Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 146 of 163
Found at i:39752335 original size:6 final size:6
Alignment explanation
Indices: 39752324--39752364 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
39752314 GCCAAGTTAA
*
39752324 CACCAT CACCAT CACCAT CACCAT CACCAT CACAAT CACCA
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCA
39752365 GCCATCTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.37, C:0.49, G:0.00, T:0.15
Consensus pattern (6 bp):
CACCAT
Found at i:39752774 original size:19 final size:19
Alignment explanation
Indices: 39752750--39752786 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39752740 AAATTTAAAC
*
39752750 TAAAAAACATAAATAAAAT
1 TAAAAAACAAAAATAAAAT
*
39752769 TAAAAAATAAAAATAAAA
1 TAAAAAACAAAAATAAAA
39752787 GACCCTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (19 bp):
TAAAAAACAAAAATAAAAT
Found at i:39753217 original size:24 final size:24
Alignment explanation
Indices: 39753185--39753243 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
39753175 TGAAGTTTTT
* *
39753185 TGTTTGTTTCTGGGGAAAATAGTC
1 TGTTTGTTTCTGCGGAAAATACTC
*
39753209 TGTTTGTTTCTTCGGAAAATACTC
1 TGTTTGTTTCTGCGGAAAATACTC
*
39753233 TTTTTGTTTCT
1 TGTTTGTTTCT
39753244 CGAAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.51
Consensus pattern (24 bp):
TGTTTGTTTCTGCGGAAAATACTC
Found at i:39753251 original size:24 final size:24
Alignment explanation
Indices: 39753185--39753255 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
39753175 TGAAGTTTTT
** * *
39753185 TGTTTGTTTCTGGGGAAAATAGTC
1 TGTTTGTTTCTTCGAAAAATACTC
*
39753209 TGTTTGTTTCTTCGGAAAATACTC
1 TGTTTGTTTCTTCGAAAAATACTC
*
39753233 TTTTTGTTTC-TCGAAAAAATACT
1 TGTTTGTTTCTTCG-AAAAATACT
39753256 AAACCCATCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 38 0.93
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (24 bp):
TGTTTGTTTCTTCGAAAAATACTC
Found at i:39753627 original size:37 final size:37
Alignment explanation
Indices: 39753585--39753665 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
39753575 GATGATGATG
**
39753585 ATTTTAATAATTATATATTTTTAAAA-AATTTAAATTA
1 ATTTTAATAATTATATATTTAAAAAATAATTTAAA-TA
* *
39753622 ATTTTAATAATTTTATATTTAAAAAATAATTTTAATA
1 ATTTTAATAATTATATATTTAAAAAATAATTTAAATA
39753659 ATTTTAA
1 ATTTTAA
39753666 AATCATTAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 32 0.82
38 7 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
ATTTTAATAATTATATATTTAAAAAATAATTTAAATA
Found at i:39753632 original size:9 final size:9
Alignment explanation
Indices: 39753585--39753665 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
39753575 GATGATGATG
39753585 ATTTTAATA
1 ATTTTAATA
*
39753594 ATTAT-ATA
1 ATTTTAATA
* *
39753602 TTTTTAAAAA
1 ATTTT-AATA
*
39753612 ATTTAAATTA
1 ATTTTAA-TA
39753622 ATTTTAATA
1 ATTTTAATA
39753631 ATTTT-AT-
1 ATTTTAATA
*
39753638 ATTTAAAAAATA
1 ATTT---TAATA
39753650 ATTTTAATA
1 ATTTTAATA
39753659 ATTTTAA
1 ATTTTAA
39753666 AATCATTAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
7 4 0.07
8 8 0.15
9 24 0.44
10 12 0.22
11 2 0.04
12 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTTAATA
Found at i:39763949 original size:22 final size:22
Alignment explanation
Indices: 39763921--39763990 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
39763911 CCGAATCAGC
* * *
39763921 TATTTTGATGTTATTTTGTTGT
1 TATTTTGCTATTATTTTGTTAT
* *
39763943 TATTTTGCTATCATTTCGTTAT
1 TATTTTGCTATTATTTTGTTAT
*
39763965 TATATTGCTATTATTTTGTTAT
1 TATTTTGCTATTATTTTGTTAT
39763987 TATT
1 TATT
39763991 GTTTGAATAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (22 bp):
TATTTTGCTATTATTTTGTTAT
Found at i:39763958 original size:11 final size:11
Alignment explanation
Indices: 39763921--39763990 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 11
39763911 CCGAATCAGC
* *
39763921 TATTTTGATGT
1 TATTTTGCTAT
* *
39763932 TATTTTGTTGT
1 TATTTTGCTAT
39763943 TATTTTGCTAT
1 TATTTTGCTAT
* * *
39763954 CATTTCGTTAT
1 TATTTTGCTAT
*
39763965 TATATTGCTAT
1 TATTTTGCTAT
*
39763976 TATTTTGTTAT
1 TATTTTGCTAT
39763987 TATT
1 TATT
39763991 GTTTGAATAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 47 1.00
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:39767700 original size:13 final size:13
Alignment explanation
Indices: 39767682--39767747 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
39767672 AATTTAGCAT
*
39767682 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
**
39767695 TGCTTTCAAAAAG
1 TGCTTTTGAAAAG
* *
39767708 TG-TAATGGAAAAG
1 TGCT-TTTGAAAAG
*
39767721 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
39767734 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
39767747 T
1 T
39767748 TTGATTTAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 1 0.03
13 38 0.95
14 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39767961 original size:24 final size:24
Alignment explanation
Indices: 39767934--39767979 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39767924 TAATATTTTA
*
39767934 ATATATGAAAT-ATTAATTTTAAAT
1 ATATAT-AAATAATTAATATTAAAT
*
39767958 ATATCTAAATAATTAATATTAA
1 ATATATAAATAATTAATATTAA
39767980 TTATTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATATAAATAATTAATATTAAAT
Found at i:39769667 original size:13 final size:13
Alignment explanation
Indices: 39769649--39769677 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39769639 CACTGAACAA
39769649 CCATACTATTGCT
1 CCATACTATTGCT
39769662 CCATACTATTGCT
1 CCATACTATTGCT
39769675 CCA
1 CCA
39769678 ACATTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.34
Consensus pattern (13 bp):
CCATACTATTGCT
Found at i:39774245 original size:129 final size:129
Alignment explanation
Indices: 39774015--39774261 Score: 424
Period size: 129 Copynumber: 1.9 Consensus size: 129
39774005 TTTTGGTTTG
39774015 AATTAGTCATGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGGCCTTTAATTGATGTTAA
1 AATTAGTCATGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGGCCTTTAATTGATGTTAA
* *
39774080 TTGAGATAGTTTTCAGTTGGTTTTCTATTAACAATTTCAATCTTGTGGCCTTCAATTGATGTTA
66 TTGAGATAGTTTTCAGTTGGTATTCTATTAACAATTTCAATCCTGTGGCCTTCAATTGATGTTA
* * *
39774144 AATTAGTTATGTACTCGTGTTCTCACTGCTGATGCTAGGTTGGATTGGCCTTTAATCT-ATGTTA
1 AATTAGTCATGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGGCCTTTAAT-TGATGTTA
*
39774208 ATTGAGATAGTTTTCAGTTTGTATTCTATTAACAATTTCAATCCTGTGGCCTTC
65 ATTGAGATAGTTTTCAGTTGGTATTCTATTAACAATTTCAATCCTGTGGCCTTC
39774262 TTCAGGTGTC
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
129 110 0.99
130 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (129 bp):
AATTAGTCATGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGGCCTTTAATTGATGTTAA
TTGAGATAGTTTTCAGTTGGTATTCTATTAACAATTTCAATCCTGTGGCCTTCAATTGATGTTA
Found at i:39786952 original size:15 final size:15
Alignment explanation
Indices: 39786928--39786963 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
39786918 AAAATAATTT
*
39786928 AAAT-TTTTTATAAA
1 AAATATTTTTAAAAA
39786942 AAATATTTTTAAAAA
1 AAATATTTTTAAAAA
39786957 AAATATT
1 AAATATT
39786964 GATGGCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTTTTAAAAA
Found at i:39789254 original size:22 final size:23
Alignment explanation
Indices: 39789229--39789272 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39789219 TCACTTTCAA
39789229 AACTATATCA-AT-TAATCACATT
1 AACTAT-TCATATATAATCACATT
39789251 AACTATTCATATATAATCACAT
1 AACTATTCATATATAATCACAT
39789273 AATTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 8 0.40
23 9 0.45
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (23 bp):
AACTATTCATATATAATCACATT
Found at i:39792063 original size:257 final size:257
Alignment explanation
Indices: 39791597--39792097 Score: 813
Period size: 257 Copynumber: 1.9 Consensus size: 257
39791587 AACACGTAAT
* *
39791597 GGAGAACGACGCGAGGGAGAGAACCGAGCGATCCAATGTCGTTTTCTCACAACGGCTATCGGTAA
1 GGAGAACGACGCGAGGGAGAGAACCGAGCGATCCAACGTCGTTTTCTCACAACGACTATCGGTAA
* * *
39791662 GAGGTGCTTGACGGATGGGTTTTGTTCGCGATACGACGACGAACCCGATGGTGGAGGTAGTGCGG
66 GAGGTGCTTGACGGATGGGATTTGTTCGCGAGACGACGACGAACCCGATGGTGGAGGCAGTGCGG
*
39791727 CGCACGAACTGCAAGAACACGATCACCAAAGCACGAACGAAAAATTGAGAAAGAGAGAGAGAGAG
131 CGCACGAACTGCAAGAACACGACCACCAAAGCACGAACGAAAAATTGAGAAAGAGAGAGAGAGAG
*
39791792 GATATTCGGTTGGGAAAGGGAAAATGGGGGATGAAGGGATTGATTTTGGCAGAACACGCGAC
196 GATATTCGGTTGGGAAAGGGAAAATGGGAGATGAAGGGATTGATTTTGGCAGAACACGCGAC
* * * * *
39791854 GGAGGACGATGCGAGGGAGAGAACCGAGCGGTCCAACGTCGTTTTCTCACAATGACTGTCGGTAA
1 GGAGAACGACGCGAGGGAGAGAACCGAGCGATCCAACGTCGTTTTCTCACAACGACTATCGGTAA
* * * ** *
39791919 GGGGTGCTTGACGGATGGGATTTGTTCGCGCGACGATGACGAATTCGATGGTGGCGGCAGTGCGG
66 GAGGTGCTTGACGGATGGGATTTGTTCGCGAGACGACGACGAACCCGATGGTGGAGGCAGTGCGG
* * *
39791984 CGCACGGACTGCAAGAACACGACCACTAAAGCACGAACGAAAAATTGAGAAAGAGAGGGAGAGAG
131 CGCACGAACTGCAAGAACACGACCACCAAAGCACGAACGAAAAATTGAGAAAGAGAGAGAGAGAG
39792049 GATATTCGGTTGGGAAAGGGAAAATGGGAGATGAAGGGATTGATTTTGG
196 GATATTCGGTTGGGAAAGGGAAAATGGGAGATGAAGGGATTGATTTTGG
39792098 ATTGAAAATT
Statistics
Matches: 223, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
257 223 1.00
ACGTcount: A:0.30, C:0.17, G:0.36, T:0.17
Consensus pattern (257 bp):
GGAGAACGACGCGAGGGAGAGAACCGAGCGATCCAACGTCGTTTTCTCACAACGACTATCGGTAA
GAGGTGCTTGACGGATGGGATTTGTTCGCGAGACGACGACGAACCCGATGGTGGAGGCAGTGCGG
CGCACGAACTGCAAGAACACGACCACCAAAGCACGAACGAAAAATTGAGAAAGAGAGAGAGAGAG
GATATTCGGTTGGGAAAGGGAAAATGGGAGATGAAGGGATTGATTTTGGCAGAACACGCGAC
Found at i:39792280 original size:30 final size:30
Alignment explanation
Indices: 39792246--39792322 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
39792236 ATAATCAGAG
*
39792246 TTCAATTTAGTCCCTAAATTTCACTAACAT
1 TTCAATTTAGTCCCTAAATTTCACTAAAAT
*
39792276 TTCAATTTAG-CCCTTAAGTTTCACTAAAAT
1 TTCAATTTAGTCCC-TAAATTTCACTAAAAT
** *
39792306 CACAATTTAGTACCTAA
1 TTCAATTTAGTCCCTAA
39792323 TGTAAAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.08
30 35 0.88
31 2 0.05
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (30 bp):
TTCAATTTAGTCCCTAAATTTCACTAAAAT
Found at i:39794008 original size:18 final size:18
Alignment explanation
Indices: 39793974--39794011 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39793964 ATCTCTCAAT
