Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_pilon, whole genome shotgun sequence
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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 46 of 49
Found at i:9395136 original size:27 final size:25
Alignment explanation
Indices: 9395080--9395145 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 25
9395070 AAAACATTAA
*
9395080 TAAAAAATAATATATATAAATATAT
1 TAAAAAATAATATATATAAAAATAT
*
9395105 AAAAATAATAAGTATATATAAAAA-AT
1 TAAAA-AATAA-TATATATAAAAATAT
* *
9395131 TTAAAAAGAAT-TATA
1 TAAAAAATAATATATA
9395146 ACTTAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 4 0.12
24 1 0.03
25 8 0.24
26 10 0.29
27 11 0.32
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
TAAAAAATAATATATATAAAAATAT
Found at i:9398072 original size:14 final size:14
Alignment explanation
Indices: 9398053--9398079 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9398043 GAGAAATTCT
9398053 ATAAGCTATATGAA
1 ATAAGCTATATGAA
9398067 ATAAGCTATATGA
1 ATAAGCTATATGA
9398080 TTCTATGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (14 bp):
ATAAGCTATATGAA
Found at i:9398535 original size:23 final size:23
Alignment explanation
Indices: 9398518--9398563 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9398508 ACAATCTTAT
9398518 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
* *
9398541 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTACGGTGCAATTCTAC
9398564 GCGGTCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:9399331 original size:21 final size:21
Alignment explanation
Indices: 9399305--9399344 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9399295 TTACAAAGTT
9399305 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
*
9399326 ACTGTAGTAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
9399345 GCATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:9399420 original size:21 final size:19
Alignment explanation
Indices: 9399394--9399441 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
9399384 TGTTCATTAC
9399394 TGTTCATACGGTACTGTTTAT
1 TGTTCATACGGTA-T-TTTAT
**
9399415 TGTTCATATTGTATTTTAT
1 TGTTCATACGGTATTTTAT
9399434 TGTTCATA
1 TGTTCATA
9399442 AAACGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 1 0.04
21 11 0.44
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (19 bp):
TGTTCATACGGTATTTTAT
Found at i:9400249 original size:3 final size:3
Alignment explanation
Indices: 9400241--9400331 Score: 82
Period size: 3 Copynumber: 31.0 Consensus size: 3
9400231 GGCCTATTTG
*
9400241 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA AAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* * * * *
9400289 TAA -AA TAG T-A TAA -ATA TAA TAT TAA AAA TAA TAT TAA AAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
9400332 AAAACAAATG
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
2 6 0.09
3 60 0.86
4 4 0.06
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:9403838 original size:30 final size:30
Alignment explanation
Indices: 9403804--9403880 Score: 147
Period size: 29 Copynumber: 2.6 Consensus size: 30
9403794 TATTTTGGAT
9403804 AAAGTTACAAAATAGTCTTTTAAATTATTA
1 AAAGTTACAAAATAGTCTTTTAAATTATTA
9403834 AAAGTTACAAAATAGTC-TTTAAATTATTA
1 AAAGTTACAAAATAGTCTTTTAAATTATTA
9403863 AAAGTTACAAAATAGTCT
1 AAAGTTACAAAATAGTCT
9403881 CTGGATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 29 0.63
30 17 0.37
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (30 bp):
AAAGTTACAAAATAGTCTTTTAAATTATTA
Found at i:9404224 original size:60 final size:60
Alignment explanation
Indices: 9404129--9404299 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
9404119 ATGGGTCGAG
* * * * *
9404129 TTTGTAACTTTTATTAGTTGATTGACTCAAAAAAACAACGTCTTATAGTCATAAGATCAT
1 TTTGTAACTTTTAATAGTCGAATGACTCAACAAAACAACGTCTTATAGTCAGAAGATCAT
*
9404189 TTTGTAACTTTTAATAATCGAATGACTCAACAAAACAACGTCTTATAGTCAGAAGATCAT
1 TTTGTAACTTTTAATAGTCGAATGACTCAACAAAACAACGTCTTATAGTCAGAAGATCAT
* **
9404249 TTTGTAGCTTTTAATAGTCGAAAAACTCAACAAAACAACG-CTCTATAGTCA
1 TTTGTAACTTTTAATAGTCGAATGACTCAACAAAACAACGTCT-TATAGTCA
9404300 AGAAACCATT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 2 0.02
60 98 0.98
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (60 bp):
TTTGTAACTTTTAATAGTCGAATGACTCAACAAAACAACGTCTTATAGTCAGAAGATCAT
Found at i:9404310 original size:60 final size:59
Alignment explanation
Indices: 9404153--9404319 Score: 205
Period size: 60 Copynumber: 2.8 Consensus size: 59
9404143 TAGTTGATTG
* * **
9404153 ACTCAAAAAAACAACGTCTTATAGTCATA-AGATCATTTTGTAACTTTTAATAATCGAATG
1 ACTCAACAAAACAACGTCTTATAGTCA-AGAAATCATTTTGT-ACTTTTAATAATCGAAAA
*
9404213 ACTCAACAAAACAACGTCTTATAGTC-AGAAGATCATTTTGTAGCTTTTAATAGTCGAAAA
1 ACTCAACAAAACAACGTCTTATAGTCAAGAA-ATCATTTTGTA-CTTTTAATAATCGAAAA
*
9404273 ACTCAACAAAACAACG-CTCTATAGTCAAGAAACCATTTATGTACTTT
1 ACTCAACAAAACAACGTCT-TATAGTCAAGAAATCATTT-TGTACTTT
9404320 ACTCATATAA
Statistics
Matches: 95, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
58 1 0.01
59 4 0.04
60 82 0.86
61 8 0.08
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (59 bp):
ACTCAACAAAACAACGTCTTATAGTCAAGAAATCATTTTGTACTTTTAATAATCGAAAA
Found at i:9404885 original size:2 final size:2
Alignment explanation
Indices: 9404878--9404914 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9404868 GGGAAAAGAG
9404878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9404915 ATAAAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9410902 original size:36 final size:36
Alignment explanation
Indices: 9410857--9410982 Score: 218
Period size: 36 Copynumber: 3.5 Consensus size: 36
9410847 AGAAGTACGA
9410857 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
1 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
* * *
9410893 AAGGAAGCATCGGCACTTTCGATTC-AAGAGAACGA
1 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
9410928 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
1 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
9410964 AAGGAAGCATCAGCACTTT
1 AAGGAAGCATCAGCACTTT
9410983 TGAATCAATT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 32 0.39
36 51 0.61
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.19
Consensus pattern (36 bp):
AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
Found at i:9412813 original size:36 final size:36
Alignment explanation
Indices: 9412768--9412902 Score: 193
Period size: 36 Copynumber: 3.8 Consensus size: 36
9412758 ATAAGTACGA
9412768 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
1 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
* * *
9412804 AAGGAAGCATCGGCACTTTCGATTC-AAGAAGAACGA
1 AAGGAAGCATCAGCACTTTCGATTCAAAG-TGAACGG
9412840 AAGGAAGCATC-GACACTTTCGATTCAAAGTGAACGG
1 AAGGAAGCATCAG-CACTTTCGATTCAAAGTGAACGG
* *
9412876 AAGGAAACATCAGCACTTTCGAATCAA
1 AAGGAAGCATCAGCACTTTCGATTCAA
9412903 TTGTTCATCT
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
35 4 0.05
36 80 0.91
37 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.19
Consensus pattern (36 bp):
AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
Found at i:9412881 original size:72 final size:72
Alignment explanation
Indices: 9412764--9412902 Score: 235
Period size: 72 Copynumber: 1.9 Consensus size: 72
9412754 AATAATAAGT
* * *
9412764 ACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTTCGATTC
1 ACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCAGCACTTTCGAATC
9412829 AAGAAGA
66 AAGAAGA
9412836 ACGAAAGGAAGCATC-GACACTTTCGATTCAAAGTGAACGGAAGGAAACATCAGCACTTTCGAAT
1 ACGAAAGGAAGCATCAG-CACTTTCGATTCAAAGTGAACGGAAGGAAACATCAGCACTTTCGAAT
9412900 CAA
65 CAA
9412903 TTGTTCATCT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 1 0.02
72 62 0.98
