Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_pilon, whole genome shotgun sequence
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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 27
Found at i:1194079 original size:10 final size:10
Alignment explanation
Indices: 1194054--1194091 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
1194044 AATGATTTGA
1194054 TAGTAATGATT
1 TAGTAATGA-T
1194065 TAGTAATGAT
1 TAGTAATGAT
1194075 TAGTAATGAT
1 TAGTAATGAT
1194085 TAGTAAT
1 TAGTAAT
1194092 AATGAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:1194086 original size:70 final size:70
Alignment explanation
Indices: 1193994--1194204 Score: 300
Period size: 70 Copynumber: 3.2 Consensus size: 70
1193984 AATGATTTGA
*
1193994 TAGTAATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTA
1 TAGTAATGA-TTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTA
1194059 ATGATT
65 ATGATT
*
1194065 TAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATTATTTGATAGTAA
1 TAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAA
1194130 T-ATT
66 TGATT
* *
1194134 TAGTAATGATTAG---T-A--A-TAAT--T-AAATTATTATTAATTTTTAATGATTTGATAGTAA
1 TAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAA
1194189 TGATT
66 TGATT
1194194 TAGTAATGATT
1 TAGTAATGATT
1194205 TGATAGTAAT
Statistics
Matches: 134, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
59 32 0.24
60 15 0.11
62 4 0.03
63 1 0.01
65 1 0.01
66 1 0.01
69 16 0.12
70 55 0.41
71 9 0.07
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (70 bp):
TAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAA
TGATT
Found at i:1194191 original size:14 final size:14
Alignment explanation
Indices: 1194172--1194219 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
1194162 TATTAATTTT
1194172 TAATGATTTGATAG
1 TAATGATTTGATAG
1194186 TAATGA-TT--TAG
1 TAATGATTTGATAG
1194197 TAATGATTTGATAG
1 TAATGATTTGATAG
1194211 TAATGATTT
1 TAATGATTT
1194220 ATTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1194200 original size:25 final size:25
Alignment explanation
Indices: 1194172--1194220 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1194162 TATTAATTTT
1194172 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
1194197 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
1194221 TTATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:1196372 original size:15 final size:16
Alignment explanation
Indices: 1196352--1196385 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1196342 CAAAAAAATT
1196352 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
1196367 TAATATAATAAACTTA
1 TAATATAATAAACTTA
1196383 TAA
1 TAA
1196386 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:1196472 original size:30 final size:30
Alignment explanation
Indices: 1196438--1196543 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
1196428 TTTCTTTAAA
1196438 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
1196468 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
1196498 AAACTAATAAAATATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
1196528 CACTACTAAAAAACTA
1 CA--ACTAATAAACTA
1196544 ATTAACTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.78
31 5 0.07
32 10 0.15
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:1196490 original size:15 final size:16
Alignment explanation
Indices: 1196442--1196496 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1196432 TTTAAACAAC
1196442 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
1196457 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
1196472 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
1196487 TAATATAACT
1 TAATATAACT
1196497 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:1196692 original size:17 final size:17
Alignment explanation
Indices: 1196670--1196705 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1196660 TAAATGTTTT
1196670 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
1196687 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
1196704 AC
1 AC
1196706 AAACTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCTAACCCTAAACTA
Found at i:1196933 original size:27 final size:27
Alignment explanation
Indices: 1196895--1196949 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1196885 AGGGTCGGCT
1196895 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
1196922 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
1196949 G
1 G
1196950 AGCCGTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.18
Consensus pattern (27 bp):
GCCATGCACCAATAATTGAAGAATCAC
Found at i:1198968 original size:41 final size:41
Alignment explanation
Indices: 1198790--1199168 Score: 318
Period size: 41 Copynumber: 9.2 Consensus size: 41
1198780 CACTTTTAGA
* * * * *
1198790 ACAAATGCCGCTAAAGACTCGTACTATAGCGGTGTTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * * *
1198831 AAAAACGACGCTAAAGAAT-GAACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * *
1198871 ACAAACGTCGCTATAGACTCGTGA-TTTAGTGGCGTTTTTTTAT
1 ACAAACGCCGCTAAAGACTAGT-ACTTTAGTGGCG--TTTTTAT
* *
1198914 ACAAACGCTGCTATAGACTAGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* *
1198955 ACAAACGCCGCTATAGACTAGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTAT
** * * * *
1198996 ACAAACGTTGCTAAAGACGCA-TACTTTAATGGCGTTTTAAGC
1 ACAAACGCCGCTAAAGAC-TAGTACTTTAGTGGCGTTTTTA-T
* * * * * *
1199038 CCAAACGCCTCCAAATACTCGTACTTTAGTGGCGCTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * * * * *
1199079 ATAAACGCCGCTAAATACT-GTACTTTAATGGTGTTTTAAGC
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTA-T
* * *
1199120 ACAAACGCCGCTAAATAATCA-TTCTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACT-AGTACTTTAGTGGCGTTTTTAT
*
1199161 ATAAACGC
1 ACAAACGC
1199169 TGATATATAT
Statistics
Matches: 272, Mismatches: 55, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
40 48 0.18
41 142 0.52
42 46 0.17
43 36 0.13
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTAT
Found at i:1199044 original size:124 final size:124
Alignment explanation
Indices: 1198790--1199105 Score: 336
Period size: 124 Copynumber: 2.6 Consensus size: 124
1198780 CACTTTTAGA
* * * * * * *
1198790 ACAAATGCC-GCTAAAGACTCGTACTATAGCGGTGTTTTTATAAAAACGACGCTAAAGAATGAAC
1 ACAAACGCCTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAAAAACGCCGCTAAAGACTGTAC
* * * * * * *
1198854 TTTAGTGGCGTTTTTATACAAACGTCGCTATAGACTCGTGATTTAGTGGCGTTTTTTTAT
66 TTTAGTGGCATTTTTATACAAACGTCGCTAAAGACGCATGATTTAATGGCG-TTTTTAAC
* * * *
1198914 ACAAACG-CTGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTAGTA
1 ACAAACGCCTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAAAAACGCCGCTAAAGACT-GTA
*
1198978 CTTTAGTGGCATTTTTATACAAACGTTGCTAAAGACGCAT-ACTTTAATGGCG-TTTTAAGC
65 CTTTAGTGGCATTTTTATACAAACGTCGCTAAAGACGCATGA-TTTAATGGCGTTTTTAA-C
* * * * * *
1199038 CCAAACGCCT-CCAAATACTCGTACTTTAGTGGCGCTTTTATATAAACGCCGCTAAATACTGTAC
1 ACAAACGCCTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAAAAACGCCGCTAAAGACTGTAC
1199102 TTTA
66 TTTA
1199106 ATGGTGTTTT
Statistics
Matches: 159, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
123 14 0.09
124 97 0.61
125 48 0.30
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (124 bp):
ACAAACGCCTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAAAAACGCCGCTAAAGACTGTAC
TTTAGTGGCATTTTTATACAAACGTCGCTAAAGACGCATGATTTAATGGCGTTTTTAAC
Found at i:1199147 original size:124 final size:124
Alignment explanation
Indices: 1198934--1199157 Score: 288
Period size: 124 Copynumber: 1.8 Consensus size: 124
1198924 CTATAGACTA
* * * * *
1198934 GTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGTGGCATTTTTATACA
1 GTACTTTAGTGGCGCTTTTATACAAACGCCGCTAAAGACTAGTACTTTAATGGCATTTTAACACA
** *
1198999 AACGTTGCTAAAGACGCATACTTTAATGGCGTTTTAAGCCCAAACGCCTCCAAATACTC
66 AACGCCGCTAAAGAAGCATACTTTAATGGCGTTTTAAGCCCAAACGCCTCCAAATACTC
* * **
1199058 GTACTTTAGTGGCGCTTTTATATAAACGCCGCTAAATACT-GTACTTTAATGGTGTTTTAAGCAC
1 GTACTTTAGTGGCGCTTTTATACAAACGCCGCTAAAGACTAGTACTTTAATGGCATTTTAA-CAC
* * * *
1199122 AAACGCCGCTAAATAATCATTCTTTAGTGGCGTTTT
65 AAACGCCGCTAAAGAAGCATACTTTAATGGCGTTTT
1199158 TATATAAACG
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
123 16 0.19
124 67 0.81
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (124 bp):
GTACTTTAGTGGCGCTTTTATACAAACGCCGCTAAAGACTAGTACTTTAATGGCATTTTAACACA
AACGCCGCTAAAGAAGCATACTTTAATGGCGTTTTAAGCCCAAACGCCTCCAAATACTC
Found at i:1201576 original size:23 final size:23
Alignment explanation
Indices: 1201548--1201593 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1201538 ATCCGATATT
1201548 ATCTTGAGGATATTAACGAGATA
1 ATCTTGAGGATATTAACGAGATA
1201571 ATCTTGAGGATATTAACGAGATA
1 ATCTTGAGGATATTAACGAGATA
1201594 CCAAAGTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (23 bp):
ATCTTGAGGATATTAACGAGATA
Found at i:1202643 original size:21 final size:22
Alignment explanation
Indices: 1202614--1202672 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
1202604 TGATTTATTA
*
1202614 TTAT-GATTTCAATTTTCTTG-
1 TTATGGATTTCAAGTTTCTTGT
* *
1202634 TTATGGATTTTAAGTTTGTTGT
1 TTATGGATTTCAAGTTTCTTGT
*
1202656 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
1202673 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 4 0.12
21 13 0.41
22 15 0.47
ACGTcount: A:0.20, C:0.05, G:0.19, T:0.56
Consensus pattern (22 bp):
TTATGGATTTCAAGTTTCTTGT
Found at i:1202953 original size:43 final size:43
Alignment explanation
Indices: 1202869--1203051 Score: 221
Period size: 43 Copynumber: 4.3 Consensus size: 43
1202859 ACCAGATCTT
* * *
1202869 TTGCGGCGTTTGTG-GGAAAACATCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTGTGGAAAACACCGCTAAATATCAACACCTA
* * *
