Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:4378988 original size:26 final size:27
Alignment explanation
Indices: 4378959--4379013 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
4378949 AAAAATAAAA
* **
4378959 TAATCTCCTTTATGTCAAGTT-AGAGT
1 TAATCTCCTTGATGAAAAGTTGAGAGT
4378985 TAATCTCCTTGATGAAAAGTTGAGAGT
1 TAATCTCCTTGATGAAAAGTTGAGAGT
4379012 TA
1 TA
4379014 TCCTTTGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (27 bp):
TAATCTCCTTGATGAAAAGTTGAGAGT
Found at i:4379778 original size:42 final size:42
Alignment explanation
Indices: 4379711--4379796 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
4379701 GTCTCAAGAA
* * * *
4379711 CAACTTCAACAGTAAGAATAGCCTCAATGTCAGGAACAACCT
1 CAACTTCAACAGCAAGAACAACCTCAATGTCAAGAACAACCT
* *
4379753 CAACTTCAACAGCAGGAACAACCTCAGTGTCAAGAACAACCT
1 CAACTTCAACAGCAAGAACAACCTCAATGTCAAGAACAACCT
4379795 CA
1 CA
4379797 TCCCGAATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (42 bp):
CAACTTCAACAGCAAGAACAACCTCAATGTCAAGAACAACCT
Found at i:4380143 original size:13 final size:13
Alignment explanation
Indices: 4380125--4380149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4380115 GAATGAGAAA
4380125 ATATATAATATAT
1 ATATATAATATAT
4380138 ATATATAATATA
1 ATATATAATATA
4380150 GAAAAAAAAG
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:4382723 original size:67 final size:67
Alignment explanation
Indices: 4382595--4382723 Score: 192
Period size: 67 Copynumber: 1.9 Consensus size: 67
4382585 TTATTATTTG
*
4382595 TATCTTGAAAATCTTATGTATATGGAAAATTATTATTACATATTCAATCAAATATTAAAAAAGTA
1 TATCTTGAAAATCTTATGTATATGGAAAATTATTATGACATATTCAATCAAATATTAAAAAAGTA
4382660 TA
66 TA
*
4382662 TATCTTGAAAATCTTATTTATATGGAGAATATTATTATGA-A-A-TCAATCAAATATTACAAAAA
1 TATCTTGAAAATCTTATGTATATGGA-AA-ATTATTATGACATATTCAATCAAATATTA-AAAAA
4382724 AAAAATATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
66 14 0.25
67 31 0.54
68 3 0.05
69 9 0.16
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (67 bp):
TATCTTGAAAATCTTATGTATATGGAAAATTATTATGACATATTCAATCAAATATTAAAAAAGTA
TA
Found at i:4383331 original size:29 final size:30
Alignment explanation
Indices: 4383282--4383370 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 30
4383272 TTTGCTTGTT
* * *
4383282 CCTTGTTCTCTTATACTTGTTCATGTACAG
1 CCTTCTTCTCTTGTACCTGTTCATGTACAG
4383312 CCTT-TTCTCTTGTACCTGTTCATGTACAG
1 CCTTCTTCTCTTGTACCTGTTCATGTACAG
* * * *
4383341 -CTTCCTCTCTTGTATCTATTCACGTACAG
1 CCTTCTTCTCTTGTACCTGTTCATGTACAG
4383370 C
1 C
4383371 TTTTTTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
28 3 0.06
29 44 0.86
30 4 0.08
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (30 bp):
CCTTCTTCTCTTGTACCTGTTCATGTACAG
Found at i:4390311 original size:3 final size:3
Alignment explanation
Indices: 4390305--4390336 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4390295 TAAAAAGGTT
4390305 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4390337 TGAAAGCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4399709 original size:22 final size:22
Alignment explanation
Indices: 4399534--4399717 Score: 92
Period size: 22 Copynumber: 8.3 Consensus size: 22
4399524 ATAATTTAGG
*
4399534 ATTTAT-A-TAAAATATAAATA
1 ATTTATAATTAAAATATTAATA
*
4399554 ATTTGTAATTAAAATATAGTAA-A
1 ATTTATAATTAAAATAT--TAATA
* **
4399577 TTTTAATAATTATTATA-TAATA
1 ATTT-ATAATTAAAATATTAATA
** *
4399599 ATTTATAATTAATTTATCAATA
1 ATTTATAATTAAAATATTAATA
* * ** *
4399621 ACTTAT-TTCTCTAAT-TTTATA
1 ATTTATAAT-TAAAATATTAATA
*
4399642 ATTTATAATTAAAATATTAATT
1 ATTTATAATTAAAATATTAATA
* * *
4399664 TTTTAAATTTATCTAAAATGTTAATA
1 ATTT--A-TAAT-TAAAATATTAATA
*
4399690 ATTTATAATTAAAATATTAACA
1 ATTTATAATTAAAATATTAATA
4399712 ATTTAT
1 ATTTAT
4399718 TCATAATTTA
Statistics
Matches: 118, Mismatches: 32, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
20 5 0.04
21 28 0.24
22 48 0.41
23 7 0.06
24 13 0.11
25 3 0.03
26 14 0.12
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTATAATTAAAATATTAATA
Found at i:4400052 original size:2 final size:2
Alignment explanation
Indices: 4400047--4400074 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4400037 ACACACACAA
4400047 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
4400075 TTCAATGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4401517 original size:21 final size:21
Alignment explanation
Indices: 4401479--4401518 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4401469 TGCTACTGGA
*
4401479 CAAAACCCTTAAATTTTAATC
1 CAAAACCCTTAAACTTTAATC
4401500 CAAAATCCCTT-AACTTTAA
1 CAAAA-CCCTTAAACTTTAA
4401519 ATTAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (21 bp):
CAAAACCCTTAAACTTTAATC
Found at i:4404967 original size:16 final size:16
Alignment explanation
Indices: 4404946--4404976 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4404936 GCGAGACTAA
*
4404946 TACCACTATCCCTATT
1 TACCACTACCCCTATT
4404962 TACCACTACCCCTAT
1 TACCACTACCCCTAT
4404977 AGGTATAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.42, G:0.00, T:0.32
Consensus pattern (16 bp):
TACCACTACCCCTATT
Found at i:4408480 original size:25 final size:25
Alignment explanation
Indices: 4408452--4408505 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
4408442 ATATATAGTT
4408452 TAATATA-TACATGTATACATATAT-A
1 TAATATATTA-ATGTATA-ATATATCA
* *
4408477 TAATTTATTAATTTATAATATATCA
1 TAATATATTAATGTATAATATATCA
4408502 TAAT
1 TAAT
4408506 GATAATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (25 bp):
TAATATATTAATGTATAATATATCA
Found at i:4409263 original size:23 final size:25
Alignment explanation
Indices: 4409235--4409289 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
4409225 AAATATATAT
4409235 TATAATTAACATAT-ACATAATT-A
1 TATAATTAACATATAACATAATTAA
* *
4409258 TATAATT-ATATATAATATAATTAA
1 TATAATTAACATATAACATAATTAA
4409282 TATAATTA
1 TATAATTA
4409290 TAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 14 0.52
24 8 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TATAATTAACATATAACATAATTAA
Found at i:4409275 original size:15 final size:14
Alignment explanation
Indices: 4409257--4409293 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
4409247 ATACATAATT
4409257 ATATAATTATATATA
1 ATATAATTA-ATATA
4409272 ATATAATTAATATA
1 ATATAATTAATATA
4409286 ATTATAAT
1 A-TATAAT
4409294 ATTTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATAATTAATATA
Found at i:4409282 original size:9 final size:9
Alignment explanation
Indices: 4409251--4409289 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
4409241 TAACATATAC
4409251 ATAATT-AT
1 ATAATTAAT
4409259 ATAATT-AT
1 ATAATTAAT
4409267 AT-A-TAAT
1 ATAATTAAT
4409274 ATAATTAAT
1 ATAATTAAT
4409283 ATAATTA
1 ATAATTA
4409290 TAATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.04
7 5 0.18
8 11 0.39
9 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATAATTAAT
Found at i:4409285 original size:18 final size:18
Alignment explanation
Indices: 4409227--4409295 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 18
4409217 TGTAAATCAA
*
4409227 ATATATATTATAATTAACAT
1 ATATATAATATAATT-A-AT
*
4409247 ATACATAAT-T-ATATAATT
1 ATATATAATATAAT-TAA-T
4409265 ATATATAATATAATTAAT
1 ATATATAATATAATTAAT
4409283 ATAATTATAATAT
1 AT-A-TATAATAT
4409296 TTTAATTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
17 1 0.03
18 15 0.38
19 7 0.17
20 17 0.43
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATATAATATAATTAAT
Found at i:4409973 original size:23 final size:23
Alignment explanation
Indices: 4409947--4410022 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
4409937 TATGTAATCA
* *
4409947 TATAAATAAAGTGTATTATAAAT
1 TATAAATAATGTATATTATAAAT
* *
4409970 TATAAA-AATGTTTATGTGTAAAT
1 TATAAATAATGTATAT-TATAAAT
*
4409993 TATATAT-ATGTATATTAT-AAT
1 TATAAATAATGTATATTATAAAT
4410014 TAATAAATA
1 T-ATAAATA
4410023 CATACTTATA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.10
22 14 0.33
23 24 0.57
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (23 bp):
TATAAATAATGTATATTATAAAT
Found at i:4412088 original size:20 final size:19
Alignment explanation
Indices: 4412063--4412144 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 19
4412053 TTTTTTCATT
4412063 AAAAGAAAGAGAAGAAAGGA
1 AAAAGAAAGA-AAGAAAGGA
*
4412083 AAAAGAGAGACAA-AAAGGGA
1 AAAAGAAAGA-AAGAAA-GGA
* *
4412103 AAAACAAA-AAAGATAAAGA
1 AAAAGAAAGAAAGA-AAGGA
*
4412122 AAAA-AAGGAAAAAGAAAGGA
1 AAAAGAA--AGAAAGAAAGGA
4412142 AAA
1 AAA
4412145 GGAGAAAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 4 0.08
19 11 0.22
20 30 0.60
21 5 0.10
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.01
Consensus pattern (19 bp):
AAAAGAAAGAAAGAAAGGA
Found at i:4412100 original size:19 final size:21
Alignment explanation
Indices: 4412063--4412106 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
4412053 TTTTTTCATT
*
4412063 AAAAGAAAGAGAAGAAA-GGA
1 AAAAGAAAGACAAGAAAGGGA
*
4412083 AAAAGAGAGACAA-AAAGGGA
1 AAAAGAAAGACAAGAAAGGGA
4412103 AAAA
1 AAAA
4412107 CAAAAAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGACAAGAAAGGGA
Found at i:4412125 original size:14 final size:15
Alignment explanation
Indices: 4412094--4412155 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 15
4412084 AAAGAGAGAC
* *
4412094 AAAAAGGGAAAAA-C
1 AAAAAAGGAAAAAGA
*
4412108 AAAAAA-GATAAAGA
1 AAAAAAGGAAAAAGA
4412122 AAAAAAGGAAAAAGA
1 AAAAAAGGAAAAAGA
4412137 AAGGAAAAGGAGAAAAGA
1 AA--AAAAGGA-AAAAGA
4412155 A
1 A
4412156 CAAGAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 5 0.13
14 11 0.28
15 9 0.23
17 7 0.18
18 7 0.18
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (15 bp):
AAAAAAGGAAAAAGA
Found at i:4412126 original size:21 final size:20
Alignment explanation
Indices: 4412102--4412144 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
4412092 ACAAAAAGGG
4412102 AAAAACAAAAAAGATAAAGAA
1 AAAAACAAAAAAGA-AAAGAA
** *
4412123 AAAAAGGAAAAAGAAAGGAA
1 AAAAACAAAAAAGAAAAGAA
