Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 124 of 313
Found at i:40099480 original size:16 final size:16
Alignment explanation
Indices: 40099443--40099484 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40099433 TTAATCATAT
*
40099443 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40099459 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40099474 TTAAAATATAT
1 TTAAAATATAT
40099485 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40099491 original size:14 final size:15
Alignment explanation
Indices: 40099452--40099493 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40099442 TTTAAACATA
*
40099452 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40099467 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40099481 A-TATAATTTAATA
1 ATTATAATTAAATA
40099494 AATTCTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40099587 original size:119 final size:120
Alignment explanation
Indices: 40099446--40099707 Score: 490
Period size: 120 Copynumber: 2.2 Consensus size: 120
40099436 ATCATATTTA
40099446 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAAT-AAATTCTTAAGAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAGAATTAA
40099510 TAATCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TAATCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
40099565 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAGAATTAA
* *
40099630 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TAATCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
40099685 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
40099708 AACTTGAAAA
Statistics
Matches: 139, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 47 0.34
120 92 0.66
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAGAATTAA
TAATCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:40099610 original size:14 final size:15
Alignment explanation
Indices: 40099561--40099612 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40099551 GTAAAATATA
40099561 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40099576 TATTAAATATATTAT
1 AATTAAATATATTAT
40099591 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40099604 AATTTAATA
1 AATTAAATA
40099613 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40104428 original size:23 final size:23
Alignment explanation
Indices: 40104389--40104451 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
40104379 TGTACTGACT
40104389 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAAGAACAATTTCCAG
40104412 CAGAC-AATCAA-AACAATTTCCAG
1 -A-ACAAATCAAGAACAATTTCCAG
*
40104435 AACAAATCAATAACAAT
1 AACAAATCAAGAACAAT
40104452 ATCAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.06
22 7 0.19
23 18 0.50
24 7 0.19
25 2 0.06
ACGTcount: A:0.54, C:0.22, G:0.06, T:0.17
Consensus pattern (23 bp):
AACAAATCAAGAACAATTTCCAG
Found at i:40104460 original size:22 final size:22
Alignment explanation
Indices: 40104389--40104463 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
40104379 TGTACTGACT
*
40104389 AACAAATCAAGAACAATTTCCAGCA
1 AACAAATCAA-AACAATATCCA--A
* * *
40104414 GAC-AATCAAAACAATTTCCAG
1 AACAAATCAAAACAATATCCAA
40104435 AACAAATCAATAACAATAT-CAA
1 AACAAATCAA-AACAATATCCAA
40104457 AACAAAT
1 AACAAAT
40104464 TGCAACAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.05
22 15 0.35
23 18 0.42
24 6 0.14
25 2 0.05
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.17
Consensus pattern (22 bp):
AACAAATCAAAACAATATCCAA
Found at i:40105729 original size:30 final size:30
Alignment explanation
Indices: 40105693--40105750 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
40105683 AGTAACCTGG
40105693 AAACCCACCAATTGAGAGCAATCGAAAGGA
1 AAACCCACCAATTGAGAGCAATCGAAAGGA
*
40105723 AAACCCACCAATTGAGAGCAATTGAAAG
1 AAACCCACCAATTGAGAGCAATCGAAAG
40105751 AGTGACACAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (30 bp):
AAACCCACCAATTGAGAGCAATCGAAAGGA
Found at i:40110810 original size:9 final size:9
Alignment explanation
Indices: 40110798--40110873 Score: 109
Period size: 9 Copynumber: 8.4 Consensus size: 9
40110788 AAATTAACTT
40110798 AATTAACCG
1 AATTAACCG
*
40110807 AATTAACCA
1 AATTAACCG
*
40110816 AATTACCCG
1 AATTAACCG
40110825 AATTAACCG
1 AATTAACCG
40110834 AATT-ACCTG
1 AATTAACC-G
40110843 AATTAACCG
1 AATTAACCG
40110852 AATTAACCG
1 AATTAACCG
*
40110861 AATTAACCA
1 AATTAACCG
40110870 AATT
1 AATT
40110874 TAATCACTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
8 3 0.05
9 54 0.90
10 3 0.05
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:40110820 original size:27 final size:27
Alignment explanation
Indices: 40110788--40110873 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
40110778 TTTTGGTTAA
**
40110788 AAATTAACTTAATTAACCGAATTAACC
1 AAATTAACCGAATTAACCGAATTAACC
*
40110815 AAATTACCCGAATTAACCGAATT-ACC
1 AAATTAACCGAATTAACCGAATTAACC
*
40110841 TGAATTAACCGAATTAACCGAATTAACC
1 -AAATTAACCGAATTAACCGAATTAACC
40110869 AAATT
1 AAATT
40110874 TAATCACTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
26 3 0.06
27 45 0.88
28 3 0.06
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (27 bp):
AAATTAACCGAATTAACCGAATTAACC
Found at i:40111025 original size:18 final size:18
Alignment explanation
Indices: 40110986--40111028 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40110976 TATGATTGGG
**
40110986 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGAATAA
*
40111004 TTGGGTTGGGTTGAATAC
1 TTGGGTTGGGTTGAATAA
40111022 TTGGGTT
1 TTGGGTT
40111029 TAGATTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.02, G:0.44, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGAATAA
Found at i:40112110 original size:20 final size:21
Alignment explanation
Indices: 40112073--40112111 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40112063 TATGTGTAGG
*
40112073 CTGCTTCAAGTTCTGCAACTT
1 CTGCTTCAAGTGCTGCAACTT
40112094 CTGCTTCAA-TGCTGCAAC
1 CTGCTTCAAGTGCTGCAAC
40112112 CTGTTCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (21 bp):
CTGCTTCAAGTGCTGCAACTT
Found at i:40112940 original size:24 final size:24
Alignment explanation
Indices: 40112891--40112942 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
40112881 AACCAAAGTC
* * *
40112891 AAATATATTATGCTAATACATGCT
1 AAATATATTATACTAATAAATACT
*
40112915 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
40112939 AAAT
1 AAAT
40112943 CTTCTAGACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:40118434 original size:50 final size:50
Alignment explanation
Indices: 40118311--40118440 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 50
40118301 TGTCATATCT
* * ** *
40118311 CAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCACATGCCATGTCC
1 CAGACATGGTCTTTCATGAGACCTCTCATATCGGTGCACACGCCATGTCC
* * * *
40118361 TAGACATTGTC-TT-ATGGGGGACCTCTCATCTCGGTGC-CAACGCCATGTCC
1 CAGACATGGTCTTTCAT--GAGACCTCTCATATCGGTGCAC-ACGCCATGTCC
40118411 CAGACATGGTCTTTCATGAGACCTCTCATA
1 CAGACATGGTCTTTCATGAGACCTCTCATA
40118441 ATCTCAATGA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
48 2 0.03
49 2 0.03
50 54 0.87
51 2 0.03
52 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
CAGACATGGTCTTTCATGAGACCTCTCATATCGGTGCACACGCCATGTCC
Found at i:40121317 original size:20 final size:19
Alignment explanation
Indices: 40121272--40121320 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
40121262 CTAGTTGTTT
40121272 TCCCTTTTGATTCACAGCC
1 TCCCTTTTGATTCACAGCC
40121291 TCCCTTTTGATTCACAGCC
1 TCCCTTTTGATTCACAGCC
*
40121310 TCCCCTTTGAT
1 TCCCTTTTGAT
40121321 CTTGTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.37, G:0.10, T:0.39
Consensus pattern (19 bp):
TCCCTTTTGATTCACAGCC
Found at i:40122371 original size:24 final size:24
Alignment explanation
Indices: 40122344--40122397 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
40122334 AATCAAAGTC
* * *
40122344 AAATATATTATGCTAATAAATGCT
1 AAATATAGTATACTAATAAATACT
*
40122368 AAATATAGTATACTCATAAATACT
1 AAATATAGTATACTAATAAATACT
40122392 AAATAT
1 AAATAT
40122398 TCTAGAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATATAGTATACTAATAAATACT
Found at i:40131136 original size:20 final size:21
Alignment explanation
Indices: 40131108--40131146 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40131098 ACAAAATTTA
40131108 AACACATAAATACATTATAGT
1 AACACATAAATACATTATAGT
*
40131129 AACA-ATAAATGCATTATA
1 AACACATAAATACATTATA
40131147 ATTATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (21 bp):
AACACATAAATACATTATAGT
Found at i:40141764 original size:16 final size:16
Alignment explanation
Indices: 40141739--40141778 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
40141729 AAATATAAAC
*
40141739 AGATAGGTTAGTATAT
1 AGATATGTTAGTATAT
40141755 AGATATGTTAGTATAT
1 AGATATGTTAGTATAT
40141771 AGATATGT
1 AGATATGT
40141779 GTGTTATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (16 bp):
AGATATGTTAGTATAT
Found at i:40142189 original size:36 final size:36
Alignment explanation
Indices: 40142149--40142243 Score: 172
Period size: 36 Copynumber: 2.6 Consensus size: 36
40142139 CCTAGATAGT
40142149 AGGAATTGCATGCTAGTAGTGTACAAGGGGCATTGC
1 AGGAATTGCATGCTAGTAGTGTACAAGGGGCATTGC
40142185 AGGAATTGCATGCTAGTAGTGTACAAGGGGCATTGC
1 AGGAATTGCATGCTAGTAGTGTACAAGGGGCATTGC
* *
40142221 AGGAATTGCCTGTTAGTAGTGTA
1 AGGAATTGCATGCTAGTAGTGTA
40142244 GAATGACTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (36 bp):
AGGAATTGCATGCTAGTAGTGTACAAGGGGCATTGC
Found at i:40144498 original size:118 final size:118
Alignment explanation
Indices: 40144290--40144526 Score: 456
Period size: 118 Copynumber: 2.0 Consensus size: 118
40144280 AAGAAGGAAA
*
40144290 ATGCGATAAAGAAGTAGGATATTCTGTACAGTACTGGGTTCAAGAATAATCGGCTTTCACAACTG
1 ATGCGATAAAGAACTAGGATATTCTGTACAGTACTGGGTTCAAGAATAATCGGCTTTCACAACTG
40144355 GACTTTCAAACAAGCTAAAGTAATTGTTATGTTTCCAATCTCAGTAACCTCTC
66 GACTTTCAAACAAGCTAAAGTAATTGTTATGTTTCCAATCTCAGTAACCTCTC
*
40144408 ATGCGATAAAGAACTAGGATATTCTGTACAGTACTGGGTTCAAGAATTATCGGCTTTCACAACTG
1 ATGCGATAAAGAACTAGGATATTCTGTACAGTACTGGGTTCAAGAATAATCGGCTTTCACAACTG
40144473 GACTTTCAAACAAGCTAAAGTAATTGTTATGTTTCCAATCTCAGTAACCTCTC
66 GACTTTCAAACAAGCTAAAGTAATTGTTATGTTTCCAATCTCAGTAACCTCTC
40144526 A
1 A
40144527 ACTGAGCATC
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (118 bp):
ATGCGATAAAGAACTAGGATATTCTGTACAGTACTGGGTTCAAGAATAATCGGCTTTCACAACTG
GACTTTCAAACAAGCTAAAGTAATTGTTATGTTTCCAATCTCAGTAACCTCTC
Found at i:40146817 original size:6 final size:6
Alignment explanation
Indices: 40146808--40146841 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
40146798 TGAAGATGAA
40146808 GATGGT GATGGT GATGGT GATGGT GATGGT GATG
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATG
40146842 CTGAAGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (6 bp):
GATGGT
Found at i:40148729 original size:20 final size:20
Alignment explanation
Indices: 40148696--40148742 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
40148686 AAAAGAGACA
*
40148696 AAAGCAAAACGAAACAGAAAG
1 AAAG-AAAAAGAAACAGAAAG
*
40148717 AAAGAAAAAGAAATAGAAAG
1 AAAGAAAAAGAAACAGAAAG
40148737 AAAGAA
1 AAAGAA
40148743 GAACTCATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAGAAACAGAAAG
Found at i:40149175 original size:20 final size:20
Alignment explanation
Indices: 40149150--40149191 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40149140 GAATTTAGGC
*
40149150 AAATATTGAATAAAAAATTG
1 AAATATTCAATAAAAAATTG
**
40149170 AAATATTCAATATGAAATTG
1 AAATATTCAATAAAAAATTG
40149190 AA
1 AA
40149192 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATTCAATAAAAAATTG
Found at i:40150631 original size:26 final size:26
Alignment explanation
Indices: 40150601--40150653 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
40150591 ATAGTTACAG
* *
40150601 AGAAGAAACGAAATAGAAAGA-GAGAA
1 AGAAGAAAAGAAA-AGAAAAAGGAGAA
40150627 AGAAGAAAAGAAAAGAAAAAGGAGAA
1 AGAAGAAAAGAAAAGAAAAAGGAGAA
40150653 A
1 A
40150654 TTCAAGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (26 bp):
AGAAGAAAAGAAAAGAAAAAGGAGAA
Found at i:40157792 original size:45 final size:46
Alignment explanation
Indices: 40157738--40157832 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 46
40157728 TAAATACATG
40157738 TATATTTAAATTATTAGTACAAATGTATATAATATATATATTTACT
