Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold184
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: 2218657
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.30
Warning! 156408 characters in sequence are not A, C, G, or T
File 7 of 13
Found at i:1089137 original size:84 final size:84
Alignment explanation
Indices: 1088982--1089146 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
1088972 CATTTTCCAC
* * * *
1088982 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
1089047 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
1089066 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
1089128 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
1089147 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1089559 original size:21 final size:21
Alignment explanation
Indices: 1089535--1089576 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1089525 ATCCATTTCT
* *
1089535 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
1089556 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCAACATCTTGA
1089577 ACAGTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:1091297 original size:23 final size:23
Alignment explanation
Indices: 1091257--1091302 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1091247 TAACGATACA
* *
1091257 TGAACAGTGATACGTGAATAGTG
1 TGAACAGTGATACATGAACAGTG
1091280 TGAACAGTGAT-CTATGAACAGTG
1 TGAACAGTGATAC-ATGAACAGTG
1091303 ATATATCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (23 bp):
TGAACAGTGATACATGAACAGTG
Found at i:1091323 original size:21 final size:22
Alignment explanation
Indices: 1091293--1091347 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
1091283 ACAGTGATCT
1091293 ATGAACAGTGATATATCGATAC
1 ATGAACAGTGATATATCGATAC
*
1091315 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATATATCGATAC
*
1091336 ATAAACAGTGAT
1 ATGAACAGTGAT
1091348 GAATAGTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATATATCGATAC
Found at i:1091454 original size:53 final size:53
Alignment explanation
Indices: 1091390--1091527 Score: 240
Period size: 53 Copynumber: 2.6 Consensus size: 53
1091380 CTACTACCAA
*
1091390 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAGTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1091443 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1091496 TGTATCGATACATATTTGTGTGTATCGATACA
1 TGTATCGATACATATTT-TGTGTATCGATACA
1091528 TTTAAAATGT
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1091613 original size:21 final size:21
Alignment explanation
Indices: 1091587--1091627 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1091577 GTCAACCTTG
1091587 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1091608 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1091628 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:1092894 original size:22 final size:23
Alignment explanation
Indices: 1092852--1092895 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1092842 TTAAAATGAC
*
1092852 TTAAACCCGATTTAACCCGAATG
1 TTAAACCCGAATTAACCCGAATG
*
1092875 TTAAACCC-AATTGACCCGAAT
1 TTAAACCCGAATTAACCCGAAT
1092896 CTAGAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.25
Consensus pattern (23 bp):
TTAAACCCGAATTAACCCGAATG
Found at i:1093704 original size:17 final size:17
Alignment explanation
Indices: 1093682--1093716 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1093672 GATTTTTTTG
*
1093682 AAATTAAGATCAAAATT
1 AAATTAAAATCAAAATT
1093699 AAATTAAAATCAAAATT
1 AAATTAAAATCAAAATT
1093716 A
1 A
1093717 CATCAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATTAAAATCAAAATT
Found at i:1093987 original size:35 final size:37
Alignment explanation
Indices: 1093948--1094108 Score: 107
Period size: 36 Copynumber: 4.4 Consensus size: 37
1093938 TCCATCGAAG
* *
1093948 CTTCAACTTTAGAAT-AGAA-AACTCTTTTACCAAGA
1 CTTCAACTTTAAAATAAAAACAACTCTTTTACCAAGA
* * *
1093983 CTTCAAATTTAAAATAAAAAACAACTCTTTTACTAAGG
1 CTTCAACTTTAAAAT-AAAAACAACTCTTTTACCAAGA
* * **
1094021 CTTCAACTTTAAAAATGAAAA-AACTCATCCACCAA-A
1 CTTCAACTTT-AAAATAAAAACAACTCTTTTACCAAGA
* * * * * *
1094057 GCTTCAACTTTTAAACAAAAA-ACCTCTTCTATCAAGG
1 -CTTCAACTTTAAAATAAAAACAACTCTTTTACCAAGA
**
1094094 CTTTGACTTTAAAAT
1 CTTCAACTTTAAAAT
1094109 GAGAAACTCC
Statistics
Matches: 96, Mismatches: 24, Indels: 11
0.73 0.18 0.08
Matches are distributed among these distances:
35 13 0.14
36 28 0.29
37 23 0.24
38 27 0.28
39 5 0.05
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.30
Consensus pattern (37 bp):
CTTCAACTTTAAAATAAAAACAACTCTTTTACCAAGA
Found at i:1094015 original size:38 final size:40
Alignment explanation
Indices: 1093967--1094044 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 40
1093957 TAGAATAGAA
1093967 AACTCTTTTACCAAGACTTCAAATTT-AAAAT-AAAAAAC
1 AACTCTTTTACCAAGACTTCAAATTTAAAAATGAAAAAAC
* * *
1094005 AACTCTTTTACTAAGGCTTCAACTTTAAAAATGAAAAAAC
1 AACTCTTTTACCAAGACTTCAAATTTAAAAATGAAAAAAC
1094045 TCATCCACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 23 0.66
39 5 0.14
40 7 0.20
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (40 bp):
AACTCTTTTACCAAGACTTCAAATTTAAAAATGAAAAAAC
Found at i:1094129 original size:35 final size:35
Alignment explanation
Indices: 1094016--1094220 Score: 126
Period size: 35 Copynumber: 5.7 Consensus size: 35
1094006 ACTCTTTTAC
* * * *
1094016 TAAGGCTTCAACTTTAAAAATGAAAAAACTCATCCAC
1 TAAGGCTTTAACTTT-AAAATG-AAAAACTCCTCTAA
* * * * ** *
1094053 CAAAGCTTCAACTTTTAAACAAAAAACCTCTTCT-A
1 TAAGGCTTTAACTTTAAAATGAAAAA-CTCCTCTAA
* *
1094088 TCAAGGCTTTGACTTTAAAATGAGAAACTCCTCTAA
1 T-AAGGCTTTAACTTTAAAATGAAAAACTCCTCTAA
* * * * * * *
1094124 TAAGGCTTTGACTTTATAATGAAAAATTTCACCAC
1 TAAGGCTTTAACTTTAAAATGAAAAACTCCTCTAA
** *
1094159 CGAGGCTTTAACTTTAAAATGAAAAACTCCTCCT-T
1 TAAGGCTTTAACTTTAAAATGAAAAACTCCT-CTAA
*
1094194 TAAGGTTTTAACTTTAAAAATGAAAAA
1 TAAGGCTTTAACTTT-AAAATGAAAAA
1094221 AAAAAACCCC
Statistics
Matches: 127, Mismatches: 36, Indels: 11
0.73 0.21 0.06
Matches are distributed among these distances:
35 74 0.58
36 40 0.31
37 13 0.10
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (35 bp):
TAAGGCTTTAACTTTAAAATGAAAAACTCCTCTAA
Found at i:1094574 original size:25 final size:27
Alignment explanation
Indices: 1094527--1094576 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1094517 CACAACATGA
*
1094527 ATGAATGTTCTGCAATAAATGAATGCC
1 ATGAATGTTATGCAATAAATGAATGCC
*
1094554 ATGAATG-TATGC-ATAATTGAATG
1 ATGAATGTTATGCAATAAATGAATG
1094577 AATCATATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 4 0.19
27 7 0.33
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (27 bp):
ATGAATGTTATGCAATAAATGAATGCC
Found at i:1095930 original size:9 final size:9
Alignment explanation
Indices: 1095916--1095958 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1095906 ACATTGTATA
1095916 TTTTTTTCT
1 TTTTTTTCT
*
1095925 TTTTTTTCA
1 TTTTTTTCT
1095934 TTTTTTTC-
1 TTTTTTTCT
*
1095942 ATTTTTTCT
1 TTTTTTTCT
1095951 TTATTTTT
1 TT-TTTTT
1095959 TCCATTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 7 0.24
9 17 0.59
10 5 0.17
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1095947 original size:20 final size:20
Alignment explanation
Indices: 1095914--1095966 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1095904 AAACATTGTA
1095914 TATTTTTTTC-TTTTTT-TT
1 TATTTTTTTCATTTTTTCTT
*
1095932 CATTTTTTTCATTTTTTCTT
1 TATTTTTTTCATTTTTTCTT
*
1095952 TATTTTTTCCATTTT
1 TATTTTTTTCATTTT
1095967 GAAGCCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 9 0.30
19 6 0.20
20 15 0.50
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTTTTCATTTTTTCTT
Found at i:1095966 original size:9 final size:9
Alignment explanation
Indices: 1095915--1095948 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1095905 AACATTGTAT
1095915 ATTTTTTTC
1 ATTTTTTTC
*
1095924 TTTTTTTTC
1 ATTTTTTTC
1095933 ATTTTTTTC
1 ATTTTTTTC
1095942 ATTTTTT
1 ATTTTTT
1095949 CTTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:1105221 original size:52 final size:52
Alignment explanation
Indices: 1105134--1105262 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
1105124 CGAAATATGA
* * *
1105134 AAATTCGCGTGCATGTATCGATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
1105186 AGATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1105238 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1105263 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1105273 original size:52 final size:52
Alignment explanation
Indices: 1105134--1105280 Score: 179
Period size: 52 Copynumber: 2.8 Consensus size: 52
1105124 CGAAATATGA
* * * ***
1105134 AAATTCGCGTGCATGTATCGATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
* * ***
1105186 AGATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
1105238 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATA
1 AAATTTGCCTGCATGTATCGATACATAAGAT-AGTGTATCGATA
1105281 TAATGTATCG
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
Found at i:1105362 original size:19 final size:19
Alignment explanation
Indices: 1105338--1105403 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
1105328 TAGCTTAAAT
1105338 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1105357 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
* *
1105370 TGTATGGATACAACACCTTA
1 TGTATCGATACAA-AACTTA
1105390 TGTATCGATACAAA
1 TGTATCGATACAAA
1105404 TCGTTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 1 0.03
19 13 0.35
20 12 0.32
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1105380 original size:32 final size:33
Alignment explanation
Indices: 1105336--1105401 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1105326 AGTAGCTTAA
1105336 ATTGTATCGATACAA-AACTTATGTATCGATAC
1 ATTGTATCGATACAACAACTTATGTATCGATAC
* *
1105368 ATTGTATGGATACAACACCTTATGTATCGATAC
1 ATTGTATCGATACAACAACTTATGTATCGATAC
1105401 A
1 A
1105402 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAACTTATGTATCGATAC
Found at i:1106200 original size:61 final size:61
Alignment explanation
Indices: 1106119--1106235 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
1106109 AAACCCAATA
**
1106119 TCACTGGCTTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCCTCAAGCCCGATC
1 TCACTGGCCATGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCCTCAAGCCCGATC
* * *
1106180 TCACTGGCCATGAATTAGCATATTGGTACCTTTATCATTCTTCTCATCTTCAAGCC
1 TCACTGGCCATGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCCTCAAGCC
1106236 TGACGTGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (61 bp):
TCACTGGCCATGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCCTCAAGCCCGATC
Found at i:1109432 original size:27 final size:27
Alignment explanation
Indices: 1109375--1109444 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
1109365 ATCATCATTG
* * * *
1109375 GGGATACTCAAACCCCATTATTCTGAG
1 GGGATACTCCAACCCCATTACTCCGAA
*
1109402 GGGATACTCCAACCCCATTCCTCCGAA
1 GGGATACTCCAACCCCATTACTCCGAA
*
1109429 GGGATACTCCAGCCCC
1 GGGATACTCCAACCCC
1109445 TTTTCAACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.20
Consensus pattern (27 bp):
GGGATACTCCAACCCCATTACTCCGAA
Found at i:1113373 original size:52 final size:52
Alignment explanation
Indices: 1113288--1113412 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
1113278 ATATGAAAAG
* *
1113288 TTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1113340 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1113392 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1113413 AAGATCAATG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
