Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 129 of 433
Found at i:39612393 original size:18 final size:17
Alignment explanation
Indices: 39612372--39612405 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39612362 TATAATAGTT
39612372 AAAATAAATAAAAGAAAC
1 AAAATAAA-AAAAGAAAC
*
39612390 AAAATAGAAAAAGAAA
1 AAAATAAAAAAAGAAA
39612406 GAACAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAAAAAAAGAAAC
Found at i:39612446 original size:6 final size:6
Alignment explanation
Indices: 39612435--39612459 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39612425 AATAGAAAGG
39612435 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
39612460 GGAAAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:39612494 original size:26 final size:26
Alignment explanation
Indices: 39612458--39612512 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
39612448 AAGAAAAAGA
39612458 AAGGAAAAATAGGGTTTTAAGGTTTG
1 AAGGAAAAATAGGGTTTTAAGGTTTG
39612484 AAGGAAAAATAGGGTTTTAAGGTTTG
1 AAGGAAAAATAGGGTTTTAAGGTTTG
39612510 AAG
1 AAG
39612513 CTTAATTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (26 bp):
AAGGAAAAATAGGGTTTTAAGGTTTG
Found at i:39614421 original size:40 final size:40
Alignment explanation
Indices: 39614257--39614423 Score: 171
Period size: 40 Copynumber: 4.2 Consensus size: 40
39614247 AAATTGAATG
* * **
39614257 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGATT
* * **
39614296 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
* *
39614336 ATATCCGGGCTAAGACCCGAAGG-TATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGATT
* *
39614376 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGATT
39614416 ATATCCGG
1 ATATCCGG
39614424 TTATATTCCG
Statistics
Matches: 104, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
39 17 0.16
40 85 0.82
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
Found at i:39618199 original size:27 final size:28
Alignment explanation
Indices: 39618169--39618238 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
39618159 ATAATAAGTC
*
39618169 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
39618196 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
39618224 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39618239 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39625407 original size:40 final size:40
Alignment explanation
Indices: 39625341--39625507 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39625331 AAATTGAATG
* * *
39625341 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
39625380 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
39625420 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
39625460 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
39625500 ATATCCGG
1 ATATCCGG
39625508 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:39628426 original size:13 final size:13
Alignment explanation
Indices: 39628410--39628435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39628400 CAAAAGACAC
39628410 GGCCGTGTGTCTT
1 GGCCGTGTGTCTT
39628423 GGCCGTGTGTCTT
1 GGCCGTGTGTCTT
39628436 AATCGTGTGA
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:0.00, C:0.23, G:0.38, T:0.38
Consensus pattern (13 bp):
GGCCGTGTGTCTT
Found at i:39637506 original size:152 final size:154
Alignment explanation
Indices: 39636934--39637527 Score: 835
Period size: 154 Copynumber: 3.9 Consensus size: 154
39636924 AATGGTATTA
* * * * *
39636934 TTTA-TGT-GTTGGTTGTTGGAATTTTGGAAGGAAAGGTTTGTTTGTGTCGGAGTTTTAGGGAGG
1 TTTATTGTAGTTGGCTGTTGGAATTTTGGAAGGAAAAGTTTGTTTGTGTTGGAGTTTTAAGGAGA
* * * * *
39636997 AAGTGTGATAGTTTTAAGGTATGTTTTTGTTGTTTGTTATAATAATTTGTATATTATATATGTTT
66 AAGTGTAATAGTTTTAAGATATATTTTTATTGTTTGTTATAATAATTTGTATATTATATATATTT
39637062 ATATTTTAATTTATTGCTAATTTT
131 ATATTTTAATTTATTGCTAATTTT
* *
39637086 TTT-TTAGCGTAGTTGGCTTTTGGAATTTTGGAAGGAAAAATTTG--TGTGTTGGAGTTTTAAGG
1 TTTATT---GTAGTTGGCTGTTGGAATTTTGGAAGGAAAAGTTTGTTTGTGTTGGAGTTTTAAGG
* *
39637148 AGAAAGTGTAATAGTTTTAAGATATATTTTTATTGTTTGTTATAATAATTTTTATATTATATATG
63 AGAAAGTGTAATAGTTTTAAGATATATTTTTATTGTTTGTTATAATAATTTGTATATTATATATA
39637213 TTTATATTTTAATTTATTGCTAATTTT
128 TTTATATTTTAATTTATTGCTAATTTT
** * * * *
39637240 TTTATCATAGTTGGCTATTGAAATTTTGGAAGGAAAAGTTTGAATT-TGTTGGAGTTTTAGGGAG
1 TTTATTGTAGTTGGCTGTTGGAATTTTGGAAGGAAAAGTTTG-TTTGTGTTGGAGTTTTAAGGAG
39637304 AAAGTGTAATAGTTTTAAGATATATTTTTATTGTTTGTTATAATAATTTGTATATTATATATATT
65 AAAGTGTAATAGTTTTAAGATATATTTTTATTGTTTGTTATAATAATTTGTATATTATATATATT
*
39637369 TATATTTTAATTTATTG-TTATTTT
130 TATATTTTAATTTATTGCTAATTTT
* * *
39637393 TTTATTGTAGTTGGCTGTTGGAATTTTTGAAGGAAAAGTTTGTTTGTGTTAGAG-TTTAAAGAGA
1 TTTATTGTAGTTGGCTGTTGGAATTTTGGAAGGAAAAGTTTGTTTGTGTTGGAGTTTTAAGGAGA
* * * * *
39637457 AAGTGTGATAGTTTTAAGGTATGTTTTTATTGTTTGTAATAATAATTTGTATATTATATATATAT
66 AAGTGTAATAGTTTTAAGATATATTTTTATTGTTTGTTATAATAATTTGTATATTATATATATTT
39637522 ATATTT
131 ATATTT
39637528 ATATTTTAAA
Statistics
Matches: 397, Mismatches: 35, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
152 112 0.28
153 50 0.13
154 202 0.51
155 4 0.01
156 29 0.07
ACGTcount: A:0.28, C:0.01, G:0.20, T:0.51
Consensus pattern (154 bp):
TTTATTGTAGTTGGCTGTTGGAATTTTGGAAGGAAAAGTTTGTTTGTGTTGGAGTTTTAAGGAGA
AAGTGTAATAGTTTTAAGATATATTTTTATTGTTTGTTATAATAATTTGTATATTATATATATTT
ATATTTTAATTTATTGCTAATTTT
Found at i:39637771 original size:2 final size:2
Alignment explanation
Indices: 39637764--39637789 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39637754 AAATTATGTT
39637764 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
39637790 ATAAAGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39643603 original size:19 final size:19
Alignment explanation
Indices: 39643579--39643616 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
39643569 TCAAGATAAT
39643579 AAAATAATTTAAAA-ATATA
1 AAAATAA-TTAAAATATATA
39643598 AAAATAATTAAAATATATA
1 AAAATAATTAAAATATATA
39643617 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATAATTAAAATATATA
Found at i:39643621 original size:12 final size:10
Alignment explanation
Indices: 39643579--39643626 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
39643569 TCAAGATAAT
39643579 AAAATAATTTA
1 AAAATAA-TTA
39643590 AAAAT-A-TA
1 AAAATAATTA
39643598 AAAATAATTA
1 AAAATAATTA
39643608 AAATATATATTA
1 AAA-ATA-ATTA
39643620 AAAATAA
1 AAAATAA
39643627 AAAAAGTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 7 0.21
11 11 0.33
12 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATAATTA
Found at i:39654580 original size:22 final size:22
Alignment explanation
Indices: 39654544--39654596 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
39654534 TTTTCATATA
*
39654544 TTTTGA-GAAGTTTCCTATGTG
1 TTTTGATGACGTTTCCTATGTG
39654565 TTTTGATGACGTTTCCTATGTG
1 TTTTGATGACGTTTCCTATGTG
39654587 TTTTGATGAC
1 TTTTGATGAC
39654597 TTAATATGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.17, C:0.11, G:0.23, T:0.49
Consensus pattern (22 bp):
TTTTGATGACGTTTCCTATGTG
Found at i:39658172 original size:43 final size:44
Alignment explanation
Indices: 39658125--39658228 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 44
39658115 CATTGACTTA
* *
39658125 TGATTTATGTGTAAGACCATGTCTGGGA-GATCGGAATCG-TATT
1 TGATTTACGTGTAAGACCATGTCTGGGATAAT-GGAATCGATATT
* *
39658168 TGATTT-CGTGTAAGACCCTGTCTGGGATAATGGCATCGATATT
1 TGATTTACGTGTAAGACCATGTCTGGGATAATGGAATCGATATT
*
39658211 TGA-TTACATGTAAGACCA
1 TGATTTACGTGTAAGACCA
39658229 CGCCTAGGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
42 27 0.52
43 25 0.48
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (44 bp):
TGATTTACGTGTAAGACCATGTCTGGGATAATGGAATCGATATT
Found at i:39663598 original size:40 final size:40
Alignment explanation
Indices: 39663543--39663760 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
39663533 CGGATGATAA
* *
39663543 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
39663583 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39663623 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39663663 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39663703 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
39663743 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39663761 TACTTGGTTG
Statistics
Matches: 169, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 17 0.10
40 151 0.89
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39671644 original size:40 final size:40
Alignment explanation
Indices: 39671589--39671766 Score: 263
Period size: 40 Copynumber: 4.5 Consensus size: 40
39671579 CGGATGATAA
* *
39671589 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
39671629 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39671669 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39671709 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
39671749 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39671767 TACTTGGTTG
Statistics
Matches: 129, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 17 0.13
40 111 0.86
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39674661 original size:12 final size:12
Alignment explanation
Indices: 39674644--39674673 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39674634 CACTTAAAGT
*
39674644 ATGCATATGAAA
1 ATGCATATAAAA
39674656 ATGCATATAAAA
1 ATGCATATAAAA
39674668 ATGCAT
1 ATGCAT
39674674 CCATCTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (12 bp):
ATGCATATAAAA
