Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 19 of 318
Found at i:4987760 original size:19 final size:18
Alignment explanation
Indices: 4987734--4987783 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
4987724 GCAAAAAAAT
*
4987734 AAATAAAATATAAATATA
1 AAATAAAATAAAAATATA
4987752 AATATAAAATAAAAATATA
1 AA-ATAAAATAAAAATATA
4987771 AAATAAAATAAAA
1 AAATAAAATAAAA
4987784 CAAAATTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAAATAAAAATATA
Found at i:4987761 original size:13 final size:12
Alignment explanation
Indices: 4987734--4987780 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
4987724 GCAAAAAAAT
4987734 AAATAAAATAT-
1 AAATAAAATATA
4987745 AAATATAAATATA
1 AAATA-AAATATA
4987758 AAATAAAAATATA
1 AAAT-AAAATATA
4987771 AAATAAAATA
1 AAATAAAATA
4987781 AAACAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.15
12 12 0.36
13 15 0.45
14 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAAAATATA
Found at i:4991465 original size:20 final size:20
Alignment explanation
Indices: 4991418--4991466 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
4991408 TTAAATTCTA
4991418 AAAGATAAATACAAATAAAT
1 AAAGATAAATACAAATAAAT
* *
4991438 AAATATAATTA-AAGATAAAT
1 AAAGATAAATACAA-ATAAAT
*
4991458 GAAGATAAA
1 AAAGATAAA
4991467 AGCTAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.22
Consensus pattern (20 bp):
AAAGATAAATACAAATAAAT
Found at i:4997050 original size:30 final size:30
Alignment explanation
Indices: 4997014--4997070 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4997004 ACGGCCCTGA
*
4997014 CACACGGGCGTGTGG-TCTGCCCGTGTGCCT
1 CACACGGGCATGTGGAT-TGCCCGTGTGCCT
4997044 CACACGGGCATGTGGATTGCCCGTGTG
1 CACACGGGCATGTGGATTGCCCGTGTG
4997071 GAAGTGCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.11, C:0.30, G:0.37, T:0.23
Consensus pattern (30 bp):
CACACGGGCATGTGGATTGCCCGTGTGCCT
Found at i:4997541 original size:81 final size:82
Alignment explanation
Indices: 4997385--4997552 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 82
4997375 ACAAAAATTG
* * * **
4997385 TAAAACACAGATCAATAGCGGCGTTTTTGGTAAAACGCCACTAAAAACAGAGCAATAGCGGCGCT
1 TAAAACACAGAGCAATAGCAGCGCTTCCGGTAAAACGCCACTAAAAACAGAGCAATAGCGGCGCT
** *
4997450 TTTTGTTAAAACGCCGC
66 TTCCGGTAAAACGCCGC
* * *
4997467 TAAAA-ACAGAGCAATAGCAGCGCTTCCGGTAAAACGCCGCTAAAAGTCGGAGCAATAGCGGCGC
1 TAAAACACAGAGCAATAGCAGCGCTTCCGGTAAAACGCCACTAAAA-ACAGAGCAATAGCGGCGC
4997531 -TTCCGGTAAAACGCCGC
65 TTTCCGGTAAAACGCCGC
4997548 TAAAA
1 TAAAA
4997553 GTCATATAAC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
81 53 0.72
82 21 0.28
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.18
Consensus pattern (82 bp):
TAAAACACAGAGCAATAGCAGCGCTTCCGGTAAAACGCCACTAAAAACAGAGCAATAGCGGCGCT
TTCCGGTAAAACGCCGC
Found at i:4997555 original size:41 final size:40
Alignment explanation
Indices: 4997385--4997552 Score: 210
Period size: 41 Copynumber: 4.1 Consensus size: 40
4997375 ACAAAAATTG
* * ** *
4997385 TAAAACACAGATCAATAGCGGCGTTTTTGGTAAAACGCCAC
1 TAAAA-ACAGAGCAATAGCGGCGCTTCCGGTAAAACGCCGC
** *
4997426 TAAAAACAGAGCAATAGCGGCGCTTTTTGTTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGC-TTCCGGTAAAACGCCGC
*
4997467 TAAAAACAGAGCAATAGCAGCGCTTCCGGTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGCTTCCGGTAAAACGCCGC
* *
4997507 TAAAAGTCGGAGCAATAGCGGCGCTTCCGGTAAAACGCCGC
1 TAAAA-ACAGAGCAATAGCGGCGCTTCCGGTAAAACGCCGC
4997548 TAAAA
1 TAAAA
4997553 GTCATATAAC
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 35 0.31
41 79 0.69
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.18
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGCTTCCGGTAAAACGCCGC
Found at i:4997790 original size:7 final size:7
Alignment explanation
Indices: 4997778--4997841 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
4997768 TTTATTTTTT
*
4997778 GGTTTAC
1 GGTTTAA
4997785 GGTTTAA
1 GGTTTAA
**
4997792 TATTTAA
1 GGTTTAA
4997799 GGTTTAA
1 GGTTTAA
* *
4997806 GGTCTAT
1 GGTTTAA
*
4997813 GGTTTAG
1 GGTTTAA
*
4997820 GGTTTTAT
1 GG-TTTAA
4997828 GGTTTAA
1 GGTTTAA
4997835 GGTTTAA
1 GGTTTAA
4997842 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:4997830 original size:15 final size:15
Alignment explanation
Indices: 4997794--4997844 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
4997784 CGGTTTAATA
*
4997794 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
4997808 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
4997823 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
4997838 TTAATGG
1 TTTATGG
4997845 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:4998455 original size:8 final size:8
Alignment explanation
Indices: 4998444--4998528 Score: 122
Period size: 8 Copynumber: 11.0 Consensus size: 8
4998434 ACTCAAAAAA
4998444 TAAAAATT
1 TAAAAATT
4998452 TAAAAATT
1 TAAAAATT
4998460 TAAAAATT
1 TAAAAATT
4998468 TAAAAATT
1 TAAAAATT
4998476 TAAAAATT
1 TAAAAATT
4998484 TAAAAA-T
1 TAAAAATT
4998491 T-AAAATT
1 TAAAAATT
4998498 TAAAAA-T
1 TAAAAATT
*
4998505 AAAAAATT
1 TAAAAATT
* *
4998513 AAAAAACT
1 TAAAAATT
4998521 TAAAAATT
1 TAAAAATT
4998529 AATATTTTAG
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
6 4 0.06
7 10 0.14
8 56 0.80
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAAATT
Found at i:4999777 original size:17 final size:17
Alignment explanation
Indices: 4999747--4999785 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4999737 TGTAATTGGA
*
4999747 AGAAGAAATAGGTTTTC
1 AGAAAAAATAGGTTTTC
* *
4999764 TGAAAAAATGGGTTTTC
1 AGAAAAAATAGGTTTTC
4999781 AGAAA
1 AGAAA
4999786 GATAAAATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (17 bp):
AGAAAAAATAGGTTTTC
Found at i:5001240 original size:17 final size:18
Alignment explanation
Indices: 5001220--5001257 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5001210 CATTGATATC
5001220 TTTA-TATTTAATTTAAT
1 TTTATTATTTAATTTAAT
* *
5001237 TTTATTATTTATTTTAGT
1 TTTATTATTTAATTTAAT
5001255 TTT
1 TTT
5001258 GATTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATTATTTAATTTAAT
Found at i:5001276 original size:19 final size:21
Alignment explanation
Indices: 5001248--5001295 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
5001238 TTATTATTTA
5001248 TTTTAGTTTTGATTCTAA-AT
1 TTTTAGTTTTGATTCTAATAT
* *
5001268 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTCTAATAT
5001288 TTTTAGTT
1 TTTTAGTT
5001296 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTCTAATAT
Found at i:5001394 original size:27 final size:27
Alignment explanation
Indices: 5001359--5001413 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5001349 TATTTTGATA
*
5001359 ATGAATTTTA-AATTTTTTATATTTTTC
1 ATGAATTTTATAATATTTTAT-TTTTTC
*
5001386 ATGACTTTTATAATATTTTATTTTTTC
1 ATGAATTTTATAATATTTTATTTTTTC
5001413 A
1 A
5001414 AAATTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (27 bp):
ATGAATTTTATAATATTTTATTTTTTC
Found at i:5001493 original size:43 final size:43
Alignment explanation
Indices: 5001432--5001531 Score: 182
Period size: 43 Copynumber: 2.3 Consensus size: 43
5001422 TTACCTTTAG
*
5001432 TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCA
1 TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCA
*
5001475 TGACCTGTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCA
1 TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCA
5001518 TGACCTTTAGCGGC
1 TGACCTTTAGCGGC
5001532 ATTTTTTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (43 bp):
TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCA
Found at i:5002738 original size:17 final size:18
Alignment explanation
Indices: 5002718--5002757 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5002708 AAATCAGTAA
*
5002718 AAATTATAAAAATTA-TT
1 AAATTATAAAAAATATTT
*
5002735 AAATTTTAAAAAATATTT
1 AAATTATAAAAAATATTT
5002753 AAATT
1 AAATT
5002758 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTATAAAAAATATTT
Found at i:5002748 original size:18 final size:18
Alignment explanation
Indices: 5002725--5002788 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 18
5002715 TAAAAATTAT
5002725 AAAAATTATTAAATTTTA
1 AAAAATTATTAAATTTTA
5002743 AAAAA-TATTTAAATTTTA
1 AAAAATTA-TTAAATTTTA
*
5002761 TTAAAAATTTTGTAAAATTTTA
1 --AAAAATTAT-T-AAATTTTA
*
5002783 TAAAAT
1 AAAAAT
5002789 CGTAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 2 0.05
18 15 0.39
20 11 0.29
21 2 0.05
22 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAAATTATTAAATTTTA
Found at i:5002777 original size:10 final size:10
Alignment explanation
Indices: 5002721--5002788 Score: 52
Period size: 10 Copynumber: 6.9 Consensus size: 10
5002711 TCAGTAAAAA
*
5002721 TTATAAAA-A
1 TTATAAAATT
*
5002730 TTATTAAATT
1 TTATAAAATT
* *
5002740 TTAAAAAATA
1 TTATAAAATT
5002750 TT-T-AAATT
1 TTATAAAATT
5002758 TTATTAAAAATT
1 TTA-T-AAAATT
*
5002770 TTGTAAAATT
1 TTATAAAATT
5002780 TTATAAAAT
1 TTATAAAAT
5002789 CGTAAAAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
8 6 0.13
9 7 0.16
10 24 0.53
11 1 0.02
12 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (10 bp):
TTATAAAATT
Found at i:5006370 original size:19 final size:20
Alignment explanation
Indices: 5006346--5006383 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5006336 GGTACCACCA
5006346 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
5006365 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
5006384 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:5006677 original size:46 final size:45
Alignment explanation
