Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 62 of 240
Found at i:20219799 original size:21 final size:21
Alignment explanation
Indices: 20219757--20219818 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
20219747 GCTAGGTGAA
* *
20219757 GTGGGACTGTAACTGGGGGAT
1 GTGGGACTGTAACTTGGAGAT
20219778 GTGGGACTGTAACTTGGAGAT
1 GTGGGACTGTAACTTGGAGAT
20219799 GTAGGG-CTGTAACTTGGAGA
1 GT-GGGACTGTAACTTGGAGA
20219819 GGTAGGGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 35 0.92
22 3 0.08
ACGTcount: A:0.23, C:0.10, G:0.42, T:0.26
Consensus pattern (21 bp):
GTGGGACTGTAACTTGGAGAT
Found at i:20219823 original size:21 final size:21
Alignment explanation
Indices: 20219784--20219842 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
20219774 GGATGTGGGA
*
20219784 CTGTAACTTGGAGATGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
20219805 CTGTAACTTGGAGAGGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
* * *
20219826 CTATAGCTTGGTGAGGT
1 CTGTAACTTGGAGAGGT
20219843 TGGAGAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.10, G:0.39, T:0.29
Consensus pattern (21 bp):
CTGTAACTTGGAGAGGTAGGG
Found at i:20219949 original size:21 final size:21
Alignment explanation
Indices: 20219886--20220046 Score: 128
Period size: 21 Copynumber: 7.7 Consensus size: 21
20219876 TGGACTTGTC
* * * *
20219886 GGACTGTATCCTGGTGAGCTA
1 GGACTGTAACCAGGAGAGGTA
** * * *
20219907 GGACTGTAAGTAGGTGATGTG
1 GGACTGTAACCAGGAGAGGTA
* *
20219928 GGGCTGTAACCAGGAGAGGTG
1 GGACTGTAACCAGGAGAGGTA
* *
20219949 GGACTGTACCCAGGAGATGTA
1 GGACTGTAACCAGGAGAGGTA
20219970 GGACTGTAACCAGGAGAGGTA
1 GGACTGTAACCAGGAGAGGTA
* *
20219991 GGACTGTAACCAGGTGATG-A
1 GGACTGTAACCAGGAGAGGTA
* *
20220011 CGGACTGTATCCAGGAGATG-A
1 -GGACTGTAACCAGGAGAGGTA
*
20220032 TGGGCTGTAACCAGG
1 -GGACTGTAACCAGG
20220047 GGATGACGTA
Statistics
Matches: 114, Mismatches: 25, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
20 1 0.01
21 113 0.99
ACGTcount: A:0.26, C:0.16, G:0.38, T:0.20
Consensus pattern (21 bp):
GGACTGTAACCAGGAGAGGTA
Found at i:20219953 original size:42 final size:42
Alignment explanation
Indices: 20219907--20220051 Score: 168
Period size: 42 Copynumber: 3.5 Consensus size: 42
20219897 TGGTGAGCTA
** * *
20219907 GGACTGTAAGTAGGTGATGTGGGGCTGTAACCAGGAGAGGTG
1 GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
* * *
20219949 GGACTGTACCCAGGAGATGTAGGACTGTAACCAGGAGAGGTA
1 GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
* *
20219991 GGACTGTAACCAGGTGATG-ACGGACTGTATCCAGGAGATGATG
1 GGACTGTAACCAGGTGATGTA-GGACTGTAACCAGGAGA-GGTG
*
20220034 GG-CTGTAACCAGGGGATG
1 GGACTGTAACCAGGTGATG
20220052 ACGTAGGAGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 83 0.94
43 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.39, T:0.19
Consensus pattern (42 bp):
GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
Found at i:20232656 original size:11 final size:11
Alignment explanation
Indices: 20232640--20232666 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20232630 TTTTTAATCA
20232640 AATATATATTT
1 AATATATATTT
20232651 AATATATATTT
1 AATATATATTT
20232662 AATAT
1 AATAT
20232667 GGGCCGGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATATATATTT
Found at i:20239210 original size:46 final size:46
Alignment explanation
Indices: 20239151--20239242 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
20239141 ACAATTGTGG
20239151 CATGTTTGAGTAATTATTATAATTAGTGGGTTTCACCGAATTGAGT
1 CATGTTTGAGTAATTATTATAATTAGTGGGTTTCACCGAATTGAGT
20239197 CATGTTTGAGTAATTATTATAATTAGTGGGTTTCACCGAATTGAGT
1 CATGTTTGAGTAATTATTATAATTAGTGGGTTTCACCGAATTGAGT
20239243 GTAATTGGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (46 bp):
CATGTTTGAGTAATTATTATAATTAGTGGGTTTCACCGAATTGAGT
Found at i:20242701 original size:20 final size:20
Alignment explanation
Indices: 20242673--20242711 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20242663 TCTTCACAAT
*
20242673 TTTGCAAGAGTTTTAGTAAA
1 TTTGCAAGAATTTTAGTAAA
*
20242693 TTTGTAAGAATTTTAGTAA
1 TTTGCAAGAATTTTAGTAA
20242712 TATCATAAAA
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:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (20 bp):
TTTGCAAGAATTTTAGTAAA
Found at i:20243878 original size:22 final size:22
Alignment explanation
Indices: 20243790--20243877 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
20243780 GCTTGAACGA
* *
20243790 GATTTGCACTATGGTGCATACT
1 GATTTGCACTACGGTGCCTACT
*
20243812 GATTTGCACTACAGTGCCTACT
1 GATTTGCACTACGGTGCCTACT
** *
20243834 GATTCACACTTCGGTGCCTACT
1 GATTTGCACTACGGTGCCTACT
20243856 -ACTTTGCACTACGGTGCCTACT
1 GA-TTTGCACTACGGTGCCTACT
20243878 ATTAAAATAC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 1 0.02
22 54 0.98
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (22 bp):
GATTTGCACTACGGTGCCTACT
Found at i:20258167 original size:23 final size:24
Alignment explanation
Indices: 20258115--20258165 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
20258105 AAAGAACAAG
*
20258115 AAAATAGCAACAAAACAATAAAAA
1 AAAACAGCAACAAAACAATAAAAA
* *
20258139 AAAACAGCAACAAAATAGTAAAAA
1 AAAACAGCAACAAAACAATAAAAA
20258163 AAA
1 AAA
20258166 CATTCGGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.75, C:0.12, G:0.06, T:0.08
Consensus pattern (24 bp):
AAAACAGCAACAAAACAATAAAAA
Found at i:20259357 original size:19 final size:19
Alignment explanation
Indices: 20259288--20259359 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
20259278 TTCAATTAAG
*
20259288 AAAATATATTTTTATTTTT
1 AAAATAAATTTTTATTTTT
** * *
20259307 AATTTTAATTTTAATTTTTT
1 AAAATAAATTTTTA-TTTTT
**
20259327 AAAATACTTTTTTATTTTT
1 AAAATAAATTTTTATTTTT
20259346 AAAATAAATTTTTA
1 AAAATAAATTTTTA
20259360 GTGTTTTATT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
19 26 0.67
20 13 0.33
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
AAAATAAATTTTTATTTTT
Found at i:20293498 original size:773 final size:772
Alignment explanation
Indices: 20291223--20294318 Score: 4885
Period size: 773 Copynumber: 4.0 Consensus size: 772
20291213 TACCAACTAC
* * * * *
20291223 AATTGGGAAGAAGAATTTTCCACCGAATGTCTTGGACATTAGATCTATGCATATGGGTCTTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
*
20291288 TACTGCAAGCCGCTTGTACAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* *
20291353 TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTGGAGTTGG
131 TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTAGAGTTAG
*
20291418 AGAACATGAAATCGCCAGAATTCTTCTTGACGAACTTGAGGACGTATGTTGTTAGAGAAGACAAT
196 AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGA-AAT
* * * * *
20291483 ATTTGTATCATATTTGATAGGTAGAAGACTAATTGCCGCAATTAGGCGCTCCGGTGTTCCCTGAA
260 ATTTGCATCATATTTGATAGGTAGAAGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATGAA
* *
20291548 AATCTATTTACTGTATCCATCATATTGCCACCAACTTCTACTGAGACTACATGAATGCAGACTAG
325 AATCTATTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACTAG
*
20291613 CGCAAACAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACTT
390 CGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACTT
* *
20291678 CCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATATATACGCAGTGTACGAGCTGGAAC
455 CCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGAAC
* * *
20291743 AACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCTACAGTGAAGCAAATACTCTT
520 AACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACTCTT
*
20291808 TTTTTAGAGTGGTTGGGTACCATAGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTCG
585 TTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTCG
*
20291873 ATATGGTCATATGACCACCAACCTAACAAGTGTTATTAACTTTGTCTTGAAGCAAACACGACATT
650 ATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACATT
* * *
20291938 TTCCAATTTTATTTATTTTTTCAACTATATTTTACAGACTGACAACATTTATGCCAAG
715 TTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
** *
20291996 AATTGGGAAGAAGAATTTTCCATAAAATGTCCTGGACATTCGATCTATGCATGTTGGTATTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
* * * *
20292061 TACTGCAAGCTGCTTGTGCAAGTTGATGACACCTGGTTATATGAAAAATATACGCAGATCATTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
*
20292126 TATTGTGGTTGCACAAGA-TGGGAACCAGAACTTGCTACGGATAGTGTTTGCCATTGTAGAGTTA
131 TATTGTGGTTGCACAAGACT-GGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTAGAGTTA
* * *
20292190 AAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGCGGATGTATGTTGTTAGAGAAGACAA
195 GAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGA-AA
* * *
20292255 TATTTGCATCATATTTGATAGGTAGAAGAGACTAATTGCTGTGATTAGGAGTTTCGGTGTTCCAT
259 TATTTGCATCATATTTGATAGGTAG-A-AGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCAT
* * * *
20292320 GAAAATCTCTTTACAGTATCCGCCATATTACCACCAACTTCTACTGAGACTACAAGAATGCAGAC
322 GAAAATCTATTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGAC
20292385 TAGCGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATA-TCTTAATA
387 TAGCGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
* *
20292449 CTTCCATAAATTAATTCGAAAATGTAGCTTGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
452 CTTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
* *
20292514 AACAACACTGTTTCAAGCAAAGGCTGACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACA
517 AACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACT
*
20292579 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAACTCAAAGTTTTGATGACGGATC
582 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATC
* *
20292644 TCGATATGGTCATATGACCACCAACCTGACAAATGTTATTAACTTTTTCTTGAAGCAAACACGAC
647 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGAC
*
20292709 ACTTTT-TAATTTTATTTATTTTCTCAACTATATTTTACAGGCCG-CAAACATTTATGCCAAG
712 A-TTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGAC-AACATTTATGCCAAG
* * * *
20292770 AATTGGAAAGAAGAATTTTTCACCAAATGTCCTGGATATTCGATCTATGCATGTGGGTCTTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
* * *
20292835 TACTACAAGCCGCTTGTGCAGGTTGATGACACCTGATTATACGAAAAATATACGCAGATACTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * * *
20292900 TATTATAGTTGCACAAGA-TGAATACCAGAACTTGCTACCGATAGTGTTTGCCATTGTAGAGTTG
131 TATTGTGGTTGCACAAGACTGGA-ACCAGAACTTGCTACCGATAGTGTTTGCCATTGTAGAGTTA
* *
20292964 GAGAACATGAAATCGCCAGAATTCTTCTTGACGAACTTGAGGACGTATGTTGTTAGAGAAG-ATT
195 GAGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGAAAT
* * * * *
20293028 ATTTGCATCATATTCGATAAGTAGAAGAGACTAATTGCCGCGATTAGGAGATCCGATGTTTCATG
260 ATTTGCATCATATTTGATAGGTAG-A-AGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATG
* * * * *
20293093 AAAATCTGTTTACTGTATCCGCCATATTGCCGCCAACTTCCACTGAGACTACAAGAATGCAGAAT
323 AAAATCTATTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACT
*
20293158 AGCGCAAA-ATAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTATTAATA
388 AGCGCAAATA-AGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATA
* *
20293222 CTTCCATAAATTAATTCGAAAACGTAGCATGTCTTTTTGAAATACATACGCAGCGTACGAGCTGG
452 CTTCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGG
*
20293287 AACAACACTGTTTCAAGCAAAGGCTGACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACT
517 AACAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACT
* *
20293352 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTTATGACAGATC
582 CTTTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATC
20293417 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGAC
647 TCGATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGAC
**
20293482 ATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACTAACAACATTTATGCCAAG
712 ATTTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
* * * * *
20293543 AATTGGGAAGAAGAATTTTTCACCAAATGTCATGGATATTCGATTTATGCATGTAGGTATTTCCC
1 AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
* *
20293608 TACTGCATGCCGCTTGTGCAGGTTGATGACACCTGGTTATACAAAAAATATACGCAGATCCTTCT
66 TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
* * * * * *
20293673 TATTGTGGTTGCACAATACGGGAACCATAACTTACTATCGATAGTGTTTGCCATTGTGGAGTTAG
131 TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTAGAGTTAG
* *
20293738 AGAATATGAAATCGCCAGAATTCTTCCTGACGAACTTGCAGG-CATATGTTGTTAGAGAAGACAA
196 AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTG-AGGACGTATGTTGTTAGAGAAGA-AA
* * *
20293802 TATTTGCATCATATTTGATAGGTAGAAGACTAATTGTCGCGATTAGGTGTTCTGGTGTTCCATGA
259 TATTTGCATCATATTTGATAGGTAGAAGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATGA
* * * * *
20293867 AAATCTATTTACTGTATCCACCACACTGCTACCAACTTCTACCGAGACTACATGAATGCAGACTA
324 AAATCTATTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACTA
*
20293932 GGGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACT
389 GCGCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACT
* * ** *
20293997 TCCATAATTTAATTCGAAAAGGTAGCTTGTCTTTTCGAAATACATACATAGCGTACGAACTGGAA
454 TCCATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGAA
* * * *
20294062 CAACATTGTTTCAAACAAAGGCTAACCAGGCTTGAGGTTGATATCTACAGTAAAACGAATACTCT
519 CAACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACTCT
*
20294127 TTTTTTTGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTC
584 TTTTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTC
* * *
20294192 GATATGGTCATATGACCACTAACCTGACAAATGTTATTAACTTTGTCTTGAAGCAAACACAACAT
649 GATATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACAT
* ** **
20294257 TTTCTAATTTTATTTATTTTTTCAACTATATTTTACAGATTGGTAACATTTATGCCAAG
714 TTTCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
20294316 AAT
1 AAT
20294319 GAGGCTAAAA
Statistics
Matches: 2137, Mismatches: 171, Indels: 30
0.91 0.07 0.01
Matches are distributed among these distances:
771 1 0.00
772 176 0.08
773 1246 0.58
774 542 0.25
775 172 0.08
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (772 bp):
AATTGGGAAGAAGAATTTTCCACCAAATGTCCTGGACATTCGATCTATGCATGTGGGTATTTCCC
TACTGCAAGCCGCTTGTGCAGGTTGATGACACCTGGTTATACGAAAAATATACGCAGATCCTTCT
TATTGTGGTTGCACAAGACTGGAACCAGAACTTGCTACCGATAGTGTTTGCCATTGTAGAGTTAG
AGAACATGAAATCGCCAGAATTCTTCCTGACGAACTTGAGGACGTATGTTGTTAGAGAAGAAATA
TTTGCATCATATTTGATAGGTAGAAGACTAATTGCCGCGATTAGGAGTTCCGGTGTTCCATGAAA
ATCTATTTACTGTATCCACCATATTGCCACCAACTTCTACTGAGACTACAAGAATGCAGACTAGC
GCAAATAAGTAGTGAGCATGGGTAAATTTTGATTTCAACATATTTTTAAATATTCTTAATACTTC
CATAAATTAATTCGAAAAGGTAGCATGTCTTTTCGAAATACATACGCAGCGTACGAGCTGGAACA
ACACTGTTTCAAGCAAAGGCTAACCAGGCTTGAGGTTGATATCCACAGTGAAACGAATACTCTTT
TTTTAGAGTGGTTGGGTACCATGGAGCCATGGTAATGAGCTCAAAGTTTTGATGACGGATCTCGA
TATGGTCATATGACCACCAACCTAACAAATGTTATTAACTTTGTCTTGAAGCAAACACGACATTT
TCTAATTTTATTTATTTTCTCAACTATATTTTACAGACCGACAACATTTATGCCAAG
Found at i:20297602 original size:43 final size:43
Alignment explanation
Indices: 20297548--20297747 Score: 206
Period size: 43 Copynumber: 4.7 Consensus size: 43
20297538 TTTTAGAAAT
* * * *
20297548 AAACGCTGTTATAGACCATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
20297591 AAACGCCGTTATAAATCAAGACCTTTAGCGGTGATTTTTCCAC
1 AAACGCCGCTATAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
20297634 AAACGCCACTATAG-CTCAAGACCTTTAGCGGCGCTTTTTCCAT
1 AAACGCCGCTATAGAC-CAAGACCTTTAGCGGCGCTTTTCCCAC
* * ** *
20297677 AAACGCCGCTATAGATCAATACCTTTAGCTACGCTTTCCCCAC
1 AAACGCCGCTATAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
20297720 AAACGCCGCTATAGAACAA-ACCTTTAGC
1 AAACGCCGCTATAGACCAAGACCTTTAGC
20297748 AACACTTCTC
Statistics
Matches: 131, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
42 9 0.07
43 122 0.93
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:20297766 original size:42 final size:43
Alignment explanation
Indices: 20297677--20297768 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 43
20297667 CTTTTTCCAT
* * * *
20297677 AAACGCCGCTATAGATCAATACCTTTAGCTACGCTTTCCCCAC
1 AAACGCCGCTATAGAACAATACCTTTAGCAACACTTTCCCCAA
*
20297720 AAACGCCGCTATAGAACAA-ACCTTTAGCAACAC-TTCTCGCAA
1 AAACGCCGCTATAGAACAATACCTTTAGCAACACTTTC-CCCAA
20297762 AAACGCC
1 AAACGCC
20297769 ACTAAAAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 3 0.07
42 22 0.51
43 18 0.42
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTATAGAACAATACCTTTAGCAACACTTTCCCCAA
Found at i:20301695 original size:14 final size:14
Alignment explanation
Indices: 20301678--20301732 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
20301668 CACTAACTCT
*
20301678 TAACCTCTAACCTC
1 TAACCTCTAACCCC
*
20301692 TAACCCCTAACCCC
1 TAACCTCTAACCCC
* *
20301706 AAACCTTTAACCCC
1 TAACCTCTAACCCC
20301720 TAA-CTACTAACCC
1 TAACCT-CTAACCC
20301733 ATATATCTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 2 0.06
14 31 0.94
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACCTCTAACCCC
Found at i:20301702 original size:21 final size:21
Alignment explanation
Indices: 20301678--20301731 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20301668 CACTAACTCT
20301678 TAACCTCTAACCTCTAACCCC
1 TAACCTCTAACCTCTAACCCC
* * *
20301699 TAACCCCAAACCTTTAACCCC
1 TAACCTCTAACCTCTAACCCC
20301720 TAA-CTACTAACC
1 TAACCT-CTAACC
20301732 CATATATCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (21 bp):
TAACCTCTAACCTCTAACCCC
Found at i:20301920 original size:15 final size:14
Alignment explanation
Indices: 20301857--20301922 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
20301847 CTTGACACCA
*
20301857 AATCCATAAACCCT
1 AATCCATAATCCCT
20301871 AAAT-CA-AA-CCCTT
1 -AATCCATAATCCC-T
* *
20301884 AAACCAGAATCCCT
1 AATCCATAATCCCT
20301898 AATCCATAATCCCT
1 AATCCATAATCCCT
20301912 AATTCCATAAT
1 AA-TCCATAAT
20301923 TTATAAACCT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 5 0.12
13 5 0.12
14 19 0.44
15 14 0.33
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.24
Consensus pattern (14 bp):
AATCCATAATCCCT
Found at i:20301991 original size:14 final size:14
Alignment explanation
Indices: 20301972--20302008 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20301962 AACCTAAATT
20301972 AACCATATACCCTA
1 AACCATATACCCTA
*
20301986 AACCATATACCTTA
1 AACCATATACCCTA
*
20302000 AATCATATA
1 AACCATATA
20302009 TATTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:20315374 original size:23 final size:24
Alignment explanation
Indices: 20315310--20315374 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
20315300 ATGTATGCAT
*
20315310 ATAA-AAAATATTTATAAATATTAA
1 ATAATAAAATA-TAATAAATATTAA
20315334 ATAATAAAAT-TAAGTAAAT-TTAA
1 ATAATAAAATATAA-TAAATATTAA
20315357 AT-ATAAAATATACATAAA
1 ATAATAAAATATA-ATAAA
20315375 AATAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 7 0.19
23 14 0.39
24 10 0.28
25 5 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAATAAAATATAATAAATATTAA
Found at i:20318800 original size:29 final size:27
Alignment explanation
Indices: 20318750--20318804 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
20318740 TGTAATTTTT
*
20318750 AAAAATTATAAAAAATGCAAAAATATG
1 AAAAATTATAAAAAATACAAAAATATG
*
20318777 AAAAATTATATAAAAATTATAAAAATAT
1 AAAAATTATA-AAAAA-TACAAAAATAT
20318805 AACAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 5 0.21
29 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (27 bp):
AAAAATTATAAAAAATACAAAAATATG
Found at i:20319804 original size:24 final size:23
Alignment explanation
Indices: 20319776--20319821 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
20319766 TTTGGAGAAT
20319776 TTTGTATTT-ACGTTTTGAGGGTTC
1 TTTGT-TTTCACGTTTTG-GGGTTC
*
20319800 TTTGTTTTCAGGTTTTGGGGTT
1 TTTGTTTTCACGTTTTGGGGTT
20319822 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.07, G:0.28, T:0.57
Consensus pattern (23 bp):
TTTGTTTTCACGTTTTGGGGTTC
Found at i:20320269 original size:17 final size:17
Alignment explanation
Indices: 20320247--20320280 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20320237 ATCAAATACG
20320247 AACATTTCATATCATTT
1 AACATTTCATATCATTT
20320264 AACATTTCATATCATTT
1 AACATTTCATATCATTT
20320281 CCAGATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
AACATTTCATATCATTT
Found at i:20321247 original size:21 final size:21
Alignment explanation