Found at i:1113423 original size:52 final size:52
Alignment explanation
Indices: 1113288--1113432 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 52
1113278 ATATGAAAAG
* *** *
1113288 TTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
***
1113340 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
1113392 TTGCCTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AATGTATCGATACA
1113433 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
Found at i:1113436 original size:13 final size:13
Alignment explanation
Indices: 1113418--1113445 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1113408 ATACAAAGAT
1113418 CAATGTATCGATA
1 CAATGTATCGATA
1113431 CAATGTATCGATA
1 CAATGTATCGATA
1113444 CA
1 CA
1113446 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1113543 original size:33 final size:33
Alignment explanation
Indices: 1113486--1113552 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1113476 AATAACTTAA
*
1113486 ATTGTATCGATACAAAAAAATATGTATTGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1113519 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1113552 A
1 A
1113553 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1114204 original size:18 final size:18
Alignment explanation
Indices: 1114181--1114232 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
1114171 TCAAGCGTTG
*
1114181 ATTCTGCACATGTTGGGT
1 ATTCTGCACATGTTGAGT
1114199 ATTCTGCA-ATGGTT-AGT
1 ATTCTGCACAT-GTTGAGT
1114216 ATTCTGCACATGTTGAG
1 ATTCTGCACATGTTGAG
1114233 GTCAAGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.38
Consensus pattern (18 bp):
ATTCTGCACATGTTGAGT
Found at i:1114444 original size:55 final size:52
Alignment explanation
Indices: 1114344--1114628 Score: 217
Period size: 43 Copynumber: 5.7 Consensus size: 52
1114334 GAAAAGTGAT
* * * * * * **
1114344 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
1114398 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
1114451 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
1114494 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
1114543 AAAGATGCCAATATGCTGATTCAAGGCCA-ATGATATTGGACTT-AA-A-GG-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCT-ACATTGAACTTAAAGATGGA
* * * *
1114591 CAAGGTGACAATATGTTGATTCAAGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
1114629 GGCTTAAAAG
Statistics
Matches: 195, Mismatches: 25, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
43 39 0.20
44 1 0.01
46 1 0.01
47 1 0.01
48 34 0.17
49 39 0.20
51 1 0.01
52 32 0.16
53 6 0.03
54 5 0.03
55 36 0.18
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:1114524 original size:95 final size:93
Alignment explanation
Indices: 1114398--1114628 Score: 304
Period size: 92 Copynumber: 2.4 Consensus size: 93
1114388 AAGATGAGAA
* *
1114398 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT---AAAGATGCCAAT
*
1114463 ATGCTGATTCAAGGCCAGCT-ATATTGGACTT
63 ATGCTGATTCAAGGCCA-ATGATATTGGACTT
*
1114494 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGATGCCAATATG
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGATGCCAATATG
1114558 CTGATTCAAGGCCAATGATATTGGACTT
66 CTGATTCAAGGCCAATGATATTGGACTT
* * * *
1114586 AAAGGCAAGGTGACAATATGTTGATTCAAGGCCAGCTATATTG
1 AAAGG--A--TGCCAATGTGCTGATTCAAGGCCAGCTACATTG
1114629 GGCTTAAAAG
Statistics
Matches: 121, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
91 1 0.01
92 44 0.36
95 42 0.35
96 5 0.04
97 29 0.24
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (93 bp):
AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGATGCCAATATG
CTGATTCAAGGCCAATGATATTGGACTT
Found at i:1114565 original size:49 final size:49
Alignment explanation
Indices: 1114341--1114636 Score: 275
Period size: 49 Copynumber: 6.0 Consensus size: 49
1114331 TGAGAAAAGT
* * * * *
1114341 GATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAA
1 GATAAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * * *
1114390 GATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1 GAT-----AAA-GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
*
1114445 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 GAT---AAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
1114497 G-----G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 GATAAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
*
1114540 GATAAAGATGCCAATATGCTGATTCAAGGCCA-ATGATATTGGACTTAAA
1 GATAAAGATGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGACTTAAA
** * * * *
1114589 G-GCAAGGTGACAATATGTTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 GATAAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1114637 AGGAGACGCC
Statistics
Matches: 206, Mismatches: 27, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
43 40 0.19
44 1 0.00
48 40 0.19
49 41 0.20
52 39 0.19
53 5 0.02
54 3 0.01
55 37 0.18
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (49 bp):
GATAAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
Found at i:1114590 original size:92 final size:94
Alignment explanation
Indices: 1114397--1114636 Score: 306
Period size: 95 Copynumber: 2.5 Consensus size: 94
1114387 AAAGATGAGA
* * *
1114397 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAA
1 AAAAGG-TGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAGATGCCAA
*
1114462 TATGCTGATTCAAGGCCAGCTATATTGGACTT
63 TATGCTGATTCAAGGCCAGATATATTGGACTT
*
1114494 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAGATGCCAATAT
1 AAAAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGATGCCAATAT
1114557 GCTGATTCAAGGCCA-ATGATATTGGACTT
66 GCTGATTCAAGGCCAGAT-ATATTGGACTT
* * * *
1114586 AAAGGCAAGGTGACAATATGTTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 -AA---AAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1114637 AGGAGACGCC
Statistics
Matches: 128, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
91 1 0.01
92 39 0.30
94 1 0.01
95 42 0.33
96 5 0.04
97 40 0.31
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (94 bp):
AAAAGGTGACAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGATGCCAATAT
GCTGATTCAAGGCCAGATATATTGGACTT
Found at i:1114713 original size:28 final size:28
Alignment explanation
Indices: 1114682--1114779 Score: 133
Period size: 28 Copynumber: 3.4 Consensus size: 28
1114672 GTTTGCATCA
* *
1114682 ACTTGTGTGCTTTTGAAGGTTGCTACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1114710 ACTTGTGGGCTTTTAAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
1114738 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
1114768 ACTTGTGGGCTT
1 ACTTGTGGGCTT
1114780 AAAAAGAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
28 39 0.63
30 23 0.37
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.37
Consensus pattern (28 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTG
Found at i:1114764 original size:30 final size:30
Alignment explanation
Indices: 1114682--1115130 Score: 134
Period size: 30 Copynumber: 14.6 Consensus size: 30
1114672 GTTTGCATCA
* * *
1114682 ACTTGTGTGCTTTTG--AAGGTTGCTACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
1114710 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
1114738 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * *
1114768 ACTTGTGGGCTTAAAAAGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * * * *
1114802 AGTTGTGAG-TTTACAAAAGAAAAAGAGTGCCACAG
1 ACTTGTGGGCTTT-----TG-AAAAGGGTGCCACTG
* * * * *
1114837 AGTTGTGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** *
1114866 ACTTGTGGGCTTCGGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* ** * *
1114896 ACTTATGGGCTTAAAAAGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * * * *
1114930 AGTTGTGAG-TTTACAAAAGAAAAAGAGTGCCACGG
1 ACTTGTGGGCTTT-----TG-AAAAGGGTGCCACTG
* * * * *
1114965 AGTTGTGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
**
1114994 ACTTGTGGGCTTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
1115024 ATTTGTGGGC-TTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
***
1115051 ACTTGTGGGCTTTTGAAAAAAAAAAATGCCACTG
1 ACTTGTGGGCTTTTG----AAAAGGGTGCCACTG
***
1115085 ACTTGTGGGC-TTTGAAAAATATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
1115114 ACTTGTGGACTTTTGAA
1 ACTTGTGGGCTTTTGAA
1115131 GGGTGAGGAA
Statistics
Matches: 325, Mismatches: 59, Indels: 72
0.71 0.13 0.16
Matches are distributed among these distances:
27 21 0.06
28 43 0.13
29 71 0.22
30 73 0.22
31 2 0.01
33 12 0.04
34 53 0.16
35 44 0.14
36 6 0.02
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
Found at i:1114862 original size:29 final size:30
Alignment explanation
Indices: 1114822--1115031 Score: 95
Period size: 29 Copynumber: 6.8 Consensus size: 30
1114812 TTACAAAAGA
* *
1114822 AAAAGAGTGCCACAGAGTTGTGGACTTTGG
1 AAAAGAGTGCCACAGACTTGTGGACTTCGG
* *
1114852 AAAAGA-TGCCACCGACTTGTGGGCTTCGG
1 AAAAGAGTGCCACAGACTTGTGGACTTCGG
* * * * *
1114881 AAAAGGGTGCCACTA-ACTTATGGGCTTAAAAAGA
1 AAAAGAGTGCCAC-AGACTTGTGGACTT----CGG
* * * * *
1114915 AAAAGAGTGCTATAGAGTTGT-GAGTTTACAAAAGA
1 AAAAGAGTGCCACAGACTTGTGGA-CTT-C----GG
* * *
1114950 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGAGTGCCACAGACTTGTGGACTTCGG
* *
1114980 AAAAGA-TGCCACCGACTTGTGGGCTTCGG
1 AAAAGAGTGCCACAGACTTGTGGACTTCGG
* * *
1115009 AAAAGGGTGCCACTGATTTGTGG
1 AAAAGAGTGCCACAGACTTGTGG
1115032 GCTTTGAAGG
Statistics
Matches: 136, Mismatches: 30, Indels: 28
0.70 0.15 0.14
Matches are distributed among these distances:
29 48 0.35
30 44 0.32
31 1 0.01
33 2 0.01
34 17 0.12
35 22 0.16
36 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.23
Consensus pattern (30 bp):
AAAAGAGTGCCACAGACTTGTGGACTTCGG
Found at i:1115033 original size:128 final size:128
Alignment explanation
Indices: 1114730--1115035 Score: 549
Period size: 128 Copynumber: 2.4 Consensus size: 128
1114720 TTTTAAAGGT
* **
1114730 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGT
1 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGT
1114795 GCTATAGAGTTGTGAGTTTACAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTTGGAAAAGA
66 GCTATAGAGTTGTGAGTTTACAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTTGGAAAAGA
*
1114858 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTATGGGCTTAAAAAGAAAAAGAGT
1 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGT
*
1114923 GCTATAGAGTTGTGAGTTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGA
66 GCTATAGAGTTGTGAGTTTACAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTTGGAAAAGA
* *
1114986 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTT
1 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTT
1115036 TGAAGGTTGC
Statistics
Matches: 170, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 170 1.00
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (128 bp):
TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGT
GCTATAGAGTTGTGAGTTTACAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTTGGAAAAGA
Found at i:1115049 original size:27 final size:27
Alignment explanation
Indices: 1114986--1115063 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
1114976 TTGGAAAAGA
* *
1114986 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGG
* *
1115016 TGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGG
1115043 TGCCACTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
1115064 TGAAAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.56
29 1 0.02
30 18 0.42
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGG
Found at i:1115112 original size:29 final size:29
Alignment explanation
Indices: 1114948--1115126 Score: 155
