Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold154
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: 1945843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 156 characters in sequence are not A, C, G, or T
File 9 of 12
Found at i:1254209 original size:10 final size:10
Alignment explanation
Indices: 1254168--1254224 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
1254158 GAGTTAGGTA
1254168 AAAAAGAAAG
1 AAAAAGAAAG
1254178 AAAGAAGATGAAG
1 AAA-AAGA--AAG
1254191 AAGAAAGAAAG
1 AA-AAAGAAAG
*
1254202 AAAAAGAAAA
1 AAAAAGAAAG
1254212 AAAAAGAAA-
1 AAAAAGAAAG
1254221 AAAA
1 AAAA
1254225 TATGAAATGG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 4 0.10
10 19 0.45
11 9 0.21
13 9 0.21
14 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:1262098 original size:32 final size:32
Alignment explanation
Indices: 1261887--1262690 Score: 774
Period size: 32 Copynumber: 26.2 Consensus size: 32
1261877 AATTTTTTTC
*
1261887 TCAAAGCCCACACAAGTCGATGGC-A--CTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TT
* * *
1261917 TCAAA-ACC-CACAAGTCAGTGGC-A-TCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* * *
1261945 TCAAAGTCCACACAAGTTGGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* *
1261975 TCAAAG-CC-CACAAGTCAGTGGC-ATCC-TT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* **
1262003 TCAAAG-CC-CATAAGTCAATGGC-A--CTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TT
* *
1262031 TCAAAG-CC-CACAAGTCAGTGGC-A-CCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
1262059 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* *
1262091 TCAAAG-CC-CACAAGTCAGTGGC-A-CCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
1262119 TCAAAGCCCACACAAGTCGGTGGC-A--CTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TT
* *
1262149 TCAAAGCCCACATAAG-CTGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTC-GGTGGCAACCCTTT
*
1262181 TCAAAGCCCACATAAGTCGGTGGCAA-CCTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TT
* *
1262213 TCAAAGCCCACACAAGTCGGTGGTAATCCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
*
1262245 TCAAAGCCCACACAAGTCGGTGGCAACCTTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* *
1262277 TCAAAG-CC-CACAAGTCAGTGGC-ACCATTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
1262306 T-AAAGCCCACACAAGTCGGTGGC-A--CTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TT
* * *
1262335 TCAAAGCCCACATAAGTCAGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* *
1262367 TCAAAGACCACACAAGTCGGTGACAA-CCTATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TT
* *
1262399 TCAAAGCCCACATAAGTCGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
*
1262431 TCAAAGCCCACACAAGTCGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* *
1262463 TCAAAGCCCACACAAGTTGGTGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* *
1262495 TCAAAGCCCATACAAGTCGGTGGTAACCCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* * *
1262527 TCAAAGCCCACACAAGTTGATGGCAACCCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
1262559 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
* * *
1262591 TCAAAGCCCACACAAGTTGATGGGAA-CCTCTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TT
* * * * *
1262623 TCAAAAGTCCACAC--TTCTGTGGAAACCGTTT
1 TC-AAAGCCCACACAAGTCGGTGGCAACCCTTT
* * * *
1262654 TAAAAACCCACGCAAGTCAGTGGCAACCCTTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
1262686 TCAAA
1 TCAAA
1262691 TCACCATTTT
Statistics
Matches: 662, Mismatches: 77, Indels: 68
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.00
28 105 0.16
29 28 0.04
30 144 0.22
31 24 0.04
32 342 0.52
33 18 0.03
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (32 bp):
TCAAAGCCCACACAAGTCGGTGGCAACCCTTT
Found at i:1262371 original size:186 final size:184
Alignment explanation
Indices: 1261887--1262607 Score: 918
Period size: 186 Copynumber: 3.9 Consensus size: 184
1261877 AATTTTTTTC
* * * * *
1261887 TCAAAGCCCACACAAGTCGATGGC-A-CTATTTCAAAACCCACAAGTCAGTGGCATCTTTTCAAA
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAA
* * * *
1261950 GTCCACACAAGTTGGTGGCA-TCCTTTCAAAGCCCAC--AAGTCAGTGGC-ATCC-TTTCAAAG-
66 GCCCACACAAGTCGGTGGCACT-ATTTCAAAGCCCACATAAGTCAGTGGCAACCCATTTCAAAGC
* ** * *
1262009 CC-CATAAGTCAATGGC-A-CTATTTCAAAG-CC-CACAAGTCAGTGGCACCATT
130 CCACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGAACCATT
*
1262059 TCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAA
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAA
*
1262124 GCCCACACAAGTCGGTGGCACTATTTCAAAGCCCACATAAG-CTGGTGGCAACCCATTTCAAAGC
66 GCCCACACAAGTCGGTGGCACTATTTCAAAGCCCACATAAGTC-AGTGGCAACCCATTTCAAAGC
* *
1262188 CCACATAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGTAATCCTTT
130 CCACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGG-AA-CCATT
** *
1262245 TCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCAAAGCCCACAAGTCAGTGGCACCATTTTAAA
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAA
*
1262310 GCCCACACAAGTCGGTGGCACTATTTCAAAGCCCACATAAGTCAGTGGCAACCCATTTCAAAGAC
66 GCCCACACAAGTCGGTGGCACTATTTCAAAGCCCACATAAGTCAGTGGCAACCCATTTCAAAGCC
* *
1262375 CACACAAGTCGGTGACAACCTATTTCAAAGCCCACATAAGTCGGTGGCAACCCATT
131 CACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGG-AA-CCATT
**
1262431 TCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTT
1 TCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-A-CCATTT
* * * *
1262496 CAAAGCCCATACAAGTCGGTGGTAACCCT-TTTCAAAGCCCACACAAGT-TGATGGCAACCCATT
62 CAAAGCCCACACAAGTCGGTGG---CACTATTTCAAAGCCCACATAAGTCAG-TGGCAACCCATT
1262559 TCAAAGCCCACACAAGTCGGTGGCAACCCT-TTTCAAAGCCCACACAAGT
123 TCAAAGCCCACACAAGTCGGTGGCAA-CCTATTTCAAAGCCCACACAAGT
1262608 TGATGGGAAC
Statistics
Matches: 485, Mismatches: 38, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
172 23 0.05
173 1 0.00
174 64 0.13
175 2 0.00
176 8 0.02
177 3 0.01
178 8 0.02
179 2 0.00
180 12 0.02
181 1 0.00
182 11 0.02
183 2 0.00
184 12 0.02
185 1 0.00
186 214 0.44
187 3 0.01
188 12 0.02
189 1 0.00
190 26 0.05
191 1 0.00
192 72 0.15
193 6 0.01
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (184 bp):
TCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAA
GCCCACACAAGTCGGTGGCACTATTTCAAAGCCCACATAAGTCAGTGGCAACCCATTTCAAAGCC
CACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGAACCATT
Found at i:1262772 original size:45 final size:46
Alignment explanation
Indices: 1262721--1262844 Score: 151
Period size: 49 Copynumber: 2.7 Consensus size: 46
1262711 AAGTCCGATA
*
1262721 TCGCTGGCCTTGAATCAGCATATTGGCACTTTT-CTAAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACTTTTACTAAGCCCAATG
* *
1262766 TCGCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCACTTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGG--CACTTTT-ACTAAGCCCAATG
* * **
1262815 TCGTTGACCTTGAATTGGCACATTGGCACT
1 TCGCTGGCCTTGAATCAGCACATTGGCACT
1262845 CCTCTTATCT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
45 24 0.36
47 11 0.16
49 32 0.48
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.31
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACTTTTACTAAGCCCAATG
Found at i:1266262 original size:97 final size:96
Alignment explanation
Indices: 1266158--1266364 Score: 231
Period size: 96 Copynumber: 2.1 Consensus size: 96
1266148 GTTTATCGAA
* ** *
1266158 GATACACCAACCTTATTCCTCCGT-A-GGGATACTTTAACCCCTTTTTTTAAACTCATCAAAATT
1 GATACACCAACC-CATTCCT--GTAAGGGGATACTCCAACCCC-ATTTTTAAACTCATCAAAATT
*** *
1266221 TTGGTCTTATTTTGTCCAAATTGTCATTATC-GGG
62 TAAATCTTATTTTGTCCAAATTATCATTATCAGGG
* *
1266255 GATACACCAATCCCATTCCTTTAAGGGGATACTCCAACCCCATTTTTAAACTTATCAAAATTTAA
1 GATACACCAA-CCCATTCCTGTAAGGGGATACTCCAACCCCATTTTTAAACTCATCAAAATTTAA
* *
1266320 ATCTTATTTTGTCTAAATTATCATTGTCAGGG
65 ATCTTATTTTGTCCAAATTATCATTATCAGGG
*
1266352 GATACTCCAACCC
1 GATACACCAACCC
1266365 CGTTTTAAAC
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
95 1 0.01
96 48 0.52
97 42 0.45
98 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (96 bp):
GATACACCAACCCATTCCTGTAAGGGGATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAA
TCTTATTTTGTCCAAATTATCATTATCAGGG
Found at i:1266344 original size:96 final size:98
Alignment explanation
Indices: 1266183--1266361 Score: 245
Period size: 96 Copynumber: 1.8 Consensus size: 98
1266173 TTCCTCCGTA
** * *** *
1266183 GGGATACTTTAACCCCTTTTTTTAAACTCATCAAAATTTTGGTCTTATTTTGTCCAAATTGTCAT
1 GGGATACTCCAACCCCTATTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
1266248 TATC-GGGGATACACCAATCCCATTCCTTTAAG
66 TATCAGGGGATACACCAATCCCATTCCTTTAAG
* *
1266280 GGGATACTCCAACCCC-ATTTTTAAACTTATCAAAATTTAAATCTTATTTTGTCTAAATTATCAT
1 GGGATACTCCAACCCCTATTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
* *
1266344 TGTCAGGGGATACTCCAA
66 TATCAGGGGATACACCAA
1266362 CCCCGTTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
96 44 0.63
97 26 0.37
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (98 bp):
GGGATACTCCAACCCCTATTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
TATCAGGGGATACACCAATCCCATTCCTTTAAG
Found at i:1266422 original size:69 final size:70
Alignment explanation
Indices: 1266278--1266433 Score: 235
Period size: 70 Copynumber: 2.2 Consensus size: 70
1266268 CATTCCTTTA
* * * * *
1266278 AGGGGATACTCCAACCCCATTTTTAAACTTATCAAAATTTAAATCTTATTTTGTCTAAATTATCA
1 AGGGGATACTCCAACCCCAGTTTTAAACTCATCAAAATTTAAATCGTATTTTGGCCAAATTATCA
1266343 TTGTC
66 TTGTC
*
1266348 AGGGGATACTCCAACCCC-GTTTTAAACTCATCAAAATTTGAAGTCGTATTTTGGCCAAATTATC
1 AGGGGATACTCCAACCCCAGTTTTAAACTCATCAAAATTT-AAATCGTATTTTGGCCAAATTATC
1266412 ATTGTC
65 ATTGTC
1266418 -GGGGATACTCCAACCC
1 AGGGGATACTCCAACCC
1266434 TATTCCTCTG
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
69 35 0.44
70 44 0.56
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (70 bp):
AGGGGATACTCCAACCCCAGTTTTAAACTCATCAAAATTTAAATCGTATTTTGGCCAAATTATCA
TTGTC
Found at i:1269090 original size:19 final size:18
Alignment explanation
Indices: 1269066--1269143 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 18
1269056 TTTCTGGATC
1269066 TATCAATACAAAGAAATTG
1 TATCAATACAAA-AAATTG
*
1269085 TATCAAT----ATAA-TG
1 TATCAATACAAAAAATTG
* *
1269098 TATCGATACATTAAAATTG
1 TATCAATACA-AAAAATTG
*
1269117 TATCGATACAAAGAAATTG
1 TATCAATACAAA-AAATTG
1269136 TATCAATA
1 TATCAATA
1269144 TAATGTATCG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
13 8 0.17
14 2 0.04
15 1 0.02
18 4 0.09
19 32 0.68
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (18 bp):
TATCAATACAAAAAATTG
Found at i:1271508 original size:13 final size:13
Alignment explanation
Indices: 1271490--1271520 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1271480 ACATTTCTTC
1271490 ATGTATCGATACA
1 ATGTATCGATACA
1271503 ATGTATCGATACA
1 ATGTATCGATACA
*
1271516 TTGTA
1 ATGTA
1271521 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1271512 original size:33 final size:33
Alignment explanation
Indices: 1271470--1271536 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
1271460 GTTACATGCT
1271470 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
1271503 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
1271536 A
1 A
1271537 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:1271650 original size:33 final size:32
Alignment explanation
Indices: 1271587--1271651 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1271577 CAATTTGGCC
* *
1271587 ATGTATTGATACAATGAACATGTATAGATACA
1 ATGTATCGATACAAAGAACATGTATAGATACA
* *
1271619 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATAGATACA
