Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_pilon, 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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3383315 original size:23 final size:23
Alignment explanation
Indices: 3383289--3383363 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
3383279 AGTCGAGGAT
* *
3383289 TCTATATGGTCCTTTAGGATAAA
1 TCTATATGGTCCTTCAGGACAAA
* * *
3383312 TCTATGTGGTTCTTCGGGACAAA
1 TCTATATGGTCCTTCAGGACAAA
*
3383335 TCTATATGGTCATTC-GAGACAAA
1 TCTATATGGTCCTTCAG-GACAAA
3383358 TTCTAT
1 -TCTAT
3383364 GTGGCACTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.02
23 36 0.86
24 5 0.12
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (23 bp):
TCTATATGGTCCTTCAGGACAAA
Found at i:3383374 original size:24 final size:23
Alignment explanation
Indices: 3383309--3383374 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
3383299 CCTTTAGGAT
** *
3383309 AAATCTATGTGGTTCTTCGGGAC
1 AAATCTATGTGGCACTTCGAGAC
*
3383332 AAATCTATATGGTCA-TTCGAGAC
1 AAATCTATGTGG-CACTTCGAGAC
3383355 AAATTCTATGTGGCACTTCG
1 AAA-TCTATGTGGCACTTCG
3383375 GTGCAAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 23 0.66
24 12 0.34
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (23 bp):
AAATCTATGTGGCACTTCGAGAC
Found at i:3388485 original size:21 final size:20
Alignment explanation
Indices: 3388461--3388505 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3388451 AACATTATTG
3388461 ATACTGAT-TGAAGTAGTATCA
1 ATACTGATGTGAAG--GTATCA
*
3388482 ATACTGATGTGGAGGTATCA
1 ATACTGATGTGAAGGTATCA
3388502 ATAC
1 ATAC
3388506 CAAGAGCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (20 bp):
ATACTGATGTGAAGGTATCA
Found at i:3389250 original size:15 final size:15
Alignment explanation
Indices: 3389227--3389283 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
3389217 ACGTGAAAAA
3389227 TGATCTATGTGAATG
1 TGATCTATGTGAATG
* *
3389242 TGATATATGTAAATG
1 TGATCTATGTGAATG
* **
3389257 TGTTCTATGTGAAAA
1 TGATCTATGTGAATG
3389272 TG-TCTATGTGAA
1 TGATCTATGTGAA
3389284 CATGTAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
14 10 0.29
15 25 0.71
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (15 bp):
TGATCTATGTGAATG
Found at i:3389495 original size:24 final size:23
Alignment explanation
Indices: 3389417--3389496 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
3389407 AGTCGAGGGT
* *
3389417 TCTATGCGGTCATTCGGGACAAA
1 TCTATGTGGTCATTCAGGACAAA
* *
3389440 TCTATGTGGCCCTTCAGGACAAA
1 TCTATGTGGTCATTCAGGACAAA
* *
3389463 TCTATGTGGTCTTTCAGGAAAAA
1 TCTATGTGGTCATTCAGGACAAA
3389486 TTCTATGTGGT
1 -TCTATGTGGT
3389497 ACTTCGGTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 39 0.80
24 10 0.20
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (23 bp):
TCTATGTGGTCATTCAGGACAAA
Found at i:3392523 original size:30 final size:30
Alignment explanation
Indices: 3392487--3392547 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3392477 AGAGTCGAGT
*
3392487 GTTACCTATGTCCTTCGGAACATATGGATA
1 GTTACCTATGTCCTTCGAAACATATGGATA
**
3392517 GTTACCTATGTTTTTCGAAACATATGGATA
1 GTTACCTATGTCCTTCGAAACATATGGATA
3392547 G
1 G
3392548 GTCCTTCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGAAACATATGGATA
Found at i:3393713 original size:32 final size:32
Alignment explanation
Indices: 3393668--3393728 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3393658 CAAAGAGTCG
* *
3393668 AGGGTTACCTATGTCCTTTGGGATATATGAAT
1 AGGGTTACCTATGTCATTCGGGATATATGAAT
*
3393700 AGGGTTACTTATGTCATTCGGGATATATG
1 AGGGTTACCTATGTCATTCGGGATATATG
3393729 GACAATTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (32 bp):
AGGGTTACCTATGTCATTCGGGATATATGAAT
Found at i:3394976 original size:30 final size:31
Alignment explanation
Indices: 3394899--3394977 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
3394889 GAGTCGAGGG
* *
3394899 TTACCTATGTCCTTCGGGATATATGGATAGTG
1 TTACCTATGTCCTTCGGGATATATGGACAG-A
*
3394931 TTACTTATGTCCTTCGGGATATATGGACA-A
1 TTACCTATGTCCTTCGGGATATATGGACAGA
*
3394961 TTACCTATGTTCTTCGG
1 TTACCTATGTCCTTCGG
3394978 ACCATATAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 15 0.36
32 27 0.64
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGATATATGGACAGA
Found at i:3396072 original size:30 final size:30
Alignment explanation
Indices: 3396036--3396092 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3396026 GAGTCGAGTG
**
3396036 TTACCTATGTCTTTCGGGACATATGGACAA
1 TTACCTATGTCTTTCGAAACATATGGACAA
*
3396066 TTACCTATGTTTTTCGAAACATATGGA
1 TTACCTATGTCTTTCGAAACATATGGA
3396093 TAGGTCCTTC
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:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (30 bp):
TTACCTATGTCTTTCGAAACATATGGACAA
Found at i:3408497 original size:20 final size:20
Alignment explanation
Indices: 3408460--3408498 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3408450 ATTCCACCAT
*
3408460 ATGCAACTATAAGCTCCTAA
1 ATGCAACTATAAGATCCTAA
* *
3408480 ATGCATCTATATGATCCTA
1 ATGCAACTATAAGATCCTA
3408499 TATGGACTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (20 bp):
ATGCAACTATAAGATCCTAA
Found at i:3410677 original size:18 final size:18
Alignment explanation
Indices: 3410650--3410685 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3410640 TGGTAATCAT
*
3410650 ATACATAATTTCATTCAC
1 ATACAAAATTTCATTCAC
3410668 ATACAAAATTTCATTCAC
1 ATACAAAATTTCATTCAC
3410686 GTAAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (18 bp):
ATACAAAATTTCATTCAC
Found at i:3410693 original size:18 final size:18
Alignment explanation
Indices: 3410656--3410693 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3410646 TCATATACAT
*
3410656 AATTTCATTCACATACAA
1 AATTTCATTCACATAAAA
*
3410674 AATTTCATTCACGTAAAA
1 AATTTCATTCACATAAAA
3410692 AA
1 AA
3410694 GTTGTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (18 bp):
AATTTCATTCACATAAAA
Found at i:3412529 original size:197 final size:196
Alignment explanation
Indices: 3412235--3412709 Score: 688
Period size: 197 Copynumber: 2.4 Consensus size: 196
3412225 TTTTCATTTC
*
3412235 TTTTAAATTCCTAAAGTACCGATACTATGGTACATATACTTATAAACGTATCGATAC---TTTCA
1 TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAACGTATCGATACAAATTTCA
* *** * * *
3412297 ACAATTCCAAAAGCGTTTTACCGGTTTTGTCAAATTGAAATC-GATTTTGTCAAATTTCAACCTG
66 ACAATTTCGGTAGC-TTTTACCAGTTTTGTCAAATTGAAA-CAGATTTTGTCAAATTTAAACATG
* * *
3412361 TTATATTGTCATGTATCGATACATGTGTTTAAGGTATCGATACTTTATAGGTGCTATTATTGCAA
129 TTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGCTGCTACTATTGCAA
3412426 TTA
194 TTA
* *
3412429 TTTTAAATTCCAAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
1 TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAACGTATCGATACAAATTTCA
*
3412494 ACAATTTCGGTAGCTCTTTACCAGTTTTGTCAAATTGAAACAGGTTTTGTCAAATTTAAACATGT
66 ACAATTTCGGTAGCT-TTTACCAGTTTTGTCAAATTGAAACAGATTTTGTCAAATTTAAACATGT
* * *
3412559 TATATTGTCATGTATTGATAGATGTGTCTAAGGTATCGATACTTTATAGCTGCTACTATTGCAGT
130 TATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGCTGCTACTATTGCAAT
*
3412624 TC
195 TA
* * *
3412626 TTTTAAAATTCCTAAAGTATCGATACCTTGGTACATATACTTATAAACGTATTGATACAAATTTC
1 TTTT-AAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAACGTATCGATACAAATTTC
*
3412691 AACAATTTTGGTAGCTTTT
65 AACAATTTCGGTAGCTTTT
3412710 TACAGGTCTT
Statistics
Matches: 251, Mismatches: 24, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
194 54 0.22
196 2 0.01
197 125 0.50
198 70 0.28
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (196 bp):
TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAACGTATCGATACAAATTTCA
ACAATTTCGGTAGCTTTTACCAGTTTTGTCAAATTGAAACAGATTTTGTCAAATTTAAACATGTT
ATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGCTGCTACTATTGCAATT
A
Found at i:3412542 original size:20 final size:20
Alignment explanation
Indices: 3412517--3412555 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3412507 CTCTTTACCA
3412517 GTTTTGTCAAATTGAAACAG
1 GTTTTGTCAAATTGAAACAG
*
3412537 GTTTTGTCAAATTTAAACA
1 GTTTTGTCAAATTGAAACA
3412556 TGTTATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
GTTTTGTCAAATTGAAACAG
Found at i:3413114 original size:20 final size:20
Alignment explanation
Indices: 3413089--3413202 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
3413079 CCCTTTACCA
3413089 GTTTTGTCAAATTGAAATCG
1 GTTTTGTCAAATTGAAATCG
**
3413109 GTTTTGTCAAATTTCAA-CTG
1 GTTTTGTCAAATTGAAATC-G
* * **
3413129 GTTTTATCAATTTCCAATCG
1 GTTTTGTCAAATTGAAATCG
* ** *
3413149 ATTTTGTCAAATTCGTTA-CTT
1 GTTTTGTCAAATT-GAAATC-G
*
3413170 GTTTTGTCAAATTAAAATCG
1 GTTTTGTCAAATTGAAATCG
3413190 GATTTT-TCAAATT
1 G-TTTTGTCAAATT
3413203 TCAACATGTT
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.01
20 51 0.72
21 19 0.27
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
GTTTTGTCAAATTGAAATCG
Found at i:3413123 original size:197 final size:196
Alignment explanation
Indices: 3412718--3413126 Score: 649
Period size: 197 Copynumber: 2.1 Consensus size: 196
3412708 TTTACAGGTC
3412718 TTTT-TCAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTATAAGGTATCGATACTT
1 TTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTATAAGGTATCGATACTT
* * *
3412782 TATAGCCGCTATTATTGTAATTCTTTTAAATTCTACAGTACTGATACTTTGGTACATATACTTAT
66 TATAGCCGCTATTATTGCAATTATTTTAAATTCTACAATACTGATACTTTGGTACATATACTTAT
* *
3412847 AAATGTGTCCATACAAATTTCAACAATTTCGGTAGCTCTTTACCAGTTTTGCCAAATGGAAACCA
131 AAATGTATCCATACAAATTTCAACAATTTCGGTAGCCCTTTACCAGTTTTGCCAAATGGAAACCA
3412912 G
196 G
* * * * *
3412913 CTTTGTCAAATTTCAGCTTGTTATATTGTCATGTATTGATACATGTGTGTAAGGTATCGATACTT
1 TTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTATAAGGTATCGATACTT
* *
3412978 TATAGCCGCTATTATTGCAATTATTTTAAATTCCTACAATATTTATACTTTGGTACATATACTTA
66 TATAGCCGCTATTATTGCAATTATTTTAAATT-CTACAATACTGATACTTTGGTACATATACTTA
* * * *
