Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 87 of 345
Found at i:28757895 original size:35 final size:35
Alignment explanation
Indices: 28757833--28757948 Score: 187
Period size: 35 Copynumber: 3.2 Consensus size: 35
28757823 CAATGATATG
*
28757833 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
28757869 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
*
28757904 CAATCTTAGATATGATTGTAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
28757941 CAATCTTA
1 CAATCTTA
28757949 AAAGATATGA
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
35 50 0.66
36 15 0.20
37 11 0.14
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:28759614 original size:27 final size:27
Alignment explanation
Indices: 28759579--28759755 Score: 185
Period size: 27 Copynumber: 6.6 Consensus size: 27
28759569 ACAACTAAGA
28759579 AATAACCTTTGTGGCATACTCTGAAAG
1 AATAACCTTTGTGGCATACTCTGAAAG
* * ** *
28759606 AATAGCCTTTATGGTGTTCTCTGAAAG
1 AATAACCTTTGTGGCATACTCTGAAAG
* ** *
28759633 AACAACCTTTGTGGTGTACTATGAAAG
1 AATAACCTTTGTGGCATACTCTGAAAG
* * *
28759660 AATAATCTTTGTGGCGTACTATGAAAG
1 AATAACCTTTGTGGCATACTCTGAAAG
* * *
28759687 AATAACTTTTATGGCATACTCTAAAAG
1 AATAACCTTTGTGGCATACTCTGAAAG
*
28759714 AATAACATTTGTGGCATACTCT-ATAAG
1 AATAACCTTTGTGGCATACTCTGA-AAG
*
28759741 AATAGCCTTTGTGGC
1 AATAACCTTTGTGGC
28759756 GTGTTCTAAT
Statistics
Matches: 126, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
26 1 0.01
27 125 0.99
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (27 bp):
AATAACCTTTGTGGCATACTCTGAAAG
Found at i:28759756 original size:81 final size:82
Alignment explanation
Indices: 28759574--28759757 Score: 210
Period size: 81 Copynumber: 2.3 Consensus size: 82
28759564 ACACGACAAC
* * * ** * *
28759574 TAAGAAATAACCTTTGTGGCATACTCTGAAAGAATAGCCTTTATGGTGTTCTCTGAAAGAACAAC
1 TAAG-AATAACCTTTGTGGCGTACTATGAAAGAATAACCTTTATGGCATACTCTAAAAGAACAAC
* **
28759639 CTTTGTGGTGTACTATGA
65 ATTTGTGGCATACTATGA
* * *
28759657 -AAGAATAATCTTTGTGGCGTACTATGAAAGAATAACTTTTATGGCATACTCTAAAAGAATAACA
1 TAAGAATAACCTTTGTGGCGTACTATGAAAGAATAACCTTTATGGCATACTCTAAAAGAACAACA
*
28759721 TTTGTGGCATACTCT-A
66 TTTGTGGCATACTATGA
*
28759737 TAAGAATAGCCTTTGTGGCGT
1 TAAGAATAACCTTTGTGGCGT
28759758 GTTCTAATTG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 80 0.95
82 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (82 bp):
TAAGAATAACCTTTGTGGCGTACTATGAAAGAATAACCTTTATGGCATACTCTAAAAGAACAACA
TTTGTGGCATACTATGA
Found at i:28760755 original size:13 final size:12
Alignment explanation
Indices: 28760725--28760758 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28760715 AAAGATAAAA
28760725 TATCATCTTTTT
1 TATCATCTTTTT
*
28760737 TGTCATCTTTTT
1 TATCATCTTTTT
28760749 TCATCATCTT
1 T-ATCATCTT
28760759 CCCCAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.15, C:0.21, G:0.03, T:0.62
Consensus pattern (12 bp):
TATCATCTTTTT
Found at i:28761926 original size:25 final size:25
Alignment explanation
Indices: 28761809--28761950 Score: 123
Period size: 24 Copynumber: 5.8 Consensus size: 25
28761799 AAGCTATTTG
*
28761809 GAGCTTCCTGTTA-ATGGCTC-TTT
1 GAGCTTCCTGTTATATGGCTCGTAT
* *
28761832 AGAGCTACCTGATAT-TGGCTCGTAT
1 -GAGCTTCCTGTTATATGGCTCGTAT
*
28761857 GAGCTTCCTGATT-TA-GGCTCTTAT
1 GAGCTTCCTG-TTATATGGCTCGTAT
* ** *
28761881 GAGCTTCTTGTTATAAAGCTCGGAT
1 GAGCTTCCTGTTATATGGCTCGTAT
* **
28761906 AAGCTTCCTGTTATATGGCTCACAT
1 GAGCTTCCTGTTATATGGCTCGTAT
*
28761931 GAGCTTCCCGTTATATGGCT
1 GAGCTTCCTGTTATATGGCT
28761951 TGAAGGAGTG
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.02
24 46 0.49
25 46 0.49
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCGTAT
Found at i:28761944 original size:50 final size:49
Alignment explanation
Indices: 28761849--28761945 Score: 115
Period size: 50 Copynumber: 2.0 Consensus size: 49
28761839 CCTGATATTG
* * ** **
28761849 GCTCGTATGAGCTTCCTGATTTAGGCTCTTATGAGCTTCTTGTTATAAA
1 GCTCGGATAAGCTTCCTGATTTAGGCTCACATGAGCTTCCCGTTATAAA
28761898 GCTCGGATAAGCTTCCTG-TTATATGGCTCACATGAGCTTCCCGTTATA
1 GCTCGGATAAGCTTCCTGATT-TA-GGCTCACATGAGCTTCCCGTTATA
28761946 TGGCTTGAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 2 0.05
49 18 0.45
50 20 0.50
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (49 bp):
GCTCGGATAAGCTTCCTGATTTAGGCTCACATGAGCTTCCCGTTATAAA
Found at i:28770888 original size:20 final size:20
Alignment explanation
Indices: 28770863--28770911 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28770853 AAATATTACT
28770863 TTAAAT-ATAAAATATTCAAA
1 TTAAATCAT-AAATATTCAAA
* *
28770883 TTAAATCATCATTATTCAAA
1 TTAAATCATAAATATTCAAA
28770903 TTAAATCAT
1 TTAAATCAT
28770912 CATTCATAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAATCATAAATATTCAAA
Found at i:28770912 original size:20 final size:20
Alignment explanation
Indices: 28770875--28770915 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28770865 AAATATAAAA
28770875 TATTCAAATTAAATCATCAT
1 TATTCAAATTAAATCATCAT
28770895 TATTCAAATTAAATCATCAT
1 TATTCAAATTAAATCATCAT
28770915 T
1 T
28770916 CATAGCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTCAAATTAAATCATCAT
Found at i:28772954 original size:63 final size:63
Alignment explanation
Indices: 28772854--28772978 Score: 205
Period size: 63 Copynumber: 2.0 Consensus size: 63
28772844 CTTAAGCAAC
* * *
28772854 CTTAGTACATCATTAACGTGATTCATGCAAGTCACATAACATCATCTATCATCTTGAAGGTAT
1 CTTAGTACATCATTAACATGATACATGCAAGTCACATAACATCATCTATCATCTTAAAGGTAT
* *
28772917 CTTAGTACATTATTAACATGATACATGCAAGTTACATAACATCATCTATCATCTTAAAGGTA
1 CTTAGTACATCATTAACATGATACATGCAAGTCACATAACATCATCTATCATCTTAAAGGTA
28772979 AGGTACAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (63 bp):
CTTAGTACATCATTAACATGATACATGCAAGTCACATAACATCATCTATCATCTTAAAGGTAT
Found at i:28774101 original size:28 final size:28
Alignment explanation
Indices: 28774070--28774126 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
28774060 TTTAAATCAG
28774070 TGGTGTGGTGCCTATTTTAATAAATAAT
1 TGGTGTGGTGCCTATTTTAATAAATAAT
* *
28774098 TGGTGTGGTGCCTATTTTGATTAATAAT
1 TGGTGTGGTGCCTATTTTAATAAATAAT
28774126 T
1 T
28774127 ACTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.46
Consensus pattern (28 bp):
TGGTGTGGTGCCTATTTTAATAAATAAT
Found at i:28774564 original size:39 final size:39
Alignment explanation
Indices: 28774510--28774588 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
28774500 AATCTATATA
28774510 TTACAGATTCCATAAATTGAGCAAGAAATGGATGGTTTC
1 TTACAGATTCCATAAATTGAGCAAGAAATGGATGGTTTC
28774549 TTACAGATTCCATAAATTGAGCAAGAAATGGATGGTTTC
1 TTACAGATTCCATAAATTGAGCAAGAAATGGATGGTTTC
28774588 T
1 T
28774589 GAAGCTGTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (39 bp):
TTACAGATTCCATAAATTGAGCAAGAAATGGATGGTTTC
Found at i:28783928 original size:30 final size:30
Alignment explanation
Indices: 28783894--28783954 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28783884 TCCTTAACTC
28783894 AAACTTTGGCAAAATTT-CAATTTTACCCCT
1 AAACTTTGGC-AAATTTACAATTTTACCCCT
* * *
28783924 AAACTTTTGCATATTTACAATTTTCCCCCT
1 AAACTTTGGCAAATTTACAATTTTACCCCT
28783954 A
1 A
28783955 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAATTTACAATTTTACCCCT
Found at i:28785578 original size:17 final size:18
Alignment explanation
Indices: 28785542--28785580 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28785532 TTTTTCTTAC
*
28785542 TTTATCTATTTTTGAATT
1 TTTATCTACTTTTGAATT
28785560 TTTATCTACTTTT-AATT
1 TTTATCTACTTTTGAATT
28785577 TTTA
1 TTTA
28785581 GAATTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTATCTACTTTTGAATT
Found at i:28787231 original size:13 final size:13
Alignment explanation
Indices: 28787213--28787237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28787203 GAACCAAAAA
28787213 TCTCTCCTTTTTC
1 TCTCTCCTTTTTC
28787226 TCTCTCCTTTTT
1 TCTCTCCTTTTT
28787238 TTTGTTTTAG
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTCTCCTTTTTC
Found at i:28788335 original size:47 final size:47
Alignment explanation
Indices: 28788275--28788405 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
28788265 CGGTAGTGCG
* * *
28788275 AATAAATTATCAATATATGCAAACAAGCTGCCAATAACGGTAATGTA
1 AATAAATTGTCAATATATGCAAACAAGCTGCCAATAACGATAATGCA
* * *
28788322 GATAAATTGTCAATATATGCAAACAAGCTGCTAGTAACGATAATGCA
1 AATAAATTGTCAATATATGCAAACAAGCTGCCAATAACGATAATGCA
* * * * *
28788369 AATAAAATGCCAATATATGTACACAAGATGCCAATAA
1 AATAAATTGTCAATATATGCAAACAAGCTGCCAATAA
28788406 TGTAATAAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (47 bp):
AATAAATTGTCAATATATGCAAACAAGCTGCCAATAACGATAATGCA
Found at i:28789559 original size:24 final size:25
Alignment explanation
Indices: 28789532--28789594 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
28789522 GCGTTTCCTC
*
28789532 GCACACATAGTGCTATATA-ATCTT
1 GCACACATAGTGCCATATAGATCTT
* * * *
28789556 GCACATATAGTGCCATGTAGTTTTT
1 GCACACATAGTGCCATATAGATCTT
28789581 GCACACATAGTGCC
1 GCACACATAGTGCC
28789595 GCATAACCTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 16 0.50
25 16 0.50
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (25 bp):
GCACACATAGTGCCATATAGATCTT
Found at i:28793275 original size:27 final size:27
Alignment explanation
Indices: 28793227--28793384 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
28793217 GCGAGGCTGC
* *
28793227 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
28793254 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
