Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold158
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: 3161772
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 138004 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:1283514 original size:7 final size:6
Alignment explanation
Indices: 1283492--1283565 Score: 62
Period size: 6 Copynumber: 12.0 Consensus size: 6
1283482 GGGCTCATCG
*** *
1283492 AGAAAGA AGAAAA AGAAAGA AG-AAA AGGGGA AGAAGAA AGAAGA A-AAAA
1 AGAAA-A AGAAAA AGAAA-A AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA
1283541 AGAAAA AGAAAA AGAAAAA AGAAAA
1 AGAAAA AGAAAA AG-AAAA AGAAAA
1283566 TAACTTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
5 7 0.13
6 29 0.53
7 19 0.35
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:1283549 original size:21 final size:21
Alignment explanation
Indices: 1283498--1283565 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
1283488 ATCGAGAAAG
*
1283498 AAGAAAAAGAAAGAAGAAAAG
1 AAGAAAAAGAAAGAAGAAAAA
** *
1283519 GGGAAGAAGAAAGAAGAAAAA
1 AAGAAAAAGAAAGAAGAAAAA
1283540 AAGAAAAAGAAA-AAG-AAAA
1 AAGAAAAAGAAAGAAGAAAAA
1283559 AAGAAAA
1 AAGAAAA
1283566 TAACTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 11 0.28
20 3 0.08
21 26 0.65
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
AAGAAAAAGAAAGAAGAAAAA
Found at i:1284249 original size:20 final size:20
Alignment explanation
Indices: 1284207--1284250 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1284197 GTAAATATTC
**
1284207 AAAAATTCTCGTGTTTTTTT
1 AAAAATTCTCGTGTTTTAAT
1284227 AAAAATTCTCGTGTTTTAAT
1 AAAAATTCTCGTGTTTTAAT
1284247 AAAA
1 AAAA
1284251 TCACGATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (20 bp):
AAAAATTCTCGTGTTTTAAT
Found at i:1284520 original size:35 final size:35
Alignment explanation
Indices: 1284407--1284814 Score: 268
Period size: 35 Copynumber: 11.5 Consensus size: 35
1284397 ATTTTCGTGC
*
1284407 TTTCGTGTTTTCAAAATTTTC-ATGTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
* * ***
1284441 CCTTT--TGTTTTCCAAAATTCCGGCATTTCAAAAAAAT
1 --TTTCGTGTTTTCAAAAATTTCGATGTTTC--AAAAAT
* *
1284478 TTTCGTGTTTTCAAGAATTTCGATGATTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
* * * *
1284513 TTCCGTGTTTTCAAGAATTTTC-ACGTTTTTATAAAAT
1 TTTCGTGTTTTCAA-AAATTTCGATG-TTTCA-AAAAT
* * *
1284550 TTTCGTGTTTTTAAAAAATTCCCG-TGTTTTAAAGATAAAT
1 TTTCGTG-TTTTCAAAAATT-TCGATG-TTT-CA-A-AAAT
* * *
1284590 TTTTGTGTTTTCGAAAATTTTC-TTGTTTCAAAAAT
1 TTTCGTGTTTTC-AAAAATTTCGATGTTTCAAAAAT
** * * *
1284625 CCTCTTGTTTTCAAAAATTCCGGTGTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
* *
1284660 CTTCGTGTTTTCAAAAATTTCGATGATTCAAAAAAT
1 TTTCGTGTTTTCAAAAATTTCGATGTTTC-AAAAAT
1284696 TTTCGTGTTTTCAAAAATTTCTCG-TGTTTCAAAAAT
1 TTTCGTGTTTTCAAAAA-TT-TCGATGTTTCAAAAAT
*
1284732 TTT--T-TTTTC-AAAATGTTCG-TGTTTTCAACAAT
1 TTTCGTGTTTTCAAAAAT-TTCGATG-TTTCAAAAAT
* * *
1284764 TCTCGTG-TTTCTAAAATTCTC-ATGTTTCCAAAAT
1 TTTCGTGTTTTCAAAAATT-TCGATGTTTCAAAAAT
*
1284798 TTTCGTGTTTTAAAAAA
1 TTTCGTGTTTTCAAAAA
1284815 AATTTGTTTC
Statistics
Matches: 292, Mismatches: 52, Indels: 57
0.73 0.13 0.14
Matches are distributed among these distances:
31 6 0.02
32 16 0.05
33 5 0.02
34 41 0.14
35 92 0.32
36 43 0.15
37 46 0.16
38 18 0.06
39 9 0.03
40 16 0.05
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (35 bp):
TTTCGTGTTTTCAAAAATTTCGATGTTTCAAAAAT
Found at i:1284531 original size:18 final size:18
Alignment explanation
Indices: 1284472--1284813 Score: 170
Period size: 18 Copynumber: 19.3 Consensus size: 18
1284462 GGCATTTCAA
*
1284472 AAAAATTTTCGTGTTTTC
1 AAAAATTTCCGTGTTTTC
* *
1284490 AAGAATTT-CGATG-ATTC
1 AAAAATTTCCG-TGTTTTC
1284507 AAAAATTTCCGTGTTTTC
1 AAAAATTTCCGTGTTTTC
*
1284525 AAGAATTTTCACGT-TTTT-
1 AA-AAATTTC-CGTGTTTTC
* *
1284543 ATAAAATTTTCGTGTTTTTA
1 A-AAAATTTCCGTG-TTTTC
* *
1284563 AAAAATTCCCGTGTTTTAA
1 AAAAATTTCCGTGTTTT-C
**
1284582 AGATAAATTTTTGTGTTTTC
1 A-A-AAATTTCCGTGTTTTC
* * *
1284602 GAAAATTTTCTTG-TTTC
1 AAAAATTTCCGTGTTTTC
* *
1284619 AAAAA-TCCTCTTGTTTTC
1 AAAAATTTC-CGTGTTTTC
1284637 AAAAA-TTCCG-GTGTTTC
1 AAAAATTTCCGTGT-TTTC
1284654 AAAAATCTT-CGTGTTTTC
1 AAAAAT-TTCCGTGTTTTC
*
1284672 AAAAATTT-CGATG-ATTC
1 AAAAATTTCCG-TGTTTTC
*
1284689 AAAAAATTTTCGTGTTTTC
1 -AAAAATTTCCGTGTTTTC
1284708 AAAAATTTCTCGTG-TTTC
1 AAAAATTTC-CGTGTTTTC
*
1284726 AAAAATTT---TTTTTTC
1 AAAAATTTCCGTGTTTTC
1284741 -AAAATGTT-CGTGTTTTC
1 AAAAAT-TTCCGTGTTTTC
*
1284758 AACAA-TTCTCGTG-TTTC
1 AAAAATTTC-CGTGTTTTC
* *
1284775 TAAAA-TTCTCATG-TTTC
1 AAAAATTTC-CGTGTTTTC
* *
1284792 CAAAATTTTCGTGTTTT-
1 AAAAATTTCCGTGTTTTC
1284809 AAAAA
1 AAAAA
1284814 AAATTTGTTT
Statistics
Matches: 258, Mismatches: 34, Indels: 65
0.72 0.10 0.18
Matches are distributed among these distances:
14 6 0.02
15 6 0.02
16 5 0.02
17 81 0.31
18 102 0.40
19 41 0.16
20 5 0.02
21 12 0.05
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
AAAAATTTCCGTGTTTTC
Found at i:1284550 original size:19 final size:19
Alignment explanation
Indices: 1284507--1284569 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
1284497 TCGATGATTC
*
1284507 AAAAA-TTTC-CGTGTTTTC
1 AAAAATTTTCACGT-TTTTA
*
1284525 AAGAATTTTCACGTTTTTA
1 AAAAATTTTCACGTTTTTA
* **
1284544 TAAAATTTTCGTGTTTTTA
1 AAAAATTTTCACGTTTTTA
1284563 AAAAATT
1 AAAAATT
1284570 CCCGTGTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 4 0.11
19 29 0.81
20 3 0.08
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (19 bp):
AAAAATTTTCACGTTTTTA
Found at i:1284575 original size:19 final size:19
Alignment explanation
Indices: 1284537--1284579 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1284527 GAATTTTCAC
* **
1284537 GTTTTTATAAAATTTTCGT
1 GTTTTTAAAAAATTCCCGT
1284556 GTTTTTAAAAAATTCCCGT
1 GTTTTTAAAAAATTCCCGT
1284575 GTTTT
1 GTTTT
1284580 AAAGATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (19 bp):
GTTTTTAAAAAATTCCCGT
Found at i:1284618 original size:17 final size:17
Alignment explanation
Indices: 1284586--1284813 Score: 178
Period size: 17 Copynumber: 13.2 Consensus size: 17
1284576 TTTTAAAGAT
* *
1284586 AAATTTTTGTGTTTTCGA
1 AAATTTTCGTG-TTTCAA
*
1284604 AAATTTTCTTGTTTCAA
1 AAATTTTCGTGTTTCAA
** *
1284621 AAATCCTCTTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
*
1284639 AAA-TTCCGGTGTTTCAA
1 AAATTTTC-GTGTTTCAA
*
1284656 AAATCTTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
*
1284674 AAA-TTTCGATGATTCAAA
1 AAATTTTCG-TGTTTC-AA
1284692 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
1284710 AAATTTCTCGTGTTTCAA
1 AAATTT-TCGTGTTTCAA
*
1284728 AAATTTT--TTTTTC-A
1 AAATTTTCGTGTTTCAA
*
1284742 AAATGTTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
* * *
1284760 CAATTCTCGTGTTTCTA
1 AAATTTTCGTGTTTCAA
* * *
1284777 AAATTCTCATGTTTCCA
1 AAATTTTCGTGTTTCAA
*
1284794 AAATTTTCGTGTTTTAA
1 AAATTTTCGTGTTTCAA
1284811 AAA
1 AAA
1284814 AAATTTGTTT
Statistics
Matches: 169, Mismatches: 28, Indels: 27
0.75 0.12 0.12
Matches are distributed among these distances:
14 7 0.04
15 5 0.03
16 1 0.01
17 74 0.44
18 69 0.41
19 13 0.08
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:1286539 original size:4 final size:4
Alignment explanation
Indices: 1286526--1286560 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1286516 GCATGACTGA
1286526 CATT CA-T CATT CATT CATT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT
1286561 GCATGTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
CATT
Found at i:1291701 original size:157 final size:156
Alignment explanation
Indices: 1291426--1291934 Score: 683
Period size: 157 Copynumber: 3.3 Consensus size: 156
1291416 TGTTTTTTGT
* *
1291426 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTTAC--GCTGAGGTA-TT-TTTCA
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTCTTTTA
* * * * *
1291487 A-TTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
66 AGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTG
1291551 AGGTATTTCTTTTAAATTTCT-ATTTTC
131 AGGTA-TT-TTTTAAATTTCTCATTTTC
*
1291578 AAAAATCAACTCATATTGTGAGAGGTGAGCTGAGCCTCGGGTCACATGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTCTTTTA
*
1291643 AGTTTCTGTTTTTAAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTG
66 AGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTG
* *
1291708 AGGTA-TTTTTCAATTTCTGTCTTTTTC
131 AGGTATTTTTTAAATTTC--TCATTTTC
* * * ** * *
1291735 AAAAATCAACTCATTTTGCT-AGAAGTGAGTTTAGTTTCGGGTCACATGCCGAGGCATTTCTTTT
1 AAAAATCAACTCATATTG-TGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTCTTTT
1291799 AAGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCT
65 AAGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCT
* * * * *
1291864 GATGTATTTTTCAATTTATGTCCTTTTC
130 GAGGTATTTTTTAAATT-TCTCATTTTC
* *
1291892 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTC
1291935 GCACGTTGAG
Statistics
Matches: 313, Mismatches: 32, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
152 43 0.14
154 19 0.06
155 3 0.01
156 6 0.02
157 233 0.74
158 8 0.03
159 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (156 bp):
AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCTGAGGTATTTCTTTTA
AGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTG
AGGTATTTTTTAAATTTCTCATTTTC
Found at i:1291708 original size:79 final size:76
Alignment explanation
Indices: 1291402--1291947 Score: 627
Period size: 78 Copynumber: 7.0 Consensus size: 76
1291392 TTTCACAAAT
*
1291402 TATTTTTCAATCTT-TGTTTTTTGTAAAAATCAACTCATATTG-TGAGAGGTGAGTTGAGCCTCG
1 TATTTTTCAAT-TTCTG-TTTTT-CAAAAATCAACTCATATTGCT-AGAGGTGAGTTGAGCCTCG
*
1291465 GGT--TACGCTGAGG
62 GGTCACACGCTGAGG
* *
1291478 TATTTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTC
* *
1291543 ACATGCCGAGG
66 ACACGCTGAGG
* * *
1291554 TATTTCTTTTAAATTTCT-ATTTTCAAAAATCAACTCATATTG-TGAGAGGTGAGCTGAGCCTCG
1 TA--T-TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCT-AGAGGTGAGTTGAGCCTCG
*
1291617 GGTCACATGCTGAGG
62 GGTCACACGCTGAGG
* * *
1291632 TATTTCTTTTAAGTTTCTGTTTTTAAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGG
1 TA-TT-TTTCAA-TTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGG
1291697 GTCACACGCTGAGG
63 GTCACACGCTGAGG
* * * **
1291711 TATTTTTCAATTTCTGTCTTTTTCAAAAATCAACTCATTTTGCTAGAAGTGAGTTTAGTTTCGGG
1 TATTTTTCAATTTCTG--TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGG
* *
1291776 TCACATGCCGAGG
64 TCACACGCTGAGG
* * *
1291789 CATTTCTTTTAAGTTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGG
1 TA-TT-TTTCAA-TTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGG
*
1291854 GTCACACGCTGATG
63 GTCACACGCTGAGG
* * *
1291868 TATTTTTCAATTTATGTCCTTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGT--TTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGG
* *
1291933 TCGCACGTTGAGG
64 TCACACGCTGAGG
1291946 TA
1 TA
1291948 NNNNNNNNNN
Statistics
Matches: 408, Mismatches: 43, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
74 40 0.10
75 6 0.01
76 35 0.09
77 17 0.04
78 176 0.43
79 122 0.30
80 6 0.01
81 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (76 bp):
TATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTC
ACACGCTGAGG
Found at i:1292207 original size:78 final size:76
Alignment explanation
Indices: 1292073--1292332 Score: 360
Period size: 78 Copynumber: 3.4 Consensus size: 76
1292063 NNNNNNAGTC
* *
1292073 GAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATGTTACGAGAGGTGAGTTGAGTCTCG
1 GAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
* *
1292138 AGTCACACGCT
66 GGTCGCACGCT
* *
1292149 GAGGTATTTTTCAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCT
1 GAGGTATTTTTCAATTTCTG-TTTTTC-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
*
1292214 CGGGTCGCATGCT
64 CGGGTCGCACGCT
*
1292227 GAGGTATTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTACGATAGGTGAGTTGAGCCT
1 GAGGTA-T-TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
*
1292292 CGGGTCGCACGCC
64 CGGGTCGCACGCT
* * * *
1292305 GAGTTA-TTCTCGATTTCTGCTTTTCAAA
1 GAGGTATTTTTCAATTTCTGTTTTTCAAA
1292333 TAAAAAGAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
75 19 0.12
76 20 0.12
77 6 0.04
78 99 0.60
79 7 0.04
80 13 0.08
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (76 bp):
GAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
GGTCGCACGCT
Found at i:1292555 original size:29 final size:29
Alignment explanation
Indices: 1292479--1292602 Score: 176
Period size: 29 Copynumber: 4.2 Consensus size: 29
1292469 AATTAATTAA
1292479 AAAATTACATTTTGACCCCTAAACTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTC
1292508 TAAAATTACATTTTGACCCCTAAACTTTTC
1 -AAAATTACATTTTGACCCCTAAACTTTTC
** *
1292538 AAAATTACATTTCAACCCCTTAACTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTC
* * *
1292567 TAAATTACATTTTGATCCCTACACTTTCTC
1 AAAATTACATTTTGACCCCTAAACTTT-TC
1292597 AAAATT
1 AAAATT
1292603 GCGTTTCTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 47 0.57
30 36 0.43
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAACTTTTC
Found at i:1292615 original size:59 final size:59
Alignment explanation
Indices: 1292479--1292602 Score: 187
Period size: 59 Copynumber: 2.1 Consensus size: 59
1292469 AATTAATTAA
**
1292479 AAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTTC
1 AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTTC
* * *
1292538 AAAATTACATTTCAACCCCTTAACTTTTCT-AAATTACATTTTGATCCCTACACTTTCTC
1 AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTT-TC
1292597 AAAATT
1 AAAATT
1292603 GCGTTTCTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 24 0.41
59 35 0.59
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTCAACCCCTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTTC
Found at i:1292979 original size:17 final size:18
Alignment explanation
Indices: 1292954--1293000 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1292944 ACAAAAAAAT
*
1292954 AAAAA-AAAAGCA-AGCA
1 AAAAAGAAAAGAATAGCA
1292970 AAAAAGAAAA-AATAGCA
1 AAAAAGAAAAGAATAGCA
1292987 AAGAAAGAAAAGAA
1 AA-AAAGAAAAGAA
1293001 AAAGAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.23
17 10 0.38
18 8 0.31
19 2 0.08
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAATAGCA
Found at i:1292979 original size:21 final size:23
Alignment explanation
Indices: 1292955--1293013 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
1292945 CAAAAAAATA
*
1292955 AAAAAAAAGC-AAGCAA-AAAAG
1 AAAAAAAAGCAAAGAAAGAAAAG
*
1292976 AAAAAATAGCAAAGAAAGAAAAG
1 AAAAAAAAGCAAAGAAAGAAAAG
* *
1292999 AAAAAGAAGAAAAGA
1 AAAAAAAAGCAAAGA
1293014 GGGGAGAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 9 0.29
22 5 0.16
23 17 0.55
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAAAAAGCAAAGAAAGAAAAG
Found at i:1293106 original size:7 final size:7
Alignment explanation
Indices: 1293096--1293185 Score: 58
Period size: 7 Copynumber: 12.4 Consensus size: 7
1293086 GGGAAAGAAG
1293096 AAAAAGA
1 AAAAAGA
1293103 AAAAAGA
1 AAAAAGA
* *
1293110 AGAGAGA
1 AAAAAGA
1293117 AAGAAAGAA
1 AA-AAAG-A
1293126 GAAAAAGA
1 -AAAAAGA
1293134 AAGAAA-A
1 AA-AAAGA
** *
1293141 AAAGGGG
1 AAAAAGA
*
1293148 AAGAAGA
1 AAAAAGA
*
1293155 AAGAAGA
1 AAAAAGA
1293162 AAAAA-A
1 AAAAAGA
1293168 GAAAAAGA
1 -AAAAAGA
1293176 AAAAAGA
1 AAAAAGA
1293183 AAA
1 AAA
1293186 TAATTTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
6 2 0.03
7 47 0.73
8 8 0.12
9 5 0.08
10 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:1293125 original size:31 final size:34
Alignment explanation
Indices: 1293089--1293178 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 34
1293079 GCTGATCGGG
*
1293089 AAAGAAGAAAAAGAAAAAAGAAGA-GAG-A-AAG
1 AAAGAAGAAAAAGAAAAAAGAAAAGGAGAAGAAG
*
1293120 AAAGAAGAAAAAGAAAGAAA-AAAAGGGGAAGAAG
1 AAAGAAGAAAAAGAAA-AAAGAAAAGGAGAAGAAG
*
1293154 AAAGAAGAAAAAAAGAAAAAGAAAA
1 AAAGAAGAAAAAGA-AAAAAGAAAA
1293179 AAGAAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
31 19 0.38
32 5 0.10
33 1 0.02
34 19 0.38
35 6 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (34 bp):
AAAGAAGAAAAAGAAAAAAGAAAAGGAGAAGAAG
Found at i:1293138 original size:21 final size:21
Alignment explanation
Indices: 1293088--1293184 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
1293078 GGCTGATCGG
* *
1293088 GAAAGAAGAAAAAGAAAAAAGAA
1 GAAAGAA-AGAAAGAAGAAA-AA
*
1293111 GAGAGAAAGAAAGAAGAAAAA
1 GAAAGAAAGAAAGAAGAAAAA
* ** *
1293132 GAAAGAAAAAAAGGGGAAGAA
1 GAAAGAAAGAAAGAAGAAAAA
*
1293153 GAAAG-AAGAAAAAAAGAAAAA
1 GAAAGAAAG-AAAGAAGAAAAA
1293174 GAAA-AAAGAAA
1 GAAAGAAAGAAA
1293185 ATAATTTTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 5 0.08
21 38 0.64
22 10 0.17
23 6 0.10
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAGAAAAA
Found at i:1293152 original size:42 final size:42
Alignment explanation
Indices: 1293106--1293185 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
1293096 AAAAAGAAAA
* *
1293106 AAGAAGAGAGAA-AGAAAGAAGAAAAAGAAAGAAA-AAAAGGGG
1 AAGAAGAAAGAAGA-AAAAAAGAAAAAGAAA-AAAGAAAAGGGG
1293148 AAGAAGAAAGAAGAAAAAAAGAAAAAGAAAAAAGAAAA
1 AAGAAGAAAGAAGAAAAAAAGAAAAAGAAAAAAGAAAA
1293186 TAATTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 3 0.09
42 30 0.88
43 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (42 bp):
AAGAAGAAAGAAGAAAAAAAGAAAAAGAAAAAAGAAAAGGGG
Found at i:1293181 original size:24 final size:24
Alignment explanation
Indices: 1293093--1293183 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
1293083 ATCGGGAAAG
* *
1293093 AAGAAAAAGAAAAAAGAAGAGAGA
1 AAGAAAAAGAAAAAAGAAGAAAAA
1293117 AAGAAAGAAG-AAAAAGAAAGAAAAA
1 AAGAAA-AAGAAAAAAG-AAGAAAAA
*** *
1293142 AAGGGGAAGAAGAAAGAAGAAAAA
1 AAGAAAAAGAAAAAAGAAGAAAAA
1293166 AAGAAAAAGAAAAAAGAA
1 AAGAAAAAGAAAAAAGAA
1293184 AATAATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 37 0.69
25 17 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (24 bp):
AAGAAAAAGAAAAAAGAAGAAAAA
Found at i:1293183 original size:31 final size:31
Alignment explanation
Indices: 1293088--1293183 Score: 97
Period size: 34 Copynumber: 3.0 Consensus size: 31
1293078 GGCTGATCGG
* *
1293088 GAAAGAAGAAAAAGA-AAAAAGAAGAGAGAAA
1 GAAAGAAGAAAAAAAGAAAAAGAAGAAAG-AA
*
1293119 GAAAGAAGAAAAAGAAAGAAAAA-AAGGGGAAGAA
1 GAAAGAAG-AAAA-AAAGAAAAAGAA--GAAAGAA
*
1293153 GAAAGAAGAAAAAAAGAAAAAGAAAAAAGAA
1 GAAAGAAGAAAAAAAGAAAAAGAAGAAAGAA
1293184 AATAATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
31 13 0.24
32 13 0.24
33 10 0.19
34 15 0.28
35 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (31 bp):
GAAAGAAGAAAAAAAGAAAAAGAAGAAAGAA
Found at i:1293433 original size:10 final size:11
Alignment explanation
Indices: 1293418--1293454 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1293408 GAGGCAGGCC
1293418 AGAAAAAAA-A
1 AGAAAAAAAGA
1293428 AGAAAAAAAGA
1 AGAAAAAAAGA
*
1293439 AGAAAGAAAGA
1 AGAAAAAAAGA
1293450 A-AAAA
1 AGAAAA
1293455 TGTTCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 12 0.50
11 12 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:1294019 original size:35 final size:33
Alignment explanation
Indices: 1293972--1294092 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 33
1293962 CGTGCTTTCG
1293972 TGTTTTCAAAATTTTCA-TGTTTCAAAAATCCTTT
1 TGTTTTCAAAA-TTTCAGTGTTTCAAAAAT-CTTT
* * *
1294006 TGTTTTCCAAAATTCCAGCGTTTCAAAAATTTTTT
1 TGTTTT-CAAAATTTCAGTGTTTCAAAAA-TCTTT
*
1294041 GTGTTTTCAAGAATTTCAGTGATTCAAAAAAT-TTCT
1 -TGTTTTCAA-AATTTCAGTGTTTC-AAAAATCTT-T
1294077 ATGTTTTCAAGAATTT
1 -TGTTTTCAA-AATTT
1294093 TCACGTTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
34 10 0.14
35 23 0.32
36 35 0.48
37 5 0.07
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (33 bp):
TGTTTTCAAAATTTCAGTGTTTCAAAAATCTTT
Found at i:1294050 original size:19 final size:18
Alignment explanation
Indices: 1294026--1294364 Score: 214
Period size: 18 Copynumber: 18.5 Consensus size: 18
1294016 AATTCCAGCG
*
1294026 TTTCAAAAATTTTTTGTGT
1 TTTCAAAAA-TTTTCGTGT
*
1294045 TTTCAAGAA-TTTCAGTG-
1 TTTCAAAAATTTTC-GTGT
* * *
1294062 ATTCAAAAAATTTCTATGT
1 TTTCAAAAATTTTC-GTGT
* *
1294081 TTTCAAGAATTTTCACGTTT
1 TTTCAAAAATTTT--CGTGT
* *
1294101 TTTTATAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
1294119 TTTTAAAAAATTCCGGTGTT
1 TTTCAAAAATTTTC-GTG-T
*
1294139 TTTAAAGATAAATTTTCGTGT
1 TTT-CA-A-AAATTTTCGTGT
*
1294160 TTTCAAAAATTTTCTTGT
1 TTTCAAAAATTTTCGTGT
** *
1294178 TTT-AAAAATCCTCCTGT
1 TTTCAAAAATTTTCGTGT
*
1294195 TTTCAAAAA-TTCCG-GT
1 TTTCAAAAATTTTCGTGT
*
1294211 GTTTCAAAAATCTTCGTGT
1 -TTTCAAAAATTTTCGTGT
1294230 TTTCAAAAA-TTTCG-GT
1 TTTCAAAAATTTTCGTGT
*
1294246 GATTCAAAAAATTTTCGTGT
1 -TTTC-AAAAATTTTCGTGT
1294266 TTTCAAAAATTTCTCGTG-
1 TTTCAAAAATTT-TCGTGT
* *
1294284 TTTCAAAAATTTTCTTTTTTT
1 TTTCAAAAATTTTC---GTGT
*
1294305 TTTC-AAAATGTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
1294322 TTTCAACAATTCTCGTG-
1 TTTCAAAAATTTTCGTGT
*
1294339 TTTCAAAAATTTCCGTGT
1 TTTCAAAAATTTTCGTGT
1294357 TTT-AAAAA
1 TTTCAAAAA
1294365 AAATTTGCTT
Statistics
Matches: 249, Mismatches: 46, Indels: 52
0.72 0.13 0.15
Matches are distributed among these distances:
16 4 0.02
17 68 0.27
18 92 0.37
19 37 0.15
20 28 0.11
21 10 0.04
22 4 0.02
23 6 0.02
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:1294356 original size:35 final size:36
Alignment explanation
Indices: 1293969--1294365 Score: 212
Period size: 35 Copynumber: 10.9 Consensus size: 36
1293959 TTTCGTGCTT
* * *
1293969 TCGTGTTTTC-AAAATTTTCATG-TTTCAAAAATCC
1 TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTC
** * * *
1294003 TTTTGTTTTCCAAAA-TTCCAGCG-TTTCAAAAATTTT
1 TCGTGTTTTCAAAAATTTCC-GTGTTTTCAAAAA-TTC
* * * *
1294039 TTGTGTTTTCAAGAATTTCAGTG-ATTCAAAAAATT-
1 TCGTGTTTTCAAAAATTTCCGTGTTTTC-AAAAATTC
* * * * * *
1294074 TCTATGTTTTCAAGAATTTTCACGTTTTTTTATAAATTT
1 TC-GTGTTTTCAA-AAATTTC-CGTGTTTTCAAAAATTC
* * * *
1294113 TCGTGTTTTTAAAAAATTCCGGTGTTTTTAAAGATAAATTT
1 TCGTGTTTTCAAAAATTTCC-GTG-TTTT-CA-A-AAATTC
* * *
1294154 TCGTGTTTTCAAAAATTTTCTTGTTTT-AAAAATCC
1 TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTC
*
1294189 TCCTGTTTTCAAAAA-TTCCG-GTGTTTCAAAAA-TC
1 TCGTGTTTTCAAAAATTTCCGTGT-TTTCAAAAATTC
* * *
1294223 TTCGTGTTTTCAAAAATTTCGGTG-ATTCAAAAAATTT
1 -TCGTGTTTTCAAAAATTTCCGTGTTTTC-AAAAATTC
1294260 TCGTGTTTTCAAAAATTTCTCGTG-TTTCAAAAATTTTC
1 TCGTGTTTTCAAAAATTTC-CGTGTTTTCAAAAA--TTC
** * *
1294298 TTTTTTTTTTC-AAAATGTT-CGTGTTTTCAACAATTC
1 -TCGTGTTTTCAAAAAT-TTCCGTGTTTTCAAAAATTC
*
1294334 TCGTG-TTTCAAAAATTTCCGTGTTTTAAAAAA
1 TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAA
1294366 AATTTGCTTC
Statistics
Matches: 278, Mismatches: 55, Indels: 59
0.71 0.14 0.15
Matches are distributed among these distances:
33 2 0.01
34 24 0.09
35 74 0.27
36 67 0.24
37 33 0.12
38 35 0.13
39 18 0.06
40 2 0.01
41 23 0.08
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (36 bp):
TCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTC
Found at i:1296400 original size:44 final size:44
Alignment explanation
Indices: 1296339--1296803 Score: 321
Period size: 44 Copynumber: 10.7 Consensus size: 44
1296329 AGATGGCAAA
* * * *
1296339 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCAATAAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-TAACAAG
* *
1296384 TC-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAAG
* *
1296427 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGAA-AACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATAACAAG
* * * *** *
1296472 TCTTATC-CCCTGAAGTTGTAGTAGG-GCAGACTGAAGATGGTAAA
1 TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGA-TTAAAATAACAAG
* ** *
1296516 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATAACAAG
* * * *
1296560 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAAG
* *
1296604 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA-AGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATAACAAG
** * * * * * *
1296649 TCTTATC-CTTTGAAGTTGTAGTGGGGCAAACTGAAGATGACGAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATAAC-AAG
* * * *
1296693 TCTTGTCTCCCTGAAGTTGCAGT-G-G-AG---AAAGTGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAAG
* * * **
1296731 TCTTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATGA-TTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAAG
** *
1296774 ATCTTATCTCTTTGAAGTTGCAGTAGAGCA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCA
1296804 AATCGCATCA
Statistics
Matches: 336, Mismatches: 62, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
37 2 0.01
38 28 0.08
39 1 0.00
40 1 0.00
41 1 0.00
42 1 0.00
43 11 0.03
44 221 0.66
45 68 0.20
46 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAAG
Found at i:1296531 original size:133 final size:132
Alignment explanation
Indices: 1296339--1296905 Score: 384
Period size: 133 Copynumber: 4.3 Consensus size: 132
1296329 AGATGGCAAA
* * * *
1296339 TCTTATCTCCCTGAAGTTGCAGTGGAACAGA-T-TA-AAACCAATAAT-TCTATCTCCCTGAAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGC-A-AATCT-TATCTCTCTGAAGT
* *
1296400 TGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGA
63 TGCAGTGGAGCAGATTAAAGTCACAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAA-A
1296465 -AAACAAG
125 TAAACAAG
* ** *
1296472 TCTTATC-CCCTGAAGTTGTAGTAGG-GCAGACTGAAGATGGTAAATCTTATCTCTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGACTGAAGAAAGCAAATCTTATCTCTCTGAAGTTG
* * * * * **
1296535 CAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATTTA
65 CAGTGGAGCAGATTAAAGTC-ACAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAATAAA
1296600 CAAG
129 CAAG
* * *
1296604 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATC-CTTTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAATCTTATCTCTCTGAAGTTGC
* * * * * * * *
1296668 AGTGGGGCAAACTGAAGATGACGAATCTTGTCTCCCTGAAGTTGCAGT-G-G-AGA--AAGT-GA
66 AGTGGAGCAGATTAAAG-TCAC-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAATAAA
*
1296727 CAAA
129 CAAG
* * * * * *
1296731 TCTTATCTCCCTGAAGTTGCAGTAGAGCGGA-TTAA-AATG-ATTGATCTTATCTCTTTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA--AATCTTATCTCTCTGAAGTT
* * *** * * ** * * * * * **
1296793 GCAGTAGAGCAAATCGCA-TCAGACT-TTAT-TTTCTCGAAATTACAGTGAAACA-AGTGGAAGC
64 GCAGTGGAGCAGATTAAAGTCACAATCTTATCTCCCT-GAAGTTGCAGTGGAGCAGA-TGAAATA
*
1296854 TACAAG
127 AACAAG
*
1296860 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAAT
1296906 GTTAACTTGA
Statistics
Matches: 339, Mismatches: 70, Indels: 53
0.73 0.15 0.11
Matches are distributed among these distances:
122 3 0.01
123 12 0.04
124 3 0.01
125 6 0.02
126 11 0.03
127 55 0.16
128 4 0.01
129 33 0.10
130 7 0.02
131 4 0.01
132 61 0.18
133 133 0.39
134 6 0.02
135 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (132 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAATCTTATCTCTCTGAAGTTGC
AGTGGAGCAGATTAAAGTCACAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAATAAACA
AG
Found at i:1296623 original size:177 final size:177
Alignment explanation
Indices: 1296327--1296766 Score: 649
Period size: 177 Copynumber: 2.5 Consensus size: 177
1296317 ATGGATTGAA
* * *
1296327 GAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCAATAATTCTATCTC
1 GAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
*
1296392 CCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAG
66 CCTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAG
*
1296457 ACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAGACT
131 ACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAAACT
* *
1296504 GAAGATGGTAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
1 GAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
* *
1296569 CCTGAAGTTGCAGTGGAGCGGATTAAATTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
66 CCTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAG
* ** *
1296634 ACTGAAGAAAGCAAGTCTTATCCTTTGAAGTTGTAGTGGGGCAAACT
131 ACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAAACT
* * * ** * *
1296681 GAAGATGACGAATCTTGTCTCCCTGAAGTTGCAGTGGAG-A-A--AGTGAC-A-AATCTTATCTC
1 GAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
*
1296740 CCTGAAGTTGCAGTAGAGCGGATTAAA
66 CCTGAAGTTGCAGTGGAGCGGATTAAA
1296767 ATGATTGATC
Statistics
Matches: 240, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
171 36 0.15
172 1 0.00
173 3 0.01
175 1 0.00
176 1 0.00
177 198 0.82
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (177 bp):
GAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
CCTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAG
ACTGAAGAAAACAAGTCTTATCCCCTGAAGTTGTAGTAGGGCAAACT
Found at i:1298262 original size:12 final size:12
Alignment explanation
Indices: 1298247--1298284 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1298237 TTATTTTTTA
1298247 TTTATTAATTAT
1 TTTATTAATTAT
1298259 TTTATTAAATTAT
1 TTTATT-AATTAT
1298272 TATTATT-ATTAT
1 T-TTATTAATTAT
1298284 T
1 T
1298285 GCCATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.50
13 7 0.29
14 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATTAATTAT
Found at i:1305814 original size:25 final size:27
Alignment explanation
Indices: 1305742--1305821 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 27
1305732 ATAAATCTTA
1305742 AAATTATATATAATTTT-AGTTTAGTATGT
1 AAATTATATATAATTTTGA-TTT-G-ATGT
*
1305771 AAATTATACATGAATTTTGATTTGA-GT
1 AAATTATATAT-AATTTTGATTTGATGT
1305798 -AATTATATATAATTTTGATTTGAT
1 AAATTATATATAATTTTGATTTGAT
1305822 TCAATTCTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
25 13 0.28
26 9 0.20
27 2 0.04
28 1 0.02
29 11 0.24
30 9 0.20
31 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.50
Consensus pattern (27 bp):
AAATTATATATAATTTTGATTTGATGT
Found at i:1307721 original size:50 final size:50
Alignment explanation
Indices: 1307662--1307841 Score: 184
Period size: 51 Copynumber: 3.6 Consensus size: 50
1307652 AAAGTGATGG
* *
1307662 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACT-AT-GA
* * * * * *
1307712 TCGCATGTGTAGTACTATGTGCAAGATACTATGCGTACCGGATACTTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACTAT-GA
** * * * *
1307763 TCATGTGTGTAGTACTATGTGCAGGGTACTACGTGTATCGGATAGTAATGT
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACT-ATGA
1307814 TCACATGTGTAGTACTATGTGCAGGCTA
1 TCACATGTGTAGTACTATGTGCAGGCTA
1307842 TTGTGTGAAC
Statistics
Matches: 104, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
50 36 0.35
51 66 0.63
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATACTATGA
Found at i:1307904 original size:45 final size:45
Alignment explanation
Indices: 1307855--1307940 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
1307845 TGTGAACCGA
* *
1307855 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCATCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCATCGG
1307900 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1307941 CTGAGTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCATCGG
Found at i:1313316 original size:2 final size:2
Alignment explanation
Indices: 1313309--1313338 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1313299 NNNNNNNNNN
*
1313309 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1313339 TTGTTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1314169 original size:7 final size:7
Alignment explanation
Indices: 1314157--1314185 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1314147 TTAAGGGTAA
1314157 ATTAGCC
1 ATTAGCC
1314164 ATTAGCC
1 ATTAGCC
1314171 ATTAGCC
1 ATTAGCC
1314178 ATTAGCC
1 ATTAGCC
1314185 A
1 A
1314186 ATAGGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (7 bp):
ATTAGCC
Found at i:1316428 original size:25 final size:25