3413043 TAAATGTATCGATACAAATTTCAACAATTTCGGTAGCCCTTTACCAGTTTTGTCAAATTGAAATC
130 TAAATGTATCCATACAAATTTCAACAATTTCGGTAGCCCTTTACCAGTTTTGCCAAATGGAAACC
*
3413108 GG
195 AG
3413110 TTTTGTCAAATTTCAAC
1 TTTTGTCAAATTTCAAC
3413127 TGGTTTTATC
Statistics
Matches: 193, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
195 3 0.02
196 86 0.45
197 104 0.54
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (196 bp):
TTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTATAAGGTATCGATACTT
TATAGCCGCTATTATTGCAATTATTTTAAATTCTACAATACTGATACTTTGGTACATATACTTAT
AAATGTATCCATACAAATTTCAACAATTTCGGTAGCCCTTTACCAGTTTTGCCAAATGGAAACCA
G
Found at i:3413189 original size:41 final size:40
Alignment explanation
Indices: 3413089--3413207 Score: 125
Period size: 40 Copynumber: 3.0 Consensus size: 40
3413079 CCCTTTACCA
* *
3413089 GTTTTGTCAAATTGAAATCGGTTTTGTCAAATTTCAACTG
1 GTTTTGTCAAATTAAAATCGATTTTGTCAAATTTCAACTG
* * ** * *
3413129 GTTTTATCAATTTCCAATCGATTTTGTCAAA-TTCGTTACTT
1 GTTTTGTCAAATTAAAATCGATTTTGTCAAATTTC--AACTG
3413170 GTTTTGTCAAATTAAAATCGGATTTT-TCAAATTTCAAC
1 GTTTTGTCAAATTAAAATC-GATTTTGTCAAATTTCAAC
3413208 ATGTTATATT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
39 3 0.05
40 28 0.44
41 23 0.37
42 9 0.14
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.45
Consensus pattern (40 bp):
GTTTTGTCAAATTAAAATCGATTTTGTCAAATTTCAACTG
Found at i:3425123 original size:21 final size:21
Alignment explanation
Indices: 3425093--3425140 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3425083 GCAGGGGTAC
* *
3425093 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
3425114 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
3425135 ATGCCA
1 ATGCCA
3425141 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:3425167 original size:42 final size:42
Alignment explanation
Indices: 3425120--3425237 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
3425110 TCATATGCCA
* * *
3425120 AGCCCACCAGTTTATATGCC-ATCTCCGCAGGGTTACATT-CT
1 AGCCCACCAGGTTACATGCCGAGC-CCGCAGGGTTACATTCCT
*
3425161 GAGCCCA-CAGGGTTACATTCCGAGCCCGCAGGGTTACATTCCT
1 -AGCCCACCA-GGTTACATGCCGAGCCCGCAGGGTTACATTCCT
* *
3425204 AGCCCGCCAGGTTACATGCCTAGCCCGCAGGGTT
1 AGCCCACCAGGTTACATGCCGAGCCCGCAGGGTT
3425238 TTATACCATA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
41 2 0.03
42 57 0.88
43 6 0.09
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.23
Consensus pattern (42 bp):
AGCCCACCAGGTTACATGCCGAGCCCGCAGGGTTACATTCCT
Found at i:3425173 original size:21 final size:21
Alignment explanation
Indices: 3425147--3425237 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
3425137 GCCATCTCCG
*
3425147 CAGGGTTACATTCTGAGCCCA
1 CAGGGTTACATTCCGAGCCCA
*
3425168 CAGGGTTACATTCCGAGCCCG
1 CAGGGTTACATTCCGAGCCCA
* *
3425189 CAGGGTTACATTCCTAGCCCGC
1 CAGGGTTACATTCCGAGCCC-A
* * *
3425211 CA-GGTTACATGCCTAGCCCG
1 CAGGGTTACATTCCGAGCCCA
3425231 CAGGGTT
1 CAGGGTT
3425238 TTATACCATA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.20, C:0.32, G:0.26, T:0.22
Consensus pattern (21 bp):
CAGGGTTACATTCCGAGCCCA
Found at i:3425841 original size:33 final size:33
Alignment explanation
Indices: 3425757--3425858 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
3425747 AATGTTTTTA
*
3425757 AAATACAAATTATATTATTCAAAATTTAAAA-T
1 AAATATAAATTATATTATTCAAAATTTAAAATT
* *
3425789 AAAAATAAA-AATAATTATTCAAAATTTAAAATT
1 AAATATAAATTAT-ATTATTCAAAATTTAAAATT
* * *
3425822 AAATATAAATTATAGTATTCGAAATTTAACATT
1 AAATATAAATTATATTATTCAAAATTTAAAATT
3425855 AAAT
1 AAAT
3425859 TTCAACTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 30 0.51
34 2 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (33 bp):
AAATATAAATTATATTATTCAAAATTTAAAATT
Found at i:3426472 original size:127 final size:128
Alignment explanation
Indices: 3426217--3426816 Score: 1029
Period size: 127 Copynumber: 4.7 Consensus size: 128
3426207 ACAATCCATC
* * *
3426217 TAGTGTCCCCGAGGGACATGAGGGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAGT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
3426282 GGAAGGCGTG-CCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
3426344 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
**
3426409 GGAAGGTACGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATA-GAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
3426471 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATATAA
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAA-ATAA
*
3426536 ---AAGGCGCGCCCCCGGGAACGCGCCTTC-AGTCCCCTGAGAAAT-ATAGGTACTGATAT-ATC
65 TGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGA-A
3426595 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
3426660 AGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGT-CCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
3426722 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
3426787 GGAAGGTGCGCCCCCGAGAACGCGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
3426817 TGTGAATAGT
Statistics
Matches: 450, Mismatches: 13, Indels: 20
0.93 0.03 0.04
Matches are distributed among these distances:
123 18 0.04
124 75 0.17
125 25 0.06
126 38 0.08
127 241 0.54
128 53 0.12
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:3426674 original size:251 final size:252
Alignment explanation
Indices: 3426217--3426816 Score: 994
Period size: 251 Copynumber: 2.4 Consensus size: 252
3426207 ACAATCCATC
* *
3426217 TAGTGTCCCCGAGGGACATGAGGGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAGT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC-AAATA-T
** *
3426282 GGAAGGCGTG-CCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
64 AAAAGGCGCGCCCCCGGGAACGCGCCTTC-AGTCCCCTGAGAAATAATAGGTACTGATATGAATA
*
3426346 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
128 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAG
*
3426411 AAGGTACGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATA-GAA
193 AAGGCACGCCCCCGGGAACGCGCCTTCAAGT-CCCTGAGAAATAATAGGTACTGATATGAA
3426471 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATATAA
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATATAA
*
3426536 AAGGCGCGCCCCCGGGAACGCGCCTTCAGTCCCCTGAGAAAT-ATAGGTACTGATAT-ATCTAGT
66 AAGGCGCGCCCCCGGGAACGCGCCTTCAGTCCCCTGAGAAATAATAGGTACTGATATGA-ATAGT
3426599 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAA
130 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAA
*
3426664 GGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCTGAGAAATAATAGGTACTGATATGAA
195 GGCACGCCCCCGGGAACGCGCCTTCAAGTCCCTGAGAAATAATAGGTACTGATATGAA
3426722 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAA-ATAA
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATATAA
* *
3426786 TGGAAGGTGCGCCCCCGAGAACGCGCCTTCA
66 ---AAGGCGCGCCCCCGGGAACGCGCCTTCA
3426817 TGTGAATAGT
Statistics
Matches: 329, Mismatches: 11, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
250 30 0.09
251 172 0.52
252 23 0.07
253 49 0.15
254 55 0.17
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (252 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAATATAA
AAGGCGCGCCCCCGGGAACGCGCCTTCAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGTG
TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAG
GCACGCCCCCGGGAACGCGCCTTCAAGTCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:3426916 original size:15 final size:17
Alignment explanation
Indices: 3426897--3426936 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
3426887 TCACAAGCTT
3426897 TCAAATTCTC-AAATTC
1 TCAAATTCTCTAAATTC
*
3426913 -CAAA-ACTCTAAATTC
1 TCAAATTCTCTAAATTC
3426928 TCAAATTCT
1 TCAAATTCT
3426937 GAAAATGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 5
0.73 0.08 0.19
Matches are distributed among these distances:
14 3 0.16
15 10 0.53
16 4 0.21
17 2 0.11
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (17 bp):
TCAAATTCTCTAAATTC
Found at i:3428284 original size:167 final size:165
Alignment explanation
Indices: 3427988--3428320 Score: 591
Period size: 167 Copynumber: 2.0 Consensus size: 165
3427978 TCAGTTAAGT
3427988 CCGAGTTTGATCGATCTAACATGGAGAAATCTGTCTGCTATGCTCCAACGTGACAACGGATGTCA
1 CCGAGTTTGATCGATCTAACATGGAGAAATCTGTCTGCTATGCTCCAACGTGACAACGGATGTCA
3428053 AGGATGGTCCGTGTATCAAAGAGGAAGAGGAAACAACTTATGGGAACTAACCAGATACAACGGTC
66 AGGATGGTCCGTGTATCAAAGAGGAAGAGGAAACAACTTATGGGAACTAACCAGATACAACGGTC
3428118 CTCATACA-TTGTGCAACA-GTATAAACCAGGATC
131 CTCATACAGTTGTGCAACAGGTATAAACCAGGATC
3428151 CCGAG-TTGATCGATCTAACATGGAGAAATCTGTCTGCTACTGCGTCCAACGTGACAACGGATGT
1 CCGAGTTTGATCGATCTAACATGGAGAAATCTGTCTGCTA-TGC-TCCAACGTGACAACGGATGT
3428215 CAATGGATGGTCCGTGTATCAAAGAGGAAGAGGAAGAACAACTTATGGGAACTAACCAGATACAA
64 CAA-GGATGGTCCGTGTATCAAAGAGGAAGAGG-A-AACAACTTATGGGAACTAACCAGATACAA
3428280 CGGTCCTCATACATGTTGTGCAACAGGTATAAACCAGGATC
126 CGGTCCTCATACA-GTTGTGCAACAGGTATAAACCAGGATC
3428321 ATCCCAACTT
Statistics
Matches: 162, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
162 34 0.21
163 8 0.05
164 23 0.14
165 29 0.18
166 1 0.01
167 42 0.26
169 10 0.06
170 15 0.09
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (165 bp):
CCGAGTTTGATCGATCTAACATGGAGAAATCTGTCTGCTATGCTCCAACGTGACAACGGATGTCA
AGGATGGTCCGTGTATCAAAGAGGAAGAGGAAACAACTTATGGGAACTAACCAGATACAACGGTC
CTCATACAGTTGTGCAACAGGTATAAACCAGGATC
Found at i:3432792 original size:2 final size:2
Alignment explanation
Indices: 3432787--3432821 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3432777 TTTATCATTA
3432787 AT AT AT AT -T AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3432822 ATGATATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3432805 original size:13 final size:12
Alignment explanation
Indices: 3432787--3432821 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
3432777 TTTATCATTA
3432787 ATATATAT-TAT
1 ATATATATATAT
3432798 ATATATATATAT
1 ATATATATATAT