Found at i:39681983 original size:40 final size:40
Alignment explanation
Indices: 39681939--39682170 Score: 313
Period size: 40 Copynumber: 5.8 Consensus size: 40
39681929 GGATATAACT
* * *
39681939 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
39681979 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
39682019 ACTCGCACAAATGCCTTCGGGACTCAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
39682059 ATTCACACAAATGCCTTTGGGACTTAGCCCGGTTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
39682099 ACTTGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* ** *
39682139 ACTAGTGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
39682171 TTATCATCCA
Statistics
Matches: 170, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 168 0.99
41 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:39685630 original size:2 final size:2
Alignment explanation
Indices: 39685623--39685669 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
39685613 TCATTTTCTG
39685623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39685665 TA TA T
1 TA TA T
39685670 TTTCCATTAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39687138 original size:188 final size:187
Alignment explanation
Indices: 39686821--39687195 Score: 680
Period size: 188 Copynumber: 2.0 Consensus size: 187
39686811 TATTTTAGGA
* *
39686821 TATTATATTAGTATTTTAGGACATTGCATGATGAAGCTTGGATTGTGCTTAAATGTTATTATGTT
1 TATTATATTAGTATTTTAGGACATTACATCATGAAGCTTGGATTGTGCTTAAATGTTATTATGTT
39686886 ACTTTTATTTGTAGATGGAAAAGATTTGTTTGGATGACAGGTGTAGAATGAGGAGAACAAATGAA
66 ACTTTTATTTGTAGATGGAAAAGATTTGTTTGGATGACAGGTGTAGAATGAGGAGAACAAATGAA
*
39686951 GGAGTGAAGTTTTTTCATTGCAAAAGGGTGGATGGATTTCCAACATTAATGCCATGGC
131 GGAGTGAAG-TTTTTCATTGCAAAAGGGTGGATGGATTACCAACATTAATGCCATGGC
*
39687009 TATTATATTAGTATTTTAGGACATTACATCATGAAGCTTTGATTGTGCTTAAATGTTATTATGTT
1 TATTATATTAGTATTTTAGGACATTACATCATGAAGCTTGGATTGTGCTTAAATGTTATTATGTT
*
39687074 ACTTTTACTTT-TAGATGGAAAAGATTTGTTTGGATGATAGGTGTAGAATGAGGAGAACAAATGA
66 ACTTTTA-TTTGTAGATGGAAAAGATTTGTTTGGATGACAGGTGTAGAATGAGGAGAACAAATGA
39687138 AGGAGTGAAGTTTTTCATTGCAAAAGGGTGGATGGATTACCAACATTAATGCCATGGC
130 AGGAGTGAAGTTTTTCATTGCAAAAGGGTGGATGGATTACCAACATTAATGCCATGGC
39687196 AATTTCAGGA
Statistics
Matches: 181, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
187 47 0.26
188 131 0.72
189 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36
Consensus pattern (187 bp):
TATTATATTAGTATTTTAGGACATTACATCATGAAGCTTGGATTGTGCTTAAATGTTATTATGTT
ACTTTTATTTGTAGATGGAAAAGATTTGTTTGGATGACAGGTGTAGAATGAGGAGAACAAATGAA
GGAGTGAAGTTTTTCATTGCAAAAGGGTGGATGGATTACCAACATTAATGCCATGGC
Found at i:39702541 original size:47 final size:47
Alignment explanation
Indices: 39702490--39703055 Score: 940
Period size: 47 Copynumber: 12.1 Consensus size: 47
39702480 TTAGGATTTT
*
39702490 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
39702537 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
39702584 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
39702631 ATGTGATGAATGTGAACATGCGA-ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGC-ATATATGTGATAAGGCCGAATGGCCA
39702678 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
39702725 ATGTAATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
39702772 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
39702819 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
39702866 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
39702913 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
39702960 A-GTAATGAATGTGAACATGCATATATGTGATAAGGCTGAATGTCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
39703006 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
39703053 ATG
1 ATG
39703056 CGAAATGTGT
Statistics
Matches: 492, Mismatches: 23, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 44 0.09
47 444 0.90
48 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:39702682 original size:24 final size:24
Alignment explanation
Indices: 39702607--39702682 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
39702597 GAACATGCAT
39702607 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * *
39702631 ATGTGATGA-ATGTG--AACAT-GCGA
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
39702654 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
39702678 ATGTG
1 ATGTG
39702683 ATGAATGTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 4 0.10
23 13 0.33
24 18 0.46
25 4 0.10
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:39702802 original size:25 final size:25
Alignment explanation
Indices: 39702773--39702850 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
39702763 GAATGGCCAA
39702773 TGTGATGAATGTGAACATGCATATG
1 TGTGATGAATGTGAACATGCATATG
* *
39702798 TGTGAT-AAGGCCG-A-ATGGCCA-A--
1 TGTGATGAATG-TGAACAT-G-CATATG
39702820 TGTGATGAATGTGAACATGCATATG
1 TGTGATGAATGTGAACATGCATATG
39702845 TGTGAT
1 TGTGAT
39702851 AAGGCCGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 9 0.22
23 8 0.20
24 8 0.20
25 15 0.38
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.29
Consensus pattern (25 bp):
TGTGATGAATGTGAACATGCATATG
Found at i:39703085 original size:46 final size:46
Alignment explanation
Indices: 39703029--39703119 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
39703019 GGAAGTGTAT
* * *
39703029 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGGGGTAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* *
39703075 ATATGGGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGGGGTAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
39703120 TGTATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGGGGTAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:39706256 original size:14 final size:14
Alignment explanation
Indices: 39706237--39706263 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39706227 AAATTTACTC
39706237 TTAAAACAAGAATA
1 TTAAAACAAGAATA
39706251 TTAAAACAAGAAT
1 TTAAAACAAGAAT
39706264 TAAGAACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (14 bp):
TTAAAACAAGAATA
Found at i:39721640 original size:25 final size:25
Alignment explanation
Indices: 39721611--39721660 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
39721601 TGTTTAAAGT
* *
39721611 CTTTTATTTATTATTTCTAT-TTTAA
1 CTTTTATCT-TTATTTATATATTTAA
39721636 CTTTTATCTTTATTTATATATTTAA
1 CTTTTATCTTTATTTATATATTTAA
39721661 AGTAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (25 bp):
CTTTTATCTTTATTTATATATTTAA
Found at i:39728120 original size:27 final size:25
Alignment explanation
Indices: 39728058--39728120 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
39728048 AGCTTGAAAT
39728058 AGCTTCCTGATAAATGGCTCACATG
1 AGCTTCCTGATAAATGGCTCACATG
* * *
39728083 AGCATCCTGATATATGGCTCGAGAGTG
1 AGCTTCCTGATAAATGGCTC-ACA-TG
*
39728110 TGCTTCCTGAT
1 AGCTTCCTGAT
39728121 TAAGTGCCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 18 0.58
26 2 0.06
27 11 0.35
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (25 bp):
AGCTTCCTGATAAATGGCTCACATG
Found at i:39737416 original size:49 final size:48
Alignment explanation
Indices: 39737336--39737466 Score: 129
Period size: 49 Copynumber: 2.7 Consensus size: 48
39737326 CACATCAAAG
* * * *
39737336 CGATGCCGTGTCCCAAAAAGGTATTATACTGACTTTCATATATCGAG-GC
1 CGATGCCGTGTCCCAACAA-GTCTTACACTGACTCTCATATATCG-GTGC
* * *
39737385 CGATGTCGTGTCCCAGACAAGTCTTACACTGACTCTCATTTATCGGTGT
1 CGATGCCGTGTCCCA-ACAAGTCTTACACTGACTCTCATATATCGGTGC
* * *
39737434 CGATGCCATGTCCCAAACAGGTCTTTCACTGAC
1 CGATGCCGTGTCCC-AACAAGTCTTACACTGAC
39737467 ACACAACAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 1 0.01
49 63 0.93
50 4 0.06
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (48 bp):
CGATGCCGTGTCCCAACAAGTCTTACACTGACTCTCATATATCGGTGC
Found at i:39745697 original size:27 final size:27
Alignment explanation
Indices: 39745661--39745859 Score: 220
Period size: 27 Copynumber: 7.4 Consensus size: 27
39745651 ACCTGAACCT
*
39745661 TTATGAGATAAAATGACTGTTTTTCCC
1 TTATGAGATAAAATGACTGTTTTGCCC
* *
39745688 TTATGTGATAAAATGA-TGATTTTACCC
1 TTATGAGATAAAATGACTG-TTTTGCCC
*
39745715 TTATGAGATAAAATGACTGTTTTGCCT
1 TTATGAGATAAAATGACTGTTTTGCCC
* * * *
39745742 TTATGTGGTAAAATAACTATTTTGCCC
1 TTATGAGATAAAATGACTGTTTTGCCC
* ***
39745769 TTATGTGATAAAATGAAAATTTTGCCC
1 TTATGAGATAAAATGACTGTTTTGCCC
* * *
39745796 TTATGAGGTAAAATGTCAGTTTTGCCC
1 TTATGAGATAAAATGACTGTTTTGCCC
* *
39745823 TTATGAGGTAAAATGACTATTTTGCCC
1 TTATGAGATAAAATGACTGTTTTGCCC
*
39745850 TTATGTGATA
1 TTATGAGATA
39745860 TATGTGTATA
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 142 0.97
28 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.40
Consensus pattern (27 bp):
TTATGAGATAAAATGACTGTTTTGCCC
Found at i:39745797 original size:81 final size:81
Alignment explanation
Indices: 39745658--39745859 Score: 296
Period size: 81 Copynumber: 2.5 Consensus size: 81
39745648 CGTACCTGAA
* * * **
39745658 CCTTTATGAGATAAAATGACTGTTTTTCCCTTATGTGATAAAATGATGATTTTACCCTTATGAGA
1 CCTTTATGAGGTAAAATGACTATTTTGCCCTTATGTGATAAAATGAAAATTTTACCCTTATGAGA
*
39745723 TAAAATGACTGTTTTG
66 TAAAATGACAGTTTTG
* * * *
39745739 CCTTTATGTGGTAAAATAACTATTTTGCCCTTATGTGATAAAATGAAAATTTTGCCCTTATGAGG
1 CCTTTATGAGGTAAAATGACTATTTTGCCCTTATGTGATAAAATGAAAATTTTACCCTTATGAGA
*
39745804 TAAAATGTCAGTTTTG
66 TAAAATGACAGTTTTG
*
39745820 CCCTTATGAGGTAAAATGACTATTTTGCCCTTATGTGATA
1 CCTTTATGAGGTAAAATGACTATTTTGCCCTTATGTGATA