28793280 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
28793307 CAGATAATTGT-GCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
28793333 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
28793360 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
28793385 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
25 2 0.02
26 28 0.24
27 80 0.70
28 5 0.04
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:28793311 original size:53 final size:54
Alignment explanation
Indices: 28793245--28793384 Score: 239
Period size: 53 Copynumber: 2.6 Consensus size: 54
28793235 GTGACGAAGT
*
28793245 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
28793299 CACCAGATCAGATAATTGT-GCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
28793352 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
28793385 GACGCTTCCT
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
53 56 0.68
54 26 0.32
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:28793790 original size:8 final size:8
Alignment explanation
Indices: 28793774--28793803 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28793764 CTCAAAATAC
28793774 CGGCTTTT
1 CGGCTTTT
*
28793782 CGGCATTT
1 CGGCTTTT
28793790 CGGCTTTT
1 CGGCTTTT
28793798 CGGCTT
1 CGGCTT
28793804 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:28800527 original size:39 final size:38
Alignment explanation
Indices: 28800443--28800557 Score: 124
Period size: 39 Copynumber: 2.9 Consensus size: 38
28800433 CTCATTCAAT
* * * *
28800443 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAAT
1 GCCTTCGGGACTTAACCC-GA-ATTATAACTCGCACAAAG
* *
28800483 G-CTTCGGGACTTAACCCGAATTGGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGAATT-ATAACTCGCACAAAG
*
28800521 GCCTTCGGGACTTAACCGGAATTAATAACTCGCACAA
1 GCCTTCGGGACTTAACCCGAATT-ATAACTCGCACAA
28800558 TACCTTCGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
37 2 0.03
38 13 0.21
39 47 0.75
40 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (38 bp):
GCCTTCGGGACTTAACCCGAATTATAACTCGCACAAAG
Found at i:28800613 original size:40 final size:38
Alignment explanation
Indices: 28800443--28800617 Score: 108
Period size: 39 Copynumber: 4.5 Consensus size: 38
28800433 CTCATTCAAT
* * * *
28800443 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAAT
1 GCCTTCGGGACTT-AGCCGGA-ATTAATAACTAGCAC-AAA
* * ** * *
28800483 G-CTTCGGGACTTAACCCGAATTGGTATCTCGCACAAA
1 GCCTTCGGGACTTAGCCGGAATTAATAACTAGCACAAA
* *
28800520 GGCCTTCGGGACTTAACCGGAATTAATAACTCGCACAATA
1 -GCCTTCGGGACTTAGCCGGAATTAATAACTAGCACAA-A
* *
28800560 -CCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA
1 GCCTTCGGGA-CTTAG-CCGGAAT-TAATAAC-TAGCACAAA
28800599 GCCTTCGGGACTTAGCCGG
1 GCCTTCGGGACTTAGCCGG
28800618 CAGCATTCAA
Statistics
Matches: 110, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
37 7 0.06
38 25 0.23
39 56 0.51
40 19 0.17
41 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (38 bp):
GCCTTCGGGACTTAGCCGGAATTAATAACTAGCACAAA
Found at i:28801300 original size:40 final size:40
Alignment explanation
Indices: 28801208--28801332 Score: 146
Period size: 40 Copynumber: 3.1 Consensus size: 40
28801198 ACTCATTCAG
* * *
28801208 CTTCGGGACTTAACCCGGATTTTAA-AACTC-CACGAATGC
1 CTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAAGGC
** *
28801247 CTTCGGGACTTAACCCGGAATTGGTATCTCGCACAAAGGC
1 CTTCGGGACTTAACCCGGAATTAATAACTCGCACAAAGGC
* **
28801287 CTTCGTGACTTAACCCGGAATTAATAACTCGCACAAATAC
1 CTTCGGGACTTAACCCGGAATTAATAACTCGCACAAAGGC
28801327 CTTCGG
1 CTTCGG
28801333 ATCTCTAGTC
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
38 2 0.03
39 23 0.32
40 46 0.65
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAACCCGGAATTAATAACTCGCACAAAGGC
Found at i:28805776 original size:37 final size:37
Alignment explanation
Indices: 28805700--28805780 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
28805690 TTGCAGCAAT
****
28805700 AGTAGG-TCTAACTATACTCAATTCAGCTCCTGTTCA
1 AGTAGGTTCTAACTATACTCAATTCAGCTCCTACAAA
*
28805736 AGTAGGTTCTAACTATACTCAATTCATCTCCTACAAA
1 AGTAGGTTCTAACTATACTCAATTCAGCTCCTACAAA
28805773 AGTAGGTT
1 AGTAGGTT
28805781 TAGCATAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 6 0.15
37 33 0.85
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (37 bp):
AGTAGGTTCTAACTATACTCAATTCAGCTCCTACAAA
Found at i:28813905 original size:16 final size:16
Alignment explanation
Indices: 28813881--28813980 Score: 137
Period size: 16 Copynumber: 6.2 Consensus size: 16
28813871 TGGTTCACTA
*
28813881 TAATGGAATAGGGTTG
1 TAATGGAATAGAGTTG
* *
28813897 TAATTGAATAGAGGTG
1 TAATGGAATAGAGTTG
*
28813913 TAAAGGAATAGAGTTG
1 TAATGGAATAGAGTTG
* *
28813929 TAATTGAATAGAGGTG
1 TAATGGAATAGAGTTG
*
28813945 TAATGTAATAGAGTTG
1 TAATGGAATAGAGTTG
28813961 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
28813977 TAAT
1 TAAT
28813981 CAGTAATTCT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 71 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:28813980 original size:32 final size:32
Alignment explanation
Indices: 28813881--28813980 Score: 155
Period size: 32 Copynumber: 3.1 Consensus size: 32
28813871 TGGTTCACTA
*
28813881 TAATGGAATAGGGTTGTAATTGAATAGAGGTG
1 TAATGGAATAGAGTTGTAATTGAATAGAGGTG
*
28813913 TAAAGGAATAGAGTTGTAATTGAATAGAGGTG
1 TAATGGAATAGAGTTGTAATTGAATAGAGGTG
* * *
28813945 TAATGTAATAGAGTTGTAATGGAATAGAGTTG
1 TAATGGAATAGAGTTGTAATTGAATAGAGGTG
28813977 TAAT
1 TAAT
28813981 CAGTAATTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (32 bp):
TAATGGAATAGAGTTGTAATTGAATAGAGGTG
Found at i:28814040 original size:43 final size:46
Alignment explanation
Indices: 28813962--28814053 Score: 120
Period size: 43 Copynumber: 2.1 Consensus size: 46
28813952 ATAGAGTTGT
* * *
28813962 AATGGAATAGAGTTGTAATCAGTAATTCTATTGTTTGGTTTAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCTATTGTTTCGTTGAATGG
28814008 AATGGAATA-AGCTGTAAT-AGT-ATTCT-TGTGTTTCGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCTAT-TGTTTCGTTGAATGG
28814051 AAT
1 AAT
28814054 AGATGTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 1 0.02
43 21 0.50
44 3 0.07
45 8 0.19
46 9 0.21
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.40
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCTATTGTTTCGTTGAATGG
Found at i:28822591 original size:49 final size:49
Alignment explanation
Indices: 28822478--28822704 Score: 191
Period size: 49 Copynumber: 4.7 Consensus size: 49
28822468 TATAAGATGT
* ** * * *
28822478 GTCAGTGCAAGACCATGTCTATGACATGGCATCGG-CACGTATAGAG-GT
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACG-ATTGTGAGA
* * * *
28822526 GTCAGTGTAAGACCATGTTTGGGACATGGCAT-TGTCACGGTATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAT-TGTGAGA
* * * *
28822575 -TCTAGTGTAAGACCATGTCTGGGACATGCCATCGGCCTCGATTTTGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATTGTGAGA
* *
28822624 GTCAGTGTAAGACCATGTCTGGGACATGGCATC-G--ACTTAATG-GATGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-GATTGTGA-GA
* *
28822671 GCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCG
28822705 ATATTACACC
Statistics
Matches: 145, Mismatches: 25, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
46 3 0.02
47 36 0.25
48 37 0.26
49 62 0.43
50 7 0.05
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (49 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATTGTGAGA
Found at i:28823732 original size:28 final size:28
Alignment explanation
Indices: 28823691--28823788 Score: 151
Period size: 28 Copynumber: 3.5 Consensus size: 28
28823681 ACACGGGCTA
* *
28823691 GGACACGGGTGTGTCATGGCTGTATGAG
1 GGACACGGGCGTGTCATGGCCGTATGAG
*
28823719 GGACACGGGCGTGTCATGGCCGTGTGAG
1 GGACACGGGCGTGTCATGGCCGTATGAG
*
28823747 GGACACGGGCGTGTCATGGCCGTATAAG
1 GGACACGGGCGTGTCATGGCCGTATGAG
*
28823775 GGACACGGACGTGT
1 GGACACGGGCGTGT
28823789 GTTAGGCCGT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.18, C:0.19, G:0.43, T:0.19
Consensus pattern (28 bp):
GGACACGGGCGTGTCATGGCCGTATGAG
Found at i:28823777 original size:56 final size:57
Alignment explanation
Indices: 28823691--28823802 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
28823681 ACACGGGCTA
* * * *
28823691 GGACACGGGTGTGTCATGGCTGTATGAGGGACACGGGCGTGTCAT-GGCCGTGTGAG
1 GGACACGGGCGTGTCATGGCCGTATAAGGGACACGGACGTGTCATAGGCCGTGTGAG
**
28823747 GGACACGGGCGTGTCATGGCCGTATAAGGGACACGGACGTGTGTTAGGCCGTGTGA
1 GGACACGGGCGTGTCATGGCCGTATAAGGGACACGGACGTGTCATAGGCCGTGTGA
28823803 AAACCCTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 39 0.80
57 10 0.20
ACGTcount: A:0.18, C:0.19, G:0.43, T:0.21
Consensus pattern (57 bp):
GGACACGGGCGTGTCATGGCCGTATAAGGGACACGGACGTGTCATAGGCCGTGTGAG
Found at i:28830217 original size:30 final size:30
Alignment explanation
Indices: 28830181--28830246 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
28830171 CACGGACAGA
28830181 GACACGGCCGTGTGTCTCAGCCATGTGGAG
1 GACACGGCCGTGTGTCTCAGCCATGTGGAG
* *
28830211 GACACGGCCGTGTGTCTTAGCCGTGTGGAG
1 GACACGGCCGTGTGTCTCAGCCATGTGGAG
28830241 GACACG
1 GACACG
28830247 ACCTCTGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.17, C:0.26, G:0.38, T:0.20
Consensus pattern (30 bp):
GACACGGCCGTGTGTCTCAGCCATGTGGAG
Found at i:28834252 original size:42 final size:41
Alignment explanation
Indices: 28834149--28834311 Score: 141
Period size: 43 Copynumber: 3.8 Consensus size: 41
28834139 ATGTGTTCTC
* * *
28834149 GTGTAAGACCATGTTTGGGACGTTGTCATCG-ACTTATGATTTAT
