Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 121 of 203
Found at i:38366524 original size:20 final size:19
Alignment explanation
Indices: 38366496--38366534 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38366486 GCAAGCTGAT
*
38366496 TTTAGCTCGATTCCAGCTCC
1 TTTACCTCG-TTCCAGCTCC
*
38366516 TTTACCTCGTTTCAGCTCC
1 TTTACCTCGTTCCAGCTCC
38366535 AACCAGCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.13, C:0.36, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTACCTCGTTCCAGCTCC
Found at i:38366561 original size:20 final size:20
Alignment explanation
Indices: 38366538--38366577 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
38366528 CAGCTCCAAC
38366538 CAGCTCACTT-GAGCTCAATT
1 CAGCTCA-TTCGAGCTCAATT
38366558 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
38366578 TAGTTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAATT
Found at i:38371089 original size:31 final size:31
Alignment explanation
Indices: 38371053--38371257 Score: 118
Period size: 31 Copynumber: 6.7 Consensus size: 31
38371043 ATATAAGTAT
* *
38371053 TACATTGCTGAAATTTATTTGTATATGGTTA
1 TACATTGCTGAAATTGATTTGTATATGATTA
* * **
38371084 TACATT-ATCGAAATTGATTTCTATATGAAGA
1 TACATTGCT-GAAATTGATTTGTATATGATTA
* *
38371115 TA-AGTTGCCG-AATTGATTCGTATATGATTA
1 TACA-TTGCTGAAATTGATTTGTATATGATTA
* * * * *
38371145 TACTTTGCTGTAATTTATTTGCATATGGTTA
1 TACATTGCTGAAATTGATTTGTATATGATTA
* * **
38371176 TACATT-ATCGAAATTGATTTGTATATAAAGA
1 TACATTGCT-GAAATTGATTTGTATATGATTA
* * *
38371207 TA-AGTTG-TCAAATTTGATTCGTATATGAATA
1 TACA-TTGCTGAAA-TTGATTTGTATATGATTA
* *
38371238 TATATTGTTG-AATTGATTTG
1 TACATTGCTGAAATTGATTTG
38371258 AGCATTGGAT
Statistics
Matches: 130, Mismatches: 33, Indels: 23
0.70 0.18 0.12
Matches are distributed among these distances:
30 37 0.28
31 91 0.70
32 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44
Consensus pattern (31 bp):
TACATTGCTGAAATTGATTTGTATATGATTA
Found at i:38371164 original size:92 final size:92
Alignment explanation
Indices: 38371031--38371257 Score: 305
Period size: 92 Copynumber: 2.5 Consensus size: 92
38371021 ATAAATTTTT
* *
38371031 GAATTAATTCGTATAT-AAGTATTACATTGCTGAAATTTATTTGTATATGGTTATACATTATCGA
1 GAATTGATTCGTATATGAA-TA-TACATTGCTGAAATTTATTTGCATATGGTTATACATTATCGA
*
38371095 AATTGATTTCTATATGAAGATAAGTTGCC
64 AATTGATTTCTATATAAAGATAAGTTGCC
* * *
38371124 GAATTGATTCGTATATGATTATACTTTGCTGTAATTTATTTGCATATGGTTATACATTATCGAAA
1 GAATTGATTCGTATATGAATATACATTGCTGAAATTTATTTGCATATGGTTATACATTATCGAAA
* *
38371189 TTGATTTGTATATAAAGATAAGTTGTC
66 TTGATTTCTATATAAAGATAAGTTGCC
* * * *
38371216 AAATTTGATTCGTATATGAATATATATTGTTG-AATTGATTTG
1 GAA-TTGATTCGTATATGAATATACATTGCTGAAATTTATTTG
38371258 AGCATTGGAT
Statistics
Matches: 118, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
92 76 0.64
93 41 0.35
94 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (92 bp):
GAATTGATTCGTATATGAATATACATTGCTGAAATTTATTTGCATATGGTTATACATTATCGAAA
TTGATTTCTATATAAAGATAAGTTGCC
Found at i:38372596 original size:50 final size:49
Alignment explanation
Indices: 38372542--38372686 Score: 157
Period size: 50 Copynumber: 2.9 Consensus size: 49
38372532 AAGGTGGAAG
* *
38372542 TATGTAGCAGTATATCTGCATATCAGTGGTGGCTAGACCACAAATTGTTA
1 TATGT-GCAGTATATCTGCATATCAGTGGTGGCTTGTCCACAAATTGTTA
* * * *
38372592 TATGTGGCAGTATATCTGCATATAAGTTGTGGCTTGTCCGCAAAGTGTTA
1 TATGT-GCAGTATATCTGCATATCAGTGGTGGCTTGTCCACAAATTGTTA
* * * *
38372642 TCAATG-GTAGTTTATCTTCAAATCAGTGGTGGCTTGTCCACAAAT
1 T--ATGTGCAGTATATCTGCATATCAGTGGTGGCTTGTCCACAAAT
38372687 GGTGATTCGG
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
50 75 0.96
52 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (49 bp):
TATGTGCAGTATATCTGCATATCAGTGGTGGCTTGTCCACAAATTGTTA
Found at i:38394322 original size:29 final size:29
Alignment explanation
Indices: 38394273--38394354 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
38394263 TGTTACAGTC
*
38394273 ACCATCCCTTTTCATAATCGATAGCCG-A
1 ACCATCCCTTTTCATATTCGATAGCCGTA
* * ** *
38394301 AGCTATCCCTTTTCATATTCGATGGTTGTC
1 A-CCATCCCTTTTCATATTCGATAGCCGTA
38394331 ACCATCCCTTTTCATATTCGATAG
1 ACCATCCCTTTTCATATTCGATAG
38394355 TCAAAGTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 1 0.02
29 42 0.95
30 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATAGCCGTA
Found at i:38396145 original size:22 final size:23
Alignment explanation
Indices: 38396115--38396159 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
38396105 TTAATATGCT
*
38396115 TTTATAAAT-CTTTACATTATAAC
1 TTTATAAATACTATA-ATTATAAC
38396138 TTTA-AAATACTATAATTATAAC
1 TTTATAAATACTATAATTATAAC
38396160 AAATAGGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTATAAATACTATAATTATAAC
Found at i:38397567 original size:37 final size:38
Alignment explanation
Indices: 38397516--38397588 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
38397506 TTTTCATAAT
** *
38397516 TTCACTTTTTCACTTTCAA-TCACTATTCAATTCAAAA
1 TTCACTTTGCCACTTTCAAGTCAATATTCAATTCAAAA
38397553 TTCACTTTGCCACTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTGCCACTTTCAAGTCAATATTCAATTCAA
38397589 TTCTACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.41
Consensus pattern (38 bp):
TTCACTTTGCCACTTTCAAGTCAATATTCAATTCAAAA
Found at i:38397851 original size:51 final size:51
Alignment explanation
Indices: 38397793--38397983 Score: 210
Period size: 51 Copynumber: 3.8 Consensus size: 51
38397783 CCGGTTCACA
* *
38397793 TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCTGATACACG
1 TAGTAGCCTACACATAGTACTACACACGCGACCATCACTATCTGATACACG
* * * * * * *
38397844 TAGTAGCCTGCACATAGTACTACATACGCGATCA-AAGCTATC-CAGTACGCA
1 TAGTAGCCTACACATAGTACTACACACGCGACCATCA-CTATCTGA-TACACG
*
38397895 TAGTAGCCTACACATAGTACTACACATGCGACCTATCA-T-TCTGATACACG
1 TAGTAGCCTACACATAGTACTACACACGCGACC-ATCACTATCTGATACACG
* * *
38397945 TAGTAGCCTGCACATAGTACTGCACACGTGACCATCACT
1 TAGTAGCCTACACATAGTACTACACACGCGACCATCACT
38397984 TTCACTTTCA
Statistics
Matches: 113, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
49 4 0.04
50 38 0.34
51 69 0.61
52 1 0.01
53 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTACACATAGTACTACACACGCGACCATCACTATCTGATACACG
Found at i:38401780 original size:44 final size:44
Alignment explanation
Indices: 38401722--38401890 Score: 243
Period size: 44 Copynumber: 3.8 Consensus size: 44
38401712 TTTGTTTACT
*
38401722 TTCAACCTATTCCACCGCTGACCAGGGAGATAGGATTCTCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATC
* *
38401766 TTCAACTTATTCCACTGTTGACCAGGGAGATAGGATT-TACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCT-CAATC
* *
38401810 TTCAACCTATTCCACTGCTGACAAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATC
* *
38401854 TTCAATCTATTCCACTGCTGCCCAGGGA-AGTAGGATT
1 TTCAACCTATTCCACTGCTGACCAGGGAGA-TAGGATT
38401891 ACTGGCTTCA
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
43 2 0.02
44 110 0.98
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATC
Found at i:38401925 original size:88 final size:89
Alignment explanation
Indices: 38401722--38401926 Score: 215
Period size: 88 Copynumber: 2.3 Consensus size: 89
38401712 TTTGTTTACT
* * * * *
38401722 TTCAACCTATTCCACCGCTGAC-CAGGGAGATAGGATTCTCAATCTTCAACTTATTCCACTGTTG
1 TTCAACCTACTCCACTGCTAACACAGGGAGATAGGATTCACAATCTTCAACTTATTCCACTGCTG
*
38401786 ACCAGGGAGATAGGATTTACAATC
66 ACCAGGGAGATAGGATTTACAAGC
* *
38401810 TTCAACCTATTCCACTGCTGACA-AGGGAGATAGGATTCACAATCTTCAA-TCTATTCCACTGCT
1 TTCAACCTACTCCACTGCTAACACAGGGAGATAGGATTCACAATCTTCAACT-TATTCCACTGCT
* **
38401873 GCCCAGGGA-AGTAGGA-TTACTGGC
65 GACCAGGGAGA-TAGGATTTACAAGC
** *
38401897 TTCAATGTACTCCGCTG-TAACCACAGGGAG
1 TTCAACCTACTCCACTGCTAA-CACAGGGAG
38401927 GTTAAAATCC
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
86 2 0.02
87 22 0.22
88 76 0.76
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (89 bp):
TTCAACCTACTCCACTGCTAACACAGGGAGATAGGATTCACAATCTTCAACTTATTCCACTGCTG
ACCAGGGAGATAGGATTTACAAGC
Found at i:38402265 original size:264 final size:265
Alignment explanation
Indices: 38401850--38402340 Score: 876
Period size: 264 Copynumber: 1.9 Consensus size: 265
38401840 TAGGATTCAC
* *
38401850 AATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGGATTACTGGCTTCAATGTACTCCGCTGT
1 AATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
38401915 AACCACAGGGAGGTTAAAATCCGCCATCTTCGATCTACTCCGCTACTGCTTAGGGAGATAAGATC
66 AACCACAGGGAGGTTAAAATCCGCCATCTTCGATCTACTCCGCTACTGCTTAGGGAGATAAGATC
*
38401980 TGAAATCTTCAATCTATTCCACTATTGTCTAGGAAAGTAGAATTACTGGCTTCAATGTATTCCAC
131 TGAAATCTTCAATCTATTCCACTATTGTCTAGGAAAGTAGAATTACTGGCTTCAATGTACTCCAC
38402045 TGTAACCACAGGGAGGTAAAATTTGCCATCTTCAATCTACTCCGCTATTACTTAGGGCGATAAGA
196 TGTAACCACAGGGAGGTAAAATTTGCCATCTTCAATCTACTCCGCTATTACTTAGGGCGATAAGA
38402110 CCTGA
261 CCTGA
* * *
38402115 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
38402180 AACCACAGGGAGG-TAAAATCCGCCATCTTCGATCTGCTCCGCTACTTCTTAGGGAGATAAGATC
66 AACCACAGGGAGGTTAAAATCCGCCATCTTCGATCTACTCCGCTACTGCTTAGGGAGATAAGATC
* * *
38402244 TGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCTAC
131 TGAAATCTTCAATCTATTCCACTATTGTCTAGGAAAGTAGAATTACTGGCTTCAATGTACTCCAC
38402309 TGTAACCACAGGGAGGTAAAATTTGCCATCTT
196 TGTAACCACAGGGAGGTAAAATTTGCCATCTT
38402341 TGATCTGCTT
Statistics
Matches: 215, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
264 142 0.66
265 73 0.34
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (265 bp):
AATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
AACCACAGGGAGGTTAAAATCCGCCATCTTCGATCTACTCCGCTACTGCTTAGGGAGATAAGATC
TGAAATCTTCAATCTATTCCACTATTGTCTAGGAAAGTAGAATTACTGGCTTCAATGTACTCCAC
TGTAACCACAGGGAGGTAAAATTTGCCATCTTCAATCTACTCCGCTATTACTTAGGGCGATAAGA
CCTGA
Found at i:38402349 original size:132 final size:132
Alignment explanation
Indices: 38401833--38402346 Score: 780
Period size: 132 Copynumber: 3.9 Consensus size: 132
38401823 ACTGCTGACA
* * * * *
38401833 AGGGAGATAGGAT-TCACAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGGATTACTGGC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGC
*
38401897 TTCAATGTACTCCGCTGTAACCACAGGGAGGTTAAAATCCGCCATCTTCGATCTACTCCGCTACT
65 TTCAATGTACTCCACTGTAACCACAGGGAGG-TAAAATCCGCCATCTTCGATCTACTCCGCTACT
*
38401962 GCTT
129 TCTT
* * *
38401966 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCTAGGAAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* ** *
38402031 TCAATGTATTCCACTGTAACCACAGGGAGGTAAAATTTGCCATCTTCAATCTACTCCGCTA-TTA
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCGCTACTT-