39745860 TATGTGTATA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 107 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (81 bp):
CCTTTATGAGGTAAAATGACTATTTTGCCCTTATGTGATAAAATGAAAATTTTACCCTTATGAGA
TAAAATGACAGTTTTG
Found at i:39753737 original size:55 final size:55
Alignment explanation
Indices: 39753653--39753775 Score: 149
Period size: 55 Copynumber: 2.2 Consensus size: 55
39753643 AAGCCCCACA
* * * *
39753653 CCCGTGTTAATTTAACAGGTTTGACCATGGGTGTTCCATACGAGCGTGTCGAATG
1 CCCGTGTTATTTTAACAGGTTTCACCATGGGTCTTCCACACGAGCGTGTCGAATG
* * *
39753708 CCCGTGTTATTTTAACAGG-TTCACCCATGGTTCTTCCACACGGGCGTGTCGCATG
1 CCCGTGTTATTTTAACAGGTTTCA-CCATGGGTCTTCCACACGAGCGTGTCGAATG
* *
39753763 CTCGTGTTGTTTT
1 CCCGTGTTATTTT
39753776 GGCAGGCTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 3 0.05
55 55 0.95
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (55 bp):
CCCGTGTTATTTTAACAGGTTTCACCATGGGTCTTCCACACGAGCGTGTCGAATG
Found at i:39760542 original size:40 final size:41
Alignment explanation
Indices: 39760505--39760729 Score: 279
Period size: 40 Copynumber: 5.7 Consensus size: 41
39760495 GCTACTCGTT
*
39760505 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATT-TAGTAACTCGCA
* *
39760545 CAGATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
*
39760585 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
*
39760625 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* * * * *
39760665 CGAATGCCTTC-GGATCTTAG-TCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAAC-TCGCA
39760705 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTCGGGATCTTAGCCCGGA
39760730 CATCATTCGA
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 25 0.15
40 140 0.84
41 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
Found at i:39765100 original size:26 final size:30
Alignment explanation
Indices: 39765071--39765126 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
39765061 ATGGGTGATA
39765071 AAATA-ATG-AAA-AAA-AAAAGAAAAAAG
1 AAATAGATGAAAACAAAGAAAAGAAAAAAG
39765097 AAATATGATGAAAACAAAGAAAAGAAAAAA
1 AAATA-GATGAAAACAAAGAAAAGAAAAAA
39765127 AAAAGTGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 5 0.20
28 3 0.12
29 3 0.12
30 3 0.12
31 11 0.44
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (30 bp):
AAATAGATGAAAACAAAGAAAAGAAAAAAG
Found at i:39766282 original size:27 final size:28
Alignment explanation
Indices: 39766226--39766295 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
39766216 AAATTTGTAC
39766226 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
39766254 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
39766281 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39766296 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:39771587 original size:40 final size:41
Alignment explanation
Indices: 39771550--39771774 Score: 252
Period size: 40 Copynumber: 5.7 Consensus size: 41
39771540 GCTACTCGTT
*
39771550 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATT-TAGTAACTCGCA
* * *
39771590 CAGATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* *
39771630 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* *
39771670 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* * * * *
39771710 CGAATGCCTTC-GGATCTTAG-TCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAAC-TCGCA
39771750 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTCGGGATCTTAGCCCGGA
39771775 CATCATTCGA
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 25 0.15
40 136 0.83
41 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (41 bp):
CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
Found at i:39778152 original size:18 final size:18
Alignment explanation
Indices: 39778125--39778177 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
39778115 TGTTAATATA
*
39778125 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCTTGATTG
*
39778143 GGAGTCAATCCTTGATTG
1 GGAGTAAATCCTTGATTG
*
39778161 GAAGTAAATCCTTGATT
1 GGAGTAAATCCTTGATT
39778178 AAGATTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (18 bp):
GGAGTAAATCCTTGATTG
Found at i:39794960 original size:34 final size:34
Alignment explanation
Indices: 39794922--39795004 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
39794912 CTGTTACGGA
*
39794922 AATGGGCTAAGGCCCACACTAATACTGATACTGC
1 AATGGGCTAAAGCCCACACTAATACTGATACTGC
39794956 AATGGGCTAAAGCCCACACTAATACTGATACTGC
1 AATGGGCTAAAGCCCACACTAATACTGATACTGC
39794990 AATGGGCTAAAGCCC
1 AATGGGCTAAAGCCC
39795005 TAACTGGAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (34 bp):
AATGGGCTAAAGCCCACACTAATACTGATACTGC
Found at i:39799005 original size:40 final size:40
Alignment explanation
Indices: 39798958--39799106 Score: 192
Period size: 40 Copynumber: 3.7 Consensus size: 40
39798948 TTTACAAAAA
39798958 TTTGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
1 TTTGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
* * *
39798998 TTCGGCTATGTATGGCACTTAGTGTGTGATTCGAGATAAC
1 TTTGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
* * * * *
39799038 TTTAGCTATGTATGACACTTAGTGTGCGGGATT-AAAATAGT
1 TTTGGCTATGTATGGCACTTAGTGTGC--GATTCGAGATAGC
39799079 TTTGGCTATGTATTGGCACTTAGTGTGC
1 TTTGGCTATGTA-TGGCACTTAGTGTGC
39799107 AAAAATTCGA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
40 60 0.65
41 15 0.16
42 18 0.19
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (40 bp):
TTTGGCTATGTATGGCACTTAGTGTGCGATTCGAGATAGC
Found at i:39805252 original size:6 final size:6
Alignment explanation
Indices: 39805222--39805296 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
39805212 AAGAAACATT
* * * *
39805222 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATTAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* *
39805271 ATCAGA ATTAGA ATCAGA AGCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCAGA AT
39805297 TGGGTGACAG
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
5 2 0.04
6 45 0.87
7 4 0.08
8 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:39805284 original size:31 final size:31
Alignment explanation
Indices: 39805243--39805352 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 31
39805233 AATCAAAATG
39805243 AGAATCAGAATTAGAATCAGGTGACAGAATC
1 AGAATCAGAATTAGAATCAGGTGACAGAATC
* * * *
39805274 AGAATTAGAATCAGAAGCAGAATTGGGTGACAGAATT
1 AGAATCAGAATTAGAATC---A---GGTGACAGAATC
* * *
39805311 AGAATCAAAATTAGTATCAGGTAACAGAATC
1 AGAATCAGAATTAGAATCAGGTGACAGAATC
*
39805342 AAAATCAGAAT
1 AGAATCAGAAT
39805353 ATGAATGCAA
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
31 34 0.57
34 2 0.03
37 24 0.40
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (31 bp):
AGAATCAGAATTAGAATCAGGTGACAGAATC
Found at i:39805284 original size:37 final size:37
Alignment explanation
Indices: 39805231--39805315 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
39805221 TATCAGAACT
* **
39805231 AGAATCAAAATGAGAATCAGAATTAGAATCAGGTGAC
1 AGAATCAGAATGAGAATCAGAAGCAGAATCAGGTGAC
* **
39805268 AGAATCAGAATTAGAATCAGAAGCAGAATTGGGTGAC
1 AGAATCAGAATGAGAATCAGAAGCAGAATCAGGTGAC
*
39805305 AGAATTAGAAT
1 AGAATCAGAAT
39805316 CAAAATTAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.20
Consensus pattern (37 bp):
AGAATCAGAATGAGAATCAGAAGCAGAATCAGGTGAC
Found at i:39805532 original size:2 final size:2
Alignment explanation
Indices: 39805525--39805560 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39805515 CTACCAGAAC
39805525 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
39805561 GTGTGGCGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39805912 original size:27 final size:27
Alignment explanation
Indices: 39805882--39806074 Score: 226
Period size: 27 Copynumber: 7.2 Consensus size: 27
39805872 AACACCCTAG
** *
39805882 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
*
39805909 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * * *
39805936 GGGTAAAGCAGTAATTCTATAAATTGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
39805963 GGGTAAAACAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* **
39805990 GGGTAAAACGGTAATTTTGTAAATTAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
39806017 AGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
39806044 -GGTAAAACAGTAATTTTGTAATTCAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
39806070 GGGTA
1 GGGTA
39806075 CTTTGATAAT
Statistics
Matches: 141, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
26 23 0.16
27 118 0.84
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (27 bp):
GGGTAAAACAGTAATTTTGTAAATCGA
Found at i:39806084 original size:27 final size:27
Alignment explanation
Indices: 39806051--39806118 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
39806041 CGAGGTAAAA
*
39806051 CAGTAATTTTGTAATTCAAGGGTACTTT
1 CAGTAATTTTGTAAGTCAAGGGTA-TTT
* ** *
39806079 GA-TAATTTTACAAGTCGAGGGTATTT
1 CAGTAATTTTGTAAGTCAAGGGTATTT
39806105 CAGTAATTTTGTAA
1 CAGTAATTTTGTAA
39806119 ACTGAGGGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
26 4 0.13
27 26 0.84
28 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (27 bp):
CAGTAATTTTGTAAGTCAAGGGTATTT
Found at i:39806117 original size:54 final size:53
Alignment explanation
Indices: 39806051--39806226 Score: 178
Period size: 54 Copynumber: 3.3 Consensus size: 53
39806041 CGAGGTAAAA
* *
39806051 CAGTAATTTTGTAATTCAAGGGTACTTTGATAATTTTACAAGTCGAGGGTATTT
1 CAGTAATTTTGTAA-ACAAGGGTACTTTGATAATTTTACAAATCGAGGGTATTT
* * *
39806105 CAGTAATTTTGTAAACTGAGGGCA-TTTCGATAATTTTACAAATCGAGGATATTT