3432810 -TATATATATAT
1 ATATATATATAT
3432821 A
1 A
3432822 ATGATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATATATATAT
Found at i:3432807 original size:15 final size:15
Alignment explanation
Indices: 3432787--3432821 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3432777 TTTATCATTA
3432787 ATATATATTATATAT
1 ATATATATTATATAT
3432802 ATATATATTATATAT
1 ATATATATTATATAT
3432817 ATATA
1 ATATA
3432822 ATGATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATTATATAT
Found at i:3434161 original size:16 final size:18
Alignment explanation
Indices: 3434122--3434161 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
3434112 AGTGCTACTT
*
3434122 TAATTATCTTAAATATTC
1 TAATTATCTTAAATATTA
3434140 TAATTA-CTTAAAT-TTA
1 TAATTATCTTAAATATTA
3434156 TAATTA
1 TAATTA
3434162 GTATATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 7 0.33
18 6 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTATCTTAAATATTA
Found at i:3434520 original size:2 final size:2
Alignment explanation
Indices: 3434515--3434548 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3434505 AATAAAGGGG
3434515 AT AT AT AT AT 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 AT AT
3434549 CAGTTGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3435166 original size:2 final size:2
Alignment explanation
Indices: 3435088--3435149 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
3435078 ACAATAACAA
3435088 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT
3435130 AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
3435150 ATTTGTATTG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3448057 original size:24 final size:21
Alignment explanation
Indices: 3448029--3448073 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 21
3448019 AAAAGTCAAA
3448029 TTAAAAATCATATTGATAGAAATT
1 TTAAAAATCA-A-TGATA-AAATT
*
3448053 TTAAATATCAATGATAAAATT
1 TTAAAAATCAATGATAAAATT
3448074 AAATTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 1 0.05
24 9 0.45
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (21 bp):
TTAAAAATCAATGATAAAATT
Found at i:3451027 original size:23 final size:25
Alignment explanation
Indices: 3450983--3451031 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
3450973 ATTTATAAAC
3450983 AGTTTAATATCATTTAACTATTTAA
1 AGTTTAATATCATTTAACTATTTAA
3451008 AGTTTAA-ATC-TTTATA-TATTTAA
1 AGTTTAATATCATTTA-ACTATTTAA
3451031 A
1 A
3451032 AAAATATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.52
24 4 0.17
25 7 0.30
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (25 bp):
AGTTTAATATCATTTAACTATTTAA
Found at i:3451319 original size:35 final size:35
Alignment explanation
Indices: 3451273--3451349 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
3451263 ATATACTACT
3451273 TTTTTATGACCTATGGATGTCTTTATTGTGATTTG
1 TTTTTATGACCTATGGATGTCTTTATTGTGATTTG
*
3451308 TTTTTATGACCTATGGATGTCTTTGTTGTGATTTG
1 TTTTTATGACCTATGGATGTCTTTATTGTGATTTG
3451343 TTTTTAT
1 TTTTTAT
3451350 AAATTATAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.16, C:0.08, G:0.19, T:0.57
Consensus pattern (35 bp):
TTTTTATGACCTATGGATGTCTTTATTGTGATTTG
Found at i:3454608 original size:9 final size:9
Alignment explanation
Indices: 3454594--3454625 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3454584 TTCTCATCAT
3454594 TTATTTTTA
1 TTATTTTTA
3454603 TTA-TTTTA
1 TTATTTTTA
3454611 TTATTTTTA
1 TTATTTTTA
3454620 TTATTT
1 TTATTT
3454626 CTAAATCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTTA
Found at i:3458870 original size:19 final size:16
Alignment explanation
Indices: 3458828--3458861 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3458818 TCTCATATGT
*
3458828 TCACATAGATCACATA
1 TCACATAGATAACATA
3458844 TCACATAGAATAACATA
1 TCACATAG-ATAACATA
3458861 T
1 T
3458862 AACACATAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (16 bp):
TCACATAGATAACATA
Found at i:3461583 original size:19 final size:19
Alignment explanation
Indices: 3461559--3461608 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3461549 ACTGTTCACT
*
3461559 GTACTATTCATATAATATA
1 GTACTATTCATACAATATA
3461578 GTACTATTCATACAATATA
1 GTACTATTCATACAATATA
*
3461597 ATACTATTCATA
1 GTACTATTCATA
3461609 AAAACATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (19 bp):
GTACTATTCATACAATATA
Found at i:3466660 original size:13 final size:13
Alignment explanation
Indices: 3466642--3466680 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3466632 TAGTGGAGAC
*
3466642 TTGATTATTTATG
1 TTGATTAGTTATG
*
3466655 TTGATTAGTTATA
1 TTGATTAGTTATG
3466668 TTGATTAGTTATG
1 TTGATTAGTTATG
3466681 GCTTGAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (13 bp):
TTGATTAGTTATG
Found at i:3468057 original size:23 final size:22
Alignment explanation
Indices: 3468014--3468100 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 22
3468004 GAGGTGCCAT
*
3468014 GTAGAAATTGT-CTAAAGGACCAC
1 GTAGAAA-TGTCCCAAA-GACCAC
* *
3468037 ATAGAAATGTCCCGAAAGACCGC
1 GTAGAAATGTCCC-AAAGACCAC
* *
3468060 GTAGATATGTCACAAAGGACCAC
1 GTAGAAATGTCCCAAA-GACCAC
*
3468083 GTAGAATTGTCCCAAAGA
1 GTAGAAATGTCCCAAAGA
3468101 ACTGCGTAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
22 8 0.16
23 40 0.78
24 3 0.06
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (22 bp):
GTAGAAATGTCCCAAAGACCAC
Found at i:3468064 original size:46 final size:46
Alignment explanation
Indices: 3468014--3468111 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 46
3468004 GAGGTGCCAT
*
3468014 GTAGAAATTGTC-TAAAGGACCACATAGAAATGTCCCGAAAG-ACCGC
1 GTAGAAA-TGTCACAAAGGACCACATAGAAATGTCCC-AAAGAACCGC
* * * *
3468060 GTAGATATGTCACAAAGGACCACGTAGAATTGTCCCAAAGAACTGC
1 GTAGAAATGTCACAAAGGACCACATAGAAATGTCCCAAAGAACCGC
3468106 GTAGAA
1 GTAGAA
3468112 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
45 8 0.18
46 36 0.82
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.18
Consensus pattern (46 bp):
GTAGAAATGTCACAAAGGACCACATAGAAATGTCCCAAAGAACCGC
Found at i:3468108 original size:23 final size:22
Alignment explanation
Indices: 3468038--3468111 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
3468028 AAGGACCACA
*
3468038 TAGAAATGTCCCGAAAGACCGCG
1 TAGAATTGTCCC-AAAGACCGCG
* *
3468061 TAG-ATATGTCACAAAGGACCACG
1 TAGAAT-TGTCCCAAA-GACCGCG
*
3468084 TAGAATTGTCCCAAAGAACTGCG
1 TAGAATTGTCCCAAAG-ACCGCG
3468107 TAGAA
1 TAGAA
3468112 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
22 5 0.12
23 34 0.83
24 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.18
Consensus pattern (22 bp):
TAGAATTGTCCCAAAGACCGCG
Found at i:3474964 original size:24 final size:23
Alignment explanation
Indices: 3474937--3474988 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
3474927 TGCACCAAAG
3474937 TAGAAATTGTCCCGAATGACCACA
1 TAGAAA-TGTCCCGAATGACCACA
** *
3474961 TAGAAATGTCTTGAATGACCGCA
1 TAGAAATGTCCCGAATGACCACA
3474984 TAGAA
1 TAGAA
3474989 CCCTTGACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (23 bp):
TAGAAATGTCCCGAATGACCACA
Found at i:3476495 original size:90 final size:88
Alignment explanation
Indices: 3476343--3476514 Score: 281
Period size: 90 Copynumber: 1.9 Consensus size: 88
3476333 ACACACCCTT
3476343 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAAATAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAAATAAATCTATATTTA
*
3476408 ATTAATTGGAATTTAATAATCCTC
66 ATTAATT-GAATTAAATAATCCTC
* * * *
3476432 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATTTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAAATAAATCTATATTT
3476497 AATTAATTGAATTAAATA
65 AATTAATTGAATTAAATA
3476515 TTCGGGATTA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 38 0.49
90 39 0.51
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAAATAAATCTATATTTA
ATTAATTGAATTAAATAATCCTC
Found at i:3478810 original size:24 final size:24
Alignment explanation
Indices: 3478728--3478822 Score: 75
Period size: 24 Copynumber: 4.0 Consensus size: 24
3478718 ATTTTTTATT
* * *
3478728 TGAATTCTGTTTTGACATCTGATC
1 TGAATTATGTTATGATATCTGATC
* * *
3478752 TGAAATATGTTATGAT-TCCTAACC
1 TGAATTATGTTATGATAT-CTGATC
* * *
3478776 TGGATTCTGTTATGATATATGATC
1 TGAATTATGTTATGATATCTGATC
* *
3478800 TGAATTATGTTTTGATTTCTGAT
1 TGAATTATGTTATGATATCTGAT
3478823 ATATCCATTT
Statistics
Matches: 52, Mismatches: 17, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 50 0.96
25 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (24 bp):
TGAATTATGTTATGATATCTGATC
Found at i:3478990 original size:2 final size:2
Alignment explanation
Indices: 3478983--3479015 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3478973 CGGATGGGGG
3478983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3479016 TAAAAGATCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3481352 original size:37 final size:37
Alignment explanation
Indices: 3481310--3481388 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
3481300 CAATAATCAA
*
3481310 AATAAAATTACTTCTAAAATAGTGTCACACACTATAC
1 AATAAAATTACTTCTAAAATAGTGACACACACTATAC
* *
3481347 AATAAAATTACTTCTAAAATAGTGACCCACACTGTAC
1 AATAAAATTACTTCTAAAATAGTGACACACACTATAC
3481384 AATAA
1 AATAA
3481389 CTTTATCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (37 bp):
AATAAAATTACTTCTAAAATAGTGACACACACTATAC
Found at i:3483036 original size:14 final size:15
Alignment explanation
Indices: 3483017--3483060 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
3483007 CGTTCGATTA
*
3483017 TATGTTCGTTTAT-T
1 TATGTTCATTTATGT
3483031 TATGTTCATTTATGT
1 TATGTTCATTTATGT
3483046 T-TGTTCATTTATGT
1 TATGTTCATTTATGT
3483060 T
1 T
3483061 CGAATATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 26 0.93
15 2 0.07
ACGTcount: A:0.16, C:0.07, G:0.14, T:0.64
Consensus pattern (15 bp):
TATGTTCATTTATGT
Found at i:3483055 original size:24 final size:26
