Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 15 of 199
Found at i:4990026 original size:123 final size:122
Alignment explanation
Indices: 4989860--4990150 Score: 327
Period size: 123 Copynumber: 2.4 Consensus size: 122
4989850 TAAATTATTT
* * * * * * *
4989860 TAAATCCCTGAGCATTAACGGCGCTTTTTAAAAAACACCGCTAAA-AATAGAGCATTCGCGGCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAACAATA-AACATTAGCAGCGC
* * * *
4989924 TTTATCAAAAACACCGCTAAAAGCCATGAGCATTAGCAGCGCTAT-CCCAAAAACGCCGC
65 TTCACCAAAAACACCGCT-AAAGCCATAAGCATTAGCAGCGCT-TCCCCAAAAACGCCAC
* * **
4989983 TAAAGCCCTAAGCATTAGCGGCGCTTTCCT-AAAAACGCTGCTAAAGCCCTAAACATTAGCAGCG
1 TAAAGCCCTGAGCATTAGCGGCGCTTT-CTAAAAAACGCCGCTAAA-CAATAAACATTAGCAGCG
* * * *
4990047 CTTCCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCCCAAAAACGCCAC
64 CTTCACCAAAAACACCGCTAAAGCCATAAGCATTAGCAGCGCTTCCCCAAAAACGCCAC
* *
4990106 TAAAGCCCTGAGCATTAGCGGCGCTTACTCAAAAACGCCGCTAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAA
4990151 GCCCCGAAAG
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
122 3 0.02
123 110 0.78
124 26 0.18
125 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.18
Consensus pattern (122 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAACAATAAACATTAGCAGCGCT
TCACCAAAAACACCGCTAAAGCCATAAGCATTAGCAGCGCTTCCCCAAAAACGCCAC
Found at i:5004086 original size:94 final size:94
Alignment explanation
Indices: 5003925--5004115 Score: 310
Period size: 94 Copynumber: 2.0 Consensus size: 94
5003915 CGCAATAAAC
* * **
5003925 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGTATAAATTGTATACACTAGAATACGGTCAT
1 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
*
5003990 GTTTAACGATAAATCAATTATGTTTAGCA
66 GTTTAACGATAAATCAACTATGTTTAGCA
*
5004019 CTTGTTACAATTATGCTTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
1 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
**
5004084 GTTTAACGATAAATCGGCTATGTTTAGCA
66 GTTTAACGATAAATCAACTATGTTTAGCA
5004113 CTT
1 CTT
5004116 AGTATGAAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 89 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (94 bp):
CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
GTTTAACGATAAATCAACTATGTTTAGCA
Found at i:5004155 original size:40 final size:42
Alignment explanation
Indices: 5004111--5004200 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 42
5004101 CTATGTTTAG
5004111 CACTTAGTATGAAATTT-GAGATAGCTTCGGCTA-AT-TATGA
1 CACTTAGTATGAAATTTGGA-ATAGCTTCGGCTATATATATGA
* ** * *
5004151 CACTTAGTGTGCGATTTGGAATAGCTTCGGTTATATATATGG
1 CACTTAGTATGAAATTTGGAATAGCTTCGGCTATATATATGA
5004193 CACTTAGT
1 CACTTAGT
5004201 GTGTGTGACT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 26 0.62
41 4 0.10
42 12 0.29
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (42 bp):
CACTTAGTATGAAATTTGGAATAGCTTCGGCTATATATATGA
Found at i:5004259 original size:41 final size:39
Alignment explanation
Indices: 5004131--5004268 Score: 111
Period size: 41 Copynumber: 3.4 Consensus size: 39
5004121 GAAATTTGAG
* *
5004131 ATAGCTTCGGCTAATTATGACACTTAGTGTGC-GATT-TGGA
1 ATAGCTTCGGCT-ATTAAGGCACTTAGTGTGCGGATTAT--A
* * * *
5004171 ATAGCTTCGGTTATATATATGGCACTTAGTGTGTGTGACTGA-G
1 ATAGCTTCGGCTAT-TA-A-GGCACTTAGTGTGCG-GA-TTATA
5004214 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGGGATTATA
1 ATAGCTTCGGCTAT-TAAGGCACTTAGTGTGC-GGATTATA
5004255 ATAGCTTCGGCTAT
1 ATAGCTTCGGCTAT
5004269 ACGATGGCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
39 2 0.03
40 15 0.19
41 29 0.37
42 14 0.18
43 15 0.19
44 2 0.03
45 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (39 bp):
ATAGCTTCGGCTATTAAGGCACTTAGTGTGCGGATTATA
Found at i:5004276 original size:83 final size:82
Alignment explanation
Indices: 5004127--5004285 Score: 198
Period size: 83 Copynumber: 1.9 Consensus size: 82
5004117 GTATGAAATT
* * *
5004127 TGAGATAGCTTCGGCTAATTATGACACTTAGTGTGCGATTTGGAATAGCTTCGGTTATATATATG
1 TGAGATAGCTTCGGCTAATTAAGACACTTAGTGTGCGATTT-GAATAGCTTCGGCTATATAGATG
*
5004192 GCACTTAGTGTGTGTGAC
65 GCAATTAGTGTGTGTGAC
* *
5004210 TGAGATAGCTTCGGCT-ATGTAAGGCACTTAGTGTGCGGGATTAT-AATAGCTTCGGCTATA-CG
1 TGAGATAGCTTCGGCTAAT-TAAGACACTTAGTGTGC--GATT-TGAATAGCTTCGGCTATATAG
5004272 ATGGCAATTAGTGT
62 ATGGCAATTAGTGT
5004286 ACAAAACATT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
82 2 0.03
83 44 0.67
84 15 0.23
85 4 0.06
86 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (82 bp):
TGAGATAGCTTCGGCTAATTAAGACACTTAGTGTGCGATTTGAATAGCTTCGGCTATATAGATGG
CAATTAGTGTGTGTGAC
Found at i:5004965 original size:46 final size:46
Alignment explanation
Indices: 5004912--5005022 Score: 159
Period size: 46 Copynumber: 2.4 Consensus size: 46
5004902 GTTGTTTTTA
** *
5004912 GATGTATAATGCTGTCCATTTTGAGCATATTGATGTTGTCCAATTT
1 GATGTATAATGCTGTCCATTTTGAGCATATAAATGCTGTCCAATTT
* *
5004958 GATGTATAATGCTGTCAATTTTGAGTATATAAATGCTGTCCAATTT
1 GATGTATAATGCTGTCCATTTTGAGCATATAAATGCTGTCCAATTT
*
5005004 GATGTATAAATGTTGTCCA
1 GATGTAT-AATGCTGTCCA
5005023 AAACAGAGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 48 0.84
47 9 0.16
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (46 bp):
GATGTATAATGCTGTCCATTTTGAGCATATAAATGCTGTCCAATTT
Found at i:5004997 original size:24 final size:22
Alignment explanation
Indices: 5004952--5005020 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
5004942 TGATGTTGTC
*
5004952 CAATTTGATGTAT-AATGCTGT
1 CAATTTGATATATAAATGCTGT
5004973 CAATTTTGAGTATATAAATGCTGT
1 CAA-TTTGA-TATATAAATGCTGT
* *
5004997 CCAATTTGATGTATAAATGTTGT
1 -CAATTTGATATATAAATGCTGT
5005020 C
1 C
5005021 CAAAACAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 3 0.07
22 6 0.15
23 16 0.39
24 13 0.32
25 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (22 bp):
CAATTTGATATATAAATGCTGT
Found at i:5005023 original size:23 final size:23
Alignment explanation
Indices: 5004912--5005023 Score: 106
Period size: 24 Copynumber: 4.9 Consensus size: 23
5004902 GTTGTTTTTA
*
5004912 GATGTAT-AATGCTGTCCATTTT
1 GATGTATAAATGCTGTCCAATTT
** *
5004934 GA-GCATATTGATGTTGTCCAATTT
1 GATG--TATAAATGCTGTCCAATTT
5004958 GATGTAT-AATGCTGT-CAATTTT
1 GATGTATAAATGCTGTCCAA-TTT
*
5004980 GAGTATATAAATGCTGTCCAATTT
1 GA-TGTATAAATGCTGTCCAATTT
*
5005004 GATGTATAAATGTTGTCCAA
1 GATGTATAAATGCTGTCCAA
5005024 AACAGAGTAG
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
21 4 0.05
22 13 0.18
23 26 0.35
24 27 0.36
25 4 0.05
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (23 bp):
GATGTATAAATGCTGTCCAATTT
Found at i:5005813 original size:13 final size:13
Alignment explanation
Indices: 5005792--5005840 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
5005782 ATGCAGGGGA
5005792 CACACGCCCAGGT
1 CACACGCCCAGGT
*
5005805 CATACGCCCAGGT
1 CACACGCCCAGGT
*
5005818 CACACACCCAGGT
1 CACACGCCCAGGT
5005831 CACACGCCCA
1 CACACGCCCA
5005841 TGTGCTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.27, C:0.47, G:0.18, T:0.08
Consensus pattern (13 bp):
CACACGCCCAGGT
Found at i:5007028 original size:26 final size:26
Alignment explanation
Indices: 5006999--5007054 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5006989 TCCTCTCTCA
5006999 AGCCATAT-AACAGGAAGCTCACAAAG
1 AGCCAT-TGAACAGGAAGCTCACAAAG
* * *
5007025 AGCCATTGATCGGGAAGCTCACAGAG
1 AGCCATTGAACAGGAAGCTCACAAAG
5007051 AGCC
1 AGCC
5007055 TATCAGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (26 bp):
AGCCATTGAACAGGAAGCTCACAAAG
Found at i:5009222 original size:21 final size:21
Alignment explanation
Indices: 5009198--5009243 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5009188 AAAATCTTAT
*
5009198 AATATA-ATTATTTAATTAATA
1 AATATATATTACTTAA-TAATA
*
5009219 AATATATTTTACTTAATAATA
1 AATATATATTACTTAATAATA
5009240 AATA
1 AATA
5009244 ATAGATATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATATATTACTTAATAATA
Found at i:5009285 original size:29 final size:27
Alignment explanation
Indices: 5009210--5009285 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 27
5009200 TATAATTATT
*
5009210 TAATTAATAAATATATTTTACTTAATAA
1 TAATTAATAAATATA-TTTACTTAAAAA
* *
5009238 TAAATAATAGATATCTATTTACTTAAAAA
1 TAATTAATA-A-ATATATTTACTTAAAAA
5009267 GTAATTAAATAAATATATT
1 -TAATT-AATAAATATATT
5009286 ACAAATGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 8 0.21
29 18 0.46
30 9 0.23
31 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (27 bp):
TAATTAATAAATATATTTACTTAAAAA
Found at i:5009924 original size:25 final size:25
Alignment explanation
Indices: 5009890--5009947 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
5009880 AGCTTCGGAT
5009890 AGCCATATATCGGGAAGTTCAAGCG
1 AGCCATATATCGGGAAGTTCAAGCG
*
5009915 AGCCATATATTGGGAAGTTCAAGCG
