Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 21 of 185
Found at i:5924674 original size:3 final size:3
Alignment explanation
Indices: 5924668--5924693 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5924658 ATTATTATTA
5924668 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
5924694 AGTATGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:5924942 original size:12 final size:12
Alignment explanation
Indices: 5924925--5924955 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5924915 ATAATTTTAG
5924925 TGTGTATTATTT
1 TGTGTATTATTT
5924937 TGTGTATTATTT
1 TGTGTATTATTT
*
5924949 TGAGTAT
1 TGTGTAT
5924956 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:5931244 original size:19 final size:20
Alignment explanation
Indices: 5931206--5931244 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5931196 TTTAAACACA
5931206 CAAATATTACAAAAAAAATT
1 CAAATATTACAAAAAAAATT
* *
5931226 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAAAAAAATT
5931245 ACCTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
CAAATATTACAAAAAAAATT
Found at i:5931341 original size:44 final size:42
Alignment explanation
Indices: 5931256--5931408 Score: 145
Period size: 44 Copynumber: 3.6 Consensus size: 42
5931246 CCTTTTTTTC
* *
5931256 CCTTTCTTCCCTCTTCTTCTTCTTTTTT-TTCTCTTCTCCTTT
1 CCTTTCTTCCTTCTT-TCCTTCTTTTTTCTTCTCTTCTCCTTT
5931298 CCCTTTCTTTCCTTCTTTCCTTCTTTTTTCTTCTCTTCTCCTTT
1 -CCTTTC-TTCCTTCTTTCCTTCTTTTTTCTTCTCTTCTCCTTT
* * *
5931342 TC-TTCTTCTTTCTTTCCTT-TTTTCTCTTCTCCTT-TCCTTGT
1 CCTTTCTTCCTTCTTTCCTTCTTTTTTCTTCT-CTTCTCCTT-T
*
5931383 -CTTTCTTTCCTCTCCTTTCTTTCTTT
1 CCTTTC-TTCCT-T-CTTTCCTTCTTT
5931409 CCCTCCTTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
40 16 0.17
41 20 0.21
42 7 0.07
43 19 0.20
44 29 0.31
45 3 0.03
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.65
Consensus pattern (42 bp):
CCTTTCTTCCTTCTTTCCTTCTTTTTTCTTCTCTTCTCCTTT
Found at i:5931389 original size:38 final size:37
Alignment explanation
Indices: 5931304--5931406 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 37
5931294 CTTTCCCTTT
* *
5931304 CTTTCC-TTCTTTCCTTCTTT--TTTCTTCTCTTCTC
1 CTTTCCTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTC
*
5931338 CTTTTC-TTC-TTCTTTCTTTCCTTTTTTCTCTTCTC
1 CTTTCCTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTC
*
5931373 CTTTCCTTGTCTTTCTTTCCTCTCCTTTCTTTCT
1 CTTTCCTT-TCTTTCTTT-CTTTCCTTT-TTTCT
5931407 TTCCCTCCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
33 9 0.16
34 8 0.14
35 18 0.32
36 1 0.02
37 2 0.04
38 6 0.11
39 8 0.14
40 5 0.09
ACGTcount: A:0.00, C:0.34, G:0.01, T:0.65
Consensus pattern (37 bp):
CTTTCCTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTC
Found at i:5931389 original size:41 final size:39
Alignment explanation
Indices: 5931267--5931406 Score: 130
Period size: 39 Copynumber: 3.5 Consensus size: 39
5931257 CTTTCTTCCC
*
5931267 TCTTCTTC-TTCTTTTTTTTCTCTTCTCCTTTCCCTTTCTT
1 TCTTCTTCTTTC-CTTTTTTCTCTTCTCCTTT-CCTTTCTT
*
5931307 TC--CTTCTTTCCTTCTTTTTTCTTCT-CTTCTCCTTT-TCT
1 TCTTCTTCTTTCCTT-TTTTCTCTTCTCCTT-TCCTTTCT-T
5931345 TCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTGTCTT
1 TCTTC-TTCTTTCCTTTTTTCTCTTCTCCTTTCCTT-TCTT
* *
5931386 TCTT-TCCTCTCCTTTCTTTCT
1 TCTTCTTCTTTCCTTT-TTTCT
5931407 TTCCCTCCTT
Statistics
Matches: 84, Mismatches: 5, Indels: 22
0.76 0.05 0.20
Matches are distributed among these distances:
37 1 0.01
38 17 0.20
39 23 0.27
40 23 0.27
41 19 0.23
42 1 0.01
ACGTcount: A:0.00, C:0.34, G:0.01, T:0.66
Consensus pattern (39 bp):
TCTTCTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTTCTT
Found at i:5931526 original size:27 final size:27
Alignment explanation
Indices: 5931450--5931516 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
5931440 TAACACCAAC
5931450 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* *
5931477 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
5931504 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
5931517 ACCATTGGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:5931623 original size:27 final size:27
Alignment explanation
Indices: 5931585--5931652 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
5931575 TTTTTTTGAT
5931585 ATATTTTGGTAAATAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAGTTGTA
5931612 ATATTTTGGTAAATAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAGTTGTA
5931639 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
5931653 TTTTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTGTA
Found at i:5934441 original size:21 final size:20
Alignment explanation
Indices: 5934378--5934442 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
5934368 ATTAATCACC
*
5934378 AAACTCTCAAACCCTAAATCGA
1 AAACTCT-AAACCCTAAAT-GT
* *
5934400 AAACACTAAA-CCTATATTGT
1 AAACTCTAAACCCTA-AATGT
5934420 AAACTCTAAACCCTAAACTGT
1 AAACTCTAAACCCTAAA-TGT
5934441 AA
1 AA
5934443 TCCAAAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 15 0.43
21 14 0.40
22 6 0.17
ACGTcount: A:0.46, C:0.26, G:0.05, T:0.23
Consensus pattern (20 bp):
AAACTCTAAACCCTAAATGT
Found at i:5934750 original size:75 final size:75
Alignment explanation
Indices: 5934545--5934752 Score: 249
Period size: 76 Copynumber: 2.7 Consensus size: 75
5934535 ATGCATGGTT
* * * *
5934545 AAGACCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTCCCGCAAGCGCCACTAACTC
1 AAGAACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTCTC-AAAGCGCCACTAACTC
*
5934610 TAGTATACATC
65 TAATATACATC
* * * ** *
5934621 AAGACCAAAACAT-TGCGTTTTGGTTAAGATATTTTGCGGTGTTTTTCTTTAAGCGCCACTAATT
1 AAGAACAAAAC-TCTGCGTTTTGGTTAAGATATTTTGCGGCG-CTTTCTCAAAGCGCCACTAACT
*
5934685 CTAATATACCTC
64 CTAATATACATC
*
5934697 AA-AACAAAACTCTACGTTTTGGTTAAGATATTTTGCGGCGCTTGTCTCAAAGCGCC
1 AAGAACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT-TCTCAAAGCGCC
5934753 GCGATTACTA
Statistics
Matches: 113, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
74 3 0.03
75 43 0.38
76 63 0.56
77 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (75 bp):
AAGAACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTCTCAAAGCGCCACTAACTCT
AATATACATC
Found at i:5935286 original size:113 final size:113
Alignment explanation
Indices: 5934918--5935341 Score: 369
Period size: 113 Copynumber: 3.7 Consensus size: 113
5934908 CCAAACCATG
* * * * * *
5934918 ACGGCGTTTTCCATAAGCGTCACTAATTCTAGTATACATTAAGACCAAAAAGCTACGTTTTGTTT
1 ACGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCG-TTT-TTT
* ** * * *
5934983 TAAGATATTTTGCGGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTG
64 TAAGATATTTTGCGGCGCTTTTCACGAAACGCCGCTAATACATTGCTTTA
* * * * * ** *
5935033 GCAGCGTTTTTCCATAATCGCCACTAATTATAATATA-ACTCAAAACC-AAACTCTGC-ATTTTT
1 ACGGCG-TTTTCCATAAGCGCCACTAATTCTAATATACA-TCAAGACCAAAACGATGCGTTTTTT
* *
5935095 TAAGATATTTTGCGGCGCTTTTCAAGAAGCGCCGCTAATACATT-CTTTA
64 TAAGATATTTTGCGGCGCTTTTCACGAAACGCCGCTAATACATTGCTTTA
* * *
5935144 GCGGCGTGTTTTCTTAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTTCTT
1 ACGGCGT-TTTCCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTT-TT
* * * * *
5935209 TAAGATTTTTTGCAGCGCTTTTCACGGATCG-CTCTAATAC-TTGCTTTA
64 TAAGATATTTTGCGGCGCTTTTCACGAAACGCCGCTAATACATTGCTTTA
* * * * *
5935257 ACGGAGTTTTCCCATAATCGCCACTAATTCTAGTATACATCAACACTAAAAC-ACTGCGTTTTGG
1 ACGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGA-TGCGTTTT--
**
5935321 TTT-AGGGATTTTGCGGCGCTT
62 TTTAAGATATTTTGCGGCGCTT
5935342 GAAGGTAAAC
Statistics
Matches: 250, Mismatches: 48, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
110 1 0.00
111 41 0.16
112 54 0.22
113 80 0.32
114 31 0.12
115 11 0.04
116 32 0.13
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (113 bp):
ACGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTTTTTA
AGATATTTTGCGGCGCTTTTCACGAAACGCCGCTAATACATTGCTTTA
Found at i:5935334 original size:227 final size:227
Alignment explanation
Indices: 5934931--5935341 Score: 488
Period size: 227 Copynumber: 1.8 Consensus size: 227
5934921 GCGTTTTCCA
* * * * *
5934931 TAAGCGTCACTAATTCTAGTATACATTAAGACCAAAAAGCTACGTTTTGTTTTAAGATATTTTGC
1 TAAGCGCCACTAATTCTAATATACATCAAGACCAAAAAGATACGTTTTGCTTTAAGATATTTTGC
* ** * *
5934996 GGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTGGCAGCGTTTTTCCATAATCGCCACTAAT
66 AGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTAACAGAGTTTTCCCATAATCGCCACTAAT
* * *
5935061 TATAATATAACTCAAAACCAAACTCTGCATTTTTTAAGATATTTTGCGGCGCTTTTCAAGAAGCG
131 TATAATATAACTCAAAACAAAACACTGCATTTTTTAAGAGATTTTGCGGCGCTTTTCAAGAAGCG
5935126 CCGCTAATACATTCTTTAGCGGCGTGTTTTCT