1202911 TTGCGGCGTTTGTGT-CAAACACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGTGGAAA-ACACCGCTAAATATCAACACCTA
* *
1202954 TTGCAGCGTTTGT-TGGAAAATACCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGTGGAAAACACCGCTAAATATCAACACCTA
* * *
1202996 TTACGGCATTTG-GTGGACAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGTGGA-AAACACCGCTAAATATCAACACCTA
1203039 TTGCGGCGTTTGT
1 TTGCGGCGTTTGT
1203052 CCAACAAACG
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
42 51 0.43
43 68 0.57
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (43 bp):
TTGCGGCGTTTGTGTGGAAAACACCGCTAAATATCAACACCTA
Found at i:1202963 original size:85 final size:85
Alignment explanation
Indices: 1202869--1203051 Score: 244
Period size: 85 Copynumber: 2.2 Consensus size: 85
1202859 ACCAGATCTT
* * * * *
1202869 TTGCGGCGTTTGTGGGAAAACATCGCTAAATCTCAAGACCTATTGCGGCGTTT-GTGTCA-AACA
1 TTGCGGCGTTTGTGGGAAAACACCGCTAAATATCAACACCTATTACGGCATTTGGTG-CACAA-A
*
1202932 CGCCGCTAAATCTCAACACCTA
64 CGCCGCTAAATATCAACACCTA
* * * *
1202954 TTGCAGCGTTTGTTGGAAAATACCGCTAAATATCAACACCTATTACGGCATTTGGTGGACAAACG
1 TTGCGGCGTTTGTGGGAAAACACCGCTAAATATCAACACCTATTACGGCATTTGGTGCACAAACG
1203019 CCGCTAAATATCAACACCTA
66 CCGCTAAATATCAACACCTA
1203039 TTGCGGCGTTTGT
1 TTGCGGCGTTTGT
1203052 CCAACAAACG
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
85 80 0.94
86 5 0.06
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (85 bp):
TTGCGGCGTTTGTGGGAAAACACCGCTAAATATCAACACCTATTACGGCATTTGGTGCACAAACG
CCGCTAAATATCAACACCTA
Found at i:1203059 original size:43 final size:42
Alignment explanation
Indices: 1202869--1203090 Score: 201
Period size: 43 Copynumber: 5.2 Consensus size: 42
1202859 ACCAGATCTT
*** ** * *
1202869 TTGCGGCGTTTGTGGGAAAACATCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTTCAAAAACGCCGCTAAATATCAACACCTA
* *
1202911 TTGCGGCGTTTGTGTCAAACACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGT-TCAAAAACGCCGCTAAATATCAACACCTA
* ** **
1202954 TTGCAGCGTTTGTTGGAAAATACCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTTCAAAAACGCCGCTAAATATCAACACCTA
* * ** *
1202996 TTACGGCATTTGGTGGACAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTT-GTTCAAAAACGCCGCTAAATATCAACACCTA
* * ***
1203039 TTGCGGCGTTTGTCCAACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTTCAA-AAACGCCGCTAAATATCAACACCTA
1203082 TTGCGGCGT
1 TTGCGGCGT
1203091 ATTTTGTTAC
Statistics
Matches: 146, Mismatches: 31, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
42 47 0.32
43 99 0.68
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (42 bp):
TTGCGGCGTTTGTTCAAAAACGCCGCTAAATATCAACACCTA
Found at i:1204302 original size:24 final size:25
Alignment explanation
Indices: 1204254--1204330 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 25
1204244 TTCAAAAGGG
* **
1204254 TGCTATTTTTGTAATTTTTTTAAAA
1 TGCTATTTTCGTAATTTTTGAAAAA
1204279 TGCTA-TTTCGTAATTTTTGAAAAAAA
1 TGCTATTTTCGTAATTTTTG--AAAAA
* *
1204305 TGATATTTTAGTAAATATTTTGAAAA
1 TGCTATTTTCGT-AAT-TTTTGAAAA
1204331 TGGTGTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 12 0.29
25 5 0.12
26 8 0.19
27 9 0.21
28 3 0.07
29 5 0.12
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.49
Consensus pattern (25 bp):
TGCTATTTTCGTAATTTTTGAAAAA
Found at i:1204376 original size:29 final size:28
Alignment explanation
Indices: 1204238--1204378 Score: 94
Period size: 29 Copynumber: 5.1 Consensus size: 28
1204228 ACATACTGAA
* * * *
1204238 AATTAATTCAAAAGGGTGCTATTTTTGT
1 AATTATTTTAAAATGGTGCTATTTTCGT
*
1204266 AATTTTTTTAAAA---TGCTA-TTTCGT
1 AATTATTTTAAAATGGTGCTATTTTCGT
* *** * *
1204290 AATT-TTTGAAAAAAATGATATTTTAGT
1 AATTATTTTAAAATGGTGCTATTTTCGT
* * * *
1204317 AAATATTTTGAAAATGGTGTTATATTGGT
1 AATTATTTT-AAAATGGTGCTATTTTCGT
1204346 AATTAATTTTAAAATGGTGCTATTTTCGT
1 AATT-ATTTTAAAATGGTGCTATTTTCGT
1204375 AATT
1 AATT
1204379 TTGAAGAAAA
Statistics
Matches: 87, Mismatches: 19, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
23 7 0.08
24 9 0.10
25 5 0.06
26 4 0.05
27 8 0.09
28 13 0.15
29 36 0.41
30 5 0.06
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (28 bp):
AATTATTTTAAAATGGTGCTATTTTCGT
Found at i:1205720 original size:21 final size:23
Alignment explanation
Indices: 1205687--1205737 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
1205677 TGGATATATA
1205687 TGTATTATTAATACA-TTTGTTC
1 TGTATTATTAATACATTTTGTTC
1205709 TGTATT-TTAATACATTTTGTTC
1 TGTATTATTAATACATTTTGTTC
1205731 TGTATTA
1 TGTATTA
1205738 AATCTAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (23 bp):
TGTATTATTAATACATTTTGTTC
Found at i:1206154 original size:2 final size:2
Alignment explanation
Indices: 1206147--1206190 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1206137 TGGTTTATTT
1206147 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1206188 TA T
1 TA T
1206191 TTTTACTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1206173 original size:23 final size:23
Alignment explanation
Indices: 1206142--1206191 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1206132 ATACATGGTT
*
1206142 TATTTTATATATATATATATATA
1 TATTATATATATATATATATATA
1206165 TATTATATATATATATATATATA
1 TATTATATATATATATATATATA
1206188 TATT
1 TATT
1206192 TTTACTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATATATATATATATATATA
Found at i:1208103 original size:30 final size:29
Alignment explanation
Indices: 1208067--1208165 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 29
1208057 AGTGATAAAT
1208067 TGGTCACTAACATTACTGATTTGTAACAAA
1 TGGTCACTAACATTA-TGATTTGTAACAAA
* *
1208097 TGGTCACTAACTTTATTGATTCGTAACAAAAA
1 TGGTCACTAACATTA-TGATTTGTAAC--AAA
* *
1208129 TGGTCACTAACGTTATAATTTGTAACAAA
1 TGGTCACTAACATTATGATTTGTAACAAA
*
1208158 TGATCACT
1 TGGTCACT
1208166 CTATCGTCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.17
30 24 0.40
31 9 0.15
32 17 0.28
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (29 bp):
TGGTCACTAACATTATGATTTGTAACAAA
Found at i:1212962 original size:31 final size:31
Alignment explanation
Indices: 1212897--1212973 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1212887 ATTACGTTGT
** * *
1212897 GGATCATATTGTAAACGGATTAAATGTCGAG
1 GGATCATATTACAAACAGATTAAATGTAGAG
1212928 GGATCATATTACAAACAGATTAAATGTTAG-G
1 GGATCATATTACAAACAGATTAAATG-TAGAG
**
1212959 GGATTGTATTACAAA
1 GGATCATATTACAAA
1212974 TTTTAAAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 37 0.95
32 2 0.05
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (31 bp):
GGATCATATTACAAACAGATTAAATGTAGAG
Found at i:1216356 original size:51 final size:55
Alignment explanation
Indices: 1216300--1216414 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 55
1216290 AACAATCAAT
* * * *
1216300 ACATACTTACACCAATATAAGTGAA-CAAA-ATAC-AAAAAA-ATATCATTTTAC
1 ACATACTTACACCAATATAAGTGAATAAAACAAACAAAAAAAGATAGCACTTTAC
** *
1216351 ACATACTTACACCGGTGTAAGTGAATAAAACAAACAAAAAAAGATAGCACTTTAC
1 ACATACTTACACCAATATAAGTGAATAAAACAAACAAAAAAAGATAGCACTTTAC
1216406 ACATACTTA
1 ACATACTTA
1216415 TATAGATGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 22 0.42
52 3 0.06
53 3 0.06
54 6 0.11
55 19 0.36
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.23
Consensus pattern (55 bp):
ACATACTTACACCAATATAAGTGAATAAAACAAACAAAAAAAGATAGCACTTTAC
Found at i:1219695 original size:16 final size:16
Alignment explanation
Indices: 1219674--1219710 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1219664 GTTATTTGTG
1219674 TAAAATTATAATAAAT
1 TAAAATTATAATAAAT
* *
1219690 TAAAATTTTAATTAAT
1 TAAAATTATAATAAAT
1219706 TAAAA
1 TAAAA
1219711 GTTAACCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATTATAATAAAT
Found at i:1222725 original size:15 final size:15
Alignment explanation
Indices: 1222705--1222735 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1222695 TTAGCTAAGT
1222705 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
1222720 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
1222735 G
1 G
1222736 ATAATGTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.68, T:0.06
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:1223454 original size:43 final size:43
Alignment explanation
Indices: 1223369--1223479 Score: 154
Period size: 43 Copynumber: 2.6 Consensus size: 43
1223359 TTTTGAATGA
* *
1223369 GGTAATAAAATGAAACAAAAA-AAATGAAGTTTTTAATCGTGG
1 GGTACTAAAATGAAACAAAAATAAATAAAGTTTTTAATCGTGG
*
1223411 GGTACTAAAATGGAACAAAAATAAATAAAGTTTTTAAAT-GTGG
1 GGTACTAAAATGAAACAAAAATAAATAAAGTTTTT-AATCGTGG
*
1223454 GGTACTAAAATGAAATAAAAACTAAA
1 GGTACTAAAATGAAACAAAAA-TAAA
1223480 CTTTAAGTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
42 19 0.31
43 35 0.57
44 7 0.11
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.25
Consensus pattern (43 bp):
GGTACTAAAATGAAACAAAAATAAATAAAGTTTTTAATCGTGG
Found at i:1225224 original size:3 final size:3
Alignment explanation
Indices: 1225216--1225261 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
1225206 TTGTTTTTAA
* *
1225216 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
1225260 TA
1 TA
1225262 AATAATTACA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1227525 original size:26 final size:26
Alignment explanation
Indices: 1227474--1227530 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
1227464 TAATTCTTTC
*
1227474 TTTTCAAATTTTTATATATACTTATTA
1 TTTTCAAATATTTATATATAC-TATTA
*
1227501 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCA-AATATTTATATATACTATTA
1227527 TTTT
1 TTTT
1227531 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 9 0.33
27 6 0.22
28 12 0.44
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTCAAATATTTATATATACTATTA
Found at i:1238176 original size:12 final size:12
Alignment explanation
Indices: 1238159--1238216 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
1238149 TATTATGCTT
