Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 89 of 226
Found at i:31361296 original size:91 final size:91
Alignment explanation
Indices: 31361141--31361320 Score: 335
Period size: 91 Copynumber: 2.0 Consensus size: 91
31361131 ACACCGATGT
*
31361141 GTGTGATTCTATGAAAACTTTGTCTCATGCTCAAAATAGGTACTTTATTTTATTCATTGATGATT
1 GTGTGATTCTATGAAAACTTCGTCTCATGCTCAAAATAGGTACTTTATTTTATTCATTGATGATT
31361206 TAACTCGTATGACATGAGTGTATTCG
66 TAACTCGTATGACATGAGTGTATTCG
31361232 GTGTGA-TCGTATGAAAACTTCGTCTCATGCTCAAAATAGGTACTTTATTTTATTCATTGATGAT
1 GTGTGATTC-TATGAAAACTTCGTCTCATGCTCAAAATAGGTACTTTATTTTATTCATTGATGAT
31361296 TTAACTCGTATGACATGAGTGTATT
65 TTAACTCGTATGACATGAGTGTATT
31361321 TTATGAGATA
Statistics
Matches: 87, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
90 2 0.02
91 85 0.98
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (91 bp):
GTGTGATTCTATGAAAACTTCGTCTCATGCTCAAAATAGGTACTTTATTTTATTCATTGATGATT
TAACTCGTATGACATGAGTGTATTCG
Found at i:31362757 original size:31 final size:32
Alignment explanation
Indices: 31362699--31362759 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
31362689 ATTATACTAT
*
31362699 TAATAGTTAGTGACCAAAATGTTACAAATTGA
1 TAATAGTTAGTGACCAAAATGTGACAAATTGA
***
31362731 TAAT-GTTAGTGACCATTTTGTGACAAATT
1 TAATAGTTAGTGACCAAAATGTGACAAATT
31362760 AAAATTCGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (32 bp):
TAATAGTTAGTGACCAAAATGTGACAAATTGA
Found at i:31371138 original size:22 final size:22
Alignment explanation
Indices: 31371113--31371169 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
31371103 TACAAATTAA
31371113 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTACAAAATCAT
* *
31371135 ATCTTCTAAGATTGC-ATATCAT
1 ATC-TCTAAGATTACAAAATCAT
31371157 A--TCTAAGATTACA
1 ATCTCTAAGATTACA
31371170 TATATTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.33
22 10 0.33
23 10 0.33
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (22 bp):
ATCTCTAAGATTACAAAATCAT
Found at i:31371146 original size:23 final size:22
Alignment explanation
Indices: 31371103--31371160 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
31371093 AAAGGGTATC
* *
31371103 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
31371124 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
31371147 TGCATATCATATCT
1 TACAAATCATATCT
31371161 AAGATTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:31372006 original size:131 final size:132
Alignment explanation
Indices: 31371593--31372018 Score: 518
Period size: 131 Copynumber: 3.2 Consensus size: 132
31371583 GAATTGGTAA
* * * *
31371593 TTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTTCCTTACTA
1 TTTCAACCTACTCCACTGCAAC-TCAGGGAGATAAGACTGGTGGCTTAAATCTGCTTCCCTACTA
* * *
31371658 CCTCA-GAAAGATAAGACTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATA
65 CCT-AGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTA
31371722 CAAT
129 CAAT
* * ** * * * *
31371726 ATTCAACCTACTCCACTACTGCACAGGGAGATAGGACTGGTGGCTTAAAT-TCACTT-CCTATTA
1 TTTCAACCTACTCCACTGCAACTCAGGGAGATAAGACTGGTGGCTTAAATCT-GCTTCCCTACTA
* * * *
31371789 TCTAGGGAATATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAC
65 CCTAGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAC
31371854 AAT
130 AAT
* * * * *
31371857 CTTCAACCTACTCTACTGCTACTCAGGGAGATAAGAC-AGTGACTTAAATCTGCTTCCCTACTAC
1 TTTCAACCTACTCCACTGCAACTCAGGGAGATAAGACTGGTGGCTTAAATCTGCTTCCCTACTAC
* * * * * *
31371921 CTTGGGAAGATAAGATTCGCTGTCTTTGATCTGCTCTAGTACTGCTTAGGGAGACAAGACCTACA
66 CTAGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACA
31371986 AT
131 AT
31371988 TTTCAACCTACTCCACTGCAAACTCAGGGAG
1 TTTCAACCTACTCCACTGC-AACTCAGGGAG
31372019 GCAGGGCTGG
Statistics
Matches: 246, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
130 14 0.06
131 178 0.72
132 37 0.15
133 17 0.07
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
TTTCAACCTACTCCACTGCAACTCAGGGAGATAAGACTGGTGGCTTAAATCTGCTTCCCTACTAC
CTAGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACA
AT
Found at i:31372096 original size:89 final size:89
Alignment explanation
Indices: 31371998--31372260 Score: 348
Period size: 89 Copynumber: 3.0 Consensus size: 89
31371988 TTTCAACCTA
* * * * * *
31371998 CTCCACTGCAAACTCAGGGAGGCAGGGCTGGTGTTTTTGATCTGCTTCACTACTAGTACAGGAAG
1 CTCCACTGCAAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAG
* * *
31372063 ACAAGATCTGTTGTTTTCAG-TCTG
66 ACAAGATCTGCTATCTTCAGCT-TG
* * * * *
31372087 GTCCGCTGCAAACTCAGGGAGGCAAGGTTGGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAG
1 CTCCACTGCAAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAG
31372152 ACAAGATCTGCTATCTTCAGCTTG
66 ACAAGATCTGCTATCTTCAGCTTG
* * *
31372176 CTCCACTACAAACTTAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAAGAAG
1 CTCCACTGCAAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAG
*
31372241 ACAAGATCTGCTATCGTCAG
66 ACAAGATCTGCTATCTTCAG
31372261 TCTGCCCGCT
Statistics
Matches: 150, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
89 149 0.99
90 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (89 bp):
CTCCACTGCAAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGCCAATACAGGAAG
ACAAGATCTGCTATCTTCAGCTTG
Found at i:31372440 original size:44 final size:44
Alignment explanation
Indices: 31372365--31372470 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
31372355 CGCTTCATTG
* * *
31372365 CAACTTCAGGGAGATAGGATTAGTAGCTTCAATCC-GCTCCACTG
1 CAACTTCAGGGAGATAAGATTAGTAGCTTCAA-CCTACTCCACTA
* * * ** *
31372409 TAACTTCAGGGAGATAATATTGGTATTTTCAACCTACTCCATTA
1 CAACTTCAGGGAGATAAGATTAGTAGCTTCAACCTACTCCACTA
31372453 CAACTTCAGGGAGATAAG
1 CAACTTCAGGGAGATAAG
31372471 GTTTGATGTG
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
43 2 0.04
44 48 0.96
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATTAGTAGCTTCAACCTACTCCACTA
Found at i:31372827 original size:44 final size:44
Alignment explanation
Indices: 31372580--31372998 Score: 262
Period size: 44 Copynumber: 9.5 Consensus size: 44
31372570 CTATCTTCAG
* * * *
31372580 TCTGTTCCACTGTAACTTCAGGGAGATAAGAC-T-TCACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA
** * * * **
31372622 TCCACTCCACTGTAACTTCAGGGAGATAGGA-TTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTTAA
* * *
31372666 TCT-CTTCCACTGTAACTTCAGGGAGATAAGA-TT-CACCATCTTTAG
1 TCTGC-TCCACTGCAACTTCAGGGAGATAAGACTTGTA--A-CTTTAA
* * * * ** * *
31372711 TTTGC-CTCACTGTAACTTCAGGGGGATAAGACCTGCTTTCTTCAG
1 TCTGCTC-CACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAA
* * *
31372756 TTTGCTCCATTGCAACTTCAGGAAGATAAGACTTGTAACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA
* * * **
31372800 TCCGCTCCACTGCAACTTTAGGGAGATAAGA-TTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTTAA
* * * * * *
31372844 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAA
* * ** * *
31372889 TCTACCCCACTGCAACTTCAAGGGA-ATAAGACTTGCTTTCTTCAG
1 TCTGCTCCACTGCAACTTC-AGGGAGATAAGACTTG-TAACTTTAA
* * *
31372934 TCTGCCCCACTGCAATTTTAGGGAGATAAGACTTGTAACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA
*
31372978 TCTGCTCCACTGCAACCTCAG
1 TCTGCTCCACTGCAACTTCAG
31372999 ATAGATAGGA
Statistics
Matches: 296, Mismatches: 63, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
42 28 0.09
43 3 0.01
44 129 0.44
45 129 0.44
46 7 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA
Found at i:31372839 original size:178 final size:178
Alignment explanation
Indices: 31372573--31372998 Score: 570
Period size: 178 Copynumber: 2.4 Consensus size: 178
31372563 AGATTTACTA
* * * * * *
31372573 TCTTCAGTCTGTTCCACTGTAACTTCAGGGAGATAAGAC-T-TCACTTCAATCCACTCCACTGTA
1 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCCGCTCCACTGCA
* * *
31372636 ACTTCAGGGAGATAGGATTATTGGCTTTAATCT-CTTCCACTGTAACTTCAGGGAGATAAGATTC
66 ACTTCAGGGAGATAAGATTATTGGCTTTAATCTGC-TCCACTGCAACTTCAAGGAGATAAGATTC
* * * * * * *
31372700 ACCATCTTTAGTTTGCCTCACTGTAACTTCAGGGGGATAAGACCTGCTT
130 ACCATCTTCAGTCTACCCCACTGCAACTTCAAGGGAATAAGACCTGCTT
* * *
31372749 TCTTCAGTTTGCTCCATTGCAACTTCAGGAAGATAAGACTTGTAACTTTAATCCGCTCCACTGCA
1 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCCGCTCCACTGCA
* **
31372814 ACTTTAGGGAGATAAGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
66 ACTTCAGGGAGATAAGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTCA
*
31372879 CCATCTTCAGTCTACCCCACTGCAACTTCAAGGGAATAAGACTTGCTT
131 CCATCTTCAGTCTACCCCACTGCAACTTCAAGGGAATAAGACCTGCTT
* * * *
31372927 TCTTCAGTCTGCCCCACTGCAATTTTAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCA
1 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCCGCTCCACTGCA
*
31372992 ACCTCAG
66 ACTTCAG
31372999 ATAGATAGGA
Statistics
Matches: 215, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
176 34 0.16
177 1 0.00
178 179 0.83
179 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (178 bp):
TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCCGCTCCACTGCA
ACTTCAGGGAGATAAGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTCA
CCATCTTCAGTCTACCCCACTGCAACTTCAAGGGAATAAGACCTGCTT
Found at i:31373005 original size:44 final size:44
Alignment explanation
Indices: 31372580--31373005 Score: 190
Period size: 45 Copynumber: 9.6 Consensus size: 44
31372570 CTATCTTCAG
* * * * *
31372580 TCTGTTCCACTGTAACTTCAGGGAGATAAGAC-T-TCACTTCAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTTAA
** * * * * **
31372622 TCCACTCCACTGTAACTTCAGGGAGATAGGA-TTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTT-GTAACTTTAA
* * * *
31372666 TCT-CTTCCACTGTAACTTCAGGGAGATAAGA-TT-CACCATCTTTAG
1 TCTGC-TCCACTGCAACTTCAGAGAGATAAGACTTGTA--A-CTTTAA
* * * * * ** * *
31372711 TTTGC-CTCACTGTAACTTCAGGGGGATAAGACCTGCTTTCTTCAG
1 TCTGCTC-CACTGCAACTTCAGAGAGATAAGACTTG-TAACTTTAA
* *
31372756 TTTGCTCCATTGCAACTTCAG-GAAGATAAGACTTGTAACTTTAA
1 TCTGCTCCACTGCAACTTCAGAG-AGATAAGACTTGTAACTTTAA
* * * * **
31372800 TCCGCTCCACTGCAACTTTAGGGAGATAAGA-TTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTT-GTAACTTTAA
* * * * *
31372844 TCTGCTCCACTGCAACTTCA-AGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGA-GAGATAAGACTTG-TAACTTTAA
* * * ** * *
31372889 TCTACCCCACTGCAACTTCA-AGGGAATAAGACTTGCTTTCTTCAG
1 TCTGCTCCACTGCAACTTCAGAGAG-ATAAGACTTG-TAACTTTAA
* * * *
31372934 TCTGCCCCACTGCAATTTTAGGGAGATAAGACTTGTAACTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTTAA
* *
31372978 TCTGCTCCACTGCAACCTCAGATAGATA
1 TCTGCTCCACTGCAACTTCAGAGAGATA
31373006 GGATTTGTGG
Statistics
Matches: 298, Mismatches: 65, Indels: 40
0.74 0.16 0.10
Matches are distributed among these distances:
42 28 0.09
43 3 0.01
44 130 0.44
45 132 0.44
46 5 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTTAA
Found at i:31373321 original size:24 final size:24
Alignment explanation
Indices: 31373294--31373369 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
31373284 TTATCCCTAT
31373294 TGTAATCTTCAAGGTTCAATCCAC
1 TGTAATCTTCAAGGTTCAATCCAC
31373318 TGTAATCTTCAAGGTTCAATCCAC
1 TGTAATCTTCAAGGTTCAATCCAC
* *
31373342 TGTAATCTTCAAGGTTTAGTCCAC
1 TGTAATCTTCAAGGTTCAATCCAC
31373366 TGTA
1 TGTA
31373370 TTTTTAGGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (24 bp):
TGTAATCTTCAAGGTTCAATCCAC
Found at i:31374295 original size:9 final size:9
Alignment explanation
Indices: 31374283--31374315 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
31374273 TATTTTTCTT
31374283 TTTTTTTAA
1 TTTTTTTAA
31374292 TTTTTTTAA
1 TTTTTTTAA
*
31374301 -TTTTTTGA
1 TTTTTTTAA
31374309 TTTTTTT
1 TTTTTTT
31374316 CTTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:31377587 original size:19 final size:20
Alignment explanation
Indices: 31377563--31377609 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
31377553 TGTGAAAATC
*
31377563 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
31377582 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
31377602 -AATGCAAA
1 TAATGCAAA
31377610 AAGAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:31379409 original size:15 final size:16
Alignment explanation
Indices: 31379391--31379423 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31379381 AAATGTAAAC
31379391 AAATTTAAAAAT-AAT
1 AAATTTAAAAATGAAT
*
31379406 AAATTTGAAAATGAAT
1 AAATTTAAAAATGAAT
31379422 AA
1 AA
31379424 TAAGGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AAATTTAAAAATGAAT
Found at i:31380346 original size:16 final size:17
Alignment explanation
Indices: 31380312--31380349 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
31380302 ATATCTAAGA
31380312 TTTATAAAATATTAAATT
1 TTTATAAAATATT-AATT
31380330 TTTATAAAATATT-ATT
1 TTTATAAAATATTAATT
31380346 TTTA
1 TTTA
31380350 AGTTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATAAAATATTAATT
Found at i:31380393 original size:7 final size:7
Alignment explanation
Indices: 31380366--31380435 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
31380356 TATTATTTGA
31380366 AAATATAT
1 AAAT-TAT
*
31380374 AAAATAT
1 AAATTAT
31380381 ATAATTAT
1 A-AATTAT
31380389 AAATTTAT
1 AAA-TTAT
*
31380397 AAAATAT
1 AAATTAT
*
31380404 AAAATAT
1 AAATTAT
*
31380411 AAAATAT
1 AAATTAT
31380418 ATAATTA-
1 A-AATTAT
31380425 AAATATAT
1 AAAT-TAT
31380433 AAA
1 AAA
31380436 AAAGCCTACA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
6 3 0.06
7 27 0.51
8 23 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAATTAT
Found at i:31380397 original size:23 final size:22
Alignment explanation
Indices: 31380366--31380431 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
31380356 TATTATTTGA
*
31380366 AAATATATAAAATATATAATTAT
1 AAATATATAAAATATA-AAATAT
*
31380389 AAATTTATAAAATATAAAATAT
1 AAATATATAAAATATAAAATAT
*
31380411 AAA-ATATATAAT-TAAAATAT
1 AAATATATAAAATATAAAATAT
31380431 A
1 A
31380432 TAAAAAAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 9 0.23
21 7 0.18
22 8 0.21
23 15 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATATATAAAATATAAAATAT
Found at i:31380411 original size:14 final size:14
Alignment explanation
Indices: 31380370--31380431 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
31380360 ATTTGAAAAT
31380370 ATATAAAATATATAA
1 ATATAAAATATA-AA
* *
31380385 TTATAAATTTATAAA
1 ATATAAA-ATATAAA
31380400 ATATAAAATATAAA
1 ATATAAAATATAAA
*
31380414 ATATATAAT-TAAA
1 ATATAAAATATAAA
31380427 ATATA
1 ATATA
31380432 TAAAAAAGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 9 0.22
14 14 0.34
15 14 0.34
16 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAAAATATAAA
Found at i:31380494 original size:17 final size:17
Alignment explanation
Indices: 31380456--31380525 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
31380446 ATATTTTGAA
*
31380456 AAATATATAAAA-ATTT
1 AAATATATAAAATATAT
*
31380472 ACAATATATAATATATAT
1 A-AATATATAAAATATAT
*
31380490 AAATA-AAAAAAT-TAT
1 AAATATATAAAATATAT
*
31380505 AAATGTATAAAAATATAT
1 AAATATAT-AAAATATAT
31380523 AAA
1 AAA
31380526 AGAACTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
15 7 0.16
16 7 0.16
17 19 0.44
18 10 0.23
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
AAATATATAAAATATAT
Found at i:31380657 original size:9 final size:9
Alignment explanation
Indices: 31380627--31380674 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
31380617 TGTAAAAACT
*
31380627 TTTTATATT
1 TTTTATATA
31380636 TTTTAT-TA
1 TTTTATATA
*
31380644 ATTTATATA
1 TTTTATATA
*
31380653 TTTTA-AAA
1 TTTTATATA
31380661 TTTTATATA
1 TTTTATATA
31380670 TTTTA
1 TTTTA
31380675 AATTTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 13 0.41
9 19 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTATATA
Found at i:31380665 original size:17 final size:17
Alignment explanation
Indices: 31380627--31380676 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
31380617 TGTAAAAACT
* *
31380627 TTTTATATTTTTTATTAA
1 TTTTATATATTTTA-AAA
31380645 -TTTATATATTTTAAAA
1 TTTTATATATTTTAAAA
31380661 TTTTATATATTTTAAA
1 TTTTATATATTTTAAA
31380677 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATATATTTTAAAA
Found at i:31383400 original size:30 final size:31
Alignment explanation
Indices: 31383366--31383434 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
31383356 ACTTAACAAC
*
31383366 TCAATGATTTAAAT-AAAACTTTTGAATAAT
1 TCAATGACTTAAATGAAAACTTTTGAATAAT
*
31383396 TCAATGACTTAAATGAAAACTTTTGAATAGT
1 TCAATGACTTAAATGAAAACTTTTGAATAAT
*
31383427 TCATTGAC
1 TCAATGAC
31383435 CATTTTGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (31 bp):
TCAATGACTTAAATGAAAACTTTTGAATAAT
Found at i:31393760 original size:45 final size:46
Alignment explanation
Indices: 31393683--31393818 Score: 145
Period size: 45 Copynumber: 3.0 Consensus size: 46
31393673 ACACATTTGC
* * * * *
31393683 AGATTAAAGCTGCTAATACGGTGTGTGTAAACCACT-AGTCGGTG-A
1 AGATAAAAGCTGCTAATACGATGTGGGGAAACCACTAAAT-GGTGCA
* *
31393728 AGATAAAAGCTTCTAATATGATGTGGGGAAACCACTAAATGGTGCA
1 AGATAAAAGCTGCTAATACGATGTGGGGAAACCACTAAATGGTGCA
**
31393774 A-ATAAAAGCTGCTAATAC-AGTGTGGATAAACCACTAAATGGTGCA
1 AGATAAAAGCTGCTAATACGA-TGTGGGGAAACCACTAAATGGTGCA
31393819 GACAAGTTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
44 1 0.01
45 72 0.94
46 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (46 bp):
AGATAAAAGCTGCTAATACGATGTGGGGAAACCACTAAATGGTGCA
Found at i:31394289 original size:24 final size:24
Alignment explanation
Indices: 31394253--31394298 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
31394243 GAAAATAGGG
* * *
31394253 GAAAAATTGTAAAATTTAAAAATA
1 GAAAAAATATAAAATCTAAAAATA
31394277 GAAAAAATATAAAATCTAAAAA
1 GAAAAAATATAAAATCTAAAAA
31394299 AATAGGGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (24 bp):
GAAAAAATATAAAATCTAAAAATA
Found at i:31395877 original size:22 final size:22
Alignment explanation
Indices: 31395828--31395881 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
31395818 CAAGTTTCGT
31395828 TTTAGATTAATTAATTTATATAC
1 TTTA-ATTAATTAATTTATATAC
*
31395851 -CTAATTATATTAATTTA-ATAC
1 TTTAATTA-ATTAATTTATATAC
31395872 TTTAATTAAT
1 TTTAATTAAT
31395882 CATTTATGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTAATTAATTAATTTATATAC
Found at i:31405328 original size:89 final size:90
Alignment explanation
Indices: 31405161--31405337 Score: 241
Period size: 90 Copynumber: 2.0 Consensus size: 90
31405151 TTTATTTTTA
* *
31405161 TTTTTTTGCACTCAATTGACCACTTGAATTTTCAAAATGCATAAAAAAAGCCCTCAAACTTCTTA
1 TTTTTTTGCACTCAATTGACCACTTGAACTTTCAAAATGCATAAAAAAAGACCTCAAACTTCTTA
*
31405226 AAAAAAACAATTAAACCCTTGCTTT
66 AAAAAAACAATTAAACCCCTGCTTT
*** *
31405251 TTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT-CAAAAAGACCTCAAAACTT-TT
1 TTTTTTTGCACTCAATTGACCACTTGAACTTTCAAAATGCATAAAAAAAGACCTC-AAACTTCTT
* * *
31405314 CAAAAAAGCAATTAAGCCCCTGCT
