Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 38 of 125
Found at i:11431087 original size:14 final size:14
Alignment explanation
Indices: 11431068--11431097 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11431058 AGTAAATATG
11431068 TATATGCGTGTATA
1 TATATGCGTGTATA
*
11431082 TATATGTGTGTATA
1 TATATGCGTGTATA
11431096 TA
1 TA
11431098 GATGTGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (14 bp):
TATATGCGTGTATA
Found at i:11432196 original size:42 final size:42
Alignment explanation
Indices: 11432139--11433173 Score: 1070
Period size: 42 Copynumber: 25.4 Consensus size: 42
11432129 TCTTGATTAA
* * *
11432139 GGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
11432181 AGGTAAGAGATTGGATG--G-CTTCAATCTGCCCCATGATTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
11432220 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
11432262 GGGTAAGAGATTGGCTGGTAG-CTTCAATCTACCCTATGATCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* * **
11432304 GGGTAAGAGATTGGATGATGTCTTCAATCCGCCCTACAATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
11432346 AGGTAAGAAATTGGAT-ATTATCTTCAATCTACCCCATGATCG
1 GGGTAAGAGATTGGATGA-TGTCTTCAATCTGCCCCATGATCG
* * * *
11432388 AGTTAAGAGATTGGATGATGTCTTCATTCTGCCTCAT-ATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
11432429 GGGTAAGAGATTGGATG--GT-TTCAATCTGCCCCATGGTTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
11432468 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
11432510 GGGTAAAAGATTAGATGATAG-CTTCAATCTGCCCCAT-AGTCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGA-TCG
* *
11432552 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCACGATTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
*
11432594 TGGTAAGAGATTGGAT-ATTGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGA-TGTCTTCAATCTGCCCCATGATCG
* * * *
11432636 AGGTAAGTGATTGGATGATGTCTTCAATCTGCCTCATGATCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
11432678 GGGTAAGAGATTAGATGA--T-TTCAATCTGCCCTATGGTTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
11432717 GGGTAAGAGATTGGATGATATCTTCAAT-TAGCCTCATGATCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCT-GCCCCATGATCG
* * * *
11432759 GGGTAAGAGATGGGATG--GT-TTCAATCTACTCCATGGTCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * * *
11432798 GGATAGGAGATTGGATGATGTCTTCAATCTACCCCATGTTTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
*
11432840 GGGTAAGAGATTGGATG--G-CTTCAATCTACCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
11432879 GGGTAAGTA-ATTGGATGATGTCTTCAATCTACCACATGATCG
1 GGGTAAG-AGATTGGATGATGTCTTCAATCTGCCCCATGATCG
*
11432921 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCACATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
11432963 AGGTAAGAGATTGGATG--GT-TTCAATCTGCCCTATGATCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * * **
11433002 AGGTATGAGATT-GATG-TGTCTTTAATCTGCCTTC-TGATTA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCC-CCATGATCG
* * * *
11433042 GGTTAAAAGATT---TGACGT-TTCAATCTGCCCCATGATCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* ** **
11433080 GGGTATGAGATTGG-TG-TGTCTTCAATCTGCCCTTTGATTA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
*
11433120 GGGTAAAAGATT-G--GATG-CTTCAATCTG-CCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
*
11433157 GGGTATGAGATTGGATG
1 GGGTAAGAGATTGGATG
11433174 GTAGCTTCGC
Statistics
Matches: 836, Mismatches: 115, Indels: 86
0.81 0.11 0.08
Matches are distributed among these distances:
37 17 0.02
38 55 0.07
39 187 0.22
40 61 0.07
41 33 0.04
42 478 0.57
43 5 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
Found at i:11432321 original size:84 final size:82
Alignment explanation
Indices: 11432139--11433173 Score: 1067
Period size: 81 Copynumber: 12.7 Consensus size: 82
11432129 TCTTGATTAA
* * * *
11432139 GGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATG-GCTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTGCTTC
*
11432203 AATCTGCCCCATGATTG
66 AATCTGCCCCATGATCG
*
11432220 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGCTGGTAGCT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-GT-GCT
* *
11432285 TCAATCTACCCTATGATCG
64 TCAATCTGCCCCATGATCG
* * ** * * * *
11432304 GGGTAAGAGATTGGATGATGTCTTCAATCCGCCCTACAATCGAGGTAAGAAATTGGATATTATCT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-GT-GCT
*
11432369 TCAATCTACCCCATGATCG
64 TCAATCTGCCCCATGATCG
* * * * *
11432388 AGTTAAGAGATTGGATGATGTCTTCATTCTGCCTCAT-ATCGGGGTAAGAGATTGGATG-GTTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTGCTTC
* *
11432451 AATCTGCCCCATGGTTG
66 AATCTGCCCCATGATCG
* *
11432468 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTAGATGATAGCT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-T-GCT
11432533 TCAATCTGCCCCAT-AGTCG
64 TCAATCTGCCCCATGA-TCG
* * * *
11432552 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCACGATTGTGGTAAGAGATTGGATATTGTCT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-GTG-CT
11432617 TCAATCTGCCCCATGATCG
64 TCAATCTGCCCCATGATCG
* * * * *
11432636 AGGTAAGTGATTGGATGATGTCTTCAATCTGCCTCATGATCAGGGTAAGAGATTAGATGAT--TT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-TGCTT
* * *
11432699 CAATCTGCCCTATGGTTG
65 CAATCTGCCCCATGATCG
* * * * *
11432717 GGGTAAGAGATTGGATGATATCTTCAAT-TAGCCTCATGATCAGGGTAAGAGATGGGATG-GTTT
1 GGGTAAGAGATTGGATGATGTCTTCAATCT-GCCCCATGATCGGGGTAAGAGATTGGATGTGCTT
* * *
11432780 CAATCTACTCCATGGTCG
65 CAATCTGCCCCATGATCG
* * * * *
11432798 GGATAGGAGATTGGATGATGTCTTCAATCTACCCCATGTTTGGGGTAAGAGATTGGATG-GCTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTGCTTC
*
11432862 AATCTACCCCATGATCG
66 AATCTGCCCCATGATCG
* *
11432879 GGGTAAGTA-ATTGGATGATGTCTTCAATCTACCACATGATCGGGGTAAGAGATTGGATGATGTC
1 GGGTAAG-AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-TG-C
*
11432943 TTCAATCTGCCACATGATCG
63 TTCAATCTGCCCCATGATCG
* * ** *
11432963 AGGTAAGAGATTGGATG--GT-TTCAATCTGCCCTATGATCAAGGTATGAGATT-GATGTGTCTT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTG-CTT
* * **
11433024 TAATCTGCCTTC-TGATTA
65 CAATCTGCC-CCATGATCG
* * * * *
11433042 GGTTAAAAGATT---TGACGT-TTCAATCTGCCCCATGATCAGGGTATGAGATTGG-TGTGTCTT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTG-CTT
** **
11433102 CAATCTGCCCTTTGATTA
65 CAATCTGCCCCATGATCG
* *
11433120 GGGTAAAAGATT-G--GATG-CTTCAATCTG-CCCATGATCGGGGTATGAGATTGGATG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG
11433174 GTAGCTTCGC
Statistics
Matches: 814, Mismatches: 111, Indels: 61
0.83 0.11 0.06
Matches are distributed among these distances:
76 2 0.00
77 23 0.03
78 79 0.10
79 28 0.03
80 56 0.07
81 302 0.37
82 5 0.01
83 21 0.03
84 297 0.36
85 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (82 bp):
GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTGCTTC
AATCTGCCCCATGATCG
Found at i:11433053 original size:40 final size:39
Alignment explanation
Indices: 11432982--11433148 Score: 121
Period size: 40 Copynumber: 4.3 Consensus size: 39
11432972 ATTGGATGGT
* * * * **
11432982 TTCAATCTGCCCTATGATCAAGGTATGAGATTGATGTGTC
1 TTCAATCTGCCTTCTGATTAGGGTAAAAGATTG-TGTGTC
* * *
11433022 TTTAATCTGCCTTCTGATTAGGTTAAAAGATT-TGACGT-
1 TTCAATCTGCCTTCTGATTAGGGTAAAAGATTGTG-TGTC
* * **
11433060 TTCAATCTGCC-CCATGATCAGGGTATGAGATTGGTGTGTC
1 TTCAATCTGCCTTC-TGATTAGGGTAAAAGATT-GTGTGTC
11433100 TTCAATCTGCCCTT-TGATTAGGGTAAAAGATTG-GATG-C
1 TTCAATCTG-CCTTCTGATTAGGGTAAAAGATTGTG-TGTC
11433138 TTCAATCTGCC
1 TTCAATCTGCC
11433149 CATGATCGGG
Statistics
Matches: 99, Mismatches: 20, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
37 3 0.03
38 37 0.37
39 7 0.07
40 50 0.51
41 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (39 bp):
TTCAATCTGCCTTCTGATTAGGGTAAAAGATTGTGTGTC
Found at i:11433077 original size:78 final size:77
Alignment explanation
Indices: 11432901--11433169 Score: 301
Period size: 78 Copynumber: 3.4 Consensus size: 77
11432891 GGATGATGTC
* * * * * *
11432901 TTCAATCTACCACATGATCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCC-ACATGATCGAG
1 TTCAATCTGCCCCATGATCAGGGTATGAGATT-GATG-TGTCTTCAATCTGCCTTC-TGAT-TAG
* *
11432965 GTAAGAGATTGGATGGT
62 GTAAAAGATTGGA-CGT
* * *
11432982 TTCAATCTGCCCTATGATCAAGGTATGAGATTGATGTGTCTTTAATCTGCCTTCTGATTAGGTTA
1 TTCAATCTGCCCCATGATCAGGGTATGAGATTGATGTGTCTTCAATCTGCCTTCTGATTAGG-TA
*
11433047 AAAGATTTGACGT
65 AAAGATTGGACGT
*
11433060 TTCAATCTGCCCCATGATCAGGGTATGAGATTGGTGTGTCTTCAATCTGCCCTT-TGATTAGGGT
1 TTCAATCTGCCCCATGATCAGGGTATGAGATTGATGTGTCTTCAATCTG-CCTTCTGATTA-GGT
* *
11433124 AAAAGATTGGATGC
64 AAAAGATTGGACGT
*
11433138 TTCAATCTG-CCCATGATCGGGGTATGAGATTG
1 TTCAATCTGCCCCATGATCAGGGTATGAGATTG
11433170 GATGGTAGCT
Statistics
Matches: 164, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
77 22 0.13
78 77 0.47
79 34 0.21
80 5 0.03
81 26 0.16
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (77 bp):
TTCAATCTGCCCCATGATCAGGGTATGAGATTGATGTGTCTTCAATCTGCCTTCTGATTAGGTAA
AAGATTGGACGT
Found at i:11433481 original size:49 final size:49
Alignment explanation
Indices: 11433423--11433696 Score: 278
Period size: 49 Copynumber: 5.6 Consensus size: 49
11433413 CATTACGACC
* ** **
11433423 TCAATCTTTCCCTTCACATCTCTAAGGTATTAGGTTCACGGTTGCGGCT
1 TCAACCTTTCCCTTCACATCTCTAAGGTACAAGGTTCACCATTGCGGCT
* * * * * * * *
11433472 TCAACCTTTCTCTCCATATCTCCATGGTACAAGATTCACCGTTGTGGCT
1 TCAACCTTTCCCTTCACATCTCTAAGGTACAAGGTTCACCATTGCGGCT
* * * * *
11433521 TCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCTCTATTACGGCT
1 TCAACCTTTCCCTTCACATCTCTAAGGTACAAGGTTCACCATTGCGGCT
* * * * * *
11433570 TCAACCTTTCCCTTCATATCTCCATGGTACAAGATTCACCATTACAGCT
1 TCAACCTTTCCCTTCACATCTCTAAGGTACAAGGTTCACCATTGCGGCT
* * *
11433619 TCAATCTTTCCCATCACATCTCTAAGATACAAGGTTCACCATTGCGGCT
1 TCAACCTTTCCCTTCACATCTCTAAGGTACAAGGTTCACCATTGCGGCT
* * *
11433668 TCAACCTTTCCCTCCATATCTCTAGGGTA
1 TCAACCTTTCCCTTCACATCTCTAAGGTA
11433697 TTAGATTTGC
Statistics
Matches: 177, Mismatches: 48, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
49 177 1.00
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (49 bp):
TCAACCTTTCCCTTCACATCTCTAAGGTACAAGGTTCACCATTGCGGCT
Found at i:11433556 original size:98 final size:98
Alignment explanation
Indices: 11433423--11433728 Score: 414
Period size: 98 Copynumber: 3.1 Consensus size: 98
11433413 CATTACGACC
* ** ** *
11433423 TCAATCTTTCCCTTCACATCTCTAAGGTATTAGGTTCACGGTTGCGGCTTCAACCTTTCTCTCCA
1 TCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCACCATTGCGGCTTCAACCTTTCCCTCCA
11433488 TATCTCCATGGTACAAGATTCACCGTTGTGGCT
66 TATCTCCATGGTACAAGATTCACCGTTGTGGCT
* * * *
11433521 TCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCTCTATTACGGCTTCAACCTTTCCCTTCA
1 TCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCACCATTGCGGCTTCAACCTTTCCCTCCA
* ***
11433586 TATCTCCATGGTACAAGATTCACCATTACAGCT
66 TATCTCCATGGTACAAGATTCACCGTTGTGGCT
*
11433619 TCAATCTTTCCCATCACATCTCTAAGATACAAGGTTCACCATTGCGGCTTCAACCTTTCCCTCCA
1 TCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCACCATTGCGGCTTCAACCTTTCCCTCCA
* * ** ** *
11433684 TATCTCTAGGGTATTAGATTTGCCGTTGTGACT
66 TATCTCCATGGTACAAGATTCACCGTTGTGGCT
11433717 TCAATCTTTCCC
1 TCAATCTTTCCC
11433729 TTGAAACTTG
Statistics
Matches: 179, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
98 179 1.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (98 bp):
TCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCACCATTGCGGCTTCAACCTTTCCCTCCA
TATCTCCATGGTACAAGATTCACCGTTGTGGCT
Found at i:11434278 original size:102 final size:103
Alignment explanation
Indices: 11434134--11434437 Score: 378
Period size: 112 Copynumber: 2.9 Consensus size: 103
11434124 CACTAACTGC
* * *
11434134 TATTTCAAATGCAAAAATGCTTGCATCAAGGTCGTAAGGTGGATGAAATTGAATTTGATTGGAGG
1 TATTTC-AATGCAAAAATGCTTG-AACAAGGTTGTAAGGTGGATAAAATTGAATTTGATTGGAGG
