Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 83 of 172
Found at i:27719863 original size:48 final size:48
Alignment explanation
Indices: 27719719--27719846 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 48
27719709 CGATTAATGA
27719719 GAGCCAGTGTAAGACCATATCTAGGACATGGCATCAGCATTGATATGAT
1 GAGCCAGTGTAAGACCATATCTAGGACATGGCATCAGCATTGATATG-T
* * *
27719768 -AGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATTGATATGT
1 GAGCCAGTGTAAGACCATATCTAGGACATGGCATCAGCATTGATATGT
* * *
27719815 GTGCCAGTATAAGACCATATCTAGGATATGGC
1 GAGCCAGTGTAAGACCATATCTAGGACATGGC
27719847 GTCGGCCTCG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.01
48 68 0.99
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATATCTAGGACATGGCATCAGCATTGATATGT
Found at i:27730600 original size:51 final size:51
Alignment explanation
Indices: 27730506--27730603 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
27730496 TTTGACTAAG
* * * ***
27730506 TTGTTACGTAAGGGTGTACCATTTAACTAGACTGATGCTCAGCAGGATAAA
1 TTGTTACATAAAGGAGTACCATTTAACTAGACTGATAAGCAGCAGGATAAA
*
27730557 TTGTTACATAAAGGAGTACCATTTAACTGGACTGATAAGCAGCAGGA
1 TTGTTACATAAAGGAGTACCATTTAACTAGACTGATAAGCAGCAGGA
27730604 AAGTTTTGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
TTGTTACATAAAGGAGTACCATTTAACTAGACTGATAAGCAGCAGGATAAA
Found at i:27736556 original size:25 final size:25
Alignment explanation
Indices: 27736523--27736587 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
27736513 GTATACATAT
*
27736523 CATATTTCATTTCAATTATTTCGTA
1 CATACTTCATTTCAATTATTTCGTA
*
27736548 CATACTTCATTTCCATTATTTCGTA
1 CATACTTCATTTCAATTATTTCGTA
27736573 CATACTTCATATTCA
1 CATACTTCAT-TTCA
27736588 CTACTTCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 33 0.92
26 3 0.08
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.48
Consensus pattern (25 bp):
CATACTTCATTTCAATTATTTCGTA
Found at i:27736837 original size:42 final size:43
Alignment explanation
Indices: 27736759--27736858 Score: 123
Period size: 42 Copynumber: 2.3 Consensus size: 43
27736749 TCCCGAACGT
* **
27736759 GGTCTTACATGTAATTCAGTATCAATGCCTCTGTCCCAGACAG
1 GGTCTTACATGTAAATCAGTATCAATGCCAATGTCCCAGACAG
* *
27736802 GGTCTTACATG-AAATCAG-ATACGATGCCAATGTCCCAGACAT
1 GGTCTTACATGTAAATCAGTAT-CAATGCCAATGTCCCAGACAG
*
27736844 GGTCTTACACGTAAA
1 GGTCTTACATGTAAA
27736859 ATCCCAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.04
42 33 0.67
43 14 0.29
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGTAAATCAGTATCAATGCCAATGTCCCAGACAG
Found at i:27743602 original size:32 final size:32
Alignment explanation
Indices: 27743565--27743643 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
27743555 TAGTTGTGCT
* *
27743565 ACAAAGGCTATCTTTTACATTCAGTACTCCCC
1 ACAAAGGCTATCCTTTACATTCAATACTCCCC
* *
27743597 ACAAAGGCTTTCCTTTACATTCAATACTCTCC
1 ACAAAGGCTATCCTTTACATTCAATACTCCCC
*
27743629 ACAAAGGCTTTCCTT
1 ACAAAGGCTATCCTT
27743644 CTCGTGGTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (32 bp):
ACAAAGGCTATCCTTTACATTCAATACTCCCC
Found at i:27754802 original size:40 final size:40
Alignment explanation
Indices: 27754734--27755709 Score: 1814
Period size: 40 Copynumber: 24.4 Consensus size: 40
27754724 GGATGATAAT
* *
27754734 CGGGCTAAGTCCCG-AGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
*
27754773 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27754813 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
*
27754853 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27754893 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27754933 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27754973 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755013 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755053 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755093 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755133 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755173 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755213 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755253 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755293 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755333 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755373 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755413 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755453 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755493 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755533 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
27755573 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
27755613 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
** * *
27755653 CGGGCTAAATCCCGAAGGCATTTGAGTGAG-TAGCTATATC
1 CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTA-CTATATC
**
27755693 C-GGCTAATTCCCGAAGG
1 CGGGCTAAGCCCCGAAGG
27755710 TACTTGGTTT
Statistics
Matches: 924, Mismatches: 11, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
39 31 0.03
40 893 0.97
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:27762960 original size:59 final size:59
Alignment explanation
Indices: 27762896--27763012 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
27762886 GTTTGATCTT
*
27762896 TTTTTGGTTCGGCATAGTACATGATATTTTGCTAGTGAGGTTTTGAATAATTTAATTAC
1 TTTTTGGTTCGGCATAGCACATGATATTTTGCTAGTGAGGTTTTGAATAATTTAATTAC
27762955 TTTTTGGTTCGGCATAGCACATGATATTTTGCTAGTGAGGTTTTGAATAATTTAATTA
1 TTTTTGGTTCGGCATAGCACATGATATTTTGCTAGTGAGGTTTTGAATAATTTAATTA
27763013 ATGTTAGATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (59 bp):
TTTTTGGTTCGGCATAGCACATGATATTTTGCTAGTGAGGTTTTGAATAATTTAATTAC
Found at i:27764706 original size:46 final size:46
Alignment explanation
Indices: 27764585--27764803 Score: 302
Period size: 46 Copynumber: 4.7 Consensus size: 46
27764575 TGTAACCCGC
* *
27764585 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
27764635 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
27764678 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
27764724 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
27764770 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
27764804 CGATGCTCAA
Statistics
Matches: 155, Mismatches: 10, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 2 0.01
45 2 0.01
46 114 0.74
47 28 0.18
48 2 0.01
49 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:27774221 original size:39 final size:40
Alignment explanation
Indices: 27774086--27774221 Score: 204
Period size: 40 Copynumber: 3.4 Consensus size: 40
27774076 GATGATAGCT
27774086 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
27774126 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* * *
27774166 GGGCTAAATCCCGAAGGCATTTGAGCAAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
*
27774206 -GGCTAATTCCCGAAGG
1 GGGCTAAGTCCCGAAGG
27774222 TAGTTGGTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 17 0.19
40 72 0.81
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:27776296 original size:14 final size:15
Alignment explanation
Indices: 27776270--27776300 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
27776260 TTCTTTATAC
27776270 TATATACCATATTCT
1 TATATACCATATTCT
27776285 TATATA-CATATTCT
1 TATATACCATATTCT
27776299 TA
1 TA
27776301 ATAGTATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATACCATATTCT
Found at i:27779012 original size:21 final size:20
Alignment explanation
Indices: 27778980--27779018 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27778970 GATGATGTTG
27778980 ATGTAGAGTTTTTCAGAAATC
1 ATGTAGAGTTTTT-AGAAATC
27779001 ATGTCAGA-TTTTTAGAAA
1 ATGT-AGAGTTTTTAGAAA
27779019 AGTTTCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 9 0.53
22 3 0.18
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (20 bp):
ATGTAGAGTTTTTAGAAATC
Found at i:27783036 original size:18 final size:18
Alignment explanation
Indices: 27783010--27783062 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
27783000 CAATTTCTCG
*
27783010 TAATTATAATGAAAATAA
1 TAATAATAATGAAAATAA
** *
27783028 TAATAATAATTCAAGTAA
1 TAATAATAATGAAAATAA
27783046 TAATAACTTAATGAAAA
1 TAATAA--TAATGAAAA
27783063 CCTTGTTACA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 20 0.77
20 6 0.23
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (18 bp):
TAATAATAATGAAAATAA
Found at i:27784249 original size:24 final size:23
Alignment explanation
Indices: 27784208--27784262 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
27784198 TACCGTAGCC
*
27784208 CAACTTTTGGCTTTTTGGCATTT
1 CAACTTTTAGCTTTTTGGCATTT
27784231 CAACTTTTCAGCTTTTTGGCATTT
1 CAACTTTT-AGCTTTTTGGCATTT
*
27784255 CAGCTTTT
1 CAACTTTT
27784263 GCCGATTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.51
Consensus pattern (23 bp):
CAACTTTTAGCTTTTTGGCATTT
Found at i:27786078 original size:69 final size:69
Alignment explanation
Indices: 27785962--27786102 Score: 246
Period size: 69 Copynumber: 2.0 Consensus size: 69
27785952 GGAGAGACCT
* *
27785962 TAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATGCTTAAGGTCAACATATGACTTT
1 TAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATACTTAAGGTCAACATATGACTTC
27786027 TGCC
66 TGCC
* *
27786031 TAAGGAAAACTAAGTCCTCCACTGCAAACTCTATTTCTTGATACTTAAGGTCAGCATATGACTTC
1 TAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATACTTAAGGTCAACATATGACTTC
27786096 TGCC
66 TGCC
27786100 TAA
1 TAA
27786103 CCGAGGCCTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (69 bp):
TAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATACTTAAGGTCAACATATGACTTC
TGCC
Found at i:27790470 original size:47 final size:47
Alignment explanation
Indices: 27790414--27790865 Score: 742
Period size: 47 Copynumber: 9.6 Consensus size: 47
27790404 TATTTGAATA
*
27790414 AATGTGAAAGTGTATCTATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
27790461 AAAGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
27790510 AATGTGAAAGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
27790557 AATGTGAAAGTGCATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27790604 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
27790651 AATGTGAAAGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
27790698 AATGTGAAAGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
27790745 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
27790792 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
27790839 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
27790866 TCCCGAAGGG
Statistics
Matches: 386, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 341 0.88
49 45 0.12
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:27794638 original size:18 final size:18
Alignment explanation
Indices: 27794611--27794664 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
27794601 TCAGGTTCTC
*
27794611 ATAATTATAATGAAAATA
1 ATAATAATAATGAAAATA
** *
27794629 ATAATAATAATTCAAGTA
1 ATAATAATAATGAAAATA
27794647 ATAATAACTTAATGAAAA
1 ATAATAA--TAATGAAAA
27794665 CCTTGTTACA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 21 0.78
20 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAATAATAATGAAAATA
Found at i:27795564 original size:29 final size:29
Alignment explanation
Indices: 27795498--27795616 Score: 136
Period size: 29 Copynumber: 4.2 Consensus size: 29
27795488 TACATACATG
*
27795498 CATATGGCCCATTAGGCCC-AATCTTATT
1 CATATGGCCCATTAGGCCCAAATCATATT
* * **
27795526 CAAATGGCCCATTTGGCCCAGTTCATATT
1 CATATGGCCCATTAGGCCCAAATCATATT
* * *
27795555 CTTATGGCCCACTAGGCCCAATTC-TCATT
1 CATATGGCCCATTAGGCCCAAATCAT-ATT
27795584 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCATTAGGCCCAAATCATATT
27795613 -ATAT
1 CATAT
27795617 TCATGCTCAC
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 22 0.29
29 52 0.69
30 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAAATCATATT
Found at i:27795602 original size:58 final size:57
Alignment explanation
Indices: 27795500--27795612 Score: 163
Period size: 58 Copynumber: 2.0 Consensus size: 57
27795490 CATACATGCA
* * * **
27795500 TATGGCCCATTAGGCCCAATCTTATTCAAATGGCCCATTTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATTAGGCCCAAATCATATTCT
*
27795557 TATGGCCCACTAGGCCCAATTCTCATTCATATGGCCCATTAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCTCATTCAAATGGCCCATTAGGCCCAAATCATATT
27795613 ATATTCATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 18 0.37
58 31 0.63
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATTAGGCCCAAATCATATTCT
Found at i:27795730 original size:19 final size:19
Alignment explanation
Indices: 27795694--27795730 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27795684 TAACCCATCA
*
27795694 GGCCCATTTAGCCCATTCC
1 GGCCCATTTAGCCAATTCC
*
27795713 GGCCCATTTGGCCAATTC
1 GGCCCATTTAGCCAATTC
27795731 TCAACCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.38, G:0.19, T:0.27
Consensus pattern (19 bp):
GGCCCATTTAGCCAATTCC
Found at i:27798116 original size:28 final size:29
Alignment explanation
Indices: 27798006--27798120 Score: 112
Period size: 29 Copynumber: 4.0 Consensus size: 29
27797996 GTGAGCATCA
* * *
27798006 ATATGAATGTGA-CTGGGCCTAACGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
* * *
27798034 ATATAAATGTCATTTGGGCCTAATGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
*
27798063 --ATGTATAGGTGATTTGGGCCTAATGGGCC
1 ATATGAATA--TGATTTGGGCCTAATGGGCC
*
27798092 ATATGAATATGA-TTGGGCTTAATGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
27798120 A
1 A
27798121 GATACAGGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
27 4 0.06
28 26 0.36
29 36 0.50
31 6 0.08
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (29 bp):
ATATGAATATGATTTGGGCCTAATGGGCC
Found at i:27803419 original size:42 final size:42
Alignment explanation
Indices: 27803356--27803439 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
27803346 CCATATCTAA
**
27803356 CATAACCTAATTAACTGCATTTCCAACATGCCAACTCTCACT
1 CATAACCTAATTAACCACATTTCCAACATGCCAACTCTCACT
27803398 CATAACCTAATTAACCACATTTCCAACATGCCAACTCTCACT
1 CATAACCTAATTAACCACATTTCCAACATGCCAACTCTCACT
27803440 ACTTTGATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.35, G:0.04, T:0.27
Consensus pattern (42 bp):
CATAACCTAATTAACCACATTTCCAACATGCCAACTCTCACT
Found at i:27804702 original size:21 final size:20
Alignment explanation
Indices: 27804674--27804713 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
27804664 TATGTATGAG
27804674 TTTTAATGATTGATGATAGA
1 TTTTAATGATTGATGATAGA
*
27804694 TTTTGAATGTTTGATGATAG
1 TTTT-AATGATTGATGATAG
27804714 TTATATAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (20 bp):
TTTTAATGATTGATGATAGA
Found at i:27807467 original size:20 final size:20
Alignment explanation
Indices: 27807421--27807468 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
27807411 AGTACGCTCG
27807421 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
* * *
27807441 ATCGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
27807461 GTTGAGCT
1 GTTGAGCT
27807469 GGACGGAGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:27809079 original size:18 final size:19
Alignment explanation
Indices: 27809056--27809094 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
27809046 TTTATCTCAA
*
27809056 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
27809074 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
27809093 TT
1 TT
27809095 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:27809110 original size:48 final size:49
Alignment explanation
Indices: 27809058--27809161 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 49
27809048 TATCTCAATT
* * *
27809058 TCTTTTTCCACTCT-TTTTTC-TTGTTCACATTCTTTTTCTCTCTCAAAC
1 TCTTTTTCCACTCTCTTTTTCAAT-CTCACATTCTTTTTCACTCTCAAAC
* ** *
27809106 TCTTTTT-CATTCTCTTTTTCAATCTCATTTTCTTTTTCACTCTCAATC
1 TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
27809154 TCTTTTTC
1 TCTTTTTC
27809162 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
47 5 0.11
48 40 0.87
49 1 0.02
ACGTcount: A:0.12, C:0.28, G:0.01, T:0.59
Consensus pattern (49 bp):
TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
Found at i:27809133 original size:18 final size:18
Alignment explanation
Indices: 27809112--27809161 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
27809102 AAACTCTTTT
27809112 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
27809130 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
27809148 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
27809162 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:27809151 original size:24 final size:24
Alignment explanation
Indices: 27809087--27809168 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
27809077 CTTGTTCACA
*
27809087 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
27809111 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
27809135 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
27809159 TTCTTTTTCT
1 TTCTTTTTCT
27809169 TTCATTTCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:27809220 original size:42 final size:42
Alignment explanation
Indices: 27809165--27809261 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
27809155 CTTTTTCTTT
* * *
27809165 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
27809206 TTCTCTCATTTTCTTTGTTTCTTCTCTTGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
27809248 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
27809262 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:27817585 original size:24 final size:24
Alignment explanation
Indices: 27817555--27817601 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
27817545 AAACCACATA
27817555 TTTACTATATATACCTAAAATGAT
1 TTTACTATATATACCTAAAATGAT
27817579 TTTACTATATATACCTAAAATGA
1 TTTACTATATATACCTAAAATGA
27817602 GCTAGTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (24 bp):
TTTACTATATATACCTAAAATGAT
Found at i:27817784 original size:29 final size:29
Alignment explanation
Indices: 27817695--27817784 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 29
27817685 AGCATTACAT
*
27817695 ACTTAGTAAGTTTGTATAATAGAAACTAA
1 ACTTAGTAAGTTCGTATAATAGAAACTAA
** * * * ** *
27817724 ACTTACCAA-TCCCATTTAATA-TTAC-AT
1 ACTTAGTAAGT-TCGTATAATAGAAACTAA
27817751 ACTTAGTAAGTTCGTATAATAGAAACTAA
1 ACTTAGTAAGTTCGTATAATAGAAACTAA
27817780 ACTTA
1 ACTTA
27817785 CCAATCTTGT
Statistics
Matches: 40, Mismatches: 17, Indels: 8
0.62 0.26 0.12
Matches are distributed among these distances:
27 15 0.38
28 6 0.15
29 19 0.47
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.34
Consensus pattern (29 bp):
ACTTAGTAAGTTCGTATAATAGAAACTAA
Found at i:27837097 original size:29 final size:29
Alignment explanation
Indices: 27837062--27837119 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
27837052 CTCTAAATTA
27837062 GGATCCACTAATTTTACCTGAAATTAGAC
1 GGATCCACTAATTTTACCTGAAATTAGAC
27837091 GGATCCACTAATTTTACCTGAAATTAGAC
1 GGATCCACTAATTTTACCTGAAATTAGAC
