Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 56 of 168
Found at i:15897239 original size:50 final size:50
Alignment explanation
Indices: 15897095--15897259 Score: 165
Period size: 50 Copynumber: 3.3 Consensus size: 50
15897085 AGATAACACG
* * *
15897095 CCACAAAGGCTTTTCACAA-GATTA-GCCACAAAGGCTTTTCTAGAGAACTTG
1 CCACAAAGGCTTTCCA-AATGA-TACGCCACAAAAGCTTTT-TAGAGAACTTA
* * ** * *
15897146 CCACAAAGGCTTTTCAAATGATATGCC-GTAAAGACTTTCTAGAGAACTCA
1 CCACAAAGGCTTTCCAAATGATACGCCACAAAAG-CTTTTTAGAGAACTTA
* * *
15897196 CTATAAAGGCTTTCCAAATGATACGCCACAAAAGCTTTTTAGAGAATTTA
1 CCACAAAGGCTTTCCAAATGATACGCCACAAAAGCTTTTTAGAGAACTTA
15897246 CCACAAAGGCTTTC
1 CCACAAAGGCTTTC
15897260 TAGAGAATTT
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
50 64 0.69
51 29 0.31
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (50 bp):
CCACAAAGGCTTTCCAAATGATACGCCACAAAAGCTTTTTAGAGAACTTA
Found at i:15897249 original size:25 final size:25
Alignment explanation
Indices: 15897221--15897269 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
15897211 AAATGATACG
*
15897221 CCACAAAAGCTTTTTAGAGAATTTA
1 CCACAAAAGCTTTCTAGAGAATTTA
*
15897246 CCACAAAGGCTTTCTAGAGAATTT
1 CCACAAAAGCTTTCTAGAGAATTT
15897270 TCAAGTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (25 bp):
CCACAAAAGCTTTCTAGAGAATTTA
Found at i:15898876 original size:44 final size:44
Alignment explanation
Indices: 15898820--15898914 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 44
15898810 AGGCAACATA
* *
15898820 CAAAATAAGCCACAAAGGCTAATAGAATGCCACAAAAG-CCAAAT
1 CAAAATAAGCCACAAAGGATAACAGAATGCCA-AAAAGCCCAAAT
* * *
15898864 TAAAATATGCCACAAAGGATAACAGAATGCCATAAAGCCCAAAT
1 CAAAATAAGCCACAAAGGATAACAGAATGCCAAAAAGCCCAAAT
15898908 CAAAATA
1 CAAAATA
15898915 CATCACAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 4 0.09
44 40 0.91
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.14
Consensus pattern (44 bp):
CAAAATAAGCCACAAAGGATAACAGAATGCCAAAAAGCCCAAAT
Found at i:15898922 original size:44 final size:44
Alignment explanation
Indices: 15898820--15898926 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 44
15898810 AGGCAACATA
* *
15898820 CAAAATA-AGCCACAAAGGCTAATAGAATGCCACAAAAGCCAAAT
1 CAAAATACA-CCACAAAGGATAACAGAATGCCACAAAAGCCAAAT
* ** *
15898864 TAAAATATGCCACAAAGGATAACAGAATGCCA-TAAAGCCCAAAT
1 CAAAATACACCACAAAGGATAACAGAATGCCACAAAAG-CCAAAT
*
15898908 CAAAATACATCACAAAGGA
1 CAAAATACACCACAAAGGA
15898927 GACCCAAGGT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
43 4 0.08
44 48 0.92
ACGTcount: A:0.52, C:0.21, G:0.13, T:0.13
Consensus pattern (44 bp):
CAAAATACACCACAAAGGATAACAGAATGCCACAAAAGCCAAAT
Found at i:15906068 original size:21 final size:22
Alignment explanation
Indices: 15906039--15906080 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
15906029 AATAATAAAC
*
15906039 AAATAAAAAG-TAGCACACTAA
1 AAATAAAAAGTTAGAACACTAA
*
15906060 AAATTAAAAGTTAGAACACTA
1 AAATAAAAAGTTAGAACACTA
15906081 TCTAGCTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.19
Consensus pattern (22 bp):
AAATAAAAAGTTAGAACACTAA
Found at i:15906452 original size:18 final size:18
Alignment explanation
Indices: 15906429--15906467 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
15906419 AAATTAAAAT
*
15906429 ATTAATTAAACTAATTAA
1 ATTAATTAAACTAATGAA
*
15906447 ATTAATTAACCTAATGAA
1 ATTAATTAAACTAATGAA
15906465 ATT
1 ATT
15906468 TCCTATTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTAATTAAACTAATGAA
Found at i:15909027 original size:13 final size:13
Alignment explanation
Indices: 15909009--15909067 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
15908999 TTCTTCATTA
15909009 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
*
15909022 CTTTTGAAAAGTG
1 CTTTTGAGAAGTG
* *
15909035 TTTTTAAGAAGTG
1 CTTTTGAGAAGTG
* *
15909048 TTTTTGAGAAGTA
1 CTTTTGAGAAGTG
15909061 CTTTTGA
1 CTTTTGA
15909068 AAAAATTGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (13 bp):
CTTTTGAGAAGTG
Found at i:15931476 original size:15 final size:17
Alignment explanation
Indices: 15931446--15931477 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
15931436 TGTCGCCAAC
15931446 TTTTGTACTGTGTTTGT
1 TTTTGTACTGTGTTTGT
15931463 TTTTG-ACT-TGTTTGT
1 TTTTGTACTGTGTTTGT
15931478 GATCTTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (17 bp):
TTTTGTACTGTGTTTGT
Found at i:15932135 original size:263 final size:263
Alignment explanation
Indices: 15931668--15932179 Score: 776
Period size: 263 Copynumber: 1.9 Consensus size: 263
15931658 CTTTCTATTC
* * * * * *
15931668 TGTTTATCTTGTGTGTGATTGTCTGGAAACTATGTACATTGATTCTATCATTAATTGACTGTTTA
1 TGTTTATCTGGTGTGTGATTGTCTGGAAACTATGTACATCGATTCTATAATTAACTAACTGCTTA
* * * *
15931733 CGAGCTTCTATGTCTGTATGACTGATAATGTATGGTGTGTATTTTTGCACATGCATTAATCTCTT
66 CGAGCTTCTATGTCTGTATGACTAATAATGTATAGTGTGCATTTTTGCACATGCATTAACCTCTT
*
15931798 TGGGTTAGGTTGCAAAGAGAAGGGAGTCTGATCTGTTTTGGCAATTTCAACTACAATACGTCTGT
131 TAGGTTAGGTTGCAAAGAGAAGGGAGTCTGATCTGTTTTGGCAATTTCAACTACAATACGTCTGT
15931863 ATAGCGGTTTACTGCACAGTACGACATATATGTTAGCTCTACAGCATATTAACAGTGTACATCGA
196 ATAGCGGTTTACTGCACAGTACGACATATATGTTAGCTCTACAGCATATTAACAGTGTACATCGA
15931928 TTA
261 TTA
* * * *
15931931 TGTTTATCTGGTTTGTGGTTGTCTGGAAAC-AGTGTACATCGATTCTGTAATTGACTAACTGCTT
1 TGTTTATCTGGTGTGTGATTGTCTGGAAACTA-TGTACATCGATTCTATAATTAACTAACTGCTT
* * *
15931995 ACGAGCTTCTATGT-TAGTGTGACTAATAATGTATAGTGTGCATTTTTGCATATGCATTAACCTT
65 ACGAGCTTCTATGTCT-GTATGACTAATAATGTATAGTGTGCATTTTTGCACATGCATTAACCTC
* * * * *
15932059 TTTAGGTTGGGTTGCGAAGAGAAGGGAGTCTGATTTGTTTTGGCAGTTTCAACTGCAATACGTCT
129 TTTAGGTTAGGTTGCAAAGAGAAGGGAGTCTGATCTGTTTTGGCAATTTCAACTACAATACGTCT
*
15932124 GTATAGCGGTTTACTGCACAGTACGACATATATGTTAGCTCTACTGCATATTAACA
194 GTATAGCGGTTTACTGCACAGTACGACATATATGTTAGCTCTACAGCATATTAACA
15932180 TTTGAGTGGC
Statistics
Matches: 223, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
262 2 0.01
263 221 0.99
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (263 bp):
TGTTTATCTGGTGTGTGATTGTCTGGAAACTATGTACATCGATTCTATAATTAACTAACTGCTTA
CGAGCTTCTATGTCTGTATGACTAATAATGTATAGTGTGCATTTTTGCACATGCATTAACCTCTT
TAGGTTAGGTTGCAAAGAGAAGGGAGTCTGATCTGTTTTGGCAATTTCAACTACAATACGTCTGT
ATAGCGGTTTACTGCACAGTACGACATATATGTTAGCTCTACAGCATATTAACAGTGTACATCGA
TTA
Found at i:15933803 original size:50 final size:50
Alignment explanation
Indices: 15933719--15933816 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
15933709 ACCAGGCTGG
* *
15933719 ACAAGTAGAATCTGTATAGAACTACTCTTCTTCTATTTGATATTGATTGT
1 ACAAGTAGAATCTATATAGAACTACTCTTCTTCTATTTGACATTGATTGT
*
15933769 ACAAGTAGAAT-TCATATAGAACTTCTC-TCATTCTATTTGACATTGATT
1 ACAAGTAGAATCT-ATATAGAACTACTCTTC-TTCTATTTGACATTGATT
15933817 AGAATAAGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 3 0.07
50 40 0.93
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (50 bp):
ACAAGTAGAATCTATATAGAACTACTCTTCTTCTATTTGACATTGATTGT
Found at i:15938958 original size:24 final size:23
Alignment explanation
Indices: 15938931--15938981 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
15938921 AGATCTTCAA
*
15938931 ACAAAGGTAAAACCTATAACTTC
1 ACAAAGGTAAAACCTACAACTTC
15938954 TACAAAGGTAAAACCTACAACTTC
1 -ACAAAGGTAAAACCTACAACTTC
15938978 ACAA
1 ACAA
15938982 GTACACAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.49, C:0.24, G:0.08, T:0.20
Consensus pattern (23 bp):
ACAAAGGTAAAACCTACAACTTC
Found at i:15945263 original size:157 final size:156
Alignment explanation
Indices: 15944966--15945278 Score: 509
Period size: 157 Copynumber: 2.0 Consensus size: 156
15944956 ATCACAATAA
* * * *
15944966 AGTGTTATATCTTTTTTCCATACCAGGAATGACTTCAAGATTAGTTAAGAACTTTCGAAGCCAAA
1 AGTGTTATAGCTTTTTTCCATACCAGGAATGACTTCAAGATCAGTTAAGAAATTTCGAAACCAAA
* *
15945031 TTGCTTCATTCATTGTCTCAAAAGCAACCACATACTTGGCCTCCATAGTAGAGTCAGTAGTGCAA
66 TTGCTTCATTCATTGTCTCAAAAACAACCACATACTTGGCCTCCATAGTAGAGTCAGCAGTGCAA
15945096 GTTTGTTTTACACTTATCCATACTAT
131 GTTTGTTTTACACTTATCCATACTAT
* *
15945122 AGTGTTATAGCTTTTTTTTCATATCAGGAATGACTTCAAGATCAGTTAAGAAATTTCGAAACCAA
1 AGTGTTATAGC-TTTTTTCCATACCAGGAATGACTTCAAGATCAGTTAAGAAATTTCGAAACCAA
* *
15945187 ATTGCTTCTTTCGTTGTCTCAAAAACAACCACATACTTGGCCTCCATAGTAGAGTCAGCAGTGCA
65 ATTGCTTCATTCATTGTCTCAAAAACAACCACATACTTGGCCTCCATAGTAGAGTCAGCAGTGCA
* *
15945252 AGTTTGTTTTACACTTCTCCATGCTAT
130 AGTTTGTTTTACACTTATCCATACTAT
15945279 GGCTACGCCA
Statistics
Matches: 144, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
156 10 0.07
157 134 0.93
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (156 bp):
AGTGTTATAGCTTTTTTCCATACCAGGAATGACTTCAAGATCAGTTAAGAAATTTCGAAACCAAA
TTGCTTCATTCATTGTCTCAAAAACAACCACATACTTGGCCTCCATAGTAGAGTCAGCAGTGCAA
GTTTGTTTTACACTTATCCATACTAT
Found at i:15946720 original size:50 final size:51
Alignment explanation
Indices: 15946645--15946780 Score: 168
Period size: 51 Copynumber: 2.7 Consensus size: 51
15946635 TGTGTAGGCG
* * *
15946645 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT-ATAGATCACA
** * * *
15946695 TGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGTTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATAGATCACA
*
15946746 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
15946781 AACATCATTG
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
50 34 0.47
51 38 0.52