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (72 bp):
ACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCAGCACTTTCGAATC
AAGAAGA
Found at i:9415584 original size:23 final size:22
Alignment explanation
Indices: 9415553--9415595 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
9415543 TTGCTACAAG
*
9415553 GTAATTTTTTAACTTCATTTTAA
1 GTAAATTTTTAA-TTCATTTTAA
*
9415576 GTAAATTTTTAATTCTTTTT
1 GTAAATTTTTAATTCATTTT
9415596 GTAATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (22 bp):
GTAAATTTTTAATTCATTTTAA
Found at i:9429105 original size:182 final size:183
Alignment explanation
Indices: 9428797--9429161 Score: 723
Period size: 182 Copynumber: 2.0 Consensus size: 183
9428787 GTTGATCTCC
9428797 GACACCACAAAACATAACTAAAGGAACCGATTCAAAAAATATTAGAATCGTACTATCAAAATCAC
1 GACACCACAAAACATAACTAAAGGAACCGATTCAAAAAATATTAGAATCGTACTATCAAAATCAC
9428862 CTGGAGGCGATGACAAATGCAGGAATTTATGTTTCGCCCCGGCTTCAGATCGAGTGACGGTAACC
66 CTGGAGGCGATGACAAATGCAGGAATTTATGTTTCGCCCCGGCTTCAGATCGAGTGACGGTAACC
9428927 GTATCGACTCACGAGTCACAGGATTCCACAAACAGCATCGACCTGATGTTCTA
131 GTATCGACTCACGAGTCACAGGATTCCACAAACAGCATCGACCTGATGTTCTA
9428980 GACACCACAAAACATAACTAAAGGAACCGATTCAAAAAATA-TAGAATCGTACTATCAAAATCAC
1 GACACCACAAAACATAACTAAAGGAACCGATTCAAAAAATATTAGAATCGTACTATCAAAATCAC
9429044 CTGGAGGCGATGACAAATGCAGGAATTTATGTTTCGCCCCGGCTTCAGATCGAGTGACGGTAACC
66 CTGGAGGCGATGACAAATGCAGGAATTTATGTTTCGCCCCGGCTTCAGATCGAGTGACGGTAACC
9429109 GTATCGACTCACGAGTCACAGGATTCCACAAACAGCATCGACCTGATGTTCTA
131 GTATCGACTCACGAGTCACAGGATTCCACAAACAGCATCGACCTGATGTTCTA
9429162 ATATGAAAAC
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 141 0.77
183 41 0.23
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (183 bp):
GACACCACAAAACATAACTAAAGGAACCGATTCAAAAAATATTAGAATCGTACTATCAAAATCAC
CTGGAGGCGATGACAAATGCAGGAATTTATGTTTCGCCCCGGCTTCAGATCGAGTGACGGTAACC
GTATCGACTCACGAGTCACAGGATTCCACAAACAGCATCGACCTGATGTTCTA
Found at i:9429688 original size:17 final size:18
Alignment explanation
Indices: 9429657--9429692 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9429647 CGAATATCCG
*
9429657 TATTCTAATATAAAATTT
1 TATTCTAATAAAAAATTT
9429675 TATT-TAATAAAAAATTT
1 TATTCTAATAAAAAATTT
9429692 T
1 T
9429693 CAAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTCTAATAAAAAATTT
Found at i:9435616 original size:83 final size:82
Alignment explanation
Indices: 9435457--9435649 Score: 183
Period size: 83 Copynumber: 2.3 Consensus size: 82
9435447 GTCGTCCCAT
* * * * * * * *
9435457 GACTTAGCATCTTTCATAGGAAAGAGAGAGATCGTCACCAGATTCAGGTTCCTTTAAAAGAATGA
1 GACTCAGCGTCTTTCA-AAGAAAGAGTGAGATCATCACCAGATTCACGTTCCTTCAAAAGAAGGA
*
9435522 GTGGATCACCCCAAATAAC
65 ATGGATCACCCC-AATAAC
* *
9435541 GACTCAGTGTCTTTCAAAGAAAGAGTGAGATCATCACCATATTCATCG-TCCTTCAGAAA-AAGG
1 GACTCAGCGTCTTTCAAAGAAAGAGTGAGATCATCACCAGATTCA-CGTTCCTTCA-AAAGAAGG
* * *
9435604 AATGGATTACCCCAATTAT
64 AATGGATCACCCCAATAAC
* *
9435623 GACTCAGCGTCCTTCAGAGAAAAGAGT
1 GACTCAGCGTCTTTCAAAG-AAAGAGT
9435650 AAAATCGTCC
Statistics
Matches: 89, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
82 20 0.22
83 52 0.58
84 17 0.19
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (82 bp):
GACTCAGCGTCTTTCAAAGAAAGAGTGAGATCATCACCAGATTCACGTTCCTTCAAAAGAAGGAA
TGGATCACCCCAATAAC
Found at i:9436160 original size:12 final size:12
Alignment explanation
Indices: 9436145--9436196 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
9436135 ATTTAAACGA
9436145 GTATTGGGCCGG
1 GTATTGGGCCGG
*
9436157 GTATTGGGTCGG
1 GTATTGGGCCGG
*
9436169 GTATTGGGCCGA
1 GTATTGGGCCGG
* *
9436181 GAATCGGGCCGG
1 GTATTGGGCCGG
9436193 GTAT
1 GTAT
9436197 ATATATATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.13, C:0.15, G:0.46, T:0.25
Consensus pattern (12 bp):
GTATTGGGCCGG
Found at i:9436907 original size:11 final size:11
Alignment explanation
Indices: 9436893--9436918 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9436883 CTTTTTATCT
9436893 TTGTCTTATTC
1 TTGTCTTATTC
9436904 TTGTCTTATTC
1 TTGTCTTATTC
9436915 TTGT
1 TTGT
9436919 TAACACAAGA
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:0.15, G:0.12, T:0.65
Consensus pattern (11 bp):
TTGTCTTATTC
Found at i:9436990 original size:3 final size:3
Alignment explanation
Indices: 9436975--9437024 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
9436965 GTTCAGGTTT
* *
9436975 TTA TTA ATA TTA TTA TTA -TA TAAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
9437020 TTA TT
1 TTA TT
9437025 TTACAGACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9438166 original size:13 final size:13
Alignment explanation
Indices: 9438132--9438170 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
9438122 TGTAATATTT
*
9438132 TTGTTTTGGTCATC
1 TTGTTTT-GTAATC
9438146 TATGTTTTGTAATC
1 T-TGTTTTGTAATC
9438160 TTGTTTTGTAA
1 TTGTTTTGTAA
9438171 CCATTGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 10 0.43
14 7 0.30
15 6 0.26
ACGTcount: A:0.15, C:0.08, G:0.18, T:0.59
Consensus pattern (13 bp):
TTGTTTTGTAATC
Found at i:9440088 original size:23 final size:24
Alignment explanation
Indices: 9440062--9440138 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 24
9440052 ACTCTTAATA
9440062 TTATGGATATTTTACGTCTACTCTTAT
1 TTATGGATATTTTACGTCTACTC---T
9440089 ATTATGGATATTTTACGTCTACTCTTAAT
1 -TTATGGATATTTTACGTCTACTC----T
9440118 GTTATGGATATTTTACGTCTA
1 -TTATGGATATTTTACGTCTA
9440139 ACCGTGTCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 23 0.50
29 23 0.50
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (24 bp):
TTATGGATATTTTACGTCTACTCT
Found at i:9440132 original size:29 final size:29
Alignment explanation
Indices: 9440049--9440138 Score: 164
Period size: 29 Copynumber: 3.1 Consensus size: 29
9440039 ATTCGTATAT
9440049 TCTACTCTTAATATTATGGATATTTTACG
1 TCTACTCTTAATATTATGGATATTTTACG
9440078 TCTACTCTT-ATATTATGGATATTTTACG
1 TCTACTCTTAATATTATGGATATTTTACG
*
9440106 TCTACTCTTAATGTTATGGATATTTTACG
1 TCTACTCTTAATATTATGGATATTTTACG
9440135 TCTA
1 TCTA
9440139 ACCGTGTCCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 28 0.47
29 31 0.53
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (29 bp):
TCTACTCTTAATATTATGGATATTTTACG
Found at i:9443426 original size:3 final size:3
Alignment explanation
Indices: 9443418--9443453 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
9443408 GTTCTTTTAT
9443418 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9443454 ACCAAGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9448661 original size:26 final size:26
Alignment explanation
Indices: 9448609--9448666 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
9448599 TGTAATGAAA
* *
9448609 ATAAATTAAAAAATAATGATTATAAT
1 ATAAATTAAAAAATAATGACTAAAAT
** *
9448635 ATAAATTTTAAAATGATGACTAAAAT
1 ATAAATTAAAAAATAATGACTAAAAT
*
9448661 AAAAAT
1 ATAAAT
9448667 GTCCTAAACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
ATAAATTAAAAAATAATGACTAAAAT
Found at i:9451103 original size:3 final size:3
Alignment explanation
Indices: 9451095--9451119 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9451085 TACATTGGTT
9451095 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
9451120 AAAATGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9458743 original size:3 final size:3
Alignment explanation
Indices: 9458737--9458776 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9458727 ATGATGACAC
9458737 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
9458777 ATTTTTAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9465372 original size:15 final size:17
Alignment explanation
Indices: 9465352--9465385 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9465342 ATAGAAGAAG
9465352 CTTCT-ATAAT-TGGAA
1 CTTCTAATAATCTGGAA