4412143 AA
1 AA
4412145 GGAGAAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAACAAAAAAGAAAAGAA
Found at i:4412580 original size:20 final size:19
Alignment explanation
Indices: 4412555--4412637 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 19
4412545 TTTTTTCATT
4412555 AAAAGAAAGAGAAGAAAGGA
1 AAAAGAAAGA-AAGAAAGGA
*
4412575 AAAAGAGAGACAA-AAAGGGA
1 AAAAGAAAGA-AAGAAA-GGA
* *
4412595 AAAACAAA-AAAGATAAAGA
1 AAAAGAAAGAAAGA-AAGGA
4412614 AAAA-AAAGGAAAAAGAAAGGA
1 AAAAGAAA-G--AAAGAAAGGA
4412635 AAA
1 AAA
4412638 GGAAGAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.10
19 11 0.22
20 22 0.44
21 7 0.14
22 5 0.10
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.01
Consensus pattern (19 bp):
AAAAGAAAGAAAGAAAGGA
Found at i:4412592 original size:19 final size:21
Alignment explanation
Indices: 4412555--4412598 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
4412545 TTTTTTCATT
*
4412555 AAAAGAAAGAGAAGAAA-GGA
1 AAAAGAAAGACAAGAAAGGGA
*
4412575 AAAAGAGAGACAA-AAAGGGA
1 AAAAGAAAGACAAGAAAGGGA
4412595 AAAA
1 AAAA
4412599 CAAAAAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGACAAGAAAGGGA
Found at i:4413072 original size:20 final size:19
Alignment explanation
Indices: 4413047--4413129 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 19
4413037 TTTTTTCATT
4413047 AAAAGAAAGAGAAGAAAGGA
1 AAAAGAAAGA-AAGAAAGGA
*
4413067 AAAAGAGAGACAA-AAAGGGA
1 AAAAGAAAGA-AAGAAA-GGA
* *
4413087 AAAACAAA-AAAGATAAAGA
1 AAAAGAAAGAAAGA-AAGGA
4413106 AAAA-AAAGGAAAAAGAAAGGA
1 AAAAGAAA-G--AAAGAAAGGA
4413127 AAA
1 AAA
4413130 GGAGAAAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.10
19 11 0.22
20 22 0.44
21 7 0.14
22 5 0.10
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.01
Consensus pattern (19 bp):
AAAAGAAAGAAAGAAAGGA
Found at i:4413084 original size:19 final size:21
Alignment explanation
Indices: 4413047--4413090 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
4413037 TTTTTTCATT
*
4413047 AAAAGAAAGAGAAGAAA-GGA
1 AAAAGAAAGACAAGAAAGGGA
*
4413067 AAAAGAGAGACAA-AAAGGGA
1 AAAAGAAAGACAAGAAAGGGA
4413087 AAAA
1 AAAA
4413091 CAAAAAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGACAAGAAAGGGA
Found at i:4413095 original size:492 final size:492
Alignment explanation
Indices: 4411710--4413171 Score: 2723
Period size: 494 Copynumber: 3.0 Consensus size: 492
4411700 AAATTAGGAG
*
4411710 TTATGATGGAGGATAAATTTATCTTGGTCCTTAAGTAGCCCTTTCATGCAGTGGAGTGATACGAC
1 TTATAATGGAGGATAAATTTATCTTGGTCCTTAAGTAGCCC-TTCATG-AGTGGAGTGATACGAC
4411775 ATTGGGGTAAGGATGTGGATGTGTTGTAGACTATTTAATTGAGCCCTTTTGGCTT-TTTTTCA-T
64 ATTGGGGTAAGGATGTGGATGTGTTGTAGACTATTTAATTGAGCCCTTTTGGCTTCTTTTTCATT
4411838 TCCTTTAGTTCGCCTTTAACTTTTCTTGCCTGTTGATTGTTTATTTATTATTTATTTTATTTTC-
129 TCCTTTAGTTCGCCTTTAACTTTTCTTGCCTGTTGATTGTTTATTTATTATTTATTTTATTTTCT
*
4411902 TCCTTAATTTTCTAAGAATTACTCTCTAACTTCCATTGTCTTCTTAAGGCAACTTCTTTT-GAAA
194 TCCTTAATTTTCTAAGAATTACTCTCTAATTTCCATTGTCTTCTTAAGGCAACTTCTTTTGGAAA
*
4411966 AGAACTGTGATTTGTGTTGTAAGTTCTTGTAGGATGGTGGTTTAAGGTTTTATGAGTCTGTTGGG
259 AGAACTGTGATTTGTGTTGTAAGTTCTTGTAGGATGGTGGTTTAAGGTTTTATGAGTCTGTTGAG
*
4412031 CAA--AAAAGTAAAGAATTTTTTATTTTTTCATTAAAAGAAAGAGAAGAAAGGAAAAAGAGAGAC
324 CAATGAAAGGTAAAGAATTTTTTATTTTTTCATTAAAAGAAAGAGAAGAAAGGAAAAAGAGAGAC
4412094 AAAAAGGGAAAAACAAAAAAGATAAAG-AAAAAAAGGAAAAAGAAAGGAAAAGGAGAAAAGAACA
389 AAAAAGGGAAAAACAAAAAAGATAAAGAAAAAAAAGGAAAAAGAAAGGAAAAGGAGAAAAGAACA
4412158 AGAAAAAAATGTATGGTATAGTTCAACATTGGGGTAAAT
454 AGAAAAAAATGTATGGTATAGTTCAACATTGGGGTAAAT
4412197 TTATAATGGAGGATAAATTTATCTTGGTCCTTAAGTAGCCCTTCATGAGTGGAGTGATACGACAT
1 TTATAATGGAGGATAAATTTATCTTGGTCCTTAAGTAGCCCTTCATGAGTGGAGTGATACGACAT
4412262 TGGGGTAAGGATGTGGATGTGTTGTAGACTATTTAATTGAGCCCTTTTGGCTTCTTTTTCATTTC
66 TGGGGTAAGGATGTGGATGTGTTGTAGACTATTTAATTGAGCCCTTTTGGCTTCTTTTTCATTTC
4412327 CTTTAGTT-GCCTTTAACTTTTCTTGCCTGTTGATTGTTTATTTATTATTTATTTTATTTTTCTT
131 CTTTAGTTCGCCTTTAACTTTTCTTGCCTGTTGATTGTTTATTTATTATTTATTTTA-TTTTCTT
4412391 -CTTAATTTTCTAAGAATTACTCTCTAATTTCCATTGTCTTCTTAAGGCAACTTC-TTTGGAAAA
195 CCTTAATTTTCTAAGAATTACTCTCTAATTTCCATTGTCTTCTTAAGGCAACTTCTTTTGGAAAA
4412454 GAAACTGTTGATTTGTGTTGTAAGTTCTTGTAGGATGGTGGTTTAAGGTTTTATGAGTCTGTTGA
260 G-AACTG-TGATTTGTGTTGTAAGTTCTTGTAGGATGGTGGTTTAAGGTTTTATGAGTCTGTTGA
4412519 GGCAATGAAAGGTAAAGAATTTTTTATTTTTTCATTAAAAGAAAGAGAAGAAAGGAAAAAGAGAG
323 -GCAATGAAAGGTAAAGAATTTTTTATTTTTTCATTAAAAGAAAGAGAAGAAAGGAAAAAGAGAG
4412584 ACAAAAAGGGAAAAACAAAAAAGATAAAGAAAAAAAAGGAAAAAGAAAGGAAAAGGAAGAAAATG
387 ACAAAAAGGGAAAAACAAAAAAGATAAAGAAAAAAAAGGAAAAAGAAAGGAAAAGG-AGAAAA-G
4412649 AACAAGAAAAAAATGTATGGTA-AGTTCAACATTGGGGTAAAT
450 AACAAGAAAAAAATGTATGGTATAGTTCAACATTGGGGTAAAT
4412691 TTATAATGGAGGATAAATTTATCTTGGTCCTTAAGTAGCCCTTCATGAGTGGAGTGATACGACAT
1 TTATAATGGAGGATAAATTTATCTTGGTCCTTAAGTAGCCCTTCATGAGTGGAGTGATACGACAT
4412756 TGGGGTAAGGATGTGGATGTGTTGTAG-CTATTTAATTGAGCCCTTTTGGCTTCTTTTTCATTTC
66 TGGGGTAAGGATGTGGATGTGTTGTAGACTATTTAATTGAGCCCTTTTGGCTTCTTTTTCATTTC
4412820 CTTTAGTTCGCCTTTAACTTTTCTTGCCTGTTGATTGTTTATTTATTATTTATTTTATTTTCTTC
131 CTTTAGTTCGCCTTTAACTTTTCTTGCCTGTTGATTGTTTATTTATTATTTATTTTATTTTCTTC
4412885 CTTAATTTTCTAAGAATTACTCTCTAATTTCCATTGTCTTCTTAAGGCAACTTCTTTTGGAAAAG
196 CTTAATTTTCTAAGAATTACTCTCTAATTTCCATTGTCTTCTTAAGGCAACTTCTTTTGGAAAAG
4412950 AACTGTGATTTGTGTTGTAAGTTCTTGTAGGATGGTGGTTTAAGGTTTTATGAGTCTGTTGAGCA
261 AACTGTGATTTGTGTTGTAAGTTCTTGTAGGATGGTGGTTTAAGGTTTTATGAGTCTGTTGAGCA
4413015 ATGAAAGGTAAAGAATTTTTTATTTTTTCATTAAAAGAAAGAGAAGAAAGGAAAAAGAGAGACAA
326 ATGAAAGGTAAAGAATTTTTTATTTTTTCATTAAAAGAAAGAGAAGAAAGGAAAAAGAGAGACAA
4413080 AAAGGGAAAAACAAAAAAGATAAAGAAAAAAAAGGAAAAAGAAAGGAAAAGGAGAAAAGGAACAA
391 AAAGGGAAAAACAAAAAAGATAAAGAAAAAAAAGGAAAAAGAAAGGAAAAGGAGAAAA-GAACAA
4413145 GAAAAAAATGTATGGTATAGTTCAACA
455 GAAAAAAATGTATGGTATAGTTCAACA
4413172 CCCTTTTCTT
Statistics
Matches: 953, Mismatches: 5, Indels: 29
0.97 0.01 0.03
Matches are distributed among these distances:
485 71 0.07
486 64 0.07
487 115 0.12
488 6 0.01
489 56 0.06
490 4 0.00
491 29 0.03
492 215 0.23
493 135 0.14
494 225 0.24
495 33 0.03
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (492 bp):
TTATAATGGAGGATAAATTTATCTTGGTCCTTAAGTAGCCCTTCATGAGTGGAGTGATACGACAT
TGGGGTAAGGATGTGGATGTGTTGTAGACTATTTAATTGAGCCCTTTTGGCTTCTTTTTCATTTC
CTTTAGTTCGCCTTTAACTTTTCTTGCCTGTTGATTGTTTATTTATTATTTATTTTATTTTCTTC
CTTAATTTTCTAAGAATTACTCTCTAATTTCCATTGTCTTCTTAAGGCAACTTCTTTTGGAAAAG
AACTGTGATTTGTGTTGTAAGTTCTTGTAGGATGGTGGTTTAAGGTTTTATGAGTCTGTTGAGCA
ATGAAAGGTAAAGAATTTTTTATTTTTTCATTAAAAGAAAGAGAAGAAAGGAAAAAGAGAGACAA
AAAGGGAAAAACAAAAAAGATAAAGAAAAAAAAGGAAAAAGAAAGGAAAAGGAGAAAAGAACAAG
AAAAAAATGTATGGTATAGTTCAACATTGGGGTAAAT
Found at i:4413119 original size:10 final size:11
Alignment explanation
Indices: 4413093--4413148 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
4413083 GGGAAAAACA
*
4413093 AAAAAGATAAAG
1 AAAAAGA-AAGG
4413105 AAAAA-AAAGG
1 AAAAAGAAAGG
4413115 AAAAAGAAAGG
1 AAAAAGAAAGG
4413126 AAAAGGAGAAAAGG
1 AAAA--AG-AAAGG
*
4413140 AACAAGAAA
1 AAAAAGAAA
4413149 AAAATGTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 8 0.21
11 13 0.34
12 7 0.18
13 2 0.05
14 8 0.21
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGG
Found at i:4413579 original size:6 final size:6
Alignment explanation
Indices: 4413558--4413593 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
4413548 ATAGGGTATG
*
4413558 AAAAGA AGAA-A AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A
4413594 GAGAGGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:4417768 original size:28 final size:29
Alignment explanation
Indices: 4417720--4417781 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
4417710 ACTAAGTATT
*
4417720 ATTTTATCATTGGTAAGTAT-ATTTTAAA
1 ATTTTATCATTGGTAAATATAATTTTAAA
*
4417748 ATTTTATCATTGG-AGAATATAATTTTAAT
1 ATTTTATCATTGGTA-AATATAATTTTAAA
4417777 ATTTT
1 ATTTT
4417782 GAAGGCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 1 0.03
28 17 0.57
29 12 0.40
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (29 bp):
ATTTTATCATTGGTAAATATAATTTTAAA
Found at i:4420478 original size:21 final size:21
Alignment explanation
Indices: 4420387--4420479 Score: 52
Period size: 21 Copynumber: 4.5 Consensus size: 21
4420377 AAAAAAAGAA
*
4420387 AACTCATAATCAAAGAAAGGG
1 AACTCATAATCAAAGAAAAGG
* *
4420408 AACTTATAAGCATAAGTAATTAAGG
1 AACTCATAATCA-AAG-AA--AAGG
* *
4420433 AATTCATAAT-TAA-AAAA--
1 AACTCATAATCAAAGAAAAGG
* *
4420450 AA-TGATAATTAAAGAAAAGG
1 AACTCATAATCAAAGAAAAGG
4420470 AACTCATAAT
1 AACTCATAAT
4420480 AAGGAGGTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 18
0.65 0.12 0.22
Matches are distributed among these distances:
16 6 0.11
17 4 0.08
18 4 0.08
19 2 0.04
20 2 0.04
21 18 0.34
22 3 0.06
23 4 0.08
25 10 0.19
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.24
Consensus pattern (21 bp):
AACTCATAATCAAAGAAAAGG
Found at i:4420757 original size:212 final size:212
Alignment explanation
Indices: 4420389--4420811 Score: 616
Period size: 212 Copynumber: 2.0 Consensus size: 212
4420379 AAAAAGAAAA
* * *
4420389 CTCATAATCAAAGAAAGGGAACTTATAAGCATAAGTAATTAAGGAATTCATAATTAAAAAAAATG
1 CTCATAATCAAAGAAAAGGAACTTATAAACATAAGTAATTAAGGAATTCATAATTAAAAAAAAGG
* *
4420454 ATAATTAAAGAAAAGGAACTCATAATAAGGAGGTTTCGTTGAACATATTTACACAACAAAGAATA
66 ATAATTAAAGAAAAGGAACTCATAATAAGAAGGTTTCGTTGAACACATTTACACAACAAAGAATA
* * * *
4420519 ATACTATCAATTCCAAAAAGTAGTTGCATTATCATCAAATAATACCAAAGTGGGTCTTGAGTTTG
131 ATACCATCAATTCCAAAAAATAGTTGCATTATCATCAAATAATACCAAAATGGGTCTTGAGCTTG
4420584 GCAG-TGCTTGTGAGATG
196 GCAGCT-CTTGTGAGATG
* * * * *
4420601 CTCATAATTAAAGAAAAGGAACTTTTAAATATAAGTAATTAA-GAATCTCATAATTAAAGAAAGG
1 CTCATAATCAAAGAAAAGGAACTTATAAACATAAGTAATTAAGGAAT-TCATAATTAAAAAAAAG
* * * * **
4420665 GATAATTAAAGAAAAGGAACTCATAATGAGAAGGTTTTGTTGAACACGTTTACAGAAGGAAGAAT
65 GATAATTAAAGAAAAGGAACTCATAATAAGAAGGTTTCGTTGAACACATTTACACAACAAAGAAT
*
4420730 AATACCATCAATTCCAAAAAATAGTTGCATTGTCATCAAATAATACCAAAATGGGTCTTGAGCTT
