Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 11 of 29
Found at i:3978039 original size:11 final size:11
Alignment explanation
Indices: 3978023--3978056 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3978013 CAGAAATTTT
3978023 AGCAACTCATG
1 AGCAACTCATG
3978034 AGCAACTCATG
1 AGCAACTCATG
*
3978045 AGCAAGTCATG
1 AGCAACTCATG
3978056 A
1 A
3978057 ATGTGTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (11 bp):
AGCAACTCATG
Found at i:3978547 original size:16 final size:17
Alignment explanation
Indices: 3978526--3978558 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3978516 CTTGGATTTG
*
3978526 TTTTCTA-TGAGGTTTT
1 TTTTCTAGTAAGGTTTT
3978542 TTTTCTAGTAAGGTTTT
1 TTTTCTAGTAAGGTTTT
3978559 AATGAGGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.15, C:0.06, G:0.18, T:0.61
Consensus pattern (17 bp):
TTTTCTAGTAAGGTTTT
Found at i:3979227 original size:11 final size:12
Alignment explanation
Indices: 3979211--3979239 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3979201 CTTTATTTCC
3979211 TTTTTTAT-ATT
1 TTTTTTATAATT
3979222 TTTTTTATAATT
1 TTTTTTATAATT
3979234 TTTTTT
1 TTTTTT
3979240 TTAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:3983396 original size:21 final size:19
Alignment explanation
Indices: 3983372--3983410 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
3983362 TAGTAATGCT
3983372 TATGTATAAATTAAATATATG
1 TATGTATAAA--AAATATATG
3983393 TATGTATAAAAAATATAT
1 TATGTATAAAAAATATAT
3983411 TACATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
TATGTATAAAAAATATATG
Found at i:3983530 original size:17 final size:17
Alignment explanation
Indices: 3983508--3983553 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
3983498 TAGTAATGCT
3983508 TATGTATAAATTAAATA
1 TATGTATAAATTAAATA
*
3983525 TATGTATATA-T-AATA
1 TATGTATAAATTAAATA
*
3983540 TATTTATACAATTA
1 TATGTATA-AATTA
3983554 TATTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (17 bp):
TATGTATAAATTAAATA
Found at i:3990363 original size:22 final size:22
Alignment explanation
Indices: 3990313--3990381 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 22
3990303 ACGGGTTAAA
*
3990313 AAAATTAATAATTTTAGTTAATTT
1 AAAATTAATAA-TTTAGTT-ATAT
*
3990337 AATAATTTTATATATTTAGTTATAT
1 AA-AA-TTAATA-ATTTAGTTATAT
3990362 AAAATTAATAATTTAGTTAT
1 AAAATTAATAATTTAGTTAT
3990382 CGATGGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.26
23 5 0.13
24 4 0.10
25 7 0.18
26 12 0.31
27 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
AAAATTAATAATTTAGTTATAT
Found at i:3992797 original size:9 final size:9
Alignment explanation
Indices: 3992783--3992812 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3992773 AATTTTTTAT
3992783 AAAAAATAA
1 AAAAAATAA
3992792 AAAAAAT-A
1 AAAAAATAA
3992800 AAAAAATAA
1 AAAAAATAA
3992809 AAAA
1 AAAA
3992813 TTAATTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:3992813 original size:7 final size:8
Alignment explanation
Indices: 3992783--3992812 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3992773 AATTTTTTAT
3992783 AAAAAATAA
1 AAAAAAT-A
3992792 AAAAAATA
1 AAAAAATA
3992800 AAAAAATA
1 AAAAAATA
3992808 AAAAA
1 AAAAA
3992813 TTAATTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:3993212 original size:3 final size:3
Alignment explanation
Indices: 3993204--3993229 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3993194 CCTATTAATA
3993204 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3993230 AATTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3993407 original size:15 final size:15
Alignment explanation
Indices: 3993387--3993424 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3993377 TATATATATA
3993387 TTATAATTAATAA-TT
1 TTATAATT-ATAATTT
3993402 TTATAAGTTATAATTT
1 TTATAA-TTATAATTT
3993418 TTATAAT
1 TTATAAT
3993425 GTTAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTATAATTT
Found at i:3997210 original size:9 final size:9
Alignment explanation
Indices: 3997196--3997225 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3997186 AAGCTTTTCA
3997196 TAGCCAAAT
1 TAGCCAAAT
3997205 TAGCCAAAT
1 TAGCCAAAT
*
3997214 TAGCTAAAT
1 TAGCCAAAT
3997223 TAG
1 TAG
3997226 ACATATAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (9 bp):
TAGCCAAAT
Found at i:3997439 original size:39 final size:40
Alignment explanation
Indices: 3997377--3997457 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
3997367 GGTTCTGAAA
* * *
3997377 AACACCAATTGTGGTGAGGTT-AAAAACCATATTAAGGTG
1 AACACCAATTGTGGTAAGATTAAAAAACCATACTAAGGTG
*
3997416 AACACCAATCT-TGGTAAGATTAAAAAACCCTACTAAGGTG
1 AACACCAAT-TGTGGTAAGATTAAAAAACCATACTAAGGTG
3997456 AA
1 AA
3997458 TAATGGTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 17 0.47
40 19 0.53
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (40 bp):
AACACCAATTGTGGTAAGATTAAAAAACCATACTAAGGTG
Found at i:4008811 original size:2 final size:2
Alignment explanation
Indices: 4008804--4008833 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4008794 TCATATGGTC
4008804 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4008834 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4008838 original size:2 final size:2
Alignment explanation
Indices: 4008833--4008857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4008823 TCTCTCTCTC
4008833 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
4008858 CTCTGCCGGC
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:4011158 original size:60 final size:60
Alignment explanation
Indices: 4011085--4011208 Score: 176
Period size: 60 Copynumber: 2.1 Consensus size: 60
4011075 CCTTTAACGT
* **
4011085 ATTTTGTAATTGAGTCCGTTGACCGTTAATGCATCAATTGAGTCAACTGACCGTTAATAG
1 ATTTTGTAATTGAGTCAGGCGACCGTTAATGCATCAATTGAGTCAACTGACCGTTAATAG
* ** * *
4011145 ATTTTGTAATTGAGTCAGGCGATCGTTAATGTTTCAATTGAGTCAACTGACTGTTAATGG
1 ATTTTGTAATTGAGTCAGGCGACCGTTAATGCATCAATTGAGTCAACTGACCGTTAATAG
4011205 ATTT
1 ATTT
4011209 GAGAAATATC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (60 bp):
ATTTTGTAATTGAGTCAGGCGACCGTTAATGCATCAATTGAGTCAACTGACCGTTAATAG
Found at i:4011161 original size:32 final size:30
Alignment explanation
Indices: 4011118--4011208 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 30
4011108 CGTTAATGCA
4011118 TCAATTGAGTCAACTGACCGTTAATAGATTT
1 TCAATTGAGTCAACTGACCGTTAAT-GATTT
* * *
4011149 TGTAATTGAGTCAGGC-GATCGTTAATG--TT
1 T-CAATTGAGTCA-ACTGACCGTTAATGATTT
*
4011178 TCAATTGAGTCAACTGACTGTTAATGGATTT
1 TCAATTGAGTCAACTGACCGTTAAT-GATTT
4011209 GAGAAATATC
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
27 1 0.02
28 18 0.38
29 4 0.09
31 4 0.09
32 19 0.40
33 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (30 bp):
TCAATTGAGTCAACTGACCGTTAATGATTT
Found at i:4011200 original size:28 final size:28
Alignment explanation
Indices: 4011104--4011203 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 28
4011094 TTGAGTCCGT
**
4011104 TGACCGTTAATGCATCAATTGAGTCAAC
1 TGACCGTTAATGTTTCAATTGAGTCAAC
* *
4011132 TGACCGTTAATAGATTTTGTAATTGAGTCAGGC
1 TGACCGTTAAT-G--TTT-CAATTGAGTCA-AC
*
4011165 -GATCGTTAATGTTTCAATTGAGTCAAC
1 TGACCGTTAATGTTTCAATTGAGTCAAC
*
4011192 TGACTGTTAATG
1 TGACCGTTAATG
4011204 GATTTGAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.02
28 30 0.53
29 4 0.07
31 2 0.04
32 19 0.33
33 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (28 bp):
TGACCGTTAATGTTTCAATTGAGTCAAC
Found at i:4011768 original size:25 final size:26
Alignment explanation
Indices: 4011721--4011769 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
4011711 ATCTTTATTA
* * *
4011721 TTTTATTTATTTATACTTTTATATCT
1 TTTTATTTATATATACATATATATCT
4011747 TTTTATTT-TATATACATATATAT
1 TTTTATTTATATATACATATATAT
4011770 ATCATTGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTATTTATATATACATATATATCT
Found at i:4019104 original size:51 final size:51
Alignment explanation
Indices: 4019036--4019135 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
4019026 AGGCTAGATA
* * *
4019036 ATACATTATATTGTTACATTTTTAACTTATTGACTATATATTTATAATGCT
1 ATACATTATATTATTACATTTATAACTTATTAACTATATATTTATAATGCT
*
4019087 ATACATTGTATTATTACATTTATAACTTATTAACTATATATTTATAATG
1 ATACATTATATTATTACATTTATAACTTATTAACTATATATTTATAATG
4019136 ATCATAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (51 bp):
ATACATTATATTATTACATTTATAACTTATTAACTATATATTTATAATGCT
Found at i:4026184 original size:20 final size:22
Alignment explanation
Indices: 4026159--4026204 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
4026149 ATTTTACATT
4026159 AATAAATA-TTAAAAAGGAAA-
1 AATAAATAGTTAAAAAGGAAAG
*
4026179 AATAAATAGTTAAAAATGAAAG
1 AATAAATAGTTAAAAAGGAAAG
4026201 AATA
1 AATA
4026205 TAAGTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 11 0.48
22 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (22 bp):
AATAAATAGTTAAAAAGGAAAG
Found at i:4027825 original size:4 final size:4
Alignment explanation
Indices: 4027816--4027842 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4027806 ACAATAATAT
4027816 ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATA
4027843 TAATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:4047193 original size:4 final size:4
Alignment explanation
Indices: 4047179--4047244 Score: 78
Period size: 4 Copynumber: 16.5 Consensus size: 4
4047169 ATAAGGAGCA
* * * *
