Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003272.1 Hibiscus syriacus cultivar Beakdansim tig00006877_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: 58950
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3652 original size:1 final size:1
Alignment explanation
Indices: 3646--3735 Score: 90
Period size: 1 Copynumber: 90.0 Consensus size: 1
3636 ATGTTTGAAG
* * * * * * * * *
3646 AAAAAAAGAAAAAAGAAAGAAAAGAAAAAAAAGAAAAGAAAAAAAAAAAGAAAAAAGAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
3711 AAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3736 GAAAGGGGGG
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:3656 original size:8 final size:8
Alignment explanation
Indices: 3643--3732 Score: 123
Period size: 8 Copynumber: 11.2 Consensus size: 8
3633 ATTATGTTTG
3643 AAGAAAAA
1 AAGAAAAA
3651 AAG-AAAA
1 AAGAAAAA
3658 AAGAAAGAA
1 AAGAAA-AA
3667 AAGAAAAAA
1 AAG-AAAAA
3676 AAGAAAAGA
1 AAGAAAA-A
*
3685 AAAAAAAA
1 AAGAAAAA
3693 AAG-AAAA
1 AAGAAAAA
3700 AAGAAAAA
1 AAGAAAAA
3708 AAGAAAAA
1 AAGAAAAA
3716 AAGAAAAA
1 AAGAAAAA
3724 AA-AAAAA
1 AAGAAAAA
3731 AA
1 AA
3733 AAAGAAAGGG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
7 21 0.28
8 34 0.45
9 17 0.23
10 3 0.04
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:3705 original size:42 final size:41
Alignment explanation
Indices: 3646--3739 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
3636 ATGTTTGAAG
*
3646 AAAAAAAGAAAAAAGAAAGAAAAGAAAAAAA-AGAAAAGAAAA
1 AAAAAAAGAAAAAAGAAA-AAAAGAAAAAAAGA-AAAAAAAAA
3688 AAAAAAAGAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAAAA
1 AAAAAAAGAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAAAA
3729 AAAAAAAGAAA
1 AAAAAAAGAAA
3740 GGGGGGGTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
41 31 0.62
42 19 0.38
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (41 bp):
AAAAAAAGAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAAAA
Found at i:5015 original size:83 final size:83
Alignment explanation
Indices: 4878--5095 Score: 427
Period size: 83 Copynumber: 2.6 Consensus size: 83
4868 AACAAATGCC
*
4878 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
4943 ATTGAATTTGAAAGATAA
66 ATTGAATTTGAAAGATAA
4961 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
5026 ATTGAATTTGAAAGATAA
66 ATTGAATTTGAAAGATAA
5044 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
5096 AGTAGGAAAC
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 134 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (83 bp):
ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
ATTGAATTTGAAAGATAA
Found at i:5293 original size:115 final size:115
Alignment explanation
Indices: 5051--5255 Score: 324
Period size: 115 Copynumber: 1.8 Consensus size: 115
5041 TAAATGTGCT
*
5051 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTAGGAAACCACAGAACCA
1 AATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTAGGAAACCACAGAACCA
* * * *
5116 ATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
66 ATCATTGGAATTAAAAGATGAATCTGCTCATAGTAGAAATAAGAAGACTC
* * *
5166 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGG-AACTACAGAACCA
1 AATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTAGGAAACCACAGAACCA
5230 ATCATTGGAATTAAAAGATGAA-CTGC
66 ATCATTGGAATTAAAAGATGAATCTGC
5256 ATGATCGTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
113 3 0.04
114 32 0.38
115 50 0.59
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (115 bp):
AATAGCAGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTAGGAAACCACAGAACCA
ATCATTGGAATTAAAAGATGAATCTGCTCATAGTAGAAATAAGAAGACTC
Found at i:6135 original size:112 final size:111
Alignment explanation
Indices: 5932--6605 Score: 931
