Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 83 of 325
Found at i:28288955 original size:139 final size:139
Alignment explanation
Indices: 28288705--28289188 Score: 729
Period size: 139 Copynumber: 3.5 Consensus size: 139
28288695 TGATGTCATA
* * * * * *
28288705 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGAT
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGT
* *
28288769 CTTATTCATTTTCCCGTCATGTTGCCATTATATCTTTCAACCATGGTCTTACTCATTTCATGTCA
65 CTTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCA
*
28288834 GGTTGCCATG
130 AGTTGCCATG
*
28288844 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
28288909 TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
66 TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
28288974 GTTGCCATG
131 GTTGCCATG
*
28288983 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
** *** * * * *
28289048 TTACACA-TTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAC
66 TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
28289112 GTTGCCATG
131 GTTGCCATG
* * * *
28289121 GTATCTTTCAACCATAGTCTTACACATTTCATATCAGGTTGTCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
28289186 TTA
66 TTA
28289189 CACATTCCAT
Statistics
Matches: 320, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
138 126 0.39
139 194 0.61
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (139 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
GTTGCCATG
Found at i:28293589 original size:22 final size:23
Alignment explanation
Indices: 28293555--28293598 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
28293545 TGAAATGGCT
*
28293555 TATTTTCCATAATAACC-AATTC
1 TATTTTACATAATAACCTAATTC
* *
28293577 TATTTTACTTAATCACCTAATT
1 TATTTTACATAATAACCTAATT
28293599 GGCACTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTTTACATAATAACCTAATTC
Found at i:28299974 original size:11 final size:11
Alignment explanation
Indices: 28299958--28299982 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28299948 TAAACTATAC
28299958 CTACTCCACTT
1 CTACTCCACTT
28299969 CTACTCCACTT
1 CTACTCCACTT
28299980 CTA
1 CTA
28299983 GTTACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (11 bp):
CTACTCCACTT
Found at i:28306278 original size:30 final size:30
Alignment explanation
Indices: 28306213--28306311 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
28306203 ACCACTAACA
* * * ** *
28306213 ATTTTTCGTTACAGACGTAACGGAATTATC
1 ATTTTTCATCACAGACTTAACGGAGCTACC
28306243 ATTTTTCATCACAGACTTAACGGAGCTACC
1 ATTTTTCATCACAGACTTAACGGAGCTACC
* * * * * * *
28306273 GTTTTTCGTTATATACTTAACGGAGTTTCC
1 ATTTTTCATCACAGACTTAACGGAGCTACC
28306303 ATTTTTCAT
1 ATTTTTCAT
28306312 TCCCTTATCA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (30 bp):
ATTTTTCATCACAGACTTAACGGAGCTACC
Found at i:28316450 original size:19 final size:20
Alignment explanation
Indices: 28316426--28316464 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28316416 TGGTCACCAC
28316426 AATATAA-ATTAA-ATATAAT
1 AATATAAGA-TAAGATATAAT
28316445 AATATAAGATAAGATATAAT
1 AATATAAGATAAGATATAAT
28316465 TATGCCCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AATATAAGATAAGATATAAT
Found at i:28318349 original size:28 final size:28
Alignment explanation
Indices: 28318309--28318371 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 28
28318299 AATTTCACAA
* *
28318309 TTTTAATAGATT-ATTATATATTTATAAT
1 TTTTAAAAGATTAATTAAATATTTAT-AT
* *
28318337 TTTTAAAATATTAAATTAAATTTTTATAT
1 TTTTAAAAGATT-AATTAAATATTTATAT
28318366 TTTTAA
1 TTTTAA
28318372 GAGGAGAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.34
29 8 0.28
30 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTAAAAGATTAATTAAATATTTATAT
Found at i:28322139 original size:15 final size:15
Alignment explanation
Indices: 28322119--28322148 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28322109 TATTTAAATT
28322119 TATTTATAAATTTTA
1 TATTTATAAATTTTA
28322134 TATTTATAAATTTTA
1 TATTTATAAATTTTA
28322149 CAAGATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTATAAATTTTA
Found at i:28322400 original size:15 final size:15
Alignment explanation
Indices: 28322382--28322428 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
28322372 TTTTTAAAGA
28322382 TTATATTTTAGTTAT
1 TTATATTTTAGTTAT
* **
28322397 TTATATTTAAAAT-T
1 TTATATTTTAGTTAT
*
28322411 TTATATTTTAGTCAT
1 TTATATTTTAGTTAT
28322426 TTA
1 TTA
28322429 CGTTATAGTT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (15 bp):
TTATATTTTAGTTAT
Found at i:28324159 original size:111 final size:115
Alignment explanation
Indices: 28323949--28324211 Score: 336
Period size: 112 Copynumber: 2.3 Consensus size: 115
28323939 CTAGTAATTT
* * * *
28323949 TTTTTTGTTCTGGCCTTATAATGGCCGGCACTAAGGACTTTTATCATGTTCCAATGCAATTTTTT
1 TTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTATCATGTCCCAATGCAATTTTTT
28324014 ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGTAAAA-AA-AAA
66 ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGTAAAACAAGAAA
* * * * **
28324062 -TTTTGGTTCTGGCCTTCTAATGGCCGACACCAGGGGCTTTTTTTGTGTCCCAATGCAATTTTTT
1 TTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTATCATGTCCCAATGCAATTTTTT
* * ** *
28324126 -TTTTACTTTTCTACATTGATGGCCGGCACCAGACTTGTAAAACAAGAAA
66 ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGTAAAACAAGAAA
28324175 TTTTTTTGGGTTCTGGCCTTCTAATGGCCGGCACCAA
1 --TTTTT-GGTTCTGGCCTTCTAATGGCCGGCACCAA
28324212 ATTTATCATC
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
111 37 0.29
112 56 0.44
113 3 0.02
116 4 0.03
117 27 0.21
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (115 bp):
TTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTATCATGTCCCAATGCAATTTTTT
ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGTAAAACAAGAAA
Found at i:28327034 original size:60 final size:60
Alignment explanation
Indices: 28326956--28327092 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
28326946 CAGTGTTAAC
* *
28326956 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
28327017 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
28327077 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
28327093 TAACACAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 53 0.78
61 13 0.19
62 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:28327056 original size:28 final size:27
Alignment explanation
Indices: 28326955--28327056 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
28326945 TCAGTGTTAA
* *
28326955 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
28326983 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
28327015 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
28327043 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
28327057 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:28331962 original size:60 final size:60
Alignment explanation
Indices: 28331884--28332020 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
28331874 CAGTGTTAAC
* *
28331884 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
28331945 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
28332005 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
28332021 TAACACAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 53 0.78
61 13 0.19
62 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:28331984 original size:28 final size:27
Alignment explanation
Indices: 28331883--28331984 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
28331873 TCAGTGTTAA
* *
28331883 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
28331911 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
28331943 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
28331971 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
28331985 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:28336873 original size:47 final size:47
Alignment explanation
Indices: 28336751--28336967 Score: 245
Period size: 47 Copynumber: 4.8 Consensus size: 47
28336741 GTTATACGTG
* * * **
28336751 TAACGCGGTGCTAAGTGGATATACCACGATTACACATATTGAAGCAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
28336798 GTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT
1 -TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* *
28336846 TAACGTGGTGCTAAGTGGATATACCACGATTA-A-ACA-TG------
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* * *
28336884 TAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTTAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* *
28336931 TAACGTGGTGCTAAGTGGATATACCACAGTTAAATAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATAT
28336968 GTAACATGGT
Statistics
Matches: 143, Mismatches: 17, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
38 29 0.20
39 1 0.01
40 2 0.01
41 2 0.01
44 2 0.01
45 2 0.01
46 1 0.01
47 63 0.44
48 41 0.29
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (47 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
Found at i:28336900 original size:85 final size:85
Alignment explanation
Indices: 28336795--28337000 Score: 360
Period size: 85 Copynumber: 2.4 Consensus size: 85