4047179 ATAT GTAT ATAT ATAT ATAT GTAT ATAT ATGT ATGT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
4047227 ATGT ATAT ATAT GTAT AT
1 ATAT ATAT ATAT ATAT AT
4047245 GAAATTTCAC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:4047197 original size:10 final size:10
Alignment explanation
Indices: 4047184--4047244 Score: 95
Period size: 10 Copynumber: 6.1 Consensus size: 10
4047174 GAGCAATATG
*
4047184 TATATATATA
1 TATATGTATA
4047194 TATATGTATA
1 TATATGTATA
*
4047204 TATATGTATG
1 TATATGTATA
*
4047214 TATATATATA
1 TATATGTATA
4047224 TATATGTATA
1 TATATGTATA
4047234 TATATGTATA
1 TATATGTATA
4047244 T
1 T
4047245 GAAATTTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (10 bp):
TATATGTATA
Found at i:4047200 original size:16 final size:16
Alignment explanation
Indices: 4047179--4047245 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
4047169 ATAAGGAGCA
4047179 ATATGTATATATATAT
1 ATATGTATATATATAT
4047195 ATATG--TATATATAT
1 ATATGTATATATATAT
*
4047209 GTATGTATATATATAT
1 ATATGTATATATATAT
*
4047225 ATATGTATATATATGT
1 ATATGTATATATATAT
4047241 ATATG
1 ATATG
4047246 AAATTTCACA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
14 13 0.28
16 33 0.72
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.49
Consensus pattern (16 bp):
ATATGTATATATATAT
Found at i:4047216 original size:30 final size:30
Alignment explanation
Indices: 4047180--4047242 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
4047170 TAAGGAGCAA
4047180 TATGTATATATATATATATGTATATATATG
1 TATGTATATATATATATATGTATATATATG
4047210 TATGTATATATATATATATGTATATATATG
1 TATGTATATATATATATATGTATATATATG
4047240 TAT
1 TAT
4047243 ATGAAATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (30 bp):
TATGTATATATATATATATGTATATATATG
Found at i:4049812 original size:79 final size:79
Alignment explanation
Indices: 4049681--4049839 Score: 219
Period size: 79 Copynumber: 2.0 Consensus size: 79
4049671 ACCCCTAAAG
* * *
4049681 CCACCTTTTTCCATCATCAAGCTAAAGTTTTTGCACTAAGCAAAGTTTGTCACTGCCCGTGTTTG
1 CCACCATTTTCCATCATCAAGCTAAAGTTTTTGCACTAAGAAAAGTTTGTCACTGCCAGTGTTTG
*
4049746 TAGCAGTTTTTCAC
66 TAGCAGGTTTTCAC
* ** * **
4049760 CCACCATTTTCCATTATCAAGCTATGGTTTTTGCACTAGGAAAAGTTTGTCACTGGTAGTGTTTG
1 CCACCATTTTCCATCATCAAGCTAAAGTTTTTGCACTAAGAAAAGTTTGTCACTGCCAGTGTTTG
*
4049825 TAGTAGGTTTTCAC
66 TAGCAGGTTTTCAC
4049839 C
1 C
4049840 ACAAATTTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (79 bp):
CCACCATTTTCCATCATCAAGCTAAAGTTTTTGCACTAAGAAAAGTTTGTCACTGCCAGTGTTTG
TAGCAGGTTTTCAC
Found at i:4051246 original size:15 final size:15
Alignment explanation
Indices: 4051226--4051263 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4051216 TTTATATACA
4051226 TTATAATTAATAA-TT
1 TTATAATT-ATAATTT
4051241 TTATAAGTTATAATTT
1 TTATAA-TTATAATTT
4051257 TTATAAT
1 TTATAAT
4051264 GTTAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTATAATTT
Found at i:4051584 original size:14 final size:14
Alignment explanation
Indices: 4051553--4051594 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
4051543 TATATAAACA
4051553 AAGTTATATATATTAT
1 AAGTTATA-AT-TTAT
4051569 AA-TTAATAATTTAT
1 AAGTT-ATAATTTAT
4051583 AAGTTATAATTT
1 AAGTTATAATTT
4051595 TAGAAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 13 0.54
15 6 0.25
16 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
AAGTTATAATTTAT
Found at i:4052487 original size:2 final size:2
Alignment explanation
Indices: 4052480--4052512 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4052470 TTAAGTAATA
4052480 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 A
4052513 AACGGGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4059648 original size:45 final size:48
Alignment explanation
Indices: 4059584--4059718 Score: 152
Period size: 49 Copynumber: 2.8 Consensus size: 48
4059574 TATGGCCCTC
*
4059584 TAAAATTTTTAAAATTTTTTA-TTA-TATATA-TATTAATGGTCCTTT
1 TAAAATTTTTAAAATTTTTTATTTATTATATATTATTAATGATCCTTT
*
4059629 TAAAATTTTTAAAATTTTTTATTTATTATATATTTTTTAATGATCCTTT
1 TAAAATTTTTAAAATTTTTTATTTATTATATA-TTATTAATGATCCTTT
* * * * *
4059678 TCAAAATTTATGAAAA-TATTAATTTACTATATATTTTTAAT
1 T-AAAATTT-TTAAAATTTTTTATTTATTATATATTATTAAT
4059719 AGTTCCCTCA
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
45 21 0.27
46 3 0.04
47 6 0.08
49 22 0.28
50 21 0.27
51 5 0.06
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (48 bp):
TAAAATTTTTAAAATTTTTTATTTATTATATATTATTAATGATCCTTT
Found at i:4059676 original size:49 final size:48
Alignment explanation
Indices: 4059584--4059715 Score: 155
Period size: 50 Copynumber: 2.8 Consensus size: 48
4059574 TATGGCCCTC
* *
4059584 TAAAATTTTTAAAATTTTTTA-TTATATATA--TATTAATGGTCCTTT
1 TAAAATTTTTAAAATTTTTTATTTATATATATTTTTTAATGATCCTTT
4059629 TAAAATTTTTAAAATTTTTTATTTATTATATATTTTTTAATGATCCTTT
1 TAAAATTTTTAAAATTTTTTATTTA-TATATATTTTTTAATGATCCTTT
* * *
4059678 TCAAAATTTATGAAAA-TATTAATTTACTATATATTTTT
1 T-AAAATTT-TTAAAATTTTTTATTTA-TATATATTTTT
4059716 AATAGTTCCC
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
45 21 0.28
46 3 0.04
47 6 0.08
49 14 0.19
50 26 0.35
51 5 0.07
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (48 bp):
TAAAATTTTTAAAATTTTTTATTTATATATATTTTTTAATGATCCTTT
Found at i:4060056 original size:16 final size:16
Alignment explanation
Indices: 4060026--4060067 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
4060016 TTCTTCTTTC
4060026 TATTTATATTATTTAAT
1 TATTTATA-TATTTAAT
4060043 TATTTATATATTTAAT
1 TATTTATATATTTAAT
4060059 TA-TTATATA
1 TATTTATATA
4060068 AAATCTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTATATATTTAAT
Found at i:4060103 original size:7 final size:7
Alignment explanation
Indices: 4060093--4060137 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
4060083 TATTTAACTA
4060093 TTTATAT
1 TTTATAT
4060100 TTTATAT
1 TTTATAT
*
4060107 ATTATAGT
1 TTTATA-T
4060115 TTTATAT
1 TTTATAT
*
4060122 TTAATAT
1 TTTATAT
*
4060129 TTTAAAT
1 TTTATAT
4060136 TT
1 TT
4060138 AAATAGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (7 bp):
TTTATAT
Found at i:4060109 original size:15 final size:15
Alignment explanation
Indices: 4060091--4060132 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4060081 CGTATTTAAC
4060091 TATTTATATTTTATA
1 TATTTATATTTTATA
4060106 TA-TTATAGTTTTATA
1 TATTTATA-TTTTATA
*
4060121 T-TTAATATTTTA
1 TATTTATATTTTA
4060133 AATTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TATTTATATTTTATA
Found at i:4060139 original size:14 final size:13
Alignment explanation
Indices: 4060091--4060138 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
4060081 CGTATTTAAC
4060091 TATTTATATTTTA
1 TATTTATATTTTA
4060104 TATATTATAGTTTTA
1 TAT-TTATA-TTTTA
4060119 TATTTAATATTTTA
1 TATTT-ATATTTTA
*
4060133 AATTTA
1 TATTTA
4060139 AATAGAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TATTTATATTTTA
Found at i:4067188 original size:3 final size:3
Alignment explanation
Indices: 4067182--4067216 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4067172 AAAAAGGGAA
4067182 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4067217 AGATACTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4068150 original size:23 final size:25
Alignment explanation
Indices: 4068117--4068164 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
4068107 TGATAATTAA
*
4068117 GGAAAATAATA-AAGAG-TTGAAAT
1 GGAAAAAAATATAAGAGTTTGAAAT
*
4068140 GGAAAAAAATATAATAGTTTGAAAT
1 GGAAAAAAATATAAGAGTTTGAAAT
4068165 AAGAGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (25 bp):
GGAAAAAAATATAAGAGTTTGAAAT
Found at i:4068990 original size:30 final size:29
Alignment explanation
Indices: 4068929--4069007 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
4068919 CCTTCAAAAG
** **
4068929 TTTTAAAATTTTATAATTTTCCCTTGCTTT
1 TTTTAAAATTTTATAATTTT-GATCACTTT
4068959 TTTTAAAATTTTATAATTTTGATCACTTT
1 TTTTAAAATTTTATAATTTTGATCACTTT
*
4068988 TTTT-AAATTTTATAGTTTTG
1 TTTTAAAATTTTATAATTTTG
4069008 TCCCTACAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 15 0.34
29 9 0.20
30 20 0.45
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.61
Consensus pattern (29 bp):
TTTTAAAATTTTATAATTTTGATCACTTT
Found at i:4077591 original size:15 final size:16
Alignment explanation
Indices: 4077571--4077604 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4077561 TGTTATGTAG
*
4077571 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
4077586 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
4077602 ATT
1 ATT
4077605 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:4082355 original size:35 final size:35
Alignment explanation
Indices: 4082309--4082383 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
4082299 TGATGCAAAC
4082309 CTAAAGAAATTGCACTAGCTTGTGCAATTTCTTCT
1 CTAAAGAAATTGCACTAGCTTGTGCAATTTCTTCT
4082344 CTAAAGAAATTGCACTAGCTTGTGCAATTTCTTCT
1 CTAAAGAAATTGCACTAGCTTGTGCAATTTCTTCT
4082379 CTAAA
1 CTAAA
4082384 CAATTAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
CTAAAGAAATTGCACTAGCTTGTGCAATTTCTTCT
Found at i:4089393 original size:150 final size:150
Alignment explanation
Indices: 4089110--4089741 Score: 614
Period size: 150 Copynumber: 4.1 Consensus size: 150
4089100 CTCAAATGAG
* * * *
4089110 GAGTTGTTTATTTTTAAAAAT-GATTTTAAATTTGTGGAGCCTCGGATGATCCGAGAAGTTGTTT
1 GAGTTGTTTATTTTT-CAAATCAATTTTAAAGTTGTGGAGCCTCAGATGA----AG-AGTTG-TT
* * * * *