38402095 CTT
130 CTT
* * *
38402098 AGGGCGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTATTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
38402163 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCGCTACTTC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCGCTACTTC
38402228 TT
131 TT
*
38402230 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* ** *
38402295 TCAATGTACTCTACTGTAACCACAGGGAGGTAAAATTTGCCATCTTTGATCT
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCT
38402347 GCTTCGCTGT
Statistics
Matches: 345, Mismatches: 33, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
131 1 0.00
132 258 0.75
133 84 0.24
134 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTCCGCTACTTC
TT
Found at i:38402463 original size:44 final size:44
Alignment explanation
Indices: 38402408--38402551 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 44
38402398 CGCTACAACC
* *
38402408 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGCG
1 CAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGGCG
* * * ** * * ** *
38402452 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACT
1 CAGGAAGGCAAG-GCTGGTATCTTCGATCTGCTTCGCTGTCGGCG
* *
38402496 CAAGG-AGGCAAGGCTGGTTTCTTCGATCTGCTTCGCTGTCGGTG
1 C-AGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGGCG
*
38402540 TAGGAAGGCAAG
1 CAGGAAGGCAAG
38402552 ATCTGCTATT
Statistics
Matches: 71, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 21 0.30
44 29 0.41
45 21 0.30
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGGCG
Found at i:38402526 original size:88 final size:88
Alignment explanation
Indices: 38402337--38402563 Score: 364
Period size: 88 Copynumber: 2.6 Consensus size: 88
38402327 AAATTTGCCA
* *
38402337 TCTTTGATCTGCTTCGCTGTCGGCGTAGGAAGGCAAGATCTGCTATTTTTTTAACTTGCTCCGCT
1 TCTTCGATCTGCTTCGCTGTCGGCGTAGGAAGGCAAGATCTGCTA--TTTTTAACCTGCTCCGCT
*
38402402 ACAACCCAGGGAGGCAAGGCTGGTG
64 ACAACCCAAGGAGGCAAGGCTGGTG
* *
38402427 TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGC
1 TCTTCGATCTGCTTCGCTGTCGGCGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTAC
* *
38402492 AACTCAAGGAGGCAAGGCTGGTT
66 AACCCAAGGAGGCAAGGCTGGTG
*
38402515 TCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTT
1 TCTTCGATCTGCTTCGCTGTCGGCGTAGGAAGGCAAGATCTGCTATTTT
38402564 CACTGATCTG
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
88 85 0.66
90 43 0.34
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (88 bp):
TCTTCGATCTGCTTCGCTGTCGGCGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTAC
AACCCAAGGAGGCAAGGCTGGTG
Found at i:38402533 original size:43 final size:43
Alignment explanation
Indices: 38402393--38402533 Score: 106
Period size: 43 Copynumber: 3.2 Consensus size: 43
38402383 TTTTTTAACT
* * *
38402393 TGCTCCGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATC
1 TGCTCCGCTGCAACCCAAGGAGGCAAGGCTGGTTTCTTCGATC
* ** * * * ** *
38402436 TGCTTCGCTGTCGGCGC-AGGAAGGCAAGATCTGCTATT-TTTAACC
1 TGCTCCGCTG-CAACCCAAGG-AGGCAAG-GCTGGT-TTCTTCGATC
*
38402481 TGCTCCGCTGCAACTCAAGGAGGCAAGGCTGGTTTCTTCGATC
1 TGCTCCGCTGCAACCCAAGGAGGCAAGGCTGGTTTCTTCGATC
*
38402524 TGCTTCGCTG
1 TGCTCCGCTG
38402534 TCGGTGTAGG
Statistics
Matches: 70, Mismatches: 22, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
42 2 0.03
43 27 0.39
44 20 0.29
45 20 0.29
46 1 0.01
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (43 bp):
TGCTCCGCTGCAACCCAAGGAGGCAAGGCTGGTTTCTTCGATC
Found at i:38403837 original size:18 final size:17
Alignment explanation
Indices: 38403780--38403844 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
38403770 TTGGCCTCTC
* **
38403780 CTTTTTCTTTTCTTTTT
1 CTTTTTTTTTTCACTTT
**
38403797 CTTTTTCTTTTTCTTTTT
1 CTTTTT-TTTTTCACTTT
38403815 CTTTTTTTTTTCACTTT
1 CTTTTTTTTTTCACTTT
38403832 CATTTTTTATTTT
1 C-TTTTTT-TTTT
38403845 GATTTTGACC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 16 0.38
18 22 0.52
19 4 0.10
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTTTTTTTTCACTTT
Found at i:38403844 original size:6 final size:6
Alignment explanation
Indices: 38403780--38403826 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
38403770 TTGGCCTCTC
38403780 CTTTTT C-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT -TTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
38403826 C
1 C
38403827 ACTTTCATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:38408862 original size:20 final size:20
Alignment explanation
Indices: 38408834--38409148 Score: 108
Period size: 20 Copynumber: 13.8 Consensus size: 20
38408824 TATATAAGAT
38408834 ATATATATAGAAAGTATAAA
1 ATATATATAGAAAGTATAAA
*
38408854 ATATGTATAGAAAGTATACGTACA
1 ATATATATAGAAAGTATA---A-A
* *
38408878 TATATATATATAAGGTAATAAA
1 -ATATATATAGAAAGT-ATAAA
* * *
38408900 TATATAAATCATAAAGATAATGATTAT
1 -ATATATAT-AGAAAG-T-AT-A--AA
38408927 ATATATATAGAAAGTATAAA
1 ATATATATAGAAAGTATAAA
*
38408947 ATATGTATAGAAAGTATACGTACA
1 ATATATATAGAAAGTATA---A-A
* *
38408971 TATATATATATAAGGTAATAAA
1 -ATATATATAGAAAGT-ATAAA
* * *
38408993 TATATAAATCATAAAGATAATGATTAT
1 -ATATATAT-AGAAAG-T-AT-A--AA
38409020 ATATATATAGAAAGTATAAA
1 ATATATATAGAAAGTATAAA
*
38409040 ATATGTATAGAAAGTATACGTACA
1 ATATATATAGAAAGTATA---A-A
* *
38409064 TATATATATATAAGGTAATAAA
1 -ATATATATAGAAAGT-ATAAA
* * *
38409086 TATATAAATCATAAAGATAATGATTAT
1 -ATATATAT-AGAAAG-T-AT-A--AA
38409113 ATATATATAGAAAGTATAAA
1 ATATATATAGAAAGTATAAA
*
38409133 ATATGTATAGAAAGTA
1 ATATATATAGAAAGTA
38409149 ATAATAATTA
Statistics
Matches: 231, Mismatches: 31, Indels: 66
0.70 0.09 0.20
Matches are distributed among these distances:
20 69 0.30
22 30 0.13
23 27 0.12
24 18 0.08
25 54 0.23
26 30 0.13
27 3 0.01
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:38408920 original size:24 final size:23
Alignment explanation
Indices: 38408827--38409121 Score: 155
Period size: 24 Copynumber: 12.7 Consensus size: 23
38408817 ACATATATAT
*
38408827 ATAAGATATATATATAGAAAG-T-
1 ATAA-ATATATATATATAAAGATA
* *
38408849 ATAAA-ATATGTATAGAAAGTATA
1 ATAAATATATATATATAAAG-ATA
* * *
38408872 CGTACATATATATATAT-AAGGTA
1 -ATAAATATATATATATAAAGATA
*
38408895 ATAAATATATAAATCATAAAGATA
1 ATAAATATATATAT-ATAAAGATA
* *
38408919 ATGATTATATATATATAGAA-AGT-
1 ATAAATATATATATATA-AAGA-TA
* *
38408942 ATAAA-ATATGTATAGAAAGTATA
1 ATAAATATATATATATAAAG-ATA
* * *
38408965 CGTACATATATATATAT-AAGGTA
1 -ATAAATATATATATATAAAGATA
*
38408988 ATAAATATATAAATCATAAAGATA
1 ATAAATATATATAT-ATAAAGATA
* *
38409012 ATGATTATATATATATAGAA-AGT-
1 ATAAATATATATATATA-AAGA-TA
* *
38409035 ATAAA-ATATGTATAGAAAGTATA
1 ATAAATATATATATATAAAG-ATA
* * *
38409058 CGTACATATATATATAT-AAGGTA
1 -ATAAATATATATATATAAAGATA
*
38409081 ATAAATATATAAATCATAAAGATA
1 ATAAATATATATAT-ATAAAGATA
* *
38409105 ATGATTATATATATATA
1 ATAAATATATATATATA
38409122 GAAAGTATAA
Statistics
Matches: 203, Mismatches: 45, Indels: 49
0.68 0.15 0.16
Matches are distributed among these distances:
20 13 0.06
21 5 0.02
22 58 0.29
23 31 0.15
24 72 0.35
25 24 0.12
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (23 bp):
ATAAATATATATATATAAAGATA
Found at i:38409166 original size:93 final size:93
Alignment explanation
Indices: 38408832--38409148 Score: 634
Period size: 93 Copynumber: 3.4 Consensus size: 93
38408822 TATATATAAG
38408832 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTATACGTACATATATATATATAAGGTAAT
1 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTATACGTACATATATATATATAAGGTAAT
38408897 AAATATATAAATCATAAAGATAATGATT
66 AAATATATAAATCATAAAGATAATGATT
38408925 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTATACGTACATATATATATATAAGGTAAT
1 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTATACGTACATATATATATATAAGGTAAT
38408990 AAATATATAAATCATAAAGATAATGATT
66 AAATATATAAATCATAAAGATAATGATT
38409018 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTATACGTACATATATATATATAAGGTAAT
1 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTATACGTACATATATATATATAAGGTAAT
38409083 AAATATATAAATCATAAAGATAATGATT
66 AAATATATAAATCATAAAGATAATGATT
38409111 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTA
1 ATATATATATAGAAAGTATAAAATATGTATAGAAAGTA
38409149 ATAATAATTA
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 224 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (93 bp):
ATATATATATAGAAAGTATAAAATATGTATAGAAAGTATACGTACATATATATATATAAGGTAAT
AAATATATAAATCATAAAGATAATGATT
Found at i:38412238 original size:10 final size:11
Alignment explanation
Indices: 38412213--38412238 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38412203 TGGTGCTGTA
38412213 TTTTTATGTTG
1 TTTTTATGTTG
38412224 TTTTTATGTTG
1 TTTTTATGTTG
38412235 TTTT
1 TTTT
38412239 GGTGTTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (11 bp):
TTTTTATGTTG
Found at i:38412251 original size:34 final size:34
Alignment explanation
Indices: 38412190--38412261 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
38412180 GTGATGCTAT
* *
38412190 TTTTTGTGTTGTTTGGTGCTGTATTTTTATGTTG
1 TTTTTATGTTGTTTGGTGCTGTATTTTTATGGTG
*
38412224 TTTTTATGTTGTTTTGGTG-T-TACTTTTTGTGGTG
1 TTTTTATGTTG-TTTGGTGCTGTA-TTTTTATGGTG
38412258 TTTT
1 TTTT
38412262 ATTGTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.06
34 24 0.73
35 7 0.21
ACGTcount: A:0.06, C:0.03, G:0.25, T:0.67
Consensus pattern (34 bp):
TTTTTATGTTGTTTGGTGCTGTATTTTTATGGTG
Found at i:38412472 original size:20 final size:19
Alignment explanation
Indices: 38412445--38412487 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
38412435 TTTAGTATCA
* *
38412445 TTTTATATTTTTTTTCTTG
1 TTTTATATTTGTTTTCATG
38412464 TTTTAATATTTGTTTTCATG
1 TTTT-ATATTTGTTTTCATG
38412484 TTTT
1 TTTT
38412488 TAAATGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTATATTTGTTTTCATG
Found at i:38415000 original size:39 final size:40
Alignment explanation
Indices: 38414940--38415067 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 40
38414930 TATGTTTAAA
* *
38414940 TTTATGTGATTATATGGGTATTGCGATATATGCTTGAATG
1 TTTAAGTGATTATATGAGTATTGCGATATATGCTTGAATG
* * * * *
38414980 TTTTA-TGATCATATGAGTATTACGATATGTGCTTGAACG
1 TTTAAGTGATTATATGAGTATTGCGATATATGCTTGAATG
* * * *
38415019 -TTAAGTAATTATATGAGTATTGTGATATTTGCTTAAATG
1 TTTAAGTGATTATATGAGTATTGCGATATATGCTTGAATG
*
38415058 -TTATGTGATT
1 TTTAAGTGATT
38415068 GTATATGTAA
Statistics
Matches: 70, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
38 3 0.04
39 64 0.91
40 3 0.04
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.45
Consensus pattern (40 bp):