Indices: 20321177--20321248 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
20321167 TCATGAGAGC
*
20321177 TAAACAAAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
* * * * *
20321198 TGAACGGAAGCTCGTAAGAGG-
1 TAAACAGAAACCCATAAG-GGT
* *
20321219 TGAGCAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
20321240 TAAACAGAA
1 TAAACAGAA
20321249 GCTTAAAAGA
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:20321271 original size:42 final size:42
Alignment explanation
Indices: 20321158--20321290 Score: 113
Period size: 42 Copynumber: 3.2 Consensus size: 42
20321148 CCGAAAGCTG
* ** * * *
20321158 AACAAAAGCTCATGAGAGCTAAACAAAAACCCATAAGGGTTG
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
* ** * *
20321200 AACGGAAGCTCGTAAGAGGTGAGCAGAAACCCATAAGGGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
* * ** * *
20321242 AACAGAAGCTTAAAAGAGCTGAACGGAAACTAATATGAGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
20321284 AACAGAA
1 AACAGAA
20321291 ACTCGTGAGA
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:20324735 original size:20 final size:21
Alignment explanation
Indices: 20324697--20324735 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20324687 TTGTTTTCAT
**
20324697 AATTTTATATAATTTTTTTGC
1 AATTTTATATAATAATTTTGC
20324718 AATTTT-TATAATAATTTT
1 AATTTTATATAATAATTTT
20324736 AATAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
AATTTTATATAATAATTTTGC
Found at i:20324762 original size:9 final size:9
Alignment explanation
Indices: 20324721--20324800 Score: 56
Period size: 9 Copynumber: 8.6 Consensus size: 9
20324711 TTTTTGCAAT
20324721 TTTTATAATA
1 TTTT-TAATA
*
20324731 ATTTTAATA
1 TTTTTAATA
20324740 GTTTTT-ATA
1 -TTTTTAATA
20324749 TTTTTAATA
1 TTTTTAATA
20324758 TTTTTTGCAAT-
1 -TTTTT--AATA
* *
20324769 TTTATATTA
1 TTTTTAATA
20324778 TTTTTAATA
1 TTTTTAATA
* *
20324787 TATTTAATG
1 TTTTTAATA
20324796 TTTTT
1 TTTTT
20324801 TTATAACTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
8 7 0.13
9 29 0.53
10 16 0.29
12 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTAATA
Found at i:20324800 original size:47 final size:47
Alignment explanation
Indices: 20324706--20324800 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
20324696 TAATTTTATA
*
20324706 TAATTTTTTTGCAATTTTTATAATAATTTTAATAGTTTTTATATTTT
1 TAATTTTTTTGCAATTTTTATAATAATTTTAATAGTTTTAATATTTT
* * *
20324753 TAATATTTTTTGCAA-TTTTATATTATTTTTAATA-TATTTAATGTTTT
1 TAAT-TTTTTTGCAATTTTTATAATAATTTTAATAGT-TTTAATATTTT
20324800 T
1 T
20324801 TTATAACTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 1 0.02
47 31 0.74
48 10 0.24
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (47 bp):
TAATTTTTTTGCAATTTTTATAATAATTTTAATAGTTTTAATATTTT
Found at i:20324880 original size:19 final size:21
Alignment explanation
Indices: 20324856--20324946 Score: 65
Period size: 18 Copynumber: 4.7 Consensus size: 21
20324846 AAAGTTTAAG
*
20324856 TATTTTAAAT-ATTTTTTAT-
1 TATTTTAAATAAATTTTTATA
*
20324875 TATTTTTAATAAATTTTTATA
1 TATTTTAAATAAATTTTTATA
*
20324896 TATTTTCAAA-AAA-ATTTATA
1 TATTTT-AAATAAATTTTTATA
*
20324916 -ACTTTAAA-AAA-TTTTA-A
1 TATTTTAAATAAATTTTTATA
*
20324933 AATTTTAAA-AAATT
1 TATTTTAAATAAATT
20324947 AACAAAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
17 1 0.02
18 20 0.33
19 14 0.23
20 14 0.23
21 9 0.15
22 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTTAAATAAATTTTTATA
Found at i:20324945 original size:18 final size:18
Alignment explanation
Indices: 20324878--20324946 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
20324868 TTTTTATTAT
* *
20324878 TTTTAATAAATTTTTATATA
1 TTTTAA-AAAATTTTA-AAA
* *
20324898 TTTTCAAAAAAATTTATAA
1 TTTT-AAAAAATTTTAAAA
*
20324917 CTTTAAAAAATTTTAAAA
1 TTTTAAAAAATTTTAAAA
20324935 TTTTAAAAAATT
1 TTTTAAAAAATT
20324947 AACAAAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 23 0.57
19 4 0.10
20 11 0.28
21 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTAAAAAATTTTAAAA
Found at i:20324957 original size:18 final size:18
Alignment explanation
Indices: 20324904--20324959 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
20324894 TATATTTTCA
* *
20324904 AAAAAATTT-ATAACTTT
1 AAAAAATTTAAAAAATTT
* *
20324921 AAAAAATTTTAAAATTTT
1 AAAAAATTTAAAAAATTT
20324939 AAAAAA-TTAACAAAATTT
1 AAAAAATTTAA-AAAATTT
20324957 AAA
1 AAA
20324960 GGAAATTACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAAATTTAAAAAATTT
Found at i:20326270 original size:14 final size:14
Alignment explanation
Indices: 20326251--20326277 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20326241 TTCTATATTC
20326251 TCAATCCTCAATTT
1 TCAATCCTCAATTT
20326265 TCAATCCTCAATT
1 TCAATCCTCAATT
20326278 ATATTTTTAA
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:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
TCAATCCTCAATTT
Found at i:20327354 original size:63 final size:63
Alignment explanation
Indices: 20327287--20327423 Score: 193
Period size: 63 Copynumber: 2.2 Consensus size: 63
20327277 CATTCCCCGT
* * * * * * *
20327287 ATCAAAACCTTCAACTCTAGTTTATTTTACCCAAGCACCATAGCATGCACAATCATTTCTTAC
1 ATCAACACCTTCAACACTAGTTTATTTTACACAAGCACCACAACATGCACAATCATTCCCTAC
* *
20327350 ATCAACACATTCAACACTAGTTTATTTTACACAAGCACCACAACATGCGCAATCATTCCCTAC
1 ATCAACACCTTCAACACTAGTTTATTTTACACAAGCACCACAACATGCACAATCATTCCCTAC
20327413 ATCAACACCTT
1 ATCAACACCTT
20327424 TAGGGATATA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.28
Consensus pattern (63 bp):
ATCAACACCTTCAACACTAGTTTATTTTACACAAGCACCACAACATGCACAATCATTCCCTAC
Found at i:20330256 original size:104 final size:104
Alignment explanation
Indices: 20330139--20330334 Score: 313
Period size: 104 Copynumber: 1.9 Consensus size: 104
20330129 GGCCAAAAAG
* *
20330139 GTATCAATATTTTTTGAATTATCGATACCCCCTCTTAAAAGCGATACCAAAA-ATGCATTTTATT
1 GTATCAATATTTTTTGAATTATCGATACCCCATCTTAAAAGCAATACCAAAATA-GCATTTTATT
*
20330203 TTTCACAAACCCTACTAAGTATCGATACCTTTTTGGTCAA
65 TTTCACAAACCCTACGAAGTATCGATACCTTTTTGGTCAA
* * *
20330243 GTATCGATATTTTTTGAATTATCGATACCCTATCTTAAAAGCAATACCAAAATAGCATTTTGTTT
1 GTATCAATATTTTTTGAATTATCGATACCCCATCTTAAAAGCAATACCAAAATAGCATTTTATTT
*
20330308 TTCTCAAACCCTACGAAGTATCGATAC
66 TTCACAAACCCTACGAAGTATCGATAC
20330335 TGTATCGATA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 83 0.99
105 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.36
Consensus pattern (104 bp):
GTATCAATATTTTTTGAATTATCGATACCCCATCTTAAAAGCAATACCAAAATAGCATTTTATTT
TTCACAAACCCTACGAAGTATCGATACCTTTTTGGTCAA
Found at i:20333282 original size:18 final size:18
Alignment explanation
Indices: 20333222--20333283 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
20333212 ATAATGTAGA
*
20333222 TGAAAAAATAATGATATT
1 TGAAATAATAATGATATT
* *
20333240 TGAAAT-ATTAT-ACATAT
1 TGAAATAATAATGATAT-T
**
20333257 AAAAATAATAATGATATT
1 TGAAATAATAATGATATT
20333275 TGAAATAAT
1 TGAAATAAT
20333284 TATTTAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
16 3 0.09
17 9 0.28
18 17 0.53
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (18 bp):
TGAAATAATAATGATATT
Found at i:20334019 original size:20 final size:20
Alignment explanation
Indices: 20333986--20334024 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20333976 TATATAAAAA
20333986 TATTTTTAGAAAAACAAAATT
1 TATTTTTAGAAAAA-AAAATT
*
20334007 TATTTTT-GTAAAAAAAAT
1 TATTTTTAGAAAAAAAAAT
20334025 ATAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TATTTTTAGAAAAAAAAATT
Found at i:20340741 original size:28 final size:26
Alignment explanation
Indices: 20340685--20340743 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
20340675 ATATTTTGGT
*
20340685 AAAATATTATTTTTAAAATTATAAAA
1 AAAATATTATTTTTAAAATAATAAAA
*
20340711 AAAATATT-TTTTGTACAAATAAATAATA
1 AAAATATTATTTT-TA-AAAT-AATAAAA
20340739 AAAAT
1 AAAAT
20340744 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.14
26 10 0.36
27 4 0.14
28 10 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATATTATTTTTAAAATAATAAAA
Found at i:20344261 original size:19 final size:20
Alignment explanation
Indices: 20344220--20344263 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
20344210 ATTTTGGAAT
* *
20344220 TTTTTTATATTTTAAAAATAG
1 TTTTTTAAATTTT-AAAAGAG
20344241 TTTTTTAAATTTT-AAAGAG
1 TTTTTTAAATTTTAAAAGAG
20344260 TTTT
1 TTTT
20344264 ATTTTTCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTTTTAAATTTTAAAAGAG
Found at i:20344500 original size:21 final size:22
Alignment explanation
Indices: 20344468--20344511 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
20344458 ATGGTATATG
20344468 TTATAAATTATTTA-TATTAAA
1 TTATAAATTATTTATTATTAAA
20344489 TTATATAA-TATTTATTATTAAA
1 TTATA-AATTATTTATTATTAAA
20344511 T
1 T
20344512 ATTTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAAATTATTTATTATTAAA
Found at i:20347254 original size:14 final size:15
Alignment explanation
Indices: 20347224--20347254 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20347214 TACTTCTACA
20347224 TTTTGATGCCACTTT
1 TTTTGATGCCACTTT
*
20347239 TTTTTATGCCACTTT
1 TTTTGATGCCACTTT
20347254 T
1 T
20347255 GATTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.10, T:0.58
Consensus pattern (15 bp):
TTTTGATGCCACTTT
Found at i:20347262 original size:61 final size:60
Alignment explanation
Indices: 20347128--20347245 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 60
20347118 AGTAGTTCTA
*
20347128 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTTGATTTATTTG
1 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTT-ATTTATATG
* *
20347189 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTGATGCCACTTTTTTTTAT
1 CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTTATTTAT
20347246 GCCACTTTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 5 0.09
61 50 0.91
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (60 bp):
CATCTGCATTATTGAACAAAATCGATACTTCTACATTTTAATGCCACTTTTATTTATATG
Found at i:20347294 original size:76 final size:76
Alignment explanation
