Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 81 of 198
Found at i:25745844 original size:24 final size:23
Alignment explanation
Indices: 25745791--25745844 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
25745781 AGTAAATCAC
* *
25745791 TAAATTGTTAAAAATTTTCTTAA
1 TAAATTATTAAAAAATTTCTTAA
* *
25745814 AACAATTATTAAAAAATTTCTTTAT
1 TA-AATTATTAAAAAATTTC-TTAA
25745839 TAAATT
1 TAAATT
25745845 TAAATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 19 0.79
25 4 0.17
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATTATTAAAAAATTTCTTAA
Found at i:25750668 original size:49 final size:47
Alignment explanation
Indices: 25750605--25750706 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 47
25750595 ACGAATAAAT
* * *
25750605 ATAAATATAAATATTTATATTAAATACA-AGATCTGAACAAATAATATAA
1 ATAAATATAAATATTTAT-GTAAAAACACAGATCT-AAAAAATAAT-TAA
**
25750654 ATAAATATTTATATTTATGTAAAAACATCAGATCTAAAAAATAATTAA
1 ATAAATATAAATATTTATGTAAAAACA-CAGATCTAAAAAATAATTAA
25750702 ATAAA
1 ATAAA
25750707 CAAGATCTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 15 0.33
49 25 0.54
50 6 0.13
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (47 bp):
ATAAATATAAATATTTATGTAAAAACACAGATCTAAAAAATAATTAA
Found at i:25751897 original size:21 final size:21
Alignment explanation
Indices: 25751865--25751910 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
25751855 TATAAAATTC
25751865 TTATTTTTAAT-A-TTATAAT
1 TTATTTTTAATAACTTATAAT
25751884 ATTATTTTTAAATAACTTATAAT
1 -TTATTTTT-AATAACTTATAAT
25751907 TTAT
1 TTAT
25751911 AATATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
22 5 0.22
23 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTTAATAACTTATAAT
Found at i:25752401 original size:13 final size:13
Alignment explanation
Indices: 25752383--25752410 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25752373 ATTATTATTT
25752383 AAACTTTCTTTTA
1 AAACTTTCTTTTA
25752396 AAACTTTCTTTTA
1 AAACTTTCTTTTA
25752409 AA
1 AA
25752411 TTAACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (13 bp):
AAACTTTCTTTTA
Found at i:25757095 original size:9 final size:9
Alignment explanation
Indices: 25757081--25757106 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
25757071 CAATTTCAAG
25757081 AATCAAGAA
1 AATCAAGAA
25757090 AATCAAGAA
1 AATCAAGAA
25757099 AATCAAGA
1 AATCAAGA
25757107 TTGCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
AATCAAGAA
Found at i:25759760 original size:31 final size:32
Alignment explanation
Indices: 25759725--25759802 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
25759715 TAAACATCAA
* *
25759725 TACATAGTAAC-TGATATAATATGGTCACTGG
1 TACATAGTAACTTGATATAATATAGTCACCGG
*
25759756 TACATAGT-ACTTGATATAATATAGTCACCGT
1 TACATAGTAACTTGATATAATATAGTCACCGG
25759787 TACATAGT-ACTTGATA
1 TACATAGTAACTTGATA
25759803 CTTCAAAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 2 0.05
31 41 0.95
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (32 bp):
TACATAGTAACTTGATATAATATAGTCACCGG
Found at i:25763107 original size:42 final size:42
Alignment explanation
Indices: 25763058--25763195 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 42
25763048 CTGGCATCGT
*
25763058 AGTGCATCATCGGATAAATTGAAGGAAATATACTGGCA-ATTA
1 AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACA-TA
* * * * *
25763100 GGTGCATCATCGGACAAGTTGAAGCAATTATATTGGCACATA
1 AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACATA
* ** * *
25763142 AGTGCATCATCGGATGAACCGAACCAAATATACTTGCACATA
1 AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACATA
25763184 AGTGCATCATCG
1 AGTGCATCATCG
25763196 ACCAAACCAA
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
42 78 0.99
43 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (42 bp):
AGTGCATCATCGGATAAATTGAAGCAAATATACTGGCACATA
Found at i:25763213 original size:42 final size:41
Alignment explanation
Indices: 25763128--25763251 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 41
25763118 TTGAAGCAAT
* * **
25763128 TATATTGGCACATAAGTGCATCATCGGA-TGAACCGAACCAAA
1 TATATT-GCACATAAGTGCATCATC-GACTAAACCAAAGTAAA
*
25763170 TATACTTGCACATAAGTGCATCATCGACCAAACCAAAGTAAA
1 TATA-TTGCACATAAGTGCATCATCGACTAAACCAAAGTAAA
* *
25763212 TATATTGACACATAATTGCATCATCGACTAAACTAAAGTA
1 TATATTG-CACATAAGTGCATCATCGACTAAACCAAAGTA
25763252 TAGACCCATA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 5 0.07
42 64 0.90
43 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (41 bp):
TATATTGCACATAAGTGCATCATCGACTAAACCAAAGTAAA
Found at i:25766351 original size:18 final size:19
Alignment explanation
Indices: 25766328--25766376 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
25766318 AAGTTTTATT
*
25766328 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
25766346 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
25766365 TTTAATTTTTAT
1 TTT-ATTTTTAT
25766377 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:25766356 original size:22 final size:22
Alignment explanation
Indices: 25766319--25766376 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
25766309 CAAGTTGTAA
* *
25766319 AGTTTTATTTTTATTTTTATTT
1 AGTTTAATTTTTATTTTTACTT
*
25766341 A-TTTATTTATTTATTTTTACTT
1 AGTTTAATT-TTTATTTTTACTT
25766363 AGTTTAATTTTTAT
1 AGTTTAATTTTTAT
25766377 GTAAATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.63
23 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (22 bp):
AGTTTAATTTTTATTTTTACTT
Found at i:25769590 original size:12 final size:12
Alignment explanation
Indices: 25769573--25769603 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25769563 AAAATCTGAT
25769573 TTCAATGTGTAA
1 TTCAATGTGTAA
25769585 TTCAATGTGTAA
1 TTCAATGTGTAA
*
25769597 CTCAATG
1 TTCAATG
25769604 AAAATTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:25783376 original size:18 final size:20
Alignment explanation
Indices: 25783340--25783377 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25783330 CTTTGTTAAA
25783340 TTTTATTTTATTAAATCTTG
1 TTTTATTTTATTAAATCTTG
25783360 TTTTATTTT-TT-AATCTTG
1 TTTTATTTTATTAAATCTTG
25783378 GGGGTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTATTTTATTAAATCTTG
Found at i:25784275 original size:53 final size:53
Alignment explanation
Indices: 25784192--25784400 Score: 267
Period size: 53 Copynumber: 3.9 Consensus size: 53
25784182 GGCACTAAAG
* * * *
25784192 GACCATATCGTGCAAGATCGTATCTGGTGGGTTATGACATCATAT-GAGAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGA-AAGAA
* * *
25784245 GACCATATTGTGTAAGACCGTAACTGGTGGGTTGTGGCATCATATGGAAAAAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAAGAA
* *
25784298 GACCATATCGTGTAAGAACGTAACTGCTGGGTTATGGCATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAAGAA
* * * * * *
25784351 TACCACATCATGTAAGACCATAACTGGTGGGTCATGTCATCATATGGAAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAA
25784401 AATTTAGGAA
Statistics
Matches: 135, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 133 0.99
54 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGGAAAGAA
Found at i:25806020 original size:20 final size:20
Alignment explanation
Indices: 25805983--25806030 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
25805973 TAAATTTTTA
*
25805983 TATTTT-ACCTTTATTATTT
1 TATTTTGACCTTTAATATTT
*
25806002 TATTTTGACTTTTAATATTT
1 TATTTTGACCTTTAATATTT
25806022 TATTGTTGA
1 TATT-TTGA
25806031 TGTAGCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (20 bp):
TATTTTGACCTTTAATATTT
Found at i:25807490 original size:15 final size:15
Alignment explanation
Indices: 25807481--25807513 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
25807471 CAAATGCTAT
25807481 AATAATAAATACAAC
1 AATAATAAATACAAC
*
25807496 AATAATAAATACATC
1 AATAATAAATACAAC
25807511 AAT
1 AAT
25807514 GACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:25809799 original size:15 final size:15
Alignment explanation
Indices: 25809779--25809808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25809769 CTCTTTCTTC
25809779 AGAATGAGATGCCAA
1 AGAATGAGATGCCAA
*
25809794 AGAATGATATGCCAA
1 AGAATGAGATGCCAA
25809809 TATTCTTCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (15 bp):
AGAATGAGATGCCAA
Found at i:25810747 original size:43 final size:43
Alignment explanation
Indices: 25810681--25810940 Score: 378
Period size: 43 Copynumber: 6.1 Consensus size: 43
25810671 TTTTATAAAT
** *
25810681 GCCGCTAAAGGTCATGACTTTTAGCGGCGCTTCTACCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* *
25810724 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTC-CCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* ** *
25810766 GCCGCTAAAGAACAAGACCTTTAGTTGCGCTTCTACCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* * *
25810809 GCCACGAAAGAACATGACCTTTAGCGGCGATTCTACCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
*
25810852 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCATAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
* *
25810895 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTATACCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
25810938 GCC
1 GCC
25810941 ACTATAAGGA
Statistics
Matches: 193, Mismatches: 23, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
42 37 0.19
43 156 0.81
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAAC
Found at i:25810884 original size:86 final size:86
Alignment explanation
Indices: 25810681--25810995 Score: 372
Period size: 86 Copynumber: 3.7 Consensus size: 86
25810671 TTTTATAAAT
** * * *
25810681 GCCGCTAAAGGTCATGACTTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGATCATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
*
25810746 AGCGGCGCTTC-CCCACAAAC
66 AGCGGCGCTTCTACCACAAAC
* ** * *
25810766 GCCGCTAAAGAACAAGACCTTTAGTTGCGCTTCTACCACAAATGCCACGAAAGAACATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
*
25810831 AGCGGCGATTCTACCACAAAC
66 AGCGGCGCTTCTACCACAAAC
* * *
25810852 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGATCATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
*
25810917 AGCGGCGCTTATACCACAAAC
66 AGCGGCGCTTCTACCACAAAC
* * * * * *
25810938 GCCACTATAAG--GATGGCTTTTAGCGGCGCTTTTTA--ACAAATGCCACTAAA-AACATGAC
1 GCCGCTA-AAGAACATGACCTTTAGCGGCGC-TTCTACCACAAACGCCACTAAAGAACATGAC
25810996 TTTTTAAAAA
Statistics
Matches: 196, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
83 7 0.04
84 12 0.06
85 80 0.41
86 94 0.48