Period size: 113 Copynumber: 6.0 Consensus size: 111
5922 GCAAAGATTT
*
5932 AAATTTATCACTTGATGGATCAGCTTTTCCAGAGAGTTTCATAATGAGAAGAACTCATCTGAAGA
1 AAATCTATCACTTGATGGATCAGCTTTTCCAGAGAG-TTCATAATGAGAAGAACTCATCTGAAGA
*
5997 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
6044 AAATCCATCACTTGATGGGTCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAAA
1 AAATCTATCACTTGATGGATCAGCTTTTCCAGAG-AGTTCATAATGAGAAGAACTCATCTGAAGA
*
6109 AGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
6156 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATCAGCTTTTCCAG--AGAGTTCATAATGAGAAGAACTCATCTGAAG
*
6221 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* ***
6269 AAATCTATCACTTGATGGATTAAAATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTACTTG
1 AAATCTATCACTTGATGGATCAGCTTTTCCA-G-AGAGTTCATAATGAGAAGAACTCA-T-C-TG
* * *
6334 AAGAAGGATGAAGAAGTTCATAACGAGAAGAATTTGTTCAACCTTTTGTTC
61 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
6385 AAATCTATCACTTGATGGA-CTATCTTTTCCTGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCTATCACTTGATGGATC-AGCTTTTCCAG--AGAGTTCATAATGAGAAGAACTCATCTGAA
* *
6449 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
6498 AAATCCATCACTTGATGGGTCAG-TTTTCCCAGAGAAGTTCATAATGAGAAGAACTCATCAGGAG
1 AAATCTATCACTTGATGGATCAGCTTTT-CCAGAG-AGTTCATAATGAGAAGAACTCATCTGAAG
* ** *
6562 AA-GAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
64 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
6606 AATGACTCTA
Statistics
Matches: 509, Mismatches: 41, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
111 38 0.07
112 164 0.32
113 199 0.39
114 5 0.01
115 3 0.01
116 100 0.20
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (111 bp):
AAATCTATCACTTGATGGATCAGCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:6437 original size:229 final size:224
Alignment explanation
Indices: 5932--6605 Score: 989
Period size: 229 Copynumber: 3.0 Consensus size: 224
5922 GCAAAGATTT
* * *
5932 AAATTTATCACTTGATGGA-TCAGCTTTTCCAG--AGAGTTTCATAATGAGAAGAACTCATCTGA
1 AAATCTATCACTTGATGGACT-ATCTTTTCCAGTTCGAG-TTCATAATGAGAAGAACTCATCTGA
5994 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGA
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGA
* ** *
6059 TGGGTCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGATGAAGAAGTTC
129 T-GGTTAAATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTC
6124 ATAATGAGAAGAATTTGTTCAACCTTTTGCTC
193 ATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
6156 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGACTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
6221 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
*
6286 GATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTACTTGAAGAAGGATGAAGAAG
131 G-TTAAATTTTCCAGAG-A-AGTTCATAATGAGAAGAACTCA-T-C-TGAAGAAGGATGAAGAAG
* *
6350 TTCATAACGAGAAGAATTTGTTCAACCTTTTGTTC
190 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
6385 AAATCTATCACTTGATGGACTATCTTTTCCTGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGACTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
6450 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
* * * * * *
6515 GGTCAGTTTTCCCAGAGAAGTTCATAATGAGAAGAACTCATCAGGAGAA-GAAGAAGAAGTTCAT
131 GTTAAATTTT-CCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCAT
* ** *
6579 AATAAGAAGAGCTTATTCAACCTTTTG
195 AATGAGAAGAATTTGTTCAACCTTTTG
6606 AATGACTCTA
Statistics
Matches: 408, Mismatches: 31, Indels: 22
0.89 0.07 0.05
Matches are distributed among these distances:
224 67 0.16
225 104 0.25
226 26 0.06
227 2 0.00
228 28 0.07
229 180 0.44
230 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (224 bp):
AAATCTATCACTTGATGGACTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
GTTAAATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:6835 original size:3 final size:3
Alignment explanation
Indices: 6829--6913 Score: 116
Period size: 3 Copynumber: 28.0 Consensus size: 3
6819 CATTTTAATG
* * * * *
6829 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TAA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6877 TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
6914 AATATTACAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
3 72 0.96
4 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:8207 original size:27 final size:26
Alignment explanation
Indices: 8177--8235 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
8167 TAAATATATA
*
8177 TAATAAATAATTATTTATATATATTTT
1 TAATAAATAATT-TTAATATATATTTT
* *
8204 TAATAAATTATTTTAATATTTATTTT
1 TAATAAATAATTTTAATATATATTTT
8230 TCAATA
1 T-AATA
8236 TCGAAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATAAATAATTTTAATATATATTTT
Found at i:10452 original size:21 final size:21
Alignment explanation
Indices: 10428--10509 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
10418 ATGCATCCCT
10428 TGAATGTGCATCGATACACTA
1 TGAATGTGCATCGATACACTA
*
10449 TGAATGTGCACCGATGTATTC-CT-
1 TGAATGTGCATCGA--TA--CACTA
10472 TGAATGTGCATCGATACACTA
1 TGAATGTGCATCGATACACTA
* *
10493 TGCA-GTGCATCGTTACA
1 TGAATGTGCATCGATACA
10510 GTCGTCAGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
19 1 0.02
20 14 0.27
21 18 0.35
23 15 0.29
24 2 0.04
25 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
TGAATGTGCATCGATACACTA
Found at i:10476 original size:44 final size:44
Alignment explanation
Indices: 10391--10494 Score: 165
Period size: 44 Copynumber: 2.4 Consensus size: 44
10381 TTGTGCAAAA
*
10391 TGCATCGATACACTA-GAAAGTGTACCGATGCATCCCTTGAATG
1 TGCATCGATACACTATGAAAGTGCACCGATGCATCCCTTGAATG
* * *
10434 TGCATCGATACACTATGAATGTGCACCGATGTATTCCTTGAATG
1 TGCATCGATACACTATGAAAGTGCACCGATGCATCCCTTGAATG
10478 TGCATCGATACACTATG
1 TGCATCGATACACTATG
10495 CAGTGCATCG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
43 15 0.27
44 41 0.73
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCACCGATGCATCCCTTGAATG
Found at i:10991 original size:13 final size:13
Alignment explanation
Indices: 10968--11006 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
10958 AAAACTCCAT
10968 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
10982 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
*
10995 ATAGTTTTCAAA
1 ATTGTTTTCAAA
11007 ATTATCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:13163 original size:64 final size:65
Alignment explanation
Indices: 13083--13235 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 65
13073 ACCCTATTAA
*
13083 GAATGCATTTTGTGTACCGATGCACA-ACCATGCATCGATGCACTCTTGAAT-TTATTGAAACAT
1 GAATGCATTTTATGTACCGATGCACATACCATGCATCGATGCACTCTTGAATCTT-TTGAAACAT
*
13146 T
65 C
* **
13147 GAATGCATTTTATGTACAGATGCACATACCATGCATCGATGCACTCTTGGCTCTTTTGAAACATC
1 GAATGCATTTTATGTACCGATGCACATACCATGCATCGATGCACTCTTGAATCTTTTGAAACATC
* *
13212 GAATGTA-ATTAGTGTACCGATGCA
1 GAATGCATTTTA-TGTACCGATGCA
13236 GCCCTAGTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.35
65 49 0.63
66 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (65 bp):
GAATGCATTTTATGTACCGATGCACATACCATGCATCGATGCACTCTTGAATCTTTTGAAACATC
Found at i:14307 original size:19 final size:20
Alignment explanation
Indices: 14285--14322 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
14275 AAGTATTTAT
14285 ACTTTTATAA-AGTATCGAA
1 ACTTTTATAAGAGTATCGAA
*
14304 ACTTTTGTAAGAGTATCGA
1 ACTTTTATAAGAGTATCGA
14323 TATTTTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ACTTTTATAAGAGTATCGAA
Found at i:16144 original size:182 final size:182