Indices: 5006610--5006774 Score: 170
Period size: 46 Copynumber: 3.6 Consensus size: 45
5006600 CGCCCCTAAG
* *
5006610 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-TTAGTATCCATAAA
* * **
5006656 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT-TACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--GCTTAGTATCCAT-AAA
* * * * * *
5006703 CGAACTCGAACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-TTAGTATCCATAAA
5006749 TGAACTCGGACTCAACTCAACGAGTT
1 TGAACTCGGACTCAACTCAACGAGTT
5006775 TGGATGCTCA
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 58 0.60
47 35 0.36
48 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCTTAGTATCCATAAA
Found at i:5006726 original size:93 final size:93
Alignment explanation
Indices: 5006611--5006781 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
5006601 GCCCCTAAGT
* * * *
5006611 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
5006676 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
5006704 GAACTCGAACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
5006769 CGAGTTTGGATGC
66 CGAGTTCGGATGC
5006782 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5012690 original size:50 final size:50
Alignment explanation
Indices: 5012615--5012736 Score: 217
Period size: 50 Copynumber: 2.4 Consensus size: 50
5012605 GGCAACAAGT
* *
5012615 GATAAGTGATAGCTTCGACTACACTTATCTGATCAAGGACAAATGAAAGC
1 GATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGC
*
5012665 GATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGT
1 GATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGC
5012715 GATAAGTAATAGCTTCGGCTAC
1 GATAAGTAATAGCTTCGGCTAC
5012737 CTGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (50 bp):
GATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGC
Found at i:5012759 original size:31 final size:31
Alignment explanation
Indices: 5012724--5012860 Score: 204
Period size: 31 Copynumber: 4.4 Consensus size: 31
5012714 TGATAAGTAA
5012724 TAGCTTCGGCTACCTGATCAGTGAAAAGTGG
1 TAGCTTCGGCTACCTGATCAGTGAAAAGTGG
** *
5012755 TAGCTTTTGCTACCTGATCAATGAAAAGTGG
1 TAGCTTCGGCTACCTGATCAGTGAAAAGTGG
*
5012786 TAGC-TCTGGCTACCTGATCAGTGAAAAATGG
1 TAGCTTC-GGCTACCTGATCAGTGAAAAGTGG
* *
5012817 TAGCTTCGACTACCTGATCAGTGAATAGTGG
1 TAGCTTCGGCTACCTGATCAGTGAAAAGTGG
5012848 TAGCTTCGGCTAC
1 TAGCTTCGGCTAC
5012861 AAGTGACAAG
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
30 1 0.01
31 90 0.97
32 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
TAGCTTCGGCTACCTGATCAGTGAAAAGTGG
Found at i:5012935 original size:46 final size:49
Alignment explanation
Indices: 5012882--5013007 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 49
5012872 GGTTTCCGTA
* * *
5012882 TAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGATT-CATG
1 TAAGACCATAGCTGGGATATGGCATCGATATGACATATGTGATTACATG
* * *
5012928 TAAGACCATAGCTGGGCTATGGCATCGATATGTCATATGTGATTACGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATGACATATGTGATTACATG
* * *
5012977 TAAGACCATAGCTTGGCTATGGAATCGATAT
1 TAAGACCATAGCTGGGATATGGCATCGATAT
5013008 ATGAATATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
46 24 0.35
47 1 0.01
48 12 0.17
49 32 0.46
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (49 bp):
TAAGACCATAGCTGGGATATGGCATCGATATGACATATGTGATTACATG
Found at i:5012988 original size:49 final size:47
Alignment explanation
Indices: 5012882--5013044 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 47
5012872 GGTTTCCGTA
* * * * *
5012882 TAAGACCATATCTGGGATATGGCATC-AGTGAGATATGTGATT-CATG
1 TAAGACCATAGCTGGGCTATGGCATCGAATG-TATATGTGATTACGTG
5012928 TAAGACCATAGCTGGGCTATGGCATCGATATGTCATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGA-ATGT-ATATGTGATTACGTG
* * * *
5012977 TAAGACCATAGCTTGGCTATGGAATCG-A--TATA--TGAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGAATGTATATGTGATTACGTG
5013019 TAAGACCATAGCTGGGCTATGGCATC
1 TAAGACCATAGCTGGGCTATGGCATC
5013045 ATTATGTGAA
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
42 32 0.31
44 3 0.03
45 1 0.01
46 24 0.24
47 2 0.02
48 12 0.12
49 28 0.27
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCGAATGTATATGTGATTACGTG
Found at i:5013023 original size:42 final size:42
Alignment explanation
Indices: 5012974--5013071 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 42
5012964 ATGTGATTAC
* *
5012974 GTGTAAGACCATAGCTTGGCTATGGAATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGAATC-ATTATATGAAGAT
* *
5013016 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGAATCATTATATGAAGAT
5013058 GTGTAAGACCATAG
1 GTGTAAGACCATAG
5013072 TTGAACTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 50 0.98
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGAATCATTATATGAAGAT
Found at i:5013081 original size:42 final size:40
Alignment explanation
Indices: 5012974--5013087 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 40
5012964 ATGTGATTAC
* *
5012974 GTGTAAGACCATAGCTTGGCTATGGAATCGATATATGAATAT
1 GTGTAAGACCATAG-TTGGCTATGGCATC-ATATATGAAGAT
* *
5013016 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAG-TTGGCTATGGCATCA-TATATGAAGAT
*
5013058 GTGTAAGACCATAGTTGAACTATGGCATCA
1 GTGTAAGACCATAGTTG-GCTATGGCATCA
5013088 AGAAAACGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
41 3 0.05
42 61 0.95
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (40 bp):
GTGTAAGACCATAGTTGGCTATGGCATCATATATGAAGAT
Found at i:5020567 original size:17 final size:17
Alignment explanation
Indices: 5020545--5020579 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5020535 AACTGTTATT
5020545 GATTTTATTGGTTTAAA
1 GATTTTATTGGTTTAAA
5020562 GATTTTATTGGTTTAAA
1 GATTTTATTGGTTTAAA
5020579 G
1 G
5020580 GCTTGAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (17 bp):
GATTTTATTGGTTTAAA
Found at i:5021338 original size:21 final size:21
Alignment explanation
Indices: 5021312--5021368 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
5021302 ATTTAACCGT
5021312 CTATTTTAGCATATATATGAA
1 CTATTTTAGCATATATATGAA
5021333 CTATTTTAGCATATATATGAA
1 CTATTTTAGCATATATATGAA
5021354 CTATTTTAGCATATA
1 CTATTTTAGCATATA
5021369 CAAGTAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (21 bp):
CTATTTTAGCATATATATGAA
Found at i:5022002 original size:3 final size:3
Alignment explanation
Indices: 5021994--5022182 Score: 72
Period size: 3 Copynumber: 61.3 Consensus size: 3
5021984 CCCTATATGT
*
5021994 TTA TTA TTA TTA TTA TTA TTA TATA TATA TATA TTA TATA TTG TTAA
1 TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA TTA T-TA TTA TT-A
* * * **
5022041 TTG TT- TTA TTT TTA -TA CCTTA TTT TTA -TA TTA TATA TTA -TA AAA
1 TTA TTA TTA TTA TTA TTA --TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
5022085 TTA TT- TTA TTA TATA TTA TT- TATA TTA TTA TTTA TTA TGTT TTA TTT
1 TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA -TTA TTA T-TA TTA TTA
** * * *
5022132 TTCA CAAA TTA TTA TTA TTA TT- TTA -CA TTA TCA TTT TTA -TA TTA
1 TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5022176 TTA TTA T
1 TTA TTA T
5022183 ATTTTTACTT
Statistics
Matches: 141, Mismatches: 24, Indels: 42
0.68 0.12 0.20
Matches are distributed among these distances:
2 16 0.11
3 94 0.67
4 29 0.21
5 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5022050 original size:43 final size:43
Alignment explanation
Indices: 5021996--5022122 Score: 118
Period size: 43 Copynumber: 2.9 Consensus size: 43
5021986 CTATATGTTT
* *
5021996 ATTATTATTATTATTATTATATATATATATATTATATATTGT-TA
1 ATTATT-TTATTATTATTAT-TATATATATATTATATATTATAAA
* * * *
5022040 ATTGTTTTATTTTTA-TACCTTATTTTTATATTATATATTATAAA
1 ATTATTTTATTATTATTA--TTATATATATATTATATATTATAAA
*
5022084 ATTATTTTATTATATATTATT-TATAT-TATTATTTATTAT
1 ATTATTTTATTAT-TATTATTATATATATATTATATATTAT
5022123 GTTTTATTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
42 14 0.21
43 29 0.43
44 20 0.30
45 2 0.03
46 2 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (43 bp):
ATTATTTTATTATTATTATTATATATATATTATATATTATAAA
Found at i:5022096 original size:16 final size:16
Alignment explanation
Indices: 5022068--5022112 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5022058 CTTATTTTTA
5022068 TATTATATATTATAAAAT
1 TATT-TATATTAT-AAAT
*
5022086 TATTT-TATTATATAT
1 TATTTATATTATAAAT
5022101 TATTTATATTAT
1 TATTTATATTAT
5022113 TATTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 8 0.32
16 12 0.48
17 1 0.04
18 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTATATTATAAAT
Found at i:5022119 original size:23 final size:23
Alignment explanation
Indices: 5022060--5022119 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
5022050 TTTTATACCT
*
5022060 TATTTTTATATTATATATTATAA
1 TATTATTATATTATATATTATAA
* * *
5022083 AATTATTTTATTATATATTATTTA
1 TATTATTATATTATATATTA-TAA
5022107 TATTATTAT-TTAT
1 TATTATTATATTAT
5022120 TATGTTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTATATTATATATTATAA
Found at i:5022345 original size:17 final size:19
Alignment explanation
Indices: 5022324--5022440 Score: 61
Period size: 19 Copynumber: 6.2 Consensus size: 19
5022314 ATTATATAAC
5022324 ATTTATTATATT-TTTATT
1 ATTTATTATATTATTTATT
5022342 -TTTATTCTATATTATTTATT
1 ATTTA-T-TATATTATTTATT
*
5022362 ATTT-TTATAGGTTATATA-T
1 ATTTATTATA--TTATTTATT
* *
5022381 A-TCA-TATATTATCTATT
1 ATTTATTATATTATTTATT
*
5022398 ATATTATT-TACGTT-TATATT
1 AT-TTATTATA--TTATTTATT
* *
5022418 ATTCATTATATTATTTATA
1 ATTTATTATATTATTTATT
5022437 ATTT
1 ATTT
5022441 TAAAATTTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 29
