Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 101 of 103
Found at i:37945890 original size:26 final size:26
Alignment explanation
Indices: 37945861--37945911 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
37945851 TCACTTAATA
*
37945861 AATTAATTATTAATATTTTAAATATT
1 AATTAATTATTAATAATTTAAATATT
** *
37945887 AATTTTTTATTTATAATTTAAATAT
1 AATTAATTATTAATAATTTAAATAT
37945912 GTTATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTAATTATTAATAATTTAAATATT
Found at i:37945918 original size:16 final size:16
Alignment explanation
Indices: 37945897--37945927 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37945887 AATTTTTTAT
*
37945897 TTATAATTTAAATATG
1 TTATAATTAAAATATG
37945913 TTATAATTAAAATAT
1 TTATAATTAAAATAT
37945928 AAAAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATAATTAAAATATG
Found at i:37945941 original size:30 final size:28
Alignment explanation
Indices: 37945907--37945975 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
37945897 TTATAATTTA
37945907 AATATGTTATAATTAAAATATAAAAATATT
1 AATAT-TTATAATTAAAAT-TAAAAATATT
* * *
37945937 AATATTTTTTAATTTAAATTTAAAATATT
1 AATA-TTTATAATTAAAATTAAAAATATT
37945966 AAT-TTTATAA
1 AATATTTATAA
37945976 GTTTAAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 6 0.18
29 12 0.35
30 15 0.44
31 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTTATAATTAAAATTAAAAATATT
Found at i:37949060 original size:2 final size:2
Alignment explanation
Indices: 37949053--37949093 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
37949043 CTTATAGGTT
37949053 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
37949094 TGCATACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:37956679 original size:37 final size:37
Alignment explanation
Indices: 37956629--37956700 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
37956619 ATAAATATAC
* * * *
37956629 TTTGACTCGAAGTCTTTGACCTCATTCCTTACAAAAT
1 TTTGACTCAAAGTCTTTGACCCCAATCCCTACAAAAT
* *
37956666 TTTGACTTAAAGTCTTTTACCCCAATCCCTACAAA
1 TTTGACTCAAAGTCTTTGACCCCAATCCCTACAAA
37956701 GTTAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.36
Consensus pattern (37 bp):
TTTGACTCAAAGTCTTTGACCCCAATCCCTACAAAAT
Found at i:37975735 original size:2 final size:2
Alignment explanation
Indices: 37975718--37975802 Score: 88
Period size: 2 Copynumber: 43.5 Consensus size: 2
37975708 TACAAACTTT
* * *
37975718 GA GA GG GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GTA GTT
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A G-A
*
37975762 NA G- GA G- GA G- GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
37975800 GA G
1 GA G
37975803 TTTATAATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
1 4 0.06
2 63 0.90
3 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.53, T:0.04
Consensus pattern (2 bp):
GA
Found at i:37988160 original size:18 final size:18
Alignment explanation
Indices: 37988117--37988153 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
37988107 TTTTATTATA
37988117 TTAATAAAACTTTTAATT
1 TTAATAAAACTTTTAATT
37988135 TTAATAAAA-TTTTAATT
1 TTAATAAAACTTTTAATT
37988152 TT
1 TT
37988154 TATTAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATAAAACTTTTAATT
Found at i:37990106 original size:13 final size:14
Alignment explanation
Indices: 37990082--37990121 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
37990072 TTGTCTTATT
*
37990082 TAAATAATTTTAAA
1 TAAATTATTTTAAA
37990096 T-AATTATTTT-AA
1 TAAATTATTTTAAA
37990108 TAAATT-TTTTAAA
1 TAAATTATTTTAAA
37990121 T
1 T
37990122 TTTATAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 7 0.30
13 15 0.65
14 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATTATTTTAAA
Found at i:37990198 original size:17 final size:17
Alignment explanation
Indices: 37990176--37990217 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
37990166 TTTAAATTTT
37990176 TGTTA-TATTATATTTGA
1 TGTTATTATTAT-TTTGA
37990193 TGTTATTATTATTTTG-
1 TGTTATTATTATTTTGA
*
37990209 TTTTATTAT
1 TGTTATTAT
37990218 AATTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (17 bp):
TGTTATTATTATTTTGA
Found at i:37990229 original size:15 final size:15
Alignment explanation
Indices: 37990195--37990243 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
37990185 ATATTTGATG
*
37990195 TTATTATTATTTTGTT
1 TTATTATTATTAT-TT
*
37990211 TTATTATAATTATTT
1 TTATTATTATTATTT
* *
37990226 TTATAATTATTAATT
1 TTATTATTATTATTT
37990241 TTA
1 TTA
37990244 AATTTAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTATTATTATTT
Found at i:37990235 original size:31 final size:31
Alignment explanation
Indices: 37990173--37990236 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
37990163 AATTTTAAAT
* *
37990173 TTTTGTTATATTATATTTGATGTTATTATTA
1 TTTTGTTATATTATAATTGATGTTATAATTA
* *
37990204 TTTTGTTTTATTATAATT-ATTTTTATAATTA
1 TTTTGTTATATTATAATTGA-TGTTATAATTA
37990235 TT
1 TT
37990237 AATTTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (31 bp):
TTTTGTTATATTATAATTGATGTTATAATTA
Found at i:37990239 original size:19 final size:20
Alignment explanation
Indices: 37990195--37990240 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
37990185 ATATTTGATG
* *
37990195 TTATT-ATTATTTTGTTTTA
1 TTATTAATTATTTTGTATAA
37990214 TTA-TAATTATTTT-TATAA
1 TTATTAATTATTTTGTATAA
37990232 TTATTAATT
1 TTATTAATT
37990241 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTAATTATTTTGTATAA
Found at i:37990270 original size:20 final size:21
Alignment explanation
Indices: 37990245--37990290 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
37990235 TTAATTTTAA
37990245 ATTTAAATAAT-AAAAATTAT
1 ATTTAAATAATAAAAAATTAT
* *
37990265 ATTT-AATTATAAAAAATTTT
1 ATTTAAATAATAAAAAATTAT
37990285 ATTTAA
1 ATTTAA
37990291 TCTATTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTAAATAATAAAAAATTAT
Found at i:37992092 original size:23 final size:23
Alignment explanation
Indices: 37992066--37992109 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
37992056 TCATTAATTT
*
37992066 TTCATGAATAAACTTGTTTAATA
1 TTCATGAACAAACTTGTTTAATA
*
37992089 TTCATGAACAAGCTTGTTTAA
1 TTCATGAACAAACTTGTTTAA
37992110 GCTAATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (23 bp):
TTCATGAACAAACTTGTTTAATA
Found at i:37995398 original size:2 final size:2
Alignment explanation
Indices: 37995391--37995428 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37995381 CGACTTCAAC
37995391 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
37995429 TCTGCTCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38001793 original size:7 final size:7
Alignment explanation
Indices: 38001781--38001805 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38001771 CGTGTTACCC
38001781 GTTTCGT
1 GTTTCGT
38001788 GTTTCGT
1 GTTTCGT
38001795 GTTTCGT
1 GTTTCGT
38001802 GTTT
1 GTTT
38001806 TAACTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.28, T:0.60
Consensus pattern (7 bp):
GTTTCGT
Found at i:38020652 original size:2 final size:2
Alignment explanation
Indices: 38020645--38020674 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38020635 CATTTGTAGC
*
38020645 AG AG AG AG AC 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
38020675 TGGAAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38025244 original size:183 final size:183
Alignment explanation
Indices: 38024930--38025293 Score: 547
Period size: 183 Copynumber: 2.0 Consensus size: 183
38024920 GGTTAGAGAG
* * *
38024930 AAAAGCTTTGAGTCAGAGTCTGGTAATTCTGAAAGTGAAATAGAAAAAAAATGTAAAAGGGGTTC
1 AAAAACTTTGAGTCAGAGTCAGGTAATTCTGAAAGTGAAATAGAAAAAAAACGTAAAAGGGGTTC
* * *
38024995 TTGTAATAAGAAGAGGAAGCGTTGCAAACAAGTAAGGGATGTACTGGAGGTGACGGAGAGGAAGA
66 TTGTAATAAGAAGAGAAAGCGTTGCAAACAAGTAAGGGATGTACTGGAGGTAAAGGAGAGGAAGA
* *
38025060 TT-AGAGCAGTTCCTGAAGTACTAAATGTTGTGGCAGGTGGAAGAGAATAAGAA
131 TTGA-AGCAGTTCCTGAAGTACTAAATGTTGTGACAGGTGGAAAAGAATAAGAA
38025113 AAAAACTTTGAGTCAGAGTCAGGTAATTCTGAAAGTG-AATGAGAAAAAAAAACGTAAAA-GGGT
1 AAAAACTTTGAGTCAGAGTCAGGTAATTCTGAAAGTGAAAT-AG-AAAAAAAACGTAAAAGGGGT
* * * *
38025176 TTTTGTAATAAGAAGAGAAAGTGTTGCAAACACGTAAGGGATGTA-TCGGAGGTAAAGGAGATGA
64 TCTTGTAATAAGAAGAGAAAGCGTTGCAAACAAGTAAGGGATGTACT-GGAGGTAAAGGAGAGGA
*
38025240 AGATTGAAGTAGTTCCTGAAGTACTAAATGTTGTGACAGGTGGAAAAGAATAAG
128 AGATTGAAGCAGTTCCTGAAGTACTAAATGTTGTGACAGGTGGAAAAGAATAAG
38025294 TGTTCTAAAT
Statistics
Matches: 164, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
182 4 0.02
183 145 0.88
184 15 0.09
ACGTcount: A:0.41, C:0.08, G:0.29, T:0.23
Consensus pattern (183 bp):
AAAAACTTTGAGTCAGAGTCAGGTAATTCTGAAAGTGAAATAGAAAAAAAACGTAAAAGGGGTTC
TTGTAATAAGAAGAGAAAGCGTTGCAAACAAGTAAGGGATGTACTGGAGGTAAAGGAGAGGAAGA
TTGAAGCAGTTCCTGAAGTACTAAATGTTGTGACAGGTGGAAAAGAATAAGAA
Found at i:38025978 original size:35 final size:35
Alignment explanation
Indices: 38025939--38026053 Score: 149
Period size: 35 Copynumber: 3.3 Consensus size: 35
38025929 TTACTTATTC
* * * *
38025939 TAGTTGTTCTGCTTTAAATAGTACTTCACTTGTTT