Alignment explanation
Indices: 15803--16404 Score: 877
Period size: 182 Copynumber: 3.3 Consensus size: 182
15793 AGGTAAAAAT
*
15803 ATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
* * *
15868 CACTTTTTGGAATTTAAAAGAGAATCAGTAATAGCGTCTATAAATTGTTGATACTTTATAAAAAT
66 CAC-TTTTGGAATTTAAAAGAGAAACAGTAATAGCGTCTATAAAGTGTCGATACTTTATAAAAAT
* * ** * *
15933 GTATCGATCCATAATAGTATAAAAGGTAAAAATATGACAAAATCAATATGGAA
130 GTATCGATCCATAATAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAA
* *
15986 ATGACAAAACCGGTAAACCACTACCGGATATGTTGAAAGTGTCGAAACTTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
* * * *
16051 CACTTTTGGAATTTAAAAGGGAACCAGTAATAACATCTATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAACAGTAATAGCGTCTATAAAGTGTCGATACTTTATAAAAATG
16116 TATCGATCCATAATAATATAACAGGTAAAAATATGACAAAA-CTGGTCTCGAA
131 TATCGATCCATAATAATATAACAGGTAAAAATATGACAAAATC-GGTCTCGAA
* * * *
16168 ATGACAAAACCGATAAAG-AGCTACTGGATATGTTGAAAGTGTTGATACTTTAATATAAGTATCA
1 ATGACAAAACCGGTAAAGCA-CTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCG
* * *
16232 ACACTTTTGGAATTTAAAAGAGAAACAGTAATAGTGCCTATAAAGTGTCAATACTTTATAAAAAT
65 ACACTTTTGGAATTTAAAAGAGAAACAGTAATAGCGTCTATAAAGTGTCGATACTTTATAAAAAT
** * * *
16297 GTATTAATCCATAACAATATAACAGGCAATAATATGACAAAATCGGTCTCGAA
130 GTATCGATCCATAATAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAA
* *
16350 ATGACAAAACCGGTAAAGCACTACCAGATATTTTGAAAGTG-CTGATACTTTAATA
1 ATGACAAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTC-GATACTTTAATA
16405 AGTATGCGTA
Statistics
Matches: 376, Mismatches: 38, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
181 2 0.01
182 307 0.82
183 67 0.18
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
ATGACAAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
CACTTTTGGAATTTAAAAGAGAAACAGTAATAGCGTCTATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAATAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAA
Found at i:18481 original size:9 final size:9
Alignment explanation
Indices: 18469--18508 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
18459 AGGCGGCAGA
18469 GGAGGAAGT
1 GGAGGAAGT
*
18478 GGAGGCAGT
1 GGAGGAAGT
*
18487 GGAGGCAGT
1 GGAGGAAGT
*
18496 GGAGGAAGA
1 GGAGGAAGT
18505 GGAG
1 GGAG
18509 AAGGAAGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.57, T:0.07
Consensus pattern (9 bp):
GGAGGAAGT
Found at i:18484 original size:18 final size:18
Alignment explanation
Indices: 18463--18508 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
18453 AGGTAGAGGC
18463 GGCAGAGGAGGAAGTGGA
1 GGCAGAGGAGGAAGTGGA
* *
18481 GGCAGTGGAGGCAGTGGA
1 GGCAGAGGAGGAAGTGGA
*
18499 GGAAGAGGAG
1 GGCAGAGGAG
18509 AAGGAAGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.57, T:0.07
Consensus pattern (18 bp):
GGCAGAGGAGGAAGTGGA
Found at i:19241 original size:128 final size:127
Alignment explanation
Indices: 18922--19233 Score: 350
Period size: 128 Copynumber: 2.4 Consensus size: 127
18912 TTTAAAGTAT
*
18922 TAGGTAAATTTACAATGTAA-GTGG--TAAAAATACACT-TTTTAAATGACAAAAT-TAGTAAAC
1 TAGGTAAATTTACAATGTAACG-GGTATAAAAATACA-TGTTTT--ATGAGAAAATAT-GTAAAC
* * * * * * *
18982 ATAATGTGTCGATATTTTTTAAAATTGTATCGATCCCAACAACATAGGAACCGATAATTATAATG
61 ATAAAGTGTCAATATTTATTAAAA-TGTATCGATCACAAAAACATAGAAACCGATAATTACAATG
19047 TAA
125 TAA
* * * * * * *
19050 TAGGTAAATTTACAATGTAACCGGTAGAAATATACCA-GTTTAATTAGAAAATAGGTCAACATAA
1 TAGGTAAATTTACAATGTAACGGGTATAAAAATA-CATGTTTTATGAGAAAATATGTAAACATAA
*
19114 AGTGTCAATACATTTATTAAAA-GTATCGATCACAAAAACATTGAAACCGATAATTACAATGTAA
65 AGTGTCAAT--ATTTATTAAAATGTATCGATCACAAAAACATAGAAACCGATAATTACAATGTAA
19178 TAGGTAAATTTACAATGTAACGGGTATAAAAATACATGTTTTATGAGAAAATATGT
1 TAGGTAAATTTACAATGTAACGGGTATAAAAATACATGTTTTATGAGAAAATATGT