Indices: 20347163--20347307 Score: 281
Period size: 76 Copynumber: 1.9 Consensus size: 76
20347153 TACTTCTACA
20347163 TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
1 TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
20347228 GATGCCACTTT
66 GATGCCACTTT
*
20347239 TTTTTATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
1 TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
20347304 GATG
66 GATG
20347308 TTCTTTCAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (76 bp):
TTTTAATGCCACTTTTGATTTATTTGCATCTGCATTATTGAACAAAATCGATACTTCTACATTTT
GATGCCACTTT
Found at i:20348347 original size:22 final size:21
Alignment explanation
Indices: 20348314--20348357 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
20348304 TAAATATAAG
*
20348314 TATTGTATTAACCAAATCATT
1 TATTGAATTAACCAAATCATT
20348335 TATTGAATATAACCAAATCATT
1 TATTGAAT-TAACCAAATCATT
20348357 T
1 T
20348358 TCATATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (21 bp):
TATTGAATTAACCAAATCATT
Found at i:20348650 original size:21 final size:21
Alignment explanation
Indices: 20348626--20348665 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20348616 CGTGTCAATA
20348626 TTTA-ATTACAAATATTTAATT
1 TTTATATT-CAAATATTTAATT
*
20348647 TTTATATTTAAATATTTAA
1 TTTATATTCAAATATTTAA
20348666 ATATAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATATTCAAATATTTAATT
Found at i:20348926 original size:13 final size:13
Alignment explanation
Indices: 20348908--20348934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20348898 AAACACTCAA
20348908 ATTTCTCAAAAGC
1 ATTTCTCAAAAGC
20348921 ATTTCTCAAAAGC
1 ATTTCTCAAAAGC
20348934 A
1 A
20348935 ATAAAGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ATTTCTCAAAAGC
Found at i:20354268 original size:21 final size:21
Alignment explanation
Indices: 20354228--20354270 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
20354218 CTTTTCCTAA
*
20354228 AATATGAATTAGATTGAATTG
1 AATATGAATTAGATTAAATTG
20354249 AATATGAATT-GTATTAAATTG
1 AATATGAATTAG-ATTAAATTG
20354270 A
1 A
20354271 GTTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (21 bp):
AATATGAATTAGATTAAATTG
Found at i:20354661 original size:24 final size:24
Alignment explanation
Indices: 20354634--20354685 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
20354624 GTTATATTGT
* *
20354634 TCTTACAAGTTTCTCGTTAATAGC
1 TCTTACAAGCTTCCCGTTAATAGC
***
20354658 TCTTGTGAGCTTCCCGTTAATAGC
1 TCTTACAAGCTTCCCGTTAATAGC
20354682 TCTT
1 TCTT
20354686 CGGAGCATCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (24 bp):
TCTTACAAGCTTCCCGTTAATAGC
Found at i:20354894 original size:24 final size:24
Alignment explanation
Indices: 20354867--20354927 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
20354857 GGCTTTTCGA
*
20354867 AGCTACCCGTTATTGGCTCTCATG
1 AGCTTCCCGTTATTGGCTCTCATG
*
20354891 AGCTTCCCGATTA-TGGCTCTTATG
1 AGCTTCCCG-TTATTGGCTCTCATG
20354915 AGCTTCCCGTTAT
1 AGCTTCCCGTTAT
20354928 ACAGCCCTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 3 0.09
24 27 0.82
25 3 0.09
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (24 bp):
AGCTTCCCGTTATTGGCTCTCATG
Found at i:20360436 original size:28 final size:28
Alignment explanation
Indices: 20360386--20360479 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
20360376 TGGAAGGTGG
* *
20360386 AAAAAGAAAGATAAAGGAAAGAGAAAAA
1 AAAAAGAAAGAGAAAGAAAAGAGAAAAA
*
20360414 AAAAAGAAA-AGAAAGAAAGAGAGAAAGA
1 AAAAAGAAAGAGAAAGAAA-AGAGAAAAA
** *
20360442 CTAAGGAAAGAGGAAAGGAAAAGGAGGAAAAA
1 AAAAAGAAAGA-GAAA-GAAAA-GA-GAAAAA
20360474 AAAAAG
1 AAAAAG
20360480 GAATGATAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
27 7 0.14
28 23 0.46
29 1 0.02
30 5 0.10
31 6 0.12
32 8 0.16
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.02
Consensus pattern (28 bp):
AAAAAGAAAGAGAAAGAAAAGAGAAAAA
Found at i:20360438 original size:17 final size:16
Alignment explanation
Indices: 20360387--20360439 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
20360377 GGAAGGTGGA
20360387 AAAAGAAAGATAAAG-G
1 AAAAGAAAGA-AAAGAG
* *
20360403 AAAGAGAAAAAAAAAAG
1 AAA-AGAAAGAAAAGAG
20360420 AAAAGAAAGAAAGAGAG
1 AAAAGAAAGAAA-AGAG
20360437 AAA
1 AAA
20360440 GACTAAGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAG
Found at i:20390117 original size:87 final size:86
Alignment explanation
Indices: 20389969--20390128 Score: 232
Period size: 87 Copynumber: 1.8 Consensus size: 86
20389959 TTTTCTTCTG
* * * *
20389969 CACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTTCTTCAAAAAAAG
1 CACTCAATTGAGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAATTCTTC-AAAAAAG
20390034 CAATTAAGCTCATACTTTTTTT
65 CAATTAAGCTCATACTTTTTTT
* * *
20390056 CACTCGATTGGGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAATGT-TTTAAAAAAG
1 CACTCAATTGAGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAAT-TCTTCAAAAAAG
20390120 CAATTAAGC
65 CAATTAAGC
20390129 CCCTGCTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 16 0.25
87 48 0.74
88 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (86 bp):
CACTCAATTGAGTACTTGAACATTCAAAATGCATCAAAAAGACCCTAAAAATTCTTCAAAAAAGC
AATTAAGCTCATACTTTTTTT
Found at i:20390183 original size:18 final size:19
Alignment explanation
Indices: 20390162--20390197 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
20390152 AAAAGATAAA
20390162 AAAAATTATT-AATTTTAG
1 AAAAATTATTGAATTTTAG
20390180 AAAAATTATTGAATTTTA
1 AAAAATTATTGAATTTTA
20390198 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
AAAAATTATTGAATTTTAG
Found at i:20390183 original size:19 final size:20
Alignment explanation
Indices: 20390161--20390211 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
20390151 GAAAAGATAA
20390161 AAAAAATTATTAATTTT-AG
1 AAAAAATTATTAATTTTAAG
*
20390180 -AAAAATTATTGAATTTTAAT
1 AAAAAATTATT-AATTTTAAG
20390200 AAAAAATT-TTAA
1 AAAAAATTATTAA
20390212 AGTTTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
19 8 0.29
20 3 0.11
21 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAAAATTATTAATTTTAAG
Found at i:20390217 original size:20 final size:21
Alignment explanation
Indices: 20390161--20390224 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
20390151 GAAAAGATAA
20390161 AAAAAATTATT-AA-TTT--T
1 AAAAAATTATTAAAGTTTAAT
* *
20390178 AGAAAAATTATTGAATTTTAAT
1 A-AAAAATTATTAAAGTTTAAT
*
20390200 AAAAAATT-TTAAAGTTTATT
1 AAAAAATTATTAAAGTTTAAT
20390220 AAAAA
1 AAAAA
20390225 TTAGAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.03
18 10 0.26
19 2 0.05
20 17 0.44
21 7 0.18
22 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AAAAAATTATTAAAGTTTAAT
Found at i:20390239 original size:21 final size:20
Alignment explanation
Indices: 20390219--20390259 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
20390209 TAAAGTTTAT
20390219 TAAAAAT-TAGAAAAAAATTA
1 TAAAAATATA-AAAAAAATTA
20390239 TAAAAATCATAAAAAAAATTA
1 TAAAAAT-ATAAAAAAAATTA
20390260 ACGACCCGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 10 0.53
22 2 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAAAATATAAAAAAAATTA
Found at i:20390483 original size:19 final size:18
Alignment explanation
Indices: 20390414--20390503 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 18
20390404 TTATACCAAA
20390414 TTTATATTTATTTAC-ATT
1 TTTATATTT-TTTACAATT
*
20390432 TTGTATAATTTTCTTACAA-C
1 TT-TAT-ATTTT-TTACAATT
**
20390452 TTTATAAAATTTTACAATT
1 TTTAT-ATTTTTTACAATT
20390471 TTTATACTTTTTT-CTAATT
1 TTTATA-TTTTTTAC-AATT
20390490 TTTAATATTTTTTA
1 TTT-ATATTTTTTA
20390504 TTAAAATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
18 10 0.18
19 33 0.58
20 13 0.23
21 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTATATTTTTTACAATT
Found at i:20390540 original size:49 final size:46
Alignment explanation
Indices: 20390452--20390552 Score: 107
Period size: 49 Copynumber: 2.2 Consensus size: 46
20390442 TTCTTACAAC
* * *
20390452 TTTATAAAATTTTACAATTTTTATACTTTTTTCTAATTTTTAATATTT
1 TTTATAAAATTTAACAATATTTATACTTTTATCTAA-TTTTAAT-TTT
* *
20390500 TTTATTAAAATTTAATAATATTTATAGCTTTTAT-TGATTTTAA-TTT
1 TTTA-TAAAATTTAACAATATTTATA-CTTTTATCTAATTTTAATTTT
20390546 TTTATAA
1 TTTATAA
20390553 TTTTTTTCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
45 3 0.07
46 7 0.15
48 10 0.22
49 20 0.43
50 6 0.13
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (46 bp):
TTTATAAAATTTAACAATATTTATACTTTTATCTAATTTTAATTTT
Found at i:20396478 original size:39 final size:39
Alignment explanation
Indices: 20396415--20396525 Score: 134
Period size: 38 Copynumber: 2.8 Consensus size: 39
20396405 TTTAAAATAT
* * *
20396415 ATATTTAAGATGTCCTAAACTATGACATAATTAAAAACCC
1 ATATTAAAGATGTTC-AAATTATGACATAATTAAAAACCC
* * *
20396455 TTATTAAAGATGTTCAGATTATGACATAATT-AAAACTC
1 ATATTAAAGATGTTCAAATTATGACATAATTAAAAACCC
* *
20396493 ATATTAATGATGTTTAAATTATGACATAATTAA
1 ATATTAAAGATGTTCAAATTATGACATAATTAA
20396526 GTACTTAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
38 33 0.55
39 15 0.25
40 12 0.20
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (39 bp):
ATATTAAAGATGTTCAAATTATGACATAATTAAAAACCC
Found at i:20399298 original size:19 final size:19
Alignment explanation
Indices: 20399274--20399310 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20399264 TCAACTACTT
20399274 GCCTTTGAAGTTTCTTAGA
1 GCCTTTGAAGTTTCTTAGA
20399293 GCCTTTGAAGTTTCTTAG
1 GCCTTTGAAGTTTCTTAG
20399311 TTTCTTCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (19 bp):
GCCTTTGAAGTTTCTTAGA
Found at i:20400401 original size:38 final size:38
Alignment explanation
Indices: 20400333--20400440 Score: 128
Period size: 38 Copynumber: 2.8 Consensus size: 38
20400323 AAGATATCCT
*
20400333 AAATTATGACATAATTAAAAACCCT-TATTAAAGAAGTTC
1 AAATTATGACATAATT-AAAA-CTTATATTAAAGAAGTTC
* * * *
20400372 AGATTATGACATAATTAAAACTTATATTAATGATGTTT
1 AAATTATGACATAATTAAAACTTATATTAAAGAAGTTC
*
20400410 AAATTATGACATAATTAAAGACTTAAATTAA
1 AAATTATGACATAATTAAA-ACTTATATTAA