28336785 CATATTGAAG
*
28336795 CATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
1 CATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
28336860 GTGGATATACCAC-GATTAAA
66 GTGGATATACCACAG-TTAAA
*
28336880 CATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTTATTAACGTGGTGCTAA
1 CATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
28336945 GTGGATATACCACAGTTAAA
66 GTGGATATACCACAGTTAAA
* *
28336965 TATGTAACATGGTGCTAAGTGGATATGCCACAGTTA
1 CATGTAACATGGTGCTAAGTGGATATGCCACGGTTA
28337001 TACATGTTAA
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
85 115 0.99
86 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (85 bp):
CATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
GTGGATATACCACAGTTAAA
Found at i:28336902 original size:38 final size:38
Alignment explanation
Indices: 28336846--28336995 Score: 149
Period size: 38 Copynumber: 3.7 Consensus size: 38
28336836 ATTGATTCAT
* *
28336846 TAACGTGGTGCTAAGTGGATATACCACGATTAAACATG
1 TAACATGGTGCTAAGTGGATATACCACGATTAAATATG
* *
28336884 TAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 TAACATGGTGCTAAGTGGATATACCACGATTA-A-ATA-TG
*
28336925 ATTTATTAACGTGGTGCTAAGTGGATATACCAC-AGTTAAATATG
1 ------TAACATGGTGCTAAGTGGATATACCACGA-TTAAATATG
*
28336969 TAACATGGTGCTAAGTGGATATGCCAC
1 TAACATGGTGCTAAGTGGATATACCAC
28336996 AGTTATACAT
Statistics
Matches: 93, Mismatches: 9, Indels: 20
0.76 0.07 0.16
Matches are distributed among these distances:
38 54 0.58
39 1 0.01
40 2 0.02
41 2 0.02
44 2 0.02
45 3 0.03
46 1 0.01
47 28 0.30
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (38 bp):
TAACATGGTGCTAAGTGGATATACCACGATTAAATATG
Found at i:28339432 original size:27 final size:26
Alignment explanation
Indices: 28339391--28339602 Score: 97
Period size: 27 Copynumber: 8.3 Consensus size: 26
28339381 GAAAGAAAGA
28339391 TAAATTTAAATGAAATAAGGAAAAAAT
1 TAAATTTAAA-GAAATAAGGAAAAAAT
* * *
28339418 TTAATTTCAAAGAAAT-GGGAAAAAAAC
1 TAAATTT-AAAGAAATAAGG-AAAAAAT
* * * *
28339445 TAAAATT-AA-AATTGAAAG-AAAGA-
1 TAAATTTAAAGAAAT-AAGGAAAAAAT
28339468 TAAATTTAAACGAAATAAGGAAAAAAT
1 TAAATTTAAA-GAAATAAGGAAAAAAT
* *
28339495 TTAATTTCAAAGAAAT-GGGAAAAAAT
1 TAAATTT-AAAGAAATAAGGAAAAAAT
* * * *
28339521 TAAAATT-AA-AATTGAAAG-AAAGA-
1 TAAATTTAAAGAAAT-AAGGAAAAAAT
**
28339544 TAAATTTAAATGAAATGGGGAAAAAAT
1 TAAATTTAAA-GAAATAAGGAAAAAAT
* * *
28339571 TTAATTTAAATTAAATGA-GAAAAAA-
1 TAAATTTAAA-GAAATAAGGAAAAAAT
28339596 TAAATTT
1 TAAATTT
28339603 GCATGGAAAG
Statistics
Matches: 137, Mismatches: 31, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
23 15 0.11
24 17 0.12
25 13 0.09
26 38 0.28
27 48 0.35
28 6 0.04
ACGTcount: A:0.59, C:0.02, G:0.13, T:0.26
Consensus pattern (26 bp):
TAAATTTAAAGAAATAAGGAAAAAAT
Found at i:28339538 original size:76 final size:76
Alignment explanation
Indices: 28339381--28339650 Score: 361
Period size: 76 Copynumber: 3.6 Consensus size: 76
28339371 AATTTACAAG
*
28339381 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAAACT
1 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGG-AAAAAATT
28339446 AAAATTAAAATT
65 AAAATTAAAATT
*
28339458 GAAAGAAAGATAAATTTAAACGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAATTA
1 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAATTA
28339523 AAATTAAAATT
66 AAATTAAAATT
** * *
28339534 GAAAGAAAGATAAATTTAAATGAAATGGGGAAAAAATTTAATTT-AAATTAAATGAGAAAAAA-T
1 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAA-GAAATGGGAAAAAATT
*** *
28339597 -AAATTTGCATG
65 AAAATTAAAATT
* * *
28339608 GAAAGATAA-AT-AATTTAAATGAAATGAGAAAAAAATTAAATTT
1 GAAAGA-AAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTT
28339651 GTATGGAAAA
Statistics
Matches: 177, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
73 29 0.16
74 15 0.08
75 6 0.03
76 72 0.41
77 55 0.31
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (76 bp):
GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAATTA
AAATTAAAATT
Found at i:28339646 original size:21 final size:21
Alignment explanation
Indices: 28339622--28339744 Score: 63
Period size: 21 Copynumber: 5.5 Consensus size: 21
28339612 GATAAATAAT
28339622 TTAAATGAAATGAGAAAAAAA
1 TTAAATGAAATGAGAAAAAAA
* *
28339643 TTAAATTTG-TATGGAAAAATAGATAA
1 TTAAA--TGAAAT-GAGAAA-A-A-AA
* **
28339669 TTTAAATGAAATGAGGAAAATT
1 -TTAAATGAAATGAGAAAAAAA
* *
28339691 TTAATTTAAAT-A-AAAAATAA
1 TTAAATGAAATGAGAAAAA-AA
28339711 TATAAATGAAATGAGAAAAAAAA
1 T-TAAATGAAATGAG-AAAAAAA
28339734 TTAAATTGAAA
1 TTAAA-TGAAA
28339745 AAAATATAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 26
0.65 0.12 0.23
Matches are distributed among these distances:
19 4 0.05
20 2 0.03
21 22 0.30
22 7 0.09
23 16 0.22
24 7 0.09
25 7 0.09
26 4 0.05
27 5 0.07
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (21 bp):
TTAAATGAAATGAGAAAAAAA
Found at i:28339669 original size:48 final size:46
Alignment explanation
Indices: 28339572--28339770 Score: 186
Period size: 48 Copynumber: 4.5 Consensus size: 46
28339562 GGAAAAAATT
* * *
28339572 TAATTTAAATTAAATGAGAAAAAA-TAAATTTGCATGGAAAGATAAA
1 TAATTTAAATGAAATGAGAAAAAATTAAATTTGAATGGAAAAAT-AA
*
28339618 TAATTTAAATGAAATGAGAAAAAAATTAAATTTGTATGGAAAAATAGA
1 TAATTTAAATGAAATGAG-AAAAAATTAAATTTGAATGGAAAAATA-A
* * * *
28339666 TAATTTAAATGAAATGAGGAAAATTTTAATTTAAAT---AAAA-AA
1 TAATTTAAATGAAATGAGAAAAAATTAAATTTGAATGGAAAAATAA
*
28339708 TAATATAAATGAAATGAGAAAAAAAATTAAA-TTGAA---AAAAAT-A
1 TAATTTAAATGAAATGAG--AAAAAATTAAATTTGAATGGAAAAATAA
*
28339751 TAGTTTAAATGAAATG-GAAA
1 TAATTTAAATGAAATGAGAAA
28339771 TGAAATGAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
40 3 0.02
42 19 0.15
43 24 0.18
44 12 0.09
46 17 0.13
47 20 0.15
48 36 0.27
ACGTcount: A:0.58, C:0.01, G:0.13, T:0.29
Consensus pattern (46 bp):
TAATTTAAATGAAATGAGAAAAAATTAAATTTGAATGGAAAAATAA
Found at i:28339775 original size:5 final size:5
Alignment explanation
Indices: 28339757--28339786 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
28339747 AATATAGTTT
28339757 AAATG AAATGG AAATG AAATG AAATG AAAT
1 AAATG AAAT-G AAATG AAATG AAATG AAAT
28339787 TTGAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:28339776 original size:16 final size:15
Alignment explanation
Indices: 28339757--28339786 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28339747 AATATAGTTT
28339757 AAATGAAATGGAAATG
1 AAATGAAAT-GAAATG
28339773 AAATGAAATGAAAT
1 AAATGAAATGAAAT
28339787 TTGAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
AAATGAAATGAAATG
Found at i:28340174 original size:5 final size:5
Alignment explanation
Indices: 28340164--28340264 Score: 51
Period size: 5 Copynumber: 18.0 Consensus size: 5
28340154 GAAAAAAATT
* *
28340164 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTA
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A AATGA
* *
28340215 TAATGA ATATGA AATTA AATAA AATGTTA AATGA ACAT-A ATATGA AATGA
1 -AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA A-ATGA AATGA
28340265 TGATTATGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
5 39 0.51
6 25 0.32
7 13 0.17
ACGTcount: A:0.54, C:0.01, G:0.14, T:0.31
Consensus pattern (5 bp):
AATGA
Found at i:28340182 original size:30 final size:30
Alignment explanation
Indices: 28340144--28340264 Score: 87
Period size: 30 Copynumber: 4.0 Consensus size: 30
28340134 GAAAAGTAAT
28340144 AAAT-TTAAATGAAA-A-AAATTAATGAAATG
1 AAATGTTAAATGAAATATAAA-T-ATGAAATG
*
28340173 AAATGTTAAATGAAATATGAATATGAAATG
1 AAATGTTAAATGAAATATAAATATGAAATG
*
28340203 AAATGTAATTTATAATG-AATATGAAAT-T-AAATA
1 AAATG----TTA-AATGAAATAT-AAATATGAAATG
*
28340236 AAATGTTAAATG-AACAT-AATATGAAATG
1 AAATGTTAAATGAAATATAAATATGAAATG
28340264 A
1 A
28340265 TGATTATGAA
Statistics
Matches: 76, Mismatches: 5, Indels: 23
0.73 0.05 0.22
Matches are distributed among these distances:
26 3 0.04
27 1 0.01
28 13 0.17
29 7 0.09
30 23 0.30
31 2 0.03
32 2 0.03
33 9 0.12
34 9 0.12
35 7 0.09
ACGTcount: A:0.56, C:0.01, G:0.12, T:0.31
Consensus pattern (30 bp):
AAATGTTAAATGAAATATAAATATGAAATG
Found at i:28340185 original size:12 final size:12
Alignment explanation
Indices: 28340168--28340249 Score: 53
Period size: 12 Copynumber: 6.6 Consensus size: 12
28340158 AAAATTAATG
28340168 AAATGAAATGTT
1 AAATGAAATGTT
* *
28340180 AAATGAAATATG
1 AAATGAAATGTT
28340192 AATATGAAATG--
1 AA-ATGAAATGTT
*
28340203 AAATGTAAT-TT
1 AAATGAAATGTT
28340214 ATAATGAATATGAAATT
1 A-AATGAA-ATG---TT
*
28340231 AAATAAAATGTT
1 AAATGAAATGTT
28340243 AAATGAA
1 AAATGAA
28340250 CATAATATGA
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
10 6 0.11
11 3 0.06
12 25 0.46
13 9 0.17
15 3 0.06
16 5 0.09
17 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (12 bp):
AAATGAAATGTT
Found at i:28340229 original size:28 final size:30
Alignment explanation
Indices: 28340165--28340264 Score: 100
Period size: 28 Copynumber: 3.3 Consensus size: 30
28340155 AAAAAAATTA
28340165 ATGAAATGAAATGTTAAATGAAATATGAAT
1 ATGAAATGAAATGTTAAATGAAATATGAAT
28340195 ATGAAATGAAATGTAATTTATAATG-AATATGAA-
1 ATGAAATGAAATG----TTA-AATGAAATATGAAT
* * *
28340228 ATTAAATAAAATGTTAAATG-AACAT-AAT