9465367 CTTCTAATAATCTGGAA
1 CTTCTAATAATCTGGAA
9465384 CT
1 CT
9465386 ATTGGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (17 bp):
CTTCTAATAATCTGGAA
Found at i:9469457 original size:2 final size:2
Alignment explanation
Indices: 9469450--9469494 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
9469440 CAAGTCCCAT
9469450 TA TA TA TA TA TA TA TA TA T- TA -A TA -A T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9469488 TA TA TA T
1 TA TA TA T
9469495 TGACGAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9471002 original size:11 final size:11
Alignment explanation
Indices: 9470986--9471021 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
9470976 AACTAATTAA
9470986 ATAAATAAAAT
1 ATAAATAAAAT
9470997 ATAAATATAAAT
1 ATAAATA-AAAT
*
9471009 ATAATTAAAAT
1 ATAAATAAAAT
9471020 AT
1 AT
9471022 TAAACGCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:9481557 original size:64 final size:64
Alignment explanation
Indices: 9481485--9481609 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 64
9481475 TGCACTAAGA
** **
9481485 GTGCATCGATGCGTAAAATGCATTCGATGTT-TTGAAA-AAACTTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGAATAAAATGCATTCGATGTTCAAGAAATAAA-TTGA-TGCATCGATGCATGGTA
9481548 T
64 T
*
9481549 GTGCATCGATGAATAAAATGCATTCGATGTTCAAGAAATTAATTGATGCATCGATGCATGG
1 GTGCATCGATGAATAAAATGCATTCGATGTTCAAGAAATAAATTGATGCATCGATGCATGG
9481610 ATTGGTGCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 44 0.81
65 8 0.15
66 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGAATAAAATGCATTCGATGTTCAAGAAATAAATTGATGCATCGATGCATGGTAT
Found at i:9481618 original size:20 final size:20
Alignment explanation
Indices: 9481590--9481628 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9481580 CAAGAAATTA
9481590 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
9481610 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
9481629 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:9482703 original size:21 final size:21
Alignment explanation
Indices: 9482679--9482722 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9482669 GAGGAGGAGG
* *
9482679 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
9482700 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
9482721 AG
1 AG
9482723 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:9487138 original size:20 final size:20
Alignment explanation
Indices: 9487113--9487156 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
9487103 ATATATATAT
9487113 ATATATATATATGGATGGATGG
1 ATATAT-TA-ATGGATGGATGG
*
9487135 ATATATTAATGGGTGGATGG
1 ATATATTAATGGATGGATGG
9487155 AT
1 AT
9487157 GGTGCTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (20 bp):
ATATATTAATGGATGGATGG
Found at i:9487140 original size:2 final size:2
Alignment explanation
Indices: 9487079--9487124 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
9487069 ACCTGCCATG
9487079 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9487120 TA TA T
1 TA TA T
9487125 GGATGGATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9489211 original size:22 final size:21
Alignment explanation
Indices: 9489169--9489208 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9489159 GAGTTTATTT
*
9489169 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
9489190 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
9489209 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:9492316 original size:49 final size:45
Alignment explanation
Indices: 9492214--9492334 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 45
9492204 GTAACCATGC
*
9492214 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
* * * * **
9492259 AAAAAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAA
*
9492308 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
9492335 AAGGTAAGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
45 23 0.37
46 1 0.02
48 1 0.02
49 37 0.60
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:9492804 original size:22 final size:22
Alignment explanation
Indices: 9492779--9492833 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
9492769 TAAAAGGAGT
9492779 ATCGATTCCCCTGCTACAGGGA
1 ATCGATTCCCCTGCTACAGGGA
9492801 ATCGATTCCCCTGCTACAGGGA
1 ATCGATTCCCCTGCTACAGGGA
9492823 ATCGATTCCCC
1 ATCGATTCCCC
9492834 CACTGTCCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.24
Consensus pattern (22 bp):
ATCGATTCCCCTGCTACAGGGA
Found at i:9494545 original size:45 final size:46
Alignment explanation
Indices: 9494459--9494547 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 46
9494449 GAAAAAACCT
* * *
9494459 GAGTGCATCTATGCATGGTCTTGTGCATCGATGCATCAAATGCACC
1 GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACC
9494505 GAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
9494548 TTCGATGTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACC
Found at i:9494595 original size:20 final size:20
Alignment explanation
Indices: 9494567--9494605 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9494557 CAAGAAAGTA
9494567 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
9494587 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
9494606 CATTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:9497129 original size:13 final size:13
Alignment explanation
Indices: 9497111--9497163 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
9497101 CATACCTTTG
9497111 AGAAACACATTTT
1 AGAAACACATTTT
* *
9497124 AGAAACAC-TGTC
1 AGAAACACATTTT
***
9497136 ATCGACACATTTT
1 AGAAACACATTTT
9497149 AGAAACACATTTT
1 AGAAACACATTTT
9497162 AG
1 AG
9497164 TGTTCGCCGG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
12 7 0.24
13 22 0.76
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (13 bp):
AGAAACACATTTT
Found at i:9501593 original size:6 final size:6
Alignment explanation
Indices: 9501582--9501606 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9501572 CCTCATCCTT
9501582 AGGCTC AGGCTC AGGCTC AGGCTC A
1 AGGCTC AGGCTC AGGCTC AGGCTC A
9501607 TTGTGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (6 bp):
AGGCTC
Found at i:9502281 original size:2 final size:2
Alignment explanation
Indices: 9502274--9502321 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
9502264 GTTCCTGTTA
9502274 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
9502316 GT GT GT
1 GT GT GT
9502322 AAATGAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:9502540 original size:2 final size:2
Alignment explanation
Indices: 9502533--9502566 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9502523 GGGATTTTTC
9502533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9502567 TTCACCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9504085 original size:2 final size:2
Alignment explanation
Indices: 9504078--9504155 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
9504068 TGAGAGTCGA
9504078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9504120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9504156 GTAAACAGTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9506659 original size:33 final size:33
Alignment explanation
Indices: 9506617--9506691 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
9506607 AAATTTTTAA
9506617 CAAAGCCTCTGTTAGCTTGGCATTCCATTGTCT
1 CAAAGCCTCTGTTAGCTTGGCATTCCATTGTCT
9506650 CAAAGCCTCTGTTAGCTTGGCATTCCATTGTCT
1 CAAAGCCTCTGTTAGCTTGGCATTCCATTGTCT
*
9506683 CGAAGCCTC
1 CAAAGCCTC
9506692 CTTTAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (33 bp):
CAAAGCCTCTGTTAGCTTGGCATTCCATTGTCT
Found at i:9508493 original size:17 final size:17
Alignment explanation
Indices: 9508473--9508505 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9508463 AAAATTAAAA
