Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 71 of 135
Found at i:28102186 original size:21 final size:21
Alignment explanation
Indices: 28102138--28102195 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
28102128 TTATGCTATT
* * *
28102138 CTACTTCCCTCGCTGTAGCCT
1 CTACTTCCCTCGCTGCAACCG
28102159 CTACTTCCCTCGCTGCAACCG
1 CTACTTCCCTCGCTGCAACCG
* *
28102180 CTGCTTCTCTCGCTGC
1 CTACTTCCCTCGCTGC
28102196 CGCATCTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.09, C:0.45, G:0.16, T:0.31
Consensus pattern (21 bp):
CTACTTCCCTCGCTGCAACCG
Found at i:28102297 original size:66 final size:64
Alignment explanation
Indices: 28102182--28102346 Score: 199
Period size: 66 Copynumber: 2.5 Consensus size: 64
28102172 TGCAACCGCT
* *
28102182 GCTTCTCTCGCTGCCGCATCTTCTTTAAGCTGCTGCTGCAGTTGCTCATA-CTTTCGTTGAACCT
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTG-TGCTGCAGTTGCTCATATCTTT--TTGAACCT
28102246 CA
63 CA
*
28102248 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTT-CTTCATATCTTTTTGAACCTC
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGT-GCTGCAGTTGC-TCATATCTTTTTGAACCTC
28102312 A
64 A
* ** * *
28102313 GCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTG
28102347 TAATTTGCTC
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
64 1 0.01
65 40 0.45
66 43 0.49
67 4 0.05
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.39
Consensus pattern (64 bp):
GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTGCTGCAGTTGCTCATATCTTTTTGAACCTCA
Found at i:28104702 original size:16 final size:16
Alignment explanation
Indices: 28104681--28104711 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28104671 CGTTTATGAG
28104681 TTAGGGATTTCAAAAC
1 TTAGGGATTTCAAAAC
*
28104697 TTAGGGATTTTAAAA
1 TTAGGGATTTCAAAA
28104712 TAGGGAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (16 bp):
TTAGGGATTTCAAAAC
Found at i:28106998 original size:114 final size:113
Alignment explanation
Indices: 28106795--28107141 Score: 532
Period size: 113 Copynumber: 3.1 Consensus size: 113
28106785 GCTTAACGCC
* * * *
28106795 AAACGCCGCTGAAGAACGGATTATTAGTGGCGTTTGGGCAAAAACCGCCACTAGTGTTCCCAAAT
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGC-AAAACCGCCACTAATGTTCCCAAAT
* *
28106860 ATATGAAAACGGCGTCGTTTTGTGTTACTCTATTTGCGACGCTTTTTGTA
65 ATATGAAAACGGCGTCGTTCTGTGTTACTCTA-TTGCGGCGCTTTTTGTA
*
28106910 AAACGCCGCTGAAGAATGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* * * *
28106975 TATGAAAACGGCATCATTCTGTGTTACTCCATTGCGGCGCTTTTTATA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
* * *
28107023 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTTATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* *
28107088 TATGAAAACGACGTCGTTCTGTGTGACTCTATTGCGGCGCTTTTTGTA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
28107136 AAACGC
1 AAACGC
28107142 TGCTAATGCT
Statistics
Matches: 211, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
113 124 0.59
114 52 0.25
115 35 0.17
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (113 bp):
AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
Found at i:28107265 original size:41 final size:40
Alignment explanation
Indices: 28107121--28107268 Score: 124
Period size: 40 Copynumber: 3.7 Consensus size: 40
28107111 TGACTCTATT
* * *
28107121 GCGGCGCTTTTT-GTAAAACGCTGCTAATGCTTGGT-TTTA
1 GCGGCG-TTTTTCGTAAAACGCCGCTAATGCTCGATATTTA
* * * *
28107160 GCGGCGTTTTT-TTATGTAGCGCCGCTAATGCTCGATATTTT
1 GCGGCGTTTTTCGTA--AAACGCCGCTAATGCTCGATATTTA
*
28107201 GCGGCGTTTTTCGTAAAATGCCGCTAATGCTCGAT-TATTA
1 GCGGCGTTTTTCGTAAAACGCCGCTAATGCTCGATAT-TTA
* * *
28107241 GTGGCGTTTTTTGTCCAAACGCCGCTAA
1 GCGGCGTTTTTCGT-AAAACGCCGCTAA
28107269 AAGTGCCGCT
Statistics
Matches: 87, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
38 7 0.08
39 7 0.08
40 46 0.53
41 25 0.29
42 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (40 bp):
GCGGCGTTTTTCGTAAAACGCCGCTAATGCTCGATATTTA
Found at i:28112314 original size:8 final size:8
Alignment explanation
Indices: 28112301--28112333 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
28112291 AAGAAAACGC
28112301 AAGAAAAT
1 AAGAAAAT
28112309 AAGAAAAT
1 AAGAAAAT
28112317 AA-AAAAT
1 AAGAAAAT
*
28112324 AAAAAAAT
1 AAGAAAAT
28112332 AA
1 AA
28112334 AACCAAGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (8 bp):
AAGAAAAT
Found at i:28112324 original size:15 final size:15
Alignment explanation
Indices: 28112304--28112335 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28112294 AAAACGCAAG
*
28112304 AAAATAAGAAAATAA
1 AAAATAAAAAAATAA
28112319 AAAATAAAAAAATAA
1 AAAATAAAAAAATAA
28112334 AA
1 AA
28112336 CCAAGTCGAA
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:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATAAAAAAATAA
Found at i:28113410 original size:44 final size:44
Alignment explanation
Indices: 28113355--28113754 Score: 256
Period size: 44 Copynumber: 8.6 Consensus size: 44
28113345 TTTTAATCCA
* *
28113355 CTCCACTGTAATCTCAGGGAGATAGGATTA-TCAGCTTCAATCTG
1 CTCCGCTGTAATCTCAGGGAGATAAGATTACT-AGCTTCAATCTG
*
28113399 CTCCGTTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
1 CTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * *
28113443 CTCTGCTGCAATCTCAGGGAGATAAGATTTCTGGTTTCAATCTGATGCG
1 CTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATC---T--G
* * * * * *
28113492 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCG
1 --CT-C-C-GCTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCTG
*
28113541 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
1 CTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * *
28113585 CTCTGCTGCAATCTCAGGGAGATAAGATTTCTGGTTTCAATCTGATGCG
1 CTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATC---T--G
* * * * * *
28113634 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCG
1 --CT-C-C-GCTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCTG
* *
28113683 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
28113727 CTCCGCTGTAATCTCAGGGAGATAAGAT
1 CTCCGCTGTAATCTCAGGGAGATAAGAT
28113755 CTGCAATTTC
Statistics
Matches: 279, Mismatches: 44, Indels: 66
0.72 0.11 0.17
Matches are distributed among these distances:
42 2 0.01
43 4 0.01
44 192 0.69
45 5 0.02
46 2 0.01
47 6 0.02
49 4 0.01
51 4 0.01
52 2 0.01
53 2 0.01
54 52 0.19
55 2 0.01
56 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
CTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
Found at i:28113583 original size:142 final size:142
Alignment explanation
Indices: 28113405--28113754 Score: 673
Period size: 142 Copynumber: 2.5 Consensus size: 142
28113395 TCTGCTCCGT
28113405 TGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCTGCTGCAATCTCAGGGAGATAAGA
1 TGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCTGCTGCAATCTCAGGGAGATAAGA
28113470 TTTCTGGTTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
66 TTTCTGGTTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
28113535 AATCCGCTCCAC
131 AATCCGCTCCAC
28113547 TGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCTGCTGCAATCTCAGGGAGATAAGA
1 TGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCTGCTGCAATCTCAGGGAGATAAGA
28113612 TTTCTGGTTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
66 TTTCTGGTTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
28113677 AATCCGCTCCAC
131 AATCCGCTCCAC
* * *
28113689 TGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 TGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCTGCTGCAATCTCAGGGAGATAAGA
28113754 T
66 T
28113755 CTGCAATTTC
Statistics
Matches: 205, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 205 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (142 bp):
TGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCTGCTGCAATCTCAGGGAGATAAGA
TTTCTGGTTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
AATCCGCTCCAC
Found at i:28115140 original size:19 final size:20
Alignment explanation
Indices: 28115108--28115145 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28115098 TTAGCTTTTC
*
28115108 CATTTTTACTTTTTCATCAT
1 CATTTTTACATTTTCATCAT
28115128 CATTTTT-CATTTTCATCA
1 CATTTTTACATTTTCATCA
28115146 CTTTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (20 bp):
CATTTTTACATTTTCATCAT
Found at i:28125410 original size:21 final size:21
Alignment explanation
Indices: 28125363--28125403 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28125353 TGTTAAGGAG
*
28125363 CACACGCCCGTGTGACTATGA
1 CACACGCCCGTGTGACCATGA
*
28125384 CACACGCCCGTGTGCCCATG
1 CACACGCCCGTGTGACCATG
28125404 GGACACGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.39, G:0.24, T:0.17
Consensus pattern (21 bp):
CACACGCCCGTGTGACCATGA
Found at i:28131747 original size:50 final size:48
Alignment explanation
Indices: 28131628--28131815 Score: 157
Period size: 50 Copynumber: 3.8 Consensus size: 48
28131618 ACATGCCAAA
* * *
28131628 GCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC-TGCAAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGTGC-CAT
* * * *
28131677 GTCATGTCTCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCTCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATC-GTGC-CAT
* ** *
28131727 GCCATGTCCCAGACATGGTCTTAC-CGGGAACCTCTCATCTCTGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGG-AGTTCTCATATC-GTGCC-AT
* **
28131777 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATA
28131816 ACCTCAATAA
Statistics
Matches: 114, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
48 4 0.04
49 33 0.29
50 74 0.65
51 3 0.03
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGTGCCAT
Found at i:28133555 original size:38 final size:38
Alignment explanation
Indices: 28133512--28133590 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