1 TATATTTAAATTATTAGTACAAATGTATATAATATATATATTTACT
40157784 TATA-TTAAATTATTAGTACAAATGTATATAATATATATATTTACT
1 TATATTTAAATTATTAGTACAAATGTATATAATATATATATTTACT
40157829 TATA
1 TATA
40157833 AATTAAGTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 45 0.92
46 4 0.08
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (46 bp):
TATATTTAAATTATTAGTACAAATGTATATAATATATATATTTACT
Found at i:40158397 original size:18 final size:19
Alignment explanation
Indices: 40158374--40158420 Score: 87
Period size: 18 Copynumber: 2.5 Consensus size: 19
40158364 AAAAATGATA
40158374 CAATCTTAGATATGAT-TG
1 CAATCTTAGATATGATATG
40158392 CAATCTTAGATATGATATG
1 CAATCTTAGATATGATATG
40158411 CAATCTTAGA
1 CAATCTTAGA
40158421 AGATATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (19 bp):
CAATCTTAGATATGATATG
Found at i:40158731 original size:18 final size:18
Alignment explanation
Indices: 40158708--40158742 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40158698 CATGTTTCCC
40158708 TTTTTTT-ATATATTTTAA
1 TTTTTTTAATA-ATTTTAA
40158726 TTTTTTTAATAATTTTA
1 TTTTTTTAATAATTTTA
40158743 GTATCATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTAATAATTTTAA
Found at i:40169084 original size:78 final size:78
Alignment explanation
Indices: 40168986--40169254 Score: 405
Period size: 78 Copynumber: 3.4 Consensus size: 78
40168976 CGAAGAAACA
* * * *
40168986 GATTTGGCATCTCTATATTAGACGGAGAGCAGATCGAAGACATAGCAAATCTGACCTTTATTAAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTAAA
40169051 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
40169064 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTAAA
*
40169129 GCAAATCCAAGAT
66 GCAGATCCAAGAT
* * * * *
40169142 GATTTGACATCTCTGTATTAGACGGGAAGTAGATCAAAGACATAACAGAT-TGGACCTTCATTAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTAA
40169206 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
*
40169220 GATTTGGTATCTCTGTATTAGACGGGGAGCAGATC
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
40169255 TGACCTTCAT
Statistics
Matches: 171, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
77 1 0.01
78 170 0.99
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTAAA
GCAGATCCAAGAT
Found at i:40169364 original size:45 final size:45
Alignment explanation
Indices: 40169280--40169477 Score: 254
Period size: 45 Copynumber: 4.4 Consensus size: 45
40169270 TACATCGAAA
* * * * *
40169280 CAGATCCAAGATGACAAATTTGGCATCTCTGTATCAGACGGAGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
* *
40169325 CAAATCGGAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
* * * * *
40169370 CAGATTGAAGA-AGCAGATTTGGCGTCTCTGTATTTGACGGTGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
*
40169414 CAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGACGGGGAG
1 CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
* *
40169459 CAGATCAAAGATAGCAGAT
1 CAGATCGAAGATAACAGAT
40169478 ATCGCCTTCC
Statistics
Matches: 132, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 39 0.30
45 93 0.70
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (45 bp):
CAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
Found at i:40169415 original size:89 final size:90
Alignment explanation
Indices: 40169280--40169477 Score: 274
Period size: 89 Copynumber: 2.2 Consensus size: 90
40169270 TACATCGAAA
* * *
40169280 CAGATCCAAGAT-GACAAATTTGGCATCTCTGTATCAGACGGAGAGCAAATCGGAGATAACAGAT
1 CAGATCAAAGATAG-CAGATTTGGCATCTCTGTATCAGACGGAGAGCAAATCGAAGATAACAGAT
40169344 TTGGCATCTCTGTATTAGACGGGGAG
65 TTGGCATCTCTGTATTAGACGGGGAG
** * ** * *
40169370 CAGATTGAAGA-AGCAGATTTGGCGTCTCTGTATTTGACGGTGAGCAGATCGAAGATAACAGATT
1 CAGATCAAAGATAGCAGATTTGGCATCTCTGTATCAGACGGAGAGCAAATCGAAGATAACAGATT
*
40169434 TGGCGTCTCTGTATTAGACGGGGAG
66 TGGCATCTCTGTATTAGACGGGGAG
40169459 CAGATCAAAGATAGCAGAT
1 CAGATCAAAGATAGCAGAT
40169478 ATCGCCTTCC
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
89 77 0.82
90 17 0.18
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (90 bp):
CAGATCAAAGATAGCAGATTTGGCATCTCTGTATCAGACGGAGAGCAAATCGAAGATAACAGATT
TGGCATCTCTGTATTAGACGGGGAG
Found at i:40169505 original size:89 final size:89
Alignment explanation
Indices: 40169323--40169512 Score: 215
Period size: 89 Copynumber: 2.1 Consensus size: 89
40169313 TCAGACGGAG
* * **
40169323 AGCAAATCGGAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGAAGCAGAT
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGAAGCAGAT
* * ** * *
40169388 TTGGCGTCTCTGTATTTGACGGTG
66 TCGCCGTCTCTGTAGCTGACAGTA
*
40169412 AGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGA
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGA-AGCAGA
*
40169477 TATCGCCTTC-CTG-AGCTG-CAGTAA
65 T-TCGCCGTCTCTGTAGCTGACAGT-A
*
40169501 AGCAGATTGAAG
1 AGCAGATCGAAG
40169513 CCGTCAAGAG
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
88 3 0.04
89 67 0.79
90 10 0.12
91 5 0.06
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (89 bp):
AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGAAGCAGAT
TCGCCGTCTCTGTAGCTGACAGTA
Found at i:40169840 original size:17 final size:19
Alignment explanation
Indices: 40169818--40169860 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
40169808 ATGGAAATAT
40169818 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
40169835 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
40169854 AATCTTA
1 AATCTTA
40169861 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:40169850 original size:19 final size:19
Alignment explanation
Indices: 40169826--40169862 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40169816 ATAATCTTCA
40169826 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
40169845 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
40169863 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:40169888 original size:22 final size:22
Alignment explanation
Indices: 40169826--40169885 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 22
40169816 ATAATCTTCA
40169826 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
40169845 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
40169867 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
40169886 GATTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:40170879 original size:13 final size:12
Alignment explanation
Indices: 40170863--40170924 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
40170853 GAGAAAAAAT
40170863 TAAATGAAATTGA
1 TAAATGAAATT-A
*
40170876 TAAATTAAATTA
1 TAAATGAAATTA
*
40170888 TTAAATGAAATGA
1 -TAAATGAAATTA
* *
40170901 GAAAGTGATATTA
1 TAAA-TGAAATTA
40170914 TAAGATGAAAT
1 TAA-ATGAAAT
40170925 GAGAAATACA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
12 4 0.11
13 33 0.87
14 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (12 bp):
TAAATGAAATTA
Found at i:40170913 original size:26 final size:25
Alignment explanation
Indices: 40170861--40170931 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
40170851 AAGAGAAAAA
* *
40170861 ATTAAATGAAATTGATAAATTAAATT
1 ATTAAATGAAA-TGAGAAATGAAATT
*
40170887 ATTAAATGAAATGAGAAAGTGATATT
1 ATTAAATGAAATGAGAAA-TGAAATT
40170913 A-TAAGATGAAATGAGAAAT
1 ATTAA-ATGAAATGAGAAAT
40170932 ACAATTTGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 10 0.25
26 30 0.75
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (25 bp):
ATTAAATGAAATGAGAAATGAAATT
Found at i:40170990 original size:32 final size:32
Alignment explanation
Indices: 40170954--40171018 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
40170944 ATGAGATTGA
40170954 AAGCATAAAACCAAGGCTCATGAATTATTCAT
1 AAGCATAAAACCAAGGCTCATGAATTATTCAT
40170986 AAGCATAAAACCAAGGCTCATGAATTATTCAT
1 AAGCATAAAACCAAGGCTCATGAATTATTCAT
40171018 A
1 A
40171019 CTTGAATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (32 bp):
AAGCATAAAACCAAGGCTCATGAATTATTCAT
Found at i:40181543 original size:26 final size:26
Alignment explanation
Indices: 40181514--40181569 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
40181504 TGGTACAAAT
40181514 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
40181540 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40181566 TGAT
1 TGAT
40181570 GGGCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.39
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40184105 original size:25 final size:25
Alignment explanation
Indices: 40184077--40184127 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40184067 CTGGTGCACA
40184077 GCTTCCATTCACTTTAACCTATAAT
1 GCTTCCATTCACTTTAACCTATAAT
40184102 GCTTCCATTCACTTTAACCTATAAT
1 GCTTCCATTCACTTTAACCTATAAT
40184127 G
1 G
40184128 AAATTATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.39
Consensus pattern (25 bp):
GCTTCCATTCACTTTAACCTATAAT
Found at i:40190076 original size:40 final size:40
Alignment explanation
Indices: 40190032--40190258 Score: 418
Period size: 40 Copynumber: 5.7 Consensus size: 40
40190022 CAATTGAGGA
40190032 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
40190072 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
40190112 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
40190152 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
40190192 TTATATCCGGGATAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* * *
40190232 TTATATCCGGGCTAAATCTCGAAGGCA
1 TTATATCCGGGTTAAGTCCCGAAGGCA
40190259 ATTGGGTTGG
Statistics
Matches: 183, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 183 1.00
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.31
Consensus pattern (40 bp):
TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:40191608 original size:26 final size:26
Alignment explanation
Indices: 40191579--40191634 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
40191569 TGGTACAAAT
40191579 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
40191605 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40191631 TGAT
1 TGAT
40191635 GGGCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.39
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40195957 original size:10 final size:9
Alignment explanation
Indices: 40195933--40195962 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
40195923 AGTAAAATAG
40195933 TTATAATTT
1 TTATAATTT
40195942 TTATAATTT
1 TTATAATTT
40195951 TTAATAATTT
1 TT-ATAATTT
40195961 TT
1 TT
40195963 TTATAGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATAATTT
Found at i:40202637 original size:43 final size:44
Alignment explanation
Indices: 40202557--40202644 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
40202547 CGAACAAAAA
* *
40202557 AAAAGATTAGGTACCAAATTAGGAAAAAAGAGTCAAGTTTAGGT
1 AAAAGATTAAGTACCAAATTAAGAAAAAAGAGTCAAGTTTAGGT
* * *
40202601 AAAATATTAAGTACCAACTTAAG-AAAAAGTGTCAAGTTTAGGT
1 AAAAGATTAAGTACCAAATTAAGAAAAAAGAGTCAAGTTTAGGT
40202644 A
1 A
40202645 TCAAATTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 20 0.51
44 19 0.49
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (44 bp):
AAAAGATTAAGTACCAAATTAAGAAAAAAGAGTCAAGTTTAGGT
Found at i:40202683 original size:32 final size:30
Alignment explanation
Indices: 40202624--40202687 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
40202614 CCAACTTAAG
40202624 AAAAAGTGTCAAGTTTAGGTATCAAATTAGA
1 AAAAAGTGTCAAGTTTAGGTATCAAATT-GA
40202655 AAAAAGTGTCAAAGTTTAGGTA-CAAAATTGA
1 AAAAAGTGTC-AAGTTTAGGTATC-AAATTGA
40202686 AA
1 AA
40202688 CAAAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (30 bp):
AAAAAGTGTCAAGTTTAGGTATCAAATTGA
Found at i:40205830 original size:86 final size:85
Alignment explanation
Indices: 40205676--40205852 Score: 291
Period size: 86 Copynumber: 2.1 Consensus size: 85
40205666 TTTACAGCTG
* * **
40205676 TAGACACTGGATTCTTTTCAATGCACAAGTACATTTAATTCAGCTAAGGAAAACAATTTTAAATG
1 TAGACACTGGACTCTTTTAAATGCACAAGTACATGCAATTCAGCTAAGGAAAACAATTTTAAATG
40205741 TGAATAAATACATATATTTA
66 TGAATAAATACATATATTTA
* *
40205761 TAGACACTGTACTCTTTTAAATGCACAAGTACATGCAACTTCAGCTAGGGAAAACAATTTTAAAT
1 TAGACACTGGACTCTTTTAAATGCACAAGTACATGCAA-TTCAGCTAAGGAAAACAATTTTAAAT
40205826 GTGAATAAATACATATATTTA
65 GTGAATAAATACATATATTTA
40205847 TAGACA
1 TAGACA
40205853 AATACATATA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 33 0.39
86 52 0.61
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (85 bp):
TAGACACTGGACTCTTTTAAATGCACAAGTACATGCAATTCAGCTAAGGAAAACAATTTTAAATG