27837120 TCACATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (29 bp):
GGATCCACTAATTTTACCTGAAATTAGAC
Found at i:27838127 original size:52 final size:52
Alignment explanation
Indices: 27838056--27838157 Score: 141
Period size: 52 Copynumber: 2.0 Consensus size: 52
27838046 ACCCAATTAT
* * * * * *
27838056 ATGTGTCGCATCCATTATGAACTCGGACCAACTGAATGAGCTCGGATGCCAC
1 ATGTATCGCATCCATTATGAACCCAGACCAACTCAACGAGCTCGAATGCCAC
*
27838108 ATGTATCGTATCCATTATGAACCCAGACCAACTCAACGAGCTCGAATGCC
1 ATGTATCGCATCCATTATGAACCCAGACCAACTCAACGAGCTCGAATGCC
27838158 GCATACATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (52 bp):
ATGTATCGCATCCATTATGAACCCAGACCAACTCAACGAGCTCGAATGCCAC
Found at i:27843073 original size:43 final size:44
Alignment explanation
Indices: 27842951--27843125 Score: 143
Period size: 43 Copynumber: 4.1 Consensus size: 44
27842941 AAAGCTCATA
* * *
27842951 CAATGCCAAC-GTCCCAGACGTGGTCTAACATGT-AATCAAATAT
1 CAATGCC-ACTGTCCCAGACATGGTCTTACACGTAAATCAAATAT
* * *
27842994 CGATGCCACTGTCCTAGACAGGGTCTTACACG-AAATCAAATA-
1 CAATGCCACTGTCCCAGACATGGTCTTACACGTAAATCAAATAT
* *
27843036 CAATGCTGA-TGTCCCAGACATGGTCTTACACGTAAATCATAA-GT
1 CAATGC-CACTGTCCCAGACATGGTCTTACACGTAAATCA-AATAT
* * *
27843080 CAATGCCAAC-GTCCCAAACGTGTTCTTACACG-AAAT-AACATAT
1 CAATGCC-ACTGTCCCAGACATGGTCTTACACGTAAATCAA-ATAT
27843123 CAA
1 CAA
27843126 AAATTCTATT
Statistics
Matches: 106, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
41 1 0.01
42 30 0.28
43 47 0.44
44 28 0.26
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (44 bp):
CAATGCCACTGTCCCAGACATGGTCTTACACGTAAATCAAATAT
Found at i:27849795 original size:50 final size:50
Alignment explanation
Indices: 27849675--27850019 Score: 278
Period size: 50 Copynumber: 6.7 Consensus size: 50
27849665 TTGTGAGAAT
* * * *** *
27849675 ACATGTGTAGTACTATGTGCAAGCTACTATGTGTTTAAGATGGTTTTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG--TTAGGTC
* * *
27849727 ACGTGTATAGTACTAAGTGCAGGCTACTACGTATACCAGATAGTTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTC
* * * * * * * * * * *
27849777 GCATGTGTAGGACTAAGTGCAAGCTCCTATGCGTACCCGAAAACCTCA-ATC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATA-GTTAGGTC
*** * ** *
27849828 TTGTGTGTAGTACTAAGTGCAGGCTACTACATGTATTAGATGGTTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTC
* * * * *
27849878 ACGTGTGCAGTCCTAAGTGCAGGCCACAACGTGTACCAGATAGTTAGGTC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTC
* * *
27849928 GCATGTGTAGTACTAAGTTCAGGTTAGGCTACTACGTGTATCAGATAGTTAGGTC
1 ACATGTGTAGTACTAAG-T---G-CAGGCTACTACGTGTACCAGATAGTTAGGTC
27849983 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACC
1 ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACC
27850020 GGATTGCTGG
Statistics
Matches: 223, Mismatches: 62, Indels: 18
0.74 0.20 0.06
Matches are distributed among these distances:
49 2 0.01
50 108 0.48
51 33 0.15
52 35 0.16
54 2 0.01
55 43 0.19
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
ACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTC
Found at i:27849979 original size:105 final size:104
Alignment explanation
Indices: 27849848--27850036 Score: 270
Period size: 105 Copynumber: 1.8 Consensus size: 104
27849838 TACTAAGTGC
* * * *
27849848 AGGCTACTACATGTATTAGATGGTTAGGTCACGTGTGCAGTCCTAAGTGCAGGCCACAACGTGTA
1 AGGCTACTACATGTATCAGATAGTTAGGTCACATGTGCAGTACTAAGTGCAGGCCACAACGTGTA
*
27849913 CCAGATAGTTAGGTCGCATGTGTAGTACTAAGTTCAGGTT
66 CCAGATAGCT-GGTCGCATGTGTAGTACTAAGTTCAGGTT
* * * *
27849953 AGGCTACTACGTGTATCAGATAGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA
1 AGGCTACTACATGTATCAGATAGTTAGGTCACATGTGCAGTACTAAGTGCAGGCCACAACGTGTA
* *
27850018 CCGGATTGCTGGTCGCATG
66 CCAGATAGCTGGTCGCATG
27850037 AGTGCAGCCT
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
104 9 0.12
105 64 0.88
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (104 bp):
AGGCTACTACATGTATCAGATAGTTAGGTCACATGTGCAGTACTAAGTGCAGGCCACAACGTGTA
CCAGATAGCTGGTCGCATGTGTAGTACTAAGTTCAGGTT
Found at i:27850283 original size:16 final size:15
Alignment explanation
Indices: 27850262--27850291 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
27850252 GAATGGAGTA
27850262 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
27850278 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
27850292 TAAAATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:27856762 original size:50 final size:50
Alignment explanation
Indices: 27856643--27856938 Score: 263
Period size: 50 Copynumber: 5.9 Consensus size: 50
27856633 ATTGTGAGAA
* * *** *
27856643 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG--TTAGGT
* *
27856695 CACATGTGTAGTACTAAGTGCAAGCTACTACATGTACCAGATAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
** * * * * * *
27856745 CGTATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCA-AT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAGTT-AGGT
* * * ** **
27856796 CACGTGTGTACTAGTAAGTGCAGGCTACTACGTGTATAAGACGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
** * *
27856846 CATGTGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGATTGTT-GGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
* * * *
27856895 CACATGTGTAGTACTAAGTACAGGCTACTATGCGTACTAGATAG
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
27856939 CTTCAGTTAC
Statistics
Matches: 195, Mismatches: 46, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
49 42 0.22
50 81 0.42
51 35 0.18
52 37 0.19
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
Found at i:27856844 original size:101 final size:101
Alignment explanation
Indices: 27856694--27856875 Score: 256
Period size: 101 Copynumber: 1.8 Consensus size: 101
27856684 TGGTTTTAGG
* * * *
27856694 TCACATGTGTAGTACTAAGTGCAAGCTACTACATGTACCAGATAGTTAGGTCGTATGTGTAGTAC
1 TCACATGTGTACTACTAAGTGCAAGCTACTACATGTACAAGACAGTTAGGTCATATGTGTAGTAC
*
27856759 TAAGTGCAGGCTACTATGCGTACCCGACAACTTCAA
66 TAAGTACAGGCTACTATGCGTACCCGACAACTTCAA
* * * * * * *
27856795 TCACGTGTGTACTAGTAAGTGCAGGCTACTACGTGTATAAGACGGTTAGGTCATGTGTGTAGTAC
1 TCACATGTGTACTACTAAGTGCAAGCTACTACATGTACAAGACAGTTAGGTCATATGTGTAGTAC
27856860 TAAGTACAGGCTACTA
66 TAAGTACAGGCTACTA
27856876 CGTGTACCAG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 69 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (101 bp):
TCACATGTGTACTACTAAGTGCAAGCTACTACATGTACAAGACAGTTAGGTCATATGTGTAGTAC
TAAGTACAGGCTACTATGCGTACCCGACAACTTCAA
Found at i:27859711 original size:29 final size:28
Alignment explanation
Indices: 27859675--27859752 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
27859665 TCATGAGATT
27859675 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
27859705 -GCACTAAGTGTGTGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
27859732 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
27859753 GATTATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.80
30 3 0.07
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.31
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:27859973 original size:174 final size:174
Alignment explanation
Indices: 27859705--27860032 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
27859695 AAATTGTACA
*
27859705 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
27859770 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTCCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
27859835 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
27859879 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
27859944 TGTGCGAACCCAATATATATTTCCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTCCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
27860009 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
27860033 ACCTTGAGTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTCCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:27861507 original size:17 final size:14
Alignment explanation
Indices: 27861471--27861498 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27861461 CATTATAACA
27861471 AAAACATATTAGCT
1 AAAACATATTAGCT
27861485 AAAACATATTAGCT
1 AAAACATATTAGCT
27861499 CATAAAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAACATATTAGCT
Found at i:27862177 original size:42 final size:41
Alignment explanation
Indices: 27862129--27862322 Score: 160
Period size: 43 Copynumber: 4.6 Consensus size: 41
27862119 TCAATGCCTC
* * *
27862129 TGTCCCATACAAGGTCTTACACGAAA-TCAGATACGATGCCGA
1 TGTCCCAGACACGGTCTTACACGAAACTCA-AT-CGAGGCCGA
* *
27862171 TGTCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTG-
1 TGTCCCAGACACGGTCTTACACG-AAA-CTCAATCGAGGCC-GA
* * ** *
27862214 TCTCCCAGACACGGTCTTACATGAAA-TCAGATACGTTGCTGA
1 TGTCCCAGACACGGTCTTACACGAAACTCA-AT-CGAGGCCGA
* * * *
27862256 TGTCCCAGACATGGTCTTATACTTAAATCTCAATCGAGGCCTA
1 TGTCCCAGACACGGTCTTACAC-GAAA-CTCAATCGAGGCCGA
27862299 TGTCCCAGACACGGTCTTACACGA
1 TGTCCCAGACACGGTCTTACACGA
27862323 TATCTCAGAC
Statistics
Matches: 119, Mismatches: 23, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 46 0.39
43 56 0.47
44 5 0.04
45 6 0.05
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (41 bp):
TGTCCCAGACACGGTCTTACACGAAACTCAATCGAGGCCGA
Found at i:27862230 original size:85 final size:85
Alignment explanation
Indices: 27862131--27862322 Score: 312
Period size: 85 Copynumber: 2.3 Consensus size: 85
27862121 AATGCCTCTG
* *
27862131 TCCCATACAAGGTCTTACACGAAATCAGATACGATGCCGATGTCCCAGACATGGTCTTATACGTA
1 TCCCAGACACGGTCTTACACGAAATCAGATACGATGCCGATGTCCCAGACATGGTCTTATACGTA
*
27862196 AATCTCAATCGAGGCCTGTC
66 AATCTCAATCGAGGCCTATC
