Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 11 of 190
Found at i:1703115 original size:30 final size:30
Alignment explanation
Indices: 1703075--1703157 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
1703065 ATAGATGAAT
* *
1703075 TAAATTGAATTAAATTTATAAAATTTAATC
1 TAAATCGAATTAAATTTAAAAAATTTAATC
* * *
1703105 TAAATCGAATTGATTTTAAAAAATTTAATT
1 TAAATCGAATTAAATTTAAAAAATTTAATC
**
1703135 TAAATTTATATTAAAATTTAAAA
1 TAAATCGA-ATT-AAATTTAAAA
1703158 TTTTATAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 31 0.74
31 3 0.07
32 8 0.19
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (30 bp):
TAAATCGAATTAAATTTAAAAAATTTAATC
Found at i:1704611 original size:6 final size:6
Alignment explanation
Indices: 1704600--1704628 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1704590 TCAAAACCTT
1704600 CTCCTG CTCCTG CTCCTG CTCCTG CTCCT
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCT
1704629 CAGCCAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.14, T:0.34
Consensus pattern (6 bp):
CTCCTG
Found at i:1705874 original size:21 final size:21
Alignment explanation
Indices: 1705848--1705887 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1705838 ATTTTTTGGG
1705848 TTTTACATGTGTTAATATGTA
1 TTTTACATGTGTTAATATGTA
* *
1705869 TTTTACGTGTGTTGATATG
1 TTTTACATGTGTTAATATG
1705888 AATCAAGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTTACATGTGTTAATATGTA
Found at i:1727053 original size:26 final size:26
Alignment explanation
Indices: 1726991--1727054 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
1726981 TCTAGTTTAA
* * *
1726991 ACCCAATTGGACCCATTCTGGCCCTG
1 ACCCAATTGGGCCCATTCTAGCCCTC
* *
1727017 ACCCAACTGGGCCCATTCTAGCCTTC
1 ACCCAATTGGGCCCATTCTAGCCCTC
1727043 ACCCAATTGGGC
1 ACCCAATTGGGC
1727055 TTATTCTGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.22
Consensus pattern (26 bp):
ACCCAATTGGGCCCATTCTAGCCCTC
Found at i:1727104 original size:26 final size:26
Alignment explanation
Indices: 1727072--1727145 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 26
1727062 GGTTCGGGCT
* * *
1727072 TAATTGGGCCTATCTTGGTCCAAGCC
1 TAATTGGGCCCATTTTGGTCCAAACC
*
1727098 TAGTTGGGCCCATTTTGGT-CAAACC
1 TAATTGGGCCCATTTTGGTCCAAACC
*
1727123 TAATTAGGCCCATTTTGGTCCAA
1 TAATTGGGCCCATTTTGGTCCAA
1727146 TTGGATTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 22 0.54
26 19 0.46
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (26 bp):
TAATTGGGCCCATTTTGGTCCAAACC
Found at i:1727169 original size:3 final size:3
Alignment explanation
Indices: 1727161--1727217 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
1727151 TTATGTTACC
*
1727161 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1727209 ATT ATT ATT
1 ATT ATT ATT
1727218 TTTTTGTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1727662 original size:23 final size:24
Alignment explanation
Indices: 1727636--1727683 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1727626 TTTTTTTTAA
* *
1727636 TTTTTCAAGATTTTTC-AGGATTT
1 TTTTTAAAAATTTTTCTAGGATTT
*
1727659 TTTTTAAAAATTTTTCTAGGCTTT
1 TTTTTAAAAATTTTTCTAGGATTT
1727683 T
1 T
1727684 CTAGGTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.58
Consensus pattern (24 bp):
TTTTTAAAAATTTTTCTAGGATTT
Found at i:1727684 original size:33 final size:32
Alignment explanation
Indices: 1727620--1727684 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
1727610 AAGATGACCT
** *
1727620 AGGATTTTTTTTTTAATTTTTCAAGATTTTTC
1 AGGATTTTTTTTAAAATTTTTCAAGACTTTTC
* *
1727652 AGGATTTTTTTTAAAAATTTTTCTAGGCTTTTC
1 AGGATTTTTTTT-AAAATTTTTCAAGACTTTTC
1727685 TAGGTTTGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.23, C:0.08, G:0.11, T:0.58
Consensus pattern (32 bp):
AGGATTTTTTTTAAAATTTTTCAAGACTTTTC
Found at i:1728093 original size:14 final size:14
Alignment explanation
Indices: 1728074--1728106 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1728064 CATGTTTTTC
1728074 TTTATTTATTTATT
1 TTTATTTATTTATT
1728088 TTTATTTATTTATT
1 TTTATTTATTTATT
1728102 TTTAT
1 TTTAT
1728107 CCATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:1728095 original size:18 final size:18
Alignment explanation
Indices: 1728068--1728102 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1728058 TGACCACATG
*
1728068 TTTTTCTTTATTTATTTA
1 TTTTTATTTATTTATTTA
1728086 TTTTTATTTATTTATTT
1 TTTTTATTTATTTATTT
1728103 TTATCCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTATTTATTTATTTA
Found at i:1739589 original size:89 final size:89
Alignment explanation
Indices: 1739381--1740172 Score: 544
Period size: 89 Copynumber: 8.9 Consensus size: 89
1739371 GTTTCGTCTC
* * * * * *
1739381 GATCACATGATTCATGGTTTCATTCTGATCATTTATTTTTGACCTCGACTCGATCTTGGTCACTT
1 GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGACTAGATCTTGGTCACTT
* ** * *
1739446 TATTTCG-CTTATGGTTTCATCCC
66 TATTTTGACTCGTGATTTCATCCT
* * * * * * * ** * *
1739469 AATCACATGATT-ATTAGTTTCGTCTTGATCATTCATTTTTTACCTTGATTAGGGCCTGGTCATT
1 GATCACATGATTCGTGA-TTTCATCCTGATCATTCATTTTTGACCTTGACTAGATCTTGGTCACT
*
1739533 TTATTTTGACTCGTGATTTTATCCT
65 TTATTTTGACTCGTGATTTCATCCT
* * * * **
1739558 GATCACATGATTCGTGATTTCATCCTGATCATTTATTTTTGACATTGACTCGATATTGGTTGCTT
1 GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGACTAGATCTTGGTCACTT
** *
1739623 TATTTTGACTTATGATTTCATCTT
66 TATTTTGACTCGTGATTTCATCCT
* * ** * *
1739647 GGTCACATGATTCGTGGTTTCATCCCAATCATTCATTTTTGA-CTTCGACTCGATCTGGGTCACT
1 GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTT-GACTAGATCTTGGTCACT
* * *
1739711 TTATTTTAACTCGTGGTTTCATCCC
65 TTATTTTGACTCGTGATTTCATCCT
* * * * * * ** * * * *
1739736 GATCACATGGTTTGTGGTTTCATCCTGATTATTTATATTAAACCTAGACTCGATCTTGATCAATT
1 GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGACTAGATCTTGGTCACTT
* * **
1739801 TATTTGGACTCATGATTTTGT-CT
66 TATTTTGACTCGTGATTTCATCCT
* ** ** * * * ** *
1739824 CGATCACATAATTTATGATTTCATTTTGATCATTTATTTTTGACATTGATTTAG-TCTTAATCGC
1 -GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGA-CTAGATCTTGGTCAC
*
1739888 TTTATTTCGACTCGT-AGTTTCAT-CT
64 TTTATTTTGACTCGTGA-TTTCATCCT
* * * * * * * * * *
1739913 CGATCATATAATTAGTGGTTTCCTCTTGATCATTCATTTTTTACCTCGACTCGATCTTGGTCGCT
1 -GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGACTAGATCTTGGTCACT
* *
1739978 TTATTTTGACTCGTGGTTTCATCCC
65 TTATTTTGACTCGTGATTTCATCCT
* * * * * * * * *
1740003 AATCACATGATTCGTGATTTCATCTTTATTATTTATTTTTAATCTCGACTCA-ATCTTGGTCATT
1 GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGACT-AGATCTTGGTCACT
*
1740067 TTATTTTGACTCGTGGTTTCAT-CT
65 TTATTTTGACTCGTGATTTCATCCT
* * * * * * *
1740091 CGGTCACATGATTCATGATTTCATCCTAATCA-TCATTTTCGACTTTGACTTGGTCTTGGTCACT
1 -GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGACTAGATCTTGGTCACT
*
1740155 TTA-TTTAACTCGTGATTT
65 TTATTTTGACTCGTGATTT
1740173 AATCTCGGTC
Statistics
Matches: 541, Mismatches: 149, Indels: 29
0.75 0.21 0.04
Matches are distributed among these distances:
87 15 0.03
88 85 0.16
89 434 0.80
90 7 0.01
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.46
Consensus pattern (89 bp):
GATCACATGATTCGTGATTTCATCCTGATCATTCATTTTTGACCTTGACTAGATCTTGGTCACTT
TATTTTGACTCGTGATTTCATCCT
Found at i:1739742 original size:178 final size:177
Alignment explanation
Indices: 1739354--1740160 Score: 688
Period size: 178 Copynumber: 4.5 Consensus size: 177
1739344 GTCTTAGTTG
** * * * *
1739354 CTTTATTTCAACTCGTAGTTTCGTCTCGATCACATGATTCATGGTTTCATTCTGATCATTTATTT
1 CTTTATTTTGACTCGTGGTTTCATCTCGATCACATGATTCGTGGTTTCATCCTGATCATTTATTT
* * * *
1739419 TTGACCTCGACTCGATCTTGGTCACTTTATTTCG-CTTATGGTTTCATCCCAATCACATGATT-A
66 TTGACCTCGACTCGATCTTGGTCACTTTATTTTGACTCATGATTTCATCCCAATCACATGATTCG
* * * * * ** *
1739482 TTAGTTTCGTCTTGATCATTCATTTTTTACCTTGATTAGGGCCTGGTCA
131 TGA-TTTCATCTTGATCATTCATTTTTGA-CTTGACTCGATCTTGGTCA
* * * *
1739531 TTTTATTTTGACTCGTGATTTTATC-CTGATCACATGATTCGTGATTTCATCCTGATCATTTATT
1 CTTTATTTTGACTCGTGGTTTCATCTC-GATCACATGATTCGTGGTTTCATCCTGATCATTTATT
* * * ** * ****
1739595 TTTGACATTGACTCGATATTGGTTGCTTTATTTTGACTTATGATTTCATCTTGGTCACATGATTC
65 TTTGACCTCGACTCGATCTTGGTCACTTTATTTTGACTCATGATTTCATCCCAATCACATGATTC
* *** *
1739660 GTGGTTTCATCCCAATCATTCATTTTTGACTTCGACTCGATCTGGGTCA
130 GTGATTTCATCTTGATCATTCATTTTTGACTT-GACTCGATCTTGGTCA
* * * * * *
1739709 CTTTATTTTAACTCGTGGTTTCATCCCGATCACATGGTTTGTGGTTTCATCCTGATTATTTATAT
1 CTTTATTTTGACTCGTGGTTTCATCTCGATCACATGATTCGTGGTTTCATCCTGATCATTTATTT
** * * * * ** * * * **
1739774 TAAACCTAGACTCGATCTTGATCAATTTATTTGGACTCATGATTTTGTCTCGATCACATAATTTA
66 TTGACCTCGACTCGATCTTGGTCACTTTATTTTGACTCATGATTTCATCCCAATCACATGATTCG
* * ** ** *
1739839 TGATTTCATTTTGATCATTTATTTTTGACATTGA-TTTAGTCTTAATCG
131 TGATTTCATCTTGATCATTCATTTTTGAC-TTGACTCGA-TCTTGGTCA
* * * * * * * *
1739887 CTTTATTTCGACTCGTAGTTTCATCTCGATCATATAATTAGTGGTTTCCTCTTGATCATTCATTT
1 CTTTATTTTGACTCGTGGTTTCATCTCGATCACATGATTCGTGGTTTCATCCTGATCATTTATTT
* * * *
1739952 TTTACCTCGACTCGATCTTGGTCGCTTTATTTTGACTCGTGGTTTCATCCCAATCACATGATTCG
66 TTGACCTCGACTCGATCTTGGTCACTTTATTTTGACTCATGATTTCATCCCAATCACATGATTCG
* * * * * *
1740017 TGATTTCATCTTTATTATTTATTTTTAATCTCGACTCAATCTTGGTCA
131 TGATTTCATCTTGATCATTCATTTTTGA-CTTGACTCGATCTTGGTCA
* * * * * *
1740065 TTTTATTTTGACTCGTGGTTTCATCTCGGTCACATGATTCATGATTTCATCCTAATCA-TCATTT
1 CTTTATTTTGACTCGTGGTTTCATCTCGATCACATGATTCGTGGTTTCATCCTGATCATTTATTT
* * * * *
1740129 TCGACTTTGACTTGGTCTTGGTCACTTTATTT
66 TTGACCTCGACTCGATCTTGGTCACTTTATTT
1740161 AACTCGTGAT
Statistics
Matches: 489, Mismatches: 132, Indels: 18
0.77 0.21 0.03
Matches are distributed among these distances:
176 1 0.00
177 117 0.24
178 364 0.74
179 7 0.01
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.46
Consensus pattern (177 bp):
CTTTATTTTGACTCGTGGTTTCATCTCGATCACATGATTCGTGGTTTCATCCTGATCATTTATTT
TTGACCTCGACTCGATCTTGGTCACTTTATTTTGACTCATGATTTCATCCCAATCACATGATTCG
TGATTTCATCTTGATCATTCATTTTTGACTTGACTCGATCTTGGTCA
Found at i:1739864 original size:267 final size:266
Alignment explanation
Indices: 1739203--1740123 Score: 852
Period size: 267 Copynumber: 3.4 Consensus size: 266
1739193 ATCATTTTTT
* * * * * * *
