Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 13 of 64
Found at i:1494207 original size:20 final size:20
Alignment explanation
Indices: 1494184--1494226 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1494174 TTGATCTTGG
1494184 TTTTTATTTTTGGTTTTTGTT
1 TTTTTATTTTTGG-TTTTGTT
* *
1494205 TTTTTGTTTTTTGTTTTGTT
1 TTTTTATTTTTGGTTTTGTT
1494225 TT
1 TT
1494227 GTCTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (20 bp):
TTTTTATTTTTGGTTTTGTT
Found at i:1494210 original size:15 final size:15
Alignment explanation
Indices: 1494190--1494221 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1494180 TTGGTTTTTA
1494190 TTTTTGGTTTTTGTT
1 TTTTTGGTTTTTGTT
*
1494205 TTTTTGTTTTTTGTT
1 TTTTTGGTTTTTGTT
1494220 TT
1 TT
1494222 GTTTTGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (15 bp):
TTTTTGGTTTTTGTT
Found at i:1494234 original size:20 final size:20
Alignment explanation
Indices: 1494198--1494236 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1494188 TATTTTTGGT
*
1494198 TTTTGTTTTTTTGTTTTTTG
1 TTTTGTTTTTCTGTTTTTTG
1494218 TTTTGTTTTGTCT-TTTTTT
1 TTTTGTTTT-TCTGTTTTTT
1494237 TTATTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.85
Consensus pattern (20 bp):
TTTTGTTTTTCTGTTTTTTG
Found at i:1494236 original size:15 final size:14
Alignment explanation
Indices: 1494190--1494249 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 14
1494180 TTGGTTTTTA
* *
1494190 TTTTTGGTTTTTGT
1 TTTTTTGTTTTTCT
1494204 TTTTTTG-TTTT-T
1 TTTTTTGTTTTTCT
*
1494216 TGTTTTGTTTTGTCT
1 TTTTTTGTTTT-TCT
*
1494231 TTTTTTTTATTTTCT
1 TTTTTTGT-TTTTCT
1494246 TTTT
1 TTTT
1494250 GTAAATTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.18
13 7 0.18
14 7 0.18
15 14 0.37
16 3 0.08
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (14 bp):
TTTTTTGTTTTTCT
Found at i:1494487 original size:84 final size:84
Alignment explanation
Indices: 1494332--1494553 Score: 250
Period size: 84 Copynumber: 2.6 Consensus size: 84
1494322 ATCATGCCGA
* * * * * * *
1494332 AAGTCTTACAAATCTTGTAATTAAAACATATTCAACTCAAGAGACTTACGAAA-CTTGTTTGAAG
1 AAGTCTTACAAATCTTGAAATTAAAATAAATTCAACTCAAAAGACTTAC-AAATCCTATTAGAAG
*
1494396 GACTTAGAAATTACATCTAG
65 GACTTAGAAATTACACCTAG
* * * *
1494416 AGGTCTTACAAATCTTGAAATCAAAATAGATTCAACTTAAAAGACTTACAAATCCTATTCAG-AG
1 AAGTCTTACAAATCTTGAAATTAAAATAAATTCAACTCAAAAGACTTACAAATCCTATT-AGAAG
*
1494480 GATTTAGAAATTACACCTAG
65 GACTTAGAAATTACACCTAG
* * * * *
1494500 AAGTCTTACAAGTCTTGAAATTAACATAAATTCAGCTCGAAAGACTTACGAATC
1 AAGTCTTACAAATCTTGAAATTAAAATAAATTCAACTCAAAAGACTTACAAATC
1494554 TTGCTTGGAA
Statistics
Matches: 115, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
83 3 0.03
84 111 0.97
85 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (84 bp):
AAGTCTTACAAATCTTGAAATTAAAATAAATTCAACTCAAAAGACTTACAAATCCTATTAGAAGG
ACTTAGAAATTACACCTAG
Found at i:1494659 original size:22 final size:22
Alignment explanation
Indices: 1494601--1494662 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1494591 ATAGATTGCA
*
1494601 CCCAGAGGTCTTAAAGATTATG
1 CCCAGAGGTCTTAAAAATTATG
** * * *
1494623 CCTGGAAGTCATAAAAATTGTG
1 CCCAGAGGTCTTAAAAATTATG
1494645 CCCAGAGGTCTTAAAAAT
1 CCCAGAGGTCTTAAAAAT
1494663 CTTAAAATCT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (22 bp):
CCCAGAGGTCTTAAAAATTATG
Found at i:1494799 original size:105 final size:106
Alignment explanation
Indices: 1494650--1494976 Score: 429
Period size: 105 Copynumber: 3.1 Consensus size: 106
1494640 TTGTGCCCAG
* * * *
1494650 AGGTCTTAA-AAATCTTAAAATCTTTGAATACTCCTCATACATTAGAGGCATTGAAACTTTAAAA
1 AGGTCTTAAGAGATCTCAAAATCTTTGAATGCTCCTCATACATTAGAGGCATTGAAACTTTGAAA
1494714 ATTTAAAATGTTTTGCCCGAAGGTCTTAAAGATTATG-TTCA
66 ATTTAAAATGTTTTGCCCGAAGGTCTTAAAGATTATGCTT-A
* *
1494755 AGGTCTTAAG-GATTTCAAAATCTTTGAATGCTCCTTATACATTAGAGGCATTGAAACTTTGAAA
1 AGGTCTTAAGAGATCTCAAAATCTTTGAATGCTCCTCATACATTAGAGGCATTGAAACTTTGAAA
* * * *
1494819 ATTTAAAATGTTTTGCCTGAAAGTCTTAAAGATTGTGCCTTG
66 ATTTAAAATGTTTTGCCCGAAGGTCTTAAAGATTATG-CTTA
*
1494861 AGGTCTT-AGAGATCTCAAAATCTTTGAATGCTCCTCATATATTAGAGGCATTGAAA--TTGAAA
1 AGGTCTTAAGAGATCTCAAAATCTTTGAATGCTCCTCATACATTAGAGGCATTGAAACTTTGAAA
* * *
1494923 ATTTAAAATGTTTTG-TCGGAGGTCTTGGAA-ATTATGCTTGA
66 ATTTAAAATGTTTTGCCCGAAGGTCTT-AAAGATTATGCTT-A
1494964 AGGTCTT-AGAGAT
1 AGGTCTTAAGAGAT
1494977 TATACCTAGA
Statistics
Matches: 196, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
102 3 0.02
103 25 0.13
104 23 0.12
105 93 0.47
106 50 0.26
107 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (106 bp):
AGGTCTTAAGAGATCTCAAAATCTTTGAATGCTCCTCATACATTAGAGGCATTGAAACTTTGAAA
ATTTAAAATGTTTTGCCCGAAGGTCTTAAAGATTATGCTTA
Found at i:1495210 original size:126 final size:124
Alignment explanation
Indices: 1494861--1495252 Score: 459
Period size: 126 Copynumber: 3.1 Consensus size: 124
1494851 TTGTGCCTTG
* * * *
1494861 AGGTCTTAGAGATCTCAAAATCTTTGAATGCTCCTCATATATTAGAGGCATTGAAA-TTGAAAAT
1 AGGTCTTACAAATCTTAAAATCTTTGAATGC-CCT-TTATATTAGAGGCATTGAAACTTGAAAAT
* * *
1494925 TTAAAATGTTTTGTCGGAGGTCTTGGAAATTATGCTTGAAGGTCTTAGAGATTATACCTAGA
64 TTAAAATGTTTTCTCGGAGGTCTTGGAAATTATGCTTGAAGGTTTTAGAGATTATACCCA-A
* *
1494987 A-GTCTTACAAATCTTAAAATCTTTGAATGCTCTTCATAATT-GAGGCATTGAAACATTGAAAAT
1 AGGTCTTACAAATCTTAAAATCTTTGAATGCCCTTTAT-ATTAGAGGCATTGAAAC-TTGAAAAT
* * * * * *
1495050 TTAAAATGTTTTGC-CTAGAAGTTTTGGAAATTATGCTCGAAGGTTTTAAAAATTATACCCAA
64 TTAAAATGTTTT-CTC-GGAGGTCTTGGAAATTATGCTTGAAGGTTTTAGAGATTATACCCAA
* * *
1495112 AGGTCTTACAAATCTTAAAATCTTTGAATGCCCTTTGTATTATAGGCATTGAAACTTTAAAAATT
1 AGGTCTTACAAATCTTAAAATCTTTGAATGCCCTTTATATTAGAGGCATTGAAAC-TTGAAAATT
* * * * **
1495177 TAAAATGTTTTACTCGGAGGTCTTAGAAGTTATGTTTGGAGGTTTTAGAGATTATGTCCAA
65 TAAAATGTTTT-CTCGGAGGTCTTGGAAATTATGCTTGAAGGTTTTAGAGATTATACCCAA
1495238 AGGTCTTACAAATCT
1 AGGTCTTACAAATCT
1495253 CAATAGCACA
Statistics
Matches: 224, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
123 14 0.06
124 5 0.02
125 52 0.23
126 152 0.68
127 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (124 bp):
AGGTCTTACAAATCTTAAAATCTTTGAATGCCCTTTATATTAGAGGCATTGAAACTTGAAAATTT
AAAATGTTTTCTCGGAGGTCTTGGAAATTATGCTTGAAGGTTTTAGAGATTATACCCAA
Found at i:1495224 original size:22 final size:22
Alignment explanation
Indices: 1495192--1495233 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1495182 TGTTTTACTC
1495192 GGAGGTCTTAGA-AGTTATGTTT
1 GGAGGTCTTAGAGA-TTATGTTT
*
1495214 GGAGGTTTTAGAGATTATGT
1 GGAGGTCTTAGAGATTATGT
1495234 CCAAAGGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.24, C:0.02, G:0.33, T:0.40
Consensus pattern (22 bp):
GGAGGTCTTAGAGATTATGTTT
Found at i:1496815 original size:17 final size:18
Alignment explanation
Indices: 1496780--1496820 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1496770 AATTAATACT
*
1496780 AAATAATAATAATAGTAA
1 AAATAATAATAAGAGTAA
*
1496798 AAATAA-AATAAGATTAA
1 AAATAATAATAAGAGTAA
1496815 AAATAA
1 AAATAA
1496821 CTAGTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAATAATAAGAGTAA
Found at i:1497119 original size:19 final size:20
Alignment explanation
Indices: 1497092--1497132 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1497082 TCTTTTAAAG
*
1497092 TTTTGTTTTGAT-TTGATTT
1 TTTTATTTTGATCTTGATTT
*
1497111 TTTTATTTTGATCTTGGTTT
1 TTTTATTTTGATCTTGATTT
1497131 TT
1 TT
1497133 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.10, C:0.02, G:0.15, T:0.73
Consensus pattern (20 bp):
TTTTATTTTGATCTTGATTT
Found at i:1497446 original size:22 final size:22
Alignment explanation
Indices: 1497421--1497479 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1497411 GATTGCACCC
*
1497421 AGAGGTCCTAAAGATTATGCCT
1 AGAGGTCCTAAAAATTATGCCT
* * *
1497443 AGAGGTCTTAAAAATTGTGCCC
1 AGAGGTCCTAAAAATTATGCCT
* *
1497465 GGAGGTCTTAAAAAT
1 AGAGGTCCTAAAAAT
1497480 CTAAAATCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (22 bp):
AGAGGTCCTAAAAATTATGCCT
Found at i:1497656 original size:105 final size:105
Alignment explanation
Indices: 1497490--1497801 Score: 395
Period size: 105 Copynumber: 3.0 Consensus size: 105
1497480 CTAAAATCTA
* *
1497490 AAAATCTTTGAATGCTTCTAATACATTAAAGGCGTTGAAACTTTAAAAATTTAAAATGTTTTGCC
1 AAAATCTTTGAATGC-TCTCATACATTAAAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCC
*
1497555 CAAAGGTCTTAAAGATTGTGC-TCAAGGTCTTAAGGATTTC
65 CAAAGGTCTTAAAGATTATGCTTCAAGGTCTTAAGGATTTC
*
1497595 AAAATCTTTAAATGCTCCTCATACATTAAAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCC
1 AAAATCTTTGAATGCT-CTCATACATTAAAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCC
* ** *
1497660 CGAAA-GTCTTAAAGATTTTGCTTGGAGGTCTT-AGAGATCTC
65 C-AAAGGTCTTAAAGATTATGCTTCAAGGTCTTAAG-GATTTC
* *
1497701 AAAATCTTTGAATGCTCTGCATATATTAAAGGCATTGAAA--TTGAAAATTTAAAATGTTTTG-C
1 AAAATCTTTGAATGCTCT-CATACATTAAAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCC
* * * *
1497763 TAGAGGTCTTGGAA-ATTATGCTTCAAGGTCTTAAAGATT
65 CAAAGGTCTT-AAAGATTATGCTTCAAGGTCTTAAGGATT
1497802 ATGCCTAGAG
Statistics
Matches: 181, Mismatches: 18, Indels: 18
0.83 0.08 0.08
Matches are distributed among these distances:
102 2 0.01
103 24 0.13
104 24 0.13
105 80 0.44
106 51 0.28
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (105 bp):
AAAATCTTTGAATGCTCTCATACATTAAAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCCC
AAAGGTCTTAAAGATTATGCTTCAAGGTCTTAAGGATTTC
Found at i:1497813 original size:22 final size:22
Alignment explanation
Indices: 1497762--1497813 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1497752 AAATGTTTTG
*
1497762 CTAGAGGTCTTGGAAATTATGC
1 CTAGAGGTCTTGAAAATTATGC
*
1497784 TTCA-AGGTCTT-AAAGATTATGC
1 CT-AGAGGTCTTGAAA-ATTATGC
1497806 CTAGAGGT
1 CTAGAGGT
1497814 TTTACAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
21 3 0.12
22 20 0.83
23 1 0.04
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (22 bp):
CTAGAGGTCTTGAAAATTATGC
Found at i:1497887 original size:125 final size:124
