Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 3 of 290
Found at i:772295 original size:159 final size:161
Alignment explanation
Indices: 772063--772517 Score: 600
Period size: 154 Copynumber: 2.9 Consensus size: 161
772053 TTTTTCCTTA
772063 AAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTT
1 AAAAACCCT--AAACCCTAAACCACTAAGCCCTAATTTAATTGA-TTTTTCTTATTTTCATAGTT
*
772128 AATTTAATTAATTAACCCTCAACTTTAAGTGTTCATTAATTTTTCCCTTAAAAAACACAAAAAAC
63 AATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCCCTTAAAAAACAC-AAAAAC
* * *
772193 TCTAAATCGCTAAAACCCTAA-CCCTAAAACAATC
127 CCTAAACCACTAAAACCCTAACCCCTAAAACAATC
* *
772227 AAAAACCCT-AACCTTAAAAACC-CTAAACCCTAATTTAATTGA-TTTT-TTATTTTCATAGTTA
1 AAAAACCCTAAACCCT--AAACCACTAAGCCCTAATTTAATTGATTTTTCTTATTTTCATAGTTA
* *
772288 ATTTAATTAATTAACCCTCAACTCTAAGTG----------TTTCCCTTAAATAACACTAAAACCC
64 ATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCCCTTAAAAAACACAAAAACCC
* *
772343 TAAACCACTAAAACCTTAACCCCTAAAATAATC
129 TAAACCACTAAAACCCTAACCCCTAAAACAATC
772376 AAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTT
1 AAAAACCCT--AAACCCTAAACCACTAAGCCCTAATTTAATTGA-TTTTTCTTATTTTCATAGTT
* *
772441 AATTTAATTAATTAACCTTCAACTCTAAGTGTTCATTAATTTTT-CCTTAAAAAACCCTAAAAAC
63 AATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCCCTTAAAAAACAC-AAAAAC
772505 CCTAAACCACTAA
127 CCTAAACCACTAA
772518 GCCCTAATTT
Statistics
Matches: 254, Mismatches: 16, Indels: 42
0.81 0.05 0.13
Matches are distributed among these distances:
148 22 0.09
149 37 0.15
150 5 0.02
151 19 0.07
152 5 0.02
153 4 0.02
154 44 0.17
159 44 0.17
160 4 0.02
161 5 0.02
162 19 0.07
163 16 0.06
164 30 0.12
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.33
Consensus pattern (161 bp):
AAAAACCCTAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTCTTATTTTCATAGTTAAT
TTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCCCTTAAAAAACACAAAAACCCTA
AACCACTAAAACCCTAACCCCTAAAACAATC
Found at i:772368 original size:15 final size:16
Alignment explanation
Indices: 772332--772370 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
772322 CCTTAAATAA
772332 CACTAAAACCCTAAAC
1 CACTAAAACCCTAAAC
*
772348 CACTAAAA-CCTTAAC
1 CACTAAAACCCTAAAC
*
772363 CCCTAAAA
1 CACTAAAA
772371 TAATCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (16 bp):
CACTAAAACCCTAAAC
Found at i:772581 original size:104 final size:109
Alignment explanation
Indices: 772376--772621 Score: 378
Period size: 114 Copynumber: 2.3 Consensus size: 109
772366 TAAAATAATC
772376 AAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTT
1 AAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTT
772441 AATTTAATTAATTAACCTTCAACTCTAAGTGTTCATTAATTTTT-CCTTA
66 AATTTAATTAATTAACC-TC-ACTC--A--GTTCATTAATTTTTCCCTTA
772490 AAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTT
1 AAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTT
772555 AATTTAATTAATTAA-C-C-CTC-GTTCATTAATTTTTCCCTTA
66 AATTTAATTAATTAACCTCACTCAGTTCATTAATTTTTCCCTTA
* *
772595 AATAACACT-AAAACCCTAAACCACTAA
1 AAAAACCCTAAAAACCCTAAACCACTAA
772622 AACCTTAACC
Statistics
Matches: 129, Mismatches: 2, Indels: 12
0.90 0.01 0.08
Matches are distributed among these distances:
104 32 0.25
105 12 0.09
109 3 0.02
111 1 0.01
113 1 0.01
114 80 0.62
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (109 bp):
AAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTT
AATTTAATTAATTAACCTCACTCAGTTCATTAATTTTTCCCTTA
Found at i:772592 original size:268 final size:268
Alignment explanation
Indices: 772244--772846 Score: 1110
Period size: 268 Copynumber: 2.3 Consensus size: 268
772234 CTAACCTTAA
*
772244 AAACC-CTAAACCCTAATTTAATTGA--TTTT-TTATTTTCATAGTTAATTTAATTAATTAACCC
1 AAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCC
772305 TCAACTCTAAGTGTTTCCCTTAAATAACACTAAAACCCTAAACCACTAAAACCTTAACCCCTAAA
66 TCAACTCTAAGTGTTTCCCTTAAATAACACTAAAACCCTAAACCACTAAAACCTTAACCCCTAAA
772370 ATAATCAAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTC
131 ATAATCAAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTC
772435 ATAGTTAATTTAATTAATTAACCTTCAACTCTAAGTGTTCATTAATTTTTCCTTAAAAAACCCTA
196 ATAGTTAATTTAATTAATTAACCTTCAACTCTAAGTGTTCATTAATTTTTCCTTAAAAAACCCTA
772500 AAAACCCT
261 AAAACCCT
772508 AAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCC
1 AAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCC
** *
772573 TC-GTTCATTAA-TTTTTCCCTTAAATAACACTAAAACCCTAAACCACTAAAACCTTAACCCCTA
66 TCAACTC--TAAGTGTTTCCCTTAAATAACACTAAAACCCTAAACCACTAAAACCTTAACCCCTA
772636 AAATAATCAAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTT
129 AAATAATCAAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTT
772701 TCATAGTTAATTTAATTAATTAACCTTCAACTCTAAGTGTTCATTAATTTTTCCTTAAAAAACCC
194 TCATAGTTAATTTAATTAATTAACCTTCAACTCTAAGTGTTCATTAATTTTTCCTTAAAAAACCC
772766 TAAAAACCCT
259 TAAAAACCCT
772776 AAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCC
1 AAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCC
772841 TCAACT
66 TCAACT
772847 NGTTTTTAAA
Statistics
Matches: 326, Mismatches: 6, Indels: 9
0.96 0.02 0.03
Matches are distributed among these distances:
264 5 0.02
265 19 0.06
267 6 0.02
268 292 0.90
269 4 0.01
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (268 bp):
AAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCC
TCAACTCTAAGTGTTTCCCTTAAATAACACTAAAACCCTAAACCACTAAAACCTTAACCCCTAAA
ATAATCAAAAACCCTAAAAACCCTAAACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTC
ATAGTTAATTTAATTAATTAACCTTCAACTCTAAGTGTTCATTAATTTTTCCTTAAAAAACCCTA
AAAACCCT
Found at i:772636 original size:15 final size:16
Alignment explanation
Indices: 772600--772638 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
772590 CCTTAAATAA
772600 CACTAAAACCCTAAAC
1 CACTAAAACCCTAAAC
*
772616 CACTAAAA-CCTTAAC
1 CACTAAAACCCTAAAC
*
772631 CCCTAAAA
1 CACTAAAA
772639 TAATCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (16 bp):
CACTAAAACCCTAAAC
Found at i:797447 original size:23 final size:22
Alignment explanation
Indices: 797404--797493 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 22
797394 GTTGATGGAC
*
797404 AGTAAGCTCTATTGAGCTGAAAT
1 AGTAAGCTCTA-CGAGCTGAAAT
*
797427 AGTAAGCTCTGACGAGTTG-AAT
1 AGTAAGCTCT-ACGAGCTGAAAT
* *
797449 CAGTAAGCTCATACGAGCTAAGAAC
1 -AGTAAGCTC-TACGAGCTGA-AAT
797474 AGTAAGCTCTTACGAGCTGA
1 AGTAAGCTC-TACGAGCTGA
797494 TATATCGGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
22 3 0.05
23 30 0.55
24 20 0.36
25 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (22 bp):
AGTAAGCTCTACGAGCTGAAAT
Found at i:800649 original size:42 final size:42
Alignment explanation
Indices: 800603--800691 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
800593 TCTGGAACAA
* **
800603 GGCATCGAAATGAGATTTCATATAAGACCATACTTGGGATAT
1 GGCATCGAAATAAGATCCCATATAAGACCATACTTGGGATAT
** * **
800645 GGCATCGATGTAAGATCCCATGTAAGACCATGTTTGGGATAT
1 GGCATCGAAATAAGATCCCATATAAGACCATACTTGGGATAT
800687 GGCAT
1 GGCAT
800692 TGGTATCTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (42 bp):
GGCATCGAAATAAGATCCCATATAAGACCATACTTGGGATAT
Found at i:801692 original size:30 final size:30
Alignment explanation
Indices: 801656--801715 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
801646 TGCACGGGAA
801656 GACACACGGGCAGGT-GTCTAGGCTGTGTGT
1 GACACACGGGCAGGTGGTCT-GGCTGTGTGT
* *
801686 GACACACGGTCATGTGGTCTGGCTGTGTGT
1 GACACACGGGCAGGTGGTCTGGCTGTGTGT
801716 CCCCTACACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.15, C:0.20, G:0.38, T:0.27
Consensus pattern (30 bp):
GACACACGGGCAGGTGGTCTGGCTGTGTGT
Found at i:814675 original size:42 final size:42
Alignment explanation
Indices: 814609--814763 Score: 166
Period size: 42 Copynumber: 3.7 Consensus size: 42
814599 TGTGTTATCA
* * * * *
814609 TGTAAGACCATATCTAGGATATGGCGTTGATATGAGATTTCG
1 TGTAAGACCATGTTTGGGACATGGCATTGATATGAGATTTCG
* *
814651 TGTAAGACCATGTTTGGAACATGGCATTGAAATGAGATTTCG
1 TGTAAGACCATGTTTGGGACATGGCATTGATATGAGATTTCG
* * * * ** *
814693 TATAAGACCATGTTTGGGATATGGCATCGATGTGAGATCCCA
1 TGTAAGACCATGTTTGGGACATGGCATTGATATGAGATTTCG
* *
814735 TGTAAGACCACGTTCGGGACATGGCATTG
1 TGTAAGACCATGTTTGGGACATGGCATTG
814764 GTATCTTATT
Statistics
Matches: 92, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATGTTTGGGACATGGCATTGATATGAGATTTCG
Found at i:829202 original size:46 final size:46
Alignment explanation
Indices: 829066--829237 Score: 149
Period size: 46 Copynumber: 3.7 Consensus size: 46
829056 ATGCCTATGC
* *
829066 CATGTCCCAGACATGGTCTTACAC-AG-ACACATCTCGT-AGCTGATG
1 CATGTCCCAGACATGGTCTTACACTAGCACTCATCTCATGA-C-GATG
* * * * * *
829111 CATGTCCCAGACA-AGTCTTACATTGGC-TTACATCTCGAGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCACT-CATCTC-ATGACGATG
*
829157 CATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATGACGATG
1 CATGTCCCAGACATGGTCTTACACTAGCACTCATCTC-ATGACGATG
* *
829203 CCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
1 -CATGTCCCAGACATGGTCTTACACTAGCACTCAT
829238 GTAGCCAATG
Statistics
Matches: 100, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
44 8 0.08
45 14 0.14
46 46 0.46
47 16 0.16
48 16 0.16
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTAGCACTCATCTCATGACGATG
Found at i:834812 original size:15 final size:15
Alignment explanation
Indices: 834794--834823 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
834784 AAAAGATCAA
*
834794 GAGGGAAAAGAAGAG
1 GAGGAAAAAGAAGAG
834809 GAGGAAAAAGAAGAG
1 GAGGAAAAAGAAGAG
834824 AGAGTAGAAA
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:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
GAGGAAAAAGAAGAG
Found at i:835557 original size:33 final size:33
Alignment explanation
Indices: 835515--835578 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
835505 CAAGACAAGT
835515 ATGGTTTGTACAAGTGGTTGGTTATGCCTTTCG
1 ATGGTTTGTACAAGTGGTTGGTTATGCCTTTCG
835548 ATGGTTTGTACAAGTGGTTGGTTATGCCTTT
1 ATGGTTTGTACAAGTGGTTGGTTATGCCTTT
835579 TGGCTTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.16, C:0.11, G:0.30, T:0.44