196 CCGCTAATACATTCTTTAGCGGCGTGTTTTCT
* * *
5935158 TAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTT-CTTTAAGATTTTTTGC
1 TAAGCGCCACTAATTCTAATATACATCAAGACCAAAAAGATACGTTTTGCTTTAAGATATTTTGC
* ** ** * * *
5935222 AGCGCTTTTCACGGATCG-CTCTAATAC-TTGCTTTAACGGAGTTTTCCCATAATCGCCACTAAT
66 AGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTAACAGAGTTTTCCCATAATCGCCACTAAT
* * * * * *
5935285 TCTAGTAT-ACATCAACACTAAAACACTGCGTTTTGGTTTAGGGATTTTGCGGCGCTT
131 TATAATATAAC-TCAAAAC-AAAACACTGCATTTT--TTAAGAGATTTTGCGGCGCTT
5935342 GAAGGTAAAC
Statistics
Matches: 150, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
223 2 0.01
224 43 0.29
225 20 0.13
226 25 0.17
227 60 0.40
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (227 bp):
TAAGCGCCACTAATTCTAATATACATCAAGACCAAAAAGATACGTTTTGCTTTAAGATATTTTGC
AGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTAACAGAGTTTTCCCATAATCGCCACTAAT
TATAATATAACTCAAAACAAAACACTGCATTTTTTAAGAGATTTTGCGGCGCTTTTCAAGAAGCG
CCGCTAATACATTCTTTAGCGGCGTGTTTTCT
Found at i:5937411 original size:32 final size:32
Alignment explanation
Indices: 5937374--5937436 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
5937364 ATTAATTTTT
5937374 ATGAGTTATCAAAAT-AAATAAATCAATTTATC
1 ATGAGTTATCAAAATCAAAT-AATCAATTTATC
* *
5937406 ATGAGTTATTAAATTCAAATAATCAATTTAT
1 ATGAGTTATCAAAATCAAATAATCAATTTAT
5937437 AAGTTTATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (32 bp):
ATGAGTTATCAAAATCAAATAATCAATTTATC
Found at i:5937470 original size:145 final size:144
Alignment explanation
Indices: 5937205--5937470 Score: 354
Period size: 145 Copynumber: 1.8 Consensus size: 144
5937195 GAGGATTATT
* * * * * *
5937205 AATCTAACAAGTTTAATTAATCAATATGAGTTATCAAATTAATTAATTAATTAATAATGTGTTAT
1 AATCTAACAAGCTCAATTAATCAATATGAGTTATCAAATAAATAAATCAATTAATAATGAGTTAT
*
5937270 TAAACTCAAGTAATCAATTTATAAGCATATGATGTTCCAAATTCATAGTAAAATATATTCTTACA
66 TAAACTCAAATAATCAATTTATAAGCATATGATGTTCCAAATTCATAGTAAAATATATTCTTACA
5937335 CGTGATTGATCATA
131 CGTGATTGATCATA
*** * *
5937349 AATCTAACAAGCTCAATTAATTTTTATGAGTTATCAAAATAAATAAATCAATTTATCATGAGTTA
1 AATCTAACAAGCTCAATTAATCAATATGAGTTATC-AAATAAATAAATCAATTAATAATGAGTTA
* ** * *
5937414 TTAAATTCAAATAATCAATTTATAAGTTTATGATGCTT-GAAATTCATAGTAGAATAT
65 TTAAACTCAAATAATCAATTTATAAGCATATGATG-TTCCAAATTCATAGTAAAATAT
5937471 TTAAGTAGAA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
144 30 0.29
145 71 0.69
146 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (144 bp):
AATCTAACAAGCTCAATTAATCAATATGAGTTATCAAATAAATAAATCAATTAATAATGAGTTAT
TAAACTCAAATAATCAATTTATAAGCATATGATGTTCCAAATTCATAGTAAAATATATTCTTACA
CGTGATTGATCATA
Found at i:5938077 original size:28 final size:28
Alignment explanation
Indices: 5938037--5938100 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
5938027 CTCGACCCCC
*
5938037 TAAAATGAAAATTTTAAATTAGTAAAGG
1 TAAAATTAAAATTTTAAATTAGTAAAGG
5938065 TAAAATTAAAATTTTAAATTAGTAAAGG
1 TAAAATTAAAATTTTAAATTAGTAAAGG
5938093 TAAAATTA
1 TAAAATTA
5938101 TACTTTGCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (28 bp):
TAAAATTAAAATTTTAAATTAGTAAAGG
Found at i:5948907 original size:26 final size:26
Alignment explanation
Indices: 5948852--5948905 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
5948842 GCCTTGCTTG
*
5948852 AAATCGAAAACTTTGATTTCGTAAGT
1 AAATCGAAAACTTTGATATCGTAAGT
5948878 AAATCGAAAACTTTGATATC-TAAGT
1 AAATCGAAAACTTTGATATCGTAAGT
5948903 AAA
1 AAA
5948906 ATAATCAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (26 bp):
AAATCGAAAACTTTGATATCGTAAGT
Found at i:5948951 original size:16 final size:16
Alignment explanation
Indices: 5948930--5948997 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
5948920 TTTGGTTCGC
5948930 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5948946 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
5948962 GGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
5948978 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
5948994 TGTA
1 TGTA
5948998 ATAGCAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5949037 original size:45 final size:41
Alignment explanation
Indices: 5948978--5949087 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
5948968 GGATTAGAGG
*
5948978 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
5949020 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
5949063 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
5949088 TAATGAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:5949250 original size:16 final size:16
Alignment explanation
Indices: 5949213--5949254 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5949203 TTAATCATAT
*
5949213 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5949229 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5949244 TTAAAATATAT
1 TTAAAATATAT
5949255 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:5949261 original size:14 final size:15
Alignment explanation
Indices: 5949222--5949263 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5949212 TTTAAACATA
*
5949222 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5949237 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5949251 A-TATAATTTAATA
1 ATTATAATTAAATA
5949264 AAATTCTTAA
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:5949313 original size:61 final size:61
Alignment explanation
Indices: 5949248--5949435 Score: 208
Period size: 61 Copynumber: 3.1 Consensus size: 61
5949238 TTATAATTAA
5949248 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
5949309 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
5949368 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
5949429 AATATAT
1 AATATAT
5949436 GATACTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 24 0.25
61 37 0.38
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:5949361 original size:120 final size:120
Alignment explanation
Indices: 5949216--5949445 Score: 460
Period size: 120 Copynumber: 1.9 Consensus size: 120
5949206 ATCATATTTA
5949216 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
5949281 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
5949336 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
5949401 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
5949446 TTTACTCAAA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:5949381 original size:14 final size:15
Alignment explanation
Indices: 5949332--5949383 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5949322 ATAAAATATA
5949332 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5949347 TATTAAATATATTAT
1 AATTAAATATATTAT
5949362 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5949375 AATTTAATA
1 AATTAAATA
5949384 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:5949434 original size:59 final size:59
Alignment explanation
Indices: 5949251--5949434 Score: 175
Period size: 59 Copynumber: 3.1 Consensus size: 59
5949241 TAATTAAAAT
5949251 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * *
5949310 ATAT-ATGATACTATAAAA-TATAAATTAA-CATAATTATTATTAAAT-ATATTATAATTAAA--
1 ATATAAT-TTA--ATAAAATTCTTAA-TAATC--AA-TATTCTTATATGA-ATT-TACTCAAATC
5949369 AT-
57 ATA
5949371 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
5949430 ATATA
1 ATATA
5949435 TGATACTATA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
56 6 0.06
57 12 0.13
58 7 0.07
59 20 0.21
60 10 0.11
61 15 0.16
62 7 0.07
63 12 0.13
64 6 0.06
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
Found at i:5953172 original size:137 final size:137
Alignment explanation
Indices: 5952926--5953203 Score: 520
Period size: 137 Copynumber: 2.0 Consensus size: 137
5952916 GAAATGCAAC
*
5952926 CATCAGGGCCATGTAAATTCTTATTTGGAAAGATCTTACATAAGATACCATTTTCACCACAAATT
1 CATCAGGGCCATGTAAATTCTCATTTGGAAAGATCTTACATAAGATACCATTTTCACCACAAATT
* *
5952991 TCTTGTTCTTTTCTTTTTTAAAATAAATAAAGAAGAGAAGAAATGGTTCTTCCCAATATACACAT
66 TCTTATGCTTTTCTTTTTTAAAATAAATAAAGAAGAGAAGAAATGGTTCTTCCCAATATACACAT
5953056 CATATAT
131 CATATAT
5953063 CATCAGGGCCATGTAAATTCTCATTTGGAAAGATCTTACATAAGATACCATTTTCACCACAAATT
1 CATCAGGGCCATGTAAATTCTCATTTGGAAAGATCTTACATAAGATACCATTTTCACCACAAATT
*
5953128 TCTTATGCTTTTCTTTTTTTAAATAAATAAAGAAGAGAAGAAATGGTTCTTCCCAATATACACAT
66 TCTTATGCTTTTCTTTTTTAAAATAAATAAAGAAGAGAAGAAATGGTTCTTCCCAATATACACAT
5953193 CATATAT
131 CATATAT
5953200 CATC
1 CATC
5953204 TAGGAACCAG
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (137 bp):
CATCAGGGCCATGTAAATTCTCATTTGGAAAGATCTTACATAAGATACCATTTTCACCACAAATT
TCTTATGCTTTTCTTTTTTAAAATAAATAAAGAAGAGAAGAAATGGTTCTTCCCAATATACACAT
CATATAT
Found at i:5955076 original size:12 final size:12