Alignment explanation
Indices: 1497656--1498035 Score: 419
Period size: 125 Copynumber: 3.0 Consensus size: 124
1497646 TAAAATGTTT
* * * * * * * *
1497656 TGCCCGAAAGTCTTAAAGATTTTGCTTGGAGGTCTTAGAGATCTCAAAATCTTTGAATGCTCTGC
1 TGCCCGAAGGTCTTAAAGATTATGCCTAGAGGTTTTACAAATCTTAAAATCTTTGAATGCTCT-C
* *
1497721 ATATATTAAAGGCATTGAA-ATTGAAAATTTAAAATGTTTTG-CTAGAGGTCTTGGAAATTA
65 ATA-ATT-GAGGCATTAAACATTGAAAATTTAAAATGTTTTGCCTAGAGGTCTTGGAAATTA
*
1497781 TGCTTC-AAGGTCTTAAAGATTATGCCTAGAGGTTTTACAAATCTTAAAATCTTTGAATGCTCTA
1 TGC-CCGAAGGTCTTAAAGATTATGCCTAGAGGTTTTACAAATCTTAAAATCTTTGAATGCTCT-
* * * * *
1497845 CATAATTGAGGCATTAAAACATTGAAAATATAAAATGTTTTGCCAACAGGTTTTGAAAATTA
64 CATAATTGAGGCATT-AAACATTGAAAATTTAAAATGTTTTGCCTAGAGGTCTTGGAAATTA
* * * * *
1497907 TGCCCGGAGGTTTTAAAGATTATGCC-CGAGGTTTTCCAAATCTTAAAATCTTTGAATGCCTCTT
1 TGCCCGAAGGTCTTAAAGATTATGCCTAGAGGTTTTACAAATCTTAAAATCTTTGAATG-CTCTC
* * * *
1497971 GTAATAGAGGCATTGAAACTTTGAAAATTTAAAATGTTTTGCCT-GTAGGTCTTGGGAATTA
65 ATAATTGAGGCATT-AAACATTGAAAATTTAAAATGTTTTGCCTAG-AGGTCTTGGAAATTA
1498032 TGCC
1 TGCC
1498036 AGAAAGTATT
Statistics
Matches: 215, Mismatches: 33, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
123 7 0.03
124 5 0.02
125 162 0.75
126 41 0.19
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (124 bp):
TGCCCGAAGGTCTTAAAGATTATGCCTAGAGGTTTTACAAATCTTAAAATCTTTGAATGCTCTCA
TAATTGAGGCATTAAACATTGAAAATTTAAAATGTTTTGCCTAGAGGTCTTGGAAATTA
Found at i:1497939 original size:21 final size:22
Alignment explanation
Indices: 1497892--1497941 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1497882 TTTTGCCAAC
1497892 AGGTTTTGAAAATTATGCCCGG
1 AGGTTTTGAAAATTATGCCCGG
1497914 AGGTTTT-AAAGATTATGCCC-G
1 AGGTTTTGAAA-ATTATGCCCGG
1497935 AGGTTTT
1 AGGTTTT
1497942 CCAAATCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (22 bp):
AGGTTTTGAAAATTATGCCCGG
Found at i:1498125 original size:104 final size:104
Alignment explanation
Indices: 1497914--1498155 Score: 294
Period size: 104 Copynumber: 2.3 Consensus size: 104
1497904 TTATGCCCGG
* * * * * * **
1497914 AGGTTTTAAAGATTATGCCCG-AGGTTTTCCAAATCTTAAAATCTTTGAATGCCTCTTGTAATAG
1 AGGTCTTAAAGATTATGCCAGAAAGTATTACAAATCTCAAAATCTTTGAATGCCTCTCATAATAG
* * *
1497978 AGGCATTGAAACTTTGAAAATTTAAAATGTTTTGCCTGT
66 AGGCATTGAAACTTTAAAAATTTAAAATCTTTTGCCAGT
**
1498017 AGGTCTT-GGGAATTATGCCAGAAAGTATTACAAATCTCAAAATCTTTGAATG-CTCCTCATAAT
1 AGGTCTTAAAG-ATTATGCCAGAAAGTATTACAAATCTCAAAATCTTTGAATGCCT-CTCATAAT
1498080 AGAGGCATTGAAACTTTAAAAATTTAAAATCTTTTGCTCAG-
64 AGAGGCATTGAAACTTTAAAAATTTAAAATCTTTTGC-CAGT
* *
1498121 AGGTCTTAAAGATTATGCCCGAAAGTATTAGAAAT
1 AGGTCTTAAAGATTATGCCAGAAAGTATTACAAAT
1498156 ATGTTTGGGT
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
102 1 0.01
103 17 0.15
104 96 0.82
105 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (104 bp):
AGGTCTTAAAGATTATGCCAGAAAGTATTACAAATCTCAAAATCTTTGAATGCCTCTCATAATAG
AGGCATTGAAACTTTAAAAATTTAAAATCTTTTGCCAGT
Found at i:1500140 original size:88 final size:84
Alignment explanation
Indices: 1499986--1500143 Score: 201
Period size: 88 Copynumber: 1.8 Consensus size: 84
1499976 CTGGCTGAAA
* * *
1499986 CTTTATTCACTTTTTACCTTGAATTCTCTCTAAGGCACATGTCTTTCTTTTCTTAGCTTTTTTTT
1 CTTTATTCACTTTTTACCTTAAATTCTCTCTAAAGCACATGTCTTTCTTTTCTTAGCTTTTATTT
1500051 TTTTGGATTTTAACTAAAG
66 TTTTGGATTTTAACTAAAG
* * **
1500070 CTTTATTCACTTTTTTACCTTAAATTCTTGTCTACGAAGTACATGTCTTTCTCTTT-TTTTCTTT
1 CTTTATTCAC-TTTTTACCTTAAATTC-TCTCTA--AAGCACATGTCTTTCT-TTTCTTAGCTTT
1500134 TATTTTTTTG
61 TATTTTTTTG
1500144 TGCAAACACC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 10 0.16
85 15 0.24
86 5 0.08
88 29 0.47
89 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56
Consensus pattern (84 bp):
CTTTATTCACTTTTTACCTTAAATTCTCTCTAAAGCACATGTCTTTCTTTTCTTAGCTTTTATTT
TTTTGGATTTTAACTAAAG
Found at i:1510683 original size:23 final size:22
Alignment explanation
Indices: 1510651--1510693 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1510641 TAGGTTTTCG
*
1510651 TGCCAACTAATCTTGGGCTTATA
1 TGCCAACTAAAC-TGGGCTTATA
*
1510674 TGCCAGCTAAACTGGGCTTA
1 TGCCAACTAAACTGGGCTTA
1510694 AAATTGGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (22 bp):
TGCCAACTAAACTGGGCTTATA
Found at i:1511056 original size:34 final size:34
Alignment explanation
Indices: 1511015--1511376 Score: 198
Period size: 33 Copynumber: 11.0 Consensus size: 34
1511005 AAGCTGGGCT
* *
1511015 TTAAAATCTTCATCGAGTACCAGGTAAACTGGGC
1 TTAAAATCTTCATCGAGTGCCAGGTAAACTAGGC
* * * **
1511049 TTAAAATCTTCCTTG-GTGCTAAATAAACTAGGC
1 TTAAAATCTTCATCGAGTGCCAGGTAAACTAGGC
* *
1511082 TTAAAATCATT-A-C--GTGCCAGCTAAGCTAGGC
1 TTAAAATC-TTCATCGAGTGCCAGGTAAACTAGGC
* * *
1511113 TTAAACT-TTCATTG-GTGCCAAGTAAACTAGGC
1 TTAAAATCTTCATCGAGTGCCAGGTAAACTAGGC
* * * *
1511145 TTAAAATTTTCATC-AGGTGCTAGGTATACTGGGC
1 TTAAAATCTTCATCGA-GTGCCAGGTAAACTAGGC
* * * * *
1511179 TTCAACT-TTCTTTG-GTGCTAGGTAAACTAGGC
1 TTAAAATCTTCATCGAGTGCCAGGTAAACTAGGC
** *
1511211 TT-AAATCTTTC-TTTAGTGCCAGATAAACTAGGC
1 TTAAAATC-TTCATCGAGTGCCAGGTAAACTAGGC
* ** *
1511244 TTAAAAT-TTCATCGAGTGCTACATAAATTAGGC
1 TTAAAATCTTCATCGAGTGCCAGGTAAACTAGGC
* * * * *
1511277 ATAAAATTTTCATC-AGGTGTCAGGTAAATTGGGC
1 TTAAAATCTTCATCGA-GTGCCAGGTAAACTAGGC
** * * *
1511311 TTAAAATCTTTTTTTG-GTGCCAGATAAACAAGGC
1 TTAAAATC-TTCATCGAGTGCCAGGTAAACTAGGC
* * *
1511345 TTAAAAT-TTCAACGAGCGCCAGGTAAATTAGG
1 TTAAAATCTTCATCGAGTGCCAGGTAAACTAGG
1511377 TGTCAGGTAA
Statistics
Matches: 247, Mismatches: 63, Indels: 37
0.71 0.18 0.11
Matches are distributed among these distances:
29 2 0.01
30 1 0.00
31 23 0.09
32 47 0.19
33 88 0.36
34 83 0.34
35 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (34 bp):
TTAAAATCTTCATCGAGTGCCAGGTAAACTAGGC
Found at i:1511083 original size:33 final size:32
Alignment explanation
Indices: 1511039--1511355 Score: 201
Period size: 33 Copynumber: 9.7 Consensus size: 32
1511029 GAGTACCAGG
* * *
1511039 TAAACTGGGCTTAAAATCTTCCTTGGTGCTAAA
1 TAAACTAGGCTTAAAAT-TTCATTGGTGCTAGA
* * *
1511072 TAAACTAGGCTTAAAA--TCATTACGTGCCAGC
1 TAAACTAGGCTTAAAATTTCATT-GGTGCTAGA
* * *
1511103 TAAGCTAGGCTTAAACTTTCATTGGTGCCA-A
1 TAAACTAGGCTTAAAATTTCATTGGTGCTAGA
* *
1511134 GTAAACTAGGCTTAAAATTTTCATCAGGTGCTAGG
1 -TAAACTAGGCTTAAAA-TTTCAT-TGGTGCTAGA
* * * * * *
1511169 TATACTGGGCTTCAACTTTCTTTGGTGCTAGG
1 TAAACTAGGCTTAAAATTTCATTGGTGCTAGA
* * * *
1511201 TAAACTAGGCTTAAATCTTTCTTTAGTGCCAGA
1 TAAACTAGGCTTAAA-ATTTCATTGGTGCTAGA
* *
1511234 TAAACTAGGCTTAAAATTTCATCGAGTGCTACA
1 TAAACTAGGCTTAAAATTTCATTG-GTGCTAGA
* * * *
1511267 TAAATTAGGCATAAAATTTTCATCAGGTG-TCAGG
1 TAAACTAGGCTTAAAA-TTTCAT-TGGTGCT-AGA
* * ** *
1511301 TAAATTGGGCTTAAAATCTTTTTTTGGTGCCAGA
1 TAAACTAGGCTTAAAA--TTTCATTGGTGCTAGA
*
1511335 TAAACAAGGCTTAAAATTTCA
1 TAAACTAGGCTTAAAATTTCA
1511356 ACGAGCGCCA
Statistics
Matches: 219, Mismatches: 51, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
30 4 0.02
31 19 0.09
32 49 0.22
33 81 0.37
34 61 0.28
35 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (32 bp):
TAAACTAGGCTTAAAATTTCATTGGTGCTAGA
Found at i:1511114 original size:31 final size:30
Alignment explanation
Indices: 1511072--1511151 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 30
1511062 TGGTGCTAAA
1511072 TAAACTAGGCTTAAAATCATTACGTGCC-AG
1 TAAACTAGGCTTAAAATCATT-CGTGCCAAG
* * *
1511102 CTAAGCTAGGCTTAAACTTTCATTGGTGCCAAG
1 -TAAACTAGGCTTAAA--ATCATTCGTGCCAAG
1511135 TAAACTAGGCTTAAAAT
1 TAAACTAGGCTTAAAAT
1511152 TTTCATCAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
30 1 0.02
31 14 0.34
32 19 0.46
33 7 0.17
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (30 bp):
TAAACTAGGCTTAAAATCATTCGTGCCAAG
Found at i:1511194 original size:66 final size:66
Alignment explanation
Indices: 1511015--1511353 Score: 280
Period size: 66 Copynumber: 5.1 Consensus size: 66
1511005 AAGCTGGGCT
* * * * *
1511015 TTAAAATCTTCATC-GAGTACCAGGTAAACTGGGCTTAAAATCTTCCTTGGTGCTAAATAAACTA
1 TTAAAATTTTCATCAG-GTGCCAGGTAAACTGGGCTTAAACT-TTCATTGGTGCTAAGTAAACTA
1511079 GGC
64 GGC
* * * * * *
1511082 TTAAAA---TCATTACGTGCCAGCTAAGCTAGGCTTAAACTTTCATTGGTGCCAAGTAAACTAGG
1 TTAAAATTTTCATCAGGTGCCAGGTAAACTGGGCTTAAACTTTCATTGGTGCTAAGTAAACTAGG
1511144 C
66 C
* * * * *
1511145 TTAAAATTTTCATCAGGTGCTAGGTATACTGGGCTTCAACTTTCTTTGGTGCTAGGTAAACTAGG
1 TTAAAATTTTCATCAGGTGCCAGGTAAACTGGGCTTAAACTTTCATTGGTGCTAAGTAAACTAGG
1511210 C
66 C
* * * * * * *
1511211 TT-AAATCTTTCTTTA-GTGCCAGATAAACTAGGCTTAAAATTTCATCGAGTGCTACA-TAAATT
1 TTAAAAT-TTTCATCAGGTGCCAGGTAAACTGGGCTTAAACTTTCATTG-GTGCTA-AGTAAACT
1511273 AGGC
63 AGGC
* * * ** * *
1511277 ATAAAATTTTCATCAGGTGTCAGGTAAATTGGGCTTAAAATCTTTTTTTGGTGC-CAGATAAACA
1 TTAAAATTTTCATCAGGTGCCAGGTAAACTGGGCTT-AAA-CTTTCATTGGTGCTAAG-TAAACT
1511341 AGGC
63 AGGC
1511345 TTAAAATTT
1 TTAAAATTT
1511354 CAACGAGCGC
Statistics
Matches: 211, Mismatches: 48, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
63 28 0.13
64 24 0.11
65 28 0.13
66 77 0.36
67 26 0.12
68 23 0.11
69 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (66 bp):
TTAAAATTTTCATCAGGTGCCAGGTAAACTGGGCTTAAACTTTCATTGGTGCTAAGTAAACTAGG
C
Found at i:1513556 original size:14 final size:13
Alignment explanation
Indices: 1513525--1513562 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1513515 TTTGACTTAA
1513525 AAAAAAATTAAAC
1 AAAAAAATTAAAC
*
1513538 -CAAAAATTAAAC
1 AAAAAAATTAAAC
1513550 TAAAAAAATTAAA
1 -AAAAAAATTAAA
1513563 ATATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
14 10 0.48
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAATTAAAC
Found at i:1524160 original size:2 final size:2
Alignment explanation
Indices: 1524153--1524177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1524143 GCAAGGAGAT
1524153 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 T
1524178 GGGTAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1524580 original size:26 final size:26
Alignment explanation