1271652 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATAGATACA
Found at i:1273152 original size:63 final size:63
Alignment explanation
Indices: 1273005--1273165 Score: 173
Period size: 63 Copynumber: 2.6 Consensus size: 63
1272995 TCATAATTGA
* *
1273005 ATTGTATCGATATATGATAAATTGTATCGATACATTGCACCTAACAGCTATAATTTCAAATGC
1 ATTGTATCGATATATGATGAATTGTATCGATACATTGCACCTAACAGCTAGAATTTCAAATGC
* ** * * * *
1273068 ACTACATCGATACATGGTGAATTGTATCGATATATTAAGC-CC-AACGGCTAGAATTTCAAATGC
1 ATTGTATCGATATATGATGAATTGTATCGATACATT--GCACCTAACAGCTAGAATTTCAAATGC
* * * *
1273131 ATTGTATTGATATATTATGAATTTTATTGATACAT
1 ATTGTATCGATATATGATGAATTGTATCGATACAT
1273166 AAGAGCGTGT
Statistics
Matches: 77, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
63 73 0.95
64 2 0.03
65 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (63 bp):
ATTGTATCGATATATGATGAATTGTATCGATACATTGCACCTAACAGCTAGAATTTCAAATGC
Found at i:1274055 original size:4 final size:4
Alignment explanation
Indices: 1274033--1274071 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
1274023 GAGTTTAGCT
* *
1274033 AAGA AAGA GAGA AAAA AAGA AAGA AAGAA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AA
1274072 AAGAGAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1274057 original size:12 final size:12
Alignment explanation
Indices: 1274036--1274083 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
1274026 TTTAGCTAAG
*
1274036 AAAGAGAGAAAA
1 AAAGAAAGAAAA
1274048 AAAGAAAGAAAGA
1 AAAGAAAGAAA-A
1274061 AAAGAAAGAAAA
1 AAAGAAAGAAAA
*
1274073 AGAG-AAGAAAA
1 AAAGAAAGAAAA
1274084 TAGAGTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 7 0.21
12 14 0.42
13 12 0.36
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:1274070 original size:25 final size:24
Alignment explanation
Indices: 1274036--1274082 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1274026 TTTAGCTAAG
*
1274036 AAAGAGAGAAAAAAAGAAAGAAAGA
1 AAAGAAAGAAAAAAAG-AAGAAAGA
*
1274061 AAAGAAAGAAAAAGAGAAGAAA
1 AAAGAAAGAAAAAAAGAAGAAA
1274083 ATAGAGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
AAAGAAAGAAAAAAAGAAGAAAGA
Found at i:1274088 original size:12 final size:11
Alignment explanation
Indices: 1274033--1274088 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
1274023 GAGTTTAGCT
*
1274033 AAGAAAGAGAG
1 AAGAAAAAGAG
1274044 AA-AAAAAGA-
1 AAGAAAAAGAG
*
1274053 AAGAAAGAAAAG
1 AAGAAA-AAGAG
1274065 AAAGAAAAAGAG
1 -AAGAAAAAGAG
1274077 AAGAAAATAGAG
1 AAGAAAA-AGAG
1274089 TGAAAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 2 0.05
10 9 0.24
11 12 0.32
12 8 0.22
13 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:1277193 original size:13 final size:13
Alignment explanation
Indices: 1277175--1277200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1277165 TACACACAAG
1277175 ATGTATCGATACA
1 ATGTATCGATACA
1277188 ATGTATCGATACA
1 ATGTATCGATACA
1277201 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1277217 original size:33 final size:32
Alignment explanation
Indices: 1277157--1277220 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1277147 CTTAACTGTT
*
1277157 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1277189 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1277221 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1283352 original size:13 final size:13
Alignment explanation
Indices: 1283334--1283366 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1283324 CATTCTCTGC
*
1283334 ATCGATACATTGT
1 ATCGATACAGTGT
1283347 ATCGATACAGTGT
1 ATCGATACAGTGT
1283360 ATCGATA
1 ATCGATA
1283367 TAAAGGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (13 bp):
ATCGATACAGTGT
Found at i:1283883 original size:274 final size:274
Alignment explanation
Indices: 1283394--1283943 Score: 1100
Period size: 274 Copynumber: 2.0 Consensus size: 274
1283384 CAGTTCGAAC
1283394 CCTTTCTTCTTCATTCTATCGATACACAACGCCAAAAACACCCAAAAATCCTCTTAAACCCTATC
1 CCTTTCTTCTTCATTCTATCGATACACAACGCCAAAAACACCCAAAAATCCTCTTAAACCCTATC
1283459 TTCAATTCATCAAAATTCATCAAATCTTTTGCAAATTTCTTGTTTTTCACTTCAAAATACATCAT
66 TTCAATTCATCAAAATTCATCAAATCTTTTGCAAATTTCTTGTTTTTCACTTCAAAATACATCAT
1283524 TTTTCATCAAAATCATCAACAAAAACAGTTTTTATTCCATCAAATCTTTCATTCAAAACTGTCAA
131 TTTTCATCAAAATCATCAACAAAAACAGTTTTTATTCCATCAAATCTTTCATTCAAAACTGTCAA
1283589 AACCCACTGTTTTTGTCACTTTTTAATCCCTTCAAAAATCACATTTAGGAGTGTTTTTAAGCCAA
196 AACCCACTGTTTTTGTCACTTTTTAATCCCTTCAAAAATCACATTTAGGAGTGTTTTTAAGCCAA
1283654 ATTTTTGTACCAAT
261 ATTTTTGTACCAAT
1283668 CCTTTCTTCTTCATTCTATCGATACACAACGCCAAAAACACCCAAAAATCCTCTTAAACCCTATC
1 CCTTTCTTCTTCATTCTATCGATACACAACGCCAAAAACACCCAAAAATCCTCTTAAACCCTATC
1283733 TTCAATTCATCAAAATTCATCAAATCTTTTGCAAATTTCTTGTTTTTCACTTCAAAATACATCAT
66 TTCAATTCATCAAAATTCATCAAATCTTTTGCAAATTTCTTGTTTTTCACTTCAAAATACATCAT
1283798 TTTTCATCAAAATCATCAACAAAAACAGTTTTTATTCCATCAAATCTTTCATTCAAAACTGTCAA
131 TTTTCATCAAAATCATCAACAAAAACAGTTTTTATTCCATCAAATCTTTCATTCAAAACTGTCAA
1283863 AACCCACTGTTTTTGTCACTTTTTAATCCCTTCAAAAATCACATTTAGGAGTGTTTTTAAGCCAA
196 AACCCACTGTTTTTGTCACTTTTTAATCCCTTCAAAAATCACATTTAGGAGTGTTTTTAAGCCAA
1283928 ATTTTTGTACCAAT
261 ATTTTTGTACCAAT
1283942 CC
1 CC
1283944 ACTCTCAAAC
Statistics
Matches: 276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
274 276 1.00
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (274 bp):
CCTTTCTTCTTCATTCTATCGATACACAACGCCAAAAACACCCAAAAATCCTCTTAAACCCTATC
TTCAATTCATCAAAATTCATCAAATCTTTTGCAAATTTCTTGTTTTTCACTTCAAAATACATCAT
TTTTCATCAAAATCATCAACAAAAACAGTTTTTATTCCATCAAATCTTTCATTCAAAACTGTCAA
AACCCACTGTTTTTGTCACTTTTTAATCCCTTCAAAAATCACATTTAGGAGTGTTTTTAAGCCAA
ATTTTTGTACCAAT
Found at i:1284117 original size:20 final size:22
Alignment explanation
Indices: 1284084--1284128 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1284074 GCAGCACTCA
**
1284084 CCAGGTCGTGACC-GGCA-CCC
1 CCAGGTCGCAACCGGGCAGCCC
1284104 CCAGGTCGCAACCGGGCAGCCC
1 CCAGGTCGCAACCGGGCAGCCC
1284126 CCA
1 CCA
1284129 CACTCACAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.18, C:0.47, G:0.29, T:0.07
Consensus pattern (22 bp):
CCAGGTCGCAACCGGGCAGCCC
Found at i:1285528 original size:51 final size:51
Alignment explanation
Indices: 1285461--1285577 Score: 225
Period size: 51 Copynumber: 2.3 Consensus size: 51
1285451 ATAAATTTTA
1285461 TGATTAAGGGGGAGAAAGAAACTTGTGATTAAAAGATATTGTTAAATTGCT
1 TGATTAAGGGGGAGAAAGAAACTTGTGATTAAAAGATATTGTTAAATTGCT
1285512 TGATTAAGGGGGAGAAAGAAACTTGTGATTAAAAGATATTGTTAAATTGCT
1 TGATTAAGGGGGAGAAAGAAACTTGTGATTAAAAGATATTGTTAAATTGCT
*
1285563 TTATTAAGGGGGAGA
1 TGATTAAGGGGGAGA
1285578 GATAAGGAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.31
Consensus pattern (51 bp):
TGATTAAGGGGGAGAAAGAAACTTGTGATTAAAAGATATTGTTAAATTGCT
Found at i:1286158 original size:13 final size:13
Alignment explanation
Indices: 1286140--1286164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1286130 ATAATGCACA
1286140 GTATCGATACATT
1 GTATCGATACATT
1286153 GTATCGATACAT
1 GTATCGATACAT
1286165 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1286282 original size:13 final size:13
Alignment explanation
Indices: 1286264--1286289 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1286254 TACACACAAG
1286264 ATGTATCGATACA
1 ATGTATCGATACA
1286277 ATGTATCGATACA
1 ATGTATCGATACA
1286290 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1286306 original size:33 final size:32
Alignment explanation
Indices: 1286246--1286309 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1286236 CTTAACTGTT
*
1286246 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1286278 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1286310 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1291191 original size:20 final size:19
Alignment explanation
Indices: 1291151--1291202 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
1291141 CGATACAGTA
* *
1291151 TATCGATACATGTTCATTG
1 TATCGATACATGATAATTG
1291170 TATCGATACATGCATAATTG
1 TATCGATACATG-ATAATTG
1291190 TATCGATACATGA
1 TATCGATACATGA
1291203 AACTGGCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (19 bp):
TATCGATACATGATAATTG
Found at i:1291274 original size:20 final size:21
Alignment explanation
Indices: 1291230--1291275 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1291220 CTACCTTTGT
**
1291230 TTGTATCGATACATGGCACAA
1 TTGTATCGATACATAACACAA
1291251 -TGTATCGATACATAACA-AA
1 TTGTATCGATACATAACACAA
1291270 TTGTAT
1 TTGTAT
1291276 TGGTACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACATAACACAA
Found at i:1292903 original size:18 final size:18
Alignment explanation
Indices: 1292880--1292917 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1292870 AACCATCAAA
1292880 GATGATGAAGATAATGAT
1 GATGATGAAGATAATGAT
*
1292898 GATGATGATGATAATGAT
1 GATGATGAAGATAATGAT
1292916 GA
1 GA
1292918 AGTTGACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (18 bp):
GATGATGAAGATAATGAT
Found at i:1292915 original size:9 final size:9
Alignment explanation
Indices: 1292884--1292917 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1292874 ATCAAAGATG
*
1292884 ATGAAGATA
1 ATGATGATA
*
1292893 ATGATGATG
1 ATGATGATA
1292902 ATGATGATA
1 ATGATGATA
1292911 ATGATGA
1 ATGATGA
1292918 AGTTGACTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
ATGATGATA
Found at i:1299840 original size:21 final size:21
Alignment explanation
Indices: 1299816--1299870 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1299806 TTTCAATATT
1299816 TATAAATGTTTTAGAG-TTATG
1 TATAAATGTTTTAGAGCTT-TG
*
1299837 TATAAATGTTTTCGAGCTTTG
1 TATAAATGTTTTAGAGCTTTG
*
1299858 AATCAAATGTTTT
1 TAT-AAATGTTTT
1299871 TAAGTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.47
Consensus pattern (21 bp):
TATAAATGTTTTAGAGCTTTG
Found at i:1300117 original size:20 final size:20
Alignment explanation
Indices: 1300076--1300126 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1300066 CCACTGTTTA
**
1300076 TATCGATACATGGCACAATG
1 TATCGATACATAACACAATG
1300096 TATCGATACATAACA-AATTG
1 TATCGATACATAACACAA-TG
*
1300116 TATTGATACAT
1 TATCGATACAT
1300127 TGTCCCAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (20 bp):
TATCGATACATAACACAATG
Found at i:1303137 original size:35 final size:35
Alignment explanation
Indices: 1303097--1303163 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
1303087 ATAGGAAATA
1303097 TATCGATACATTAGTAATTATATCGATACAATATG
1 TATCGATACATTAGTAATTATATCGATACAATATG
* * * * *
1303132 TATCGATATATTATTCATTGTATTGATACAAT
1 TATCGATACATTAGTAATTATATCGATACAAT
1303164 CTGGAAATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (35 bp):
TATCGATACATTAGTAATTATATCGATACAATATG
Found at i:1312725 original size:72 final size:72
Alignment explanation
Indices: 1312635--1312780 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
1312625 ATCCTAAAAA
1312635 AATTACAAAAATGCCTTTAGGGGATACCTTCAATATAAAAGTACCTAGCACCATAAAAGGCTCGA
1 AATTACAAAAATGCCTTTAGGGGATACCTTCAATATAAAAGTACCTAGCACCATAAAAGGCTCGA
1312700 AAAAATG
66 AAAAATG
1312707 AATTACAAAAATGCCTTTAGGGGATACCTTCAATATAAAAGTACCTAGCACCATAAAAGGCTCGA
1 AATTACAAAAATGCCTTTAGGGGATACCTTCAATATAAAAGTACCTAGCACCATAAAAGGCTCGA
1312772 AAAAATG
66 AAAAATG
1312779 AA
1 AA
1312781 AAAAAATGAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (72 bp):
AATTACAAAAATGCCTTTAGGGGATACCTTCAATATAAAAGTACCTAGCACCATAAAAGGCTCGA
AAAAATG
Found at i:1314387 original size:15 final size:16
Alignment explanation
Indices: 1314367--1314404 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
1314357 CCATCTTCTC
*
1314367 TCTTTTTTT-CTTTTA
1 TCTTTTTTTATTTTTA
1314382 T-TTTTTTTATTTTTA