28133502 AAAACCATAG
* *
28133512 TATATTGTTAGTTATGTCATCTTGATTAAAACTTTGAT
1 TATATTGTTAGTTATGCCATCTTGATTAAAACTCTGAT
28133550 TATATTGTTAGTTATGCCATCTTGATTAAAACTCTGAT
1 TATATTGTTAGTTATGCCATCTTGATTAAAACTCTGAT
28133588 TAT
1 TAT
28133591 GAATAGAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (38 bp):
TATATTGTTAGTTATGCCATCTTGATTAAAACTCTGAT
Found at i:28135984 original size:16 final size:17
Alignment explanation
Indices: 28135963--28135994 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28135953 TTCAAATTTT
28135963 TAGAAATT-TAAAAAAA
1 TAGAAATTATAAAAAAA
28135979 TAGAAATTATAAAAAA
1 TAGAAATTATAAAAAA
28135995 TATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
TAGAAATTATAAAAAAA
Found at i:28136004 original size:19 final size:20
Alignment explanation
Indices: 28135982--28136025 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
28135972 AAAAAAATAG
*
28135982 AAATTATAAAAAAT-ATTTA
1 AAATAATAAAAAATCATTTA
*
28136001 AAATAATAGAAAATCATTTA
1 AAATAATAAAAAATCATTTA
28136021 AAATA
1 AAATA
28136026 TTTTTTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AAATAATAAAAAATCATTTA
Found at i:28136024 original size:29 final size:28
Alignment explanation
Indices: 28135968--28136028 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
28135958 ATTTTTAGAA
*
28135968 ATTTAAAAAAATAGAAATTATAAAAAAT
1 ATTTAAAAAAATAGAAATCATAAAAAAT
* **
28135996 ATTTAAAATAATAGAAAATCATTTAAAAT
1 ATTTAAAAAAATAG-AAATCATAAAAAAT
28136025 ATTT
1 ATTT
28136029 TTTTCTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (28 bp):
ATTTAAAAAAATAGAAATCATAAAAAAT
Found at i:28136066 original size:30 final size:30
Alignment explanation
Indices: 28136030--28136089 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
28136020 AAAATATTTT
* **
28136030 TTTCTCT-TTTGCTTTTTTTTTTTTACTTTC
1 TTTCTCTCTTTCCTTTAATTTTTTT-CTTTC
28136060 TTTCTCTCTTTCCTTTAATTTTTTTCTTTC
1 TTTCTCTCTTTCCTTTAATTTTTTTCTTTC
28136090 AATTTTCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (30 bp):
TTTCTCTCTTTCCTTTAATTTTTTTCTTTC
Found at i:28136678 original size:23 final size:23
Alignment explanation
Indices: 28136651--28136706 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28136641 TGAGAAAATG
*
28136651 GAAAATGAAAAGAA-AAAAAAAA
1 GAAAAAGAAAAGAAGAAAAAAAA
* *
28136673 GAAAAAGGAAAGAAGTAAAAAAA
1 GAAAAAGAAAAGAAGAAAAAAAA
* *
28136696 GGAAAACAAAA
1 GAAAAAGAAAA
28136707 ATAACTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (23 bp):
GAAAAAGAAAAGAAGAAAAAAAA
Found at i:28136777 original size:14 final size:14
Alignment explanation
Indices: 28136758--28136784 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28136748 CCATTTTTAT
28136758 AATTTTTAAAATTC
1 AATTTTTAAAATTC
28136772 AATTTTTAAAATT
1 AATTTTTAAAATT
28136785 TTGTGAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTTTTAAAATTC
Found at i:28141547 original size:41 final size:41
Alignment explanation
Indices: 28141484--28141566 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
28141474 TTTGATATGA
* * **
28141484 GATTACGTGTAAAACCATGTCTAGGACATTGGCATCGTATAT
1 GATTACGTGTAAAACCACGTCTAGAACAGAGGCATCG-ATAT
* *
28141526 GATT-CGTGTAAGACCCCGTCTAGAACAGAGGCATCGATAT
1 GATTACGTGTAAAACCACGTCTAGAACAGAGGCATCGATAT
28141566 G
1 G
28141567 TGATAACATG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 5 0.14
41 26 0.74
42 4 0.11
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (41 bp):
GATTACGTGTAAAACCACGTCTAGAACAGAGGCATCGATAT
Found at i:28148967 original size:43 final size:42
Alignment explanation
Indices: 28148915--28149032 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 42
28148905 TGTGATCACA
*
28148915 TGTAAGACCATGTCTGAGACATTAGCATCGATATAAGATTACG
1 TGTAAGACCATGTCTGGGACATTAGCATCGATATAAGATT-CG
* * *
28148958 TGTCAGACCATGTCTGGGACATTAGCACCG-TATATGATTCG
1 TGTAAGACCATGTCTGGGACATTAGCATCGATATAAGATTCG
* *
28148999 TGTAAGACCCTGTCTGGGACA-AAGGCATCGATAT
1 TGTAAGACCATGTCTGGGACATTA-GCATCGATAT
28149033 GTGATAACAT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
40 1 0.02
41 26 0.40
42 11 0.17
43 27 0.42
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTAGCATCGATATAAGATTCG
Found at i:28149013 original size:41 final size:43
Alignment explanation
Indices: 28148915--28149019 Score: 151
Period size: 43 Copynumber: 2.5 Consensus size: 43
28148905 TGTGATCACA
* *
28148915 TGTAAGACCATGTCTGAGACATTAGCATCGATATAAGATTACG
1 TGTAAGACCATGTCTGGGACATTAGCACCGATATAAGATTACG
* *
28148958 TGTCAGACCATGTCTGGGACATTAGCACCG-TATATGATT-CG
1 TGTAAGACCATGTCTGGGACATTAGCACCGATATAAGATTACG
*
28148999 TGTAAGACCCTGTCTGGGACA
1 TGTAAGACCATGTCTGGGACA
28149020 AAGGCATCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 21 0.38
42 8 0.14
43 27 0.48
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTAGCACCGATATAAGATTACG
Found at i:28149318 original size:22 final size:22
Alignment explanation
Indices: 28149287--28149329 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28149277 TACACCAAAA
* *
28149287 TAGGCTTTTAGCGGTGCTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
28149309 TAGGCCTTTAGCGGCGCTTTT
1 TAGGCCTTTAGCGGCGCTTTT
28149330 GAGCGCCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
TAGGCCTTTAGCGGCGCTTTTT
Found at i:28149445 original size:43 final size:43
Alignment explanation
Indices: 28149375--28149644 Score: 202
Period size: 43 Copynumber: 6.3 Consensus size: 43
28149365 GCGCCGGAAA
* * * * *
28149375 AAACGCCGCTAAAGACAAAAACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* * * *
28149418 AAACACCATTAAAGACCAAGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* ** * *
28149461 AAACGCCGCTAAAGGTCATGATCTTTAGCGGCGCTTTTACCAC
1 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* ** * * *
28149504 AAACGCAACTAAAGTTCATGACCTTTAGTGGCGCTTCTACCAC
1 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* * * * * * * *
28149547 AAACGCCGCTAAAGATCATGACCTTGAGCGACACTTCTACAAC
1 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* * * ***
28149590 AAACGCCACTATAA-A-GATGACTTTTAGCGGCGCTTTTTTGAC
1 AAACGCCACTA-AAGACCAAGACCTTTAGCGGCGCTTTTACCAC
*
28149632 AAACACCACTAAA
1 AAACGCCACTAAA
28149645 ATCATGACTT
Statistics
Matches: 185, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 2 0.01
42 28 0.15
43 153 0.83
44 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
Found at i:28149488 original size:86 final size:86
Alignment explanation
Indices: 28149375--28149576 Score: 235
Period size: 86 Copynumber: 2.3 Consensus size: 86
28149365 GCGCCGGAAA
** * * * *
28149375 AAACGCCGCTAAAGA-CAAAAACTTTTAGCGGCGCTTTTCCCACAAACACCATTAAAGACCAAGA
1 AAACGCCGCTAAAGATC-ATGACCTTTAGCGGCGCTTTTACCACAAACACAACTAAAGACCAAGA
* *
28149439 CCTTTAGCGACGCTTTTCCCAC
65 CCTTTAGCGACGCTTCTACCAC
* * * ** *
28149461 AAACGCCGCTAAAGGTCATGATCTTTAGCGGCGCTTTTACCACAAACGCAACTAAAGTTCATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACAAACACAACTAAAGACCAAGAC
* *
28149526 CTTTAGTGGCGCTTCTACCAC
66 CTTTAGCGACGCTTCTACCAC
*
28149547 AAACGCCGCTAAAGATCATGACCTTGAGCG
1 AAACGCCGCTAAAGATCATGACCTTTAGCG
28149577 ACACTTCTAC
Statistics
Matches: 96, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
86 95 0.99
87 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (86 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACAAACACAACTAAAGACCAAGAC
CTTTAGCGACGCTTCTACCAC
Found at i:28150972 original size:491 final size:491
Alignment explanation
Indices: 28150048--28151030 Score: 1822
Period size: 491 Copynumber: 2.0 Consensus size: 491
28150038 AATTCCATTC
28150048 ATCTAAAGACATCCTTAGAACATTTATGAGCACTATGTCATACTCATTTATCAGCTCTTAAAAAA
1 ATCTAAAGACATCCTTAGAACATTTATGAGCACTATGTCATACTCATTTATCAGCTCTTAAAAAA
* *
28150113 TTAACAGCATGTATGACCTAGGAGTTTAATTAATCACCACATTTCGTCCAGCAAGCACTTTATTG
66 TTAACAGCATGTATGACCTAGCAGTTCAATTAATCACCACATTTCGTCCAGCAAGCACTTTATTG
* * *
28150178 GCTTTCTATAAAATTTAAGATTCTTAGACTTTCCCTAGAAAATATTTTTCAGTCCAAAAAGAATC
131 GCTTTCTAAAAAAATTAAGATTCTTAGACTTTCCCCAGAAAATATTTTTCAGTCCAAAAAGAATC
* *
28150243 CAACATAAAATTATTAATAGCAATTGACTTGCATATTTAAAATGACAAGCAAGTTAGTTACCGAC
196 CAACAGAAAATTATTAATAGCAATTGACTTGCATATTTAAAATCACAAGCAAGTTAGTTACCGAC
*
28150308 ATCAAGGGGAGGATTTAGATATTCTATTCCATTGCTTATCTGACCATATGGCTCCATTAAATCAA
261 ATCAAGGGGAGGATATAGATATTCTATTCCATTGCTTATCTGACCATATGGCTCCATTAAATCAA
* *
28150373 CCATGTTTTGCAGATCATCTTTGGTCAAATTTAGTCCAAGGTGATTCACCCGCATTTGGCTAATT
326 CCACGTTTTGCAGATCATCTTTGGTCAAATTTAGTCCAAGGTGATTCACCAGCATTTGGCTAATT
* * *
28150438 TGCTTGACAATTTTGGGATCATGCTGCTGAAAGTCTGCAAGCAGTACAAATTACAGTTAGATAAT
391 TGCTTGACAACTTTGGGATCATGCTGCTGAAAGTCTACAAGCAGTACAAACTACAGTTAGATAAT
28150503 TTGGTTAAAATTGATTAGTGCCTAAAACATGAATTT
456 TTGGTTAAAATTGATTAGTGCCTAAAACATGAATTT
28150539 ATCTAAAGACATCCTTAGAACATTTATGAGCACTATGTCATACTCATTTATCAGCTCTTAAAAAA
1 ATCTAAAGACATCCTTAGAACATTTATGAGCACTATGTCATACTCATTTATCAGCTCTTAAAAAA
*
28150604 TTAACAGCATGTATGACCTAGCAGTTCAATTAATCCCCACATTTCGTCCAGCAAGCACTTTATTG
66 TTAACAGCATGTATGACCTAGCAGTTCAATTAATCACCACATTTCGTCCAGCAAGCACTTTATTG
*
28150669 GCTTTCTAAAAAAATTAAGATTCTTAGACTTTCCCCAGAAATTATTTTTCAGTCCAAAAAGAATC
131 GCTTTCTAAAAAAATTAAGATTCTTAGACTTTCCCCAGAAAATATTTTTCAGTCCAAAAAGAATC
*
28150734 CAACAGAAAATTATTAATAGCAATTGACTTGCATATTTAAAATCACAAGCAAGTTAGTTACTGAC
196 CAACAGAAAATTATTAATAGCAATTGACTTGCATATTTAAAATCACAAGCAAGTTAGTTACCGAC
28150799 ATCAAGGGGAGGATATAGATATTCTATTCCATTGCTTATCTGACCATATGGCTCCATTAAATCAA
261 ATCAAGGGGAGGATATAGATATTCTATTCCATTGCTTATCTGACCATATGGCTCCATTAAATCAA
28150864 CCACGTTTTGCAGATCATCTTTGGTCAAATTTAGTCCAAGGTGATTCACCAGCATTTGGCTAATT
326 CCACGTTTTGCAGATCATCTTTGGTCAAATTTAGTCCAAGGTGATTCACCAGCATTTGGCTAATT
28150929 TGCTTGACAACTTTGGGATCATGCTGCTGAAAGTCTACAAGCAGTACAAACTACAGTTAGATAAT
391 TGCTTGACAACTTTGGGATCATGCTGCTGAAAGTCTACAAGCAGTACAAACTACAGTTAGATAAT
28150994 TTGGTTAAAATTGATTAGTGCCTAAAACATGAATTT