Indices: 1524538--1524587 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1524528 CATGTAAAAA
*
1524538 TTTTAACCAAAC-CTTTTCTTTTTTT
1 TTTTAACCAAACATTTTTCTTTTTTT
*
1524563 TTTTCAACCAAATATTTTTCTTTTT
1 TTTT-AACCAAACATTTTTCTTTTT
1524588 ATATGTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 7 0.33
27 10 0.48
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTAACCAAACATTTTTCTTTTTTT
Found at i:1526481 original size:116 final size:116
Alignment explanation
Indices: 1526361--1526602 Score: 432
Period size: 116 Copynumber: 2.1 Consensus size: 116
1526351 ATAAATGGTT
* *
1526361 ATAACTATTTCAATATAAATAGATTATTATTCATAAAAGTCATGATTATGCATAAGGTCATAACC
1 ATAACTATTTCAATATAAATAGATTATTATTCATAAAAGTCATGATTATACAGAAGGTCATAACC
*
1526426 ATTTGAATAGAAATTTAT-TTCTGTTCATTCATTATAAATAAATATTTTAGC
66 ATTTAAATAGAAATTTATCTT-TGTTCATTCATTATAAATAAATATTTTAGC
1526477 ATAACTATTTCAATATAAATAGATTATTATTCATAAAAGTCATGATTATACAGAAGGTCATAACC
1 ATAACTATTTCAATATAAATAGATTATTATTCATAAAAGTCATGATTATACAGAAGGTCATAACC
1526542 ATTTAAATAGAAATTTATCTTTGTTCATTCATTATAAATAAATATTTTAGC
66 ATTTAAATAGAAATTTATCTTTGTTCATTCATTATAAATAAATATTTTAGC
*
1526593 ATAACCATTT
1 ATAACTATTT
1526603 TTACTACTTC
Statistics
Matches: 121, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
116 119 0.98
117 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (116 bp):
ATAACTATTTCAATATAAATAGATTATTATTCATAAAAGTCATGATTATACAGAAGGTCATAACC
ATTTAAATAGAAATTTATCTTTGTTCATTCATTATAAATAAATATTTTAGC
Found at i:1526601 original size:57 final size:56
Alignment explanation
Indices: 1526419--1526602 Score: 149
Period size: 57 Copynumber: 3.2 Consensus size: 56
1526409 TGCATAAGGT
*
1526419 CATAACCATTTGAATAGAAATTTATTTCTGTTCATTCATTATAAATAAATATTTTAG
1 CATAACCATTTAAATAGAAATTTATTT-TGTTCATTCATTATAAATAAATATTTTAG
* * * ** * * * * * ***
1526476 CATAACTATTTCAATATAAATAGATTATTATTCATAAAAGTCATGAT-TATACAGAAGGT--
1 CATAACCATTTAAATAGAAATTTATT-TTGTTCAT-----TCATTATAAATAAATATTTTAG
1526535 CATAACCATTTAAATAGAAATTTATCTTTGTTCATTCATTATAAATAAATATTTTAG
1 CATAACCATTTAAATAGAAATTTAT-TTTGTTCATTCATTATAAATAAATATTTTAG
1526592 CATAACCATTT
1 CATAACCATTT
1526603 TTACTACTTC
Statistics
Matches: 91, Mismatches: 26, Indels: 20
0.66 0.19 0.15
Matches are distributed among these distances:
54 6 0.07
55 6 0.07
57 38 0.42
58 1 0.01
59 27 0.30
60 1 0.01
61 6 0.07
62 6 0.07
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (56 bp):
CATAACCATTTAAATAGAAATTTATTTTGTTCATTCATTATAAATAAATATTTTAG
Found at i:1535055 original size:14 final size:15
Alignment explanation
Indices: 1535036--1535064 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1535026 ATTTTTTATG
1535036 TTTTATA-TATTAAT
1 TTTTATATTATTAAT
1535050 TTTTATATTATTAAT
1 TTTTATATTATTAAT
1535065 AATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTATATTATTAAT
Found at i:1536876 original size:18 final size:18
Alignment explanation
Indices: 1536834--1536876 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
1536824 TCTTTCATCA
1536834 TTTTTTAGTTATTTTATT
1 TTTTTTAGTTATTTTATT
1536852 TTATTTTA-TTATTTTATAT
1 TT-TTTTAGTTATTTTAT-T
1536871 TTTTTT
1 TTTTTT
1536877 GGGAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTAGTTATTTTATT
Found at i:1542077 original size:39 final size:39
Alignment explanation
Indices: 1542023--1542202 Score: 127
Period size: 39 Copynumber: 4.6 Consensus size: 39
1542013 TCCAGAACTA
* *
1542023 GATGCACCCAAATCTGGTTCCAACAAGACCCCCAGTCTG
1 GATGCGCCCGAATCTGGTTCCAACAAGACCCCCAGTCTG
* * * *
1542062 GATGCGCCCGAATCTGGTTCCAACTAGTCGCCCA-CCTG
1 GATGCGCCCGAATCTGGTTCCAACAAGACCCCCAGTCTG
** * ** * * ** *
1542100 CCTGAGGTCG-ATC-CG-TCGGAA-GGGACTACGCCCAGAACTG
1 GATGCGCCCGAATCTGGTTC-CAACAAGAC--C-CCCAG-TCTG
*
1542140 GATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTG
1 GATGCGCCCGAATCTGGTTCCAACAAGACCCCCAGTCTG
1542179 GATGCGCCCGAATCTGGTTCCAAC
1 GATGCGCCCGAATCTGGTTCCAAC
1542203 CAGTCGCCCA
Statistics
Matches: 101, Mismatches: 30, Indels: 20
0.67 0.20 0.13
Matches are distributed among these distances:
35 4 0.04
36 3 0.03
37 3 0.03
38 12 0.12
39 55 0.54
40 12 0.12
41 4 0.04
42 3 0.03
43 5 0.05
ACGTcount: A:0.23, C:0.34, G:0.24, T:0.18
Consensus pattern (39 bp):
GATGCGCCCGAATCTGGTTCCAACAAGACCCCCAGTCTG
Found at i:1542165 original size:117 final size:117
Alignment explanation
Indices: 1541959--1542282 Score: 549
Period size: 117 Copynumber: 2.8 Consensus size: 117
1541949 NNNNNNNNNN
* * *
1541959 TGGTTCTAACCAGTCGCCCACCTGCCTGAGGTCGATCCGTCAGAAGGGACTACGTCCAGAACTAG
1 TGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATCCGTCAGAAGGGACTACGCCCAGAACTGG
*
1542024 ATGCACCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCCCGAATC
66 ATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCCCGAATC
* *
1542076 TGGTTCCAACTAGTCGCCCACCTGCCTGAGGTCGATCCGTCGGAAGGGACTACGCCCAGAACTGG
1 TGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATCCGTCAGAAGGGACTACGCCCAGAACTGG
1542141 ATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCCCGAATC
66 ATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCCCGAATC
* * *
1542193 TGGTTCCAACCAGTCGCCCACCACTGCTTGAGGTCAATCCGTCAGAAGGGACTATGCCCAGAACT
1 TGGTTCCAACCAGTCGCCCA-C-CTGCCTGAGGTCGATCCGTCAGAAGGGACTACGCCCAGAACT
1542258 GGATGCGCCCAAATCTGGTTCCAAC
64 GGATGCGCCCAAATCTGGTTCCAAC
1542283 CAGTCGCCCA
Statistics
Matches: 194, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
117 130 0.67
118 1 0.01
119 63 0.32
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (117 bp):
TGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATCCGTCAGAAGGGACTACGCCCAGAACTGG
ATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCCCGAATC
Found at i:1542274 original size:80 final size:79
Alignment explanation
Indices: 1542176--1542361 Score: 309
Period size: 80 Copynumber: 2.3 Consensus size: 79
1542166 GACCCCCAGT
* * *
1542176 CTGGATGCGCCCGAATCTGGTTCCAACCAGTCGCCCACCACTGCTTGAGGTCAATCCGTCAGAAG
1 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCAATCCATCAGAAG
*
1542241 GGACTATGCCCAGAA
66 GGACTACG-CCAGAA
* *
1542256 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
1 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCAATCCATCAGAAG
1542321 GGACTACGCCAGAA
66 GGACTACGCCAGAA
1542335 CTGGATGCGCCCAAATCTGGTTCCAAC
1 CTGGATGCGCCCAAATCTGGTTCCAAC
1542362 AAGACCCCCA
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 33 0.33
80 67 0.67
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (79 bp):
CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCAATCCATCAGAAG
GGACTACGCCAGAA
Found at i:1542399 original size:198 final size:199
Alignment explanation
Indices: 1542059--1542504 Score: 785
Period size: 198 Copynumber: 2.3 Consensus size: 199
1542049 GACCCCCAGT
* * *
1542059 CTGGATGCGCCCGAATCTGGTTCCAACTAGTCGCCCA-C-CTGCCTGAGGTCGATCCGTCGGAAG
1 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
1542122 GGACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCC
66 GGACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCC
*
1542187 CGAATCTGGTTCCAACCAGTCGCCCACCACTG-CTTGAGGTCAATCCGTCAGAAGGGACTATGCC
131 CGAATCTGGTTCCAACCAGTCGCCCACCACTGTC-TGAGGTCAATCCGTCAGAAGGGACTACGCC
1542251 CAGAA
195 CAGAA
1542256 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
1 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
1542321 GGACTACG-CCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCC
66 GGACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCC
* * *
1542385 CGAATCTTGTTCCAACCAGTCGCCCACCACTGTCTGAGGTCGATCCGTCGGAAGGGACTACGCCC
131 CGAATCTGGTTCCAACCAGTCGCCCACCACTGTCTGAGGTCAATCCGTCAGAAGGGACTACGCCC
1542450 AGAA
196 AGAA
1542454 CTGGATGCGCCCAAATCT-GTTCCAACCAGTCGCCCACCACTGCCTGAGGTC
1 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTC
1542505 CAGTCGCCCA
Statistics
Matches: 239, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
197 68 0.28
198 138 0.58
199 33 0.14
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.18
Consensus pattern (199 bp):
CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
GGACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGTCTGGATGCGCC
CGAATCTGGTTCCAACCAGTCGCCCACCACTGTCTGAGGTCAATCCGTCAGAAGGGACTACGCCC
AGAA
Found at i:1542476 original size:118 final size:118
Alignment explanation
Indices: 1542256--1542479 Score: 396
Period size: 118 Copynumber: 1.9 Consensus size: 118
1542246 ATGCCCAGAA
1542256 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
1 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
1542321 GGACTACGCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGT
66 GGACTACGCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGT
* * * *
1542374 CTGGATGCGCCCGAATCTTGTTCCAACCAGTCGCCCACCACTGTCTGAGGTCGATCCGTCGGAAG
1 CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
1542439 GGACTACGCCCAGAACTGGATGCGCCCAAATCT-GTTCCAAC
66 GGACTACG-CCAGAACTGGATGCGCCCAAATCTGGTTCCAAC
1542480 CAGTCGCCCA
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 77 0.76
119 24 0.24
ACGTcount: A:0.23, C:0.34, G:0.24, T:0.18
Consensus pattern (118 bp):
CTGGATGCGCCCAAATCTGGTTCCAACCAGTCGCCCACCACTGCCTGAGGTCGATCCATCGGAAG
GGACTACGCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACCCCCAGT
Found at i:1542509 original size:25 final size:25
Alignment explanation
Indices: 1542479--1542529 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1542469 TCTGTTCCAA
1542479 CCAGTCGCCCACCACTGCCTGAGGT
1 CCAGTCGCCCACCACTGCCTGAGGT
1542504 CCAGTCGCCCACCACTGCCTGAGGT
1 CCAGTCGCCCACCACTGCCTGAGGT
1542529 C
1 C
1542530 GATCCGTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.45, G:0.24, T:0.16
Consensus pattern (25 bp):
CCAGTCGCCCACCACTGCCTGAGGT
Found at i:1546308 original size:25 final size:22
Alignment explanation
Indices: 1546266--1546312 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 22
1546256 AAAAAAAAAA
1546266 GAAAAAAAGGAAATTGAAAATT
1 GAAAAAAAGGAAATTGAAAATT
1546288 GAAAAATAAGGAAAATATGAAAATT
1 GAAAAA-AAGG-AAAT-TGAAAATT