Alignment explanation
Indices: 3483008--3483068 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
3482998 GTTCGTGAAC
*
3483008 GTTCGATTATATGTTCGTTTATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
*
3483034 GTTC-ATT-TATGTTTGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
*
3483058 GTTCGAATATA
1 GTTCGATTATA
3483069 GGGCAAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 19 0.63
25 5 0.17
26 6 0.20
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (26 bp):
GTTCGATTATATGTTCGTTCATTTAT
Found at i:3483338 original size:10 final size:10
Alignment explanation
Indices: 3483338--3483367 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3483328 GTTTATGTTC
*
3483338 GTTCGTTTGT
1 GTTCGTTTAT
3483348 GTTCGTTTAT
1 GTTCGTTTAT
3483358 GTTCGTTTAT
1 GTTCGTTTAT
3483368 CATTTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:3483343 original size:14 final size:13
Alignment explanation
Indices: 3483320--3483360 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3483310 TTTGTGGTTG
3483320 TGTTGTTCGTTTA
1 TGTTGTTCGTTTA
3483333 TGTTCGTTCG-TT-
1 TGTT-GTTCGTTTA
3483345 TG-TGTTCGTTTA
1 TGTTGTTCGTTTA
3483357 TGTT
1 TGTT
3483361 CGTTTATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 5 0.21
11 3 0.12
12 4 0.17
13 7 0.29
14 5 0.21
ACGTcount: A:0.05, C:0.10, G:0.24, T:0.61
Consensus pattern (13 bp):
TGTTGTTCGTTTA
Found at i:3483466 original size:16 final size:16
Alignment explanation
Indices: 3483445--3483475 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3483435 AATTTTTTTG
3483445 TTCGTTTATGTTCGTA
1 TTCGTTTATGTTCGTA
3483461 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
3483476 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTA
Found at i:3484798 original size:26 final size:27
Alignment explanation
Indices: 3484750--3484805 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
3484740 GGACATATTT
3484750 AATTTAATTTTAAAAAAATAAAATAAA
1 AATTTAATTTTAAAAAAATAAAATAAA
* *
3484777 AATTTAATTTT-AAAATATAAAATATA
1 AATTTAATTTTAAAAAAATAAAATAAA
3484803 AAT
1 AAT
3484806 GATTATTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AATTTAATTTTAAAAAAATAAAATAAA
Found at i:3486017 original size:2 final size:2
Alignment explanation
Indices: 3486010--3486034 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3486000 GTCACTTCCC
3486010 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
3486035 GTATGTATGT
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:3487298 original size:36 final size:34
Alignment explanation
Indices: 3487245--3487319 Score: 80
Period size: 36 Copynumber: 2.1 Consensus size: 34
3487235 CAAAGGGCTC
*
3487245 GTTCGTTCATTTACGTTCGTGAATGTTCGATTATAT
1 GTTCGTTCATTTACGTTCATGAATGTTC-ATT-TAT
* **
3487281 GTTCGTTTATGTT-CGTTCATTTATGTTCATTTAT
1 GTTCGTTCAT-TTACGTTCATGAATGTTCATTTAT
3487315 GTTCG
1 GTTCG
3487320 AAAAGATGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
34 8 0.24
35 3 0.09
36 21 0.62
37 2 0.06
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.52
Consensus pattern (34 bp):
GTTCGTTCATTTACGTTCATGAATGTTCATTTAT
Found at i:3487313 original size:24 final size:26
Alignment explanation
Indices: 3487269--3487319 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
3487259 GTTCGTGAAT
*
3487269 GTTCGATTATATGTTCGTTTATGTTC
1 GTTCGATTATATGTTCATTTATGTTC
3487295 GTTC-ATT-TATGTTCATTTATGTTC
1 GTTCGATTATATGTTCATTTATGTTC
3487319 G
1 G
3487320 AAAAGATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.71
25 3 0.12
26 4 0.17
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.55
Consensus pattern (26 bp):
GTTCGATTATATGTTCATTTATGTTC
Found at i:3487597 original size:10 final size:10
Alignment explanation
Indices: 3487580--3487683 Score: 73
Period size: 10 Copynumber: 9.1 Consensus size: 10
3487570 GTGTTTGTGT
3487580 TGTTCGTTTA
1 TGTTCGTTTA
*
3487590 TATTCGTTTA
1 TGTTCGTTTA
3487600 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
3487613 TGTTCGTTTATTA
1 TGTTCG--T-TTA
3487626 TGTTCGTTTATTA
1 TGTTCG--T-TTA
3487639 TGTTCGTTTA
1 TGTTCGTTTA
*
3487649 TGTTTGTTCGTTTG
1 ----TGTTCGTTTA
3487663 TGTTCGTTTA
1 TGTTCGTTTA
3487673 TGTTCGTTTA
1 TGTTCGTTTA
3487683 T
1 T
3487684 CATTTAAATG
Statistics
Matches: 80, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
10 38 0.47
11 1 0.01
12 1 0.01
13 31 0.39
14 9 0.11
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:3487606 original size:23 final size:23
Alignment explanation
Indices: 3487580--3487673 Score: 107
Period size: 23 Copynumber: 3.9 Consensus size: 23
3487570 GTGTTTGTGT
*
3487580 TGTTCGTTTATATTCGTTTATTG
1 TGTTCGTTTATATTCGTTTATTA
*
3487603 TGTTCGTTTATGTTCGTTTATTA
1 TGTTCGTTTATATTCGTTTATTA
*
3487626 TGTTCGTTTATTATGTTCGTTTATGTT
1 TGTTCGTTTA-TA--TTCGTTTAT-TA
* *
3487653 TGTTCGTTTGTGTTCGTTTAT
1 TGTTCGTTTATATTCGTTTAT
3487674 GTTCGTTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
23 31 0.51
24 10 0.16
26 10 0.16
27 10 0.16
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.62
Consensus pattern (23 bp):
TGTTCGTTTATATTCGTTTATTA
Found at i:3487610 original size:13 final size:13
Alignment explanation
Indices: 3487580--3487661 Score: 95
Period size: 13 Copynumber: 6.7 Consensus size: 13
3487570 GTGTTTGTGT
3487580 TGTTCGTTTA-TA
1 TGTTCGTTTATTA
*
3487592 --TTCGTTTATTG
1 TGTTCGTTTATTA
3487603 TGTTCG--T-TTA
1 TGTTCGTTTATTA
3487613 TGTTCGTTTATTA
1 TGTTCGTTTATTA
3487626 TGTTCGTTTATTA
1 TGTTCGTTTATTA
*
3487639 TGTTCGTTTATGTT
1 TGTTCGTTTAT-TA
3487653 TGTTCGTTT
1 TGTTCGTTT
3487662 GTGTTCGTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
10 16 0.27
11 2 0.03
12 1 0.02
13 31 0.52
14 10 0.17
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (13 bp):
TGTTCGTTTATTA
Found at i:3515597 original size:23 final size:23
Alignment explanation
Indices: 3515563--3515625 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
3515553 CATCTTATCT
*
3515563 GGCACTTTGGTGCATTTCTACGC
1 GGCACTTAGGTGCATTTCTACGC
* *
3515586 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTAGGTGCATTTCTACGC
* *
3515609 GGCACTTCGGTGTATTT
1 GGCACTTAGGTGCATTT
3515626 ATATGAGCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (23 bp):
GGCACTTAGGTGCATTTCTACGC
Found at i:3552171 original size:147 final size:142
Alignment explanation
Indices: 3551858--3552120 Score: 395
Period size: 147 Copynumber: 1.8 Consensus size: 142
3551848 AACCCGCTAC
* *
3551858 CCCTTTTCTTTTACGACTTTGAGAGCTCTGGACGTGACACTCATTCACCTCATCAGTTTGTTCCT
1 CCCTTTTATTGTACGACTTTGAGAGCTCTGGACGTGACACTCATTCACCTCATCAGTTTGTTCCT
*
3551923 TTTGATCGGTTGGGTTTTTAGAAGTGTCTTTCAAGTTTCCTTTGCTGATTGCATTCTTTGGACGT
66 TTTGATCGGTTGGG-TTTTAGAAGTGTCTTTCAAGTTTCCTTTGCTGATTGCATTCATT-GACGT
* * *
3551988 CTCGAGTAACCCGCTAC
129 CTCCAG--A-CCGATAA
* *
3552005 CCCTTTTCTTTTACGACTTTGAGAGCTCTGGACGTGACACTCATTCACCTCATCAGTTT-TTCCT
1 CCCTTTTATTGTACGACTTTGAGAGCTCTGGACGTGACACTCATTCACCTCATCAGTTTGTTCCT
3552069 TTTGATCGGTTGGG-TTTAGAAGTGTCTTTCAAGTTTCCTTTGCTGATTGCAT
66 TTTGATCGGTTGGGTTTTAGAAGTGTCTTTCAAGTTTCCTTTGCTGATTGCAT
3552121 CCTCAATTAC
Statistics
Matches: 116, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
144 38 0.33
146 19 0.16
147 59 0.51
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.41
Consensus pattern (142 bp):
CCCTTTTATTGTACGACTTTGAGAGCTCTGGACGTGACACTCATTCACCTCATCAGTTTGTTCCT
TTTGATCGGTTGGGTTTTAGAAGTGTCTTTCAAGTTTCCTTTGCTGATTGCATTCATTGACGTCT
CCAGACCGATAA
Found at i:3558327 original size:210 final size:212
Alignment explanation
Indices: 3558088--3558511 Score: 818
Period size: 211 Copynumber: 2.0 Consensus size: 212
3558078 TTTGATCATG
3558088 TAAACAAAAAAGTGAATTTTACAATATTCAAAAACACCCAAATTAATTAAATT-AAATTACCTAG
1 TAAACAAAAAAGTGAATTTTACAATATTCAAAAACACCCAAATTAATTAAATTAAAATTACCTAG
3558152 TCA-TTTAGAAAAGATAAAGAATGTTCGATTATTTACAAATATCGAGACCAGATCTTAAAATTTA
66 TCATTTTAG-AAAGATAAAGAATGTTCGATTATTTACAAATATCGAGACCAGATCTTAAAATTTA
3558216 TAACAACCTTTTCTCGATAAATTTAAATAAACGAACATTTCCTTTTCTTTCGTTCCCAAATTTT-
130 TAACAACCTTTTCTCGATAAATTTAAATAAACGAACATTTCCTTTTCTTTCGTTCCCAAATTTTA
3558280 GAGTGATGGATCAATTTT
195 GAGTGATGGATCAATTTT
3558298 TAAACAAAAAAGTGAATTTTACAATATTCAAAAACACCCAAATTAATTAAATTAAAATTACCTAG
1 TAAACAAAAAAGTGAATTTTACAATATTCAAAAACACCCAAATTAATTAAATTAAAATTACCTAG
3558363 TCATTTTAGAAAGATAAAGAATGTTCGATTATTTACAAATATCGAGACCAGATCTTAAAATTTAT
66 TCATTTTAGAAAGATAAAGAATGTTCGATTATTTACAAATATCGAGACCAGATCTTAAAATTTAT
3558428 AACAACCTTTTCTCGATAAATTTAAATAAACGAACATTTCCTTTTCTTTCGTTCCCAAATTTTAG
131 AACAACCTTTTCTCGATAAATTTAAATAAACGAACATTTCCTTTTCTTTCGTTCCCAAATTTTAG
3558493 AGTGATGGATCAATTTT
196 AGTGATGGATCAATTTT
3558510 TA
1 TA
3558512 GGCGTCACTA
Statistics
Matches: 211, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
210 53 0.25
211 133 0.63
212 25 0.12
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (212 bp):
TAAACAAAAAAGTGAATTTTACAATATTCAAAAACACCCAAATTAATTAAATTAAAATTACCTAG
TCATTTTAGAAAGATAAAGAATGTTCGATTATTTACAAATATCGAGACCAGATCTTAAAATTTAT
AACAACCTTTTCTCGATAAATTTAAATAAACGAACATTTCCTTTTCTTTCGTTCCCAAATTTTAG
AGTGATGGATCAATTTT
Found at i:3560720 original size:53 final size:53
Alignment explanation
Indices: 3560618--3560879 Score: 292
Period size: 53 Copynumber: 4.9 Consensus size: 53
3560608 TCTTCGAATG
* * * * * ***
3560618 ACGGGTCCGCTCCCTCTTG-TTCATGGATTAAGGAGCTCAAACAATCTTCTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTACTT
* * * * * * *
3560672 ATGAGTTTGCTCCCTATTGCTTCAGGGAGTAGAATTCGAATAATCTTCTGCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
* *
3560725 ACGGGTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATATTCTACTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
* * * * *
3560778 ACGGGTTCGCTCCCTCTTACTTCAAGGAGTAGAACTCGAACAATCGTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
*
3560831 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATTTTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
