Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 9 of 79
Found at i:3076393 original size:160 final size:160
Alignment explanation
Indices: 3076063--3076461 Score: 619
Period size: 160 Copynumber: 2.5 Consensus size: 160
3076053 TAATATAAAT
* *
3076063 AACTTTATATTTATGTAATGATTTTTTTGCCATTTT-TTTATCAAATTTATGGGTTTTTTTTTTT
1 AACTTTGTATTTATGTAATGATTTTTTTGCCATTTTATTTATCAATTTTATGGG-----TTTTTT
3076127 TTTTGCAATTTAAATAGTCAACTTCATATTTATGTAATGAATTTGTTTCCATTTTATTTATCAAT
61 TTTTGCAATTTAAATAGTCAACTTCATATTTATGTAATGAATTTGTTTCCATTTTATTTATCAAT
*
3076192 TTTATAAGGTTTTTTTTTTTTGCAATTTAAATAGTC
126 GTTAT-AGGTTTTTTTTTTTTGCAATTTAAATAGTC
*
3076228 AACTTTGTATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTG
1 AACTTTGTATTTATGTAATGATTTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTG
** *
3076293 CAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTT-TTTGCCATTTTATTTATCAATGTTA
66 CAATTTAAATAGTCAACTTCATATTTATGTAATGAATTTGTTT-CCATTTTATTTATCAATGTTA
3076357 T-GTGTTTTTTTTTTTTGCAATTTAAATAGTC
130 TAG-GTTTTTTTTTTTTGCAATTTAAATAGTC
*
3076388 AACTTTGTATTTATGTAATGATTTTTTTGCCATTTTATTTATTAATTTTAT-GG-TTTTTTTTTG
1 AACTTTGTATTTATGTAATGATTTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTG
3076451 CAATTTAAATA
66 CAATTTAAATA
3076462 AATAAACTTT
Statistics
Matches: 222, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
158 21 0.09
159 3 0.01
160 80 0.36
161 68 0.31
165 34 0.15
166 16 0.07
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (160 bp):
AACTTTGTATTTATGTAATGATTTTTTTGCCATTTTATTTATCAATTTTATGGGTTTTTTTTTTG
CAATTTAAATAGTCAACTTCATATTTATGTAATGAATTTGTTTCCATTTTATTTATCAATGTTAT
AGGTTTTTTTTTTTTGCAATTTAAATAGTC
Found at i:3076406 original size:81 final size:80
Alignment explanation
Indices: 3076063--3076461 Score: 594
Period size: 81 Copynumber: 5.0 Consensus size: 80
3076053 TAATATAAAT
* * *
3076063 AACTTTATATTTATGTAATGATTTTTTTGCCATTTT-TTTATCAAATTTATGGGTTTTTTTTTTT
1 AACTTTGTATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTAT-GG---TTTTTTTT
3076127 TTTTGCAATTTAAATAGTC
62 TTTTGCAATTTAAATAGTC
**
3076146 AACTTCATATTTATGTAATGAATTTGTTT-CCATTTTATTTATCAATTTTATAAGGTTTTTTTTT
1 AACTTTGTATTTATGTAATGAATTT-TTTGCCATTTTATTTATCAATTTTAT--GGTTTTTTTTT
3076210 TTTGCAATTTAAATAGTC
63 TTTGCAATTTAAATAGTC
*
3076228 AACTTTGTATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGG-GTTTTTTTTTT
1 AACTTTGTATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTTTTT
3076292 GCAATTTAAATAGTC
66 GCAATTTAAATAGTC
* *
3076307 AACTTTGTATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATGTTATGTGTTTTTTTTTTT
1 AACTTTGTATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATG-GTTTTTTTTTTT
3076372 TGCAATTTAAATAGTC
65 TGCAATTTAAATAGTC
* *
3076388 AACTTTGTATTTATGTAATGATTTTTTTGCCATTTTATTTATTAATTTTATGG---TTTTTTTTT
1 AACTTTGTATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTTTTT
3076450 GCAATTTAAATA
66 GCAATTTAAATA
3076462 AATAAACTTT
Statistics
Matches: 297, Mismatches: 13, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
77 21 0.07
79 75 0.25
80 4 0.01
81 77 0.26
82 72 0.24
83 30 0.10
84 16 0.05
85 2 0.01
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (80 bp):
AACTTTGTATTTATGTAATGAATTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTTTTT
GCAATTTAAATAGTC
Found at i:3079297 original size:46 final size:46
Alignment explanation
Indices: 3079247--3079613 Score: 272
Period size: 46 Copynumber: 7.9 Consensus size: 46
3079237 TTTTTCACCA
* * *
3079247 AAAATTAGGCAGTATACATATATCAATTTGGACAGCACTTATACAC
1 AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTATACAC
* *** * *
3079293 AAAATTTA-ACAGCATGTGTATACAAAATTGGACAGCA-TTGATTCACC
1 AAAA-TTAGGCAGCATACATATACCAAATTGGACAGCACTT-ATACA-C
* * * *
3079340 AAAAATTAAGAAGCATACATATACCAATTTGGACAGCACTTATATAC
1 -AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTATACAC
* * ** * * * *
3079387 AAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCACC
1 AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTATACA-C
* * * *
3079434 AAAATTGGGCAGCATACATACACCAACTTGGACAACACTTATACAC
1 AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTATACAC
* * ** * * * *
3079480 AAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCACC
1 AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTATACA-C
* * *
3079527 AAAATTGGGCAGCATACATAGACCAATTTGGACAGCACTTATACAC
1 AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTATACAC
* * ** * * *
3079573 -AAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTAT
1 AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTAT
3079614 NNNNNNNNNN
Statistics
Matches: 242, Mismatches: 71, Indels: 17
0.73 0.22 0.05
Matches are distributed among these distances:
45 34 0.14
46 98 0.40
47 79 0.33
48 29 0.12
49 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (46 bp):
AAAATTAGGCAGCATACATATACCAAATTGGACAGCACTTATACAC
Found at i:3079384 original size:23 final size:22
Alignment explanation
Indices: 3079358--3079610 Score: 172
Period size: 23 Copynumber: 11.0 Consensus size: 22
3079348 AGAAGCATAC
* *
3079358 ATATACCAATTTGGACAGCACTT
1 ATATACAAAATTGGACAGCA-TT
*
3079381 ATATACAAAATTTGACAGCATGT
1 ATATACAAAATTGGACAGCAT-T
*
3079404 ATATGCAAAATTGGACAGCATT
1 ATATACAAAATTGGACAGCATT
*
3079426 -TATTCACCAAAATTGGGCAGCA-T
1 ATA-T-A-CAAAATTGGACAGCATT
* * *
3079449 ACATACACCAACTTGGACAACACTT
1 ATATACA--AAATTGGACAGCA-TT
* *
3079474 ATACACAAAATTTGACAGCATGT
1 ATATACAAAATTGGACAGCAT-T
*
3079497 ATATGCAAAATTGGACAGCATT
1 ATATACAAAATTGGACAGCATT
* *
3079519 -TATTCACCAAAATTGGGCAGCATAC
1 ATA-T-A-CAAAATTGGACAGCAT-T
* * * *
3079544 ATAGACCAATTTGGACAGCACT
1 ATATACAAAATTGGACAGCATT
*
3079566 -TATACACAAATTTGACAGCATGT
1 ATATACA-AAATTGGACAGCAT-T
*
3079589 ATATGCAAAATTGGACAGCATT
1 ATATACAAAATTGGACAGCATT
3079611 TATNNNNNNN
Statistics
Matches: 177, Mismatches: 35, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
21 10 0.06
22 19 0.11
23 104 0.59
24 36 0.20
25 6 0.03
26 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (22 bp):
ATATACAAAATTGGACAGCATT
Found at i:3079487 original size:93 final size:94
Alignment explanation
Indices: 3079173--3079613 Score: 600
Period size: 93 Copynumber: 4.7 Consensus size: 94
3079163 ATCTACCCTG
* * * * ** *
3079173 TTTGGACAGCTCTTATACATCAAAAATTGAGCAGCATATATGTATAAAATTAGACAGCATTTTTT
1 TTTGGACAGCACTTATACA-CAAAATTTGA-CAGCATGTATATGCAAAATTGGACAGCA----TT
* * *
3079238 TTTTCACCAAAAATTAGGCAGTATACATATATCAA
60 TATTCACCAAAAATTAGGCAGCATACATATACCAA
* * * *
3079273 TTTGGACAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTGATTCA
1 TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCA
* *
3079338 CCAAAAATTAAGAAGCATACATATACCAA
66 CCAAAAATTAGGCAGCATACATATACCAA
*
3079367 TTTGGACAGCACTTATATACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCA
1 TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCA
* *
3079432 CC-AAAATTGGGCAGCATACATACACCAA
66 CCAAAAATTAGGCAGCATACATATACCAA
* *
3079460 CTTGGACAACACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCA
1 TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCA
* *
3079525 CC-AAAATTGGGCAGCATACATAGACCAA
66 CCAAAAATTAGGCAGCATACATATACCAA
3079553 TTTGGACAGCACTTATACAC-AAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTAT
1 TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTAT
3079614 NNNNNNNNNN
Statistics
Matches: 312, Mismatches: 29, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
92 41 0.13
93 129 0.41
94 93 0.30
98 23 0.07
99 8 0.03
100 18 0.06
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (94 bp):
TTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCA
CCAAAAATTAGGCAGCATACATATACCAA
Found at i:3080173 original size:28 final size:28
Alignment explanation
Indices: 3080141--3080266 Score: 164
Period size: 28 Copynumber: 4.5 Consensus size: 28
3080131 TTTAATAAGT
* * *
3080141 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
* *
3080169 TCGCACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
*
3080197 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
*
3080225 TCGCACACTTAGTGCT-TCACAATTAAAT
1 TCGCACACTTAGTGCTCT-ACAATTAAAC
*
3080253 TTGCACACTTAGTG
1 TCGCACACTTAGTG
3080267 TCGAAAGTCA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 1 0.01
28 88 0.99
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTCTACAATTAAAC
Found at i:3080910 original size:190 final size:190
Alignment explanation
Indices: 3080587--3082864 Score: 4529
Period size: 190 Copynumber: 12.0 Consensus size: 190
3080577 GAAGAAAATG
3080587 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3080652 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3080717 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3080777 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3080842 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3080907 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3080967 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3081032 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3081097 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3081157 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3081222 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3081287 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3081347 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3081412 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3081477 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3081537 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3081602 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3081667 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3081727 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3081792 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3081857 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3081917 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3081982 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3082047 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3082107 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3082172 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3082237 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3082297 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3082362 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3082427 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