TTTAAGTGATTATATGAGTATTGCGATATATGCTTGAATG
Found at i:38415085 original size:78 final size:78
Alignment explanation
Indices: 38414948--38415094 Score: 170
Period size: 78 Copynumber: 1.9 Consensus size: 78
38414938 AATTTATGTG
* * * * * *
38414948 ATTATATGGGTATTGCGATATATGCTTGAATGTTTTATGATCATATGAGTATTACGATATGTGCT
1 ATTATATGAGTATTGCGATATATGCTTAAATGTTATATGATCATATGAGTAATACGATATATACT
38415013 TGAACGTTAAGTA
66 TGAACGTTAAGTA
* * * ** *
38415026 ATTATATGAGTATTGTGATATTTGCTTAAATGTTATGTGATTGTAT-ATGTAATATGATATATAC
1 ATTATATGAGTATTGCGATATATGCTTAAATGTTATATGATCATATGA-GTAATACGATATATAC
38415090 TTGAA
65 TTGAA
38415095 AGCGAATATG
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
77 1 0.02
78 55 0.98
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (78 bp):
ATTATATGAGTATTGCGATATATGCTTAAATGTTATATGATCATATGAGTAATACGATATATACT
TGAACGTTAAGTA
Found at i:38419603 original size:48 final size:48
Alignment explanation
Indices: 38419527--38419623 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
38419517 GCAAATTGAA
*
38419527 CAATGGAAAGGCAACTAGATTTAAATTGAATAGTAGTGGTGGTGTGTG
1 CAATAGAAAGGCAACTAGATTTAAATTGAATAGTAGTGGTGGTGTGTG
*
38419575 CAATAGAAAGGCAAGTAGATTTAAATTGAATAGTAGTGGTGGTGTGTG
1 CAATAGAAAGGCAACTAGATTTAAATTGAATAGTAGTGGTGGTGTGTG
38419623 C
1 C
38419624 TTTGAAGGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.29
Consensus pattern (48 bp):
CAATAGAAAGGCAACTAGATTTAAATTGAATAGTAGTGGTGGTGTGTG
Found at i:38427303 original size:19 final size:19
Alignment explanation
Indices: 38427279--38427316 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
38427269 TTATTCACTC
38427279 TGTTTATTATTTTGATACT
1 TGTTTATTATTTTGATACT
38427298 TGTTTATTATTTTGATACT
1 TGTTTATTATTTTGATACT
38427317 GACCTCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (19 bp):
TGTTTATTATTTTGATACT
Found at i:38427976 original size:72 final size:73
Alignment explanation
Indices: 38427891--38428037 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 73
38427881 CCCACACAAA
*
38427891 ATATCTTTTCTAATATCCCATCCTTA-GAAAGAAAACAAATATTCTCTAAAATTTTGTGTGCTAA
1 ATATCTTTTCTAATATCCCATCCTTAGGAAAGAAAACAAATATTCTCTAAAATTTTGTGTACTAA
38427955 TTTGGAAG
66 TTTGGAAG
** *
38427963 ATATCTTTTCTAATATCCCATCCTTAGGAAAGAAAGTAAATATTCTCTGAAATTTTGTGTACTAA
1 ATATCTTTTCTAATATCCCATCCTTAGGAAAGAAAACAAATATTCTCTAAAATTTTGTGTACTAA
38428028 TTTGGAAG
66 TTTGGAAG
38428036 AT
1 AT
38428038 CAAATCTCCA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
72 26 0.37
73 44 0.63
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (73 bp):
ATATCTTTTCTAATATCCCATCCTTAGGAAAGAAAACAAATATTCTCTAAAATTTTGTGTACTAA
TTTGGAAG
Found at i:38435255 original size:36 final size:36
Alignment explanation
Indices: 38435187--38435255 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
38435177 GAAAAGCTGT
*
38435187 TTTTACATATATTAATAAATTTATATTTTAAATTGG
1 TTTTACATATATTAATAAATTTATATTATAAATTGG
38435223 TTTTACATATATTGCAAT-AATTTAT-TTATAAAT
1 TTTTACATATATT--AATAAATTTATATTATAAAT
38435256 AAATCAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 20 0.67
37 7 0.23
38 3 0.10
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (36 bp):
TTTTACATATATTAATAAATTTATATTATAAATTGG
Found at i:38436511 original size:32 final size:32
Alignment explanation
Indices: 38436468--38436557 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
38436458 CAATCATTTC
38436468 AATATCTAACAAGCTTAAAACATAATAAATTG
1 AATATCTAACAAGCTTAAAACATAATAAATTG
* *
38436500 AATATCCAACAAGCTTAAAACATAATAAATTT
1 AATATCTAACAAGCTTAAAACATAATAAATTG
38436532 AATATCTAACAAGCTTAAAACATAAT
1 AATATCTAACAAGCTTAAAACATAAT
38436558 CAATATCTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.28
Consensus pattern (32 bp):
AATATCTAACAAGCTTAAAACATAATAAATTG
Found at i:38436581 original size:27 final size:27
Alignment explanation
Indices: 38436532--38436584 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
38436522 TAATAAATTT
*
38436532 AATATCTAACAAGCTTAAAACATAATC
1 AATATCTAACAAGATTAAAACATAATC
*
38436559 AATATCTAACAA-ATTCAAGACATAAT
1 AATATCTAACAAGATT-AAAACATAAT
38436585 AATTTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (27 bp):
AATATCTAACAAGATTAAAACATAATC
Found at i:38438865 original size:3 final size:3
Alignment explanation
Indices: 38438857--38438976 Score: 240
Period size: 3 Copynumber: 40.0 Consensus size: 3
38438847 TATTTTTTCC
38438857 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38438905 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38438953 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
38438977 CATATATTTT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38439123 original size:20 final size:20
Alignment explanation
Indices: 38439091--38439132 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38439081 ACAAATGTAT
*
38439091 ATATATTTAAATATACATAC
1 ATATATTTAAATACACATAC
38439111 ATAT-TTTAGAATACACATAC
1 ATATATTTA-AATACACATAC
38439131 AT
1 AT
38439133 TTCCCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATATTTAAATACACATAC
Found at i:38443328 original size:145 final size:145
Alignment explanation
Indices: 38443065--38443356 Score: 476
Period size: 145 Copynumber: 2.0 Consensus size: 145
38443055 ATCTTGTGTA
* * *
38443065 GTAGTCTTTCAAATGTTGAAGTTGGCAATGCCTTAGTAAAAAGATCTACTAAATTCTCACTAGAA
1 GTAGTCTTTCAAAGGTTGAAGTTGGCAATGCCTTAGTAAAAAAATCTACTAAATTCTCACTAAAA
* * *
38443130 CAAATTTTTTGAACATTTATATCACCTCTTTTCGCAAGATCATAGGTGAAGAATAATTTTGGTGA
66 CAAATTTTTTAAACATTTATATCACCTCTTTTCGCAAGATCATAGGTAAAGAATAATTTTGGTAA
*
38443195 AATACGTTTCGTTCT
131 AATACATTTCGTTCT
38443210 GTAGTCTTTCAAAGGTTGAAGTTGGCAATGCCTTAGTAAAAAAATCTACTAAATTCTCACTAAAA
1 GTAGTCTTTCAAAGGTTGAAGTTGGCAATGCCTTAGTAAAAAAATCTACTAAATTCTCACTAAAA
** * * *
38443275 TGATTTTTTTAAACATTTATATCACCTCTTTTCTCAAGATCATGGGTAAAGAATAATTTTGGTAA
66 CAAATTTTTTAAACATTTATATCACCTCTTTTCGCAAGATCATAGGTAAAGAATAATTTTGGTAA
38443340 AATACATTTCGTTCT
131 AATACATTTCGTTCT
38443355 GT
1 GT
38443357 CACCTTTGAT
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
145 135 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (145 bp):
GTAGTCTTTCAAAGGTTGAAGTTGGCAATGCCTTAGTAAAAAAATCTACTAAATTCTCACTAAAA
CAAATTTTTTAAACATTTATATCACCTCTTTTCGCAAGATCATAGGTAAAGAATAATTTTGGTAA
AATACATTTCGTTCT
Found at i:38445101 original size:21 final size:21
Alignment explanation
Indices: 38445072--38445120 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
38445062 TTTTTTGCAC
38445072 TAACAGTTTGCCCTATTAGGA
1 TAACAGTTTGCCCTATTAGGA
* *
38445093 TATCAGTTTGCCCTATTGGGA
1 TAACAGTTTGCCCTATTAGGA
38445114 TAACAGT
1 TAACAGT
38445121 CTTCTATGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (21 bp):
TAACAGTTTGCCCTATTAGGA
Found at i:38446129 original size:24 final size:24
Alignment explanation
Indices: 38446097--38446145 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
38446087 TTAATGGGTG
*
38446097 TCCAATTGAATTTTCAATTATTTT
1 TCCAATTGAATTCTCAATTATTTT
38446121 TCCAATTGAATTCTCAATTATTTT
1 TCCAATTGAATTCTCAATTATTTT
38446145 T
1 T
38446146 TGCATCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (24 bp):
TCCAATTGAATTCTCAATTATTTT
Found at i:38446301 original size:18 final size:18
Alignment explanation
Indices: 38446278--38446318 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
38446268 ACCTGATGAA
38446278 AAAACAAGTA-GTCTTTCC
1 AAAACAA-TATGTCTTTCC
*
38446296 AAAAC-ATATTTCTTTCC
1 AAAACAATATGTCTTTCC
38446313 AAAACA
1 AAAACA
38446319 TATTTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAACAATATGTCTTTCC
Found at i:38446311 original size:17 final size:17
Alignment explanation
Indices: 38446289--38446330 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
38446279 AAACAAGTAG
38446289 TCTTTCCAAAACATATT
1 TCTTTCCAAAACATATT
38446306 TCTTTCCAAAACATATT
1 TCTTTCCAAAACATATT
*
38446323 TATTTCCA
1 TCTTTCCA
38446331 CATTCAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (17 bp):
TCTTTCCAAAACATATT
Found at i:38455061 original size:15 final size:16
Alignment explanation
Indices: 38455041--38455070 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38455031 TTTTATATGT
38455041 TAAAATAAA-TAATAA
1 TAAAATAAAGTAATAA
38455056 TAAAATAAAGTAATA
1 TAAAATAAAGTAATA
38455071 TATTAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
TAAAATAAAGTAATAA
Found at i:38463989 original size:20 final size:20
Alignment explanation
Indices: 38463966--38464009 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
38463956 ATCACTTTCC
38463966 ATTTCAAGTATGAACTTACT
1 ATTTCAAGTATGAACTTACT
38463986 ATTTCAAGTATGAACTTACT
1 ATTTCAAGTATGAACTTACT
38464006 ATTT
1 ATTT
38464010 TATTACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (20 bp):
ATTTCAAGTATGAACTTACT
Found at i:38470180 original size:110 final size:110
Alignment explanation
Indices: 38469987--38470208 Score: 419
Period size: 110 Copynumber: 2.0 Consensus size: 110
38469977 TATATATTTA
38469987 TTGTTGAAATGAGAATAAAATAAAAATGCAAAAACTGAATAAATGATCAAATTGAGCGGAACGCC
1 TTGTTGAAATGAGAATAAAATAAAAATGCAAAAACTGAATAAATGATCAAATTGAGCGGAACGCC
38470052 GGATTTGAGTACTTCTGATCAAGTGACAAAGTGATAAGTGGTAGC
66 GGATTTGAGTACTTCTGATCAAGTGACAAAGTGATAAGTGGTAGC
38470097 TTGTTGAAATGAGAATAAAATAAAAATGCAAAAACTGAATAAATGATCAAATTGAGCGGAACGCC
1 TTGTTGAAATGAGAATAAAATAAAAATGCAAAAACTGAATAAATGATCAAATTGAGCGGAACGCC
*
38470162 GGATTTGAGT-TTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC
66 GGATTTGAGTACT-TCTGATCAAGTGACAAAGTGATAAGTGGTAGC
38470207 TT
1 TT
38470209 TAGCTACACT
Statistics
Matches: 110, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
109 1 0.01
110 109 0.99
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (110 bp):
TTGTTGAAATGAGAATAAAATAAAAATGCAAAAACTGAATAAATGATCAAATTGAGCGGAACGCC
GGATTTGAGTACTTCTGATCAAGTGACAAAGTGATAAGTGGTAGC
Found at i:38470239 original size:46 final size:46
Alignment explanation
Indices: 38470172--38470291 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
38470162 GGATTTGAGT
*
38470172 TTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAC
1 TTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACAC
*
38470218 TTATCTAATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACAC
1 TTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACAC
*
38470264 TTATCTGATC-AGGGAC-AAGTGATAAGTG
1 TTATCTGATCAAGTGACAAAGTGATAAGTG
38470292 ATCATACGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 12 0.17
45 5 0.07
46 53 0.76
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
TTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACAC
Found at i:38471147 original size:49 final size:50
Alignment explanation
Indices: 38471055--38471152 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 50
38471045 ATCTATTTAT
* * * *
38471055 AGGTTGAAAAAATCTTATTCTAATAAATGATAAATAGATGAAGTGTAGTA
1 AGGTTGAAAAAACCTTATTCTAATAAATGATAAATAAAAGAAGTATAGTA
* *
38471105 AGGTTG-AAAAACCTTATTCTAATCACTAGA-AAATAAAAGAAGTATAGT
1 AGGTTGAAAAAACCTTATTCTAATAAAT-GATAAATAAAAGAAGTATAGT
38471153 TCTTATGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 33 0.80
50 8 0.20
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (50 bp):
AGGTTGAAAAAACCTTATTCTAATAAATGATAAATAAAAGAAGTATAGTA
Found at i:38475648 original size:13 final size:13
Alignment explanation
Indices: 38475626--38475657 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
38475616 ATTAACACTG
*
38475626 TTAAAATTCTCTA
1 TTAAATTTCTCTA
38475639 TTAAATTTCTCTA
1 TTAAATTTCTCTA
38475652 TTAAAT
1 TTAAAT
38475658 CCAGGTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAATTTCTCTA
Found at i:38476614 original size:12 final size:12
Alignment explanation
Indices: 38476597--38476622 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38476587 TAATCCTCTC
38476597 AATTTCCTTCCA
1 AATTTCCTTCCA
38476609 AATTTCCTTCCA
1 AATTTCCTTCCA
38476621 AA
1 AA
38476623 ATTCTCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTCCTTCCA
Found at i:38476653 original size:40 final size:40
Alignment explanation
Indices: 38476609--38476695 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
38476599 TTTCCTTCCA
38476609 AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTC
1 AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTC
*
38476649 AATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTC
1 AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTC
38476689 AATTTCC
1 AATTTCC
38476696 CCTCAATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.41
Consensus pattern (40 bp):
AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTC
Found at i:38477833 original size:7 final size:7
Alignment explanation
Indices: 38477821--38477845 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38477811 AGTCGATTGA
38477821 TATTTAG
1 TATTTAG
38477828 TATTTAG
1 TATTTAG
38477835 TATTTAG
1 TATTTAG
38477842 TATT
1 TATT
38477846 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:38479067 original size:18 final size:18
Alignment explanation
Indices: 38479044--38479096 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 18
38479034 TTTGATGTAA
38479044 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAATTTAAT
38479062 TAAAAACCCTAACCTAATTTAAT
1 TAAAAA--C---CCTAATTTAAT
38479085 TAAAAACCCTAA
1 TAAAAACCCTAA
38479097 CCCTAACCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 11 0.37
20 1 0.03
21 1 0.03
23 17 0.57
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAACCCTAATTTAAT
Found at i:38479122 original size:23 final size:23
Alignment explanation
Indices: 38479051--38479098 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
38479041 TAATAAAAAC
38479051 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
38479074 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
38479097 CC
1 CC
38479099 CTAACCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (23 bp):
CCTAATTTAATTAAAAACCCTAA
Found at i:38479135 original size:30 final size:29
Alignment explanation
Indices: 38479066--38479122 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
38479056 TTTAATTAAA
38479066 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
38479095 AACCCTAACCTATTTTAATTAAAAACCC
1 AACCCTAACCTAATTTAATTAAAAACCC
38479123 ACTGCCCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:38481689 original size:124 final size:124
Alignment explanation
Indices: 38481394--38481742 Score: 601
Period size: 124 Copynumber: 2.8 Consensus size: 124
38481384 CCCAAACTTG
38481394 CTACTATAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTATAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
38481459 TAGAAGCAATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTACTTCTTACATGAC
* ** * *
38481517 CAACTATAGCAAAATCGCGTCCACGAGGGCATGATTTCACAATTTCTTCTGAAATAACATCCTGG
1 CTACTATAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
38481582 TAGAAGCGATTTTATACTATTTGCTTAGAAACATCAAAAAAAATTACTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTACTTCTTACATGAC
*
38481641 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTATAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
38481706 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
38481743 CTCGAAATAA
Statistics
Matches: 208, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
123 92 0.44
124 116 0.56
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTATAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTACTTCTTACATGAC
Found at i:38481797 original size:23 final size:23
Alignment explanation
Indices: 38481769--38481825 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
38481759 TCAGGACCTA
38481769 AAACCCTAAAAAGCCTGAACCCT
1 AAACCCTAAAAAGCCTGAACCCT
*
38481792 AAACCCTAAAAAGCTTGAACCCT
1 AAACCCTAAAAAGCCTGAACCCT
38481815 AAACCCTAAAA
1 AAACCCTAAAA
38481826 GCCAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.47, C:0.32, G:0.07, T:0.14
Consensus pattern (23 bp):
AAACCCTAAAAAGCCTGAACCCT
Found at i:38483205 original size:2 final size:2
Alignment explanation
Indices: 38483198--38483229 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38483188 CTTCACGCCG
38483198 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
38483230 AATGACATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38483600 original size:6 final size:6
Alignment explanation
Indices: 38483589--38483616 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38483579 ATCTAGTTCT
38483589 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
38483617 AAATTGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:38483674 original size:6 final size:6
Alignment explanation
Indices: 38483665--38483704 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
38483655 TCGGTTTTAG
38483665 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTG
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTG
38483705 TTGAGTTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.17, T:0.68
Consensus pattern (6 bp):
TTTGAT
Found at i:38487032 original size:24 final size:26
Alignment explanation
Indices: 38486985--38487033 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
38486975 GTTTTTGAAT
*
38486985 TTATTTTAAAGTTATTTTGTTAGTTA
1 TTATTATAAAGTTATTTTGTTAGTTA
38487011 TTATTATAAA-TTA-TTTGTTAGTT
1 TTATTATAAAGTTATTTTGTTAGTT
38487034 TAATGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 3 0.14
26 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (26 bp):
TTATTATAAAGTTATTTTGTTAGTTA
Found at i:38493420 original size:16 final size:17
Alignment explanation
Indices: 38493397--38493433 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
38493387 AAAAACAAAT
38493397 AAAA-TTACATT-ATAA
1 AAAATTTACATTCATAA
*
38493412 AAAATTTACTTTCATAA
1 AAAATTTACATTCATAA
38493429 AAAAT
1 AAAAT
38493434 CACAAAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTTACATTCATAA
Found at i:38493530 original size:101 final size:100
Alignment explanation
Indices: 38493411--38493840 Score: 515
Period size: 101 Copynumber: 4.2 Consensus size: 100
38493401 TTACATTATA
*
38493411 AAAAATTTACTTTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATC
1 AAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATC
*
38493476 ATAAATTAATAACAAAATAACTATAAAATAAATTTT
66 ATAAATTACTAACAAAATAACTATAAAAT-AATTTT
* * *
38493512 AAAAATTTACATTCATAAAAAATTACAAAACACTAAACTAAACACTATCAACTTATAACCTAATC
1 AAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATC
*
38493577 ATAAATTACTAGCAAAATAACTATAAAATAATCTTTT
66 ATAAATTACTAACAAAATAACTATAAAATAA--TTTT
* * * *
38493614 AAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAGCAC-AACAATTTATGACCTAATC
1 AAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATC
* * *
38493678 TTAAGTTATTAACAAAATAACTATAAAATAATTTT
66 ATAAATTACTAACAAAATAACTATAAAATAATTTT
** * * * * *
38493713 AAAAAATAAAAAAATTTACAT-GAAATTCACAAAACACTAAACTAAAACACAAACAAATTA-AAC
1 -AAAAAT--TTACA-TT-CATAAAAAATCACAAAACACTAAACT-AAACACTAACAATTTATAAC
* * * *
38493776 ATAATCATAAATTACTAACAAAATAATTTTAAAATAATTATAA
60 CTAATCATAAATTACTAACAAAATAACTATAAAATAATT-T-T
*
38493819 AAAAAATTACATTCATAAAAAA
1 AAAAATTTACATTCATAAAAAA
38493841 AATTAAACCA
Statistics
Matches: 277, Mismatches: 40, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
99 4 0.01
100 7 0.03
101 134 0.48
102 52 0.19
103 24 0.09
104 42 0.15
105 14 0.05
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.27
Consensus pattern (100 bp):
AAAAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATC
ATAAATTACTAACAAAATAACTATAAAATAATTTT
Found at i:38493800 original size:205 final size:203
Alignment explanation
Indices: 38493407--38493840 Score: 570
Period size: 205 Copynumber: 2.1 Consensus size: 203
38493397 AAAATTACAT
*
38493407 TATAAAAAATTTACTTTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCT
1 TATAAAAAA-TTACATTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCT
** * *
38493472 AATCATAAATTAATAACAAAATAACTATAAAATAAATTTTAAAAATTTACATTCATAAAAAATTA
65 AATCATAAATTAATAACAAAATAACTATAAAATAAATTTTAAAAATAAAAATTCACAAAAAATTA
* * * * *
38493537 CAAAACACTAAACTAAACACTATCAACTTATAACCTAATCATAAATTACTAGCAAAATAACTATA
130 CAAAACACTAAACTAAACACAAACAAATTATAACATAATCATAAATTACTAACAAAATAACTATA
38493602 AAATAATCT-
195 AAATAAT-TA
* * * *
38493611 TTTAAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAGCAC-AACAATTTATGACCTA
1 TATAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTA
* * * * **
38493675 ATCTTAAGTTATTAACAAAATAACTATAAAAT-AATTTTAAAAAATAAAAAAATTTACATGAAAT
66 ATCATAAATTAATAACAAAATAACTATAAAATAAATTTT-AAAAAT--AAAAATTCACAAAAAAT
*
38493739 TCACAAAACACTAAACTAAAACACAAACAAATTA-AACATAATCATAAATTACTAACAAAATAAT
128 T-ACAAAACACTAAACT-AAACACAAACAAATTATAACATAATCATAAATTACTAACAAAATAAC
*
38493803 TTTAAAATAATTA
191 TATAAAATAATTA
*
38493816 TAAAAAAAATTACATTCATAAAAAA
1 TATAAAAAATTACATTCATAAAAAA
38493841 AATTAAACCA
Statistics
Matches: 199, Mismatches: 25, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
201 6 0.03
202 50 0.25
203 36 0.18
204 20 0.10
205 74 0.37
206 13 0.07
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (203 bp):
TATAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTA
ATCATAAATTAATAACAAAATAACTATAAAATAAATTTTAAAAATAAAAATTCACAAAAAATTAC
AAAACACTAAACTAAACACAAACAAATTATAACATAATCATAAATTACTAACAAAATAACTATAA
AATAATTA
Found at i:38493852 original size:17 final size:18
Alignment explanation
Indices: 38493815--38493854 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38493805 TAAAATAATT
**
38493815 ATAAAAAAAATTACATTC
1 ATAAAAAAAATTACAACC
38493833 ATAAAAAAAATTA-AACC
1 ATAAAAAAAATTACAACC
38493850 ATAAA
1 ATAAA
38493855 CCCTAAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAAAAATTACAACC
Found at i:38494420 original size:9 final size:9
Alignment explanation
Indices: 38494408--38494438 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38494398 CCCAAACTTA
*
38494408 AATAACTCG
1 AATAATTCG
38494417 AATAATTCG
1 AATAATTCG
38494426 AATAATTCG
1 AATAATTCG
38494435 AATA
1 AATA
38494439 TAAACTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (9 bp):
AATAATTCG
Found at i:38494484 original size:29 final size:29
Alignment explanation
Indices: 38494444--38494502 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
38494434 GAATATAAAC
*
38494444 TATATTTTTTATTTTTAAAATACACCACA
1 TATATTTTTTATTTTTAAAAAACACCACA
*
38494473 TATATTTTTTATTTTTAAAAAACACTACA
1 TATATTTTTTATTTTTAAAAAACACCACA
38494502 T
1 T
38494503 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAAAACACCACA
Found at i:38497533 original size:19 final size:19
Alignment explanation
Indices: 38497509--38497552 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
38497499 GTATTATTTT
38497509 TGTTGTTTATTTGGAATGA
1 TGTTGTTTATTTGGAATGA
**
38497528 TGTTGTTTATTTGGGTTGA
1 TGTTGTTTATTTGGAATGA
38497547 TGTTGT
1 TGTTGT
38497553 GTTACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (19 bp):
TGTTGTTTATTTGGAATGA
Found at i:38497707 original size:5 final size:5
Alignment explanation
Indices: 38497699--38497751 Score: 63
Period size: 5 Copynumber: 10.4 Consensus size: 5
38497689 CGAACAAATA
* *
38497699 ATTCG ATTCG ATTCG ATTCG ATTCG ATTTCT ATCTC- ACTCG ATTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG A-TTCG AT-TCG ATTCG ATTCG ATTCG
38497750 AT
1 AT
38497752 AAAACTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 34 0.81
6 6 0.14
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (5 bp):
ATTCG
Found at i:38498124 original size:17 final size:17
Alignment explanation
Indices: 38498102--38498143 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
38498092 CATCACTAAT
*
38498102 AAAATAATATTTTTTAA
1 AAAATAATATTTATTAA
*
38498119 AAAATAAAATTTATTAA
1 AAAATAATATTTATTAA
38498136 AAAA-AATA
1 AAAATAATA
38498144 ATGGTGCCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATAATATTTATTAA
Found at i:38511382 original size:58 final size:60
Alignment explanation
Indices: 38511271--38511404 Score: 150
Period size: 58 Copynumber: 2.3 Consensus size: 60
38511261 TCAACTTACT
* * * * * *
38511271 AATTTTTTCCATATTGAGGTCTAAACTTTTTTTTTATCCAAGTTAGGCCCTAAACGTAG-C
1 AATTGTTTCCACATTGAGGTATAAACATTTTTTGTATCCAAGTTAGGCACTAAAC-TAGAC
* *
38511331 AATTGTTTCCACATTGAGGTATGAACATTTTTTGT-T-CAAGTTAGGCACTAAACTTGAC
1 AATTGTTTCCACATTGAGGTATAAACATTTTTTGTATCCAAGTTAGGCACTAAACTAGAC
38511389 AATTG-TTCTCACATTG
1 AATTGTTTC-CACATTG
38511405 GGACTTCAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 5 0.08
58 29 0.45
59 1 0.02
60 29 0.45
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (60 bp):
AATTGTTTCCACATTGAGGTATAAACATTTTTTGTATCCAAGTTAGGCACTAAACTAGAC
Found at i:38512543 original size:7 final size:6
Alignment explanation
Indices: 38512507--38512539 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
38512497 GAATTTGTGT
38512507 AAAA-A AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
38512540 ATAAGGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:38513308 original size:17 final size:17
Alignment explanation
Indices: 38513286--38513321 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38513276 TATTGGATGT
*
38513286 TTGTGATAAGGAGTAAA
1 TTGTGATAAGGACTAAA
*
38513303 TTGTGATAATGACTAAA
1 TTGTGATAAGGACTAAA
38513320 TT
1 TT
38513322 ATATGTGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (17 bp):
TTGTGATAAGGACTAAA
Found at i:38515993 original size:4 final size:4
Alignment explanation
Indices: 38515984--38516008 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
38515974 GTTGGATTAT
38515984 ACTA ACTA ACTA ACTA ACTA ACTA A
1 ACTA ACTA ACTA ACTA ACTA ACTA A
38516009 AAGTTGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACTA
Found at i:38526464 original size:24 final size:24
Alignment explanation
Indices: 38526419--38526464 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38526409 GGGTTATAAT
**
38526419 TTATATGTTTAAAATACTTAAAGA
1 TTATATGTTTAAAATAAATAAAGA
38526443 TTATAT-TTTAAATATAAATAAA
1 TTATATGTTTAAA-ATAAATAAA
38526465 CAGAGATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
TTATATGTTTAAAATAAATAAAGA
Found at i:38534854 original size:18 final size:18
Alignment explanation
Indices: 38534831--38534869 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38534821 AACCTATGCA
38534831 TAATATA-TTTAATTTGTT
1 TAATATATTTTAATTT-TT
38534849 TAATATATTTTAATTTTT
1 TAATATATTTTAATTTTT
38534867 TAA
1 TAA
38534870 ACTTAATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATATATTTTAATTTTT
Found at i:38534959 original size:19 final size:21
Alignment explanation
Indices: 38534927--38534968 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
38534917 TTATTTTTAT
*
38534927 AAAATTATATTTAAAA-TTAA
1 AAAATTATACTTAAAACTTAA
38534947 AAAATTAT-CTTAAAACTTAA
1 AAAATTATACTTAAAACTTAA
38534967 AA
1 AA
38534969 TACACCTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTATACTTAAAACTTAA
Found at i:38541439 original size:24 final size:24
Alignment explanation
Indices: 38541411--38541456 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38541401 ATATTTTCTC
*
38541411 TTTTACATGTAAT-TTTAATTTTAA
1 TTTTACA-ATAATATTTAATTTTAA
*
38541435 TTTTATAATAATATTTAATTTT
1 TTTTACAATAATATTTAATTTT
38541457 TAGGATGAAA
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:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTACAATAATATTTAATTTTAA
Found at i:38543742 original size:43 final size:43
Alignment explanation
Indices: 38543637--38543757 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 43
38543627 GATTTGAGAT
* * * *
38543637 TTACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGA
1 TTACATGTAAGACCACGTCTGGGACAGTGGCATTGTTATATGA
* *
38543679 TT--TTGCATAAGACC-CTGTCTGGGACAGTGGCATTGTTATTTGA
1 TTACATG--TAAGACCAC-GTCTGGGACAGTGGCATTGTTATATGA
38543722 TTACATGTAAGACCACGTCTGGGAC-GTTGGCATTGT
1 TTACATGTAAGACCACGTCTGGGACAG-TGGCATTGT
38543758 ATGAGCTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
40 2 0.03
42 27 0.42
43 33 0.51
44 1 0.02
45 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TTACATGTAAGACCACGTCTGGGACAGTGGCATTGTTATATGA
Found at i:38549668 original size:50 final size:50
Alignment explanation
Indices: 38549613--38549799 Score: 180
Period size: 50 Copynumber: 3.8 Consensus size: 50
38549603 TATTGGGGTT
* * * *
38549613 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
* *
38549663 ATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
** * * * * * * **
38549713 ATGAGAACTCCCATGTAAGACCATATCTGAGATATGACATTGGTAGTACAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCA-AG
* **
38549764 --GAAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
38549800 TTTGGCATGT
Statistics
Matches: 111, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
49 29 0.26
50 81 0.73
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
Found at i:38550034 original size:20 final size:20
Alignment explanation
Indices: 38550009--38550054 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
38549999 TGAGTTATTT
38550009 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
*
38550029 AAGTAAGAGAGTAAGTAAAG
1 AAGTAAGAGAGTAAGTAAAC
38550049 AAGTAA
1 AAGTAA
38550055 AGACCACGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:38565521 original size:40 final size:40
Alignment explanation
Indices: 38565477--38565738 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
38565467 GCTCCTCGTT
* *
38565477 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
38565517 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
38565557 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
38565596 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
38565635 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
38565674 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
38565715 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38565739 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:38571324 original size:20 final size:20
Alignment explanation
Indices: 38571299--38571336 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38571289 GTTTTTCTAG
38571299 TTTAAATTATTT-TGTTAAAT
1 TTTAAATT-TTTATGTTAAAT
38571319 TTTAAATTTTTATGTTAA
1 TTTAAATTTTTATGTTAA
38571337 TAAAGGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTTATGTTAAAT
Found at i:38582432 original size:42 final size:43
Alignment explanation
Indices: 38582329--38582477 Score: 133
Period size: 42 Copynumber: 3.5 Consensus size: 43
38582319 TGTGATATCG
* * * * *
38582329 TGTAAGACCACGTCTGGTACATTGGCATCGATT-TGA-GATTTACG
1 TGTAAGACCATGTCTGGGACAGTAGCATCG-TTAT-ATGA-TTACA
* *
38582373 TGTAAGACCATGTCTGGGACATTAGCATCG-TATATGATTTCA
1 TGTAAGACCATGTCTGGGACAGTAGCATCGTTATATGATTACA
** * * *
38582415 TGTAAGACTTTGTCTGGGACAGTGGCATCGTTATTTGATTACG
1 TGTAAGACCATGTCTGGGACAGTAGCATCGTTATATGATTACA
*
38582458 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
38582478 GTTGGCACTG
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 31 0.36
43 29 0.33
44 27 0.31
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTAGCATCGTTATATGATTACA
Found at i:38582484 original size:43 final size:42
Alignment explanation
Indices: 38582327--38582484 Score: 174
Period size: 43 Copynumber: 3.7 Consensus size: 42
38582317 TATGTGATAT
*
38582327 CGTGTAAGACCACGTCTGGTACATTGGCATCG-ATTTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTT--GA-TTA
* * * *
38582371 CGTGTAAGACCATGTCTGGGACATTAGCATCGTATATGATTT
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
* *** *
38582413 CATGTAAGACTTTGTCTGGGACAGTGGCATCGTTATTTGATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCG-TATTTGATTA
*
38582456 CGTGTAAGACCACGTCTGGGACGTTGGCA
1 CGTGTAAGACCACGTCTGGGACATTGGCA