* *
11434199 CAAAGCTCGCATGAATGAAAAGATTA-GTCCATTAATAGT
64 CAAAGCTCGTATGAATGAAAAGATTATGTCCACTAATAGT
11434238 TATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAATTTGATTGGAGGCA
1 TATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAATTTGATTGGAGGCA
*
11434303 AAGCTCGTATGAATGAAAAGATTACGAATTATTGGTCCACTAATCGT
66 AAGCTCGTATGAATG--AA-A--A-G-ATTA-T-GTCCACTAATAGT
** * * * * *
11434350 TATTTCAATATAGAAATGCTTAAACAAGGTTGTAGGGTAGATAAAATTGAATTTTATTGGA-GCA
1 TATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAATTTGATTGGAGGCA
11434414 AAGCTCGTATGAATGAAAAGATTA
66 AAGCTCGTATGAATGAAAAGATTA
11434438 AAAATGACCC
Statistics
Matches: 177, Mismatches: 13, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
102 54 0.31
103 16 0.09
104 12 0.07
105 2 0.01
106 1 0.01
107 1 0.01
108 2 0.01
109 6 0.03
111 18 0.10
112 65 0.37
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (103 bp):
TATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAATTTGATTGGAGGCA
AAGCTCGTATGAATGAAAAGATTATGTCCACTAATAGT
Found at i:11434813 original size:9 final size:9
Alignment explanation
Indices: 11434753--11434820 Score: 52
Period size: 9 Copynumber: 7.8 Consensus size: 9
11434743 TCGCCCTCTC
*
11434753 CTTTTTCTT
1 CTTTTTTTT
11434762 CTTTTTTTT
1 CTTTTTTTT
* *
11434771 CTTTCATTTC
1 CTTT-TTTTT
*
11434781 CTTTCTTTT
1 CTTTTTTTT
11434790 C---TTTTT
1 CTTTTTTTT
*
11434796 CTCTTTTTT
1 CTTTTTTTT
11434805 CTTTTTTTT
1 CTTTTTTTT
*
11434814 ATTTTTT
1 CTTTTTT
11434821 GGGTGAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
6 5 0.11
9 35 0.74
10 7 0.15
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:11435712 original size:15 final size:14
Alignment explanation
Indices: 11435667--11435721 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
11435657 CCTTTGCGGG
11435667 TTTTCTT-TTTTTC
1 TTTTCTTCTTTTTC
11435680 TTTTCTTGACTCTTTT-
1 TTTTCTT--CT-TTTTC
*
11435696 TTTT-TCCTTTTTC
1 TTTTCTTCTTTTTC
11435709 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
11435722 GATCTCCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
12 4 0.12
13 13 0.38
14 7 0.21
15 1 0.03
16 5 0.15
17 4 0.12
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:11439877 original size:30 final size:29
Alignment explanation
Indices: 11439806--11439914 Score: 103
Period size: 30 Copynumber: 3.7 Consensus size: 29
11439796 GTCAAAAATG
* * * *
11439806 AAATTTTGA-AAAGTTTGGGGCCAAATTC
1 AAATTTTTAGAAAGTTTAGGGTCAAATCC
* *
11439834 GAATTTTTGGAAAGTTTGAGGGTCAAATCC
1 AAATTTTTAGAAAGTTT-AGGGTCAAATCC
* * *
11439864 AAATATTTAGAAAGTTTAGGGGTCAAAACT
1 AAATTTTTAGAAAGTTTA-GGGTCAAATCC
*
11439894 TAATTTTTAGAAAGTTTAGGG
1 AAATTTTTAGAAAGTTTAGGG
11439915 GTTAAAACAT
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
28 6 0.09
29 11 0.17
30 48 0.74
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (29 bp):
AAATTTTTAGAAAGTTTAGGGTCAAATCC
Found at i:11439915 original size:30 final size:30
Alignment explanation
Indices: 11439835--11439959 Score: 121
Period size: 30 Copynumber: 4.2 Consensus size: 30
11439825 GCCAAATTCG
* *
11439835 AATTTTTGGAAAGTTT-GAGGGTCAAATCCA-
1 AATTTTTAGAAAGTTTAG-GGGTCAAA-ACAT
* *
11439865 AATATTTAGAAAGTTTAGGGGTCAAAACTT
1 AATTTTTAGAAAGTTTAGGGGTCAAAACAT
*
11439895 AATTTTTAGAAAGTTTAGGGGTTAAAACAT
1 AATTTTTAGAAAGTTTAGGGGTCAAAACAT
* * * *
11439925 AATTTTTGGATAG-TTCGGGGATCAAAACAC
1 AATTTTTAGAAAGTTTAGGGG-TCAAAACAT
11439955 AATTT
1 AATTT
11439960 CTTAATAAAG
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.09
30 72 0.90
31 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTAGGGGTCAAAACAT
Found at i:11441638 original size:68 final size:68
Alignment explanation
Indices: 11441529--11441666 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
11441519 AATATCATCC
*
11441529 AAATGCTCAAACAAGAATATGCATTATTCTATACTACCATCACAAAAACAATAATCAAAGTCTAT
1 AAATGCTCAAACAAGAATATGCATTATTCTATACTACCATCACAAAAACAATAATCAAAGTATAT
11441594 CTA
66 CTA
* * *
11441597 AAATGGTCAAATAAGAATATGCATTATTCTATACTACCATCACAAGAACAATAATCAAAGTATAT
1 AAATGCTCAAACAAGAATATGCATTATTCTATACTACCATCACAAAAACAATAATCAAAGTATAT
11441662 CTA
66 CTA
11441665 AA
1 AA
11441667 GTCCCTATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (68 bp):
AAATGCTCAAACAAGAATATGCATTATTCTATACTACCATCACAAAAACAATAATCAAAGTATAT
CTA
Found at i:11442472 original size:108 final size:109
Alignment explanation
Indices: 11442321--11442522 Score: 266
Period size: 108 Copynumber: 1.9 Consensus size: 109
11442311 ATGTGAGCTC
* ** * * *
11442321 AGCTTTAGTTGGATAAACCAACGATAATTGCACTTAACGCTAGTCGAATAAACCGA-CAATGTGT
1 AGCTCTAGTTGGATAAACCAACGATAATTGCACCCAACACTAGTCAAATAAACCGATCAATGTAT
* *
11442385 GCCCAGCACTAGTCAGATAAACTGACGAAAGGATTATTGAGCCT
66 GCCCAGCACTAGCCAGATAAACCGACGAAAGGATTATTGAGCCT
* * *
11442429 AGCTCTAGTTGGATAAACCCACGATAATTG-AGCCCAGA-ACTAGTCAAATAAACTGATGAATGT
1 AGCTCTAGTTGGATAAACCAACGATAATTGCA-CCCA-ACACTAGTCAAATAAACCGATCAATGT
11442492 ATGCCCAGCACTAGCCAGATAAACCGACGAA
64 ATGCCCAGCACTAGCCAGATAAACCGACGAA
11442523 TGTGTGCCCA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
107 1 0.01
108 45 0.56
109 34 0.43
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (109 bp):
AGCTCTAGTTGGATAAACCAACGATAATTGCACCCAACACTAGTCAAATAAACCGATCAATGTAT
GCCCAGCACTAGCCAGATAAACCGACGAAAGGATTATTGAGCCT
Found at i:11442505 original size:34 final size:34
Alignment explanation
Indices: 11442360--11442552 Score: 124
Period size: 34 Copynumber: 5.5 Consensus size: 34
11442350 GCACTTAACG
* *
11442360 CTAGTC-GAATAAACCGAC-AATGTGTGCCCAGCA
1 CTAGTCAG-ATAAACTGACGAATGTATGCCCAGCA
* * *
11442393 CTAGTCAGATAAACTGACGAAAGGATTATTGAGCCTAGCT
1 CTAGTCAGATAAACTGACG-AATG--TA-T--GCCCAGCA
** ** *
11442433 CTAGTTGGATAAACCCACGATAAT-TGA-GCCCAGAA
1 CTAGTCAGATAAACTGACG--AATGT-ATGCCCAGCA
* *
11442468 CTAGTCAAATAAACTGATGAATGTATGCCCAGCA
1 CTAGTCAGATAAACTGACGAATGTATGCCCAGCA
* * *
11442502 CTAGCCAGATAAACCGACGAATGTGTGCCCAGCA
1 CTAGTCAGATAAACTGACGAATGTATGCCCAGCA
*
11442536 CTAGTCCGATAAACTGA
1 CTAGTCAGATAAACTGA
11442553 AGAAAAAGTT
Statistics
Matches: 119, Mismatches: 29, Indels: 23
0.70 0.17 0.13
Matches are distributed among these distances:
33 19 0.16
34 52 0.44
35 21 0.18
37 1 0.01
38 2 0.02
39 1 0.01
40 21 0.18
41 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (34 bp):
CTAGTCAGATAAACTGACGAATGTATGCCCAGCA
Found at i:11444277 original size:21 final size:23
Alignment explanation
Indices: 11444251--11444302 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
11444241 GGACTAGCTA
11444251 CCACATATTTTCCA-AT-AATGG
1 CCACATATTTTCCAGATAAATGG
* * *
11444272 CCACATAATTTGCAGATAAATTG
1 CCACATATTTTCCAGATAAATGG
11444295 CCACATAT
1 CCACATAT
11444303 CTTCTTCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 11 0.44
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (23 bp):
CCACATATTTTCCAGATAAATGG
Found at i:11447230 original size:17 final size:16
Alignment explanation
Indices: 11447182--11447231 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
11447172 TGTAGTAAAC
*
11447182 TAAGAGAAATGCATTGA
1 TAAGAAAAATGCA-TGA
11447199 TAATG-AAAATGCATGCA
1 TAA-GAAAAATGCATG-A
11447216 TAAGAAAAATGCATGA
1 TAAGAAAAATGCATGA
11447232 AAACTAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.14
17 24 0.83
18 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (16 bp):
TAAGAAAAATGCATGA
Found at i:11450697 original size:555 final size:555
Alignment explanation
Indices: 11449646--11450762 Score: 1740
Period size: 555 Copynumber: 2.0 Consensus size: 555
11449636 TTTAAGATGT
*
11449646 TGGCCATTCACTTTGAACTGTTGCCCATCCTTTAAGTTTTCGATTGTCACTGCACCTCTTGGAAA
1 TGGCCATTCACTTTGAACTGTTGCCCATCCTTTAAGTTTTCGATTGTCACAGCACCTCTTGGAAA
* * * *
11449711 TGCTTCAACAACTTTTAATGGTCCTGACCACCTTGATCGTAATTTTCTGGATGTAATTTCAAACG
66 TACTACAACAACTTTTAATGGTCCTGACAACCTTGATCGCAATTTTCTGGATGTAATTTCAAACG
11449776 TGAATTAAATAAAAGTACCAACTGACCAGGATGAAATTGTCGATGCAATATGAGGTTGTCATACC
131 TGAATTAAATAAAAGTACCAACTGACCAGGATGAAATTGTCGATGCAATATGAGGTTGTCATACC
* *
11449841 ATCTCTTTGTCTTTTCGTTACATATCGCAGCATTCTCATAAGCATGGCGACGGATCTCTTCTAAT
196 ATCGCTTTGTCTTTTCGTTACATATCGCAACATTCTCATAAGCATGGCGACGGATCTCTTCTAAT
* * * *
11449906 TCAGTGATGTCCAGCAATCTTTTCTTCCCAGTAGCATCACAATCTAAATTTACCTGCTTAATTGC
261 TCAGTGATGTCCAACAATCTTTTCTTCCCAGCAGCATCACAATCCAAATTTACCTACTTAATTGC
* * *
11449971 CCACATGGCTTTATGTTCAAGTTCGTCAGGTAGGTTACAAGATTTTCCAAACACTAACTGATATG
326 CCACATGGCTTTATGTTCAAGTTCGACACGTAGGTGACAAGATTTTCCAAACACTAACTGATATG
* **
11450036 GCCACATTCCCAATAGGGTTTTGTAAGCGGTGCAAAGCACCCACAATGCATCATGTAGCCGTACT
391 GCAACATTCCCAATAGGGTTTTGTAAGCGGTGCAAAGCACCCACAATGCATCATGTAGCCACACT
* *
11450101 GACCAATCCTTTCTAGATGGATTAACCATCTTTTTAAGTATACCTTTAATTTGGCGATTGGATAC
456 GACCAATCCTTCCTAGATGGATTAACCATCTTTTCAAGTATACCTTTAATTTGGCGATTGGATAC
*
11450166 TTCAGCTTGACCATTAGTTAGTGCGTGATACGTGG
521 TTCAGCTTGACCATTAGTTAGTGCGTGATAAGTGG
* *
11450201 TGGCCATTCACTTTGAATTGTTGCCCATCCTTTAGGTTTTCGATTGTCACAGCA-CTGCTTGGAA
1 TGGCCATTCACTTTGAACTGTTGCCCATCCTTTAAGTTTTCGATTGTCACAGCACCT-CTTGGAA
*
11450265 ATACTACGACAACTTTTAATGGTCCTGACAACCTTGATCGCAATTTTCCTGGATGTAATTTCAAA
65 ATACTACAACAACTTTTAATGGTCCTGACAACCTTGATCGCAATTTT-CTGGATGTAATTTCAAA
*
11450330 TGTGAATTAAATAAAAGTACCAACTGACCAGGATGAAATTGTCGATGCAATATGAGGTTGTCAT-
129 CGTGAATTAAATAAAAGTACCAACTGACCAGGATGAAATTGTCGATGCAATATGAGGTTGTCATA
** * *
11450394 CTCATCGCTTTGTCTTTTC-TTGTATATCGTAACATTTTCATAAGCATGGC-ATCGGATCTCTTC
194 C-CATCGCTTTGTCTTTTCGTTACATATCGCAACATTCTCATAAGCATGGCGA-CGGATCTCTTC
*
11450457 TAATTCCA-TGATGTCCAACAATCTTTTCTTCCCAGCAGCATCATAATCCAAATTTACCTACTTA
257 TAATT-CAGTGATGTCCAACAATCTTTTCTTCCCAGCAGCATCACAATCCAAATTTACCTACTTA
* *
11450521 ATTGCCCACATGGCTTTATGTTCAAGTTCGACACGTAGGTGATAAGATTTTCCAAACACTAGCTG
321 ATTGCCCACATGGCTTTATGTTCAAGTTCGACACGTAGGTGACAAGATTTTCCAAACACTAACTG
* *** * * * *
11450586 ATATTGCAACATTTTTAATGGGGTTTTGTAAGCTGTGCGAAGCGCCCACAATGCATCATGTAGCC
386 ATATGGCAACATTCCCAATAGGGTTTTGTAAGCGGTGCAAAGCACCCACAATGCATCATGTAGCC
* *
11450651 ACACTGACCAATCCTTCCTAGATGGATTAACCATCTTTTCAAGTATAGCTTTAATTTGGTGATTG
451 ACACTGACCAATCCTTCCTAGATGGATTAACCATCTTTTCAAGTATACCTTTAATTTGGCGATTG
** * * *
11450716 GATACTTTGGCTTGATCATTAGTTTGTGGGTGATAAGTGG
516 GATACTTCAGCTTGACCATTAGTTAGTGCGTGATAAGTGG
11450756 TGGCCAT
1 TGGCCAT
11450763 ACGATGCTTC
Statistics
Matches: 511, Mismatches: 46, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
554 3 0.01
555 410 0.80
556 98 0.19
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (555 bp):
TGGCCATTCACTTTGAACTGTTGCCCATCCTTTAAGTTTTCGATTGTCACAGCACCTCTTGGAAA
TACTACAACAACTTTTAATGGTCCTGACAACCTTGATCGCAATTTTCTGGATGTAATTTCAAACG
TGAATTAAATAAAAGTACCAACTGACCAGGATGAAATTGTCGATGCAATATGAGGTTGTCATACC
ATCGCTTTGTCTTTTCGTTACATATCGCAACATTCTCATAAGCATGGCGACGGATCTCTTCTAAT
TCAGTGATGTCCAACAATCTTTTCTTCCCAGCAGCATCACAATCCAAATTTACCTACTTAATTGC
CCACATGGCTTTATGTTCAAGTTCGACACGTAGGTGACAAGATTTTCCAAACACTAACTGATATG
GCAACATTCCCAATAGGGTTTTGTAAGCGGTGCAAAGCACCCACAATGCATCATGTAGCCACACT
GACCAATCCTTCCTAGATGGATTAACCATCTTTTCAAGTATACCTTTAATTTGGCGATTGGATAC
TTCAGCTTGACCATTAGTTAGTGCGTGATAAGTGG
Found at i:11458019 original size:10 final size:10
Alignment explanation
Indices: 11458006--11458041 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
11457996 GAAGAATAGA
11458006 AGAGAAAATG
1 AGAGAAAATG
11458016 AGAGAAAATG
1 AGAGAAAATG
11458026 AGAGAAAA-G
1 AGAGAAAATG
11458035 AGAGAAA
1 AGAGAAA
11458042 TAGAAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.06
Consensus pattern (10 bp):
AGAGAAAATG
Found at i:11463910 original size:23 final size:22
Alignment explanation
Indices: 11463860--11463923 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
11463850 CAATTCGATG
* *
11463860 GTGGCGACGGCGATGGTCCAGC
1 GTGGCGACGGCGACGGTCCAAC
*
11463882 GATGGCGACGGTGACGGTCCAAC
1 G-TGGCGACGGCGACGGTCCAAC
*
11463905 AGTGGCGACGACGACGGTC
1 -GTGGCGACGGCGACGGTC