1 TAGTTGTTCTGCGTGAAGTAGCACTTCACTTGTTT
* * *
38025974 TAGTTGTTTTGCGTGAAGTAGCGCTTCACTTGTTC
1 TAGTTGTTCTGCGTGAAGTAGCACTTCACTTGTTT
*
38026009 TAGTTATTCTGCGTGAAGTAGCACTTCACTTGTTT
1 TAGTTGTTCTGCGTGAAGTAGCACTTCACTTGTTT
*
38026044 AAGTTGTTCT
1 TAGTTGTTCT
38026054 CTGTACAATA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.46
Consensus pattern (35 bp):
TAGTTGTTCTGCGTGAAGTAGCACTTCACTTGTTT
Found at i:38026010 original size:70 final size:70
Alignment explanation
Indices: 38025920--38026051 Score: 183
Period size: 70 Copynumber: 1.9 Consensus size: 70
38025910 TTCCATATGG
* * * * * * *
38025920 AGTAGTGCTTTACTTATTCTAGTTGTTCTGCTTTAAATAGTACTTCACTTGTTTTAGTTGTTTTG
1 AGTAGCGCTTCACTTATTCTAGTTATTCTGCGTGAAATAGCACTTCACTTGTTTAAGTTGTTTTG
38025985 CGTGA
66 CGTGA
* *
38025990 AGTAGCGCTTCACTTGTTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTGTTTAAGTTGTT
1 AGTAGCGCTTCACTTATTCTAGTTATTCTGCGTGAAATAGCACTTCACTTGTTTAAGTTGTT
38026052 CTCTGTACAA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
70 53 1.00
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (70 bp):
AGTAGCGCTTCACTTATTCTAGTTATTCTGCGTGAAATAGCACTTCACTTGTTTAAGTTGTTTTG
CGTGA
Found at i:38029953 original size:8 final size:8
Alignment explanation
Indices: 38029940--38029966 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
38029930 GTAGCAAATG
38029940 TGATGTGA
1 TGATGTGA
38029948 TGATGTGA
1 TGATGTGA
38029956 TGATGTGA
1 TGATGTGA
38029964 TGA
1 TGA
38029967 CTTTTGAGTC
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:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (8 bp):
TGATGTGA
Found at i:38030414 original size:6 final size:6
Alignment explanation
Indices: 38030405--38030500 Score: 53
Period size: 6 Copynumber: 15.8 Consensus size: 6
38030395 TAATAATTTA
38030405 TAATAT TAATATTT TAATA- T-A-AT TAATAT TAATATT TAATA- TAAT-T
1 TAATAT TAATA--T TAATAT TAATAT TAATAT TAATA-T TAATAT TAATAT
* *
38030451 TAAATTAT TAATATTT TAATAT AAAT-T TAATTAT TAATAT TTA-AT TAATA
1 T-AA-TAT TAATA--T TAATAT TAATAT TAA-TAT TAATAT TAATAT TAATA
38030501 ATATTTTATT
Statistics
Matches: 71, Mismatches: 4, Indels: 30
0.68 0.04 0.29
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 14 0.20
6 27 0.38
7 13 0.18
8 14 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:38030426 original size:33 final size:32
Alignment explanation
Indices: 38030389--38030524 Score: 112
Period size: 31 Copynumber: 4.4 Consensus size: 32
38030379 TTAAAAATAT
38030389 TATAATTAATAATTTATAATATTAATATTTTAA
1 TATAATTAAT-ATTTATAATATTAATATTTTAA
*
38030422 TATAATTAATATTAAT-AT-TTAATATAATTTAA
1 TATAATTAATATTTATAATATTAATAT--TTTAA
*
38030454 -ATTATTAATATTT-TAATA-TAA-A-TTTAA
1 TATAATTAATATTTATAATATTAATATTTTAA
* * *
38030481 T-T-ATTAATATTTA-ATTAATAATATTTTATT
1 TATAATTAATATTTATAATATTAATATTTTA-A
38030511 TATAATTTAATATT
1 TATAA-TTAATATT
38030525 ATTTTGATTA
Statistics
Matches: 85, Mismatches: 5, Indels: 26
0.73 0.04 0.22
Matches are distributed among these distances:
26 13 0.15
27 9 0.11
28 1 0.01
29 4 0.05
30 10 0.12
31 19 0.22
32 11 0.13
33 18 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TATAATTAATATTTATAATATTAATATTTTAA
Found at i:38030429 original size:48 final size:46
Alignment explanation
Indices: 38030354--38030499 Score: 156
Period size: 48 Copynumber: 3.0 Consensus size: 46
38030344 ATTTTATTTT
*
38030354 TTTAAATATTAATAATTATAAT-TAATTAA-A-AATATTATAATTAATAA
1 TTTAAATATTAAT-ATTTTAATATAATTAATATAATATT-TAA-T-ATAA
38030401 TTTATAATATTAATATTTTAATATAATTAATATTAATATTTAATATAA
1 TTTA-AATATTAATATTTTAATATAATTAATA-TAATATTTAATATAA
38030449 TTTAAATTATTAATATTTTAATATAAATTTAATTATTAATATTTAAT-TAA
1 TTTAAA-TATTAATATTTTAATAT-AA-TTAA-TA-TAATATTTAATATAA
38030499 T
1 T
38030500 AATATTTTAT
Statistics
Matches: 89, Mismatches: 1, Indels: 15
0.85 0.01 0.14
Matches are distributed among these distances:
47 13 0.15
48 41 0.46
49 4 0.04
50 11 0.12
51 20 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (46 bp):
TTTAAATATTAATATTTTAATATAATTAATATAATATTTAATATAA
Found at i:38030434 original size:23 final size:23
Alignment explanation
Indices: 38030358--38030525 Score: 124
Period size: 23 Copynumber: 7.3 Consensus size: 23
38030348 TATTTTTTTA
*
38030358 AATATTAATAATTATAAT-TAATTAAA
1 AATATTAAT-ATT-TAATATAATT--T
* *
38030384 AATATT-ATAATTAATA-ATTTAT
1 AATATTAATATTTAATATAATT-T
38030406 AATATTAATATTTTAATATAA-TT
1 AATATTAATA-TTTAATATAATTT
38030429 AATATTAATATTTAATATAATTT
1 AATATTAATATTTAATATAATTT
38030452 AAATTATTAATATTTTAATATAAATTT
1 -AA-TATTAATA-TTTAATAT-AATTT
38030479 AATTATTAATATTTAAT-TAA--T
1 AA-TATTAATATTTAATATAATTT
*
38030500 AATATT-TTA-TT--TATAATTT
1 AATATTAATATTTAATATAATTT
38030519 AATATTA
1 AATATTA
38030526 TTTTGATTAA
Statistics
Matches: 123, Mismatches: 6, Indels: 32
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.01
17 3 0.02
18 2 0.02
19 9 0.07
20 4 0.03
21 3 0.02
22 17 0.14
23 25 0.20
24 12 0.10
25 17 0.14
26 25 0.20
27 5 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTAATATTTAATATAATTT
Found at i:38030482 original size:26 final size:25
Alignment explanation
Indices: 38030370--38030499 Score: 137
Period size: 26 Copynumber: 5.2 Consensus size: 25
38030360 TATTAATAAT
** *
38030370 TATAA-TTAATTAAAAATATTATAA
1 TATAATTTAATTATTAATATTTTAA
*
38030394 TTAATAATTTATAATATTAATATTTTAA
1 -T-ATAATTTA-ATTATTAATATTTTAA
38030422 TATAA-TTAA-TATTAATA-TTTAA
1 TATAATTTAATTATTAATATTTTAA
38030444 TATAATTTAAATTATTAATATTTTAA
1 TATAATTT-AATTATTAATATTTTAA
38030470 TATAAATTTAATTATTAATA-TTTAA
1 TAT-AATTTAATTATTAATATTTTAA
38030495 T-TAAT
1 TATAAT
38030500 AATATTTTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 18
0.81 0.03 0.16
Matches are distributed among these distances:
22 10 0.11
23 13 0.14
24 4 0.04
25 18 0.19
26 27 0.29
27 9 0.10
28 12 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TATAATTTAATTATTAATATTTTAA
Found at i:38030510 original size:51 final size:49
Alignment explanation
Indices: 38030370--38030523 Score: 161
Period size: 51 Copynumber: 3.1 Consensus size: 49
38030360 TATTAATAAT
**
38030370 TATAATTAATTAAAAATATTATAATTAATAAT-TTATAATATTAATATTTTAA
1 TATAATTAATTATTAATATT-TAATTAATAATATT-T--TATTAATATTTTAA
* **
38030422 TATAATTAA-TATTAATATTTAATATAAT-TTAAATTATTAATATTTTAA
1 TATAATTAATTATTAATATTTAAT-TAATAATATTTTATTAATATTTTAA
* *
38030470 TATAAATTTAATTATTAATATTTAATTAATAATATTTTATTTATAATTTAA
1 TAT-AA-TTAATTATTAATATTTAATTAATAATATTTTATTAATATTTTAA
38030521 TAT
1 TAT
38030524 TATTTTGATT
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
48 17 0.20
49 2 0.02
50 14 0.16
51 44 0.51
52 9 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (49 bp):
TATAATTAATTATTAATATTTAATTAATAATATTTTATTAATATTTTAA
Found at i:38030665 original size:16 final size:16
Alignment explanation
Indices: 38030644--38030678 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
38030634 CAAATTTTAA
38030644 TAAAATATTAATAGTT
1 TAAAATATTAATAGTT
*
38030660 TAAAATATTAATATTT
1 TAAAATATTAATAGTT
38030676 TAA
1 TAA
38030679 TATTTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TAAAATATTAATAGTT
Found at i:38034005 original size:17 final size:18
Alignment explanation
Indices: 38033988--38034033 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
38033978 TATTATTATT
38033988 ATTGATAAATTAAAATTA
1 ATTGATAAATTAAAATTA
* *
38034006 ATTTAT-GATTAAAATTA
1 ATTGATAAATTAAAATTA
38034023 ATTAGATAAAT
1 ATT-GATAAAT
38034034 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 13 0.59
18 7 0.32
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (18 bp):
ATTGATAAATTAAAATTA
Found at i:38034131 original size:11 final size:10
Alignment explanation
Indices: 38034106--38034173 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
38034096 TGACATAATA
*
38034106 TTTTTAAAAA
1 TTTTTAAAAT
38034116 TTTTTAAAAT
1 TTTTTAAAAT
38034126 TATTTTAAAA-
1 T-TTTTAAAAT
38034136 TTTTT-AAAT
1 TTTTTAAAAT
*
38034145 TATTTTTAAAT
1 T-TTTTAAAAT
*
38034156 TTTTAAATAAAT
1 TTTT-TA-AAAT
38034168 TTTTTA
1 TTTTTA
38034174 TTATATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
8 3 0.06
9 5 0.10
10 18 0.38
11 14 0.29
12 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:38034144 original size:19 final size:19
Alignment explanation
Indices: 38034107--38034163 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
38034097 GACATAATAT
38034107 TTTTAAAAATTTTTAAAATTA
1 TTTT-AAAATTTTT-AAATTA
38034128 TTTTAAAATTTTTAAATTA
1 TTTTAAAATTTTTAAATTA
*
38034147 TTTTTAAATTTTTAAAT
1 TTTTAAAATTTTTAAAT
38034164 AAATTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 22 0.63
20 9 0.26
21 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAAATTTTTAAATTA
Found at i:38034169 original size:20 final size:20
Alignment explanation
Indices: 38034103--38034171 Score: 79
Period size: 19 Copynumber: 3.4 Consensus size: 20
38034093 TTATGACATA
38034103 ATATTTTTAAAAATTTTTAAA-
1 ATATTTTT--AAATTTTTAAAT
*
38034124 ATTATTTTAAAATTTTTAAAT
1 A-TATTTTTAAATTTTTAAAT
38034145 -TATTTTTAAATTTTTAAAT
1 ATATTTTTAAATTTTTAAAT
*