0.66 0.08 0.26
Matches are distributed among these distances:
16 6 0.08
17 6 0.08
18 12 0.16
19 24 0.32
20 22 0.29
21 5 0.07
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTATTATATTATTTATT
Found at i:5022346 original size:31 final size:30
Alignment explanation
Indices: 5022310--5022367 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
5022300 TTAAAATAAA
5022310 TTTTATTATATAACATTTATTATATTTTTAT
1 TTTTATTATATAACATTTATTAT-TTTTTAT
* **
5022341 TTTTATTCTATATTATTTATTATTTTT
1 TTTTATTATATAACATTTATTATTTTT
5022368 ATAGGTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (30 bp):
TTTTATTATATAACATTTATTATTTTTTAT
Found at i:5025298 original size:266 final size:266
Alignment explanation
Indices: 5024824--5025326 Score: 911
Period size: 266 Copynumber: 1.9 Consensus size: 266
5024814 TTTTTGCTTT
* *
5024824 AAGTTTGTATGTACTAATGGTTTTTCCTAGGGCTTTGGGATATGTGGACGAGGCAACCACAGATC
1 AAGTTTGTATGTACTAATGATTTTTCCTAGGGCTTTGGGATATGTGGACGAGGCAACCACAGATA
*
5024889 TTTTTCATCGACTCAGTAAAAGGGTCACTTCCGTCCCTGCGATTTTAACAGAGACGTTCAGGTCC
66 TTTTTCATCGACTCAGTAAAAGGGTCACTTCCGTCCCTGCGATTTTAACAGAGACATTCAGGTCC
5024954 TTAGGCGCATGTAAGAGGGCTGGTGCAGGCAGATTTGTTGGTTGTGCTCAGTTACTTTTAGCTTG
131 TTAGGCGCATGTAAGAGGGCTGGTGCAGGCAGATTTGTTGGTTGTGCTCAGTTACTTTTAGCTTG
*
5025019 GTTCTACAGTCATTTTCGATTGATAGATAAGGTGGTTTGTCGGGTCTTCTTCGAGGATTATTCAC
196 GTTCTACAGTCATTTTCAATTGATAGATAAGGTGGTTTGTCGGGTCTTCTTCGAGGATTATTCAC
5025084 CGTTGA
261 CGTTGA
*
5025090 AAGTTTGTATAG-ACTGATGATTTTTCCTAGGGCTTTGGGATATGTGGACGAGGCAACCACAGAT
1 AAGTTTGTAT-GTACTAATGATTTTTCCTAGGGCTTTGGGATATGTGGACGAGGCAACCACAGAT
*
5025154 ATTTTTCATCGACTCAGTAAAAGGGTCACTTCCGTCCCTGCGATTTTAGC-GAAGACATTCAGGT
65 ATTTTTCATCGACTCAGTAAAAGGGTCACTTCCGTCCCTGCGATTTTAACAG-AGACATTCAGGT
*
5025218 TCTTAGGCGCATGTAAGAGGGCTGGTGCAGGCAGATTTGTTGGTTGTGCTCAGTTACTTTTAGCT
129 CCTTAGGCGCATGTAAGAGGGCTGGTGCAGGCAGATTTGTTGGTTGTGCTCAGTTACTTTTAGCT
5025283 TGGTTCTACAGTCATTTTCAATTGATAGATAAGGTGGTTTGTCG
194 TGGTTCTACAGTCATTTTCAATTGATAGATAAGGTGGTTTGTCG
5025327 AGGATTATTC
Statistics
Matches: 228, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
265 1 0.00
266 226 0.99
267 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (266 bp):
AAGTTTGTATGTACTAATGATTTTTCCTAGGGCTTTGGGATATGTGGACGAGGCAACCACAGATA
TTTTTCATCGACTCAGTAAAAGGGTCACTTCCGTCCCTGCGATTTTAACAGAGACATTCAGGTCC
TTAGGCGCATGTAAGAGGGCTGGTGCAGGCAGATTTGTTGGTTGTGCTCAGTTACTTTTAGCTTG
GTTCTACAGTCATTTTCAATTGATAGATAAGGTGGTTTGTCGGGTCTTCTTCGAGGATTATTCAC
CGTTGA
Found at i:5026589 original size:14 final size:14
Alignment explanation
Indices: 5026570--5026599 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5026560 AAGATATTCT
5026570 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
5026584 TTTTCTAAATGAAG
1 TTTTCTAAATAAAG
5026598 TT
1 TT
5026600 GAACCAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:5034903 original size:44 final size:44
Alignment explanation
Indices: 5034840--5034932 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
5034830 GGAACAATTT
* * *
5034840 GAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
1 GAAGATACCAAATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
5034884 GAAGATACCAAATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
1 GAAGATACCAAATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
*
5034928 AAAGA
1 GAAGA
5034933 CATAGCTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (44 bp):
GAAGATACCAAATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
Found at i:5035328 original size:204 final size:205
Alignment explanation
Indices: 5034919--5035427 Score: 885
Period size: 204 Copynumber: 2.5 Consensus size: 205
5034909 TATTGGCAGA
* * * *
5034919 GAGCAGATCAAAGACATAGCTGATTTGGCTTTCACATGTTTACGTTGAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTCGAAGCAAATCTAAGATGAT
* * * *
5034984 TTGGCATCTCTGTATTGTTAGAGAACGAATCGAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGAGGGCAGA
5035049 CACATAGCAGATCCAAACTTCAGATGTCTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAAACTTCAGATGTCTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
5035114 TGCTTACAAG
196 TGCTTACAAG
5035124 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTCGAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTCGAAGCAAATCTAAGATGAT
* * *
5035189 TTGGCATCTCTATATTGTCAGAGAGCAAATCGAAGTGTGGCATCTCCACTTCAATGG-GGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGAGGGCAGA
5035253 CACATAGCAGATCCAAACTTCAGATGTCTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAAACTTCAGATGTCTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
5035318 TGCTTACAAG
196 TGCTTACAAG
* * *
5035328 GAGCAAATCGAAGATATAACTGATTTGGCTTTCACGTGCTTACGTCGAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTCGAAGCAAATCTAAGATGAT
5035393 TTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAG
66 TTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAG
5035428 ACACAGCTAA
Statistics
Matches: 289, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
204 178 0.62
205 111 0.38
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (205 bp):
GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTCGAAGCAAATCTAAGATGAT
TTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGAGGGCAGA
CACATAGCAGATCCAAACTTCAGATGTCTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
TGCTTACAAG
Found at i:5035444 original size:87 final size:87
Alignment explanation
Indices: 5035328--5035515 Score: 286
Period size: 87 Copynumber: 2.2 Consensus size: 87
5035318 TGCTTACAAG
* * * *
5035328 GAGCAAATCGAAGATATAACTGATTTGGCTTTCACGTGCTTACGTCGAAGCAAATCTAAGATGAT
1 GAGCAAATCGAAGACACAACTAATTTGGCTTTCACGTGCTTACGTCAAAGCAAATCTAAGATGAT
*
5035393 TTGGCATCTCTGTATTGTCAGA
66 TTGGCATCTCTGTATTGGCAGA
* * * *
5035415 GAGCAAATCGAAGACACAGCTAATTTGGCTTTCATGTGTTTACGTTAAAGCAAATCTAAGATGAT
1 GAGCAAATCGAAGACACAACTAATTTGGCTTTCACGTGCTTACGTCAAAGCAAATCTAAGATGAT
5035480 TTGGCATCTCTGTATTGGCAGA
66 TTGGCATCTCTGTATTGGCAGA
*
5035502 GAGCAGATCGAAGA
1 GAGCAAATCGAAGA
5035516 TACCAGATTT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (87 bp):
GAGCAAATCGAAGACACAACTAATTTGGCTTTCACGTGCTTACGTCAAAGCAAATCTAAGATGAT
TTGGCATCTCTGTATTGGCAGA
Found at i:5037026 original size:2 final size:2
Alignment explanation
Indices: 5037008--5037061 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
5036998 TATAGTGTAT
*
5037008 TA TA TT TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5037049 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
5037062 GTGTTTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5041741 original size:9 final size:9
Alignment explanation
Indices: 5041729--5041761 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
5041719 GATTTATTCG
5041729 AATCGAGTT
1 AATCGAGTT
5041738 AATCGAGTT
1 AATCGAGTT
*
5041747 AATCGAATT
1 AATCGAGTT
5041756 AATCGA
1 AATCGA
5041762 ATCAACTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:5041762 original size:9 final size:9
Alignment explanation
Indices: 5041729--5041774 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
5041719 GATTTATTCG
*
5041729 AATCGAGTT
1 AATCGAATT
*
5041738 AATCGAGTT
1 AATCGAATT
5041747 AATCGAATT
1 AATCGAATT
*
5041756 AATCGAATC
1 AATCGAATT
5041765 AACTCGAATT
1 AA-TCGAATT
5041775 TTTTTTTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (9 bp):
AATCGAATT
Found at i:5042166 original size:24 final size:24
Alignment explanation
Indices: 5042137--5042184 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5042127 TTATTCAAAC
5042137 CCCTTACCCCCCATTTCAACGAAA
1 CCCTTACCCCCCATTTCAACGAAA
*
5042161 CCCTTACCCCCCATTTCTACGAAA
1 CCCTTACCCCCCATTTCAACGAAA
5042185 GACGAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.46, G:0.04, T:0.23
Consensus pattern (24 bp):
CCCTTACCCCCCATTTCAACGAAA
Found at i:5047866 original size:125 final size:125
Alignment explanation
Indices: 5047649--5047873 Score: 330
Period size: 125 Copynumber: 1.8 Consensus size: 125
5047639 ATTTTAGTCA
* * * *
5047649 TATTTAAATGGCTTTTGTAATCTTGTTTAGAGGGTTGACAGAATATATCTTACGAGAGGTTTGAT
1 TATTTAAATGGCTTTTGTAATCCTATTTAGAAGGTTGACAGAATATATCTTACGAGAGATTTGAT
* *
5047714 GAAGAGTTTTATGGAGAGTTTTTGAGAGAGCTTTGGCATATTAGGACTTTGATATTTGCC
66 GAAGAGTTTTATGGAGAGCTTGTGAGAGAGCTTTGGCATATTAGGACTTTGATATTTGCC
* *
5047774 TATTTAAA-GAGCTTTTGTAATCCTATTTAGAAGGTTGACAGAATATCTTTTAC-ATGAGATTTG
1 TATTTAAATG-GCTTTTGTAATCCTATTTAGAAGGTTGACAGAATATATCTTACGA-GAGATTTG
5047837 ATGAAGAGTTTTGA-GGAGAGCTTGTGAGAGAGCTTTG
64 ATGAAGAGTTTT-ATGGAGAGCTTGTGAGAGAGCTTTG
5047874 TATTTGGGTT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
124 2 0.02
125 86 0.97
126 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (125 bp):
TATTTAAATGGCTTTTGTAATCCTATTTAGAAGGTTGACAGAATATATCTTACGAGAGATTTGAT
GAAGAGTTTTATGGAGAGCTTGTGAGAGAGCTTTGGCATATTAGGACTTTGATATTTGCC
Found at i:5049168 original size:22 final size:23
Alignment explanation
Indices: 5049141--5049185 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5049131 GGGTATCTAC
5049141 AAATCAAATC-TCTAAGAATACA
1 AAATCAAATCTTCTAAGAATACA
* *
5049163 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGAATACA
5049186 TATCATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGAATACA
Found at i:5049190 original size:22 final size:22
Alignment explanation
Indices: 5049138--5049195 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
5049128 AAAGGGTATC
*
5049138 TACAAATCAAATC-TCTAAGAA
1 TACAAATCATATCTTCTAAGAA
*
5049159 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAA
*
5049182 TACATATCATATCT
