Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 176 of 198
Found at i:55087224 original size:8 final size:8
Alignment explanation
Indices: 55087211--55087241 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
55087201 CCTCATGAAG
55087211 GCCTTGTT
1 GCCTTGTT
55087219 GCCTTGTT
1 GCCTTGTT
55087227 GCCTTGTT
1 GCCTTGTT
*
55087235 GCATTGT
1 GCCTTGT
55087242 AGGCCCGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.23, G:0.26, T:0.48
Consensus pattern (8 bp):
GCCTTGTT
Found at i:55087626 original size:21 final size:21
Alignment explanation
Indices: 55087600--55087649 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
55087590 GTTTTAATTA
55087600 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
55087621 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
55087642 AAGCAGAG
1 AAGCAGAG
55087650 CAGAGCAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.50, T:0.00
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGGG
Found at i:55088007 original size:44 final size:44
Alignment explanation
Indices: 55087958--55088054 Score: 160
Period size: 44 Copynumber: 2.2 Consensus size: 44
55087948 CAAAATTAGT
*
55087958 GGCGTTT-TTAGAAAAAGCGCCGCTAAAGGTCACCAAACAATAGC
1 GGCGTTTGTT-GAAAAAGCACCGCTAAAGGTCACCAAACAATAGC
*
55088002 GGCGTTTGTTGGAAAAGCACCGCTAAAGGTCACCAAACAATAGC
1 GGCGTTTGTTGAAAAAGCACCGCTAAAGGTCACCAAACAATAGC
55088046 GGCGTTTGT
1 GGCGTTTGT
55088055 GGGAAAAACG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
44 48 0.96
45 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (44 bp):
GGCGTTTGTTGAAAAAGCACCGCTAAAGGTCACCAAACAATAGC
Found at i:55088060 original size:44 final size:44
Alignment explanation
Indices: 55087970--55088061 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
55087960 CGTTTTTAGA
* *
55087970 AAAAGCGCCGCTAAAGGTCACCAAACAATAGCGGCGTTTGTTGG
1 AAAAGCACCGCTAAAGGTCACCAAACAATAGCGGCGTTTGTGGG
55088014 AAAAGCACCGCTAAAGGTCACCAAACAATAGCGGCGTTTGTGGG
1 AAAAGCACCGCTAAAGGTCACCAAACAATAGCGGCGTTTGTGGG
55088058 AAAA
1 AAAA
55088062 ACGCCGCGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (44 bp):
AAAAGCACCGCTAAAGGTCACCAAACAATAGCGGCGTTTGTGGG
Found at i:55088095 original size:87 final size:86
Alignment explanation
Indices: 55087998--55088179 Score: 220
Period size: 86 Copynumber: 2.1 Consensus size: 86
55087988 CACCAAACAA
* ** *
55087998 TAGCGGCGTTTGTTGGAAAAGCACCGCTAAAGGTCACCAAACAATAGCGGCGTTTGTGGGAAAAA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGAACA-CAAACAATAGCGGCGTTTGTAGGAAAAA
55088063 CGCCGCGAAAGAACATGACATT
65 CGCCGCGAAAGAACATGACATT
* * * ** * ** *
55088085 TATCGGCGTTTGTGGGAATAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTAGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGAACACAAACAATAGCGGCGTTTGTAGGAAAAAC
* *
55088150 GCCGCTAAAGAACATGACCTT
66 GCCGCGAAAGAACATGACATT
55088171 TAGCGGCGT
1 TAGCGGCGT
55088180 GTATTTCTAT
Statistics
Matches: 79, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
86 49 0.62
87 30 0.38
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.21
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGAACACAAACAATAGCGGCGTTTGTAGGAAAAAC
GCCGCGAAAGAACATGACATT
Found at i:55088098 original size:43 final size:43
Alignment explanation
Indices: 55088042--55088179 Score: 222
Period size: 43 Copynumber: 3.2 Consensus size: 43
55088032 CACCAAACAA
* * *
55088042 TAGCGGCGTTTGTGGGAAAAACGCCGCGAAAGAACATGACATT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTT
* *
55088085 TATCGGCGTTTGTGGGAATAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTT
*
55088128 TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTT
55088171 TAGCGGCGT
1 TAGCGGCGT
55088180 GTATTTCTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 87 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTT
Found at i:55094159 original size:16 final size:16
Alignment explanation
Indices: 55094138--55094170 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55094128 TTTTTAATTG
55094138 TTTTTTAATATTATAC
1 TTTTTTAATATTATAC
*
55094154 TTTTTTAATATTTTAC
1 TTTTTTAATATTATAC
55094170 T
1 T
55094171 ATATTTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAATATTATAC
Found at i:55116986 original size:21 final size:21
Alignment explanation
Indices: 55116960--55117011 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
55116950 TCACTTCGTT
55116960 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
55116981 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
55117002 TCTTTTTGTC
1 TCTTTTTGTC
55117012 TAACTCACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.23, G:0.12, T:0.56
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:55117022 original size:21 final size:21
Alignment explanation
Indices: 55116940--55117022 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
55116930 ACAAAAAAAA
*
55116940 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCCAAGTCACTTC---TCTT
*
55116964 TTTGTCCAAGTTACTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
**
55116985 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
* *
55117006 TTTGTCTAACTCACTTC
1 TTTGTCCAAGTCACTTC
55117023 CTTAGGGGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 37 0.71
24 15 0.29
ACGTcount: A:0.13, C:0.24, G:0.11, T:0.52
Consensus pattern (21 bp):
TTTGTCCAAGTCACTTCTCTT
Found at i:55117478 original size:16 final size:16
Alignment explanation
Indices: 55117432--55117480 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
55117422 TTGGGGAAAT
55117432 AGTGTAAATATGCAAA
1 AGTGTAAATATGCAAA
* **
55117448 AGT-TTAA-GGGCAAA
1 AGTGTAAATATGCAAA
55117462 AGTGTAAATATGCAAA
1 AGTGTAAATATGCAAA
55117478 AGT
1 AGT
55117481 TTAGGGGCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 8 0.32
15 6 0.24
16 11 0.44
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.24
Consensus pattern (16 bp):
AGTGTAAATATGCAAA
Found at i:55117512 original size:30 final size:30
Alignment explanation
Indices: 55117432--55117492 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
55117422 TTGGGGAAAT
55117432 AGTGTAAATATGCAAAAGTTTAAGGGCAAA
1 AGTGTAAATATGCAAAAGTTTAAGGGCAAA
*
55117462 AGTGTAAATATGCAAAAGTTTAGGGGCAAA
1 AGTGTAAATATGCAAAAGTTTAAGGGCAAA
55117492 A
1 A
55117493 TAGTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.23
Consensus pattern (30 bp):
AGTGTAAATATGCAAAAGTTTAAGGGCAAA
Found at i:55117730 original size:18 final size:17
Alignment explanation
Indices: 55117697--55117735 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
55117687 TTTTATAAAT
55117697 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
55117715 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
55117732 TGTG
1 TGTG
55117736 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:55117980 original size:23 final size:23
Alignment explanation
Indices: 55117953--55118074 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
55117943 AGTGTTATTG
55117953 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
55117976 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
55117999 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
55118022 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
55118045 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55118068 ATCAGTG
1 ATCAGTG
55118075 TGGCACTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:55118007 original size:46 final size:46
Alignment explanation
Indices: 55117953--55118074 Score: 217
Period size: 46 Copynumber: 2.7 Consensus size: 46
55117943 AGTGTTATTG
55117953 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
55117999 ATCAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
55118045 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
55118075 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:55121782 original size:11 final size:11
Alignment explanation
Indices: 55121766--55121796 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
55121756 CTTTCAATTC
55121766 CAATTTAATCA
1 CAATTTAATCA
55121777 CAATTTAATCA
1 CAATTTAATCA
55121788 CAATTTAAT
1 CAATTTAAT
55121797 TCAATACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (11 bp):
CAATTTAATCA
Found at i:55122933 original size:14 final size:13
Alignment explanation
Indices: 55122907--55122956 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
55122897 ATTTATTTGA
55122907 AATATAATAATAT
1 AATATAATAATAT
55122920 AATATAATTAATAT
1 AATATAA-TAATAT
* *
55122934 AAT-TTACAATAT
1 AATATAATAATAT
55122946 AATA-AATAATA