38034164 AAATTTTT
1 ATATTTTT
38034172 TATTATATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 18 0.43
20 17 0.40
21 1 0.02
22 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTTAAATTTTTAAAT
Found at i:38037760 original size:49 final size:47
Alignment explanation
Indices: 38037669--38037853 Score: 174
Period size: 49 Copynumber: 3.8 Consensus size: 47
38037659 GTGCACACTA
** * * * *
38037669 TTTTAGTAGAATAAATAGAAAACAGCAGGCTATAAAAGGCGCACTCTG
1 TTTTAGTAGCCTAAATAGAAAACAAC-GACTATATAACGCGCACTCTG
* *
38037717 TTTTAATAGCCTAAATAGCAAAACAACGTACTATATAACGCGCACACTG
1 TTTTAGTAGCCTAAATAG-AAAACAACG-ACTATATAACGCGCACTCTG
* * *
38037766 TTTTAGTAGCCTAAATAGGAAACAATGCG-CTGTATAAGGCGCACATTCTG
1 TTTTAGTAGCCTAAATAGAAAACAA--CGACTATATAACGCGCAC--TCTG
* *
38037816 TTTTCGTAGCCTAAATAGAAAACAGCGAGCTATATAAC
1 TTTTAGTAGCCTAAATAGAAAACAACGA-CTATATAAC
38037854 CTAAACCCCA
Statistics
Matches: 111, Mismatches: 18, Indels: 14
0.78 0.13 0.10
Matches are distributed among these distances:
48 37 0.33
49 40 0.36
50 34 0.31
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (47 bp):
TTTTAGTAGCCTAAATAGAAAACAACGACTATATAACGCGCACTCTG
Found at i:38037808 original size:48 final size:47
Alignment explanation
Indices: 38037661--38037852 Score: 183
Period size: 48 Copynumber: 3.9 Consensus size: 47
38037651 TACATATGGT
* ** *
38037661 GCACACTATTTTAGTAGAATAAATAGAAAAC-AGCAGGCTATAAAAGGC
1 GCACACTGTTTTAGTAGCCTAAATAGAAAACAAGC--GCTATATAAGGC
* * *
38037709 GCACTCTGTTTTAATAGCCTAAATAGCAAAACAA-CGTACTATATAACGC
1 GCACACTGTTTTAGTAGCCTAAATAG-AAAACAAGCG--CTATATAAGGC
* *
38037758 GCACACTGTTTTAGTAGCCTAAATAGGAAACAATGCGCTGTATAAGGC
1 GCACACTGTTTTAGTAGCCTAAATAGAAAACAA-GCGCTATATAAGGC
*
38037806 GCACATTCTGTTTTCGTAGCCTAAATAGAAAAC-AGCGAGCTATATAA
1 GCACA--CTGTTTTAGTAGCCTAAATAGAAAACAAGC--GCTATATAA
38037853 CCTAAACCCC
Statistics
Matches: 119, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
47 1 0.01
48 43 0.36
49 40 0.34
50 35 0.29
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.25
Consensus pattern (47 bp):
GCACACTGTTTTAGTAGCCTAAATAGAAAACAAGCGCTATATAAGGC
Found at i:38044315 original size:35 final size:35
Alignment explanation
Indices: 38044269--38044341 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
38044259 CAGCAATCCT
38044269 AAAATTAAAAATCCTTCCTTTCTGCAACAGATGAG
1 AAAATTAAAAATCCTTCCTTTCTGCAACAGATGAG
38044304 AAAATTAAAAATCCTTCCTTTCTGCAACAGATGAG
1 AAAATTAAAAATCCTTCCTTTCTGCAACAGATGAG
38044339 AAA
1 AAA
38044342 CACTTTAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.27
Consensus pattern (35 bp):
AAAATTAAAAATCCTTCCTTTCTGCAACAGATGAG
Found at i:38056708 original size:22 final size:22
Alignment explanation
Indices: 38056676--38056730 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
38056666 CGCCTAGGAC
38056676 AAGTT-AGAACTCTTCCATGAA
1 AAGTTAAGAACTCTTCCATGAA
38056697 AAGTTAAGAACTCTTCCATGAA
1 AAGTTAAGAACTCTTCCATGAA
38056719 AAGTTAAGAACT
1 AAGTTAAGAACT
38056731 GGATTTGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (22 bp):
AAGTTAAGAACTCTTCCATGAA
Found at i:38062457 original size:27 final size:27
Alignment explanation
Indices: 38062427--38062499 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
38062417 CATCATTTGT
38062427 TTAATGTAGAAAATTCATGGGAAGGCG
1 TTAATGTAGAAAATTCATGGGAAGGCG
* *
38062454 TTAAGTATACTTCCAAAATTCATGGGAAGGCG
1 TTAA-TGTA----GAAAATTCATGGGAAGGCG
38062486 TTAATGTAGAAAAT
1 TTAATGTAGAAAAT
38062500 CCAGACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
27 9 0.24
28 3 0.08
31 3 0.08
32 22 0.59
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (27 bp):
TTAATGTAGAAAATTCATGGGAAGGCG
Found at i:38063065 original size:147 final size:147
Alignment explanation
Indices: 38062788--38063087 Score: 537
Period size: 147 Copynumber: 2.0 Consensus size: 147
38062778 GGTCAGCTTC
38062788 TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAATGTGTTTGCATGT
1 TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAATGTGTTTGCATGT
* *
38062853 ATCAGTCAATGGAACTGTGATTCTTTGTCTTTCTTTCTTTTTCTGAAACTTTTTGTGTGGGGTTG
66 ATCAGTCAATGGAACTGTGATTCTTTGTCTCTCTTTCTTTTTCTGAAACATTTTGTGTGGGGTTG
38062918 GACCCAAAGATATTTTT
131 GACCCAAAGATATTTTT
* * *
38062935 TCATGTTCTGTCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAATGTGTTTGCGTGT
1 TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAATGTGTTTGCATGT
*
38063000 ATCAGTCAATGGAACTGTGATTCTTTGTCTCTCTTTCTTTTTCTGAAACATTTTGTTTGGGGTTG
66 ATCAGTCAATGGAACTGTGATTCTTTGTCTCTCTTTCTTTTTCTGAAACATTTTGTGTGGGGTTG
38063065 GACCCAAAGATATTTTT
131 GACCCAAAGATATTTTT
38063082 TGCATA
1 T-CATA
38063088 GTAGTTTGTT
Statistics
Matches: 145, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
147 142 0.98
148 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (147 bp):
TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAATGTGTTTGCATGT
ATCAGTCAATGGAACTGTGATTCTTTGTCTCTCTTTCTTTTTCTGAAACATTTTGTGTGGGGTTG
GACCCAAAGATATTTTT
Found at i:38082906 original size:21 final size:21
Alignment explanation
Indices: 38082881--38082940 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
38082871 GGCCCATGTG
* *
38082881 ACCCATTTGACTCATATTATA
1 ACCCATCTGACCCATATTATA
38082902 ACCCATCTGACCCATATTATTGTA
1 ACCCATCTGACCCATATTA---TA
38082926 ACCCATCTGACCCAT
1 ACCCATCTGACCCAT
38082941 CTGACCACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 17 0.50
24 17 0.50
ACGTcount: A:0.30, C:0.32, G:0.07, T:0.32
Consensus pattern (21 bp):
ACCCATCTGACCCATATTATA
Found at i:38082927 original size:24 final size:24
Alignment explanation
Indices: 38082895--38082940 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
38082885 ATTTGACTCA
38082895 TATTATAACCCATCTGACCCATAT
1 TATTATAACCCATCTGACCCATAT
*
38082919 TATTGTAACCCATCTGACCCAT
1 TATTATAACCCATCTGACCCAT
38082941 CTGACCACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (24 bp):
TATTATAACCCATCTGACCCATAT
Found at i:38083580 original size:12 final size:12
Alignment explanation
Indices: 38083563--38083628 Score: 75
Period size: 12 Copynumber: 5.8 Consensus size: 12
38083553 TTCCTCCTCA
38083563 TCATCATCAAAC
1 TCATCATCAAAC
*
38083575 TCATCATCAAAT
1 TCATCATCAAAC
* *
38083587 TCATCACCGAAC
1 TCATCATCAAAC
*
38083599 TCATCATCGAAC
1 TCATCATCAAAC
38083611 TCATCAT--AA-
1 TCATCATCAAAC
38083620 TCATCATCA
1 TCATCATCA
38083629 GAGTCATCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
9 7 0.15
10 2 0.04
12 38 0.81
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.27
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:38083592 original size:21 final size:21
Alignment explanation
Indices: 38083566--38083645 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
38083556 CTCCTCATCA
*
38083566 TCATCA-AACTCATCATCAAAT
1 TCATCACAA-TCATCATCAAAC
*
38083587 TCATCACCGAACTCATCATCGAAC
1 TCATCA-C-AA-TCATCATCAAAC
* * *
38083611 TCATCATAATCATCATCAGAG
1 TCATCACAATCATCATCAAAC
38083632 TCATCTA-AATCATC
1 TCATC-ACAATCATC
38083646 CTCAGGCAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
21 27 0.55
22 3 0.06
24 19 0.39
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.28
Consensus pattern (21 bp):
TCATCACAATCATCATCAAAC
Found at i:38094064 original size:2 final size:2
Alignment explanation
Indices: 38094051--38094099 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
38094041 ATCAACATTC
*
38094051 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38094093 AT AT AT A
1 AT AT AT A
38094100 GATAAAACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38095551 original size:41 final size:41
Alignment explanation
Indices: 38095483--38095593 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
38095473 CATTAATATC
* * **
38095483 AAAGTAAACTCGAATCTTCATAGATGTGAGCAGAGTCAGAT
1 AAAGTAAACTCGAATCTTCACAAATGTGAGCAGACCCAGAT
* * * * *
38095524 AAAGTAAACTTGAATATTTACAAATGTGAGTAGACCCGGAT
1 AAAGTAAACTCGAATCTTCACAAATGTGAGCAGACCCAGAT
38095565 AAAGTAAACTCGAATCTTCACAAATGTGA
1 AAAGTAAACTCGAATCTTCACAAATGTGA
38095594 CTAGATAGAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (41 bp):
AAAGTAAACTCGAATCTTCACAAATGTGAGCAGACCCAGAT
Found at i:38110763 original size:15 final size:15
Alignment explanation
Indices: 38110740--38110797 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
38110730 ACACTTATTT
*
38110740 TAAAAAATAAAAAAA
1 TAAATAATAAAAAAA
**
38110755 TAAATAATAATGAAA
1 TAAATAATAAAAAAA
*
38110770 TATAATAA-AAAATAA
1 TA-AATAATAAAAAAA
38110785 TAAAT--TAAAAAAA
1 TAAATAATAAAAAAA
38110798 GAAAGGAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
13 6 0.18
14 3 0.09
15 20 0.59
16 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAATAATAAAAAAA
Found at i:38110778 original size:20 final size:19
Alignment explanation
Indices: 38110741--38110797 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 19
38110731 CACTTATTTT
*
38110741 AAAA-AATAAA-AAAATAA
1 AAAATAATAAATATAATAA
*
38110758 ATAATAATGAAATATAATAA
1 AAAATAAT-AAATATAATAA
38110778 AAAATAATAAAT-TAA-AA
1 AAAATAATAAATATAATAA
38110795 AAA
1 AAA