1 TACAAATCATATCT
5049196 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.59
23 10 0.31
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAA
Found at i:5054306 original size:22 final size:23
Alignment explanation
Indices: 5054279--5054323 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5054269 GGGTATCTAC
5054279 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
5054301 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
5054324 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:5054327 original size:17 final size:17
Alignment explanation
Indices: 5054305--5054355 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
5054295 ATTACAAAAT
5054305 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
5054322 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
*
5054341 CATATCTTCAAAGAT
1 CATATCTTCTAAGAT
5054356 CATGTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:5054328 original size:22 final size:22
Alignment explanation
Indices: 5054276--5054333 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
5054266 AAAGGGTATC
*
5054276 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
5054297 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
5054320 TACATATCATATCT
1 TACAAATCATATCT
5054334 AAGATTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.58
23 11 0.33
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:5054336 original size:19 final size:20
Alignment explanation
Indices: 5054289--5054346 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
5054279 AAATCAAATC
*
5054289 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
5054312 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
5054331 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
5054347 TTCAAAGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:5054718 original size:6 final size:6
Alignment explanation
Indices: 5054707--5054738 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
5054697 TATGTTGGGT
*
5054707 TTGTGG TTGTGG TTGTGG TTGTGA TTGTGG TT
1 TTGTGG TTGTGG TTGTGG TTGTGG TTGTGG TT
5054739 TATAAACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.00, G:0.44, T:0.53
Consensus pattern (6 bp):
TTGTGG
Found at i:5055462 original size:15 final size:15
Alignment explanation
Indices: 5055444--5055473 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5055434 TTTGTTGAGG
5055444 GATAAAAACAATATA
1 GATAAAAACAATATA
5055459 GATAAAAACAATATA
1 GATAAAAACAATATA
5055474 AATATTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
GATAAAAACAATATA
Found at i:5056038 original size:2 final size:2
Alignment explanation
Indices: 5056031--5056068 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5056021 ATTATGTTAA
5056031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5056069 TGTATCTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5056146 original size:14 final size:15
Alignment explanation
Indices: 5056127--5056160 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5056117 TCTTTGACCC
5056127 AAAAAGAA-ACAAAG
1 AAAAAGAAGACAAAG
*
5056141 AAAAAGAAGACAAAT
1 AAAAAGAAGACAAAG
5056156 AAAAA
1 AAAAA
5056161 ATAAAGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAGAAGACAAAG
Found at i:5056558 original size:23 final size:23
Alignment explanation
Indices: 5056528--5056575 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5056518 CTGTTAGAAC
5056528 TACTTCCTTAATTTTCCTAACAA
1 TACTTCCTTAATTTTCCTAACAA
*
5056551 TACTTCCTTGATTTTCCTAACAA
1 TACTTCCTTAATTTTCCTAACAA
5056574 TA
1 TA
5056576 GTCATAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.44
Consensus pattern (23 bp):
TACTTCCTTAATTTTCCTAACAA
Found at i:5062953 original size:176 final size:178
Alignment explanation
Indices: 5062590--5063311 Score: 854
Period size: 176 Copynumber: 4.1 Consensus size: 178
5062580 CAACTTTAGG
** ** * * *
5062590 GAGATAAGGCTGGTGGCTTCAATCTGCTCCTGTTACTACATTGGAAAGATAAGATTCGCCATCTT
1 GAGATAAGGCTGGTGGCTAAAATCTGCTCC-CCTACTACCTCGGGAAGATAAGATTCGCCATCTT
* * *
5062655 CAATCTGTTCCACTAC-AGCTTAGGGAGAT-A-A-----AATC-T-AGTCTGCTTCCTTGCTACC
65 CGATCTGCTCCACTACTATCTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACC
* *
5062710 TCAGGAAGATAAGACTATCATATTT-AAGCTGCTCTCTTGCTACCTTAGA
130 TCAGGAAGATAAGACTA-CATATTTCAACCTGCTCTCTTGCTACCTCAGA
* * *
5062759 GAGATAAGGCTGGTGGCTAAAATCTTCTCCCCTACTACCTCAGGAAGATAAGATTCGCCATTTTC
1 GAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTACTACCTCGGGAAGATAAGATTCGCCATCTTC
* * * * *
5062824 GATCTGCCCCACTACTATCTCAAGGAGATGAGATCTTCAATCTTCAGTTTGCTTCCTTGCTACCT
66 GATCTGCTCCACTACTATCTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCT
* * *
5062889 CAGGAAGATAAGACTTCA-A-TTCAGCCTGCTCCCTTGCTACCTCAGA
131 CAGGAAGATAAGACTACATATTTCAACCTGCTCTCTTGCTACCTCAGA
* * *
5062935 GAGATAAGGCTAGTGGCTAAAATCTGCTCCCTTGCTACCTCGGGAAGATAAGATAT-GCCATCTT
1 GAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTACTACCTCGGGAAGATAAGAT-TCGCCATCTT
* * * * *
5062999 CAATCTGCTCTACTACTGT-TTAGGGAGATAAGATCTTC-ATCATCAGTCTGCTTCCTTACTACC
65 CGATCTGCTCCACTACTATCTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACC
* * *
5063062 TCTGGAAGATAAGACTACA-ATCTTCAACCTGCTCTCTTACTGCCTCAGA
130 TCAGGAAGATAAGACTACATAT-TTCAACCTGCTCTCTTGCTACCTCAGA
* * *
5063111 GAGATAAGGATGGTAGCTAAAACCTGCTCCCCTACTACCTCGGGAAGATAAGATTCGCCATCTTC
1 GAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTACTACCTCGGGAAGATAAGATTCGCCATCTTC
* * * * *
5063176 GAGCTGCTCCACTACTA-CTTAGGGAGATAAGATCTACAACCTT-AGTCTACTTCTTTGCTACCT
66 GATCTGCTCCACTACTATCTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCT
* *
5063239 CAGGAAGATAAGACTACGAT-CTTCAACCTGCTCTCTTGCTACCTTAGA
131 CAGGAAGATAAGACTAC-ATATTTCAACCTGCTCTCTTGCTACCTCAGA
*
5063287 GAGATAAAGCTGGTGGCTAAAATCT
1 GAGATAAGGCTGGTGGCTAAAATCT
5063312 TCTTGTAACA
Statistics
Matches: 465, Mismatches: 69, Indels: 31
0.82 0.12 0.05
Matches are distributed among these distances:
168 40 0.09
169 37 0.08
170 1 0.00
171 1 0.00
174 40 0.09
175 19 0.04
176 285 0.61
177 8 0.02
178 34 0.07
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (178 bp):
GAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTACTACCTCGGGAAGATAAGATTCGCCATCTTC
GATCTGCTCCACTACTATCTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCT
CAGGAAGATAAGACTACATATTTCAACCTGCTCTCTTGCTACCTCAGA
Found at i:5063061 original size:88 final size:86
Alignment explanation
Indices: 5062957--5063272 Score: 260
Period size: 88 Copynumber: 3.6 Consensus size: 86
5062947 GTGGCTAAAA
* * *
5062957 TCTGCTCCCTTGCTACCTCGGGAAGATAAGA-TATGCCATCTTCAATCTGCTCTACTACTGTTTA
1 TCTGCTCCCTTACTACCTCGGGAAGATAAGACTA--CCATCTTCAACCTGCTCTACTACTGCTTA
* *
5063021 GGGAGATAAGATCTTCATCATCAG
64 GGGAGATAAGATCTTCAAC-TAAG
* * * *
5063045 TCTGCTTCCTTACTACCTCTGGAAGATAAGACTACAATCTTCAACCTGCTCT-CTTACTGCCTCA
1 TCTGCTCCCTTACTACCTCGGGAAGATAAGACTACCATCTTCAACCTGCTCTAC-TACTG-CTTA
* ** * *
5063109 GAGAGATAAGGATGGT-AGCTAAAA
64 GGGAGATAA-GATCTTCAACT-AAG
* * * * * * * *
5063133 CCTGCTCCCCTACTACCTCGGGAAGATAAGATTCGCCATCTTCGAGCTGCTCCACTACTACTTAG
1 TCTGCTCCCTTACTACCTCGGGAAGATAAGACT-ACCATCTTCAACCTGCTCTACTACTGCTTAG
* *
5063198 GGAGATAAGATCTACAACCTTAG
65 GGAGATAAGATCTTCAA-CTAAG
* * * * * *
5063221 TCTACTTCTTTGCTACCTCAGGAAGATAAGACTACGATCTTCAACCTGCTCT
1 TCTGCTCCCTTACTACCTCGGGAAGATAAGACTACCATCTTCAACCTGCTCT
5063273 CTTGCTACCT
Statistics
Matches: 174, Mismatches: 45, Indels: 19
0.73 0.19 0.08
Matches are distributed among these distances:
86 1 0.01
87 39 0.22
88 107 0.61
89 26 0.15
90 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (86 bp):
TCTGCTCCCTTACTACCTCGGGAAGATAAGACTACCATCTTCAACCTGCTCTACTACTGCTTAGG
GAGATAAGATCTTCAACTAAG
Found at i:5063094 original size:44 final size:44
Alignment explanation
Indices: 5063046--5063270 Score: 104
Period size: 44 Copynumber: 5.1 Consensus size: 44
5063036 CATCATCAGT
5063046 CTGCTTCCTTACTACCTCTGGAAGATAAGACTACAATCTTCAAC
1 CTGCTTCCTTACTACCTCTGGAAGATAAGACTACAATCTTCAAC
* * *** * **
5063090 CTGC-TCTCTTACTGCCTC-AGAGAGATAAGGA-TGGTAGCTAAAAC
1 CTGCTTC-CTTACTACCTCTGGA-AGATAA-GACTACAATCTTCAAC
* * * * * * * *
5063134 CTGCTCCCCTACTACCTCGGGAAGATAAGATTCGCCATCTTCGAG
1 CTGCTTCCTTACTACCTCTGGAAGATAAGACT-ACAATCTTCAAC
* * * **
5063179 CTGC-TCCACTACTA-CT-TAGGGAGATAAGATCTACAACCTT-AGT
1 CTGCTTCC-TTACTACCTCT-GGAAGATAAGA-CTACAATCTTCAAC
* * * * *
5063222 CTACTTCTTTGCTACCTCAGGAAGATAAGACTACGATCTTCAAC
1 CTGCTTCCTTACTACCTCTGGAAGATAAGACTACAATCTTCAAC
5063266 CTGCT
1 CTGCT
5063271 CTCTTGCTAC
Statistics
Matches: 127, Mismatches: 40, Indels: 28
0.65 0.21 0.14
Matches are distributed among these distances:
43 21 0.17
44 85 0.67
45 21 0.17
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (44 bp):
CTGCTTCCTTACTACCTCTGGAAGATAAGACTACAATCTTCAAC
Found at i:5064772 original size:40 final size:40
Alignment explanation
Indices: 5064698--5064918 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
5064688 AACCCAAGTA
* *
5064698 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
5064737 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * *
5064777 CCTTCGAGACTTAGCCCGGATATAG-CAACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
5064817 CCTTCGGGACTTAGCCC-GAGTATAGTCAATAGCACAACTA
1 CCTTCGGGACTTAGCCCGGA-TATAGTCACTAGCACAAATG
*
5064857 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
5064896 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
5064919 TATCCGAATA
Statistics
Matches: 158, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
39 39 0.25
40 115 0.73
41 4 0.03