456 TTGGTTAAAATTGATTAGTGCCTAAAACATGAATTT
28151030 A
1 A
28151031 CCACCAATTA
Statistics
Matches: 476, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
491 476 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (491 bp):
ATCTAAAGACATCCTTAGAACATTTATGAGCACTATGTCATACTCATTTATCAGCTCTTAAAAAA
TTAACAGCATGTATGACCTAGCAGTTCAATTAATCACCACATTTCGTCCAGCAAGCACTTTATTG
GCTTTCTAAAAAAATTAAGATTCTTAGACTTTCCCCAGAAAATATTTTTCAGTCCAAAAAGAATC
CAACAGAAAATTATTAATAGCAATTGACTTGCATATTTAAAATCACAAGCAAGTTAGTTACCGAC
ATCAAGGGGAGGATATAGATATTCTATTCCATTGCTTATCTGACCATATGGCTCCATTAAATCAA
CCACGTTTTGCAGATCATCTTTGGTCAAATTTAGTCCAAGGTGATTCACCAGCATTTGGCTAATT
TGCTTGACAACTTTGGGATCATGCTGCTGAAAGTCTACAAGCAGTACAAACTACAGTTAGATAAT
TTGGTTAAAATTGATTAGTGCCTAAAACATGAATTT
Found at i:28153937 original size:13 final size:13
Alignment explanation
Indices: 28153901--28153947 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
28153891 AGTTATGTGA
*
28153901 TTTTATAAAATAT
1 TTTTATAAACTAT
28153914 TTTT-TATAACTAT
1 TTTTATA-AACTAT
28153927 TTTTATAAACTGGAT
1 TTTTATAAACT--AT
28153942 TTTTAT
1 TTTTAT
28153948 TAAAAAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 17 0.59
14 2 0.07
15 8 0.28
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (13 bp):
TTTTATAAACTAT
Found at i:28154587 original size:33 final size:34
Alignment explanation
Indices: 28154550--28154620 Score: 135
Period size: 33 Copynumber: 2.1 Consensus size: 34
28154540 CACTAATTAA
28154550 TAACCTGACACCGAATCCATAAACCTTAAA-CCC
1 TAACCTGACACCGAATCCATAAACCTTAAATCCC
28154583 TAACCTGACACCGAATCCATAAACCTTAAATCCC
1 TAACCTGACACCGAATCCATAAACCTTAAATCCC
28154617 TAAC
1 TAAC
28154621 TCTTAATCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.39, C:0.35, G:0.06, T:0.20
Consensus pattern (34 bp):
TAACCTGACACCGAATCCATAAACCTTAAATCCC
Found at i:28154654 original size:21 final size:21
Alignment explanation
Indices: 28154615--28154654 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28154605 ACCTTAAATC
* * *
28154615 CCTAACTCTTAATCTCTAACA
1 CCTAACACTTAACCCCTAACA
28154636 CCTAACACTTAACCCCTAA
1 CCTAACACTTAACCCCTAA
28154655 ATCACAACCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.28
Consensus pattern (21 bp):
CCTAACACTTAACCCCTAACA
Found at i:28155165 original size:41 final size:39
Alignment explanation
Indices: 28155107--28155342 Score: 197
Period size: 41 Copynumber: 5.8 Consensus size: 39
28155097 AAGTGTTTTT
*
28155107 GCGGCGTTTTTTGAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTT-AAAAACGCCGCTAAAG-CCTGAGCATTA
* *
28155148 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGTCTAAGCATTA
1 GCGGCGCTTTTT-AAAAACGCCGCTAAA-GCCTGAGCATTA
**** * * *
28155189 GTAATGCTTTCTTAAGAATGCTGCTAAAAG-CTAGAGCATTA
1 GCGGCGCTTT-TTAAAAACGCCGCT-AAAGCCT-GAGCATTA
* *
28155230 GCGGCGCATTTCTAAAAATGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGC-TTTTTAAAAACGCCGCTAAAGC-CTGAGCATTA
*
28155271 GCGGCGCTTTATTAAAAACGCTGCTAAAAG-CTAGAGCATTA
1 GCGGCGCTTT-TTAAAAACGCCGCT-AAAGCCT-GAGCATTA
* * *
28155312 GCGTCGCTTTTGAAAAAATGCCGCTAAAGCC
1 GCGGCGCTTTT-TAAAAACGCCGCTAAAGCC
28155343 CCGAAAGGTC
Statistics
Matches: 157, Mismatches: 26, Indels: 24
0.76 0.13 0.12
Matches are distributed among these distances:
40 16 0.10
41 126 0.80
42 15 0.10
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (39 bp):
GCGGCGCTTTTTAAAAACGCCGCTAAAGCCTGAGCATTA
Found at i:28155268 original size:82 final size:81
Alignment explanation
Indices: 28155140--28155341 Score: 253
Period size: 82 Copynumber: 2.5 Consensus size: 81
28155130 CTAAAGCCCT
* * * * * * *
28155140 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTCTAAGCATTAGTAATGCTTTCTTAAG
1 GAGCATTAGCGGCGCTTTCT-AAAAATGCCGCTAAAGCTCTAAGCATTAGCAACGCTTTATTAAA
*
28155205 AATGCTGCTAAAAGCTA
65 AACGCTGCTAAAAGCTA
* **
28155222 GAGCATTAGCGGCGCATTTCTAAAAATGCCGCTAAAGCTCTGAGCATTAGCGGCGCTTTATTAAA
1 GAGCATTAGCGGCGC-TTTCTAAAAATGCCGCTAAAGCTCTAAGCATTAGCAACGCTTTATTAAA
28155287 AACGCTGCTAAAAGCTA
65 AACGCTGCTAAAAGCTA
*
28155304 GAGCATTAGCGTCGCTTT-TGAAAAAATGCCGCTAAAGC
1 GAGCATTAGCGGCGCTTTCT--AAAAATGCCGCTAAAGC
28155342 CCCGAAAGGT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
80 1 0.01
81 3 0.03
82 97 0.92
83 4 0.04
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (81 bp):
GAGCATTAGCGGCGCTTTCTAAAAATGCCGCTAAAGCTCTAAGCATTAGCAACGCTTTATTAAAA
ACGCTGCTAAAAGCTA
Found at i:28155451 original size:39 final size:40
Alignment explanation
Indices: 28155408--28155513 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
28155398 AAAAACACCA
* *
28155408 CTAATGCTC-ATTTTTAGCGGCGCTTTTCTG-AAAGCGCTG
1 CTAATGCTCAATTTTTAGCGGCG-TTTTATGTAAAGCGCCG
* * **
28155447 CTAATGCTCGATCTTTAGCGGCGTTTTATGTTTAGCGCCG
1 CTAATGCTCAATTTTTAGCGGCGTTTTATGTAAAGCGCCG
* *
28155487 CTAATGCTCAATTTTTAGTGGTGTTTT
1 CTAATGCTCAATTTTTAGCGGCGTTTT
28155514 TTGTCCAAAC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
39 15 0.27
40 41 0.73
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.41
Consensus pattern (40 bp):
CTAATGCTCAATTTTTAGCGGCGTTTTATGTAAAGCGCCG
Found at i:28163483 original size:20 final size:20
Alignment explanation
Indices: 28163447--28163485 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28163437 TTGCTTCTTC
*
28163447 TTTACTTACTCTCTTACTTG
1 TTTACTTACTCTATTACTTG
28163467 TTTACTTACT-TGATTACTT
1 TTTACTTACTCT-ATTACTT
28163486 AAATAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTCTATTACTTG
Found at i:28163873 original size:56 final size:50
Alignment explanation
Indices: 28163744--28163879 Score: 146
Period size: 50 Copynumber: 2.6 Consensus size: 50
28163734 TACTGCAAAG
* **
28163744 GCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATTTCGGTGCCAAC
1 GCCATGTCCCAAACATGGTCTTACGTGGGACCTCTCATTTCAATGCCAAC
* * * *
28163794 GCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATAACGTTAATAATGCCAAT
1 GCCATGTCCCAAACATGGTCTTACGTGGGACCTCTCAT----TT--CAATGCCAAC
*
28163850 GCCATGTCCCAAACATGGTCTTACATGGGA
1 GCCATGTCCCAAACATGGTCTTACGTGGGA
28163880 TCTCATCCCC
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 35 0.50
54 2 0.03
56 33 0.47
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAAACATGGTCTTACGTGGGACCTCTCATTTCAATGCCAAC
Found at i:28166053 original size:40 final size:40
Alignment explanation
Indices: 28165998--28166154 Score: 201
Period size: 40 Copynumber: 3.9 Consensus size: 40
28165988 GCCTTTAGGA
* *
28165998 GTATCGAAGTACAAACAGGGGCACATATGCGCATTCAAGG
1 GTATCGAAGTACAAACAGGGGCACATATGTGCATTCAGGG
*
28166038 GTATC-AAGGTACAAACAGGGGCACGTATGTGCATTCAGGG
1 GTATCGAA-GTACAAACAGGGGCACATATGTGCATTCAGGG
* ** * *
28166078 GTA-CCATAGTACAAACAGAAGCACGTGTGTGCATTCAGGG
1 GTATCGA-AGTACAAACAGGGGCACATATGTGCATTCAGGG
*
28166118 GTATCGAAGTACAAATAGGGGCACATATGTGCATTCA
1 GTATCGAAGTACAAACAGGGGCACATATGTGCATTCA
28166155 TACAATAATT
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
39 3 0.03
40 95 0.94
41 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.20
Consensus pattern (40 bp):
GTATCGAAGTACAAACAGGGGCACATATGTGCATTCAGGG
Found at i:28169780 original size:35 final size:35
Alignment explanation
Indices: 28169734--28169804 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
28169724 ATCAAGAATG
28169734 TATGATAAATAAGCTTCACATCCCTTTTTAATCAA
1 TATGATAAATAAGCTTCACATCCCTTTTTAATCAA
28169769 TATGATAAATAAGCTTCACATCCCTTTTTAATCAA
1 TATGATAAATAAGCTTCACATCCCTTTTTAATCAA
28169804 T
1 T
28169805 TTTTTAGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.38
Consensus pattern (35 bp):
TATGATAAATAAGCTTCACATCCCTTTTTAATCAA
Found at i:28171978 original size:46 final size:46
Alignment explanation
Indices: 28171922--28172013 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
28171912 AGTAATACTA
28171922 GAATGATTCTAATGTTGCAAACAATGAGTGGCATCTAGCAATGCAT
1 GAATGATTCTAATGTTGCAAACAATGAGTGGCATCTAGCAATGCAT
28171968 GAATGATTCTAATGTTGCAAACAATGAGTGGCATCTAGCAATGCAT
1 GAATGATTCTAATGTTGCAAACAATGAGTGGCATCTAGCAATGCAT
28172014 CATTGCTACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
GAATGATTCTAATGTTGCAAACAATGAGTGGCATCTAGCAATGCAT
Found at i:28173464 original size:15 final size:15
Alignment explanation
Indices: 28173444--28173473 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28173434 ATATACAACT
28173444 GGGTTTTAAATCAGA
1 GGGTTTTAAATCAGA
28173459 GGGTTTTAAATCAGA
1 GGGTTTTAAATCAGA
28173474 CCTTTGAGGC
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:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
GGGTTTTAAATCAGA
Found at i:28174559 original size:40 final size:40
Alignment explanation
Indices: 28174514--28174738 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 40
28174504 AGGAGTATTA
*
28174514 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACTG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTACTG
* * **
28174554 AAGTACAAATAGGGACATGTATGTGCATTCAGGGGTA-TCG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTACT-G
* * *
28174594 AAGTACGAACAGGGGCACATATGTGCATTCAAGGGCACTG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTACTG
* * * *
28174634 ATGTACAAACAGGGCCACATATGTGCATTTAGGGGTACGG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTACTG
* * ** *
28174674 AAGTAC-AA-A--GGAACATATGGGCATTCAACGGTACCG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTACTG
*
28174710 AAGTACAAACAGGGGCACGTATGTGCATT
1 AAGTACAAACAGGGGCACATATGTGCATT
28174739 TATACAATAA
Statistics
Matches: 151, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
36 26 0.17
37 2 0.01
38 2 0.01
39 3 0.02
40 117 0.77
41 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACATATGTGCATTCAGGGGTACTG
Found at i:28174631 original size:20 final size:19
Alignment explanation
Indices: 28174606--28174667 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
28174596 GTACGAACAG
28174606 GGGCACATATGTGCATTCAA