1 AGCCATATATCGGGAAGTTCAAGCG
*
5009940 AGTCATAT
1 AGCCATAT
5009948 CAAGACGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (25 bp):
AGCCATATATCGGGAAGTTCAAGCG
Found at i:5011044 original size:30 final size:30
Alignment explanation
Indices: 5010995--5011054 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5010985 TTTATTTATC
5010995 ATTTATCATCTTTTATTATTTCACTTTCCA
1 ATTTATCATCTTTTATTATTTCACTTTCCA
* * *
5011025 ATTTCATCAT-TTTTTTTATTTTATTTTCCA
1 ATTT-ATCATCTTTTATTATTTCACTTTCCA
5011055 TGGATGAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTATCATCTTTTATTATTTCACTTTCCA
Found at i:5015833 original size:28 final size:28
Alignment explanation
Indices: 5015783--5015846 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
5015773 GACTCACATT
5015783 CCCAAATC-TCAAATTAAAAAAAAAAAC
1 CCCAAATCTTCAAATTAAAAAAAAAAAC
* *
5015810 CCCAAATCTTTAAA-TAATAAAAAAAATC
1 CCCAAATCTTCAAATTAA-AAAAAAAAAC
5015838 CCCAAATCT
1 CCCAAATCT
5015847 CGTCTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.20
Consensus pattern (28 bp):
CCCAAATCTTCAAATTAAAAAAAAAAAC
Found at i:5022330 original size:31 final size:32
Alignment explanation
Indices: 5022252--5022330 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 32
5022242 GATTAAAAAA
5022252 GGGCCCGGCCTCGGGCACCACTTTTTTGGCCC
1 GGGCCCGGCCTCGGGCACCACTTTTTTGGCCC
*
5022284 GGGCCCAGCCTCGGGCACCACTTTTTTGGCCC
1 GGGCCCGGCCTCGGGCACCACTTTTTTGGCCC
5022316 GGGCCCGGCC-CGGGC
1 GGGCCCGGCCTCGGGC
5022331 TCAGCCCGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 5 0.11
32 40 0.89
ACGTcount: A:0.06, C:0.42, G:0.34, T:0.18
Consensus pattern (32 bp):
GGGCCCGGCCTCGGGCACCACTTTTTTGGCCC
Found at i:5022401 original size:9 final size:9
Alignment explanation
Indices: 5022387--5022418 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5022377 TAAAATACTT
5022387 TTTTTTAAA
1 TTTTTTAAA
5022396 TTTTTTAAA
1 TTTTTTAAA
*
5022405 GTTTTTAAA
1 TTTTTTAAA
5022414 TTTTT
1 TTTTT
5022419 AAAAAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:5022410 original size:39 final size:38
Alignment explanation
Indices: 5022357--5022480 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 38
5022347 AAATATTTTT
**
5022357 ATTTTTTATTTTTTTAATTTT-AAAATACTTTTTTTTAA
1 ATTTTTTAAATTTTTAATTTTAAAAATAC-TTTTTTTAA
5022395 ATTTTTTAAAGTTTTTAAATTTTTAAAAAATAC-TTTTTTAA
1 ATTTTTTAAA-TTTTT-AA-TTTT-AAAAATACTTTTTTTAA
* * *
5022436 ATTTTTTTAATTTTAAAATATTTCAAAATACTTTTTTT-A
1 ATTTTTTAAATTTT-TAAT-TTTAAAAATACTTTTTTTAA
5022475 ATTTTT
1 ATTTTT
5022481 GTTTTAATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
38 8 0.11
39 20 0.27
40 17 0.23
41 21 0.29
43 7 0.10
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (38 bp):
ATTTTTTAAATTTTTAATTTTAAAAATACTTTTTTTAA
Found at i:5022486 original size:42 final size:41
Alignment explanation
Indices: 5022373--5022498 Score: 139
Period size: 41 Copynumber: 3.0 Consensus size: 41
5022363 TATTTTTTTA
* * *
5022373 ATTTTAAAATACTTTTTTTTAAATTTTTTAAAGTTTTTAAAT
1 ATTTAAAAATAC-TTTTTTTAAATTTTTTTAAGTTTTAAAAT
*
5022415 TTTTAAAAAATAC-TTTTTTAAATTTTTTTAA-TTTTAAAAT
1 ATTT-AAAAATACTTTTTTTAAATTTTTTTAAGTTTTAAAAT
* * *
5022455 ATTTCAAAATACTTTTTTTAATTTTTGTTTTAATTTTTAAAAT
1 ATTTAAAAATACTTTTTTTAA-ATTT-TTTTAAGTTTTAAAAT
5022498 A
1 A
5022499 AATTTTTGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
39 7 0.10
40 19 0.26
41 20 0.28
42 9 0.12
43 17 0.24
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (41 bp):
ATTTAAAAATACTTTTTTTAAATTTTTTTAAGTTTTAAAAT
Found at i:5025249 original size:20 final size:20
Alignment explanation
Indices: 5025224--5025321 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 20
5025214 ATTATAAAAA
*
5025224 ATAAAAATTAATAAAAAGTT
1 ATAAAAATTAATAAAAATTT
* *
5025244 AT-AAAATTTATAAAATTTT
1 ATAAAAATTAATAAAAATTT
* * **
5025263 AATAAAAAATATTTTAAATTT
1 -ATAAAAATTAATAAAAATTT
* *
5025284 ATTAAAAATTAGAAAAAAAATT
1 A-TAAAAATTA-ATAAAAATTT
*
5025306 AT-AAAATTCATAAAAA
1 ATAAAAATTAATAAAAA
5025322 ATATAAAATG
Statistics
Matches: 57, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
19 20 0.35
20 11 0.19
21 20 0.35
22 6 0.11
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAAATTAATAAAAATTT
Found at i:5025267 original size:30 final size:29
Alignment explanation
Indices: 5025209--5025329 Score: 113
Period size: 31 Copynumber: 4.1 Consensus size: 29
5025199 ACATGTGGCA
*
5025209 AAAAAATTATAAAA--AATAAAAATTAAT
1 AAAAAATTATAAAATTTATAAAAATTAAT
* *
5025236 AAAAAGTTATAAAATTTATAAAATTTTAAT
1 AAAAAATTATAAAATTTATAAAA-ATTAAT
* * *
5025266 AAAAAATATTTTAAATTTATTAAAAATTAGAA
1 AAAAAAT-TATAAAATTTA-TAAAAATTA-AT
* *
5025298 AAAAAATTATAAAATTCATAAAAAAT-AT
1 AAAAAATTATAAAATTTATAAAAATTAAT
5025326 AAAA
1 AAAA
5025330 TGCATAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
27 13 0.17
28 5 0.07
29 6 0.08
30 18 0.24
31 20 0.27
32 13 0.17
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAAATTATAAAATTTATAAAAATTAAT
Found at i:5025293 original size:11 final size:10
Alignment explanation
Indices: 5025224--5025270 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
5025214 ATTATAAAAA
*
5025224 ATAAAAATTA
1 ATAAAAATTT
*
5025234 ATAAAAAGTT
1 ATAAAAATTT
5025244 AT-AAAATTT
1 ATAAAAATTT
*
5025253 ATAAAATTTT
1 ATAAAAATTT
5025263 AATAAAAA
1 -ATAAAAA
5025271 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.27
10 16 0.53
11 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:5025326 original size:18 final size:19
Alignment explanation
Indices: 5025298--5025339 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
5025288 AAAATTAGAA
*
5025298 AAAAAATTATAAAATTCAT
1 AAAAAATTATAAAATGCAT
5025317 AAAAAA-TATAAAATGCAT
1 AAAAAATTATAAAATGCAT
5025335 AAAAA
1 AAAAA
5025340 GGACATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAAATTATAAAATGCAT
Found at i:5025530 original size:9 final size:9
Alignment explanation
Indices: 5025516--5025742 Score: 54
Period size: 10 Copynumber: 24.9 Consensus size: 9
5025506 CTTTGGTAAG
5025516 ATAATTTTT
1 ATAATTTTT
5025525 ATAATTCTTTTT
1 ATAA---TTTTT
* *
5025537 ACAAATTTT
1 ATAATTTTT
5025546 AT-ATTTTT
1 ATAATTTTT
5025554 ATATATTTTT
1 ATA-ATTTTT
5025564 ATAATTTTCT
1 ATAATTTT-T
*
5025574 -TACGA-CTTT
1 ATA--ATTTTT
*
5025583 ATAAAATTTT
1 AT-AATTTTT
5025593 ATAATTTTTT
1 ATAA-TTTTT
* *
5025603 CTATATTTCT
1 ATA-ATTTTT
5025613 AT-ATATTTT
1 ATAAT-TTTT
*
5025622 ATACTTTTT
1 ATAATTTTT
5025631 -TACGATTTTT
1 ATA--ATTTTT
5025641 ATAA--TTT
1 ATAATTTTT
5025648 -T--TTTTT
1 ATAATTTTT
*
5025654 CTAATTTTT
1 ATAATTTTT
5025663 ATAA--TTT
1 ATAATTTTT
5025670 -T--TTTTT
1 ATAATTTTT
*
5025676 CTAATTTTT
1 ATAATTTTT
*
5025685 AGTAAATTTT
1 A-TAATTTTT
*
5025695 AAATATTTTT
1 ATA-ATTTTT
5025705 ATTAAAATTTTT
1 A-T--AATTTTT
5025717 AATAATTTTT
1 -ATAATTTTT
*
5025727 AT-TTTTTT
1 ATAATTTTT
*
5025735 ATTATTTT
1 ATAATTTT
5025743 GTTACCACAT
Statistics
Matches: 162, Mismatches: 21, Indels: 70
0.64 0.08 0.28
Matches are distributed among these distances:
6 8 0.05
7 8 0.05
8 18 0.11
9 50 0.31
10 56 0.35
11 5 0.03
12 15 0.09
13 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5025593 original size:39 final size:38
Alignment explanation
Indices: 5025516--5025601 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
5025506 CTTTGGTAAG
* * *
5025516 ATAATTTTTATAATTCTTTTTACAAATTTTATATTTTT
1 ATAATTTTTATAATTCTTCTTACAAATTTTAAAATTTT
* *
5025554 ATATATTTTTATAATT-TTCTTACGACTTTATAAAATTTT
1 ATA-ATTTTTATAATTCTTCTTACAAATTT-TAAAATTTT
5025593 ATAATTTTT
1 ATAATTTTT
5025602 TCTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 19 0.46
39 22 0.54
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (38 bp):
ATAATTTTTATAATTCTTCTTACAAATTTTAAAATTTT
Found at i:5025650 original size:29 final size:28
Alignment explanation
Indices: 5025548--5025648 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 28
5025538 CAAATTTTAT
5025548 ATTTTTATATATTTTTATAATTTTCTTACG
1 ATTTTTATATA-TTTTATAATTTT-TTACG
* * *
5025578 A-CTTTATAAAATTTTATAATTTTTT-CT
1 ATTTTTAT-ATATTTTATAATTTTTTACG
*
5025605 ATATTTCTATATATTTTATACTTTTTTACG
1 AT-TTT-TATATATTTTATAATTTTTTACG
5025635 ATTTTTATA-ATTTT
1 ATTTTTATATATTTT
5025649 TTTTTCTAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
27 7 0.12
28 6 0.10
29 37 0.63
30 9 0.15
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTTTTATATATTTTATAATTTTTTACG
Found at i:5025658 original size:13 final size:13
Alignment explanation
Indices: 5025636--5025684 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
5025626 TTTTTTACGA
5025636 TTTTTATAATTTT
1 TTTTTATAATTTT
*
5025649 TTTTTCTAA----
1 TTTTTATAATTTT
5025658 TTTTTATAATTTT
1 TTTTTATAATTTT
*
5025671 TTTTTCTAATTTT
1 TTTTTATAATTTT
5025684 T
1 T