1 GTGTAAGACCACGTCTGGGACATTG-CATCGTA-TT-TGATTT-T
*
28834193 GTGTAAGACCACATCTGGGACATTAGCATCGTATTTGATTTT
1 GTGTAAGACCACGTCTGGGACATT-GCATCGTATTTGATTTT
* * **
28834235 GTGTAAGACC-CTGTCTGGGACAGTGGCATTGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGACA-TTGCATCG-TATTTGATTTT
* *
28834278 ATGTAAGACCACGTCTGGGACATTTGCATTGTAT
1 GTGTAAGACCACGTCTGGGACA-TTGCATCGTAT
28834312 GAGTTTTTCA
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 28 0.28
43 42 0.42
44 28 0.28
45 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
GTGTAAGACCACGTCTGGGACATTGCATCGTATTTGATTTT
Found at i:28834271 original size:43 final size:42
Alignment explanation
Indices: 28834185--28834311 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 42
28834175 CATCGACTTA
* *
28834185 TGATTTATGTGTAAGACCACATCTGGGACATTAGCATCGTATT
1 TGATTT-TGTGTAAGACCACGTCTGGGACATTAGCATTGTATT
* *
28834228 TGATTTTGTGTAAGACC-CTGTCTGGGACAGTGGCATTGATATT
1 TGATTTTGTGTAAGACCAC-GTCTGGGACATTAGCATTG-TATT
*** *
28834271 TGATTACATGTAAGACCACGTCTGGGACATTTGCATTGTAT
1 TGATTTTGTGTAAGACCACGTCTGGGACATTAGCATTGTAT
28834312 GAGTTTTTCA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 29 0.40
43 41 0.57
44 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (42 bp):
TGATTTTGTGTAAGACCACGTCTGGGACATTAGCATTGTATT
Found at i:28838653 original size:30 final size:30
Alignment explanation
Indices: 28838619--28838679 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28838609 TCCTTAACTC
*
28838619 AAACTTTGGTAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
28838649 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
28838679 A
1 A
28838680 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:28849466 original size:55 final size:55
Alignment explanation
Indices: 28849360--28849467 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
28849350 GACAGTTTTG
* * *
28849360 ACCACGGGTGGTAGGCACGAGAGTGTCGCACGCCCGTGTTAATTGGACAGGATCA
1 ACCACAGGTGGTAGGCACGAGAGTGTCACACGCCCGTATTAATTGGACAGGATCA
* * *
28849415 ACCACAGGTGGTGGGCACGAGCGTGTCACACGCCCGTATTGATTTGG-CAGGAT
1 ACCACAGGTGGTAGGCACGAGAGTGTCACACGCCCGTATT-AATTGGACAGGAT
28849468 TGCCCACGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 41 0.89
56 5 0.11
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.19
Consensus pattern (55 bp):
ACCACAGGTGGTAGGCACGAGAGTGTCACACGCCCGTATTAATTGGACAGGATCA
Found at i:28852720 original size:93 final size:93
Alignment explanation
Indices: 28852561--28852731 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
28852551 GGATGGTTGA
* * *
28852561 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
28852626 TGAGT-TCGAGTTCGTGAGATGTAACTAG
66 TGAGTCT-GAGTTCGTGAGATGTAACTAG
* * *
28852654 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
28852719 TGAGTCTGAGTTC
66 TGAGTCTGAGTTC
28852732 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 70 0.99
94 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCTGAGTTCGTGAGATGTAACTAG
Found at i:28852734 original size:46 final size:46
Alignment explanation
Indices: 28852567--28852736 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 46
28852557 TTGAGCATCT
* * *
28852567 GAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
* * * * *
28852613 GAACTCATTGAGTTGAGTTCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC--CC
28852660 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
* *
28852706 GAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28852737 GGGGCGGGTT
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 55 0.55
47 26 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
Found at i:28854957 original size:16 final size:16
Alignment explanation
Indices: 28854933--28855032 Score: 139
Period size: 16 Copynumber: 6.2 Consensus size: 16
28854923 TGGTTCACTA
*
28854933 TAATGGAATAGGGTTG
1 TAATGGAATAGAGTTG
*
28854949 TAATTGAATAGA-TGTG
1 TAATGGAATAGAGT-TG
28854965 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
* *
28854981 TAATTGAATAGAGGTG
1 TAATGGAATAGAGTTG
*
28854997 TAATGTAATAGAGTTG
1 TAATGGAATAGAGTTG
28855013 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
28855029 TAAT
1 TAAT
28855033 CAGTAATTCT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.01
16 71 0.97
17 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:28855105 original size:44 final size:46
Alignment explanation
Indices: 28855017--28855105 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 46
28855007 GAGTTGTAAT
* * *
28855017 GGAATAGAGTTGTAATCAGTAATTCTATTGTGTGGTTTAATGGAAC
1 GGAATAGAGCTGTAATCAGTAATTCTATTGTGTCGTTGAATGGAAC
*
28855063 GGAATAGAGCTGTAAT-AGT-ATTCT-TGTGTTTCGTTGAATGGAA
1 GGAATAGAGCTGTAATCAGTAATTCTAT-TGTGTCGTTGAATGGAA
28855106 TAGATGTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 19 0.50
45 3 0.08
46 15 0.39
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (46 bp):
GGAATAGAGCTGTAATCAGTAATTCTATTGTGTCGTTGAATGGAAC
Found at i:28858132 original size:43 final size:43
Alignment explanation
Indices: 28857983--28858141 Score: 182
Period size: 43 Copynumber: 3.7 Consensus size: 43
28857973 TATGTGTTCT
* * *
28857983 CGTGTAAGACCATGTCTGGGACTTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTA
* *
28858027 CGTGCAAGACCACGTCTGGGACGTTGGCATCG-TATTTGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
*
28858069 CGTGTAAGACC-CTGTTTGGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTA
* *
28858112 CATGTAAGACCACATCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
28858142 TGTACATGTT
Statistics
Matches: 98, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.31
43 37 0.38
44 30 0.31
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:28863594 original size:48 final size:48
Alignment explanation
Indices: 28863493--28863758 Score: 187
Period size: 47 Copynumber: 5.6 Consensus size: 48
28863483 ATTGTGCGCT
* *
28863493 AGTGTAAGA-CATGTCTAGGACAT-GCATC--CGC-TATGAGATGTGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGTAT-AGAGGTGTC
* *
28863537 AGTGCAAGACCATGTCTATGACATGGCATCGGCACGTATAGAGGTGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGTATAGAGGTGTC
* * * * * * *
28863585 AGTGTAAGACCATGTTTGGGACATGGCATTGTCACGGTATGTGAGATCT-
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-GTAT-AGAGGTGTC
* * * *
28863634 AGTGTAAGACCAT-TC-AGGACATGCCATCGGCCTCGATTTCGA--TAGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGG-CACG-TATAGAGGT-GTC
* * * * * *
28863681 AGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTAATGGATGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGT-ATAGAGGTGTC
*
28863728 AGTGTAAGACCATGTCTAGGACGTGGCATCG
1 AGTGTAAGACCATGTCTAGGACATGGCATCG
28863759 ATATTACACC
Statistics
Matches: 173, Mismatches: 32, Indels: 30
0.74 0.14 0.13
Matches are distributed among these distances:
44 8 0.05
45 15 0.09
46 10 0.06
47 57 0.33
48 47 0.27
49 31 0.18
50 5 0.03
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGTATAGAGGTGTC
Found at i:28863749 original size:96 final size:93
Alignment explanation
Indices: 28863493--28863758 Score: 242
Period size: 96 Copynumber: 2.8 Consensus size: 93
28863483 ATTGTGCGCT
* * * *
28863493 AGTGTAAGA-CATGTCTAGGACAT-GCATCCG-CTATGAGATGTGTCAGTGCAAGACCATGTCTA
1 AGTGTAAGACCATGTCTGGGACATGGCAT-CGACTATGAGATGAGCCAGTGTAAGACCATGTCTA
*
28863555 TGACATGGCATCGGCACGTATAGAGGTGTC
65 GGACATGGCATCGGCACGTATAGA-GTGTC
* * * * *
28863585 AGTGTAAGACCATGTTTGGGACATGGCATTGTCACGGTATGTGA-GATCTAGTGTAAGACCAT-T
1 AGTGTAAGACCATGTCTGGGACATGGCATCG--AC--TATGAGATGAGCCAGTGTAAGACCATGT
* * * *
28863648 C-AGGACATGCCATCGGCCTCGATTTCGA-TAGTC
62 CTAGGACATGGCATCGG-CACG-TATAGAGT-GTC
28863681 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAATG-GATGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-T-ATGAGATGAGCCAGTGTAAGACCATGTCT
*
28863745 AGGACGTGGCATCG
64 AGGACATGGCATCG
28863759 ATATTACACC
Statistics
Matches: 139, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
92 9 0.06
93 16 0.12
94 25 0.18
95 16 0.12
96 50 0.36
97 17 0.12
98 6 0.04
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (93 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTATGAGATGAGCCAGTGTAAGACCATGTCTAG
GACATGGCATCGGCACGTATAGAGTGTC
Found at i:28864779 original size:28 final size:27
Alignment explanation
Indices: 28864738--28864833 Score: 122
Period size: 28 Copynumber: 3.5 Consensus size: 27
28864728 ACACGGGCTA
*
28864738 GGACACGGGTGTGTCATGGCCGTATGAG
1 GGACACGGGCGTGTCATGGCCGT-TGAG
* *
28864766 GGACACGGGCGTGTCATGGTCGTGTAAG
1 GGACACGGGCGTGTCATGGCCGT-TGAG
*
28864794 GGACACGGGCGTGTCATGGCCG-TGTG
1 GGACACGGGCGTGTCATGGCCGTTGAG
*
28864820 GGACACGGACGTGT
1 GGACACGGGCGTGT
28864834 GTTAGGCCGT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 15 0.25
28 45 0.75
ACGTcount: A:0.17, C:0.20, G:0.44, T:0.20
Consensus pattern (27 bp):
GGACACGGGCGTGTCATGGCCGTTGAG
Found at i:28871179 original size:48 final size:48
Alignment explanation
Indices: 28871073--28871297 Score: 198
Period size: 48 Copynumber: 4.8 Consensus size: 48
28871063 TCAATTGTGC
* *
28871073 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATC-G--C-TATGAGATGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTAT-AGAGGA
* * *
28871116 G-TCAGTGTAATACCATGTTTGGGACATGGCATCGGCACGTATAGAGGT
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGA
* * * * *
28871164 GTTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATGGATATGTGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATA-GAG-GA