Period size: 29 Copynumber: 6.0 Consensus size: 29
1114938 GTTTACAAAA
* * *
1114948 GAAAAAGAGTGCCACGGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
* * *
1114978 GGAAAAGATGCCACCGACTTGTGGGCTTCG
1 GAAAAAGATGCCACTGACTTGTGGGCTT-T
* * *
1115008 GAAAAGGGTGCCACTGATTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
1115037 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGC-TTT
*
1115065 GAAAAAAAAAAATGCCACTGACTTGTGGGCTTT
1 G----AAAAAGATGCCACTGACTTGTGGGCTTT
* *
1115098 GAAAAATATGCCACTGACTTGTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
1115127 TGAAGGGTGA
Statistics
Matches: 123, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
27 21 0.17
28 4 0.03
29 44 0.36
30 30 0.24
33 4 0.03
34 20 0.16
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:1116512 original size:1 final size:1
Alignment explanation
Indices: 1116506--1116575 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
1116496 TCCGGACCCC
* * * * * * * * *
1116506 TTTTTTTGTTTTTGTTTGTTGTTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1116571 TTTTT
1 TTTTT
1116576 GTGGAGGACG
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:1116532 original size:21 final size:20
Alignment explanation
Indices: 1116506--1116577 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
1116496 TCCGGACCCC
1116506 TTTTTTTGTTTTTGTTTGTT
1 TTTTTTTGTTTTTGTTTGTT
*
1116526 GTTTTTTT-TGTTTTGTTTTTT
1 -TTTTTTTGT-TTTTGTTTGTT
*
1116547 TTTTGTTTTTTTTTGTTTTGTT
1 TTTT-TTTGTTTTTG-TTTGTT
1116569 TTTTTTTGT
1 TTTTTTTGT
1116578 GGAGGACGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 5 0.11
21 29 0.66
22 10 0.23
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (20 bp):
TTTTTTTGTTTTTGTTTGTT
Found at i:1116535 original size:16 final size:15
Alignment explanation
Indices: 1116508--1116575 Score: 86
Period size: 15 Copynumber: 4.4 Consensus size: 15
1116498 CGGACCCCTT
1116508 TTTTTGTTTTTGTTTG
1 TTTTT-TTTTTGTTTG
1116524 TTGTTTTTTTTGTTTTG
1 TT-TTTTTTTTG-TTTG
1116541 TTTTTTTTTTGTTT-
1 TTTTTTTTTTGTTTG
1116555 TTTTTTGTTTTGTTT-
1 TTTTTT-TTTTGTTTG
1116570 TTTTTT
1 TTTTTT
1116576 GTGGAGGACG
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.12
15 17 0.35
16 17 0.35
17 9 0.18
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTGTTTG
Found at i:1116556 original size:26 final size:25
Alignment explanation
Indices: 1116509--1116575 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 25
1116499 GGACCCCTTT
1116509 TTTTGTTTTTGTTTGTTGTTTTTTTTG
1 TTTTGTTTTT-TTT-TTGTTTTTTTTG
1116536 TTTTGTTTTTTTTTTGTTTTTTTTTG
1 TTTTGTTTTTTTTTTG-TTTTTTTTG
1116562 TTTTGTTTTTTTTT
1 TTTTGTTTTTTTTT
1116576 GTGGAGGACG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 3 0.08
26 26 0.67
27 10 0.26
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (25 bp):
TTTTGTTTTTTTTTTGTTTTTTTTG
Found at i:1130494 original size:52 final size:52
Alignment explanation
Indices: 1130409--1130533 Score: 180
Period size: 52 Copynumber: 2.4 Consensus size: 52
1130399 ATATAAAAAG
* * * * * *
1130409 TTGCTTGCATGTATCGATAAATTTTATAGTGTATCGATACAT-CTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTATAAAATGTATCGATACATGC-AGGCAAAT
1130461 TTGCCTGCATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAAT
1 TTGCCTGCATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAAT
1130513 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1130534 AAGATCAATG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 65 0.98
53 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAAT
Found at i:1130544 original size:52 final size:52
Alignment explanation
Indices: 1130438--1130554 Score: 166
Period size: 52 Copynumber: 2.2 Consensus size: 52
1130428 AATTTTATAG
* **
1130438 TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTATAAAA
1 TGTATCGATACATCTAGGCAAATTTGCCTGCATGTATCGATACAAGATAAAA
*
1130490 TGTATCGATACATGC-AGGCAAATTTGCCTGCATGTATCGATACAAAGAT-CAA
1 TGTATCGATACAT-CTAGGCAAATTTGCCTGCATGTATCGATAC-AAGATAAAA
1130542 TGTATCGATACAT
1 TGTATCGATACAT
1130555 TTTTTGGCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
52 55 0.93
53 4 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATCTAGGCAAATTTGCCTGCATGTATCGATACAAGATAAAA
Found at i:1130630 original size:33 final size:33
Alignment explanation
Indices: 1130573--1130639 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1130563 AATAACTTAA
*
1130573 ATTGTATCGATACAAAAAAATATGTATTGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1130606 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1130639 A
1 A
1130640 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1134197 original size:20 final size:21
Alignment explanation
Indices: 1134172--1134222 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
1134162 TTTTCACAAT
1134172 TTGTATCGATACATTGTT-CA
1 TTGTATCGATACATTGTTACA
*
1134192 TTGTATCAATACATTGTT-CA
1 TTGTATCGATACATTGTTACA
1134212 TTGTATCGATA
1 TTGTATCGATA
1134223 TATTATGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (21 bp):
TTGTATCGATACATTGTTACA
Found at i:1134267 original size:20 final size:19
Alignment explanation
Indices: 1134242--1134315 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
1134232 TTTACCCAGA
1134242 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
1134262 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
1134282 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
1134302 TGTATCGATACATT
1 TGTATCGATACATT
1134316 CAGGAATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:1136744 original size:51 final size:51
Alignment explanation
Indices: 1136667--1136797 Score: 180
Period size: 51 Copynumber: 2.6 Consensus size: 51
1136657 GTTATTTCCG
* *
1136667 AGGGGATACTCCAACCCCGGTTTTATTT-CTAAACTACCAATTTTTCACAAT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAAC-ACCAATTTTTCACAAT
* * *
1136718 CGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAGT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAAT
1136769 AGGGGATACTCCAACCCC-A--TTATTTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAA
1136798 GGGGATACTT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 10 0.14
50 1 0.01
51 56 0.78
52 5 0.07
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAAT
Found at i:1136997 original size:78 final size:78
Alignment explanation
Indices: 1136719--1137017 Score: 291
Period size: 79 Copynumber: 3.8 Consensus size: 78
1136709 TTTCACAATC
* * * *
1136719 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCA-CAGTAGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCATAATTA-GGGATACTCCAA
* **
1136783 CCCCATTATTTCCAA
65 CCCTATTATTT-TGA
* *** * * * * **
1136798 GGGGATACTTCAACCCCGGCCTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAA-
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCATAATTAGGGATACTCCAAC
*
1136862 CCTCGTTATTTTCGA
66 CCT-ATTATTTT-GA
* * * *
1136877 GGGGATACTCCAACCCCGATTTCATTT-TCAAAATATCGATTTTT-ATAATTAGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTTCATAATTAGGGATACTCCAA
1136940 CCCTATTATTTATGA
65 CCCTATTATTT-TGA
** *
1136955 GGGGATACTCCAACCCCGATTTTATTTCTGGAACACCAATTTTCCATAATTAGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCATAATTAGGGATACTCCA
1137018 GCCCCGTTGT
Statistics
Matches: 177, Mismatches: 35, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
78 62 0.35
79 114 0.64
80 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCATAATTAGGGATACTCCAAC
CCTATTATTTTGA
Found at i:1137011 original size:157 final size:158
Alignment explanation
Indices: 1136719--1137017 Score: 352
Period size: 157 Copynumber: 1.9 Consensus size: 158
1136709 TTTCACAATC
* * *
1136719 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAGTAGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAATTTTTCAAAGTAGGGGATACTCCAAC
* * * * * *
1136784 CCCATTATTTCCAAGGGGATACTTCAACCCCGGCCTTATTTCTAAATCATCGATTTTTCACAATC
66 CCCATTATTTACAAGGGGATACTCCAACCCCGACCTTATTTCTAAATCACCAATTTTCCACAATC
*
1136849 GGGGATACTCCAACCTCGTTATTTTCGA
131 AGGGATACTCCAACCTCGTTATTTTCGA
* * * * *
1136877 GGGGATACTCCAACCCCGATTTCATTTTCAAAATATCGATTTTT-ATAATTA-GGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAATTTTTCA-AAGTAGGGGATACTCCAA
* ** ** * *
1136940 CCCTATTATTTATGAGGGGATACTCCAACCCCGATTTTATTTCTGGAA-CACCAATTTTCCATAA
65 CCCCATTATTTACAAGGGGATACTCCAACCCCGACCTTATTTCT-AAATCACCAATTTTCCACAA
*
1137004 TTAGGGATACTCCA
129 TCAGGGATACTCCA
1137018 GCCCCGTTGT
Statistics
Matches: 116, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
157 73 0.63
158 43 0.37
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (158 bp):
GGGGATACTCCAACCCCGATTTCATTTCCAAAACACCAATTTTTCAAAGTAGGGGATACTCCAAC
CCCATTATTTACAAGGGGATACTCCAACCCCGACCTTATTTCTAAATCACCAATTTTCCACAATC
AGGGATACTCCAACCTCGTTATTTTCGA
Found at i:1138724 original size:16 final size:16
Alignment explanation
Indices: 1138703--1138798 Score: 70
Period size: 19 Copynumber: 5.5 Consensus size: 16
1138693 TAAAGATAAA
1138703 ATAAATTATTAAAAAT
1 ATAAATTATTAAAAAT
1138719 ATAAATTA--AAAAAT
1 ATAAATTATTAAAAAT
*
1138733 ATATATATATTAAATAATT
1 ATAAAT-TATTAAA-AA-T
*
1138752 AAAAATTATTAAAATTAT
1 ATAAATTATTAAAA--AT
1138770 AGTTAAATTAAATTATAAAAT
1 A--TAAATT--ATTA-AAAAT
1138791 ATAAATTA
1 ATAAATTA
1138799 AAATTATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 23
0.70 0.04 0.25
Matches are distributed among these distances:
14 11 0.17
15 2 0.03
16 8 0.12
17 5 0.08
18 11 0.17
19 12 0.19
20 5 0.08
21 3 0.05
22 4 0.06
23 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAAATTATTAAAAAT
Found at i:1138730 original size:14 final size:15
Alignment explanation
Indices: 1138703--1138798 Score: 53
Period size: 14 Copynumber: 6.5 Consensus size: 15
1138693 TAAAGATAAA
1138703 ATAAATTATTAAAAAT
1 ATAAATTA-TAAAAAT
1138719 ATAAATTA-AAAAAT
1 ATAAATTATAAAAAT
* **
1138733 ATATA-TATATTAA-
1 ATAAATTATAAAAAT
*
1138746 AT-AATTA-AAAATT
1 ATAAATTATAAAAAT
*
1138759 ATTAAAATTATAGTTAAAT
1 A-T-AAATTATA--AAAAT
1138778 -TAAATTAT-AAAAT
1 ATAAATTATAAAAAT
1138791 ATAAATTA
1 ATAAATTA
1138799 AAATTATATT
Statistics
Matches: 60, Mismatches: 10, Indels: 22
0.65 0.11 0.24
Matches are distributed among these distances:
12 3 0.05
13 11 0.18
14 21 0.35
16 20 0.33
17 2 0.03
19 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (15 bp):
ATAAATTATAAAAAT
Found at i:1138818 original size:36 final size:37
Alignment explanation
Indices: 1138704--1138834 Score: 121
Period size: 36 Copynumber: 3.6 Consensus size: 37
1138694 AAAGATAAAA
* * *
1138704 TAAATTATTAAAAATATAAATTAAAAAATATATATATAT
1 TAAATAATT-AAAATATAAATT-AAAATTATATTTATAT
* * *
1138743 TAAATAATTAAAA-AT-TATTAAAATTATAGTTAAAT
1 TAAATAATTAAAATATAAATTAAAATTATATTTATAT
*
1138778 TAAATTA-TAAAATATAAATTAAAATTATATTTATGA-
1 TAAATAATTAAAATATAAATTAAAATTATATTTAT-AT
1138814 TAAATAA-TAATAAT-TAAATTA
1 TAAATAATTAA-AATATAAATTA
1138835 TTAAAAATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
34 5 0.06
35 20 0.26
36 34 0.44
37 6 0.08
38 4 0.05
39 8 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (37 bp):
TAAATAATTAAAATATAAATTAAAATTATATTTATAT
Found at i:1139795 original size:18 final size:18
Alignment explanation
Indices: 1139764--1139800 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1139754 TTATATTGGT
1139764 AAGAAGGAAAGAAAAAAA
1 AAGAAGGAAAGAAAAAAA
* *
1139782 AAGAATGAAGGAAAAAAA
1 AAGAAGGAAAGAAAAAAA
1139800 A
1 A
1139801 TTTAAGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (18 bp):
AAGAAGGAAAGAAAAAAA
Found at i:1139840 original size:19 final size:19
Alignment explanation
Indices: 1139816--1139855 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1139806 GTATTGTGTT