19234 TTACATAATG
Statistics
Matches: 153, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
127 2 0.01
128 130 0.85
130 19 0.12
131 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (127 bp):
TAGGTAAATTTACAATGTAACGGGTATAAAAATACATGTTTTATGAGAAAATATGTAAACATAAA
GTGTCAATATTTATTAAAATGTATCGATCACAAAAACATAGAAACCGATAATTACAATGTAA
Found at i:19271 original size:128 final size:126
Alignment explanation
Indices: 18922--19271 Score: 345
Period size: 128 Copynumber: 2.7 Consensus size: 126
18912 TTTAAAGTAT
*
18922 TAGGTAAATTTACAATGTAA-GTGG--TAAAAATACACT-TTTTAAATGACAAAAT-TAGTAAAC
1 TAGGTAAATTTACAATGTAACG-GGTATAAAAATACA-TGTTTT--ATGAGAAAATAT-GTAAAC
* * * * *
18982 ATAATGTGTCGATATTTTTTAAAATTGTATCGATCCCAACAACATAGGAACCGATAATTATAATG
61 ATAATGTGTCGACA-TTTTT-AAATTGTATCGATCACAAAAACATAGAAACCGATAATTACAATG
19047 TAA
124 TAA
* * * * * * *
19050 TAGGTAAATTTACAATGTAACCGGTAGAAATATACCA-GTTTAATTAGAAAATAGGTCAACATAA
1 TAGGTAAATTTACAATGTAACGGGTATAAAAATA-CATGTTTTATGAGAAAATATGTAAACATAA
* * * *
19114 AGTGTCAATACATTTATTAAA-AGTATCGATCACAAAAACATTGAAACCGATAATTACAATGTAA
65 TGTGTC--GACATTT-TTAAATTGTATCGATCACAAAAACATAGAAACCGATAATTACAATGTAA
**
19178 TAGGTAAATTTACAATGTAACGGGTATAAAAATACATGTTTTATGAGAAAATATGTTTACATAAT
1 TAGGTAAATTTACAATGTAACGGGTATAAAAATACATGTTTTATGAGAAAATATGTAAACATAAT
* *
19243 GTATCGACATATTTTAAATTTGTGTCGAT
66 GTGTCGACAT-TTTTAAA-TTGTATCGAT
19272 ACTTTTTGTC
Statistics
Matches: 179, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
126 9 0.05
127 4 0.02
128 145 0.81
129 6 0.03
130 13 0.07
131 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.33
Consensus pattern (126 bp):
TAGGTAAATTTACAATGTAACGGGTATAAAAATACATGTTTTATGAGAAAATATGTAAACATAAT
GTGTCGACATTTTTAAATTGTATCGATCACAAAAACATAGAAACCGATAATTACAATGTAA
Found at i:19648 original size:199 final size:199
Alignment explanation
Indices: 19109--20672 Score: 2099
Period size: 199 Copynumber: 7.8 Consensus size: 199
19099 AATAGGTCAA
* * * *
19109 CATAAAGTGTCAATACATTTATTAAA-AGTATCGATCACAAAAACATTGAAACCGATAATTACAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAA
* * * ** * *
19173 TGTAATAGGTAAATTTACAATGTAACGGGTATAAAAATACATGTTTTATGAGAAAATATGTTTAC
64 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTAC
* * * * *
19238 ATAATGTATCG-ACATATTTTAAATTTGTGTCGATACTTTTTGTCCAGAATAAATGACAAACTAG
129 ATAAAGTATCGAACA-CTTTTAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAG
19302 GTGCACG
193 GTGCACG
* * * * * * *
19309 CATAAAGTGTCGATACATTTATTAAA-AGAATCAATCCTAAAAATATCAAAACCGATAATTATAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAA
* * * * *
19373 TGTAATAGGTAAACTTACAATGTAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAAC
64 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTAC
* *
19438 ATAATGTATCGAA-ACTTTCTAAATATGTGTCGATACATTTTGTCCAGAATGAATGCCAAACTAG
129 ATAAAGTATCGAACACTTT-TAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAG
19502 GTGCACG
193 GTGCACG
* * * *
19509 GATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAATATCAAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
*
19574 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAAGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
** * * *
19639 AAAGTATCGACACAAATTTAAA-AAGTGTCGATACTTTTTGTCCAGAATGAATGTCAAACTAGGA
131 AAAGTATCGA-ACACTTTTAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGT
19703 GCACG
195 GCACG
* * * **
19708 CATAAAGTGTCGATAAATTTAAAATTGTATCAATCCCAAAAATATTAAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
* * *
19773 TAATGGGTAAATTTACAATGTACCCGGTAGAAATATACTGGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
* * * * * *
19838 AAAGTAT-TAACACAAATTTAAA-ATGTGTCGGTACGTTTTGACCAGAATGAATGTCAAACTAGG