5025685 AGTAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
9 8 0.28
13 21 0.72
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATAATTTT
Found at i:5025660 original size:22 final size:22
Alignment explanation
Indices: 5025635--5025694 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
5025625 CTTTTTTACG
5025635 ATTTTTATAATTTTTTTTTCTA
1 ATTTTTATAATTTTTTTTTCTA
5025657 ATTTTTATAATTTTTTTTTCTA
1 ATTTTTATAATTTTTTTTTCTA
*
5025679 ATTTTTAGTAAATTTT
1 ATTTTTA-TAATTTTT
5025695 AAATATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 29 0.81
23 7 0.19
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTTTATAATTTTTTTTTCTA
Found at i:5025672 original size:19 final size:19
Alignment explanation
Indices: 5025608--5025672 Score: 51
Period size: 22 Copynumber: 3.2 Consensus size: 19
5025598 TTTTTCTATA
*
5025608 TTTCTATATATTTTATACTTT
1 TTTCTA-AT-TTTTATAATTT
*
5025629 TTTAC-GATTTTTATAATTTTTT
1 TTT-CTAATTTTTATAA---TTT
5025651 TTTCTAATTTTTATAATTT
1 TTTCTAATTTTTATAATTT
5025670 TTT
1 TTT
5025673 TTTCTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
19 13 0.36
20 2 0.06
21 4 0.11
22 17 0.47
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTCTAATTTTTATAATTT
Found at i:5025684 original size:32 final size:33
Alignment explanation
Indices: 5025655--5025728 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
5025645 TTTTTTTTTC
* ** *
5025655 TAATTTTTATAAT-TTTTTTTTCTAATTTTTAG
1 TAATTTTTATAATATTTTTATTAAAATTTTTAA
*
5025687 TAAATTTTA-AATATTTTTATTAAAATTTTTAA
1 TAATTTTTATAATATTTTTATTAAAATTTTTAA
5025719 TAATTTTTAT
1 TAATTTTTAT
5025729 TTTTTTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 3 0.09
32 31 0.91
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (33 bp):
TAATTTTTATAATATTTTTATTAAAATTTTTAA
Found at i:5025724 original size:22 final size:21
Alignment explanation
Indices: 5025677--5025729 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
5025667 TTTTTTTTTC
*
5025677 TAATTTTTAGTAAATTTTAAA
1 TAATTTTTATTAAATTTTAAA
*
5025698 T-ATTTTTATTAAAATTTTTAA
1 TAATTTTTATT-AAATTTTAAA
5025719 TAATTTTTATT
1 TAATTTTTATT
5025730 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 11 0.39
22 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATTTTTATTAAATTTTAAA
Found at i:5037686 original size:46 final size:46
Alignment explanation
Indices: 5037616--5037800 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
5037606 CATGGCAAAG
* *
5037616 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
5037662 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
5037708 TGTGAAAAGTAGGTATGGTGTTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
5037754 TGTGAAAAGTAGGTACGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
5037800 T
1 T
5037801 ATAGCAATGT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:5052273 original size:28 final size:27
Alignment explanation
Indices: 5052242--5052304 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
5052232 GGTTAGGGTT
*
5052242 AAAATAATTTAAGGTTTAGGGATTTTAA
1 AAAATAATTTAAGGTAT-GGGATTTTAA
* * * *
5052270 AAAATAAATTAGGGTATGTGTTTTTAA
1 AAAATAATTTAAGGTATGGGATTTTAA
5052297 AAAATAAT
1 AAAATAAT
5052305 AATTAAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (27 bp):
AAAATAATTTAAGGTATGGGATTTTAA
Found at i:5052312 original size:34 final size:33
Alignment explanation
Indices: 5052274--5052397 Score: 133
Period size: 34 Copynumber: 3.7 Consensus size: 33
5052264 TTTTAAAAAA
* *
5052274 TAAATTAGGGTAT-GTGTTTTTAAAAAATAATAAT
1 TAAATTAGGGTTTAGAGTTTTTAAAAAAT--TAAT
** * *
5052308 TAAATTAGATTTTAGGGGTTTTAAATAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAAA-AAATTAAT
*
5052342 TAACTTAGGGTTTAGAGTTTTTAAGAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAA-AAAATTAAT
*
5052376 TAAATTAGGGTTTAGATTTTTT
1 TAAATTAGGGTTTAGAGTTTTT
5052398 TAAATAAGTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
34 61 0.81
35 10 0.13
36 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.44
Consensus pattern (33 bp):
TAAATTAGGGTTTAGAGTTTTTAAAAAATTAAT
Found at i:5052588 original size:127 final size:127
Alignment explanation
Indices: 5052453--5052712 Score: 466
Period size: 127 Copynumber: 2.0 Consensus size: 127
5052443 GACAATAAGG
*
5052453 ATTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACTGTTCTGAACAAATAGTGTCAA
1 ATTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
* * *
5052518 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTGACGAAAAAAGCTTCTACGTGGACGCT
66 AAACGCTACAAGCAGGATGCACTGTCAGCAAAATTGACGAAAAAAGCTCCCACGTGGACGCT
5052580 ATTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
1 ATTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
*
5052645 AAACGCTACAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCACGTGGACGCT
66 AAACGCTACAAGCAGGATGCACTGTCAGCAAAATTGACGAAAAAAGCTCCCACGTGGACGCT
*
5052707 CTTTTT
1 ATTTTT
5052713 CTACATTAGT
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (127 bp):
ATTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
AAACGCTACAAGCAGGATGCACTGTCAGCAAAATTGACGAAAAAAGCTCCCACGTGGACGCT
Found at i:5053863 original size:18 final size:18
Alignment explanation
Indices: 5053826--5053869 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5053816 GACTGAGAAA
*
5053826 AGGAAACATATAAGGTTT
1 AGGATACATATAAGGTTT
*
5053844 AGGGTACATATAAAGG-TT
1 AGGATACATAT-AAGGTTT
5053862 AGGATACA
1 AGGATACA
5053870 CATCTAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAGGTTT
Found at i:5054466 original size:7 final size:7
Alignment explanation
Indices: 5054456--5054480 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5054446 TTATATACAT
5054456 AATACTA
1 AATACTA
5054463 AATACTA
1 AATACTA
5054470 AATACTA
1 AATACTA
5054477 AATA
1 AATA
5054481 TGAAACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:5056825 original size:28 final size:28
Alignment explanation
Indices: 5056794--5056849 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5056784 TTGTTGTTTC
*
5056794 TGATGATGGGTTAAGAGAAGTAAAATGA
1 TGATGATGGGTTAAAAGAAGTAAAATGA
5056822 TGATGATGGGTTAAAAGAAGTAAAATGA
1 TGATGATGGGTTAAAAGAAGTAAAATGA
5056850 AGATTATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (28 bp):
TGATGATGGGTTAAAAGAAGTAAAATGA
Found at i:5063923 original size:26 final size:26
Alignment explanation
Indices: 5063891--5063945 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5063881 CGCACTTCCC
5063891 TTGTTTTCCTAATTTAGCTTCAATGT
1 TTGTTTTCCTAATTTAGCTTCAATGT
5063917 TTGTTTTCCTAATTTAGCTTCAATGT
1 TTGTTTTCCTAATTTAGCTTCAATGT
5063943 TTG
1 TTG
5063946 GATGCCCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.55
Consensus pattern (26 bp):
TTGTTTTCCTAATTTAGCTTCAATGT
Found at i:5068593 original size:20 final size:20
Alignment explanation
Indices: 5068568--5068607 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5068558 CTAAATGATT
5068568 GTTCAAACAGAAGGTACAAC
1 GTTCAAACAGAAGGTACAAC
5068588 GTTCAAACAGAAGGTACAAC
1 GTTCAAACAGAAGGTACAAC
5068608 ACATGGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (20 bp):
GTTCAAACAGAAGGTACAAC
Found at i:5078239 original size:32 final size:33
Alignment explanation
Indices: 5078177--5078248 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
5078167 ATTTGCATAT
5078177 AAAAATTGATAAAATTATTATTTAGACCCCC-A
1 AAAAATTGATAAAATTATTATTTAGACCCCCTA
* * *
5078209 AAAATATTGATAAAA-TGTTATTTGGTCCCCCTA
1 AAAA-ATTGATAAAATTATTATTTAGACCCCCTA
5078242 AAAAATT
1 AAAAATT
5078249 ACTTGACTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (33 bp):
AAAAATTGATAAAATTATTATTTAGACCCCCTA
Found at i:5079432 original size:11 final size:11
Alignment explanation
Indices: 5079398--5079426 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5079388 TTTTAGAATA
5079398 TTTT-TAAAAT
1 TTTTATAAAAT
5079408 TTTTATAAAAT
1 TTTTATAAAAT
5079419 TTTTATAA
1 TTTTATAA
5079427 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTATAAAAT
Found at i:5079437 original size:20 final size:20
Alignment explanation
Indices: 5079397--5079457 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
5079387 ATTTTAGAAT
*
5079397 ATTTTTA-AAATTTTTATAAA
1 ATTTTTATAATTTTTTA-AAA
5079417 ATTTTTATAATTTTTTAAAA
1 ATTTTTATAATTTTTTAAAA
** *
5079437 AAATTTAT-ATTTTTAAAAA
1 ATTTTTATAATTTTTTAAAA
5079456 AT
1 AT
5079458 ATATATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 11 0.31
20 16 0.46
21 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTTATAATTTTTTAAAA
Found at i:5079464 original size:19 final size:18
Alignment explanation
Indices: 5079428--5079463 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5079418 TTTTTATAAT
*
5079428 TTTTTAAAAAAATTTATA
1 TTTTTAAAAAAATATATA