87 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (86 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTACCACAAACGCCACTAAAGAACATGACCTTT
AGCGGCGCTTCTACCACAAAC
Found at i:25810960 original size:128 final size:127
Alignment explanation
Indices: 25810693--25810965 Score: 386
Period size: 128 Copynumber: 2.1 Consensus size: 127
25810683 CGCTAAAGGT
* * *
25810693 CATGACTTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCC
1 CATGACTTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCA
** * *
25810758 CCACAAACGCCGCTAAAGAACAAGACCTTTAGTTGCGCTTCTACCACAAATGCCACGAAAGAA
66 CCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTATACCACAAACGCCACGAAAG-A
*
25810821 CATGACCTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCT
1 CATGACTTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTC-
* * * *
25810886 ACCATAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTATACCACAAACGCCACTATAAG-
65 ACCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTATACCACAAACGCCACGA-AAGA
* *
25810949 GATGGCTTTTAGCGGCG
1 CATGACTTTTAGCGGCG
25810966 CTTTTTAACA
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
128 75 0.59
129 50 0.39
130 3 0.02
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (127 bp):
CATGACTTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCA
CCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTATACCACAAACGCCACGAAAGA
Found at i:25811001 original size:42 final size:42
Alignment explanation
Indices: 25810693--25810995 Score: 317
Period size: 43 Copynumber: 7.1 Consensus size: 42
25810683 CGCTAAAGGT
* * *
25810693 CATGACTTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAT
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
** *
25810736 CATGACCTTTAGCGGCGCTTCCCCACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTCTACACAAACGCCACTAAAGAA
* ** * *
25810778 CAAGACCTTTAGTTGCGCTTCTACCACAAATGCCACGAAAGAA
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
* *
25810821 CATGACCTTTAGCGGCGATTCTACCACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
* * *
25810864 CATGACCTTTAGCGGCGCTTCTACCATAAACGCCGCTAAAGAT
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTAAAGAA
*
25810907 CATGACCTTTAGCGGCGCTTATACCACAAACGCCACTATAAG--
1 CATGACCTTTAGCGGCGCTTCTA-CACAAACGCCACTA-AAGAA
* * * * *
25810949 GATGGCTTTTAGCGGCGCTTTTTA-ACAAATGCCACTAAA-AA
1 CATGACCTTTAGCGGCGC-TTCTACACAAACGCCACTAAAGAA
25810990 CATGAC
1 CATGAC
25810996 TTTTTAAAAA
Statistics
Matches: 223, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.01
41 16 0.07
42 51 0.23
43 151 0.68
44 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (42 bp):
CATGACCTTTAGCGGCGCTTCTACACAAACGCCACTAAAGAA
Found at i:25813894 original size:15 final size:16
Alignment explanation
Indices: 25813874--25813903 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25813864 AAAAAAAGAA
25813874 AAGC-AATTATAAAAG
1 AAGCAAATTATAAAAG
25813889 AAGCAAATTATAAAA
1 AAGCAAATTATAAAA
25813904 CCCAGAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (16 bp):
AAGCAAATTATAAAAG
Found at i:25815724 original size:16 final size:17
Alignment explanation
Indices: 25815703--25815737 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25815693 ATCTAATAAT
25815703 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
25815719 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
25815736 TT
1 TT
25815738 CGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:25821533 original size:3 final size:3
Alignment explanation
Indices: 25821525--25821575 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
25821515 GGTACACTAG
25821525 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25821573 TAT
1 TAT
25821576 GATTCTGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25822998 original size:43 final size:43
Alignment explanation
Indices: 25822950--25823196 Score: 415
Period size: 43 Copynumber: 5.7 Consensus size: 43
25822940 TTCCCAAAAA
* * *
25822950 CGCCGCTAAAGGTCATGTCCTTTAGCGGCGTTTGTAGAG-AAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GGGTAAAG
* *
25822993 TGCCGCTAAAGATTATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
*
25823036 CACCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
*
25823079 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
25823122 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
25823165 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTT
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTT
25823197 GTCAATAGCG
Statistics
Matches: 192, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 2 0.01
43 190 0.99
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAG
Found at i:25823448 original size:116 final size:117
Alignment explanation
Indices: 25823307--25823521 Score: 335
Period size: 117 Copynumber: 1.8 Consensus size: 117
25823297 GCGGCGTTTT
* * *
25823307 TATTTTATTTGGAATAAAATGACACTATTTTGCTAT-AT-AAAATGGCGCTAATTTTTTAAACTA
1 TATTTCATTTGGAATAAAACGACACTATTTTGCTATGATAAAAATCGCGCT-ATTTTTTAAACTA
25823370 AAATTATTTTTGGTGGCGTTTTTTATAAAAACGCCGCTAACGCCGCAAAAAAG
65 AAATTATTTTTGGTGGCGTTTTTTATAAAAACGCCGCTAACGCCGCAAAAAAG
* * * *
25823423 TATTTCATTTGGAATAAAACGACACTGTTTTGCTATGCTAAAAATCTCGCTATTTTTTAAAGTAA
1 TATTTCATTTGGAATAAAACGACACTATTTTGCTATGATAAAAATCGCGCTATTTTTTAAACTAA
*
25823488 AATTATTTTTTGTGGCGTTTTTTATAAAAACGCC
66 AATTATTTTTGGTGGCGTTTTTTATAAAAACGCC
25823522 CAAAAAATTT
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
116 33 0.37
117 47 0.53
118 9 0.10
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (117 bp):
TATTTCATTTGGAATAAAACGACACTATTTTGCTATGATAAAAATCGCGCTATTTTTTAAACTAA
AATTATTTTTGGTGGCGTTTTTTATAAAAACGCCGCTAACGCCGCAAAAAAG
Found at i:25824030 original size:22 final size:22
Alignment explanation
Indices: 25824005--25824049 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
25823995 CCGACCCTTG
*
25824005 AATCCCTAAATCTTAACCCCTA
1 AATCACTAAATCTTAACCCCTA
*
25824027 AATCACTAACTCTTAACCCCTA
1 AATCACTAAATCTTAACCCCTA
25824049 A
1 A
25824050 CTACTAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.27
Consensus pattern (22 bp):
AATCACTAAATCTTAACCCCTA
Found at i:25831754 original size:131 final size:131
Alignment explanation
Indices: 25831579--25831862 Score: 471
Period size: 131 Copynumber: 2.2 Consensus size: 131
25831569 TCTTCTGTCA
* * *
25831579 GCTCCACTACTGCTTAGGGAGATAAGACTTGTAATTTCCAACCTATTCCATTGCTGGTCAGGGAC
1 GCTCCGCTACTGCTTAGGGAGATAAGACTTGCAATTTCCAACCTATTCCACTGCTGGTCAGGGAC
* * *
25831644 ATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATC
66 ATAGGACTTGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCATCCTCGATC
25831709 T
131 T
25831710 GCTCCGCTACTGCTTAGGGAGATAAGA-TCTGCAATTTCCAACCTATTCCACTGCTGGTCAGGGA
1 GCTCCGCTACTGCTTAGGGAGATAAGACT-TGCAATTTCCAACCTATTCCACTGCTGGTCAGGGA
*
25831774 CATAGGACTTGTGGCTTAAATCTATTTCTCTACTCCTGGGGAAGATAAGATTCGCCATCCTCGAT
65 CATAGGACTTGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCATCCTCGAT
25831839 CT
130 CT
* *
25831841 GCTCCGCCACTACTTAGGGAGA
1 GCTCCGCTACTGCTTAGGGAGA
25831863 CCAAATCTGC
Statistics
Matches: 143, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
130 1 0.01
131 142 0.99
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (131 bp):
GCTCCGCTACTGCTTAGGGAGATAAGACTTGCAATTTCCAACCTATTCCACTGCTGGTCAGGGAC
ATAGGACTTGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCATCCTCGATC
T
Found at i:25832208 original size:171 final size:168
Alignment explanation
Indices: 25831873--25832250 Score: 531
Period size: 171 Copynumber: 2.2 Consensus size: 168
25831863 CCAAATCTGC
* * * *
25831873 AACCAGCTCTACTGCAACTGATGGAGGCAAGGTTTTATTTTCGATCTGCTTCGCTGTTAACGCAG
1 AACCAGCTCCATTGCAACCGATGGAGGCAAGG--CT-TTTTCGATCTGCTTCGCTGTTAACGCAG
* * *
25831938 GAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTAGATC
63 GAAGGCAAAATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGACGCAAGGCTTTTTAGATC
*
25832003 TGCTTCGCTGTTAATACAGGAAGGCAAAATCTGCTATCTTT
128 TGCTTCGCTGTTAACACAGGAAGGCAAAATCTGCTATCTTT
* *
25832044 GACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTTTCGATCTGCTTCGCTGTTAATGCAGGAA
1 AACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTTTCGATCTGCTTCGCTGTTAACGCAGGAA
* * * *
25832109 GGCAAAATCTGCTATCTTTGACTAGCTCCACTGCAACCGATGGACGCAATGCTTTGTTTTCGATT
66 GGCAAAATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGACGCAAGGC--T-TTTTAGATC
* * *
25832174 TGCTTTGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
128 TGCTTCGCTGTTAACACAGGAAGGCAAAATCTGCTATCTTT
* *
25832215 AACCAGCTCCATTACAACCGATAGAGGCAAGGCTTT
1 AACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTT
25832251 GTTTTCGATT
Statistics
Matches: 184, Mismatches: 20, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
168 77 0.42
169 1 0.01
170 1 0.01
171 105 0.57
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (168 bp):
AACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTTTCGATCTGCTTCGCTGTTAACGCAGGAA
GGCAAAATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGACGCAAGGCTTTTTAGATCTGC
TTCGCTGTTAACACAGGAAGGCAAAATCTGCTATCTTT
Found at i:25832261 original size:87 final size:86
Alignment explanation
Indices: 25831874--25832259 Score: 537
Period size: 84 Copynumber: 4.5 Consensus size: 86
25831864 CAAATCTGCA
* * *
25831874 ACCAGCTCTACTGCAACTGATGGAGGCAAGGTTTTATTTTCGATCTGCTTCGCTGTTAACGCAGG
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTT-TTTTCGATCTGCTTCGCTGTTAACGCAGG
* *
25831939 AAGGCAAGATCTGTTATCTTTG
65 AAGGCAAAATCTGCTATCTTTG
* **
25831961 ACCAGCTCCACTGCAACCGATGGAGGCAAGGC--TTTTTAGATCTGCTTCGCTGTTAATACAGGA
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTCGATCTGCTTCGCTGTTAACGCAGGA
25832024 AGGCAAAATCTGCTATCTTTG
66 AGGCAAAATCTGCTATCTTTG
* *
25832045 ACCAGCTCCATTGCAACCGATGGAGGCAAGGC--TTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTCGATCTGCTTCGCTGTTAACGCAGGA
25832108 AGGCAAAATCTGCTATCTTTG
66 AGGCAAAATCTGCTATCTTTG
* * * * *
25832129 ACTAGCTCCACTGCAACCGATGGACGCAATGCTTTGTTTTCGATTTGCTTTGCTGTTAACGCAGG
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTT-TTTTCGATCTGCTTCGCTGTTAACGCAGG
* *
25832194 AAGGCAAGATCTGCTATCTTTA
65 AAGGCAAAATCTGCTATCTTTG
* * *
25832216 ACCAGCTCCATTACAACCGATAGAGGCAAGGCTTTGTTTTCGAT
1 ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTT-TTTTCGAT
25832260 TTTCACTGAT
Statistics
Matches: 270, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
84 155 0.57
85 1 0.00
86 1 0.00
87 113 0.42