38582485 CTGTACGAGC
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
42 29 0.31
43 33 0.35
44 29 0.31
45 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
Found at i:38599007 original size:2 final size:2
Alignment explanation
Indices: 38599002--38599716 Score: 1430
Period size: 2 Copynumber: 357.5 Consensus size: 2
38598992 TGAATTGTGT
38599002 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599044 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599086 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599128 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599170 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599212 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599254 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599296 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599338 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599380 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599422 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599464 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599506 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599548 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599590 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599632 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599674 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38599716 T
1 T
38599717 TTCTTCTCCA
Statistics
Matches: 713, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 713 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:38599921 original size:73 final size:73
Alignment explanation
Indices: 38599802--38599939 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 73
38599792 ACCAATGCAT
* *
38599802 GATCTTCCGTTCCAATGTAATTTTGATCCTTAGATTTGAATTTTTTACCGAGATTGACACACCTG
1 GATCTTCCGATACAATGTAATTTTGATCCTTAGATTTGAATTTTTTACCGAGATTGACACACCTG
38599867 CTATGAAA
66 CTATGAAA
* * *
38599875 GATCTTCCGATACAATGTAATTTTGATCCTTAGCTTTGAATTTTTTACCGAGTTTGACCCACCTG
1 GATCTTCCGATACAATGTAATTTTGATCCTTAGATTTGAATTTTTTACCGAGATTGACACACCTG
38599940 ATTGACTCAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (73 bp):
GATCTTCCGATACAATGTAATTTTGATCCTTAGATTTGAATTTTTTACCGAGATTGACACACCTG
CTATGAAA
Found at i:38604018 original size:31 final size:31
Alignment explanation
Indices: 38603978--38604040 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
38603968 TATCTAAATG
* *
38603978 ACTTAAATAAAAACTTTTAAATAGTTTAGTA
1 ACTTAAATAAAAACTTTCAAATAATTTAGTA
*
38604009 ACTTTAATAAAAACTTTCAAATAATTTAGTA
1 ACTTAAATAAAAACTTTCAAATAATTTAGTA
38604040 A
1 A
38604041 TCAAATTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTTAGTA
Found at i:38605066 original size:40 final size:40
Alignment explanation
Indices: 38605011--38605086 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
38605001 CAATCTAGTA
38605011 TATATATATATACTTATATTAAGTCACTGTTTGAGTCTAG
1 TATATATATATACTTATATTAAGTCACTGTTTGAGTCTAG
38605051 TATATATATATACTTATATTAAGTCACTGTTTGAGT
1 TATATATATATACTTATATTAAGTCACTGTTTGAGT
38605087 TAGCGTCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (40 bp):
TATATATATATACTTATATTAAGTCACTGTTTGAGTCTAG
Found at i:38610395 original size:122 final size:123
Alignment explanation
Indices: 38610153--38610496 Score: 602
Period size: 123 Copynumber: 2.8 Consensus size: 123
38610143 TTTCGAGTTG
38610153 ACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTA-TTGAGAAGAAATTGTGAA
1 ACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
*
38610216 ATCGCGCCCTCGCGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTA
65 ATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTA
* *
38610275 ACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTATGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
* *
38610340 TCGCCCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTG
66 TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTA
*
38610398 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATACTATTTGAGAAGAAATTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
*
38610463 TCGCGCCCTCGTGGACGCAATTTTGCTACAGTAG
66 TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
38610497 CAAGTTTGGG
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
122 42 0.20
123 168 0.80
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (123 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTA
Found at i:38611740 original size:6 final size:6
Alignment explanation
Indices: 38611736--38611769 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
38611726 CAAAGGTTTA
* *
38611736 GGTTTG GGTTAG GGTTAG GGTTAG AGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTT
38611770 TTTAATTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (6 bp):
GGTTAG
Found at i:38611781 original size:18 final size:18
Alignment explanation
Indices: 38611760--38612142 Score: 174
Period size: 18 Copynumber: 22.8 Consensus size: 18
38611750 TTAGGGTTAG
38611760 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
38611778 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
38611796 AGTTA-GG---TT-A--G
1 AGTTAGGGTTTTTAATTA
* * **
38611807 GGTTTGTATTTTTAATTA
1 AGTTAGGGTTTTTAATTA
38611825 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
38611843 AATTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
* * *
38611861 AGATCGGGTTTGTAATTA
1 AGTTAGGGTTTTTAATTA
*
38611879 AGTTA-GG---TT-A--G
1 AGTTAGGGTTTTTAATTA
* *
38611890 GGTTTGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
* *
38611908 AATTA-GG---TT-A--G
1 AGTTAGGGTTTTTAATTA
38611919 AGTTAGGGTTTTTAATTAA
1 AGTTAGGGTTTTTAATT-A
38611938 GTTAGGTTAGGGTTTTTAATTA
1 ---A-GTTAGGGTTTTTAATTA
* ** *
38611960 AATTA-GG-TTAGAGTTA
1 AGTTAGGGTTTTTAATTA
* *
38611976 GGGTTAGGATTTTTAATTA
1 -AGTTAGGGTTTTTAATTA
*
38611995 AGTTAGGTTAGGGTTTTAATTA
1 AGTTA-G---GGTTTTTAATTA
* *
38612017 AATTA-GG---TT-A--G
1 AGTTAGGGTTTTTAATTA
38612028 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
38612046 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
38612064 AGTTA-GG---TT-A--G
1 AGTTAGGGTTTTTAATTA
*
38612075 GGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
38612093 ACTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
38612111 AATTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
38612129 AGTTAGGGTTTTTA
1 AGTTAGGGTTTTTA
38612143 TTACATCAAA
Statistics
Matches: 266, Mismatches: 52, Indels: 94
0.65 0.13 0.23
Matches are distributed among these distances:
11 18 0.07
12 8 0.03
13 5 0.02
14 9 0.03
15 10 0.04
16 11 0.04
17 15 0.06
18 150 0.56
19 8 0.03
22 16 0.06
23 16 0.06
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.47
Consensus pattern (18 bp):
AGTTAGGGTTTTTAATTA
Found at i:38611806 original size:47 final size:47
Alignment explanation
Indices: 38611749--38612117 Score: 270
Period size: 47 Copynumber: 8.1 Consensus size: 47
38611739 TTGGGTTAGG
*
38611749 GTTAGGGTTAGAGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
1 GTTA-GGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
* **
38611797 GTTAGGTTAGGGTTTGTATTTTTAATTAAGTTAGGGTTTTTAATT-A
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
* * *
38611843 ---A----A---TTAGGGTTTTTAATTAAGATCGGGTTTGTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
* *
38611880 GTTAGGTTAGGGTTTGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTT--TTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATT--A--A-GTTAGGGTT----TTTAATTAA
* *
38611934 -TTAAGTTA-GGTTAGGGTTTTTAATTAAATTA-GG-------TT-A
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
* *
38611970 G--A-GTTAGGGTTAGGATTTTTAATTAAGTTAGGTTAGGGTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA-G---GGTTTTTAATTAA
* *
38612018 ATTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
*
38612065 GTTAGGTTAGGGTTAGGGTTTTTAATTAACTTAGGGTTTTTAATTAA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
*
38612112 ATTAGG
1 GTTAGG
38612118 GTTTTTAATT
Statistics
Matches: 254, Mismatches: 29, Indels: 77
0.71 0.08 0.21
Matches are distributed among these distances:
34 4 0.02
35 22 0.09
36 28 0.11
37 3 0.01
39 1 0.00
40 3 0.01
43 1 0.00
44 1 0.00
46 2 0.01
47 117 0.46
48 6 0.02
49 1 0.00
50 3 0.01
51 27 0.11
52 22 0.09
53 7 0.03
54 4 0.02
56 2 0.01
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (47 bp):
GTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
Found at i:38611899 original size:29 final size:29
Alignment explanation
Indices: 38611866--38612052 Score: 178
Period size: 29 Copynumber: 6.7 Consensus size: 29
38611856 AATTAAGATC
*
38611866 GGGTTTGTAATTAAGTTAGGTTAGGGTTT
1 GGGTTTTTAATTAAGTTAGGTTAGGGTTT
* * *
38611895 GGGTTTTTAATTAAATTAGGTTAGAGTTA
1 GGGTTTTTAATTAAGTTAGGTTAGGGTTT
38611924 GGGTTTTTAATTAAGTTAGGTTAGGGTTT
1 GGGTTTTTAATTAAGTTAGGTTAGGGTTT
* * *
38611953 ---TTAATTAAATTAGGTTAGAGTTAGGGTTA
1 GGGTT--TTTAATTAAGTTAG-GTTAGGGTTT
*
38611982 GGATTTTTAATTAAGTTAGGTTA------
1 GGGTTTTTAATTAAGTTAGGTTAGGGTTT
* * *
38612005 GGG-TTTTAATTAAATTAGGTTAGAGTTA
1 GGGTTTTTAATTAAGTTAGGTTAGGGTTT
38612033 GGGTTTTTAATTAAGTTAGG
1 GGGTTTTTAATTAAGTTAGG
38612053 GTTTTTAATT
Statistics
Matches: 130, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
22 18 0.14
23 2 0.02
26 2 0.02
28 15 0.12
29 79 0.61
30 12 0.09
32 2 0.02
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
GGGTTTTTAATTAAGTTAGGTTAGGGTTT
Found at i:38611937 original size:58 final size:56
Alignment explanation
Indices: 38611866--38612099 Score: 241
Period size: 52 Copynumber: 4.4 Consensus size: 56
38611856 AATTAAGATC
*
38611866 GGGTTTGTAATTAAGTTAGGTTAGGGTTTGGGTTTTTAATTAAATTAGGTTAGAGTTA
1 GGGTTTTTAATTAAGTTAGGTTA-GG-TTGGGTTTTTAATTAAATTAGGTTAGAGTTA
38611924 GGGTTTTTAATTAAGTTAGGTTA----GGGTTTTTAATTAAATTAGGTTAGAGTTA
1 GGGTTTTTAATTAAGTTAGGTTAGGTTGGGTTTTTAATTAAATTAGGTTAGAGTTA
*
38611976 GGGTTAGGATTT--TTAA-TTAAGTTAGGTTAGGG-TTTTAATTAAATTAGGTTAGAGTTA
1 GGGTT----TTTAATTAAGTTAGGTTAGGTT-GGGTTTTTAATTAAATTAGGTTAGAGTTA
* *
38612033 GGGTTTTTAATT-A---A-GTTA----GGGTTTTTAATTAAGTTAGGTTAGGGTTA
1 GGGTTTTTAATTAAGTTAGGTTAGGTTGGGTTTTTAATTAAATTAGGTTAGAGTTA
*
38612080 GGGTTTTTAATTAACTTAGG
1 GGGTTTTTAATTAAGTTAGG
38612100 GTTTTTAATT
Statistics
Matches: 155, Mismatches: 4, Indels: 40
0.78 0.02 0.20
Matches are distributed among these distances:
46 3 0.02
47 35 0.23
48 1 0.01
51 5 0.03
52 36 0.23
53 10 0.06
54 5 0.03
55 2 0.01
56 3 0.02
57 30 0.19
58 25 0.16
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (56 bp):