Alignment explanation
Indices: 1316385--1316434 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1316375 AGCCAATGAG
*
1316385 GATTTTTTTTATATTTTC-GTTGTT
1 GATTTTTTTGATATTTTCGGTTGTT
*
1316409 GATTTTATTTGATGTTTTCGGTTGTT
1 GATTTT-TTTGATATTTTCGGTTGTT
1316435 AATCGAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 10 0.45
26 6 0.27
ACGTcount: A:0.12, C:0.04, G:0.18, T:0.66
Consensus pattern (25 bp):
GATTTTTTTGATATTTTCGGTTGTT
Found at i:1317399 original size:15 final size:15
Alignment explanation
Indices: 1317363--1317404 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1317353 TTTAATCGAG
1317363 TATATGTATTATTAT
1 TATATGTATTATTAT
*
1317378 TATTATGT-TTATCTTT
1 TA-TATGTATTAT-TAT
1317394 TATATGTATTA
1 TATATGTATTA
1317405 AGCTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (15 bp):
TATATGTATTATTAT
Found at i:1322235 original size:15 final size:14
Alignment explanation
Indices: 1322215--1322248 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1322205 GATCCTTTCA
*
1322215 AAAAAAATCAAAAT
1 AAAAAAATAAAAAT
1322229 CAAAAAAATAAAAAT
1 -AAAAAAATAAAAAT
1322244 AAAAA
1 AAAAA
1322249 TAAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:1324611 original size:44 final size:45
Alignment explanation
Indices: 1324559--1324771 Score: 116
Period size: 44 Copynumber: 4.6 Consensus size: 45
1324549 GATTGAAGCT
*
1324559 AGAAATCTTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAA
1 AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAA
* * * * *
1324604 AG-GATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATCACATCAGATTGAA
1 AGAAATCTTATCTCCCT-AAGATTACAGTGGAGCAGATTA-A--A-A-T-AA
* * **
1324654 GCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--
1 ---AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATT-AAAATAA
* * * **
1324701 AGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAA
1 AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAA
*
1324746 ATG--ATCTTATCTCTCTGAAG-TTACAG
1 A-GAAATCTTATCTCCCT-AAGATTACAG
1324772 CAGAGTAGAT
Statistics
Matches: 126, Mismatches: 25, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
43 3 0.02
44 76 0.60
45 9 0.07
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 3 0.02
53 4 0.03
54 26 0.21
55 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
AGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAA
Found at i:1324726 original size:98 final size:97
Alignment explanation
Indices: 1324547--1324733 Score: 234
Period size: 98 Copynumber: 1.9 Consensus size: 97
1324537 ATTTAAGCCA
* * * * *
1324547 CAGATTGAAGCTAGAAATCTTATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCT
*
1324612 ATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATCACAT
* **
1324645 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCC
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATT-AAAATAAG-AATCC
*
1324709 TATCTCCCTG-AGATTACAGTGGAGT
64 TATCTCCCTGAAG-TTACAGTAGAGT
1324734 GGATTAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
97 4 0.05
98 69 0.91
99 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (97 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTAAAATAAGAATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATCACAT
Found at i:1324888 original size:23 final size:23
Alignment explanation
Indices: 1324858--1324904 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1324848 TGGCGATGCA
1324858 GTGGAGCAGATTAAAGCCACATC
1 GTGGAGCAGATTAAAGCCACATC
1324881 GTGGAGCAGATTAAAGCCACATC
1 GTGGAGCAGATTAAAGCCACATC
1324904 G
1 G
1324905 GTAAATCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (23 bp):
GTGGAGCAGATTAAAGCCACATC
Found at i:1324971 original size:50 final size:49
Alignment explanation
Indices: 1324888--1325245 Score: 225
Period size: 50 Copynumber: 7.2 Consensus size: 49
1324878 ATCGTGGAGC
* * ** **
1324888 AGATTAAAGCCACATCGGTAAATCTCGCTTCCCTGACACTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACA-TGCAGTTAAAA
* * * * ** **
1324938 ATATTAAAGCTACAACAGCGAATCTTACCTCCCTGGCGATGCAGTGGAGT
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGAC-ATGCAGTTAAAA
* * * * * *
1324988 AGATTAAAGCCACATCGGTGAA-CTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACA-TGCAGTTAAAA
* * ** *
1325037 AGATTAAAGCCACAACAGCAAATCTTACCTCCCTGACGATGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGAC-ATGCAGTTAAAA
* * * * *
1325087 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACA-TGCAGTTAAAA
* * * * * * * ** *
1325137 GGATTAAAGCTACAATAGCGAATCTTACTTCCCAGGCGGTGTAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGAC-ATGCAGTTAAAA
* * * * *
1325187 AGATTGAAGCTACAACAGCGAATCTTGCTT-CCTCGACATCACAGTTAAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCT-GACAT-GCAGTTAAAA
1325237 AGATTAAAG
1 AGATTAAAG
1325246 TTGCGAGTTA
Statistics
Matches: 225, Mismatches: 75, Indels: 16
0.71 0.24 0.05
Matches are distributed among these distances:
48 1 0.00
49 38 0.17
50 184 0.82
51 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (49 bp):
AGATTAAAGCCACAACAGCGAATCTTACTTCCCTGACATGCAGTTAAAA
Found at i:1325183 original size:100 final size:100
Alignment explanation
Indices: 1324881--1325245 Score: 480
Period size: 100 Copynumber: 3.7 Consensus size: 100
1324871 AAGCCACATC
* * * * * *
1324881 GTGGAGCAGATTAAAGCCACATCGGTAAATCTCGCTTCCCTGACACTGCAGTTAAAAATATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
1324946 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
66 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
** *
1324981 GTGGAGTAGATTAAAGCCACATCGGTGAA-CTTGCTTCCCCGACATTGTAGTTAAAAAGATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
* * *
1325045 GCCACAACAGCAAATCTTACCTCCCTGACGATGCA
66 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
*
1325080 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAGGATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
* * * * *
1325145 GCTACAATAGCGAATCTTACTTCCCAGGCGGTGTA
66 GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
* * * * * * ** *
1325180 GTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCTCGACATCACAGTTAAACAGATTAAA
1 GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
1325245 G
66 G
1325246 TTGCGAGTTA
Statistics
Matches: 232, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 89 0.38
100 143 0.62
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (100 bp):
GTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAA
GCTACAACAGCGAATCTTACCTCCCTGGCGATGCA
Found at i:1326786 original size:15 final size:15
Alignment explanation
Indices: 1326750--1326791 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1326740 TTTAATCGAG
1326750 TATATGTATTATTAT
1 TATATGTATTATTAT
*
1326765 TATTATGT-TTATCTTT
1 TA-TATGTATTAT-TAT
1326781 TATATGTATTA
1 TATATGTATTA
1326792 AGCTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (15 bp):
TATATGTATTATTAT
Found at i:1326864 original size:11 final size:11
Alignment explanation
Indices: 1326850--1326902 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
1326840 ATTCAATGGT
1326850 TATTTTAATTC
1 TATTTTAATTC
* *
1326861 TATTTTGAGTC
1 TATTTTAATTC
1326872 TATTTTGAATTC
1 TATTTT-AATTC
1326884 ATATATTTAATT-
1 -TAT-TTTAATTC
1326896 TATTTTA
1 TATTTTA
1326903 GAACTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (11 bp):
TATTTTAATTC
Found at i:1332227 original size:43 final size:42
Alignment explanation
Indices: 1332176--1332327 Score: 168
Period size: 43 Copynumber: 3.6 Consensus size: 42
1332166 TGTGTTTTTG
* *
1332176 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TTGTGATTACA
* * * *
1332219 TGTAAGACCATGTCTGGGACATTGGCATTGTATT-TAATT-CA
1 TGTAAGACCACGTCTGGGACGTTGGCATCG-ATTGTGATTACA
1332260 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TGTGATTACA
*
1332303 TGTAAGAACACGTCTGGGACGTTGG
1 TGTAAGACCACGTCTGGGACGTTGG
1332328 TATTGTACGA
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
40 2 0.02
41 27 0.30
42 8 0.09
43 51 0.57
44 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATTGTGATTACA
Found at i:1332276 original size:41 final size:42
Alignment explanation
Indices: 1332214--1332334 Score: 129
Period size: 41 Copynumber: 2.9 Consensus size: 42
1332204 CGACTTGTGT
* * *
1332214 TTACGTGTAAGACCATGTCTGGGACATTGGCATTGTATTTAA
1 TTACATGTAAGACCCTGTCTGGGACATTGGCATTGTATGTAA
* * *
1332256 TT-CATGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGA
1 TTACATGTAAGACCCTGTCTGGGACATTGGCATTG-TATGTAA
* * *
1332298 TTACATGTAAGAACAC-GTCTGGGACGTTGGTATTGTA
1 TTACATGTAAG-ACCCTGTCTGGGACATTGGCATTGTA
1332335 CGAGCCTTCC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
41 28 0.43
42 11 0.17
43 23 0.35
44 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (42 bp):
TTACATGTAAGACCCTGTCTGGGACATTGGCATTGTATGTAA
Found at i:1332318 original size:84 final size:84
Alignment explanation
Indices: 1332176--1332334 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 84
1332166 TGTGTTTTTG
* * * *
1332176 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGAACACGTCTGGGACAT
1332241 TGGCATTGTATTTAATTCA
66 TGGCATTGTATTTAATTCA
1332260 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGAACACGTCTGGGA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGAACACGTCTGGGA
* *
1332322 CGTTGGTATTGTA
63 CATTGGCATTGTA
1332335 CGAGCCTTCC
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
83 2 0.03
84 63 0.95
85 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (84 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGAACACGTCTGGGACAT
TGGCATTGTATTTAATTCA
Found at i:1333304 original size:27 final size:28
Alignment explanation
Indices: 1333266--1333319 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
1333256 AAGAGTATGT
1333266 TATATGACTGTTTTGGTTGAT-TGCTTC
1 TATATGACTGTTTTGGTTGATATGCTTC
1333293 TATATGACTGTTTTGGTTGATATGCTT
1 TATATGACTGTTTTGGTTGATATGCTT
1333320 GCTTGAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.17, C:0.09, G:0.22, T:0.52
Consensus pattern (28 bp):
TATATGACTGTTTTGGTTGATATGCTTC
Found at i:1336824 original size:37 final size:39
Alignment explanation
Indices: 1336783--1336920 Score: 100
Period size: 40 Copynumber: 3.5 Consensus size: 39
1336773 TTATCTACAT
* *
1336783 TACTGGTGGTTTGTCCACA-T-TGGCAGTTTATCTGTAA
1 TACTGGTAGCTTGTCCACATTATGGCAGTTTATCTGTAA
* * *
1336820 TACTGGTAGCTTGTCTACATTACTGGCAGTTTATCTGCAT
1 TACTGGTAGCTTGTCCACATTA-TGGCAGTTTATCTGTAA
* * * * * * *
1336860 TATTGATGGCTTGTCCATATTACTGGCAGCTTGTCTGCAA
1 TACTGGTAGCTTGTCCACATTA-TGGCAGTTTATCTGTAA