1546313 TTTTGGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 4 0.18
24 4 0.18
25 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (22 bp):
GAAAAAAAGGAAATTGAAAATT
Found at i:1552443 original size:14 final size:14
Alignment explanation
Indices: 1552424--1552451 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1552414 AATATTTTTA
1552424 TTAAAAATATATAT
1 TTAAAAATATATAT
1552438 TTAAAAATATATAT
1 TTAAAAATATATAT
1552452 CAAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:1552457 original size:12 final size:13
Alignment explanation
Indices: 1552422--1552456 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1552412 TTAATATTTT
1552422 TATTAAAAATATA
1 TATTAAAAATATA
1552435 TATTTAAAAATATA
1 TA-TTAAAAATATA
*
1552449 TATCAAAA
1 TATTAAAA
1552457 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
TATTAAAAATATA
Found at i:1552553 original size:19 final size:20
Alignment explanation
Indices: 1552512--1552561 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1552502 AAATCTTTCA
*
1552512 ATTTATTAATTTTAATTTTTT
1 ATTT-TTAATTTTAATTTATT
1552533 A-TTTTAATTTT-ATTTAATT
1 ATTTTTAATTTTAATTT-ATT
1552552 ATTTTTAATT
1 ATTTTTAATT
1552562 AAAAACTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 11 0.42
20 10 0.38
21 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTAATTTTAATTTATT
Found at i:1554445 original size:17 final size:18
Alignment explanation
Indices: 1554425--1554459 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1554415 CTTAACCACC
1554425 ACAAAG-CCAACACCATT
1 ACAAAGTCCAACACCATT
*
1554442 ACAAAGTCCCACACCATT
1 ACAAAGTCCAACACCATT
1554460 CACCAAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.37, G:0.06, T:0.14
Consensus pattern (18 bp):
ACAAAGTCCAACACCATT
Found at i:1555670 original size:10 final size:9
Alignment explanation
Indices: 1555657--1555699 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
1555647 TTATTTTCCC
1555657 AAAAAAATA
1 AAAAAAATA
*
1555666 TAAAATAATA
1 -AAAAAAATA
1555676 AAATAAAATA
1 AAA-AAAATA
*
1555686 AAATAAATA
1 AAAAAAATA
1555695 AAAAA
1 AAAAA
1555700 TGATGAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1556021 original size:15 final size:17
Alignment explanation
Indices: 1555991--1556027 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1555981 GACATAAAAA
1555991 TAAAACAATTAGAT-AAT
1 TAAAACAA-TAGATAAAT
1556008 TAAAACAA-AGATAAAT
1 TAAAACAATAGATAAAT
1556024 TAAA
1 TAAA
1556028 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 7 0.37
17 8 0.42
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (17 bp):
TAAAACAATAGATAAAT
Found at i:1557645 original size:4 final size:4
Alignment explanation
Indices: 1557636--1557699 Score: 67
Period size: 4 Copynumber: 16.0 Consensus size: 4
1557626 TTGATAATAA
* ** * *
1557636 TATT TATT TACT TAAC TATT TATT TAATT TA-T TAGT TATG TATT TATT
1 TATT TATT TATT TATT TATT TATT T-ATT TATT TATT TATT TATT TATT
1557684 TATT TATT TATT TATT
1 TATT TATT TATT TATT
1557700 ATCTTATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
3 3 0.06
4 43 0.86
5 4 0.08
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (4 bp):
TATT
Found at i:1557706 original size:8 final size:7
Alignment explanation
Indices: 1557652--1557708 Score: 51
Period size: 8 Copynumber: 7.3 Consensus size: 7
1557642 TTTACTTAAC
1557652 TATTTATT
1 TATTTA-T
1557660 TAATTTAT
1 T-ATTTAT
*
1557668 TAGTTAT
1 TATTTAT
1557675 GTATTTATT
1 -TATTTA-T
1557684 TATTTATT
1 TATTTA-T
1557692 TATTTAT
1 TATTTAT
1557699 TATCTTAT
1 TAT-TTAT
1557707 TA
1 TA
1557709 AATAAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 9 0.21
8 28 0.65
9 6 0.14
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (7 bp):
TATTTAT
Found at i:1566201 original size:131 final size:131
Alignment explanation
Indices: 1565977--1566236 Score: 450
Period size: 131 Copynumber: 2.0 Consensus size: 131
1565967 TTAGAAGTAG
* *
1565977 TAAAAATGGTTATGCTAAAATATTTATTTATAATGAATGAACATAGATAAAATTTCTATTTAAAT
1 TAAAAATGGTTATGCTAAAATATTTATTTATAATAAATGAACAGAGATAAAATTTCTATTTAAAT
* *
1566042 AGTTATGACTTTCTGTATAATCATACTTTTATGAATAATAATCTATTTATATTGAAATAGTTATG
66 AGTTATGACCTTATGTATAATCATACTTTTATGAATAATAATCTATTTATATTGAAATAGTTATG
1566107 T
131 T
*
1566108 TAAAAATGGTTATGCTAAAATATTTATTTATAATAAATGAATAGAGAT-AAATTTCTATTTAAAT
1 TAAAAATGGTTATGCTAAAATATTTATTTATAATAAATGAACAGAGATAAAATTTCTATTTAAAT
*
1566172 GGTTATGACCTTATGTATAATCATGACTTTTATGAATAATAATCTATTTATATTGAAATAGTTAT
66 AGTTATGACCTTATGTATAATCAT-ACTTTTATGAATAATAATCTATTTATATTGAAATAGTTAT
1566237 AACCATTTAT
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
130 37 0.30
131 85 0.70
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (131 bp):
TAAAAATGGTTATGCTAAAATATTTATTTATAATAAATGAACAGAGATAAAATTTCTATTTAAAT
AGTTATGACCTTATGTATAATCATACTTTTATGAATAATAATCTATTTATATTGAAATAGTTATG
T
Found at i:1573710 original size:28 final size:28
Alignment explanation
Indices: 1573659--1573715 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1573649 AAGCATGTAA
**
1573659 GAAAAAAAAATGAAAAAGGAATGAAAAT
1 GAAAAAAAAATGAAAAAAAAATGAAAAT
1573687 GAAAAAAAAA-GAAAAAAAAGATGAAAAT
1 GAAAAAAAAATGAAAAAAAA-ATGAAAAT
1573715 G
1 G
1573716 CATGTTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (28 bp):
GAAAAAAAAATGAAAAAAAAATGAAAAT
Found at i:1579894 original size:20 final size:21
Alignment explanation
Indices: 1579869--1579911 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1579859 TGACACCCAC
1579869 ATATTTGTCATAGCCA-CCTA
1 ATATTTGTCATAGCCACCCTA
1579889 ATATTTGTCATAGCCACCCTA
1 ATATTTGTCATAGCCACCCTA
1579910 AT
1 AT
1579912 GTCTTTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (21 bp):
ATATTTGTCATAGCCACCCTA
Found at i:1584529 original size:5 final size:5
Alignment explanation
Indices: 1584519--1584556 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
1584509 AAATGGGTTA
*
1584519 AAAAT AAAAT AAAAT -AAAT AAAAT CAAA- AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1584557 GGAAAAGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1584539 original size:9 final size:10
Alignment explanation
Indices: 1584519--1584556 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
1584509 AAATGGGTTA
1584519 AAAATAAAAT
1 AAAATAAAAT
1584529 AAAAT-AAAT
1 AAAATAAAAT
*
1584538 AAAATCAAA-
1 AAAATAAAAT
1584547 AAAATAAAAT
1 AAAATAAAAT
1584557 GGAAAAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:1584539 original size:14 final size:14
Alignment explanation
Indices: 1584518--1584556 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1584508 AAAATGGGTT
1584518 AAAAATAAAAT-AA
1 AAAAATAAAATCAA
1584531 AATAAATAAAATCAA
1 AA-AAATAAAATCAA
1584546 AAAAATAAAAT
1 AAAAATAAAAT
1584557 GGAAAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 2 0.08
14 18 0.75
15 4 0.17
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATAAAATCAA
Found at i:1585013 original size:22 final size:22
Alignment explanation
Indices: 1584988--1585031 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1584978 ATATTTTTTT
* * *
1584988 CAAACTTTCCCCAGATTTCTCC
1 CAAAATTTCCCCAAATTACTCC
*
1585010 CAAAATTTGCCCAAATTACTCC
1 CAAAATTTCCCCAAATTACTCC
1585032 TAGAATCTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (22 bp):
CAAAATTTCCCCAAATTACTCC
Found at i:1585400 original size:3 final size:3
Alignment explanation
Indices: 1585387--1585426 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1585377 AAGAAATGAA
1585387 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1585427 ATATAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1585499 original size:3 final size:3
Alignment explanation
Indices: 1585493--1585521 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1585483 TATAATAATA
1585493 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1585522 AATCGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1585636 original size:25 final size:24
Alignment explanation
Indices: 1585603--1585665 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
1585593 CCTGAGCGTT
1585603 AATGCGCCTAAATGGGCCGGACACC
1 AATG-GCCTAAATGGGCCGGACACC
* *
1585628 AATGTGCCTAATTTGGGCTGGACACC
1 AATG-GCCTAA-ATGGGCCGGACACC
*
1585654 AATGGACTAAAT
1 AATGGCCTAAAT
1585666 TAAGCTCGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 1 0.03
25 15 0.47
26 16 0.50
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (24 bp):
AATGGCCTAAATGGGCCGGACACC
Found at i:1585666 original size:26 final size:26
Alignment explanation
Indices: 1585615--1585663 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1585605 TGCGCCTAAA
*
1585615 TGGGCCGGACACCAATGTGCCTAATT
1 TGGGCCGGACACCAATGTGACTAATT
*
1585641 TGGGCTGGACACCAATG-GACTAA
1 TGGGCCGGACACCAATGTGACTAA
1585664 ATTAAGCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (26 bp):
TGGGCCGGACACCAATGTGACTAATT
Found at i:1587120 original size:53 final size:53
Alignment explanation
Indices: 1587063--1587166 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
1587053 CTGATACCCC
*
1587063 ATAGGTTTGAAAGAATGAATATTTGATTTACAAAAATGTTTGTTTAACCATAG
1 ATAGGTTTGAAAGAATGAATATTTGATTTACAAAAAAGTTTGTTTAACCATAG
* *
1587116 ATAGGTTTGAAAGAATGAATATTTGATTTTCAAAAAAGTTTGTTTAGCCAT
1 ATAGGTTTGAAAGAATGAATATTTGATTTACAAAAAAGTTTGTTTAACCAT
1587167 CGAGATTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (53 bp):
ATAGGTTTGAAAGAATGAATATTTGATTTACAAAAAAGTTTGTTTAACCATAG
Found at i:1588536 original size:13 final size:13
Alignment explanation
Indices: 1588518--1588542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1588508 AAAAATAATA
1588518 AAAGATGAAAATT
1 AAAGATGAAAATT
1588531 AAAGATGAAAAT
1 AAAGATGAAAAT
1588543 AATAATAATA
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:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (13 bp):
AAAGATGAAAATT
Found at i:1588780 original size:21 final size:21
Alignment explanation
Indices: 1588755--1588806 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1588745 CTAAACCCAT