Alignment explanation
Indices: 5955061--5955086 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5955051 AGCAAAAAAA
5955061 TATTGCATAAAT
1 TATTGCATAAAT
5955073 TATTGCATAAAT
1 TATTGCATAAAT
5955085 TA
1 TA
5955087 AATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
TATTGCATAAAT
Found at i:5957844 original size:6 final size:6
Alignment explanation
Indices: 5957833--5957881 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
5957823 CATCACTCGT
5957833 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
5957881 A
1 A
5957882 GTGTAGGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:5958680 original size:29 final size:28
Alignment explanation
Indices: 5958645--5958699 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
5958635 GTACTTGCAT
* *
5958645 AAAATGTCTAATATAATCCTTGTACTTTG
1 AAAATGTCCAATATAATACTT-TACTTTG
*
5958674 AAAATGTCCAATGTAATACTTTACTT
1 AAAATGTCCAATATAATACTTTACTT
5958700 GAAGTGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (28 bp):
AAAATGTCCAATATAATACTTTACTTTG
Found at i:5959342 original size:29 final size:29
Alignment explanation
Indices: 5959287--5959343 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
5959277 ACATATATTG
* * *
5959287 ATAGTTCAAATACCACATTAGATATTTTC
1 ATAGTACAAATACCACATTAAACATTTTC
* *
5959316 ATAGTACAATTACTACATTAAACATTTT
1 ATAGTACAAATACCACATTAAACATTTT
5959344 ATAAATAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (29 bp):
ATAGTACAAATACCACATTAAACATTTTC
Found at i:5964393 original size:6 final size:6
Alignment explanation
Indices: 5964359--5964392 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5964349 GAAAATGTAA
* *
5964359 GCAGCT GCAGTT GCAGTT GCAGTT GCAGGT GCAG
1 GCAGTT GCAGTT GCAGTT GCAGTT GCAGTT GCAG
5964393 GCCATGGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.24
Consensus pattern (6 bp):
GCAGTT
Found at i:5966219 original size:2 final size:2
Alignment explanation
Indices: 5966212--5966237 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5966202 GCAGAAATCC
5966212 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5966238 AAAGCAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5972300 original size:24 final size:24
Alignment explanation
Indices: 5972280--5972357 Score: 147
Period size: 24 Copynumber: 3.2 Consensus size: 24
5972270 AAACTCATAA
5972280 GAGCCATATTCAGGAAGCTCATGC
1 GAGCCATATTCAGGAAGCTCATGC
*
5972304 GAGCGATATTCAGGAAGCTCATGC
1 GAGCCATATTCAGGAAGCTCATGC
5972328 GAGCCATATTCAGGAAGCTCATGC
1 GAGCCATATTCAGGAAGCTCATGC
5972352 GAGCCA
1 GAGCCA
5972358 ATAACGGGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.19
Consensus pattern (24 bp):
GAGCCATATTCAGGAAGCTCATGC
Found at i:5972380 original size:48 final size:49
Alignment explanation
Indices: 5972278--5972396 Score: 136
Period size: 48 Copynumber: 2.4 Consensus size: 49
5972268 GGAAACTCAT
* * *
5972278 AAGAGCCATATTCAGGAAGCTCATGCGAGCGATATTCAGGAAGCTCATG
1 AAGAGCCATATTCAGGAAGCTCATGCGAGCAATATACAGGAAGCTCACG
* * *
5972327 -CGAGCCATATTCAGGAAGCTCATGCGAGCCAATA-ACGGGTAGCTC-CG
1 AAGAGCCATATTCAGGAAGCTCATGCGAG-CAATATACAGGAAGCTCACG
*
5972374 AAGAGCCATTAATCAGGAAGCTC
1 AAGAGCCA-TATTCAGGAAGCTC
5972397 CGGATAGCCA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.02
48 41 0.69
49 17 0.29
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (49 bp):
AAGAGCCATATTCAGGAAGCTCATGCGAGCAATATACAGGAAGCTCACG
Found at i:5972406 original size:73 final size:71
Alignment explanation
Indices: 5972329--5972467 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 71
5972319 AGCTCATGCG
* ** *
5972329 AGCCATAT-TCAGGAAGCTCATGCGAGCCAATAACGGGTAGCTCCGAAGAGCCATTAATCAGGAA
1 AGCCATATATCAGGAAGCTCAAGCGAGCC-ATAACGGAAAGCTCCG--GAGCCATTAATAAGGAA
5972393 GCTCCGGAT
63 GCTCCGGAT
* * * * *
5972402 AGCCATATATCGGGGAGTTCAAGCGAGTCATATCGGAAAGCTCCGGAGCCATTAATAAGGAAGCT
1 AGCCATATATCAGGAAGCTCAAGCGAGCCATAACGGAAAGCTCCGGAGCCATTAATAAGGAAGCT
5972467 C
66 C
5972468 ACAAAGAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
71 20 0.36
73 21 0.38
74 15 0.27
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.19
Consensus pattern (71 bp):
AGCCATATATCAGGAAGCTCAAGCGAGCCATAACGGAAAGCTCCGGAGCCATTAATAAGGAAGCT
CCGGAT
Found at i:5973256 original size:21 final size:20
Alignment explanation
Indices: 5973232--5973270 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5973222 AAGTTGTTTA
*
5973232 TCTATCAACAACATTTCATTT
1 TCTA-CAACAAAATTTCATTT
*
5973253 TCTACCACAAAATTTCAT
1 TCTACAACAAAATTTCAT
5973271 AGTTCAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (20 bp):
TCTACAACAAAATTTCATTT
Found at i:5977194 original size:34 final size:34
Alignment explanation
Indices: 5977156--5977222 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
5977146 ACACAATAGA
5977156 TAAATTTTTATTATTCACTAAATTCGTGCAAATG
1 TAAATTTTTATTATTCACTAAATTCGTGCAAATG
5977190 TAAATTTTTATTATTCACTAAATTCGTGCAAAT
1 TAAATTTTTATTATTCACTAAATTCGTGCAAAT
5977223 ATATAAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (34 bp):
TAAATTTTTATTATTCACTAAATTCGTGCAAATG
Found at i:5978823 original size:26 final size:26
Alignment explanation
Indices: 5978772--5978823 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5978762 CGGGTAGCTT
* *
5978772 CAAAGAGCCATTAATCAGAAATCTCA
1 CAAAGAACCATTAATCAGAAAGCTCA
* *
5978798 CAAAGAACCTTTAATCAGGAAGCTCA
1 CAAAGAACCATTAATCAGAAAGCTCA
5978824 TGAAGATCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.19
Consensus pattern (26 bp):
CAAAGAACCATTAATCAGAAAGCTCA
Found at i:5982501 original size:25 final size:25
Alignment explanation
Indices: 5982463--5982538 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
5982453 TAAAAATCCG
*
5982463 TTCTCTTTTGCTCTCTTATTTTTTA
1 TTCTCTTTTACTCTCTTATTTTTTA
5982488 TTCTCTTTTACTCT-TATATTTTCTTA
1 TTCTCTTTTACTCTCT-TATTTT-TTA
*
5982514 -T-TC-TTTACTCTCTTTATTATTTA
1 TTCTCTTTTACTCTC-TTATTTTTTA
5982537 TT
1 TT
5982539 TCATAACACA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
23 11 0.25
24 9 0.20
25 21 0.48
26 3 0.07
ACGTcount: A:0.13, C:0.18, G:0.01, T:0.67
Consensus pattern (25 bp):
TTCTCTTTTACTCTCTTATTTTTTA
Found at i:5982537 original size:23 final size:23
Alignment explanation
Indices: 5982494--5982538 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5982484 TTTATTCTCT
*
5982494 TTTACTCTTATATTTTCTTATTC
1 TTTACTCTTATATTATCTTATTC
*
5982517 TTTACTCTCTTTATTAT-TTATT
1 TTTACTCT-TATATTATCTTATT
5982539 TCATAACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTACTCTTATATTATCTTATTC
Found at i:5990384 original size:31 final size:31
Alignment explanation
Indices: 5990346--5990408 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5990336 TTTAATTGCA
5990346 ATATGAGAACTAGTATGAAACAAAAGCCACT
1 ATATGAGAACTAGTATGAAACAAAAGCCACT
*
5990377 ATATGAGAACTTGTATGAAACAAAAGCCACT
1 ATATGAGAACTAGTATGAAACAAAAGCCACT
5990408 A
1 A
5990409 AAAGATAAAG
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:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (31 bp):
ATATGAGAACTAGTATGAAACAAAAGCCACT
Found at i:5999566 original size:18 final size:18
Alignment explanation
Indices: 5999518--5999569 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
5999508 TATTTTAAAA
5999518 ATTATAAAGATAAAAGCT
1 ATTATAAAGATAAAAGCT
*
5999536 ATTA-AAATTATAAAAGCT
1 ATTATAAA-GATAAAAGCT
5999554 ATTATAAAGATAAAAG
1 ATTATAAAGATAAAAG
5999570 ATAAAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.29
Consensus pattern (18 bp):
ATTATAAAGATAAAAGCT
Found at i:6001724 original size:39 final size:39
Alignment explanation
Indices: 6001673--6001753 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
6001663 ATTACAAAAA
6001673 AAATAAAATTTAAATATCAAATATTATATTAACCCAAAT
1 AAATAAAATTTAAATATCAAATATTATATTAACCCAAAT
*
6001712 AAATAAAGTTTAAATATCAAATATTATATTAACCCAAAT
1 AAATAAAATTTAAATATCAAATATTATATTAACCCAAAT
6001751 AAA
1 AAA
6001754 AATTTATCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.32
Consensus pattern (39 bp):
AAATAAAATTTAAATATCAAATATTATATTAACCCAAAT
Found at i:6005276 original size:32 final size:32
Alignment explanation
Indices: 6005235--6005299 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
6005225 ACGATTTATC
6005235 AAACAATGCTGACAATGGGTCTTTATCATAGG
1 AAACAATGCTGACAATGGGTCTTTATCATAGG
6005267 AAACAATGCTGACAATGGGTCTTTATCATAGG
1 AAACAATGCTGACAATGGGTCTTTATCATAGG
6005299 A
1 A
6005300 TGTTGAGGGG
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:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (32 bp):
AAACAATGCTGACAATGGGTCTTTATCATAGG
Found at i:6007213 original size:18 final size:18
Alignment explanation
