Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 124 of 131
Found at i:40829115 original size:14 final size:14
Alignment explanation
Indices: 40829096--40829123 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40829086 TCACGATGTG
40829096 TATGTATGTATATA
1 TATGTATGTATATA
40829110 TATGTATGTATATA
1 TATGTATGTATATA
40829124 GATACACACA
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:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
TATGTATGTATATA
Found at i:40832559 original size:17 final size:17
Alignment explanation
Indices: 40832533--40832576 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
40832523 CATCCACTAC
* *
40832533 ATATAAATACACTTACT
1 ATATATATACACATACT
*
40832550 ATATATATACACATATT
1 ATATATATACACATACT
40832567 ATATATATAC
1 ATATATATAC
40832577 GGACACAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATATATACACATACT
Found at i:40838750 original size:16 final size:18
Alignment explanation
Indices: 40838728--40838772 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
40838718 TTATTATTTG
*
40838728 TTTTATAATATTTTAA-A
1 TTTTATAATATTTAAACA
40838745 -TTTAT-AT-TTTAAACA
1 TTTTATAATATTTAAACA
40838760 TTTTATAATATTT
1 TTTTATAATATTT
40838773 GTTTATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 10 0.43
17 2 0.09
18 3 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATAATATTTAAACA
Found at i:40843520 original size:23 final size:23
Alignment explanation
Indices: 40843494--40843550 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
40843484 TATATTTACT
*
40843494 TTATAGAATATTTAG-TTTTATTA
1 TTATA-AATATTTAGCATTTATTA
40843517 TTATAATATATTTAGCATTTATTA
1 TTATAA-ATATTTAGCATTTATTA
*
40843541 GTATAAATAT
1 TTATAAATAT
40843551 CTTTGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.03
23 17 0.57
24 12 0.40
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (23 bp):
TTATAAATATTTAGCATTTATTA
Found at i:40852731 original size:18 final size:17
Alignment explanation
Indices: 40852704--40852761 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
40852694 CAGCTCACAT
*
40852704 CTTTGGTGAGCTCGCAA
1 CTTTGGTGAGCTCGCAC
*
40852721 CTTTGGGTGAGCTTGCAC
1 CTTT-GGTGAGCTCGCAC
**
40852739 CTTTCATGAGCTCGCAC
1 CTTTGGTGAGCTCGCAC
40852756 CTTTGG
1 CTTTGG
40852762 GAAGTTTGCA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.33
Consensus pattern (17 bp):
CTTTGGTGAGCTCGCAC
Found at i:40861141 original size:23 final size:22
Alignment explanation
Indices: 40861096--40861141 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
40861086 GAGAAATACA
* *
40861096 TATTTTAATTTTAATTTTTATT
1 TATTTTAATTTTAACTTTAATT
*
40861118 TATTTGTATTTTTAACTTTAATT
1 TATTT-TAATTTTAACTTTAATT
40861141 T
1 T
40861142 TTATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTAATTTTAACTTTAATT
Found at i:40861156 original size:29 final size:29
Alignment explanation
Indices: 40861098--40861157 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
40861088 GAAATACATA
* *
40861098 TTTTAATTTTAATTTTTATTTATTTGTAT
1 TTTTAACTTTAATTTTTATATATTTGTAT
40861127 TTTTAACTTTAATTTTTATATATATT-TAT
1 TTTTAACTTTAATTTTTATATAT-TTGTAT
40861156 TT
1 TT
40861158 ATTTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTAACTTTAATTTTTATATATTTGTAT
Found at i:40861699 original size:576 final size:576
Alignment explanation
Indices: 40860607--40861759 Score: 2306
Period size: 576 Copynumber: 2.0 Consensus size: 576
40860597 TCGCTGGTAA
40860607 TATTCGATCCAAATGGATAGGTCCATTCATTATAACTAATTTATTCTCGAATGGTGCAGTGGAAA
1 TATTCGATCCAAATGGATAGGTCCATTCATTATAACTAATTTATTCTCGAATGGTGCAGTGGAAA
40860672 TTCAAAGTGAAGAAACCCGAAAGTGCTTTAAGGTGAATGGTCAACGGGTAAAACCCTTTTACGAG
66 TTCAAAGTGAAGAAACCCGAAAGTGCTTTAAGGTGAATGGTCAACGGGTAAAACCCTTTTACGAG
40860737 AATTTTAAAATGCACATAGTTGAGGAGATTGTTCTCGAGGAGCCCAGAACTTGAATAACAGGTCG
131 AATTTTAAAATGCACATAGTTGAGGAGATTGTTCTCGAGGAGCCCAGAACTTGAATAACAGGTCG
40860802 TCGAGCTAACGACGTTAAACAAAGCGCTGTTGAGAGACAACCCAAATTTTCTCTTTATGTAAATA
196 TCGAGCTAACGACGTTAAACAAAGCGCTGTTGAGAGACAACCCAAATTTTCTCTTTATGTAAATA
40860867 AATTTTTAGATGGTAAAAGGAAAGTGAAAATGCATGTCAAGGATCGGTTCTGTCTAAGGAAAGAC
261 AATTTTTAGATGGTAAAAGGAAAGTGAAAATGCATGTCAAGGATCGGTTCTGTCTAAGGAAAGAC
40860932 TTGGTACTTAAGAATATCCATTGTGACTCACCTCTCTTTCCTGGGAACTTACTTGGTGCATTTAT
326 TTGGTACTTAAGAATATCCATTGTGACTCACCTCTCTTTCCTGGGAACTTACTTGGTGCATTTAT
40860997 CGCGGCTATTTTACTAAATCCCATAATCTTGGTTTTTAATAATTTATTTCTCGAATATTTAAGCA
391 CGCGGCTATTTTACTAAATCCCATAATCTTGGTTTTTAATAATTTATTTCTCGAATATTTAAGCA
40861062 TAGCATTAGCAAAGCCATATATTCGAGAAATACATATTTTAATTTTAATTTTTATTTATTTGTAT
456 TAGCATTAGCAAAGCCATATATTCGAGAAATACATATTTTAATTTTAATTTTTATTTATTTGTAT
40861127 TTTTAACTTTAATTTTTATATATATTTATTTATTTATATTTATATTTTTTTATTTT
521 TTTTAACTTTAATTTTTATATATATTTATTTATTTATATTTATATTTTTTTATTTT
40861183 TATTCGATCCAAATGGATAGGTCCATTCATTATAACTAATTTATTCTCGAATGGTGCAGTGGAAA
1 TATTCGATCCAAATGGATAGGTCCATTCATTATAACTAATTTATTCTCGAATGGTGCAGTGGAAA
40861248 TTCAAAGTGAAGAAACCCGAAAGTGCTTTAAGGTGAATGGTCAACGGGTAAAACCCTTTTACGAG
66 TTCAAAGTGAAGAAACCCGAAAGTGCTTTAAGGTGAATGGTCAACGGGTAAAACCCTTTTACGAG
40861313 AATTTTAAAATGCACATAGTTGAGGAGATTGTTCTCGAGGAGCCCAGAACTTGAATAACAGGTCG
131 AATTTTAAAATGCACATAGTTGAGGAGATTGTTCTCGAGGAGCCCAGAACTTGAATAACAGGTCG
40861378 TCGAGCTAACGACGTTAAACAAAGCGCTGTTGAGAGACAACCCAAATTTTCTCTTTATGTAAATA
196 TCGAGCTAACGACGTTAAACAAAGCGCTGTTGAGAGACAACCCAAATTTTCTCTTTATGTAAATA
40861443 AATTTTTAGATGGTAAAAGGAAAGTGAAAATGCATGTCAAGGATCGGTTCTGTCTAAGGAAAGAC
261 AATTTTTAGATGGTAAAAGGAAAGTGAAAATGCATGTCAAGGATCGGTTCTGTCTAAGGAAAGAC
40861508 TTGGTACTTAAGAATATCCATTGTGACTCACCTCTCTTTCCTGGGAACTTACTTGGTGCATTTAT
326 TTGGTACTTAAGAATATCCATTGTGACTCACCTCTCTTTCCTGGGAACTTACTTGGTGCATTTAT
40861573 CGCGGCTATTTTACTAAATCCCATAATCTTGGTTTTTAATAATTTATTTCTCGAATATTTAAGCA
391 CGCGGCTATTTTACTAAATCCCATAATCTTGGTTTTTAATAATTTATTTCTCGAATATTTAAGCA
40861638 TAGCATTAGCAAAGCCATATATTCGAGAAATACATATTTTAATTTTAATTTTTATTTATTTGTAT
456 TAGCATTAGCAAAGCCATATATTCGAGAAATACATATTTTAATTTTAATTTTTATTTATTTGTAT
40861703 TTTTAACTTTAATTTTTATATATATTTATTTATTTATATTTATATTTTTTTATTTT
521 TTTTAACTTTAATTTTTATATATATTTATTTATTTATATTTATATTTTTTTATTTT
40861759 T
1 T
40861760 GCAGGTAGAC
Statistics
Matches: 577, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
576 577 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (576 bp):
TATTCGATCCAAATGGATAGGTCCATTCATTATAACTAATTTATTCTCGAATGGTGCAGTGGAAA
TTCAAAGTGAAGAAACCCGAAAGTGCTTTAAGGTGAATGGTCAACGGGTAAAACCCTTTTACGAG
AATTTTAAAATGCACATAGTTGAGGAGATTGTTCTCGAGGAGCCCAGAACTTGAATAACAGGTCG
TCGAGCTAACGACGTTAAACAAAGCGCTGTTGAGAGACAACCCAAATTTTCTCTTTATGTAAATA
AATTTTTAGATGGTAAAAGGAAAGTGAAAATGCATGTCAAGGATCGGTTCTGTCTAAGGAAAGAC
TTGGTACTTAAGAATATCCATTGTGACTCACCTCTCTTTCCTGGGAACTTACTTGGTGCATTTAT
CGCGGCTATTTTACTAAATCCCATAATCTTGGTTTTTAATAATTTATTTCTCGAATATTTAAGCA
TAGCATTAGCAAAGCCATATATTCGAGAAATACATATTTTAATTTTAATTTTTATTTATTTGTAT
TTTTAACTTTAATTTTTATATATATTTATTTATTTATATTTATATTTTTTTATTTT
Found at i:40861717 original size:23 final size:22
Alignment explanation
Indices: 40861672--40861717 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
40861662 GAGAAATACA
* *
40861672 TATTTTAATTTTAATTTTTATT
1 TATTTTAATTTTAACTTTAATT
*
40861694 TATTTGTATTTTTAACTTTAATT
1 TATTT-TAATTTTAACTTTAATT
40861717 T
1 T
40861718 TTATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTAATTTTAACTTTAATT
Found at i:40861732 original size:29 final size:29
Alignment explanation
Indices: 40861674--40861733 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
40861664 GAAATACATA
* *
40861674 TTTTAATTTTAATTTTTATTTATTTGTAT
1 TTTTAACTTTAATTTTTATATATTTGTAT
40861703 TTTTAACTTTAATTTTTATATATATT-TAT
1 TTTTAACTTTAATTTTTATATAT-TTGTAT
40861732 TT
1 TT
40861734 ATTTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTAACTTTAATTTTTATATATTTGTAT
Found at i:40861757 original size:14 final size:14
Alignment explanation
Indices: 40861688--40861745 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
40861678 AATTTTAATT
*
40861688 TTTATTTATTTGTA
1 TTTATTTATTTATA
*
40861702 TTT-TTAACTTTA-A
1 TTTATTTA-TTTATA
*
40861715 -TT-TTTATATATA
1 TTTATTTATTTATA
40861727 TTTATTTATTTATA
1 TTTATTTATTTATA
40861741 TTTAT
1 TTTAT
40861746 ATTTTTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 6 0.17
14 20 0.57
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTATTTATTTATA
Found at i:40869510 original size:36 final size:36
Alignment explanation
Indices: 40869458--40869536 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
40869448 ATCTTTGCTG
* * * *
40869458 GAGGATTCACATGGTGCAACAAATTGGGCTTTACAA
1 GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
* *
40869494 GAGGGTTCACATGGTGCAGCGAACTAGGCTTCACAA
1 GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
40869530 GAGGGTT
1 GAGGGTT
40869537 TGCATAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (36 bp):
GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
Found at i:40870911 original size:17 final size:16
Alignment explanation
Indices: 40870887--40870982 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 16
40870877 GCTTGCAGCC
40870887 TTGGTGAGCTCACAAT
1 TTGGTGAGCTCACAAT
* * * *
40870903 ATTGATGAGATCGCAGT
1 -TTGGTGAGCTCACAAT
40870920 CTTGGTGAGCTCGTAC-AT
1 -TTGGTGAGCTC--ACAAT
40870938 TTGGTGAGCTCACAATT
1 TTGGTGAGCTCACAA-T
*
40870955 TTGGTGAGCTCTCAACT
1 TTGGTGAGCTCACAA-T
40870972 TTGGGTGAGCT
1 TT-GGTGAGCT
40870983 TACATCTTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.03
16 1 0.02
17 50 0.79
18 9 0.14
19 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (16 bp):
TTGGTGAGCTCACAAT
Found at i:40870991 original size:18 final size:18
Alignment explanation
Indices: 40870940--40870993 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
40870930 TCGTACATTT
*
40870940 GGTGAGCTCACAAT-TTT-
1 GGTGAGCTTAC-ATCTTTG
*
40870957 GGTGAGCTCT-CAACTTTG
1 GGTGAGCT-TACATCTTTG
40870975 GGTGAGCTTACATCTTTG
1 GGTGAGCTTACATCTTTG
40870993 G
1 G
40870994 TAAGCTCGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.43
18 16 0.53
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (18 bp):
GGTGAGCTTACATCTTTG
Found at i:40870993 original size:35 final size:35
Alignment explanation
Indices: 40870921--40871025 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 35
40870911 GATCGCAGTC
* *
40870921 TTGGTGAGCTCGT-ACATTT-GGTGAGCTCACAAT-T
1 TTGGTAAGCTCGTAAC-TTTGGGTGAGCTTAC-ATCT
*
40870955 TTGGTGAGCTC-TCAACTTTGGGTGAGCTTACATCT
1 TTGGTAAGCTCGT-AACTTTGGGTGAGCTTACATCT
* * *
40870990 TTGGTAAGCTCGTACCTTTGGG-GAGTTTGCATCT
1 TTGGTAAGCTCGTAACTTTGGGTGAGCTTACATCT
40871024 TT
1 TT
40871026 ACGACCTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
33 1 0.02
34 28 0.46
35 31 0.51
36 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (35 bp):
TTGGTAAGCTCGTAACTTTGGGTGAGCTTACATCT
Found at i:40874499 original size:26 final size:26
Alignment explanation
Indices: 40874470--40874551 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
40874460 TGATGAGGCT
*