1 GGGCACATATGTGCATTC-A
* **
28174626 GGGCAC-TGATGTACAAACA
1 GGGCACAT-ATGTGCATTCA
*
28174645 GGGCCACATATGTGCATTTA
1 GGG-CACATATGTGCATTCA
28174665 GGG
1 GGG
28174668 GTACGGAAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.16
20 26 0.81
21 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (19 bp):
GGGCACATATGTGCATTCA
Found at i:28174657 original size:80 final size:79
Alignment explanation
Indices: 28174514--28174738 Score: 269
Period size: 80 Copynumber: 2.9 Consensus size: 79
28174504 AGGAGTATTA
* * * *
28174514 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACTGAAGTACAAATAGGGACATGTATGTG
1 AAGTAC-AACAGGGGCACATATGTGCATTCAAGGGTACTGAAGTACAAACAGGGACACGTATGTG
28174579 CATTCAGGGGTATC-G
65 CATTCAGGGGTA-CGG
* * * *
28174594 AAGTACGAACAGGGGCACATATGTGCATTCAAGGGCACTGATGTACAAACAGGGCCACATATGTG
1 AAGTAC-AACAGGGGCACATATGTGCATTCAAGGGTACTGAAGTACAAACAGGGACACGTATGTG
*
28174659 CATTTAGGGGTACGG
65 CATTCAGGGGTACGG
* * * * *
28174674 AAGTACAA-A--GGAACATATGGGCATTCAACGGTACCGAAGTACAAACAGGGGCACGTATGTGC
1 AAGTACAACAGGGGCACATATGTGCATTCAAGGGTACTGAAGTACAAACAGGGACACGTATGTGC
28174736 ATT
66 ATT
28174739 TATACAATAA
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
76 48 0.38
78 1 0.01
79 3 0.02
80 74 0.59
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Consensus pattern (79 bp):
AAGTACAACAGGGGCACATATGTGCATTCAAGGGTACTGAAGTACAAACAGGGACACGTATGTGC
ATTCAGGGGTACGG
Found at i:28182233 original size:42 final size:42
Alignment explanation
Indices: 28182138--28182244 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
28182128 GCCAAGCCAT
* *
28182138 ACGCCCGTGTGCCAAGCCGTGTACCTCTCGAAATGGCCTCAC
1 ACGCCCGTGTGCCAGGCCGTGTACCTCTCAAAATGGCCTCAC
* * * *
28182180 ACGCTCATGTGCCAGGCCATGTACCTCTCAAAATGGCCTTAC
1 ACGCCCGTGTGCCAGGCCGTGTACCTCTCAAAATGGCCTCAC
* *
28182222 ATGCCCGTGTGCTAGGCCGTGTA
1 ACGCCCGTGTGCCAGGCCGTGTA
28182245 ACTACCTGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.20, C:0.34, G:0.24, T:0.22
Consensus pattern (42 bp):
ACGCCCGTGTGCCAGGCCGTGTACCTCTCAAAATGGCCTCAC
Found at i:28190332 original size:64 final size:64
Alignment explanation
Indices: 28190248--28190376 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
28190238 TTTCTCCCAC
* * * *
28190248 TTCTCTTTCTAGAAAGACACCAGTCTGAA-CAGCAAATATTTTGTTCTTAGTGGGATTAAAAAAA
1 TTCTCTCTCTACAAACACACCAGTCT-AAGCAACAAATATTTTGTTCTTAGTGGGATTAAAAAAA
28190312 TTCTCTCTCTACAAACACACCAGTCTAAGCAACAAATATTTTGTTCTTAGTGGGATTAAAAAAA
1 TTCTCTCTCTACAAACACACCAGTCTAAGCAACAAATATTTTGTTCTTAGTGGGATTAAAAAAA
28190376 T
1 T
28190377 AATATCCTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 2 0.03
64 58 0.97
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (64 bp):
TTCTCTCTCTACAAACACACCAGTCTAAGCAACAAATATTTTGTTCTTAGTGGGATTAAAAAAA
Found at i:28190557 original size:15 final size:16
Alignment explanation
Indices: 28190537--28190566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28190527 ATGGCGTCTT
28190537 TTGAAC-CGATTTAGA
1 TTGAACACGATTTAGA
28190552 TTGAACACGATTTAG
1 TTGAACACGATTTAG
28190567 TGTGAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (16 bp):
TTGAACACGATTTAGA
Found at i:28193152 original size:12 final size:13
Alignment explanation
Indices: 28193135--28193163 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28193125 CTCATACATG
28193135 AATAAATAAA-GC
1 AATAAATAAATGC
28193147 AATAAATAAATGC
1 AATAAATAAATGC
28193160 AATA
1 AATA
28193164 GTTATAGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:28206437 original size:17 final size:17
Alignment explanation
Indices: 28206415--28206447 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28206405 ATAAGTACAC
*
28206415 ATTGTCATTGCATTTTT
1 ATTGTCATTACATTTTT
28206432 ATTGTCATTACATTTT
1 ATTGTCATTACATTTT
28206448 CATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:28216069 original size:29 final size:29
Alignment explanation
Indices: 28216036--28216097 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
28216026 TAATAAAAAG
28216036 TATATAATGATTCAATCACAATAGAATCA
1 TATATAATGATTCAATCACAATAGAATCA
28216065 TATATAATGATTCAATCACAATAGAATCA
1 TATATAATGATTCAATCACAATAGAATCA
28216094 TATA
1 TATA
28216098 CTAACATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
TATATAATGATTCAATCACAATAGAATCA
Found at i:28216106 original size:29 final size:29
Alignment explanation
Indices: 28216036--28216109 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
28216026 TAATAAAAAG
*
28216036 TATATAATGATTCAATCACAATAGAATCA
1 TATATAATCATTCAATCACAATAGAATCA
*
28216065 TATATAATGATTCAATCACAATAGAATCA
1 TATATAATCATTCAATCACAATAGAATCA
28216094 TATACTAA-CATTCAAT
1 TATA-TAATCATTCAAT
28216110 TTAATCAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 40 0.93
30 3 0.07
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.32
Consensus pattern (29 bp):
TATATAATCATTCAATCACAATAGAATCA
Found at i:28219714 original size:49 final size:53
Alignment explanation
Indices: 28219660--28219770 Score: 131
Period size: 49 Copynumber: 2.2 Consensus size: 53
28219650 ACCATCCAAG
* *
28219660 AACACACCTGGGCACCAAGTTCCAAGCCCGTAGGC-TAACAT-C-CCTCC-GA
1 AACACACCTGGGCACCAAGTGCCAAGCCCGAAGGCTTAACATCCGCCTCCAGA
* * * * *
28219709 AACACAACTTGTCACTAAGTGCCAAGCCCGAAGGCTTTACATCCGCCTCCAGA
1 AACACACCTGGGCACCAAGTGCCAAGCCCGAAGGCTTAACATCCGCCTCCAGA
28219762 AACACACCT
1 AACACACCT
28219771 AAATCATTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 29 0.58
50 5 0.10
51 1 0.02
52 5 0.10
53 10 0.20
ACGTcount: A:0.31, C:0.37, G:0.16, T:0.16
Consensus pattern (53 bp):
AACACACCTGGGCACCAAGTGCCAAGCCCGAAGGCTTAACATCCGCCTCCAGA
Found at i:28224504 original size:6 final size:6
Alignment explanation
Indices: 28224493--28224518 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28224483 AACAAATATT
28224493 AATTTA AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
28224519 ACTTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:28225139 original size:17 final size:17
Alignment explanation
Indices: 28225117--28225153 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
28225107 TACTTTCCAT
28225117 ATATCAATAACAAGGAC
1 ATATCAATAACAAGGAC
28225134 ATATCAATAACAAGGAC
1 ATATCAATAACAAGGAC
28225151 ATA
1 ATA
28225154 CTTTTATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (17 bp):
ATATCAATAACAAGGAC
Found at i:28225270 original size:18 final size:19
Alignment explanation
Indices: 28225228--28225273 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
28225218 TTACAATCAC
*
28225228 CATATTTCAAGTCATGCAAA
1 CATATTT-AATTCATGCAAA
28225248 -A-ATTTAATTCATG-AAA
1 CATATTTAATTCATGCAAA
28225264 CATATTTAAT
1 CATATTTAAT
28225274 AAACACACCG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 11 0.48
19 1 0.04
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (19 bp):
CATATTTAATTCATGCAAA
Found at i:28226573 original size:51 final size:49
Alignment explanation
Indices: 28226483--28226601 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 49
28226473 TATCCTGAAT
*
28226483 TTTAAAACCTCTTTTAAATAATAATTGAAATTCTATTTAATTATCT-TTTA
1 TTTAAAA-CTCTTTTAAATAATAATTGAAATTATATTTAATTAT-TATTTA
* * *
28226533 TTTAAAACTTTTTTAAATAATAATAATTAAATTATGTTTAATTATTATTTA
1 TTTAAAACTCTTTTAAATAATAAT--TGAAATTATATTTAATTATTATTTA
* *
28226584 TCTAAAAATCTTTTAAAT
1 TTTAAAACTCTTTTAAAT
28226602 TAAAATTCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
49 16 0.27
50 8 0.14
51 35 0.59
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (49 bp):
TTTAAAACTCTTTTAAATAATAATTGAAATTATATTTAATTATTATTTA
Found at i:28226611 original size:16 final size:16
Alignment explanation
Indices: 28226586--28226617 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28226576 ATTATTTATC
28226586 TAAAAATCTTTTAAAT
1 TAAAAATCTTTTAAAT
*
28226602 TAAAATTCTTTTAAAT
1 TAAAAATCTTTTAAAT
28226618 AATAACTAAA
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:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAAATCTTTTAAAT
Found at i:28229635 original size:17 final size:19
Alignment explanation
Indices: 28229615--28229654 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28229605 AATAAATTCC
28229615 TTTTATAG-GA-AAACACT
1 TTTTATAGTGACAAACACT
*
28229632 TTTTCTAGTGACAAACACT
1 TTTTATAGTGACAAACACT
28229651 TTTT
1 TTTT
28229655 TCTCTGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (19 bp):
TTTTATAGTGACAAACACT
Found at i:28232544 original size:16 final size:16
Alignment explanation
Indices: 28232520--28232557 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
28232510 TATGTAATAT
28232520 AAAAA-ATTAAATTTG
1 AAAAATATTAAATTTG
28232535 AAAAATATTAAATTTG
1 AAAAATATTAAATTTG
28232551 AAAAATA
1 AAAAATA
28232558 CTGACATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
AAAAATATTAAATTTG
Found at i:28235628 original size:44 final size:44
Alignment explanation
Indices: 28235539--28235629 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 44
28235529 AACTCTATTT
* * * *
28235539 TTAGTTTACCACTTAAATTGTGATTAGTGTAAGTTATTTTCATA
1 TTAGTTTACCACTTAAACTCTGATTAGTGTAAGTTATTATAATA
* * *
28235583 TTAGTTT-CTCACTTAAACTCTTATTAGTGTAGGTTGTTATAATA
1 TTAGTTTAC-CACTTAAACTCTGATTAGTGTAAGTTATTATAATA
28235627 TTA
1 TTA
28235630 TTTGACCTGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.03
44 38 0.97
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (44 bp):
TTAGTTTACCACTTAAACTCTGATTAGTGTAAGTTATTATAATA
Found at i:28237982 original size:137 final size:138
Alignment explanation
Indices: 28237774--28238040 Score: 367
Period size: 137 Copynumber: 1.9 Consensus size: 138
28237764 ATGTCATTAG
* * * * * *
28237774 GGTTACCATGTTTTGGGTGCTGGTCTTGAATGTCCTACCGGTGGCTGAGTTCTGGCATATGTTGC
1 GGTTACCAAGTTTCGGGTGCTGGTCTTGAATGTCCTACCGATGGCTGAGGTCCGACATATGTTGC
* * * * **
28237839 GAATACTTGACAGCTTGTGTGAGCAACACCTTGTAGC-TATATTTCGACTGATAGCTTGTGTGAG