* * * *
27862216 TCCCAGACACGGTCTTACATGAAATCAGATACGTTGCTGATGTCCCAGACATGGTCTTATACTTA
1 TCCCAGACACGGTCTTACACGAAATCAGATACGATGCCGATGTCCCAGACATGGTCTTATACGTA
*
27862281 AATCTCAATCGAGGCCTATG
66 AATCTCAATCGAGGCCTATC
27862301 TCCCAGACACGGTCTTACACGA
1 TCCCAGACACGGTCTTACACGA
27862323 TATCTCAGAC
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 98 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (85 bp):
TCCCAGACACGGTCTTACACGAAATCAGATACGATGCCGATGTCCCAGACATGGTCTTATACGTA
AATCTCAATCGAGGCCTATC
Found at i:27865870 original size:66 final size:66
Alignment explanation
Indices: 27865764--27865894 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
27865754 TGAAATGTAT
27865764 ACAAATGTATATGTAAGTAGAGATGAAATTTGTCGAATGTAAAAAGGAACTGAAGCCTATAGAGT
1 ACAAATGTATATGTAAGTAGAGATGAAATTTGTCGAATGTAAAAAGGAACTGAAGCCTATAGAGT
27865829 G
66 G
* *
27865830 ACAAATGTATATGTAAGTAGAGATGAAATTTGTCGAATGTAAAAAGGAAGTGAAGCCTATTGAGT
1 ACAAATGTATATGTAAGTAGAGATGAAATTTGTCGAATGTAAAAAGGAACTGAAGCCTATAGAGT
27865895 AGCTGGTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (66 bp):
ACAAATGTATATGTAAGTAGAGATGAAATTTGTCGAATGTAAAAAGGAACTGAAGCCTATAGAGT
G
Found at i:27865985 original size:29 final size:28
Alignment explanation
Indices: 27865949--27866026 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
27865939 TCATGAGATT
27865949 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
27865979 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
27866006 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
27866027 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:27866291 original size:172 final size:174
Alignment explanation
Indices: 27865979--27866304 Score: 539
Period size: 172 Copynumber: 1.9 Consensus size: 174
27865969 AAATTGTACA
* *
27865979 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
27866044 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
27866109 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
27866153 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* * *
27866218 -GTGC-AATCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
27866281 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
27866305 ACCTTGAGTT
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
172 78 0.55
173 4 0.03
174 59 0.42
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:27866550 original size:62 final size:62
Alignment explanation
Indices: 27866453--27866707 Score: 510
Period size: 62 Copynumber: 4.1 Consensus size: 62
27866443 TGATTATAAC
27866453 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
1 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
27866515 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
1 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
27866577 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
1 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
27866639 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
1 TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
27866701 TCTAGGT
1 TCTAGGT
27866708 TTCTTGGACT
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 193 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (62 bp):
TCTAGGTGAATGCTTATGGCTTACTGAGTTATATACTCATTCGGTGTTTGCTTGTCACCTAT
Found at i:27870425 original size:14 final size:14
Alignment explanation
Indices: 27870406--27870436 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
27870396 AGCTTTGTGG
27870406 GCATATTCTATTGT
1 GCATATTCTATTGT
27870420 GCATATTCTATTGT
1 GCATATTCTATTGT
27870434 GCA
1 GCA
27870437 AATATGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (14 bp):
GCATATTCTATTGT
Found at i:27880039 original size:19 final size:19
Alignment explanation
Indices: 27880015--27880060 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
27880005 GGGGTATATC
27880015 GGTAATTTTGCTCTTTAGG
1 GGTAATTTTGCTCTTTAGG
27880034 GGTAATTTTGCTCTTTAGG
1 GGTAATTTTGCTCTTTAGG
27880053 GGTAATTT
1 GGTAATTT
27880061 GCCCATCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.48
Consensus pattern (19 bp):
GGTAATTTTGCTCTTTAGG
Found at i:27883793 original size:39 final size:40
Alignment explanation
Indices: 27883642--27883811 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
27883632 GGACTAAGAT
* * *
27883642 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
27883682 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** * *
27883722 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGAC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * * *
27883762 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
27883801 CCGAAGGCATT
1 CCGAAGGCATT
27883812 TGAACGAGGA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
39 31 0.28
40 79 0.72
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:27883831 original size:79 final size:80
Alignment explanation
Indices: 27883664--27883846 Score: 192
Period size: 79 Copynumber: 2.3 Consensus size: 80
27883654 GTGCGAGATA
* * * * *
27883664 CTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGACCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
27883729 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
27883744 TTAAATCCGGGTTACGACCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGACCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
27883808 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
*
27883823 CTATATCC-GGTTAA-ATCCCGAAGG
1 CTAAATCCGGGTTAAGA-CCCGAAGG
27883847 TACGTGAATT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
77 1 0.01
78 13 0.15
79 47 0.56
80 23 0.27
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGACCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:27889906 original size:5 final size:5
Alignment explanation
Indices: 27889896--27889921 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27889886 NAAAATTATA
27889896 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
27889922 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:27897124 original size:23 final size:23
Alignment explanation
Indices: 27897094--27897155 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
27897084 CTAGAATGCG
*
27897094 TGCTAGGGAAGCAGACTTTTTCA
1 TGCTAGGGTAGCAGACTTTTTCA
27897117 TGCTAGGGTAGCAGACTTTTTCA
1 TGCTAGGGTAGCAGACTTTTTCA
27897140 TGCTAGGGTAGCAGAC
1 TGCTAGGGTAGCAGAC
27897156 ATTAAGTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (23 bp):
TGCTAGGGTAGCAGACTTTTTCA
Found at i:27901772 original size:48 final size:48
Alignment explanation
Indices: 27901679--27901772 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
27901669 TGGGTATTAG
* * **
27901679 TCATGTGCTTAATGATGTTCAGGATTCATAGTTTTCTCTGTAACAATA
1 TCATGTGCTTAATGATATTCAGGATTCATAGTTATCTCTCCAACAATA
*
27901727 TCATGTGCTTAATGATATTTAGGATTCATAGTTATCTCTCCAACAA
1 TCATGTGCTTAATGATATTCAGGATTCATAGTTATCTCTCCAACAA
27901773 CATTGTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (48 bp):
TCATGTGCTTAATGATATTCAGGATTCATAGTTATCTCTCCAACAATA
Found at i:27902575 original size:36 final size:35
Alignment explanation
Indices: 27902516--27902583 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
27902506 ATAGTAAAAT
* *
27902516 TAATAATAAAATAAGAGTTAGATAATATACAAAGAA
1 TAATAATAAAATAAGAATAAGATAATA-ACAAAGAA
27902552 TAATAATAAAAT-AGTAATAAGATAATAACAAA
1 TAATAATAAAATAAG-AATAAGATAATAACAAA
27902584 AATGACAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 7 0.24
36 22 0.76
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.25
Consensus pattern (35 bp):
TAATAATAAAATAAGAATAAGATAATAACAAAGAA
Found at i:27903056 original size:9 final size:10
Alignment explanation
Indices: 27903030--27903056 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
27903020 AATATAATAT
27903030 TAATTTTTTA
1 TAATTTTTTA
27903040 TAATTTTTTA
1 TAATTTTTTA
27903050 TAATTTT
1 TAATTTT
27903057 AAAACTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:27904060 original size:39 final size:41
Alignment explanation
Indices: 27904009--27904168 Score: 186
Period size: 41 Copynumber: 4.0 Consensus size: 41
27903999 TTTTAAAATT
* ** *
27904009 CAGAGCAATAGCGGCG-TTCTAAAAAAACGCCGCTAAAA-A
1 CAGAGCATTAGCGGCGCTTCTAGTAAAACGCCGCTAAAAGC
*
27904048 CAGAGCATTAGCGGCGCTTTCT-GTAAAACGCCGTTAAAAGC
1 CAGAGCATTAGCGGCGC-TTCTAGTAAAACGCCGCTAAAAGC
*
27904089 CAGAGCATTAGCGGCGCGT-TAGGTAAAACGCCGCTAAAAGC
1 CAGAGCATTAGCGGCGCTTCTA-GTAAAACGCCGCTAAAAGC
* *
27904130 CAAAGCATTAGCGGCGCTT-TCGGTAAAACGCCGCTAAAA
1 CAGAGCATTAGCGGCGCTTCT-AGTAAAACGCCGCTAAAA
27904169 ATCTCATAAC
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
39 16 0.15
40 15 0.14
41 74 0.70
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (41 bp):
CAGAGCATTAGCGGCGCTTCTAGTAAAACGCCGCTAAAAGC
Found at i:27904102 original size:41 final size:41
Alignment explanation
Indices: 27904032--27904168 Score: 213
Period size: 41 Copynumber: 3.4 Consensus size: 41
27904022 GCGTTCTAAA
* *
27904032 AAAACGCCGCTAAAA-ACAGAGCATTAGCGGCGCTTTCTGT
1 AAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTCGGT
* * *
27904072 AAAACGCCGTTAAAAGCCAGAGCATTAGCGGCGCGTTAGGT
1 AAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTCGGT
*
27904113 AAAACGCCGCTAAAAGCCAAAGCATTAGCGGCGCTTTCGGT
1 AAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTCGGT
27904154 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
27904169 ATCTCATAAC
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 14 0.16
41 73 0.84
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (41 bp):
AAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTCGGT
Found at i:27905199 original size:15 final size:15
Alignment explanation
Indices: 27905179--27905210 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27905169 TTTAATTTAG
*
27905179 AAGATAAATGTATAT
1 AAGATAAATATATAT
27905194 AAGATAAATATATAT
1 AAGATAAATATATAT
27905209 AA
1 AA
27905211 AATATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:27905249 original size:24 final size:24
Alignment explanation
Indices: 27905199--27905249 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
27905189 TATATAAGAT
* *
27905199 AAATATATATAAAATATTATTTTA
1 AAATATATATAAAATATTATATGA
27905223 AAATATATAT-AAATATGTATATGA
1 AAATATATATAAAATAT-TATATGA
27905247 AAA
1 AAA
27905250 GTGGTTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
AAATATATATAAAATATTATATGA
Found at i:27909640 original size:289 final size:289
Alignment explanation
Indices: 27909121--27910115 Score: 1990
Period size: 289 Copynumber: 3.4 Consensus size: 289
27909111 CCAACCTTGT
27909121 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
27909186 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
27909251 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACCTTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACCTTAATTTATT
27909316 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATAATATTATATTCAAAATACTATT
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATAATATTATATTCAAAATACTATT
27909381 TTTTATATTAATAATGTTTGATTTTAATA
261 TTTTATATTAATAATGTTTGATTTTAATA
27909410 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
27909475 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
27909540 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACCTTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACCTTAATTTATT
27909605 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATAATATTATATTCAAAATACTATT
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATAATATTATATTCAAAATACTATT
27909670 TTTTATATTAATAATGTTTGATTTTAATA
261 TTTTATATTAATAATGTTTGATTTTAATA
27909699 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
27909764 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
27909829 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACCTTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACCTTAATTTATT
27909894 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATAATATTATATTCAAAATACTATT
196 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATAATATTATATTCAAAATACTATT
27909959 TTTTATATTAATAATGTTTGATTTTAATA
261 TTTTATATTAATAATGTTTGATTTTAATA
27909988 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
27910053 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
27910116 TCCGTTTTAT
Statistics
Matches: 706, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 706 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (289 bp):
TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACCTTAATTTATT
TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATAATATTATATTCAAAATACTATT
TTTTATATTAATAATGTTTGATTTTAATA
Found at i:27910369 original size:15 final size:15
Alignment explanation
Indices: 27910325--27910380 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
27910315 AACGACATGT
*
27910325 ATATTACTTAATTAAA
1 ATATTATTTAATT-AA
27910341 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
27910354 ATATTATTTAATTAA
1 ATATTATTTAATTAA
27910369 ATATTATTTAAT
1 ATATTATTTAAT
27910381 CCCGCTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:27910496 original size:9 final size:9
Alignment explanation
Indices: 27910482--27910632 Score: 187
Period size: 9 Copynumber: 16.9 Consensus size: 9
27910472 ATATATTTGA
27910482 TTATATAAC
1 TTATATAAC
27910491 TTATATAAC
1 TTATATAAC
* *
27910500 TTACAAAAC
1 TTATATAAC
* *
27910509 GTACATAAC
1 TTATATAAC
27910518 TTATATAAC
1 TTATATAAC
27910527 TTATATAAC
1 TTATATAAC
*
27910536 TTACATAAC
1 TTATATAAC
27910545 TTATATAAC
1 TTATATAAC
*
27910554 ATATATAAC
1 TTATATAAC
*
27910563 TTACATAAC
1 TTATATAAC
27910572 TTATATAAC
1 TTATATAAC
* *
27910581 ATACATAAC
1 TTATATAAC
27910590 TTATATAAC
1 TTATATAAC
27910599 TTATATAAC
1 TTATATAAC
*
27910608 TTAGATAA-
1 TTATATAAC
*
27910616 ATATATAAC
1 TTATATAAC
*
27910625 TTACATAA
1 TTATATAA
27910633 AATACATAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
8 6 0.05
9 114 0.95
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.37
Consensus pattern (9 bp):
TTATATAAC
Found at i:27910516 original size:27 final size:27
Alignment explanation
Indices: 27910486--27910702 Score: 211
Period size: 27 Copynumber: 7.8 Consensus size: 27
27910476 ATTTGATTAT
* *
27910486 ATAACTTATATAACTTACAAAACGTAC
1 ATAACTTATATAACTTACATAACTTAC
*
27910513 ATAACTTATATAACTTATATAACTTAC
1 ATAACTTATATAACTTACATAACTTAC
* *
27910540 ATAACTTATATAACATATATAACTTAC
1 ATAACTTATATAACTTACATAACTTAC
* *
27910567 ATAACTTATATAACATACATAACTTAT
1 ATAACTTATATAACTTACATAACTTAC
* * *
27910594 ATAACTTATATAACTTAGATAA-ATAT
1 ATAACTTATATAACTTACATAACTTAC
* ** *
27910620 ATAACTTACATAAAATACATAATACTTAA
1 ATAACTTATATAACTTACAT-A-ACTTAC
* *
27910649 ATATATTTTATATCATAATTTACATAACTTAC
1 ATA-A--CT-TAT-ATAACTTACATAACTTAC
*
27910681 ATAACTTATATAACTTAGATAA
1 ATAACTTATATAACTTACATAA
27910703 ATATATAATT
Statistics
Matches: 159, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
26 19 0.12
27 107 0.67
28 4 0.03
29 6 0.04
30 1 0.01
31 1 0.01
32 9 0.06
33 3 0.02
34 9 0.06
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.37
Consensus pattern (27 bp):
ATAACTTATATAACTTACATAACTTAC
Found at i:27910518 original size:18 final size:18
Alignment explanation
Indices: 27910482--27910755 Score: 203
Period size: 18 Copynumber: 14.9 Consensus size: 18
27910472 ATATATTTGA
*
27910482 TTATATAACTTATATAAC
1 TTATATAACTTACATAAC
* * *
27910500 TTACAAAACGTACATAAC
1 TTATATAACTTACATAAC
*
27910518 TTATATAACTTATATAAC
1 TTATATAACTTACATAAC
* *
27910536 TTACATAACTTATATAAC
1 TTATATAACTTACATAAC
*
27910554 ATATATAACTTACATAAC
1 TTATATAACTTACATAAC
*
27910572 TTATATAACATACATAAC
1 TTATATAACTTACATAAC
*
27910590 TTATATAACTTATATAAC
1 TTATATAACTTACATAAC
* * *
27910608 TTAGATAA-ATATATAAC
1 TTATATAACTTACATAAC
* **
27910625 TTACATAAAATACATAATAC
1 TTATATAACTTACAT-A-AC
** *
27910645 TTAAATATATTTTATATCATAAT
1 TT--ATATA-ACT-TA-CATAAC
*
27910668 TTACATAACTTACATAAC
1 TTATATAACTTACATAAC
*
27910686 TTATATAACTTAGATAA-
1 TTATATAACTTACATAAC
* *
27910703 ATATATAATTTACATAA-
1 TTATATAACTTACATAAC
* * * *
27910720 ATATATATCATATCATAAA
1 TTATATAACTTA-CATAAC
*
27910739 TTACATAACTTACATAA
1 TTATATAACTTACATAA
27910756 TACTTAAATA
Statistics
Matches: 205, Mismatches: 41, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
17 38 0.19
18 134 0.65
19 11 0.05
20 5 0.02
21 4 0.02
22 4 0.02
23 3 0.01
24 3 0.01
25 3 0.01
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.38
Consensus pattern (18 bp):
TTATATAACTTACATAAC
Found at i:27910674 original size:9 final size:9
Alignment explanation
Indices: 27910662--27910756 Score: 50
Period size: 9 Copynumber: 10.7 Consensus size: 9
27910652 TATTTTATAT
27910662 CATAATTTA
1 CATAATTTA
*
27910671 CATAACTTA
1 CATAATTTA
*
27910680 CATAACTTA
1 CATAATTTA
* *
27910689 TATAACTTA
1 CATAATTTA
* *
27910698 GATAA-ATA
1 CATAATTTA
*
27910706 TATAATTTA
1 CATAATTTA
*
27910715 CATAAATATA
1 CAT-AATTTA
* * *
27910725 TATCATAT-
1 CATAATTTA
*
27910733 CATAAATTA
1 CATAATTTA
*
27910742 CATAACTTA
1 CATAATTTA
27910751 CATAAT
1 CATAAT
27910757 ACTTAAATAT
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
8 10 0.15
9 50 0.75
10 7 0.10
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.38
Consensus pattern (9 bp):
CATAATTTA
Found at i:27910692 original size:114 final size:114
Alignment explanation
Indices: 27910558--27910779 Score: 295
Period size: 114 Copynumber: 1.9 Consensus size: 114
27910548 TATAACATAT
* * *
27910558 ATAACTTACATAACTTATATAACATACATAACTTATATAACTTATATAACTTAGATA-AATAT-A
1 ATAACTTACATAACTTATATAACATACATAA-ATATATAACTTACATAA-ATAGATATAATATCA
* * *
27910621 TAACTTACATAAAATACATAATACTTAAATATATTTTATATCATAATTTAC
64 TAAATTACATAAAATACATAATACTTAAATATATATCATATCATAATTTAC
* * * * *
27910672 ATAACTTACATAACTTATATAACTTAGATAAATATATAATTTACATAAATATATATCATATCATA
1 ATAACTTACATAACTTATATAACATACATAAATATATAACTTACATAAATAGATATAATATCATA
**
27910737 AATTACATAACTTACATAATACTTAAATATATATCATATCATA
66 AATTACATAAAATACATAATACTTAAATATATATCATATCATA
27910780 CATAACTAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
112 5 0.05
113 18 0.19
114 70 0.75
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (114 bp):
ATAACTTACATAACTTATATAACATACATAAATATATAACTTACATAAATAGATATAATATCATA
AATTACATAAAATACATAATACTTAAATATATATCATATCATAATTTAC
Found at i:27916419 original size:21 final size:21
Alignment explanation
Indices: 27916395--27916445 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
27916385 ACAATTTAGA
*
27916395 GCAGAGGCAGCAGAGAGGGAG
1 GCAGAGGCAGCAGAGAGAGAG
* * *
27916416 GCAGCGGCTGCAGCGAGAGAG
1 GCAGAGGCAGCAGAGAGAGAG
27916437 GCAGAGGCA
1 GCAGAGGCA
27916446 CGAGCGATGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.49, T:0.02
Consensus pattern (21 bp):
GCAGAGGCAGCAGAGAGAGAG
Found at i:27916755 original size:16 final size:16
Alignment explanation
Indices: 27916734--27916803 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
27916724 TTTGGTTCGT
* * *
27916734 TGTATTGGATTAGAGA
1 TGTAATGGAATAGAGG
* *
27916750 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
27916766 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