1 AATATAATAATA
55122957 ATATACTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 13 0.42
13 9 0.29
14 9 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:55126874 original size:2 final size:2
Alignment explanation
Indices: 55126867--55126891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55126857 TGGGAAATTG
55126867 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55126892 AATTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55139773 original size:17 final size:17
Alignment explanation
Indices: 55139751--55139785 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
55139741 CCTGCATAAT
55139751 ATGTTAGTAAAGGTAAA
1 ATGTTAGTAAAGGTAAA
55139768 ATGTTAGTAAAGGTAAA
1 ATGTTAGTAAAGGTAAA
55139785 A
1 A
55139786 CAGGTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (17 bp):
ATGTTAGTAAAGGTAAA
Found at i:55140598 original size:18 final size:16
Alignment explanation
Indices: 55140577--55140621 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
55140567 ATTTTGGGTG
55140577 TTTTATTTTTTCGTTTTC
1 TTTT-TTTTTTC-TTTTC
*
55140595 TTTTTTTTCTCTTTTC
1 TTTTTTTTTTCTTTTC
*
55140611 TCTTTTTTTTC
1 TTTTTTTTTTC
55140622 CTTGTGGTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 6 0.25
18 4 0.17
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTTCTTTTC
Found at i:55140601 original size:16 final size:16
Alignment explanation
Indices: 55140582--55140621 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
55140572 GGGTGTTTTA
55140582 TTTTTTCGTTTTCT-TT
1 TTTTTTC-TTTTCTCTT
55140598 TTTTTCTCTTTTCTCTT
1 TTTTT-TCTTTTCTCTT
55140615 TTTTTTC
1 TTTTTTC
55140622 CTTGTGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTCTCTT
Found at i:55142360 original size:9 final size:9
Alignment explanation
Indices: 55142346--55142377 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
55142336 TTTCGGATTT
*
55142346 GAATAACTC
1 GAATAATTC
55142355 GAATAATTC
1 GAATAATTC
55142364 GAATAATTC
1 GAATAATTC
55142373 GAATA
1 GAATA
55142378 TCAAACTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (9 bp):
GAATAATTC
Found at i:55142462 original size:29 final size:31
Alignment explanation
Indices: 55142426--55142486 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
55142416 AAACCTTTTT
* *
55142426 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
55142456 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
55142487 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:55142619 original size:19 final size:20
Alignment explanation
Indices: 55142579--55142619 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
55142569 CCAAAACCCT
*
55142579 CAAAACCTTTTATTTTCCCC
1 CAAAACCTTTTATCTTCCCC
55142599 CAAAA-CTTTTA-CTTCCTCC
1 CAAAACCTTTTATCTTCC-CC
55142618 CA
1 CA
55142620 CTTTTTCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (20 bp):
CAAAACCTTTTATCTTCCCC
Found at i:55142768 original size:17 final size:17
Alignment explanation
Indices: 55142742--55142774 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55142732 ACTTTCCCTT
55142742 AAACTTTTA-TTCCCCA
1 AAACTTTTATTTCCCCA
55142758 AAACTTTTTATTTCCCC
1 AAAC-TTTTATTTCCCC
55142775 CCTAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (17 bp):
AAACTTTTATTTCCCCA
Found at i:55154612 original size:21 final size:21
Alignment explanation
Indices: 55154586--55154627 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55154576 TTTCTCCCAT
* *
55154586 GTTAGGTTTTGGGTTTCTAGG
1 GTTAGGGTTAGGGTTTCTAGG
*
55154607 GTTAGGGTTAGGGTTTTTAGG
1 GTTAGGGTTAGGGTTTCTAGG
55154628 ATTTTTAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.02, G:0.40, T:0.45
Consensus pattern (21 bp):
GTTAGGGTTAGGGTTTCTAGG
Found at i:55155203 original size:124 final size:125
Alignment explanation
Indices: 55154810--55155222 Score: 666
Period size: 125 Copynumber: 3.3 Consensus size: 125
55154800 ATTTATTAAG
* *
55154810 GAAATCGCTACCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * *
55154875 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAAGATGCTTTATCAGAAGAATTTTT
66 GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
* *
55154935 AAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTAAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* *
55155000 GCTTCTGAGCAAATAGTATAAAAAACGCTTGAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
* *
55155060 GAAATCGCTCCTACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* *
55155125 GCTTCTGAGCAAATAGTAT-AAAAACGCTTCAAACAAGATGCTTTATCAGAAAAATTTCT
66 GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
* * *
55155184 GAAATCTCTCCCACGTGGACGCGTTTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCG-CTTTTACTACAGTAG
55155223 CATATTTGGG
Statistics
Matches: 267, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 57 0.21
125 210 0.79
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
Found at i:55155448 original size:9 final size:9
Alignment explanation
Indices: 55155434--55155464 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
55155424 GTTAAACGAA
55155434 TCGAGTTAT
1 TCGAGTTAT
55155443 TCGAGTTAT
1 TCGAGTTAT
55155452 TCGAGTTAT
1 TCGAGTTAT
55155461 TCGA
1 TCGA
55155465 ATCAACTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:55155808 original size:30 final size:31
Alignment explanation
Indices: 55155760--55155819 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
55155750 AAACCTTTTA
*
55155760 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
55155790 TTTTCTCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
55155820 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:55159164 original size:49 final size:49
Alignment explanation
Indices: 55159046--55159166 Score: 224
Period size: 49 Copynumber: 2.5 Consensus size: 49
55159036 TAAGAATATT
* *
55159046 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
55159095 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
55159144 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
55159167 TAATATAAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:55165581 original size:21 final size:21
Alignment explanation
Indices: 55165555--55165599 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
55165545 ATTATTGCTA
55165555 AAGCCATTGCCAATCATTTTC
1 AAGCCATTGCCAATCATTTTC
*
55165576 AAGCCATTGCCAATCGTTTTC
1 AAGCCATTGCCAATCATTTTC
55165597 AAG
1 AAG
55165600 AAGTCATCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (21 bp):
AAGCCATTGCCAATCATTTTC
Found at i:55176651 original size:42 final size:42
Alignment explanation
Indices: 55176597--55176693 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
55176587 CTATATGAAT
*
55176597 GGCACTAAGTGTGCA-AAACTAAAATGACGATGTTGAATAATG
1 GGCACTAAGTGTG-AGAAACTAAAATGACGATGTTGAATAACG
* * *
55176639 GGCACTAAGTGTGAGAAATTAATATGATGATGTTGAATAACG
1 GGCACTAAGTGTGAGAAACTAAAATGACGATGTTGAATAACG
55176681 GGCACTAAGTGTG
1 GGCACTAAGTGTG
55176694 TGACACCGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (42 bp):
GGCACTAAGTGTGAGAAACTAAAATGACGATGTTGAATAACG
Found at i:55180407 original size:2 final size:2
Alignment explanation
Indices: 55180400--55180424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55180390 AATGAGATAA
55180400 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55180425 ATGTATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55198274 original size:23 final size:21
Alignment explanation
Indices: 55198240--55198296 Score: 96
Period size: 23 Copynumber: 2.6 Consensus size: 21
55198230 TTAAATCATG
55198240 TCTCTCAAATTCTCTCATATT
1 TCTCTCAAATTCTCTCATATT
55198261 TCTCTCCAATATTCTCTCATATT
1 TCTCT-CAA-ATTCTCTCATATT
55198284 TCTCTCAAATTCT
1 TCTCTCAAATTCT
55198297 TCTAAAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.29
22 6 0.18
23 18 0.53
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (21 bp):
TCTCTCAAATTCTCTCATATT
Found at i:55201007 original size:23 final size:23
Alignment explanation
Indices: 55200981--55201102 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
55200971 ATAAGTGCAA
55200981 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55201004 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55201027 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
55201050 CACTGTTATGTGGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
55201073 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55201096 CACTGAT
1 CACTGAT
55201103 CAATAACACT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55201048 original size:46 final size:46