3082487 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
3082552 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
3082617 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
*
3082677 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACCTTTGTA
1 ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
*
3082742 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGCCGTCCACTATATTTTAAAT
66 AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
*
3082807 GGGTTTATTGCCCTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTA
131 GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTA
3082865 CACTTTAAGT
Statistics
Matches: 2085, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 2085 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (190 bp):
ACTTTATTTTATAATATTTATGATATAATATACATTATTATTCGTTTACTATTTTAACATTTGTA
AAATAATATTTAAAACATAGAATACATGGCTTTTTAGCCATCTTGTCGTCCACTATATTTTAAAT
GGGTTTATTGCCTTTTAAGGACTTCAAGTTAAAAAGCCATTACCAAATAGGTGCTTTATA
Found at i:3083866 original size:27 final size:27
Alignment explanation
Indices: 3083802--3083890 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
3083792 TGTCAGATAA
*
3083802 GCTCCACCAATCGCGCATACCAAATAG
1 GCTCCACCAGTCGCGCATACCAAATAG
3083829 GCTCCACCAGTCGCGTC-TACCAAATAG
1 GCTCCACCAGTCGCG-CATACCAAATAG
* * * * *
3083856 GCTCCATCAGTCACGCCTACTAGATAG
1 GCTCCACCAGTCGCGCATACCAAATAG
*
3083883 GCGCCACC
1 GCTCCACC
3083891 TACCCCATAC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.02
27 51 0.96
28 1 0.02
ACGTcount: A:0.27, C:0.38, G:0.18, T:0.17
Consensus pattern (27 bp):
GCTCCACCAGTCGCGCATACCAAATAG
Found at i:3084005 original size:20 final size:20
Alignment explanation
Indices: 3083980--3084017 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3083970 AGGCGTCACC
*
3083980 AATAAAATAATAATTTAAAA
1 AATAAAAAAATAATTTAAAA
*
3084000 AATAAAAAAATATTTTAA
1 AATAAAAAAATAATTTAA
3084018 TATAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAAAAAATAATTTAAAA
Found at i:3084635 original size:17 final size:16
Alignment explanation
Indices: 3084585--3084637 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
3084575 ATTTTTTTAG
3084585 AAATAAAATAAAATAATA
1 AAATAAAA-AAAATAA-A
*
3084603 AAA-ACAAAAACATAAA
1 AAATA-AAAAAAATAAA
3084619 AAATAAAAAAAAGTAAA
1 AAATAAAAAAAA-TAAA
3084636 AA
1 AA
3084638 TGCATAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 10 0.33
17 14 0.47
18 6 0.20
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (16 bp):
AAATAAAAAAAATAAA
Found at i:3090963 original size:10 final size:10
Alignment explanation
Indices: 3090948--3090984 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
3090938 GGTGCTGCCG
3090948 GAAAAAGAGA
1 GAAAAAGAGA
3090958 GAAAAAGAGA
1 GAAAAAGAGA
*
3090968 GAAAGAGAAGA
1 GAAAAAG-AGA
3090979 GAAAAA
1 GAAAAA
3090985 AAAAGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:3096457 original size:155 final size:155
Alignment explanation
Indices: 3096279--3096713 Score: 568
Period size: 155 Copynumber: 2.8 Consensus size: 155
3096269 CGGCCATTTA
3096279 TTCGTACTATTTTCCCGAATTTTATTACTTTCAATAAAAATATCATATTTTCTAATTTTATTATT
1 TTCGTACTATTTTCCCGAATTTTATTACTTTCAATAAAAATATCATATTTTCTAATTTTATTATT
3096344 TTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTA-
66 TTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTAG
*
3096408 AAAAAGCCCCTT-ATTC-ATGCCCTTTG
131 AAAAA-ACCCTTGATTCGA--CCCTTTG
*
3096434 TTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAATAT-ATTATTTT-TATATTTTATTA
1 TTCGTACTATTTTCCCGAATTTTATTACTTTCAATAAAAATATCA-TATTTTCTA-ATTTTATTA
* * * * * *
3096497 TTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTTAAA-
64 TTTTACATTATTTTAGTACATTATGTTTG-AA-A-TT-TATTAATTTA-GTGTG-TTTTTTAAAT
* *
3096560 AAATTTAGTAAAAAACTCTTGCTTCGACCCTTTG
123 AAATTTAG-AAAAAACCCTTGATTCGACCCTTTG
*
3096594 TTCGTACT-TTTTCTCCGTATTTTATTACTTT--A-AAAAATATCATATTTTCTAATTTTATTAT
1 TTCGTACTATTTTC-CCGAATTTTATTACTTTCAATAAAAATATCATATTTTCTAATTTTATTAT
*
3096655 TTTACATTATTTTAGTACATTATGTTTGAAATTTATCAATTTAGTGTGTTTTTTAAATA
65 TTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATA
3096714 TACCATTTTT
Statistics
Matches: 244, Mismatches: 19, Indels: 36
0.82 0.06 0.12
Matches are distributed among these distances:
152 8 0.03
153 9 0.04
154 8 0.03
155 84 0.34
156 4 0.02
157 50 0.20
158 9 0.04
159 21 0.09
160 42 0.17
161 8 0.03
162 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.52
Consensus pattern (155 bp):
TTCGTACTATTTTCCCGAATTTTATTACTTTCAATAAAAATATCATATTTTCTAATTTTATTATT
TTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTAG
AAAAAACCCTTGATTCGACCCTTTG
Found at i:3096502 original size:15 final size:16
Alignment explanation
Indices: 3096476--3096505 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3096466 AATAAAAATA
3096476 TATTATTTTTATATTT
1 TATTATTTTTATATTT
3096492 TATTA-TTTTATATT
1 TATTATTTTTATATT
3096506 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTTTTATATTT
Found at i:3097079 original size:31 final size:31
Alignment explanation
Indices: 3097043--3097118 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
3097033 TCACATTTTC
3097043 TTTCTTTCTTTTTCCTTCCTTC-CCTCTTCTTCT
1 TTTCTTTCTTTTTCCTTCCTTCTCCT-TTC--CT
3097076 TCTTCTTT-TTTTT--TTCCTTCTCCTTTCCT
1 T-TTCTTTCTTTTTCCTTCCTTCTCCTTTCCT
3097105 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
3097119 TTTTTCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
28 6 0.15
29 8 0.21
31 10 0.26
32 3 0.08
33 6 0.15
34 6 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (31 bp):
TTTCTTTCTTTTTCCTTCCTTCTCCTTTCCT
Found at i:3097090 original size:35 final size:38
Alignment explanation
Indices: 3097051--3097146 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 38
3097041 TCTTTCTTTC
3097051 TTTTTCC-T-TCCTTCCCTCTTC-TTCTTCTTCTTTTT
1 TTTTTCCTTCTCCTTCCCTCTTCTTTCTTCTTCTTTTT
* * *
3097086 TTTTTCCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTTT
1 TTTTTCCTTCTCCTTCCCTCTTCTTTCTTCTTCTTTTT
*
3097124 CTTTCTTTCTTCTCCTTTCCCTC
1 -TTT-TTCCTTCTCC-TTCCCTC
3097147 CCATCGATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
35 7 0.14
36 1 0.02
37 11 0.22
38 13 0.27
39 3 0.06
40 9 0.18
41 5 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (38 bp):
TTTTTCCTTCTCCTTCCCTCTTCTTTCTTCTTCTTTTT
Found at i:3097110 original size:37 final size:39
Alignment explanation
Indices: 3097047--3097143 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 39
3097037 ATTTTCTTTC
*
3097047 TTTCTTTTTCC-T-TCCTTCCCTCTTC-TTCTTCTTCTT
1 TTTCTTTTTCCTTCTCCTTTCCTCTTCTTTCTTCTTCTT
* *
3097083 TTT-TTTTTCCTTCTCCTTTCCTTTTCTTTCTTTTTCTT
1 TTTCTTTTTCCTTCTCCTTTCCTCTTCTTTCTTCTTCTT
*
3097121 TTTCTTTCTTTCTTCTCCTTTCC
1 TTTCTTT-TTCCTTCTCCTTTCC
3097144 CTCCCATCGA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
35 7 0.13
36 4 0.08
37 11 0.21
38 13 0.25
39 3 0.06
40 14 0.27
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (39 bp):
TTTCTTTTTCCTTCTCCTTTCCTCTTCTTTCTTCTTCTT
Found at i:3097141 original size:10 final size:10
Alignment explanation
Indices: 3097067--3097142 Score: 56
Period size: 10 Copynumber: 7.9 Consensus size: 10
3097057 CTTCCTTCCC
3097067 TCTTC-TTCT
1 TCTTCTTTCT
3097076 TCTTCTTT-T
1 TCTTCTTTCT
3097085 T-TT-TTTCCT
1 TCTTCTTT-CT
*
3097094 TCTCCTTTCCT
1 TCTTCTTT-CT
3097105 T-TTCTTTCT
1 TCTTCTTTCT
*
3097114 TTTTCTTT-T
1 TCTTCTTTCT
3097123 TCTTTCTTTCT
1 TC-TTCTTTCT
*
3097134 TCTCCTTTC
1 TCTTCTTTC
3097143 CCTCCCATCG
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
7 3 0.05
8 2 0.04
9 14 0.25
10 26 0.47
11 10 0.18
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TCTTCTTTCT
Found at i:3097141 original size:20 final size:20
Alignment explanation
Indices: 3097072--3097141 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
3097062 TTCCCTCTTC
*
3097072 TTCTTCTTCTTTTT-TTT-T
1 TTCTTCTCCTTTTTCTTTCT
* *
3097090 TCCTTCTCC-TTTCCTTTTCT
1 TTCTTCTCCTTTTTC-TTTCT
* *
3097110 TTCTTTTTCTTTTTCTTTCT
1 TTCTTCTCCTTTTTCTTTCT
3097130 TTCTTCTCCTTT
1 TTCTTCTCCTTT
3097142 CCCTCCCATC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
17 3 0.08
18 7 0.18
19 3 0.08
20 22 0.56
21 4 0.10
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TTCTTCTCCTTTTTCTTTCT
Found at i:3102093 original size:66 final size:65
Alignment explanation
Indices: 3101988--3102122 Score: 216
Period size: 66 Copynumber: 2.1 Consensus size: 65
3101978 GCCTTGAATC
* *
3101988 TTTATAAAATTTTTTGAGTACTCCCAAGATCTTTCAATATGATTATAAGCCTTTTCAAAGTAGGA
1 TTTATAAAATTTTTTGAGTACTCCCAAGACCTTTCAATATGATTATAAGCCTTTTCAAAGCAGGA
* *
3102053 TTTATAAAGATTTTTTTAGTACTCCCAAGACCTTTCAATATGTTTATAAGCCTTTTCAAAGCAGG
1 TTTATAAA-ATTTTTTGAGTACTCCCAAGACCTTTCAATATGATTATAAGCCTTTTCAAAGCAGG
*
3102118 T
65 A
3102119 TTTA
1 TTTA
3102123 GAGTAAGGCT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
65 8 0.12
66 56 0.88
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (65 bp):
TTTATAAAATTTTTTGAGTACTCCCAAGACCTTTCAATATGATTATAAGCCTTTTCAAAGCAGGA
Found at i:3106410 original size:66 final size:66
Alignment explanation
Indices: 3106304--3106438 Score: 261
Period size: 66 Copynumber: 2.0 Consensus size: 66
3106294 TCATCTTATC
*
3106304 GCTATGCTTCTTATTGATCTACCGTAATTTGATACGTCAAATTAGACTCTCTAATACACTCGAGG
1 GCTATGCTTCTTATTGATCTACCGTAATTTGATACATCAAATTAGACTCTCTAATACACTCGAGG
3106369 A
66 A
3106370 GCTATGCTTCTTATTGATCTACCGTAATTTGATACATCAAATTAGACTCTCTAATACACTCGAGG
1 GCTATGCTTCTTATTGATCTACCGTAATTTGATACATCAAATTAGACTCTCTAATACACTCGAGG
3106435 A
66 A
3106436 GCT
1 GCT
