Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 143 of 187
Found at i:42801372 original size:6 final size:7
Alignment explanation
Indices: 42801344--42801411 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
42801334 GAGTATGAGT
42801344 TTAGGGA
1 TTAGGGA
*
42801351 TTATGGA
1 TTAGGGA
42801358 TTAGGGA
1 TTAGGGA
42801365 TT-GGGA
1 TTAGGGA
* *
42801371 TTTAAGGT
1 -TTAGGGA
42801379 TTAGGGA
1 TTAGGGA
*
42801386 TTAGAGGG
1 TTAG-GGA
*
42801394 TTAGGGGT
1 TTA-GGGA
42801402 TTAGGGA
1 TTAGGGA
42801409 TTA
1 TTA
42801412 AAAGTTAGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
6 4 0.08
7 31 0.65
8 12 0.25
9 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (7 bp):
TTAGGGA
Found at i:42801421 original size:22 final size:23
Alignment explanation
Indices: 42801376--42801429 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
42801366 TGGGATTTAA
**
42801376 GGTTTAGGGATTAGAGGGTTAGG
1 GGTTTAGGGATTAGAAAGTTAGG
42801399 GGTTTAGGGATTA-AAAGTTAGG
1 GGTTTAGGGATTAGAAAGTTAGG
*
42801421 GATTTAGGG
1 GGTTTAGGG
42801430 GTCGAGTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.26, C:0.00, G:0.43, T:0.31
Consensus pattern (23 bp):
GGTTTAGGGATTAGAAAGTTAGG
Found at i:42801615 original size:15 final size:15
Alignment explanation
Indices: 42801595--42801641 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
42801585 TATTTTAATG
*
42801595 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
42801610 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
42801624 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
42801638 TTTA
1 TTTA
42801642 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:42801662 original size:21 final size:22
Alignment explanation
Indices: 42801625--42801677 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
42801615 GGATTATGAA
*
42801625 TTAGGGA-TTATGGTTTAAGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
42801646 TT-GGGATTTAAGGTTTAGGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
42801667 TTAGGGGTTTA
1 TTAGGGATTTA
42801678 GGGGTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
TTAGGGATTTAAGGTTTAAGGG
Found at i:42801670 original size:7 final size:7
Alignment explanation
Indices: 42801660--42801698 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
42801650 GATTTAAGGT
42801660 TTAGGGG
1 TTAGGGG
42801667 TTAGGGG
1 TTAGGGG
42801674 TTTAGGGG
1 -TTAGGGG
**
42801682 TTAGATG
1 TTAGGGG
42801689 TTAGGGG
1 TTAGGGG
42801696 TTA
1 TTA
42801699 AGAGTTAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:42801677 original size:15 final size:15
Alignment explanation
Indices: 42801656--42801698 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
42801646 TTGGGATTTA
42801656 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
42801671 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
42801686 ATG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
42801699 AGAGTTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:42801685 original size:22 final size:22
Alignment explanation
Indices: 42801643--42801707 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
42801633 TATGGTTTAA
* *
42801643 GGGTT-GGGATTTAAGGTTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
*
42801664 GGGTTAGGGGTTTAGGGGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
** *
42801686 ATGTTAGGGG-TTAAGAGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
42801707 G
1 G
42801708 AATTTAAGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.20, C:0.00, G:0.46, T:0.34
Consensus pattern (22 bp):
GGGTTAGGGGTTTAAGGGTTAG
Found at i:42801694 original size:14 final size:13
Alignment explanation
Indices: 42801660--42801707 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
42801650 GATTTAAGGT
*
42801660 TTAGGGGTTAGGGG
1 TTAGGGGTTA-GAG
42801674 TTTAGGGGTTAGATG
1 -TTAGGGGTTAGA-G
42801689 TTAGGGGTTAAGAG
1 TTAGGGGTT-AGAG
42801703 TTAGG
1 TTAGG
42801708 AATTTAAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 16 0.53
15 14 0.47
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:42802424 original size:83 final size:83
Alignment explanation
Indices: 42802279--42802436 Score: 271
Period size: 83 Copynumber: 1.9 Consensus size: 83
42802269 TTTATTTTAT
* *
42802279 AAAAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAATAGTGTCATTTTGTT
1 AAAAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACAGCGTCATTTTGTT
42802344 CAAAATGAAACGCCGCAA
66 CAAAATGAAACGCCGCAA
* * *
42802362 AAAAAATTAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCGTTTTGTT
1 AAAAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACAGCGTCATTTTGTT
42802427 CAAAATGAAA
66 CAAAATGAAA
42802437 AAATTTTGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.28
Consensus pattern (83 bp):
AAAAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACAGCGTCATTTTGTT
CAAAATGAAACGCCGCAA
Found at i:42806802 original size:85 final size:85
Alignment explanation
Indices: 42806641--42806809 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 85
42806631 CATGATATGT
* * * * * *
42806641 TTTTAGCGGAGTTTTTGCGAGAAGCGTCGCTAAAGGTTTGTTCTATAGCGGCGTTTGTGGGAAAC
1 TTTTAGCGGAGTTTGTGCGAAAAGCGCCGCTAAAGGTATGGTCTATAGCGGCGTTTGTGGGAAAA
* *
42806706 AGTGCCGCTAAAGGTCATGG
66 AGCGCCACTAAAGGTCATGG
* * *
42806726 TTTTAGCGGCGTTTGTG-GAAACAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-GTAA
1 TTTTAGCGGAGTTTGTGCGAAA-AGCGCCGCTAAAGGT-ATGGTCTATAGCGGCGTTTGTGGGAA
42806789 AAAGCGCCACTAAAGGTCATG
64 AAAGCGCCACTAAAGGTCATG
42806810 ACCTTTAGCA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
84 3 0.04
85 50 0.70
86 18 0.25
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (85 bp):
TTTTAGCGGAGTTTGTGCGAAAAGCGCCGCTAAAGGTATGGTCTATAGCGGCGTTTGTGGGAAAA
AGCGCCACTAAAGGTCATGG
Found at i:42806807 original size:43 final size:43
Alignment explanation
Indices: 42806663--42806825 Score: 204
Period size: 43 Copynumber: 3.8 Consensus size: 43
42806653 TTTTGCGAGA
* * * *
42806663 AGCGTCGCTAAAGGT-TTGTTCTATAGCGGCGTTTGTGGGAAAC
1 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-GGAAAC
*
42806706 AGTGCCGCTAAAGGTCATGGT-TTTAGCGGCGTTTGTGGAAAC
1 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAC
* *
42806748 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGTAAAA
1 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAC
* ** *
42806791 AGCGCCACTAAAGGTCATGACCTTTAGCAGCGTTT
1 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
42806826 ATTTTAAAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
42 26 0.25
43 77 0.73
44 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAC
Found at i:42808809 original size:40 final size:39
Alignment explanation
Indices: 42808756--42809008 Score: 247
Period size: 40 Copynumber: 6.3 Consensus size: 39
42808746 TGCCCCTATT
**
42808756 TGCACATCAGTGCCTCTGTTTGTACTTCGGTACCCCTGAA
1 TGCACATTTGTGCC-CTGTTTGTACTTCGGTACCCCTGAA
* *
42808796 TGCACATTTGTGCCCTGTTTGCACTTCGGTGCCCCTGAA
1 TGCACATTTGTGCCCTGTTTGTACTTCGGTACCCCTGAA
*
42808835 TGCACATTTGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
1 TGCACATTTGTG-CCCTGTTTGTACTTCGGTACCCCTGAA
* * * * * * *
42808875 CGAACATTTATGCCCTCCGTTTGCACTTTGGTGCCCCTAAA
1 TGCACATTTGTGCCCT--GTTTGTACTTCGGTACCCCTGAA
* * *
42808916 TGCACATCTGTGCCCTTATTTGTACTTCGGTACCCCTAAA
1 TGCACATTTGTGCCC-TGTTTGTACTTCGGTACCCCTGAA
* ** * *
42808956 TACACATACGTGCCCCTGTTT-TCACTTCGGTGCCCCTGAT
1 TGCACATTTGTG-CCCTGTTTGT-ACTTCGGTACCCCTGAA
*
42808996 TGCACATTCGTGC
1 TGCACATTTGTGC
42809009 TCTTGATTGC
Statistics
Matches: 175, Mismatches: 32, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
39 41 0.23
40 101 0.58
41 32 0.18
42 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (39 bp):
TGCACATTTGTGCCCTGTTTGTACTTCGGTACCCCTGAA
Found at i:42808938 original size:81 final size:79
Alignment explanation
Indices: 42808745--42809002 Score: 277
Period size: 81 Copynumber: 3.2 Consensus size: 79
42808735 AAATGAAGAA
** * * * *
42808745 GTGCCCCTATTTGCACATCAGTG-CCTCTGTTTGTACTTCGGTACCCCTGAATGCACATTTGTGC
1 GTGCCCCTAAATGCACATCTGTGCCCT-TGTTTGTACTTCGGTACCCCTGAACGAACATTTATGC
42808809 CCTGTTTGCACTTCG
65 CCTGTTTGCACTTCG
* * * *
42808824 GTGCCCCTGAATGCACATTTGTGCCCCTGTTTGTACTTCAGTACCCCTGAACGAACATTTATGCC
1 GTGCCCCTAAATGCACATCTGTGCCCTTGTTTGTACTTCGGTACCCCTGAACGAACATTTATGCC
*
42808889 CTCCGTTTGCACTTTG
66 CT--GTTTGCACTTCG
* ** ***
42808905 GTGCCCCTAAATGCACATCTGTGCCCTTATTTGTACTTCGGTACCCCT-AAATACACATACGTGC
1 GTGCCCCTAAATGCACATCTGTGCCCTTGTTTGTACTTCGGTACCCCTGAACGA-ACATTTATG-
*
42808969 CCCTGTTTTCACTTCG
64 CCCTGTTTGCACTTCG
* *
42808985 GTGCCCCTGATTGCACAT
1 GTGCCCCTAAATGCACAT
42809003 TCGTGCTCTT
Statistics
Matches: 149, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
79 54 0.36
80 31 0.21
81 60 0.40
82 4 0.03
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.33
Consensus pattern (79 bp):
GTGCCCCTAAATGCACATCTGTGCCCTTGTTTGTACTTCGGTACCCCTGAACGAACATTTATGCC
CTGTTTGCACTTCG
Found at i:42809008 original size:20 final size:21
Alignment explanation
Indices: 42808745--42809020 Score: 89
Period size: 20 Copynumber: 13.8 Consensus size: 21
42808735 AAATGAAGAA
*
42808745 GTGCCCCT-ATTTGCACA-TCA
1 GTGCCCCTGA-TTGCACATTCG
* * *
42808765 GTGCCTCTGTTTGTAC-TTCG
1 GTGCCCCTGATTGCACATTCG
* * *
42808785 GTACCCCTGAATGCACATT-T
1 GTGCCCCTGATTGCACATTCG
*
42808805 GTG-CCCTGTTTGCAC-TTCG
1 GTGCCCCTGATTGCACATTCG
* *
42808824 GTGCCCCTGAATGCACATT-T
1 GTGCCCCTGATTGCACATTCG
* * *
42808844 GTGCCCCTGTTTGTAC-TTCA
1 GTGCCCCTGATTGCACATTCG
* ** * *
42808864 GTACCCCTGAACGAACATT-T
1 GTGCCCCTGATTGCACATTCG
* * * *
42808884 ATGCCCTCCGTTTGCAC-TTTG
1 GTGCCC-CTGATTGCACATTCG
* * *
42808905 GTGCCCCTAAATGCACA-TCT
1 GTGCCCCTGATTGCACATTCG
* *
42808925 GTG-CCCTTATTTGTAC-TTCG
1 GTGCCCCTGA-TTGCACATTCG
* * * * *
42808945 GTACCCCTAAATACACATAC-
1 GTGCCCCTGATTGCACATTCG
* *
42808965 GTGCCCCTGTTTTCAC-TTCG
1 GTGCCCCTGATTGCACATTCG
42808985 GTGCCCCTGATTGCACATTC-
1 GTGCCCCTGATTGCACATTCG
* *
42809005 GTGCTCTTGATTGCAC
1 GTGCCCCTGATTGCAC
42809021 TTTGGTTCCC
Statistics
Matches: 177, Mismatches: 62, Indels: 34
0.65 0.23 0.12
Matches are distributed among these distances:
18 2 0.01
19 22 0.12
20 127 0.72
21 26 0.15