11463924 TGGCGATGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 1 0.03
23 33 0.94
24 1 0.03
ACGTcount: A:0.19, C:0.27, G:0.42, T:0.12
Consensus pattern (22 bp):
GTGGCGACGGCGACGGTCCAAC
Found at i:11464040 original size:12 final size:12
Alignment explanation
Indices: 11464000--11464042 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
11463990 TTAGAGAGAA
*
11464000 AAAGAAGAAGAG
1 AAAGAAAAAGAG
11464012 AAGAGAAAAGAGAG
1 AA-AGAAAA-AGAG
*
11464026 AAAGAGAAAGAG
1 AAAGAAAAAGAG
11464038 AAAGA
1 AAAGA
11464043 TACTCACGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 11 0.41
13 10 0.37
14 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAGAG
Found at i:11467932 original size:23 final size:23
Alignment explanation
Indices: 11467894--11467938 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11467884 TGTTGGAAAT
*
11467894 ATAATCTACTGCAAAACAAGTCC
1 ATAATCTACTACAAAACAAGTCC
* *
11467917 ATAATCTACTATAAAATAAGTC
1 ATAATCTACTACAAAACAAGTC
11467939 TGCTAGTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (23 bp):
ATAATCTACTACAAAACAAGTCC
Found at i:11475067 original size:23 final size:23
Alignment explanation
Indices: 11475019--11475061 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
11475009 TCCATAGCGC
*
11475019 GCTCATGTATTTAGCACTTTTCT
1 GCTCATGTATTTAACACTTTTCT
*
11475042 GCTCGTGT-TTTAACACTTTT
1 GCTCATGTATTTAACACTTTT
11475062 AGTGCTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (23 bp):
GCTCATGTATTTAACACTTTTCT
Found at i:11475811 original size:24 final size:25
Alignment explanation
Indices: 11475757--11475812 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
11475747 TGAATTTTCT
11475757 CTGTTTTCCTACAAAATTTTCAAGA
1 CTGTTTTCCTACAAAATTTTCAAGA
*
11475782 CT-TTTTCCTGC-AAATTTTCAA-A
1 CTGTTTTCCTACAAAATTTTCAAGA
11475804 CCTGTTTTC
1 -CTGTTTTC
11475813 AGTGATAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.04
23 12 0.43
24 13 0.46
25 2 0.07
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (25 bp):
CTGTTTTCCTACAAAATTTTCAAGA
Found at i:11479884 original size:48 final size:48
Alignment explanation
Indices: 11479802--11479917 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
11479792 TTGATCTGAA
* * * *
11479802 TAGTTGACAAGCGTAAACATACATTAAATAACGAGCGTAAACGTATAT
1 TAGTTGACGAGCGTAAATATACAATAAATAACGAGCGTAAACGTACAT
* * *
11479850 TAGTTGACGAGCGTAAATGTACAATAACTGACGAGCGTAAACGTACAT
1 TAGTTGACGAGCGTAAATATACAATAAATAACGAGCGTAAACGTACAT
* *
11479898 TAGTTTACGAGCATAAATAT
1 TAGTTGACGAGCGTAAATAT
11479918 TCTGACCGAG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (48 bp):
TAGTTGACGAGCGTAAATATACAATAAATAACGAGCGTAAACGTACAT
Found at i:11479907 original size:24 final size:24
Alignment explanation
Indices: 11479802--11479914 Score: 118
Period size: 24 Copynumber: 4.7 Consensus size: 24
11479792 TTGATCTGAA
* *
11479802 TAGTTGACAAGCGTAAACATACAT
1 TAGTTGACGAGCGTAAACGTACAT
** * *
11479826 TAAATAACGAGCGTAAACGTATAT
1 TAGTTGACGAGCGTAAACGTACAT
* *
11479850 TAGTTGACGAGCGTAAATGTACAA
1 TAGTTGACGAGCGTAAACGTACAT
**
11479874 TAACTGACGAGCGTAAACGTACAT
1 TAGTTGACGAGCGTAAACGTACAT
* *
11479898 TAGTTTACGAGCATAAA
1 TAGTTGACGAGCGTAAA
11479915 TATTCTGACC
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (24 bp):
TAGTTGACGAGCGTAAACGTACAT
Found at i:11482558 original size:21 final size:21
Alignment explanation
Indices: 11482532--11482574 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11482522 TGCAAGGGTC
11482532 ATAGGCAATCTAATGTACCTT
1 ATAGGCAATCTAATGTACCTT
11482553 ATAGGCAATCTAATGTACCTT
1 ATAGGCAATCTAATGTACCTT
11482574 A
1 A
11482575 CGAGTTGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
ATAGGCAATCTAATGTACCTT
Found at i:11485486 original size:17 final size:17
Alignment explanation
Indices: 11485456--11485496 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
11485446 AAACTAAAAT
11485456 GAATGCAACGACAATTAA
1 GAATGCAACGACAA-TAA
11485474 -AATGCAA-GCACAATAA
1 GAATGCAACG-ACAATAA
11485490 GAATGCA
1 GAATGCA
11485497 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (17 bp):
GAATGCAACGACAATAA
Found at i:11500197 original size:14 final size:14
Alignment explanation
Indices: 11500178--11500205 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11500168 ATGTTCTCAT
11500178 GCATCTTCATGTGG
1 GCATCTTCATGTGG
11500192 GCATCTTCATGTGG
1 GCATCTTCATGTGG
11500206 AAAACCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (14 bp):
GCATCTTCATGTGG
Found at i:11505327 original size:6 final size:6
Alignment explanation
Indices: 11505318--11505360 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
11505308 TTTGAATATG
* * *
11505318 AAATGA AAATGA GAATG- ATATGA AAATGG AAATGA AAATGA AA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AA
11505361 TGGATGTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
5 3 0.10
6 27 0.90
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (6 bp):
AAATGA
Found at i:11505351 original size:17 final size:17
Alignment explanation
Indices: 11505315--11505360 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
11505305 TGATTTGAAT
11505315 ATGAAATGAAAATGAGA
1 ATGAAATGAAAATGAGA
*
11505332 ATGATATGAAAATG-GAA
1 ATGAAATGAAAATGAG-A
11505349 ATGAAAATGAAA
1 ATG-AAATGAAA
11505361 TGGATGTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 17 0.68
18 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.20
Consensus pattern (17 bp):
ATGAAATGAAAATGAGA
Found at i:11505744 original size:55 final size:55
Alignment explanation
Indices: 11505624--11505745 Score: 181
Period size: 55 Copynumber: 2.2 Consensus size: 55
11505614 GCTTCTTTTG
* * * * *
11505624 AATCAATTGTCATATTGAAATATTGCTTCTTTTGAATAGATTGTTTATATGTTTA
1 AATCAATTGTTATGTTAAAATACTGCTTCTTTTGAATAGAGTGTTTATATGTTTA
*
11505679 AATCAATTGTTATGTTAAAATACTGCTTCTTTTGAATCGAGTGTTTATATGTTTA
1 AATCAATTGTTATGTTAAAATACTGCTTCTTTTGAATAGAGTGTTTATATGTTTA
*
11505734 AATCGATTGTTA
1 AATCAATTGTTA
11505746 CATAGCACAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
AATCAATTGTTATGTTAAAATACTGCTTCTTTTGAATAGAGTGTTTATATGTTTA
Found at i:11508398 original size:6 final size:6
Alignment explanation
Indices: 11508387--11508412 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11508377 CAACAAGATA
11508387 ATTAAT ATTAAT ATTAAT ATTAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT AT
11508413 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTAAT
Found at i:11508900 original size:20 final size:20
Alignment explanation
Indices: 11508875--11508912 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11508865 AATGACAAAA
11508875 CAATCACTCAACTTTCAATT
1 CAATCACTCAACTTTCAATT
*
11508895 CAATCATTCAACTTTCAA
1 CAATCACTCAACTTTCAA
11508913 AAAATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (20 bp):
CAATCACTCAACTTTCAATT
Found at i:11512832 original size:6 final size:6
Alignment explanation
Indices: 11512823--11512855 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
11512813 CATGTTGTTG
11512823 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCT
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCT
11512856 GAGATAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
TCTCCC
Found at i:11521589 original size:109 final size:109
Alignment explanation
Indices: 11521398--11521621 Score: 439
Period size: 109 Copynumber: 2.1 Consensus size: 109
11521388 TGTTCATTCA
*
11521398 GTTAATCGACTCGAACTATCAAAAATCGAATTAGTCGACCCCTTAAATATTTAATCGTTAATTTA
1 GTTAATCGACTCGAACTACCAAAAATCGAATTAGTCGACCCCTTAAATATTTAATCGTTAATTTA
11521463 ATTGAATTTTTTTCAAAAAAAATTAACCGAACCAAAATTTTTCG
66 ATTGAATTTTTTTCAAAAAAAATTAACCGAACCAAAATTTTTCG
11521507 GTTAATCGACTCGAACTACCAAAAATCGAATTAGTCGACCCCTTAAATATTTAATCGTTAATTTA
1 GTTAATCGACTCGAACTACCAAAAATCGAATTAGTCGACCCCTTAAATATTTAATCGTTAATTTA
11521572 ATTGAATTTTTTTCAAAAAAAATTAACCGAACCAAAATTTTTCG
66 ATTGAATTTTTTTCAAAAAAAATTAACCGAACCAAAATTTTTCG
11521616 GTTAAT
1 GTTAAT
11521622 TCGATCGGTT
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 114 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (109 bp):
GTTAATCGACTCGAACTACCAAAAATCGAATTAGTCGACCCCTTAAATATTTAATCGTTAATTTA
ATTGAATTTTTTTCAAAAAAAATTAACCGAACCAAAATTTTTCG
Found at i:11522635 original size:22 final size:22
Alignment explanation
Indices: 11522607--11522650 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11522597 TGAAAAGTTG
*
11522607 TAATGTAATTCAAATTTGAAAA
1 TAATGTAATTAAAATTTGAAAA
11522629 TAATGTAATTAAAATTTGAAAA
1 TAATGTAATTAAAATTTGAAAA
11522651 CTTAAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATGTAATTAAAATTTGAAAA
Found at i:11524303 original size:22 final size:22
Alignment explanation
Indices: 11524277--11524337 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
11524267 ATATTGCCAT
*
11524277 AGAATCTTACTGTTCATGCCAAG
1 AGAATCTCACTGTTCATG-CAAG
* * *
11524300 -GAATCTCACTATTCACGTAAG
1 AGAATCTCACTGTTCATGCAAG
11524321 AGAATCTCACTGTTCAT
1 AGAATCTCACTGTTCAT
11524338 TTTGTTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (22 bp):
AGAATCTCACTGTTCATGCAAG
Found at i:11532258 original size:24 final size:24
Alignment explanation
Indices: 11532221--11532441 Score: 244
Period size: 24 Copynumber: 9.2 Consensus size: 24
11532211 ATGAAATAAA
* *
11532221 GTAAACATATTCATGCTAACGAGC
1 GTAAACATACTCATGCTGACGAGC
* * *
11532245 GTAAACGTACTCATGTTGATGAGC
1 GTAAACATACTCATGCTGACGAGC
* *
11532269 GTAAACATACTCATGCTGATGAGT
1 GTAAACATACTCATGCTGACGAGC
*
11532293 GTAAACATATTCATGCTGACGAGC
1 GTAAACATACTCATGCTGACGAGC
* *
11532317 GTAAACGTATTCATGCTGACGAGC
1 GTAAACATACTCATGCTGACGAGC
** *
11532341 GTAAATGTACTCATGCTGGCGAGC
1 GTAAACATACTCATGCTGACGAGC
* *
11532365 GTAAACATACTCATGCTGACGGGT
1 GTAAACATACTCATGCTGACGAGC
* * *
11532389 GTAAACTTATTCATGTTGACGAGC
1 GTAAACATACTCATGCTGACGAGC
* * * *
11532413 GTAAACGTACTCAAGTTGACAAGC
1 GTAAACATACTCATGCTGACGAGC
11532437 GTAAA
1 GTAAA
11532442 TGTAAAGAAG
Statistics
Matches: 168, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 168 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (24 bp):
GTAAACATACTCATGCTGACGAGC
Found at i:11532341 original size:72 final size:72
Alignment explanation
Indices: 11532221--11532441 Score: 298
Period size: 72 Copynumber: 3.1 Consensus size: 72
11532211 ATGAAATAAA
* * * *
11532221 GTAAACATATTCATGCTAACGAGCGTAAACGTACTCATGTTGATGAGCGTAAACATACTCATGCT
1 GTAAACATATTCATGCTGACGAGCGTAAACGTATTCATGTTGACGAGCGTAAACGTACTCATGCT
* *
11532286 GATGAGT
66 GACGAGC
* *
11532293 GTAAACATATTCATGCTGACGAGCGTAAACGTATTCATGCTGACGAGCGTAAATGTACTCATGCT
1 GTAAACATATTCATGCTGACGAGCGTAAACGTATTCATGTTGACGAGCGTAAACGTACTCATGCT
*
11532358 GGCGAGC
66 GACGAGC
* * * * * *
11532365 GTAAACATACTCATGCTGACGGGTGTAAACTTATTCATGTTGACGAGCGTAAACGTACTCAAGTT
1 GTAAACATATTCATGCTGACGAGCGTAAACGTATTCATGTTGACGAGCGTAAACGTACTCATGCT
*
11532430 GACAAGC
66 GACGAGC
11532437 GTAAA
1 GTAAA
11532442 TGTAAAGAAG
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 130 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (72 bp):
GTAAACATATTCATGCTGACGAGCGTAAACGTATTCATGTTGACGAGCGTAAACGTACTCATGCT
GACGAGC
Found at i:11534095 original size:54 final size:54
Alignment explanation
Indices: 11534010--11534152 Score: 259
Period size: 54 Copynumber: 2.6 Consensus size: 54
11534000 CCGTAAATGC
*
11534010 AAAAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
1 AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
*
11534064 AAAAGGTCCGATGACTCTGTGTCATCTTGAGTTATATGAATCCTATTACGGATT
1 AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
*
11534118 AAAGGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
11534153 CAAACGTGAA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 85 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (54 bp):
AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
Found at i:11538427 original size:27 final size:27
