Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 154 of 240
Found at i:48561961 original size:5 final size:6
Alignment explanation
Indices: 48561946--48561976 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
48561936 CAAACCCTAG
*
48561946 TTTTTC TTTTTC TTTTTC TTTTTA TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
48561977 CGTTTCTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:48562147 original size:18 final size:18
Alignment explanation
Indices: 48562124--48562159 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
48562114 ATTAATAACC
48562124 AATACATATTTATTATTA
1 AATACATATTTATTATTA
*
48562142 AATACATGTTTATTATTA
1 AATACATATTTATTATTA
48562160 CACATGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
AATACATATTTATTATTA
Found at i:48565779 original size:30 final size:30
Alignment explanation
Indices: 48565742--48565823 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
48565732 TTGGCACATG
* **
48565742 GGCGTGTGTCCAGCCCGTGTGGCTTGCACA
1 GGCGTGTGTCCAGCCCATGTGGCTCACACA
* *
48565772 TGCGTGTGTCTAGCCCATGTGGCTCACACA
1 GGCGTGTGTCCAGCCCATGTGGCTCACACA
* *
48565802 GGCATGTATCCAGCCCATGTGG
1 GGCGTGTGTCCAGCCCATGTGG
48565824 AAATGCTCAG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.24
Consensus pattern (30 bp):
GGCGTGTGTCCAGCCCATGTGGCTCACACA
Found at i:48566779 original size:17 final size:17
Alignment explanation
Indices: 48566757--48566792 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
48566747 AGTATTATAA
48566757 TATTTATCATAA-AATTT
1 TATTTATCA-AATAATTT
48566774 TATTTATCAAATAATTT
1 TATTTATCAAATAATTT
48566791 TA
1 TA
48566793 AAAACAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTATCAAATAATTT
Found at i:48567661 original size:17 final size:18
Alignment explanation
Indices: 48567630--48567671 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
48567620 ATAATATCAT
*
48567630 TAAAAAACTCATAAATAC
1 TAAAAAACTCATAAAAAC
* *
48567648 TAAAAAACT-TTAAAAAT
1 TAAAAAACTCATAAAAAC
48567665 TAAAAAA
1 TAAAAAA
48567672 AAGTTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAAACTCATAAAAAC
Found at i:48572265 original size:14 final size:14
Alignment explanation
Indices: 48572246--48572272 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48572236 TTGTTTGCAT
48572246 ATAAAATATTTTTC
1 ATAAAATATTTTTC
48572260 ATAAAATATTTTT
1 ATAAAATATTTTT
48572273 ATTATTGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAAATATTTTTC
Found at i:48573192 original size:21 final size:22
Alignment explanation
Indices: 48573139--48573192 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
48573129 CTTAATTAAG
48573139 TAAATTAAGATTAATTAAAACTA
1 TAAA-TAAGATTAATTAAAACTA
* *
48573162 -AAACATGATTAATTAAAA-TA
1 TAAATAAGATTAATTAAAACTA
48573182 TAAATAAGATT
1 TAAATAAGATT
48573193 TATGAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (22 bp):
TAAATAAGATTAATTAAAACTA
Found at i:48573369 original size:19 final size:19
Alignment explanation
Indices: 48573331--48573369 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
48573321 TCATCCAAAC
*
48573331 TCCAAAAAATATTAGTTTT
1 TCCAAAAAATATAAGTTTT
48573350 TCCAAAAAA-ATAAGTCTTT
1 TCCAAAAAATATAAGT-TTT
48573369 T
1 T
48573370 TCCAGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (19 bp):
TCCAAAAAATATAAGTTTT
Found at i:48573957 original size:19 final size:19
Alignment explanation
Indices: 48573933--48573972 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
48573923 TAAATGGCTC
48573933 TTCAATTTATTTTTTCATT
1 TTCAATTTATTTTTTCATT
*
48573952 TTCAATTTGTTTTTTCATT
1 TTCAATTTATTTTTTCATT
48573971 TT
1 TT
48573973 GCTTCAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (19 bp):
TTCAATTTATTTTTTCATT
Found at i:48576724 original size:13 final size:13
Alignment explanation
Indices: 48576708--48576734 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48576698 ACTTCTCAAA
48576708 AGCATTTTTCCAC
1 AGCATTTTTCCAC
48576721 AGCATTTTTCCAC
1 AGCATTTTTCCAC
48576734 A
1 A
48576735 ACACTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (13 bp):
AGCATTTTTCCAC
Found at i:48586280 original size:54 final size:54
Alignment explanation
Indices: 48586217--48586449 Score: 225
Period size: 54 Copynumber: 4.1 Consensus size: 54
48586207 AGTATCATAT
* *
48586217 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAAAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
*
48586271 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * * *
48586325 ATTATATATTTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
1 ATTAT-GA-TTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTT-TA-T-T-A-
48586389 A
54 A
*
48586390 TATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
48586445 ATTAT
1 ATTAT
48586450 ATATTTTAAT
Statistics
Matches: 142, Mismatches: 23, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
54 61 0.43
55 2 0.01
56 7 0.05
57 12 0.08
58 5 0.04
59 4 0.03
60 16 0.11
61 4 0.03
62 5 0.04
63 12 0.08
64 7 0.05
65 2 0.01
66 5 0.04
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:48586306 original size:28 final size:27
Alignment explanation
Indices: 48586221--48586307 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
48586211 TCATATATTA
48586221 TGATTTGAGTAAATTCATATAAAAATAT
1 TGATTTGAGTAAATTCATAT-AAAATAT
* * * * *
48586249 TAATTATTA-AAAATT-TTATTAAAT-T
1 TGATT-TGAGTAAATTCATATAAAATAT
48586274 ATGATTTGAGTAAATTCATATAAGAATAT
1 -TGATTTGAGTAAATTCATATAA-AATAT
48586303 TGATT
1 TGATT
48586308 ATTAAGAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 7 0.16
28 17 0.40
29 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (27 bp):
TGATTTGAGTAAATTCATATAAAATAT
Found at i:48586354 original size:15 final size:15
Alignment explanation
Indices: 48586319--48586370 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
48586309 TTAAGAATTT
*
48586319 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48586333 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48586347 TATTTAATAATAAT-
1 TATTTAATTATAATA
48586361 TATGTTAATT
1 TAT-TTAATT
48586371 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48586396 original size:120 final size:120
Alignment explanation
Indices: 48586271--48586486 Score: 432
Period size: 120 Copynumber: 1.8 Consensus size: 120
48586261 ATTTTATTAA
48586271 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
48586336 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
66 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
48586391 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
48586456 TAATTATAATATATTTAATAATAATTATGTT
66 TAATTATAATATATTTAATAATAATTATGTT
48586487 TAAATATGAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 96 1.00
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (120 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
Found at i:48586469 original size:16 final size:16
Alignment explanation
Indices: 48586448--48586489 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
48586438 TTATTAAATT
*
48586448 ATATATTTTAATTATA
1 ATATATTTTAATAATA
48586464 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
48586479 AT-TATGTTTAA
1 ATATAT-TTTAA
48586490 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:48586474 original size:15 final size:15
Alignment explanation
Indices: 48586439--48586480 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48586429 TTAAGAATTT
*
48586439 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48586453 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48586467 TATTTAATAATAAT
1 TATTTAATTATAAT
48586481 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48586714 original size:45 final size:41
Alignment explanation
Indices: 48586616--48586725 Score: 107
Period size: 45 Copynumber: 2.6 Consensus size: 41
48586606 TTTTCCATTA
48586616 TGCTATTACACCTCTATTCCATT-C-AACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACAAACCAAACACAAGAT
* * ***
48586655 TACTATTACGCCTCTATTCCATTACATTTAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACA---AACCAAACACAAGA-T
* *
48586700 TGCTATTACACCTCTAATCCAATACA
1 TGCTATTACACCTCTATTCCATTACA
48586726 CCTCTAATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 21 0.38
40 1 0.02
44 11 0.20
45 23 0.41
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (41 bp):
TGCTATTACACCTCTATTCCATTACAAACCAAACACAAGAT
Found at i:48586727 original size:16 final size:16
Alignment explanation
Indices: 48586706--48586741 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
48586696 GATTTGCTAT
48586706 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48586722 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48586738 TACA
1 TACA
48586742 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:48586945 original size:16 final size:17
Alignment explanation
Indices: 48586926--48586957 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
48586916 TGAACATTAA
48586926 AATCAAAT-TCAAATAC
1 AATCAAATATCAAATAC
48586942 AATCAAATATCAAATA
1 AATCAAATATCAAATA
48586958 GGAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (17 bp):
AATCAAATATCAAATAC
Found at i:48607158 original size:22 final size:22
Alignment explanation
Indices: 48607119--48607165 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
48607109 ACATTAATAT
* *
48607119 AACAGTAGGCATCAAAGTGTAA
1 AACAATAGGCATCAAAGTGCAA
**
48607141 AACAATAGGCATTGAAGTGCAA
1 AACAATAGGCATCAAAGTGCAA
48607163 AAC
1 AAC
48607166 GATAAGCACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (22 bp):
AACAATAGGCATCAAAGTGCAA
Found at i:48608573 original size:22 final size:21
Alignment explanation
Indices: 48608548--48608592 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48608538 AAGAACCAAG
48608548 TTGTAAAGAAAAATTTTTTCTT
1 TTGTAAAG-AAAATTTTTTCTT
**
48608570 TTGTAAAGAATTTTTTTTCTT