27916782 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
27916798 TGTAAT
1 TGTAAT
27916804 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:27922553 original size:21 final size:21
Alignment explanation
Indices: 27922529--27922579 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
27922519 ACAATTTAGA
*
27922529 GCAGAGGCAGCAGAGAGGGAG
1 GCAGAGGCAGCAGAGAGAGAG
* * *
27922550 GCAGCGGCTGCAGCGAGAGAG
1 GCAGAGGCAGCAGAGAGAGAG
27922571 GCAGAGGCA
1 GCAGAGGCA
27922580 CGAGCGATGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.49, T:0.02
Consensus pattern (21 bp):
GCAGAGGCAGCAGAGAGAGAG
Found at i:27922799 original size:16 final size:16
Alignment explanation
Indices: 27922777--27922845 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
27922767 TTTGGTTCGC
27922777 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
27922793 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
27922809 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
27922826 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
27922842 TGTA
1 TGTA
27922846 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:27922823 original size:33 final size:32
Alignment explanation
Indices: 27922777--27922845 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
27922767 TTTGGTTCGC
27922777 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
27922809 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
27922842 TGTA
1 TGTA
27922846 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:27922910 original size:44 final size:45
Alignment explanation
Indices: 27922826--27923000 Score: 202
Period size: 45 Copynumber: 4.0 Consensus size: 45
27922816 GGATTAGAGG
* * * *
27922826 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
**
27922871 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T---
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
* * *
27922911 TG-AATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
**
27922955 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
27922999 TG
1 TG
27923001 GAATAGAGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
39 20 0.19
40 13 0.12
41 1 0.01
43 1 0.01
44 32 0.30
45 41 0.38
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
Found at i:27922931 original size:39 final size:39
Alignment explanation
Indices: 27922874--27923017 Score: 180
Period size: 39 Copynumber: 3.5 Consensus size: 39
27922864 GGTTGAATGT
27922874 AATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTG
1 AATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTG
* * ***
27922913 AATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATG
1 AATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T---TG
27922957 TAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTG
1 -AATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTG
*
27922997 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
27923018 CATAATGAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
39 40 0.45
40 13 0.15
41 1 0.01
43 1 0.01
44 13 0.15
45 20 0.23
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.33
Consensus pattern (39 bp):
AATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTG
Found at i:27922977 original size:84 final size:84
Alignment explanation
Indices: 27922831--27923019 Score: 351
Period size: 84 Copynumber: 2.2 Consensus size: 84
27922821 AGAGGTGTAT
* * *
27922831 TGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGT
1 TGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGT
27922896 AATCTTGTGTTTGGTTGAA
66 AATCTTGTGTTTGGTTGAA
27922915 TGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGT
1 TGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGT
27922980 AATCTTGTGTTTGGTTGAA
66 AATCTTGTGTTTGGTTGAA
27922999 TGGAATAGAGGTGTAATAGCA
1 TGGAATAGAGGTGTAATAGCA
27923020 TAATGAAAAA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 102 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.33
Consensus pattern (84 bp):
TGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGT
AATCTTGTGTTTGGTTGAA
Found at i:27923195 original size:17 final size:18
Alignment explanation
Indices: 27923165--27923198 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
27923155 TTATTATTTG
27923165 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
27923183 CGGTCGC-GTCGCGTTT
1 CGGTCGCGGTCGCGTTT
27923199 GTCGCGGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:27925023 original size:14 final size:14
Alignment explanation
Indices: 27924985--27925027 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
27924975 TAAAATGTAC
27924985 AATATAATTAAA-T
1 AATATAATTAAATT
27924998 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
27925013 AA-ATAATTTAATT
1 AATATAATTAAATT
27925026 AA
1 AA
27925028 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:27927508 original size:3 final size:3
Alignment explanation
Indices: 27927500--27927592 Score: 69
Period size: 3 Copynumber: 31.0 Consensus size: 3
27927490 TAAAACAATT
** * *
27927500 TAA TAA TAA TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA TAA TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * ** * *
27927548 TGA TGA TGA TGA TGA TGG TAT TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27927593 AAATCTTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.54, C:0.01, G:0.12, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27932689 original size:20 final size:20
Alignment explanation
Indices: 27932664--27932701 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27932654 TTTTTTGAAT
*
27932664 TTTTTATAAAATCTGAAAAG
1 TTTTTAAAAAATCTGAAAAG
*
27932684 TTTTTAAAAAATTTGAAA
1 TTTTTAAAAAATCTGAAA
27932702 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTTTAAAAAATCTGAAAAG
Found at i:27932705 original size:18 final size:18
Alignment explanation
Indices: 27932657--27932707 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
27932647 TAGTTTTTTT
* *
27932657 TTTGAATTTTTTATAAAA
1 TTTGAAATTTTTAAAAAA
*
27932675 TCTGAAAAGTTTTTAAAAAA
1 TTTG-AAA-TTTTTAAAAAA
27932695 TTTGAAATTTTTA
1 TTTGAAATTTTTA
27932708 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 9 0.33
19 5 0.19
20 13 0.48
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTGAAATTTTTAAAAAA
Found at i:27936156 original size:6 final size:6
Alignment explanation
Indices: 27936145--27936169 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27936135 CACCCAAGCC
27936145 ATCCAA ATCCAA ATCCAA ATCCAA A
1 ATCCAA ATCCAA ATCCAA ATCCAA A
27936170 CACAAGATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ATCCAA
Found at i:27938827 original size:5 final size:5
Alignment explanation
Indices: 27938807--27938839 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
27938797 TGAAGGAATT
27938807 AAAAG ACAAA- AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAA
27938840 CAGGTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:27938882 original size:7 final size:7
Alignment explanation
Indices: 27938870--27938897 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
27938860 AATGAGACCG
27938870 GTTCCAA
1 GTTCCAA
27938877 GTTCCAA
1 GTTCCAA
27938884 GTTCCAA
1 GTTCCAA
27938891 GTTCCAA
1 GTTCCAA
27938898 TTTCTAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
GTTCCAA
Found at i:27939945 original size:20 final size:20
Alignment explanation
Indices: 27939891--27939945 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
27939881 TCAAATATAC
*
27939891 TATATTAAAAAATAATTTAAAA
1 TATATT-AAAAAT-ATTCAAAA
*
27939913 TTTA-TAAAAATATTCAAAA
1 TATATTAAAAATATTCAAAA
27939932 TATATTAAAAATAT
1 TATATTAAAAATAT
27939946 ATAGAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 10 0.34
20 15 0.52
21 1 0.03
22 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATTAAAAATATTCAAAA
Found at i:27939953 original size:11 final size:11
Alignment explanation
Indices: 27939891--27939947 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
27939881 TCAAATATAC
27939891 TATATTAAAAA
1 TATATTAAAAA
*
27939902 -ATAATTTAAAA
1 TAT-ATTAAAAA
*
27939913 TTTA-T-AAAA
1 TATATTAAAAA
*
27939922 -ATATTCAAAA
1 TATATTAAAAA
27939932 TATATTAAAAA
1 TATATTAAAAA
27939943 TATAT
1 TATAT
27939948 AGAAAAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
8 2 0.05
9 5 0.14
10 7 0.19
11 22 0.59
12 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TATATTAAAAA
Found at i:27943294 original size:21 final size:21
Alignment explanation
Indices: 27943253--27943307 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
27943243 TATTGAATTG
27943253 TTTTGAATTTA-ATA-A-AAT
1 TTTTGAATTTATATATATAAT
27943271 TTTAT-AATTTATATATATAAT
1 TTT-TGAATTTATATATATAAT
*
27943292 TTTTGAATTTTTATAT
1 TTTTGAATTTATATAT
27943308 TAGTAGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.29
19 4 0.13
20 2 0.06
21 16 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTGAATTTATATATATAAT
Found at i:27944759 original size:18 final size:19
Alignment explanation
Indices: 27944736--27944772 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27944726 AAGTTCAATG
27944736 ATTAAA-AAAAGACAAAAA
1 ATTAAATAAAAGACAAAAA
*
27944754 ATTAAATGAAAGACAAAAA
1 ATTAAATAAAAGACAAAAA
27944773 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.14
Consensus pattern (19 bp):
ATTAAATAAAAGACAAAAA
Found at i:27947007 original size:14 final size:14
Alignment explanation
Indices: 27946988--27947018 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27946978 TCAAGTTGAG
*
27946988 TTGAATTTTAAAAT