65 AAAAAAAACAATTAAACCCCTGCT
31405338 CTAATTAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
89 32 0.42
90 44 0.58
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.32
Consensus pattern (90 bp):
TTTTTTTGCACTCAATTGACCACTTGAACTTTCAAAATGCATAAAAAAAGACCTCAAACTTCTTA
AAAAAAACAATTAAACCCCTGCTTT
Found at i:31405413 original size:19 final size:20
Alignment explanation
Indices: 31405362--31405420 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
31405352 GAAAAAATTT
*
31405362 ATAAAAAATAATAAATTTT-
1 ATAAAAAATATTAAATTTTA
*
31405381 AGAAAAAATATTAAATTTTA
1 ATAAAAAATATTAAATTTTA
*
31405401 ATAAAAAAT-TTAAAATTTA
1 ATAAAAAATATTAAATTTTA
31405420 A
1 A
31405421 AATTTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 27 0.77
20 8 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAAAAATATTAAATTTTA
Found at i:31405465 original size:19 final size:19
Alignment explanation
Indices: 31405343--31405473 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
31405333 CTGCTCTAAT
*
31405343 TAAAAATTAGAAAAAATTTA
1 TAAAAATTA-AAAAATTTTA
* *
31405363 TAAAAAATAATAAATTTTA
1 TAAAAATTAAAAAATTTTA
* * **
31405382 GAAAAAATATTAAATTTTAA
1 TAAAAATTAAAAAATTTT-A
*
31405402 TAAAAAATTTAAAATTTAAAATTTA
1 T-AAAAA-TT-AAA---AAATTTTA
***
31405427 TTAAAAATTATAATTTTTTTA
1 -TAAAAATTA-AAAAATTTTA
31405448 TAAAAATTAAAAAATTTTA
1 TAAAAATTAAAAAATTTTA
31405467 TAAAAAT
1 TAAAAAT
31405474 CAGAAAAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
19 38 0.45
20 18 0.21
21 9 0.11
22 1 0.01
23 2 0.02
24 4 0.05
25 6 0.07
26 7 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAAAATTAAAAAATTTTA
Found at i:31405480 original size:19 final size:19
Alignment explanation
Indices: 31405443--31405481 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
31405433 ATTATAATTT
*
31405443 TTTTATAAAAATTAAAAAA
1 TTTTATAAAAATCAAAAAA
31405462 TTTTATAAAAATCAGAAAAA
1 TTTTATAAAAATCA-AAAAA
31405482 AATTAACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
TTTTATAAAAATCAAAAAA
Found at i:31407264 original size:38 final size:38
Alignment explanation
Indices: 31407193--31407273 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
31407183 GAGATGTTTC
* **
31407193 ACATGTATTCAGTCCAATAGTAGAAATTTACATGCTTA
1 ACATGTATTCAGTCCAACAGTAGAAATAGACATGCTTA
* * *
31407231 ACATGTATTCAGTTCAACGGTAGCAATAGACATGCTTA
1 ACATGTATTCAGTCCAACAGTAGAAATAGACATGCTTA
31407269 ACATG
1 ACATG
31407274 CAATTAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (38 bp):
ACATGTATTCAGTCCAACAGTAGAAATAGACATGCTTA
Found at i:31410774 original size:21 final size:22
Alignment explanation
Indices: 31410728--31410780 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
31410718 CAATCATTTT
31410728 AAAACATTT-GTCTATTTTGGTAG
1 AAAAC-TTTAGTCTATTTT-GTAG
31410751 AAAACTTTAGTCTATTTT-TAG
1 AAAACTTTAGTCTATTTTGTAG
*
31410772 AAAAGTTTA
1 AAAACTTTA
31410781 CAAGTTTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.39
22 3 0.11
23 14 0.50
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (22 bp):
AAAACTTTAGTCTATTTTGTAG
Found at i:31426325 original size:25 final size:25
Alignment explanation
Indices: 31426296--31426348 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
31426286 TCAAGTATGG
31426296 AATTATCTGCCAAAGACAGAGAAGA
1 AATTATCTGCCAAAGACAGAGAAGA
*
31426321 AATTATCTGCCAAAGATAGAGAAGA
1 AATTATCTGCCAAAGACAGAGAAGA
31426346 AAT
1 AAT
31426349 CCAAAATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (25 bp):
AATTATCTGCCAAAGACAGAGAAGA
Found at i:31433346 original size:22 final size:22
Alignment explanation
Indices: 31433316--31433366 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
31433306 GACAAGCCAT
* *
31433316 CACTAATTTGCAGTTAAACTAC
1 CACTGATTTGCAGATAAACTAC
* * *
31433338 TACTGATTTGTAGATAAACTGC
1 CACTGATTTGCAGATAAACTAC
31433360 CACTGAT
1 CACTGAT
31433367 AACACTGATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (22 bp):
CACTGATTTGCAGATAAACTAC
Found at i:31440307 original size:20 final size:20
Alignment explanation
Indices: 31440273--31440340 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
31440263 CACAAGGGAA
* *
31440273 GAAAAAGAAAGAAGATGAAGG
1 GAAAAAG-AATAAGAAGAAGG
31440294 GAAAAAGAATAAGAAGAA--
1 GAAAAAGAATAAGAAGAAGG
* *
31440312 G-AAAAGAA-GAGAGGAAGAG
1 GAAAAAGAATAAGAAGAAG-G
31440331 GAAAAAGAAT
1 GAAAAAGAAT
31440341 GTCACAGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
16 6 0.16
17 7 0.18
18 1 0.03
19 1 0.03
20 16 0.42
21 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (20 bp):
GAAAAAGAATAAGAAGAAGG
Found at i:31443456 original size:23 final size:23
Alignment explanation
Indices: 31443404--31443457 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
31443394 CACGTACCTC
* * * *
31443404 TCTGTGATGCCTTTGTGGCGTAT
1 TCTGTAATACCTTTGTGACATAT
31443427 T-TCGTAATACCTTTGTGACATAT
1 TCT-GTAATACCTTTGTGACATAT
31443450 TCTGTAAT
1 TCTGTAAT
31443458 GCTTCTGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (23 bp):
TCTGTAATACCTTTGTGACATAT
Found at i:31447347 original size:23 final size:22
Alignment explanation
Indices: 31447321--31447363 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
31447311 TAGATCTCAT
31447321 AATAAGATGTA-AATCCCTAATCG
1 AATAAG-TGTATAA-CCCTAATCG
*
31447344 AATATGTGTATAACCCTAAT
1 AATAAGTGTATAACCCTAAT
31447364 GACATGCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (22 bp):
AATAAGTGTATAACCCTAATCG
Found at i:31465531 original size:21 final size:23
Alignment explanation
Indices: 31465488--31465532 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
31465478 TTATTTTTAG
* *
31465488 TTTTTATATTTTTTCAAATTTAT
1 TTTTTATATGTTTTCAAACTTAT
31465511 TTTTTATA-GTTTT-AAACTTAT
1 TTTTTATATGTTTTCAAACTTAT
31465532 T
1 T
31465533 ATTGATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATATGTTTTCAAACTTAT
Found at i:31476926 original size:14 final size:14
Alignment explanation
Indices: 31476907--31476937 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
31476897 ATAAAAGAAG
31476907 TAAAGATCTAATTC
1 TAAAGATCTAATTC
31476921 TAAAGATCTAATTC
1 TAAAGATCTAATTC
31476935 TAA
1 TAA
31476938 TAATTATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (14 bp):
TAAAGATCTAATTC
Found at i:31480908 original size:19 final size:19
Alignment explanation
Indices: 31480881--31480918 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31480871 ATAATAAAAT
* *
31480881 ATTTTTTAAAACTTATAAA
1 ATTTATTAAAAATTATAAA
31480900 ATTTATTAAAAATTATAAA
1 ATTTATTAAAAATTATAAA
31480919 TACTTAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTATTAAAAATTATAAA
Found at i:31480972 original size:30 final size:30
Alignment explanation
Indices: 31480938--31480995 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
31480928 CAACTATAAA
* *
31480938 ATATAACTAATTGTTGAAAA-ATAAAAATAT
1 ATATAA-TAATTATTAAAAATATAAAAATAT
31480968 ATATAATAATTATTAAAAATATAAAAAT
1 ATATAATAATTATTAAAAATATAAAAAT
31480996 TCTAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (30 bp):
ATATAATAATTATTAAAAATATAAAAATAT
Found at i:31482256 original size:19 final size:20
Alignment explanation
Indices: 31482224--31482262 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
31482214 AGAGACTAAA
31482224 ATGTATAAAATTTGAAATTG
1 ATGTATAAAATTTGAAATTG
* *
31482244 ATGT-TAAATTTTGTAATTG
1 ATGTATAAAATTTGAAATTG
31482263 TAGATAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (20 bp):
ATGTATAAAATTTGAAATTG
Found at i:31487012 original size:21 final size:21
Alignment explanation
Indices: 31486987--31487069 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 21
31486977 AGTCATATAA
31486987 GTTTCAGTTTAACCCTTCTGG
1 GTTTCAGTTTAACCCTTCTGG
* * * * *
31487008 GTTTCAGTTCAGCTCTTTTGA
1 GTTTCAGTTTAACCCTTCTGG
* **
31487029 GCTTCAGTTTAACCCTAATGG
1 GTTTCAGTTTAACCCTTCTGG
* *
31487050 GTTTCAGTTTAGCTCTTCTG
1 GTTTCAGTTTAACCCTTCTG
31487070 ATCTTTAGAT
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTCTGG
Found at i:31487038 original size:42 final size:42
Alignment explanation
Indices: 31486989--31487159 Score: 157
Period size: 42 Copynumber: 4.1 Consensus size: 42
31486979 TCATATAAGT
* *
31486989 TTCAGTTTAACCCTTCTGGGTTTCAGTTCAGCTCTTTTGAGC
1 TTCAGTTTAACCCTTATGGGTTTCAGTTCAGCTCTTATGAGC
* * * *
31487031 TTCAGTTTAACCCTAATGGGTTTCAGTTTAGCTCTTCTGATC
1 TTCAGTTTAACCCTTATGGGTTTCAGTTCAGCTCTTATGAGC
* * * * *
31487073 TTTAGATTAACACTGATGGGTTTTC-GTTCAGCTCCTATGAGC
1 TTCAGTTTAACCCTTATGGG-TTTCAGTTCAGCTCTTATGAGC
* * * * * *
31487115 TTCCGTTCAACCCTTACGGGTTTTC-GTTTAGCACTTATGTGC
1 TTCAGTTTAACCCTTATGGG-TTTCAGTTCAGCTCTTATGAGC
31487157 TTC
1 TTC
31487160 TGTGCAACCT
Statistics
Matches: 104, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 100 0.96
43 4 0.04
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (42 bp):
TTCAGTTTAACCCTTATGGGTTTCAGTTCAGCTCTTATGAGC
Found at i:31494383 original size:21 final size:21
Alignment explanation
Indices: 31494259--31494424 Score: 70
Period size: 21 Copynumber: 8.0 Consensus size: 21
31494249 TTTGCTTTCC
*
31494259 GTTTAGCTCTCATGAGCTTCA
1 GTTTAGCTCTTATGAGCTTCA
** * *
31494280 GTCAAG-TCATATGAGTTTCA
1 GTTTAGCTCTTATGAGCTTCA
* * * *
31494300 GTTTAACCCTT-TTACGTTTCA
1 GTTTAGCTCTTATGA-GCTTCA
* *
31494321 GTTCAGCTCTTTTGAGCTTCA
1 GTTTAGCTCTTATGAGCTTCA
* * * * * *
31494342 ATTTAACCCTAATGGGTTTCA
1 GTTTAGCTCTTATGAGCTTCA
*
31494363 GTTTAGCTCTTCTGAGCTTCA