1 TTGTAAAGAAAATTTTTTCTT
48608591 TT
1 TT
48608593 TCTCACGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (21 bp):
TTGTAAAGAAAATTTTTTCTT
Found at i:48613978 original size:31 final size:31
Alignment explanation
Indices: 48613943--48614004 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
48613933 AAAAGAACAA
48613943 GATTGAATCGTGCTAGCATGTTGCATATTTC
1 GATTGAATCGTGCTAGCATGTTGCATATTTC
48613974 GATTGAATCGTGCTAGCATGTTGCATATTTC
1 GATTGAATCGTGCTAGCATGTTGCATATTTC
48614005 ATAACTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (31 bp):
GATTGAATCGTGCTAGCATGTTGCATATTTC
Found at i:48614770 original size:5 final size:5
Alignment explanation
Indices: 48614760--48614795 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
48614750 GGAAAGAAAA
*
48614760 AGAAG AGAAG AGAAG AGAAG AGAAG CGAAG AGAAG A
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG A
48614796 AAACTTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:48629950 original size:29 final size:30
Alignment explanation
Indices: 48629877--48629942 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
48629867 ATCAAATCAT
* * *
48629877 TTAAATAAGAATTTATAAATAATTTAATGAC
1 TTAAATAAAAATTT-CAAATAATTTAATGAA
48629908 TTAAATAAAAATTTCAAATAATTTAAT-AA
1 TTAAATAAAAATTTCAAATAATTTAATGAA
48629937 TTAAAT
1 TTAAAT
48629943 TGTAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 7 0.22
30 12 0.38
31 13 0.41
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
TTAAATAAAAATTTCAAATAATTTAATGAA
Found at i:48639657 original size:30 final size:30
Alignment explanation
Indices: 48639607--48639663 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
48639597 CTGGCAAATG
*
48639607 GCCATGTGGTAGCCCTTGTGG-ATCACACA
1 GCCATGTGCTAGCCCTTGTGGAATCACACA
48639636 GCCATGTGCCTAG-CCTGTGTGGAATCAC
1 GCCATGTG-CTAGCCCT-TGTGGAATCAC
48639664 CCAACCTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 11 0.46
30 8 0.33
31 5 0.21
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (30 bp):
GCCATGTGCTAGCCCTTGTGGAATCACACA
Found at i:48648455 original size:16 final size:16
Alignment explanation
Indices: 48648434--48648467 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
48648424 TCAATCCTGA
*
48648434 GTAAGTGATGAGCTAT
1 GTAAGTGATGAACTAT
48648450 GTAAGTGATGAACTAT
1 GTAAGTGATGAACTAT
48648466 GT
1 GT
48648468 GTGCATCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (16 bp):
GTAAGTGATGAACTAT
Found at i:48656555 original size:26 final size:26
Alignment explanation
Indices: 48656532--48656629 Score: 96
Period size: 26 Copynumber: 3.8 Consensus size: 26
48656522 AAAATTTATT
* *
48656532 TTAAAAATTTAAAAAATTATTTTAAA
1 TTAAAAAATTAAAAAAATATTTTAAA
48656558 TTAAAAAATTAAAAAAATATTTT--A
1 TTAAAAAATTAAAAAAATATTTTAAA
* **
48656582 --AAAATATTTTAAAAATATTTTAAA
1 TTAAAAAATTAAAAAAATATTTTAAA
*
48656606 TTAAAAAAATTTAAAAAAGTATTT
1 TT-AAAAAA-TTAAAAAAATATTT
48656630 AAAAGTATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
22 18 0.32
24 2 0.04
26 21 0.37
27 5 0.09
28 11 0.19
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (26 bp):
TTAAAAAATTAAAAAAATATTTTAAA
Found at i:48656563 original size:18 final size:20
Alignment explanation
Indices: 48656521--48656568 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
48656511 AATAAATACC
*
48656521 AAAAATTTATTTTAAAAATTT
1 AAAAAATTATTTT-AAAATTT
48656542 AAAAAATTATTTT-AAA-TT
1 AAAAAATTATTTTAAAATTT
48656560 AAAAAATTA
1 AAAAAATTA
48656569 AAAAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
21 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAAATTATTTTAAAATTT
Found at i:48656572 original size:27 final size:26
Alignment explanation
Indices: 48656534--48656629 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 26
48656524 AATTTATTTT
48656534 AAAAATTTAAAAAATTATTTTAAATTA
1 AAAAATTTAAAAAA-TATTTTAAATTA
*
48656561 AAAAATTAAAAAAATATTTT--A--A
1 AAAAATTTAAAAAATATTTTAAATTA
* *
48656583 AAATATTTTAAAAATATTTTAAATTAA
1 AAAAATTTAAAAAATATTTTAAATT-A
48656610 AAAAATTTAAAAAAGTATTT
1 AAAAATTTAAAAAA-TATTT
48656630 AAAAGTATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 18 0.32
24 2 0.04
26 6 0.11
27 26 0.46
28 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (26 bp):
AAAAATTTAAAAAATATTTTAAATTA
Found at i:48656584 original size:11 final size:11
Alignment explanation
Indices: 48656570--48656605 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
48656560 AAAAAATTAA
48656570 AAAAATATTTT
1 AAAAATATTTT
48656581 AAAAATATTTT
1 AAAAATATTTT
48656592 AAAAATATTTT
1 AAAAATATTTT
48656603 AAA
1 AAA
48656606 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:48656605 original size:48 final size:51
Alignment explanation
Indices: 48656528--48656644 Score: 165
Period size: 49 Copynumber: 2.4 Consensus size: 51
48656518 ACCAAAAATT
*
48656528 TATTTT-AAAA-ATTTAAAAAATTATTTTAAATT-AAAAAA-TTAAAAAAA
1 TATTTTAAAAATATTTTAAAAATTATTTTAAATTAAAAAAATTTAAAAAAA
*
48656575 TATTTTAAAAATATTTTAAAAA-TATTTTAAATTAAAAAAATTTAAAAAAG
1 TATTTTAAAAATATTTTAAAAATTATTTTAAATTAAAAAAATTTAAAAAAA
*
48656625 TA-TTTAAAAGTATTTTAAAA
1 TATTTTAAAAATATTTTAAAA
48656645 TTAAAAAATA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
47 6 0.10
48 15 0.24
49 32 0.51
50 10 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (51 bp):
TATTTTAAAAATATTTTAAAAATTATTTTAAATTAAAAAAATTTAAAAAAA
Found at i:48656612 original size:38 final size:39
Alignment explanation
Indices: 48656562--48656652 Score: 123
Period size: 38 Copynumber: 2.3 Consensus size: 39
48656552 TTTAAATTAA
*
48656562 AAAATTAAAAAAATATTTTAAAAA-TATTTTAAAAATATTTT
1 AAAATT-AAAAAA-ATTTAAAAAAGTA-TTTAAAAATATTTT
*
48656603 -AAATTAAAAAAATTTAAAAAAGTATTTAAAAGTATTTT
1 AAAATTAAAAAAATTTAAAAAAGTATTTAAAAATATTTT
48656641 AAAATTAAAAAA
1 AAAATTAAAAAA
48656653 TAAAAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 22 0.48
39 19 0.41
40 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (39 bp):
AAAATTAAAAAAATTTAAAAAAGTATTTAAAAATATTTT
Found at i:48656653 original size:38 final size:38
Alignment explanation
Indices: 48656534--48656652 Score: 120
Period size: 38 Copynumber: 3.1 Consensus size: 38
48656524 AATTTATTTT
***
48656534 AAAAATTTAAAAAATTATTTT--AAAT-TAAAAAATTAAA
1 AAAAATTTAAAAAA-TATTTTAAAAATATTTTAAATT-AA
*
48656571 AAAATATTTTAAAAATATTTTAAAAATATTTTAAATTAA
1 AAAA-ATTTAAAAAATATTTTAAAAATATTTTAAATTAA
*
48656610 AAAAATTTAAAAAAGTA-TTTAAAAGTATTTTAAAATTAA
1 AAAAATTTAAAAAA-TATTTTAAAAATATTTT-AAATTAA
48656649 AAAA
1 AAAA
48656653 TAAAAAATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
37 10 0.14
38 31 0.44
39 23 0.33
40 6 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (38 bp):
AAAAATTTAAAAAATATTTTAAAAATATTTTAAATTAA
Found at i:48668937 original size:29 final size:28
Alignment explanation
Indices: 48668895--48669004 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 28
48668885 TCCCAGACCA
* * * * *
48668895 TGTGTCTGATACGGTCCAACACATAGTTG
1 TGTGTCTCACACGGTCTAGCACAT-GTCG
*
48668924 TGTGTCTCACACGGTCTAGCATATGGTCG
1 TGTGTCTCACACGGTCTAGCACAT-GTCG
*
48668953 TGTGTCTCACATGGTCTAGCACATGATCG
1 TGTGTCTCACACGGTCTAGCACATG-TCG
* * *
48668982 TGTGTCACACACGGCCTGGCACA
1 TGTGTCTCACACGGTCTAGCACA
48669005 CATTTGTGTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
28 1 0.01
29 66 0.99
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (28 bp):
TGTGTCTCACACGGTCTAGCACATGTCG
Found at i:48672971 original size:51 final size:51
Alignment explanation
Indices: 48672895--48673105 Score: 334
Period size: 51 Copynumber: 4.2 Consensus size: 51
48672885 CGGATCACAT
*
48672895 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* ** * *
48672946 TTATCACTTGTCACTTATCACTGATCAGATATGTACAACTAAAGCTATCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
48672997 TTATCACTTGTCACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
48673048 TTATCACTAGTCACTTATCACTGATCACATAAGTGTAGCTAAA-CTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
48673098 TTATCACT
1 TTATCACT
48673106 GATCACATAA
Statistics
Matches: 145, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 15 0.10
51 130 0.90
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:48673065 original size:102 final size:101
Alignment explanation
Indices: 48672895--48673204 Score: 342
Period size: 102 Copynumber: 3.2 Consensus size: 101
48672885 CGGATCACAT
* * *
48672895 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCAC
1 TTATCACTTGTCACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCAC
* * *
48672960 TTATCACTGATCAGATATGTACAACTAAAGCTATCAC
66 TTATCACTGATCACATAAGTACAACTAAA-CTACCAC
48672997 TTATCACTTGTCACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCAC
1 TTATCACTTGTCACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCAC
** *
48673062 TTATCACTGATCACATAAGTGTAGCTAAACTACCAC
66 TTATCACTGATCACATAAGTACAACTAAACTACCAC
* * *
48673098 TTATCAC-TG------AT--C--A-C--ATAAGTGTATCTAAAGCTACCATTTATCACTTGTCAC
1 TTATCACTTGTCACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCAC
* * * ** *
48673149 TTATCACTGATTAGATAAATGTAGCTAAACTACCAC
66 TTATCACTGATCACATAAGTACAACTAAACTACCAC
*
48673185 TTATCACTTGTCACTGATCA
1 TTATCACTTGTCACTTATCA
48673205 AAAGTACTCA
Statistics
Matches: 184, Mismatches: 15, Indels: 24
0.83 0.07 0.11
Matches are distributed among these distances:
87 74 0.40
88 2 0.01
89 1 0.01
90 1 0.01
92 1 0.01
94 4 0.02
100 2 0.01
101 13 0.07
102 86 0.47
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (101 bp):
TTATCACTTGTCACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCAC
TTATCACTGATCACATAAGTACAACTAAACTACCAC
Found at i:48673106 original size:36 final size:37
Alignment explanation
Indices: 48673059--48673142 Score: 143
Period size: 36 Copynumber: 2.3 Consensus size: 37
48673049 TATCACTAGT
48673059 CACTTATCACTGATCACATAAGTGTAGCTAAA-CTAC
1 CACTTATCACTGATCACATAAGTGTAGCTAAAGCTAC