20400441 TTTAACTAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
37 2 0.03
38 33 0.55
39 25 0.42
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (38 bp):
AAATTATGACATAATTAAAACTTATATTAAAGAAGTTC
Found at i:20400451 original size:38 final size:38
Alignment explanation
Indices: 20400374--20400451 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
20400364 AGAAGTTCAG
* ***
20400374 ATTATGACATAATTAAAACTTATATTAATGATGTTTAA
1 ATTATGACATAATTAAAACTTAAATTAATGATAACTAA
*
20400412 ATTATGACATAATTAAAGACTTAAATTAAT-TTAACTAA
1 ATTATGACATAATTAAA-ACTTAAATTAATGATAACTAA
20400450 AT
1 AT
20400452 AATTAGAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 23 0.68
39 11 0.32
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (38 bp):
ATTATGACATAATTAAAACTTAAATTAATGATAACTAA
Found at i:20402964 original size:9 final size:9
Alignment explanation
Indices: 20402935--20403005 Score: 54
Period size: 10 Copynumber: 7.4 Consensus size: 9
20402925 ATTTTATCTT
20402935 TTTTTATAAA
1 TTTTTAT-AA
*
20402945 TTTCCTATAA
1 TTT-TTATAA
20402955 TTTTTATAA
1 TTTTTATAA
20402964 TATTTTATATA
1 T-TTTTATA-A
* *
20402975 TTGTTATAT
1 TTTTTATAA
20402984 TTATTTATAA
1 TT-TTTATAA
*
20402994 TTTCTAT-A
1 TTTTTATAA
20403002 TTTT
1 TTTT
20403006 ATGTATTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 4 0.08
9 12 0.24
10 28 0.57
11 5 0.10
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:20402981 original size:20 final size:20
Alignment explanation
Indices: 20402913--20402982 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
20402903 TGGTTTTTTA
* *
20402913 ATTTTTAAATATATTTTATCT
1 ATTTTTATA-ATATTTTATAT
*
20402934 TTTTTTATAA-ATTTCCTATA-
1 ATTTTTATAATATTT--TATAT
20402954 ATTTTTATAATATTTTATAT
1 ATTTTTATAATATTTTATAT
*
20402974 ATTGTTATA
1 ATTTTTATA
20402983 TTTATTTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 8 0.20
20 18 0.45
21 14 0.35
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (20 bp):
ATTTTTATAATATTTTATAT
Found at i:20402983 original size:10 final size:9
Alignment explanation
Indices: 20402956--20403014 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
20402946 TTCCTATAAT
20402956 TTTTATAATA
1 TTTTAT-ATA
20402966 TTTTATATA
1 TTTTATATA
20402975 TTGTTATAT-
1 TT-TTATATA
20402984 TTATT-TATA
1 TT-TTATATA
* *
20402993 ATTTCTATA
1 TTTTATATA
*
20403002 TTTTATGTA
1 TTTTATATA
20403011 TTTT
1 TTTT
20403015 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 5 0.12
9 24 0.59
10 12 0.29
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATATA
Found at i:20403485 original size:9 final size:9
Alignment explanation
Indices: 20403456--20403500 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
20403446 GGTTTTTGGA
20403456 TTTTAGGG-
1 TTTTAGGGT
20403464 -TTTAGGG-
1 TTTTAGGGT
20403471 TTTTAGGGT
1 TTTTAGGGT
*
20403480 TTTTAGGAT
1 TTTTAGGGT
*
20403489 TTTTAAGGT
1 TTTTAGGGT
20403498 TTT
1 TTT
20403501 GGAGAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 7 0.22
8 7 0.22
9 18 0.56
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.56
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:20411226 original size:27 final size:27
Alignment explanation
Indices: 20411188--20411241 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
20411178 TCATGAGAAA
20411188 ATGAAAGGGTCAAGTCGAGGCACCGTG
1 ATGAAAGGGTCAAGTCGAGGCACCGTG
20411215 ATGAAAGGGTCAAGTCGAGGCACCGTG
1 ATGAAAGGGTCAAGTCGAGGCACCGTG
20411242 GATAGGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.37, T:0.15
Consensus pattern (27 bp):
ATGAAAGGGTCAAGTCGAGGCACCGTG
Found at i:20427427 original size:3 final size:3
Alignment explanation
Indices: 20427407--20427479 Score: 119
Period size: 3 Copynumber: 24.0 Consensus size: 3
20427397 ATTCACCAAG
* *
20427407 ATA ATA ACA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20427455 ATA ATA ATA ATA ATA ATA ATCA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA
20427480 TATCATATGT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20427667 original size:17 final size:17
Alignment explanation
Indices: 20427619--20427668 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
20427609 TTAACATAGG
*
20427619 TAATACATATAAAATAA
1 TAATACATATATAATAA
*
20427636 -AA-ACATA-ATAGTAA
1 TAATACATATATAATAA
*
20427650 TAATACATATATACTAA
1 TAATACATATATAATAA
20427667 TA
1 TA
20427669 TATATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 7 0.26
17 8 0.30
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (17 bp):
TAATACATATATAATAA
Found at i:20428132 original size:45 final size:45
Alignment explanation
Indices: 20428062--20428198 Score: 147
Period size: 45 Copynumber: 3.0 Consensus size: 45
20428052 TAAATAGTAC
* * *
20428062 ATAATGAATTTAAAATATTGATATATGTTAAAT-TTAAATAATATTA
1 ATAATAAATTTAAAATAATG-TATA-GTTAAATATTAAATAATACTA
20428108 ATAAT-AATTTAAAATAATAGTATA-TTAAATATTAAAATAATACTA
1 ATAATAAATTTAAAATAAT-GTATAGTTAAATATT-AAATAATACTA
* *
20428153 ATGATAAATTTAAAACAATGT-TAAGCTTAAATATTAAATAATACTA
1 ATAATAAATTTAAAATAATGTAT-AG-TTAAATATTAAATAATACTA
20428199 TTTGTCAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
43 6 0.08
44 3 0.04
45 33 0.41
46 29 0.36
47 9 0.11
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (45 bp):
ATAATAAATTTAAAATAATGTATAGTTAAATATTAAATAATACTA
Found at i:20428165 original size:23 final size:22
Alignment explanation
Indices: 20428068--20428167 Score: 82
Period size: 23 Copynumber: 4.4 Consensus size: 22
20428058 GTACATAATG
* *
20428068 AATTTAAAATATTGATATATGTTA
1 AATTTAAAATAAT-ATA-ATGATA
*
20428092 AATTT-AAATAATATTAATAAT-
1 AATTTAAAATAATA-TAATGATA
20428113 AATTTAAAATAATAGT-AT-ATTA
1 AATTTAAAATAATA-TAATGA-TA
20428135 AATATTAAAATAATACTAATGATA
1 AAT-TTAAAATAATA-TAATGATA
20428159 AATTTAAAA
1 AATTTAAAA
20428168 CAATGTTAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.02
21 8 0.12
22 16 0.25
23 26 0.41
24 12 0.19
25 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTTAAAATAATATAATGATA
Found at i:20428192 original size:46 final size:44
Alignment explanation
Indices: 20428089--20428198 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 44
20428079 TTGATATATG
* *
20428089 TTAAAT-TTAAATAATATTAATAATAATTTAAAATAATAGTATA
1 TTAAATATTAAATAATACTAATAATAATTTAAAACAATAGTATA
*
20428132 TTAAATATTAAAATAATACTAATGATAAATTTAAAACAAT-GT-TAA
1 TTAAATATT-AAATAATACTAATAAT-AATTTAAAACAATAGTAT-A
20428177 GCTTAAATATTAAATAATACTA
1 --TTAAATATTAAATAATACTA
20428199 TTTGTCAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
43 6 0.10
44 3 0.05
45 17 0.29
46 23 0.40
47 9 0.16
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (44 bp):
TTAAATATTAAATAATACTAATAATAATTTAAAACAATAGTATA
Found at i:20441469 original size:23 final size:23
Alignment explanation
Indices: 20441441--20441488 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
20441431 CTTTTATTCA
20441441 AGTTTTAGTTTGCAACTTTATTT
1 AGTTTTAGTTTGCAACTTTATTT
* * *
20441464 AGTTTTAGTTTTCAATTTTCTTT
1 AGTTTTAGTTTGCAACTTTATTT
20441487 AG
1 AG
20441489 GTTATTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.58
Consensus pattern (23 bp):
AGTTTTAGTTTGCAACTTTATTT
Found at i:20442528 original size:187 final size:187
Alignment explanation
Indices: 20442213--20442585 Score: 728
Period size: 187 Copynumber: 2.0 Consensus size: 187
20442203 CCATTGGGCA
20442213 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
1 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
20442278 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAGAGGCGG
66 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAGAGGCGG
*
20442343 TCACTTACTGGATTCTTTACTTTCCAGACTTGAGTCTTACATTTACCTCCTTATGCT
131 TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTCTTACATTTACCTCCTTATGCT
*
20442400 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACTCGTATACTTGC
1 CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
20442465 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAGAGGCGG
66 GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAGAGGCGG
20442530 TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTCTTACATTTACCTCCTTATGC
131 TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTCTTACATTTACCTCCTTATGC
20442586 AAAGTGTAAC
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 184 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (187 bp):
CGATTCTCAGATTACTTCCATACTTCATTGTATAAACTATATTACAACTTGACCCGTATACTTGC
GAAAACTGCCTAACAATATTTGGTTGCAATATTCACACTCTAGACATTAGTACGTCAAGAGGCGG
TCACTTACTGGATTCTTTACTGTCCAGACTTGAGTCTTACATTTACCTCCTTATGCT
Found at i:20442807 original size:12 final size:12
Alignment explanation
Indices: 20442790--20442828 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
20442780 AGGTACTCAG
20442790 AAAATTTTTCAC
1 AAAATTTTTCAC
20442802 AAAA--TTT--C
1 AAAATTTTTCAC
20442810 AAAATTTTTCAC
1 AAAATTTTTCAC
20442822 AAAATTT
1 AAAATTT
20442829 CAAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 5 0.22
10 6 0.26
12 12 0.52
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTTTTCAC
Found at i:20442815 original size:20 final size:20
Alignment explanation
Indices: 20442790--20442839 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
20442780 AGGTACTCAG
20442790 AAAATTTTTCACAAAATTTC
1 AAAATTTTTCACAAAATTTC
20442810 AAAATTTTTCACAAAATTTC
1 AAAATTTTTCACAAAATTTC
20442830 AAAATTTTTC
1 AAAATTTTTC
20442840 CAATGTGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTTTTCACAAAATTTC
Found at i:20442819 original size:10 final size:10
Alignment explanation
Indices: 20442790--20442839 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
20442780 AGGTACTCAG
20442790 AAAATTTTTC
1 AAAATTTTTC
*
20442800 ACAAA-ATTTC
1 A-AAATTTTTC
20442810 AAAATTTTTC
1 AAAATTTTTC
*
20442820 ACAAA-ATTTC
1 A-AAATTTTTC
20442830 AAAATTTTTC
1 AAAATTTTTC
20442840 CAATGTGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 6 0.19
10 20 0.62
11 6 0.19
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAATTTTTC
Found at i:20444045 original size:13 final size:13