3106439 TATTTTCAAG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (66 bp):
GCTATGCTTCTTATTGATCTACCGTAATTTGATACATCAAATTAGACTCTCTAATACACTCGAGG
A
Found at i:3107179 original size:10 final size:10
Alignment explanation
Indices: 3107131--3107185 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
3107121 TTAGTTTAGG
3107131 TTTTCATTT-T
1 TTTTC-TTTCT
*
3107141 TTTTCCTTTCC
1 TTTT-CTTTCT
3107152 TTTTCTCTTC-
1 TTTTCT-TTCT
3107162 TTTTCTTTCT
1 TTTTCTTTCT
3107172 TTTTCTTTACT
1 TTTTCTTT-CT
3107183 TTT
1 TTT
3107186 GTTGTTGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 3 0.08
10 23 0.59
11 13 0.33
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:3107184 original size:20 final size:21
Alignment explanation
Indices: 3107141--3107185 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3107131 TTTTCATTTT
3107141 TTTTCCTTTCCTTTTCTCTTC
1 TTTTCCTTTCCTTTTCTCTTC
*
3107162 TTTT-CTTTCTTTTTCT-TTAC
1 TTTTCCTTTCCTTTTCTCTT-C
3107182 TTTT
1 TTTT
3107186 GTTGTTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 16 0.73
21 4 0.18
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCCTTTCCTTTTCTCTTC
Found at i:3109122 original size:29 final size:31
Alignment explanation
Indices: 3109075--3109139 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
3109065 TTTTTAAAAG
*
3109075 TAAAATTGTATTTTGACTT-TTCTAAAAATAA
1 TAAAATTGTAATTTGACTTATT-TAAAAATAA
*
3109106 TAAAATT-TAATTT-ACTTATTTAAAAATTA
1 TAAAATTGTAATTTGACTTATTTAAAAATAA
3109135 TAAAA
1 TAAAA
3109140 ATATAGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.55
30 7 0.23
31 7 0.23
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (31 bp):
TAAAATTGTAATTTGACTTATTTAAAAATAA
Found at i:3117306 original size:5 final size:5
Alignment explanation
Indices: 3117298--3117327 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3117288 GTACAAAGTA
*
3117298 AAATA AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
3117328 CTAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:3127041 original size:46 final size:44
Alignment explanation
Indices: 3126988--3127140 Score: 155
Period size: 46 Copynumber: 3.6 Consensus size: 44
3126978 TTTGAGTACT
*
3126988 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGA-AAAGTGATAAGTGGTAGC-TTAGCTACACTTA
3127034 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTG-AAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
3127070 TCTGATCAAGTGACAAAGTAATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGA-AAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
3127116 TCTGATC-AGGGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAGTGATAAGTG
3127141 ATCATACGTA
Statistics
Matches: 90, Mismatches: 5, Indels: 26
0.74 0.04 0.21
Matches are distributed among these distances:
35 1 0.01
36 29 0.32
37 2 0.02
40 2 0.02
42 2 0.02
44 11 0.12
45 6 0.07
46 36 0.40
47 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTGATCAAGTGAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:3127065 original size:36 final size:36
Alignment explanation
Indices: 3127024--3127096 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
3127014 GGTAGCTTTA
*
3127024 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTAATAAGT
*
3127060 GCTACACTTATCTGATCAAGTGACAAAGTAATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTAATAAGT
3127096 G
1 G
3127097 GTAGCCTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTAATAAGT
Found at i:3135151 original size:13 final size:13
Alignment explanation
Indices: 3135130--3135195 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
3135120 TTTAAACCAA
3135130 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
3135143 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
3135156 ACTTTTTCACAA-C
1 AC-TTTTCAAAAGC
*
3135169 ACTTTTCAAAAGA
1 ACTTTTCAAAAGC
*
3135182 ATTTTTCAAAAGC
1 ACTTTTCAAAAGC
3135195 A
1 A
3135196 ATGAATAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 8 0.18
13 29 0.66
14 7 0.16
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3140478 original size:25 final size:25
Alignment explanation
Indices: 3140450--3140531 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
3140440 AAGTAACGGA
*** *
3140450 AAGCTCATACAAGCTGTATATTGGG
1 AAGCTCATACAAGCCAAATATCGGG
*
3140475 AAGCTCTTACAAGCCAAATATCGGG
1 AAGCTCATACAAGCCAAATATCGGG
* * *
3140500 AAGCTCATGA-GAGCCAAGTATCAGG
1 AAGCTCAT-ACAAGCCAAATATCGGG
3140525 AAGCTCA
1 AAGCTCA
3140532 AGTGAGCTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 46 0.98
26 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (25 bp):
AAGCTCATACAAGCCAAATATCGGG
Found at i:3140538 original size:25 final size:25
Alignment explanation
Indices: 3140486--3140538 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3140476 AGCTCTTACA
* *
3140486 AGCCAAATATCGGGAAGCTCATGAG
1 AGCCAAATATCAGGAAGCTCAAGAG
* *
3140511 AGCCAAGTATCAGGAAGCTCAAGTG
1 AGCCAAATATCAGGAAGCTCAAGAG
3140536 AGC
1 AGC
3140539 TATGATGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (25 bp):
AGCCAAATATCAGGAAGCTCAAGAG
Found at i:3144583 original size:26 final size:26
Alignment explanation
Indices: 3144547--3144612 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
3144537 AAACGAACAC
* *
3144547 TAACGGAAAGCTCACAAAGAGCC-TT
1 TAACGGGAAGCTCACAAAGAGCCATG
* *
3144572 TAATCGGGAAGCTTACGAAGAGCCATG
1 TAA-CGGGAAGCTCACAAAGAGCCATG
*
3144599 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
3144613 TAAGAGCTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.09
26 26 0.79
27 4 0.12
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.17
Consensus pattern (26 bp):
TAACGGGAAGCTCACAAAGAGCCATG
Found at i:3149659 original size:4 final size:4
Alignment explanation
Indices: 3149650--3149693 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
3149640 CATCAATCTT
3149650 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3149694 GCATAACTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:3153981 original size:48 final size:49
Alignment explanation
Indices: 3153889--3153984 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 49
3153879 GTGTAATTAC
* * *
3153889 ACAAAATATCACCCAATAACAAAAAATTATTACAATATTTGTAATGTTT
1 ACAAAACATCACCCAATAACAAAAAATTATTACAATACTCGTAATGTTT
* * *
3153938 ACAAAACATTACCCAATAA-TACAAATTATTACAACT-CTCGTAATGTT
1 ACAAAACATCACCCAATAACAAAAAATTATTACAA-TACTCGTAATGTT
3153985 GTGTAACACG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 22 0.55
49 18 0.45
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (49 bp):
ACAAAACATCACCCAATAACAAAAAATTATTACAATACTCGTAATGTTT
Found at i:3165802 original size:31 final size:31
Alignment explanation
Indices: 3165754--3165812 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3165744 AATTGGTCAT
3165754 TGAAATATTCAAAAATTTTCATTTAAGTTAC
1 TGAAATATTCAAAAATTTTCATTTAAGTTAC
* * *
3165785 TGAACTATTTAAAAATTTTTATTTAAGT
1 TGAAATATTCAAAAATTTTCATTTAAGT
3165813 CATTGGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (31 bp):
TGAAATATTCAAAAATTTTCATTTAAGTTAC
Found at i:3170507 original size:21 final size:21
Alignment explanation
Indices: 3170482--3170553 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
3170472 TTCTACAGTT
*
3170482 AAATATAACTAATTTTAATTA
1 AAATATAACTAATTATAATTA
** *
3170503 AAATATATTTAATTCGACAATTA
1 AAATATAACTAATT--ATAATTA
* * *
3170526 AAGTTTAACTAATTGTAATTA
1 AAATATAACTAATTATAATTA
3170547 AAATATA
1 AAATATA
3170554 TTTGAAGGAA
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
21 22 0.59
23 15 0.41
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATATAACTAATTATAATTA
Found at i:3170514 original size:43 final size:44
Alignment explanation
Indices: 3170466--3170556 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
3170456 TTATCTAAAA
* * *
3170466 ATTTAATTCTACAGTTAAA-TATAACTAATTTTAATTAAAATAT
1 ATTTAATTCGACAATTAAAGTATAACTAATTGTAATTAAAATAT
*
3170509 ATTTAATTCGACAATTAAAGTTTAACTAATTGTAATTAAAATAT
1 ATTTAATTCGACAATTAAAGTATAACTAATTGTAATTAAAATAT
3170553 ATTT
1 ATTT
3170557 GAAGGAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 17 0.40
44 26 0.60
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (44 bp):
ATTTAATTCGACAATTAAAGTATAACTAATTGTAATTAAAATAT
Found at i:3170657 original size:3 final size:3
Alignment explanation
Indices: 3170649--3170678 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3170639 TGGATTGTTG
3170649 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3170679 TGTATGTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3181014 original size:9 final size:9
Alignment explanation
Indices: 3181000--3181039 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
3180990 TTTGGTTAAA
3181000 AATTAACCG
1 AATTAACCG
*
3181009 AATTAACTG
1 AATTAACCG
*
3181018 AATTACCCG
1 AATTAACCG
3181027 AATTAACCG
1 AATTAACCG
3181036 AATT
1 AATT
3181040 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:3182221 original size:27 final size:25
Alignment explanation
Indices: 3182164--3182214 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3182154 AATCGATGAA
*
3182164 CACTAATGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
3182189 CACTAACGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
3182214 C
1 C
3182215 GCACTAAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (25 bp):
CACTAACGTGCTAATAATCAGAGAG
Found at i:3182818 original size:15 final size:15
Alignment explanation
Indices: 3182798--3182827 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3182788 AATATCTGTA
3182798 CATTATTTCACATAT
1 CATTATTTCACATAT
*
3182813 CATTATTTCAGATAT
1 CATTATTTCACATAT
3182828 TTCTCTTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTATTTCACATAT
Found at i:3188903 original size:13 final size:13
Alignment explanation
Indices: 3188887--3188912 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3188877 AAATTTATTT
3188887 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3188900 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3188913 ATATATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:3192623 original size:46 final size:47