1739203 ATGATTCGTGGTTTCGT-TTCGATAATTTATTTTCAACCTCGACTC-AGTCCTAGTCATTTTATT
1 ATGATTTGTGGTTTCATCTT-GATTATTTATTTTTAACCTAGACTCGA-TCTTGGTCATTTTATT
** * * * ** **
1739266 TTGACTCGTGATTTCGTCTCAAGCACATGATTCGTGGATTT-ATCCCAATCATTTATTTTCAACC
64 TTGACTCGTGATTTTATCTCGATCACATGATTCAT-GATTTCATCCTGATCATTTATTTTTGA--
* * * * * *
1739330 TCTACTTGGACTTG-GTCTTAGTTGCTTTATTTCAACTCGTAGTTTCGTCTCGATCACATGATTC
126 -C-A-TT-GA-TCGAGTATTAATCGCTTTATTTCGACTC-TAGTTTCATCTCGATCACATGATTC
* * * ** **
1739394 ATGGTTTCATTCTGATCATTTATTTTTGACCTCGACTCGATCTTGGTCACTTTA-TTTCGCTTAT
185 GTGGTTTCATCCTGATCATTCATTTTTGACCTCGACTCGATCTTGGTCACTTTATTTTAACTCGT
1739458 GGTTTCATCCCAATCAC
250 GGTTTCATCCCAATCAC
* * * * * * * * ** *
1739475 ATGATTAT-TAGTTTCGTCTTGATCATTCATTTTTTACCTTGATTAGGGCCTGGTCATTTTATTT
1 ATGATT-TGTGGTTTCATCTTGATTATTTATTTTTAACCTAGACTCGATCTTGGTCATTTTATTT
*
1739539 TGACTCGTGATTTTATC-CTGATCACATGATTCGTGATTTCATCCTGATCATTTATTTTTGACAT
65 TGACTCGTGATTTTATCTC-GATCACATGATTCATGATTTCATCCTGATCATTTATTTTTGACAT
** * * * *
1739603 TGACTCGA-TATTGGTTGCTTTATTTTGACT-TATGATTTCATCTTGGTCACATGATTCGTGGTT
129 TGA-TCGAGTATTAATCGCTTTATTTCGACTCTA-G-TTTCATCTCGATCACATGATTCGTGGTT
** * *
1739666 TCATCCCAATCATTCATTTTTGACTTCGACTCGATCTGGGTCACTTTATTTTAACTCGTGGTTTC
191 TCATCCTGATCATTCATTTTTGACCTCGACTCGATCTTGGTCACTTTATTTTAACTCGTGGTTTC
*
1739731 ATCCCGATCAC
256 ATCCCAATCAC
* * * * * * *
1739742 ATGGTTTGTGGTTTCATCCTGATTATTTATATTAAACCTAGACTCGATCTTGATCAATTTATTTG
1 ATGATTTGTGGTTTCATCTTGATTATTTATTTTTAACCTAGACTCGATCTTGGTCATTTTATTTT
* * * * **
1739807 GACTCATGATTTTGTCTCGATCACATAATTTATGATTTCATTTTGATCATTTATTTTTGACATTG
66 GACTCGTGATTTTATCTCGATCACATGATTCATGATTTCATCCTGATCATTTATTTTTGACATTG
** * * * * *
1739872 ATTTAGTCTTAATCGCTTTATTTCGACTCGTAGTTTCATCTCGATCATATAATTAGTGGTTTCCT
131 ATCGAGTATTAATCGCTTTATTTCGACTC-TAGTTTCATCTCGATCACATGATTCGTGGTTTCAT
* * * *
1739937 CTTGATCATTCATTTTTTACCTCGACTCGATCTTGGTCGCTTTATTTTGACTCGTGGTTTCATCC
195 CCTGATCATTCATTTTTGACCTCGACTCGATCTTGGTCACTTTATTTTAACTCGTGGTTTCATCC
1740002 CAATCAC
260 CAATCAC
* * * * * *
1740009 ATGATTCGTGATTTCATCTTTATTATTTATTTTTAATCTCGACTCAATCTTGGTCATTTTATTTT
1 ATGATTTGTGGTTTCATCTTGATTATTTATTTTTAACCTAGACTCGATCTTGGTCATTTTATTTT
* * * *
1740074 GACTCGTGGTTTCATCTCGGTCACATGATTCATGATTTCATCCTAATCAT
66 GACTCGTGATTTTATCTCGATCACATGATTCATGATTTCATCCTGATCAT
1740124 CATTTTCGAC
Statistics
Matches: 525, Mismatches: 110, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
264 2 0.00
265 1 0.00
266 92 0.18
267 324 0.62
268 3 0.01
269 3 0.01
271 6 0.01
272 92 0.18
273 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (266 bp):
ATGATTTGTGGTTTCATCTTGATTATTTATTTTTAACCTAGACTCGATCTTGGTCATTTTATTTT
GACTCGTGATTTTATCTCGATCACATGATTCATGATTTCATCCTGATCATTTATTTTTGACATTG
ATCGAGTATTAATCGCTTTATTTCGACTCTAGTTTCATCTCGATCACATGATTCGTGGTTTCATC
CTGATCATTCATTTTTGACCTCGACTCGATCTTGGTCACTTTATTTTAACTCGTGGTTTCATCCC
AATCAC
Found at i:1740352 original size:26 final size:26
Alignment explanation
Indices: 1740302--1740383 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 26
1740292 TATAGACACT
* * * *
1740302 CATTTTAGTTCGAGCCCAATCGGACC
1 CATTTTAGTCCAAGCCCAGTTGGACC
* *
1740328 CATTGTT-GTCCAAGCTCAGTTGGACT
1 CATT-TTAGTCCAAGCCCAGTTGGACC
1740354 CATTTTAGTCCAAGCCCAGTTGGACC
1 CATTTTAGTCCAAGCCCAGTTGGACC
1740380 CATT
1 CATT
1740384 CTGGCCTTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 2 0.04
26 42 0.91
27 2 0.04
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (26 bp):
CATTTTAGTCCAAGCCCAGTTGGACC
Found at i:1741516 original size:16 final size:16
Alignment explanation
Indices: 1741498--1741548 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
1741488 AGACTTTTTC
1741498 AAAAAA-AAAAA-AAA
1 AAAAAACAAAAACAAA
*
1741512 ACAAAACAAAAACAAA
1 AAAAAACAAAAACAAA
*
1741528 AAAAGACAAAAACAAA
1 AAAAAACAAAAACAAA
1741544 AAAAA
1 AAAAA
1741549 GGAAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 5 0.16
15 5 0.16
16 21 0.68
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAACAAA
Found at i:1745680 original size:9 final size:9
Alignment explanation
Indices: 1745666--1745695 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1745656 TTGTTGTTTT
1745666 AAAAAATTA
1 AAAAAATTA
1745675 AAAAAATTAA
1 AAAAAATT-A
1745685 AAAAAATTA
1 AAAAAATTA
1745694 AA
1 AA
1745696 CTTTTACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:1745687 original size:10 final size:10
Alignment explanation
Indices: 1745666--1745695 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1745656 TTGTTGTTTT
1745666 AAAAAATT-A
1 AAAAAATTAA
1745675 AAAAAATTAA
1 AAAAAATTAA
1745685 AAAAAATTAA
1 AAAAAATTAA
1745695 A
1 A
1745696 CTTTTACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:1749157 original size:20 final size:19
Alignment explanation
Indices: 1749132--1749175 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
1749122 AAAAAAAAGA
*
1749132 TTATATATTTTTATTAATTT
1 TTATATATTTTT-TAAATTT
1749152 TTATATATTTTTTAAATTT
1 TTATATATTTTTTAAATTT
1749171 TTATA
1 TTATA
1749176 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATATTTTTTAAATTT
Found at i:1749179 original size:11 final size:10
Alignment explanation
Indices: 1749132--1749177 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
1749122 AAAAAAAAGA
*
1749132 TTATATATTT
1 TTATAAATTT
*
1749142 TTATTAATTT
1 TTATAAATTT
*
1749152 TTATATATTT
1 TTATAAATTT
1749162 TT-TAAATTT
1 TTATAAATTT
1749171 TTATAAA
1 TTATAAA
1749178 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATAAATTT
Found at i:1749272 original size:26 final size:25
Alignment explanation
Indices: 1749220--1749272 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
1749210 TAAATACATT
*
1749220 AAAAATTTTATTAAAATAATATATAA
1 AAAAATTTTA-TAAAATAATAAATAA
1749246 AAAAATTTTA-AAAATCAATAAACTAA
1 AAAAATTTTATAAAAT-AATAAA-TAA
1749272 A
1 A
1749273 TCAAATCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
25 5 0.21
26 14 0.58
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAAATTTTATAAAATAATAAATAA
Found at i:1749452 original size:2 final size:2
Alignment explanation
Indices: 1749445--1749493 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1749435 TCATTGAGTT
*
1749445 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1749487 TA TA TA T
1 TA TA TA T
1749494 GATTAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1749726 original size:2 final size:2
Alignment explanation
Indices: 1749721--1749761 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1749711 TGTGTGTGTG
1749721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1749762 TTGTCAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1750564 original size:13 final size:12
Alignment explanation
Indices: 1750520--1750563 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1750510 GGCTCTGTTA
1750520 TATTTTTAATTCT
1 TATTTTTAATT-T
*
1750533 GATTTTTAATTT
1 TATTTTTAATTT
*
1750545 TAATTTTAATTT
1 TATTTTTAATTT
1750557 TATTTTT
1 TATTTTT
1750564 TTACATTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (12 bp):
TATTTTTAATTT
Found at i:1754451 original size:25 final size:25
Alignment explanation
Indices: 1754417--1754466 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1754407 GCATGAACCA
*
1754417 CTTAAAGTTTTATACAGTATAAAGG
1 CTTAAAGTTTTACACAGTATAAAGG
1754442 CTTAAAGTTTTACACAGTATAAAGG
1 CTTAAAGTTTTACACAGTATAAAGG
1754467 TTTATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (25 bp):
CTTAAAGTTTTACACAGTATAAAGG
Found at i:1760103 original size:21 final size:21
Alignment explanation
Indices: 1760079--1760153 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
1760069 AATTAATTGA
1760079 ATAAAAATTAAATATTATATT
1 ATAAAAATTAAATATTATATT
* * * *
1760100 ATAAGAATT-ATTTTTAGAATT
1 ATAAAAATTAAATATTA-TATT
* * *
1760121 GTTAAGAAATTAAATGTTATATG
1 -ATAA-AAATTAAATATTATATT
1760144 ATAAAAATTA
1 ATAAAAATTA
1760154 TTTTTAAAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
20 5 0.13
21 17 0.44
22 6 0.15
23 6 0.15
24 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (21 bp):
ATAAAAATTAAATATTATATT
Found at i:1760121 original size:44 final size:44
Alignment explanation
Indices: 1760073--1760164 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
1760063 AATGATAATT
* * *
1760073 AATTGAATAA-AAATTAAATATTATATTATAAGAATTATTTTTAG
1 AATTG-ATAAGAAATTAAATATTATATGATAAAAATTATTTTTAA
* *
1760117 AATTGTTAAGAAATTAAATGTTATATGATAAAAATTATTTTTAA
1 AATTGATAAGAAATTAAATATTATATGATAAAAATTATTTTTAA
1760161 AATT
1 AATT
1760165 TTAATATTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.07
44 39 0.93
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (44 bp):
AATTGATAAGAAATTAAATATTATATGATAAAAATTATTTTTAA
Found at i:1760908 original size:16 final size:18
Alignment explanation
Indices: 1760887--1760929 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 18
1760877 TGAACTGTTG
1760887 AAATTACAAAAA-AAAA-
1 AAATTACAAAAACAAAAC
1760903 AAATTACAAAAACAAAAC
1 AAATTACAAAAACAAAAC
1760921 AAAGTTACA
1 AAA-TTACA
1760930 TTACAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.50
17 4 0.17
18 3 0.12
19 5 0.21
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (18 bp):
AAATTACAAAAACAAAAC
Found at i:1760935 original size:18 final size:18
Alignment explanation
Indices: 1760914--1760950 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1760904 AATTACAAAA
1760914 ACAAAACAAAGTTACATT
1 ACAAAACAAAGTTACATT
*
1760932 ACAAAACAAAGTTCCATT
1 ACAAAACAAAGTTACATT
1760950 A
1 A
1760951 TAATGTTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.19, G:0.05, T:0.22
Consensus pattern (18 bp):
ACAAAACAAAGTTACATT
Found at i:1765725 original size:21 final size:22
Alignment explanation
Indices: 1765683--1765747 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
1765673 GGTTGTAAGG
1765683 ATTTTTATTCATTTCTATTTTA-A
1 ATTTTT-TT-ATTTCTATTTTATA
*
1765706 ATTTTTTTATTTC-ATATTTATC
1 ATTTTTTTATTTCTAT-TTTATA
*
1765728 A-TTTTTTATTTTTATTTTAT
1 ATTTTTTTATTTCTATTTTAT
1765748 GGTCTATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 2 0.05
21 24 0.65
22 5 0.14
23 6 0.16
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTTTTATTTCTATTTTATA
Found at i:1767428 original size:58 final size:57
Alignment explanation
Indices: 1767365--1767578 Score: 283
Period size: 58 Copynumber: 3.7 Consensus size: 57
1767355 TAAAAAGATT
*
1767365 TAAAAAATATTTTTGAAAAAAAGTTAAAAGTATCAATTTTTCCTGAAAATAAGCTTTC
1 TAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCCTGAAAATAAG-TTTC
*
1767423 TAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAA-TTTTCCTTAAACATAAGTTT-
1 TAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCCTGAAA-ATAAGTTTC
* ** * *
1767479 TCAAAAATAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTT-CTCGAAATTAAAGTTTT
1 T-AAAAA-ATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCCT-GAAAAT-AAGTTTC
1767539 TAAAAAATA-TTTTGAAAAAAAGTTGAAAGTATCAATTTTT
1 TAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTT
1767579 TATGTACAAA
Statistics
Matches: 139, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
56 1 0.01
57 47 0.34
58 72 0.52
59 18 0.13
60 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (57 bp):
TAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCCTGAAAATAAGTTTC
Found at i:1774364 original size:24 final size:24
Alignment explanation
Indices: 1774337--1774383 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1774327 TTATGTTATC
*
1774337 TTCGTATT-TTTTATTCGTATCATT
1 TTCGTATTATATTATT-GTATCATT
1774361 TTCGTATTATATTATTGTATCAT
1 TTCGTATTATATTATTGTATCAT
1774384 GTTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.60
Consensus pattern (24 bp):
TTCGTATTATATTATTGTATCATT
Found at i:1776035 original size:16 final size:15
Alignment explanation
Indices: 1776014--1776054 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1776004 TTTTGTAAAA
1776014 TTTTTTCTTTTCTCGC
1 TTTTTTCTTTTC-CGC
*
1776030 TTTTTTCTTTTCCTC
1 TTTTTTCTTTTCCGC
1776045 TATTTTTCTT
1 T-TTTTTCTT
1776055 CTTTACTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTTTCTTTTCCGC
Found at i:1776862 original size:41 final size:41
Alignment explanation
Indices: 1776817--1776941 Score: 130
Period size: 41 Copynumber: 3.0 Consensus size: 41
1776807 TTAAATCAAA
*
1776817 TTTAATTTGACTAACTTATCAATAATTATCATACTAGTTAT
1 TTTAATTTGACTAACTTATCAATAATTATCATACTAGTAAT
** * * * * *
1776858 TTTAATTTGACTAAAGATATCTATTA-TATCGT--TAAATCAAA
1 TTTAATTTGACT-AACTTATCAATAATTATCATACT-AGT-AAT
1776899 TTTAATTTGACTAACTTATCAATAATTATCATACTAGTAAT
1 TTTAATTTGACTAACTTATCAATAATTATCATACTAGTAAT
1776940 TT
1 TT
1776942 AAAAAAAATA
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
39 1 0.02
40 11 0.17
41 39 0.62
42 11 0.17
43 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (41 bp):
TTTAATTTGACTAACTTATCAATAATTATCATACTAGTAAT
Found at i:1778848 original size:24 final size:24
Alignment explanation
Indices: 1778803--1778848 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1778793 ATTATCATTA
*
1778803 TTTATTTTATTTGTATTTGCTATC
1 TTTATTTTATTTGTATTAGCTATC
*
1778827 TTTATTTTCTTTGT-TTGAGCTA
1 TTTATTTTATTTGTATT-AGCTA
1778849 CTATAGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.15, C:0.09, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTATTTTATTTGTATTAGCTATC
Found at i:1779658 original size:31 final size:28
Alignment explanation
Indices: 1779620--1779692 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 28
1779610 AATTTATTCT
1779620 TTAATAAAATAGTATAATTTAATTT-ATTTAA
1 TTAATAAAATA-TATAATTT--TTTGATTT-A
1779651 TTAATAAAATA-AT-ATTTTTTGATTTA
1 TTAATAAAATATATAATTTTTTGATTTA
1779677 TTAATAAAATATATAA
1 TTAATAAAATATATAA
1779693 ATATAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
26 15 0.38
27 6 0.15
28 5 0.13
29 2 0.05
31 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
TTAATAAAATATATAATTTTTTGATTTA
Found at i:1779698 original size:6 final size:6
Alignment explanation
Indices: 1779687--1779738 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
1779677 TTAATAAAAT
* * *
1779687 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAT ATATAT ATATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1779735 ATAT
1 ATAT
1779739 TAACAACTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:1783733 original size:58 final size:58
Alignment explanation
Indices: 1783488--1783785 Score: 264
Period size: 59 Copynumber: 5.1 Consensus size: 58
1783478 TTTGTACAAG
* * * *
1783488 GAAAAATTGATACTTTCAACTTTT-TTCCAAAATATTTTTTCTTGAAATTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCCAAAATATTTTTT-TAGAAA-CTTAATTTCAA
* ** * * * * * *
1783547 GAAAAATTGATACTTTTAACTTTTCCTTAAAAAAAACTTTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCC-TCCAAAATATTTTTTTAGAAACTTAATTTCAA
* * * *
1783606 AAAAAATTGATACTTTCAACTTTT-TTCCAAAATTATTTTTTTGGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCCAAAA-TATTTTTTTAGAAAC-TTAATTTCAA
* *
1783665 GAAAAATTGATACTTTAAACTTTTCCT-CAAAATATTTTTTTAGAAAGCTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTCCAAAATATTTTTTTAGAAA-CTTAATTTCAA
* * * * * * * *
1783723 GGAAAATTGATATTTTTAATTTTTCCTCAAAAATATTTTTTT-G-AATTTTATTTAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCCAAAATATTTTTTTAGAAACTTAATTTCAA
1783779 GAAAAAT
1 GAAAAAT
1783786 AATAATAATA
Statistics
Matches: 192, Mismatches: 40, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
56 13 0.07
57 7 0.04
58 55 0.29
59 101 0.53
60 5 0.03
61 11 0.06
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTCCAAAATATTTTTTTAGAAACTTAATTTCAA
Found at i:1783763 original size:118 final size:118
Alignment explanation
Indices: 1783484--1783764 Score: 347
Period size: 118 Copynumber: 2.4 Consensus size: 118
1783474 CGCCTTTGTA
* *
1783484 CAAGGAAAAATTGATACTTTCAACTTTTT-TCCAAAATATTTTTTCTTGAAATTTTAATTTCGAG
1 CAAGG-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT-TTGAAACTTTAATTTCGAG
* *
1783548 AAAAATTGATACTTTTAACTTTTCCTTAAAAAAAACTTTTTTAAAAATTTATTTT
64 AAAAATTGATACTTTAAACTTTTCCTTAAAAAAAACTTTTTTAAAAACTTATTTT
* ** * *
1783603 TAAAAAAAATTGATACTTTCAACTTTTT-TCCAAAATTATTTTTTTGGAAACTTTAATTTCGAGA
1 CAAGGAAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTTTGAAACTTTAATTTCGAGA
* * * *
1783667 AAAATTGATACTTTAAACTTTTCC-T-CAAAATATTTTTTTAGAAAGCTTATTTT
65 AAAATTGATACTTTAAACTTTTCCTTAAAAAAAACTTTTTTA-AAAACTTATTTT
* *
1783720 CAAGGAAAATTGATATTTTTAA-TTTTTCCTCAAAAATATTTTTTT
1 CAAGGAAAATTGATACTTTCAACTTTTT-CTCAAAAATATTTTTTT
1783765 GAATTTTATT
Statistics
Matches: 139, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
116 17 0.12
117 42 0.30
118 66 0.47
119 14 0.10
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (118 bp):
CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAACTTTAATTTCGAGAA
AAATTGATACTTTAAACTTTTCCTTAAAAAAAACTTTTTTAAAAACTTATTTT
Found at i:1783800 original size:15 final size:14
Alignment explanation
Indices: 1783780--1783833 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 14
1783770 TTATTTAAAG
1783780 AAAAATAATAATAAT
1 AAAAATAA-AATAAT
*
1783795 AAAAATGAAAATAAA
1 AAAAAT-AAAATAAT
1783810 AATAAAGTAAAATAAAT
1 AA-AAA-TAAAAT-AAT
1783827 AAAAATA
1 AAAAATA
1783834 GAGAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 15 0.45
16 13 0.39
17 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:1783831 original size:10 final size:10
Alignment explanation
Indices: 1783782--1783833 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
1783772 ATTTAAAGAA
*
1783782 AAATAATAAT
1 AAATAAAAAT
1783792 -AATAAAAAT
1 AAATAAAAAT
1783801 GAAAATAAAAAT
1 --AAATAAAAAT
1783813 AAAGT-AAAAT
1 AAA-TAAAAAT
1783823 AAATAAAAAT
1 AAATAAAAAT
1783833 A
1 A
1783834 GAGAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
9 9 0.25
10 17 0.47
11 1 0.03
12 9 0.25
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1783846 original size:20 final size:19
Alignment explanation
Indices: 1783802--1783847 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1783792 AATAAAAATG
1783802 AAAATAAAAATAAAGTAAA
1 AAAATAAAAATAAAGTAAA
1783821 ATAAATAAAAATAGAGAG-AAA
1 A-AAATAAAAATA-A-AGTAAA
1783842 AAAATA
1 AAAATA
1783848 TTAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 16 0.67
21 5 0.21
22 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATAAAGTAAA
Found at i:1783888 original size:16 final size:16
Alignment explanation
Indices: 1783844--1783897 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1783834 GAGAGAAAAA
* *
1783844 AATATTAAACAAATAT
1 AATAATAAATAAATAT
*
1783860 AATCTAATCAATAAATAT
1 AA--TAATAAATAAATAT
1783878 AATAATAAATAAATA-
1 AATAATAAATAAATAT
1783893 AATAA
1 AATAA
1783898 ATATACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 5 0.16
16 14 0.44
18 13 0.41
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAAATAAATAT
Found at i:1784796 original size:21 final size:20
Alignment explanation
Indices: 1784772--1784862 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 20
1784762 TTTTAAAAAA
*
1784772 TAATCAGATAAGTAATAATAT
1 TAAT-AGATAAATAATAATAT
* * *
1784793 TAATAGATAACTAAAAATAAA
1 TAATAGATAAATAATAAT-AT
*
1784814 TAATAGATAAATTATAATAT
1 TAATAGATAAATAATAATAT
1784834 ATAATAAGATTAATATATATAAATAT
1 -TAAT-AGA-TAA-ATA-AT-AATAT
1784860 TAA
1 TAA
1784863 CAAAAAAGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 13 0.24
21 24 0.44
22 3 0.05
23 3 0.05
24 2 0.04
25 5 0.09
26 5 0.09
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
TAATAGATAAATAATAATAT
Found at i:1784796 original size:41 final size:41
Alignment explanation
Indices: 1784751--1784839 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 41
1784741 ATAAAAGGTG
* ** *
1784751 TTAATAGATAATTTTAAA-AAATAATCAGATAAGTAATAATA
1 TTAATAGATAACTAAAAATAAATAAT-AGATAAATAATAATA
*
1784792 TTAATAGATAACTAAAAATAAATAATAGATAAATTATAATA
1 TTAATAGATAACTAAAAATAAATAATAGATAAATAATAATA
1784833 TATAATA
1 T-TAATA
1784840 AGATTAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 29 0.71
42 12 0.29
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (41 bp):
TTAATAGATAACTAAAAATAAATAATAGATAAATAATAATA
Found at i:1784922 original size:4 final size:4
Alignment explanation
Indices: 1784915--1785036 Score: 54
Period size: 4 Copynumber: 29.5 Consensus size: 4
1784905 GATATATATT
*