*
48673095 CACTTATCACTGATCACATAAGTGTATCTAAAGCTAC
1 CACTTATCACTGATCACATAAGTGTAGCTAAAGCTAC
*
48673132 CATTTATCACT
1 CACTTATCACT
48673143 TGTCACTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 31 0.69
37 14 0.31
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.31
Consensus pattern (37 bp):
CACTTATCACTGATCACATAAGTGTAGCTAAAGCTAC
Found at i:48673126 original size:87 final size:87
Alignment explanation
Indices: 48673008--48673192 Score: 298
Period size: 87 Copynumber: 2.1 Consensus size: 87
48672998 TATCACTTGT
*
48673008 CACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCACTTATCACTGAT
1 CACTTATCACTAATCACATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCACTTATCACTGAT
*
48673073 CACATAAGTGTAGCTAAACTAC
66 CACATAAATGTAGCTAAACTAC
* * * *
48673095 CACTTATCACTGATCACATAAGTGTATCTAAAGCTACCATTTATCACTTGTCACTTATCACTGAT
1 CACTTATCACTAATCACATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCACTTATCACTGAT
* *
48673160 TAGATAAATGTAGCTAAACTAC
66 CACATAAATGTAGCTAAACTAC
48673182 CACTTATCACT
1 CACTTATCACT
48673193 TGTCACTGAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (87 bp):
CACTTATCACTAATCACATAAGTGTAGCTAAAGCTACCACTTATCACTAGTCACTTATCACTGAT
CACATAAATGTAGCTAAACTAC
Found at i:48673197 original size:50 final size:51
Alignment explanation
Indices: 48673095--48673204 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 51
48673085 GCTAAACTAC
* * *
48673095 CACTTATCACTGATCACATAAGTGTATCTAAAGCTACCATTTATCACTTGT
1 CACTTATCACTGATCACATAAATGTAGCTAAAGCTACCACTTATCACTTGT
* *
48673146 CACTTATCACTGATTAGATAAATGTAGCTAAA-CTACCACTTATCACTTGT
1 CACTTATCACTGATCACATAAATGTAGCTAAAGCTACCACTTATCACTTGT
*
48673196 CACTGATCA
1 CACTTATCA
48673205 AAAGTACTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 25 0.47
51 28 0.53
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.34
Consensus pattern (51 bp):
CACTTATCACTGATCACATAAATGTAGCTAAAGCTACCACTTATCACTTGT
Found at i:48673300 original size:17 final size:17
Alignment explanation
Indices: 48673278--48673310 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48673268 TATTCTCAAT
48673278 TCATCAATA-AATATATC
1 TCATC-ATACAATATATC
48673295 TCATCATACAATATAT
1 TCATCATACAATATAT
48673311 AATTCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:48676891 original size:15 final size:16
Alignment explanation
Indices: 48676866--48676896 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
48676856 ATGAGTCTCT
48676866 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
48676882 TTTTTT-AAATATTTA
1 TTTTTTAAAATATTTA
48676897 CTACACCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:48695725 original size:29 final size:30
Alignment explanation
Indices: 48695679--48695742 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 30
48695669 GTTTAGCCTT
*
48695679 GGAAGAAAATTTTGAGATTTGGTCAAAAAG
1 GGAAGAAAATTTTAAGATTTGGTCAAAAAG
48695709 GGAA-AAAATTTTAAGATTTGGTCAAAAAG
1 GGAAGAAAATTTTAAGATTTGGTCAAAAAG
48695738 GGAAG
1 GGAAG
48695743 TTGAGCCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 28 0.88
30 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.27, T:0.25
Consensus pattern (30 bp):
GGAAGAAAATTTTAAGATTTGGTCAAAAAG
Found at i:48704481 original size:21 final size:21
Alignment explanation
Indices: 48704422--48704489 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
48704412 AATCAATAGT
* *
48704422 TCAAAAACTAACTACGAAAAA
1 TCAAATACTAACTAAGAAAAA
* * * * *
48704443 TC-TATAGTCAGTAGGAAAAA
1 TCAAATACTAACTAAGAAAAA
48704463 TCAAATACTAACTAAGAAAAA
1 TCAAATACTAACTAAGAAAAA
48704484 TCAAAT
1 TCAAAT
48704490 TGGTGTGAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.21
Consensus pattern (21 bp):
TCAAATACTAACTAAGAAAAA
Found at i:48706719 original size:18 final size:18
Alignment explanation
Indices: 48706685--48706719 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48706675 ATAAATAATT
* *
48706685 TTTTTAATATTTTAAAAC
1 TTTTAAATATTTAAAAAC
48706703 TTTTAAATATTTAAAAA
1 TTTTAAATATTTAAAAA
48706720 AATTTAGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAATATTTAAAAAC
Found at i:48706725 original size:18 final size:19
Alignment explanation
Indices: 48706690--48706740 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
48706680 TAATTTTTTT
* **
48706690 AATATTTTAAAACTTTTA-
1 AATATTTAAAAAAATTTAG
48706708 AATATTTAAAAAAATTTAG
1 AATATTTAAAAAAATTTAG
* *
48706727 AAAATCTAAAAAAA
1 AATATTTAAAAAAA
48706741 AAGTTAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
AATATTTAAAAAAATTTAG
Found at i:48707866 original size:20 final size:19
Alignment explanation
Indices: 48707829--48707867 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
48707819 TATTTACAGC
* *
48707829 TTTTAATATTTTTTTATTT
1 TTTTAATATTTATGTATTT
48707848 TTTTAAATATTTATGTATTT
1 TTTT-AATATTTATGTATTT
48707868 ATATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTAATATTTATGTATTT
Found at i:48708509 original size:16 final size:16
Alignment explanation
Indices: 48708488--48708520 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48708478 TTATATATAT
48708488 ATTTTTA-AAGATTTTA
1 ATTTTTATAA-ATTTTA
48708504 ATTTTTATAAATTTTA
1 ATTTTTATAAATTTTA
48708520 A
1 A
48708521 ATCATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTTATAAATTTTA
Found at i:48710409 original size:5 final size:5
Alignment explanation
Indices: 48710399--48710429 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
48710389 TTTGCATTGT
*
48710399 TTTTA TTTTA TTTTA TTTTA TTTTT TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
48710430 AACATTTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:48720689 original size:32 final size:28
Alignment explanation
Indices: 48720670--48720740 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
48720660 ATTAATTTAT
48720670 AATTTATTATCTAAAATATTAAAATTGA
1 AATTTATTATCTAAAATATTAAAATTGA
* * *
48720698 AATTTATTATCTAAATTA-TACAATTTA
1 AATTTATTATCTAAAATATTAAAATTGA
*
48720725 AACATTATTATCTAAA
1 AA-TTTATTATCTAAA
48720741 CATTAATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (28 bp):
AATTTATTATCTAAAATATTAAAATTGA
Found at i:48722432 original size:16 final size:16
Alignment explanation
Indices: 48722411--48722444 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
48722401 TTATAAGAAA
48722411 TCAAAAAAAAATAGTC
1 TCAAAAAAAAATAGTC
48722427 TC--AAAAAAATAGTC
1 TCAAAAAAAAATAGTC
48722441 TCAA
1 TCAA
48722445 TCGGACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 4
0.80 0.00 0.20
Matches are distributed among these distances:
14 14 0.88
16 2 0.12
ACGTcount: A:0.59, C:0.15, G:0.06, T:0.21
Consensus pattern (16 bp):
TCAAAAAAAAATAGTC
Found at i:48722434 original size:14 final size:14
Alignment explanation
Indices: 48722415--48722444 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
48722405 AAGAAATCAA
48722415 AAAAAAATAGTCTC
1 AAAAAAATAGTCTC
48722429 AAAAAAATAGTCTC
1 AAAAAAATAGTCTC
48722443 AA
1 AA
48722445 TCGGACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAAAATAGTCTC
Found at i:48723710 original size:21 final size:21
Alignment explanation
Indices: 48723684--48723724 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48723674 ATAGTATCCC
48723684 CCATGTG-CAACATGATGAGCT
1 CCATGTGACAA-ATGATGAGCT
*
48723705 CCATGTGACAAATGGTGAGC
1 CCATGTGACAAATGATGAGC
48723725 CCCGTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
CCATGTGACAAATGATGAGCT
Found at i:48723957 original size:18 final size:18
Alignment explanation
Indices: 48723931--48723991 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
48723921 TGAGGTGGAT
*
48723931 GAGGGTATCCTCCATGAG
1 GAGGATATCCTCCATGAG
*
48723949 GAGGATATCCTGCA-G-G
1 GAGGATATCCTCCATGAG
*
48723965 TG-GG-TATCCGCCATGAG
1 -GAGGATATCCTCCATGAG
48723982 GAGGATATCC
1 GAGGATATCC
48723992 CGCTGGTGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 5 0.15
18 17 0.50
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (18 bp):
GAGGATATCCTCCATGAG
Found at i:48723979 original size:33 final size:33
Alignment explanation
Indices: 48723933--48724000 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
48723923 AGGTGGATGA
* *
48723933 GGGTATCCTCCATGAGGAGGATATCCTGCAGGT
1 GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
*
48723966 GGGTATCCGCCATGAGGAGGATATCCCGCTGGT
1 GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
48723999 GG
1 GG
48724001 AGGATATCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.37, T:0.22
Consensus pattern (33 bp):
GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
Found at i:48724017 original size:18 final size:18
Alignment explanation
Indices: 48723981--48724018 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
48723971 TCCGCCATGA
* *
48723981 GGAGGATATCCCGCTGGT
1 GGAGGATATCCAGCCGGT
48723999 GGAGGATATCCAGCCGGT
1 GGAGGATATCCAGCCGGT
48724017 GG
1 GG
48724019 GTATCCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.42, T:0.18
Consensus pattern (18 bp):
GGAGGATATCCAGCCGGT
Found at i:48724038 original size:15 final size:15
Alignment explanation
Indices: 48724020--48724063 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
48724010 AGCCGGTGGG
*
48724020 TATCCTTGTGGGGGA
1 TATCCTTGTGGAGGA
*
48724035 TATCCTTGAGGAGGA
1 TATCCTTGTGGAGGA
48724050 TATCCTTGTGGAGG
1 TATCCTTGTGGAGG
48724064 GTAGGATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (15 bp):
TATCCTTGTGGAGGA
Found at i:48733916 original size:51 final size:50
Alignment explanation
Indices: 48733857--48733953 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 50
48733847 CAGGAATCGA
48733857 TTTCAAATACTCTTACAAAGGACTAAACTTAGATTTATGAACCATAACAAT
1 TTTCAAATACTCTTACAAAGGACTAAACTTAGA-TTATGAACCATAACAAT
*
48733908 TTTCAAATACTCTTACAAAGGGCTAAACTTAGATTATGAACCATAA
1 TTTCAAATACTCTTACAAAGGACTAAACTTAGATTATGAACCATAA