Alignment explanation
Indices: 20444027--20444052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20444017 AGAACATTGC
20444027 TCGTTGAATCTTT
1 TCGTTGAATCTTT
20444040 TCGTTGAATCTTT
1 TCGTTGAATCTTT
20444053 CATAATATCG
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:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TCGTTGAATCTTT
Found at i:20444198 original size:25 final size:24
Alignment explanation
Indices: 20444170--20444226 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
20444160 CATAAATGGA
**
20444170 AAGCTCATGTGAGCCATGTAACGGG
1 AAGCTCATGAAAGCCAT-TAACGGG
** *
20444195 AAGCTTTTGAAAGCCATTAATGGG
1 AAGCTCATGAAAGCCATTAACGGG
20444219 AAGCTCAT
1 AAGCTCAT
20444227 ACGAGCCAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (24 bp):
AAGCTCATGAAAGCCATTAACGGG
Found at i:20444243 original size:24 final size:24
Alignment explanation
Indices: 20444216--20444270 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
20444206 AGCCATTAAT
20444216 GGGAAGCTCATA-CGAGCCAATATC
1 GGGAAGCTCA-AGCGAGCCAATATC
*
20444240 GGGAAGGTTCAAGCGAGCCAATATC
1 GGGAA-GCTCAAGCGAGCCAATATC
20444265 GGGAAG
1 GGGAAG
20444271 TTCCGGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.15
Consensus pattern (24 bp):
GGGAAGCTCAAGCGAGCCAATATC
Found at i:20444281 original size:24 final size:25
Alignment explanation
Indices: 20444229--20444285 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
20444219 AAGCTCATAC
*
20444229 GAGCCAATATCGGGAAGGTTCAAGC
1 GAGCCAATATCGGGAAGGTTCAAGA
**
20444254 GAGCCAATATCGGGAA-GTTCCGGA
1 GAGCCAATATCGGGAAGGTTCAAGA
20444278 GAGCCAAT
1 GAGCCAAT
20444286 TAATTAGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.32, C:0.21, G:0.32, T:0.16
Consensus pattern (25 bp):
GAGCCAATATCGGGAAGGTTCAAGA
Found at i:20451292 original size:262 final size:262
Alignment explanation
Indices: 20450827--20451615 Score: 1542
Period size: 262 Copynumber: 3.0 Consensus size: 262
20450817 AAGCTTCTCC
20450827 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
1 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
* *
20450892 CTCAGTTATGTTAAGAAAGTTATAAATGCAGAAAAAACAATAACAGTTGTGTTGTAATGTTCTTT
66 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATATCAGTTGTGTTGTAATGTTCTTT
20450957 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
131 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
20451022 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
196 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
20451087 GA
261 GA
20451089 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
1 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
20451154 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATATCAGTTGTGTTGTAATGTTCTTT
66 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATATCAGTTGTGTTGTAATGTTCTTT
20451219 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
131 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
20451284 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
196 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
20451349 GA
261 GA
20451351 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
1 ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
20451416 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATATCAGTTGTGTTGTAATGTTCTTT
66 CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATATCAGTTGTGTTGTAATGTTCTTT
*
20451481 ATGTTGCCACTGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
131 ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
*
20451546 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAGTGAAAAACTGATAAAGTAATCT
196 AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
20451611 GA
261 GA
20451613 ATA
1 ATA
20451616 GAACATACTC
Statistics
Matches: 523, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
262 523 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (262 bp):
ATATTACACATCAATCTGCATAACAAGCAATTATACCTTCAAACTACATAGTTATTTCTCCAAAC
CTCAGTTATGGTAAGAAAGTTATAAATGCAGAAAAAACAATATCAGTTGTGTTGTAATGTTCTTT
ATGTTGCCACCGAAACAACATTACCTGTGTACCCTTTGATCTTGCTGTTTTATGAATGTTATTTA
AATCAAATAGAACATACTTCTTCTGTCAATTAGTAGAATGCAATGAAAAACTGATAAAGTAATCT
GA
Found at i:20455541 original size:20 final size:20
Alignment explanation
Indices: 20455516--20455561 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
20455506 AACAAATAAG
*
20455516 GGCACCGAAGTGCAATTAGA
1 GGCACCGAAGTGCAATCAGA
* *
20455536 GGCACCGGAGTGCAATCAGT
1 GGCACCGAAGTGCAATCAGA
20455556 GGCACC
1 GGCACC
20455562 TTTCTTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.33, T:0.13
Consensus pattern (20 bp):
GGCACCGAAGTGCAATCAGA
Found at i:20458695 original size:45 final size:44
Alignment explanation
Indices: 20458617--20458721 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 44
20458607 TATTTCTCAT
** * *
20458617 TTTCA-TT-TCCATTTCGAGAAAACCACATTCATTTCCACATGA
1 TTTCATTTCTCCATTTCGAGAAAACCACAACCATTTACAAATGA
* * *
20458659 TTTCATTTCTCCATTTCGGAGAAAACCATAACCATTTATAAATGT
1 TTTCATTTCTCCATTTC-GAGAAAACCACAACCATTTACAAATGA
20458704 TTTCTATTTCTCCATTTC
1 TTTC-ATTTCTCCATTTC
20458722 CATTCATTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 5 0.10
43 2 0.04
44 8 0.15
45 24 0.46
46 13 0.25
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.41
Consensus pattern (44 bp):
TTTCATTTCTCCATTTCGAGAAAACCACAACCATTTACAAATGA
Found at i:20463250 original size:25 final size:24
Alignment explanation
Indices: 20463213--20463259 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
20463203 ATTTATCATT
*
20463213 AAAAACTTCAAACATTATCAATGA
1 AAAAACTTCAAACATTAACAATGA
* *
20463237 AAAAATTTCAAAACTTTAACAAT
1 AAAAACTTC-AAACATTAACAAT
20463260 TTCGTGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAACTTCAAACATTAACAATGA
Found at i:20478196 original size:23 final size:22
Alignment explanation
Indices: 20478164--20478225 Score: 97
Period size: 22 Copynumber: 2.7 Consensus size: 22
20478154 CCCGGATCAT
20478164 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAATTA-A
20478188 TTTTTATTAAAATTAAAATTAA
1 TTTTTATTAAAATTAAAATTAA
*
20478210 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
20478226 TTGTTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
22 16 0.43
23 16 0.43
24 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAATTAA
Found at i:20478220 original size:16 final size:16
Alignment explanation
Indices: 20478199--20478239 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
20478189 TTTTATTAAA
20478199 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
20478215 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
20478231 ATTAAAATT
1 ATTAAAATT
20478240 GTATCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:20487456 original size:76 final size:74
Alignment explanation
Indices: 20487341--20487596 Score: 245
Period size: 75 Copynumber: 3.4 Consensus size: 74
20487331 ATTTTGCATC
* * *
20487341 AATA-ATACTTATTTACAATCTACAAAATAAAATTTAAAAATTGTTTGTATTGTATTATATTTAT
1 AATATATACTTATTTACAATCTAC-AAA-AAAATTAAAAAATTGTTTGTATTGTATTCTATGTAT
20487405 TTTATATCAAT
64 TTTATATCAAT
* ** *
20487416 AATATATACTTATTTACAATCTATAAAAAAAGTTAAAAAAAGGCTTGTATTGTATTCTATCGTAT
1 AATATATACTTATTTACAATCTACAAAAAAA-TTAAAAAATTGTTTGTATTGTATTCTAT-GTAT
*
20487481 GTCTTCT-T-AAT
64 -T-TTATATCAAT
* * * *
20487492 -A-ATATACTTATTTACAACCTACGAAAAAAA-TAAAAAATTGTTTATATTATATTCTACCGTAT
1 AATATATACTTATTTACAATCTAC-AAAAAAATTAAAAAATTGTTTGTATTGTATTCTA-TGTAT
*
20487554 TTTACATCAAT
64 TTTATATCAAT
* * * *
20487565 AATATATACTTACTAACAATTTACCAAAAAAT
1 AATATATACTTATTTACAATCTACAAAAAAAT
20487597 GAGAAGCAAT
Statistics
Matches: 146, Mismatches: 23, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
71 2 0.01
72 2 0.01
73 28 0.19
74 30 0.21
75 55 0.38
76 24 0.16
77 2 0.01
78 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (74 bp):
AATATATACTTATTTACAATCTACAAAAAAATTAAAAAATTGTTTGTATTGTATTCTATGTATTT
TATATCAAT
Found at i:20487566 original size:73 final size:73
Alignment explanation
Indices: 20487329--20487570 Score: 242
Period size: 73 Copynumber: 3.3 Consensus size: 73
20487319 TTTCTCTATT
* *
20487329 GTATTTTGCATCAAT-A-ATACTTATTTACAATCTACAAAATAAAATTTAAAAATTGTTTGTATT
1 GTATTTTACATCAATAATATACTTATTTACAATCTACAAAA-AAAATTAAAAAATTGTTTGTATT
* *
20487392 GTATTATAT
65 GTATTCTAC
* * * * ** *
20487401 TTATTTTATATCAATAATATATACTTATTTACAATCTATAAAAAAAGTTAAAAAAAGGCTTGTAT
1 GTATTTTACATCAAT-A-ATATACTTATTTACAATCTACAAAAAAAATTAAAAAATTGTTTGTAT
20487466 TGTATTCTATC
64 TGTATTCTA-C
* * * *
20487477 GTATGTCTT-C-TTAATAATATACTTATTTACAACCTACGAAAAAAA-TAAAAAATTGTTTATAT
1 GTAT-T-TTACATCAATAATATACTTATTTACAATCTACAAAAAAAATTAAAAAATTGTTTGTAT
*
20487539 TATATTCTACC
64 TGTATTCTA-C
20487550 GTATTTTACATCAATAATATA
1 GTATTTTACATCAATAATATA
20487571 TACTTACTAA
Statistics
Matches: 136, Mismatches: 25, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
71 2 0.01
72 14 0.10
73 36 0.26
74 25 0.18
75 27 0.20
76 29 0.21
77 1 0.01
78 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.42
Consensus pattern (73 bp):
GTATTTTACATCAATAATATACTTATTTACAATCTACAAAAAAAATTAAAAAATTGTTTGTATTG
TATTCTAC
Found at i:20488842 original size:28 final size:29
Alignment explanation
Indices: 20488810--20488864 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
20488800 CCCTTATTCA
20488810 TTGAATGGTAA-AC-CATTCTTTTGTTTGG
1 TTGAA-GGTAATACTCATTCTTTTGTTTGG
*
20488838 TTGAAGGTAATACTTATTCTTTTGTTT
1 TTGAAGGTAATACTCATTCTTTTGTTT
20488865 CATTTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 7 0.29
29 12 0.50
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (29 bp):
TTGAAGGTAATACTCATTCTTTTGTTTGG
Found at i:20489008 original size:17 final size:17
Alignment explanation
Indices: 20488988--20489041 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
20488978 GAAATATTTT
20488988 AATATAATTTAATAT-A
1 AATATAATTTAATATAA
*
20489004 AA-AT-ATTTAATTTTAA
1 AATATAATTTAA-TATAA
* *
20489020 AATATAATTCAAAATAA
1 AATATAATTTAATATAA
20489037 AATAT
1 AATAT