TGAATAAATACATATATTTA
Found at i:40205857 original size:20 final size:20
Alignment explanation
Indices: 40205832--40205872 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40205822 AAATGTGAAT
40205832 AAATACATATATTTATAGAC
1 AAATACATATATTTATAGAC
40205852 AAATACATATATTTATAGAC
1 AAATACATATATTTATAGAC
40205872 A
1 A
40205873 CTGTATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATACATATATTTATAGAC
Found at i:40205883 original size:106 final size:106
Alignment explanation
Indices: 40205746--40205938 Score: 377
Period size: 106 Copynumber: 1.8 Consensus size: 106
40205736 AAATGTGAAT
40205746 AAATACATATATTTATAGACACTGTACTCTTTTAAATGCACAAGTACATGCAACTTCAGCTAGGG
1 AAATACATATATTTATAGACACTGTACTCTTTTAAATGCACAAGTACATGCAACTTCAGCTAGGG
40205811 AAAACAATTTTAAATGTGAATAAATACATATATTTATAGAC
66 AAAACAATTTTAAATGTGAATAAATACATATATTTATAGAC
*
40205852 AAATACATATATTTATAGACACTGTATTCTTTTAAATGCACAAGTACATGCAACTTCAGCTAGGG
1 AAATACATATATTTATAGACACTGTACTCTTTTAAATGCACAAGTACATGCAACTTCAGCTAGGG
40205917 AAAACAATTTTAAATGTGAATA
66 AAAACAATTTTAAATGTGAATA
40205939 TGTATATACA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 86 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (106 bp):
AAATACATATATTTATAGACACTGTACTCTTTTAAATGCACAAGTACATGCAACTTCAGCTAGGG
AAAACAATTTTAAATGTGAATAAATACATATATTTATAGAC
Found at i:40206894 original size:30 final size:30
Alignment explanation
Indices: 40206854--40206941 Score: 124
Period size: 30 Copynumber: 2.9 Consensus size: 30
40206844 TATGGATCAA
* * *
40206854 AGGGACAAACC-ACGAAGAAGCACCGATACC
1 AGGGAGAAACCAAGGAA-AAGCACTGATACC
40206884 AGGGAGAAACCAAGGAAAAGCACTGATACC
1 AGGGAGAAACCAAGGAAAAGCACTGATACC
*
40206914 AGGGAGAAACCGAGGAAAAGCACTGATA
1 AGGGAGAAACCAAGGAAAAGCACTGATA
40206942 GACCCCCAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.45, C:0.22, G:0.27, T:0.06
Consensus pattern (30 bp):
AGGGAGAAACCAAGGAAAAGCACTGATACC
Found at i:40209305 original size:23 final size:23
Alignment explanation
Indices: 40209195--40209313 Score: 64
Period size: 23 Copynumber: 5.1 Consensus size: 23
40209185 ATCAGGTAGT
* *
40209195 TCACAAAGAACCATATCGGAAAGC
1 TCACAAAGAGCC-TATCGGGAAGC
* *
40209219 TCACGAAGAGCCTATCGGGAAGT
1 TCACAAAGAGCCTATCGGGAAGC
** * * *
40209242 TC-CGGATAGCCGTATATCAGGAAGT
1 TCACAAAGAGCC---TATCGGGAAGC
**
40209267 TCA-AGCGAGCAC-ATCGGGAAGC
1 TCACAAAGAGC-CTATCGGGAAGC
*
40209289 TCACAAAGAGCCTATCGGGATGC
1 TCACAAAGAGCCTATCGGGAAGC
40209312 TC
1 TC
40209314 TTAAGAGCTA
Statistics
Matches: 73, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
22 19 0.26
23 27 0.37
24 10 0.14
25 16 0.22
26 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (23 bp):
TCACAAAGAGCCTATCGGGAAGC
Found at i:40211436 original size:3 final size:3
Alignment explanation
Indices: 40211422--40211470 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
40211412 TTTTATACTA
*
40211422 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40211465 AA- AAT A
1 AAT AAT A
40211471 TCTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:40211444 original size:11 final size:11
Alignment explanation
Indices: 40211428--40211466 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
40211418 ACTAAATAAT
40211428 TAATAATAAAA
1 TAATAATAAAA
*
40211439 TAATAATGAAA
1 TAATAATAAAA
40211450 TAATAATAAAA
1 TAATAATAAAA
40211461 TAATAA
1 TAATAA
40211467 AATATCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:40211453 original size:19 final size:19
Alignment explanation
Indices: 40211429--40211470 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40211419 CTAAATAATT
*
40211429 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
40211448 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
40211467 AATA
1 AATA
40211471 TCTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:40211493 original size:20 final size:21
Alignment explanation
Indices: 40211440--40211504 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 21
40211430 ATAATAAAAT
* *
40211440 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
40211459 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
40211480 AATAAT-ATATATCTAATT-A
1 AATAATAAAATATCTAATTAA
40211499 AATAAT
1 AATAAT
40211505 CATAAAAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 18 0.46
20 12 0.31
21 9 0.23
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:40211769 original size:30 final size:31
Alignment explanation
Indices: 40211713--40211771 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
40211703 CACTCTTAAA
** *
40211713 ATATTTACACTATTGGCCCTTCAAATTTTTT
1 ATATTTACACTATTAACCCCTCAAATTTTTT
40211744 ATATTTACACT-TTAACCCCTCAAATTTT
1 ATATTTACACTATTAACCCCTCAAATTTT
40211772 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.46
Consensus pattern (31 bp):
ATATTTACACTATTAACCCCTCAAATTTTTT
Found at i:40211779 original size:30 final size:31
Alignment explanation
Indices: 40211713--40211781 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
40211703 CACTCTTAAA
** * *
40211713 ATATTTACACTATTGGCCCTTCAAATTTTTT
1 ATATTTACACTATTAACCCCTCAAATTTTTG
40211744 ATATTTACACT-TTAACCCCTCAAA-TTTTG
1 ATATTTACACTATTAACCCCTCAAATTTTTG
40211773 AGTATTTAC
1 A-TATTTAC
40211782 TCTTATGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 17 0.52
31 11 0.33
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (31 bp):
ATATTTACACTATTAACCCCTCAAATTTTTG
Found at i:40212597 original size:18 final size:18
Alignment explanation
Indices: 40212574--40212612 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40212564 CTAGGTAACT
40212574 TTTATCTCAAA-TGATGAA
1 TTTATCTCAAACT-ATGAA
40212592 TTTATCTCAAACTATGAA
1 TTTATCTCAAACTATGAA
40212610 TTT
1 TTT
40212613 GATATTCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
TTTATCTCAAACTATGAA
Found at i:40214156 original size:22 final size:23
Alignment explanation
Indices: 40214129--40214180 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
40214119 ATAAAATAAA
*
40214129 AAAAGAGGA-AAAAATCATGGGT
1 AAAAGAGGACAAAAATCATGGGC
40214151 AAAAGA-GACAAAAATCATGGGC
1 AAAAGAGGACAAAAATCATGGGC
40214173 AAAAGAGG
1 AAAAGAGG
40214181 CATCGACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.07
22 24 0.89
23 1 0.04
ACGTcount: A:0.56, C:0.08, G:0.27, T:0.10
Consensus pattern (23 bp):
AAAAGAGGACAAAAATCATGGGC
Found at i:40221604 original size:16 final size:17
Alignment explanation
Indices: 40221583--40221617 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40221573 TAATGTCTAG
40221583 GAAAATTA-TTAATTGA
1 GAAAATTAGTTAATTGA
40221599 GAAAATTAGTTTAATTGA
1 GAAAATTAG-TTAATTGA
40221617 G
1 G
40221618 GGGTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (17 bp):
GAAAATTAGTTAATTGA
Found at i:40222244 original size:31 final size:31
Alignment explanation
Indices: 40222209--40222271 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
40222199 ATCTTAAGAT
40222209 ATAAATAATTTAGTGACTATAACGCAAATGG
1 ATAAATAATTTAGTGACTATAACGCAAATGG
*
40222240 ATAAATAATTTAGTGACTATGACGCAAATGG
1 ATAAATAATTTAGTGACTATAACGCAAATGG
40222271 A
1 A
40222272 CAGTTTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (31 bp):
ATAAATAATTTAGTGACTATAACGCAAATGG
Found at i:40224438 original size:84 final size:84
Alignment explanation
Indices: 40224297--40224465 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
40224287 AGAGGCTAAG
* * *
40224297 TCCTCTCCATTCTCAGTTTTTCAACTCTCGACCCCGTTGTTGGTGAATCAGCCTTCTTCTATATG
1 TCCTCTCCATTCTCAGTTTTTCAACTCTCGACCCCGTTGTTGATGAATCAACCTTCTTCTATACG
40224362 ACCCTTTCTCTACTCTTAT
66 ACCCTTTCTCTACTCTTAT
40224381 TCCTCTCCATTCTCAGTTTTTCAACTCTCGACCCCGTTGTTGATGAATCAACCTTCTTCTATACG
1 TCCTCTCCATTCTCAGTTTTTCAACTCTCGACCCCGTTGTTGATGAATCAACCTTCTTCTATACG
40224446 ACCCTTTCTCTACTCTTAT
66 ACCCTTTCTCTACTCTTAT
40224465 T
1 T
40224466 GATACTCTGT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.17, C:0.33, G:0.09, T:0.41
Consensus pattern (84 bp):
TCCTCTCCATTCTCAGTTTTTCAACTCTCGACCCCGTTGTTGATGAATCAACCTTCTTCTATACG
ACCCTTTCTCTACTCTTAT
Found at i:40224603 original size:14 final size:15
Alignment explanation
Indices: 40224586--40224616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40224576 ATGAAATATA
40224586 TTAAG-TAAATAAAT
1 TTAAGTTAAATAAAT
40224600 TTAAGTTAAATAAAT
1 TTAAGTTAAATAAAT
40224615 TT
1 TT
40224617 TAAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TTAAGTTAAATAAAT
Found at i:40224987 original size:42 final size:42
Alignment explanation
Indices: 40224918--40225005 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
40224908 TTGTAGGTCT
*
40224918 TTATACGTTAGCTTGAGCTATACGTGGCACGCTGCTATCTAA
1 TTATACGTTAGCTTGAGCTATAAGTGGCACGCTGCTATCTAA
* * *
40224960 TTATACGTTAGCTTGAGTTATAAGTGGCACGTTGCTGTCTAA
1 TTATACGTTAGCTTGAGCTATAAGTGGCACGCTGCTATCTAA
40225002 TTAT
1 TTAT
40225006 TCTATCAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (42 bp):
TTATACGTTAGCTTGAGCTATAAGTGGCACGCTGCTATCTAA
Found at i:40225476 original size:21 final size:21
Alignment explanation
Indices: 40225431--40225470 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40225421 AATTATTATA
40225431 ATAAAAATATTAAATATATGT
1 ATAAAAATATTAAATATATGT
*
40225452 ATAATAAATA-TAATTATAT
1 ATAA-AAATATTAAATATAT
40225471 TGATAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
ATAAAAATATTAAATATATGT
Found at i:40227356 original size:27 final size:26
Alignment explanation
Indices: 40227297--40227376 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
40227287 ATTTGCTTTG
** * *
40227297 TGTATTATAGATTTTAAAATGCTTTA
1 TGTATTATTCATTTTAAATTGTTTTA
** *
40227323 TACATTATTTATTTTAAACTTGTTTTA
1 TGTATTATTCATTTTAAA-TTGTTTTA
40227350 TGTATTATTCATTTTAAATTGTTTTA
1 TGTATTATTCATTTTAAATTGTTTTA
40227376 T
1 T
40227377 TGTTTACTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 23 0.52
27 21 0.48
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (26 bp):
TGTATTATTCATTTTAAATTGTTTTA
Found at i:40232353 original size:14 final size:15
Alignment explanation
Indices: 40232326--40232354 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40232316 CCAACATTAT
40232326 CATCCATGGATTGCA
1 CATCCATGGATTGCA
40232341 CATCCAT-GATTGCA
1 CATCCATGGATTGCA
40232355 AACAAGGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (15 bp):
CATCCATGGATTGCA
Found at i:40241137 original size:43 final size:42
Alignment explanation
Indices: 40241070--40241215 Score: 193
Period size: 43 Copynumber: 3.4 Consensus size: 42
40241060 AAAAATTACT
* *
40241070 GGCGCTTTTTTAGAAAATGCCGCTAAAGAACAGGACCTTTAGC
1 GGCGCTTTTTTA-AAAACGCCGCTAAAGACCAGGACCTTTAGC
* *
40241113 GGCGCTTTTTGTAAAAACGGCGCTAAAGACCAGGACCTTTAGT
1 GGCGCTTTTT-TAAAAACGCCGCTAAAGACCAGGACCTTTAGC
* *
40241156 GGCGCTTTTTTTTAAAAGCGCCGCTAAAGACCAAGACCTTTAGC
1 GGCGC--TTTTTTAAAAACGCCGCTAAAGACCAGGACCTTTAGC
*
40241200 GGCGCTTTTCTAAAAA
1 GGCGCTTTTTTAAAAA
40241216 ACGATGATCT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
42 9 0.10
43 41 0.46
44 35 0.39
45 5 0.06
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (42 bp):
GGCGCTTTTTTAAAAACGCCGCTAAAGACCAGGACCTTTAGC
Found at i:40245796 original size:73 final size:75
Alignment explanation
Indices: 40245613--40245797 Score: 311
Period size: 73 Copynumber: 2.5 Consensus size: 75
40245603 GGCGTTTTTT
* *
40245613 TCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTATTTTTTGTGGCGTTTTTTAAAAAA
1 TCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTAGTTTTTGTGGCGTGTTTTAAAAAA
*
40245678 ATGCCACTAA
66 ACGCCACTAA
*
40245688 TCTCTCAATTTTCATATTTATTTTTATTTGTTATAATAGT-GTTTTTGTGGCGTGTTTT-AAAAA
1 TCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTAGTTTTTGTGGCGTGTTTTAAAAAA
40245751 ACGCCACTAA
66 ACGCCACTAA
*
40245761 TCTCTTAATTTTCATATTTATTTTTATTTGATATAAT
1 TCTCTTAATTTTCATATTTATTTTTATTTGTTATAAT
40245798 TTGGAAGCCA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
73 49 0.47
74 16 0.15
75 39 0.38
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.54
Consensus pattern (75 bp):
TCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTAGTTTTTGTGGCGTGTTTTAAAAAA
ACGCCACTAA
Found at i:40246169 original size:21 final size:21
Alignment explanation
Indices: 40246143--40246293 Score: 131
Period size: 21 Copynumber: 6.8 Consensus size: 21
40246133 CTCTTAAACA
*
40246143 TTAAACCCTAAACCATATATC
1 TTAAACCATAAACCATATATC
* *
40246164 TTAAACCATAGTTAACTCATAAACC
1 TTAAACCATA---AAC-CATATATC