Alignment explanation
Indices: 3192557--3192658 Score: 197
Period size: 46 Copynumber: 2.2 Consensus size: 47
3192547 TTATGTTAAT
3192557 ATCTCTTTCGAGAGTAAGAACTACTGACTCTAGGTTGATTAATTGAA
1 ATCTCTTTCGAGAGTAAGAACTACTGACTCTAGGTTGATTAATTGAA
3192604 ATCTCTTTCG-GAGTAAGAACTACTGACTCTAGGTTGATTAATTGAA
1 ATCTCTTTCGAGAGTAAGAACTACTGACTCTAGGTTGATTAATTGAA
3192650 ATCTCTTTC
1 ATCTCTTTC
3192659 TAATTAAAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 45 0.82
47 10 0.18
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (47 bp):
ATCTCTTTCGAGAGTAAGAACTACTGACTCTAGGTTGATTAATTGAA
Found at i:3192978 original size:74 final size:74
Alignment explanation
Indices: 3192851--3193008 Score: 264
Period size: 74 Copynumber: 2.1 Consensus size: 74
3192841 AATATCTCAA
* * * *
3192851 AAATATTAA-AACAAGAAATAAGCATACATAATTGAGGACAAGAATCAATTATTTATCGCGTAAA
1 AAATAATAAGAACAAGAAATAAGCATAAATAATTGAGAACAAGAATCAAGTATTTATCGCGTAAA
3192915 TCAGAAATC
66 TCAGAAATC
*
3192924 AAATAATAAGAACAAGAAATAAGCATAAATAATTGAGAATAAGAATCAAGTATTTATCGCGTAAA
1 AAATAATAAGAACAAGAAATAAGCATAAATAATTGAGAACAAGAATCAAGTATTTATCGCGTAAA
3192989 TCAGAAATC
66 TCAGAAATC
3192998 AAATAATAAGA
1 AAATAATAAGA
3193009 TTCATCATAG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 8 0.10
74 71 0.90
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (74 bp):
AAATAATAAGAACAAGAAATAAGCATAAATAATTGAGAACAAGAATCAAGTATTTATCGCGTAAA
TCAGAAATC
Found at i:3197032 original size:3 final size:3
Alignment explanation
Indices: 3197024--3197069 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3197014 AAAAGTATAT
3197024 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
3197070 AAAACTCATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:3201224 original size:21 final size:21
Alignment explanation
Indices: 3201198--3201244 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3201188 GAGAGTTAAA
3201198 TTGAGAAGT-AGGTGTTGTAGG
1 TTGAGAA-TCAGGTGTTGTAGG
3201219 TTGAGAATCAGGTGTTGTAGG
1 TTGAGAATCAGGTGTTGTAGG
*
3201240 GTGAG
1 TTGAG
3201245 TATTAGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.23, C:0.02, G:0.43, T:0.32
Consensus pattern (21 bp):
TTGAGAATCAGGTGTTGTAGG
Found at i:3205546 original size:30 final size:30
Alignment explanation
Indices: 3205510--3205570 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
3205500 TCATATTCGA
3205510 GAGAAAGACCATTGAGAATCGCAGTAACAT
1 GAGAAAGACCATTGAGAATCGCAGTAACAT
3205540 GAGAAAGACCATTGAGAATCGCAGTAACAT
1 GAGAAAGACCATTGAGAATCGCAGTAACAT
3205570 G
1 G
3205571 CTCATGTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (30 bp):
GAGAAAGACCATTGAGAATCGCAGTAACAT
Found at i:3206358 original size:12 final size:12
Alignment explanation
Indices: 3206341--3206366 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3206331 CTAACTAGTT
3206341 ACAGTTTTAACA
1 ACAGTTTTAACA
3206353 ACAGTTTTAACA
1 ACAGTTTTAACA
3206365 AC
1 AC
3206367 TTCATTAATT
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:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (12 bp):
ACAGTTTTAACA
Found at i:3208772 original size:21 final size:21
Alignment explanation
Indices: 3208740--3208797 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
3208730 ATTTTTAAAT
*
3208740 AATTAATATTAATTATTTATA
1 AATTAATATTAAATATTTATA
3208761 AATTCAAT-TTAAATA-TT-TA
1 AATT-AATATTAAATATTTATA
*
3208780 AATTATATTTTAAATATT
1 AATTA-ATATTAAATATT
3208798 AAAATACCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 1 0.03
19 8 0.25
20 9 0.28
21 11 0.34
22 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTAATATTAAATATTTATA
Found at i:3215872 original size:14 final size:14
Alignment explanation
Indices: 3215853--3215883 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3215843 TTTAAAATAC
3215853 TTTAAAAATATTTT
1 TTTAAAAATATTTT
3215867 TTTAAAAATATTTT
1 TTTAAAAATATTTT
3215881 TTT
1 TTT
3215884 GTGTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAAAAATATTTT
Found at i:3219739 original size:16 final size:16
Alignment explanation
Indices: 3219718--3219748 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3219708 TTAAGAAATT
*
3219718 ATTATTATTATATTAC
1 ATTATTATAATATTAC
3219734 ATTATTATAATATTA
1 ATTATTATAATATTA
3219749 TAGTAGTTAA
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:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATTATAATATTAC
Found at i:3222891 original size:21 final size:21
Alignment explanation
Indices: 3222841--3222892 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3222831 ATAAAGCTTC
* *
3222841 AAAAACTTAAAATTTATTATA
1 AAAAACATAAAATTTAATATA
3222862 AAAATACATAAAATTTAA-ATTA
1 AAAA-ACATAAAATTTAATA-TA
3222884 AAAAACATA
1 AAAAACATA
3222893 TAAAAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAACATAAAATTTAATATA
Found at i:3223746 original size:11 final size:11
Alignment explanation
Indices: 3223710--3223747 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3223700 AAAAATGTTA
3223710 TTTT-TTGCTG
1 TTTTCTTGCTG
* *
3223720 TTTTGTTGCTA
1 TTTTCTTGCTG
3223731 TTTTCTTGCTG
1 TTTTCTTGCTG
3223742 TTTTCT
1 TTTTCT
3223748 CACTATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.03, C:0.13, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTTCTTGCTG
Found at i:3223753 original size:22 final size:21
Alignment explanation
Indices: 3223708--3223756 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
3223698 AAAAAAATGT
* **
3223708 TATTTTTTGCTGTTTTGTTGC
1 TATTTTTTGCTGTTTTCTCAC
3223729 TATTTTCTTGCTGTTTTCTCAC
1 TATTTT-TTGCTGTTTTCTCAC
3223751 TATTTT
1 TATTTT
3223757 GCTACTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.08, C:0.14, G:0.12, T:0.65
Consensus pattern (21 bp):
TATTTTTTGCTGTTTTCTCAC
Found at i:3223769 original size:19 final size:19
Alignment explanation
Indices: 3223747--3223784 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3223737 TGCTGTTTTC
*
3223747 TCACTATTTTGCTACTATT
1 TCACTATTATGCTACTATT
*
3223766 TCACTATTATGTTACTATT
1 TCACTATTATGCTACTATT
3223785 ATTTTATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (19 bp):
TCACTATTATGCTACTATT
Found at i:3235867 original size:13 final size:13
Alignment explanation
Indices: 3235849--3235873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3235839 TAAAGGAATA
3235849 AGAAAGAAAAAAT
1 AGAAAGAAAAAAT
3235862 AGAAAGAAAAAA
1 AGAAAGAAAAAA
3235874 AAGAGATAAA
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AGAAAGAAAAAAT
Found at i:3238684 original size:20 final size:19
Alignment explanation
Indices: 3238659--3238723 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
3238649 CATTTTGACA
3238659 TATCAAAGTTTCTAAGGATT
1 TATCAAA-TTTCTAAGGATT
*
3238679 TATCAAAATTTCTAAGGCTT
1 TATC-AAATTTCTAAGGATT
** *
3238699 TGCCATAATTTCTAAGGGTT
1 TATCA-AATTTCTAAGGATT
3238719 TATCA
1 TATCA
3238724 GTATGTCTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.89
21 3 0.08
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (19 bp):
TATCAAATTTCTAAGGATT
Found at i:3238827 original size:20 final size:19
Alignment explanation
Indices: 3238804--3238870 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
3238794 AAGGATTTCT
3238804 CAAAATTTTTAAGATTATAC
1 CAAAATTTTTAAGATT-TAC
* *
3238824 C-AAATATCTAAAGATTTAC
1 CAAAAT-TTTTAAGATTTAC
* *
3238843 CAAAAATTTTAAGGTTCTAC
1 CAAAATTTTTAAGATT-TAC
3238863 CAAAATTT
1 CAAAATTT
3238871 CCAATATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 15 0.41
20 22 0.59
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (19 bp):
CAAAATTTTTAAGATTTAC
Found at i:3238869 original size:19 final size:18
Alignment explanation
Indices: 3238804--3238870 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
3238794 AAGGATTTCT
3238804 CAAAATTTTTAAGATTATAC
1 CAAAA-TTTTAAGATT-TAC
* *
3238824 CAAATATCTAAAGATTTAC
1 CAAA-ATTTTAAGATTTAC
*
3238843 CAAAAATTTTAAGGTTCTAC
1 C-AAAATTTTAAGATT-TAC
3238863 CAAAATTT
1 CAAAATTT
3238871 CCAATATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 19 0.49
20 19 0.49
21 1 0.03
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (18 bp):
CAAAATTTTAAGATTTAC
Found at i:3238886 original size:20 final size:20
Alignment explanation
Indices: 3238863--3238901 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3238853 AAGGTTCTAC
3238863 CAAAATTTCCAATATTTTAT
1 CAAAATTTCCAATATTTTAT
* *
3238883 CAAAATTTCTAATGTTTTA
1 CAAAATTTCCAATATTTTA
3238902 CTAACATGAT
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:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
CAAAATTTCCAATATTTTAT
Found at i:3239209 original size:20 final size:20
Alignment explanation
Indices: 3239134--3239225 Score: 57
Period size: 20 Copynumber: 4.6 Consensus size: 20
3239124 TAGCAAAGCA
* *
3239134 TTAAAAATTTCT-ATAAATCC
1 TTAAAAATTT-TGGTAAATTC
* *
3239154 TTAAATATTTTGGTATAA-AC
1 TTAAAAATTTTGGTA-AATTC
* *
3239174 -TAAAAAATATGAGTAAATTC
1 TTAAAAATTTTG-GTAAATTC
3239194 TTAAAAATTTTGGT-AATTC
1 TTAAAAATTTTGGTAAATTC
*
3239213 TTTAAATATTTTG
1 -TTAAAAATTTTG
3239226 ATCTGATCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
19 16 0.29
20 29 0.52
21 11 0.20
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (20 bp):
TTAAAAATTTTGGTAAATTC
Found at i:3240013 original size:29 final size:30
Alignment explanation
Indices: 3239974--3240047 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
3239964 ACAAAACAAT
*
3239974 AACATAAGTGACTAAAACATAACAT-TTCA
1 AACATAAGTGACTAAAACATAACATAGTCA
* *
3240003 AACATAAGTGACTAAAATATAATATGAGTCA
1 AACATAAGTGACTAAAACATAACAT-AGTCA
*
3240034 AACAAAAGTGACTA
1 AACATAAGTGACTA
3240048 CTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.23
Consensus pattern (30 bp):
AACATAAGTGACTAAAACATAACATAGTCA
Found at i:3255459 original size:21 final size:22
Alignment explanation
Indices: 3255421--3255479 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
3255411 ATTAAGTCAT
*
3255421 AATAACTATTACACTAAAAATAAA