1 ATGAAATGAAATGTTAAATGAAATATGAAT
28340256 ATGAAATGA
1 ATGAAATGA
28340265 TGATTATGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
27 2 0.03
28 15 0.25
29 3 0.05
30 13 0.22
33 11 0.19
34 11 0.19
35 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.14, T:0.31
Consensus pattern (30 bp):
ATGAAATGAAATGTTAAATGAAATATGAAT
Found at i:28340410 original size:17 final size:18
Alignment explanation
Indices: 28340378--28340414 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28340368 AAATGGAAAG
*
28340378 ATAGATAATTTAAATGAA
1 ATAGATAATGTAAATGAA
28340396 ATAGA-AATGTAAATGAA
1 ATAGATAATGTAAATGAA
28340413 AT
1 AT
28340415 GCAAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.30
Consensus pattern (18 bp):
ATAGATAATGTAAATGAA
Found at i:28342748 original size:85 final size:85
Alignment explanation
Indices: 28342633--28342872 Score: 238
Period size: 89 Copynumber: 2.7 Consensus size: 85
28342623 AGAAATTGAC
*
28342633 AAATTAAATTTACAGACACAATAAAATACAAACATTCTAAAATATTAATACA-AAAAA-TAAAAT
1 AAATTAAATTTA-AAACACAA-AAAATACAAACATTCTAAAA-ATTAATACACAAAAATTAAAAT
28342696 TCAAAC-A-AAAATAATACGCACT
63 TCAAACTACAAAA-AATACGCACT
* * *
28342718 AAATTAAATTTAAACACCCAAAAAACTACAAACATATGGGT-AAAATTAATACACAAAAATTTTA
1 AAATTAAATTTAAA-ACACAAAAAA-TACAAACAT-T--CTAAAAATTAATACACAAAAA-TTAA
* * *
28342782 AATTCAAACTACATAAAATATGGACT
60 AATTCAAACTACAAAAAATACGCACT
* *
28342808 AAATTAAATTTACAAATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
1 AAATTAAATTTA-AAACAC-AAAAAATACAAACATTCTAA-AAATTAATACACAAAAAT-TAAAA
28342873 AATGAATCCT
Statistics
Matches: 128, Mismatches: 12, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
84 5 0.04
85 26 0.20
86 10 0.08
87 9 0.07
88 3 0.02
89 32 0.25
90 32 0.25
91 11 0.09
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (85 bp):
AAATTAAATTTAAAACACAAAAAATACAAACATTCTAAAAATTAATACACAAAAATTAAAATTCA
AACTACAAAAAATACGCACT
Found at i:28342866 original size:89 final size:86
Alignment explanation
Indices: 28342633--28342872 Score: 256
Period size: 90 Copynumber: 2.7 Consensus size: 86
28342623 AGAAATTGAC
* *
28342633 AAATTAAATTTACAGACACAATAAAATACAAACATTCTAAAATATTAATACA-AAAA-ATAAAAT
1 AAATTAAATTTACAAACACAAAAAAATACAAACATTCTAAAA-ATTAATACACAAAATATAAAAT
28342696 TCAAACAAAAATAATACGCACT
65 TCAAACAAAAATAATACGCACT
* * * * *
28342718 AAATTAAATTTA-AACACCCAAAAAACTACAAACATATGGGT-AAAATTAATACACAAAAATTTT
1 AAATTAAATTTACAA-ACACAAAAAAATACAAACAT-T--CTAAAAATTAATACAC-AAAATATA
* * *
28342781 AAATTCAAACTACATAA-AATATGGACT
61 AAATTCAAAC-A-AAAATAATACGCACT
*
28342808 AAATTAAATTTACAAATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
1 AAATTAAATTTACAAACACAAAAAAATACAAACATTCTAA-AAATTAATACAC-AAAATATAAAA
28342873 AATGAATCCT
Statistics
Matches: 126, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
84 1 0.01
85 29 0.23
86 10 0.08
87 4 0.03
88 6 0.05
89 33 0.26
90 38 0.30
91 5 0.04
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (86 bp):
AAATTAAATTTACAAACACAAAAAAATACAAACATTCTAAAAATTAATACACAAAATATAAAATT
CAAACAAAAATAATACGCACT
Found at i:28343380 original size:27 final size:27
Alignment explanation
Indices: 28343342--28343407 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
28343332 TTCGATTGTA
* *
28343342 CACTACAAAAAACTCTCATCTACAATC
1 CACTACAAAAAACTCCCATATACAATC
28343369 CACTACAAAAAACTCCCATATACAATC
1 CACTACAAAAAACTCCCATATACAATC
28343396 CACTACAAAAAA
1 CACTACAAAAAA
28343408 AAACTCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (27 bp):
CACTACAAAAAACTCCCATATACAATC
Found at i:28343650 original size:47 final size:47
Alignment explanation
Indices: 28343599--28343701 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 47
28343589 GCCAGCAACG
* * **
28343599 ATTTTTTTTTTA-CTCTGGTGTTAGTCAATA-AGTGCCCAACACTCCAA
1 ATTTTTTTTTCATCTCTGGTGTCAACCAATATA-TGCCCAACAC-CCAA
*
28343646 ATTTTTTTTTCATTTCTGGTGTCAACCAATATATGCCCAACACCCAA
1 ATTTTTTTTTCATCTCTGGTGTCAACCAATATATGCCCAACACCCAA
28343693 ATTTTTTTT
1 ATTTTTTTT
28343702 AAAATTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 24 0.49
48 24 0.49
49 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (47 bp):
ATTTTTTTTTCATCTCTGGTGTCAACCAATATATGCCCAACACCCAA
Found at i:28343881 original size:113 final size:113
Alignment explanation
Indices: 28343711--28343918 Score: 287
Period size: 112 Copynumber: 1.8 Consensus size: 113
28343701 TAAAATTTAA
* * **
28343711 TGGTGCCAACCATCAGTGTAGAAAAGTAAGAAAAAAAATTACATTGGTACACGAAAAAAGTCTTT
1 TGGTGCCAACCATCAGTGTAAAAAAGTAACAAAAAAAATTACATTGGTACACGAAAAAAGTCCGT
*
28343776 GGTGCT-GGCCATTAGAAGGCCAGAACCAAAACTTTTTTTTTGTTGGTC
66 GGTG-TGGGCCATTAAAAGGCCAGAACCAAAACTTTTTTTTTGTTGGTC
* * * **
28343824 TGGTGCCGACTATCAGTGTAAAAAAGT-ACAAAAAAATTTGTATTAGG-ACACGAAAAAAGTCCG
1 TGGTGCCAACCATCAGTGTAAAAAAGTAACAAAAAAAATTACATT-GGTACACGAAAAAAGTCCG
28343887 TGGTGTGGGCCATTAAAAGGCCAGAACCAAAA
65 TGGTGTGGGCCATTAAAAGGCCAGAACCAAAA
28343919 AAAAAATTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
111 1 0.01
112 56 0.67
113 26 0.31
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (113 bp):
TGGTGCCAACCATCAGTGTAAAAAAGTAACAAAAAAAATTACATTGGTACACGAAAAAAGTCCGT
GGTGTGGGCCATTAAAAGGCCAGAACCAAAACTTTTTTTTTGTTGGTC
Found at i:28344012 original size:113 final size:113
Alignment explanation
Indices: 28343710--28344030 Score: 328
Period size: 113 Copynumber: 2.8 Consensus size: 113
28343700 TTAAAATTTA
* * * * * *
28343710 ATGGTGCCAACCATCAGTGTAGAAAAGTAAGAAAAAAAA-TTACATTGGTACACGAAAAAAGTCT
1 ATGGTGCCGACTATCAGTGTAGAAAAGTAAAAAAAAAAATTTGCATTGGGACACGAAAAAAGTCC
* ****** ** *
28343774 TTGGTGCTGGCCATTAGAAGGCCAGAACCAAAACTTTTTTTTTGTTGGT
66 CTGGTGCT-GCCATTAGAAGGCCAGAACCAAAACAAAAAATTTACTAGT
* * * * *
28343823 CTGGTGCCGACTATCAGTGTAAAAAAGT--ACAAAAAAATTTGTATTAGGACACGAAAAAAGTCC
1 ATGGTGCCGACTATCAGTGTAGAAAAGTAAAAAAAAAAATTTGCATTGGGACACGAAAAAAGTCC
* *
28343886 GTGGTG-TGGGCCATTAAAAGGCCAGAACCAAAA-AAAAAATTTACTAGT
66 CTGGTGCT--GCCATTAGAAGGCCAGAACCAAAACAAAAAATTTACTAGT
* * **
28343934 ATGGTGTCGGCTATCAGTGTAGAAAAGTAAAAAAAAAAATTTGCGGTGGGACACGAAAAAAGTCC
1 ATGGTGCCGACTATCAGTGTAGAAAAGTAAAAAAAAAAATTTGCATTGGGACACGAAAAAAGTCC
28343999 CTGGTGCCTGCCATTAGAAGGCCAGAACCAAA
66 CTGGTG-CTGCCATTAGAAGGCCAGAACCAAA
28344031 TTTTTTTTAA
Statistics
Matches: 169, Mismatches: 33, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
111 38 0.22
112 49 0.29
113 81 0.48
115 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (113 bp):
ATGGTGCCGACTATCAGTGTAGAAAAGTAAAAAAAAAAATTTGCATTGGGACACGAAAAAAGTCC
CTGGTGCTGCCATTAGAAGGCCAGAACCAAAACAAAAAATTTACTAGT
Found at i:28345412 original size:31 final size:31
Alignment explanation
Indices: 28345365--28345423 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28345355 AACCCTTCCT
* *
28345365 ACATTAAATCCGACAAAAAACAGCAAATATA
1 ACATGAAATCCAACAAAAAACAGCAAATATA
28345396 ACATGAAATCCAACAAAAAACAGCAAAT
1 ACATGAAATCCAACAAAAAACAGCAAAT
28345424 GTAGCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.14
Consensus pattern (31 bp):
ACATGAAATCCAACAAAAAACAGCAAATATA
Found at i:28345710 original size:21 final size:21
Alignment explanation
Indices: 28345686--28345734 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28345676 GCTGCCATCA
* *
28345686 CTGCTGTCTCTACCTCCCTCG
1 CTGCTGCCGCTACCTCCCTCG
* *
28345707 CTGCTACCGCTGCCTCCCTCG
1 CTGCTGCCGCTACCTCCCTCG
28345728 CTGCTGC
1 CTGCTGC
28345735 ATCCACTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.49, G:0.18, T:0.29
Consensus pattern (21 bp):
CTGCTGCCGCTACCTCCCTCG
Found at i:28346173 original size:13 final size:14
Alignment explanation
Indices: 28346147--28346175 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28346137 ACTAACGACG
28346147 AATTAAATCATTAT
1 AATTAAATCATTAT
28346161 AATTAAA-CATTAT
1 AATTAAATCATTAT
28346174 AA
1 AA
28346176 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAATCATTAT
Found at i:28352729 original size:11 final size:11
Alignment explanation
Indices: 28352715--28352759 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
28352705 AGATAAATAT
28352715 TATTTTATTAA
1 TATTTTATTAA
*
28352726 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
28352739 TATTTTATTAT
1 TATTTTATTAA
28352750 TATTTTATTA
1 TATTTTATTA
28352760 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:28354580 original size:46 final size:46
Alignment explanation
Indices: 28354509--28354969 Score: 485
Period size: 46 Copynumber: 10.0 Consensus size: 46
28354499 GTGTGCTTTC
28354509 TGAAATGAAATGT-ATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGTGA-AAGACCATGGTTGAAAGATACCATGGCAACA
*
28354555 TGAAATGAAATGTGAAAGACTATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGTGAAAGACCATGGTTGAAAGATACCATGGCAACA
* *
28354601 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGTGAAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
28354647 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACA
1 TGAAATGAAATGTGAAAGACCATGGTTGAAAGATACCATGGCAACA
* *
28354693 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGTGAAAGACCATGGTTGAAAGATACCATGGCAACA
** * * *
28354739 T-AACGGGAAATGAAT-AAA-ACCATGGTTG-AAGATACCATGGTAGCG
1 TGAA-ATGAAATG--TGAAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