1784915 AATA AATA GTAAT- AATA AATA AATA AAT- AATA AATA CATA AGATA ATCATAA
1 AATA AATA --AATA AATA AATA AATA AATA AATA AATA AATA A-ATA A--AT-A
* * * * * * * *
1784967 AAGA AAAA AAAA AATA TATA TATA TATA TA-A AATA AAAA AAT- AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
1785013 ATATA AATAA AATA AAAA AATA AA
1 A-ATA AAT-A AATA AATA AATA AA
1785037 ATGGGCTTAC
Statistics
Matches: 95, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
3 11 0.12
4 64 0.67
5 13 0.14
6 5 0.05
7 2 0.02
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:1785005 original size:25 final size:25
Alignment explanation
Indices: 1784925--1785035 Score: 102
Period size: 25 Copynumber: 4.2 Consensus size: 25
1784915 AATAAATAGT
1784925 AATAATAA-ATAAAT-AAATAATAAA
1 AATAATAATATAAATAAAATAA-AAA
*
1784949 TACATAAGATAATCATAAA-AGAAAAAAAAA
1 -A-AT-A-ATAAT-ATAAATA-AAATAAAAA
*
1784979 AATATATATATATATATAAAATAAAAA
1 AATA-ATA-ATATAAATAAAATAAAAA
1785006 AATAATAATATAAATAAAATAAAAA
1 AATAATAATATAAATAAAATAAAAA
1785031 AATAA
1 AATAA
1785036 AATGGGCTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
25 23 0.32
26 5 0.07
27 21 0.29
28 9 0.12
29 1 0.01
30 8 0.11
31 5 0.07
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (25 bp):
AATAATAATATAAATAAAATAAAAA
Found at i:1785318 original size:42 final size:41
Alignment explanation
Indices: 1785217--1785678 Score: 406
Period size: 42 Copynumber: 10.9 Consensus size: 41
1785207 ATGATCAAAA
* * *
1785217 CTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATATAAACAATG
1 CTCCTCTAATCAGAGGCTCAACAACTTTG-AAAA-ATAAA-TA-G
**
1785262 CTCCTCTAATCAGAGGCTCAATGACTTT-AAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAAT--AG
** * * * * *
1785304 CTTTTCTAAACAGAGGCTCAACGACTTTTGAAGAGTAAATTG
1 CTCCTCTAATCAGAGGCTCAACAAC-TTTGAAAAATAAATAG
* * * *
1785346 CTCTTCTAATCAGAGGTTCAACAATTTTGAAAAATAAATGG
1 CTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAG
*
1785387 CTCTTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAAT--AG
* * ** * * *
1785430 CTCTTCTAAACAGAGGCTCAATGACTTTTGAAGAGTAAATGG
1 CTCCTCTAATCAGAGGCTCAACAAC-TTTGAAAAATAAATAG
* * *
1785472 CTCAT-TCAATCAGAGGCTCAATAACTTTGAAAAATAAATAAAA
1 CTCCTCT-AATCAGAGGCTCAACAACTTTGAAAAATAAAT--AG
* * * * ** *
1785515 CTCCTCTAAACAGAGGTTCAACGACTTTTGAAGAGGAAATGG
1 CTCCTCTAATCAGAGGCTCAACAAC-TTTGAAAAATAAATAG
*
1785557 CTCCTCTAATCAGAGGCTCAATAACTTTGAAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAAT--AG
* * *
1785600 CTCCTCTAAACAGAGGCTCAACAACTTTTGAAGAGTAAATAG
1 CTCCTCTAATCAGAGGCTCAACAAC-TTTGAAAAATAAATAG
*
1785642 CTCCTCTAATCAGAGGCTCAATAACTTTGAAAAATAA
1 CTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAA
1785679 TTGGCTCATT
Statistics
Matches: 342, Mismatches: 60, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
41 84 0.25
42 115 0.34
43 73 0.21
44 44 0.13
45 26 0.08
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (41 bp):
CTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAG
Found at i:1785483 original size:85 final size:85
Alignment explanation
Indices: 1785221--1785678 Score: 525
Period size: 85 Copynumber: 5.4 Consensus size: 85
1785211 TCAAAACTCC
* * * *
1785221 TCTAAGCAGAGGCTCAACGACTTTGAAAAATATAA-ACAATGCTCCTCTAATCAGAGGCTCAATG
1 TCTAATCAGAGGCTCAACAACTTTGAAAAATA-AATA-AA-GCTCCTCTAAACAGAGGCTCAACG
* * * *
1785285 AC-TTT-AAAAATAAATAAAGCTTT
63 ACTTTTGAAGAGTAAAT--GGCTCT
* * * * * * * * *
1785308 TCTAAACAGAGGCTCAACGACTTTTGAAGAGTAAAT--TGCTCTTCTAATCAGAGGTTCAAC-AA
1 TCTAATCAGAGGCTCAACAAC-TTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGAC
* *
1785370 TTTTGAAAAATAAATGGCTCT
65 TTTTGAAGAGTAAATGGCTCT
* *
1785391 TCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCTTCTAAACAGAGGCTCAATGACT
1 TCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACT
1785456 TTTGAAGAGTAAATGGCTCAT
66 TTTGAAGAGTAAATGGCTC-T
* * *
1785477 TC-AATCAGAGGCTCAATAACTTTGAAAAATAAATAAAACTCCTCTAAACAGAGGTTCAACGACT
1 TCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACT
* *
1785541 TTTGAAGAGGAAATGGCTCC
66 TTTGAAGAGTAAATGGCTCT
* *
1785561 TCTAATCAGAGGCTCAATAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACT
1 TCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACT
* *
1785626 TTTGAAGAGTAAATAGCTCC
66 TTTGAAGAGTAAATGGCTCT
*
1785646 TCTAATCAGAGGCTCAATAACTTTGAAAAATAA
1 TCTAATCAGAGGCTCAACAACTTTGAAAAATAA
1785679 TTGGCTCATT
Statistics
Matches: 329, Mismatches: 33, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
82 12 0.04
83 24 0.07
84 45 0.14
85 214 0.65
86 3 0.01
87 22 0.07
88 9 0.03
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (85 bp):
TCTAATCAGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACT
TTTGAAGAGTAAATGGCTCT
Found at i:1786688 original size:20 final size:20
Alignment explanation
Indices: 1786665--1786713 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1786655 TGAGTCCTCC
1786665 TTTTTCATTCACTTTTTTC-T
1 TTTTTCATTCA-TTTTTTCAT
**
1786685 TTTTTTTTTCATTTTTTCAT
1 TTTTTCATTCATTTTTTCAT
1786705 TTTTTCATT
1 TTTTTCATT
1786714 TTTTCTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTCATTCATTTTTTCAT
Found at i:1786690 original size:8 final size:8
Alignment explanation
Indices: 1786688--1786718 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1786678 TTTTTCTTTT
1786688 TTTTTTCA
1 TTTTTTCA
1786696 TTTTTTCA
1 TTTTTTCA
1786704 TTTTTTCA
1 TTTTTTCA
1786712 TTTTTTC
1 TTTTTTC
1786719 TTCAAGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1794778 original size:205 final size:205
Alignment explanation
Indices: 1794423--1795039 Score: 1072
Period size: 205 Copynumber: 3.0 Consensus size: 205
1794413 AAGTGAATAC
* * *
1794423 CATTTCTTGTCTTCATTTTGTTCTCCAAACCAAGTACCCTAGAGTGACTTTATTAGTAAATGGTC
1 CATTTCTTATCTTCATTTTGCTCTCCAAACCAAGTACCCTAGAGTGACTTTATCAGTAAATGGTC
* * *
1794488 CAGCACTTACTTTTCGAGGATTTTTCCATACTTTAATCATCTCATTTATCCTCTAAAATGCTTTG
66 CAGAACTTACTTTTCGAGGATTTTTCCATGCTTTAATCATCTCATTCATCCTCTAAAATGCTTTG
* * * *
1794553 GCTTACTATAAGAGAAATCTAATTGATGAAGCTCATAAGTCATAGGAATAAACTGTTCTCACCAA
131 GCTCACTATAAGAAAAATCTAACTGATGAAGCTCATAAGTCATAGGAATGAACTGTTCTCACCAA
1794618 ACTGCCTTCT
196 ACTGCCTTCT
*
1794628 CATTTCTTATCTTCATTTTGCTCTCCAAACCAAGTACCTTAGAGTGACTTTATCAGTAAATGGTC
1 CATTTCTTATCTTCATTTTGCTCTCCAAACCAAGTACCCTAGAGTGACTTTATCAGTAAATGGTC
1794693 CAGAACTTACTTTTCGAGGATTTTTCCATGCTTTAATCATCTCATTCATCCTCTAAAATGCTTTG
66 CAGAACTTACTTTTCGAGGATTTTTCCATGCTTTAATCATCTCATTCATCCTCTAAAATGCTTTG
* * *
1794758 GCTCACTATAAGAAAAATCTAACTGATGAAGCTTATAAGTCATAGGAATGAACTATTCTCGCCAA
131 GCTCACTATAAGAAAAATCTAACTGATGAAGCTCATAAGTCATAGGAATGAACTGTTCTCACCAA
1794823 ACTGCCTTCT
196 ACTGCCTTCT
1794833 CATTTCTTATCTTCATTTTGCTCTCCAAACCAAGTACCCTAGAGTGACTTTATCAGTAAATGGTC
1 CATTTCTTATCTTCATTTTGCTCTCCAAACCAAGTACCCTAGAGTGACTTTATCAGTAAATGGTC
*
1794898 CAGAACTTACTTTTCAAGGATTTTTCCATGCTTTAATCATCTCATTCATCCTCTAAAATGCTTTG
66 CAGAACTTACTTTTCGAGGATTTTTCCATGCTTTAATCATCTCATTCATCCTCTAAAATGCTTTG
* *
1794963 GCTCACTATAAGAAAAATCTAACTGATGAAGCCCATAAGTCATAGGAATGAACTGTTCTCCCCAA
131 GCTCACTATAAGAAAAATCTAACTGATGAAGCTCATAAGTCATAGGAATGAACTGTTCTCACCAA
*
1795028 ACTGTCTTCT
196 ACTGCCTTCT
1795038 CA
1 CA
1795040 CTAGGAGTGA
Statistics
Matches: 391, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
205 391 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (205 bp):
CATTTCTTATCTTCATTTTGCTCTCCAAACCAAGTACCCTAGAGTGACTTTATCAGTAAATGGTC
CAGAACTTACTTTTCGAGGATTTTTCCATGCTTTAATCATCTCATTCATCCTCTAAAATGCTTTG
GCTCACTATAAGAAAAATCTAACTGATGAAGCTCATAAGTCATAGGAATGAACTGTTCTCACCAA
ACTGCCTTCT
Found at i:1797118 original size:60 final size:60
Alignment explanation
Indices: 1796971--1797252 Score: 310
Period size: 59 Copynumber: 4.8 Consensus size: 60
1796961 CGCTTTTGTA
* * * *
1796971 TAAGGAAAAATTGATACTTTCAACTTTTTCC-CAAAATATTTTTTTTTAAAATTTTAATTT
1 TAAGG-AAAATTGATACTTTCAACTTTTTCCTCAAAAAAATTTTTTTGAAAACTTTAATTT
** * * *
1797031 CGAGAAAAATTGATACTTTCAAC-TTTTCCTCAAAAAAACTTTTTTTGAGAA-TTTATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTTCCTCAAAAAAA-TTTTTTTGAAAACTTTAATTT
* * *
1797090 TAAGGAAAATTGATACTTTCAACTTTTT-CTCAAAAAGA-TTTTTTGGAAACTTTAAGTT
1 TAAGGAAAATTGATACTTTCAACTTTTTCCTCAAAAAAATTTTTTTGAAAACTTTAATTT
* * * * *
1797148 TGAGGAAAATTGATATTTTCAACTTTTT-CTAAAAAAAAACCTTTTTTGAAAA-TTTATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTTCCT-CAAAAAAA-TTTTTTTGAAAACTTTAATTT
1797208 TAAGGAAAATTGATACTTTCAACTTTTTCC-CAAAAATAATTTTTT
1 TAAGGAAAATTGATACTTTCAACTTTTTCCTCAAAAA-AATTTTTT
1797253 GAATTTTATT
Statistics
Matches: 186, Mismatches: 27, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
57 9 0.05
58 40 0.22
59 76 0.41
60 50 0.27
61 11 0.06
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (60 bp):
TAAGGAAAATTGATACTTTCAACTTTTTCCTCAAAAAAATTTTTTTGAAAACTTTAATTT
Found at i:1797132 original size:118 final size:117
Alignment explanation
Indices: 1796971--1797255 Score: 394
Period size: 118 Copynumber: 2.4 Consensus size: 117
1796961 CGCTTTTGTA
* * *
1796971 TAAGGAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTTTTAAAATTTTAA-TTTCGAG
1 TAAGG-AAAATTGATACTTTCAACTTTTTCCCAAAA-A-ATTTTTTGAAAACTTTAAGTTT-GAG
* * *
1797035 AAAAATTGATACTTTCAACTTTTCCT-CAAAAAAACTTTTTTTGAGAATTTATTTT
62 AAAAATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTGAAAATTTATTTT
* * *
1797090 TAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAGATTTTTTGGAAACTTTAAGTTTGAGGAA
1 TAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAA-ATTTTTTGAAAACTTTAAGTTTGAGAAA
* *
1797155 AATTGATATTTTCAACTTTTTCTAAAAAAAAACCTTTTTTGAAAATTTATTTT
65 AATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTGAAAATTTATTTT
1797208 TAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATAATTTTTTGAA
1 TAAGGAAAATTGATACTTTCAACTTTTTCCC-AAAA-AATTTTTTGAA
1797256 TTTTATTTAA
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
117 41 0.28
118 88 0.59
119 18 0.12
120 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (117 bp):
TAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAAATTTTTTGAAAACTTTAAGTTTGAGAAAA
ATTGATACTTTCAACTTTTCCTAAAAAAAAACCTTTTTTGAAAATTTATTTT
Found at i:1797319 original size:10 final size:10
Alignment explanation