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.34
Consensus pattern (21 bp):
GTGCCCCTGATTGCACATTCG
Found at i:42809033 original size:20 final size:20
Alignment explanation
Indices: 42808978--42809033 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
42808968 CCCCTGTTTT
* *
42808978 CACTTCGGTGCCCCTGATTG
1 CACTTTGGTGCCCTTGATTG
* * *
42808998 CACATTCGTGCTCTTGATTG
1 CACTTTGGTGCCCTTGATTG
*
42809018 CACTTTGGTTCCCTTG
1 CACTTTGGTGCCCTTG
42809034 TTATGCATCT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (20 bp):
CACTTTGGTGCCCTTGATTG
Found at i:42811424 original size:16 final size:18
Alignment explanation
Indices: 42811403--42811438 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42811393 CCTATAAGAA
42811403 TGAATG-CCAAC-AAATT
1 TGAATGACCAACAAAATT
42811419 TGAATGACCAACAAAATT
1 TGAATGACCAACAAAATT
42811437 TG
1 TG
42811439 CCAGGGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (18 bp):
TGAATGACCAACAAAATT
Found at i:42813712 original size:13 final size:13
Alignment explanation
Indices: 42813694--42813718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42813684 TTTTCGTACT
42813694 ATAGTTTTTTATC
1 ATAGTTTTTTATC
42813707 ATAGTTTTTTAT
1 ATAGTTTTTTAT
42813719 TTAATTCAAC
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:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
ATAGTTTTTTATC
Found at i:42814168 original size:21 final size:21
Alignment explanation
Indices: 42814142--42814189 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
42814132 ACACTCTAGG
42814142 ATTTTCTGCAACAA-CTTTTCT
1 ATTTTCT-CAACAAGCTTTTCT
**
42814163 ATTTTC-CATTAAGCTTTTCT
1 ATTTTCTCAACAAGCTTTTCT
42814183 ATTTTCT
1 ATTTTCT
42814190 TTGACAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTTTCTCAACAAGCTTTTCT
Found at i:42817123 original size:16 final size:16
Alignment explanation
Indices: 42817102--42817132 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42817092 CCCAGATTTT
42817102 GATACCCATATCTTTC
1 GATACCCATATCTTTC
42817118 GATACCCATATCTTT
1 GATACCCATATCTTT
42817133 GACTTTCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (16 bp):
GATACCCATATCTTTC
Found at i:42821738 original size:17 final size:17
Alignment explanation
Indices: 42821716--42821748 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42821706 TCCCAGATTT
42821716 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
42821733 TGATACCCATATCTTT
1 TGATACCCATATCTTT
42821749 GGCTTCCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:42822412 original size:22 final size:22
Alignment explanation
Indices: 42822387--42822428 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42822377 GGTATTTGGG
*
42822387 TGAGTGAGGCATTATTAAGTTC
1 TGAGCGAGGCATTATTAAGTTC
*
42822409 TGAGCGATGCATTATTAAGT
1 TGAGCGAGGCATTATTAAGT
42822429 GTTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (22 bp):
TGAGCGAGGCATTATTAAGTTC
Found at i:42826536 original size:2 final size:2
Alignment explanation
Indices: 42826529--42826578 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
42826519 GAATGAATGA
* * * *
42826529 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AA AT TT AT GAT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
42826572 AT AT AT A
1 AT AT AT A
42826579 CGTTAGGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:42827190 original size:24 final size:23
Alignment explanation
Indices: 42827150--42827195 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
42827140 ATGTATGATA
* *
42827150 GATTATTGAATTTGTGATTATTT
1 GATTATTAAATTTGTGAATATTT
42827173 GATTGATTAAATTTGTGAATATT
1 GATT-ATTAAATTTGTGAATATT
42827196 GAGATACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (23 bp):
GATTATTAAATTTGTGAATATTT
Found at i:42828268 original size:21 final size:19
Alignment explanation
Indices: 42828238--42828277 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
42828228 TGATGAATTT
*
42828238 GTGATGATTTTTTAAGTTTG
1 GTGATGA-TTTATAAGTTTG
42828258 GTGATAGATTTATAAGTTTG
1 GTGAT-GATTTATAAGTTTG
42828278 ATAGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (19 bp):
GTGATGATTTATAAGTTTG
Found at i:42829010 original size:29 final size:29
Alignment explanation
Indices: 42828920--42829013 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 29
42828910 ACACTAGTTG
* * * *
42828920 TCGGTGATTACAGTATCAGGTACTTTATA
1 TCGGTGATTATAGTTTCAGGTACTATGTA
* * *
42828949 ACGGTG-TTATAGTTTCAGGCACTCA-GTG
1 TCGGTGATTATAGTTTCAGGTACT-ATGTA
* *
42828977 CCGGTGATTATAGTTTTAGGTACTATGTA
1 TCGGTGATTATAGTTTCAGGTACTATGTA
42829006 TCGGTGAT
1 TCGGTGAT
42829014 GGATATCATA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
28 21 0.42
29 29 0.58
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (29 bp):
TCGGTGATTATAGTTTCAGGTACTATGTA
Found at i:42834874 original size:20 final size:19
Alignment explanation
Indices: 42834741--42834875 Score: 85
Period size: 20 Copynumber: 6.7 Consensus size: 19
42834731 TACGGAATTC
42834741 CCTCATAATTCTTTTTGTATAT
1 CCTCATAA-T-TTTTTGTAT-T
* *
42834763 GCCTCATGATTTTTTTGTACT
1 -CCTCAT-AATTTTTTGTATT
**
42834784 CTCTCATGGTTTTTTGGTATT
1 C-CTCATAATTTTTT-GTATT
* *
42834805 CCCTCAGAATTTTTGGTATGT
1 -CCTCATAATTTTTTGTAT-T
*
42834826 CTTCATAATTTTTT-TA-T
1 CCTCATAATTTTTTGTATT
* *
42834843 ACTCATATTTTTTTGTATT
1 CCTCATAATTTTTTGTATT
42834862 CCATCATAATTTTT
1 CC-TCATAATTTTT
42834876 GGCACTCTTT
Statistics
Matches: 87, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
17 12 0.14
18 2 0.02
19 4 0.05
20 32 0.37
21 20 0.23
22 9 0.10
23 7 0.08
24 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (19 bp):
CCTCATAATTTTTTGTATT
Found at i:42834875 original size:21 final size:20
Alignment explanation
Indices: 42834741--42834875 Score: 91
Period size: 21 Copynumber: 6.7 Consensus size: 20
42834731 TACGGAATTC
42834741 CCTCATAATTCTTTTTGTATAT
1 CCTCATAATT-TTTTTGTAT-T
* *
42834763 GCCTCATGATTTTTTTGTACT
1 -CCTCATAATTTTTTTGTATT
** *
42834784 CTCTCATGGTTTTTTGGTATT
1 C-CTCATAATTTTTTTGTATT
* *
42834805 CCCTCAGAA-TTTTTGGTATGT
1 -CCTCATAATTTTTTTGTAT-T
*
42834826 CTTCATAA-TTTTTT-TA-T
1 CCTCATAATTTTTTTGTATT
*
42834843 ACTCAT-ATTTTTTTGTATT
1 CCTCATAATTTTTTTGTATT
42834862 CCATCATAATTTTT
1 CC-TCATAATTTTT
42834876 GGCACTCTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
16 1 0.01
17 11 0.12
18 2 0.02
19 4 0.04
20 26 0.29
21 28 0.31
22 9 0.10
23 9 0.10
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (20 bp):
CCTCATAATTTTTTTGTATT
Found at i:42835300 original size:37 final size:40
Alignment explanation
Indices: 42835259--42835332 Score: 109
Period size: 37 Copynumber: 1.9 Consensus size: 40
42835249 GTAAATTCTT
* *
42835259 ATAATTTTTTGTACTC-CC-CAT-TTTTTGGTATTCTATA
1 ATAATTTTTTATACACACCTCATATTTTTGGTATTCTATA
42835296 ATAATTTTTTATACACACCTCATATTTTTGGTATTCT
1 ATAATTTTTTATACACACCTCATATTTTTGGTATTCT
42835333 CTCATGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 14 0.44
38 2 0.06
39 3 0.09
40 13 0.41
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (40 bp):
ATAATTTTTTATACACACCTCATATTTTTGGTATTCTATA
Found at i:42835343 original size:20 final size:20
Alignment explanation
Indices: 42835313--42835404 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 20
42835303 TTTATACACA
42835313 CCTCATA-TTTTTGGTATTC
1 CCTCATAGTTTTTGGTATTC
* * *
42835332 TCTCATGGTTTTTTGGTATCC
1 CCTCATAG-TTTTTGGTATTC
* * * *
42835353 CCTCAGAATTTTTAGTATGC
1 CCTCATAGTTTTTGGTATTC
*
42835373 CCTCATAGTTTTTTGTATTC
1 CCTCATAGTTTTTGGTATTC
*
42835393 TCTCATAGTTTT
1 CCTCATAGTTTT
42835405 ATACAAACCT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
19 5 0.09
20 37 0.65
21 15 0.26
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.51
Consensus pattern (20 bp):
CCTCATAGTTTTTGGTATTC
Found at i:42837359 original size:101 final size:102
Alignment explanation
Indices: 42837242--42837426 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
42837232 AAAGTGATGG
*
42837242 TCACGTGTGTACTACTATGTGCAGGCTACTACATGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTACTACTATGTGCAGGCTACTACATGTACCGG-ATGATAATGGTCACATGTGTAGT
*
42837305 ATTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* ** * *
42837343 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTACTACTATGTGCAGGCTACTACATGTACCGGATGATAATGGTCACATGTGTAGTA
*
42837408 CTATGTGTAGGCTACTATG
66 CTATGTGCAGGCTACTATG
42837427 TGAACTGAAC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 32 0.43
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTACTACTATGTGCAGGCTACTACATGTACCGGATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:42837372 original size:51 final size:51
Alignment explanation
Indices: 42837238--42837428 Score: 217
Period size: 51 Copynumber: 3.8 Consensus size: 51
42837228 AGTGAAAGTG
* * ** *
42837238 ATGGTCACGTGTGTACTACTATGTGCAGGCTACTACATGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* * *
42837287 ATAGGTCGCATGTGTAGTATTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* * * * *
42837338 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
*
42837390 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTATGTG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
42837429 AACTGAACAT
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 37 0.31
51 77 0.65
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
Found at i:42837486 original size:45 final size:45
Alignment explanation
Indices: 42837435--42837523 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
42837425 TGTGAACTGA
* *
42837435 ACATCATTGATTAGTAAGGTGGTTGCGATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCGATGTGCTGAATCCACCGG
*
42837480 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCGATGTGCTGAATCCACCG
42837524 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCGATGTGCTGAATCCACCGG
Found at i:42837644 original size:38 final size:37
Alignment explanation
Indices: 42837599--42837671 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
42837589 AGGTGTTGAA
*
42837599 TTGAATTGAA-TATCGACTTAGAAA-TGGAAAAGTGAATT
1 TTGAATTGAATTAT-GA-TT-GAAAGTGAAAAAGTGAATT
42837637 TTGAATTGAATTATGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTATGATTGAAAGTGAAAAAGTGAA