4089174 ATATTTTTCAAATTGATTTTTAAAGTTGTGGAGCCTCAGATGAGAAGTTGTTTATTTCTCAAATT
59 -TATTTTTCAAATCGA-TTTTAAAGTTGTGGAGCCTCGGATGAGGAGTTGTTTATTTTTCAAATC
* * * *
4089239 GATTTCAAAGTTATGGAGCTTTGGAAGAA
122 AATTTTAAAGTTATGGAGCCTCGGAAGAA
* *
4089268 GAATTGTTTATTTTTCAAATCAATTTTTAAAGTTGTGGAGCCTCAAATGAAGAGTTGTTTA-TTT
1 GAGTTGTTTATTTTTCAAATCAA-TTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATTTT
* * * *
4089332 TCAAATCGATTTTAAATTTGTGGAGCCTCGGATTAGGAGTTGTTTATTTTTTAAATCGATTTTAA
65 TCAAATCGATTTTAAAGTTGTGGAGCCTCGGATGAGGAGTTGTTTATTTTTCAAATCAATTTTAA
* * *
4089397 AGTTGTGGAGCCTCAGATGAA
130 AGTTATGGAGCCTCGGAAGAA
* * * * *
4089418 GAGTTGTTTATCTTTCAAATCAATTTTAAACTTGTGCAGCCTCGGATGATGAGTTGTTTATTTTT
1 GAGTTGTTTATTTTTCAAATCAATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTA-TTTT
* * * *
4089483 TAAAAT-GATTTTAAAGTTGTGGAGTCTTGGATAAGGAGTTGTTTATTTTTCAAA-CTAATTTTT
65 TCAAATCGATTTTAAAGTTGTGGAGCCTCGGATGAGGAGTTGTTTATTTTTCAAATC-AA-TTTT
* *
4089546 AAAGTTATGAAGCCTC--ATATAA
128 AAAGTTATGGAGCCTCGGA-AGAA
* ** *
4089568 GGAGTTATTT-TTTTAAAAAAAAATCAATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTATTTA
1 -GAGTTGTTTATTTT----TCAAATCAATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTA
* * ** *
4089632 TTTTTCAAATCAATTTTTATCTTGTGGAGCTTCGGATGAGGAGTTGTTTATTTTTCAAAAT-AAT
61 TTTTTCAAATCGATTTTAAAGTTGTGGAGCCTCGGATGAGGAGTTGTTTATTTTTC-AAATCAAT
* * * *
4089696 TTTAAAGTTGTGGAGCCGCGGATGAG
125 TTTAAAGTTATGGAGCCTCGGAAGAA
4089722 GAGTTGTTTATTTTTCAAAT
1 GAGTTGTTTATTTTTCAAAT
4089742 TGTCTTTAAA
Statistics
Matches: 391, Mismatches: 65, Indels: 44
0.78 0.13 0.09
Matches are distributed among these distances:
149 34 0.09
150 138 0.35
151 45 0.12
152 2 0.01
153 36 0.09
154 88 0.23
155 6 0.02
157 4 0.01
158 15 0.04
159 23 0.06
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (150 bp):
GAGTTGTTTATTTTTCAAATCAATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATTTTT
CAAATCGATTTTAAAGTTGTGGAGCCTCGGATGAGGAGTTGTTTATTTTTCAAATCAATTTTAAA
GTTATGGAGCCTCGGAAGAA
Found at i:4089434 original size:100 final size:100
Alignment explanation
Indices: 4089061--4089741 Score: 626
Period size: 100 Copynumber: 6.7 Consensus size: 100
4089051 GCACCTGGAT
* * * * * * *
4089061 GTTGCTTATTTTTCAAATTGTTTTTAAAGTTGCCT-AAGCCTCAAATGAGGAGTTGTTTATTTTT
1 GTTGTTTATTTTTTAAATCGATTTTAAAGTTG--TGGAGCCTCAGATGAAGAGTTGTTTATTTTT
* *
4089125 AAAAAT-GATTTTAAATTTGTGGAGCCTCGGATGATCCGAGAA
64 -CAAATCAATTTTAAATTTGTGGAGCCTCGGATGA---G-G-A
*
4089167 GTTGTTTATATTTTTCAAATTGATTTTTAAAGTTGTGGAGCCTCAGATG-AGAAGTTGTTTATTT
1 GTTGTTTAT-TTTTT-AAATCGA-TTTTAAAGTTGTGGAGCCTCAGATGAAG-AGTTGTTTATTT
* ** * * * * * * *
4089231 CTCAAATTGATTTCAAAGTTATGGAGCTTTGGAAGAAGA
62 TTCAAATCAATTTTAAATTTGTGGAGCCTCGGATGAGGA
* * * *
4089270 ATTGTTTATTTTTCAAATCAATTTTTAAAGTTGTGGAGCCTCAAATGAAGAGTTGTTTA-TTTTC
1 GTTGTTTATTTTTTAAATCGA-TTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATTTTTC
* *
4089334 AAATCGATTTTAAATTTGTGGAGCCTCGGATTAGGA
65 AAATCAATTTTAAATTTGTGGAGCCTCGGATGAGGA
*
4089370 GTTGTTTATTTTTTAAATCGATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATCTTTCA
1 GTTGTTTATTTTTTAAATCGATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATTTTTCA
* * *
4089435 AATCAATTTTAAACTTGTGCAGCCTCGGATGATGA
66 AATCAATTTTAAATTTGTGGAGCCTCGGATGAGGA
* **
4089470 GTTGTTTATTTTTTAAAAT-GATTTTAAAGTTGTGGAGTCTTGGAT-AAGGAGTTGTTTATTTTT
1 GTTGTTTATTTTTT-AAATCGATTTTAAAGTTGTGGAGCCTCAGATGAA-GAGTTGTTTATTTTT
* * * ** *
4089533 CAAA-CTAATTTTTAAAGTTATGAAGCCTCATATAAGGA
64 CAAATC-AA-TTTTAAATTTGTGGAGCCTCGGATGAGGA
* ** * *
4089571 GTTATTT-TTTTAAAAAAAAATCAATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTATTTATTT
1 GTTGTTTATTTT----TTAAATCGATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATTT
* *
4089635 TTCAAATCAATTTT-TATCTTGTGGAGCTTCGGATGAGGA
62 TTCAAATCAATTTTAAAT-TTGTGGAGCCTCGGATGAGGA
* * * * *
4089674 GTTGTTTATTTTTCAAAAT-AATTTTAAAGTTGTGGAGCCGCGGATGAGGAGTTGTTTATTTTTC
1 GTTGTTTATTTTT-TAAATCGATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATTTTTC
4089738 AAAT
65 AAAT
4089742 TGTCTTTAAA
Statistics
Matches: 480, Mismatches: 73, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
99 39 0.08
100 190 0.40
101 76 0.16
102 7 0.01
103 38 0.08
104 47 0.10
105 3 0.01
106 8 0.02
107 10 0.02
108 51 0.11
109 11 0.02
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (100 bp):
GTTGTTTATTTTTTAAATCGATTTTAAAGTTGTGGAGCCTCAGATGAAGAGTTGTTTATTTTTCA
AATCAATTTTAAATTTGTGGAGCCTCGGATGAGGA
Found at i:4089750 original size:50 final size:49
Alignment explanation
Indices: 4089061--4089756 Score: 520
Period size: 50 Copynumber: 13.7 Consensus size: 49
4089051 GCACCTGGAT
* * * **
4089061 GTTGCTTATTTTTCAAATTGTTTTTAAAGTTGCCT-AAGCCTCAAATGAGGA
1 GTTGTTTATTTTTCAAATAG-TTTTAAAGTTG--TGGAGCCTCGGATGAGGA
* *
4089112 GTTGTTTATTTTT-AAAAATGATTTTAAATTTGTGGAGCCTCGGATGATCCGAGAA
1 GTTGTTTATTTTTCAAATA-G-TTTTAAAGTTGTGGAGCCTCGGATGA---G-G-A
* * *
4089167 GTTGTTTATATTTTTCAAATTGATTTTTAAAGTTGTGGAGCCTCAGATGAGAA
1 GTTG-TT-TATTTTTCAAA-T-AGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * * * * * * *
4089220 GTTGTTTATTTCTCAAATTGATTTCAAAGTTATGGAGCTTTGGAAGAAGA
1 GTTGTTTATTTTTCAAATAG-TTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * ** *
4089270 ATTGTTTATTTTTCAAATCAATTTTTAAAGTTGTGGAGCCTCAAATGAAGA
1 GTTGTTTATTTTTCAAAT--AGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * *
4089321 GTTGTTTA-TTTTCAAATCGATTTTAAATTTGTGGAGCCTCGGATTAGGA
1 GTTGTTTATTTTTCAAATAG-TTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * * *
4089370 GTTGTTTATTTTTTAAATCGATTTTAAAGTTGTGGAGCCTCAGATGAAGA
1 GTTGTTTATTTTTCAAATAG-TTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * * * *
4089420 GTTGTTTATCTTTCAAATCAATTTTAAACTTGTGCAGCCTCGGATGATGA
1 GTTGTTTATTTTTCAAAT-AGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * * *
4089470 GTTGTTTATTTTTTAAA-ATGATTTTAAAGTTGTGGAGTCTTGGATAAGGA
1 GTTGTTTATTTTTCAAATA-G-TTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * * ** *
4089520 GTTGTTTATTTTTCAAACTAATTTTTAAAGTTATGAAGCCTCATATAAGGA
1 GTTGTTTATTTTTCAAA-T-AGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
* ** * * *
4089571 GTTATTT-TTTTAAAAAAAAATCAATTTTAAAGTTGTGGAGCCTCAGATGAAGA
1 GTTGTTTATTTT----TCAAAT-AGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
* * * ** *
4089624 GTTATTTATTTTTCAAATCAATTTTTATCTTGTGGAGCTTCGGATGAGGA
1 GTTGTTTATTTTTCAAAT-AGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
* *
4089674 GTTGTTTATTTTTCAAAATAATTTTAAAGTTGTGGAGCCGCGGATGAGGA
1 GTTGTTTATTTTTC-AAATAGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
* *
4089724 GTTGTTTATTTTTCAAATTGTCTTTAAAATTGT
1 GTTGTTTATTTTTCAAATAGT-TTTAAAGTTGT
4089757 TTCAACCATG
Statistics
Matches: 515, Mismatches: 100, Indels: 61
0.76 0.15 0.09
Matches are distributed among these distances:
48 1 0.00
49 38 0.07
50 288 0.56
51 95 0.18
52 2 0.00
53 40 0.08
54 8 0.02
55 6 0.01
56 2 0.00
57 7 0.01
58 27 0.05
60 1 0.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (49 bp):
GTTGTTTATTTTTCAAATAGTTTTAAAGTTGTGGAGCCTCGGATGAGGA
Found at i:4089929 original size:22 final size:21
Alignment explanation
Indices: 4089902--4089955 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
4089892 TTATATGTGT
4089902 TTTCATTGTTTATTTTATTTCA
1 TTTCATTGTTT-TTTTATTTCA
*
4089924 TTTCATT-TCATTTTTTATTTTA
1 TTTCATTGT--TTTTTTATTTCA
4089946 TTTCATTGTT
1 TTTCATTGTT
4089956 ACCTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.07
22 23 0.82
23 3 0.11
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTCATTGTTTTTTTATTTCA
Found at i:4089980 original size:18 final size:18
Alignment explanation
Indices: 4089929--4089982 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
4089919 TTTCATTTCA
* *
4089929 TTTCATTTTTTATTT-TA
1 TTTCATTTGTTATTTATT
*
4089946 TTTCA-TTGTTACCTTATT
1 TTTCATTTGTTA-TTTATT
4089964 TTTCATTTGTTATTTATT
1 TTTCATTTGTTATTTATT
4089982 T
1 T
4089983 ATTTACTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.17
17 7 0.23
18 12 0.40
19 6 0.20
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTGTTATTTATT
Found at i:4089993 original size:35 final size:35
Alignment explanation
Indices: 4089929--4089995 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
4089919 TTTCATTTCA
* *
4089929 TTTCATTTTTTATTTTATTTCATTGTTACCTTATT
1 TTTCATTTGTTATTTTATTTCATTCTTACCTTATT
4089964 TTTCATTTGTTA-TTTATTT-ATTTACTTACCTT
1 TTTCATTTGTTATTTTATTTCA-TT-CTTACCTT
4089996 TCTTATGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 1 0.04
34 9 0.32
35 18 0.64
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (35 bp):
TTTCATTTGTTATTTTATTTCATTCTTACCTTATT
Found at i:4095332 original size:33 final size:33
Alignment explanation
Indices: 4095287--4095385 Score: 101
Period size: 34 Copynumber: 3.0 Consensus size: 33
4095277 ATGAAAAGCC
4095287 ATTGTGAAGGTTTCACTTGAT-TTAGTAAAAAGT
1 ATTGTGAAGGTTTCACTTGATCTTA-TAAAAAGT
* *
4095320 ATTGTGAGGGTTTCACTTGATCTTATAAAAGGCT
1 ATTGTGAAGGTTTCACTTGATCTTATAAAAAG-T
* * ** * *
4095354 ATCGTGATGGTTTTGCTCGATCTCATAAAAAG
1 ATTGTGAAGGTTTCACTTGATCTTATAAAAAG
4095386 CTCATTTCGC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
33 26 0.47
34 29 0.53
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (33 bp):
ATTGTGAAGGTTTCACTTGATCTTATAAAAAGT
Found at i:4100959 original size:235 final size:233
Alignment explanation
Indices: 4100545--4101006 Score: 630
Period size: 235 Copynumber: 2.0 Consensus size: 233