38110798 GAAAGGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 7 0.21
20 13 0.38
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAATAAATATAATAA
Found at i:38114665 original size:23 final size:23
Alignment explanation
Indices: 38114639--38114688 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
38114629 TTTTTTACGC
*
38114639 TTTAAAATTA-AAAATATTACATA
1 TTTAAAATTATAAAATATTA-AAA
*
38114662 TTT-ATATTATAAAATATTAAAA
1 TTTAAAATTATAAAATATTAAAA
38114684 TTTAA
1 TTTAA
38114689 TATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAAAATTATAAAATATTAAAA
Found at i:38116268 original size:3 final size:3
Alignment explanation
Indices: 38116260--38116297 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
38116250 AATGAGCTCT
38116260 ATA ATA ATA ATA ATA ATA ATA ACT- ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA AT
38116298 GATGATGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:38118557 original size:14 final size:14
Alignment explanation
Indices: 38118538--38118567 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38118528 CCAGCTTGGA
*
38118538 AAAGAAAAGCAAAT
1 AAAGAAAAGAAAAT
38118552 AAAGAAAAGAAAAT
1 AAAGAAAAGAAAAT
38118566 AA
1 AA
38118568 GGGTTTTCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (14 bp):
AAAGAAAAGAAAAT
Found at i:38125502 original size:165 final size:166
Alignment explanation
Indices: 38125230--38125559 Score: 637
Period size: 165 Copynumber: 2.0 Consensus size: 166
38125220 GGTAGCTTAG
38125230 GATGCCACGTGTACGGTCTTGAATCATCCATGAAGGTGCTCTTTCCAAATGCATGATGACAAACT
1 GATGCCACGTGTACGGTCTTGAATCATCCATGAAGGTGCTCTTTCCAAATGCATGATGACAAACT
38125295 TCCTCCTTTATGTCATTTCCATTCAACAGGTGGGGAGGATTGTTAAACGTTAATCAGGGCAAAGA
66 TCCTCCTTTATGTCATTTCCATTCAACAGGTGGGGAGGATTGTTAAACGTTAATCAGGGCAAAGA
38125360 TCCTACTGCA-G-GGAGAGAGAGAGAGAGAGAGAGA
131 TCCTACTGCAGGAGGAGAGAGAGAGAGAGAGAGAGA
38125394 NGATGCCACGTGTACGGTCTTGAATCATCCATGAAGGTGCTCTTTCCAAATGCATGATGACAAAC
1 -GATGCCACGTGTACGGTCTTGAATCATCCATGAAGGTGCTCTTTCCAAATGCATGATGACAAAC
38125459 TTCCTCCTTTATGTCATTTCCATTCAACAGGTGGGGAGGATTGTTAAACGTTAATCAGGGCAAAG
65 TTCCTCCTTTATGTCATTTCCATTCAACAGGTGGGGAGGATTGTTAAACGTTAATCAGGGCAAAG
38125524 ATCCTACTGCAGGAGGAGAGAGAGAGAGAGAGAGAG
130 ATCCTACTGCAGGAGGAGAGAGAGAGAGAGAGAGAG
38125560 GACTGACTGA
Statistics
Matches: 163, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
165 140 0.86
166 1 0.01
167 22 0.13
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (166 bp):
GATGCCACGTGTACGGTCTTGAATCATCCATGAAGGTGCTCTTTCCAAATGCATGATGACAAACT
TCCTCCTTTATGTCATTTCCATTCAACAGGTGGGGAGGATTGTTAAACGTTAATCAGGGCAAAGA
TCCTACTGCAGGAGGAGAGAGAGAGAGAGAGAGAGA
Found at i:38128621 original size:2 final size:2
Alignment explanation
Indices: 38128614--38128650 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38128604 CTTCAAAAAT
38128614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38128651 TTAATTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38128733 original size:2 final size:2
Alignment explanation
Indices: 38128726--38128763 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
38128716 AAAGAAANTA
38128726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38128764 TAATTCTAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38133505 original size:5 final size:5
Alignment explanation
Indices: 38133495--38133526 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
38133485 GGCAGCCTTC
38133495 TTCTT TTCTT TTCTT TTCTT TT-TT TT-TT TTCT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCT
38133527 GTTTTGATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTCTT
Found at i:38133519 original size:18 final size:18
Alignment explanation
Indices: 38133492--38133526 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38133482 AATGGCAGCC
38133492 TTCTTCTTTTCTTTTCTT
1 TTCTTCTTTTCTTTTCTT
* *
38133510 TTCTTTTTTTTTTTTCT
1 TTCTTCTTTTCTTTTCT
38133527 GTTTTGATCT
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTCTTCTTTTCTTTTCTT
Found at i:38138518 original size:86 final size:86
Alignment explanation
Indices: 38138371--38138543 Score: 314
Period size: 86 Copynumber: 2.0 Consensus size: 86
38138361 GAGTGGGAAA
38138371 AACAAAGCATATATATATATATATATATATAGAAAAGAAAAAAAGAAAAATACAGAAAGAGATAC
1 AACAAAGCATATATATATATATATATATATAGAAAAGAAAAAAAGAAAAATACAGAAAGAGATAC
38138436 AAAATTAAGCTTTTTTAACAAC
66 AAAATTAAGC-TTTTTAACAAC
38138458 NAACAAAGCATATATATATATATATATATATAG-AAAG-AAAAAAGAAAAATACAGAAAGAGATA
1 -AACAAAGCATATATATATATATATATATATAGAAAAGAAAAAAAGAAAAATACAGAAAGAGATA
38138521 CAAAATTAAGCTTTTTAACAAC
65 CAAAATTAAGCTTTTTAACAAC
38138543 A
1 A
38138544 TATATGCTAT
Statistics
Matches: 85, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
84 1 0.01
85 11 0.13
86 37 0.44
87 4 0.05
88 32 0.38
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.24
Consensus pattern (86 bp):
AACAAAGCATATATATATATATATATATATAGAAAAGAAAAAAAGAAAAATACAGAAAGAGATAC
AAAATTAAGCTTTTTAACAAC
Found at i:38156692 original size:34 final size:35
Alignment explanation
Indices: 38156648--38156719 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 35
38156638 TAGAATCAAC
*
38156648 AACAATAAACATAATAATCTGATGTTCGCACAAGG
1 AACAATAAACATAATAATCGGATGTTCGCACAAGG
*
38156683 AACAA-AAACATAATAATCGGATGTTTGCACAAGG
1 AACAATAAACATAATAATCGGATGTTCGCACAAGG
38156717 AAC
1 AAC
38156720 GTGACAAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 30 0.86
35 5 0.14
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (35 bp):
AACAATAAACATAATAATCGGATGTTCGCACAAGG
Found at i:38159910 original size:22 final size:23
Alignment explanation
Indices: 38159885--38159936 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
38159875 CGTGGATAAA
38159885 AAAATTAAT-TA-AATATTAAATT
1 AAAATTAATGTATAAT-TTAAATT
**
38159907 AAAA-TAATGTATAATTTTTATT
1 AAAATTAATGTATAATTTAAATT
38159929 AAAATTAA
1 AAAATTAA
38159937 AATTTATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 15 0.60
23 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATTAATGTATAATTTAAATT
Found at i:38159971 original size:21 final size:22
Alignment explanation
Indices: 38159927--38159973 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
38159917 ATAATTTTTA
* * *
38159927 TTAAAATTAAAATTTATTTGAT
1 TTAAAATAAAAATTTATATAAT
38159949 TTAAAATAAAAATTTA-ATAAT
1 TTAAAATAAAAATTTATATAAT
38159970 TTAA
1 TTAA
38159974 TTTTTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAAAATAAAAATTTATATAAT
Found at i:38165548 original size:20 final size:20
Alignment explanation
Indices: 38165525--38165571 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
38165515 TTTTTATTAC
38165525 TTGTTTCATTCATACAAATA
1 TTGTTTCATTCATACAAATA
38165545 TTGTTTCATTCATACAAATA
1 TTGTTTCATTCATACAAATA
38165565 TTGTTTC
1 TTGTTTC
38165572 TGATATTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (20 bp):
TTGTTTCATTCATACAAATA
Found at i:38169710 original size:60 final size:59
Alignment explanation
Indices: 38169613--38169726 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
38169603 ATTTGGAGCA
* *
38169613 TTTTGGAATGATTTTTGATACACGAAATAAACATTTGAGCGTTTTGAGTATTTTTATAT
1 TTTTGGAATGATTTTTGATACACGAAATAAACATTTGAGCATTTTGAGCATTTTTATAT
* * *
38169672 TTTTTGAAGTGATTTTTGATACATGAAGA-AAACGTTTGAGCATTTTGAGCATTTT
1 TTTTGGAA-TGATTTTTGATACACGAA-ATAAACATTTGAGCATTTTGAGCATTTT
38169727 CAATATGGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 7 0.15
60 40 0.83
61 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (59 bp):
TTTTGGAATGATTTTTGATACACGAAATAAACATTTGAGCATTTTGAGCATTTTTATAT
Found at i:38169959 original size:23 final size:23
Alignment explanation
Indices: 38169896--38169959 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
38169886 AGTTGATATG
* * *
38169896 GCATTACGTGACTGGTAAGTAAA
1 GCATTACGTGATTGATTAGTAAA
*
38169919 GCATTACTTTGATTGATTAGTAAA
1 GCATTAC-GTGATTGATTAGTAAA
*
38169943 GTATTACGTGATTGATT
1 GCATTACGTGATTGATT
38169960 TTTAGGTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (23 bp):
GCATTACGTGATTGATTAGTAAA
Found at i:38175486 original size:17 final size:17
Alignment explanation
Indices: 38175466--38175513 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
38175456 AATTTGAAAA
38175466 TTAATTAAATTATTAAT
1 TTAATTAAATTATTAAT
* *
38175483 TTAATTTAAGTATT-A-
1 TTAATTAAATTATTAAT
38175498 TTAA-TAAATTATTAAT
1 TTAATTAAATTATTAAT
38175514 AAATAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
14 7 0.28
15 5 0.20
16 1 0.04
17 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAATTAAATTATTAAT
Found at i:38175518 original size:15 final size:16
Alignment explanation
Indices: 38175500--38175539 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
38175490 AAGTATTATT
*
38175500 AATAAATTATT-AATA
1 AATAAATAATTCAATA
38175515 AATAAATAATTCAATA
1 AATAAATAATTCAATA
38175531 AAT-AATAAT
1 AATAAATAAT
38175540 AATTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAATAATTCAATA
Found at i:38183015 original size:83 final size:82
Alignment explanation
Indices: 38182859--38183108 Score: 349