42837672 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 12 0.38
39 3 0.09
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATTATGATTGAAAGTGAAAAAGTGAATT
Found at i:42840175 original size:50 final size:50
Alignment explanation
Indices: 42840060--42840353 Score: 390
Period size: 50 Copynumber: 5.7 Consensus size: 50
42840050 GATCATAACA
* ** * *
42840060 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
42840111 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
42840161 TGCCAACGTCATGTCCCAGGCATGGCCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
42840211 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
42840261 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
42840316 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
42840354 TCTTTTTACC
Statistics
Matches: 214, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 138 0.64
51 34 0.16
53 4 0.02
55 2 0.01
56 36 0.17
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:42844783 original size:30 final size:31
Alignment explanation
Indices: 42844747--42844805 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
42844737 TTCGAGCTTG
42844747 GGGACAAAAATGTAATTATG-CAAAAGTTTA
1 GGGACAAAAATGTAATTATGACAAAAGTTTA
* *
42844777 GGGACAAAATTGTAATTTTGACAAAAGTT
1 GGGACAAAAATGTAATTATGACAAAAGTT
42844806 GAGTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (31 bp):
GGGACAAAAATGTAATTATGACAAAAGTTTA
Found at i:42845360 original size:51 final size:50
Alignment explanation
Indices: 42845278--42845563 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
42845268 GATGAACACG
* **
42845278 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * * * * * * *
42845329 TGTGTAGTACTAAGTGAAAGCTACAATGTGTACCGAGAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACA
* * *
42845380 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * *
42845431 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCTTTGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATGGTCACA
* * *
42845482 TGTGTAGTACTATGTGAAGGCTACTACGTGAACC-ATAAA-ACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACA
42845532 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
42845564 TCGAATGATA
Statistics
Matches: 193, Mismatches: 35, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
50 42 0.22
51 149 0.77
52 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGGTCACA
Found at i:42845454 original size:102 final size:102
Alignment explanation
Indices: 42845274--42845555 Score: 424
Period size: 102 Copynumber: 2.8 Consensus size: 102
42845264 AATCGATGAA
* *
42845274 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
42845339 TAAGTGAAAGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
*
42845376 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
*
42845441 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* * * * * *
42845478 CACATGTGTAGTACTATGTGAAGGCTACTACGTGAA-CCATAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
*
42845541 CTATGTGAAGGCTAC
65 CTAAGTGAAGGCTAC
42845556 TACGTGTATC
Statistics
Matches: 165, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
101 35 0.21
102 130 0.79
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:42845584 original size:101 final size:102
Alignment explanation
Indices: 42845278--42845600 Score: 319
Period size: 102 Copynumber: 3.2 Consensus size: 102
42845268 GATGAACACG
* ** *
42845278 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATA-ATGGTCACATGTGTAGTACTAA
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAA-ACATGATCACATGTGTAGTACTAA
* * * * * *** * *
42845342 GTGAAAGCTACAATGTGTACCGAGAAGCTTTGGTCACG
65 GTGAAGGCTACTACGTGTACCGAAAAGATAAAGTAACA
* ** *
42845380 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAAACATGATCACATGTGTAGTACTAAG
* * *** *
42845445 TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACA
66 TGAAGGCTACTACGTGTACCGAAAAGATAAAGTAACA
* * * *
42845482 TGTGTAGTACTATGTGAAGGCTACTACGTGAA-CCATAAAACTTGATCACGTGTGTAGTACTATG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAAACATGATCACATGTGTAGTACTAAG
* *
42845546 TGAAGGCTACTACGTGTATCG-AATGATAAAAGTAACA
66 TGAAGGCTACTACGTGTACCGAAAAGAT-AAAGTAACA
* *
42845583 TGGGTAGTATTGTGTGAA
1 TGTGTAGTACTGTGTGAA
42845601 AAACCCCAAA
Statistics
Matches: 193, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
100 4 0.02
101 64 0.33
102 125 0.65
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (102 bp):
TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCCATAAAACATGATCACATGTGTAGTACTAAG
TGAAGGCTACTACGTGTACCGAAAAGATAAAGTAACA
Found at i:42849207 original size:113 final size:114
Alignment explanation
Indices: 42848976--42849301 Score: 550
Period size: 113 Copynumber: 2.9 Consensus size: 114
42848966 AAAAAAAGCA
42848976 TTAGCGGCGTTTTT-GAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCT
1 TTAGCGGCGTTTTTGGA-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCT
42849039 TTCGGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
* * * *
42849089 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCTAACGACGCCATTTTCTAAACTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTT
*
42849154 TCAGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATG-CCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
*
42849202 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTT
* *
42849267 TCGGGGATTTAGCGGCGTTTTTTGAAAAGCGCCGC
66 TCGGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGC
42849302 AAAAAATATT
Statistics
Matches: 198, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 124 0.63
114 74 0.37
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
Found at i:42849569 original size:15 final size:15
Alignment explanation
Indices: 42849551--42849581 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42849541 CATATTCTAA
42849551 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
42849566 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
42849581 G
1 G
42849582 ATTAGGGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:42849841 original size:15 final size:15
Alignment explanation
Indices: 42849821--42849867 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
42849811 TATTTTAAGG
*
42849821 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
42849836 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
42849850 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
42849864 TTTA
1 TTTA
42849868 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:42849888 original size:21 final size:20
Alignment explanation
Indices: 42849854--42849894 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
42849844 TTATGAATTA
*
42849854 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
42849874 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
42849895 AGGGGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:42851896 original size:21 final size:21
Alignment explanation
Indices: 42851843--42851896 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
42851833 TAAAGATTAT
42851843 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
42851864 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
42851885 TAATTTAAAATT
1 TAATTTAAAATT
42851897 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:42851911 original size:8 final size:8
Alignment explanation
Indices: 42851886--42851929 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
42851876 TGAATATAAT
42851886 AATT-TAA
1 AATTGTAA
42851893 AATTGTAAA
1 AATTGT-AA
42851902 AATTGTAA
1 AATTGTAA
42851910 AATTGTAAAA
1 AATTGT--AA
42851920 AATTGTAA
1 AATTGTAA
42851928 AA
1 AA
42851930 ATTATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 4 0.12
8 13 0.39
9 8 0.24
10 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (8 bp):
AATTGTAA
Found at i:42851923 original size:10 final size:9
Alignment explanation
Indices: 42851891--42851939 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
42851881 ATAATAATTT
42851891 AAAATTGTA
1 AAAATTGTA
42851900 AAAATTGT-
1 AAAATTGTA
42851908 AAAATTGTAA
1 AAAATTGT-A
42851918 AAAATTGTA
1 AAAATTGTA
*
42851927 AAAATTATA
1 AAAATTGTA
42851936 AAAA
1 AAAA
42851940 ATAAAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 8 0.22
9 21 0.57
10 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (9 bp):
AAAATTGTA
Found at i:42851940 original size:10 final size:10
Alignment explanation
Indices: 42851908--42851967 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 10
42851898 TAAAAATTGT
*
42851908 AAAATTGTAA
1 AAAATTATAA
*
42851918 AAAATTGT-A
1 AAAATTATAA
42851927 AAAATTATAA
1 AAAATTATAA
* *
42851937 AAAATAAAAA
1 AAAATTATAA
42851947 TAAAATTA-AA
1 -AAAATTATAA
42851957 AAAATTA-AA
1 AAAATTATAA
42851966 AA
1 AA
42851968 GAAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
9 19 0.43
10 19 0.43
11 6 0.14
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
AAAATTATAA
Found at i:42851951 original size:21 final size:21
Alignment explanation
Indices: 42851927--42851967 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42851917 AAAAATTGTA
42851927 AAAATTATAAAAAA-TAAAAAT
1 AAAATTA-AAAAAATTAAAAAT
42851948 AAAATTAAAAAAATTAAAAA
1 AAAATTAAAAAAATTAAAAA
42851968 GAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAATTAAAAAAATTAAAAAT
Found at i:42851962 original size:9 final size:9
Alignment explanation
Indices: 42851916--42851977 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
42851906 GTAAAATTGT
*
42851916 AAAAAATTG
1 AAAAAATTA
*
42851925 TAAAAATTA
1 AAAAAATTA
*
42851934 TAAAAAATAAA
1 -AAAAAAT-TA
42851945 AATAAAATTA
1 AA-AAAATTA
42851955 AAAAAATTA
1 AAAAAATTA
*
42851964 AAAAGAAATA
1 AAAA-AATTA
42851974 AAAA
1 AAAA
42851978 CACTAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
9 18 0.42
10 19 0.44
11 6 0.14
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAAAATTA
Found at i:42851977 original size:20 final size:20
Alignment explanation
Indices: 42851935--42851977 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
42851925 TAAAAATTAT
42851935 AAAAAATAAAAATAAAATTAA
1 AAAAAATAAAAATAAAA-TAA
* *
42851956 AAAAATTAAAAA-GAAATAA
1 AAAAAATAAAAATAAAATAA
42851975 AAA
1 AAA