Alignment explanation
Indices: 11538376--11538430 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
11538366 TCACCAGAGG
* **
11538376 GGCACTGAATGTGCCTTATTGATAGGC
1 GGCACTAAATGTGCCTTATCAATAGGC
*
11538403 GGCACTAAATGTGCCTTGTCAATAGGC
1 GGCACTAAATGTGCCTTATCAATAGGC
11538430 G
1 G
11538431 TCACCACTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (27 bp):
GGCACTAAATGTGCCTTATCAATAGGC
Found at i:11538778 original size:22 final size:22
Alignment explanation
Indices: 11538725--11538780 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
11538715 ATTATAGTTT
11538725 AAATTTTAATTTTTTATTTATTA
1 AAATTTT-ATTTTTTATTTATTA
11538748 AAATTTTATTTTTTATTTATTA
1 AAATTTTATTTTTTATTTATTA
11538770 AAATTTTATTT
1 AAATTTTATTT
11538781 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
AAATTTTATTTTTTATTTATTA
Found at i:11542084 original size:12 final size:12
Alignment explanation
Indices: 11542069--11542108 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
11542059 CTTCCTCTTC
11542069 CTCTTGCTCTGG
1 CTCTTGCTCTGG
*
11542081 CTCTTGCTTTGG
1 CTCTTGCTCTGG
* *
11542093 CTCTAGCTGTGG
1 CTCTTGCTCTGG
11542105 CTCT
1 CTCT
11542109 GGTGTAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.25, T:0.42
Consensus pattern (12 bp):
CTCTTGCTCTGG
Found at i:11542629 original size:43 final size:43
Alignment explanation
Indices: 11542563--11542659 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
11542553 AACTGCACAA
* ** *
11542563 TTAATAACATGTTATTATATTAACAAGGGTCAACTAATATAAT
1 TTAATAACATGCTACGATATTAACAAGAGTCAACTAATATAAT
* * *
11542606 TTAATAACATGCTACGATGTTAACACGAGTCAAGTAATATAAT
1 TTAATAACATGCTACGATATTAACAAGAGTCAACTAATATAAT
*
11542649 TGAATAACATG
1 TTAATAACATG
11542660 TCAAGGAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (43 bp):
TTAATAACATGCTACGATATTAACAAGAGTCAACTAATATAAT
Found at i:11545094 original size:21 final size:22
Alignment explanation
Indices: 11545068--11545115 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
11545058 CTACGTTTAT
* * *
11545068 AAATGGTGTTTTGAAGAAGA-A
1 AAATGGCGTTTTAAAAAAGAGA
11545089 AAATGGCGTTTTAAAAAAGAGA
1 AAATGGCGTTTTAAAAAAGAGA
11545111 AAATG
1 AAATG
11545116 AGAGATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.25, T:0.25
Consensus pattern (22 bp):
AAATGGCGTTTTAAAAAAGAGA
Found at i:11545542 original size:23 final size:22
Alignment explanation
Indices: 11545486--11545542 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
11545476 AATCTACTCT
* *
11545486 ACTAAATAAA-AAAAATTAATA
1 ACTAAACAAATAAAAATTAAAA
*
11545507 AC-AAATCATATAAAAATTAAAAA
1 ACTAAA-CAAATAAAAATT-AAAA
11545530 ACTAAACAAATAA
1 ACTAAACAAATAA
11545543 TTTATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 3 0.11
21 4 0.14
22 7 0.25
23 11 0.39
24 3 0.11
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (22 bp):
ACTAAACAAATAAAAATTAAAA
Found at i:11545727 original size:16 final size:17
Alignment explanation
Indices: 11545696--11545728 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11545686 AACAACAACA
*
11545696 AAACTTACCTTTTCTTT
1 AAACTTACCATTTCTTT
11545713 AAACTTA-CATTTCTTT
1 AAACTTACCATTTCTTT
11545729 CTCTCCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (17 bp):
AAACTTACCATTTCTTT
Found at i:11547116 original size:11 final size:11
Alignment explanation
Indices: 11547097--11547199 Score: 73
Period size: 11 Copynumber: 9.0 Consensus size: 11
11547087 TTTTGATTTT
*
11547097 TTAAGTTTAAA
1 TTAAATTTAAA
*
11547108 TTAATTTTAAA
1 TTAAATTTAAA
**
11547119 TTTTATTTAAA
1 TTAAATTTAAA
**
11547130 TTTAAATTTATC
1 -TTAAATTTAAA
11547142 TTAAATTTAAA
1 TTAAATTTAAA
*
11547153 TTTATTTATTTAAA
1 -TTA--AATTTAAA
* *
11547167 TTTATTTTAAA
1 TTAAATTTAAA
11547178 TTTAAATTT-AA
1 -TTAAATTTAAA
11547189 TTAAATTTAAA
1 TTAAATTTAAA
11547200 ATGATATTAA
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
10 8 0.11
11 37 0.53
12 16 0.23
13 2 0.03
14 7 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:11547117 original size:6 final size:6
Alignment explanation
Indices: 11547096--11547199 Score: 87
Period size: 6 Copynumber: 18.0 Consensus size: 6
11547086 ATTTTGATTT
* * *
11547096 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
11547140 TCTTAAA TTTAAA TTTATTTA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
11547189 -TTAAA TTTAAA
1 TTTAAA TTTAAA
11547200 ATGATATTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.05
5 18 0.23
6 50 0.63
7 2 0.03
8 5 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:11547208 original size:17 final size:17
Alignment explanation
Indices: 11547096--11547215 Score: 124
Period size: 17 Copynumber: 7.3 Consensus size: 17
11547086 ATTTTGATTT
* * *
11547096 TTTAAGTTTAAATTAAT
1 TTTAAATTTATATTAAA
11547113 TTTAAATTT-TATTTAAA
1 TTTAAATTTATA-TTAAA
*
11547130 TTTAAATTTATCTTAAA
1 TTTAAATTTATATTAAA
11547147 TTTAAATTTAT-TT--A
1 TTTAAATTTATATTAAA
*
11547161 TTTAAATTTATTTTAAA
1 TTTAAATTTATATTAAA
11547178 TTTAAATTTA-ATTAAA
1 TTTAAATTTATATTAAA
* *
11547194 TTTAAAATGATATTAAA
1 TTTAAATTTATATTAAA
*
11547211 ATTAA
1 TTTAA
11547216 TAAATTAAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.13
15 2 0.02
16 16 0.18
17 58 0.65
18 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:11547955 original size:12 final size:13
Alignment explanation
Indices: 11547920--11547958 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
11547910 GTTAACATTA
11547920 AATACTATTAATG
1 AATACTATTAATG
*
11547933 AATATTATTAATG
1 AATACTATTAATG
11547946 AATA-TATTAATG
1 AATACTATTAATG
11547958 A
1 A
11547959 TAATAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
AATACTATTAATG
Found at i:11548261 original size:20 final size:19
Alignment explanation
Indices: 11548236--11548279 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
11548226 GTTTTTTTTA
* *
11548236 AAAAAAATAAAGAGAGAAAG
1 AAAAAAACAAAAAG-GAAAG
11548256 AAAAAAACAAAAAGGAAAG
1 AAAAAAACAAAAAGGAAAG
11548275 AAAAA
1 AAAAA
11548280 GAAGAGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAAACAAAAAGGAAAG
Found at i:11548314 original size:11 final size:11
Alignment explanation
Indices: 11548298--11548327 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
11548288 ATCCTACCTT
11548298 GGACGGCGGTC
1 GGACGGCGGTC
*
11548309 GGACGGTGGTC
1 GGACGGCGGTC
11548320 GGACGGCG
1 GGACGGCG
11548328 CGTGTAGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.57, T:0.10
Consensus pattern (11 bp):
GGACGGCGGTC
Found at i:11549041 original size:29 final size:29
Alignment explanation
Indices: 11548980--11549070 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
11548970 AAACAGTCCG
* * *
11548980 AAAATTGCATCTTGACCCCAAAA-TTTTA
1 AAAATTACATTTTGACCCCAAAACTTCTA
*
11549008 GAAAATTACATTTTGACCCCAAAACTTCCA
1 -AAAATTACATTTTGACCCCAAAACTTCTA
*
11549038 AAAATTACCATTTTG-CCCTCAAACCTTCTA
1 AAAATTA-CATTTTGACCC-CAAAACTTCTA
11549068 AAA
1 AAA
11549071 TTCTATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 31 0.58
30 22 0.42
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAAACTTCTA
Found at i:11549428 original size:58 final size:58
Alignment explanation
Indices: 11549038--11549404 Score: 576
Period size: 58 Copynumber: 6.3 Consensus size: 58
11549028 AAAACTTCCA
* * * * *
11549038 AAAATTACCATTTT-GCCCTCAAACCTTCTAAAATTCTATTTTTAACCCCGATTTAACC
1 AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
11549096 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
11549154 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCTCGATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* **
11549212 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCCTAATTTCACC
1 -AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
11549270 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
**
11549328 AAAATTACCATTTTACCCCTAAGTTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
11549386 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
11549405 CGAGTATCCA
Statistics
Matches: 285, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
57 37 0.13
58 208 0.73
59 40 0.14
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:11551338 original size:13 final size:13
Alignment explanation
Indices: 11551320--11551347 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11551310 CCCTTTGTTT
11551320 GGTAGAAAATGAA
1 GGTAGAAAATGAA
11551333 GGTAGAAAATGAA
1 GGTAGAAAATGAA
11551346 GG
1 GG
11551348 ATAAGGTATA
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:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (13 bp):
GGTAGAAAATGAA
Found at i:11552713 original size:15 final size:15
Alignment explanation
Indices: 11552690--11552719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11552680 ATATCTTTTG
*
11552690 ATTTTAAAGTAACTT
1 ATTTGAAAGTAACTT
11552705 ATTTGAAAGTAACTT
1 ATTTGAAAGTAACTT
11552720 TAATTATATA
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:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
ATTTGAAAGTAACTT
Found at i:11557740 original size:2 final size:2
Alignment explanation
Indices: 11557733--11557781 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
11557723 TAATTATACA
11557733 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11557775 AG AG AG A
1 AG AG AG A
11557782 TTATATTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11567304 original size:16 final size:16
Alignment explanation
Indices: 11567283--11567313 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11567273 CACCTAAGTC
11567283 ACACCTCAACCTTATA
1 ACACCTCAACCTTATA
*
11567299 ACACCTCAATCTTAT
1 ACACCTCAACCTTAT
11567314 CTAATTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
ACACCTCAACCTTATA
Found at i:11570913 original size:22 final size:22
Alignment explanation
Indices: 11570887--11570934 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
11570877 ATAAAAATCA
11570887 ATATGTATCTATTTACATATAT
1 ATATGTATCTATTTACATATAT
11570909 ATATGTATCTATTTACATATAT
1 ATATGTATCTATTTACATATAT
11570931 ATAT
1 ATAT
11570935 ATATATGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (22 bp):
ATATGTATCTATTTACATATAT
Found at i:11570949 original size:24 final size:24
Alignment explanation
Indices: 11570903--11570950 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11570893 ATCTATTTAC
* **
11570903 ATATATATATGTATCTATTTACAT
1 ATATATATATATATCTACGTACAT
*
11570927 ATATATATATATATGTACGTACAT
1 ATATATATATATATCTACGTACAT
11570951 GTGTATATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (24 bp):
ATATATATATATATCTACGTACAT
Found at i:11571002 original size:62 final size:66
Alignment explanation
Indices: 11570935--11571071 Score: 167
Period size: 66 Copynumber: 2.1 Consensus size: 66
11570925 ATATATATAT
* * * *
11570935 ATATATGTACGTACATGTGTATATGA-AT-AAAAT-AA-AAA-AATGAAATCAAGATGTATGTTT
1 ATATATATACGTACATGCGTATAT-ATATAAAAATAAATAAAGAATAAAATCAAAATGTATGTTT
11570995 GC
65 GC
* *
11570997 ATATATATATGTACATGCGTATATATATAAAAATAAATAAAGAATAAAATCAAAATGTATGTTTA
1 ATATATATACGTACATGCGTATATATATAAAAATAAATAAAGAATAAAATCAAAATGTATGTTTG
*
11571062 T
66 C
11571063 ATATATATA
1 ATATATATA
11571072 TGCCTACGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
61 1 0.02
62 23 0.37
63 5 0.08
64 2 0.03
65 3 0.05
66 29 0.46
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (66 bp):
ATATATATACGTACATGCGTATATATATAAAAATAAATAAAGAATAAAATCAAAATGTATGTTTG
C
Found at i:11572148 original size:39 final size:39
Alignment explanation
Indices: 11572080--11572749 Score: 653
Period size: 39 Copynumber: 17.0 Consensus size: 39
11572070 AGATTGGGTT
* **
11572080 ATGGTTTCAATCTACCCCATGATTAGGGTAAGAGATTGG
1 ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * * * * *
11572119 ATGGTTGCGATCTGCCTCATAATTGGGGTAAGAGATCGG
1 ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * * *
11572158 ATGATTTTTAATATGCCCCATGATCGGGGTAAGAGATCGG