48733954 AAATCCAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 13 0.29
51 32 0.71
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (50 bp):
TTTCAAATACTCTTACAAAGGACTAAACTTAGATTATGAACCATAACAAT
Found at i:48758937 original size:13 final size:13
Alignment explanation
Indices: 48758921--48758946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48758911 AAATATATAT
48758921 TTTTTAATTTTAA
1 TTTTTAATTTTAA
48758934 TTTTTAATTTTAA
1 TTTTTAATTTTAA
48758947 AATAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTTAA
Found at i:48758954 original size:11 final size:11
Alignment explanation
Indices: 48758938--48758967 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
48758928 TTTTAATTTT
48758938 TAATTTTAAAA
1 TAATTTTAAAA
48758949 TAATTTTAAAA
1 TAATTTTAAAA
*
48758960 TATTTTTA
1 TAATTTTA
48758968 GTTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:48761630 original size:18 final size:18
Alignment explanation
Indices: 48761608--48761653 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
48761598 TTGATGATAT
48761608 CGATATTGATGA-TAGTGA
1 CGATATTGAT-ACTAGTGA
*
48761626 TGATATTGATACTAGTGA
1 CGATATTGATACTAGTGA
*
48761644 CGCTATTGAT
1 CGATATTGAT
48761654 CGTGACTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (18 bp):
CGATATTGATACTAGTGA
Found at i:48763605 original size:15 final size:15
Alignment explanation
Indices: 48763585--48763617 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
48763575 ATTAAAATAC
48763585 AAAACC-AAATTTTAT
1 AAAACCAAAATTTT-T
48763600 AAAACCAAAATTTTT
1 AAAACCAAAATTTTT
48763615 AAA
1 AAA
48763618 CACTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAACCAAAATTTTT
Found at i:48772077 original size:157 final size:157
Alignment explanation
Indices: 48771791--48772104 Score: 628
Period size: 157 Copynumber: 2.0 Consensus size: 157
48771781 AAATAAGAAA
48771791 TAAACCTATCATTCTGCACAATTATCAGAAGTAAACCGATAAGAACTGGGAAAAGGATATTCTCT
1 TAAACCTATCATTCTGCACAATTATCAGAAGTAAACCGATAAGAACTGGGAAAAGGATATTCTCT
48771856 CTATACTAAGATCCTCAATCAAGCTACTTAAGCAAGGAACCACTTAGTAATAACTCAAGATTCTG
66 CTATACTAAGATCCTCAATCAAGCTACTTAAGCAAGGAACCACTTAGTAATAACTCAAGATTCTG
48771921 TCATCTAGATATCGAGAAACTCATGTC
131 TCATCTAGATATCGAGAAACTCATGTC
48771948 TAAACCTATCATTCTGCACAATTATCAGAAGTAAACCGATAAGAACTGGGAAAAGGATATTCTCT
1 TAAACCTATCATTCTGCACAATTATCAGAAGTAAACCGATAAGAACTGGGAAAAGGATATTCTCT
48772013 CTATACTAAGATCCTCAATCAAGCTACTTAAGCAAGGAACCACTTAGTAATAACTCAAGATTCTG
66 CTATACTAAGATCCTCAATCAAGCTACTTAAGCAAGGAACCACTTAGTAATAACTCAAGATTCTG
48772078 TCATCTAGATATCGAGAAACTCATGTC
131 TCATCTAGATATCGAGAAACTCATGTC
48772105 CACAACTCAA
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (157 bp):
TAAACCTATCATTCTGCACAATTATCAGAAGTAAACCGATAAGAACTGGGAAAAGGATATTCTCT
CTATACTAAGATCCTCAATCAAGCTACTTAAGCAAGGAACCACTTAGTAATAACTCAAGATTCTG
TCATCTAGATATCGAGAAACTCATGTC
Found at i:48774242 original size:16 final size:17
Alignment explanation
Indices: 48774202--48774243 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
48774192 ATTATCGAAT
48774202 ATTTATAAGGGAAAACTTGG
1 ATTT-TAAGGGAAAAC-T-G
48774222 ATTTTAAGGGAAAAC-G
1 ATTTTAAGGGAAAACTG
48774238 ATTTTA
1 ATTTTA
48774244 TCTTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
19 11 0.50
20 4 0.18
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (17 bp):
ATTTTAAGGGAAAACTG
Found at i:48774854 original size:45 final size:46
Alignment explanation
Indices: 48774804--48774899 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 46
48774794 TCATTGACCA
*
48774804 AGTATAAATAATTAATAATAAATAATATGTAAATTAGTTAA-ATTT
1 AGTATAAATAATTAATAATAAATAATATGTAAATTAATTAACATTT
*
48774849 AGTATAAATAATTAATAATAAATACTATGTAAATTAATTAACTATTT
1 AGTATAAATAATTAATAATAAATAATATGTAAATTAATTAAC-ATTT
48774896 AGTA
1 AGTA
48774900 GGTCAACATA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 39 0.83
47 8 0.17
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (46 bp):
AGTATAAATAATTAATAATAAATAATATGTAAATTAATTAACATTT
Found at i:48777564 original size:28 final size:28
Alignment explanation
Indices: 48777501--48777604 Score: 136
Period size: 28 Copynumber: 3.7 Consensus size: 28
48777491 TGACTTTCGA
*
48777501 CACTAAGTGTGTGAGTTTAATTTGTAAAG
1 CACTAAGTGTGCGAGTTTAA-TTGTAAAG
*
48777530 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
48777558 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
48777586 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAGTTTA
48777605 TTAAATATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 47 0.71
29 19 0.29
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:48778374 original size:23 final size:23
Alignment explanation
Indices: 48778327--48778385 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
48778317 TTATGCTTAA
* *
48778327 ATGCTGCCC-AATTGATGTATTT
1 ATGCTGCCCAAATTGATATATAT
48778349 ATGCTGCCCAAATTG-TCATATAT
1 ATGCTGCCCAAATTGAT-ATATAT
*
48778372 ATGCTGTCCAAATT
1 ATGCTGCCCAAATT
48778386 TTTGATGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (23 bp):
ATGCTGCCCAAATTGATATATAT
Found at i:48778402 original size:49 final size:48
Alignment explanation
Indices: 48778349--48778627 Score: 114
Period size: 48 Copynumber: 5.9 Consensus size: 48
48778339 TGATGTATTT
*
48778349 ATGCTGCCCAA-ATTGTCATATATATGCTGTCCAAATTTT-TGATGTAAAA
1 ATGCTGCCCAATATTGT-ATATACATGCTGT-CAAATTTTGTG-TGTAAAA
* * *
48778398 ATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTGT--AA
1 ATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTGTGTGTAAAA
* * * * ** * * *
48778444 GTGTTGTCCAA-ATTGGTGTATGTATGCTGCCTAATTTT-TG-GTGAATTA
1 ATGCTGCCCAATATT-GTATATACATGCTGTCAAATTTTGTGTGT-AA-AA
** * * *
48778492 ATGCTATCCAATTTTGTATATACATGCTGTTAAA-TTT-TGTGTATAA
1 ATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTGTGTGTAAAA
* * * ** * * *
48778538 GTGCTGTCCAA-ATTGGTGTATGTATGCTGCCTAATTTT-TG-GTGAATCA
1 ATGCTGCCCAATATT-GTATATACATGCTGTCAAATTTTGTGTGT-AA-AA
* * * * *
48778586 ATGTTGTCCAATTTTGTATACACATGCTGTTAAATTTTGTGT
1 ATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTGTGT
48778628 ATAAGTGCTG
Statistics
Matches: 167, Mismatches: 47, Indels: 31
0.68 0.19 0.13
Matches are distributed among these distances:
44 2 0.01
45 6 0.04
46 53 0.32
47 12 0.07
48 60 0.36
49 30 0.18
50 4 0.02
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (48 bp):
ATGCTGCCCAATATTGTATATACATGCTGTCAAATTTTGTGTGTAAAA
Found at i:48778472 original size:46 final size:46
Alignment explanation
Indices: 48778350--48778660 Score: 211
Period size: 46 Copynumber: 6.6 Consensus size: 46
48778340 GATGTATTTA
* * * *
48778350 TGCTGCCCAAATT-GTCATATATATGCTGTCCAAATTTT-TGATGTAAAAA
1 TGCTGTCCAAATTGGT-ATATGTATGCTGT-TAAATTTTGTG-TGT--AAG
* * **
48778399 TGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTGTAAG
1 TGCTGTCCAAATTGGTATATGTATGCTGTTAAATTTTGTGTGTAAG
* * * *
48778445 TGTTGTCCAAATTGGTGTATGTATGCTGCCTAATTTTTG-GTGAATTAA-
1 TGCTGTCCAAATTGGTATATGTATGCTG-TTAAATTTTGTGTG---TAAG
* * * ** *
48778493 TGCTATCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATGTATGCTGTTAAATTTTGTGTGTAAG
* * *
48778539 TGCTGTCCAAATTGGTGTATGTATGCTGCCTAATTTTTG-GTGAATCAA-
1 TGCTGTCCAAATTGGTATATGTATGCTG-TTAAATTTTGTGTG--T-AAG
* * * *** *
48778587 TGTTGTCCAATTTTGTATACACATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATGTATGCTGTTAAATTTTGTGTGTAAG
48778633 TGCTGTCCAAATTGGTATATGTATGCTG
1 TGCTGTCCAAATTGGTATATGTATGCTG
48778661 CCTAATTTTT
Statistics
Matches: 200, Mismatches: 48, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
45 5 0.03
46 74 0.37
47 32 0.16
48 57 0.28
49 30 0.15
50 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (46 bp):
TGCTGTCCAAATTGGTATATGTATGCTGTTAAATTTTGTGTGTAAG
Found at i:48778502 original size:94 final size:95
Alignment explanation
Indices: 48778371--48778737 Score: 515
Period size: 94 Copynumber: 3.9 Consensus size: 95
48778361 TTGTCATATA
* * *
48778371 TATGCTGTCCAAATTTTTGATGTAA-AAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
1 TATGCTG-CCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
* *
48778435 TGTGTGTAAGTGTTGTCCAAATTGGTGTATG
65 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
* *
48778466 TATGCTGCCTAATTTTTGGTG-AATTAATGCTATCCAATTTTGTATATACATGCTGTTAAATTTT
1 TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
48778530 GTGTATAAGTGCTGTCCAAATTGGTGTATG
66 GTGTATAAGTGCTGTCCAAATTGGTGTATG
* * *
48778560 TATGCTGCCTAATTTTTGGTG-AATCAATGTTGTCCAATTTTGTATACACATGCTGTTAAATTTT
1 TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
*
48778624 GTGTATAAGTGCTGTCCAAATTGGTATATG
66 GTGTATAAGTGCTGTCCAAATTGGTGTATG
* * * * * *
48778654 TATGCTGCCTAATTTTTGGTGAAAAAAAATGCTGTCCAATTTTATATATATATGCTACTCAATTT
1 TATGCTGCCTAATTTTTGGTG-AAATAAATGCTGTCCAATTTTGTATATACATGCT-GTTAAATT
*
48778719 TTGATGTATAAGAGCTGTC
64 TTG-TGTATAAGTGCTGTC
48778738 GAAACAGGGT
Statistics
Matches: 246, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
93 2 0.01
94 188 0.76
95 7 0.03
96 27 0.11
97 8 0.03
98 14 0.06
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.43
Consensus pattern (95 bp):
TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
GTGTATAAGTGCTGTCCAAATTGGTGTATG
Found at i:48778527 original size:23 final size:22
Alignment explanation
Indices: 48778501--48778638 Score: 73
Period size: 23 Copynumber: 5.9 Consensus size: 22
48778491 AATGCTATCC
48778501 AATTTTGTATATACATGCTGTTA
1 AATTTTGTATATA-ATGCTGTTA
* *
48778524 AATTTTGTGTATAAGTGCTGTCCA
1 AATTTTGTATATAA-TGCTGT-TA
* * *
48778548 AATTGGTGTATGT-ATGCTGCCTA
1 AATT-TTGTATATAATGCTG-TTA
* * **
48778571 ATTTTTGGTGA-ATCAATGTTGTCC
1 AATTTT-GT-ATAT-AATGCTGTTA
*
48778595 AATTTTGTATACACATGCTGTTA
1 AATTTTGTATATA-ATGCTGTTA
*
48778618 AATTTTGTGTATAAGTGCTGT
1 AATTTTGTATATAA-TGCTGT
48778639 CCAAATTGGT
Statistics
Matches: 83, Mismatches: 21, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