Alignment explanation
Indices: 55200981--55201100 Score: 213
Period size: 46 Copynumber: 2.6 Consensus size: 46
55200971 ATAAGTGCAA
*
55200981 CACTGATATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
*
55201027 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTGGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
*
55201073 CACTGAAACGTAGCCGAAGCTACCACTG
1 CACTGAAATGTAGCCGAAGCTACCACTG
55201101 ATCAATAACA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
Found at i:55202144 original size:30 final size:30
Alignment explanation
Indices: 55202090--55202150 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55202080 GACGACGACA
* * *
55202090 CAGGCCCATCAACAGCGCCCACACAATCAC
1 CAGGCCCAGCAACAGCACACACACAATCAC
* *
55202120 CAGGCCCAGCAACAGCACATACACAGTCAC
1 CAGGCCCAGCAACAGCACACACACAATCAC
55202150 C
1 C
55202151 CGACCCAACA
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:0.34, C:0.44, G:0.15, T:0.07
Consensus pattern (30 bp):
CAGGCCCAGCAACAGCACACACACAATCAC
Found at i:55202242 original size:18 final size:18
Alignment explanation
Indices: 55202211--55202253 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
55202201 TACGAGGTGC
*
55202211 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
55202229 GTATCCTAAG-CCTTATAT
1 GTATCCT-AGCCCTTATAT
*
55202247 GTTTCCT
1 GTATCCT
55202254 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.44
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:55203454 original size:126 final size:126
Alignment explanation
Indices: 55203229--55203516 Score: 459
Period size: 126 Copynumber: 2.3 Consensus size: 126
55203219 GCCAAATAGG
* *
55203229 AACTACGGTAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCAGTACTTTTGCTGACAAAGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCAGAACTTTTGCTGACAAAGCATCC
* * *
55203294 TGTTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTGTTTCAGA
66 TGCTTAAAGCGTTTTTGACACAATTTGCTCAGAAACGTCTTCTCAAAATTATTGTTTCAGA
* * *
55203355 AACTACTGTAGCAAAAGAGCGTCCACATGGGAGCTTCTTTCAGAACTTTTGCTGACAATGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCAGAACTTTTGCTGACAAAGCATCC
* * *
55203420 TGCTTAAAGCGTTTTTGCCACAATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTCAGT
66 TGCTTAAAGCGTTTTTGACACAATTTGCTCAGAAACGTCTTCTCAAAATTATTGTTTCAGA
* *
55203481 AACTACTGTAGCAAAAAAGTGTCCACGTGGGAGCTT
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
55203517 TTTTAAATTA
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 148 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (126 bp):
AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCAGAACTTTTGCTGACAAAGCATCC
TGCTTAAAGCGTTTTTGACACAATTTGCTCAGAAACGTCTTCTCAAAATTATTGTTTCAGA
Found at i:55203648 original size:53 final size:53
Alignment explanation
Indices: 55203591--55203747 Score: 136
Period size: 53 Copynumber: 3.1 Consensus size: 53
55203581 TTTCCTTAAA
55203591 AACCCTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
1 AACCCTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
* * * ** **
55203644 AACCCTAAGCCCTAAT-TTATTTAATTTT----TTT-T-CTTAA-AAAC-C-CTT
1 AACCCTAAACCCTAATCTAATTT--TTTTAAAATTTATAATTAATTTACTCAAGT
* * *
55203689 AACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTGCTCAAGT
1 AACCCTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
55203742 AACCCT
1 AACCCT
55203748 CAACTATAAT
Statistics
Matches: 74, Mismatches: 18, Indels: 24
0.64 0.16 0.21
Matches are distributed among these distances:
44 3 0.04
45 15 0.20
46 6 0.08
47 2 0.03
48 7 0.09
49 2 0.03
50 7 0.09
51 1 0.01
52 6 0.08
53 21 0.28
54 4 0.05
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (53 bp):
AACCCTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
Found at i:55203650 original size:46 final size:46
Alignment explanation
Indices: 55203598--55203747 Score: 113
Period size: 48 Copynumber: 3.1 Consensus size: 46
55203588 AAAAACCCTA
55203598 AACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
1 AACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
* * ** * ** ** * *
55203644 AACCCTAAGCCCTAATTTATTTAATTTTTTTTCTTAA-AAACCCTTAACACT
1 AACCCTAA--TCTAATTTTTTTAAAATTTATAATTAATTTA--C-TCA-AGT
* *
55203695 AAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTGCTCAAGT
1 -AACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
55203742 AACCCT
1 AACCCT
55203748 CAACTATAAT
Statistics
Matches: 72, Mismatches: 24, Indels: 16
0.64 0.21 0.14
Matches are distributed among these distances:
46 14 0.19
47 3 0.04
48 22 0.31
49 2 0.03
50 21 0.29
51 2 0.03
52 8 0.11
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (46 bp):
AACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
Found at i:55203697 original size:98 final size:95
Alignment explanation
Indices: 55203590--55203895 Score: 344
Period size: 98 Copynumber: 3.2 Consensus size: 95
55203580 TTTTCCTTAA
* *
55203590 AAACCCTAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAGCC
1 AAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAA-CC
*
55203655 CTAATTTATTTAATTTTTTTTCTTAAAAACCCT
65 CTAATTTATTTAA-TTTTTTTCTT-AAAACCAT
* * *
55203688 TAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTGCTCAAGTAACCCTCAACT
1 AAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCT-AACC
* * * *
55203753 ATAATTTAATTGATTTTTTCCTTAAAACCAT
65 CTAATTTATTTAATTTTTTTCTTAAAACCAT
* * *** * * **
55203784 AAACACAAAACCCTAATCTAA-TTTTGAATTTTTTATAATTAATTTAATTAAAAAACCCTAATCC
1 AAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAA-CC
* *
55203848 CTTATTTATTTAATTTTTTTCTTTAAAACCAA
65 CTAATTTATTTAATTTTTTTC-TTAAAACCAT
* *
55203880 AAACTCAAAACCCTAA
1 AAACACTAAACCCTAA
55203896 CCCTAACGCA
Statistics
Matches: 176, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
94 2 0.01
95 46 0.26
96 50 0.28
97 9 0.05
98 67 0.38
99 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (95 bp):
AAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAACCC
TAATTTATTTAATTTTTTTCTTAAAACCAT
Found at i:55205049 original size:18 final size:16
Alignment explanation
Indices: 55205019--55205096 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 16
55205009 CATATTGACA
55205019 ATAAATAATTTAAAAAT
1 ATAAA-AATTTAAAAAT
*
55205036 CATAAAAATATTAAAAAA
1 -ATAAAAAT-TTAAAAAT
55205054 AGTAAAAATTTAAAAGCAT
1 A-TAAAAATTTAAAA--AT
55205073 ATAAAAATTTTATAAAAT
1 ATAAAAA-TTTA-AAAAT
55205091 -TAAAAA
1 ATAAAAA
55205097 AAACATAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
17 16 0.31
18 27 0.52
19 6 0.12
20 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAAAAATTTAAAAAT
Found at i:55210925 original size:20 final size:21
Alignment explanation
Indices: 55210899--55210953 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
55210889 GTAACGAATT
55210899 TTTTTCTGTCTTTTGACACGC
1 TTTTTCTGTCTTTTGACACGC
55210920 TTTTCTCTGTCTTTTGACACG-
1 TTTT-TCTGTCTTTTGACACGC
55210941 TTTTTCTGCTCTT
1 TTTTTCTG-TCTT
55210954 GTTAGCACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
22 16 0.50
ACGTcount: A:0.07, C:0.24, G:0.13, T:0.56
Consensus pattern (21 bp):
TTTTTCTGTCTTTTGACACGC
Found at i:55217738 original size:18 final size:18
Alignment explanation
Indices: 55217715--55217754 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
55217705 GCCCTCAGCA
55217715 TCTTCTCCTACATTTCCT
1 TCTTCTCCTACATTTCCT
*
55217733 TCTTCTCCTACGTTTCCT
1 TCTTCTCCTACATTTCCT
55217751 TCTT
1 TCTT
55217755 TTCCAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.38, G:0.03, T:0.53
Consensus pattern (18 bp):
TCTTCTCCTACATTTCCT
Found at i:55219899 original size:30 final size:30
Alignment explanation
Indices: 55219865--55219923 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
55219855 GTTCATCACT
*
55219865 ATTCAGTTATTGCCTACTTTATCTTGGCTA
1 ATTCAGGTATTGCCTACTTTATCTTGGCTA
55219895 ATTCAGGTATTGCCTACTTTATCTTGGCT
1 ATTCAGGTATTGCCTACTTTATCTTGGCT
55219924 TAATACTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (30 bp):
ATTCAGGTATTGCCTACTTTATCTTGGCTA
Found at i:55221186 original size:45 final size:44
Alignment explanation
Indices: 55221100--55221192 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
55221090 ATTACAACAT
* *
55221100 CATTTCATTCAACCAAACACAATAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAATAATACTATTACAGCTCTATTC
*
55221144 CATTCCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTC
1 CATTCCATTCAACCAAACACAAT-AA-TACTATTACAG-CTCTATTC
55221189 CATT
1 CATT
55221193 ATAACTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 2 0.05