1238159 GAAGAAAAAAAA
1 GAAGAAAAAAAA
1238171 GAAGAAAAAAAA
1 GAAGAAAAAAAA
1238183 -AGAGAAAAAGAAA
1 GA-AGAAAAA-AAA
1238196 -AAGAAGAAAAAA
1 GAAGAA-AAAAAA
1238208 GAAGAAAAA
1 GAAGAAAAA
1238217 GATGGGTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.02
12 29 0.69
13 12 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:1238183 original size:15 final size:15
Alignment explanation
Indices: 1238163--1238207 Score: 60
Period size: 13 Copynumber: 3.2 Consensus size: 15
1238153 ATGCTTGAAG
1238163 AAAAAAAAGAAG--A
1 AAAAAAAAGAAGAAA
1238176 AAAAAAAAG-AGAAA
1 AAAAAAAAGAAGAAA
*
1238190 AAGAAAAAGAAGAAA
1 AAAAAAAAGAAGAAA
1238205 AAA
1 AAA
1238208 GAAGAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.07
13 9 0.33
14 9 0.33
15 7 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAGAAA
Found at i:1238189 original size:24 final size:25
Alignment explanation
Indices: 1238159--1238218 Score: 88
Period size: 24 Copynumber: 2.4 Consensus size: 25
1238149 TATTATGCTT
1238159 GAAGAAAAA-AAAGAAGAAAAAAAAA
1 GAAGAAAAAGAAA-AAGAAAAAAAAA
*
1238184 G-AGAAAAAGAAAAAGAAGAAAAAA
1 GAAGAAAAAGAAAAAGAAAAAAAAA
1238208 GAAGAAAAAGA
1 GAAGAAAAAGA
1238219 TGGGTCAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 19 0.59
25 13 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (25 bp):
GAAGAAAAAGAAAAAGAAAAAAAAA
Found at i:1238204 original size:27 final size:26
Alignment explanation
Indices: 1238166--1238216 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
1238156 CTTGAAGAAA
1238166 AAAAAGAAGAAAAAAAAAGAGAAAAAG
1 AAAAAGAAGAAAAAAAAAGA-AAAAAG
*
1238193 AAAAAGAAGAAAAAAGAAGAAAAA
1 AAAAAGAAGAAAAAAAAAGAAAAA
1238217 GATGGGTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAAGAAGAAAAAAAAAGAAAAAAG
Found at i:1238612 original size:19 final size:17
Alignment explanation
Indices: 1238570--1238618 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
1238560 TATTTTCTTT
1238570 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
1238586 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
1238604 AAAATTCAATTTATT
1 -AAATTCAATTTATT
1238619 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 1 0.04
19 13 0.46
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:1239126 original size:114 final size:115
Alignment explanation
Indices: 1238876--1239213 Score: 502
Period size: 114 Copynumber: 3.0 Consensus size: 115
1238866 TACCACGTTA
* * *
1238876 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
*
1238941 TTTGCTATGAACCCCAAAAACCAATCATTAGATTTGAAAG-ATGAATTTGC
66 TTTGGTATGAACCCC-AAAACCAATCATTAGATTTGAAAGAATGAATTTGC
* *
1238991 TCATAGTAGAAATAAGAAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
* *
1239056 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGAAT-CATTTGC
66 TTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGAATGAATTTGC
* *
1239105 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTTGAAGTGTTCTTTGAGTTATCTGATTTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
* * * * * *
1239170 TTCGGTAGGAACCACAGAACCATTCATTAGAATTGAAAG-ATGAA
66 TTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGAATGAA
1239214 CTGCATGATC
Statistics
Matches: 201, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
113 2 0.01
114 123 0.61
115 76 0.38
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (115 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
TTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGAATGAATTTGC
Found at i:1240285 original size:215 final size:216
Alignment explanation
Indices: 1239914--1240398 Score: 911
Period size: 215 Copynumber: 2.2 Consensus size: 216
1239904 ATGGATCATC
*
1239914 AACATTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAAGAAGAATTTGTTCAACAT
1 AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAATTTGTTCAACAT
1239979 TTTGCTCAAATTCATCATTCAATGGATCAGCGTTGCCAGAAGGTTCATAATGAGAAGAACTTATC
66 TTTGCTCAAATTCATCATTCAATGGATCAGCGTTGCCAGAAGGTTCATAATGAGAAGAACTTATC
1240044 TGAAGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA-TTTTTTTGCTTGACTCTATCAC
131 TGAAGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACTTTTTTTGCTTGACTCTATCAC
1240108 AGAAGAAGATAGATCAGCATT
196 AGAAGAAGATAGATCAGCATT
*
1240129 AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAATG-AGAATTTGTTCAACC
1 AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAA-GAAGAATTTGTTCAACA
1240193 TTTTGCTCAAATTCATCATTCAATGGATCAGCGTTGCCAGAAGGTTCATAATGAGAAGAACTTAT
65 TTTTGCTCAAATTCATCATTCAATGGATCAGCGTTGCCAGAAGGTTCATAATGAGAAGAACTTAT
1240258 CTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAATCTTTTTTTGCTTGACTCTATC
130 CTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA-CTTTTTTTGCTTGACTCTATC
1240323 ACAGAAGAAGATAGATCAGCATT
194 ACAGAAGAAGATAGATCAGCATT
*
1240346 AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA
1240399 GAAGTTCATA
Statistics
Matches: 263, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
215 168 0.64
216 2 0.01
217 93 0.35
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (216 bp):
AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAATTTGTTCAACAT
TTTGCTCAAATTCATCATTCAATGGATCAGCGTTGCCAGAAGGTTCATAATGAGAAGAACTTATC
TGAAGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACTTTTTTTGCTTGACTCTATCAC
AGAAGAAGATAGATCAGCATT
Found at i:1240624 original size:115 final size:114
Alignment explanation
Indices: 1240361--1240782 Score: 420
Period size: 116 Copynumber: 3.7 Consensus size: 114
1240351 TTCCAGTTCG
*
1240361 AGTTCATAATGAGAAGAACTCATCTGAAGAAG--GAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * * *
1240424 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAG
66 TCAACCTTTTG-CTAAATCCATCACTTGATGGATCAACTTTTCCAGAG-AA
* *
1240474 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAA-AA-AAGAAATTCATAATGAGAAGAATT
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACT
*
1240537 TGTTCAACCTTTTGCTAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
63 TGTTCAACCTTTTGCTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAA
* * *
1240589 AGTTCATAATGAGAAGAACTCATCT------GAAGAAGAAGAAGTTCACAATAAGAAGAGCTTGT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
1240648 TCAACCTTTTGCATAATTCTATCACAGAAAGAGATAGATTAGCATCAACTTTTCCAGAGAA
66 TCAACCTTTTGC-TAAATCCATCAC---------TTGA-T-GGATCAACTTTTCCAGAGAA
* *
1240709 AGTTTATAATGAGAAGAACTCATCTGAAGAA-AA-AAGAAGAAGTTCATAATGAGAAGAACTTAT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1240772 TCAACCTTTTG
66 TCAACCTTTTG
1240783 AATGACTCTA
Statistics
Matches: 259, Mismatches: 24, Indels: 41
0.80 0.07 0.13
Matches are distributed among these distances:
106 3 0.01
107 2 0.01
108 34 0.13
109 10 0.04
112 6 0.02
113 19 0.07
115 47 0.18
116 51 0.20
117 2 0.01
118 3 0.01
119 1 0.00
120 42 0.16
124 37 0.14
125 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (114 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTAAATCCATCACTTGATGGATCAACTTTTCCAGAGAA
Found at i:1240818 original size:124 final size:123
Alignment explanation
Indices: 1240571--1240870 Score: 369
Period size: 124 Copynumber: 2.5 Consensus size: 123
1240561 CACTTGATGG
*
1240571 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG---AAGAAGAAGTTCACA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGAAGTTCACA
* * * * * * *
1240633 ATAAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAAGAGATAGATTAGC
66 ATAAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAAC
* *
1240691 ATCAACTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAAAAGAAGAAGTTCAC
* * * * *
1240756 AATGAGAAGAACTTATTCAACCTTTTGAATGACTCTATCACATAAGGAAATAGGTCAAC
65 AATAAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAAC
** * *
1240815 ATC-A--TCCCCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 ATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGAA
1240871 TTTATTCAAT
Statistics
Matches: 155, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
120 45 0.29
121 15 0.10
122 31 0.20
123 1 0.01
124 63 0.41
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGAAGTTCACA
ATAAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAAC
Found at i:1241023 original size:3 final size:3
Alignment explanation
Indices: 1241015--1241060 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
1241005 TTGTTTTTAA
* *
1241015 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
1241059 TA
1 TA
1241061 AATAATTACA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1246590 original size:34 final size:30
Alignment explanation
Indices: 1246552--1246620 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1246542 TTGATATAAC
1246552 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1246586 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1246615 AATTTA
1 AATTTA
1246621 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1246631 original size:29 final size:30
Alignment explanation
Indices: 1246561--1246620 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1246551 CAATTTAAGG
1246561 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1246592 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1246621 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1246725 original size:21 final size:20
Alignment explanation
Indices: 1246699--1246797 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
1246689 AATGTGTCAA
1246699 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1246720 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
1246741 AGTACATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* * *
1246762 TAGTGCATCGATGTACCATGC
1 -AGTGCATCCATGCACCCTGC
1246783 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1246798 TCAAACACCG
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.20
21 35 0.53
22 11 0.17