* *
1588755 AAAAATCCAATTTTTTTAAGA
1 AAAAAACCAATATTTTTAAGA
* *
1588776 AAAAAACCTATATTTTTCAGA
1 AAAAAACCAATATTTTTAAGA
*
1588797 AAAAACCCAA
1 AAAAAACCAA
1588807 AAAAGTTTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAAACCAATATTTTTAAGA
Found at i:1589817 original size:18 final size:17
Alignment explanation
Indices: 1589793--1589962 Score: 79
Period size: 17 Copynumber: 9.8 Consensus size: 17
1589783 TAGGTTAAAA
1589793 AAGATTTCAAGTTTCAC
1 AAGATTTCAAGTTTCAC
*
1589810 AGAGATTTC-AGATTTGA-
1 A-AGATTTCAAG-TTTCAC
1589827 AAGATTTCAAGTTTCAC
1 AAGATTTCAAGTTTCAC
* *
1589844 AGAGATTGCAA-ATTCAC
1 A-AGATTTCAAGTTTCAC
* *
1589861 AAAGGTTTCAA-ATTCAC
1 -AAGATTTCAAGTTTCAC
*
1589878 AAGAATTTCCAAGTTTCGC
1 AAG-ATTT-CAAGTTTCAC
*
1589897 AA-AGGTTCTAA-TTTGCA-
1 AAGA-TTTC-AAGTTT-CAC
*
1589914 AAGGTTTCAAGTTTCAC
1 AAGATTTCAAGTTTCAC
*
1589931 AA-ATGTTCTAGATTTGCA-
1 AAGAT-TTCAAG-TTT-CAC
*
1589949 AAGATTCCAAGTTT
1 AAGATTTCAAGTTT
1589963 TGCAAAGGTT
Statistics
Matches: 117, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
16 19 0.16
17 51 0.44
18 37 0.32
19 10 0.09
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (17 bp):
AAGATTTCAAGTTTCAC
Found at i:1589960 original size:35 final size:35
Alignment explanation
Indices: 1589884--1589986 Score: 136
Period size: 35 Copynumber: 3.0 Consensus size: 35
1589874 TCACAAGAAT
*
1589884 TTCCAAGTTTCGCAAAGGTTCTA-ATTTGCAAAGG
1 TTCCAAGTTTCGCAAAGGTTCTAGATTTGCAAAGA
* * *
1589918 TTTCAAGTTTCACAAATGTTCTAGATTTGCAAAGA
1 TTCCAAGTTTCGCAAAGGTTCTAGATTTGCAAAGA
* * *
1589953 TTCCAAGTTTTGCAAAGGTTCCAGATTCGCAAAG
1 TTCCAAGTTTCGCAAAGGTTCTAGATTTGCAAAG
1589987 GTTTCATATT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
34 20 0.34
35 38 0.66
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (35 bp):
TTCCAAGTTTCGCAAAGGTTCTAGATTTGCAAAGA
Found at i:1589997 original size:17 final size:17
Alignment explanation
Indices: 1589892--1589989 Score: 72
Period size: 17 Copynumber: 5.7 Consensus size: 17
1589882 ATTTCCAAGT
*
1589892 TTCGCAAAGGTTCTA-A
1 TTCGCAAAGGTTCCAGA
* * *
1589908 TTTGCAAAGGTTTCAAGT
1 TTCGCAAAGG-TTCCAGA
* * *
1589926 TTCACAAATGTTCTAGA
1 TTCGCAAAGGTTCCAGA
* * *
1589943 TTTGCAAAGATTCCAAGT
1 TTCGCAAAGGTTCC-AGA
*
1589961 TTTGCAAAGGTTCCAGA
1 TTCGCAAAGGTTCCAGA
1589978 TTCGCAAAGGTT
1 TTCGCAAAGGTT
1589990 TCATATTCAC
Statistics
Matches: 62, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
16 9 0.15
17 31 0.50
18 22 0.35
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (17 bp):
TTCGCAAAGGTTCCAGA
Found at i:1590015 original size:17 final size:17
Alignment explanation
Indices: 1589995--1590091 Score: 72
Period size: 17 Copynumber: 5.8 Consensus size: 17
1589985 AGGTTTCATA
1589995 TTCACAAGAATTTTAGT
1 TTCACAAGAATTTTAGT
* *
1590012 TTCACAATAATTTCAGT
1 TTCACAAGAATTTTAGT
** *
1590029 TTTGCAAGAGTTTTAGGT
1 TTCACAAGAATTTTA-GT
* * **
1590047 TT-GCAAGAAATCAAG-
1 TTCACAAGAATTTTAGT
* *
1590062 TTCACAAGAACTTTAGG
1 TTCACAAGAATTTTAGT
1590079 TTCACAAGAATTT
1 TTCACAAGAATTT
1590092 CAAGTTCACT
Statistics
Matches: 61, Mismatches: 16, Indels: 6
0.73 0.19 0.07
Matches are distributed among these distances:
15 2 0.03
16 10 0.16
17 45 0.74
18 4 0.07
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (17 bp):
TTCACAAGAATTTTAGT
Found at i:1590098 original size:17 final size:17
Alignment explanation
Indices: 1590057--1590108 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1590047 TTGCAAGAAA
1590057 TCAAGTTCACAAGAACTT
1 TCAAGTTCACAAGAA-TT
*
1590075 T-AGGTTCACAAGAATT
1 TCAAGTTCACAAGAATT
*
1590091 TCAAGTTCACTAGAATT
1 TCAAGTTCACAAGAATT
1590108 T
1 T
1590109 AAGGTTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (17 bp):
TCAAGTTCACAAGAATT
Found at i:1590100 original size:34 final size:34
Alignment explanation
Indices: 1589994--1590160 Score: 108
Period size: 34 Copynumber: 4.9 Consensus size: 34
1589984 AAGGTTTCAT
* *
1589994 ATTCACAAGAATTTTAGTTTCACAATAATTTC-AG
1 ATTCACAAGAA-TTTAGGTTCACAAGAATTTCAAG
* ** * ** *
1590028 TTTTGCAAGAGTTTTAGGTTTGCAAGAA-ATCAAG
1 ATTCACAAGA-ATTTAGGTTCACAAGAATTTCAAG
1590062 -TTCACAAGAACTTTAGGTTCACAAGAATTTCAAG
1 ATTCACAAGAA-TTTAGGTTCACAAGAATTTCAAG
* ** * *
1590096 -TTCACTAGAATTTAAGGTTTGCAAGAGTTTAAAAG
1 ATTCACAAGAATTT-AGGTTCACAAGAATTT-CAAG
* *
1590131 ATTCTCAAGAGATTTAGGTTCATAAGAATT
1 ATTCACAAGA-ATTTAGGTTCACAAGAATT
1590161 CGTAAGAGTT
Statistics
Matches: 99, Mismatches: 26, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
33 26 0.26
34 48 0.48
35 3 0.03
36 18 0.18
37 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
ATTCACAAGAATTTAGGTTCACAAGAATTTCAAG
Found at i:1590114 original size:67 final size:67
Alignment explanation
Indices: 1589995--1590121 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 67
1589985 AGGTTTCATA
* * * ** * *
1589995 TTCACAAGAATTTTAGTTTCACAATAATTTCAGTTTTGCAAGAGTTTTAGGTTTGCAAGAAATCA
1 TTCACAAGAACTTTAGGTTCACAAGAATTTCAGTTTCACAAGAATTTAAGGTTTGCAAGAAATCA
1590060 AG
66 AG
*
1590062 TTCACAAGAACTTTAGGTTCACAAGAATTTCAAG-TTCACTAGAATTTAAGGTTTGCAAGA
1 TTCACAAGAACTTTAGGTTCACAAGAATTTC-AGTTTCACAAGAATTTAAGGTTTGCAAGA
1590122 GTTTAAAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
67 49 0.96
68 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (67 bp):
TTCACAAGAACTTTAGGTTCACAAGAATTTCAGTTTCACAAGAATTTAAGGTTTGCAAGAAATCA
AG
Found at i:1590518 original size:22 final size:22
Alignment explanation
Indices: 1590487--1590571 Score: 93
Period size: 22 Copynumber: 3.8 Consensus size: 22
1590477 AGATTTTTCT
1590487 TCAAAAATTTTAAAGATTCACA
1 TCAAAAATTTTAAAGATTCACA
* *
1590509 TCCAAAATTTTAAAAATTCACA
1 TCAAAAATTTTAAAGATTCACA
1590531 TTCAACAAATTTTATAA-ATTCACA
1 -TCAA-AAATTTTA-AAGATTCACA
* *
1590555 TCTAAAA-GTTAAAGATT
1 TCAAAAATTTTAAAGATT
1590572 TTTATTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
20 2 0.04
21 6 0.11
22 23 0.43
23 6 0.11
24 15 0.28
25 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (22 bp):
TCAAAAATTTTAAAGATTCACA
Found at i:1590544 original size:24 final size:23
Alignment explanation
Indices: 1590486--1590555 Score: 97
Period size: 22 Copynumber: 3.0 Consensus size: 23
1590476 AAGATTTTTC
*
1590486 TTCAAAAATTTTAAAGATTCACA
1 TTCAAAAATTTTAAAAATTCACA
*
1590509 -TCCAAAATTTTAAAAATTCACA
1 TTCAAAAATTTTAAAAATTCACA
*
1590531 TTCAACAAATTTTATAAATTCACA
1 TTCAA-AAATTTTAAAAATTCACA
1590555 T
1 T
1590556 CTAAAAGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
22 20 0.49
23 3 0.07
24 18 0.44
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (23 bp):
TTCAAAAATTTTAAAAATTCACA
Found at i:1590703 original size:44 final size:45
Alignment explanation
Indices: 1590615--1590705 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
1590605 GATTTAAAAG
*
1590615 AAAATTAGAAATTCACATCCAAAGATTTCAAAGATTCATATTCAA
1 AAAATTAGAAATTCACATCCAAAGATTTCAAAAATTCATATTCAA
* * * *
1590660 AAAATTAGAGATTCACATCCAATG-TTTCAAAAATTCTTTTTCAA
1 AAAATTAGAAATTCACATCCAAAGATTTCAAAAATTCATATTCAA
1590704 AA
1 AA
1590706 GCTTTATGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (45 bp):
AAAATTAGAAATTCACATCCAAAGATTTCAAAAATTCATATTCAA
Found at i:1597080 original size:19 final size:19
Alignment explanation
Indices: 1597001--1597081 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 19
1596991 TTAACCTAAA
*
1597001 GTTTAGGATTCCACCTAAGG
1 GTTTAGGATTTCACCT-AGG
* * **
1597021 TTTTAGGGTTTCATTTAGG
1 GTTTAGGATTTCACCTAGG
** * * *
1597040 GTTTAAAATTTTATCTAAG
1 GTTTAGGATTTCACCTAGG
*
1597059 GTTTAGGGTTTCACCTAGG
1 GTTTAGGATTTCACCTAGG
1597078 GTTT
1 GTTT
1597082 CAGACATAAG
Statistics
Matches: 43, Mismatches: 18, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
19 32 0.74
20 11 0.26
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.43
Consensus pattern (19 bp):
GTTTAGGATTTCACCTAGG
Found at i:1598577 original size:31 final size:31
Alignment explanation
Indices: 1598539--1598601 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1598529 ATGTACTTCA
* * *
1598539 TTTTTCATTCAAAATTTCAATAAAAAACTTT
1 TTTTTCATTCAAAAATTCAAGAAAAAAATTT
1598570 TTTTTCATTCAAAAATTCAAGAAAAAAATTT
1 TTTTTCATTCAAAAATTCAAGAAAAAAATTT
1598601 T
1 T
1598602 CATTTAACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (31 bp):
TTTTTCATTCAAAAATTCAAGAAAAAAATTT
Found at i:1599700 original size:35 final size:35
Alignment explanation
Indices: 1599661--1599788 Score: 150
Period size: 35 Copynumber: 3.7 Consensus size: 35
1599651 TTTTGTGTTT
* *
1599661 CTACTGCAATATTTTTTTTGGTTTTTATTATGTTA
1 CTACTGCAATATTTTTTTTGGTTTTTGTTATGCTA
** * * *
1599696 CTACTATAGTATTTTTTTAGGTTTTTGTTCTGCTA
1 CTACTGCAATATTTTTTTTGGTTTTTGTTATGCTA
* * * *
1599731 CT-TTTCAGTATTGTTTTTGGTTTTTGTTATGCTA
1 CTACTGCAATATTTTTTTTGGTTTTTGTTATGCTA
1599765 CTACTGCAATATTTTTTTTGGTTT
1 CTACTGCAATATTTTTTTTGGTTT
1599789 CCTCTTTTTC
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
34 28 0.37
35 47 0.63
ACGTcount: A:0.16, C:0.10, G:0.14, T:0.59
Consensus pattern (35 bp):
CTACTGCAATATTTTTTTTGGTTTTTGTTATGCTA
Found at i:1600253 original size:10 final size:11
Alignment explanation
Indices: 1600233--1600257 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1600223 TGGGCCAAGC
1600233 TTTTTGTTTTT
1 TTTTTGTTTTT
1600244 TTTTTGTTTTT
1 TTTTTGTTTTT
1600255 TTT
1 TTT
1600258 ACTAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:1600599 original size:8 final size:8
Alignment explanation
Indices: 1600588--1600654 Score: 57
Period size: 8 Copynumber: 8.1 Consensus size: 8
1600578 CTAAAATTCC
1600588 TTTTTTG-
1 TTTTTTGT
1600595 TTTTTTGT
1 TTTTTTGT
*
1600603 TGTTTTGT
1 TTTTTTGT
*
1600611 TTTTTTAT
1 TTTTTTGT
1600619 TTTGTGTTGT
1 TTT-T-TTGT
1600629 TTTTGTCT-T
1 TTTT-T-TGT
1600638 TTTTTTGT
1 TTTTTTGT
*
1600646 TGTTTTGT
1 TTTTTTGT
1600654 T
1 T
1600655 AAAAAACAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
7 8 0.16
8 26 0.52
9 9 0.18
10 7 0.14
ACGTcount: A:0.01, C:0.01, G:0.16, T:0.81