5079446 TTTTT-AAAAAATATATA
1 TTTTTAAAAAAATATATA
5079463 T
1 T
5079464 AAATTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAAAAAATATATA
Found at i:5079484 original size:18 final size:17
Alignment explanation
Indices: 5079461--5079504 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5079451 AAAAAATATA
5079461 TATAAATTTTAGAATGTT
1 TATAAATTTTAGAAT-TT
*
5079479 TATAAATATTTTGAATTT
1 TATAAAT-TTTAGAATTT
5079497 TA-AAATTT
1 TATAAATTT
5079505 ATTTTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 4 0.17
18 11 0.46
19 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (17 bp):
TATAAATTTTAGAATTT
Found at i:5081275 original size:20 final size:21
Alignment explanation
Indices: 5081247--5081286 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5081237 AATAAAATAT
*
5081247 AATATTAAT-TATATATTTTA
1 AATAATAATATATATATTTTA
5081267 AATAATAATACTATATATTT
1 AATAATAATA-TATATATTT
5081287 ATATTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATAATATATATATTTTA
Found at i:5081466 original size:40 final size:40
Alignment explanation
Indices: 5081387--5081473 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
5081377 CTAAACATCA
* * *
5081387 TATT-TAATAAAATATTTATTATATCTATTTGAGTTTTTT
1 TATTATAATAAAACATTTATTATATCTATGTGAGTGTTTT
* *
5081426 TATTATAATAAAGCATTTATTATATTTATG-GTAGTGTTTT
1 TATTATAATAAAACATTTATTATATCTATGTG-AGTGTTTT
*
5081466 TAATATAA
1 TATTATAA
5081474 ATACTTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 5 0.12
40 35 0.88
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (40 bp):
TATTATAATAAAACATTTATTATATCTATGTGAGTGTTTT
Found at i:5088527 original size:36 final size:36
Alignment explanation
Indices: 5088480--5088551 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
5088470 TGTGAAAGCT
5088480 ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
1 ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
5088516 ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
1 ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
5088552 TTACTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (36 bp):
ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
Found at i:5091869 original size:59 final size:59
Alignment explanation
Indices: 5091790--5091909 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
5091780 TTAGACTTAA
5091790 TTTTTATTATATATGAGCCCAATATTATATTTGTCAGATCTTATTATTTTATTATTATT
1 TTTTTATTATATATGAGCCCAATATTATATTTGTCAGATCTTATTATTTTATTATTATT
5091849 TTTTTATTATATATGAGCCCAATATTATATTTGTCAGATCTTATTATTTTATTATTATT
1 TTTTTATTATATATGAGCCCAATATTATATTTGTCAGATCTTATTATTTTATTATTATT
5091908 TT
1 TT
5091910 ATTCCAAATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.57
Consensus pattern (59 bp):
TTTTTATTATATATGAGCCCAATATTATATTTGTCAGATCTTATTATTTTATTATTATT
Found at i:5092371 original size:18 final size:18
Alignment explanation
Indices: 5092340--5092374 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5092330 TGATTTATTG
5092340 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
5092358 TTTTAATTTT-TTTATTT
1 TTTT-ATTTTATTTATTT
5092375 GACATGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:5119276 original size:9 final size:9
Alignment explanation
Indices: 5119262--5119298 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5119252 TATAGTTTGA
5119262 TATTCGAAT
1 TATTCGAAT
5119271 TATTCGAAT
1 TATTCGAAT
*
5119280 TATTCGAGT
1 TATTCGAAT
5119289 TATTCGAAT
1 TATTCGAAT
5119298 T
1 T
5119299 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5122070 original size:96 final size:96
Alignment explanation
Indices: 5121960--5122153 Score: 379
Period size: 96 Copynumber: 2.0 Consensus size: 96
5121950 TGATATGCTA
5121960 GGTAGATTTTCATGCATGATGATACGTACTCTACTTTAAGATTAATACGTGTATATTTAAAGTGG
1 GGTAGATTTTCATGCATGATGATACGTACTCTACTTTAAGATTAATACGTGTATATTTAAAGTGG
*
5122025 ATTTGCGTACACTAGAGGTGCTCATGGGCCG
66 ATTCGCGTACACTAGAGGTGCTCATGGGCCG
5122056 GGTAGATTTTCATGCATGATGATACGTACTCTACTTTAAGATTAATACGTGTATATTTAAAGTGG
1 GGTAGATTTTCATGCATGATGATACGTACTCTACTTTAAGATTAATACGTGTATATTTAAAGTGG
5122121 ATTCGCGTACACTAGAGGTGCTCATGGGCCG
66 ATTCGCGTACACTAGAGGTGCTCATGGGCCG
5122152 GG
1 GG
5122154 CGGCCCGTCC
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (96 bp):
GGTAGATTTTCATGCATGATGATACGTACTCTACTTTAAGATTAATACGTGTATATTTAAAGTGG
ATTCGCGTACACTAGAGGTGCTCATGGGCCG
Found at i:5122400 original size:11 final size:11
Alignment explanation
Indices: 5122345--5122412 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
5122335 TATTTTTTAA
5122345 TTTTAAAATAT
1 TTTTAAAATAT
* *
5122356 TTTTTACATACT
1 TTTTAAAATA-T
5122368 TTTT-AAAT-T
1 TTTTAAAATAT
**
5122377 TTTTTTAA-A-
1 TTTTAAAATAT
5122386 TTTTAAAATAT
1 TTTTAAAATAT
5122397 TTTTAAAATACT
1 TTTTAAAATA-T
5122409 TTTT
1 TTTT
5122413 TTTTTTAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
9 11 0.24
10 3 0.07
11 21 0.47
12 10 0.22
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5122417 original size:46 final size:45
Alignment explanation
Indices: 5122337--5122459 Score: 148
Period size: 41 Copynumber: 2.8 Consensus size: 45
5122327 AATATATTTA
* *
5122337 TTTTTTAATTTTAAAATATTTTTTACATAC-----TTTTTAAATT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTTAAATT
*
5122377 TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTTTTAATTT
1 TTTTTT-AATTTTAAAATATTTTTAAAATAC-TTTTTTTTTTAAATT
* *
5122424 TTTTTTAATTTAAAAATATTTTTAAAATAATTTTTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
5122460 AAATTTTTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
40 6 0.08
41 22 0.31
45 6 0.08
46 22 0.31
47 15 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (45 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTTAAATT
Found at i:5122426 original size:10 final size:11
Alignment explanation
Indices: 5122410--5122434 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5122400 TAAAATACTT
5122410 TTTTTTTTTAA
1 TTTTTTTTTAA
5122421 TTTTTTTTTAA
1 TTTTTTTTTAA
5122432 TTT
1 TTT
5122435 AAAAATATTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:5122458 original size:31 final size:31
Alignment explanation
Indices: 5122423--5122484 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
5122413 TTTTTTAATT
*
5122423 TTTTTTTAA-TTTAAAAATATTTTTAAAATAA
1 TTTTTTAAATTTTAAAAA-ATTTTTAAAATAA
*
5122454 TTTTTTAAATTTTTAAAAATTTTTAAAATAA
1 TTTTTTAAATTTTAAAAAATTTTTAAAATAA
5122485 AAATGGGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTTTTAAATTTTAAAAAATTTTTAAAATAA
Found at i:5128078 original size:6 final size:6
Alignment explanation
Indices: 5128060--5128097 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
5128050 CAAGGAGAGA
*
5128060 AGGGAG A-GGAG AGGGAG AGGGAG AGGGAG AGGCAG AGG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGG
5128098 AGGTGGTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.34, C:0.03, G:0.63, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:5130044 original size:3 final size:3
Alignment explanation
Indices: 5130025--5130058 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5130015 GTGGCACTGC
*
5130025 CAT CAT CAA CAT GCAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT -CAT CAT CAT CAT CAT CAT CAT
5130059 TGGTCGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:5135068 original size:9 final size:9
Alignment explanation
Indices: 5135044--5135080 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5135034 TGAGTTTTCA
*
5135044 AATTCGAAG
1 AATTCGAAT
*
5135053 AACTCGAAT
1 AATTCGAAT
5135062 AATTCGAAT
1 AATTCGAAT
5135071 AATTCGAAT
1 AATTCGAAT
5135080 A
1 A
5135081 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5135328 original size:30 final size:31
Alignment explanation
Indices: 5135294--5135353 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
5135284 AAACCTTTTA
*
5135294 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
5135324 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
5135354 TCCCATCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:5135622 original size:9 final size:9
Alignment explanation
Indices: 5135608--5135636 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5135598 AATTTCACAT
5135608 TTTATATTA
1 TTTATATTA
5135617 TTTATATTA
1 TTTATATTA
5135626 TTTATATTA
1 TTTATATTA
5135635 TT
1 TT
5135637 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:5147853 original size:21 final size:21
Alignment explanation
Indices: 5147827--5147881 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
5147817 GGTTAGGTAA
*
5147827 TGAAGAAGAAAATTGGTGTTT
1 TGAAGAAGAAAAATGGTGTTT
5147848 TGAAGAAGAAAAATGGTGTTT
1 TGAAGAAGAAAAATGGTGTTT
*
5147869 GGCAAG-AGAAAAA
1 TG-AAGAAGAAAAA