40874470 TAAAATAAGTTACTTGTGTAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
* * * **
40874496 TAAAA-ATGTTAACCATG-ATA-AGGCT
1 TAAAATAAGTT-A-CTTGTATAGTGGAA
40874521 TAAAATAAGTTACTTGTATAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
40874547 TAAAA
1 TAAAA
40874552 ATGTTAACCA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (26 bp):
TAAAATAAGTTACTTGTATAGTGGAA
Found at i:40874523 original size:51 final size:51
Alignment explanation
Indices: 40874460--40874564 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
40874450 TAAAGTCAGT
* *
40874460 TGATGAGGCTTAAAATAAGTTACTTGTGTAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
40874511 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
40874562 TGA
1 TGA
40874565 ATTTGAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (51 bp):
TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
Found at i:40882333 original size:14 final size:14
Alignment explanation
Indices: 40882314--40882344 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
40882304 TGGAATGAAA
40882314 TTATTTTTTTCTCT
1 TTATTTTTTTCTCT
40882328 TTA-TTTTTTCTCT
1 TTATTTTTTTCTCT
40882341 TTAT
1 TTAT
40882345 ACAGGCTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.81
14 3 0.19
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTTTTTCTCT
Found at i:40883007 original size:16 final size:15
Alignment explanation
Indices: 40882988--40883017 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40882978 TCATATATAT
40882988 ATATATATATATTTAG
1 ATATATAT-TATTTAG
40883004 ATATATATTATTTA
1 ATATATATTATTTA
40883018 TACTTTAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATATATTATTTAG
Found at i:40889379 original size:17 final size:19
Alignment explanation
Indices: 40889344--40889381 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
40889334 TTAACTTTTC
40889344 TTATTTTTATCAGATTATT
1 TTATTTTTATCAGATTATT
40889363 TTATTTTT-TCA-ATTATT
1 TTATTTTTATCAGATTATT
40889380 TT
1 TT
40889382 TTTCAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTTTTATCAGATTATT
Found at i:40889383 original size:19 final size:21
Alignment explanation
Indices: 40889339--40889383 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
40889329 ATTAATTAAC
40889339 TTTTCTTATTTTTATCAGATTA
1 TTTT-TTATTTTTATCAGATTA
40889361 --TTTTATTTTT-TCA-ATTA
1 TTTTTTATTTTTATCAGATTA
40889378 TTTTTT
1 TTTTTT
40889384 TCAACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
17 4 0.19
18 3 0.14
19 12 0.57
20 2 0.10
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTATTTTTATCAGATTA
Found at i:40897885 original size:18 final size:18
Alignment explanation
Indices: 40897862--40897896 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40897852 ACAACCACGT
*
40897862 CTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTCTTTTTC
40897880 CTTTTTTTTGTCTTTTT
1 CTTTTTTTTGTCTTTTT
40897897 GCATGCATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
CTTTTTTTTGTCTTTTTC
Found at i:40898890 original size:17 final size:17
Alignment explanation
Indices: 40898868--40898919 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
40898858 ATGGAAACAT
* *
40898868 AATCTTCAAGGATATGC
1 AATCTTAAAAGATATGC
*
40898885 AATCTTAGATATGATATGC
1 AATCTTA-A-AAGATATGC
40898904 AATCTTAAAAGATATG
1 AATCTTAAAAGATATG
40898920 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (17 bp):
AATCTTAAAAGATATGC
Found at i:40911355 original size:44 final size:44
Alignment explanation
Indices: 40911292--40911491 Score: 198
Period size: 44 Copynumber: 4.6 Consensus size: 44
40911282 AACCGTTACA
40911292 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* *
40911336 CGGTGGAATTAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* * * *** * *
40911380 CGATGGAATCAGTACTTAGCAACCACCTTATAATC-AATGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
* * *
40911422 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAATT--AAGGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACC--TCAC-GTTCAAAGGATCC
*
40911464 CGGTGGAATCAACACTTAGCAACCACCT
1 CGGTGGAATCAGCACTTAGCAACCACCT
40911492 TTATTGTTAG
Statistics
Matches: 132, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.02
41 18 0.14
42 14 0.11
43 25 0.19
44 73 0.55
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (44 bp):
CGGTGGAATCAGCACTTAGCAACCACCTCACGTTCAAAGGATCC
Found at i:40916399 original size:41 final size:40
Alignment explanation
Indices: 40916354--40916430 Score: 127
Period size: 41 Copynumber: 1.9 Consensus size: 40
40916344 CACATTTATA
*
40916354 ATCAATAATTCAGGGAATCTGCACTTAGTAACCCTTTTTTG
1 ATCAATAATTCAGGGAATCTGC-CTTAGCAACCCTTTTTTG
*
40916395 ATCAATGATTCAGGGAATCTGCCTTAGCAACCCTTT
1 ATCAATAATTCAGGGAATCTGCCTTAGCAACCCTTT
40916431 ACATTCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 13 0.38
41 21 0.62
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (40 bp):
ATCAATAATTCAGGGAATCTGCCTTAGCAACCCTTTTTTG
Found at i:40934537 original size:30 final size:30
Alignment explanation
Indices: 40934498--40934572 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
40934488 TTAGGCACAG
*
40934498 AGGACACATGCCCATCTGGCTCATACAGCC
1 AGGAGACATGCCCATCTGGCTCATACAGCC
* * *
40934528 AGGAGACATGCCCGTGTGGCTCATACGGCC
1 AGGAGACATGCCCATCTGGCTCATACAGCC
*
40934558 AGGAGACACGCCCAT
1 AGGAGACATGCCCAT
40934573 GTCTTAGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.33, G:0.27, T:0.15
Consensus pattern (30 bp):
AGGAGACATGCCCATCTGGCTCATACAGCC
Found at i:40940801 original size:25 final size:25
Alignment explanation
Indices: 40940772--40940836 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
40940762 GTCCTATTTG
* *
40940772 TTATTTTTGCTATTAATTAATTTTA
1 TTATTTTTGATATTAATTAATCTTA
*
40940797 TTATTATTT-ATTATT-ATTACTCTTA
1 TTATT-TTTGA-TATTAATTAATCTTA
*
40940822 TTATTATTGATATTA
1 TTATTTTTGATATTA
40940837 TTATTATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
24 6 0.19
25 19 0.59
26 7 0.22
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (25 bp):
TTATTTTTGATATTAATTAATCTTA
Found at i:40940802 original size:3 final size:3
Alignment explanation
Indices: 40940794--40940843 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
40940784 TTAATTAATT
* *
40940794 TTA TTA TTA TTTA TTA TTA TTA CTC TTA TTA TTA TTGA -TA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
40940840 TTA T
1 TTA T
40940844 GTTTGGTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 35 0.88
4 4 0.10
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:40940824 original size:15 final size:13
Alignment explanation
Indices: 40940794--40940843 Score: 64
Period size: 15 Copynumber: 3.5 Consensus size: 13
40940784 TTAATTAATT
40940794 TTATTATTATTTA
1 TTATTATTATTTA
40940807 TTATTATTACTCTTA
1 TTATTATTA-T-TTA
40940822 TTATTATTGATATTA
1 TTATTATT-AT-TTA
40940837 TTATTAT
1 TTATTAT
40940844 GTTTGGTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 22 0.67
16 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:40941013 original size:21 final size:22
Alignment explanation
Indices: 40940987--40941035 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
40940977 TTATTATTAG
40940987 TATTA-TAAATTTGTTATGTAT
1 TATTATTAAATTTGTTATGTAT
*
40941008 TATTATCTTAGATTTGTTATGTAT
1 TATTA--TTAAATTTGTTATGTAT
40941032 TATT
1 TATT
40941036 GTTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 5 0.21
24 19 0.79
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (22 bp):
TATTATTAAATTTGTTATGTAT
Found at i:40941075 original size:49 final size:51
Alignment explanation
Indices: 40940978--40941077 Score: 123
Period size: 49 Copynumber: 2.0 Consensus size: 51
40940968 TATAATGTAT
* * * *
40940978 TATTATTAGTATTATAAATTTGTTATGTATTATTATCTTAGATTTGTTATG
1 TATTATTAGTATTATAAATTTATTACGTATTATTATCTTAAATATGTTATG
* * *
40941029 TATTATT-GTTTTA-AAATTTATTACGTATTCTTATTTTAAATATGTTATG
1 TATTATTAGTATTATAAATTTATTACGTATTATTATCTTAAATATGTTATG
40941078 CATCATTACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 30 0.71
50 5 0.12
51 7 0.17
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (51 bp):
TATTATTAGTATTATAAATTTATTACGTATTATTATCTTAAATATGTTATG
Found at i:40941658 original size:19 final size:19
Alignment explanation
Indices: 40941634--40941744 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
40941624 AATCTTCAGG
40941634 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40941653 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* ** *
40941672 AATATATAATCTTAAATAT
1 GATATGCAATCTTAGATAT
40941691 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
40941710 GATATATAATCTTAGACAT
1 GATATGCAATCTTAGATAT
40941729 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40941745 AGATATGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 79 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40941684 original size:38 final size:38
Alignment explanation
Indices: 40941641--40941744 Score: 181
Period size: 38 Copynumber: 2.7 Consensus size: 38
40941631 AGGGATATGC
40941641 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
* *
40941679 AATCTTAAATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
40941717 AATCTTAGACATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
40941745 AGATATGATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:40942062 original size:24 final size:25
Alignment explanation
Indices: 40942035--40942087 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
40942025 CCTTTTAATG
* *
40942035 TTTTTGTAA-TTAAGCTTTT-TTTA
1 TTTTTTTAATTTAACCTTTTATTTA
*
40942058 TTTTTTTAATTTACCCTTTTATTTA
1 TTTTTTTAATTTAACCTTTTATTTA
40942083 TTTTT
1 TTTTT
40942088 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
24 8 0.32
25 9 0.36
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTTTTAATTTAACCTTTTATTTA
Found at i:40948180 original size:132 final size:132
Alignment explanation
Indices: 40948005--40948660 Score: 1053
Period size: 132 Copynumber: 5.0 Consensus size: 132
40947995 ACAGCGAAGC
* *
40948005 AGATCGAAGTTTGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
*
40948070 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCCAAGCAGTAGTGGA
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGGA
40948135 GA
131 GA
*
40948137 AGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* * *
40948202 AATTCCCTGGACAATAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCCAAGCAGTAGTGGA
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGGA
40948267 GA
131 GA
* *
40948269 AGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* * *
40948334 ACTTTCCTGGACAAC-GATGGAATAGATTGAAGATTTCAAGTTTTATCTCCCTAAGCAGTAGTGG
66 ACTTCCCTGGACAACAG-TGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGG
*
40948398 AGT
130 AGA
* * *
40948401 AGATCGAAGATGGCAGATTTTACCTCACTGTGGTTACAGTGGAGTACATTAAAGCCAGTAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* * * * *
40948466 ACTTCCATGGACAACAGTGGATTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAATGGTGGA
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGGA
*
40948531 GC
131 GA
* *
40948533 AGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCT
1 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* * *
40948598 ACTTCCATGGACAACAGTGGATTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTG
40948661 NNNNNNNNNN
Statistics
Matches: 488, Mismatches: 34, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 486 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (132 bp):
AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGGA
GA
Found at i:40949339 original size:19 final size:19
Alignment explanation
Indices: 40949298--40949342 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40949288 NNNNNNNNNN
*
40949298 AATCTTAGATATGATATAT
1 AATCTTAGATATGATATAC
*
40949317 AATCTTAGATATGATATGC
1 AATCTTAGATATGATATAC
40949336 AATCTTA
1 AATCTTA
40949343 AAAGATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (19 bp):
AATCTTAGATATGATATAC
Found at i:40949669 original size:24 final size:26
Alignment explanation
Indices: 40949642--40949695 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
40949632 CCTTTTAATG
*
40949642 TTTTTGTAA-TTAAGCTTTT-TTTAT
1 TTTTTGTAATTTAACCTTTTATTTAT
* *
40949666 TTTTTTTAATTTACCCTTTTATTTAT
1 TTTTTGTAATTTAACCTTTTATTTAT
40949692 TTTT
1 TTTT
40949696 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.32
25 8 0.32
26 9 0.36
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTGTAATTTAACCTTTTATTTAT
Found at i:40950411 original size:26 final size:26
Alignment explanation
Indices: 40950356--40950411 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
40950346 TTCTCAAGGA
*
40950356 AATTGAGCCCTAACGTATTGGGTTCG
1 AATTGAGCCCTAACGTATTGGGTCCG
*
40950382 AATTGTGCCCTAACGTATTGGG-CCG
1 AATTGAGCCCTAACGTATTGGGTCCG
40950407 CAATT
1 -AATT
40950412 TCTTAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (26 bp):
AATTGAGCCCTAACGTATTGGGTCCG
Found at i:40951748 original size:14 final size:14
Alignment explanation
Indices: 40951729--40951756 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40951719 CAAGGAGATC
40951729 CGATCACACCTCAA
1 CGATCACACCTCAA
40951743 CGATCACACCTCAA
1 CGATCACACCTCAA
40951757 AGAAATGTCG
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:0.36, C:0.43, G:0.07, T:0.14
Consensus pattern (14 bp):
CGATCACACCTCAA
Found at i:40957577 original size:46 final size:46
Alignment explanation
Indices: 40957508--40957633 Score: 173
Period size: 46 Copynumber: 2.7 Consensus size: 46
40957498 AAGGAGAAGG
* * * *
40957508 GACCAAGGTGAAAACCTGGAAAGGGTGCTTTAAG-TCCTAAAAAAGA
1 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAGCT-CTAAAAAAAA
*
40957554 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTGAGCTCTAAAAAAAA
1 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAGCTCTAAAAAAAA
* *
40957600 GACCAAGGTGAAAACCCGCAAAGGGCACCTTAAG
1 GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAG
40957634 ACCAAAAAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 70 0.99
47 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (46 bp):
GACCAAGGTGAAAACCTGCAAAGGGCGCCTTAAGCTCTAAAAAAAA
Found at i:40958933 original size:45 final size:45
Alignment explanation
Indices: 40958869--40959080 Score: 203
Period size: 45 Copynumber: 4.7 Consensus size: 45
40958859 CATTATGGCG
* *
40958869 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGATCATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
* * * * * *
40958914 AATCTTATCTCCCTTAAGTTGTAGTAGAGCAAATTGAAGC-TA-CT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-CATAGCA
* * * * * * * * *
40958958 AATCCTATCTGCCTAAAGTTGTAGTGGAGCGGATTAAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
** *
40959003 AGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
* *
40959048 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
40959081 TTAAAGCTAT
Statistics
Matches: 133, Mismatches: 31, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
44 34 0.26
45 98 0.74
46 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAACATAGCA
Found at i:40959041 original size:89 final size:90
Alignment explanation
Indices: 40958917--40959086 Score: 207
Period size: 89 Copynumber: 1.9 Consensus size: 90
40958907 CATAGCAAAT
* * * * * * *
40958917 CTTATCTCCCTTAAGTTGTAGTAGAGCAAATTGAAGCTA-CTAATCCTATCTGCCTAAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAAACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCA
* *
40958981 GTGGAGCGGATTAAAGATAGCGAGC
66 GTGGAACAGATTAAAGATAGCGAGC
* * * * *
40959006 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAAACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCA
40959071 GTGGAACAGATTAAAG
66 GTGGAACAGATTAAAG
40959087 CTATAAATTA
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
89 33 0.50
90 33 0.50
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (90 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAAACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCA
GTGGAACAGATTAAAGATAGCGAGC
Found at i:40959421 original size:143 final size:142
Alignment explanation
Indices: 40959164--40959471 Score: 442
Period size: 143 Copynumber: 2.2 Consensus size: 142
40959154 AAAGTTGTAG
* *
40959164 GCCTTATCTCCCTAAAGTTGCAGCGGGGCAGACTGAAGACAGCGAAACTTATTCCCTAGCGTTGC
1 GCCTTATCTCCCTAAAGTTGCAGCGGAGCAAACTGAAGACAGCGAAACTTATTCCCTAGCGTTGC
* *
40959229 AGTGGAACAGGTTAAAGCTACAAATTATCGCAGAACTTATCTTCCTGAAGTTGCAGTGGAGCAGA
66 AGTGGAACAGATTAAAGCTACAAATTATCGCAGAACTTATCTTCCTGAAGTTGCAGTGAAGCAGA
*
40959294 TTGAAGCCACCA
131 TTAAAGCCACCA
* *
40959306 GCCTTATCTCCCTAATGTTGCAGCGGAGCAAACTGAAGACAGCGAATCTTATTTCCCTAGCGTTG
1 GCCTTATCTCCCTAAAGTTGCAGCGGAGCAAACTGAAGACAGCGAAACTTA-TTCCCTAGCGTTG
* *
40959371 CAGTGGAATAGATTATAGCTACAAATTAT-G-ACGAATCTTATCTTCCTGAAGTTGCAGTGAAGC
65 CAGTGGAACAGATTAAAGCTACAAATTATCGCA-GAA-CTTATCTTCCTGAAGTTGCAGTGAAGC
*
40959434 AGATTAAAGCCAACAA
128 AGATTAAAGCC-ACCA
* * *
40959450 TCC-TATTTCCCTGAAGTTGCAG
1 GCCTTATCTCCCTAAAGTTGCAG
40959472 TCGAGCGGAT
Statistics
Matches: 148, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
141 1 0.01
142 51 0.34
143 91 0.61
144 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (142 bp):
GCCTTATCTCCCTAAAGTTGCAGCGGAGCAAACTGAAGACAGCGAAACTTATTCCCTAGCGTTGC
AGTGGAACAGATTAAAGCTACAAATTATCGCAGAACTTATCTTCCTGAAGTTGCAGTGAAGCAGA
TTAAAGCCACCA
Found at i:40960929 original size:10 final size:10
Alignment explanation
Indices: 40960914--40961064 Score: 90
Period size: 10 Copynumber: 14.0 Consensus size: 10
40960904 TATTAATTAA
40960914 TTTTATTATT
1 TTTTATTATT
40960924 TTTTATTATT
1 TTTTATTATT
40960934 TTTTATTATT
1 TTTTATTATT
40960944 TATTTATTATT
1 T-TTTATTATT
*
40960955 ACTCTTATTATT
1 --TTTTATTATT
* *
40960967 ATTGA-TA-T
1 TTTTATTATT
*
40960975 TATTATTATGT
1 TTTTATTAT-T
* **
40960986 GTCAATTTAGTCT
1 TTTTA-TTA-T-T
* *
40960999 GTTTGTTATT
1 TTTTATTATT
40961009 TTTGCTATTAATT
1 TTT--TATT-ATT
40961022 AATTTTATTATT
1 --TTTTATTATT
40961034 TTTTATTATT
1 TTTTATTATT
40961044 TTTTATTATT
1 TTTTATTATT
40961054 TATTTATTATT
1 T-TTTATTATT
40961065 ACTCTTATTA
Statistics
Matches: 110, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
8 3 0.03
9 4 0.04
10 47 0.43
11 21 0.19
12 20 0.18
13 12 0.11
15 3 0.03
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTATTATT
Found at i:40960932 original size:3 final size:3
Alignment explanation
Indices: 40960916--40960983 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
40960906 TTAATTAATT
* *
40960916 TTA TTA TT- TT- TTA TTA TT- TT- TTA TTA TTTA TTTA TTA TTA CTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA
40960959 TTA TTA TTA TTGA -TA TTA TTA TTA T
1 TTA TTA TTA TT-A TTA TTA TTA TTA T
40960984 GTGTCAATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 9 0.16
3 39 0.70
4 8 0.14
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40960963 original size:33 final size:33
Alignment explanation
Indices: 40960926--40961077 Score: 103
Period size: 33 Copynumber: 4.3 Consensus size: 33
40960916 TTATTATTTT
40960926 TTATTATTTTTTATTATTTATTTATTATTACTC
1 TTATTATTTTTTATTATTTATTTATTATTACTC
* * *
40960959 TTATTATTATTGATATTA-TTATTATGTGTCAATTTAGTCTGT
1 TTATTATT-TT-TTATTATTTATT-TAT-T--A-TTA--CT-C
* * *
40961001 TTGTTATTTTTGCTATTAATTAATTTTATTATT--TT
1 TTATTATTTTT--TATTATTTA--TTTATTATTACTC
40961036 TTATTATTTTTTATTATTTATTTATTATTACTC
1 TTATTATTTTTTATTATTTATTTATTATTACTC
40961069 TTATTATTT
1 TTATTATTT
40961078 ATGATATTAT
Statistics
Matches: 93, Mismatches: 9, Indels: 34
0.68 0.07 0.25
Matches are distributed among these distances:
31 9 0.10
33 26 0.28
34 7 0.08
35 18 0.19
36 2 0.02
38 1 0.01
39 3 0.03
40 2 0.02
41 5 0.05
42 12 0.13
43 4 0.04
44 2 0.02
45 2 0.02
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (33 bp):
TTATTATTTTTTATTATTTATTTATTATTACTC
Found at i:40961008 original size:110 final size:111
Alignment explanation
Indices: 40960876--40961089 Score: 405
Period size: 110 Copynumber: 1.9 Consensus size: 111
40960866 TGTTTTAGTT
40960876 TCAATTTAGTCCTGTTTGTTATTTTTGCTATTAATTAATTTTATTATTTTTTATTATTTTTTATT
1 TCAATTTAGTCCTGTTTGTTATTTTTGCTATTAATTAATTTTATTATTTTTTATTATTTTTTATT
40960941 ATTTATTTATTATTACTCTTATTA-TTATTGATATTATTATTATGTG
66 ATTTATTTATTATTACTCTTATTATTTA-TGATATTATTATTATGTG
40960987 TCAATTTAGT-CTGTTTGTTATTTTTGCTATTAATTAATTTTATTATTTTTTATTATTTTTTATT
1 TCAATTTAGTCCTGTTTGTTATTTTTGCTATTAATTAATTTTATTATTTTTTATTATTTTTTATT
40961051 ATTTATTTATTATTACTCTTATTATTTATGATATTATTA
66 ATTTATTTATTATTACTCTTATTATTTATGATATTATTA
40961090 CATTTGGTTA
Statistics
Matches: 102, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
110 89 0.87
111 13 0.13
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.64
Consensus pattern (111 bp):
TCAATTTAGTCCTGTTTGTTATTTTTGCTATTAATTAATTTTATTATTTTTTATTATTTTTTATT
ATTTATTTATTATTACTCTTATTATTTATGATATTATTATTATGTG
Found at i:40963142 original size:10 final size:10
Alignment explanation
Indices: 40963127--40963167 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
40963117 TATTAATTAA
40963127 TTTTATTATT
1 TTTTATTATT
40963137 TTTTATTATT
1 TTTTATTATT
40963147 TTTTATTATT
1 TTTTATTATT
40963157 TATTTATTATT
1 T-TTTATTATT
40963168 ACTCTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTATTATT
Found at i:40963145 original size:3 final size:3
Alignment explanation
Indices: 40963129--40963196 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
40963119 TTAATTAATT
* *
40963129 TTA TTA TT- TT- TTA TTA TT- TT- TTA TTA TTTA TTTA TTA TTA CTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA
40963172 TTA TTA TTA TTGA -TA TTA TTA TTA T
1 TTA TTA TTA TT-A TTA TTA TTA TTA T
40963197 GTTTGGTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 9 0.16
3 39 0.70
4 8 0.14
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40963159 original size:24 final size:25
Alignment explanation
Indices: 40963132--40963196 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