Consensus pattern (33 bp):
ATGGTTTGTACAAGTGGTTGGTTATGCCTTTCG
Found at i:843708 original size:20 final size:21
Alignment explanation
Indices: 843683--843727 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
843673 ACACGGCTAA
843683 CCACACG-CCCATGTGCTAGG
1 CCACACGACCCATGTGCTAGG
*
843703 CCACACGCACCCGTGTGCTAGG
1 CCACACG-ACCCATGTGCTAGG
843725 CCA
1 CCA
843728 TATGCCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.13
Consensus pattern (21 bp):
CCACACGACCCATGTGCTAGG
Found at i:845058 original size:43 final size:42
Alignment explanation
Indices: 844894--845059 Score: 149
Period size: 43 Copynumber: 3.9 Consensus size: 42
844884 CATAAGCTCG
* * ** *
844894 TACAATGCC-ATATCCCAGATATGGTCTTACTTGTTA-CCATA
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCCA-A
* * * * * *
844935 TATCGATGCCACT-TCCCAGACAGGGTCTTACACGAAATCGAT
1 TA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCCAA
* *
844977 TAACCATGCCAATGTCCCAAACATGGTCTTACACGTAATCTCAA
1 T-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC-CAA
*
845021 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC
845060 AAGTCTCGAT
Statistics
Matches: 99, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
41 2 0.02
42 33 0.33
43 62 0.63
44 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCCAA
Found at i:850444 original size:43 final size:43
Alignment explanation
Indices: 850383--850571 Score: 283
Period size: 43 Copynumber: 4.4 Consensus size: 43
850373 ACATATCATT
* *
850383 TCACCGGCATTACGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
850426 TCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
850469 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* * *
850512 TCACCGGCACTAAACCTGCTAGGCATGAAGGCCCGAATATA-A
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
850554 T-ACCAGCACTAGGCCTGC
1 TCACCGGCACTAAGCCTGC
850572 GAGATTTATC
Statistics
Matches: 134, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 14 0.10
42 2 0.01
43 118 0.88
ACGTcount: A:0.30, C:0.34, G:0.23, T:0.13
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:850596 original size:38 final size:38
Alignment explanation
Indices: 850543--850626 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
850533 GGCATGAAGG
* * *
850543 CCCGAATATAATACCAGCACTAGGCCTGCGAGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAA
* *
850581 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAA
850619 CCCGAATA
1 CCCGAATA
850627 CACATCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAA
Found at i:859862 original size:27 final size:27
Alignment explanation
Indices: 859832--860009 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
859822 ATATTGAGTC
* * * *
859832 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
859859 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
859886 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
859914 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
859941 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
859968 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
859995 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
860010 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:859971 original size:82 final size:81
Alignment explanation
Indices: 859853--860008 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
859843 TGCTATATAA
* *
859853 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
859918 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
859935 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
859999 CACTTAGTGC
65 CACTTAGTGC
860009 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:880540 original size:27 final size:26
Alignment explanation
Indices: 880482--880588 Score: 124
Period size: 27 Copynumber: 4.0 Consensus size: 26
880472 TGGCTGCCAA
* *
880482 AACAGATAATGTGACAGAGTCACCAG
1 AACAGATAATGTGGCAGAGCCACCAG
880508 ATACAGATAATCGTGGCAGAGCCACCAG
1 A-ACAGATAAT-GTGGCAGAGCCACCAG
*
880536 AACAGATATATGTGGTAGAGCCACCAG
1 AACAGATA-ATGTGGCAGAGCCACCAG
* * *
880563 ATCAGATATTTGTGGCATAGCCACCA
1 AACAGATA-ATGTGGCAGAGCCACCA
880589 TAACGCTTCC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.01
27 53 0.75
28 17 0.24
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (26 bp):
AACAGATAATGTGGCAGAGCCACCAG
Found at i:880541 original size:54 final size:54
Alignment explanation
Indices: 880482--880588 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
880472 TGGCTGCCAA
*
880482 AACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACCAG
1 AACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCACCAG
** * * *
880536 AACAGATATATGTGGTAGAGCCACCAGATCAGATATTTGTGGCATAGCCACCA
1 AACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCACCA
880589 TAACGCTTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 29 0.63
55 17 0.37
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (54 bp):
AACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCACCAG
Found at i:887748 original size:39 final size:39
Alignment explanation
Indices: 887688--887811 Score: 146
Period size: 39 Copynumber: 3.2 Consensus size: 39
887678 CTTTAACCCT
* *
887688 GATATTTTC-CAGC-TCGTAGCCTGCGGACCTCAAGTCCG
1 GATATTTTCTCAGCAT-ATAGCCTGCGGACCTCATGTCCG
*
887726 GATATATTTCT-AGCATATAGCCTGCGGATCTCATGTCCG
1 GATAT-TTTCTCAGCATATAGCCTGCGGACCTCATGTCCG
* * * *
887765 GATGTTTTTTCAGCATATAGCCTGCGGACCTTATGTTCG
1 GATATTTTCTCAGCATATAGCCTGCGGACCTCATGTCCG
887804 GATATTTT
1 GATATTTT
887812 TCCAATCTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
38 9 0.12
39 63 0.86
40 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (39 bp):
GATATTTTCTCAGCATATAGCCTGCGGACCTCATGTCCG
Found at i:887812 original size:39 final size:40
Alignment explanation
Indices: 887704--887812 Score: 150
Period size: 39 Copynumber: 2.8 Consensus size: 40
887694 TTCCAGCTCG
* *
887704 TAGCCTGCGGACCTCAAGTCCGGATA-TATTTCTAGCATA
1 TAGCCTGCGGACCTCATGTCCGGATATTTTTTCTAGCATA
* *
887743 TAGCCTGCGGATCTCATGTCCGGATGTTTTTTC-AGCATA
1 TAGCCTGCGGACCTCATGTCCGGATATTTTTTCTAGCATA
* *
887782 TAGCCTGCGGACCTTATGTTCGGATATTTTT
1 TAGCCTGCGGACCTCATGTCCGGATATTTTT
887813 CCAATCTCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 56 0.92
40 5 0.08
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (40 bp):
TAGCCTGCGGACCTCATGTCCGGATATTTTTTCTAGCATA
Found at i:889332 original size:30 final size:30
Alignment explanation
Indices: 889297--889357 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
889287 TAACCATAAG
889297 AACAACAATCTATCCCCTTCAATTTCTCCC
1 AACAACAATCTATCCCCTTCAATTTCTCCC
889327 AACAACAATCTATCCCCTTCAATTTCTCCC
1 AACAACAATCTATCCCCTTCAATTTCTCCC
889357 A
1 A
889358 TGGCCGAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.30
Consensus pattern (30 bp):
AACAACAATCTATCCCCTTCAATTTCTCCC
Found at i:891433 original size:93 final size:93
Alignment explanation
Indices: 891325--891495 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
891315 GCCCCTAAGT
* * *
891325 GAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
891390 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
891418 GAACTCGGACTCAACTCAACAAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
891483 CGAGTTCGGATGC
66 CGAGTTCGGATGC
891496 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:891492 original size:46 final size:46
Alignment explanation
Indices: 891320--891492 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
891310 AACCCGCCCC
* * * * *
891320 TAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
891366 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* * *
891414 TCA-CGAACTCGGACTCAACTCAACAAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
891459 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
891493 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 28 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:898531 original size:35 final size:35
Alignment explanation
Indices: 898485--898555 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
898475 TACTTAAGTA
898485 GTTGTACAAGCCATTTACCAAGATAAAAGTCCTTT
1 GTTGTACAAGCCATTTACCAAGATAAAAGTCCTTT
*
898520 GTTGTGCAAGCCATTTACCAAGATAAAAGTCCTTT
1 GTTGTACAAGCCATTTACCAAGATAAAAGTCCTTT
898555 G
1 G
898556 GATAGTGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (35 bp):
GTTGTACAAGCCATTTACCAAGATAAAAGTCCTTT
Found at i:900253 original size:46 final size:47
Alignment explanation
Indices: 900200--900322 Score: 169
Period size: 46 Copynumber: 2.7 Consensus size: 47
900190 TGGTATGTGA
*
900200 GCCAGTGTAAGATATGTTTGGGACATGCATCA-GCCACATCATGAGT
1 GCCAGTGTAAGACATGTTTGGGACATGCATCAGGCCACATCATGAGT
* * * *
900246 GCCAGTGTAAGACATGTCTGGGATATGAAT-AGGCTACATCATGAGT
1 GCCAGTGTAAGACATGTTTGGGACATGCATCAGGCCACATCATGAGT
* *
900292 GTCAGTGTAAGACATGTTTGGGACACGCATC
1 GCCAGTGTAAGACATGTTTGGGACATGCATC
900323 GGCATTGAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 1 0.02
46 64 0.98
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTTTGGGACATGCATCAGGCCACATCATGAGT
Found at i:902950 original size:12 final size:12
Alignment explanation
Indices: 902918--902951 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
902908 AAGAATGTAA
902918 GGCCGAAGAATT
1 GGCCGAAGAATT
*
902930 GGCTGAAGAATT
1 GGCCGAAGAATT
*
902942 GGCCAAAGAA
1 GGCCGAAGAA
902952 AAGAGAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.32, T:0.15
Consensus pattern (12 bp):
GGCCGAAGAATT
Found at i:908271 original size:49 final size:49
Alignment explanation
Indices: 908199--908368 Score: 164
Period size: 49 Copynumber: 3.5 Consensus size: 49
908189 TGTTTGTCAA
* * * *
908199 TGTAAGACCTATCTGGGACATGGCATCGACACCGATAGATGAGAGCCAG
1 TGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGCCAG
* * **
908248 TGTAAGACCTGTCTGAGACATGGCATCGGCATCGATATATGAAAGTTAG
1 TGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGCCAG
* * * * * * **
908297 TGTAAGACTTGTCTCAGACACGACATCGACTTCAAT-G-TGCCAGCCAG
1 TGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGCCAG
*
908344 TGTAAGACCATGTCTGGGACATGGC