1 AATAATTATTA-A-TAAAAATAAA
*
3255445 AAT-ATTATTAAT-AAAATAAT
1 AATAATTATTAATAAAAATAAA
*
3255465 TATAATTATTAATAA
1 AATAATTATTAATAA
3255480 TTTTTTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 9 0.30
21 10 0.33
22 2 0.07
23 6 0.20
24 3 0.10
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAATTATTAATAAAAATAAA
Found at i:3261794 original size:2 final size:2
Alignment explanation
Indices: 3261787--3261820 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3261777 GTGCCTGCAG
3261787 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3261821 ACACACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3263771 original size:3 final size:3
Alignment explanation
Indices: 3263763--3263789 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3263753 TGTTGCTGTG
3263763 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3263790 TATTGGTTTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3270901 original size:4 final size:4
Alignment explanation
Indices: 3270894--3270920 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3270884 ATTGGATAAG
3270894 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3270921 TTGAAAGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3271657 original size:15 final size:15
Alignment explanation
Indices: 3271637--3271666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3271627 AAAACATGAG
3271637 TTAATTTAATCCAAA
1 TTAATTTAATCCAAA
*
3271652 TTAATTTGATCCAAA
1 TTAATTTAATCCAAA
3271667 ACTAACTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.40
Consensus pattern (15 bp):
TTAATTTAATCCAAA
Found at i:3275694 original size:2 final size:2
Alignment explanation
Indices: 3275687--3275716 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3275677 AAGTTACCTT
3275687 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
3275717 CACAAAACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3285027 original size:16 final size:16
Alignment explanation
Indices: 3285006--3285038 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3284996 GAACACTAAG
3285006 GCAGGAAAAAACGAAA
1 GCAGGAAAAAACGAAA
3285022 GCAGGAAAAAACGAAA
1 GCAGGAAAAAACGAAA
3285038 G
1 G
3285039 TGAAACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.12, G:0.27, T:0.00
Consensus pattern (16 bp):
GCAGGAAAAAACGAAA
Found at i:3299517 original size:17 final size:16
Alignment explanation
Indices: 3299495--3299527 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3299485 GAGAATTTTT
3299495 TTAATATTAATTATTAA
1 TTAATATTAA-TATTAA
3299512 TTAATATTAATATTAA
1 TTAATATTAATATTAA
3299528 AATCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATATTAATATTAA
Found at i:3302035 original size:2 final size:2
Alignment explanation
Indices: 3302028--3302074 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3302018 TTCATTCCAC
3302028 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
3302070 AT AT A
1 AT AT A
3302075 AACACATAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3343542 original size:35 final size:34
Alignment explanation
Indices: 3343472--3343549 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
3343462 TAAATATATA
*
3343472 TTTTTAATTTTTAATTTTAAAATACTTTTAAAATT
1 TTTTTAATTTTTAATTTTAAAATAATTTT-AAATT
* *
3343507 TTTTTATTTTTTATTTTTAAAATAAATATTT-AATT
1 TTTTTAATTTTTAATTTTAAAAT-AAT-TTTAAATT
3343542 TTTATTAA
1 TTT-TTAA
3343550 AAATGAGCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 28 0.78
36 5 0.14
37 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTTTAATTTTTAATTTTAAAATAATTTTAAATT
Found at i:3356108 original size:124 final size:124
Alignment explanation
Indices: 3355962--3356202 Score: 457
Period size: 124 Copynumber: 1.9 Consensus size: 124
3355952 TATTCAGATG
3355962 ATAAAATTATATTTTTATTATCATAAAAATTAAAATTTAATTTCAGCTCCTAAATTTTTTATTTA
1 ATAAAATTATATTTTTATTATCATAAAAATTAAAATTTAATTTCAGCTCCTAAATTTTTTATTTA
3356027 TTTTTAAGTATAGTCATCGGATCATGTAAATGTAAGAAGGTAATGGGACTCACTTAAAT
66 TTTTTAAGTATAGTCATCGGATCATGTAAATGTAAGAAGGTAATGGGACTCACTTAAAT
3356086 ATAAAATATATATTTTTA-TATCATAAAAATTAAAATTTAATTTCAGCTCCTAAATTTTTTATTT
1 ATAAAAT-TATATTTTTATTATCATAAAAATTAAAATTTAATTTCAGCTCCTAAATTTTTTATTT
*
3356150 ATTTTTAAGTATAGTCATCGGATCATGTAAATGTAAGAAGGTAATGGGTCTCA
65 ATTTTTAAGTATAGTCATCGGATCATGTAAATGTAAGAAGGTAATGGGACTCA
3356203 TCAAAACACC
Statistics
Matches: 115, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
124 105 0.91
125 10 0.09
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (124 bp):
ATAAAATTATATTTTTATTATCATAAAAATTAAAATTTAATTTCAGCTCCTAAATTTTTTATTTA
TTTTTAAGTATAGTCATCGGATCATGTAAATGTAAGAAGGTAATGGGACTCACTTAAAT
Found at i:3359272 original size:16 final size:16
Alignment explanation
Indices: 3359231--3359274 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3359221 CCGATATAAT
*
3359231 AAATATATTTATTTTTA
1 AAATAT-TTTAATTTTA
* *
3359248 AATTTTTTTAATTTTA
1 AAATATTTTAATTTTA
3359264 AAATATTTTAA
1 AAATATTTTAA
3359275 AAATACTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATATTTTAATTTTA
Found at i:3359296 original size:39 final size:40
Alignment explanation
Indices: 3359242--3359328 Score: 126
Period size: 39 Copynumber: 2.2 Consensus size: 40
3359232 AATATATTTA
3359242 TTTTTAAATTTTTTTAATTTTAAAAT-ATTTTAAAAATACT
1 TTTTTAAATTTTTTTAATTTTAAAATCATTTT-AAAATACT
* *
3359282 TTTTTTAA-TTTTTTAATTTTAAAATCCTTTTAAAATAC-
1 TTTTTAAATTTTTTTAATTTTAAAATCATTTTAAAATACT
3359320 TTTTTAAAT
1 TTTTTAAAT
3359329 CGGACTTATG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 7 0.17
39 24 0.57
40 11 0.26
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (40 bp):
TTTTTAAATTTTTTTAATTTTAAAATCATTTTAAAATACT
Found at i:3369867 original size:12 final size:12
Alignment explanation
Indices: 3369850--3369874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3369840 ACTATATATA
3369850 TATGTGTGTGTG
1 TATGTGTGTGTG
3369862 TATGTGTGTGTG
1 TATGTGTGTGTG
3369874 T
1 T
3369875 GTCTTTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.40, T:0.52
Consensus pattern (12 bp):
TATGTGTGTGTG
Found at i:3379186 original size:20 final size:20
Alignment explanation
Indices: 3379161--3379198 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3379151 TAAACCATAC
3379161 TTTTTTATTTTTAAAATATA
1 TTTTTTATTTTTAAAATATA
3379181 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
3379199 CACTACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTTATTTTTAAAATATA
Found at i:3379428 original size:15 final size:15
Alignment explanation
Indices: 3379405--3379440 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3379395 CTTTTATTTG
*
3379405 TTTCCTTACACTGTA
1 TTTCTTTACACTGTA
3379420 TTTCTTTACACTGTA
1 TTTCTTTACACTGTA
3379435 TTTCTT
1 TTTCTT
3379441 CCTCCTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTCTTTACACTGTA
Found at i:3380620 original size:14 final size:14
Alignment explanation
Indices: 3380584--3380621 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
3380574 TTATTTCCCA
*
3380584 ATCCACCCCCACCG
1 ATCCACCTCCACCG
3380598 ATCCACCTCCACCG
1 ATCCACCTCCACCG
*
3380612 ATCCCCCTCC
1 ATCCACCTCC
3380622 GGTCCTCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.18, C:0.63, G:0.05, T:0.13
Consensus pattern (14 bp):
ATCCACCTCCACCG
Found at i:3382288 original size:21 final size:20
Alignment explanation
Indices: 3382264--3382305 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3382254 AATATAAACC
3382264 ATAT-TTTTTTATTTTTAAA
1 ATATATTTTTTATTTTTAAA
3382283 ATATATTTTTTATTTTTAAA
1 ATATATTTTTTATTTTTAAA
3382303 ATA
1 ATA
3382306 CACCACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATATTTTTTATTTTTAAA
Found at i:3385021 original size:22 final size:21
Alignment explanation
Indices: 3384995--3385054 Score: 53
Period size: 22 Copynumber: 3.1 Consensus size: 21
3384985 CGGGTCATAA
3384995 TTAATTAAATAGTTAGTGAAT
1 TTAATTAAATAGTTAGTGAAT
3385016 TCTAATCT-AAT-G---GTG-AT
1 T-TAAT-TAAATAGTTAGTGAAT
3385033 TT-ATTAAATAGTTAGTGAAT
1 TTAATTAAATAGTTAGTGAAT
3385053 TT
1 TT
3385055 TAATCTAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 17
0.65 0.00 0.35
Matches are distributed among these distances:
14 1 0.03
15 5 0.16
16 2 0.06
17 3 0.10
18 3 0.10
19 3 0.10
20 4 0.13
21 2 0.06
22 7 0.23
23 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (21 bp):
TTAATTAAATAGTTAGTGAAT
Found at i:3391096 original size:170 final size:170
Alignment explanation
Indices: 3390814--3391121 Score: 571
Period size: 170 Copynumber: 1.8 Consensus size: 170
3390804 GAAGAAACTG
*
3390814 AAAAAGTAGGCTGTTCTCGAATCACCTGTGGCACTTGCTCTTAGCCTCGATAAGTTCACCGAACA
1 AAAAAGTAGGCTATTCTCGAATCACCTGTGGCACTTGCTCTTAGCCTCGATAAGTTCACCGAACA
*
3390879 AAGCCGAGAATAATGAGTAGGATCATTAAGGGAATTATTAAGGAAATTAGTAATTGATTAAAAGT
66 AAGCCGAGAATAATGAGTAAGATCATTAAGGGAATTATTAAGGAAATTAGTAATTGATTAAAAGT
3390944 TAGTAATTAAAGGGAATGAACTAAATTGTGAAGCAACTAA
131 TAGTAATTAAAGGGAATGAACTAAATTGTGAAGCAACTAA
* * *
3390984 AAAAAGTAGGCTATTCTTGAATCACGTGTGGCACTTGCTCTTAGCCTCGATAAGTTCACCGGACA
1 AAAAAGTAGGCTATTCTCGAATCACCTGTGGCACTTGCTCTTAGCCTCGATAAGTTCACCGAACA
3391049 AAGCCGAGAATAATGAGTAAGATCATTAAGGGAATTATTAAGGAAATTAGTAATTGATTAAAAGT
66 AAGCCGAGAATAATGAGTAAGATCATTAAGGGAATTATTAAGGAAATTAGTAATTGATTAAAAGT
3391114 TAGTAATT
131 TAGTAATT
3391122 CAAGTATATT
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 133 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (170 bp):
AAAAAGTAGGCTATTCTCGAATCACCTGTGGCACTTGCTCTTAGCCTCGATAAGTTCACCGAACA
AAGCCGAGAATAATGAGTAAGATCATTAAGGGAATTATTAAGGAAATTAGTAATTGATTAAAAGT
TAGTAATTAAAGGGAATGAACTAAATTGTGAAGCAACTAA
Found at i:3393500 original size:23 final size:22
Alignment explanation
Indices: 3393455--3393504 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 22
3393445 AGGTAAACAA
*
3393455 AAATTTTAAAATCTATAATTAT
1 AAATTTTAAAATCAATAATTAT
3393477 AAATTTTAAAAAGTCAATAATATAT
1 AAATTTT-AAAA-TCAATAAT-TAT
3393502 AAA
1 AAA
3393505 AATTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 4 0.17
24 7 0.29