130 AATACCATCAATTCCAAAAAATAGTTGCATTATCATCAAATAATACCAAAATGGGTCTTGAGCTT
*
4420795 GGCGGCTCTTGTGAGAT
195 GGCAGCTCTTGTGAGAT
4420812 AATTACAAGT
Statistics
Matches: 187, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
211 4 0.02
212 182 0.97
213 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.27
Consensus pattern (212 bp):
CTCATAATCAAAGAAAAGGAACTTATAAACATAAGTAATTAAGGAATTCATAATTAAAAAAAAGG
ATAATTAAAGAAAAGGAACTCATAATAAGAAGGTTTCGTTGAACACATTTACACAACAAAGAATA
ATACCATCAATTCCAAAAAATAGTTGCATTATCATCAAATAATACCAAAATGGGTCTTGAGCTTG
GCAGCTCTTGTGAGATG
Found at i:4423472 original size:18 final size:18
Alignment explanation
Indices: 4423444--4423487 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
4423434 TTAATTGGAT
* *
4423444 ATAAAAA-TATTTTTAGA
1 ATAAAAATTATTTGTAAA
*
4423461 ATGAAAATTATTTGTAAA
1 ATAAAAATTATTTGTAAA
4423479 ATAAAAATT
1 ATAAAAATT
4423488 CTATTTGCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (18 bp):
ATAAAAATTATTTGTAAA
Found at i:4426680 original size:36 final size:37
Alignment explanation
Indices: 4426615--4426686 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
4426605 CTTGCGTATG
* *
4426615 GGCTAGTAATTAGAAGATTTGATTTTCAAAAATCTTA
1 GGCTAATAATTAGAAGATTTGATTCTCAAAAATCTTA
*
4426652 GGCTAATAATTAGACG-TTTGATTCTCAAAAATCTT
1 GGCTAATAATTAGAAGATTTGATTCTCAAAAATCTT
4426687 GGTTGTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (37 bp):
GGCTAATAATTAGAAGATTTGATTCTCAAAAATCTTA
Found at i:4429572 original size:20 final size:20
Alignment explanation
Indices: 4429547--4429588 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4429537 AAAACTCGTG
*
4429547 TAAATGTATTGACACATTCC
1 TAAATGTATTGACACATCCC
*
4429567 TAAATGTATTGATACATCCC
1 TAAATGTATTGACACATCCC
4429587 TA
1 TA
4429589 GGTGTTGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
TAAATGTATTGACACATCCC
Found at i:4439482 original size:30 final size:30
Alignment explanation
Indices: 4439448--4439522 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
4439438 ATCTCTTAAT
4439448 TGAAGATGAAGAAGATGACATGCAAAGAGA
1 TGAAGATGAAGAAGATGACATGCAAAGAGA
* **
4439478 TGAAGATGAAGAAGATGACATGGACGGAGA
1 TGAAGATGAAGAAGATGACATGCAAAGAGA
*
4439508 TAAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
4439523 AGAAGTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.49, C:0.05, G:0.32, T:0.13
Consensus pattern (30 bp):
TGAAGATGAAGAAGATGACATGCAAAGAGA
Found at i:4439493 original size:15 final size:15
Alignment explanation
Indices: 4439448--4439534 Score: 63
Period size: 15 Copynumber: 5.8 Consensus size: 15
4439438 ATCTCTTAAT
4439448 TGAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
*
4439463 TG-ACATGCAA-AGAGA
1 TGAAGATG-AAGA-AGA
4439478 TGAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
* * *
4439493 TG-ACATGGACGGAGA
1 TGAAGAT-GAAGAAGA
*
4439508 TAAAGATGAAGAAGA
1 TGAAGATGAAGAAGA
* *
4439523 AGAAGTTGAAGA
1 TGAAGATGAAGA
4439535 TGAAAATGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
14 8 0.15
15 38 0.70
16 8 0.15
ACGTcount: A:0.49, C:0.05, G:0.32, T:0.14
Consensus pattern (15 bp):
TGAAGATGAAGAAGA
Found at i:4442099 original size:30 final size:29
Alignment explanation
Indices: 4442063--4442203 Score: 123
Period size: 30 Copynumber: 4.8 Consensus size: 29
4442053 AATGTCGAAT
*
4442063 AGAAAATTTCGTTGG-AAAGTCAAT-TCCAAC
1 AGAAAATTTCGTTGGCAAAG---ATGGCCAAC
* **
4442093 AGAAAATTTTGTTGG--AA-ATTTCCAAC
1 AGAAAATTTCGTTGGCAAAGATGGCCAAC
4442119 -GAAAAATTTCGTTGGCAAAGAATGGCCAAC
1 AG-AAAATTTCGTTGGCAAAG-ATGGCCAAC
*
4442149 AAAAAATTTCGTTGGCAAAGCATGGCCAAC
1 AGAAAATTTCGTTGGCAAAG-ATGGCCAAC
*
4442179 AAAAAATTTCGTTGGCAAAGCATGG
1 AGAAAATTTCGTTGGCAAAG-ATGG
4442204 AACTGAATTT
Statistics
Matches: 98, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
25 3 0.03
26 18 0.18
28 2 0.02
29 2 0.02
30 73 0.74
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (29 bp):
AGAAAATTTCGTTGGCAAAGATGGCCAAC
Found at i:4442111 original size:56 final size:56
Alignment explanation
Indices: 4442033--4442203 Score: 143
Period size: 56 Copynumber: 3.0 Consensus size: 56
4442023 AAAGAATTTT
* * * * *
4442033 CAACGGAAAATTCCGTTTGAAATGTCGAATAG-AAAATTTCGTTGG-AAAGTCAAT-TC
1 CAACAGAAAATTTCGTTGGAAATGTCCAA-AGAAAAATTTCGTTGGCAAAG--AATGGC
* * *
4442089 CAACAGAAAATTTTGTTGGAAATTTCCAACGAAAAATTTCGTTGGCAAAGAATGGC
1 CAACAGAAAATTTCGTTGGAAATGTCCAAAGAAAAATTTCGTTGGCAAAGAATGGC
* * *
4442145 CAACAAAAAATTTCGTTGGCAAAGCATGGCCAACA-AAAAATTTCGTTGGCAAAGCATGG
1 CAACAGAAAATTTCGTTGG--AA--ATGTCCAA-AGAAAAATTTCGTTGGCAAAGAATGG
4442204 AACTGAATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
55 4 0.04
56 54 0.58
57 4 0.04
58 2 0.02
60 29 0.31
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (56 bp):
CAACAGAAAATTTCGTTGGAAATGTCCAAAGAAAAATTTCGTTGGCAAAGAATGGC
Found at i:4444768 original size:27 final size:27
Alignment explanation
Indices: 4444737--4444800 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
4444727 ATTCCTTGTT
4444737 AGGACCAATAGAAACAAGTCTATATAG
1 AGGACCAATAGAAACAAGTCTATATAG
4444764 AGGACCAATAGAAACAAGTCTATATAG
1 AGGACCAATAGAAACAAGTCTATATAG
* *
4444791 AAGACTAATA
1 AGGACCAATA
4444801 CATTTCAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (27 bp):
AGGACCAATAGAAACAAGTCTATATAG
Found at i:4448124 original size:34 final size:32
Alignment explanation
Indices: 4448076--4448148 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
4448066 ATAAACATAG
** *
4448076 TCATCATCTGGAGTAATCTCCCAATGGATGGCAA
1 TCATCATCCAGAGTAATCT-CAAATGGATGGC-A
* *
4448110 TCATCATCCAGAGTAGTCTCAAATGGGTGGCA
1 TCATCATCCAGAGTAATCTCAAATGGATGGCA
4448142 TCATCAT
1 TCATCAT
4448149 AATTGTCATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 8 0.24
33 10 0.29
34 16 0.47
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (32 bp):
TCATCATCCAGAGTAATCTCAAATGGATGGCA
Found at i:4448598 original size:2 final size:2
Alignment explanation
Indices: 4448591--4448615 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4448581 TAAATCAAAC
4448591 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 A
4448616 AAAGTCCTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4449331 original size:18 final size:18
Alignment explanation
Indices: 4449308--4449353 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4449298 GGGTATCCCT
4449308 TTTCATTTCAATTTTACA
1 TTTCATTTCAATTTTACA
* *
4449326 TTTCATTTC-CTTTTTCA
1 TTTCATTTCAATTTTACA
4449343 TTTACATTTCA
1 TTT-CATTTCA
4449354 TTTGATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTCATTTCAATTTTACA
Found at i:4449334 original size:23 final size:21
Alignment explanation
Indices: 4449308--4449361 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
4449298 GGGTATCCCT
4449308 TTTCATTTCAATTTTACATTTCA
1 TTTCATTTC-A-TTTACATTTCA
*
4449331 TTTCCTTTTTCATTTACATTTCA
1 TTT-C-ATTTCATTTACATTTCA
*
4449354 TTTGATTT
1 TTTCATTT
4449362 TGTCGGTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 3 0.12
23 17 0.65
24 2 0.08
25 4 0.15
ACGTcount: A:0.20, C:0.17, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTCATTTCATTTACATTTCA
Found at i:4454518 original size:18 final size:19
Alignment explanation
Indices: 4454490--4454533 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
4454480 GGTCATGAAA
4454490 TTTTTCAAAATTTAT-TTGT
1 TTTTTCAAAATTT-TCTTGT
4454509 TTTTTC-AAATTTTCTTGT
1 TTTTTCAAAATTTTCTTGT
4454527 TCTTTTC
1 T-TTTTC
4454534 TTAACTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTCAAAATTTTCTTGT
Found at i:4462402 original size:24 final size:24
Alignment explanation
Indices: 4462375--4462428 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4462365 ATGTTTCTGG
* *
4462375 TCAATGTATCATTGAGACTGGATA
1 TCAATGTATCATTGAGACTAGACA
4462399 TCAATGTATCATTGAGACTAGACA
1 TCAATGTATCATTGAGACTAGACA
4462423 TCAATG
1 TCAATG
4462429 ATGCTTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (24 bp):
TCAATGTATCATTGAGACTAGACA
Found at i:4462683 original size:14 final size:14
Alignment explanation
Indices: 4462664--4462699 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
4462654 ACGTGAAATG
4462664 CTATACTTGAGTGT
1 CTATACTTGAGTGT
4462678 CTATACACTTGAGTGT
1 CTAT--ACTTGAGTGT
4462694 CTATAC
1 CTATAC
4462700 AACACTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
16 14 0.70
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (14 bp):
CTATACTTGAGTGT
Found at i:4462706 original size:19 final size:16
Alignment explanation
Indices: 4462668--4462700 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4462658 GAAATGCTAT
4462668 ACTTGAGTGTCTATAC
1 ACTTGAGTGTCTATAC
4462684 ACTTGAGTGTCTATAC
1 ACTTGAGTGTCTATAC
4462700 A
1 A
4462701 ACACTTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (16 bp):
ACTTGAGTGTCTATAC
Found at i:4462761 original size:108 final size:108
Alignment explanation
Indices: 4462572--4462779 Score: 380
Period size: 108 Copynumber: 1.9 Consensus size: 108
4462562 TGTCTTGGTA
*
4462572 ATACACTTGAGTGTCTATACAAAACTTCTTATGTCTCAGTCGTGTAAATACTCCTTACACTTAAG
1 ATACACTTGAGTGTCTATACAAAACTTCTCATGTCTCAGTCGTGTAAATACTCCTTACACTTAAG
*
4462637 ACACTAGATTATCTTTTACGTGAAATGCTATACTTGAGTGTCT
66 ACACTAGATTATCTTTTACGTAAAATGCTATACTTGAGTGTCT
*
4462680 ATACACTTGAGTGTCTATACAACACTTCTCATGTCTCAGTCGTGTAAATACTCCTTACACTTAAG
1 ATACACTTGAGTGTCTATACAAAACTTCTCATGTCTCAGTCGTGTAAATACTCCTTACACTTAAG
*
4462745 ACACTAGGTTATCTTTTACGTAAAATGCTATACTT
66 ACACTAGATTATCTTTTACGTAAAATGCTATACTT
4462780 TAATTTCATC
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 96 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (108 bp):
ATACACTTGAGTGTCTATACAAAACTTCTCATGTCTCAGTCGTGTAAATACTCCTTACACTTAAG
ACACTAGATTATCTTTTACGTAAAATGCTATACTTGAGTGTCT
Found at i:4466041 original size:36 final size:36
Alignment explanation
Indices: 4465992--4466061 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
4465982 TCTAAGAGAG
* *
4465992 AGAAAATGCTGAAACTATAAGAATGAGAGATTGACA
1 AGAAAATGCTGAAACCATAAGAAGGAGAGATTGACA
* * *
4466028 AGAAATTGTTGAAACCCTAAGAAGGAGAGATTGA