*
39793974 CTTTATTTTTCAGTTTTA
1 CTTTATTTGTCAGTTTTA
39793992 CTTTATTTGT-AGCTTTTA
1 CTTTATTTGTCAG-TTTTA
39794010 CT
1 CT
39794012 ATTAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.13, G:0.08, T:0.63
Consensus pattern (18 bp):
CTTTATTTGTCAGTTTTA
Found at i:39796085 original size:132 final size:130
Alignment explanation
Indices: 39795892--39796307 Score: 333
Period size: 132 Copynumber: 3.1 Consensus size: 130
39795882 CAATTACAAC
* * * * **
39795892 TCTTCCCTATCAAATTCCCATCTAAG-GTAAGAGCATAAAGCACAACGGAACCAATAAATCCTAC
1 TCTTCCCTATCAAATCCCCACCTAAGAG-AAAAGCAAAAAGCACAGTGGAACCAATAAATCCTAC
*
39795956 TTCAGAAAATCTGTCACAGTGCATTCACAAATCATTGAAAACCATAGGAATTTATAGTCTATTAC
65 TTCAGAAAATCTG-CATAGTGCATTCACAAATCATTGAAAA-CATAGGAATTTATAGTCTATTAC
*
39796021 GGT
128 AGT
***
39796024 TCTTCCCTATCAAATCCCCACCTAAG-GAAAATGTGTAAAGCACCA-TGG-ACCAGGA-AAATCC
1 TCTTCCCTATCAAATCCCCACCTAAGAGAAAA-GCAAAAAGCA-CAGTGGAACCA--ATAAATCC
* * * * * * * * *
39796085 T-CCTCGTGAGAATCTGCTATTGTGCTTTCACAAATTATTGAAAACTTATGAATTCACATAGGGT
62 TACTTC-AGAAAATCTGC-ATAGTGCATTCACAAATCATTGAAAACATAGGAATT--TATA--GT
**
39796149 AACCTATTACAAC
121 ---CTATTACAGT
* * * * *
39796162 TCTTCCCTAGCAAATCCCCATCTAAGAGAAGAGCAAAAAGCATAGTGGAACCAATAAATTCTACT
1 TCTTCCCTATCAAATCCCCACCTAAGAGAAAAGCAAAAAGCACAGTGGAACCAATAAATCCTACT
* * * *
39796227 TCAGAAAATCTGCCATAGCGCACTCACAAATTC-TTGAAAAGCATAGGAATTTATAGTTTATCAC
66 TCAGAAAATCTG-CATAGTGCATTCACAAA-TCATTGAAAA-CATAGGAATTTATAGTCTATTAC
39796291 AGT
128 AGT
39796294 TCTTCCCTATCAAA
1 TCTTCCCTATCAAA
39796308 ACTCCATCAA
Statistics
Matches: 220, Mismatches: 43, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
131 19 0.09
132 91 0.41
133 6 0.03
135 4 0.02
137 5 0.02
138 74 0.34
139 21 0.10
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (130 bp):
TCTTCCCTATCAAATCCCCACCTAAGAGAAAAGCAAAAAGCACAGTGGAACCAATAAATCCTACT
TCAGAAAATCTGCATAGTGCATTCACAAATCATTGAAAACATAGGAATTTATAGTCTATTACAGT
Found at i:39796214 original size:270 final size:269
Alignment explanation
Indices: 39795812--39796548 Score: 869
Period size: 270 Copynumber: 2.7 Consensus size: 269
39795802 CAGACTCAAA
* * * * * * * *
39795812 CCCACTTCTGAGAATCAGCCGTTGTGCCTTCACAAATTATTGTGAAGGTTAGAAATTCACTTTGG
1 CCCACTTCGGAGAATCTGCCATTGTGCATTCACAAATTATTG-AAAAGTTAG-AATTCACATAGG
* * * *
39795877 GTAGCCAATTACAACTCTTCCCTATCAAATTCCCATCTAAGGTAAGAGCATAAAGCACAACGGAA
64 GTAGCCTATTACAACTCTTCCCTATCAAATCCCCATCTAAGGTAAGAGCAAAAAGCACAATGGAA
* * *
39795942 CCAATAAATCCTACTTCAGAAAATCTGTCACAGTGCATTCACAAATCATTGAAAACCATAGGAAT
129 CCAATAAATCCTACTTCAGAAAATCTGCCATAGTGCATTCACAAATCATTGAAAAGCATAGGAAT
* * * * *
39796007 TTATAGTCTATTACGGTTCTTCCCTATCAAATCCCCACCTAA-GGAAAATGTGTAAAGCACCAT-
194 TTATAGTCTATCACAGTTCTTCCCTATCAAAACCCCACC-AATGGAAAAGGTGTAAAGCACAATC
*
39796070 GGACCAGGAAAAT
258 GAACCA-GAAAAT
* * *
39796083 CCTC-C-TCGTGAGAATCTGCTATTGTGCTTTCACAAATTATTGAAAACTTATGAATTCACATAG
1 CC-CACTTCG-GAGAATCTGCCATTGTGCATTCACAAATTATTGAAAAGTTA-GAATTCACATAG
* * * *
39796146 GGTAACCTATTACAACTCTTCCCTAGCAAATCCCCATCTAAGAG-AAGAGCAAAAAGCATAGTGG
63 GGTAGCCTATTACAACTCTTCCCTATCAAATCCCCATCTAAG-GTAAGAGCAAAAAGCACAATGG
* * *
39796210 AACCAATAAATTCTACTTCAGAAAATCTGCCATAGCGCACTCACAAATTC-TTGAAAAGCATAGG
127 AACCAATAAATCCTACTTCAGAAAATCTGCCATAGTGCATTCACAAA-TCATTGAAAAGCATAGG
* * * *
39796274 AATTTATAGTTTATCACAGTTCTTCCCTATCAAAACTCCATCAATGGCAAAGGTGTAAAGCACAA
191 AATTTATAGTCTATCACAGTTCTTCCCTATCAAAACCCCACCAATGGAAAAGGTGTAAAGCACAA
* **
39796339 TCGAACTATTAAAT
256 TCGAACCAGAAAAT
* * * *
39796353 CCCACTTCGGAGAATCTGCCGTTGTGCAGTCACAAATTATTTAAAAGGTTAGAACTTCACATCGG
1 CCCACTTCGGAGAATCTGCCATTGTGCATTCACAAATTATTGAAAA-GTTAGAA-TTCACATAGG
* * * *
39796418 GTAGCCTATGACTACTCTTCCCTATCAAATCCCCATCAAAGGTAAGGGCAAAAA-CACAATGGAA
64 GTAGCCTATTACAACTCTTCCCTATCAAATCCCCATCTAAGGTAAGAGCAAAAAGCACAATGGAA
* * * *
39796482 GCAGTAAATCCTACTTCAGAAAACCTGCCATAGTGCATTCAC-ATTCATTGAAAAGCATAGGAAT
129 CCAATAAATCCTACTTCAGAAAATCTGCCATAGTGCATTCACAAATCATTGAAAAGCATAGGAAT
39796546 TTA
194 TTA
39796549 CATCGTGTAG
Statistics
Matches: 394, Mismatches: 59, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
268 2 0.01
269 24 0.06
270 266 0.68
271 101 0.26
272 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (269 bp):
CCCACTTCGGAGAATCTGCCATTGTGCATTCACAAATTATTGAAAAGTTAGAATTCACATAGGGT
AGCCTATTACAACTCTTCCCTATCAAATCCCCATCTAAGGTAAGAGCAAAAAGCACAATGGAACC
AATAAATCCTACTTCAGAAAATCTGCCATAGTGCATTCACAAATCATTGAAAAGCATAGGAATTT
ATAGTCTATCACAGTTCTTCCCTATCAAAACCCCACCAATGGAAAAGGTGTAAAGCACAATCGAA
CCAGAAAAT
Found at i:39804123 original size:12 final size:12
Alignment explanation
Indices: 39804106--39804130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39804096 CTCTTTTAAC
39804106 AAAAAAATTCAA
1 AAAAAAATTCAA
39804118 AAAAAAATTCAA
1 AAAAAAATTCAA
39804130 A
1 A
39804131 TTTTCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:39804187 original size:26 final size:27
Alignment explanation
Indices: 39804139--39804190 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39804129 AATTTTCAAA
*
39804139 ATATTTGTAAAAAAATTCTAAAATTTT
1 ATATTTGTAAAAAAATTCAAAAATTTT
*
39804166 ATATTTTTAAAAAAATT-AAAAATTT
1 ATATTTGTAAAAAAATTCAAAAATTT
39804191 AAAAAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATTTGTAAAAAAATTCAAAAATTTT
Found at i:39804203 original size:27 final size:29
Alignment explanation
Indices: 39804173--39804226 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
39804163 TTTATATTTT
39804173 TAAA-AAAAT-TAAAAATTTAAAAAAAAG
1 TAAAGAAAATATAAAAATTTAAAAAAAAG
* **
39804200 TAAAGAATATATAAATTTTTAAAAAAA
1 TAAAGAAAATATAAAAATTTAAAAAAA
39804227 TTTCCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.18
28 4 0.18
29 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (29 bp):
TAAAGAAAATATAAAAATTTAAAAAAAAG
Found at i:39808736 original size:26 final size:27
Alignment explanation
Indices: 39808679--39808743 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
39808669 TCCGAATCAC
*
39808679 ATTAAA-TTAATTTTTTTTATTAAATA
1 ATTAAATTTAATTTTTATTATTAAATA
*
39808705 AATAAATTTAATTTTATATTATT-AA-A
1 ATTAAATTTAATTTT-TATTATTAAATA
*
39808731 ATTAAATTAAATT
1 ATTAAATTTAATT
39808744 AAAATATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 17 0.52
27 10 0.30
28 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTAAATTTAATTTTTATTATTAAATA
Found at i:39809855 original size:12 final size:12
Alignment explanation
Indices: 39809838--39809864 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39809828 TCTCTATTAT
39809838 AATTATTTTTTA
1 AATTATTTTTTA
39809850 AATTATTTTTTA
1 AATTATTTTTTA
39809862 AAT
1 AAT
39809865 AATCATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
AATTATTTTTTA
Found at i:39809900 original size:25 final size:27
Alignment explanation
Indices: 39809854--39809919 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 27
39809844 TTTTTAAATT
*
39809854 ATTTTTTAAATA-ATCATGAA-TT-AA
1 ATTTTTTAATTATATCATGAATTTAAA
* *
39809878 ATTTTTTAATTATATTATTAATTTAAA
1 ATTTTTTAATTATATCATGAATTTAAA
*
39809905 ATTTTATAAATTATA
1 ATTTT-TTAATTATA
39809920 AAAATATGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 11 0.32
25 6 0.18
26 2 0.06
27 7 0.21
28 8 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTTTTAATTATATCATGAATTTAAA
Found at i:39810287 original size:15 final size:16
Alignment explanation
Indices: 39810257--39810292 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
39810247 GGTGTCCAAA
*
39810257 AAATTAATCGTTAATT
1 AAATTAATCATTAATT
39810273 AAATTAAT-ATTAATT
1 AAATTAATCATTAATT
39810288 AAATT
1 AAATT
39810293 GATTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATTAATCATTAATT
Found at i:39810345 original size:17 final size:18
Alignment explanation
Indices: 39810325--39810359 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39810315 TTATTAATTG
*
39810325 AATTAATC-AATTAAAAA
1 AATTAATCTAATCAAAAA
39810342 AATTAATCTAATCAAAAA
1 AATTAATCTAATCAAAAA
39810360 TATTTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTAATCTAATCAAAAA
Found at i:39810545 original size:30 final size:29
Alignment explanation
Indices: 39810490--39810546 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
39810480 TAAAAAAACT
*
39810490 TTAACTAACCTTTAATCAAACTAAATTGA
1 TTAACTAACCATTAATCAAACTAAATTGA
* *
39810519 TTAACTAACCGATTAATCGAATTAAATT
1 TTAACTAACC-ATTAATCAAACTAAATT
39810547 TATTTAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (29 bp):
TTAACTAACCATTAATCAAACTAAATTGA
Found at i:39810941 original size:3 final size:3
Alignment explanation
Indices: 39810935--39810978 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
39810925 TATAATAATG
39810935 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39810979 GTTGTTGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39810983 original size:3 final size:3
Alignment explanation
Indices: 39810977--39811006 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39810967 ATTATTATTA
39810977 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
39811007 ATTCAGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:39812186 original size:4 final size:4
Alignment explanation
Indices: 39812179--39812212 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
39812169 TAAAGAAAGG
39812179 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
39812213 GTATATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:39816813 original size:16 final size:16
Alignment explanation
Indices: 39816786--39816819 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
39816776 TATTGTAAGT
39816786 AAAATTTT-AAAATAA
1 AAAATTTTAAAAATAA
39816801 AAAATTATTAAAAATAA
1 AAAATT-TTAAAAATAA
39816818 AA
1 AA
39816820 TAAGATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTTTAAAAATAA
Found at i:39817508 original size:17 final size:18
Alignment explanation
Indices: 39817464--39817508 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
39817454 ATTTAAGATA
39817464 TATATAAATATTAATGTAT
1 TATA-AAATATTAATGTAT
*
39817483 TGATAAAATTTTAATGTAT
1 T-ATAAAATATTAATGTAT
39817502 T-TAAAAT
1 TATAAAAT
39817509 CGATAGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
19 15 0.62
20 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (18 bp):
TATAAAATATTAATGTAT
Found at i:39822929 original size:10 final size:10