1 ATG-GTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * ** *
11572198 ATGTTTTTCAATCTG-CCCATAATTAGGGTAAGAGATTAG
1 ATG-GTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * *
11572237 ATGGTTTTTAATATGCCCTATGATCGGGGTAAGAGATTGG
1 ATGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * *
11572277 ATGGTTTTTAATCTGCCCTATGATTGGGGTAAGAGATTGG
1 ATGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * * *
11572317 ATGGTTACGATCTGCCTCATGATCGGGGTAAGAGATCGG
1 ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
*
11572356 ATGGTTTTCAATCTGCCCCATGATTGGGGTAAGAGATTGG
1 ATGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * * * * *
11572396 ATGGCTACAATCTGCACCATGATCGAGTTAAGAGATCGG
1 ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* ** **
11572435 ATGATTTTCAATCTGCTTCATGATCTAGGTAAGAGATTGG
1 ATG-GTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * ** *
11572475 GTGGTTGT-GATCTGCCTTATGATCGGGGTAAGAGATCGG
1 ATGGTT-TCAATCTGCCCCATGATCGGGGTAAGAGATTGG
*
11572514 ATGGTTTTCAATCTGCCTCATGATCGGGGTAAGAGATTGG
1 ATGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* *
11572554 ATGGTTGCAATTTGCCCCATGATCGGGGTAAGAGATTGG
1 ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* *
11572593 -TGGTTTTTAATCTGCCCCATGATCGAGGTAAGAGATTGG
1 ATGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * * * * *
11572632 ATTGCTGCGATATGCCCCATGATCGGGGTAAGAGATCGG
1 ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * * *
11572671 ATGGTTTTCAATTTTCCCCATGATCGAGTTAAGAGATTGG
1 ATGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
* * * *
11572711 GTGGTTGCGATCTGCCCCATGATCGAGGTAAGAGATTGG
1 ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
11572750 TGCAGCTTCG
Statistics
Matches: 518, Mismatches: 102, Indels: 22
0.81 0.16 0.03
Matches are distributed among these distances:
38 3 0.01
39 283 0.55
40 232 0.45
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31
Consensus pattern (39 bp):
ATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
Found at i:11572188 original size:79 final size:79
Alignment explanation
Indices: 11572080--11572746 Score: 705
Period size: 79 Copynumber: 8.5 Consensus size: 79
11572070 AGATTGGGTT
* * * ** * * * *
11572080 ATGGTTTCAATCTACCCCATGATTAGGGTAAGAGATTGGATGG-TTGCGATCTGCCTCATAATTG
1 ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATTG
*
11572144 GGGTAAGAGATCGG
66 GGGTAAGAGATTGG
* ** * *
11572158 ATGATTTTTAATATGCCCCATGATCGGGGTAAGAGATCGGATGTTTTTCAATCTGCC-CATAATT
1 ATG-GTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATT
* *
11572222 AGGGTAAGAGATTAG
65 GGGGTAAGAGATTGG
** * * *
11572237 ATGGTTTTTAATATGCCCTATGATCGGGGTAAGAGATTGGATGGTTTTTAATCTGCC-CTATGAT
1 ATGG-TTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTC-ATGAT
11572301 TGGGGTAAGAGATTGG
64 TGGGGTAAGAGATTGG
* * * * *
11572317 ATGGTTACGATCTGCCTCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCCCATGATTG
1 ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATTG
11572382 GGGTAAGAGATTGG
66 GGGTAAGAGATTGG
* * * * * * * *
11572396 ATGGCTACAATCTGCACCATGATCGAGTTAAGAGATCGGATGATTTTCAATCTGCTTCATGATCT
1 ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGAT-T
*
11572461 -AGGTAAGAGATTGG
65 GGGGTAAGAGATTGG
* ** * ** *
11572475 GTGGTTGTGATCTGCCTTATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATCG
1 ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATTG
11572540 GGGTAAGAGATTGG
66 GGGTAAGAGATTGG
* * * * *
11572554 ATGGTTGCAATTTGCCCCATGATCGGGGTAAGAGATTGG-TGGTTTTTAATCTGCCCCATGATCG
1 ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATTG
*
11572618 AGGTAAGAGATTGG
66 GGGTAAGAGATTGG
* * * * * * *
11572632 ATTGCTGCGATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATTTTCCCCATGATCG
1 ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATTG
* *
11572697 AGTTAAGAGATTGG
66 GGGTAAGAGATTGG
* * * *
11572711 GTGGTTGCGATCTGCCCCATGATCGAGGTAAGAGAT
1 ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGAT
11572747 TGGTGCAGCT
Statistics
Matches: 504, Mismatches: 77, Indels: 15
0.85 0.13 0.03
Matches are distributed among these distances:
78 73 0.14
79 397 0.79
80 34 0.07
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (79 bp):
ATGGTTGCAATATGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTCAATCTGCCTCATGATTG
GGGTAAGAGATTGG
Found at i:11572913 original size:49 final size:49
Alignment explanation
Indices: 11572848--11573022 Score: 158
Period size: 49 Copynumber: 3.5 Consensus size: 49
11572838 TTACCGTTGT
* *
11572848 GGCCTCAATCTTTCCCTTCATATCTCTAAGGTGTAAGGTTCGCCGTTGC
1 GGCCTCAACCTTTCCCTTCATATCTCTAAGGTGTAAGGTTCGCCGTTAC
* * * ** * *
11572897 GGCTTCAACCTTTCCCTCCATATCTCTATGGTACAAGATTCACCGTTAC
1 GGCCTCAACCTTTCCCTTCATATCTCTAAGGTGTAAGGTTCGCCGTTAC
* * * *
11572946 GGCCTCAATCC-TTCCCATCACATCTTCTAA-G-GTACCGAGTTCGCCATTAC
1 GGCCTCAA-CCTTTCCCTTCATATC-TCTAAGGTGTA-AG-GTTCGCCGTTAC
*
11572996 GGCCTCAAACCTTTCCCTTCAAATCTC
1 GGCCTC-AACCTTTCCCTTCATATCTC
11573023 CATGGTACTG
Statistics
Matches: 98, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
48 1 0.01
49 59 0.60
50 25 0.26
51 13 0.13
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (49 bp):
GGCCTCAACCTTTCCCTTCATATCTCTAAGGTGTAAGGTTCGCCGTTAC
Found at i:11573158 original size:99 final size:97
Alignment explanation
Indices: 11572835--11573204 Score: 397
Period size: 99 Copynumber: 3.7 Consensus size: 97
11572825 TAGGGTATGA
* * * * ** * *
11572835 GATTTACCGTTGTGGCCTCAATCTTTCCCT-TCATATC-TCTAAGGTGTAAGGTTCGCCGTTGCG
1 GATTCACCGTTG-CGCCTCAATCCTT-CCTATCACATCTTCTAAGGTACAGGGTTCGCCATTGCG
* * *
11572898 GCTTCAACCTTTCCCTCCATATCTCTATGGTACAA
64 GCCTCAACCTTTCCCTTCATATCTC-ATGGTACAG
* * * * *
11572933 GATTCACCGTTACGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGAGTTCGCCATTACGG
1 GATTCACCGTTGC-GCCTCAATCCTTCCTATCACATCTTCTAAGGTACAGGGTTCGCCATTGCGG
* *
11572998 CCTCAAACCTTTCCCTTCAAATCTCCATGGTACTG
65 CCTC-AACCTTTCCCTTCATATCT-CATGGTACAG
* * * *
11573033 GATTCACCATTGCAGCCTCAATCCTTCCTATCACATCTTTTAAGGTACAGGGTTTGCCGTTGCGG
1 GATTCACCGTTGC-GCCTCAATCCTTCCTATCACATCTTCTAAGGTACAGGGTTCGCCATTGCGG
11573098 CCTCAACCTTTCCCTTCATATCTACATGGTATC-G
65 CCTCAACCTTTCCCTTCATATCT-CATGGTA-CAG
* *
11573132 GATTCACTGTTGCGTCCTCAATCCTT-CTCATCACGTCTTCTAAGGTACAGGGTTCGCCATTGCG
1 GATTCACCGTTGCG-CCTCAATCCTTCCT-ATCACATCTTCTAAGGTACAGGGTTCGCCATTGCG
11573196 GCCTCAACC
64 GCCTCAACC
11573205 CTGCCCATCA
Statistics
Matches: 228, Mismatches: 36, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
97 2 0.01
98 30 0.13
99 111 0.49
100 84 0.37
101 1 0.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (97 bp):
GATTCACCGTTGCGCCTCAATCCTTCCTATCACATCTTCTAAGGTACAGGGTTCGCCATTGCGGC
CTCAACCTTTCCCTTCATATCTCATGGTACAG
Found at i:11573252 original size:199 final size:198
Alignment explanation
Indices: 11572835--11573264 Score: 467
Period size: 199 Copynumber: 2.2 Consensus size: 198
11572825 TAGGGTATGA
* * * * **
11572835 GATTTACCGTTGTGGCCTCAATCTTTCCCTTCATATCTCTAAGGTGTAAGGTTCGCCGTTGCGGC
1 GATTCACCGTTGCGGCCTCAATCCTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGC
*
11572900 TTCAACCTTTCCCTCCATATCTCTATGGTACAAGATTCACCGTTACGGCCTCAATCCTTCCCATC
66 CTCAACCTTTCCCTCCATATCTCTATGGTACAAGATTCACCGTTACGGCCTCAATCCTTCCCATC
* * * * *
11572965 ACATCTTCTAAGGTACCGAGTTCGCCATTACGGCCTCAAACCTTTCCCTTCAAATCTCCATGGTA
131 ACATCTTCTAAGGTACAGAGTTCGCCATTACGGCCTCAAACCCTGCCCATCAAATCTCCAAGGTA
11573030 CTG
196 CTG
* * * * *
11573033 GATTCACCATTGCAGCCTCAATCCTT-CCTATCACATCTTTTAAGGTACAGGGTTTGCCGTTGCG
1 GATTCACCGTTGCGGCCTCAATCCTTCCCT-TCACATC-TCTAAGGTACAAGGTTCGCCGTTGCG
* * * * * *
11573097 GCCTCAACCTTTCCCTTCATATCTAC-ATGGTATC-GGATTCACTGTTGCGTCCTCAATCCTTCT
64 GCCTCAACCTTTCCCTCCATATCT-CTATGGTA-CAAGATTCACCGTTACGGCCTCAATCCTTCC
* * * ** *
11573160 CATCACGTCTTCTAAGGTACAGGGTTCGCCATTGCGGCCTC-AACCCTGCCCATCATGTCTTCTA
127 CATCACATCTTCTAAGGTACAGAGTTCGCCATTACGGCCTCAAACCCTGCCCATCAAATC-TCCA
11573224 AGGTA-TCG
191 AGGTACT-G
* **
11573232 GGTTTGCCGTTGCGGCCTCAA-CCTTTCCCTTCA
1 GATTCACCGTTGCGGCCTCAATCC-TTCCCTTCA
11573265 TGTCTTCATT
Statistics
Matches: 190, Mismatches: 34, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
197 3 0.02
198 43 0.23
199 139 0.73
200 5 0.03
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (198 bp):
GATTCACCGTTGCGGCCTCAATCCTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGC
CTCAACCTTTCCCTCCATATCTCTATGGTACAAGATTCACCGTTACGGCCTCAATCCTTCCCATC
ACATCTTCTAAGGTACAGAGTTCGCCATTACGGCCTCAAACCCTGCCCATCAAATCTCCAAGGTA
CTG
Found at i:11573266 original size:50 final size:50
Alignment explanation
Indices: 11572841--11573271 Score: 315
Period size: 50 Copynumber: 8.7 Consensus size: 50
11572831 ATGAGATTTA
* * ** *
11572841 CCGTTGTGGCCTCAATCTTTCCCTTCATATC-TCTAAGGTGTAAGGTTCG
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACAGGGTTCG
* * * * * *
11572890 CCGTTGCGGCTTCAACCTTTCCCTCCATATC-TCTATGGTACAAGATTCA
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACAGGGTTCG
* * * * *
11572939 CCGTTACGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACCGAGTTCG
1 CCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTCTAAGGTACAGGGTTCG
* * * * * * * *
11572989 CCATTACGGCCTCAAACCTTTCCCTTCAAATC-TCCATGGTACTGGATTCA
1 CCGTTGCGGCCTC-AACCTTTCCCTTCATATCTTCTAAGGTACAGGGTTCG
* * * * *
11573039 CCATTGCAGCCTCAATCC-TT-CCTATCACATCTTTTAAGGTACAGGGTTTG
1 CCGTTGCGGCCTCAA-CCTTTCCCT-TCATATCTTCTAAGGTACAGGGTTCG
* * * *
11573089 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTAC-ATGGTATC-GGATTCA
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTA-CAGGGTTCG
* * * * **
11573138 CTGTTGCGTCCTCAATCC-TTCTCATCACGTCTTCTAAGGTACAGGGTTCG
1 CCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTCTAAGGTACAGGGTTCG
* * * * * *
11573188 CCATTGCGGCCTCAACCCTGCCCATCATGTCTTCTAAGGTATC-GGGTTTG
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTA-CAGGGTTCG
*
11573238 CCGTTGCGGCCTCAACCTTTCCCTTCATGTCTTC
1 CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTC
11573272 ATTTTTCCTT
Statistics
Matches: 298, Mismatches: 69, Indels: 29
0.75 0.17 0.07
Matches are distributed among these distances:
48 3 0.01
49 111 0.37
50 167 0.56
51 17 0.06
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.32
Consensus pattern (50 bp):
CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACAGGGTTCG
Found at i:11582422 original size:14 final size:14
Alignment explanation
Indices: 11582403--11582439 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
11582393 GATCTCCAAG
11582403 GCAACTTCTGTTCA
1 GCAACTTCTGTTCA
11582417 GCAACTTCTGTTCA
1 GCAACTTCTGTTCA
11582431 GCAACTTCT
1 GCAACTTCT
11582440 TTCGACATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.35
Consensus pattern (14 bp):
GCAACTTCTGTTCA
Found at i:11590116 original size:25 final size:23
Alignment explanation
Indices: 11590088--11590133 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
11590078 GTTGGATCCA
11590088 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
11590113 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
11590134 CCATAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:11590141 original size:25 final size:26
Alignment explanation
Indices: 11590084--11590142 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
11590074 TCTAGTTGGA
11590084 TCCAAATTAAATTCTAAAAAGATAAT
1 TCCAAATTAAATTCTAAAAAGATAAT
*
11590110 T--AGAATTAAA-TCTAAACA-ATAAT
1 TCCA-AATTAAATTCTAAAAAGATAAT
11590133 TCCATAATTA
1 TCCA-AATTA
11590143 GATCCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 6 0.21
24 8 0.29
25 13 0.46
26 1 0.04
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (26 bp):
TCCAAATTAAATTCTAAAAAGATAAT
Found at i:11596348 original size:21 final size:21
Alignment explanation
Indices: 11596314--11596356 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
11596304 ATTTCAAAAA