3560880 GGTGTAATTC
Statistics
Matches: 172, Mismatches: 35, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
53 149 0.87
54 15 0.09
55 8 0.05
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACTT
Found at i:3561343 original size:41 final size:42
Alignment explanation
Indices: 3561291--3561399 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
3561281 GGTGTGAAAA
* *
3561291 CATCTTACCCGAAGGACTTA-TGGATGACAC-GAAGGATTT-AT
1 CATCTTGCCCGAAAGACTTACT-GATGAC-CTGAAGGATTTCAT
* *
3561332 CATCTTGCCCGAACGACTTACTGATGGCCTGAAGGATTTCAT
1 CATCTTGCCCGAAAGACTTACTGATGACCTGAAGGATTTCAT
* *
3561374 CATCATGCTCGAAAGACTTACTGATG
1 CATCTTGCCCGAAAGACTTACTGATG
3561400 GCACTTACTG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.02
41 32 0.54
42 26 0.44
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (42 bp):
CATCTTGCCCGAAAGACTTACTGATGACCTGAAGGATTTCAT
Found at i:3561392 original size:42 final size:41
Alignment explanation
Indices: 3561321--3561401 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
3561311 TGGATGACAC
* *
3561321 GAAGGATTTATCATCTTGCCCGAACGACTTACTGATGGCCT
1 GAAGGATTTATCATCATGCCCGAAAGACTTACTGATGGCCT
*
3561362 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 GAAGGATTT-ATCATCATGCCCGAAAGACTTACTGATGGC
3561402 ACTTACTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 9 0.25
42 27 0.75
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (41 bp):
GAAGGATTTATCATCATGCCCGAAAGACTTACTGATGGCCT
Found at i:3561407 original size:13 final size:13
Alignment explanation
Indices: 3561389--3561413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3561379 TGCTCGAAAG
3561389 ACTTACTGATGGC
1 ACTTACTGATGGC
3561402 ACTTACTGATGG
1 ACTTACTGATGG
3561414 ATTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:3561535 original size:80 final size:80
Alignment explanation
Indices: 3561402--3561573 Score: 317
Period size: 80 Copynumber: 2.1 Consensus size: 80
3561392 TACTGATGGC
*
3561402 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAATGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
3561467 CATCATGCTCGAAAG
66 CATCATGCTCGAAAG
* *
3561482 ACTTACTGATGGGTTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
3561547 CATCATGCTCGAAAG
66 CATCATGCTCGAAAG
3561562 ACTTACTGATGG
1 ACTTACTGATGG
3561574 CCTGAAGGAT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 89 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (80 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
CATCATGCTCGAAAG
Found at i:3561582 original size:42 final size:42
Alignment explanation
Indices: 3561535--3561617 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
3561525 CAAATTACCC
*
3561535 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCT
1 GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCT
*
3561577 GAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCC
1 GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
3561618 CGAATGACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (42 bp):
GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCT
Found at i:3577738 original size:6 final size:6
Alignment explanation
Indices: 3577727--3577792 Score: 61
Period size: 6 Copynumber: 11.3 Consensus size: 6
3577717 TTTAGTCATT
3577727 TTTTTA TTTTTA TTTTT- TTTCTTA TTTCTTA --TTTA TTGTTTA -TTTTA
1 TTTTTA TTTTTA TTTTTA TTT-TTA TTT-TTA TTTTTA TT-TTTA TTTTTA
*
3577774 TTTTTA -CTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TT
3577793 ATTTTTTCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.06
5 12 0.24
6 25 0.49
7 11 0.22
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:3577763 original size:23 final size:22
Alignment explanation
Indices: 3577735--3577812 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 22
3577725 TTTTTTTATT
*
3577735 TTTATTTTTTTTCTTATTTCTTA
1 TTTATTTTTATT-TTATTTCTTA
3577758 TTTATTGTTTATTTTATTT-TTA
1 TTTATT-TTTATTTTATTTCTTA
*
3577780 CTTTATTTTTATTATTTTTTCTAATA
1 -TTTATTTTTATT-TTATTTCT--TA
3577806 TTTATTT
1 TTTATTT
3577813 ATACGTTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.19
23 23 0.49
24 6 0.13
25 7 0.15
26 2 0.04
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTATTTTTATTTTATTTCTTA
Found at i:3577769 original size:11 final size:11
Alignment explanation
Indices: 3577729--3577798 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
3577719 TAGTCATTTT
3577729 TTTATTTTTA-
1 TTTATTTTTAC
3577739 TTT-TTTTT-C
1 TTTATTTTTAC
3577748 -TTATTTCTTA-
1 TTTATTT-TTAC
*
3577758 TTTATTGTTTAT
1 TTTATT-TTTAC
3577770 TTTATTTTTAC
1 TTTATTTTTAC
3577781 TTTATTTTTA-
1 TTTATTTTTAC
3577791 -TTATTTTT
1 TTTATTTTT
3577799 TCTAATATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
8 2 0.04
9 16 0.31
10 5 0.10
11 22 0.42
12 7 0.13
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTATTTTTAC
Found at i:3577990 original size:36 final size:33
Alignment explanation
Indices: 3577936--3578059 Score: 95
Period size: 36 Copynumber: 3.5 Consensus size: 33
3577926 ATACACATTA
*
3577936 TTTTTATTTATTCTTTTTTCTTTAATTTCTTTTACT
1 TTTTTATTT-TTTTTTTTTCTTT-ATTT-TTTTACT
* *
3577972 TTTTTATTTTTTTGTTTTTGTTTTTTTTATTTTACT
1 TTTTTATTTTTTT-TTTTT-CTTTATTT-TTTTACT
* * *
3578008 TCCTTTACTTTTTTTTCTTTCTTTATTTTTTTATT
1 T-TTTTA-TTTTTTTTTTTTCTTTATTTTTTTACT
* *
3578043 TGTTTTGTTTTATTTTT
1 T-TTTTATTTTTTTTTT
3578060 ATTATGTTAC
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
34 8 0.11
35 13 0.19
36 31 0.44
37 11 0.16
38 7 0.10
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (33 bp):
TTTTTATTTTTTTTTTTTCTTTATTTTTTTACT
Found at i:3578060 original size:55 final size:55
Alignment explanation
Indices: 3577955--3578058 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
3577945 ATTCTTTTTT
*
3577955 CTTTAATTTCTTTTACTTTTTTATTTTTTTGTTTTTGTTTTTTTTATTTTACTTC
1 CTTTAATTTCTTTTACTTTTTTATTTTTTTGTATTTGTTTTTTTTATTTTACTTC
* *
3578010 CTTTACTTT-TTTTTCTTTCTTTA-TTTTTT-TATTTGTTTTGTTTTATTTT
1 CTTTAATTTCTTTTACTTT-TTTATTTTTTTGTATTTGTTTT-TTTTATTTT
3578059 TATTATGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
53 9 0.20
54 23 0.52
55 12 0.27
ACGTcount: A:0.10, C:0.09, G:0.04, T:0.78
Consensus pattern (55 bp):
CTTTAATTTCTTTTACTTTTTTATTTTTTTGTATTTGTTTTTTTTATTTTACTTC
Found at i:3578076 original size:36 final size:36
Alignment explanation
Indices: 3578036--3578138 Score: 102
Period size: 37 Copynumber: 2.8 Consensus size: 36
3578026 TTCTTTATTT
3578036 TTTTATTTGTTTTGTTTTATTTTTATTATGTTACCA
1 TTTTATTTGTTTTGTTTTATTTTTATTATGTTACCA
* * **
3578072 TTTTATTT-TATTT-ATTTATTTTTTACTTATTTTATTA
1 TTTTATTTGT-TTTGTTTTA-TTTTTA-TTATGTTACCA
*
3578109 TTTTTTTTGTTTTGTTATTATTTTATATTA
1 TTTTATTTGTTTTGTT-TTATTTT-TATTA
3578139 CACACTTCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
35 5 0.09
36 17 0.31
37 18 0.33
38 9 0.17
39 5 0.09
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (36 bp):
TTTTATTTGTTTTGTTTTATTTTTATTATGTTACCA
Found at i:3578101 original size:11 final size:10
Alignment explanation
Indices: 3578072--3578138 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 10
3578062 TATGTTACCA
3578072 TTTTATT-TT
1 TTTTATTATT
*
3578081 ATTTATTTATT
1 TTTTA-TTATT
3578092 TTTTACTTA--
1 TTTTA-TTATT
3578101 TTTTATTATT
1 TTTTATTATT
*
3578111 TTTT-TTGTT
1 TTTTATTATT
3578120 TTGTTATTATT
1 TT-TTATTATT
*
3578131 TTATATTA
1 TTTTATTA
3578139 CACACTTCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
8 3 0.07
9 15 0.33
10 13 0.28
11 15 0.33
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTTATTATT
Found at i:3578116 original size:57 final size:57
Alignment explanation
Indices: 3578016--3578134 Score: 125
Period size: 57 Copynumber: 2.1 Consensus size: 57
3578006 CTTCCTTTAC
* * * * *
3578016 TTTT-TTTTCTTTCTTTATTTTTTTATTTGTTTTGTTTTATTTTTATTATGTTACCA
1 TTTTATTTTATTTATTTATTTTTTTACTTATTTTATTTTATTTTTATTATGTTACCA
* * * **
3578072 TTTTATTTTATTTATTTA-TTTTTTACTTATTTTATTATTTTTTTTGTTTTGTTATTA
1 TTTTATTTTATTTATTTATTTTTTTACTTATTTTATT-TTATTTTTATTATGTTACCA
3578129 TTTTAT
1 TTTTAT
3578135 ATTACACACT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
56 19 0.37
57 32 0.63
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (57 bp):
TTTTATTTTATTTATTTATTTTTTTACTTATTTTATTTTATTTTTATTATGTTACCA
Found at i:3578987 original size:15 final size:16
Alignment explanation
Indices: 3578961--3578990 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3578951 TATTAGAAAT
3578961 ATTTGTTTTAATTTTC
1 ATTTGTTTTAATTTTC
3578977 ATTTG-TTTAATTTT
1 ATTTGTTTTAATTTT
3578991 AAAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (16 bp):
ATTTGTTTTAATTTTC
Found at i:3583318 original size:32 final size:32
Alignment explanation
Indices: 3583282--3583352 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
3583272 GTGGTATATT
* *
3583282 TTTTAAGCTACCTATGGTTCTG-TATGATATGC
1 TTTTAAGCTACCTATGATTCTGCGATG-TATGC
* * *
3583314 TTTTAAGTTACCTTTGATTCTGCGCTGTATGC
1 TTTTAAGCTACCTATGATTCTGCGATGTATGC
3583346 TTTTAAG
1 TTTTAAG
3583353 AGTATTTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.46
Consensus pattern (32 bp):
TTTTAAGCTACCTATGATTCTGCGATGTATGC
Found at i:3583626 original size:167 final size:169
Alignment explanation
Indices: 3583350--3583685 Score: 658
Period size: 167 Copynumber: 2.0 Consensus size: 169
3583340 GTATGCTTTT
3583350 AAGAGTATTTTCTGGTAACTTTCAAGCACTATGTTTTATTTTCTCAAATAAAGTATTGATTTTTA
1 AAGAGTATTTTCTGGTAACTTTCAAGCACTATGTTTTATTTTCTCAAATAAAGTATTGATTTTTA
3583415 TAATTGGGATGATTTAAATAATGCAGGTAGATTTAGTTAAGAGACACAGTTTTCCTGTTACTGGA
66 TAATTGGGATGATTTAAATAATGCAGGTAGATTTAGTTAAGAGACACAGTTTTCCTGTTACTGGA
3583480 AT-GGAG-AAATCGACGTGTTCTAAGAGGTCACTGGTTC
131 ATGGGAGAAAATCGACGTGTTCTAAGAGGTCACTGGTTC
3583517 AAGAGTATTTTCTGGTAACTTTCAAGCACTATGTTTTATTTTCTCAAATAAAGTATTGATTTTTA
1 AAGAGTATTTTCTGGTAACTTTCAAGCACTATGTTTTATTTTCTCAAATAAAGTATTGATTTTTA