Alignment explanation
Indices: 39822914--39822950 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
39822904 GTGTTAATTG
*
39822914 TATCATATCA
1 TATCATACCA
39822924 TATCATACCA
1 TATCATACCA
39822934 TATCATACCA
1 TATCATACCA
*
39822944 TACCATA
1 TATCATA
39822951 ATTAAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (10 bp):
TATCATACCA
Found at i:39822937 original size:15 final size:15
Alignment explanation
Indices: 39822917--39822950 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
39822907 TTAATTGTAT
*
39822917 CATATCATATCATAC
1 CATATCATACCATAC
39822932 CATATCATACCATAC
1 CATATCATACCATAC
39822947 CATA
1 CATA
39822951 ATTAAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
CATATCATACCATAC
Found at i:39824933 original size:15 final size:15
Alignment explanation
Indices: 39824913--39824942 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39824903 GTTATTTAGT
*
39824913 TATCTTAAAATGTCA
1 TATCTTAAAACGTCA
39824928 TATCTTAAAACGTCA
1 TATCTTAAAACGTCA
39824943 CATCATCGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (15 bp):
TATCTTAAAACGTCA
Found at i:39826045 original size:21 final size:21
Alignment explanation
Indices: 39826019--39826065 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
39826009 ACCTCATATC
39826019 TTTAAT-AATGTTAATAATTTA
1 TTTAATAAAT-TTAATAATTTA
* *
39826040 TTTAATAAATTTTATAATTTT
1 TTTAATAAATTTAATAATTTA
39826061 TTTAA
1 TTTAA
39826066 AATTTTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAATAAATTTAATAATTTA
Found at i:39828650 original size:23 final size:23
Alignment explanation
Indices: 39828603--39828659 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
39828593 TCAATATAAA
*
39828603 ATTATATTAAATTATTCTATCTT
1 ATTATATTAAATTATTCTATATT
*
39828626 ATTATATTATATTATT-TATA--
1 ATTATATTAAATTATTCTATATT
39828646 ATTATATTTAAATT
1 ATTATA-TTAAATT
39828660 TTAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.20
21 6 0.20
22 3 0.10
23 15 0.50
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATATTAAATTATTCTATATT
Found at i:39828758 original size:2 final size:2
Alignment explanation
Indices: 39828751--39828793 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39828741 TTAAGACCAT
*
39828751 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39828793 A
1 A
39828794 ACTGGCTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39831779 original size:30 final size:30
Alignment explanation
Indices: 39831745--39832021 Score: 140
Period size: 30 Copynumber: 9.4 Consensus size: 30
39831735 TATGGATACC
* *
39831745 CGGGGGTGAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTAGGTGAAAT
* * ** **
39831775 CGGGGTTAAAAACGG-AATTTTAGAAG-CTT
1 CGGGGGT-AAAATGGTAATTTTAGGTGAAAT
* * *
39831804 CGGGGGCAAAATGGTAATTTTCGGTGAAAA
1 CGGGGGTAAAATGGTAATTTTAGGTGAAAT
* * ** **
39831834 CGGGGTTGAAAACGG-AATTTTAGAAG-CTT
1 CGGGGGT-AAAATGGTAATTTTAGGTGAAAT
*
39831863 CGGGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTAGGTGAAAT
* ** **
39831893 CGGGGTTAAAAATGG-AATTTTAGAAG-CTT
1 CGGGGGT-AAAATGGTAATTTTAGGTGAAAT
* *
39831922 CGGGGGCAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTAGGTGAAAT
* * * **
39831952 TGGGGTTAAAAATAG-AATTTTAGAG-G-CTT
1 CGGGGGT-AAAATGGTAATTTTAG-GTGAAAT
* *
39831981 CGGGGGTAAAATGGTAATTTTCGATGAAAT
1 CGGGGGTAAAATGGTAATTTTAGGTGAAAT
* *
39832011 TGGGGTTAAAA
1 CGGGGGTAAAA
39832022 ACGGAATTTT
Statistics
Matches: 171, Mismatches: 62, Indels: 28
0.66 0.24 0.11
Matches are distributed among these distances:
28 25 0.15
29 56 0.33
30 65 0.38
31 25 0.15
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.29
Consensus pattern (30 bp):
CGGGGGTAAAATGGTAATTTTAGGTGAAAT
Found at i:39831808 original size:59 final size:59
Alignment explanation
Indices: 39831745--39832060 Score: 481
Period size: 59 Copynumber: 5.4 Consensus size: 59
39831735 TATGGATACC
* *
39831745 CGGGGGTGAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
* * *
39831804 CGGGGGCAAAATGGTAATTTTCGGTGAAAACGGGGTTGAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
*
39831863 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
* * ** *
39831922 CGGGGGCAAAATGGTAATTTTCGGTGAAATTGGGGTTAAAAATAGAATTTTAGAGGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
* * *
39831981 CGGGGGTAAAATGGTAATTTTCGATGAAATTGGGGTTAAAAACGGAATTTTAGAAACTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
*
39832040 CGGGGGTCAAAAT-ATAATTTT
1 CGGGGGT-AAAATGGTAATTTT
39832061 GGAAAAGTTT
Statistics
Matches: 236, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
59 231 0.98
60 5 0.02
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
Found at i:39832078 original size:30 final size:30
Alignment explanation
Indices: 39832042--39832287 Score: 375
Period size: 30 Copynumber: 8.2 Consensus size: 30
39832032 AGAAACTTCG
39832042 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
39832072 GGGGTCAAAATATAATTTTGGAAAAGTCTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
39832102 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
39832132 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
**
39832162 AAGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
39832192 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
39832222 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* * * *
39832252 AGGGTTAAAATGTAATTTTGGAAAAGTTTC
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
39832282 GGGGTC
1 GGGGTC
39832288 GAAAGATGAT
Statistics
Matches: 196, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 196 1.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:39832082 original size:118 final size:117
Alignment explanation
Indices: 39831745--39832120 Score: 451
Period size: 118 Copynumber: 3.2 Consensus size: 117
39831735 TATGGATACC
* *
39831745 CGGGGGTGAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGG
* * **
39831810 CAAAATGGTAATTTTCGGTGAAAACG--GGGTTGAAAACGGAATTTTAGAAGCTT
66 CAAAATGGTAATTTTC-G-GAAAA-GTTGGGGTAAAAATAGAATTTTAGAAGCTT
*
39831863 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGG
* *
39831928 CAAAATGGTAATTTTCGGTGAAA-TTGGGGTTAAAAATAGAATTTTAGAGGCTT
66 CAAAATGGTAATTTTCGG-AAAAGTTGGGG-TAAAAATAGAATTTTAGAAGCTT
* * *
39831981 CGGGGGTAAAATGGTAATTTTCGATGAAATTGGGGTTAAAAACGGAATTTTAGAAACTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGG
* * * *
39832046 TCAAAAT-ATAATTTT-GGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTCTT
66 -CAAAATGGTAATTTTCGGAAAAG--TTGGGGTAAAAATAGAATTTT--AGAAG-CTT
*
39832102 -GGGGTTAAAAT-GTAATTTT
1 CGGGGGTAAAATGGTAATTTT
39832121 GGAAAAGTTT
Statistics
Matches: 227, Mismatches: 20, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
116 4 0.02
117 9 0.04
118 178 0.78
119 20 0.09
120 13 0.06
121 3 0.01
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGG
CAAAATGGTAATTTTCGGAAAAGTTGGGGTAAAAATAGAATTTTAGAAGCTT
Found at i:39832739 original size:160 final size:162
Alignment explanation
Indices: 39832452--39832756 Score: 415
Period size: 160 Copynumber: 1.9 Consensus size: 162
39832442 TTAAGGACTA
* *
39832452 AATTAAAATAAATTAAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAATTGACACGTGGCA
1 AATTAAAACAAATTAAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAAATGACACGTGGCA
* * ** **
39832517 ATCTCTGGTGCAGTCAAACAGTCAAATGACTAGTTTATAAACCTTGAAAAATTATTGGGCCAATT
66 ATCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACAGGGCCAATT
39832582 T-C-ATAATTAAAACAAAGTTGATTTAGGATTT
130 TGCAATAATTAAAACAAAGTTGATTTAGGATTT
* *
39832613 AATTAAAACAAATTAAAAACA-A-AA-GGACTAAATGCATAAATAATCCAAAACATGACACGTGG
1 AATTAAAACAAATTAAAAA-ATAGAAGGGACTAAATGCAGAAATAAGCCAAAA-ATGACACGTGG
*
39832675 CAATCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCAATT-AAAATTGCAGGGCCA
64 CAATCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTACAGGGCCA
39832739 ATTTGCAAATAATTAAAA
127 ATTTGC-AATAATTAAAA
39832757 AGATGCAAAA
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
159 24 0.19
160 69 0.55
161 20 0.16
162 3 0.02
163 10 0.08
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (162 bp):
AATTAAAACAAATTAAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAAATGACACGTGGCA
ATCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAGGGCCAATTT
GCAATAATTAAAACAAAGTTGATTTAGGATTT
Found at i:39834313 original size:6 final size:6
Alignment explanation
Indices: 39834284--39834356 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
39834274 TATAATAATA
* *
39834284 TTAAATT TTAAA- TTAAAT TCAAAT TTAAAT TTAAA- TTGAAT TT-AAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
39834330 GTAAAT TTAAGA- TTAAA- ATAAAT TTAA
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAA
39834357 TTTTTCAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
5 18 0.33
6 30 0.56
7 6 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:39834325 original size:11 final size:11
Alignment explanation
Indices: 39834283--39834359 Score: 68
Period size: 11 Copynumber: 6.8 Consensus size: 11
39834273 TTATAATAAT
39834283 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
39834295 ATTAAATTCAA
1 ATTAAATTTAA
39834306 ATTTAAATTTAA
1 A-TTAAATTTAA
*
39834318 ATTGAATTT-A
1 ATTAAATTTAA
39834328 ATGTAAATTTAA
1 AT-TAAATTTAA
*
39834340 GATTAAA-ATAA
1 -ATTAAATTTAA
*
39834351 ATTTAATTT
1 ATTAAATTT
39834360 TTCAAATGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.15
11 22 0.42
12 21 0.40
13 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:39834325 original size:28 final size:29
Alignment explanation
Indices: 39834294--39834348 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
39834284 TTAAATTTTA
*
39834294 AATTAAAT-TCAAATTTAA-ATTTAAATTG
1 AATTAAATGT-AAATTTAAGATTAAAATTG
*
39834322 AATTTAATGTAAATTTAAGATTAAAAT
1 AATTAAATGTAAATTTAAGATTAAAAT
39834349 AAATTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTAAATGTAAATTTAAGATTAAAATTG
Found at i:39834353 original size:28 final size:28
Alignment explanation
Indices: 39834304--39834357 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
39834294 AATTAAATTC
* *
39834304 AAATTTAAATTTAAATTGAATTTAATGT
1 AAATTTAAATTTAAAATAAATTTAATGT
39834332 AAATTTAAGA-TTAAAATAAATTTAAT
1 AAATTTAA-ATTTAAAATAAATTTAAT
39834358 TTTTCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
AAATTTAAATTTAAAATAAATTTAATGT