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:5064830 original size:80 final size:80
Alignment explanation
Indices: 5064697--5064918 Score: 310
Period size: 80 Copynumber: 2.8 Consensus size: 80
5064687 AAACCCAAGT
* *
5064697 ACCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 ACCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
*
5064761 GTCACTAGCACAA-A
66 GTCAATAGCACAACA
* *
5064775 AGCCTTCGAGACTTAGCCCGGATATAGCAACTCGCACAAACGCCTTCGGGACTTAGCCC-GAGTA
1 A-CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-TA
*
5064839 TAGTCAATAGCACAACT
64 TAGTCAATAGCACAACA
* *
5064856 ACCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCAC-CATGCCTTCGGGACTTAGCCCGGATAT
1 ACCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
5064919 TATCCGAATA
Statistics
Matches: 128, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 36 0.28
80 89 0.70
81 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (80 bp):
ACCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GTCAATAGCACAACA
Found at i:5068530 original size:8 final size:8
Alignment explanation
Indices: 5068517--5068567 Score: 70
Period size: 8 Copynumber: 6.6 Consensus size: 8
5068507 TTTTTGATTG
5068517 ATTTTTTT
1 ATTTTTTT
5068525 ATTTTTTT
1 ATTTTTTT
5068533 A--TTTTT
1 ATTTTTTT
5068539 ATTTTTTT
1 ATTTTTTT
* *
5068547 ACTTTTTG
1 ATTTTTTT
5068555 ATTTTTTT
1 ATTTTTTT
5068563 ATTTT
1 ATTTT
5068568 ATTTTTGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 6 0.16
8 31 0.84
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:5068537 original size:14 final size:14
Alignment explanation
Indices: 5068520--5068573 Score: 83
Period size: 14 Copynumber: 3.8 Consensus size: 14
5068510 TTGATTGATT
5068520 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
5068534 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
5068548 CTTTTTGATTTTTTTA
1 -TTTTT-ATTTTTTTA
5068564 -TTTTATTTTT
1 TTTTTATTTTT
5068574 GTCTTAAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.16
14 18 0.47
15 5 0.13
16 9 0.24
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:5073574 original size:112 final size:112
Alignment explanation
Indices: 5073388--5073616 Score: 325
Period size: 112 Copynumber: 2.0 Consensus size: 112
5073378 CGGCCATGTG
* * * *
5073388 ACACGGTCGTATGAAGTACACGGCCTGGACACACGAAAGTGCCCTAGGCCGTGTGAAAATTGGAG
1 ACACGGTCGGATGAAGCACACGACCTGGACACACGAAAGTGCCCTAGGCCGTGTGAAAACTGGAG
* *
5073453 CTAAGTTTTCAAATTTTAAATAAGTCAGGGAGCCACACGGGTAAGGC
66 CTAAGTTTTCAAATTTTAAATAAGTCAGGAAGCCACACGGGCAAGGC
* * **
5073500 ACACGGTCGGGTGAAGCACGCGACCTGGACACAC-AAGAGTTTCCTAGGCCGTGTGAAAACTGGA
1 ACACGGTCGGATGAAGCACACGACCTGGACACACGAA-AGTGCCCTAGGCCGTGTGAAAACTGGA
* * *
5073564 GCTAATTTTTCAAATTTTAAATAAGTCAGGAAGCTAGACGGGCAAGGC
65 GCTAAGTTTTCAAATTTTAAATAAGTCAGGAAGCCACACGGGCAAGGC
5073612 ACACG
1 ACACG
5073617 ACCGTGTGTT
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 2 0.02
112 101 0.98
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (112 bp):
ACACGGTCGGATGAAGCACACGACCTGGACACACGAAAGTGCCCTAGGCCGTGTGAAAACTGGAG
CTAAGTTTTCAAATTTTAAATAAGTCAGGAAGCCACACGGGCAAGGC
Found at i:5076919 original size:6 final size:6
Alignment explanation
Indices: 5076908--5076939 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
5076898 AAAAATAAAC
*
5076908 AAAAAT AAAAAT AAAAGT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
5076940 TATGAGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:5088835 original size:93 final size:93
Alignment explanation
Indices: 5088727--5088897 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
5088717 GCCCCTAAGT
* * *
5088727 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5088792 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
5088820 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5088885 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5088898 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:5088894 original size:46 final size:46
Alignment explanation
Indices: 5088722--5088894 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
5088712 AACCCGCCCC
* * *
5088722 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
5088768 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
5088816 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
5088861 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5088895 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:5094289 original size:93 final size:93
Alignment explanation
Indices: 5094181--5094350 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
5094171 ACCCATAAGT
* * *
5094181 GAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
5094246 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
5094274 GAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
5094339 CGTGTTCGGATG
66 CGAGTTCGGATG
5094351 TTCAACCATC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5094348 original size:46 final size:46
Alignment explanation
Indices: 5094168--5094348 Score: 217
Period size: 46 Copynumber: 3.9 Consensus size: 46
5094158 TATCATGTAA
* * * *
5094168 CACACCCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCATT
1 CACATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT
*
5094214 CGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT
1 CACATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TT
* *
5094265 -ACAT-C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATT
1 CACATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT
*
5094307 CACATCCATAAGTGAACTCGGACTCAACTCAACGTGTTCGGA
1 CACATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5094349 TGTTCAACCA
Statistics
Matches: 115, Mismatches: 11, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
44 2 0.02
45 2 0.02
46 65 0.57
47 29 0.25
48 2 0.02
49 2 0.02
50 4 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CACATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT
Found at i:5094799 original size:30 final size:30
Alignment explanation
Indices: 5094765--5094824 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5094755 CCTTAATACG
5094765 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* * *
5094795 AACTTTTGCATAATTATACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
5094825 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:5095189 original size:47 final size:47
Alignment explanation
Indices: 5095118--5095285 Score: 202
Period size: 47 Copynumber: 3.6 Consensus size: 47
5095108 TAAGCTAAAT
5095118 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
* * * * *
5095165 CGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATG---C--GGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA--TC
*
5095212 TGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
5095259 CGAACTCGTTGAGTTGAGTCCGAGTTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC
5095286 ACTTATGGAT
Statistics
Matches: 99, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
44 4 0.04
45 3 0.03
46 2 0.02
47 81 0.82
48 2 0.02
49 3 0.03
50 4 0.04
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
Found at i:5095283 original size:94 final size:93
Alignment explanation
Indices: 5095118--5095331 Score: 365
Period size: 94 Copynumber: 2.3 Consensus size: 93
5095108 TAAGCTAAAT
5095118 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAG
* * **
5095183 TTCGAGTTCACTTATGGATGCGGAATGTT
66 TCCGAGTTCACTTATGGATGC-GAACGCC
*
5095212 TGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAG
5095277 TCCGAGTTCACTTATGGATGCGAACGCC
66 TCCGAGTTCACTTATGGATGCGAACGCC
*
5095305 CGAGCTCGTTGAGTTGAGTCCGAGTTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC
5095332 ACTTATGGGT
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 29 0.26
94 84 0.74
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.29
Consensus pattern (93 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAG
TCCGAGTTCACTTATGGATGCGAACGCC
Found at i:5099374 original size:47 final size:47
Alignment explanation
Indices: 5099323--5099499 Score: 222
Period size: 47 Copynumber: 3.8 Consensus size: 47
5099313 TGGTTCAACA
*
5099323 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
5099370 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA--A--CG
5099417 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
*
5099463 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5099500 GCGGGTTACA
Statistics
Matches: 113, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
43 2 0.02
44 5 0.04
45 2 0.02
46 37 0.33
47 58 0.51
48 3 0.03
50 6 0.05
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:5116064 original size:28 final size:29
Alignment explanation
Indices: 5115991--5116078 Score: 101
Period size: 28 Copynumber: 3.1 Consensus size: 29
5115981 AGCATGGCTG
* * *
5115991 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCAGAGCCA
* *
5116018 CCAGATACAGATATTTTGTGGCAGGGCCA
1 CCAGATACAGATAATTTGTGGCAGAGCCA
*
5116047 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCAGAGCCA
5116075 CCAG
1 CCAG
5116079 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 11 0.22
28 25 0.49
29 15 0.29
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCAGAGCCA
Found at i:5116231 original size:28 final size:28
Alignment explanation
Indices: 5116184--5116275 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
5116174 AAATTAACCC
*
5116184 TAGGGGTATAGA-GGTCATTTTGCATACA
1 TAGGGGTATA-ATGGTAATTTTGCATACA
5116212 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
5116240 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