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATAGATCACA
Found at i:15946770 original size:51 final size:50
Alignment explanation
Indices: 15946643--15946773 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
15946633 TGTGTGTAGG
* ** * *
15946643 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCG
1 CGTGTGTAGTACTATGTGCAGGCTACTATGCATACCGGAATGATAGATCA
* * *
15946693 CATGTGTAGTACTATGTGCAGGCTACTATGCATACCGG-ATAGTTTCGATCA
1 CGTGTGTAGTACTATGTGCAGGCTACTATGCATACCGGAAT-G-ATAGATCA
15946744 CGTGTGTAGTACTATGTGCAGGCTACTATG
1 CGTGTGTAGTACTATGTGCAGGCTACTATG
15946774 TGAACCGAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.03
50 35 0.50
51 33 0.47
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (50 bp):
CGTGTGTAGTACTATGTGCAGGCTACTATGCATACCGGAATGATAGATCA
Found at i:15946833 original size:45 final size:45
Alignment explanation
Indices: 15946782--15946869 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
15946772 TGTGAACCGA
* *
15946782 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
15946827 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
15946870 GAGTATCTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:15950161 original size:16 final size:15
Alignment explanation
Indices: 15950137--15950167 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
15950127 TATTTATTTT
15950137 TATTAATATTATATA
1 TATTAATATTATATA
15950152 TATTACATATTATATA
1 TATTA-ATATTATATA
15950168 ATCTAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATATTATATA
Found at i:15956769 original size:27 final size:27
Alignment explanation
Indices: 15956731--15956786 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
15956721 AACCGACTAT
15956731 TAGGGATTTTGAATCATTTGAATAAAA
1 TAGGGATTTTGAATCATTTGAATAAAA
15956758 TAGGGATTTTGAATCATTTGAATAAAA
1 TAGGGATTTTGAATCATTTGAATAAAA
15956785 TA
1 TA
15956787 ATCTTATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.38
Consensus pattern (27 bp):
TAGGGATTTTGAATCATTTGAATAAAA
Found at i:15959248 original size:51 final size:50
Alignment explanation
Indices: 15959118--15959309 Score: 226
Period size: 51 Copynumber: 3.8 Consensus size: 50
15959108 ATTATTATCA
* * *
15959118 TTCGATACACGTAATAGCCTTCACATAGTACCACACACGTGACC-AAGTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * *
15959167 TTACGGTCCATGTAGTAACCTTCACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * *
15959219 TTCGGTATACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
*
15959269 TATCGATACACGTAGTAGCCTTCACATAGTACTACACACGT
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACACGT
15959310 ATTCATCGAT
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.02
50 39 0.33
51 73 0.61
52 5 0.04
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Found at i:15961594 original size:50 final size:50
Alignment explanation
Indices: 15961468--15961759 Score: 262
Period size: 50 Copynumber: 5.7 Consensus size: 50
15961458 GAATATAACA
* * * ** * * * *
15961468 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * * * **
15961517 TACCAATGTCATATCCCAGATATGGTCTTAAATGGGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * * *
15961567 TGCCCATGCCATGTCCCATACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * *
15961617 TGCCAACGCCATGTCCCAAACATGGTCTTACACGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
*
15961667 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GG
*
15961723 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
15961760 TCTCATCCTC
Statistics
Matches: 199, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
49 35 0.18
50 126 0.63
53 1 0.01
56 37 0.19
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:15962137 original size:30 final size:30
Alignment explanation
Indices: 15962103--15962160 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
15962093 CCTCGACTCT
15962103 AACTTTGACAAAATTACAATTTTGCCCCTA
1 AACTTTGACAAAATTACAATTTTGCCCCTA
* * * *
15962133 AACTTTTACATAATTACACTTTTTCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
15962161 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:15967303 original size:23 final size:23
Alignment explanation
Indices: 15967272--15967322 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
15967262 ACCTATTTTC
* *
15967272 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
15967295 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
15967318 TTACA
1 TTACA
15967323 ACTTCGTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:15971186 original size:51 final size:50
Alignment explanation
Indices: 15971126--15971346 Score: 189
Period size: 51 Copynumber: 4.4 Consensus size: 50
15971116 TATGAACACG
*
15971126 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATAAATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAAAT--TGGTCACA
* * * *** *
15971177 TGTGTAGTACTATGTGCAGGCTACTAAGTGTACCGGATGGCCTTGGTCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAT-AAATTGGTCACA
* * * * * *
15971228 TGTGTAGTACTATGTGTAGGCTACTACGTG-AACTGGA-AAGCTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATC-AGATAA-ATTGGTCACA
*
15971278 TGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGATGACAA-TGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAT-A-AATTGGTCACA
* * *
15971329 TGGGTGGTACCATGTGCA
1 TGTGTAGTACTATGTGCA
15971347 AACCACCGAA
Statistics
Matches: 140, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
50 43 0.31
51 91 0.65
52 4 0.03
53 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAAATTGGTCACA
Found at i:15971294 original size:50 final size:50
Alignment explanation
Indices: 15971122--15971309 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
15971112 TACCTATGAA
* * *
15971122 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCGATAA-ATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGA-AAGCT--TGGT
* * * **
15971173 CACATGTGTAGTACTATGTGCAGGCTACTAAGTGTACCGGATGGCCTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAAAG-CTTGGT
* * *
15971224 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACTGGAAAGCTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAAAGCTTGGT
*
15971274 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
15971310 TCAGATGACA
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 40 0.34
51 74 0.63
52 2 0.02
53 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAAAGCTTGGT
Found at i:15971325 original size:101 final size:101
Alignment explanation
Indices: 15971122--15971327 Score: 245
Period size: 101 Copynumber: 2.0 Consensus size: 101
15971112 TACCTATGAA
* *
15971122 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAATCGATAAAT-ATGATCACATGTGTAGTAC
* * **
15971187 TATGTGCAGGCTACTAAGTGTACCGGATGGCCTTGGT
65 TATGTGCAGGCTACTAAGTGTACCAGATGACAATGGT
* * * * *
15971224 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACTGGA-AAGCT-TGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAA-TCGATAA-ATATGATCACATGTGTAGTA
* * *
15971287 CTATGTGTAGGCTACTACGTGTATCAGATGACAATGGT
64 CTATGTGCAGGCTACTAAGTGTACCAGATGACAATGGT
15971325 CAC
1 CAC
15971328 ATGGGTGGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
101 49 0.56
102 35 0.40
103 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAATCGATAAATATGATCACATGTGTAGTACT
ATGTGCAGGCTACTAAGTGTACCAGATGACAATGGT
Found at i:15972868 original size:14 final size:14
Alignment explanation
Indices: 15972845--15972874 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15972835 AAATATAGAC
15972845 ATCCACATTTATAT
1 ATCCACATTTATAT
*
15972859 ATCCATATTTATAT
1 ATCCACATTTATAT
15972873 AT
1 AT
15972875 TTGTAACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (14 bp):
ATCCACATTTATAT
Found at i:15976657 original size:21 final size:21
Alignment explanation
Indices: 15976639--15976746 Score: 99
Period size: 21 Copynumber: 5.1 Consensus size: 21
15976629 AGGTTGAATG
*
15976639 GAAGCTCATAAGAGCTGAACT
1 GAAGCTCATAAGAGCTGAACA
* * * * *
15976660 GAAACCCATAAGGGTTAAACA
1 GAAGCTCATAAGAGCTGAACA
* *
15976681 GAAGCTCAAAAGAGCTGAACG
1 GAAGCTCATAAGAGCTGAACA
* * *
15976702 GAAACTCATATGAGTTGAACA
1 GAAGCTCATAAGAGCTGAACA
* *
15976723 GAAGCTCGTAAGAGCTAAACA
1 GAAGCTCATAAGAGCTGAACA
15976744 GAA
1 GAA
15976747 AGTAAACACG
Statistics
Matches: 64, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
GAAGCTCATAAGAGCTGAACA
Found at i:15976668 original size:42 final size:42
Alignment explanation
Indices: 15976586--15976747 Score: 148
Period size: 42 Copynumber: 3.9 Consensus size: 42
15976576 CAAAAGCCTG
* * * *
15976586 AAGGCTGAACAAAAG-TACATAAGTGCTAAACAGAATCCCATA
1 AAGGTTGAACAGAAGCT-CATAAGAGCTAAACAGAAACCCATA
** * *
15976628 AAGGTTGAATGGAAGCTCATAAGAGCTGAACTGAAACCCATA
1 AAGGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATA
* * * * * *
15976670 AGGGTTAAACAGAAGCTCAAAAGAGCTGAACGGAAACTCAT-
1 AAGGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATA
* *
15976711 ATGAGTTGAACAGAAGCTCGTAAGAGCTAAACAGAAA
1 AAG-GTTGAACAGAAGCTCATAAGAGCTAAACAGAAA
15976748 GTAAACACGA
Statistics
Matches: 97, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 2 0.02
42 94 0.97
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
AAGGTTGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATA
Found at i:15984437 original size:21 final size:21
Alignment explanation