22 5 0.06
23 56 0.67
24 12 0.14
25 10 0.12
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (22 bp):
AATTTTGTATATAATGCTGTTA
Found at i:48785090 original size:28 final size:28
Alignment explanation
Indices: 48785027--48785130 Score: 145
Period size: 28 Copynumber: 3.7 Consensus size: 28
48785017 TGACTTTCGA
48785027 CACTAAGTGTGCGAGTTTAATTTGTAAAG
1 CACTAAGTGTGCGAGTTTAA-TTGTAAAG
*
48785056 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
48785084 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
48785112 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAGTTTA
48785131 TTAAATATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 47 0.70
29 20 0.30
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:48785980 original size:94 final size:93
Alignment explanation
Indices: 48785876--48786261 Score: 524
Period size: 94 Copynumber: 4.1 Consensus size: 93
48785866 GATGTATTTA
* * * *
48785876 TGCTGCCCAAATT-GTCATATATATGCTGTCCAAATTTTTGATGTAA-AATGCTGTCCAATTTTG
1 TGCTGTCCAAATTGGT-ATATGTATGCTG-CCTAATTTTTGGTG-AACAATGCTGTCCAATTTTG
*
48785939 CATATACATGCTGTTAAATTTTGTGTATAAG
63 TATATACATGCTGTTAAATTTTGTGTATAAG
*
48785970 TGCTGTCCAAATTGGTGTATGTATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTA
1 TGCTGTCCAAATTGGTATATGTATGCTGCCTAATTTTTGGTGAA-CAATGCTGTCCAATTTTGTA
48786035 TATACATGCTGTTAAATTTTGTGTATAAG
65 TATACATGCTGTTAAATTTTGTGTATAAG
* *
48786064 TGCTATCCAAATTGGTGTATGTATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTA
1 TGCTGTCCAAATTGGTATATGTATGCTGCCTAATTTTTGGTGAA-CAATGCTGTCCAATTTTGTA
*
48786129 TACACATGCTGTTAAATTTTGTGTATAAG
65 TATACATGCTGTTAAATTTTGTGTATAAG
* * * *
48786158 TGCTGTCCAAATTGGTATATGTATGCTGCCTAATTTTTGGTGAAAAAAATGCTGTCTAATTATAT
1 TGCTGTCCAAATTGGTATATGTATGCTGCCTAATTTTTGGTG--AACAATGCTGTCCAATTTTGT
* * *
48786223 ATATATATGCTGCTCAATTTTTGATGTATAAG
64 ATATACATGCTG-TTAAATTTTG-TGTATAAG
*
48786255 AGCTGTC
1 TGCTGTC
48786262 GAAACAGGGT
Statistics
Matches: 266, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
92 2 0.01
93 12 0.05
94 201 0.76
95 27 0.10
96 10 0.04
97 14 0.05
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.41
Consensus pattern (93 bp):
TGCTGTCCAAATTGGTATATGTATGCTGCCTAATTTTTGGTGAACAATGCTGTCCAATTTTGTAT
ATACATGCTGTTAAATTTTGTGTATAAG
Found at i:48785987 original size:23 final size:22
Alignment explanation
Indices: 48785852--48786173 Score: 91
Period size: 23 Copynumber: 13.8 Consensus size: 22
48785842 TTTATGCTTA
* *
48785852 AATGCTG-CCCAATTGATGTATT
1 AATGCTGTCCAAATTGGTGTA-T
* * *
48785874 TATGCTGCCCAAATT-GTCATAT
1 AATGCTGTCCAAATTGGT-GTAT
* *
48785896 ATATGCTGTCCAAATTTTTGATGTAA
1 A-ATGCTGTCCAAA---TTGGTGTAT
* * **
48785922 AATGCTGTCCAATTTTGCATAT
1 AATGCTGTCCAAATTGGTGTAT
* *
48785944 ACATGCTGT-TAAATTTTGTGTAT
1 A-ATGCTGTCCAAA-TTGGTGTAT
48785967 AAGTGCTGTCCAAATTGGTGTAT
1 AA-TGCTGTCCAAATTGGTGTAT
* * *
48785990 GTATGCTG-CCTAATTTTTGGTGAAT
1 -AATGCTGTCC-AA--ATTGGTGTAT
* * *
48786015 CAATGCTGTCCAATTTTGTATAT
1 -AATGCTGTCCAAATTGGTGTAT
* *
48786038 ACATGCTGT-TAAATTTTGTGTAT
1 A-ATGCTGTCCAAA-TTGGTGTAT
*
48786061 AAGTGCTATCCAAATTGGTGTAT
1 AA-TGCTGTCCAAATTGGTGTAT
* * *
48786084 GTATGCTG-CCTAATTTTTGGTGAAT
1 -AATGCTGTCC-AA--ATTGGTGTAT
* * * *
48786109 CAATGCTGTCCAATTTTGTATAC
1 -AATGCTGTCCAAATTGGTGTAT
* *
48786132 ACATGCTGT-TAAATTTTGTGTAT
1 A-ATGCTGTCCAAA-TTGGTGTAT
48786155 AAGTGCTGTCCAAATTGGT
1 AA-TGCTGTCCAAATTGGT
48786174 ATATGTATGC
Statistics
Matches: 220, Mismatches: 51, Indels: 57
0.67 0.16 0.17
Matches are distributed among these distances:
22 28 0.13
23 128 0.58
24 11 0.05
25 43 0.20
26 9 0.04
27 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (22 bp):
AATGCTGTCCAAATTGGTGTAT
Found at i:48786984 original size:6 final size:6
Alignment explanation
Indices: 48786973--48787012 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
48786963 GTTTCCCAAA
*
48786973 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGA AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
48787013 ATGAAATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:48791219 original size:26 final size:25
Alignment explanation
Indices: 48791190--48791260 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
48791180 ATCACTTTAA
48791190 TATTAAATTAATATAATATTTAATCT
1 TATTAAATTAATATAATATTT-ATCT
* * *
48791216 TATTAAAATAATAAAATGTTTATCT
1 TATTAAATTAATATAATATTTATCT
*
48791241 TACATTAAAATTAATTTAAT
1 T--ATT-AAATTAATATAAT
48791261 CTTAAGATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 5 0.14
26 18 0.50
27 3 0.08
28 10 0.28
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (25 bp):
TATTAAATTAATATAATATTTATCT
Found at i:48794187 original size:51 final size:52
Alignment explanation
Indices: 48794111--48794265 Score: 208
Period size: 51 Copynumber: 3.0 Consensus size: 52
48794101 AAGATGGTTA
* *
48794111 TGGTCACATGTGTAGTACTAAGTGCAGGTTAATATGTGTACCGGATAGCT-T
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
* * * *
48794162 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTAT
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
* * *
48794213 TGGTCACATGTGTGGTACTAAGTGTAGGCTACTATGTGTACCAGATAGC-AT
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
48794264 TG
1 TG
48794266 ATCATAAGGG
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.02
51 86 0.97
52 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (52 bp):
TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
Found at i:48799208 original size:21 final size:21
Alignment explanation
Indices: 48799184--48799227 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48799174 GAATCTTTAG
*
48799184 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
48799205 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
48799226 TA
1 TA
48799228 ATTAGTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:48803813 original size:6 final size:6
Alignment explanation
Indices: 48803804--48803828 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48803794 TTATTTTTAT
48803804 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
48803829 AAAATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:48803880 original size:17 final size:17
Alignment explanation
Indices: 48803860--48803898 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
48803850 ATTTTTAAAA
**
48803860 ATATTTGAGTATTTTAT
1 ATATTTGAACATTTTAT
*
48803877 ATATTTTAACATTTTAT
1 ATATTTGAACATTTTAT
48803894 ATATT
1 ATATT
48803899 ATTTCTTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (17 bp):
ATATTTGAACATTTTAT
Found at i:48803958 original size:12 final size:13
Alignment explanation
Indices: 48803943--48803989 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
48803933 AATTTTTTAA
48803943 ATTTAT-TATTAT
1 ATTTATGTATTAT
48803955 ATTTAT-TATTAT
1 ATTTATGTATTAT
*
48803967 ATTT-TGTATAAT
1 ATTTATGTATTAT
48803979 ATTTATGTATT
1 ATTTATGTATT
48803990 TGCATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 1 0.03
12 25 0.81
13 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATTTATGTATTAT
Found at i:48805054 original size:15 final size:15
Alignment explanation
Indices: 48805031--48805060 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48805021 GTAAGGATGT
48805031 GAACACACCATGTGC
1 GAACACACCATGTGC
*
48805046 GAACCCACCATGTGC
1 GAACACACCATGTGC
48805061 CAGCCCCTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.37, G:0.20, T:0.13
Consensus pattern (15 bp):
GAACACACCATGTGC
Found at i:48807740 original size:6 final size:6
Alignment explanation
Indices: 48807729--48807773 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
48807719 AGGTTTCCAA
* * * *
48807729 AAATGG AAATGG AAATGG AAATGA AAATGA AAATGA AAATTG AAA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAA
48807774 CTTACAATCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.22, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:48807746 original size:12 final size:12
Alignment explanation
Indices: 48807728--48807773 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
48807718 TAGGTTTCCA
48807728 AAAATGGAAATG
1 AAAATGGAAATG
*
48807740 GAAATGGAAATG
1 AAAATGGAAATG
*
48807752 AAAATGAAAATG
1 AAAATGGAAATG
*
48807764 AAAATTGAAA
1 AAAATGGAAA
48807774 CTTACAATCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:48807961 original size:27 final size:27
Alignment explanation
Indices: 48807914--48807978 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
48807904 GTGAAATTTC
* **
48807914 TCAAAATTTTA-CTGGGAGTAAAATTG
1 TCAAAATTTTATCAGGGAGTAAAATCA
48807940 TCAAAATTTTATCAAGGG-GTAAAATCA
1 TCAAAATTTTATC-AGGGAGTAAAATCA
48807967 TCAAAATTTTAT
1 TCAAAATTTTAT
48807979 TCGAGCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.32
27 20 0.59
28 3 0.09
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (27 bp):
TCAAAATTTTATCAGGGAGTAAAATCA
Found at i:48810194 original size:23 final size:23
Alignment explanation
Indices: 48810168--48810247 Score: 151
Period size: 23 Copynumber: 3.5 Consensus size: 23
48810158 AACGTCAAGT
48810168 GAATTAATTCACAAACGAATTCA
1 GAATTAATTCACAAACGAATTCA
*
48810191 GAATTAATTCATAAACGAATTCA
1 GAATTAATTCACAAACGAATTCA
48810214 GAATTAATTCACAAACGAATTCA
1 GAATTAATTCACAAACGAATTCA
48810237 GAATTAATTCA
1 GAATTAATTCA
48810248 TCTTGGGTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (23 bp):
GAATTAATTCACAAACGAATTCA
Found at i:48810201 original size:11 final size:11
Alignment explanation
Indices: 48810185--48810247 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
48810175 TTCACAAACG
48810185 AATTCAGAATT
1 AATTCAGAATT
* **
48810196 AATTCATAAACG
1 AATTCA-GAATT
48810208 AATTCAGAATT
1 AATTCAGAATT
* **
48810219 AATTCACAAACG
1 AATTCA-GAATT
48810231 AATTCAGAATT
1 AATTCAGAATT
48810242 AATTCA
1 AATTCA
48810248 TCTTGGGTCC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