* * * *
28871214 GCTAGTGTAAGACCATGTCTGGGACATGGCAT-TG-ACTTAATGGATGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGT-ATAGAGGA
* *
28871261 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
28871298 TTACACCTTA
Statistics
Matches: 149, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
42 1 0.01
43 9 0.06
44 13 0.09
45 5 0.03
46 1 0.01
47 32 0.21
48 47 0.32
49 10 0.07
50 31 0.21
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.26
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGA
Found at i:28872158 original size:30 final size:30
Alignment explanation
Indices: 28872122--28872187 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
28872112 CACGGGCAGA
28872122 GACACGG-CTGTGTGTCTCAGCCATGTGGAG
1 GACACGGTC-GTGTGTCTCAGCCATGTGGAG
* *
28872152 GACACGGTCGTGTGTCTTAGCCGTGTGGAG
1 GACACGGTCGTGTGTCTCAGCCATGTGGAG
28872182 GACACG
1 GACACG
28872188 ACCTCTGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.23
Consensus pattern (30 bp):
GACACGGTCGTGTGTCTCAGCCATGTGGAG
Found at i:28880151 original size:39 final size:39
Alignment explanation
Indices: 28879947--28880169 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
28879937 TTGAATGCTG
* * * * * *
28879947 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
28879987 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
28880027 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
28880067 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
28880107 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
28880146 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28880170 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:28880189 original size:79 final size:80
Alignment explanation
Indices: 28880027--28880204 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
28880017 AGATACAAGT
* * * *
28880027 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
28880092 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
28880107 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
28880171 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
28880186 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28880205 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:28884847 original size:10 final size:11
Alignment explanation
Indices: 28884833--28884861 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
28884823 AAATAAACTG
28884833 GTAAAATAAAA
1 GTAAAATAAAA
28884844 -TAAAATAAAA
1 GTAAAATAAAA
28884854 GTAAAATA
1 GTAAAATA
28884862 CATATAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (11 bp):
GTAAAATAAAA
Found at i:28886917 original size:28 final size:28
Alignment explanation
Indices: 28886880--28886935 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28886870 TTTTGGAGAA
28886880 AGAAATCACCATTTTTGGTGCTTTGAAG
1 AGAAATCACCATTTTTGGTGCTTTGAAG
28886908 AGAAATCACCATTTTTGGTGCTTTGAAG
1 AGAAATCACCATTTTTGGTGCTTTGAAG
28886936 GTCCGGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (28 bp):
AGAAATCACCATTTTTGGTGCTTTGAAG
Found at i:28887953 original size:15 final size:16
Alignment explanation
Indices: 28887927--28887956 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28887917 TGTTATTGCG
28887927 AAAATAAAAAAGAAAT
1 AAAATAAAAAAGAAAT
28887943 AAAAT-AAAAAGAAA
1 AAAATAAAAAAGAAA
28887957 CAAGGTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAGAAAT
Found at i:28889087 original size:34 final size:35
Alignment explanation
Indices: 28889041--28889127 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 35
28889031 AGGTAAGTAT
28889041 ATGT-AAGCTTATATTGAACTTGAT-TATTCGATTAC
1 ATGTGAAG-TTATATTGAACTT-ATATATTCGATTAC
* **
28889076 ATGTGAA-TTATATTGAACTTATATATTCGGTTTT
1 ATGTGAAGTTATATTGAACTTATATATTCGATTAC
*
28889110 ATGTGAAGTTATTTTGAA
1 ATGTGAAGTTATATTGAA
28889128 TGTGCATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.04
34 28 0.62
35 13 0.29
36 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (35 bp):
ATGTGAAGTTATATTGAACTTATATATTCGATTAC
Found at i:28892806 original size:30 final size:30
Alignment explanation
Indices: 28892772--28892832 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28892762 TCCTTAACTC
*
28892772 AAACTTTTGCAAAATTACAATTTTGCCCCT
1 AAACTGTTGCAAAATTACAATTTTGCCCCT
* * *
28892802 AAACTGTTGCATATTTACACTTTTGCCCCT
1 AAACTGTTGCAAAATTACAATTTTGCCCCT
28892832 A
1 A
28892833 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTGTTGCAAAATTACAATTTTGCCCCT
Found at i:28894346 original size:29 final size:30
Alignment explanation
Indices: 28894317--28894392 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
28894307 TTCAGCTATC
*
28894317 AATTATGAAAAGGGATGGTGATGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
**
28894347 AACAATGAAAAGGGATGGTGACGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
28894377 AATTATGAAAAGGGAT
1 AATTATGAAAAGGGAT
28894393 ATCTTCGACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (30 bp):
AATTATGAAAAGGGATGGTGACGACCATCA
Found at i:28894414 original size:30 final size:30
Alignment explanation
Indices: 28894380--28894452 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
28894370 ACCATCAAAT
* * *
28894380 TATGAAAAGGGATATCTTCGACTGTCGAAC
1 TATGAAAAGGGATAACTTCAACTATCGAAC
* *
28894410 TATGAAAAGGGATAACTTCAATTATCGAAT
1 TATGAAAAGGGATAACTTCAACTATCGAAC
28894440 TATGAAAAGGGAT
1 TATGAAAAGGGAT
28894453 GGATCAACCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (30 bp):
TATGAAAAGGGATAACTTCAACTATCGAAC
Found at i:28904574 original size:12 final size:12
Alignment explanation
Indices: 28904557--28904581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28904547 TGAAATATGC
28904557 TATTTATATTAT
1 TATTTATATTAT
28904569 TATTTATATTAT
1 TATTTATATTAT
28904581 T
1 T
28904582 TATACTTACA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTATATTAT
Found at i:28904594 original size:21 final size:20
Alignment explanation
Indices: 28904557--28904598 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
28904547 TGAAATATGC
*
28904557 TATTTATATTATTATTTATAT
1 TATTTATATTATCATTT-TAT
28904578 TATTTATACTTA-CATTTTAT
1 TATTTATA-TTATCATTTTAT
28904598 T
1 T
28904599 TATTATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTATATTATCATTTTAT
Found at i:28904975 original size:16 final size:16
Alignment explanation
Indices: 28904954--28904994 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
28904944 TAATAATAAA
28904954 ATATTATAGGCCCAAT
1 ATATTATAGGCCCAAT
*
28904970 ATATTAGATAGGTCCAAT
1 ATATT--ATAGGCCCAAT
28904988 ATATTAT
1 ATATTAT
28904995 GTATGCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (16 bp):
ATATTATAGGCCCAAT
Found at i:28905004 original size:18 final size:18
Alignment explanation
Indices: 28904959--28904993 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28904949 ATAAAATATT
28904959 ATAGGCCCAATATATTAG
1 ATAGGCCCAATATATTAG
*
28904977 ATAGGTCCAATATATTA
1 ATAGGCCCAATATATTA
28904994 TGTATGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (18 bp):
ATAGGCCCAATATATTAG
Found at i:28916664 original size:49 final size:47
Alignment explanation
Indices: 28916490--28916852 Score: 609
Period size: 47 Copynumber: 7.6 Consensus size: 47
28916480 CCCTTCGGGA
28916490 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28916537 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28916584 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28916631 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28916680 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28916727 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28916778 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28916827 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
28916853 CACAATTATC
Statistics
Matches: 300, Mismatches: 8, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
47 160 0.53
49 94 0.31
51 46 0.15
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28916677 original size:96 final size:96
Alignment explanation
Indices: 28916490--28916852 Score: 635
Period size: 96 Copynumber: 3.8 Consensus size: 96
28916480 CCCTTCGGGA
*
28916490 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
28916553 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
28916584 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
28916649 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
28916680 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATATAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAT
28916745 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
28916778 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
28916843 ACA--TTCACAT
64 ACACTTTCACAT
28916853 CACAATTATC
Statistics
Matches: 259, Mismatches: 4, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
94 54 0.21
96 99 0.38
98 61 0.24
100 45 0.17
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28920568 original size:50 final size:50
Alignment explanation
Indices: 28920494--28920786 Score: 385
Period size: 50 Copynumber: 5.9 Consensus size: 50
28920484 ATCAAAGTTG
* *
28920494 ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCGTATATCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATCGAGGCCA
* * * ** *
28920544 ATGTCATGTCCCAGACATGATCTTACATTGGCTCTCATCTATCG-GTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATCGAG-GCCA
* * *