44 21 0.49
45 20 0.47
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAATAATACTATTACAGCTCTATTC
Found at i:55221805 original size:10 final size:11
Alignment explanation
Indices: 55221790--55221839 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
55221780 CAACTAAATC
55221790 ATTTCTCTC-A
1 ATTTCTCTCAA
*
55221800 ATTTCTCTCTA
1 ATTTCTCTCAA
55221811 ATATTCTCTCAA
1 AT-TTCTCTCAA
*
55221823 ATTCCTCTCAA
1 ATTTCTCTCAA
55221834 ATTTCT
1 ATTTCT
55221840 ATTTAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.26
11 16 0.46
12 10 0.29
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTCTCTCAA
Found at i:55221817 original size:22 final size:22
Alignment explanation
Indices: 55221790--55221839 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
55221780 CAACTAAATC
* *
55221790 ATTTCTCTC-AATTTCTCTCTA
1 ATTTCTCTCAAATTCCTCTCAA
55221811 ATATTCTCTCAAATTCCTCTCAA
1 AT-TTCTCTCAAATTCCTCTCAA
55221834 ATTTCT
1 ATTTCT
55221840 ATTTAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 11 0.44
23 12 0.48
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTCTCTCAAATTCCTCTCAA
Found at i:55223984 original size:21 final size:22
Alignment explanation
Indices: 55223938--55223985 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
55223928 CCAACACCGA
55223938 CAACCAGATCCCCTACCGGATG
1 CAACCAGATCCCCTACCGGATG
*
55223960 -AACCAGAGTCCCC-GCCGGA-G
1 CAACCAGA-TCCCCTACCGGATG
55223980 CAACCA
1 CAACCA
55223986 CAACCCCCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.29, C:0.42, G:0.21, T:0.08
Consensus pattern (22 bp):
CAACCAGATCCCCTACCGGATG
Found at i:55224186 original size:48 final size:49
Alignment explanation
Indices: 55224118--55224286 Score: 304
Period size: 49 Copynumber: 3.5 Consensus size: 49
55224108 GTTTATTTTA
55224118 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
55224167 ATGTAATAAAATA-AAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
* *
55224215 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
*
55224264 ATTTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
55224287 AATATTCTTA
Statistics
Matches: 116, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
48 48 0.41
49 68 0.59
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
Found at i:55227691 original size:123 final size:124
Alignment explanation
Indices: 55227472--55227756 Score: 455
Period size: 123 Copynumber: 2.3 Consensus size: 124
55227462 GCCCAACATT
* * *
55227472 CTACTGTAACAAAAACGCGTCCACATAGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTAGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
**
55227537 TTGAAGCGTTTCTATACTATTTGCTCAGAAACGTCAACTTGAAATTA-CTTTTCAAGAC
66 TTGAAGCGTTTCTATACTATTTGCTCAGAAACGTCAACTCAAAATTATCTTTTCAAGAC
* * * *
55227595 CTACTGTAGCAAAAGCGCGTCCATGTGGGAGTGATTTCAGAAATTCTTCTGATAAAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTAGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* * *
55227660 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTCTATACTATTTGCTCAGAAACGTCAACTCAAAATTATCTTTTCAAGAC
55227719 CTACTGTAGCAAAAGCGCGTCCACGTAGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTAGGAGCGATTTC
55227757 CTTAATAAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
123 102 0.70
124 44 0.30
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTAGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTCTATACTATTTGCTCAGAAACGTCAACTCAAAATTATCTTTTCAAGAC
Found at i:55227974 original size:15 final size:15
Alignment explanation
Indices: 55227942--55227975 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
55227932 CCTAAAAATA
* *
55227942 CTAAAAACCCTAACC
1 CTAAAAACCCAAAAC
55227957 CTAAAAACCCAAAAC
1 CTAAAAACCCAAAAC
55227972 CTAA
1 CTAA
55227976 CGTAGGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (15 bp):
CTAAAAACCCAAAAC
Found at i:55229716 original size:197 final size:193
Alignment explanation
Indices: 55229303--55229862 Score: 591
Period size: 193 Copynumber: 2.9 Consensus size: 193
55229293 TAGCGATCTG
* * * * *
55229303 TAAACTCAGCTTAGTCTGTTTGTTGTTTTTGACGAGGGTGAAAAGTAAATACTATTCAGATTTAT
1 TAAACTCAGTTTAGTCTGCTTG-TGTTTTTGATGAGGGTGAAAAGTAAATACCATTCAGATTTAG
* *
55229368 CTCTATGATGAATTTATCA-TACGTTCATAACACTATACAGTTAGTGGTGAGCTTTGTATTTTCT
65 CTCTATGATGAA-TTATCATTA-GTTCATAACAC-ATA-AATTAGTGGTGAGCTTTGCATTTTCT
* * *
55229432 GAATGATTCTGCTATGTTA-T--AAAGTTCACTAATTGCTATACAGATTTAGCTTCGCTAGCTGA
126 GAATGATTCTGATATGTTATTGAAAAGTTCACTCATTGC-ATACAGATTTAACTTCGCTAGCTGA
55229494 TCCT
190 TCCT
*
55229498 TAAACTCAGCTTT-GTCTGCTTGTCGTTTTTGATGAGGGTGAAAAGTAGATACCATTCAGATTTA
1 TAAACTCAG-TTTAGTCTGCTTGT-GTTTTTGATGAGGGTGAAAAGTAAATACCATTCAGATTTA
* ** *
55229562 GCTCAATGATGAATTGCCATTAGTTCATAGCAGCATAAACTTCA-TGGTGAGCTTTGCATTTTCT
64 GCTCTATGATGAATTATCATTAGTTCATAACA-CATAAA-TT-AGTGGTGAGCTTTGCATTTTCT
*
55229626 GAATGATTCTGGTATGTTATTGAAAAGTTCACTCATTGACATACAGATTTAACTGT-GCTAGCTG
126 GAATGATTCTGATATGTTATTGAAAAGTTCACTCATTG-CATACAGATTTAACT-TCGCTAGCTG
55229690 ATCCT
189 ATCCT
* * ** * *** *
55229695 TAAGCTCAGTTTAATCTGC-T-TGTTTCGGGTGCCAGTG-AAAGTAAATATCATTCAGATTTAGC
1 TAAACTCAGTTTAGTCTGCTTGTGTTTTTGATGAGGGTGAAAAGTAAATACCATTCAGATTTAGC
* ** * * * *
55229757 TTTATGAAAAATTATCATAAGTTCATAACATCATAAATTTATTGGTGAGTTTTTCATTTTCTGAA
66 TCTATGATGAATTATCATTAGTTCATAACA-CATAAA-TTAGTGGTGAGCTTTGCATTTTCTGAA
* * *
55229822 TGATTCTAATATGTTATAGAAAAGATCACTCATTGCCATAC
129 TGATTCTGATATGTTATTGAAAAGTTCACTCATTG-CATAC
55229863 TGTTTTAAGA
Statistics
Matches: 310, Mismatches: 42, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
192 1 0.00
193 111 0.36
194 66 0.21
195 71 0.23
196 6 0.02
197 53 0.17
198 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (193 bp):
TAAACTCAGTTTAGTCTGCTTGTGTTTTTGATGAGGGTGAAAAGTAAATACCATTCAGATTTAGC
TCTATGATGAATTATCATTAGTTCATAACACATAAATTAGTGGTGAGCTTTGCATTTTCTGAATG
ATTCTGATATGTTATTGAAAAGTTCACTCATTGCATACAGATTTAACTTCGCTAGCTGATCCT
Found at i:55234218 original size:12 final size:12
Alignment explanation
Indices: 55234203--55234232 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55234193 AGGAACATTT
*
55234203 CGAGGATTTCTA
1 CGAGGATATCTA
55234215 CGAGGATATCTA
1 CGAGGATATCTA
55234227 CGAGGA
1 CGAGGA
55234233 ACTAAGCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (12 bp):
CGAGGATATCTA
Found at i:55239933 original size:2 final size:2
Alignment explanation
Indices: 55239926--55239960 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55239916 TGAAGTTTGA
55239926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55239961 ATAAGACCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55244308 original size:2 final size:2
Alignment explanation
Indices: 55244301--55244329 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55244291 CATTTTAATG
55244301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55244330 GTGGTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55245159 original size:22 final size:22
Alignment explanation
Indices: 55245108--55245159 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
55245098 CTCGTTTGAT
* *
55245108 AAATTAAAAAAATTAAATGTTA
1 AAATTAAAAAAATTAAATATCA
* *
55245130 AAAATAAAAAAATTAATTATCA
1 AAATTAAAAAAATTAAATATCA
*
55245152 AATTTAAA
1 AAATTAAA
55245160 TTATAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTAAAAAAATTAAATATCA
Found at i:55248487 original size:21 final size:21
Alignment explanation
Indices: 55248463--55248503 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55248453 ATAGATTAAA
*
55248463 TCTTA-AATTTGAACAAAATAT
1 TCTTACAATTAGAA-AAAATAT
55248484 TCTTACAATTAGAAAAAATA
1 TCTTACAATTAGAAAAAATA
55248504 GAGAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (21 bp):
TCTTACAATTAGAAAAAATAT
Found at i:55262462 original size:2 final size:2
Alignment explanation
Indices: 55262455--55262483 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55262445 AAATTCACAA
55262455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55262484 GGGACTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55263501 original size:17 final size:17
Alignment explanation
Indices: 55263479--55263579 Score: 76
Period size: 17 Copynumber: 5.6 Consensus size: 17
55263469 CGAATTGAAT
55263479 CACTACATAATTAAAAA
1 CACTACATAATTAAAAA
** *
55263496 CACTACATAAGTATTTGAAT
1 CACTACAT-A--ATTAAAAA
55263516 CACTACATAATTAAAAA
1 CACTACATAATTAAAAA
* ** *
55263533 CATTACATAAGTCTTTGAAT
1 CACTACATAA---TTAAAAA
55263553 CACTACATAATTAAAAA
1 CACTACATAATTAAAAA
*