4100535 ATTTCAGAGC
* * *
4100545 TTGTGATGTGGCCACAAGATAGATGGAAGAGTGAAATAGTATGCAGTATTTGTACACCATGTCGA
1 TTGTGATGTAGCCACAAGAAAGATGGAAGAGTGAAATAGTATGCAGTATTTGAACACCATGTCGA
*
4100610 ATAGGGTTTCTTATAACTCGAGCTTAGTAATGATAATAATTGGGTGTTAGGCCTAGATTGCATCA
66 ATAGGGCTTCTTATAACTCGAGCTTAGTAATGATAATAATTGGGTGTTAGGCCTAGATTGCATCA
** * * *
4100675 AAGTTTGCTTTTCTTTTCTCTCATTGGTGTGGAGAAGCTTTTCTCCAAGATAACATAAACATGTT
131 AAGTTCACTTTTCTTTTCTCTCATTGGTATGGACAAGCTTTTCTCCAAGAGAAC--AAACATGTT
*
4100740 AACCGTTTGAACTTAA-CCTAAAACTGCCCACTTTTAGGGT
194 AACC-TTTGAACATAAGCCTAAAACTGCCCACTTTTAGGGT
*
4100780 TTGTGATGTAG-CAGCAAGAAAGATTGAAGAGTGAAATAGTATGCAGTATTTGAACACCATGT-G
1 TTGTGATGTAGCCA-CAAGAAAGATGGAAGAGTGAAATAGTATGCAGTATTTGAACACCATGTCG
* * *
4100843 TATTTGGGCTTCTGT-TAACTTGAGCTTAGTAATGATAATAATTGGGTGTTAGGCCTAGATTGCA
65 -AATAGGGCTTCT-TATAACTCGAGCTTAGTAATGATAATAATTGGGTGTTAGGCCTAGATTGC-
* * * *
4100907 AT-TAAGTTCACTTTTCTTTTCT-TGCATTGGTATGGACAAGCTTTTGTCCAAGAGAGCAAACGT
127 ATCAAAGTTCACTTTTCTTTTCTCT-CATTGGTATGGACAAGCTTTTCTCCAAGAGAACAAACAT
* *
4100970 GTTAATCTTTGAACATAAGCCTAAAATTGCCCACTTT
191 GTTAACCTTTGAACATAAGCCTAAAACTGCCCACTTT
4101007 ACGAGCACCA
Statistics
Matches: 201, Mismatches: 20, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
232 10 0.05
233 28 0.14
234 4 0.02
235 156 0.78
236 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (233 bp):
TTGTGATGTAGCCACAAGAAAGATGGAAGAGTGAAATAGTATGCAGTATTTGAACACCATGTCGA
ATAGGGCTTCTTATAACTCGAGCTTAGTAATGATAATAATTGGGTGTTAGGCCTAGATTGCATCA
AAGTTCACTTTTCTTTTCTCTCATTGGTATGGACAAGCTTTTCTCCAAGAGAACAAACATGTTAA
CCTTTGAACATAAGCCTAAAACTGCCCACTTTTAGGGT
Found at i:4113385 original size:6 final size:6
Alignment explanation
Indices: 4113376--4113414 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4113366 AGAAACACAG
* * *
4113376 ATAAAT ATAAAT ATAAAT ATATAT ATACAT ATATAT ATA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA
4113415 CAGTGAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (6 bp):
ATAAAT
Found at i:4113393 original size:12 final size:12
Alignment explanation
Indices: 4113376--4113414 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
4113366 AGAAACACAG
*
4113376 ATAAATATAAAT
1 ATAAATATATAT
4113388 ATAAATATATAT
1 ATAAATATATAT
*
4113400 ATACATATATAT
1 ATAAATATATAT
4113412 ATA
1 ATA
4113415 CAGTGAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:4115576 original size:2 final size:2
Alignment explanation
Indices: 4115571--4115609 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4115561 AAAAGGGGGT
*
4115571 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4115610 AATATGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4115621 original size:3 final size:3
Alignment explanation
Indices: 4115613--4115639 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4115603 AGGGAGAAAT
4115613 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
4115640 GGAATAAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:4120126 original size:2 final size:2
Alignment explanation
Indices: 4120115--4120143 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4120105 TTCATAGTGA
4120115 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4120144 CAATAGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4122738 original size:26 final size:27
Alignment explanation
Indices: 4122691--4122743 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
4122681 TTTTAACTCG
* *
4122691 AAATAAAATATAAAAATTTA-TTAAAT
1 AAATAAAAAATAAAAATATATTTAAAT
*
4122717 AAATAAAAAATAAAAGTATATTTAAAT
1 AAATAAAAAATAAAAATATATTTAAAT
4122744 TTTTATCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATAAAAAATAAAAATATATTTAAAT
Found at i:4124639 original size:20 final size:20
Alignment explanation
Indices: 4124614--4124651 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4124604 TTATTACTTG
*
4124614 GAATATTGTTGTTGATATTA
1 GAATATTATTGTTGATATTA
4124634 GAATATTATTGTTGATAT
1 GAATATTATTGTTGATAT
4124652 CCATACAAAT
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:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
GAATATTATTGTTGATATTA
Found at i:4129260 original size:24 final size:26
Alignment explanation
Indices: 4129233--4129282 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
4129223 TTGTTGTGGA
*
4129233 AAAAATGT-TGTTA-ATGCCATGTTG
1 AAAAATGTATGTTATATACCATGTTG
4129257 AAAAATGTAGTGTTATATACCATGTT
1 AAAAATGTA-TGTTATATACCATGTT
4129283 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
26 5 0.23
27 9 0.41
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (26 bp):
AAAAATGTATGTTATATACCATGTTG
Found at i:4129316 original size:27 final size:27
Alignment explanation
Indices: 4129285--4129484 Score: 160
Period size: 27 Copynumber: 7.6 Consensus size: 27
4129275 ACCATGTTCT
*
4129285 AAAATTTAGTTGTTACACGCTATATTG
1 AAAATTTAGTTGTTACACGCTATGTTG
* *
4129312 GAAATATT--TT-TTACACACTATGTTG
1 AAAAT-TTAGTTGTTACACGCTATGTTG
* * * *
4129337 TAAATGTAGTTGTTACATGCTATGTTC
1 AAAATTTAGTTGTTACACGCTATGTTG
* * *
4129364 AAGATTTAGTTGTTACACTCCATGTTG
1 AAAATTTAGTTGTTACACGCTATGTTG
* * *
4129391 AAAATTTAGTTGTTACATGTTATATTG
1 AAAATTTAGTTGTTACACGCTATGTTG
* *
4129418 AAAAATGTAGTTGTTACACGTTATGTT-
1 -AAAATTTAGTTGTTACACGCTATGTTG
* * * *
4129445 AAAATAT-G-TATCACACGCCATGTTG
1 AAAATTTAGTTGTTACACGCTATGTTG
*
4129470 AAAATTTATTTGTTA
1 AAAATTTAGTTGTTA
4129485 TACATCATAT
Statistics
Matches: 132, Mismatches: 33, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
24 13 0.10
25 24 0.18
26 10 0.08
27 60 0.45
28 25 0.19
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (27 bp):
AAAATTTAGTTGTTACACGCTATGTTG
Found at i:4129404 original size:54 final size:54
Alignment explanation
Indices: 4129239--4129436 Score: 172
Period size: 54 Copynumber: 3.7 Consensus size: 54
4129229 TGGAAAAAAT
* * * * * *
4129239 GTTGTTA-ATGCCATGTTGAAAAATGTAG-TGTTATATACCATGTTCTAAAATTTA
1 GTTGTTACATGCTATATTG-AAAATTTAGTTGTTACACACCATGTT-GAAAATTTA
* * * * *
4129293 GTTGTTACACGCTATATTGGAAATATT--TT-TTACACACTATGTTGTAAATGTA
1 GTTGTTACATGCTATATTGAAAAT-TTAGTTGTTACACACCATGTTGAAAATTTA
* * * *
4129345 GTTGTTACATGCTATGTTCAAGATTTAGTTGTTACACTCCATGTTGAAAATTTA
1 GTTGTTACATGCTATATTGAAAATTTAGTTGTTACACACCATGTTGAAAATTTA
* *
4129399 GTTGTTACATGTTATATTGAAAAATGTAGTTGTTACAC
1 GTTGTTACATGCTATATTG-AAAATTTAGTTGTTACAC
4129437 GTTATGTTAA
Statistics
Matches: 112, Mismatches: 25, Indels: 13
0.75 0.17 0.09
Matches are distributed among these distances:
51 2 0.02
52 25 0.22
53 13 0.12
54 47 0.42
55 25 0.22
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (54 bp):
GTTGTTACATGCTATATTGAAAATTTAGTTGTTACACACCATGTTGAAAATTTA
Found at i:4129431 original size:28 final size:27
Alignment explanation
Indices: 4129239--4129454 Score: 118
Period size: 27 Copynumber: 8.0 Consensus size: 27
4129229 TGGAAAAAAT
*
4129239 GTTGTTA-ATGCCATGTTGAAAAATGTA
1 GTTGTTACATGCTATGTT-AAAAATGTA
* * * * *
4129266 G-TGTTATATACCATGTTCTAAAATTTA
1 GTTGTTACATGCTATGTT-AAAAATGTA
* * **
4129293 GTTGTTACACGCTATATTGGAAA--TA
1 GTTGTTACATGCTATGTTAAAAATGTA
* * ** **
4129318 TTTTTTACACACTATGTTGTAAATGTA
1 GTTGTTACATGCTATGTTAAAAATGTA
* * *
4129345 GTTGTTACATGCTATGTTCAAGATTTA
1 GTTGTTACATGCTATGTTAAAAATGTA
* * *
4129372 GTTGTTACACT-CCATGTTGAAAATTTA
1 GTTGTTACA-TGCTATGTTAAAAATGTA
* *
4129399 GTTGTTACATGTTATATTGAAAAATGTA
1 GTTGTTACATGCTATGTT-AAAAATGTA
* *
4129427 GTTGTTACACGTTATGTTAAAATATGTA
1 GTTGTTACATGCTATGTTAAAA-ATGTA
4129455 TCACACGCCA
Statistics
Matches: 147, Mismatches: 34, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
25 20 0.14
26 6 0.04
27 81 0.55
28 40 0.27
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (27 bp):
GTTGTTACATGCTATGTTAAAAATGTA
Found at i:4129573 original size:62 final size:62
Alignment explanation
Indices: 4129457--4129574 Score: 141
Period size: 62 Copynumber: 1.9 Consensus size: 62
4129447 AATATGTATC
* **
4129457 ACACGCCATGTTGAAAATTTATTTGTTATACATCATATTGAAAAATGTAATTGTTAGTTGTT
1 ACACGCCATGTTGAAAATTTAATTGTTATACATCATATTGAAAAAAATAATTGTTAGTTGTT
* * * *
4129519 ACACGCCATGTTGGAGATTTAATTG-T-TACATGCCATGTTGAAAAAAATAGTTGTTA
1 ACACGCCATGTTGAAAATTTAATTGTTATACAT--CATATTGAAAAAAATAATTGTTA
4129575 CATACCATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 5 0.11
61 1 0.02
62 41 0.87
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (62 bp):
ACACGCCATGTTGAAAATTTAATTGTTATACATCATATTGAAAAAAATAATTGTTAGTTGTT
Found at i:4129613 original size:26 final size:25
Alignment explanation
Indices: 4129561--4129607 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
4129551 CCATGTTGAA
*
4129561 AAAAATAGTTGTTACATACCATGAT
1 AAAAATAGTTGTTACACACCATGAT
*
4129586 AAAAA-AGTTGTTACACAGCATG
1 AAAAATAGTTGTTACACACCATG
4129608 TCATAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (25 bp):
AAAAATAGTTGTTACACACCATGAT
Found at i:4129770 original size:127 final size:127
Alignment explanation
Indices: 4129589--4129845 Score: 496
Period size: 127 Copynumber: 2.0 Consensus size: 127
4129579 CCATGATAAA
4129589 AAAGTTGTTACACAGCATGTCATAATTTGAACTGTTTTGACTTGACAGAAAATATTTTGTAACAA
1 AAAGTTGTTACACAGCATGTCATAATTTGAACTGTTTTGACTTGACAGAAAATATTTTGTAACAA
*
4129654 AACTACCCTTTTGTGCCTTACATGACAAGATGTTTCATCTCTTTTTAATTTTTGAATTGCTT
66 AACTACCCTTTTGTGCCTTACATGACAAGATGTTTCATCTCTTTTTAATTTTTGAATTACTT
4129716 AAAGTTGTTACACAGCATGTCATAATTTGAACTGTTTTGACTTGACAGAAAATATTTTGTAACAA