1 CAGTAATTTTGTAAAC-AAGGGTACTTT-GATAATTTTACAAATCGAGGGTATTT
** * * * *
39806159 GGGTAATTTTATAAACCAGGGGTACTTTGGTAATTTTACAACT-G-GGGTATTT
1 CAGTAATTTTGTAAA-CAAGGGTACTTTGATAATTTTACAAATCGAGGGTATTT
* *
39806211 CAATAATTTGGTAAAC
1 CAGTAATTTTGTAAAC
39806227 TAAAGTATTC
Statistics
Matches: 99, Mismatches: 19, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
51 1 0.01
52 17 0.17
53 5 0.05
54 72 0.73
55 4 0.04
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.38
Consensus pattern (53 bp):
CAGTAATTTTGTAAACAAGGGTACTTTGATAATTTTACAAATCGAGGGTATTT
Found at i:39806125 original size:27 final size:27
Alignment explanation
Indices: 39806095--39806219 Score: 82
Period size: 27 Copynumber: 4.7 Consensus size: 27
39806085 TTTACAAGTC
*
39806095 GAGGGTATTTCAGTAATTTTGTAAACT
1 GAGGGTATTTCAGTAATTTTATAAACT
* *
39806122 GAGGGCATTTC-GATAATTTTACAAA-T
1 GAGGGTATTTCAG-TAATTTTATAAACT
* **
39806148 CGAGGATATTTGGGTAATTTTATAAAC-
1 -GAGGGTATTTCAGTAATTTTATAAACT
* * *
39806175 CAGGGGTACTTT-GGTAATTTTA-CAACT
1 GA-GGGTA-TTTCAGTAATTTTATAAACT
*
39806202 G-GGGTATTTCAATAATTT
1 GAGGGTATTTCAGTAATTT
39806220 GGTAAACTAA
Statistics
Matches: 77, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
24 3 0.04
25 11 0.14
26 6 0.08
27 53 0.69
28 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (27 bp):
GAGGGTATTTCAGTAATTTTATAAACT
Found at i:39808999 original size:80 final size:80
Alignment explanation
Indices: 39808915--39809063 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
39808905 TATGGTAACC
* * * *
39808915 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
39808979 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
39808995 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
39809060 CCGG
66 CCGG
39809064 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:39809005 original size:40 final size:38
Alignment explanation
Indices: 39808956--39809063 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
39808946 ATCACGATTT
*
39808956 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
39808996 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
39809036 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
39809064 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:39816293 original size:80 final size:80
Alignment explanation
Indices: 39816209--39816357 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
39816199 TATGGTAACC
* * * *
39816209 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
39816273 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
39816289 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
39816354 CCGG
66 CCGG
39816358 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:39816299 original size:40 final size:38
Alignment explanation
Indices: 39816250--39816357 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
39816240 ATCACGATTT
*
39816250 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
39816290 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
39816330 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
39816358 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:39824137 original size:23 final size:23
Alignment explanation
Indices: 39824111--39824160 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
39824101 ACCCCATGCA
39824111 ATGCAACATA-ATATCATACATGG-
1 ATGCAACATACATAT-A-ACATGGC
39824134 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
39824157 ATGC
1 ATGC
39824161 TCAAATACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:39824290 original size:27 final size:27
Alignment explanation
Indices: 39824195--39824309 Score: 122
Period size: 27 Copynumber: 4.3 Consensus size: 27
39824185 GAAAAAATCT
* * *
39824195 GTCATTTTACCTTACCGGGGTATTACA
1 GTCATTTTACCCTACGGGGGTATTTCA
** *
39824222 GTCATTTTACCCTACATGTGTATTTCA
1 GTCATTTTACCCTACGGGGGTATTTCA
* *
39824249 GTCATTCTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTACGGGGGTATTTCA
* * **
39824276 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTACGGGGGTATTTCA
39824303 GTCATTT
1 GTCATTT
39824310 GATCACATAA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTACGGGGGTATTTCA
Found at i:39824566 original size:27 final size:27
Alignment explanation
Indices: 39824303--39824565 Score: 339
Period size: 27 Copynumber: 9.7 Consensus size: 27
39824293 GGGTATTTTG
*
39824303 GTCATTTGATCACATAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* *
39824330 ATCATTTTATCACGTAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* *
39824357 CTCATTTTATCACGTAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
39824384 GTCATTTTATCACATAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
*
39824411 GTCATTTTATCACATAAGGGTAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* *
39824438 TTCATTTTATCATATAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* * *
39824465 CTCATTTTATCACATAGGGGTAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
* * * *
39824492 GTCATTTTATCATATGACGGTAAAATTC
1 GTCATTTTATCACATAAGGGCAAAA-TC
* * *
39824520 -TCATTTTATCACTTGAGGGTAAAATC
1 GTCATTTTATCACATAAGGGCAAAATC
*
39824546 GTCATTTTATCACATGAGGG
1 GTCATTTTATCACATAAGGG
39824566 TTGAAGTACA
Statistics
Matches: 211, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
26 2 0.01
27 207 0.98
28 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (27 bp):
GTCATTTTATCACATAAGGGCAAAATC
Found at i:39824813 original size:2 final size:2
Alignment explanation
Indices: 39824806--39824830 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39824796 ACCGTAAGAT
39824806 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
39824831 AAAGCAACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39829972 original size:22 final size:22
Alignment explanation
Indices: 39829944--39830002 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 22
39829934 AACACGTTAT
*
39829944 AAAGGCTAACAGAATGCCCCAC
1 AAAGGCTAACAGAATGCACCAC
*
39829966 AAAGGCTAACA-AA-GTACCAC
1 AAAGGCTAACAGAATGCACCAC
*
39829986 AAAGGCTAATAGAATGC
1 AAAGGCTAACAGAATGC
39830003 TACTATAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.48
21 4 0.13
22 12 0.39
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAGGCTAACAGAATGCACCAC
Found at i:39831279 original size:20 final size:20
Alignment explanation
Indices: 39831256--39831298 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
39831246 ATGCCATAGT
39831256 GGCTAACAGAAAGCCACAAA
1 GGCTAACAGAAAGCCACAAA
*
39831276 GGCTAACAGAATGCCACAAA
1 GGCTAACAGAAAGCCACAAA
39831296 GGC
1 GGC
39831299 CCTTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.26, G:0.23, T:0.07
Consensus pattern (20 bp):
GGCTAACAGAAAGCCACAAA
Found at i:39842553 original size:43 final size:44
Alignment explanation
Indices: 39842505--39842651 Score: 158
Period size: 43 Copynumber: 3.4 Consensus size: 44
39842495 ATCGATATGT
*
39842505 GATTACATGTAAGACCATGTCTAGAACATTGGCAT-TATAATGA
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATCTATAATGA
* * *
39842548 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGT-TAAT-C
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATC-TATAATGA
* * * * * *
39842591 GATTTCGTGTAAGACCCTGTCTAGGACAGTGGCATCGAT-ATGT
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATCTATAATGA
*
39842634 GATAACATGTAAGACCAT
1 GATTACATGTAAGACCAT
39842652 ATCTGGGATA
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.02
43 79 0.92
44 4 0.05
45 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
GATTACATGTAAGACCATGTCTAGGACATTGGCATCTATAATGA
Found at i:39858677 original size:42 final size:42
Alignment explanation
Indices: 39858570--39858719 Score: 183
Period size: 42 Copynumber: 3.5 Consensus size: 42
39858560 CATATCTTAG
* * * * *
39858570 ATATGGTCTTAAATGAAATCTCGTATCGATGCCAATAGCCCAG
1 ATATGGTCTTACACGAAATCTCATATCGATGCC-ATATCCCAA
* * * * *
39858613 CTATGGTCTTACATGAAGTCTCATATCGATGTCATATCCCAT
1 ATATGGTCTTACACGAAATCTCATATCGATGCCATATCCCAA
*
39858655 ATATGGTCTTACACGAAATCTCATATAGATGCCATATCCCAA
1 ATATGGTCTTACACGAAATCTCATATCGATGCCATATCCCAA
*
39858697 ATATGGTCTTACACGTAATCTCA
1 ATATGGTCTTACACGAAATCTCA
39858720 GTAACCCTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 65 0.70
43 28 0.30
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (42 bp):
ATATGGTCTTACACGAAATCTCATATCGATGCCATATCCCAA
Found at i:39862705 original size:6 final size:6
Alignment explanation
Indices: 39862687--39862786 Score: 80
Period size: 6 Copynumber: 16.3 Consensus size: 6
39862677 AAGAAACATT
* * *
39862687 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAGA ATTAGA ATCAGA ATCAGGTG
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
* * *
39862737 AT-AGA ATCAGA ATTAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA
39862785 AT
1 AT
39862787 GGGAATGCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
5 5 0.07
6 62 0.82
7 6 0.08
8 3 0.04
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (6 bp):
ATCAGA
Found at i:39862749 original size:31 final size:31
Alignment explanation
Indices: 39862707--39862786 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
39862697 GAATCAGAAT
* *
39862707 CAGAATTAGAATTAGAATCAGAATCAGGTGA
1 CAGAATCAGAATTAGAATCAGAATCAGGTAA
* *
39862738 TAGAATCAGAATTAGAATCAGTATCAGGTAA
1 CAGAATCAGAATTAGAATCAGAATCAGGTAA
* *
39862769 CAGAATCAAAATCAGAAT
1 CAGAATCAGAATTAGAAT
39862787 GGGAATGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (31 bp):
CAGAATCAGAATTAGAATCAGAATCAGGTAA