Indices: 15984399--15984439 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15984389 AAGCTTGAAC
* *
15984399 GCTAAACAGAAGCACATAAGT
1 GCTAAACAAAAACACATAAGT
*
15984420 GCTAAACAAAAACCCATAAG
1 GCTAAACAAAAACACATAAG
15984440 GGTTGAATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (21 bp):
GCTAAACAAAAACACATAAGT
Found at i:15984475 original size:42 final size:42
Alignment explanation
Indices: 15984403--15984548 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 42
15984393 TTGAACGCTA
* * *
15984403 AACAGAAGC-ACATAAGTGCTAAACAAAAACCCATAAGGGTTG
1 AACAGAAGCTA-ATAAGAGCTGAACGAAAACCCATAAGGGTTG
** * *
15984445 AATGGAAGCTAATAAGAGCTGAACGGAAACCCATAAGGGTTA
1 AACAGAAGCTAATAAGAGCTGAACGAAAACCCATAAGGGTTG
* * ** *
15984487 AACAGAAGCTCAA-AAGAGCTGGACGAAAACTCATTTGAGTTG
1 AACAGAAGCT-AATAAGAGCTGAACGAAAACCCATAAGGGTTG
*
15984529 AACAGAAGCTCATAAGAGCT
1 AACAGAAGCTAATAAGAGCT
15984549 AAATTGAAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
41 1 0.01
42 80 0.95
43 3 0.04
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTAATAAGAGCTGAACGAAAACCCATAAGGGTTG
Found at i:15984480 original size:21 final size:21
Alignment explanation
Indices: 15984429--15984481 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
15984419 TGCTAAACAA
* * *
15984429 AAACCCATAAGGGTTGAATGG
1 AAACCCATAAGAGCTGAACGG
* **
15984450 AAGCTAATAAGAGCTGAACGG
1 AAACCCATAAGAGCTGAACGG
15984471 AAACCCATAAG
1 AAACCCATAAG
15984482 GGTTAAACAG
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (21 bp):
AAACCCATAAGAGCTGAACGG
Found at i:15988988 original size:18 final size:18
Alignment explanation
Indices: 15988965--15989017 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
15988955 TATTTAATAG
* *
15988965 AACCAAATGGACCGATCA
1 AACCAATTGAACCGATCA
* *
15988983 AACCAATTGTACCAATCA
1 AACCAATTGAACCGATCA
*
15989001 AACTAATTGAACCGATC
1 AACCAATTGAACCGATC
15989018 GAATCGATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.19
Consensus pattern (18 bp):
AACCAATTGAACCGATCA
Found at i:15990617 original size:19 final size:19
Alignment explanation
Indices: 15990572--15990622 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
15990562 AAGTATAAAG
15990572 TCAAGTTAAAATGATTTCAA
1 TCAAGTTAAAAT-ATTTCAA
**
15990592 TTGAGTTAAACAT-TTTCAA
1 TCAAGTTAAA-ATATTTCAA
15990611 TCAAGTTAAAAT
1 TCAAGTTAAAAT
15990623 TGTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 8 0.31
21 2 0.08
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (19 bp):
TCAAGTTAAAATATTTCAA
Found at i:15991231 original size:173 final size:172
Alignment explanation
Indices: 15990907--15991233 Score: 528
Period size: 173 Copynumber: 1.9 Consensus size: 172
15990897 CTAATTTTAA
*
15990907 CTATTTTTAATAATTTATTCAATTGAACCGATTGTATCGATCAAACTGGTTGAACTAGGAACTAG
1 CTATTTTTAATAATTTATTCAATTGAACCGATTGTATCGATCAAACTGGTTGAACTAGGAACAAG
** * * *
15990972 TGGTTTGACCAATTGCCTACCAATCAAATTCTGAAAACCTTGAGCTTCGTTAATGATATACTATA
66 TAATCTAACCAATTGCCTACCAATCAAATGCTGAAAACCTTGAGCTTCGTTAATGATATACTATA
15991037 AGTAAAATTAATTATTTATTATTTTTTAATCAAATTAATTAT
131 AGTAAAATTAATTATTTATTATTTTTTAATCAAATTAATTAT
* *
15991079 CTATTTTTAATAATTTATTCAATTGAACCGATTGTATCGATCAAACTGGTTGAATTGGGAACAAG
1 CTATTTTTAATAATTTATTCAATTGAACCGATTGTATCGATCAAACTGGTTGAACTAGGAACAAG
* * * *
15991144 TAATCTAACCAATTTGCTTAGCAATCAAATGCTGAAAACCTTGAGCTTCGTTGATTATATACTAT
66 TAATCTAACCAA-TTGCCTACCAATCAAATGCTGAAAACCTTGAGCTTCGTTAATGATATACTAT
*
15991209 AAGTAAAATTATTTATTTATTATTT
130 AAGTAAAATTAATTATTTATTATTT
15991234 GAGTTTTGAA
Statistics
Matches: 141, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
172 70 0.50
173 71 0.50
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (172 bp):
CTATTTTTAATAATTTATTCAATTGAACCGATTGTATCGATCAAACTGGTTGAACTAGGAACAAG
TAATCTAACCAATTGCCTACCAATCAAATGCTGAAAACCTTGAGCTTCGTTAATGATATACTATA
AGTAAAATTAATTATTTATTATTTTTTAATCAAATTAATTAT
Found at i:15991698 original size:33 final size:31
Alignment explanation
Indices: 15991658--15991742 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
15991648 AGCTAATTTT
15991658 TTTTTAAATAACAACATATTAATTTAAAT-AAAA
1 TTTTTAAATAA-AACA-A-TAATTTAAATAAAAA
**
15991691 TTTTTAAATAATTCAATAATTTAAATAAAAA
1 TTTTTAAATAAAACAATAATTTAAATAAAAA
* **
15991722 TTTTCAAATAATTCAATAATT
1 TTTTTAAATAAAACAATAATT
15991743 ATTTAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
30 10 0.21
31 25 0.52
32 2 0.04
33 11 0.23
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTTAAATAAAACAATAATTTAAATAAAAA
Found at i:15991715 original size:17 final size:17
Alignment explanation
Indices: 15991693--15991742 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
15991683 AAATAAAATT
15991693 TTTAAATAATTCAATAA
1 TTTAAATAATTCAATAA
*
15991710 TTTAAATAA---AA-AT
1 TTTAAATAATTCAATAA
15991723 TTTCAAATAATTCAATAA
1 TTT-AAATAATTCAATAA
15991741 TT
1 TT
15991743 ATTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
13 4 0.15
14 8 0.31
17 11 0.42
18 3 0.12
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATAATTCAATAA
Found at i:15991752 original size:31 final size:31
Alignment explanation
Indices: 15991677--15991742 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
15991667 AACAACATAT
*
15991677 TAATTTAAAT-AAAATTTTTAAATAATTCAA
1 TAATTTAAATAAAAATTTTCAAATAATTCAA
15991707 TAATTTAAATAAAAATTTTCAAATAATTCAA
1 TAATTTAAATAAAAATTTTCAAATAATTCAA
15991738 TAATT
1 TAATT
15991743 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (31 bp):
TAATTTAAATAAAAATTTTCAAATAATTCAA
Found at i:15995180 original size:20 final size:20
Alignment explanation
Indices: 15995152--15995202 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
15995142 AAATTTAAAT
* *
15995152 TGATTCAATATCTTTATTAC
1 TGATACAATATCTCTATTAC
15995172 TGATACAATATCTCTATTAC
1 TGATACAATATCTCTATTAC
*
15995192 TGATATAATAT
1 TGATACAATAT
15995203 TAATATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (20 bp):
TGATACAATATCTCTATTAC
Found at i:15997884 original size:43 final size:44
Alignment explanation
Indices: 15997834--15998072 Score: 235
Period size: 43 Copynumber: 5.6 Consensus size: 44
15997824 AGTGATACGG
* * *
15997834 GGAATCAGCACATAGCAACC-CCTTTCACAATTAAGGATTTGGT
1 GGAATCAGCACTTAGCAACCACCTTTCACAATTAAAGATATGGT
* ** *
15997877 GGAATCAGCACTTAGCAACCACCTTT-A-TATTCAGTGATACGG-
1 GGAATCAGCACTTAGCAACCACCTTTCACAATT-AAAGATATGGT
* * * *
15997919 GGAATCAACACTTAGCAACC-CCATTCACAATTAAAAATATTGT
1 GGAATCAGCACTTAGCAACCACCTTTCACAATTAAAGATATGGT
* * * * *
15997962 GGATTCAGCACATAGCAACCACCTTT-A-TATTCAATGATACGG-
1 GGAATCAGCACTTAGCAACCACCTTTCACAATT-AAAGATATGGT
*
15998004 GGAATCAGCACTTAGCAACC-CCTTTCACAATTAAAAATATGGT
1 GGAATCAGCACTTAGCAACCACCTTTCACAATTAAAGATATGGT
*
15998047 GGGATCAGCACTTAGCAACCACCTTT
1 GGAATCAGCACTTAGCAACCACCTTT
15998073 AGAGTCAATA
Statistics
Matches: 155, Mismatches: 30, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
41 9 0.06
42 57 0.37
43 75 0.48
44 14 0.09
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (44 bp):
GGAATCAGCACTTAGCAACCACCTTTCACAATTAAAGATATGGT
Found at i:15997935 original size:85 final size:85
Alignment explanation
Indices: 15997791--15998111 Score: 439
Period size: 85 Copynumber: 3.8 Consensus size: 85
15997781 CCGTTACTCA
* * * * * *
15997791 GTGGATTCAACACTTAGCAACCA-CTATAAATTCAGTGATACGGGGAATCAGCACATAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAACCC
**
15997855 CTTTCACAATTAAGGATTTG
66 CTTTCACAATTAAAAATTTG
* *
15997875 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACTTAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAACCC
*
15997940 CATTCACAATTAAAAATATT-
66 CTTTCACAATTAAAAAT-TTG
* *
15997960 GTGGATTCAGCACATAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAACCC
*
15998025 CTTTCACAATTAAAAATATG
66 CTTTCACAATTAAAAATTTG
* * * * * *
15998045 GTGGGATCAGCACTTAGCAACCACCTTTAGAGTCAATAATTCGGGGAATCAGCACTTAGAAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAACCC
15998110 CT
66 CT
15998112 CGGGGAATCA
Statistics
Matches: 211, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
84 22 0.10
85 187 0.89
86 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (85 bp):
GTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAACCC
CTTTCACAATTAAAAATTTG
Found at i:15998115 original size:26 final size:26
Alignment explanation
Indices: 15998085--15998137 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
15998075 AGTCAATAAT
*
15998085 TCGGGGAATCAGCACTTAGAAACCCC
1 TCGGGGAATCAGCACCTAGAAACCCC
* *
15998111 TCGGGGAATCAGTACCTAGCAACCCC
1 TCGGGGAATCAGCACCTAGAAACCCC
15998137 T
1 T
15998138 TTTTATTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (26 bp):
TCGGGGAATCAGCACCTAGAAACCCC
Found at i:16003011 original size:8 final size:8
Alignment explanation
Indices: 16002998--16003039 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
16002988 TGAAAGTTAG
16002998 TTATCCAA
1 TTATCCAA
16003006 TTATCCAA
1 TTATCCAA
*
16003014 TTAT--AT
1 TTATCCAA
16003020 TTATCCAA
1 TTATCCAA
*
16003028 TTATTCAA
1 TTATCCAA
16003036 TTAT
1 TTAT
16003040 ATAATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.17
8 24 0.83
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.48
Consensus pattern (8 bp):
TTATCCAA
Found at i:16003026 original size:22 final size:22
Alignment explanation
Indices: 16002998--16003041 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16002988 TGAAAGTTAG