1139816 TATGTTATTTATTATATTA
1 TATGTTATTTATTATATTA
1139835 TATGTTATTTATTATATTA
1 TATGTTATTTATTATATTA
1139854 TA
1 TA
1139856 ATTTTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TATGTTATTTATTATATTA
Found at i:1139978 original size:11 final size:12
Alignment explanation
Indices: 1139947--1140009 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
1139937 TATTTTTACC
1139947 ATATTTATATTATT
1 ATATTT-TA-TATT
1139961 ATATTTTA-ATT
1 ATATTTTATATT
*
1139972 ATTTTTTATATT
1 ATATTTTATATT
*
1139984 ATATTTGTATCTT
1 ATATTT-TATATT
*
1139997 ATAATATTATATT
1 AT-ATTTTATATT
1140010 TAGAATTATC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 10 0.24
12 8 0.20
13 14 0.34
14 9 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:1144149 original size:2 final size:2
Alignment explanation
Indices: 1144144--1144168 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1144134 ATATTTTTTG
1144144 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1144169 CAAAACAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1144910 original size:19 final size:19
Alignment explanation
Indices: 1144886--1144922 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1144876 ATAACGATTA
* *
1144886 TAAATTATATAATTTGATC
1 TAAATTACATAATATGATC
1144905 TAAATTACATAATATGAT
1 TAAATTACATAATATGAT
1144923 ATTATTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
TAAATTACATAATATGATC
Found at i:1146163 original size:20 final size:19
Alignment explanation
Indices: 1146115--1146166 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1146105 CTGCTAGTTT
* *
1146115 CATATATCGATGCAATGAA
1 CATATATCGATACAAAGAA
*
1146134 CATGTATCGATACAAAGCAA
1 CATATATCGATACAAAG-AA
*
1146154 TATATATCGATAC
1 CATATATCGATAC
1146167 TTTTGAGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (19 bp):
CATATATCGATACAAAGAA
Found at i:1154961 original size:13 final size:13
Alignment explanation
Indices: 1154943--1154967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1154933 CATTTTACTA
1154943 TGTATCGATACAT
1 TGTATCGATACAT
1154956 TGTATCGATACA
1 TGTATCGATACA
1154968 ATGTCTCATG
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):
TGTATCGATACAT
Found at i:1154965 original size:33 final size:33
Alignment explanation
Indices: 1154923--1154987 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1154913 TTGGGCACAA
* *
1154923 TGTATCGATACATTTTACT-ATGTATCGATACAT
1 TGTATCGATACAATGT-CTCATGTATCGATACAT
1154956 TGTATCGATACAATGTCTCATGTATCGATACA
1 TGTATCGATACAATGTCTCATGTATCGATACA
1154988 AATAGTGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATGTCTCATGTATCGATACAT
Found at i:1155051 original size:20 final size:20
Alignment explanation
Indices: 1155015--1155052 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1155005 TACTACCAGT
*
1155015 TTCATGTATCTACACAATTC
1 TTCATGTATCGACACAATTC
*
1155035 TTCATGTATCGATACAAT
1 TTCATGTATCGACACAAT
1155053 GAACATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGACACAATTC
Found at i:1157956 original size:50 final size:51
Alignment explanation
Indices: 1157895--1158015 Score: 174
Period size: 51 Copynumber: 2.4 Consensus size: 51
1157885 TGAACTATAC
* *
1157895 ATGTATCGATACATTCT-GTTTTTTACCTAGATGTATCAATATATTTTTCA
1 ATGTATTGATACATTCTAGTTTTTTACCTAGATGTATCAATACATTTTTCA
* * * *
1157945 ATGTATTGATACATTTTATTTTTTTACCTAGATGTATCGATACATTTTTTA
1 ATGTATTGATACATTCTAGTTTTTTACCTAGATGTATCAATACATTTTTCA
1157996 ATGTATTGATACA-TCTAGTT
1 ATGTATTGATACATTCTAGTT
1158016 AATTTTTAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 20 0.32
51 42 0.68
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.50
Consensus pattern (51 bp):
ATGTATTGATACATTCTAGTTTTTTACCTAGATGTATCAATACATTTTTCA
Found at i:1158918 original size:20 final size:20
Alignment explanation
Indices: 1158893--1158933 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1158883 TAGCCTTTGA
* *
1158893 TCATGCATTTTCACTATGTT
1 TCATGCATTTTAAATATGTT
1158913 TCATGCATTTTAAATATGTT
1 TCATGCATTTTAAATATGTT
1158933 T
1 T
1158934 GGCATCTCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (20 bp):
TCATGCATTTTAAATATGTT
Found at i:1174003 original size:28 final size:28
Alignment explanation
Indices: 1173530--1174027 Score: 432
Period size: 28 Copynumber: 17.6 Consensus size: 28
1173520 CAATACGACC
* *
1173530 TCTTTTCAAAGCCCATAAGTTAGTGGTC-
1 TCTTTTCAAAGCCCACAAGTCAGTGG-CA
* * * * *
1173558 CCTTTTTAAAGCCTACAAGTTAGTGGTA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
1173586 CCTTTTTAAAGCTCACAAGTTAGTGGCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGC-A
* *
1173615 CTCTTTTCAAAGCTCACAAGTTAGTGGCAA
1 -TCTTTTCAAAGCCCACAAGTCAGTGGC-A
* *
1173645 CCCTTTTCGAAA-CCCATAAGTCAGTGGCA
1 -TCTTTTC-AAAGCCCACAAGTCAGTGGCA
* * * *
1173674 TCCTTTC-AAGCCCACAAGTTAATGACAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGC-A
* *
1173702 CCCTTTTTAAAGCCCACAAGTCAGTGGCA
1 -TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1173731 TCCTTTCAAAGCCTACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1173759 -CATTTTCAAAGCCCATAAGTCAATGGCA
1 TC-TTTTCAAAGCCCACAAGTCAGTGGCA
1173787 TCCTTTT-AAAGCCCACAAGTCAGTGGCA
1 T-CTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
1173815 TCCTTTCAGAGCCCACAAGTTAGTGGCT
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* ** *
1173843 TCTTTTCAAAGCCCATAAGTCAACGGTA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
1173871 CCTTTCCAAAGCCCGCAAGTCAATGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1173899 CCTTCTT-AAGGCCCACAAGTCAGTGGCA
1 TCTT-TTCAAAGCCCACAAGTCAGTGGCA
* *
1173927 CCTTTTCAAAGCTCACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
1173955 TCCTTTCAAAGCCTACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1173983 TCTTTTTAAAGCCCACAAGTCGGTAGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
1174011 TCCTTTCAAAGCCCACA
1 TCTTTTCAAAGCCCACA
1174028 CAAGTTAGTG
Statistics
Matches: 385, Mismatches: 71, Indels: 28
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.01
27 19 0.05
28 285 0.74
29 12 0.03
30 64 0.17
31 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (28 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:1175196 original size:50 final size:50
Alignment explanation
Indices: 1175139--1175247 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
1175129 ACAGTACATG
** *
1175139 TATCGATACATTCTATTTTTTACCCAGATGTATCGAGACATTTTTCAATA
1 TATCGATACATTCTATTTTTTAAACAGATGTATCGAGACATTTTTCAACA
* * *
1175189 TATCGATACATTCTTTTTTTTAAACAGATGTATCGATACATTTTTCAACG
1 TATCGATACATTCTATTTTTTAAACAGATGTATCGAGACATTTTTCAACA
1175239 TATCGATAC
1 TATCGATAC
1175248 CTCTAATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (50 bp):
TATCGATACATTCTATTTTTTAAACAGATGTATCGAGACATTTTTCAACA
Found at i:1183895 original size:20 final size:20
Alignment explanation
Indices: 1183870--1183907 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1183860 TACTACCAGT
1183870 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
1183890 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
1183908 AAACATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:1183916 original size:19 final size:20
Alignment explanation
Indices: 1183872--1183922 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1183862 CTACCAGTTT
***
1183872 CATGTATCGATACAATTCTT
1 CATGTATCGATACAATTAAA
1183892 CATGTATCGATACAA-TAAA
1 CATGTATCGATACAATTAAA
1183911 CATGTATCGATA
1 CATGTATCGATA
1183923 TAATGTATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:1190062 original size:19 final size:19
Alignment explanation
Indices: 1190040--1190076 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1190030 AAAATTCAAA
1190040 AATTTATGAAAAATGATTG
1 AATTTATGAAAAATGATTG
* *
1190059 AATTTTTGAAAACTGATT
1 AATTTATGAAAAATGATT
1190077 TAATATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.41
Consensus pattern (19 bp):
AATTTATGAAAAATGATTG
Found at i:1190104 original size:167 final size:167
Alignment explanation
Indices: 1189669--1190118 Score: 439
Period size: 167 Copynumber: 2.7 Consensus size: 167
1189659 AAAGTCGATT
* * ** * * * * *
1189669 TTTC-AAAAATAAGAAAATTTTAAAGAAAAAAATTCAAAACTCATAAAAATAAATAAAATTTTCA
1 TTTCGAAAAA-AAGAGAA-TTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGA
* * * **
1189733 AAACT-AATTTAATATGAATCAAATAATAATAATATTTAAT-AA-AATAAAAATTAAAAATCGAA
64 AAACTGAA-TTAATATAAATTAAATAAT-A-AA-ATTTGATGAATTTTAAAAATTAAAAATCGAA
* *
1189795 AAAAATTCCTCTTGAAAAAATTTACGGAGTAAAAAACTTCGTA
125 AAAAATTCCTCTTGAAAAAATTTACGGAGTAAAAAACTCCATA
* * *
1189838 TTTCGAAAACAAGAGAATTTCAAGAAAAAAATAAAAAACTCATGAAGATGAATGAATTTTTTAAA
1 TTTCGAAAAAAAGAGAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAA
* * * * * *
1189903 ACTGAATTAATGTGAGTTAAATCATAAAATTTGATGAATTTTGAAAATTAAAAATCGAGAAAAA-
66 ACTGAATTAATATAAATTAAATAATAAAATTTGATGAATTTTAAAAATTAAAAATCGAAAAAAAT
*
1189967 TCCT-TTCGAAAACATTTACGGAGTAAAAAA-TACCATA
131 TCCTCTT-GAAAAAATTTACGGAGTAAAAAACT-CCATA
* * * * * * *
1190004 TTTCGAAAAAAAG-GAGTTTTAAGGAAAAAATTCAAAAATTTATGAAAAATGATTGAATTTTTGA
1 TTTCGAAAAAAAGAGAATTTCAA-GAAAAAAATAAAAAACTCATG-AAAATGAATGAATTTTTGA
* *
1190068 AAACTGATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATT
64 AAACTGAATTAATATAAATTAAATAATAAAATTTGATGAATTTTAAAAATT
1190119 TTAAACCAAC
Statistics
Matches: 233, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
165 16 0.07
166 62 0.27
167 82 0.35
168 57 0.24
169 12 0.05
170 4 0.02
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.31
Consensus pattern (167 bp):
TTTCGAAAAAAAGAGAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAA
ACTGAATTAATATAAATTAAATAATAAAATTTGATGAATTTTAAAAATTAAAAATCGAAAAAAAT
TCCTCTTGAAAAAATTTACGGAGTAAAAAACTCCATA
Found at i:1197887 original size:20 final size:20
Alignment explanation
Indices: 1197862--1197935 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
1197852 TTTTAACTAG
1197862 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
*
1197882 ATGTATCGATACATT-CATA
1 ATGTATCGATACATTGAATA
* *
1197901 CATGTATCGATATATTGAAAA
1 -ATGTATCGATACATTGAATA
1197922 ATGTATCGATACAT
1 ATGTATCGATACAT
1197936 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.89
21 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:1198593 original size:57 final size:58
Alignment explanation
Indices: 1198458--1199395 Score: 1191
Period size: 57 Copynumber: 16.3 Consensus size: 58
1198448 TCACTAACTG
* * * * *
1198458 TTGTGGGCGTTGAAAAGAGTTGCCACTGTCTCGTGTGGGCTTTGAAAAGAGTTACCATTGGC
1 TTGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAAGAG-TGCCACTGAC
* * * * * *
1198520 TTATGGGCTTTGAAAAGAGTGCCACTAACTTGTAGACTTTGAAAGGA-TGCCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * * *
1198577 TTGTGAGCTTTGAAAAGAGTACCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * * *
1198634 TTGTGAGCTTTGAAAAGAGTGTCACTGATTTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1198691 TTGTGGGCTTTG-AAAGGGTGCCGCTGACTTGTAGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1198748 TTGTGGGCTTTGAAAAGAGTTGCCA-TCGACTCGTGTGGGCTTTGAAACGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAG-TGCCACT-GACT--TGTGGGCTTTGAAAAGAGTGCCACTGAC
* * * *
1198809 TTATGGGCTTTG-AAAGGGTGCTACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAA
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * * * *
1198866 TTGTGAGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCTACTGAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * * * *
1198923 TTATGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAAAGTGTCACTAAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1198980 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGGCTTTGAAAGGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1199038 TTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1199094 TTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGA-TGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1199151 TTGTGGGCTTTGAAAAGAATGCCATTGATTTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
** * *
1199209 TTGTGGGCTTTGAACGGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1199266 ATGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * ** *
1199324 TTGTGGGCTTTG-AAAGGGTGCCACTAACTCATGGGCTTTGAAAAGAGTGCCACTGAG
1 TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
1199381 TTGTGGGCTTTGAAA
1 TTGTGGGCTTTGAAA
1199396 GGGATGAACA
Statistics
Matches: 769, Mismatches: 92, Indels: 34
0.86 0.10 0.04
Matches are distributed among these distances:
56 52 0.07
57 486 0.63
58 132 0.17
59 30 0.04
60 6 0.01
61 46 0.06
62 17 0.02
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (58 bp):
TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
Found at i:1198603 original size:29 final size:29
Alignment explanation
Indices: 1198458--1199395 Score: 1191
Period size: 29 Copynumber: 32.5 Consensus size: 29
1198448 TCACTAACTG
* *
1198458 TTGTGGGCGTTGAAAAGAGTTGCCACTGTC
1 TTGTGGGCTTTGAAAAGAG-TGCCACTGAC
* * *
1198488 TCGTGTGGGCTTTGAAAAGAGTTACCATTGGC
1 T--TGTGGGCTTTGAAAAGAG-TGCCACTGAC
* *
1198520 TTATGGGCTTTGAAAAGAGTGCCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * * *
1198549 TTGTAGACTTTGAAAGGA-TGCCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1198577 TTGTGAGCTTTGAAAAGAGTACCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1198606 TTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1198634 TTGTGAGCTTTGAAAAGAGTGTCACTGAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1198663 TTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1198691 TTGTGGGCTTTG-AAAGGGTGCCGCTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1198719 TTGTAGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1198748 TTGTGGGCTTTGAAAAGAGTTGCCA-TCGAC
1 TTGTGGGCTTTGAAAAGAG-TGCCACT-GAC
*
1198778 TCGTGTGGGCTTTGAAACGAGTGCCACTGAC
1 T--TGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1198809 TTATGGGCTTTG-AAAGGGTGCTACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1198837 TTGTGGGCTTTGAAAAGAGTGCCACTGAA
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1198866 TTGTGAGCTTTG-AAAGGGTGCCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1198894 TTGTGGGCTTTGAAAAGAGTGCTACTGAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1198923 TTATGGGCTTTGAAAAG-GTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * * *
1198951 TTGTGGGCTTTGAAAAAAGTGTCACTAAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1198980 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1199009 TTGTAGGCTTTGAAAGGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1199038 TTGTGGGCTTTG-AAAGGGTGCCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1199066 TTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1199094 TTGTGGGCTTTGAAAAGAGTGCCACTGAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1199123 TTGTGGGCTTTGAAAGGA-TGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* * *
1199151 TTGTGGGCTTTGAAAAGAATGCCATTGAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1199180 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
** *
1199209 TTGTGGGCTTTGAACGGAGTGCCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1199238 TTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1199266 ATGTGGGCTTTGAAAAGAGTGCCACTGAT
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1199295 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1199324 TTGTGGGCTTTG-AAAGGGTGCCACTAAC
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
** *
1199352 TCATGGGCTTTGAAAAGAGTGCCACTGAG
1 TTGTGGGCTTTGAAAAGAGTGCCACTGAC
1199381 TTGTGGGCTTTGAAA
1 TTGTGGGCTTTGAAA
1199396 GGGATGAACA
Statistics
Matches: 788, Mismatches: 103, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
28 296 0.38
29 412 0.52
30 27 0.03
31 9 0.01
32 44 0.06
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (29 bp):
TTGTGGGCTTTGAAAAGAGTGCCACTGAC
Found at i:1198617 original size:86 final size:86
Alignment explanation
Indices: 1198449--1199395 Score: 1136
Period size: 86 Copynumber: 10.9 Consensus size: 86
1198439 CAAATGTTGT
* * * *
1198449 CACTAACTGTTGTGGGCGTTGAAAAGAGTTGCCACTGTCTCGTGTGGGCTTTGAAAAGAGTTACC
1 CACTAAC--TTGTGGGCTTTG-AAAG-GATGCCACTGACT--TGTGGGCTTTGAAAAGAG-TGCC
* * *
1198514 ATTGGCTTATGGGCTTTGAAAAGAGTGC
59 ACTGACTTGTGGGCTTTGAAAAGAGTGC
* * * * * *
1198542 CACTAACTTGTAGACTTTGAAAGGATGCCACTAACTTGTGAGCTTTGAAAAGAGTACCACTAACT
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
*
1198607 TGTGGGCTTTG-AAAGGGTGC
66 TGTGGGCTTTGAAAAGAGTGC
* * * * * *
1198627 CACTGACTTGTGAGCTTTGAAAAGAGTGTCACTGATTTGTGGGCTTTG-AAAGGGTGCCACTGAC
1 CACTAACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1198691 TTGTGGGCTTTG-AAAGGGTGC
65 TTGTGGGCTTTGAAAAGAGTGC
* * * *
1198712 CGCTGACTTGTAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCA-TCG
1 CACTAACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACT-G
*
1198776 ACTCGTGTGGGCTTTGAAACGAGTGC
63 ACT--TGTGGGCTTTGAAAAGAGTGC
* * * * *
1198802 CACTGACTTATGGGCTTTGAAAGGGTGCTACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAAT
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
1198867 TGTGAGCTTTG-AAAGGGTGC
66 TGTGGGCTTTGAAAAGAGTGC
* * * *
1198887 CACTAACTTGTGGGCTTTGAAAAGAGTGCTACTGATTTATGGGCTTTGAAAAG-GTGCCACTGAC
1 CACTAACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
* *
1198951 TTGTGGGCTTTGAAAAAAGTGT
65 TTGTGGGCTTTGAAAAGAGTGC
* * * *
1198973 CACTAATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGGCTTTGAAAGGAGTGCCACTGAC
1 CACTAACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
*
1199038 TTGTGGGCTTTG-AAAGGGTGC
65 TTGTGGGCTTTGAAAAGAGTGC
* *
1199059 CACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
*
1199124 TGTGGGCTTTGAAAGGA-TGC
66 TGTGGGCTTTGAAAAGAGTGC
* * * *
1199144 CACTGACTTGTGGGCTTTGAAAAGAATGCCATTGATTTGTGGGCTTTGAAAAGAGTGCCACTGAC
1 CACTAACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC
**
1199209 TTGTGGGCTTTGAACGGAGTGC
65 TTGTGGGCTTTGAAAAGAGTGC
* * *
1199231 CACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACATGTGGGCTTTGAAAAGAGTGCCACTGATT
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1199296 TGTGGGCTTTGAAAAGAGTGC
66 TGTGGGCTTTGAAAAGAGTGC
* * * ** *
1199317 CACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTCATGGGCTTTGAAAAGAGTGCCACTGAGT
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1199382 TGTGGGCTTTGAAA
66 TGTGGGCTTTGAAA
1199396 GGGATGAACA
Statistics
Matches: 748, Mismatches: 92, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
85 223 0.30
86 350 0.47
87 70 0.09
88 8 0.01
89 50 0.07
90 31 0.04
91 9 0.01
93 7 0.01
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (86 bp):
CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
TGTGGGCTTTGAAAAGAGTGC
Found at i:1200650 original size:18 final size:19
Alignment explanation
Indices: 1200627--1200668 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1200617 TTTTTGCTAT
1200627 TTTTTTCTTAGTTTT-TTG
1 TTTTTTCTTAGTTTTATTG
* *
1200645 TTTTTTTTTTGTTTTATTG
1 TTTTTTCTTAGTTTTATTG
1200664 TTTTT
1 TTTTT
1200669 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.05, C:0.02, G:0.10, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTAGTTTTATTG
Found at i:1200650 original size:19 final size:19
Alignment explanation
Indices: 1200626--1200685 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1200616 TTTTTTGCTA
1200626 TTTTTTTCTTAGTTTT-TTG
1 TTTTTTT-TTAGTTTTATTG
*
1200645 TTTTTTTTTTGTTTTATTG
1 TTTTTTTTTAGTTTTATTG
*
1200664 TTTTTATTT--TTTTATT-
1 TTTTTTTTTAGTTTTATTG
1200680 TTTTTT
1 TTTTTT
1200686 GGGTATAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.14
17 7 0.19
18 7 0.19
19 18 0.49
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTAGTTTTATTG
Found at i:1200651 original size:8 final size:8
Alignment explanation
Indices: 1200628--1200684 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
1200618 TTTTGCTATT
1200628 TTTTTCTTA
1 TTTTT-TTA
* *
1200637 GTTTTTTG
1 TTTTTTTA
1200645 TTTTTTT-
1 TTTTTTTA
1200652 TTTGTTTTA
1 TTT-TTTTA
1200661 TTGTTTTTA
1 TT-TTTTTA
1200670 TTTTTTTA
1 TTTTTTTA
1200678 TTTTTTT
1 TTTTTTT
1200685 TGGGTATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
7 3 0.07
8 25 0.60
9 13 0.31
10 1 0.02
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1200656 original size:11 final size:11
Alignment explanation
Indices: 1200614--1200685 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
1200604 GACCTCTTTC
*
1200614 TTTTTTTTGCT
1 TTTTTTTTGTT
* *
1200625 ATTTTTTTCTT
1 TTTTTTTTGTT
**
1200636 AGTTTTTTGTT
1 TTTTTTTTGTT
1200647 TTTTTTTTGTT
1 TTTTTTTTGTT
*
1200658 TTATTGTTT-TT
1 TT-TTTTTTGTT
* *
1200669 ATTTTTTTATT
1 TTTTTTTTGTT
1200680 TTTTTT
1 TTTTTT
1200686 GGGTATAAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
10 5 0.10
11 38 0.79
12 5 0.10
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:1212465 original size:20 final size:19
Alignment explanation
Indices: 1212436--1212510 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1212426 AAAAAGACAT
1212436 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
1212455 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
1212476 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
1212496 AATGTATCGATACAT
1 AATGTATCGATACAT
1212511 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1212493 original size:40 final size:39
Alignment explanation
Indices: 1212433--1212510 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
1212423 GGTAAAAAGA
*
1212433 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1212472 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1212511 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1215059 original size:29 final size:30
Alignment explanation
Indices: 1214997--1215069 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
1214987 TACAATGAAT
*
1214997 AATGTATCAATATC-TCTAGGCAAAATCTAG
1 AATGTATCAATA-CATCTAGGCAAAATCCAG
*
1215027 AATGTATCAATACATCT-GGTAAAATCCAG
1 AATGTATCAATACATCTAGGCAAAATCCAG
*
1215056 AATGTATCGATACA
1 AATGTATCAATACA
1215070 ATGAATAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (30 bp):
AATGTATCAATACATCTAGGCAAAATCCAG
Found at i:1220217 original size:15 final size:15
Alignment explanation
Indices: 1220184--1220248 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
1220174 AAGAGTTTCC
*
1220184 TTTTCTTGTTCAACTA
1 TTTTCTT-TTCAACAA
*
1220200 TTTTCTTTTCAAGAA
1 TTTTCTTTTCAACAA
* *
1220215 TTTTATTTTCAATAA
1 TTTTCTTTTCAACAA
1220230 -TTTCATTTTCAACAA
1 TTTTC-TTTTCAACAA
1220245 TTTT
1 TTTT
1220249 TTATTTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 3 0.07
15 28 0.68
16 10 0.24
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTCTTTTCAACAA
Found at i:1220226 original size:30 final size:30
Alignment explanation
Indices: 1220192--1220248 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1220182 CCTTTTCTTG
* *
1220192 TTCAACTATTTTC-TTTTCAAGAATTTTATT
1 TTCAA-TAATTTCATTTTCAACAATTTTATT
1220222 TTCAATAATTTCATTTTCAACAATTTT
1 TTCAATAATTTCATTTTCAACAATTTT
1220249 TTATTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.54
Consensus pattern (30 bp):
TTCAATAATTTCATTTTCAACAATTTTATT
Found at i:1220821 original size:20 final size:20