42851978 CACTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 3 0.15
21 11 0.55
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAATAAAAATAAAATAA
Found at i:42852030 original size:47 final size:48
Alignment explanation
Indices: 42851972--42852070 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
42851962 TAAAAAGAAA
** * *
42851972 TAAAAACACTAAAATTTTTATTTTTACCTAATTTTTATAAATACTACT
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
* *
42852020 TAAAAA-ACTAAAATTGATAATTTTATCTAATTTTTATAAATATTACC
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
42852067 TAAA
1 TAAA
42852071 CAAAATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 39 0.87
48 6 0.13
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.43
Consensus pattern (48 bp):
TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
Found at i:42853745 original size:26 final size:26
Alignment explanation
Indices: 42853714--42853764 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
42853704 CATTGAAGTT
* * *
42853714 TGGTTTATCTTTTTACATGCATGAAG
1 TGGTTTATATTTATACACGCATGAAG
42853740 TGGTTTATATTTATACACGCATGAA
1 TGGTTTATATTTATACACGCATGAA
42853765 ATCATAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
TGGTTTATATTTATACACGCATGAAG
Found at i:42855009 original size:13 final size:13
Alignment explanation
Indices: 42854993--42855018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42854983 TTATAAAATT
42854993 TTTACATTTTACA
1 TTTACATTTTACA
42855006 TTTACATTTTACA
1 TTTACATTTTACA
42855019 AAGCTTCAGC
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:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTACATTTTACA
Found at i:42855976 original size:50 final size:50
Alignment explanation
Indices: 42855906--42856032 Score: 245
Period size: 50 Copynumber: 2.5 Consensus size: 50
42855896 CTAGATTCAG
42855906 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
1 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
42855956 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
1 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
*
42856006 GCTTATATGCAAGATGTGAGTTATGGA
1 GCTTATATGCAAAATGTGAGTTATGGA
42856033 GTTGGTTTTC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (50 bp):
GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
Found at i:42857473 original size:43 final size:43
Alignment explanation
Indices: 42857423--42857693 Score: 314
Period size: 43 Copynumber: 6.3 Consensus size: 43
42857413 TTTTTTATGA
* * *
42857423 TCTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGGTCAGGT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
* * * * *
42857466 TTTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGAACTTG-
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
* * * * * *
42857508 ACTTTTAGTGGCTTTTTTGG-AAAAGCGTCGCTAAAGGTCATGT
1 TC-TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
*
42857551 TCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGATCATGT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
*** *
42857594 TC-TTAGCGATATTTGTGAAAAAAGCGCCGCTAAAGATCATGT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
* *
42857636 TCTTTAGCGGCATTTGTGAAAAAAGCGCCGCTAAAGATCATGT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
*
42857679 TCTTTAGCGGTGTTT
1 TCTTTAGCGGCGTTT
42857694 TTTCAAATAA
Statistics
Matches: 194, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
42 70 0.36
43 124 0.64
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
Found at i:42857673 original size:85 final size:83
Alignment explanation
Indices: 42857436--42857687 Score: 310
Period size: 85 Copynumber: 3.0 Consensus size: 83
42857426 TTAGCGGCGT
* * *
42857436 TTTTG-GAAAAAGCGCCGCTAAAGGTCAGGTTTTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAA
1 TTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAA
* * * *
42857500 AGAACTTGACTT-TTAGTGGC
66 AGATCATG--TTCTTAG-CGA
* * *
42857520 TTTTTTGGAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAA
1 TTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAA
42857585 AGATCATGTTCTTAGCGA
66 AGATCATGTTCTTAGCGA
* * * *
42857603 TATTTGTGAAAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGAAAAAAGCGCCGCT
1 T-TTTGTG-AAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCT
42857668 AAAGATCATGTTCTTTAGCG
64 AAAGATCATGTTC-TTAGCG
42857688 GTGTTTTTTC
Statistics
Matches: 146, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
83 4 0.03
84 13 0.09
85 123 0.84
86 6 0.04
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (83 bp):
TTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAA
AGATCATGTTCTTAGCGA
Found at i:42859963 original size:10 final size:10
Alignment explanation
Indices: 42859948--42860100 Score: 73
Period size: 10 Copynumber: 16.1 Consensus size: 10
42859938 TTATTTTTAA
42859948 ATTTTAAAAT
1 ATTTTAAAAT
*
42859958 ATTTT-ACAT
1 ATTTTAAAAT
*
42859967 ACTTTT-TAAT
1 A-TTTTAAAAT
*
42859977 -TTTT-TAAT
1 ATTTTAAAAT
42859985 -TTT-AAAAT
1 ATTTTAAAAT
42859993 ATTTTAAAAT
1 ATTTTAAAAT
*
42860003 ACTTTT-TAAT
1 A-TTTTAAAAT
*
42860013 -TTTT--TA-
1 ATTTTAAAAT
42860019 ATTTTAAAAT
1 ATTTTAAAAT
42860029 ATTTTAAAAT
1 ATTTTAAAAT
* *
42860039 ACTTTTTTAATT
1 A--TTTTAAAAT
*
42860051 TTTTTAAAAT
1 ATTTTAAAAT
42860061 ATTTTAAAATAT
1 ATTTT-AAA-AT
*
42860073 ATTTTTAAA-
1 ATTTTAAAAT
42860082 ATTTT-AAA-
1 ATTTTAAAAT
42860090 ATTTTAAAAT
1 ATTTTAAAAT
42860100 A
1 A
42860101 AAAATGGGCC
Statistics
Matches: 114, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
7 5 0.04
8 26 0.23
9 16 0.14
10 44 0.39
11 9 0.08
12 14 0.12
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:42860005 original size:36 final size:36
Alignment explanation
Indices: 42859940--42860100 Score: 199
Period size: 36 Copynumber: 4.5 Consensus size: 36
42859930 AAATATATTT
* *
42859940 ATTTTTAAATTTTAAAATATTTT-ACATACTTTTTA
1 ATTTTTTAATTTTAAAATATTTTAAAATACTTTTTA
42859975 ATTTTTTAATTTTAAAATATTTTAAAATACTTTTTA
1 ATTTTTTAATTTTAAAATATTTTAAAATACTTTTTA
42860011 ATTTTTTAATTTTAAAATATTTTAAAATACTTTTTTA
1 ATTTTTTAATTTTAAAATATTTTAAAATAC-TTTTTA
*
42860048 A---TTT--TTTTAAAATATTTTAAAATATATTTTTAAA
1 ATTTTTTAATTTTAAAATATTTTAAAATA-CTTTTT--A
**
42860082 ATTTTAAAATTTTAAAATA
1 ATTTTTTAATTTTAAAATA
42860101 AAAATGGGCC
Statistics
Matches: 111, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
32 25 0.23
34 5 0.05
35 22 0.20
36 41 0.37
37 8 0.07
39 10 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (36 bp):
ATTTTTTAATTTTAAAATATTTTAAAATACTTTTTA
Found at i:42860061 original size:32 final size:31
Alignment explanation
Indices: 42860018--42860100 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 31
42860008 TTAATTTTTT
42860018 AATTTTAAAATATTTTAAAATACT-TTTTTAA
1 AATTTTAAAATATTTTAAAATA-TATTTTTAA
**
42860049 TTTTTTTAAAATATTTTAAAATATATTTTTAA
1 -AATTTTAAAATATTTTAAAATATATTTTTAA
42860081 AATTTT-AAA-ATTTTAAAATA
1 AATTTTAAAATATTTTAAAATA
42860101 AAAATGGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 11 0.24
30 3 0.07
31 5 0.11
32 27 0.59
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
AATTTTAAAATATTTTAAAATATATTTTTAA
Found at i:42860088 original size:8 final size:8
Alignment explanation
Indices: 42860075--42860099 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42860065 TAAAATATAT
42860075 TTTTAAAA
1 TTTTAAAA
42860083 TTTTAAAA
1 TTTTAAAA
42860091 TTTTAAAA
1 TTTTAAAA
42860099 T
1 T
42860100 AAAAATGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:42861248 original size:32 final size:32
Alignment explanation
Indices: 42861212--42861313 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
42861202 CCAACTCTCT
42861212 CTTTCTTTATTTTTTCTTATTCACTTTTTGTG
1 CTTTCTTTATTTTTTCTTATTCACTTTTTGTG
* *
42861244 CTTTCTTTA--TTTT-TT-TT---TTTCTCT-
1 CTTTCTTTATTTTTTCTTATTCACTTTTTGTG
*
42861268 CTTTCCTTATTTTTTCTTATTCACTTTTTGTG
1 CTTTCTTTATTTTTTCTTATTCACTTTTTGTG
* *
42861300 TTTTCTTTGTTTTT
1 CTTTCTTTATTTTT
42861314 GTTTGCAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
24 8 0.15
25 5 0.09
26 4 0.07
27 2 0.04
28 4 0.07
29 2 0.04
30 4 0.07
31 5 0.09
32 20 0.37
ACGTcount: A:0.07, C:0.16, G:0.05, T:0.73
Consensus pattern (32 bp):
CTTTCTTTATTTTTTCTTATTCACTTTTTGTG
Found at i:42861272 original size:56 final size:56
Alignment explanation
Indices: 42861207--42861313 Score: 187
Period size: 56 Copynumber: 1.9 Consensus size: 56
42861197 TCCCTCCAAC
*
42861207 TCTCTCTTTCTTTATTTTTTCTTATTCACTTTTTGTGCTTTCTTTATTTTTTTTTT
1 TCTCTCTTTCCTTATTTTTTCTTATTCACTTTTTGTGCTTTCTTTATTTTTTTTTT
* *
42861263 TCTCTCTTTCCTTATTTTTTCTTATTCACTTTTTGTGTTTTCTTTGTTTTT
1 TCTCTCTTTCCTTATTTTTTCTTATTCACTTTTTGTGCTTTCTTTATTTTT
42861314 GTTTGCAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.72
Consensus pattern (56 bp):
TCTCTCTTTCCTTATTTTTTCTTATTCACTTTTTGTGCTTTCTTTATTTTTTTTTT
Found at i:42862433 original size:14 final size:17
Alignment explanation
Indices: 42862397--42862433 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42862387 ATTTTTCAAT
42862397 ATATATTATTATGTTAA
1 ATATATTATTATGTTAA
42862414 ATATATT-TTAT-TTAA
1 ATATATTATTATGTTAA
42862429 A-ATAT
1 ATATAT
42862434 CAACTACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 5 0.25
16 4 0.20
17 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATTATTATGTTAA
Found at i:42864152 original size:21 final size:21
Alignment explanation
Indices: 42864093--42864176 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
42864083 TGATCAGTAT
*
42864093 ACGACACAT-AAGTGCCTGTA
1 ACGACACATAAAGTGCCTGAA
** *
42864113 ACGACACACGAGGTGCCTGAA
1 ACGACACATAAAGTGCCTGAA
*
42864134 ACGACACATAAAGTTCCTGAGA
1 ACGACACATAAAGTGCCTGA-A
42864156 TACGACACATAAAGTGCCTGA
1 -ACGACACATAAAGTGCCTGA
42864177 TCGGCAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 8 0.15
21 25 0.47
22 1 0.02
23 19 0.36
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (21 bp):
ACGACACATAAAGTGCCTGAA
Found at i:42865211 original size:15 final size:16
Alignment explanation
Indices: 42865193--42865224 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42865183 TTAATTAATA
42865193 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
42865208 TAATTTAATAATATTT
1 TAATTTAATAATATTT
42865224 T
1 T