* *
40246189 CTAAACCCTAAACCATATATC
1 TTAAACCATAAACCATATATC
*
40246210 TTAAACCTTAAACCATATATC
1 TTAAACCATAAACCATATATC
* *
40246231 TTAAACCATAATTAACTCATAAACC
1 TTAAACCAT-A--AAC-CATATATC
**
40246256 TTAAACCCCAAACCATATATC
1 TTAAACCATAAACCATATATC
*
40246277 TCAAACCATAAACCATA
1 TTAAACCATAAACCATA
40246294 AACTATAATG
Statistics
Matches: 103, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
21 62 0.60
22 7 0.07
24 7 0.07
25 27 0.26
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (21 bp):
TTAAACCATAAACCATATATC
Found at i:40246180 original size:46 final size:46
Alignment explanation
Indices: 40246127--40246216 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
40246117 TTCAAATTCG
* *
40246127 AGTTAACTCTTAAACATTAAACCCTAAACCATATATCTTAAACCAT
1 AGTTAACTCATAAACACTAAACCCTAAACCATATATCTTAAACCAT
*
40246173 AGTTAACTCATAAACCCTAAACCCTAAACCATATATCTTAAACC
1 AGTTAACTCATAAACACTAAACCCTAAACCATATATCTTAAACC
40246217 TTAAACCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.28
Consensus pattern (46 bp):
AGTTAACTCATAAACACTAAACCCTAAACCATATATCTTAAACCAT
Found at i:40246226 original size:67 final size:67
Alignment explanation
Indices: 40246143--40246293 Score: 248
Period size: 67 Copynumber: 2.3 Consensus size: 67
40246133 CTCTTAAACA
* * *
40246143 TTAAACCCTAAACCATATATCTTAAACCATAGTTAACTCATAAACCCTAAACCCTAAACCATATA
1 TTAAACCATAAACCATATATCTTAAACCATAATTAACTCATAAACCCTAAACCCCAAACCATATA
40246208 TC
66 TC
* *
40246210 TTAAACCTTAAACCATATATCTTAAACCATAATTAACTCATAAACCTTAAACCCCAAACCATATA
1 TTAAACCATAAACCATATATCTTAAACCATAATTAACTCATAAACCCTAAACCCCAAACCATATA
40246275 TC
66 TC
*
40246277 TCAAACCATAAACCATA
1 TTAAACCATAAACCATA
40246294 AACTATAATG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 78 1.00
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (67 bp):
TTAAACCATAAACCATATATCTTAAACCATAATTAACTCATAAACCCTAAACCCCAAACCATATA
TC
Found at i:40246291 original size:7 final size:7
Alignment explanation
Indices: 40246144--40246301 Score: 57
Period size: 7 Copynumber: 21.4 Consensus size: 7
40246134 TCTTAAACAT
*
40246144 TAAACCC
1 TAAACCA
40246151 TAAACCA
1 TAAACCA
* * *
40246158 TATATCT
1 TAAACCA
40246165 TAAACCA
1 TAAACCA
40246172 TAGTTAACTCA
1 TA---AAC-CA
*
40246183 TAAACCC
1 TAAACCA
*
40246190 TAAACCC
1 TAAACCA
40246197 TAAACCA
1 TAAACCA
* * *
40246204 TATATCT
1 TAAACCA
*
40246211 TAAACCT
1 TAAACCA
40246218 TAAACCA
1 TAAACCA
* * *
40246225 TATATCT
1 TAAACCA
40246232 TAAACCA
1 TAAACCA
40246239 TAATTAACTCA
1 T-A--AAC-CA
*
40246250 TAAACCT
1 TAAACCA
*
40246257 TAAACCC
1 TAAACCA
*
40246264 CAAACCA
1 TAAACCA
* *
40246271 TATATC-
1 TAAACCA
40246277 TCAAACCA
1 T-AAACCA
40246285 TAAACCA
1 TAAACCA
*
40246292 TAAACTA
1 TAAACCA
40246299 TAA
1 TAA
40246302 TGATAATTAA
Statistics
Matches: 110, Mismatches: 31, Indels: 20
0.68 0.19 0.12
Matches are distributed among these distances:
6 1 0.01
7 87 0.79
8 8 0.07
10 7 0.06
11 7 0.06
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCA
Found at i:40246540 original size:30 final size:31
Alignment explanation
Indices: 40246484--40246543 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40246474 CCAAAAGCGC
*
40246484 CGCTAATGCTCTGGTTTTTAGCGGCGTTTTA
1 CGCTAATGCACTGGTTTTTAGCGGCGTTTTA
* *
40246515 CGCTATTGCACTGG-TTTTAGTGGCGTTTT
1 CGCTAATGCACTGGTTTTTAGCGGCGTTTT
40246544 TGTTAAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.43
Consensus pattern (31 bp):
CGCTAATGCACTGGTTTTTAGCGGCGTTTTA
Found at i:40249994 original size:8 final size:8
Alignment explanation
Indices: 40249983--40250008 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40249973 AAAAAAATGA
40249983 ATTTAAAT
1 ATTTAAAT
40249991 ATTTAAAT
1 ATTTAAAT
40249999 ATTTAAAT
1 ATTTAAAT
40250007 AT
1 AT
40250009 GAATTCGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTAAAT
Found at i:40251011 original size:6 final size:6
Alignment explanation
Indices: 40251000--40251042 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
40250990 TAAAAATCTC
* *
40251000 AATTTA AATTTA AATGTAA ATATTTG AATTTA AATTTA AATTT
1 AATTTA AATTTA AAT-TTA A-ATTTA AATTTA AATTTA AATTT
40251043 GACCATAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 24 0.77
7 5 0.16
8 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (6 bp):
AATTTA
Found at i:40251019 original size:26 final size:26
Alignment explanation
Indices: 40250990--40251040 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
40250980 GAACTAGTAT
40250990 TAAAAATCTCAATTTAAATTTAAATG
1 TAAAAATCTCAATTTAAATTTAAATG
* * *
40251016 TAAATATTTGAATTTAAATTTAAAT
1 TAAAAATCTCAATTTAAATTTAAAT
40251041 TTGACCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
TAAAAATCTCAATTTAAATTTAAATG
Found at i:40251024 original size:20 final size:20
Alignment explanation
Indices: 40251001--40251040 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40250991 AAAAATCTCA
40251001 ATTTAAATTTAAATGTAAAT
1 ATTTAAATTTAAATGTAAAT
* *
40251021 ATTTGAATTTAAATTTAAAT
1 ATTTAAATTTAAATGTAAAT
40251041 TTGACCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTTAAATTTAAATGTAAAT
Found at i:40255263 original size:88 final size:88
Alignment explanation
Indices: 40255115--40255288 Score: 239
Period size: 88 Copynumber: 2.0 Consensus size: 88
40255105 AAGCCTCACC
* * *
40255115 TAGTCACACATTCATTTCATGCTTTTAACATAGAAAAATATCAACCTATATTCTATGGTGGGTCT
1 TAGTCACACATTCATTTCATGCTTCTAACATAGAAAAATATCAACCTACATGCTATGGTGGGTCT
40255180 TAAAAGATTCCATTT-TTTTTGG
66 TAAAAGATTCCATTTCTTTTTGG
*
40255202 TAGTCAC-C-TTCATTTCATGC-TCTAACATAAAAGAAAAAATATCAACCTACCTGCTATGGTGG
1 TAGTCACACATTCATTTCATGCTTCTAACAT---AG-AAAAATATCAACCTACATGCTATGGTGG
*
40255264 GTCTTAAAAGGTTCCATTTCTTTTT
62 GTCTTAAAAGATTCCATTTCTTTTT
40255289 ACAGCTCATA
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
84 7 0.09
85 12 0.16
86 1 0.01
87 9 0.12
88 43 0.56
89 5 0.06
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (88 bp):
TAGTCACACATTCATTTCATGCTTCTAACATAGAAAAATATCAACCTACATGCTATGGTGGGTCT
TAAAAGATTCCATTTCTTTTTGG
Found at i:40259659 original size:6 final size:6
Alignment explanation
Indices: 40259648--40259673 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40259638 ACATCTTTTA
40259648 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
40259674 TGAGTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:40262017 original size:3 final size:3
Alignment explanation
Indices: 40262009--40262036 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40261999 TCAAACGGTA
40262009 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40262037 GATAGTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40262625 original size:31 final size:31
Alignment explanation
Indices: 40262590--40262649 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
40262580 TAATTAAATC
40262590 AAAGTACAGAGACTAA-ATTCATAATTTTTGT
1 AAAGTACAGAGACTAACA-TCATAATTTTTGT
** *
40262621 AAAGTGTAGAGATTAACATCATAATTTTT
1 AAAGTACAGAGACTAACATCATAATTTTT
40262650 TGGTGCAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (31 bp):
AAAGTACAGAGACTAACATCATAATTTTTGT
Found at i:40263154 original size:31 final size:32
Alignment explanation
Indices: 40263118--40263186 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
40263108 ATAACATTAA
*
40263118 TTTTAA-CAATTTAATAACTTAAAA-GAAATTT
1 TTTTAAGCAATTTAATAA-ATAAAACGAAATTT
*
40263149 TTTTAAGTAATTTAATAAATAAAACGAAATTT
1 TTTTAAGCAATTTAATAAATAAAACGAAATTT
40263181 TATTTA
1 T-TTTA
40263187 TGATTTAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 11 0.33
32 18 0.55
33 4 0.12
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (32 bp):
TTTTAAGCAATTTAATAAATAAAACGAAATTT
Found at i:40263162 original size:32 final size:33
Alignment explanation
Indices: 40263125--40263186 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
40263115 TAATTTTAAC
*
40263125 AATTTAATAACTTAAAA-GAAATTTT-TTTAAGT
1 AATTTAATAA-ATAAAACGAAATTTTATTTAAGT
40263157 AATTTAATAAATAAAACGAAATTTTATTTA
1 AATTTAATAAATAAAACGAAATTTTATTTA
40263187 TGATTTAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 5 0.19
32 18 0.67
33 4 0.15
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (33 bp):
AATTTAATAAATAAAACGAAATTTTATTTAAGT
Found at i:40268378 original size:44 final size:44
Alignment explanation
Indices: 40268329--40268415 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
40268319 AAATTTAATA
40268329 TTTAGTCATTGAGTATAATTTAGTCATTTATTTTTATGTTTTTT
1 TTTAGTCATTGAGTATAATTTAGTCATTTATTTTTATGTTTTTT
*
40268373 TTTAGTCATTGAGTATAATTTAGTCCTTTATTTTTATGTTTTT
1 TTTAGTCATTGAGTATAATTTAGTCATTTATTTTTATGTTTTT
40268416 ATGACGAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (44 bp):
TTTAGTCATTGAGTATAATTTAGTCATTTATTTTTATGTTTTTT
Found at i:40277993 original size:31 final size:31
Alignment explanation
Indices: 40277958--40278020 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
40277948 AAAAAAAAAA
*
40277958 TTGAATAG-CCTAGTGACTTAAATAAAAACTT
1 TTGAATAGTCC-AGTAACTTAAATAAAAACTT
40277989 TTGAATAGTCCAGTAACTTAAATAAAAACTT
1 TTGAATAGTCCAGTAACTTAAATAAAAACTT
40278020 T
1 T
40278021 AAAATAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (31 bp):
TTGAATAGTCCAGTAACTTAAATAAAAACTT
Found at i:40288672 original size:25 final size:25
Alignment explanation
Indices: 40288638--40288687 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40288628 CTTGCCCCTG
40288638 TAGAAAAGCCTCCATACACAACCTT
1 TAGAAAAGCCTCCATACACAACCTT
40288663 TAGAAAAGCCTCCATACACAACCTT
1 TAGAAAAGCCTCCATACACAACCTT
40288688 CAGTAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.20
Consensus pattern (25 bp):
TAGAAAAGCCTCCATACACAACCTT
Found at i:40292611 original size:20 final size:21
Alignment explanation
Indices: 40292586--40292635 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
40292576 TTGAAAATAT
*
40292586 TTGAATTCAACTCGACTC-AC
1 TTGAATTCAACTCAACTCAAC
40292606 TTGAATTCAACTCAACTCAAC
1 TTGAATTCAACTCAACTCAAC
*
40292627 TTGATTTCA
1 TTGAATTCA
40292636 CTTCTAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (21 bp):
TTGAATTCAACTCAACTCAAC
Found at i:40299682 original size:9 final size:9
Alignment explanation
Indices: 40299668--40299707 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
40299658 TTAATTAACC
40299668 TAAATTAAT
1 TAAATTAAT
40299677 TAAATTAAT
1 TAAATTAAT
40299686 TAAATTAAT
1 TAAATTAAT
*
40299695 CAAACTTAAT
1 TAAA-TTAAT
40299705 TAA
1 TAA
40299708 CATAATAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAATTAAT
Found at i:40301479 original size:40 final size:40
Alignment explanation
Indices: 40301356--40301487 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 40
40301346 GAACTTAAAT
* * *
40301356 CGATGAGACATTGGGTGTCAAATTATTA-TTTCAGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGA-ATT-ATC
* * * ** *
40301397 CGATGAGGCATTGGGTGTC-AA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
*
40301434 AGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
*
40301474 CGATGAGGCACTGG
1 CGATGAGACACTGG
40301488 ATGCCAAACT
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 17 0.24
38 7 0.10
39 4 0.06
40 25 0.35
41 18 0.25
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
Found at i:40303659 original size:567 final size:567
Alignment explanation
Indices: 40302579--40303713 Score: 2261
Period size: 567 Copynumber: 2.0 Consensus size: 567
40302569 TACAAATACC
40302579 AATATTAAACCAATCCAAACGCATTTTATATATTATCTAATACTTAAATTTAAACACTTATCATG
1 AATATTAAACCAATCCAAACGCATTTTATATATTATCTAATACTTAAATTTAAACACTTATCATG
40302644 TATTATTATCAATTATCAATTTACTTATTTCACTATTACAATCACAATCCAATATAACACACTGA
66 TATTATTATCAATTATCAATTTACTTATTTCACTATTACAATCACAATCCAATATAACACACTGA
40302709 AGACATCCTAGGTACATGTCATTACCGATAATTAACATGCTTTACCTTTTTAAGTTCGAGATCGG
131 AGACATCCTAGGTACATGTCATTACCGATAATTAACATGCTTTACCTTTTTAAGTTCGAGATCGG
40302774 CTTATGATGGTGATTCGACGATCTGTCTTTAACCTAACCTGCGCACGGAAACAAACCGTACGCTG
196 CTTATGATGGTGATTCGACGATCTGTCTTTAACCTAACCTGCGCACGGAAACAAACCGTACGCTG
40302839 AGTATGAACTCAGTGGTATTTCTATAAATCGATACTTAAGTCAATAATAAATCATATATCAATGA
261 AGTATGAACTCAGTGGTATTTCTATAAATCGATACTTAAGTCAATAATAAATCATATATCAATGA
40302904 ACCTTGAGAATTCAATCTATTACTCCTAATAGTTCAATCATTTGTTTTCGAAATATAATGCTAAG
326 ACCTTGAGAATTCAATCTATTACTCCTAATAGTTCAATCATTTGTTTTCGAAATATAATGCTAAG
40302969 ATCTTGTTAATCACTTTCGATGAAATGTATACAATTTCAATGTTTGTTCATTATCCGTCGATTTT