23 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:1246843 original size:20 final size:19
Alignment explanation
Indices: 1246818--1246912 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 19
1246808 AATGCAATTA
1246818 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTT-T
* **
1246838 GTGCATCGATGTATCAAGGTT
1 GTGCATCGATGCATC--CTTT
*
1246859 GTGCATCGATGCATCTTGTT
1 GTGCATCGATGCATCCT-TT
*
1246879 GTGCATGGATGCATCCTGTT
1 GTGCATCGATGCATCCT-TT
*
1246899 GTGCATCCATGCAT
1 GTGCATCGATGCAT
1246913 GAAGGTTGGA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
20 46 0.74
21 15 0.24
22 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (19 bp):
GTGCATCGATGCATCCTTT
Found at i:1246865 original size:41 final size:40
Alignment explanation
Indices: 1246818--1246912 Score: 111
Period size: 41 Copynumber: 2.4 Consensus size: 40
1246808 AATGCAATTA
*
1246818 GTGCATCGATGCATCCTT-CTGTGCATCGATGTATCAAGGTT
1 GTGCATCGATGCAT-CTTGCTGTGCATCGATGCATC-AGGTT
* * **
1246859 GTGCATCGATGCATCTTGTTGTGCATGGATGCATCCTGTT
1 GTGCATCGATGCATCTTGCTGTGCATCGATGCATCAGGTT
*
1246899 GTGCATCCATGCAT
1 GTGCATCGATGCAT
1246913 GAAGGTTGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 19 0.40
41 28 0.60
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (40 bp):
GTGCATCGATGCATCTTGCTGTGCATCGATGCATCAGGTT
Found at i:1248306 original size:15 final size:15
Alignment explanation
Indices: 1248275--1248305 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1248265 GATGATGGTG
1248275 AAGGAAGATGAAGAA
1 AAGGAAGATGAAGAA
1248290 AAGGAAGA-GAAGAA
1 AAGGAAGATGAAGAA
1248304 AA
1 AA
1248306 ACAAGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (15 bp):
AAGGAAGATGAAGAA
Found at i:1249921 original size:21 final size:21
Alignment explanation
Indices: 1249895--1249934 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1249885 AAACAATGGG
1249895 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
1249916 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
1249935 CATTAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1250074 original size:34 final size:30
Alignment explanation
Indices: 1250036--1250104 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1250026 TTGATATAAC
1250036 AATTTAAGGCAAAATGGTTTTTGGAATTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGAATT-AATTG
*
1250070 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGAATTAATTG
1250099 AATTTA
1 AATTTA
1250105 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGAATTAATTG
Found at i:1250115 original size:29 final size:30
Alignment explanation
Indices: 1250045--1250104 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1250035 CAATTTAAGG
1250045 CAAAATGGTTTTTGGAATTGAATTGAATTTA
1 CAAAAT-GTTTTTGGAATTGAATTGAATTTA
*
1250076 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGAATTGAATTGAATTTA
1250105 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGAATTGAATTGAATTTA
Found at i:1250279 original size:20 final size:21
Alignment explanation
Indices: 1250233--1250288 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
1250223 CTGCATCCCT
1250233 GTGCATCGATGCACCTGCACTA
1 GTGCATCGATGCACCTGCAC-A
1250255 GTGCATCGATGCACCATG-A-A
1 GTGCATCGATGCACC-TGCACA
*
1250275 GTGCATCTATGCAC
1 GTGCATCGATGCAC
1250289 TCAAACACCG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 14 0.44
22 16 0.50
23 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (21 bp):
GTGCATCGATGCACCTGCACA
Found at i:1250334 original size:20 final size:20
Alignment explanation
Indices: 1250309--1250381 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
1250299 AATGCAATTA
1250309 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
1250329 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
1250349 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
1250369 GTGCATCCATGCA
1 GTGCATCGATGCA
1250382 CGAAGGCTGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.16, C:0.30, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:1251581 original size:13 final size:13
Alignment explanation
Indices: 1251544--1251582 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1251534 AGTTAAAAAA
*
1251544 TAATTTAATATTT
1 TAATTTAAGATTT
*
1251557 TATTTTATAGATTT
1 TAATTTA-AGATTT
1251571 TAATTTAAGATT
1 TAATTTAAGATT
1251583 AATCAAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (13 bp):
TAATTTAAGATTT
Found at i:1254244 original size:20 final size:20
Alignment explanation
Indices: 1254215--1254286 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1254205 AAATGACCAA
1254215 CAAATTCGCAACGCGA-ACT
1 CAAATTCGCAACGCGATACT
* *
1254234 CCAATTTCGCAACGCGATAGT
1 -CAAATTCGCAACGCGATACT
*
1254255 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATACT
1254275 CAAATTCGCAAC
1 CAAATTCGCAAC
1254287 ATAAAGTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 46 0.96
21 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGATACT
Found at i:1254283 original size:40 final size:38
Alignment explanation
Indices: 1254215--1254327 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 38
1254205 AAATGACCAA
* * * *
1254215 CAAATTCGCAACGCGAACTCCAATTTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAGT-CAAATTCGCAAC-AGAAAGT
*
1254255 CAAATTCGCAACGCGATAGTCAAATTCGCAACATAAAGT
1 CAAATTCGCAACGCGA-AGTCAAATTCGCAACAGAAAGT
**
1254294 CAAATTTCATAACGCGAAAGTCAAATTCGCAACA
1 CAAA-TTCGCAACGCG-AAGTCAAATTCGCAACA
1254328 TGTTTTAGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 8 0.13
40 52 0.83
41 3 0.05
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (38 bp):
CAAATTCGCAACGCGAAGTCAAATTCGCAACAGAAAGT
Found at i:1255091 original size:12 final size:12
Alignment explanation
Indices: 1255073--1255106 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1255063 CCACATTTCC
1255073 CAATATCAAACA
1 CAATATCAAACA
*
1255085 TAATATCAAACA
1 CAATATCAAACA
*
1255097 CAATCTCAAA
1 CAATATCAAA
1255107 ACCCACAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.21
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1255282 original size:24 final size:24
Alignment explanation
Indices: 1255231--1255284 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1255221 GTATTCGAAA
*
1255231 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1255255 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1255279 TTTGAT
1 TTTGAT
1255285 GATATGTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1257571 original size:18 final size:18
Alignment explanation
Indices: 1257548--1257583 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1257538 AAGCAAAAGG
*
1257548 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1257566 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1257584 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1258407 original size:24 final size:24
Alignment explanation
Indices: 1258355--1258407 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1258345 TTTCATATGT
* *
1258355 AATTGGAGTTTGAATTTAAATTTA
1 AATTTGAGTTTGAATTTAAATATA
*
1258379 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1258403 AATTT
1 AATTT
1258408 CGACTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1258752 original size:39 final size:39
Alignment explanation
Indices: 1258709--1258795 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1258699 TCCGATGCTC
* *
1258709 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATACGGTGCCAAGCAAAAGGAA
*
1258748 ATCAAAATCCAAATCTCATACGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATACGGTGCCAAGCAAAAGGAA
1258787 ATCAAAATC
1 ATCAAAATC
1258796 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATACGGTGCCAAGCAAAAGGAA
Found at i:1259208 original size:67 final size:65
Alignment explanation
Indices: 1259129--1259274 Score: 195
Period size: 67 Copynumber: 2.2 Consensus size: 65
1259119 TTTTAGAAAC
* *
1259129 AACAAATCAACTTTTACAAATC-AATTAAACAAGCAAAAATAATAATTCTTATTTACACATCAAA
1 AACAAATCAACTTTTACAAATCAAATCAAACAAGC-AAAA-AATAAATCTTATTTACACATC-AA
1259193 TTA
63 TTA
** * * *
1259196 AACAAATCAACTTTTACAAATCAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAAATCAAACAAGCAAAAAATAAATCTTATTTACACATCAATTA
1259261 AACAAATCAACTTT
1 AACAAATCAACTTT
1259275 CAATGTAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
65 19 0.27
66 18 0.25
67 26 0.37
68 8 0.11
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.31
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAAATCAAACAAGCAAAAAATAAATCTTATTTACACATCAATTA
Found at i:1260655 original size:20 final size:21
Alignment explanation
Indices: 1260597--1260655 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
1260587 TGAATCGGGA
* *
1260597 TCTTGAACGGAGGGCGGGACC
1 TCTTGAACGGTGGGAGGGACC
* **
1260618 TCTTGAACGATGACAGGG-CC
1 TCTTGAACGGTGGGAGGGACC
1260638 TCTTGAACGGTGGGAGGG
1 TCTTGAACGGTGGGAGGG
1260656 GCTTCTTCGA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.19
Consensus pattern (21 bp):
TCTTGAACGGTGGGAGGGACC
Found at i:1260662 original size:21 final size:21
Alignment explanation
Indices: 1260597--1260687 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 21
1260587 TGAATCGGGA
* * *
1260597 TCTTGAACGGAGGGCGGGACC
1 TCTTGAACGGTGGGAGGGGCC
* **
1260618 TCTTGAACGATGACA-GGGCC
1 TCTTGAACGGTGGGAGGGGCC
*
1260638 TCTTGAACGGTGGGAGGGGCT
1 TCTTGAACGGTGGGAGGGGCC
* * *
1260659 TCTTCG-ATGATGAGAGGGGCC
1 TCTT-GAACGGTGGGAGGGGCC
1260680 TCTTGAAC
1 TCTTGAAC
1260688 AATAGGATAC
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
20 17 0.33
21 34 0.65
22 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.37, T:0.22
Consensus pattern (21 bp):
TCTTGAACGGTGGGAGGGGCC
Found at i:1263349 original size:20 final size:20
Alignment explanation
Indices: 1263324--1263469 Score: 131
Period size: 20 Copynumber: 7.3 Consensus size: 20