9508473 ATAAATAAAAGTTTAAG
1 ATAAATAAAAGTTTAAG
9508490 ATAAATAAAAGTTTAA
1 ATAAATAAAAGTTTAA
9508506 AATGCTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
ATAAATAAAAGTTTAAG
Found at i:9508690 original size:4 final size:4
Alignment explanation
Indices: 9508681--9508713 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
9508671 CTGTGTAAAC
9508681 AATA AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA A
9508714 CCAGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:9509355 original size:13 final size:14
Alignment explanation
Indices: 9509337--9509366 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9509327 ATATGAATTG
9509337 TAAAAATAAAA-AA
1 TAAAAATAAAATAA
9509350 TAAAAATAAAATAA
1 TAAAAATAAAATAA
9509364 TAA
1 TAA
9509367 CATGTGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAAATAAAATAA
Found at i:9514967 original size:21 final size:21
Alignment explanation
Indices: 9514943--9514985 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9514933 TTCATATTCG
* *
9514943 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
9514964 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
9514985 T
1 T
9514986 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:9530703 original size:6 final size:6
Alignment explanation
Indices: 9530689--9530758 Score: 72
Period size: 6 Copynumber: 11.7 Consensus size: 6
9530679 TTTTGACCTA
* * *
9530689 ACACAC ACACGC ACACGC ACACG- -CACGC GCACGC GCACGC ACACGC
1 ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC
*
9530735 GCACGC ACACGCGC ACACGC ACAC
1 ACACGC ACA--CGC ACACGC ACAC
9530759 ACCTTGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 4 0.07
6 46 0.82
8 6 0.11
ACGTcount: A:0.30, C:0.50, G:0.20, T:0.00
Consensus pattern (6 bp):
ACACGC
Found at i:9535730 original size:3 final size:3
Alignment explanation
Indices: 9535722--9535748 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9535712 GAGAATAGTA
9535722 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
9535749 GGTTTTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9547266 original size:39 final size:39
Alignment explanation
Indices: 9547215--9547291 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
9547205 AAAATACAGA
9547215 ATTATGAAACTTTAATGAACTCGAGAATTAAGTAATATT
1 ATTATGAAACTTTAATGAACTCGAGAATTAAGTAATATT
9547254 ATTATGAAACTTTAATGAACTCGAGAATTAAGTAATAT
1 ATTATGAAACTTTAATGAACTCGAGAATTAAGTAATAT
9547292 ATAGCTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (39 bp):
ATTATGAAACTTTAATGAACTCGAGAATTAAGTAATATT
Found at i:9554435 original size:33 final size:34
Alignment explanation
Indices: 9554393--9554465 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 34
9554383 ATTTTATTTA
9554393 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
9554426 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
9554460 TATATA
1 TATATA
9554466 ATACAAACCC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 20 0.51
34 19 0.49
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:9554500 original size:15 final size:14
Alignment explanation
Indices: 9554470--9554513 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
9554460 TATATAATAC
* *
9554470 AAACCCTAACCCCT
1 AAACCTTAAACCCT
9554484 AAACCTTTAAACCCT
1 AAACC-TTAAACCCT
9554499 AAACCTTAAACCCT
1 AAACCTTAAACCCT
9554513 A
1 A
9554514 TCTTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:9554501 original size:7 final size:7
Alignment explanation
Indices: 9554470--9554513 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
9554460 TATATAATAC
9554470 AAACCCT
1 AAACCCT
*
9554477 AACCCCT
1 AAACCCT
*
9554484 AAACCTTT
1 AAACC-CT
9554492 AAACCCT
1 AAACCCT
*
9554499 AAACCTT
1 AAACCCT
9554506 AAACCCT
1 AAACCCT
9554513 A
1 A
9554514 TCTTTTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:9558271 original size:18 final size:18
Alignment explanation
Indices: 9558248--9558293 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
9558238 ATCATTCCCA
9558248 GTAATCTTATTCCCGCCG
1 GTAATCTTATTCCCGCCG
* *
9558266 GTAATCCTATTCCCGCTG
1 GTAATCTTATTCCCGCCG
*
9558284 ATAATCTTAT
1 GTAATCTTAT
9558294 ATTCCGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (18 bp):
GTAATCTTATTCCCGCCG
Found at i:9568252 original size:9 final size:9
Alignment explanation
Indices: 9568240--9568291 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
9568230 TAATATTTTG
9568240 TATTTAATT
1 TATTTAATT
*
9568249 TATTTAA-G
1 TATTTAATT
9568257 TATTTAATT
1 TATTTAATT
9568266 TATTTAA--
1 TATTTAATT
* *
9568273 TATTTTACT
1 TATTTAATT
9568282 TATTTAATT
1 TATTTAATT
9568291 T
1 T
9568292 TTTTTGCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:9568261 original size:17 final size:17
Alignment explanation
Indices: 9568239--9568288 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
9568229 TTAATATTTT
9568239 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
9568256 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
9568273 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
9568289 TTTTTTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:9568284 original size:16 final size:16
Alignment explanation
Indices: 9568248--9568293 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
9568238 TGTATTTAAT
* *
9568248 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
9568265 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
9568281 TTATTTAAT-TTTT
1 TTATTTAATATTTT
9568294 TTTGCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:9570854 original size:22 final size:21
Alignment explanation
Indices: 9570820--9570864 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
9570810 GATTGTAAAG
* *
9570820 TTTAATTTTTAAATATTAATA
1 TTTAATTTTTAAACATAAATA
*
9570841 TTTATTTTATTAAACATAAATA
1 TTTAATTT-TTAAACATAAATA
9570863 TT
1 TT
9570865 ACGGGGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATTTTTAAACATAAATA
Found at i:9571098 original size:3 final size:3
Alignment explanation
Indices: 9571049--9571085 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
9571039 ATTAAGAGAC
9571049 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9571086 TGAAATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9574480 original size:21 final size:21
Alignment explanation
Indices: 9574454--9574526 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
9574444 AAGTGAACTC
9574454 AGTATCGATACCTAATGTATG
1 AGTATCGATACCTAATGTATG
* * * ** *
9574475 AGTATCGAAACATTACCTA-C
1 AGTATCGATACCTAATGTATG
* **
9574495 AATATATATACCTAATGTATG
1 AGTATCGATACCTAATGTATG
9574516 AGTATCGATAC
1 AGTATCGATAC
9574527 TTCTAGCCCC
Statistics
Matches: 33, Mismatches: 18, Indels: 2
0.62 0.34 0.04
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (21 bp):
AGTATCGATACCTAATGTATG
Found at i:9576998 original size:35 final size:35
Alignment explanation
Indices: 9576880--9577019 Score: 199
Period size: 36 Copynumber: 3.9 Consensus size: 35
9576870 TGAATAAGAA
*
9576880 GAACGAAAGGAAGCATCAGTACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTC-AAGT
* * * *
9576916 GAACGGAAGGAAGCATCGGCACTTTTGATTCAAGAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAG-T
*
9576952 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
*
9576987 GAACGGAAGGAAGCATCAGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAA
9577020 TTGTTCATCT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 34 0.37
36 59 0.63
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:9577019 original size:71 final size:72
Alignment explanation
Indices: 9576875--9577019 Score: 247
Period size: 71 Copynumber: 2.0 Consensus size: 72
9576865 GAAGGTGAAT
* *
9576875 AAGAAGAACGAAAGGAAGCATCAGTACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTT
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
*
9576940 TTGATTC
66 TCGATTC
*
9576947 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTC-AAGTGAACGGAAGGAAGCATCAGCACTT
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
9577011 TCGATTC
66 TCGATTC
9577018 AA
1 AA
9577020 TTGTTCATCT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 35 0.51
72 34 0.49
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
TCGATTC
Found at i:9578366 original size:35 final size:35
Alignment explanation
Indices: 9578248--9578387 Score: 199
Period size: 36 Copynumber: 3.9 Consensus size: 35
9578238 TGAATAAGAA
*
9578248 GAACGAAAGGAAGCATCAGTACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTC-AAGT
* * * *
9578284 GAACGGAAGGAAGCATCGGCACTTTTGATTCAAGAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAG-T
*
9578320 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
*
9578355 GAACGGAAGGAAGCATCAGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAA
9578388 TTGTTCATCT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 34 0.37
36 59 0.63
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:9578387 original size:71 final size:72
Alignment explanation
Indices: 9578243--9578387 Score: 247
Period size: 71 Copynumber: 2.0 Consensus size: 72
9578233 GAAGGTGAAT
* *
9578243 AAGAAGAACGAAAGGAAGCATCAGTACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTT
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
*
9578308 TTGATTC
66 TCGATTC
*
9578315 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTC-AAGTGAACGGAAGGAAGCATCAGCACTT
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
9578379 TCGATTC
66 TCGATTC
9578386 AA
1 AA
9578388 TTGTTCATCT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 35 0.51
72 34 0.49
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
TCGATTC
Found at i:9582102 original size:16 final size:17
Alignment explanation
Indices: 9582069--9582106 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
9582059 AAAATCGTCA
*
9582069 ACCCAAAAATTTCAGGT
1 ACCCAAAAATTCCAGGT
*
9582086 ACCCAAAAA-TCCGGGT
1 ACCCAAAAATTCCAGGT
9582102 ACCCA
1 ACCCA
9582107 TATTTGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.39, C:0.32, G:0.13, T:0.16
Consensus pattern (17 bp):
ACCCAAAAATTCCAGGT
Found at i:9582555 original size:31 final size:30
Alignment explanation
Indices: 9582496--9582583 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
9582486 CAAACGGATT
* * *
9582496 ACAAAATGATCATTAAACTATTCAAATTGTT
1 ACAAAATGATTATTAAATTA-TCAAATTGTC
* *
9582527 ATAAAATGATTATTAAATTTATCGAATTGTC
1 ACAAAATGATTATTAAA-TTATCAAATTGTC
9582558 ACAAAATGA-TACTTAAAATTATCAAA
1 ACAAAATGATTA-TT-AAATTATCAAA
9582584 ATTTATCACT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 2 0.04
31 40 0.85
32 5 0.11
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (30 bp):
ACAAAATGATTATTAAATTATCAAATTGTC
Found at i:9584729 original size:16 final size:16
Alignment explanation
Indices: 9584707--9584755 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
9584697 CAGGTTTCAG
9584707 ATTCAGATTTCAATTC
1 ATTCAGATTTCAATTC
* *
9584723 CTTCAGATTTCAAATC
1 ATTCAGATTTCAATTC
9584739 ATTCACAGATTTCAATT
1 ATT--CAGATTTCAATT
9584756 TCCTCAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 16 0.59
18 11 0.41
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTCAGATTTCAATTC
Found at i:9585860 original size:5 final size:5
Alignment explanation
Indices: 9585850--9585875 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9585840 TATTTTGTCT
9585850 ATTTA ATTTA ATTTA ATTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA A
9585876 CTATTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:9586518 original size:24 final size:24
Alignment explanation
Indices: 9586485--9586542 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
9586475 TCATAAGGTT
9586485 CGTGCCACAAGACCAAAGAAAACA
1 CGTGCCACAAGACCAAAGAAAACA
* * *
9586509 CGTGCTACAAGACCAGAGAAAACG
1 CGTGCCACAAGACCAAAGAAAACA
*
9586533 TGTGCCACAA
1 CGTGCCACAA
9586543 AGACATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.28, G:0.21, T:0.09
Consensus pattern (24 bp):
CGTGCCACAAGACCAAAGAAAACA
Found at i:9586782 original size:3 final size:3
Alignment explanation
Indices: 9586774--9586808 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9586764 ATAAGAAAAG
*
9586774 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
9586809 GAGAAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:9587455 original size:29 final size:28
Alignment explanation
Indices: 9587422--9587513 Score: 73
Period size: 29 Copynumber: 3.3 Consensus size: 28
9587412 GTTGAGTTTC
9587422 TTTATTAGTAAAAGTTTTAAAATGATCAT
1 TTTATTA-TAAAAGTTTTAAAATGATCAT
* **
9587451 TTTATTATAAGA-TTTT--TTTGAGTCAT
1 TTTATTATAAAAGTTTTAAAATGA-TCAT
* **
9587477 TTAATTATTAAAAGTTACAAAATGATCAT
1 TTTATTA-TAAAAGTTTTAAAATGATCAT
*
9587506 TTGATTAT
1 TTTATTAT
9587514 TCATATGTTC
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
25 3 0.06
26 10 0.21
27 8 0.17
28 7 0.15
29 17 0.35
30 3 0.06
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (28 bp):
TTTATTATAAAAGTTTTAAAATGATCAT
Found at i:9592554 original size:50 final size:50
Alignment explanation
Indices: 9592429--9592554 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 50
9592419 GTAGCAGTAA
*
9592429 AGCGCGCCCCCTGAACCGCGCTATACGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCGCCACGTGGGTAT
** * * *
9592479 AGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGTCGCCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCGCCACGTGGGTAT
* *
9592529 AGCGCGCCCCCTGATCCACGCTATAC
1 AGCGCGCCCCCTGAACCGCGCTATAC
9592555 CTGGGTATCT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.16, C:0.37, G:0.28, T:0.19
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCGCCACGTGGGTAT
Found at i:9593036 original size:111 final size:111
Alignment explanation
Indices: 9592842--9593063 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
9592832 TGGAAATCAT
*
9592842 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
* *
9592907 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGACTAAAAATTAA
*
9592953 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
*
9593018 TAATTAGTTGATTTATTTAATGCATGATTATTAGACTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGACTAAAAATTAA
9593064 TTTTTGTAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGACTAAAAATTAA
Found at i:9599532 original size:21 final size:21
Alignment explanation
Indices: 9599495--9599534 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9599485 CCCCCTTTGA
*
9599495 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
9599516 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
9599535 TGGGGTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:9600243 original size:12 final size:12
Alignment explanation
Indices: 9600228--9600254 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9600218 CACCTCTAAA
9600228 TCCTCCTCCTAT
1 TCCTCCTCCTAT
9600240 TCCTCCTCCTAT
1 TCCTCCTCCTAT
9600252 TCC
1 TCC
9600255 AATTTCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (12 bp):
TCCTCCTCCTAT
Found at i:9602046 original size:22 final size:23
Alignment explanation
Indices: 9602021--9602064 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
9602011 AATTAAGTTT
9602021 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
9602043 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
9602065 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:9604225 original size:3 final size:3
Alignment explanation
Indices: 9604217--9604266 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
9604207 ACCTGCTCAG