16002998 TTATCCAATTATCCAATTATAT
1 TTATCCAATTATCCAATTATAT
*
16003020 TTATCCAATTATTCAATTATAT
1 TTATCCAATTATCCAATTATAT
16003042 AATTAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATCCAATTATCCAATTATAT
Found at i:16008947 original size:19 final size:19
Alignment explanation
Indices: 16008922--16008964 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
16008912 TATAGTTCTC
*
16008922 AAATAATAGG-AATTATAA
1 AAATAATAGGTAAATATAA
16008940 ATAATAATAGGTAAATATAA
1 A-AATAATAGGTAAATATAA
16008960 AAATA
1 AAATA
16008965 TTAATAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
AAATAATAGGTAAATATAA
Found at i:16008963 original size:22 final size:19
Alignment explanation
Indices: 16008923--16008970 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
16008913 ATAGTTCTCA
*
16008923 AATAATAGGAATTATAAAT
1 AATAATAGGAATTAAAAAT
16008942 AATAATAGGTAAATATAAAAAT
1 AATAATAGG--AAT-TAAAAAT
*
16008964 ATTAATA
1 AATAATA
16008971 AAACTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
21 3 0.12
22 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.31
Consensus pattern (19 bp):
AATAATAGGAATTAAAAAT
Found at i:16014639 original size:29 final size:27
Alignment explanation
Indices: 16014607--16014677 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
16014597 TATACTTACC
16014607 ATTCCTTCAGAGTTCGCCATATATATACT
1 ATTCCTTCAGAGTTCGCC--ATATATACT
*
16014636 ATTCCTTCAGAGTTCGCCATGTATACT
1 ATTCCTTCAGAGTTCGCCATATATACT
* *
16014663 ACTCCTTCATAGTTC
1 ATTCCTTCAGAGTTC
16014678 ACCAAGAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 21 0.54
29 18 0.46
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (27 bp):
ATTCCTTCAGAGTTCGCCATATATACT
Found at i:16014688 original size:27 final size:27
Alignment explanation
Indices: 16014609--16014688 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
16014599 TACTTACCAT
* * *
16014609 TCCTTCAGAGTTCGCCATATATATACTAT
1 TCCTTCAGAGTTCACCA-AGA-ATACTAC
* * *
16014638 TCCTTCAGAGTTCGCCATGTATACTAC
1 TCCTTCAGAGTTCACCAAGAATACTAC
*
16014665 TCCTTCATAGTTCACCAAGAATAC
1 TCCTTCAGAGTTCACCAAGAATAC
16014689 CACTTCTTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 26 0.60
29 17 0.40
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.34
Consensus pattern (27 bp):
TCCTTCAGAGTTCACCAAGAATACTAC
Found at i:16014843 original size:27 final size:27
Alignment explanation
Indices: 16014796--16014862 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
16014786 TTCACCATAG
* *
16014796 AGGCTTCTATTATAATAGATTTCCAAAA
1 AGGCTTCCATT-TAATAGATTGCCAAAA
*
16014824 AGGCTTCCATTTCATAGATTGCCAAAA
1 AGGCTTCCATTTAATAGATTGCCAAAA
*
16014851 AGGTTTCCATTT
1 AGGCTTCCATTT
16014863 TCTAGTGTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (27 bp):
AGGCTTCCATTTAATAGATTGCCAAAA
Found at i:16016539 original size:13 final size:13
Alignment explanation
Indices: 16016504--16016603 Score: 87
Period size: 13 Copynumber: 7.6 Consensus size: 13
16016494 GTAAATTTTG
16016504 TATATGAAATGGT
1 TATATGAAATGGT
16016517 TAT-TCGAAATGGT
1 TATAT-GAAATGGT
* **
16016530 TATATAAAATGAA
1 TATATGAAATGGT
*
16016543 TATATGAATTGGT
1 TATATGAAATGGT
*
16016556 TATATGAATTGGT
1 TATATGAAATGGT
**
16016569 TATATGGAAATATT
1 TATAT-GAAATGGT
*
16016583 TATACTG-AATGAT
1 TATA-TGAAATGGT
16016596 TATATGAA
1 TATATGAA
16016604 TCAGTTATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
12 3 0.04
13 55 0.79
14 11 0.16
15 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:16016586 original size:53 final size:52
Alignment explanation
Indices: 16016504--16016619 Score: 126
Period size: 53 Copynumber: 2.2 Consensus size: 52
16016494 GTAAATTTTG
* **
16016504 TATATGAAATGGTTATTCGAAATGGTTATA-TAAAATGAATATATGAATTGGT
1 TATATGAAATGGTTATTCGAAATAGTTATACT-AAATGAATATATGAATCAGT
* * * * *
16016556 TATATGAATTGGTTATATGGAAATATTTATACTGAATGATTATATGAATCAGT
1 TATATGAAATGGTTAT-TCGAAATAGTTATACTAAATGAATATATGAATCAGT
16016609 TATATGGAAAT
1 TATAT-GAAAT
16016620 AATTATATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
52 15 0.29
53 32 0.62
54 5 0.10
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.40
Consensus pattern (52 bp):
TATATGAAATGGTTATTCGAAATAGTTATACTAAATGAATATATGAATCAGT
Found at i:16016611 original size:13 final size:13
Alignment explanation
Indices: 16016543--16016614 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
16016533 ATAAAATGAA
*
16016543 TATATGAATTGGT
1 TATATGAATTAGT
*
16016556 TATATGAATTGGT
1 TATATGAATTAGT
* *
16016569 TATATGGAAATATT
1 TATAT-GAATTAGT
*
16016583 TATACTGAATGA-T
1 TATA-TGAATTAGT
*
16016596 TATATGAATCAGT
1 TATATGAATTAGT
16016609 TATATG
1 TATATG
16016615 GAAATAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.12
13 30 0.60
14 13 0.26
15 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (13 bp):
TATATGAATTAGT
Found at i:16022992 original size:26 final size:26
Alignment explanation
Indices: 16022960--16023025 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
16022950 CATCCCAATC
*
16022960 CACAGCTCGTGTGAGTATACCCATTT
1 CACAGCTCGTGTGAGTAGACCCATTT
* *
16022986 CATAGCTCGTGTGAGTAGGCCCATTT
1 CACAGCTCGTGTGAGTAGACCCATTT
16023012 CACAGCTCGTGTGA
1 CACAGCTCGTGTGA
16023026 AATGTATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (26 bp):
CACAGCTCGTGTGAGTAGACCCATTT
Found at i:16030962 original size:18 final size:18
Alignment explanation
Indices: 16030939--16030996 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
16030929 CCTAATAACA
16030939 AACAGAAGCTTGAAAGCT
1 AACAGAAGCTTGAAAGCT
*
16030957 AACAGAAGCTCGTGAGAGCT
1 AACAGAAGCT--TGAAAGCT
*
16030977 GAA-AGAAGCTCGAAAGCT
1 -AACAGAAGCTTGAAAGCT
16030995 AA
1 AA
16030997 ACAAAAGCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.06
18 16 0.47
20 14 0.41
21 2 0.06
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (18 bp):
AACAGAAGCTTGAAAGCT
Found at i:16030993 original size:38 final size:39
Alignment explanation
Indices: 16030942--16031015 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
16030932 AATAACAAAC
* * *
16030942 AGAAGCTTGAAAGCT-AACAGAAGCTCGTGAGAGCTGAA
1 AGAAGCTCGAAAGCTAAACAAAAGCTCGTAAGAGCTGAA
16030980 AGAAGCTCGAAAGCTAAACAAAAGCTCGTAAGAGCT
1 AGAAGCTCGAAAGCTAAACAAAAGCTCGTAAGAGCT
16031016 AATCCACCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 14 0.44
39 18 0.56
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.15
Consensus pattern (39 bp):
AGAAGCTCGAAAGCTAAACAAAAGCTCGTAAGAGCTGAA
Found at i:16037273 original size:21 final size:21
Alignment explanation
Indices: 16037249--16037288 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16037239 AGATTAAATC
* *
16037249 GAAAACATTTGGAAATTTTAG
1 GAAAACAGTTGAAAATTTTAG
*
16037270 GAAAAGAGTTGAAAATTTT
1 GAAAACAGTTGAAAATTTT
16037289 GAATTGCAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (21 bp):
GAAAACAGTTGAAAATTTTAG
Found at i:16042639 original size:126 final size:126
Alignment explanation
Indices: 16042486--16042740 Score: 483
Period size: 126 Copynumber: 2.0 Consensus size: 126
16042476 GAAAGACCTC
16042486 TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
1 TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
*
16042551 TTTGACAAACAAGTTGCCCCGAAATTAAAAGATCCTAAGAGCTTTACCATCCCATGTTTAA
66 TTTGACAAACAAGTTGCCCCGAAATTAAAAGATCCTAAGAGCTTTACCATCCCATGTTCAA
*
16042612 TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTTT
1 TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
*
16042677 TTTGACAAACAAGTTGCCCCGAAATTAAAAGATCCTAGGAGCTTTACCATCCCATGTTCAA
66 TTTGACAAACAAGTTGCCCCGAAATTAAAAGATCCTAAGAGCTTTACCATCCCATGTTCAA
16042738 TTG
1 TTG
16042741 ACAATCATTA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (126 bp):
TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
TTTGACAAACAAGTTGCCCCGAAATTAAAAGATCCTAAGAGCTTTACCATCCCATGTTCAA
Found at i:16057367 original size:21 final size:21
Alignment explanation
Indices: 16057317--16057373 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
16057307 ACTGTTGTTG
*
16057317 AGAAGGAAGTTGCTGCTACAGA
1 AGAA-GAAGTTGTTGCTACAGA
* *
16057339 TGAGGAAGTTGTTGCTGA-AGA
1 AGAAGAAGTTGTTGCT-ACAGA
16057360 AGAAGAAGTTGTTG
1 AGAAGAAGTTGTTG
16057374 AAAATGAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.33, C:0.07, G:0.35, T:0.25
Consensus pattern (21 bp):
AGAAGAAGTTGTTGCTACAGA
Found at i:16065676 original size:67 final size:67
Alignment explanation
Indices: 16065602--16065740 Score: 251
Period size: 67 Copynumber: 2.1 Consensus size: 67
16065592 TGTGTGTTCT
16065602 ATTTTTCTTTCTTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGAC
1 ATTTTTCTTTCTTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGAC
16065667 AA
66 AA
* * *
16065669 ATTTTTCTTTCTTTTCTTTGTGATATATTGTCATTATCATCCTTCTATTTTTAACAATTATTGAC
1 ATTTTTCTTTCTTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGAC
16065734 AA
66 AA
16065736 ATTTT
1 ATTTT
16065741 GTTTTACTTC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (67 bp):
ATTTTTCTTTCTTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGAC
AA
Found at i:16066135 original size:28 final size:28
Alignment explanation
Indices: 16066095--16066152 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16066085 TCACAAATTA
16066095 ATTGATATTCCAAACTTAAACACGTTTT
1 ATTGATATTCCAAACTTAAACACGTTTT
16066123 ATTGATATTCCAAACTTAAACACGTTTT