42865225 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:42865215 original size:25 final size:26
Alignment explanation
Indices: 42865180--42865232 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
42865170 TATTATCTTA
42865180 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
42865204 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
42865231 AT
1 AT
42865233 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:42871216 original size:43 final size:42
Alignment explanation
Indices: 42871159--42871440 Score: 232
Period size: 43 Copynumber: 6.6 Consensus size: 42
42871149 ATTCAGTGAC
*
42871159 ACGGGGAATCAGCACATAGCAACCCCTTTCACAATTAAGGAT
1 ACGGGGAATCAGCACTTAGCAACCCCTTTCACAATTAAGGAT
* * * * *
42871201 ACGATGGAATTAGCACTTAGCAACCACCTTT-A-TATTCAGTGAA
1 ACG-GGGAATCAGCACTTAGCAACC-CCTTTCACAATTAAG-GAT
* * *
42871244 ACGGGGAATCAGCACTTAGCAACCCCTTTCACGATCAAAGAT
1 ACGGGGAATCAGCACTTAGCAACCCCTTTCACAATTAAGGAT
* * * *
42871286 ACGGTGGAATCAGCACATAGCAACCACCTTT-A-TATTCAGTGCT
1 ACGG-GGAATCAGCACTTAGCAACC-CCTTTCACAATTAAG-GAT
* *
42871329 ACGGGGAATCAGCACTTAGCAACCCCTTTCACAATCAAAGAT
1 ACGGGGAATCAGCACTTAGCAACCCCTTTCACAATTAAGGAT
* * * * * * **
42871371 ACGGTGGGATCAGCATTTAGCAACCACCTCT-AGAGTCAATAAT
1 ACGG-GGAATCAGCACTTAGCAACC-CCTTTCACAATTAAGGAT
* *
42871414 TCGGGGAATCAGCACTTAACAACCCCT
1 ACGGGGAATCAGCACTTAGCAACCCCT
42871441 CGGGGAATCA
Statistics
Matches: 192, Mismatches: 36, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
41 13 0.07
42 80 0.42
43 85 0.44
44 14 0.07
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (42 bp):
ACGGGGAATCAGCACTTAGCAACCCCTTTCACAATTAAGGAT
Found at i:42871270 original size:85 final size:85
Alignment explanation
Indices: 42871118--42871440 Score: 425
Period size: 85 Copynumber: 3.8 Consensus size: 85
42871108 ATCCGCTACT
* ** * * *
42871118 CGGTGGATTCAGCACTTAGCAACCACC-AAAAATTCAGTGACACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGAAACGGGGAATCAGCACTTAGCAAC
* *
42871182 CCCTTTCACAATTAAGGATA
66 CCCTTTCACAATCAAAGATA
* *
42871202 CGATGGAATTAGCACTTAGCAACCACCTTTATATTCAGTGAAACGGGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGAAACGGGGAATCAGCACTTAGCAAC
*
42871267 CCCTTTCACGATCAAAGATA
66 CCCTTTCACAATCAAAGATA
* **
42871287 CGGTGGAATCAGCACATAGCAACCACCTTTATATTCAGTGCTACGGGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGAAACGGGGAATCAGCACTTAGCAAC
42871352 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
* * * * * * * *
42871372 CGGTGGGATCAGCATTTAGCAACCACCTCTAGAGTCAAT-AATTCGGGGAATCAGCACTTAACAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGAA-ACGGGGAATCAGCACTTAGCAA
42871436 CCCCT
65 CCCCT
42871441 CGGGGAATCA
Statistics
Matches: 209, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
84 24 0.11
85 185 0.89
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGAAACGGGGAATCAGCACTTAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:42876649 original size:29 final size:29
Alignment explanation
Indices: 42876581--42876655 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
42876571 AAATTTTTAA
42876581 ATAA-TAATTTTAAAAAAAATTCTAAAATT
1 ATAATTAATTTT-AAAAAAATTCTAAAATT
* * *
42876610 AT-CTTAGTTTTAAAAAAA-TCTGAAATTT
1 ATAATTAATTTTAAAAAAATTCT-AAAATT
*
42876638 ATAATTAATTTTTAAAAA
1 ATAATTAATTTTAAAAAA
42876656 TTATAGATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 3 0.08
28 14 0.38
29 20 0.54
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (29 bp):
ATAATTAATTTTAAAAAAATTCTAAAATT
Found at i:42879651 original size:27 final size:26
Alignment explanation
Indices: 42879621--42879873 Score: 202
Period size: 27 Copynumber: 9.4 Consensus size: 26
42879611 AAAACCCTCA
*
42879621 AAGGGTAAAATTACCAAAATATCCTTG
1 AAGGGTAAAATTACCGAAATA-CCTTG
**
42879648 AAGGGTAAAATTACCGAAATACCCTCA
1 AAGGGTAAAATTACCGAAATA-CCTTG
* *
42879675 AAGGGTAAAATTACTGAAATACCCTCG
1 AAGGGTAAAATTACCGAAATA-CCTTG
* *
42879702 AAGGGAAAAATTACCAAAATACCTTCG
1 AAGGGTAAAATTACCGAAATACCTT-G
* * *
42879729 AAGGGTAAAATTACTGAAATACCCTC
1 AAGGGTAAAATTACCGAAATACCTTG
* *
42879755 AAGGGGTAAAATTACTGAAACACCTTCG
1 AA-GGGTAAAATTACCGAAATACCTT-G
** *
42879783 AAGGGTAAAATTACAAAAATACCCTCG
1 AAGGGTAAAATTACCGAAATA-CCTTG
* * ***
42879810 AAGGGT-AAATTATCGAAGTACCCCCA
1 AAGGGTAAAATTACCGAAATA-CCTTG
* * **
42879836 AAGGATAAAATTATCGAAATACCCCCG
1 AAGGGTAAAATTACCGAAATA-CCTTG
42879863 AAGGGTAAAAT
1 AAGGGTAAAAT
42879874 GACTGTTATA
Statistics
Matches: 189, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
26 24 0.13
27 160 0.85
28 5 0.03
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (26 bp):
AAGGGTAAAATTACCGAAATACCTTG
Found at i:42879672 original size:54 final size:54
Alignment explanation
Indices: 42879597--42879873 Score: 315
Period size: 54 Copynumber: 5.1 Consensus size: 54
42879587 TGCGATTCGT
** * * * *
42879597 GGTAAAATTATTGAAAAACCCTCAAAGGGTAAAATTACCAAAATATCCTTGAAG
1 GGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAG
*
42879651 GGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTACTGAAATACCCTCGAAG
1 GGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAG
* * * * *
42879705 GGAAAAATTACCAAAATACCTTCGAAGGGTAAAATTACTGAAATACCCTC-AAGG
1 GGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAA-G
* * * * **
42879759 GGTAAAATTACTGAAACACCTTCGAAGGGTAAAATTACAAAAATACCCTCGAAG
1 GGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAG
* * * * * *
42879813 GGT-AAATTATCGAAGTACCCCCAAAGGATAAAATTATCGAAATACCCCCGAAG
1 GGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAG
42879866 GGTAAAAT
1 GGTAAAAT
42879874 GACTGTTATA
Statistics
Matches: 191, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
53 43 0.23
54 146 0.76
55 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (54 bp):
GGTAAAATTACCGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAG
Found at i:42879732 original size:81 final size:81
Alignment explanation
Indices: 42879597--42879873 Score: 380
Period size: 81 Copynumber: 3.4 Consensus size: 81
42879587 TGCGATTCGT
* * *
42879597 GGTAAAATTATTGAAAAACCCTCAAAGGGTAAAATTACCAAAATATCCTT-GAAGGGTAAAATTA
1 GGTAAAATTACTGAAATACCCTCGAAGGGTAAAATTACCAAAATA-CCTTCGAAGGGTAAAATTA
42879661 CCGAAATACCCTCAAAG
65 CCGAAATACCCTCAAAG
*
42879678 GGTAAAATTACTGAAATACCCTCGAAGGGAAAAATTACCAAAATACCTTCGAAGGGTAAAATTAC
1 GGTAAAATTACTGAAATACCCTCGAAGGGTAAAATTACCAAAATACCTTCGAAGGGTAAAATTAC
* *
42879743 TGAAATACCCTCAAGG
66 CGAAATACCCTCAAAG
* * * * *
42879759 GGTAAAATTACTGAAACACCTTCGAAGGGTAAAATTACAAAAATACCCTCGAAGGGT-AAATTAT
1 GGTAAAATTACTGAAATACCCTCGAAGGGTAAAATTACCAAAATACCTTCGAAGGGTAAAATTAC
* *
42879823 CGAAGTACCCCCAAAG
66 CGAAATACCCTCAAAG
* *
42879839 GATAAAATTA-TCGAAATACCCCCGAAGGGTAAAAT
1 GGTAAAATTACT-GAAATACCCTCGAAGGGTAAAAT
42879874 GACTGTTATA
Statistics
Matches: 174, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
79 1 0.01
80 51 0.29
81 122 0.70
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (81 bp):
GGTAAAATTACTGAAATACCCTCGAAGGGTAAAATTACCAAAATACCTTCGAAGGGTAAAATTAC
CGAAATACCCTCAAAG
Found at i:42880808 original size:20 final size:20
Alignment explanation
Indices: 42880783--42880825 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
42880773 TTCCAAAATT
* *
42880783 AAGAAACGAGTTTTATCAAC
1 AAGAAACGAGTTTCACCAAC
42880803 AAGAAACGAGTTTCACCAAC
1 AAGAAACGAGTTTCACCAAC
42880823 AAG
1 AAG
42880826 TCTAAGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (20 bp):
AAGAAACGAGTTTCACCAAC
Found at i:42891778 original size:82 final size:82
Alignment explanation
Indices: 42891637--42891793 Score: 235
Period size: 82 Copynumber: 1.9 Consensus size: 82
42891627 GGTTAGTTCT
* *
42891637 TATGGACTCTTGCTTGAAGAATAGTCCCTGCGGACTCCTGCTTGAAGAATAATCATTACGAACTC
1 TATGGACTCTTGCTTGAAGAATAGTCCATACGGACTCCTGCTTGAAGAATAATCATTACGAACTC
42891702 TTGCTTGAAATAGTCCA
66 TTGCTTGAAATAGTCCA
* * * * *
42891719 TATGGACTCTTTCTTGAA-AGATAGTCCATACGGACTCTTTCTTGAAGAATAGTCTTTACGAACT
1 TATGGACTCTTGCTTGAAGA-ATAGTCCATACGGACTCCTGCTTGAAGAATAATCATTACGAACT
42891783 CTTGCTTGAAA
65 CTTGCTTGAAA
42891794 GATAGTCTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 66 0.99
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (82 bp):
TATGGACTCTTGCTTGAAGAATAGTCCATACGGACTCCTGCTTGAAGAATAATCATTACGAACTC
TTGCTTGAAATAGTCCA
Found at i:42891791 original size:56 final size:57
Alignment explanation
Indices: 42891640--42891800 Score: 179
Period size: 56 Copynumber: 2.9 Consensus size: 57
42891630 TAGTTCTTAT
* * * *
42891640 GGACTCTTGCTTGAAGAATAGTCCCTGCGGACTCCTGCTTG-AAGAATAAT-CATTAC
1 GGACTCTTGCTTGAAGAATAGTCCATACGGACTCTTGCTTGAAAG-ATAGTCCATTAC
* * *
42891696 GAACTCTTGCTTG-A-AATAGTCCATATGGACTCTTTCTTGAAAGATAGTCCA-TAC
1 GGACTCTTGCTTGAAGAATAGTCCATACGGACTCTTGCTTGAAAGATAGTCCATTAC
* ** *
42891750 GGACTCTTTCTTGAAGAATAGTCTTTACGAACTCTTGCTTGAAAGATAGTC
1 GGACTCTTGCTTGAAGAATAGTCCATACGGACTCTTGCTTGAAAGATAGTC
42891801 TATTTAGACT
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
54 38 0.44
55 7 0.08
56 42 0.48
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (57 bp):
GGACTCTTGCTTGAAGAATAGTCCATACGGACTCTTGCTTGAAAGATAGTCCATTAC
Found at i:42891801 original size:28 final size:28
Alignment explanation
Indices: 42891640--42891800 Score: 161
Period size: 28 Copynumber: 5.8 Consensus size: 28
42891630 TAGTTCTTAT
* *
42891640 GGACTCTTGCTTGAAGAATAGTCCCTGC
1 GGACTCTTGCTTGAAGAATAGTCCATAC
* *
42891668 GGACTCCTGCTTGAAGAATAAT-CATTAC
1 GGACTCTTGCTTGAAGAATAGTCCA-TAC
* *
42891696 GAACTCTTGCTTG-A-AATAGTCCATAT
1 GGACTCTTGCTTGAAGAATAGTCCATAC
*
42891722 GGACTCTTTCTTGAA-AGATAGTCCATAC
1 GGACTCTTGCTTGAAGA-ATAGTCCATAC
* **
42891750 GGACTCTTTCTTGAAGAATAGTCTTTAC
1 GGACTCTTGCTTGAAGAATAGTCCATAC
*
42891778 GAACTCTTGCTTGAA-AGATAGTC
1 GGACTCTTGCTTGAAGA-ATAGTC
42891801 TATTTAGACT
Statistics
Matches: 112, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
26 18 0.16
27 7 0.06
28 86 0.77
29 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (28 bp):
GGACTCTTGCTTGAAGAATAGTCCATAC
Found at i:42892262 original size:26 final size:25
Alignment explanation
Indices: 42892224--42892272 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
42892214 ATCATTCATT
*
42892224 TTCACCAAAATAACACATATCAATCA
1 TTCAACAAAATAACACA-ATCAATCA
* *
42892250 TTCAACAATATAACATAATCAAT