25 6 0.25
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTTTAAAATCAATAATTAT
Found at i:3395570 original size:853 final size:851
Alignment explanation
Indices: 3394227--3395865 Score: 3152
Period size: 853 Copynumber: 1.9 Consensus size: 851
3394217 TTAAAGTAAA
* *
3394227 TTTAATGATAAATTTGTGATTTTAATATATTTCTTTACACAACGAAATAACATAATACTATTGCT
1 TTTAATGATAAATTTGTGATTTTAATATATTCCTTTACACAACAAAATAACATAATACTATTGCT
*
3394292 TGTTATTTCCATTTAATTAATACAACTATGTAATACTATTATGCTTATAATCATACTCTATTCCA
66 TGTTATTTCCATTTAATTAATACAACTATGTAACACTATTATGCTTATAATCATACTCTATTCCA
*
3394357 TTATAGCGAACTAAATATGTATCTTTTAGAATTTCATATACTTATTTCTTAATTTAGACAAGGTT
131 TTATAGCGAACTAAATATGTATCTTTCAGAATTTCATATACTTATTTCTTAATTTAGACAAGGTT
* *
3394422 AAATCTTTAAGTCTTTAAATATTTAATTTTTTTATTTTTTAAATCTTATCTATCATTTTTACTCG
196 AAATCTTTAAATCTTTAAATATTTAATTTTTTTATTTTTTAAATCTTATCTATCATTTTTACTCA
*
3394487 AGGGTTTTGCTTATAAAGCACTACCTTTCTTTTGGAGTTTGGGTATTTTAAATTTTGAAGAATTA
261 AGGGTTTTCCTTATAAAGCACTACCTTTCTTTTGGAGTTTGGGTATTTTAAATTTTGAAGAATTA
3394552 AAGTTTTTAATTATTTATTTTAGTTTATCTATCATTGTTGACTCAAAGATTCTGCTACAAAAACA
326 AAGTTTTTAATTATTTATTTTAGTTTATCTATCATTGTTGACTCAAAGATTCTGCTACAAAAACA
3394617 CCACATTTCTTAAAAAGTTGTAATATTAAAATGATTTAACTCACGATTTAGCTCTTGAAGTATAC
391 CCACATTTCTTAAAAAGTTGTAATATTAAAATGATTTAACTCACGATTTAGCTCTTGAAGTATAC
3394682 ATATTTTTTTATTTTGATACTTAAATATTTTTTTGTTCTAATTTGGTATATAAAGTATCAAGTTC
456 ATATTTTTTTATTTTGATACTTAAATATTTTTTTGTTCTAATTTGGTATATAAAGTATCAAGTTC
3394747 TTCTATGTTTGGACCATTTTATAACGGTCATTAAAAAAAATTAGGTCACTTTGGCCAATAGAAAA
521 TTCTATGTTTGGACCATTTTATAACGGTCATTAAAAAAAATTAGGTCACTTTGGCCAATAGAAAA
3394812 GTGTCACATAGCTTGTCTTTTACCAATTAAAAATGTCACATGTCAATTAGATTTATTTAAAATAA
586 GTGTCACATAGCTTGTCTTTTACCAATTAAAAATGTCACATGTCAATTAGATTTATTTAAAATAA
3394877 AATTATTAAATTTAAATTAAAAATAAAAAATATTAGTATTAAATATTTAATTATTAAAAAAATTG
651 AATTATTAAATTTAAATTAAAAATAAAAAATATTAGTATTAAATATTTAATTATTAAAAAAATTG
3394942 TTGATTTTGAGCAGTCGTTGATCAATGTTGAGCGGGCATTGACTTGTCATGTGGCTCTATTAGAA
716 TTGATTTTGAGCAGTCGTTGATCAATGTTGAGCGGGCATTGACTTGTCATGTGGCTCTATTAGAA
3395007 TACGTCTTGCTTCCTAGGCCCGAGCTAGGGCCTGGCCCGTAGAAAAAATATGAAGCTCGGGCCCG
781 TACGTCTTGCTTCCTAGGCCCGAGCTAGGGCCTGGCCCGTAGAAAAAATATGAAGCTCGGGCCCG
3395072 ACCCAT
846 ACCCAT
*
3395078 TTTAATGGTAAATTTGTGATTTTAATATATTCCTTTACACAACAAAATAACATAATACTATTGCT
1 TTTAATGATAAATTTGTGATTTTAATATATTCCTTTACACAACAAAATAACATAATACTATTGCT
* **
3395143 TGTTATTTTCATTTAATTAATACAACTATGTAACGTTATTATGCTTATAATCATACTCTATTCCA
66 TGTTATTTCCATTTAATTAATACAACTATGTAACACTATTATGCTTATAATCATACTCTATTCCA
*
3395208 TTATAGCGAACTAAATATGTATCTTTCAGAATTTCATATACTTGTTTCTTAATTTAGACAAGGTT
131 TTATAGCGAACTAAATATGTATCTTTCAGAATTTCATATACTTATTTCTTAATTTAGACAAGGTT
3395273 AAATCTTTAAATCTTTAAATATTTAATTTTTTTTATTTTTTAAATCTTATCTATCATTTTTACTC
196 AAATCTTTAAATCTTTAAATATTTAA-TTTTTTTATTTTTTAAATCTTATCTATCATTTTTACTC
3395338 AAGGGTTTTTCCTTATAAAGCACTACCTTTCTTTTGGAGTTTGGGTATTTTAAATTTTGAAGAAT
260 AAGGG-TTTTCCTTATAAAGCACTACCTTTCTTTTGGAGTTTGGGTATTTTAAATTTTGAAGAAT
3395403 TAAAGTTTTTAATTATTTATTTTAGTTTATCTATCATTGTTGACTCAAAGATTCTGCTACAAAAA
324 TAAAGTTTTTAATTATTTATTTTAGTTTATCTATCATTGTTGACTCAAAGATTCTGCTACAAAAA
3395468 CACCACATTTCTTAAAAAGTTGTAATATTAAAATGATTTAACTCACGATTTAGCTCTTGAAGTAT
389 CACCACATTTCTTAAAAAGTTGTAATATTAAAATGATTTAACTCACGATTTAGCTCTTGAAGTAT
3395533 ACATATTTTTTTATTTTGATACTTAAATATTTTTTTGTTCTAATTTGGTATATAAAGTATCAAGT
454 ACATATTTTTTTATTTTGATACTTAAATATTTTTTTGTTCTAATTTGGTATATAAAGTATCAAGT
3395598 TCTTCTATGTTTGGACCATTTTATAACGGTCATTAAAAAAAATTAGGTCACTTTGGCCAATAGAA
519 TCTTCTATGTTTGGACCATTTTATAACGGTCATTAAAAAAAATTAGGTCACTTTGGCCAATAGAA
3395663 AAGTGTCACATAGCTTGTCTTTTACCAATTAAAAATGTCACATGTCAATTAGATTTATTTAAAAT
584 AAGTGTCACATAGCTTGTCTTTTACCAATTAAAAATGTCACATGTCAATTAGATTTATTTAAAAT
3395728 AAAATTATTAAATTTAAATTAAAAATAAAAAATATTAGTATTAAATATTTAATTATTAAAAAAAT
649 AAAATTATTAAATTTAAATTAAAAATAAAAAATATTAGTATTAAATATTTAATTATTAAAAAAAT
3395793 TGTTGATTTTGAGCAGTCGTTGATCAATGTTGAGCGGGCATTGACTTGTCATGTGGCTCTATTAG
714 TGTTGATTTTGAGCAGTCGTTGATCAATGTTGAGCGGGCATTGACTTGTCATGTGGCTCTATTAG
3395858 AATACGTC
779 AATACGTC
3395866 ACATGTCCTT
Statistics
Matches: 774, Mismatches: 12, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
851 211 0.27
852 42 0.05
853 521 0.67
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (851 bp):
TTTAATGATAAATTTGTGATTTTAATATATTCCTTTACACAACAAAATAACATAATACTATTGCT
TGTTATTTCCATTTAATTAATACAACTATGTAACACTATTATGCTTATAATCATACTCTATTCCA
TTATAGCGAACTAAATATGTATCTTTCAGAATTTCATATACTTATTTCTTAATTTAGACAAGGTT
AAATCTTTAAATCTTTAAATATTTAATTTTTTTATTTTTTAAATCTTATCTATCATTTTTACTCA
AGGGTTTTCCTTATAAAGCACTACCTTTCTTTTGGAGTTTGGGTATTTTAAATTTTGAAGAATTA
AAGTTTTTAATTATTTATTTTAGTTTATCTATCATTGTTGACTCAAAGATTCTGCTACAAAAACA
CCACATTTCTTAAAAAGTTGTAATATTAAAATGATTTAACTCACGATTTAGCTCTTGAAGTATAC
ATATTTTTTTATTTTGATACTTAAATATTTTTTTGTTCTAATTTGGTATATAAAGTATCAAGTTC
TTCTATGTTTGGACCATTTTATAACGGTCATTAAAAAAAATTAGGTCACTTTGGCCAATAGAAAA
GTGTCACATAGCTTGTCTTTTACCAATTAAAAATGTCACATGTCAATTAGATTTATTTAAAATAA
AATTATTAAATTTAAATTAAAAATAAAAAATATTAGTATTAAATATTTAATTATTAAAAAAATTG
TTGATTTTGAGCAGTCGTTGATCAATGTTGAGCGGGCATTGACTTGTCATGTGGCTCTATTAGAA
TACGTCTTGCTTCCTAGGCCCGAGCTAGGGCCTGGCCCGTAGAAAAAATATGAAGCTCGGGCCCG
ACCCAT
Found at i:3396003 original size:23 final size:22
Alignment explanation
Indices: 3395958--3396007 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 22
3395948 AGGTAAACAA
*
3395958 AAATTTTAAAATCTATAATTAT
1 AAATTTTAAAATCAATAATTAT
3395980 AAATTTTAAAAAGTCAATAATATAT
1 AAATTTT-AAAA-TCAATAAT-TAT
3396005 AAA
1 AAA
3396008 AATTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 4 0.17
24 7 0.29
25 6 0.25
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTTTAAAATCAATAATTAT
Found at i:3407923 original size:30 final size:30
Alignment explanation
Indices: 3407868--3407932 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3407858 TTTATCATTA
* * *
3407868 TTATTATTATTATTGCCATTGTTATTGTAT
1 TTATTATTATTATTACCATTATTATTATAT
*
3407898 TTATTATTATTACTTACC-TTATTATTATTT
1 TTATTATTATTA-TTACCATTATTATTATAT
3407928 TTATT
1 TTATT
3407933 TACCCATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.63
Consensus pattern (30 bp):
TTATTATTATTATTACCATTATTATTATAT
Found at i:3407943 original size:21 final size:20
Alignment explanation
Indices: 3407896--3407944 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3407886 TTGTTATTGT
3407896 ATTTATTATTATTACTTACC
1 ATTTATTATTATTACTTACC
* * *
3407916 TTATTATTATTTTTATTTACCC
1 AT-TTATTATTATTACTTA-CC
3407938 ATTTATT
1 ATTTATT
3407945 CCCCTTTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTATTATTATTACTTACC
Found at i:3408072 original size:17 final size:17
Alignment explanation
Indices: 3408050--3408085 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3408040 ATATTTTTAA
3408050 ATTTTGTAAATAAATAT
1 ATTTTGTAAATAAATAT
*
3408067 ATTTTGTAAATATATAT
1 ATTTTGTAAATAAATAT
3408084 AT
1 AT
3408086 ACTTACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTTGTAAATAAATAT
Found at i:3408719 original size:30 final size:30
Alignment explanation
Indices: 3408664--3408728 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3408654 TTTATCATTA
* * *
3408664 TTATTATTATTATTGCCATTGTTATTGTAT
1 TTATTATTATTATTACCATTATTATTATAT
*
3408694 TTATTATTATTACTTACC-TTATTATTATTT
1 TTATTATTATTA-TTACCATTATTATTATAT
3408724 TTATT
1 TTATT
3408729 TACCCATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.63
Consensus pattern (30 bp):
TTATTATTATTATTACCATTATTATTATAT
Found at i:3408739 original size:21 final size:20
Alignment explanation
Indices: 3408692--3408740 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3408682 TTGTTATTGT
3408692 ATTTATTATTATTACTTACC
1 ATTTATTATTATTACTTACC
* * *
3408712 TTATTATTATTTTTATTTACCC
1 AT-TTATTATTATTACTTA-CC
3408734 ATTTATT
1 ATTTATT
3408741 CCCCTTTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTATTATTATTACTTACC
Found at i:3408892 original size:12 final size:12
Alignment explanation
Indices: 3408859--3408910 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
3408849 TTGTAAATAA
*
3408859 ATATATATACTT
1 ATATATATATTT
*
3408871 ACATATATATTT
1 ATATATATATTT
3408883 ATATATATATTT
1 ATATATATATTT
3408895 A-ATA-AT-TTT
1 ATATATATATTT
3408904 ATA-ATAT
1 ATATATAT
3408911 GTATATAGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 5 0.14
10 5 0.14
11 3 0.09
12 22 0.63
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATATATATTT
Found at i:3412942 original size:6 final size:6
Alignment explanation
Indices: 3412931--3412971 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
3412921 AAAAAGGGAA
3412931 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
3412972 AAGAAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:3413890 original size:7 final size:7
Alignment explanation
Indices: 3413872--3413932 Score: 74
Period size: 7 Copynumber: 9.0 Consensus size: 7
3413862 CTGAGTCAAA
3413872 AAAAATG
1 AAAAATG
3413879 AAAAAATG
1 -AAAAATG
3413887 AAAAATG
1 AAAAATG
*
3413894 -AGAATG
1 AAAAATG
3413900 AAAAATG
1 AAAAATG
*
3413907 AAGAAT-
1 AAAAATG
3413913 AAAAATG
1 AAAAATG
3413920 AAAAAT-
1 AAAAATG
3413926 AAAAATG
1 AAAAATG
3413933 GAGAGGCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
6 16 0.35
7 23 0.50
8 7 0.15
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:3413905 original size:20 final size:20
Alignment explanation
Indices: 3413873--3413932 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3413863 TGAGTCAAAA
3413873 AAAATGAAAAAATGAAAAATG
1 AAAATG-AAAAATGAAAAATG
* * *
3413894 AGAATGAAAAATGAAGAATA
1 AAAATGAAAAATGAAAAATG
3413914 AAAATGAAAAAT-AAAAATG
1 AAAATGAAAAATGAAAAATG
3413933 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATGAAAAATGAAAAATG
Found at i:3413921 original size:13 final size:14
Alignment explanation
Indices: 3413872--3413932 Score: 74
Period size: 13 Copynumber: 4.5 Consensus size: 14
3413862 CTGAGTCAAA
3413872 AAAAATGAAAAAATG
1 AAAAATG-AAAAATG
*
3413887 AAAAATG-AGAATG