1 GTTTAGCTCTTATGAGCTTCA
* * * *
31494384 -TATTAACCCTTATGGGTTTCCA
1 GT-TTAGCTCTTATGAGCTT-CA
*
31494406 -TTTAGCTCCTATGAGCTTC
1 GTTTAGCTCTTATGAGCTTC
31494425 TGTTCAACCC
Statistics
Matches: 99, Mismatches: 41, Indels: 11
0.66 0.27 0.07
Matches are distributed among these distances:
20 18 0.18
21 76 0.77
22 5 0.05
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTTAGCTCTTATGAGCTTCA
Found at i:31494399 original size:42 final size:42
Alignment explanation
Indices: 31494289--31494459 Score: 154
Period size: 42 Copynumber: 4.1 Consensus size: 42
31494279 AGTCAAGTCA
* * ** *
31494289 TATGAGTTTCAGT-TTAACCCTTTTACGTTTCAGTTCAGCTCT
1 TATGAGCTTCA-TATTAACCCTTATGGGTTTCAGTTTAGCTCT
* *
31494331 TTTGAGCTTCA-ATTTAACCCTAATGGGTTTCAGTTTAGCTCT
1 TATGAGCTTCATA-TTAACCCTTATGGGTTTCAGTTTAGCTCT
* *
31494373 TCTGAGCTTCATATTAACCCTTATGGGTTTCCA-TTTAGCTCC
1 TATGAGCTTCATATTAACCCTTATGGGTTT-CAGTTTAGCTCT
* * *
31494415 TATGAGCTTC-TGTTCAACCCTTACGGGTTGTC-GTTTAGCACT
1 TATGAGCTTCATATT-AACCCTTATGGGTT-TCAGTTTAGCTCT
31494457 TAT
1 TAT
31494460 ATGCTTCTGT
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
41 3 0.03
42 100 0.93
43 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.42
Consensus pattern (42 bp):
TATGAGCTTCATATTAACCCTTATGGGTTTCAGTTTAGCTCT
Found at i:31498185 original size:24 final size:24
Alignment explanation
Indices: 31498158--31498255 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 24
31498148 GTTATTAGGG
*
31498158 TTACTGATTACAGCTCTTATGAGC
1 TTACTGATTACAGCTCGTATGAGC
* *
31498182 TTACTGATT-CTTAGCTTGCATGAGC
1 TTACTGATTAC--AGCTCGTATGAGC
*
31498207 TTACTG-TTAATCAGCTCGTAAGAGC
1 TTACTGATT-A-CAGCTCGTATGAGC
*
31498232 TTACTGTTTACAGCTCGTATGAGC
1 TTACTGATTACAGCTCGTATGAGC
31498256 ATACATGTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.02
24 24 0.39
25 33 0.54
26 2 0.03
27 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (24 bp):
TTACTGATTACAGCTCGTATGAGC
Found at i:31500032 original size:45 final size:45
Alignment explanation
Indices: 31499967--31500140 Score: 170
Period size: 45 Copynumber: 3.9 Consensus size: 45
31499957 TCATTTTTCG
* ** * ** *
31499967 TTGTGTTGCCATAGTGTCTTTCAGCTATGGTCTTATTTCTTTA-AT
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTA-CTCGATAGAA
*
31500012 TTGTGATGCCATAGCATCTTTTAGCTATGGTCTTACTCGATAGAA
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCGATAGAA
* * * *
31500057 TTGTGATGCCATAACTTCTTTCAGCCATGGTCTTACTCGATTGAA
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCGATAGAA
* * ** * *
31500102 TCGTGATTCCATAATATCTTTTAGCCATGGTCTTACTCG
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCG
31500141 TTTCTGGTAT
Statistics
Matches: 110, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
44 4 0.04
45 106 0.96
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.42
Consensus pattern (45 bp):
TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCGATAGAA
Found at i:31500167 original size:90 final size:89
Alignment explanation
Indices: 31499924--31500182 Score: 204
Period size: 90 Copynumber: 2.9 Consensus size: 89
31499914 ATTCTCGTCT
* * * * * * * *
31499924 TGATTCCATATTATCTTTCAGTCATGTTCTTATTCATTTTTCGTTGTGTTGCCATAGTGTCTTTC
1 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGTTG-G-TGCCATAGTGTCTTTC
* * *
31499989 AGCTATGGTCTTATTTCTTTAATTTG
64 AGCTATGGTCTTATCTCTTGAATTCG
* ** * * ** * *
31500015 TGATGCCATAGCATCTTTTAGCTATGGTCTTACTCG-ATAGAATTGTGATGCCATAACT-TCTTT
1 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGTTG-G-TGCCAT-AGTGTCTTT
*
31500078 CAGCCATGGTCTTA-CTCGATTGAA-TCG
63 CAGCTATGGTCTTATCTC--TTGAATTCG
*
31500105 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTGGTATGGTGCCATAGTGTCTTTCT
1 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGT-TGGTGCCATAGTGTCTTTC-
31500170 A-CTATGGTCTTAT
64 AGCTATGGTCTTAT
31500183 TTATTTTCGG
Statistics
Matches: 129, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
89 4 0.03
90 86 0.67
91 37 0.29
92 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (89 bp):
TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGTTGGTGCCATAGTGTCTTTCAG
CTATGGTCTTATCTCTTGAATTCG
Found at i:31500281 original size:15 final size:15
Alignment explanation
Indices: 31500252--31500285 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31500242 CCAACAAACT
31500252 CAATTCATATATAAA
1 CAATTCATATATAAA
31500267 CAATT-ATATATTAAA
1 CAATTCATATA-TAAA
31500282 CAAT
1 CAAT
31500286 CAAAAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (15 bp):
CAATTCATATATAAA
Found at i:31501862 original size:24 final size:23
Alignment explanation
Indices: 31501835--31501882 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
31501825 GAGTAAAGAA
* *
31501835 TTTTATTTTTTTATTTCATTTAGT
1 TTTTATTTTTTAATTT-AATTAGT
31501859 TTTTATTTTTTAATTTAATTAGT
1 TTTTATTTTTTAATTTAATTAGT
31501882 T
1 T
31501883 AAAGTTGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTAATTTAATTAGT
Found at i:31506309 original size:27 final size:27
Alignment explanation
Indices: 31506269--31506350 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
31506259 AACACGTCAG
* *
31506269 GAAAGAAAAACCTTTATGGCAAACTCT
1 GAAAGAAAAGCCTTTATGGCGAACTCT
31506296 GAAAGAAAAGCCTTTATGGCGAACTCT
1 GAAAGAAAAGCCTTTATGGCGAACTCT
* *
31506323 GAAAGAAGAGCCTTTATGGTGAACTCT
1 GAAAGAAAAGCCTTTATGGCGAACTCT
31506350 G
1 G
31506351 TATGGACTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTATGGCGAACTCT
Found at i:31506575 original size:35 final size:35
Alignment explanation
Indices: 31506493--31506589 Score: 131
Period size: 35 Copynumber: 2.8 Consensus size: 35
31506483 TTCATGATGT
* *
31506493 CACTTCGTAGAGCCAATAGATCATTTTCGTGATGC
1 CACTTCGTAGAGCCAGTAGATCATTTTCGTGATAC
* **
31506528 CACTCCACAGAGCCAGTAGATCATTTTCGTGATAC
1 CACTTCGTAGAGCCAGTAGATCATTTTCGTGATAC
* *
31506563 CACTTTGTAGAGCTAGTAGATCATTTT
1 CACTTCGTAGAGCCAGTAGATCATTTT
31506590 TCCAACCAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (35 bp):
CACTTCGTAGAGCCAGTAGATCATTTTCGTGATAC
Found at i:31507176 original size:20 final size:20
Alignment explanation
Indices: 31507151--31507199 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
31507141 CTAGAAACTT
*
31507151 ACAGAAACCTTTCAAATTTG
1 ACAGAAACCTTTCAAATATG
*
31507171 ACAGAAACTTTTCAAATATG
1 ACAGAAACCTTTCAAATATG
*
31507191 ACAAAAACC
1 ACAGAAACC
31507200 GTTAACTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (20 bp):
ACAGAAACCTTTCAAATATG
Found at i:31508351 original size:23 final size:23
Alignment explanation
Indices: 31508321--31508375 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
31508311 GCTCTATACG
*
31508321 TGTTATATTCAAAGCTTTATGCA
1 TGTTATATTCAAAGCTATATGCA
* *
31508344 TGTTATATTCCATGCTATATGCA
1 TGTTATATTCAAAGCTATATGCA
31508367 TGTTATATT
1 TGTTATATT
31508376 TGATTCAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (23 bp):
TGTTATATTCAAAGCTATATGCA
Found at i:31510954 original size:3 final size:3
Alignment explanation
Indices: 31510946--31511009 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
31510936 CTTTTTAAGC
*
31510946 CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31510994 CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT C
31511010 ACACCACCGC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:31519189 original size:76 final size:75
Alignment explanation
Indices: 31519100--31519358 Score: 394
Period size: 76 Copynumber: 3.4 Consensus size: 75
31519090 GAATACATTG
* *
31519100 AATATGAA-GGGGTTGCTAAGTGCTGATTCCGCAACTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCC-CAATTCATTGGTGGTTGCTAAGTGCTGATTCCA
31519164 CCGTATCCTTA
65 CCGTATCCTTA
*
31519175 AATATAAAGGGGGTTGCTAAGTGTTGATTCCCTAATTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCCC-AATTCATTGGTGGTTGCTAAGTGCTGATTCCA
*
31519240 CCATATCCTTA
65 CCGTATCCTTA
* *
31519251 AATATAAAGAGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 AATATAAAGGGGGTTGCTAAGTGCTGATTC-CCAATTCATTGGTGGTTGCTAAGTGCTGATTCCA
**
31519316 CCGTATTTTTA
65 CCGTATCCTTA
* *
31519327 AATGTGAAGGGGGTTGCTAAGTGCTGATTCCC
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCCC
31519359 CCAAGGGGTT
Statistics
Matches: 168, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
75 10 0.06
76 156 0.93
77 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (75 bp):
AATATAAAGGGGGTTGCTAAGTGCTGATTCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCAC
CGTATCCTTA
Found at i:31519204 original size:43 final size:40
Alignment explanation
Indices: 31519143--31519357 Score: 161
Period size: 43 Copynumber: 5.5 Consensus size: 40
31519133 ACTCATTGGT
31519143 GGTTGCTAAGTGCTGATTCCACCGTATCCTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-CTTAAAT-T-AAGGG
* * * *
31519186 GGTTGCTAAGTGTTGATT-C-CC-TA-ATT-CATT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATTAAGGG
* *
31519219 GGTTGCTAAGTGCTGATTCCACCATATCCTTAAATATAAAGAG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-CTTAAAT-T-AAGGG
* * *
31519262 GGTTGCTAAGTGCTGATT-CTCCG-A--TT-CATT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATTAAGGG
*
31519295 GGTTGCTAAGTGCTGATTCCACCGTATTTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTA-TCTTAAAT-T-AAGGG
31519338 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
31519358 CCCAAGGGGT
Statistics
Matches: 135, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