1 ATTGATATTCCAAACTTAAACACGTTTT
16066151 AT
1 AT
16066153 CCCTCTAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (28 bp):
ATTGATATTCCAAACTTAAACACGTTTT
Found at i:16069384 original size:16 final size:16
Alignment explanation
Indices: 16069365--16069395 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16069355 GTTAAAAATA
16069365 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
16069381 ATATAACATTTATAA
1 ATATAAAATTTATAA
16069396 GCAAAGTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:16070664 original size:11 final size:11
Alignment explanation
Indices: 16070638--16070695 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
16070628 AACTAATCCT
*
16070638 CTCTCAAATTTT
1 CTCTC-AATTTC
16070650 CTCTCAATTTC
1 CTCTCAATTTC
16070661 CTCTCAATTTC
1 CTCTCAATTTC
* *
16070672 CTCTCAAATTG
1 CTCTCAATTTC
*
16070683 CTCTCAAATTC
1 CTCTCAATTTC
16070694 CT
1 CT
16070696 TCCAAATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
11 37 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:16070675 original size:22 final size:22
Alignment explanation
Indices: 16070638--16070703 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
16070628 AACTAATCCT
* *
16070638 CTCTCAAATTTTCTCTCAATTTC
1 CTCTC-AATTTCCTCTCAAATTC
*
16070661 CTCTCAATTTCCTCTCAAATTG
1 CTCTCAATTTCCTCTCAAATTC
*
16070683 CTCTCAAATTCCT-TCCAAATT
1 CTCTCAATTTCCTCT-CAAATT
16070704 TCACTCAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.03
22 32 0.84
23 5 0.13
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.42
Consensus pattern (22 bp):
CTCTCAATTTCCTCTCAAATTC
Found at i:16070710 original size:22 final size:22
Alignment explanation
Indices: 16070640--16070715 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
16070630 CTAATCCTCT
* * * *
16070640 CTCAAATTTTCTCTCAATTTCCT
1 CTCAAA-TTCCTCTCAAATTGCA
* *
16070663 CTCAATTTCCTCTCAAATTGCT
1 CTCAAATTCCTCTCAAATTGCA
*
16070685 CTCAAATTCCT-TCCAAATTTCA
1 CTCAAATTCCTCT-CAAATTGCA
16070707 CTCAAATTC
1 CTCAAATTC
16070716 ATATTTAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 1 0.02
22 39 0.87
23 5 0.11
ACGTcount: A:0.26, C:0.32, G:0.01, T:0.41
Consensus pattern (22 bp):
CTCAAATTCCTCTCAAATTGCA
Found at i:16070711 original size:33 final size:33
Alignment explanation
Indices: 16070640--16070714 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 33
16070630 CTAATCCTCT
* * *
16070640 CTCAAATTTTCTCTCAATTTCCTCTCAATTTCCT
1 CTCAAA-TTGCTCTCAAATTCCTCTCAATTTCCA
16070674 CTCAAATTGCTCTCAAATTCCT-TCCAAATTT-CA
1 CTCAAATTGCTCTCAAATTCCTCT-C-AATTTCCA
16070707 CTCAAATT
1 CTCAAATT
16070715 CATATTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 1 0.03
33 24 0.67
34 11 0.31
ACGTcount: A:0.27, C:0.31, G:0.01, T:0.41
Consensus pattern (33 bp):
CTCAAATTGCTCTCAAATTCCTCTCAATTTCCA
Found at i:16070772 original size:51 final size:51
Alignment explanation
Indices: 16070673--16070772 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
16070663 CTCAATTTCC
*
16070673 TCTCAAATTGCTCTCAAATTCCTTCCAAATTTCACTCAAATTCATATTTAA
1 TCTCAAATTGCTCTCAAATTCCTTCCAAATTTCACTCAAATCCATATTTAA
* * * * * *
16070724 TCTCAATTTGCTCTCAAGTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAATTGCTCTCAAATTCCTTC-CAAATTTCACTCAAATCCATATTT
16070773 TTAAATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.43
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAAATTCCTTCCAAATTTCACTCAAATCCATATTTAA
Found at i:16070804 original size:15 final size:14
Alignment explanation
Indices: 16070778--16070816 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
16070768 TATTTTTAAA
16070778 TATTTTTAAAAAAAT
1 TATTTTT-AAAAAAT
16070793 TAATTTTTAAAAAAT
1 T-ATTTTTAAAAAAT
16070808 T-TTTTTAAA
1 TATTTTTAAA
16070817 CCGTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.35
15 9 0.39
16 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTTTTAAAAAAT
Found at i:16074211 original size:127 final size:125
Alignment explanation
Indices: 16073936--16074378 Score: 611
Period size: 127 Copynumber: 3.5 Consensus size: 125
16073926 CCCAAACATG
* *
16073936 CTACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
16074001 TAGAAGCG-ATTTTATACTGTTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* *
16074060 CTACTGTAGCAAAAGCGCATCCACGAGGGCACGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * *
16074124 CTTGCAGCGTTGTTTTATACTATTTGCTCAAAAACATCAACTCGAAATTATTTCTTCCAGGAC
65 CTTGAAGCGTT-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* *
16074187 CAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
16074252 TTGAAGCGTTTTTTAAACTATTTGCTTAGAAACGTCAACTCGAAATTATTTTTCTAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * * * * *
16074312 CTACTGTAGCAAAAGTGCGTACACGTGGGCGCGACTTAAAAAATCCTTCTGATAAATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
16074377 TT
66 TT
16074379 CGATTTTATC
Statistics
Matches: 283, Mismatches: 31, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
123 2 0.01
124 64 0.23
125 66 0.23
126 73 0.26
127 76 0.27
128 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:16075192 original size:21 final size:21
Alignment explanation
Indices: 16075168--16075212 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16075158 TAAAAAAATA
* *
16075168 TTATTAAGTAAATGGAATTTT
1 TTATGAAGTAAATGGAAATTT
*
16075189 TTATGAATTAAATGGAAATTT
1 TTATGAAGTAAATGGAAATTT
16075210 TTA
1 TTA
16075213 ATGCAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (21 bp):
TTATGAAGTAAATGGAAATTT
Found at i:16077463 original size:26 final size:26
Alignment explanation
Indices: 16077416--16077484 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 26
16077406 TATCCTCCTA
** * *
16077416 TTTGAGTTGGTTGGAGGTCCCTTGAG
1 TTTGAGTTGGTCAGAGGACCCTTAAG
*
16077442 TTTGAGTTGGTCAGATGACCCTTAAG
1 TTTGAGTTGGTCAGAGGACCCTTAAG
* * *
16077468 GTTAAGTTGGCCAGAGG
1 TTTGAGTTGGTCAGAGG
16077485 TGTTGGATTT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.33
Consensus pattern (26 bp):
TTTGAGTTGGTCAGAGGACCCTTAAG
Found at i:16079188 original size:6 final size:6
Alignment explanation
Indices: 16079177--16079212 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
16079167 TAGGTTTCTA
* *
16079177 GAAATG GAAATG GAAATG AAAATG AAAATG GAAATG
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG
16079213 AAAACTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.17
Consensus pattern (6 bp):
GAAATG
Found at i:16079205 original size:18 final size:18
Alignment explanation
Indices: 16079178--16079216 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
16079168 AGGTTTCTAG
*
16079178 AAATGGAAATGGAAATGA
1 AAATGAAAATGGAAATGA
16079196 AAATGAAAATGGAAATGA
1 AAATGAAAATGGAAATGA
16079214 AAA
1 AAA
16079217 CTTGCAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (18 bp):
AAATGAAAATGGAAATGA
Found at i:16079213 original size:12 final size:12
Alignment explanation
Indices: 16079178--16079216 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
16079168 AGGTTTCTAG
*
16079178 AAATGGAAATGG
1 AAATGGAAATGA
*
16079190 AAATGAAAATGA
1 AAATGGAAATGA
16079202 AAATGGAAATGA
1 AAATGGAAATGA
16079214 AAA
1 AAA
16079217 CTTGCAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (12 bp):
AAATGGAAATGA
Found at i:16080157 original size:39 final size:40
Alignment explanation
Indices: 16080079--16080159 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 40
16080069 CCTCTATGTA
16080079 AGAAAATCATTTTCAAACAAAGTTTTTTTTTTCAACAATTGG
1 AGAAAATCATTTTCAAACAAA--TTTTTTTTTCAACAATTGG
16080121 AGAAAATCATTTTCAAACAAA-TTTTTTTTCAACAATTGG
1 AGAAAATCATTTTCAAACAAATTTTTTTTTCAACAATTGG
16080160 TATAAGAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 18 0.46
42 21 0.54
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (40 bp):
AGAAAATCATTTTCAAACAAATTTTTTTTTCAACAATTGG
Found at i:16087428 original size:40 final size:40
Alignment explanation
Indices: 16087343--16087486 Score: 207
Period size: 41 Copynumber: 3.5 Consensus size: 40
16087333 TTTAACATAT
* * *
16087343 TCACTGGCACTTAGCCTGCTAGGCTTACAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGG-TTATAACCTGATTCAGA
*
16087384 TCACCGGCACGTAGCCTGCTAGGTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTATAACCTGATTCAGA
* *
16087424 TCACCGGCACTTAGCCTGCTAGGTTCATAACATGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTT-ATAACCTGATTCAGA
*
16087465 TCACCGACACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
16087487 ACTTAAAGTC
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 39 0.41
41 55 0.59
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGTTATAACCTGATTCAGA
Found at i:16089519 original size:13 final size:13
Alignment explanation
Indices: 16089501--16089525 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16089491 CAATCAAATG
16089501 CACACAAAATAAA
1 CACACAAAATAAA
16089514 CACACAAAATAA
1 CACACAAAATAA
16089526 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:16097486 original size:19 final size:20
Alignment explanation
Indices: 16097462--16097500 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
16097452 TTTGTGTACG
16097462 CTATTT-TTCTGTGG-TTTTT
1 CTATTTGTTC-GTGGATTTTT
16097481 CTATTTGTTCGTGGATTTTT
1 CTATTTGTTCGTGGATTTTT
16097501 TTTTCTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.08, C:0.10, G:0.18, T:0.64
Consensus pattern (20 bp):