Consensus pattern (8 bp):
TTTTTTGT
Found at i:1600621 original size:23 final size:22
Alignment explanation
Indices: 1600588--1600654 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
1600578 CTAAAATTCC
*
1600588 TTTTTTGTTTTTTGTTGTTTTG
1 TTTTTTTTTTTTTGTTGTTTTG
*
1600610 TTTTTTTATTTTGTGTTG-TTT-
1 TTTTTTT-TTTTTTGTTGTTTTG
* *
1600631 TTGTCTTTTTTTTGTTGTTTTG
1 TTTTTTTTTTTTTGTTGTTTTG
1600653 TT
1 TT
1600655 AAAAAACAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 9 0.24
21 8 0.22
22 11 0.30
23 9 0.24
ACGTcount: A:0.01, C:0.01, G:0.16, T:0.81
Consensus pattern (22 bp):
TTTTTTTTTTTTTGTTGTTTTG
Found at i:1600766 original size:35 final size:34
Alignment explanation
Indices: 1600713--1600872 Score: 115
Period size: 35 Copynumber: 4.6 Consensus size: 34
1600703 TCACCACCCT
*
1600713 AAGTAATAAATAAAGGATGATTAAAACAACACTAC
1 AAGTAA-AAATAAAGGATGATTAAAACAACACCAC
* *
1600748 AAGTTAAAAATAAAGGATGACTAGAAA-AACACCAT
1 AAG-TAAAAATAAAGGATGATTA-AAACAACACCAC
* * ** *
1600783 AAGTAAAAATAAAAGATGACTAGGACAACACCGC
1 AAGTAAAAATAAAGGATGATTAAAACAACACCAC
* * * ** * * * *
1600817 AAGCCAAAAATAATGAACAATTGAGACAACTCTAC
1 AAG-TAAAAATAAAGGATGATTAAAACAACACCAC
*
1600852 AAATAAAAATAAAGGATGATT
1 AAGTAAAAATAAAGGATGATT
1600873 GGGACAACAT
Statistics
Matches: 95, Mismatches: 26, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
33 1 0.01
34 40 0.42
35 48 0.51
36 6 0.06
ACGTcount: A:0.56, C:0.13, G:0.14, T:0.17
Consensus pattern (34 bp):
AAGTAAAAATAAAGGATGATTAAAACAACACCAC
Found at i:1600795 original size:34 final size:34
Alignment explanation
Indices: 1600707--1600814 Score: 119
Period size: 35 Copynumber: 3.1 Consensus size: 34
1600697 ACTGGGTCAC
* *
1600707 CACCCTAAGTAATAAATAAAGGATGATTA-AAACAA
1 CACCATAAGTAA-AAATAAAGGATGACTAGAAA-AA
* *
1600742 CACTACAAGTTAAAAATAAAGGATGACTAGAAAAA
1 CACCATAAG-TAAAAATAAAGGATGACTAGAAAAA
* * *
1600777 CACCATAAGTAAAAATAAAAGATGACTAGGACAA
1 CACCATAAGTAAAAATAAAGGATGACTAGAAAAA
1600811 CACC
1 CACC
1600815 GCAAGCCAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
34 26 0.42
35 30 0.48
36 6 0.10
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.17
Consensus pattern (34 bp):
CACCATAAGTAAAAATAAAGGATGACTAGAAAAA
Found at i:1600859 original size:69 final size:69
Alignment explanation
Indices: 1600786--1600915 Score: 179
Period size: 69 Copynumber: 1.9 Consensus size: 69
1600776 ACACCATAAG
* * *
1600786 TAAAAATAAAAGATGACTAGGACAACACCGCAAGCCAAAAATAATGAACAATTGAGACAACTCTA
1 TAAAAATAAAAGATGACTAGGACAACACCGCAAGCAAAAAATAACGAACAACTGAGACAACTCTA
1600851 CAAA
66 CAAA
* * * * * *
1600855 TAAAAATAAAGGATGATTGGGACAACATCGTAAGTAAAAAATAACGAACAACTGAGACAAC
1 TAAAAATAAAAGATGACTAGGACAACACCGCAAGCAAAAAATAACGAACAACTGAGACAAC
1600916 ACATTAAGTC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 52 1.00
ACGTcount: A:0.53, C:0.16, G:0.15, T:0.15
Consensus pattern (69 bp):
TAAAAATAAAAGATGACTAGGACAACACCGCAAGCAAAAAATAACGAACAACTGAGACAACTCTA
CAAA
Found at i:1601208 original size:35 final size:35
Alignment explanation
Indices: 1601152--1601222 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 35
1601142 TAAAACCTAG
*
1601152 GTGCTAGCTAAACTGGACTTAAATCTTTTCA-TGAT
1 GTGCCAGCTAAACTGGACTTAAAT-TTTTCATTGAT
1601187 GTGCCAGCTAAACT-GAGCTTAAATTTTTCATTGAT
1 GTGCCAGCTAAACTGGA-CTTAAATTTTTCATTGAT
1601222 G
1 G
1601223 CCAGTCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 8 0.24
35 25 0.76
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (35 bp):
GTGCCAGCTAAACTGGACTTAAATTTTTCATTGAT
Found at i:1601240 original size:33 final size:33
Alignment explanation
Indices: 1601161--1601317 Score: 117
Period size: 33 Copynumber: 4.7 Consensus size: 33
1601151 GGTGCTAGCT
1601161 AAACT-GGACTTAAATCTTTTCA-TGATGTGCCAG-C
1 AAACTAGG-CTTAAAT-TTTTCATTGA--TGCCAGTC
1601195 TAAACT-GAGCTTAAATTTTTCATTGATGCCAGTC
1 -AAACTAG-GCTTAAATTTTTCATTGATGCCAGTC
* * * * **
1601229 AAATTAGGCTTAAGTCTTTCATTAATGTTAGTC
1 AAACTAGGCTTAAATTTTTCATTGATGCCAGTC
* * *
1601262 AAACTGGGTTTAAATATTTCATTGATGCCAG-C
1 AAACTAGGCTTAAATTTTTCATTGATGCCAGTC
*
1601294 TAAACTAGGTTTAAATCTTTTCAT
1 -AAACTAGGCTTAAAT-TTTTCAT
1601318 GAGTTACCAA
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
32 1 0.01
33 68 0.68
34 14 0.14
35 16 0.16
36 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (33 bp):
AAACTAGGCTTAAATTTTTCATTGATGCCAGTC
Found at i:1601308 original size:99 final size:98
Alignment explanation
Indices: 1601156--1601375 Score: 238
Period size: 99 Copynumber: 2.2 Consensus size: 98
1601146 ACCTAGGTGC
* *
1601156 TAGCTAAACTGGACTTAAATCTTTTCA-TGATGTGCCAGCTAAACTGAGCTTAAAT-TTTTCATT
1 TAGCTAAACTGGGCTTAAAT-ATTTCATTGA--TGCCAGCTAAACTGAGCTTAAATCTTTTCA-T
* *
1601219 GA-TGCC-AGTCAAATT-AGGCTTAAGTCTTTCATTAATGT
62 GAGTACCAAAT-AAATTGA-GCTTAA-T-TTTCATTAATGT
* *
1601257 TAG-TCAAACTGGGTTTAAATATTTCATTGATGCCAGCTAAACT-AGGTTTAAATCTTTTCATGA
1 TAGCT-AAACTGGGCTTAAATATTTCATTGATGCCAGCTAAACTGA-GCTTAAATCTTTTCATGA
1601320 GTTACCAAATAAATTGAGCTTAATTTTCATTAATGT
64 G-TACCAAATAAATTGAGCTTAATTTTCATTAATGT
1601356 TAGCTAAACTGGGCTTAAAT
1 TAGCTAAACTGGGCTTAAAT
1601376 TTTTTCATGA
Statistics
Matches: 103, Mismatches: 7, Indels: 20
0.79 0.05 0.15
Matches are distributed among these distances:
98 1 0.01
99 52 0.50
100 14 0.14
101 33 0.32
102 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (98 bp):
TAGCTAAACTGGGCTTAAATATTTCATTGATGCCAGCTAAACTGAGCTTAAATCTTTTCATGAGT
ACCAAATAAATTGAGCTTAATTTTCATTAATGT
Found at i:1601459 original size:32 final size:32
Alignment explanation
Indices: 1601418--1601581 Score: 181
Period size: 32 Copynumber: 5.1 Consensus size: 32
1601408 AAAGTTCCTT
1601418 GGGCCAGGTAATCTAAGCTTAAATTTTCATGA
1 GGGCCAGGTAATCTAAGCTTAAATTTTCATGA
* *
1601450 GGGCTAGGTAATTTAAGCTTAAATTTTCATGA
1 GGGCCAGGTAATCTAAGCTTAAATTTTCATGA
*
1601482 GGGCCAAGTAATCTAAGCTTAAATTTTTTCATGA
1 GGGCCAGGTAATCTAAGCTTAAA--TTTTCATGA
* * * *
1601516 GCGCCAAGTAATCTAAGCTTGAAACTTT-ATTCA
1 GGGCCAGGTAATCTAAGCTT-AAATTTTCA-TGA
* * *
1601549 --ACCAGATAATCTGAGCTTAAATTTTCATGA
1 GGGCCAGGTAATCTAAGCTTAAATTTTCATGA
1601579 GGG
1 GGG
1601582 GTAGGTAAGT
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
30 8 0.07
31 15 0.14
32 51 0.46
33 5 0.05
34 28 0.25
35 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (32 bp):
GGGCCAGGTAATCTAAGCTTAAATTTTCATGA
Found at i:1601486 original size:64 final size:65
Alignment explanation
Indices: 1601418--1601589 Score: 190
Period size: 66 Copynumber: 2.7 Consensus size: 65
1601408 AAAGTTCCTT
* * *
1601418 GGGCCAGGTAATCTAAGCTTAAATTTTCATGAGGGCTAGGTAATTTAAGCTT-AAATTTTCA-TG
1 GGGCCAGGTAATCTAAGCTTAAATTTTCATGAGGGCTAGGTAATCTAAGCTTGAAACTTT-ATTC
1601481 A
65 A
* * * *
1601482 GGGCCAAGTAATCTAAGCTTAAATTTTTTCATGAGCGCCAAGTAATCTAAGCTTGAAACTTTATT
1 GGGCCAGGTAATCTAAGCTTAAA--TTTTCATGAGGGCTAGGTAATCTAAGCTTGAAACTTTATT
1601547 CA
64 CA
* * * *
1601549 --ACCAGATAATCTGAGCTTAAATTTTCATGAGGGGTAGGTAA
1 GGGCCAGGTAATCTAAGCTTAAATTTTCATGAGGGCTAGGTAA
1601590 GTAGGGCTTA
Statistics
Matches: 89, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
63 16 0.18
64 22 0.25
65 17 0.19
66 26 0.29
67 8 0.09
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (65 bp):
GGGCCAGGTAATCTAAGCTTAAATTTTCATGAGGGCTAGGTAATCTAAGCTTGAAACTTTATTCA
Found at i:1601868 original size:33 final size:33
Alignment explanation
Indices: 1601726--1602008 Score: 160
Period size: 33 Copynumber: 8.6 Consensus size: 33
1601716 GGTAATCTTG
* *
1601726 GCCAACTAAGCTGGGCTTAAAT-TTTCATTTGGT
1 GCCAACTAAACTAGGCTTAAATCTTTCA-TTGGT
* * * *
1601759 GCCTATTAAACTGGGCTTAAAT-TTTCA-TGAAT
1 GCCAACTAAACTAGGCTTAAATCTTTCATTG-GT
*** * *
1601791 ATTAGCTAAGCTAGGCTTAAATCTTTTCA-TGAGT
1 GCCAACTAAACTAGGCTTAAATC-TTTCATTG-GT
*
1601825 GCCATA-TAAACTAGGCTTAAAAC-TTCATTAGGT
1 GCCA-ACTAAACTAGGCTTAAATCTTTCATT-GGT
1601858 GCCAACTAAACTAGGCTTAAATCTTTCATTGGT
1 GCCAACTAAACTAGGCTTAAATCTTTCATTGGT
*
1601891 GCCAGA-TAATCT-GGACTTAAATCTTTCCA-TGAAG-
1 GCCA-ACTAAACTAGG-CTTAAATCTTT-CATTG--GT
* ** * * *
1601925 GCTAGGTAATCTAGGCTTAAAAC-TTCATT-GA
1 GCCAACTAAACTAGGCTTAAATCTTTCATTGGT
** *
1601956 GCCAGGT-AACTAGGCTTAAACCTTTCATTGGAT
1 GCCAACTAAACTAGGCTTAAATCTTTCATTGG-T
*
1601989 GCCAGCTAAACTAGGCTTAA
1 GCCAACTAAACTAGGCTTAA
1602009 GTTTCCATTG
Statistics
Matches: 200, Mismatches: 29, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
30 14 0.07
31 14 0.07
32 25 0.12
33 81 0.41
34 63 0.31
35 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (33 bp):
GCCAACTAAACTAGGCTTAAATCTTTCATTGGT
Found at i:1602018 original size:64 final size:63
Alignment explanation
Indices: 1601833--1602018 Score: 155
Period size: 64 Copynumber: 2.9 Consensus size: 63
1601823 GTGCCATATA
* *
1601833 AACTAGGCTTAAAAC-TTCATTAGG-TGCCAACTAAACTAGGCTTAAATCTTTCATTGGTGCCAG
1 AACTAGGCTTAAAACTTTCATT-GGATGCCAGCTAAACTAGGCTTAAA--TTTCATT-GAGCCAG
1601896 AT
62 AT
* * * * * * *
1601898 AATCT-GGACTTAAATCTTTCCA-TGAAGGCTAGGTAATCTAGGCTTAAAACTTCATTGAGCCAG
1 AA-CTAGG-CTTAAAACTTT-CATTGGATGCCAGCTAAACTAGGCTT-AAATTTCATTGAGCCAG
*
1601961 GT
62 AT
* *
1601963 AACTAGGCTTAAACCTTTCATTGGATGCCAGCTAAACTAGGCTTAAGTTTCCATTG
1 AACTAGGCTTAAAACTTTCATTGGATGCCAGCTAAACTAGGCTTAAATTT-CATTG
1602019 TTGCCAGCTG
Statistics
Matches: 94, Mismatches: 18, Indels: 19
0.72 0.14 0.15
Matches are distributed among these distances:
63 6 0.06
64 35 0.37
65 15 0.16
66 16 0.17
67 17 0.18
68 5 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (63 bp):
AACTAGGCTTAAAACTTTCATTGGATGCCAGCTAAACTAGGCTTAAATTTCATTGAGCCAGAT
Found at i:1603188 original size:10 final size:10
Alignment explanation
Indices: 1603170--1603230 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
1603160 CATTCATTTC
*
1603170 TTCTCTTTTT
1 TTCTTTTTTT
1603180 TTCTTTTTTT
1 TTCTTTTTTT
*
1603190 TTCTTTGTTT
1 TTCTTTTTTT
**
1603200 TTCTTTATTCC
1 TTCTTT-TTTT
*
1603211 TTCATTTTTT
1 TTCTTTTTTT
*
1603221 TTCTCTTTTT
1 TTCTTTTTTT
1603231 CCTCACCTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
10 34 0.85
11 6 0.15