** *
1336900 TTTTGGTAGTTTCGTCCACAT
1 TACTGGTAGCTT-GTCCACAT
1336921 ATATTGGAGT
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
37 16 0.20
38 1 0.01
40 55 0.70
41 7 0.09
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (39 bp):
TACTGGTAGCTTGTCCACATTATGGCAGTTTATCTGTAA
Found at i:1336845 original size:20 final size:20
Alignment explanation
Indices: 1336820--1336895 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
1336810 TTATCTGTAA
*
1336820 TACTGGTAGCTTGTCTACAT
1 TACTGGCAGCTTGTCTACAT
* * *
1336840 TACTGGCAGTTTATCTGCAT
1 TACTGGCAGCTTGTCTACAT
* *** * *
1336860 TATTGATGGCTTGTCCATAT
1 TACTGGCAGCTTGTCTACAT
1336880 TACTGGCAGCTTGTCT
1 TACTGGCAGCTTGTCT
1336896 GCAATTTTGG
Statistics
Matches: 38, Mismatches: 18, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
TACTGGCAGCTTGTCTACAT
Found at i:1336872 original size:40 final size:40
Alignment explanation
Indices: 1336763--1336898 Score: 143
Period size: 40 Copynumber: 3.5 Consensus size: 40
1336753 AAGGAGGAAG
* * *
1336763 TACTGGCAATTTATCTACATTACTGGTGGTTTGTCCACA-
1 TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
* * * *
1336802 T--TGGCAGTTTATCTGTAATACTGGTAGCTTGTCTACAT
1 TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
* * *
1336840 TACTGGCAGTTTATCTGCATTATTGATGGCTTGTCCATAT
1 TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
* *
1336880 TACTGGCAGCTTGTCTGCA
1 TACTGGCAGTTTATCTGCA
1336899 ATTTTGGTAG
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
37 29 0.37
38 1 0.01
39 1 0.01
40 47 0.60
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGGCAGTTTATCTGCATTACTGGTGGCTTGTCCACAT
Found at i:1340410 original size:12 final size:13
Alignment explanation
Indices: 1340383--1340415 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1340373 TTAAAAACCC
*
1340383 TTTCATTTATTTT
1 TTTCCTTTATTTT
1340396 TTTCCTTTA-TTT
1 TTTCCTTTATTTT
1340408 TTTCCTTT
1 TTTCCTTT
1340416 GAAATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCCTTTATTTT
Found at i:1341717 original size:22 final size:22
Alignment explanation
Indices: 1341678--1341719 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1341668 TGAATAAACC
* * *
1341678 AAATAAATTTTATTTCTGTAGA
1 AAATAAACTTAATATCTGTAGA
1341700 AAATAAACTTAATATCTGTA
1 AAATAAACTTAATATCTGTA
1341720 AACTGAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATAAACTTAATATCTGTAGA
Found at i:1343929 original size:2 final size:2
Alignment explanation
Indices: 1343922--1343952 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1343912 AAGATAATAG
*
1343922 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1343953 TTATCCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1349869 original size:6 final size:6
Alignment explanation
Indices: 1349858--1349885 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1349848 AGGATTACAA
1349858 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1349886 TTAGAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTCC
Found at i:1359341 original size:79 final size:79
Alignment explanation
Indices: 1359210--1359367 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
1359200 GATAAGTTGA
1359210 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
1 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
1359275 TTTTACAGCATTCC
66 TTTTACAGCATTCC
*
1359289 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACTATAAGCATGCACAAAGGCGTGAAACTCAT
1 AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
1359354 TTTTACAGCATTCC
66 TTTTACAGCATTCC
1359368 TTCGTTTATA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.23
Consensus pattern (79 bp):
AAGAAGCCAGTTAAAAGCACATTCTGTAAAATGACAATAAGCATGCACAAAGGCGTGAAACTCAT
TTTTACAGCATTCC
Found at i:1367366 original size:31 final size:30
Alignment explanation
Indices: 1367298--1367366 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
1367288 TGGTTTCAAT
1367298 TCAGTCACTTAACTTTCAAAAAATGAAAAA
1 TCAGTCACTTAACTTTCAAAAAATGAAAAA
* * * *
1367328 TCGGTCAC-TAACGTTATCGAAAAGTGACAAA
1 TCAGTCACTTAAC-TT-TCAAAAAATGAAAAA
1367359 TCAGTCAC
1 TCAGTCAC
1367367 CCACTAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 4 0.12
30 9 0.28
31 19 0.59
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (30 bp):
TCAGTCACTTAACTTTCAAAAAATGAAAAA
Found at i:1367501 original size:3 final size:3
Alignment explanation
Indices: 1367495--1367530 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1367485 CTAATAACAA
*
1367495 AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG -AG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1367531 GACTGTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1369248 original size:36 final size:36
Alignment explanation
Indices: 1369191--1369284 Score: 127
Period size: 35 Copynumber: 2.6 Consensus size: 36
1369181 AAATTTTTTT
* *
1369191 AAAAATTAATTGAATTAGGTTTTAGGAGTTTT-AAG
1 AAAAATTAATTAAATTAGGTTTTAGGAGTTTTAAAA
* * *
1369226 TAAAATTAATTAAATTAGGGTTTAGGATTTTTAAAA
1 AAAAATTAATTAAATTAGGTTTTAGGAGTTTTAAAA
1369262 AAAAATTAATTAAATTAAGGTTT
1 AAAAATTAATTAAATT-AGGTTT
1369285 AGTTTTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 28 0.56
36 17 0.34
37 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (36 bp):
AAAAATTAATTAAATTAGGTTTTAGGAGTTTTAAAA
Found at i:1369292 original size:35 final size:36
Alignment explanation
Indices: 1369191--1369298 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
1369181 AAATTTTTTT
* * *
1369191 AAAAATTAATTGAATT-AGGTTTTAGGAGTTTT-AAG
1 AAAAATTAATTAAATTAAGG-TTTAGGATTTTTAAAA
* *
1369226 TAAAATTAATTAAATTAGGGTTTAGGATTTTTAAAA
1 AAAAATTAATTAAATTAAGGTTTAGGATTTTTAAAA
**
1369262 AAAAATTAATTAAATTAAGGTTTAGTTTTTTTAAAA
1 AAAAATTAATTAAATTAAGGTTTAGGATTTTTAAAA
1369298 A
1 A
1369299 TAATTTTGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 25 0.40
36 37 0.60
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (36 bp):
AAAAATTAATTAAATTAAGGTTTAGGATTTTTAAAA
Found at i:1369610 original size:124 final size:124
Alignment explanation
Indices: 1369385--1369707 Score: 452
Period size: 124 Copynumber: 2.6 Consensus size: 124
1369375 GAATTTTGTT
* * *
1369385 TTTTTCTATAGTAGTTCTTGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAA
1 TTTTTCTATAGTAGTTCTTG-AAAA-TAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAA
*
1369450 ACGCTTTAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAAGCTCCCACGTGGACGCTA
64 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTG-AAAAAAGCTCCCACGTGGACGCTA
*
1369512 TTTTTCTACAGTAGTTCTTGAAAA-AATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
1 TTTTTCTATAGTAGTTCTTGAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
* * * * *
1369576 TCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
66 GCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTA
* * * *
1369635 TTTTTCTATAGTAGTTCTTGAGAAAATAAATTTGAGAAGACGGTTAC-GTAAAAATAGTGTCAAT
1 TTTTTCTATAGTAGTTCTT--GAAAATAATTTTGAGAAGACGGTT-CTGAAAAAATAGTGTAAAA
1369699 AACGCTTCA
63 AACGCTTCA
1369708 CGGCATACTT
Statistics
Matches: 176, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
123 39 0.22
124 69 0.39
125 5 0.03
126 43 0.24
127 20 0.11
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (124 bp):
TTTTTCTATAGTAGTTCTTGAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
GCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTA
Found at i:1371545 original size:24 final size:24
Alignment explanation
Indices: 1371495--1371545 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1371485 AAAAAAGAAT
* * *
1371495 GCGGAGGTGTTTGCATCACCCATG
1 GCGGAGGTGTTTGAATCACACAAG
* *
1371519 GCGGAGGTGTTTGAATCTCATAAG
1 GCGGAGGTGTTTGAATCACACAAG
1371543 GCG
1 GCG
1371546 ATGGGGACTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (24 bp):
GCGGAGGTGTTTGAATCACACAAG
Found at i:1375042 original size:16 final size:16
Alignment explanation
Indices: 1375021--1375077 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
1375011 TTTGGTTCGC
*
1375021 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
1375037 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
1375053 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
1375069 TGTAATGGA
1 TGTAATGGA
1375078 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:1375344 original size:18 final size:17
Alignment explanation
Indices: 1375323--1375357 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1375313 TTATTATTAA
*
1375323 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1375341 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1375358 TCTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1385829 original size:28 final size:29
Alignment explanation
Indices: 1385748--1385843 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
1385738 AAGATATAAC
* * *
1385748 AATTTTTACTAT-TTTTAAATTTTTTAAAT
1 AATTTTTACAATATTTTAAAATTTCT-AAT
*
1385777 AATTTTTTACAATCTTTTAAAATTTCTAAT
1 AA-TTTTTACAATATTTTAAAATTTCTAAT
* *
1385807 AATTTTTACAGTATTTT-CAATTTCTAAT
1 AATTTTTACAATATTTTAAAATTTCTAAT
1385835 ATATTTTTA
1 A-ATTTTTA
1385844 ANNNNNNNNN
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.19
29 22 0.38
30 14 0.24
31 11 0.19
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (29 bp):
AATTTTTACAATATTTTAAAATTTCTAAT
Found at i:1389133 original size:139 final size:139
Alignment explanation
Indices: 1388883--1389161 Score: 558
Period size: 139 Copynumber: 2.0 Consensus size: 139
1388873 AGGCGTCATG
1388883 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
1 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
1388948 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
66 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
1389013 TTTTTACTT
131 TTTTTACTT
1389022 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
1 TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
1389087 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
66 CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
1389152 TTTTTACTT
131 TTTTTACTT
1389161 T
1 T
1389162 GATTCTAATG
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (139 bp):
TAATACGCGCGTATTCGGCCTGTATTGTATTAGGTAATACACTGAACCAAACGCCTCCTTAGATT
CTTTTACTATTCGATTCAATTAATGTTAAGGTTTAATGCATACTTTAATTTTGGAGTAAACTTTT
TTTTTACTT
Found at i:1389817 original size:28 final size:29
Alignment explanation
Indices: 1389736--1389830 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
1389726 AAGATATAAC
* * *
1389736 AATTTTTACTAT-TTTTAAATTTTTTAAAT
1 AATTTTTACAATATTTTAAAATTTCT-AAT
*