28354784 TGACATGAAATG-AATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGAAATGAAATGTGA-AAGACCATGGTTGAAAGATACCATGGCAACA
* * *
28354830 T-AACATGAAAAG-AATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGAA-ATGAAATGTGA-AAGACCATGGTTGAAAGATACCATGGCAACA
* * * *
28354876 TGACATGAAAAGAAT-AAA-ACCATAGTTGAAAGATTCCATGGCAACA
1 TGAAATGAAATG--TGAAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * * * *
28354922 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGAAATG-AAATGTGAAAGACCATGGTTGAAAGATACCATGGCAACA
28354968 TG
1 TG
28354970 TCAAAGATAA
Statistics
Matches: 367, Mismatches: 31, Indels: 34
0.85 0.07 0.08
Matches are distributed among these distances:
43 1 0.00
44 2 0.01
45 36 0.10
46 320 0.87
47 6 0.02
48 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
TGAAATGAAATGTGAAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:28354672 original size:92 final size:92
Alignment explanation
Indices: 28354513--28354969 Score: 585
Period size: 92 Copynumber: 5.0 Consensus size: 92
28354503 GCTTTCTGAA
* * * *
28354513 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTGAAAGACTAT
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCAT
*
28354578 GGTTGAAAGATACCATGGCAACATGAT
66 GGTTGAAAGATACCATGGCAACATGAC
* * *
28354605 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCAT
* *
28354670 GGTTGAAAGATACCATTGCAACATGAT
66 GGTTGAAAGATACCATGGCAACATGAC
* * ** * *
28354697 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATAACGGGAAATGAATAAAACCAT
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCAT
* * *
28354762 GGTTG-AAGATACCATGGTAGCGTGAC
66 GGTTGAAAGATACCATGGCAACATGAC
* * * * *
28354788 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTAACATGAAAAGAATAAGACCAT
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCAT
*
28354853 GGTTGAAAGATACCATGGCAACGTGAC
66 GGTTGAAAGATACCATGGCAACATGAC
* * * * *
28354880 ATGAAAAGAATAAAACCATAGTTGAAAGATTCCATGGCAACATGACA-GAAAATGAGTAAGACCA
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCA
* * * *
28354944 TAGTTGAAAGACACTATGGCATCATG
65 TGGTTGAAAGATACCATGGCAACATG
28354970 TCAAAGATAA
Statistics
Matches: 324, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
91 80 0.25
92 244 0.75
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (92 bp):
ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCAT
GGTTGAAAGATACCATGGCAACATGAC
Found at i:28354941 original size:229 final size:230
Alignment explanation
Indices: 28354515--28354964 Score: 609
Period size: 229 Copynumber: 2.0 Consensus size: 230
28354505 TTTCTGAAAT
* * * *
28354515 GAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTGAAAGACTATGG
1 GAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTAAAAGACCATGG
* * * **
28354580 TTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
66 TTGAAAGATACCATGGCAACATAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAA
* * ** * * * * *
28354645 CATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACATGATATGAAATGTGTAA
131 CATGACATGAAAAGAATAAAACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAA
* *
28354710 GACCATGGTTGAAAGATACCATGGCAACATAACGG
196 GACCATAGTTGAAAGACACCATGGCAACATAACGG
* * * *
28354745 GAAATGAATAAAACCATGGTTG-AAGATACCATGGTAGCGTGACATGAAATG-AATAAGACCATG
1 GAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTAA-AAGACCATG
*
28354808 GTTGAAAGATACCATGGCAACGTAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCA
65 GTTGAAAGATACCATGGCAACATAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCA
* *
28354873 ACGTGACATGAAAAGAATAAAACCATAGTTGAAAGATTCCATGGCAACATGACA-GAAAATGAGT
130 ACATGACATGAAAAGAATAAAACCATAGTTGAAAGATACCATGGCAACATGACATG-AAATGAGT
*
28354937 AAGACCATAGTTGAAAGACACTATGGCA
194 AAGACCATAGTTGAAAGACACCATGGCA
28354965 TCATGTCAAA
Statistics
Matches: 190, Mismatches: 28, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
228 2 0.01
229 168 0.88
230 20 0.11
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (230 bp):
GAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTAAAAGACCATGG
TTGAAAGATACCATGGCAACATAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAA
CATGACATGAAAAGAATAAAACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAA
GACCATAGTTGAAAGACACCATGGCAACATAACGG
Found at i:28355270 original size:16 final size:17
Alignment explanation
Indices: 28355249--28355281 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28355239 ATGATGGAGC
28355249 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
28355265 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
28355282 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:28359339 original size:15 final size:14
Alignment explanation
Indices: 28359319--28359359 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28359309 AATTCGAAAG
28359319 AAAAAAAATAAAGAA
1 AAAAAAAATAAA-AA
*
28359334 AAAAAAACTAAAAA
1 AAAAAAAATAAAAA
*
28359348 AAAGAAAATAAA
1 AAAAAAAATAAA
28359360 TATACCGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.85, C:0.02, G:0.05, T:0.07
Consensus pattern (14 bp):
AAAAAAAATAAAAA
Found at i:28360672 original size:9 final size:9
Alignment explanation
Indices: 28360594--28360724 Score: 74
Period size: 9 Copynumber: 14.7 Consensus size: 9
28360584 TAAGTATAAT
*
28360594 TAAGTTATA
1 TAAGTTATG
28360603 TAAGTTATG
1 TAAGTTATG
28360612 TAAGTTATG
1 TAAGTTATG
* * *
28360621 ATATGATATA
1 -TAAGTTATG
*
28360631 T-ATTTATG
1 TAAGTTATG
28360639 T-A-TTATG
1 TAAGTTATG
*
28360646 TAAGTTATA
1 TAAGTTATG
*
28360655 TAAATTATG
1 TAAGTTATG
28360664 TAAGTTATG
1 TAAGTTATG
* * *
28360673 AAATTTGATCTT
1 TAAGTT-A--TG
*
28360685 TAAATTATG
1 TAAGTTATG
28360694 TAAGTTATG
1 TAAGTTATG
28360703 T-A-TTATG
1 TAAGTTATG
*
28360710 TAAATTATG
1 TAAGTTATG
*
28360719 TGAGTT
1 TAAGTT
28360725 GCTGGTGAAC
Statistics
Matches: 93, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
7 12 0.13
8 8 0.09
9 60 0.65
10 7 0.08
11 1 0.01
12 5 0.05
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:28360709 original size:16 final size:16
Alignment explanation
Indices: 28360688--28360719 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28360678 TGATCTTTAA
*
28360688 ATTATGTAAGTTATGT
1 ATTATGTAAATTATGT
28360704 ATTATGTAAATTATGT
1 ATTATGTAAATTATGT
28360720 GAGTTGCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (16 bp):
ATTATGTAAATTATGT
Found at i:28363524 original size:15 final size:15
Alignment explanation
Indices: 28363501--28363532 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28363491 AAATAATAAT
28363501 TTATATATATTTATC
1 TTATATATATTTATC
*
28363516 TTATTTATATTTATC
1 TTATATATATTTATC
28363531 TT
1 TT
28363533 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTTATC
Found at i:28365871 original size:22 final size:22
Alignment explanation
Indices: 28365845--28365904 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
28365835 AAAACCATGT
* * *
28365845 TATTTTTGTTGTTGTTTTTCCA
1 TATTTTTGCTATTATTTTTCCA
28365867 TA-TTTTGCTATTATTTTTCCA
1 TATTTTTGCTATTATTTTTCCA
* *
28365888 -ATTTTTGCCACTATTTT
1 TATTTTTGCTATTATTTT
28365905 GCTATAGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.91
22 2 0.06
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.63
Consensus pattern (22 bp):
TATTTTTGCTATTATTTTTCCA
Found at i:28366419 original size:22 final size:22
Alignment explanation
Indices: 28366361--28366429 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
28366351 ATATTCAAAC
*
28366361 AATAACAACAAAATAAGTAGCAA
1 AATAACAACAAAATGA-TAGCAA
* * ** *
28366384 TATAATAATGAAATGATAGTAA
1 AATAACAACAAAATGATAGCAA
*
28366406 AATAACAACAAAATGGTAGCAA
1 AATAACAACAAAATGATAGCAA
28366428 AA
1 AA
28366430 CAGCTGATTT
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.19
Consensus pattern (22 bp):
AATAACAACAAAATGATAGCAA
Found at i:28369912 original size:13 final size:13
Alignment explanation
Indices: 28369894--28369932 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
28369884 TTGGATGCCA
28369894 AGAAAATCAATAG
1 AGAAAATCAATAG
*
28369907 AGAAAATGAA-AG
1 AGAAAATCAATAG
28369919 AGATAAATCAATAG
1 AGA-AAATCAATAG
28369933 TATCTCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 15 0.68
14 2 0.09
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (13 bp):
AGAAAATCAATAG
Found at i:28374462 original size:47 final size:47
Alignment explanation
Indices: 28374411--28374501 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
28374401 CCTAAGAATA
* *
28374411 CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATCAAT
1 CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATCAAT
28374458 CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATC
1 CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATC
28374502 GAATTGCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (47 bp):
CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATCAAT
Found at i:28379882 original size:13 final size:13
Alignment explanation
Indices: 28379864--28379888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28379854 TTTAAATGTG
28379864 AAATGAATATATT
1 AAATGAATATATT