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (86 bp):
ACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTCGATCTGCTTCGCTGTTAACGCAGGA
AGGCAAAATCTGCTATCTTTG
Found at i:25833485 original size:7 final size:7
Alignment explanation
Indices: 25833473--25833517 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
25833463 ATTTTTACTC
25833473 TTTCATT
1 TTTCATT
25833480 TTTCATT
1 TTTCATT
25833487 TTTCA-T
1 TTTCATT
*
25833493 TTTCACT
1 TTTCATT
25833500 TTTCATT
1 TTTCATT
25833507 TTTCATCT
1 TTTCAT-T
25833515 TTT
1 TTT
25833518 TTTTTACATC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
6 6 0.17
7 25 0.71
8 4 0.11
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTCATT
Found at i:25833510 original size:14 final size:14
Alignment explanation
Indices: 25833462--25833517 Score: 71
Period size: 14 Copynumber: 4.0 Consensus size: 14
25833452 TTAGCCTCTC
25833462 CATTTTT-ACTCTTT
1 CATTTTTCACT-TTT
*
25833476 CATTTTTCATTTTT
1 CATTTTTCACTTTT
25833490 CA-TTTTCACTTTT
1 CATTTTTCACTTTT
25833503 CATTTTTCATCTTTT
1 CATTTTTCA-CTTTT
25833518 TTTTTACATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.32
14 18 0.49
15 7 0.19
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (14 bp):
CATTTTTCACTTTT
Found at i:25833522 original size:14 final size:14
Alignment explanation
Indices: 25833471--25833528 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 14
25833461 CCATTTTTAC
*
25833471 TCTTTCATTTTTCA
1 TCTTTTATTTTTCA
25833485 T-TTTTCA-TTTTCA
1 TCTTTT-ATTTTTCA
25833498 -CTTTTCATTTTTCA
1 TCTTTT-ATTTTTCA
25833512 TCTTTT-TTTTTACA
1 TCTTTTATTTTT-CA
25833526 TCT
1 TCT
25833529 GTTGTCTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 20 0.53
14 13 0.34
15 5 0.13
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTTATTTTTCA
Found at i:25833522 original size:20 final size:20
Alignment explanation
Indices: 25833473--25833512 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
25833463 ATTTTTACTC
25833473 TTTCATTTTTCATTTTTCAT
1 TTTCATTTTTCATTTTTCAT
*
25833493 TTTCACTTTTCATTTTTCAT
1 TTTCATTTTTCATTTTTCAT
25833513 CTTTTTTTTT
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:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCATTTTTCATTTTTCAT
Found at i:25843033 original size:13 final size:14
Alignment explanation
Indices: 25843010--25843087 Score: 56
Period size: 15 Copynumber: 5.4 Consensus size: 14
25843000 CTAGTTAATC
25843010 TAAACCTTAAACCA
1 TAAACCTTAAACCA
*
25843024 TAAA-CTTAAACCC
1 TAAACCTTAAACCA
25843037 TAAAATCC-TAAACCCA
1 T-AAA-CCTTAAA-CCA
25843053 TAAACCCTT-AACACA
1 TAAA-CCTTAAAC-CA
*
25843068 T-AACCTTTAAACCT
1 TAAACC-TTAAACCA
25843082 TAAACC
1 TAAACC
25843088 CTAGCCTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
13 11 0.22
14 14 0.27
15 21 0.41
16 5 0.10
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:25843084 original size:21 final size:21
Alignment explanation
Indices: 25843010--25843114 Score: 81
Period size: 21 Copynumber: 4.9 Consensus size: 21
25843000 CTAGTTAATC
*
25843010 TAAACCTTAAACCATAAAC-T
1 TAAACCTTAAACCATAACCTT
* **
25843030 TAAACCCTAAAATCC-TAAACCCA
1 TAAA-CCTTAAA-CCAT-AACCTT
25843053 TAAACCCTT-AACACATAACCTT
1 TAAA-CCTTAAAC-CATAACCTT
* *
25843075 TAAACCTTAAACCCTAGCCTT
1 TAAACCTTAAACCATAACCTT
*
25843096 TAAACCATAAACCATAACC
1 TAAACCTTAAACCATAACC
25843115 CCAAACCTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.06
21 35 0.52
22 19 0.28
23 9 0.13
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAACCATAACCTT
Found at i:25843719 original size:114 final size:114
Alignment explanation
Indices: 25843366--25843913 Score: 803
Period size: 114 Copynumber: 4.8 Consensus size: 114
25843356 ATTTTAAATC
* * *
25843366 CCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
* *
25843431 GTTGGGTTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGC
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* *** *
25843480 CCTGAGCATTAGCGGCGCTTTCTTAAAAACACTATTAAATCCCCGAAAGCTCA-AAAAAGGCGTC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
* *
25843544 ATTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAGGA
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * *
25843593 CCTGAACATTAGCGACGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTT
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
*
25843658 GTTGGACTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * * *
25843707 CTTGAGCATTAGCGGTGCTTTCTTAAAAACACCGCTAAATCTCCAAAAGTTCAGAAAACGGCGTC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
* * *
25843772 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGC
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * *
25843821 CCTGAGCATTAGCGGCGCTTTTTTAAAAAAGTCGCTAAATCACCGAAATCTCAGAAAACGGCGTC
1 CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
25843886 GTTGGGCTTAGG-TTTTTTGCGGCGCTTT
66 GTTGGGCTTAGGTTTTTTTGCGGCGCTTT
25843914 TTGAAAAACG
Statistics
Matches: 385, Mismatches: 48, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
113 117 0.30
114 268 0.70
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (114 bp):
CCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
Found at i:25843925 original size:227 final size:227
Alignment explanation
Indices: 25843360--25843913 Score: 822
Period size: 227 Copynumber: 2.4 Consensus size: 227
25843350 TAAATTATTT
* * *
25843360 TAAATCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * *
25843425 GGCATCGTTGGGTTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATT
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATT
* * *
25843490 AGCGGCGCTTTCTTAAAAACACTATTAAATCCCCGAAAGCTCAAAAAAGGCGTCATTGGGCTTAG
131 AGCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCAAAAAAGGCGTCATTGGGCTTAG
25843555 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
196 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * *
25843587 TAAGGACCTGAACATTAGCGACGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * * *
25843652 AGCGTTGTTGGACTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACTTGAGCATT
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATT
* * * * * *
25843717 AGCGGTGCTTTCTTAAAAACACCGCTAAATCTCCAAAAGTTCAGAAAACGGCGTCGTTGGGCTTA
131 AGCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCA-AAAAAGGCGTCATTGGGCTTA
* *
25843782 GGTTTTTTTGCGGCGCTTTCTCAAAAACGTCGC
195 GGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * * *
25843815 TAAAGCCCTGAGCATTAGCGGCGCTTTTTTAAAAAAGTCGCTAAATCACCGAAATCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
25843880 GGCGTCGTTGGGCTTAGG-TTTTTTGCGGCGCTTT
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTT
25843914 TTGAAAAACG
Statistics
Matches: 289, Mismatches: 37, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
227 168 0.58
228 121 0.42
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (227 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCTGAGCATT
AGCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCAAAAAAGGCGTCATTGGGCTTAG
GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:25851010 original size:28 final size:25
Alignment explanation
Indices: 25850978--25851035 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 25
25850968 GACCCTAAGC
25850978 CCAAATATCAAAATCCATACCCATTACA
1 CCAAATAT-AAAAT--ATACCCATTACA
25851006 CC-AA-ATAAAATATACCCATTACA
1 CCAAATATAAAATATACCCATTACA
25851029 CCAAATA
1 CCAAATA
25851036 AAATAACAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
23 14 0.50
24 2 0.07
25 6 0.21
26 2 0.07
27 2 0.07
28 2 0.07
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (25 bp):
CCAAATATAAAATATACCCATTACA
Found at i:25851021 original size:23 final size:23
Alignment explanation
Indices: 25850994--25851040 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
25850984 ATCAAAATCC
25850994 ATACCCATTACACCAAATAAAAT
1 ATACCCATTACACCAAATAAAAT
25851017 ATACCCATTACACCAAATAAAAT
1 ATACCCATTACACCAAATAAAAT
25851040 A
1 A
25851041 ACAGCCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (23 bp):
ATACCCATTACACCAAATAAAAT
Found at i:25860017 original size:46 final size:45
Alignment explanation
Indices: 25859965--25860082 Score: 147
Period size: 40 Copynumber: 2.7 Consensus size: 45
25859955 CCAACCATTA
*
25859965 ATTAACTAAAATGAGTTTAATGAAAATAAAGTCCAACAACTCAATT
1 ATTAACTAAGATGAGTTTAAT-AAAATAAAGTCCAACAACTCAATT
*
25860011 ATTAACTAAGATGAGTTTAAT---AT--AGTCCAGCAACTCAATT
1 ATTAACTAAGATGAGTTTAATAAAATAAAGTCCAACAACTCAATT
* *
25860051 ATTAACTACGATGAGTTTAATTAAATTAAAGT
1 ATTAACTAAGATGAGTTTAA-TAAAATAAAGT
25860083 TCAGCTTGCA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
40 35 0.56
41 1 0.02
42 2 0.03
44 1 0.02
46 23 0.37
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (45 bp):
ATTAACTAAGATGAGTTTAATAAAATAAAGTCCAACAACTCAATT
Found at i:25860925 original size:21 final size:21
Alignment explanation
Indices: 25860872--25860926 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
25860862 CCTGCTCCAG
*
25860872 GTCTTGAGACAAGAGCCTCTT
1 GTCTTGAGACATGAGCCTCTT
25860893 GTCTTGAGACATGAGCCTCTT
1 GTCTTGAGACATGAGCCTCTT
25860914 GTCTTGAGACATG
1 GTCTTGAGACATG
25860927 CAAACATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (21 bp):
GTCTTGAGACATGAGCCTCTT
Found at i:25866927 original size:46 final size:46
Alignment explanation
Indices: 25866811--25866995 Score: 183
Period size: 46 Copynumber: 4.0 Consensus size: 46
25866801 CAGGGATTAA
* * * * * *
25866811 TATTACTGTATTCTCGAGT-TCACAATACATGCAAGAGCTCGAAACC
1 TATTCCTGTATTCTCAAGTCT-GCAACACATGCAGGAGCTCGGAACC
** * * *
25866857 TAAACCTGTATTCTCAAGTCTGCAATACATGCATGAGCTTGGAACC
1 TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
* * * * *
25866903 TATTCCTATATTCTCAAGTTTGCAACATATGTAGGAGCTTGGAACC
1 TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
* * *
25866949 TATTCTTGTATTCTCGAGTCTGCAACATATGCAGGAGCTCGGAACC
1 TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
25866995 T
1 T
25866996 GGGCAAAACT
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
46 115 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (46 bp):
TATTCCTGTATTCTCAAGTCTGCAACACATGCAGGAGCTCGGAACC
Found at i:25879427 original size:50 final size:49
Alignment explanation
Indices: 25879361--25879543 Score: 213
Period size: 51 Copynumber: 3.6 Consensus size: 49
25879351 AAAGTGATGG
* * * * * *
25879361 TCACGTGTGTAGTACTATGTACAAGCTACTACGTTTACCGGAAAGATAGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG-TAGA
* * *