1 TGTAAGACC-TGTCTGAGACATGGC
908369 GTCGGCATTT
Statistics
Matches: 95, Mismatches: 25, Indels: 3
0.77 0.20 0.02
Matches are distributed among these distances:
47 14 0.15
48 11 0.12
49 70 0.74
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (49 bp):
TGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGCCAG
Found at i:914694 original size:14 final size:14
Alignment explanation
Indices: 914647--914694 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
914637 GTACGAATGG
*
914647 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
914661 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
914675 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
914689 ATTGGT
1 AATGGT
914695 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:917919 original size:12 final size:12
Alignment explanation
Indices: 917902--917936 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
917892 TAGGTTTCCA
917902 AAAATGAAAATT
1 AAAATGAAAATT
917914 AAAATGAAAATT
1 AAAATGAAAATT
*
917926 AAAATGGAAAT
1 AAAATGAAAAT
917937 GGAAATTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (12 bp):
AAAATGAAAATT
Found at i:918119 original size:26 final size:25
Alignment explanation
Indices: 918090--918157 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
918080 TCTCGAAATT
918090 TTACTAGGGGTAAAATTGTCAAAAAC
1 TTACTAGGGGTAAAATTGTC-AAAAC
* * *
918116 TTACCAGGGGTAAAATTTTCAAAAT
1 TTACTAGGGGTAAAATTGTCAAAAC
918141 TTAACT-GGGGTAAAATT
1 TT-ACTAGGGGTAAAATT
918158 AGGGTGAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 17 0.46
26 20 0.54
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
TTACTAGGGGTAAAATTGTCAAAAC
Found at i:918150 original size:25 final size:26
Alignment explanation
Indices: 918085--918157 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
918075 AATTTTCTCG
*
918085 AAATTTTACTAGGGGTAAAATTGTCAA
1 AAATTTAACT-GGGGTAAAATTGTCAA
* * * *
918112 AAACTTACCAGGGGTAAAATTTTC-A
1 AAATTTAACTGGGGTAAAATTGTCAA
918137 AAATTTAACTGGGGTAAAATT
1 AAATTTAACTGGGGTAAAATT
918158 AGGGTGAGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 19 0.50
26 13 0.34
27 6 0.16
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (26 bp):
AAATTTAACTGGGGTAAAATTGTCAA
Found at i:919468 original size:15 final size:15
Alignment explanation
Indices: 919448--919477 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
919438 CAACACTTGT
919448 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
919463 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
919478 AAATACATTA
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:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:921252 original size:19 final size:20
Alignment explanation
Indices: 921228--921267 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
921218 CGCGCAAAGA
* *
921228 TTCCAA-AAATTAAATGTTT
1 TTCCAAGAAAATAAATATTT
921247 TTCCAAGAAAATAAATATTT
1 TTCCAAGAAAATAAATATTT
921267 T
1 T
921268 AAGCAGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TTCCAAGAAAATAAATATTT
Found at i:944960 original size:41 final size:41
Alignment explanation
Indices: 944903--944985 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
944893 AAAATAGGTA
944903 TGGTTGATAAATGGGTTTAATGTAGAGTTTGGATTATATGC
1 TGGTTGATAAATGGGTTTAATGTAGAGTTTGGATTATATGC
944944 TGGTTGATAAATGGGTTTAATGTAGAGTTTGGATTATATGC
1 TGGTTGATAAATGGGTTTAATGTAGAGTTTGGATTATATGC
944985 T
1 T
944986 CGTAAGTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (41 bp):
TGGTTGATAAATGGGTTTAATGTAGAGTTTGGATTATATGC
Found at i:948825 original size:93 final size:93
Alignment explanation
Indices: 948666--948838 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
948656 CGCCCATAAG
* * * * *
948666 CGAACTTGGACTCAACTTAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
948731 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
948759 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
948824 ACGAGTTCGGATGCC
66 ACGAGTTCGGATGCC
948839 CAAACATCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:948834 original size:46 final size:46
Alignment explanation
Indices: 948659--948834 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
948649 TGTAACCCGC
* * * * *
948659 CCATAAGCGAACTTGGACTCAACTTAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
948705 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
948755 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
948798 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
948835 TGCCCAAACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:948853 original size:46 final size:45
Alignment explanation
Indices: 948710--948853 Score: 157
Period size: 46 Copynumber: 3.1 Consensus size: 45
948700 CGCATCCATG
*
948710 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATCT
* * * * *
948757 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCT
*
948803 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACAT-CT
948849 AGTGA
1 AGTGA
948854 CATGTCACTT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
44 8 0.10
45 1 0.01
46 33 0.42
47 32 0.41
48 1 0.01
49 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCT
Found at i:951269 original size:30 final size:30
Alignment explanation
Indices: 951234--951313 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
951224 CAAGGAAACC
*
951234 GAATAAAGAAATCCAAGATAGAGAAATCCA
1 GAATAAAGAAATCCAAGATAAAGAAATCCA
* * *
951264 GAATAAAGAATTCC-AGAATAAAGAGATCTA
1 GAATAAAGAAATCCAAG-ATAAAGAAATCCA
* *
951294 GGATAAAGAAACCCAAGATA
1 GAATAAAGAAATCCAAGATA
951314 TGATACTATG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 2 0.05
30 37 0.90
31 2 0.05
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (30 bp):
GAATAAAGAAATCCAAGATAAAGAAATCCA
Found at i:951273 original size:15 final size:15
Alignment explanation
Indices: 951234--951304 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
951224 CAAGGAAACC
951234 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
951249 -AGATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
*
951264 GAATAAAGAATTCCA
1 GAATAAAGAAATCCA
* *
951279 GAATAAAGAGATCTA
1 GAATAAAGAAATCCA
*
951294 GGATAAAGAAA
1 GAATAAAGAAA
951305 CCCAAGATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
14 1 0.02
15 44 0.96
16 1 0.02
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.15
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:951313 original size:15 final size:15
Alignment explanation
Indices: 951236--951313 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
951226 AGGAAACCGA
951236 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
951251 ATAGAGAAATCC-AG
1 ATAAAGAAATCCAAG
*
951265 AATAAAGAATTCC-AG
1 -ATAAAGAAATCCAAG
* * *
951280 AATAAAGAGATCTAGG
1 -ATAAAGAAATCCAAG
*
951296 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
951311 ATA
1 ATA
951314 TGATACTATG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
14 2 0.04
15 47 0.94
16 1 0.02
ACGTcount: A:0.55, C:0.13, G:0.17, T:0.15
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:951862 original size:18 final size:20
Alignment explanation
Indices: 951839--951880 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
951829 CAGTTAAATT
951839 ATTCAATT-A-AAATATTTC
1 ATTCAATTAAGAAATATTTC
951857 ATTCAATTACAGAAATATTTC
1 ATTCAATTA-AGAAATATTTC
951878 ATT
1 ATT
951881 TCGGTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
20 1 0.05
21 12 0.57
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTCAATTAAGAAATATTTC
Found at i:954030 original size:100 final size:100
Alignment explanation
Indices: 953857--954056 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
953847 CTTCACAGAT
953857 ATCTTTGACGTTGATTGGTTCATATCATTTTTGTCAAAAGATGTTAAAATCATAAAGCAGCTGCC
1 ATCTTTGACGTTGATTGGTTCATATCATTTTTGTCAAAAGATGTTAAAATCATAAAGCAGCTGCC
953922 TAAAAGGGGATGGAGGACTTGGACTCCATACACCA
66 TAAAAGGGGATGGAGGACTTGGACTCCATACACCA
953957 ATCTTTGACGTTGATTGGTTCATATCATTTTTGTCAAAAGATGTTAAAATCATAAAGCAGCTGCC
1 ATCTTTGACGTTGATTGGTTCATATCATTTTTGTCAAAAGATGTTAAAATCATAAAGCAGCTGCC
954022 TAAAAGGGGATGGAGGACTTGGACTCCATACACCA
66 TAAAAGGGGATGGAGGACTTGGACTCCATACACCA
954057 TGCGCGTTCC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (100 bp):
ATCTTTGACGTTGATTGGTTCATATCATTTTTGTCAAAAGATGTTAAAATCATAAAGCAGCTGCC
TAAAAGGGGATGGAGGACTTGGACTCCATACACCA
Found at i:954509 original size:22 final size:22
Alignment explanation
Indices: 954484--954529 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
954474 TTGTACTCTT
954484 AGGTCTGATTTTGTGTGCTTTA
1 AGGTCTGATTTTGTGTGCTTTA
954506 AGGTCTGATTTTGTGTGCTTTA
1 AGGTCTGATTTTGTGTGCTTTA
954528 AG
1 AG
954530 TTCTAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.09, G:0.28, T:0.48
Consensus pattern (22 bp):
AGGTCTGATTTTGTGTGCTTTA
Found at i:956542 original size:6 final size:6
Alignment explanation
Indices: 956531--956563 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
956521 GGCCTGATCT
*
956531 GGATGA GGATGA GGATGA GGATGA GGAAGA GGA
1 GGATGA GGATGA GGATGA GGATGA GGATGA GGA
956564 GGACGAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.12
Consensus pattern (6 bp):
GGATGA
Found at i:956906 original size:22 final size:22
Alignment explanation
Indices: 956878--956922 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
956868 AAGATGGATG
956878 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
956900 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
956922 T
1 T
956923 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:960680 original size:22 final size:22
Alignment explanation
Indices: 960652--960696 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
960642 AGGGGGAGTG
960652 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
960674 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
960696 T
1 T
960697 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:964016 original size:14 final size:14
Alignment explanation
Indices: 963997--964030 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
963987 CAGTTTGATC