40963122 ATTAATTTTA
* *
40963132 TTATTTTTTATTAT-TTTTTATTAT
1 TTATTTATTATTATCTTATTATTAT
40963156 TTATTTATTATTACTCTTATTATTAT
1 TTATTTATTATTA-TCTTATTATTAT
*
40963182 TGATATTATTATTAT
1 TTAT-TTATTATTAT
40963197 GTTTGGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.34
25 1 0.03
26 13 0.37
27 9 0.26
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (25 bp):
TTATTTATTATTATCTTATTATTAT
Found at i:40964391 original size:21 final size:20
Alignment explanation
Indices: 40964344--40964391 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
40964334 CTCAACTCTA
*
40964344 TTTTTAATTTCTCTAATTTT
1 TTTTTAATTTCTCTAATTTG
40964364 TTATTTAATATTCT-TAATTCTG
1 TT-TTTAAT-TTCTCTAATT-TG
40964386 TTTTTA
1 TTTTTA
40964392 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTCTCTAATTTG
Found at i:40964779 original size:24 final size:24
Alignment explanation
Indices: 40964680--40964780 Score: 96
Period size: 24 Copynumber: 4.2 Consensus size: 24
40964670 AATTATAATG
* *
40964680 TATTA-GTATTAGTATTATAAATT
1 TATTACGTATTATTATTTTAAATT
* * * *
40964703 TGTTATGTATTATTATCTTAGATT
1 TATTACGTATTATTATTTTAAATT
* *
40964727 TATTATGTATTATTGTTTTAAAATT
1 TATTACGTATTATTATTTT-AAATT
* *
40964752 TATTACGTATTTTTATTTTAAATA
1 TATTACGTATTATTATTTTAAATT
40964776 TATTA
1 TATTA
40964781 TGCATCATTA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
23 4 0.06
24 39 0.62
25 20 0.32
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (24 bp):
TATTACGTATTATTATTTTAAATT
Found at i:40968655 original size:45 final size:46
Alignment explanation
Indices: 40968606--40968703 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
40968596 AGATAGAAAC
*
40968606 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
40968651 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
40968697 GAAAATA
1 CAAAATA
40968704 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:40972301 original size:45 final size:46
Alignment explanation
Indices: 40972252--40972349 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
40972242 AGATAGAAAC
*
40972252 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
40972297 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
40972343 GAAAATA
1 CAAAATA
40972350 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:40974275 original size:24 final size:25
Alignment explanation
Indices: 40974223--40974286 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 25
40974213 AAAAAGCTTT
*
40974223 TATTTTTATAATTTTT--T-AAAAA
1 TATTTTTATACTTTTTAATAAAAAA
40974245 TATTTTTATACTTTTTAATAAAAAA
1 TATTTTTATACTTTTTAATAAAAAA
*
40974270 TA-TTTTATATTTTTTAA
1 TATTTTTATACTTTTTAA
40974287 CTTTCTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.41
24 15 0.41
25 7 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTTTTATACTTTTTAATAAAAAA
Found at i:40974317 original size:6 final size:7
Alignment explanation
Indices: 40974298--40974323 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40974288 TTTCTATATA
40974298 AATTTTT
1 AATTTTT
40974305 AATTTTT
1 AATTTTT
40974312 AATTTTT
1 AATTTTT
40974319 AATTT
1 AATTT
40974324 ATGCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:40984463 original size:12 final size:12
Alignment explanation
Indices: 40984448--40984479 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
40984438 ACTCATCGTT
40984448 TTTTATTTTTTA
1 TTTTATTTTTTA
40984460 TTTTA-TTTTTA
1 TTTTATTTTTTA
40984471 TTTT-TTTTT
1 TTTTATTTTT
40984480 ACGAATCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:40985386 original size:22 final size:22
Alignment explanation
Indices: 40985342--40985400 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
40985332 ATGAATGTTG
*
40985342 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
40985366 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
40985388 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
40985401 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:40990675 original size:30 final size:29
Alignment explanation
Indices: 40990639--40990729 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 29
40990629 GTTCAGATTC
*
40990639 AAAAAAGAAAAATCAAAATCAAAATAAAA
1 AAAAAAGAAAAATCAAAGTCAAAATAAAA
**
40990668 AACAAAAGAAAAAATCAAAGTCAAAA-GCAA
1 AA-AAAAG-AAAAATCAAAGTCAAAATAAAA
*
40990698 AAAAGAGAAATCAATCAAAGTCAAAATAAAA
1 AAAAAAGAAA--AATCAAAGTCAAAATAAAA
40990729 A
1 A
40990730 TATGAAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 3 0.06
29 6 0.12
30 23 0.45
31 19 0.37
ACGTcount: A:0.73, C:0.10, G:0.08, T:0.10
Consensus pattern (29 bp):
AAAAAAGAAAAATCAAAGTCAAAATAAAA
Found at i:40990681 original size:19 final size:20
Alignment explanation
Indices: 40990638--40990701 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 20
40990628 AGTTCAGATT
* * *
40990638 CAAAAAAGAAAAATCAAAAT
1 CAAAAAATAAAAAACAAAAG
40990658 C--AAAATAAAAAACAAAAG
1 CAAAAAATAAAAAACAAAAG
* **
40990676 -AAAAAATCAAAGTCAAAAG
1 CAAAAAATAAAAAACAAAAG
40990695 CAAAAAA
1 CAAAAAA
40990702 GAGAAATCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 14 0.40
19 14 0.40
20 7 0.20
ACGTcount: A:0.75, C:0.11, G:0.06, T:0.08
Consensus pattern (20 bp):
CAAAAAATAAAAAACAAAAG
Found at i:40993093 original size:87 final size:87
Alignment explanation
Indices: 40992914--40993140 Score: 262
Period size: 87 Copynumber: 2.6 Consensus size: 87
40992904 AGATCAGTGA
* * * * *
40992914 AGATCGAA-A-ACAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGATTAAAAATAGCGGATCTT
1 AGATCGAAGATAC-AAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTC
* *
40992977 GCCTCCCTAAGCAATAGTGGAGC
65 GCCTCCCTAAGCAACAGTGAAGC
* *
40993000 AGATCGAAGATACCAGCCTTGCCTCCCTC-GTTGCAGTGGAGTAGGTTGAAGATAGCAGATCTCG
1 AGATCGAAGATACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTCG
* ** * *
40993064 CCTTCCTGCGTCGACGGTGAAGC
66 CCTCCCTAAG-CAACAGTGAAGC
* * *
40993087 AGATCGAAGGTACAAGTCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGAT
1 AGATCGAAGATACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGAT
40993141 TAGAAATTAC
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
86 44 0.37
87 50 0.42
88 24 0.20
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.23
Consensus pattern (87 bp):
AGATCGAAGATACAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTCG
CCTCCCTAAGCAACAGTGAAGC
Found at i:40993307 original size:131 final size:131
Alignment explanation
Indices: 40993143--40993989 Score: 794
Period size: 131 Copynumber: 6.4 Consensus size: 131
40993133 TTGAAGATTA
*
40993143 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAACAGATCGAAGATGGCGAATCTTATCTTC
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTC
40993208 CCCAGGAATAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGTT
66 CCCAGGAATAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGTT
40993273 G
131 G
* ** *
40993274 GAAACTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGTGAATCTTATCTTC
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTC
* * * * * *
40993339 CCTAGGAGTATGGAAGCAGATTTAAGCCGCAAGTCCTATCTCCCTG-GTCAGCAGTGGAATAGGT
66 CCCAGGAATAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAG-CAGCAGTGGAATAGGT
40993403 TG
130 TG
* * * * * * *
40993405 G-GATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATAGC-AGATCTCACCTT
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGA-ATCTTATCTT
* * * ** * *
40993468 CCTGC-GTCG-A-CGGCGAAGCAGATCGAAGGCACAAG-CCT-TGCCTTCCTCGATTGTAGTGGA
65 CC-CCAG--GAATAGG-GAAACAGATTTAAGCCACAAGTCCTAT---TTCC-C---TG-A--GCA
* *
40993528 GCAGGTTG-A-AGATTG
116 GCA-GTGGAATAGGTTG
* * *
40993543 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCATATTGAAGACGGCGAATCTTATCTTC
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTC
* *
40993608 CCTAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGTT
66 CCCAGGAATAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGTT
40993673 G
131 G
** * **
40993674 GAAACCACAGGTCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTC
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTC
* ** *
40993739 CCCAGGAGTAGGGAAGTAGATTTAAGCCACAAGTCCTATCTCCCTG-GTCAGCAGTGGAATAGGT
66 CCCAGGAATAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAG-CAGCAGTGGAATAGGT
40993803 TG
130 TG
** * * * * * *
40993805 GAAACCACAGGTCTTATCTCCCTAAGCAGTAGTGGAGTAGATAGAAGATGGC-AGATTTTA-CCT
1 GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGA-ATCTTATCTT
** * * * * * * *
40993868 CCCTGTGGTTATAGTGGAGTAC--ATTGAAGCCAGTAA-TTCTATATCCCTGGGCAGCAGTGGAA
65 CCC-CAGG-AATAG-GGA-AACAGATTTAAGCCA-CAAGTCCTATTTCCCTGAGCAGCAGTGGAA
*
40993930 TAGATT-
125 TAGGTTG
*
40993936 GAAGATTACAGATCTTATCTCCCTAAG-AAGTAGTGGAGCAGATCGAGGATGGCG
1 GAA-ATTACAGATCTTATCTCCCTAAGCAA-TAGTGGAGCAGATCGAAGATGGCG
40993990 GATTTTACCT
Statistics
Matches: 588, Mismatches: 90, Indels: 74
0.78 0.12 0.10
Matches are distributed among these distances:
129 5 0.01
130 72 0.12
131 318 0.54
132 84 0.14
133 9 0.02
136 3 0.01
137 5 0.01
138 23 0.04
139 63 0.11
140 6 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (131 bp):
GAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTC
CCCAGGAATAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGTT
G
Found at i:40993693 original size:400 final size:401
Alignment explanation
Indices: 40993047--40993860 Score: 1360
Period size: 400 Copynumber: 2.0 Consensus size: 401
40993037 GGAGTAGGTT
* * * *
40993047 GAAGATAGCAGATCTCGCCTTCCTGCGTCGACGGTGAAGCAGATCGAAGGTACAAGTCTTGCCTC
1 GAAGATAGCAGATCTCACCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
*
40993112 CCTCGGTTGTAGTGGAGCAGGTTGAAGATTAGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
66 CCTCGATTGTAGTGGAGCAGGTTGAAGATTAGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
*
40993177 GAACAGATCGAAGATGGCGAATCTTATCTTCCCCAGGAATAGGGAAACAGATTTAAGCCACAAGT
131 GAACAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAATAGGGAAACAGATTTAAGCCACAAGT
*
40993242 CCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACTACAGATCTTATCTCCCTAAGCAATAGT
196 CCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACCACAGATCTTATCTCCCTAAGCAATAGT
* * * *
40993307 GGAGCAGATCGAAGACAGTGAATCTTATCTTCCCTAGGAGTATGGAAGCAGATTTAAGCCGCAAG
261 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
* *** *
40993372 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGG-GATTTCAGATCTTATCTCCCTAAGTAGTAG
326 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAACCACAGATCTTATCTCCCTAAGCAGTAG
*
40993436 TGGAGCAGATC
391 TGGAGCAGATA
*
40993447 GAAGATAGCAGATCTCACCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTT
1 GAAGATAGCAGATCTCACCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
*
40993512 CCTCGATTGTAGTGGAGCAGGTTGAAGATTGGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
66 CCTCGATTGTAGTGGAGCAGGTTGAAGATTAGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
* * * * *
40993577 GAGCATATTGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAACAGATTTAAGCCACAAGT
131 GAACAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAATAGGGAAACAGATTTAAGCCACAAGT
*
40993642 CCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACCACAGGTCTTATCTCCCTAAGCAATAGT
196 CCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACCACAGATCTTATCTCCCTAAGCAATAGT
*
40993707 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGTAGATTTAAGCCACAAG
261 GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
*
40993772 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAACCACAGGTCTTATCTCCCTAAGCAGTAG
326 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAACCACAGATCTTATCTCCCTAAGCAGTAG
*
40993837 TGGAGTAGATA
391 TGGAGCAGATA
*
40993848 GAAGATGGCAGAT
1 GAAGATAGCAGAT
40993861 TTTACCTCCC
Statistics
Matches: 384, Mismatches: 29, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
400 339 0.88
401 45 0.12
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (401 bp):
GAAGATAGCAGATCTCACCTTCCTGCGTCGACGGCGAAGCAGATCGAAGGCACAAGCCTTGCCTC
CCTCGATTGTAGTGGAGCAGGTTGAAGATTAGAAATTACAGATCTTATCTCCCTAAGCAATAGTG
GAACAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAATAGGGAAACAGATTTAAGCCACAAGT
CCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACCACAGATCTTATCTCCCTAAGCAATAGT
GGAGCAGATCGAAGACAGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAAG
TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAACCACAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATA
Found at i:40993708 original size:44 final size:44
Alignment explanation
Indices: 40993634--40993840 Score: 131
Period size: 44 Copynumber: 4.7 Consensus size: 44
40993624 CAGATTTAAG
* * * * *
40993634 CCACAAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAA
1 CCACAGGTCTTATCTCCCTAAGCAGTAGTGGAATAGGTTGGAAA
* ** * *
40993678 CCACAGGTCTTATCTCCCTAAGCAATAGTGGAGCA-GATCGAAGA
1 CCACAGGTCTTATCTCCCTAAGCAGTAGTGGAATAGGTTGGAA-A
* * * * * *
40993722 -CAGC-GAATCTTATCTTCCC-CAGGAGTAG-GGAAGTAGATT-TAAG
1 CCA-CAG-GTCTTATC-TCCCTAAGCAGTAGTGGAA-TAGGTTGGAAA
* * * *
40993765 CCACAAGTCCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGGAAA
1 CCACAGGTCTTATCTCCCTAAG-CAGTAGTGGAATAGGTTGGAAA
40993809 CCACAGGTCTTATCTCCCTAAGCAGTAGTGGA
1 CCACAGGTCTTATCTCCCTAAGCAGTAGTGGA
40993841 GTAGATAGAA
Statistics
Matches: 117, Mismatches: 33, Indels: 26
0.66 0.19 0.15
Matches are distributed among these distances:
42 5 0.04
43 27 0.23
44 79 0.68
45 6 0.05
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (44 bp):
CCACAGGTCTTATCTCCCTAAGCAGTAGTGGAATAGGTTGGAAA
Found at i:40993999 original size:132 final size:132
Alignment explanation
Indices: 40993631--40994048 Score: 431
Period size: 132 Copynumber: 3.2 Consensus size: 132
40993621 AAACAGATTT
* * * *
40993631 AAGCCAC-AAGTCCTATTTCCCTGAGCAGCAGTGGAATAGGTTGGAAACCACAGGTCTTATCTCC
1 AAGCCACTAA-TCCTATCTCCCTGGGCAGCAGTGGAATAGATTGGAAACCACAGATCTTATCTCC
* ** * * * *
40993695 CTAAGCAA-TAGTGGAGCAGATCGAAGACAGC-GAATCTTATCTTCCC-CAGG--AGTAG-GGAA
65 CTAAG-AAGTAGTGGAGCAGATAGAAGATGGCAG-ATTTTA-CCTCCCTGAGGTTA-CAGTGG-A
* *
40993754 GTAGATTT
125 GTACATTG
* * *
40993762 AAGCCAC-AAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAACCACAGGTCTTATCTCC
1 AAGCCACTAA-TCCTATCTCCCTGGGCAGCAGTGGAATAGATTGGAAACCACAGATCTTATCTCC
* * * *
40993826 CTAAGCAGTAGTGGAGTAGATAGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACA
65 CTAAGAAGTAGTGGAGCAGATAGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACA
40993891 TTG
130 TTG
* * * **
40993894 AAGCCAGTAATTCTATATCCCTGGGCAGCAGTGGAATAGATT-GAAGATTACAGATCTTATCTCC
1 AAGCCACTAATCCTATCTCCCTGGGCAGCAGTGGAATAGATTGGAA-ACCACAGATCTTATCTCC
* * * * *
40993958 CTAAGAAGTAGTGGAGCAGATCGAGGATGGCGGATTTTACCTTCCTGAGGTTACAGTGGAGTATA
65 CTAAGAAGTAGTGGAGCAGATAGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACA
40994023 TTG
130 TTG
40994026 AAGCCACTAATCCTATCTCCCTG
1 AAGCCACTAATCCTATCTCCCTG
40994049 AAATTACAGT
Statistics
Matches: 245, Mismatches: 34, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
130 6 0.02
131 95 0.39
132 139 0.57
133 5 0.02
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (132 bp):
AAGCCACTAATCCTATCTCCCTGGGCAGCAGTGGAATAGATTGGAAACCACAGATCTTATCTCCC
TAAGAAGTAGTGGAGCAGATAGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACAT
TG
Found at i:40994305 original size:50 final size:50
Alignment explanation
Indices: 40994237--40994398 Score: 164
Period size: 50 Copynumber: 3.2 Consensus size: 50
40994227 GGTACAGTGG
* * * * *
40994237 AACAGATTAACGTCACAACGGTGAATCTTGCTTCCCAGACATTGCAGTTA
1 AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGACATTGCAGTTA
* * ** ** **
40994287 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCTTA-AGCGGTGCAGTGG
1 AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGA-CATTGCAGTTA
* * *
40994337 AACAGATTAAAGCCATAACAGCGAATCTTACTTCCCCGACATTTCAGTTA
1 AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGACATTGCAGTTA
40994387 AACAGATTAAAG
1 AACAGATTAAAG
40994399 TTACGAGTTA
Statistics
Matches: 86, Mismatches: 24, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
49 1 0.01
50 84 0.98
51 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (50 bp):
AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGACATTGCAGTTA
Found at i:40998703 original size:43 final size:43
Alignment explanation
Indices: 40998647--40998882 Score: 211
Period size: 43 Copynumber: 5.4 Consensus size: 43
40998637 ATGCACTTCA
* * *
40998647 TGTGCCAGTATATTTACTTTGGTTCGTCCGATGATGCACTGTG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * * * * *
40998690 TGTGCCAACATATTTGTTTTGGTTCGTTCGATAATGCATTGTG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* *
40998733 TGTGCCAATATATTTGCTTCGGTTCATCCGGTGATTTGCACTGTG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGA--TGCACTGTG
* * * ** * ** * *
40998778 TCTGTCAGTATATTTGCTTCAATTCATGTGATAATGCACTATG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
* * * * *
40998821 TGTGCCAGTATATTTGCTTCAGTTCGTCCAATGATGCGCTATG
1 TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
*
40998864 TGTGCCAATATATTCGCTT
1 TGTGCCAATATATTTGCTT
40998883 TGATTTATCC
Statistics
Matches: 155, Mismatches: 36, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
43 122 0.79
45 33 0.21
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (43 bp):
TGTGCCAATATATTTGCTTCGGTTCGTCCGATGATGCACTGTG
Found at i:41033660 original size:27 final size:27
Alignment explanation
Indices: 41033602--41033660 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
41033592 TTTCCATTTT
* *
41033602 CTTTTCCTTCTCTTTTTTCTCCTTTAG
1 CTTTTACTTCTCTTTTTTCTCCATTAG
41033629 C-TTTACTT-TCTTTTTTCCTCCATTAG
1 CTTTTACTTCTCTTTTTT-CTCCATTAG
41033655 CTTTTA
1 CTTTTA
41033661 AGACCTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.29
26 15 0.54
27 5 0.18
ACGTcount: A:0.08, C:0.27, G:0.03, T:0.61
Consensus pattern (27 bp):
CTTTTACTTCTCTTTTTTCTCCATTAG
Found at i:41041894 original size:94 final size:94
Alignment explanation
Indices: 41041633--41041899 Score: 338
Period size: 94 Copynumber: 2.8 Consensus size: 94
41041623 GTGTCACAGT
** * * ** * *
41041633 TTCATCTTGCTCCATTACAACTTCAATGAGATAAGGTTTGTTGTTGTAGTTTCATTCCAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
* * *
41041698 TACAACTTAAGAGGTATAGGATTTGTAGC
66 TACAACTTCAGGGGCATAGGATTTGTAGC
* * * *
41041727 TTCATCTTGCTCCATTGTAACTT-TAGGAAGATAAGATTTTCTATGGTAGCTTCACTCCAACCCA
1 TTCATCTTGCTCCATTGTAACTTCAAGG-AGATAAGATTTACTATTGTAGCTTCATTCCAACCCA
* *
41041791 CTGCCACTTCAGGGGCATAGGATTTGTAGC
65 CTACAACTTCAGGGGCATAGGATTTGTAGC
* * *
41041821 TTCATTTTGCTCCATTGTAACTTCAAGGAGATAAGATTCACTATTGTAGCTTCATTCAAACCCAC
1 TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
41041886 TACAACTTCAGGGG
66 TACAACTTCAGGGG
41041900 GACTGGAGTT
Statistics
Matches: 146, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
93 2 0.01
94 141 0.97
95 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (94 bp):
TTCATCTTGCTCCATTGTAACTTCAAGGAGATAAGATTTACTATTGTAGCTTCATTCCAACCCAC
TACAACTTCAGGGGCATAGGATTTGTAGC
Found at i:41042841 original size:213 final size:213
Alignment explanation
Indices: 41042474--41043101 Score: 1229
Period size: 213 Copynumber: 2.9 Consensus size: 213
41042464 CTGTTTTAGG
*
41042474 TCCTTGTACTATTTAGAAATCTTTCAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
1 TCCTTGTACTATTTAGAAATCTTTTAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
41042539 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAACTAAAATGAAAAAATCTTAACGAAAA
66 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAACTAAAATGAAAAAATCTTAACGAAAA
41042604 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTTCCCCA
131 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTTCCCCA
41042669 GATATCGATATGTAATAA
196 GATATCGATATGTAATAA
41042687 TCCTTGTACTATTTAGAAATCTTTTAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
1 TCCTTGTACTATTTAGAAATCTTTTAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
41042752 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAACTAAAATGAAAAAATCTTAACGAAAA
66 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAACTAAAATGAAAAAATCTTAACGAAAA
41042817 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTTCCCCA
131 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTTCCCCA
41042882 GATATCGATATGTAATAA
196 GATATCGATATGTAATAA
41042900 TCCTTGTACTATTTAGAAATCTTTTAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
1 TCCTTGTACTATTTAGAAATCTTTTAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
*
41042965 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAAATAAAATGAAAAAATCTTAACGAAAA
66 AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAACTAAAATGAAAAAATCTTAACGAAAA
*
41043030 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTGCCCCA
131 AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTTCCCCA
41043095 GATATCG
196 GATATCG
41043102 TATTGTGAGC
Statistics
Matches: 412, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 412 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (213 bp):
TCCTTGTACTATTTAGAAATCTTTTAGAGCGATATGTAATAATCCTTTTACTTTATAACATTGCT
AGTCTATTGATTGTTATTTCAATGCAAAAAATACTTAAACTAAAATGAAAAAATCTTAACGAAAA
AGATTAACTAAAATGACAAATATTACTAGAACACGAAGTGAGTGAAAATGAAATTAGGTTCCCCA
GATATCGATATGTAATAA
Found at i:41054839 original size:20 final size:20
Alignment explanation
Indices: 41054810--41054861 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
41054800 AATTTTCTCC
41054810 TCTTCCAACTTCTCTATCCT
1 TCTTCCAACTTCTCTATCCT
* *
41054830 TCTTCTAACTTCTCTATCTT
1 TCTTCCAACTTCTCTATCCT
*
41054850 TTTTCCAA-TTCT
1 TCTTCCAACTTCT
41054862 GAACTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (20 bp):
TCTTCCAACTTCTCTATCCT
Found at i:41057706 original size:13 final size:13
Alignment explanation
Indices: 41057690--41057716 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41057680 ATTAGTACTT
41057690 ATAATAATTAATG
1 ATAATAATTAATG
41057703 ATAATAATTAATG
1 ATAATAATTAATG
41057716 A
1 A