131 AAAGTATCGAACAC--TTTTAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGG
*
19901 TACACG
194 TGCACG
* *
19907 CATAAAGTGTTGATACATTTAAAATTGTATCGATCTCAAAAACATCGAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
* * * *
19972 TAATAGGTAAATTTAGAATCTAACTGGTAGAAATATACC-ATTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
** * *
20036 AAAGTATCGACACAAATTTAAA-AAGTGTCGATACTTTTTGACCAGAATGAATGCCAAACTAGGT
131 AAAGTATCGA-ACACTTTTAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGT
*
20100 GTACG
195 GCACG
20105 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
* *
20170 TAATAGGTAAATTTACAATGTAACCAGTAGAAATATACCGGTTTTATAAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
*
20235 AAAGTATCG-ACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGT
131 AAAGTATCGAACACTTT-TAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGT
20299 GCACG
195 GCACG
* * *
20304 CATAAAATGTCGATACATTTTAAATTGTATCGATCCCAAAAACATTGAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
* **
20369 TAATAGGTAAATTTACAATGTAACCGGTATACGTATACCGGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
* * * * * *
20434 AATGTATCG-ACGCTTTCTATATTTGTGTCGATACGTTTTGTCCAGAATAAATGCCAAACTAGGT
131 AAAGTATCGAACACTTT-TAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGT
20498 GCACG
195 GCACG
* * * *
20503 CATGAAGTGTCGATACATTTAAAATTTTATCGATCCCAAAACCATCGAAACTGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
* * *
20568 TAATAGGTAAATTTACAATGTAACCGTTATAAATATATCGGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
** *
20633 ATTGTATC-AACACTTTCTAAATTTGTGTCGATACCTTTTT
131 AAAGTATCGAACACTTT-TAAATATGTGTCGATA-CTTTTT
20673 TAAATTGCGC
Statistics
Matches: 1226, Mismatches: 124, Indels: 28
0.89 0.09 0.02
Matches are distributed among these distances:
197 8 0.01
198 185 0.15
199 825 0.67
200 204 0.17
201 4 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTACAATG
TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
AAAGTATCGAACACTTTTAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAGGTG
CACG
Found at i:20188 original size:596 final size:594
Alignment explanation
Indices: 19109--20633 Score: 2166
Period size: 596 Copynumber: 2.6 Consensus size: 594
19099 AATAGGTCAA
* * *
19109 CATAAAGTGTCAATACATTTATTAAA-AGTATCGATCACAAAAACATTGAAACCGATAATTACAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCGATCCCAAAAACATTGAAACCGATAATTACAA
* * * *
19173 TGTAATAGGTAAATTTACAATGTAACGGGTATAAAAATACAT-GTTTTATGAGAAAATATGTTTA
64 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATAC-TGGTTTTATGAGAAAATAGGTCTA
* *
19237 CATAATGTATCGACATATTTTAAATTTGTGTCGATACTTTTTGTCCAGAATAAATGACAAACTAG
128 CATAATGTATCGACACATTTTAAA-TTGTGTCGATACGTTTTGTCCAGAATAAATGACAAACTAG
* * * * *
19302 GTGCACGCATAAAGTGTCGATACATTTATTAAA-AGAATCAATCCTAAAAATATCAAAACCGATA
192 GTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATCGATCC-AAAAACATCGAAACCGATA
* * *
19366 ATTATAATGTAATAGGTAAACTTACAATGTAACTGGTATAAATATACCGGTTTTATGAGAGAATA
254 ATTACAATGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACC-GTTTTATGAGAAAATA
* * ** * *
19431 GGTCAACATAATGTATCGAAACTTTCTAAATATGTGTCGATACATTTTGTCCAGAATGAATGCCA
318 GGTCTACATAAAGTATCGAAAAATTCTAAATAAGTGTCGATACATTTTGACCAGAATGAATGCCA
* *
19496 AACTAGGTGCACGGATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAATATCAAAACC
383 AACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCAAAACC
* *
19561 GATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAA
448 GATAATTACAATGTAATAGGTAAATTTACAATGTAACCAGTAGAAATATACCGGTTTTATAAGAA
19626 AATAAGTCTACATAAAGTATCGACACAAATT-TAAA-AAGTGTCGATACTTTTTGTCCAGAATGA
513 AATAAGTCTACATAAAGTATCGACAC--ATTCTAAATAAGTGTCGATACTTTTTGTCCAGAATGA
*
19689 ATGTCAAACTAGGAGCACG
576 ATGCCAAACTAGGAGCACG
* * * *