963997 TTAATTCTAAAAAT
1 TTAATTCTAAAAAT
* *
964011 TTAATTCTGAATAT
1 TTAATTCTAAAAAT
964025 TTAATT
1 TTAATT
964031 TGATCTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (14 bp):
TTAATTCTAAAAAT
Found at i:967900 original size:17 final size:17
Alignment explanation
Indices: 967869--967902 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
967859 ATTTTGCAAA
**
967869 GAACCTAAATCAGTTGT
1 GAACCTAAAAAAGTTGT
967886 GAACCTAAAAAAGTTGT
1 GAACCTAAAAAAGTTGT
967903 TGCTATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (17 bp):
GAACCTAAAAAAGTTGT
Found at i:968225 original size:15 final size:15
Alignment explanation
Indices: 968207--968247 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
968197 TTAGTTTAAA
968207 ATTATTTTTTGAATT
1 ATTATTTTTTGAATT
968222 ATTATTTTTT--A-T
1 ATTATTTTTTGAATT
968234 A-TATTTTTTGAATT
1 ATTATTTTTTGAATT
968248 TTTTAGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
ATTATTTTTTGAATT
Found at i:970836 original size:8 final size:8
Alignment explanation
Indices: 970823--970848 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
970813 ATTACAGTCC
970823 AAAATAAT
1 AAAATAAT
970831 AAAATAAT
1 AAAATAAT
970839 AAAATAAT
1 AAAATAAT
970847 AA
1 AA
970849 GGTTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:972145 original size:10 final size:11
Alignment explanation
Indices: 972117--972149 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
972107 GTGGCTAAGG
972117 CAAAATAAACAT
1 CAAAATAAA-AT
972129 CAAAATAAAAT
1 CAAAATAAAAT
972140 -AAAATAAAAT
1 CAAAATAAAAT
972150 GAATGAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 2 0.10
12 9 0.43
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
CAAAATAAAAT
Found at i:972193 original size:19 final size:19
Alignment explanation
Indices: 972169--972206 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
972159 TATAAATTTA
972169 TTAACAATTTAAGAAAAGT
1 TTAACAATTTAAGAAAAGT
*
972188 TTAACAATTTTAGAAAAGT
1 TTAACAATTTAAGAAAAGT
972207 AAAATGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (19 bp):
TTAACAATTTAAGAAAAGT
Found at i:975723 original size:78 final size:77
Alignment explanation
Indices: 975582--975747 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 77
975572 ATTTGATGTG
975582 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTATATCCGGGTTAAATCCCGCAGGCTT
1 TATCCGGG-TTAAAGACCCGCAGGCTATATGCTAGAATTATATCCGGGTTAAATCCCGCAGGCTT
975647 CGTGCTGGTATTA
65 CGTGCTGGTATTA
* * * * * * *
975660 TATCCGGGTTAAA-TCCCGCAGGCCTA-GTGCTGGTATTATATCTGAGTTTAAAGTCCCGTAGGC
1 TATCCGGGTTAAAGACCCGCAGG-CTATATGCTAGAATTATATCCG-GGTTAAA-TCCCGCAGGC
*
975723 TTCGTGCTGGTGTTA
63 TTCGTGCTGGTATTA
* *
975738 TGTTCGGGTT
1 TATCCGGGTT
975748 TTATACCTCG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
76 22 0.29
77 14 0.19
78 39 0.52
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (77 bp):
TATCCGGGTTAAAGACCCGCAGGCTATATGCTAGAATTATATCCGGGTTAAATCCCGCAGGCTTC
GTGCTGGTATTA
Found at i:975730 original size:40 final size:38
Alignment explanation
Indices: 975582--975747 Score: 172
Period size: 38 Copynumber: 4.3 Consensus size: 38
975572 ATTTGATGTG
* * * *
975582 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTAGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGTATTA
975622 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* *
975660 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* * * *
975698 TATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCTGGTGTTA
1 TATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
* *
975738 TGTTCGGGTT
1 TATCCGGGTT
975748 TTATACCTCG
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
37 1 0.01
38 60 0.56
39 14 0.13
40 32 0.30
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
Found at i:979696 original size:40 final size:39
Alignment explanation
Indices: 979665--979874 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
979655 GGACTAAGAT
* *
979665 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
979705 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
979745 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
979785 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
979825 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
979864 CCGAAGGCATT
1 CCGAAGGCATT
979875 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:979828 original size:120 final size:120
Alignment explanation
Indices: 979612--979874 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
979602 TTGAATGCTG
* *
979612 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
979676 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
979732 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
979795 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
979851 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
979875 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:979894 original size:79 final size:80
Alignment explanation
Indices: 979613--979909 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
979603 TGAATGCTGT
* ** * * * **
979613 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
979676 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
979693 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
979757 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
979773 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
979837 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
979852 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
979910 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:987726 original size:39 final size:39
Alignment explanation
Indices: 987562--987744 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
987552 TTGAATGCTG
* * * * * * *
987562 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
987602 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
987642 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
987682 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
987721 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
987745 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:987764 original size:79 final size:80
Alignment explanation
Indices: 987598--987779 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
987588 GCTAAGTGAA
* * * *
987598 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
987662 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
987678 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
987742 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
987757 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
987780 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:989961 original size:50 final size:50
Alignment explanation
Indices: 989851--989962 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 50
989841 ACTACTCATT
* * *
989851 TGGCCGAATATGCAAGATCAAGAATAATATCACATATGTACATATCTATA
1 TGGCCGAATATGCAAGATCAAGAATAACATCACATAAGTACATACCTATA
* * * * *
989901 AGGCCGAATATGCAAGTTCCAA-TATAACATCACATAAGTATATACCTATG
1 TGGCCGAATATGCAAGAT-CAAGAATAACATCACATAAGTACATACCTATA
*
989951 TGGCCAAATATG
1 TGGCCGAATATG
989963 AAAGGTCATT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 48 0.94
51 3 0.06
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (50 bp):
TGGCCGAATATGCAAGATCAAGAATAACATCACATAAGTACATACCTATA
Found at i:1001639 original size:4 final size:4
Alignment explanation
Indices: 1001630--1001805 Score: 271
Period size: 4 Copynumber: 44.0 Consensus size: 4
1001620 TTAAAAGTAC
1001630 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * *
1001678 GCAT ACAT GCAT GCAT GCAT CCAT GCAT GCAT ACAT GCAT ACAA ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1001726 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1001774 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1001806 CCAAGCTGTA
Statistics
Matches: 162, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 162 1.00
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1002061 original size:21 final size:21
Alignment explanation
Indices: 1002012--1002061 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1002002 CTTGTAAGCA
1002012 AGATACACGGCTGTGTGGCTG
1 AGATACACGGCTGTGTGGCTG
*
1002033 AGACACAC-GCTCGTGTGGCTG
1 AGATACACGGCT-GTGTGGCTG
*
1002054 AGGTACAC
1 AGATACAC
1002062 AACCGTGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.20
Consensus pattern (21 bp):
AGATACACGGCTGTGTGGCTG
Found at i:1003578 original size:165 final size:161
Alignment explanation
Indices: 1003296--1003632 Score: 462
Period size: 165 Copynumber: 2.1 Consensus size: 161
1003286 TCCCGTTTTT
* * ** *
1003296 AATGATTTTTATGTTTTTGAAGTCGTTGTAGCTTTTTCTAGCTAGCCTAGAGACTATTTTGCAAA
1 AATGATTTTTATGTTTTTGAAGTCGCTATAGCTTAATCTAGCTAGCCTAGAGACTAATTTGCAAA
* * *
1003361 AATATTAAAGTTTTAGGGTTTTTCCATGAGAATTTTTGCATGATTTTTGAAATTTAATGAAATAT
66 AATATTAAAGGTTTAGGGTTTTTCCATGAGAATTTTTGCATGATTCTTGAAATTTAATGAAAGAT
1003426 TATGAGTCATTGTTGTTAAATAAACAAGTTTTGTA
131 TATGAG----TGTTGTTAAATAAACAAGTTTTGTA
*
1003461 AATGATTTTTATGTTTTTGAAGTCGCTATAGCTTAATCTAGCTAGCCTAGGGACTAATTTGC-AA
1 AATGATTTTTATGTTTTTGAAGTCGCTATAGCTTAATCTAGCTAGCCTAGAGACTAATTTGCAAA
* * * * *
1003525 AATTTATAAAGGTTTAGGGTTTTTCCTTGAGCATATTTT-CTTGATTCTTGAAATTTAATGAACG
66 AATAT-TAAAGGTTTAGGGTTTTTCCATGAGAAT-TTTTGCATGATTCTTGAAATTTAATGAAAG
*
1003589 ATTATGAGTGTTGTTAAATAAACAAGTTTTTTA
129 ATTATGAGTGTTGTTAAATAAACAAGTTTTGTA
1003622 AATGGATTTTT
1 AAT-GATTTTT
1003633 GATGAAATTA
Statistics
Matches: 154, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
161 27 0.18
162 7 0.05
164 6 0.04
165 110 0.71
166 4 0.03
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (161 bp):
AATGATTTTTATGTTTTTGAAGTCGCTATAGCTTAATCTAGCTAGCCTAGAGACTAATTTGCAAA
AATATTAAAGGTTTAGGGTTTTTCCATGAGAATTTTTGCATGATTCTTGAAATTTAATGAAAGAT
TATGAGTGTTGTTAAATAAACAAGTTTTGTA
Found at i:1006009 original size:39 final size:40
Alignment explanation
Indices: 1005955--1006131 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
1005945 AAACCAAGTA
* * * *