CTATTTGTTCGTGGATTTTT
Found at i:16101712 original size:7 final size:7
Alignment explanation
Indices: 16101700--16101726 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
16101690 TCTTTCGTTT
16101700 TTTTATA
1 TTTTATA
16101707 TTTTATA
1 TTTTATA
16101714 TTTTATA
1 TTTTATA
16101721 TTTTAT
1 TTTTAT
16101727 CTTATTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTATA
Found at i:16104395 original size:36 final size:36
Alignment explanation
Indices: 16104352--16104423 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
16104342 AGCTGAGAGA
16104352 ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
1 ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
*
16104388 ATGAATAAAACCTTGCTTGACATGGTTCGTTCAATG
1 ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
16104424 TTAAGTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (36 bp):
ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
Found at i:16106070 original size:12 final size:12
Alignment explanation
Indices: 16106053--16106078 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16106043 TAGTATAGAG
16106053 AAGTGTAAAACA
1 AAGTGTAAAACA
16106065 AAGTGTAAAACA
1 AAGTGTAAAACA
16106077 AA
1 AA
16106079 CTTGGATTGC
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:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (12 bp):
AAGTGTAAAACA
Found at i:16113768 original size:35 final size:34
Alignment explanation
Indices: 16113719--16113988 Score: 252
Period size: 35 Copynumber: 7.5 Consensus size: 34
16113709 CCGACATTTA
* *
16113719 AAAAAGGTTGGGATAAACCTGTCTGAAGAAATCTT
1 AAAAAGGTTGGGATAGACCTGTCT-AAGAAACCTT
* *
16113754 AAAAAGGTTAGGATAGACCTATCTAAGACAACCTT
1 AAAAAGGTTGGGATAGACCTGTCTAAGA-AACCTT
** * *
16113789 AAAAAATTTGGAATAGACCTTGTCTAAAGCAACCTTT
1 AAAAAGGTTGGGATAGACC-TGTCT-AAGAAACC-TT
* *
16113826 AAAAAAGGTTAGGATAGACCTGTCTAAAATAACCTT
1 -AAAAAGGTTGGGATAGACCTGTCTAAGA-AACCTT
* * * *
16113862 AGAAAGGTTGGGATAGACCTTGTCGAAAGCAACCCT
1 AAAAAGGTTGGGATAGACC-TGTC-TAAGAAACCTT
* * * *
16113898 AAAAAGGTTGAGATAGACATTGTCTAAGGCAATCTTT
1 AAAAAGGTTGGGATAGAC-CTGTCTAA-G-AAACCTT
16113935 AAAAAAGGTTGGGATAGACCTGTCTAAGACAACCTT
1 -AAAAAGGTTGGGATAGACCTGTCTAAGA-AACCTT
16113971 AAAAAGGTTGGGATAGAC
1 AAAAAGGTTGGGATAGAC
16113989 ACGTTTAAGG
Statistics
Matches: 188, Mismatches: 34, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
34 4 0.02
35 79 0.42
36 47 0.25
37 26 0.14
38 32 0.17
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (34 bp):
AAAAAGGTTGGGATAGACCTGTCTAAGAAACCTT
Found at i:16113815 original size:36 final size:35
Alignment explanation
Indices: 16113716--16113988 Score: 198
Period size: 36 Copynumber: 7.6 Consensus size: 35
16113706 AGGCCGACAT
* * *
16113716 TTAAAAAAGGTTGGGATAAACCTGTCTGAAGA-AATC
1 TTAAAAAA-GTTGGAATAGACCTGTCT-AAGACAACC
* *
16113752 TTAAAAAGGTTAGG-ATAGACCTATCTAAGACAACC
1 TTAAAAAAGTT-GGAATAGACCTGTCTAAGACAACC
*
16113787 TTAAAAAATTTGGAATAGACCTTGTCTAA-AGCAACC
1 TTAAAAAAGTTGGAATAGACC-TGTCTAAGA-CAACC
* *
16113823 TTTAAAAAAGGTTAGG-ATAGACCTGTCTAAAATAACC
1 -TTAAAAAA-GTT-GGAATAGACCTGTCTAAGACAACC
* * * *
16113860 TTAGAAAGGTTGGGATAGACCTTGTCGAA-AGCAACC
1 TTAAAAAAGTTGGAATAGACC-TGTCTAAGA-CAACC
* * * * *
16113896 CTAAAAAGGTT-GAGATAGACATTGTCTAAGGCAATCT
1 TTAAAAAAGTTGGA-ATAGAC-CTGTCTAAGACAA-CC
*
16113933 TTAAAAAAGGTTGGGATAGACCTGTCTAAGACAACC
1 TTAAAAAA-GTTGGAATAGACCTGTCTAAGACAACC
* *
16113969 TTAAAAAGGTTGGGATAGAC
1 TTAAAAAAGTTGGAATAGAC
16113989 ACGTTTAAGG
Statistics
Matches: 192, Mismatches: 27, Indels: 37
0.75 0.11 0.14
Matches are distributed among these distances:
34 8 0.04
35 57 0.30
36 68 0.35
37 37 0.19
38 19 0.10
39 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (35 bp):
TTAAAAAAGTTGGAATAGACCTGTCTAAGACAACC
Found at i:16113950 original size:109 final size:107
Alignment explanation
Indices: 16113715--16113988 Score: 354
Period size: 109 Copynumber: 2.5 Consensus size: 107
16113705 AAGGCCGACA
* * * *
16113715 TTTAAAAAAGGTTGGGATAAACCTGTCTGAAGAAATCTTAAAAAGGTTAGGATAGACCTATCTAA
1 TTTAAAAAAGGTTGGGATAGACCTGTCT-AAGAAACCTTAAAAAGGTTGGGATAGACCTATCAAA
* * *
16113780 GACAACCTTAAAAAATTTGGAATAGACCTTGTCTAAAGCAACC
65 GACAACCCTAAAAAAGTTGGAATAGACATTGTCTAAAGCAACC
* * * *
16113823 TTTAAAAAAGGTTAGGATAGACCTGTCTAAAATAACCTTAGAAAGGTTGGGATAGACCTTGTCGA
1 TTTAAAAAAGGTTGGGATAGACCTGTCTAAGA-AACCTTAAAAAGGTTGGGATAGACC-TATC-A
* * *
16113888 AAG-CAACCCTAAAAAGGTT-GAGATAGACATTGTCTAAGGCAATC
63 AAGACAACCCTAAAAAAGTTGGA-ATAGACATTGTCTAAAGCAACC
16113932 TTTAAAAAAGGTTGGGATAGACCTGTCTAAGACAACCTTAAAAAGGTTGGGATAGAC
1 TTTAAAAAAGGTTGGGATAGACCTGTCTAAGA-AACCTTAAAAAGGTTGGGATAGAC
16113989 ACGTTTAAGG
Statistics
Matches: 144, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.02
108 50 0.35
109 88 0.61
110 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (107 bp):
TTTAAAAAAGGTTGGGATAGACCTGTCTAAGAAACCTTAAAAAGGTTGGGATAGACCTATCAAAG
ACAACCCTAAAAAAGTTGGAATAGACATTGTCTAAAGCAACC
Found at i:16113989 original size:73 final size:72
Alignment explanation
Indices: 16113716--16113988 Score: 306
Period size: 73 Copynumber: 3.8 Consensus size: 72
16113706 AGGCCGACAT
* * * * *
16113716 TTAAAAAAGGTTGGGATAAACC-TGTCTGAAGAAATCTTAAAAAGGTTAGGATAGACCTATCTAA
1 TTAAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGACCTGTCTAA
16113780 GACAACC
66 GACAACC
* *
16113787 TTAAAAAA-TTTGGAATAGACCTTGTCTAAAGCAACCTTTAAAAAAGGTTAGGATAGACCTGTCT
1 TTAAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACC-TT-AAAAAGGTTAGGATAGACCTGTCT
* *
16113851 AAAATAACC
64 AAGACAACC
* * * *
16113860 TT-AGAAAGGTTGGGATAGACCTTGTCGAAAGCAACCCTAAAAAGGTT-GAGATAGACATTGTCT
1 TTAAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTTAAAAAGGTTAG-GATAGAC-CTGTCT
* *
16113923 AAGGCAATCT
64 AAGACAA-CC
*
16113933 TTAAAAAAGGTTGGGATAGACC-TGTCT-AAGACAACCTTAAAAAGGTTGGGATAGAC
1 TTAAAAAAGGTTGGGATAGACCTTGTCTAAAG-CAACCTTAAAAAGGTTAGGATAGAC
16113989 ACGTTTAAGG
Statistics
Matches: 170, Mismatches: 22, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
70 11 0.06
71 35 0.21
72 19 0.11
73 86 0.51
74 19 0.11
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (72 bp):
TTAAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGACCTGTCTAA
GACAACC
Found at i:16116619 original size:41 final size:41
Alignment explanation
Indices: 16116574--16116675 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
16116564 GCTTAGCGCT
*
16116574 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTAAATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
* * *
16116615 TAGCAGGCTTAATGCTGGTGAAACATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
16116656 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
16116676 TACTGAATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 3 0.05
41 52 0.95
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
Found at i:16117281 original size:16 final size:15
Alignment explanation
Indices: 16117255--16117288 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
16117245 GATTAACAGG
*
16117255 TTATATTATATATAT
1 TTATATTATATACAT
16117270 TTATATTTATATACAT
1 TTATA-TTATATACAT
16117286 TTA
1 TTA
16117289 GTTATGCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTATATACAT
Found at i:16118245 original size:29 final size:31
Alignment explanation
Indices: 16118213--16118283 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 31
16118203 AATATATGTC
16118213 ATTAAAAA-G-AACATAATATAATATTTTTA
1 ATTAAAAATGAAACATAATATAATATTTTTA
16118242 ATTAAAAAATGCATAACATAATATAATATTTTTA
1 ATT-AAAAATG-A-AACATAATATAATATTTTTA
16118276 ATTAAAAA
1 ATTAAAAA
16118284 ATGCATAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.08
30 5 0.14
31 1 0.03
33 5 0.14
34 23 0.62
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (31 bp):
ATTAAAAATGAAACATAATATAATATTTTTA
Found at i:16118261 original size:34 final size:34
Alignment explanation
Indices: 16118222--16118290 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
16118212 CATTAAAAAG
16118222 AACATAATATAATATTTTTAATTAAAAAATGCAT
1 AACATAATATAATATTTTTAATTAAAAAATGCAT
16118256 AACATAATATAATATTTTTAATTAAAAAATGCAT
1 AACATAATATAATATTTTTAATTAAAAAATGCAT
16118290 A
1 A
16118291 GTTTTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (34 bp):
AACATAATATAATATTTTTAATTAAAAAATGCAT
Found at i:16118729 original size:139 final size:140
Alignment explanation
Indices: 16118478--16118733 Score: 374
Period size: 139 Copynumber: 1.8 Consensus size: 140
16118468 GGACAAAGTC
* *
16118478 GACTCTTATTTAAGAGTTGTCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAG
1 GACTCTTATTTAAGAGTTGCCTTAGGCATGCATATCCCAAACCTTATACAAAGAGTTGGCCAAAG
* * * * *
16118543 CGTATGTTGGCAGGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAAAAGTGTCAACATAATGTT
66 CATATGCTGGCAAGTCAATCCCAACACTTAGAAAAGTGTCGGCCCAAAAGTGTCAACATAATGTT
16118608 AGATACAACT
131 AGATACAACT
* *
16118618 GACTCTTATTTAAGTA-TTGCCTTAGGCATGTATATCCCAAATCTTAT-CAAAGAGTTGGCCAAA
1 GACTCTTATTTAAG-AGTTGCCTTAGGCATGCATATCCCAAACCTTATACAAAGAGTTGGCCAAA
* *
16118681 GCATCTGCTGGCAAGTCAATCCCGACACTTAGAAAAGTG-CTGGCCCAAAAGTG
65 GCATATGCTGGCAAGTCAATCCCAACACTTAGAAAAGTGTC-GGCCCAAAAGTG
16118734 CCGTATTAGG
Statistics
Matches: 103, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
138 1 0.01
139 60 0.58
140 41 0.40
141 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (140 bp):