5116268 TAGGGGTA
1 TAGGGGTA
5116276 CTCTAGTACA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
27 1 0.02
28 61 0.98
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:5120101 original size:6 final size:6
Alignment explanation
Indices: 5120053--5120087 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5120043 TATGATCTTT
* *
5120053 TTTTTA TTCTTC TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
5120088 GTACTTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:5140327 original size:25 final size:25
Alignment explanation
Indices: 5140293--5140344 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
5140283 AGTTGATTCG
5140293 AAGAAATGATCTAAAAACTTAAATT
1 AAGAAATGATCTAAAAACTTAAATT
5140318 AAGAAATGATCTAAAAACTTAAATT
1 AAGAAATGATCTAAAAACTTAAATT
5140343 AA
1 AA
5140345 TTTAACTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (25 bp):
AAGAAATGATCTAAAAACTTAAATT
Found at i:5143512 original size:18 final size:18
Alignment explanation
Indices: 5143489--5143523 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5143479 ACCCCTTAGA
5143489 ATCTGACCCATCTTTTAT
1 ATCTGACCCATCTTTTAT
5143507 ATCTGACCCATCTTTTA
1 ATCTGACCCATCTTTTA
5143524 CTCCATCGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.43
Consensus pattern (18 bp):
ATCTGACCCATCTTTTAT
Found at i:5150915 original size:6 final size:6
Alignment explanation
Indices: 5150904--5150979 Score: 89
Period size: 6 Copynumber: 12.3 Consensus size: 6
5150894 GAAGTCTCTC
* * * *
5150904 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAGTAC AACTGA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
*
5150952 AAATAA AAATAA ATAAAAA CAAATAA AA
1 AAATAA AAATAA A-AATAA -AAATAA AA
5150980 TGAAAATAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
6 50 0.85
7 8 0.14
8 1 0.02
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:5153144 original size:11 final size:11
Alignment explanation
Indices: 5153130--5153159 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5153120 AACATTATAC
*
5153130 AATAATTAAAT
1 AATAATAAAAT
5153141 AATAATAAAAT
1 AATAATAAAAT
5153152 AATAATAA
1 AATAATAA
5153160 TAACAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:5155970 original size:19 final size:19
Alignment explanation
Indices: 5155946--5156023 Score: 115
Period size: 19 Copynumber: 4.1 Consensus size: 19
5155936 ATCTTTAAGA
5155946 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
5155965 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
5155984 ATA--CACTCTTAGATATG
1 ATATGCAATCTTAGATATG
5156001 ATATGCAATCTTAAAGATATG
1 ATATGCAATCTT--AGATATG
5156022 AT
1 AT
5156024 CTTGTAATCT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.30
19 28 0.53
21 9 0.17
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:5155975 original size:36 final size:36
Alignment explanation
Indices: 5155935--5156021 Score: 108
Period size: 36 Copynumber: 2.4 Consensus size: 36
5155925 ATGGAAATAT
5155935 AATCTTTAAGAATATGCAATCTTAGATATGATATGC
1 AATCTTTAAGAATATGCAATCTTAGATATGATATGC
* *
5155971 AATC-TT-AGATATGATACACTCTTAGATATGATATGC
1 AATCTTTAAGA-AT-ATGCAATCTTAGATATGATATGC
*
5156007 AATCTTAAAG-ATATG
1 AATCTTTAAGAATATG
5156022 ATCTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
34 3 0.07
35 6 0.14
36 31 0.72
37 1 0.02
38 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (36 bp):
AATCTTTAAGAATATGCAATCTTAGATATGATATGC
Found at i:5160634 original size:9 final size:9
Alignment explanation
Indices: 5160620--5160672 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
5160610 TCTATTTCAA
5160620 AAAAAAAAG
1 AAAAAAAAG
5160629 AAAAAAGAA-
1 AAAAAA-AAG
* *
5160638 AAGAAAAAT
1 AAAAAAAAG
*
5160647 AATAAAAAG
1 AAAAAAAAG
*
5160656 AATAAAAAG
1 AAAAAAAAG
5160665 AAAAAAAA
1 AAAAAAAA
5160673 TGGAGAGGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 2 0.05
9 34 0.89
10 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:5160639 original size:12 final size:11
Alignment explanation
Indices: 5160618--5160672 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 11
5160608 CTTCTATTTC
5160618 AAAAAAAAAAG
1 AAAAAAAAAAG
5160629 AAAAAAGAAAAG
1 AAAAAA-AAAAG
5160641 AAAAATAATAAA-
1 AAAAA-AA-AAAG
*
5160653 AAGAATAAAAAG
1 AA-AAAAAAAAG
5160665 AAAAAAAA
1 AAAAAAAA
5160673 TGGAGAGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 14 0.38
12 17 0.46
13 6 0.16
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.05
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5161751 original size:44 final size:43
Alignment explanation
Indices: 5161557--5162030 Score: 340
Period size: 44 Copynumber: 10.8 Consensus size: 43
5161547 GAAACAAGAT
5161557 TTGGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAG-TCGAAGATAGCAGA
* * * * **
5161600 TCT--AATACTCCTGTGCTTACAGCGAAGC-AGATCGAAGATTTCAGCA
1 T-TGGCAT-C-CCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGCAG-A
* * * **
5161646 -TGGCATCCCTATGTTTATAAGGAACAAGTTGAAGATTTCAGCA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGCAG-A
* *
5161689 -TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAACAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGCAGA
* * *
5161731 TTTTGCATCCCTATGTTTATAGGGAAGAA-TCGAAGATAGCAGA
1 -TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGCAGA
* * * * * **
5161774 TCTGACATTCCTGTGCTTACAGTGAA-ACAGATCGAAGATTTCAGCA
1 T-TGGCATCCCTGTGTTTATAGGGAACA-AG-TCGAAGATAGCAG-A
*
5161820 -TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGCAGA
* * *
5161862 TTTGGCATCGCTGTGTTTATAGGGAACAAATCAAAGATAGCAGA
1 -TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGCAGA
* * * * * **
5161906 TCTGACATTCCTGTGCTTACAGTGAA-ATAGATCGAAGATTTCAGCA
1 T-TGGCATCCCTGTGTTTATAGGGAACA-AG-TCGAAGATAGCAG-A
*
5161952 -TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
1 TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGCAGA
* * * * *
5161994 TTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA
1 -TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGA
5162031 CATAGCTGAA
Statistics
Matches: 339, Mismatches: 67, Indels: 49
0.75 0.15 0.11
Matches are distributed among these distances:
42 7 0.02
43 106 0.31
44 182 0.54
45 39 0.12
46 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (43 bp):
TTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGCAGA
Found at i:5161851 original size:174 final size:175
Alignment explanation
Indices: 5161553--5161890 Score: 527
Period size: 174 Copynumber: 1.9 Consensus size: 175
5161543 CAGAGAAACA
* *
5161553 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTAATACTCCTGTGCTT
1 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCAGATCTAACACTCCTGTGCTT
* *
5161618 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAAGGAACAAGTTGAAGATT
66 ACAGCGAAACAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAAGGAACAAGTTGAAGATA
*
5161683 TCAGCA-TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAAC
131 GCAG-ATTGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAAC
* * * *
5161728 AGATTTTGCATCCCTATGTTTATAGGGAAGA-ATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCAGATCTAACACTCCTGTGCTT
* * *
5161792 ACAGTGAAACAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAACAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAAGGAACAAGTTGAAGATA
*
5161857 GCAGATTTGGCATCGCTGTGTTTATAGGGAACAA
131 GCAGA-TTGGCATCCCTGTGTTTATAGGGAACAA
5161891 ATCAAAGATA
Statistics
Matches: 148, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
173 1 0.01
174 93 0.63
175 54 0.36
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (175 bp):
AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCAGATCTAACACTCCTGTGCTT
ACAGCGAAACAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAAGGAACAAGTTGAAGATA
GCAGATTGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAAC
Found at i:5161970 original size:132 final size:131
Alignment explanation
Indices: 5161676--5162030 Score: 595
Period size: 132 Copynumber: 2.7 Consensus size: 131
5161666 GGAACAAGTT
* *
5161676 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAACAGATTTTGCATCC
1 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCAT-C
* *
5161741 CTATGTTTATAGGGAA-GAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAACAGA
65 CTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAACAGA
5161805 TC
130 TC
5161807 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCG
1 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATC-
* *
5161872 CTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAATAGA
65 CTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAACAGA
5161937 TC
130 TC
5161939 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
1 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
* * *
5162004 TTGTGCTTACAAGGAACAAATCGAAGA
66 -TGTGTTTATAGGGAACAAATCGAAGA
5162031 CATAGCTGAA
Statistics
Matches: 211, Mismatches: 10, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
130 1 0.00
131 77 0.36
132 133 0.63
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (131 bp):
GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
TGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAACAGAT
C
Found at i:5162317 original size:19 final size:19
Alignment explanation
Indices: 5162293--5162355 Score: 103
Period size: 19 Copynumber: 3.4 Consensus size: 19
5162283 TTTAAGAATT
5162293 TGCAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
5162312 TGCAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
*
5162331 --CACTCTTAGATATGATA