1 TCTTTTTTTATTTTTA
1314397 TCTTTTTT
1 TCTTTTTT
1314405 CATCCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 7 0.35
16 6 0.30
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (16 bp):
TCTTTTTTTATTTTTA
Found at i:1314589 original size:16 final size:17
Alignment explanation
Indices: 1314568--1314620 Score: 76
Period size: 16 Copynumber: 3.3 Consensus size: 17
1314558 TTAGCCAATA
1314568 AAATTTAAAA-TAAAAT
1 AAATTTAAAATTAAAAT
1314584 AAATTTAAAATTAAAA-
1 AAATTTAAAATTAAAAT
1314600 AAA-TTAAAATTAAAAT
1 AAATTTAAAATTAAAAT
*
1314616 CAATT
1 AAATT
1314621 CTCAGTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 12 0.36
16 15 0.45
17 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTTAAAATTAAAAT
Found at i:1314608 original size:15 final size:15
Alignment explanation
Indices: 1314567--1314614 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1314557 TTTAGCCAAT
*
1314567 AAAATTTAAAA-TAA
1 AAAAATTAAAATTAA
1314581 AATAAATTTAAAATTAA
1 AA-AAA-TTAAAATTAA
1314598 AAAAATTAAAATTAA
1 AAAAATTAAAATTAA
1314613 AA
1 AA
1314615 TCAATTCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.07
15 14 0.47
16 9 0.30
17 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTAAAATTAA
Found at i:1314899 original size:153 final size:154
Alignment explanation
Indices: 1314724--1315149 Score: 372
Period size: 154 Copynumber: 2.8 Consensus size: 154
1314714 ATGTATATGA
* **
1314724 AAAAATTC-AAAACTTAAAAAATAAATTAAATTTTCTAAAACTGATTTAATGTGAATTTAATGAA
1 AAAAATTCTAAAACTTATAAAATAAATTAAATTTTCTAAAACTGATTTAATGTGAATTTAAACAA
* *
1314788 -AATAGTTGATGAAATTTAAAAAGTT-TGAACCAAGAAAAAT-CTAACCGAAAAATTTTACAGAG
66 TAATAGTTGAAGAAATTTAAAAA-TTATAAACCAAGAAAAATCCT-ACCG-AAAATTTTACAGAG
* * *
1314850 TAGAAAA-TTTCATATTTTGGA-AATA-G
128 TAAAAAACTTT-ATATTTT-AATAACAGG
* * * * * * *
1314876 AAAAATTCTAAAACTCATAAAATAAATTGAATTTTTCAAAAAATAATTTACTATGAA-TTAAACA
1 AAAAATTCTAAAACTTATAAAATAAATT-AAATTTTCTAAAACTGATTTAATGTGAATTTAAACA
* * * ** **
1314940 ATAATATTTGAAGAATTTTGAAAATTATAAACTTAGAAAAATCCTATTGAAAATTTTACAGAGTA
65 ATAATAGTTGAAGAAATTTAAAAATTATAAACCAAGAAAAATCCTACCGAAAATTTTACAGAGTA
*
1315005 AAAAACTTTGTATTTTAATAACAGG
130 AAAAACTTTATATTTTAATAACAGG
** * * * *
1315030 AAAAATTCTAAAACTTATAAAATAAATTGTATTTTTTCAAACTGATTGAATGTCAA-TTACAA-A
1 AAAAATTCTAAAACTTATAAAATAAATTAAATTTTCTAAAACTGATTTAATGTGAATTTA-AACA
* * ** * * *
1315093 AGAATATTTGAAG-AATTTTGAAATTACAAA-CATAGAAAAATCCTACCAAAAAATTTA
65 ATAATAGTTGAAGAAATTTAAAAATTATAAACCA-AGAAAAATCCTACCGAAAATTTTA
1315150 TGAAAAAGAA
Statistics
Matches: 217, Mismatches: 47, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
152 42 0.19
153 86 0.40
154 87 0.40
155 2 0.01
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (154 bp):
AAAAATTCTAAAACTTATAAAATAAATTAAATTTTCTAAAACTGATTTAATGTGAATTTAAACAA
TAATAGTTGAAGAAATTTAAAAATTATAAACCAAGAAAAATCCTACCGAAAATTTTACAGAGTAA
AAAACTTTATATTTTAATAACAGG
Found at i:1315043 original size:154 final size:151
Alignment explanation
Indices: 1314836--1315137 Score: 378
Period size: 153 Copynumber: 2.0 Consensus size: 151
1314826 ATCTAACCGA
* * *
1314836 AAAATTTTACAGAGTAGAAAATTTCATATTTTGGAAATAGAAAAATTCTAAAACTCATAAAATAA
1 AAAATTTTACAGAGTAAAAAATTTCATATTTTGAAAACAGAAAAATTCTAAAACTCATAAAATAA
* * * *
1314901 ATTG-AATTTTTCAAAAAATAATTTACTATGAATTA-AACAATAATATTTGAAGAATTTTGAAAA
66 ATTGTAATTTTTC--AAAATAATTGAATATCAATTACAA-AAGAATATTTGAAGAATTTTG-AAA
* *
1314964 TTATAAACTTAGAAAAATCCTATTG
127 TTACAAACATAGAAAAATCCTATTG
* *
1314989 AAAATTTTACAGAGTAAAAAACTTT-GTATTTT-AATAACAGGAAAAATTCTAAAACTTATAAAA
1 AAAATTTTACAGAGTAAAAAA-TTTCATATTTTGAA-AACA-GAAAAATTCTAAAACTCATAAAA
* * * *
1315052 TAAATTGTATTTTTTCAAACTGATTGAATGTCAATTACAAAAGAATATTTGAAGAATTTTGAAAT
63 TAAATTGTAATTTTTCAAAATAATTGAATATCAATTACAAAAGAATATTTGAAGAATTTTGAAAT
1315117 TACAAACATAGAAAAATCCTA
128 TACAAACATAGAAAAATCCTA
1315138 CCAAAAAATT
Statistics
Matches: 129, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
152 24 0.19
153 64 0.50
154 34 0.26
155 7 0.05
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (151 bp):
AAAATTTTACAGAGTAAAAAATTTCATATTTTGAAAACAGAAAAATTCTAAAACTCATAAAATAA
ATTGTAATTTTTCAAAATAATTGAATATCAATTACAAAAGAATATTTGAAGAATTTTGAAATTAC
AAACATAGAAAAATCCTATTG
Found at i:1316831 original size:20 final size:19
Alignment explanation
Indices: 1316785--1316841 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1316775 TTATATCGAT
* *
1316785 ACATTGTATTGATACATGT
1 ACATTGTATCGATACATGC
*
1316804 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
1316823 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1316842 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1320181 original size:13 final size:13
Alignment explanation
Indices: 1320162--1320200 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1320152 ACTATTTATG
1320162 ATGTATCGATACA
1 ATGTATCGATACA
*
1320175 CTGTATCGATACA
1 ATGTATCGATACA
1320188 ATGTATCGATACA
1 ATGTATCGATACA
1320201 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1320312 original size:22 final size:22
Alignment explanation
Indices: 1320258--1320312 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
1320248 GTGAATAGTG
1320258 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
1320280 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
1320301 TGAACAGTGATG
1 TGAACAGTGATG
1320313 AATAGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:1320319 original size:10 final size:10
Alignment explanation
Indices: 1320300--1320330 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1320290 GTATCGATAC
1320300 ATGAACAGTG
1 ATGAACAGTG
*
1320310 ATGAATAGTG
1 ATGAACAGTG
1320320 ATGAACAGTG
1 ATGAACAGTG
1320330 A
1 A
1320331 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1320418 original size:53 final size:53
Alignment explanation
Indices: 1320354--1320490 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
1320344 CTACTACCAA
* *
1320354 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCTAGTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1320407 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1320460 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1320491 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1320526 original size:21 final size:20
Alignment explanation
Indices: 1320478--1320532 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1320468 TACATATTTG
**
1320478 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATAAAA
* *
1320498 TCTGTATCGATACATTTAAAA
1 TGTGTATCGATAC-TATAAAA
1320519 TGTGTATCGATACT
1 TGTGTATCGATACT
1320533 TTTCAGGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (20 bp):
TGTGTATCGATACTATAAAA
Found at i:1320597 original size:21 final size:21
Alignment explanation
Indices: 1320571--1320611 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1320561 GTCAACCTTG
1320571 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1320592 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1320612 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1324544 original size:13 final size:13
Alignment explanation
Indices: 1324522--1324558 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1324512 AACCTAGATA
1324522 TATCGATACATTG
1 TATCGATACATTG
* *
1324535 TATTGATACAATG
1 TATCGATACATTG
1324548 TATCGATACAT
1 TATCGATACAT
1324559 AGGTTACTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1327021 original size:13 final size:13
Alignment explanation
Indices: 1327003--1327029 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1326993 ACATTATGTT
1327003 TTGTATCGATACA
1 TTGTATCGATACA
1327016 TTGTATCGATACA
1 TTGTATCGATACA
1327029 T
1 T
1327030 GTTCATGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1327065 original size:20 final size:19
Alignment explanation
Indices: 1327013--1327069 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1327003 TTGTATCGAT
*
1327013 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
* * *
1327032 TCATGGTATTGATACATGC
1 ACATTGTATCGATACATGC
1327051 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1327070 AAACTGCAGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1330740 original size:17 final size:17
Alignment explanation
Indices: 1330718--1330754 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1330708 TTAAATAATA
1330718 TTTA-TTTATTATTTTAT
1 TTTATTTTATT-TTTTAT
1330735 TTTATTTTATTTTTTAT
1 TTTATTTTATTTTTTAT
1330752 TTT
1 TTT
1330755 TAAAATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTATTTTTTAT
Found at i:1332378 original size:15 final size:15
Alignment explanation
Indices: 1332345--1332377 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1332335 ATCCCAAGTA
1332345 TTTTCTTTCTTTTTC
1 TTTTCTTTCTTTTTC
1332360 TTTTCTTTCTTTTT-
1 TTTTCTTTCTTTTTC
1332374 TTTT
1 TTTT
1332378 TTTTTTTGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:1332382 original size:19 final size:19
Alignment explanation
Indices: 1332346--1332380 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1332336 TCCCAAGTAT
1332346 TTTCTTTCTTTTTCTTTTC
1 TTTCTTTCTTTTTCTTTTC
1332365 TTTCTTT-TTTTT-TTTT
1 TTTCTTTCTTTTTCTTTT
1332381 TTTTGCGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTCTTTCTTTTTCTTTTC
Found at i:1333667 original size:14 final size:14
Alignment explanation
Indices: 1333648--1333683 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1333638 TAATTAATTA
1333648 ATTATTACTA-TTTT
1 ATTATTA-TATTTTT
1333662 ATTATTATATTTTT
1 ATTATTATATTTTT
1333676 ATTATTAT
1 ATTATTAT
1333684 TTTGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTATATTTTT
Found at i:1334276 original size:43 final size:42
Alignment explanation
Indices: 1334229--1334363 Score: 123
Period size: 43 Copynumber: 3.2 Consensus size: 42
1334219 AAAGGGTGGA
* * *
1334229 AAAGTCTTTAGGGTGAAAGCTGATAAGTAGACTTGAGGGTAAG
1 AAAGTCTTTA-GGTCAAAGCTGATAGGCAGACTTGAGGGTAAG
* * *
1334272 AAAGT-TTCCAAGGTCAAAG-TAGATAGGCAAAC-GGAGGGTAAG
1 AAAGTCTT--TAGGTCAAAGCT-GATAGGCAGACTTGAGGGTAAG
* * *
1334314 AAAATCTCCTAGGTCAAAGCTGATAGGCAGACTTGAAGGTAAG
1 AAAGTCT-TTAGGTCAAAGCTGATAGGCAGACTTGAGGGTAAG
1334357 AAAGTCT
1 AAAGTCT
1334364 CCAAGGTAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
42 35 0.49
43 36 0.50
44 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (42 bp):
AAAGTCTTTAGGTCAAAGCTGATAGGCAGACTTGAGGGTAAG
Found at i:1334513 original size:42 final size:42
Alignment explanation
Indices: 1334257--1335868 Score: 939
Period size: 42 Copynumber: 38.2 Consensus size: 42
1334247 GCTGATAAGT
* * ** *
1334257 AGACTTGAGGGTAAGAAAGTTTCCAAGGTCAAAGTAGATAGGC
1 AGACTTGA-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * * *
1334300 AAAC-GGAGGGTAAGAAAATCTCCTAGGTCAAAGCTGATAGGC
1 AGACTTGA-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * *
1334342 AGACTTGAAGGTAAGAAAGTCTCCAAGGTAAAAGTCGACATGT
1 AGACTTG-AGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * *
1334385 AGACTTGAGGTGAGGCAA-TCTCCATGGTCAAAGCCAATAGGC
1 AGACTTGAGGTAAGG-AAGTCTCCAAGGTCAAAGCCGACAGGC
* ** * ** * *
1334427 AGAC-TAACGGTAAAAAAGTCTCCAAGGTTAAAGTTGAAAGGT
1 AGACTTGA-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * *
1334469 AGACTTGAGGTGAGGTAGTCTCTAAGGTCAAAGCCAACAAGT
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * **
1334511 AGAC-TAATGGTAAGAAAGTCTCTAAGGTCAAAGCCAACAGAA
1 AGACTTGA-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * *
1334553 AAACTTGAGATTAGGCAGTCTCCAGGGTCAAAGCCGACAGGT
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
** * * * *
1334595 AGACTAAAGAT-AGGAAAATCTCCAAAGTCAAAGCCGACAGAC
1 AGACTTGAGGTAAGG-AAGTCTCCAAGGTCAAAGCCGACAGGC
* * * *