1 TTCAACAAAATAACACAATCAAT
42892273 AGTACTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (25 bp):
TTCAACAAAATAACACAATCAATCA
Found at i:42898970 original size:20 final size:20
Alignment explanation
Indices: 42898945--42898984 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
42898935 TAACGGGACC
42898945 GCTGATGTGGCAAGTTAACT
1 GCTGATGTGGCAAGTTAACT
*
42898965 GCTGATGTGGCCAGTTAACT
1 GCTGATGTGGCAAGTTAACT
42898985 TGCCACGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (20 bp):
GCTGATGTGGCAAGTTAACT
Found at i:42899765 original size:3 final size:3
Alignment explanation
Indices: 42899757--42899797 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42899747 AATCTCTATC
42899757 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42899798 CTTAAATTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42899954 original size:29 final size:31
Alignment explanation
Indices: 42899894--42899962 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
42899884 ACTATTAATC
* *
42899894 AGTGACTGTTTTGTCACTTTTTTATAATGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
* *
42899925 AGTGGCTGTTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
42899954 AAGTGACTG
1 -AGTGACTG
42899963 AAATGAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.16
30 13 0.41
31 14 0.44
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:42901647 original size:22 final size:22
Alignment explanation
Indices: 42901621--42901744 Score: 88
Period size: 25 Copynumber: 5.3 Consensus size: 22
42901611 GCCCTTATGG
42901621 TATTCTATTAGCCTTTGTGGCA
1 TATTCTATTAGCCTTTGTGGCA
* * *
42901643 TATTCTGTTAGCTTTTGTGGCG
1 TATTCTATTAGCCTTTGTGGCA
* *
42901665 TATTATGTATGTTGCCTTTGTGGCA
1 TA-T-TCTAT-TAGCCTTTGTGGCA
*
42901690 TATTCTGTATGTTA-CCTTTGTGGCG
1 TATTC--TA--TTAGCCTTTGTGGCA
* *
42901715 TATTCTGATTGGCCCTTGTGGCA
1 TATTCT-ATTAGCCTTTGTGGCA
*
42901738 TACTCTA
1 TATTCTA
42901745 ATAAGTCTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
22 24 0.31
23 17 0.22
24 5 0.06
25 30 0.38
26 1 0.01
27 1 0.01
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.46
Consensus pattern (22 bp):
TATTCTATTAGCCTTTGTGGCA
Found at i:42901719 original size:25 final size:25
Alignment explanation
Indices: 42901656--42901721 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
42901646 TCTGTTAGCT
* *
42901656 TTTGTGGCGTATTATGTATGTTGCC
1 TTTGTGGCGTATTCTGTATGTTACC
*
42901681 TTTGTGGCATATTCTGTATGTTACC
1 TTTGTGGCGTATTCTGTATGTTACC
42901706 TTTGTGGCGTATTCTG
1 TTTGTGGCGTATTCTG
42901722 ATTGGCCCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.48
Consensus pattern (25 bp):
TTTGTGGCGTATTCTGTATGTTACC
Found at i:42908552 original size:19 final size:19
Alignment explanation
Indices: 42908491--42908552 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
42908481 ACGGACTACC
42908491 AACACCTCCACCACCGAGT
1 AACACCTCCACCACCGAGT
* * **
42908510 AACATCATCCA-CAGCCCACC
1 AACA-CCTCCACCA-CCGAGT
42908530 AACACCTCCACCACCGAGT
1 AACACCTCCACCACCGAGT
42908549 AACA
1 AACA
42908553 TCATCCATAG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.35, C:0.47, G:0.08, T:0.10
Consensus pattern (19 bp):
AACACCTCCACCACCGAGT
Found at i:42908579 original size:39 final size:39
Alignment explanation
Indices: 42908488--42908580 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 39
42908478 GTTACGGACT
**
42908488 ACCAACACCTCCACCACCGAGTAACATCATCCACAGCCC
1 ACCAACAAATCCACCACCGAGTAACATCATCCACAGCCC
** * *
42908527 ACCAACACCTCCACCACCGAGTAACATCATCCATAGTCC
1 ACCAACAAATCCACCACCGAGTAACATCATCCACAGCCC
* *
42908566 GCCAGCAAATCCACC
1 ACCAACAAATCCACC
42908581 GGAAGCAGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.33, C:0.46, G:0.09, T:0.12
Consensus pattern (39 bp):
ACCAACAAATCCACCACCGAGTAACATCATCCACAGCCC
Found at i:42918826 original size:406 final size:406
Alignment explanation
Indices: 42918074--42918885 Score: 1516
Period size: 406 Copynumber: 2.0 Consensus size: 406
42918064 GAGGAGAAGA
* *
42918074 AAATTCACCGTGTCAAATTCGAATGATACAAGAGGAGAGACATTAACATCTATTTATAGCATACA
1 AAATTCACCGTGTCAAATTCGAATGATACAAGAGAAGAGACATGAACATCTATTTATAGCATACA
42918139 TAAGAGATCCCACTGCACTAGAATATGGAATATGTGACATGTAGTCAATCTCATCATCTGATTGT
66 TAAGAGATCCCACTGCACTAGAATATGGAATATGTGACATGTAGTCAATCTCATCATCTGATTGT
42918204 GGAGACAAAGCCGATAAAAGTCTGAAATGGGCTACTAAAGGAGTACTAACAGGCTTAGCAATCTG
131 GGAGACAAAGCCGATAAAAGTCTGAAATGGGCTACTAAAGGAGTACTAACAGGCTTAGCAATCTG
42918269 CATATTCAACCTACAAAGAACTTTCTCAATGTACCCTTTTCTGACTTAGGTACAATTTACTTGTT
196 CATATTCAACCTACAAAGAACTTTCTCAATGTACCCTTTTCTGACTTAGGTACAATTTACTTGTT
42918334 TTTCTATCTCTAAGAATCTCCATACCAAGTATTTTCTTTGTTGCTCCCAAATCCTTCATCTCAAA
261 TTTCTATCTCTAAGAATCTCCATACCAAGTATTTTCTTTGTTGCTCCCAAATCCTTCATCTCAAA
*
42918399 TTCTTCATTAAGTTGGGTTTTAACATTTCTTATTTCTCATTTATCTTTAGCTACTATTAATATGT
326 TTCTTCATTAAGTTGGGTTTTAACATTTCTTATTTCTCATTTATCTTTAGCTACTATCAATATGT
42918464 CATCAACATAGGGGAG
391 CATCAACATAGGGGAG
* *
42918480 AAATTCACTGTGTCAAATTCGAATGATACAAGAGAAGAGGCATGAACATCTATTTATAGCATACA
1 AAATTCACCGTGTCAAATTCGAATGATACAAGAGAAGAGACATGAACATCTATTTATAGCATACA
* *
42918545 TAAGAGATCCCACTGTAGTAGAATATGGAATATGTGACATGTAGTCAATCTCATCATCTGATTGT
66 TAAGAGATCCCACTGCACTAGAATATGGAATATGTGACATGTAGTCAATCTCATCATCTGATTGT
* *
42918610 GGAGACAAAGCCGATGAAAGTCTGAAATGGGCTGCTAAAGGAGTACTAACAGGCTTAGCAATCTG
131 GGAGACAAAGCCGATAAAAGTCTGAAATGGGCTACTAAAGGAGTACTAACAGGCTTAGCAATCTG
42918675 CATATTCAACCTACAAAGAACTTTCTCAATGTACCCTTTTCTGACTTAGGTACAATTTACTTGTT
196 CATATTCAACCTACAAAGAACTTTCTCAATGTACCCTTTTCTGACTTAGGTACAATTTACTTGTT
*
42918740 TTTCTATCTCTAAGAATCTCCATAGCAAGTATTTTCTTTGTTGCTCCCAAATCCTTCATCTCAAA
261 TTTCTATCTCTAAGAATCTCCATACCAAGTATTTTCTTTGTTGCTCCCAAATCCTTCATCTCAAA
* *
42918805 TTCTTTATTAAGTTGGGTTTTAACATTTCTTATTTCTCATTTATCTTTCGCTACTATCAATATGT
326 TTCTTCATTAAGTTGGGTTTTAACATTTCTTATTTCTCATTTATCTTTAGCTACTATCAATATGT
42918870 CATCAACATAGGGGAG
391 CATCAACATAGGGGAG
42918886 TAGATACACA
Statistics
Matches: 394, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
406 394 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (406 bp):
AAATTCACCGTGTCAAATTCGAATGATACAAGAGAAGAGACATGAACATCTATTTATAGCATACA
TAAGAGATCCCACTGCACTAGAATATGGAATATGTGACATGTAGTCAATCTCATCATCTGATTGT
GGAGACAAAGCCGATAAAAGTCTGAAATGGGCTACTAAAGGAGTACTAACAGGCTTAGCAATCTG
CATATTCAACCTACAAAGAACTTTCTCAATGTACCCTTTTCTGACTTAGGTACAATTTACTTGTT
TTTCTATCTCTAAGAATCTCCATACCAAGTATTTTCTTTGTTGCTCCCAAATCCTTCATCTCAAA
TTCTTCATTAAGTTGGGTTTTAACATTTCTTATTTCTCATTTATCTTTAGCTACTATCAATATGT
CATCAACATAGGGGAG
Found at i:42923500 original size:13 final size:13
Alignment explanation
Indices: 42923482--42923526 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
42923472 ACACTGTTAA
42923482 ACTTTTTAAAAGC
1 ACTTTTTAAAAGC
* *
42923495 ACTTTTTCACAGC
1 ACTTTTTAAAAGC
*
42923508 ACTTTTCAAAAGC
1 ACTTTTTAAAAGC
42923521 A-TTTTT
1 ACTTTTT
42923527 CAACCTCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (13 bp):
ACTTTTTAAAAGC
Found at i:42925753 original size:22 final size:22
Alignment explanation
Indices: 42925728--42925773 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42925718 TCAGGAGCCC
42925728 AAAACCGAGACCAAAACCAAAA
1 AAAACCGAGACCAAAACCAAAA
* * *
42925750 AAAACTGAGACCAAGACCCAAA
1 AAAACCGAGACCAAAACCAAAA
42925772 AA
1 AA
42925774 CTGGTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.26, G:0.11, T:0.02
Consensus pattern (22 bp):
AAAACCGAGACCAAAACCAAAA
Found at i:42926219 original size:62 final size:59
Alignment explanation
Indices: 42926146--42926260 Score: 176
Period size: 62 Copynumber: 1.9 Consensus size: 59
42926136 AATGATTATC
* * *
42926146 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAGAT
42926208 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAA
42926261 CATTAAAGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
59 20 0.40
60 1 0.02
61 1 0.02
62 28 0.56
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGAT
Found at i:42926508 original size:148 final size:148
Alignment explanation
Indices: 42926240--42926655 Score: 787
Period size: 148 Copynumber: 2.8 Consensus size: 148
42926230 ATTTATCTTG
42926240 ATAAATATTATATTAATTTAACATTAAAGTGATTAAGTTTAATCATAGTTAAACTCTCTAAACTC
1 ATAAATATTATATTAATTTAACATTAAAGTGATTAAGTTTAATCATAGTTAAACTCTCTAAACTC
* * *
42926305 TCTCTATATAAAGAGAGCCTTGGATCATTATTTACACACATTTGAATTCAAGAGAGTTTAATCTA
66 TCCCTATATAAAGAGAGTCTTGGATCATTATTTACACACATTTGAATTCAAGAGAGTTTAATATA
42926370 ATATTAAATTTAATCTAA
131 ATATTAAATTTAATCTAA
*
42926388 ATAAATATTATATTAATTTAACATTAAAGTGATTAAGTTTAATCATAGTTAAACTTTCTAAACTC
1 ATAAATATTATATTAATTTAACATTAAAGTGATTAAGTTTAATCATAGTTAAACTCTCTAAACTC
42926453 TCCCTATATAAAGAGAGTCTTGGATCATTATTTACACACATTTGAATTCAAGAGAGTTTAATATA
66 TCCCTATATAAAGAGAGTCTTGGATCATTATTTACACACATTTGAATTCAAGAGAGTTTAATATA
42926518 ATATTAAATTTAATCTAA
131 ATATTAAATTTAATCTAA
*
42926536 ATAAATATTATATTAATTTAACATTAAAGTGATTAAGTTTAGTCATAGTTAAACTCTCTAAACTC
1 ATAAATATTATATTAATTTAACATTAAAGTGATTAAGTTTAATCATAGTTAAACTCTCTAAACTC
42926601 TCCCTATATAAAGAGAGTCTTGGATCATTATTTACACACATTTGAATTCAAGAGA
66 TCCCTATATAAAGAGAGTCTTGGATCATTATTTACACACATTTGAATTCAAGAGA
42926656 AAGTTGTAGA
Statistics
Matches: 262, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
148 262 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (148 bp):
ATAAATATTATATTAATTTAACATTAAAGTGATTAAGTTTAATCATAGTTAAACTCTCTAAACTC
TCCCTATATAAAGAGAGTCTTGGATCATTATTTACACACATTTGAATTCAAGAGAGTTTAATATA
ATATTAAATTTAATCTAA
Found at i:42927537 original size:2 final size:2
Alignment explanation
Indices: 42927530--42927555 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42927520 TATAATTGTG
42927530 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42927556 GAGATGATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42928843 original size:17 final size:19
Alignment explanation
Indices: 42928814--42928848 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42928804 CCCTCGTCCT
42928814 CTAAGGAGAAAT-AGAAAG
1 CTAAGGAGAAATAAGAAAG
42928832 CTAAGG-GAAATAAGAAA
1 CTAAGGAGAAATAAGAAA
42928849 TTGATTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.06, G:0.26, T:0.11
Consensus pattern (19 bp):
CTAAGGAGAAATAAGAAAG
Found at i:42931371 original size:51 final size:50