1 AAAAATGAAAAATG
*
3413900 AAAAATGAAGAAT-
1 AAAAATGAAAAATG
3413913 AAAAATGAAAAAT-
1 AAAAATGAAAAATG
3413926 AAAAATG
1 AAAAATG
3413933 GAGAGGCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 31 0.72
14 5 0.12
15 7 0.16
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:3415434 original size:44 final size:44
Alignment explanation
Indices: 3415339--3415437 Score: 105
Period size: 44 Copynumber: 2.2 Consensus size: 44
3415329 CCTAAGCAGT
* *
3415339 AGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGC
1 AGTGGAGCAGACAGAAGAAAACAATCCTATCTCCCTGAAGTTAC
* * *
3415383 AGCGGAGCAGACTG-AGAAAACAAGTCTTATCCTCCC-G-AGATTAC
1 AGTGGAGCAGACAGAAGAAAACAA-TCCTAT-CTCCCTGAAG-TTAC
3415427 AGTGGAGCAGA
1 AGTGGAGCAGA
3415438 TTAAAACAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
43 10 0.22
44 31 0.67
45 5 0.11
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (44 bp):
AGTGGAGCAGACAGAAGAAAACAATCCTATCTCCCTGAAGTTAC
Found at i:3415783 original size:141 final size:141
Alignment explanation
Indices: 3415423--3416055 Score: 864
Period size: 141 Copynumber: 4.5 Consensus size: 141
3415413 CCTCCCGAGA
* *
3415423 TTACAGTGGAGCAGATTAAAACAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
1 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
* * * *
3415488 CAGATTGAAGCCTGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAG-CTGA-TAATC
66 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGAC--ACT-ATC
3415551 CTATCTCCCTG-AG
128 CTATCTCCCTGAAG
* * * ** *
3415564 ATTACAGTGAAACGAATTAAAGTAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCA
1 -TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA
* * *
3415629 TCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGAAGCAGATGGAA-ACTAGTATCC
65 TCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGAC-ACTATCC
3415693 TATCTCCCTGAAG
129 TATCTCCCTGAAG
* ** * *
3415706 TTAAAGTGGAGTTGATTAAAACAAAGGATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCACAT
1 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
* * * * *
3415771 CCGATTGAAGCCAGAGATCTTATCTCCCTGTGATTACAGCAGAA-TAAATCGAAGACACTATCCT
66 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGC-GAAGCAGATCGAAGACACTATCCT
3415835 ATCTCCCTGAAG
130 ATCTCCCTGAAG
*
3415847 TTACAGTGGAGCGGATTAAAACAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
1 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
* * * *
3415912 CAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACACTATCCTA
66 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGACACTATCCTA
3415977 TCTCCCTGAAG
131 TCTCCCTGAAG
* * *
3415988 TTACAGTGGGGCGGATTAAAATAATA-GATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGCA
1 TTACAGTGGAGCGGATTAAAACAA-AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA
3416052 TCAG
65 TCAG
3416056 GTCTTATCTC
Statistics
Matches: 433, Mismatches: 51, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
140 2 0.00
141 316 0.73
142 115 0.27
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (141 bp):
TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGACACTATCCTA
TCTCCCTGAAG
Found at i:3415889 original size:44 final size:43
Alignment explanation
Indices: 3415830--3416250 Score: 149
Period size: 44 Copynumber: 9.4 Consensus size: 43
3415820 CGAAGACACT
3415830 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAATG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAC-AATG
* * ** * *
3415874 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGTA
1 ATCCTATCTCCCTGAAGTTACAGT-G-G-AG--CG-----GATT-AAAACAATG
* * * *
3415928 ATCCTATCTCCCTG-AGATTACAGTGGAGCAGATCGAAGACACT-
1 ATCCTATCTCCCTGAAG-TTACAGTGGAGCGGAT-TAAAACAATG
* *
3415971 ATCCTATCTCCCTGAAGTTACAGTGGGGCGGATTAAAATAATAG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAT-G
* * * * *** *
3416015 ATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGCATC-A-G
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAATG
* * * * * * *
3416056 GTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAA-ACA-G
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTA-AAACA-ATG
* ** * * * * *
3416100 GTTTTATCCCCCTGAAGTCACAGTGGGGCAGACTGAAGAAACAA--
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-T-TA-AAACAATG
* * * * * *
3416144 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCGGATA
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAC-AATG
**
3416188 ATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGA-AATAG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA-ACAAT-G
* * *
3416232 ATCTTTTCTCTCTGAAGTT
1 ATCCTATCTCCCTGAAGTT
3416251 GCAGCAGAGT
Statistics
Matches: 282, Mismatches: 68, Indels: 54
0.70 0.17 0.13
Matches are distributed among these distances:
41 28 0.10
42 7 0.02
43 33 0.12
44 166 0.59
45 7 0.02
46 2 0.01
47 2 0.01
49 3 0.01
51 2 0.01
52 1 0.00
53 3 0.01
54 25 0.09
55 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAATG
Found at i:3416222 original size:217 final size:217
Alignment explanation
Indices: 3415927--3416431 Score: 664
Period size: 217 Copynumber: 2.3 Consensus size: 217
3415917 TGAAGCCAGT
* *
3415927 AATCCTATCTCCCTG-AGATTACAGTGGAGCAGATCGAAGAC-ACT-ATCCTATCTCCCTGAAGT
1 AATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTGAAGACGA-TAATCCTATCTCCCTGAAGT
* *
3415989 TACAGTGGGGCGGATTAAA-ATAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGCAT
64 TACAGTGGAGCGGATTAAAGA-AATAGATCTTATCTCTCTGAAGTTACAGCAGAGTGGATCGCAT
* * * * * *
3416053 CA-GGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAACAGGTTTTATCCCCCTGAAG
128 -AGGGTCTCATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAA
** *
3416117 TCACAGTGGGGCAGACTGAAGAAACA
192 TCACAGTGAAGCAGACCGAAGAAACA
3416143 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAG-CGGATAATCCTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAC-GATAATCCTATCTCCCTGAAGTT
** * *
3416207 GTAGTGGAGCGGATTAAAGAAATAGATCTTTTCTCTCTGAAGTTGCAGCAGAGTGGATCGCATAG
65 ACAGTGGAGCGGATTAAAGAAATAGATCTTATCTCTCTGAAGTTACAGCAGAGTGGATCGCATAG
* * *
3416272 GGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTGAGAAAACAAGTCTTATCTCCCTAAAATCA
130 GGTCTCATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAATCA
*
3416337 CAGTGAAGCAGACCGAAGAAGCA
195 CAGTGAAGCAGACCGAAGAAACA
* * * * *
3416360 AATCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGTCGATAATCCTATCTTCCC-GACGTT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGACGATAATCCTATC-TCCCTGAAGTT
*
3416424 ACGGTGGA
65 ACAGTGGA
3416432 ATGGATCGAA
Statistics
Matches: 253, Mismatches: 28, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
215 1 0.00
216 36 0.14
217 210 0.83
218 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (217 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAGAAATAGATCTTATCTCTCTGAAGTTACAGCAGAGTGGATCGCATAGG
GTCTCATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAATCAC
AGTGAAGCAGACCGAAGAAACA
Found at i:3416385 original size:44 final size:44
Alignment explanation
Indices: 3416278--3416385 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 44
3416268 ATAGGGTCTC
* ** *
3416278 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAGAAAACAAGTCTT
1 ATCTCCCTGAAGTTGCAGTGAAGCAGACCGAGAAAACAAATCTT
* * ** *
3416322 ATCTCCCTAAAATCACAGTGAAGCAGACCGA-AGAAGCAAATCTT
1 ATCTCCCTGAAGTTGCAGTGAAGCAGACCGAGA-AAACAAATCTT
*
3416366 ATCTCCCTGAGGTTGCAGTG
1 ATCTCCCTGAAGTTGCAGTG
3416386 GAGTAGATTG
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
43 1 0.02
44 48 0.98
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (44 bp):
ATCTCCCTGAAGTTGCAGTGAAGCAGACCGAGAAAACAAATCTT
Found at i:3420331 original size:30 final size:30
Alignment explanation
Indices: 3420276--3420340 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3420266 TTTATCATTA
* * *
3420276 TTATTATTATTATTGCCATTGTTATTGTAT
1 TTATTATTATTATTACCATTATTATTATAT
*
3420306 TTATTATTATTACTTACC-TTATTATTATTT
1 TTATTATTATTA-TTACCATTATTATTATAT
3420336 TTATT
1 TTATT
3420341 TACTCATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.63
Consensus pattern (30 bp):
TTATTATTATTATTACCATTATTATTATAT
Found at i:3420351 original size:21 final size:20
Alignment explanation
Indices: 3420304--3420352 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3420294 TTGTTATTGT
3420304 ATTTATTATTATTACTTACC
1 ATTTATTATTATTACTTACC
* * *
3420324 TTATTATTATTTTTATTTACTC
1 AT-TTATTATTATTACTTAC-C
3420346 ATTTATT
1 ATTTATT
3420353 CCCCTTTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTATTATTATTACTTACC
Found at i:3421598 original size:16 final size:16
Alignment explanation
Indices: 3421561--3421600 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3421551 TTAATAAAAT
* *
3421561 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3421577 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3421593 TAAAATTA
1 TAAAATTA
3421601 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3421630 original size:33 final size:33
Alignment explanation
Indices: 3421582--3421664 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
3421572 GTTATTAAAA
** *
3421582 TTAATTGTTAGTAAAATTATCAAATTATTAATTG
1 TTAATTG-TAGTAAAACCAACAAATTATTAATTG
* *
3421616 TTAATTGTATTAAAACCAACCAATTATTAATTG
1 TTAATTGTAGTAAAACCAACAAATTATTAATTG
3421649 TTAATTGTTAGTAAAA
1 TTAATTG-TAGTAAAA
3421665 GTATTTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 28 0.67
34 14 0.33
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.43
Consensus pattern (33 bp):
TTAATTGTAGTAAAACCAACAAATTATTAATTG
Found at i:3427276 original size:22 final size:23
Alignment explanation
Indices: 3427223--3427278 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3427213 TTTAATTAAA
* * *
3427223 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
3427246 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
3427268 ATTAAAATTAA
1 ATTAAAATTAA
3427279 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:3427291 original size:16 final size:16
Alignment explanation