Found at i:39863236 original size:27 final size:27
Alignment explanation
Indices: 39863216--39863760 Score: 666
Period size: 27 Copynumber: 20.2 Consensus size: 27
39863206 GGGTTTCTCG
39863216 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
39863243 GT-ATTCCTACCCTACAAGGGTATTTC-
1 GTAATT-CTACCCTACAGGGGTATTTCA
39863269 GATAATTCTACCCTACAGGGGTATTTCA
1 G-TAATTCTACCCTACAGGGGTATTTCA
39863297 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
39863324 GT-ATTCCTACCCTACAGGGGTATTTCG
1 GTAATT-CTACCCTACAGGGGTATTTCA
* *
39863351 GTAATTTTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
39863378 GTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
39863405 GTAATTCTACCATATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
39863432 GTAGTTCTACCTTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
39863459 GTAATTTTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
39863486 GTAATTCTACCTTACAGGGATATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
39863513 GTAATTCTACACTACAGGGGTA-TTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * * *
39863539 GTATTTCTACCTTACAAGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* **
39863566 GTAATTCTACCCTACAAGGGTATTTTG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
39863593 GTAATTCTACCTTACAGGAGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * * * *
39863620 ATAATTGTACCTTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
39863647 GTAATTCTACCTTACAGGGGCATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
** *
39863674 GTAATTCTACTATATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
39863701 GTAATTTTACCTTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
39863728 GTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
39863755 GTAATT
1 GTAATT
39863761 TTACAAATCG
Statistics
Matches: 453, Mismatches: 58, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
26 29 0.06
27 417 0.92
28 7 0.02
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:39863783 original size:26 final size:27
Alignment explanation
Indices: 39863749--39863819 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
39863739 TTACAGGGGT
39863749 ATTTCGGTAATTTTACAAATC-GAGG-A
1 ATTT-GGTAATTTTACAAATCGGAGGTA
* *
39863775 ATTTGGGTAATTTTATAAATCGGGGGTA
1 ATTT-GGTAATTTTACAAATCGGAGGTA
*
39863803 CTTTGGTAATTTTACAA
1 ATTTGGTAATTTTACAA
39863820 CTGGGGGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 19 0.50
27 15 0.39
28 4 0.11
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
ATTTGGTAATTTTACAAATCGGAGGTA
Found at i:39863815 original size:27 final size:26
Alignment explanation
Indices: 39863637--39863840 Score: 108
Period size: 27 Copynumber: 7.7 Consensus size: 26
39863627 TACCTTACAA
* **
39863637 GGGTATTTCGGTAATTCTAC-CTTACAG
1 GGGTATTTCGGTAATTTTACAAAT-C-G
* * * * *
39863664 GGGCATTTCAGTAATTCTACTATATAG
1 GGGTATTTCGGTAATTTTAC-AAATCG
* ** *
39863691 GGGTATTTCAGTAATTTTACCTTATAG
1 GGGTATTTCGGTAATTTTA-CAAATCG
* * **
39863718 GGGTATTTCAGTAATTCTAC-CTTACAG
1 GGGTATTTCGGTAATTTTACAAAT-C-G
39863745 GGGTATTTCGGTAATTTTACAAATCG
1 GGGTATTTCGGTAATTTTACAAATCG
* * * *
39863771 AGGAATTTGGGTAATTTTATAAATCGG
1 GGGTATTTCGGTAATTTTACAAATC-G
* *
39863798 GGGTACTTT-GGTAATTTTACAACTGG
1 GGGTA-TTTCGGTAATTTTACAAATCG
*
39863824 GGGTATTTCAGTAATTT
1 GGGTATTTCGGTAATTT
39863841 GGTAAACTAA
Statistics
Matches: 142, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.03
26 36 0.25
27 96 0.68
28 5 0.04
29 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.39
Consensus pattern (26 bp):
GGGTATTTCGGTAATTTTACAAATCG
Found at i:39865401 original size:26 final size:26
Alignment explanation
Indices: 39865372--39865475 Score: 174
Period size: 26 Copynumber: 4.0 Consensus size: 26
39865362 TGGTACAAAT
39865372 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39865398 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39865424 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39865450 TGATAAT-GGTTCAGGTAAATGTTCCA
1 TGATAATGGGTT-AGGTAAATGTTCCA
39865476 AGATGGGAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
25 4 0.05
26 69 0.95
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39876293 original size:25 final size:25
Alignment explanation
Indices: 39876264--39876311 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39876254 TTATAATATG
* * *
39876264 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
39876289 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
39876312 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:39876380 original size:20 final size:20
Alignment explanation
Indices: 39876355--39876413 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
39876345 TAAATATGGT
39876355 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
39876375 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
39876395 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
39876414 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:39876395 original size:11 final size:11
Alignment explanation
Indices: 39876359--39876413 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
39876349 TATGGTATGT
39876359 ATGATATGCAC
1 ATGATATGCAC
* *
39876370 ATGAAATG--T
1 ATGATATGCAC
39876379 ATGATATGCAC
1 ATGATATGCAC
*
39876390 ATGATATG--T
1 ATGATATGCAC
39876399 ATGATATGCAC
1 ATGATATGCAC
39876410 ATGA
1 ATGA
39876414 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:39876491 original size:24 final size:24
Alignment explanation
Indices: 39876464--39876582 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
39876454 GAGGAAGTGA
*
39876464 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
39876488 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
39876511 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
39876535 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39876559 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39876583 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:39876533 original size:47 final size:48
Alignment explanation
Indices: 39876464--39876582 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
39876454 GAGGAAGTGA
39876464 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
39876511 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
39876559 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39876583 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:39876809 original size:31 final size:31
Alignment explanation
Indices: 39876774--39876837 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
39876764 CGTTTACAGT
39876774 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
39876805 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
39876836 AA
1 AA
39876838 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:39884376 original size:25 final size:25
Alignment explanation
Indices: 39884347--39884394 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39884337 TTATAATATG
* * *
39884347 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
39884372 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
39884395 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:39884463 original size:20 final size:20
Alignment explanation
Indices: 39884438--39884496 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
39884428 TAAATATGGT
39884438 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
39884458 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
39884478 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
39884497 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:39884478 original size:11 final size:11
Alignment explanation
Indices: 39884442--39884496 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
39884432 TATGGTATGT
39884442 ATGATATGCAC
1 ATGATATGCAC
* *
39884453 ATGAAATG--T
1 ATGATATGCAC
39884462 ATGATATGCAC
1 ATGATATGCAC
*
39884473 ATGATATG--T
1 ATGATATGCAC
39884482 ATGATATGCAC
1 ATGATATGCAC
39884493 ATGA
1 ATGA
39884497 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:39884616 original size:47 final size:48
Alignment explanation
Indices: 39884547--39884665 Score: 161
Period size: 47 Copynumber: 2.5 Consensus size: 48
39884537 GAGGAAGTGA
39884547 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATACCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATACCCCAGTTATT
** * *
39884594 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATACCCCAGTTATT
*
39884642 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39884666 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 42 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATACCCCAGTTATT
Found at i:39884661 original size:25 final size:24
Alignment explanation
Indices: 39884547--39884665 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
39884537 GAGGAAGTGA
*
39884547 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
39884571 AAAAGGGCTTATACCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
39884594 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
39884618 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39884642 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39884666 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
23 21 0.25
24 52 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:39884892 original size:31 final size:31
Alignment explanation
Indices: 39884857--39884920 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