1 TTGAATATTAAAAT
27947002 TTGAATATTAAAAT
1 TTGAATATTAAAAT
27947016 TTG
1 TTG
27947019 GATAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
TTGAATATTAAAAT
Found at i:27948094 original size:16 final size:18
Alignment explanation
Indices: 27948068--27948101 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
27948058 TAGAATTAGG
27948068 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
27948085 TTGA-AAAATTAATTTAA
1 TTGAGAAAATTAATTTAA
27948102 CAAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:27948736 original size:15 final size:15
Alignment explanation
Indices: 27948716--27948781 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
27948706 AGTATACTTG
27948716 TTATTTTAAATAATA
1 TTATTTTAAATAATA
*
27948731 TTATTTTAAATTA-A
1 TTATTTTAAATAATA
* * *
27948745 TTACTTAAAATAAAA
1 TTATTTTAAATAATA
*
27948760 TTATATTATCAATAAT-
1 TTAT-TT-TAAATAATA
27948776 TTATTT
1 TTATTT
27948782 AAACATAGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 11 0.28
15 18 0.45
16 6 0.15
17 5 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTTTAAATAATA
Found at i:27949346 original size:9 final size:9
Alignment explanation
Indices: 27949321--27949360 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
27949311 TCAAAGTCTT
27949321 TAATATTTTA
1 TAAT-TTTTA
27949331 T-ATTTTTA
1 TAATTTTTA
27949339 TAATTTTTAA
1 TAATTTTT-A
27949349 TAATTTTTA
1 TAATTTTTA
27949358 TAA
1 TAA
27949361 GTTTATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.21
9 12 0.43
10 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TAATTTTTA
Found at i:27954307 original size:4 final size:4
Alignment explanation
Indices: 27954300--27954324 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27954290 ATATACTGTT
27954300 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
27954325 GACTATACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:27957272 original size:23 final size:23
Alignment explanation
Indices: 27957240--27957284 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
27957230 TGAAAAATAA
* *
27957240 ATTTTTAATTTTTAATTGAAAAC
1 ATTTTCAATTTTAAATTGAAAAC
27957263 ATTTTCAATTTTAAATTGAAAA
1 ATTTTCAATTTTAAATTGAAAA
27957285 ATTAAAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTTCAATTTTAAATTGAAAAC
Found at i:27962075 original size:18 final size:18
Alignment explanation
Indices: 27962008--27962162 Score: 181
Period size: 18 Copynumber: 8.7 Consensus size: 18
27961998 TTCAAGGATA
*
27962008 TGCAATCTTAGATGTGAT
1 TGCAATCTTAGATATGAT
*
27962026 ATGCCATCTTAGATATGA-
1 -TGCAATCTTAGATATGAT
*
27962044 TACAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
* *
27962062 TGCAGTCTTCGATATGA-
1 TGCAATCTTAGATATGAT
*
27962079 TCCAATCTTAGATATGAT
1 TGCAATCTTAGATATGAT
27962097 TGCAATCTTAGATATGA-
1 TGCAATCTTAGATATGAT
* *
27962114 TACAATCTTAGACATGAT
1 TGCAATCTTAGATATGAT
*
27962132 TGCAAACTTAGATATGAT
1 TGCAATCTTAGATATGAT
*
27962150 ATACAATCTTAGA
1 -TGCAATCTTAGA
27962163 AGATATGATT
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
17 44 0.39
18 45 0.39
19 25 0.22
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (18 bp):
TGCAATCTTAGATATGAT
Found at i:27962085 original size:35 final size:35
Alignment explanation
Indices: 27962010--27962162 Score: 216
Period size: 35 Copynumber: 4.3 Consensus size: 35
27962000 CAAGGATATG
* *
27962010 CAATCTTAGATGTGATATGCCATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
* * *
27962046 CAATCTTAGATATGATTGCAGTCTTCGATATGATC
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
27962081 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
* *
27962116 CAATCTTAGACATGATTGCAAACTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
27962153 CAATCTTAGA
1 CAATCTTAGA
27962163 AGATATGATT
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
35 77 0.73
36 15 0.14
37 13 0.12
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:27963585 original size:43 final size:43
Alignment explanation
Indices: 27963516--27963610 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
27963506 TCCTTGATAT
** * *
27963516 GGTCTTACATGTTATCACTTATCGATG-TCACTGTCTCACTCAG
1 GGTCTTACATGAAATCACTTAACGATGCTCA-TGTCTCACACAG
* *
27963559 GGTCTTACATGAAATCGA-TTAACGATGCTGATGTCTCACACAT
1 GGTCTTACATGAAATC-ACTTAACGATGCTCATGTCTCACACAG
27963602 GGTCTTACA
1 GGTCTTACA
27963611 CGTAATTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
43 41 0.93
44 3 0.07
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (43 bp):
GGTCTTACATGAAATCACTTAACGATGCTCATGTCTCACACAG
Found at i:27967981 original size:23 final size:23
Alignment explanation
Indices: 27967955--27967999 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
27967945 GTTTTTCCTT
27967955 TTGTAGGAGTGTTTTTTTCTCAA
1 TTGTAGGAGTGTTTTTTTCTCAA
27967978 TTGTAGGAGTGTTTTTTTCTCA
1 TTGTAGGAGTGTTTTTTTCTCA
27968000 GTTGATTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.22, T:0.53
Consensus pattern (23 bp):
TTGTAGGAGTGTTTTTTTCTCAA
Found at i:27972441 original size:10 final size:10
Alignment explanation
Indices: 27972419--27972470 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
27972409 AATTCTATCG
*
27972419 AAAA-TAATC
1 AAAATTAATT
27972428 AAAATTAATT
1 AAAATTAATT
*
27972438 AAAATTTATTAT
1 AAAA-TTAAT-T
27972450 AAAATTAATT
1 AAAATTAATT
*
27972460 AAAATTCATT
1 AAAATTAATT
27972470 A
1 A
27972471 TGTTAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 4 0.11
10 19 0.53
11 8 0.22
12 5 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTAATT
Found at i:27972481 original size:22 final size:22
Alignment explanation
Indices: 27972428--27972471 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27972418 GAAAATAATC
*
27972428 AAAATTAATTAAAATTTATTAT
1 AAAATTAATTAAAATTCATTAT
27972450 AAAATTAATTAAAATTCATTAT
1 AAAATTAATTAAAATTCATTAT
27972472 GTTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTAATTAAAATTCATTAT
Found at i:27988712 original size:22 final size:23
Alignment explanation
Indices: 27988674--27988723 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
27988664 TCTGTCAAAA
* *
27988674 ATTATCAAAGTTAATTAAAATTT
1 ATTATCAAAATTAATTAAAATTC
27988697 ATTAT-AAAATTAATTAAAATTC
1 ATTATCAAAATTAATTAAAATTC
27988719 ATTAT
1 ATTAT
27988724 GTTAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTATCAAAATTAATTAAAATTC
Found at i:27990611 original size:20 final size:18
Alignment explanation
Indices: 27990588--27990626 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
27990578 ATAATAATTA
27990588 TATTTTATTAAATTATGTAT
1 TATTTTATT-AATT-TGTAT
27990608 TATTTTATTAATTTGTAT
1 TATTTTATTAATTTGTAT
27990626 T
1 T
27990627 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
TATTTTATTAATTTGTAT
Found at i:27990626 original size:15 final size:15
Alignment explanation
Indices: 27990558--27990627 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 15
27990548 ATATTATAAT
*
27990558 TTTTATTAATTCATA
1 TTTTATTAATTTATA
*
27990573 TTTTAATAATAATTATA
1 TTTTATTAAT--TTATA
27990590 TTTTATTAAATTATGTATTA
1 TTTTATT-AA-T-T-TA-TA
*
27990610 TTTTATTAATTTGTA
1 TTTTATTAATTTATA
27990625 TTT
1 TTT
27990628 AATAAAAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
15 14 0.31
16 1 0.02
17 11 0.24
18 5 0.11
19 5 0.11
20 9 0.20
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTTATTAATTTATA
Found at i:27990873 original size:16 final size:16
Alignment explanation
Indices: 27990852--27990886 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27990842 TGAATTACTG
*
27990852 ATTACAACTTTATTTC
1 ATTACAACTCTATTTC
27990868 ATTACAACTCTATTTC
1 ATTACAACTCTATTTC
27990884 ATT
1 ATT
27990887 CCCCTAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTACAACTCTATTTC
Found at i:27992044 original size:16 final size:16
Alignment explanation
Indices: 27992008--27992057 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
27991998 TCCATATTTG
27992008 ATTTTTTTAAAAT-TA
1 ATTTTTTTAAAATATA
*
27992023 GTTTTTATTTAAAA-ATA
1 -ATTTT-TTTAAAATATA
27992040 ATTTTTTTAAAATATA
1 ATTTTTTTAAAATATA
27992056 AT
1 AT
27992058 ACACTAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 7 0.24
16 13 0.45
17 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTTTTTTAAAATATA
Found at i:27992291 original size:18 final size:18
Alignment explanation
Indices: 27992245--27992293 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
27992235 TTAATGATTT
*
27992245 AATATAAATATATATAATT
1 AATAT-AATATATATAATC
*
27992264 ATTATTTAATATATATAATC
1 A--ATATAATATATATAATC
27992284 AATATAATAT
1 AATATAATAT
27992294 TTTTTTATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 8 0.32
19 1 0.04
20 13 0.52
21 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATAATATATATAATC
Found at i:27993353 original size:16 final size:18
Alignment explanation
Indices: 27993332--27993364 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
27993322 AAATATCTTT
27993332 ATTTTTA-GTA-AATATA
1 ATTTTTATGTATAATATA
27993348 ATTTTTATGTATAATAT
1 ATTTTTATGTATAATAT
27993365 TTATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
ATTTTTATGTATAATATA
Found at i:27993474 original size:32 final size:32
Alignment explanation
Indices: 27993438--27993538 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 32
27993428 TTAACTAATG
27993438 TTTATAATTAATAAATATATTATTTTAATTTT
1 TTTATAATTAATAAATATATTATTTTAATTTT
** * *
27993470 TTTATTTTTAATTAAAGTA-AATATTTTTAATTAATG
1 TTTATAATTAA-TAAA-TATATTA-TTTTAATT--TT
*
27993506 TTTATAATTAATAAATATATTA-TTCAATTTT
1 TTTATAATTAATAAATATATTATTTTAATTTT
27993537 TT