20489042 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.20
15 4 0.13
16 5 0.17
17 10 0.33
18 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAATTTAATATAA
Found at i:20489008 original size:25 final size:25
Alignment explanation
Indices: 20488979--20489063 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 25
20488969 AAAATATTTG
20488979 AAATATTTTAATATAATTTAATATAA
1 AAATATTTTAATATAATTTAATAT-A
* *
20489005 AATATTTAATTTTAAAATATAATTCAAAATA
1 AA-A--T-ATTTT--AATATAATTTAATATA
* *
20489036 AAATATTTTAAAATAATTTGATATA
1 AAATATTTTAATATAATTTAATATA
20489061 AAA
1 AAA
20489064 CTAAAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
25 15 0.32
26 2 0.04
27 6 0.13
28 1 0.02
29 1 0.02
30 6 0.13
31 3 0.06
32 13 0.28
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (25 bp):
AAATATTTTAATATAATTTAATATA
Found at i:20489022 original size:15 final size:15
Alignment explanation
Indices: 20488983--20489024 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
20488973 TATTTGAAAT
*
20488983 ATTTTAATATAATTTA
1 ATTTTAAAAT-ATTTA
*
20488999 A-TATAAAATATTTA
1 ATTTTAAAATATTTA
20489013 ATTTTAAAATAT
1 ATTTTAAAATAT
20489025 AATTCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.27
15 15 0.68
16 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTAAAATATTTA
Found at i:20489037 original size:32 final size:33
Alignment explanation
Indices: 20488964--20489043 Score: 101
Period size: 32 Copynumber: 2.4 Consensus size: 33
20488954 AGAAAATATA
* *
20488964 AAAATAAAATATTTGAAATATTTTAATATAATTT
1 AAAATAAAATATTT-AAATATTTAAATATAATTC
*
20488998 AATATAAAATATTT-AAT-TTTAAAATATAATTC
1 AAAATAAAATATTTAAATATTT-AAATATAATTC
20489030 AAAATAAAATATTT
1 AAAATAAAATATTT
20489044 TAAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.07
32 25 0.61
34 13 0.32
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
AAAATAAAATATTTAAATATTTAAATATAATTC
Found at i:20489163 original size:21 final size:22
Alignment explanation
Indices: 20489099--20489164 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
20489089 ATATAACAAT
20489099 AATTATATTAAAA-ATGTTATTA
1 AATTATATTAAAATATG-TATTA
** * *
20489121 AATTATA-TATTATTTTTATTA
1 AATTATATTAAAATATGTATTA
20489142 AATTATATTAAAATATGT-TTA
1 AATTATATTAAAATATGTATTA
20489163 AA
1 AA
20489165 GTATTTATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
AATTATATTAAAATATGTATTA
Found at i:20489184 original size:44 final size:43
Alignment explanation
Indices: 20489099--20489191 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 43
20489089 ATATAACAAT
*
20489099 AATTATATTAAAAATGTTATTAAATTATATATTATTTTTATTA
1 AATTATATTAAAAATGTTATTAAAGTATATATTATTTTTATTA
* *
20489142 AATTATATTAAAATATG-T-TTAAAGTATTTATTTTTATTTTATTA
1 AATTATATTAAAA-ATGTTATTAAAGTATATA-TTAT-TTTTATTA
20489186 AATTAT
1 AATTAT
20489192 TTTTAATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
42 10 0.23
43 17 0.39
44 17 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (43 bp):
AATTATATTAAAAATGTTATTAAAGTATATATTATTTTTATTA
Found at i:20490324 original size:40 final size:39
Alignment explanation
Indices: 20490275--20490363 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 39
20490265 TCCACGTCAG
* * *
20490275 CGCGCTTTGCTG-ACGTGCACAGAAATCGCGCTGACGTGGA
1 CGCGATTTGCTGAACGTGC-C-CAAAGCGCGCTGACGTGGA
* *
20490315 CGCGATTTGCTGACACGTTCCCAAAGCGCGCTGACGTGTA
1 CGCGATTTGCTGA-ACGTGCCCAAAGCGCGCTGACGTGGA
20490355 CGCGATTTG
1 CGCGATTTG
20490364 TTGCCACGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 36 0.86
41 1 0.02
42 5 0.12
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.22
Consensus pattern (39 bp):
CGCGATTTGCTGAACGTGCCCAAAGCGCGCTGACGTGGA
Found at i:20490827 original size:249 final size:251
Alignment explanation
Indices: 20490386--20490934 Score: 904
Period size: 249 Copynumber: 2.2 Consensus size: 251
20490376 GCGCCCCTGG
* * * *
20490386 GGATGCTTTATGAGAGGAATTTGTGAAATCTCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCATTTGCTACAGTAGGTC
* *
20490451 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCACATAGTATAAAAAAACGCTTCAAGCAGGA
66 CTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTAT-AAAAAACGCTTCAAGCAGGA
* * * *
20490516 TGCTTTATGATAAGCATTTGTGAAATCGCACCCTCGTGTACGCGCTTTTGCTATAGTAGGTCCTG
130 TGCTTTATGAGAAGAATTTATGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTG
20490581 GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
195 GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
*
20490638 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCTCATTTGCTACAGTAGGT-
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCATTTGCTACAGTAGGTC
*
20490702 CTTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAGGAT
66 CTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGAT
*
20490766 GCTTTATGAGAAGAATTTATGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGG
131 GCTTTATGAGAAGAATTTATGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGG
20490831 AAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
196 AAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
* * * * * *
20490887 TGATACTTTATCAAAAGAATTTGTGAAATCGCGCCCACGTCGACGCGC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGC
20490935 TTTTTTTATA
Statistics
Matches: 277, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
249 177 0.64
251 41 0.15
252 59 0.21
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (251 bp):
GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCATTTGCTACAGTAGGTC
CTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGAT
GCTTTATGAGAAGAATTTATGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGG
AAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
Found at i:20490945 original size:125 final size:125
Alignment explanation
Indices: 20490386--20490948 Score: 894
Period size: 125 Copynumber: 4.5 Consensus size: 125
20490376 GCGCCCCTGG
* * * *
20490386 GGATGCTTTATGAGAGGAATTTGTGAAATCTCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
*
20490451 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCACATAGTATAAAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAAACGCTTCAAGCA
* * * *
20490513 GGATGCTTTATGATAAGCATTTGTGAAATCGCACCCTCGTGTACGCGCTTTTGCTATAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
20490578 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
* * *
20490638 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCTCATTTGCTACAGTAGGT-
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
* *
20490702 CTTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
*
20490762 GGATGCTTTATGAGAAGAATTTATGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
20490827 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
66 CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
* * * * * * **
20490887 TGATACTTTATCAAAAGAATTTGTGAAATCGCGCCCACGTCGACGCGCTTTTTTTATAGTAG
1 GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAG
20490949 CATGTTTGGG
Statistics
Matches: 402, Mismatches: 33, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
124 118 0.29
125 184 0.46
127 100 0.25
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (125 bp):
GGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTC
CTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCA
Found at i:20494069 original size:21 final size:21
Alignment explanation
Indices: 20494044--20494184 Score: 96
Period size: 22 Copynumber: 6.6 Consensus size: 21
20494034 GTCAAGGGTT
20494044 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
* *
20494065 AGGGTTAGGG--TTTAGGGTTT
1 AGGGTTAGGGTTTTTA-AGTTA
* * *
20494085 AGTGTTAGGGGTTTTAGGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
20494106 TGGGGTT----TTTAAGTTAAGTTA
1 -AGGGTTAGGGTTT---TTAAGTTA
20494127 AGGGTTTAGGGTTTTTAAGTTA
1 AGGG-TTAGGGTTTTTAAGTTA
* *
20494149 AGGGTTTAGGGGTTCTAAGTTA
1 AGGG-TTAGGGTTTTTAAGTTA
20494171 AGGGTTTAGGGTTT
1 AGGG-TTAGGGTTT
20494185 GTCAATTAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 15 0.16
21 23 0.24
22 49 0.51
25 3 0.03
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.43
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:20494075 original size:27 final size:28
Alignment explanation
Indices: 20494039--20494159 Score: 119
Period size: 27 Copynumber: 4.3 Consensus size: 28
20494029 TACCAGTCAA
20494039 GGGTTAGGG-TTAGGGTTTTTAAGTTAA
1 GGGTTAGGGTTTAGGGTTTTTAAGTTAA
* *
20494066 GGGTTAGGGTTTAGGG--TTTAGTGTTAG
1 GGGTTAGGGTTTAGGGTTTTTA-AGTTAA
*
20494093 GGGTTTTA-GGTTATGGGGTTTTTAAGTTAA
1 GGG--TTAGGGTT-TAGGGTTTTTAAGTTAA
20494123 --GTTAAGGGTTTAGGGTTTTTAAGTTAA
1 GGGTT-AGGGTTTAGGGTTTTTAAGTTAA
20494150 GGGTTTAGGG
1 GGG-TTAGGG
20494160 GTTCTAAGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
26 6 0.08
27 33 0.43
28 15 0.20
29 12 0.16
30 6 0.08
31 4 0.05
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (28 bp):
GGGTTAGGGTTTAGGGTTTTTAAGTTAA
Found at i:20494110 original size:15 final size:15
Alignment explanation
Indices: 20494082--20494114 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20494072 GGGTTTAGGG
20494082 TTTAGTGTTAGGGGT
1 TTTAGTGTTAGGGGT
20494097 TTTAG-GTTATGGGGT
1 TTTAGTGTTA-GGGGT
20494112 TTT
1 TTT
20494115 TAAGTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.36, T:0.52
Consensus pattern (15 bp):
TTTAGTGTTAGGGGT
Found at i:20494146 original size:22 final size:22
Alignment explanation
Indices: 20494119--20494184 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
20494109 GGTTTTTAAG
20494119 TTAAGTTAAGGGTTTAGGGTTT
1 TTAAGTTAAGGGTTTAGGGTTT
*
20494141 TTAAGTTAAGGGTTTAGGGGTT
1 TTAAGTTAAGGGTTTAGGGTTT
*
20494163 CTAAGTTAAGGGTTTAGGGTTT
1 TTAAGTTAAGGGTTTAGGGTTT
20494185 GTCAATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.23, C:0.02, G:0.33, T:0.42
Consensus pattern (22 bp):
TTAAGTTAAGGGTTTAGGGTTT
Found at i:20495631 original size:20 final size:20
Alignment explanation
Indices: 20495594--20495631 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20495584 ATTATTTTTA