GACTCTTATTTAAGAGTTGCCTTAGGCATGCATATCCCAAACCTTATACAAAGAGTTGGCCAAAG
CATATGCTGGCAAGTCAATCCCAACACTTAGAAAAGTGTCGGCCCAAAAGTGTCAACATAATGTT
AGATACAACT
Found at i:16120038 original size:27 final size:27
Alignment explanation
Indices: 16119981--16120038 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
16119971 ATTAATTGGT
* * * *
16119981 GAACCCCATCTCGCTAAACCGACTGGT
1 GAACCCCATCTCGCCAAACCAACTAGC
16120008 GAACCCCAGT-TCGCCAAACCAACTAGC
1 GAACCCCA-TCTCGCCAAACCAACTAGC
16120035 GAAC
1 GAAC
16120039 ACTCCTTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.31, C:0.38, G:0.17, T:0.14
Consensus pattern (27 bp):
GAACCCCATCTCGCCAAACCAACTAGC
Found at i:16125223 original size:27 final size:26
Alignment explanation
Indices: 16125179--16125243 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 26
16125169 TTTTATCAAG
* *
16125179 TTTATTAGTTAATCGATAAATAAATA
1 TTTATTAATTTATCGATAAATAAATA
* *
16125205 TTTTATTAATTTATTGATAAATTAATA
1 -TTTATTAATTTATCGATAAATAAATA
16125232 TTTATTAATTTA
1 TTTATTAATTTA
16125244 GAGAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (26 bp):
TTTATTAATTTATCGATAAATAAATA
Found at i:16128083 original size:37 final size:36
Alignment explanation
Indices: 16128034--16128104 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
16128024 CATAGATATT
* *
16128034 CCACCTGAAACACGCCA-ACCGCTCATAAGAGCTAAA
1 CCACCCGAAACACGCCAGA-CGCTCATAAAAGCTAAA
*
16128070 CCACCCGATAACACGCCAGATGCTCATAAAAGCTA
1 CCACCCGA-AACACGCCAGACGCTCATAAAAGCTA
16128105 GTCTATCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 7 0.23
37 22 0.73
38 1 0.03
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.13
Consensus pattern (36 bp):
CCACCCGAAACACGCCAGACGCTCATAAAAGCTAAA
Found at i:16130145 original size:2 final size:2
Alignment explanation
Indices: 16130138--16130170 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16130128 TATCTAGTAT
16130138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16130171 CAAAGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16130647 original size:7 final size:8
Alignment explanation
Indices: 16130630--16130654 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16130620 TTGGAATATT
16130630 AAAATTAA
1 AAAATTAA
16130638 AAAATTAA
1 AAAATTAA
16130646 AAAATTAA
1 AAAATTAA
16130654 A
1 A
16130655 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:16131138 original size:3 final size:3
Alignment explanation
Indices: 16131130--16131168 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
16131120 TTAACATGAT
16131130 TAA 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 TAA
16131169 AATGATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16134653 original size:17 final size:17
Alignment explanation
Indices: 16134631--16134664 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16134621 GAGATAACAA
16134631 ACAACTCCAATAAAAAG
1 ACAACTCCAATAAAAAG
16134648 ACAACTCCAATAAAAAG
1 ACAACTCCAATAAAAAG
16134665 GAGGTTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.24, G:0.06, T:0.12
Consensus pattern (17 bp):
ACAACTCCAATAAAAAG
Found at i:16137684 original size:13 final size:14
Alignment explanation
Indices: 16137666--16137694 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16137656 TATACCAAAG
16137666 AAAAAAC-AAACAA
1 AAAAAACAAAACAA
16137679 AAAAAACAAAACAA
1 AAAAAACAAAACAA
16137693 AA
1 AA
16137695 CAGAGAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAACAA
Found at i:16138217 original size:20 final size:20
Alignment explanation
Indices: 16138183--16138222 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16138173 TAGGCCCTTA
** *
16138183 GATTATTAACTTTAATGGTT
1 GATTATTAAAGTTAACGGTT
16138203 GATTATTAAAGTTAACGGTT
1 GATTATTAAAGTTAACGGTT
16138223 TGACTTTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (20 bp):
GATTATTAAAGTTAACGGTT
Found at i:16142282 original size:27 final size:27
Alignment explanation
Indices: 16142248--16142299 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
16142238 CAACGAATCA
16142248 GGGAATCAGCACACAGCAACCCCTTGG
1 GGGAATCAGCACACAGCAACCCCTTGG
**
16142275 GGGAATCAGCACTTAGCAACCCCTT
1 GGGAATCAGCACACAGCAACCCCTT
16142300 CACATTTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (27 bp):
GGGAATCAGCACACAGCAACCCCTTGG
Found at i:16142353 original size:101 final size:102
Alignment explanation
Indices: 16142110--16142373 Score: 476
Period size: 101 Copynumber: 2.6 Consensus size: 102
16142100 TAACCGTTAT
* * *
16142110 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAACAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
16142175 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
* *
16142212 CGGTGGAATCAGCACTTAGCAACCACCAACGAATCAGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
16142277 GAATCAGCACTTAGCAA-CCCCTTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
16142313 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
16142374 TATATGCAAT
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 78 0.50
102 77 0.50
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (102 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
Found at i:16144706 original size:19 final size:18
Alignment explanation
Indices: 16144679--16144726 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
16144669 GAAGCCAAAC
*
16144679 GAAACAGAAAGAAAGAAAA
1 GAAAAAGAAA-AAAGAAAA
* *
16144698 GAAAAAGAAAAAGGGAAA
1 GAAAAAGAAAAAAGAAAA
16144716 GAAATAAGAAA
1 GAAA-AAGAAA
16144727 CGCAAGGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAAAAGAAAA
Found at i:16152740 original size:51 final size:50
Alignment explanation
Indices: 16152673--16152804 Score: 149
Period size: 51 Copynumber: 2.6 Consensus size: 50
16152663 TGATAGGTCG
*
16152673 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGATCA
1 CATGTGTAGTACTATGTGCACGCTACTATGCGTACCGGATAG-TAT-GATCA
* * * * * *
16152724 CGTGTGTAGCACTATGTGCACGCTACTACGTGTATCGGATAGTGATGGTCA
1 CATGTGTAGTACTATGTGCACGCTACTATGCGTACCGGATAGT-ATGATCA
* *
16152775 CATGTGTAGTACTATATGCATGCTACTATG
1 CATGTGTAGTACTATGTGCACGCTACTATG
16152805 TGAACCGGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 1 0.01
51 65 0.97
52 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTATGTGCACGCTACTATGCGTACCGGATAGTATGATCA
Found at i:16152740 original size:101 final size:102
Alignment explanation
Indices: 16152620--16152804 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
16152610 AAAGTGATGG
* * * *
16152620 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTA-C-CAAAATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGCACTATGTGCACGCTACTACGTGTATCGCAAAATGAT-GGTCACATGTGTAGT
*
16152683 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATATGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * *
16152721 TCACGTGTGTAGCACTATGTGCACGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGCACTATGTGCACGCTACTACGTGTATCGCAAAATGATGGTCACATGTGTAGTA
*
16152786 CTATATGCATGCTACTATG
66 CTATATGCAGGCTACTATG
16152805 TGAACCGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 34 0.47
102 33 0.45
103 6 0.08
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGCACTATGTGCACGCTACTACGTGTATCGCAAAATGATGGTCACATGTGTAGTA
CTATATGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:16162422 original size:17 final size:17
Alignment explanation
Indices: 16162396--16162429 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16162386 ATATTTTAGA
16162396 TTTATTATTTA-AAACT
1 TTTATTATTTAGAAACT
16162412 TTTAGTTATTTAGAAACT
1 TTTA-TTATTTAGAAACT
16162430 ATGATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTATTATTTAGAAACT
Found at i:16165036 original size:91 final size:91
Alignment explanation
Indices: 16164881--16165054 Score: 240
Period size: 91 Copynumber: 1.9 Consensus size: 91
16164871 TCATCCACAT
* * **
16164881 ATTATCTGGCAGCTTTTATCTAAAATTAAGTTGTGTATTCACAACCATCTGGCGGCGTATTAACC
1 ATTATCTGGCAGCTTTTATCTAAAATTAAGTTGTGTACTCACAACCATCTAGCAACGTATTAACC
* *
16164946 TACAACTTTTGGTTGTTCGCCCACCC
66 TACAACATTTGGTGGTTCGCCCACCC
* ** * *
16164972 ATTATCTGGTAGCTTTTATCTGCAATTATGTTGTGTACTCACAATCATCTAGCAACGTATTAACC
1 ATTATCTGGCAGCTTTTATCTAAAATTAAGTTGTGTACTCACAACCATCTAGCAACGTATTAACC
*
16165037 TGCAACATTTGGTGGTTC
66 TACAACATTTGGTGGTTC
16165055 ATCCACAACT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (91 bp):
ATTATCTGGCAGCTTTTATCTAAAATTAAGTTGTGTACTCACAACCATCTAGCAACGTATTAACC
TACAACATTTGGTGGTTCGCCCACCC
Found at i:16167626 original size:18 final size:19
Alignment explanation
Indices: 16167574--16167628 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
16167564 TTACAAAAAG
*
16167574 AAATTCAAAATAGTTT-TTA
1 AAATTCAAAATA-TTTATAA
16167593 AAATTCAAAATATTTATAA
1 AAATTCAAAATATTTATAA
*
16167612 AAATTCTAAAT-TTTATA
1 AAATTCAAAATATTTATA
16167629 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 9 0.27
19 24 0.73
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATTCAAAATATTTATAA
Found at i:16167685 original size:30 final size:28
Alignment explanation
Indices: 16167633--16167700 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 28
16167623 TTTATATTTT
16167633 TAAAAAATATATAAAATATTAAAAATTC
1 TAAAAAATATATAAAATATTAAAAATTC
* *
16167661 TAAAGAATATATTAAAAATTTTAAAAATTC
1 TAAAAAATATA-T-AAAATATTAAAAATTC
16167691 TAAAATAATA
1 TAAAA-AATA