** *
9604217 GAC GAC GAC GAC GAC GAC GAC GGT GAT GAC GAC GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
9604265 GA
1 GA
9604267 TAACAGCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.32, C:0.28, G:0.36, T:0.04
Consensus pattern (3 bp):
GAC
Found at i:9604514 original size:35 final size:33
Alignment explanation
Indices: 9604475--9604559 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
9604465 ATATTTCAGT
*
9604475 TAATTTTGTT-TATTATCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
9604510 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
9604545 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
9604560 TAAATACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:9607452 original size:12 final size:12
Alignment explanation
Indices: 9607435--9607465 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
9607425 TTCCAACATG
9607435 AATCTTCCTCGA
1 AATCTTCCTCGA
9607447 AATCTTCCTCGA
1 AATCTTCCTCGA
9607459 AATCTTC
1 AATCTTC
9607466 GTTATCAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (12 bp):
AATCTTCCTCGA
Found at i:9608789 original size:23 final size:23
Alignment explanation
Indices: 9608743--9608793 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
9608733 AACGATAATA
*
9608743 AAATAATTAAAATATTCACTAAT
1 AAATAATTAAAATATTCACAAAT
*
9608766 AAATAATTAATAATATTTA-AAAT
1 AAATAATTAA-AATATTCACAAAT
9608789 AAATA
1 AAATA
9608794 TTATTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAATTAAAATATTCACAAAT
Found at i:9609802 original size:21 final size:21
Alignment explanation
Indices: 9609776--9609815 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9609766 TTTTATATTC
9609776 AATTAAACC-TTTATATTAAAA
1 AATTAAACCATTTA-ATTAAAA
9609797 AATTAAACCATTTAATTAA
1 AATTAAACCATTTAATTAA
9609816 TTTTGACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAAACCATTTAATTAAAA
Found at i:9613587 original size:3 final size:3
Alignment explanation
Indices: 9613579--9613633 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
9613569 ATTCCCCCCA
9613579 TCT TCT TCT TCT TCT TCT TCT TCT T-T AT-T TC- TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT
*
9613621 TCT TCT TCC TCT T
1 TCT TCT TCT TCT T
9613634 ATCACACATA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:9614591 original size:26 final size:27
Alignment explanation
Indices: 9614562--9614621 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
9614552 TGTGTGTGAT
*
9614562 AAGAGGAAAAGTGAAG-AGAAAGAA-AG
1 AAGAAGAAAAGTGAAGAAG-AAGAAGAG
9614588 AAGAAGAAAAGTGAAGAAGAAGAAGAG
1 AAGAAGAAAAGTGAAGAAGAAGAAGAG
9614615 AAGAAGA
1 AAGAAGA
9614622 TGGGGAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (27 bp):
AAGAAGAAAAGTGAAGAAGAAGAAGAG
Found at i:9614593 original size:16 final size:16
Alignment explanation
Indices: 9614574--9614611 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9614564 GAGGAAAAGT
9614574 GAAGAGAAAG-AAAGAA
1 GAAGA-AAAGTAAAGAA
*
9614590 GAAGAAAAGTGAAGAA
1 GAAGAAAAGTAAAGAA
9614606 GAAGAA
1 GAAGAA
9614612 GAGAAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (16 bp):
GAAGAAAAGTAAAGAA
Found at i:9621574 original size:19 final size:19
Alignment explanation
Indices: 9621552--9621590 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9621542 ATGTGTGCTC
*
9621552 TTCAGTTTTAGAAGTTGAG
1 TTCAGTTTTAGAAGTCGAG
9621571 TTCAGTTTTAGAAGTCGAG
1 TTCAGTTTTAGAAGTCGAG
9621590 T
1 T
9621591 ATTGTCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (19 bp):
TTCAGTTTTAGAAGTCGAG
Found at i:9622137 original size:36 final size:35
Alignment explanation
Indices: 9622050--9622163 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
9622040 CGGCAACCAA
9622050 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
9622085 CTTTGAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
9622120 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
9622155 -GTTGAAAAT
1 CTTTGAAAAT
9622164 AGGAATGGGT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
33 5 0.07
34 3 0.04
35 43 0.57
36 24 0.32
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:9622589 original size:16 final size:17
Alignment explanation
Indices: 9622568--9622601 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9622558 ACTATTCACA
*
9622568 TGAATAGT-GAATTTTG
1 TGAATAGTAAAATTTTG
9622584 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
9622601 T
1 T
9622602 CGGCGATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:9626659 original size:21 final size:21
Alignment explanation
Indices: 9626635--9626695 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
9626625 ACCAACTTTG
9626635 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
9626656 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
9626670 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
9626691 AAATG
1 AAATG
9626696 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:9626716 original size:36 final size:35
Alignment explanation
Indices: 9626630--9626733 Score: 176
Period size: 35 Copynumber: 3.0 Consensus size: 35
9626620 TGGCAACCAA
9626630 CTTTG-AAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
9626664 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
9626699 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
9626734 GCTAGATGTT
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
34 5 0.07
35 38 0.57
36 24 0.36
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:9630179 original size:64 final size:64
Alignment explanation
Indices: 9630126--9630288 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
9630116 CGGTGCACCA
*
9630126 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * *
9630190 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATCCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
9630255 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
9630289 CAATTAATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 40 0.47
65 46 0.53
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:9630260 original size:19 final size:19
Alignment explanation
Indices: 9630236--9630286 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
9630226 GAAAATATCC
9630236 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
9630255 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
9630274 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
9630287 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:9670681 original size:20 final size:20
Alignment explanation
Indices: 9670656--9670700 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
9670646 GTCATCCAAT
*
9670656 TTTTTAAACCTCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
9670676 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
9670696 TTTTT
1 TTTTT
9670701 TTCCAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:9676498 original size:18 final size:18
Alignment explanation
Indices: 9676475--9676527 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
9676465 CGTAGAAATT
* * *
9676475 TGTCCCGTAGGATCACTG
1 TGTCCCGAAGGACCACTA
9676493 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
**
9676511 TGTCTAGAAGGACCACT
1 TGTCCCGAAGGACCACT
9676528 GATAATCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:9680633 original size:19 final size:17
Alignment explanation
Indices: 9680599--9680630 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9680589 TATTTCACTA
9680599 AGAACACATATATTATC
1 AGAACACATATATTATC
9680616 AGAACACATAT-TTAT
1 AGAACACATATATTAT
9680631 TATATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (17 bp):
AGAACACATATATTATC
Found at i:9683597 original size:17 final size:17
Alignment explanation
Indices: 9683575--9683632 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
9683565 ATTCATACAT
9683575 ACATATATACATACAAC