Indices: 1797270--1797321 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
1797260 ATTTAAAGAA
*
1797270 AAATAATAAT
1 AAATAAAAAT
1797280 -AATAAAAAT
1 AAATAAAAAT
1797289 GAAAATAAAAAT
1 --AAATAAAAAT
1797301 AAAGT-AAAAT
1 AAA-TAAAAAT
1797311 AAATAAAAAT
1 AAATAAAAAT
1797321 A
1 A
1797322 GAGAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
9 9 0.25
10 17 0.47
11 1 0.03
12 9 0.25
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1797334 original size:20 final size:19
Alignment explanation
Indices: 1797290--1797335 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1797280 AATAAAAATG
1797290 AAAATAAAAATAAAGTAAA
1 AAAATAAAAATAAAGTAAA
1797309 ATAAATAAAAATAGAGAG-AAA
1 A-AAATAAAAATA-A-AGTAAA
1797330 AAAATA
1 AAAATA
1797336 TTAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 16 0.67
21 5 0.21
22 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATAAAGTAAA
Found at i:1797370 original size:16 final size:15
Alignment explanation
Indices: 1797347--1797377 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1797337 TAAACAAATC
1797347 TAATATAATAAATAA
1 TAATATAATAAATAA
1797362 TAATAATAATAAATAA
1 TAAT-ATAATAAATAA
1797378 ATATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATATAATAAATAA
Found at i:1798266 original size:41 final size:41
Alignment explanation
Indices: 1798230--1798310 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 41
1798220 TAGATAGTTT
1798230 AAAA-AAATAATCAAATAAATAATAATATTAACAGATAACTA
1 AAAATAAATAAT-AAATAAATAATAATATTAACAGATAACTA
* *
1798271 AAAATAAATAATAGATAAATTATAATATATAATCAGATAA
1 AAAATAAATAATAAATAAATAATAATAT-TAA-CAGATAA
1798311 ACATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 18 0.51
42 10 0.29
43 7 0.20
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (41 bp):
AAAATAAATAATAAATAAATAATAATATTAACAGATAACTA
Found at i:1798320 original size:22 final size:21
Alignment explanation
Indices: 1798273--1798321 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1798263 GATAACTAAA
* *
1798273 AATAAATAATAGATAAATTAT
1 AATATATAATAGATAAAATAT
1798294 AATATATAATCAGATAAACATAT
1 AATATATAAT-AGATAAA-ATAT
1798317 -ATATA
1 AATATA
1798322 AAAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 12 0.50
23 3 0.12
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (21 bp):
AATATATAATAGATAAAATAT
Found at i:1798417 original size:7 final size:7
Alignment explanation
Indices: 1798385--1798504 Score: 58
Period size: 7 Copynumber: 17.0 Consensus size: 7
1798375 GTATATATAT
1798385 TAATAAA
1 TAATAAA
*
1798392 TAGT-AA
1 TAATAAA
1798398 TAATAAA
1 TAATAAA
1798405 TAAATAAA
1 T-AATAAA
1798413 TAATAAA
1 TAATAAA
1798420 TACATAAGA
1 TA-ATAA-A
*
1798429 TAAT-CA
1 TAATAAA
1798435 TAA-AAGA
1 TAATAA-A
*
1798442 -AAAAAA
1 TAATAAA
1798448 TATATAAAA
1 TA-AT-AAA
1798457 TAAT-AA
1 TAATAAA
*
1798463 TAAAATAA
1 TAATA-AA
1798471 TAATAAA
1 TAATAAA
1798478 -AATACAA
1 TAATA-AA
1798485 -AATACAA
1 TAATA-AA
1798492 -AATAAA
1 TAATAAA
*
1798498 AAATAAA
1 TAATAAA
1798505 ATGGACTTAC
Statistics
Matches: 92, Mismatches: 7, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
6 23 0.25
7 39 0.42
8 22 0.24
9 8 0.09
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (7 bp):
TAATAAA
Found at i:1798499 original size:6 final size:6
Alignment explanation
Indices: 1798453--1798505 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
1798443 AAAAATATAT
* *
1798453 AAAATA ATAAT- AAAATA ATAATA AAAATA CAAAATA CAAAATAA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA -AAAATA -AAAAT-A AAAATA
1798503 AAA
1 AAA
1798506 TGGACTTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 4 0.10
6 18 0.45
7 17 0.43
8 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:1798503 original size:30 final size:31
Alignment explanation
Indices: 1798444--1798503 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1798434 ATAAAAGAAA
* *
1798444 AAAATATATAAAATAATAATAAAATAATAAT
1 AAAATATACAAAATAAAAATAAAATAATAAT
1798475 AAAA-ATACAAAATACAAAATAAAA-AATAA
1 AAAATATACAAAATA-AAAATAAAATAATAA
1798504 AATGGACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (31 bp):
AAAATATACAAAATAAAAATAAAATAATAAT
Found at i:1800298 original size:16 final size:16
Alignment explanation
Indices: 1800277--1800307 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1800267 ATATTTCAAA
*
1800277 AAAATAAATGAATGAT
1 AAAATAAATAAATGAT
1800293 AAAATAAATAAATGA
1 AAAATAAATAAATGA
1800308 AAACCATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (16 bp):
AAAATAAATAAATGAT
Found at i:1801201 original size:3 final size:3
Alignment explanation
Indices: 1801193--1801237 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1801183 AGATAAATAC
1801193 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1801238 TGCATTGAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1806955 original size:19 final size:18
Alignment explanation
Indices: 1806938--1806972 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1806928 AAATTAATAA
1806938 AATAAAATATT-TTTAAT
1 AATAAAATATTATTTAAT
1806955 -ATAAAATATTATTTAAT
1 AATAAAATATTATTTAAT
1806972 A
1 A
1806973 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAAATATTATTTAAT
Found at i:1806971 original size:17 final size:16
Alignment explanation
Indices: 1806939--1806993 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
1806929 AATTAATAAA
1806939 ATAAAATATTTTTAAT
1 ATAAAATATTTTTAAT
1806955 ATAAAATATTATTTAAT
1 ATAAAATATT-TTTAAT
1806972 AT----TATTTTTAAAT
1 ATAAAATATTTTT-AAT
1806985 ATAAAATAT
1 ATAAAATAT
1806994 ATAAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 3 0.09
13 9 0.27
16 10 0.30
17 11 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATATTTTTAAT
Found at i:1807001 original size:8 final size:8
Alignment explanation
Indices: 1806980--1807041 Score: 62
Period size: 7 Copynumber: 8.2 Consensus size: 8
1806970 ATATTATTTT
1806980 TAAATATA
1 TAAATATA
1806988 -AAATATA
1 TAAATATA
1806995 TAAATATA
1 TAAATATA
1807003 TAAATATA
1 TAAATATA
*
1807011 -AAATTAAA
1 TAAA-TATA
1807019 TAAATA-A
1 TAAATATA
*
1807026 TAAA-AAA
1 TAAATATA
1807033 T-AATATA
1 TAAATATA
1807040 TA
1 TA
1807042 TTTGAATAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 3 0.07
7 20 0.43
8 20 0.43
9 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
TAAATATA
Found at i:1807006 original size:23 final size:22
Alignment explanation
Indices: 1806980--1807041 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
1806970 ATATTATTTT
1806980 TAAATATAAAATATATAAATATA
1 TAAATATAAAATATATAAATA-A
*
1807003 TAAATATAAAATTAAATAAATAA
1 TAAATATAAAA-TATATAAATAA
1807026 TAAA-A-AATAATATATA
1 TAAATATAA-AATATATA
1807042 TTTGAATAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 7 0.20
22 3 0.09
23 16 0.46
24 9 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATATAAAATATATAAATAA
Found at i:1807033 original size:10 final size:11
Alignment explanation
Indices: 1806980--1807037 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 11
1806970 ATATTATTTT
1806980 TAAATATAA-AA
1 TAAATA-AATAA
*
1806991 TATATAAATATA
1 TAAATAAATA-A
1807003 TAAATATAA-AA
1 TAAATA-AATAA
1807014 TTAAATAAATAA
1 -TAAATAAATAA
1807026 TAAA-AAATAA
1 TAAATAAATAA
1807036 TA
1 TA
1807038 TATATTTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 10 0.25
11 13 0.32
12 15 0.38
13 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:1807997 original size:2 final size:2
Alignment explanation
Indices: 1807990--1808028 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1807980 ATATGAAGGA
1807990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1808029 GACACACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1808127 original size:27 final size:26
Alignment explanation
Indices: 1808063--1808127 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
1808053 GAATTTACCA
1808063 AAATTCAACTTCAACCCAACTCAATTT
1 AAATTCAA-TTCAACCCAACTCAATTT
** **
1808090 AAATAAAAATTCAACCCAACTTGATTT
1 AAAT-TCAATTCAACCCAACTCAATTT
1808117 GAAATTCAATT
1 -AAATTCAATT
1808128 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.31
Consensus pattern (26 bp):
AAATTCAATTCAACCCAACTCAATTT
Found at i:1810167 original size:14 final size:14
Alignment explanation
Indices: 1810141--1810179 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1810131 TTGCAATGTT
*
1810141 AGAAAAAATAAATA
1 AGAAAAAAGAAATA
*
1810155 AGAGAAAAGAAATA
1 AGAAAAAAGAAATA
*
1810169 ATAAAAAAGAA
1 AGAAAAAAGAA
1810180 TTTTGACTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (14 bp):
AGAAAAAAGAAATA
Found at i:1822830 original size:7 final size:7
Alignment explanation
Indices: 1822818--1822843 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1822808 TATATATCCG
1822818 AAATTTA
1 AAATTTA
1822825 AAATTTA
1 AAATTTA
1822832 AAATTTA
1 AAATTTA
1822839 AAATT
1 AAATT
1822844 CTTTAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:1823076 original size:3 final size:3
Alignment explanation
Indices: 1823070--1823105 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1823060 AATAATAATG
1823070 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1823106 AAAGTGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1824430 original size:19 final size:18
Alignment explanation
Indices: 1824406--1824441 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1824396 CAATAGCGAT
1824406 CCGCTATTGCCCGCTATTA
1 CCGCTATTG-CCGCTATTA
1824425 CCGCTATTGCCGCTATT
1 CCGCTATTGCCGCTATT
1824442 CCTATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.14, C:0.36, G:0.17, T:0.33
Consensus pattern (18 bp):
CCGCTATTGCCGCTATTA
Found at i:1826717 original size:5 final size:5
Alignment explanation
Indices: 1826709--1826738 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1826699 AAAGAGAGAA
*
1826709 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1826739 CTAGCAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1829151 original size:17 final size:18
Alignment explanation
Indices: 1829129--1829163 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1829119 AAATATAAAA
1829129 TTTTTACTTT-AAAATTG