33 38 0.28
34 5 0.04
35 3 0.02
36 4 0.03
37 4 0.03
38 8 0.06
39 4 0.03
40 4 0.03
41 3 0.02
42 4 0.03
43 58 0.43
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (40 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATTAAGGG
Found at i:31519394 original size:103 final size:103
Alignment explanation
Indices: 31519261--31519462 Score: 332
Period size: 103 Copynumber: 2.0 Consensus size: 103
31519251 AATATAAAGA
* * * * *
31519261 GGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTT
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
*
31519326 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAG
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAG
*
31519364 GGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
*
31519429 GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
31519463 GAATCACTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (103 bp):
GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAG
Found at i:31519407 original size:33 final size:33
Alignment explanation
Indices: 31519338--31519485 Score: 103
Period size: 33 Copynumber: 4.4 Consensus size: 33
31519328 ATGTGAAGGG
*
31519338 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
31519365 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
31519398 GGTTGCTAAGAGCTGATTCCACC-ATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATC-----AT-TG---GT
*
31519441 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
31519474 GGTTGCTAAGTG
1 GGTTGCTAAGTG
31519486 TTGAATCCAC
Statistics
Matches: 95, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
27 21 0.22
31 2 0.02
32 2 0.02
33 32 0.34
34 5 0.05
36 2 0.02
37 1 0.01
39 2 0.02
40 2 0.02
42 5 0.05
43 21 0.22
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:31524792 original size:22 final size:21
Alignment explanation
Indices: 31524717--31524799 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 21
31524707 CCTTCCTCTC
31524717 CCTTTTCTTTTCTTATCGTTC-TT
1 CCTTTTCTTTTCTT-T--TTCTTT
*
31524740 CCTTTTCTATTTCCTTATTCTTT
1 CCTTTTCT-TTT-CTTTTTCTTT
*
31524763 -ATTCTTCTTTTCTTTTTCCTTT
1 CCTT-TTCTTTTCTTTTT-CTTT
*
31524785 CCTTTTCTTTCCTTT
1 CCTTTTCTTTTCTTT
31524800 GGGTTGTTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
21 5 0.10
22 22 0.45
23 16 0.33
24 3 0.06
25 3 0.06
ACGTcount: A:0.05, C:0.27, G:0.01, T:0.67
Consensus pattern (21 bp):
CCTTTTCTTTTCTTTTTCTTT
Found at i:31526515 original size:127 final size:128
Alignment explanation
Indices: 31526362--31526618 Score: 426
Period size: 127 Copynumber: 2.0 Consensus size: 128
31526352 GATTGTTGAA
*
31526362 TTATCGACTGGGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
1 TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
*
31526427 TGG-TTTTTTTATAATAACGTTACTGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
66 TGGTTTTTTTTATAATAACGTTAATGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
*
31526489 TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATACAAGT
1 TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
* * * * * *
31526554 TGGTTTTTTTTCTAATAATGTTAATGTAACTTTTTAGAGTTGGTCTTAACGTCTAGGCTGAGT
66 TGGTTTTTTTTATAATAACGTTAATGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
31526617 TT
1 TT
31526619 GGGGTGTTAC
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
127 66 0.55
128 54 0.45
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.47
Consensus pattern (128 bp):
TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
TGGTTTTTTTTATAATAACGTTAATGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
Found at i:31526899 original size:30 final size:30
Alignment explanation
Indices: 31526865--31526921 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
31526855 ACAGGAATAA
31526865 GTTGCTCACACAAGCTGACAGTATATCAAG
1 GTTGCTCACACAAGCTGACAGTATATCAAG
* *
31526895 GTTGCTCACACAAGTTGACATTATATC
1 GTTGCTCACACAAGCTGACAGTATATC
31526922 GAGACTACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
GTTGCTCACACAAGCTGACAGTATATCAAG
Found at i:31529340 original size:13 final size:13
Alignment explanation
Indices: 31529322--31529369 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
31529312 CCACTCGCTC
31529322 TATTATTAAATTT
1 TATTATTAAATTT
* *
31529335 TATTATTAGA-TA
1 TATTATTAAATTT
*
31529347 TAATATTAAATTT
1 TATTATTAAATTT
31529360 TATTATTAAA
1 TATTATTAAA
31529370 ATTGTCCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TATTATTAAATTT
Found at i:31530379 original size:22 final size:23
Alignment explanation
Indices: 31530353--31530396 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
31530343 GTGATGAGGT
**
31530353 TATCTTATGAATATGTT-AAATC
1 TATCTTAAAAATATGTTGAAATC
31530375 TATCTTAAAAATATGTTGAAAT
1 TATCTTAAAAATATGTTGAAAT
31530397 ATATTGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (23 bp):
TATCTTAAAAATATGTTGAAATC
Found at i:31539399 original size:13 final size:13
Alignment explanation
Indices: 31539381--31539406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31539371 TCTGTTGCTG
31539381 CACAAAACTTTAT
1 CACAAAACTTTAT
31539394 CACAAAACTTTAT
1 CACAAAACTTTAT
31539407 TTTGTTTATG
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:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CACAAAACTTTAT
Found at i:31539656 original size:5 final size:5
Alignment explanation
Indices: 31539648--31539673 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31539638 TAACTAAGAT
31539648 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
31539674 TAAATCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:31549429 original size:18 final size:18
Alignment explanation
Indices: 31549389--31549425 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
31549379 CCATGATGTT
*
31549389 TGCCCGTGTGGGCCGACA
1 TGCCCGTGTGGGCCCACA
31549407 TGCCCGTGT-GGCCCACA
1 TGCCCGTGTGGGCCCACA
31549424 TG
1 TG
31549426 GCCCAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.35, G:0.35, T:0.19
Consensus pattern (18 bp):
TGCCCGTGTGGGCCCACA
Found at i:31551006 original size:16 final size:16
Alignment explanation
Indices: 31550985--31551054 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
31550975 TTTGGTTCGC
* *
31550985 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
31551001 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
31551017 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31551033 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31551049 TGTAAT
1 TGTAAT
31551055 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:31551138 original size:39 final size:43
Alignment explanation
Indices: 31551033--31551142 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
31551023 GGAATAGAGG
31551033 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
31551078 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
31551118 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
31551143 TAATGAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:31551305 original size:16 final size:16
Alignment explanation
Indices: 31551268--31551309 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31551258 TTAATCATAT
*
31551268 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
31551284 TT-AAATATATTATAA
1 TTAAAATATATTATAA
31551299 TTAAAATATAT
1 TTAAAATATAT
31551310 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:31551316 original size:14 final size:15
Alignment explanation
Indices: 31551277--31551318 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31551267 TTTAAACATA
*
31551277 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31551292 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
31551306 A-TATAATTTAATA
1 ATTATAATTAAATA
31551319 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31551491 original size:47 final size:46
Alignment explanation
Indices: 31551425--31551591 Score: 146
Period size: 47 Copynumber: 3.6 Consensus size: 46
31551415 TTAATTAAAA
*
31551425 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTATCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTATCT
* * * * * *
31551472 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
* * * *
31551517 TA-AT-AATAATATATAATTTCATAA-AATTCTTAATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTATCT
*
31551563 TATATGAATTTATACAATTTAAAATAATT
1 TATATGAATTTATATAATTTAAAATAATT
31551592 CGGATCAATC
Statistics
Matches: 92, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
43 3 0.03
44 15 0.16
45 14 0.15
46 13 0.14
47 40 0.43
48 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
Found at i:31551513 original size:26 final size:28
Alignment explanation
Indices: 31551484--31551555 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
31551474 TATGAATTTG
*
31551484 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
31551510 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
31551538 TAAAATTCTTAATAATAA
1 TATAA-T-TTAATAATAA
31551556 ATTTTCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 12 0.31
29 1 0.03
30 10 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:31551751 original size:22 final size:22
Alignment explanation
Indices: 31551723--31551767 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
31551713 ACTAAGCTTG
31551723 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