55263570 CATTACATAA
1 CACTACATAA
55263580 GTCTTGAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
17 35 0.56
18 1 0.02
19 1 0.02
20 26 0.41
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.30
Consensus pattern (17 bp):
CACTACATAATTAAAAA
Found at i:55263521 original size:20 final size:20
Alignment explanation
Indices: 55263496--55263562 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
55263486 TAATTAAAAA
55263496 CACTACATAAGTATTTGAAT
1 CACTACATAAGTATTTGAAT
** *
55263516 CACTACAT-A--ATTAAAAA
1 CACTACATAAGTATTTGAAT
* *
55263533 CATTACATAAGTCTTTGAAT
1 CACTACATAAGTATTTGAAT
55263553 CACTACATAA
1 CACTACATAA
55263563 TTAAAAACAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
17 12 0.34
18 1 0.03
19 1 0.03
20 21 0.60
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (20 bp):
CACTACATAAGTATTTGAAT
Found at i:55263582 original size:37 final size:37
Alignment explanation
Indices: 55263473--55263584 Score: 206
Period size: 37 Copynumber: 3.0 Consensus size: 37
55263463 ATTAACCGAA
* *
55263473 TTGAATCACTACATAATTAAAAACACTACATAAGTAT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
55263510 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
55263547 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
55263584 T
1 T
55263585 GAAATTAACA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:55269587 original size:36 final size:36
Alignment explanation
Indices: 55269546--55269618 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
55269536 GGTAGCTTTA
*
55269546 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
*
55269582 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
55269618 G
1 G
55269619 GTAGCTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
Found at i:55269713 original size:36 final size:36
Alignment explanation
Indices: 55269667--55269776 Score: 202
Period size: 36 Copynumber: 3.1 Consensus size: 36
55269657 TATGTTGCGA
55269667 TGCTATACTTATCTGATCAAGTGAAAAAGTGATAAG
1 TGCTATACTTATCTGATCAAGTGAAAAAGTGATAAG
*
55269703 TGTTATACTTATCTGATCAAGTGAAAAAGTGATAAG
1 TGCTATACTTATCTGATCAAGTGAAAAAGTGATAAG
*
55269739 TGCTATACTTATCTGATCAAGTGACAAAGTGATAAG
1 TGCTATACTTATCTGATCAAGTGAAAAAGTGATAAG
55269775 TG
1 TG
55269777 GTAGCTTAGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (36 bp):
TGCTATACTTATCTGATCAAGTGAAAAAGTGATAAG
Found at i:55273383 original size:2 final size:2
Alignment explanation
Indices: 55273376--55273406 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55273366 CAATAATAAA
55273376 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
55273407 TATATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:55275585 original size:17 final size:15
Alignment explanation
Indices: 55275548--55275578 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55275538 ATAGCTGAAC
*
55275548 ACAAAAAAGTAATCT
1 ACAAAAAAGTAATAT
55275563 ACAAAAAAGTAATAT
1 ACAAAAAAGTAATAT
55275578 A
1 A
55275579 AACAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (15 bp):
ACAAAAAAGTAATAT
Found at i:55276835 original size:21 final size:24
Alignment explanation
Indices: 55276790--55276835 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
55276780 TATACTTAAG
*
55276790 AATATATATATATCTTTATAAATT
1 AATATATATAAATCTTTATAAATT
55276814 AATATA-ATAAAT-TTTA-AAATT
1 AATATATATAAATCTTTATAAATT
55276835 A
1 A
55276836 TTAATTAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 4 0.19
23 5 0.24
24 6 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AATATATATAAATCTTTATAAATT
Found at i:55280204 original size:13 final size:13
Alignment explanation
Indices: 55280186--55280220 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
55280176 GAATCGTTAC
55280186 ACTCGTTGGTACA
1 ACTCGTTGGTACA
55280199 ACTCGTTGGTACA
1 ACTCGTTGGTACA
*
55280212 TCTCGTTGG
1 ACTCGTTGG
55280221 CAATAAGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (13 bp):
ACTCGTTGGTACA
Found at i:55282682 original size:43 final size:42
Alignment explanation
Indices: 55282612--55282738 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 42
55282602 AGCTCGTATA
* *
55282612 ATGCCAACGTCCCAGACGTGGTTTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGCGGTCTTACATGTAA-CACATATCG
*
55282655 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GCGGTCTTACATGT-AACACATA-TCG
55282698 ATGCCAACGTCCCAGACGCGGTCTTACATGATAACACATAT
1 ATGCCAACGTCCCAGACGCGGTCTTACATG-TAACACATAT
55282739 TGAAAATCCT
Statistics
Matches: 73, Mismatches: 3, Indels: 16
0.79 0.03 0.17
Matches are distributed among these distances:
42 4 0.05
43 62 0.85
44 7 0.10
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGCGGTCTTACATGTAACACATATCG
Found at i:55297948 original size:10 final size:10
Alignment explanation
Indices: 55297878--55297948 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 10
55297868 GACATGATTT
55297878 TTAAATAATTA
1 TTAAA-AATTA
55297889 TTAAAAA-TA
1 TTAAAAATTA
55297898 TCATAAAAAGTTA
1 T--TAAAAA-TTA
*
55297911 TAAAAAATTA
1 TTAAAAATTA
* * *
55297921 TTTAAACTCA
1 TTAAAAATTA
*
55297931 TTAGAAATTA
1 TTAAAAATTA
55297941 TTAAAAAT
1 TTAAAAAT
55297949 ATTTTTTAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
9 3 0.07
10 24 0.52
11 16 0.35
13 3 0.07
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:55311858 original size:17 final size:19
Alignment explanation
Indices: 55311825--55311859 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
55311815 AATTTTCATT
55311825 AAATATAAAAATCAAATTA
1 AAATATAAAAATCAAATTA
55311844 AAATA-AAAAAT-AAATT
1 AAATATAAAAATCAAATT
55311860 TTATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATATAAAAATCAAATTA
Found at i:55318135 original size:2 final size:2
Alignment explanation
Indices: 55318111--55318167 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
55318101 AACACATCAA
* * *
55318111 AT AT AC AT AT AC AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55318153 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
55318168 CGATACAAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55322821 original size:3 final size:3
Alignment explanation
Indices: 55322813--55322862 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
55322803 GGGCACAAAC
55322813 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
55322861 AA
1 AA
55322863 CAGTTTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:55323389 original size:44 final size:45
Alignment explanation
Indices: 55323321--55323732 Score: 155
Period size: 44 Copynumber: 9.1 Consensus size: 45
55323311 ATCTGCCATA
* * * *
55323321 ACAAATCTTATCTCCTTGGAGTTGCAGTGGAGCAAGA-TGAAGCT
1 ACAAATCCTATATCCCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
* ** *
55323365 ACAAATCCTATATCCCTGAGGTTGCAGTGGA-CCGGATTGAAGTT
1 ACAAATCCTATATCCCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
* * * * * * * *
55323409 ATAATTTCTATACCCCTGAAATTGCATTGG-GTC-TGATTTAATCTGCCAT
1 ACAAATCCTATATCCCTGAAGTTGCAGTGGAG-CAAGATTGAA---G-C-T
* * *
55323458 AGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCT
1 A-CAAATCCTATATCCCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
* * * * *
55323503 ACAAATCTTATATTCCTGAAGTTGCAGTGGATC-GGATTGAAACT
1 ACAAATCCTATATCCCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
* * * * * *** * * *
55323547 ACAATTTCTATA-CTCCTAAAATTGTAGTGG-GTTGGAATAAAACT
1 ACAAATCCTATATC-CCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
* * * * * *
55323591 ACAGTAGCGAATCTTATCTCCATAAAGTCGCAGTGGAGCGAGA-TGAAGCT
1 AC---A---AATCCTATATCCCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
* ** * * *
55323641 GCAAATTTTATCTCCCTAAAGTTGCAATGGAGCAAGA-TGAAGCT
1 ACAAATCCTATATCCCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
* * *
55323685 ACAAATCCTATATCCCTAAAGTTGTAGTGGA--ATAGATTGAAACT
1 ACAAATCCTATATCCCTGAAGTTGCAGTGGAGCA-AGATTGAAGCT
55323729 ACAA
1 ACAA
55323733 CAGCAAATCT
Statistics
Matches: 272, Mismatches: 72, Indels: 48
0.69 0.18 0.12
Matches are distributed among these distances:
42 1 0.00
43 8 0.03
44 199 0.73
45 3 0.01
46 1 0.00
47 4 0.01
49 2 0.01
50 47 0.17
51 7 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (45 bp):
ACAAATCCTATATCCCTGAAGTTGCAGTGGAGCAAGATTGAAGCT
Found at i:55323540 original size:138 final size:138
Alignment explanation
Indices: 55323292--55323671 Score: 467
Period size: 138 Copynumber: 2.8 Consensus size: 138
55323282 ATCCCTTAAG
* * * * *
55323292 TTGCAGTGGGTTGGATTGAATCTGCCATAACAAATCTTATCTCCTTGGAGTTGCAGTGGAGCAAG