1389765 AATTTTTTACAATCTTTTAAAATTTCTAAT
1 AA-TTTTTACAATATTTTAAAATTTCTAAT
* *
1389795 AATTTTTACAGTATTTT-CAATTTCTAAT
1 AATTTTTACAATATTTTAAAATTTCTAAT
1389823 ATATTTTT
1 A-ATTTTT
1389831 TCAAAATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.19
29 21 0.37
30 14 0.25
31 11 0.19
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (29 bp):
AATTTTTACAATATTTTAAAATTTCTAAT
Found at i:1396548 original size:21 final size:21
Alignment explanation
Indices: 1396522--1396566 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1396512 CAAAACTTAT
1396522 TAATTATGGTAGTTAAGTGAC
1 TAATTATGGTAGTTAAGTGAC
1396543 TAATTATGGTAGTTAAGTGAC
1 TAATTATGGTAGTTAAGTGAC
1396564 TAA
1 TAA
1396567 ATAGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (21 bp):
TAATTATGGTAGTTAAGTGAC
Found at i:1399567 original size:7 final size:7
Alignment explanation
Indices: 1399555--1399592 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1399545 ATGGGTACAT
1399555 ATGTATA
1 ATGTATA
1399562 ATGTATA
1 ATGTATA
1399569 ATGTATA
1 ATGTATA
1399576 ATGTATA
1 ATGTATA
1399583 ATGTATA
1 ATGTATA
1399590 ATG
1 ATG
1399593 CTATTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (7 bp):
ATGTATA
Found at i:1401208 original size:12 final size:12
Alignment explanation
Indices: 1401193--1401217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1401183 TAATGTTTGA
1401193 GGGATTAATATG
1 GGGATTAATATG
1401205 GGGATTAATATG
1 GGGATTAATATG
1401217 G
1 G
1401218 TGTGTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (12 bp):
GGGATTAATATG
Found at i:1402361 original size:30 final size:29
Alignment explanation
Indices: 1402288--1402361 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
1402278 GAATTAAAAA
*
1402288 TAAATTAATAAATATTTTCATATTTTATC
1 TAAATTAATAAATATTTACATATTTTATC
* *
1402317 TAAATTAAAAAAATATTTAGAT-TTTTCCAT-
1 TAAATT-AATAAATATTTACATATTTT--ATC
1402347 TAAATTAGATAAATA
1 TAAATTA-ATAAATA
1402362 AGATAACAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
29 11 0.30
30 24 0.65
31 2 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (29 bp):
TAAATTAATAAATATTTACATATTTTATC
Found at i:1404359 original size:32 final size:32
Alignment explanation
Indices: 1404305--1404365 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1404295 CTTTTAACAA
* * *
1404305 TATTATTTTTAAAATTTAAATTCTATTTTTTT
1 TATTATTTCTAAAATTGAAATTCGATTTTTTT
* *
1404337 TATTGTTTCTAAAATTGGAATTCGATTTT
1 TATTATTTCTAAAATTGAAATTCGATTTT
1404366 CCTTTTAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (32 bp):
TATTATTTCTAAAATTGAAATTCGATTTTTTT
Found at i:1405606 original size:24 final size:24
Alignment explanation
Indices: 1405591--1405642 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1405581 AATCAATGTC
*
1405591 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
1405615 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
1405639 AAAT
1 AAAT
1405643 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:1405766 original size:29 final size:29
Alignment explanation
Indices: 1405733--1405791 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1405723 TCCACATTGA
*
1405733 CACGAATTCTCAACGAACAAGTTCTTCAC
1 CACGAACTCTCAACGAACAAGTTCTTCAC
*
1405762 CACGAACTCTCAATGAACAAGTTCTTCAC
1 CACGAACTCTCAACGAACAAGTTCTTCAC
1405791 C
1 C
1405792 TCTTCCACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (29 bp):
CACGAACTCTCAACGAACAAGTTCTTCAC
Found at i:1409283 original size:24 final size:24
Alignment explanation
Indices: 1409268--1409320 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1409258 AATCAATGTC
1409268 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
** *
1409292 AAATATATTAAACTAATAAAATACT
1 AAATATATTATGCTAAT-AAATGCT
1409317 AAAT
1 AAAT
1409321 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:1410181 original size:17 final size:19
Alignment explanation
Indices: 1410148--1410182 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1410138 TATGCTAATT
1410148 TTATTACTATAAAATAGAG
1 TTATTACTATAAAATAGAG
1410167 TTATTACT-T-AAATAGA
1 TTATTACTATAAAATAGA
1410183 ATTAATAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (19 bp):
TTATTACTATAAAATAGAG
Found at i:1412242 original size:16 final size:16
Alignment explanation
Indices: 1412223--1412264 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1412213 TTATTATTAT
1412223 TATTAATTATATTTAA
1 TATTAATTATATTTAA
*
1412239 TATTAATATAAATTTAA
1 TATTAAT-TATATTTAA
*
1412256 -ATTTATTAT
1 TATTAATTAT
1412265 TATGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTATATTTAA
Found at i:1412882 original size:16 final size:17
Alignment explanation
Indices: 1412857--1412896 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1412847 AAAAACAATA
*
1412857 TAAT-AAATTATTAAT-
1 TAATAAAATTATAAATC
1412872 TAATAAAATTATAAATC
1 TAATAAAATTATAAATC
1412889 T-ATAAAAT
1 TAATAAAAT
1412897 CATTGCATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 17 0.77
17 1 0.05
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAAAATTATAAATC
Found at i:1415934 original size:66 final size:65
Alignment explanation
Indices: 1415852--1415976 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 65
1415842 CCACCAATCT
1415852 TTTATTGAGGTGTGATTGGATCACCTAAAAA-ATAGCTTTGGTCTACGAGTTTTAGAAAAATGGA
1 TTTATTGAGGTGTGATTGGATCACCTAAAAACA-A-CTTTGGTCTACGAGTTTTAGAAAAATGGA
1415916 TC
64 TC
1415918 TTTATTGAGGTGTGATTGGATCACCTAAAAACAACTTTGGTCTACGAGTTTTAGAAAAA
1 TTTATTGAGGTGTGATTGGATCACCTAAAAACAACTTTGGTCTACGAGTTTTAGAAAAA
1415977 CGGGTTCGGG
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
65 25 0.43
66 32 0.55
67 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (65 bp):
TTTATTGAGGTGTGATTGGATCACCTAAAAACAACTTTGGTCTACGAGTTTTAGAAAAATGGATC
Found at i:1416652 original size:17 final size:17
Alignment explanation
Indices: 1416630--1416675 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1416620 AATGGTATAG
1416630 AAATAATATAAAC-AAAT
1 AAATAA-ATAAACGAAAT
1416647 AAATAAATAAACGAAATT
1 AAATAAATAAACGAAA-T
1416665 AATATAAATAA
1 AA-ATAAATAA
1416676 TAAAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.23
17 9 0.35
18 3 0.12
19 8 0.31
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATAAATAAACGAAAT
Found at i:1416939 original size:20 final size:20
Alignment explanation
Indices: 1416911--1416957 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1416901 AAAGATATAT
*
1416911 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
1416931 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
1416951 ATATATA
1 ATATATA
1416958 CGTACATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:1417581 original size:22 final size:21
Alignment explanation
Indices: 1417546--1417641 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 21
1417536 AAAGGGTATC
* *
1417546 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
1417567 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
1417590 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
1417609 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
1417628 TGCATATCATATCT
1 TACAAATCATATCT
1417642 AAGGTTGCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.03
19 26 0.43
21 7 0.12
22 15 0.25
23 10 0.17
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:1417589 original size:23 final size:22
Alignment explanation
Indices: 1417546--1417603 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1417536 AAAGGGTATC
* *
1417546 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1417567 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
1417590 TGCATATCATATCT
1 TACAAATCATATCT
1417604 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1417606 original size:19 final size:19
Alignment explanation
Indices: 1417582--1417654 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
1417572 AATCATATCT
1417582 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
1417601 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
1417620 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
1417639 TCTAAGGTTGCATATC
1 TCTAAGATTGCATATC
1417655 CTCGAAGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1424311 original size:19 final size:20
Alignment explanation
Indices: 1424287--1424336 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
1424277 TGATAAACTT
*
1424287 TCTTTATATATTTTT-AGAA
1 TCTTTATATATTTTTGAAAA
1424306 TCTTTA-ATATTTTTGAAAA
1 TCTTTATATATTTTTGAAAA
1424325 T-TTTATA-ATTTT
1 TCTTTATATATTTT
1424337 ACATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (20 bp):
TCTTTATATATTTTTGAAAA
Found at i:1426900 original size:21 final size:20
Alignment explanation
Indices: 1426886--1426941 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
1426876 TTGAGGATTG
1426886 AAAATTGGAAATTGAAAATT
1 AAAATTGGAAATTGAAAATT
*
1426906 AAAATTTGGAGATTGAAAATAT
1 AAAA-TTGGAAATTGAAAAT-T
*
1426928 AAAATTGAAAATTG
1 AAAATTGGAAATTG
1426942 GGGATTGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 22 0.71
22 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (20 bp):
AAAATTGGAAATTGAAAATT
Found at i:1426925 original size:28 final size:28
Alignment explanation
Indices: 1426889--1426961 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
1426879 AGGATTGAAA
*
1426889 ATTGGAAATTGAAAATT-AAAATTTGGAG
1 ATTGAAAATTGAAAATTGAAAA-TTGGAG
*
1426917 ATTGAAAATAT-AAAATTGAAAATTGGGG
1 ATTGAAAAT-TGAAAATTGAAAATTGGAG
* *
1426945 ATTGAAGATTGAGAATT
1 ATTGAAAATTGAAAATT
1426962 TAGGAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 1 0.03
28 32 0.84
29 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.32
Consensus pattern (28 bp):
ATTGAAAATTGAAAATTGAAAATTGGAG
Found at i:1426956 original size:7 final size:7
Alignment explanation
Indices: 1426882--1426941 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
1426872 AGGATTGAGG
1426882 ATTGAAA
1 ATTGAAA
*
1426889 ATTGGAA
1 ATTGAAA
1426896 ATTGAAA
1 ATTGAAA
1426903 ATT-AAA
1 ATTGAAA
* *
1426909 ATTTGGAG
1 A-TTGAAA
1426917 ATTGAAA
1 ATTGAAA
1426924 ATAT-AAA
1 AT-TGAAA
1426931 ATTGAAA
1 ATTGAAA
1426938 ATTG
1 ATTG
1426942 GGGATTGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 5 0.12
7 35 0.81
8 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.32
Consensus pattern (7 bp):
ATTGAAA
Found at i:1427716 original size:17 final size:18
Alignment explanation
Indices: 1427689--1427724 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1427679 AAAAATATAA
1427689 AAAAGTTATAAAAATTTT
1 AAAAGTTATAAAAATTTT
*
1427707 AAAA-TTATAAAATTTTT
1 AAAAGTTATAAAAATTTT