Indices: 6007183--6007233 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
6007173 AGTTTTATTT
6007183 AAAA-ATTATAAAAAATAA
1 AAAATATTA-AAAAAATAA
* *
6007201 AAAATATTAAAAATATAT
1 AAAATATTAAAAAAATAA
*
6007219 AAAATTTTAAAAAAA
1 AAAATATTAAAAAAA
6007234 ATATTTTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATATTAAAAAAATAA
Found at i:6007436 original size:45 final size:47
Alignment explanation
Indices: 6007385--6007478 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 47
6007375 ATTCTTCGAT
*
6007385 TTTTATAA-T-TTAGTATGATTGCTTTAAAACATTGAAATTGCACCC
1 TTTTATAATTGTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
6007430 TTTTATAATTGAGTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
1 TTTTATAATT--GTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
6007479 CAATTAGGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 8 0.18
46 1 0.02
49 35 0.80
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (47 bp):
TTTTATAATTGTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
Found at i:6008140 original size:10 final size:11
Alignment explanation
Indices: 6008108--6008141 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6008098 GATGTATTAT
*
6008108 ATAATTTAAAA
1 ATAATATAAAA
*
6008119 ATTATATAAAA
1 ATAATATAAAA
6008130 ATAATATAAAA
1 ATAATATAAAA
6008141 A
1 A
6008142 ATTAATATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:6013519 original size:21 final size:21
Alignment explanation
Indices: 6013493--6013535 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
6013483 TTCAGTAACT
6013493 TCTTCTGTAGCAACAACTTCC
1 TCTTCTGTAGCAACAACTTCC
* *
6013514 TCTTCTGTAGTAGCAACTTCC
1 TCTTCTGTAGCAACAACTTCC
6013535 T
1 T
6013536 TATCAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (21 bp):
TCTTCTGTAGCAACAACTTCC
Found at i:6018487 original size:24 final size:24
Alignment explanation
Indices: 6018455--6018505 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
6018445 ACACTGAAGG
6018455 TGACTTGCTCATCATTAAGTCACA
1 TGACTTGCTCATCATTAAGTCACA
6018479 TGACTTGCTCATCATTAAGTCACA
1 TGACTTGCTCATCATTAAGTCACA
6018503 TGA
1 TGA
6018506 TTAGTTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (24 bp):
TGACTTGCTCATCATTAAGTCACA
Found at i:6042871 original size:8 final size:8
Alignment explanation
Indices: 6042858--6042883 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6042848 GCCCACATAA
6042858 TTCACAAT
1 TTCACAAT
6042866 TTCACAAT
1 TTCACAAT
6042874 TTCACAAT
1 TTCACAAT
6042882 TT
1 TT
6042884 TTACCATAAA
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (8 bp):
TTCACAAT
Found at i:6051713 original size:16 final size:15
Alignment explanation
Indices: 6051687--6051716 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6051677 TTGTATCAAG
6051687 AGAAAATCAATACAC
1 AGAAAATCAATACAC
6051702 AGAAAGATCAATACA
1 AGAAA-ATCAATACA
6051717 AAAAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (15 bp):
AGAAAATCAATACAC
Found at i:6052803 original size:33 final size:35
Alignment explanation
Indices: 6052772--6052881 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 35
6052762 TTTTTATGTT
6052772 TATATAATATTGTTTTCTTAGTATGCGTATGTATG
1 TATATAATATTGTTTTCTTAGTATGCGTATGTATG
* *
6052807 TATATAATGATATCTCATTT-TT--T-T--TTATGT-T-
1 TATATAAT-AT-TGT--TTTCTTAGTATGCGTATGTATG
6052838 TATATAATATTGTTTTCTTAGTATGCGTATGTATG
1 TATATAATATTGTTTTCTTAGTATGCGTATGTATG
6052873 TATATAATA
1 TATATAATA
6052882 ATATATTAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
27 3 0.05
28 2 0.03
29 2 0.03
30 3 0.05
31 9 0.15
32 1 0.02
33 10 0.17
34 1 0.02
35 18 0.31
36 3 0.05
37 2 0.03
38 2 0.03
39 3 0.05
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (35 bp):
TATATAATATTGTTTTCTTAGTATGCGTATGTATG
Found at i:6052814 original size:64 final size:65
Alignment explanation
Indices: 6052746--6052885 Score: 255
Period size: 66 Copynumber: 2.2 Consensus size: 65
6052736 ATTTTTTTTC
6052746 ATAATGATATCTCA-TTTTTTTATGTTTATATAATATTGTTTTCTTAGTATGCGTATGTATGTAT
1 ATAATGATATCTCATTTTTTTTATGTTTATATAATATTGTTTTCTTAGTATGCGTATGTATGTAT
6052810 ATAATGATATCTCATTTTTTTTTATGTTTATATAATATTGTTTTCTTAGTATGCGTATGTATGTA
1 ATAATGATATCTCA-TTTTTTTTATGTTTATATAATATTGTTTTCTTAGTATGCGTATGTATGTA
6052875 T
65 T
*
6052876 ATAATAATAT
1 ATAATGATAT
6052886 ATTAGCAATT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
64 14 0.19
66 59 0.81
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (65 bp):
ATAATGATATCTCATTTTTTTTATGTTTATATAATATTGTTTTCTTAGTATGCGTATGTATGTAT
Found at i:6066197 original size:20 final size:21
Alignment explanation
Indices: 6066167--6066208 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
6066157 AAATATTTTA
6066167 AAAAAATAAAGATATAAAAAT
1 AAAAAATAAAGATATAAAAAT
*
6066188 AAAAAA-AAAGTTATAAAAAT
1 AAAAAATAAAGATATAAAAAT
6066208 A
1 A
6066209 TTGAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (21 bp):
AAAAAATAAAGATATAAAAAT
Found at i:6069292 original size:26 final size:27
Alignment explanation
Indices: 6069253--6069304 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
6069243 TTTAGAATTC
* *
6069253 TTTTACTTGTTTTTTTTTAAAATCAAA
1 TTTTACTTGATTTTTCTTAAAATCAAA
*
6069280 TTTTACTT-ATTTTTCTTGAAATCAA
1 TTTTACTTGATTTTTCTTAAAATCAA
6069305 TGTGCAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTTACTTGATTTTTCTTAAAATCAAA
Found at i:6069628 original size:17 final size:17
Alignment explanation
Indices: 6069606--6069640 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6069596 ACTGAGCTAA
6069606 ACTCGGCAAACGTAGGG
1 ACTCGGCAAACGTAGGG
6069623 ACTCGGCAAACGTAGGG
1 ACTCGGCAAACGTAGGG
6069640 A
1 A
6069641 AATGGACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.34, T:0.11
Consensus pattern (17 bp):
ACTCGGCAAACGTAGGG
Found at i:6083792 original size:3 final size:3
Alignment explanation
Indices: 6083777--6083850 Score: 96
Period size: 3 Copynumber: 24.3 Consensus size: 3
6083767 ATTAGGTTTA
*
6083777 TAT TAT TAC TAT TAT TAT TAT TAT CT-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* *
6083822 TAT TAG TAT TAT GTAG TAT TAT TAT TAT T
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT T
6083851 TACTTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 58 0.94
4 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:6097973 original size:45 final size:45
Alignment explanation
Indices: 6097906--6098179 Score: 379
Period size: 45 Copynumber: 6.1 Consensus size: 45
6097896 AACAAATCAA
* * * *
6097906 CGAATATAGCAGATCTTATCTTCCTGTATTGGCAGTGAAGCAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * **
6097951 CAAAGATAGCAGATCTTGTCTTCGTGTATTGGCAATGAAGTAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
6097996 CGAAGATAGCAAGA-CTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 CGAAGATAGC-AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
*
6098041 CGAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * *
6098086 CGAAGATAACAGATCTTGTCCTCCTATATTGGCAGCGAAGTAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * * * *
6098131 CGAAGATAGCAGATCATGCCTTCCTGTACTGGCAACGAAGCAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
6098176 CGAA
1 CGAA
6098180 AAACAACGAA
Statistics
Matches: 204, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
44 3 0.01
45 198 0.97
46 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (45 bp):
CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
Found at i:6103898 original size:22 final size:23
Alignment explanation
Indices: 6103866--6103908 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
6103856 AAGTATCTAC
6103866 AAATCAAATC-TCTAAGATTAGT
1 AAATCAAATCTTCTAAGATTAGT
*
6103888 AAATCATATCTTCTAAGATTA
1 AAATCAAATCTTCTAAGATTA
6103909 CATATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTAGT
Found at i:6103914 original size:17 final size:17
Alignment explanation
Indices: 6103892--6103944 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 17
6103882 ATTAGTAAAT
6103892 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
* *
6103909 CATATCATATCTACGATTG
1 CATATC-T-TCTAAGATTA
* *
6103928 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
6103945 TGTTTCTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:6103915 original size:22 final size:22
Alignment explanation
Indices: 6103863--6103920 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
6103853 GAAAAGTATC
*
6103863 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
6103884 TAGTAAATCATATCTTCTAAGAT
1 TA-CAAATCATATCTTCTAAGAT
*
6103907 TACATATCATATCT
1 TACAAATCATATCT
6103921 ACGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 2 0.06
22 19 0.61