5147882 ATTACAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (21 bp):
TGAAGAAGAAAAATGGTGTTT
Found at i:5147882 original size:22 final size:21
Alignment explanation
Indices: 5147830--5147883 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
5147820 TAGGTAATGA
*
5147830 AGAAGAAAATTGGTGTTTTGAAG
1 AGAA-AAAA-TGGTGTTTGGAAG
5147853 A-AGAAAAATGGTGTTTGGCAAG
1 AGA-AAAAATGGTGTTTGG-AAG
5147875 AGAAAAAAT
1 AGAAAAAAT
5147884 TACAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 9 0.33
22 15 0.56
23 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (21 bp):
AGAAAAAATGGTGTTTGGAAG
Found at i:5148481 original size:15 final size:16
Alignment explanation
Indices: 5148448--5148481 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5148438 CAATCTTTCA
5148448 CTTTTCTTCCAACTTT
1 CTTTTCTTCCAACTTT
*
5148464 CTTTTCTTCTAA-TTT
1 CTTTTCTTCCAACTTT
5148479 CTT
1 CTT
5148482 ACTTCTTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTTCTTCCAACTTT
Found at i:5148764 original size:21 final size:19
Alignment explanation
Indices: 5148715--5148766 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
5148705 AATATCTCAA
5148715 CTAATTTAATAATAAAATT
1 CTAATTTAATAATAAAATT
* *
5148734 TTATTGTTTAATATATAAAATT
1 CTA--ATTTAATA-ATAAAATT
5148756 CTAACTTTAAT
1 CTAA-TTTAAT
5148767 CATTTTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (19 bp):
CTAATTTAATAATAAAATT
Found at i:5161416 original size:19 final size:20
Alignment explanation
Indices: 5161392--5161436 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5161382 TTCTAGGCAT
* *
5161392 ATTTTTTAAT-AATTTTTAA
1 ATTTTTTAATAAAATATTAA
5161411 ATTTTTTAATAAAATATTAA
1 ATTTTTTAATAAAATATTAA
5161431 ATTTTT
1 ATTTTT
5161437 ACATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTTAATAAAATATTAA
Found at i:5161498 original size:19 final size:18
Alignment explanation
Indices: 5161457--5161501 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5161447 TTTAAAATTT
*
5161457 AAAATATATAAAATCTAA
1 AAAATATTTAAAATCTAA
*
5161475 AAAATATTTAAAATTTATA
1 AAAATATTTAAAATCTA-A
5161494 AAAATATT
1 AAAATATT
5161502 ATTTAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATTTAAAATCTAA
Found at i:5167180 original size:29 final size:31
Alignment explanation
Indices: 5167122--5167187 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
5167112 TGGACCAAAA
*
5167122 TTTTAAAATATGAAAAATAAAAAGATTAAAT
1 TTTTAAAATATGAAAAATAAAAAGACTAAAT
* *
5167153 TTTTAAAA-ATG-AAAATATATAGACTAAAT
1 TTTTAAAATATGAAAAATAAAAAGACTAAAT
*
5167182 TCTTAA
1 TTTTAA
5167188 TTTGTAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.65
30 3 0.10
31 8 0.26
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (31 bp):
TTTTAAAATATGAAAAATAAAAAGACTAAAT
Found at i:5167519 original size:21 final size:20
Alignment explanation
Indices: 5167487--5167525 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5167477 ATGATAATAT
5167487 TTATTTTTTTTATTTTTATC
1 TTATTTTTTTTATTTTTATC
5167507 TTATTTCTTTTTATTTTTA
1 TTATTT-TTTTTATTTTTA
5167526 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (20 bp):
TTATTTTTTTTATTTTTATC
Found at i:5168821 original size:25 final size:25
Alignment explanation
Indices: 5168775--5168822 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5168765 AGCTATTTAC
**
5168775 TTTTTAAAAGTATAAATTAAAAATG
1 TTTTTAAAAGTATAAAAGAAAAATG
5168800 TTTTTAAAAAGTA-AAAAGAAAAA
1 TTTTT-AAAAGTATAAAAGAAAAA
5168823 ACACATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTTTTAAAAGTATAAAAGAAAAATG
Found at i:5168822 original size:26 final size:25
Alignment explanation
Indices: 5168775--5168823 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5168765 AGCTATTTAC
* **
5168775 TTTTTAAAAGTATAAATTAAAAATG
1 TTTTTAAAAGTAAAAAGAAAAAATG
5168800 TTTTTAAAAAGTAAAAAGAAAAAA
1 TTTTT-AAAAGTAAAAAGAAAAAA
5168824 CACATTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTTTTAAAAGTAAAAAGAAAAAATG
Found at i:5169222 original size:5 final size:5
Alignment explanation
Indices: 5169212--5169238 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5169202 ACAATAAACT
5169212 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
5169239 GAAATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:5169346 original size:18 final size:19
Alignment explanation
Indices: 5169311--5169348 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5169301 AAAATGAACA
*
5169311 TTTTATTTCTCAAAAATAC
1 TTTTATTTCACAAAAATAC
*
5169330 TTTT-TTTCACAATAATAC
1 TTTTATTTCACAAAAATAC
5169348 T
1 T
5169349 AAACTCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTATTTCACAAAAATAC
Found at i:5174838 original size:21 final size:22
Alignment explanation
Indices: 5174790--5174843 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
5174780 CCTTTTGAAC
*
5174790 TATT-TTATTTATGTTCTTAAT
1 TATTATTATTTATATTCTTAAT
*
5174811 TA-TATTATTTATATT-TTATT
1 TATTATTATTTATATTCTTAAT
5174831 TATTATTAATTTA
1 TATTATT-ATTTA
5174844 GGGAATACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 7 0.25
21 16 0.57
22 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTATTTATATTCTTAAT
Found at i:5175647 original size:36 final size:36
Alignment explanation
Indices: 5175606--5175674 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
5175596 ATAAAGATTC
5175606 AATATGATAA-GCAATTCAATAATATAAATAGTACAA
1 AATATGA-AATGCAATTCAATAATATAAATAGTACAA
** *
5175642 AATATGAAATTTAATTTAATAATATAAATAGTA
1 AATATGAAATGCAATTCAATAATATAAATAGTA
5175675 GATATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.33
Consensus pattern (36 bp):
AATATGAAATGCAATTCAATAATATAAATAGTACAA
Found at i:5181723 original size:2 final size:2
Alignment explanation
Indices: 5181716--5181741 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5181706 CAGCATTTGC
5181716 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
5181742 GCAATGATGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5187980 original size:46 final size:46
Alignment explanation
Indices: 5187902--5188040 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
5187892 GCAATGCTAT
* * *
5187902 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACTTCTCAC
* *
5187948 AACTCAGTATGATTTTCTTTACTAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACTTCTCAC
5187994 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACGTTC-CAC
1 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTAC-TTCTCAC
5188040 A
1 A
5188041 CTTTGCCATG
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
46 83 0.98
47 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACTTCTCAC
Found at i:5205962 original size:24 final size:24
Alignment explanation
Indices: 5205935--5205986 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5205925 AATCAAAGTC
* *
5205935 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
5205959 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
5205983 AAAT
1 AAAT
5205987 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:5210409 original size:24 final size:24
Alignment explanation
Indices: 5210367--5210418 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5210357 AATCAAAGTC
** *
5210367 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
5210391 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
5210415 AAAT
1 AAAT
5210419 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:5213455 original size:27 final size:27
Alignment explanation
Indices: 5213425--5213485 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
5213415 TATACATATA
5213425 TTAAGTATGATTAGTTTAGTTTCTTGT
1 TTAAGTATGATTAGTTTAGTTTCTTGT
5213452 TTAAGTATGATTAGTTTAGTTTCTTGT
1 TTAAGTATGATTAGTTTAGTTTCTTGT
5213479 TTAAGTA
1 TTAAGTA
5213486 AAAATGGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (27 bp):
TTAAGTATGATTAGTTTAGTTTCTTGT
Found at i:5219152 original size:21 final size:22
Alignment explanation
Indices: 5219128--5219174 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
5219118 AATCATTTGG
* * *
5219128 ATTTTATTTTTTAAA-TTAAAT
1 ATTTTATTATTAAAAGTTAAAA
5219149 ATTTTATTATTAAAAGTTAAAA
1 ATTTTATTATTAAAAGTTAAAA
5219171 ATTT
1 ATTT
5219175 AACATAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTATTATTAAAAGTTAAAA
Found at i:5219484 original size:3 final size:3
Alignment explanation
Indices: 5219476--5219513 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5219466 CCCAGATTTT
5219476 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5219514 TTTTTCTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5222090 original size:3 final size:3
Alignment explanation
Indices: 5222084--5222130 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
5222074 GAATAAGACA
*