28379877 AAATGAATATAT
1 AAATGAATATAT
28379889 AAAAGTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAATGAATATATT
Found at i:28380973 original size:36 final size:36
Alignment explanation
Indices: 28380932--28381004 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
28380922 TATAGGCTAG
28380932 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
1 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
28380968 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
1 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
28381004 T
1 T
28381005 ATAATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
Found at i:28382985 original size:2 final size:2
Alignment explanation
Indices: 28382978--28383040 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
28382968 CCTCCCTTCG
28382978 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28383020 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
28383041 CCCATGTATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:28383078 original size:4 final size:4
Alignment explanation
Indices: 28383063--28383096 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
28383053 TTTCTTTGTG
*
28383063 TGTA TATA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
28383097 CATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:28384559 original size:2 final size:2
Alignment explanation
Indices: 28384552--28384579 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28384542 ACAGGATTTG
28384552 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28384580 TTATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28387798 original size:22 final size:22
Alignment explanation
Indices: 28387744--28387796 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
28387734 CTTTCAATAT
* * **
28387744 TCTCTCAAATTCCTCTCAAATC
1 TCTCTTAAATTCCTCTAAAAAA
28387766 TCTCTTAAATTCCTCTAAAAAA
1 TCTCTTAAATTCCTCTAAAAAA
28387788 TCTCGTTAA
1 TCTC-TTAA
28387797 TTTTTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (22 bp):
TCTCTTAAATTCCTCTAAAAAA
Found at i:28389504 original size:30 final size:30
Alignment explanation
Indices: 28389463--28389528 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
28389453 CGACGACGCA
*
28389463 GGCCCATCAACAGCACCCACACAATCACCC
1 GGCCCAGCAACAGCACCCACACAATCACCC
* * * *
28389493 GGCCCAGCAACAGGACCTACACAGTCACCG
1 GGCCCAGCAACAGCACCCACACAATCACCC
28389523 GGCCCA
1 GGCCCA
28389529 ACAGTTCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.45, G:0.18, T:0.06
Consensus pattern (30 bp):
GGCCCAGCAACAGCACCCACACAATCACCC
Found at i:28389605 original size:18 final size:18
Alignment explanation
Indices: 28389582--28389624 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
28389572 TGCCAGGTAC
*
28389582 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
28389600 GTATCCTAGCCCTTATAT
1 GTATCCTAGCCCTTATAT
*
28389618 GTTTCCT
1 GTATCCT
28389625 TTTCCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:28390213 original size:116 final size:116
Alignment explanation
Indices: 28390009--28390275 Score: 489
Period size: 116 Copynumber: 2.3 Consensus size: 116
28389999 TATTTGTACA
* *
28390009 AACATTTTGAATCTTTATATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* * *
28390074 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
28390125 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
28390190 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
66 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
28390241 AACATTTTGAATATTTTTATATTATTTCATGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAAT
28390276 AAAATATAAA
Statistics
Matches: 146, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 146 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (116 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
Found at i:28390238 original size:54 final size:54
Alignment explanation
Indices: 28390058--28390239 Score: 172
Period size: 54 Copynumber: 3.2 Consensus size: 54
28390048 TAAAAGGTTG
* *
28390058 TTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTA
1 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
* * * * * *
28390112 TTTTAAATAAGGCAACATTTTGAATATT--TTTATATTATTTCATGTAATTAGAT-AAAAGGTTG
1 TTTTAAATAAAG-TA-ATTAT-AAT-TTACTTT-TA-TATTT--T-TAATAAAATGAAAA--TTA
28390174 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
1 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
28390228 TTTTAAATAAAG
1 TTTTAAATAAAG
28390240 CAACATTTTG
Statistics
Matches: 101, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
54 25 0.25
55 8 0.08
56 12 0.12
57 5 0.05
58 14 0.14
59 5 0.05
60 11 0.11
61 8 0.08
62 13 0.13
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (54 bp):
TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
Found at i:28393771 original size:125 final size:126
Alignment explanation
Indices: 28393285--28393821 Score: 839
Period size: 126 Copynumber: 4.3 Consensus size: 126
28393275 GCCCAAGTTA
* * *
28393285 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGTTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*** *
28393350 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACATGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* * * * * * *
28393411 TTTTAGAGACCACTGTAGTAAAAGAGCATCCACGTGGGAGTTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
28393476 TGCATCCTACTTGAAGCGTTTTT-ACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCACAGACACGTCTTCTCAAAATTATTT
*
28393537 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCT-AACA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAA-A
* *
28393601 ATGCATCCTGCTTGAAGCGTTTTTTACACTATTTGCATAGACACGTCTTCTCAAAATTATTT
65 ATGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* *
28393663 TTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTG-CAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
28393727 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTA-TT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
28393787 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
28393822 AGAAGCTTTT
Statistics
Matches: 378, Mismatches: 29, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
124 36 0.10
125 61 0.16
126 280 0.74
127 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (126 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
Found at i:28394033 original size:97 final size:96
Alignment explanation
Indices: 28393932--28394106 Score: 264
Period size: 97 Copynumber: 1.8 Consensus size: 96
28393922 CTTAAAATCC
* * **
28393932 TAATCTAATTTTTTTAAATTTA-TAATTAATTTACTTAAGTAAC-CTTAAACCCTAATTTATTTG
1 TAATCTAA-TTTTTTAAAATTAGTAATTAATTTAATTAACAAACAC-TAAACCCTAATTTATTT-
28393995 ATTTTTTTCCTTAAAAACCATAAACACTAAACCA
63 ATTTTTTTCCTTAAAAACCATAAACACTAAACCA
*
28394029 TAATCTAATTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCTTAATTTATTTATT
1 TAATCTAATTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCCTAATTTATTTATT
28394094 TTTTTCCTTAAAA
66 TTTTTCCTTAAAA
28394107 CCCTAAAATT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
96 28 0.39
97 42 0.59
98 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (96 bp):
TAATCTAATTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCCTAATTTATTTATT
TTTTTCCTTAAAAACCATAAACACTAAACCA
Found at i:28398349 original size:9 final size:9
Alignment explanation
Indices: 28398335--28398367 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
28398325 TCTTATATTT
28398335 TTTTTTTAC
1 TTTTTTTAC
28398344 TTTTTTTAAC
1 TTTTTTT-AC
28398354 -TTTTTTAC
1 TTTTTTTAC
28398362 TTTTTT
1 TTTTTT
28398368 CTTATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:28398452 original size:36 final size:36
Alignment explanation
Indices: 28398383--28398456 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 36
28398373 ATTTTGTCTC
*
28398383 TTTCTTAGATTTTTTTCTTTTTTAAGTTTTATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAG-TTTATATTAT
28398420 TTTCTTA-ATTTATTTTACTTATTTAA-TTTATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTATATTAT
28398456 T
1 T
28398457 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 15 0.44
37 11 0.32
38 8 0.24
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (36 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTATATTAT
Found at i:28398461 original size:18 final size:17
Alignment explanation
Indices: 28398410--28398457 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
28398400 TTTTTTAAGT
*
28398410 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
*
28398428 TTTATTTTACTTATTTAA
1 TTTATATTA-TTATTTAA
28398446 TTTATATTATTA
1 TTTATATTATTA
28398458 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:28398494 original size:23 final size:22
Alignment explanation
Indices: 28398460--28398534 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 22
28398450 TATTATTAAT
*
28398460 TTTAAAAATTTTGTAATATATA
1 TTTAAAAATTTTATAATATATA
*
28398482 TTTAAAATGTTTTATAATAT-T-
1 TTTAAAA-ATTTTATAATATATA
** *
28398503 TTTTTAAATTTTA-AATTATTATT
1 TTTAAAAATTTTATAA-TA-TATA
28398526 TTTAAAAAT
1 TTTAAAAAT