1 TTGCAGTGGGTTGGATTAAATCTGCCATAGCGAATCTTATCTCCATGAAGTTGCAGTGGAGCAAG
* * ** *
55323357 ATGAAGCTACAAATCCTATATCCCTGAGGTTGCAGTGGACCGGATTGAAGTTATAATTTCTATAC
66 ATGAAGCTACAAATCTTATATCCCTGAAGTTGCAGTGGACCGGATTGAAACTACAATTTCTATAC
*
55323422 CCCTGAAA
131 CCCTAAAA
* * *
55323430 TTGCATTGGGTCT-GATTTAATCTGCCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAA
1 TTGCAGTGGGT-TGGATTAAATCTGCCATAGCGAATCTTATCTCCATGAAGTTGCAGTGGAGCAA
* *
55323494 GATGAAGCTACAAATCTTATATTCCTGAAGTTGCAGTGGATCGGATTGAAACTACAATTTCTATA
65 GATGAAGCTACAAATCTTATATCCCTGAAGTTGCAGTGGACCGGATTGAAACTACAATTTCTATA
*
55323559 CTCCTAAAA
130 CCCCTAAAA
* * * * * * *
55323568 TTGTAGTGGGTTGGAATAAAACT-ACAGTAGCGAATCTTATCTCCATAAAGTCGCAGTGGAGCGA
1 TTGCAGTGGGTTGGATTAAATCTGCCA-TAGCGAATCTTATCTCCATGAAGTTGCAGTGGAGCAA
* * * * *
55323632 GATGAAGCTGCAAATTTTATCTCCCTAAAGTTGCAATGGA
65 GATGAAGCTACAAATCTTATATCCCTGAAGTTGCAGTGGA
55323672 GCAAGATGAA
Statistics
Matches: 208, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
137 3 0.01
138 204 0.98
139 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (138 bp):
TTGCAGTGGGTTGGATTAAATCTGCCATAGCGAATCTTATCTCCATGAAGTTGCAGTGGAGCAAG
ATGAAGCTACAAATCTTATATCCCTGAAGTTGCAGTGGACCGGATTGAAACTACAATTTCTATAC
CCCTAAAA
Found at i:55323687 original size:138 final size:137
Alignment explanation
Indices: 55323324--55323714 Score: 430
Period size: 138 Copynumber: 2.8 Consensus size: 137
55323314 TGCCATAACA
* * * *
55323324 AATCTTATCTCCTTGGAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATATCCCTGAGGTTG
1 AATCTTATCTCCATGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCTTATATCCCTGAAGTTG
* * * * * * * * *
55323389 CAGTGGACCGGATTGAAGTTATAATTTCTATACCCCTGAAATTGCATTGGGTCTGATTTAATCTG
66 CAGTGGA-CGGATTGAAGCTACAATTTCTATACTCCTAAAATTGTAGTGGGTCTGAATAAAACTG
*
55323454 CCATAGCG
130 ACATAGCG
* *
55323462 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCTTATATTCCTGAAGTTG
1 AATCTTATCTCCATGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCTTATATCCCTGAAGTTG
*
55323527 CAGTGGATCGGATTGAAACTACAATTTCTATACTCCTAAAATTGTAGTGGGT-TGGAATAAAACT
66 CAGTGGA-CGGATTGAAGCTACAATTTCTATACTCCTAAAATTGTAGTGGGTCT-GAATAAAACT
55323591 -ACAGTAGCG
129 GACA-TAGCG
* * * * * * *
55323600 AATCTTATCTCCATAAAGTCGCAGTGGAGCGAGATGAAGCTGCAAATTTTATCTCCCTAAAGTTG
1 AATCTTATCTCCATGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCTTATATCCCTGAAGTTG
* * * * *
55323665 CAATGGAGCAAGA-TGAAGCTACAAATCCTATA-TCCCTAAAGTTGTAGTGG
66 CAGTGGA-C-GGATTGAAGCTACAATTTCTATACT-CCTAAAATTGTAGTGG
55323715 AATAGATTGA
Statistics
Matches: 216, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
137 4 0.02
138 210 0.97
139 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (137 bp):
AATCTTATCTCCATGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCTTATATCCCTGAAGTTG
CAGTGGACGGATTGAAGCTACAATTTCTATACTCCTAAAATTGTAGTGGGTCTGAATAAAACTGA
CATAGCG
Found at i:55325352 original size:3 final size:3
Alignment explanation
Indices: 55325344--55325379 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55325334 TGTCATTAGA
55325344 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55325380 GCTATAGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:55325466 original size:9 final size:9
Alignment explanation
Indices: 55325452--55325477 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55325442 TTAAATGTTG
55325452 ATACTATTA
1 ATACTATTA
55325461 ATACTATTA
1 ATACTATTA
55325470 ATACTATT
1 ATACTATT
55325478 TGTATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (9 bp):
ATACTATTA
Found at i:55329251 original size:2 final size:2
Alignment explanation
Indices: 55329246--55329293 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
55329236 AAGAGCCTAA
55329246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55329288 AT AT AT
1 AT AT AT
55329294 TAAATATGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55329365 original size:12 final size:12
Alignment explanation
Indices: 55329348--55329385 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
55329338 TATAGAAAAT
55329348 ATGATAATAATA
1 ATGATAATAATA
*
55329360 ATGATAGTAAATA
1 ATGATAAT-AATA
55329373 ATG-TAATAATA
1 ATGATAATAATA
55329384 AT
1 AT
55329386 AGTAATGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.26
12 10 0.43
13 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:55329371 original size:24 final size:24
Alignment explanation
Indices: 55329339--55329385 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
55329329 ATGTATATGT
55329339 ATAGAAAAT-ATGATAATAATAATG
1 ATAGAAAATAATG-TAATAATAATG
*
55329363 ATAGTAAATAATGTAATAATAAT
1 ATAGAAAATAATGTAATAATAAT
55329386 AGTAATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
ATAGAAAATAATGTAATAATAATG
Found at i:55343102 original size:17 final size:17
Alignment explanation
Indices: 55343082--55343114 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55343072 TTCAATATTA
55343082 TATTTCAAACAATAAAT
1 TATTTCAAACAATAAAT
*
55343099 TATTTCTAACAATAAA
1 TATTTCAAACAATAAA
55343115 ATGTATATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (17 bp):
TATTTCAAACAATAAAT
Found at i:55344681 original size:17 final size:16
Alignment explanation
Indices: 55344640--55344682 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
55344630 CTTCTCCTAA
55344640 TTTCTCTCTATTACTTC
1 TTTCT-TCTATTACTTC
*
55344657 TCTTCTTCTGTTATCTTC
1 T-TTCTTCTATTA-CTTC
55344675 TTTCTTCT
1 TTTCTTCT
55344683 CTGATCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.07, C:0.28, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTCTTCTATTACTTC
Found at i:55344689 original size:17 final size:18
Alignment explanation
Indices: 55344653--55344693 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
55344643 CTCTCTATTA
* *
55344653 CTTCTCTTCTTCTGTTAT
1 CTTCTCTTCTTCTCTGAT
55344671 CTTCT-TTCTTCTCTGAT
1 CTTCTCTTCTTCTCTGAT
55344688 C-TCTCT
1 CTTCTCT
55344694 ATTACTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.15
17 12 0.60
18 5 0.25
ACGTcount: A:0.05, C:0.32, G:0.05, T:0.59
Consensus pattern (18 bp):
CTTCTCTTCTTCTCTGAT
Found at i:55345335 original size:3 final size:3
Alignment explanation
Indices: 55345327--55345363 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
55345317 TCAGGTTATA
55345327 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55345364 TAAATCAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55346329 original size:26 final size:26
Alignment explanation
Indices: 55346300--55346349 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
55346290 TTATAAAAAG
55346300 GAAACAAATCCTGATAAAAATTATCA
1 GAAACAAATCCTGATAAAAATTATCA
* *
55346326 GAAACAAATCTTGATAAAATTTAT
1 GAAACAAATCCTGATAAAAATTAT
55346350 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (26 bp):
GAAACAAATCCTGATAAAAATTATCA
Found at i:55351427 original size:3 final size:3
Alignment explanation
Indices: 55351419--55351498 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
55351409 CCACTCATCT
55351419 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
55351467 TAA TAA TAC TAT TAC TAA TAC TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55351499 CTTACCTCAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:55352422 original size:14 final size:17
Alignment explanation
Indices: 55352403--55352440 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
55352393 ATTTATTTCT
55352403 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
55352417 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
55352434 TAATATA
1 TAATATA
55352441 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:55352448 original size:12 final size:11
Alignment explanation
Indices: 55352420--55352463 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
55352410 ATATTTATAA
55352420 TATAATTAATT
1 TATAATTAATT
*
55352431 TAATAATATACTT
1 T-ATAAT-TAATT
55352444 TATAATTAATT
1 TATAATTAATT
55352455 TATATATTA
1 TATA-ATTA
55352464 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:55352467 original size:20 final size:23
Alignment explanation
Indices: 55352415--55352477 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
55352405 ATATAATATT
55352415 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
55352437 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
55352462 TATATAAATAAATAAT
1 TATATATATAATTAAT
55352478 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:55352479 original size:20 final size:20
Alignment explanation
Indices: 55352432--55352480 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