1334637 AGACTTGAGGTAAAGTAGTCTACAAGGTCAAAGCCGACAGAC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* ** * ** *
1334679 AAACTAAAGAT-AGGAAAGTCTCCAAGGTCAAAGTTGACAGGT
1 AGACTTGAGGTAAGG-AAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * *
1334721 AGACTTCAGGTAAGGCAGTCTCTAGGGTCAAAGCTGGCAGGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * *
1334763 AGAC-TGAAGGGT-AGGAAAGTCTCTAGGGTTAAAGCC-ATAAGGT
1 AGACTTG-A-GGTAAGG-AAGTCTCCAAGGTCAAAGCCGA-CAGGC
* * *
1334806 AGACTTGAGGTAA-GTAGTCTCCAAGGTCAAAACCGACAAGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * *
1334847 A-AATTGAAAGGTAAAGAAGTCTCCAAGGTCAAAGTCAACAGGT
1 AGACTTG--AGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * ** *
1334890 AGACTTGAGGTAA-GACAGTCTCTAGGGTCAAAG-TTAGTAGGC
1 AGACTTGAGGTAAGGA-AGTCTCCAAGGTCAAAGCCGA-CAGGC
** * * * *
1334932 AGACTAAAGGGTAAGAAAGTTTCTAAGGTCAAAACCGACAGGC
1 AGACTTGA-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* ** * ** * * *
1334975 AAACTTGAGGTAAGGTTGTTTTTAGGGTCAATGCCGACAAGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * *
1335017 A-AATTGAATGATAAGAAAGTTTCCAGGGTCAAAGCCGATAGGC
1 AGACTTG-A-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * * *
1335060 TGACTTAAGGTAAGGTAGTCTCTAGGGTCAATGCCGATAGGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
*
1335102 AGACTTGAGGTAAGGCAGTCTCCAAGGTCAAAGCCGACAGGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * ** *
1335144 AGAC-TGAAGGTAAGAAAGTCTCCAAGATCAAAGCAAACAGGT
1 AGACTTG-AGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * *
1335186 AGACTTGAGGTGAGGTAGTCTCCAGGGTCAAAGCCGATAGGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
*** * *
1335228 AGACAAAAGGTAAGAAAGTCTCCAAGGTCAAAGTCGACAGGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * *
1335270 AGACTTGAGGTGAGGCAGTCTCCAAAGTCAAAGCCGACAGGT
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * *
1335312 AGAC-TGAAGGTACGAAAGTCTCCAAGGTCAAAACCGACAGGC
1 AGACTTG-AGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* ** * * **
1335354 AGACTTGAGGTGAGGCGGTCTCCAAGGTCAAAGTCGACCGAT
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * *
1335396 AGA-TTGAAGGT-AGAAAAGTCTCCAAGGTTAAAGCTGACAGGC
1 AGACTTG-AGGTAAG-GAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * * * *
1335438 AGACTTAAGGTGAGGCAGTCTCTAAGGTCAAAGTCAAAAGAC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* *
1335480 AGAC-TGAGGGTAAGAAAGTCTCCAAGGTCAAAGCCAACAGGC
1 AGACTTGA-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * * * *
1335522 AAACTTAAGGTGAGGTAGTCTCC-TGCGTCAAAGTCGATAGGT
1 AGACTTGAGGTAAGGAAGTCTCCAAG-GTCAAAGCCGACAGGC
** * * * ** *
1335564 AGACTAAAGAGTAAGAAAGTTTCCAGGGTCAAAGTGGATAGGC
1 AGACTTGAG-GTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * *
1335607 AAACTTGAGGTGAGGTAGTCTCTAAGATCAAAGTCGACAGGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* ** * * * *
1335649 AAACTAAAGGGTAAGAAAGTCTCCAAGGTCAAAGCTGATAGGT
1 AGACTTGA-GGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * *
1335692 AGACTTGAGGTAAGGCAGTCTCTAGGGTCAAAGCCGATAGGT
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * *
1335734 AGAC-TGAAGGTAAGAAAGTCTCCAGGGTCAAAGCTGACAGGC
1 AGACTTG-AGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * *
1335776 AGACTTTAAGTGAGGCAGTCTCCAAGGTCAAAGCTGACAAGC
1 AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * *
1335818 AGACTAGAGGT-AGAAAAGACTCCAAGGTCAAAACTGACAGGC
1 AGACTTGAGGTAAG-GAAGTCTCCAAGGTCAAAGCCGACAGGC
*
1335860 AAAC-TGAGG
1 AGACTTGAGG
1335869 GGTAAGAAAT
Statistics
Matches: 1191, Mismatches: 330, Indels: 98
0.74 0.20 0.06
Matches are distributed among these distances:
40 4 0.00
41 57 0.05
42 892 0.75
43 225 0.19
44 13 0.01
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.18
Consensus pattern (42 bp):
AGACTTGAGGTAAGGAAGTCTCCAAGGTCAAAGCCGACAGGC
Found at i:1336013 original size:45 final size:45
Alignment explanation
Indices: 1335900--1336013 Score: 110
Period size: 45 Copynumber: 2.5 Consensus size: 45
1335890 GACTAAGGTA
*
1335900 GAACCATCATGTCAAACAGAAA-G-GAAAAGGATTTGACCAGGGTGG
1 GAACCA-CATGTCAATCAGAAATGAGAAAA-GATTTGACCAGGGTGG
* * * * *
1335945 TAACTAGATGTCAAATTAG-AATGAGAAAA-ATCTTGACTAGGGTGG
1 GAACCACATGTC-AATCAGAAATGAGAAAAGAT-TTGACCAGGGTGG
1335990 GAACCACATGTCAATCAGAAATGA
1 GAACCACATGTCAATCAGAAATGA
1336014 TGGGAAGTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
44 14 0.26
45 35 0.65
46 5 0.09
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (45 bp):
GAACCACATGTCAATCAGAAATGAGAAAAGATTTGACCAGGGTGG
Found at i:1348992 original size:188 final size:190
Alignment explanation
Indices: 1348715--1349123 Score: 543
Period size: 188 Copynumber: 2.2 Consensus size: 190
1348705 TGCCCTTTCA
* * * * ** *
1348715 GAAAACCCATAGGAATATGAAAATATAACTCGAGTAAATAAACGACCACACATTTTTAAAAAATA
1 GAAAA-CCATAAGAATATGAAAACATGACTCCAACAAATAAACAACCACACATTTTTAAAAAATA
** * * * *
1348780 TTAATTTTTTGGAAATCGAATTTTTTTAAATTTTTAAATTTACCTTCTAAATTTTGAAAATTATT
65 TTAATTTTAAGGAAACCGAATTTTTCTAAATTTTTAAATTTAACTTCTAAATTTTGAAAATTATG
* * * *
1348845 TTTCGGACCCGATGGAAAACCAAGGGATACGAAAGGTATTAAAAAATTTCATACCCTGACG
130 TTTCGGACCCGACGAAAAACCAAGGGATACGAAAAGTATTAAAAAATTTCATACCCCGACG
* * **
1348906 GAAAACCATAAGAATATGAAAACATGACTCCAACAAATAAACAATCACA-TTTTTTTTAAAATAT
1 GAAAACCATAAGAATATGAAAACATGACTCCAACAAATAAACAACCACACATTTTTAAAAAATAT
*
1348970 TAA-TTTAAGGAAACCGAATTTTTCTAAATTTTTAAATTTAACTTCTAAATTTTGAACATTATGT
66 TAATTTTAAGGAAACCGAATTTTTCTAAATTTTTAAATTTAACTTCTAAATTTTGAAAATTATGT
* * * **
1349034 TTCGTACCCGACGAAAAATCAAGGGATATGAAAAGTATTAAAATTTTTCATACCCCGACG
131 TTCGGACCCGACGAAAAACCAAGGGATACGAAAAGTATTAAAAAATTTCATACCCCGACG
*
1349094 AAAAACCATAAGAATATGAAAACATGACTC
1 GAAAACCATAAGAATATGAAAACATGACTC
1349124 GAGTGGGCAT
Statistics
Matches: 190, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
188 134 0.71
189 15 0.08
190 36 0.19
191 5 0.03
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (190 bp):
GAAAACCATAAGAATATGAAAACATGACTCCAACAAATAAACAACCACACATTTTTAAAAAATAT
TAATTTTAAGGAAACCGAATTTTTCTAAATTTTTAAATTTAACTTCTAAATTTTGAAAATTATGT
TTCGGACCCGACGAAAAACCAAGGGATACGAAAAGTATTAAAAAATTTCATACCCCGACG
Found at i:1349722 original size:1 final size:1
Alignment explanation
Indices: 1349711--1349755 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
1349701 ATCCCAAGTA
* * * *
1349711 TTTTCTTTTTTTTTTCTTTTCTTTTTCTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1349756 GCGTCAACTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:1349727 original size:11 final size:11
Alignment explanation
Indices: 1349711--1349755 Score: 74
Period size: 11 Copynumber: 4.2 Consensus size: 11
1349701 ATCCCAAGTA
1349711 TTTTCTTTTTT
1 TTTTCTTTTTT
*
1349722 TTTTCTTTTCT
1 TTTTCTTTTTT
1349733 TTTTCTTTTTT
1 TTTTCTTTTTT
1349744 TTTT-TTTTTT
1 TTTTCTTTTTT
1349754 TT
1 TT
1349756 GCGTCAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 8 0.25
11 24 0.75
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:1350239 original size:36 final size:36
Alignment explanation
Indices: 1350197--1350276 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
1350187 TTCTTGCTCC
1350197 TTCGATTCTATTTT-TTTCTATTTTCATTTCT-GCTAT
1 TTCGATTCTATTTTCTTT-TATTTTCATTTCTAG-TAT
* * *
1350233 TTCGATTCTGTTTTCTTTTTTTTTCGTTTCTAGTAT
1 TTCGATTCTATTTTCTTTTATTTTCATTTCTAGTAT
*
1350269 TTTGATTC
1 TTCGATTC
1350277 CCTCTTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 34 0.89
37 4 0.11
ACGTcount: A:0.11, C:0.15, G:0.09, T:0.65
Consensus pattern (36 bp):
TTCGATTCTATTTTCTTTTATTTTCATTTCTAGTAT
Found at i:1350522 original size:29 final size:29
Alignment explanation
Indices: 1350478--1350546 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
1350468 TAATTTCATT
* * *
1350478 TTGCAGCAGCTGTTTCTTTTTTGTCTTTA
1 TTGCTGCAGCTATTTCTTTTTTGTCTTCA
1350507 TTGCTGCAGCTATTTCTTTTTTGTCTTCA
1 TTGCTGCAGCTATTTCTTTTTTGTCTTCA
*
1350536 TTGCTACAGCT
1 TTGCTGCAGCT
1350547 TTCATTTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.52
Consensus pattern (29 bp):
TTGCTGCAGCTATTTCTTTTTTGTCTTCA
Found at i:1351054 original size:14 final size:14
Alignment explanation
Indices: 1351027--1351087 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
1351017 TAATTAATTA
1351027 ATTATTACTA-TTTT
1 ATTATTA-TATTTTT
1351041 ATTATTATATTTTT
1 ATTATTATATTTTT
* *
1351055 ATGATTATTTTATTT
1 ATTATTATATT-TTT
*
1351070 TTTATT-T-TTTTT
1 ATTATTATATTTTT
1351082 ATTATT
1 ATTATT
1351088 CATGTTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 8 0.20
13 4 0.10
14 21 0.52
15 7 0.17
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (14 bp):
ATTATTATATTTTT
Found at i:1351074 original size:12 final size:12
Alignment explanation
Indices: 1351037--1351087 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1351027 ATTATTACTA
*
1351037 TTTTATTATTAT
1 TTTTTTTATTAT
*
1351049 ATTTTTATGATTAT
1 -TTTTT-TTATTAT
1351063 TTTATTTT-TTAT
1 TTT-TTTTATTAT
1351075 TTTTTTTATTAT
1 TTTTTTTATTAT
1351087 T
1 T
1351088 CATGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.12
12 12 0.38
13 8 0.25
14 8 0.25
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTATTAT
Found at i:1352876 original size:87 final size:88
Alignment explanation
Indices: 1352571--1352965 Score: 386
Period size: 88 Copynumber: 4.5 Consensus size: 88
1352561 AACAAGTTCT
* * * ** * * *
1352571 ACCACGGCTGAACCATCACGTCGAACAAAGATGAAAGGAGTTTGACTAGGGCTAAACCATCACGT
1 ACCAAGGCAGAACCATCACGTCAAATGAATATGAAAAGAGTTTGACCAGGGCTAAACCATCACGT
* * *
1352636 TAAACGA-TAGTGAAAGGAGTTTG
66 CAAACGAGGA-TGAAAAGAGTTTG
* ** * * * *
1352659 ACCAAGGCAAAACCATCGA-GTCAAATGAGGATAAAAAGAGTTTGACTATGGTTAAACCATCACG
1 ACCAAGGCAGAACCATC-ACGTCAAATGAATATGAAAAGAGTTTGACCAGGGCTAAACCATCACG
**
1352723 TCAAATAAGGATGAAAAGAGTTTG
65 TCAAACGAGGATGAAAAGAGTTTG
* * * * * * *
1352747 ACCAAGGTAGAACCCTCACATCAAATGAAAATGAAAAAAGTTTGACCAAGGCTGAACCATCACGT
1 ACCAAGGCAGAACCATCACGTCAAATGAATATGAAAAGAGTTTGACCAGGGCTAAACCATCACGT
* *
1352812 TAAACGAGGAT-AAAAGAGTTAG
66 CAAACGAGGATGAAAAGAGTTTG
* * * * * *
1352834 ACTAAGGCAGAACCATCATGTTAAACGAATATGAAAGGAGTTTGACCAGGGCTGAACCATCACGT
1 ACCAAGGCAGAACCATCACGTCAAATGAATATGAAAAGAGTTTGACCAGGGCTAAACCATCACGT
* *
1352899 CAAATGAGGATG-AAGGAGTTTG
66 CAAACGAGGATGAAAAGAGTTTG
*
1352921 ACCAAGGCAGAACTATCACGTCAAATG-ATAGTGAAAAGAGTTTGA
1 ACCAAGGCAGAACCATCACGTCAAATGAATA-TGAAAAGAGTTTGA
1352966 TATCTACGTC
Statistics
Matches: 249, Mismatches: 53, Indels: 11
0.80 0.17 0.04
Matches are distributed among these distances:
86 3 0.01
87 117 0.47
88 127 0.51
89 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (88 bp):
ACCAAGGCAGAACCATCACGTCAAATGAATATGAAAAGAGTTTGACCAGGGCTAAACCATCACGT
CAAACGAGGATGAAAAGAGTTTG
Found at i:1352942 original size:43 final size:44
Alignment explanation
Indices: 1352571--1352965 Score: 327
Period size: 44 Copynumber: 9.0 Consensus size: 44
1352561 AACAAGTTCT
* * * ** * *
1352571 ACCACGGCTGAACCATCACGTCGAACAAAGATGAAAGGAGTTTG
1 ACCAAGGCAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTG
* * * * * *
1352615 ACTAGGGCTA-AACCATCACGTTAAACGA-TAGTGAAAGGAGTTTG
1 ACCAAGGC-AGAACCATCACGTCAAATGAGGA-TGAAAAGAGTTTG
* *
1352659 ACCAAGGCAAAACCATCGA-GTCAAATGAGGATAAAAAGAGTTTG
1 ACCAAGGCAGAACCATC-ACGTCAAATGAGGATGAAAAGAGTTTG
* * * *
1352703 ACTATGGTTA-AACCATCACGTCAAATAAGGATGAAAAGAGTTTG
1 ACCAAGG-CAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTG
* * * ** *
1352747 ACCAAGGTAGAACCCTCACATCAAATGAAAATGAAAAAAGTTTG
1 ACCAAGGCAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTG
* * * *
1352791 ACCAAGGCTGAACCATCACGTTAAACGAGGAT-AAAAGAGTTAG
1 ACCAAGGCAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTG
* * * * ** *
1352834 ACTAAGGCAGAACCATCATGTTAAACGAATATGAAAGGAGTTTG
1 ACCAAGGCAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTG
* * *
1352878 ACCAGGGCTGAACCATCACGTCAAATGAGGATG-AAGGAGTTTG
1 ACCAAGGCAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTG
* *
1352921 ACCAAGGCAGAACTATCACGTCAAATGA-TAGTGAAAAGAGTTTG
1 ACCAAGGCAGAACCATCACGTCAAATGAGGA-TGAAAAGAGTTTG
1352965 A
1 A
1352966 TATCTACGTC
Statistics
Matches: 283, Mismatches: 57, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.00
43 78 0.28
44 201 0.71
45 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (44 bp):
ACCAAGGCAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTG
Found at i:1353775 original size:171 final size:171
Alignment explanation
Indices: 1353466--1353782 Score: 386
Period size: 171 Copynumber: 1.9 Consensus size: 171
1353456 ACTAAAAGAG
* * * *
1353466 AATGGTATGAGTAGGAATATATGGGAGGTACCCCTTGTGGTCATTTGATGCATCAATACCATCTA
1 AATGGTATGAGTAGAAATATATGGGAGGTACCCCTTATGGGCATGTGATGCATCAATACCATCTA
* ** * * *
1353531 GTAGTTGAGAGAAAAAGGGATACGATTAGGAATGTGGGGTCGGGATGTTCTTACCTCAAAGAACT
66 GTAGTTGAGAGAAAAAGGGATACGATTAGGAATGTAGGGTCGAAATATCCTTACATCAAAGAACT
1353596 CAGATTATGTGATGCATTCATACCATCTAACGGTTGAAGGA
131 CAGATTATGTGATGCATTCATACCATCTAACGGTTGAAGGA
* * * *
1353637 AATGGTATGATTAGAAATATGTGGGCGGTTCCCCCTTTATGGGCATGTGATGCATCAATACCATC
1 AATGGTATGAGTAGAAATATATGGGAGG-TACCCC-TTATGGGCATGTGATGCATCAATACCATC
* * * * * * **
1353702 TAGTGGTTGA-AGGAAAATGG-TATGATTAGGAATGTAGGGTTGAAATATCCTTGCATCGGAGAA
64 TAGTAGTTGAGAGAAAAAGGGATACGATTAGGAATGTAGGGTCGAAATATCCTTACATCAAAGAA
**
1353765 CTTGGATTATGTGATGCA
129 CTCAGATTATGTGATGCA
1353783 CTAATATCAT
Statistics
Matches: 120, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
171 72 0.60
172 13 0.11
173 35 0.29
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (171 bp):
AATGGTATGAGTAGAAATATATGGGAGGTACCCCTTATGGGCATGTGATGCATCAATACCATCTA
GTAGTTGAGAGAAAAAGGGATACGATTAGGAATGTAGGGTCGAAATATCCTTACATCAAAGAACT
CAGATTATGTGATGCATTCATACCATCTAACGGTTGAAGGA
Found at i:1354731 original size:50 final size:49
Alignment explanation
Indices: 1354622--1354734 Score: 145
Period size: 50 Copynumber: 2.3 Consensus size: 49
1354612 TGAACAGTAC
* ****
1354622 ATGTATCGATACATTCTTTTTTTACCCAGATGTATCAATACATTTTTCA
1 ATGTATCGATACATTCTTTTTTTACCCAGATATATCAATACATTGAAAA
* * *
1354671 ATGCAACGATACATTCTATTTTTTACCCAGATATATCGATACATTGAAAA
1 ATGTATCGATACATTCT-TTTTTTACCCAGATATATCAATACATTGAAAA
1354721 ATGTATCGATACAT
1 ATGTATCGATACAT
1354735 CTAGTTTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
49 15 0.28
50 38 0.72
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (49 bp):
ATGTATCGATACATTCTTTTTTTACCCAGATATATCAATACATTGAAAA
Found at i:1357568 original size:14 final size:13
Alignment explanation
Indices: 1357536--1357585 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
1357526 TGTCTGAGTG
1357536 AGGAAGAAGGAAAA
1 AGGAAGAA-GAAAA
1357550 A-GAAGAAG--AA
1 AGGAAGAAGAAAA
1357560 AGGAAGAAGAAAA
1 AGGAAGAAGAAAA
*
1357573 A-GAAAAAGAAAA
1 AGGAAGAAGAAAA
1357585 A
1 A
1357586 AAAGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
10 3 0.09
11 7 0.22
12 12 0.38
13 9 0.28
14 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAAA
Found at i:1357568 original size:24 final size:23
Alignment explanation
Indices: 1357536--1357583 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
1357526 TGTCTGAGTG
*
1357536 AGGAAGAAGGAAAAAGAAGAAGAA
1 AGGAAGAA-GAAAAAGAAAAAGAA
1357560 AGGAAGAAGAAAAAGAAAAAGAA
1 AGGAAGAAGAAAAAGAAAAAGAA
1357583 A
1 A
1357584 AAAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (23 bp):
AGGAAGAAGAAAAAGAAAAAGAA
Found at i:1357587 original size:15 final size:15
Alignment explanation
Indices: 1357563--1357594 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1357553 AGAAGAAAGG
*
1357563 AAGAAGAAAAAGAAA
1 AAGAAAAAAAAGAAA
1357578 AAGAAAAAAAAGAAA
1 AAGAAAAAAAAGAAA
1357593 AA
1 AA
1357595 AAATGCAACA
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:0.16, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:1357595 original size:23 final size:23
Alignment explanation
Indices: 1357539--1357597 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
1357529 CTGAGTGAGG
* **
1357539 AAGAAGGAAAAAGAAGAAGAAAGG
1 AAGAA-GAAAAAGAAAAAGAAAAA
1357563 AAGAAGAAAAAGAAAAAGAAAAAA
1 AAGAAGAAAAAGAAAAAG-AAAAA
*
1357587 AAGAAAAAAAA
1 AAGAAGAAAAA
1357598 TGCAACAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
AAGAAGAAAAAGAAAAAGAAAAA
Found at i:1358213 original size:19 final size:19
Alignment explanation
Indices: 1358189--1358243 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1358179 AATTCAACAG
1358189 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1358208 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1358227 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1358244 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1358301 original size:13 final size:13
Alignment explanation
Indices: 1358283--1358308 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1358273 CATTTTTCCG
1358283 TGTATCGATACAT
1 TGTATCGATACAT
1358296 TGTATCGATACAT
1 TGTATCGATACAT
1358309 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1360846 original size:28 final size:27
Alignment explanation
Indices: 1360779--1360851 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1360769 CTTCACAATC
* *
1360779 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1360806 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1360834 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1360852 ACTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1360901 original size:51 final size:52
Alignment explanation
Indices: 1360834--1360969 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
1360824 TTATTTCTGA
* * ***
1360834 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATATTT-C-ATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAT-TTTCCTATAATC
* * * *
1360885 GGGGATACTCCCACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCTATAATC
*
1360937 GGGGATACTCCAACACCGATTTTATTTCCAAAA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAA
1360970 ATACTAATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
50 3 0.04
51 33 0.47
52 34 0.49
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCTATAATC
Found at i:1361057 original size:211 final size:211
Alignment explanation
Indices: 1360670--1361062 Score: 565
Period size: 211 Copynumber: 1.9 Consensus size: 211
1360660 AATTCTCCAC
* * * *
1360670 AATCGGGGATATTCTAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* **
1360735 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTTA
* * * *
1360800 ATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
1360865 AATATTGATATTTCAT
196 AATATTGATATTTCAT
* * *
1360881 AATCGGGGATACTCCCACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* * * * *
1360946 CCAACACCGATTTTATTTCC-AAAAATACTAATTT-TTCACAATTAAGGATACTCCAACCTCGTC
65 CCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGT-
* *
1361009 TATTCATCGGGGATACTCCAACTCCGTTACTTCCGAGGGAACACTCCAACCCCG
129 TAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
1361063 TTATTATCTC
Statistics
Matches: 159, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
210 23 0.14
211 101 0.64
212 35 0.22
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
AATATTGATATTTCAT
Found at i:1367725 original size:51 final size:50
Alignment explanation
Indices: 1367665--1367807 Score: 144
Period size: 52 Copynumber: 2.8 Consensus size: 50
1367655 TTTCAAGGGA
* * ***
1367665 ATACTCCAACCCTGACTTTATTTCCAAAATATTGATTTT-TTATAATCGGGG
1 ATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTTCTT-TAATCGGGG
* * *
1367716 ATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTCATCGGGG
1 ATACTCCAA-CCCGATTTTATTTCCAAAACACCAATTTT-CTTTAATCGGGG
*
1367768 ATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTT
1 ATACTCCAAC-CCGATTTTATTTCC-AAAACACCAATTTT
1367808 TCACAATTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
51 29 0.38
52 32 0.42
53 15 0.20
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (50 bp):
ATACTCCAACCCGATTTTATTTCCAAAACACCAATTTTCTTTAATCGGGG
Found at i:1367884 original size:211 final size:211
Alignment explanation
Indices: 1367497--1367887 Score: 570
Period size: 211 Copynumber: 1.9 Consensus size: 211
1367487 AATTCTCCAC
* * *
1367497 AATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* ** *
1367562 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTCA
* * * *
1367627 ATCATCGTGGATACTCCAACCCCGTTATTTTCAAGGGAATACTCCAACCCTGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCCTGACTTTATTTCCAA
1367692 AATATTGATTTTTTAT
196 AATATTGATTTTTTAT
* * * *
1367708 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTCATCGGGGATACT
1 AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* * * *
1367773 CCAACACCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATTAAGGATACTCCAACCTCGTC
65 CCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTC
*
1367836 AATTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCC
130 AA-TCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCC
1367888 CGTTATTATC
Statistics
Matches: 158, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
210 25 0.16
211 99 0.63
212 34 0.22
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (211 bp):
AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTCA
ATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCCTGACTTTATTTCCAA
AATATTGATTTTTTAT
Found at i:1375034 original size:22 final size:24
Alignment explanation
Indices: 1374985--1375035 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
1374975 TCAAAATGAT
*
1374985 GAAAAAGTCAAAAGAAAAAGCACA
1 GAAAAAGTCAAAAGAAAAAGCAAA
*
1375009 -AAAAA-TGAAAAGAAAAA-CAAA
1 GAAAAAGTCAAAAGAAAAAGCAAA
1375030 GAAAAA
1 GAAAAA
1375036 AAGCAAAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.12
22 16 0.67
23 5 0.21
ACGTcount: A:0.75, C:0.08, G:0.14, T:0.04
Consensus pattern (24 bp):
GAAAAAGTCAAAAGAAAAAGCAAA
Found at i:1375043 original size:19 final size:18
Alignment explanation
Indices: 1375016--1375058 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1375006 ACAAAAAATG
1375016 AAAAGAAAAACAAAGA-AA
1 AAAAGAAAAACAAA-ATAA
*
1375034 AAAAGCAAAAGCAAAATAA
1 AAAAG-AAAAACAAAATAA
1375053 AAAAGA
1 AAAAGA
1375059 GAACAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAACAAAATAA
Found at i:1376643 original size:110 final size:112
Alignment explanation
Indices: 1376445--1376751 Score: 379
Period size: 110 Copynumber: 2.7 Consensus size: 112
1376435 TAACCTCTTC
* * *
1376445 AAAGTCCACAA-TTCAGTGGCACTCCCTTTTAAAGGCCACAACTCCATGGCACCCTTTCAAAGTC
1 AAAGTCCACAACTTC-GTGGCAC-CCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT-TAAGTC
* * *
1376509 TACAACTCTATGGCACCCTGTTTAAGTCCACAACTCCATGGCACC-TTTT
63 CACAACTCCATGGCACCCTATTTAAGTCCACAACTCCATGGCACCATTTT
*
1376558 TAAGTCCACAACTTCGTGGCA-CCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAGAGTCCA
1 AAAGTCCACAACTTCGTGGCACCCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTA-AGTCCA
* * * *
1376621 TAACTCCATGGCACCCTATTTAAGTCCATAACTTCGTGGCACCATTTT
65 CAACTCCATGGCACCCTATTTAAGTCCACAACTCCATGGCACCATTTT
* * * *
1376669 AAAGTCCATAACTTCGTGGCACCCCTTTTTGAAGTCCACAACTCCGTAGCACTCTTTTTAAGTCC
1 AAAGTCCACAACTTCGTGGCACCCC-TTTTAAAGTCCACAACTCCGTGGCAC-CCTTTTAAGTCC
* *
1376734 ACAACTCCGTGGTACCCT
64 ACAACTCCATGGCACCCT
1376752 TTTCAAAGAC
Statistics
Matches: 169, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