1 TGCAATCTTAGATATGATA
5162348 TGCAATCT
1 TGCAATCT
5162356 CAAAGATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.40
19 24 0.60
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (19 bp):
TGCAATCTTAGATATGATA
Found at i:5162562 original size:16 final size:16
Alignment explanation
Indices: 5162541--5162576 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5162531 TCAATCAAAT
5162541 TTCTCTCCCTCTTGCG
1 TTCTCTCCCTCTTGCG
5162557 TTCTCTCCCTCTTGCG
1 TTCTCTCCCTCTTGCG
5162573 TTCT
1 TTCT
5162577 TACTCCCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.42, G:0.11, T:0.47
Consensus pattern (16 bp):
TTCTCTCCCTCTTGCG
Found at i:5165860 original size:40 final size:39
Alignment explanation
Indices: 5165768--5165862 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 39
5165758 ACCATCTCTG
* * *
5165768 TCCAACCCAACACACC-ATGTGGGGATAAAATAGACCTA
1 TCCAACCCTACACACCAATATGGGGATAAAATAGACCCA
* * *
5165806 CCCAGCCCTGCACACCAACTATGGGGATAAAATCA-ACCCA
1 TCCAACCCTACACACCAA-TATGGGGATAAAAT-AGACCCA
5165846 TCCAACCCTACACACCA
1 TCCAACCCTACACACCA
5165863 CATGGTACCG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
38 12 0.27
39 1 0.02
40 31 0.69
41 1 0.02
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.14
Consensus pattern (39 bp):
TCCAACCCTACACACCAATATGGGGATAAAATAGACCCA
Found at i:5170817 original size:24 final size:24
Alignment explanation
Indices: 5170763--5170890 Score: 158
Period size: 24 Copynumber: 5.4 Consensus size: 24
5170753 GAGACATGGC
*
5170763 CAGTAAGCTCT-TCATGAGCTGATAA
1 CAGTAAGCTCTAT--TGAGCTGAAAA
5170788 CAGTAAGCTCTATTGAGCTGAAAA
1 CAGTAAGCTCTATTGAGCTGAAAA
*
5170812 CGGTAAGCTCTATTGAGCTGAAAA
1 CAGTAAGCTCTATTGAGCTGAAAA
*
5170836 CAGTAAGCTCTATTAAGCTG--AA
1 CAGTAAGCTCTATTGAGCTGAAAA
*
5170858 CAGTAAGCTCT-TCTAAGCTG-AAA
1 CAGTAAGCTCTAT-TGAGCTGAAAA
5170881 CAGTAAGCTC
1 CAGTAAGCTC
5170891 ATACAAGCTA
Statistics
Matches: 96, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.01
22 20 0.21
23 12 0.12
24 51 0.53
25 11 0.11
26 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (24 bp):
CAGTAAGCTCTATTGAGCTGAAAA
Found at i:5173828 original size:25 final size:24
Alignment explanation
Indices: 5173794--5173846 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
5173784 AAGTTCAAGC
* *
5173794 GAGCCATATCAGGAA-GCTCATAAA
1 GAGCCATATCA-AAACGCTCAGAAA
5173818 GAGCCTATATCAAAACGCTCAGAAA
1 GAGCC-ATATCAAAACGCTCAGAAA
5173843 GAGC
1 GAGC
5173847 TATGTATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAAAACGCTCAGAAA
Found at i:5180148 original size:5 final size:5
Alignment explanation
Indices: 5180132--5180225 Score: 122
Period size: 5 Copynumber: 18.6 Consensus size: 5
5180122 GCAACCCAAT
*
5180132 TTTTA -TTT- TTTTA TTTTTA TTTTA TAATTTA TTATT- TATTA TTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA T--TTTA TT-TTA TTTTA TTTTA
5180178 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
5180226 ATTAATTTAT
Statistics
Matches: 80, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
4 8 0.10
5 60 0.75
6 7 0.09
7 5 0.06
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5182102 original size:12 final size:12
Alignment explanation
Indices: 5182085--5182118 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5182075 TTTAAAGAAA
*
5182085 TAATAATGATAT
1 TAATAATAATAT
5182097 TAATAATAATAT
1 TAATAATAATAT
5182109 TAAT-ATAATA
1 TAATAATAATA
5182119 ATAAATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:5189962 original size:12 final size:12
Alignment explanation
Indices: 5189926--5189973 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
5189916 TATACTTTAA
5189926 AAAATAATATTT
1 AAAATAATATTT
5189938 AATAATAAT-TTT
1 AA-AATAATATTT
*
5189950 AAAATAGTATTT
1 AAAATAATATTT
5189962 AATATATAATAT
1 AA-A-ATAATAT
5189974 GATAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 5 0.17
12 12 0.40
13 7 0.23
14 6 0.20
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
AAAATAATATTT
Found at i:5190203 original size:20 final size:21
Alignment explanation
Indices: 5190170--5190210 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5190160 AATATGAAAG
*
5190170 TATATATATGTAAAAATAACA
1 TATATATATATAAAAATAACA
5190191 TATA-ATATATAAAAATAACA
1 TATATATATATAAAAATAACA
5190211 CAATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
TATATATATATAAAAATAACA
Found at i:5190294 original size:10 final size:10
Alignment explanation
Indices: 5190261--5190315 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
5190251 ATTTGTGAAA
5190261 AATAATATAT
1 AATAATATAT
* *
5190271 AGTAA-ACAAT
1 AATAATA-TAT
5190281 AATAATATAT
1 AATAATATAT
5190291 AATAATATAAT
1 AATAATAT-AT
*
5190302 TATAATATAT
1 AATAATATAT
5190312 AATA
1 AATA
5190316 CAAAGATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 1 0.03
10 25 0.69
11 10 0.28
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AATAATATAT
Found at i:5190300 original size:18 final size:18
Alignment explanation
Indices: 5190279--5190329 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
5190269 ATAGTAAACA
5190279 ATAATAATATATAATAAT
1 ATAATAATATATAATAAT
*
5190297 ATAATTATA-ATATATAAT
1 ATAATAATATATA-ATAAT
*
5190315 ACAA-AGATATATAAT
1 ATAATA-ATATATAAT
5190330 CATTACGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
ATAATAATATATAATAAT
Found at i:5191589 original size:15 final size:15
Alignment explanation
Indices: 5191569--5191607 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
5191559 CCCTCAACTT
5191569 CGCCACCATGCATTG
1 CGCCACCATGCATTG
*
5191584 CGCCACTATGCATTG
1 CGCCACCATGCATTG
*
5191599 TGCCACCAT
1 CGCCACCAT
5191608 CAGCGCGCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (15 bp):
CGCCACCATGCATTG
Found at i:5192534 original size:15 final size:15
Alignment explanation
Indices: 5192496--5192534 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
5192486 TCGCGCGCTG
*
5192496 ATGGTGGCACAATGC
1 ATGGTGGCGCAATGC
5192511 ATGGTGGCGCAATGC
1 ATGGTGGCGCAATGC
5192526 ATGGTGGCG
1 ATGGTGGCG
5192535 AAGTTGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.41, T:0.21
Consensus pattern (15 bp):
ATGGTGGCGCAATGC
Found at i:5196746 original size:21 final size:21
Alignment explanation
Indices: 5196722--5196761 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5196712 AACTGACTTT
*
5196722 TAACTAAACTAGATCAATTAA
1 TAACCAAACTAGATCAATTAA
* *
5196743 TAACCAAATTAGATTAATT
1 TAACCAAACTAGATCAATT
5196762 CGATCAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (21 bp):
TAACCAAACTAGATCAATTAA
Found at i:5198203 original size:29 final size:30
Alignment explanation
Indices: 5198165--5198221 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
5198155 AGCCAGAAAA
* *
5198165 TTTATATTTTCCATCTTTCTATTTTTTCCC
1 TTTATATTTTCCATATTTCTAATTTTTCCC
5198195 TTTA-ATTTTCCATATTTCTAATTTTTC
1 TTTATATTTTCCATATTTCTAATTTTTC
5198222 ATTCCACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.18, C:0.19, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTATATTTTCCATATTTCTAATTTTTCCC
Found at i:5199004 original size:20 final size:21
Alignment explanation
Indices: 5198947--5199005 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
5198937 GGTTAACATG
5198947 ATAATAACTATAATAAAATAAA
1 ATAATAAC-ATAATAAAATAAA
*
5198969 ATAATTACATAA-AAAAT-AA
1 ATAATAACATAATAAAATAAA
5198988 ATAA-AACATAGATAAAAT
1 ATAATAACATA-ATAAAAT
5199006 TTGAAATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.15
19 7 0.21
20 10 0.30
21 4 0.12
22 7 0.21
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (21 bp):
ATAATAACATAATAAAATAAA
Found at i:5206934 original size:13 final size:13
Alignment explanation
Indices: 5206916--5206940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5206906 TATTATGATA
5206916 ATTTAGTATTGAG
1 ATTTAGTATTGAG
5206929 ATTTAGTATTGA
1 ATTTAGTATTGA
5206941 TTTCAAAAAA
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:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
ATTTAGTATTGAG
Found at i:5211223 original size:382 final size:383
Alignment explanation
Indices: 5210513--5211280 Score: 1029
Period size: 382 Copynumber: 2.0 Consensus size: 383
5210503 CTACTCGTAA
* * * * ** * *
5210513 CTAAGTATCATTCCCATTCAAAGTATGTTACACAATCATTTTTGAGTCCCACGCGAGCTTATGGA
1 CTAAGTACCATTCCCATTAAAAGTATGTTACACAATCATTTCTAAGTCCCACAAGAGCTTACGAA
** * * *
5210578 AGCTCTTTTGCTAACTCGGGCATGAATTAGGACCAAATTATAATGTTCTAAAAATTTCGGGTCGA
66 AGCTCTTTTGCTAACTCGAACATGAATTAGGACCAAATTATAAAGTTCTAAAAATTTCAGGCCGA
* * * *
5210643 CATCGCGACTTCATAATTTTCTTGATGCAACCACATCAACTCAGTGAGTTAGGTTGCAACATCAA
131 CATCACGACTTCATAATTTCCTTGATCCAACCACATCAACTCAGTGAGTTACGTTGCAACATCAA
* * *
5210708 GCCTTTCAACATCGCGACACCACTTACTGTCGGACGAAGTTGCGAAGTCAAAATTTCTTGGTTGC
196 ACCTCTCAACATCGCAACACCACTTACTGTCGGACGAAGTTGCGAAGTCAAAATTTCTTGGTTGC
* * * *
5210773 AACGTTGCCCCTATTTTTTACAAAATACACTTTTTTTTGTACCTATTCAATAATTTCCAACCAAA
261 AACGTTGCCCATATTCTTGACAAAATACACTTTTTTTTGTACCTATTCAATAATTTCCAACAAAA
5210838 TCATATGTTCACATTCAATC-ATTTACCAATCCTACCTATGCCAAATCATGACAAAAC
326 TCATATGTTCACATTCAATCAATTTACCAATCCTACCTATGCCAAATCATGACAAAAC
* *
5210895 CTAAGTACCATTCCTATTAAAAGTATGTTACACAATCATTTCTAAGTCCTACAAGAGCTTACGAA
1 CTAAGTACCATTCCCATTAAAAGTATGTTACACAATCATTTCTAAGTCCCACAAGAGCTTACGAA
* * *
5210960 AGCTCTTTTGCTAACTTGAACATGAATTAGGACCAAATTATAAAGTTTTAAAAATTTTAGGCCGA
66 AGCTCTTTTGCTAACTCGAACATGAATTAGGACCAAATTATAAAGTTCTAAAAATTTCAGGCCGA
* * * *
5211025 CGTCACGACTTCATAATTTCCTT-ATCCTGACCACGTCAACTCAGTGAGTTACGTTGCAACGTCA
131 CATCACGACTTCATAATTTCCTTGATCC-AACCACATCAACTCAGTGAGTTACGTTGCAACATCA