1 AGAAAATGCTGAAACCATAAGAAGGAGAGATTGA
4466062 AGAATTTGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.20
Consensus pattern (36 bp):
AGAAAATGCTGAAACCATAAGAAGGAGAGATTGACA
Found at i:4468735 original size:13 final size:13
Alignment explanation
Indices: 4468713--4468760 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
4468703 TCTTTACACC
*
4468713 TCTTTCTCTTTTT
1 TCTTTTTCTTTTT
4468726 TCTTTTTC-TTTT
1 TCTTTTTCTTTTT
4468738 TCTCTTTTCTTTTCT
1 TCT-TTTTCTTTT-T
4468753 GTCTTTTT
1 -TCTTTTT
4468761 ATATTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 7 0.23
13 12 0.40
14 3 0.10
15 5 0.17
16 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (13 bp):
TCTTTTTCTTTTT
Found at i:4468745 original size:19 final size:19
Alignment explanation
Indices: 4468713--4468750 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4468703 TCTTTACACC
*
4468713 TCTTTCTCTTTTTTCTTTT
1 TCTTTCTCTCTTTTCTTTT
*
4468732 TCTTTTTCTCTTTTCTTTT
1 TCTTTCTCTCTTTTCTTTT
4468751 CTGTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTTTCTCTCTTTTCTTTT
Found at i:4468980 original size:14 final size:14
Alignment explanation
Indices: 4468954--4469008 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
4468944 TGAAATCCTG
4468954 TATTTCATA-TTTAT
1 TATTT-ATATTTTAT
4468968 TATTTATATTTTAT
1 TATTTATATTTTAT
*
4468982 TTTTTATATTTTAT
1 TATTTATATTTTAT
*
4468996 GT-TTTATTTTTTA
1 -TATTTATATTTTA
4469009 AGTTTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
13 3 0.08
14 33 0.89
15 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (14 bp):
TATTTATATTTTAT
Found at i:4468986 original size:7 final size:7
Alignment explanation
Indices: 4468963--4469008 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
4468953 GTATTTCATA
*
4468963 TTTATTA
1 TTTATTT
*
4468970 TTTATAT
1 TTTATTT
4468977 TTTATTT
1 TTTATTT
*
4468984 TTTATAT
1 TTTATTT
*
4468991 TTTATGT
1 TTTATTT
4468998 TTTATTT
1 TTTATTT
4469005 TTTA
1 TTTA
4469009 AGTTTAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (7 bp):
TTTATTT
Found at i:4469013 original size:14 final size:14
Alignment explanation
Indices: 4468970--4469013 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4468960 ATATTTATTA
**
4468970 TTTATATTTTATTT
1 TTTATATTTTAAGT
*
4468984 TTTATATTTTATGT
1 TTTATATTTTAAGT
*
4468998 TTTATTTTTTAAGT
1 TTTATATTTTAAGT
4469012 TT
1 TT
4469014 AAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (14 bp):
TTTATATTTTAAGT
Found at i:4472788 original size:31 final size:31
Alignment explanation
Indices: 4472750--4472843 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 31
4472740 AACAATGACT
**
4472750 AGGTAGGTGGGAGCT-AAGCAGGTTAAAGAGA
1 AGGTAGGTGAAAGCTAAAG-AGGTTAAAGAGA
**
4472781 AGGTAGGTGAAAGCTAAAGAGGTTCGAGAGA
1 AGGTAGGTGAAAGCTAAAGAGGTTAAAGAGA
* * * *
4472812 AAGTAGGTGAAAGGTATAGAGGTTACAGAGA
1 AGGTAGGTGAAAGCTAAAGAGGTTAAAGAGA
4472843 A
1 A
4472844 CATGAGAGGC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 50 0.94
32 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.38, T:0.17
Consensus pattern (31 bp):
AGGTAGGTGAAAGCTAAAGAGGTTAAAGAGA
Found at i:4473189 original size:24 final size:24
Alignment explanation
Indices: 4473156--4473210 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
4473146 AGTTGCTAAA
*
4473156 ATTTTGTGTTGTTTCTTTCATATG
1 ATTTTTTGTTGTTTCTTTCATATG
* **
4473180 ATTTTTTGTTGTTTGTTTTGTATG
1 ATTTTTTGTTGTTTCTTTCATATG
4473204 ATTTTTT
1 ATTTTTT
4473211 AGGAAATAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.11, C:0.04, G:0.16, T:0.69
Consensus pattern (24 bp):
ATTTTTTGTTGTTTCTTTCATATG
Found at i:4475856 original size:21 final size:20
Alignment explanation
Indices: 4475832--4475872 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4475822 AATGTAACTT
4475832 AGTTATATATAAATATCTATA
1 AGTTATATATAAATAT-TATA
*
4475853 AGTTATATATTAATATTATA
1 AGTTATATATAAATATTATA
4475873 TAGTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (20 bp):
AGTTATATATAAATATTATA
Found at i:4481701 original size:16 final size:16
Alignment explanation
Indices: 4481680--4481712 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4481670 CACTAATATA
*
4481680 TTTATTTAATTATAAC
1 TTTATTTAACTATAAC
4481696 TTTATTTAACTATAAC
1 TTTATTTAACTATAAC
4481712 T
1 T
4481713 CAATTTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATTTAACTATAAC
Found at i:4487839 original size:152 final size:153
Alignment explanation
Indices: 4487563--4487864 Score: 364
Period size: 152 Copynumber: 2.0 Consensus size: 153
4487553 TTCTGCTTCA
* *
4487563 AAAGTGTTTGGTAAACATTGACACACAAGACTTGGTTGAAAGAAGGGTTAGAACAGCTAAACAGT
1 AAAGTGCTTGGTAAACATTGACACACAAGACTTGATTGAAAGAAGGGTTAGAACAGCTAAACAGT
* ** *
4487628 TACCTATATGAGTTAAGTTGAAGTACTTTAATAATTTGATGGTTTTCATTTGGATTA-TTTTATT
66 TACCTATATGAGTTAAGTTGAAATACTTTAATAAACTGAGGGTTTTCATTTGGATTATTTTTATT
*
4487692 ACAGCCTCATCTCTTACTTGGGT
131 ACAACCTCATCTCTTACTTGGGT
* * * * * * * *
4487715 AAAGTGCTTGGTAAACATTGGCACATAGGACTTGATTGAAGGATGGGTTA-ATATAGTTAAATAG
1 AAAGTGCTTGGTAAACATTGACACACAAGACTTGATTGAAAGAAGGGTTAGA-ACAGCTAAACAG
*
4487779 TTACCTA-AGTGAGTT-AGTATGAAATA-TTCTGATAAACTGAGGGTTTTCATCTT-GATTATTT
65 TTACCTATA-TGAGTTAAGT-TGAAATACTT-TAATAAACTGAGGGTTTTCAT-TTGGATTATTT
*
4487840 TTATTGCAACCTCATCTCTTACTTG
126 TTATTACAACCTCATCTCTTACTTG
4487865 AGTTGGTCTT
Statistics
Matches: 127, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
151 7 0.06
152 93 0.73
153 27 0.21
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (153 bp):
AAAGTGCTTGGTAAACATTGACACACAAGACTTGATTGAAAGAAGGGTTAGAACAGCTAAACAGT
TACCTATATGAGTTAAGTTGAAATACTTTAATAAACTGAGGGTTTTCATTTGGATTATTTTTATT
ACAACCTCATCTCTTACTTGGGT
Found at i:4490904 original size:101 final size:101
Alignment explanation
Indices: 4490784--4491066 Score: 404
Period size: 101 Copynumber: 2.8 Consensus size: 101
4490774 AATTGCAAGT
4490784 TATATCGCTCAATCTTTGACCATAATTTATCATTACGTTTCAGCCGCTAGCTTTATCGCTCATGA
1 TATATCGCTCAATCTTTGACCATAATTTATCATTACGTTTCAGCCGCTAGCTTTATCGCTCATGA
*
4490849 TTTGGATGTAATGATAATATATTATTGGTCGCAAAC
66 TTTGGCTGTAATGATAATATATTATTGGTCGCAAAC
* * *
4490885 TATATCGCTCAATCTTTGACCGTAATTTATCATTACGTTTCAGTCGCTAGCTTTATCACTCATGA
1 TATATCGCTCAATCTTTGACCATAATTTATCATTACGTTTCAGCCGCTAGCTTTATCGCTCATGA
********** *
4490950 TTTGGCTGTAATGATNNNNNNNNNNTGGTCGCAAGC
66 TTTGGCTGTAATGATAATATATTATTGGTCGCAAAC
* *
4490986 TATATCGCTCAATCTTTGACCTTAATTTATCATTAACGTTTCAGCCGCTAGCTTTATCGCTCATA
1 TATATCGCTCAATCTTTGACCATAATTTATCATT-ACGTTTCAGCCGCTAGCTTTATCGCTCATG
4491051 ATTTGGCTGTAATGAT
65 ATTTGGCTGTAATGAT
4491067 TGGCCGCAAG
Statistics
Matches: 162, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 119 0.73
102 43 0.27
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.38
Consensus pattern (101 bp):
TATATCGCTCAATCTTTGACCATAATTTATCATTACGTTTCAGCCGCTAGCTTTATCGCTCATGA
TTTGGCTGTAATGATAATATATTATTGGTCGCAAAC
Found at i:4507112 original size:31 final size:31
Alignment explanation
Indices: 4507077--4507153 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
4507067 ATATAAAGAT
4507077 TAAATTGAAAAAAATTGAAATGTTAAGGGAC
1 TAAATTGAAAAAAATTGAAATGTTAAGGGAC
* *
4507108 TAAATTGAAAAAAATTGAGATGTTAAGGGAT
1 TAAATTGAAAAAAATTGAAATGTTAAGGGAC
4507139 TAAATTGAAAAAAAT
1 TAAATTGAAAAAAAT
4507154 ATTTGAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.53, C:0.01, G:0.18, T:0.27
Consensus pattern (31 bp):
TAAATTGAAAAAAATTGAAATGTTAAGGGAC
Found at i:4508459 original size:19 final size:19
Alignment explanation
Indices: 4508435--4508474 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
4508425 TTGTACTGAT
4508435 ATGTCAGCA-TATCAATGTC
1 ATGTCAGCACTATC-ATGTC
4508454 ATGTCAGCACTATCATGTC
1 ATGTCAGCACTATCATGTC
4508473 AT
1 AT
4508475 TTTATAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (19 bp):
ATGTCAGCACTATCATGTC
Found at i:4513268 original size:17 final size:17
Alignment explanation
Indices: 4513248--4513280 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4513238 AAAGTAACGT
4513248 TTTCTCTCTTTT-TTTTC
1 TTTCT-TCTTTTGTTTTC
4513265 TTTCTTCTTTTGTTTT
1 TTTCTTCTTTTGTTTT
4513281 TGCATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTCTTCTTTTGTTTTC
Found at i:4515706 original size:196 final size:197
Alignment explanation
Indices: 4515193--4515978 Score: 1209
Period size: 197 Copynumber: 3.9 Consensus size: 197
4515183 CTAAAAGAAT
* * *
4515193 TACTATGTCGCTATCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGCATTTGAGGAGAACTT
1 TACTATGTTGCTAGCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGCATTTGAGGAGAACTG
4515258 TTGATCTTCTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACCTTGT
66 TTGATCTTCTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACCTTGT
* * * * *
4515323 GAATCATTCAACACCAAAATGTCTTTTGATTTGTTTTAAGTTTGCACGTTTTCCCGGGTCTGCTC
131 GAATCATTCAACACCAAATTGTCTTTTGACTTGTTTTAAGTTTGCACATTTTCCCAGGACTGCTC
4515388 AG
196 AG
* *
4515390 TACCATGTTGCTAGCTCTGTTCAGTTATTTTATAATTATTTCAAGAGAGCATTTGAGGAGAACTG
1 TACTATGTTGCTAGCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGCATTTGAGGAGAACTG
*
4515455 TTGATCTTCTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCCCCCAGATTGACCTTGT
66 TTGATCTTCTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACCTTGT
*
4515520 GAATCGTTCAACACCAAATTGTCTTTTGACTTGTTTTAAGTTTGCACATTTTCCCAGG-CTGCTC
131 GAATCATTCAACACCAAATTGTCTTTTGACTTGTTTTAAGTTTGCACATTTTCCCAGGACTGCTC
4515584 AG
196 AG
* * * *
4515586 TAGTATGTTGCTAGCTCTGTTCAGTTATTTCATAATCACTTCAAGAGAGCATTTGAGGAGATCTG
1 TACTATGTTGCTAGCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGCATTTGAGGAGAACTG
* *
4515651 TTGATCTTTTTTAACAAATTACAATTGCAATGGTCTGGTTGTGGCCTCTCCCAGATTGACCTTGT
66 TTGATCTTCTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACCTTGT
**
4515716 GAATCATTCAACACCAAATTGTCTTTTGACTTGTCATAAGTTTGCACATTCCCTAAGATTTTAGC
131 GAATCATTCAACACCAAATTGTCTTTTGACTTGTTTTAAGTTTG--CA----C----ATTTT--C
** *
4515781 TTGAGGACTGATCAG
184 -CCAGGACTGCTCAG
*