31551745 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
31551767 A
1 A
31551768 GTTAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTCATTAAATTACTTTCAA
Found at i:31555464 original size:40 final size:40
Alignment explanation
Indices: 31555409--31555511 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 40
31555399 TTATTGAATT
*
31555409 ATTGCACTTACGTGCCCCTGTTTGTTCTTCGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* *
31555449 ATTGCACTTACGTGCCCCCTATTTGTACTTCGGTACCCTTG
1 ATTGCACTTACGTG-CCCCTGTTTGTACTTCGGTACCCCTG
* * *
31555490 AATGCACATATGTGCCCCTGTT
1 ATTGCACTTACGTGCCCCTGTT
31555512 GCACTTTGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 21 0.38
41 34 0.62
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (40 bp):
ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
Found at i:31555466 original size:20 final size:19
Alignment explanation
Indices: 31555409--31555567 Score: 72
Period size: 20 Copynumber: 7.9 Consensus size: 19
31555399 TTATTGAATT
31555409 ATTGCACTTACGTGCCCCTG
1 ATTGCACTT-CGTGCCCCTG
* ** *
31555429 TTTGTTCTTCGGTACCCCTG
1 ATTGCACTTC-GTGCCCCTG
31555449 ATTGCACTTACGTGCCCCCT-
1 ATTGCACTT-CGTG-CCCCTG
* * *
31555469 ATTTGTACTTCGGTACCCTTG
1 A-TTGCACTTC-GTGCCCCTG
*
31555490 AATGCACATAT-GTGCCCCTG
1 ATTGCAC-T-TCGTGCCCCTG
* *
31555510 -TTGCACTTTGATGCCTCTG
1 ATTGCACTTCG-TGCCCCTG
* * *
31555529 ATCGCACATTCATGCTCCTG
1 ATTGCAC-TTCGTGCCCCTG
*
31555549 ATTGCACTTTGGTGCCCCT
1 ATTGCAC-TTCGTGCCCCT
31555568 ATTATGCGTC
Statistics
Matches: 100, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
17 1 0.01
18 2 0.02
19 13 0.13
20 64 0.64
21 19 0.19
22 1 0.01
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.35
Consensus pattern (19 bp):
ATTGCACTTCGTGCCCCTG
Found at i:31561967 original size:12 final size:13
Alignment explanation
Indices: 31561950--31561983 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
31561940 TTTACTAGGG
31561950 TTAGGGTTTTTA-
1 TTAGGGTTTTTAT
31561962 TTAGGGTTTTTAT
1 TTAGGGTTTTTAT
31561975 TTAGGGTTT
1 TTAGGGTTT
31561984 AGAGTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (13 bp):
TTAGGGTTTTTAT
Found at i:31563626 original size:9 final size:9
Alignment explanation
Indices: 31563614--31563664 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
31563604 ATTAAAAAGA
31563614 AGAGAGTTG
1 AGAGAGTTG
*
31563623 AGAGACTTG
1 AGAGAGTTG
* *
31563632 AAAGGGTTTG
1 AGAGAG-TTG
31563642 AGAG-GATTG
1 AGAGAG-TTG
31563651 AGAGAGTTG
1 AGAGAGTTG
31563660 AGAGA
1 AGAGA
31563665 AGAATGTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 27 0.79
10 7 0.21
ACGTcount: A:0.35, C:0.02, G:0.41, T:0.22
Consensus pattern (9 bp):
AGAGAGTTG
Found at i:31565296 original size:3 final size:3
Alignment explanation
Indices: 31565288--31565319 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31565278 GAGTGAAAAA
31565288 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
31565320 CGACAAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:31565933 original size:3 final size:3
Alignment explanation
Indices: 31565925--31565955 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31565915 TTTGAATTTA
31565925 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
31565956 GTAAGAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31566831 original size:6 final size:6
Alignment explanation
Indices: 31566816--31566849 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
31566806 ATCTACCCAA
* *
31566816 CCCTGG CCCTGC CCCTGC CCCTGC CTCTGC CCCT
1 CCCTGC CCCTGC CCCTGC CCCTGC CCCTGC CCCT
31566850 TTTCTCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.62, G:0.18, T:0.21
Consensus pattern (6 bp):
CCCTGC
Found at i:31569196 original size:3 final size:3
Alignment explanation
Indices: 31569188--31569221 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
31569178 CCATGATCTT
31569188 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31569222 CATCATCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31580681 original size:47 final size:45
Alignment explanation
Indices: 31580605--31580727 Score: 113
Period size: 46 Copynumber: 2.6 Consensus size: 45
31580595 GTGGTTTAAC
* * * *
31580605 CACATATCTATTCTGGCAGCTTAGTTGCAATTATAGTGGCTCGACCA
1 CACATATCTATTTTGGTAGCTTA-CTGCAA-TATAGTAGCTCGACCA
* *
31580652 CACATATCTATTTTGGTAGCTTGACTGCAATGTAGTAGCTTGACCA
1 CACATATCTATTTTGGTAGCTT-ACTGCAATATAGTAGCTCGACCA
* * *
31580698 CATATATTTGA-TTTGGTAGTTTAACTGCAA
1 CACATATCT-ATTTTGGTAGCTT-ACTGCAA
31580728 CTTTGGTGGC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
46 37 0.58
47 26 0.41
48 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (45 bp):
CACATATCTATTTTGGTAGCTTACTGCAATATAGTAGCTCGACCA
Found at i:31581523 original size:29 final size:30
Alignment explanation
Indices: 31581480--31581557 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
31581470 AAATTGAATC
* *
31581480 AAATCAAATTTTCATGTATAAAATCGCACA-
1 AAATCAAA-GTTCATGTACAAAATCGCACAT
* * *
31581510 AAATCAAAGTTCATGTACGACATTGCACATT
1 AAATCAAAGTTCATGTACAAAATCGCACA-T
31581541 AAATCAAAGTTCATGTA
1 AAATCAAAGTTCATGTA
31581558 AATATTCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.39
30 8 0.20
31 17 0.41
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (30 bp):
AAATCAAAGTTCATGTACAAAATCGCACAT
Found at i:31583748 original size:18 final size:18
Alignment explanation
Indices: 31583727--31583771 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
31583717 CATTCGTTTG
31583727 CAAAACATTATTC-ATTT
1 CAAAACATTATTCAATTT
* *
31583744 ACAAATCGTTATTCAATTT
1 -CAAAACATTATTCAATTT
31583763 CAAAACATT
1 CAAAACATT
31583772 TTCTTATTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (18 bp):
CAAAACATTATTCAATTT
Found at i:31587527 original size:20 final size:20
Alignment explanation
Indices: 31587502--31587566 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
31587492 AGTACAACAA
31587502 GGGTACGTAAGTGCGTTCAG
1 GGGTACGTAAGTGCGTTCAG
* ** *
31587522 GGGTACCG-AAGTAC-AACAA
1 GGGTA-CGTAAGTGCGTTCAG
*
31587541 GGGCACGTAAGTGCGTTCAG
1 GGGTACGTAAGTGCGTTCAG
31587561 GGGTAC
1 GGGTAC
31587567 CGAAGTACAA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 17 0.53
21 2 0.06
ACGTcount: A:0.26, C:0.18, G:0.37, T:0.18
Consensus pattern (20 bp):
GGGTACGTAAGTGCGTTCAG
Found at i:31587539 original size:39 final size:39
Alignment explanation
Indices: 31587480--31587618 Score: 188
Period size: 39 Copynumber: 3.6 Consensus size: 39
31587470 AAAGTACTAA
* * *
31587480 CAGGAGTACCAAAGTACAACAAGGGTACGTAAGTGCGTT
1 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
31587519 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
1 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
* * *
31587558 CAGGGGTACCGAAGTACAACAGGGGCACGTACGTGCATT
1 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
** **
31587597 CAAAGGTACTTAAGTACAACAA
1 CAGGGGTACCGAAGTACAACAA
31587619 TTTTTCTACA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.17
Consensus pattern (39 bp):
CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
Found at i:31587580 original size:19 final size:20
Alignment explanation
Indices: 31587471--31587582 Score: 63
Period size: 19 Copynumber: 5.8 Consensus size: 20
31587461 TGCGATACGA
* * *
31587471 AAGTACTAACAGGAGTACCA
1 AAGTACGAACAGGGGTACCG
*
31587491 AAGTAC-AACAAGGGTA-CG
1 AAGTACGAACAGGGGTACCG
* **
31587509 TAAGTGCGTTCAGGGGTACCG
1 -AAGTACGAACAGGGGTACCG
* *
31587530 AAGTAC-AACAAGGGCA-CG
1 AAGTACGAACAGGGGTACCG
* **
31587548 TAAGTGCGTTCAGGGGTACCG
1 -AAGTACGAACAGGGGTACCG
31587569 AAGTAC-AACAGGGG
1 AAGTACGAACAGGGG
31587583 CACGTACGTG
Statistics
Matches: 66, Mismatches: 20, Indels: 13
0.67 0.20 0.13
Matches are distributed among these distances:
18 3 0.05
19 30 0.45
20 29 0.44
21 4 0.06
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (20 bp):
AAGTACGAACAGGGGTACCG
Found at i:31594448 original size:22 final size:22
Alignment explanation
Indices: 31594412--31594455 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31594402 TAGCATGTTG
*
31594412 AAATTTTCTTAATTTT-ATAAT
1 AAATTTTATTAATTTTGATAAT
31594433 AAATTTTGATTAATTTTGATAAT
1 AAATTTT-ATTAATTTTGATAAT
31594456 TTTCGACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
AAATTTTATTAATTTTGATAAT
Found at i:31595148 original size:54 final size:54
Alignment explanation
Indices: 31595084--31595193 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
31595074 CCCTTTCTGA
*
31595084 TTTCATCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
1 TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
31595138 TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
1 TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
31595192 TT
1 TT
31595194 CATAAGAGCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (54 bp):
TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
Found at i:31595176 original size:26 final size:26
Alignment explanation
Indices: 31595093--31595177 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
31595083 ATTTCATCTC
31595093 TTGAAAAAGAGTCAATCTACCACCAT
1 TTGAAAAAGAGTCAATCTACCACCAT
** * * **
31595119 TTGAAGCAGCATTCAAGTTTTTCACC-T
1 TTGAAAAAG-AGTCAA-TCTACCACCAT
31595146 CTTGAAAAAGAGTCAATCTACCACCAT
1 -TTGAAAAAGAGTCAATCTACCACCAT
31595173 TTGAA
1 TTGAA
31595178 GCAGCATTCA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