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:6104432 original size:16 final size:16
Alignment explanation
Indices: 6104411--6104442 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6104401 TATTTATTTC
6104411 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
6104427 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
6104443 ATTACTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAATTGTATCTTTTA
Found at i:6104896 original size:7 final size:7
Alignment explanation
Indices: 6104863--6104939 Score: 64
Period size: 7 Copynumber: 11.0 Consensus size: 7
6104853 TAATTGATTA
*
6104863 TAAATCC
1 TAAACCC
6104870 TAAACCC
1 TAAACCC
* **
6104877 CAAACTA
1 TAAACCC
6104884 TAAACCC
1 TAAACCC
*
6104891 TTAACCC
1 TAAACCC
6104898 TAAACCC
1 TAAACCC
*
6104905 CAAACCC
1 TAAACCC
* *
6104912 CAAACCG
1 TAAACCC
* *
6104919 TAAAACT
1 TAAACCC
6104926 TAAACCC
1 TAAACCC
6104933 TAAACCC
1 TAAACCC
6104940 ACCAATTAAC
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.44, C:0.39, G:0.01, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:6111087 original size:24 final size:24
Alignment explanation
Indices: 6111025--6111076 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
6111015 TTTCTAAAAG
* * *
6111025 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
6111049 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
6111073 ATTT
1 ATTT
6111077 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:6114886 original size:46 final size:46
Alignment explanation
Indices: 6114808--6115127 Score: 439
Period size: 46 Copynumber: 6.9 Consensus size: 46
6114798 ACATTGTTAT
* * *
6114808 AACTTAGTATGGTTTTCTTCACGGAAATACCATTCCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
6114854 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * * *
6114900 AATTCAATATGGTTTTCTTCACTAAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
6114946 AACTTAGTATGGTTTTCTTTA-TCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
6114992 AACTCAGTATGGTTTTCTTTA-TCGAAATACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
6115038 AACTCAGTATGGTTTTCTTTA-TCGAAATACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
6115084 AACTCAGTATGGTTTTCTTCACTAAAATACCATGCCTACGTTTT
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTAC-TTTT
6115128 ACACTTTTCC
Statistics
Matches: 252, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.00
46 246 0.98
47 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:6117015 original size:24 final size:23
Alignment explanation
Indices: 6116983--6117030 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
6116973 TAATCTAAAA
6116983 TATCTCCAACATCATCATTACTTT
1 TATCTCCAACATCATCATTA-TTT
6117007 TATCTCCAACATCATCATTATTT
1 TATCTCCAACATCATCATTATTT
6117030 T
1 T
6117031 CTAGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (23 bp):
TATCTCCAACATCATCATTATTT
Found at i:6120341 original size:8 final size:8
Alignment explanation
Indices: 6120328--6120359 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
6120318 AGTAAAATAT
*
6120328 ATATTATC
1 ATATTATA
6120336 ATATTATA
1 ATATTATA
6120344 ATATTATA
1 ATATTATA
6120352 ATATTATA
1 ATATTATA
6120360 TCTTAAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTATA
Found at i:6122971 original size:30 final size:30
Alignment explanation
Indices: 6122928--6122985 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
6122918 AATGGGCTGG
*
6122928 CACATGGGCGTGTGGCCAGTCCGTGTGGCT
1 CACATGGGCGTGTGGCCAGCCCGTGTGGCT
** **
6122958 CACATGGTTGTGTGTTCAGCCCGTGTGG
1 CACATGGGCGTGTGGCCAGCCCGTGTGG
6122986 AAATGCCCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.10, C:0.24, G:0.38, T:0.28
Consensus pattern (30 bp):
CACATGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:6140802 original size:19 final size:20
Alignment explanation
Indices: 6140762--6140799 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6140752 AGTTTGTTTA
6140762 AAAATAAAATTTTAAAAAAT
1 AAAATAAAATTTTAAAAAAT
6140782 AAAATAAAATTTTAAAAA
1 AAAATAAAATTTTAAAAA
6140800 TAATTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAAATTTTAAAAAAT
Found at i:6142667 original size:91 final size:90
Alignment explanation
Indices: 6142487--6142657 Score: 216
Period size: 91 Copynumber: 1.9 Consensus size: 90
6142477 AACGTTACAA
* * * * *
6142487 GTTAATATGTTGTTAGACAGTTGTGAATACACAACATAATTGCAGATAAAAGCTGCCAGATAATG
1 GTTAATATGCTGCTAGACAGTTGTGAATACACAACATAATTACAGATAAAAGCTGCCAAATAATA
* *
6142552 GGTGGATGGATCACCCATGTTGTAG
66 GGTGGATGAACCACCCATGTTGTAG
** ** *
6142577 GTTAATATGCTGCTAGATGGTTGTGAATACACAACATTTTTTACAGATAAAAGTTGCCAAATAAT
1 GTTAATATGCTGCTAGACAGTTGTGAATACACAACA-TAATTACAGATAAAAGCTGCCAAATAAT
*
6142642 ATGTGGATGAACCACC
65 AGGTGGATGAACCACC
6142658 AGATTTGTAG
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
90 32 0.48
91 35 0.52
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (90 bp):
GTTAATATGCTGCTAGACAGTTGTGAATACACAACATAATTACAGATAAAAGCTGCCAAATAATA
GGTGGATGAACCACCCATGTTGTAG
Found at i:6147059 original size:32 final size:31
Alignment explanation
Indices: 6147023--6147101 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 31
6147013 TAAAATAAGG
**
6147023 TTTTAGGTTTCTTAAAAGTTGAAG-AAAAAAAT
1 TTTTAGGTCCCTTAAAAGTTG--GTAAAAAAAT
6147055 TTTTAGGTCCCTTAAAAGTTGGTAAAAAAA-
1 TTTTAGGTCCCTTAAAAGTTGGTAAAAAAAT
*
6147085 TTTT-GGGCCCTTAAAAG
1 TTTTAGGTCCCTTAAAAG
6147102 CTAAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 12 0.28
30 5 0.12
31 7 0.16
32 19 0.44
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (31 bp):
TTTTAGGTCCCTTAAAAGTTGGTAAAAAAAT
Found at i:6147095 original size:29 final size:31
Alignment explanation
Indices: 6147033--6147114 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 31
6147023 TTTTAGGTTT
*
6147033 CTTAAAAGTTGAAGAAAAAAATTTTTAGGTCC
1 CTTAAAAGTTG-AGAAAAAAATTTTTAGGGCC
6147065 CTTAAAAGTTG-GTAAAAAAA-TTTT-GGGCC
1 CTTAAAAGTTGAG-AAAAAAATTTTTAGGGCC
* *
6147094 CTTAAAAGCT-AAAAAAAAATT
1 CTTAAAAGTTGAGAAAAAAATT
6147115 CTAGATCCCC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 7 0.16
29 14 0.32
30 5 0.11
31 7 0.16
32 11 0.25
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (31 bp):
CTTAAAAGTTGAGAAAAAAATTTTTAGGGCC
Found at i:6148513 original size:17 final size:17
Alignment explanation
Indices: 6148472--6148514 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
6148462 GTAATAGCCC
*
6148472 AAATTTAAT-ATTAAAT
1 AAATTTTATAATTAAAT
**
6148488 AAAAATTATAATTAAAT
1 AAATTTTATAATTAAAT
6148505 AAATTTTATA
1 AAATTTTATA
6148515 GGTATTGGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTTATAATTAAAT
Found at i:6149214 original size:29 final size:29
Alignment explanation
Indices: 6149164--6149219 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
6149154 GTTCAACATG
* *
6149164 TAATGTTATATATGAACTTTTATTTTGTA
1 TAATGTTATATATGAACGTTTACTTTGTA
*
6149193 TAATTTTATATATG-ACAGTTTACTTTG
1 TAATGTTATATATGAAC-GTTTACTTTG
6149220 ATTTTCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (29 bp):
TAATGTTATATATGAACGTTTACTTTGTA
Found at i:6151920 original size:21 final size:22
Alignment explanation
Indices: 6151894--6151942 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
6151884 AATACCTTCT
*
6151894 GAAAAAAAACA-TATTTTAAAA
1 GAAAAAAAACATTATTCTAAAA
* *
6151915 GAAAAAAAATATTATTCTAATA
1 GAAAAAAAACATTATTCTAAAA
6151937 GAAAAA
1 GAAAAA
6151943 CTGAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (22 bp):
GAAAAAAAACATTATTCTAAAA
Found at i:6154723 original size:24 final size:24
Alignment explanation
Indices: 6154694--6154775 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
6154684 GTCTTCATCT
**
6154694 TCTTCATCTTCCCCTCGACCCCCG
1 TCTTCATCTTCATCTCGACCCCCG
* *
6154718 TATTCATCTTCATCTCGACCCTCG
1 TCTTCATCTTCATCTCGACCCCCG
* * *
6154742 CCTTCATTTTCATCTCTACCCCCG
1 TCTTCATCTTCATCTCGACCCCCG
6154766 TCTTCATCTT
1 TCTTCATCTT
6154776 TGTCTCCATC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.12, C:0.44, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTTCATCTTCATCTCGACCCCCG
Found at i:6156730 original size:16 final size:18
Alignment explanation
Indices: 6156699--6156733 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
6156689 AAAATAGTTT
6156699 AAAATATTTTAGAAATTA
1 AAAATATTTTAGAAATTA
6156717 AAAAT-TTTTA-AAATTA
1 AAAATATTTTAGAAATTA
6156733 A
1 A
6156734 CTTAGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATATTTTAGAAATTA
Found at i:6156934 original size:9 final size:9
Alignment explanation
Indices: 6156910--6156953 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
6156900 CGAACAAATC
*
6156910 TTGAGAAAA
1 TTGAGAGAA