55352422 TAATTAATTT
*
55352432 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
55352452 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
55352472 AATAATATA
1 AATAATATA
55352481 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:55352960 original size:36 final size:36
Alignment explanation
Indices: 55352908--55352981 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
55352898 TTGTATAGGC
**
55352908 ATCAAAAAATTTTTAGCTTTCTTTTCTTTTTGAAAA
1 ATCAAAAAATACTTAGCTTTCTTTTCTTTTTGAAAA
*
55352944 ATCAAAAAATACTTAGCTTTCTTTTCTTTTTGTAAA
1 ATCAAAAAATACTTAGCTTTCTTTTCTTTTTGAAAA
55352980 AT
1 AT
55352982 TCCATTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (36 bp):
ATCAAAAAATACTTAGCTTTCTTTTCTTTTTGAAAA
Found at i:55359753 original size:16 final size:16
Alignment explanation
Indices: 55359705--55359754 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
55359695 GAAATTTTAT
55359705 ATTTTTCAT-CTTACTA
1 ATTTTTCATCCTT-CTA
*
55359721 A-TTTTCTACCCTT-TA
1 ATTTTTC-ATCCTTCTA
55359736 ATTTTTCATCCTTCTA
1 ATTTTTCATCCTTCTA
55359752 ATT
1 ATT
55359755 CATGCCAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 13 0.46
16 12 0.43
17 3 0.11
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTTCATCCTTCTA
Found at i:55362898 original size:10 final size:10
Alignment explanation
Indices: 55362883--55362934 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
55362873 TTTAGAAAAA
55362883 TTTTAAAATT
1 TTTTAAAATT
55362893 TTTTAATATATT
1 TTTTAA-A-ATT
*
55362905 TTTTAGAATT
1 TTTTAAAATT
55362915 TTTTAAGAATT
1 TTTTAA-AATT
*
55362926 TTTAAAAAT
1 TTTTAAAAT
55362935 ATAAAATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 17 0.47
11 11 0.31
12 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:55362914 original size:22 final size:21
Alignment explanation
Indices: 55362883--55362934 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
55362873 TTTAGAAAAA
*
55362883 TTTTAAAATTTTTTAATATATT
1 TTTTAAAATTTTTTAAGA-ATT
*
55362905 TTTTAGAATTTTTTAAGAATT
1 TTTTAAAATTTTTTAAGAATT
*
55362926 TTTAAAAAT
1 TTTTAAAAT
55362935 ATAAAATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTAAAATTTTTTAAGAATT
Found at i:55362917 original size:11 final size:11
Alignment explanation
Indices: 55362883--55362928 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
55362873 TTTAGAAAAA
55362883 TTTTAA-AATT
1 TTTTAAGAATT
*
55362893 TTTTAATATATT
1 TTTTAAGA-ATT
55362905 TTTT-AGAATT
1 TTTTAAGAATT
55362915 TTTTAAGAATT
1 TTTTAAGAATT
55362926 TTT
1 TTT
55362929 AAAAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 13 0.41
11 12 0.38
12 7 0.22
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (11 bp):
TTTTAAGAATT
Found at i:55363336 original size:38 final size:38
Alignment explanation
Indices: 55363294--55363373 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
55363284 TAAATATAGA
55363294 CTTTAAATAGACCCTTATTAGTGGCTAATCTTTATTAG
1 CTTTAAATAGACCCTTATTAGTGGCTAATCTTTATTAG
55363332 CTTTAAATAGACCCTTATTAGTGGCTAATCTTTATTAG
1 CTTTAAATAGACCCTTATTAGTGGCTAATCTTTATTAG
55363370 CTTT
1 CTTT
55363374 GAAGTGTACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (38 bp):
CTTTAAATAGACCCTTATTAGTGGCTAATCTTTATTAG
Found at i:55366781 original size:14 final size:14
Alignment explanation
Indices: 55366762--55366788 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55366752 GTTTGCCATG
55366762 CATGTATATATATA
1 CATGTATATATATA
55366776 CATGTATATATAT
1 CATGTATATATAT
55366789 GCATCAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
CATGTATATATATA
Found at i:55367952 original size:2 final size:2
Alignment explanation
Indices: 55367945--55367986 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
55367935 ACTTGTCTCA
*
55367945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55367987 GTTATAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:55375215 original size:15 final size:15
Alignment explanation
Indices: 55375195--55375226 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55375185 CATCAACCTA
55375195 TACAAGTCTCTTAAT
1 TACAAGTCTCTTAAT
55375210 TACAAGTCTCTTAAT
1 TACAAGTCTCTTAAT
55375225 TA
1 TA
55375227 TATACAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (15 bp):
TACAAGTCTCTTAAT
Found at i:55378295 original size:99 final size:101
Alignment explanation
Indices: 55378112--55378309 Score: 312
Period size: 99 Copynumber: 2.0 Consensus size: 101
55378102 AGATCATAAC
*
55378112 TAAATATTAAATTGAACTTGTATTTTAAAAATTAAGATAACACACGTTTAATAGTATCAATTTTG
1 TAAATATTAAATTGAACTCGTATTTTAAAAATTAAGATAACACACGTTTAATAGTATCAATTTTG
*
55378177 AGCGTAACGAAAATGCTAAAACCGTCCTCGCACAAT
66 AGCGTAACGAAAATGCTAAAACCATCCTCGCACAAT
* * *
55378213 TAAATATTGAATTGAACTCGTGTTTTAAAAATTAAGAT-A-ACACGTTTAATAGTATTAATTTTG
1 TAAATATTAAATTGAACTCGTATTTTAAAAATTAAGATAACACACGTTTAATAGTATCAATTTTG
*
55378276 AGCGTAAC-AAAAGTGCTAAAACTATCCTCGCACA
66 AGCGTAACGAAAA-TGCTAAAACCATCCTCGCACA
55378310 GTAATTGATT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
98 4 0.04
99 50 0.56
100 1 0.01
101 35 0.39
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (101 bp):
TAAATATTAAATTGAACTCGTATTTTAAAAATTAAGATAACACACGTTTAATAGTATCAATTTTG
AGCGTAACGAAAATGCTAAAACCATCCTCGCACAAT
Found at i:55383276 original size:23 final size:23
Alignment explanation
Indices: 55383249--55383324 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
55383239 AGTGTTATTG
55383249 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* * * *
55383272 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCAGCTACAT
55383295 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
*
55383318 ATTAGTG
1 ATCAGTG
55383325 TGGCACTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCAGCTACAT
Found at i:55384359 original size:2 final size:2
Alignment explanation
Indices: 55384352--55384384 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55384342 TGTATTATTC
55384352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55384385 TCATGGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55388286 original size:13 final size:13
Alignment explanation
Indices: 55388268--55388305 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
55388258 AATTTAGCAA
55388268 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
55388281 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
55388294 TGCTTTTGAAAA
1 TGCTTTTGAAAA
55388306 ATTTGGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:55392065 original size:14 final size:14
Alignment explanation
Indices: 55392046--55392081 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
55392036 AAAAAGTAAG
55392046 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
55392060 TCATTTTCCGGAAA
1 TCATTTTCCAGAAA
*
55392074 CCATTTTC
1 TCATTTTC
55392082 AGTGAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:55394125 original size:232 final size:232
Alignment explanation
Indices: 55393719--55394182 Score: 885
Period size: 232 Copynumber: 2.0 Consensus size: 232
55393709 AAGTGTATGA
55393719 CTTGAATTCTGCTTCTTCTATTGAACCCTAAAGTCAAACTAAAAAAGCAGAGCATCTCTTAGAAA
1 CTTGAATTCTGCTTCTTCTATTGAACCCTAAAGTCAAACTAAAAAAGCAGAGCATCTCTTAGAAA
55393784 AAAAATGGAAGTACATGGATTCGTGTTGTTTAGTACTAACCTTAGCATCTGAATAAATGGAACCA
66 AAAAATGGAAGTACATGGATTCGTGTTGTTTAGTACTAACCTTAGCATCTGAATAAATGGAACCA
* *
55393849 ATTAAAAGTTACATATTGTTGTTGTTGAAATATTGTTGGTTATTTTCAAGTTGGAATCAAAGAGG
131 ACTAAAAGTTACATATTGTTGGTGTTGAAATATTGTTGGTTATTTTCAAGTTGGAATCAAAGAGG
55393914 AAACTTCCAAATATTTGAC-TTCTGTTATCTACTTTGT
196 AAACTTCCAAATATTTGACTTTC-GTTATCTACTTTGT
55393951 CTTGAATTCTGCTTCTTCTATTGAACCCTAAAGTCAAACTAAAAAAGCAGAGCATCTCTTAGAAA
1 CTTGAATTCTGCTTCTTCTATTGAACCCTAAAGTCAAACTAAAAAAGCAGAGCATCTCTTAGAAA
55394016 AAAAATGGAAGTACATGGATTCGTGTTGTTTAGTACTAACCTTAGCATCTGAATAAATGGAACCA
66 AAAAATGGAAGTACATGGATTCGTGTTGTTTAGTACTAACCTTAGCATCTGAATAAATGGAACCA
*
55394081 ACTAAAAGTTACATATTGTTGGTGTTGAAATCTTGTTGGTTATTTTCAAGTTGGAATCAAAGAGG
131 ACTAAAAGTTACATATTGTTGGTGTTGAAATATTGTTGGTTATTTTCAAGTTGGAATCAAAGAGG
55394146 AAACTTCCAAATATTTGACTTTCGTTATCTACTTTGT
196 AAACTTCCAAATATTTGACTTTCGTTATCTACTTTGT
55394183 TGACATATTT
Statistics
Matches: 228, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
232 225 0.99
233 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (232 bp):
CTTGAATTCTGCTTCTTCTATTGAACCCTAAAGTCAAACTAAAAAAGCAGAGCATCTCTTAGAAA
AAAAATGGAAGTACATGGATTCGTGTTGTTTAGTACTAACCTTAGCATCTGAATAAATGGAACCA
ACTAAAAGTTACATATTGTTGGTGTTGAAATATTGTTGGTTATTTTCAAGTTGGAATCAAAGAGG