5222084 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5222131 ATACTAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5237392 original size:17 final size:17
Alignment explanation
Indices: 5237370--5237405 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5237360 TAAATTTTAT
5237370 TGCTTGAATTTTTAAAG
1 TGCTTGAATTTTTAAAG
5237387 TGCTTGAATTTTTAAAG
1 TGCTTGAATTTTTAAAG
5237404 TG
1 TG
5237406 GGGTGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (17 bp):
TGCTTGAATTTTTAAAG
Found at i:5259622 original size:34 final size:33
Alignment explanation
Indices: 5259581--5259649 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
5259571 TCAACATTTA
*
5259581 AAAAACAAAACATTATCACAAAAGGTGAAAAACT
1 AAAAACAAAACATTATCACAAAAGGAG-AAAACT
*
5259615 AAAAACAAAACATTATCACAGAAGGAGAAAACT
1 AAAAACAAAACATTATCACAAAAGGAGAAAACT
5259648 AA
1 AA
5259650 TACTTACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.13
Consensus pattern (33 bp):
AAAAACAAAACATTATCACAAAAGGAGAAAACT
Found at i:5264643 original size:26 final size:26
Alignment explanation
Indices: 5264607--5264660 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5264597 GCAAGAGATG
5264607 TTGTCACCTTAAATCTCACTTTGTGA
1 TTGTCACCTTAAATCTCACTTTGTGA
5264633 TTGTCACCTTAAATCTCACTTTGTGA
1 TTGTCACCTTAAATCTCACTTTGTGA
5264659 TT
1 TT
5264661 CTTCTGACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (26 bp):
TTGTCACCTTAAATCTCACTTTGTGA
Found at i:5276802 original size:22 final size:22
Alignment explanation
Indices: 5276777--5276825 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5276767 TGTTTTCTCC
5276777 TTATTTTGCTACCATTTTACTA
1 TTATTTTGCTACCATTTTACTA
* * * **
5276799 TTATGTTGTTACTATTTTGTTA
1 TTATTTTGCTACCATTTTACTA
5276821 TTATT
1 TTATT
5276826 GTTTGGATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (22 bp):
TTATTTTGCTACCATTTTACTA
Found at i:5280545 original size:20 final size:20
Alignment explanation
Indices: 5280516--5280560 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5280506 AAATTCAGTT
* * *
5280516 AATTATCCAATTTCAAATCG
1 AATTAACCAACTTCAAACCG
*
5280536 AATTAACCAACTTCCAACCG
1 AATTAACCAACTTCAAACCG
5280556 AATTA
1 AATTA
5280561 GATTGATTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.29
Consensus pattern (20 bp):
AATTAACCAACTTCAAACCG
Found at i:5282856 original size:15 final size:15
Alignment explanation
Indices: 5282836--5282866 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5282826 AAAAGACTTT
5282836 TTCCTTCTATTATTA
1 TTCCTTCTATTATTA
5282851 TTCCTTCTATTATTA
1 TTCCTTCTATTATTA
5282866 T
1 T
5282867 AATAATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (15 bp):
TTCCTTCTATTATTA
Found at i:5283745 original size:40 final size:40
Alignment explanation
Indices: 5283692--5283831 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 40
5283682 AACACACCAG
* * *
5283692 TTTGGCACGCAGTGTCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* *
5283732 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* * *
5283770 TTAG-CACCCAGTGCCTCATCGAATTAATCCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGA-TAATCCGAAGTAATAA
*
5283810 ATTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGTCTCATCG
5283832 ACTCAAAGTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
37 16 0.19
38 15 0.18
39 2 0.02
40 34 0.41
41 16 0.19
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
Found at i:5283819 original size:41 final size:40
Alignment explanation
Indices: 5283701--5283832 Score: 155
Period size: 41 Copynumber: 3.4 Consensus size: 40
5283691 GTTTGGCACG
* * *
5283701 CAGTGTCTCATCGGATAATTCGAAGTAATAATTTGACACC
1 CAGTGTCTCATCGAATAATCCGAAGTAATAAATTGACACC
** *
5283741 CAGTGTCTCATCGGCTAAACCGAAG---TAAATT-AGCACC
1 CAGTGTCTCATCGAATAATCCGAAGTAATAAATTGA-CACC
*
5283778 CAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGACACC
1 CAGTGTCTCATCGAA-TAATCCGAAGTAATAAATTGACACC
5283819 CAGTGTCTCATCGA
1 CAGTGTCTCATCGA
5283833 CTCAAAGTTG
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
36 1 0.01
37 21 0.27
38 9 0.12
40 22 0.29
41 23 0.30
42 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
CAGTGTCTCATCGAATAATCCGAAGTAATAAATTGACACC
Found at i:5284835 original size:19 final size:20
Alignment explanation
Indices: 5284811--5284858 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
5284801 ATTAATAAGC
*
5284811 AATACATAT-TTTATTATTA
1 AATACACATGTTTATTATTA
5284830 AATACACATGTTTATTATT-
1 AATACACATGTTTATTATTA
*
5284849 ATTACACATG
1 AATACACATG
5284859 AATTTACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (20 bp):
AATACACATGTTTATTATTA
Found at i:5290124 original size:34 final size:34
Alignment explanation
Indices: 5290062--5290126 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
5290052 TTTGTAGTAA
5290062 TTTATTTTTTCTTTCATATTTCAATTATATATTT
1 TTTATTTTTTCTTTCATATTTCAATTATATATTT
*
5290096 TTTATTATTTTCTTCTC-TATTT-AGTTATATA
1 TTTATT-TTTTCTT-TCATATTTCAATTATATA
5290127 GATAAAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 14 0.50
35 12 0.43
36 2 0.07
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (34 bp):
TTTATTTTTTCTTTCATATTTCAATTATATATTT
Found at i:5294072 original size:22 final size:20
Alignment explanation
Indices: 5294047--5294093 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
5294037 GATATTTTAA
*
5294047 ATATTAATATTTATTTTATTTT
1 ATATTAATATTT-GTTTA-TTT
*
5294069 ATATAAATATTTGTTTATTT
1 ATATTAATATTTGTTTATTT
5294089 ATATT
1 ATATT
5294094 TATTCGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATATTAATATTTGTTTATTT
Found at i:5296297 original size:20 final size:20
Alignment explanation
Indices: 5296271--5296318 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
5296261 AACAATGAAT
5296271 CTGTTCATCAAAAGATACAA
1 CTGTTCATCAAAAGATACAA
* *
5296291 TTG-T--TCAAAAGATACGA
1 CTGTTCATCAAAAGATACAA
5296308 CTGTTCATCAA
1 CTGTTCATCAA
5296319 GTGACAGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 6
0.71 0.10 0.19
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 1 0.05
20 6 0.27
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
CTGTTCATCAAAAGATACAA
Found at i:5300963 original size:19 final size:21
Alignment explanation
Indices: 5300925--5300963 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5300915 AATAATTGAT
*
5300925 TATATTGTTGTTATTGTTTTG
1 TATATTGTTGTTAATGTTTTG
5300946 TATATT-TTG-TAATGTTTT
1 TATATTGTTGTTAATGTTTT
5300964 TTGTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATGTTTTG
Found at i:5301023 original size:3 final size:3
Alignment explanation
Indices: 5301015--5301051 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5301005 ATAGTTTTAG
5301015 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5301052 GACTGTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5301891 original size:18 final size:18
Alignment explanation
Indices: 5301868--5301905 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5301858 GGTTGGTGGT
5301868 GAAGAAGAAAGTGCTGGC
1 GAAGAAGAAAGTGCTGGC
* *
5301886 GAAGAAGAATGTGGTGGC
1 GAAGAAGAAAGTGCTGGC
5301904 GA
1 GA
5301906 TCATTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.42, T:0.13
Consensus pattern (18 bp):
GAAGAAGAAAGTGCTGGC
Found at i:5306852 original size:27 final size:27
Alignment explanation
Indices: 5306810--5306865 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
5306800 TTAGCCACAT
*
5306810 ATTGGTGCCGCCTTTTTATTCCTCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
*
5306837 ATTGGTGCCGCTTTTTTATTCCCCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
5306864 AT
1 AT
5306866 CACCCTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.09, C:0.32, G:0.14, T:0.45
Consensus pattern (27 bp):
ATTGGTGCCGCCTTTTTATTCCCCTCC
Found at i:5307657 original size:5 final size:5
Alignment explanation
Indices: 5307649--5307802 Score: 59
Period size: 5 Copynumber: 32.6 Consensus size: 5
5307639 TTTTCTCTTC
* * * *
5307649 TCCTT TCCTT TTCTT TCC-T TCTTT TTCTT T-CTT T--TT TCTTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
* * *
5307695 TCCTCT T-C-T TCTTCT TCCTTT TCTTTT TCTCTT CTCCTT TCCTT TTCTT
1 TCCT-T TCCTT TCCT-T TCC-TT TC-CTT TC-CTT -TCCTT TCCTT TCCTT
* * *
5307744 TCC-T TCTTT TTCTT T-CTT TCCTC TCC-T T-CTT TCCTT T-CTT T-CTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
5307788 T-CTT T-CTT T-CTT TCC
1 TCCTT TCCTT TCCTT TCC
5307803 CTCTCCTTCT
Statistics
Matches: 117, Mismatches: 17, Indels: 30
0.71 0.10 0.18
Matches are distributed among these distances:
3 6 0.05
4 37 0.32
5 53 0.45
6 18 0.15
7 3 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (5 bp):
TCCTT
Found at i:5307674 original size:36 final size:36
Alignment explanation