3583582 TAATTGGGATGATTTAAATAATGCAGGTAGATTTAGTTAAGAGACACAGTTTTCCTGTTACTGGA
66 TAATTGGGATGATTTAAATAATGCAGGTAGATTTAGTTAAGAGACACAGTTTTCCTGTTACTGGA
3583647 ATGGGAGAAAATCGACGTGTTCTAAGAGGTCACTGGTTC
131 ATGGGAGAAAATCGACGTGTTCTAAGAGGTCACTGGTTC
3583686 GCTCGTAAAG
Statistics
Matches: 167, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
167 132 0.79
168 4 0.02
169 31 0.19
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (169 bp):
AAGAGTATTTTCTGGTAACTTTCAAGCACTATGTTTTATTTTCTCAAATAAAGTATTGATTTTTA
TAATTGGGATGATTTAAATAATGCAGGTAGATTTAGTTAAGAGACACAGTTTTCCTGTTACTGGA
ATGGGAGAAAATCGACGTGTTCTAAGAGGTCACTGGTTC
Found at i:3584379 original size:2 final size:2
Alignment explanation
Indices: 3584368--3584398 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3584358 CTCCAATTCT
3584368 TA TA -A 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 TA
3584399 ATTATCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3592685 original size:83 final size:80
Alignment explanation
Indices: 3592537--3592699 Score: 290
Period size: 80 Copynumber: 2.0 Consensus size: 80
3592527 TCAAGGTATG
*
3592537 ATGAATAGTAACTATTTTTCTATCATTAACAAATCCCCTTGTCTTGTGATAAAGTAGCTTCTTTT
1 ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTGTCTTGTGATAAAGTAGCTTCTTTT
3592602 TAAGATAGACTACAT
66 TAAGATAGACTACAT
3592617 ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTGTCTTCTTGTGATAAAGTAGCTTCT
1 ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTG---TCTTGTGATAAAGTAGCTTCT
3592682 TTTTAAGATAGACTACAT
63 TTTTAAGATAGACTACAT
3592700 TCATTATGGT
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
80 40 0.51
83 39 0.49
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (80 bp):
ATGAATAGTAACTAATTTTCTATCATTAACAAATCCCCTTGTCTTGTGATAAAGTAGCTTCTTTT
TAAGATAGACTACAT
Found at i:3596754 original size:20 final size:20
Alignment explanation
Indices: 3596729--3596768 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3596719 AGCAACAGAA
*
3596729 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
3596749 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
3596769 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:3596784 original size:51 final size:52
Alignment explanation
Indices: 3596725--3596869 Score: 230
Period size: 51 Copynumber: 2.9 Consensus size: 52
3596715 AATTAGCAAC
3596725 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
3596776 AGAATAAAAAACTGATTC--TCTAATTAAAAATGATCCTA--TAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
3596825 AGAATAAAAACTGATTCTATCTAATT-AAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
3596870 TTTAATTTAG
Statistics
Matches: 87, Mismatches: 1, Indels: 12
0.87 0.01 0.12
Matches are distributed among these distances:
48 12 0.14
49 27 0.31
50 7 0.08
51 30 0.34
52 5 0.06
53 6 0.07
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:3596856 original size:19 final size:19
Alignment explanation
Indices: 3596832--3596868 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3596822 AATAGAATAA
*
3596832 AAACTGATTCTATCTAATT
1 AAACTGATCCTATCTAATT
3596851 AAACTGATCCTATCTAAT
1 AAACTGATCCTATCTAAT
3596869 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (19 bp):
AAACTGATCCTATCTAATT
Found at i:3596859 original size:49 final size:50
Alignment explanation
Indices: 3596725--3596863 Score: 214
Period size: 49 Copynumber: 2.8 Consensus size: 50
3596715 AATTAGCAAC
3596725 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTA--TAATAACTAAT
3596776 AGAATAAAAAACTGATTC--TCTAATTAAAAATGATCCTATAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATAATAACTAAT
*
3596825 AGAATAAAAACTGATTCTATCTAATT-AAACTGATCCTAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
3596864 CTAATATTTA
Statistics
Matches: 83, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
48 12 0.14
49 28 0.34
50 7 0.08
51 25 0.30
52 5 0.06
53 6 0.07
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (50 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATAATAACTAAT
Found at i:3604018 original size:20 final size:20
Alignment explanation
Indices: 3603993--3604032 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3603983 AGCAACAGAA
3603993 TAAAAATGATTC-TATCTAAT
1 TAAAAATGA-TCATATCTAAT
3604013 TAAAAATGATCATATCTAAT
1 TAAAAATGATCATATCTAAT
3604033 AACTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCATATCTAAT
Found at i:3604061 original size:53 final size:53
Alignment explanation
Indices: 3603989--3604139 Score: 254
Period size: 53 Copynumber: 2.9 Consensus size: 53
3603979 AATTAGCAAC
3603989 AGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
1 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
*
3604040 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
*
3604093 AGAATAAAAAACTGATTCTATCTAATTAAAACTGATCCA-ATCTAATA
1 AGAATAAAAAACTGATTCTATCTAATTAAAAATGAT-CATATCTAATA
3604140 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
51 5 0.05
52 5 0.05
53 83 0.88
54 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.32
Consensus pattern (53 bp):
AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCATATCTAATAACTAAT
Found at i:3604075 original size:20 final size:21
Alignment explanation
Indices: 3604046--3604085 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3604036 TAATAGAATA
*
3604046 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
3604067 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
3604086 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:3604125 original size:20 final size:20
Alignment explanation
Indices: 3604100--3604138 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3604090 AATAGAATAA
* *
3604100 AAAACTGATTCTATCTAATT
1 AAAACTGATCCAATCTAATT
3604120 AAAACTGATCCAATCTAAT
1 AAAACTGATCCAATCTAAT
3604139 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAACTGATCCAATCTAATT
Found at i:3604535 original size:125 final size:128
Alignment explanation
Indices: 3604293--3604548 Score: 401
Period size: 125 Copynumber: 2.0 Consensus size: 128
3604283 CTCTACCAAG
* * *
3604293 CAAGGTATGGAAAGAAAATTACTTTTTCTCTCTAGTTTTTTCATCTTTCCTACCTAGCTCCTCAA
1 CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAG--TTTTCATCTTTCCTACCAAGCACCTCAA
* * *
3604358 TGGAAAAAATATATGAACTCTCAATCTTTTACTAATCTCCTCTAATTTTTCATCTTTCCAATTTT
64 TGGAAAAAATATATGAACTCTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTTT
3604423 CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAG-TTT-ATCTTTCCTACCAAGCACCTCAATG
1 CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAGTTTTCATCTTTCCTACCAAGCACCTCAATG
* *
3604486 G-AAAAATATATGCACTTTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTTT
66 GAAAAAATATATGAACTCTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTTT
3604548 C
1 C
3604549 TTTATGTTAC
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
125 57 0.48
126 24 0.20
127 3 0.03
130 34 0.29
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (128 bp):
CAAGGCATGGAAAGAAAATTACTTTTTCTCTCTAGTTTTCATCTTTCCTACCAAGCACCTCAATG
GAAAAAATATATGAACTCTCAAACCTTTACTAATCTCCTCTAATTTTTCATCATTCCAATTTT
Found at i:3607542 original size:57 final size:57
Alignment explanation
Indices: 3607449--3607563 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3607439 ATACTAAATC
* *
3607449 TGTTCAAGTTTTACATTTAGCAAGTCCTGACCATCAGCATCTCTTACAACACCCATT
1 TGTTCAAGTTTTACATTTAGCAACTCCTAACCATCAGCATCTCTTACAACACCCATT
*
3607506 TGTTCAAGTTTTACATTTAGCAACTCCTAACTATCAGCATCTCTTACAACACCCATT
1 TGTTCAAGTTTTACATTTAGCAACTCCTAACCATCAGCATCTCTTACAACACCCATT
3607563 T
1 T
3607564 CTCTATCTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.35
Consensus pattern (57 bp):
TGTTCAAGTTTTACATTTAGCAACTCCTAACCATCAGCATCTCTTACAACACCCATT
Found at i:3612895 original size:2 final size:2
Alignment explanation
Indices: 3612888--3612918 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3612878 CATGAGTTAG
3612888 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 A
3612919 GGAATTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3613792 original size:32 final size:31
Alignment explanation
Indices: 3613751--3613847 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 31
3613741 GAGTCGAGGG
3613751 TTTACCTATGTTATACGGAACATATGGACAGT
1 TTTACCTATGTT-TACGGAACATATGGACAGT
*
3613783 TTTACCTATGTCTTTC-GAGACATATGGACAG-
1 TTTACCTATGT-TTACGGA-ACATATGGACAGT
* *
3613814 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTT-TACGGAACATATGGACAGT
3613846 TT
1 TT
3613848 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.02
31 25 0.45
32 28 0.51
33 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (31 bp):
TTTACCTATGTTTACGGAACATATGGACAGT
Found at i:3613823 original size:31 final size:31
Alignment explanation
Indices: 3613750--3613850 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
3613740 AGAGTCGAGG
*
3613750 GTTTACCTATGTTAT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
3613781 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
3613813 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
3613844 GTTTACC
1 GTTTACC
3613851 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:3613882 original size:30 final size:30
Alignment explanation
Indices: 3613838--3613911 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
3613828 AAGGAACATA
3613838 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
3613869 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
3613899 TGGATAGTTACCG
1 TGGACAGTTACCG
3613912 GGTCGTGTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 35 0.83
31 7 0.17
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:3617083 original size:2 final size:2
Alignment explanation
Indices: 3617076--3617118 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3617066 CATGAGTTAG
3617076 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT
3617118 A
1 A