1 AAAGTTGTTACACAGCATGTCATAATTTGAACTGTTTTGACTTGACAGAAAATATTTTGTAACAA
*
4129781 AACTACCCTTTTGTGCCTTACATGATAAGATGTTTCATCTCTTTTTAATTTTTGAATTACTT
66 AACTACCCTTTTGTGCCTTACATGACAAGATGTTTCATCTCTTTTTAATTTTTGAATTACTT
4129843 AAA
1 AAA
4129846 AGCTAGGGAT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (127 bp):
AAAGTTGTTACACAGCATGTCATAATTTGAACTGTTTTGACTTGACAGAAAATATTTTGTAACAA
AACTACCCTTTTGTGCCTTACATGACAAGATGTTTCATCTCTTTTTAATTTTTGAATTACTT
Found at i:4131240 original size:38 final size:38
Alignment explanation
Indices: 4131198--4131273 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
4131188 TTATATGCTA
*
4131198 ATAAATAAGTTGACAATAAACTTGTTCTTTTAAAAACT
1 ATAAACAAGTTGACAATAAACTTGTTCTTTTAAAAACT
*
4131236 ATAAACAAGTTGACAATAGACTTGTTCTTTTAAAAACT
1 ATAAACAAGTTGACAATAAACTTGTTCTTTTAAAAACT
4131274 TTGTAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (38 bp):
ATAAACAAGTTGACAATAAACTTGTTCTTTTAAAAACT
Found at i:4132928 original size:9 final size:9
Alignment explanation
Indices: 4132911--4132967 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
4132901 AGAGAATATA
*
4132911 TTAAGAATT
1 TTAAAAATT
4132920 TTAAAAATT
1 TTAAAAATT
* ***
4132929 TTATATGGT
1 TTAAAAATT
*
4132938 ATAAAAAATT
1 TTAA-AAATT
4132948 TTAAAAATT
1 TTAAAAATT
4132957 TTAAAAATT
1 TTAAAAATT
4132966 TT
1 TT
4132968 GGGCCCCCAC
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
9 31 0.86
10 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (9 bp):
TTAAAAATT
Found at i:4132962 original size:8 final size:9
Alignment explanation
Indices: 4132941--4132967 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4132931 ATATGGTATA
4132941 AAAAATTTT
1 AAAAATTTT
4132950 AAAAATTTT
1 AAAAATTTT
4132959 AAAAATTTT
1 AAAAATTTT
4132968 GGGCCCCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAAATTTT
Found at i:4137358 original size:63 final size:63
Alignment explanation
Indices: 4137229--4137347 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
4137219 CTTATGAGAG
* * * * *
4137229 GAATCGATTCTTCAAAAAGAAAAAGTCAATTTTGGACAATGCAGAAGCTACTAGAAGCAAGAA
1 GAATCGATTCTTCAAAAAGAAAAAGTCAATTCTAGAAAATACAAAAGCTACTAGAAGCAAGAA
* * *
4137292 GAATTGATTCTTTAAAAAGAAAAAGTCAATTCTATAAAATACAAAAGCTACTAGAA
1 GAATCGATTCTTCAAAAAGAAAAAGTCAATTCTAGAAAATACAAAAGCTACTAGAA
4137348 TATGCAAGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.24
Consensus pattern (63 bp):
GAATCGATTCTTCAAAAAGAAAAAGTCAATTCTAGAAAATACAAAAGCTACTAGAAGCAAGAA
Found at i:4138005 original size:20 final size:20
Alignment explanation
Indices: 4137982--4138026 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4137972 AGAAAGAGAG
4137982 GAAAAAAAACTAGAAAACGA
1 GAAAAAAAACTAGAAAACGA
* * * *
4138002 GAAAATAAGCTGGGAAACGA
1 GAAAAAAAACTAGAAAACGA
4138022 GAAAA
1 GAAAA
4138027 TGGAACTAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.62, C:0.09, G:0.22, T:0.07
Consensus pattern (20 bp):
GAAAAAAAACTAGAAAACGA
Found at i:4138833 original size:71 final size:70
Alignment explanation
Indices: 4138758--4138987 Score: 178
Period size: 71 Copynumber: 3.0 Consensus size: 70
4138748 ATGTTTAATA
* *
4138758 TTAAAAATAATAATACTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTCATTT
1 TTAAAAATATTAATA-TTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTAATTT
4138823 TATTTT
65 TATTTT
* *
4138829 TTAAATATTATTAAT-TATAATTTATAATATTAATAATTTATCATTTAAAT-ATTAATATTTTTA
1 TTAAA-AATATTAATAT-TAATTTATAAT-TT-A-AATGT-T-A-TT--ATGA-T--TA--TTTA
*
4138892 TTTATATATTAATTATTAATTTT
51 TTTTTAT-TTAATT-TT-ATTTT
* * *
4138915 TT-AAAATATTAATATTTTATTTATAATTTAACTGTTATTATGATTATTTATTTTTATTAAATTT
1 TTAAAAATATTAATA-TTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTAATTT
*
4138979 TATCTT
65 TATTTT
4138985 TTA
1 TTA
4138988 GATATTCATA
Statistics
Matches: 125, Mismatches: 12, Indels: 44
0.69 0.07 0.24
Matches are distributed among these distances:
70 7 0.06
71 18 0.14
72 14 0.11
73 11 0.09
74 4 0.03
75 3 0.02
76 1 0.01
77 5 0.04
78 2 0.02
79 5 0.04
80 1 0.01
81 3 0.02
82 3 0.02
83 11 0.09
84 15 0.12
85 14 0.11
86 8 0.06
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (70 bp):
TTAAAAATATTAATATTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTAATTTT
ATTTT
Found at i:4138860 original size:22 final size:22
Alignment explanation
Indices: 4138828--4138934 Score: 94
Period size: 22 Copynumber: 4.9 Consensus size: 22
4138818 CATTTTATTT
*
4138828 TTTAAATATTATTAA-TTATAA
1 TTTAAATATTAATAATTTATAA
*
4138849 TTTATAATATTAATAATTTATCA
1 TTTA-AATATTAATAATTTATAA
*
4138872 TTTAAATATTAAT-ATTT-TTA
1 TTTAAATATTAATAATTTATAA
* * * **
4138892 TTTATATATTAATTATTAATTT
1 TTTAAATATTAATAATTTATAA
*
4138914 TTTAAAATATTAATATTTTAT
1 TTT-AAATATTAATAATTTAT
4138935 TTATAATTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
20 14 0.20
21 11 0.15
22 24 0.34
23 22 0.31
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAAATATTAATAATTTATAA
Found at i:4138868 original size:87 final size:84
Alignment explanation
Indices: 4138775--4138945 Score: 197
Period size: 84 Copynumber: 2.0 Consensus size: 84
4138765 TAATAATACT
* * *
4138775 TAATTTATAATTTAAATGTTATTATGATTATTTATTTTTAT-TTCATT-TT-ATTTTTTAAATAT
1 TAATTTATAATTTAAATATTA--AT-ATT-TTTATTTATATATTAATTATTAATTTTTTAAA-A-
4138837 TATTAAT-TATAATTTATAATATTAA
60 TATTAATATATAATTTATAAT-TTAA
*
4138862 TAATTTATCATTTAAATATTAATATTTTTATTTATATATTAATTATTAATTTTTTAAAATATTAA
1 TAATTTATAATTTAAATATTAATATTTTTATTTATATATTAATTATTAATTTTTTAAAATATTAA
* *
4138927 TATTTTATTTATAATTTAA
66 TATATAATTTATAATTTAA
4138946 CTGTTATTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
83 10 0.14
84 19 0.26
85 16 0.22
86 10 0.14
87 19 0.26
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (84 bp):
TAATTTATAATTTAAATATTAATATTTTTATTTATATATTAATTATTAATTTTTTAAAATATTAA
TATATAATTTATAATTTAA
Found at i:4138903 original size:27 final size:26
Alignment explanation
Indices: 4138864--4138917 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
4138854 AATATTAATA
4138864 ATTTATCATTTAAATATTAATATTTTT
1 ATTTATCATTTAAATATTAAT-TTTTT
*
4138891 ATTTAT-ATATTAATTATTAATTTTTT
1 ATTTATCAT-TTAAATATTAATTTTTT
4138917 A
1 A
4138918 AAATATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTATCATTTAAATATTAATTTTTT
Found at i:4139219 original size:153 final size:154
Alignment explanation
Indices: 4138568--4139269 Score: 661
Period size: 153 Copynumber: 4.5 Consensus size: 154
4138558 TATTTTATTT
* * * *
4138568 TTTAAATATTAATATTTTATTTATAATCTAATCATTAACA-T-T---AT-A-AATATTCT-TTTG
1 TTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATAATAATATTTTATTTA
**
4138625 TAATTTAAATGTTATTATGATTATTTATTTTGAAATTATT-TTACTTTTAAATATTAATAATTTA
66 TAATTTAAATGTTATTATGATTATTT-TTTT--AATT-TTATT--TTTTATGTATTAATAATTTA
*** * * *
4138689 TAATTAT-TCAAAATATTAAAAATAGATAG
125 TAATTATATTTGAATATTAATAATTGATAA
* * * ** * *
4138718 TTTAAATATTAATATGTTACTTATAATTTCATGTTTAATATTA-AAAATAATAATACTTAATTTA
1 TTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATAATAATATTTTATTTA
* *
4138782 TAATTTAAATGTTATTATGATTATTTATTTTTATTTCATTTTATT-T-T-TT-A-AATATTATTA
66 TAATTTAAATGTTATTATGATTATTT-TTTTAATTTTATTTT-TTATGTATTAATAAT-TTA-TA
* * *
4138842 ATTATAATTTATAATATTAATAATTTATCA
127 ATTAT-ATTT-GAATATTAATAATTGATAA
* * * *
4138872 TTTAAATATTAATATTTTTATTTAT-ATATTAATTATTAATTTTTTAAAATATTAATATTTTATT
1 TTTAAATATTAATA-TTTTATTTATAAT-TTAATCATTAATATTATAAAATAATAATATTTTATT
* * *
4138936 TATAATTTAACTGTTATTATGATTATTTATTTTTATTAAATTTTATCTTTTA-GATATTCATAAT
64 TATAATTTAAATGTTATTATG---A-TTATTTTT-TT-AATTTTATTTTTTATG-TATTAATAAT
* * * * *
4139000 TTTTATTTTTATTTGAAATATTAATAATTGTTCA
122 TTATAATTATATTTG-AATATTAATAATTGATAA
4139034 TTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATAATAATATTTTATTTA
1 TTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATAATAATATTTTATTTA
* *
4139099 TAATTTAAATGTTATTATGATTATTTTTTT-ATTTTATTTTTTATGTGTTAATCATTTATAATTG
66 TAATTTAAATGTTATTATGATTATTTTTTTAATTTTATTTTTTATGTATTAATAATTTATAATT-
*
4139163 AT-TTTGAATATTAATAATTGGTAA
130 ATATTTGAATATTAATAATTGATAA
* * * *
4139187 TTTAAATATTAATATTTTATTTATAATTTAATCATTAAAATTTTAAAATATTAATATTTTGTTTA
1 TTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATAATAATATTTTATTTA
*
4139252 TAATTTAAATATTATTAT
66 TAATTTAAATGTTATTAT
4139270 TAAAATATTA
Statistics
Matches: 457, Mismatches: 61, Indels: 65
0.78 0.10 0.11
Matches are distributed among these distances:
149 3 0.01
150 37 0.08
151 10 0.02
152 1 0.00
153 97 0.21
154 63 0.14
155 27 0.06
156 43 0.09
157 42 0.09
158 1 0.00
159 3 0.01
160 10 0.02
161 70 0.15
162 37 0.08
163 7 0.02
164 3 0.01
165 3 0.01
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (154 bp):
TTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTATAAAATAATAATATTTTATTTA
TAATTTAAATGTTATTATGATTATTTTTTTAATTTTATTTTTTATGTATTAATAATTTATAATTA
TATTTGAATATTAATAATTGATAA
Found at i:4139242 original size:42 final size:40
Alignment explanation
Indices: 4139190--4139287 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 40
4139180 TTGGTAATTT
4139190 AAATATTAATATTTTATTTATAATTT-AATCATTAAAATT-TTA
1 AAATATTAATATTTTATTTATAATTTAAAT-ATT---ATTATTA
*
4139232 AAATATTAATATTTTGTTTATAATTTAAATATTATTATTA
1 AAATATTAATATTTTATTTATAATTTAAATATTATTATTA
*
4139272 AAATATTAATACTTTA
1 AAATATTAATATTTTA
4139288 ACTAATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
39 3 0.06
40 17 0.33
42 28 0.55
43 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (40 bp):