4515796 TACTAT-TTGCTAGCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGGATTTGAGGAGAACTG
1 TACTATGTTGCTAGCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGCATTTGAGGAGAACTG
4515860 TTGATCTT-TTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACCTTGT
66 TTGATCTTCTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACCTTGT
*
4515924 GAATCATTCAACACCAAATTATCTTTTGACTTGTTTTAAGTTTGCACATTTTCCC
131 GAATCATTCAACACCAAATTGTCTTTTGACTTGTTTTAAGTTTGCACATTTTCCC
4515979 TAAGATTTTA
Statistics
Matches: 538, Mismatches: 37, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
196 171 0.32
197 177 0.33
198 7 0.01
202 2 0.00
206 7 0.01
208 97 0.18
209 65 0.12
210 12 0.02
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (197 bp):
TACTATGTTGCTAGCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGCATTTGAGGAGAACTG
TTGATCTTCTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACCTTGT
GAATCATTCAACACCAAATTGTCTTTTGACTTGTTTTAAGTTTGCACATTTTCCCAGGACTGCTC
AG
Found at i:4515952 original size:208 final size:211
Alignment explanation
Indices: 4515582--4515997 Score: 712
Period size: 208 Copynumber: 2.0 Consensus size: 211
4515572 CCCAGGCTGC
*
4515582 TCAGTAGTATGTTGCTAGCTCTGTTCAGTTATTTCATAATCACTTCAAGAGAGCATTTGAGGAGA
1 TCAGTACTATGTTGCTAGCTCTGTTCAGTTATTTCATAATCACTTCAAGAGAGCATTTGAGGAGA
*
4515647 TCTGTTGATCTTTTTTAACAAATTACAATTGCAATGGTCTGGTTGTGGCCTCTCCCAGATTGACC
66 ACTGTTGATCTTTTTTAACAAATTACAATTGCAATGGTCTGGTTGTGGCCTCTCCCAGATTGACC
*
4515712 TTGTGAATCATTCAACACCAAATTGTCTTTTGACTTGTCATAAGTTTGCACA-TTCCCTAAGATT
131 TTGTGAATCATTCAACACCAAATTATCTTTTGACTTGTCATAAGTTTGCACATTTCCCTAAGATT
4515776 TTAGCTTGAGGACTGA
196 TTAGCTTGAGGACTGA
* * *
4515792 TCAGTACTAT-TTGCTAGCTCTGTTCAGTTATTTTATAATTACTTCAAGAGAGGATTTGAGGAGA
1 TCAGTACTATGTTGCTAGCTCTGTTCAGTTATTTCATAATCACTTCAAGAGAGCATTTGAGGAGA
*
4515856 ACTGTTGATC-TTTTTAACAAATTACAATTGCAATGGTCTGGTTGTTGCCTCTCCCAGATTGACC
66 ACTGTTGATCTTTTTTAACAAATTACAATTGCAATGGTCTGGTTGTGGCCTCTCCCAGATTGACC
**
4515920 TTGTGAATCATTCAACACCAAATTATCTTTTGACTTGTTTTAAGTTTGCACATTTTCCCTAAGAT
131 TTGTGAATCATTCAACACCAAATTATCTTTTGACTTGTCATAAGTTTGCACA-TTTCCCTAAGAT
*
4515985 TTTAGTTTGAGGA
195 TTTAGCTTGAGGA
4515998 TGCTCATAAA
Statistics
Matches: 194, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
208 102 0.53
209 60 0.31
210 32 0.16
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (211 bp):
TCAGTACTATGTTGCTAGCTCTGTTCAGTTATTTCATAATCACTTCAAGAGAGCATTTGAGGAGA
ACTGTTGATCTTTTTTAACAAATTACAATTGCAATGGTCTGGTTGTGGCCTCTCCCAGATTGACC
TTGTGAATCATTCAACACCAAATTATCTTTTGACTTGTCATAAGTTTGCACATTTCCCTAAGATT
TTAGCTTGAGGACTGA
Found at i:4522388 original size:18 final size:18
Alignment explanation
Indices: 4522361--4522402 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
4522351 AATTCGGAAG
* *
4522361 CTTTTGCTTTATTTGTTT
1 CTTTTCCTTTATTTATTT
*
4522379 CTTTTCCTTTCTTTATTT
1 CTTTTCCTTTATTTATTT
4522397 -TTTTCC
1 CTTTTCC
4522403 CCAAAGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.71
Consensus pattern (18 bp):
CTTTTCCTTTATTTATTT
Found at i:4523430 original size:2 final size:2
Alignment explanation
Indices: 4523423--4523455 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4523413 TTGCTTTGTT
4523423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4523456 ATGTTTTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4536087 original size:25 final size:25
Alignment explanation
Indices: 4536026--4536099 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 25
4536016 GGAAAAACCA
*
4536026 ACAATTGTGTCTATTTGAAATAG--
1 ACAATTGTGTCTGTTTGAAATAGAC
* *
4536049 ACAGTTGTGACTGTTTGAAATAGAC
1 ACAATTGTGTCTGTTTGAAATAGAC
4536074 ACAATTGTGTCTG-TTGAGAATAGAC
1 ACAATTGTGTCTGTTTGA-AATAGAC
4536099 A
1 A
4536100 TCTTTGCCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 20 0.47
24 4 0.09
25 19 0.44
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.34
Consensus pattern (25 bp):
ACAATTGTGTCTGTTTGAAATAGAC
Found at i:4537814 original size:21 final size:22
Alignment explanation
Indices: 4537785--4537827 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4537775 AATACTTTTT
*
4537785 ATTATAATATTTAAT-TTTTAA
1 ATTAAAATATTTAATATTTTAA
*
4537806 ATTAAAATATTTATTATTTTAA
1 ATTAAAATATTTAATATTTTAA
4537828 TAATTTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAAATATTTAATATTTTAA
Found at i:4542589 original size:31 final size:30
Alignment explanation
Indices: 4542545--4542617 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
4542535 TTTGATATAA
* *
4542545 AAAAATA-TGTTTGTCTTAATTTAGGACAAG
1 AAAAATATTTTTTGTCTTAATCTA-GACAAG
4542575 AAAAATATTTTTTGTCTTAATCTAGACAAG
1 AAAAATATTTTTTGTCTTAATCTAGACAAG
4542605 AAAACATATTTTT
1 AAAA-ATATTTTT
4542618 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (30 bp):
AAAAATATTTTTTGTCTTAATCTAGACAAG
Found at i:4542617 original size:30 final size:30
Alignment explanation
Indices: 4542545--4542617 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
4542535 TTTGATATAA
* *
4542545 AAAAATATGTTTGTCTTAATTTAGGACAAG
1 AAAAATATTTTTGTCTTAATCTAGGACAAG
4542575 AAAAATATTTTTTGTCTTAATCTA-GACAAG
1 AAAAATA-TTTTTGTCTTAATCTAGGACAAG
4542605 AAAACATATTTTT
1 AAAA-ATATTTTT
4542618 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (30 bp):
AAAAATATTTTTGTCTTAATCTAGGACAAG
Found at i:4549267 original size:14 final size:16
Alignment explanation
Indices: 4549248--4549284 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
4549238 CACTGTAATT
4549248 TTTATAA-TA-TATTG
1 TTTATAATTAGTATTG
4549262 TTTATAATTAGTTATTG
1 TTTATAATTAG-TATTG
4549279 TTTATA
1 TTTATA
4549285 CAAACTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
17 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (16 bp):
TTTATAATTAGTATTG
Found at i:4549375 original size:15 final size:16
Alignment explanation
Indices: 4549333--4549376 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
4549323 TGTCATTAAT
4549333 TATATA-TATAATAAAG
1 TATATACTAT-ATAAAG
4549349 TA-ATAC-ATATAAA-
1 TATATACTATATAAAG
4549362 TATATACTATATAAA
1 TATATACTATATAAA
4549377 ATTAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 12 0.48
16 2 0.08
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
TATATACTATATAAAG
Found at i:4553734 original size:21 final size:20
Alignment explanation
Indices: 4553686--4553743 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
4553676 GATTTTGATA
* *
4553686 AATATTTATCAATAGATGAG
1 AATATTTATCGATAGATGAC
**
4553706 TCTATTTATCGATAGATGCAC
1 AATATTTATCGATAGATG-AC
4553727 AATATTTATCGATAGAT
1 AATATTTATCGATAGAT
4553744 AAAAACCCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (20 bp):
AATATTTATCGATAGATGAC
Found at i:4557904 original size:25 final size:25
Alignment explanation
Indices: 4557855--4557908 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
4557845 TATGAGGTGA
**
4557855 AATAAAAAATAAAATAATATTTAAT
1 AATAAAAAATAAAATAATAAATAAT
4557880 AATAAAAAAT-AAATAATAAAATAAT
1 AATAAAAAATAAAATAAT-AAATAAT
4557905 AATA
1 AATA
4557909 TTTTATTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (25 bp):
AATAAAAAATAAAATAATAAATAAT
Found at i:4560643 original size:60 final size:60
Alignment explanation
Indices: 4560569--4560908 Score: 341
Period size: 60 Copynumber: 5.7 Consensus size: 60
4560559 GGAAGACACA
* * * *
4560569 ACTTTATGCTTGGTGGCGTGGGGAGTCCCACGAGTAGGTACTAGGAGGACAAAAGCCTCA
1 ACTTTATACTTGGTGGCATGGGGAGTCCCACGAGTAGGCACTAGGAGGACAAAAGCCTCG
* * * *
4560629 ACTTTATA-TCTGGTGGCATGGTGAGTCCTACGAGTAGGCACTGGGAGGACAGAAGCCTCG
1 ACTTTATACT-TGGTGGCATGGGGAGTCCCACGAGTAGGCACTAGGAGGACAAAAGCCTCG
*
4560689 ACTTTATACTTGGTGGCATGGGGAGTCCCATGAG-ATGGCACTAGGAGGA-AAGAAGCCTCG
1 ACTTTATACTTGGTGGCATGGGGAGTCCCACGAGTA-GGCACTAGGAGGACAA-AAGCCTCG
* * * * * * *
4560749 ACTTTATACTTGGTGGCGT-GGGAGTCCCACGAGTAAGTATTAAGG-GGACGAAAGCCCCA
1 ACTTTATACTTGGTGGCATGGGGAGTCCCACGAGTAGGCACT-AGGAGGACAAAAGCCTCG
* * * * * * * *
4560808 ATTTTATACTTGGTGGCACGAGGGAATCCTACCAATAGGCATTAAGG-GGACAGAAGCCTCG
1 ACTTTATACTTGGTGGCATG-GGGAGTCCCACGAGTAGGCACT-AGGAGGACAAAAGCCTCG
* * *
4560869 ACTTTATATTTGGTAGCATGGGGAGTCCCATGAGTAGGCA
1 ACTTTATACTTGGTGGCATGGGGAGTCCCACGAGTAGGCA
4560909 TTGATATATG
Statistics
Matches: 228, Mismatches: 43, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
59 44 0.19
60 137 0.60
61 47 0.21
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (60 bp):
ACTTTATACTTGGTGGCATGGGGAGTCCCACGAGTAGGCACTAGGAGGACAAAAGCCTCG
Found at i:4560871 original size:180 final size:180
Alignment explanation
Indices: 4560569--4560902 Score: 469
Period size: 180 Copynumber: 1.9 Consensus size: 180
4560559 GGAAGACACA
* * *
4560569 ACTTTATGCTTGGTGGCGTGGGGAGTCCCACGAGTAGGTACTAGGAGGACAAAAGCCTCAACTTT
1 ACTTTATACTTGGTGGCGTGGGGAGTCCCACGAGTAAGTACTAGGAGGACAAAAGCCCCAACTTT
* * * * * *
4560634 ATATCTGGTGGCATGGTGAGTCCTACGAGTAGGCACTGGGAGGACAGAAGCCTCGACTTTATACT
66 ATATCTGGTGGCACGGGGAATCCTACCAATAGGCACTAGGAGGACAGAAGCCTCGACTTTATACT
*
4560699 TGGTGGCATGGGGAGTCCCATGAGATGGCACTAGGAGGAAAGAAGCCTCG
131 TGGTAGCATGGGGAGTCCCATGAGATGGCACTAGGAGGAAAGAAGCCTCG
* * *
4560749 ACTTTATACTTGGTGGCGT-GGGAGTCCCACGAGTAAGTATTAAGG-GGACGAAAGCCCCAATTT
1 ACTTTATACTTGGTGGCGTGGGGAGTCCCACGAGTAAGTACT-AGGAGGACAAAAGCCCCAACTT
*
4560812 TATA-CTTGGTGGCACGAGGGAATCCTACCAATAGGCATTAAGG-GGACAGAAGCCTCGACTTTA
65 TATATC-TGGTGGCACG-GGGAATCCTACCAATAGGCACT-AGGAGGACAGAAGCCTCGACTTTA
*
4560875 TATTTGGTAGCATGGGGAGTCCCATGAG
127 TACTTGGTAGCATGGGGAGTCCCATGAG
4560903 TAGGCATTGA
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
178 1 0.01
179 48 0.36
180 84 0.62
181 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (180 bp):
ACTTTATACTTGGTGGCGTGGGGAGTCCCACGAGTAAGTACTAGGAGGACAAAAGCCCCAACTTT
ATATCTGGTGGCACGGGGAATCCTACCAATAGGCACTAGGAGGACAGAAGCCTCGACTTTATACT
TGGTAGCATGGGGAGTCCCATGAGATGGCACTAGGAGGAAAGAAGCCTCG
Found at i:4560956 original size:14 final size:14
Alignment explanation
Indices: 4560937--4560966 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4560927 GTGGAGACTC
4560937 ACACGATTTCTTAG
1 ACACGATTTCTTAG