Indices: 3427254--3427293 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3427244 TTAATAAAAT
* *
3427254 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3427270 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3427286 TAAAATTA
1 TAAAATTA
3427294 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3427399 original size:9 final size:9
Alignment explanation
Indices: 3427366--3427393 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3427356 TTTATCAAAT
3427366 TATTAATTG
1 TATTAATTG
3427375 TATTAATTG
1 TATTAATTG
3427384 TATTAATTG
1 TATTAATTG
3427393 T
1 T
3427394 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3427403 original size:68 final size:68
Alignment explanation
Indices: 3427282--3427623 Score: 661
Period size: 68 Copynumber: 5.1 Consensus size: 68
3427272 AAATTAATTG
*
3427282 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3427345 TGA
66 TGA
3427348 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3427413 TGA
66 TGA
3427416 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3427481 TGA
66 TGA
3427484 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3427549 TGA
66 TGA
3427552 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3427617 TGA
66 TGA
3427620 TTAG
1 TTAG
3427624 GGCCCCATGG
Statistics
Matches: 273, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
66 26 0.10
68 247 0.90
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:3427467 original size:9 final size:9
Alignment explanation
Indices: 3427434--3427461 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3427424 TTTATCAAAT
3427434 TATTAATTG
1 TATTAATTG
3427443 TATTAATTG
1 TATTAATTG
3427452 TATTAATTG
1 TATTAATTG
3427461 T
1 T
3427462 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3427535 original size:9 final size:9
Alignment explanation
Indices: 3427502--3427529 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3427492 TTTATCAAAT
3427502 TATTAATTG
1 TATTAATTG
3427511 TATTAATTG
1 TATTAATTG
3427520 TATTAATTG
1 TATTAATTG
3427529 T
1 T
3427530 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3427603 original size:9 final size:9
Alignment explanation
Indices: 3427570--3427597 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3427560 TTTATCAAAT
3427570 TATTAATTG
1 TATTAATTG
3427579 TATTAATTG
1 TATTAATTG
3427588 TATTAATTG
1 TATTAATTG
3427597 T
1 T
3427598 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3435328 original size:25 final size:26
Alignment explanation
Indices: 3435293--3435349 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
3435283 TAAATTTTAA
* **
3435293 TTTTAATTTAAAATATAGTTTAATAT
1 TTTTAATTTAAAAAATAACTTAATAT
*
3435319 TTTTAA-TTAAAAAATAACTTACTAT
1 TTTTAATTTAAAAAATAACTTAATAT
3435344 TTTTAA
1 TTTTAA
3435350 ATATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTAATTTAAAAAATAACTTAATAT
Found at i:3435640 original size:19 final size:21
Alignment explanation
Indices: 3435613--3435654 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3435603 CTTTTAAAAA
*
3435613 ATAAAAA-ATTAAATTAATAT
1 ATAAAAATATTAAAATAATAT
3435633 ATAAAAATATTAAAATAATAT
1 ATAAAAATATTAAAATAATAT
3435654 A
1 A
3435655 CAAATTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAATATTAAAATAATAT
Found at i:3436307 original size:20 final size:20
Alignment explanation
Indices: 3436273--3436314 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3436263 AACTATTTAA
** *
3436273 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
3436293 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
3436313 AT
1 AT
3436315 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:3439225 original size:156 final size:151
Alignment explanation
Indices: 3438939--3439345 Score: 591
Period size: 154 Copynumber: 2.7 Consensus size: 151
3438929 AACATGTTCG
* * * * *
3438939 TATTTCGACCATTTGTTCGTATTTTTTTTCTGGATTTTATTATTTTTAAAAAATATACTATTTT-
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCTGGATTTTATTA-CTTTAAAAAATATATTATTTTC
* * * * * *
3439003 TTAAATTTATTATTTTACATTATTTTAGTACATTATTTTTGAAATGTATTCATTTAGTTTGATTT
65 GT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGATTT
*
3439068 TTAAATAAATTTTAAAAAAAACCCT
129 TTAAATAAA-ATT-AAAAAAACCCT
*
3439093 TATTTCGGCCCTTTGTTCATATTTTTTTCCTGGATTTTATTACTTTCAATAAAAATATATTATTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCTGGATTTTATTACTTT--A-AAAAATATATTATTT
*
3439158 TCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTT
63 TCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGATT
3439223 TTTAAATAAAATTAAAAAAACCCT
128 TTTAAATAAAATTAAAAAAACCCT
* **
3439247 TATTCCGGCCCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTAAAAAATATATTATTTTCG
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCTGGATTTTATTACTTTAAAAAATATATTATTTTCG
3439312 TATTTTATTATTTTACATTATTTTAGTACATTAT
66 TATTTTATTATTTTACATTATTTTAGTACATTAT
3439346 CTTCAGCTGA
Statistics
Matches: 231, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
151 52 0.23
152 1 0.00
153 3 0.01
154 91 0.39
155 3 0.01
156 80 0.35
157 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (151 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTTCCTGGATTTTATTACTTTAAAAAATATATTATTTTCG
TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGATTTTT
AAATAAAATTAAAAAAACCCT
Found at i:3439469 original size:15 final size:16
Alignment explanation
Indices: 3439445--3439477 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3439435 GGAGGGAAGG
3439445 AAAAAGAAAGAAAAAT
1 AAAAAGAAAGAAAAAT
*
3439461 AAAAA-AAAGAAAGAT
1 AAAAAGAAAGAAAAAT
3439476 AA
1 AA
3439478 TTTTTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAT
Found at i:3439702 original size:34 final size:35
Alignment explanation
Indices: 3439638--3439716 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
3439628 AAATAGCATT
* * *
3439638 AAAAATAAAAATACTAAAAAATTATGTTTA-TGAA
1 AAAAATAAAAAAACTAAAAAAGTATATTTATTGAA
3439672 AAAAATAAAAAAAC-AAAAATAGTATATTTATTGAA
1 AAAAATAAAAAAACTAAAAA-AGTATATTTATTGAA
**
3439707 AGTAATAAAA
1 AAAAATAAAA
3439717 TCCGGAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
33 5 0.13
34 21 0.55
35 12 0.32
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.27
Consensus pattern (35 bp):
AAAAATAAAAAAACTAAAAAAGTATATTTATTGAA
Found at i:3439968 original size:153 final size:149
Alignment explanation
Indices: 3439730--3440195 Score: 624
Period size: 153 Copynumber: 3.1 Consensus size: 149
3439720 GGAAAAAAAG
* * *
3439730 AAAAATACGAACAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAAAACACACT-AA
1 AAAAATAAGAACAAAGGGCCGAAATAAGAGTTTTTT--TAAATTTAT-TTAAAAAACACACTAAA
*
3439794 TTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATATTATATT
63 TGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA-TAGAAAATA-TATATT
3439859 TTTTAAAAGTAATAAAATCCGGGGA
126 TTTT-AAAGTAATAAAATCCGGGGA
*
3439884 AAAAATAAGAACAAAGGGCCGAAATAATAGTTTTTTTAAATTTTATTTAAAAAACACACTAAATG
1 AAAAATAAGAACAAAGGGCCGAAATAAGAGTTTTTTTAAA-TTTATTTAAAAAACACACTAAATG
3439949 AATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAACTAGAAAATAGTATATTTT
65 AATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA-TAGAAAATA-TATATTTT
3440014 TTAAAGTAATAAAATCCGGGGGA
128 TTAAAGTAATAAAATCC-GGGGA
* * * *
3440037 AAAAATACA-AACAAATGGCCGAAATAAGAGTTTTTTTTAAATTTATTTATAAATCAAACTAAAT
1 AAAAATA-AGAACAAAGGGCCGAAATAAGAG-TTTTTTTAAATTTATTTAAAAAACACACTAAAT
* * *
3440101 GAATACATTTCAAAAATAATGTACTAAAATAA--TAAAAT--TAGAA-A-ATAATATATATTTTT
64 GAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAGAAAATATATATTTTT
* * *
3440160 TAAAGTAATAAAATTCTGGAA
129 TAAAGTAATAAAATCCGGGGA
*
3440181 AAAAATACGAACAAA
1 AAAAATAAGAACAAA
3440196 TATTGGTGCA
Statistics
Matches: 287, Mismatches: 19, Indels: 22
0.88 0.06 0.07
Matches are distributed among these distances:
144 16 0.06
145 24 0.08
146 5 0.02
147 1 0.00
149 4 0.01
151 6 0.02
152 32 0.11
153 155 0.54
154 44 0.15
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (149 bp):
AAAAATAAGAACAAAGGGCCGAAATAAGAGTTTTTTTAAATTTATTTAAAAAACACACTAAATGA
ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAGAAAATATATATTTTTTA
AAGTAATAAAATCCGGGGA
Found at i:3443106 original size:19 final size:19
Alignment explanation
Indices: 3443056--3443117 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
3443046 GCCTAATTTG
*
3443056 AACTATAATGATAATTCTAAA
1 AACTATAA-AATAATTCT-AA
3443077 CAACTTATAAAATAATTCTAA
1 -AAC-TATAAAATAATTCTAA
*
3443098 AACTATAAAAAAATT-TAA
1 AACTATAAAATAATTCTAA
3443116 AA
1 AA
3443118 TTCTGAACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 5 0.14
19 11 0.30
20 3 0.08
21 2 0.05
22 11 0.30
23 5 0.14
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
AACTATAAAATAATTCTAA
Found at i:3444859 original size:18 final size:18
Alignment explanation
Indices: 3444838--3444872 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3444828 AATCATTTTC
* *
3444838 AAAACCAAAATAAAAAAA
1 AAAACAAAAACAAAAAAA
3444856 AAAACAAAAACAAAAAA
1 AAAACAAAAACAAAAAA
3444873 TCCTTCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (18 bp):
AAAACAAAAACAAAAAAA
Found at i:3445074 original size:15 final size:14
Alignment explanation
Indices: 3445048--3445094 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
3445038 TTTTTCATTT
3445048 ATAAAAATAAAAAA
1 ATAAAAATAAAAAA
3445062 ATAAAAATGAAAAAA
1 ATAAAAAT-AAAAAA
3445077 ATATAACAATAATAAAA
1 ATA-AA-AATAA-AAAA
3445094 A
1 A
3445095 ATATGATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 4 0.14
17 8 0.28
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:3445093 original size:18 final size:18
Alignment explanation
Indices: 3445053--3445098 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
3445043 CATTTATAAA
3445053 AATAAAAAA-ATAAAAAT
1 AATAAAAAATATAAAAAT
* *
3445070 GA-AAAAAATATAACAAT
1 AATAAAAAATATAAAAAT
3445087 AATAAAAAATAT
1 AATAAAAAATAT
3445099 GATGAACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAAAAATATAAAAAT
Done.