Found at i:39834857 original size:68 final size:68
Alignment explanation
Indices: 39834653--39835361 Score: 1139
Period size: 68 Copynumber: 10.4 Consensus size: 68
39834643 GTCCAACTTC
* * * * * * *
39834653 ACTTCAATTCCAAGAGGATGACGTTGCTCTTACTTCAATTTTAGAGGTAAAGATGTGTTATCCAC
1 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
39834718 TCT
66 TCT
* *
39834721 ACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGATGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTG-TTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
39834786 CTCT
65 CTCT
*
39834790 ACTTCAATTTCGAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
1 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
39834855 TCT
66 TCT
* * * * *
39834858 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
1 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
39834923 TCT
66 TCT
*
39834926 ACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTG-TTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
39834991 CTCT
65 CTCT
* *
39834995 ACTTCAATTTCCAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGTTATCCAC
1 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
39835060 TCT
66 TCT
* * * * *
39835063 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
1 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
39835128 TCT
66 TCT
*
39835131 ACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTG-TTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
39835196 CTCT
65 CTCT
*
39835200 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGTTATCCAC
1 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
39835265 TCT
66 TCT
* *
39835268 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
1 ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
39835333 TCT
66 TCT
*
39835336 ACTTCAATTTCAAGGGGATGATGTTG
1 ACTTCAATTTCAAGGGGATGACGTTG
39835362 AGATCTGCAA
Statistics
Matches: 596, Mismatches: 42, Indels: 6
0.93 0.07 0.01
Matches are distributed among these distances:
68 406 0.68
69 190 0.32
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (68 bp):
ACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
TCT
Found at i:39834959 original size:137 final size:137
Alignment explanation
Indices: 39834653--39835361 Score: 1147
Period size: 137 Copynumber: 5.2 Consensus size: 137
39834643 GTCCAACTTC
* * * * * *
39834653 ACTTCAATTCCAAGAGGATGACGTTGC-TCTTACTTCAATTTTAGAGGTAAAGATGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
* *
39834717 CTCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGATGTGTTA
66 CTCTACTTCAATTTCAAGGGGATGACGTTGC-TCTTACTTCAATTTCAGAGATGAAGACGTGTTA
39834782 TCCACTCT
130 TCCACTCT
*
39834790 ACTTCAATTTCGAGGGGATGACGTTG-TTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
* * * *
39834854 CTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTAT
66 CTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
39834919 CCACTCT
131 CCACTCT
*
39834926 ACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
* * *
39834991 CTCTACTTCAATTTCCAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGTTAT
66 CTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
39835056 CCACTCT
131 CCACTCT
* * * *
39835063 ACTTCAATTTCAAGGGAATGACGTTGC-TCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
*
39835127 CTCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTA
66 CTCTACTTCAATTTCAAGGGGATGACGTTGC-TCTTACTTCAATTTCAGAGATGAAGACGTGTTA
39835192 TCCACTCT
130 TCCACTCT
*
39835200 ACTTCAATTTCAAGGGGATGACGTTG-TTCTTACTTCAATTTTAGAGATGAAGACGTGTTATCCA
1 ACTTCAATTTCAAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
*
39835264 CTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
66 CTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
39835329 CCACTCT
131 CCACTCT
*
39835336 ACTTCAATTTCAAGGGGATGATGTTG
1 ACTTCAATTTCAAGGGGATGACGTTG
39835362 AGATCTGCAA
Statistics
Matches: 534, Mismatches: 34, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
136 194 0.36
137 340 0.64
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (137 bp):
ACTTCAATTTCAAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA
CTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
CCACTCT
Found at i:39835005 original size:205 final size:205
Alignment explanation
Indices: 39834653--39835361 Score: 1303
Period size: 205 Copynumber: 3.5 Consensus size: 205
39834643 GTCCAACTTC
* *
39834653 ACTTCAATTCCAAGAGG-ATGACGTTGCTCTTACTTCAATTTTAGAGGTAAAGATGTGTTATCCA
1 ACTTCAATTTCAAG-GGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCA
*
39834717 CTCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGATGTGTTA
65 CTCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTA
* *
39834782 TCCACTCTACTTCAATTTCGAGGGGATGACGTTGTTCTTACTTCAATTTCAGAGATGAAGACGTG
130 TCCACTCTACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTG
39834847 TTATCCACTCT
195 TTATCCACTCT
39834858 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
1 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
39834923 TCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
66 TCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
*
39834988 CCACTCTACTTCAATTTCCAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGT
131 CCACTCTACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGT
39835053 TATCCACTCT
196 TATCCACTCT
39835063 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
1 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
39835128 TCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
66 TCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
39835193 CCACTCTACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGT
131 CCACTCTACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGT
39835258 TATCCACTCT
196 TATCCACTCT
* * *
39835268 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
1 ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
* *
39835333 TCTACTTCAATTTCAAGGGGATGATGTTG
66 TCTACTTCAATTTCGAGGGGATGACGTTG
39835362 AGATCTGCAA
Statistics
Matches: 492, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
204 2 0.00
205 490 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (205 bp):
ACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAGATGTGTTATCCAC
TCTACTTCAATTTCGAGGGGATGACGTTGCTTCTTACTTCAATTTCAGAGATGAAGACGTGTTAT
CCACTCTACTTCAATTTCAAGGGGATGACGTTGTTCTTACTTCAATTTTAGAGATGAAGACGTGT
TATCCACTCT
Found at i:39847503 original size:117 final size:118
Alignment explanation
Indices: 39847299--39847554 Score: 399
Period size: 117 Copynumber: 2.2 Consensus size: 118
39847289 TATGGATACC
* * *
39847299 CGGGGGCGAAATGGTAATTTTCGGTGAAAACGGGGTTGAAAACGGAATTTTAGAAGCTTCGGGGG
1 CGGGGGCAAAATGGTAATTTTCAGTGAAAACGGGGTTGAAAACAGAATTTTAGAAGCTTCGGGGG
*
39847364 TAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTT
66 TAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAACGGAATTTTAGAAGCTT
* * *
39847417 CGGGGGCAAAATGGTAATTTTCAGTGAAATCGGGGTT-AAAATAGAATTTTAGAGGCTTCGGGGG
1 CGGGGGCAAAATGGTAATTTTCAGTGAAAACGGGGTTGAAAACAGAATTTTAGAAGCTTCGGGGG
* *
39847481 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
66 TAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAACGGAATTTTAGAAGCTT
*
39847534 CGGGGGTCAAAAT-ATAATTTT
1 CGGGGG-CAAAATGGTAATTTT
39847555 GGAAAAGTTT
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
117 87 0.69
118 40 0.31
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (118 bp):
CGGGGGCAAAATGGTAATTTTCAGTGAAAACGGGGTTGAAAACAGAATTTTAGAAGCTTCGGGGG
TAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAACGGAATTTTAGAAGCTT
Found at i:39847556 original size:58 final size:59
Alignment explanation
Indices: 39847307--39847554 Score: 376
Period size: 59 Copynumber: 4.2 Consensus size: 59
39847297 CCCGGGGGCG
* *
39847307 AAATGGTAATTTTCGGTGAAAACGGGGTTGAAAACGGAATTTTAGAAGCTTCGGGGGTA
1 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGGTA
* * *
39847366 AAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGCA
1 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGGTA
* *
39847425 AAATGGTAATTTTCAGTGAAATCGGGGTTAAAATA--GAATTTTAGAGGCTTCGGGGGTA
1 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAA-ACGGAATTTTAGAAGCTTCGGGGGTA
*
39847483 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGGTCA
1 AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGGT-A
*
39847543 AAAT-ATAATTTT
1 AAATGGTAATTTT
39847555 GGAAAAGTTT
Statistics
Matches: 172, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
57 1 0.01
58 52 0.30
59 113 0.66
60 6 0.03
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (59 bp):
AAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTCGGGGGTA
Found at i:39847824 original size:30 final size:30
Alignment explanation
Indices: 39847536--39847811 Score: 426
Period size: 30 Copynumber: 9.2 Consensus size: 30
39847526 AGAAGCTTCG
39847536 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
39847566 GGGGTCAAAATATAATTTTGGAAAAGTCTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
39847596 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
39847626 GGGGTCAAAATGTAATTTTGGAAAAGTTTC
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
39847656 CGGGTCAAAATATAATTTTGGAAAAGTTTC
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
39847686 AGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
39847716 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
39847746 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* * * *
39847776 AGGGTTAAAATGTAATTTTGGAAAAGTTTC
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
39847806 GGGGTC
1 GGGGTC
39847812 GAAAGATGAT
Statistics
Matches: 225, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 225 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:39848242 original size:160 final size:163
Alignment explanation
Indices: 39847899--39848244 Score: 431
Period size: 160 Copynumber: 2.1 Consensus size: 163
39847889 GTATCCAGAG
* * * * *
39847899 GTCAAGGGACTAATTTGA-AAACTTTGAAAAAATTTTGGACCAATTTTGTAATTAATTAAGAGTT
1 GTCAAAGGACTAATTT-ATAAACCTTGAAAAAATTTTGGACCAATTTCGTAATTAATAAAAAGTT
* *
39847963 AATTTAAGGACTAAATTAAAATAAATTAAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAA
65 AATTTAAGGACTAAATTAAAACAAATTAAAAAATAGAAAGGACTAAATGCAGAAATAAGCCAAAA