6156919 TTGAGAGAA
1 TTGAGAGAA
*
6156928 TTGAGAG-T
1 TTGAGAGAA
6156936 TTAGAGAGAA
1 TT-GAGAGAA
6156946 TTGAGAGA
1 TTGAGAGA
6156954 GTTAGATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 2 0.07
9 26 0.87
10 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:6158481 original size:18 final size:16
Alignment explanation
Indices: 6158449--6158482 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
6158439 CAAAATATCT
6158449 AAAAATTTTAAATTTA
1 AAAAATTTTAAATTTA
6158465 AAAAATTATTAAAATTTA
1 AAAAATT-TT-AAATTTA
6158483 CTTTAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAATTTTAAATTTA
Found at i:6159203 original size:17 final size:17
Alignment explanation
Indices: 6159181--6159214 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6159171 TTAGATCTAT
6159181 TCTATCAAGTTATTTGA
1 TCTATCAAGTTATTTGA
*
6159198 TCTATCGAGTTATTTGA
1 TCTATCAAGTTATTTGA
6159215 AGATGCACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (17 bp):
TCTATCAAGTTATTTGA
Found at i:6159348 original size:19 final size:19
Alignment explanation
Indices: 6159324--6159363 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6159314 TTTATTTTTT
* *
6159324 ATTAGAACCGAAAAGTTTA
1 ATTAGAACAGAAAAGTATA
*
6159343 ATTAGAATAGAAAAGTATA
1 ATTAGAACAGAAAAGTATA
6159362 AT
1 AT
6159364 AAAAGTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (19 bp):
ATTAGAACAGAAAAGTATA
Found at i:6166877 original size:27 final size:28
Alignment explanation
Indices: 6166838--6166891 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
6166828 GTTCGGTTCG
*
6166838 GTTTTCGATTTTTCTATACTAATTTTTT
1 GTTTTCGATTTTTCTAGACTAATTTTTT
* *
6166866 GTTTT-GATTTTTTTAGACTTATTTTT
1 GTTTTCGATTTTTCTAGACTAATTTTT
6166892 ATATGTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.17, C:0.07, G:0.09, T:0.67
Consensus pattern (28 bp):
GTTTTCGATTTTTCTAGACTAATTTTTT
Found at i:6172115 original size:18 final size:18
Alignment explanation
Indices: 6172088--6172123 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6172078 ATTATTCTAT
*
6172088 AATTTTTAAAAAGTATTA
1 AATTTATAAAAAGTATTA
*
6172106 AATTTATAAAATGTATTA
1 AATTTATAAAAAGTATTA
6172124 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AATTTATAAAAAGTATTA
Found at i:6172147 original size:22 final size:23
Alignment explanation
Indices: 6172105--6172161 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
6172095 AAAAAGTATT
*
6172105 AAATTTATAAAATGTATTATAAA
1 AAATATATAAAATGTATTATAAA
*
6172128 AAATATATATAAT-TATTATAAA
1 AAATATATAAAATGTATTATAAA
* *
6172150 AATTAAATAAAA
1 AAATATATAAAA
6172162 ATATTGATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATATATAAAATGTATTATAAA
Found at i:6172166 original size:22 final size:21
Alignment explanation
Indices: 6172141--6172202 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 21
6172131 TATATATAAT
6172141 TATTATAAAAATTAAATAAAAA
1 TATTAT-AAAATTAAATAAAAA
6172163 TATTGAT---ATTAAATAAAAA
1 TATT-ATAAAATTAAATAAAAA
*
6172182 TATTATAAAATAAAATAAAAA
1 TATTATAAAATTAAATAAAAA
6172203 ACCGTCCCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.06
19 16 0.46
21 11 0.31
22 4 0.11
23 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TATTATAAAATTAAATAAAAA
Found at i:6172793 original size:13 final size:13
Alignment explanation
Indices: 6172775--6172801 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6172765 TAATATTAAT
6172775 TAATTTTTTATAA
1 TAATTTTTTATAA
6172788 TAATTTTTTATAA
1 TAATTTTTTATAA
6172801 T
1 T
6172802 TTTTATAATA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATTTTTTATAA
Found at i:6172816 original size:13 final size:12
Alignment explanation
Indices: 6172779--6172817 Score: 55
Period size: 10 Copynumber: 3.3 Consensus size: 12
6172769 ATTAATTAAT
6172779 TTTTTATAATAA
1 TTTTTATAATAA
6172791 TTTTT-T-ATAA
1 TTTTTATAATAA
6172801 TTTTTATAATACA
1 TTTTTATAATA-A
6172814 TTTT
1 TTTT
6172818 ATATTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 2 0.08
12 8 0.33
13 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTTATAATAA
Found at i:6172817 original size:21 final size:20
Alignment explanation
Indices: 6172779--6172831 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
6172769 ATTAATTAAT
6172779 TTTTTATAATAATTTTTTATAA
1 TTTTTATAATAA-TTTTTAT-A
6172801 TTTTTATAATACA-TTTTATA
1 TTTTTATAATA-ATTTTTATA
6172821 TTTTTAGTAAT
1 TTTTTA-TAAT
6172832 TTTAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.24
21 10 0.34
22 11 0.38
23 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTATAATAATTTTTATA
Found at i:6185506 original size:21 final size:21
Alignment explanation
Indices: 6185459--6185512 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
6185449 ACCATTGTTT
** *
6185459 CTAATCTCATTGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
*
6185480 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
*
6185501 CTAATCTTACCG
1 CTAATCTCACCG
6185513 TTACTGCTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:6207538 original size:15 final size:15
Alignment explanation
Indices: 6207520--6207565 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
6207510 GTAGGAGGCT
6207520 GAGCAATTGGTGGAG
1 GAGCAATTGGTGGAG
* * *
6207535 GAGCCATAGGTGGCG
1 GAGCAATTGGTGGAG
*
6207550 GAGCAAGTGGTGGAG
1 GAGCAATTGGTGGAG
6207565 G
1 G
6207566 GGGTGAGGGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.24, C:0.11, G:0.50, T:0.15
Consensus pattern (15 bp):
GAGCAATTGGTGGAG
Found at i:6210253 original size:67 final size:69
Alignment explanation
Indices: 6210170--6210301 Score: 189
Period size: 69 Copynumber: 1.9 Consensus size: 69
6210160 ATACACAATA
* **
6210170 TAATGGTTTTGCCTTTTAAC-TTA-ATGA-GTAAACATTTATCAAAACAACGTAATTTTGCCTTT
1 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATC-AAACAACGTAATTTTGCCTTT
6210232 TAACT
65 TAACT
* *
6210237 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAGAGCGTAATTTTGCCTTTT
1 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAACAACGTAATTTTGCCTTTT
6210302 CTTATTCAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 19 0.33
68 3 0.05
69 22 0.39
70 13 0.23
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (69 bp):
TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAACAACGTAATTTTGCCTTTT
AACT
Found at i:6211542 original size:31 final size:31
Alignment explanation
Indices: 6211507--6211608 Score: 73
Period size: 31 Copynumber: 3.3 Consensus size: 31
6211497 TGTTAACACA
6211507 ATGTACCACATTAGATATTTTATGAAAGTAC
1 ATGTACCACATTAGATATTTTATGAAAGTAC
* * * * * * *
6211538 ATGTATCATAATAAAGCACATATTA--ATAGTTC
1 ATGTACCA-CAT-TAG-ATATTTTATGAAAGTAC
* *
6211570 ATGTATCACATTGGATATTTTATGAAAGTAC
1 ATGTACCACATTAGATATTTTATGAAAGTAC
*
6211601 AAGTACCA
1 ATGTACCA
6211609 AATGTGACAT
Statistics
Matches: 50, Mismatches: 16, Indels: 10
0.66 0.21 0.13
Matches are distributed among these distances:
29 6 0.12
30 1 0.02
31 20 0.40
32 15 0.30
33 2 0.04
34 6 0.12
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (31 bp):
ATGTACCACATTAGATATTTTATGAAAGTAC
Found at i:6211808 original size:14 final size:15
Alignment explanation
Indices: 6211789--6211817 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6211779 GAGTGTTGAG
6211789 GTCTAATTTT-TTTT
1 GTCTAATTTTATTTT
6211803 GTCTAATTTTATTTT
1 GTCTAATTTTATTTT
6211818 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (15 bp):
GTCTAATTTTATTTT
Found at i:6224761 original size:3 final size:3
Alignment explanation
Indices: 6224747--6224797 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
6224737 ACACTAGTAC
* * * * *
6224747 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6224794 ATA A
1 ATA A
6224798 GGATATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6226442 original size:20 final size:19
Alignment explanation
Indices: 6226414--6226454 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6226404 TTGAAAATTC
6226414 AATAATATATAAAAATTAAA
1 AATAATATA-AAAAATTAAA
* *
6226434 AATATTATAAAAATTTAAA
1 AATAATATAAAAAATTAAA
6226453 AA
1 AA
6226455 ATGTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATATAAAAAATTAAA
Found at i:6226463 original size:19 final size:18
Alignment explanation
Indices: 6226407--6226454 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
6226397 ATAATTTTTG
*
6226407 AAAATTCAATAATA-TATA
1 AAAATT-AAAAATATTATA
6226425 AAAATTAAAAATATTATA
1 AAAATTAAAAATATTATA
6226443 AAAATTTAAAAA
1 AAAA-TTAAAAA
6226455 ATGTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.22
18 14 0.52
19 7 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTAAAAATATTATA
Found at i:6231404 original size:24 final size:24
Alignment explanation