39884847 CGTTTACAGT
39884857 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
39884888 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
39884919 AA
1 AA
39884921 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:39894966 original size:25 final size:25
Alignment explanation
Indices: 39894932--39894982 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
39894922 AGGGCCTGAG
39894932 TTAGTGCGATCGACTAGTGATTTCT
1 TTAGTGCGATCGACTAGTGATTTCT
39894957 TTAGTGCGATCGACTAGTGATTTCT
1 TTAGTGCGATCGACTAGTGATTTCT
39894982 T
1 T
39894983 CTCGTAAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.41
Consensus pattern (25 bp):
TTAGTGCGATCGACTAGTGATTTCT
Found at i:39896404 original size:44 final size:44
Alignment explanation
Indices: 39896341--39896428 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
39896331 CTTTCATCTA
39896341 ACTAAATGTCTGACTCCAGATATTACCAGACGATACACCTTTTT
1 ACTAAATGTCTGACTCCAGATATTACCAGACGATACACCTTTTT
39896385 ACTAAATGTCTGACTCCAGATATTACCAGACGATACACCTTTTT
1 ACTAAATGTCTGACTCCAGATATTACCAGACGATACACCTTTTT
39896429 CTCTTCTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (44 bp):
ACTAAATGTCTGACTCCAGATATTACCAGACGATACACCTTTTT
Found at i:39898933 original size:37 final size:37
Alignment explanation
Indices: 39898862--39898934 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
39898852 TACCCTCTAC
39898862 ATCCCTCAACAATCATCCATCAATCCTTCTTCATTTT
1 ATCCCTCAACAATCATCCATCAATCCTTCTTCATTTT
* * *
39898899 ATCCCTTAACATATGCATTCATCCATCC-TC-TCATTT
1 ATCCCTCAACA-AT-CATCCATCAATCCTTCTTCATTT
39898935 CTCTCTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 16 0.52
38 4 0.13
39 11 0.35
ACGTcount: A:0.26, C:0.34, G:0.01, T:0.38
Consensus pattern (37 bp):
ATCCCTCAACAATCATCCATCAATCCTTCTTCATTTT
Found at i:39904420 original size:47 final size:47
Alignment explanation
Indices: 39904360--39904531 Score: 167
Period size: 47 Copynumber: 3.7 Consensus size: 47
39904350 ATAAGAGCCT
*
39904360 GTGTAAGACCATGTCTGGGACATGGCATCGGTATTGAGACGAGAGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGTATCGAGA-GAGAGCTA
* * * *
39904408 CTGTAAGA-CATGTCTGGGACAT-CCATCAGCTA-CGAGATGATAG-TCA
1 GTGTAAGACCATGTCTGGGACATGGCATC-GGTATCGAGA-GAGAGCT-A
* * * *
39904454 GTGTAAGACCATGTCTGGAACATGGCATC-G-ACTGGAGATATGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGTA-TCGAGAGA-GAGCTA
39904501 GTGTAAGACCATGTCTGGGACATGGCATCGG
1 GTGTAAGACCATGTCTGGGACATGGCATCGG
39904532 CACCTTATCC
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
45 2 0.02
46 21 0.21
47 65 0.65
48 12 0.12
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGTATCGAGAGAGAGCTA
Found at i:39907689 original size:49 final size:49
Alignment explanation
Indices: 39907617--39907716 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
39907607 ATGGTGAACA
* * *
39907617 CTTAGTACCACCCATGTGACCTAGACAATTTATCTCGTTGCTCTCTTGT
1 CTTAGTACCACCCATGTGACCTAGACAATTTATCTCATAGATCTCTTGT
39907666 CTTAGTACCACCCATGTGACCTAGACAATTTATCTCATAGATCTCTTGT
1 CTTAGTACCACCCATGTGACCTAGACAATTTATCTCATAGATCTCTTGT
39907715 CT
1 CT
39907717 ACATGGTGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (49 bp):
CTTAGTACCACCCATGTGACCTAGACAATTTATCTCATAGATCTCTTGT
Found at i:39920444 original size:70 final size:71
Alignment explanation
Indices: 39920331--39920493 Score: 301
Period size: 70 Copynumber: 2.3 Consensus size: 71
39920321 CGATTTGTCT
*
39920331 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGTGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
39920395 CTTTCA
66 CTTTCA
*
39920401 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
39920466 CTTTCA
66 CTTTCA
39920472 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
39920494 GATACATCTC
Statistics
Matches: 90, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
70 50 0.56
71 40 0.44
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:39920531 original size:71 final size:70
Alignment explanation
Indices: 39920331--39920527 Score: 240
Period size: 70 Copynumber: 2.8 Consensus size: 70
39920321 CGATTTGTCT
* * * * *
39920331 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGTGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
39920395 CTTTCA
65 CTTTCA
* * * *
39920401 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
39920466 CTTTCA
65 CTTTCA
* *
39920472 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
39920528 TACAGGGTGT
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 51 0.44
71 43 0.37
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:39921786 original size:44 final size:42
Alignment explanation
Indices: 39921721--39921809 Score: 160
Period size: 44 Copynumber: 2.1 Consensus size: 42
39921711 ACAATTATTT
39921721 CTATCTCGATTTGTGTCACGAAACCACTATTCCGATTAGGCC
1 CTATCTCGATTTGTGTCACGAAACCACTATTCCGATTAGGCC
39921763 CTATCTCGGATTTGTGGTCACGAAACCACTATTCCGATTAGGCC
1 CTATCTC-GATTTGT-GTCACGAAACCACTATTCCGATTAGGCC
39921807 CTA
1 CTA
39921810 ATTCGGGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 7 0.16
43 7 0.16
44 31 0.69
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (42 bp):
CTATCTCGATTTGTGTCACGAAACCACTATTCCGATTAGGCC
Found at i:39925370 original size:27 final size:27
Alignment explanation
Indices: 39925340--39925406 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
39925330 GTCTTTAGAG
*
39925340 GCAAATATTTGTACTAAAGTATCATAT
1 GCAAATATTTGTACTAAAGTATAATAT
* * *
39925367 GCAAAAATATCTATACTAAAGTATAATTT
1 GC--AAATATTTGTACTAAAGTATAATAT
39925396 GCAAATATTTG
1 GCAAATATTTG
39925407 CGCCAGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 9 0.28
29 23 0.72
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
GCAAATATTTGTACTAAAGTATAATAT
Found at i:39925383 original size:29 final size:29
Alignment explanation
Indices: 39925342--39925400 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
39925332 CTTTAGAGGC
* * *
39925342 AAATATTTGTACTAAAGTATCATATGCAA
1 AAATATCTATACTAAAGTATAATATGCAA
*
39925371 AAATATCTATACTAAAGTATAATTTGCAA
1 AAATATCTATACTAAAGTATAATATGCAA
39925400 A
1 A
39925401 TATTTGCGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (29 bp):
AAATATCTATACTAAAGTATAATATGCAA
Found at i:39928729 original size:18 final size:18
Alignment explanation
Indices: 39928706--39928742 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39928696 CTATATTTTG
39928706 AGTTTGGGAACTCAAGTT
1 AGTTTGGGAACTCAAGTT
39928724 AGTTTGGGAACTCAAGTT
1 AGTTTGGGAACTCAAGTT
39928742 A
1 A
39928743 TCACTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (18 bp):
AGTTTGGGAACTCAAGTT
Found at i:39929422 original size:17 final size:19
Alignment explanation
Indices: 39929381--39929422 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
39929371 TATTTTCTTC
39929381 TTTATTGTTCTAAGTTTTGA
1 TTTATTGTTCT-AGTTTTGA
39929401 TTTATTGTTCT-GTTTT-A
1 TTTATTGTTCTAGTTTTGA
39929418 TTTAT
1 TTTAT
39929423 CATAGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
20 11 0.50
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.67
Consensus pattern (19 bp):
TTTATTGTTCTAGTTTTGA
Found at i:39930991 original size:26 final size:26
Alignment explanation
Indices: 39930962--39931016 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
39930952 TAAGAAGAGA
39930962 TGACCAAATGAAAGGAGGAGTACAAC
1 TGACCAAATGAAAGGAGGAGTACAAC
39930988 TGACCAAATGAAAGGAGGAGTACAAC
1 TGACCAAATGAAAGGAGGAGTACAAC
39931014 TGA
1 TGA
39931017 TCTCTCACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.13
Consensus pattern (26 bp):
TGACCAAATGAAAGGAGGAGTACAAC
Found at i:39931195 original size:96 final size:96
Alignment explanation
Indices: 39931021--39931196 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 96
39931011 AACTGATCTC
* * * *
39931021 TCACCTATTGTGAAATGTTATTGGTGTAGTTCCAAAGATCATAAGGGTTTCCGATGTCCAATTAA
1 TCACCTATTGTGAAATGTTATTAGTGTAGTTCAAAAGATAATAAGGGTTTCCAATGTCCAATTAA
*
39931086 GTATCCAAATAGAGAGAATACGATTGAGCTA
66 ATATCCAAATAGAGAGAATACGATTGAGCTA
* * *
39931117 TCACCTTTTGTGTAATGTTATTAGTTTAGTTCAAAAGATAATAAGGGTTTCCAATGTCCAATTAA
1 TCACCTATTGTGAAATGTTATTAGTGTAGTTCAAAAGATAATAAGGGTTTCCAATGTCCAATTAA
* *
39931182 ATATTCAACTAGAGA
66 ATATCCAAATAGAGA
39931197 AGAAAGTATG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (96 bp):
TCACCTATTGTGAAATGTTATTAGTGTAGTTCAAAAGATAATAAGGGTTTCCAATGTCCAATTAA
ATATCCAAATAGAGAGAATACGATTGAGCTA
Found at i:39931390 original size:37 final size:37
Alignment explanation
Indices: 39931340--39931413 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
39931330 ATAGAAACGT
39931340 CATGTTCTCCTACTAAGATGTATTGTACTAAATTGAA
1 CATGTTCTCCTACTAAGATGTATTGTACTAAATTGAA
39931377 CATGTTCTCCTACTAAGATGTATTGTACTAAATTGAA
1 CATGTTCTCCTACTAAGATGTATTGTACTAAATTGAA
39931414 TATTTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (37 bp):
CATGTTCTCCTACTAAGATGTATTGTACTAAATTGAA
Found at i:39932925 original size:18 final size:19
Alignment explanation
Indices: 39932889--39932928 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
39932879 ATGAGCTCAA
39932889 TATTTTTTTATTAGCTTTTAT
1 TATTTTTTTATTA--TTTTAT
39932910 TATTTTTTTATT-TTTTAT
1 TATTTTTTTATTATTTTAT
39932928 T
1 T
39932929 CGAACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
21 12 0.63
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (19 bp):
TATTTTTTTATTATTTTAT
Found at i:39933605 original size:236 final size:234
Alignment explanation
Indices: 39933193--39933896 Score: 1031
Period size: 236 Copynumber: 3.0 Consensus size: 234
39933183 CAAAGTTGCC