1 ACATATATACATACAAC
* *
9683592 ACATATAGTCCATATAAC
1 ACATATA-TACATACAAC
9683610 ACATATATACATACAAC
1 ACATATATACATACAAC
9683627 ACATAT
1 ACATAT
9683633 GTATAAGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (17 bp):
ACATATATACATACAAC
Found at i:9683659 original size:4 final size:4
Alignment explanation
Indices: 9683650--9683705 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
9683640 ACAAATTTGG
* * * *
9683650 CATA CATA CAATA CATA CATA CATT CATA CATT CATA CATT CATA CATT
1 CATA CATA C-ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
9683699 CATA CAT
1 CATA CAT
9683706 GTGGAGAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
4 39 0.91
5 4 0.09
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (4 bp):
CATA
Found at i:9683673 original size:8 final size:8
Alignment explanation
Indices: 9683650--9683705 Score: 85
Period size: 8 Copynumber: 6.9 Consensus size: 8
9683640 ACAAATTTGG
*
9683650 CATACATA
1 CATACATT
*
9683658 CAATACATA
1 C-ATACATT
9683667 CATACATT
1 CATACATT
9683675 CATACATT
1 CATACATT
9683683 CATACATT
1 CATACATT
9683691 CATACATT
1 CATACATT
9683699 CATACAT
1 CATACAT
9683706 GTGGAGAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
8 38 0.83
9 8 0.17
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (8 bp):
CATACATT
Found at i:9684532 original size:22 final size:23
Alignment explanation
Indices: 9684505--9684567 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 23
9684495 TAAATTACAC
9684505 AAAGAAGTTGCATTAAACATTCT
1 AAAGAAGTTGCATTAAACATTCT
9684528 AAGAAGATTAAGTTGCATTAAACATTCT
1 -A-AAG---AAGTTGCATTAAACATTCT
*
9684556 -AAGAAGATGCAT
1 AAAGAAGTTGCAT
9684568 GGTAACTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 8 0.24
24 1 0.03
25 6 0.18
28 19 0.56
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (23 bp):
AAAGAAGTTGCATTAAACATTCT
Found at i:9684543 original size:28 final size:28
Alignment explanation
Indices: 9684509--9684563 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
9684499 TTACACAAAG
9684509 AAGTTGCATTAAACATTCTAAGAAGATT
1 AAGTTGCATTAAACATTCTAAGAAGATT
9684537 AAGTTGCATTAAACATTCTAAGAAGAT
1 AAGTTGCATTAAACATTCTAAGAAGAT
9684564 GCATGGTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (28 bp):
AAGTTGCATTAAACATTCTAAGAAGATT
Found at i:9687255 original size:55 final size:55
Alignment explanation
Indices: 9687187--9687296 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
9687177 CGTTTTATGT
* *
9687187 TTGTTAACTGAGTGACCTGAATGGTGGCCGAAAAGAGTCAAAGTTGAGTCAATGA
1 TTGTTAACCGAGTGACCTGAAAGGTGGCCGAAAAGAGTCAAAGTTGAGTCAATGA
9687242 TTGTTAACCGAGTGACCTGAAAGGTGGCCGAAAAGAGTCAAAGTTGAGTCAATGA
1 TTGTTAACCGAGTGACCTGAAAGGTGGCCGAAAAGAGTCAAAGTTGAGTCAATGA
9687297 ACGTGGCATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.24
Consensus pattern (55 bp):
TTGTTAACCGAGTGACCTGAAAGGTGGCCGAAAAGAGTCAAAGTTGAGTCAATGA
Found at i:9696513 original size:22 final size:22
Alignment explanation
Indices: 9696482--9696528 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9696472 AACTACAGTG
9696482 CAAGCAGTGCAAGATATGATGA
1 CAAGCAGTGCAAGATATGATGA
*
9696504 CAAGCGGTGCAAGATATGATGA
1 CAAGCAGTGCAAGATATGATGA
9696526 CAA
1 CAA
9696529 ACAGAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17
Consensus pattern (22 bp):
CAAGCAGTGCAAGATATGATGA
Found at i:9698611 original size:5 final size:5
Alignment explanation
Indices: 9698592--9698635 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
9698582 GTCCGTCCGT
* * *
9698592 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
9698636 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.02, C:0.41, G:0.34, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:9698644 original size:6 final size:6
Alignment explanation
Indices: 9698633--9698687 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
9698623 TCGGCTCGGC
*
9698633 TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
9698681 TCGTGG T
1 TCGTGG T
9698688 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:9698990 original size:22 final size:22
Alignment explanation
Indices: 9698965--9699019 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
9698955 TCAGGAGTTA
* *
9698965 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
9698987 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
9699009 CGGGAGTTATA
1 CAGGAGTTATA
9699020 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:9704562 original size:5 final size:5
Alignment explanation
Indices: 9704543--9704581 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
9704533 GTCCGTCCGT
* * *
9704543 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
9704582 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:9704590 original size:6 final size:6
Alignment explanation
Indices: 9704579--9704669 Score: 155
Period size: 6 Copynumber: 15.2 Consensus size: 6
9704569 TCGGCTCGGC
* * *
9704579 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
9704627 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
9704670 AATACGTGTC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:9704969 original size:22 final size:22
Alignment explanation
Indices: 9704944--9704998 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
9704934 TCAGGAGTTA
* *
9704944 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
9704966 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
9704988 CGGGAGTTATA
1 CAGGAGTTATA
9704999 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:9708547 original size:21 final size:20
Alignment explanation
Indices: 9708461--9708618 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
9708451 AAATGACCAA
**
9708461 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
9708480 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
9708500 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
9708520 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
9708541 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
9708562 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
9708582 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
9708603 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
9708619 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:9708847 original size:26 final size:26
Alignment explanation
Indices: 9708824--9708875 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
9708814 AATGCGTATC
9708824 CGTAAATCGCAACGCGTATCCGTAAA
1 CGTAAATCGCAACGCGTATCCGTAAA
9708850 CGTAAATCGCAACGCGTATCCGTAAA
1 CGTAAATCGCAACGCGTATCCGTAAA
9708876 TCGCAACGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (26 bp):
CGTAAATCGCAACGCGTATCCGTAAA
Found at i:9708989 original size:20 final size:20
Alignment explanation
Indices: 9708586--9709002 Score: 448
Period size: 20 Copynumber: 20.4 Consensus size: 20
9708576 GATTTTCAAT
* ** *
9708586 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
9708606 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
9708626 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9708646 AATCGCAACGTGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A
**
9708667 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
9708687 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9708707 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
9708727 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
9708748 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9708768 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
9708788 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9708808 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
9708828 AATCGCAACGCGTATCCGTAAACGTA
1 AATCGCAACGCGTAT-C-----CGTA