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:1604835 original size:33 final size:34
Alignment explanation
Indices: 1604763--1605009 Score: 149
Period size: 33 Copynumber: 7.5 Consensus size: 34
1604753 ATGATATTAG
* *
1604763 CTAAGCTAGGCTTAAATCTTTTCATGA-GTGCCATA
1 CTAAACTAGGCTTAAATC-TTTCATTAGGTGCCA-A
*
1604798 -TAAACTAGGCTTAAAAC-TTCATTAGGTGCCAA
1 CTAAACTAGGCTTAAATCTTTCATTAGGTGCCAA
1604830 CTAAACTAGGCTTAAATCTTTCATT-GGTGCCAGA
1 CTAAACTAGGCTTAAATCTTTCATTAGGTGCCA-A
* * * * * *
1604864 -TAATCTAGACTTAAATCTTTCCATGAAG-GCTAG
1 CTAAACTAGGCTTAAATCTTT-CATTAGGTGCCAA
* * * * *
1604897 GTAATCTAGGCTTAAAAC-TTCATTA--AGCCAG
1 CTAAACTAGGCTTAAATCTTTCATTAGGTGCCAA
* * * * *
1604928 GT-AACTAGGCTTAAACCTTTCACTAGATGCCAG
1 CTAAACTAGGCTTAAATCTTTCATTAGGTGCCAA
* * * *
1604961 CTAAACTAGGCTTAAGT-TTCCATT-GTTGCCAG
1 CTAAACTAGGCTTAAATCTTTCATTAGGTGCCAA
*
1604993 CTAATACTAGGTTTAAA
1 CTAA-ACTAGGCTTAAA
1605010 ACCTAGGCGC
Statistics
Matches: 173, Mismatches: 26, Indels: 28
0.76 0.11 0.12
Matches are distributed among these distances:
30 13 0.08
31 12 0.07
32 22 0.13
33 70 0.40
34 55 0.32
35 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (34 bp):
CTAAACTAGGCTTAAATCTTTCATTAGGTGCCAA
Found at i:1606711 original size:8 final size:7
Alignment explanation
Indices: 1606694--1606750 Score: 50
Period size: 6 Copynumber: 8.4 Consensus size: 7
1606684 GTCATAACCA
1606694 TTTTTC-
1 TTTTTCT
1606700 TTTTTCT
1 TTTTTCT
1606707 CTTTTTC-
1 -TTTTTCT
*
1606714 TTTTTCC
1 TTTTTCT
1606721 TTTTT-T
1 TTTTTCT
*
1606727 TTTTACTT
1 TTTTTC-T
1606735 TTTTTCT
1 TTTTTCT
1606742 TTTTT-T
1 TTTTTCT
1606748 TTT
1 TTT
1606751 GACATGCCCC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 20 0.47
7 11 0.26
8 12 0.28
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:1606726 original size:9 final size:8
Alignment explanation
Indices: 1606700--1606747 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
1606690 ACCATTTTTC
*
1606700 TTTTTCTC
1 TTTTTCTT
1606708 TTTTTCTT
1 TTTTTCTT
*
1606716 TTTCCTTTTT
1 TTT--TTCTT
1606726 TTTTTACTT
1 TTTTT-CTT
1606735 TTTTTCTT
1 TTTTTCTT
1606743 TTTTT
1 TTTTT
1606748 TTTGACATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 20 0.59
9 7 0.21
10 7 0.21
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1606750 original size:14 final size:14
Alignment explanation
Indices: 1606694--1606750 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
1606684 GTCATAACCA
*
1606694 TTTTTCTTTTTCTC
1 TTTTTCTTTTTCTT
*
1606708 TTTTTCTTTTTCCT
1 TTTTTCTTTTTCTT
*
1606722 TTTTT-TTTTACTT
1 TTTTTCTTTTTCTT
1606735 TTTTTCTTTTT-TT
1 TTTTTCTTTTTCTT
1606748 TTT
1 TTT
1606751 GACATGCCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 16 0.43
14 21 0.57
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:1607618 original size:23 final size:23
Alignment explanation
Indices: 1607587--1607635 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1607577 TTCCTTTTCA
** *
1607587 TTTTTTTTTGTCTTTTTCTTCTT
1 TTTTTTTTTCACTTTTTCTCCTT
1607610 TTTTTTTTTCACTTTTTCTCCTT
1 TTTTTTTTTCACTTTTTCTCCTT
1607633 TTT
1 TTT
1607636 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTTTTTTCACTTTTTCTCCTT
Found at i:1611316 original size:22 final size:20
Alignment explanation
Indices: 1611275--1611328 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
1611265 TTTTTTTGAG
*
1611275 AAATTAAAATAAAAAGAATT
1 AAATTAAAATAAAAACAATT
*
1611295 AAATTAAATATCAAAACCAATT
1 AAATTAAA-AT-AAAAACAATT
1611317 AAA-TAAAA-AAAA
1 AAATTAAAATAAAA
1611329 TTGTAATAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 4 0.13
20 9 0.30
21 6 0.20
22 11 0.37
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATTAAAATAAAAACAATT
Found at i:1613957 original size:35 final size:35
Alignment explanation
Indices: 1613893--1614058 Score: 179
Period size: 35 Copynumber: 4.7 Consensus size: 35
1613883 TTTGTGTTTT
*
1613893 TGCTGCAGTATTTTCTTCTGGTTTCTGTTCTGTTTC
1 TGCTGCAGTATTTT-TTCTGGTTTCTGTTCTGTTGC
* * * **
1613929 CGCAGCAGTATTTTTTTTGGTTTCTGTTCTACTGC
1 TGCTGCAGTATTTTTTCTGGTTTCTGTTCTGTTGC
*
1613964 TGTTGCAGTATTTTTTCTGGTTTCTGTTCTGTTGC
1 TGCTGCAGTATTTTTTCTGGTTTCTGTTCTGTTGC
* * * ** *
1613999 TGCTGCAGTATTTTTTCTGATTTTTGTTTTCCTGT
1 TGCTGCAGTATTTTTTCTGGTTTCTGTTCTGTTGC
* *
1614034 TGCTGTAGTATTTTATTTTGGTTTC
1 TGCTGCAGTATTTT-TTCTGGTTTC
1614059 CTCCTTTTAT
Statistics
Matches: 106, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
35 87 0.82
36 19 0.18
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (35 bp):
TGCTGCAGTATTTTTTCTGGTTTCTGTTCTGTTGC
Found at i:1614044 original size:70 final size:71
Alignment explanation
Indices: 1613892--1614058 Score: 210
Period size: 70 Copynumber: 2.4 Consensus size: 71
1613882 CTTTGTGTTT
* * * *
1613892 TTGCTGCAGTATTTTCTTCTGGTTTCTGTTCTGTTTCCGCAGCAGTATTTTTTTTGGTTTCTGTT
1 TTGCTGCAGTATTTTATTCTGGTTTCTGTTCTGTTGCCGCAGCAGTATTTTTTCTGATTTCTGTT
1613957 CTACTG
66 CTACTG
* * * * *
1613963 CTGTTGCAGTATTTT-TTCTGGTTTCTGTTCTGTTGCTGCTGCAGTATTTTTTCTGATTTTTGTT
1 TTGCTGCAGTATTTTATTCTGGTTTCTGTTCTGTTGCCGCAGCAGTATTTTTTCTGATTTCTGTT
* *
1614027 TTCCTG
66 CTACTG
* *
1614033 TTGCTGTAGTATTTTATTTTGGTTTC
1 TTGCTGCAGTATTTTATTCTGGTTTC
1614059 CTCCTTTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
70 59 0.73
71 22 0.27
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (71 bp):
TTGCTGCAGTATTTTATTCTGGTTTCTGTTCTGTTGCCGCAGCAGTATTTTTTCTGATTTCTGTT
CTACTG
Found at i:1615669 original size:22 final size:22
Alignment explanation
Indices: 1615622--1615673 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1615612 AAAATTGGTG
*
1615622 TGAAAAATATTTAAAATAACTA
1 TGAAATATATTTAAAATAACTA
*
1615644 TGAAATATATTTAGAAATAAGT-
1 TGAAATATATTTA-AAATAACTA
1615666 TGAAATAT
1 TGAAATAT
1615674 TAATTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.35
Consensus pattern (22 bp):
TGAAATATATTTAAAATAACTA
Found at i:1617567 original size:21 final size:21
Alignment explanation
Indices: 1617529--1617612 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
1617519 AAGTTAGAAA
**
1617529 AAAATGCAAAAAAGGAAAAAAG
1 AAAAT-CAAAAATTGAAAAAAG
* **
1617551 GAAATCAAAAATTGAAAATTG
1 AAAATCAAAAATTGAAAAAAG
* **
1617572 AAAATCAAAACTTGAAAATTG
1 AAAATCAAAAATTGAAAAAAG
**
1617593 AAAATTGAAAATTGAAAAAA
1 AAAATCAAAAATTGAAAAAA
1617613 ATAAGGAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 46 0.92
22 4 0.08
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (21 bp):
AAAATCAAAAATTGAAAAAAG
Found at i:1617593 original size:7 final size:7
Alignment explanation
Indices: 1617558--1617610 Score: 81
Period size: 7 Copynumber: 7.6 Consensus size: 7
1617548 AAGGAAATCA
1617558 AAAATTG
1 AAAATTG
1617565 AAAATTG
1 AAAATTG
*
1617572 AAAA-TC
1 AAAATTG
1617578 AAAACTTG
1 AAAA-TTG
1617586 AAAATTG
1 AAAATTG
1617593 AAAATTG
1 AAAATTG
1617600 AAAATTG
1 AAAATTG
1617607 AAAA
1 AAAA
1617611 AAATAAGGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 5 0.12
7 32 0.76
8 5 0.12
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (7 bp):
AAAATTG
Found at i:1619457 original size:20 final size:21
Alignment explanation
Indices: 1619420--1619459 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1619410 TCTCATTCAA
1619420 ATTTTTTTTAGTTAATATTTC
1 ATTTTTTTTAGTTAATATTTC
1619441 ATTTTTTGTTA-TT-ATATTT
1 ATTTTTT-TTAGTTAATATTT
1619460 TTATTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 9 0.50
22 3 0.17
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (21 bp):
ATTTTTTTTAGTTAATATTTC
Found at i:1620144 original size:20 final size:20
Alignment explanation
Indices: 1620121--1620168 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1620111 TTTATACTTG
1620121 AACAATTTGAAAATATTTCT
1 AACAATTTGAAAATATTTCT
* * *
1620141 AACACTTTTAAAATATTTTT
1 AACAATTTGAAAATATTTCT
*
1620161 AAAAATTT
1 AACAATTT
1620169 CTTTGCGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (20 bp):
AACAATTTGAAAATATTTCT
Found at i:1621216 original size:22 final size:20
Alignment explanation
Indices: 1621188--1621252 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
1621178 AGAGTTTTTG
*
1621188 GGATTTGAAGAAGAAAAATCT
1 GGATTTGAAGAAGAAAAA-AT
*
1621209 AGGATTTGAAGAATAAAAAAT
1 -GGATTTGAAGAAGAAAAAAT
*
1621230 GGTACTTGAAGAAGAAAAAAT
1 GG-ATTTGAAGAAGAAAAAAT
1621251 GG
1 GG
1621253 TGGCCACCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 17 0.45
ACGTcount: A:0.51, C:0.03, G:0.25, T:0.22
Consensus pattern (20 bp):
GGATTTGAAGAAGAAAAAAT
Found at i:1621721 original size:43 final size:43
Alignment explanation
Indices: 1621649--1621876 Score: 206
Period size: 43 Copynumber: 5.2 Consensus size: 43
1621639 AACAAAAGCA
* *
1621649 TGACAACTTTTTGAAAATTTGAAAAGCTCCTTTAAACAGAGGCT
1 TGACAAC-TTTTGAAAATTTAAAAAGCTCCTTTAAGCAGAGGCT
* * * * *
1621693 CGACAACTTTTAAAAATTTAAAAAGCTCCTCTAAGTAGAGCCT
1 TGACAACTTTTGAAAATTTAAAAAGCTCCTTTAAGCAGAGGCT
* * * *
1621736 TGACAACATTTGAAAATTTCAAATGCTCCTTTAAGCAAAGGCT
1 TGACAACTTTTGAAAATTTAAAAAGCTCCTTTAAGCAGAGGCT
* * * *
1621779 TAACAACTTTTGAAAATTTAAAAAGCT-TTTCTAAGTAGAAAAGCT
1 TGACAACTTTTGAAAATTTAAAAAGCTCCTT-TAAGCAG--AGGCT
* ** * * * *
1621824 TAACAAAATTTAAAAATTTAAAAAGCCCCTCTAAGCAAAGGCT
1 TGACAACTTTTGAAAATTTAAAAAGCTCCTTTAAGCAGAGGCT
*
1621867 TAACAACTTT
1 TGACAACTTT
1621877 AAAATTCTCA
Statistics
Matches: 145, Mismatches: 35, Indels: 9
0.77 0.19 0.05
Matches are distributed among these distances:
42 2 0.01
43 104 0.72
44 6 0.04
45 32 0.22
46 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (43 bp):
TGACAACTTTTGAAAATTTAAAAAGCTCCTTTAAGCAGAGGCT
Found at i:1621785 original size:86 final size:86
Alignment explanation
Indices: 1621644--1621880 Score: 271
Period size: 86 Copynumber: 2.7 Consensus size: 86
1621634 ATCTAAACAA
* * * * * **
1621644 AAGCATGACAACTTTTTGAAAATTTGAAAAGCTCCTTTAAACAGAGGCTCGACAACTTTTAAAAA
1 AAGCTTGACAAC-ATTTGAAAATTTAAAAAGCTCCTTTAAGCAAAGGCTTAACAACTTTTAAAAA
1621709 TTTAAAAAGCTCCTCTAAGTAG