Period size: 83 Copynumber: 3.0 Consensus size: 82
38182849 TACATTGCTC
* * *
38182859 TGGTGAGAT-TTGGTCCCATGGATGTAATGTGTGGCCTTGATGAGAACATCAAGAATTTGAGTGG
1 TGGTGAGATCTTAGTCCCATGGATGTAATGTGTGGCCTTGATGAGGACATCAAGGATTTGAGTGG
*
38182923 GTGGGATTGTAATAAACT
66 GT-GAATTGTAATAAACT
*
38182941 TGGTGAGATCTTAGTCTCATGGATGTAATGTGTGGCCTTGATGAGGACATCAAGGATTTGAGTGG
1 TGGTGAGATCTTAGTCCCATGGATGTAATGTGTGGCCTTGATGAGGACATCAAGGATTTGAGTGG
38183006 GTAGAATTGTAATAAACT
66 GT-GAATTGTAATAAACT
* * * * * * * *
38183024 TAGTGAGATCTTAGTCCCGTAGATGCAATGTATGGCATTGATGAAGACATCAAGGATTTGAGTAG
1 TGGTGAGATCTTAGTCCCATGGATGTAATGTGTGGCCTTGATGAGGACATCAAGGATTTGAGTGG
38183089 GTGAAATTGTAATAAACT
66 GTG-AATTGTAATAAACT
38183107 TG
1 TG
38183109 AACTTAAGTT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
82 10 0.07
83 140 0.93
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (82 bp):
TGGTGAGATCTTAGTCCCATGGATGTAATGTGTGGCCTTGATGAGGACATCAAGGATTTGAGTGG
GTGAATTGTAATAAACT
Found at i:38183172 original size:44 final size:44
Alignment explanation
Indices: 38183102--38183186 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
38183092 AAATTGTAAT
** *
38183102 AAACTTGAACTTAAGTTACGTGGTTTAGGCCCAAAAAGATGCTG
1 AAACTTGAACTTAAGCCACGTAGTTTAGGCCCAAAAAGATGCTG
*
38183146 AAACTTGAACTTAAGCCACGTAGTTTAGGCCCAAAATGATG
1 AAACTTGAACTTAAGCCACGTAGTTTAGGCCCAAAAAGATG
38183187 TTGGGTCAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (44 bp):
AAACTTGAACTTAAGCCACGTAGTTTAGGCCCAAAAAGATGCTG
Found at i:38188001 original size:30 final size:30
Alignment explanation
Indices: 38187967--38188026 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
38187957 TAAAACCCTT
38187967 GAAATTGCCGAAG-AAGAGGAGATTGAGGAA
1 GAAATTGCC-AAGAAAGAGGAGATTGAGGAA
38187997 GAAATTGCCAAGAAAGAGGAGATTGAGGAA
1 GAAATTGCCAAGAAAGAGGAGATTGAGGAA
38188027 AAAGATGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.45, C:0.07, G:0.35, T:0.13
Consensus pattern (30 bp):
GAAATTGCCAAGAAAGAGGAGATTGAGGAA
Found at i:38188061 original size:78 final size:78
Alignment explanation
Indices: 38187923--38188137 Score: 304
Period size: 78 Copynumber: 2.8 Consensus size: 78
38187913 GCCCTTGCAG
* * * ** *
38187923 CTGCCAAGGAAGAGAAGATTGATGAAGAAGATGCTAAAACCCTTGAAATTGCCGAAGAAGAGGAG
1 CTGCCAAGGAAGAGGAGATTGAGGAAAAAGATGCTAAAACCCTTGAAATTGTTGAGGAAGAGGAG
*
38187988 ATTGAGGAAGAAA
66 ATTGAGGAAAAAA
* * *
38188001 TTGCCAAGAAAGAGGAGATTGAGGAAAAAGATGCTAAAACCCTTGAAACTGTTGAGGAAGAGGAG
1 CTGCCAAGGAAGAGGAGATTGAGGAAAAAGATGCTAAAACCCTTGAAATTGTTGAGGAAGAGGAG
38188066 ATTGAGGAAAAAA
66 ATTGAGGAAAAAA
** * *
38188079 CTGCTGAGGAAGAGGAGACTGAGGAAAAAGATGCTAAAATCCTTGAAATTGTTGAGGAA
1 CTGCCAAGGAAGAGGAGATTGAGGAAAAAGATGCTAAAACCCTTGAAATTGTTGAGGAA
38188138 ATGAACAAAA
Statistics
Matches: 120, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 120 1.00
ACGTcount: A:0.43, C:0.10, G:0.30, T:0.17
Consensus pattern (78 bp):
CTGCCAAGGAAGAGGAGATTGAGGAAAAAGATGCTAAAACCCTTGAAATTGTTGAGGAAGAGGAG
ATTGAGGAAAAAA
Found at i:38188087 original size:30 final size:30
Alignment explanation
Indices: 38188046--38188107 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
38188036 AAAACCCTTG
* *
38188046 AAACTGTTGAGGAAGAGGAGATTGAGGAAA
1 AAACTGCTGAGGAAGAGGAGACTGAGGAAA
38188076 AAACTGCTGAGGAAGAGGAGACTGAGGAAA
1 AAACTGCTGAGGAAGAGGAGACTGAGGAAA
38188106 AA
1 AA
38188108 GATGCTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.35, T:0.13
Consensus pattern (30 bp):
AAACTGCTGAGGAAGAGGAGACTGAGGAAA
Found at i:38188547 original size:62 final size:62
Alignment explanation
Indices: 38188429--38188546 Score: 145
Period size: 62 Copynumber: 1.9 Consensus size: 62
38188419 TAAAATTTAT
*
38188429 TAATGATTATAAATATAATTTTAAATTTTAATTTATAAATTTATAAATTTAATTTTTATCAA
1 TAATGATTATAAATATAATTTTAAATTTTAATTTATAAATTTACAAATTTAATTTTTATCAA
* * *
38188491 TAAT-ATTCATAAATATTATTTTTAATTTCTTATTT-TAAA-TT-CAAATTTAAGTTTTT
1 TAATGATT-ATAAATATAATTTTAAATTT-TAATTTATAAATTTACAAATTTAA-TTTTT
38188547 TTATAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
60 8 0.16
61 10 0.20
62 26 0.53
63 5 0.10
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (62 bp):
TAATGATTATAAATATAATTTTAAATTTTAATTTATAAATTTACAAATTTAATTTTTATCAA
Found at i:38207007 original size:57 final size:57
Alignment explanation
Indices: 38206946--38207061 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
38206936 GAAGAATCCA
38206946 CCTTGTATTATAAATTTATAACTTTCCATATATATTTTTGATTTCCTTGTCTCTTCT
1 CCTTGTATTATAAATTTATAACTTTCCATATATATTTTTGATTTCCTTGTCTCTTCT
* *
38207003 CCTTGTATTATAAATTTATAACTTTCTATATATATTTTTTATTTCCTTGTCTCTTCT
1 CCTTGTATTATAAATTTATAACTTTCCATATATATTTTTGATTTCCTTGTCTCTTCT
38207060 CC
1 CC
38207062 AGGTGAAGTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.55
Consensus pattern (57 bp):
CCTTGTATTATAAATTTATAACTTTCCATATATATTTTTGATTTCCTTGTCTCTTCT
Found at i:38210767 original size:6 final size:6
Alignment explanation
Indices: 38210756--38210783 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38210746 CTTATTTATT
38210756 TATAAA TATAAA TATAAA TATAAA TATA
1 TATAAA TATAAA TATAAA TATAAA TATA
38210784 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:38226033 original size:20 final size:19
Alignment explanation
Indices: 38226005--38226045 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
38225995 TTTACATTCC
*
38226005 CTTCCGATTGATAACATTT
1 CTTCCGATTGATAACACTT
*
38226024 CTTCCTGATTTATAACACTT
1 CTTCC-GATTGATAACACTT
38226044 CT
1 CT
38226046 CGTCTCTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.44
Consensus pattern (19 bp):
CTTCCGATTGATAACACTT
Found at i:38236759 original size:173 final size:170
Alignment explanation
Indices: 38236440--38236806 Score: 495
Period size: 174 Copynumber: 2.1 Consensus size: 170
38236430 AGTACAGGGA
* * * *
38236440 TTACCAATTTTTCCATATTGTTCTGAAGAAAACCTATATTCTAAAGAGAAATTTCTTCACCCTTT
1 TTACCAGTATTTCCATATTGTTCTAAAGAAAACCTATATTCTAAAGAGAAATATCTTCACCCTTT
* * *
38236505 CTGGATGTTTCAGGACTACCCAGGAAAGACATTGCTAATTCAAATGTTTACGAAAGGCTTGATAT
66 CTGGATGTTTCAGGACTACCCAGGAAAGACATTGCTAATTAAAATGTTTACGAAAGGCTGGATAC
* * *
38236570 ATGCCCTTTTTTTTTTTTTTCCATATTGTTAGTTCAAATG
131 ATGCCTTTTTTTTTTTTTTTCCATATTGTTAGTTAAAATC
* * * *
38236610 TTACCAGTATTTCCATAATGTTCTTAAAGGAAACCTATTTTTCTATAGAGAAATATCTTCACCCT
1 TTACCAGTATTTCCATATTGTTC-TAAAGAAAACCTA-TATTCTAAAGAGAAATATCTTCACCCT
* * * *
38236675 TT-TCGGATGTTTCAGGAACTACCCTGGAAAGACATTGTTAGTTAAAATGTTTATGAAAGGCTGG
64 TTCT-GGATGTTTCAGG-ACTACCCAGGAAAGACATTGCTAATTAAAATGTTTACGAAAGGCTGG
*
38236739 ATACATG-CTTCTTCTTTTTTTTTTTCCATATTGTTATTTAAAATC
127 ATACATGCCTT-TT-TTTTTTTTTTTCCATATTGTTAGTTAAAATC
38236784 TTACCAGTATTTCCATATTGTTC
1 TTACCAGTATTTCCATATTGTTC
38236807 AAATGTTTGA
Statistics
Matches: 171, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
170 20 0.12
171 12 0.07
172 40 0.23
173 49 0.29
174 50 0.29
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (170 bp):
TTACCAGTATTTCCATATTGTTCTAAAGAAAACCTATATTCTAAAGAGAAATATCTTCACCCTTT
CTGGATGTTTCAGGACTACCCAGGAAAGACATTGCTAATTAAAATGTTTACGAAAGGCTGGATAC
ATGCCTTTTTTTTTTTTTTTCCATATTGTTAGTTAAAATC
Found at i:38240352 original size:161 final size:160
Alignment explanation
Indices: 38240078--38240399 Score: 405
Period size: 161 Copynumber: 2.0 Consensus size: 160
38240068 AATGGTACTT
* * * ** * * *** *
38240078 AATTGATTTGGAAACCCTAGACCTGAGTTCTAAACTGCTGTACATGGTTTATAGTAACTCACTGG
1 AATTAATTCGGAAACCCTAAACCCAAGTTCAAAACTGCTGCACACAATTCATAGTAACTCACTGG
* ** * *
38240143 CATATACTAGTGATACTACTGGTAATTAGACAATTCTTATGCCATTTTCTGAAACAATCATTTGA
66 CATATACTAGTGATACTACTGGTAATTAGACAATTCTCATAACATTTTCCGAAACAATCAGTTGA
* *
38240208 TGCACCATTCAAAACAACAGAAGAAGTAGG
131 CGCACCAGTCAAAACAACAGAAGAAGTAGG
38240238 AATTAATTCGGAAACCCTAAACCCAAGTTCAAAACTGCTGCACACAATTCATAG-AACTCACTGG
1 AATTAATTCGGAAACCCTAAACCCAAGTTCAAAACTGCTGCACACAATTCATAGTAACTCACTGG
* * * *
38240302 CTTTTACTAGT-ACTGCTGCTGGCCTAATTAGACAATTCTCATAACATTTTCCGAAACAATCAGT
66 CATATACTAGTGA-TACTACTGG--TAATTAGACAATTCTCATAACATTTTCCGAAACAATCAGT
38240366 TGACGCACCAGTCAAAACAACAGAAGAAGTAGG
128 TGACGCACCAGTCAAAACAACAGAAGAAGTAGG
38240399 A
1 A
38240400 CCATCGGCAT
Statistics
Matches: 137, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
158 1 0.01
159 26 0.19
160 43 0.31
161 67 0.49
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (160 bp):
AATTAATTCGGAAACCCTAAACCCAAGTTCAAAACTGCTGCACACAATTCATAGTAACTCACTGG
CATATACTAGTGATACTACTGGTAATTAGACAATTCTCATAACATTTTCCGAAACAATCAGTTGA
CGCACCAGTCAAAACAACAGAAGAAGTAGG
Found at i:38243980 original size:73 final size:73
Alignment explanation
Indices: 38243903--38244074 Score: 197
Period size: 73 Copynumber: 2.4 Consensus size: 73
38243893 TTATGACTCG
** * *
38243903 AACTTGAAATCTT-TAAGATATCTTGTTCAACCTTTCT-CACTTTTCTGCTGCAAGAAGAGAATA
1 AACTTGAAAT-TTCTAAGATATCTTACT-AACCTTTCTCCACTTTTATACTGCAAGAAGAGAATA
38243966 TTAGGATTGC
64 TTAGGATTGC
* *
38243976 AACTTGAAATTTCTAAGATATCTTACTAACCTTTTTCCACTTTTATATTGCAAGAAGAGAATATT
1 AACTTGAAATTTCTAAGATATCTTACTAACCTTTCTCCACTTTTATACTGCAAGAAGAGAATATT
* * *
38244041 A-CAATCC