11 22 0.58
12 16 0.42
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (11 bp):
AATTCAGAATT
Found at i:48813691 original size:27 final size:27
Alignment explanation
Indices: 48813661--48814094 Score: 395
Period size: 27 Copynumber: 16.1 Consensus size: 27
48813651 TAACAGTCAA
*
48813661 TTTACCCTAT-AAGGGTATTTTAGTAAT
1 TTTACCC-ATCAAGGGTATTTTGGTAAT
* * * *
48813688 TTTACCCATCAGGGGTATTTCGATTAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* * *** *
48813715 TTTACTCTTTGGGGGTATCTTGGTAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* * *
48813742 TTTACCCATCAAAGGTATTTCGGTAAA
1 TTTACCCATCAAGGGTATTTTGGTAAT
* *
48813769 TTTACCCATCAAGGGTATTTCGATAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* *
48813796 TTTACCCGTTAAGGGTATTTTGGTAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* * * * *
48813823 TTAACCCATCGAGGGTATTTCGATAGT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* *
48813850 TTTATCCATCGAA-GGTATTTCGGTAAT
1 TTTACCCATC-AAGGGTATTTTGGTAAT
* ** * * *
48813877 TATACCCATTGAGGATATTTCGATAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
*
48813904 TTTACCCATCGAGGGTATTTTGGTAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* *
48813931 TTTACCCATCGAGGGTATTTTGATAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
*
48813958 TTTACCCATCTAGGGTATTTTGGTAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* * *
48813985 TTTACCCATCGAGAGTATTTTGGTAGT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* * * *
48814012 ATTACCCATCGAGGGTATTTCGATAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* * * *
48814039 TTTACTCGTCGAGGGTATTTTGATAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
* * *
48814066 TTTACCCATCGAGGGTATTTCGATAAT
1 TTTACCCATCAAGGGTATTTTGGTAAT
48814093 TT
1 TT
48814095 AGGCCCATTA
Statistics
Matches: 334, Mismatches: 70, Indels: 6
0.81 0.17 0.01
Matches are distributed among these distances:
26 3 0.01
27 330 0.99
28 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (27 bp):
TTTACCCATCAAGGGTATTTTGGTAAT
Found at i:48813743 original size:54 final size:54
Alignment explanation
Indices: 48813672--48814094 Score: 481
Period size: 54 Copynumber: 7.8 Consensus size: 54
48813662 TTACCCTATA
* * * * *
48813672 AGGGTATTTT-AGTAATTTTACCCATC-AGGGGTATTTCGATTATTTTACTCTTTG
1 AGGGTATTTTGA-TAATTTTACCCATCGA-GGGTATTTCGGTAATTTTACCCATCG
* * * * * * *
48813726 GGGGTATCTTGGTAATTTTACCCATCAAAGGTATTTCGGTAAATTTACCCATCA
1 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATCG
* * ** * *
48813780 AGGGTATTTCGATAATTTTACCCGTTAAGGGTATTTTGGTAATTTAACCCATCG
1 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATCG
* * * * * *
48813834 AGGGTATTTCGATAGTTTTATCCATCGAAGGTATTTCGGTAATTATACCCATTG
1 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATCG
* * *
48813888 AGGATATTTCGATAATTTTACCCATCGAGGGTATTTTGGTAATTTTACCCATCG
1 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATCG
* *
48813942 AGGGTATTTTGATAATTTTACCCATCTAGGGTATTTTGGTAATTTTACCCATCG
1 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATCG
* * * * * * *
48813996 AGAGTATTTTGGTAGTATTACCCATCGAGGGTATTTCGATAATTTTACTCGTCG
1 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATCG
*
48814050 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGATAATTT
1 AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTT
48814095 AGGCCCATTA
Statistics
Matches: 312, Mismatches: 55, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
54 311 1.00
55 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (54 bp):
AGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATCG
Found at i:48813798 original size:81 final size:81
Alignment explanation
Indices: 48813672--48814094 Score: 499
Period size: 81 Copynumber: 5.2 Consensus size: 81
48813662 TTACCCTATA
** * * * * * *
48813672 AGGGTATTTTAGTAATTTTACCCATCAGGGGTATTTCGATTATTTTACTCTTTGGGGGTATCTTG
1 AGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCGTTGAGGGTATTTTG
*
48813737 GTAATTTTACCCATCA
66 GTAATTTTACCCATCG
* * *
48813753 AAGGTATTTCGGTAAATTTACCCATCAAGGGTATTTCGATAATTTTACCCGTTAAGGGTATTTTG
1 AGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCGTTGAGGGTATTTTG
*
48813818 GTAATTTAACCCATCG
66 GTAATTTTACCCATCG
* * * * * * * *
48813834 AGGGTATTTCGATAGTTTTATCCATCGAA-GGTATTTCGGTAATTATACCCATTGAGGATATTTC
1 AGGGTATTTCGGTAATTTTACCCATC-AAGGGTATTTCGATAATTTTACCCGTTGAGGGTATTTT
*
48813898 GATAATTTTACCCATCG
65 GGTAATTTTACCCATCG
* * * *
48813915 AGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTTGATAATTTTACCCATCT-AGGGTATTTT
1 AGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCGT-TGAGGGTATTTT
48813979 GGTAATTTTACCCATCG
65 GGTAATTTTACCCATCG
* * * * * * *
48813996 AGAGTATTTTGGTAGTATTACCCATCGAGGGTATTTCGATAATTTTACTCGTCGAGGGTATTTTG
1 AGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCGTTGAGGGTATTTTG
*
48814061 ATAATTTTACCCATCG
66 GTAATTTTACCCATCG
*
48814077 AGGGTATTTCGATAATTT
1 AGGGTATTTCGGTAATTT
48814095 AGGCCCATTA
Statistics
Matches: 288, Mismatches: 50, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
80 1 0.00
81 284 0.99
82 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (81 bp):
AGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCCGTTGAGGGTATTTTG
GTAATTTTACCCATCG
Found at i:48815307 original size:22 final size:22
Alignment explanation
Indices: 48815252--48815307 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
48815242 CCTCTGACCT
*
48815252 CCTTACCACACCTGTGACGCCA
1 CCTTGCCACACCTGTGACGCCA
*
48815274 CCTTATTGCCACACCTGTGTCGCCA
1 CC---TTGCCACACCTGTGACGCCA
48815299 CCTTGCCAC
1 CCTTGCCAC
48815308 TACACCACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 9 0.31
25 20 0.69
ACGTcount: A:0.18, C:0.45, G:0.14, T:0.23
Consensus pattern (22 bp):
CCTTGCCACACCTGTGACGCCA
Found at i:48817892 original size:27 final size:27
Alignment explanation
Indices: 48817851--48818352 Score: 589
Period size: 27 Copynumber: 18.7 Consensus size: 27
48817841 GGTAATTTTA
**
48817851 AGGGTATTTTAGTAATTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
*
48817878 GGGGTATTTCGGTAATTTTACCCATC-
1 AGGGTATTTCGGTAATTTTACCCATCG
* ** **
48817904 ATGGGTATTTTGAAAATTTTACCTTTCG
1 A-GGGTATTTCGGTAATTTTACCCATCG
* *
48817932 GGGGTATTTCGGTAATTTTACCCACCG
1 AGGGTATTTCGGTAATTTTACCCATCG
***
48817959 AGGGTATTTTAATAATTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
* ***
48817986 AAGGTATTTTAATAATTTTACCCATC-
1 AGGGTATTTCGGTAATTTTACCCATCG
48818012 AGGGGTATTTCGGTAATTTTACCCATCG
1 A-GGGTATTTCGGTAATTTTACCCATCG
*
48818040 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
* * *
48818067 AGGGTATTTCGATAGTTTTA-CCATTG
1 AGGGTATTTCGGTAATTTTACCCATCG
* *
48818093 AGGTTATTTTGGTAATTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
* * * *
48818120 AGAGTATTTCGGTAGTTTTACTCATCT
1 AGGGTATTTCGGTAATTTTACCCATCG
* **
48818147 AGGTTATTTTAGTAATTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
* *
48818174 AGGGTATTTTGGTAGTTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
* *
48818201 AGGGTATTTCGATAGTTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
* *
48818228 AGGGTATTTCGATAGTTTTA-CCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
*
48818254 AGGGTATTTCAGTAATTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
*
48818281 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGGTAATTTTACCCATCG
* *
48818308 AGGGTATTTCGATAATTTTACCCATTG
1 AGGGTATTTCGGTAATTTTACCCATCG
*
48818335 AGTGTATTTCGGTAATTT
1 AGGGTATTTCGGTAATTT
48818353 AGGCCCATTA
Statistics
Matches: 409, Mismatches: 60, Indels: 12
0.85 0.12 0.02
Matches are distributed among these distances:
26 45 0.11
27 363 0.89
28 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACCCATCG
Found at i:48819538 original size:25 final size:25
Alignment explanation
Indices: 48819504--48819554 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
48819494 ACCTCTAACG
48819504 TCCTTACCACACCTGTGACGCCACC
1 TCCTTACCACACCTGTGACGCCACC
* *
48819529 TCCTTGCCACACCTGTGTCGCCACC
1 TCCTTACCACACCTGTGACGCCACC
48819554 T
1 T
48819555 TGCCACTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.47, G:0.14, T:0.24
Consensus pattern (25 bp):
TCCTTACCACACCTGTGACGCCACC
Found at i:48819558 original size:22 final size:23
Alignment explanation
Indices: 48819505--48819560 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
48819495 CCTCTAACGT
*
48819505 CCTTACCACACCTGTGACGCCACC
1 CCTTGCCACACCTGTGACGCCA-C
*
48819529 TCCTTGCCACACCTGTGTCGCCA-
1 -CCTTGCCACACCTGTGACGCCAC
48819552 CCTTGCCAC
1 CCTTGCCAC
48819561 TACACCACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
25 20 0.69
ACGTcount: A:0.16, C:0.48, G:0.14, T:0.21
Consensus pattern (23 bp):
CCTTGCCACACCTGTGACGCCAC
Found at i:48821867 original size:40 final size:40
Alignment explanation
Indices: 48821685--48821867 Score: 207
Period size: 39 Copynumber: 4.7 Consensus size: 40
48821675 GCTACTCATT
* *
48821685 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
48821725 CAATTGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
48821764 CAAATGCCTTCGGG-CTTAG-CCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
48821802 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
48821843 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
48821868 CATCATTCAA
Statistics
Matches: 121, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
37 2 0.02
38 27 0.22
39 43 0.36
40 37 0.31
41 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:48837624 original size:32 final size:32
Alignment explanation
Indices: 48837580--48837644 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
48837570 GAACGGATCA
*
48837580 AAAGCATTACACTATCACAAGGTATATGTGGC
1 AAAGCATCACACTATCACAAGGTATATGTGGC
48837612 AAAGCATCACACTATCACAAGGTATATGTGGC
1 AAAGCATCACACTATCACAAGGTATATGTGGC
48837644 A
1 A