*
11596314 TAATATTATTTTAATAG-ATT
1 TAATATTATCTTAATAGTATT
11596334 TAATACTTATCTTAATAGTATT
1 TAATA-TTATCTTAATAGTATT
11596356 T
1 T
11596357 TATTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
TAATATTATCTTAATAGTATT
Found at i:11596460 original size:47 final size:48
Alignment explanation
Indices: 11596334--11596469 Score: 150
Period size: 47 Copynumber: 2.8 Consensus size: 48
11596324 TTAATAGATT
* * * * *
11596334 TAATACTTATCTTAAT-AGTATTTTATTAATTTAATATTAAATTTAATT
1 TAATATTTATCTTGATAAATATTATATTAATTTAATA-TAAATTTAATA
* * *
11596382 TAATGTTTATCTTCTAGAAAAATATTCTATTAATTTAATA-AAATTTAATA
1 TAATATTTATC-T-T-GATAAATATTATATTAATTTAATATAAATTTAATA
11596432 TAATATTTATCTTGATAAATATTATATTAATTTAATAT
1 TAATATTTATCTTGATAAATATTATATTAATTTAATAT
11596470 TAAAGTGATT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
47 22 0.30
48 10 0.14
49 2 0.03
50 20 0.27
51 1 0.01
52 18 0.25
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (48 bp):
TAATATTTATCTTGATAAATATTATATTAATTTAATATAAATTTAATA
Found at i:11599882 original size:29 final size:29
Alignment explanation
Indices: 11599850--11599911 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
11599840 ATCTAAATAA
* * *
11599850 TTGACATGATGTGTTCTGAAAAAACAATT
1 TTGACAAGATGGGTTCTAAAAAAACAATT
* **
11599879 TTGAGAAGATGGGTTCTAAAAAAATTATT
1 TTGACAAGATGGGTTCTAAAAAAACAATT
11599908 TTGA
1 TTGA
11599912 TGAGATGGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (29 bp):
TTGACAAGATGGGTTCTAAAAAAACAATT
Found at i:11599917 original size:29 final size:29
Alignment explanation
Indices: 11599857--11599919 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
11599847 TAATTGACAT
* *
11599857 GATGTGTTCTGAAAAAACAATTTTGAGAA
1 GATGGGTTCTAAAAAAACAATTTTGAGAA
**
11599886 GATGGGTTCTAAAAAAATTATTTTGATG-A
1 GATGGGTTCTAAAAAAACAATTTTGA-GAA
11599915 GATGG
1 GATGG
11599920 ATTTTGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (29 bp):
GATGGGTTCTAAAAAAACAATTTTGAGAA
Found at i:11603569 original size:30 final size:32
Alignment explanation
Indices: 11603535--11603594 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
11603525 CAAAATAGCA
11603535 AAATTTAGATATCTT-GTTTTG-AATTTTTAG
1 AAATTTAGATATCTTAGTTTTGAAATTTTTAG
*
11603565 AAATTTAGATATGTTAGTTTTGAAATTTTT
1 AAATTTAGATATCTTAGTTTTGAAATTTTT
11603595 GACTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.52
31 6 0.22
32 7 0.26
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (32 bp):
AAATTTAGATATCTTAGTTTTGAAATTTTTAG
Found at i:11603695 original size:38 final size:38
Alignment explanation
Indices: 11603653--11603731 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
11603643 TGTAATATTG
*
11603653 TTTAAAAGTTAAATACTTCTTTAATTTTTATATAAAAT
1 TTTAAAAGTAAAATACTTCTTTAATTTTTATATAAAAT
* *
11603691 TTTAAAAGTAAAATACTTTTTTAATTTTTATATAATAT
1 TTTAAAAGTAAAATACTTCTTTAATTTTTATATAAAAT
11603729 TTT
1 TTT
11603732 GAAATCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (38 bp):
TTTAAAAGTAAAATACTTCTTTAATTTTTATATAAAAT
Found at i:11604303 original size:13 final size:13
Alignment explanation
Indices: 11604245--11604310 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
11604235 AGTTTAGTAT
*
11604245 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
11604258 TGCTTCTAAAAAG
1 TGCTTTTGAAAAG
11604271 TG-TTTTGGAAAAG
1 TGCTTTT-GAAAAG
*
11604284 TGATTTTGAAAAG
1 TGCTTTTGAAAAG
*
11604297 TTCTTTTTGAAAAG
1 TGC-TTTTGAAAAG
11604311 CTTAGTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
12 3 0.07
13 26 0.60
14 14 0.33
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:11616923 original size:7 final size:7
Alignment explanation
Indices: 11616911--11616955 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
11616901 CAAGATGAAC
11616911 GAACAAA
1 GAACAAA
11616918 GAACAAA
1 GAACAAA
11616925 GAACAAA
1 GAACAAA
11616932 G-ACAAA
1 GAACAAA
*
11616938 GAAACTAA
1 G-AACAAA
11616946 GAACACAA
1 GAACA-AA
11616954 GA
1 GA
11616956 GAGAGAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
6 6 0.18
7 18 0.55
8 9 0.27
ACGTcount: A:0.67, C:0.16, G:0.16, T:0.02
Consensus pattern (7 bp):
GAACAAA
Found at i:11623546 original size:100 final size:101
Alignment explanation
Indices: 11623346--11623546 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 101
11623336 GAAAATTTAC
11623346 AAAAGAAAGTTATTAAATAAAAAATAGAAAAGAGAAGGTTGGAGATTTCCACCAACTGAGATGAT
1 AAAAGAAAGTTATTAAATAAAAAATAGAAAAGAGAAGGTTGGAGATTTCCACCAACTGAGATGAT
*
11623411 AAAAAAAATAAAAGAAAGACTAAAAACTAAATTCAA
66 AAAAAAAATAAAAGAAAAACTAAAAACTAAATTCAA
11623447 AAAAGAAAGTTATTAAATAAAAAATAGAAAAGAGAAGGTTGGAGATTTCCACCAACTGAGATGAT
1 AAAAGAAAGTTATTAAATAAAAAATAGAAAAGAGAAGGTTGGAGATTTCCACCAACTGAGATGAT
11623512 -AAAAAAATAAAAGAAAAACTAAAAACTAAATTCAA
66 AAAAAAAATAAAAGAAAAACTAAAAACTAAATTCAA
11623547 CCGAAAACAA
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
100 34 0.34
101 65 0.66
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.19
Consensus pattern (101 bp):
AAAAGAAAGTTATTAAATAAAAAATAGAAAAGAGAAGGTTGGAGATTTCCACCAACTGAGATGAT
AAAAAAAATAAAAGAAAAACTAAAAACTAAATTCAA
Found at i:11628241 original size:6 final size:6
Alignment explanation
Indices: 11628230--11628259 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11628220 TAGCACATAT
11628230 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
1 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
11628260 TGATAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
ATCTCA
Found at i:11637016 original size:15 final size:15
Alignment explanation
Indices: 11636996--11637025 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11636986 GATGAAGGAG
*
11636996 AAGGAAGAAGAAGAA
1 AAGGAAGAAAAAGAA
11637011 AAGGAAGAAAAAGAA
1 AAGGAAGAAAAAGAA
11637026 GAAAAGAATG
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:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGGAAGAAAAAGAA
Found at i:11638135 original size:12 final size:11
Alignment explanation
Indices: 11638085--11638135 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
11638075 CAGTCACTTG
11638085 AAAAAG-GAAA
1 AAAAAGAGAAA
*
11638095 AAAATGAGAAA
1 AAAAAGAGAAA
11638106 AAGAAAGAGAAA
1 AA-AAAGAGAAA
11638118 AGAAAAGGAGAAA
1 A-AAAA-GAGAAA
11638131 AAAAA
1 AAAAA
11638136 TTATTGCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 6 0.17
12 16 0.46
13 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:11643780 original size:18 final size:18
Alignment explanation
Indices: 11643759--11643803 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
11643749 GAACCTATGG
11643759 CTGCATCTGAGTTTGTGA
1 CTGCATCTGAGTTTGTGA
*
11643777 CTGCATCTGATTTTGTGA
1 CTGCATCTGAGTTTGTGA
11643795 -TCGCATCTG
1 CT-GCATCTG
11643804 GTCAAGCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (18 bp):
CTGCATCTGAGTTTGTGA
Found at i:11647868 original size:37 final size:37
Alignment explanation
Indices: 11647812--11647989 Score: 171
Period size: 37 Copynumber: 4.8 Consensus size: 37
11647802 ATAATTTTAA
11647812 TCTAGAATTGCGCCCAAACATGTCGCTGCATGAGAACT
1 TCTAG-ATTGCGCCCAAACATGTCGCTGCATGAGAACT
* * * *
11647850 TTTAGATTGCGTCCAAACATGTCACTGCATGAGCACT
1 TCTAGATTGCGCCCAAACATGTCGCTGCATGAGAACT
* * * *
11647887 TCTAGATTACGCCCAAACATGTCGCCGCATGAGTACC
1 TCTAGATTGCGCCCAAACATGTCGCTGCATGAGAACT
* * * * ** *
11647924 TCTAGATTACACCCAAAAACTGTCACCACATGAGCACT
1 TCTAGATTGCGCCCAAACA-TGTCGCTGCATGAGAACT
* *
11647962 TCTAGATTGCACCAAAAC-TGT-GCTGCAT
1 TCTAGATTGCGCCCAAACATGTCGCTGCAT
11647990 AAATATTCTT
Statistics
Matches: 116, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
35 4 0.03
36 3 0.03
37 76 0.66
38 33 0.28
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (37 bp):
TCTAGATTGCGCCCAAACATGTCGCTGCATGAGAACT
Found at i:11647965 original size:75 final size:74
Alignment explanation
Indices: 11647812--11647969 Score: 199
Period size: 74 Copynumber: 2.1 Consensus size: 74
11647802 ATAATTTTAA
* * * * * ** * **
11647812 TCTAGAATTGCGCCCAAACATGTCGCTGCATGAGAACTTTTAGATTGCGTCCAAACATGTCACTG
1 TCTAG-ATTACGCCCAAACATGTCGCCGCATGAGAACCTCTAGATTACACCCAAAAATGTCACCA
11647877 CATGAGCACT
65 CATGAGCACT
*
11647887 TCTAGATTACGCCCAAACATGTCGCCGCATGAGTACCTCTAGATTACACCCAAAAACTGTCACCA
1 TCTAGATTACGCCCAAACATGTCGCCGCATGAGAACCTCTAGATTACACCCAAAAA-TGTCACCA
11647952 CATGAGCACT
65 CATGAGCACT
11647962 TCTAGATT
1 TCTAGATT
11647970 GCACCAAAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 42 0.59
75 29 0.41
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (74 bp):
TCTAGATTACGCCCAAACATGTCGCCGCATGAGAACCTCTAGATTACACCCAAAAATGTCACCAC
ATGAGCACT
Found at i:11648493 original size:37 final size:37
Alignment explanation
Indices: 11648443--11648517 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
11648433 TCGAGTAGCC
11648443 TGAGAATAGTATTCTCCATTTGTTCTTTTATATTTCT
1 TGAGAATAGTATTCTCCATTTGTTCTTTTATATTTCT
11648480 TGAGAATAGTATTCTCCATTTGTTCTTTTATATTTCT
1 TGAGAATAGTATTCTCCATTTGTTCTTTTATATTTCT
11648517 T
1 T
11648518 TCTTAAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (37 bp):
TGAGAATAGTATTCTCCATTTGTTCTTTTATATTTCT
Found at i:11653842 original size:14 final size:15
Alignment explanation
Indices: 11653823--11653853 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11653813 ATCTTTCATG
11653823 TTTAAAT-TTTTTTA
1 TTTAAATGTTTTTTA
11653837 TTTAAATGTTTTTTA
1 TTTAAATGTTTTTTA
11653852 TT
1 TT
11653854 ACATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTAAATGTTTTTTA
Found at i:11655241 original size:17 final size:17
Alignment explanation
Indices: 11655206--11655243 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
11655196 TTGGACACCA
11655206 TTCATTAGACTTTAGTT
1 TTCATTAGACTTTAGTT
*
11655223 TTCAGTTAGATTTTA-TT
1 TTCA-TTAGACTTTAGTT
11655240 TTCA
1 TTCA
11655244 CTATCGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (17 bp):
TTCATTAGACTTTAGTT
Found at i:11657004 original size:3 final size:3
Alignment explanation
Indices: 11656998--11657023 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11656988 ATAATAATTT
11656998 ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC AC
11657024 AAAAAGAACA
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:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:11661718 original size:35 final size:35
Alignment explanation
Indices: 11661668--11661938 Score: 373
Period size: 35 Copynumber: 7.7 Consensus size: 35
11661658 TGGTTAAAGT
* *
11661668 GTAAGGCTTTGGATTGCTTACGTCTAAGTTAGAGC
1 GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
* * *
11661703 GTAAGGCTTTAGATTGCTTACGTCTCGGTTAGAGC
1 GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
* * *
11661738 CTAAGGCTTTGGATTGCTTACGTCTCAGTTAGAGT
1 GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
* * *
11661773 GTAAGGCTATGGATTGCTTCCATCTCGGTTAGAGC
1 GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
* * *
11661808 GTAAGGCTTTGGATTGCTTAAGTCTCGGTTAGAGC
1 GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
11661843 GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
1 GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
*
11661878 GTAAGGCTATGGATTTCTTACGTCTC-GATTAGAGC
1 GTAAGGCTATGGATTGCTTACGTCTCAG-TTAGAGC
* *
11661913 ATAAGGCTATGGATTGCTTACATCTC
1 GTAAGGCTATGGATTGCTTACGTCTC
11661939 GAATAAAGCG
Statistics
Matches: 211, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
34 1 0.00
35 210 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (35 bp):
GTAAGGCTATGGATTGCTTACGTCTCAGTTAGAGC
Found at i:11661848 original size:105 final size:105
Alignment explanation
Indices: 11661660--11661932 Score: 411
Period size: 105 Copynumber: 2.6 Consensus size: 105
11661650 GGATAGCTTG
* * ** * *
11661660 GTTAAAGTGTAAGGCTTTGGATTGCTTACGTCTAAGTTAGAGCGTAAGGCTTTAGATTGCTTACG
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCGGTTAGAGCGTAAGGCTTTGGATTGCTTAAG