66 AGGATTGC
* *
38244048 AAATTTGAAATTTCTAAAATATCTTAC
1 -AACTTGAAATTTCTAAGATATCTTAC
38244075 ATACTAACTC
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
72 13 0.15
73 72 0.85
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (73 bp):
AACTTGAAATTTCTAAGATATCTTACTAACCTTTCTCCACTTTTATACTGCAAGAAGAGAATATT
AGGATTGC
Found at i:38249671 original size:2 final size:2
Alignment explanation
Indices: 38249655--38249691 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
38249645 ACGACACTTT
* *
38249655 TC TC TC CC TC CC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38249692 ACTACCACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:38254241 original size:93 final size:93
Alignment explanation
Indices: 38254181--38254350 Score: 227
Period size: 93 Copynumber: 1.8 Consensus size: 93
38254171 TGCTCTGTCG
*
38254181 ATTAATTTAGCTTCTCCAATGAA-ACGACAAAGATTAAATGCTTGTGCTAAGACAGAGACAAGTC
1 ATTAATTTAGCTTCTCCAATGAAGA-GACAAAGATTAAATGCTTGTGCTAATACAGAGACAAGTC
*
38254245 ACCTCACTGAGAATATCTCTAGTAATCCA
65 ACCTCACCGAGAATATCTCTAGTAATCCA
* * ** * *
38254274 ATTAATTTAGTTTCTCCTATGAAGAGACGGAGATTAAATGCTTGTGCTGATACAGAG-CAAAGCC
1 ATTAATTTAGCTTCTCCAATGAAGAGACAAAGATTAAATGCTTGTGCTAATACAGAGAC-AAGTC
*
38254338 ACCTCACTGAGAA
65 ACCTCACCGAGAA
38254351 GATTTCCGCT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
92 1 0.01
93 66 0.97
94 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (93 bp):
ATTAATTTAGCTTCTCCAATGAAGAGACAAAGATTAAATGCTTGTGCTAATACAGAGACAAGTCA
CCTCACCGAGAATATCTCTAGTAATCCA
Found at i:38257258 original size:12 final size:12
Alignment explanation
Indices: 38257233--38257265 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
38257223 GTAACATCAA
38257233 TTTTATTTT-AT
1 TTTTATTTTAAT
38257244 TTTT-TTTTAAT
1 TTTTATTTTAAT
38257255 TTTTATTTTAA
1 TTTTATTTTAA
38257266 AATTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 10 0.50
12 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTAAT
Found at i:38258809 original size:2 final size:2
Alignment explanation
Indices: 38258792--38258825 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
38258782 ACTTTGAAAC
*
38258792 AT AT TT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38258826 AACAAGTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:38258988 original size:2 final size:2
Alignment explanation
Indices: 38258981--38259009 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38258971 TGTGCAATTA
38258981 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38259010 TNAGTGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:38259106 original size:182 final size:184
Alignment explanation
Indices: 38258797--38259193 Score: 703
Period size: 182 Copynumber: 2.2 Consensus size: 184
38258787 GAAACATATT
38258797 TATATATTATATATATATATATATATATAAACAAGTGAGAATACATATTCGAGATTTTAAAAAAT
1 TATATA-TATATATATATATATATATATAAACAAGTGAGAATACATATTCGAGATTTTAAAAAAT
38258862 TATTATATATATAATTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACA
65 TATTATATATATAATTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACA
*
38258927 AGCAAATGAAGCAACAAATTAATGACATATATGCCGTACGTTAATGTGCA-ATTAA
130 AGCAAATGAAGCAACAAAATAATGACATATATGCCGTACGTTAATGTGCATA-TAA
***
38258982 TATATATATATATATATATAT-TATAT-ATTNAGTGAGAATACATATTCGAGATTTTAAAAAATT
1 TATATATATATATATATATATATATATAAACAAGTGAGAATACATATTCGAGATTTTAAAAAATT
38259045 ATTATATATATAATTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAA
66 ATTATATATATAATTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAA
38259110 GCAAATGAAGCAACAAAATAATGACATATATGCCGTACGTTAATGTGCATATAA
131 GCAAATGAAGCAACAAAATAATGACATATATGCCGTACGTTAATGTGCATATAA
38259164 TATATATATATATATATATATAGT-TATAAA
1 TATATATATATATATATATATA-TATATAAA
38259194 GAGAAGAAAA
Statistics
Matches: 203, Mismatches: 5, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
182 171 0.84
183 9 0.04
184 17 0.08
185 6 0.03
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (184 bp):
TATATATATATATATATATATATATATAAACAAGTGAGAATACATATTCGAGATTTTAAAAAATT
ATTATATATATAATTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAA
GCAAATGAAGCAACAAAATAATGACATATATGCCGTACGTTAATGTGCATATAA
Found at i:38259153 original size:91 final size:91
Alignment explanation
Indices: 38258876--38259154 Score: 229
Period size: 91 Copynumber: 3.1 Consensus size: 91
38258866 ATATATATAA
38258876 TTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAAGCAAATGAAGCAA
1 TTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAAGCAAATGAAGCAA
*
38258941 CAAATTAATGACATATATGCCGTACG
66 CAAAATAATGACATATATGCCGTACG
* * * * * * * * * *
38258967 TTAATGTG-CAATTAATATATATATATATATAT-AT-ATTATA-TATTNAGTGAGAATACATATT
1 TTAATG-GACAATTATTGTTTATGT-TATCT-TCATCATTAAAGTATT-A-TAACAA-GCA-AAT
** * * * *
38259028 CG-AG-ATTTTAAAA-AATTATTATATAT---ATA-A
59 -GAAGCA--ACAAAATAATGA-CATATATGCCGTACG
38259058 TTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAAGCAAATGAAGCAA
1 TTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAAGCAAATGAAGCAA
38259123 CAAAATAATGACATATATGCCGTACG
66 CAAAATAATGACATATATGCCGTACG
38259149 TTAATG
1 TTAATG
38259155 TGCATATAAT
Statistics
Matches: 133, Mismatches: 33, Indels: 44
0.63 0.16 0.21
Matches are distributed among these distances:
87 11 0.08
88 8 0.06
89 4 0.03
90 17 0.13
91 54 0.41
92 17 0.13
93 4 0.03
94 8 0.06
95 10 0.08
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (91 bp):
TTAATGGACAATTATTGTTTATGTTATCTTCATCATTAAAGTATTATAACAAGCAAATGAAGCAA
CAAAATAATGACATATATGCCGTACG
Found at i:38267119 original size:31 final size:31
Alignment explanation
Indices: 38267076--38267137 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
38267066 ATCTTCCAAT
*
38267076 AATTGGTACACGTTAGCTTTTCTTTAAAAAA
1 AATTAGTACACGTTAGCTTTTCTTTAAAAAA
38267107 AATTAGTACACGTTAGCTTTTCTTTAAAAAA
1 AATTAGTACACGTTAGCTTTTCTTTAAAAAA
38267138 TTAAGTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (31 bp):
AATTAGTACACGTTAGCTTTTCTTTAAAAAA
Found at i:38275893 original size:86 final size:86
Alignment explanation
Indices: 38275780--38275976 Score: 299
Period size: 86 Copynumber: 2.3 Consensus size: 86
38275770 CCCAAAACAT
*
38275780 AAAAAATAGTAAAACAATGAAACAAAGAAGCAATCATGTGAATTATCAAAGAAAACCCATATTCT
1 AAAAAAT-GTAAAACAA-AAAACAAAGAAGCAATCATGTGAATTATCAAAGAAAACCCATATTCT
*
38275845 TAAACCCCAGAAGCAACTTAAA-
64 TAAACCCCAGAAACAACTTAAAG
*
38275867 AAGAAAATGTAAAACAAAAAACAAAGAAGCAATCATGTGACTTATCAAAGAAAACCCATATTCTT
1 AA-AAAATGTAAAACAAAAAACAAAGAAGCAATCATGTGAATTATCAAAGAAAACCCATATTCTT
*
38275932 AAACCCCAGAAATAACTTAAAG
65 AAACCCCAGAAACAACTTAAAG
* *
38275954 AAACAATGTAAAAC-CAAAACAAA
1 AAAAAATGTAAAACAAAAAACAAA
38275977 CCCCCGCCCC
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
85 8 0.08
86 76 0.75
87 13 0.13
88 5 0.05
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (86 bp):
AAAAAATGTAAAACAAAAAACAAAGAAGCAATCATGTGAATTATCAAAGAAAACCCATATTCTTA
AACCCCAGAAACAACTTAAAG
Found at i:38277505 original size:68 final size:70
Alignment explanation
Indices: 38277374--38277505 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 70
38277364 TACATTATGC
* ** *
38277374 CGTTAGTTGATTGAAAATAAAATAAATAAGTGAGAAAAAATAGCTGTTGGAGACCATTAAATATA
1 CGTTAGTTGATTGAAAATAAAATAAAT-AGTAAGAAAAAATAGAGGTTAGAGACCATTAAATATA
38277439 TCTTAT
65 TCTTAT
**
38277445 CGTTAGTTGATT-ATAAATAAAA-AAAT-GTAAGAAAAAATAGAGGTTAGAGATTATTAAATAT
1 CGTTAGTTGATTGA-AAATAAAATAAATAGTAAGAAAAAATAGAGGTTAGAGACCATTAAATAT
38277506 GTATTACCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 29 0.54
70 5 0.09
71 20 0.37
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (70 bp):
CGTTAGTTGATTGAAAATAAAATAAATAGTAAGAAAAAATAGAGGTTAGAGACCATTAAATATAT
CTTAT
Found at i:38278978 original size:24 final size:25
Alignment explanation
Indices: 38278951--38279014 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
38278941 ATTTTAATCA
* *
38278951 TTTTTACTTAACATTTAAT-AATTT
1 TTTTTAATTAACATCTAATGAATTT
*
38278975 TTTTTAATTAGCATCTAATGAATTTT
1 TTTTTAATTAACATCTAATGAA-TTT
38279001 TTTTTCAATTAACA
1 TTTTT-AATTAACA
38279015 CCTTATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 16 0.48
25 2 0.06
26 8 0.24
27 7 0.21
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (25 bp):
TTTTTAATTAACATCTAATGAATTT
Found at i:38289080 original size:20 final size:21
Alignment explanation
Indices: 38289051--38289094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38289041 TCACTTAATT
38289051 AATCTCC-TTTAATTTAGAAG
1 AATCTCCTTTTAATTTAGAAG
* *
38289071 AATCTTCTTTTAATTTCGAAG
1 AATCTCCTTTTAATTTAGAAG
38289092 AAT
1 AAT
38289095 GGTTATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (21 bp):
AATCTCCTTTTAATTTAGAAG
Found at i:38292319 original size:78 final size:78
Alignment explanation
Indices: 38292190--38292348 Score: 273
Period size: 78 Copynumber: 2.0 Consensus size: 78
38292180 AATTAACATA
*
38292190 TTCTTCCTCAATCTCCTCTTCCTCGACAGTTTCAAAGGTTTTAGCATCTTCTTCCTCAGTCTCCT
1 TTCTTCCTCAATCTCCTCTTCCTCGACAGTTTCAAAGGTTTTAGCATCTTCTTCCTCAATCTCCT
38292255 CTTCCTCGGCAAT