25879411 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGCTTAGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG--TAGA
* *
25879462 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT-A-GA
*
25879513 TCACATGTGTAGTACTATGTGTAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
25879544 TGTGAACCGG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 37 0.33
51 75 0.66
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTAGA
Found at i:25879621 original size:46 final size:43
Alignment explanation
Indices: 25879549--25879647 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
25879539 TACTATGTGA
*
25879549 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
25879592 ACCGGATATCATTGATTACAAAGGGTGGTTGTTATGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
25879638 ACCGTGTATC
1 ACCG-GTATC
25879648 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 27 0.56
47 3 0.06
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:25880510 original size:2 final size:2
Alignment explanation
Indices: 25880503--25880560 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
25880493 GGAAAATTAA
25880503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25880545 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
25880561 GAATGATTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25881676 original size:3 final size:3
Alignment explanation
Indices: 25881668--25881693 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25881658 ATGGAGAAAG
25881668 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
25881694 GTGAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:25883005 original size:20 final size:20
Alignment explanation
Indices: 25882980--25883019 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25882970 CGTAAAATGA
*
25882980 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
25883000 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
25883020 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:25883009 original size:34 final size:35
Alignment explanation
Indices: 25882965--25883031 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
25882955 CAGTAAAATA
*
25882965 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
25882999 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
25883032 CCAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:25883750 original size:111 final size:111
Alignment explanation
Indices: 25883556--25883777 Score: 426
Period size: 111 Copynumber: 2.0 Consensus size: 111
25883546 TGATAAAGTA
*
25883556 TTGTTGTCTAAAAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTATTTTTTCTAAA
1 TTGTTGTCTAAAAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
25883621 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
*
25883667 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
1 TTGTTGTCTAAAAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
25883732 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
25883778 CATGGTATTG
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (111 bp):
TTGTTGTCTAAAAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
Found at i:25886498 original size:10 final size:9
Alignment explanation
Indices: 25886454--25886496 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
25886444 TTTTTTTCTA
25886454 ATTTTTAAT
1 ATTTTTAAT
*
25886463 ATTTTTATT
1 ATTTTTAAT
**
25886472 AAAATTTAAT
1 -ATTTTTAAT
25886482 ATTTTTAAT
1 ATTTTTAAT
25886491 ATTTTT
1 ATTTTT
25886497 TATTGATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 21 0.78
10 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:25886498 original size:19 final size:19
Alignment explanation
Indices: 25886455--25886524 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
25886445 TTTTTTCTAA
* *
25886455 TTTTTAATATTTTTATTAA
1 TTTTTAATATTTTTAATAT
**
25886474 AATTTAATATTTTTAATAT
1 TTTTTAATATTTTTAATAT
*
25886493 TTTTTATTGATTTTT-AT-T
1 TTTTTAAT-ATTTTTAATAT
25886511 TTTTATAAT-TTTTT
1 TTTT-TAATATTTTT
25886525 GCCACATGTC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 25 0.61
20 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (19 bp):
TTTTTAATATTTTTAATAT
Found at i:25886524 original size:17 final size:17
Alignment explanation
Indices: 25886490--25886523 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25886480 ATATTTTTAA
*
25886490 TATTTTTTATTGATTTT
1 TATTTTTTATTAATTTT
25886507 TATTTTTTA-TAATTTT
1 TATTTTTTATTAATTTT
25886523 T
1 T
25886524 TGCCACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTTATTAATTTT
Found at i:25886737 original size:92 final size:88
Alignment explanation
Indices: 25886629--25886861 Score: 229
Period size: 92 Copynumber: 2.6 Consensus size: 88
25886619 GCAAATGACT
* * * * *
25886629 TTTTTAATGTATTTTAACAGTTCAAGTACTCAATTGAGTAAAAAAAATAAAG-CAGGAGTTTAAT
1 TTTTTGATGCATTTTAA-AGTTAAAGTACTCAATTGAGT-AAAAAAATAAAGTAAGG-GCTTAAT
* * *
25886693 TGCTTTTTTTGAAAAAGTTTTGAGGGTC
63 TACTTTTTTGGAAAAAG-TTTGAGAG-C
* *
25886721 TTTTTGATGCATTTTAAAAGTTTAAGTACTCAATTGAGTGTAAAAAAA-AAAGTAATGGCTTAAT
1 TTTTTGATGCATTTT-AAAGTTAAAGTACTCAATTGA--GTAAAAAAATAAAGTAAGGGCTTAAT
*
25886785 TACTTTTTTGGAAATAGTTTGAGAGC
63 TACTTTTTTGGAAAAAGTTTGAGAGC
* * *
25886811 CTTTTGATGCATTTTTAAAGTTAAAGTAAC-CAATTGAATAAGAAAATAAAG
1 TTTTTGATGCA-TTTTAAAGTTAAAGT-ACTCAATTGAGTAAAAAAATAAAG
25886862 ACTTAATTAC
Statistics
Matches: 120, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
88 7 0.06
89 4 0.03
90 28 0.23
91 13 0.11
92 55 0.46
93 11 0.09
94 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (88 bp):
TTTTTGATGCATTTTAAAGTTAAAGTACTCAATTGAGTAAAAAAATAAAGTAAGGGCTTAATTAC
TTTTTTGGAAAAAGTTTGAGAGC
Found at i:25887443 original size:19 final size:20
Alignment explanation
Indices: 25887421--25887461 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
25887411 TATTTTTTGA
25887421 ATTTA-ATATTATTTA-AAAT
1 ATTTATATATT-TTTACAAAT
25887440 ATTTATATATTTTTACAAAT
1 ATTTATATATTTTTACAAAT
25887460 AT
1 AT
25887462 AATGATATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTATATATTTTTACAAAT
Found at i:25893620 original size:17 final size:18
Alignment explanation
Indices: 25893595--25893640 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
25893585 TATAAGAATA
*
25893595 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
25893612 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
25893630 ATTAAATTATA
1 ATTAAATTATA
25893641 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:25893862 original size:44 final size:45
Alignment explanation
Indices: 25893799--25893895 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
25893789 CTATTACACC
* *
25893799 TCCATTTCATTTAACCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* *
25893843 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
25893888 TCCATTAC
1 TCCATTAC
25893896 GCCTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:25893896 original size:16 final size:16
Alignment explanation
Indices: 25893875--25893927 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
25893865 TTGAATTGCT
25893875 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
25893891 ATTACGCCTCTATTCT
1 ATTACGCCTCTATTCC
25893907 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
25893923 ATTAC
1 ATTAC
25893928 AGCGAACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:25903590 original size:34 final size:34
Alignment explanation
Indices: 25903547--25903614 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
25903537 GCATTTTTGA
*
25903547 CACTGTACTGAAATGGGCTAAGGCACAA-ACTGT
1 CACTGTACTGAAAAGGGCTAAGGCACAAGACTGT
* *
25903580 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTAAGGCACAAGACTGT
25903615 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTAAGGCACAAGACTGT
Found at i:25906278 original size:17 final size:17
Alignment explanation
Indices: 25906258--25906290 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25906248 TAATATTTTG
25906258 TATTAATTAAATTCATA
1 TATTAATTAAATTCATA
*
25906275 TATTAATTATATTCAT
1 TATTAATTAAATTCAT
25906291 TCCAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAATTAAATTCATA
Found at i:25906508 original size:135 final size:138
Alignment explanation
Indices: 25906194--25906693 Score: 801
Period size: 138 Copynumber: 3.6 Consensus size: 138
25906184 ATAGAGAAGT
* *
25906194 GAAATTAATTAATATAACTGTTTATATTGATAAATTTGGTAAAATATATACTATTAATATTTTGT
1 GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGT
* * * * *
25906259 ATTAATTAAATTCATATATTAATTATATTCATTCCAAAAGAATATTAATTTTCATATCTTTTATA
66 ATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATA
25906324 TTTTGACC
131 TTTTGACC
*
25906332 GAAATTAA-TACATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTG
1 GAAATTAATTA-ATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTG
* *
25906396 TATGTATCAAATTCATATATTAATTATATTCTTTCC-AAA-AA-ATTAATTTCCACGTCTTTTAT
65 TATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTAT
25906458 ATTTTGACC
130 ATTTTGACC
* * *
25906467 GAAATTAATTAATATAATTGTTTATATTAATAAATTTGGTAATATATATACAGTTAATATTTTGT
1 GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGT
*
25906532 ACGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATA
66 ATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATA
*
25906597 TTTTAACC
131 TTTTGACC
* *
25906605 GAAATTAATTAATTTAACTGTTTACATTAATAAATTTGGTAAAATATATACAATTAATATTTTGT
1 GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGT
*
25906670 ATGAATCAAATTCTTATATTAATT
66 ATGAATCAAATTCATATATTAATT
25906694 TTATATATGT
Statistics
Matches: 332, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
135 118 0.36
136 7 0.02
137 7 0.02
138 200 0.60
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGT
ATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATA
TTTTGACC
Found at i:25906681 original size:273 final size:273
Alignment explanation
Indices: 25906194--25906693 Score: 833
Period size: 273 Copynumber: 1.8 Consensus size: 273
25906184 ATAGAGAAGT
*
25906194 GAAATTAATTAATATAACTGTTTATATTGATAAATTTGGTAAAATATATACTATTAATATTTTGT
1 GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACTATTAATATTTTGT
** * *
25906259 ATTAATTAAATTCATATATTAATTATATTCATTCCAAAAGAATATTAATTTTCATATCTTTTATA
66 ACGAATCAAATTCATATATTAATTATATTCATTCCAAAAGAATATTAATTTCCATATCTTTTATA
* *
25906324 TTTTGACCGAAATTAATACATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAA
131 TTTTAACCGAAATTAATACATATAACTGTTTACATTAATAAATTCGGTAAAATATATACAATTAA
*
25906389 TATTTTGTATGTATCAAATTCATATATTAATTATATTCTTTCCAAAAAATTAATTTCCACGTCTT
196 TATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAAATTAATTTCCACGTCTT
25906454 TTATATTTTGACC
261 TTATATTTTGACC
* *
25906467 GAAATTAATTAATATAATTGTTTATATTAATAAATTTGGTAATATATATAC-AGTTAATATTTTG
1 GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACTA-TTAATATTTTG
* *
25906531 TACGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTAT
65 TACGAATCAAATTCATATATTAATTATATTCATTCCAAAAGAATATTAATTTCCATATCTTTTAT
* *
25906596 ATTTTAACCGAAATTAATTA-ATTTAACTGTTTACATTAATAAATTTGGTAAAATATATACAATT
130 ATTTTAACCGAAATTAA-TACATATAACTGTTTACATTAATAAATTCGGTAAAATATATACAATT
*
25906660 AATATTTTGTATGAATCAAATTCTTATATTAATT
194 AATATTTTGTATGAATCAAATTCATATATTAATT
25906694 TTATATATGT
Statistics
Matches: 210, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
272 1 0.00
273 207 0.99
274 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (273 bp):
GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACTATTAATATTTTGT
ACGAATCAAATTCATATATTAATTATATTCATTCCAAAAGAATATTAATTTCCATATCTTTTATA
TTTTAACCGAAATTAATACATATAACTGTTTACATTAATAAATTCGGTAAAATATATACAATTAA
TATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAAATTAATTTCCACGTCTT
TTATATTTTGACC
Found at i:25930308 original size:7 final size:6
Alignment explanation
Indices: 25930292--25930342 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25930282 TCTTTCCTGC
* *
25930292 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
25930342 A
1 A
25930343 GGAAAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.13
6 22 0.56
7 7 0.18
8 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:25934815 original size:12 final size:12
Alignment explanation
Indices: 25934768--25934863 Score: 59
Period size: 12 Copynumber: 7.4 Consensus size: 12
25934758 TATGAAAAGG
*
25934768 CTTGATGAAAAA
1 CTTGATAAAAAA
*
25934780 CTTTA-AAAAGAA
1 CTTGATAAAA-AA
* *
25934792 CTTGCTACAAAA
1 CTTGATAAAAAA
25934804 CTTGATAAAAAAA
1 CTTGAT-AAAAAA
*
25934817 CTTGGTAATTAAAAA
1 CTT-G--ATAAAAAA
25934832 CTTGATAAAATAA
1 CTTGATAAAA-AA
*
25934845 CTAGATGAAAAATA
1 CTTGAT-AAAAA-A
25934859 CTTGA
1 CTTGA
25934864 AGAAAGAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
11 3 0.05
12 21 0.33
13 19 0.30
14 11 0.17
15 8 0.12
16 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.27
Consensus pattern (12 bp):
CTTGATAAAAAA
Found at i:25934832 original size:15 final size:13
Alignment explanation
Indices: 25934775--25934863 Score: 67
Period size: 13 Copynumber: 6.8 Consensus size: 13
25934765 AGGCTTGATG
25934775 AAAAACTT--TAA
1 AAAAACTTGATAA
*
25934786 AAAGAACTTGCT-A
1 AAA-AACTTGATAA
*
25934799 CAAAACTTGATAA
1 AAAAACTTGATAA
*
25934812 AAAAACTTGGTAA
1 AAAAACTTGATAA
25934825 TTAAAAACTTGATAA
1 --AAAAACTTGATAA
* *
25934840 AATAACTAGATGAA
1 AAAAACTTGAT-AA
*
25934854 AAATACTTGA
1 AAAAACTTGA
25934864 AGAAAGAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
11 3 0.05
12 12 0.20
13 24 0.39
14 10 0.16
15 12 0.20
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (13 bp):
AAAAACTTGATAA
Found at i:25934880 original size:19 final size:19
Alignment explanation
Indices: 25934852--25934889 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25934842 TAACTAGATG
*
25934852 AAAAATACTTGAA-GAAAGA
1 AAAAACACTT-AATGAAAGA
25934871 AAAAACACTTAATGAAAGA
1 AAAAACACTTAATGAAAGA
25934890 CTTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.16
Consensus pattern (19 bp):
AAAAACACTTAATGAAAGA
Found at i:25938127 original size:79 final size:79
Alignment explanation
Indices: 25937976--25938210 Score: 254
Period size: 79 Copynumber: 3.0 Consensus size: 79
25937966 AGCTTAATTG
* * ** * * * * * *
25937976 TTTACAACTTGCATACAATGTTTGGAGAGAACTCGCACTTCACCAATTCGTAGTTCCATCTTAGT
1 TTTACAACTCGCATGCAGCGTTTGGAGACAGCTCACACTTCACCAGTTTGTAGCTCCATCTTAGT
25938041 TCACAAGCTCTCTA
66 TCACAAGCTCTCTA
** * * *
25938055 TTTGTAGCTCTCATGTAGCGTTTGGAGACAGCTCACACTTCACCAGTTTGTAGCTCCATCTTAGT
1 TTTACAACTCGCATGCAGCGTTTGGAGACAGCTCACACTTCACCAGTTTGTAGCTCCATCTTAGT
**
25938120 TTGCAAGCTCTCTA
66 TCACAAGCTCTCTA
* * * * * * *
25938134 TTTACAACTCGCATGCAGTGCTTGGACATAGCTCACACTTCACCAGTTTGTAGCTCCATATCAAT
1 TTTACAACTCGCATGCAGCGTTTGGAGACAGCTCACACTTCACCAGTTTGTAGCTCCATCTTAGT
25938199 TCACAAGCTCTC
66 TCACAAGCTCTC
25938211 CGTTACAACT
Statistics
Matches: 125, Mismatches: 31, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
79 125 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.33
Consensus pattern (79 bp):
TTTACAACTCGCATGCAGCGTTTGGAGACAGCTCACACTTCACCAGTTTGTAGCTCCATCTTAGT
TCACAAGCTCTCTA
Found at i:25938479 original size:13 final size:14
Alignment explanation
Indices: 25938461--25938493 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
25938451 ACGTTCTTAG
*
25938461 CTCGCA-TATACTA
1 CTCGCAGTATACAA
25938474 CTCGCAGTATACAA
1 CTCGCAGTATACAA
25938488 CTCGCA
1 CTCGCA
25938494 AGCAACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.24
Consensus pattern (14 bp):
CTCGCAGTATACAA
Found at i:25942822 original size:30 final size:30
Alignment explanation
Indices: 25942788--25942986 Score: 125
Period size: 30 Copynumber: 6.7 Consensus size: 30
25942778 AGCTGAAGCT
*
25942788 ATCCCTTTTCATTATTTGATGGTCGTCATA
1 ATCCCTTTTCATTATTTGATGGTCGTCACA
* * *
25942818 ATCCCTTTTCATT-GTTGATGGTTGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACA
* * * * *
25942847 ATCCCTTTTCATAATTTGATTGCCG-AAGCT
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CA
* * * * *** *
25942877 ATCCCTTTTCATAATTCGATAGCCAAAACT
1 ATCCCTTTTCATTATTTGATGGTCGTCACA
* * *** *
25942907 ATCCCTTTTCATAATTTGATAG-CCAAAGCT
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CA
* *
25942937 ATCCCTTTTCATTATTCGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACA
*
25942967 ATCCCTTTTCATAATTTGAT
1 ATCCCTTTTCATTATTTGAT
25942987 AGCCAAGGCT
Statistics
Matches: 139, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
29 29 0.21
30 106 0.76
31 4 0.03
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (30 bp):
ATCCCTTTTCATTATTTGATGGTCGTCACA
Found at i:25942850 original size:29 final size:30
Alignment explanation
Indices: 25942788--25942858 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
25942778 AGCTGAAGCT
* *
25942788 ATCCCTTTTCATTATTTGATGGTCGTCATA
1 ATCCCTTTTCATTAGTTGATGGTCGTCACA
* *
25942818 ATCCCTTTTCATT-GTTGATGGTTGTCACC
1 ATCCCTTTTCATTAGTTGATGGTCGTCACA
25942847 ATCCCTTTTCAT
1 ATCCCTTTTCAT
25942859 AATTTGATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (30 bp):
ATCCCTTTTCATTAGTTGATGGTCGTCACA
Found at i:25943001 original size:30 final size:30
Alignment explanation
Indices: 25942847--25943020 Score: 206
Period size: 30 Copynumber: 5.8 Consensus size: 30
25942837 GGTTGTCACC
* *
25942847 ATCCCTTTTCATAATTTGATTGCCGAAGCT
1 ATCCCTTTTCATAATTTGATAGCCAAAGCT
* *
25942877 ATCCCTTTTCATAATTCGATAGCCAAAACT
1 ATCCCTTTTCATAATTTGATAGCCAAAGCT
25942907 ATCCCTTTTCATAATTTGATAGCCAAAGCT
1 ATCCCTTTTCATAATTTGATAGCCAAAGCT
* * * *** *
25942937 ATCCCTTTTCATTATTCGATGGTCGTCA-CC
1 ATCCCTTTTCATAATTTGATAG-CCAAAGCT
*
25942967 ATCCCTTTTCATAATTTGATAGCCAAGGCT
1 ATCCCTTTTCATAATTTGATAGCCAAAGCT
*
25942997 ATCCCTTTTCATTATTTTGATAGC
1 ATCCCTTTTCA-TAATTTGATAGC
25943021 TGAGGATCGT
Statistics
Matches: 119, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
29 1 0.01
30 105 0.88
31 13 0.11
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATAGCCAAAGCT
Found at i:25943009 original size:60 final size:59
Alignment explanation
Indices: 25942818--25943012 Score: 266
Period size: 60 Copynumber: 3.3 Consensus size: 59
25942808 GGTCGTCATA
* * *
25942818 ATCCCTTTTCATTGTT-GATGGTTGTCACCATCCCTTTTCATAATTTGATTGCCGAAGCT
1 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCC-AAGCT
* * * *** *
25942877 ATCCCTTTTCATAATTCGATAGCCAAAACTATCCCTTTTCATAATTTGATAGCCAAAGCT
1 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCC-AAGCT
25942937 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCAAGGCT
1 ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCAA-GCT
25942997 ATCCCTTTTCATTATT
1 ATCCCTTTTCATTATT
25943013 TTGATAGCTG
Statistics
Matches: 116, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
59 16 0.14
60 100 0.86
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (59 bp):
ATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCAAGCT
Found at i:25947461 original size:40 final size:40
Alignment explanation
Indices: 25947411--25947519 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
25947401 AGAGCATTCT
* * *
25947411 TTTCAATAGATTCAGTAGGTATGACTTGAGAGCGCATACA
1 TTTCAGTAGATTCAGTAGGTATGACTCGAAAGCGCATACA
* * * * **
25947451 TTTTAGTAGATTCAGTAAGTATGGCTCGAAAGTGCATATG
1 TTTCAGTAGATTCAGTAGGTATGACTCGAAAGCGCATACA
25947491 TTTCAGTAGATTCAGTAGGTACTG-CTCGA
1 TTTCAGTAGATTCAGTAGGTA-TGACTCGA
25947520 TGATCTCATT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 55 0.96
41 2 0.04
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGACTCGAAAGCGCATACA
Found at i:25951606 original size:27 final size:27
Alignment explanation
Indices: 25951549--25951606 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
25951539 ATTTATCTAT
* * * ***
25951549 TTTTTATTTTAATTTTAATATTCTTTG
1 TTTTTAATTTAATTGTAACATTCTAAA
25951576 TTTTTAATTTAATTGTAACATTCTAAA
1 TTTTTAATTTAATTGTAACATTCTAAA
25951603 TTTT
1 TTTT
25951607 CTTTTGTTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTAATTTAATTGTAACATTCTAAA
Found at i:25955866 original size:23 final size:23
Alignment explanation
Indices: 25955821--25955866 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
25955811 CTTTCTTACT
* *
25955821 GTAGTAACTTTTGGGGTATTACA
1 GTAGTAACTTTTGGGATACTACA
25955844 GTAGTAA-TTTTCGGGATACTACA
1 GTAGTAACTTTT-GGGATACTACA
25955867 TTTCCCTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (23 bp):
GTAGTAACTTTTGGGATACTACA
Found at i:25957458 original size:50 final size:50
Alignment explanation
Indices: 25957340--25957728 Score: 369
Period size: 50 Copynumber: 7.7 Consensus size: 50
25957330 TGATAATAAC
* * ** * * *
25957340 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGT--
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * **
25957388 ACTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* **
25957439 ATGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCAT-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATCG
* * * * *