28920594 ATGTCATGTCCCAGACATGGTCTTACACTAACTCTCATATCTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATCGAGGCCA
* * * *
28920644 ATGCCATGTCTCAGACATGGTCTTACGCTAGCTCCCATAT-TCGAGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATCGAGGCCA
* *
28920693 ATGCCATG-CCCTAGACATGGTCTTACAACTAGCTCTCATATCTCGAGGCCA
1 ATGCCATGTCCC-AGACATGGTCTTAC-ACTAACTCTCATATATCGAGGCCA
28920744 ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATC
1 ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATC
28920787 CGGTCTATTC
Statistics
Matches: 211, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
48 2 0.01
49 31 0.15
50 143 0.68
51 32 0.15
52 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATCGAGGCCA
Found at i:28920624 original size:100 final size:99
Alignment explanation
Indices: 28920448--28920783 Score: 399
Period size: 100 Copynumber: 3.4 Consensus size: 99
28920438 AGGTGCTGAC
* * * * * * ***
28920448 GCCATGTCCCGGACATGGTCTTACACTGGCTCACACA-TCAAAGTTGATGCCATGTCCCAGACAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCCCATATTCGAGGCCAATGCCATGTCCCAGACAT
* *
28920512 GGTCTTACACTAACTCTCGTATATCGAGGCCGAT
66 GGTCTTACACTAACTCTCATATCTCGAGGCCGAT
* * * * * * *
28920546 GTCATGTCCCAGACATGATCTTACATTGGCTCTCATCTATCG-GTGCCAATGTCATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCCCATAT-TCGAG-GCCAATGCCATGTCCCAGAC
28920610 ATGGTCTTACACTAACTCTCATATCTCGAGGCCGAT
64 ATGGTCTTACACTAACTCTCATATCTCGAGGCCGAT
* *
28920646 GCCATGTCTCAGACATGGTCTTACGCTAGCTCCCATATTCGAGGCCAATGCCATG-CCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCCCATATTCGAGGCCAATGCCATGTCCC-AGACA
* *
28920710 TGGTCTTACAACTAGCTCTCATATCTCGAGGCCAAT
65 TGGTCTTAC-ACTAACTCTCATATCTCGAGGCCGAT
* *
28920746 GCCATGTCCCAGACATGGTCTTACACTAACTCTCATAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCCCATAT
28920784 ATCCGGTCTA
Statistics
Matches: 202, Mismatches: 30, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
98 33 0.16
99 28 0.14
100 141 0.70
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (99 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTCCCATATTCGAGGCCAATGCCATGTCCCAGACAT
GGTCTTACACTAACTCTCATATCTCGAGGCCGAT
Found at i:28926543 original size:13 final size:14
Alignment explanation
Indices: 28926520--28926548 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28926510 AATGGGTGCA
28926520 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
28926534 AAAA-AAAAAAAAG
1 AAAAGAAAAAAAAG
28926547 AA
1 AA
28926549 CCCCACAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:28930018 original size:38 final size:38
Alignment explanation
Indices: 28929975--28930050 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
28929965 ATCAGATTAA
28929975 ATCAAAATTCACATATACAATTACACATTAATTAAAGT
1 ATCAAAATTCACATATACAATTACACATTAATTAAAGT
28930013 ATCAAAATTCACATATACAATTACACATTAATTAAAGT
1 ATCAAAATTCACATATACAATTACACATTAATTAAAGT
28930051 TTATGTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (38 bp):
ATCAAAATTCACATATACAATTACACATTAATTAAAGT
Found at i:28931173 original size:57 final size:57
Alignment explanation
Indices: 28931052--28931235 Score: 169
Period size: 57 Copynumber: 3.2 Consensus size: 57
28931042 CAAGGAAATA
* * * * * * * * *
28931052 TCAAGAATTAATTTGGAGAAAAAAAATTCAAATCCCAATATGAGATTAATCGACAAGT
1 TCAAAAATTAATTTAGACAAAAAAAATTCAAAACCCTATATAAGA-AAATTGTCAAGT
* * *
28931110 TCAAAAATTAATTTGGACAAAAAAAATT-TAAATCCTATGA-AAGAACAATTG-CGAAGT
1 TCAAAAATTAATTTAGACAAAAAAAATTCAAAACCCTAT-ATAAGAA-AATTGTC-AAGT
* *
28931167 TCAAAAA-TAACTTAGACAAAAAAAATTCAAAACCCTATATAAGAATATTGTCAAGT
1 TCAAAAATTAATTTAGACAAAAAAAATTCAAAACCCTATATAAGAAAATTGTCAAGT
*
28931223 TCAAATATTAATT
1 TCAAAAATTAATT
28931236 CGCATAAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
56 34 0.33
57 42 0.41
58 27 0.26
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (57 bp):
TCAAAAATTAATTTAGACAAAAAAAATTCAAAACCCTATATAAGAAAATTGTCAAGT
Found at i:28931248 original size:57 final size:54
Alignment explanation
Indices: 28931052--28931235 Score: 138
Period size: 56 Copynumber: 3.2 Consensus size: 54
28931042 CAAGGAAATA
* * * * * * *
28931052 TCAAGAATTAATTTGGAGAAAAAAAATTCAAATCCCAATATGAGATTAATCGACAAGT
1 TCAA-AATTAA-TTAGACAAAAAAAATTCAAAACCCTATATAAGAAT-ATTG-CAAGT
* * * *
28931110 TCAAAAATTAATTTGGACAAAAAAAATT-TAAATCCTATGA-AAGAACAATTGCGAAGT
1 TC-AAAATTAA-TTAGACAAAAAAAATTCAAAACCCTAT-ATAAGAA-TATTGC-AAGT
*
28931167 TCAAAAATAACTTAGACAAAAAAAATTCAAAACCCTATATAAGAATATTGTCAAGT
1 TCAAAATTAA-TTAGACAAAAAAAATTCAAAACCCTATATAAGAATATTG-CAAGT
28931223 TCAAATATTAATT
1 TCAAA-ATTAATT
28931236 CGCATAAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
56 39 0.38
57 36 0.35
58 25 0.25
59 2 0.02
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (54 bp):
TCAAAATTAATTAGACAAAAAAAATTCAAAACCCTATATAAGAATATTGCAAGT
Found at i:28933602 original size:46 final size:46
Alignment explanation
Indices: 28933522--28933836 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
28933512 TTTGACATGA
* * * * * * *
28933522 TGCCATAGTGTCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *** * *
28933568 TGTCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATTACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
28933614 TGCCATGGTATCTTTCAACCATGATCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
28933660 TGCCATGGTATCTTCCAACCATGGTCTTACACATTT--TAT-A--T
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
28933701 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
28933747 TGTCATGGTATCTTCCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
28933793 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
28933837 AAAGCACACT
Statistics
Matches: 239, Mismatches: 24, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
41 36 0.15
43 4 0.02
44 4 0.02
45 4 0.02
46 191 0.80
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:28933766 original size:133 final size:133
Alignment explanation
Indices: 28933562--28933833 Score: 436
Period size: 133 Copynumber: 2.0 Consensus size: 133
28933552 TCATTTTCTG
* * *** *
28933562 TCATGTTGTCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATTACGTTGCCATGGTATCT
1 TCATATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCT
*
28933627 TTCAACCATGATCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCATGGTCTTACAC
66 TCCAACCATGATCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCATGGTCTTACAC
28933692 ATT
131 ATT
* * *
28933695 TTATATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGTCATGGTATCT
1 TCATATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCT
* *
28933760 TCCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
66 TCCAACCATGATCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCATGGTCTTACAC
28933825 ATT
131 ATT
28933828 TCATAT
1 TCATAT
28933834 CAGAAAGCAC
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 126 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (133 bp):
TCATATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCT
TCCAACCATGATCTTACACATTTCATATCAGGTTGCCATGGTATCTTCCAACCATGGTCTTACAC
ATT
Found at i:28938258 original size:19 final size:19
Alignment explanation
Indices: 28938207--28938268 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
28938197 ATATTTATTG
*
28938207 ATTTCTTTATAAAAATACTA
1 ATTT-TTTATAAAATTACTA
* * * *
28938227 AATATTAAAAAAATTACTA
1 ATTTTTTATAAAATTACTA
*
28938246 ATTTTTTATAAAATTATTA
1 ATTTTTTATAAAATTACTA
28938265 ATTT
1 ATTT
28938269 AAAATAATTA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
19 30 0.94
20 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTTTATAAAATTACTA
Found at i:28938286 original size:37 final size:38
Alignment explanation
Indices: 28938207--28938291 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 38
28938197 ATATTTATTG
28938207 ATTTCTTTATAAAAATACTAAATATTAAAAAAATTACTA
1 ATTT-TTTATAAAAATACTAAATATTAAAAAAATTACTA
* * *
28938246 ATTTTTTATAAAATTA-TTAAT-TTAAAATAATTACTGA
1 ATTTTTTATAAAAATACTAAATATTAAAAAAATTACT-A
*
28938283 ATTTCTTAT
1 ATTTTTTAT
28938292 CATGTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 13 0.32
37 13 0.32
38 11 0.27
39 4 0.10
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (38 bp):
ATTTTTTATAAAAATACTAAATATTAAAAAAATTACTA
Found at i:28938708 original size:21 final size:21
Alignment explanation
Indices: 28938682--28938723 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28938672 GATTAAGAGA
28938682 AAGTAAAATCTTAATATTTAC
1 AAGTAAAATCTTAATATTTAC
28938703 AAGTAAAATCTTAATATTTAC
1 AAGTAAAATCTTAATATTTAC
28938724 TTGTAGTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
AAGTAAAATCTTAATATTTAC
Found at i:28955943 original size:14 final size:15
Alignment explanation
Indices: 28955917--28955945 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28955907 ATTTTATGAA
28955917 TTTCATGATGTGTTG
1 TTTCATGATGTGTTG
28955932 TTTCAT-ATGTGTTG
1 TTTCATGATGTGTTG
28955946 ATGATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (15 bp):
TTTCATGATGTGTTG
Found at i:28956139 original size:50 final size:51
Alignment explanation
Indices: 28956060--28956188 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
28956050 GACCATGGCA
* *
28956060 ACAAGTGATAAGTGATAGCCTCGGTTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
28956111 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
28956161 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
28956189 CTGATCAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 43 0.61
51 27 0.39