*
11661725 TCTCGGTTAGAGCCTAAGGCTTTGGATTGCTTACGTCTCA
66 TCTCGGTTAGAGCCTAAGGCTATGGATTGCTTACGTCTCA
* *
11661765 GTTAGAGTGTAAGGCTATGGATTGCTTCCATCTCGGTTAGAGCGTAAGGCTTTGGATTGCTTAAG
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCGGTTAGAGCGTAAGGCTTTGGATTGCTTAAG
*
11661830 TCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTCA
66 TCTCGGTTAGAGCCTAAGGCTATGGATTGCTTACGTCTCA
* * * * *
11661870 GTTAGAGCGTAAGGCTATGGATTTCTTACGTCTCGATTAGAGCATAAGGCTATGGATTGCTTA
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCGGTTAGAGCGTAAGGCTTTGGATTGCTTA
11661933 CATCTCGAAT
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 151 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (105 bp):
GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCGGTTAGAGCGTAAGGCTTTGGATTGCTTAAG
TCTCGGTTAGAGCCTAAGGCTATGGATTGCTTACGTCTCA
Found at i:11664450 original size:35 final size:35
Alignment explanation
Indices: 11664172--11664468 Score: 357
Period size: 35 Copynumber: 8.5 Consensus size: 35
11664162 GAAAGCTTGG
* * *
11664172 TTAGAGTGTAAGGCTTTGGATTGCTTACGTCTCTA
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11664207 TTAGAGCGTAAGGCTTTGAATTGCTTACGTCTCGG
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11664242 TTAGAGCATAAGGCTTTGGATTGCTTACGTATC-A
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11664276 GTTAGAGTGTAAGGTTATGGATTGCTTATGTCTC-A
1 -TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11664311 GTTAGAGCGTAAGGCTTTGGATTGCTTAAGTCTCGG
1 -TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
11664347 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTC-A
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
*
11664381 GTTAGAGCGTAAGGCTATGGATTTCTTACGTCTCGA
1 -TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* *
11664417 TTAGAGCATAAGGCTATGGATTGCTTACATCTCGA
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11664452 ATAAAGCGTAAAGCTAT
1 TTAGAGCGTAAGGCTAT
11664469 TGCAGCTTAG
Statistics
Matches: 228, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
35 227 1.00
36 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (35 bp):
TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
Found at i:11664450 original size:105 final size:104
Alignment explanation
Indices: 11664171--11664468 Score: 409
Period size: 105 Copynumber: 2.8 Consensus size: 104
11664161 GGAAAGCTTG
* * *
11664171 GTTAGAGTGTAAGGCTTTGGATTGCTTACGTCTCTATTAGAGCGTAAGGCTTTGAATTGCTTACG
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTC-ATTAGAGCGTAAGGCTTTGGATTGCTTACA
* *
11664236 TCTCGGTTAGAGCATAAGGCTTTGGATTGCTTACGTATCA
65 TCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTATCA
* *
11664276 GTTAGAGTGTAAGGTTATGGATTGCTTATGTCTCAGTTAGAGCGTAAGGCTTTGGATTGCTTA-A
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCA-TTAGAGCGTAAGGCTTTGGATTGCTTACA
*
11664340 GTCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTCA
65 -TCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTATCA
* * * *
11664381 GTTAGAGCGTAAGGCTATGGATTTCTTACGTCTCGATTAGAGCATAAGGCTATGGATTGCTTACA
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTC-ATTAGAGCGTAAGGCTTTGGATTGCTTACA
** * *
11664446 TCTCGAATAAAGCGTAAAGCTAT
65 TCTCGGTTAGAGCGTAAGGCTAT
11664469 TGCAGCTTAG
Statistics
Matches: 171, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
104 1 0.01
105 168 0.98
106 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (104 bp):
GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCATTAGAGCGTAAGGCTTTGGATTGCTTACAT
CTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTATCA
Found at i:11664468 original size:70 final size:70
Alignment explanation
Indices: 11664171--11664449 Score: 398
Period size: 70 Copynumber: 4.0 Consensus size: 70
11664161 GGAAAGCTTG
* * * *
11664171 GTTAGAGTGTAAGGCTTTGGATTGCTTACGTCTCTATTAGAGCGTAAGGCTTTGAATTGCTTACG
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
*
11664236 TCTCG
66 TCTCA
* * * * *
11664241 GTTAGAGCATAAGGCTTTGGATTGCTTACGTATC-AGTTAGAGTGTAAGGTTATGGATTGCTTAT
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGA-TTAGAGCGTAAGGCTATGGATTGCTTAC
11664305 GTCTCA
65 GTCTCA
* *
11664311 GTTAGAGCGTAAGGCTTTGGATTGCTTAAGTCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACG
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
11664376 TCTCA
66 TCTCA
* * * *
11664381 GTTAGAGCGTAAGGCTATGGATTTCTTACGTCTCGATTAGAGCATAAGGCTATGGATTGCTTACA
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
11664446 TCTC
66 TCTC
11664450 GAATAAAGCG
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
69 1 0.01
70 184 0.99
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (70 bp):
GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
TCTCA
Found at i:11666962 original size:35 final size:35
Alignment explanation
Indices: 11666684--11666980 Score: 357
Period size: 35 Copynumber: 8.5 Consensus size: 35
11666674 GAAAGCTTGG
* * *
11666684 TTAGAGTGTAAGGCTTTGGATTGCTTACGTCTCTA
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11666719 TTAGAGCGTAAGGCTTTGAATTGCTTACGTCTCGG
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11666754 TTAGAGCATAAGGCTTTGGATTGCTTACGTATC-A
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11666788 GTTAGAGTGTAAGGTTATGGATTGCTTATGTCTC-A
1 -TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11666823 GTTAGAGCGTAAGGCTTTGGATTGCTTAAGTCTCGG
1 -TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
11666859 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTC-A
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
*
11666893 GTTAGAGCGTAAGGCTATGGATTTCTTACGTCTCGA
1 -TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* *
11666929 TTAGAGCATAAGGCTATGGATTGCTTACATCTCGA
1 TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
* * *
11666964 ATAAAGCGTAAAGCTAT
1 TTAGAGCGTAAGGCTAT
11666981 TGCAGCTTAG
Statistics
Matches: 228, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
35 227 1.00
36 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (35 bp):
TTAGAGCGTAAGGCTATGGATTGCTTACGTCTCGA
Found at i:11666962 original size:105 final size:104
Alignment explanation
Indices: 11666683--11666980 Score: 409
Period size: 105 Copynumber: 2.8 Consensus size: 104
11666673 GGAAAGCTTG
* * *
11666683 GTTAGAGTGTAAGGCTTTGGATTGCTTACGTCTCTATTAGAGCGTAAGGCTTTGAATTGCTTACG
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTC-ATTAGAGCGTAAGGCTTTGGATTGCTTACA
* *
11666748 TCTCGGTTAGAGCATAAGGCTTTGGATTGCTTACGTATCA
65 TCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTATCA
* *
11666788 GTTAGAGTGTAAGGTTATGGATTGCTTATGTCTCAGTTAGAGCGTAAGGCTTTGGATTGCTTA-A
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCA-TTAGAGCGTAAGGCTTTGGATTGCTTACA
*
11666852 GTCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTCA
65 -TCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTATCA
* * * *
11666893 GTTAGAGCGTAAGGCTATGGATTTCTTACGTCTCGATTAGAGCATAAGGCTATGGATTGCTTACA
1 GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTC-ATTAGAGCGTAAGGCTTTGGATTGCTTACA
** * *
11666958 TCTCGAATAAAGCGTAAAGCTAT
65 TCTCGGTTAGAGCGTAAGGCTAT
11666981 TGCAGCTTAG
Statistics
Matches: 171, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
104 1 0.01
105 168 0.98
106 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (104 bp):
GTTAGAGTGTAAGGCTATGGATTGCTTACGTCTCATTAGAGCGTAAGGCTTTGGATTGCTTACAT
CTCGGTTAGAGCGTAAGGCTATGGATTGCTTACGTATCA
Found at i:11666980 original size:70 final size:70
Alignment explanation
Indices: 11666683--11666961 Score: 398
Period size: 70 Copynumber: 4.0 Consensus size: 70
11666673 GGAAAGCTTG
* * * *
11666683 GTTAGAGTGTAAGGCTTTGGATTGCTTACGTCTCTATTAGAGCGTAAGGCTTTGAATTGCTTACG
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
*
11666748 TCTCG
66 TCTCA
* * * * *
11666753 GTTAGAGCATAAGGCTTTGGATTGCTTACGTATC-AGTTAGAGTGTAAGGTTATGGATTGCTTAT
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGA-TTAGAGCGTAAGGCTATGGATTGCTTAC
11666817 GTCTCA
65 GTCTCA
* *
11666823 GTTAGAGCGTAAGGCTTTGGATTGCTTAAGTCTCGGTTAGAGCGTAAGGCTATGGATTGCTTACG
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
11666888 TCTCA
66 TCTCA
* * * *
11666893 GTTAGAGCGTAAGGCTATGGATTTCTTACGTCTCGATTAGAGCATAAGGCTATGGATTGCTTACA
1 GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
11666958 TCTC
66 TCTC
11666962 GAATAAAGCG
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
69 1 0.01
70 184 0.99
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (70 bp):
GTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTCGATTAGAGCGTAAGGCTATGGATTGCTTACG
TCTCA
Found at i:11669473 original size:35 final size:35
Alignment explanation
Indices: 11669193--11669491 Score: 382
Period size: 35 Copynumber: 8.5 Consensus size: 35
11669183 TGGAAAGCTT
* *
11669193 GGTTAGAGTGTAAGGCTTTGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
** * *
11669228 TATTAGAGCGTAAGGCTTTGAATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * *
11669263 GGTTAGAGCATAAGGCTTTGGATTGCTTACGTATC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * * *
11669298 AGTTAGAGTGTAAGGTTATGGATTGCTTATGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * *
11669333 AGTTAGAGCGTAAGGCTTTGGATTGCTTAAGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
11669368 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* *
11669403 AGTTAGAGCGTAAGGCTATGGATTGCTTACATCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* *
11669438 GGTTAGAGCATAAGGCTATGGATTGCTTACATCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
** * *
11669473 GAATAAAGCGTAAAGCTAT
1 GGTTAGAGCGTAAGGCTAT
11669492 TTCAGCTCAG
Statistics
Matches: 232, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 232 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (35 bp):
GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
Found at i:11671985 original size:35 final size:35
Alignment explanation
Indices: 11671705--11672003 Score: 382
Period size: 35 Copynumber: 8.5 Consensus size: 35
11671695 TGGAAAGCTT
* *
11671705 GGTTAGAGTGTAAGGCTTTGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
** * *
11671740 TATTAGAGCGTAAGGCTTTGAATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * *
11671775 GGTTAGAGCATAAGGCTTTGGATTGCTTACGTATC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * * *
11671810 AGTTAGAGTGTAAGGTTATGGATTGCTTATGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * *
11671845 AGTTAGAGCGTAAGGCTTTGGATTGCTTAAGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
11671880 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* *
11671915 AGTTAGAGCGTAAGGCTATGGATTGCTTACATCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* *
11671950 GGTTAGAGCATAAGGCTATGGATTGCTTACATCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
** * *
11671985 GAATAAAGCGTAAAGCTAT
1 GGTTAGAGCGTAAGGCTAT
11672004 TTCAGCTCAG
Statistics
Matches: 232, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 232 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (35 bp):
GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
Found at i:11674161 original size:35 final size:35
Alignment explanation
Indices: 11674122--11674420 Score: 420
Period size: 35 Copynumber: 8.5 Consensus size: 35
11674112 TGGATAGCTT
* *
11674122 GGTTAGA-CTGTAAAGCTTTGGATTGCTTACGTCTC
1 GGTTAGAGC-GTAAGGCTATGGATTGCTTACGTCTC
* *
11674157 GGTTAGAGCATAAGGCTTTGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* *
11674192 GATTAGAGTGTAAGGCTATGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* *
11674227 TGTTAGAGCGTAAGGCTTTGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * *
11674262 AGTTAGAGCGTAAGGCTTTGGATTGCTTACATCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* *
11674297 TGTTAGAGAGTAAGGCTATGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
*