28398535 ATTCTTAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
19 2 0.05
20 7 0.17
21 6 0.15
22 9 0.22
23 17 0.41
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTAAAAATTTTATAATATATA
Found at i:28398529 original size:21 final size:20
Alignment explanation
Indices: 28398491--28398531 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28398481 ATTTAAAATG
28398491 TTTTATAATATTTTTTTAAA
1 TTTTATAATATTTTTTTAAA
28398511 TTTTA-AATTATTATTTTTAAA
1 TTTTATAA-TATT-TTTTTAAA
28398532 AATATTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 9 0.47
21 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTATAATATTTTTTTAAA
Found at i:28399306 original size:9 final size:9
Alignment explanation
Indices: 28399294--28399380 Score: 68
Period size: 9 Copynumber: 9.4 Consensus size: 9
28399284 TAAAATTTAA
28399294 AAAATATTT
1 AAAATATTT
*
28399303 AAAATATTA
1 AAAATATTT
*
28399312 AAAATATTA
1 AAAATATTT
28399321 AAAATATTT
1 AAAATATTT
*
28399330 TAAATCATTT
1 AAAAT-ATTT
* *
28399340 TAAATGTTTT
1 AAAAT-ATTT
* *
28399350 ATAATATTA
1 AAAATATTT
28399359 AAAATATATT
1 AAAATAT-TT
*
28399369 -TAATATTT
1 AAAATATTT
28399377 AAAA
1 AAAA
28399381 AATAATTTGA
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
8 2 0.03
9 44 0.71
10 16 0.26
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:28399307 original size:18 final size:18
Alignment explanation
Indices: 28399284--28399328 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
28399274 AAATTCTATG
28399284 TAAAAT-TTAAAAAATATT
1 TAAAATATT-AAAAATATT
28399302 TAAAATATTAAAAATATT
1 TAAAATATTAAAAATATT
*
28399320 AAAAATATT
1 TAAAATATT
28399329 TTAAATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATATTAAAAATATT
Found at i:28399334 original size:18 final size:18
Alignment explanation
Indices: 28399295--28399381 Score: 77
Period size: 19 Copynumber: 4.7 Consensus size: 18
28399285 AAAATTTAAA
* **
28399295 AAATATTTAAAATATTAA
1 AAATATTAAAAATATTTT
28399313 AAATATTAAAAATATTTT
1 AAATATTAAAAATATTTT
** *
28399331 AAATCATTTTAAATGTTTT
1 AAAT-ATTAAAAATATTTT
28399350 ATAATATTAAAAATATATTT
1 A-AATATTAAAAATAT-TTT
28399370 -AATATTTAAAAA
1 AAATA-TTAAAAA
28399382 ATAATTTGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
18 23 0.41
19 27 0.48
20 6 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (18 bp):
AAATATTAAAAATATTTT
Found at i:28399397 original size:31 final size:34
Alignment explanation
Indices: 28399350--28399416 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
28399340 TAAATGTTTT
28399350 ATAATATTAAAAATATA-TTTAATATTTA-AAAA
1 ATAATATTAAAAATATATTTTAATATTTATAAAA
*
28399382 ATAAT-TTGAAAATATATTTTTAATATTTATAAAA
1 ATAATATTAAAAATATA-TTTTAATATTTATAAAA
28399416 A
1 A
28399417 ATACATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 10 0.32
32 5 0.16
33 11 0.35
34 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
ATAATATTAAAAATATATTTTAATATTTATAAAA
Found at i:28399515 original size:28 final size:27
Alignment explanation
Indices: 28399482--28399554 Score: 128
Period size: 28 Copynumber: 2.7 Consensus size: 27
28399472 ATAAATAAGG
28399482 ACTTAAAAAAGAAAAAAGAAAGTCAAA
1 ACTTAAAAAAGAAAAAAGAAAGTCAAA
28399509 ACTTTAAAAAAGAAAAAAGAAAGTCAAA
1 AC-TTAAAAAAGAAAAAAGAAAGTCAAA
*
28399537 ACTTAAAAAAAAAAAAAG
1 ACTTAAAAAAGAAAAAAG
28399555 GCTGAAACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 17 0.39
28 27 0.61
ACGTcount: A:0.71, C:0.07, G:0.10, T:0.12
Consensus pattern (27 bp):
ACTTAAAAAAGAAAAAAGAAAGTCAAA
Found at i:28402955 original size:30 final size:30
Alignment explanation
Indices: 28402921--28403023 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
28402911 CCTATATCCT
28402921 GGTGATATGAACTCGAACCACCCATGTCCG
1 GGTGATATGAACTCGAACCACCCATGTCCG
*
28402951 GGTGATATAAACTCGAACCACCCATGTCCG
1 GGTGATATGAACTCGAACCACCCATGTCCG
*
28402981 GGTGATATGAACTCGAACCACCTATGTCCG
1 GGTGATATGAACTCGAACCACCCATGTCCG
*
28403011 GGTTATATGAACT
1 GGTGATATGAACT
28403024 GCTCTGGGAC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (30 bp):
GGTGATATGAACTCGAACCACCCATGTCCG
Found at i:28406196 original size:23 final size:23
Alignment explanation
Indices: 28406170--28406239 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
28406160 AAAAAAAATT
28406170 AAAAATAATATT-T-AAAATTTTA
1 AAAAAT-ATATTATAAAAATTTTA
28406192 AAAAATATATTATAAAAATTTT-
1 AAAAATATATTATAAAAATTTTA
* * * *
28406214 AAATATACATTACAAAATTTTTA
1 AAAAATATATTATAAAAATTTTA
28406237 AAA
1 AAA
28406240 TTAATAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.12
22 25 0.61
23 11 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAAATATATTATAAAAATTTTA
Found at i:28406251 original size:21 final size:22
Alignment explanation
Indices: 28406168--28406252 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
28406158 TTAAAAAAAA
*
28406168 TTAAAAATA-ATATTTAAAATTT
1 TTAAAAATACATA-ATAAAATTT
* * * *
28406190 TAAAAAATATATTATAAAAATT
1 TTAAAAATACATAATAAAATTT
* * *
28406212 TTAAATATACATTACAAAATTT
1 TTAAAAATACATAATAAAATTT
*
28406234 TTAAAATTA-ATAATAAAAT
1 TTAAAAATACATAATAAAAT
28406253 AAATAAACAA
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
21 8 0.16
22 39 0.80
23 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAAATACATAATAAAATTT
Found at i:28406268 original size:18 final size:19
Alignment explanation
Indices: 28406245--28406287 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28406235 TAAAATTAAT
* *
28406245 AATAAAATAAATA-AACAA
1 AATAAAATAAAAAGAAAAA
28406263 AATAAAATAAAAAGAAAAA
1 AATAAAATAAAAAGAAAAA
28406282 AATAAA
1 AATAAA
28406288 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (19 bp):
AATAAAATAAAAAGAAAAA
Found at i:28406314 original size:34 final size:34
Alignment explanation
Indices: 28406261--28406332 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
28406251 ATAAATAAAC
28406261 AAAATAAAATAAAAAGAAAAA-A-ATAAATTTCAA
1 AAAATAAAATAAAAAGAAAAAGACA-AAATTTCAA
*
28406294 AAAAGTAAAA-AAAAAGGAAAAAGACAAAATTTTAA
1 AAAA-TAAAATAAAAA-GAAAAAGACAAAATTTCAA
28406329 AAAA
1 AAAA
28406333 ATATTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 9 0.26
34 11 0.32
35 13 0.38
36 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (34 bp):
AAAATAAAATAAAAAGAAAAAGACAAAATTTCAA
Found at i:28406364 original size:27 final size:28
Alignment explanation
Indices: 28406334--28406397 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
28406324 TTTAAAAAAA
* * *
28406334 TATTTAAAATATTATGATTTCTTATAT-
1 TATTTAAAAAATTATAATTTCTTAAATG
*
28406361 TA-TTAAAAAATTATAATTTTTTAAATG
1 TATTTAAAAAATTATAATTTCTTAAATG
28406388 TATTTAAAAA
1 TATTTAAAAA
28406398 TTGTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 20 0.65
27 4 0.13
28 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (28 bp):
TATTTAAAAAATTATAATTTCTTAAATG
Found at i:28406405 original size:26 final size:26
Alignment explanation
Indices: 28406334--28406399 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
28406324 TTTAAAAAAA
* *
28406334 TATTTAAAATATTATGATTTCTTATAT
1 TATTTAAAA-ATTATAATTTCTTAAAT
* *
28406361 TATTAAAAAATTATAATTTTTTAAAT
1 TATTTAAAAATTATAATTTCTTAAAT
28406387 GTATTTAAAAATT
1 -TATTTAAAAATT
28406400 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:28406459 original size:22 final size:23
Alignment explanation
Indices: 28406426--28406470 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
28406416 AAAATAATCT
*
28406426 CAAAATACATATCTA-AAATTTA
1 CAAAATACATATATATAAATTTA
28406448 CAAATATA-ATATATATAAATTTA
1 CAAA-ATACATATATATAAATTTA
28406471 ATAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (23 bp):
CAAAATACATATATATAAATTTA
Found at i:28406587 original size:18 final size:16
Alignment explanation
Indices: 28406558--28406594 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
28406548 TAATATTTAA
28406558 TATATTTTTTTAAATT
1 TATATTTTTTTAAATT
28406574 TATATTTATATTTAAATT
1 TATATTT-T-TTTAAATT
28406592 TAT
1 TAT
28406595 TAATAGTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTTTTTTAAATT
Found at i:28406901 original size:23 final size:22
Alignment explanation
Indices: 28406848--28406943 Score: 63
Period size: 22 Copynumber: 4.3 Consensus size: 22
28406838 ATAAAGTTAA
28406848 AAAATATTTTTAAAAATAATAAT
1 AAAA-ATTTTTAAAAATAATAAT
* *
28406871 TAAAATTTTTAAAAA-ATATTAT
1 AAAAATTTTTAAAAATA-ATAAT
* *
28406893 AAAACA-TTTTAAATAT-ATATT
1 AAAA-ATTTTTAAAAATAATAAT
* * *
28406914 ACCAATTTTTTAAAATTAATAAT
1 A-AAAATTTTTAAAAATAATAAT
*
28406937 ATAAATT
1 AAAAATT
28406944 AAATAAGCAA
Statistics
Matches: 54, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
21 5 0.09
22 40 0.74
23 9 0.17
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAATTTTTAAAAATAATAAT
Found at i:28406976 original size:18 final size:18
Alignment explanation
Indices: 28406926--28406977 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
28406916 CAATTTTTTA
*
28406926 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
28406944 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
28406962 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
28406978 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:28407026 original size:9 final size:9