41057717 CCAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATAATAATTAATG
Found at i:41058795 original size:7 final size:7
Alignment explanation
Indices: 41058785--41058813 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41058775 ATATTTTTTG
41058785 TTTTGTT
1 TTTTGTT
41058792 TTTTGTT
1 TTTTGTT
41058799 TTTTGTT
1 TTTTGTT
41058806 TTTTGTT
1 TTTTGTT
41058813 T
1 T
41058814 ATCTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTGTT
Found at i:41060542 original size:9 final size:9
Alignment explanation
Indices: 41060513--41060549 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41060503 TGAGTTTTCG
41060513 AATTCGAAT
1 AATTCGAAT
*
41060522 AACTCGAAT
1 AATTCGAAT
41060531 AATTCGAAT
1 AATTCGAAT
*
41060540 AATTCAAAT
1 AATTCGAAT
41060549 A
1 A
41060550 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41063470 original size:21 final size:20
Alignment explanation
Indices: 41063440--41063478 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41063430 GTACATGCAT
41063440 ACATACATTTTTATAATATTG
1 ACATACA-TTTTATAATATTG
*
41063461 ACATATATTTTATAATAT
1 ACATACATTTTATAATAT
41063479 ATATACGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
ACATACATTTTATAATATTG
Found at i:41063990 original size:107 final size:108
Alignment explanation
Indices: 41063785--41063991 Score: 326
Period size: 107 Copynumber: 1.9 Consensus size: 108
41063775 AAGAAATTTT
* * * * * * *
41063785 TTTCTAAATAAGGCAATGGTTTTGAGTTTGGAAAATCGAGAAAACGTGCCCTAATGTGCTGGGTT
1 TTTCAAAACAAGGCAATGATTTTGAGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTT
41063850 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
66 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
*
41063893 TTTCAAAACAAGGCAAT-ATTTTGCGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTT
1 TTTCAAAACAAGGCAATGATTTTGAGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTT
*
41063957 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCT
66 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCT
41063992 CTTAAATCTC
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
107 75 0.83
108 15 0.17
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (108 bp):
TTTCAAAACAAGGCAATGATTTTGAGTTTGAAAAATCAAAAAAACGTGCCCTAACGTGCTGGGTT
TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
Found at i:41069030 original size:16 final size:17
Alignment explanation
Indices: 41069009--41069046 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41068999 ACAGCAGATT
41069009 TATTTTGATTT-TTTTC
1 TATTTTGATTTCTTTTC
**
41069025 TATTTTTCTTTCTTTTC
1 TATTTTGATTTCTTTTC
41069042 TATTT
1 TATTT
41069047 CGGCTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTGATTTCTTTTC
Found at i:41071511 original size:58 final size:58
Alignment explanation
Indices: 41071395--41071532 Score: 145
Period size: 58 Copynumber: 2.4 Consensus size: 58
41071385 CCGGGTTTTT
* * ******
41071395 TTTATAAAAATATTA-TAAAAAATAAAAAAATATCAAAATAATATAACTTTTTTATTA
1 TTTATAAAAATATTACAAAAAAATAAAAAAATACCAAAATAATATAAAAAAAGTATTA
*
41071452 TTTATGAAAATATTACAAAAAAATAAAAAAATACCAAAATAATATACAAAAAAGT-TTA
1 TTTATAAAAATATTACAAAAAAATAAAAAAATACCAAAATAATATA-AAAAAAGTATTA
** *
41071510 TTTACCAAAATAATACAAAAAAA
1 TTTATAAAAATATTACAAAAAAA
41071533 AAACGGCTGA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
57 14 0.21
58 51 0.76
59 2 0.03
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (58 bp):
TTTATAAAAATATTACAAAAAAATAAAAAAATACCAAAATAATATAAAAAAAGTATTA
Found at i:41072178 original size:154 final size:157
Alignment explanation
Indices: 41071994--41072314 Score: 540
Period size: 154 Copynumber: 2.1 Consensus size: 157
41071984 TACATTTTAA
*
41071994 AAAAATATACTATTTTAGTATTTTATTATTTTACATTATTTTAGTTCATTATGTTTGAAATGTAT
1 AAAAATATACTATTTTAGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
*
41072059 TCATTTAGTGTG-TTTTTAAATAAA-TTT-AAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTT
66 TCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTACTT
41072121 TTTTCCCCGGATTTTATTACTTTCAAT
131 TTTTCCCCGGATTTTATTACTTTCAAT
* *
41072148 AAAAATATAGTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
1 AAAAATATACTATTTTAGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
* * *
41072213 TCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAACTCTTATTTCGGCTCTTTGTTTGTACTT
66 TCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTACTT
*
41072278 TTTTCTCCGGATTTTATTACTTTCAAT
131 TTTTCCCCGGATTTTATTACTTTCAAT
*
41072305 AAAAAAATAC
1 AAAAATATAC
41072315 ACTAAATGAA
Statistics
Matches: 154, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
154 74 0.48
155 12 0.08
156 3 0.02
157 65 0.42
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (157 bp):
AAAAATATACTATTTTAGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
TCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTACTT
TTTTCCCCGGATTTTATTACTTTCAAT
Found at i:41076345 original size:2 final size:2
Alignment explanation
Indices: 41076338--41076368 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
41076328 GAAAAACAAA
*
41076338 AT AT AT AT AT GT 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 A
41076369 ACAAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41078652 original size:2 final size:2
Alignment explanation
Indices: 41078647--41078682 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
41078637 TCTGTCTCTT
*
41078647 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41078683 AGTTTAATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41081701 original size:20 final size:20
Alignment explanation
Indices: 41081676--41081713 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41081666 GGACTATGCA
*
41081676 AAACAATGTTGTTTTACCCT
1 AAACAATGCTGTTTTACCCT
41081696 AAACAATGCTGTTTTACC
1 AAACAATGCTGTTTTACC
41081714 TTGATCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
AAACAATGCTGTTTTACCCT
Found at i:41082418 original size:9 final size:9
Alignment explanation
Indices: 41082406--41082446 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
41082396 AAAAAGAATT
*
41082406 TTTTTATAA
1 TTTTTAAAA
41082415 TTTTTAAACAA
1 TTTTT-AA-AA
41082426 TTTTTAAAA
1 TTTTTAAAA
41082435 TTTTTAAAA
1 TTTTTAAAA
41082444 TTT
1 TTT
41082447 CAAAAGTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 19 0.66
10 3 0.10
11 7 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:41083077 original size:21 final size:21
Alignment explanation
Indices: 41083052--41083093 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41083042 AAACCCTTAT
41083052 TTTAATTGAATTAATAATATA
1 TTTAATTGAATTAATAATATA
***
41083073 TTTAATTTTTTTAATAATATA
1 TTTAATTGAATTAATAATATA
41083094 AATGTTAAAT
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:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAATTGAATTAATAATATA
Found at i:41087814 original size:3 final size:3
Alignment explanation
Indices: 41087806--41087896 Score: 155
Period size: 3 Copynumber: 30.3 Consensus size: 3
41087796 CCAATACACT
41087806 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
41087854 GAA GAA TAA GAA GAA GAA GAA TAA GAA GAA GAA GAA AAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
41087897 TCCTTAACTG
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:41092642 original size:5 final size:5
Alignment explanation
Indices: 41092632--41092659 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41092622 TAAAGCCTCC
41092632 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
41092660 TTACTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:41095580 original size:23 final size:23
Alignment explanation
Indices: 41095534--41095583 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
41095524 GTTTTAAGTT
*
41095534 TTTATATGTATTATTATTTGAAA
1 TTTATATGTATCATTATTTGAAA
41095557 TTTACTATGTATCATTATTT-AAA
1 TTTA-TATGTATCATTATTTGAAA
41095580 TTTA
1 TTTA
41095584 ACATATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTATATGTATCATTATTTGAAA
Found at i:41099365 original size:13 final size:13
Alignment explanation
Indices: 41099349--41099373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41099339 TAATATATTT
41099349 ATTAATTATAAAC
1 ATTAATTATAAAC
41099362 ATTAATTATAAA
1 ATTAATTATAAA
41099374 TAAAAAAGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAATTATAAAC
Found at i:41100291 original size:18 final size:18
Alignment explanation
Indices: 41100268--41100303 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41100258 GTAATATGTT
*
41100268 ATATTATGTTATTTATAA
1 ATATTATGTAATTTATAA
41100286 ATATTATGTAATTTATAA
1 ATATTATGTAATTTATAA
41100304 TACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATTATGTAATTTATAA
Found at i:41105450 original size:266 final size:267
Alignment explanation
Indices: 41104965--41105498 Score: 1061
Period size: 266 Copynumber: 2.0 Consensus size: 267
41104955 GGATGCACAA
41104965 ATACATGGTTATAATAATACCATAGTAATGATATTATATAATAGTATTAATAATGTTAAAATAAT
1 ATACATGGTTATAATAATACCATAGTAATGATATTATATAATAGTATTAATAATGTTAAAATAAT
41105030 TAATTTAATAATAAAATAACTAAAATAACAAATAGAGGATTAAATTGGAAACTAAACGAAATTTT
66 TAATTTAATAATAAAATAACTAAAATAACAAATAGAGGATTAAATTGGAAACTAAACGAAATTTT
41105095 GGGATTGAAATTAAAAACAAACAACGAAAAGGATTAAATCATAACGCGTGTGAAAGGAAGAGGAC
131 GGGATTGAAATTAAAAACAAACAACGAAAAGGATTAAATCATAACGCGTGTGAAAGGAAGAGGAC
41105160 CAAAAGGAAAATATTCCCACGTTGATAAAACGACGTCGTTCTAGCGAGGCCTATGCGCATGGTCA
196 CAAAAGGAAAATATTCCCACGTTGATAAAACGACGTCGTTCTAGCGAGGCCTATGCGCATGGTCA
41105225 ATGGACC
261 ATGGACC
41105232 ATACATGGTT-TAATAATACCATAGTAATGATATTATATAATAGTATTAATAATGTTAAAATAAT
1 ATACATGGTTATAATAATACCATAGTAATGATATTATATAATAGTATTAATAATGTTAAAATAAT
41105296 TAATTTAATAATAAAATAACTAAAATAACAAATAGAGGATTAAATTGGAAACTAAACGAAATTTT
66 TAATTTAATAATAAAATAACTAAAATAACAAATAGAGGATTAAATTGGAAACTAAACGAAATTTT
41105361 GGGATTGAAATTAAAAACAAACAACGAAAAGGATTAAATCATAACGCGTGTGAAAGGAAGAGGAC
131 GGGATTGAAATTAAAAACAAACAACGAAAAGGATTAAATCATAACGCGTGTGAAAGGAAGAGGAC
41105426 CAAAAGGAAAATATTCCCACGTTGATAAAACGACGTCGTTCTAGCGAGGCCTATGCGCATGGTCA
196 CAAAAGGAAAATATTCCCACGTTGATAAAACGACGTCGTTCTAGCGAGGCCTATGCGCATGGTCA
41105491 ATGGACC
261 ATGGACC
41105498 A
1 A
41105499 GGTTGAAATA
Statistics
Matches: 267, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
266 257 0.96
267 10 0.04
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.26
Consensus pattern (267 bp):
ATACATGGTTATAATAATACCATAGTAATGATATTATATAATAGTATTAATAATGTTAAAATAAT
TAATTTAATAATAAAATAACTAAAATAACAAATAGAGGATTAAATTGGAAACTAAACGAAATTTT
GGGATTGAAATTAAAAACAAACAACGAAAAGGATTAAATCATAACGCGTGTGAAAGGAAGAGGAC
CAAAAGGAAAATATTCCCACGTTGATAAAACGACGTCGTTCTAGCGAGGCCTATGCGCATGGTCA
ATGGACC
Found at i:41106035 original size:11 final size:11
Alignment explanation
Indices: 41106019--41106043 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41106009 AAAGTAAAAT
41106019 AAATAAATGAA
1 AAATAAATGAA
41106030 AAATAAATGAA
1 AAATAAATGAA
41106041 AAA
1 AAA
41106044 CTCAAGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATAAATGAA
Found at i:41106037 original size:15 final size:15
Alignment explanation
Indices: 41105993--41106042 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
41105983 TCGAAAGAGG
41105993 AAAAGAAAAAATAAA-
1 AAAAG-AAAAATAAAT
*
41106008 AAAAGTAAAATAAAT
1 AAAAGAAAAATAAAT
*
41106023 AAATGAAAAATAAAT
1 AAAAGAAAAATAAAT
41106038 GAAAA
1 -AAAA
41106043 ACTCAAGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 8 0.28
15 18 0.62
16 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAGAAAAATAAAT
Found at i:41106902 original size:45 final size:43
Alignment explanation
Indices: 41106851--41107176 Score: 171
Period size: 45 Copynumber: 7.3 Consensus size: 43
41106841 TAATCCGTTT
* *
41106851 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTACTC
1 CACTGCAACTTCAGGGAGATAAGA-TTG-TATCTTCAGTCTACTC
* * * **
41106896 CACTGCAACTCCAAGGAGATAAGACTTGTATCATCAACCTA-TC
1 CACTGCAACTTCAGGGAGATAAGA-TTGTATCTTCAGTCTACTC
* * * *
41106939 CTACTGCAACTTCAGGGATATAAGGATTG-A-CATGA-TCTGCTC
1 C-ACTGCAACTTCAGGGAGATAA-GATTGTATCTTCAGTCTACTC
* * * * * *
41106981 TACTGCAACTTTAGAGAGATAAGATCGATAAT-TTATAGTTTTAATCTGTTC
1 CACTGCAACTTCAGGGAGATAAGATTG-T-ATCTT-CAG-TCT-A-C---TC
* * * *
41107032 CACTGCAACTTTAGGGAAATAAGAGTCGCTATCTTCAGTCTGCTC
1 CACTGCAACTTCAGGGAGATAAGA-TTG-TATCTTCAGTCTACTC
* * *
41107077 CACTGCAACTTCAGGGAGATAAGATTG-GTCGTGA-TCTACTC
1 CACTGCAACTTCAGGGAGATAAGATTGTATCTTCAGTCTACTC
* * * *
41107118 TACTGCAACTTTAGAGAGATAAGATCTACTATCTTCAGTCTACTC
1 CACTGCAACTTCAGGGAGATAAGAT-T-GTATCTTCAGTCTACTC
* *
41107163 TACTGCAACCTCAG
1 CACTGCAACTTCAG
41107177 TAAGAGAAGA
Statistics
Matches: 214, Mismatches: 46, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
40 4 0.02
41 48 0.22
42 11 0.05
43 6 0.03
44 37 0.17
45 69 0.32
46 2 0.01
48 2 0.01
50 2 0.01
51 27 0.13
52 6 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGATTGTATCTTCAGTCTACTC
Found at i:41106962 original size:44 final size:45
Alignment explanation
Indices: 41106851--41106962 Score: 120
Period size: 44 Copynumber: 2.5 Consensus size: 45
41106841 TAATCCGTTT
* * * **
41106851 CACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTACTC
1 CACTGCAACTTCAGGGAAATAAGACTTGCTATCATCAACCTACTC
* * *
41106896 CACTGCAACTCCAAGGAGATAAGACTTG-TATCATCAACCTA-TC
1 CACTGCAACTTCAGGGAAATAAGACTTGCTATCATCAACCTACTC
*
41106939 CTACTGCAACTTCAGGGATATAAG
1 C-ACTGCAACTTCAGGGAAATAAG
41106963 GATTGACATG
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.05
44 28 0.51
45 24 0.44
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (45 bp):
CACTGCAACTTCAGGGAAATAAGACTTGCTATCATCAACCTACTC
Found at i:41107101 original size:96 final size:94
Alignment explanation
Indices: 41106794--41107101 Score: 271
Period size: 96 Copynumber: 3.3 Consensus size: 94
41106784 TTGTTATGAC
* * *
41106794 CTGCTCTACTGCAACTTCAAAGAGATAAGATCGGTAATTTATAGCTTTAATCCGTTTCACTGCAA
1 CTGCTCCACTGCAACTTCAAAGAGATAAGATC-GTAATTTATAG-TTTAATCTGTTCCACTGCAA
* *
41106859 CTTCAGGGAAATAAGATTTGCTATCTTTAGT
64 CTTCAGGGAAATAAGAGTTGCTATCTTCAGT
* * * * * * *
41106890 CTACTCCACTGCAACTCCAAGGAGATAAGA-C-T--TGTATCA--TCAACCT-ATCCTACTGCAA
1 CTGCTCCACTGCAACTTCAAAGAGATAAGATCGTAATTTAT-AGTTTAATCTGTTCC-ACTGCAA
* * *
41106948 CTTCAGGGATATAAG-GATTG--A-CATGA-T
64 CTTCAGGGAAATAAGAG-TTGCTATCTTCAGT
* * *
41106975 CTGCTCTACTGCAACTTTAGAGAGATAAGATCGATAATTTATAGTTTTAATCTGTTCCACTGCAA
1 CTGCTCCACTGCAACTTCAAAGAGATAAGATCG-TAATTTATAG-TTTAATCTGTTCCACTGCAA
* *
41107040 CTTTAGGGAAATAAGAGTCGCTATCTTCAGT
64 CTTCAGGGAAATAAGAGTTGCTATCTTCAGT
**
41107071 CTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 CTGCTCCACTGCAACTTCAAAGAGATAAGAT
41107102 TGGTCGTGAT
Statistics
Matches: 163, Mismatches: 32, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
85 25 0.15
86 4 0.02
87 1 0.01
88 3 0.02
89 29 0.18
90 4 0.02
91 4 0.02
92 28 0.17
93 5 0.03
94 1 0.01
95 4 0.02
96 55 0.34
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (94 bp):
CTGCTCCACTGCAACTTCAAAGAGATAAGATCGTAATTTATAGTTTAATCTGTTCCACTGCAACT
TCAGGGAAATAAGAGTTGCTATCTTCAGT
Found at i:41120058 original size:38 final size:38
Alignment explanation
Indices: 41120007--41120082 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
41119997 TTTATAAGTT
41120007 AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
1 AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
*
41120045 AGTTTTTTTTTTCAATTTTCATCTTTCTCCTTTCTTCC
1 AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
41120083 CAAAAAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.11, C:0.25, G:0.03, T:0.62
Consensus pattern (38 bp):
AGTTTTTTTTTTCAATTTTCATCTTTCTCCCTTCTTCC
Found at i:41125488 original size:91 final size:91
Alignment explanation
Indices: 41125340--41125598 Score: 326
Period size: 91 Copynumber: 2.9 Consensus size: 91
41125330 ACACTAGATG
* * * * *
41125340 CACATAGTGTAAA-CCTGTAGGCTAAATGTT-TTCCCCGATAACATGCCATATTGCTCATAAGAG
1 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
*
41125403 CTTTCCCGTCGATATAATGCTAAATA
66 CTTTCCCGTCGATATAATGCCAAATA
* *
41125429 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGTTAGATTGCTCATTAGAG
1 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
* * * *
41125494 CTTTCTCG-CTGATATCATGCCAAGTG
66 CTTTCCCGTC-GATATAATGCCAAATA
* * * * *
41125520 TACATAGTGCAAAGCCCGTAGGCTAAATATTCTCCCCCAATAACACGGTAGATTGCTCATAAGAG
1 CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
*
41125585 CTTTCCCATCGATA
66 CTTTCCCGTCGATA
41125599 ACACACTAGA
Statistics
Matches: 146, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
89 12 0.08
90 17 0.12
91 116 0.79
92 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (91 bp):
CACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCCGATAACATGCTAGATTGCTCATAAGAG
CTTTCCCGTCGATATAATGCCAAATA
Found at i:41130945 original size:13 final size:13
Alignment explanation
Indices: 41130927--41130952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41130917 CGTGTTTCCA
41130927 AAAACCATTTGTT
1 AAAACCATTTGTT
41130940 AAAACCATTTGTT
1 AAAACCATTTGTT
41130953 TGTGTAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:41143833 original size:11 final size:11
Alignment explanation
Indices: 41143807--41143864 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
41143797 CTCTTAGTCT
41143807 TTATTTTATT-
1 TTATTTTATTA
41143817 TTATTTTATTA
1 TTATTTTATTA
41143828 TTATTTCT-TTA
1 TTATTT-TATTA
41143839 TT-TTTTATTA
1 TTATTTTATTA
41143849 GTT-TTTTATTA
1 -TTATTTTATTA
41143860 TTATT
1 TTATT
41143865 CTTAATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.02
10 18 0.42
11 23 0.53
12 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:41143833 original size:21 final size:23
Alignment explanation
Indices: 41143807--41143864 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
41143797 CTCTTAGTCT
41143807 TTATTTTATT-TTATTTTATTA-
1 TTATTTTATTATTATTTTATTAG
41143828 TTATTTCT-TTATT-TTTTATTAG
1 TTATTT-TATTATTATTTTATTAG
41143850 TT-TTTTATTATTATT
1 TTATTTTATTATTATT
41143865 CTTAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.03
21 24 0.75
22 7 0.22
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTATTTTATTATTATTTTATTAG
Found at i:41143838 original size:29 final size:29
Alignment explanation
Indices: 41143804--41143861 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
41143794 CTCCTCTTAG
41143804 TCTTTATTTTATT-TTA-TTTTATTATTATT
1 TCTTTATTTT-TTATTAGTTTT-TTATTATT
41143833 TCTTTATTTTTTATTAGTTTTTTATTATT
1 TCTTTATTTTTTATTAGTTTTTTATTATT
41143862 ATTCTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 2 0.07
29 21 0.78
30 4 0.15
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (29 bp):
TCTTTATTTTTTATTAGTTTTTTATTATT
Found at i:41143846 original size:18 final size:19
Alignment explanation
Indices: 41143815--41143864 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
41143805 CTTTATTTTA
41143815 TTTTATTTTATTATTA-TT
1 TTTTATTTTATTATTAGTT
41143833 TCTTTATTTT-TTATTAGTT
1 T-TTTATTTTATTATTAGTT
41143852 TTTTATTATTATT
1 TTTTATT-TTATT
41143865 CTTAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 13 0.46
19 13 0.46
20 2 0.07
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTTTATTATTAGTT
Found at i:41143937 original size:71 final size:72
Alignment explanation
Indices: 41143843--41143991 Score: 291
Period size: 71 Copynumber: 2.1 Consensus size: 72
41143833 TCTTTATTTT
41143843 TTATTAGTTTTTTATTATTATTCTTAATTAATTCTCATTTATTTTTATTCTAGTTCATTTCTTCT
1 TTATTAGTTTTTTATTATTATTCTTAATTAATTCTCATTTATTTTTATTCTAGTTCATTTCTTCT
41143908 CTTGTTC
66 CTTGTTC
41143915 TTATTAG-TTTTTATTATTATTCTTAATTAATTCTCATTTATTTTTATTCTAGTTCATTTCTTCT
1 TTATTAGTTTTTTATTATTATTCTTAATTAATTCTCATTTATTTTTATTCTAGTTCATTTCTTCT
41143979 CTTGTTC
66 CTTGTTC
41143986 TTATTA
1 TTATTA
41143992 TATATTGGTG
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 70 0.91
72 7 0.09
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.64
Consensus pattern (72 bp):
TTATTAGTTTTTTATTATTATTCTTAATTAATTCTCATTTATTTTTATTCTAGTTCATTTCTTCT
CTTGTTC
Found at i:41143959 original size:33 final size:33
Alignment explanation
Indices: 41143851--41143962 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 33
41143841 TTTTATTAGT
41143851 TTTTTATTATTATTCTTAATTAATTCTCATTTA
1 TTTTTATTATTATTCTTAATTAATTCTCATTTA
* ** *
41143884 TTTTTATTCTAGTTCATTTCTT-CTCTTGTTCTTA-TTA
1 TTTTTA-T-TA-TT-A-TTCTTAAT-TAATTCTCATTTA
41143921 GTTTTTATTATTATTCTTAATTAATTCTCATTTA
1 -TTTTTATTATTATTCTTAATTAATTCTCATTTA
41143955 TTTTTATT
1 TTTTTATT
41143963 CTAGTTCATT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
33 25 0.40
34 6 0.10
35 4 0.06
36 4 0.06
37 6 0.10
38 17 0.27
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.65
Consensus pattern (33 bp):
TTTTTATTATTATTCTTAATTAATTCTCATTTA
Found at i:41145882 original size:6 final size:6
Alignment explanation
Indices: 41145871--41145913 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
41145861 AGTCTATTTG
* * *
41145871 TTTTAT TTTTAT TTTTA- TTTTAT GTTTAT GTTTAT TGTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
41145914 GCTTAGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:41149286 original size:42 final size:42
Alignment explanation
Indices: 41149227--41149320 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
41149217 CTTTCTTTTC
41149227 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
1 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
41149269 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
1 CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
*
41149311 CACATGGCCA
1 CACACGGCCA
41149321 TACGACACGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.18
Consensus pattern (42 bp):
CACACGGCCAAAGGCATAGGCATGTGTCTCAGCCGTGTATGA
Found at i:41160751 original size:12 final size:12
Alignment explanation
Indices: 41160734--41160761 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41160724 CCCCACAGAA
41160734 AATAGACTCATT
1 AATAGACTCATT