109 1 0.01
110 66 0.39
111 30 0.18
112 3 0.02
113 20 0.12
114 43 0.25
115 6 0.04
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.28
Consensus pattern (112 bp):
AAAGTCCACAACTTCGTGGCACCCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC
AACTCCATGGCACCCTATTTAAGTCCACAACTCCATGGCACCATTTT
Found at i:1376765 original size:29 final size:28
Alignment explanation
Indices: 1376445--1377022 Score: 368
Period size: 28 Copynumber: 20.4 Consensus size: 28
1376435 TAACCTCTTC
* *
1376445 AAAGTCCACAATTCAGTGGCACTCCCTTTT
1 AAAGTCCACAACTCCGTGGCA--CCCTTTT
* * *
1376475 AAAGGCCACAACTCCATGGCACCCTTTC
1 AAAGTCCACAACTCCGTGGCACCCTTTT
* **
1376503 AAAGTCTACAACTCTATGGCACCCTGTTT
1 AAAGTCCACAACTCCGTGGCACCCT-TTT
*
1376532 -AAGTCCACAACTCCATGGCA-CCTTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
* *
1376558 TAAGTCCACAACTTCGTGGCACCCTTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
1376586 -AAGTCCACAACTCCGTGGCACCCTTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
* * *
1376613 AGAGTCCATAACTCCATGGCACCCTATTT
1 AAAGTCCACAACTCCGTGGCACCCT-TTT
* * *
1376642 -AAGTCCATAACTTCGTGGCACCATTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
* *
1376669 AAAGTCCATAACTTCGTGGCACCCCTTTTT
1 AAAGTCCACAACTCCGTGGCA-CCC-TTTT
* * *
1376699 GAAGTCCACAACTCCGTAGCACTCTTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
* *
1376727 TAAGTCCACAACTCCGTGGTACCCTTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
1376755 CAAAGACCACACAAGTCGGTGGCAACCTTTT
1 -AAAG-TC-CACAACTCCGTGGCACCCTTTT
* *
1376786 CAAAG-CCTACAAGTCAGTGGCACCCTTTT
1 -AAAGTCC-ACAACTCCGTGGCACCCTTTT
* * * *
1376815 CAAAGCCCACAAGTCAGTGGCACCTTTTT
1 -AAAGTCCACAACTCCGTGGCACCCTTTT
** * * *
1376844 CAAACCCCACAAGTCAGTGACACCCTTTT
1 -AAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
1376873 CATAG-CTCACAAGTCAGTGACA-CCTTTT
1 -AAAGTC-CACAACTCCGTGGCACCCTTTT
* ** * *
1376901 AAAG-CTCACAAGTTAGTGGCA-TCTTTC
1 AAAGTC-CACAACTCCGTGGCACCCTTTT
* * * * *
1376928 AAAGCCCATAAGTCAGTGGCACACTTTTT
1 AAAGTCCACAACTCCGTGGCAC-CCTTTT
* *
1376957 AAAGTCCACAAGTCAGTGGCA-CCTTTT
1 AAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
1376984 CAAAGCCCATAAGTCAGTGGCA-CCTTTT
1 -AAAGTCCACAACTCCGTGGCACCCTTTT
*
1377012 CAAAGCCCACA
1 -AAAGTCCACA
1377023 CAAGTTGATG
Statistics
Matches: 469, Mismatches: 61, Indels: 38
0.83 0.11 0.07
Matches are distributed among these distances:
26 3 0.01
27 94 0.20
28 185 0.39
29 123 0.26
30 41 0.09
31 23 0.05
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (28 bp):
AAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:1376959 original size:56 final size:58
Alignment explanation
Indices: 1376733--1377307 Score: 487
Period size: 56 Copynumber: 9.8 Consensus size: 58
1376723 TTTTTAAGTC
* * * *
1376733 CACAACTCCGTGGTACCCTTTTCAAAGACCACACAAGTCGGTGGCA-ACCTTTTCAAAGC-
1 CACAAGTCAGTGGCACCCTTTTCAAAG-CC-CACAAGTCAGTGGCACA-CTTTTCAAAGCT
* *
1376792 CTACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTTCAAACCC
1 C-ACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACAC-TTTTCAAAGCT
* * * *
1376851 CACAAGTCAGTGACACCCTTTTCATAGCTCACAAGTCAGTGACAC-CTTTT-AAAGCT
1 CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCT
* * * *
1376907 CACAAGTTAGTGGCA-TC-TTTCAAAGCCCATAAGTCAGTGGCACACTTTTTAAAG-T
1 CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCT
* *
1376962 CCACAAGTCAGTGGCA-CCTTTTCAAAGCCCATAAGTCAGTGGCAC-CTTTTCAAAGCCCA
1 -CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACACTTTTCAAAG--CT
* * * *
1377021 CACAAGT-TGATGGCAACTCTTTTTAAAGCCCACATAAGTCGGTGGCA-ACCTTTTCAAAGCT
1 CACAAGTCAG-TGGC-ACCCTTTTCAAAGCCCAC--AAGTCAGTGGCACA-CTTTTCAAAGCT
* * * * *
1377082 CACAATTCAGTGGCACCCTTTTCAAAGCTCACAAGTCAATAGCACA--TTTCAAAGCC
1 CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCT
* * * * *
1377138 CACAAGTCAGTGGCACACTTTTCAAAGCCCACAAGTTAGTAGCAC-CCTTTCAAAGCCCA
1 CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACACTTTTCAAAG--CT
* * * * *
1377197 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACACTTTTCAAAG--CT
* * *
1377261 CACAAGTCGGTGGCAAACTTTTTCAAAGTCCACACAAGTCAGTGGCA
1 CACAAGTCAGTGGC-ACCCTTTTCAAAG-CC-CACAAGTCAGTGGCA
1377308 ACCTTTTTCA
Statistics
Matches: 434, Mismatches: 53, Indels: 54
0.80 0.10 0.10
Matches are distributed among these distances:
54 22 0.05
55 7 0.02
56 94 0.22
57 40 0.09
58 84 0.19
59 20 0.05
60 62 0.14
61 13 0.03
62 23 0.05
63 13 0.03
64 56 0.13
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (58 bp):
CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCACACTTTTCAAAGCT
Found at i:1377104 original size:29 final size:29
Alignment explanation
Indices: 1376442--1377377 Score: 579
Period size: 29 Copynumber: 32.1 Consensus size: 29
1376432 ATGTAACCTC
* *
1376442 TTCAAAGTCCACAATTCAGTGGCACTCCCTT
1 TTCAAAGCCCACAAGTCAGTGGCA--CCCTT
* *
1376473 TT-AAAGGCCACAACTCCA-TGGCACCC-T
1 TTCAAAGCCCACAAGT-CAGTGGCACCCTT
* * *
1376500 TTCAAAGTCTACAACTCTA-TGGCACCCTGT
1 TTCAAAGCCCACAAGTC-AGTGGCACCCT-T
* *
1376530 TT--AAGTCCACAACTCCA-TGGCA-CCTT
1 TTCAAAGCCCACAAGT-CAGTGGCACCCTT
* * *
1376556 TT-TAAGTCCACAACTTC-GTGGCACCCTT
1 TTCAAAGCCCACAA-GTCAGTGGCACCCTT
* * *
1376584 TT--AAGTCCACAACTCCGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* * * *
1376611 TT-AGAGTCCATAACTCCA-TGGCACCCTAT
1 TTCAAAGCCCACAAGT-CAGTGGCACCCT-T
* * * *
1376640 TT--AAGTCCATAACTTC-GTGGCACCATT
1 TTCAAAGCCCACAA-GTCAGTGGCACCCTT
* * *
1376667 TT-AAAGTCCATAACTTC-GTGGCACCCCTT
1 TTCAAAGCCCACAA-GTCAGTGGCA-CCCTT
** * * * * *
1376696 TTTGAAGTCCACAACTCCGTAGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* * * * *
1376725 TT-TAAGTCCACAACTCCGTGGTACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
1376753 TTCAAAGACCACACAAGTCGGTGGCAACCTT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCTT
*
1376784 TTCAAAGCCTACAAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
*
1376813 TTCAAAGCCCACAAGTCAGTGGCACCTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
1376842 TTCAAACCCCACAAGTCAGTGACACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* * *
1376871 TTCATAGCTCACAAGTCAGTGACA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* * *
1376899 TT-AAAGCTCACAAGTTAGTGGCA-TC-T
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
1376925 TTCAAAGCCCATAAGTCAGTGGCACACTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
1376954 TTTAAAGTCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
*
1376982 TTCAAAGCCCATAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
1377010 TTCAAAGCCCACACAAGT-TGATGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAG-TGGC-ACCCTT
* * *
1377042 TTTAAAGCCCACATAAGTCGGTGGCAACCTT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCTT
* *
1377073 TTCAAAGCTCACAATTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* * * *
1377102 TTCAAAGCTCACAAGTCAATAGCA--CAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
*
1377129 TTCAAAGCCCACAAGTCAGTGGCACACTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
1377158 TTCAAAGCCCACAAGTTAGTAGCACCC-T
1 TTCAAAGCCCACAAGTCAGTGGCACCCTT
* *
1377186 TTCAAAGCCCACACAAGTCGGTGGCAACCTTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACCCTT
* *
1377218 TTCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACCCTT
* * *
1377250 TTCAAAGCCCACACAAGTCGGTGGCAAACTTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACCCTT
*
1377282 TTCAAAGTCCACACAAGTCAGTGGCAACCTTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACCCTT
*
1377314 TTC-AAGCCCATACAAGTCAGT-GTACCTCTTT
1 TTCAAAGCCC--ACAAGTCAGTGGCACC-C-TT
*
1377345 TTC-AAGCCCACACAAGTCAATGGCAACCCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ACCCTT
1377376 TT
1 TT
1377378 TAAAACACCA
Statistics
Matches: 763, Mismatches: 94, Indels: 96
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.01
27 109 0.14
28 178 0.23
29 206 0.27
30 63 0.08
31 81 0.11
32 113 0.15
33 5 0.01
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTT
Found at i:1377483 original size:54 final size:53
Alignment explanation
Indices: 1377424--1377537 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 53
1377414 TCAATGTCAT
* *
1377424 TGGCCTTAAATCAACATATTGGCACTCATCCTC-TTTCTTAGAGTCCAATATT-GC
1 TGGCCTTAAATCAACATATTGGCACTCACCCTCATCT-TTA-AGTCCAAT-TTAGC
* * *
1377478 TGGCCTTGAATCAGCATATTGGCACTTACCCTCATCTTTAAGTCCAATTTAGC
1 TGGCCTTAAATCAACATATTGGCACTCACCCTCATCTTTAAGTCCAATTTAGC
1377531 TGGCCTT
1 TGGCCTT
1377538 TAATTGGCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
52 2 0.04
53 17 0.32
54 32 0.60
55 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (53 bp):
TGGCCTTAAATCAACATATTGGCACTCACCCTCATCTTTAAGTCCAATTTAGC
Found at i:1378605 original size:17 final size:16
Alignment explanation
Indices: 1378569--1378618 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1378559 ATGGGTGAGG
* *
1378569 AAGAAAGAATAAGAAG
1 AAGAAAGAAGAAGAAA
1378585 AAGAAAGGAAGAAGAAA
1 AAGAAA-GAAGAAGAAA
*
1378602 AAGAAA-AAAAAGAAA
1 AAGAAAGAAGAAGAAA
1378617 AA
1 AA
1378619 AATGAAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.33
16 6 0.20
17 14 0.47
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
AAGAAAGAAGAAGAAA
Found at i:1382807 original size:39 final size:39
Alignment explanation
Indices: 1382753--1382828 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1382743 AGATAAGGTG
*
1382753 CCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTATA
* * * *
1382792 CCAATGTGTTGATTCAAGGCCAGTGACATTGGTCTTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA
1382829 GAGACAAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (39 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTATA
Found at i:1382813 original size:87 final size:87
Alignment explanation
Indices: 1382651--1382863 Score: 282
Period size: 87 Copynumber: 2.4 Consensus size: 87
1382641 CTTAAAAATG
* * * *
1382651 TTAAAGATGAAGGCGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTGGTGCCAACGTGCTG
1 TTAAAGAT-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTGATACCAACGTGCTG
* *
1382716 ATTCACGGCCAGCAACGTTGATC
65 ATTCAAGGCCAGCAACATTGATC
* * *
1382739 TTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATACCAATGTGTTGA
1 TTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTGATACCAACGTGCTGA
** *
1382804 TTCAAGGCCAGTGACATTGGTC
66 TTCAAGGCCAGCAACATTGATC
* * *
1382826 TTAGAGACAAGGTGCCAATGTGCTGATTCAAGGCCAGC
1 TTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGC
1382864 AACATTGGAC
Statistics
Matches: 110, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
87 102 0.93
88 8 0.07
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (87 bp):
TTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTGATACCAACGTGCTGA
TTCAAGGCCAGCAACATTGATC
Found at i:1382869 original size:48 final size:46
Alignment explanation
Indices: 1382792--1382922 Score: 151
Period size: 43 Copynumber: 2.9 Consensus size: 46
1382782 TGGGCTTATA
* * *
1382792 CCAATGTGTTGATTCAAGGCCAGTGACATTGGTCTTAGAGACAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGA-A-AAGGTG
*
1382840 CCAATGTGCTGATTCAAGGCCAGCAACATTGGACTT---AAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAAAAGGTG
** * *
1382883 CCAATAAGCTGATTCAAGTCCAGCGATATTGGACTTAGAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAA
1382923 GAAAATGCCA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
43 37 0.52
44 1 0.01
46 1 0.01
48 32 0.45
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (46 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAGAAAAGGTG
Found at i:1382895 original size:43 final size:43
Alignment explanation