66 GAATACTTGACAGCTTGTGTGAGCAACACCATGCAGCTTACATTCCGACCAATAGCTTGTGTGAG
28237903 CAGACCTA
131 CAGACCTA
**
28237911 GGTTACCAAGTTTCGGGTGCTGGTCTTGGTTGTCCTACCGATGGCTGAGGTCCGACAT-TAGTTG
1 GGTTACCAAGTTTCGGGTGCTGGTCTTGAATGTCCTACCGATGGCTGAGGTCCGACATAT-GTTG
* *
28237975 CGGATACTTGACAGCTTGTGTGAGCAACATCATGCAGCTTACATTCCGACCAATAGCTTGTGTGA
65 CGAATACTTGACAGCTTGTGTGAGCAACACCATGCAGCTTACATTCCGACCAATAGCTTGTGTGA
28238040 G
130 G
28238041 TAGCATCATA
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
136 1 0.01
137 88 0.79
138 23 0.21
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (138 bp):
GGTTACCAAGTTTCGGGTGCTGGTCTTGAATGTCCTACCGATGGCTGAGGTCCGACATATGTTGC
GAATACTTGACAGCTTGTGTGAGCAACACCATGCAGCTTACATTCCGACCAATAGCTTGTGTGAG
CAGACCTA
Found at i:28238075 original size:42 final size:42
Alignment explanation
Indices: 28237985--28238085 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
28237975 CGGATACTTG
*
28237985 ACAGCTTGTGTGAGCAACATCATGCAGCTTACATTCCGACCA
1 ACAGCTTGTGTGAGCAACATCATACAGCTTACATTCCGACCA
* * * * ** *
28238027 ATAGCTTGTGTGAGTAGCATCATATAGCTTACATTCTTACCG
1 ACAGCTTGTGTGAGCAACATCATACAGCTTACATTCCGACCA
*
28238069 GCAGCTTGTGTGAGCAA
1 ACAGCTTGTGTGAGCAA
28238086 ACCCATTTTA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (42 bp):
ACAGCTTGTGTGAGCAACATCATACAGCTTACATTCCGACCA
Found at i:28243460 original size:14 final size:15
Alignment explanation
Indices: 28243443--28243473 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28243433 AATTTTATTT
28243443 TTAATTTTAAAA-AA
1 TTAATTTTAAAATAA
28243457 TTAATTTTAAAATAA
1 TTAATTTTAAAATAA
28243472 TT
1 TT
28243474 TTAACGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATTTTAAAATAA
Found at i:28244349 original size:30 final size:30
Alignment explanation
Indices: 28244301--28244368 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
28244291 ACAACTTTTT
* *
28244301 TTAATTATATAATAAGAAAGCATGTTT-ATA
1 TTAATTATATAATAAGAAAACAT-TTTAACA
*
28244331 TTAATTATAGT-ATGAGAAAACATTTTAACA
1 TTAATTATA-TAATAAGAAAACATTTTAACA
28244361 TTAATTAT
1 TTAATTAT
28244369 GTTATCGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.09
30 29 0.88
31 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (30 bp):
TTAATTATATAATAAGAAAACATTTTAACA
Found at i:28263388 original size:24 final size:24
Alignment explanation
Indices: 28263356--28263412 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
28263346 TTCAATTTTT
28263356 TTCATTTTCATT-TTTCTTTTCTTG
1 TTCATTTTCATTCTTT-TTTTCTTG
28263380 TTCATTTTCATTCTTTTTTTCTTG
1 TTCATTTTCATTCTTTTTTTCTTG
28263404 TTCATTTTC
1 TTCATTTTC
28263413 TCTCAACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.09, C:0.18, G:0.04, T:0.70
Consensus pattern (24 bp):
TTCATTTTCATTCTTTTTTTCTTG
Found at i:28263423 original size:24 final size:24
Alignment explanation
Indices: 28263356--28263424 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
28263346 TTCAATTTTT
***
28263356 TTCATTTTCATTTTTCTTTTCTTG
1 TTCATTTTCATTCAACTTTTCTTG
***
28263380 TTCATTTTCATTCTTTTTTTCTTG
1 TTCATTTTCATTCAACTTTTCTTG
28263404 TTCATTTTC-TCTCAACTTTTC
1 TTCATTTTCAT-TCAACTTTTC
28263425 AACAGAAGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.03
24 38 0.97
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (24 bp):
TTCATTTTCATTCAACTTTTCTTG
Found at i:28276207 original size:15 final size:15
Alignment explanation
Indices: 28276184--28276220 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
28276174 GGAATCAATT
*
28276184 AAATAAAATAATAAA
1 AAATTAAATAATAAA
28276199 AAATTAAATAATAAA
1 AAATTAAATAATAAA
28276214 AAATTAA
1 AAATTAA
28276221 GTTAAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATTAAATAATAAA
Found at i:28277566 original size:18 final size:18
Alignment explanation
Indices: 28277543--28277578 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28277533 CTAGTGCATT
28277543 ATATGAA-AGTGATAAGTG
1 ATATGAACA-TGATAAGTG
28277561 ATATGAACATGATAAGTG
1 ATATGAACATGATAAGTG
28277579 TGCATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (18 bp):
ATATGAACATGATAAGTG
Found at i:28282172 original size:51 final size:50
Alignment explanation
Indices: 28282039--28282233 Score: 198
Period size: 51 Copynumber: 3.8 Consensus size: 50
28282029 AAAGTGATGG
*
28282039 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGATAGGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA-G-TATGT
* * * * *
28282090 TGCA--TGTGTAGTACTGTATGTGCAAGCTACTATGCGTACCAGATAGCTTTGA
1 T-CACGTGTGTAGTAC--TATGTGCAGGCTACTACGTGTACCAGATAG-TATGT
* *
28282142 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT-ATGT
* * * *
28282193 TCACATGTTTAGTACTATGTGCAGGCTACTATGTGAACCAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG
28282234 TATAATTAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
50 11 0.09
51 65 0.56
52 30 0.26
53 11 0.09
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTATGT
Found at i:28282472 original size:16 final size:16
Alignment explanation
Indices: 28282451--28282482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28282441 TGATTGAAAG
*
28282451 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
28282467 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
28282483 GCAACAAAAT
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:28290155 original size:24 final size:24
Alignment explanation
Indices: 28290119--28290191 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
28290109 TGCAATCGAT
*
28290119 AGGGTGAATAGAGGAGCTATGGAA
1 AGGGTGAAGAGAGGAGCTATGGAA
*
28290143 AGGGTGAAGAGAGGAAC-AGTGGAA
1 AGGGTGAAGAGAGGAGCTA-TGGAA
* * *
28290167 AGGTTGAAGGGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTATGGAA
28290191 A
1 A
28290192 ATGTCTTACC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.37, C:0.04, G:0.45, T:0.14
Consensus pattern (24 bp):
AGGGTGAAGAGAGGAGCTATGGAA
Found at i:28292014 original size:21 final size:21
Alignment explanation
Indices: 28291963--28292024 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
28291953 TAATTAGCAC
*
28291963 ACTCAGATGCATCCACAACAA
1 ACTCAGATGCACCCACAACAA
* * *
28291984 AGTC-GTATGCACCCACACCAT
1 ACTCAG-ATGCACCCACAACAA
*
28292005 ACTCAGATGCAGCCACAACA
1 ACTCAGATGCACCCACAACA
28292025 CTCTTCAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15
Consensus pattern (21 bp):
ACTCAGATGCACCCACAACAA
Found at i:28301958 original size:18 final size:18
Alignment explanation
Indices: 28301935--28301977 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28301925 AATTAGAATG
28301935 CAAAAATTA-AACTAAAAA
1 CAAAAATTATAA-TAAAAA
28301953 CAAAAATTATAATAAAAA
1 CAAAAATTATAATAAAAA
*
28301971 TAAAAAT
1 CAAAAAT
28301978 GGCTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (18 bp):
CAAAAATTATAATAAAAA
Found at i:28306248 original size:38 final size:38
Alignment explanation
Indices: 28306195--28306273 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
28306185 TTATGATAGA
*
28306195 AAAAAAATAAACTAAATACTTCATAATAAAGACATGTT
1 AAAAAAATAAACTAAATACTTCATAATAAAGACATATT
**
28306233 AAAAAAATAGGCTAAATACTTCATAATAAAGACATATT
1 AAAAAAATAAACTAAATACTTCATAATAAAGACATATT
28306271 AAA
1 AAA
28306274 TCCCTACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.25
Consensus pattern (38 bp):
AAAAAAATAAACTAAATACTTCATAATAAAGACATATT
Found at i:28306604 original size:11 final size:11
Alignment explanation
Indices: 28306588--28306613 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28306578 ACATATGCTC
28306588 TTTTTTTCTTT
1 TTTTTTTCTTT
28306599 TTTTTTTCTTT
1 TTTTTTTCTTT
28306610 TTTT
1 TTTT
28306614 CTTTTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:28306610 original size:19 final size:19
Alignment explanation
Indices: 28306586--28306625 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28306576 GTACATATGC
*
28306586 TCTTTTTTTCTTTTTTTTT
1 TCTTTTTTTCTTTTTTCTT
28306605 TCTTTTTTTCTTTTTTCTT
1 TCTTTTTTTCTTTTTTCTT
28306624 TC
1 TC
28306626 AAGAACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (19 bp):
TCTTTTTTTCTTTTTTCTT
Found at i:28306625 original size:11 final size:10
Alignment explanation
Indices: 28306588--28306625 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28306578 ACATATGCTC
28306588 TTTTTTTCTT
1 TTTTTTTCTT
*
28306598 TTTTTTT-TC
1 TTTTTTTCTT
28306607 TTTTTTTCTT
1 TTTTTTTCTT
28306617 TTTTCTTTC
1 TTTT-TTTC
28306626 AAGAACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 12 0.50
11 4 0.17
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:28307906 original size:3 final size:3
Alignment explanation
Indices: 28307898--28307922 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28307888 CTCTGTGGGA
28307898 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
28307923 TAGGATCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:28310621 original size:48 final size:48
Alignment explanation
Indices: 28310565--28310705 Score: 282
Period size: 48 Copynumber: 2.9 Consensus size: 48
28310555 AAAATATTTT
28310565 CAAAAAGAGACATCTAATTTTAAATATTTACAAAAACAACAACCATTA
1 CAAAAAGAGACATCTAATTTTAAATATTTACAAAAACAACAACCATTA
28310613 CAAAAAGAGACATCTAATTTTAAATATTTACAAAAACAACAACCATTA
1 CAAAAAGAGACATCTAATTTTAAATATTTACAAAAACAACAACCATTA
28310661 CAAAAAGAGACATCTAATTTTAAATATTTACAAAAACAACAACCA
1 CAAAAAGAGACATCTAATTTTAAATATTTACAAAAACAACAACCA
28310706 AGTCTTGAAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 93 1.00
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.24
Consensus pattern (48 bp):
CAAAAAGAGACATCTAATTTTAAATATTTACAAAAACAACAACCATTA
Found at i:28312008 original size:13 final size:13
Alignment explanation
Indices: 28311990--28312019 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
28311980 GCCGCAGTAC
28311990 GTGTACCTTTGAA
1 GTGTACCTTTGAA
28312003 GTGTACCTTTGAA