65 TTTAAAAAGCTCCTCTAAGTAG
* * *
1621731 -AGCCTTGACAACATTTGAAAATTTCAAATGCTCCTTTAAGCAAAGGCTTAACAACTTTTGAAAA
1 AAG-CTTGACAACATTTGAAAATTTAAAAAGCTCCTTTAAGCAAAGGCTTAACAACTTTTAAAAA
**
1621795 TTTAAAAAGCTTTTCTAAGTAG
65 TTTAAAAAGCTCCTCTAAGTAG
* * * * *
1621817 AAAAGCTTAACAAAATTTAAAAATTTAAAAAGCCCCTCTAAGCAAAGGCTTAACAAC-TTTAAAA
1 --AAGCTTGACAACATTTGAAAATTTAAAAAGCTCCTTTAAGCAAAGGCTTAACAACTTTTAAAA
1621881 TTCTCATCTT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
86 66 0.52
87 14 0.11
88 45 0.35
89 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (86 bp):
AAGCTTGACAACATTTGAAAATTTAAAAAGCTCCTTTAAGCAAAGGCTTAACAACTTTTAAAAAT
TTAAAAAGCTCCTCTAAGTAG
Found at i:1635832 original size:77 final size:78
Alignment explanation
Indices: 1635704--1635885 Score: 262
Period size: 77 Copynumber: 2.3 Consensus size: 78
1635694 AGTAATGTAG
* * *
1635704 TGGGAAAAGAAAA-AAAATGAACAAGAAATGGAGATACCTTTAACTATCATGGAAAAAAGGAAAA
1 TGGGAAAAGAAAAGAAAATG--GAAGAAATGGAGATACATCTAACTATCATGGAAAAAAGGAAAA
1635768 TGGAAAAGAA-AAGA
64 TGGAAAAGAAGAAGA
* * *
1635782 TGGGAAGAGAAAAGAAAATGGAAGAAATGGAGATACATCTAACTATCATGGAAGAAATGAAAATG
1 TGGGAAAAGAAAAGAAAATGGAAGAAATGGAGATACATCTAACTATCATGGAAAAAAGGAAAATG
*
1635847 GAAGAGAAGAAGA
66 GAAAAGAAGAAGA
1635860 T-GGAAAAGAAAAGAAAATGGAAGAAA
1 TGGGAAAAGAAAAGAAAATGGAAGAAA
1635886 CAAACAGTGA
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
77 71 0.76
78 17 0.18
79 6 0.06
ACGTcount: A:0.57, C:0.05, G:0.25, T:0.13
Consensus pattern (78 bp):
TGGGAAAAGAAAAGAAAATGGAAGAAATGGAGATACATCTAACTATCATGGAAAAAAGGAAAATG
GAAAAGAAGAAGA
Found at i:1635849 original size:15 final size:14
Alignment explanation
Indices: 1635829--1635885 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 14
1635819 TCTAACTATC
1635829 ATGGAAGAAATGAAA
1 ATGGAAGAAA-GAAA
*
1635844 ATGGAAGAGAAGAAG
1 ATGGAAGA-AAGAAA
1635859 ATGGAAAAGAAAAGAAA
1 ATGG--AAG-AAAGAAA
1635876 ATGGAAGAAA
1 ATGGAAGAAA
1635886 CAAACAGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 3 0.08
15 18 0.50
16 2 0.06
17 12 0.33
18 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (14 bp):
ATGGAAGAAAGAAA
Found at i:1635868 original size:17 final size:17
Alignment explanation
Indices: 1635833--1635881 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1635823 ACTATCATGG
*
1635833 AAGAAATGAAAATGG--
1 AAGAAAAGAAAATGGAA
* *
1635848 AAGAGAAGAAGATGGAA
1 AAGAAAAGAAAATGGAA
1635865 AAGAAAAGAAAATGGAA
1 AAGAAAAGAAAATGGAA
1635882 GAAACAAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.44
17 15 0.56
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (17 bp):
AAGAAAAGAAAATGGAA
Found at i:1643353 original size:23 final size:21
Alignment explanation
Indices: 1643303--1643353 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
1643293 AGTCTTAGGT
1643303 CATTTTCCATACATTTTTAAC
1 CATTTTCCATACATTTTTAAC
*
1643324 TATTTTTCCAATA-AGTTTTTAAGC
1 CA-TTTTCC-ATACA-TTTTTAA-C
1643348 CATTTT
1 CATTTT
1643354 TGGTTCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.04
22 7 0.29
23 14 0.58
24 2 0.08
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (21 bp):
CATTTTCCATACATTTTTAAC
Found at i:1647175 original size:33 final size:35
Alignment explanation
Indices: 1647102--1647186 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 35
1647092 AGGTGAAAAG
*
1647102 AAAG-AAAAGAAAGAAAAAGTGAATAAAGTTGTTGT
1 AAAGAAAAAGAAAGAAAAAG-AAATAAAGTTGTTGT
*
1647137 -TAGAAAAAGAAAGAAAAA-AAATAAAGTTG-TGT
1 AAAGAAAAAGAAAGAAAAAGAAATAAAGTTGTTGT
*
1647169 AAAGAAAAGGAAAAGAAA
1 AAAGAAAAAG-AAAGAAA
1647187 GGTGAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
32 3 0.07
33 17 0.40
34 9 0.21
35 14 0.33
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (35 bp):
AAAGAAAAAGAAAGAAAAAGAAATAAAGTTGTTGT
Found at i:1650096 original size:31 final size:29
Alignment explanation
Indices: 1650061--1650133 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
1650051 ATTATTCCAT
*
1650061 GTCCTTATATTTTAAAATAACTATCATTTTG
1 GTCCTTATATTTTAAAA-AA-TAACATTTTG
*
1650092 GTCCTTAAATTTTAAAAAATAACATTTTG
1 GTCCTTATATTTTAAAAAATAACATTTTG
* *
1650121 ATCCCTATATTTT
1 GTCCTTATATTTT
1650134 GTTGGTCGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (29 bp):
GTCCTTATATTTTAAAAAATAACATTTTG
Found at i:1654997 original size:40 final size:41
Alignment explanation
Indices: 1654953--1655029 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1654943 TTGATACTTG
*** *
1654953 CTTAAC-TTACACTCAACACTGAACGCACTTTAGTAAAACA
1 CTTAACTTTACACTCAACAAAAAACGCACTTCAGTAAAACA
*
1654993 CTTAACTTTAGACTCAACAAAAAACGCACTTCAGTAA
1 CTTAACTTTACACTCAACAAAAAACGCACTTCAGTAA
1655030 GATATAGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 6 0.19
41 25 0.81
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.25
Consensus pattern (41 bp):
CTTAACTTTACACTCAACAAAAAACGCACTTCAGTAAAACA
Found at i:1658645 original size:19 final size:19
Alignment explanation
Indices: 1658623--1658660 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1658613 AGCAATTAGG
*
1658623 CCTTTGGATCCTTTGCACA
1 CCTTTGGAGCCTTTGCACA
*
1658642 CCTTTGGAGGCTTTGCACA
1 CCTTTGGAGCCTTTGCACA
1658661 TTAACATTTG
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:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (19 bp):
CCTTTGGAGCCTTTGCACA
Found at i:1661197 original size:21 final size:21
Alignment explanation
Indices: 1661173--1661217 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1661163 ATTCACACTT
1661173 AAATTCAAAGATTCGTATATG
1 AAATTCAAAGATTCGTATATG
* * *
1661194 AAATTGAAAGATTTGTATTTG
1 AAATTCAAAGATTCGTATATG
1661215 AAA
1 AAA
1661218 AATTTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (21 bp):
AAATTCAAAGATTCGTATATG
Found at i:1661293 original size:44 final size:43
Alignment explanation
Indices: 1661209--1661295 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
1661199 GAAAGATTTG
* *
1661209 TATTTGAAAAATTTATAAATTAGCATCTATATTCATATATTCA
1 TATTTGAAAAATTTATAAATTAGCATCTAAATTCAAATATTCA
* * *
1661252 TATTTGAAAATTTTA-AAGATTTGCATTTACAATTCAAATATTCA
1 TATTTGAAAAATTTATAA-ATTAGCATCTA-AATTCAAATATTCA
1661296 CAATTAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 2 0.05
43 23 0.62
44 12 0.32
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (43 bp):
TATTTGAAAAATTTATAAATTAGCATCTAAATTCAAATATTCA
Found at i:1661590 original size:38 final size:38
Alignment explanation
Indices: 1661540--1661620 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
1661530 TTAAAACCCC
*
1661540 AAAATTTTCTCAATTGAAAACTAAAATCTCATCTTT-G
1 AAAATTTTCTCAATCGAAAACTAAAATCTCATCTTTGG
* * * *
1661577 AAAATTCTTCTCAATCGAGAATTAAAATCTTATGTTTGG
1 AAAATT-TTCTCAATCGAAAACTAAAATCTCATCTTTGG
1661616 AAAAT
1 AAAAT
1661621 GTTCCTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 6 0.16
38 25 0.68
39 6 0.16
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (38 bp):
AAAATTTTCTCAATCGAAAACTAAAATCTCATCTTTGG
Found at i:1668460 original size:16 final size:16
Alignment explanation
Indices: 1668429--1668461 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1668419 ACAAGCTAAC
1668429 TTTCTTAGTTGTCCCA
1 TTTCTTAGTTGTCCCA
1668445 TTTCATTAGTTG-CCCA
1 TTTC-TTAGTTGTCCCA
1668461 T
1 T
1668462 ACTTAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.48
Consensus pattern (16 bp):
TTTCTTAGTTGTCCCA
Found at i:1670471 original size:53 final size:53
Alignment explanation
Indices: 1670408--1670513 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1670398 CATATTGCAA
1670408 TATGTTTAGAATATTTATAGAGATGGAACATAAAATTTCCTTTAAACACTGAG
1 TATGTTTAGAATATTTATAGAGATGGAACATAAAATTTCCTTTAAACACTGAG
1670461 TATGTTTAGAATATTTATAGAGATGGAACATAAAATTTCCTTTAAACACTGAG
1 TATGTTTAGAATATTTATAGAGATGGAACATAAAATTTCCTTTAAACACTGAG
1670514 GTCATTTAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (53 bp):
TATGTTTAGAATATTTATAGAGATGGAACATAAAATTTCCTTTAAACACTGAG
Found at i:1671635 original size:16 final size:15
Alignment explanation
Indices: 1671611--1671669 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
1671601 AAAGAATGGG
*
1671611 AAAAC-AAAAAAGAT
1 AAAACAAAAAAAAAT
*
1671625 AAAACAAAAAAAAACA
1 AAAACAAAAAAAAA-T
1671641 AAAACAAAAGAAAAAAT
1 AAAAC-AAA-AAAAAAT
1671658 AGAAA-AAAAAAA
1 A-AAACAAAAAAA
1671670 CAAGCTAGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 8 0.22
17 4 0.11
18 9 0.24
ACGTcount: A:0.85, C:0.07, G:0.05, T:0.03
Consensus pattern (15 bp):
AAAACAAAAAAAAAT
Found at i:1675445 original size:18 final size:18
Alignment explanation
Indices: 1675424--1675459 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1675414 CGCTTAGCCA
*
1675424 TTTTTGGTTTTTTTTCTT
1 TTTTTCGTTTTTTTTCTT
*
1675442 TTTTTCTTTTTTTTTCTT
1 TTTTTCGTTTTTTTTCTT
1675460 CCTTGTGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (18 bp):
TTTTTCGTTTTTTTTCTT
Found at i:1678445 original size:14 final size:16
Alignment explanation
Indices: 1678426--1678462 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1678416 GCCAAATAAG
1678426 AAAGAAAA-TA-ACTA
1 AAAGAAAACTACACTA
1678440 AAAGAAAACTACACTA
1 AAAGAAAACTACACTA
*
1678456 AGAGAAA
1 AAAGAAA
1678463 CTAAAATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAGAAAACTACACTA
Found at i:1695932 original size:14 final size:16
Alignment explanation
Indices: 1695903--1695934 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1695893 GGAAAGATTG
1695903 ATCAAGATTGCATCAC
1 ATCAAGATTGCATCAC
1695919 ATCAAGA-T-CATCAC
1 ATCAAGATTGCATCAC
1695933 AT
1 AT
1695935 TCAACGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (16 bp):
ATCAAGATTGCATCAC
Found at i:1698858 original size:16 final size:16
Alignment explanation
Indices: 1698827--1698864 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1698817 CATTAAAAAT
*
1698827 TTATTT-TTATTTTTA
1 TTATTTATTAATTTTA
1698842 TTATTTATTAATTTTA
1 TTATTTATTAATTTTA
1698858 TTATTTA
1 TTATTTA
1698865 ATTTTATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTATTAATTTTA
Done.