4560951 ACACGATTTCTTAG
1 ACACGATTTCTTAG
4560965 AC
1 AC
4560967 CTACCCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (14 bp):
ACACGATTTCTTAG
Found at i:4563137 original size:12 final size:12
Alignment explanation
Indices: 4563106--4563163 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
4563096 GAGGAAATGT
* *
4563106 AATGCAAATACA
1 AATGTAAATGCA
*
4563118 AATATAAATGCA
1 AATGTAAATGCA
*
4563130 TATGTAAATGCCA
1 AATGTAAATG-CA
* *
4563143 AATGAAAATTCA
1 AATGTAAATGCA
4563155 AATGTAAAT
1 AATGTAAAT
4563164 TTCAAGCCCA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
12 27 0.75
13 9 0.25
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.26
Consensus pattern (12 bp):
AATGTAAATGCA
Found at i:4567595 original size:18 final size:19
Alignment explanation
Indices: 4567572--4567619 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
4567562 TTTTGGAGGG
4567572 TTTTCTTTCTT-TTGCTCT
1 TTTTCTTTCTTCTTGCTCT
* *
4567590 TTTTCTTT-TTCTTTCTTT
1 TTTTCTTTCTTCTTGCTCT
4567608 TTTTGCTTTCTT
1 TTTT-CTTTCTT
4567620 AATTTGGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 17 0.68
19 4 0.16
20 2 0.08
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTCTTGCTCT
Found at i:4568280 original size:15 final size:13
Alignment explanation
Indices: 4568246--4568273 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4568236 TTTTGATCGG
4568246 TGTTATAATTCCT
1 TGTTATAATTCCT
4568259 TGTTATAATTCCT
1 TGTTATAATTCCT
4568272 TG
1 TG
4568274 GGTTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (13 bp):
TGTTATAATTCCT
Found at i:4570095 original size:12 final size:12
Alignment explanation
Indices: 4570078--4570104 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4570068 ATTTCATTAC
4570078 TTTTTTGTTCAA
1 TTTTTTGTTCAA
4570090 TTTTTTGTTCAA
1 TTTTTTGTTCAA
4570102 TTT
1 TTT
4570105 CTTCTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTGTTCAA
Found at i:4577210 original size:118 final size:117
Alignment explanation
Indices: 4577035--4577404 Score: 465
Period size: 118 Copynumber: 3.1 Consensus size: 117
4577025 AACAAATCCA
* * * * *
4577035 CTTGTGACCTTGC-AAAAGCAAGAAAGCAGCATACAGAGAAAAAATAGACTCTAATCTCTAAAAA
1 CTTGTGACCCTGCAAAAAGCAAGAAAGAAGCAGATAGAGAAAAAGTAGACTCT-ATCTCTAAAAA
** * *
4577099 AGAGAATCACAAGGAAAAAGCAGTAGACAGTGATCTTGTAGAAAAAGCAGACT
65 AGAGAATCACAAGGAAAAAGCAACAGACAGTGATCCTGTAGAAAAAGCAAACT
* * * *
4577152 CTTGTGACCCTACAAAAAGCAAGAAAGAAGTAGATAGAGAAAAAGTAGATTTTGATCTCTAAAAA
1 CTTGTGACCCTGCAAAAAGCAAGAAAGAAGCAGATAGAGAAAAAGTAGACTCT-ATCTCTAAAAA
* *
4577217 AGAGAATCACGAGGAAAAAGCAACAGACAGTGATCCTGCAGAAAAAGCAAACT
65 AGAGAATCACAAGGAAAAAGCAACAGACAGTGATCCTGTAGAAAAAGCAAACT
* * * *
4577270 CTTATGACCCTGCAAAAAGCAAGAAGGCAA-CAGATAGAGAAAAAGCAGACTCTAGTCTCTAAGA
1 CTTGTGACCCTGCAAAAAGCAAGAAAG-AAGCAGATAGAGAAAAAGTAGACTCTA-TCTCTAAAA
* * * * *
4577334 AAGAGAATCACCAGGAAAGAGCAACAGACAATAATCCTGTAGAAAAAGAAAACT
64 AAGAGAATCACAAGGAAAAAGCAACAGACAGTGATCCTGTAGAAAAAGCAAACT
*
4577388 CTTGTGACTCTGCAAAA
1 CTTGTGACCCTGCAAAA
4577405 GAATCACGAG
Statistics
Matches: 218, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
117 12 0.06
118 204 0.94
119 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (117 bp):
CTTGTGACCCTGCAAAAAGCAAGAAAGAAGCAGATAGAGAAAAAGTAGACTCTATCTCTAAAAAA
GAGAATCACAAGGAAAAAGCAACAGACAGTGATCCTGTAGAAAAAGCAAACT
Found at i:4584672 original size:211 final size:211
Alignment explanation
Indices: 4584338--4584720 Score: 524
Period size: 211 Copynumber: 1.8 Consensus size: 211
4584328 TTCTGGTCGC
* * *
4584338 AACAATTTCCTTTCTTCGACTTCCAACCATCTAATGGGCAACTTACACCTCCACTTGTACAATGC
1 AACAATTTCCTTTCTTCGACTTCCAACCATCTAATGGGCAACCTACACCTCCACTGGTACAATAC
* * *
4584403 CTCAAATATTGACTAGATACCATAATCATCATCCAAAGCTAAAGCCATTGATGGAATATCATAAT
66 CTCAAATACTGACTAGATACCATAATCATCATCCAAAGCTAAAGCCACTGACGGAATATCATAAT
4584468 CATCATCCAAAATCACTCATT-GAATGGCATCATAGCACTGCAGGTGTTCCTTCCACTGCCACTT
131 CATCATCCAAAATCACTCATTAG-ATGGCATCATAGCACTGCAGGTGTTCCTTCCACTGCCACTT
4584532 ATACCATCTCCGGCCTT
195 ATACCATCTCCGGCCTT
* *** * *
4584549 AACAATTTCCTTTC-TCTGACTTCTAACCAT-TCAATGGGTGGCCTACACCTCTACTGGTACAGT
1 AACAATTTCCTTTCTTC-GACTTCCAACCATCT-AATGGGCAACCTACACCTCCACTGGTACAAT
* * * *
4584612 ACCTCAAATACTGAC-AGAATATCATAATCATCGTTCAATG-TCAAAGCCACTGACGGAATATCA
64 ACCTCAAATACTGACTAG-ATACCATAATCATCATCCAAAGCT-AAAGCCACTGACGGAATATCA
* *
4584675 TAGTCATCATCCAAAATCACTTATTAGATGGCATCATAGCACTGCA
127 TAATCATCATCCAAAATCACTCATTAGATGGCATCATAGCACTGCA
4584721 AGCGGGAATC
Statistics
Matches: 149, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
210 6 0.04
211 142 0.95
212 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (211 bp):
AACAATTTCCTTTCTTCGACTTCCAACCATCTAATGGGCAACCTACACCTCCACTGGTACAATAC
CTCAAATACTGACTAGATACCATAATCATCATCCAAAGCTAAAGCCACTGACGGAATATCATAAT
CATCATCCAAAATCACTCATTAGATGGCATCATAGCACTGCAGGTGTTCCTTCCACTGCCACTTA
TACCATCTCCGGCCTT
Found at i:4592329 original size:12 final size:13
Alignment explanation
Indices: 4592310--4592345 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
4592300 CAGAATAGTT
4592310 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
4592323 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
4592334 TCTTGCTGCCTC
1 TCTTGCTGCCTC
4592346 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:4604067 original size:28 final size:28
Alignment explanation
Indices: 4604019--4604122 Score: 90
Period size: 26 Copynumber: 3.8 Consensus size: 28
4604009 AGAGAAAATG
**
4604019 TTGTTACACGCCATGTT--AAAAAAAAA
1 TTGTTACATTCCATGTTGGAAAAAAAAA
* *
4604045 TTGTTACATTCTATGTTGG--AAAAATA
1 TTGTTACATTCCATGTTGGAAAAAAAAA
* * * * *
4604071 TTATCACATGCCATGTCGAAAAAAAAAA
1 TTGTTACATTCCATGTTGGAAAAAAAAA
4604099 TTGTTACATTCCATGTTGAGAAAA
1 TTGTTACATTCCATGTTG-GAAAA
4604123 TGTTACATGC
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
26 33 0.58
28 20 0.35
29 4 0.07
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (28 bp):
TTGTTACATTCCATGTTGGAAAAAAAAA
Found at i:4604226 original size:26 final size:26
Alignment explanation
Indices: 4604196--4604279 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
4604186 CGTTTTTGCA
* *
4604196 AAAAAAAAATTCTACACGTCATGTTC
1 AAAAAAAATTTCTACACGCCATGTTC
* *
4604222 AAAAACAATTTGCTACACGCCATTTTC
1 AAAAAAAATTT-CTACACGCCATGTTC
* *
4604249 ATAAAAAATTTCTACACACCATGTTC
1 AAAAAAAATTTCTACACGCCATGTTC
*
4604275 GAAAA
1 AAAAA
4604280 TAGTGTGCCA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 25 0.53
27 22 0.47
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.27
Consensus pattern (26 bp):
AAAAAAAATTTCTACACGCCATGTTC
Found at i:4617559 original size:17 final size:19
Alignment explanation
Indices: 4617519--4617561 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4617509 AAAATTAAAA
4617519 AAAAAAGCATAATACTTAT
1 AAAAAAGCATAATACTTAT
*
4617538 AAAAAATCATAA-AC-TATT
1 AAAAAAGCATAATACTTA-T
4617556 AAAAAA
1 AAAAAA
4617562 AGTCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 11 0.50
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAAAGCATAATACTTAT
Found at i:4619979 original size:25 final size:25
Alignment explanation
Indices: 4619951--4620003 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
4619941 CTTACCCATT
*
4619951 TATGCAACCCTTTTATTTGTGTTAA
1 TATGCAACCCTTTTACTTGTGTTAA
*
4619976 TATGCAACGCTTTTACTTGTGTTAA
1 TATGCAACCCTTTTACTTGTGTTAA
4620001 TAT
1 TAT
4620004 TCCTGTGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (25 bp):
TATGCAACCCTTTTACTTGTGTTAA
Found at i:4646107 original size:32 final size:32
Alignment explanation
Indices: 4646066--4646138 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
4646056 TTTCAAAAGC
* ** *
4646066 TTATAATTTTTTTC-TTATTTTGTTTTAAATAT
1 TTATAATTTTTATCTTTATTTT-TTAAAAAAAT
4646098 TTATAA-TTTTATCTTTATTTTTTAAAAAAAT
1 TTATAATTTTTATCTTTATTTTTTAAAAAAAT
4646129 TTATAATTTT
1 TTATAATTTT
4646139 ATTTTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
31 19 0.54
32 16 0.46
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (32 bp):
TTATAATTTTTATCTTTATTTTTTAAAAAAAT
Found at i:4646523 original size:16 final size:17
Alignment explanation
Indices: 4646502--4646533 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4646492 AAGGTAAGCT
4646502 TTAAAT-AAAAATGAGC
1 TTAAATCAAAAATGAGC
4646518 TTAAATCAAAAATGAG
1 TTAAATCAAAAATGAG
4646534 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (17 bp):
TTAAATCAAAAATGAGC
Found at i:4646906 original size:12 final size:12
Alignment explanation
Indices: 4646889--4646926 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4646879 TTAGTAAGCA
*
4646889 ATATATATATAT
1 ATATATGTATAT
4646901 ATATATGTATAT
1 ATATATGTATAT
*
4646913 GTATATGTATAT
1 ATATATGTATAT
4646925 AT
1 AT
4646927 GGTATCAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:4669366 original size:113 final size:112
Alignment explanation
Indices: 4669189--4669400 Score: 289
Period size: 113 Copynumber: 1.9 Consensus size: 112
4669179 TTTATAGATT
* * * * * *
4669189 GATGGTATGAATATGAGGTAATGACTAATGTTTTAATTAAGGCTTGTTCGGGACTTGGCGGGTTC
1 GATGGCATGAATATGAAGTAATAACTAACGATTTAAGTAAGGCTTGTTCGGGACTTGGCGGGTTC
* * * *
4669254 TCCTGCTAGACTCGGACGCCGGTAGCAATCGAGGTGCAGTCGTTATA
66 ACCCGCGAGACTCAGACGCCGGTAGCAATCGAGGTGCAGTCGTTATA
* *
4669301 GATGGCATGAATATGAAGTAATAATCTAACGATTTAAGTAAGGCTTGTTTGGGACTTTGCGGGTT
1 GATGGCATGAATATGAAGTAATAA-CTAACGATTTAAGTAAGGCTTGTTCGGGACTTGGCGGGTT
* *
4669366 CACCCGCGAGACTCAGACGCTGGTAGCGATCGAGG
65 CACCCGCGAGACTCAGACGCCGGTAGCAATCGAGG
4669401 AATGGTCGTT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
112 21 0.25
113 64 0.75
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (112 bp):
GATGGCATGAATATGAAGTAATAACTAACGATTTAAGTAAGGCTTGTTCGGGACTTGGCGGGTTC
ACCCGCGAGACTCAGACGCCGGTAGCAATCGAGGTGCAGTCGTTATA
Found at i:4683371 original size:17 final size:17
Alignment explanation
Indices: 4683338--4683372 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4683328 GCTTCTGGGG
*
4683338 TTCTATTTTTAAGTTAT
1 TTCTATTTTTAACTTAT