* * ** * * * * ***
5211089 AATCTCTCCACATCGCAACGTCACTTATTGTTGGATGAAGTTGCGATGTTGGAATTTCTTGGTTG
195 AACCTCTCAACATCGCAACACCACTTACTGTCGGACGAAGTTGCGAAGTCAAAATTTCTTGGTTG
* * **
5211154 CAACGTTGCCCATGTTCTTGGCAAAATACA-TTTTCTTTTGTACCTATTCAATAATTTTGAACAA
260 CAACGTTGCCCATATTCTTGACAAAATACACTTTT-TTTTGTACCTATTCAATAATTTCCAACAA
* * * *
5211218 AATCATATGTTTATATTCAATCAATTTACCAATTCTACCTATGCCAGATCATGACAAAAC
324 AATCATATGTTCACATTCAATCAATTTACCAATCCTACCTATGCCAAATCATGACAAAAC
5211278 CTA
1 CTA
5211281 TTATAGCAAG
Statistics
Matches: 331, Mismatches: 52, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
381 7 0.02
382 286 0.86
383 38 0.11
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (383 bp):
CTAAGTACCATTCCCATTAAAAGTATGTTACACAATCATTTCTAAGTCCCACAAGAGCTTACGAA
AGCTCTTTTGCTAACTCGAACATGAATTAGGACCAAATTATAAAGTTCTAAAAATTTCAGGCCGA
CATCACGACTTCATAATTTCCTTGATCCAACCACATCAACTCAGTGAGTTACGTTGCAACATCAA
ACCTCTCAACATCGCAACACCACTTACTGTCGGACGAAGTTGCGAAGTCAAAATTTCTTGGTTGC
AACGTTGCCCATATTCTTGACAAAATACACTTTTTTTTGTACCTATTCAATAATTTCCAACAAAA
TCATATGTTCACATTCAATCAATTTACCAATCCTACCTATGCCAAATCATGACAAAAC
Found at i:5211569 original size:30 final size:30
Alignment explanation
Indices: 5211529--5211586 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5211519 CTGGGCATTT
* *
5211529 CCACACGGGCTGGGCACACGCCCGTGTGAG
1 CCACACGGGCTGGACACACGCCCATGTGAG
* *
5211559 CCACATGGGCTGGACACACTCCCATGTG
1 CCACACGGGCTGGACACACGCCCATGTG
5211587 CCAACCGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.14
Consensus pattern (30 bp):
CCACACGGGCTGGACACACGCCCATGTGAG
Found at i:5219531 original size:83 final size:83
Alignment explanation
Indices: 5219400--5219570 Score: 333
Period size: 83 Copynumber: 2.1 Consensus size: 83
5219390 GACACACGGG
5219400 CGTGTCCTAGGCCGTGTGAAACTTGGAGCTAAAATTTTCAATTTTAAAACAAGTTAGAGAGTTAT
1 CGTGTCCTAGGCCGTGTGAAACTTGGAGCTAAAATTTTCAATTTTAAAACAAGTTAGAGAGTTAT
5219465 ACGGGCAAGGCACACAGC
66 ACGGGCAAGGCACACAGC
*
5219483 TGTGTCCTAGGCCGTGTGAAACTTGGAGCTAAAATTTTCAATTTTAAAACAAGTTAGAGAGTTAT
1 CGTGTCCTAGGCCGTGTGAAACTTGGAGCTAAAATTTTCAATTTTAAAACAAGTTAGAGAGTTAT
5219548 ACGGGCAAGGCACACAGC
66 ACGGGCAAGGCACACAGC
5219566 CGTGT
1 CGTGT
5219571 ATGAGACACA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (83 bp):
CGTGTCCTAGGCCGTGTGAAACTTGGAGCTAAAATTTTCAATTTTAAAACAAGTTAGAGAGTTAT
ACGGGCAAGGCACACAGC
Found at i:5220416 original size:14 final size:13
Alignment explanation
Indices: 5220361--5220427 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 13
5220351 TTTTCCTATT
5220361 TTATTTTTTGTTTA
1 TTATTTTTT-TTTA
*
5220375 TTATTATTTTTTA
1 TTATTTTTTTTTA
** *
5220388 TTAATTCATTCTTA
1 TT-ATTTTTTTTTA
5220402 TTATTTTTATTTTA
1 TTATTTTT-TTTTA
5220416 TT-TTATTTTTTT
1 TTATT-TTTTTTT
5220428 GTATCTTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
13 16 0.37
14 27 0.63
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (13 bp):
TTATTTTTTTTTA
Found at i:5220425 original size:6 final size:5
Alignment explanation
Indices: 5220357--5220442 Score: 54
Period size: 5 Copynumber: 17.0 Consensus size: 5
5220347 CTCATTTTCC
* * * *
5220357 TATTT TATTT TTTGTT TATTAT TATTT T-TTAT TAATT CATTCT TATTA
1 TATTT TATTT TAT-TT TATT-T TATTT TATT-T TATTT TATT-T TATTT
*
5220405 T-TTT TATTT TATTT TATTT T-TTT GTATCT TA-TT TATTT
1 TATTT TATTT TATTT TATTT TATTT -TATTT TATTT TATTT
5220443 CATTATTCTA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
4 11 0.18
5 35 0.56
6 16 0.26
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:5220439 original size:19 final size:19
Alignment explanation
Indices: 5220372--5220442 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
5220362 TATTTTTTGT
5220372 TTATTATTATTTTTTATTAAT-
1 TTATT-TTATTTTTT-TT-ATC
* * *
5220393 TCATTCTTATTATTTTTATT
1 TTATT-TTATTTTTTTTATC
5220413 TTATTTTATTTTTTTGTATC
1 TTATTTTATTTTTTT-TATC
5220433 TTA-TTTATTT
1 TTATTTTATTT
5220443 CATTATTCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 18 0.43
20 12 0.29
21 12 0.29
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (19 bp):
TTATTTTATTTTTTTTATC
Found at i:5222189 original size:6 final size:6
Alignment explanation
Indices: 5222173--5222234 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
5222163 ATTTATTTTC
* * *
5222173 TTTTA- TTTTAT TTTTAT CTTTAT TTTTAG TTTTAT TTCTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
5222220 GTTTT-T TGTTAT TTT
1 -TTTTAT TTTTAT TTT
5222235 CTTAGACTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
5 8 0.17
6 34 0.74
7 4 0.09
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:5222196 original size:12 final size:11
Alignment explanation
Indices: 5222164--5222234 Score: 65
Period size: 12 Copynumber: 6.2 Consensus size: 11
5222154 ATTGAGTCCA
*
5222164 TTTATTTT-CT
1 TTTATTTTATT
5222174 TTTATTTTATT
1 TTTATTTTATT
5222185 TTTATCTTTATT
1 TTTAT-TTTATT
5222197 TTTAGTTTTATT
1 TTTA-TTTTATT
*
5222209 TCTATTTTTATGT
1 TTTA-TTTTAT-T
5222222 TTT-TTGTTATT
1 TTTATT-TTATT
5222233 TT
1 TT
5222235 CTTAGACTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
10 8 0.15
11 11 0.21
12 29 0.56
13 4 0.08
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:5222199 original size:18 final size:17
Alignment explanation
Indices: 5222164--5222234 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 17
5222154 ATTGAGTCCA
*
5222164 TTTA-TTTTCTTTTA-T
1 TTTATTTTTATTTTATT
5222179 TTTATTTTTATCTTTATT
1 TTTATTTTTAT-TTTATT
*
5222197 TTTAGTTTTATTTCTATT
1 TTTATTTTTATTT-TATT
5222215 TTTATGTTTT-TTGTTATT
1 TTTAT-TTTTATT-TTATT
5222233 TT
1 TT
5222235 CTTAGACTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
15 4 0.09
16 5 0.11
17 6 0.13
18 27 0.57
19 5 0.11
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTATTTTTATTTTATT
Found at i:5224112 original size:30 final size:30
Alignment explanation
Indices: 5224076--5224154 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
5224066 CTAGGCATTT
* * *
5224076 CCATACGGGCTAGTCACGCGCCCGTGTAAG
1 CCATACGGGCTAGGCACACACCCGTGTAAG
* * *
5224106 CCATACGAGCTGGGCACACACCCGTGTGAG
1 CCATACGGGCTAGGCACACACCCGTGTAAG
*
5224136 CCACACGGGCT-GG-ACACAC
1 CCATACGGGCTAGGCACACAC
5224155 GCCCATGTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 6 0.15
29 2 0.05
30 33 0.80
ACGTcount: A:0.23, C:0.35, G:0.29, T:0.13
Consensus pattern (30 bp):
CCATACGGGCTAGGCACACACCCGTGTAAG
Found at i:5230924 original size:22 final size:22
Alignment explanation
Indices: 5230882--5230943 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
5230872 AAATTTTTAA
* *
5230882 ATTTTAAAAATAGAGATACTAT
1 ATTTTAAAAATAGAAAGACTAT
*
5230904 ATTTATAAAAATA-AAAGACTAA
1 ATTT-TAAAAATAGAAAGACTAT
* * *
5230926 ATTCTAAATATACAAAGA
1 ATTTTAAAAATAGAAAGA
5230944 ATTGGAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 7 0.21
22 18 0.55
23 8 0.24
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
ATTTTAAAAATAGAAAGACTAT
Found at i:5231410 original size:5 final size:6
Alignment explanation
Indices: 5231398--5231426 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5231388 TAAAATTAAA
5231398 TTATTT TTATTT TTATTT TTATTT TTATT
1 TTATTT TTATTT TTATTT TTATTT TTATT
5231427 ATTTCAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:5234562 original size:19 final size:19
Alignment explanation
Indices: 5234520--5234559 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5234510 TCACTCCCCC
5234520 CTTCTCTTCTTTCACCTTT
1 CTTCTCTTCTTTCACCTTT
5234539 CTTCTC-TCTTT-ACCCTTT
1 CTTCTCTTCTTTCA-CCTTT
5234557 CTT
1 CTT
5234560 TCTGCCGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 13 0.65
19 6 0.30
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (19 bp):
CTTCTCTTCTTTCACCTTT
Found at i:5235802 original size:38 final size:38
Alignment explanation
Indices: 5235751--5235831 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
5235741 TTGGAAAAGA
5235751 TGGCATGGGAGTATATAGTGTTGTTGAAATATTGGCTT
1 TGGCATGGGAGTATATAGTGTTGTTGAAATATTGGCTT
5235789 TGGCATGGGAGTATATAGTGTTGTTGAAATATTGGCTT
1 TGGCATGGGAGTATATAGTGTTGTTGAAATATTGGCTT
*
5235827 AGGCA
1 TGGCA
5235832 ACTAATATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.25, C:0.06, G:0.32, T:0.37
Consensus pattern (38 bp):
TGGCATGGGAGTATATAGTGTTGTTGAAATATTGGCTT
Found at i:5240448 original size:18 final size:18
Alignment explanation
Indices: 5240415--5240460 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5240405 AAATTATAAT
* *
5240415 ATTAATTTTGAGATTTTT
1 ATTAATTTTTAGATTTTA
* *
5240433 TTTAATTTTTATATTTTA
1 ATTAATTTTTAGATTTTA
5240451 ATTAATTTTT
1 ATTAATTTTT
5240461 CATTAATCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTAATTTTTAGATTTTA
Found at i:5249787 original size:17 final size:17
Alignment explanation
Indices: 5249767--5249801 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5249757 AATAATTTTA
5249767 AATTAATT-ATTATAATT
1 AATTAATTAATTA-AATT
5249784 AATTAATTAATTAAATT
1 AATTAATTAATTAAATT
5249801 A
1 A
5249802 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAATTAATTAAATT
Found at i:5252170 original size:18 final size:18
Alignment explanation
Indices: 5252147--5252207 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
5252137 TGTCAAGCGC
*
5252147 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
5252165 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
5252183 GTATCATAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
5252201 GTTTCCT
1 GTATCCT
5252208 TTTTCCAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.41
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Done.