Indices: 6231376--6231427 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
6231366 TTCGTAGATA
* *
6231376 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
6231400 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
6231424 AAAT
1 AAAT
6231428 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:6233219 original size:13 final size:13
Alignment explanation
Indices: 6233194--6233227 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6233184 AGTGAAGAGT
6233194 ACAAAAGTGTAAAC
1 ACAAAA-TGTAAAC
6233208 ACAAAATGTAAAC
1 ACAAAATGTAAAC
*
6233221 ATAAAAT
1 ACAAAAT
6233228 TCTCTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (13 bp):
ACAAAATGTAAAC
Found at i:6233344 original size:24 final size:24
Alignment explanation
Indices: 6233317--6233368 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
6233307 TTCGTAGGTC
6233317 AAATAAATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
*
6233341 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
6233365 AAAT
1 AAAT
6233369 CTTCTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:6233956 original size:15 final size:15
Alignment explanation
Indices: 6233936--6233967 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6233926 TTTATATTTT
6233936 TATATAATTTTAATA
1 TATATAATTTTAATA
6233951 TATATAATTTTAATA
1 TATATAATTTTAATA
6233966 TA
1 TA
6233968 GATGCAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATAATTTTAATA
Found at i:6242434 original size:16 final size:16
Alignment explanation
Indices: 6242414--6242466 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
6242404 AAAAATTATG
*
6242414 TTTTCCATCCTTCTAG
1 TTTTCCATCCTTCTAA
* *
6242430 TTTTCTACCCCTTC-AA
1 TTTTCCA-TCCTTCTAA
*
6242446 TTTTCCATCCTCCTAA
1 TTTTCCATCCTTCTAA
6242462 TTTTC
1 TTTTC
6242467 TTTCCACTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 20 0.69
17 5 0.17
ACGTcount: A:0.15, C:0.34, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTCCATCCTTCTAA
Found at i:6263539 original size:8 final size:8
Alignment explanation
Indices: 6263526--6263575 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
6263516 AATTGAGAGA
6263526 AGAGAGGG
1 AGAGAGGG
6263534 AGAGA-GG
1 AGAGAGGG
6263541 -GAGA-GG
1 AGAGAGGG
6263547 -GAGAGGG
1 AGAGAGGG
*
6263554 AGGGAGGG
1 AGAGAGGG
*
6263562 AGGGAGGG
1 AGAGAGGG
6263570 AGAGAG
1 AGAGAG
6263576 AGGGAATGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 10 0.26
7 4 0.11
8 24 0.63
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:6263558 original size:4 final size:4
Alignment explanation
Indices: 6263529--6263571 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
6263519 TGAGAGAAGA
* *
6263529 GAGG GAGA GAGG GAGAG G-GA GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAG-G GAGG GAGG GAGG GAGG GAGG GAGG GAG
6263572 AGAGAGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 1 0.03
4 30 0.91
5 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:6263564 original size:12 final size:12
Alignment explanation
Indices: 6263529--6263575 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
6263519 TGAGAGAAGA
6263529 GAGGGAGAGAGG
1 GAGGGAGAGAGG
6263541 GAGAGG-GAGAGG
1 GAG-GGAGAGAGG
*
6263553 GAGGGAGGGAGG
1 GAGGGAGAGAGG
6263565 GAGGGAGAGAG
1 GAGGGAGAGAG
6263576 AGGGAATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (12 bp):
GAGGGAGAGAGG
Found at i:6272985 original size:20 final size:20
Alignment explanation
Indices: 6272959--6273008 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
6272949 AGAGCCATTA
6272959 ATATCGATACC-AATAGAAAT
1 ATATCGATACCAAATAG-AAT
*
6272979 TTATCGATACCAAATAGAAT
1 ATATCGATACCAAATAGAAT
6272999 ATATCGATAC
1 ATATCGATAC
6273009 TTGATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (20 bp):
ATATCGATACCAAATAGAAT
Found at i:6283400 original size:18 final size:18
Alignment explanation
Indices: 6283359--6283393 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6283349 TGCCTCGACC
6283359 CCTCTGCCACGATAACCA
1 CCTCTGCCACGATAACCA
*
6283377 CCTCTGCCATGATAACC
1 CCTCTGCCACGATAACC
6283394 TCTTCTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.20
Consensus pattern (18 bp):
CCTCTGCCACGATAACCA
Found at i:6284984 original size:15 final size:15
Alignment explanation
Indices: 6284939--6284985 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
6284929 TCCTAAAATG
6284939 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
**
6284954 A-AGTCATTTATAATTT
1 ATA-AAATTT-TAATTT
6284970 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
6284985 A
1 A
6284986 GAAATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 1 0.04
15 12 0.48
16 11 0.44
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:6287696 original size:17 final size:18
Alignment explanation
Indices: 6287665--6287700 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6287655 AATTTAACTT
6287665 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
6287683 TAATT-AATTTTTTAAAA
1 TAATTAAATTATTTAAAA
6287700 T
1 T
6287701 TATAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:6288461 original size:36 final size:36
Alignment explanation
Indices: 6288421--6288495 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
6288411 ATAAAAAAAG
*
6288421 TAATAAAAAATAAAATTATT-AAATATTAAAA-TAATA
1 TAAT-AAAAAT-AAATTATTAAAAAATTAAAATTAATA
* *
6288457 TAATAAAAATATATTTTTAAAAAATTAAAATTAATA
1 TAATAAAAATAAATTATTAAAAAATTAAAATTAATA
6288493 TAA
1 TAA
6288496 ATAGATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 6 0.18
35 16 0.47
36 12 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (36 bp):
TAATAAAAATAAATTATTAAAAAATTAAAATTAATA
Found at i:6289877 original size:20 final size:20
Alignment explanation
Indices: 6289852--6289898 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
6289842 AATAAGAAAG
6289852 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
6289872 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
6289892 ATATAAA
1 ATATAAA
6289899 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:6291566 original size:44 final size:44
Alignment explanation
Indices: 6291452--6291568 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
6291442 TTTTAACCCA
* * ** * *
6291452 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
*
6291495 CTCCTCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
*
6291539 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
6291569 GTAATTTCCA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 4 0.07
43 19 0.32
44 32 0.53
45 5 0.08
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:6291808 original size:86 final size:86
Alignment explanation
Indices: 6291702--6291887 Score: 282
Period size: 86 Copynumber: 2.2 Consensus size: 86
6291692 AATCTGTAAC
*
6291702 CTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAAT
1 CTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
6291767 GCAGGAAGGCAAGATCTGCTT
66 GCAGGAAGGCAAGATCTGCTT
* * * *
6291788 CTTTAACTAGCTCCACTGCAATCGATGGATGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
1 CTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
* **
6291853 GTAGGAAGGCAAGATCTTTTGT
66 GCAGGAAGGCAAGATCTGCT-T
*
6291875 CTTCAACCAGCTC
1 CTTTAACCAGCTC
6291888 TATCACAACC
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 77 0.87
87 12 0.13
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (86 bp):
CTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAT
GCAGGAAGGCAAGATCTGCTT
Found at i:6291915 original size:86 final size:86
Alignment explanation
Indices: 6291706--6291915 Score: 262
Period size: 86 Copynumber: 2.4 Consensus size: 86
6291696 TGTAACCTTT
* * *
6291706 AACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAATGCAG
1 AACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAG
*
6291771 GAAGGCAAGATCTGCTTCTTT
66 GAAGGCAAGATCTGCTTCTTC
* * * * *
6291792 AACTAGCTCCACTGCAATCGATGGATGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGTAG
1 AACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAG
**
6291857 GAAGGCAAGATCTTTTGTCTTC
66 GAAGGCAAGATCTGCT-TCTTC
* **
6291879 AACCAGCTCTA-TCACAACCGAAAGAGGCAAGG-TTTGT
1 AACCAGCTCCACT-ACAACCGATGGAGGCAAGGCTTTGT
6291916 GTCTTCGCTT
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
86 79 0.75
87 27 0.25
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (86 bp):
AACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAG
GAAGGCAAGATCTGCTTCTTC
Found at i:6292134 original size:44 final size:44
Alignment explanation
Indices: 6292085--6292239 Score: 161
Period size: 44 Copynumber: 3.5 Consensus size: 44
6292075 TCTACTCTGT