AAACTTCCAAATATTTGACTTTCGTTATCTACTTTGT
Found at i:55397400 original size:11 final size:11
Alignment explanation
Indices: 55397369--55397413 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
55397359 TTTCATTTTT
*
55397369 TTATA-TATTT
1 TTATACTATTA
*
55397379 TTTTACTATTA
1 TTATACTATTA
55397390 TTATACTATTA
1 TTATACTATTA
55397401 -T-TACTATTA
1 TTATACTATTA
55397410 TTAT
1 TTAT
55397414 GTTACATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
9 8 0.28
10 6 0.21
11 15 0.52
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATACTATTA
Found at i:55401361 original size:20 final size:20
Alignment explanation
Indices: 55401332--55401371 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55401322 TCCACCTCAT
* *
55401332 GCATCGCATCATATGCATTA
1 GCATCACATCACATGCATTA
55401352 GCATCACATCACATGCATTA
1 GCATCACATCACATGCATTA
55401372 AAGACCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (20 bp):
GCATCACATCACATGCATTA
Found at i:55408788 original size:10 final size:9
Alignment explanation
Indices: 55408773--55408799 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55408763 CTTTGATTTC
55408773 AAAAAAAAT
1 AAAAAAAAT
55408782 AAAAAAAAT
1 AAAAAAAAT
55408791 AAAAAAAAT
1 AAAAAAAAT
55408800 GGAGAGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:55409765 original size:100 final size:100
Alignment explanation
Indices: 55409642--55409827 Score: 282
Period size: 100 Copynumber: 1.9 Consensus size: 100
55409632 GTTGAAAAGT
* *
55409642 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTA
*
55409707 CGACGGCGGATCTAGCTTCCCTGATATTACAATTG
66 CGACGGCAGATCTAGCTTCCCTGATATTACAATTG
* * * * * *
55409742 AAAAGATTGAAGCCACAATGGCGGATCTTACTTCCCTAACGGTGCGGTGGGATAGATTTAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTA
*
55409807 CGACGGCAGATCTGGCTTCCC
66 CGACGGCAGATCTAGCTTCCC
55409828 CAACATTGCA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 76 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTA
CGACGGCAGATCTAGCTTCCCTGATATTACAATTG
Found at i:55409799 original size:50 final size:50
Alignment explanation
Indices: 55409642--55409853 Score: 167
Period size: 50 Copynumber: 4.2 Consensus size: 50
55409632 GTTGAAAAGT
* *
55409642 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGG
* * * * * * * * *
55409692 AACAGATTGAAGCTACGACGGCGGATC-TAGCTTCCCTGATATTACAATTG
1 AAAAGATTGAAGCCACAACGGCGGATCTTA-CTTCCCTAACAGTGCAGTGG
* * *
55409742 AAAAGATTGAAGCCACAATGGCGGATCTTACTTCCCTAACGGTGCGGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGG
* * * * * * ** * * *
55409792 GATAGATTTAAGCTACGACGGCAGATCTGGCTTCCCCAACATTGCAGTTG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGG
55409842 AACAA-ATTGAAG
1 AA-AAGATTGAAG
55409854 ATTACAGATC
Statistics
Matches: 119, Mismatches: 40, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
49 2 0.02
50 114 0.96
51 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (50 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGG
Found at i:55409843 original size:100 final size:100
Alignment explanation
Indices: 55409642--55409853 Score: 273
Period size: 100 Copynumber: 2.1 Consensus size: 100
55409632 GTTGAAAAGT
* *
55409642 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTA
* ** *
55409707 CGACGGCGGATCTAGCTTCCCTGATATTACAATTG
66 CGACGGCAGATCTAGCTTCCCCAACATTACAATTG
* * * * * *
55409742 AAAAGATTGAAGCCACAATGGCGGATCTTACTTCCCTAACGGTGCGGTGGGATAGATTTAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTA
* * *
55409807 CGACGGCAGATCTGGCTTCCCCAACATTGCAGTTG
66 CGACGGCAGATCTAGCTTCCCCAACATTACAATTG
55409842 AACAA-ATTGAAG
1 AA-AAGATTGAAG
55409854 ATTACAGATC
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
100 94 0.98
101 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTAACAGTGCAGTGGAACAGATTGAAGCTA
CGACGGCAGATCTAGCTTCCCCAACATTACAATTG
Found at i:55411517 original size:11 final size:11
Alignment explanation
Indices: 55411486--55411530 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
55411476 TTTCATTTTT
*
55411486 TTATA-TATTT
1 TTATACTATTA
*
55411496 TTTTACTATTA
1 TTATACTATTA
55411507 TTATACTATTA
1 TTATACTATTA
55411518 -T-TACTATTA
1 TTATACTATTA
55411527 TTAT
1 TTAT
55411531 GTTACATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
9 8 0.28
10 6 0.21
11 15 0.52
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATACTATTA
Found at i:55411842 original size:2 final size:2
Alignment explanation
Indices: 55411835--55411877 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
55411825 TCCATTATTT
* * *
55411835 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TC TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55411877 T
1 T
55411878 GCGAATGCAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55413508 original size:93 final size:93
Alignment explanation
Indices: 55413344--55413520 Score: 228
Period size: 93 Copynumber: 1.9 Consensus size: 93
55413334 TTGCAGCTCG
* * * * * * *
55413344 TGTGGTTCCTACCGACCATTCTTCTGCACCAGTTATCGGTTGTAACGCGAAAGGGTATACCCCTG
1 TGTGCTTCCTACCGAACATTCGTCAGCACCAGTCATCGGTGGTAACGCGAAAGGGCATACCCCTG
* *
55413409 TTTATGGAGAATCATGTCCTCCTCCAAA
66 TTTATGGAAAATCAGGTCCTCCTCCAAA
* ** * *
55413437 TGTGCTTCCTACTGAACATTCGTCAGCACCAGTCATCGGTGGTAACGTTACAGGGCATACCTCTG
1 TGTGCTTCCTACCGAACATTCGTCAGCACCAGTCATCGGTGGTAACGCGAAAGGGCATACCCCTG
55413502 TTTATGGAAAATCAGGTCC
66 TTTATGGAAAATCAGGTCC
55413521 CTCACCAAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (93 bp):
TGTGCTTCCTACCGAACATTCGTCAGCACCAGTCATCGGTGGTAACGCGAAAGGGCATACCCCTG
TTTATGGAAAATCAGGTCCTCCTCCAAA
Found at i:55425716 original size:42 final size:42
Alignment explanation
Indices: 55425654--55425806 Score: 272
Period size: 42 Copynumber: 3.6 Consensus size: 42
55425644 GCTACAGAAG
55425654 AAGAAGAAAAGGACAGTGGAAAAGAAGAAAAGGACATTGGAA
1 AAGAAGAAAAGGACAGTGGAAAAGAAGAAAAGGACATTGGAA
*
55425696 AAGAAGAAAAGGACAATGGAAAAGAAGAAAAGGACATTGGAA
1 AAGAAGAAAAGGACAGTGGAAAAGAAGAAAAGGACATTGGAA
*
55425738 AAGAAGAAAAGGAC-GTTGGAAAAGAAGAAAAGGACGTTGGAA
1 AAGAAGAAAAGGACAG-TGGAAAAGAAGAAAAGGACATTGGAA
55425780 AAGAAGAAAAGGACAGTGGAAAAGAAG
1 AAGAAGAAAAGGACAGTGGAAAAGAAG
55425807 TCGAGGAACC
Statistics
Matches: 106, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
42 105 0.99
43 1 0.01
ACGTcount: A:0.57, C:0.05, G:0.31, T:0.07
Consensus pattern (42 bp):
AAGAAGAAAAGGACAGTGGAAAAGAAGAAAAGGACATTGGAA
Found at i:55425813 original size:21 final size:21
Alignment explanation
Indices: 55425654--55425806 Score: 247
Period size: 21 Copynumber: 7.3 Consensus size: 21
55425644 GCTACAGAAG
55425654 AAGAAGAAAAGGACAGTGGAA
1 AAGAAGAAAAGGACAGTGGAA
*
55425675 AAGAAGAAAAGGACATTGGAA
1 AAGAAGAAAAGGACAGTGGAA
*
55425696 AAGAAGAAAAGGACAATGGAA
1 AAGAAGAAAAGGACAGTGGAA
*
55425717 AAGAAGAAAAGGACATTGGAA
1 AAGAAGAAAAGGACAGTGGAA
55425738 AAGAAGAAAAGGAC-GTTGGAA
1 AAGAAGAAAAGGACAG-TGGAA
55425759 AAGAAGAAAAGGAC-GTTGGAA
1 AAGAAGAAAAGGACAG-TGGAA
55425780 AAGAAGAAAAGGACAGTGGAA
1 AAGAAGAAAAGGACAGTGGAA
55425801 AAGAAG
1 AAGAAG
55425807 TCGAGGAACC
Statistics
Matches: 126, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
21 125 0.99
22 1 0.01
ACGTcount: A:0.57, C:0.05, G:0.31, T:0.07
Consensus pattern (21 bp):
AAGAAGAAAAGGACAGTGGAA
Found at i:55426651 original size:25 final size:25
Alignment explanation
Indices: 55426617--55426670 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
55426607 GTTTAAACTA
55426617 TGAATTTCTGAACTGTCTGAGAATT
1 TGAATTTCTGAACTGTCTGAGAATT
*
55426642 TGAATTTCTGCACTGTCTGAGAATT
1 TGAATTTCTGAACTGTCTGAGAATT
55426667 TGAA
1 TGAA
55426671 AGTTGAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (25 bp):
TGAATTTCTGAACTGTCTGAGAATT
Found at i:55429710 original size:2 final size:2
Alignment explanation
Indices: 55429703--55429731 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55429693 ATGCTATGTA
55429703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55429732 GCCATTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55442572 original size:45 final size:46
Alignment explanation
Indices: 55442518--55442628 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
55442508 ATCACTTGTC
*
55442518 CTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
*
55442563 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
55442609 CTTGATCAGATAAGTGTAGC
1 CTTGATCAGATAAGTGTAGC
55442629 CACTTATCAC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 21 0.33
46 42 0.67
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
Done.