1 GTGTACCTTTGAA
28312016 GTGT
1 GTGT
28312020 CCCCCACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (13 bp):
GTGTACCTTTGAA
Found at i:28313902 original size:15 final size:16
Alignment explanation
Indices: 28313872--28313905 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28313862 TAATATGGAA
*
28313872 AATGGGAGTTTGTTTT
1 AATGGGAGTTTATTTT
28313888 AATGGG-GTTTATTTT
1 AATGGGAGTTTATTTT
28313903 AAT
1 AAT
28313906 ATTGAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (16 bp):
AATGGGAGTTTATTTT
Found at i:28320479 original size:347 final size:346
Alignment explanation
Indices: 28319838--28320531 Score: 1379
Period size: 347 Copynumber: 2.0 Consensus size: 346
28319828 TAATTATATA
28319838 TTAAAATATAAACTATTTAATATATTGTTAGTGAAAAATTTTAATTCCATAAATAAATTTCTATT
1 TTAAAATATAAACTATTTAATATATTGTTAGTGAAAAATTTTAATTCCATAAATAAATTTCTATT
28319903 ATTACCACCTATTTTAAGGGTTAATATTTGGTACATATAATTTTTTTTATTTTATAAGTAATTTT
66 ATTACCACCTATTTTAAGGGTTAATATTTGGTACATATAATTTTTTTTATTTTATAAGTAATTTT
28319968 TAAAAATTACCTTGCGTTTTTTCAAAATATTTTACTATATTATTATAAGATACTTAAAATCTCCA
131 TAAAAATTACCTTGCGTTTTTTCAAAATATTTTACTATATTATTATAAGATACTTAAAATCTCCA
28320033 TTAACAATGTACCAAATATTATATTTTTTAATACATAAATTTTTATTTTTTATTACGAATAAAAC
196 TTAACAATGTACCAAATATTATATTTTTTAATACATAAATTTTTATTTTTTATTACGAATAAAAC
28320098 CCAAACCTTTTTTTTAGAGGACAACGAGTAGTGATGAGATTGAAATTGATGGGGAATAGCAACTA
261 CCAAACCTTTTTTTTAGAGGACAACGAGTAGTGATGAGATTGAAATTGATGGGGAATAGCAACTA
28320163 GTCAACTTCGTTTTATTACGC
326 GTCAACTTCGTTTTATTACGC
28320184 TTAAAATTATAAACTATTTAATATATTGTTAGTGAAAAATTTTAATTCCATAAATAAATTTCTAT
1 TTAAAA-TATAAACTATTTAATATATTGTTAGTGAAAAATTTTAATTCCATAAATAAATTTCTAT
28320249 TATTACCACCTATTTTAAGGGTTAATATTTGGTACATATAATTTTTTTTATTTTATAAGTAATTT
65 TATTACCACCTATTTTAAGGGTTAATATTTGGTACATATAATTTTTTTTATTTTATAAGTAATTT
28320314 TTAAAAATTACCTTGCGTTTTTTCAAAATATTTTACTATATTATTATAAGATACTTAAAATCTCC
130 TTAAAAATTACCTTGCGTTTTTTCAAAATATTTTACTATATTATTATAAGATACTTAAAATCTCC
28320379 ATTAACAATGTACCAAATATTATATTTTTTAATACATAAATTTTTATTTTTTATTACGAATAAAA
195 ATTAACAATGTACCAAATATTATATTTTTTAATACATAAATTTTTATTTTTTATTACGAATAAAA
28320444 CCCAAACCTTTTTTTTAGAGGACAACGAGTAGTGATGAGATTGAAATTGATGGGGAATAGCAACT
260 CCCAAACCTTTTTTTTAGAGGACAACGAGTAGTGATGAGATTGAAATTGATGGGGAATAGCAACT
28320509 AGTCAACTTCGTTTTATTACGC
325 AGTCAACTTCGTTTTATTACGC
28320531 T
1 T
28320532 ACCAGCTTAG
Statistics
Matches: 347, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
346 6 0.02
347 341 0.98
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (346 bp):
TTAAAATATAAACTATTTAATATATTGTTAGTGAAAAATTTTAATTCCATAAATAAATTTCTATT
ATTACCACCTATTTTAAGGGTTAATATTTGGTACATATAATTTTTTTTATTTTATAAGTAATTTT
TAAAAATTACCTTGCGTTTTTTCAAAATATTTTACTATATTATTATAAGATACTTAAAATCTCCA
TTAACAATGTACCAAATATTATATTTTTTAATACATAAATTTTTATTTTTTATTACGAATAAAAC
CCAAACCTTTTTTTTAGAGGACAACGAGTAGTGATGAGATTGAAATTGATGGGGAATAGCAACTA
GTCAACTTCGTTTTATTACGC
Found at i:28321367 original size:17 final size:17
Alignment explanation
Indices: 28321341--28321391 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
28321331 ATTTTTTTTA
28321341 TTTAAATAAATAATTAT
1 TTTAAATAAATAATTAT
*
28321358 TTTTAATAAA-AATAATAT
1 TTTAAATAAATAAT--TAT
*
28321376 TTTAAATAAGTAATTA
1 TTTAAATAAATAATTA
28321392 ATCTTTAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 11 0.39
19 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATAAATAATTAT
Found at i:28321376 original size:18 final size:19
Alignment explanation
Indices: 28321348--28321384 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28321338 TTATTTAAAT
*
28321348 AAATAATTATTTTTAATAA
1 AAATAATTATTTTAAATAA
28321367 AAATAA-TATTTTAAATAA
1 AAATAATTATTTTAAATAA
28321385 GTAATTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATTATTTTAAATAA
Found at i:28321785 original size:27 final size:27
Alignment explanation
Indices: 28321748--28321800 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28321738 GTAATGGCTA
* * *
28321748 AATAATCATATAAAATTGTTTTAAATT
1 AATAATAATATAAAATTCTGTTAAATT
28321775 AATAATAATATAAAATTCTGTTAAAT
1 AATAATAATATAAAATTCTGTTAAAT
28321801 AATTATATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
AATAATAATATAAAATTCTGTTAAATT
Found at i:28321808 original size:23 final size:23
Alignment explanation
Indices: 28321746--28321809 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 23
28321736 TAGTAATGGC
* * *
28321746 TAAATAATCATATAAAATTGTTT
1 TAAATAATTATATAAAATTCTGT
28321769 TAAATTAATAATAATATAAAATTCTGT
1 TAAA-TAAT--T-ATATAAAATTCTGT
28321796 TAAATAATTATATA
1 TAAATAATTATATA
28321810 GTTATATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
23 9 0.26
24 5 0.15
26 4 0.12
27 16 0.47
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAATAATTATATAAAATTCTGT
Found at i:28325327 original size:18 final size:19
Alignment explanation
Indices: 28325299--28325334 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28325289 AAAAAATTAT
28325299 ATACTTTTTTTTTCAATTG
1 ATACTTTTTTTTTCAATTG
28325318 ATAC-TTTTTTTTCAATT
1 ATACTTTTTTTTTCAATT
28325335 TTCAGTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.64
Consensus pattern (19 bp):
ATACTTTTTTTTTCAATTG
Found at i:28330730 original size:21 final size:19
Alignment explanation
Indices: 28330706--28330753 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
28330696 CTTTTTCTGT
28330706 TTATAGAAAATTATAAAAAAA
1 TTATAGAAAA-TA-AAAAAAA
*
28330727 TTATATTAAAATAAAAAAAA
1 TTATA-GAAAATAAAAAAAA
28330747 TTATAGA
1 TTATAGA
28330754 CTAGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 7 0.29
22 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
TTATAGAAAATAAAAAAAA
Found at i:28338547 original size:2 final size:2
Alignment explanation
Indices: 28338542--28338569 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28338532 AAGTAATATA
28338542 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28338570 ATAGACATAG
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28351437 original size:19 final size:19
Alignment explanation
Indices: 28351415--28351476 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
28351405 ATTTTTGAAT
*
28351415 TATTGAATGATTTTAGCTC
1 TATTGAATGATTTTCGCTC
* *
28351434 TATTTGCAT-TTGTTTCGCTC
1 TA-TTGAATGAT-TTTCGCTC
28351454 TATTGAATGATTTTCGCTC
1 TATTGAATGATTTTCGCTC
28351473 TATT
1 TATT
28351477 TTCCTTCTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (19 bp):
TATTGAATGATTTTCGCTC
Found at i:28351897 original size:17 final size:17
Alignment explanation
Indices: 28351875--28351927 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
28351865 ATTCCCAAAG
28351875 TAATAATGTAATATTAA
1 TAATAATGTAATATTAA
* *
28351892 TAATAATATAATATTAG
1 TAATAATGTAATATTAA
*
28351909 TAATAACGTAATATTAA
1 TAATAATGTAATATTAA
28351926 TA
1 TA
28351928 GAGAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (17 bp):
TAATAATGTAATATTAA
Found at i:28352308 original size:75 final size:75
Alignment explanation
Indices: 28352223--28352365 Score: 259
Period size: 75 Copynumber: 1.9 Consensus size: 75
28352213 CTTCAATTAA
* *
28352223 TTAATTTATGCTGTTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
1 TTAATTTATGCTATTGCACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
28352288 TGTTTTTTTT
66 TGTTTTTTTT
*
28352298 TTAATTTATGCTATTGCACTATTATATTAATTTAGGCTTCAATTAATTAACTTTAAAGTTTAAAC
1 TTAATTTATGCTATTGCACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
28352363 TGT
66 TGT
28352366 AGTTTAACAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (75 bp):
TTAATTTATGCTATTGCACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAC
TGTTTTTTTT
Found at i:28352429 original size:96 final size:90
Alignment explanation
Indices: 28352290--28352583 Score: 439
Period size: 90 Copynumber: 3.2 Consensus size: 90
28352280 GTTTAAACTG
* *
28352290 TTTTTTT-TTTAATTTATGCTATTGCACTATTATATTAATTTAGGCTTCAATTAATTAACTTTAA
1 TTTTTTTGTTTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAA
28352354 AGTTTAAACTGTAGTTTAACATACT
66 AGTTTAAACTGTAGTTTAACATACT
28352379 TTTTTTTGTTTAATTTATGCTGTTGTACTTGTACTATTATATTAATTTAGGCTTCAATTAACTAA
1 TTTTTTTGTTTAATTTATGC-----TA-TTGTACTATTATATTAATTTAGGCTTCAATTAACTAA
* *
28352444 CTTTAAAGTTTAAAC-GATAGCTTAACAGACT
60 CTTTAAAGTTTAAACTG-TAGTTTAACATACT
* * *
28352475 TTTTTTTGTTTAATTTATGCTATTTTACAATAATATTAATTTAGGCTTCAATTAACTAACTTTAA
1 TTTTTTTGTTTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAA
*
28352540 AGTTTAAAATGTAGTTTAACATACT
66 AGTTTAAACTGTAGTTTAACATACT
28352565 TTTTTTTGTTTAATTTATG
1 TTTTTTTGTTTAATTTATG
28352584 AGTGATCCAA
Statistics
Matches: 186, Mismatches: 10, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
89 7 0.04
90 91 0.49
91 3 0.02
95 3 0.02
96 82 0.44
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (90 bp):
TTTTTTTGTTTAATTTATGCTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAA
AGTTTAAACTGTAGTTTAACATACT
Found at i:28355151 original size:19 final size:19
Alignment explanation
Indices: 28355127--28355175 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
28355117 GTATTATTTT
28355127 TGTTGTTTATTTGGAATGA
1 TGTTGTTTATTTGGAATGA
28355146 TGTTGTTTATTTGGAATGA
1 TGTTGTTTATTTGGAATGA
*
28355165 TGTTTTTTATT
1 TGTTGTTTATT
28355176 ATAACCGTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.22, T:0.59
Consensus pattern (19 bp):
TGTTGTTTATTTGGAATGA
Found at i:28357687 original size:6 final size:6
Alignment explanation
Indices: 28357678--28357730 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
28357668 CACACACACG
28357678 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
28357726 TATAC
1 TATAC
28357731 CAACTAAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TATACA
Found at i:28363721 original size:23 final size:23
Alignment explanation