Indices: 1382660--1382919 Score: 169
Period size: 48 Copynumber: 6.0 Consensus size: 43
1382650 GTTAAAGATG
* * * *
1382660 AAGGCGCCAATATGCTGATTCAAGGCCAGTGATATTGGGC-T-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
** * * *
1382701 --GGTGCCAACGTGCTGATTCACGGCCAGCAACGTT-GATCTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGA-CTT----A
* *
1382746 TAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * * * *
1382789 -A--TACCAATGTGTTGATTCAAGGCCAGTGACATTGGTCTTAGAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A
* *
1382833 CAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTA
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * *
1382877 AAGGTGCCAATAAGCTGATTCAAGTCCAGCGATATTGGACTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
1382920 GAAGAAAATG
Statistics
Matches: 167, Mismatches: 32, Indels: 38
0.70 0.14 0.16
Matches are distributed among these distances:
38 1 0.01
39 59 0.35
40 1 0.01
41 1 0.01
43 38 0.23
44 1 0.01
46 1 0.01
48 64 0.38
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (43 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
Found at i:1383006 original size:28 final size:28
Alignment explanation
Indices: 1382941--1383321 Score: 416
Period size: 28 Copynumber: 13.7 Consensus size: 28
1382931 CACCAACTCG
* **
1382941 TGTGGGCCTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTG-AA-GGTTGCCACTGACT
*
1382970 TGTGTGCTTTTGAAGGTTGCCACT-ACCT
1 TGTGGGCTTTTGAAGGTTGCCACTGA-CT
*
1382998 TATGGGC-TTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
** *
1383025 TGTGGGCTTTAAAAAGG-TGCCACTAACT
1 TGTGGGCTTT-TGAAGGTTGCCACTGACT
* * *
1383053 TGTGGGCTTCTGAAGGTTGCTATTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
1383081 TGTGGGCTTTTGAGGGTTACCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
1383109 TGTGGGC-TTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
1383136 TGTGGGCTTTTGAGGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
1383164 TGTGGGC-TTTGAAGATTGCCATTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
1383191 TGTGGGCTTTTGAGGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
1383219 TGTGGGCTTTTAAAAGATGCCACTGGCT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
1383247 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * *
1383275 TATGGG-ATTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
*
1383303 TGTGGGCTTCTGAAGGTTG
1 TGTGGGCTTTTGAAGGTTG
1383322 AGGAATGTCT
Statistics
Matches: 292, Mismatches: 50, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
27 86 0.29
28 189 0.65
29 17 0.06
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.34
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:1383028 original size:55 final size:55
Alignment explanation
Indices: 1382941--1383321 Score: 435
Period size: 55 Copynumber: 6.8 Consensus size: 55
1382931 CACCAACTCG
** *
1382941 TGTGGGCCTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACT-ACCT
1 TGTGGG-CTTTG-AA-GGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGA-CT
* ** *
1382998 TATGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTAAAAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTT-TGAAGGTTGCCACTGACT
* * * *
1383053 TGTGGGCTTCTGAAGGTTGCTATTGACTTGTGGGCTTTTGAGGGTTACCACTGACT
1 TGTGGGCTT-TGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
*
1383109 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAGGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
1383164 TGTGGGCTTTGAAGATTGCCATTAACTTGTGGGCTTTTGAGGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
1383219 TGTGGGCTTTTAAAAGATGCCACTGGCTTGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * * *
1383275 TATGGGATTTGAAAAGATGCCACTAACTTGTGGGCTTCTGAAGGTTG
1 TGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTG
1383322 AGGAATGTCT
Statistics
Matches: 283, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
54 5 0.02
55 142 0.50
56 131 0.46
57 5 0.02
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.34
Consensus pattern (55 bp):
TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:1383165 original size:111 final size:110
Alignment explanation
Indices: 1382966--1383321 Score: 457
Period size: 111 Copynumber: 3.2 Consensus size: 110
1382956 GGGTTGCACC
* * *
1382966 AACTTGTGTGCTTTTGAAGGTTGCCACT-ACCTTATGGGCTTTGAAGGTTGCCACTGACTTGTGG
1 AACTTGTGGGCTTTTGAGGGTTGCCACTGA-CTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGG
** * * *
1383030 GCTTTAAAAAGG-TGCCACTAACTTGTGGGCTTCTGAAGGTTGCTATT
65 GCTTT-TGAAGGTTGCCACTGACTTGTGGGCTT-TGAAGATTGCCATT
* *
1383077 GACTTGTGGGCTTTTGAGGGTTACCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGG
1 AACTTGTGGGCTTTTGAGGGTTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGG
*
1383142 CTTTTGAGGGTTGCCACTGACTTGTGGGCTTTGAAGATTGCCATT
66 CTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAGATTGCCATT
* * * *
1383187 AACTTGTGGGCTTTTGAGGGTTGCCACTGACTTGTGGGCTTTTAAAAGATGCCACTGGCTTGTGG
1 AACTTGTGGGCTTTTGAGGGTTGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGG
* * *
1383252 GCTTTTGAAGGTTGCCACTGACTTATGGGATTTGAAAAGA-TGCCACT
65 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG--AAGATTGCCATT
* *
1383299 AACTTGTGGGCTTCTGAAGGTTG
1 AACTTGTGGGCTTTTGAGGGTTG
1383322 AGGAATGTCT
Statistics
Matches: 217, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
110 52 0.24
111 133 0.61
112 28 0.13
113 4 0.02
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.35
Consensus pattern (110 bp):
AACTTGTGGGCTTTTGAGGGTTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGG
CTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAGATTGCCATT
Found at i:1383729 original size:37 final size:37
Alignment explanation
Indices: 1383683--1383764 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
1383673 GATGAAGCAT
*
1383683 AAATACATCATGCAAAATGAAATGTTATGAATGTCAC
1 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
1383720 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
1 AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
1383757 AAATGCAT
1 AAATGCAT
1383765 GATTGTGGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (37 bp):
AAATGCATCATGCAAAATGAAATGTTATGAATGTCAC
Found at i:1384810 original size:14 final size:14
Alignment explanation
Indices: 1384790--1384826 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1384780 CCGGACCCTT
1384790 TTTGTTTTTTTATTG
1 TTTGTTTTTTT-TTG
1384805 -TTG-TTTTTTTTG
1 TTTGTTTTTTTTTG
1384817 TTTGTTTTTT
1 TTTGTTTTTT
1384827 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.15
13 9 0.45
14 8 0.40
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.84
Consensus pattern (14 bp):
TTTGTTTTTTTTTG
Found at i:1384815 original size:16 final size:14
Alignment explanation
Indices: 1384788--1384855 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
1384778 ATCCGGACCC
*
1384788 TTTTTGTTTTTTTA
1 TTTTTGTTTTTTTT
*
1384802 TTGTTG-TTTTTTT
1 TTTTTGTTTTTTTT
*
1384815 TGTTTGTTTTTTCTT
1 TTTTTGTTTTTT-TT
1384830 TTTTT-TTCTCTCTTTT
1 TTTTTGTT-T-T-TTTT
1384846 TTTTT-TTTTT
1 TTTTTGTTTTT
1384856 GCGGAGGATG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
13 11 0.25
14 13 0.30
15 8 0.18
16 10 0.23
17 2 0.05
ACGTcount: A:0.01, C:0.06, G:0.07, T:0.85
Consensus pattern (14 bp):
TTTTTGTTTTTTTT
Found at i:1384817 original size:23 final size:22
Alignment explanation
Indices: 1384788--1384836 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1384778 ATCCGGACCC
*
1384788 TTTTTGTTT-TTTTATTGTTGTTT
1 TTTTTGTTTGTTTT-TTCTT-TTT
1384811 TTTTTGTTTGTTTTTTCTTTTT
1 TTTTTGTTTGTTTTTTCTTTTT
1384833 TTTT
1 TTTT
1384837 CTCTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 13 0.54
24 4 0.17
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (22 bp):
TTTTTGTTTGTTTTTTCTTTTT
Found at i:1400679 original size:24 final size:26
Alignment explanation
Indices: 1400652--1400699 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1400642 AATCAAATTT
1400652 TATTTAT-C-AGGGATACTCCAACAC
1 TATTTATCCGAGGGATACTCCAACAC
*
1400676 TATTTCTCCGAGGGATACTCCAAC
1 TATTTATCCGAGGGATACTCCAAC
1400700 TCCCCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 1 0.05
26 14 0.67
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (26 bp):
TATTTATCCGAGGGATACTCCAACAC
Found at i:1402670 original size:20 final size:20
Alignment explanation
Indices: 1402645--1402684 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1402635 ACATTTGAGA
1402645 TATGTATCGATACATTCACT
1 TATGTATCGATACATTCACT
*
1402665 TATGTATCGATGCATTCACT
1 TATGTATCGATACATTCACT
1402685 AATTGTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (20 bp):
TATGTATCGATACATTCACT
Found at i:1403364 original size:31 final size:31
Alignment explanation
Indices: 1403287--1403381 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
1403277 CAACTTATCG
* **
1403287 CCAACTTATGTGGGCTTTGACTCAGGTGCTG
1 CCAACTTATGTGAGCTTTGACTCAGGTGCCA
** **
1403318 CCAACTCCTACGAGCTTTGACT-AGGGTGCCA
1 CCAACTTATGTGAGCTTTGACTCA-GGTGCCA
* *
1403349 CCAACTTATGTGAGCTTTGACTCAAGTGTCA
1 CCAACTTATGTGAGCTTTGACTCAGGTGCCA
1403380 CC
1 CC
1403382 TGTAGTTACC
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 1 0.02
31 47 0.96
32 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (31 bp):
CCAACTTATGTGAGCTTTGACTCAGGTGCCA
Found at i:1404463 original size:167 final size:164
Alignment explanation
Indices: 1404196--1404514 Score: 462
Period size: 167 Copynumber: 1.9 Consensus size: 164
1404186 AATACGGAGT
* * *
1404196 TTTTCACTCCATAAATATTTTCGAGAGGCTTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAAT
1 TTTTCACTCCATAAATATTTTCGAGAGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAAC
* * * **
1404261 ATCATTATTTATTTTATATTAATTCAATTTTAAAAAACTTAATTCATTTTCATGAGTTTTTTATT
66 ATCATCATTTATTTCATATTAATTCAATATTAAAAAA-TTAATTCATTTTCATGAGTTTTAGATT
1404326 TTTTCCTTGAAATTCTCATTTTTTCGAAATACGGTA
130 TTTTCCTTGAAATT-TCATTTTTTCGAAATACGGTA
*
1404362 TTTTCTACTCCATAAAT-TTTTCCGAGGGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAA
1 TTTTC-ACTCCATAAATATTTT-CGAGAGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAA
*
1404426 ACATCATCATTTGA-TTCATATTAATTCAGTATTAAAAAATTAATTCATTTTCATGAGTTTTAGA
64 ACATCATCATTT-ATTTCATATTAATTCAATATTAAAAAATTAATTCATTTTCATGAGTTTTAGA
** *
1404490 TTTTTTTGTTGAAATTTCCTTTTTT
128 TTTTTTCCTTGAAATTTCATTTTTT
1404515 TAGAAACTGA
Statistics
Matches: 137, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
165 8 0.06
166 46 0.34
167 82 0.60
168 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (164 bp):
TTTTCACTCCATAAATATTTTCGAGAGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAAC
ATCATCATTTATTTCATATTAATTCAATATTAAAAAATTAATTCATTTTCATGAGTTTTAGATTT
TTTCCTTGAAATTTCATTTTTTCGAAATACGGTA
Found at i:1404604 original size:164 final size:164
Alignment explanation
Indices: 1404196--1404606 Score: 451
Period size: 167 Copynumber: 2.5 Consensus size: 164
1404186 AATACGGAGT
* * *
1404196 TTTTC-ACTCCATAAATATTTTCGAGAGGCTTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
1 TTTTCTACTCCATAAAT-TTTTC-AGGGGATTTTTCTTGGTTTTAAATTTTTAAAATTCATCAAA
* * **
1404260 TATCATTATTT-ATTTTATATTAATTCAATTTTAAAAAACTTAATTCATTTTCATGAGTTTTTTA
64 TATCATTATTTGA-TTCATATTAATTCAATATTAAAAAACTTAATTCATTTTCATGAGTTTTAGA
*
1404324 TTTTTTCCTTGAAATTCTCATTTTTTCGAAATACGGTA
128 TTTTTTCCTTGAAATTCTCATTTTTTAGAAATAC-GTA
*
1404362 TTTTCTACTCCATAAATTTTTCCGAGGGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAA
1 TTTTCTACTCCATAAATTTTT-C-AGGGGATTTTTCTTGGTTTTAAATTTTTAAAATTCATCAAA
* * *
1404427 CATCATCATTTGATTCATATTAATTCAGTATTAAAAAA-TTAATTCATTTTCATGAGTTTTAGAT