*
39848028 ATTGACACGTGGCAACTTCTGGTGCAGTCAAACA
130 ATTGACACGTGGCAACTTCTGGTACAGTCAAACA
**
39848062 GTCAAAGGACTTGTTTATAAACCTTG-AAAAATTATTGTG-CCAATTTCGTAATTAA-AACAAAG
1 GTCAAAGGACTAATTTATAAACCTTGAAAAAATT-TTG-GACCAATTTCGTAATTAATAA-AAAG
* * * * *
39848124 TTGATTT-AGGATTTAATTAAAACAAATT-AAAAATA-AAAGGACTAAATGCATAAATAATCCAA
63 TTAATTTAAGGACTAAATTAAAACAAATTAAAAAATAGAAAGGACTAAATGCAGAAATAAGCCAA
39848186 AACA-TGACACGTGGCAA-TCTCTGGTACAGTCAAACA
128 AA-ATTGACACGTGGCAACT-TCTGGTACAGTCAAACA
*
39848222 GTCAAAGGACTAAATTATAAACC
1 GTCAAAGGACTAATTTATAAACC
39848245 AATTAAAATT
Statistics
Matches: 159, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
159 1 0.01
160 75 0.47
161 8 0.05
162 27 0.17
163 47 0.30
164 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (163 bp):
GTCAAAGGACTAATTTATAAACCTTGAAAAAATTTTGGACCAATTTCGTAATTAATAAAAAGTTA
ATTTAAGGACTAAATTAAAACAAATTAAAAAATAGAAAGGACTAAATGCAGAAATAAGCCAAAAA
TTGACACGTGGCAACTTCTGGTACAGTCAAACA
Found at i:39849619 original size:20 final size:20
Alignment explanation
Indices: 39849581--39849621 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39849571 AGAGCTGGTG
* * *
39849581 GATGGAGCTGGTGGTCAGCA
1 GATGGAGCCGATGGCCAGCA
39849601 GATGGAGCCGATGGCCAGCA
1 GATGGAGCCGATGGCCAGCA
39849621 G
1 G
39849622 CAGTAGGCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.44, T:0.15
Consensus pattern (20 bp):
GATGGAGCCGATGGCCAGCA
Found at i:39849698 original size:14 final size:13
Alignment explanation
Indices: 39849664--39849702 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
39849654 ATTTGGACTA
39849664 TTGTAATTGGGCC
1 TTGTAATTGGGCC
*
39849677 CT-TAATTGGGCC
1 TTGTAATTGGGCC
39849689 TTTGTAATTGGGCC
1 -TTGTAATTGGGCC
39849703 ATTGATTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 10 0.45
13 2 0.09
14 10 0.45
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.38
Consensus pattern (13 bp):
TTGTAATTGGGCC
Found at i:39849833 original size:6 final size:6
Alignment explanation
Indices: 39849804--39849876 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
39849794 TATAATAATA
* *
39849804 TTAAATT TTAAA- TTAAAT TCAAAT TTAAAT TTAAA- TTGAAT TT-AAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
39849850 GTAAAT TTAAGA- TTAAA- ATAAAT TTAA
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAA
39849877 TTTTTCAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
5 18 0.33
6 30 0.56
7 6 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:39849845 original size:11 final size:11
Alignment explanation
Indices: 39849803--39849879 Score: 68
Period size: 11 Copynumber: 6.8 Consensus size: 11
39849793 TTATAATAAT
39849803 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
39849815 ATTAAATTCAA
1 ATTAAATTTAA
39849826 ATTTAAATTTAA
1 A-TTAAATTTAA
*
39849838 ATTGAATTT-A
1 ATTAAATTTAA
39849848 ATGTAAATTTAA
1 AT-TAAATTTAA
*
39849860 GATTAAA-ATAA
1 -ATTAAATTTAA
*
39849871 ATTTAATTT
1 ATTAAATTT
39849880 TTCAAATGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.15
11 22 0.42
12 21 0.40
13 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:39849845 original size:28 final size:29
Alignment explanation
Indices: 39849814--39849868 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
39849804 TTAAATTTTA
*
39849814 AATTAAAT-TCAAATTTAA-ATTTAAATTG
1 AATTAAATGT-AAATTTAAGATTAAAATTG
*
39849842 AATTTAATGTAAATTTAAGATTAAAAT
1 AATTAAATGTAAATTTAAGATTAAAAT
39849869 AAATTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTAAATGTAAATTTAAGATTAAAATTG
Found at i:39849873 original size:28 final size:28
Alignment explanation
Indices: 39849824--39849877 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
39849814 AATTAAATTC
* *
39849824 AAATTTAAATTTAAATTGAATTTAATGT
1 AAATTTAAATTTAAAATAAATTTAATGT
39849852 AAATTTAAGA-TTAAAATAAATTTAAT
1 AAATTTAA-ATTTAAAATAAATTTAAT
39849878 TTTTCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
AAATTTAAATTTAAAATAAATTTAATGT
Found at i:39851767 original size:19 final size:19
Alignment explanation
Indices: 39851745--39851783 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39851735 TTATTGTCAC
39851745 TCACCGTAATCAAATTTGT
1 TCACCGTAATCAAATTTGT
* *
39851764 TCACTGTAATTAAATTTGT
1 TCACCGTAATCAAATTTGT
39851783 T
1 T
39851784 ATTAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (19 bp):
TCACCGTAATCAAATTTGT
Found at i:39853420 original size:76 final size:76
Alignment explanation
Indices: 39853333--39853538 Score: 278
Period size: 78 Copynumber: 2.7 Consensus size: 76
39853323 AATATAGGGA
* * * *
39853333 TTAAATATCAAATGATACAAGAATCTTTGGCATATAAATCCAAAAAACAGCGAAATTAAAATATA
1 TTAAATTTCAAATGATACAAGAACCTTTGGCATATAACTCCAAAAAACAGCAAAATTAAAATATA
39853398 GAGATTAA-TAT
66 GAGATTAACT-T
*
39853409 TTAAATTTCAAATGATACATA-AACCTTTGGCATATTAACCCCCAAAAAACAGCAAAATTAAAAT
1 TTAAATTTCAAATGATACA-AGAACCTTTGGCATA-TAA-CTCCAAAAAACAGCAAAATTAAAAT
*
39853473 ATAGGGATTAACTT
63 ATAGAGATTAACTT
*
39853487 TTAAATTTCAAATGATGCAAGAACCTTTGGC-T-TAACT-CAAAAAACAGCAAAA
1 TTAAATTTCAAATGATACAAGAACCTTTGGCATATAACTCCAAAAAACAGCAAAA
39853539 AAATTCCGTT
Statistics
Matches: 117, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
73 15 0.13
74 1 0.01
75 3 0.03
76 30 0.26
77 6 0.05
78 61 0.52
79 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (76 bp):
TTAAATTTCAAATGATACAAGAACCTTTGGCATATAACTCCAAAAAACAGCAAAATTAAAATATA
GAGATTAACTT
Found at i:39859064 original size:22 final size:23
Alignment explanation
Indices: 39859032--39859075 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
39859022 CCAAGTCAAG
*
39859032 CTTGTCATT-GGTATTGTGATAT
1 CTTGTCATTGGGTATCGTGATAT
*
39859054 CTTGTCCTTGGGTATCGTGATA
1 CTTGTCATTGGGTATCGTGATA
39859076 CCAACATCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.45
Consensus pattern (23 bp):
CTTGTCATTGGGTATCGTGATAT
Found at i:39863681 original size:43 final size:43
Alignment explanation
Indices: 39863631--39863718 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
39863621 TTACAGAAGT
39863631 AATTCTTTCTTTTCTTCAATAAATAAATAAATTTTTATATATA
1 AATTCTTTCTTTTCTTCAATAAATAAATAAATTTTTATATATA
39863674 AATTCTTTCTTTTCTTCAATAAATAAATAAATTTTTATATATA
1 AATTCTTTCTTTTCTTCAATAAATAAATAAATTTTTATATATA
39863717 AA
1 AA
39863719 ATCAAACCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (43 bp):
AATTCTTTCTTTTCTTCAATAAATAAATAAATTTTTATATATA
Found at i:39875007 original size:15 final size:16
Alignment explanation
Indices: 39874978--39875012 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39874968 TAATTAATTG
39874978 TTTTTTAAAATTTTTA
1 TTTTTTAAAATTTTTA
* *
39874994 TTTTTTGAAATTTTAA
1 TTTTTTAAAATTTTTA
39875010 TTT
1 TTT
39875013 AAAGAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTTTAAAATTTTTA
Found at i:39875656 original size:19 final size:19
Alignment explanation
Indices: 39875627--39875664 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
39875617 TAAATTTAAA
39875627 TAAACAAATACAAACAAATT
1 TAAACAAATACAAA-AAATT
39875647 TAAA-AAATACAAAAAATT
1 TAAACAAATACAAAAAATT
39875665 ATTCATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAACAAATACAAAAAATT
Found at i:39876774 original size:29 final size:29
Alignment explanation
Indices: 39876736--39876791 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
39876726 TAAAAGTAAT
* *
39876736 TTTTTTTAATTAATTACGTAAATAACTCA
1 TTTTTTTAATTAAATACGAAAATAACTCA
*
39876765 TTTTTTTAATTAAATATGAAAATAACT
1 TTTTTTTAATTAAATACGAAAATAACT
39876792 TAAAATCTAC
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:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTTTTTAATTAAATACGAAAATAACTCA
Found at i:39877213 original size:17 final size:17
Alignment explanation
Indices: 39877193--39877246 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
39877183 AAATAATATT
39877193 TTTAAATTAGAAATAAA
1 TTTAAATTAGAAATAAA
* **
39877210 TTTAAAATAG---TATT
1 TTTAAATTAGAAATAAA
*
39877224 TTTAAATTAAAAATAAA
1 TTTAAATTAGAAATAAA
39877241 TTTAAA
1 TTTAAA
39877247 ATTTAAAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
14 10 0.37
17 17 0.63
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
TTTAAATTAGAAATAAA
Found at i:39877216 original size:31 final size:31
Alignment explanation
Indices: 39877181--39877248 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
39877171 TTTTCTTCTC
*
39877181 TAAAATAATATTTTTAAATTAGAAATAAATT
1 TAAAATAATATTTTTAAATTAAAAATAAATT
*
39877212 TAAAATAGTATTTTTAAATTAAAAATAAATT
1 TAAAATAATATTTTTAAATTAAAAATAAATT
39877243 TAAAAT
1 TAAAAT
39877249 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (31 bp):
TAAAATAATATTTTTAAATTAAAAATAAATT
Found at i:39877243 original size:19 final size:19
Alignment explanation
Indices: 39877206--39877261 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
39877196 AAATTAGAAA
* *
39877206 TAAATTTAAAATAGTATTTT
1 TAAATTAAAAATA-AATTTT
39877226 TAAATTAAAAATAAA-TTT
1 TAAATTAAAAATAAATTTT
*
39877244 AAAATTTAAAAAATAAAT
1 TAAA-TT-AAAAATAAAT
39877262 AATAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.20
19 3 0.10
20 21 0.70
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAATTAAAAATAAATTTT
Found at i:39877366 original size:17 final size:18
Alignment explanation
Indices: 39877344--39877381 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
39877334 TTATTAATTA
39877344 TTAATT-AAATATATAAT
1 TTAATTAAAATATATAAT
*
39877361 TTAATTAAAATATATATT
1 TTAATTAAAATATATAAT
39877379 TTA
1 TTA
39877382 TTTTTGGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTAAAATATATAAT
Found at i:39877397 original size:98 final size:103
Alignment explanation
Indices: 39877287--39877510 Score: 352
Period size: 105 Copynumber: 2.2 Consensus size: 103
39877277 TCATCGGGAA
* *
39877287 TTGGTGGCGCCAT-TTAACATGGCTCCACCCGATTAATTATTTATTATTTATTA-ATTAT-T-A-
1 TTGGTGGAGCCATGTTAA-ATGGCGCCACCCGATTAATTATTTATTATTTATTATATTATCTAAT
39877347 A-TTAAATATATAATTTAATTAAAATATATATTTTATTT
65 ATTTAAATATATAATTTAATTAAAATATATATTTTATTT
39877385 TTGGTGGAGCCATGTTAAATGGCGCCACCCGATTAATTATTTATTATTTATTATTTATTATCTAA
1 TTGGTGGAGCCATGTTAAATGGCGCCACCCGATTAATTATTTATTATTTATTA--TATTATCTAA
*
39877450 TATTTAAATATATAGTTTAATTAAAATATATATTTTATTT
64 TATTTAAATATATAATTTAATTAAAATATATATTTTATTT
39877490 TTGGTGGAGCCATGTTAAATG
1 TTGGTGGAGCCATGTTAAATG
39877511 ACACCATCAA
Statistics