*
4683355 TTCTATTTTTACCTTAT
1 TTCTATTTTTAACTTAT
4683372 T
1 T
4683373 GTATTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (17 bp):
TTCTATTTTTAACTTAT
Found at i:4686093 original size:30 final size:30
Alignment explanation
Indices: 4686057--4686115 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4686047 TATGAGATAC
4686057 ATACATTGAATAGGATCTAATTAAAGAGCT
1 ATACATTGAATAGGATCTAATTAAAGAGCT
4686087 ATACATTGAATAGGATCTAATTAAAGAGC
1 ATACATTGAATAGGATCTAATTAAAGAGC
4686116 ACCATATCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (30 bp):
ATACATTGAATAGGATCTAATTAAAGAGCT
Found at i:4687904 original size:31 final size:31
Alignment explanation
Indices: 4687866--4687929 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
4687856 TTTACTTTCT
4687866 TTAAATATCATAGATATTAATGAGTTTAAGC
1 TTAAATATCATAGATATTAATGAGTTTAAGC
4687897 TTAAATATCATAGATATTAATGAGTTTAAGC
1 TTAAATATCATAGATATTAATGAGTTTAAGC
4687928 TT
1 TT
4687930 TCTCCTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (31 bp):
TTAAATATCATAGATATTAATGAGTTTAAGC
Found at i:4690255 original size:81 final size:81
Alignment explanation
Indices: 4690170--4690499 Score: 360
Period size: 81 Copynumber: 4.1 Consensus size: 81
4690160 TATTAAACAT
* * * * * **
4690170 CATGTACAAAAATATGTTATACACCATGGTCAAAAAAGGTTATTACACGTTATGTTGAAAAAAAA
1 CATGTACAAAAATATGTTACACGCCATGATTAAAAAAGGTTGTTACACGCCATGTTGAAAAAAAA
*
4690235 TATTGTTGTTGCACGC
66 TATTGTTGTTACACGC
4690251 CATGTACAAAAATATGTTACACGCCATGATTAACAAAA-GTTGTTACACGCCATGTTGAAAAAAA
1 CATGTACAAAAATATGTTACACGCCATGATTAA-AAAAGGTTGTTACACGCCATGTTGAAAAAAA
*
4690315 ATATTGTTGTTACATGC
65 ATATTGTTGTTACACGC
* * * * * * * *
4690332 CATGTATGAAACA-ATGTTATATGCTATGGTT-AAAAAGGTTGTTATACGCCATGTTAAAAAAAA
1 CATGTA-CAAAAATATGTTACACGCCATGATTAAAAAAGGTTGTTACACGCCATGTTGAAAAAAA
**
4690395 TATATTGTCATTACACGC
65 -ATATTGTTGTTACACGC
* * * * * *
4690413 TATGTACAAAAACATGTTACATGTCATGATTAAAAAAAGTTGTTACACGTCATGTTGATAAAAAA
1 CATGTACAAAAATATGTTACACGCCATGATTAAAAAAGGTTGTTACACGCCATGTTGA-AAAAAA
* *
4690478 ATATTATTGTTACACAC
65 ATATTGTTGTTACACGC
4690495 CATGT
1 CATGT
4690500 TGAAAAAAAT
Statistics
Matches: 206, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
79 4 0.02
80 29 0.14
81 120 0.58
82 47 0.23
83 6 0.03
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (81 bp):
CATGTACAAAAATATGTTACACGCCATGATTAAAAAAGGTTGTTACACGCCATGTTGAAAAAAAA
TATTGTTGTTACACGC
Found at i:4690268 original size:24 final size:24
Alignment explanation
Indices: 4690240--4690305 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 24
4690230 AAAAATATTG
*
4690240 TTGTTGCACGCCATGT-ACAAAAA
1 TTGTTACACGCCATGTAACAAAAA
*
4690263 TATGTTACACGCCATGATTAACAAAAG
1 T-TGTTACACGCCATG--TAACAAAAA
4690290 TTGTTACACGCCATGT
1 TTGTTACACGCCATGT
4690306 TGAAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 1 0.03
24 14 0.38
26 15 0.41
27 7 0.19
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (24 bp):
TTGTTACACGCCATGTAACAAAAA
Found at i:4690314 original size:26 final size:25
Alignment explanation
Indices: 4690239--4690393 Score: 86
Period size: 24 Copynumber: 6.0 Consensus size: 25
4690229 AAAAAATATT
* *
4690239 GTTGTTGCACGCCATG-TACAAAAA
1 GTTGTTACACGCCATGTTAAAAAAA
*
4690263 -TATGTTACACGCCATGATTAACAAAA
1 GT-TGTTACACGCCATG-TTAAAAAAA
4690289 GTTGTTACACGCCATGTTGAAAAAAAATA
1 GTTGTTACACGCCATGTT---AAAAAA-A
* * *
4690318 TTGTTGTTACATGCCATGTATGAAACAA
1 --GTTGTTACACGCCATGT-TAAAAAAA
* * * *
4690346 --TGTTATATGCTATGGTT-AAAAAG
1 GTTGTTACACGCCAT-GTTAAAAAAA
*
4690369 GTTGTTATACGCCATGTTAAAAAAA
1 GTTGTTACACGCCATGTTAAAAAAA
4690394 ATATATTGTC
Statistics
Matches: 102, Mismatches: 14, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
23 5 0.05
24 28 0.27
25 20 0.20
26 20 0.20
27 1 0.01
28 6 0.06
29 5 0.05
31 16 0.16
32 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (25 bp):
GTTGTTACACGCCATGTTAAAAAAA
Found at i:4690422 original size:162 final size:161
Alignment explanation
Indices: 4690202--4690504 Score: 428
Period size: 162 Copynumber: 1.9 Consensus size: 161
4690192 ACCATGGTCA
** * ** * *
4690202 AAAAAGGTTATTACACGTTATGTTGAAAAAAAATATTGTTGTTGCACGCCATGTACAAAAATATG
1 AAAAAGGTTATTACACGCCATGTTAAAAAAAAATATTGTCATTACACGCCATGTACAAAAACATG
* * **
4690267 TTACACGCCATGATTAACAAAAGTTGTTACACGCCATGTTGA-AAAAAAATATTGTTGTTACATG
66 TTACACGCCATGATTAAAAAAAGTTGTTACACGCCATGTTGATAAAAAAATATTATTGTTACACA
4690331 CCATGTATGAAACAATGTTATATGCTATGGTT
131 CCATGT-TGAAACAATGTTATATGCTATGGTT
* * *
4690363 AAAAAGGTTGTTATACGCCATGTTAAAAAAAATATATTGTCATTACACGCTATGTACAAAAACAT
1 AAAAAGGTTATTACACGCCATGTTAAAAAAAA-ATATTGTCATTACACGCCATGTACAAAAACAT
* * *
4690428 GTTACATGTCATGATTAAAAAAAGTTGTTACACGTCATGTTGATAAAAAAATATTATTGTTACAC
65 GTTACACGCCATGATTAAAAAAAGTTGTTACACGCCATGTTGATAAAAAAATATTATTGTTACAC
4690493 ACCATGTTGAAA
130 ACCATGTTGAAA
4690505 AAAATATTGT
Statistics
Matches: 123, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
161 27 0.22
162 71 0.58
163 25 0.20
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (161 bp):
AAAAAGGTTATTACACGCCATGTTAAAAAAAAATATTGTCATTACACGCCATGTACAAAAACATG
TTACACGCCATGATTAAAAAAAGTTGTTACACGCCATGTTGATAAAAAAATATTATTGTTACACA
CCATGTTGAAACAATGTTATATGCTATGGTT
Found at i:4690506 original size:30 final size:31
Alignment explanation
Indices: 4690452--4690517 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
4690442 TTAAAAAAAG
**
4690452 TTGTTACACGTCATGTTGATAAAAAAATATTA
1 TTGTTACACACCATGTTGA-AAAAAAATATTA
*
4690484 TTGTTACACACCATGTTG-AAAAAAATATTG
1 TTGTTACACACCATGTTGAAAAAAAATATTA
4690514 TTGT
1 TTGT
4690518 CACATGTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 15 0.48
32 16 0.52
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (31 bp):
TTGTTACACACCATGTTGAAAAAAAATATTA
Found at i:4690529 original size:30 final size:30
Alignment explanation
Indices: 4690451--4690545 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
4690441 ATTAAAAAAA
4690451 GTTGTTACACGTCATGTTGATAAAAAAATATT
1 GTTGTTACACGTCATGTTG--AAAAAAATATT
* **
4690483 ATTGTTACACACCATGTTGAAAAAAATATT
1 GTTGTTACACGTCATGTTGAAAAAAATATT
* * * *
4690513 GTTGTCACATGTCATGTTCAAAAAAATTTT
1 GTTGTTACACGTCATGTTGAAAAAAATATT
4690543 GTT
1 GTT
4690546 ACACTTTAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 37 0.70
32 16 0.30
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (30 bp):
GTTGTTACACGTCATGTTGAAAAAAATATT
Found at i:4703816 original size:19 final size:19
Alignment explanation
Indices: 4703782--4703833 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4703772 ATAATTTTGA
* * *
4703782 TTATTAAATATATTATTATT
1 TTATTTAAT-TATTATAAAT
4703802 TTATTTAATTATTATAAAT
1 TTATTTAATTATTATAAAT
*
4703821 TTATTTATTTATT
1 TTATTTAATTATT
4703834 TTGGAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTTAATTATTATAAAT
Found at i:4707997 original size:29 final size:30
Alignment explanation
Indices: 4707956--4708038 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 30
4707946 ATGTAACCAA
** * *
4707956 ATTTTTTTGAACATGGCGTGTAATAACAAT
1 ATTTTTTTGAACATAACGTGTAACAACAAC
*
4707986 ATTTTTTT-AACATAACGTGTAGCAACAAC
1 ATTTTTTTGAACATAACGTGTAACAACAAC
* *
4708015 ATTTTTTTTCAACATAACTTGTAA
1 A-TTTTTTTGAACATAACGTGTAA
4708039 TATGTTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 17 0.39
30 15 0.34
31 12 0.27
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (30 bp):
ATTTTTTTGAACATAACGTGTAACAACAAC
Found at i:4710011 original size:2 final size:2
Alignment explanation
Indices: 4710004--4710029 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4709994 TATCATAGTA
4710004 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
4710030 GTTGAGATGC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4715585 original size:34 final size:34
Alignment explanation
Indices: 4715542--4715606 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
4715532 AACAAGCGAA
4715542 AATCGATCCCTTAAGACCCTTAGTGCTCTGACAC
1 AATCGATCCCTTAAGACCCTTAGTGCTCTGACAC
4715576 AATCGATCCCTTAAGACCCTTAGTGCTCTGA
1 AATCGATCCCTTAAGACCCTTAGTGCTCTGA
4715607 TACCATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (34 bp):
AATCGATCCCTTAAGACCCTTAGTGCTCTGACAC
Found at i:4720825 original size:15 final size:16
Alignment explanation
Indices: 4720795--4720827 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4720785 ATCGTTCAAG
4720795 TTCGATATTCAAATTA
1 TTCGATATTCAAATTA
*
4720811 TTCGAT-TTTAAATTA
1 TTCGATATTCAAATTA
4720826 TT
1 TT
4720828 TAAATTCCAT
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:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (16 bp):
TTCGATATTCAAATTA
Found at i:4721007 original size:38 final size:38
Alignment explanation
Indices: 4720956--4721032 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
4720946 TGTCAGCCGT
4720956 AAATAAGTTATTTATCATTACACTT-TTATCAACTTGTG
1 AAATAAGTTATTTATCATTACA-TTGTTATCAACTTGTG
* *
4720994 AAATAAGTTATTTATTATTACATTGTTGTCAACTTGTG
1 AAATAAGTTATTTATCATTACATTGTTATCAACTTGTG
4721032 A
1 A
4721033 CATTCGCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (38 bp):
AAATAAGTTATTTATCATTACATTGTTATCAACTTGTG
Found at i:4727877 original size:59 final size:59
Alignment explanation
Indices: 4727811--4727928 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
4727801 CCTCAAAAGA
* *
4727811 TTTAAAATCCACAAATGCCCAATTCTGATTTTCAAACACTTTGTTAAATATACAAGGAC
1 TTTAAAATCCACAAATGCCCAATTCTGAATTTCAAACACTTTGTTAAATACACAAGGAC
* * * *
4727870 TTTAAAATCCACAAATGCCCAGTTCTGAATTTCACACGCTTTGTTAATTACACAAGGAC
1 TTTAAAATCCACAAATGCCCAATTCTGAATTTCAAACACTTTGTTAAATACACAAGGAC
4727929 ATATATTCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (59 bp):
TTTAAAATCCACAAATGCCCAATTCTGAATTTCAAACACTTTGTTAAATACACAAGGAC
Found at i:4730123 original size:22 final size:22
Alignment explanation
Indices: 4730085--4730131 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4730075 TAATTCAAAA
*
4730085 ATATACTTTTAGTTCTTTTTTT
1 ATATACTTTTAGTTCTTCTTTT
*
4730107 ATATA-TTTTATTGTCTTCTTTT
1 ATATACTTTTAGT-TCTTCTTTT