Alignment explanation
Indices: 1220796--1220875 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
1220786 TTTTCACAAT
1220796 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
*
1220816 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTATTCA
* *
1220836 TTGTATCAATACATTGA-GCA
1 TTGTATCGATACATT-ATTCA
* *
1220856 ATGTATCGATACAATATTCA
1 TTGTATCGATACATTATTCA
1220876 GGCATTTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:1223376 original size:28 final size:28
Alignment explanation
Indices: 1223325--1223387 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1223315 AGGGTACTTT
1223325 AACCCCGTTATTTCATCGAAGATACTCC
1 AACCCCGTTATTTCATCGAAGATACTCC
* **
1223353 AATCCCGTTATTTCCAT-GGGGATACTCC
1 AACCCCGTTATTT-CATCGAAGATACTCC
1223381 AACCCCG
1 AACCCCG
1223388 ATTTTATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.90
29 3 0.10
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.27
Consensus pattern (28 bp):
AACCCCGTTATTTCATCGAAGATACTCC
Found at i:1223427 original size:51 final size:51
Alignment explanation
Indices: 1223370--1223488 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
1223360 TTATTTCCAT
* **
1223370 GGGGATACTCCAACCCCGATTTTATTTCTAAAGTACCAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
* * *
1223421 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
1223472 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
1223489 ATTATTTTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:1223504 original size:79 final size:79
Alignment explanation
Indices: 1223421--1223683 Score: 303
Period size: 79 Copynumber: 3.3 Consensus size: 79
1223411 TTCCACAATC
* * * *
1223421 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAAC
* *
1223486 CCCATTATTTTCAA
66 CCTATTATTTTCGA
* * *** * *
1223500 GGGGATACTTCAACCCTGGCCTTATTTCTAAATCATCGATTTTTCACAATTGGGAATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAAC
*
1223565 CCTGTTATTTTCGA
66 CCTATTATTTTCGA
* * * * * **
1223579 GGGGATACTCTAACCCCGATTTCATTTTTAAAATATCGATTTTT-ATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAAC
* * *
1223643 ACTTTTATTTCCGA
66 CCTATTATTTTCGA
1223657 GGGGATACTCCAACCCCGATTTTATTT
1 GGGGATACTCCAACCCCGATTTTATTT
1223684 TTGGAACACC
Statistics
Matches: 151, Mismatches: 33, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
78 52 0.34
79 99 0.66
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACAATTGGGGATACTCCAAC
CCTATTATTTTCGA
Found at i:1223662 original size:78 final size:78
Alignment explanation
Indices: 1223421--1223717 Score: 222
Period size: 79 Copynumber: 3.8 Consensus size: 78
1223411 TTCCACAATC
* * ** * * * * **
1223421 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTCATTTTTAAAATATCGATTTTT-ATAATCAGGGATACTCCAAC
* ** * *
1223486 CCCATTATTTTCAA
65 ACTGTTATTTCCGA
* * ** * * *
1223500 GGGGATACTTCAACCCTGGCCTT-ATTTCT-AAATCATCGATTTTTCACAAT-TGGGAATACTCC
1 GGGGATACTCCAACCC-CGATTTCATTTTTAAAAT-ATCGATTTTT-ATAATCAGGG-ATACTCC
* *
1223562 AACCCTGTTATTTTCGA
62 AACACTGTTATTTCCGA
*
1223579 GGGGATACTCTAACCCCGATTTCATTTTTAAAATATCGATTTTTATAATCAGGGATACTCCAACA
1 GGGGATACTCCAACCCCGATTTCATTTTTAAAATATCGATTTTTATAATCAGGGATACTCCAACA
*
1223644 CTTTTATTTCCGA
66 CTGTTATTTCCGA
* ** * * * *
1223657 GGGGATACTCCAACCCCGATTTTATTTTTGGAACACCAATTTTCCATAATCAGGGATACTC
1 GGGGATACTCCAACCCCGATTTCATTTTTAAAATATCGATTTT-TATAATCAGGGATACTC
1223718 TAGCCCTGTT
Statistics
Matches: 179, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
78 70 0.39
79 102 0.57
80 7 0.04
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTCATTTTTAAAATATCGATTTTTATAATCAGGGATACTCCAACA
CTGTTATTTCCGA
Found at i:1224266 original size:20 final size:20
Alignment explanation
Indices: 1224241--1224294 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1224231 GTATCGATAC
**
1224241 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
1224261 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
1224281 AATGTATCGATACA
1 AATGTATCGATACA
1224295 AGTCGTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:1224363 original size:13 final size:13
Alignment explanation
Indices: 1224345--1224370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1224335 ACACATAGTA
1224345 TGTATCGATACAT
1 TGTATCGATACAT
1224358 TGTATCGATACAT
1 TGTATCGATACAT
1224371 CATAAAATGT
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:1224386 original size:33 final size:32
Alignment explanation
Indices: 1224325--1224392 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1224315 GTAGCTAAAC
**
1224325 TTGTATCGATACACATAGTATGTATCGATACA
1 TTGTATCGATACACATAAAATGTATCGATACA
1224357 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CATAAAATGTATCGATACA
1224390 TTG
1 TTG
1224393 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACACATAAAATGTATCGATACA
Found at i:1229922 original size:21 final size:21
Alignment explanation
Indices: 1229879--1229924 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1229869 TAATTCACGC
* *
1229879 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
1229900 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
1229921 ATTC
1 ATTC
1229925 ATATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:1231747 original size:13 final size:13
Alignment explanation
Indices: 1231729--1231754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1231719 ATAATCACCT
1231729 TGTATCGATACAA
1 TGTATCGATACAA
1231742 TGTATCGATACAA
1 TGTATCGATACAA
1231755 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:1235130 original size:13 final size:13
Alignment explanation
Indices: 1235112--1235137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1235102 CAATTTTTTG
1235112 TGTATCGATACAT
1 TGTATCGATACAT
1235125 TGTATCGATACAT
1 TGTATCGATACAT
1235138 ACTTGGTGAA
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:1236396 original size:29 final size:29
Alignment explanation
Indices: 1236162--1238132 Score: 2229
Period size: 29 Copynumber: 67.1 Consensus size: 29
1236152 TTTTTTTAAA
* *
1236162 AAAAGGGTGCCACTAACTTATGTGGGCCTTG
1 AAAAGGGTGCCACTGAC-T-TGTGGGCTTTG
* * *
1236193 AAAATAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAA-GGGTGCCACTGACT--TGTGGGCTTTG
* * *
1236225 AAAAGAGTTACCACTGGCTTGTGGGCTTT-
1 AAAAG-GGTGCCACTGACTTGTGGGCTTTG
* *
1236254 AAAAGGGTGCCACTGACTTGTGAGTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1236283 -GAAGGGTGCCACTGATTTGTGTGGGCTTTG
1 AAAAGGGTGCCACTGA-CT-TGTGGGCTTTG
* * *
1236313 AAAAGAGTTGCTACCGACTTGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGAC-T-TGTGGGCTTTG
* *
1236345 AAAAGAGTG-CACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1236373 AAAAGAGTGCCACTGACTTGTGGGTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1236402 AAAA-GGAGCCACTGACTTGTAGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1236430 AAAAGAGTGCCACTAACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1236458 AAAAGGGTGCCACTAACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
1236489 AAAGGGGTGCCACT-ATCTTGTGGGCTTTG
1 AAAAGGGTGCCACTGA-CTTGTGGGCTTTG
* *
1236518 AAAAGAGTGCCACTAACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1236546 AAAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
* *
1236577 AAAGGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1236606 AAAGGGGTGCCACTAACTTGTGAGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1236635 -GAAGGGTGCCACTGATTTGTGTGGGCTTTG
1 AAAAGGGTGCCACTGA-CT-TGTGGGCTTTG
* * *
1236665 AAAAGAGTTGCTACCGACTTGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGAC-T-TGTGGGCTTTG
* *
1236697 AAAAGAGTG-CACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1236725 AAAAGAGTGCCACTGACTTGTGGGTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1236754 AAAA-GGAGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1236782 AAAGGGGTGCCACTGACTTGTGGGCATTTG
1 AAAAGGGTGCCACTGACTTGTGGGC-TTTG
* * * *
1236812 AAAAGAGTGCTACTAACTTGTGAGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1236840 AAAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
1236871 AAAGGGGTGCCACT-ATCTTGTGGGCTTTG
1 AAAAGGGTGCCACTGA-CTTGTGGGCTTTG
* *
1236900 AAAAGAGTGCCACTAACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1236928 AAAAAGGTGCCATTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
* *
1236959 AAAGGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
** *
1236988 AAGGGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237017 AAAGGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237046 AAAGGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237075 AAAGGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237104 AAAGGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237133 -AAAGGGTGCCACTGACTTGTGAGCTTTA
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237161 AAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
* *
1237193 AAAAGAGTGTCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237222 AAAAGAGTGCTACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
1237253 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1237282 -AAAGGGTGCCACTGACTTGCTTGGGGTTTG
1 AAAAGGGTGCCACTGACTTG--TGGGCTTTG
**
1237312 AATGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1237341 -AAAGGGTACCACTGACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237368 AAAAGGGTGCCACTAACTTGCTTGGGGTTTG
1 AAAAGGGTGCCACTGACTTG--TGGGCTTTG
*
1237399 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1237428 -AAAGGGTACCAATGACTTGGGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1237456 -AAAGGGTGCCAATGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
* *
1237486 AAAGGGGTGCCACTGACTTATGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237515 AAAAGAGTGCCACTAACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1237543 AAAAGGGTGCCATTGACTTGCATGGGCTTTG
1 AAAAGGGTGCCACTGACTTG--TGGGCTTTG
*
1237574 -AAAGAGGTGCCACT-ATCTTGTGGTCTTTG
1 AAAAG-GGTGCCACTGA-CTTGTGGGCTTTG
* *
1237603 AAAAGAGTGCCACTAACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1237631 AAAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
1237662 -AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237690 AAAGGGGTGCCATTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1237719 -AAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
* * *
1237749 AAAGGGGTACCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1237778 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1237806 AAAGGGGTGCCACTAACTTATGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1237835 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1237864 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1237892 AAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
* *
1237924 AAAAGAGTGCCACTGACTTGTGGGTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1237953 AAAAGAGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
1237984 -AAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
1238014 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1238043 -AAAGGGTACCACTGACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1238070 AAAAGGGTGCCACTGACTTGCGTGTGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
1238101 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1238130 AAA
1 AAA
1238133 GGGATGAACA
Statistics
Matches: 1685, Mismatches: 178, Indels: 156
0.83 0.09 0.08
Matches are distributed among these distances:
28 476 0.28
29 611 0.36
30 237 0.14
31 246 0.15
32 115 0.07
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (29 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:1237462 original size:615 final size:604