391 ATCTTGTTAATCACTTTCGATGAAATGTATACAATTTCAATGTTTGTTCATTATCCGTCGATTTT
*
40303034 TCATATTTATTCAGTAATAACCTGTGTTCAGTATCATTCAGACATTCAGTAGCAGACAATTATTC
456 TCATATTTATTCAGTAATAACCTGTGTTCAGTATCATTCAGACATTCAGTAACAGACAATTATTC
40303099 AGTAACAATTAGTTTTTCAGTACTTTTATTTACAATTCATTTGAGTA
521 AGTAACAATTAGTTTTTCAGTACTTTTATTTACAATTCATTTGAGTA
40303146 AATATTAAACCAATCCAAACGCATTTTATATATTATCTAATACTTAAATTTAAACACTTATCATG
1 AATATTAAACCAATCCAAACGCATTTTATATATTATCTAATACTTAAATTTAAACACTTATCATG
40303211 TATTATTATCAATTATCAATTTACTTATTTCACTATTACAATCACAATCCAATATAACACACTGA
66 TATTATTATCAATTATCAATTTACTTATTTCACTATTACAATCACAATCCAATATAACACACTGA
40303276 AGACATCCTAGGTACATGTCATTACCGATAATTAACATGCTTTACCTTTTTAAGTTCGAGATCGG
131 AGACATCCTAGGTACATGTCATTACCGATAATTAACATGCTTTACCTTTTTAAGTTCGAGATCGG
40303341 CTTATGATGGTGATTCGACGATCTGTCTTTAACCTAACCTGCGCACGGAAACAAACCGTACGCTG
196 CTTATGATGGTGATTCGACGATCTGTCTTTAACCTAACCTGCGCACGGAAACAAACCGTACGCTG
40303406 AGTATGAACTCAGTGGTATTTCTATAAATCGATACTTAAGTCAATAATAAATCATATATCAATGA
261 AGTATGAACTCAGTGGTATTTCTATAAATCGATACTTAAGTCAATAATAAATCATATATCAATGA
40303471 ACCTTGAGAATTCAATCTATTACTCCTAATAGTTCAATCATTTGTTTTCGAAATATAATGCTAAG
326 ACCTTGAGAATTCAATCTATTACTCCTAATAGTTCAATCATTTGTTTTCGAAATATAATGCTAAG
40303536 ATCTTGTTAATCACTTTCGATGAAATGTATACAATTTCAATGTTTGTTCATTATCCGTCGATTTT
391 ATCTTGTTAATCACTTTCGATGAAATGTATACAATTTCAATGTTTGTTCATTATCCGTCGATTTT
40303601 TCATATTTATTCAGTAATAACCTGTGTTCAGTATCATTCAGACATTCAGTAACAGACAATTATTC
456 TCATATTTATTCAGTAATAACCTGTGTTCAGTATCATTCAGACATTCAGTAACAGACAATTATTC
40303666 AGTAACAATTAGTTTTTCAGTACTTTTATTTACAATTCATTTGAGTA
521 AGTAACAATTAGTTTTTCAGTACTTTTATTTACAATTCATTTGAGTA
40303713 A
1 A
40303714 TAATATTATT
Statistics
Matches: 567, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
567 567 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (567 bp):
AATATTAAACCAATCCAAACGCATTTTATATATTATCTAATACTTAAATTTAAACACTTATCATG
TATTATTATCAATTATCAATTTACTTATTTCACTATTACAATCACAATCCAATATAACACACTGA
AGACATCCTAGGTACATGTCATTACCGATAATTAACATGCTTTACCTTTTTAAGTTCGAGATCGG
CTTATGATGGTGATTCGACGATCTGTCTTTAACCTAACCTGCGCACGGAAACAAACCGTACGCTG
AGTATGAACTCAGTGGTATTTCTATAAATCGATACTTAAGTCAATAATAAATCATATATCAATGA
ACCTTGAGAATTCAATCTATTACTCCTAATAGTTCAATCATTTGTTTTCGAAATATAATGCTAAG
ATCTTGTTAATCACTTTCGATGAAATGTATACAATTTCAATGTTTGTTCATTATCCGTCGATTTT
TCATATTTATTCAGTAATAACCTGTGTTCAGTATCATTCAGACATTCAGTAACAGACAATTATTC
AGTAACAATTAGTTTTTCAGTACTTTTATTTACAATTCATTTGAGTA
Found at i:40304732 original size:17 final size:15
Alignment explanation
Indices: 40304707--40304746 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
40304697 CTTTTTCTCC
40304707 TTCTTTCTTCCCTTGT
1 TTCTTTCTTCCC-TGT
*
40304723 TTCGTTTCTTCTCTGT
1 TTC-TTTCTTCCCTGT
40304739 TTCTTTCT
1 TTCTTTCT
40304747 ATTCTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 9 0.41
17 8 0.36
ACGTcount: A:0.00, C:0.28, G:0.07, T:0.65
Consensus pattern (15 bp):
TTCTTTCTTCCCTGT
Found at i:40304810 original size:11 final size:11
Alignment explanation
Indices: 40304785--40304826 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 11
40304775 TTTATAATAA
40304785 TAATAATAA--
1 TAATAATAACT
40304794 TAATAATAACT
1 TAATAATAACT
40304805 TAATAATATACT
1 TAATAATA-ACT
40304817 TATATAATAA
1 TA-ATAATAA
40304827 GTAAATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.31
11 8 0.28
12 6 0.21
13 6 0.21
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAATAACT
Found at i:40304826 original size:3 final size:3
Alignment explanation
Indices: 40304778--40304812 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
40304768 TTTTGTTTTT
40304778 ATA ATA ATA ATA ATA ATA ATA ATA ACTTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A--TA ATA ATA
40304813 TACTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 27 0.90
5 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40306393 original size:23 final size:24
Alignment explanation
Indices: 40306347--40306394 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
40306337 AAATATTATT
*
40306347 TTTTAGAAATATTTATGAAAAATA
1 TTTTAGAAATATTTATCAAAAATA
40306371 TTTT-GAAATA-TTATCAAATAATA
1 TTTTAGAAATATTTATCAAA-AATA
40306394 T
1 T
40306395 ACAAAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 11 0.50
24 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
TTTTAGAAATATTTATCAAAAATA
Found at i:40307732 original size:140 final size:139
Alignment explanation
Indices: 40307348--40307775 Score: 635
Period size: 139 Copynumber: 3.1 Consensus size: 139
40307338 GACGAGTTTT
* * * * * * * * *
40307348 TATTGTATTCTACTGTTTTGTTTTCTC-AGTTGCTTTTAATTTTTTTTAAACTGCTACT-CAAGA
1 TATTGTATTTTACTGTTTTTTTTTTTCTAATTGCTTTTGATTGTTTTT-CACTTCTAATCCAAGA
* * * *
40307411 TTTGTTTAATTAATTGTTTATTCGAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTC
65 TTTCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTC
40307476 GATGTGATTG
130 GATGTGATTG
*
40307486 TATTGTATTTTACTGTTTTTCTTTTTCTAATTGCTTTTGATTGTTTTTCACTTCTAATCCAAGAT
1 TATTGTATTTTACTGTTTTTTTTTTTCTAATTGCTTTTGATTGTTTTTCACTTCTAATCCAAGAT
* *
40307551 TTCTTTGATGAGTTGTTTATTCCAATTGAACTTAGTCCATCAGATAACAGTGTAATACTTAGTCG
66 TTCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTCG
*
40307616 TTGTGATTG
131 ATGTGATTG
40307625 TATTGTATTTTACTGTTTTTTTTTTTCTAATTTGCTTTTGATTGTTTTTCACTTCTAATCCAAGA
1 TATTGTATTTTACTGTTTTTTTTTTTCTAA-TTGCTTTTGATTGTTTTTCACTTCTAATCCAAGA
* *
40307690 TTTCTTTGATTAGTTGTTTATTCCAATTGAACTTATTTCATCAGATAACAGTGTAATACTTACTC
65 TTTCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTC
*
40307755 GATGTGATTT
130 GATGTGATTG
*
40307765 TATTGCATTTT
1 TATTGTATTTT
40307776 GCTTTTGGTT
Statistics
Matches: 262, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
138 30 0.11
139 119 0.45
140 113 0.43
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (139 bp):
TATTGTATTTTACTGTTTTTTTTTTTCTAATTGCTTTTGATTGTTTTTCACTTCTAATCCAAGAT
TTCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTCG
ATGTGATTG
Found at i:40307790 original size:140 final size:138
Alignment explanation
Indices: 40307348--40307775 Score: 626
Period size: 140 Copynumber: 3.1 Consensus size: 138
40307338 GACGAGTTTT
* * * * * * * *
40307348 TATTGTATTCTACTG-TTTTGTTTTCTCAGTTGCTTTTAATTTTTTTTAAACTGCTACT-CAAGA
1 TATTGTATTTTACTGTTTTTTTTTTCT-AATTGCTTTTGATTGTTTTT-CACTTCTAATCCAAGA
* * * *
40307411 TTTGTTTAATTAATTGTTTATTCGAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTC
64 TTTCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTC
40307476 GATGTGATTG
129 GATGTGATTG
40307486 TATTGTATTTTACTGTTTTTCTTTTTCTAATTGCTTTTGATTGTTTTTCACTTCTAATCCAAGAT
1 TATTGTATTTTACTGTTTTT-TTTTTCTAATTGCTTTTGATTGTTTTTCACTTCTAATCCAAGAT
* *
40307551 TTCTTTGATGAGTTGTTTATTCCAATTGAACTTAGTCCATCAGATAACAGTGTAATACTTAGTCG
65 TTCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTCG
*
40307616 TTGTGATTG
130 ATGTGATTG
40307625 TATTGTATTTTACTGTTTTTTTTTTTCTAATTTGCTTTTGATTGTTTTTCACTTCTAATCCAAGA
1 TATTGTATTTTACTG-TTTTTTTTTTCTAA-TTGCTTTTGATTGTTTTTCACTTCTAATCCAAGA
* *
40307690 TTTCTTTGATTAGTTGTTTATTCCAATTGAACTTATTTCATCAGATAACAGTGTAATACTTACTC
64 TTTCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTC
*
40307755 GATGTGATTT
129 GATGTGATTG
*
40307765 TATTGCATTTT
1 TATTGTATTTT
40307776 GCTTTTGGTT
Statistics
Matches: 263, Mismatches: 22, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
138 21 0.08
139 118 0.45
140 124 0.47
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (138 bp):
TATTGTATTTTACTGTTTTTTTTTTCTAATTGCTTTTGATTGTTTTTCACTTCTAATCCAAGATT
TCTTTGATTAGTTGTTTATTCCAATTGAACTTAGTTCATCAGATAACAGTGTAATACTTAGTCGA
TGTGATTG
Found at i:40307813 original size:119 final size:120
Alignment explanation
Indices: 40307669--40308148 Score: 389
Period size: 119 Copynumber: 3.9 Consensus size: 120
40307659 CTTTTGATTG
* * * * *
40307669 TTTTTCACTTCTAATCCAAGATTTCTTTGATTAGTTGTTTATTCCAATTGAACTTATTTCAT-CA
1 TTTTTCACTGCTAATCCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAACATAGTTCATCCA
* * * * *
40307733 GATAACAGTGTAATACTTACTCGATGTGATTTTATTGCATTTTGCTTTTGGTTTTT
66 -AAAACAGTGTAATACTTAATCGACGAGATTGTATTGCATTTTGCTTTTGGTTTTT
40307789 TTTTTCACTGCTAAT-CAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAACATAGTTCATCCA
1 TTTTTCACTGCTAATCCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAACATAGTTCATCCA
* *
40307853 AAAACAGTGTAATACTTAATCGACGAGATTGTATTGCATTTTACTGGTTT-CTCTCCGTTGCT
66 AAAACAGTGTAATACTTAATCGACGAGATTGTATTGCATTTTGCT--TTTGGT-T---TT--T
** * * ** * * * * * * * * *
40307915 TTTGAAGTTCTTTTACTGCTAATCGAGATTTCTTCAGTTAATTGTTAATTCCAATTTACCTTAGT
1 TTT----TTC-ACTGCT--AATCCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAACATAGT
* * * * * *
40307980 TCA-ACAGAAAACAGTGTAATACTTAGTCAGATGTGATT-AATTGCATTTTGCTTTTGATTCTTT
59 TCATCCA-AAAACAGTGTAATACTTAATC-GACGAGATTGTATTGCATTTTGCTTTTGGTT-TTT
* * *
40308043 TTGTTCACTGCTAAT-CAAGATTTCTTTAATTAGCTGTTTATTCAAGTTGAACATAGTTCAGT-C
1 TTTTTCACTGCTAATCCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAACATAGTTCA-TCC
* *
40308106 AAAAACAGTGTAATACTTAGTTGACGAGATTGTATTGCATTTT
65 AAAAACAGTGTAATACTTAATCGACGAGATTGTATTGCATTTT
40308149 ATTGGTTTCT
Statistics
Matches: 282, Mismatches: 55, Indels: 46
0.74 0.14 0.12
Matches are distributed among these distances:
119 88 0.31
120 81 0.29
121 7 0.02
123 3 0.01
124 5 0.02
126 4 0.01
128 3 0.01
130 5 0.02
131 3 0.01
132 4 0.01
133 4 0.01
134 68 0.24
135 7 0.02
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (120 bp):
TTTTTCACTGCTAATCCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAACATAGTTCATCCA
AAAACAGTGTAATACTTAATCGACGAGATTGTATTGCATTTTGCTTTTGGTTTTT
Found at i:40307980 original size:134 final size:133
Alignment explanation
Indices: 40307790--40308251 Score: 483
Period size: 134 Copynumber: 3.5 Consensus size: 133
40307780 TTGGTTTTTT
* *
40307790 TTTTCACTGCTAATCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAACATAGTTCATCCAAA
1 TTTTCACTGCTAATCAAGATTTCTTTAATTAATTGTTTATTCCAATTGAACATAGTTCAT-CAAA
*
40307855 AACAGTGTAATACTTAATCGACGAGATTGTATTGCATTTTACTGGTTTCTCTCCGTTGCTTTTGA
65 AACAGTGTAATACTTAGTCGACGAGATTGTATTGCATTTTA-TGGTTTCTCTCCGTTGCTTTTGA
40307920 AGTTC
129 AGTTC
* * * * * * * *
40307925 TTTT-ACTGCTAATCGAGATTTCTTCAGTTAATTGTTAATTCCAATTTACCTTAGTTCAACAGAA
1 TTTTCACTGCTAATCAAGATTTCTTTAATTAATTGTTTATTCCAATTGAACATAGTTCATCA-AA
* * * *
40307989 AACAGTGTAATACTTAGTCAGATGTGATT-AATTGCA-TTT-T-G---CT-T---TTGATTCTT-
65 AACAGTGTAATACTTAGTC-GACGAGATTGTATTGCATTTTATGGTTTCTCTCCGTTGCTT-TTG
40308042 ---TT-
128 AAGTTC
* **
40308044 TGTTCACTGCTAATCAAGATTTCTTTAATTAGCTGTTTATT-CAAGTTGAACATAGTTCAGTCAA
1 TTTTCACTGCTAATCAAGATTTCTTTAATTAATTGTTTATTCCAA-TTGAACATAGTTCA-TCAA
*
40308108 AAACAGTGTAATACTTAGTTGACGAGATTGTATTGCATTTTATTGGTTTCTCTCCGTTGCTTTTG
64 AAACAGTGTAATACTTAGTCGACGAGATTGTATTGCATTTTA-TGGTTTCTCTCCGTTGCTTTTG
*
40308173 AAGTTTT
128 AAG-TTC
* * * * *
40308180 TTTTCACTGCTACTCGAGATTTCTTTAATTAATTGTTTATTCCAATTAAACATGGTTCATACGAA
1 TTTTCACTGCTAATCAAGATTTCTTTAATTAATTGTTTATTCCAATTGAACATAGTTCAT-CAAA
40308245 AACAGTG
65 AACAGTG
40308252 CAAACTAAGA
Statistics
Matches: 262, Mismatches: 39, Indels: 51
0.74 0.11 0.14
Matches are distributed among these distances:
119 13 0.05
120 69 0.26
121 5 0.02
123 6 0.02
124 3 0.01
126 1 0.00
127 4 0.02
128 1 0.00
130 3 0.01
131 6 0.02
133 5 0.02
134 71 0.27
135 14 0.05
136 58 0.22
137 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (133 bp):
TTTTCACTGCTAATCAAGATTTCTTTAATTAATTGTTTATTCCAATTGAACATAGTTCATCAAAA
ACAGTGTAATACTTAGTCGACGAGATTGTATTGCATTTTATGGTTTCTCTCCGTTGCTTTTGAAG
TTC
Found at i:40308074 original size:254 final size:249
Alignment explanation
Indices: 40307516--40308251 Score: 866
Period size: 254 Copynumber: 2.9 Consensus size: 249
40307506 CTTTTTCTAA
* * * * *
40307516 TTGCTTTTGA-TTGTTTTTCACTTCTAATCCAAGATTTCTTTGATGAGTTGTTTATTCCAATTGA
1 TTGCTTTTGATTTTTTTTTCACTGCTAAT-CAAGATTTCTTTAATTAGTTGTTTATTCAAATTGA
* * * ** * *
40307580 ACTTAGTCCATCAGATAACAGTGTAATACTTAGTCGTTGTGATTGTATTGTATTTTACTGTTTTT
65 ACATAGTTCATCA-AAAACAGTGTAATACTTAGTCGACGAGATTGTATTGCATTTTACTG-----
* * *** * * * * * *
40307645 TTTTTTCTAATTTGCTTTTGATTGTTTTTCACTTCTAATCCAAGATTTCTTTGATTAGTTGTTTA
124 GTTTCTCTCCGTTGCTTTTGA-AGTTTTTTACTGCTAAT-CGAGATTTCTTAG-TTAATTGTTTA
* * * *
40307710 TTCCAATTGAACTTATTTCATCAGATAACAGTGTAATACTTACTCGATGTGATTTTATTGCATT
186 TTCCAATTGAACTTAGTTCAACAGAAAACAGTGTAATACTTACTCGATGTGATTTAATTGCATT
*