1263314 GCGTAAAAAC
1263324 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1263344 ATTTGACTTTTGTGTTGCG-
1 ATTTGACTTTCGCGTTGCGA
* *
1263363 ATTT-ACAAATTCGCGTTACGA
1 ATTTGAC--TTTCGCGTTGCGA
* *
1263384 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1263404 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1263424 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
*
1263443 ATTT-ACAGATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
1263464 ATTTGA
1 ATTTGA
1263470 GAAATCGCAA
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
18 4 0.04
19 10 0.10
20 72 0.72
21 11 0.11
22 3 0.03
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1263387 original size:40 final size:40
Alignment explanation
Indices: 1263332--1263469 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
1263322 ACATTTGACT
1263332 TTCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAAA
1 TTCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAAA
* *
1263372 TTCGCGTTACGAATTTGACTTTTGTGTTGCGAATTTGAC-TA
1 TTCGCGTTGCGAATTTGACTTTTGTGTTGCG-ATTT-ACAAA
* *
1263413 -TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAGA
1 TTCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAAA
1263452 TTCGCGTTGCGAATTTGA
1 TTCGCGTTGCGAATTTGA
1263470 GAAATCGCAA
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.02
39 5 0.06
40 75 0.84
41 5 0.06
42 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (40 bp):
TTCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAAA
Found at i:1263541 original size:20 final size:21
Alignment explanation
Indices: 1263494--1263549 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
1263484 ATTTACATAT
1263494 TCGCGTTGCGAAA-TTGAAAA
1 TCGCGTTGCGAAATTTGAAAA
* * *
1263514 TTGGGTTGCGAAATTTG-AGA
1 TCGCGTTGCGAAATTTGAAAA
1263534 TCGCGTTGCG-AATTTG
1 TCGCGTTGCGAAATTTG
1263550 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 6 0.20
20 21 0.70
21 3 0.10
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGAAATTTGAAAA
Found at i:1264074 original size:6 final size:6
Alignment explanation
Indices: 1264065--1264102 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1264055 ATCCCCATTC
* *
1264065 AAAATC AAAATA AAAATA AAAATA AAGATA AAAA-A AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
1264103 TGCTACGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:1267677 original size:20 final size:20
Alignment explanation
Indices: 1267629--1267683 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1267619 TTAGAAACGA
1267629 CGAATCA-CTTATTATTATTT
1 CGAATCACCTT-TTATTATTT
*
1267649 AGAATCACCTTTTATTATTT
1 CGAATCACCTTTTATTATTT
*
1267669 CGAATCACCATTTAT
1 CGAATCACCTTTTAT
1267684 CCTACTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.45
Consensus pattern (20 bp):
CGAATCACCTTTTATTATTT
Found at i:1268087 original size:2 final size:2
Alignment explanation
Indices: 1268082--1268139 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1268072 ACACACACAC
1268082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1268124 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1268140 GGTGGGGCAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1268264 original size:28 final size:28
Alignment explanation
Indices: 1268223--1268279 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
1268213 ATCTATTTCG
1268223 CCCCTAAAATTTTATAAGATT-AAGTTCA
1 CCCCTAAAATTTTATAAG-TTCAAGTTCA
1268251 CCCCTTAAAA-TTTATAAGTTCAAGTTCA
1 CCCC-TAAAATTTTATAAGTTCAAGTTCA
1268279 C
1 C
1268280 TCTTAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 2 0.07
28 20 0.74
29 5 0.19
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (28 bp):
CCCCTAAAATTTTATAAGTTCAAGTTCA
Found at i:1279630 original size:3 final size:3
Alignment explanation
Indices: 1279622--1279659 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1279612 ACATTGAGAC
*
1279622 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1279660 GATTTGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1280915 original size:7 final size:7
Alignment explanation
Indices: 1280903--1280927 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1280893 TGCAACAACC
1280903 CTTCTCT
1 CTTCTCT
1280910 CTTCTCT
1 CTTCTCT
1280917 CTTCTCT
1 CTTCTCT
1280924 CTTC
1 CTTC
1280928 CCTCGCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
CTTCTCT
Found at i:1282725 original size:9 final size:9
Alignment explanation
Indices: 1282698--1282746 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1282688 CATTTTCATC
1282698 AAAATA-TT
1 AAAATATTT
1282706 -AAATA-TT
1 AAAATATTT
1282713 AAAATATTT
1 AAAATATTT
1282722 AAAATATTT
1 AAAATATTT
*
1282731 ATTAATATTT
1 A-AAATATTT
*
1282741 ATAATA
1 AAAATA
1282747 ATATATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.19
8 5 0.14
9 17 0.46
10 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAAATATTT
Found at i:1282830 original size:26 final size:27
Alignment explanation
Indices: 1282801--1282869 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
1282791 AGATATTATA
1282801 TTTTTAT-TTTAATAAT-ATATAATAATTT
1 TTTTTATATTTAATAATGA-ATAAT-A-TT
1282829 TTTTTATATTTAATAATGAATAATATT
1 TTTTTATATTTAATAATGAATAATATT
*
1282856 ATTTATATATTTAA
1 -TTTTTATATTTAA
1282870 AACATATACT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 2 0.05
28 20 0.54
29 14 0.38
30 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTTTATATTTAATAATGAATAATATT
Found at i:1283117 original size:20 final size:20
Alignment explanation
Indices: 1283069--1283118 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1283059 TTTCCAGATG
1283069 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1283089 TTTACCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1283109 TTTTTCAGAA
1 TTTTCCAGAA
1283119 TTCAAATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1283137 original size:15 final size:15
Alignment explanation
Indices: 1283117--1283167 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
1283107 CATTTTTCAG
1283117 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
1283132 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
1283147 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
1283162 AATTCA
1 AATTCA
1283168 TTTTTCGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:1283153 original size:30 final size:29
Alignment explanation
Indices: 1283101--1283171 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 29
1283091 TACCAGAAAT
*
1283101 GTAATTCATTTTTCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
1283130 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
1283160 GTAATTCATTTT
1 GTAATTCATTTT
1283172 TCGGAAAACC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:1289977 original size:171 final size:171
Alignment explanation
Indices: 1289692--1290027 Score: 654
Period size: 171 Copynumber: 2.0 Consensus size: 171
1289682 TGATTTACCC
1289692 AAACATGCCATATGCATACTTGTTGAAACTTCATTTGGGTTATCATCTAAAATAACCCTCAGCAA
1 AAACATGCCATATGCATACTTGTTGAAACTTCATTTGGGTTATCATCTAAAATAACCCTCAGCAA
1289757 CTCTATAGGACTGAAATTCATTTAGGGACGTAGGTTCCGACAAAACTTATAAGAATGAAACAAAG
66 CTCTATAGGACTGAAATTCATTTAGGGACGTAGGTTCCGACAAAACTTATAAGAATGAAACAAAG
*
1289822 TAAAAACTGAAAAATAGATTCTGAGAAAGATATACTTGTTG
131 TAAAAACTGAAAAATAAATTCTGAGAAAGATATACTTGTTG
*
1289863 AAACATGCCATATGCATACTTGTTGAAACTTCATTTGGGTTATCATCTAAAATAACCCTCGGCAA
1 AAACATGCCATATGCATACTTGTTGAAACTTCATTTGGGTTATCATCTAAAATAACCCTCAGCAA
1289928 CTCTATAGGACTGAAATTCATTTAGGGACGTAGGTTCCGACAAAACTTATAAGAATGAAACAAAG
66 CTCTATAGGACTGAAATTCATTTAGGGACGTAGGTTCCGACAAAACTTATAAGAATGAAACAAAG
1289993 TAAAAACTGAAAAATAAATTCTGAGAAAGATATAC
131 TAAAAACTGAAAAATAAATTCTGAGAAAGATATAC
1290028 CTGTAGCTAC
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 163 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (171 bp):
AAACATGCCATATGCATACTTGTTGAAACTTCATTTGGGTTATCATCTAAAATAACCCTCAGCAA
CTCTATAGGACTGAAATTCATTTAGGGACGTAGGTTCCGACAAAACTTATAAGAATGAAACAAAG
TAAAAACTGAAAAATAAATTCTGAGAAAGATATACTTGTTG
Found at i:1293680 original size:16 final size:16
Alignment explanation
Indices: 1293659--1293697 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1293649 TTTCTAAAAG
*
1293659 CTAAAAGCTTTTGCAA
1 CTAAAAGCTATTGCAA
1293675 CTAAAAGCTATTGCAA
1 CTAAAAGCTATTGCAA
*
1293691 CAAAAAG
1 CTAAAAG
1293698 AACTTATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
CTAAAAGCTATTGCAA
Found at i:1293792 original size:16 final size:16
Alignment explanation
Indices: 1293771--1293809 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1293761 TTTCTAAAAG
*
1293771 CTAAAAGCTTTTGCAA
1 CTAAAAGCTATTGCAA
1293787 CTAAAAGCTATTGCAA
1 CTAAAAGCTATTGCAA
*
1293803 CAAAAAG
1 CTAAAAG
1293810 AATTTATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
CTAAAAGCTATTGCAA
Found at i:1293792 original size:112 final size:112
Alignment explanation
Indices: 1293594--1293869 Score: 516
Period size: 112 Copynumber: 2.5 Consensus size: 112
1293584 CAGTAAAATC
*
1293594 ATAGGACGTAAAAACAGTTGATTCATTTAAGCAACAAAAAAACAACTTGTTTATGTTTCTAAAAG
1 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAAC-AAAAAACAACTTGTTTATGTTTCTAAAAG
1293659 CTAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
65 CTAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
1293707 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTTATGTTTCTAAAAGC
1 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTTATGTTTCTAAAAGC
*
1293772 TAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAATTTATCT
66 TAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
*
1293819 ATAGGACGTAAAAACAATTCATTCATTTAAGCAACAAAAAACAACTTGTTT
1 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTT
1293870 TAGTACACAT
Statistics
Matches: 160, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