Alignment explanation
Indices: 1236235--1238132 Score: 2258
Period size: 615 Copynumber: 3.0 Consensus size: 604
1236225 AAAAGAGTTA
* * * * * ** * *
1236235 CCACTGGCTTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGAGTTTTGGAAGGGTGCCACTGAT
1 CCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCATTGA-
* * **
1236299 TTGTGTGGGCTTTGAAAAGAGTTGCTACCGACTTGTGTGGGCTTTGAAAAGAGTG-CACTAACTT
65 CT-TGTGGGCTTTGAAAAGAG-TGCCACTAAC-T-TGTGGGCTTTGAAAAGAGTGCCACTAACTT
* * * * *
1236363 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGTTTTGAAAA-GGAGCCACTGACTTGTAGGCT
126 GTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCT
* * *
1236427 TTGAAAAGAGTGCCACTAACTTGTGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGAA
190 TTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTAACTT--GTGGGCTTTGAA
* * * *
1236491 AGGGGTGCCACTATCTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTT-AAAAGGGTG
253 A-GGGTGCCACTAACTTGTGGGCTTT--AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTG
* *
1236555 CCACTGACTTGCGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACT
315 CCACTAACTT--GTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAA-GGGTG---C-
*
1236620 AACTTGTGAGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAAGAGTTGCTACCGACTT
373 --C-----A-C----------TG--AC-----T-TGTGGGCTTTGAAAAGAGTTGCCACCGACTT
*
1236685 GTGTGGGCTTTGAAAAGAGTG-CACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
412 GTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
* * *
1236749 TTTTGAAAAGGAGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCATTTGAA
477 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGC-TTTG-A
* * * * *
1236814 AAGAGTGCTACTAACTTGTGAGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGGGT
540 AAGGGTACCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTT-CGTGGGCTTTGAAAGGGGT
1236879 G
604 G
1236880 CCACT-ATCTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCATTGA
1 CCACTGA-CTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCATTGA
* * ** *
1236944 CTTGCGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAGGGGGTGCCACTAACTTGT
65 CTT--GTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGT
* *
1237009 GGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTT
128 GGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTT
1237074 GAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGG
192 GAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGG
* * * * * * *
1237139 TGCCACTGACTTGTGAGCTTTAAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGTC
257 TGCCACTAACTTGTGGGCTTT--AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAGGGGTGCC
* * * *
1237204 ACTGACTTGTGGGCTTTGAAAAGAGTGCTACTGACTTGCGTGGGCTTTGAAAGGGGTGCCACTGA
317 ACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGACTT--GTGGGCTTTGAAA-GGGTGCCACTGA
* * * ** *
1237269 CTTGTGGGCTTTG-AAAG-GGTGCCACTGACTTGCT-TGGGGTTTGAATGGGGTGCCACTGACTT
379 CTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTG-TGTGGGCTTTGAAAAGAGTGCCACTGACTT
* * * * *
1237331 GTGGGCTTTG-AAAGGGTACCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCTTGGGG
443 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG--TGGGC
* * *
1237395 TTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTACCAATGACTTGGGGGCTTTGAAAG
506 TTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTAAAAG
*
1237460 GGTGCCAATGACTTGCGTGGGCTTTGAAAGGGGTG
571 GGTGCCACTGACTT-CGTGGGCTTTGAAAGGGGTG
* *
1237495 CCACTGACTTATGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCATTGAC
1 CCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCATTGAC
* *
1237560 TTGCATGGGCTTTG-AAAGAGGTGCCACTATCTTGTGGTCTTTGAAAAGAGTGCCACTAACTTGT
66 TTG--TGGGCTTTGAAAAGA-GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGT
*
1237624 GGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTT
128 GGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTT
* * *
1237688 TGAAAGGGGTGCCATTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGCGTGGGCTTTGAAA
191 TGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTAACTT--GTGGGCTTTGAAA
*
1237752 GGGGTACCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCC
254 -GGGTGCCACTAACTTGTGGGCTTT-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCC
*
1237817 ACTAACTTATGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT
317 ACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT
*
1237882 GTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
382 GTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
*
1237947 GTTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTT
447 GCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTT
1238012 TGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTAAAAGGG
508 TGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTAAAAGGG
*
1238077 TGCCACTGACTTGCGTGTGCTTTGAAAGGGGTG
573 TGCCACTGACTT-CGTGGGCTTTGAAAGGGGTG
1238110 CCACTGACTTGTGGGCTTTGAAA
1 CCACTGACTTGTGGGCTTTGAAA
1238133 GGGATGAACA
Statistics
Matches: 1103, Mismatches: 115, Indels: 100
0.84 0.09 0.08
Matches are distributed among these distances:
610 25 0.02
611 18 0.02
612 45 0.04
613 68 0.06
614 31 0.03
615 460 0.42
616 55 0.05
617 66 0.06
618 1 0.00
623 2 0.00
625 2 0.00
635 1 0.00
636 1 0.00
641 1 0.00
643 46 0.04
644 69 0.06
645 97 0.09
646 79 0.07
647 36 0.03
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (604 bp):
CCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCATTGAC
TTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGG
CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAA
GGGGTGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCC
ACTAACTTGTGGGCTTTAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTAACTTG
TGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
GAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
AGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCC
ACTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTC
GTGGGCTTTGAAAGGGGTG
Found at i:1239364 original size:1 final size:1
Alignment explanation
Indices: 1239360--1239409 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
1239350 TTTTTTGCTA
* * * * *
1239360 TTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1239410 GGGTGTAAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:1239374 original size:11 final size:11
Alignment explanation
Indices: 1239360--1239409 Score: 73
Period size: 11 Copynumber: 4.4 Consensus size: 11
1239350 TTTTTTGCTA
*
1239360 TTTTTTCTTTT
1 TTTTTTGTTTT
1239371 TTTTTTGTTTTT
1 TTTTTTG-TTTT
1239383 TTGTTTTGTTTT
1 TT-TTTTGTTTT
1239395 TTTTTTGTTTT
1 TTTTTTGTTTT
1239406 TTTT
1 TTTT
1239410 GGGTGTAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
11 19 0.53
12 12 0.33
13 5 0.14
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:1239410 original size:25 final size:24
Alignment explanation
Indices: 1239362--1239408 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1239352 TTTTGCTATT
1239362 TTTTCTTTTTTTTTTGTTTTTTTG
1 TTTTCTTTTTTTTTTGTTTTTTTG
*
1239386 TTTTGTTTTTTTTTTGTTTTTTT
1 TTTTCTTTTTTTTTTGTTTTTTT
1239409 TGGGTGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (24 bp):
TTTTCTTTTTTTTTTGTTTTTTTG
Found at i:1253435 original size:20 final size:20
Alignment explanation
Indices: 1253406--1253480 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1253396 AAAAAGACAT
*
1253406 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
1253426 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
1253446 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
1253466 AATGTATCGATACAT
1 AATGTATCGATACAT
1253481 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:1253474 original size:40 final size:39
Alignment explanation
Indices: 1253403--1253480 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1253393 GGTAAAAAGA
* *
1253403 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1253442 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1253481 CAGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1268711 original size:20 final size:19
Alignment explanation
Indices: 1268686--1268766 Score: 83
Period size: 20 Copynumber: 4.2 Consensus size: 19
1268676 TGCATCCTCC
* *
1268686 ACAAAAAAAAAATAAATAA
1 ACAAAAAAAAAAAAAAAAA
1268705 ACAAAAAAAAGAAAAAAAAA
1 ACAAAAAAAA-AAAAAAAAA
**
1268725 ACAAAAAACAAAAAACCAAA
1 ACAAAAAA-AAAAAAAAAAA
* *
1268745 A-AAAAAAAAACAAAAACA
1 ACAAAAAAAAAAAAAAAAA
1268763 ACAA
1 ACAA
1268767 CAACAAAAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
18 8 0.16
19 18 0.35
20 23 0.45
21 2 0.04
ACGTcount: A:0.85, C:0.11, G:0.01, T:0.02
Consensus pattern (19 bp):
ACAAAAAAAAAAAAAAAAA
Found at i:1268719 original size:27 final size:28
Alignment explanation
Indices: 1268689--1268775 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 28
1268679 ATCCTCCACA
* *
1268689 AAAAAAAAATAAATAAACAAAAAA-AAGA
1 AAAAAAAAACAAA-AAACAAAAAACAAAA
1268717 AAAAAAAAACAAAAAACAAAAAACCAAAA
1 AAAAAAAAACAAAAAACAAAAAA-CAAAA
1268746 AAAAAAAAAC-AAAAACAACAACAACAAAA
1 AAAAAAAAACAAAAAACAA-AA-AACAAAA
1268775 A
1 A
1268776 GGGTCCGGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
27 10 0.19
28 20 0.38
29 21 0.40
30 2 0.04
ACGTcount: A:0.85, C:0.11, G:0.01, T:0.02
Consensus pattern (28 bp):
AAAAAAAAACAAAAAACAAAAAACAAAA
Found at i:1268721 original size:7 final size:7
Alignment explanation
Indices: 1268688--1268775 Score: 85
Period size: 7 Copynumber: 12.4 Consensus size: 7
1268678 CATCCTCCAC
1268688 AAAA-AA
1 AAAACAA
*
1268694 AAAATAA
1 AAAACAA
1268701 ATAAACAA
1 A-AAACAA
1268709 AAAA-AA
1 AAAACAA
1268715 GAAAA-AA
1 -AAAACAA
1268722 AAAACAA
1 AAAACAA
1268729 AAAACAA
1 AAAACAA
1268736 AAAACCAA
1 AAAA-CAA
*
1268744 AAAAAAA
1 AAAACAA
1268751 AAAAC-A
1 AAAACAA
1268757 AAAACAA
1 AAAACAA
1268764 CAACAACAA
1 -AA-AACAA
1268773 AAA
1 AAA
1268776 GGGTCCGGAT
Statistics
Matches: 71, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
6 16 0.23
7 33 0.46
8 17 0.24
9 5 0.07
ACGTcount: A:0.85, C:0.11, G:0.01, T:0.02
Consensus pattern (7 bp):
AAAACAA
Found at i:1268771 original size:15 final size:13
Alignment explanation
Indices: 1268686--1268775 Score: 69
Period size: 13 Copynumber: 6.5 Consensus size: 13
1268676 TGCATCCTCC
1268686 ACAAAAA-AAAAA
1 ACAAAAACAAAAA
1268698 TA-AATAAACAAAAA
1 -ACAA-AAACAAAAA
*
1268712 A-AAGAAAAAAAAA
1 ACAA-AAACAAAAA
1268725 ACAAAAAACAAAAA
1 AC-AAAAACAAAAA
*
1268739 ACCAAAAAAAAAAAA
1 A-C-AAAAACAAAAA
1268754 ACAAAAACAACAACA
1 ACAAAAACAA-AA-A
1268769 ACAAAAA
1 ACAAAAA
1268776 GGGTCCGGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.03
13 23 0.35
14 17 0.26
15 23 0.35
ACGTcount: A:0.84, C:0.12, G:0.01, T:0.02
Consensus pattern (13 bp):
ACAAAAACAAAAA
Found at i:1268775 original size:1 final size:1
Alignment explanation
Indices: 1268688--1268760 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
1268678 CATCCTCCAC
* * * * * * **
1268688 AAAAAAAAAATAAATAAACAAAAAAAAGAAAAAAAAAACAAAAAACAAAAAACCAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1268753 AACAAAAA
1 AAAAAAAA
1268761 CAACAACAAC
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.88, C:0.08, G:0.01, T:0.03
Consensus pattern (1 bp):
A
Found at i:1270252 original size:30 final size:29
Alignment explanation
Indices: 1270216--1270742 Score: 734
Period size: 30 Copynumber: 17.9 Consensus size: 29
1270206 TCACCCTTCA
* *
1270216 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
*
1270246 AAAGCCCACAAGTCAGTGGCACTATTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