GGGTTTTTAATTAAGTTAGGTTAGGTTGGGTTTTTAATTAAATTAGGTTAGAGTTA
Found at i:38611955 original size:52 final size:52
Alignment explanation
Indices: 38611876--38612117 Score: 290
Period size: 47 Copynumber: 4.7 Consensus size: 52
38611866 GGGTTTGTAA
* *
38611876 TTAAGTTAGGTTAGGGTTTGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTT
1 TTAA-TTAAGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTT
38611930 TTAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTAGGATTT
1 TTAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTA--G---GG-TTT
38611988 TTAATTAAGTTAGGTTAGGG-TTTTAATTAAATTAGGTTAGAGTTAGGGTTT
1 TTAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTT
* *
38612039 TTAATT-A---A-GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTT
1 TTAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTT
*
38612086 TTAATT-A---A-CTTAGGGTTTTTAATTAAATTAGG
1 TTAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGG
38612118 GTTTTTAATT
Statistics
Matches: 175, Mismatches: 6, Indels: 21
0.87 0.03 0.10
Matches are distributed among these distances:
46 7 0.04
47 60 0.34
50 1 0.01
51 9 0.05
52 35 0.20
53 7 0.04
54 5 0.03
55 1 0.01
57 27 0.15
58 23 0.13
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (52 bp):
TTAATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTT
Found at i:38611983 original size:35 final size:34
Alignment explanation
Indices: 38611937--38612005 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
38611927 TTTTTAATTA
*
38611937 AGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
1 AGTTAGGTTAGGGATTTTAATTAAATTAGGTTAG
*
38611971 AGTTAGGGTTA-GGATTTTTAATTAAGTTAGGTTAG
1 AGTTA-GGTTAGGGA-TTTTAATTAAATTAGGTTAG
38612006 GGTTTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (34 bp):
AGTTAGGTTAGGGATTTTAATTAAATTAGGTTAG
Found at i:38612193 original size:25 final size:26
Alignment explanation
Indices: 38612138--38612201 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
38612128 AAGTTAGGGT
38612138 TTTTATTACATCAAATAGAAATTCTA
1 TTTTATTACATCAAATAGAAATTCTA
* * *
38612164 TTTTATTATATTAAATA-AACTTCTA
1 TTTTATTACATCAAATAGAAATTCTA
38612189 TTTTATTACATCA
1 TTTTATTACATCA
38612202 GATAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTATTACATCAAATAGAAATTCTA
Found at i:38612349 original size:21 final size:21
Alignment explanation
Indices: 38612302--38612351 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
38612292 CTTCCTCTAG
* *
38612302 CTTCCGGTGGCGATTGTTCTT
1 CTTCCGATGGCGATTGTGCTT
* * *
38612323 CCTCCGATGGTGATTGTGGTT
1 CTTCCGATGGCGATTGTGCTT
38612344 CTTCCGAT
1 CTTCCGAT
38612352 TCGACATCTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.08, C:0.24, G:0.28, T:0.40
Consensus pattern (21 bp):
CTTCCGATGGCGATTGTGCTT
Found at i:38614501 original size:29 final size:29
Alignment explanation
Indices: 38614469--38614552 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
38614459 AATTGAAATT
38614469 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
38614498 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
38614520 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
38614549 AAAT
1 AAAT
38614553 TAAGAGGATT
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
22 9 0.23
23 4 0.10
24 4 0.10
27 5 0.13
28 4 0.10
29 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:38614501 original size:51 final size:51
Alignment explanation
Indices: 38614446--38614560 Score: 203
Period size: 51 Copynumber: 2.3 Consensus size: 51
38614436 TTTCAAAAAT
*
38614446 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
38614497 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
38614548 GAAATTAAGAGGA
1 GAAATTGAGAGGA
38614561 TTAGAGAGGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:38615756 original size:9 final size:9
Alignment explanation
Indices: 38615742--38615831 Score: 72
Period size: 9 Copynumber: 9.6 Consensus size: 9
38615732 TTTGATTAAA
*
38615742 AATTACCTG
1 AATTACCCG
38615751 AATTACCCG
1 AATTACCCG
* *
38615760 AATAACCCA
1 AATTACCCG
*
38615769 AATTACCTG
1 AATTACCCG
*
38615778 AAAAATACCCG
1 --AATTACCCG
*
38615789 AATTACCTG
1 AATTACCCG
*
38615798 AAAATTACTCG
1 --AATTACCCG
38615809 AATTACCCG
1 AATTACCCG
*
38615818 AATTACCCA
1 AATTACCCG
38615827 AATTA
1 AATTA
38615832 AATCACTACA
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
9 49 0.78
11 14 0.22
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:38615792 original size:20 final size:20
Alignment explanation
Indices: 38615764--38615815 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
38615754 TACCCGAATA
*
38615764 ACCCAAATTACCTGAAAAAT
1 ACCCGAATTACCTGAAAAAT
*
38615784 ACCCGAATTACCTGAAAATT
1 ACCCGAATTACCTGAAAAAT
*
38615804 ACTCGAATTACC
1 ACCCGAATTACC
38615816 CGAATTACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (20 bp):
ACCCGAATTACCTGAAAAAT
Found at i:38615860 original size:17 final size:17
Alignment explanation
Indices: 38615838--38615935 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
38615828 ATTAAATCAC
*
38615838 TACATAATTAAAAGCAT
1 TACATAATTAAAAACAT
* * *
38615855 TACATAAATATTTAAATCAC
1 TACAT--A-ATTAAAAACAT
*
38615875 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
38615892 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
38615912 TACATAATTAAACACAT
1 TACATAATTAAAAACAT
38615929 TACATAA
1 TACATAA
38615936 GTCTTGAATT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 31 0.53
18 1 0.02
19 1 0.02
20 25 0.43
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:38615880 original size:20 final size:19
Alignment explanation
Indices: 38615829--38615881 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
38615819 ATTACCCAAA
38615829 TTAAATCACTACAT--AAT
1 TTAAATCACTACATAAAAT
* * *
38615846 TAAAAGCATTACATAAATAT
1 TTAAATCACTACATAAA-AT
38615866 TTAAATCACTACATAA
1 TTAAATCACTACATAA
38615882 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 11 0.41
19 1 0.04
20 15 0.56
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (19 bp):
TTAAATCACTACATAAAAT
Found at i:38615936 original size:37 final size:36
Alignment explanation
Indices: 38615832--38615944 Score: 156
Period size: 37 Copynumber: 3.1 Consensus size: 36
38615822 ACCCAAATTA
* * *
38615832 AATCACTACATAATTAAAAGCATTACATAAATATTTA
1 AATCACTACATAATTAAAA-CATTACATAAGTCTTTG
*
38615869 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATT-AAAACATTACATAAGTCTTTG
38615906 AATCACTACATAATTAAACACATTACATAAGTC-TTG
1 AATCACTACATAATTAAA-ACATTACATAAGTCTTTG
38615942 AAT
1 AAT
38615945 TAACACATAA
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
36 9 0.13
37 56 0.81
38 4 0.06
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (36 bp):
AATCACTACATAATTAAAACATTACATAAGTCTTTG
Found at i:38623085 original size:42 final size:42
Alignment explanation
Indices: 38623039--38623122 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
38623029 CATTAAGCAC
38623039 ATATTACTTT-ATAC-TTTCTAATGATGCACTGAGGTGCCAGAT
1 ATATTACTTTGA-ACTTTTC-AATGATGCACTGAGGTGCCAGAT
* *
38623081 ATATTACTTTGAACTTTTCGATGATGCACTGAGGTGCTAGAT
1 ATATTACTTTGAACTTTTCAATGATGCACTGAGGTGCCAGAT
38623123 TGGTGTGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 33 0.87
43 5 0.13
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (42 bp):
ATATTACTTTGAACTTTTCAATGATGCACTGAGGTGCCAGAT
Found at i:38629612 original size:31 final size:31
Alignment explanation
Indices: 38629560--38629619 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
38629550 TGAGGGATGA
* * *
38629560 AAATAGGGTTAGTTTGATATTTTACTTAATT
1 AAATAGAGTTAATTTGATATTTTAATTAATT
38629591 AAATAGAGTTAATTT-ATTATTTTAATTAA
1 AAATAGAGTTAATTTGA-TATTTTAATTAA
38629620 ATAAGGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (31 bp):
AAATAGAGTTAATTTGATATTTTAATTAATT
Found at i:38629637 original size:27 final size:27
Alignment explanation
Indices: 38629585--38629645 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
38629575 GATATTTTAC
*
38629585 TTAATTAAATAGAGTTAATTTATTATT
1 TTAATTAAATAGAGTTAAATTATTATT
*
38629612 TTAATTAAATA-AGGATTAAATTTTATATT
1 TTAATTAAATAGA-G-TTAAATTAT-TATT
38629641 TTAAT
1 TTAAT
38629646 GTAGTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 12 0.41
28 7 0.24
29 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (27 bp):
TTAATTAAATAGAGTTAAATTATTATT
Found at i:38629894 original size:20 final size:21
Alignment explanation
Indices: 38629865--38629904 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38629855 TTTTTTGCTT
*
38629865 ATTA-GTTTTTTAGGGTTTTC
1 ATTAGGTTTTCTAGGGTTTTC
38629885 ATTAGGTTTTCTAGGGTTTT
1 ATTAGGTTTTCTAGGGTTTT
38629905 GTATGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.57
Consensus pattern (21 bp):
ATTAGGTTTTCTAGGGTTTTC
Found at i:38643422 original size:52 final size:52
Alignment explanation
Indices: 38643365--38643469 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
38643355 TGTAGAACAA
* * * *
38643365 CATATATTCTAAAAAGGCACCCACCTTCCTTACACCTAGCCATAGTCCTCCC
1 CATATATTCAAAAAAGACACCCACCATCCCTACACCTAGCCATAGTCCTCCC
38643417 CATATATTCAAAAAAGACACCCACCATCCCTACACCTAGCCATAGTCCTCCC
1 CATATATTCAAAAAAGACACCCACCATCCCTACACCTAGCCATAGTCCTCCC
38643469 C
1 C
38643470 TTTTCATTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.31, C:0.40, G:0.07, T:0.22
Consensus pattern (52 bp):
CATATATTCAAAAAAGACACCCACCATCCCTACACCTAGCCATAGTCCTCCC
Found at i:38644532 original size:30 final size:30
Alignment explanation
Indices: 38644496--38644699 Score: 191
Period size: 30 Copynumber: 7.2 Consensus size: 30
38644486 AAAGTGAGTG
*
38644496 ACATAATATAAACATTAATATACATAACAT
1 ACATAATATAAACAGTAATATACATAACAT
* * *
38644526 AAATAATGTAAACAGTAGTATACATAACAT
1 ACATAATATAAACAGTAATATACATAACAT
* *
38644556 ACATAATATCAACA-T--TA-ATAT-ACAT
1 ACATAATATAAACAGTAATATACATAACAT
*
38644581 ACATAATATAAATAGTAATATACATAACAT
1 ACATAATATAAACAGTAATATACATAACAT
* *
38644611 ACATGATATAAACAGTAATATATATAACAT
1 ACATAATATAAACAGTAATATACATAACAT
* *
38644641 AC---ATA-AAA-AGTAATATGCATAAAAT
1 ACATAATATAAACAGTAATATACATAACAT
* *
38644666 ACATAAATAGAAATA-TAA-A-ACATAACAT
1 ACAT-AATATAAACAGTAATATACATAACAT
38644694 ACATAA
1 ACATAA
38644700 ATAGTAATAT
Statistics
Matches: 144, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
25 32 0.22
26 7 0.05
27 7 0.05
28 13 0.09
29 8 0.06
30 76 0.53
31 1 0.01
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.27
Consensus pattern (30 bp):
ACATAATATAAACAGTAATATACATAACAT
Found at i:38644606 original size:55 final size:56
Alignment explanation