Alignment explanation
Indices: 42931297--42931594 Score: 283
Period size: 51 Copynumber: 5.9 Consensus size: 50
42931287 CAATGATGTT
* * * * *
42931297 CGGTTCACATAGTAGTCTACACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * ** * *
42931348 CGATACACGTAGTAGCCTGCACATAGTTCTACACACGTGATTGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * *
42931399 TGGTACGCATAGTAGCCTGCACATAGTACTACACATGTTACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * *
42931450 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
** * * * * *
42931501 CGGTATGCATATTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
* *
42931551 TGGTACACGTAGTAGCCTGCACATAATACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
42931595 CACTTTCACT
Statistics
Matches: 192, Mismatches: 50, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
49 2 0.01
50 38 0.20
51 149 0.78
52 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:42931442 original size:102 final size:102
Alignment explanation
Indices: 42931304--42931590 Score: 434
Period size: 102 Copynumber: 2.8 Consensus size: 102
42931294 GTTCGGTTCA
* *
42931304 CATAGTAGTCTACACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
* * *
42931369 CATAGTTCTACACACGTGATTGAAACTATCTGGTACG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
*
42931406 CATAGTAGCCTGCACATAGTACTACACATGTTACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
*
42931471 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * * *
42931508 CATATTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA-TCCGATACACGTAGTAGCCTGC
*
42931571 ACATAATACTACACACGTGA
65 ACATAGTACTACACACGTGA
42931591 CCATCACTTT
Statistics
Matches: 170, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
100 4 0.02
101 39 0.23
102 127 0.75
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:42937252 original size:37 final size:36
Alignment explanation
Indices: 42937201--42937308 Score: 105
Period size: 37 Copynumber: 2.9 Consensus size: 36
42937191 ATTCCAAAAA
*
42937201 TAATA-TTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATACTTATCTTAATA-TTTAATATT-AATTTAATAT
**
42937237 TAATACTTATCTTAATATTATTTTATTAATTTAATAT
1 TAATACTTATCTTAATATT-TAATATTAATTTAATAT
* *
42937274 TAAAACGATTATCTTAATATTAAAT-TTAATTTAAT
1 TAATAC--TTATCTTAATATTTAATATTAATTTAAT
42937309 GTTTATCTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
36 15 0.25
37 31 0.52
38 1 0.02
39 13 0.22
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (36 bp):
TAATACTTATCTTAATATTTAATATTAATTTAATAT
Found at i:42937274 original size:11 final size:11
Alignment explanation
Indices: 42937201--42937276 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 11
42937191 ATTCCAAAAA
*
42937201 TAATATTATTT
1 TAATATTAATT
42937212 TAATAGTTTAATAT
1 TAATA--TTAAT-T
42937226 TAA-ATTTAATT
1 TAATA-TTAATT
42937237 TAATACTT-ATCT
1 TAATA-TTAAT-T
42937249 TAATATT-ATT
1 TAATATTAATT
42937259 T--TATTAATT
1 TAATATTAATT
42937268 TAATATTAA
1 TAATATTAA
42937277 AACGATTATC
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 2 0.04
11 21 0.38
12 15 0.27
13 5 0.09
14 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:42937290 original size:39 final size:37
Alignment explanation
Indices: 42937223--42937295 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
42937213 AATAGTTTAA
*
42937223 TATTAAATTTAATTTAATACTTATCTTAATATTATTT
1 TATTAAATTTAATTTAAAACTTATCTTAATATTATTT
42937260 TATT-AATTTAATATTAAAACGATTATCTTAATATTA
1 TATTAAATTTAAT-TTAAAAC--TTATCTTAATATTA
42937296 AATTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 8 0.25
37 10 0.31
39 14 0.44
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.52
Consensus pattern (37 bp):
TATTAAATTTAATTTAAAACTTATCTTAATATTATTT
Found at i:42937356 original size:62 final size:60
Alignment explanation
Indices: 42937287--42937404 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 60
42937277 AACGATTATC
* * * * *
42937287 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTAAAATTAATCTAATATTTATCTTG-A-ATAAACATTATATTAATTTAATAAGAT
*
42937349 TTAATATTAAAATTAATCTAATATTTATCTTGAATAAATATTATATTAATTTAATA
1 TTAATATTAAAATTAATCTAATATTTATCTTGAATAAACATTATATTAATTTAATA
42937405 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (60 bp):
TTAATATTAAAATTAATCTAATATTTATCTTGAATAAACATTATATTAATTTAATAAGAT
Found at i:42941768 original size:2 final size:2
Alignment explanation
Indices: 42941761--42941789 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42941751 TCATTAAGTT
42941761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42941790 TTAATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42943604 original size:23 final size:24
Alignment explanation
Indices: 42943576--42943621 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
42943566 GGGATAAAAA
42943576 ATGGTTTTG-AAAAAATAAATGAG
1 ATGGTTTTGAAAAAAATAAATGAG
42943599 ATGGTTTTGAAAAAAATAAATGA
1 ATGGTTTTGAAAAAAATAAATGA
42943622 TCGACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (24 bp):
ATGGTTTTGAAAAAAATAAATGAG
Found at i:42944603 original size:15 final size:15
Alignment explanation
Indices: 42944583--42944611 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42944573 ATAGCAAATG
42944583 TTTGACTTAATTTTA
1 TTTGACTTAATTTTA
42944598 TTTGACTTAATTTT
1 TTTGACTTAATTTT
42944612 CAAGTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTGACTTAATTTTA
Found at i:42950948 original size:21 final size:21
Alignment explanation
Indices: 42950909--42950949 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42950899 GGCCATAATG
*
42950909 ATGTTCACACATGCCATTAAC
1 ATGTTCACACATGCAATTAAC
* *
42950930 ATGTTCATACATGGAATTAA
1 ATGTTCACACATGCAATTAA
42950950 AAGCCATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (21 bp):
ATGTTCACACATGCAATTAAC
Found at i:42958985 original size:33 final size:32
Alignment explanation
Indices: 42958916--42959089 Score: 109
Period size: 27 Copynumber: 5.4 Consensus size: 32
42958906 ATATAAAGGG
42958916 GGTTGCTAAGTGCTGATTCTCCC-A--A--GG-
1 GGTTGCTAAGTGCTGATTC-CCCAATCATTGGT
42958943 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCC-AATCATTGGT
* *
42958976 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCA-A---T-CAT-T---GGT
*
42959018 GGTTGCTAAGTGCTGATTCCCC---CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCAATCATTGGT
* *
42959045 GGTTGCTAAGTGTTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCC-AATCATTGGT
42959078 GGTTGCTAAGTG
1 GGTTGCTAAGTG
42959090 TTCAATCCAC
Statistics
Matches: 118, Mismatches: 6, Indels: 40
0.72 0.04 0.24
Matches are distributed among these distances:
26 3 0.03
27 40 0.34
28 3 0.03
30 1 0.01
31 2 0.02
32 4 0.03
33 34 0.29
34 3 0.03
37 1 0.01
38 2 0.02
39 1 0.01
41 2 0.02
42 22 0.19
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCAATCATTGGT
Found at i:42959099 original size:102 final size:102
Alignment explanation
Indices: 42958911--42959100 Score: 326
Period size: 102 Copynumber: 1.9 Consensus size: 102
42958901 ATTGAATATA
* *
42958911 AAGGGGGTTGCTAAGTGCTGATTCTCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
* *
42958976 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTG
66 GGTTGCTAAGTGCTCAATCCACCATATTTTAAATGTG
*
42959013 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
*
42959078 GGTTGCTAAGTGTTCAATCCACC
66 GGTTGCTAAGTGCTCAATCCACC
42959101 GATAACGGAC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 82 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
GGTTGCTAAGTGCTCAATCCACCATATTTTAAATGTG
Found at i:42963321 original size:21 final size:22
Alignment explanation
Indices: 42963269--42963326 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
42963259 GATCGGATGA
*
42963269 AATAAAAAGAATAATAACAGTAGT
1 AATAAAAAGAAT-ATAACA-TAAT
**
42963293 AACGAAAAGAATATAAC-TAAT
1 AATAAAAAGAATATAACATAAT
42963314 AATAAAAAGAATA
1 AATAAAAAGAATA
42963327 GATAATAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.48
23 5 0.17
24 10 0.34
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.19
Consensus pattern (22 bp):
AATAAAAAGAATATAACATAAT
Found at i:42963387 original size:20 final size:20
Alignment explanation
Indices: 42963362--42963405 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
42963352 TAAATGAACG
*
42963362 AATAATCATAATAGAT-AATA
1 AATAATCA-AATAAATAAATA
42963382 AATAATCAAATAAATAAATA
1 AATAATCAAATAAATAAATA
42963402 AATA
1 AATA
42963406 GGGCAAACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
AATAATCAAATAAATAAATA
Found at i:42964371 original size:18 final size:17
Alignment explanation
Indices: 42964338--42964371 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42964328 GGGTCAAAAA
*
42964338 AATTAATTTCAAAAATT
1 AATTAATTTAAAAAATT
42964355 AATTAATTTTAAAAAAT
1 AATTAA-TTTAAAAAAT
42964372 ATATATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAATTTAAAAAATT
Found at i:42972545 original size:16 final size:16
Alignment explanation
Indices: 42972512--42972555 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
42972502 AATATATATT
*
42972512 ATTTTTA-AT-TTAAT
1 ATTTTTATATATTAAA
*
42972526 ATTTTTATTTATTAAA
1 ATTTTTATATATTAAA
42972542 ATTTTTATATATTA
1 ATTTTTATATATTA
42972556 TCATCTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTATATATTAAA
Found at i:42974065 original size:20 final size:21
Alignment explanation
Indices: 42974037--42974086 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
42974027 AATAATCAAA
* * *
42974037 GTATTAATAT-TTTAAGGCTT
1 GTATCAATATCTTTAAAGCAT
42974057 GTATCAATATCTTTAAAGCAT
1 GTATCAATATCTTTAAAGCAT
42974078 GTATCAATA
1 GTATCAATA
42974087 CCTAATGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
GTATCAATATCTTTAAAGCAT
Found at i:42983167 original size:14 final size:15
Alignment explanation
Indices: 42983143--42983171 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42983133 CCAATTTAAG
42983143 TTTTTATGAATTTTT
1 TTTTTATGAATTTTT
42983158 TTTTTA-GAATTTTT
1 TTTTTATGAATTTTT
42983172 ATAAGCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTATGAATTTTT
Found at i:42983199 original size:9 final size:9
Alignment explanation
Indices: 42983185--42983392 Score: 50
Period size: 9 Copynumber: 21.7 Consensus size: 9