1 TTTTTACTTTGAAAATTG
*
1829146 TTTTTATTTTGAAAATTG
1 TTTTTACTTTGAAAATTG
1829164 ATTTATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTTTACTTTGAAAATTG
Found at i:1830270 original size:6 final size:6
Alignment explanation
Indices: 1830261--1830345 Score: 62
Period size: 6 Copynumber: 14.2 Consensus size: 6
1830251 TAATAGTAAC
* * * * * *
1830261 AACAAT AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAT
1 AACAAT AACAAT AACAAT AACAAT AACAAT AACAAT AACAAT AACAAT
* * * * * *
1830309 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT A
1 AACAAT AACAAT AACAAT AACAAT AACAAT AACAAT A
1830346 TAATAGCATA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AACAAT
Found at i:1830273 original size:3 final size:3
Alignment explanation
Indices: 1830258--1830307 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1830248 TAGTAATAGT
*
1830258 AAC AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1830306 AA
1 AA
1830308 TAATAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.30, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:1830312 original size:3 final size:3
Alignment explanation
Indices: 1830306--1830462 Score: 134
Period size: 3 Copynumber: 54.7 Consensus size: 3
1830296 CAACAACAAC
1830306 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AGCAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT
*
1830355 AAT -AT AAT -AT AAT -AT ACT -AT AAT -AT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
1830397 AAT -AT GAT -AT AAT AGT AGT GAT AAT AAT AAG AAT AAC GAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1830443 AAA AAT AAT AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1830463 CAGAAATATA
Statistics
Matches: 125, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
2 17 0.14
3 105 0.84
5 3 0.02
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1830808 original size:55 final size:54
Alignment explanation
Indices: 1830695--1830889 Score: 187
Period size: 55 Copynumber: 3.5 Consensus size: 54
1830685 AGTGATTGGG
* * * * * *
1830695 GATTGAACCACAAGTAAAAAAAAATAATTTGGACTTGAATCGAGATCGAATGATTGA
1 GATTGAACCACAAGT-TAGAAAAATAATATGGA-TCGAGTCAAGATCGAATGA-TGA
*
1830752 GATTGAACCATAAGTTAGAAAAATAATATGGATCGAGTCAAGATCGAATGACTGA
1 GATTGAACCACAAGTTAGAAAAATAATATGGATCGAGTCAAGATCGAATGA-TGA
* * * * * *
1830807 GATTGAACCGCAAGTCA-AAAAGATAATCTAGATCGAG-CTTAGATCGAATGATCA
1 GATTGAACCACAAGTTAGAAAA-ATAATATGGATCGAGTC-AAGATCGAATGATGA
1830861 GGATTGAACCACAAGTTAGAAAAACTAAT
1 -GATTGAACCACAAGTTAGAAAAA-TAAT
1830890 TGACTTAGAC
Statistics
Matches: 116, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
54 7 0.06
55 73 0.63
56 22 0.19
57 14 0.12
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (54 bp):
GATTGAACCACAAGTTAGAAAAATAATATGGATCGAGTCAAGATCGAATGATGA
Found at i:1831872 original size:43 final size:41
Alignment explanation
Indices: 1831805--1831903 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 41
1831795 TTGGCTTTTT
* * * *
1831805 TTTTTTTTTGCTCAAGCCATCTTTTTGGGTTTTCAACTTGAA
1 TTTTTTTTTGCTCAAACCACCTTTTCGGGTTGTCAACTT-AA
**
1831847 CTTTTTTTTTGCTCAAATTACCTTTTCGGGTTGTCAACTTAA
1 -TTTTTTTTTGCTCAAACCACCTTTTCGGGTTGTCAACTTAA
*
1831889 TTTTTTTTGGCTCAA
1 TTTTTTTTTGCTCAA
1831904 GCAGCCCTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 14 0.29
42 2 0.04
43 33 0.67
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (41 bp):
TTTTTTTTTGCTCAAACCACCTTTTCGGGTTGTCAACTTAA
Found at i:1834168 original size:18 final size:18
Alignment explanation
Indices: 1834145--1834184 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1834135 CAAAAGACTT
1834145 TGGTCTTCCTAAAATGAA
1 TGGTCTTCCTAAAATGAA
*
1834163 TGGTCTTCCTGAAATGAA
1 TGGTCTTCCTAAAATGAA
1834181 TGGT
1 TGGT
1834185 GCTAATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (18 bp):
TGGTCTTCCTAAAATGAA
Found at i:1842604 original size:27 final size:23
Alignment explanation
Indices: 1842574--1842635 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
1842564 ATGTTTAATT
*
1842574 TAAAATTAGTAAAATAACAATGATAAA
1 TAAAATTAG--AAATAA-AAAGA-AAA
1842601 TAAAA-TAGAAATAAAAAGAAAA
1 TAAAATTAGAAATAAAAAGAAAA
1842623 TAAAA-TA-AAATAA
1 TAAAATTAGAAATAA
1842636 GACTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 6 0.18
22 10 0.29
23 4 0.12
24 6 0.18
26 3 0.09
27 5 0.15
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (23 bp):
TAAAATTAGAAATAAAAAGAAAA
Found at i:1842614 original size:11 final size:11
Alignment explanation
Indices: 1842598--1842635 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1842588 TAACAATGAT
1842598 AAATAAAATAG
1 AAATAAAATAG
1842609 AAATAAAA-AG
1 AAATAAAATAG
1842619 AAAATAAAATA-
1 -AAATAAAATAG
1842630 AAATAA
1 AAATAA
1842636 GACTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.32
11 16 0.64
12 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (11 bp):
AAATAAAATAG
Found at i:1842622 original size:5 final size:5
Alignment explanation
Indices: 1842583--1842635 Score: 52
Period size: 5 Copynumber: 9.6 Consensus size: 5
1842573 TTAAAATTAG
*
1842583 TAAAA TAACAA TGATAAA TAAAA TAGAAA TAAAAA GAAAA TAAAA TAAAA
1 TAAAA TAA-AA T-A-AAA TAAAA TA-AAA T-AAAA TAAAA TAAAA TAAAA
1842633 TAA
1 TAA
1842636 GACTAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 24 0.59
6 11 0.27
7 5 0.12
8 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:1842674 original size:13 final size:13
Alignment explanation
Indices: 1842639--1842686 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1842629 AAAATAAGAC
*
1842639 TAAAAAAGGAAAA
1 TAAAAAATGAAAA
1842652 TTATAAAAAT-AAAA
1 -TA-AAAAATGAAAA
1842666 TCAAAAAATGAAAA
1 T-AAAAAATGAAAA
1842680 TAAAAAA
1 TAAAAAA
1842687 AAATTACGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.43
14 12 0.40
15 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (13 bp):
TAAAAAATGAAAA
Found at i:1842687 original size:28 final size:27
Alignment explanation
Indices: 1842596--1842688 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 27
1842586 AATAACAATG
*
1842596 ATAAATAAAATAGAAAT--AAAAAGAAA
1 ATAAAAAAAATA-AAATCAAAAAAGAAA
*
1842622 ATAAAATAAAATAAGA-CTAAAAAAGGAAA
1 ATAAAA-AAAATAAAATC-AAAAAA-GAAA
* *
1842651 ATTATAAAAATAAAATCAAAAAATGAAA
1 ATAAAAAAAATAAAATCAAAAAA-GAAA
1842679 ATAAAAAAAA
1 ATAAAAAAAA
1842689 ATTACGATTG
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
26 7 0.13
27 6 0.11
28 31 0.58
29 9 0.17
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.16
Consensus pattern (27 bp):
ATAAAAAAAATAAAATCAAAAAAGAAA
Found at i:1843035 original size:21 final size:21
Alignment explanation
Indices: 1843002--1843042 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1842992 CATGAACCCA
* *
1843002 AATTTTTCCAAAATTTTCCAT
1 AATTCTTCAAAAATTTTCCAT
1843023 AATTCTTCAAAAATTTTCCA
1 AATTCTTCAAAAATTTTCCA
1843043 AAAATACAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTCTTCAAAAATTTTCCAT
Found at i:1843047 original size:11 final size:10
Alignment explanation
Indices: 1842999--1843045 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
1842989 CATCATGAAC
*
1842999 CCAAATTTTT
1 CCAAAATTTT
1843009 CCAAAATTTT
1 CCAAAATTTT
*
1843019 CCATAATTCTT
1 CCAAAATT-TT
*
1843030 CAAAAATTTT
1 CCAAAATTTT
1843040 CCAAAA
1 CCAAAA
1843046 ATACAGCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (10 bp):
CCAAAATTTT
Found at i:1843519 original size:3 final size:3
Alignment explanation
Indices: 1843511--1843660 Score: 87
Period size: 3 Copynumber: 52.0 Consensus size: 3
1843501 TAATAGCAAC
* * * * *
1843511 AAT AAT AAT AAC AAC AAC AAC AAG AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
1843558 ACT -AT AAT -CT AAT AAT AAT -AT GAT -AT GAT -AT AAT ACT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
1843601 AGT AAG AAT AAT GAT AAT AAT AAA AAT AAT AAT ACT AAT AAC AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1843649 AAT AAT AGT AAT
1 AAT AAT AAT AAT
1843661 GACAAAAAAT
Statistics
Matches: 116, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
2 10 0.09
3 106 0.91
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1843631 original size:21 final size:21
Alignment explanation
Indices: 1843607--1843668 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1843597 TAATAGTAAG
*
1843607 AATAATGA-TAATAATAAAAAT
1 AATAAT-ACTAATAACAAAAAT
1843628 AATAATACTAATAACAAAAAT
1 AATAATACTAATAACAAAAAT
* *
1843649 AATAATAGTAATGACAAAAA
1 AATAATACTAATAACAAAAA
1843669 ATCAACACCG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
AATAATACTAATAACAAAAAT
Found at i:1844820 original size:153 final size:151
Alignment explanation
Indices: 1844530--1844824 Score: 502
Period size: 153 Copynumber: 1.9 Consensus size: 151
1844520 TGATTTAAAT
* *
1844530 GAAATACATATATGTTAACGTGAAGTGTCGGTTTCACACTTTTTTCTTAAGTCATGTTGAAATAG
1 GAAATACATATATGTTAACGTGAAGCGTCGGTTTCACACTTTTTTCCTAAGTCATGTTGAAATAG
* *
1844595 TTTATTTTCAAATTTAATTAAACTTGTCCTTTGTTTGTAATCCTTATCCCCTTCCAAGCCACAAC
66 TTTATTTTCAAATTTAATTAAACTTGTCCTTTGTTTATAACCCTTATCCCCTTCCAAGCCACAAC
1844660 AAGAAAAAAAAAAAACTCTAA
131 AAGAAAAAAAAAAAACTCTAA
1844681 GAAATACATATATATGTTAACGTGAAGCGTCGGTTTCACACTTTTTTCCTAAGTCATGTTGAAAT
1 GAAATAC--ATATATGTTAACGTGAAGCGTCGGTTTCACACTTTTTTCCTAAGTCATGTTGAAAT
*
1844746 ATTTTATTTTCAAATTTAATTAAACTTGTCCTTTGTTTATAACCCCTTATCCCCTTCCAAGCCAC
64 AGTTTATTTTCAAATTTAATTAAACTTGTCCTTTGTTTATAA-CCCTTATCCCCTTCCAAGCCAC
*
1844811 AACCA-AAAAAAAAA
128 AACAAGAAAAAAAAA
1844825 TTCTAAAATT
Statistics
Matches: 135, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
151 7 0.05
153 103 0.76
154 25 0.19
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (151 bp):
GAAATACATATATGTTAACGTGAAGCGTCGGTTTCACACTTTTTTCCTAAGTCATGTTGAAATAG
TTTATTTTCAAATTTAATTAAACTTGTCCTTTGTTTATAACCCTTATCCCCTTCCAAGCCACAAC
AAGAAAAAAAAAAAACTCTAA
Found at i:1846688 original size:41 final size:41
Alignment explanation
Indices: 1846631--1846713 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
1846621 ACTATGAAGC
1846631 TAGTATTCTCAGTTGCAAAAGAAAGATTCTAACAATTTCCT
1 TAGTATTCTCAGTTGCAAAAGAAAGATTCTAACAATTTCCT
*
1846672 TAGTATTCTCAGTTGCAAAAGAAAGATTCTTACAATTTCCT