66 CTTCCTCGGCAAT
* *
38292268 TTCTTCCTCAATCTCCTCTTCCTCGACAGTTTCAAGGGTTTTAGCATCTTCTTCCTCAATCTTCT
1 TTCTTCCTCAATCTCCTCTTCCTCGACAGTTTCAAAGGTTTTAGCATCTTCTTCCTCAATCTCCT
* *
38292333 CTTCCTTGGCAGT
66 CTTCCTCGGCAAT
38292346 TTC
1 TTC
38292349 AAGGGCTTCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.14, C:0.33, G:0.11, T:0.42
Consensus pattern (78 bp):
TTCTTCCTCAATCTCCTCTTCCTCGACAGTTTCAAAGGTTTTAGCATCTTCTTCCTCAATCTCCT
CTTCCTCGGCAAT
Found at i:38309809 original size:29 final size:29
Alignment explanation
Indices: 38309776--38309831 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
38309766 ATTCAAATAA
38309776 ATTTAAATAAGTTCTTATATTTTTATTAC
1 ATTTAAATAAGTTCTTATATTTTTATTAC
* * *
38309805 ATTTAATTAATTTTTTATATTTTTATT
1 ATTTAAATAAGTTCTTATATTTTTATT
38309832 TTGAATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAGTTCTTATATTTTTATTAC
Found at i:38310138 original size:26 final size:25
Alignment explanation
Indices: 38310097--38310148 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
38310087 TTAATCACTT
38310097 ATTTAATTTAAAATAAAAATAAATAA
1 ATTTAATTTAAAATAAAAA-AAATAA
*
38310123 ATTTAA-TTAAATATAATAAAAATAA
1 ATTTAATTTAAA-ATAAAAAAAATAA
38310148 A
1 A
38310149 AATTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTTAATTTAAAATAAAAAAAATAA
Found at i:38310172 original size:31 final size:30
Alignment explanation
Indices: 38310102--38310189 Score: 74
Period size: 30 Copynumber: 2.9 Consensus size: 30
38310092 CACTTATTTA
38310102 ATTTAAAATAAAAATAAATAA--ATTTAATT
1 ATTTAAAATAAAAATAAA-AATTATTTAATT
** *
38310131 AAATATAATAAAAATAAAAATTTATTTAATT
1 ATTTAAAATAAAAATAAAAA-TTATTTAATT
* **
38310162 TTTTAAAAT-AATTTAAAAACTTATTTAA
1 ATTTAAAATAAAAATAAAAA-TTATTTAA
38310190 ACACTATGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
28 2 0.04
29 15 0.33
30 16 0.35
31 13 0.28
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
ATTTAAAATAAAAATAAAAATTATTTAATT
Found at i:38311119 original size:21 final size:21
Alignment explanation
Indices: 38311095--38311137 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
38311085 TATTGTTTCT
*
38311095 TAAAATTATAAAAGTCCGACA
1 TAAAATTATAAAAGCCCGACA
*
38311116 TAAAATTATAAATGCCCGACA
1 TAAAATTATAAAAGCCCGACA
38311137 T
1 T
38311138 TAACTAGATC
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:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (21 bp):
TAAAATTATAAAAGCCCGACA
Found at i:38314799 original size:15 final size:15
Alignment explanation
Indices: 38314779--38314813 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
38314769 GAATTTTCAT
38314779 TATCACTTTCGTCAA
1 TATCACTTTCGTCAA
*
38314794 TATCACTTTCTTCAA
1 TATCACTTTCGTCAA
38314809 TATCA
1 TATCA
38314814 TTCAAATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.43
Consensus pattern (15 bp):
TATCACTTTCGTCAA
Found at i:38317981 original size:16 final size:16
Alignment explanation
Indices: 38317960--38318002 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
38317950 TGATAATTTT
38317960 TTATTAATTTTAAAAA
1 TTATTAATTTTAAAAA
* *
38317976 TTATTAAATTATATAAA
1 TTATT-AATTTTAAAAA
38317993 TTA-TAATTTT
1 TTATTAATTTT
38318003 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATTTTAAAAA
Found at i:38338107 original size:2 final size:2
Alignment explanation
Indices: 38338060--38338095 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
38338050 CCTCACAGTT
38338060 TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38338096 GTGCTCCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:38347085 original size:22 final size:20
Alignment explanation
Indices: 38347045--38347087 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
38347035 GTCAAAAAAT
*
38347045 AATTTATCATTTTTTTTAAA
1 AATTTATCATTTTTATTAAA
38347065 AATTTATCATGTTTTAATTAAA
1 AATTTATCAT-TTTT-ATTAAA
38347087 A
1 A
38347088 CAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (20 bp):
AATTTATCATTTTTATTAAA
Found at i:38365674 original size:31 final size:31
Alignment explanation
Indices: 38365610--38365674 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
38365600 AATTTTGTTT
*
38365610 ATTAAAACTACAAAAATATCCTTAAACATGG
1 ATTAAAACTACAAAAATATCCTTAAACAAGG
* * * *
38365641 ATTAAAATTACAAAAATTTCTTTAAATAAGG
1 ATTAAAACTACAAAAATATCCTTAAACAAGG
38365672 ATT
1 ATT
38365675 TGTTGCCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (31 bp):
ATTAAAACTACAAAAATATCCTTAAACAAGG
Found at i:38371912 original size:21 final size:20
Alignment explanation
Indices: 38371873--38371914 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
38371863 ATTATGTCTG
* *
38371873 TTGCTTTTTTTTTTCTTCCT
1 TTGCTTTTTTTATCCTTCCT
38371893 TTGCTTTTTTTATCCTTTCCT
1 TTGCTTTTTTTATCC-TTCCT
38371914 T
1 T
38371915 CTTCCATGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.71
Consensus pattern (20 bp):
TTGCTTTTTTTATCCTTCCT
Found at i:38379852 original size:127 final size:126
Alignment explanation
Indices: 38379646--38379968 Score: 497
Period size: 127 Copynumber: 2.6 Consensus size: 126
38379636 GAAGGATGGT
* **
38379646 GGATGGAGGTTAGGTCATTGGTCAAAAT-CCATTTGGACT-CGTGAGTTTATCTCATTGTTAATC
1 GGATGGAGGTTAGGTCATTGGTCAAAATCCCATTTGGA-TGCATGAGTTTATGACATTGTTAATC
* * *
38379709 ATATACATTCTTGTCTCTGCAATCTTTATTCACTCGAACATTATATCTTCCTTGCATGAGCA
65 ATATGCATTCTTGTCTCTGCAATCTTTATTCACTCAAACAATATATCTTCCTTGCATGAGCA
* *
38379771 GGATGGAGGTTTAGGTCAATGGTTAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATC
1 GGATGGAGG-TTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATC
* * **
38379836 ATATGCATTCTTGTCTCTGCAATCTTTCTTCACTCAAACAATGTATCTTTGTTGCATGAGCA
65 ATATGCATTCTTGTCTCTGCAATCTTTATTCACTCAAACAATATATCTTCCTTGCATGAGCA
38379898 GGATGGAGGGTTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATC
1 GGATGGA-GGTTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATC
38379963 ATATGC
65 ATATGC
38379969 TATAGTTGCT
Statistics
Matches: 180, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
125 9 0.05
126 18 0.10
127 151 0.84
128 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (126 bp):
GGATGGAGGTTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATCA
TATGCATTCTTGTCTCTGCAATCTTTATTCACTCAAACAATATATCTTCCTTGCATGAGCA
Found at i:38381381 original size:3 final size:3
Alignment explanation
Indices: 38381373--38381398 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38381363 GTTGTAAGGA
38381373 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
38381399 AAAGTTAATG
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:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:38387670 original size:53 final size:56
Alignment explanation
Indices: 38387610--38387717 Score: 150
Period size: 56 Copynumber: 2.0 Consensus size: 56
38387600 TGGGACGGGA
* **
38387610 GAGCA-TTT-CACTGTGA-AGAAGGGGCCTTTTGAGCCAATGTCAAGGAGGTGGCC
1 GAGCATTTTACACTCTGAGAGAAGGGGCCTTTCAAGCCAATGTCAAGGAGGTGGCC
* *
38387663 GAGCATTTTACAGTCTGAGAGAAGGTGCCTTTCAAGCCAATGTCAAGGAGGTGGC
1 GAGCATTTTACACTCTGAGAGAAGGGGCCTTTCAAGCCAATGTCAAGGAGGTGGC
38387718 TTCTTCCTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
53 5 0.11
54 3 0.06
55 6 0.13
56 33 0.70
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (56 bp):
GAGCATTTTACACTCTGAGAGAAGGGGCCTTTCAAGCCAATGTCAAGGAGGTGGCC
Found at i:38403109 original size:19 final size:19
Alignment explanation
Indices: 38403085--38403125 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
38403075 ATGGAATCAT
*
38403085 AAGCCTATGGTAAGAGAAC
1 AAGCCTATAGTAAGAGAAC
* *
38403104 AAGCCTATAGTCAGAGAGC
1 AAGCCTATAGTAAGAGAAC
38403123 AAG
1 AAG
38403126 TGTTACGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.15
Consensus pattern (19 bp):
AAGCCTATAGTAAGAGAAC
Found at i:38411578 original size:26 final size:26
Alignment explanation
Indices: 38411540--38411591 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
38411530 ATGACTCTCC
38411540 ATATGACTCGGATAAATGTTTATTAG
1 ATATGACTCGGATAAATGTTTATTAG
* *
38411566 ATATGACTTGGATAAATGTTTCTTAG
1 ATATGACTCGGATAAATGTTTATTAG
38411592 GTCTATAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (26 bp):
ATATGACTCGGATAAATGTTTATTAG
Found at i:38414502 original size:8 final size:8
Alignment explanation
Indices: 38414489--38414514 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
38414479 TTTCCAAGCC
38414489 CCTTTCTT
1 CCTTTCTT
38414497 CCTTTCTT
1 CCTTTCTT
38414505 CCTTTCTT
1 CCTTTCTT
38414513 CC
1 CC
38414515 CAACCAATTA
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:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (8 bp):
CCTTTCTT
Found at i:38416930 original size:48 final size:48
Alignment explanation
Indices: 38416859--38416955 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
38416849 CCGTTCATCA
38416859 TTAATATGTATACACCAATGAAAGAGGGTAGGAGTAGTAAATTTTTCT
1 TTAATATGTATACACCAATGAAAGAGGGTAGGAGTAGTAAATTTTTCT
38416907 TTAATATGTATACACCAATGAAAGAGGGTAGGAGTAGTAAATTTTTCT
1 TTAATATGTATACACCAATGAAAGAGGGTAGGAGTAGTAAATTTTTCT
38416955 T
1 T