41160746 AATAGACTCATT
1 AATAGACTCATT
41160758 AATA
1 AATA
41160762 ATTTAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (12 bp):
AATAGACTCATT
Found at i:41167602 original size:41 final size:41
Alignment explanation
Indices: 41167557--41167792 Score: 224
Period size: 41 Copynumber: 5.8 Consensus size: 41
41167547 GGCATTGAGT
* *
41167557 CTAGCAGGCTTTGTGTCGGTGTGTTATATCAGGCTTTATGC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
* * * * *
41167598 CTAGCAAGCTTCGTGTCAGTGTATTGTATTAAGCTTTATGC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
* * *
41167639 CTAGCAGGCATCGTGCCGGTGTATTATATCAGGCTTTGTGC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
* * * * *
41167680 CTAGCATGCTTTGTG-CTGGTGTATTATATTAGGCATTGTGC
1 CTAGCAGGCTTCGTGTC-GGTGTATTATATCAGGCTTTATGC
* * ** * *
41167721 CTAGCAAGCTTTGTACCGATGTTTTATATCAGGCTTTGA-GC
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTT-ATGC
* * *
41167762 CTAGTAGGCTTCGTGTCAGTGTATTGTATCA
1 CTAGCAGGCTTCGTGTCGGTGTATTATATCA
41167793 AGTAAATTGT
Statistics
Matches: 156, Mismatches: 36, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
40 1 0.01
41 154 0.99
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (41 bp):
CTAGCAGGCTTCGTGTCGGTGTATTATATCAGGCTTTATGC
Found at i:41167681 original size:82 final size:82
Alignment explanation
Indices: 41167557--41167790 Score: 281
Period size: 82 Copynumber: 2.9 Consensus size: 82
41167547 GGCATTGAGT
* * *
41167557 CTAGCAGGCTTTGTGTCGGTGTGTTATATCAGGCTTTATGCCTAGCAAGCTTCGTGTCAGTGTAT
1 CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTCAGTGTAT
*
41167622 TGTATTAAGCTTTATGC
66 TGTATTAAGCATTATGC
* * * * *
41167639 CTAGCAGGCATCGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCATGCTTTGTG-CTGGTGTA
1 CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTC-AGTGTA
* * *
41167703 TTATATTAGGCATTGTGC
65 TTGTATTAAGCATTATGC
* * * * * * *
41167721 CTAGCAAGCTTTGTACCGATGTTTTATATCAGGCTTTGAGCCTAGTAGGCTTCGTGTCAGTGTAT
1 CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTCAGTGTAT
41167786 TGTAT
66 TGTAT
41167791 CAAGTAAATT
Statistics
Matches: 126, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
81 1 0.01
82 124 0.98
83 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (82 bp):
CTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTTGTGCCTAGCAAGCTTCGTGTCAGTGTAT
TGTATTAAGCATTATGC
Found at i:41167776 original size:123 final size:122
Alignment explanation
Indices: 41167557--41167792 Score: 271
Period size: 123 Copynumber: 1.9 Consensus size: 122
41167547 GGCATTGAGT
* *
41167557 CTAGCAGGCTTTGTGTCGGTGTGTTATATCAGGCTTTATGCCTAGCAAGCTTCGTGTCAGTGTAT
1 CTAGCAGGCTTTGTGTCGGTGTATTATATCAGGCATTATGCCTAGCAAGCTTC-TGTCAGTGTAT
* * *
41167622 TGTATTAAGCTTTATGCCTAGCAGGCATCGTGCCGGTGTATTATATCAGGCTTTGTGC
65 TATATCAAGCTTTATGCCTAGCAGGCATCGTGCCAGTGTATTATATCAGGCTTTGTGC
* * * *
41167680 CTAGCATGCTTTGTG-CTGGTGTATTATATTAGGCATTGTGCCTAGCAAGCTT-TGTACCGATGT
1 CTAGCAGGCTTTGTGTC-GGTGTATTATATCAGGCATTATGCCTAGCAAGCTTCTGT-CAG-TGT
* * * * * *
41167743 TTTATATCAGGCTTTGA-GCCTAGTAGGCTTCGTGTCAGTGTATTGTATCA
63 ATTATATCAAGCTTT-ATGCCTAGCAGGCATCGTGCCAGTGTATTATATCA
41167793 AGTAAATTGT
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
121 3 0.03
122 3 0.03
123 87 0.93
124 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (122 bp):
CTAGCAGGCTTTGTGTCGGTGTATTATATCAGGCATTATGCCTAGCAAGCTTCTGTCAGTGTATT
ATATCAAGCTTTATGCCTAGCAGGCATCGTGCCAGTGTATTATATCAGGCTTTGTGC
Found at i:41175799 original size:13 final size:13
Alignment explanation
Indices: 41175783--41175807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41175773 CCATTGCCAG
41175783 AAATAATAATAAC
1 AAATAATAATAAC
41175796 AAATAATAATAA
1 AAATAATAATAA
41175808 ATATCTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:41176124 original size:2 final size:2
Alignment explanation
Indices: 41176117--41176148 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
41176107 TCTCCATGCA
*
41176117 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41176149 TTACTGGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:41195469 original size:19 final size:20
Alignment explanation
Indices: 41195421--41195472 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
41195411 GTATTTGATT
* *
41195421 TTGGATTCTTCTAGATAATG
1 TTGGACTCTTCTAGATAATC
* *
41195441 TAGGAGTCTTCTAG-TAATC
1 TTGGACTCTTCTAGATAATC
41195460 TTGGACTCTTCTA
1 TTGGACTCTTCTA
41195473 ATGCATTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (20 bp):
TTGGACTCTTCTAGATAATC
Found at i:41212775 original size:3 final size:3
Alignment explanation
Indices: 41212769--41212796 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41212759 TAATAATAAT
41212769 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
41212797 GGAGGAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:41213593 original size:15 final size:15
Alignment explanation
Indices: 41213573--41213603 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41213563 AAAACAACAT
41213573 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41213588 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41213603 A
1 A
41213604 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:41217929 original size:15 final size:15
Alignment explanation
Indices: 41217909--41217939 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41217899 AAAACAACAT
41217909 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41217924 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
41217939 A
1 A
41217940 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:41219008 original size:111 final size:111
Alignment explanation
Indices: 41218814--41219034 Score: 363
Period size: 111 Copynumber: 2.0 Consensus size: 111
41218804 CTTATTATTT
* * *
41218814 AAATCTTCATTTCGAGAAAACGACACGTCACATCCAATACATTAGGACACGACATATCGAATTCC
1 AAATCTTCATTTCGAGAAAACGACACGACACATCCAATACATTAGAACACGACATATCAAATTCC
*
41218879 CGAAAGTGAGTTTTTGGTTTATGCGTTTTGATTGTAGAAAATTTTA
66 CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTA
* * *
41218925 AAATCTTCATTTCTAGAAAAATGACAC-ACACATCCAATACATTAGAACACGACGTATCAAATTC
1 AAATCTTCATTTCGAG-AAAACGACACGACACATCCAATACATTAGAACACGACATATCAAATTC
41218989 CCGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTT
65 CCGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTT
41219035 TGATTATTTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 93 0.91
112 9 0.09
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (111 bp):
AAATCTTCATTTCGAGAAAACGACACGACACATCCAATACATTAGAACACGACATATCAAATTCC
CGAAAGTGAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTA
Found at i:41219603 original size:365 final size:365
Alignment explanation
Indices: 41218933--41219664 Score: 1394
Period size: 365 Copynumber: 2.0 Consensus size: 365
41218923 TAAAATCTTC
41218933 ATTTCTAGAAAAATGACACACACATCCAATACATTAGAACACGACGTATCAAATTCCCGAAAGTG
1 ATTTCTAGAAAAATGACACACACATCCAATACATTAGAACACGACGTATCAAATTCCCGAAAGTG
41218998 AGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTTGATTATTTAGATTCAACGAGGAAAATT
66 AGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTTGATTATTTAGATTCAACGAGGAAAATT
*
41219063 GGAACCCAATACGTTAGGGCTCCATTCTCTCGAAGATTCCAAATTCCGGGTATTGCGTTATTTTG
131 GGAACCCAATACGTTAGGGCTCCATTCCCTCGAAGATTCCAAATTCCGGGTATTGCGTTATTTTG
41219128 AAAGTTTTTGGATAAATTGCTTTTGATACTCAAATGAAATTAAATGTAATTCTTTAAAATAAAAA
196 AAAGTTTTTGGATAAATTGCTTTTGATACTCAAATGAAATTAAATGTAATTCTTTAAAATAAAAA
41219193 GGATTGATTAAGGATGTACAATGCAAGATGATGATTCATGAACTAAAACGTATACTAACGAACGC
261 GGATTGATTAAGGATGTACAATGCAAGATGATGATTCATGAACTAAAACGTATACTAACGAACGC
41219258 CAAACAATCAATAAATATAAATAAACAATACAATATAACA
326 CAAACAATCAATAAATATAAATAAACAATACAATATAACA
41219298 ATTTCTAG-AAAATGACACATCACATCCAATACATTAGAACACGACGTATCAAATTCCCGAAAGT
1 ATTTCTAGAAAAATGACACA-CACATCCAATACATTAGAACACGACGTATCAAATTCCCGAAAGT
41219362 GAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTTGATTATTTAGATTCAACGAGGAAAAT
65 GAGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTTGATTATTTAGATTCAACGAGGAAAAT
*
41219427 TGGAACCCAATACGTTAGGGCTCCATTCCCTCGAAGATTCCAAATTTCGGGTATTGCGTTATTTT
130 TGGAACCCAATACGTTAGGGCTCCATTCCCTCGAAGATTCCAAATTCCGGGTATTGCGTTATTTT
*
41219492 GAAAGTTTTTGGATAAATTGGTTTTGATACTCAAATGAAATTAAATGTAATTCTTTAAAATAAAA
195 GAAAGTTTTTGGATAAATTGCTTTTGATACTCAAATGAAATTAAATGTAATTCTTTAAAATAAAA
* *
41219557 AGGATTGATTAATGATGTACAATGCGAGATGATGATTCATGAACTAAAACGTATACTAACGAACG
260 AGGATTGATTAAGGATGTACAATGCAAGATGATGATTCATGAACTAAAACGTATACTAACGAACG
*
41219622 TCAAACAATCAATAAATATAAATAAACAATACAATATAACA
325 CCAAACAATCAATAAATATAAATAAACAATACAATATAACA
41219663 AT
1 AT
41219665 GGCAAGAATC
Statistics
Matches: 360, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
364 11 0.03
365 349 0.97
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (365 bp):
ATTTCTAGAAAAATGACACACACATCCAATACATTAGAACACGACGTATCAAATTCCCGAAAGTG
AGTTTTTGGTTTATGCGCTTTGATTGTAGAAAATTTTTGATTATTTAGATTCAACGAGGAAAATT
GGAACCCAATACGTTAGGGCTCCATTCCCTCGAAGATTCCAAATTCCGGGTATTGCGTTATTTTG
AAAGTTTTTGGATAAATTGCTTTTGATACTCAAATGAAATTAAATGTAATTCTTTAAAATAAAAA
GGATTGATTAAGGATGTACAATGCAAGATGATGATTCATGAACTAAAACGTATACTAACGAACGC
CAAACAATCAATAAATATAAATAAACAATACAATATAACA
Found at i:41221669 original size:44 final size:44
Alignment explanation
Indices: 41221634--41221820 Score: 241
Period size: 44 Copynumber: 4.2 Consensus size: 44
41221624 ACTACTGCTT
41221634 AGGGAGATAGGA-TCCACAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACT-CACAATCTTCAACCTATTCCACTGCTGGTC
* ** * *
41221678 AGGGAGTTAGGACTTGCGATCTTCAACCTATTCCACTACTGGTC
1 AGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGGTC
* * ** * *
41221722 AGGGAGTTAGGCCTTGCAATCTTCTACCTATTCCTCTGCTGGTC
1 AGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGGTC
*
41221766 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGGTC
*
41221810 AGGGAGCTAGG
1 AGGGAGATAGG
41221821 TTTTGTGATT
Statistics
Matches: 126, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 125 0.99
45 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (44 bp):
AGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGGTC
Found at i:41221742 original size:88 final size:88
Alignment explanation
Indices: 41221650--41221820 Score: 279
Period size: 88 Copynumber: 1.9 Consensus size: 88
41221640 ATAGGATCCA
* * *
41221650 CAATCTTCAACCTATTCCACTGCTGGTCAGGGAGTTAGGACTTGCGATCTTCAACCTATTCCACT
1 CAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
*
41221715 ACTGGTCAGGGAGTTAGGCCTTG
66 ACTGGTCAGGGAGCTAGGCCTTG
* *
41221738 CAATCTTCTACCTATTCCTCTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
1 CAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
*
41221803 GCTGGTCAGGGAGCTAGG
66 ACTGGTCAGGGAGCTAGG
41221821 TTTTGTGATT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 76 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (88 bp):
CAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACT
ACTGGTCAGGGAGCTAGGCCTTG
Done.