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:28956202 original size:31 final size:31
Alignment explanation
Indices: 28956164--28956280 Score: 207
Period size: 31 Copynumber: 3.8 Consensus size: 31
28956154 ACAAATGACA
*
28956164 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28956195 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28956226 AGTGAAAAGTGGTAGTTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
28956257 AGTGAAAAGTGGTAGCTTCGGCTA
1 AGTGAAAAGTGGTAGCTTCGGCTA
28956281 TAAGTGACAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:28960215 original size:14 final size:14
Alignment explanation
Indices: 28960174--28960216 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
28960164 TATTAAATTT
*
28960174 TTTTATAAATTTAA
1 TTTTATAAATATAA
* *
28960188 TTTAATTAATATAA
1 TTTTATAAATATAA
*
28960202 TTTTATAAAAATAA
1 TTTTATAAATATAA
28960216 T
1 T
28960217 ATATCTAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTATAAATATAA
Found at i:28963078 original size:45 final size:44
Alignment explanation
Indices: 28962998--28963128 Score: 174
Period size: 45 Copynumber: 2.9 Consensus size: 44
28962988 GCTATACTCC
*
28962998 TAAAATGAGTAAGATCATAGCTGAAAA-ATGCTATGGCATCAGGA
1 TAAAATGAGTAAGACCATAGCT-AAAAGATGCTATGGCATCAGGA
* *
28963042 TAAAGATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGA
1 TAAA-ATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCAGGA
* * *
28963087 TGAAAATGAGTAAGACCATAGCTGAAAGACGCTATGACATCA
1 T-AAAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCA
28963129 AATGAAAACA
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
44 8 0.10
45 66 0.86
46 3 0.04
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (44 bp):
TAAAATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCAGGA
Found at i:28971890 original size:43 final size:43
Alignment explanation
Indices: 28971829--28971914 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
28971819 TCTTTGCATA
28971829 TCTCACAAACTTTGCGGCCTTTATCCTTTCTTTTAGCTAACTT
1 TCTCACAAACTTTGCGGCCTTTATCCTTTCTTTTAGCTAACTT
28971872 TCTCACAAACTTTGCGGCCTTTATCCTTTCTTTTAGCTAACTT
1 TCTCACAAACTTTGCGGCCTTTATCCTTTCTTTTAGCTAACTT
28971915 CTTTCTTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (43 bp):
TCTCACAAACTTTGCGGCCTTTATCCTTTCTTTTAGCTAACTT
Found at i:28973261 original size:12 final size:12
Alignment explanation
Indices: 28973244--28973277 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
28973234 GAAGGTGTAA
28973244 GAAGAGGAAGTT
1 GAAGAGGAAGTT
28973256 GAAGAGGAAGTT
1 GAAGAGGAAGTT
28973268 GAAGAGGAAG
1 GAAGAGGAAG
28973278 AGGATGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (12 bp):
GAAGAGGAAGTT
Found at i:28977371 original size:44 final size:45
Alignment explanation
Indices: 28977264--28977379 Score: 137
Period size: 44 Copynumber: 2.6 Consensus size: 45
28977254 GACAGGACAG
*
28977264 AACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGATTTGGA
1 AACAGAAATAAGCCATGTAAGTCCATATTA-AAATATGGATTTGGA
* * *
28977310 AACAGGATTAAGCCATGTAAGTCCATATT-ATATATGGCA-TTGGA
1 AACAGAAATAAGCCATGTAAGTCCATATTAAAATATGG-ATTTGGA
* **
28977354 GACAGAAATAATTCATGTAAGTCCAT
1 AACAGAAATAAGCCATGTAAGTCCAT
28977380 GTCAAAGACA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 33 0.55
45 1 0.02
46 26 0.43
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (45 bp):
AACAGAAATAAGCCATGTAAGTCCATATTAAAATATGGATTTGGA
Found at i:28984723 original size:44 final size:45
Alignment explanation
Indices: 28984633--28984760 Score: 150
Period size: 44 Copynumber: 2.8 Consensus size: 45
28984623 ACAGAGCAGA
*
28984633 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
28984679 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
28984723 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTG
28984761 ACAGGATATT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.52
45 1 0.01
46 32 0.46
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:28988600 original size:5 final size:5
Alignment explanation
Indices: 28988590--28988639 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
28988580 GGCAGTTAAG
* *
28988590 ATTTT ATTTT ATTTTT ATCTT ATCTT ATTTT A--TT ATCTTT ATTTT ATTTT
1 ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT
28988640 GAAATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 3 0.08
5 27 0.69
6 9 0.23
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:28991347 original size:23 final size:23
Alignment explanation
Indices: 28991275--28991383 Score: 111
Period size: 23 Copynumber: 5.0 Consensus size: 23
28991265 CCTGATTAAT
28991275 ATACGACACAT-AAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
* * ** *
28991296 A-AAGACAGACGAGGTGCCTG--
1 ATACGACACATAAAGTGCCTGAA
* *
28991316 ATACAACACATAAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
28991339 ATACGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAA
28991362 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
28991384 TCAGAAAAGC
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 7 0.10
21 22 0.31
23 42 0.59
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:28991501 original size:17 final size:18
Alignment explanation
Indices: 28991469--28991502 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28991459 TAATAGGGTA
28991469 TTTTAATTCTCAATTCAC
1 TTTTAATTCTCAATTCAC
*
28991487 TTTTATTTC-CAATTCA
1 TTTTAATTCTCAATTCA
28991503 AGATCACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAATTCTCAATTCAC
Found at i:28991551 original size:35 final size:37
Alignment explanation
Indices: 28991512--28991585 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 37
28991502 AAGATCACTT
*
28991512 TTCAATTATA-ATTTCACATTCA-AA-TCAATATACAG
1 TTCAATTATACA-TACACATTCACAATTCAATATACAG
28991547 TTCAATTATACATACACATTCACAATTCAATATACAG
1 TTCAATTATACATACACATTCACAATTCAATATACAG
28991584 TT
1 TT
28991586 TAACTTAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 19 0.54
36 3 0.09
37 13 0.37
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (37 bp):
TTCAATTATACATACACATTCACAATTCAATATACAG
Found at i:28991738 original size:47 final size:46
Alignment explanation
Indices: 28991669--28991986 Score: 188
Period size: 47 Copynumber: 6.7 Consensus size: 46
28991659 GTATAATGTT
28991669 GATGCCATGTCCCAGACATGGTCTTACACTGGCTGATTCATCAAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-ATTCATCAAGTC
* * * *
28991716 GATGCCATGTCCCAGACATGGTCTTACACTGACTATTAAAATCGAGGC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATT--CATCAAGTC
* * *
28991764 AGACGCCATGTCCCAGACATGGTCTTACACTAGCT-CTCA-CATATCCGTGCC
1 -GATGCCATGTCCCAGACATGGTCTTACACTGGCTATTCATCA-A---GT--C
* * * * * *
28991815 GATGCCATGTCCCAGATAGGGTCTTACACTGACACATCTCGT-AACT-
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TAT-TCATCAAGTC
* * * * *
28991861 GATG-CATGTCCTAGACAT-GTCTTACACTAGCTTACGTCATGAGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TA-TTCATCAAGTC
* * * *
28991907 GATG-AATGTCCCAGACAT-GTCTTACAATAGCTCTCGTC-TCAA-TACC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTAT--TCATCAAGT--C
* *
28991953 GATGCCATGTCTCAGACATGGTCTTACATTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT
28991987 CTCATAATGT
Statistics
Matches: 207, Mismatches: 42, Indels: 43
0.71 0.14 0.15
Matches are distributed among these distances:
44 16 0.08
45 17 0.08
46 44 0.21
47 45 0.22
48 19 0.09
49 33 0.16
50 28 0.14
51 1 0.00
52 1 0.00
53 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTATTCATCAAGTC
Found at i:28993536 original size:21 final size:21
Alignment explanation
Indices: 28993510--28993599 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 21
28993500 CGATACATAA
* *
28993510 GTGCCTGAAACCACACATGAG
1 GTGCCTGATACCACACACGAG
* * * *
28993531 GAGCCTGATACGACACATGAA
1 GTGCCTGATACCACACACGAG
28993552 GTGCCTGATA-CA-ACACGAG
1 GTGCCTGATACCACACACGAG
* *
28993571 GCGCCTGATACAACACACGAG
1 GTGCCTGATACCACACACGAG
28993592 GTGCCTGA
1 GTGCCTGA
28993600 AATATGACAC
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.25
20 2 0.04
21 40 0.71
ACGTcount: A:0.32, C:0.28, G:0.26, T:0.14
Consensus pattern (21 bp):
GTGCCTGATACCACACACGAG
Found at i:28993587 original size:40 final size:42
Alignment explanation
Indices: 28993504--28993601 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 42
28993494 AGTATACGAT
* *
28993504 ACAT-AAGTGCCTGAAACCACACATGAGGAGCCTGATACGAC
1 ACATGAAGTGCCTGAAACCACACACGAGGAGCCTGATACAAC
* *
28993545 ACATGAAGTGCCTGATA-CA-ACACGAGGCGCCTGATACAAC
1 ACATGAAGTGCCTGAAACCACACACGAGGAGCCTGATACAAC
* *
28993585 ACACGAGGTGCCTGAAA
1 ACATGAAGTGCCTGAAA
28993602 TATGACACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 32 0.65
41 6 0.12
42 11 0.22
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (42 bp):
ACATGAAGTGCCTGAAACCACACACGAGGAGCCTGATACAAC
Found at i:28993646 original size:23 final size:23
Alignment explanation
Indices: 28993592--28993646 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
28993582 AACACACGAG
* *
28993592 GTGCCTGAAATATGACACATAAA
1 GTGCCTGATATACGACACATAAA
*
28993615 GTGTCTGATATACGACACATAAA
1 GTGCCTGATATACGACACATAAA
28993638 GTGCCTGAT
1 GTGCCTGAT
28993647 CGGCAAAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (23 bp):
GTGCCTGATATACGACACATAAA
Found at i:28993771 original size:23 final size:22
Alignment explanation
Indices: 28993745--28993797 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
28993735 AATTCTCAAT