1 TAGTATTCTCAGTTGCAAAAGAAAGATTCTAACAATTTCCT
1846713 T
1 T
1846714 GTTTTCATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (41 bp):
TAGTATTCTCAGTTGCAAAAGAAAGATTCTAACAATTTCCT
Found at i:1851519 original size:14 final size:15
Alignment explanation
Indices: 1851500--1851532 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1851490 ATTTTTCTTA
*
1851500 AAAAT-AAAATTTCT
1 AAAATAAAAATTTCC
1851514 AAAATAAAAATTTCC
1 AAAATAAAAATTTCC
1851529 AAAA
1 AAAA
1851533 GCATTTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAAATTTCC
Found at i:1851567 original size:71 final size:71
Alignment explanation
Indices: 1851436--1851713 Score: 310
Period size: 71 Copynumber: 4.0 Consensus size: 71
1851426 TATTTTGATT
* **
1851436 TTTCTAAAATAAAAATTTTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1 TTTCTAAAATAAAAA-TTTCCAAAAGCA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1851501 AAATAAAA
64 AAATAAAA
* * * *
1851509 TTTCTAAAATAAAAATTTCCAAAAGCATTTTGGGGGAAAGTTGAAAATATCAATTTTTCTTGAAA
1 TTTCTAAAATAAAAATTTCCAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAA
1851574 ATAAAAA
66 AT-AAAA
* *
1851581 TGTT-T--AA-AAAAA--T---ATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAA
1 T-TTCTAAAATAAAAATTTCCAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAA
1851635 AATAAAA
65 AATAAAA
* *
1851642 TTTCTAAAATAAAAATTTTCAAAAGCATTTTG-GGAGAAAGTTGAAAGTATCAATTTTCCTTGAA
1 TTTCTAAAATAAAAATTTCCAAAAGCATTTTGAGGA-AAAGTTGAAAGTATCAATTTTTCTT-AA
*
1851706 AATTAAAA
64 AAATAAAA
1851714 GGTTTAAAAA
Statistics
Matches: 173, Mismatches: 17, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
60 2 0.01
61 6 0.03
62 36 0.21
63 2 0.01
64 7 0.04
66 1 0.01
67 1 0.01
69 7 0.04
70 5 0.03
71 65 0.38
72 24 0.14
73 17 0.10
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (71 bp):
TTTCTAAAATAAAAATTTCCAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAA
ATAAAA
Found at i:1851608 original size:133 final size:131
Alignment explanation
Indices: 1851441--1851892 Score: 597
Period size: 133 Copynumber: 3.4 Consensus size: 131
1851431 TGATTTTTCT
*
1851441 AAAATAAAAATTTT-CAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
1 AAAATAAAAATTTTAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
* *
1851505 AAAATTTCTAAAATAAAAATTTCCAAAAGCATTTTGGGGGAAAGTTGAAAATATCAATTTTTCTT
66 AAAATTTCTAAAATAAAAATTTCCAAAAGCATTTTGGGGGAAAGTTGAAAGTATCAATTTTCCTT
1851570 G
131 G
1851571 AAAATAAAAATGTTTAAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAA
1 AAAATAAAAAT-TTTAAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAA
* *
1851636 ATAAAATTTCTAAAATAAAAATTTTCAAAAGCATTTTGGGAGAAAGTTGAAAGTATCAATTTTCC
64 ATAAAATTTCTAAAATAAAAATTTCCAAAAGCATTTTGGGGGAAAGTTGAAAGTATCAATTTTCC
1851701 TTG
129 TTG
** * * *
1851704 AAAATTAAAAGGTTTAAAAATATATATTTTTG-GGAAAAGTTGAAAGTATCGA-TTTTCTTTGAA
1 AAAA-TAAAAATTTTAAAAA-AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAA
* ** * * * * *
1851767 AATAAAATTTCTAAAATAAAAATTATCAAAAAAAATTTTTGAGGAAAAGTTGGAAGTACCAATAT
63 AATAAAATTTCTAAAATAAAAATT-TCCAAAAGCA-TTTTGGGGGAAAGTTGAAAGTATCAATTT
*
1851832 TCCTTA
126 TCCTTG
* * * *
1851838 AAAATAAAAATTATCAAGAAAAATA-TTTTAAGAAAAAGTTGAAAGTATCAATTTT
1 AAAATAAAAATT-TTAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1851893 CCTTGTACAA
Statistics
Matches: 282, Mismatches: 29, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
130 11 0.04
131 8 0.03
132 56 0.20
133 161 0.57
134 46 0.16
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (131 bp):
AAAATAAAAATTTTAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
AAAATTTCTAAAATAAAAATTTCCAAAAGCATTTTGGGGGAAAGTTGAAAGTATCAATTTTCCTT
G
Found at i:1851895 original size:60 final size:59
Alignment explanation
Indices: 1851779--1851896 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 59
1851769 TAAAATTTCT
* * *
1851779 AAAATAAAAATTATCAAAAAAAATTTTTGAGGAAAAGTTGGAAGTACCAATATTCCTTA
1 AAAATAAAAATTATCAAAAAAAATTTTTAAGAAAAAGTTGAAAGTACCAATATTCCTTA
* * *
1851838 AAAATAAAAATTATCAAGAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAATAAAAATTATCAAAAAAAAT-TTTTAAGAAAAAGTTGAAAGTACCAATATTCCTT
1851897 GTACAAAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 23 0.44
60 29 0.56
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.31
Consensus pattern (59 bp):
AAAATAAAAATTATCAAAAAAAATTTTTAAGAAAAAGTTGAAAGTACCAATATTCCTTA
Found at i:1862389 original size:9 final size:9
Alignment explanation
Indices: 1862375--1862406 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1862365 ATTATGCTTG
1862375 AAAAAATTA
1 AAAAAATTA
1862384 AAAAAATTA
1 AAAAAATTA
1862393 AAAAAA-TA
1 AAAAAATTA
1862401 AAAAAA
1 AAAAAA
1862407 GAAAACTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAATTA
Found at i:1863548 original size:44 final size:44
Alignment explanation
Indices: 1863429--1863568 Score: 172
Period size: 44 Copynumber: 3.2 Consensus size: 44
1863419 CTGTTACCTT
* * *
1863429 TGTTTAGAGGAGCTTTATTTATTTTTTCAAAATCATTGAACCTC
1 TGTTTAGAGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTC
* * * * *
1863473 TATTTATATGAGCTTTACTTATTTTTCCAAAGTCGTTGAGCCTC
1 TGTTTAGAGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTC
* * *
1863517 TGTTTAGAGGAGCTTTGTTTATTTTTCCAAAGTTACTGAGCCTC
1 TGTTTAGAGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTC
*
1863561 TGCTTAGA
1 TGTTTAGA
1863569 TAAGGGTGTA
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 79 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (44 bp):
TGTTTAGAGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTC
Found at i:1864286 original size:8 final size:8
Alignment explanation
Indices: 1864273--1864301 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1864263 TAGGTTTATA
1864273 TATTTTTT
1 TATTTTTT
1864281 TA-TTTTT
1 TATTTTTT
1864288 TATTTTTT
1 TATTTTTT
1864296 TATTTT
1 TATTTT
1864302 ATTTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TATTTTTT
Found at i:1864303 original size:20 final size:20
Alignment explanation
Indices: 1864278--1864315 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1864268 TTATATATTT
1864278 TTTTATTTTTTATTTTTTTA
1 TTTTATTTTTTATTTTTTTA
*
1864298 TTTTATTTTTTGTTTTTT
1 TTTTATTTTTTATTTTTT
1864316 GTGATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.87
Consensus pattern (20 bp):
TTTTATTTTTTATTTTTTTA
Found at i:1864308 original size:15 final size:15
Alignment explanation
Indices: 1864273--1864301 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1864263 TAGGTTTATA
1864273 TATTTTTTTATTTTT
1 TATTTTTTTATTTTT
1864288 TATTTTTTTATTTT
1 TATTTTTTTATTTT
1864302 ATTTTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TATTTTTTTATTTTT
Found at i:1864317 original size:7 final size:7
Alignment explanation
Indices: 1864276--1864315 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1864266 GTTTATATAT
1864276 TTTTTTA
1 TTTTTTA
1864283 TTTTTTA
1 TTTTTTA
1864290 TTTTTT-
1 TTTTTTA
*
1864296 TATTTTA
1 TTTTTTA
*
1864303 TTTTTTG
1 TTTTTTA
1864310 TTTTTT
1 TTTTTT
1864316 GTGATTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:1865407 original size:71 final size:70
Alignment explanation
Indices: 1865308--1865555 Score: 237
Period size: 71 Copynumber: 3.6 Consensus size: 70
1865298 CAAAAAATAT
* * *
1865308 TTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTTAAATAGAAATTTTCA
1 TTTTGAGGGAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAATTTCTTAAATA-AAATTTTCA
1865373 AAAGCA
65 AAAGCA
* * * ** *
1865379 TTTTGGGGGAAAGTTGAAAATATCAATTTCTCTTGAAAATAAAAAAGT-TT--A-AAAA-TAT--
1 TTTTGAGGGAAAGTTGAAAATATCAATTTTTCTTAAAAAT-AAAATTTCTTAAATAAAATTTTCA
* *
1865437 ATA--T
65 AAAGCA
* * *
1865441 TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA-ATAAATTTCTAAAATAAAAATTTTC
1 TTTTGAGGGAAAGTTGAAAATATCAATTTTTCTTAAAAATA-AAATTTCTTAAAT-AAAATTTTC
1865505 AAAAGCA
64 AAAAGCA
* * *
1865512 TTTTGAGAGAAAGTTGAAAATATCAATTTTCCTTGAAAATAAAA
1 TTTTGAGGGAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAA
1865556 AGATTTAAAA
Statistics
Matches: 137, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
60 1 0.01
61 4 0.03
62 35 0.26
64 3 0.02
66 6 0.04
67 5 0.04
68 1 0.01
69 3 0.02
71 73 0.53
72 6 0.04
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (70 bp):
TTTTGAGGGAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAATTTCTTAAATAAAATTTTCAA
AAGCA
Found at i:1865462 original size:133 final size:130
Alignment explanation
Indices: 1865299--1865740 Score: 536
Period size: 133 Copynumber: 3.3 Consensus size: 130
1865289 AAAAATTCCC
*
1865299 AAAAA-ATATTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTTAAATA
1 AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTTAAATA
* *
1865363 GAAATTTTCAAAAGCATTTTGGGGGAAAGTTGAAAATATCAATTTCTCTTGAAAATAAAAAAGTT
66 AAAATTTTCAAAAGCATTTTGAGGGAAAGTTGAAAATATCAATTT-TCTTGAAAAT-AAAAAGTT
1865428 TA
129 TA
*
1865430 AAAATATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA-ATAAATTTCTAAAA
1 AAAA-ATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATA-AAATTTCTTAAA
*
1865494 TAAAAATTTTCAAAAGCATTTTGAGAGAAAGTTGAAAATATCAATTTTCCTTGAAAATAAAAAGA
64 TAAAAATTTTCAAAAGCATTTTGAGGGAAAGTTGAAAATATCAATTTT-CTTGAAAATAAAAAG-
1865559 TTTA
127 TTTA
* * ** * *
1865563 AAAAATATTTTTTTTAAAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTT-TTAAAAT
1 AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTT-AAAT
** * * * * * *
1865627 AAAAATCATCAAAAAAACATTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAA-
65 AAAAATTTTC--AAAAGCATTTTGAGGGAAAGTTGAAAATATCAA-TTTTCTTGAAAATAAAAAG
1865691 TTATCA
127 TT-T-A
* *
1865697 AGAAAA-ACA-TTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTA
1 A-AAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA
1865741 TACAAAAGCA
Statistics
Matches: 270, Mismatches: 28, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
131 5 0.02
132 68 0.25
133 146 0.54
134 43 0.16
135 8 0.03
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (130 bp):
AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTTAAATA
AAAATTTTCAAAAGCATTTTGAGGGAAAGTTGAAAATATCAATTTTCTTGAAAATAAAAAGTTTA