1005955 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
1005994 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1006034 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
1006074 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
1006113 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
1006132 TTATCATCCG
Statistics
Matches: 126, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
38 1 0.01
39 48 0.38
40 77 0.61
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:1006108 original size:79 final size:80
Alignment explanation
Indices: 1005955--1006131 Score: 245
Period size: 79 Copynumber: 2.2 Consensus size: 80
1005945 AAACCAAGTA
* * * * *
1005955 CCTTCGGAATTTAG-CCGGATATAGCTACTTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
1006019 TAACTCGCACAAATG
66 TAACTAGCACAAATG
1006034 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGA-ATT
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-T
*
1006096 AGTCACTAGCACAAATG
64 AGTAACTAGCACAAATG
1006113 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
1006132 TTATCATCCG
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
78 1 0.01
79 58 0.66
80 29 0.33
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TAACTAGCACAAATG
Found at i:1008456 original size:17 final size:18
Alignment explanation
Indices: 1008434--1008467 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1008424 CACATTGAAG
1008434 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
1008451 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
1008468 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:1010164 original size:40 final size:40
Alignment explanation
Indices: 1010099--1010206 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
1010089 GGACTAAGAT
* * * *
1010099 CCGAAGGCATTTGTGCTAGTGACTATATCCAGGTTAAGTT
1 CCGAAGGCATTTGTGCGAGTTACTATATCCAGGCTAAGTC
* *
1010139 TCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCAGGCTAAGTC
* *
1010179 CCGAAGGTATTTGTGCGAGTTGCTATAT
1 CCGAAGGCATTTGTGCGAGTTACTATAT
1010207 TCGACTAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCAGGCTAAGTC
Found at i:1012098 original size:28 final size:28
Alignment explanation
Indices: 1012013--1012115 Score: 118
Period size: 28 Copynumber: 3.7 Consensus size: 28
1012003 TGGCCATTTT
* * *
1012013 AGGCCCAATCTCATCCATATGGCCCATC
1 AGGCCCAATCACTTTCATATGGCCCATC
* *
1012041 -GAGCCCAATCACATGCATATGGCCCATC
1 AG-GCCCAATCACTTTCATATGGCCCATC
* **
1012069 AGGCCCTATCACTTTCATATGGCCTGTC
1 AGGCCCAATCACTTTCATATGGCCCATC
1012097 AGGCCCAATCACTTTCATA
1 AGGCCCAATCACTTTCATA
1012116 GTCATGCAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
27 1 0.02
28 63 0.97
29 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCACTTTCATATGGCCCATC
Found at i:1031351 original size:40 final size:40
Alignment explanation
Indices: 1031296--1031477 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
1031286 TATTCGGATG
*
1031296 ATATCCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
1031336 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
1031376 ACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
1031416 GTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
1031456 ATATCC-GGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
1031478 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 14 0.11
40 114 0.88
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:1037844 original size:200 final size:200
Alignment explanation
Indices: 1037501--1037901 Score: 775
Period size: 200 Copynumber: 2.0 Consensus size: 200
1037491 TTTACCCTTT
1037501 CGACCGAACCGGAGAACTTTCTTCCAAGGAGACACTTTTAAGAATACTTTATCACCCACCTGAAA
1 CGACCGAACCGGAGAACTTTCTTCCAAGGAGACACTTTTAAGAATACTTTATCACCCACCTGAAA
1037566 TTCAATCTCCCTTCGTTTAAGATCGGCGTATGACTTTTGACGATCGAAAGCTGCTTTTAAACTAT
66 TTCAATCTCCCTTCGTTTAAGATCGGCGTATGACTTTTGACGATCGAAAGCTGCTTTTAAACTAT
1037631 CCCAAATCAGTCTTACTTTTTCTTCTGTTTCCCGAATCAAATCAACCCCGTGTATCTTCTTTTCA
131 CCCAAATCAGTCTTACTTTTTCTTCTGTTTCCCGAATCAAATCAACCCCGTGTATCTTCTTTTCA
1037696 CTGAG
196 CTGAG
1037701 CGACCGAACCGGAGAACTTTCTTCCAAGGAGACACTTTTAAGAATACTTTATCACCCACCTGAAA
1 CGACCGAACCGGAGAACTTTCTTCCAAGGAGACACTTTTAAGAATACTTTATCACCCACCTGAAA
*
1037766 TTCAATCTCCCTTCGTTTAAGATCGGCGTATGACTTTTGACGATCGGAAGCTGCTTTTAAACTAT
66 TTCAATCTCCCTTCGTTTAAGATCGGCGTATGACTTTTGACGATCGAAAGCTGCTTTTAAACTAT
* *
1037831 CCCGAATCAGTCTTACTTTTTCTTCTGTTTCCCGAATCAAATCAACCCCGTGTATCTTGTTTTCA
131 CCCAAATCAGTCTTACTTTTTCTTCTGTTTCCCGAATCAAATCAACCCCGTGTATCTTCTTTTCA
1037896 CTGAG
196 CTGAG
1037901 C
1 C
1037902 TCTGTCCAAT
Statistics
Matches: 198, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 198 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (200 bp):
CGACCGAACCGGAGAACTTTCTTCCAAGGAGACACTTTTAAGAATACTTTATCACCCACCTGAAA
TTCAATCTCCCTTCGTTTAAGATCGGCGTATGACTTTTGACGATCGAAAGCTGCTTTTAAACTAT
CCCAAATCAGTCTTACTTTTTCTTCTGTTTCCCGAATCAAATCAACCCCGTGTATCTTCTTTTCA
CTGAG
Found at i:1048936 original size:39 final size:39
Alignment explanation
Indices: 1048891--1049044 Score: 221
Period size: 39 Copynumber: 4.1 Consensus size: 39
1048881 ATTCAAGACA
* *
1048891 CTGGAAATGTATCCAGGCTAAAGTCCCGTAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1048930 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
1048969 CTGGAAATGTATCCGGGCTAAAGTCCCGTAGG---C-T-
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
1049003 -TGGAAATGTATCCGGGCTAAAGTTCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1049041 CTGG
1 CTGG
1049045 TAATATAATT
Statistics
Matches: 103, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
33 29 0.28
35 1 0.01
36 1 0.01
37 1 0.01
39 71 0.69
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:1049042 original size:72 final size:75
Alignment explanation
Indices: 1048891--1049044 Score: 233
Period size: 72 Copynumber: 2.1 Consensus size: 75
1048881 ATTCAAGACA
1048891 CTGGAAATGTATCCAGGCTAAAGTCCCGTAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCC
1 CTGGAAATGTATCCAGGCTAAAGTCCCGTAGG--TCGT-CTGGAAATGTATCCGGGCTAAAGTCC
1048956 CGCAGGCTTCGTG
63 CGCAGGCTTCGTG
* *
1048969 CTGGAAATGTATCCGGGCTAAAGTCCCGTAGG-C-T-TGGAAATGTATCCGGGCTAAAGTTCCGC
1 CTGGAAATGTATCCAGGCTAAAGTCCCGTAGGTCGTCTGGAAATGTATCCGGGCTAAAGTCCCGC
*
1049031 AGGCTTTGTG
66 AGGCTTCGTG
1049041 CTGG
1 CTGG
1049045 TAATATAATT
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
72 40 0.55
74 1 0.01
75 1 0.01
78 31 0.42
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (75 bp):
CTGGAAATGTATCCAGGCTAAAGTCCCGTAGGTCGTCTGGAAATGTATCCGGGCTAAAGTCCCGC
AGGCTTCGTG
Found at i:1058346 original size:16 final size:18
Alignment explanation
Indices: 1058319--1058351 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1058309 ATTTAATTCT
1058319 TATAAGTTTTTA-ATAAA
1 TATAAGTTTTTACATAAA
1058336 TATAA-TTTTTACATAA
1 TATAAGTTTTTACATAA
1058352 TACTTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (18 bp):
TATAAGTTTTTACATAAA
Found at i:1059498 original size:9 final size:9
Alignment explanation
Indices: 1059475--1059509 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
1059465 TAGTTTTATC
1059475 TATTTATTA
1 TATTTATTA
1059484 -ATTTATTA
1 TATTTATTA
1059492 TATTTATTA
1 TATTTATTA
1059501 TATTATATT
1 TATT-TATT
1059510 TTAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 12 0.50
10 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTATTA
Found at i:1059506 original size:14 final size:13
Alignment explanation
Indices: 1059469--1059510 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1059459 TGTAAATAGT
*
1059469 TTTATCTATT-TA
1 TTTATTTATTATA
*
1059481 TTAATTTATTATA
1 TTTATTTATTATA
1059494 TTTATTATATTATA
1 TTTATT-TATTATA
1059508 TTT
1 TTT
1059511 TAATAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 8 0.32
13 7 0.28
14 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:1059929 original size:22 final size:23
Alignment explanation
Indices: 1059888--1059936 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1059878 AATTATTTAA
* *
1059888 AAATGTTTTGTTCAAAAAAATGT
1 AAATGTATTGTTCAAAAAAAAGT
1059911 AAATGTATTGTT-AAAAAAAAGT
1 AAATGTATTGTTCAAAAAAAAGT
1059933 AAAT
1 AAAT
1059937 ATAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (23 bp):
AAATGTATTGTTCAAAAAAAAGT
Found at i:1064577 original size:13 final size:13
Alignment explanation
Indices: 1064559--1064637 Score: 89
Period size: 13 Copynumber: 6.5 Consensus size: 13
1064549 TAGATTTTTT
1064559 CTAAATATTATCA
1 CTAAATATTATCA
1064572 CTAAATA--ATC-
1 CTAAATATTATCA
1064582 CTAAATATTATCA
1 CTAAATATTATCA
*
1064595 CTAAATATTGTCA
1 CTAAATATTATCA
*
1064608 CTAAATA--AT-T
1 CTAAATATTATCA
*
1064618 CTAAATATTTTCA
1 CTAAATATTATCA
1064631 CTAAATA
1 CTAAATA
1064638 AATCAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 14 0.25
11 4 0.07
12 4 0.07
13 33 0.60
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:1064599 original size:36 final size:36
Alignment explanation
Indices: 1064559--1064637 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
1064549 TAGATTTTTT
1064559 CTAAATATTATCACTAAATAATCCTAAATATTATCA
1 CTAAATATTATCACTAAATAATCCTAAATATTATCA
* * *
1064595 CTAAATATTGTCACTAAATAATTCTAAATATTTTCA
1 CTAAATATTATCACTAAATAATCCTAAATATTATCA
1064631 CTAAATA
1 CTAAATA
1064638 AATCAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (36 bp):
CTAAATATTATCACTAAATAATCCTAAATATTATCA
Found at i:1064621 original size:23 final size:23
Alignment explanation
Indices: 1064595--1064638 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1064585 AATATTATCA
1064595 CTAAATATTGTCACTAAATAATT
1 CTAAATATTGTCACTAAATAATT
*
1064618 CTAAATATTTTCACTAAATAA
1 CTAAATATTGTCACTAAATAA
1064639 ATCAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (23 bp):
CTAAATATTGTCACTAAATAATT
Found at i:1064656 original size:14 final size:14
Alignment explanation
Indices: 1064637--1064664 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1064627 TTCACTAAAT
1064637 AAATCAAATTTTAA
1 AAATCAAATTTTAA
1064651 AAATCAAATTTTAA
1 AAATCAAATTTTAA
1064665 CTAGAATTTA