28993745 TCACTTTCATTCCCAATTCAAGA
1 TCACTTTC-TTCCCAATTCAAGA
*
28993768 TCACTTTTCTTTCCAATTCAAGA
1 TCAC-TTTCTTCCCAATTCAAGA
28993791 TCACTTT
1 TCACTTT
28993798 TTAATTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 3 0.11
23 21 0.75
24 4 0.14
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.42
Consensus pattern (22 bp):
TCACTTTCTTCCCAATTCAAGA
Found at i:28994606 original size:23 final size:24
Alignment explanation
Indices: 28994557--28994607 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
28994547 AATAAATTAT
28994557 TTTATAACAAGTGTACATATATCTA
1 TTTATAACAAGTGTACA-ATATCTA
* *
28994582 TTTATTACAAGTGTAC-ATATGTA
1 TTTATAACAAGTGTACAATATCTA
28994605 TTT
1 TTT
28994608 GTTTAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
25 15 0.62
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (24 bp):
TTTATAACAAGTGTACAATATCTA
Found at i:28995081 original size:14 final size:14
Alignment explanation
Indices: 28995046--28995085 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 14
28995036 AATTTAGATT
28995046 TTAT-TTTATTTTA
1 TTATCTTTATTTTA
28995059 --ATC-TTATTTTA
1 TTATCTTTATTTTA
28995070 TTATCTTTATTTTA
1 TTATCTTTATTTTA
28995084 TT
1 TT
28995086 TTGAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 10 0.43
13 3 0.13
14 10 0.43
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATCTTTATTTTA
Found at i:28996698 original size:16 final size:17
Alignment explanation
Indices: 28996677--28996711 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28996667 GTTTCAGACA
28996677 TTTTGGACTGCT-TTTG
1 TTTTGGACTGCTATTTG
*
28996693 TTTTGGACTTCTATTTG
1 TTTTGGACTGCTATTTG
28996710 TT
1 TT
28996712 GTTTTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.60
Consensus pattern (17 bp):
TTTTGGACTGCTATTTG
Found at i:28998772 original size:112 final size:113
Alignment explanation
Indices: 28998574--28998799 Score: 418
Period size: 112 Copynumber: 2.0 Consensus size: 113
28998564 ATCTACTTTA
* *
28998574 GACTTCTTATTATGGGCCTACGAGTTCCAAATCGATTATTGAAAACTAATCGGGACCATTCCGAG
1 GACTTCTTATTATGGGCCTACGAGTCCCAAATCGATCATTGAAAACTAATCGGGACCATTCCGAG
28998639 TCCCTAAACCAACTATGAAAATTTCGTCATTGAACAGGTCACACGCCT
66 TCCCTAAACCAACTATGAAAATTTCGTCATTGAACAGGTCACACGCCT
28998687 GACTTCTTATTATGGGCCTACGA-TCCCAAATCGATCATTGAAAACTAATCGGGACCATTCCGAG
1 GACTTCTTATTATGGGCCTACGAGTCCCAAATCGATCATTGAAAACTAATCGGGACCATTCCGAG
*
28998751 TCCCTAAACCAACTATGAAAATTTCGTCATTGAACAGGTCATACGCCT
66 TCCCTAAACCAACTATGAAAATTTCGTCATTGAACAGGTCACACGCCT
28998799 G
1 G
28998800 TATGACCATT
Statistics
Matches: 110, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
112 87 0.79
113 23 0.21
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (113 bp):
GACTTCTTATTATGGGCCTACGAGTCCCAAATCGATCATTGAAAACTAATCGGGACCATTCCGAG
TCCCTAAACCAACTATGAAAATTTCGTCATTGAACAGGTCACACGCCT
Found at i:29000094 original size:46 final size:47
Alignment explanation
Indices: 28999884--29000202 Score: 217
Period size: 46 Copynumber: 6.7 Consensus size: 47
28999874 CGGGCAAGTT
* * *
28999884 GCCGATGCCATGTCCCAGACATAGTCTTACATTAGCTAACATCACCGAG
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTTACATC-CCGAG
* * * *
28999933 GTCGATGCCATGTCCCAGACATGGTTTTACACTAGCTCTCACATATCC-AT
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCT-T-ACAT-CCCGAG
* **
28999983 GCCGACGGCATGTCCCAGACATGGTCTTACACT-GAC--ACATTTCGTA-
1 GCCGA-TGCATGTCCCAGACATGGTCTTACACTAG-CTTACATCCCG-AG
* *
29000029 GCCGATGCATGTCCCAGACAT-GTCTTACACTGGCTTACGTCCCGAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTTACATCCCGAG
* * * *** *
29000075 GCCGATGCATGTCCTAGACAT-GTCTTACACTAGCACT-CGTCTTAAT
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGC-TTACATCCCGAG
* * *** *
29000121 GCCGATGCCATGTCTCAGACATGGTCTTACACTGGCTCT-CATAATGTG
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCT-TACATCCCGAG
* *
29000169 GCCGATGCATGTCCCAGATAT-GTCTTACAATAGC
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGC
29000203 CCACAATAAT
Statistics
Matches: 219, Mismatches: 36, Indels: 33
0.76 0.12 0.11
Matches are distributed among these distances:
44 11 0.05
45 19 0.09
46 69 0.32
47 26 0.12
48 23 0.11
49 34 0.16
50 30 0.14
51 7 0.03
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTTACATCCCGAG
Found at i:29000151 original size:94 final size:93
Alignment explanation
Indices: 28999884--29000202 Score: 285
Period size: 94 Copynumber: 3.4 Consensus size: 93
28999874 CGGGCAAGTT
* ** *
28999884 GCCGATGCCATGTCCCAGACATAGTCTTACATTAGCTAACATCACCG-AGGTCGATGCCATGTCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC--ACAT-GTCGTA-GCCGATGCCATGTCC
* * *
28999948 CAGACATGGTTTTACACTAGCTCTCACATATCC-AT
60 CAGACATGGTCTTACACTGGCTCT-ACATA-CCGAG
* *
28999983 GCCGACGGCATGTCCCAGACATGGTCTTACACT-GACACATTTCGTAGCCGATG-CATGTCCCAG
1 GCCGA-TGCATGTCCCAGACAT-GTCTTACACTAG-CACATGTCGTAGCCGATGCCATGTCCCAG
* *
29000046 ACAT-GTCTTACACTGGCT-TACGTCCCGAG
63 ACATGGTCTTACACTGGCTCTACATACCGAG
* * *
29000075 GCCGATGCATGTCCTAGACATGTCTTACACTAGCAC-TCGTCTTAATGCCGATGCCATGTCTCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACAT-GTCGT-A-GCCGATGCCATGTCCCAG
** *
29000139 ACATGGTCTTACACTGGCTCT-CATAATGTG
63 ACATGGTCTTACACTGGCTCTACATACCGAG
* *
29000169 GCCGATGCATGTCCCAGATATGTCTTACAATAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
29000203 CCACAATAAT
Statistics
Matches: 185, Mismatches: 24, Indels: 27
0.78 0.10 0.11
Matches are distributed among these distances:
89 1 0.01
90 16 0.09
91 18 0.10
92 16 0.09
93 14 0.08
94 61 0.33
95 15 0.08
96 8 0.04
97 5 0.03
98 1 0.01
99 29 0.16
100 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (93 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACATGTCGTAGCCGATGCCATGTCCCAGACA
TGGTCTTACACTGGCTCTACATACCGAG
Found at i:29000192 original size:140 final size:143
Alignment explanation
Indices: 28999884--29000202 Score: 364
Period size: 140 Copynumber: 2.2 Consensus size: 143
28999874 CGGGCAAGTT
* *
28999884 GCCGATGCCATGTCCCAGACATAGTCTTACATTAGCTAACATCACCGAGGTCGATGCCATGTCCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTAACATCACCGAGGCCGATGCCATGTCCC
* * * *
28999949 AGACATGGTTTTACACTAGCTCTCACATATCCATGCCGACGGCATGTCCCAGACATGGTCTTACA
64 AGACATGGTCTTACACTAGCACTCACATATCAATGCCGACGCCATGTCCCAGACATGGTCTTACA
*
29000014 CTGACACATTTCGTA
129 CTGACACATATCGTA
* * * *
29000029 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTC-CCGAGGCCGATG-CATGTCCTAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTAACATCACCGAGGCCGATGCCATGTCCCAG
* * *
29000092 ACAT-GTCTTACACTAGCACTCGTC-T-T-AATGCCGATGCCATGTCTCAGACATGGTCTTACAC
66 ACATGGTCTTACACTAGCACTC-ACATATCAATGCCGACGCCATGTCCCAGACATGGTCTTACAC
* * *
29000153 TGGCTCTCATAAT-GTG
130 T-G-ACACAT-ATCGTA
* *
29000169 GCCGATGCATGTCCCAGATATGTCTTACAATAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
29000203 CCACAATAAT
Statistics
Matches: 150, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
138 32 0.21
139 2 0.01
140 53 0.35
141 15 0.10
142 11 0.07
143 16 0.11
144 14 0.09
145 7 0.05
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (143 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTAACATCACCGAGGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCACTCACATATCAATGCCGACGCCATGTCCCAGACATGGTCTTACACT
GACACATATCGTA
Found at i:29002273 original size:7 final size:7
Alignment explanation
Indices: 29002261--29002290 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
29002251 TTCTTGGATG
29002261 ATATATA
1 ATATATA
29002268 ATATATA
1 ATATATA
29002275 ATATATA
1 ATATATA
29002282 ATATATA
1 ATATATA
29002289 AT
1 AT
29002291 TCTATACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:29004568 original size:12 final size:12
Alignment explanation
Indices: 29004537--29004570 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
29004527 ACAATGCTTT
*
29004537 TGAAAAGTGTTG
1 TGAAAAGTGATG
29004549 TGGAAAAGTGATG
1 T-GAAAAGTGATG
29004562 TGAAAAGTG
1 TGAAAAGTG
29004571 CTTTTGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (12 bp):
TGAAAAGTGATG
Found at i:29004904 original size:14 final size:16
Alignment explanation
Indices: 29004885--29004916 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
29004875 GTAATTAGTA
29004885 TTTTAAAA-AAT-ATT
1 TTTTAAAATAATGATT
29004899 TTTTAAAATAATGATT
1 TTTTAAAATAATGATT
29004915 TT
1 TT
29004917 AACACATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTAAAATAATGATT
Found at i:29010324 original size:42 final size:43
Alignment explanation
Indices: 29010224--29010376 Score: 127
Period size: 43 Copynumber: 3.6 Consensus size: 43
29010214 AATGCCAACA
* *
29010224 TCCCAGACGTGGTCTTACATGTAATCAAACATCGATGCCACTG
1 TCCCAGACATGGTCTTACATGAAATCAAACATCGATGCCACTG
* * * *
29010267 TCCCAGACAGGGTCTTACATGAAATCAGATAT-GATGTCGA-TG
1 TCCCAGACATGGTCTTACATGAAATCAAACATCGATG-CCACTG
* * * *
29010309 TCCTAGACATGGTCTTACACAT-AAAACAGAA-GTCGATGCCAAC-A
1 TCCCAGACATGGTCTT--ACATGAAATCA-AACATCGATGCC-ACTG
*
29010353 TCCCAGACATGGTCTTACACGAAA
1 TCCCAGACATGGTCTTACATGAAA
29010377 ACACATATCG
Statistics
Matches: 87, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
42 23 0.26
43 39 0.45
44 25 0.29
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGAAATCAAACATCGATGCCACTG
Found at i:29012299 original size:3 final size:3
Alignment explanation
Indices: 29012293--29012327 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
29012283 AAATAAAAAA
*