Found at i:1865643 original size:61 final size:61
Alignment explanation
Indices: 1865521--1865643 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 61
1865511 ATTTTGAGAG
* * ** ***
1865521 AAAGTTGAAAATATCAATTTTCCTTGAAAATAAAAAGATTTAAAAAATATTTTTTTTAAAA
1 AAAGTTGAAAATATCAATTTTCCTTGAAAATAAAAAGATTTAAAAAAAAATCATCAAAAAA
* **
1865582 AAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAATTTTTAAAATAAAAATCATCAAAAAA
1 AAAGTTGAAAATATCAATTTTCCTTGAAAATAAAAAGATTTAAAA-AAAAATCATCAAAAAA
1865643 A
1 A
1865644 CATTTTAAGG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 11 0.22
61 40 0.78
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (61 bp):
AAAGTTGAAAATATCAATTTTCCTTGAAAATAAAAAGATTTAAAAAAAAATCATCAAAAAA
Found at i:1865685 original size:59 final size:60
Alignment explanation
Indices: 1865622--1865740 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
1865612 TAAAATTTTT
1865622 AAAATAAAAATCATCAA-AAAAACATTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTA
1 AAAATAAAAATCATCAAGAAAAACATTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTA
* *
1865681 AAAATAAAAATTATCAAGAAAAACATTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTA
1 AAAATAAAAATCATCAAGAAAAACATTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTA
1865741 TACAAAAGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 16 0.28
60 41 0.72
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.30
Consensus pattern (60 bp):
AAAATAAAAATCATCAAGAAAAACATTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTA
Found at i:1870066 original size:95 final size:96
Alignment explanation
Indices: 1869873--1870067 Score: 277
Period size: 95 Copynumber: 2.0 Consensus size: 96
1869863 AGGAAACAAG
1869873 AAAATAAAATAAAATTACAACTCAAAATTTTCTTGCATTATTAATTAGTGTCATTTCTAGAATTT
1 AAAATAAAATAAAATTACAACTCAAAATTTTCTTGC-----T-ATTAGTGTCATTTCTAGAATTT
* *
1869938 TGTCAGTTGATATTATAAATTAGATTATATTTTAGTA
60 TGTCAGCTGATATTATAAATTAGAATATATTTTAGTA
* *
1869975 AAAATAAAATGAAATTACAACTCAAAATTTTCTTGGC-ATTAGTGTCATTTCTATAA-TTTGTCA
1 AAAATAAAATAAAATTACAACTCAAAATTTTCTT-GCTATTAGTGTCATTTCTAGAATTTTGTCA
1870038 GCTGATATTATAAATTAGAATATATTTTAG
65 GCTGATATTATAAATTAGAATATATTTTAG
1870068 AGGTTGATAC
Statistics
Matches: 88, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
95 35 0.40
96 18 0.20
102 33 0.38
103 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (96 bp):
AAAATAAAATAAAATTACAACTCAAAATTTTCTTGCTATTAGTGTCATTTCTAGAATTTTGTCAG
CTGATATTATAAATTAGAATATATTTTAGTA
Found at i:1870228 original size:21 final size:21
Alignment explanation
Indices: 1870202--1870292 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
1870192 TAACATTTTA
1870202 TAACTTTTGATA-AATTTTTGG
1 TAACTTTTGATACAA-TTTTGG
** *
1870223 TAAC-TTCAATACAATTTTAG
1 TAACTTTTGATACAATTTTGG
* * *
1870243 TAACTTATGATATAATTTTGA
1 TAACTTTTGATACAATTTTGG
*
1870264 TAACTTTTGATACAATTTTGA
1 TAACTTTTGATACAATTTTGG
*
1870285 TAATTTTT
1 TAACTTTT
1870293 AACAAAATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
20 14 0.25
21 42 0.75
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (21 bp):
TAACTTTTGATACAATTTTGG
Found at i:1870282 original size:11 final size:10
Alignment explanation
Indices: 1870250--1870318 Score: 57
Period size: 11 Copynumber: 6.5 Consensus size: 10
1870240 TAGTAACTTA
1870250 TGATATAATTT
1 TGATA-AATTT
*
1870261 TGATAACTTT
1 TGATAAATTT
1870271 TGATACAATTT
1 TGATA-AATTT
*
1870282 TGATAATTTT
1 TGATAAATTT
* *
1870292 TAACAAAATTT
1 TGA-TAAATTT
*
1870303 TAATAAACTTT
1 TGATAAA-TTT
1870314 TGATA
1 TGATA
1870319 TCATTTCTAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
10 18 0.38
11 29 0.62
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (10 bp):
TGATAAATTT
Found at i:1870301 original size:21 final size:21
Alignment explanation
Indices: 1870256--1870314 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1870246 CTTATGATAT
* * *
1870256 AATTTTGATAACTTTTGATAC
1 AATTTTGATAACTTTTAACAA
*
1870277 AATTTTGATAATTTTTAACAA
1 AATTTTGATAACTTTTAACAA
*
1870298 AATTTTAATAAACTTTT
1 AATTTTGAT-AACTTTT
1870315 GATATCATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (21 bp):
AATTTTGATAACTTTTAACAA
Found at i:1870581 original size:21 final size:21
Alignment explanation
Indices: 1870515--1870610 Score: 99
Period size: 21 Copynumber: 4.6 Consensus size: 21
1870505 TTGATAACCT
*
1870515 TTGATA-AACTTTTGGTAA-TT
1 TTGATACAA-TTTTGGTAACTA
*
1870535 TTAATACAATTTTGGTAACT-
1 TTGATACAATTTTGGTAACTA
*
1870555 TATGATATAATTTTGGTAACTA
1 T-TGATACAATTTTGGTAACTA
* * *
1870577 TTGATACAATATCGGTAACCA
1 TTGATACAATTTTGGTAACTA
1870598 TTGATACAATTTT
1 TTGATACAATTTT
1870611 TATAATCTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 15 0.24
21 47 0.75
22 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (21 bp):
TTGATACAATTTTGGTAACTA
Found at i:1871087 original size:22 final size:22
Alignment explanation
Indices: 1871024--1871191 Score: 128
Period size: 22 Copynumber: 7.7 Consensus size: 22
1871014 GATATACAGC
* *
1871024 TAAATTATCAATGATTTATTA-
1 TAAATTATTAATGATTTACTAT
* * *
1871045 CAAATTAATATTGATTTACTAT
1 TAAATTATTAATGATTTACTAT
* *
1871067 TAATTTA-TAATTAGTTTACTAT
1 TAAATTATTAATGA-TTTACTAT
*
1871089 TAAATTATTGATGATTTACTAT
1 TAAATTATTAATGATTTACTAT
* * * **
1871111 TAAATAACTGATGATTTGTTAT
1 TAAATTATTAATGATTTACTAT
*
1871133 AAAATT-TTAATTGATTTACTAT
1 TAAATTATTAA-TGATTTACTAT
* * *
1871155 TAATTTATCAATAATTTACTA-
1 TAAATTATTAATGATTTACTAT
*
1871176 TAAATTATCAATGATT
1 TAAATTATTAATGATT
1871192 AATTAATTTA
Statistics
Matches: 114, Mismatches: 28, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
21 36 0.32
22 71 0.62
23 7 0.06
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (22 bp):
TAAATTATTAATGATTTACTAT
Found at i:1871194 original size:51 final size:52
Alignment explanation
Indices: 1871139--1871243 Score: 124
Period size: 51 Copynumber: 2.0 Consensus size: 52
1871129 TTATAAAATT
* * * *
1871139 TTAATTGATTTACTAT-TAATTTATCAATAATTTACTA-TAAATTATCAATGA
1 TTAATTAATTTACT-TCTAAATCATCAATAATTTACCACTAAATTATCAATGA
* * *
1871190 TTAATTAATTTACTTCTAAATCATCATTTATTTACCACTAAATTATTAATGA
1 TTAATTAATTTACTTCTAAATCATCAATAATTTACCACTAAATTATCAATGA
1871242 TT
1 TT
1871244 TACTATTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.02
51 29 0.64
52 15 0.33
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (52 bp):
TTAATTAATTTACTTCTAAATCATCAATAATTTACCACTAAATTATCAATGA
Found at i:1871504 original size:22 final size:22
Alignment explanation
Indices: 1871479--1871529 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1871469 AATAACACAA
1871479 TTATTATTGATTTATTACTAAG-
1 TTATTATT-ATTTATTACTAAGT
1871501 TTATTTATTATTTATTACTAAGT
1 TTA-TTATTATTTATTACTAAGT
1871524 TTATTA
1 TTATTA
1871530 ATTAATTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (22 bp):
TTATTATTATTTATTACTAAGT
Found at i:1871528 original size:19 final size:21
Alignment explanation
Indices: 1871482--1871540 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
1871472 AACACAATTA
*
1871482 TTATTGATTTATTACTAAGTTAT
1 TTATTAATTTATTACTAAG-T-T
1871505 TTATT-ATTTATTACTAAG-T
1 TTATTAATTTATTACTAAGTT
*
1871524 TTATTAATTAATTACTA
1 TTATTAATTTATTACTA
1871541 TTAAACTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.18
20 10 0.29
22 13 0.38
23 5 0.15
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TTATTAATTTATTACTAAGTT
Found at i:1871852 original size:22 final size:21
Alignment explanation
Indices: 1871827--1871906 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
1871817 CCCTGTAGTG
1871827 ATTACATTATCACTAATTTACT
1 ATTA-ATTATCACTAATTTACT
* *
1871849 ATTAAATTATCATTAATTTATT
1 ATT-AATTATCACTAATTTACT
* * *
1871871 ATTAAGTTATCAATTATTAACT
1 ATTAA-TTATCACTAATTTACT
*
1871893 ACTAAGTTATCACT
1 ATTAA-TTATCACT
1871907 TTTTTTATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.04
22 45 0.94
23 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTAATTATCACTAATTTACT
Found at i:1875003 original size:95 final size:96
Alignment explanation
Indices: 1874820--1875014 Score: 293
Period size: 95 Copynumber: 2.0 Consensus size: 96
1874810 AGGAAACAAG
1874820 AAAATAAAATAAAATTACAACTCAAAATTTTCTTGCATTATTAATTAGTGTCATTTCTAGAATTT
1 AAAATAAAATAAAATTACAACTCAAAATTTTCTTGC-----T-ATTAGTGTCATTTCTAGAATTT
* *
1874885 TGTCAGTTGATATTATAAATTAGATTATATTTTAGTA
60 TGTCAGCTGATATTATAAATTAGAATATATTTTAGTA
* *
1874922 AAAATAAAATGAAATTACAACTCAAAATTTTCTTGC-ATTAGTGTCATTTCTATAATTTTGTCAG
1 AAAATAAAATAAAATTACAACTCAAAATTTTCTTGCTATTAGTGTCATTTCTAGAATTTTGTCAG
1874986 CTGATATTATAAATTAGAATATATTTTAG
66 CTGATATTATAAATTAGAATATATTTTAG
1875015 AGGTTGATAC
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
95 54 0.61
102 35 0.39
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (96 bp):
AAAATAAAATAAAATTACAACTCAAAATTTTCTTGCTATTAGTGTCATTTCTAGAATTTTGTCAG
CTGATATTATAAATTAGAATATATTTTAGTA
Found at i:1875175 original size:21 final size:21
Alignment explanation
Indices: 1875149--1875239 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
1875139 TAACATTTTA
1875149 TAACTTTTGATA-AATTTTTGG
1 TAACTTTTGATACAA-TTTTGG
** *
1875170 TAAC-TTCAATACAATTTTAG
1 TAACTTTTGATACAATTTTGG
* * *
1875190 TAACTTATGATATAATTTTGA
1 TAACTTTTGATACAATTTTGG
*
1875211 TAACTTTTGATACAATTTTGA
1 TAACTTTTGATACAATTTTGG
*
1875232 TAATTTTT
1 TAACTTTT
1875240 AACAAAATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
20 14 0.25
21 42 0.75
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (21 bp):
TAACTTTTGATACAATTTTGG
Found at i:1875229 original size:11 final size:10
Alignment explanation
Indices: 1875197--1875265 Score: 57
Period size: 11 Copynumber: 6.5 Consensus size: 10
1875187 TAGTAACTTA
1875197 TGATATAATTT
1 TGATA-AATTT
*
1875208 TGATAACTTT
1 TGATAAATTT
1875218 TGATACAATTT
1 TGATA-AATTT
*
1875229 TGATAATTTT
1 TGATAAATTT
* *
1875239 TAACAAAATTT
1 TGA-TAAATTT
*
1875250 TAATAAACTTT
1 TGATAAA-TTT
1875261 TGATA
1 TGATA
1875266 TCATTTCTAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
10 18 0.38
11 29 0.62
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (10 bp):
TGATAAATTT
Done.