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:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATCAAATTTTAA
Found at i:1065240 original size:20 final size:20
Alignment explanation
Indices: 1065217--1065257 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1065207 TATACTTTCA
*
1065217 TTTA-TATATATTTTTTATTT
1 TTTATTATA-ATTATTTATTT
1065237 TTTATTATAATTATTTATTT
1 TTTATTATAATTATTTATTT
1065257 T
1 T
1065258 CAAACGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTATAATTATTTATTT
Found at i:1068987 original size:49 final size:49
Alignment explanation
Indices: 1068921--1069208 Score: 333
Period size: 49 Copynumber: 5.8 Consensus size: 49
1068911 TAGACAAAGC
* * *
1068921 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * * *
1068970 TATCCGATACACGTAGTAGCCTGCATTTAGTACTACACACGTGATCGAAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
** * *
1069021 TATTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * * *
1069070 TATCCGATACACGTAGTAGCCTGCATTTAGTACTACACACGTGATCGAAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
** *
1069121 TATTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
*
1069170 TATCCGGTACACATAGTAGCCTACACTTAGTACTACACA
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
1069209 CGTGACCTCA
Statistics
Matches: 193, Mismatches: 42, Indels: 8
0.79 0.17 0.03
Matches are distributed among these distances:
49 109 0.56
50 12 0.06
51 72 0.37
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:1069061 original size:100 final size:100
Alignment explanation
Indices: 1068926--1069213 Score: 531
Period size: 100 Copynumber: 2.9 Consensus size: 100
1068916 AAAGCTATCT
1068926 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACGTAGTAGCC
1068991 TGCATTTAGTACTACACACGTGATCGAAGTTATTG
66 TGCATTTAGTACTACACACGTGATCGAAGTTATTG
1069026 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACGTAGTAGCC
1069091 TGCATTTAGTACTACACACGTGATCGAAGTTATTG
66 TGCATTTAGTACTACACACGTGATCGAAGTTATTG
* * *
1069126 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACATAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACGTAGTAGCC
* *
1069191 TACACTTAGTACTACACACGTGA
66 TGCATTTAGTACTACACACGTGA
1069214 CCTCACAATA
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 183 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACGTAGTAGCC
TGCATTTAGTACTACACACGTGATCGAAGTTATTG
Found at i:1069515 original size:27 final size:27
Alignment explanation
Indices: 1069452--1069515 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
1069442 GTGTAGCAAT
* * * *
1069452 TCATGCAATCCATGTAATAGTAATTTA
1 TCATTCAATTCATGTAACAATAATTTA
* *
1069479 ACATTCAATTCATGTAACAATAATTTG
1 TCATTCAATTCATGTAACAATAATTTA
1069506 TCATTCAATT
1 TCATTCAATT
1069516 TCACATGACA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (27 bp):
TCATTCAATTCATGTAACAATAATTTA
Found at i:1070819 original size:24 final size:26
Alignment explanation
Indices: 1070790--1070838 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1070780 CTTGTTTTAA
* *
1070790 TATTTG-TTT-TTATGTTTTTAAATG
1 TATTTGATTTATTATATTTTAAAATG
1070814 TATTTGATTTATTATATTTTAAAAT
1 TATTTGATTTATTATATTTTAAAAT
1070839 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (26 bp):
TATTTGATTTATTATATTTTAAAATG
Found at i:1076781 original size:13 final size:13
Alignment explanation
Indices: 1076763--1076805 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1076753 TAGATTTTTC
1076763 CTAAATATTATCA
1 CTAAATATTATCA
1076776 CTAAATA--ATC-
1 CTAAATATTATCA
1076786 CTAAATATTATCA
1 CTAAATATTATCA
*
1076799 TTAAATA
1 CTAAATA
1076806 ATTCAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:1076788 original size:23 final size:23
Alignment explanation
Indices: 1076761--1076807 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1076751 GTTAGATTTT
1076761 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
1076784 TCCTAAATATTATCATTAAATAA
1 TCCTAAATATTATCACTAAATAA
1076807 T
1 T
1076808 TCAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:1080515 original size:33 final size:33
Alignment explanation
Indices: 1080473--1080724 Score: 190
Period size: 33 Copynumber: 7.7 Consensus size: 33
1080463 TCTGAGGTGC
1080473 ACAT-TCCTTTTTCAAGTGGTACACACAAAGT-T
1 ACATATCC-TTTTCAAGTGGTACACACAAAGTAT
* * * **
1080505 ACATACCCTTTTCAATTTGTACACACAAAGTGC
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * * * *
1080538 AGATAACCTTTTCAAGT-GTACACGCATAGTGT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * *
1080570 ACTTTTCCTTTTCAAGTGGTATACACAAAGTAT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * * * *
1080603 ACTTTTCCTTTTCAAGTGGCATAAACAAAGTAT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * *
1080636 ACCTTTCCTTTTCATA-TGGTATACACAAAGTAT
1 ACATATCCTTTTCA-AGTGGTACACACAAAGTAT
** * * * *
1080669 ACCCAACCTTTCCAAGT-GTACGCACAAAGTGT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* *
1080701 ACATAGCCTTTTCAAGTTGTACAC
1 ACATATCCTTTTCAAGTGGTACAC
1080725 TTTCGGGTTA
Statistics
Matches: 179, Mismatches: 35, Indels: 11
0.80 0.16 0.05
Matches are distributed among these distances:
32 76 0.42
33 102 0.57
34 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (33 bp):
ACATATCCTTTTCAAGTGGTACACACAAAGTAT
Found at i:1080558 original size:32 final size:31
Alignment explanation
Indices: 1080481--1080560 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
1080471 GCACATTCCT
* *
1080481 TTTTCAAGTGGTACACACAAAGTTACATACCC
1 TTTTCAAGT-GTACACACAAAGTCACATAACC
* *
1080513 TTTTCAATTTGTACACACAAAGTGCAGATAACC
1 TTTTCAA-GTGTACACACAAAGT-CACATAACC
1080546 TTTTCAAGTGTACAC
1 TTTTCAAGTGTACAC
1080561 GCATAGTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 27 0.66
33 14 0.34
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (31 bp):
TTTTCAAGTGTACACACAAAGTCACATAACC
Found at i:1081417 original size:21 final size:22
Alignment explanation
Indices: 1081371--1081413 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1081361 TGTAAAAGTG
*
1081371 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
1081393 ATTTC-CTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
1081413 A
1 A
1081414 ATTTACAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:1083770 original size:40 final size:40
Alignment explanation
Indices: 1083579--1083763 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
1083569 TCGAATGATG
* * * *
1083579 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
1083619 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
1083659 TCCGGGCTAAG-CCCAAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1083698 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
1083739 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1083764 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 32 0.26
40 80 0.66
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:1083785 original size:79 final size:79
Alignment explanation
Indices: 1083632--1083796 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
1083622 GGACTAAGAT
* * **
1083632 CCGAAGGCATTTGTGTGAGATACTAATTCCGGGCTAAGCCCAAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
*
1083697 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * * *
1083711 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-C
* *
1083774 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
1083790 CCGAAGG
1 CCGAAGG
1083797 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.65
80 23 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:1090066 original size:66 final size:65
Alignment explanation
Indices: 1089987--1090111 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 65
1089977 GGACCTTTCC
* * **
1089987 TTTTCTAATTGTACAC-CTGAGGTGCACATTCCCTTTTCAAGTGGTACACACGA-AGTGTACATA
1 TTTTCTAATTGTACACAC-AAAGTGCACATAACCTTTTCAAGT-GTACACAC-ATAGTGTACATA
1090050 CCT
63 CCT
*
1090053 TTTTC-AATTTGTACACACAAAGTGCAGATAACCTTTTCAAGTGTACACACATAGTGTAC
1 TTTTCTAA-TTGTACACACAAAGTGCACATAACCTTTTCAAGTGTACACACATAGTGTAC
1090112 CTTTCCTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
64 1 0.02
65 17 0.33
66 32 0.63
67 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (65 bp):
TTTTCTAATTGTACACACAAAGTGCACATAACCTTTTCAAGTGTACACACATAGTGTACATACCT
Found at i:1090103 original size:32 final size:32
Alignment explanation
Indices: 1090018--1090262 Score: 167
Period size: 33 Copynumber: 7.5 Consensus size: 32
1090008 GTGCACATTC
*
1090018 CCTTTTCAAGTGGTACACACGAAGTGTACATA
1 CCTTTTCAAGTGGTACACACAAAGTGTACATA
* * * *
1090050 CCTTTTTCAATTTGTACACACAAAGTGCAGATAA
1 CC-TTTTCAAGTGGTACACACAAAGTGTACAT-A
* * *
1090084 CCTTTTCAAGT-GTACACACATAGTGTACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTGTA-CATA
* * *
1090116 CCTTTTCAAGTGGTATACACAAAGTATACATTT
1 CCTTTTCAAGTGGTACACACAAAGTGTACA-TA
* * * * * *
1090149 TCTTTTCATA-TTGTATACACAAAGTATACCTTT
1 CCTTTTCA-AGTGGTACACACAAAGTGTA-CATA
* *
1090182 CCTTTTCATA-TGGTATACACAAAGTATACCCA-A
1 CCTTTTCA-AGTGGTACACACAAAGTGTA--CATA
*
1090215 CCTTTCCAAGT-GTACACACAAAGTGTACATA
1 CCTTTTCAAGTGGTACACACAAAGTGTACATA
* *
1090246 GCCTTTTAAAGTTGTAC
1 -CCTTTTCAAGTGGTAC
1090263 CCTTTCAGGA
Statistics
Matches: 174, Mismatches: 27, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
30 2 0.01
31 1 0.01
32 52 0.30
33 112 0.64
34 7 0.04
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (32 bp):
CCTTTTCAAGTGGTACACACAAAGTGTACATA
Found at i:1090120 original size:66 final size:65
Alignment explanation
Indices: 1090018--1090242 Score: 229
Period size: 66 Copynumber: 3.4 Consensus size: 65
1090008 GTGCACATTC
* * * * * ** *
1090018 CCTTTTCAAGTGGTACACACGAAGTGTA-CATACCTTTTTCAATTTGTACACACAAAGTGCAGAT
1 CCTTTTCAAGT-GTACACACAAAGTGTACCTTTCC-TTTTCAATTGGTATACACAAAGTATACAT
1090082 AA
64 AA
* * **
1090084 CCTTTTCAAGTGTACACACATAGTGTACCTTTCCTTTTCAAGTGGTATACACAAAGTATACATTT
1 CCTTTTCAAGTGTACACACAAAGTGTACCTTTCCTTTTCAATTGGTATACACAAAGTATACATAA
* * * * **
1090149 TCTTTTCATATTGTATACACAAAGTATACCTTTCCTTTTC-ATATGGTATACACAAAGTATACCC
1 CCTTTTCA-AGTGTACACACAAAGTGTACCTTTCCTTTTCAAT-TGGTATACACAAAGTATACAT