Matches: 115, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
98 46 0.40
99 4 0.03
101 5 0.04
102 1 0.01
103 1 0.01
104 1 0.01
105 57 0.50
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (103 bp):
TTGGTGGAGCCATGTTAAATGGCGCCACCCGATTAATTATTTATTATTTATTATATTATCTAATA
TTTAAATATATAATTTAATTAAAATATATATTTTATTT
Found at i:39877432 original size:7 final size:7
Alignment explanation
Indices: 39877420--39877455 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
39877410 CACCCGATTA
39877420 ATTATTT
1 ATTATTT
39877427 ATTATTT
1 ATTATTT
39877434 ATTATTT
1 ATTATTT
*
39877441 ATTATCT
1 ATTATTT
*
39877448 AATATTT
1 ATTATTT
39877455 A
1 A
39877456 AATATATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (7 bp):
ATTATTT
Found at i:39877575 original size:11 final size:11
Alignment explanation
Indices: 39877559--39877604 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
39877549 TATTTTTAAA
39877559 ATTTTAAATTT
1 ATTTTAAATTT
39877570 ATTTTAAATTT
1 ATTTTAAATTT
*
39877581 A---AAAATATT
1 ATTTTAAAT-TT
39877590 ATTTTAAATTT
1 ATTTTAAATTT
39877601 ATTT
1 ATTT
39877605 CTAATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 4 0.14
9 3 0.10
11 18 0.62
12 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:39877591 original size:20 final size:19
Alignment explanation
Indices: 39877546--39877601 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
39877536 TTTGTTTATT
*
39877546 ATTTATTTTTAAAATTT-TAA
1 ATTTA-TTTT-AAATTTAAAA
39877566 ATTTATTTTAAATTTAAAA
1 ATTTATTTTAAATTTAAAA
39877585 ATATTATTTTAAATTTA
1 AT-TTATTTTAAATTTA
39877602 TTTCTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 19 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATTTTAAATTTAAAA
Found at i:39877594 original size:31 final size:31
Alignment explanation
Indices: 39877559--39877625 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
39877549 TATTTTTAAA
39877559 ATTTTAAATTTATTT-TAAATTTAAAAATATT
1 ATTTTAAATTTATTTCT-AATTTAAAAATATT
39877590 ATTTTAAATTTATTTCTAATTTAAAAATATT
1 ATTTTAAATTTATTTCTAATTTAAAAATATT
39877621 ATTTT
1 ATTTT
39877626 GGAGAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTTTAAATTTATTTCTAATTTAAAAATATT
Found at i:39878078 original size:29 final size:29
Alignment explanation
Indices: 39878013--39878069 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
39878003 CCGTAAATTT
* *
39878013 TAAATTATTTTCGTATTTAATTAAAAAAA
1 TAAATTATTTACGTAATTAATTAAAAAAA
39878042 TAAATTATTTACGTAATTAATTAAAAAA
1 TAAATTATTTACGTAATTAATTAAAAAA
39878070 GTTACTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (29 bp):
TAAATTATTTACGTAATTAATTAAAAAAA
Found at i:39886314 original size:30 final size:29
Alignment explanation
Indices: 39886274--39886342 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
39886264 AGTTTATATA
* *
39886274 TTTATAATTTTTAAAAATTTAAAT-TAAATT
1 TTTATCATTTTTAAAAATTAAAATGT-AA-T
*
39886304 TTTATCATTTTTTAAAAGTTAAAATGTAAT
1 TTTATCA-TTTTTAAAAATTAAAATGTAAT
39886334 TTTATCATT
1 TTTATCATT
39886343 ACTAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 14 0.41
31 17 0.50
32 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTATCATTTTTAAAAATTAAAATGTAAT
Found at i:39886319 original size:31 final size:30
Alignment explanation
Indices: 39886281--39886342 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
39886271 ATATTTATAA
*
39886281 TTTTTAAAAATTTAAAT-TAAATTTTTATCAT
1 TTTTTAAAAATTAAAATGT-AA-TTTTATCAT
*
39886312 TTTTTAAAAGTTAAAATGTAATTTTATCAT
1 TTTTTAAAAATTAAAATGTAATTTTATCAT
39886342 T
1 T
39886343 ACTAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.36
31 17 0.61
32 1 0.04
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTTTAAAAATTAAAATGTAATTTTATCAT
Found at i:39903803 original size:43 final size:42
Alignment explanation
Indices: 39903679--39903946 Score: 272
Period size: 43 Copynumber: 6.3 Consensus size: 42
39903669 TTTGTTAATA
* * * *
39903679 TTAGTGGCGTTTGTGGGAAAAACGCCACTAAAGATCAT-GTTCT
1 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGGTT-T
* * * *
39903722 TTAGCGGCGTTTGCGGAAAAGTGCCACTAAAGATCATGGTTT
1 TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGGTTT
* *
39903764 TTAGCGGCATTTGTGGAATAAGCGCCGCTAAAGACCATGGTCT
1 TTAGCGGCGTTTGTGGAA-AAGCGCCGCTAAAGACCATGGTTT
* *
39903807 TTAGCGACGTTTGTTGGAAAAGCGCCGCTAAAGACCATGTTTT
1 TTAGCGGCGTTTG-TGGAAAAGCGCCGCTAAAGACCATGGTTT
* *
39903850 TTAGCGGCGTTTGTGAGATAAGCGCCGTTAAAGACCAT-GTTCT
1 TTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGACCATGGTT-T
* * * * *
39903893 TTAGTGGAGTTTTTGGAAAAGCGTCGCTAAAGACCAT-ATTCT
1 TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGGTT-T
*
39903935 ATAGCGGCGTTT
1 TTAGCGGCGTTT
39903947 TTCCTCATAA
Statistics
Matches: 192, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
42 74 0.39
43 113 0.59
44 5 0.03
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGGTTT
Found at i:39903849 original size:85 final size:87
Alignment explanation
Indices: 39903679--39903946 Score: 300
Period size: 85 Copynumber: 3.1 Consensus size: 87
39903669 TTTGTTAATA
* * * * * *
39903679 TTAGTGGCGTTTGTGGGAA-AAACGCCACTAAAGATCATGTTCTTTAGCGGCGTTTG-CGGAAAA
1 TTAGCGGCGTTTGT-GGAATAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTTGGAAAA
* * *
39903742 GTGCCACTAAAGATCATGG-TTT
65 GCGCCGCTAAAGACCATGGTTTT
* *
39903764 TTAGCGGCATTTGTGGAATAAGCGCCGCTAAAGACCATGGTCTTTAGCGACGTTTGTTGGAAAAG
1 TTAGCGGCGTTTGTGGAATAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTTGGAAAAG
39903829 CGCCGCTAAAGACCAT-GTTTT
66 CGCCGCTAAAGACCATGGTTTT
* *
39903850 TTAGCGGCGTTTGT-GAGATAAGCGCCGTTAAAGACCATGTTCTTTAGTGGA-GTTT-TTGGAAA
1 TTAGCGGCGTTTGTGGA-ATAAGCGCCGCTAAAGACCATGTTCTTTAG-CGACGTTTGTTGGAAA
* * *
39903912 AGCGTCGCTAAAGACCAT-ATTCT
64 AGCGCCGCTAAAGACCATGGTTTT
*
39903935 ATAGCGGCGTTT
1 TTAGCGGCGTTT
39903947 TTCCTCATAA
Statistics
Matches: 159, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
84 4 0.03
85 85 0.53
86 68 0.43
87 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (87 bp):
TTAGCGGCGTTTGTGGAATAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTTGGAAAAG
CGCCGCTAAAGACCATGGTTTT
Found at i:39903940 original size:128 final size:128
Alignment explanation
Indices: 39903686--39903946 Score: 312
Period size: 128 Copynumber: 2.0 Consensus size: 128
39903676 ATATTAGTGG
* *
39903686 CGTTTGTGGGAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGTTTGCGGAAAAGTGCCACTA
1 CGTTTGTGGGAAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGTTTGCGGAAAAGCGCCACTA
* * *
39903751 AAGATCATGGTTTTTAGCGGCATTTGTGGAATAAGCGCCGCTAAAGACCATGGTCTTTAGCGA
66 AAGACCATGGTTTTTAGCGGCATTTGTGGAATAAGCGCCGCTAAAGACCATAGTCTATAGCGA
* * * * * * **
39903814 CGTTTGTTGGAAAAGCGCCGCTAAAGACCATGTTTTTTAGCGGCGTTTGTGAGATAAGCGCCGTT
1 CGTTTGTGGGAAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGTTTGCG-GAAAAGCGCCACT
* * * *
39903879 AAAGACCAT-GTTCTTTAGTGG-AGTTTTTGGAA-AAGCGTCGCTAAAGACCATATTCTATAGCG
65 AAAGACCATGGTT-TTTAGCGGCA-TTTGTGGAATAAGCGCCGCTAAAGACCATAGTCTATAGCG
*
39903941 G
128 A
39903942 CGTTT
1 CGTTT
39903947 TTCCTCATAA
Statistics
Matches: 112, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
128 80 0.71
129 32 0.29
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (128 bp):
CGTTTGTGGGAAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGTTTGCGGAAAAGCGCCACTA
AAGACCATGGTTTTTAGCGGCATTTGTGGAATAAGCGCCGCTAAAGACCATAGTCTATAGCGA
Found at i:39905522 original size:27 final size:27
Alignment explanation
Indices: 39905463--39905524 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
39905453 TATAAGTGGG
* * *
39905463 TGGTACCTACCTGACAGGCGGCACTAG
1 TGGTGCCTACCTGACAGGCGGCACCAA
* *
39905490 TAGTGCCTACCTGTCAGGCGGCACCAA
1 TGGTGCCTACCTGACAGGCGGCACCAA
39905517 TGGTGCCT
1 TGGTGCCT
39905525 TTCTGTCAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (27 bp):
TGGTGCCTACCTGACAGGCGGCACCAA
Found at i:39905606 original size:15 final size:14
Alignment explanation
Indices: 39905560--39905613 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
39905550 TTTTTATTAC
*
39905560 AAAACTAATACAAA
1 AAAATTAATACAAA
* **
39905574 AAAATTTATACACC
1 AAAATTAATACAAA
39905588 AAAATATAATACAAAA
1 AAAAT-TAATAC-AAA
39905604 AAAATTAATA
1 AAAATTAATA
39905614 ACTTAAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 15 0.48
15 10 0.32
16 6 0.19
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAATACAAA
Found at i:39905832 original size:57 final size:56
Alignment explanation
Indices: 39905733--39905864 Score: 153
Period size: 57 Copynumber: 2.4 Consensus size: 56
39905723 AAAAATTAAA
* * * *
39905733 TTAAATATTAAATAAGAATAACTCAATATTTTTAAATAAATAATATAA-AAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAGAAAAAAT
** *
39905788 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAAAAAAT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAAGAAAAAAT
39905846 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
39905865 CACTTTTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
55 6 0.09
56 18 0.28
57 25 0.39
58 15 0.23
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (56 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAGAAAAAAT
Found at i:39906586 original size:27 final size:27
Alignment explanation
Indices: 39906543--39906598 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
39906533 TTCTGTTGCG
* * *
39906543 GTAATGGGCGAGGAGGAGTAGAGTACT
1 GTAATGGGCGAGAAGGAATAGAGAACT
39906570 GTAATGGGCTGA-AAGGAATAGAGAACT
1 GTAATGGGC-GAGAAGGAATAGAGAACT
39906597 GT
1 GT
39906599 GGTGGTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.34, C:0.07, G:0.39, T:0.20
Consensus pattern (27 bp):
GTAATGGGCGAGAAGGAATAGAGAACT
Found at i:39906811 original size:6 final size:6
Alignment explanation
Indices: 39906800--39906835 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
39906790 ATAGTGCCGC
*
39906800 GGCTCA GGCTCA AGCTCA GGCTCA GGCTCA GGCTCA
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA
39906836 ACCGGCTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.17
Consensus pattern (6 bp):
GGCTCA
Found at i:39908838 original size:17 final size:17
Alignment explanation
Indices: 39908809--39908856 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
39908799 AATATTTTTA
39908809 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