48837645 TGTATATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (32 bp):
AAAGCATCACACTATCACAAGGTATATGTGGC
Found at i:48838141 original size:12 final size:12
Alignment explanation
Indices: 48838126--48838152 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
48838116 TGCTAGGTCG
48838126 TGTGCTAGGCTA
1 TGTGCTAGGCTA
48838138 TGTGCTAGGCTA
1 TGTGCTAGGCTA
48838150 TGT
1 TGT
48838153 AACTGCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.37
Consensus pattern (12 bp):
TGTGCTAGGCTA
Found at i:48847843 original size:13 final size:13
Alignment explanation
Indices: 48847825--48847850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48847815 GGTCTTAAGT
48847825 GTTGAGTTGAATC
1 GTTGAGTTGAATC
48847838 GTTGAGTTGAATC
1 GTTGAGTTGAATC
48847851 CATTATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
GTTGAGTTGAATC
Found at i:48855646 original size:26 final size:26
Alignment explanation
Indices: 48855617--48855666 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
48855607 TACCAATATT
* * *
48855617 AGTATTGCAGCAAAGCTGCTAGTAAC
1 AGTATCGCAACAAAGCTGCCAGTAAC
*
48855643 AGTATCGTAACAAAGCTGCCAGTA
1 AGTATCGCAACAAAGCTGCCAGTA
48855667 CAATATACTT
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:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
AGTATCGCAACAAAGCTGCCAGTAAC
Found at i:48864339 original size:8 final size:8
Alignment explanation
Indices: 48864320--48864349 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
48864310 TTTATTGATC
48864320 TCAATATCA
1 TCAAT-TCA
48864329 TCAATTCA
1 TCAATTCA
48864337 TCAATTCA
1 TCAATTCA
48864345 TCAAT
1 TCAAT
48864350 CAAGACAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (8 bp):
TCAATTCA
Found at i:48877428 original size:26 final size:26
Alignment explanation
Indices: 48877399--48877456 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
48877389 ATTATAGGCC
* * *
48877399 TTTTATATATTT-TTAATTGTATATAT
1 TTTTATAAATTTATAAATT-TATAAAT
48877425 TTTTATAAATTTATAAATTTATAAAT
1 TTTTATAAATTTATAAATTTATAAAT
48877451 TTTTAT
1 TTTTAT
48877457 TTTATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTATAAATTTATAAATTTATAAAT
Found at i:48877437 original size:8 final size:8
Alignment explanation
Indices: 48877426--48877452 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
48877416 TGTATATATT
48877426 TTTATAAA
1 TTTATAAA
48877434 TTTATAAA
1 TTTATAAA
48877442 TTTATAAA
1 TTTATAAA
48877450 TTT
1 TTT
48877453 TTATTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTATAAA
Found at i:48877439 original size:16 final size:16
Alignment explanation
Indices: 48877420--48877464 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
48877410 TTTAATTGTA
48877420 TATATTTTTATAAATT
1 TATATTTTTATAAATT
**
48877436 TATAAATTTATAAATT
1 TATATTTTTATAAATT
*
48877452 TTTATTTTATATA
1 TATATTTT-TATA
48877465 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTTTTATAAATT
Found at i:48879919 original size:15 final size:15
Alignment explanation
Indices: 48879899--48879928 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48879889 TTTATTACTC
*
48879899 TTTTGAATTATTTAA
1 TTTTGAATGATTTAA
48879914 TTTTGAATGATTTAA
1 TTTTGAATGATTTAA
48879929 AAAATATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
TTTTGAATGATTTAA
Found at i:48881140 original size:45 final size:44
Alignment explanation
Indices: 48881072--48881159 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
48881062 ATGTTTTTAA
* *
48881072 TTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTAG
1 TTTCCCACTTAAACTCTAATTAGTGTAAGTTATTTTAATATTAG
48881116 TTTCCCACTTAAAACTCTAATTAGTGTAAGTTATTTTAATATTA
1 TTTCCCACTT-AAACTCTAATTAGTGTAAGTTATTTTAATATTA
48881160 TTTGACCTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 10 0.24
45 31 0.76
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (44 bp):
TTTCCCACTTAAACTCTAATTAGTGTAAGTTATTTTAATATTAG
Found at i:48882911 original size:10 final size:10
Alignment explanation
Indices: 48882880--48882913 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
48882870 TGAGAATTCT
*
48882880 CCTAAGTCAT
1 CCTAAGTCAG
48882890 CCTAAGTCAG
1 CCTAAGTCAG
*
48882900 CCTAAGTTAG
1 CCTAAGTCAG
48882910 CCTA
1 CCTA
48882914 GCTCTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (10 bp):
CCTAAGTCAG
Found at i:48888321 original size:3 final size:3
Alignment explanation
Indices: 48888306--48888455 Score: 192
Period size: 3 Copynumber: 50.0 Consensus size: 3
48888296 TTTAAGATTT
* * **
48888306 TTA TTA TTG TTA TTA TTA TTA TTA TTA ATA CCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** *
48888354 TTA TTA TTA TTA TTG TTA TTA TTG TTA TTA TTA TTA ATA CCA TTA TTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
48888402 TTA TTA TTA TTA TTA TTA CCA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48888450 TTA TTA
1 TTA TTA
48888456 AATTGTTTTA
Statistics
Matches: 125, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 125 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:48891934 original size:18 final size:18
Alignment explanation
Indices: 48891907--48891945 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
48891897 GTATCACCCA
* *
48891907 CCTTCACCTCACATGTAT
1 CCTTCACCTCAAATATAT
*
48891925 CCTTCTCCTCAAATATAT
1 CCTTCACCTCAAATATAT
48891943 CCT
1 CCT
48891946 CCATATCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.03, T:0.36
Consensus pattern (18 bp):
CCTTCACCTCAAATATAT
Found at i:48892325 original size:48 final size:48
Alignment explanation
Indices: 48892266--48892369 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
48892256 TAAATTATAT
*
48892266 ATGAAAGTAGAATGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTA
1 ATGAAAATAGAATGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTA
48892314 ATGAAAATAGAATGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTA
1 ATGAAAATAGAATGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTA
48892362 ATGAAAAT
1 ATGAAAAT
48892370 CTATACATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (48 bp):
ATGAAAATAGAATGAGTGAGAATAAGTGGTAGGAAATAGGAATAATTA
Found at i:48895068 original size:2 final size:2
Alignment explanation
Indices: 48895063--48895107 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
48895053 TTTTTTACAT
48895063 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
48895105 AG A
1 AG A
48895108 TGGGGCGTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48899320 original size:282 final size:282
Alignment explanation
Indices: 48898816--48900166 Score: 1711
Period size: 282 Copynumber: 4.9 Consensus size: 282
48898806 ATGAAGGCGA
** * *
48898816 AGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGAAATTTATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* * * *
48898881 CAACTTCATGAAGGAGTCGACATTGAGGAAGTAACTGTTCTGAGTATGATCGAGAAACCGCCAGA
66 CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* *
48898946 TCATGGAGGTAACAAATCAAAATTACCTGTT-TTCGAGGCAAGGTCTCTGGAGGATATACATAAA
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCTGGAGGATATACATAAA
* *
48899010 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAAGAATGA
195 GCTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGA
*
48899075 ATCATCAAAAGATACGAAAACTG
260 ATCATCAAAAGATACGAAGACTG
* *
48899098 AGACTAATGTGGTGCTGCCTA-TTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGACTTTTAA
1 AGACTAATGTGGTGCTGCC-AGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAA
* * * * *
48899162 GCAACTTCATGAAGGAGTCGACGTTGAGGAAGTCATTGTTCCAAGTATGATCGAGAAACTGACAG
65 GCAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAG
* * *
48899227 ATCATGGAGATATCAAATCAAAATTACCTATTGTTGAGGCAAGGTCTCTGGAGGATATACATAAA
130 ATCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAA
* * *
48899292 GCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCGCATTCTTCAGGCTTAAGGAATGA
195 GCTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGA
* *
48899357 ATCATCAACAGATACGAATACTG
260 ATCATCAAAAGATACGAAGACTG
* * *
48899380 AGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
48899445 CAACTTCATGAAGGAGT---C-----------AA-TGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * * * *
48899495 TCTTGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATTTAGACAAAT
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAAG
* * * * *
48899560 CTATTCAACAACTTGCGAAACCTAAT-C--C--A---G-CATATTCTTCAGGCTCAAGGAATGAA
196 CTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* *
48899616 TCATCAAAAGATGCGAAGACCG
261 TCATCAAAAGATACGAAGACTG
*
48899638 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
*
48899703 CAACTTCATGAAGGAGTGGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
66 CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
* * ** * * *
48899768 CCATGGAGATAACAAATCAAAATTACGTGTTGTCAAGGCAAGATCTCTGGAGGACATAGACAAAG
131 TCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAAG
* * * * **
48899833 CTATCCAACAACTTCCGAAATCTAATCCAGCTGAGCTGCCACATTCTTCAGTTTCAAGGAATGAA
196 CTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
* *
48899898 CCATCAAAAGATATGAAGACTG
261 TCATCAAAAGATACGAAGACTG
48899920 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
1 AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
* ** * * *
48899985 CAACTGCATGAAGGAG-CTGATGTTGAGGAAGTAATTGTTCCAAGTATGATTGTGGAAC--CACA
66 CAACTTCATGAAGGAGTC-GACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGC-CA
* *** * *
48900047 GGATGACACAGATAACAAATCAAAATTACCTGTTGTGGAGGCAAGATCTCTGAAGGA-ATTACAT
129 -GATCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATA-TACAT
* * ** * * *
48900111 AATGCTGTCCAACAA-GGCCTGGAATCTGATCCAGCTAAGCTGCCACATTCTTCAGG
192 AAAGCTGTTCAACAACTTCC-GGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGG
48900167 TGTAAACAAT
Statistics
Matches: 938, Mismatches: 99, Indels: 64
0.85 0.09 0.06