9708854 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9708874 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
9708894 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9708914 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
9708934 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
9708954 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
9708974 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
9708994 AATCACAAC
1 AATCGCAAC
9709003 ACTGAAATTT
Statistics
Matches: 339, Mismatches: 40, Indels: 36
0.82 0.10 0.09
Matches are distributed among these distances:
19 4 0.01
20 278 0.82
21 36 0.11
22 1 0.00
25 1 0.00
26 19 0.06
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:9709715 original size:24 final size:24
Alignment explanation
Indices: 9709676--9709722 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
9709666 AAATTTGGTC
9709676 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
9709700 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
9709723 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:9712212 original size:19 final size:19
Alignment explanation
Indices: 9712190--9712517 Score: 347
Period size: 19 Copynumber: 18.7 Consensus size: 19
9712180 CGGAAAATAC
*
9712190 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
9712209 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
9712223 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
9712243 AATCGCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
9712257 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
9712277 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
9712291 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
9712310 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
9712324 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
9712344 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
9712358 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
9712377 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
9712396 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
9712410 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
9712429 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
*
9712448 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
9712467 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
9712486 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
9712505 AATCGCAATGCGA
1 AATCGCAATGCGA
9712518 TTTTGGTTTC
Statistics
Matches: 264, Mismatches: 12, Indels: 66
0.77 0.04 0.19
Matches are distributed among these distances:
14 67 0.25
15 3 0.01
16 9 0.03
17 6 0.02
18 6 0.02
19 134 0.51
20 39 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:9712255 original size:14 final size:15
Alignment explanation
Indices: 9712237--9712436 Score: 68
Period size: 14 Copynumber: 11.9 Consensus size: 15
9712227 GCAATGCGGA
9712237 AATGAAAATCGCAAC
1 AATGAAAATCGCAAC
9712252 -ATGAAAATCGCAATGC
1 AATGAAAATCGCAA--C
9712268 GGAAATGAAAATCGCAAC
1 ---AATGAAAATCGCAAC
* *
9712286 GA-GAGAATCGCAATGC
1 AATGAAAATCGCAA--C
*
9712302 GAAATGAAAATCCCAAC
1 --AATGAAAATCGCAAC
9712319 -ATGAAAATCGCAATGC
1 AATGAAAATCGCAA--C
9712335 GGAAATGAAAATCGCAAC
1 ---AATGAAAATCGCAAC
* *
9712353 GA-GAGAATCGCAATGC
1 AATGAAAATCGCAA--C
9712369 GAAATGAAAATCGCAATGC
1 --AATGAAAATCGCAA--C
9712388 GAAATGAAAATCGCAAC
1 --AATGAAAATCGCAAC
* *
9712405 GA-GAGAATCGCAATGC
1 AATGAAAATCGCAA--C
9712421 GAAATGAAAATCGCAA
1 --AATGAAAATCGCAA
9712437 TGCGAAATGG
Statistics
Matches: 144, Mismatches: 14, Indels: 50
0.69 0.07 0.24
Matches are distributed among these distances:
14 55 0.38
15 3 0.02
16 5 0.03
17 2 0.01
18 5 0.03
19 48 0.33
20 26 0.18
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (15 bp):
AATGAAAATCGCAAC
Found at i:9712311 original size:33 final size:34
Alignment explanation
Indices: 9712190--9712517 Score: 343
Period size: 34 Copynumber: 9.4 Consensus size: 34
9712180 CGGAAAATAC
* *
9712190 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
9712223 AATCGCAATGCGGAAATGAAAATCGCAAC-ATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
*
9712257 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
*
9712291 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
9712324 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
9712358 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
9712396 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
9712429 AATCGCAATGCGAAATGGAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
9712467 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
9712505 AATCGCAATGCGA
1 AATCGCAATGCGA
9712518 TTTTGGTTTC
Statistics
Matches: 266, Mismatches: 14, Indels: 25
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.00
33 84 0.32
34 93 0.35
35 6 0.02
36 2 0.01
37 2 0.01
38 78 0.29
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:9712319 original size:67 final size:67
Alignment explanation
Indices: 9712190--9712380 Score: 314
Period size: 67 Copynumber: 2.9 Consensus size: 67
9712180 CGGAAAATAC
* * * *
9712190 AATCGCAACGC-GAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAACA
1 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATCCCAACA
9712253 TGAA
64 TGAA
9712257 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATG
1 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATG
9712322 AA
66 AA
9712324 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATC
9712381 GCAATGCGAA
Statistics
Matches: 118, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
67 88 0.75
68 29 0.25
69 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (67 bp):
AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATG
AA
Found at i:9712535 original size:19 final size:19
Alignment explanation
Indices: 9712513--9712641 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
9712503 AAAATCGCAA
9712513 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
9712532 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
9712546 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
9712565 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
9712579 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
9712598 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
9712617 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
9712637 TGCGA
1 TGCGA
9712642 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:9712536 original size:57 final size:54
Alignment explanation
Indices: 9712218--9712518 Score: 323
Period size: 52 Copynumber: 5.7 Consensus size: 54
9712208 AAATCCCAAC
*
9712218 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--C-ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGATG-GAATCGCAATGC-GAA
* * * *
9712272 ATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGA---AAT-GAAAATCCCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGATGGAATCG-CAATGCGAA
9712318 CATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CGA-GAGAATCGCAATGCGAA
1 -ATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGATG-GAATCGCAATGCGAA
9712372 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGA-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGATG-GAATCGCAATGCGAA
*
9712424 ATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCG--ATGG-AATCGCAATGCGAA
9712481 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAT
9712519 TTTGGTTTCG
Statistics
Matches: 216, Mismatches: 10, Indels: 41
0.81 0.04 0.15
Matches are distributed among these distances:
46 3 0.01
47 20 0.09
48 10 0.05
49 2 0.01
50 2 0.01
51 5 0.02
52 69 0.32
53 26 0.12
54 24 0.11
55 3 0.01
56 2 0.01
57 50 0.23
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (54 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGATGGAATCGCAATGCGAA
Done.