* * * * * *
39933193 GATTTGAATTAGGG-TTCTAAACGTTCAGAAAGAAAC-TTGTAATTTGGCACAACCTGAAACACA
1 GATTTGACTTAGGGCTT-TAGATGTTCGGAAAGAAACTTTG-AATTTGACACAACCTGAAACGCA
* *
39933256 ATTGAATCCAAGTCAGATAAAACAATTAAAATAGATAACTAAGATAAATAGAATAATAAATAAAA
64 ATTGAATCCAAGTCAGATAAAAAAATTAAAATAGATAACTAAGATAAATAGAATAATAAATCAAA
* * * *
39933321 GATTAGAACAATAAAGAAGAAAATGA-GGAAGATAGATGGAAAAGATAGAACGTGGTATATAGAA
129 GATTAGAACACTAAAGAATAAAAT-ATGAAAGATAGATGGAAAAGATAGAACGTGGTGTATA-AA
39933385 GTCCTAAGGAGCCTTGGAAACAAGAAGAATCCACAACCCTGTG
192 GTCCTAAGGAGCCTTGGAAACAAGAAGAATCCACAACCCTGTG
* *
39933428 GATTTGACTTAGGGCTTTAGCTGTTCGGAAAGAAACTTTGACTTTGACACAACCTGAAACGCAAT
1 GATTTGACTTAGGGCTTTAGATGTTCGGAAAGAAACTTTGAATTTGACACAACCTGAAACGCAAT
* *
39933493 TGAATCTAAGTTAGATAAAAAAAATTAAAATAGATAACTAAGATAAATAGAATAATAAATCAAAG
66 TGAATCCAAGTCAGAT-AAAAAAATTAAAATAGATAACTAAGATAAATAGAATAATAAATCAAAG
* *
39933558 ATTAGAACACTAAAGAATAAAATATGAAAGATAGATGAAAAAGATAGAACGTGGTGTGTATAAGT
130 ATTAGAACACTAAAGAATAAAATATGAAAGATAGATGGAAAAGATAGAACGTGGTGTATA-AAGT
* * *
39933623 CCTAAGGACCCTTGGAAACAAGAAGGATCCACAACCCTGTT
194 CCTAAGGAGCCTTGGAAACAAGAAGAATCCACAACCCTGTG
* * * *
39933664 GATTTGACTTAGGGCTTTAGATGTTCGAAAAGAAACTTGGATTTTGACACAACCTGAAACGTAAT
1 GATTTGACTTAGGGCTTTAGATGTTCGGAAAGAAACTTTGAATTTGACACAACCTGAAACGCAAT
* *
39933729 TGAATCCAAGTCAGATAAAAAATTTAAAATAGATATCTAAGATAAATAGAATAATAAATCAAAGA
66 TGAATCCAAGTCAGATAAAAAAATTAAAATAGATAACTAAGATAAATAGAATAATAAATCAAAGA
*
39933794 TTAGAACACTAAAG-ATGAAAATATGAAAGATAGATGGAAAAGATAGAACATAGCGTGTAT-AAG
131 TTAGAACACTAAAGAAT-AAAATATGAAAGATAGATGGAAAAGATAGAACGT-G-GTGTATAAAG
*
39933857 TCCTAAGGAGCCTTGGAAACAAGAAAAATCCACAACCCTG
193 TCCTAAGGAGCCTTGGAAACAAGAAGAATCCACAACCCTG
39933897 GAAACATGAA
Statistics
Matches: 425, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
234 2 0.00
235 198 0.47
236 220 0.52
237 5 0.01
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.23
Consensus pattern (234 bp):
GATTTGACTTAGGGCTTTAGATGTTCGGAAAGAAACTTTGAATTTGACACAACCTGAAACGCAAT
TGAATCCAAGTCAGATAAAAAAATTAAAATAGATAACTAAGATAAATAGAATAATAAATCAAAGA
TTAGAACACTAAAGAATAAAATATGAAAGATAGATGGAAAAGATAGAACGTGGTGTATAAAGTCC
TAAGGAGCCTTGGAAACAAGAAGAATCCACAACCCTGTG
Found at i:39937508 original size:27 final size:27
Alignment explanation
Indices: 39937478--39937723 Score: 163
Period size: 27 Copynumber: 9.3 Consensus size: 27
39937468 TATTTACTTG
39937478 AAAATGACTGAAATACCCCTATAGGGT
1 AAAATGACTGAAATACCCCTATAGGGT
** *
39937505 AAAATGACCAAAATA-CCC--TACGGT
1 AAAATGACTGAAATACCCCTATAGGGT
* * * *
39937529 AAAAT-ACCGAGATA-CCCTCACAAGGT
1 AAAATGACTGAAATACCCCT-ATAGGGT
* *
39937555 AGAATGA-TCGAAATACCCCCATAGGGT
1 AAAATGACT-GAAATACCCCTATAGGGT
* *
39937582 AAAATGATTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCTATAGGGT
* * * *
39937609 AAAATTACTGAAATGCCCCCATATGGT
1 AAAATGACTGAAATACCCCTATAGGGT
**
39937636 AAAATGACCAAAATA-CCCTCATAGGGT
1 AAAATGACTGAAATACCCCT-ATAGGGT
* * * *
39937663 AAAAT-AATCG-AATA--CCGAGTAAGAT
1 AAAATGACT-GAAATACCCCTA-TAGGGT
* *
39937688 AAAATGACTGTAATACCCCTATAAGGT
1 AAAATGACTGAAATACCCCTATAGGGT
39937715 AAAATGACT
1 AAAATGACT
39937724 ATTTTTCCCT
Statistics
Matches: 172, Mismatches: 33, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
23 10 0.06
24 11 0.06
25 12 0.07
26 25 0.15
27 107 0.62
28 7 0.04
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCTATAGGGT
Found at i:39937622 original size:54 final size:54
Alignment explanation
Indices: 39937478--39937667 Score: 183
Period size: 54 Copynumber: 3.6 Consensus size: 54
39937468 TATTTACTTG
* * **
39937478 AAAATGACTGAAATACCCCTATAGGGTAAAATGACCAAAATA--CCC-TACGGT
1 AAAATGACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATACGGT
* * * * * *
39937529 AAAAT-ACCGAGATACCCTCACAAGGTAGAATGA-TCGAAATACCCCCATAGGGT
1 AAAATGACCGAAATACCCCCATAGGGTAAAATGACT-GAAATACCCCCATACGGT
** * * *
39937582 AAAATGATTGAAATACCCCCATAGGGTAAAATTACTGAAATGCCCCCATATGGT
1 AAAATGACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATACGGT
* *
39937636 AAAATGACCAAAATACCCTCATAGGGTAAAAT
1 AAAATGACCGAAATACCCCCATAGGGTAAAAT
39937668 AATCGAATAC
Statistics
Matches: 109, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
50 26 0.24
51 5 0.05
52 3 0.03
53 10 0.09
54 64 0.59
55 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (54 bp):
AAAATGACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATACGGT
Found at i:39937744 original size:27 final size:27
Alignment explanation
Indices: 39937712--39937831 Score: 150
Period size: 27 Copynumber: 4.4 Consensus size: 27
39937702 ACCCCTATAA
* *
39937712 GGTAAAATGACTATTTTTCCCTTATGC
1 GGTAAAATGACTATTTTGCCCTTATGT
* * *
39937739 GATAAACTGACTATTTTGCCCTCATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
*
39937766 GGTAAAATGACGATTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* * *
39937793 GGTAAAATGACTAATTTCCCCTTACGT
1 GGTAAAATGACTATTTTGCCCTTATGT
*
39937820 GGTAAGATGACT
1 GGTAAAATGACT
39937832 GTTTCACCCC
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAAAATGACTATTTTGCCCTTATGT
Found at i:39937845 original size:27 final size:27
Alignment explanation
Indices: 39937764--39937847 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
39937754 TTGCCCTCAT
* * * * *
39937764 GTGGTAAAATGACGATTTTGCCCTTAT
1 GTGGTAAAATGACTAATTTCCCCCTAC
*
39937791 GTGGTAAAATGACTAATTTCCCCTTAC
1 GTGGTAAAATGACTAATTTCCCCCTAC
* *
39937818 GTGGTAAGATGACT-GTTTCACCCCTAC
1 GTGGTAAAATGACTAATTTC-CCCCTAC
39937845 GTG
1 GTG
39937848 ATGTATGTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
26 4 0.08
27 45 0.92
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (27 bp):
GTGGTAAAATGACTAATTTCCCCCTAC
Found at i:39951872 original size:40 final size:39
Alignment explanation
Indices: 39951826--39952013 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 39
39951816 TGAATGATAC
* * *
39951826 CCGGGCTAAG-CCCTGAAGGCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCC-GAAGGCATTTGTGCGAGTG-TTATAT
*
39951866 TCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* *
39951906 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGCGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* *
39951946 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* *
39951986 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTTGTGC
39952014 TTGTGGATAT
Statistics
Matches: 131, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 126 0.96
41 5 0.04
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:39952025 original size:80 final size:79
Alignment explanation
Indices: 39951822--39952033 Score: 300
Period size: 80 Copynumber: 2.7 Consensus size: 79
39951812 CATTTGAATG
* * *
39951822 ATACCCGGGCTAAG-CCCTGAAGGCATTTATGCTAGTGAATATATTCGGGCTAAGACCCGAAGGC
1 ATACCCGGGTTAAGACCC-GAAGGCATTTGTGCTAGTGGATATA-TCGGGCTAAGACCCGAAGGC
*
39951886 ATTTGTGCGAGTTGTT
64 ATTTGTGCGAGTTGCT
* * * *
39951902 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGCGGTTATATCCGGGCTAAGACCCGAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGATATAT-CGGGCTAAGACCCGAAGGCA
39951967 TTTGTGCGAGTTGCT
65 TTTGTGCGAGTTGCT
* *
39951982 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGATATATCGGGCTAA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGATATATCGGGCTAA
39952034 ATTCCGAAGA
Statistics
Matches: 116, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
79 9 0.08
80 104 0.90
81 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (79 bp):
ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGGATATATCGGGCTAAGACCCGAAGGCAT
TTGTGCGAGTTGCT
Found at i:39954020 original size:13 final size:13
Alignment explanation
Indices: 39954002--39954035 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39953992 TGAATATTGG
39954002 TTTTATTTTTATA
1 TTTTATTTTTATA
*
39954015 TTTTATATTTATA
1 TTTTATTTTTATA
39954028 -TTTATTTT
1 TTTTATTTT
39954036 ATTTGGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTATA
Found at i:39961504 original size:18 final size:17
Alignment explanation
Indices: 39961481--39961514 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
39961471 GCCCACAATA
39961481 AGGCCCATGTAGGCCCAT
1 AGGCCCATGT-GGCCCAT
39961499 AGGCCCATGTGGCCCA
1 AGGCCCATGTGGCCCA
39961515 CAAAGCCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.21, C:0.35, G:0.29, T:0.15
Consensus pattern (17 bp):
AGGCCCATGTGGCCCAT
Found at i:39964632 original size:40 final size:40
Alignment explanation
Indices: 39964577--39964821 Score: 338
Period size: 40 Copynumber: 6.2 Consensus size: 40
39964567 TGAATGATAC
* * *
39964577 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
39964617 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATA-
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
39964656 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTGCTAT-T
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
39964694 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
39964734 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
39964774 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
39964814 CC-GGCTAA
1 CCGGGCTAA
39964822 ATTCCGAAGA
Statistics
Matches: 184, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
38 35 0.19
39 41 0.22
40 106 0.58
41 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:39972850 original size:40 final size:40
Alignment explanation
Indices: 39972795--39973042 Score: 336
Period size: 40 Copynumber: 6.2 Consensus size: 40
39972785 TGAATGATAC
* * ** *