1090213 AA
64 AA
*
1090215 CCTTTCCAAGTGTACACACAAAGTGTAC
1 CCTTTTCAAGTGTACACACAAAGTGTAC
1090243 ATAGCCTTTT
Statistics
Matches: 129, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
65 62 0.48
66 67 0.52
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (65 bp):
CCTTTTCAAGTGTACACACAAAGTGTACCTTTCCTTTTCAATTGGTATACACAAAGTATACATAA
Found at i:1090952 original size:21 final size:22
Alignment explanation
Indices: 1090906--1090948 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1090896 TGTAAAAGTG
*
1090906 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
1090928 ATTTC-CTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
1090948 A
1 A
1090949 ATTTAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:1091202 original size:47 final size:47
Alignment explanation
Indices: 1091141--1091235 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
1091131 TTTTATGAAG
1091141 AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
1 AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
*
1091188 AAGAAGATGATATAAAATGGGTTTAATTCTATTTAATCATTTATCAT
1 AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
1091235 A
1 A
1091236 CTTTATTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (47 bp):
AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
Found at i:1094931 original size:50 final size:50
Alignment explanation
Indices: 1094866--1095112 Score: 377
Period size: 50 Copynumber: 4.9 Consensus size: 50
1094856 ACCGAAGCTC
* *
1094866 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * * *
1094916 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAACCA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* *
1094966 CCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * * *
1095016 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAACCA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
*
1095066 CCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
1095113 AACCGTCCTA
Statistics
Matches: 175, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 175 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (50 bp):
TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
Found at i:1095040 original size:100 final size:100
Alignment explanation
Indices: 1094867--1095112 Score: 474
Period size: 100 Copynumber: 2.5 Consensus size: 100
1094857 CCGAAGCTCT
*
1094867 CTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
1 CTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
1094932 GCCTACACTTAGTACTACACACGTGACCTAACCAC
66 GCCTACACTTAGTACTACACACGTGACCTAACCAC
1094967 CTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
1 CTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
1095032 GCCTACACTTAGTACTACACACGTGACCTAACCAC
66 GCCTACACTTAGTACTACACACGTGACCTAACCAC
*
1095067 CTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
1 CTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAA
1095113 AACCGTCCTA
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 144 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (100 bp):
CTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
GCCTACACTTAGTACTACACACGTGACCTAACCAC
Found at i:1097800 original size:43 final size:42
Alignment explanation
Indices: 1097624--1098186 Score: 388
Period size: 43 Copynumber: 13.7 Consensus size: 42
1097614 AAAAGGCCAT
* * * *
1097624 TAAAGAACATGACTTTTAGTGACG-TTTT-TGAGAAAGCGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTCT-ACAAA-CGCCGC
* * * * * **
1097666 TAAAGAACGTGACCTTTAGCGGTGCCTTCCACACAAACATCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTC-TACAAACGCCGC
* * * * *
1097709 TAAAGGACGTGACCTTTAGAGGCGCTTTTTTAAAAACGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTCTACAAACGCCGC
*
1097751 TAAAGAACATGACCTTTAGCGGTGCTTTTCATACAAACGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTC-TACAAACGCCGC
* * * *
1097794 TAAAGAACAT-AACTTATAGTGGCACTTTT-T--------TGC
1 TAAAGAACATGACCTT-TAGCGGCGCTTTTCTACAAACGCCGC
* *
1097827 TAAAGAA-ATGACCTTTAGCGGCACTTTTCT-CGAAAACGCGGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTCTAC--AAACGCCGC
* * * * *
1097869 TAAAGAACATGACATTTAGCGGCGCTTTTCTAAAAAATGACAC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTCT-ACAAACGCCGC
* *
1097912 TAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTC-TACAAACGCCGC
*
1097955 TAAAGAACATGACCTTTAGTGGCGCTTTTCT-CAAAATCGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTCTAC-AAA-CGCCGC
* * * *
1097998 TAAAGAACAT-AACTTATAGTGGCACTTTT-T--------TGC
1 TAAAGAACATGACCTT-TAGCGGCGCTTTTCTACAAACGCCGC
* *
1098031 TAAAGAA-ATGACCTTTAGCGGCACTTTTCT-CGAAAACGCGGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTCTAC--AAACGCCGC
* * * * *
1098073 TAAAGAACATGACATTTAGCGGCGCTTTTCTAAAAAATGACAC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTCT-ACAAACGCCGC
* *
1098116 TAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTC-TACAAACGCCGC
*
1098159 TAAAGAACATGACCTTTAGCGGAGCTTT
1 TAAAGAACATGACCTTTAGCGGCGCTTT
1098187 CCTAAAAAAT
Statistics
Matches: 409, Mismatches: 74, Indels: 75
0.73 0.13 0.13
Matches are distributed among these distances:
32 28 0.07
33 28 0.07
41 2 0.00
42 83 0.20
43 262 0.64
44 6 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
TAAAGAACATGACCTTTAGCGGCGCTTTTCTACAAACGCCGC
Found at i:1097822 original size:85 final size:85
Alignment explanation
Indices: 1097624--1098007 Score: 242
Period size: 85 Copynumber: 4.6 Consensus size: 85
1097614 AAAAGGCCAT
* * * *
1097624 TAAAGAACATGACTTTTAGT-G-ACGTTTTTGAGAAAGCGCCGCTAAAGAACGTGACCTTTAGCG
1 TAAAGAACATAAC-TTTAGTGGCAC-TTTTTTAGAAAACGCCGCTAAAGAACATGACCTTTAGCG
*
1097687 GTGCCTTCCACACAAACATCGC
64 GTGCCTTCCACACAAACACCGC
* * * * *
1097709 TAAAGGACGTGACCTTTAGAGGCGCTTTTTTA-AAAACGCCGCTAAAGAACATGACCTTTAGCGG
1 TAAAGAACAT-AACTTTAGTGGCACTTTTTTAGAAAACGCCGCTAAAGAACATGACCTTTAGCGG
* * * *
1097773 TGCTTTTCATACAAACGCCGC
65 TGCCTTCCACACAAACACCGC
1097794 TAAAGAACATAACTTATAGTGGCACTTTTTT----------GCTAAAGAA-ATGACCTTTAGCGG
1 TAAAGAACATAACTT-TAGTGGCACTTTTTTAGAAAACGCCGCTAAAGAACATGACCTTTAGCGG
** * * * * *
1097848 CACTTTTCTCGA-AAACGCGGC
65 TGCCTTCCAC-ACAAACACCGC
* * * * * * * * *
1097869 TAAAGAACATGACATTTAGCGGCGCTTTTCTAAAAAATGACACTAAAGAACGTGACCTTTAGCGG
1 TAAAGAACATAAC-TTTAGTGGCACTTTTTTAGAAAACGCCGCTAAAGAACATGACCTTTAGCGG
* * * *
1097934 TGCTTTTCATACAAACGCCGC
65 TGCCTTCCACACAAACACCGC
* * * *
1097955 TAAAGAACATGACCTTTAGTGGCGCTTTTCTCA-AAATCGCCGCTAAAGAACAT
1 TAAAGAACAT-AACTTTAGTGGCACTTTT-TTAGAAAACGCCGCTAAAGAACAT
1098008 AACTTATAGT
Statistics
Matches: 234, Mismatches: 45, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
75 52 0.22
76 12 0.05
84 4 0.02
85 89 0.38
86 74 0.32
87 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (85 bp):
TAAAGAACATAACTTTAGTGGCACTTTTTTAGAAAACGCCGCTAAAGAACATGACCTTTAGCGGT
GCCTTCCACACAAACACCGC
Found at i:1097854 original size:32 final size:33
Alignment explanation
Indices: 1097792--1097854 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
1097782 TACAAACGCC
*
1097792 GCTAAAGAACATAACTTATAGTGGCACTTTTTT
1 GCTAAAGAACATAACTTATAGCGGCACTTTTTT
*
1097825 GCTAAAGAA-ATGACCTT-TAGCGGCACTTTT
1 GCTAAAGAACAT-AACTTATAGCGGCACTTTT
1097855 CTCGAAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (33 bp):
GCTAAAGAACATAACTTATAGCGGCACTTTTTT
Found at i:1097897 original size:75 final size:76
Alignment explanation
Indices: 1097749--1097897 Score: 189
Period size: 75 Copynumber: 2.0 Consensus size: 76
1097739 TAAAAACGCC
** *
1097749 GCTAAAGAACATGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATAACTTATAGT
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCATACAAACGCCGCTAAAGAACATAACTTATAGC
1097814 GGCACTTTTTT
66 GGCACTTTTTT
* *
1097825 GCTAAAGAA-ATGACCTTTAGCGGCACTTTTC-T-CGAAAACGCGGCTAAAGAACATGACATT-T
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCATAC--AAACGCCGCTAAAGAACATAAC-TTAT
*
1097886 AGCGGCGCTTTT
63 AGCGGCACTTTT
1097898 CTAAAAAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
73 1 0.02
74 1 0.02
75 51 0.80
76 11 0.17
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (76 bp):
GCTAAAGAACATGACCTTTAGCGGCACTTTTCATACAAACGCCGCTAAAGAACATAACTTATAGC
GGCACTTTTTT
Found at i:1097998 original size:204 final size:204
Alignment explanation
Indices: 1097708--1098186 Score: 847
Period size: 204 Copynumber: 2.4 Consensus size: 204
1097698 ACAAACATCG
* * * * *
1097708 CTAAAGGACGTGACCTTTAGAGGCGCTTTT-TTAAAAACGCCGCTAAAGAACATGACCTTTAGCG
1 CTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATGACCTTTAGCG
*
1097772 GTGCTTTTCATACAAACGCCGCTAAAGAACATAACTTATAGTGGCACTTTTTTGCTAAAGAAATG
66 GAGCTTTTCATACAAACGCCGCTAAAGAACATAACTTATAGTGGCACTTTTTTGCTAAAGAAATG
1097837 ACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGGCGCTTTTCTAA
131 ACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGGCGCTTTTCTAA
1097902 AAAATGACA
196 AAAATGACA
*
1097911 CTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATGACCTTTAGTG
1 CTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATGACCTTTAGCG
*
1097976 GCGCTTTTC-T-CAAAATCGCCGCTAAAGAACATAACTTATAGTGGCACTTTTTTGCTAAAGAAA
66 GAGCTTTTCATAC-AAA-CGCCGCTAAAGAACATAACTTATAGTGGCACTTTTTTGCTAAAGAAA
1098039 TGACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGGCGCTTTTCT
129 TGACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGGCGCTTTTCT
1098104 AAAAAATGACA
194 AAAAAATGACA
1098115 CTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATGACCTTTAGCG
1 CTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATGACCTTTAGCG
1098180 GAGCTTT
66 GAGCTTT
1098187 CCTAAAAAAT
Statistics
Matches: 264, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
202 1 0.00
203 31 0.12
204 232 0.88
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (204 bp):
CTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATGACCTTTAGCG
GAGCTTTTCATACAAACGCCGCTAAAGAACATAACTTATAGTGGCACTTTTTTGCTAAAGAAATG
ACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGGCGCTTTTCTAA
AAAATGACA
Found at i:1098050 original size:161 final size:162
Alignment explanation