1427724 A
1 A
1427725 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAAGTTATAAAAATTTT
Found at i:1428630 original size:30 final size:29
Alignment explanation
Indices: 1428596--1428652 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
1428586 GTCCTAAATA
1428596 ATATTATTTTAGAATTTTTAA-ATTTTTTAT
1 ATATTA-TTTA-AATTTTTAATATTTTTTAT
*
1428626 ATATTATTTACATTTTTAATATTTTTT
1 ATATTATTTAAATTTTTAATATTTTTT
1428653 TAAAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 11 0.44
30 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
ATATTATTTAAATTTTTAATATTTTTTAT
Found at i:1429561 original size:21 final size:22
Alignment explanation
Indices: 1429510--1429562 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1429500 TTGTTTGAAT
* * *
1429510 TTTTAATTAATTAATTAATTAA
1 TTTTATTTAATTAATAAATAAA
1429532 TTTGT-TTTAATT-ATAAATAAA
1 TTT-TATTTAATTAATAAATAAA
1429553 TTTTATTTAA
1 TTTTATTTAA
1429563 AATTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 15 0.58
22 9 0.35
23 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATTTAATTAATAAATAAA
Found at i:1429570 original size:16 final size:18
Alignment explanation
Indices: 1429536--1429577 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1429526 AATTAATTTG
*
1429536 TTTTAATTATAAATAAA-
1 TTTTATTTATAAATAAAT
*
1429553 TTTTATTTA-AAATTAAT
1 TTTTATTTATAAATAAAT
1429570 TTTTATTT
1 TTTTATTT
1429578 GATTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATTTATAAATAAAT
Found at i:1430259 original size:16 final size:17
Alignment explanation
Indices: 1430230--1430262 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1430220 AAATGTTTTT
1430230 TAAAAAATTATTTAATA
1 TAAAAAATTATTTAATA
*
1430247 TAAAATATT-TTTAATA
1 TAAAAAATTATTTAATA
1430263 CTATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAAAATTATTTAATA
Found at i:1444849 original size:44 final size:44
Alignment explanation
Indices: 1444785--1444875 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
1444775 GTAGGTCAAA
* *
1444785 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTGAAGTGAGAAAC
* * *
1444829 TAATATTAAAATAACTTACACTTATCAAAGTTGAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTGAAGTGAGAAAC
1444873 TAA
1 TAA
1444876 AAAAAAAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTGAAGTGAGAAAC
Found at i:1445078 original size:26 final size:27
Alignment explanation
Indices: 1445049--1445104 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1445039 TGGGAATTGA
*
1445049 TAATTAT-AAATAAAATTATTGTATTC
1 TAATTATAAAAAAAAATTATTGTATTC
*
1445075 TAATTGTAAAAAAAAATTATTGTATTC
1 TAATTATAAAAAAAAATTATTGTATTC
1445102 TAA
1 TAA
1445105 AAAAAAGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (27 bp):
TAATTATAAAAAAAAATTATTGTATTC
Found at i:1445095 original size:22 final size:21
Alignment explanation
Indices: 1445070--1445110 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1445060 AAAATTATTG
*
1445070 TATTCTAATTGTAAAAAAAAAT
1 TATTCT-ATTCTAAAAAAAAAT
*
1445092 TATTGTATTCTAAAAAAAA
1 TATTCTATTCTAAAAAAAA
1445111 GCCTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
TATTCTATTCTAAAAAAAAAT
Found at i:1445661 original size:58 final size:59
Alignment explanation
Indices: 1445550--1445661 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 59
1445540 AGGATTGACA
** *
1445550 TTGATTTTTTAAAAATACAACTCTTTCACTATTTACTTTTTTAACTTAAAAAAATTACT
1 TTGATTTTTTAAAAATACAACTCTACCACTATTTACTTTTATAACTTAAAAAAATTACT
* * *
1445609 TTGATTTTTT-TAAATACAACTCTACCACTATTTACTCTTTATGACTTCAAAAA
1 TTGATTTTTTAAAAATACAACTCTACCACTATTTACT-TTTATAACTTAAAAAA
1445662 GGTAATATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 23 0.50
59 23 0.50
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.46
Consensus pattern (59 bp):
TTGATTTTTTAAAAATACAACTCTACCACTATTTACTTTTATAACTTAAAAAAATTACT
Found at i:1449500 original size:43 final size:43
Alignment explanation
Indices: 1449420--1449563 Score: 155
Period size: 43 Copynumber: 3.3 Consensus size: 43
1449410 TATGTGAAAA
* * * * * *
1449420 AAACACCGCTAAAGAAC-TCGACATTTAACAGCGCTTTACCCGC
1 AAACACTGCTAAAGAACAT-GACCTTTAGCGGCACTTTACCCAC
*
1449463 AAACACTGCTAAAGAATATGACCTTTAGCGGCACTTTACCCAC
1 AAACACTGCTAAAGAACATGACCTTTAGCGGCACTTTACCCAC
* * * *
1449506 AAACGCTGCTAAAGAACATGACCTTTAGCGGCGCTTGACCCAT
1 AAACACTGCTAAAGAACATGACCTTTAGCGGCACTTTACCCAC
* *
1449549 AAACGCCGCTAAAGA
1 AAACACTGCTAAAGA
1449564 GCATAATATT
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 86 0.99
44 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (43 bp):
AAACACTGCTAAAGAACATGACCTTTAGCGGCACTTTACCCAC
Found at i:1449596 original size:43 final size:41
Alignment explanation
Indices: 1449549--1449682 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 41
1449539 CTTGACCCAT
*
1449549 AAACGCCGCTAAAGAGCATAATATTTAGCAACACTTTTATCAC
1 AAACGCCGCTAAAGAGCATAAT-TTTAGCAGC-CTTTTATCAC
* * * * *
1449592 AAACGTCGCTATAA-AGAATGACTTTTAG-AGGCTTTTTTTCAC
1 AAACGCCGCTA-AAGAGCAT-AATTTTAGCA-GCCTTTTATCAC
* * *
1449634 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAGCATAAT-TTTAGCAGC-CTTTTATCAC
1449677 AAACGC
1 AAACGC
1449683 TAAAAGTACC
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
41 3 0.04
42 29 0.41
43 34 0.49
44 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (41 bp):
AAACGCCGCTAAAGAGCATAATTTTAGCAGCCTTTTATCAC
Found at i:1455213 original size:14 final size:14
Alignment explanation
Indices: 1455196--1455421 Score: 113
Period size: 14 Copynumber: 15.9 Consensus size: 14
1455186 ACTAATTAAT
*
1455196 CTAAACCCTAACCC
1 CTAAACCCTAAACC
*
1455210 CT-AACCCTTAACC
1 CTAAACCCTAAACC
*
1455223 CTTAAACCCTAAATC
1 C-TAAACCCTAAACC
* * *
1455238 ATAAATCCTAACCCC
1 CTAAACCCTAA-ACC
*
1455253 CT-AACCCTTAACC
1 CTAAACCCTAAACC
* * *
1455266 TTTAACCCTTAACCC
1 CTAAACCC-TAAACC
*
1455281 CT-AACCCTTAACTC
1 CTAAACCCTAAAC-C
*
1455295 CTAACCCCTAAACC
1 CTAAACCCTAAACC
*
1455309 TTAAATCCC--AACC
1 CTAAA-CCCTAAACC
*
1455322 CTTAAACCATAAACC
1 C-TAAACCCTAAACC
* * *
1455337 ATAAACCATAATCC
1 CTAAACCCTAAACC
* *
1455351 CTAAATCCATAATCC
1 CTAAA-CCCTAAACC
* * *
1455366 ATAAACCTTAAAATC
1 CTAAACCCT-AAACC
*
1455381 GT-AACTCCTAAACC
1 CTAAAC-CCTAAACC
*
1455395 TTAAACCCTAAACC
1 CTAAACCCTAAACC
1455409 CTAAACCCTAAAC
1 CTAAACCCTAAAC
1455422 TATAATGATA
Statistics
Matches: 161, Mismatches: 36, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
13 22 0.14
14 86 0.53
15 53 0.33
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAACCCTAAACC
Found at i:1455232 original size:8 final size:7
Alignment explanation
Indices: 1455199--1455312 Score: 81
Period size: 7 Copynumber: 16.3 Consensus size: 7
1455189 AATTAATCTA
1455199 AACCC-T
1 AACCCTT
*
1455205 AACCCCT
1 AACCCTT
1455212 AACCCTT
1 AACCCTT
1455219 AACCCTT
1 AACCCTT
*
1455226 AAACCCTA
1 -AACCCTT
* * *
1455234 AATCATA
1 AACCCTT
*
1455241 AATCC-T
1 AACCCTT
*
1455247 AACCCCCT
1 AA-CCCTT
1455255 AACCCTT
1 AACCCTT
*
1455262 AACCTTT
1 AACCCTT
1455269 AACCCTT
1 AACCCTT
*
1455276 AACCCCT
1 AACCCTT
1455283 AACCCTT
1 AACCCTT
1455290 AACTCC-T
1 AAC-CCTT
*
1455297 AACCCCT
1 AACCCTT
*
1455304 AAACCTT
1 AACCCTT
1455311 AA
1 AA
1455313 ATCCCAACCC
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
6 9 0.10
7 68 0.77
8 11 0.12
ACGTcount: A:0.34, C:0.42, G:0.00, T:0.24
Consensus pattern (7 bp):
AACCCTT
Found at i:1455234 original size:21 final size:21
Alignment explanation
Indices: 1455199--1455421 Score: 93
Period size: 21 Copynumber: 10.5 Consensus size: 21
1455189 AATTAATCTA
*
1455199 AACCC-TAACCCCTAACCCTT
1 AACCCTTAAACCCTAACCCTT
* * *
1455219 AACCCTTAAACCCTAAATCATA
1 AACCCTTAAACCCT-AACCCTT
* *
1455241 AATCC-TAACCCCCTAACCCTT
1 AACCCTTAA-ACCCTAACCCTT
* *
1455262 AA-CCTTTAACCCTTAACCCCT
1 AACCCTTAAACCC-TAACCCTT
*
1455283 AACCCTT-AACTCCTAACCCCT
1 AACCCTTAAAC-CCTAACCCTT
*
1455304 AAACCTTAAATCCC-AACCCTT
1 AACCCTTAAA-CCCTAACCCTT
* * * * *
1455325 AAACCATAAACCATAAACCAT
1 AACCCTTAAACCCTAACCCTT
* * *
1455346 AATCCC-TAAATCCATAATCCAT
1 AA-CCCTTAAA-CCCTAACCCTT
* * *
1455368 AAACCTTAAAATCGTAACTCC-T
1 AACCCTT-AAACCCTAAC-CCTT
* *
1455390 AAACCTTAAACCCTAAACCCTA
1 AACCCTTAAACCCT-AACCCTT
1455412 AACCC-TAAAC
1 AACCCTTAAAC
1455422 TATAATGATA
Statistics
Matches: 158, Mismatches: 28, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
20 12 0.08
21 84 0.53
22 56 0.35
23 6 0.04
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTTAAACCCTAACCCTT
Found at i:1455336 original size:7 final size:7
Alignment explanation
Indices: 1455324--1455426 Score: 64
Period size: 7 Copynumber: 14.4 Consensus size: 7
1455314 TCCCAACCCT
1455324 TAAACCA
1 TAAACCA
1455331 TAAACCA
1 TAAACCA
1455338 TAAACCA
1 TAAACCA
* *
1455345 TAATCCC
1 TAAACCA
1455352 TAAATCCA
1 TAAA-CCA
*
1455360 TAATCCA
1 TAAACCA
*
1455367 TAAACCT
1 TAAACCA
* *
1455374 TAAAATCG
1 T-AAACCA
*
1455382 T-AACTCC
1 TAAAC-CA
*
1455389 TAAACCT
1 TAAACCA
*
1455396 TAAACCC
1 TAAACCA
*
1455403 TAAACCC
1 TAAACCA
*
1455410 TAAACCC
1 TAAACCA
*
1455417 TAAACTA
1 TAAACCA
1455424 TAA
1 TAA
1455427 TGATAGTTAA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
6 2 0.03
7 62 0.81
8 13 0.17
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:1455377 original size:22 final size:21
Alignment explanation
Indices: 1455252--1455420 Score: 103
Period size: 21 Copynumber: 8.0 Consensus size: 21
1455242 ATCCTAACCC
* * *
1455252 CCTAACCC-TTAACCTTTAAC
1 CCTAACCCATAAACCTTAAAT
* * *
1455272 CCTTAACCCCTAACCCTTAACT
1 CC-TAACCCATAAACCTTAAAT
*
1455294 CCTAACCCCTAAACCTTAAAT
1 CCTAACCCATAAACCTTAAAT
* * *
1455315 CCCAACCCTTAAACCATAAA-
1 CCTAACCCATAAACCTTAAAT
* * *
1455335 CCATAAACCATAATCCCTAAAT
1 CC-TAACCCATAAACCTTAAAT
*
1455357 CCATAATCCATAAACCTTAAAAT
1 CC-TAACCCATAAACCTT-AAAT
* *
1455380 CGTAACTCC-TAAACCTTAAAC
1 CCTAAC-CCATAAACCTTAAAT
*
1455401 CCTAAACCC-TAAACCCTAAA
1 CCT-AACCCATAAACCTTAAA
1455421 CTATAATGAT
Statistics
Matches: 119, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.03
21 70 0.59
22 38 0.32
23 7 0.06
ACGTcount: A:0.40, C:0.37, G:0.01, T:0.23
Consensus pattern (21 bp):
CCTAACCCATAAACCTTAAAT
Found at i:1455917 original size:41 final size:41
Alignment explanation
Indices: 1455844--1455965 Score: 145
Period size: 41 Copynumber: 3.0 Consensus size: 41
1455834 TTCAAAAAAT
* * * *
1455844 ATAAATGCCGCCAATGCTTCACTTTTTGTGGCATTTTTCTC
1 ATAAACGCCGCTAATGCTTAACCTTTTGTGGCATTTTTCTC
* * * *
1455885 ATAGACGCCGCTATTGCTTGACCTTTTATGGCATTTTTCTC
1 ATAAACGCCGCTAATGCTTAACCTTTTGTGGCATTTTTCTC
* *
1455926 ATAAACGCTGCTAAAGCTCTAACCTTTTGTGGCATTTTTC