Indices: 28363685--28363740 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
28363675 CAGCAGCTGA
28363685 AAAGCC-AGAAGACAGAACAATC
1 AAAGCCTAGAAGACAGAACAATC
28363707 AAAGCCTAGAAGACAGAACAATC
1 AAAGCCTAGAAGACAGAACAATC
28363730 AAAGCCTAGAA
1 AAAGCCTAGAA
28363741 ACTACCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.18
23 27 0.82
ACGTcount: A:0.54, C:0.21, G:0.18, T:0.07
Consensus pattern (23 bp):
AAAGCCTAGAAGACAGAACAATC
Found at i:28365574 original size:31 final size:29
Alignment explanation
Indices: 28365505--28365580 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
28365495 TTATCTCAAC
28365505 TTATATTTTAGTCATTTATGTTTAAAATG
1 TTATATTTTAGTCATTTATGTTTAAAATG
**
28365534 TTATATTTTAGTCATTTAT-TTTATCATG
1 TTATATTTTAGTCATTTATGTTTAAAATG
28365562 TTGTAATATTTTAGTCATT
1 -T-T-ATATTTTAGTCATT
28365581 AAGCCATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 7 0.17
29 20 0.48
30 1 0.02
31 14 0.33
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (29 bp):
TTATATTTTAGTCATTTATGTTTAAAATG
Found at i:28367003 original size:2 final size:2
Alignment explanation
Indices: 28366996--28367021 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28366986 CAAGATTAGA
28366996 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28367022 TTTTTAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28367964 original size:2 final size:2
Alignment explanation
Indices: 28367957--28367982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28367947 CAAGATTAGA
28367957 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28367983 TTTTTAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28368815 original size:961 final size:962
Alignment explanation
Indices: 28366954--28368878 Score: 3843
Period size: 961 Copynumber: 2.0 Consensus size: 962
28366944 TATTATCTTC
28366954 AATAACTTCATGTTCCTTTCGCATCATGACAACAAGATTAGAATATATATATATATATATATATA
1 AATAACTTCATGTTCCTTTCGCATCATGACAACAAGATTAGAATATATATATATATATATATATA
28367019 TATTTTTTAGAATCATTTGATTTAGGTTAGAACCCTAGCATTTGACTTATTGATTCAGGGTGTTC
66 TATTTTTTAGAATCATTTGATTTAGGTTAGAACCCTAGCATTTGACTTATTGATTCAGGGTGTTC
28367084 AATATATCTTTAAGGTCAAGCCGTGCATGTGTAGTAGTTTAGATGGGTGTGGTAGCTGCTATGTT
131 AATATATCTTTAAGGTCAAGCCGTGCATGTGTAGTAGTTTAGATGGGTGTGGTAGCTGCTATGTT
28367149 ATCTTTTAAATATCCAATCTTTAAAGTGGTTCTGTAACAGTTTGATTTTTCAGTGGTGTTAGAAA
196 ATCTTTTAAATATCCAATCTTTAAAGTGGTTCTGTAACAGTTTGATTTTTCAGTGGTGTTAGAAA
28367214 TAGTGGTTCGGGATCACCAAATTCGGTGAGTAAGATATTTATGAGTCAAATATGGTTTTAAAAAG
261 TAGTGGTTCGGGATCACCAAATTCGGTGAGTAAGATATTTATGAGTCAAATATGGTTTTAAAAAG
28367279 GTTTTTGAATTAGTAATTTGTGTTTTATAATGATTTATTAGATCAAGTGGTTTTAGAAAGTGAGC
326 GTTTTTGAATTAGTAATTTGTGTTTTATAATGATTTATTAGATCAAGTGGTTTTAGAAAGTGAGC
28367344 TATCGAGACCTCGTTTCTATAAACCGAGCTGTAAATATTTATAAAAATATTTACGGAGTGTCATT
391 TATCGAGACCTCGTTTCTATAAACCGAGCTGTAAATATTTATAAAAATATTTACGGAGTGTCATT
28367409 AAGGTAGTATTAAAGTTTCGTTGAAAAATTTTTAATATTTCAATAGTTAATTAATTAAAAAGCAC
456 AAGGTAGTATTAAAGTTTCGTTGAAAAATTTTTAATATTTCAATAGTTAATTAATTAAAAAGCAC
28367474 TAAATTGAAAAAGATGCAAAACTTGCTAACAATAGAATTTAAGTGATTAAATGGCTTGATAAATA
521 TAAATTGAAAAAGATGCAAAACTTGCTAACAATAGAATTTAAGTGATTAAATGGCTTGATAAATA
28367539 AATGAGGGAGGACTTAAGAAGCAATTAAACCTAACTTAAAAGGATGAGGCGGCATAAGAGAAAAA
586 AATGAGGGAGGACTTAAGAAGCAATTAAACCTAACTTAAAAGGATGAGGCGGCATAAGAGAAAAA
28367604 AATAATAAAATAAAGCCTTTAATGGCAAAATTGTATTTTTTATGAAATTAAATAAAACAAATTGA
651 AATAATAAAATAAAGCCTTTAATGGCAAAATTGTATTTTTTATGAAATTAAATAAAACAAATTGA
28367669 AATTGAAAAGCTTTTTATGCATTTCTTTTACAATATTCTGCCAAAAATCGACATAGGAGAAGAGC
716 AATTGAAAAGCTTTTTATGCATTTCTTTTACAATATTCTGCCAAAAATCGACATAGGAGAAGAGC
28367734 TTAAGCTGGTTTTTTTTTTTTTATATTTTTGCTTCAAGTGAATTCAATTCTTACCCGTTTCTTGT
781 TTAAGCTGGTTTTTTTTTTTTTATATTTTTGCTTCAAGTGAATTCAATTCTTACCCGTTTCTTGT
28367799 AATTTTTATGTTTTTGAGATTGTTACAATTAGGTTCAACTAAATATTACCCTAGTTTTTGATTTT
846 AATTTTTATGTTTTTGAGATTGTTACAATTAGGTTCAACTAAATATTACCCTAGTTTTTGATTTT
28367864 ATTAAAAAATTTGGAAGTTATCATTGATGAATATTAGATG-TTTTGATGAAT
911 ATTAAAAAATTTGGAAGTTATCATTGATGAATATTAGATGTTTTTGATGAAT
28367915 AATAACTTCATGTTCCTTTCGCATCATGACAACAAGATTAGAATATATATATATATATATATATA
1 AATAACTTCATGTTCCTTTCGCATCATGACAACAAGATTAGAATATATATATATATATATATATA
28367980 TATTTTTTAGAATCATTTGATTTAGGTTAGAACCCTAGCATTTGACTTATTGATTCAGGGTGTTC
66 TATTTTTTAGAATCATTTGATTTAGGTTAGAACCCTAGCATTTGACTTATTGATTCAGGGTGTTC
28368045 AATATATCTTTAAGGTCAAGCCGTGCATGTGTAGTAGTTTAGATGGGTGTGGTAGCTGCTATGTT
131 AATATATCTTTAAGGTCAAGCCGTGCATGTGTAGTAGTTTAGATGGGTGTGGTAGCTGCTATGTT
28368110 ATCTTTTAAATATCCAATCTTTAAAGTGGTTCTGTAACAGTTTGATTTTTCAGTGGTGTTAGAAA
196 ATCTTTTAAATATCCAATCTTTAAAGTGGTTCTGTAACAGTTTGATTTTTCAGTGGTGTTAGAAA
28368175 TAGTGGTTCGGGATCACCAAATTCGGTGAGTAAGATATTTATGAGTCAAATATGGTTTTAAAAAG
261 TAGTGGTTCGGGATCACCAAATTCGGTGAGTAAGATATTTATGAGTCAAATATGGTTTTAAAAAG
28368240 GTTTTTGAATTAGTAATTTGTGTTTTATAATGATTTATTAGATCAAGTGGTTTTAGAAAGTGAGC
326 GTTTTTGAATTAGTAATTTGTGTTTTATAATGATTTATTAGATCAAGTGGTTTTAGAAAGTGAGC
28368305 TATCGAGACCTCGTTTCTATAAACCGAGCTGTAAATATTTATAAAAATATTTACGGAGTGTCATT
391 TATCGAGACCTCGTTTCTATAAACCGAGCTGTAAATATTTATAAAAATATTTACGGAGTGTCATT
28368370 AAGGTAGTATTAAAGTTTCGTTGAAAAATTTTTAATATTTCAATAGTTAATTAATTAAAAAGCAC
456 AAGGTAGTATTAAAGTTTCGTTGAAAAATTTTTAATATTTCAATAGTTAATTAATTAAAAAGCAC
28368435 TAAATTGAAAAAGATGCAAAACTTGCTAACAATAGAATTTAAGTGATTAAATGGCTTGATAAATA
521 TAAATTGAAAAAGATGCAAAACTTGCTAACAATAGAATTTAAGTGATTAAATGGCTTGATAAATA
28368500 AATGAGGGAGGACTTAAGAAGCAATTAAACCTAACTTAAAAGGATGAGGCGGCATAAGAGAAAAA
586 AATGAGGGAGGACTTAAGAAGCAATTAAACCTAACTTAAAAGGATGAGGCGGCATAAGAGAAAAA
28368565 AATAATAAAATAAAGCCTTTAATGGCAAAATTGTATTTTTTATGAAATTAAATAAAACAAATTGA
651 AATAATAAAATAAAGCCTTTAATGGCAAAATTGTATTTTTTATGAAATTAAATAAAACAAATTGA
28368630 AATTGAAAAGCTTTTTATGCATTTCTTTTACAATATTCTGCCAAAAATCGACATAGGAGAAGAGC
716 AATTGAAAAGCTTTTTATGCATTTCTTTTACAATATTCTGCCAAAAATCGACATAGGAGAAGAGC
28368695 TTAAGCTGGTTTTTTTTTTTTTATATTTTTGCTTCAAGTGAATTCAATTCTTACCCGTTTCTTGT
781 TTAAGCTGGTTTTTTTTTTTTTATATTTTTGCTTCAAGTGAATTCAATTCTTACCCGTTTCTTGT
28368760 AATTTTTATGTTTTTGAGATTGTTACAATTAGGTTCAACTAAATATTACCCTAGTTTTTGATTTT
846 AATTTTTATGTTTTTGAGATTGTTACAATTAGGTTCAACTAAATATTACCCTAGTTTTTGATTTT
28368825 ATTAAAAAATTTGGAAGTTATCATTGATGAATATTAGATGTTTTTGATGAAT
911 ATTAAAAAATTTGGAAGTTATCATTGATGAATATTAGATGTTTTTGATGAAT
28368877 AA
1 AA
28368879 CATGGATTTA
Statistics
Matches: 963, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
961 950 0.99
962 13 0.01
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (962 bp):
AATAACTTCATGTTCCTTTCGCATCATGACAACAAGATTAGAATATATATATATATATATATATA
TATTTTTTAGAATCATTTGATTTAGGTTAGAACCCTAGCATTTGACTTATTGATTCAGGGTGTTC
AATATATCTTTAAGGTCAAGCCGTGCATGTGTAGTAGTTTAGATGGGTGTGGTAGCTGCTATGTT
ATCTTTTAAATATCCAATCTTTAAAGTGGTTCTGTAACAGTTTGATTTTTCAGTGGTGTTAGAAA
TAGTGGTTCGGGATCACCAAATTCGGTGAGTAAGATATTTATGAGTCAAATATGGTTTTAAAAAG
GTTTTTGAATTAGTAATTTGTGTTTTATAATGATTTATTAGATCAAGTGGTTTTAGAAAGTGAGC
TATCGAGACCTCGTTTCTATAAACCGAGCTGTAAATATTTATAAAAATATTTACGGAGTGTCATT
AAGGTAGTATTAAAGTTTCGTTGAAAAATTTTTAATATTTCAATAGTTAATTAATTAAAAAGCAC
TAAATTGAAAAAGATGCAAAACTTGCTAACAATAGAATTTAAGTGATTAAATGGCTTGATAAATA
AATGAGGGAGGACTTAAGAAGCAATTAAACCTAACTTAAAAGGATGAGGCGGCATAAGAGAAAAA
AATAATAAAATAAAGCCTTTAATGGCAAAATTGTATTTTTTATGAAATTAAATAAAACAAATTGA
AATTGAAAAGCTTTTTATGCATTTCTTTTACAATATTCTGCCAAAAATCGACATAGGAGAAGAGC
TTAAGCTGGTTTTTTTTTTTTTATATTTTTGCTTCAAGTGAATTCAATTCTTACCCGTTTCTTGT
AATTTTTATGTTTTTGAGATTGTTACAATTAGGTTCAACTAAATATTACCCTAGTTTTTGATTTT
ATTAAAAAATTTGGAAGTTATCATTGATGAATATTAGATGTTTTTGATGAAT
Found at i:28375383 original size:2 final size:2
Alignment explanation
Indices: 28375376--28375402 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28375366 CAGACCTTTA
28375376 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28375403 GACAACTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28375923 original size:3 final size:3
Alignment explanation
Indices: 28375917--28375947 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28375907 TTTGCTGCTG
28375917 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
28375948 ATATTCTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:28376856 original size:2 final size:2
Alignment explanation
Indices: 28376849--28376874 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28376839 ATTTGAGGTT
28376849 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28376875 ATGAATATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28378970 original size:43 final size:43
Alignment explanation
Indices: 28378910--28378993 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
28378900 GTTTAACAGT
*
28378910 AAAAATCAGGCGCATACAGTCTGAAAATGAATGGAAGTCCTCA
1 AAAAATCAGGCGCATACAGTCTGAAAATGAATGAAAGTCCTCA
28378953 AAAAATCAGGCGCATACAGTCTGAAAATGAATGAAAGTCCT
1 AAAAATCAGGCGCATACAGTCTGAAAATGAATGAAAGTCCT
28378994 ACCCTAGTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (43 bp):
AAAAATCAGGCGCATACAGTCTGAAAATGAATGAAAGTCCTCA
Found at i:28385389 original size:16 final size:15
Alignment explanation
Indices: 28385361--28385399 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
28385351 TTTTTAATGT
* *
28385361 TTATATAATATTATA
1 TTATATAAAATTAAA
28385376 TTATTATAAAATTAAA
1 TTA-TATAAAATTAAA
28385392 TTATATAA
1 TTATATAA
28385400 TATACCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATATAAAATTAAA
Found at i:28390191 original size:25 final size:28
Alignment explanation
Indices: 28390127--28390194 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
28390117 AAGGTTCAAG
*
28390127 AGAGCC-A-ATATCGAGAAGCTCATGAA
1 AGAGCCTATATATCGAGAAGCTCACGAA
*
28390153 AGAGCCTTTA-ATCGAGAAGCTC-CG-A
1 AGAGCCTATATATCGAGAAGCTCACGAA
28390178 AGAG-CTATATATCGAGA
1 AGAGCCTATATATCGAGA
28390195 CACTCATAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 4 0.11
25 12 0.33
26 7 0.19
27 12 0.33