26 18 0.42
27 12 0.28
28 13 0.30
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (26 bp):
TTGAAAAAGAGTCAATCTACCACCAT
Found at i:31604985 original size:28 final size:28
Alignment explanation
Indices: 31604953--31605008 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
31604943 CAGTGACGGT
* *
31604953 ACAGTGAGGGCCTTAGCCCAATTCAGTA
1 ACAGTGAGGGCCTTAACCCAATACAGTA
*
31604981 ACAGTGTGGGCCTTAACCCAATACAGTA
1 ACAGTGAGGGCCTTAACCCAATACAGTA
31605009 TCATTACAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (28 bp):
ACAGTGAGGGCCTTAACCCAATACAGTA
Found at i:31605412 original size:26 final size:27
Alignment explanation
Indices: 31605383--31605519 Score: 170
Period size: 27 Copynumber: 5.1 Consensus size: 27
31605373 TATAAAGATC
*
31605383 ATTTTACCCTTAG-GGGTATTACGGTA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
**
31605409 ATTTTACCCTTAG-GGGTATTTTAGTA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
* *
31605435 ATTTTACCCTTTGAGGGTATTTCGATA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
* **
31605462 ATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
* *
31605489 ATTTTACCCTTTGAGGGTATTTCGATA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
31605516 ATTT
1 ATTT
31605520 ACTCATGAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
26 35 0.37
27 60 0.63
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTAGAGGGTATTTCGGTA
Found at i:31605495 original size:54 final size:53
Alignment explanation
Indices: 31605383--31605519 Score: 222
Period size: 54 Copynumber: 2.6 Consensus size: 53
31605373 TATAAAGATC
* * *
31605383 ATTTTACCCTTAG-GGGTATTACGGTAATTTTACCCTTAGGGGTATTTTAGTA
1 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTAGGGGTATTTTAGTA
*
31605435 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTAG-GGGTATTTTAGTA
31605489 ATTTTACCCTTTGAGGGTATTTCGATAATTT
1 ATTTTACCCTTTGAGGGTATTTCGATAATTT
31605520 ACTCATGAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 12 0.15
53 23 0.29
54 44 0.56
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (53 bp):
ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTAGGGGTATTTTAGTA
Found at i:31606679 original size:570 final size:570
Alignment explanation
Indices: 31605600--31606740 Score: 1957
Period size: 570 Copynumber: 2.0 Consensus size: 570
31605590 ACGGCTTTTT
*
31605600 GGCTTTTCGCTGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
1 GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
* * *
31605665 TCCACGGACACCAACCTAGATTTCATCAAATCACAAGTCAGCCGTTAAAGCAATACACCCTATTA
66 TCCACGCACACCAACCTAGATTTCATCAAATCACAAGTCAGCCCTTAAAGCAAGACACCCTATTA
* * *
31605730 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAGGGTGACTTAACTCCTTCAATAT
131 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
** *
31605795 TCCCAACCGAAAATGGTCACCCACTTAATGATTACCTGTACCACAACACAAATCTTCATAAACTA
196 TCCCAACCGAAAATGGTCACCCACTTAATGATTACCAATACCACAACACAAATATTCATAAACTA
* *
31605860 ACTTGGCCAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAAT
261 ACTAGGACAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAAT
31605925 TTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGAC
326 TTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGAC
* *
31605990 AGTAAAAATAGTGAAGAGAAGATCGGTGTAGAGGAATAGAGCAAAAGGTGATAATCGGCTGAACC
391 AGTAAAAATAGTCAAGAGAAGATCGGTGCAGAGGAATAGAGCAAAAGGTGATAATCGGCTGAACC
31606055 ACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAATAAAA
456 ACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAATAAAA
31606120 TCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
521 TCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
*
31606170 GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGTGCAAACC
1 GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
* * *
31606235 TCCATGCACACCAACCTAGATTTCATCAAATCACAAGTTAGCCCTTAAAGCAAGACACCCTTTTA
66 TCCACGCACACCAACCTAGATTTCATCAAATCACAAGTCAGCCCTTAAAGCAAGACACCCTATTA
31606300 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
131 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
*
31606365 TCCCAACCGAAAATGGTCACCCACTTAACT-ATTACCAATACCACAACACAGATATTCATAAACT
196 TCCCAACCGAAAATGGTCACCCACTTAA-TGATTACCAATACCACAACACAAATATTCATAAACT
* * *
31606429 AACTAGGACAAAATAGTGGCTAAGAGGAGTATTCGATTTTAATGAAAAGAAAGAAAGAGAACCGA
260 AACTAGGACAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAA
* * *
31606494 TTTTAAACAAAAATTGAAGAGTATTCAAACTTTACCGATAATCAGGAATACTTGCAGCACTGAGA
325 TTTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGA
* * *
31606559 CAGTAAAAATAG-CAAGGAGAATATCGGCT-CAGAGGAATA-ATGCAAAAGGTGATAATCTGTTG
390 CAGTAAAAATAGTCAA-GAGAAGATCGG-TGCAGAGGAATAGA-GCAAAAGGTGATAATCGGCTG
*
31606621 AACTACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAAT
452 AACCACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAAT
31606686 AAAATCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
517 AAAATCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
31606740 G
1 G
31606741 AGGTCAGAGA
Statistics
Matches: 538, Mismatches: 29, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
569 3 0.01
570 533 0.99
571 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (570 bp):
GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
TCCACGCACACCAACCTAGATTTCATCAAATCACAAGTCAGCCCTTAAAGCAAGACACCCTATTA
ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
TCCCAACCGAAAATGGTCACCCACTTAATGATTACCAATACCACAACACAAATATTCATAAACTA
ACTAGGACAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAAT
TTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGAC
AGTAAAAATAGTCAAGAGAAGATCGGTGCAGAGGAATAGAGCAAAAGGTGATAATCGGCTGAACC
ACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAATAAAA
TCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
Found at i:31615703 original size:13 final size:13
Alignment explanation
Indices: 31615685--31615709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31615675 CGGCGATCAT
31615685 CCATCTGATTCCC
1 CCATCTGATTCCC
31615698 CCATCTGATTCC
1 CCATCTGATTCC
31615710 ATCATTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.08, T:0.32
Consensus pattern (13 bp):
CCATCTGATTCCC
Found at i:31617308 original size:13 final size:14
Alignment explanation
Indices: 31617289--31617326 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
31617279 CAATGACATA
31617289 GAAATAATATAAAC
1 GAAATAATATAAAC
31617303 -AAATAA-ATAAAC
1 GAAATAATATAAAC
31617315 GAAATTAATATA
1 GAAA-TAATATA
31617327 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:31617720 original size:28 final size:26
Alignment explanation
Indices: 31617682--31617762 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 26
31617672 AAAAATATAT
31617682 AAATATATACATGTACATATATATAAAA
1 AAATAT-TACAT-TACATATATATAAAA
* *
31617710 AAATATCTACA-TATATATAGATTATAAA
1 AAATAT-TACATTACATATATA-TA-AAA
*
31617738 AAAGA-TA-ATTACATATATATAAAA
1 AAATATTACATTACATATATATAAAA
31617762 A
1 A
31617763 CAAATAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
24 4 0.09
25 3 0.07
26 18 0.41
27 2 0.05
28 17 0.39
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (26 bp):
AAATATTACATTACATATATATAAAA
Found at i:31617945 original size:17 final size:17
Alignment explanation
Indices: 31617923--31617957 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31617913 TAGGAAATAA
* *
31617923 AAAATGTATATGTATAT
1 AAAATGTAAATATATAT
31617940 AAAATGTAAATATATAT
1 AAAATGTAAATATATAT
31617957 A
1 A
31617958 TGTATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AAAATGTAAATATATAT
Found at i:31618473 original size:21 final size:22
Alignment explanation
Indices: 31618415--31618473 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
31618405 AAATTAAATC
*
31618415 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATATATCATA--T
**
31618438 TCTAAGATTGTATATATCATA-
1 TCTAAGATTACATATATCATAT
31618459 TCTAAGATTACATAT
1 TCTAAGATTACATAT
31618474 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 13 0.43
23 10 0.33
24 7 0.23
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (22 bp):
TCTAAGATTACATATATCATAT
Found at i:31623252 original size:29 final size:30
Alignment explanation
Indices: 31623210--31623272 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 30
31623200 ACAATATCAA
*
31623210 AAATAATTTGATCTTTATCCAGCCAA-TTT
1 AAATAATTTAATCTTTATCCAGCCAACTTT
31623239 CAAAT-ATTTAATCTTTATCCAGCCAACTTT
1 -AAATAATTTAATCTTTATCCAGCCAACTTT
31623269 AAAT
1 AAAT
31623273 CTCCAATCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATAATTTAATCTTTATCCAGCCAACTTT
Found at i:31623280 original size:29 final size:29
Alignment explanation
Indices: 31623220--31623283 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
31623210 AAATAATTTG
**
31623220 ATCTTTATCCAGCCAATTTCAAATATTTA
1 ATCTTTATCCAGCCAATTTCAAATATCCA
*
31623249 ATCTTTATCCAGCCAACTTT-AAATCTCCA
1 ATCTTTATCCAGCCAA-TTTCAAATATCCA
31623278 ATCTTT
1 ATCTTT
31623284 CAATCTACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (29 bp):
ATCTTTATCCAGCCAATTTCAAATATCCA
Found at i:31624148 original size:26 final size:27
Alignment explanation
Indices: 31624060--31624168 Score: 118
Period size: 26 Copynumber: 4.2 Consensus size: 27
31624050 TCATTAGGCG
* *
31624060 TAGCAGGCTTTGTGCCA-ATGTATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