AAATATTAATATTTTATTTATAATTTAAATATTATTATTA
Found at i:4139428 original size:14 final size:15
Alignment explanation
Indices: 4139411--4139444 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4139401 TCACTTAGTA
4139411 ATTTAAAA-ATTAAT
1 ATTTAAAATATTAAT
4139425 ATTTTAAAATATTAAT
1 A-TTTAAAATATTAAT
4139441 ATTT
1 ATTT
4139445 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.06
15 10 0.56
16 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAAATATTAAT
Found at i:4139432 original size:15 final size:16
Alignment explanation
Indices: 4139412--4139446 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4139402 CACTTAGTAA
4139412 TTTAAAA-ATTAATAT
1 TTTAAAATATTAATAT
4139427 TTTAAAATATTAATAT
1 TTTAAAATATTAATAT
4139443 TTTA
1 TTTA
4139447 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAAATATTAATAT
Found at i:4149337 original size:14 final size:15
Alignment explanation
Indices: 4149318--4149347 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4149308 TTTAGGTATT
4149318 AAATTTTTTT-TAAA
1 AAATTTTTTTATAAA
4149332 AAATTTTTTTATAAA
1 AAATTTTTTTATAAA
4149347 A
1 A
4149348 TGAGAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTTTTTTATAAA
Found at i:4151068 original size:21 final size:20
Alignment explanation
Indices: 4151038--4151079 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4151028 CGTCTGTCCT
*
4151038 GAAAAAAAAAATAGTAAAAAA
1 GAAAAAAAAAAGA-TAAAAAA
*
4151059 GAAAAGAAAAAGATAAAAAA
1 GAAAAAAAAAAGATAAAAAA
4151079 G
1 G
4151080 GTAATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (20 bp):
GAAAAAAAAAAGATAAAAAA
Found at i:4154321 original size:2 final size:2
Alignment explanation
Indices: 4154314--4154343 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4154304 CCTATGTTAT
4154314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4154344 ACGGTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4155515 original size:6 final size:6
Alignment explanation
Indices: 4155506--4155549 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
4155496 CCCCTTTCTC
* *
4155506 TTTTTA TTTTTA TTTTT- TTTAT- TTTTTA TTTTTA TTTTTC TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
4155550 CTAATAACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 8 0.24
6 26 0.76
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:4155522 original size:7 final size:7
Alignment explanation
Indices: 4155506--4155544 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
4155496 CCCCTTTCTC
4155506 TTTTTAT
1 TTTTTAT
*
4155513 TTTTATTT
1 TTTT-TAT
4155521 TTTTTAT
1 TTTTTAT
4155528 TTTTTA-
1 TTTTTAT
4155534 TTTTTAT
1 TTTTTAT
4155541 TTTT
1 TTTT
4155545 CTTTTCTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.21
7 16 0.57
8 6 0.21
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:4155526 original size:15 final size:16
Alignment explanation
Indices: 4155506--4155538 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4155496 CCCCTTTCTC
4155506 TTTTTA-TTTTTATTT
1 TTTTTATTTTTTATTT
4155521 TTTTTATTTTTTATTT
1 TTTTTATTTTTTATTT
4155537 TT
1 TT
4155539 ATTTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTATTTTTTATTT
Found at i:4156270 original size:12 final size:12
Alignment explanation
Indices: 4156249--4156278 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4156239 ACTATTAGTG
4156249 AATT-TATGTAA
1 AATTATATGTAA
4156260 AATTATATGTAA
1 AATTATATGTAA
4156272 AATTATA
1 AATTATA
4156279 ATCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
AATTATATGTAA
Found at i:4160640 original size:12 final size:12
Alignment explanation
Indices: 4160623--4160647 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4160613 TATTATATAA
4160623 TTTTTATTAATT
1 TTTTTATTAATT
4160635 TTTTTATTAATT
1 TTTTTATTAATT
4160647 T
1 T
4160648 AAAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATTAATT
Found at i:4163266 original size:68 final size:68
Alignment explanation
Indices: 4163152--4163283 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 68
4163142 ATTTTAGAAT
* * * *
4163152 TAGATTTTAGTATAATCTGATTAAATTCAAGAATGAATTTTTTTAAAGGTAAAAGAATGTGAAAT
1 TAGAGTTTAGTATAATCCGATTAAATTCAAGAACGAATTTTCTTAAAGGTAAAAGAATGTGAAAT
4163217 TTC
66 TTC
*
4163220 TAGAGTTTAGTATAATCCGATTAAATTCAAGAACGAATTTTCTTAAAGGTGAAAGAATGTGAAA
1 TAGAGTTTAGTATAATCCGATTAAATTCAAGAACGAATTTTCTTAAAGGTAAAAGAATGTGAAA
4163284 CTTGTCAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (68 bp):
TAGAGTTTAGTATAATCCGATTAAATTCAAGAACGAATTTTCTTAAAGGTAAAAGAATGTGAAAT
TTC
Found at i:4177228 original size:3 final size:3
Alignment explanation
Indices: 4177220--4177248 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4177210 TACTAACTGT
4177220 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
4177249 TTGTTTGTGA
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:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:4177892 original size:2 final size:2
Alignment explanation
Indices: 4177885--4177910 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4177875 CTCAAAGAAG
4177885 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
4177911 TACGGGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4179704 original size:18 final size:19
Alignment explanation
Indices: 4179678--4179718 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
4179668 TTATATAAGT
4179678 ATAAATTTTT-TTAAAAAA
1 ATAAATTTTTATTAAAAAA
*
4179696 ATAATTTTTTATT-AAAAA
1 ATAAATTTTTATTAAAAAA
4179714 ATAAA
1 ATAAA
4179719 ATTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAATTTTTATTAAAAAA
Found at i:4184887 original size:14 final size:13
Alignment explanation
Indices: 4184864--4184897 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4184854 AATAAGAGAG
4184864 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
* *
4184877 AAAAGGAAAAAGG
1 AAAAGAAAAAAGA
4184890 AAAAGAAA
1 AAAAGAAA
4184898 GAAAAACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:4191368 original size:25 final size:25
Alignment explanation
Indices: 4191322--4191369 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
4191312 CTTTAATTGC
* * *
4191322 AAAAAATGAATAGAAAGCAAAAGGT
1 AAAAAAAGAAAAGAAAACAAAAGGT
*
4191347 AAAAAAAGAAAAGAAAATAAAAG
1 AAAAAAAGAAAAGAAAACAAAAG
4191370 ACAAATAGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (25 bp):
AAAAAAAGAAAAGAAAACAAAAGGT
Found at i:4196540 original size:15 final size:16
Alignment explanation
Indices: 4196517--4196549 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4196507 ACATTGATAC
4196517 TTTTAAATAAT-ATAA
1 TTTTAAATAATAATAA
*
4196532 TTTTTAATAATAATAA
1 TTTTAAATAATAATAA
4196548 TT
1 TT
4196550 GAAGCGCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAATAATAATAA
Found at i:4206935 original size:53 final size:54
Alignment explanation
Indices: 4206860--4206986 Score: 150
Period size: 53 Copynumber: 2.4 Consensus size: 54
4206850 ATTATTGTAT
* * ** * *
4206860 AACTATTAATGAAAAACCATGAATGTCCATTTCCTGAAGTAAAT-GTGACAAATG
1 AACTACTAATAAAAAATTATGAATGTCCATTTCCTAAAGTAAATACT-ACAAATG
* *
4206914 AACTACTAAT-AAAAATTATGAATGTTCATTTCTTAAAGTAAATACTACAAATG
1 AACTACTAATAAAAAATTATGAATGTCCATTTCCTAAAGTAAATACTACAAATG
*
4206967 AGCTACTAATAAAAAATTAT
1 AACTACTAATAAAAAATTAT
4206987 ATATTTGTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 44 0.70
54 19 0.30
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (54 bp):
AACTACTAATAAAAAATTATGAATGTCCATTTCCTAAAGTAAATACTACAAATG
Found at i:4207196 original size:26 final size:25
Alignment explanation
Indices: 4207167--4207254 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
4207157 ATTTTATTAC
4207167 CAAAAGTGGATGGATAATTTTACCA
1 CAAAAGTGGATGGATAATTTTACCA
** ** *
4207192 TCAAAA-TCTAAAGATAATTTTGCCA
1 -CAAAAGTGGATGGATAATTTTACCA
*
4207217 CAAAAAGTGAATGGATAA-TTTACCA
1 C-AAAAGTGGATGGATAATTTTACCA
*
4207242 CCAGAAGTGGATG
1 -CAAAAGTGGATG
4207255 AATGCCATAA
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
24 1 0.02
25 33 0.70
26 13 0.28
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (25 bp):
CAAAAGTGGATGGATAATTTTACCA
Found at i:4207242 original size:25 final size:26
Alignment explanation
Indices: 4207154--4207242 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 26
4207144 AATTTTAAAA
** * *
4207154 ATAATTTTATTACCAAAAGTGGATGG
1 ATAATTTTACCACAAAAAGTGAATGG
** *
4207180 ATAATTTTACCATCAAAATCT-AA-AG
1 ATAATTTTACCA-CAAAAAGTGAATGG
*
4207205 ATAATTTTGCCACAAAAAGTGAATGG
1 ATAATTTTACCACAAAAAGTGAATGG
4207231 ATAA-TTTACCAC
1 ATAATTTTACCAC
4207243 CAGAAGTGGA
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
24 6 0.12
25 21 0.44
26 16 0.33
27 5 0.10
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (26 bp):
ATAATTTTACCACAAAAAGTGAATGG
Found at i:4211806 original size:17 final size:18
Alignment explanation
Indices: 4211771--4211807 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4211761 ATCCTCTTAC
4211771 TCCCTCTAAATACTTTTT
1 TCCCTCTAAATACTTTTT
4211789 TCCCTCTAAATA-TTTTT
1 TCCCTCTAAATACTTTTT
4211806 TC
1 TC
4211808 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (18 bp):
TCCCTCTAAATACTTTTT
Found at i:4213161 original size:30 final size:30
Alignment explanation
Indices: 4213127--4213184 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
4213117 ATTATAAGAG
4213127 TTTA-TTTGACTCAAAATAAAAATATAAAAA
1 TTTATTTTG-CTCAAAATAAAAATATAAAAA
* *