38416956 CTTTTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (48 bp):
TTAATATGTATACACCAATGAAAGAGGGTAGGAGTAGTAAATTTTTCT
Found at i:38417154 original size:2 final size:2
Alignment explanation
Indices: 38417147--38417171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38417137 TGACTTGTTG
38417147 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
38417172 ACCCTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:38418498 original size:5 final size:6
Alignment explanation
Indices: 38418482--38418506 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38418472 AAATATTAAA
38418482 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
38418507 AAAATTAAAA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:38419411 original size:108 final size:108
Alignment explanation
Indices: 38419218--38419650 Score: 516
Period size: 108 Copynumber: 4.0 Consensus size: 108
38419208 GATGCTAAGA
* * * *
38419218 AGTTCACT-AGGCCAAACTTCTTGGATTGGA-ATAGAAATTTGAGAATCGTTCTGGAA-GCAAAG
1 AGTTCACTGA-GCCAAACTTCTTGGATT-AACATAGAAATTTGAGAATCGTTCTCGAATCCAAGG
* * * *
38419280 ACAAAGTCGTGTGCCTTTAAGAAAGCTTTGCCAGACGTCCCTGCTC
64 A-AAAGTCGTATGACTTTAAGAAAGCTTTGCCAGAAGTCCCTGCTG
* * * *
38419326 AGTTCACTGAGCCAAACTTCTTGGATTAACATTGAACTTTGAAAATCGTTCTTGAATCCAAGGAA
1 AGTTCACTGAGCCAAACTTCTTGGATTAACATAGAAATTTGAGAATCGTTCTCGAATCCAAGGAA
* * *
38419391 AAGTTGTATGACTTTGAGAAAGCTTTGCCAGAAGTCCTTGCTG
66 AAGTCGTATGACTTTAAGAAAGCTTTGCCAGAAGTCCCTGCTG
* * * *
38419434 AGTTCACTG-GCCCAAAATTCTTGGATTAACATTGAAATTTGAGAATTGTTCTCAAATCCAAGG-
1 AGTTCACTGAG-CCAAACTTCTTGGATTAACATAGAAATTTGAGAATCGTTCTCGAATCCAAGGA
* * *
38419497 AAAGTTGTATGACTTTAAGAAAGCTTTGCCAGATGTCCTTGCTG
65 AAAGTCGTATGACTTTAAGAAAGCTTTGCCAGAAGTCCCTGCTG
* ** * * *
38419541 AGATCACTGAGCCAAACTTCTTGGATTGGCATAGAAATTTGAGAATCGTTCTCCAATCTAAGAAA
1 AGTTCACTGAGCCAAACTTCTTGGATTAACATAGAAATTTGAGAATCGTTCTCGAATCCAAGGAA
* * *
38419606 AAGTCGTATTACTTTAAGAAAACTTTGTCAGAAGTCCCTGCTG
66 AAGTCGTATGACTTTAAGAAAGCTTTGCCAGAAGTCCCTGCTG
38419649 AG
1 AG
38419651 GATGCTGAGG
Statistics
Matches: 282, Mismatches: 37, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
107 96 0.34
108 180 0.64
109 6 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (108 bp):
AGTTCACTGAGCCAAACTTCTTGGATTAACATAGAAATTTGAGAATCGTTCTCGAATCCAAGGAA
AAGTCGTATGACTTTAAGAAAGCTTTGCCAGAAGTCCCTGCTG
Found at i:38419590 original size:215 final size:216
Alignment explanation
Indices: 38419218--38419650 Score: 548
Period size: 215 Copynumber: 2.0 Consensus size: 216
38419208 GATGCTAAGA
* * **
38419218 AGTTCACTAGGCCAAACTTCTTGGATTGGAATAGAAATTTGAGAATCGTTCTGGAAGCAAAGACA
1 AGTTCACTAGGCCAAAATTCTTGGATTGAAATAGAAATTTGAGAATCGTTCTCAAAGCAAAGACA
* * *
38419283 AAGTCGTGTGCCTTTAAGAAAGCTTTGCCAGACGTCCCTGCTCAGTTCACTGAGCCAAACTTCTT
66 AAGTCGTATGACTTTAAGAAAGCTTTGCCAGACGTCCCTGCTCAGATCACTGAGCCAAACTTCTT
* * ** * * * *
38419348 GGATTAACATTGAACTTTGAAAATCGTTCTTGAATCCAAGGAAAAGTTGTATGACTTTGAGAAAG
131 GGATTAACATAGAAATTTGAAAATCGTTCTCCAATCCAAGAAAAAGTCGTATGACTTTAAGAAAA
*
38419413 CTTTGCCAGAAGTCCTTGCTG
196 CTTTGCCAGAAGTCCCTGCTG
* * * *
38419434 AGTTCACT-GGCCCAAAATTCTTGGATT-AACATTGAAATTTGAGAATTGTTCTCAAATCCAAG-
1 AGTTCACTAGG-CCAAAATTCTTGGATTGAA-ATAGAAATTTGAGAATCGTTCTCAAAGCAAAGA
* * * * *
38419496 GAAAGTTGTATGACTTTAAGAAAGCTTTGCCAGATGTCCTTGCTGAGATCACTGAGCCAAACTTC
64 CAAAGTCGTATGACTTTAAGAAAGCTTTGCCAGACGTCCCTGCTCAGATCACTGAGCCAAACTTC
** * * *
38419561 TTGGATTGGCATAGAAATTTGAGAATCGTTCTCCAATCTAAGAAAAAGTCGTATTACTTTAAGAA
129 TTGGATTAACATAGAAATTTGAAAATCGTTCTCCAATCCAAGAAAAAGTCGTATGACTTTAAGAA
*
38419626 AACTTTGTCAGAAGTCCCTGCTG
194 AACTTTGCCAGAAGTCCCTGCTG
38419649 AG
1 AG
38419651 GATGCTGAGG
Statistics
Matches: 184, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
215 135 0.73
216 49 0.27
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (216 bp):
AGTTCACTAGGCCAAAATTCTTGGATTGAAATAGAAATTTGAGAATCGTTCTCAAAGCAAAGACA
AAGTCGTATGACTTTAAGAAAGCTTTGCCAGACGTCCCTGCTCAGATCACTGAGCCAAACTTCTT
GGATTAACATAGAAATTTGAAAATCGTTCTCCAATCCAAGAAAAAGTCGTATGACTTTAAGAAAA
CTTTGCCAGAAGTCCCTGCTG
Found at i:38437207 original size:3 final size:3
Alignment explanation
Indices: 38437199--38437229 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
38437189 ACATGATAAC
38437199 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
38437230 TTGGTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:38445790 original size:2 final size:2
Alignment explanation
Indices: 38445783--38445808 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38445773 ATACATTGCC
38445783 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38445809 GCAAGTTACA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38447464 original size:17 final size:15
Alignment explanation
Indices: 38447423--38447465 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
38447413 ACCAAATAAT
38447423 TAAATAAAA-AATGA
1 TAAATAAAATAATGA
38447437 TAAATTAAAATAATGA
1 TAAA-TAAAATAATGA
38447453 CTAAATACAAATA
1 -TAAATA-AAATA
38447466 TTGTTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.16
15 5 0.20
16 7 0.28
17 9 0.36
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (15 bp):
TAAATAAAATAATGA
Found at i:38448488 original size:16 final size:16
Alignment explanation
Indices: 38448459--38448490 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38448449 TCTCTCTCTC
38448459 TCTCTTTCTCTTCTTT
1 TCTCTTTCTCTTCTTT
*
38448475 TCTCTTTCTTTTCTTT
1 TCTCTTTCTCTTCTTT
38448491 GCTTTCTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TCTCTTTCTCTTCTTT
Found at i:38449061 original size:11 final size:12
Alignment explanation
Indices: 38449030--38449063 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
38449020 TTGATTTAAA
38449030 AATACTTTTTAT
1 AATACTTTTTAT
38449042 AATACTTTTTAT
1 AATACTTTTTAT
*
38449054 -ATATTTTTTA
1 AATACTTTTTA
38449064 CAGTACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (12 bp):
AATACTTTTTAT
Found at i:38471530 original size:20 final size:20
Alignment explanation
Indices: 38471505--38471547 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
38471495 AGAAAGAGTA
38471505 AACATTTTATTAGAAGTCTG
1 AACATTTTATTAGAAGTCTG
38471525 AACATTTTATTAGAAGTCTG
1 AACATTTTATTAGAAGTCTG
38471545 AAC
1 AAC
38471548 TCAGTTCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (20 bp):
AACATTTTATTAGAAGTCTG
Found at i:38473211 original size:82 final size:82
Alignment explanation
Indices: 38472967--38473212 Score: 447
Period size: 82 Copynumber: 3.0 Consensus size: 82
38472957 GAGTAAATGC
38472967 AGGCAACGGAAAGTGTTCAATAGTTACGTTACTACTTCGGGAATAGGCTTTGCTCGACTTTCGAA
1 AGGCAACGGAAAGTGTTCAATAGTTACGTTACTACTTCGGGAATAGGCTTTGCTCGACTTTCGAA
*
38473032 GGCCAGAATTCGTTTGT
66 GGCCAGAATTCGTTTTT
*
38473049 AGGCAACGGAAAGTGTTCAATAGTTACGTTACTACTTTGGGAATAGGCTTTGCTCGACTTTCGAA
1 AGGCAACGGAAAGTGTTCAATAGTTACGTTACTACTTCGGGAATAGGCTTTGCTCGACTTTCGAA
38473114 GGCCAGAATTCGTTTTT
66 GGCCAGAATTCGTTTTT
* *
38473131 AGGCAACGGAAAGTGTTCAACACTTACGTTACTACTTCGGGAATAGGCTTTGCTCGACTTTCGAA
1 AGGCAACGGAAAGTGTTCAATAGTTACGTTACTACTTCGGGAATAGGCTTTGCTCGACTTTCGAA
*
38473196 GGCCAAAATTCGTTTTT
66 GGCCAGAATTCGTTTTT
38473213 CCAAAGCATG
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 158 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (82 bp):
AGGCAACGGAAAGTGTTCAATAGTTACGTTACTACTTCGGGAATAGGCTTTGCTCGACTTTCGAA
GGCCAGAATTCGTTTTT
Found at i:38474792 original size:26 final size:26
Alignment explanation
Indices: 38474754--38474816 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
38474744 ACCCTTTCTC
38474754 CCCAGAAAACTCTACAGTTCCAAAAA
1 CCCAGAAAACTCTACAGTTCCAAAAA
* *
38474780 CGCAGAAAACTCTTCAGTTCCAAAAA
1 CCCAGAAAACTCTACAGTTCCAAAAA
38474806 CCCAGAAAACT
1 CCCAGAAAACT
38474817 TCTTTTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.44, C:0.30, G:0.10, T:0.16
Consensus pattern (26 bp):
CCCAGAAAACTCTACAGTTCCAAAAA
Found at i:38476334 original size:2 final size:2
Alignment explanation
Indices: 38476327--38476352 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38476317 GCAGGTTAGT
38476327 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
38476353 TGGCATATCA
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38483891 original size:2 final size:2
Alignment explanation
Indices: 38483886--38483932 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
38483876 ATAATTCGTG
*
38483886 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38483928 TA TA T
1 TA TA T
38483933 TATTTGAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38488126 original size:22 final size:23
Alignment explanation
Indices: 38488089--38488145 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
38488079 TTATTTTTTG
* *
38488089 TATTAAAAAGTATTTAACATTTA
1 TATTAAAAAATATTTAAAATTTA
38488112 TATTAAAAAAT-TTTAAAATTT-
1 TATTAAAAAATATTTAAAATTTA
* *
38488133 TAATATAAAATAT
1 TATTAAAAAATAT
38488146 GTCAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 9 0.31
22 10 0.34
23 10 0.34
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TATTAAAAAATATTTAAAATTTA
Done.