4730129 ATA
1 ATA
4730132 AAAAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (22 bp):
ATATACTTTTAGTTCTTCTTTT
Found at i:4733029 original size:71 final size:71
Alignment explanation
Indices: 4732950--4733113 Score: 222
Period size: 71 Copynumber: 2.3 Consensus size: 71
4732940 TAAATTATTT
* * * * * *
4732950 AATTAAGTTATTGGGTCC-AATTGATTAAATTTGTTTAATCAAGTTATTGGGTCTCATTGATTAA
1 AATTAAGTTATTGGG-CCTAATTAAATAAATTTATTTAATCAAGTTATTGGGCCTAATTAATTAA
4733014 ATTAAAC
65 ATTAAAC
4733021 AATTAAGTTATTGGGCCTAATTAAATAAATTTATTTAATCAAGTTATTGGGCCTAATTAATTAAA
1 AATTAAGTTATTGGGCCTAATTAAATAAATTTATTTAATCAAGTTATTGGGCCTAATTAATTAAA
***
4733086 TTATTT
66 TTAAAC
*
4733092 AATTAAGTTATTAGGCCTAATT
1 AATTAAGTTATTGGGCCTAATT
4733114 GNNNNNNNNN
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
70 2 0.02
71 80 0.98
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (71 bp):
AATTAAGTTATTGGGCCTAATTAAATAAATTTATTTAATCAAGTTATTGGGCCTAATTAATTAAA
TTAAAC
Found at i:4733050 original size:35 final size:35
Alignment explanation
Indices: 4732938--4733113 Score: 210
Period size: 35 Copynumber: 5.0 Consensus size: 35
4732928 NNNNNNNNTC
*
4732938 ATTAAATTATTTAATTAAGTTATTGGGTCC-AATTG
1 ATTAAATTATTTAATTAAGTTATTGGG-CCTAATTA
* * * * *
4732973 ATTAAATTTGTTTAATCAAGTTATTGGGTCTCATTG
1 ATTAAA-TTATTTAATTAAGTTATTGGGCCTAATTA
***
4733009 ATTAAATTAAACAATTAAGTTATTGGGCCTAATTA
1 ATTAAATTATTTAATTAAGTTATTGGGCCTAATTA
* *
4733044 AATAAATTTATTTAATCAAGTTATTGGGCCTAATTA
1 ATTAAA-TTATTTAATTAAGTTATTGGGCCTAATTA
*
4733080 ATTAAATTATTTAATTAAGTTATTAGGCCTAATT
1 ATTAAATTATTTAATTAAGTTATTGGGCCTAATT
4733114 GNNNNNNNNN
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
35 59 0.50
36 59 0.50
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.44
Consensus pattern (35 bp):
ATTAAATTATTTAATTAAGTTATTGGGCCTAATTA
Found at i:4736658 original size:36 final size:36
Alignment explanation
Indices: 4736602--4736810 Score: 208
Period size: 36 Copynumber: 5.9 Consensus size: 36
4736592 NNNNNNNNNN
* *
4736602 ATTAAA-TTGTTTAATTAAGTTATTGGGCGTAATTG
1 ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTG
*
4736637 ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTA
1 ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTG
* *
4736673 ATTAAATTTATTTAATCAAGTTATTGGGCCTCATTG
1 ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTG
********** *
4736709 ATT-NNNNNNNNNNATTAAGTTATTGGGCCTAATTG
1 ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTG
* * * *
4736744 AATAAATTTATTTAATCAAGTTGTTGGGCCTAATTA
1 ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTG
*
4736780 ATTAAA-TTGTTTAATTAAGTTATTGGGCCTA
1 ATTAAATTTGTTTAATCAAGTTATTGGGCCTA
4736811 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 36, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
35 50 0.37
36 86 0.63
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.42
Consensus pattern (36 bp):
ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTG
Found at i:4736742 original size:107 final size:96
Alignment explanation
Indices: 4736615--4736809 Score: 237
Period size: 107 Copynumber: 1.9 Consensus size: 96
4736605 AAATTGTTTA
* * *
4736615 ATTAAGTTATTGGGCGTAATTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTAATTAAAT
1 ATTAAGTTATTGGGCCTAATTGAATAAATTTATTTAATCAAGTTATTGGGCCTAATTAATTAAA-
4736680 TTATTTAATCAAGTTATTGGGCCTCATTGATT
65 TTATTTAATCAAGTTATTGGGCCTCATTGATT
*
4736712 NNNNNNNNNNATTAAGTTATTGGGCCTAATTGAATAAATTTATTTAATCAAGTTGTTGGGCCTAA
1 ----------ATTAAGTTATTGGGCCTAATTGAATAAATTTATTTAATCAAGTTATTGGGCCTAA
* *
4736777 TTAATTAAATTGTTTAATTAAGTTATTGGGCCT
56 TTAATTAAATTATTTAATCAAGTTATTGGGCCT
4736810 ANNNNNNNNN
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
106 22 0.27
107 60 0.73
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.42
Consensus pattern (96 bp):
ATTAAGTTATTGGGCCTAATTGAATAAATTTATTTAATCAAGTTATTGGGCCTAATTAATTAAAT
TATTTAATCAAGTTATTGGGCCTCATTGATT
Found at i:4736797 original size:71 final size:71
Alignment explanation
Indices: 4736602--4736810 Score: 233
Period size: 71 Copynumber: 2.9 Consensus size: 71
4736592 NNNNNNNNNN
* * * *
4736602 ATTAAA-TTGTTTAATTAAGTTATTGGGCGTAATTGATTAAATTTGTTTAATCAAGTTATTGGGC
1 ATTAAATTTATTTAATCAAGTTATTGGGCCTAATTGATTAAA-TTGTTTAATTAAGTTATTGGGC
4736666 CTAATTA
65 CTAATTA
* **********
4736673 ATTAAATTTATTTAATCAAGTTATTGGGCCTCATTGATTNNNNNNNNNNATTAAGTTATTGGGCC
1 ATTAAATTTATTTAATCAAGTTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCC
4736738 TAATTGA
66 TAATT-A
* *
4736745 A-TAAATTTATTTAATCAAGTTGTTGGGCCTAATTAATTAAATTGTTTAATTAAGTTATTGGGCC
1 ATTAAATTTATTTAATCAAGTTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCC
4736809 TA
66 TA
4736811 NNNNNNNNNN
Statistics
Matches: 108, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
71 78 0.72
72 30 0.28
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.42
Consensus pattern (71 bp):
ATTAAATTTATTTAATCAAGTTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCC
TAATTA
Found at i:4746387 original size:20 final size:20
Alignment explanation
Indices: 4746347--4746387 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4746337 TAATAGTTAG
* *
4746347 TAATGGCTAGAAACTATCTC
1 TAATGGCTAGAAACAACCTC
*
4746367 TAATGGCTAGAATCAACCTC
1 TAATGGCTAGAAACAACCTC
4746387 T
1 T
4746388 CAAGTATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (20 bp):
TAATGGCTAGAAACAACCTC
Found at i:4747936 original size:14 final size:13
Alignment explanation
Indices: 4747905--4747957 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
4747895 TTTTTGTTAA
*
4747905 AAAAAGAAAAAAGAG
1 AAAAA-AAAAAA-TG
4747920 AAAAAGAAAAAATG
1 AAAAA-AAAAAATG
*
4747934 AAATAAAATAAATG
1 AAA-AAAAAAAATG
4747948 AAAAAAAAAA
1 AAAAAAAAAA
4747958 GACGAAGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.18
14 14 0.41
15 14 0.41
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAAATG
Found at i:4749064 original size:29 final size:30
Alignment explanation
Indices: 4749029--4749087 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
4749019 TGGTATGTAA
4749029 CAATA-TTTTCTCAACATGGCAAGTAACAG
1 CAATATTTTTCTCAACATGGCAAGTAACAG
* *
4749058 CAATATTTTTTTTCAACATGGCATGTAACA
1 CAATA-TTTTTCTCAACATGGCAAGTAACA
4749088 TCTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
31 21 0.81
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (30 bp):
CAATATTTTTCTCAACATGGCAAGTAACAG
Found at i:4749267 original size:75 final size:74
Alignment explanation
Indices: 4749110--4749285 Score: 205
Period size: 75 Copynumber: 2.3 Consensus size: 74
4749100 TATGGTGTGC
* * *
4749110 AACATGTTTTGTGCATGGTGTGTAACAACAGTATTTTTTTTCAACATGACGTGTAACAACCTAAT
1 AACATGTTTTGTACATGGCGTGTAACAACAGTATTTTTTTTCAACATGACGTGTAACAACCTAAC
4749175 CATAGCATAT
66 CATAGCA-AT
* * * * *
4749185 AATATGTTTTAGTCCGTGGCGTGTAACAACAGTA-TTTTTTTCAATAT-AGTGTGTAACAACCTA
1 AACATGTTTT-GTACATGGCGTGTAACAACAGTATTTTTTTTCAACATGA-CGTGTAACAACCTA
4749248 ACCATGATGC-AT
64 ACCAT-A-GCAAT
4749260 AACATGTTTTTGTACATGGCGTGTAA
1 AACATG-TTTTGTACATGGCGTGTAA
4749286 AATCATGGCA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
74 1 0.01
75 58 0.67
76 25 0.29
77 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (74 bp):
AACATGTTTTGTACATGGCGTGTAACAACAGTATTTTTTTTCAACATGACGTGTAACAACCTAAC
CATAGCAAT
Found at i:4750739 original size:212 final size:212
Alignment explanation
Indices: 4750230--4750832 Score: 875
Period size: 212 Copynumber: 2.8 Consensus size: 212
4750220 ACTATAATGC
* * * * *
4750230 TATAATATTTCATATCAAAATTTGTATAAATAATAACTAATTATGAACAATGTGTTATAAAAACT
1 TATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAACT
* *
4750295 AAGGTGATAACTAATAAAGTTATTAAGTGTAATCATATAAAGAAAA-TTTATTATAAGTTATAGG
66 AAGGTGATAACTAATAAAGTTATTAAGTGTAATTATATAAA-AAAAGTTTATTATAAGTTATAGT
* *
4750359 AATACTTATATATAAATTAAATATATGTATATATATATAATATCACTTTATTATATATATAAAAT
130 AATTCTTATGTATAAATTAAATATATG--TATATATATAATATCACTTTATTATATATATAAAAT
4750424 TAATGACACAACTTATATAT
193 TAATGACACAACTTATATAT
*
4750444 TATAATATTTTAAGTTTTATATCAAAGTTTGTAAAAATAATAACTAATTATAAACAATATGTTAT
1 TAT-A-A---T--GTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTAT
* * * * *
4750509 AAAAACTAAGATGATAACTAATAAAGTTTTTAAGCGTAATTATATTAATAAAGTTTATTATAAGT
59 AAAAACTAAGGTGATAACTAATAAAGTTATTAAGTGTAATTATATAAAAAAAGTTTATTATAAGT
* * * *
4750574 TATAGTAATTCTTATGTATAAATTAAATATATGCATATATAGAATATTACTTTATTATATATATG
124 TATAGTAATTCTTATGTATAAATTAAATATATGTATATATATAATATCACTTTATTATATATATA
* *
4750639 AAATTAATGATACAACTTATATGT
189 AAATTAATGACACAACTTATATAT
**
4750663 TATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATAAATTATAAAAACT
1 TATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAACT
* * *
4750728 AAGGTGATAACTAATAAAGGTATTAATTGTGATTATATAAAAAAAGTTTATTATAAGTTATAGTA
66 AAGGTGATAACTAATAAAGTTATTAAGTGTAATTATATAAAAAAAGTTTATTATAAGTTATAGTA
4750793 ATTCTTATGTATAAATTAAATATATGTATATATATAATAT
131 ATTCTTATGTATAAATTAAATATATGTATATATATAATAT
4750833 ATTTATACAA
Statistics
Matches: 347, Mismatches: 34, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
212 151 0.44
214 4 0.01
215 1 0.00
216 1 0.00
217 1 0.00
218 1 0.00
219 54 0.16
220 3 0.01
221 131 0.38
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (212 bp):
TATAATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAACT
AAGGTGATAACTAATAAAGTTATTAAGTGTAATTATATAAAAAAAGTTTATTATAAGTTATAGTA
ATTCTTATGTATAAATTAAATATATGTATATATATAATATCACTTTATTATATATATAAAATTAA
TGACACAACTTATATAT
Found at i:4750820 original size:17 final size:17
Alignment explanation
Indices: 4750798--4750852 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
4750788 TAGTAATTCT
4750798 TATGTATAAATTAAATA
1 TATGTATAAATTAAATA
*
4750815 TATGTATATA-TATAATA
1 TATGTATAAATTA-AATA
* *
4750832 TATTTATACAATTATATA
1 TATGTATA-AATTAAATA
4750850 TAT
1 TAT
4750853 TTATTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 2 0.06
17 20 0.65
18 7 0.23
19 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
TATGTATAAATTAAATA
Done.