112 126 0.79
113 34 0.21
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.29
Consensus pattern (112 bp):
ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTTATGTTTCTAAAAGC
TAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
Found at i:1294226 original size:19 final size:20
Alignment explanation
Indices: 1294202--1294246 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1294192 ACGCATCGGC
1294202 CCGCATCAGACCGCATCAG-
1 CCGCATCAGACCGCATCAGA
* *
1294221 CCGCATCGGATCGCATCAGA
1 CCGCATCAGACCGCATCAGA
1294241 CCGCAT
1 CCGCAT
1294247 TATGTACCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.24, C:0.40, G:0.22, T:0.13
Consensus pattern (20 bp):
CCGCATCAGACCGCATCAGA
Found at i:1298362 original size:229 final size:227
Alignment explanation
Indices: 1297952--1298395 Score: 780
Period size: 229 Copynumber: 1.9 Consensus size: 227
1297942 GTAAATTATC
* * *
1297952 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1298017 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
1298082 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATT-AAAAAATTG
1298147 AAACATAAATTACATAACTTTCAAAAAAGTATA
195 AAACATAAATTACATAACTTTCAAAAAAGTATA
*
1298180 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1298245 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
1298310 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAATTG
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAATTG
1298375 AAACATAAATTACATAACTTT
195 AAACATAAATTACATAACTTT
1298396 AAAGCAGTTT
Statistics
Matches: 205, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 65 0.32
229 140 0.68
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAATTGA
AACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:1301030 original size:33 final size:33
Alignment explanation
Indices: 1300988--1301053 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1300978 AAATAGATGG
*
1300988 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1301021 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1301054 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1302866 original size:18 final size:18
Alignment explanation
Indices: 1302843--1302895 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
1302833 TCGAGTTAAT
*
1302843 TTTGTATAAGATTTATAA
1 TTTGTATACGATTTATAA
1302861 TTTGTATACGATTTATAA
1 TTTGTATACGATTTATAA
1302879 TTTGTATACGATTTATA
1 TTTGTATACGATTTATA
1302896 TTTTTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGTATACGATTTATAA
Found at i:1303322 original size:199 final size:199
Alignment explanation
Indices: 1302982--1304596 Score: 2809
Period size: 199 Copynumber: 8.1 Consensus size: 199
1302972 TTAAGGGTCA
* *** *
1302982 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
*
1303047 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1303112 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1303177 AATG
196 AATG
1303181 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1303245 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1303310 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT-AA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1303374 TAATG
195 TAATG
1303379 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1303444 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1303509 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1303573 TAATG
195 TAATG
* *** *
1303578 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
1303643 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1303707 TAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
1303771 AATA
196 AATG
1303775 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1303840 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1303905 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAAAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1303970 TAATG
195 TAATG
* ** *
1303975 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
1304039 ATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1304102 TAATATGTAATTTTTTAATCTAACCAGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1304167 AATG
196 AATG
* * *** *
1304171 TGTCGACACTAATATTGTTTGTGTCGATATTTTTTT-TCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
1304235 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1304299 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1304364 AATG
196 AATG
1304368 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1304433 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
1304498 GTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1304563 TAATG
195 TAATG
*
1304568 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1304597 CTAATTTAAA
Statistics
Matches: 1360, Mismatches: 45, Indels: 21
0.95 0.03 0.01
Matches are distributed among these distances:
195 11 0.01
196 180 0.13
197 300 0.22
198 211 0.16
199 416 0.31
200 242 0.18
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:1303923 original size:397 final size:399
Alignment explanation
Indices: 1302982--1304596 Score: 2813
Period size: 397 Copynumber: 4.1 Consensus size: 399
1302972 TTAAGGGTCA
* *** *
1302982 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
*
1303047 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1303112 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1303177 AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
1303241 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 CACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
*
1303306 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
326 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1303371 T-AATAATG
391 TAAATAATG
1303379 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1303444 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1303509 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
* ***
1303573 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGT
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
*
1303637 GCATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
260 GCACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
1303701 ATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
325 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
*
1303765 CTAAATAATA
390 CTAAATAATG
1303775 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1303840 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1303905 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAAAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
* **
1303970 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT--TTACAAGGT
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
*
1304033 GCATCAATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
260 GCACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
* *
1304096 ATAATGTAATATGTAATTTTTTAATCTAACCAGTACAATTATACCGGTTTTATGAGAGAATAAGT
325 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
1304161 CTAAATAATG
390 CTAAATAATG
* * *** *
1304171 TGTCGACACTAATATTGTTTGTGTCGATATTTTTTT-TCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
1304235 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1304299 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1304364 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
1304429 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
261 CACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
* *
1304494 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTC
326 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1304559 TAAATAATG
391 TAAATAATG
*
1304568 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1304597 CTAATTTAAA
Statistics
Matches: 1169, Mismatches: 40, Indels: 18
0.95 0.03 0.01
Matches are distributed among these distances:
393 157 0.13
394 32 0.03
395 144 0.12
396 326 0.28
397 407 0.35
398 103 0.09
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (399 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
CACCAATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
TAAATAATG
Found at i:1304386 original size:593 final size:595
Alignment explanation
Indices: 1302982--1304596 Score: 3008
Period size: 593 Copynumber: 2.7 Consensus size: 595
1302972 TTAAGGGTCA
1302982 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
*
1303047 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1303112 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1303177 AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTG
195 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
1303241 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
260 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
1303306 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1303371 T-AATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACA
390 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACA
*
1303435 AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
454 AGGTGCACCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAA
*
1303500 AAGTATAATGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
518 AAGTATAATGTAATATGTAATTTTTAATCTAACCAGTACAATTATACCGGTTTTATGAGAGAATA
1303565 AGTCTAAATAATG
583 AGTCTAAATAATG
1303578 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1303643 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1303708 AATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
*
1303772 ATATGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGC
196 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGC
1303837 ACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 ACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
*
1303902 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAAAAGTCT
326 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
* **
1303967 AAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTACAAG
391 AAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAG
*
1304031 GTGCATCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
456 GTGCACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
1304095 TATAATGTAATATGTAATTTTTTAATCTAACCAGTACAATTATACCGGTTTTATGAGAGAATAAG
521 TATAATGTAATATGTAA-TTTTTAATCTAACCAGTACAATTATACCGGTTTTATGAGAGAATAAG
1304160 TCTAAATAATG
585 TCTAAATAATG
*
1304171 TGTCGACACTAATATTGTTTGTGTCGATATTTTTTTT-CAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1304235 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
1304300 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
1304365 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGC
196 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGC
1304430 ACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 ACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* * *
1304495 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCT
326 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
*
1304560 AAATAATGTGTCGACACTAATATATTTTGTGTCGATA
391 AAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1304597 CTAATTTAAA
Statistics
Matches: 997, Mismatches: 18, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
592 153 0.15
593 373 0.37
594 117 0.12
595 213 0.21
596 141 0.14
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (595 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGC
ACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAG
GTGCACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
TATAATGTAATATGTAATTTTTAATCTAACCAGTACAATTATACCGGTTTTATGAGAGAATAAGT
CTAAATAATG
Found at i:1306076 original size:18 final size:18
Alignment explanation
Indices: 1306053--1306114 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1306043 ATCGGTCGCA
* * *
1306053 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
1306071 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
1306089 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
1306107 GAAGATGA
1 GAAGATGA
1306115 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:1306077 original size:6 final size:6
Alignment explanation
Indices: 1306053--1306114 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
1306043 ATCGGTCGCA
* * * * * *
1306053 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
1306101 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
1306115 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1306088 original size:3 final size:3
Alignment explanation
Indices: 1306068--1306118 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
1306058 TGAAGCTGAC
* * * *
1306068 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1306116 GAT
1 GAT
1306119 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1306115 original size:12 final size:12
Alignment explanation
Indices: 1306056--1306118 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
1306046 GGTCGCAGAA
* *
1306056 GATGAAGCTGAC
1 GATGAAGATGAT
*
1306068 GATGAAGATGAC
1 GATGAAGATGAT
*
1306080 GATGATGATGAT
1 GATGAAGATGAT
*
1306092 GATGACGATGAT
1 GATGAAGATGAT
1306104 GATGAAGATGAT
1 GATGAAGATGAT
1306116 GAT
1 GAT
1306119 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:1307818 original size:191 final size:184
Alignment explanation
Indices: 1307477--1308151 Score: 1196
Period size: 191 Copynumber: 3.7 Consensus size: 184
1307467 CTTTCAACAT
**
1307477 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1307542 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
1307607 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1307661 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1307726 GGTCTACAACCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTG
66 GG--T-----CTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTG
1307791 GAAGAAAAATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
124 GAAGAAAAATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1307852 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1307917 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
1307982 ATTGTGTCGATATAATTTAAAAAAGTGTCGACA-TTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
1308035 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1308099 GGTCTACAACCTATATCGACACTTTTTAATA-T-TGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
1308152 CCATTTAAAA
Statistics
Matches: 477, Mismatches: 7, Indels: 18
0.95 0.01 0.04
Matches are distributed among these distances:
180 21 0.04
181 1 0.00
182 54 0.11
183 59 0.12
184 158 0.33
186 1 0.00
189 1 0.00
191 182 0.38
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:1310724 original size:23 final size:23
Alignment explanation
Indices: 1310693--1310755 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1310683 ATAGGTAAAC
*
1310693 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1310716 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1310739 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1310756 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1310763 original size:23 final size:23
Alignment explanation
Indices: 1310693--1310765 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1310683 ATAGGTAAAC
* * **
1310693 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1310716 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1310739 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1310762 ATAT
1 ATAT
1310766 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1311148 original size:23 final size:23
Alignment explanation
Indices: 1311117--1311179 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1311107 ATAGGTAAAC
*
1311117 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1311140 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1311163 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1311180 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1311187 original size:23 final size:23
Alignment explanation
Indices: 1311117--1311189 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1311107 ATAGGTAAAC
* * **
1311117 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1311140 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1311163 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1311186 ATAT
1 ATAT
1311190 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1318179 original size:2 final size:2
Alignment explanation
Indices: 1318172--1318274 Score: 190
Period size: 2 Copynumber: 52.0 Consensus size: 2
1318162 ATCTCATACG
*
1318172 TC TC TC TC TC TC TA TC TC TC TC TC TC TC T- TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1318213 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1318255 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
1318275 CCTCACTCAC
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 97 0.99
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1325278 original size:2 final size:2
Alignment explanation
Indices: 1325271--1325295 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1325261 AAGATCTTTG
1325271 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1325296 AATGAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1326474 original size:23 final size:23
Alignment explanation
Indices: 1326448--1326507 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
1326438 AATCTTATAT
1326448 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
1326471 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
1326494 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1326508 TTTATATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1335072 original size:3 final size:3
Alignment explanation
Indices: 1335064--1335101 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1335054 TTTTAATTTT
1335064 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
1335102 AACACGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1344393 original size:2 final size:2
Alignment explanation
Indices: 1344386--1344414 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1344376 AATACACGTG
1344386 TA TA 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 TA TA T
1344415 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1349084 original size:2 final size:2
Alignment explanation
Indices: 1349079--1349289 Score: 107
Period size: 2 Copynumber: 105.5 Consensus size: 2
1349069 TTGAAATAAT
* * *
1349079 TA TA TA TA -A TA TA TA TA TA TA CA TA TA TG TA AA CT- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
1349119 TA -A TA TA TA TG TA TA AA CTA TG TA TA AA T- TA TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
1349161 TT TA TA TA GTA TG TA TA AA T- TA TA CTA TA TA TA AA CTA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* *
1349203 TA TA TA AA TA TA AA TA TA TA -A TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1349243 TA TA TA CCA TG TA GTT TA TA TT TA TA CTA TA TA TA AA T- TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
1349285 TA TA T
1 TA TA T
1349290 TATGTATAAA
Statistics
Matches: 153, Mismatches: 38, Indels: 36
0.67 0.17 0.16
Matches are distributed among these distances:
1 9 0.06
2 133 0.87
3 11 0.07
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1349227 original size:36 final size:34
Alignment explanation
Indices: 1349080--1349248 Score: 98
Period size: 33 Copynumber: 4.8 Consensus size: 34
1349070 TGAAATAATT
1349080 ATATATAATATATATATATACATATATGTAAACTTATA-
1 ATATATAATATATATATATA-A-ATA--TAAA-TTATAC
* * **
1349118 ATA-ATATATATGTATAAACTATGTATAAATTAT--
1 ATATATA-ATATATATATA-TAAATATAAATTATAC
* * **