39972795 CCGGGCTAAGTCCCGAAGGCATTTATGTTAGTTATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
39972835 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
39972875 CCGGGCTAAGACTCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
39972915 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
39972955 CTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
39972995 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
39973035 -CGGGCTAA
1 CCGGGCTAA
39973043 ATTTCGAAGA
Statistics
Matches: 183, Mismatches: 25, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
39 7 0.04
40 176 0.96
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:39974845 original size:29 final size:29
Alignment explanation
Indices: 39974812--39974904 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
39974802 TGACGAGATT
* *
39974812 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
*
39974841 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
* * * *
39974870 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
39974899 GGCACT
1 GGCACT
39974905 GGGTGTGCGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAAAATAA
Found at i:39974917 original size:29 final size:29
Alignment explanation
Indices: 39974812--39974917 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 29
39974802 TGACGAGATT
* *
39974812 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
*
39974841 GGCACTAAGTGTGC-ATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGA-GCTGGAAAAATAA
* * * *
39974870 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
**
39974899 GGCACTGGGTGTGCGAGCT
1 GGCACTAAGTGTGCGAGCT
39974918 CGGAGGGTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 64 0.98
30 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAGCTGGAAAAATAA
Found at i:39979316 original size:24 final size:24
Alignment explanation
Indices: 39979289--39979334 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39979279 AGTGTTATGT
*
39979289 GGAGGAAATCAA-GAAGAGGATTGG
1 GGAGAAAATCAAGGAA-AGGATTGG
39979313 GGAGAAAATCAAGGAAAGGATT
1 GGAGAAAATCAAGGAAAGGATT
39979335 ATGGAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.46, C:0.04, G:0.37, T:0.13
Consensus pattern (24 bp):
GGAGAAAATCAAGGAAAGGATTGG
Found at i:39988008 original size:9 final size:9
Alignment explanation
Indices: 39987996--39988035 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
39987986 ATCATTTTAG
39987996 TATTACTAT
1 TATTACTAT
**
39988005 TATTTTTAT
1 TATTACTAT
39988014 TATTACTAT
1 TATTACTAT
*
39988023 TATTACTCT
1 TATTACTAT
39988032 TATT
1 TATT
39988036 TCTTTATCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTACTAT
Found at i:39988017 original size:18 final size:18
Alignment explanation
Indices: 39987990--39988026 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39987980 ATTTTAATCA
39987990 TTTTAGTATTACTATTAT
1 TTTTAGTATTACTATTAT
*
39988008 TTTTATTATTACTATTAT
1 TTTTAGTATTACTATTAT
39988026 T
1 T
39988027 ACTCTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTAGTATTACTATTAT
Found at i:39994493 original size:22 final size:19
Alignment explanation
Indices: 39994468--39994509 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
39994458 TGATAATCAT
39994468 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
39994490 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
39994509 T
1 T
39994510 CAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:39994568 original size:16 final size:17
Alignment explanation
Indices: 39994547--39994582 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39994537 TAAATTTGAT
39994547 AATATTT-TATTTAATA
1 AATATTTATATTTAATA
*
39994563 AATATTTATTTTTAATA
1 AATATTTATATTTAATA
39994580 AAT
1 AAT
39994583 TAATAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATTTATATTTAATA
Found at i:39999094 original size:21 final size:21
Alignment explanation
Indices: 39999070--39999111 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
39999060 GAAGAAGAAG
39999070 AAGAAGAAGAAGAAGATCCTA
1 AAGAAGAAGAAGAAGATCCTA
39999091 AAGAAGAAGAAGAAGATCCTA
1 AAGAAGAAGAAGAAGATCCTA
39999112 CAGAGATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.24, T:0.10
Consensus pattern (21 bp):
AAGAAGAAGAAGAAGATCCTA
Found at i:39999105 original size:3 final size:3
Alignment explanation
Indices: 39999058--39999085 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39999048 GAGGATCCTA
39999058 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39999086 TCCTAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40005546 original size:28 final size:29
Alignment explanation
Indices: 40005514--40005575 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
40005504 TACCTGTATC
*
40005514 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAAGCCCAAATCACATTTATA
**
40005542 TGGCCCATTTGGCCCAAATCACATTTATA
1 TGGCCCATTAAGCCCAAATCACATTTATA
40005571 TGGCC
1 TGGCC
40005576 TGTTAGGCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (29 bp):
TGGCCCATTAAGCCCAAATCACATTTATA
Found at i:40005584 original size:29 final size:28
Alignment explanation
Indices: 40005514--40005599 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
40005504 TACCTGTATC
* *
40005514 TGGCCCATTAAGCCCAATCATATTTATA
1 TGGCCCATTAGGCCCAATCACATTTATA
*
40005542 TGGCCCATTTGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTTATA
** * * *
40005571 TGGCCTGTTAGGCCTAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTTATA
40005599 T
1 T
40005600 TCATGCTCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
28 25 0.52
29 23 0.48
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTTATA
Found at i:40005840 original size:24 final size:24
Alignment explanation
Indices: 40005810--40005860 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
40005800 GTAGCCAAAC
*
40005810 TTTCGGCTTTTAAGCATTTCAGCT
1 TTTCGGCATTTAAGCATTTCAGCT
** *
40005834 TTTCGGCATTTCGGCATTTCGGCT
1 TTTCGGCATTTAAGCATTTCAGCT
40005858 TTT
1 TTT
40005861 GCCGATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (24 bp):
TTTCGGCATTTAAGCATTTCAGCT
Found at i:40005845 original size:8 final size:8
Alignment explanation
Indices: 40005823--40005856 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
40005813 CGGCTTTTAA
*
40005823 GCATTTCA
1 GCATTTCG
*
40005831 GCTTTTCG
1 GCATTTCG
40005839 GCATTTCG
1 GCATTTCG
40005847 GCATTTCG
1 GCATTTCG
40005855 GC
1 GC
40005857 TTTTGCCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (8 bp):
GCATTTCG
Found at i:40008505 original size:46 final size:45
Alignment explanation
Indices: 40008439--40008528 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 45
40008429 ATGGCTAATG
40008439 TAACCTTCTCAGTCTAGTCATAACGTTTAGGCCAGGTTAGGGAGA
1 TAACCTTCTCAGTCTAGTCATAACGTTTAGGCCAGGTTAGGGAGA
*
40008484 TAACCTTTCTCAGTCTAGTCATAACGTTTAGGCCGGGTTAGGGAG
1 TAACC-TTCTCAGTCTAGTCATAACGTTTAGGCCAGGTTAGGGAG
40008529 GTTACAAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 5 0.12
46 38 0.88
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (45 bp):
TAACCTTCTCAGTCTAGTCATAACGTTTAGGCCAGGTTAGGGAGA
Found at i:40009193 original size:2 final size:2
Alignment explanation
Indices: 40009186--40009214 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40009176 TTTGTTGATG
40009186 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40009215 ATTCCCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:40011420 original size:40 final size:40
Alignment explanation
Indices: 40011373--40011472 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
40011363 AGAGGTATCG
40011373 AAATACAAACAGGGGCACATATGTGCATTCAAGGGTACCA
1 AAATACAAACAGGGGCACATATGTGCATTCAAGGGTACCA
* * * * * *
40011413 AAGTACAAACAAGGGTA-AGCATGTGCATTTAGGGGTACCA
1 AAATACAAACAGGGGCACA-TATGTGCATTCAAGGGTACCA
*
40011453 AAATACAAACAGGGTCACAT
1 AAATACAAACAGGGGCACAT
40011473 TCCATTCAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
39 1 0.02
40 45 0.96
41 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (40 bp):
AAATACAAACAGGGGCACATATGTGCATTCAAGGGTACCA
Found at i:40013295 original size:20 final size:19
Alignment explanation
Indices: 40013270--40013345 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
40013260 TGCATAACAA
*
40013270 AGGCACCAACGTGCAGAAAG
1 AGGCACCAAAGTGCA-AAAG
* ** *
40013290 AGGCACGATTGTGCAACCAG
1 AGGCACCAAAGTGCAA-AAG
40013310 AGGCACCAAAGTGCAAACAG
1 AGGCACCAAAGTGCAAA-AG
*
40013330 AGGCACCTAAGTGCAA
1 AGGCACCAAAGTGCAA
40013346 TTCTTTACAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.38, C:0.25, G:0.28, T:0.09
Consensus pattern (19 bp):
AGGCACCAAAGTGCAAAAG
Found at i:40023433 original size:33 final size:33
Alignment explanation
Indices: 40023390--40023495 Score: 94
Period size: 33 Copynumber: 3.3 Consensus size: 33
40023380 AAACCCTGAA
40023390 CCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAG
1 CCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAG
* * ** *** * *
40023423 CCAAGTGTTGAACTTG-A-ATTTACC-CTGAA-
1 CCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAG
40023452 CCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAG
1 CCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAG
*
40023485 CCAAGTGTTGA
1 CCAAGGGTTGA
40023496 ACTTGAATTT
Statistics
Matches: 50, Mismatches: 19, Indels: 8
0.65 0.25 0.10
Matches are distributed among these distances:
29 12 0.24
30 4 0.08
31 8 0.16
32 4 0.08
33 22 0.44
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (33 bp):
CCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAG
Done.