Indices: 38644496--38644718 Score: 239
Period size: 55 Copynumber: 4.0 Consensus size: 56
38644486 AAAGTGAGTG
* *
38644496 ACATAATATAAACATTAATATACATAACATAAATAATGTAAACAGTAGTATACATAACAT
1 ACATAATATAAACATTAATATACATAACAT-AAT-A--TAAATAGTAATATACATAACAT
*
38644556 ACATAATATCAACATTAATATACAT-ACATAATATAAATAGTAATATACATAACAT
1 ACATAATATAAACATTAATATACATAACATAATATAAATAGTAATATACATAACAT
* * * * *
38644611 ACATGATATAAACAGTAATATATATAACATACATA-AAA-AGTAATATGCATAAAAT
1 ACATAATATAAACATTAATATACATAACATA-ATATAAATAGTAATATACATAACAT
*
38644666 ACATAA-ATAGAA-ATATAA-A-ACATAACAT-ACATAAATAGTAATATACAT-ACAT
1 ACATAATATA-AACAT-TAATATACATAACATAATATAAATAGTAATATACATAACAT
38644718 A
1 A
38644719 AAAAACATAC
Statistics
Matches: 142, Mismatches: 15, Indels: 20
0.80 0.08 0.11
Matches are distributed among these distances:
51 2 0.01
52 7 0.05
53 19 0.13
54 5 0.04
55 66 0.46
56 8 0.06
57 4 0.03
58 3 0.02
59 4 0.03
60 24 0.17
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (56 bp):
ACATAATATAAACATTAATATACATAACATAATATAAATAGTAATATACATAACAT
Found at i:38644667 original size:25 final size:25
Alignment explanation
Indices: 38644534--38644718 Score: 140
Period size: 25 Copynumber: 6.9 Consensus size: 25
38644524 ATAAATAATG
* *
38644534 TAAACAGTAGTATACATAACATACA
1 TAAATAGTAATATACATAACATACA
* *
38644559 TAATATCAACATTAATATACAT-ACATAATA
1 TAA-AT----AGTAATATACATAACAT-ACA
38644589 TAAATAGTAATATACATAACATACATGATA
1 TAAATAGTAATATACATAACATAC-----A
* *
38644619 TAAACAGTAATATATATAACATACA
1 TAAATAGTAATATACATAACATACA
* * *
38644644 TAAAAAGTAATATGCATAAAATACA
1 TAAATAGTAATATACATAACATACA
*
38644669 TAAATAGAAATATAAAACATAACATACA
1 TAAATAGTAATAT---ACATAACATACA
38644697 TAAATAGTAATATACAT-ACATA
1 TAAATAGTAATATACATAACATA
38644719 AAAAACATAC
Statistics
Matches: 128, Mismatches: 17, Indels: 31
0.73 0.10 0.18
Matches are distributed among these distances:
24 5 0.04
25 52 0.41
26 5 0.04
28 22 0.17
29 6 0.05
30 38 0.30
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (25 bp):
TAAATAGTAATATACATAACATACA
Found at i:38644668 original size:85 final size:84
Alignment explanation
Indices: 38644496--38644699 Score: 227
Period size: 85 Copynumber: 2.4 Consensus size: 84
38644486 AAAGTGAGTG
* * * *
38644496 ACATAATATAAACATTAATATACATAACATAAATAATGTAAACAGTAGTATACATAACATACATA
1 ACATAATATAAATA-TAATATACATAACATACATAATATAAACAGTAATATACATAACATACATA
* * *
38644561 ATATCAACATTAATATACAT
65 AAATCAACATGAATATAAAT
* *
38644581 ACATAATATAAATAGTAATATACATAACATACATGATATAAACAGTAATATATATAACATACATA
1 ACATAATATAAATA-TAATATACATAACATACATAATATAAACAGTAATATACATAACATACAT-
* *
38644646 AAAAGT-AATATGCATA-AAAT
64 AAAA-TCAACATGAATATAAAT
*
38644666 ACATAAATAGAAATATAA-A-ACATAACATACATAA
1 ACAT-AATATAAATATAATATACATAACATACATAA
38644700 ATAGTAATAT
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
83 14 0.14
84 1 0.01
85 67 0.66
86 19 0.19
87 1 0.01
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.27
Consensus pattern (84 bp):
ACATAATATAAATATAATATACATAACATACATAATATAAACAGTAATATACATAACATACATAA
AATCAACATGAATATAAAT
Found at i:38644734 original size:53 final size:53
Alignment explanation
Indices: 38644634--38644735 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 53
38644624 AGTAATATAT
* * * *
38644634 ATAACATACATAAAAAGTAATATGCATAAAATACATAAATAGAAATATAAAAC
1 ATAACATACATAAAAAGTAATATACATAAAATAAAAAAATACAAATATAAAAC
* * *
38644687 ATAACATACATAAATAGTAATATACAT-ACATAAAAAACATACTAATATA
1 ATAACATACATAAAAAGTAATATACATAAAATAAAAAA-ATACAAATATA
38644736 TCAATTGACT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 7 0.17
53 34 0.83
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.25
Consensus pattern (53 bp):
ATAACATACATAAAAAGTAATATACATAAAATAAAAAAATACAAATATAAAAC
Found at i:38645475 original size:33 final size:33
Alignment explanation
Indices: 38645432--38645500 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
38645422 AAACGTCTGG
*
38645432 TAATCAAAAAGGTCTCTTTAGCAATCGACTCAC
1 TAATCAAAAAGGTCTCTTCAGCAATCGACTCAC
* *
38645465 TAATCGAAAAGGTTTCTTCAGCAATCGACTCAC
1 TAATCAAAAAGGTCTCTTCAGCAATCGACTCAC
38645498 TAA
1 TAA
38645501 GATTTTGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (33 bp):
TAATCAAAAAGGTCTCTTCAGCAATCGACTCAC
Found at i:38650605 original size:68 final size:68
Alignment explanation
Indices: 38650496--38650632 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
38650486 TAATTGATAA
*
38650496 GTCCACATCCCTTTGACGAATTTTTAGTTGGTTTACAACTGCATCAAGTTTTTGGCGTCGTTGTT
1 GTCCACATCACTTTGACGAATTTTTAGTTGGTTTACAACTGCATCAAGTTTTTGGCGTCGTTGTT
38650561 GAT
66 GAT
38650564 GTCCACATCACTTTGACGAATTTTTAGTTGGTTTACAACTGCATCAAGTTTTTGGCGTCGTTGTT
1 GTCCACATCACTTTGACGAATTTTTAGTTGGTTTACAACTGCATCAAGTTTTTGGCGTCGTTGTT
38650629 GAT
66 GAT
38650632 G
1 G
38650633 ACTAAAATAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (68 bp):
GTCCACATCACTTTGACGAATTTTTAGTTGGTTTACAACTGCATCAAGTTTTTGGCGTCGTTGTT
GAT
Found at i:38650704 original size:20 final size:19
Alignment explanation
Indices: 38650673--38650722 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
38650663 TAATTTAGCC
*
38650673 ATTTTTTATTTTTATTTTA
1 ATTTTTTATTTTTAATTTA
*
38650692 ATATTTTTGTTTTTAATTTA
1 AT-TTTTTATTTTTAATTTA
38650712 ATTTTTATATT
1 ATTTTT-TATT
38650723 CTAATTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTTTATTTTTAATTTA
Found at i:38663005 original size:26 final size:26
Alignment explanation
Indices: 38662954--38663023 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
38662944 TAGAAAAATA
38662954 TAATGTAATTA-TAAAATAATTAAATTG
1 TAAT-TAATTATTAAAAT-ATTAAATTG
* * *
38662981 TACTTAATTATTAAAATATTTAATTT
1 TAATTAATTATTAAAATATTAAATTG
*
38663007 TAATTAATT-TTATAATA
1 TAATTAATTATTAAAATA
38663024 AATTTTCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 7 0.19
26 21 0.57
27 9 0.24
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (26 bp):
TAATTAATTATTAAAATATTAAATTG
Found at i:38664486 original size:13 final size:13
Alignment explanation
Indices: 38664470--38664499 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38664460 TTTTTACCTT
*
38664470 TTAATTTTCTTAG
1 TTAATTTTCTTAA
38664483 TTAATTTTCTTAA
1 TTAATTTTCTTAA
38664496 TTAA
1 TTAA
38664500 AATCTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (13 bp):
TTAATTTTCTTAA
Found at i:38666600 original size:43 final size:43
Alignment explanation
Indices: 38666551--38666841 Score: 390
Period size: 43 Copynumber: 6.8 Consensus size: 43
38666541 TTAATAAAAG
**
38666551 CGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTTATACACAAA
1 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTA-ACACAAA
** *
38666594 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT-ATACAAA
1 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACACAAA
* * *
38666636 CGCCGTTAAAGTTCATGTTCTTTAGCGGCACTTTTAACACAAA
1 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACACAAA
* *
38666679 CGCCACTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACAAAAA
1 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACACAAA
* * *
38666722 CGCCGCTAAAGTTCATGTTCTTTAGCGGCGATTTTTACACAAA
1 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACACAAA
* * *
38666765 TGCCACTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACAAAAA
1 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACACAAA
* *
38666808 CGCTGCAAAAGCTC-TGTTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTT
38666842 TTTAAAAACG
Statistics
Matches: 220, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
42 57 0.26
43 160 0.73
44 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
CGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTAACACAAA
Found at i:38666770 original size:86 final size:86
Alignment explanation
Indices: 38666541--38666858 Score: 419
Period size: 85 Copynumber: 3.7 Consensus size: 86
38666531 GCGGTGTTTA
* * ** * * * *
38666541 TTAATAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGA
1 TTAACAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGATTTTTACACAAACGCCACTAAAGC
*
38666606 ACATGTTCTTTAGCGGCGCTT
66 TCATGTTCTTTAGCGGCGCTT
* *
38666627 TTATAC--AAACGCCGTTAAAGTTCATGTTCTTTAGCGGC-ACTTTTAACACAAACGCCACTAAA
1 TTA-ACAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGA-TTTTTACACAAACGCCACTAAA
38666689 GCTCATGTTCTTTAGCGGCGCTT
64 GCTCATGTTCTTTAGCGGCGCTT
*
38666712 TTAACAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGATTTTTACACAAATGCCACTAAAGC
1 TTAACAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGATTTTTACACAAACGCCACTAAAGC
38666777 TCATGTTCTTTAGCGGCGCTT
66 TCATGTTCTTTAGCGGCGCTT
* * * * ** *
38666798 TTAACAAAAACGCTGCAAAAGCTC-TGTTCTTTAGCGGCGCTTTTTTTAAAAACGCCACTAA
1 TTAACAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGATTTTTACACAAACGCCACTAA
38666859 TTTTGGGGTT
Statistics
Matches: 205, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
84 2 0.01
85 103 0.50
86 98 0.48
87 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (86 bp):
TTAACAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGATTTTTACACAAACGCCACTAAAGC
TCATGTTCTTTAGCGGCGCTT
Found at i:38666853 original size:171 final size:171
Alignment explanation
Indices: 38666541--38666858 Score: 433
Period size: 171 Copynumber: 1.9 Consensus size: 171
38666531 GCGGTGTTTA
* * * *
38666541 TTAATAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGA
1 TTAACAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTATACACAAACGCCACTAAAGA
** *
38666606 ACATGTTCTTTAGCGGCGCTTTTATACAAACGCCGTTAAAGTTCATGTTCTTTAGCGGCACTTTT
66 ACATGTTCTTTAGCGGCGCTTTTATACAAACGCCGCAAAAGCTCATGTTCTTTAGCGGCACTTTT
*
38666671 AACACAAACGCCACTAAAGCTCATGTTCTTTAGCGGCGCTT
131 AACAAAAACGCCACTAAAGCTCATGTTCTTTAGCGGCGCTT
** * * *
38666712 TTAACAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGATTTTTACACAAATGCCACTAAAGC
1 TTAACAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTATACACAAACGCCACTAAAGA
* * *
38666777 TCATGTTCTTTAGCGGCGCTTTTA-ACAAAAACGCTGCAAAAGCTC-TGTTCTTTAGCGGCGCTT
66 ACATGTTCTTTAGCGGCGCTTTTATAC--AAACGCCGCAAAAGCTCATGTTCTTTAGCGGCACTT
***
38666840 TTTTTAAAAACGCCACTAA
129 TTAACAAAAACGCCACTAA
38666859 TTTTGGGGTT
Statistics
Matches: 126, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
170 2 0.02
171 111 0.88
172 13 0.10
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (171 bp):
TTAACAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTTATACACAAACGCCACTAAAGA
ACATGTTCTTTAGCGGCGCTTTTATACAAACGCCGCAAAAGCTCATGTTCTTTAGCGGCACTTTT
AACAAAAACGCCACTAAAGCTCATGTTCTTTAGCGGCGCTT
Done.