Matches are distributed among these distances:
258 119 0.13
259 1 0.00
261 1 0.00
262 1 0.00
264 1 0.00
266 1 0.00
267 105 0.11
268 1 0.00
272 2 0.00
273 110 0.12
274 1 0.00
276 1 0.00
278 1 0.00
279 1 0.00
280 1 0.00
281 7 0.01
282 581 0.62
283 3 0.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (282 bp):
AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATTGATTTGGCTTTTAAG
CAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGA
TCATGGAGATAACAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGGAGGATATACATAAAG
CTGTTCAACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTCAGGCTCAAGGAATGAA
TCATCAAAAGATACGAAGACTG
Found at i:48899961 original size:540 final size:548
Alignment explanation
Indices: 48898801--48900000 Score: 1623
Period size: 540 Copynumber: 2.2 Consensus size: 548
48898791 TTGTTACAGG
* ** *
48898801 AAGATATGAAGGC-GAAGACTAATGCAGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGAAAT
1 AAGATATGAAGACTG-AGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATAT
* *
48898865 TTATTTGGCTTTTAAGCAACTTCATGAAGGAGTCGACATTGAGGAAGTAACTGTTCTGAGTATGA
65 TGATTTGGCTTTTAAGCAACTTCATGAAGGAGT--AC--------A--AACTGTTCCGAGTATGA
* *
48898930 TCGAGAAACCGCCAGATCATGGAGGTAACAAATCAAAATTACCTGTTTTCGAGGCAAGGTCTCTG
118 TCGAGAAACCGCCAGATCATGGAGATAACAAATCAAAATTACCTGTTTTCGAGGCAAGATCTCTG
* * * * *
48898995 GAGGATATACATAAAGCTGTTCGACAACTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTTC
183 GAGGATATACACAAAGCTATTCAACAACTTCCGAAACCTAATCCA-C-GA--CGCCACATTCTTC
*
48899060 AGGCTCAAAGAATGAATCATCAAAAGATACGAAAACTGAGACTAATGTGGTGCTGCCTATTCTTG
244 AGGCTCAAAGAATGAATCATCAAAAGATACGAAAACCGAGACTAATGTGGTGCTGCCTATTCTTG
*
48899125 AAGCAAGATCAGCCGAAGATATTGATTTGACTTTTAAGCAACTTCATGAAGGAGTCGACGTTGAG
309 AAGCAAGATCAGCCGAAGATATTGATTTGACTTTTAAGCAACTTCATGAAGGAGTCGACATTGAG
* * *
48899190 GAAGTCATTGTTCCAAGTATGATCGAGAAACTGACAGATCATGGAGATATCAAATCAAAATTACC
374 GAAGTAATTGTTCCAAGTATGATCGAGAAACTGACAGACCATGGAGATAACAAATCAAAATTACC
** * * * * * * *
48899255 TATTGTTGAGGCAAGGTCTCTGGAGGATATACATAAAGCTGTTCGACAACTTCCGGAATCTAATC
439 TATTGTCAAGGCAAGATCTCTGGAGGACATACACAAAGCTATCCAACAACTTCCGAAATCTAATC
* *
48899320 CAGCTGAGCCGCCGCATTCTTCAGGCTTAAGGAATGAATCATCAA
504 CAGCTGAGCCGCCACATTCTTCAGGCTTAAGGAATGAACCATCAA
* * * * * *
48899365 CAGATACGAATACTGAGACTAATGTGGTGCTTCCAGTTCTTGAAACAAGGTCAGCAGAAGATATT
1 AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
* *
48899430 GATTTGGCTTTTAAGCAACTTCATGAAGGAGT-C-AA-TGTTCCGAGTATGATTGAGAAACTGCC
66 GATTTGGCTTTTAAGCAACTTCATGAAGGAGTACAAACTGTTCCGAGTATGATCGAGAAACCGCC
* * *
48899492 AGATCTTGGAGATAACAAATCAAAATTACCTGTTGTT-GAGGCAAGATCTCTGGAGGATTTAGAC
131 AGATCATGGAGATAACAAATCAAAATTACCTGTT-TTCGAGGCAAGATCTCTGGAGGATATACAC
* * * *
48899556 AAATCTATTCAACAACTTGCGAAACCTAAT-C-C-A-G-CATATTCTTCAGGCTCAAGGAATGAA
195 AAAGCTATTCAACAACTTCCGAAACCTAATCCACGACGCCACATTCTTCAGGCTCAAAGAATGAA
* *
48899616 TCATCAAAAGATGCGAAGACCGAGACTAATGTGGTGCTGCC-AGTTCTTGAAGCAAGATCAGCCG
260 TCATCAAAAGATACGAAAACCGAGACTAATGTGGTGCTGCCTA-TTCTTGAAGCAAGATCAGCCG
* * *
48899680 AAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTGGACATTGAGGAAGTAATTGTTCCG
324 AAGATATTGATTTGACTTTTAAGCAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCA
* * * *
48899745 AGTATGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACGTGTTGTCAAGGCAAG
389 AGTATGATCGAGAAACTGACAGACCATGGAGATAACAAATCAAAATTACCTATTGTCAAGGCAAG
* *
48899810 ATCTCTGGAGGACATAGACAAAGCTATCCAACAACTTCCGAAATCTAATCCAGCTGAGCTGCCAC
454 ATCTCTGGAGGACATACACAAAGCTATCCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCAC
*
48899875 ATTCTTCA-GTTTCAAGGAATGAACCATCAA
519 ATTCTTCAGGCTT-AAGGAATGAACCATCAA
48899905 AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
1 AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
*
48899970 GATTTGGCTTTTAAGCAACTGCATGAAGGAG
66 GATTTGGCTTTTAAGCAACTTCATGAAGGAG
48900001 CTGATGTTGA
Statistics
Matches: 569, Mismatches: 63, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
539 4 0.01
540 368 0.65
541 1 0.00
544 1 0.00
546 1 0.00
548 1 0.00
549 103 0.18
550 4 0.01
561 1 0.00
564 84 0.15
565 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (548 bp):
AAGATATGAAGACTGAGACTAATGTGGTGCTGCCAGTTCTTGAAGCAAGATCAGCAGAAGATATT
GATTTGGCTTTTAAGCAACTTCATGAAGGAGTACAAACTGTTCCGAGTATGATCGAGAAACCGCC
AGATCATGGAGATAACAAATCAAAATTACCTGTTTTCGAGGCAAGATCTCTGGAGGATATACACA
AAGCTATTCAACAACTTCCGAAACCTAATCCACGACGCCACATTCTTCAGGCTCAAAGAATGAAT
CATCAAAAGATACGAAAACCGAGACTAATGTGGTGCTGCCTATTCTTGAAGCAAGATCAGCCGAA
GATATTGATTTGACTTTTAAGCAACTTCATGAAGGAGTCGACATTGAGGAAGTAATTGTTCCAAG
TATGATCGAGAAACTGACAGACCATGGAGATAACAAATCAAAATTACCTATTGTCAAGGCAAGAT
CTCTGGAGGACATACACAAAGCTATCCAACAACTTCCGAAATCTAATCCAGCTGAGCCGCCACAT
TCTTCAGGCTTAAGGAATGAACCATCAA
Found at i:48902673 original size:5 final size:5
Alignment explanation
Indices: 48902663--48902703 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
48902653 AATTTTAAAA
* *
48902663 TATTT TATTT TATTT TATTT TA--T TATTT CAGTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
48902704 AATATTTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
3 3 0.10
5 27 0.90
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:48902690 original size:18 final size:18
Alignment explanation
Indices: 48902676--48902716 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
48902666 TTTATTTTAT
48902676 TTTATTTTATTATTTCAG
1 TTTATTTTATTATTTCAG
48902694 TTTATTTTATAATATTT-AG
1 TTTATTTTAT--TATTTCAG
48902713 TTTA
1 TTTA
48902717 AAGTATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTATTTTATTATTTCAG
Found at i:48906961 original size:31 final size:31
Alignment explanation
Indices: 48906926--48906991 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
48906916 AACAAACTAG
*
48906926 TGACTTAAATAAAAAATTTTGAATAGCTCAA
1 TGACTTAAATAAAAAATTTCGAATAGCTCAA
* * * *
48906957 TGACTTAAATGAAAACTTTCGAATAGTTCAG
1 TGACTTAAATAAAAAATTTCGAATAGCTCAA
48906988 TGAC
1 TGAC
48906992 CAAAACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTCGAATAGCTCAA
Found at i:48908830 original size:25 final size:25
Alignment explanation
Indices: 48908792--48908841 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
48908782 TTGAGTTAAT
48908792 AAAATTCTCTTTAAGTTTTCTTTTA
1 AAAATTCTCTTTAAGTTTTCTTTTA
48908817 AAAATT-TCTCTTAAGTTTTCTTTTA
1 AAAATTCTCT-TTAAGTTTTCTTTTA
48908842 GAAGAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (25 bp):
AAAATTCTCTTTAAGTTTTCTTTTA
Found at i:48910232 original size:59 final size:58
Alignment explanation
Indices: 48910142--48910264 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 58
48910132 TAGAAATGGT
* * *
48910142 AAAATCGAGAAATAGGAAACATTTGAGAATGATTACGGTTTTCTCCAAAATGAAAAATGA
1 AAAATCGAGAAATA-GAAACATTTGAAAATGAATACGATTTTCTCCAAAAT-AAAAATGA
* **
48910202 AAAATGGAGAAAT-GAAATCATTTGAAAATGAATGTGATTTTCTCCAAAATAAAAATGA
1 AAAATCGAGAAATAGAAA-CATTTGAAAATGAATACGATTTTCTCCAAAATAAAAATGA
48910260 AAAAT
1 AAAAT
48910265 AAAATTTCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 17 0.30
59 27 0.48
60 12 0.21
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (58 bp):
AAAATCGAGAAATAGAAACATTTGAAAATGAATACGATTTTCTCCAAAATAAAAATGA
Found at i:48913277 original size:58 final size:60
Alignment explanation
Indices: 48913150--48913262 Score: 144
Period size: 58 Copynumber: 1.9 Consensus size: 60
48913140 AATATTAAAT
* * *
48913150 AATTTAAATTTAATATTTATCTTATAGATAAATATTTTATTAATTTAATAGATTTAATAATA
1 AATTT-AATATAATATTTATCTTATAGATAAATATTATATTAATTTAATA-ATTAAATAATA
*
48913212 AATTTAATATAATATTTATC-T-T-GATAAGTATTATATTAATTTAAT-ATTAAA
1 AATTTAATATAATATTTATCTTATAGATAAATATTATATTAATTTAATAATTAAA
48913263 GTGATTAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
56 5 0.11
58 21 0.45
59 1 0.02
60 1 0.02
61 14 0.30
62 5 0.11
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (60 bp):
AATTTAATATAATATTTATCTTATAGATAAATATTATATTAATTTAATAATTAAATAATA
Found at i:48916675 original size:12 final size:12
Alignment explanation
Indices: 48916658--48916682 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48916648 ACCGAGCCAT
48916658 AAATATTTTTAG
1 AAATATTTTTAG
48916670 AAATATTTTTAG
1 AAATATTTTTAG
48916682 A
1 A
48916683 GTGTCATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
AAATATTTTTAG
Found at i:48917830 original size:36 final size:36
Alignment explanation
Indices: 48917789--48917979 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
48917779 GGTAGCTTTA
48917789 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
*
48917825 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGACAAAGTGAT-A-----AG---T
*
48917870 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
* * *
48917907 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
*
48917943 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
48917979 G
1 G
48917980 GTAGCTTAGC
Statistics
Matches: 138, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 100 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
Found at i:48917863 original size:82 final size:82
Alignment explanation
Indices: 48917753--48917979 Score: 321
Period size: 82 Copynumber: 2.9 Consensus size: 82
48917743 TTTGAGTACT
* *
48917753 TCTGTTCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
48917818 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* *
48917835 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
* *
48917900 GATAAGTGTTATACTTA
66 GATAAGTGCTACACTTA
*
48917917 TCTGATCAAGTGAAAAAGTGATAA---GT-GC--TA--T--ACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
48917972 GATAAGTG
66 GATAAGTG
48917980 GTAGCTTAGC
Statistics
Matches: 137, Mismatches: 8, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
72 31 0.23
74 1 0.01
76 2 0.01
78 2 0.01
79 2 0.01
82 99 0.72
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGCTACACTTA
Done.