40307774 TTGCTTTTGGTTTTTTTTTTCACTGCTAATCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGA
1 TTGCTTTT-GATTTTTTTTTCACTGCTAATCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGA
*
40307839 ACATAGTTCATCCAAAAACAGTGTAATACTTAATCGACGAGATTGTATTGCATTTTACTGGTTTC
65 ACATAGTTCAT-CAAAAACAGTGTAATACTTAGTCGACGAGATTGTATTGCATTTTACTGGTTTC
*
40307904 TCTCCGTTGCTTTTGAAGTTCTTTTACTGCTAATCGAGATTTCTTCAGTTAATTGTTAATTCCAA
129 TCTCCGTTGCTTTTGAAGTT-TTTTACTGCTAATCGAGATTTCTT-AGTTAATTGTTTATTCCAA
* * *
40307969 TTTACCTTAGTTCAACAGAAAACAGTGTAATACTTAGTCAGATGTGA-TTAATTGCATT
192 TTGAACTTAGTTCAACAGAAAACAGTGTAATACTTACTC-GATGTGATTTAATTGCATT
* *
40308027 TTGCTTTTGATTCTTTTTGTTCACTGCTAATCAAGATTTCTTTAATTAGCTGTTTATTCAAGTTG
1 TTGCTTTTGATT-TTTTT-TTCACTGCTAATCAAGATTTCTTTAATTAGTTGTTTATTCAAATTG
* *
40308092 AACATAGTTCAGTCAAAAACAGTGTAATACTTAGTTGACGAGATTGTATTGCATTTTATTGGTTT
64 AACATAGTTCA-TCAAAAACAGTGTAATACTTAGTCGACGAGATTGTATTGCATTTTACTGGTTT
* *
40308157 CTCTCCGTTGCTTTTGAAGTTTTTTTTCACTGCTACTCGAGATTTCTTTAATTAATTGTTTATTC
128 CTCTCCGTTGCTTTTGAAG--TTTTTT-ACTGCTAATCGAGATTTC-TTAGTTAATTGTTTATTC
* * *
40308222 CAATTAAACATGGTTCATAC-GAAAACAGTG
189 CAATTGAACTTAGTTCA-ACAGAAAACAGTG
40308252 CAAACTAAGA
Statistics
Matches: 418, Mismatches: 46, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
252 3 0.01
253 84 0.20
254 158 0.38
255 5 0.01
256 56 0.13
257 4 0.01
258 8 0.02
259 82 0.20
260 18 0.04
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (249 bp):
TTGCTTTTGATTTTTTTTTCACTGCTAATCAAGATTTCTTTAATTAGTTGTTTATTCAAATTGAA
CATAGTTCATCAAAAACAGTGTAATACTTAGTCGACGAGATTGTATTGCATTTTACTGGTTTCTC
TCCGTTGCTTTTGAAGTTTTTTACTGCTAATCGAGATTTCTTAGTTAATTGTTTATTCCAATTGA
ACTTAGTTCAACAGAAAACAGTGTAATACTTACTCGATGTGATTTAATTGCATT
Found at i:40310540 original size:503 final size:503
Alignment explanation
Indices: 40309593--40310599 Score: 1978
Period size: 503 Copynumber: 2.0 Consensus size: 503
40309583 TTTAGCACTA
40309593 GTGATGTGGAATTGGCAGCATCCGACCTCAAAGATCTTGGCTCAAGTGAATTTCATCCTTATTTT
1 GTGATGTGGAATTGGCAGCATCCGACCTCAAAGATCTTGGCTCAAGTGAATTTCATCCTTATTTT
*
40309658 CTTAAGAGGCTTGTCTCCATTGCCATGGACAGGCATGATAAAGAGAAGGAAATGGCCTCGGTTTT
66 CTTAAGAGGCTTGTCTCCATTGCCATGGACAGACATGATAAAGAGAAGGAAATGGCCTCGGTTTT
40309723 GCTTTCTTCATTATATGCTGATGTCATCAGCCCAAACCAGATTAGGGATGGTTTTGTTATGCTTC
131 GCTTTCTTCATTATATGCTGATGTCATCAGCCCAAACCAGATTAGGGATGGTTTTGTTATGCTTC
40309788 TCGATGCTGCGGATGACCTTGCTGTGGACATACTGGATGCAGTCAATATCCTTGCTCTGTTCGTA
196 TCGATGCTGCGGATGACCTTGCTGTGGACATACTGGATGCAGTCAATATCCTTGCTCTGTTCGTA
40309853 GCTCGTGCTGTGGTTGATGAGATTCTGCCTCCAGCATTCCTCACAAGGGCAAAGAAGACACTTCC
261 GCTCGTGCTGTGGTTGATGAGATTCTGCCTCCAGCATTCCTCACAAGGGCAAAGAAGACACTTCC
*
40309918 TGAATCTTCCAAGGGATATCAGGTTCTTCAAACTGCGGAGAAGAGCTATCTCTCGGCACCCCACC
326 TGAATCTTCCAAGGGATATCAGGTTCTTCAAACTGCGGAGAAGAGCTATCTCTCAGCACCCCACC
*
40309983 ATGCTGAACTTGTAGAGAGGAGGTGGGGTGGTAGCATTCATGTCACAGTTGAGGAAATGAAGAAA
391 ATGCTGAACTTGTAGAGAGGAGGTGGGGCGGTAGCATTCATGTCACAGTTGAGGAAATGAAGAAA
40310048 AAGATTGCTGATCTTTTAAGGGAGTATGTGGAGAGTGGTGACACATTT
456 AAGATTGCTGATCTTTTAAGGGAGTATGTGGAGAGTGGTGACACATTT
40310096 GTGATGTGGAATTGGCAGCATCCGACCTCAAAGATCTTGGCTCAAGTGAATTTCATCCTTATTTT
1 GTGATGTGGAATTGGCAGCATCCGACCTCAAAGATCTTGGCTCAAGTGAATTTCATCCTTATTTT
40310161 CTTAAGAGGCTTGTCTCCATTGCCATGGACAGACATGATAAAGAGAAGGAAATGGCCTCGGTTTT
66 CTTAAGAGGCTTGTCTCCATTGCCATGGACAGACATGATAAAGAGAAGGAAATGGCCTCGGTTTT
40310226 GCTTTCTTCATTATATGCTGATGTCATCAGCCCAAACCAGATTAGGGATGGTTTTGTTATGCTTC
131 GCTTTCTTCATTATATGCTGATGTCATCAGCCCAAACCAGATTAGGGATGGTTTTGTTATGCTTC
40310291 TCGATGCTGCGGATGACCTTGCTGTGGACATACTGGATGCAGTCAATATCCTTGCTCTGTTCGTA
196 TCGATGCTGCGGATGACCTTGCTGTGGACATACTGGATGCAGTCAATATCCTTGCTCTGTTCGTA
40310356 GCTCGTGCTGTGGTTGATGAGATTCTGCCTCCAGCATTCCTCACAAGGGCAAAGAAGACACTTCC
261 GCTCGTGCTGTGGTTGATGAGATTCTGCCTCCAGCATTCCTCACAAGGGCAAAGAAGACACTTCC
40310421 TGAATCTTCCAAGGGATATCAGGTTCTTCAAACTGCGGAGAAGAGCTATCTCTCAGCACCCCACC
326 TGAATCTTCCAAGGGATATCAGGTTCTTCAAACTGCGGAGAAGAGCTATCTCTCAGCACCCCACC
*
40310486 ATGCTGAACTTTTAGAGAGGAGGTGGGGCGGTAGCATTCATGTCACAGTTGAGGAAATGAAGAAA
391 ATGCTGAACTTGTAGAGAGGAGGTGGGGCGGTAGCATTCATGTCACAGTTGAGGAAATGAAGAAA
40310551 AAGATTGCTGATCTTTTAAGGGAGTATGTGGAGAGTGGTGACACATTT
456 AAGATTGCTGATCTTTTAAGGGAGTATGTGGAGAGTGGTGACACATTT
40310599 G
1 G
40310600 AGGCCTGTAG
Statistics
Matches: 500, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
503 500 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (503 bp):
GTGATGTGGAATTGGCAGCATCCGACCTCAAAGATCTTGGCTCAAGTGAATTTCATCCTTATTTT
CTTAAGAGGCTTGTCTCCATTGCCATGGACAGACATGATAAAGAGAAGGAAATGGCCTCGGTTTT
GCTTTCTTCATTATATGCTGATGTCATCAGCCCAAACCAGATTAGGGATGGTTTTGTTATGCTTC
TCGATGCTGCGGATGACCTTGCTGTGGACATACTGGATGCAGTCAATATCCTTGCTCTGTTCGTA
GCTCGTGCTGTGGTTGATGAGATTCTGCCTCCAGCATTCCTCACAAGGGCAAAGAAGACACTTCC
TGAATCTTCCAAGGGATATCAGGTTCTTCAAACTGCGGAGAAGAGCTATCTCTCAGCACCCCACC
ATGCTGAACTTGTAGAGAGGAGGTGGGGCGGTAGCATTCATGTCACAGTTGAGGAAATGAAGAAA
AAGATTGCTGATCTTTTAAGGGAGTATGTGGAGAGTGGTGACACATTT
Found at i:40315353 original size:30 final size:30
Alignment explanation
Indices: 40315312--40315375 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
40315302 GTCCTTTTCC
*
40315312 AATCTTGTCATATCCTTTTCATCAATAAAG
1 AATCTTATCATATCCTTTTCATCAATAAAG
40315342 AATCTTATCATATCCTTTTCATCAATAAAG
1 AATCTTATCATATCCTTTTCATCAATAAAG
40315372 AATC
1 AATC
40315376 ACCACTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (30 bp):
AATCTTATCATATCCTTTTCATCAATAAAG
Found at i:40321168 original size:37 final size:38
Alignment explanation
Indices: 40321084--40321171 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 38
40321074 TTTTATCATA
*
40321084 AAATTATTA-AAAAATTATAAAAATAAGAAAAAAATAT
1 AAATTATTATAAATATTATAAAAATAAGAAAAAAATAT
*
40321121 AAA-CACTTATAAATATTAT-AAAATACA-AAAAACAA-AT
1 AAATTA-TTATAAATATTATAAAAATA-AGAAAAA-AATAT
40321158 AAATTATTATAAAT
1 AAATTATTATAAAT
40321172 TACAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
36 1 0.02
37 30 0.70
38 12 0.28
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.28
Consensus pattern (38 bp):
AAATTATTATAAATATTATAAAAATAAGAAAAAAATAT
Found at i:40321189 original size:28 final size:28
Alignment explanation
Indices: 40321134--40321189 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
40321124 CACTTATAAA
*
40321134 TATTATAAAATACAAAAAACAAATAAAT
1 TATTATAAAATACAAAAAACAAAAAAAT
*
40321162 TATTATAAATTACAAAAAA-ATAAAAAAT
1 TATTATAAAATACAAAAAACA-AAAAAAT
40321190 AAAATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (28 bp):
TATTATAAAATACAAAAAACAAAAAAAT
Found at i:40321236 original size:17 final size:18
Alignment explanation
Indices: 40321216--40321250 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
40321206 ATTTAAATTT
40321216 TTATAAAAAATTA-AAAA
1 TTATAAAAAATTATAAAA
40321233 TTATAAAAAATTATAAAA
1 TTATAAAAAATTATAAAA
40321251 AAAAATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTATAAAAAATTATAAAA
Found at i:40321264 original size:10 final size:10
Alignment explanation
Indices: 40321216--40321252 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
40321206 ATTTAAATTT
40321216 TTATAAAAAA
1 TTATAAAAAA
40321226 -T-T-AAAAA
1 TTATAAAAAA
40321233 TTATAAAAAA
1 TTATAAAAAA
40321243 TTATAAAAAA
1 TTATAAAAAA
40321253 AAATCATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
7 5 0.21
8 2 0.08
9 2 0.08
10 15 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:40321735 original size:22 final size:22
Alignment explanation
Indices: 40321710--40321752 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40321700 ATATTTTTAT
* *
40321710 TTTTTATAGAATTTTTAATATG
1 TTTTTATAAAATTTTAAATATG
40321732 TTTTTATAAAATTTTAAATAT
1 TTTTTATAAAATTTTAAATAT
40321753 TTTAAGCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTTTATAAAATTTTAAATATG
Found at i:40322094 original size:28 final size:27
Alignment explanation
Indices: 40322027--40322096 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
40322017 ATTATTATAA
*
40322027 TATTTTATATTTTTATAAGTTTATATT
1 TATTTTATATTTTTATAAATTTATATT
* *
40322054 TATTTTAGCATTTTTTTAATATTTAATATT
1 TATTTTA-TATTTTTATAA-ATTT-ATATT
40322084 T-TTTTATATTTTT
1 TATTTTATATTTTT
40322097 GATTTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.19
28 15 0.42
29 8 0.22
30 6 0.17
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (27 bp):
TATTTTATATTTTTATAAATTTATATT
Found at i:40322115 original size:26 final size:26
Alignment explanation
Indices: 40322066--40322115 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
40322056 TTTTAGCATT
* *
40322066 TTTTTAATATTTAATATTTTTTTATA
1 TTTTTAATATTTAATAATTCTTTATA
* *
40322092 TTTTTGATTTTTAATAATTCTTTA
1 TTTTTAATATTTAATAATTCTTTA
40322116 AGATTTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTTAATATTTAATAATTCTTTATA
Found at i:40324487 original size:265 final size:262
Alignment explanation
Indices: 40323650--40325499 Score: 1228
Period size: 265 Copynumber: 7.0 Consensus size: 262
40323640 CTTGATGGCT
* * *
40323650 ATGGAGGAGAGTTCAATCCTCTTGGTGAGTTATAGTGAACTATTGATTGTGTTTCCTCTGTTTTT
1 ATGGAGGGGAGTTCAATCCTCTTGGTGAGTT-TAGTGAACTATTAATTGTGTTTCCTCTGTTTCT
* * * * * *
40323715 TAGCTAGCTATATGTGAAATA-TTTTGTATGGACTCTGCATGTGTAAGTAATACTTCATTTAAGA
65 T-GCTAACTATATGTGAAATACTTCTGT-T-GACTCTGCATATGTAAGTAGT-C--CATGTAGGA
** * * * * ** *** * *
40323779 TTAA-CCCA-TTGGTGTGATCGACTTGTTTGAGCAAATCAA-AACCTTAAAAGACTAGGACCAGC
124 -TAATGGCATTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAA--TTAACCTAATA-GACTA--
* * * * * * *
40323841 TGGTGCTTGAAA-TTGACTTCTTCTTGA-ATGGTGTCAATGGCGC-CTATAAGAGGTTTTAATTA
183 -GGTGC-TCAAATTTGACTTCTTGTTGAGA-AGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTA
* ** *
40323903 TTTGTTAGCACTATGTGTCA
245 -TGGTTAG-TGTGTGTGTCA
* * * * *
40323923 ATGGAGGGGAGTTCAGTCCTCTTGGCGAGTTTAGTGAATTATTAATCGTGTTTTCTCTGTTTCTT
1 ATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTT
* * *** * * * * *
40323988 CACTAGCTGCGTGTGAAACACTTGGTGTTGGCTCTGTATATGTAAGTAGTAACCCATATAGGATT
66 -GCTAACTATATGTGAAATACTT-CTGTTGACTCTGCATATGTAAGTAGT---CCATGTAGGA-T
** * * * * * ** *
40324053 AA-CCCA-TTGGTGTGATTGACCAGTTTGAGCAAAGGAAAAACTTAGTAGACTAGGACCACTAGG
125 AATGGCATTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAA-TTA--A-CCTAATA-GACTAGG
** * * * * *
40324116 TGCTTGAATTTGACTTATTCTTGA-ATGGTGTCCATGGCA-CCTTTTAAGGGGTTTTAATTATCG
185 TGCTCAAATTTGACTTCTTGTTGAGA-AGTGTCAATGG-AGCTTTTTAAGGGGTTTTAATTAT-G
*
40324179 GTTAGCAT-TTTGTGTCA
247 GTTAG--TGTGTGTGTCA
*
40324196 ATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTGGTGAACTATTAATTGTGTTTCCTCTGTTTCTC
1 ATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCT-
** * * *
40324261 TGCTAGTTATGTGTGAAATAC-TGTGTTGACTCTGCATGTGTAAGTAGTCCATGTAGGATAATTT
65 TGCTAACTATATGTGAAATACTTCTGTTGACTCTGCATATGTAAGTAGTCCATGTAGGATAA--T
* * * * * * *
40324325 GGCATTTTGGTGTGATTGACTAGTTTGACCAATGGAAGAATTAACCTAGTAGACTATGTGCTCCA
128 GGCA-TTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCAA
*
40324390 ATTTGACTTCTTGTTGAGAAGTGTCAATGGAGATTTTTAAGGGGTTTTAATTATGGATTAGTGT-
192 ATTTGACTTCTTGTTGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATGG-TTAGTGTG
40324454 TGTGTCA
256 TGTGTCA
* * * *
40324461 ATGGAGGGGAGTTCAATCATCTTGGTGAGTTCAGTGAACTGTTAATTGTGTTTCCCCTGTTTCTT
1 ATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTT
* * * * * * * * * *
40324526 CACTAACTAAATGGGAAATTCTTTCTGTTGACTATGCATACGGAAGTAGTAGCTTGTCTGGGAT-
66 -GCTAACTATATGTGAAATAC-TTCTGTTGACTCTGCATATGTAAGTAGT-CCATG--TAGGATA
* *
40324590 AT-G---TTGATGAGATTGACTAGTTTGAGCAAAGGAAGACTTAACTTAATAGACTAGGTGCTCA
126 ATGGCATTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCA
* * * * * * *
40324651 GATTTGACTTCTTGTTGAGCAGTCTCAATGGAGGTTTTTAA-GGGTTTTAACTATCTGTTAGCGC
191 AATTTGACTTCTTGTTGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTAT-GGTTAGTG-
40324715 TGTGTGTCA
254 TGTGTGTCA
* * *
40324724 ATTGGAGGGGAGTTCAATCCTCTTGGTGAGTTTTGTGAAC---T-A--GT-TTTCTTTTGTTTCT
1 A-TGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTC-
* *
40324782 TTGCTAACTATATGTGAAATACTTTGTGTTGACTCTGCATATGTAAGTTGTAGCCCATGTAGG--
64 TTGCTAACTATATGTGAAATAC-TTCTGTTGACTCTGCATATGTAA---GTAGTCCATGTAGGAT
* * ** * * * *
40324845 -ATGACA-TTGGTGAGATTGACTAGTTTGAGTGAGGGAAGAATTTGACCTTATAGACTAAGTGCT
125 AATGGCATTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAA-TTAACCTAATAGACTAGGTGCT
* ** * * *