Alignment explanation
Indices: 28407012--28407053 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
28407002 AAAATATAAG
28407012 AAAAAAAGT
1 AAAAAAAGT
28407021 -AAAAAAGT
1 AAAAAAAGT
28407029 AAAAAAAGT
1 AAAAAAAGT
*
28407038 AAGAAAAGT
1 AAAAAAAGT
28407047 AAAAAAA
1 AAAAAAA
28407054 AAATATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:28407034 original size:17 final size:18
Alignment explanation
Indices: 28407012--28407053 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
28407002 AAAATATAAG
28407012 AAAAAAAGTAA-AAAAGT
1 AAAAAAAGTAAGAAAAGT
28407029 AAAAAAAGTAAGAAAAGT
1 AAAAAAAGTAAGAAAAGT
28407047 AAAAAAA
1 AAAAAAA
28407054 AAATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAAAAGTAAGAAAAGT
Found at i:28409502 original size:109 final size:110
Alignment explanation
Indices: 28409386--28409595 Score: 307
Period size: 110 Copynumber: 1.9 Consensus size: 110
28409376 ATCTTCATAG
* *
28409386 TTTTTAAATG-ATTAAATAAAATTTTTATCATTTTT-AAAAGCTAAAGTACAATTTTATCATTAC
1 TTTTTAAA-GAATTAAATAAAATTTTTATCATTTTTAAAAAACTAAAGTAAAATTTTATCATTAC
* *
28409449 TAATTTAAAGTTTTATAAATTATAAAAGGTTTAAATTGATTTATAA
65 TAAATTAAAATTTTATAAATTATAAAAGGTTTAAATTGATTTATAA
* * * * *
28409495 TTTTTAAAGAATTAAATTAATTTTTTATTATTTTTAAAAAATTAAAGTAAAATTTTATTATTACT
1 TTTTTAAAGAATTAAATAAAATTTTTATCATTTTTAAAAAACTAAAGTAAAATTTTATCATTACT
*
28409560 AAATTAAAATTTTATAAATTGTAAAAGGTTTAAATT
66 AAATTAAAATTTTATAAATTATAAAAGGTTTAAATT
28409596 ACAATTTTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
108 1 0.01
109 30 0.34
110 58 0.65
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (110 bp):
TTTTTAAAGAATTAAATAAAATTTTTATCATTTTTAAAAAACTAAAGTAAAATTTTATCATTACT
AAATTAAAATTTTATAAATTATAAAAGGTTTAAATTGATTTATAA
Found at i:28409509 original size:27 final size:28
Alignment explanation
Indices: 28409479--28409540 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
28409469 TATAAAAGGT
* *
28409479 TTAAATTGA-TTTATAATTTTTAAAGAA
1 TTAAATTAATTTTATAATTTTTAAAAAA
*
28409506 TTAAATTAATTTTTTATTATTTTTAAAAAA
1 TTAAATTAA--TTTTATAATTTTTAAAAAA
28409536 TTAAA
1 TTAAA
28409541 GTAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 8 0.28
30 21 0.72
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TTAAATTAATTTTATAATTTTTAAAAAA
Found at i:28409528 original size:30 final size:30
Alignment explanation
Indices: 28409488--28409556 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
28409478 TTTAAATTGA
* * * **
28409488 TTTATAATTTTTAAAGAATTAAATTAATTT
1 TTTATTATTTTTAAAAAATTAAAGTAAAAT
28409518 TTTATTATTTTTAAAAAATTAAAGTAAAAT
1 TTTATTATTTTTAAAAAATTAAAGTAAAAT
28409548 TTTATTATT
1 TTTATTATT
28409557 ACTAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTATTATTTTTAAAAAATTAAAGTAAAAT
Found at i:28409972 original size:13 final size:13
Alignment explanation
Indices: 28409954--28409984 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28409944 GTATAAATGT
*
28409954 ATATTGAATATAA
1 ATATTGAATAAAA
28409967 ATATTGAATAAAA
1 ATATTGAATAAAA
28409980 ATATT
1 ATATT
28409985 TAAAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (13 bp):
ATATTGAATAAAA
Found at i:28418931 original size:14 final size:14
Alignment explanation
Indices: 28418907--28418940 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28418897 AACCCTGAAT
*
28418907 TCAAA-CCTAAACC
1 TCAAACCCTAAAAC
28418920 TCAAACCCTAAAAC
1 TCAAACCCTAAAAC
28418934 TCAAACC
1 TCAAACC
28418941 TCAAATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (14 bp):
TCAAACCCTAAAAC
Found at i:28418953 original size:14 final size:14
Alignment explanation
Indices: 28418922--28418967 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
28418912 CCTAAACCTC
*
28418922 AAACCCTAAAAC-T
1 AAACCCTAAATCAT
28418935 CAAA-CCTCAAATCAT
1 -AAACCCT-AAATCAT
28418950 AAACCCTAAATCAT
1 AAACCCTAAATCAT
28418964 AAAC
1 AAAC
28418968 TTGGCCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.11
14 21 0.75
15 4 0.14
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:28420273 original size:30 final size:30
Alignment explanation
Indices: 28420237--28420298 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28420227 TACCATTGAA
*
28420237 GAATAAATCTCCAATAGTTCACTTTATATC
1 GAATAAATCTCCAACAGTTCACTTTATATC
28420267 GAATAAATCTCCAACAGTTCACTTTATATC
1 GAATAAATCTCCAACAGTTCACTTTATATC
28420297 GA
1 GA
28420299 TCTTTATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (30 bp):
GAATAAATCTCCAACAGTTCACTTTATATC
Found at i:28429854 original size:12 final size:13
Alignment explanation
Indices: 28429837--28429873 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
28429827 GAACCGGACA
28429837 CGAACCGAA-CTC
1 CGAACCGAAGCTC
28429849 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
28429861 CGAACCGTAGCTC
1 CGAACCGAAGCTC
28429874 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:28443313 original size:46 final size:44
Alignment explanation
Indices: 28443209--28443316 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
28443199 TGTATTTGAC
** * * *
28443209 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
28443253 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
28443299 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
28443317 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:28452971 original size:3 final size:3
Alignment explanation
Indices: 28452963--28453002 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
28452953 AGAAAAGGCT
28452963 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
28453003 GATGGCTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:28455951 original size:23 final size:23
Alignment explanation
Indices: 28455917--28455986 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
28455907 GGATACACGA
28455917 ATTCCAACCAAACACACCAGAATG
1 ATTCC-ACCAAACACACCAGAATG
28455941 ATTCCACCAAACACACCAGAAT-
1 ATTCCACCAAACACACCAGAATG
* *
28455963 AATCCACCCAAACACACCGGAATG
1 ATTCCA-CCAAACACACCAGAATG
28455987 GCACTAAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.12
23 32 0.76
24 5 0.12
ACGTcount: A:0.44, C:0.36, G:0.09, T:0.11
Consensus pattern (23 bp):
ATTCCACCAAACACACCAGAATG
Found at i:28459426 original size:47 final size:47
Alignment explanation
Indices: 28459317--28459427 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
28459307 CCGGGATAAG
* *
28459317 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
28459364 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
28459411 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
28459428 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:28460201 original size:4 final size:4
Alignment explanation
Indices: 28460192--28460216 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28460182 CCCTTTTCTA
28460192 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
28460217 CACGTTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:28461699 original size:20 final size:21
Alignment explanation
Indices: 28461658--28461700 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
28461648 AAATTTAAAA
*
28461658 TTAAGAATTAAATATTTTTTT
1 TTAAGAATTAAATATTTATTT
*
28461679 TTAA-AATT-AATATTTAATT
1 TTAAGAATTAAATATTTATTT
28461698 TTA
1 TTA
28461701 TCAAACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAAGAATTAAATATTTATTT
Found at i:28474985 original size:44 final size:45
Alignment explanation
Indices: 28474932--28475035 Score: 131
Period size: 44 Copynumber: 2.3 Consensus size: 45
28474922 TGTCTTTGAC
* * *
28474932 ATGGACTTACA-GGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGG-ATCAATCCTGTCTCCAAAGCCATATTATAAT
* *
28474976 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGATCAATCCTGTCTCCAAAGCCATA-TTATAAT
28475022 ATGGACTTACATGG
1 ATGGACTTACATGG
28475036 CTCATTTCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 31 0.60
45 2 0.04
46 19 0.37
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (45 bp):
ATGGACTTACATGGATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:28475036 original size:46 final size:44
Alignment explanation
Indices: 28474951--28475039 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 44
28474941 CAGGAATTAT
*
28474951 TCCTGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAA
*
28474995 TCCTGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TCCTGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
28475040 TTTCTGTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 18 0.44
46 23 0.56
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (44 bp):
TCCTGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAA
Found at i:28476547 original size:24 final size:22
Alignment explanation
Indices: 28476514--28476565 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
28476504 TACTCTCTTT
*
28476514 TTTTCCTTTTTTCTTTCTTTTCA
1 TTTTCTTTTTTTCTTTCTTTT-A
*
28476537 GTTTTCTTTTTTTTTTTCTTTTA
1 -TTTTCTTTTTTTCTTTCTTTTA
28476560 TTTTCT
1 TTTTCT
28476566 CTAATCATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 6 0.23
23 1 0.04
24 19 0.73
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTTTTCTTTCTTTTA
Found at i:28476553 original size:12 final size:12
Alignment explanation
Indices: 28476511--28476563 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
28476501 TTTTACTCTC
*
28476511 TTTTTTTCCTTT
1 TTTTTTTCTTTT
*
28476523 TTTCTTTCTTTT
1 TTTTTTTCTTTT
***
28476535 CAGTTTTCTTTT
1 TTTTTTTCTTTT
28476547 TTTTTTTCTTTT
1 TTTTTTTCTTTT
28476559 ATTTT
1 -TTTT
28476564 CTCTAATCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
12 27 0.87
13 4 0.13
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:28478520 original size:30 final size:30
Alignment explanation
Indices: 28478486--28478545 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28478476 TATTTTATTA
28478486 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
28478516 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
28478546 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:28479213 original size:12 final size:13
Alignment explanation
Indices: 28479198--28479235 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
28479188 CTGAAATTTT
28479198 TTATTTTT-AAAA
1 TTATTTTTGAAAA
28479210 TTATTTTTGAAAA
1 TTATTTTTGAAAA
**
28479223 GCATTTTTGAAAA
1 TTATTTTTGAAAA
28479236 ACACTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (13 bp):
TTATTTTTGAAAA
Found at i:28479410 original size:22 final size:24
Alignment explanation
Indices: 28479380--28479427 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
28479370 CAAATATGTT
*
28479380 AAAATTATTTATT-AAA-AATAAA
1 AAAAATATTTATTGAAATAATAAA
*
28479402 AAAAATATTTTTTGAAATAATAAA
1 AAAAATATTTATTGAAATAATAAA
28479426 AA
1 AA
28479428 TATGTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 3 0.14
24 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAATATTTATTGAAATAATAAA
Found at i:28479470 original size:21 final size:21
Alignment explanation
Indices: 28479425--28479477 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
28479415 GAAATAATAA
28479425 AAATATGTTAATATCTAATTAT
1 AAATAT-TTAATATCTAATTAT
28479447 AAATATTTAATGAT-TATATT-T
1 AAATATTTAAT-ATCTA-ATTAT
28479468 AAATATTTAA
1 AAATATTTAA
28479478 AATATAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
AAATATTTAATATCTAATTAT
Found at i:28479532 original size:24 final size:24
Alignment explanation
Indices: 28479505--28479550 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28479495 CTAATTAAAT
* *
28479505 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
28479529 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
28479551 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:28481581 original size:22 final size:21
Alignment explanation
Indices: 28481541--28481589 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
28481531 TCTGAAATTT
*
28481541 TAATTTTTTTGAG-ATTTTTC
1 TAATTTTTTTGAGAATTTTTG
*
28481561 TGAATTTGTTTTGATAATTTTTG
1 T-AATTT-TTTTGAGAATTTTTG
28481584 TAATTT
1 TAATTT
28481590 CACCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
22 11 0.46
23 7 0.29
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (21 bp):
TAATTTTTTTGAGAATTTTTG
Found at i:28482580 original size:10 final size:10
Alignment explanation
Indices: 28482565--28482594 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28482555 AACAAAATTG
28482565 AAACATTATT
1 AAACATTATT
*
28482575 AAACATAATT
1 AAACATTATT
28482585 AAACATTATT
1 AAACATTATT
28482595 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (10 bp):
AAACATTATT
Found at i:28482590 original size:20 final size:21
Alignment explanation
Indices: 28482555--28482594 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
28482545 GATAATCAAC
28482555 AACAAAATTGAAACATTATTA
1 AACAAAATTGAAACATTATTA
*
28482576 AACATAATT-AAACATTATT
1 AACAAAATTGAAACATTATT
28482595 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
AACAAAATTGAAACATTATTA
Found at i:28497987 original size:26 final size:26
Alignment explanation
Indices: 28497958--28498154 Score: 99
Period size: 26 Copynumber: 7.8 Consensus size: 26
28497948 ATCCTCTCTC
28497958 GAGCCATATAA-CAGGAAGCTCACAAA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
* *
28497984 GAGCCATTAATCGGGAAGCTCATAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * *
28498010 GAGCC-TT--TTAGGAAGCTTATC--C
1 GAGCCATTAATCAGGAAGCTCA-CAAA
* ** * *
28498032 GGGTTATATAA-CGGGAAGCTCACATA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
* * *
28498058 GAG--ATATAATCAGAAAGTTCACATA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
* ** *
28498083 GAACTTTTAATTAGGAAGCTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * *
28498109 GAGCCTTTAAACGGGAAGCTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
*
28498135 GTGCCATTAATCAGG-AGCTC
1 GAGCCATTAATCAGGAAGCTC
28498155 TAGATAGCCA
Statistics
Matches: 127, Mismatches: 33, Indels: 23
0.69 0.18 0.13
Matches are distributed among these distances:
22 2 0.02
23 10 0.08
24 8 0.06
25 32 0.25
26 74 0.58
27 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAAA
Found at i:28499291 original size:29 final size:30
Alignment explanation
Indices: 28499234--28499293 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
28499224 TTATTTAATT
28499234 AATTATCATCTTTTATTTTTTTCACTTTCC
1 AATTATCATCTTTTATTTTTTTCACTTTCC
*
28499264 AATT-TCATCCTTTT-TTTATTTT-ATTTTCC
1 AATTATCAT-CTTTTATTT-TTTTCACTTTCC
28499293 A
1 A
28499294 TGGATGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.62
Consensus pattern (30 bp):
AATTATCATCTTTTATTTTTTTCACTTTCC
Found at i:28503515 original size:13 final size:14
Alignment explanation
Indices: 28503499--28503534 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
28503489 CAATCTCATA
28503499 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
28503512 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
28503525 TCTC-ATTTCA
1 TCTCAATTTCA
28503535 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:28503716 original size:39 final size:38
Alignment explanation
Indices: 28503649--28503783 Score: 92
Period size: 39 Copynumber: 3.4 Consensus size: 38
28503639 ACCAATATGG
* * *
28503649 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
28503688 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * * *
28503726 TACCCGGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
28503767 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
28503784 ACTCGAGGTC
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
38 17 0.24
39 35 0.49
40 4 0.06
41 15 0.21
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:28504598 original size:5 final size:5
Alignment explanation
Indices: 28504588--28504644 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
28504578 TTACTTATTT
* *
28504588 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
28504636 ATAT- ATATA
1 ATATA ATATA
28504645 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:28504604 original size:12 final size:12
Alignment explanation
Indices: 28504587--28504642 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
28504577 TTTACTTATT
28504587 TATATAATATAA
1 TATATAATATAA
28504599 TATATAATATAATA
1 TATATAATAT-A-A
28504613 TACTATAATATAA
1 TA-TATAATATAA
*
28504626 TA-ATAATTTAA
1 TATATAATATAA
28504637 TATATA
1 TATATA
28504643 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:28504657 original size:26 final size:26
Alignment explanation
Indices: 28504589--28504644 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
28504579 TACTTATTTA
*
28504589 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
28504616 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
28504641 TATA
1 TATA
28504645 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:28508963 original size:18 final size:18
Alignment explanation
Indices: 28508942--28509002 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
28508932 TTTTATGAAC
*
28508942 TTTTTATAATTTATAAAT
1 TTTTTATAATTTTTAAAT
* *
28508960 TTTTTTTACTTTTTGAAA-
1 TTTTTATAATTTTT-AAAT
28508978 TTTTTATAATTTTTAAAT
1 TTTTTATAATTTTTAAAT
*
28508996 TATTTAT
1 TTTTTAT
28509003 TACGATAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 3 0.09
18 29 0.83
19 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTATAATTTTTAAAT
Found at i:28508983 original size:36 final size:38
Alignment explanation
Indices: 28508932--28509005 Score: 107
Period size: 36 Copynumber: 2.0 Consensus size: 38
28508922 TTGTAAAAAG
* *
28508932 TTTTATGAACTTTTTATAATTTATAAATT-TTTTTTAC
1 TTTTATGAAATTTTTATAATTTATAAATTATTTATTAC
*
28508969 TTTT-TGAAATTTTTATAATTTTTAAATTATTTATTAC
1 TTTTATGAAATTTTTATAATTTATAAATTATTTATTAC
28509006 GATAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 22 0.67
37 11 0.33
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (38 bp):
TTTTATGAAATTTTTATAATTTATAAATTATTTATTAC
Found at i:28515156 original size:17 final size:17
Alignment explanation
Indices: 28515134--28515167 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28515124 TAGCTGATAC
28515134 TCTATTAATCCATCAAA
1 TCTATTAATCCATCAAA
28515151 TCTATTAATCCATCAAA
1 TCTATTAATCCATCAAA
28515168 CCCTAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
TCTATTAATCCATCAAA
Done.