Indices: 5307600--5307810 Score: 139
Period size: 36 Copynumber: 5.6 Consensus size: 36
5307590 CCTTTTTTTC
* *
5307600 TTTTTTTC-CTTCCTTCCTTCCCTCTTC-TT-CTTCTTT
1 TTTTTTTCTCTT-C-TCCTTTCCTTTTCTTTCCTTC-TT
5307636 TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTT
1 TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTC---TT
* * * *
5307675 CTTTCTTTTTTCTTTTCCTTTCCTCTTCTTCTTCTTCCTT
1 -TTT-TTTTCTCTTCTCCTTTCCTTTTCTT-TCCTT-CTT
5307715 TTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT
1 TT-TTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT
* * * *
5307752 TTTCTTTCT-TTCCTCTCCTT-CTTTCCTTTCTTTCTT
1 TTTTTTTCTCTT-CTC-CTTTCCTTTTCTTTCCTTCTT
*
5307788 TCTTTCTTTCT-TTC-CCTCTCCTT
1 T-TTT-TTTCTCTTCTCCTTTCCTT
5307811 CTCCCCCCCA
Statistics
Matches: 143, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
35 15 0.10
36 39 0.27
37 18 0.13
38 11 0.08
39 27 0.19
40 6 0.04
41 22 0.15
42 4 0.03
43 1 0.01
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (36 bp):
TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT
Found at i:5307679 original size:4 final size:4
Alignment explanation
Indices: 5307658--5307801 Score: 79
Period size: 4 Copynumber: 35.0 Consensus size: 4
5307648 CTCCTTTCCT
*
5307658 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTTTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTT-C T-TTC
* *
5307703 -TTC -TTC TTCC TTTTC TTT- TTCTC TTCTCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC -TTTC TTTC TT-TC TT-T-C TTT-C -TTTC TTTC TTTC
* *
5307750 -TT- TTTC TTTC TTTCC TCTC CTTC TTTCC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC
5307798 TTTC
1 TTTC
5307802 CCTCTCCTTC
Statistics
Matches: 116, Mismatches: 8, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
3 19 0.16
4 60 0.52
5 28 0.24
6 9 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:5307752 original size:13 final size:13
Alignment explanation
Indices: 5307656--5307800 Score: 67
Period size: 13 Copynumber: 11.3 Consensus size: 13
5307646 TTCTCCTTTC
5307656 CTTTTCTTTCCTT
1 CTTTTCTTTCCTT
5307669 CTTTTTCTTT-CTT
1 C-TTTTCTTTCCTT
5307682 -TTTTCTTTTCCTTT
1 CTTTTC-TTTCC-TT
*
5307696 CCTCTTC-TT-CTT
1 -CTTTTCTTTCCTT
* *
5307708 C-TTCCTTTTCTT
1 CTTTTCTTTCCTT
5307720 -TTTCTCTTCTCCTTT
1 CTTT-TCTT-TCC-TT
5307735 CCTTTTCTTTCCTT
1 -CTTTTCTTTCCTT
*
5307749 C--TT-TTTCTTT
1 CTTTTCTTTCCTT
* *
5307759 CTTTCCTCTCCTT
1 CTTTTCTTTCCTT
* *
5307772 CTTTCCTTTCTTT
1 CTTTTCTTTCCTT
*
5307785 C-TTTCTTTCTTT
1 CTTTTCTTTCCTT
5307797 CTTT
1 CTTT
5307801 CCCTCTCCTT
Statistics
Matches: 102, Mismatches: 12, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
10 9 0.09
11 10 0.10
12 22 0.22
13 29 0.28
14 16 0.16
15 5 0.05
16 8 0.08
17 3 0.03
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTTTCTTTCCTT
Found at i:5307756 original size:6 final size:6
Alignment explanation
Indices: 5307624--5307758 Score: 62
Period size: 6 Copynumber: 22.0 Consensus size: 6
5307614 TCCTTCCCTC
* * * *
5307624 TTCTTC TTCTTT TT-TTT TTC-TC TTCTCCT TTCCTT TTCTTT CCTTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT TTCTTT --TTCTTT
* * * * * *
5307673 TTCTTT CT-TTT TTCTTT TCCTTT CCTCTTC TTCTTC TTCCTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT -TTCTTT TTCTTT TTCTTT TTCTTT
* * *
5307721 TTC-TC TTCTCCT TTCCTT TTCTTT CCTTCTTT TTCTTT
1 TTCTTT TTCT-TT TTCTTT TTCTTT --TTCTTT TTCTTT
5307759 CTTTCCTCTC
Statistics
Matches: 95, Mismatches: 23, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
5 17 0.18
6 57 0.60
7 9 0.09
8 12 0.13
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTCTTT
Found at i:5307776 original size:80 final size:79
Alignment explanation
Indices: 5307590--5307800 Score: 274
Period size: 80 Copynumber: 2.7 Consensus size: 79
5307580 AAAAAAATTA
* * *
5307590 CCTT-TTTTTCTTTTTTTCCT-TCCTTCCTTCC-C-TCTTCTTCTTCTTTTTTTTTTCTCTTCTC
1 CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCTCTTCTTCTTCTTCTTTTCTTTTTCTCTTCTC
5307651 CTTTCCTTTTCTTT
66 CTTTCCTTTTCTTT
** *
5307665 CCTTCTTTTTCTTTCTTTTTTCT-TTTCCTTTCCTCTTCTTCTTCTTCCTTTTCTTTTTCTCTTC
1 CCTTCTTTTTCTTTCTTTCCTCTCCTT-CTTTCCTCTTCTTCTTCTT-CTTTTCTTTTTCTCTTC
5307729 TCCTTTCCTTTTCTTT
64 TCCTTTCCTTTTCTTT
5307745 CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCT-TTCTTTCTTTCTT-TCTTTCTTT
1 CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCTCTTC-TTC-TTCTTCT-TTTCTTT
5307801 CCCTCTCCTT
Statistics
Matches: 117, Mismatches: 9, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
75 4 0.03
76 15 0.13
77 6 0.05
78 1 0.01
79 14 0.12
80 70 0.60
81 7 0.06
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (79 bp):
CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCTCTTCTTCTTCTTCTTTTCTTTTTCTCTTCTC
CTTTCCTTTTCTTT
Found at i:5307957 original size:30 final size:28
Alignment explanation
Indices: 5307919--5307990 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
5307909 TTTTGTTTTT
5307919 TTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTATAATATTTTGGTAAATAA-AAAAA-AA
* *
5307948 TTATAATATTTTAGTAAATAAAAAAAAG
1 TTATAATATTTTGGTAAATAAAAAAAAA
5307976 TTATAATATTTTGGT
1 TTATAATATTTTGGT
5307991 TATTTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 15 0.38
29 9 0.23
30 15 0.38
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (28 bp):
TTATAATATTTTGGTAAATAAAAAAAAA
Found at i:5307980 original size:28 final size:30
Alignment explanation
Indices: 5307919--5307987 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
5307909 TTTTGTTTTT
*
5307919 TTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTATAATATTTTAGTAAATAATAAAAATAA
*
5307948 TTATAATATTTTAGTAAATAA-AAAAA-AG
1 TTATAATATTTTAGTAAATAATAAAAATAA
5307976 TTATAATATTTT
1 TTATAATATTTT
5307988 GGTTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 13 0.35
29 9 0.24
30 15 0.41
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (30 bp):
TTATAATATTTTAGTAAATAATAAAAATAA
Found at i:5311457 original size:22 final size:23
Alignment explanation
Indices: 5311421--5311466 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5311411 TTATCTGTAC
* *
5311421 TTTTATTTTTAAAAATTTAGTCT
1 TTTTAATTTTAAAAATTAAGTCT
5311444 TTTTAATTTTAAAAATTAAGTCT
1 TTTTAATTTTAAAAATTAAGTCT
5311467 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTAATTTTAAAAATTAAGTCT
Found at i:5312607 original size:36 final size:36
Alignment explanation
Indices: 5312537--5312607 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
5312527 ATAACAAAAT
* *
5312537 TAATAATAAAACAAGTGTTATACAATATCTAAATAA
1 TAATAATAAAACAAGTGTAATACAATATCGAAATAA
*
5312573 TAATAATAAAAC-AGTAGTAATATAATAGT-GAAATA
1 TAATAATAAAACAAGT-GTAATACAATA-TCGAAATA
5312608 GTAACAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
35 3 0.10
36 26 0.87
37 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (36 bp):
TAATAATAAAACAAGTGTAATACAATATCGAAATAA
Found at i:5314238 original size:20 final size:21
Alignment explanation
Indices: 5314182--5314239 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
5314172 CACGCCAAAA
5314182 TTTTAA-AT-TTTTATAAAATT
1 TTTTAACATATTTT-TAAAATT
*
5314202 TTTTAACATATTGTTAAAA-T
1 TTTTAACATATTTTTAAAATT
* *
5314222 TTTTGATATATTTTTAAA
1 TTTTAACATATTTTTAAA
5314240 GCATTTGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 22 0.69
21 7 0.22
22 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTAACATATTTTTAAAATT
Found at i:5318012 original size:16 final size:18
Alignment explanation
Indices: 5317991--5318031 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5317981 CAAGTTTCAC
5317991 GAAAAT-TAA-AAAACTA
1 GAAAATATAACAAAACTA
5318007 GAAAATATAACAAAACTA
1 GAAAATATAACAAAACTA
*
5318025 AAAAATA
1 GAAAATA
5318032 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 13 0.59
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (18 bp):
GAAAATATAACAAAACTA
Found at i:5318042 original size:26 final size:25
Alignment explanation
Indices: 5318013--5318064 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
5318003 ACTAGAAAAT
*
5318013 ATAACAAAACTAAAAAATAAT-TTAAA
1 ATAA-AAAA-TAAAAAAAAATCTTAAA
*
5318039 ATAAAGAATAAAAAAAAATCTTAAA
1 ATAAAAAATAAAAAAAAATCTTAAA
5318064 A
1 A
5318065 CTCAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 9 0.39
26 4 0.17
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (25 bp):
ATAAAAAATAAAAAAAAATCTTAAA
Found at i:5339238 original size:31 final size:31
Alignment explanation
Indices: 5339203--5339274 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
5339193 AAACAGGGGA
5339203 TCCCCAAAAAGAATAGAGTGAAAATAAAAGT
1 TCCCCAAAAAGAATAGAGTGAAAATAAAAGT
5339234 TCCCCAAAAAGAATAGAGTGAAAATAAAAGT
1 TCCCCAAAAAGAATAGAGTGAAAATAAAAGT
5339265 TCCCCAAAAA