3617119 GGAATTGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3617989 original size:32 final size:32
Alignment explanation
Indices: 3617948--3618044 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
3617938 GAGTCGAGGG
3617948 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
3617980 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
3618011 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
3618043 TT
1 TT
3618045 ACTGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:3618034 original size:31 final size:31
Alignment explanation
Indices: 3617950--3618042 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
3617940 GTCGAGGGTT
* *
3617950 TACCTATGTTCTACGGAACATATGGACAGTTT
1 TACCTATGTTCTAAGGAACATATGGACAG-TA
***
3617982 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGA-ACATATGGACAGTA
3618013 TACCTATGTTCTAAGGAACATATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
3618043 TTACTGAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 27 0.52
32 25 0.48
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:3618084 original size:30 final size:30
Alignment explanation
Indices: 3618035--3618127 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
3618025 AAGGAACATA
*
3618035 TGGACAGTTTACTGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
3618066 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
3618096 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3618125 TGG
1 TGG
3618128 GTAGGTCCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.28
30 34 0.60
31 7 0.12
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:3627766 original size:6 final size:6
Alignment explanation
Indices: 3627755--3627793 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3627745 ACTGTGATTG
* * *
3627755 GCACTA GCACTA GCACTA GCACTA CCATTA CCACTA GCA
1 GCACTA GCACTA GCACTA GCACTA GCACTA GCACTA GCA
3627794 ATATGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.36, G:0.13, T:0.18
Consensus pattern (6 bp):
GCACTA
Found at i:3630918 original size:256 final size:256
Alignment explanation
Indices: 3630415--3630941 Score: 741
Period size: 255 Copynumber: 2.0 Consensus size: 256
3630405 GGTTGGGTCG
3630415 GGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGTTGGGTCGAGTTCGAGTTTAGGGTGAAAAAT
1 GGTCGGGTCAGTTTTTTTAAGTGTGATATTC--G--GGGTCGAGTTCGAGTTTAGGGTGAAAAAT
* *
3630480 ACCCGACCCGATCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAAT
62 ACCCGA--C-ACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAAT
*
3630545 AATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTTAACAAAAATAATTTTT
124 AATACCCCTCTATATATAATTTTTTTCAATTAAGTCAC--TTTTTATTGAACAAAAATAATTTTT
3630610 TTATTATTTCGGGTTAGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGATCAGGTGAAAT
187 TTATTATTT---GTTAGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGATCAGGTGAAAT
3630675 TTTATTTT
249 TTTATTTT
* * *
3630683 GGTCGGGTC-GTTTTTTTTAGTGTGATATTC-GGGTCGGGTTCGGGTTTAGGGTGAAAAATACCC
1 GGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCC
3630746 -A-ACCCGACCC-AAAAAATATATAA-TTTACCTTATATATTTAGGAATAATTACAATAATACCC
66 GACACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
*
3630807 CTCTATATATAATTTTTTTCTTTCAATTAAGTCA-TTTTTATTGAATAAAAATAATTTTTTTATT
131 CTCTATATATAA---TTTT-TTTCAATTAAGTCACTTTTTATTGAACAAAAATAATTTTTTTATT
* * *
3630871 A-TT-TTGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTC-GGTGAAACTTTATTTT
192 ATTTGTTAGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGATCAGGTGAAATTTTATTTT
*
3630933 GGTAGGGTC
1 GGTCGGGTC
3630942 GGGTCTCGGA
Statistics
Matches: 244, Mismatches: 11, Indels: 26
0.87 0.04 0.09
Matches are distributed among these distances:
250 23 0.09
251 41 0.17
255 52 0.21
256 41 0.17
257 8 0.03
258 4 0.02
259 14 0.06
261 1 0.00
262 31 0.13
267 20 0.08
268 9 0.04
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (256 bp):
GGTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCC
GACACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
CTCTATATATAATTTTTTTCAATTAAGTCACTTTTTATTGAACAAAAATAATTTTTTTATTATTT
GTTAGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGATCAGGTGAAATTTTATTTT
Found at i:3634235 original size:30 final size:30
Alignment explanation
Indices: 3634108--3634325 Score: 149
Period size: 30 Copynumber: 7.3 Consensus size: 30
3634098 AAATAATAGT
* *
3634108 AACTTAAAGGACCAAAATAGTACAAACA-A
1 AACTTAAAGGACTAAAATAGTAAAAACAGA
* * **
3634137 GAATTTAAAGAACTAAAATAGCCAAAACAGA
1 -AACTTAAAGGACTAAAATAGTAAAAACAGA
* * * ** *
3634168 AACTCAAAGGGCTAAAACAGCCAAAACATA
1 AACTTAAAGGACTAAAATAGTAAAAACAGA
** * *
3634198 AGTTTAAAGGACTAAACTAGTAAAAAAAGA
1 AACTTAAAGGACTAAAATAGTAAAAACAGA
* * *
3634228 AACTTAAAAGG-CCAAAATAATAAAAACATA
1 AACTT-AAAGGACTAAAATAGTAAAAACAGA
* *
3634258 AACTTAAGGGTCT-AAATAG-AAAATACAGA
1 AACTTAAAGGACTAAAATAGTAAAA-ACAGA
* * *
3634287 AACTTAAAGGACAAAAATA-TATAAACAGT
1 AACTTAAAGGACTAAAATAGTAAAAACAGA
*
3634316 AACATAAAGG
1 AACTTAAAGG
3634326 GCCTAACAAT
Statistics
Matches: 143, Mismatches: 39, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
28 4 0.03
29 36 0.25
30 97 0.68
31 6 0.04
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (30 bp):
AACTTAAAGGACTAAAATAGTAAAAACAGA
Found at i:3634314 original size:29 final size:28
Alignment explanation
Indices: 3634201--3634325 Score: 97
Period size: 29 Copynumber: 4.2 Consensus size: 28
3634191 AAACATAAGT
* *
3634201 TTAAAGGACTAAACTAGTAAAAAAAGAAAC
1 TTAAAGGAC-AAAATA-TAAAAACAGAAAC
* *
3634231 TTAAAAGGCCAAAATAATAAAAACATAAAC
1 TT-AAAGGACAAAAT-ATAAAAACAGAAAC
* * * *
3634261 TTAAGGGTCTAAATAGAAAATACAGAAAC
1 TTAAAGGACAAAATATAAAA-ACAGAAAC
* *
3634290 TTAAAGGACAAAAATATATAAACAGTAAC
1 TTAAAGGAC-AAAATATAAAAACAGAAAC
*
3634319 ATAAAGG
1 TTAAAGG
3634326 GCCTAACAAT
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
28 5 0.07
29 36 0.48
30 27 0.36
31 7 0.09
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.18
Consensus pattern (28 bp):
TTAAAGGACAAAATATAAAAACAGAAAC
Found at i:3635757 original size:3 final size:3
Alignment explanation
Indices: 3635749--3635816 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
3635739 TGTATCATTG
*
3635749 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
3635798 T-A TAA -AA TAAA TAA -AA TAA
1 TAA TAA TAA T-AA TAA TAA TAA
3635817 AAAAGGATCC
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.10
3 46 0.79
4 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3636302 original size:130 final size:133
Alignment explanation
Indices: 3636004--3636348 Score: 398
Period size: 130 Copynumber: 2.6 Consensus size: 133
3635994 GTCCTCTAAA
* * * *
3636004 GGTGACATGACTCCTACGTGATGAGGAGATATGGTCGAGGGATGACACGGCTT-ATACGGGATGA
1 GGTGACATGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGG-TTCATACGTGATGA
* * *
3636068 AGAGTTCTGACCATCTTTAGGAAGGGTGATAACTCGATTCCTACGTGATGAGGACGACTGGTTAT
65 AGAGGTCAGACCATCTTTAGG-AGGATGATAACTCGATTCCTACGTGATGAGGACGACTGGTTAT
*
3636133 ATAGG
129 ACAGG
* * * *
3636138 GGTGACACGAATCCTACGTGATGAGGAGGTCTGGTTGGGGGATGACACGGTTCCTACGTGATGAA
1 GGTGACATGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCATACGTGATGAA
* * * *
3636203 GATGGT-AGGCCATCTTTA-G-GGATGATAACTTGGTTCCTACGTGATGAGGATTG-CTGGTTAT
66 GA-GGTCAGACCATCTTTAGGAGGATGATAACTCGATTCCTACGTGATGAGGA-CGACTGGTTAT
3636264 -CAGG
129 ACAGG
* * * * *
3636268 GGTGACATGACTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACATGGTTCTTACGTGATGAG
1 GGTGACATGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCATACGTGATGAA
*
3636333 GACGG-CAAACCATCTT
66 GA-GGTCAGACCATCTT
3636349 CAGGGAATTA
Statistics
Matches: 180, Mismatches: 27, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
130 72 0.40
131 36 0.20
132 1 0.01
133 3 0.02
134 66 0.37
135 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.26
Consensus pattern (133 bp):
GGTGACATGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCATACGTGATGAA
GAGGTCAGACCATCTTTAGGAGGATGATAACTCGATTCCTACGTGATGAGGACGACTGGTTATAC
AGG
Found at i:3636468 original size:31 final size:31
Alignment explanation
Indices: 3636424--3636575 Score: 98
Period size: 31 Copynumber: 4.8 Consensus size: 31
3636414 GACAAAATTC
* *
3636424 GTTTCAAGCGAAACGACTCAAAGATGATTTT
1 GTTTCAAGAGAAACAACTCAAAGATGATTTT
* * * * *
3636455 GTTTTAAGAGAAACTATCTC-AAGATACAAAATTA
1 GTTTCAAGAGAAAC-AACTCAAAGAT---GATTTT
* *
3636489 GTTTCAAGGGAAACAACTCAAAGATTGGTTTCT
1 GTTTCAAGAGAAACAACTCAAAGA-TGATTT-T
* *
3636522 -TTT-AATAGAAACAGACTCAAAG--GCTTTT
1 GTTTCAAGAGAAACA-ACTCAAAGATGATTTT
3636550 GTTTCAAGAGAAACAAACTCAAAGAT
1 GTTTCAAGAGAAAC-AACTCAAAGAT
3636576 ACTGTCTCAT
Statistics
Matches: 90, Mismatches: 18, Indels: 25
0.68 0.14 0.19
Matches are distributed among these distances:
28 1 0.01
29 7 0.08
30 16 0.18
31 26 0.29
32 16 0.18
33 4 0.04
34 19 0.21
35 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (31 bp):
GTTTCAAGAGAAACAACTCAAAGATGATTTT
Found at i:3636513 original size:34 final size:34
Alignment explanation
Indices: 3636405--3636513 Score: 82
Period size: 34 Copynumber: 3.3 Consensus size: 34
3636395 TAGAAACTGT
* * * *
3636405 CTCAAGAGAGACAAAATTCGTTTCAAGCGAAACGA
1 CTCAA-AGATACAAAATTAGTTTCAAGAGAAACAA
* * * * *
3636440 CTCAAAGAT---GATTTTGTTTTAAGAGAAACTAT
1 CTCAAAGATACAAAATTAGTTTCAAGAGAAAC-AA
*
3636472 CTC-AAGATACAAAATTAGTTTCAAGGGAAACAA
1 CTCAAAGATACAAAATTAGTTTCAAGAGAAACAA
3636505 CTCAAAGAT
1 CTCAAAGAT
3636514 TGGTTTCTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
31 20 0.36
32 3 0.05
33 4 0.07
34 23 0.42
35 5 0.09
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.25
Consensus pattern (34 bp):
CTCAAAGATACAAAATTAGTTTCAAGAGAAACAA
Found at i:3636525 original size:65 final size:66
Alignment explanation
Indices: 3636360--3636533 Score: 210
Period size: 65 Copynumber: 2.6 Consensus size: 66
3636350 AGGGAATTAC
* * * *