Indices: 1097867--1098168 Score: 389
Period size: 161 Copynumber: 1.9 Consensus size: 162
1097857 CGAAAACGCG
* * * *
1097867 GCTAAAGAACATGACATTTAGCGGCGCTTTTCTAAAAAATGAC-ACTAAAGAACGTGACCTTTAG
1 GCTAAAGAACATGACATTTAGCGGCACTTTTCTAAAAAACG-CGACTAAAGAACATGACATTTAG
* * * * *
1097931 CGGTGCTTTTC-ATACAAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTTC-T-CAAAATC
65 CGGCGCTTTTCTA-AAAAACGACACTAAAGAACATGACCTTTAGCGGCGCTTTTCATAC-AAA-C
1097993 GCCGCTAAAGAACATAACTTATAGTGGCACTTTTTT
127 GCCGCTAAAGAACATAACTTATAGTGGCACTTTTTT
* ** *
1098029 GCTAAAGAA-ATGACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGC
1 GCTAAAGAACATGACATTTAGCGGCACTTTTCTAAAAAACGCGACTAAAGAACATGACATTTAGC
* * *
1098093 GGCGCTTTTCTAAAAAATGACACTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCG
66 GGCGCTTTTCTAAAAAACGACACTAAAGAACATGACCTTTAGCGGCGCTTTTCATACAAACGCCG
1098158 CTAAAGAACAT
131 CTAAAGAACAT
1098169 GACCTTTAGC
Statistics
Matches: 120, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
160 1 0.01
161 104 0.87
162 14 0.12
163 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (162 bp):
GCTAAAGAACATGACATTTAGCGGCACTTTTCTAAAAAACGCGACTAAAGAACATGACATTTAGC
GGCGCTTTTCTAAAAAACGACACTAAAGAACATGACCTTTAGCGGCGCTTTTCATACAAACGCCG
CTAAAGAACATAACTTATAGTGGCACTTTTTT
Found at i:1098058 original size:32 final size:33
Alignment explanation
Indices: 1097996--1098058 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
1097986 CAAAATCGCC
*
1097996 GCTAAAGAACATAACTTATAGTGGCACTTTTTT
1 GCTAAAGAACATAACTTATAGCGGCACTTTTTT
*
1098029 GCTAAAGAA-ATGACCTT-TAGCGGCACTTTT
1 GCTAAAGAACAT-AACTTATAGCGGCACTTTT
1098059 CTCGAAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (33 bp):
GCTAAAGAACATAACTTATAGCGGCACTTTTTT
Found at i:1098101 original size:75 final size:76
Alignment explanation
Indices: 1097953--1098101 Score: 205
Period size: 75 Copynumber: 2.0 Consensus size: 76
1097943 TACAAACGCC
* * *
1097953 GCTAAAGAACATGACCTTTAGTGGCGCTTTTCTCAAAATCGCCGCTAAAGAACATAACTTATAGT
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCTCAAAATCGCCGCTAAAGAACATAACTTATAGC
1098018 GGCACTTTTTT
66 GGCACTTTTTT
* *
1098029 GCTAAAGAA-ATGACCTTTAGCGGCACTTTTCTCGAAAA-CGCGGCTAAAGAACATGACATT-TA
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCTC-AAAATCGCCGCTAAAGAACATAAC-TTATA
*
1098091 GCGGCGCTTTT
64 GCGGCACTTTT
1098102 CTAAAAAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
75 50 0.77
76 15 0.23
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (76 bp):
GCTAAAGAACATGACCTTTAGCGGCACTTTTCTCAAAATCGCCGCTAAAGAACATAACTTATAGC
GGCACTTTTTT
Found at i:1098192 original size:86 final size:84
Alignment explanation
Indices: 1098030--1098204 Score: 235
Period size: 86 Copynumber: 2.0 Consensus size: 84
1098020 CACTTTTTTG
*
1098030 CTAAAGAAATGACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGG
1 CTAAAGAAATGACCTTTAGCGGCACTTTTCTC-AAAACGCCGCTAAAGAACATGACATTTAGCGG
* *
1098095 CGCTTTTCTAAAAAATGACA
65 AGCTTTCCTAAAAAATGACA
* ** *
1098115 CTAAAGAACGTGACCTTTAGCGGTGCTTTTCAT-ACAAACGCCGCTAAAGAACATGACCTTTAGC
1 CTAAAGAA-ATGACCTTTAGCGGCACTTTTC-TCA-AAACGCCGCTAAAGAACATGACATTTAGC
*
1098179 GGAGCTTTCCTAAAAAATGCCA
63 GGAGCTTTCCTAAAAAATGACA
1098201 CTAA
1 CTAA
1098205 TTTTAGTAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
85 9 0.11
86 69 0.87
87 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (84 bp):
CTAAAGAAATGACCTTTAGCGGCACTTTTCTCAAAACGCCGCTAAAGAACATGACATTTAGCGGA
GCTTTCCTAAAAAATGACA
Found at i:1101964 original size:50 final size:49
Alignment explanation
Indices: 1101857--1102054 Score: 182
Period size: 50 Copynumber: 4.0 Consensus size: 49
1101847 CAATTATAGA
* * * * *
1101857 AAATCAAATATAATATCACATATGTGCATACCTATATGGCCGAATATGC
1 AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
* * *
1101906 AAGATCAAATTTAACATTAAATATGTACTTACTTATATGGCCGAATATAC
1 AA-ATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
* * * * * *
1101956 GAATTCAAATATAATATCAAATTTGTGCATACCTT-CATGGCCGAATATTC
1 -AAATCAAATATAACATCAAATATGTACATA-CTTATATGGCCGAATATAC
* * * * *
1102006 TAAATCCAATATAACATCACATACGTACATACCTATGTGGCCGAATATA
1 -AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATA
1102055 TGCAAGGTCA
Statistics
Matches: 116, Mismatches: 29, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 4 0.03
50 107 0.92
51 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (49 bp):
AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
Found at i:1102047 original size:100 final size:100
Alignment explanation
Indices: 1101860--1102054 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 100
1101850 TTATAGAAAA
* * *
1101860 TCAAATATAATATCACATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATTTAACATTA
1 TCAAATATAATATCAAATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATATAACATCA
* * *
1101925 AATATGTACTTACTTATATGGCCGAATATACGAAT
66 AATACGTACATACCTATATGGCCGAATATACGAAT
* * *
1101960 TCAAATATAATATCAAATTTGTGCATACCT-TCATGGCCGAATATTCTAA-ATCCAATATAACAT
1 TCAAATATAATATCAAATATGTGCATACCTAT-ATGGCCGAATATGC-AAGATCAAATATAACAT
* *
1102023 CACATACGTACATACCTATGTGGCCGAATATA
64 CAAATACGTACATACCTATATGGCCGAATATA
1102055 TGCAAGGTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
99 1 0.01
100 79 0.96
101 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (100 bp):
TCAAATATAATATCAAATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATATAACATCA
AATACGTACATACCTATATGGCCGAATATACGAAT
Found at i:1106967 original size:27 final size:27
Alignment explanation
Indices: 1106937--1107114 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
1106927 ATATTGAGTC
* *
1106937 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
1106964 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
1106991 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
1107019 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
1107046 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
1107073 CGTACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
1107100 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1107115 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:1107080 original size:82 final size:81
Alignment explanation
Indices: 1106958--1107113 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
1106948 TGCTATATAA
* *
1106958 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
1107023 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
1107040 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGTACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
1107104 CACTTAGTGC
65 CACTTAGTGC
1107114 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:1112227 original size:27 final size:27
Alignment explanation
Indices: 1112195--1112260 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
1112185 TAGTTGAACT
1112195 ATGGCAAAGTGATAAAGTGTGCCAAAC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
*
1112222 ATGGCAAAGTGATAAAGTGTGCCAAAT
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
1112249 ATGGCAAAGTGA
1 ATGGCAAAGTGA
1112261 AATGTGACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGTGTGCCAAAC
Found at i:1117222 original size:23 final size:22
Alignment explanation
Indices: 1117191--1117234 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1117181 TTGATTGTAT
*
1117191 GTTTAGGTATGATTTTAGTTTAA
1 GTTTAGGTATGAATTTA-TTTAA
*
1117214 GTTTTGGTATGAATTTATTTA
1 GTTTAGGTATGAATTTATTTA
1117235 TGAATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTAGGTATGAATTTATTTAA
Found at i:1126967 original size:40 final size:40
Alignment explanation
Indices: 1126890--1127068 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
1126880 ACCCAAGTAT
* ** *
1126890 CTTCGGGATTTAG-CCGGATATAACCACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
1126929 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
1126969 CTTCGGGACTTAGCCCGGATATAGTCGCCAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
1127009 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAAGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
1127049 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGAT
1127069 TTCATTCGAA
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
39 12 0.10
40 108 0.90
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:1130304 original size:23 final size:22
Alignment explanation
Indices: 1130273--1130316 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1130263 TTGATCGTAT
*
1130273 GTTTAGGTATGATTTTAGTTTAA
1 GTTTAGGTATGAATTTA-TTTAA
*
1130296 GTTTTGGTATGAATTTATTTA
1 GTTTAGGTATGAATTTATTTA
1130317 TGAATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTAGGTATGAATTTATTTAA
Found at i:1134113 original size:28 final size:29
Alignment explanation
Indices: 1134080--1134151 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
1134070 TATAGTAAGT
* *
1134080 CCGCACACTTAGTGTTATATAA-TCGAAC
1 CCGCACACTTAGTGCTATACAACTCGAAC
* *
1134108 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAACTCGAAC
1134137 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
1134152 CAATTTCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 19 0.50
29 19 0.50
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATACAACTCGAAC
Found at i:1138084 original size:9 final size:9
Alignment explanation
Indices: 1138070--1138195 Score: 84
Period size: 9 Copynumber: 14.0 Consensus size: 9
1138060 TATTACGTAA
*
1138070 GTAAGTTTT
1 GTAAGTTAT
1138079 GTAAGTTAT
1 GTAAGTTAT
1138088 GTAAGTTAT
1 GTAAGTTAT
*
1138097 G-ATA-TGAT
1 GTA-AGTTAT
* *
1138105 ATACATTTAT
1 GTA-AGTTAT
*
1138115 GT-A-TTAC
1 GTAAGTTAT
1138122 GTAAGTTAT
1 GTAAGTTAT
1138131 GTCAAGTATGAT
1 GT-AAGT-T-AT
* *
1138143 ATATATTTAT
1 GTA-AGTTAT
1138153 GT-A-TTAT
1 GTAAGTTAT
1138160 GTAAGTTAT
1 GTAAGTTAT
*
1138169 GTAAGTTTT
1 GTAAGTTAT
1138178 GTAAGTTAT
1 GTAAGTTAT
1138187 GTAAGTTAT
1 GTAAGTTAT
1138196 TATATGCTAT
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
7 11 0.12
8 8 0.09
9 55 0.59
10 11 0.12
11 3 0.03
12 5 0.05
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Done.