1349151 ATAGT-TTATATTTATATAGTATGTATAAATTATAC
1 ATA-TATAATATATATATA-TAAATATAAATTATAC
1349186 TATATATAAACTATATATATATAAATATAAATATATA-
1 -ATATAT-AA-TATATATATATAAATATAAAT-TATAC
*
1349223 ATATATAATATATATATATATATATA
1 ATATATAATATATATATATAAATATA
1349249 CCATGTAGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
33 26 0.24
34 22 0.21
35 7 0.07
36 10 0.09
37 15 0.14
38 25 0.23
39 2 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (34 bp):
ATATATAATATATATATATAAATATAAATTATAC
Found at i:1349297 original size:9 final size:9
Alignment explanation
Indices: 1349077--1349297 Score: 58
Period size: 9 Copynumber: 26.1 Consensus size: 9
1349067 AATTGAAATA
1349077 ATTATATAT
1 ATTATATAT
*
1349086 AATATATAT
1 ATTATATAT
*
1349095 A-TATACAT
1 ATTATATAT
* *
1349103 A-TATGTAA
1 ATTATATAT
1349111 ACTTATA-AT
1 A-TTATATAT
1349120 A--ATATAT
1 ATTATATAT
*
1349127 ATGTATAAACT
1 AT-TATATA-T
1349138 ATGTATA-A-
1 AT-TATATAT
1349146 ATTATATA-
1 ATTATATAT
*
1349154 GTT-TATAT
1 ATTATATAT
1349162 -TTATATAGT
1 ATTATATA-T
1349171 ATGTATA-A-
1 AT-TATATAT
1349179 ATTATACTAT
1 ATTATA-TAT
1349189 A-TATA-A-
1 ATTATATAT
*
1349195 ACTATATAT
1 ATTATATAT
*
1349204 A-TATAAAT
1 ATTATATAT
*
1349212 A-TAAATAT
1 ATTATATAT
*
1349220 ATAATATAT
1 ATTATATAT
*
1349229 AATATATAT
1 ATTATATAT
1349238 A-TATATAT
1 ATTATATAT
* *
1349246 A-TACCATGT
1 ATTA-TATAT
1349255 AGTT-TATAT
1 A-TTATATAT
1349264 -TTATACTAT
1 ATTATA-TAT
1349273 A-TATA-A-
1 ATTATATAT
1349279 ATTATATAT
1 ATTATATAT
*
1349288 ATTATGTAT
1 ATTATATAT
1349297 A
1 A
1349298 AACTAGTTAA
Statistics
Matches: 162, Mismatches: 21, Indels: 58
0.67 0.09 0.24
Matches are distributed among these distances:
6 5 0.03
7 29 0.18
8 50 0.31
9 54 0.33
10 11 0.07
11 13 0.08
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (9 bp):
ATTATATAT
Found at i:1356010 original size:16 final size:17
Alignment explanation
Indices: 1355960--1356011 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1355950 ATTAAAAATA
1355960 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1355977 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
1355992 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1356008 AATT
1 AATT
1356012 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1357335 original size:29 final size:29
Alignment explanation
Indices: 1357281--1357348 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
1357271 GTGTTTATAA
* *
1357281 ATTTTATAACAGATGAATCAATTTTA-TT
1 ATTTTATAATAGATGAACCAATTTTATTT
1357309 ATTTTATAATATGCATGAACCAA-TTTATTT
1 ATTTTATAATA-G-ATGAACCAATTTTATTT
1357339 ATTTT-TAATA
1 ATTTTATAATA
1357349 AGATCACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 10 0.29
29 10 0.29
30 15 0.43
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (29 bp):
ATTTTATAATAGATGAACCAATTTTATTT
Found at i:1361577 original size:21 final size:19
Alignment explanation
Indices: 1361551--1361598 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1361541 AACACAGAAG
1361551 TCAAATTCGCAATACTGAATT
1 TCAAATTCG-AA-ACTGAATT
* *
1361572 TCAAATTCGTAACTTAATT
1 TCAAATTCGAAACTGAATT
1361591 TCAAATTC
1 TCAAATTC
1361599 ACAACTCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
21 9 0.36
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (19 bp):
TCAAATTCGAAACTGAATT
Found at i:1361604 original size:19 final size:19
Alignment explanation
Indices: 1361568--1361604 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1361558 CGCAATACTG
**
1361568 AATTTCAAATTCGTAACTT
1 AATTTCAAATTCACAACTT
1361587 AATTTCAAATTCACAACT
1 AATTTCAAATTCACAACT
1361605 CGATTTTTGA
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:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTCAAATTCACAACTT
Found at i:1361610 original size:19 final size:19
Alignment explanation
Indices: 1361568--1361610 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1361558 CGCAATACTG
** *
1361568 AATTTCAAATTCGTAACTT
1 AATTTCAAATTCACAACTC
1361587 AATTTCAAATTCACAACTC
1 AATTTCAAATTCACAACTC
*
1361606 GATTT
1 AATTT
1361611 TTGAATTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (19 bp):
AATTTCAAATTCACAACTC
Found at i:1361643 original size:19 final size:19
Alignment explanation
Indices: 1361614--1361662 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
1361604 TCGATTTTTG
1361614 AATTT-GCAACACGAATTT
1 AATTTCGCAACACGAATTT
**
1361632 AATTTCGCAACA-GGTTTT
1 AATTTCGCAACACGAATTT
*
1361650 AGTTTCGCAACAC
1 AATTTCGCAACAC
1361663 AAATGTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (19 bp):
AATTTCGCAACACGAATTT
Found at i:1362448 original size:12 final size:12
Alignment explanation
Indices: 1362427--1362460 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1362417 ACCACATTTC
*
1362427 CAATACCAAACA
1 CAATATCAAACA
1362439 CAATATCAAACA
1 CAATATCAAACA
*
1362451 CAATCTCAAA
1 CAATATCAAA
1362461 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1365219 original size:34 final size:34
Alignment explanation
Indices: 1365173--1365241 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1365163 TGTTGCGATT
* *
1365173 GTTGCGAAAGTCAAATTTG-AATTGCGATTTTCGC
1 GTTGCGAAAGTCAAATTCGCAA-CGCGATTTTCGC
*
1365207 GTTGCGATAGTCAAATTCGCAACGCGATTTTCGC
1 GTTGCGAAAGTCAAATTCGCAACGCGATTTTCGC
1365241 G
1 G
1365242 ATACAATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (34 bp):
GTTGCGAAAGTCAAATTCGCAACGCGATTTTCGC
Found at i:1365459 original size:64 final size:64
Alignment explanation
Indices: 1365380--1365537 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
1365370 TGAATTTAAC
1365380 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
* * *
1365444 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTTTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
1365508 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
1365538 ATTCAATTAA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 86 0.96
65 4 0.04
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:1366913 original size:21 final size:21
Alignment explanation
Indices: 1366887--1367004 Score: 125
Period size: 21 Copynumber: 5.6 Consensus size: 21
1366877 ATGAATCGAA
* *
1366887 CTCTTGAACGGTGGAAGGGAC
1 CTCTTGAACGATGGAAGGGGC
*
1366908 CTCTTGAATGAT-GACAGGGGC
1 CTCTTGAACGATGGA-AGGGGC
* *
1366929 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGAAGGGGC
1366950 CTCTTGAACGAT-GAGAGGGGC
1 CTCTTGAACGATGGA-AGGGGC
**
1366971 CTCTTGAACGATAGG-AGGCAC
1 CTCTTGAACGAT-GGAAGGGGC
1366992 CTCTTGAACGATG
1 CTCTTGAACGATG
1367005 ACAGGTGAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
20 4 0.05
21 76 0.93
22 1 0.01
23 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGAAGGGGC
Found at i:1366953 original size:42 final size:42
Alignment explanation
Indices: 1366887--1367009 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
1366877 ATGAATCGAA
* *
1366887 CTCTTGAACGGTGGAAGGGACCTCTTGAATGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
* *
1366929 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
* * *
1366971 CTCTTGAACGATAGGAGGCACCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGG
1367010 TGAATCGGGC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:1369616 original size:22 final size:22
Alignment explanation
Indices: 1369587--1369644 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1369577 GATAGAGATA
1369587 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
1369609 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1369631 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1369645 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1369817 original size:20 final size:20
Alignment explanation
Indices: 1369792--1369837 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1369782 TAAACGCGCT
1369792 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
1369812 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
1369832 TTGCGA
1 TTGCGA
1369838 TTTACATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:1369874 original size:20 final size:20
Alignment explanation
Indices: 1369808--1369878 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
1369798 ATTTGACTTC
**
1369808 TGTGTTGCGAATTT-GACTT
1 TGTGTTGCGAATTTAGAAAT
* *
1369827 CTGTGTTGCG-ATTTACATAT
1 -TGTGTTGCGAATTTAGAAAT
*
1369847 TCGCGTTGCGAATTTAGAAAT
1 T-GTGTTGCGAATTTAGAAAT
1369868 TGTGTTGCGAA
1 TGTGTTGCGAA
1369879 AATGGAGTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.12
20 27 0.66
21 9 0.22
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (20 bp):
TGTGTTGCGAATTTAGAAAT
Found at i:1374271 original size:40 final size:41
Alignment explanation
Indices: 1374200--1374290 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 41
1374190 CAAAGCGATC
* **
1374200 TCAAATTTCGCATCGCGAATTTGTAAATCGCAACACAGAA-G
1 TCAAA-TTCGCAACGCGAATTTCCAAATCGCAACACAGAATG
* * *
1374241 TCAAATTCGCAACGCG-ATTTCCAAATTCGCAATACTGAATT
1 TCAAATTCGCAACGCGAATTTCCAAA-TCGCAACACAGAATG
1374282 TCAAATTCG
1 TCAAATTCG
1374291 TAACTAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 7 0.17
40 21 0.50
41 14 0.33
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (41 bp):
TCAAATTCGCAACGCGAATTTCCAAATCGCAACACAGAATG
Found at i:1374320 original size:19 final size:19
Alignment explanation
Indices: 1374241--1374320 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
1374231 AACACAGAAG
*
1374241 TCAAATTCGCAACGCGATT
1 TCAAATTCGCAACTCGATT
1374260 TCCAAATTCGCAA-TACTGAATT
1 T-CAAATTCGCAACT-C-G-ATT
* **
1374282 TCAAATTCGTAACTAAATT
1 TCAAATTCGCAACTCGATT
*
1374301 TCAAATTCACAACTCGATT
1 TCAAATTCGCAACTCGATT
1374320 T
1 T
1374321 TTGAATTTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
19 20 0.42
20 12 0.25
21 11 0.23
22 5 0.10
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTCGATT
Done.