25957489 ATGCCAACGCCATGTCCCAAACTTGGTCTTACATGAGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * *
25957539 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC-
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
25957588 AGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---G
* *
25957645 ATGCTAATGCCATGTCCCAGACATGGTCTTACACT-GG--CTCACATATCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATATCG
** * * * *
25957693 ATATCGATGCCATATCTCAGATATGGTCTTACATGG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGG
25957729 AAATCACATA
Statistics
Matches: 286, Mismatches: 40, Indels: 30
0.80 0.11 0.08
Matches are distributed among these distances:
47 1 0.00
48 29 0.10
49 39 0.14
50 168 0.59
51 5 0.02
53 3 0.01
54 6 0.02
56 33 0.12
57 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
Found at i:25960528 original size:19 final size:19
Alignment explanation
Indices: 25960497--25960546 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
25960487 CATCCGGAGG
25960497 AAGAAGAAA--AAA-TAAA
1 AAGAAGAAAGGAAATTAAA
*
25960513 AAGAAGACAAGGAAATTAAG
1 AAGAAGA-AAGGAAATTAAA
25960533 AAGAAGAAAGGAAA
1 AAGAAGAAAGGAAA
25960547 ATCGGGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.24
17 2 0.07
19 10 0.34
20 10 0.34
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (19 bp):
AAGAAGAAAGGAAATTAAA
Found at i:25967431 original size:18 final size:17
Alignment explanation
Indices: 25967398--25967436 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
25967388 TTTTATAAAT
25967398 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
25967416 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
25967433 TGTG
1 TGTG
25967437 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:25967777 original size:23 final size:23
Alignment explanation
Indices: 25967663--25967780 Score: 182
Period size: 23 Copynumber: 5.1 Consensus size: 23
25967653 GTGTTATTGA
*
25967663 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
*
25967686 TCAATGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* * *
25967709 TCAATGGTAGCTTCGGGTACATA
1 TCAGTGGTAGCTTCGGCTACATT
*
25967732 TCAGTGGTAGCTTCGACTACATT
1 TCAGTGGTAGCTTCGGCTACATT
25967755 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
25967778 TCA
1 TCA
25967781 ATGTGGCACT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:25971574 original size:13 final size:13
Alignment explanation
Indices: 25971517--25971633 Score: 55
Period size: 13 Copynumber: 8.8 Consensus size: 13
25971507 TCCATTAAAC
*
25971517 ATTTCATATAA-C
1 ATTTCATATAATT
*
25971529 ACTTCATATAATT
1 ATTTCATATAATT
**
25971542 ATTTCCATATAACCG
1 ATTT-CATATAA-TT
25971557 A-TTCATATAATT
1 ATTTCATATAATT
*
25971569 ATTTCAT-TTATCT
1 ATTTCATATAAT-T
* *
25971582 ATTTCCGTATAACTG
1 ATTT-CATATAA-TT
*
25971597 A-TTCATATAATC
1 ATTTCATATAATT
*
25971609 ATTTCGTAT-ATCT
1 ATTTCATATAAT-T
25971622 ATTTCTATATAA
1 ATTTC-ATATAA
25971634 CCAATTCTTA
Statistics
Matches: 77, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
12 18 0.23
13 37 0.48
14 16 0.21
15 5 0.06
16 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.46
Consensus pattern (13 bp):
ATTTCATATAATT
Found at i:25971585 original size:40 final size:40
Alignment explanation
Indices: 25971519--25971654 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
25971509 CATTAAACAT
*
25971519 TTCATATAA-CACTTCATATAAT-TATTTCCATATAACCGA
1 TTCATATAATCATTTCATAT-ATCTATTTCCATATAACCGA
* * * *
25971558 TTCATATAATTATTTCATTTATCTATTTCCGTATAACTGA
1 TTCATATAATCATTTCATATATCTATTTCCATATAACCGA
* * *
25971598 TTCATATAATCATTTCGTATATCTATTTCTATATAACCAA
1 TTCATATAATCATTTCATATATCTATTTCCATATAACCGA
* *
25971638 TTCTTATGATCATTTCA
1 TTCATATAATCATTTCA
25971655 CATAACCAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
39 11 0.14
40 69 0.86
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.46
Consensus pattern (40 bp):
TTCATATAATCATTTCATATATCTATTTCCATATAACCGA
Found at i:25971660 original size:26 final size:26
Alignment explanation
Indices: 25971630--25971680 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
25971620 CTATTTCTAT
* * *
25971630 ATAACCAATTCTTATGATCATTTCAC
1 ATAACCAATTCATATAACCATTTCAC
25971656 ATAACCAATTCATATAACCATTTCA
1 ATAACCAATTCATATAACCATTTCA
25971681 AAGTGTTAAC
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:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (26 bp):
ATAACCAATTCATATAACCATTTCAC
Found at i:25971672 original size:13 final size:13
Alignment explanation
Indices: 25971628--25971680 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
25971618 ATCTATTTCT
25971628 ATATAACCAATTC
1 ATATAACCAATTC
* * * *
25971641 TTATGATCATTTC
1 ATATAACCAATTC
*
25971654 ACATAACCAATTC
1 ATATAACCAATTC
*
25971667 ATATAACCATTTC
1 ATATAACCAATTC
25971680 A
1 A
25971681 AAGTGTTAAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.36
Consensus pattern (13 bp):
ATATAACCAATTC
Found at i:25971779 original size:15 final size:14
Alignment explanation
Indices: 25971748--25971787 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
25971738 ATGGATATTC
25971748 AGAATTC-ATA-AA
1 AGAATTCAATATAA
25971760 AGAATTCAATATACA
1 AGAATTCAATATA-A
25971775 AGAATTCAATATA
1 AGAATTCAATATA
25971788 TAGAGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 3 0.12
14 1 0.04
15 14 0.56
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (14 bp):
AGAATTCAATATAA
Found at i:25973994 original size:126 final size:122
Alignment explanation
Indices: 25973834--25974185 Score: 472
Period size: 126 Copynumber: 2.8 Consensus size: 122
25973824 TAATTTCGAG
* ** * *
25973834 TTGACGTTTTTGATAAAATAATATAAAATCGCTTCTAGCAGGATGGTATTTGAGAAGATTTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
25973899 AAATCGTGCCATCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCG-GCC-TCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAAT-ATT-TTTTT
* *
25973960 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAAAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * *
25974025 AAATTGCGGCCTCGT-CAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTT
66 AAA-T-CGGCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATATTTTTTT
* * ** *
25974084 TTGACGATTCTGAGCAAATAATATAAGATCATTTCTACCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
25974149 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCG-G-CCTCGTGGACGCGCTTTTGCTACAGTAG
25974186 CATGTTTGGG
Statistics
Matches: 201, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
122 2 0.01
123 2 0.01
124 90 0.45
125 5 0.02
126 96 0.48
127 4 0.02
128 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (122 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATATTTTTTT
Found at i:25974145 original size:124 final size:126
Alignment explanation
Indices: 25973849--25974185 Score: 477
Period size: 124 Copynumber: 2.7 Consensus size: 126
25973839 GTTTTTGATA
* *
25973849 AAATAATATAAAATCGCTTCTAGCAGGATGGTATTTGAGAAGATTTTGTGAAA-T-CGTGCCATC
1 AAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTGCG-GCC-TC
*
25973912 GTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGC
64 GTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGATTCTGAGC
* *
25973975 AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAAAATTTGTGAAATTGCGGCCTCGT
1 AAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTGCGGCCTCGT
* * *
25974040 -CAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAAT-ATT-TTTTTTTGACGATTCTGAGC
66 GGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGATTCTGAGC
* ** * * *
25974099 AAATAATATAAGATCATTTCTACCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGT
1 AAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTGCGGCCTCGT
*
25974164 GGACGCGATTTTGCTACAGTAG
66 GGACGCGCTTTTGCTACAGTAG
25974186 CATGTTTGGG
Statistics
Matches: 189, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
124 94 0.50
125 5 0.03
126 84 0.44
127 4 0.02
128 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (126 bp):
AAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTGCGGCCTCGT
GGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGATTCTGAGC
Found at i:25977418 original size:116 final size:116
Alignment explanation
Indices: 25977214--25977430 Score: 380
Period size: 116 Copynumber: 1.9 Consensus size: 116
25977204 TGATAAATTG
* * *
25977214 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTGTTAAATTATATACAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
25977279 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTGTGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTGTGTGAATGTAAAAT
* * *
25977330 TATTAAGTCAAAAAATTGTATTAATGTTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
25977395 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATT
25977431 ACGTTAAGGT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 95 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTGTGTGAATGTAAAAT
Found at i:25977456 original size:20 final size:22
Alignment explanation
Indices: 25977428--25977473 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
25977418 CAAATCTAAC
*
25977428 ATTACGTTAA-GG-TTAGGGTT
1 ATTAAGTTAAGGGTTTAGGGTT
25977448 ATTAAGTTAAGGGTTTAGGGTT
1 ATTAAGTTAAGGGTTTAGGGTT
25977470 -TTAA
1 ATTAA
25977474 TTGAATTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 6 0.26
22 8 0.35
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.41
Consensus pattern (22 bp):
ATTAAGTTAAGGGTTTAGGGTT
Found at i:25977511 original size:20 final size:21
Alignment explanation
Indices: 25977486--25977527 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
25977476 GAATTAGCTT
*
25977486 AGGG-TTAGGGTTTTTAATTA
1 AGGGTTTAAGGTTTTTAATTA
25977506 AGGGTTTAAGGTTTTTAATTA
1 AGGGTTTAAGGTTTTTAATTA
25977527 A
1 A
25977528 ATTAAGTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (21 bp):
AGGGTTTAAGGTTTTTAATTA
Found at i:25977538 original size:50 final size:50
Alignment explanation
Indices: 25977428--25977538 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
25977418 CAAATCTAAC
* * *
25977428 ATTACGTTAAGGTTAGGGTTATTAAGTTAAGGGTTTAGGGTTTTAATTGA
1 ATTAAGTTAGGGTTAGGGTTATTAAGTTAAGGGTTTAGGGTTTTAATTAA
* *
25977478 ATT-AGCTTAGGGTTAGGGTTTTTAA-TTAAGGGTTTAAGGTTTTTAATTAA
1 ATTAAG-TTAGGGTTAGGGTTATTAAGTTAAGGGTTT-AGGGTTTTAATTAA
25977528 ATTAAGTTAGG
1 ATTAAGTTAGG
25977539 TTTTTAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
49 11 0.21