28 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (28 bp):
AGAGCCTATATATCGAGAAGCTCACGAA
Found at i:28391254 original size:30 final size:31
Alignment explanation
Indices: 28391192--28391255 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
28391182 TTATTTAATT
*
28391192 AATTTATCATCTTTTATTATTTCATCTTTCC
1 AATTTATCATCTTTTATTATTTAATCTTTCC
28391223 AATTTAGTCAT-TTTCT-TTATTTAAT-TTTCC
1 AATTTA-TCATCTTT-TATTATTTAATCTTTCC
28391253 AAT
1 AAT
28391256 GATGAATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 8 0.27
31 17 0.57
32 5 0.17
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.58
Consensus pattern (31 bp):
AATTTATCATCTTTTATTATTTAATCTTTCC
Found at i:28391582 original size:6 final size:6
Alignment explanation
Indices: 28391571--28391641 Score: 81
Period size: 6 Copynumber: 11.8 Consensus size: 6
28391561 CACATATTAT
* * * * *
28391571 TACACA TACACA CACACA CACACG TACACG TACACGA -ACACG TACACA
1 TACACA TACACA TACACA TACACA TACACA TACAC-A TACACA TACACA
28391619 TACACA TACACA TACACA TACAC
1 TACACA TACACA TACACA TACAC
28391642 TTTTACTTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.45, C:0.37, G:0.06, T:0.13
Consensus pattern (6 bp):
TACACA
Found at i:28393377 original size:20 final size:19
Alignment explanation
Indices: 28393351--28393421 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
28393341 AGACACATTA
28393351 AAAATATAAAAATAGAAAT
1 AAAATATAAAAATAGAAAT
28393370 AAATATATAAAAATTCAGAAA-
1 AAA-ATATAAAAA-T-AGAAAT
* *
28393391 AAAATATAAAATCTAGAAAA
1 AAAATATAAAA-ATAGAAAT
28393411 AAACATATAAA
1 AAA-ATATAAA
28393422 TTATAAAACT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
19 8 0.18
20 21 0.47
21 11 0.24
22 5 0.11
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAATATAAAAATAGAAAT
Found at i:28393412 original size:18 final size:18
Alignment explanation
Indices: 28393350--28393429 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 18
28393340 TAGACACATT
*
28393350 AAAAATATAAAAATAGAA
1 AAAAATATAAAATTAGAA
28393368 ATAAATATATAAAAATTCAGAA
1 A-AAA-ATAT-AAAATT-AGAA
28393390 AAAAATATAAAATCTAGAA
1 AAAAATATAAAAT-TAGAA
* *
28393409 AAAAACATATAAATTATAA
1 AAAAATATA-AAATTAGAA
28393428 AA
1 AA
28393430 CTAAAATTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
18 1 0.02
19 26 0.49
20 13 0.25
21 8 0.15
22 5 0.09
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAAATATAAAATTAGAA
Found at i:28399900 original size:23 final size:25
Alignment explanation
Indices: 28399873--28399926 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
28399863 TTTGAAGATT
*
28399873 ATATTTAGCAAC-T-AAATATTTTG
1 ATATTTAGCAACATGAAATATTGTG
28399896 ATA-TTA-CAACATGAAATATTGTG
1 ATATTTAGCAACATGAAATATTGTG
*
28399919 AAATTTAG
1 ATATTTAG
28399927 TTGTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.16
22 4 0.16
23 14 0.56
24 3 0.12
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (25 bp):
ATATTTAGCAACATGAAATATTGTG
Found at i:28419300 original size:25 final size:26
Alignment explanation
Indices: 28419247--28419309 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
28419237 ATTTGTACAT
28419247 ATTATAAAAAATGTATAAACATATGA
1 ATTATAAAAAATGTATAAACATATGA
*
28419273 ATTATAAAACATG-A-AAACATAAAT-A
1 ATTATAAAAAATGTATAAACAT--ATGA
28419298 ATTATAAAAAAT
1 ATTATAAAAAAT
28419310 ATGAATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 6 0.18
25 13 0.39
26 14 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
ATTATAAAAAATGTATAAACATATGA
Found at i:28419322 original size:2 final size:2
Alignment explanation
Indices: 28419317--28419354 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
28419307 AATATGAATG
*
28419317 TA TA TA -A TA TA TA TA TA TA TA TA AA CTA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
28419355 AAATATGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:28419335 original size:15 final size:15
Alignment explanation
Indices: 28419317--28419360 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
28419307 AATATGAATG
28419317 TATATAATATATATATA
1 TATATAA-A-ATATATA
*
28419334 TATATAAACTATATA
1 TATATAAAATATATA
28419349 TATATAAAATAT
1 TATATAAAATAT
28419361 GGTAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 17 0.68
16 1 0.04
17 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TATATAAAATATATA
Found at i:28419337 original size:17 final size:17
Alignment explanation
Indices: 28419317--28419360 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
28419307 AATATGAATG
28419317 TATATAATATATATATA
1 TATATAATATATATATA
28419334 TATATAA-ACTATATATA
1 TATATAATA-TATATATA
*
28419351 TATAAAATAT
1 TATATAATAT
28419361 GGTAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATAATATATATATA
Found at i:28419482 original size:12 final size:12
Alignment explanation
Indices: 28419467--28419526 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
28419457 ATATGTAAGT
28419467 ATAATAAATATA
1 ATAATAAATATA
* *
28419479 ATAATAATTGTA
1 ATAATAAATATA
*
28419491 ATAATAAAAATA
1 ATAATAAATATA
*
28419503 ATAATAACTATA
1 ATAATAAATATA
*
28419515 TTAATAAA-ATA
1 ATAATAAATATA
28419526 A
1 A
28419527 ACAAAAAAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 3 0.08
12 35 0.92
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
ATAATAAATATA
Found at i:28419503 original size:24 final size:24
Alignment explanation
Indices: 28419467--28419523 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
28419457 ATATGTAAGT
* * *
28419467 ATAATAAATATAATAATAATTGTA
1 ATAATAAAAATAATAATAACTATA
28419491 ATAATAAAAATAATAATAACTATA
1 ATAATAAAAATAATAATAACTATA
*
28419515 TTAATAAAA
1 ATAATAAAA
28419524 TAAACAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAATAAAAATAATAATAACTATA
Found at i:28420550 original size:13 final size:14
Alignment explanation
Indices: 28420524--28420557 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
28420514 TACAATTATA
28420524 TATAATTCTTAAAT
1 TATAATTCTTAAAT
28420538 TATAATT-TTAAAT
1 TATAATTCTTAAAT
*
28420551 TACAATT
1 TATAATT
28420558 ACACAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAATTCTTAAAT
Found at i:28424513 original size:27 final size:27
Alignment explanation
Indices: 28424447--28424573 Score: 157
Period size: 27 Copynumber: 4.7 Consensus size: 27
28424437 CTTGGGCTAA
* *
28424447 AAAAGTACTGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
28424474 AAAAATTACCGAAATACCCTCGAAGGGT
1 -AAAATTACCGAAATACCCTCGAAGGGT
*
28424502 AAAATTACCGAAATACCC-CCATAGGGT
1 AAAATTACCGAAATACCCTCGA-AGGGT
* * * *
28424529 AAAATGACCAAAATACCTTCGAATGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
*
28424556 AAAATGACCGAAATACCC
1 AAAATTACCGAAATACCC
28424574 CTATTGGGTA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.02
27 58 0.67
28 27 0.31
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (27 bp):
AAAATTACCGAAATACCCTCGAAGGGT
Found at i:28424557 original size:54 final size:54
Alignment explanation
Indices: 28424447--28424590 Score: 173
Period size: 54 Copynumber: 2.6 Consensus size: 54
28424437 CTTGGGCTAA
* * * * *
28424447 AAAAGTACTGAAATACCCTCGA-AGGGTAAAAATTACCGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCC-CCATAGGGT-AAAATGACCAAAATACCCTCGAAGGGT
* *
28424502 AAAATTACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCTTCGAATGGT
1 AAAATTACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCTCGAAGGGT
* * *
28424556 AAAATGACCGAAATACCCCTATTGGGTAAAATGAC
1 AAAATTACCGAAATACCCCCATAGGGTAAAATGAC
28424591 TGTTGTACCC
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 57 0.73
55 21 0.27
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.19
Consensus pattern (54 bp):
AAAATTACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCTCGAAGGGT
Found at i:28424583 original size:27 final size:27
Alignment explanation
Indices: 28424456--28424590 Score: 141
Period size: 27 Copynumber: 5.0 Consensus size: 27
28424446 AAAAAGTACT
*
28424456 GAAATACCCTCGA-AGGGTAAAAATTACC
1 GAAATACCC-CGATAGGGT-AAAATGACC
*
28424484 GAAATACCCTCGA-AGGGTAAAATTACC
1 GAAATACCC-CGATAGGGTAAAATGACC
*
28424511 GAAATACCCCCATAGGGTAAAATGACC
1 GAAATACCCCGATAGGGTAAAATGACC
* * *
28424538 AAAATACCTTCGA-ATGGTAAAATGACC
1 GAAATACC-CCGATAGGGTAAAATGACC
* *
28424565 GAAATACCCCTATTGGGTAAAATGAC
1 GAAATACCCCGATAGGGTAAAATGAC
28424591 TGTTGTACCC
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.04
27 69 0.74
28 20 0.22
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (27 bp):
GAAATACCCCGATAGGGTAAAATGACC
Found at i:28424845 original size:26 final size:26
Alignment explanation
Indices: 28424773--28424847 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
28424763 ATATACTGTC
* * * *
28424773 ACTGGCAGCTTTGATGCGTTACTGTT
1 ACTGGCAGCTTTGCTGCGATATTATT
* **
28424799 ATTGGCAGCTTTGCTATGATATTATT
1 ACTGGCAGCTTTGCTGCGATATTATT
28424825 ACTGGCAGCTTTGCTGCGATATT
1 ACTGGCAGCTTTGCTGCGATATT
28424848 GGTGTGTTGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (26 bp):
ACTGGCAGCTTTGCTGCGATATTATT
Found at i:28426288 original size:42 final size:42
Alignment explanation
Indices: 28426229--28426396 Score: 336
Period size: 42 Copynumber: 4.0 Consensus size: 42
28426219 GAAACAAGGA
28426229 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
1 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
28426271 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
1 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
28426313 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
1 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
28426355 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
1 ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
28426397 TAGTTAAATT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (42 bp):
ATAGGAAAAGTTGATACATTAACCTAGGAGTACATTTAGGTT
Done.