11674332 AGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
* * *
11674367 GATTAGAGCATAAGGCTATGGATTGCTTACATCTC
1 GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
*
11674402 GGTTAAAGCGTAAGGCTAT
1 GGTTAGAGCGTAAGGCTAT
11674421 TTCAGCTCAG
Statistics
Matches: 238, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
35 237 1.00
36 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (35 bp):
GGTTAGAGCGTAAGGCTATGGATTGCTTACGTCTC
Found at i:11676647 original size:21 final size:21
Alignment explanation
Indices: 11676621--11676670 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
11676611 CTAGGCGTTT
11676621 TCGCGACACGCTATGCCCATG
1 TCGCGACACGCTATGCCCATG
*
11676642 TCGCGACACGCTATGCCCGTG
1 TCGCGACACGCTATGCCCATG
11676663 TCGCGACA
1 TCGCGACA
11676671 TAGAAGACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.38, G:0.26, T:0.18
Consensus pattern (21 bp):
TCGCGACACGCTATGCCCATG
Found at i:11680821 original size:149 final size:152
Alignment explanation
Indices: 11680523--11680806 Score: 357
Period size: 149 Copynumber: 1.9 Consensus size: 152
11680513 CGTTGTCGAC
*
11680523 TTTATTAACGAGATAAGTTCCTCAGGTGGATACTTAGACACTTTCTTTCTTTTGTATTTGTTTAT
1 TTTATTAACGAGATAAGTTCCTCAGGTGGATACTTAGACACTTTCTTTCTTTTATATTTGTTTAT
* * * * *
11680588 TCAGTTTTATGCTTTTGGTATATAATTGTTTTTTAATCGCCTCGATTGTGTTTGATGATTTGCTT
66 TCAGTCTGATGCTTTTGGTATATAACTGTTCTTTAATCGCATCGATTGTGTTTGATGATTTGCTT
11680653 GAATGACTTTAGACCTTGTGTT
131 GAATGACTTTAGACCTTGTGTT
*
11680675 TTTATTAACGAGATAAGTTCC-CTGGTGGATACTT-GA-AC-TT-TTTCTTTTATA-TTGTTTAT
1 TTTATTAACGAGATAAGTTCCTCAGGTGGATACTTAGACACTTTCTTTCTTTTATATTTGTTTAT
* ** * * * *
11680734 TTAGTCTGATGCTTATTTTTAGATATGAACT-TTCTTTAGTTGCATTGATTTTGTTTGATGATTT
66 TCAGTCTGATGCTT-TTGGT--ATAT-AACTGTTCTTTAATCGCATCGATTGTGTTTGATGATTT
11680798 GCTTGAATG
127 GCTTGAATG
11680807 GCTTCTTACC
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
146 19 0.17
147 13 0.11
148 2 0.02
149 42 0.37
150 5 0.04
151 12 0.11
152 21 0.18
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (152 bp):
TTTATTAACGAGATAAGTTCCTCAGGTGGATACTTAGACACTTTCTTTCTTTTATATTTGTTTAT
TCAGTCTGATGCTTTTGGTATATAACTGTTCTTTAATCGCATCGATTGTGTTTGATGATTTGCTT
GAATGACTTTAGACCTTGTGTT
Found at i:11683498 original size:19 final size:19
Alignment explanation
Indices: 11683452--11683488 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11683442 TTTTAGTTCT
*
11683452 GTTTTTAAAAATATATATA
1 GTTTTTAAAAATATAAATA
11683471 GTTTTTAAAAATATAAAT
1 GTTTTTAAAAATATAAAT
11683489 TTTTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
GTTTTTAAAAATATAAATA
Found at i:11687168 original size:21 final size:21
Alignment explanation
Indices: 11687142--11687183 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11687132 TACCGACACT
11687142 TCATCGAAGGCTACTCTAAAA
1 TCATCGAAGGCTACTCTAAAA
11687163 TCATCGAAGGCTACTCTAAAA
1 TCATCGAAGGCTACTCTAAAA
11687184 GCCGAGTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (21 bp):
TCATCGAAGGCTACTCTAAAA
Found at i:11687567 original size:37 final size:37
Alignment explanation
Indices: 11687517--11687689 Score: 224
Period size: 37 Copynumber: 4.7 Consensus size: 37
11687507 TTAATCCAGA
11687517 ATTGCGCCCAAACATGTCGCTGCATGAGCACTTCTAG
1 ATTGCGCCCAAACATGTCGCTGCATGAGCACTTCTAG
*
11687554 ATTGCGCCCAAACATGTCGCTACATGAGCACTTCTAG
1 ATTGCGCCCAAACATGTCGCTGCATGAGCACTTCTAG
* *
11687591 ATTGCGCCCAAACATGTCGCCGCATGAGCACCTCTAG
1 ATTGCGCCCAAACATGTCGCTGCATGAGCACTTCTAG
* * * **
11687628 ATTGCACCCAAAAACTATCGCCACATGAGCACTTCTAG
1 ATTGCGCCCAAACA-TGTCGCTGCATGAGCACTTCTAG
* *
11687666 ATTAC-ACCAAA-ATTGTCGCTGCAT
1 ATTGCGCCCAAACA-TGTCGCTGCAT
11687690 AAATATTCTT
Statistics
Matches: 120, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
36 9 0.08
37 87 0.73
38 24 0.20
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
ATTGCGCCCAAACATGTCGCTGCATGAGCACTTCTAG
Found at i:11687761 original size:34 final size:36
Alignment explanation
Indices: 11687676--11687761 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 36
11687666 ATTACACCAA
*
11687676 AATTGTCGCTGCATAAATATTCTTCAAATTGCATCCAG
1 AATTGTCGCTGCATAAATA-T-TTCAAATTGCACCCAG
* * *
11687714 AATTATCGTTGCATAAGTA-TTC-AATTGCACCCAGG
1 AATTGTCGCTGCATAAATATTTCAAATTGCACCCA-G
11687749 AA-TGTCGCTGCAT
1 AATTGTCGCTGCAT
11687762 GAACATGTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
34 19 0.46
35 6 0.15
38 16 0.39
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (36 bp):
AATTGTCGCTGCATAAATATTTCAAATTGCACCCAG
Found at i:11687800 original size:26 final size:26
Alignment explanation
Indices: 11687751--11687804 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
11687741 CACCCAGGAA
*
11687751 TGTCGCTGCATGAACATGTACAAAAT
1 TGTCGCTGCATGAACACGTACAAAAT
* *
11687777 TGTCGCTGCATGAACGCGTCCAAAAT
1 TGTCGCTGCATGAACACGTACAAAAT
11687803 TG
1 TG
11687805 CACCCAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (26 bp):
TGTCGCTGCATGAACACGTACAAAAT
Found at i:11691635 original size:17 final size:17
Alignment explanation
Indices: 11691615--11691663 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
11691605 AACTAAGTTA
11691615 ACAAAAGCAATGCAGTG
1 ACAAAAGCAATGCAGTG
11691632 ACAAAA-CAAAATGCAGTG
1 ACAAAAGC--AATGCAGTG
11691650 ACAATAAG-AATGCA
1 ACAA-AAGCAATGCA
11691664 TGAGAACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 13 0.46
19 2 0.07
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (17 bp):
ACAAAAGCAATGCAGTG
Found at i:11701434 original size:21 final size:20
Alignment explanation
Indices: 11701390--11701435 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
11701380 CATCCCTATG
*
11701390 TCAATAACTACACTTTGTCA
1 TCAATAACTACACTTAGTCA
11701410 TCAATAAACTACACATTAGTC-
1 TCAAT-AACTACAC-TTAGTCA
11701431 TCAAT
1 TCAAT
11701436 GCTTTATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAATAACTACACTTAGTCA
Found at i:11701985 original size:36 final size:36
Alignment explanation
Indices: 11701938--11702011 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
11701928 GGATCCACTT
*
11701938 ATCCAAAAACAAAGGTACAGTTTCAGTATAAGGTTA
1 ATCCAAAAACAAAGGTACAGTTTCAGTATAAGATTA
**
11701974 ATCCAAAAACAAAGGTACAGTTTTGGTATAAGATTA
1 ATCCAAAAACAAAGGTACAGTTTCAGTATAAGATTA
11702010 AT
1 AT
11702012 TGTTATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (36 bp):
ATCCAAAAACAAAGGTACAGTTTCAGTATAAGATTA
Found at i:11703161 original size:45 final size:45
Alignment explanation
Indices: 11703094--11703216 Score: 147
Period size: 45 Copynumber: 2.7 Consensus size: 45
11703084 TCAAAGGACA
* * *
11703094 CCATAGCGTCTTTCAGCCATGGTCTTACTCATTTCCGTCATGATG
1 CCATAGCATCTTTCAGCTATGGTCTTACTCATTTCCATCATGATG
* ** ** *
11703139 CCATAGCATCTTTCAACTATGGTCTTACTTTTTTTTATCCTGATG
1 CCATAGCATCTTTCAGCTATGGTCTTACTCATTTCCATCATGATG
* *
11703184 TCATAACATCTTTCAGCTATGGTCTTACTCATT
1 CCATAGCATCTTTCAGCTATGGTCTTACTCATT
11703217 CTAGGCGTAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.41
Consensus pattern (45 bp):
CCATAGCATCTTTCAGCTATGGTCTTACTCATTTCCATCATGATG
Found at i:11722035 original size:4 final size:4
Alignment explanation
Indices: 11722026--11722060 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
11722016 GTGCTCCAAT
* *
11722026 TTCA TTCA TTCA CTCA TTCA TTCA TTTA TTCA TTC
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTC
11722061 GCTCATTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (4 bp):
TTCA
Found at i:11722044 original size:12 final size:12
Alignment explanation
Indices: 11722027--11722067 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
11722017 TGCTCCAATT
11722027 TCATTCATTCAC
1 TCATTCATTCAC
*
11722039 TCATTCATTCAT
1 TCATTCATTCAC
* *
11722051 TTATTCATTCGC
1 TCATTCATTCAC
11722063 TCATT
1 TCATT
11722068 TGTTTATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.02, T:0.49
Consensus pattern (12 bp):
TCATTCATTCAC
Found at i:11726165 original size:3 final size:3
Alignment explanation
Indices: 11726157--11726184 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11726147 GAAGGTGAAT
11726157 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
11726185 GACCAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11726639 original size:17 final size:17
Alignment explanation
Indices: 11726614--11726666 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
11726604 ATGCATCTCA
11726614 TTTAATTGTCATTTCAT
1 TTTAATTGTCATTTCAT
* * *
11726631 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTTCAT
* * *
11726648 TTTACTTGTTAGTTCAT
1 TTTAATTGTCATTTCAT
11726665 TT
1 TT
11726667 GCATTGTAGT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.58
Consensus pattern (17 bp):
TTTAATTGTCATTTCAT
Found at i:11741966 original size:43 final size:43
Alignment explanation
Indices: 11741918--11742247 Score: 412
Period size: 43 Copynumber: 7.7 Consensus size: 43
11741908 TACTAAAAGA
* * *
11741918 AAGACTCATGTCTCGGATAGAGCATGAGATTATTTATAAATGG
1 AAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGG
* *
11741961 AAGACTTATGTCTCGATTAGAGCATAAGATTATTTATAAAAGG
1 AAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGG
* *
11742004 AAGACTTATGTCTTGGTTAGAGCATAAGATTATTTATAAATTG
1 AAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGG
* *
11742047 AAGACTTATGTCTCGGTTGGAGCATAAGATTGTTTATAAAAT-G
1 AAGACTTATGTCTCGGTTAGAGCATAAGATTATTTAT-AAATGG
* *
11742090 AAGACTTATGTCTCGGTTAGAGCATAAGATTATTCATAAAAGG
1 AAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGG
* * * * *
11742133 AAGACTTATGTCTCGGTTGGAGTATAAAATTGTTTATAAAAGG
1 AAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGG
* * * * *
11742176 AAGACTAATGTCTCGG-CAGGATCATAAGGTTATTTGTAAATGG
1 AAGACTTATGTCTCGGTTA-GAGCATAAGATTATTTATAAATGG
* *
11742219 AAGAACTTATGACTCGGTTGGAGCATAAG
1 AAG-ACTTATGTCTCGGTTAGAGCATAAG
11742248 GTTAATACAG
Statistics
Matches: 246, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
42 3 0.01
43 220 0.89
44 23 0.09
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.32
Consensus pattern (43 bp):
AAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGG
Found at i:11742056 original size:86 final size:86
Alignment explanation
Indices: 11741911--11742247 Score: 469
Period size: 86 Copynumber: 3.9 Consensus size: 86
11741901 TGGTGATTAC
* * * *
11741911 TAAAAGAAAGACTCATGTCTCGGATAGAGCATGAGATTATTTATAAATGGAAGACTTATGTCTCG
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGGAAGACTTATGTCTCG
* * *
11741976 ATTAGAGCATAAGATTATTTA
66 GTTGGAGCATAAGATTGTTTA
* *
11741997 TAAAAGGAAGACTTATGTCTTGGTTAGAGCATAAGATTATTTATAAATTGAAGACTTATGTCTCG
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGGAAGACTTATGTCTCG
11742062 GTTGGAGCATAAGATTGTTTA
66 GTTGGAGCATAAGATTGTTTA
* * *
11742083 TAAAATGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTCATAAAAGGAAGACTTATGTCTCG
1 TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGGAAGACTTATGTCTCG
* *
11742148 GTTGGAGTATAAAATTGTTTA
66 GTTGGAGCATAAGATTGTTTA
* * * * * *
11742169 TAAAAGGAAGACTAATGTCTCGG-CAGGATCATAAGGTTATTTGTAAATGGAAGAACTTATGACT
1 TAAAAGGAAGACTTATGTCTCGGTTA-GAGCATAAGATTATTTATAAATGGAAG-ACTTATGTCT
11742233 CGGTTGGAGCATAAG
64 CGGTTGGAGCATAAG
11742248 GTTAATACAG
Statistics
Matches: 222, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
85 1 0.00
86 199 0.90
87 22 0.10
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (86 bp):
TAAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTATTTATAAATGGAAGACTTATGTCTCG
GTTGGAGCATAAGATTGTTTA
Found at i:11743005 original size:16 final size:17
Alignment explanation
Indices: 11742984--11743031 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
11742974 TTATCAAAAA
11742984 TTTCTTTCTTTTTCT-T
1 TTTCTTTCTTTTTCTAT
*
11743000 TTTCTTCCTTTTTCTCAT
1 TTTCTTTCTTTTTCT-AT
*
11743018 TTTGTTTCTTTTTC
1 TTTCTTTCTTTTTC
11743032 AAATGACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTAT
Done.