39908825 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
* *
39908842 CAAATGAATTAAATA
1 AAAAT-ATTTAAATA
39908857 AAATAATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 11 0.39
18 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:39911543 original size:20 final size:22
Alignment explanation
Indices: 39911513--39911557 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
39911503 TCGAAGTCTC
39911513 TCCCCCATTTCCCCTTTCCC-T
1 TCCCCCATTTCCCCTTTCCCGT
*
39911534 TCCCCC-TTTCTCCTTTCCCGT
1 TCCCCCATTTCCCCTTTCCCGT
39911555 TCC
1 TCC
39911558 TTGTCACACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.02, C:0.56, G:0.02, T:0.40
Consensus pattern (22 bp):
TCCCCCATTTCCCCTTTCCCGT
Found at i:39911960 original size:20 final size:20
Alignment explanation
Indices: 39911924--39911970 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
39911914 TTGATATTTT
*
39911924 TATTTTTATCATCTTTTTAA
1 TATTTTTATCATATTTTTAA
*
39911944 TATTTTTAT-ATAATTTTTTA
1 TATTTTTATCAT-ATTTTTAA
39911964 -ATTTTTA
1 TATTTTTA
39911971 ATTTTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTTATCATATTTTTAA
Found at i:39919323 original size:23 final size:23
Alignment explanation
Indices: 39919293--39919415 Score: 122
Period size: 23 Copynumber: 5.3 Consensus size: 23
39919283 ATGAGATATG
* *
39919293 ATTAGCACTTGGATGCTTTTGTA
1 ATTAGCACTTCGATGCTTCTGTA
* * *
39919316 ATTAGCACTTTGGTGCTTTTGT-
1 ATTAGCACTTCGATGCTTCTGTA
* *
39919338 ATGTAGCACATCTATGCTTCTGTA
1 AT-TAGCACTTCGATGCTTCTGTA
*
39919362 TTTAGCACTTCGATGCTTCTGTA
1 ATTAGCACTTCGATGCTTCTGTA
* * *
39919385 GTTAGCACTTCGGTTCTTCTGTA
1 ATTAGCACTTCGATGCTTCTGTA
*
39919408 GTTAGCAC
1 ATTAGCAC
39919416 ATCAGTGCTT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.02
23 82 0.96
24 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (23 bp):
ATTAGCACTTCGATGCTTCTGTA
Found at i:39919367 original size:46 final size:46
Alignment explanation
Indices: 39919294--39919429 Score: 130
Period size: 46 Copynumber: 3.0 Consensus size: 46
39919284 TGAGATATGA
* * * *
39919294 TTAGCACTTGGATGCTTTTGTAATTAGCACTTTGGTGCTTTTGTA-
1 TTAGCACATCGATGCTTCTGTAATTAGCACTTCGGTGCTTTTGTAG
* * * *
39919339 TGTAGCACATCTATGCTTCTGTATTTAGCACTTCGATGCTTCTGTAG
1 T-TAGCACATCGATGCTTCTGTAATTAGCACTTCGGTGCTTTTGTAG
* * * * * *
39919386 TTAGCACTTCGGTTCTTCTGTAGTTAGCACATCAGTGCTTTTGT
1 TTAGCACATCGATGCTTCTGTAATTAGCACTTCGGTGCTTTTGT
39919430 TACTAACACT
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
45 1 0.01
46 70 0.97
47 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (46 bp):
TTAGCACATCGATGCTTCTGTAATTAGCACTTCGGTGCTTTTGTAG
Found at i:39920298 original size:17 final size:19
Alignment explanation
Indices: 39920276--39920310 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
39920266 TGTAAGATAT
39920276 AAACATA-AATG-TGAATG
1 AAACATAGAATGTTGAATG
39920293 AAACATAGAATGTTGAAT
1 AAACATAGAATGTTGAAT
39920311 CAATGGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (19 bp):
AAACATAGAATGTTGAATG
Found at i:39923632 original size:29 final size:28
Alignment explanation
Indices: 39923590--39923967 Score: 126
Period size: 29 Copynumber: 13.0 Consensus size: 28
39923580 GCTCTCTAGT
39923590 CCCTAAACTTTCCAAAATTCCATTTTTGA
1 CCCTAAACTTTCCAAAATTCCATTTTT-A
39923619 CCCTGAAAC-TTCCAAAAATTACCA-TTTTA
1 CCCT-AAACTTTCC-AAAATT-CCATTTTTA
* *
39923648 CCCTCAAGCTTTCCAAAATTCCATTTTAA
1 CCCT-AAACTTTCCAAAATTCCATTTTTA
** *
39923677 CCC-CGA-TTTCACCCAAAATTATCA-TTTTA
1 CCCTAAACTTT---CCAAAATT-CCATTTTTA
39923706 CCCCTAAACTTTCCAAAATTCCA-TTTTA
1 -CCCTAAACTTTCCAAAATTCCATTTTTA
* ** * *
39923734 ACCTCGATTTTAGCTAAAATTACCA-TTTTA
1 CCCTAAACTTT--CCAAAATT-CCATTTTTA
* * * *
39923764 TCCTTGAACTCTT-CGAAA-TCTCATTTTGA
1 -CCCTAAACT-TTCCAAAATTC-CATTTTTA
**
39923793 CCC-CGA-TTTCACCAAAAATTACCA-TTTTA
1 CCCTAAACTTT--CC-AAAATT-CCATTTTTA
** *
39923822 CCCCCGAACTTTCTAAAATTCCATTTTTGA
1 -CCCTAAACTTTCCAAAATTCCATTTTT-A
* *
39923852 CCC-AGATTTTACCTAAAATTACCA-TTTTA
1 CCCTAAACTTT-CC-AAAATT-CCATTTTTA
*
39923881 CCCCTAAACTTTCCAAAA-TCTCATTTTGA
1 -CCCTAAACTTTCCAAAATTC-CATTTTTA
*
39923910 CCCT-GA-TTTCACCTAAAATTACCA-TTTTA
1 CCCTAAACTTT--CC-AAAATT-CCATTTTTA
*
39923939 CCCCTAAACTTTCCAAAATCCCATTTTTA
1 -CCCTAAACTTTCCAAAATTCCATTTTTA
39923968 ACCTCGAATG
Statistics
Matches: 260, Mismatches: 43, Indels: 92
0.66 0.11 0.23
Matches are distributed among these distances:
25 2 0.01
26 7 0.03
27 11 0.04
28 35 0.13
29 111 0.43
30 63 0.24
31 20 0.08
32 11 0.04
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTCCATTTTTA
Found at i:39923721 original size:58 final size:58
Alignment explanation
Indices: 39923590--39923965 Score: 431
Period size: 58 Copynumber: 6.4 Consensus size: 58
39923580 GCTCTCTAGT
* * *
39923590 CCCTAAACTTTCCAAAATTCCATTTTTGACCCTGAAACTT--CCAAAAATTACCATTTTA-
1 CCCTAAACTTTCCAAAATTCCA-TTTTGACCCCG--ATTTCACCTAAAATTACCATTTTAC
* * * *
39923648 CCCTCAAGCTTTCCAAAATTCCATTTTAACCCCGATTTCACCCAAAATTATCATTTTAC
1 CCCT-AAACTTTCCAAAATTCCATTTTGACCCCGATTTCACCTAAAATTACCATTTTAC
* * * * *
39923707 CCCTAAACTTTCCAAAATTCCATTTTAACCTCGATTTTAGCTAAAATTACCATTTTAT
1 CCCTAAACTTTCCAAAATTCCATTTTGACCCCGATTTCACCTAAAATTACCATTTTAC
* * * *
39923765 CCTTGAACTCTT-CGAAA-TCTCATTTTGACCCCGATTTCACCAAAAATTACCATTTTAC
1 CCCTAAACT-TTCCAAAATTC-CATTTTGACCCCGATTTCACCTAAAATTACCATTTTAC
** * * *
39923823 CCCCGAACTTTCTAAAATTCCATTTTTGACCCAGATTTTACCTAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAATTCCA-TTTTGACCCCGATTTCACCTAAAATTACCATTTTAC
*
39923882 CCCTAAACTTTCCAAAA-TCTCATTTTGACCCTGATTTCACCTAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAATTC-CATTTTGACCCCGATTTCACCTAAAATTACCATTTTAC
*
39923940 CCCTAAACTTTCCAAAATCCCATTTT
1 CCCTAAACTTTCCAAAATTCCATTTT
39923966 TAACCTCGAA
Statistics
Matches: 272, Mismatches: 35, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
56 3 0.01
57 4 0.01
58 190 0.70
59 75 0.28
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAATTCCATTTTGACCCCGATTTCACCTAAAATTACCATTTTAC
Found at i:39923913 original size:28 final size:28
Alignment explanation
Indices: 39923874--39923965 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
39923864 CTAAAATTAC
39923874 CATTTTACCCCTAAACTTTCCAAAATCT
1 CATTTTACCCCTAAACTTTCCAAAATCT
*
39923902 CATTTTGA-CCCT-GA-TTTCACCTAAAAT-T
1 CATTTT-ACCCCTAAACTTT--CC-AAAATCT
*
39923930 ACCATTTTACCCCTAAACTTTCCAAAATCC
1 --CATTTTACCCCTAAACTTTCCAAAATCT
39923960 CATTTT
1 CATTTT
39923966 TAACCTCGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 19 0.37
29 12 0.24
30 12 0.24
31 1 0.02
32 3 0.06
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.37
Consensus pattern (28 bp):
CATTTTACCCCTAAACTTTCCAAAATCT
Found at i:39923921 original size:117 final size:115
Alignment explanation
Indices: 39923590--39923966 Score: 483
Period size: 117 Copynumber: 3.2 Consensus size: 115
39923580 GCTCTCTAGT
** *
39923590 CCCTAAACTTTCCAAAATTCCATTTTTGACCCTGAAACTT-CCAAAAATTACCATTTTACCCTCA
1 CCCTAAACTTTCCAAAATTCCATTTTTGACCC-G-ATTTTACCTAAAATTACCATTTTACCCT-A
* * * *
39923654 AGCTTTCCAAAAT-TCCATTTTAACCCCGATTTCACCCAAAATTATCATTTTAC
63 AACTTTCCAAAATCT-CATTTTGACCCCGATTTCACCAAAAATTACCATTTTAC
* * * *
39923707 CCCTAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTTAGCTAAAATTACCATTTTATCCTTGA
1 CCCTAAACTTTCCAAAATTCCATTTTTGACC-CGATTTTACCTAAAATTACCATTTTA-CCCTAA
*
39923771 ACTCTT-CGAAATCTCATTTTGACCCCGATTTCACCAAAAATTACCATTTTAC
64 ACT-TTCCAAAATCTCATTTTGACCCCGATTTCACCAAAAATTACCATTTTAC
** *
39923823 CCCCGAACTTTCTAAAATTCCATTTTTGACCCAGATTTTACCTAAAATTACCATTTTACCCCTAA
1 CCCTAAACTTTCCAAAATTCCATTTTTGACCC-GATTTTACCTAAAATTACCATTTTA-CCCTAA
* *
39923888 ACTTTCCAAAATCTCATTTTGACCCTGATTTCACCTAAAATTACCATTTTAC
64 ACTTTCCAAAATCTCATTTTGACCCCGATTTCACCAAAAATTACCATTTTAC
*
39923940 CCCTAAACTTTCCAAAATCCCATTTTT
1 CCCTAAACTTTCCAAAATTCCATTTTT
39923967 AACCTCGAAT
Statistics
Matches: 225, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
115 3 0.01
116 89 0.40
117 133 0.59
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (115 bp):
CCCTAAACTTTCCAAAATTCCATTTTTGACCCGATTTTACCTAAAATTACCATTTTACCCTAAAC
TTTCCAAAATCTCATTTTGACCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:39931213 original size:30 final size:30
Alignment explanation
Indices: 39931179--39931274 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 30
39931169 AGTTTGAGGG
39931179 TAAAATGGTAATTTTTGGTGAAATCGGGGT
1 TAAAATGGTAATTTTTGGTGAAATCGGGGT
* *
39931209 TAAAAATGG-GA-TTTT-G-GAAAGTTCGGGGG
1 T-AAAATGGTAATTTTTGGTGAAA--TCGGGGT
*
39931238 TAAAATGGTAATTTTTGGTGAAATCGGTGT
1 TAAAATGGTAATTTTTGGTGAAATCGGGGT
*
39931268 CAAAATG
1 TAAAATG
39931275 AGATTTTGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
27 4 0.08
28 8 0.15
29 12 0.23
30 17 0.32
31 8 0.15
32 4 0.08
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.33
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGTGAAATCGGGGT
Found at i:39931223 original size:59 final size:58
Alignment explanation
Indices: 39931147--39931408 Score: 307
Period size: 59 Copynumber: 4.5 Consensus size: 58
39931137 GGAAAATTTA
39931147 GGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAATCG
* * *
39931205 GGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGTT-AAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAATCG
* * * * * * *
39931264 GTGTCAAAAT-GAGATTTTGAAAAG-TTCAGGGATAAAATGGTAATTTTAGCTAAAATCG
1 GGGTTAAAATGGA-ATTTTGGAAAGTTTGAGGG-TAAAATGGTAATTTTTGGTGAAATCG
* * * *
39931322 AGGTTAAAATGGAATTTTGGAAAGCTTGAGGGTAAAATGGTAATTTTT-G-GAAGTTTCA
1 GGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAA--ATCG
*
39931380 GGGTCAAAAATGGAATTTTGGAAAGTTTG
1 GGGT-TAAAATGGAATTTTGGAAAGTTTG
39931409 GGGACTAGAG
Statistics
Matches: 170, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
56 2 0.01
57 5 0.03
58 80 0.47
59 83 0.49
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (58 bp):
GGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAATCG
Found at i:39931406 original size:30 final size:28
Alignment explanation
Indices: 39931123--39931407 Score: 139
Period size: 29 Copynumber: 9.8 Consensus size: 28
39931113 CTCAATGGCA
* *
39931123 AAAATGTAATTTTGGGAAAATTT-AGGGTT
1 AAAATGGAATTTT-GGAAAGTTTCAGGG-T
*
39931152 AAAATGGAATTTTGGAAAGTTTGAGGGT
1 AAAATGGAATTTTGGAAAGTTTCAGGGT
*