* * * *
6292085 TGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCAC
1 TGTAACCTCAGGGAGATAAGATCCTCTATTTCAATCTGCTCCAC
* * ** * * *
6292129 TGTAACTTCAGGGAGATAGGATAGTGT-TTTCGATCTGCTCCGC
1 TGTAACCTCAGGGAGATAAGATCCTCTATTTCAATCTGCTCCAC
* *
6292172 TGTAATCTCAGGGAGATAAGAT-CTCTAGCTTCAATCTGCTCCAC
1 TGTAACCTCAGGGAGATAAGATCCTCTA-TTTCAATCTGCTCCAC
*
6292216 TGTAACCTCAGGGAGAAAAGATCC
1 TGTAACCTCAGGGAGATAAGATCC
6292240 GAAATTCTTT
Statistics
Matches: 88, Mismatches: 20, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.02
43 31 0.35
44 54 0.61
45 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
TGTAACCTCAGGGAGATAAGATCCTCTATTTCAATCTGCTCCAC
Found at i:6292305 original size:87 final size:88
Alignment explanation
Indices: 6292171--6292496 Score: 287
Period size: 87 Copynumber: 3.8 Consensus size: 88
6292161 ATCTGCTCCG
* * * *
6292171 CTGTAATCTCAGGGAGATAAGATCTCTAGCT-TCAATCTGCTCCACTGTAACCTCAGGGAGAAAA
1 CTGTAATCTCAGGGAGATAAGATC-CT-GATGT-GATCTGCTCCACTGTAACCTCAGAGAGATAA
*
6292235 GATCCGAAATTCTTTGGTCCATTCCA
63 GATCCGAAATTCTTTGGTCCGTTCCA
* * * *
6292261 CTGTAATCTCAGGGAGATAAGA-CCTGATGTGATCTTCTCTACTGTAACTTTAGAGAGATAAGAT
1 CTGTAATCTCAGGGAGATAAGATCCTGATGTGATCTGCTCCACTGTAACCTCAGAGAGATAAGAT
** *
6292325 -C------CTTTAATCCGCTCCA
66 CCGAAATTCTTTGGTCCGTTCCA
* * * * * * * *
6292341 TTGTAATCTCAAGGAGATAGGATTACT-ATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAA
1 CTGTAATCTCAGGGAGATAAGA-TCCTGA--TGTGATCTGCTCCACTGTAACCTCAGAGAGATAA
* *
6292405 GATCTGAAATTCTTTGGTCTGTTCCA
63 GATCCGAAATTCTTTGGTCCGTTCCA
* * * *
6292431 CTATAATCTCAGGGAGATAAGA-CCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGAT
1 CTGTAATCTCAGGGAGATAAGATCCTGATGTGATCTGCTCCACTGTAACCTCAGAGAGATAAGAT
6292495 CC
66 CC
6292497 TTTAATCCGC
Statistics
Matches: 181, Mismatches: 42, Indels: 29
0.72 0.17 0.12
Matches are distributed among these distances:
80 30 0.17
81 1 0.01
82 2 0.01
83 29 0.16
86 1 0.01
87 60 0.33
88 5 0.03
89 2 0.01
90 51 0.28
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (88 bp):
CTGTAATCTCAGGGAGATAAGATCCTGATGTGATCTGCTCCACTGTAACCTCAGAGAGATAAGAT
CCGAAATTCTTTGGTCCGTTCCA
Found at i:6292401 original size:44 final size:44
Alignment explanation
Indices: 6292122--6292604 Score: 228
Period size: 44 Copynumber: 11.3 Consensus size: 44
6292112 ATTTTAATCC
* * *
6292122 GCTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGT-TTTCGATCT
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTT-GATCT
* * **
6292165 GCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTTGATCT
* * * * * *
6292209 GCTCCACTGTAACCTCAGGGAGAAAAGA-TCCGAAATTCTTTGGTCC
1 GCTCCACTGTAATCTCAGGGAGATAAGATTAC--TA-TCTTTGATCT
** * *
6292255 ATTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TGTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTTGATCT
* * * * * *
6292296 TCTCTACTGTAA-CTTTAGAGAGATAAGA-T-C---CTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGATCT
* * *
6292335 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
* * *
6292379 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTTGATCT
* * * *
6292425 GTTCCACTATAATCTCAGGGAGATAAGA--CCTGA--TGTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTTGATCT
* * * * *
6292466 TCTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGATCT
* * * *
6292505 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCCTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
* * * * *
6292549 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCT-TCTTTAACCG
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTTGATCT
6292593 GCTCCACTGTAA
1 GCTCCACTGTAA
6292605 CCAATGAAGG
Statistics
Matches: 326, Mismatches: 81, Indels: 65
0.69 0.17 0.14
Matches are distributed among these distances:
39 49 0.15
40 6 0.02
41 57 0.17
42 1 0.00
43 25 0.08
44 113 0.35
45 11 0.03
46 64 0.20
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
Found at i:6292402 original size:83 final size:83
Alignment explanation
Indices: 6292315--6292578 Score: 277
Period size: 83 Copynumber: 3.1 Consensus size: 83
6292305 TAACTTTAGA
6292315 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
1 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
6292380 CTCCGCTGTAATCTCAGG
66 CTCCGCTGTAATCTCAGG
** * * * * * * *
6292398 GAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGATAAGA--CCTGA--T
1 GAGATAAGATC-------CTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACT-ATCT
* * ** *
6292459 GTGATCTTCTCTACTGTAA-CTTCAGA
58 TTGATCTGCTCCGCTGTAATC-TCAGG
*
6292485 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCCTTGATCTG
1 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
6292550 CTCCGCTGTAATCTCAGG
66 CTCCGCTGTAATCTCAGG
6292568 GAGATAAGATC
1 GAGATAAGATC
6292579 TGCTTCTTTA
Statistics
Matches: 138, Mismatches: 29, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
80 29 0.21
81 1 0.01
82 2 0.01
83 41 0.30
84 1 0.01
86 1 0.01
87 31 0.22
88 2 0.01
89 1 0.01
90 29 0.21
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (83 bp):
GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
CTCCGCTGTAATCTCAGG
Found at i:6292439 original size:46 final size:46
Alignment explanation
Indices: 6292369--6292457 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
6292359 AGGATTACTA
* * *
6292369 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
1 TCTTTGATCTGCTCCACTATAATCTCAGGGAGATAAGACCTGAAAT
* *
6292415 TCTTTGGTCTGTTCCACTATAATCTCAGGGAGATAAGACCTGA
1 TCTTTGATCTGCTCCACTATAATCTCAGGGAGATAAGACCTGA
6292458 TGTGATCTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (46 bp):
TCTTTGATCTGCTCCACTATAATCTCAGGGAGATAAGACCTGAAAT
Found at i:6292579 original size:170 final size:170
Alignment explanation
Indices: 6292205--6292580 Score: 671
Period size: 170 Copynumber: 2.2 Consensus size: 170
6292195 TCTAGCTTCA
* * * * *
6292205 ATCTGCTCCACTGTAACCTCAGGGAGAAAAGATCCGAAATTCTTTGGTCCATTCCACTGTAATCT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCCATTCCACTATAATCT
*
6292270 CAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTTAGAGAGATAAGATCCTTTAATCC
66 CAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
*
6292335 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTG
131 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCCTTG
**
6292375 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCT
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCCATTCCACTATAATCT
6292440 CAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
66 CAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
6292505 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCCTTG
131 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCCTTG
6292545 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG
1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG
6292581 CTTCTTTAAC
Statistics
Matches: 197, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 197 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (170 bp):
ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCCATTCCACTATAATCT
CAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCCTTG
Found at i:6292761 original size:45 final size:45
Alignment explanation
Indices: 6292710--6292848 Score: 124
Period size: 44 Copynumber: 3.1 Consensus size: 45
6292700 GCAAGGTTTG
*
6292710 TGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCACTGTCAATGAAGGAAGGCAAGATCTTT
* * ** * * * *
6292755 TGTCTTCAACCAGC-TCTA-TCACAACCGAAAG-AGGCAAGGT-TTG
1 TGTCTTCGACCTGCTTC-ACTGTCAA-TGAAGGAAGGCAAGATCTTT
* * *
6292798 TGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCACTGTCAATGAAGGAAGGCAAGATCTTT
6292843 TGTCTT
1 TGTCTT
6292849 TAACCAGCTC
Statistics
Matches: 68, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
43 16 0.24
44 28 0.41
45 24 0.35
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (45 bp):
TGTCTTCGACCTGCTTCACTGTCAATGAAGGAAGGCAAGATCTTT
Found at i:6292790 original size:44 final size:44
Alignment explanation
Indices: 6292742--6292880 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 44
6292732 CAATGCAGGA
6292742 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
* * * * * ** ** * * *
6292786 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAA-TGTAGG
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TCTATCACAACCGAAAG
*
6292829 AAGGCAAGATCTTTTGTCTTTAACCAGCTCTATCACAACCGAAAG
1 -AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
6292874 AGGCAAG
1 AGGCAAG
6292881 GTTTGTGTCT
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
43 16 0.24
44 35 0.53
45 15 0.23
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAG
Done.