40324908 CAAATTTGACTTCATGTTGAGCGGTGTCAATGGGGCTTTTTAAGGGGTTTT-ATTATGGCTTTGC
189 CAAATTTGACTTCTTGTTGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATGG-TTAGT
*
40324972 GTTGTGTGTTA
253 G-TGTGTGTCA
* * **
40324983 ATGGAGGGGAGTTCAATCTTCTCGGTGAGTTTAGTGAACTGCTAATTGTGTTTCCTCTGTTTCTT
1 ATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTT
* * * * * * *
40325048 CCCTAACTGA-ATGGGAAATACTTTCTGTTGACTTTGCATTTGGT-CGTAGCTGC-T-TA-TATA
66 -GCTAACT-ATATGTGAAATAC-TTCTGTTGACTCTGCATAT-GTAAGTAG-TCCATGTAGGATA
*
40325108 GGAT-GC-TTTGATGAGATTGACTAGTTTGAGAAAAGGAAGAATTAA-CTCAATAGACT-GGATG
126 --ATGGCATTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCT-AATAGACTAGG-TG
* * * * *
40325169 CTCAAATTTGACTTATTGTTGA-ACAGTGTCAAAGGAGCCTTTTAAGGGGGTTTTTGA-TATCAG
187 CTCAAATTTGACTTCTTGTTGAGA-AGTGTCAATGGAGCTTTTTAA-GGGG-TTTTAATTAT-GG
40325232 TTAGCAT-TGTGTGTCA
248 TTAG--TGTGTGTGTCA
* * * *
40325248 ATTGGAGGAGAGTTCAATCCTCTTGGTGAGTTCT-GTGAACTAGTAATCGTGTTTCCTTTGTTTC
1 A-TGGAGGGGAGTTCAATCCTCTTGGTGAGTT-TAGTGAACTATTAATTGTGTTTCCTCTGTTTC
* *
40325312 TTTGCTAACTATATGTGAAATACTT-TGTTGACTCTGCATATTTAAGTTGTAGCCCATGTAGGAT
64 -TTGCTAACTATATGTGAAATACTTCTGTTGACTCTGCATATGTAA---GTAGTCCATGTAGGAT
* * * * * *
40325376 AA---CA-TTGTTGAGATTGACTAGTTTGAGCAAAGGAAGAATTGACTTTAGAGACTAGGTGCTT
125 AATGGCATTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTC
* * * * *
40325437 GAATTTGACTTCTTGTTCA-ACGGTGTCAATGGAGCCTTTTAAGGGGTTTTAGTTATCGGTTAG
190 AAATTTGACTTCTTGTTGAGA-AGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTAT-GGTTAG
40325500 CTAGCTGCGT
Statistics
Matches: 1275, Mismatches: 218, Indels: 177
0.76 0.13 0.11
Matches are distributed among these distances:
255 2 0.00
257 49 0.04
258 69 0.05
259 76 0.06
260 12 0.01
261 21 0.02
262 97 0.08
263 63 0.05
264 102 0.08
265 231 0.18
266 83 0.07
267 93 0.07
268 20 0.02
269 5 0.00
270 7 0.01
271 29 0.02
272 169 0.13
273 135 0.11
274 6 0.00
275 6 0.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (262 bp):
ATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTT
GCTAACTATATGTGAAATACTTCTGTTGACTCTGCATATGTAAGTAGTCCATGTAGGATAATGGC
ATTTGATGAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCAAATTT
GACTTCTTGTTGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATGGTTAGTGTGTGTGT
CA
Found at i:40325037 original size:522 final size:522
Alignment explanation
Indices: 40324155--40325500 Score: 1662
Period size: 522 Copynumber: 2.6 Consensus size: 522
40324145 GTCCATGGCA
* *
40324155 CCTTTTAAGGGGTTTTAATTATCGGTTAGCATTTTGTGTCAA-TGGAGGGGAGTTCAATCCTCTT
1 CCTTTTAAGGGGTTTTAA-TATCAGTTAGCATTGTGTGTCAATTGGAGGGGAGTTCAATCCTCTT
* * * ** *
40324219 GGTGAGTTTGGTGAACTATTAATTGTGTTTCCTCTGTTTCTCTGCTAGTTATGTGTGAAATAC-T
65 GGTGAGTTTTGTGAAC--TTAA-TGTGTTTCCTTTGTTTCTTTGCTAACTATATGTGAAATACTT
* * * *
40324283 GTGTTGACTCTGCATGTGTAA---GTAGTCCATGTAGGATAATTTGGCATTTTGGTGTGATTGAC
127 GTGTTGACTCTGCATATGTAAGTTGTAGCCCATGTAGG---A--TGACA--TTGGTGAGATTGAC
* * * * * *
40324345 TAGTTTGACCAATGGAAGAATTAACC-TAGTAGACTATGTGCTCCAATTTGACTTCTTGTTGAGA
185 TAGTTTGAGCAAAGGAAGAATTGACCTTA-TAGACTAAGTGCTCAAATTTGACTTCTTGTTGAGC
* * *
40324409 AGTGTCAATGGAGATTTTTAAGGGGTTTTAATTATGGATTAGTGTTGTGTCAATGGAGGGGAGTT
249 GGTGTCAATGGAGCTTTTTAAGGGGTTTT-ATTATGGATTAGCGTTGTGTCAATGGAGGGGAGTT
* *
40324474 CAATCATCTTGGTGAGTTCAGTGAACTGTTAATTGTGTTTCCCCTGTTTCTTCACTAACTAAATG
313 CAATCATCTCGGTGAGTTCAGTGAACTGCTAATTGTGTTTCCCCTGTTTCTTCACTAACTAAATG
* * * *
40324539 GGAAATTCTTTCTGTTGACTATGCATACGGAAGTAG-TAGCTTGTCTGGGAT-ATGTTGATGAGA
378 GGAAATACTTTCTGTTGACTATGCATACGGAAGTAGCT-GCTTATATAGGATGAT-TTGATGAGA
* * * * *
40324602 TTGACTAGTTTGAGCAAAGGAAGACTTAACTTAATAGACTAGG-TGCTCAGATTTGACTTCTTGT
441 TTGACTAGTTTGAGAAAAGGAAGAATTAACTCAATAGACT-GGATGCTCAAATTTGACTTATTGT
* *
40324666 TGAGCAGTCTCAATGGAG
505 TGAACAGTCTCAAAGGAG
** * **
40324684 GTTTTTAA-GGGTTTTAACTATCTGTTAGCGCTGTGTGTCAATTGGAGGGGAGTTCAATCCTCTT
1 CCTTTTAAGGGGTTTTAA-TATCAGTTAGCATTGTGTGTCAATTGGAGGGGAGTTCAATCCTCTT
*
40324748 GGTGAGTTTTGTGAAC-T-A-GT-TTTCTTTTGTTTCTTTGCTAACTATATGTGAAATACTTTGT
65 GGTGAGTTTTGTGAACTTAATGTGTTTCCTTTGTTTCTTTGCTAACTATATGTGAAATAC-TTGT
40324809 GTTGACTCTGCATATGTAAGTTGTAGCCCATGTAGGATGACATTGGTGAGATTGACTAGTTTGAG
129 GTTGACTCTGCATATGTAAGTTGTAGCCCATGTAGGATGACATTGGTGAGATTGACTAGTTTGAG
** * *
40324874 TGAGGGAAGAATTTGACCTTATAGACTAAGTGCTCAAATTTGACTTCATGTTGAGCGGTGTCAAT
194 CAAAGGAAGAA-TTGACCTTATAGACTAAGTGCTCAAATTTGACTTCTTGTTGAGCGGTGTCAAT
* * * * *
40324939 GGGGCTTTTTAAGGGGTTTTATTATGGCTTTGCGTTGTGTGTTAATGGAGGGGAGTTCAATCTTC
258 GGAGCTTTTTAAGGGGTTTTATTATGGATTAGCG-T-TGTGTCAATGGAGGGGAGTTCAATCATC
* * * *
40325004 TCGGTGAGTTTAGTGAACTGCTAATTGTGTTTCCTCTGTTTCTTCCCTAACTGAATGGGAAATAC
321 TCGGTGAGTTCAGTGAACTGCTAATTGTGTTTCCCCTGTTTCTTCACTAACTAAATGGGAAATAC
* ** ** *
40325069 TTTCTGTTGACTTTGCATTTGGTCGTAGCTGCTTATATAGGATGCTTTGATGAGATTGACTAGTT
386 TTTCTGTTGACTATGCATACGGAAGTAGCTGCTTATATAGGATGATTTGATGAGATTGACTAGTT
*
40325134 TGAGAAAAGGAAGAATTAACTCAATAGACTGGATGCTCAAATTTGACTTATTGTTGAACAGTGTC
451 TGAGAAAAGGAAGAATTAACTCAATAGACTGGATGCTCAAATTTGACTTATTGTTGAACAGTCTC
40325199 AAAGGAG
516 AAAGGAG
* *
40325206 CCTTTTAAGGGGGTTTTTGATATCAGTTAGCATTGTGTGTCAATTGGAGGAGAGTTCAATCCTCT
1 CCTTTTAA-GGGG-TTTTAATATCAGTTAGCATTGTGTGTCAATTGGAGGGGAGTTCAATCCTCT
*
40325271 TGGTGAGTTCTGTGAACTAGTAATCGTGTTTCCTTTGTTTCTTTGCTAACTATATGTGAAATACT
64 TGGTGAGTTTTGTGAACT--TAAT-GTGTTTCCTTTGTTTCTTTGCTAACTATATGTGAAATACT
* * *
40325336 T-TGTTGACTCTGCATATTTAAGTTGTAGCCCATGTAGGATAACATTGTTGAGATTGACTAGTTT
126 TGTGTTGACTCTGCATATGTAAGTTGTAGCCCATGTAGGATGACATTGGTGAGATTGACTAGTTT
* * * ** * *
40325400 GAGCAAAGGAAGAATTGACTTTAGAGACTAGGTGCTTGAATTTGACTTCTTGTTCAACGGTGTCA
191 GAGCAAAGGAAGAATTGACCTTATAGACTAAGTGCTCAAATTTGACTTCTTGTTGAGCGGTGTCA
*
40325465 ATGGAGCCTTTTAAGGGGTTTTAGTTATCGG-TTAGC
256 ATGGAGCTTTTTAAGGGGTTTTA-TTAT-GGATTAGC
40325501 TAGCTGCGTG
Statistics
Matches: 707, Mismatches: 85, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
520 40 0.06
521 65 0.09
522 239 0.34
523 4 0.01
524 82 0.12
525 6 0.01
526 1 0.00
527 14 0.02
528 93 0.13
529 122 0.17
530 6 0.01
531 35 0.05
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (522 bp):
CCTTTTAAGGGGTTTTAATATCAGTTAGCATTGTGTGTCAATTGGAGGGGAGTTCAATCCTCTTG
GTGAGTTTTGTGAACTTAATGTGTTTCCTTTGTTTCTTTGCTAACTATATGTGAAATACTTGTGT
TGACTCTGCATATGTAAGTTGTAGCCCATGTAGGATGACATTGGTGAGATTGACTAGTTTGAGCA
AAGGAAGAATTGACCTTATAGACTAAGTGCTCAAATTTGACTTCTTGTTGAGCGGTGTCAATGGA
GCTTTTTAAGGGGTTTTATTATGGATTAGCGTTGTGTCAATGGAGGGGAGTTCAATCATCTCGGT
GAGTTCAGTGAACTGCTAATTGTGTTTCCCCTGTTTCTTCACTAACTAAATGGGAAATACTTTCT
GTTGACTATGCATACGGAAGTAGCTGCTTATATAGGATGATTTGATGAGATTGACTAGTTTGAGA
AAAGGAAGAATTAACTCAATAGACTGGATGCTCAAATTTGACTTATTGTTGAACAGTCTCAAAGG
AG
Found at i:40325671 original size:194 final size:184
Alignment explanation
Indices: 40325325--40325694 Score: 454
Period size: 194 Copynumber: 2.0 Consensus size: 184
40325315 GCTAACTATA
* * * * *
40325325 TGTGAAATACTTTGTTGACTCTGCATATTTAAGTTGTAGCCCATGTAGGATAACATTGTTGAGAT
1 TGTGAAATACTTTGTTGACTCTGCATATGTAAGTAGTAACCCATATAGGATAACATTGGTGAGAT
* * ** * *
40325390 TGACTAGTTTGAGCAAAGGAAGAATTGACTTTAGAGACTAGGTGCTTGAATTTGACTTCTTGTTC
66 TGACCAGTTTGAGCAAAGGAAAAATTGACACTAGACACTAGGTGCTTGAATTTGACTTCTTCTTC
* *
40325455 AACGGTGTCAATGGAGCCTTTTAAGGGGTTTTAGTTATCGGTTAGCTAGCTGCG
131 AACAGTGTCAATGGAGCCTTTTAAGGGGTTTTAATTATCGGTTAGCTAGCTGCG
* *
40325509 TGTGAAATACTTGGTGTTGGCTCTGTATATGTAAGTAGTAACCCATATAGGATTAACCCATTGGT
1 TGTGAAATACTT--TGTTGACTCTGCATATGTAAGTAGTAACCCATATAGGA-TAA--CATTGGT
* *
40325574 GTGATTGACCAGTTTGAGCAAAGGAAAAACTTAGTAGACTAGGACCACTAGGTGCTTGAATTTGA
61 GAGATTGACCAGTTTGAGCAAAGGAAAAA-TT-G-ACACTA-GA-CACTAGGTGCTTGAATTTGA
* * *
40325639 CTTGTTCTTGAACAGTGTCCATGGCA-CCTTTTAAGGGGTTTTAATTATCGGTTAGC
121 CTTCTTCTTCAACAGTGTCAATGG-AGCCTTTTAAGGGGTTTTAATTATCGGTTAGC
40325695 ATTTTGTTTC
Statistics
Matches: 155, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
184 12 0.08
186 32 0.21
187 3 0.02
189 32 0.21
190 2 0.01
191 1 0.01
192 3 0.02
193 2 0.01
194 67 0.43
195 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (184 bp):
TGTGAAATACTTTGTTGACTCTGCATATGTAAGTAGTAACCCATATAGGATAACATTGGTGAGAT
TGACCAGTTTGAGCAAAGGAAAAATTGACACTAGACACTAGGTGCTTGAATTTGACTTCTTCTTC
AACAGTGTCAATGGAGCCTTTTAAGGGGTTTTAATTATCGGTTAGCTAGCTGCG
Found at i:40325998 original size:265 final size:263
Alignment explanation
Indices: 40325509--40327264 Score: 1307
Period size: 265 Copynumber: 6.7 Consensus size: 263
40325499 GCTAGCTGCG
* * * **
40325509 TGTGAAATACTTGGTGTTGGCTCTGTATATGTAAGTAGTAACCCATATAGGATTAA-CCCA-TTG
1 TGTGAAATACTT-GTGTTGACTCTGCATATGTAAGTAGT---CCATGTAGGA-TAATGGCATTTG
* * * * * ** * **
40325572 GTGTGATTGACCAGTTTGAGCAAAGGAAAAACTTAGTAGACTAGGACCACTAGGTGCTTGAATTT
61 ATGAGATTGACTAGTTTGAGCAAAGGAAGAA-TTA--A-CCTAATA-GACTAGGTGCTCAAATTT
* * * * * *
40325637 GACTTGTTCTTGA-ACAGTGTCCATGGCA-CCTTTTAAGGGGTTTTAATTATCGGTTAGCATTTT
121 GACTTCTTGTTGAGA-AGTGTCAATGG-AGCTTTTTAAGGGGTTTTAATTATCGGTTAGC-GTGT
* * *
40325700 GTTTCAATGGAGGGGAGTTCAATCTTCTTGGTGAGTTTAGTGAATTATTAATTGTGTTTCCTCTG
183 GTGTCAATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTG
** * *
40325765 TTTCTCTGCTAGTTGTG
248 TTTCT-TGCTAACTATA
* *
40325782 TGTGAAATAC-TGTGTTGACTCTGCATGTGTAAGTAGTCCATGTAGGATAATTTGGCATTTTGGT
1 TGTGAAATACTTGTGTTGACTCTGCATATGTAAGTAGTCCATGTAGGATAA--TGGCA-TTTGAT
* * * * * *
40325846 GTGATTGACTAGTTTGACCAATGGAAGAATTAACCTAGTAGACTATGTGCTCCAATTTGACTTCT
63 GAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCAAATTTGACTTCT
* *
40325911 TGTTGAGAAGTGTCAATGGAGATTTTTAAGGGGTTTTAATTAT-GGATTAGTGT-TGTGTCAATG
128 TGTTGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATCGG-TTAGCGTGTGTGTCAATG
* * * * *
40325974 GAGGGGAGTTCAATCATCTTGGTGAGTTCAGTGAACTGTTAATTGTGTTTCCCCTGTTTCTTCAC
192 GAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTT-GC
*
40326039 TAACTAAA
256 TAACTATA
* * * * * * * * *
40326047 TGGGAAATTCTTTCTGTTGACTATGCATACGGAAGTAGTAGCTTGTCTGGGAT-AT-G---TTGA
1 TGTGAAATAC-TTGTGTTGACTCTGCATATGTAAGTAGT-CCATG--TAGGATAATGGCATTTGA
* * *
40326107 TGAGATTGACTAGTTTGAGCAAAGGAAGACTTAACTTAATAGACTAGGTGCTCAGATTTGACTTC
62 TGAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCAAATTTGACTTC
* * * * *
40326172 TTGTTGAGCAGTCTCAATGGAGGTTTTTAA-GGGTTTTAACTATCTGTTAGCGCTGTGTGTCAAT
127 TTGTTGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATCGGTTAGCG-TGTGTGTCAA-
* * *
40326236 TGGAGGGGAGTTCAATCCTCTTGGTGAGTTTTGTGAAC---T-A--GT-TTTCTTTTGTTTCTTT
190 TGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTC-TT
40326294 GCTAACTATA
254 GCTAACTATA
* * *
40326304 TGTGAAATACTTTGTGTTGACTCTGCATATGTAAGTTGTAGCCCATGTAGG---ATGACA-TTGG
1 TGTGAAATAC-TTGTGTTGACTCTGCATATGTAA---GTAGTCCATGTAGGATAATGGCATTTGA
** * * * *
40326365 TGAGATTGACTAGTTTGAGTGAGGGAAGAATTTGACCTTATAGACTAAGTGCTCAAATTTGACTT
62 TGAGATTGACTAGTTTGAGCAAAGGAAGAA-TTAACCTAATAGACTAGGTGCTCAAATTTGACTT
* ** * * *
40326430 CATGTTGAGCGGTGTCAATGGGGCTTTTTAAGGGGTTTT-ATTAT-GGCTTTGCGTTGTGTGTTA
126 CTTGTTGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATCGG-TTAGCG-TGTGTGTCA
* * **
40326493 ATGGAGGGGAGTTCAATCTTCTCGGTGAGTTTAGTGAACTGCTAATTGTGTTTCCTCTGTTTCTT
189 ATGGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTT
*
40326558 CCCTAACTGA-A
254 -GCTAACT-ATA
* * * * * * *
40326569 TGGGAAATACTTTCTGTTGACTTTGCATTTGGT-CGTAGCTGC-T-TA-TATAGGAT-GC-TTTG
1 TGTGAAATAC-TTGTGTTGACTCTGCATAT-GTAAGTAG-TCCATGTAGGATA--ATGGCATTTG
*
40326628 ATGAGATTGACTAGTTTGAGAAAAGGAAGAATTAA-CTCAATAGACT-GGATGCTCAAATTTGAC
61 ATGAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCT-AATAGACTAGG-TGCTCAAATTTGAC
* * * * * *
40326691 TTATTGTTGA-ACAGTGTCAAAGGAGCCTTTTAAGGGGGTTTTTGA-TATCAGTTAGCATTGTGT
124 TTCTTGTTGAGA-AGTGTCAATGGAGCTTTTTAA-GGGG-TTTTAATTATCGGTTAGC-GTGTGT
* * * *
40326754 GTCAATTGGAGGAGAGTTCAATCCTCTTGGTGAGTTCT-GTGAACTAGTAATCGTGTTTCCTTTG
185 GTCAA-TGGAGGGGAGTTCAATCCTCTTGGTGAGTT-TAGTGAACTATTAATTGTGTTTCCTCTG
40326818 TTTCTTTGCTAACTATA
248 TTTC-TTGCTAACTATA
* * *
40326835 TGTGAAATACTT-TGTTGACTCTGCATATTTAAGTTGTAGCCCATGTAGGATAA---CA-TTGTT
1 TGTGAAATACTTGTGTTGACTCTGCATATGTAA---GTAGTCCATGTAGGATAATGGCATTTGAT
* * * * **
40326895 GAGATTGACTAGTTTGAGCAAAGGAAGAATTGACTTTAGAGACTAGGTGCTTGAATTTGACTTCT
63 GAGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCAAATTTGACTTCT
* * * *
40326960 TGTTCA-ACGGTGTCAATGGAGCCTTTTAAGGGGTTTTAGTTATCGGTTAGCGTCGTGTGTCAAT
128 TGTTGAGA-AGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATCGGTTAGCGT-GTGTGTCAAT