1 ATAAACGCCGCTAATGCT-TAACCTTTTGTGGCATTTTTC
1455966 GATTAGCACC
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 48 0.72
42 19 0.28
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (41 bp):
ATAAACGCCGCTAATGCTTAACCTTTTGTGGCATTTTTCTC
Found at i:1456427 original size:40 final size:40
Alignment explanation
Indices: 1456293--1456457 Score: 163
Period size: 40 Copynumber: 4.1 Consensus size: 40
1456283 TGAATTTTTT
* * * * *
1456293 GCGGCGTTTTTCAAGAAGCACTGCTCATGCTTGATCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
* ** *
1456333 ACGGTGTTTTTCAAGAAGAGCA--GCTAATGCTCGACCTATA
1 GCGGCATTTTTCAA-AA-AGCACCGCTAATGCTTGACCTATA
* * *
1456373 ACGGCATTTTTCAAAAAGCGCCGCTAATGGTTGACCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
* * *
1456413 GCGGCATTTTTCAAAAACCACCGTTAATGCTTGATCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
1456453 GCGGC
1 GCGGC
1456458 GCTTTTTGAT
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 94 0.90
41 1 0.01
42 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
Found at i:1456479 original size:27 final size:26
Alignment explanation
Indices: 1456439--1456490 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1456429 ACCACCGTTA
* * *
1456439 ATGCTTGATCTATAGCGGCGCTTTTTG
1 ATGCTCGATATATAGCAGCG-TTTTTG
1456466 ATGCTCGATATATAGCAGCGTTTTT
1 ATGCTCGATATATAGCAGCGTTTTT
1456491 CAAAAAGCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATGCTCGATATATAGCAGCGTTTTTG
Found at i:1457842 original size:32 final size:32
Alignment explanation
Indices: 1457804--1457867 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1457794 AATAAGTACT
1457804 AAACATGCATTAGGACCATTTAAAAAAATATC
1 AAACATGCATTAGGACCATTTAAAAAAATATC
*
1457836 AAACATGCATTAGGACCATTTAACAAAATATC
1 AAACATGCATTAGGACCATTTAAAAAAATATC
1457868 CCAAAACTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.25
Consensus pattern (32 bp):
AAACATGCATTAGGACCATTTAAAAAAATATC
Found at i:1461329 original size:12 final size:12
Alignment explanation
Indices: 1461312--1461359 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
1461302 GTTCACGAAC
*
1461312 AAGCTCGTTTAA
1 AAGCTCGTTTAT
*
1461324 AAGCTCATTTAT
1 AAGCTCGTTTAT
* *
1461336 TAGCTTGTTTAT
1 AAGCTCGTTTAT
1461348 AAGCTCGTTTAT
1 AAGCTCGTTTAT
1461360 TGACTCGTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:1461345 original size:24 final size:24
Alignment explanation
Indices: 1461313--1461383 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
1461303 TTCACGAACA
1461313 AGCTCGTTTAAAAGCTCATTTATT
1 AGCTCGTTTAAAAGCTCATTTATT
* * *
1461337 AGCTTGTTTATAAGCTCGTTTATT
1 AGCTCGTTTAAAAGCTCATTTATT
**
1461361 -GACTCGTTTATGA-CTCATTTATT
1 AG-CTCGTTTAAAAGCTCATTTATT
1461384 TATTCATGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 10 0.25
24 30 0.75
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.46
Consensus pattern (24 bp):
AGCTCGTTTAAAAGCTCATTTATT
Found at i:1461366 original size:12 final size:12
Alignment explanation
Indices: 1461351--1461383 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1461341 TGTTTATAAG
1461351 CTCGTTTATTGA
1 CTCGTTTATTGA
1461363 CTCGTTTA-TGA
1 CTCGTTTATTGA
*
1461374 CTCATTTATT
1 CTCGTTTATT
1461384 TATTCATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:1461574 original size:12 final size:12
Alignment explanation
Indices: 1461552--1461598 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1461542 ATTATTTTTT
1461552 AACATTGTTCATG
1 AACA-TGTTCATG
1461565 AACATGTTCACT-
1 AACATGTTCA-TG
* *
1461577 TATATGTTCATG
1 AACATGTTCATG
1461589 AACATGTTCA
1 AACATGTTCA
1461599 ATTAAGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.79
13 5 0.18
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (12 bp):
AACATGTTCATG
Found at i:1461589 original size:24 final size:23
Alignment explanation
Indices: 1461557--1461619 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
1461547 TTTTTAACAT
*
1461557 TGTTCATGAACATGTTCACTTATA
1 TGTTCATGAACATGTTCAATTA-A
1461581 TGTTCATGAACATGTTCAATTAA
1 TGTTCATGAACATGTTCAATTAA
*
1461604 -GTTAAATGAACATGTT
1 TGTT-CATGAACATGTT
1461620 TGTGAACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 3 0.08
23 12 0.33
24 21 0.58
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:1465988 original size:134 final size:133
Alignment explanation
Indices: 1465748--1466195 Score: 513
Period size: 134 Copynumber: 3.4 Consensus size: 133
1465738 GGCTATAATG
* * * * * * *
1465748 GGGTATAACATGTAAGATCATAACTCGACTATGATAATATAGAGAGTCCACCATGACGTTAAACA
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
* *
1465813 TGTGGTATTATGTGTAAGACCATAGCTCATCTATGGAAACATAGAGAGTCTGCCAGGACATTAAA
66 TGTGGTATAATGTGTAAGACCATAGCTCA-CTATGGAAACATAGAGAGTCTACCAGGACATTAAA
1465878 CATA
130 CATA
* * * *
1465882 GGGTATAATGTGTAAGACCATAGCTCGACAATGACAACATAGAGAGTTCACCAGGACATTAAACA
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
* * * * *
1465947 TGTGGTATAATGTGTAAGACCATAGCTCGACTATGGTAACATAAAAAGTCCACTAGGACATTAAA
66 TGTGGTATAATGTGTAAGACCATAGCTC-ACTATGGAAACATAGAGAGTCTACCAGGACATTAAA
1466012 CATA
130 CATA
* * * * * * *
1466016 GGGTATAATATGTAAAAACATAGTTCG-CTATGACAACTTAAAGAGTCCGCCAAGATATTAAACA
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
* * * * *
1466080 TATGGTATATTGTGTAAGACCATAGCTTAACTATGGCAACATAGAGAGT-TTCCTAGGACATTAA
66 TGTGGTATAATGTGTAAGACCATAGC-TCACTATGGAAACATAGAGAGTCTACC-AGGACATTAA
*
1466144 ACATG
129 ACATA
* * * * * *
1466149 GGGTATGATGTGTAAGACCACAGCTCAACTATGACAGCATATAGAGT
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGT
1466196 TTGTCGGGAT
Statistics
Matches: 262, Mismatches: 48, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
132 1 0.00
133 105 0.40
134 155 0.59
135 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (133 bp):
GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
TGTGGTATAATGTGTAAGACCATAGCTCACTATGGAAACATAGAGAGTCTACCAGGACATTAAAC
ATA
Found at i:1466127 original size:200 final size:201
Alignment explanation
Indices: 1465745--1466182 Score: 524
Period size: 200 Copynumber: 2.2 Consensus size: 201
1465735 ATGGGCTATA
** * * * * * * *
1465745 ATGGGGTATAACATGTAAGATCATAACTCGACTATGATAATATAGAGAGTCCACCATGACGTTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGATAACATAAAAAGTCCACCAGGACATTAA
* * * * * * * *
1465810 ACATGTGGTATTATGTGTAAGACCATAGCTCATCTATGGAAACATAGAGAGTCTGCCAGGACATT
66 ACATGTGGTATAATATGTAAAAACATAGCTCAGCTATGGAAACATAAAGAGTCCGCCAAGACATT
*
1465875 AAACATAGGGTATAATGTGTAAGACCATAGCTCGACAATGACAACATAGAGAG-TTCACCAGGAC
131 AAACATAGGGTATAATGTGTAAGACCATAGCTCAACAATGACAACATAGAGAGTTTC-CCAGGAC
1465939 ATTAAAC
195 ATTAAAC
* * *
1465946 ATGTGGTATAATGTGTAAGACCATAGCTCGACTATGGTAACATAAAAAGTCCACTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGATAACATAAAAAGTCCACCAGGACATTAA
* * *
1466011 ACATAG-GGTATAATATGTAAAAACATAGTTC-GCTAT-GACAACTTAAAGAGTCCGCCAAGATA
66 ACAT-GTGGTATAATATGTAAAAACATAGCTCAGCTATGGA-AACATAAAGAGTCCGCCAAGACA
* * * * * *
1466073 TTAAACATATGGTATATTGTGTAAGACCATAGCTTAACTATGGCAACATAGAGAGTTTCCTAGGA
129 TTAAACATAGGGTATAATGTGTAAGACCATAGCTCAACAATGACAACATAGAGAGTTTCCCAGGA
1466138 CATTAAAC
194 CATTAAAC
* * *
1466146 ATGGGGTATGATGTGTAAGACCACAGCTCAACTATGA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGA
1466183 CAGCATATAG
Statistics
Matches: 199, Mismatches: 35, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
199 2 0.01
200 116 0.58
201 80 0.40
202 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (201 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGATAACATAAAAAGTCCACCAGGACATTAA
ACATGTGGTATAATATGTAAAAACATAGCTCAGCTATGGAAACATAAAGAGTCCGCCAAGACATT
AAACATAGGGTATAATGTGTAAGACCATAGCTCAACAATGACAACATAGAGAGTTTCCCAGGACA
TTAAAC
Found at i:1466197 original size:67 final size:67
Alignment explanation
Indices: 1465748--1466196 Score: 424
Period size: 67 Copynumber: 6.7 Consensus size: 67
1465738 GGCTATAATG
** * * * * * * * *
1465748 GGGTATAACATGTAAGATCATAACTCGACTATGATAATATAGAGAGTCCACCATGACGTTAAACA
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
1465813 T-
66 TA
* * *
1465814 GTGGTATTATGTGTAAGACCATAGCTCATCTATGGA-AACATAGAGAG-TCTGCCAGGACATTAA
1 G-GGTATAATGTGTAAGACCATAGCTCAACTAT-GACAACATAGAGAGTTC-ACCAGGACATTAA
1465877 ACATA
63 ACATA
* *
1465882 GGGTATAATGTGTAAGACCATAGCTCGACAATGACAACATAGAGAGTTCACCAGGACATTAAACA
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
1465947 T-
66 TA
* ** * * * *
1465948 GTGGTATAATGTGTAAGACCATAGCTCGACTATGGTAACATAAAAAGTCCACTAGGACATTAAAC
1 G-GGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAAC
1466013 ATA
65 ATA
* * * * * * * * * * *
1466016 GGGTATAATATGTAAAAACATAGTTC-GCTATGACAACTTAAAGAGTCCGCCAAGATATTAAACA
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
1466080 TA
66 TA
* * * * *
1466082 TGGTATATTGTGTAAGACCATAGCTTAACTATGGCAACATAGAGAGTTTC-CTAGGACATTAAAC
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAG-TTCACCAGGACATTAAAC
*
1466146 ATG
65 ATA
* * * *
1466149 GGGTATGATGTGTAAGACCACAGCTCAACTATGACAGCATATAGAGTT
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTT
1466197 TGTCGGGATA
Statistics
Matches: 312, Mismatches: 61, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
66 57 0.18
67 247 0.79
68 8 0.03
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (67 bp):
GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
TA
Found at i:1480578 original size:21 final size:20
Alignment explanation
Indices: 1480540--1480590 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1480530 CAAATACGTC
*
1480540 AACAGAAGCT-TGAAAGCTG
1 AACAGAAGCTCTAAAAGCTG
1480559 AACAGAAGCTCGTAAAAGCTG
1 AACAGAAGCTC-TAAAAGCTG
*
1480580 AACAAAAGCTC
1 AACAGAAGCTC
1480591 ATAAGAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
21 18 0.64
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (20 bp):
AACAGAAGCTCTAAAAGCTG
Found at i:1481141 original size:17 final size:18
Alignment explanation
Indices: 1481111--1481152 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1481101 AGTTAATTCA
*
1481111 TCAAATTAACTAATTT-TC
1 TCAAA-TAAATAATTTATC
1481129 TCAAATAAATAATTTATC
1 TCAAATAAATAATTTATC
1481147 -CAAATA
1 TCAAATA
1481153 TTCTAAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAAATAAATAATTTATC
Found at i:1483601 original size:16 final size:16
Alignment explanation
Indices: 1483580--1483610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1483570 TGTTTCATTT
*
1483580 GTATTTGTATCAATTG
1 GTATTTGGATCAATTG
1483596 GTATTTGGATCAATT
1 GTATTTGGATCAATT
1483611 TGTAGTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
GTATTTGGATCAATTG
Done.