1270276 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1270305 AAAGCCCACAAGTCAGTGGCACTCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* *
1270335 AAAGCCCACAAGTTAGTGGTATCTTTT-C
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
* *
1270363 AAAG-CCACAAGTCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
1270392 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
* *
1270421 AAAGCCCACAAGTTAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
*
1270451 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCATC-TTTTCC
* * * *
1270481 AAAGACCATAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1270510 AAAGTCCACAAGTCAGTGGCAATCTTTTCC
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTCC
* *
1270540 AAAGCCCACAAGTCAATGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1270569 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* *
1270599 AAAGCCCACAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1270628 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
1270658 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1270687 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* *
1270717 AAAGCCCACAAGTCAATGGCAACTTT
1 AAAGCCCACAAGTCAGTGGCATCTTT
1270743 CAGAAGCACA
Statistics
Matches: 448, Mismatches: 39, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.03
28 10 0.02
29 175 0.39
30 249 0.56
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCC
Found at i:1270319 original size:59 final size:58
Alignment explanation
Indices: 1270216--1270802 Score: 743
Period size: 59 Copynumber: 10.0 Consensus size: 58
1270206 TCACCCTTCA
* *
1270216 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCACTATTTTCC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCA-TCTTTTCC
*
1270276 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* * * * *
1270335 AAAGCCCACAAGTTAGTGGTATCTTTT-CAAAG-CCACAAGTCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* * *
1270392 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTTAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* * * *
1270451 AAAGCCCACAAGTCAGTGGCACCTTTTTCCAAAGACCATAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACC-TTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
* * * *
1270510 AAAGTCCACAAGTCAGTGGCAATCTTTTCCAAAGCCCACAAGTCAATGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
* *
1270569 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
1270628 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
* *
1270687 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAATGGCAAC-TTT-C
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
* ** * * **
1270744 AGAAGCACACAAGTTGGT-GCAACCCTTTCAAAAGCCCACACAAGTTGGTGGCATCTTTT
1 A-AAGCCCACAAGTCAGTGGC-ACCTTTTCCAAAG-CC-CACAAGTCAGTGGCATCTTTT
1270803 TCTAAGTCCA
Statistics
Matches: 476, Mismatches: 41, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
57 62 0.13
58 30 0.06
59 335 0.70
60 49 0.10
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (58 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
Found at i:1270494 original size:89 final size:90
Alignment explanation
Indices: 1270216--1270742 Score: 759
Period size: 89 Copynumber: 6.0 Consensus size: 90
1270206 TCACCCTTCA
* * *
1270216 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCACTATTTTCCAAAGC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGC
*
1270281 CCACAAGTCAGTGGCATC-TTTTCC
66 CCACAAGTCAGTGGCACCTTTTTCC
* *
1270305 AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTTAGTGGTA-TCTTTT-CAAAG-
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGC
1270367 CCACAAGTCAGTGGCACCCTTTTT-C
66 CCACAAGTCAGTGGCA-CCTTTTTCC
* *
1270392 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTTAGTGGCACCCTTTTCCAAAGC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGC
1270456 CCACAAGTCAGTGGCACCTTTTTCC
66 CCACAAGTCAGTGGCACCTTTTTCC
* * * * * *
1270481 AAAGACCATAAGTCAGTGGTA-TCTTTTCAAAAGTCCACAAGTCAGTGGCAATCTTTTCCAAAGC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGC
* * *
1270545 CCACAAGTCAATGGCATC-TTTTCA
66 CCACAAGTCAGTGGCACCTTTTTCC
* * *
1270569 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTA-TCTTTTCAAAAGC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGC
*
1270633 CCACAAGTCAGTGGCACCCTTTTCC
66 CCACAAGTCAGTGGCACCTTTTTCC
*
1270658 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGC
* *
1270722 CCACAAGTCAATGGCAACTTT
66 CCACAAGTCAGTGGCACCTTT
1270743 CAGAAGCACA
Statistics
Matches: 392, Mismatches: 37, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
86 44 0.11
87 33 0.08
88 99 0.25
89 216 0.55
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (90 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCCAAAGC
CCACAAGTCAGTGGCACCTTTTTCC
Found at i:1270857 original size:43 final size:43
Alignment explanation
Indices: 1270805--1270983 Score: 259
Period size: 43 Copynumber: 4.0 Consensus size: 43
1270795 CATCTTTTTC
* * *
1270805 TAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1270848 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
* *
1270897 TAAGTCCAATGTAGTTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1270940 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1270983 T
1 T
1270984 TCCATCTTTA
Statistics
Matches: 123, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
43 81 0.66
45 1 0.01
47 1 0.01
49 40 0.33
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (43 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
Found at i:1270917 original size:49 final size:49
Alignment explanation
Indices: 1270805--1271041 Score: 255
Period size: 43 Copynumber: 5.0 Consensus size: 49
1270795 CATCTTTTTC
* * *
1270805 TAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1270848 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
* *
1270897 TAAGTCCAATGTAGTTGGCCTTGAATCAGCATATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
*
1270940 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CTTCTT
* * * * *
1270992 TAAGTTCAATCTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTCTTCTT
1271042 ATCTTTGAAC
Statistics
Matches: 165, Mismatches: 13, Indels: 25
0.81 0.06 0.12
Matches are distributed among these distances:
43 76 0.46
45 1 0.01
47 1 0.01
49 40 0.24
50 5 0.03
51 2 0.01
52 38 0.23
53 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
Found at i:1270962 original size:92 final size:94
Alignment explanation
Indices: 1270805--1271036 Score: 351
Period size: 92 Copynumber: 2.5 Consensus size: 94
1270795 CATCTTTTTC
* *
1270805 TAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
*
1270870 GAATCAGCATATTGGCACC-TT-CTTCTT
66 GAATCAGCATATTGGCACCTTTCCATCTT
* * *
1270897 TAAGTCCAATGTAGTTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1270962 GAATCAGCATATTGGCACCTTTTCCATCTT
66 GAATCAGCATATTGGCACC-TTTCCATCTT
* * *
1270992 TAAGTTCAATCTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
1271037 TTCTTATCTT
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
92 79 0.63
94 2 0.02
95 39 0.31
96 5 0.04
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (94 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
GAATCAGCATATTGGCACCTTTCCATCTT
Found at i:1271015 original size:52 final size:53
Alignment explanation
Indices: 1270937--1271037 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 53
1270927 ATATTGGCAC
* *
1270937 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
* *
1270989 CTTTAAGTTCAATCTAGCTGGCCTTGAATCAGCACATTGACATCCTTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTT
1271038 TCTTATCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 38 0.86
53 6 0.14
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
Found at i:1272436 original size:13 final size:13
Alignment explanation
Indices: 1272418--1272474 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1272408 CATAAAGTGT
1272418 TGTATCGATACAA
1 TGTATCGATACAA
1272431 TGTATCGATACATAA
1 TGTATCGATAC--AA
1272446 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1272463 TGTATCGATACA
1 TGTATCGATACA
1272475 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1272453 original size:32 final size:32
Alignment explanation
Indices: 1272398--1272495 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
1272388 TTCAACGATT
1272398 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1272431 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1272463 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1272495 T
1 T
1272496 TTAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1272455 original size:19 final size:18
Alignment explanation
Indices: 1272396--1272493 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1272386 ATTTCAACGA
1272396 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1272415 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1272431 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1272447 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1272463 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1272479 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1272494 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1277977 original size:13 final size:13
Alignment explanation
Indices: 1277958--1277996 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1277948 ACAGCATTCT
1277958 CTGTATCGATACA
1 CTGTATCGATACA
*
1277971 TTGTATCGATACA
1 CTGTATCGATACA
*
1277984 CTGTATTGATACA
1 CTGTATCGATACA
1277997 AGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:1278171 original size:22 final size:21
Alignment explanation
Indices: 1278129--1278168 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1278119 AAATTTCTTG
1278129 TTTTTCACTTCAAAATACATCT
1 TTTTTCAC-TCAAAATACATCT
1278151 TTTTTCA-TCAAAAT-CATC
1 TTTTTCACTCAAAATACATC
1278169 ATCAAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
22 7 0.39
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTTCACTCAAAATACATCT
Found at i:1279840 original size:23 final size:19
Alignment explanation
Indices: 1279798--1279835 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1279788 AATAAATTTT
1279798 TATGATTAAGGGGGAGAAA
1 TATGATTAAGGGGGAGAAA
1279817 TATGATTAAGGGGGAGAAA
1 TATGATTAAGGGGGAGAAA
1279836 GAAATGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.21
Consensus pattern (19 bp):
TATGATTAAGGGGGAGAAA
Found at i:1279886 original size:22 final size:21
Alignment explanation
Indices: 1279865--1279904 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1279855 AGTGTTAAAT
*
1279865 TATTTTACTAAGGGGGAGAAA
1 TATTTGACTAAGGGGGAGAAA
* *
1279886 TGTTTGATTAAGGGGGAGA
1 TATTTGACTAAGGGGGAGA
1279905 GAAAAGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.30
Consensus pattern (21 bp):
TATTTGACTAAGGGGGAGAAA
Found at i:1280495 original size:20 final size:20
Alignment explanation
Indices: 1280470--1280523 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1280460 GTATCGATAC
**
1280470 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
1280490 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
1280510 AATGTATCGATACA
1 AATGTATCGATACA
1280524 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:1280592 original size:17 final size:18
Alignment explanation
Indices: 1280556--1280593 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1280546 TAGCTAAACT
1280556 TGTATCGATACACATAGTA
1 TGTATCGATA-ACATAGTA
*
1280575 TGTATCGAT-ACATTGTA
1 TGTATCGATAACATAGTA
1280592 TG
1 TG
1280594 GATACACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (18 bp):
TGTATCGATAACATAGTA
Done.