* * *
40327024 ----NGGAGTTAAAT-CTCTTGGTGAGTTTAGTAAACTATTAATTGTGTTTCCTCTGTTTCTT--
191 GGAGGGGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTTGC
*
40327082 T-GC--T-
256 TAACTATA
* * * * *
40327086 TGTGAAATAC-TGTGTTGACTCTGCATATGTAACTATTAGCCATAT-GGATAA---CA-TCGGTG
1 TGTGAAATACTTGTGTTGACTCTGCATATGTAAGTAGT--CCATGTAGGATAATGGCATTTGATG
* * * * * ***
40327145 AGATTGACTGGTTTGAGCGATGGAAGAATTAACTTGATAGACTAGGTGCTCGTGTTTGACTTCTT
64 AGATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCAAATTTGACTTCTT
** * * * * *
40327210 CCTGA-ATGGTGTCAATGGGGCCTTTTAAGGGGCTTTAGTTATCGGTTAGC-TGTGT
129 GTTGAGA-AGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATCGGTTAGCGTGTGT
40327265 TTAGTGAGGC
Statistics
Matches: 1215, Mismatches: 195, Indels: 172
0.77 0.12 0.11
Matches are distributed among these distances:
247 4 0.00
248 3 0.00
249 112 0.09
250 6 0.00
251 29 0.02
252 1 0.00
254 1 0.00
255 3 0.00
257 52 0.04
258 108 0.09
259 84 0.07
260 12 0.01
261 21 0.02
262 97 0.08
263 65 0.05
264 112 0.09
265 229 0.19
266 83 0.07
267 94 0.08
268 20 0.02
269 5 0.00
270 7 0.01
271 26 0.02
272 31 0.03
273 10 0.01
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (263 bp):
TGTGAAATACTTGTGTTGACTCTGCATATGTAAGTAGTCCATGTAGGATAATGGCATTTGATGAG
ATTGACTAGTTTGAGCAAAGGAAGAATTAACCTAATAGACTAGGTGCTCAAATTTGACTTCTTGT
TGAGAAGTGTCAATGGAGCTTTTTAAGGGGTTTTAATTATCGGTTAGCGTGTGTGTCAATGGAGG
GGAGTTCAATCCTCTTGGTGAGTTTAGTGAACTATTAATTGTGTTTCCTCTGTTTCTTGCTAACT
ATA
Found at i:40326631 original size:522 final size:521
Alignment explanation
Indices: 40325632--40327081 Score: 1682
Period size: 522 Copynumber: 2.8 Consensus size: 521
40325622 TAGGTGCTTG
* * * * * *
40325632 AATTTGACTTGTTCTTGAACAGTGTCCATGGCA-CCTTTTAAGGGGTTTTAATTATCGGTTAGCA
1 AATTTGACTTATTGTTGAACAGTCTCAAAGG-AGCCTTTTAAGGGGTTTTAA-TATCAGTTAGCA
* * * * *
40325696 TTTTGTTTCAA-TGGAGGGGAGTTCAATCTTCTTGGTGAGTTTAGTGAATTATTAATTGTGTTTC
64 TTGTGTGTCAATTGGAGGGGAGTTCAATCCTCTTGGTGAGTTTTGTG-A--ACTAA-TGTGTTTC
* * ** * * * *
40325760 CTCTGTTTCTCTGCTAGTTGTGTGTGAAATAC-TGTGTTGACTCTGCATGTGTAA---GTAGTCC
125 CTTTGTTTCTTTGCTAACTATATGTGAAATACTTGTGTTGACTCTGCATATGTAAGTTGTAGCCC
* * * * *
40325821 ATGTAGGATAATTTGGCATTTTGGTGTGATTGACTAGTTTGACCAATGGAAGAATTAACC-TAGT
190 ATGTAGG---A--TGACA--TTGGTGAGATTGACTAGTTTGAGCAAAGGAAGAATTGACCTTA-T
* * ** *
40325885 AGACTATGTGCTCCAATTTGACTTCTTGTTGAGAAGTGTCAATGGAGATTTTTAAGGGGTTTTAA
247 AGACTAAGTGCTCAAATTTGACTTCTTGTTGAGCGGTGTCAATGGAGCTTTTTAAGGGGTTTT-A
* *
40325950 TTATGGATTAGTG-T-TGTGTCAATGGAGGGGAGTTCAATCATCTTGGTGAGTTCAGTGAACTGT
311 TTATGG-TTAGCGTTGTGTGTCAATGGAGGGGAGTTCAATC-TCTTGGTGAGTTTAGTGAACTGT
* *
40326013 TAATTGTGTTTCCCCTGTTTCTTCACTAACTAAATGGGAAATTCTTTCTGTTGACTATGCATACG
374 TAATTGTGTTTCCTCTGTTTCTTCACTAACTAAATGGGAAATACTTTCTGTTGACTATGCATACG
* * * * *
40326078 GAAGTAGTAGCTTGTCTGGGATATGTTGATGAGATTGACTAGTTTGAGCAAAGGAAGACTTAACT
439 GAAGTAGTAGCTTATATAGGATATGTTGATGAGATTGACTAGTTTGAGAAAAGGAAGAATTAACT
*
40326143 TAATAGACTAGG-TGCTCA
504 CAATAGACT-GGATGCTCA
* * * * ** * **
40326161 GATTTGACTTCTTGTTGAGCAGTCTCAATGGAGGTTTTTAA-GGGTTTTAACTATCTGTTAGCGC
1 AATTTGACTTATTGTTGAACAGTCTCAAAGGAGCCTTTTAAGGGGTTTTAA-TATCAGTTAGCAT
*
40326225 TGTGTGTCAATTGGAGGGGAGTTCAATCCTCTTGGTGAGTTTTGTGAACT-A-GT-TTTCTTTTG
65 TGTGTGTCAATTGGAGGGGAGTTCAATCCTCTTGGTGAGTTTTGTGAACTAATGTGTTTCCTTTG
40326287 TTTCTTTGCTAACTATATGTGAAATACTTTGTGTTGACTCTGCATATGTAAGTTGTAGCCCATGT
130 TTTCTTTGCTAACTATATGTGAAATAC-TTGTGTTGACTCTGCATATGTAAGTTGTAGCCCATGT
** *
40326352 AGGATGACATTGGTGAGATTGACTAGTTTGAGTGAGGGAAGAATTTGACCTTATAGACTAAGTGC
194 AGGATGACATTGGTGAGATTGACTAGTTTGAGCAAAGGAAGAA-TTGACCTTATAGACTAAGTGC
* * *
40326417 TCAAATTTGACTTCATGTTGAGCGGTGTCAATGGGGCTTTTTAAGGGGTTTTATTATGGCTTTGC
258 TCAAATTTGACTTCTTGTTGAGCGGTGTCAATGGAGCTTTTTAAGGGGTTTTATTATGG-TTAGC
* * *
40326482 GTTGTGTGTTAATGGAGGGGAGTTCAATCTTCTCGGTGAGTTTAGTGAACTGCTAATTGTGTTTC
322 GTTGTGTGTCAATGGAGGGGAGTTCAATC-TCTTGGTGAGTTTAGTGAACTGTTAATTGTGTTTC
* * * ** **
40326547 CTCTGTTTCTTCCCTAACTGAATGGGAAATACTTTCTGTTGACTTTGCATTTGGTCGTAGCT-GC
386 CTCTGTTTCTTCACTAACTAAATGGGAAATACTTTCTGTTGACTATGCATACGGAAGTAG-TAGC
*
40326611 TTATATAGGATGCT-TTGATGAGATTGACTAGTTTGAGAAAAGGAAGAATTAACTCAATAGACTG
450 TTATATAGGAT-ATGTTGATGAGATTGACTAGTTTGAGAAAAGGAAGAATTAACTCAATAGACTG
40326675 GATGCTCA
514 GATGCTCA
* *
40326683 AATTTGACTTATTGTTGAACAGTGTCAAAGGAGCCTTTTAAGGGGGTTTTTGATATCAGTTAGCA
1 AATTTGACTTATTGTTGAACAGTCTCAAAGGAGCCTTTTAA-GGGG-TTTTAATATCAGTTAGCA
* *
40326748 TTGTGTGTCAATTGGAGGAGAGTTCAATCCTCTTGGTGAGTTCTGTGAACTAGTAATCGTGTTTC
64 TTGTGTGTCAATTGGAGGGGAGTTCAATCCTCTTGGTGAGTTTTGTGAAC---TAAT-GTGTTTC
*
40326813 CTTTGTTTCTTTGCTAACTATATGTGAAATACTT-TGTTGACTCTGCATATTTAAGTTGTAGCCC
125 CTTTGTTTCTTTGCTAACTATATGTGAAATACTTGTGTTGACTCTGCATATGTAAGTTGTAGCCC
* * * * *
40326877 ATGTAGGATAACATTGTTGAGATTGACTAGTTTGAGCAAAGGAAGAATTGACTTTAGAGACTAGG
190 ATGTAGGATGACATTGGTGAGATTGACTAGTTTGAGCAAAGGAAGAATTGACCTTATAGACTAAG
** * * *
40326942 TGCTTGAATTTGACTTCTTGTTCAACGGTGTCAATGGAGCCTTTTAAGGGGTTTTAGTTATCGGT
255 TGCTCAAATTTGACTTCTTGTTGAGCGGTGTCAATGGAGCTTTTTAAGGGGTTTTA-TTAT-GGT
* * * * *
40327007 TAGCGTCGTGTGTCAAT----NGGAGTTAAATCTCTTGGTGAGTTTAGTAAACTATTAATTGTGT
318 TAGCGTTGTGTGTCAATGGAGGGGAGTTCAATCTCTTGGTGAGTTTAGTGAACTGTTAATTGTGT
40327068 TTCCTCTGTTTCTT
383 TTCCTCTGTTTCTT
40327082 TGCTTGTGAA
Statistics
Matches: 792, Mismatches: 103, Indels: 57
0.83 0.11 0.06
Matches are distributed among these distances:
520 40 0.05
521 65 0.08
522 238 0.30
523 4 0.01
524 124 0.16
525 16 0.02
526 2 0.00
527 14 0.02
528 94 0.12
529 154 0.19
530 6 0.01
531 35 0.04
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.39
Consensus pattern (521 bp):
AATTTGACTTATTGTTGAACAGTCTCAAAGGAGCCTTTTAAGGGGTTTTAATATCAGTTAGCATT
GTGTGTCAATTGGAGGGGAGTTCAATCCTCTTGGTGAGTTTTGTGAACTAATGTGTTTCCTTTGT
TTCTTTGCTAACTATATGTGAAATACTTGTGTTGACTCTGCATATGTAAGTTGTAGCCCATGTAG
GATGACATTGGTGAGATTGACTAGTTTGAGCAAAGGAAGAATTGACCTTATAGACTAAGTGCTCA
AATTTGACTTCTTGTTGAGCGGTGTCAATGGAGCTTTTTAAGGGGTTTTATTATGGTTAGCGTTG
TGTGTCAATGGAGGGGAGTTCAATCTCTTGGTGAGTTTAGTGAACTGTTAATTGTGTTTCCTCTG
TTTCTTCACTAACTAAATGGGAAATACTTTCTGTTGACTATGCATACGGAAGTAGTAGCTTATAT
AGGATATGTTGATGAGATTGACTAGTTTGAGAAAAGGAAGAATTAACTCAATAGACTGGATGCTC
A
Found at i:40338844 original size:20 final size:20
Alignment explanation
Indices: 40338819--40338869 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
40338809 CATTTCACAA
40338819 TTCACAAATATCACACGTTT
1 TTCACAAATATCACACGTTT
40338839 TTCACAAATATCACACGTTT
1 TTCACAAATATCACACGTTT
*
40338859 TTCACATATAT
1 TTCACAAATAT
40338870 ACTTTTTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (20 bp):
TTCACAAATATCACACGTTT
Found at i:40338975 original size:30 final size:28
Alignment explanation
Indices: 40338941--40339001 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
40338931 TATAATTTTC
40338941 TTTACAAATTT-CATAATTCCATAATATATA
1 TTTACAAATTTACA-AATT-CA-AATATATA
*
40338971 TTTACAAATTTACAAATTTAAATATATA
1 TTTACAAATTTACAAATTCAAATATATA
40338999 TTT
1 TTT
40339002 TACATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 11 0.38
29 1 0.03
30 15 0.52
31 2 0.07
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTACAAATTTACAAATTCAAATATATA
Found at i:40342018 original size:36 final size:36
Alignment explanation
Indices: 40341971--40342063 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 36
40341961 GTCTCCAAAT
* *
40341971 TCACATTTCAATTCAATTGCACTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATT-CACTTTTCCACTTTCAAG
*
40342007 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACAATTCAATTC--AATTCACTTTTCCACTTTCAAG
40342045 TCA-ATATTCAATTCAATTC
1 TCACA-ATTCAATTCAATTC
40342064 CACACATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
36 18 0.36
37 16 0.32
38 16 0.32
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.42
Consensus pattern (36 bp):
TCACAATTCAATTCAATTCACTTTTCCACTTTCAAG
Found at i:40342458 original size:13 final size:13
Alignment explanation
Indices: 40342440--40342464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40342430 GACTAAACTC
40342440 ATAATTATTTATA
1 ATAATTATTTATA
40342453 ATAATTATTTAT
1 ATAATTATTTAT
40342465 GACTCGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAATTATTTATA
Found at i:40349805 original size:23 final size:21
Alignment explanation
Indices: 40349779--40349830 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
40349769 AGCAAACAAC
*
40349779 AACAAAAGGGACAAGAAAAAAAT
1 AACAAAA-GGAC-AGAAAAAAAG
* *
40349802 AACAGAAATGACAGCAAAAAAG
1 AACA-AAAGGACAGAAAAAAAG
40349824 AACAAAA
1 AACAAAA
40349831 TGTATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 12 0.48
23 7 0.28
24 3 0.12
ACGTcount: A:0.69, C:0.12, G:0.15, T:0.04
Consensus pattern (21 bp):
AACAAAAGGACAGAAAAAAAG
Found at i:40350355 original size:7 final size:7
Alignment explanation
Indices: 40350345--40350378 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
40350335 AATGTTTTTT
40350345 TTTTTGC
1 TTTTTGC
40350352 TTTTTGC
1 TTTTTGC
40350359 TTTTTGC
1 TTTTTGC
40350366 TTTTTGC
1 TTTTTGC
40350373 TTTTTG
1 TTTTTG
40350379 AAACAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.74
Consensus pattern (7 bp):
TTTTTGC
Found at i:40353179 original size:9 final size:9
Alignment explanation
Indices: 40353167--40353199 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
40353157 GAATTATTCG
40353167 AATCGAGTT
1 AATCGAGTT
40353176 AATCGAGTT
1 AATCGAGTT
*
40353185 AATCGAATT
1 AATCGAGTT
40353194 AATCGA
1 AATCGA
40353200 ATCAACTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:40356712 original size:125 final size:128
Alignment explanation
Indices: 40356476--40356738 Score: 329
Period size: 125 Copynumber: 2.1 Consensus size: 128
40356466 GAGTATGAGC
** *
40356476 TTGCCTTCTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATATTCGGATATTTAGAT
1 TTGCCTT-TATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAACCGGATACTTAGAT
* * * * * *
40356541 CAAATGAAAAAATCGAAACCCAATACGTTAGGGCACGACTATTCGAA-TTTCTAAATACGGGATA
65 CAAACGAAAAAACCGAAACCCAACACGTTAGGACACGACTATTCGAATTTTC-AAATACCGAATA
* * *
40356605 TTGCCTTTATTTTATTTAAAACTCATGTATTTTAA-TTT-AAAAGGATAACCGGTTACTTAGATC
1 TTGCCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAACCGGATACTTAGATC
* * *
40356668 AAACG-AAAAACCGAAACCCAGCACGTTAGGACACGA-TTTCTCGAATTTTCAATTACCGAATA
66 AAACGAAAAAACCGAAACCCAACACGTTAGGACACGACTAT-TCGAATTTTCAAATACCGAATA
40356730 TTGCCTTTA
1 TTGCCTTTA
40356739 CTTGAAAAAT
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
124 2 0.02
125 50 0.43
126 29 0.25
127 3 0.03
128 26 0.22
129 7 0.06
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (128 bp):
TTGCCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAAAAAGGATAACCGGATACTTAGATC
AAACGAAAAAACCGAAACCCAACACGTTAGGACACGACTATTCGAATTTTCAAATACCGAATA
Found at i:40356922 original size:3 final size:3
Alignment explanation
Indices: 40356900--40357260 Score: 83
Period size: 3 Copynumber: 120.3 Consensus size: 3
40356890 AATAGGACGG
* * * * *
40356900 ATA ATA AAA AAA ATA GTA ATA ATA ATA ATA AT- ATA ATG GTA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * * *
40356946 ATT TTA A-A AAA ATT A-A AT- ATA ATG ATG ATA ATA GTG TTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
40356991 ATA ATA ATA ATA ATA ATA A-A CA-A ACGA CATA TTA ATG ATA ATA GAAA
1 ATA ATA ATA ATA ATA ATA ATA -ATA A-TA -ATA ATA ATA ATA ATA -ATA
**
40357038 ATA ACG ATA ATA ATA ATGGA AGTA ATGA A-A ATA ATA ATA ATA GA-A
1 ATA ATA ATA ATA ATA AT--A A-TA AT-A ATA ATA ATA ATA ATA -ATA
* * *
40357083 ACA ATA GTA ATA A-A AGTA ATA ATA A-A ATA A-A A-A ATA ACA ATGA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * * * *
40357126 CACA TTA ATA ATA ATA AT- ATA CGTG CTA ATA ATA ATA ACA ATA TATA
1 -ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * * *
40357173 A-A AAA ATA ATA CT- ATA TTA ATA AAA ATA ATA ATA GTA GGTTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA
* * *
40357218 ATA ATA GTA AT- ATA AAA AGGTA AAA ATA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA A
40357261 AAACACTATT
Statistics
Matches: 258, Mismatches: 66, Indels: 68
0.66 0.17 0.17
Matches are distributed among these distances:
2 31 0.12
3 201 0.78
4 17 0.07
5 8 0.03
6 1 0.00
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.28
Consensus pattern (3 bp):
ATA
Done.