50 40 0.75
51 2 0.04
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (50 bp):
ATTAAGTTAGGGTTAGGGTTATTAAGTTAAGGGTTTAGGGTTTTAATTAA
Found at i:25977630 original size:23 final size:23
Alignment explanation
Indices: 25977488--25977981 Score: 445
Period size: 23 Copynumber: 20.6 Consensus size: 23
25977478 ATTAGCTTAG
*
25977488 GGTTAGGGTTTTTAATT-AA--G
1 GGTTAGGGTTTTTAATTAAATTA
*
25977508 GGTTTAAGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTA
*
25977532 AGTTA-GGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
25977554 GGTTAGGCTATGGTTTTTAATCAAATTA
1 GGTTA-G----GGTTTTTAATTAAATTA
*
25977582 --TTAGGGTTTTTAAGTT-AA--G
1 GGTTAGGGTTTTTAA-TTAAATTA
25977601 GGTTTAGGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTA
25977625 GGTTAGGCTAGGGTTTTTAATTAAATTA
1 GG-T----TAGGGTTTTTAATTAAATTA
* ** *
25977653 GATTAGGGTTTTTGGTACAAATTA
1 GGTTAGGGTTTTTAAT-TAAATTA
* *
25977677 GGTTAGGATTTTAAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
25977700 GGTTAGGCTAGGGTTTTTAATTAAATTA
1 GG-T----TAGGGTTTTTAATTAAATTA
*
25977728 GGTTAGGGTTTTTAAGT---TTA
1 GGTTAGGGTTTTTAATTAAATTA
25977748 GGGTTTAGGGTTTTTAATTAAATTA
1 -GG-TTAGGGTTTTTAATTAAATTA
*
25977773 GGTTAGGTTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
25977796 GGTTAGGCTAGGGTTTTTAATTAAATTA
1 GG-T----TAGGGTTTTTAATTAAATTA
*
25977824 GGTTAGAGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
** *
25977847 GGTTAGGGTTTTTGGTACAAATTA
1 GGTTAGGGTTTTTAAT-TAAATTA
25977871 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
25977894 GGTTAGGCTAGGGTTTTTAATTAAATTA
1 GG-T----TAGGGTTTTTAATTAAATTA
25977922 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
25977945 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
* *
25977968 GGCTAAGGTTTTTA
1 GGTTAGGGTTTTTA
25977982 TTACATCAAA
Statistics
Matches: 397, Mismatches: 34, Indels: 83
0.77 0.07 0.16
Matches are distributed among these distances:
20 5 0.01
21 29 0.07
22 53 0.13
23 152 0.38
24 47 0.12
25 4 0.01
26 3 0.01
27 4 0.01
28 100 0.25
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:25977705 original size:75 final size:70
Alignment explanation
Indices: 25977462--25977981 Score: 335
Period size: 75 Copynumber: 7.2 Consensus size: 70
25977452 AGTTAAGGGT
* * * * ** * *
25977462 TTAGGGTTTTAATTGAATTAGCTTAGGGTTAGGGTTTTTAATT-AA-GGGTTTAAGGTTTTTAAT
1 TTAGGTTTTTAATTAAATTAGGTTA-GGCTAGGGTTTTTAATTAAATTAGATT-AGGGTTTT--T
*
25977525 TAAATTAAG
62 TAAATTAGG
* * *
25977534 TTAGGTTTTTAATTAAATTAGGTTAGGCTATGGTTTTTAATCAAATT--ATTAGGG-TTTTTAAG
1 TTAGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTTAAA
25977596 TTAAGGG
66 TT-A-GG
25977603 TTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTGG
1 -TTA-GGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTT--
25977668 TACAAATTAGG
62 T--AAATTAGG
* *
25977679 TTAGGATTTTAAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTTTAA
1 TTAGG-TTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTTAA
*
25977743 GTTTAGGG
65 -ATTA-GG
*
25977751 TTTAGGGTTTTTAATTAAATTAGGTTAGG-T----TTTTTAATTAAATTAGGTTAGGCTAGGGTT
1 -TTA-GGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTA-G--A--TTAGGG-T
25977811 TTTAATTAAATTAGG
58 TTT--TTAAATTAGG
** * *
25977826 TTAGAGTTTTTAATTAAATTAGG-T----TAGGGTTTTTGGTACAAATTAGGTTAGGGTTTTTAA
1 TTAG-GTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAAT-TAAATTAGATTAGGG-TTTT--
25977886 TTAAATTAGG
61 TTAAATTAGG
*
25977896 TTAGGCTAGGGTTTTTAATTAAATTAGG-T----TAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 -T----TA-GGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGG-TT
25977956 TTAATTAAATTAGG
59 TT--TTAAATTAGG
*
25977970 CTAAGGTTTTTA
1 -TTAGGTTTTTA
25977982 TTACATCAAA
Statistics
Matches: 378, Mismatches: 31, Indels: 81
0.77 0.06 0.17
Matches are distributed among these distances:
67 6 0.02
68 16 0.04
69 13 0.03
70 32 0.08
71 62 0.16
72 28 0.07
73 38 0.10
74 72 0.19
75 95 0.25
76 7 0.02
77 5 0.01
78 4 0.01
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (70 bp):
TTAGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTTAAA
TTAGG
Found at i:25977742 original size:98 final size:98
Alignment explanation
Indices: 25977605--25977957 Score: 534
Period size: 98 Copynumber: 3.6 Consensus size: 98
25977595 GTTAAGGGTT
*
25977605 TAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTGGTA
1 TAGGGTTTTTAATTAAATTAGG-T----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTGGTA
*
25977670 CAAATTAGGTTAGGATTTTAAATTAAATTAGGTTAGGC
61 CAAATTAGGTTAGGATTTTTAATTAAATTAGGTTAGGC
* ** *
25977708 TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGT---TTAGGGTTTAGGGTTTTTAAT-TAA
1 TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTA-GG-TTAGGGTTTTTGGTACAA
*
25977769 ATTAGGTTAGGTTTTTTAATTAAATTAGGTTAGGC
64 ATTAGGTTAGGATTTTTAATTAAATTAGGTTAGGC
*
25977804 TAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTGGTACAAAT
1 TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTGGTACAAAT
*
25977869 TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGC
66 TAGGTTAGGATTTTTAATTAAATTAGGTTAGGC
25977902 TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTT
1 TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTT
25977958 AATTAAATTA
Statistics
Matches: 230, Mismatches: 14, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
95 3 0.01
96 71 0.31
97 24 0.10
98 106 0.46
99 3 0.01
102 1 0.00
103 22 0.10
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46
Consensus pattern (98 bp):
TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTGGTACAAAT
TAGGTTAGGATTTTTAATTAAATTAGGTTAGGC
Found at i:25977857 original size:194 final size:197
Alignment explanation
Indices: 25977605--25977980 Score: 618
Period size: 194 Copynumber: 1.9 Consensus size: 197
25977595 GTTAAGGGTT
25977605 TAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTGGTA
1 TAGGGTTTTTAATTAAATTAGGTTAGGC-A-GGTTTTTAATTAAATTAGATTAGGGTTTTTGGTA
25977670 CAAATTAGGTTAGGATTTTAAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGG
64 CAAATTAGGTTAGGATTTTAAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGG
*
25977735 GTTTTTAAGT-TTAGGGTTTAGGGTTTTTAATTAAATTAGG-TTAGGTTTTTTAATTAAATTAGG
129 GTTTTTAAGTATTA-GG-TTAGGGTTTTTAATTAAATTAGGCTAAGGTTTTTTAATTAAATTAGG
25977798 TTAGGC
192 TTAGGC
*
25977804 TAGGGTTTTTAATTAAATTAGGTTA-G-A-GTTTTTAATTAAATTAGGTTAGGGTTTTTGGTACA
1 TAGGGTTTTTAATTAAATTAGGTTAGGCAGGTTTTTAATTAAATTAGATTAGGGTTTTTGGTACA
* *
25977866 AATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGT
66 AATTAGGTTAGGATTTTAAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
25977931 TTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAAGGTTTTT
131 TTTTAAGT--ATTAGGTTAGGGTTTTTAATTAAATTAGGCTAAGGTTTTT
25977981 ATTACATCAA
Statistics
Matches: 168, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
194 104 0.62
195 23 0.14
196 12 0.07
197 3 0.02
198 1 0.01
199 25 0.15
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (197 bp):
TAGGGTTTTTAATTAAATTAGGTTAGGCAGGTTTTTAATTAAATTAGATTAGGGTTTTTGGTACA
AATTAGGTTAGGATTTTAAATTAAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGT
TTTTAAGTATTAGGTTAGGGTTTTTAATTAAATTAGGCTAAGGTTTTTTAATTAAATTAGGTTAG
GC
Found at i:25978061 original size:43 final size:45
Alignment explanation
Indices: 25977987--25978072 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
25977977 TTTTATTACA
*
25977987 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
*
25978032 TCAAA-AAATTTCTATTTT-TTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
25978073 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:25978517 original size:18 final size:18
Alignment explanation
Indices: 25978494--25978528 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25978484 TGGAAAAGGA
*
25978494 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
25978512 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
25978529 AACCGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:25979181 original size:7 final size:7
Alignment explanation
Indices: 25979171--25979195 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25979161 ATACATACAT
25979171 AATACTA
1 AATACTA
25979178 AATACTA
1 AATACTA
25979185 AATACTA
1 AATACTA
25979192 AATA
1 AATA
25979196 TCAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:25980424 original size:51 final size:51
Alignment explanation
Indices: 25980332--25980455 Score: 196
Period size: 51 Copynumber: 2.4 Consensus size: 51
25980322 TATTTTAAAA
* * * *
25980332 AAGGAAATTGAGAAGAAATTTAAAATTAAATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAGGAAA-TTGAAATTAAATATAGATTTGAGAGAATTTTGG
25980384 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
25980435 AAGGAAATTGAGAGG-AATTGA
1 AAGGAAATTGAGAGGAAATTGA
25980456 GAGGAAATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 6 0.09
51 45 0.66
52 17 0.25
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
Found at i:25980470 original size:12 final size:11
Alignment explanation
Indices: 25980436--25980470 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
25980426 GAATTTTGGA
25980436 AGGAAATTGAG
1 AGGAAATTGAG
25980447 AGG-AATTGAG
1 AGGAAATTGAG
25980457 AGGAAATATGAG
1 AGGAAAT-TGAG
25980469 AG
1 AG
25980471 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:25981184 original size:19 final size:18
Alignment explanation
Indices: 25981151--25981188 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
25981141 TTCATGTTAT
*
25981151 AATTTTAATTTAATAATA
1 AATTTTAAATTAATAATA
25981169 AATTTTAAAATTAATAATA
1 AATTTT-AAATTAATAATA
25981188 A
1 A
25981189 TTTGAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTTAAATTAATAATA
Found at i:25981190 original size:18 final size:17
Alignment explanation
Indices: 25981149--25981191 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
25981139 ATTTCATGTT
*
25981149 ATAATTTTAATTTAATA
1 ATAATTTTAAATTAATA
25981166 ATAAATTTTAAAATTAATA
1 AT-AATTTT-AAATTAATA
25981185 ATAATTT
1 ATAATTT
25981192 GAGAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 11 0.48
19 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTTAAATTAATA
Found at i:25981198 original size:18 final size:19
Alignment explanation
Indices: 25981160--25981198 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
25981150 TAATTTTAAT
*
25981160 TTAATAATAAATTTTAAAA
1 TTAATAATAAATTTGAAAA
*
25981179 TTAATAAT-AATTTGAGAA
1 TTAATAATAAATTTGAAAA
25981197 TT
1 TT