4213157 TTTATTTTGTTTAAAATAAAAATATAAA
1 TTTATTTTGCTCAAAATAAAAATATAAA
4213185 GGCTCGACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTATTTTGCTCAAAATAAAAATATAAAAA
Found at i:4219262 original size:3 final size:3
Alignment explanation
Indices: 4219248--4219277 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4219238 ACATCCAAAC
*
4219248 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4219278 CAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4224473 original size:126 final size:125
Alignment explanation
Indices: 4224231--4224606 Score: 368
Period size: 126 Copynumber: 3.0 Consensus size: 125
4224221 AGATGGGATT
* * * * * * *
4224231 CATGAATGGATCGATAGCAAAACCCGATGTCAATTTTGGAGATTTTCAATATTGGATCTAATGGT
1 CATGGATGGACCGATAGCAAAACCCGATGTCAATTTT-GAGATTTCCAATCTTGGATCCAAAGAT
* **
4224296 TCATGGATGGATTAATAGTAAAACTTGATGTCAA-TTCTGGAGAGTTT-CAATCTTGGATC-TA
65 TCATGGATGGATTGATAGTAAAAC-TGATGTCAATTTCAAG-GA-TTTCCAATCTTGGATCGTA
* ** * *
4224357 CATGGATGGACTGATAGCAAAACTTGATATCAATTTTGAGTATTTCCAATCTTGGGTCCAAAGAT
1 CATGGATGGACCGATAGCAAAACCCGATGTCAATTTTGAG-ATTTCCAATCTTGGATCCAAAGAT
* *
4224422 TCATGGATGGATTGATAATAAAACTCGATGTCAATTTCAAGGATTTCCAATCTTGGATCTCGTT
65 TCATGGATGGATTGATAGTAAAACT-GATGTCAATTTCAAGGATTTCCAATCTTGGA--TCGTA
* * *
4224486 CATGGATGGACCAATAGCAAAACCCGATGTCAATTCTAAGGATTTCCAATCTTGGATCC--A-AT
1 CATGGATGGACCGATAGCAAAACCCGATGTCAATTTTGA-GATTTCCAATCTTGGATCCAAAGAT
** * * * * * *
4224548 TCATCAATAGTTTGATAGCAAAACGTTAAGTCAATTTCAAAGATTTCCAATCTTGGATC
65 TCATGGATGGATTGATAGTAAAAC-TGATGTCAATTTCAAGGATTTCCAATCTTGGATC
4224607 CAATGCATAA
Statistics
Matches: 207, Mismatches: 34, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
124 2 0.01
125 7 0.03
126 139 0.67
127 6 0.03
128 2 0.01
129 50 0.24
130 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (125 bp):
CATGGATGGACCGATAGCAAAACCCGATGTCAATTTTGAGATTTCCAATCTTGGATCCAAAGATT
CATGGATGGATTGATAGTAAAACTGATGTCAATTTCAAGGATTTCCAATCTTGGATCGTA
Found at i:4224551 original size:63 final size:62
Alignment explanation
Indices: 4224228--4224668 Score: 311
Period size: 63 Copynumber: 7.0 Consensus size: 62
4224218 ACAAGATGGG
* * * ** * * *
4224228 ATTCATGAATGGATCGATAGCAAAACCCGATGTCAATTTTGGAGATTTTCAATATTGGATCTA
1 ATTCATGGATGGATTGATAGCAAAACTCGATGTCAATTTAAG-GATTTCCAATCTTGGATCCA
* * * *
4224291 ATGGTTCATGGATGGATTAATAGTAAAACTTGATGTCAATTCT-GGAGAGTTT-CAATCTTGGAT
1 A---TTCATGGATGGATTGATAGCAAAACTCGATGTCAATT-TAAG-GA-TTTCCAATCTTGGAT
4224354 -C-
60 CCA
* * * * * * *
4224355 -TACATGGATGGACTGATAGCAAAACTTGATATCAATTTTGAGTATTTCCAATCTTGGGTCCAAA
1 ATTCATGGATGGATTGATAGCAAAACTCGATGTCAA-TTTAAGGATTTCCAATCTTGGATCC--A
**
4224419 GATTCATGGATGGATTGATAATAAAACTCGATGTCAATTTCAAGGATTTCCAATCTTGGATCTC-
1 -ATTCATGGATGGATTGATAGCAAAACTCGATGTCAATTT-AAGGATTTCCAATCTTGGATC-CA
* *** *
4224483 GTTCATGGATGGACCAATAGCAAAACCCGATGTCAATTCTAAGGATTTCCAATCTTGGATCCA
1 ATTCATGGATGGATTGATAGCAAAACTCGATGTCAATT-TAAGGATTTCCAATCTTGGATCCA
** * * * * *
4224546 ATTCATCAATAGTTTGATAGCAAAACGT-TAAGTCAATTTCAAAGATTTCCAATCTTGGATCCA
1 ATTCATGGATGGATTGATAGCAAAAC-TCGATGTCAATTT-AAGGATTTCCAATCTTGGATCCA
* ** * * ** *
4224609 ATGCATAAATGGATTAATAGCAAAACTGGATGTCAATTATGGGGATTTCTAATCTTGGAT
1 ATTCATGGATGGATTGATAGCAAAACTCGATGTCAATT-TAAGGATTTCCAATCTTGGAT
4224669 ATACTGTAAA
Statistics
Matches: 301, Mismatches: 55, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
59 3 0.01
60 42 0.14
61 4 0.01
62 3 0.01
63 146 0.49
64 2 0.01
65 3 0.01
66 93 0.31
67 5 0.02
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (62 bp):
ATTCATGGATGGATTGATAGCAAAACTCGATGTCAATTTAAGGATTTCCAATCTTGGATCCA
Found at i:4225824 original size:24 final size:24
Alignment explanation
Indices: 4225792--4225841 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
4225782 AATATATATC
*
4225792 AACCATGAACCATTCCAAACACCA
1 AACCATGAACAATTCCAAACACCA
*
4225816 AACCATGAACAATTCCTAACACCA
1 AACCATGAACAATTCCAAACACCA
4225840 AA
1 AA
4225842 TCAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.34, G:0.04, T:0.14
Consensus pattern (24 bp):
AACCATGAACAATTCCAAACACCA
Found at i:4240255 original size:30 final size:30
Alignment explanation
Indices: 4240219--4240275 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
4240209 TCTCAAGTTC
*
4240219 TTATATTATTATTTTGAACTAGATAAACCT
1 TTATATTATTATTTTGAACTAAATAAACCT
* *
4240249 TTATATTTTTATTTTGAATTAAATAAA
1 TTATATTATTATTTTGAACTAAATAAA
4240276 TCATTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (30 bp):
TTATATTATTATTTTGAACTAAATAAACCT
Found at i:4240283 original size:30 final size:30
Alignment explanation
Indices: 4240219--4240283 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
4240209 TCTCAAGTTC
* *
4240219 TTATATTATTATTTTGAACTAGATAAACCT
1 TTATATTATTATTTTGAACTAAATAAACCA
* * *
4240249 TTATATTTTTATTTTGAATTAAATAAATCA
1 TTATATTATTATTTTGAACTAAATAAACCA
4240279 TTATA
1 TTATA
4240284 ATTAATTGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (30 bp):
TTATATTATTATTTTGAACTAAATAAACCA
Found at i:4243788 original size:2 final size:2
Alignment explanation
Indices: 4243750--4243778 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4243740 TCAATAAACC
4243750 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 T
4243779 GCCTTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4249087 original size:34 final size:35
Alignment explanation
Indices: 4248985--4249156 Score: 181
Period size: 35 Copynumber: 4.9 Consensus size: 35
4248975 GTTATATAAG
* * * *
4248985 ATGAATAAAGCCTATCAT-GAGGGTAAGAATACCAT
1 ATGAATAAAGCCCATCGTAG-GGGTAAAAATACCAC
* * *
4249020 ATGAATAAAGCCCAACGTGGGGGTAAAAGTACCAC
1 ATGAATAAAGCCCATCGTAGGGGTAAAAATACCAC
*
4249055 ATGAATAAAGCCTATCGT-GGGGTAAAAATACCAC
1 ATGAATAAAGCCCATCGTAGGGGTAAAAATACCAC
* * * *
4249089 TTGAATTAAGCCCATTGTAGGGGTAAAAACACCAC
1 ATGAATAAAGCCCATCGTAGGGGTAAAAATACCAC
4249124 ATGAATAAAGCCCA-C-TACGAGGGTAAAAATACC
1 ATGAATAAAGCCCATCGTA-G-GGGTAAAAATACC
4249157 GCACTAAAAT
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
33 2 0.02
34 30 0.26
35 82 0.71
36 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (35 bp):
ATGAATAAAGCCCATCGTAGGGGTAAAAATACCAC
Found at i:4249094 original size:69 final size:70
Alignment explanation
Indices: 4248985--4249156 Score: 215
Period size: 69 Copynumber: 2.5 Consensus size: 70
4248975 GTTATATAAG
* * **
4248985 ATGAATAAAGCCTATCATGAGGGTAAGAATACCATATGAATAAAGCCCAACGTGGGGGTAAAAGT
1 ATGAATAAAGCCTATCATGAGGGTAAAAATACCATATGAATAAAGCCCAACGTAGGGGTAAAAAC
4249050 ACCAC
66 ACCAC
* * **
4249055 ATGAATAAAGCCTATCGTG-GGGTAAAAATACCACT-TGAATTAAGCCCATTGTAGGGGTAAAAA
1 ATGAATAAAGCCTATCATGAGGGTAAAAATACCA-TATGAATAAAGCCCAACGTAGGGGTAAAAA
4249118 CACCAC
65 CACCAC
* *
4249124 ATGAATAAAGCCCA-CTACGAGGGTAAAAATACC
1 ATGAATAAAGCCTATC-ATGAGGGTAAAAATACC
4249157 GCACTAAAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
68 1 0.01
69 55 0.62
70 32 0.36
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (70 bp):
ATGAATAAAGCCTATCATGAGGGTAAAAATACCATATGAATAAAGCCCAACGTAGGGGTAAAAAC
ACCAC
Found at i:4255315 original size:35 final size:35
Alignment explanation
Indices: 4255269--4255390 Score: 136
Period size: 35 Copynumber: 3.5 Consensus size: 35
4255259 TGTGAGGGAT
4255269 AAGAATACCACATGAATAAAGCCCAAAATGGGGGC
1 AAGAATACCACATGAATAAAGCCCAAAATGGGGGC
* * *** *
4255304 AAGAGTACCACATGAATAAAGTCCATTGTGGGGGT
1 AAGAATACCACATGAATAAAGCCCAAAATGGGGGC
** * *
4255339 AAGAATACCACATGAATAAAGCCCACTATGAGGGT
1 AAGAATACCACATGAATAAAGCCCAAAATGGGGGC
*
4255374 AAGAATACTACAATGAA
1 AAGAATACCAC-ATGAA
4255391 ATTTGTGAAC
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
35 69 0.93
36 5 0.07
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (35 bp):
AAGAATACCACATGAATAAAGCCCAAAATGGGGGC
Found at i:4261920 original size:15 final size:15
Alignment explanation
Indices: 4261891--4261945 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
4261881 TTTACAATGC
*
4261891 AATGTGATTATAAGT
1 AATGTGATTACAAGT
* *
4261906 AATATGATTGCAAGT
1 AATGTGATTACAAGT
*
4261921 AATGTGATTACAAGC
1 AATGTGATTACAAGT
4261936 AATGTGATTA
1 AATGTGATTA
4261946 TAGAGAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:4262158 original size:60 final size:58
Alignment explanation
Indices: 4262085--4262306 Score: 194
Period size: 58 Copynumber: 3.8 Consensus size: 58
4262075 ATAATTATTA
**
4262085 AAATATAAGTTTAATATATTTATATTTCTTATTATTAATTTTTATATAATATCATCTCTT
1 AAATATATTTTTAATATA-TTATATTT-TTATTATTAATTTTTATATAATATCATCTCTT
* * * * * *
4262145 AAATATATTTTTAATGTCA-TATA-TTTTATT-TTTATTTATTATTATAATTTTATATATT
1 AAATATATTTTTAATAT-ATTATATTTTTATTATTAATTT-TTA-TATAATATCATCTCTT
4262203 ---T-TATTTTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATCTCTT
1 AAATATATTTTTAATATA-TTATATTT-TTATTATTAATTTTTATATAATATCATCTCTT
* *
4262259 AAATATATTTTTAATGTGA-TATA-TTTTATT-TTTATTTATTATTATAAT
1 AAATATATTTTTAATAT-ATTATATTTTTATTATTAATTT-TTA-TATAAT
4262307 CTTATATATT
Statistics
Matches: 131, Mismatches: 16, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
53 1 0.01
54 11 0.08
55 5 0.04
56 26 0.20
57 24 0.18
58 28 0.21
59 9 0.07
60 25 0.19
61 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (58 bp):
AAATATATTTTTAATATATTATATTTTTATTATTAATTTTTATATAATATCATCTCTT
Found at i:4262211 original size:39 final size:39
Alignment explanation
Indices: 4262168--4262446 Score: 109
Period size: 39 Copynumber: 7.1 Consensus size: 39
4262158 ATGTCATATA