1 TT
27993539 ATTTTTAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
31 3 0.06
32 9 0.17
33 13 0.24
34 12 0.22
35 7 0.13
36 10 0.19
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTATAATTAATAAATATATTATTTTAATTTT
Found at i:27993523 original size:68 final size:66
Alignment explanation
Indices: 27993414--27993548 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 66
27993404 TATAGGTGGA
*
27993414 TAAAGTAAATATTTTTAACTAATGTTTATAATTAATAAATATATTATTTTAATTTTTTTATTTTT
1 TAAAGTAAATATTTTTAACTAATGTTTATAATTAATAAATATATTA-TTCAA-TTTTTTATTTTT
27993479 AAT
64 AAT
*
27993482 TAAAGTAAATATTTTTAATTAATGTTTATAATTAATAAATATATTATTCAATTTTTTATTTTTAA
1 TAAAGTAAATATTTTTAACTAATGTTTATAATTAATAAATATATTATTCAATTTTTTATTTTTAA
27993547 T
66 T
27993548 T
1 T
27993549 CATCTTTTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 16 0.25
67 4 0.06
68 45 0.69
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (66 bp):
TAAAGTAAATATTTTTAACTAATGTTTATAATTAATAAATATATTATTCAATTTTTTATTTTTAA
T
Found at i:27993617 original size:32 final size:35
Alignment explanation
Indices: 27993581--27993644 Score: 80
Period size: 32 Copynumber: 1.9 Consensus size: 35
27993571 TTTATTTATA
27993581 AAATAAAATAATTAT-TGT-A-ATTTATTTTTAGT
1 AAATAAAATAATTATGTGTAATATTTATTTTTAGT
* **
27993613 AAATATAATTTTTATGTGTAATATTTATTTTT
1 AAATAAAATAATTATGTGTAATATTTATTTTT
27993645 CAATCCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 12 0.46
33 3 0.12
34 1 0.04
35 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (35 bp):
AAATAAAATAATTATGTGTAATATTTATTTTTAGT
Found at i:27996996 original size:37 final size:37
Alignment explanation
Indices: 27996946--27997021 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
27996936 TTAGCAAGTG
*
27996946 GTTAGATAAGTGCATAGACAAAGCCCAAAGCATTTTT
1 GTTAGATAAGTGCATAGACAAAGCCCAAAGCACTTTT
27996983 GTTAGATAAGTGCATAGACAAAGCCCAAAGCACTTTT
1 GTTAGATAAGTGCATAGACAAAGCCCAAAGCACTTTT
27997020 GT
1 GT
27997022 ACCAAGTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (37 bp):
GTTAGATAAGTGCATAGACAAAGCCCAAAGCACTTTT
Found at i:28001488 original size:30 final size:30
Alignment explanation
Indices: 28001444--28001503 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28001434 ACTTAACAAG
*
28001444 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
28001474 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
28001504 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:28010722 original size:14 final size:13
Alignment explanation
Indices: 28010684--28010732 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
28010674 AAAAAATATG
28010684 ATATTTAATAATA
1 ATATTTAATAATA
28010697 AT-TTTAA-AATA
1 ATATTTAATAATA
28010708 ATATTTAATATATA
1 ATATTTAATA-ATA
*
28010722 ATATATAATAA
1 ATATTTAATAA
28010733 CAAAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.19
12 10 0.31
13 4 0.12
14 12 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:28011139 original size:7 final size:7
Alignment explanation
Indices: 28011127--28011193 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 7
28011117 ATATGTAAAA
28011127 ATAATAT
1 ATAATAT
28011134 ATAATAT
1 ATAATAT
*
28011141 AT-ATAA
1 ATAATAT
*
28011147 ATAAAAT
1 ATAATAT
*
28011154 GAATAATAA
1 --ATAATAT
*
28011163 ATAATAAA
1 ATAAT-AT
28011171 ATAATTAT
1 ATAA-TAT
28011179 ATAATAT
1 ATAATAT
28011186 ATAATAT
1 ATAATAT
28011193 A
1 A
28011194 AAAATAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
6 5 0.10
7 27 0.55
8 11 0.22
9 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:28011140 original size:22 final size:21
Alignment explanation
Indices: 28011115--28011187 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
28011105 ATATGAAAGT
28011115 ATATATGTAAAAATAATATATA
1 ATATAT-TAAAAATAATATATA
28011137 ATATATATAAATAA-AATGA-ATA
1 ATATAT-TAAA-AATAAT-ATATA
* *
28011159 ATAAATAATAAAATAATTATATA
1 ATATATTA-AAAATAA-TATATA
28011182 ATATAT
1 ATATAT
28011188 AATATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
21 3 0.07
22 26 0.63
23 12 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
ATATATTAAAAATAATATATA
Found at i:28011148 original size:20 final size:20
Alignment explanation
Indices: 28011030--28011188 Score: 91
Period size: 20 Copynumber: 7.8 Consensus size: 20
28011020 AAAACTTTTG
*
28011030 ATAATA-ATAATATAGATAA
1 ATAATATATAATATATATAA
*
28011049 AAAATATATAATAGTATA-AA
1 ATAATATATAATA-TATATAA
*
28011069 A-AATGACATAATA-ATATAAA
1 ATAAT-ATATAATATATAT-AA
* *
28011089 ATAA-ATATAATATGTA-AT
1 ATAATATATAATATATATAA
* *
28011107 ATGAA-AGTAT-ATATGTAAAA
1 AT-AATA-TATAATATATATAA
28011127 ATAATATATAATATATATAA
1 ATAATATATAATATATATAA
* *
28011147 ATAAAATGAATAATAAATAATAAA
1 ATAATAT--ATAATATAT-AT-AA
28011171 ATAATTATATAATATATA
1 ATAA-TATATAATATATA
28011189 ATATAAAAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 31
0.71 0.08 0.20
Matches are distributed among these distances:
18 6 0.05
19 30 0.27
20 42 0.38
21 5 0.05
22 9 0.08
23 10 0.09
24 6 0.05
25 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAATATATAATATATATAA
Found at i:28011189 original size:20 final size:19
Alignment explanation
Indices: 28011030--28011200 Score: 100
Period size: 19 Copynumber: 9.2 Consensus size: 19
28011020 AAAACTTTTG
28011030 ATAATA-ATAATATAGATAAA
1 ATAATATATAATAT--ATAAA
28011050 A-AATATATAATAGTATAAA
1 ATAATATATAATA-TATAAA
*
28011069 A-AATGACATAATAATATAAA
1 ATAAT-ATATAAT-ATATAAA
* *
28011089 ATAA-ATATAATATGTAAT
1 ATAATATATAATATATAAA
*
28011107 ATGAA-AGTAT-ATATGTAAAA
1 AT-AATA-TATAATATAT-AAA
28011127 ATAATATATAATATATATAA
1 ATAATATATAATATATA-AA
28011147 ATAA-A-ATGAATA-AT-AA
1 ATAATATAT-AATATATAAA
* *
28011163 ATAATA-A-AATA-ATTAT
1 ATAATATATAATATATAAA
28011179 ATAATATATAATATA-AAA
1 ATAATATATAATATATAAA
28011197 ATAA
1 ATAA
28011201 AATTAAAAAT
Statistics
Matches: 125, Mismatches: 9, Indels: 36
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.05
16 13 0.10
17 3 0.02
18 20 0.16
19 40 0.32
20 39 0.31
21 4 0.03
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAATATATAATATATAAA
Found at i:28011212 original size:50 final size:54
Alignment explanation
Indices: 28011127--28011242 Score: 152
Period size: 52 Copynumber: 2.2 Consensus size: 54
28011117 ATATGTAAAA
* * *
28011127 ATAATATATAATATATATAAATAAAATGAATAAT-AAATA-ATAAAATAATTAT
1 ATAATATATAATATATATAAATAAAATGAAAAATAAAACAGATAAAAAAATTAT
*
28011179 ATAATATATAATATA-A-AAATAAAATTAAAAATAAAACAGATAAAAAAATTAT
1 ATAATATATAATATATATAAATAAAATGAAAAATAAAACAGATAAAAAAATTAT
*
28011231 AT-TTATATAATA
1 ATAATATATAATA
28011243 ACAACAGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
50 14 0.25
51 14 0.25
52 29 0.51
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (54 bp):
ATAATATATAATATATATAAATAAAATGAAAAATAAAACAGATAAAAAAATTAT
Found at i:28013295 original size:205 final size:206
Alignment explanation
Indices: 28012840--28013394 Score: 866
Period size: 205 Copynumber: 2.7 Consensus size: 206
28012830 AAATCTACTT
*
28012840 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATCGTAAACAC
*
28012905 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGCAAGCACAAGAATG-TCAAATCATCT
66 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGAATGCT-AAATCATCT
** *
28012969 TGGATCTTGCTTCAGTGATATTATCTGAAAGTGAGATCTGCTATGTATCTACTCCCCGTTGAAGT
130 TGGATCTTGCTTCAGTGATAACATCTGAAAGTGAGATCTACTATGTATCTACTCCCCGTTGAAGT
*
28013034 GGAGATGCCGGA
195 GGAGATGCCAGA
*
28013046 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATCGTAAACAC
* * *
28013111 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAATG-ATGCTAAATCATCT
66 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAA-GAATGCTAAATCATCT
* * *
28013175 TGGATC-TGCTTCAGT-ATAAACATCTGAAGGTGAGATCTACTATTTATCTGCTCCCCGTTGAAG
130 TGGATCTTGCTTCAGTGAT-AACATCTGAAAGTGAGATCTACTATGTATCTACTCCCCGTTGAAG
*
28013238 TGGAGATGTCAGA
194 TGGAGATGCCAGA
* * *
28013251 CTTTGATTTGCTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTACTTCAACGTAAACAC
1 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATCGTAAACAC
* * * *
28013316 GTGAAAGCCAAATCAGCTATGTCTTTGGTTTGTTCATTGTAAGCACAAGAATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGAATGCTAAATCATCTT
28013381 GGATCTTGCTTCAG
131 GGATCTTGCTTCAG
28013395 CCAGATCTGT
Statistics
Matches: 319, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
204 3 0.01
205 181 0.57
206 133 0.42
207 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (206 bp):
CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGAATGCTAAATCATCTT
GGATCTTGCTTCAGTGATAACATCTGAAAGTGAGATCTACTATGTATCTACTCCCCGTTGAAGTG
GAGATGCCAGA
Found at i:28025210 original size:14 final size:13
Alignment explanation
Indices: 28025172--28025220 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
28025162 AAAAAATATG
28025172 ATATTTAATAATA
1 ATATTTAATAATA
28025185 AT-TTTAA-AATA
1 ATATTTAATAATA
28025196 ATATTTAATATATA
1 ATATTTAATA-ATA
*
28025210 ATATATAATAA
1 ATATTTAATAA
28025221 CAAATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.19
12 10 0.31
13 4 0.12
14 12 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:28030105 original size:21 final size:21
Alignment explanation
Indices: 28030081--28030136 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
28030071 AACAGCGGTG
*
28030081 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
28030102 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
28030123 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
28030137 AACATCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Done.