16167701 ATTGTTGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 10 0.29
29 1 0.03
30 19 0.56
31 4 0.12
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (28 bp):
TAAAAAATATATAAAATATTAAAAATTC
Found at i:16167689 original size:9 final size:9
Alignment explanation
Indices: 16167630--16167695 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
16167620 AATTTTATAT
16167630 TTTTAAAAA
1 TTTTAAAAA
* *
16167639 ATATATAAAA
1 TTTTA-AAAA
*
16167649 TATTAAAAA
1 TTTTAAAAA
*
16167658 TTCTAAAGAA
1 TTTTAAA-AA
16167668 TATATTAAAAA
1 T-T-TTAAAAA
16167679 TTTTAAAAA
1 TTTTAAAAA
*
16167688 TTCTAAAA
1 TTTTAAAA
16167696 TAATAATTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 26 0.59
10 10 0.23
11 4 0.09
12 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:16170273 original size:24 final size:24
Alignment explanation
Indices: 16170227--16170273 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16170217 AAAATGGAAG
*
16170227 AGAAAAGAAAAGGGAGAAAAGAGA
1 AGAAAAGAAAAGAGAGAAAAGAGA
*
16170251 AGAAAAGAAGAAGAG-GAAGAGAG
1 AGAAAAGAA-AAGAGAGAAAAGAG
16170274 GGAAGCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
AGAAAAGAAAAGAGAGAAAAGAGA
Found at i:16174455 original size:19 final size:22
Alignment explanation
Indices: 16174423--16174462 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
16174413 TTGAAAATAA
16174423 ATTTATATTATTAAT-TATTTT
1 ATTTATATTATTAATGTATTTT
16174444 ATTTAT-TT-TTAATGTATTT
1 ATTTATATTATTAATGTATTT
16174463 AAAGATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
ATTTATATTATTAATGTATTTT
Found at i:16174847 original size:29 final size:30
Alignment explanation
Indices: 16174814--16174879 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
16174804 TAAAAAATTT
*
16174814 ATGTATAAAATTGCACA-AAATCAAAGTTC
1 ATGTATAAAATTGCACATAAACCAAAGTTC
* **
16174843 ATGTATATAATTGCACATAAACCCTAGTTC
1 ATGTATAAAATTGCACATAAACCAAAGTTC
16174873 ATGTATA
1 ATGTATA
16174880 GTTTTGAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAACCAAAGTTC
Found at i:16176788 original size:93 final size:95
Alignment explanation
Indices: 16176691--16176868 Score: 208
Period size: 93 Copynumber: 1.9 Consensus size: 95
16176681 GGGTTTGTCA
* * *
16176691 AGTAAATTAATT-ATAATTTTTTCAAAATT-GTATTA-GGTTTCA-TGTTTATG-GTTTTTAAAG
1 AGTAAA-TAATTAAAAATTGTTTAAAAATTAG-ATTAGGGTTT-AGTGTTTA-GAGTTTTT-AAG
*
16176751 -AAAAA-AAATTAAATTAGGGTTTACGATTTCTTG
61 TAAAAACAAATTAAATTAAGGTTTACGATTTCTTG
16176784 AGTAAATAATTAAAAATTGTTTAAAAATTAGATTAGGGTTTAGTGTTTAGAGTTTTTAAGTAAAA
1 AGTAAATAATTAAAAATTGTTTAAAAATTAGATTAGGGTTTAGTGTTTAGAGTTTTTAAGTAAAA
*
16176849 ACTTAATTAAATTAAGGTTT
66 AC-AAATTAAATTAAGGTTT
16176869 GGGGTTTAGG
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
92 5 0.07
93 29 0.40
94 23 0.32
96 15 0.21
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (95 bp):
AGTAAATAATTAAAAATTGTTTAAAAATTAGATTAGGGTTTAGTGTTTAGAGTTTTTAAGTAAAA
ACAAATTAAATTAAGGTTTACGATTTCTTG
Found at i:16177285 original size:125 final size:126
Alignment explanation
Indices: 16176907--16177327 Score: 727
Period size: 126 Copynumber: 3.3 Consensus size: 126
16176897 TTGTTAATTT
* * *
16176907 AAAGAAGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTCCTGAAAAAATAAATTTGAATTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGAC
*
16176972 GTTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
* * *
16177033 AAAGAAGCTCCCACGTGGATGCGCTTTTGCTATAGTAGCTCCTGAAAAAATAATTTCGAGTTGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGAC
16177098 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
* *
16177159 AAAGAAACTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG-AAAAATAATTTTGAGTTGAT
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGAC
*
16177223 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
* *
16177284 AAAGAAGCTCCCACGTGGACGCGTTTTTGCTGCAGTAGCTCCTG
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
16177328 TTAGGCCTGA
Statistics
Matches: 279, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
125 119 0.43
126 160 0.57
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
Found at i:16178439 original size:7 final size:7
Alignment explanation
Indices: 16178427--16178458 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
16178417 TTAGTTATAT
16178427 ATACTAA
1 ATACTAA
16178434 ATACTAA
1 ATACTAA
16178441 ATACTAA
1 ATACTAA
*
16178448 ATACTGA
1 ATACTAA
16178455 ATAC
1 ATAC
16178459 CAATTGACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (7 bp):
ATACTAA
Found at i:16179616 original size:29 final size:29
Alignment explanation
Indices: 16179579--16179635 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
16179569 TTCAAAAAAT
*
16179579 AAAATTTAAAACTTTTTTAAAAATAATTA
1 AAAAATTAAAACTTTTTTAAAAATAATTA
*
16179608 AAAAATTAAAGCTTTTTTAAAAATAATT
1 AAAAATTAAAACTTTTTTAAAAATAATT
16179636 TGAGAGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAAATTAAAACTTTTTTAAAAATAATTA
Found at i:16179687 original size:12 final size:10
Alignment explanation
Indices: 16179632--16179698 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 10
16179622 TTTTAAAAAT
16179632 AATTTGAGAGG
1 AATTTGAGA-G
* *
16179643 AATTAGAAAGG
1 AATTTGAGA-G
*
16179654 CATTTGAGAAG
1 AATTTGAG-AG
16179665 AATTTGAGAG
1 AATTTGAGAG
16179675 AATATTAGAGAG
1 AAT-TT-GAGAG
16179687 AATTTGAGAG
1 AATTTGAGAG
16179697 AA
1 AA
16179699 AGGATTAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
10 12 0.26
11 26 0.55
12 9 0.19
ACGTcount: A:0.45, C:0.01, G:0.28, T:0.25
Consensus pattern (10 bp):
AATTTGAGAG
Found at i:16179692 original size:33 final size:33
Alignment explanation
Indices: 16179632--16179695 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
16179622 TTTTAAAAAT
* *
16179632 AATTTGAGAGGAATTAGAAAGGCATTTGAGAAG
1 AATTTGAGAGAAATTAGAAAGGAATTTGAGAAG
*
16179665 AATTTGAGAGAATATTAGAGA-GAATTTGAGA
1 AATTTGAGAGAA-ATTAGAAAGGAATTTGAGA
16179696 GAAAGGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.44, C:0.02, G:0.28, T:0.27
Consensus pattern (33 bp):
AATTTGAGAGAAATTAGAAAGGAATTTGAGAAG
Found at i:16181012 original size:40 final size:40
Alignment explanation
Indices: 16180942--16181017 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
16180932 GAAGCCCACG
* ** *
16180942 GGAGAGCTCGCGTAAGCCTTGCAGGAATGAGGTCGCAAGA
1 GGAGAGCTCGCGTAAACCTCACAGGAATGAGATCGCAAGA
* *
16180982 GGAGAGCTCGTGTAAACCTCACAGGGATGAGATCGC
1 GGAGAGCTCGCGTAAACCTCACAGGAATGAGATCGC
16181018 GAGCCATGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.36, T:0.16
Consensus pattern (40 bp):
GGAGAGCTCGCGTAAACCTCACAGGAATGAGATCGCAAGA
Found at i:16188604 original size:92 final size:92
Alignment explanation
Indices: 16188447--16188635 Score: 369
Period size: 92 Copynumber: 2.1 Consensus size: 92
16188437 TTCCAATGTT
16188447 AGAGGAAAGTAGTTTCAATTAGCTGACCTTGTGCTAAGAAACACTGAAGCCAGATTTTCAGCTTC
1 AGAGGAAAGTAGTTTCAATTAGCTGACCTTGTGCTAAGAAACACTGAAGCCAGATTTTCAGCTTC
16188512 CCAACACAATAAAAATACCTCGAGCTG
66 CCAACACAATAAAAATACCTCGAGCTG
*
16188539 AGAGGAAAGTAGTTTCAATTAGCTGACCTTGTGCTAAGAAACACTGAAGCCAGATTTTCCGCTTC
1 AGAGGAAAGTAGTTTCAATTAGCTGACCTTGTGCTAAGAAACACTGAAGCCAGATTTTCAGCTTC
16188604 CCAACACAATAAAAATACCTCGAGCTG
66 CCAACACAATAAAAATACCTCGAGCTG
16188631 AGAGG
1 AGAGG
16188636 GACCATACAA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (92 bp):
AGAGGAAAGTAGTTTCAATTAGCTGACCTTGTGCTAAGAAACACTGAAGCCAGATTTTCAGCTTC
CCAACACAATAAAAATACCTCGAGCTG
Found at i:16188912 original size:69 final size:69
Alignment explanation
Indices: 16188827--16189017 Score: 220
Period size: 69 Copynumber: 2.8 Consensus size: 69
16188817 GAAGAGCATT
* * *** * *
16188827 AACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTAGCTATAAAATTCAGGTTTGTAGATGAAGAG
1 AACCTCCAACATAGTTAGCGAGAGCAAAGCTCCTAGCTATAAAATTAAGGTTCACAGACGAACAG
*
16188892 CTGC
66 CCGC
* * *
16188896 AACCTCCAATATAGTTAGTGAGAGCAAAGCTCCTAGCTATAAAATTAAGGTTCACAGGCGAACAG
1 AACCTCCAACATAGTTAGCGAGAGCAAAGCTCCTAGCTATAAAATTAAGGTTCACAGACGAACAG
16188961 CCGC
66 CCGC
* * * * * * *
16188965 GACCTCCAACATGGTTAGCAAGAGCAAAGCTCCCAACTGTAAAACTAAGGTTC
1 AACCTCCAACATAGTTAGCGAGAGCAAAGCTCCTAGCTATAAAATTAAGGTTC
16189018 GTATGTAAAA
Statistics
Matches: 102, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 102 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (69 bp):
AACCTCCAACATAGTTAGCGAGAGCAAAGCTCCTAGCTATAAAATTAAGGTTCACAGACGAACAG
CCGC
Found at i:16193720 original size:23 final size:21
Alignment explanation
Indices: 16193689--16193739 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
16193679 TTTTGTTATA
*
16193689 TATATATATACATGCATACATTTT
1 TATA-ATATACATACAT--ATTTT
*
16193713 TATAATATACGTACATATTTT
1 TATAATATACATACATATTTT
16193734 TATAAT
1 TATAAT
16193740 TTATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.44
23 10 0.40
24 4 0.16
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (21 bp):
TATAATATACATACATATTTT
Found at i:16200502 original size:9 final size:9
Alignment explanation
Indices: 16200488--16200524 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
16200478 ACATTAATCA
16200488 AAAGAAAAG
1 AAAGAAAAG
*
16200497 AAAGAAAAT
1 AAAGAAAAG
16200506 AAAG-AAAG
1 AAAGAAAAG
16200514 AAAGAAAAG
1 AAAGAAAAG
16200523 AA
1 AA
16200525 GTTTAACGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Done.