4262168 TTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
1 TTTTATTTTTATTTATTATTATAATTTTATATATTTTA-T
**
4262208 TTTAATATATTTATATTTATTATTATTAATTTT-TATATAATAT
1 TTT--TAT-TTT-TATTTATTATTA-TAATTTTATATATTTTAT
* * * ** * * *
4262251 CATCT-CTTAAATATATT-TT-TAATGTGATATATTTTAT
1 -TTTTATTTTTATTTATTATTATAATTTTATATATTTTAT
*
4262288 TTTTA------TTTATTATTATAATCTTATATATTTTAT
1 TTTTATTTTTATTTATTATTATAATTTTATATATTTTAT
* * *
4262321 TTTTATTTTTTAATATATT-TT-TTATATTATATATTTTAT
1 TTTTA-TTTTT-ATTTATTATTATAATTTTATATATTTTAT
* * *
4262360 TTTAATTTGT-TTTACCTATATTATATAAATTTTA-ATTTTTTAT
1 TTTTATTTTTATTTA--T-TA-T-TAT-AATTTTATATATTTTAT
* * * * *
4262403 ATTTTATTTTAATTTTTTATTCTTATTTTAATATTTTTTAT
1 -TTTTATTTTTATTTATTATTATAATTTT-ATATATTTTAT
4262444 TTT
1 TTT
4262447 AATTATAACA
Statistics
Matches: 177, Mismatches: 32, Indels: 60
0.66 0.12 0.22
Matches are distributed among these distances:
31 5 0.03
32 2 0.01
33 21 0.12
36 10 0.06
37 8 0.05
38 7 0.04
39 32 0.18
40 13 0.07
41 16 0.09
42 7 0.04
43 14 0.08
44 32 0.18
45 10 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (39 bp):
TTTTATTTTTATTTATTATTATAATTTTATATATTTTAT
Found at i:4262246 original size:24 final size:24
Alignment explanation
Indices: 4262177--4262246 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
4262167 ATTTTATTTT
4262177 TATTTATTATTA-TAA-TTTTATA
1 TATTTATTATTATTAATTTTTATA
* *
4262199 TA-TT-TTATTTTTAATATATT-TA
1 TATTTATTATTATTAAT-TTTTATA
4262221 TATTTATTATTATTAATTTTTATA
1 TATTTATTATTATTAATTTTTATA
4262245 TA
1 TA
4262247 ATATCATCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.13
21 5 0.13
22 6 0.16
23 8 0.21
24 14 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTATTATTATTAATTTTTATA
Found at i:4262314 original size:33 final size:32
Alignment explanation
Indices: 4262277--4262361 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
4262267 TTTTAATGTG
*
4262277 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATAT-ATCTT
* *
4262310 ATATATTTTATTTTTATTTTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTAATATATCTT
* *
4262342 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
4262362 TAATTTGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 13 0.28
33 33 0.72
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTATTAATATATCTT
Found at i:4262322 original size:54 final size:53
Alignment explanation
Indices: 4262150--4262325 Score: 181
Period size: 54 Copynumber: 3.2 Consensus size: 53
4262140 CTCTTAAATA
*
4262150 TATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTT
1 TATTTTTAATGT-ATATATTTTATTTTTATTTATTATTATAATATTATATATTT
* * * * * * * *
4262204 TATTTTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATCTCTTAAAT
1 TATTTTTAATGTATATAT-TTTATTTTTATTTA-TTAT-TATAATATTATATATT---T
*
4262263 ATATTTTTAATGTGATATATTTTATTTTTATTTATTATTATAATCTTATATATTT
1 -TATTTTTAATGT-ATATATTTTATTTTTATTTATTATTATAATATTATATATTT
4262318 TATTTTTA
1 TATTTTTA
4262326 TTTTTTAATA
Statistics
Matches: 96, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
53 5 0.05
54 31 0.32
55 4 0.04
56 12 0.12
58 12 0.12
59 4 0.04
60 23 0.24
61 5 0.05
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (53 bp):
TATTTTTAATGTATATATTTTATTTTTATTTATTATTATAATATTATATATTT
Found at i:4262339 original size:12 final size:14
Alignment explanation
Indices: 4262308--4262412 Score: 58
Period size: 14 Copynumber: 7.6 Consensus size: 14
4262298 TATTATAATC
*
4262308 TTATATATTTTAT-
1 TTATATTTTTTATA
*
4262321 TTTTATTTTTTA-A
1 TTATATTTTTTATA
4262334 -TATATTTTTTATA
1 TTATATTTTTTATA
* *
4262347 TTATATATTTTATT
1 TTATATTTTTTATA
4262361 TTA-ATTTGTTT-TA
1 TTATATTT-TTTATA
* * * *
4262374 CCTATATTATATAAA
1 -TTATATTTTTTATA
*
4262389 TTTTAATTTTTTATA
1 TTAT-ATTTTTTATA
*
4262404 TTTTATTTT
1 TTATATTTT
4262413 AATTTTTTAT
Statistics
Matches: 68, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
12 10 0.15
13 15 0.22
14 28 0.41
15 15 0.22
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.69
Consensus pattern (14 bp):
TTATATTTTTTATA
Found at i:4262349 original size:114 final size:114
Alignment explanation
Indices: 4262094--4262325 Score: 437
Period size: 114 Copynumber: 2.0 Consensus size: 114
4262084 AAAATATAAG
*
4262094 TTTAATATATTTATATTTCTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
*
4262159 TGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
66 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
4262208 TTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
*
4262273 TGTGATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
4262322 TTTA
1 TTTA
4262326 TTTTTTAATA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (114 bp):
TTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
TGTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
Found at i:4262384 original size:72 final size:75
Alignment explanation
Indices: 4262260--4262422 Score: 174
Period size: 72 Copynumber: 2.2 Consensus size: 75
4262250 TCATCTCTTA
* * * *
4262260 AATATATTTTTAATGTGATATATTTTATTTTTATTTATTATTATAATCTTATAT-ATTTT-A-TT
1 AATATATTTTTTATATGATATATTTTATTTTAATTTATTATTATAATATTATATAATTTTAATTT
*
4262322 TTTATTTTTT
66 TTTATATTTT
* *
4262332 AATATATTTTTTATATTATATATTTTATTTTAATTTGTT-TTACCT-ATATTATATAAATTTTAA
1 AATATATTTTTTATATGATATATTTTATTTTAATTTATTATTA--TAATATTATAT-AATTTTAA
4262395 TTTTTTATATTTT
63 TTTTTTATATTTT
* *
4262408 ATTTTAATTTTTTAT
1 AATAT-ATTTTTTAT
4262423 TCTTATTTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
71 3 0.04
72 42 0.56
73 1 0.01
74 5 0.07
75 1 0.01
76 14 0.19
77 9 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (75 bp):
AATATATTTTTTATATGATATATTTTATTTTAATTTATTATTATAATATTATATAATTTTAATTT
TTTATATTTT
Found at i:4262404 original size:19 final size:20
Alignment explanation
Indices: 4262380--4262422 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4262370 TTTACCTATA
4262380 TTATA-TAAATTTTAATTTT
1 TTATATTAAATTTTAATTTT
**
4262399 TTATATTTTATTTTAATTTT
1 TTATATTAAATTTTAATTTT
4262419 TTAT
1 TTAT
4262423 TCTTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATATTAAATTTTAATTTT
Found at i:4262428 original size:19 final size:20
Alignment explanation
Indices: 4262388--4262440 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
4262378 TATTATATAA
*
4262388 ATTTTAATTTTTTATATTTT
1 ATTTTAATTTTTTATATCTT
4262408 ATTTTAATTTTTTAT-TCTT
1 ATTTTAATTTTTTATATCTT
4262427 ATTTTAATATTTTT
1 ATTTTAAT-TTTTT
4262441 TATTTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTAATTTTTTATATCTT
Found at i:4262428 original size:26 final size:25
Alignment explanation
Indices: 4262315--4262447 Score: 66
Period size: 24 Copynumber: 5.4 Consensus size: 25
4262305 ATCTTATATA
*
4262315 TTTTATTTT-TATTTT-TTAATATATT
1 TTTTATTTTATATTTTATT-TTA-ATT
4262340 TTTTATATTATATATTTTATTTTAATT
1 TTTTAT-TT-TATATTTTATTTTAATT
* *** * * *
4262367 TGTT-TTACCTATATTATATAAATT
1 TTTTATTTTATATTTTATTTTAATT
4262391 TTAATT-TTTTATATTTTATTTTAATT
1 TT--TTATTTTATATTTTATTTTAATT
* *
4262417 TTTTATTCT-TATTTTA--AT-ATT
1 TTTTATTTTATATTTTATTTTAATT
4262438 TTTTATTTTA
1 TTTTATTTTA
4262448 ATTATAACAA
Statistics
Matches: 82, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
21 11 0.13
22 1 0.01
24 22 0.27
25 10 0.12
26 21 0.26
27 7 0.09
28 8 0.10
29 2 0.02
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.70
Consensus pattern (25 bp):
TTTTATTTTATATTTTATTTTAATT
Found at i:4262453 original size:50 final size:50
Alignment explanation
Indices: 4262333--4262453 Score: 133
Period size: 50 Copynumber: 2.4 Consensus size: 50
4262323 TTATTTTTTA
*
4262333 ATATATTTTTTATATTA-TATATTTTATTTTAATTTGTTTTACCTATATT
1 ATATATTTTTTATTTTATTATATTTTATTTTAATTTGTTTTACCTATATT
* * * * *
4262382 ATATAAATTTTAATTTT-TTATATTTTATTTTAATTT-TTTATTCTTATTTT
1 ATAT-ATTTTTTATTTTATTATATTTTATTTTAATTTGTTT-TACCTATATT
4262432 A-ATATTTTTTATTTTAATTATA
1 ATATATTTTTTATTTT-ATTATA
4262454 ACAATATAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
48 10 0.17
49 9 0.15
50 40 0.68
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (50 bp):
ATATATTTTTTATTTTATTATATTTTATTTTAATTTGTTTTACCTATATT
Found at i:4263463 original size:25 final size:23
Alignment explanation
Indices: 4263435--4263495 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
4263425 TTTACATGTA
4263435 TAATTAAAAAATTCAAATAA-AATTT
1 TAATT-AAAAATT-AAA-AATAATTT
*
4263460 TAATTATAAATTAAAAATAATTT
1 TAATTAAAAATTAAAAATAATTT
4263483 TAACTTTAAAAAT
1 TAA--TTAAAAAT
4263496 AATTTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 11 0.35
24 6 0.19
25 12 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATTAAAAATTAAAAATAATTT
Found at i:4263472 original size:54 final size:54
Alignment explanation
Indices: 4263337--4263482 Score: 167
Period size: 53 Copynumber: 2.7 Consensus size: 54
4263327 TTCTCTCTCT
* * * *
4263337 AAATT-AAATTAAAATTTTAATATAAATTATGAA-ACTTAATATTGTAAATTTAA
1 AAATTCAAATTAAAATTTTAATATAAATTAT-AATAATTTACATTGTAAATTAAA
*
4263390 AAA-TCAAATTAAAGTTTTAATATAAATTATAATAATTTACA-TGTATAATTAAA
1 AAATTCAAATTAAAATTTTAATATAAATTATAATAATTTACATTGTA-AATTAAA
*
4263443 AAATTCAAA-TAAAATTTTAATTATAAATTAAAAATAATTT
1 AAATTCAAATTAAAATTTTAA-TATAAATT-ATAATAATTT
4263483 TAACTTTAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
52 7 0.09
53 51 0.64
54 13 0.16
55 9 0.11
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (54 bp):
AAATTCAAATTAAAATTTTAATATAAATTATAATAATTTACATTGTAAATTAAA
Done.