* * * *
31624086 TAGTAGGCTTCGAGCC-GATATATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
*
31624112 TAGTAAGCTTTGAG-CAGATGTATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
*
31624138 TAGCAAGCTTTGTGCCAG-TGTATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
31624164 TAGCA
1 TAGCA
31624169 GGTACTATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.01
26 67 0.94
27 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (27 bp):
TAGCAAGCTTTGAGCCAGATGTATATT
Found at i:31625653 original size:37 final size:37
Alignment explanation
Indices: 31625596--31625701 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
31625586 TATGATCACT
*
31625596 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
*
31625631 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
31625668 TATCACTTTGTTTCTTGATCAGATAAGTATAGCC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
31625702 GAAGCTATCA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 6 0.09
36 5 0.08
37 54 0.83
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:31625731 original size:46 final size:46
Alignment explanation
Indices: 31625664--31625833 Score: 232
Period size: 46 Copynumber: 3.6 Consensus size: 46
31625654 TAAGTGTAGC
**
31625664 CACTTATCACTTTGTTTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
31625710 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
31625756 TACTTATCACTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
31625807 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
31625834 AGTACTCAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
46 69 0.62
48 1 0.01
49 1 0.01
51 40 0.36
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:31625804 original size:51 final size:52
Alignment explanation
Indices: 31625707--31625819 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 52
31625697 TAGCCGAAGC
* **
31625707 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTT-TCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
* *
31625760 TATCACTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
31625811 TATCACTTT
1 TATCACTTT
31625820 GTCACTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 43 0.78
52 4 0.07
53 8 0.15
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (52 bp):
TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
Found at i:31629350 original size:30 final size:31
Alignment explanation
Indices: 31629316--31629383 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
31629306 TTCCCCAAGA
** * * *
31629316 GTAAATACTCAAAATTTGAGGGGTTAA-AGT
1 GTAAATACGAAAAATTTGAAGGATCAATAGT
31629346 GTAAATACGAAAAATTTGAAGGATCAATAGT
1 GTAAATACGAAAAATTTGAAGGATCAATAGT
31629377 GTAAATA
1 GTAAATA
31629384 TTTTAAGAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.28
Consensus pattern (31 bp):
GTAAATACGAAAAATTTGAAGGATCAATAGT
Found at i:31633821 original size:50 final size:50
Alignment explanation
Indices: 31633763--31633885 Score: 165
Period size: 50 Copynumber: 2.5 Consensus size: 50
31633753 ATTGAGGTTC
* * *
31633763 TGAGAGGTCCCATGTAAGACCATGTCTCGGACATGGCGTTGGCACCGAGA
1 TGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGA
* * * *
31633813 TGAGAGGTCCCCTGTAAAACCATGTCTATGACATGGCATGGGCACCGATA
1 TGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGA
**
31633863 TGAGAACTCCCATGTAAGACCAT
1 TGAGAGGTCCCATGTAAGACCAT
31633886 ATCTGGGTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (50 bp):
TGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGA
Found at i:31634183 original size:20 final size:20
Alignment explanation
Indices: 31634158--31634196 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31634148 TGATTTATTT
31634158 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
31634178 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
31634197 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:31657411 original size:24 final size:24
Alignment explanation
Indices: 31657352--31657416 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 24
31657342 TTAAAACGTT
31657352 TTCTAT-A-AGTCTTTTTTGTCTG
1 TTCTATAAGAGTCTTTTTTGTCTG
31657374 TTCTGTACTTTAAGAGTCTTTTTTGTCTG
1 TTC--TA---TAAGAGTCTTTTTTGTCTG
31657403 TTCTATAAGAGTCT
1 TTCTATAAGAGTCT
31657417 ATAATACTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
22 3 0.08
24 11 0.31
27 3 0.08
28 1 0.03
29 18 0.50
ACGTcount: A:0.17, C:0.14, G:0.15, T:0.54
Consensus pattern (24 bp):
TTCTATAAGAGTCTTTTTTGTCTG
Found at i:31657768 original size:21 final size:21
Alignment explanation
Indices: 31657744--31657783 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
31657734 TTTTACGTTT
31657744 TTTCTCTCAAAGGCCTAAAAC
1 TTTCTCTCAAAGGCCTAAAAC
31657765 TTTCTCTCAAAGGCCTAAA
1 TTTCTCTCAAAGGCCTAAA
31657784 GTCTCACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCTCTCAAAGGCCTAAAAC
Found at i:31661242 original size:29 final size:29
Alignment explanation
Indices: 31661210--31661267 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
31661200 TGTATAACCC
* *
31661210 ATATTAATTTGA-AAATAATTTCTTATTTT
1 ATATTAATTTGATAAA-AATCTCTAATTTT
*
31661239 ATATTATTTTGATAAAAATCTCTAATTTT
1 ATATTAATTTGATAAAAATCTCTAATTTT
31661268 TAAACTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (29 bp):
ATATTAATTTGATAAAAATCTCTAATTTT
Found at i:31662611 original size:18 final size:17
Alignment explanation
Indices: 31662588--31662647 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
31662578 TATGATATGG
31662588 AACTTATTCAGTTTATTA
1 AACTTATTCAGTTTA-TA
*
31662606 AACTTAATTAAAG--TATA
1 AACTT-ATT-CAGTTTATA
31662623 AACTTATTTCAGTTTATA
1 AACTTA-TTCAGTTTATA
31662641 AA-TTATT
1 AACTTATT
31662648 TGAAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 5 0.14
17 12 0.34
18 13 0.37
19 3 0.09
20 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (17 bp):
AACTTATTCAGTTTATA
Found at i:31663806 original size:22 final size:22
Alignment explanation
Indices: 31663778--31663827 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
31663768 ACAAATCCTA
31663778 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
* *
31663800 TCTCAATTTCCTTTCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
31663822 TCTCAA
1 TCTCAA
31663828 ACTCTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:31663833 original size:30 final size:30
Alignment explanation
Indices: 31663799--31663857 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
31663789 TTCCAAAATC
* *
31663799 CTCTCAATTTCCTTTCAAAATTCTCTCAAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
31663829 CTCTCAATTTCCTTCCAAAATCCTCTCAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAA
31663858 TTTCCTTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (30 bp):
CTCTCAATTTCCTTCCAAAATCCTCTCAAA
Found at i:31663840 original size:52 final size:52
Alignment explanation
Indices: 31663778--31663880 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
31663768 ACAAATCCTA
* *
31663778 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTTCAAAATTCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAC
31663830 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
31663881 TCCATATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAC
Found at i:31663855 original size:22 final size:22
Alignment explanation
Indices: 31663829--31663879 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
31663819 TTCTCTCAAA
31663829 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCCTTCCAAAAAT
31663850 CCTCTCAATTTCCTTCCAAAAAT
1 -CTCTCAATTTCCTTCCAAAAAT
31663873 CTCTCAA
1 CTCTCAA
31663880 ATCCATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAAAT
Found at i:31663955 original size:29 final size:29
Alignment explanation
Indices: 31663915--31663978 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
31663905 TCAATTTCAT
31663915 TTTTTTAAAATAATTTTAAATTTTTTATA
1 TTTTTTAAAATAATTTTAAATTTTTTATA
*
31663944 TTTTTTAAAATAATTTTAAATTTTTTTTA
1 TTTTTTAAAATAATTTTAAATTTTTTATA
*
31663973 TATTTT
1 TTTTTT
31663979 CATCAATGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTTTAAAATAATTTTAAATTTTTTATA
Found at i:31665063 original size:7 final size:7
Alignment explanation
Indices: 31665051--31665082 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
31665041 AGTAGATTGA
31665051 TATTTAG
1 TATTTAG
31665058 TATTTAG
1 TATTTAG
31665065 TATTTAG
1 TATTTAG
*
31665072 TATTTTG
1 TATTTAG
31665079 TATT
1 TATT
31665083 ATGTATGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TATTTAG
Found at i:31666355 original size:29 final size:29
Alignment explanation
Indices: 31666289--31666458 Score: 268
Period size: 29 Copynumber: 5.8 Consensus size: 29
31666279 AAAAAAAATT
*
31666289 TAATTTAATTAAAAACCCTAAACACTAACC
1 TAATTTAATTAAAAACCCT-AACCCTAACC
****
31666319 TAATTTAACCCTAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
31666348 TAATTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
31666377 TAATTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACC
*
31666406 TAATTTAATTAAAAACCCTAAACCCTAACT
1 TAATTTAATTAAAAACCCT-AACCCTAACC
31666436 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
31666459 ATTAACAAAA
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
29 86 0.67
30 43 0.33
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (29 bp):
TAATTTAATTAAAAACCCTAACCCTAACC
Done.