39931180 AAAATGGTAATTTTTGGTGAAA---TCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTTCAGGG-T
* *
39931210 AAAAATGGGATTTTGGAAAG-TTCGGGGGT
1 -AAAATGGAATTTTGGAAAGTTTC-AGGGT
39931239 AAAATGGTAATTTTTGGTGAAA---TC-GGTGT
1 AAAATGG-AA-TTTT-G-GAAAGTTTCAGG-GT
*
39931268 CAAAAT-GAGATTTTGAAAAG-TTCAGGGAT
1 -AAAATGGA-ATTTTGGAAAGTTTCAGGG-T
* * *
39931297 AAAATGGTAATTTTAGCTAAA--ATCGAGGTT
1 AAAATGG-AATTTT-G-GAAAGTTTC-AGGGT
* *
39931327 AAAATGGAATTTTGGAAAGCTTGAGGGT
1 AAAATGGAATTTTGGAAAGTTTCAGGGT
39931355 AAAATGGTAATTTTTGG-AAGTTTCAGGGT
1 AAAATGG-AA-TTTTGGAAAGTTTCAGGGT
39931384 CAAAAATGGAATTTTGGAAAGTTT
1 --AAAATGGAATTTTGGAAAGTTT
39931408 GGGGACTAGA
Statistics
Matches: 207, Mismatches: 16, Indels: 65
0.72 0.06 0.23
Matches are distributed among these distances:
26 3 0.01
27 8 0.04
28 51 0.25
29 68 0.33
30 47 0.23
31 22 0.11
32 8 0.04
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTCAGGGT
Found at i:39934724 original size:17 final size:19
Alignment explanation
Indices: 39934691--39934725 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
39934681 TTCACCATTG
39934691 ATTCAACATTCTATGTTTC
1 ATTCAACATTCTATGTTTC
39934710 ATTC-ACATT-TATGTTT
1 ATTCAACATTCTATGTTT
39934726 ATATCTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (19 bp):
ATTCAACATTCTATGTTTC
Found at i:39935648 original size:23 final size:23
Alignment explanation
Indices: 39935586--39935707 Score: 127
Period size: 23 Copynumber: 5.3 Consensus size: 23
39935576 AAGCACTGAT
* * *
39935586 GTGCTAACTACAGAAGAACCGAA
1 GTGCTAAATACAGAAGCATCGAA
*
39935609 GTGCTAACTACAGAAGCATCGAA
1 GTGCTAAATACAGAAGCATCGAA
* *
39935632 GTGCTAAATACAGAAGCATAGAT
1 GTGCTAAATACAGAAGCATCGAA
* * * *
39935655 GTGCTACATACAAAAGCACCAAA
1 GTGCTAAATACAGAAGCATCGAA
* * *
39935678 GTGCTAATTACAAAAGCATCCAA
1 GTGCTAAATACAGAAGCATCGAA
39935701 GTGCTAA
1 GTGCTAA
39935708 TCATATCTCA
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (23 bp):
GTGCTAAATACAGAAGCATCGAA
Found at i:39935659 original size:46 final size:46
Alignment explanation
Indices: 39935572--39935706 Score: 119
Period size: 46 Copynumber: 2.9 Consensus size: 46
39935562 AGTGTTAGTA
** * * * **
39935572 ACAAAAGCACTGATGTGCTAACTACAGAAGAACCGAAGTGCTA-ACT
1 ACAAAAGCACCAAAGTGCTAAATACAGAAGCATAGAAGTGCTACA-T
* * * *
39935618 ACAGAAGCATCGAAGTGCTAAATACAGAAGCATAGATGTGCTACAT
1 ACAAAAGCACCAAAGTGCTAAATACAGAAGCATAGAAGTGCTACAT
* * **
39935664 ACAAAAGCACCAAAGTGCTAATTACAAAAGCATCCAAGTGCTA
1 ACAAAAGCACCAAAGTGCTAAATACAGAAGCATAGAAGTGCTA
39935707 ATCATATCTC
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
46 70 0.99
47 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.18
Consensus pattern (46 bp):
ACAAAAGCACCAAAGTGCTAAATACAGAAGCATAGAAGTGCTACAT
Found at i:39947432 original size:52 final size:51
Alignment explanation
Indices: 39947370--39947479 Score: 132
Period size: 52 Copynumber: 2.1 Consensus size: 51
39947360 CTGTTAGAAA
* * *
39947370 CCTTCATAAAGTAGAGCAA-ATGAGTCATGTTTCATGATTTAATACGTACAAT
1 CCTTAATAAAGTAGA-AAAGATGAATCATGTTTCATGATTTAATA-GTACAAT
* * *
39947422 CCTTAATAAAGTAGAAAAGATGAATTATGTTTCATGATTTGATAGTATAAT
1 CCTTAATAAAGTAGAAAAGATGAATCATGTTTCATGATTTAATAGTACAAT
*
39947473 CTTTAAT
1 CCTTAAT
39947480 GAATTAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 14 0.28
52 36 0.72
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (51 bp):
CCTTAATAAAGTAGAAAAGATGAATCATGTTTCATGATTTAATAGTACAAT
Found at i:39954178 original size:62 final size:62
Alignment explanation
Indices: 39954076--39954207 Score: 174
Period size: 62 Copynumber: 2.1 Consensus size: 62
39954066 GGTTATATTT
* * * ** *
39954076 CAATGATGCATTATGTGTCAATATGATATGATAGCGCTAAGCGTAAATTACTTTAGTCTTTC
1 CAATGATGCATTAAGTGCCAATATGATATGATAGCACTAAGCACAAATTACTTTAGACTTTC
* * *
39954138 CAATGATGCATTAAGTGCCAGTATGATTTGATAGCACTAAGCACATATTACTTTAGACTTTC
1 CAATGATGCATTAAGTGCCAATATGATATGATAGCACTAAGCACAAATTACTTTAGACTTTC
*
39954200 CGATGATG
1 CAATGATG
39954208 TACCGAGATG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (62 bp):
CAATGATGCATTAAGTGCCAATATGATATGATAGCACTAAGCACAAATTACTTTAGACTTTC
Found at i:39960696 original size:19 final size:19
Alignment explanation
Indices: 39960667--39960717 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
39960657 TCTCAATCAT
39960667 TTTTAAATAATTT-TTATTAA
1 TTTT-AATAATTTGTTA-TAA
39960687 TTTTAATAATTTGTTATAA
1 TTTTAATAATTTGTTATAA
*
39960706 TTCTCAATAATT
1 TT-TTAATAATT
39960718 ATAACTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAATAATTTGTTATAA
Found at i:39960958 original size:18 final size:18
Alignment explanation
Indices: 39960935--39960971 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39960925 TTTTATAACT
39960935 ATTTGAAAAATCATGTGA
1 ATTTGAAAAATCATGTGA
39960953 ATTTGAAAAATCATGTGA
1 ATTTGAAAAATCATGTGA
39960971 A
1 A
39960972 GGATGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (18 bp):
ATTTGAAAAATCATGTGA
Found at i:39969762 original size:17 final size:16
Alignment explanation
Indices: 39969742--39969797 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
39969732 TTCACTTAGG
39969742 TAATGAAATTTATTATA
1 TAAT-AAATTTATTATA
39969759 TAATAAA-TT-TT-T-
1 TAATAAATTTATTATA
39969771 T-ATAAA-TTATTATA
1 TAATAAATTTATTATA
39969785 TAATAAATTTATT
1 TAATAAATTTATT
39969798 TTACATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
11 7 0.21
12 3 0.09
13 2 0.06
14 3 0.09
15 7 0.21
16 8 0.24
17 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATAAATTTATTATA
Found at i:39969768 original size:16 final size:15
Alignment explanation
Indices: 39969751--39969793 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
39969741 GTAATGAAAT
39969751 TTATTATATAATAAA
1 TTATTATATAATAAA
39969766 TT-TT-T-T-ATAAA
1 TTATTATATAATAAA
39969777 TTATTATATAATAAA
1 TTATTATATAATAAA
39969792 TT
1 TT
39969794 TATTTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 7 0.29
12 3 0.12
13 2 0.08
14 3 0.12
15 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTATATAATAAA
Found at i:39973705 original size:27 final size:27
Alignment explanation
Indices: 39973675--39973729 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
39973665 ATCAAAGAGC
39973675 GGCGATTGAGAGCATTGCTTCAACTTT
1 GGCGATTGAGAGCATTGCTTCAACTTT
39973702 GGCGATTGAGAGCATTGCTTCAACTTT
1 GGCGATTGAGAGCATTGCTTCAACTTT
39973729 G
1 G
39973730 ACTTTGTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (27 bp):
GGCGATTGAGAGCATTGCTTCAACTTT
Found at i:39980360 original size:16 final size:15
Alignment explanation
Indices: 39980315--39980363 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
39980305 AAGCTTGTTT
*
39980315 TATA-TATATTTTAA
1 TATATTATATTTTTA
*
39980329 TATATTTTTATTTTTA
1 TATA-TTATATTTTTA
39980345 TATATTATATTATTTA
1 TATATTATATT-TTTA
39980361 TAT
1 TAT
39980364 TACATAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 19 0.66
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTATATTTTTA
Found at i:39980928 original size:32 final size:32
Alignment explanation
Indices: 39980888--39980951 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
39980878 GATGTTAAAA
* *
39980888 TCGTTGCTATATAGTATTTTCTGTTCACATCG
1 TCGTTGCTATATAGTAGTTTATGTTCACATCG
*
39980920 TCGTTGCTATATGGTAGTTTATGTTCACATCG
1 TCGTTGCTATATAGTAGTTTATGTTCACATCG
39980952 CTTGTATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (32 bp):
TCGTTGCTATATAGTAGTTTATGTTCACATCG
Found at i:39989118 original size:24 final size:23
Alignment explanation
Indices: 39989086--39989132 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
39989076 TATAGTATAT
39989086 GTTAAATATAATTTATTTCTAAA
1 GTTAAATATAATTTATTTCTAAA
* *
39989109 GTTAATATATAGTTTATTTTTAAA
1 GTTAA-ATATAATTTATTTCTAAA
39989133 AAAATCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (23 bp):
GTTAAATATAATTTATTTCTAAA
Found at i:39989958 original size:20 final size:21
Alignment explanation
Indices: 39989935--39989976 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
39989925 TAAAAAAAAT
39989935 AAATCTAAATA-AAAATT-CTA
1 AAATCTAAA-ACAAAATTACTA
*
39989955 AAATTTAAAACAAAATTACTA
1 AAATCTAAAACAAAATTACTA
39989976 A
1 A
39989977 TGGGGTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 1 0.05
20 14 0.74
21 4 0.21
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATCTAAAACAAAATTACTA
Found at i:39992369 original size:31 final size:31
Alignment explanation
Indices: 39992328--39992394 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
39992318 TACAAAATGA
* * * * *
39992328 TCACTGAACTATTCGAAAGTTTTTATTTAAG
1 TCACTAAACTAATCAAAACTTTCTATTTAAG
39992359 TCACTAAACTAATCAAAACTTTCTATTTAAG
1 TCACTAAACTAATCAAAACTTTCTATTTAAG
39992390 TCACT
1 TCACT
39992395 GGGCTGTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (31 bp):
TCACTAAACTAATCAAAACTTTCTATTTAAG
Found at i:39993272 original size:13 final size:13
Alignment explanation
Indices: 39993238--39993269 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39993228 TTAATATCAT
39993238 AATCA-TTAACAA
1 AATCATTTAACAA
39993250 AATCATTTAA-AA
1 AATCATTTAACAA
39993262 AATCATTT
1 AATCATTT
39993270 TAATTTAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (13 bp):
AATCATTTAACAA
Found at i:39993690 original size:3 final size:3
Alignment explanation
Indices: 39993682--39993715 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
39993672 TTTGTATTAC
39993682 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39993716 GGGTTAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40001429 original size:12 final size:12
Alignment explanation
Indices: 40001412--40001446 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40001402 TGTTGGTCTT
*
40001412 TCTCTTTCACCC
1 TCTCTTACACCC
*
40001424 TCTCTTGCACCC
1 TCTCTTACACCC
40001436 TCTCTTACACC
1 TCTCTTACACC
40001447 AAATTTGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.11, C:0.49, G:0.03, T:0.37
Consensus pattern (12 bp):
TCTCTTACACCC
Found at i:40002979 original size:14 final size:15
Alignment explanation
Indices: 40002950--40002980 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40002940 TAACTTAAAG
40002950 GGAGCCAATCTTGAA
1 GGAGCCAATCTTGAA
40002965 GGAGCCAAT-TTGAA
1 GGAGCCAATCTTGAA
40002979 GG
1 GG
40002981 TAAAAGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19
Consensus pattern (15 bp):
GGAGCCAATCTTGAA
Done.