1 TCCCCAAAAA
5339275 AACTACAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.15
Consensus pattern (31 bp):
TCCCCAAAAAGAATAGAGTGAAAATAAAAGT
Found at i:5346493 original size:150 final size:150
Alignment explanation
Indices: 5345930--5346786 Score: 1263
Period size: 150 Copynumber: 5.7 Consensus size: 150
5345920 CACATTTTGT
* *
5345930 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTTTCTATACATTTCAAATACATAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* * * * *
5345995 TCAACCTTAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAAATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* * *
5346059 CAGCTTTTCATAGCTTATAA
131 TAGCTTCTCATACCTTATAA
* * **
5346079 AATCATAAATTCTTAAGATTTTGAAATTTATGTTTTTCTTAATACATTTCAAATACATAATCAGC
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTT-TT-ATACATTTCAAATACATAATCAAA
* * * *
5346144 GTTCAACCTTAACTAATTTGGCCTTTTCATAGCTCAAAATTAATAAAAGAAATGAAAAATCCAAA
64 GTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAA
* * *
5346209 TTCAGCTTTTCATAGCTTATAA
129 TTTAGCTTCTCATACCTTATAA
* * *
5346231 AATCATAAATTCCTAAGATTTTGAAATTCTTGTTTTCTTATACATTTCAAATACATGATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* *
5346296 TCAACCTTAACCAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAATATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
*
5346360 TAACTTCTCATACCTTATAA
131 TAGCTTCTCATACCTTATAA
* *
5346380 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATATATTTCAAATACATAGTCAAAG
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTT-ATACATTTCAAATACATAATCAAAG
* * *
5346445 TTCAACCTTGACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAGTGAAATATCCAAAT
65 TTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
5346509 TTAGCTTCTCATACCTTATAA
130 TTAGCTTCTCATACCTTATAA
* *
5346530 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTTAATATATTTCAAATACATAGTCAAA
1 AATCATAAATTCCTAAGATTTTGAAATTCATG-TTTTTTT-ATACATTTCAAATACATAATCAAA
*
5346595 GTTCAACCTTAACTAATTTGGCTTTTTCA-AGCTCAAAATCAGTATAACAAATGAAAAATCCAAA
64 GTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAA
5346659 TTTAGCTTCTCATACCTTATAA
129 TTTAGCTTCTCATACCTTATAA
* * * * *
5346681 AATCCTAAATTCCTAAGATTTTGACATTCATGTTTTCTTATACAATTCAAATACAGAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
*
5346746 TCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCA
66 TCAACCTTAACT-AATTTGGCTTTTTCATAGCTCAAAATCA
5346787 TAAATTTCAA
Statistics
Matches: 652, Mismatches: 49, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
149 154 0.24
150 205 0.31
151 201 0.31
152 92 0.14
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (150 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
TAGCTTCTCATACCTTATAA
Found at i:5346581 original size:301 final size:299
Alignment explanation
Indices: 5345930--5346790 Score: 1271
Period size: 301 Copynumber: 2.9 Consensus size: 299
5345920 CACATTTTGT
* *
5345930 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTTTCTATACATTTCAAATACATAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACAT-ATCAAAGT
* * * * *
5345995 TCAACCTTAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAAATCCAAATT
65 TCAACCTTAACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* * * * *
5346059 CAGCTTTTCATAGCTTATAAAATCATAAATTCTTAAGATTTTGAAATTTATGTTTTTCTTAATAC
129 TAGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTT-TTAATAC
** * * *
5346124 ATTTCAAATACATAATCAGCGTTCAACCTTAACTAATTTGGCCTTTTCATAGCTCAAAATTAATA
193 ATTTCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATA
* * *
5346189 AAAGAAATGAAAAATCCAAATTCAGCTTTTCATAGCTTATAA
258 AAACAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
* *
5346231 AATCATAAATTCCTAAGATTTTGAAATTCTTGTTTTCTTATACATTTCAAATACATGATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACAT-ATCAAAGT
* *
5346296 TCAACCTTAACCAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAATATCCAAATTT
65 TCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAATTT
* *
5346361 AACTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATATAT
130 AGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATACAT
* * *
5346426 TTCAAATACATAGTCAAAGTTCAACCTTGACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATA
195 TTCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATAAA
* * *
5346490 ACAAGTGAAATATCCAAATTTAGCTTCTCATACCTTATAA
260 ACAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
*
5346530 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTTAATATATTTCAAATACATAGTCAAA
1 AATCATAAATTCCTAAGATTTTGAAATTCATG-TTTTTTT-ATACATTTCAAATACATA-TCAAA
*
5346595 GTTCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAGTATAACAAATGAAAAATCCAAAT
63 GTTCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
* * *
5346660 TTAGCTTCTCATACCTTATAAAATCCTAAATTCCTAAGATTTTGACATTCATGTTTTCTT-ATAC
128 TTAGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATAC
* *
5346724 AATTCAAATACAGAATCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATC-AT
193 ATTTCAAATACATAATCAAAGTTCAACCTTAACT-AATTTGGCTTTTTCAGAGCTCAAAATCAAT
5346788 AAA
257 AAA
5346791 TTTCAAAATT
Statistics
Matches: 506, Mismatches: 48, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
299 80 0.16
300 90 0.18
301 319 0.63
302 17 0.03
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (299 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATATCAAAGTT
CAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAATTTA
GCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATACATT
TCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATAAAA
CAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
Found at i:5346833 original size:109 final size:107
Alignment explanation
Indices: 5346687--5346891 Score: 286
Period size: 109 Copynumber: 1.9 Consensus size: 107
5346677 ATAAAATCCT
* * *
5346687 AAATTCCTAAGATTTTGACATTCATGTTTTCTTATACAATTC-AAATACAGAATCAAAGTTCAAC
1 AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
5346751 CTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATTTCA
66 CTTAAC-AAATTT-GC-TTTTCAGAGCTCAAAATCATAAATTTCA
* ** * * *
5346796 AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
1 AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
*
5346861 CTTAACAAATTTGCTTTTCATAGCTCAAAAT
66 CTTAACAAATTTGCTTTTCAGAGCTCAAAAT
5346892 TAATATAACA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 16 0.19
108 2 0.02
109 41 0.48
110 26 0.31
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (107 bp):
AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
CTTAACAAATTTGCTTTTCAGAGCTCAAAATCATAAATTTCA
Found at i:5351510 original size:42 final size:42
Alignment explanation
Indices: 5351464--5351617 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 42
5351454 TGCTACGCAA
* * * *
5351464 AAACCCGTAAGGGTTAAACGGAAGCTCATAAGAGCTAAACGG
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
* **
5351506 AAACCCATAAAGGTTAATTTGAAGCTCAAAAGAGCTAAACTG
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
* * * * *
5351548 AAACCCATTAGGGTAAAACTAAAGCTCAAAATAGCTGAACTG
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
* *
5351590 AAACCCAGAAGGGTTAAACTGAAACTCA
1 AAACCCATAAGGGTTAAACTGAAGCTCA
5351618 TATGAGTTGA
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
Found at i:5351514 original size:21 final size:21
Alignment explanation
Indices: 5351464--5351515 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
5351454 TGCTACGCAA
* * *
5351464 AAACCCGTAAGGGTTAAACGG
1 AAACCCATAAGAGCTAAACGG
* *
5351485 AAGCTCATAAGAGCTAAACGG
1 AAACCCATAAGAGCTAAACGG
5351506 AAACCCATAA
1 AAACCCATAA
5351516 AGGTTAATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (21 bp):
AAACCCATAAGAGCTAAACGG
Found at i:5351549 original size:21 final size:21
Alignment explanation
Indices: 5351478--5351545 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
5351468 CCGTAAGGGT
*
5351478 TAAACGGAAGCTCATAAGAGC
1 TAAACGGAAGCTCAAAAGAGC
* * *
5351499 TAAACGGAAACCCATAAAG-GT
1 TAAACGGAAGCTCA-AAAGAGC
***
5351520 TAATTTGAAGCTCAAAAGAGC
1 TAAACGGAAGCTCAAAAGAGC
5351541 TAAAC
1 TAAAC
5351546 TGAAACCCAT
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.79
22 3 0.09
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (21 bp):
TAAACGGAAGCTCAAAAGAGC
Found at i:5353262 original size:14 final size:14
Alignment explanation
Indices: 5353243--5353269 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5353233 AATGTAAAAC
5353243 TATAAAAATTCAAT
1 TATAAAAATTCAAT
5353257 TATAAAAATTCAA
1 TATAAAAATTCAA
5353270 AAAGTAGCAA
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:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
TATAAAAATTCAAT
Done.