*
20495594 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
20495614 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
20495632 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:20496631 original size:11 final size:11
Alignment explanation
Indices: 20496617--20496682 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
20496607 TTAAACATAG
20496617 ATTTGAGAGAA
1 ATTTGAGAGAA
*
20496628 ATTTG-GAAGGA
1 ATTTGAG-AGAA
20496639 ATTTGAGAGCAA
1 ATTTGAGAG-AA
20496651 A-TTGAGAGGAA
1 ATTTGAGA-GAA
20496662 A-TTGAGA-AA
1 ATTTGAGAGAA
20496671 ATAGTTGAGAGA
1 AT--TTGAGAGA
20496683 GGATTAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 3 0.07
10 1 0.02
11 30 0.67
12 10 0.22
13 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:20496666 original size:22 final size:22
Alignment explanation
Indices: 20496619--20496672 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
20496609 AAACATAGAT
*
20496619 TTGAGAGAAATTTGGAAGGAAT
1 TTGAGAGAAATTTGGAAGGAAA
20496641 TTGAGAGCAAA-TT-GAGAGGAAA
1 TTGAGAG-AAATTTGGA-AGGAAA
20496663 TTGAGA-AAAT
1 TTGAGAGAAAT
20496673 AGTTGAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.11
21 2 0.07
22 20 0.71
23 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTGGAAGGAAA
Found at i:20498356 original size:23 final size:23
Alignment explanation
Indices: 20498327--20498376 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20498317 CTTGATTCTT
*
20498327 AAAAATTCAAAA-AATAAATATTA
1 AAAAATT-AAAATAAAAAATATTA
*
20498350 AAAAATTAAAATAAAAAATATTT
1 AAAAATTAAAATAAAAAATATTA
20498373 AAAA
1 AAAA
20498377 GTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAATTAAAATAAAAAATATTA
Found at i:20500454 original size:18 final size:18
Alignment explanation
Indices: 20500430--20500465 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
20500420 ATTTTTTTCA
20500430 AAAAAAATTAAAAAAAAAC
1 AAAAAAA-TAAAAAAAAAC
20500449 AAAAAAATAAAAAAAAA
1 AAAAAAATAAAAAAAAA
20500466 ACTAAACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.08
Consensus pattern (18 bp):
AAAAAAATAAAAAAAAAC
Found at i:20500454 original size:19 final size:19
Alignment explanation
Indices: 20500430--20500467 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20500420 ATTTTTTTCA
*
20500430 AAAAAAATTAAAAAAAAAC
1 AAAAAAATAAAAAAAAAAC
20500449 AAAAAAATAAAAAAAAAAC
1 AAAAAAATAAAAAAAAAAC
20500468 TAAACGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.87, C:0.05, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAAAAATAAAAAAAAAAC
Found at i:20504165 original size:31 final size:31
Alignment explanation
Indices: 20504090--20504166 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
20504080 ATTCATATTT
* *
20504090 TCAG-ATAACTCGAATTTTTATTCGAGTTAA
1 TCAGAATAACTTGATTTTTTATTCGAGTTAA
* * *
20504120 TCAGAAAAAATTGATTTTTTATTCGAGTTAG
1 TCAGAATAACTTGATTTTTTATTCGAGTTAA
20504151 TCCA-AATAACTTGATT
1 T-CAGAATAACTTGATT
20504167 AACTCGAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 4 0.11
31 32 0.84
32 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (31 bp):
TCAGAATAACTTGATTTTTTATTCGAGTTAA
Found at i:20506519 original size:9 final size:9
Alignment explanation
Indices: 20506493--20506529 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20506483 GATAAAAAAA
20506493 TTAAAATTT
1 TTAAAATTT
* *
20506502 TGAAGATTT
1 TTAAAATTT
20506511 TTAAAATTT
1 TTAAAATTT
20506520 TTAAAATTT
1 TTAAAATTT
20506529 T
1 T
20506530 AAGTTCCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (9 bp):
TTAAAATTT
Found at i:20511017 original size:23 final size:22
Alignment explanation
Indices: 20510980--20511048 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 22
20510970 GGACTCACCA
*
20510980 CAGCTCGTATGAGCTTACCGTTT
1 CAGCTCATA-GAGCTTACCGTTT
20511003 CAGCTC-TACGAAGCTTACCGTTT
1 CAGCTCATA-G-AGCTTACCGTTT
20511026 CAGCTCAATAGAGCTTACCGTTT
1 CAGCTC-ATAGAGCTTACCGTTT
20511049 ATCAGCTCGG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
22 3 0.07
23 36 0.86
24 1 0.02
25 2 0.05
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.32
Consensus pattern (22 bp):
CAGCTCATAGAGCTTACCGTTT
Found at i:20511071 original size:26 final size:23
Alignment explanation
Indices: 20510990--20511071 Score: 89
Period size: 23 Copynumber: 3.4 Consensus size: 23
20510980 CAGCTCGTAT
20510990 GAGCTTACCGTTTCAGCTC--TA
1 GAGCTTACCGTTTCAGCTCAATA
20511011 CGAAGCTTACCGTTTCAGCTCAATA
1 -G-AGCTTACCGTTTCAGCTCAATA
20511036 GAGCTTACCGTTTATCAGCTCGGAAT-
1 GAGCTTACCG-TT-TCAGCTC--AATA
20511062 GAGCTTACCG
1 GAGCTTACCG
20511072 ATCATGGCTC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.02
23 27 0.51
24 3 0.06
25 9 0.17
26 10 0.19
27 3 0.06
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCAATA
Found at i:20517799 original size:26 final size:27
Alignment explanation
Indices: 20517768--20517837 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 27
20517758 GTTTTTGAAG
20517768 TTTTAGAATTTGTTAGAAGTTAATATATTTA
1 TTTTAGAATTTGTTAGAAGTT-A-ATA--TA
*
20517799 GTTTTTGAATTTGTTAGAAGTTAATATA
1 -TTTTAGAATTTGTTAGAAGTTAATATA
20517827 TTTTA-AATTTG
1 TTTTAGAATTTG
20517838 GTTTAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 6 0.17
27 4 0.11
28 2 0.06
30 3 0.08
31 1 0.03
32 20 0.56
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
TTTTAGAATTTGTTAGAAGTTAATATA
Found at i:20517809 original size:32 final size:32
Alignment explanation
Indices: 20517766--20517829 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20517756 ATGTTTTTGA
20517766 AGTTTTAGAATTTGTTAGAAGTTAATATATTT
1 AGTTTTAGAATTTGTTAGAAGTTAATATATTT
*
20517798 AGTTTTTGAATTTGTTAGAAGTTAATATATTT
1 AGTTTTAGAATTTGTTAGAAGTTAATATATTT
20517830 TAAATTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.52
Consensus pattern (32 bp):
AGTTTTAGAATTTGTTAGAAGTTAATATATTT
Found at i:20518186 original size:19 final size:18
Alignment explanation
Indices: 20518162--20518205 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20518152 AAAAGTTATA
*
20518162 AAAAAATTTACAAAAATAT
1 AAAAAATTTA-AAAAAAAT
20518181 AAAAAATTTAAAAAAAAT
1 AAAAAATTTAAAAAAAAT
*
20518199 AGAAAAT
1 AAAAAAT
20518206 AGAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAAATTTAAAAAAAAT
Found at i:20518195 original size:9 final size:9
Alignment explanation
Indices: 20518162--20518195 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
20518152 AAAAGTTATA
20518162 AAAAAATTT
1 AAAAAATTT
*
20518171 ACAAAAATAT
1 A-AAAAATTT
20518181 AAAAAATTT
1 AAAAAATTT
20518190 AAAAAA
1 AAAAAA
20518196 AATAGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAAATTT
Found at i:20518544 original size:26 final size:25
Alignment explanation
Indices: 20518498--20518560 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
20518488 ATATATAATT
* *
20518498 ATTAAAATAAATTAGAATTTTGGAAA
1 ATTAAAATAAATGAGAATTTT-AAAA
*
20518524 ATTAAAATAAA-GAGATTTTTTAAAA
1 ATTAAAATAAATGAGA-ATTTTAAAA
20518549 ATTATAAA-AAAT
1 ATTA-AAATAAAT
20518561 ATAAAAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (25 bp):
ATTAAAATAAATGAGAATTTTAAAA
Found at i:20518549 original size:25 final size:26
Alignment explanation
Indices: 20518498--20518560 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
20518488 ATATATAATT
* *
20518498 ATTAAAATAAATTAGAATTTTGGAAA
1 ATTAAAATAAATGAGAATTTTGAAAA
* *
20518524 ATTAAAATAAA-GAGATTTTTTAAAA
1 ATTAAAATAAATGAGAATTTTGAAAA
20518549 ATTATAAA-AAAT
1 ATTA-AAATAAAT
20518561 ATAAAAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (26 bp):
ATTAAAATAAATGAGAATTTTGAAAA
Found at i:20518560 original size:10 final size:10
Alignment explanation
Indices: 20518545--20518655 Score: 68
Period size: 10 Copynumber: 11.0 Consensus size: 10
20518535 GAGATTTTTT
20518545 AAAAATTATA
1 AAAAATTATA
20518555 AAAAA-TAT-
1 AAAAATTATA
20518563 AAAAA-TACTA
1 AAAAATTA-TA
* *
20518573 GAAAATTATT
1 AAAAATTATA
* *
20518583 AAAAATGACAA
1 AAAAATTA-TA
*
20518594 ATATAGAATTTTA
1 A-A-A-AATTATA
*
20518607 GAAAATTATA
1 AAAAATTATA
20518617 AAAAATTATA
1 AAAAATTATA
20518627 AAAAATTATA
1 AAAAATTATA
**
20518637 TGAAA-TATA
1 AAAAATTATA
*
20518646 ACAAATTATA
1 AAAAATTATA
20518656 TTTTTTATGG
Statistics
Matches: 77, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
8 7 0.09
9 11 0.14
10 48 0.62
11 4 0.05
12 2 0.03
13 2 0.03
14 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:20518857 original size:20 final size:20
Alignment explanation
Indices: 20518834--20518908 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
20518824 TTTTTAATAA
*
20518834 TTTTATAATTTTTATATTTT
1 TTTTACAATTTTTATATTTT
*
20518854 TTTTACAATTTATA-ATTTTT
1 TTTTACAATTTTTATA-TTTT
** *
20518874 TTTTGTAA--TTTATAATTT
1 TTTTACAATTTTTATATTTT
20518892 TTTT-CAATTTTTATATT
1 TTTTACAATTTTTATATT
20518909 GAAAAAGTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.05
18 10 0.23
19 9 0.21
20 22 0.51
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTACAATTTTTATATTTT
Found at i:20532108 original size:26 final size:26
Alignment explanation
Indices: 20532079--20532139 Score: 97
Period size: 25 Copynumber: 2.3 Consensus size: 26
20532069 CTTCTGCTAA
20532079 GAACATCTTCTAAGCAGAATGTTTTT
1 GAACATCTTCTAAGCAGAATGTTTTT
*
20532105 GAAC-TATTCTAAGCAGAATGTTTTT
1 GAACATCTTCTAAGCAGAATGTTTTT
20532130 GAACTATCTT
1 GAAC-ATCTT
20532140 AAGATGGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 24 0.77
26 4 0.13
27 3 0.10
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (26 bp):
GAACATCTTCTAAGCAGAATGTTTTT
Found at i:20532142 original size:25 final size:25
Alignment explanation
Indices: 20532086--20532136 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
20532076 TAAGAACATC
20532086 TTCTAAGCAGAATGTTTTTGAACTA
1 TTCTAAGCAGAATGTTTTTGAACTA
20532111 TTCTAAGCAGAATGTTTTTGAACTA
1 TTCTAAGCAGAATGTTTTTGAACTA
20532136 T
1 T
20532137 CTTAAGATGG
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:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (25 bp):
TTCTAAGCAGAATGTTTTTGAACTA
Done.