29012293 AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29012328 ATGTTATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29012621 original size:11 final size:10
Alignment explanation
Indices: 29012601--29012634 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
29012591 GAACTTTTAA
29012601 AATAATTTTT
1 AATAATTTTT
29012611 AATAATCTTTT
1 AATAAT-TTTT
*
29012622 TATAATTTTT
1 AATAATTTTT
29012632 AAT
1 AAT
29012635 TTTTTTCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
AATAATTTTT
Found at i:29018221 original size:55 final size:55
Alignment explanation
Indices: 29018155--29018264 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
29018145 ATAAAATACC
* *
29018155 TTATAATTGTCACACATTTATCACTACAAATGTCGCTGAAATTCTGCCAAATATT
1 TTATAACTGTCACACATTTATCACCACAAATGTCGCTGAAATTCTGCCAAATATT
*
29018210 TTATAACTGTCACACATTTATCACCACAAATGTCGTTGAAATTCTGCCAAATATT
1 TTATAACTGTCACACATTTATCACCACAAATGTCGCTGAAATTCTGCCAAATATT
29018265 AGTTTAGCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (55 bp):
TTATAACTGTCACACATTTATCACCACAAATGTCGCTGAAATTCTGCCAAATATT
Found at i:29020426 original size:23 final size:23
Alignment explanation
Indices: 29020376--29020427 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
29020366 AATAAACTTC
* * *
29020376 AAAAATAATAATAGAAATGATCT
1 AAAAGTAATAATAGAAATAACCT
29020399 AAAAGTAATAATAGAAATAACCT
1 AAAAGTAATAATAGAAATAACCT
29020422 AAAAGT
1 AAAAGT
29020428 TATAGTGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.23
Consensus pattern (23 bp):
AAAAGTAATAATAGAAATAACCT
Found at i:29022276 original size:60 final size:59
Alignment explanation
Indices: 29022139--29022287 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 59
29022129 CTATTCAGAA
* * * *
29022139 ATCAGAGT-TAACTAGGCCTCAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTATAG
1 ATCAGAGTAT-ACTGGGCCT-AGCCCATATCAATATCAATCTGGGCCATAGCCCATTAAAG
* *
29022199 TATCAGAGTATACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAG
1 -ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTA-AAG
* *
29022261 -TC-GAGATATATTGGGCCTTGCCCATAT
1 ATCAGAG-TATACTGGGCCTAGCCCATAT
29022288 TAACATAGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
59 3 0.04
60 51 0.67
61 19 0.25
62 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (59 bp):
ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTAAAG
Found at i:29022305 original size:20 final size:20
Alignment explanation
Indices: 29022280--29022325 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29022270 ATTGGGCCTT
29022280 GCCCATATT-AACATAGTTGG
1 GCCCATATTCAACATAGTT-G
*
29022300 GCCCAT-TTCAATATAGTTG
1 GCCCATATTCAACATAGTTG
29022319 GCCCATA
1 GCCCATA
29022326 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (20 bp):
GCCCATATTCAACATAGTTG
Found at i:29024475 original size:12 final size:12
Alignment explanation
Indices: 29024445--29024469 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29024435 CTAAATATAC
29024445 AAAATAATAATA
1 AAAATAATAATA
29024457 AAAATAATAATA
1 AAAATAATAATA
29024469 A
1 A
29024470 TGATAACATT
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:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:29029195 original size:23 final size:23
Alignment explanation
Indices: 29029168--29029215 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
29029158 AGTAGGCATG
29029168 TAAGGTCTAGTATACGAAATGTA
1 TAAGGTCTAGTATACGAAATGTA
* *
29029191 TAAGGTCTGGTATACGAAATTTA
1 TAAGGTCTAGTATACGAAATGTA
29029214 TA
1 TA
29029216 GTCAGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (23 bp):
TAAGGTCTAGTATACGAAATGTA
Found at i:29030758 original size:17 final size:18
Alignment explanation
Indices: 29030736--29030774 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29030726 AGTTTTCAGC
*
29030736 TTTGGAAG-TTTGTTTCA
1 TTTGGAAGATTTCTTTCA
*
29030753 TTTGGAAGATTTCTTTCT
1 TTTGGAAGATTTCTTTCA
29030771 TTTG
1 TTTG
29030775 ATTTTTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.15, C:0.08, G:0.21, T:0.56
Consensus pattern (18 bp):
TTTGGAAGATTTCTTTCA
Found at i:29031742 original size:35 final size:30
Alignment explanation
Indices: 29031671--29031730 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
29031661 AGAGGGGGTG
29031671 AGCTACACGAGCTTAGTGTAAGGTCAGAAC
1 AGCTACACGAGCTTAGTGTAAGGTCAGAAC
29031701 AGCTACACGAGCTTAGTGTAAGGTCAGAAC
1 AGCTACACGAGCTTAGTGTAAGGTCAGAAC
29031731 TATCTAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (30 bp):
AGCTACACGAGCTTAGTGTAAGGTCAGAAC
Found at i:29035993 original size:22 final size:22
Alignment explanation
Indices: 29035968--29036012 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29035958 ATTTAGTCAT
29035968 AATATAAATTATTAATATAATA
1 AATATAAATTATTAATATAATA
* * *
29035990 AATATAATTTATTATTTTAATA
1 AATATAAATTATTAATATAATA
29036012 A
1 A
29036013 TAAATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATAAATTATTAATATAATA
Found at i:29036043 original size:16 final size:17
Alignment explanation
Indices: 29036007--29036043 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
29035997 TTTATTATTT
29036007 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
29036024 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
29036039 TAATA
1 TAATA
29036044 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:29042381 original size:23 final size:23
Alignment explanation
Indices: 29042349--29042392 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29042339 ACTACCATTT
29042349 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
29042372 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
29042393 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:29042385 original size:13 final size:11
Alignment explanation
Indices: 29042353--29042395 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
29042343 CCATTTTCTA
*
29042353 AATAAAATAAT
1 AATAAAATATT
29042364 AAT-AAATATCT
1 AATAAAATAT-T
29042375 AAGTAAAATATT
1 AA-TAAAATATT
29042387 AATAAAATA
1 AATAAAATA
29042396 ATATTTAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:29042774 original size:3 final size:3
Alignment explanation
Indices: 29042766--29042817 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
29042756 GCCTACTTCT
29042766 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29042814 TTA T
1 TTA T
29042818 ACTCCTCAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29048132 original size:19 final size:19
Alignment explanation
Indices: 29048107--29048163 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
29048097 CAAAAATAAA
29048107 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
* *
29048126 TAAAATTAAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
29048145 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
29048163 A
1 A
29048164 TTTTATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 11 0.34
19 21 0.66
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:29048188 original size:25 final size:24
Alignment explanation
Indices: 29048133--29048189 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
29048123 TTTTAAAATT
29048133 AAAA-ATA-TTTATAAAAATTCCA
1 AAAATATATTTTATAAAAATTCCA
* *
29048155 AAATTTATATTTTATAAAAAATTCTA
1 AAA-ATATATTTTAT-AAAAATTCCA
29048181 AAAATATAT
1 AAAATATAT
29048190 AAAGAAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.11
24 3 0.11
25 10 0.36
26 12 0.43
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATATATTTTATAAAAATTCCA
Found at i:29048401 original size:5 final size:5
Alignment explanation
Indices: 29048391--29048426 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
29048381 ATTTCACTCA
* *
29048391 ATTCG ATTCG ATTTG ATTCG ATTCG ATTCG ACTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
29048427 CTTGAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:29048468 original size:36 final size:36
Alignment explanation
Indices: 29048401--29048483 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
29048391 ATTCGATTCG
*
29048401 ATTTGATTCGATTCGATTCGACTCGACTTGAATTTA
1 ATTTCATTCGATTCGATTCGACTCGACTTGAATTTA
* * * *
29048437 ATTTCATTCTATTCGATTTC-ACTTGATTTGAATTTC
1 ATTTCATTCGATTCGA-TTCGACTCGACTTGAATTTA
29048473 ATTTCATTCGA
1 ATTTCATTCGA
29048484 CTCAATTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
36 37 0.93
37 3 0.08
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (36 bp):
ATTTCATTCGATTCGATTCGACTCGACTTGAATTTA
Found at i:29049336 original size:20 final size:21
Alignment explanation
Indices: 29049311--29049354 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29049301 AAAAAATTAC
29049311 TTAAAT-TTATTTTAAAATAT
1 TTAAATATTATTTTAAAATAT
*
29049331 TTAAATATTATTTTAAAATTT
1 TTAAATATTATTTTAAAATAT
29049352 TTA
1 TTA
29049355 TTACTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAATATTATTTTAAAATAT
Found at i:29068133 original size:40 final size:40
Alignment explanation
Indices: 29068066--29068230 Score: 219
Period size: 40 Copynumber: 4.2 Consensus size: 40
29068056 ACCCAAGTAT
*
29068066 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
29068105 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
29068145 CTTCGGGTCTTAGCCCGAATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
29068185 CTTCGGGACATAGCCCGGATATAGCAACTCGCGCAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
29068225 CTTCGG
1 CTTCGG
29068231 ATTTTAGTCC
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.12
40 94 0.85
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Done.