25981199 TAAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TTAATAATAAATTTGAAAA
Found at i:25981201 original size:19 final size:18
Alignment explanation
Indices: 25981157--25981207 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
25981147 TTATAATTTT
*
25981157 AATTTAATAATAAATTTTA
1 AATTTAATAAT-AATTTGA
*
25981176 AAATTAATAATAATTTGA
1 AATTTAATAATAATTTGA
25981194 GAATTTAAATAATA
1 -AATTT-AATAATA
25981208 TTCCTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.22
19 14 0.52
20 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
AATTTAATAATAATTTGA
Found at i:25981616 original size:26 final size:26
Alignment explanation
Indices: 25981582--25981666 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
25981572 CAACAACTTT
*
25981582 CAAACAATGAATTCAATAAAATTTAC
1 CAAATAATGAATTCAATAAAATTTAC
* * *
25981608 CAAATAATGGA--GAAT-AAATTTGGAT
1 CAAATAATGAATTCAATAAAATTT--AC
* *
25981633 GAAGT-ATGAATTCAATAAAATTTAC
1 CAAATAATGAATTCAATAAAATTTAC
25981658 CAAATAATG
1 CAAATAATG
25981667 GAGAATAAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
23 6 0.14
24 7 0.17
25 8 0.19
26 15 0.36
27 6 0.14
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (26 bp):
CAAATAATGAATTCAATAAAATTTAC
Found at i:25981646 original size:50 final size:50
Alignment explanation
Indices: 25981588--25981687 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
25981578 CTTTCAAACA
25981588 ATGAATTCAATAAAATTTACCAAATAATGGAGAATAAATTTGGATGAAGT
1 ATGAATTCAATAAAATTTACCAAATAATGGAGAATAAATTTGGATGAAGT
25981638 ATGAATTCAATAAAATTTACCAAATAATGGAGAATAAATTTGGATGAAGT
1 ATGAATTCAATAAAATTTACCAAATAATGGAGAATAAATTTGGATGAAGT
25981688 CATCCAAACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (50 bp):
ATGAATTCAATAAAATTTACCAAATAATGGAGAATAAATTTGGATGAAGT
Found at i:25981678 original size:23 final size:23
Alignment explanation
Indices: 25981600--25981678 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
25981590 GAATTCAATA
25981600 AAATTTACCAAATAATGGAGAAT
1 AAATTTACCAAATAATGGAGAAT
** * * *
25981623 AAATTTGGATGAAGT-ATGAATTCAAT
1 AAATTT--ACCAAATAATGGA--GAAT
25981649 AAAATTTACCAAATAATGGAGAAT
1 -AAATTTACCAAATAATGGAGAAT
25981673 AAATTT
1 AAATTT
25981679 GGATGAAGTC
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 12 0.30
24 7 0.17
25 8 0.20
26 7 0.17
27 6 0.15
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.30
Consensus pattern (23 bp):
AAATTTACCAAATAATGGAGAAT
Found at i:25983180 original size:50 final size:50
Alignment explanation
Indices: 25983101--25983337 Score: 224
Period size: 50 Copynumber: 4.7 Consensus size: 50
25983091 GTGATGTTGC
** * *
25983101 TAGGTCATGTGTGTAGTACTATGTACAGGCTACTACGTATATCGAAAGGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAAGGA
** * *
25983151 TAGGTCGTATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CCAGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGA-AAGGA
* * * * * **
25983201 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAAAGGA
* * * *** *
25983252 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGTTGAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAAGGA
* *
25983302 AATGGTCAAATGTGTAGTACTATGTGCAGGCTACTA
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTA
25983338 TGTGAACCGG
Statistics
Matches: 153, Mismatches: 30, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
49 2 0.01
50 82 0.54
51 68 0.44
52 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAAGGA
Found at i:25983285 original size:51 final size:49
Alignment explanation
Indices: 25983110--25983347 Score: 219
Period size: 51 Copynumber: 4.7 Consensus size: 49
25983100 CTAGGTCATG
* * * * **
25983110 TGTGTAGTACTATGTACAGGCTACTACGTATATC-GAAAGGATAGGTCGTA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAT-GGTCACA
* *
25983160 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAT-GGTCACA
* * * * *
25983210 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-AT-GGTCACA
* * * *
25983261 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGTTGAAAATGGTCAAA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT--AGATGGTCACA
* *
25983312 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
25983348 GTATCATTTA
Statistics
Matches: 158, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
50 77 0.49
51 79 0.50
52 1 0.01
53 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGATGGTCACA
Found at i:25983347 original size:102 final size:101
Alignment explanation
Indices: 25983160--25983347 Score: 279
Period size: 102 Copynumber: 1.9 Consensus size: 101
25983150 ATAGGTCGTA
* **
25983160 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTATGT
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAAAGGTCAAATGTGTAGTACTATGT
*
25983225 GCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
66 GCAGGCTACTATGCGAACCGGATAGCTTCGATCACG
* **
25983261 TGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GGTTGAAAATGGTCAAATGTGTAGTACTAT
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATG-AAA-GGTCAAATGTGTAGTACTAT
*
25983325 GTGCAGGCTACTATGTGAACCGG
64 GTGCAGGCTACTATGCGAACCGG
25983348 GTATCATTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 3 0.04
101 35 0.45
102 39 0.51
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (101 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAAAGGTCAAATGTGTAGTACTATGT
GCAGGCTACTATGCGAACCGGATAGCTTCGATCACG
Found at i:25989754 original size:2 final size:2
Alignment explanation
Indices: 25989747--25989773 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25989737 CTCGACATTC
25989747 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 T
25989774 TGAACTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25994493 original size:44 final size:44
Alignment explanation
Indices: 25994410--25994500 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
25994400 CTAGTTGTCG
*
25994410 CCAACCACCACAGGACCTTCGCCGACCACCACCGTCTGCCCCTA
1 CCAACCACCACAGGACCTTCGCCGACCACCACCGCCTGCCCCTA
** **
25994454 CCAACCACCACAGGACCTTCGCCGACCGTCGTCGCCTGCCCCTA
1 CCAACCACCACAGGACCTTCGCCGACCACCACCGCCTGCCCCTA
25994498 CCA
1 CCA
25994501 TCAATCACCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.21, C:0.52, G:0.15, T:0.12
Consensus pattern (44 bp):
CCAACCACCACAGGACCTTCGCCGACCACCACCGCCTGCCCCTA
Found at i:25995264 original size:19 final size:19
Alignment explanation
Indices: 25995230--25995268 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
25995220 GGTAGAATTG
*
25995230 TTATTCTTAGAAAATAGAAT
1 TTATACTTAGAAAATA-AAT
25995250 TTATACTTA-AAAATAAAT
1 TTATACTTAGAAAATAAAT
25995268 T
1 T
25995269 CTCACTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATACTTAGAAAATAAAT
Found at i:26001106 original size:14 final size:15
Alignment explanation
Indices: 26001081--26001113 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
26001071 AAACTAAAAA
26001081 AAATTCGAGTTAATC
1 AAATTCGAGTTAATC
*
26001096 AAATT-GAGTTATTC
1 AAATTCGAGTTAATC
26001110 AAAT
1 AAAT
26001114 CATTCGAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (15 bp):
AAATTCGAGTTAATC
Found at i:26001297 original size:20 final size:18
Alignment explanation
Indices: 26001273--26001332 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
26001263 AATTAGAAAA
*
26001273 AAAATTTAAAATAATTTT
1 AAAATTCAAAATAATTTT
*
26001291 CATAAATTCAAAACAATTTT
1 -A-AAATTCAAAATAATTTT
26001311 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTT-T
26001329 AAAA
1 AAAA
26001333 ATTTCAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.11
18 15 0.42
19 2 0.06
20 15 0.42
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTCAAAATAATTTT
Found at i:26001332 original size:18 final size:18
Alignment explanation
Indices: 26001273--26001321 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
26001263 AATTAGAAAA
* *
26001273 AAAATTTAAAATAATTTT
1 AAAATTCAAAACAATTTT
26001291 CATAAATTCAAAACAATTTT
1 -A-AAATTCAAAACAATTTT
26001311 AAAATTCAAAA
1 AAAATTCAAAA
26001322 TATTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 10 0.37
19 2 0.07
20 15 0.56
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTCAAAACAATTTT
Found at i:26011230 original size:18 final size:18
Alignment explanation
Indices: 26011207--26011241 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
26011197 TTATTTTATT
26011207 TTATTTTT-TAATATTTAG
1 TTATTTTTGTAAT-TTTAG
26011225 TTATTTTTGTAATTTTA
1 TTATTTTTGTAATTTTA
26011242 TCATATCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTATTTTTGTAATTTTAG
Found at i:26012695 original size:20 final size:21
Alignment explanation
Indices: 26012657--26012695 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
26012647 TGCCCACGTA
**
26012657 ATAATGACAAAAATCAATAAC
1 ATAATGACAAAAAAAAATAAC
26012678 ATAA-GACAAAAAAAAATA
1 ATAATGACAAAAAAAAATA
26012696 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.15
Consensus pattern (21 bp):
ATAATGACAAAAAAAAATAAC
Found at i:26020321 original size:15 final size:15
Alignment explanation
Indices: 26020301--26020330 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26020291 CATCGTTAGG
*
26020301 CTTTCTCCCCTATCA
1 CTTTCTCCCCCATCA
26020316 CTTTCTCCCCCATCA
1 CTTTCTCCCCCATCA
26020331 ATTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.50, G:0.00, T:0.37
Consensus pattern (15 bp):
CTTTCTCCCCCATCA
Found at i:26023435 original size:16 final size:17
Alignment explanation
Indices: 26023409--26023442 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
26023399 TTTATTGTAT
*
26023409 TTAAGTTTTGTTTAAAA
1 TTAAGTTTTGTTAAAAA
26023426 TTAA-TTTTGTTAAAAA
1 TTAAGTTTTGTTAAAAA
26023442 T
1 T
26023443 AATATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
TTAAGTTTTGTTAAAAA
Found at i:26024555 original size:20 final size:20
Alignment explanation
Indices: 26024530--26024569 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
26024520 CGTAAAATAA
*
26024530 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
26024550 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
26024570 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:26024559 original size:34 final size:35
Alignment explanation
Indices: 26024515--26024581 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
26024505 CAGTAAAATA
*
26024515 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
26024549 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
26024582 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Done.