64 TATCATTATTTGATTCATATTAATTCAATATTAAAAAACTTAATTCATTTTCATGAGTTTTAGAT
** *
1404491 TTTTTTGTTGAAATT-TCCTTTTTTTAGAAACTGA-GT-
129 TTTTTCCTTGAAATTCT-CATTTTTTAGAAA-T-ACGTA
* * * * **
1404527 TTTT-TTCTCCATAGATATTTTT-AGGGAGATTTTTCTTGATTTAAAATTTTTAAAATTTATTTA
1 TTTTCTACTCCATA-A-ATTTTTCAGGG-GATTTTTCTTGGTTTTAAATTTTTAAAATTCATCAA
**
1404590 ATATTGTTATTTGATTC
63 ATATCATTATTTGATTC
1404607 CCATTAAATT
Statistics
Matches: 211, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
163 4 0.02
164 51 0.24
165 6 0.03
166 65 0.31
167 83 0.39
168 2 0.01
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (164 bp):
TTTTCTACTCCATAAATTTTTCAGGGGATTTTTCTTGGTTTTAAATTTTTAAAATTCATCAAATA
TCATTATTTGATTCATATTAATTCAATATTAAAAAACTTAATTCATTTTCATGAGTTTTAGATTT
TTTCCTTGAAATTCTCATTTTTTAGAAATACGTA
Found at i:1405597 original size:23 final size:23
Alignment explanation
Indices: 1405563--1405606 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
1405553 GGATGAGGAA
1405563 AAGGAAAAAAAAAGAG-GAAGAG
1 AAGGAAAAAAAAAGAGAGAAGAG
1405585 AAGGAAAAAAAAAGAGAGAAGA
1 AAGGAAAAAAAAAGAGAGAAGA
1405607 AAAAATGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (23 bp):
AAGGAAAAAAAAAGAGAGAAGAG
Found at i:1410826 original size:13 final size:13
Alignment explanation
Indices: 1410808--1410834 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1410798 ACATAAAGTG
1410808 TTGTATCGATACA
1 TTGTATCGATACA
1410821 TTGTATCGATACA
1 TTGTATCGATACA
1410834 T
1 T
1410835 AAGTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1410849 original size:32 final size:33
Alignment explanation
Indices: 1410788--1410852 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1410778 TTTCAACGAT
1410788 TTGTATCGATACATAAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
*
1410821 TTGTATCGATACAT-AAGTTTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
1410853 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATAAAGTGTTGTATCGATACA
Found at i:1410951 original size:52 final size:52
Alignment explanation
Indices: 1410895--1411023 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1410885 CACTGATCTT
*
1410895 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1410947 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1410999 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1411024 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1426310 original size:30 final size:30
Alignment explanation
Indices: 1426255--1426412 Score: 124
Period size: 30 Copynumber: 5.0 Consensus size: 30
1426245 TCACCCTTCA
* *
1426255 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC
*
1426284 AAAGCCCACAACTCCGTGACACTCTTTTTTCTTC
1 AAAGCCCACAACTCCGTGGCACTC---TTT-TTC
* * * *
1426318 TAAGTCCACGACTCTGTGGCAC-CTTCTTTC
1 AAAGCCCACAACTCCGTGGCACTCTT-TTTC
1426348 AAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--C
*
1426380 TTTTAAAGCCTACAACTCCGTGGCAC-CTTTTTC
1 ----AAAGCCCACAACTCCGTGGCACTCTTTTTC
1426413 TTTTCTAAAG
Statistics
Matches: 103, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
29 18 0.17
30 28 0.27
31 4 0.04
32 1 0.01
33 5 0.05
34 20 0.19
35 6 0.06
36 21 0.20
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.31
Consensus pattern (30 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTC
Found at i:1426388 original size:36 final size:34
Alignment explanation
Indices: 1426279--1426428 Score: 139
Period size: 36 Copynumber: 4.4 Consensus size: 34
1426269 AGTGGCATCT
* *
1426279 TTTTCAAAGCCCACAACTCCGTGACACTCTTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCAC-CTTTTTCC
* * * *
1426315 TTCT-AAGTCCACGACTCTGTGGCACC---TT-C
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCC
*
1426344 TTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CC
* *
1426380 TTTTAAAGCCTACAACTCCGTGGCACCTTTTTCT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCC
1426414 TTTCTAAAGCCCACA
1 TTT-TAAAGCCCACA
1426429 CAAGTCGGTG
Statistics
Matches: 92, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
29 3 0.03
30 20 0.22
31 1 0.01
33 1 0.01
34 23 0.25
35 16 0.17
36 28 0.30
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.33
Consensus pattern (34 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCC
Found at i:1426457 original size:33 final size:34
Alignment explanation
Indices: 1426415--1426482 Score: 129
Period size: 33 Copynumber: 2.0 Consensus size: 34
1426405 CCTTTTTCTT
1426415 TTCTAAAGCCCACACAAGTCGGTGGCAA-CCTTC
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1426448 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1426482 T
1 T
1426483 AAGTCCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22
Consensus pattern (34 bp):
TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
Found at i:1426598 original size:49 final size:49
Alignment explanation
Indices: 1426482--1426720 Score: 277
Period size: 43 Copynumber: 5.1 Consensus size: 49
1426472 GCAACCCTTC
*
1426482 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T--TC--
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1426526 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1426574 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
1426617 TAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC-AC-CT-TCATCTT
*
1426669 TAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1426718 TAA
1 TAA
1426721 CATTCCTAAG
Statistics
Matches: 163, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
43 74 0.45
44 1 0.01
45 1 0.01
46 2 0.01
49 45 0.28
50 2 0.01
51 1 0.01
52 37 0.23
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:1426639 original size:92 final size:95
Alignment explanation
Indices: 1426482--1426713 Score: 389
Period size: 92 Copynumber: 2.5 Consensus size: 95
1426472 GCAACCCTTC
1426482 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAAGTCCAATATCGCTGGCCTT
1426547 GAATCAGCATATTGGC-AC-CT-TCATCTT
66 GAATCAGCATATTGGCGACTCTGTCATCTT
* *
1426574 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCTAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAAGTCCAATATCGCTGGCCTT
* *
1426639 GAATCAGCATATTGGCGTCTTTGTCATCTT
66 GAATCAGCATATTGGCGACTCTGTCATCTT
* *
1426669 TAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTCA
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1426714 TCTTTAACAT
Statistics
Matches: 130, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 79 0.61
93 1 0.01
94 1 0.01
95 49 0.38
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (95 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAAGTCCAATATCGCTGGCCTT
GAATCAGCATATTGGCGACTCTGTCATCTT
Found at i:1427567 original size:13 final size:13
Alignment explanation
Indices: 1427549--1427575 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1427539 ACATAAAGTG
1427549 TTGTATCGATACA
1 TTGTATCGATACA
1427562 TTGTATCGATACA
1 TTGTATCGATACA
1427575 T
1 T
1427576 AAGTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1427590 original size:32 final size:33
Alignment explanation
Indices: 1427529--1427593 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1427519 TTTCAATGAT
1427529 TTGTATCGATACATAAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
*
1427562 TTGTATCGATACAT-AAGTTTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
1427594 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATAAAGTGTTGTATCGATACA
Found at i:1431419 original size:99 final size:100
Alignment explanation
Indices: 1431234--1431433 Score: 303
Period size: 99 Copynumber: 2.0 Consensus size: 100
1431224 ATTATGAAAA
* *
1431234 ATGATTCAAATGCATAAACCTTTGCATAATAATTCTTAAGTCATGGAAAATAACTTATATCTCTA
1 ATGATTCAAATGCATAAACCTTTGCATAATAATTCCTAAGTCATGAAAAATAACTTATATCTCTA
* * *
1431299 AAATATATAAAATTACGTG-AAATTTCTAGATCAT
66 AAATATATAAAATTACATGAAAATTTCCAAATCAT
* *
1431333 ATGATTTAAATGCATAAACCTTTGTATAATAATTCCTAAGTCATGAAAAATAACTTATATCTCTA
1 ATGATTCAAATGCATAAACCTTTGCATAATAATTCCTAAGTCATGAAAAATAACTTATATCTCTA
* * *
1431398 AAATGTATGAAATTGCATGAAAATTTCCAAATCAT
66 AAATATATAAAATTACATGAAAATTTCCAAATCAT
1431433 A
1 A
1431434 AAAAATTAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 76 0.84
100 14 0.16
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (100 bp):
ATGATTCAAATGCATAAACCTTTGCATAATAATTCCTAAGTCATGAAAAATAACTTATATCTCTA
AAATATATAAAATTACATGAAAATTTCCAAATCAT
Found at i:1431605 original size:58 final size:58
Alignment explanation
Indices: 1431477--1431606 Score: 156
Period size: 58 Copynumber: 2.2 Consensus size: 58
1431467 AAGTCCTCAT
* * * *
1431477 ATCATGAAAAATGACCTAAATAACTTTAATATATATTAAATTACATAAAAGTCCCTAG
1 ATCATGAAAAATGACCTAAATAACTTTAAAATATATGAAATGACATAAAAATCCCTAG
* * * *
1431535 ATTAT-AATAAATGACCTAAATGACTTTAAAATGTATGAAATGACATAAAAATTCCTAGG
1 ATCATGAA-AAATGACCTAAATAACTTTAAAATATATGAAATGACATAAAAATCCCTA-G
1431594 A-CATGAAAAATGA
1 ATCATGAAAAATGA
1431607 GTAAAATGAC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.03
58 54 0.90
59 4 0.07
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (58 bp):
ATCATGAAAAATGACCTAAATAACTTTAAAATATATGAAATGACATAAAAATCCCTAG
Found at i:1432358 original size:25 final size:24
Alignment explanation
Indices: 1432324--1432393 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
1432314 CTTAAAGAAA
*
1432324 CTTTTCTTCTTATCTTTTAT-TTTTT
1 CTTTTTTTCTTAT-TTTT-TCTTTTT
1432349 CTTTTTTTCTTTATTTTTTCTTTTT
1 CTTTTTTTC-TTATTTTTTCTTTTT
*
1432374 ATTTTTTTCTCTAGTTTTTT
1 CTTTTTTTCT-TA-TTTTTT
1432394 TCCTAAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 2 0.05
25 27 0.69
26 10 0.26
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (24 bp):
CTTTTTTTCTTATTTTTTCTTTTT
Found at i:1432361 original size:19 final size:20
Alignment explanation
Indices: 1432325--1432379 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
1432315 TTAAAGAAAC
*
1432325 TTTTCTTCTTATCTTTTATT
1 TTTTCTTTTTATCTTTTATT
*
1432345 TTTTCTTTTTTTC-TTTATT
1 TTTTCTTTTTATCTTTTATT
1432364 TTTTCTTTTTAT-TTTT
1 TTTTCTTTTTATCTTTT
1432380 TTCTCTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTCTTTTTATCTTTTATT
Found at i:1434093 original size:2 final size:2
Alignment explanation
Indices: 1434080--1434114 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
1434070 CAAACCAATC
*
1434080 TA TA TG TA TA TA TA TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
1434115 ATTATCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1435170 original size:17 final size:18
Alignment explanation
Indices: 1435148--1435190 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1435138 ATGTGATTAT
1435148 TATTTTTATGA-TTTTAA
1 TATTTTTATGATTTTTAA
*
1435165 TATTTTT-TTATTTTTAA
1 TATTTTTATGATTTTTAA
*
1435182 TATTATTAT
1 TATTTTTAT
1435191 TTATATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTTTTATGATTTTTAA
Found at i:1439256 original size:16 final size:16
Alignment explanation
Indices: 1439231--1439272 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1439221 AAAATAAATT
* *
1439231 TTTAAATTAATTTAAA
1 TTTAGATTAACTTAAA
*
1439247 TTTAGTTTAACTTAAA
1 TTTAGATTAACTTAAA
1439263 TTTAGATTAA
1 TTTAGATTAA
1439273 AAAATAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTAGATTAACTTAAA
Found at i:1439475 original size:33 final size:33
Alignment explanation
Indices: 1439436--1439501 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1439426 TTATCTTGAT
* * *
1439436 TTTAATAGTATTGAAGATAAATATTATTTTTAA
1 TTTAATAATATTAAAGACAAATATTATTTTTAA
* *
1439469 TTTAATAATATTAAAGACGAATGTTATTTTTAA
1 TTTAATAATATTAAAGACAAATATTATTTTTAA
1439502 AAAATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (33 bp):
TTTAATAATATTAAAGACAAATATTATTTTTAA
Done.