3636360 TTCAAGGGAAACAGACTCAAAGAT-GATTGTTTCAATAGAAACTGTCTCAAGAGAGACAAAATTC
1 TTCAAGGGAAACA-ACTCAAAGATGGTTTGTTTTAATAGAAACTATCTCAAGAGAGACAAAATTA
3636424 GT
65 GT
* * * * *
3636426 TTCAAGCGAAACGACTCAAAGATGATTTTGTTTTAAGAGAAACTATCTC-A-AGATACAAAATTA
1 TTCAAGGGAAACAACTCAAAGATG-GTTTGTTTTAATAGAAACTATCTCAAGAGAGACAAAATTA
3636489 GT
65 GT
*
3636491 TTCAAGGGAAACAACTCAAAGATTGGTTTCTTTTAATAGAAAC
1 TTCAAGGGAAACAACTCAAAGA-TGGTTTGTTTTAATAGAAAC
3636534 AGACTCAAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
65 58 0.64
66 14 0.15
67 19 0.21
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (66 bp):
TTCAAGGGAAACAACTCAAAGATGGTTTGTTTTAATAGAAACTATCTCAAGAGAGACAAAATTAG
T
Found at i:3636743 original size:37 final size:38
Alignment explanation
Indices: 3636680--3636766 Score: 140
Period size: 37 Copynumber: 2.3 Consensus size: 38
3636670 AAAGAAATAA
* *
3636680 ACTCAAAGATTTTTTTCATTTTGTTTCAAGTGAAACCG
1 ACTCAAAGATTTTTTTCATTTCGTTTCAAGTGAAACAG
*
3636718 ACTCAAAGATTTTTTT-GTTTCGTTTCAAGTGAAACAG
1 ACTCAAAGATTTTTTTCATTTCGTTTCAAGTGAAACAG
3636755 ACTCAAAGATTT
1 ACTCAAAGATTT
3636767 CTCAAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 30 0.65
38 16 0.35
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (38 bp):
ACTCAAAGATTTTTTTCATTTCGTTTCAAGTGAAACAG
Found at i:3636856 original size:135 final size:137
Alignment explanation
Indices: 3636610--3636914 Score: 438
Period size: 135 Copynumber: 2.2 Consensus size: 137
3636600 TTTTTCCAAA
* * *
3636610 GAAACAAACTCAAAGATTTTTCAAAAGAAACTATTTCAAAAGAGACAAAATTTTGTTACCAAAGA
1 GAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACAAAACTTTGTTACCAAAGA
* *
3636675 AATAAACTCAAAGATTTTTTTCATTTTGTTTCAAGTGAAACCGACTCAAAGA-TTTTTTTGTTTC
66 AACAAACTCAAAGA-TTTTTTCATTTTGTTTCAAGTGAAACAGACTCAAA-ATTTTTTTTGTTTC
*
3636739 GTTTCAAGT
129 GTTTCAACT
* * * * *
3636748 GAAACAGACTCAAAGATTTCTCAAGA-AAATTATCTCAAGAGAGACAAAACTTTGTT-TCAAGAG
1 GAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACAAAACTTTGTTACCAA-AG
* *
3636811 AAACATACTCAAAGA-TTTTTCATTTTGTTTCAAGTGAAACAGACTCAAAATTTTTTTTGTTTTG
65 AAACAAACTCAAAGATTTTTTCATTTTGTTTCAAGTGAAACAGACTCAAAATTTTTTTTGTTTCG
3636875 TTTCAACT
130 TTTCAACT
3636883 GAAACAGACTCAAAGATTTTTCAAAAGAAACT
1 GAAACAGACTCAAAGATTTTTCAAAAGAAACT
3636915 GTCTTGAGAG
Statistics
Matches: 148, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
134 1 0.01
135 76 0.51
136 7 0.05
137 41 0.28
138 23 0.16
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (137 bp):
GAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACAAAACTTTGTTACCAAAGA
AACAAACTCAAAGATTTTTTCATTTTGTTTCAAGTGAAACAGACTCAAAATTTTTTTTGTTTCGT
TTCAACT
Found at i:3636876 original size:37 final size:38
Alignment explanation
Indices: 3636798--3636903 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 38
3636788 GAGACAAAAC
* *
3636798 TTTGTTTCAAGAGAAACATACTCAAAGA--TTTTTCAT
1 TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTTTCAT
**
3636834 TTTGTTTCAAGTGAAACAGACTCAAA-ATTTTTTTTGT
1 TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTTTCAT
*
3636871 TTTGTTTCAACTGAAACAGACTCAAAGATTTTT
1 TTTGTTTCAAGTGAAACAGACTCAAAGATTTTT
3636904 CAAAAGAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 1 0.02
36 24 0.39
37 31 0.50
38 6 0.10
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (38 bp):
TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTTTCAT
Found at i:3637117 original size:32 final size:34
Alignment explanation
Indices: 3637055--3637122 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 34
3637045 GTCGAATCCC
*
3637055 CAAAGATGCCCTAATCATTCGATGTTGATTGCTT
1 CAAAGATGCCCTAATCATTCAATGTTGATTGCTT
*
3637089 CAAAGATGCCC-AAT-ATTCAATGTTGATTGTTT
1 CAAAGATGCCCTAATCATTCAATGTTGATTGCTT
3637121 CA
1 CA
3637123 GCACTAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 18 0.56
33 3 0.09
34 11 0.34
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (34 bp):
CAAAGATGCCCTAATCATTCAATGTTGATTGCTT
Found at i:3637817 original size:30 final size:29
Alignment explanation
Indices: 3637783--3637840 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
3637773 ATCAGAAAGT
3637783 AAATAATTA-AAATTACAAGGACCAAAATGA
1 AAATAA-TAGAAATTA-AAGGACCAAAATGA
*
3637813 AAATAATAGTAACTTAAAGGACCAAAAT
1 AAATAATAG-AAATTAAAGGACCAAAAT
3637841 AGTACAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 2 0.08
30 18 0.72
31 5 0.20
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (29 bp):
AAATAATAGAAATTAAAGGACCAAAATGA
Found at i:3637920 original size:29 final size:28
Alignment explanation
Indices: 3637826--3637927 Score: 87
Period size: 30 Copynumber: 3.5 Consensus size: 28
3637816 TAATAGTAAC
* * *
3637826 TTAAAGGACCAAAATAGTACAAACAAGAAT
1 TTAAAGGACTAAAACAG-CCAAAC-AGAAT
* * *
3637856 TTAAAGAACTAAAATAGCCAAAACAGAAAC
1 TTAAAGGACTAAAACAGCC-AAACAG-AAT
* *
3637886 TCAAAGGGCTAAAACAGCCAAACAGAAGT
1 TTAAAGGACTAAAACAGCCAAACAGAA-T
3637915 TTAAAGGACTAAA
1 TTAAAGGACTAAA
3637928 CTAGTAAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
28 2 0.03
29 20 0.34
30 36 0.62
ACGTcount: A:0.55, C:0.16, G:0.15, T:0.15
Consensus pattern (28 bp):
TTAAAGGACTAAAACAGCCAAACAGAAT
Found at i:3637966 original size:30 final size:30
Alignment explanation
Indices: 3637915--3638025 Score: 84
Period size: 30 Copynumber: 3.7 Consensus size: 30
3637905 AAACAGAAGT
* *
3637915 TTAAAGGACTAAACTAG-TAAAAAAAGAAAC
1 TTAAAGG-CCAAAATAGATAAAAAAAGAAAC
* *
3637945 TTAAAAGGCCAAAATA-ATAAAAATATAAAC
1 TT-AAAGGCCAAAATAGATAAAAAAAGAAAC
* * * * *
3637975 TTAAGGGTCTAAATAGA-AAATACAGAAAC
1 TTAAAGGCCAAAATAGATAAAAAAAGAAAC
*
3638004 TTAAAGGACCAAAATATATAAA
1 TTAAAGG-CCAAAATAGATAAA
3638026 CAGTAACATA
Statistics
Matches: 62, Mismatches: 14, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
29 25 0.40
30 29 0.47
31 8 0.13
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.20
Consensus pattern (30 bp):
TTAAAGGCCAAAATAGATAAAAAAAGAAAC
Found at i:3639490 original size:3 final size:3
Alignment explanation
Indices: 3639482--3639534 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
3639472 TGTATCCCAG
*
3639482 TAA TAA TAA TAA TAA TAA TTAA TAT TAA TAA TAA TTAA T-A TAA -AA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA
*
3639527 TAA AAA TA
1 TAA TAA TA
3639535 GACCCAGACA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3639504 original size:16 final size:16
Alignment explanation
Indices: 3639485--3639529 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3639475 ATCCCAGTAA
3639485 TAATAATAATAATAAT
1 TAATAATAATAATAAT
*
3639501 TAATATTAATAATAAT
1 TAATAATAATAATAAT
3639517 TAAT-ATAA-AATAA
1 TAATAATAATAATAA
3639530 AAATAGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 5 0.19
15 3 0.11
16 19 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATAATAATAAT
Found at i:3640184 original size:31 final size:32
Alignment explanation
Indices: 3640141--3640290 Score: 101
Period size: 31 Copynumber: 4.8 Consensus size: 32
3640131 ATAAAATTCA
* *
3640141 TTTCAAGCGAAAC-GATTCAAAGACAATTTTG
1 TTTCAAGAGAAACAGACTCAAAGACAATTTTG
* * * * *
3640172 TTTTAAGAGAAACTGTCTCAAGAGACAAAATTCG
1 TTTCAAGAGAAACAGACTCAA-AGAC-AATTTTG
* ***
3640206 TTTCAAGGGAAAC-GACTCAAAGATTGTTTTG
1 TTTCAAGAGAAACAGACTCAAAGACAATTTTG
* * * *
3640237 TTTTAATAGAAACAGGCTCAAATAC--TTTTG
1 TTTCAAGAGAAACAGACTCAAAGACAATTTTG
* *
3640267 TTTCAAGAGAAACAAACTCGAAGA
1 TTTCAAGAGAAACAGACTCAAAGA
3640291 TATTGTCTCA
Statistics
Matches: 89, Mismatches: 26, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
30 23 0.26
31 24 0.27
32 16 0.18
33 10 0.11
34 16 0.18
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (32 bp):
TTTCAAGAGAAACAGACTCAAAGACAATTTTG
Found at i:3640184 original size:67 final size:67
Alignment explanation
Indices: 3640102--3640258 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 67
3640092 TCAATGATGA
* * *
3640102 TTGTTTCAATAGAAACTGTCTCAAAAGAGATAAAATTCATTTCAAGCGAAACGATTCAAAGACAA
1 TTGTTTTAATAGAAACTGTCTCAAAAGAGACAAAATTCATTTCAAGCGAAACGACTCAAAGACAA
3640167 TT
66 TT
* * * ***
3640169 TTGTTTTAAGAGAAACTGTCTC--AAGAGACAAAATTCGTTTCAAGGGAAACGACTCAAAGATTG
1 TTGTTTTAATAGAAACTGTCTCAAAAGAGACAAAATTCATTTCAAGCGAAACGACTCAAAGACAA
3640232 TT
66 TT
* *
3640234 TTGTTTTAATAGAAACAGGCTCAAA
1 TTGTTTTAATAGAAACTGTCTCAAA
3640259 TACTTTTGTT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 55 0.72
67 21 0.28
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (67 bp):
TTGTTTTAATAGAAACTGTCTCAAAAGAGACAAAATTCATTTCAAGCGAAACGACTCAAAGACAA
TT
Found at i:3640225 original size:33 final size:33
Alignment explanation
Indices: 3640126--3640225 Score: 96
Period size: 34 Copynumber: 3.1 Consensus size: 33
3640116 ACTGTCTCAA
* * * *
3640126 AAGAGATAAAATTCATTTCAAGCGAAACGATTC
1 AAGAGACAAAATTCGTTTCAAGAGAAACGACTC
* * * *
3640159 AA-AGAC-AATTTTGTTTTAAGAGAAACTGTCTC
1 AAGAGACAAAATTCGTTTCAAGAGAAAC-GACTC
*
3640191 AAGAGACAAAATTCGTTTCAAGGGAAACGACTC
1 AAGAGACAAAATTCGTTTCAAGAGAAACGACTC
3640224 AA
1 AA
3640226 AGATTGTTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
31 15 0.29
32 8 0.16
33 12 0.24
34 16 0.31
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (33 bp):
AAGAGACAAAATTCGTTTCAAGAGAAACGACTC
Found at i:3640555 original size:36 final size:36
Alignment explanation
Indices: 3640515--3640622 Score: 171
Period size: 37 Copynumber: 3.0 Consensus size: 36
3640505 GAGACAAAAC
* *
3640515 TTTGTTTCAAGGGAAACATACTCAAAGATTTTTCAT
1 TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTCAT
**
3640551 TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTTTGT
1 TTTGTTTCAAGTGAAACAGACTCAAAGA-TTTTTCAT
3640588 TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTCA
1 TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTCA
3640623 AAAGAAACTG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 31 0.48
37 34 0.52
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTCAT
Done.