42983175 AGCTTATATC
42983185 AATTTTAAT
1 AATTTTAAT
42983194 AATTTTAATT
1 AATTTTAA-T
*
42983204 ATTTTTAATT
1 AATTTTAA-T
* *
42983214 ATTTTTTAAG
1 A-ATTTTAAT
42983224 AATTTTAAT
1 AATTTTAAT
* *
42983233 ATGTTTTTACAA
1 A--ATTTTA-AT
*
42983245 AACTTTAA-
1 AATTTTAAT
*
42983253 ATATTTAAAAT
1 A-ATTT-TAAT
*
42983264 AATTTTTATT
1 AA-TTTTAAT
42983274 AATTTT-AT
1 AATTTTAAT
*
42983282 AATTTT-TT
1 AATTTTAAT
* *
42983290 ACAATTTATT
1 A-ATTTTAAT
*
42983300 AGA-TTTATT
1 A-ATTTTAAT
42983309 ATATTGTTAAT
1 A-ATT-TTAAT
42983320 AATATTT-AT
1 AAT-TTTAAT
*
42983329 AAGTTTTCAT
1 AA-TTTTAAT
42983339 AATTTCT-AT
1 AATTT-TAAT
*
42983348 AAGTTTATAT
1 AATTTTA-AT
42983358 CAATTTTAAT
1 -AATTTTAAT
* **
42983368 ATTTTTTTT
1 AATTTTAAT
42983377 AATTTTCAAT
1 AATTTT-AAT
42983387 AATTTT
1 AATTTT
42983393 TTAAATTTTT
Statistics
Matches: 152, Mismatches: 26, Indels: 41
0.69 0.12 0.19
Matches are distributed among these distances:
8 11 0.07
9 62 0.41
10 49 0.32
11 28 0.18
12 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (9 bp):
AATTTTAAT
Found at i:42983222 original size:11 final size:10
Alignment explanation
Indices: 42983187--42983219 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42983177 CTTATATCAA
*
42983187 TTTTAA-TAA
1 TTTTAATTAT
42983196 TTTTAATTAT
1 TTTTAATTAT
42983206 TTTTAATTAT
1 TTTTAATTAT
42983216 TTTT
1 TTTT
42983220 TAAGAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:42983276 original size:10 final size:9
Alignment explanation
Indices: 42983262--42983402 Score: 65
Period size: 9 Copynumber: 15.0 Consensus size: 9
42983252 AATATTTAAA
42983262 ATAATTTTT
1 ATAATTTTT
42983271 ATTAA-TTTT
1 A-TAATTTTT
42983280 ATAATTTTTT
1 ATAA-TTTTT
*
42983290 ACAATTTATT
1 ATAATTT-TT
*
42983300 A-GATTTATT
1 ATAATTT-TT
*
42983309 AT-ATTGTTA
1 ATAATT-TTT
*
42983318 ATAATATTT
1 ATAATTTTT
*
42983327 ATAAGTTTTC
1 ATAA-TTTTT
*
42983337 ATAATTTCT
1 ATAATTTTT
*
42983346 ATAAGTTTAT
1 ATAA-TTTTT
*
42983356 ATCAATTTTA
1 AT-AATTTTT
*
42983366 ATATTTTTT
1 ATAATTTTT
* *
42983375 TTAATTTTCA
1 ATAATTTT-T
42983385 ATAATTTTT
1 ATAATTTTT
42983394 -TAAATTTTT
1 AT-AATTTTT
42983403 TAAGCATTTT
Statistics
Matches: 101, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
8 4 0.04
9 54 0.53
10 41 0.41
11 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:42983382 original size:18 final size:19
Alignment explanation
Indices: 42983359--42983401 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
42983349 AGTTTATATC
* *
42983359 AATTTT-AATATTTTTTTT
1 AATTTTCAATAATTTTTTA
42983377 AATTTTCAATAATTTTTTA
1 AATTTTCAATAATTTTTTA
42983396 AATTTT
1 AATTTT
42983402 TTAAGCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTCAATAATTTTTTA
Found at i:42987474 original size:25 final size:25
Alignment explanation
Indices: 42987441--42987491 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 25
42987431 TAAATTATAG
42987441 TTTCATCC-TCAAAGTCTTTTTATTTT
1 TTTCATCCTTCAAAG--TTTTTATTTT
42987467 TTTC-TCCTTCAAAGTTTTTATTTT
1 TTTCATCCTTCAAAGTTTTTATTTT
42987491 T
1 T
42987492 ATTTTGACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 11 0.46
25 3 0.12
26 10 0.42
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTCATCCTTCAAAGTTTTTATTTT
Found at i:42988556 original size:10 final size:10
Alignment explanation
Indices: 42988541--42988588 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
42988531 TAAAATGTTA
42988541 AAATAAATTG
1 AAATAAATTG
42988551 AAATAAATT-
1 AAATAAATTG
*
42988560 AACA-ATATTG
1 AA-ATAAATTG
*
42988570 AAATAAGTTG
1 AAATAAATTG
42988580 AAATAAATT
1 AAATAAATT
42988589 AAAAATGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.31
Consensus pattern (10 bp):
AAATAAATTG
Found at i:42988602 original size:29 final size:29
Alignment explanation
Indices: 42988528--42988603 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
42988518 ATAATATATG
*
42988528 AATT-AAAATGTTAAAATAAATTGAAATA
1 AATTAAAAATGTGAAAATAAATTGAAATA
*
42988556 AATTAACAATAT-TG-AAATAAGTTGAAATA
1 AATTAA-AA-ATGTGAAAATAAATTGAAATA
42988585 AATTAAAAATGTGAAAATA
1 AATTAAAAATGTGAAAATA
42988604 TTTGAAAGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 2 0.05
28 8 0.20
29 26 0.63
30 3 0.07
31 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.30
Consensus pattern (29 bp):
AATTAAAAATGTGAAAATAAATTGAAATA
Found at i:42989055 original size:16 final size:17
Alignment explanation
Indices: 42989014--42989056 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
42989004 GTTAAATTTT
* *
42989014 AAAATAAATATATCAAA
1 AAAATAAAAATATAAAA
*
42989031 AAAGTAAAAATA-AAAA
1 AAAATAAAAATATAAAA
42989047 AAAATAAAAA
1 AAAATAAAAA
42989057 AGTAAACAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAATAAAAATATAAAA
Found at i:42990531 original size:50 final size:50
Alignment explanation
Indices: 42990477--42990959 Score: 285
Period size: 50 Copynumber: 9.7 Consensus size: 50
42990467 TGCACCGCCT
*
42990477 GGGAGGTAAGATTCGCTGCTGTAGCTTTAACCTTTTTAACTGCAATGTCA
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * * * ** * ** * *
42990527 GGGAGGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGTACCGCCT
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
42990577 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * *** * * * ** * *
42990627 GGGAGGCAAGATTCACCATTGTGGCTTTAATCTGTTCT-GCTGCACCGCCT
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCT-TTTTAACTGCAATGTCA
* *
42990677 GGGAGGTAAGATTCGCTGCTGTAGCTTTAACCTTTTTAACTGCAATGTCG
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * * * * * * *** * * *
42990727 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCGCTGTACTG-CTT
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTC-A
* * * * *
42990777 GAGAAGT-AGAATTCGCTGTTGTAGCTTTAATCTTTTAAACTGCAATGTCG
1 GGGAGGTAAG-ATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * * * * ** ** *
42990827 GGGAAGCAAGGTTCG-TCGCTGTGGCGTTAAT-TTGTTCCAC-GTCACCGCCA
1 GGGAGGTAAGATTCGCT-GCTGTAGCTTTAATCTT-TTTAACTG-CAATGTCA
* * * * *
42990877 GAGAAGTAAGATTCGCTGCTGTGGCTTTAATCTTTTTAATTGCAATGTCG
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * * * * *
42990927 GGGAAGCAAGATTCACCGATGTGGCTTTAATCT
1 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCT
42990960 GCTCCACTGC
Statistics
Matches: 318, Mismatches: 103, Indels: 24
0.71 0.23 0.05
Matches are distributed among these distances:
49 10 0.03
50 298 0.94
51 10 0.03
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (50 bp):
GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCA
Found at i:42990983 original size:100 final size:100
Alignment explanation
Indices: 42990452--42990989 Score: 713
Period size: 100 Copynumber: 5.4 Consensus size: 100
42990442 CACGTTGTGA
* *
42990452 TTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAACCTTTTTAAC
1 TTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAAC
* * * *
42990517 TGCAATGTCAGGGAGGTAAGATTCACCGCTGTGGC
66 TGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
* *
42990552 TTTAATCTGTTCCACTGTACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAAC
1 TTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAAC
* *
42990617 TGCAATGTCAGGGAGGCAAGATTCACC-ATTGTGGC
66 TGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGC
** * *
42990652 TTTAATCTGTTCTGCTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAACCTTTTTAAC
1 TTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAAC
42990717 TGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
66 TGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
* * * * * * *
42990752 TTTAATCTGTTCCGCTGTACTGCTTGAGAAGT-AGAATTCGCTGTTGTAGCTTTAATCTTTTAAA
1 TTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAG-ATTCGCTGCTGTAGCTTTAATCTTTTTAA
* ** *
42990816 CTGCAATGTCGGGGAAGCAAGGTTCGTCGCTGTGGC
65 CTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
* * * * *
42990852 GTTAATTTGTTCCAC-GTCACCGCCAGAGAAGTAAGATTCGCTGCTGTGGCTTTAATCTTTTTAA
1 TTTAATCTGTTCCACTG-CACCGCCTGGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAA
*
42990916 TTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
65 CTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
* * * *
42990952 TTTAATCTGCTCCACTGCATCACCAGGGAAGTAAGATT
1 TTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATT
42990990 TGTAATTTTT
Statistics
Matches: 388, Mismatches: 44, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
99 3 0.01
100 381 0.98
101 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (100 bp):
TTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAAC
TGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
Found at i:42991133 original size:44 final size:44
Alignment explanation
Indices: 42991085--42991177 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
42991075 CCTTTATTTT
* * *
42991085 AATCTGCTCCATTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTC
* * *
42991129 AATCTGCTCCGCTGTAATATCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTC
42991173 AATCT
1 AATCT
42991178 AATGCGATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTC
Found at i:42991256 original size:44 final size:44
Alignment explanation
Indices: 42991051--42991260 Score: 122
Period size: 44 Copynumber: 4.5 Consensus size: 44
42991041 GATCTACTCT
* * *
42991051 ACTGTAA-CTTCAGAGAGATAATATCCTTTATTTTAATCTGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCCGCTCC
* * * * * *
42991095 ATTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTAATCCGCTCC
* * * * * *
42991139 GCTGTAATATCAGGGAGATAAGATTTCTGGCTTCAATCTAATGCGATCTACTC
1 ACTGTAATCTCAGGGAGATAAGA--TC---CTTTATTTTAATCCG--CT-C-C
*
42991192 TACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 -ACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCCGCTCC
42991237 ACTGTAATCTCAGGGAGATAAGAT
1 ACTGTAATCTCAGGGAGATAAGAT
42991261 TTCTAGCTTC
Statistics
Matches: 123, Mismatches: 26, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
42 1 0.01
43 2 0.02
44 70 0.57
45 3 0.02
46 2 0.02
47 2 0.02
49 16 0.13
50 1 0.01
51 3 0.02
52 3 0.02
53 1 0.01
54 19 0.15
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
ACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCC
Done.