19708 CATAAAGTGTCGATAAATTTAAAATTGTATCAATCCCAAAAATATTAAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATTGAAACCGATAATTACAATG
* * *
19773 TAATGGGTAAATTTACAATGTACCCGGTAGAAATATACTGGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTATAAATATACTGGTTTTATGAGAAAATAGGTCTACAT
* ** * * * * * * *
19838 AAAGTATTAACACAAATTTAAAATGTGTCGGTACGTTTTGACCAGAATGAATGTCAAACTAGGTA
131 AATGTATCGACAC-ATTTTAAATTGTGTCGATACGTTTTGTCCAGAATAAATGACAAACTAGGTG
*
19903 CACGCATAAAGTGTTGATACATTTAAAATTGTATCGATCTCAAAAACATCGAAACCGATAATTAC
195 CACGCATAAAGTGTCGATACATTTAAAATTGTATCGATC-CAAAAACATCGAAACCGATAATTAC
* * * *
19968 AATGTAATAGGTAAATTTAGAATCTAACTGGTAGAAATATACCATTTTATGAGAAAATAGGTCTA
259 AATGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGTTTTATGAGAAAATAGGTCTA
*
20033 CATAAAGTATCGACACAAATT-TAAA-AAGTGTCGATACTTTTTGACCAGAATGAATGCCAAACT
324 CATAAAGTATCGA-A-AAATTCTAAATAAGTGTCGATACATTTTGACCAGAATGAATGCCAAACT
* * *
20096 AGGTGTACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATA
387 AGGTGCACGCATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCAAAACCGATA
20161 ATTACAATGTAATAGGTAAATTTACAATGTAACCAGTAGAAATATACCGGTTTTATAAGAAAATA
452 ATTACAATGTAATAGGTAAATTTACAATGTAACCAGTAGAAATATACCGGTTTTATAAGAAAATA
* * **
20226 GGTCTACATAAAGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCA
517 AGTCTACATAAAGTATCGACACATTCTAAATAAGTGTCGATACTTTTTGTCCAGAATGAATGCCA
*
20291 AACTAGGTGCACG
582 AACTAGGAGCACG
* *
20304 CATAAAATGTCGATACATTTTAAATTGTATCGATCCCAAAAACATTGAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATTGAAACCGATAATTACAATG
** *
20369 TAATAGGTAAATTTACAATGTAACCGGTATACGTATACCGGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTATAAATATACTGGTTTTATGAGAAAATAGGTCTACAT
* * *
20434 AATGTATCGACGC-TTTCTATATTTGTGTCGATACGTTTTGTCCAGAATAAATGCCAAACTAGGT
131 AATGTATCGACACATTT-TA-AATTGTGTCGATACGTTTTGTCCAGAATAAATGACAAACTAGGT
* * * *
20498 GCACGCATGAAGTGTCGATACATTTAAAATTTTATCGATCCCAAAACCATCGAAACTGATAATTA
194 GCACGCATAAAGTGTCGATACATTTAAAATTGTATCGAT-CCAAAAACATCGAAACCGATAATTA
* * *
20563 CAATGTAATAGGTAAATTTACAATGTAACCGTTATAAATATATCGGTTTTATGAGAAAATAGGTC
258 CAATGTAATAGGTAAATTTACAATGTAACTGGTATAAATATA-CCGTTTTATGAGAAAATAGGTC
20628 TACATA
322 TACATA
20634 TTGTATCAAC
Statistics
Matches: 818, Mismatches: 95, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
594 4 0.00
595 6 0.01
596 515 0.63
597 103 0.13
598 164 0.20
599 26 0.03
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (594 bp):
CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATTGAAACCGATAATTACAATG
TAATAGGTAAATTTACAATGTAACCGGTATAAATATACTGGTTTTATGAGAAAATAGGTCTACAT
AATGTATCGACACATTTTAAATTGTGTCGATACGTTTTGTCCAGAATAAATGACAAACTAGGTGC
ACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAACATCGAAACCGATAATTACAA
TGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGTTTTATGAGAAAATAGGTCTACA
TAAAGTATCGAAAAATTCTAAATAAGTGTCGATACATTTTGACCAGAATGAATGCCAAACTAGGT
GCACGCATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCAAAACCGATAATTA
CAATGTAATAGGTAAATTTACAATGTAACCAGTAGAAATATACCGGTTTTATAAGAAAATAAGTC
TACATAAAGTATCGACACATTCTAAATAAGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACT
AGGAGCACG
Found at i:21291 original size:2 final size:2
Alignment explanation
Indices: 21284--21319 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21274 ATGGGGAATG
21284 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
21320 CTCCAAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25645 original size:199 final size:199
Alignment explanation
Indices: 25060--26708 Score: 2206
Period size: 199 Copynumber: 8.2 Consensus size: 199
25050 ATCTATAATT
*
25060 TTTAAAATTGTATCGATCCTAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
* ** * * *
25125 ATATAACTGGTAGAAATATACCGCCTTTATGAGAAAACAGGTCTACATAATGTATCGTCACTTTC
66 ATATAACCGGTAGAAATATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTA
*
25190 TAAATTTGTATCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGA
131 TAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGA
25255 TACA
196 TACA
25259 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
* * *
25324 ATGTAA-CGGTAGAAATATACC-AGTATATTGAGAAAATAGGTCTACATAATGTATCGACACTTT
66 ATATAACCGGTAGAAATATACCGATTTTA-TGAGAAAATAGGTCTACATAATGTATCGACACTTT
* * * * *
25387 ATAAATTTGTGTCGATACTTTTTTTCCAGAATGAATACCCAACGAGGTACACGCATAAAGTATTG
130 ATAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCG
25452 ATACA
195 ATACA
*
25457 TTTAAAATTGTATCGATCTCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
* * * * *
25522 ATGTAACCAGTAAAAATATACTGATTTTAGGAGAAAATAGGTCTACATAATGTATCGACACTTTA
66 ATATAACCGGTAGAAATATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTA
* * **
25587 TAAATTTGTGTCGATACTTTTTATCCAGAATGAATTCCCAATAAGGTGCACGCATAAAGTGTCGA
131 TAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGA
25652 TACA
196 TACA
* * *
25656 TTTAAAATTATATCGATCTCAAAAGCATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
* * *
25721 ATATAATCGGTAGAAATATACC-AGTTTTATGAGAAAATAGGTATACATAATGTATCGATACTTT
66 ATATAACCGGTAGAAATATACCGA-TTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTT
* * *
25785 CTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGTCCAACGAGGTGCACCCATAAAGTGTCG
130 ATAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCG
25850 ATACA
195 ATACA
* * * *
25855 TTTAAAATTGTATCGGTCACAAAAACATTGAAACCTATAATTATAATGTAATAGGTAAATTTAAA
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
* * *
25920 ATATAACCGGTAGAAATATACCAATTTTATGAGAAAATATGTCTACATAATGTATCGACACTTTC
66 ATATAACCGGTAGAAATATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTA
*
25985 TAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGTACGCATAAAGTGTCGA
131 TAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGA
26050 TACA
196 TACA
* * *
26054 TTTAAAATTGTATCGATCCCAAAAATATCGAAATCTATAATTATAATGTAATATGTAAATTTACA
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
*
26119 ATGTAACCGGTAAATTTACAATGTAATCGGTAGAAATATACCGATTTTAGGAGAAAATAGGTCTA
66 A--T-A----T--A---AC--------CGGTAGAAATATACCGATTTTATGAGAAAATAGGTCTA
* * * *
26184 TATAATGTATCGATACTTTATAAATTTGTGTCAATACTTTTTTTCCAGAATGAATGCCCAACGAG
111 CATAATGTATCGACACTTTATAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAG
*
26249 GTGCACGTATAAAGTGTCGATACA
176 GTGCACGCATAAAGTGTCGATACA
* *
26273 TTTAAAATTGTATCGATCACAAAAGCATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
* * * * *
26338 ATATAACCGGTA-AAATATACCGGTTTTATGAGAAAATAAGTCTACATATTGTATCGATACTTTT
66 ATATAACCGGTAGAAATATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTA
* * * ** * * *
26402 TAAATTTTTGTCGATA----TTGTCCAAAATGAATGCCCAACAAAATGCACGCATAAAATGCCAA
131 TAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGA
26463 TACA
196 TACA
*
26467 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACA-TTAC
1 TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAA-ATTTAC
* * * * * *
26531 AATGTAACCGGTAGAAATATACC-AGTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTT
65 AATATAACCGGTAGAAATATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTT
* * * * * * * * *
26595 TTAAA-TTGTGTCGATATTTTTTGTCCAGAATGAATGTCAAACGAGATCCACGCGTAAACTATCG
130 ATAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCG
26659 ATACA
195 ATACA
* * * *
26664 TTTATTAAA-AGTATCAATCTCAAAAACATCGAAACCCATAATTAT
1 TTTA--AAATTGTATCGATCCCAAAAACATCGAAACCTATAATTAT
26709 GTTATATAAG
Statistics
Matches: 1292, Mismatches: 125, Indels: 67
0.87 0.08 0.05
Matches are distributed among these distances:
193 10 0.01
194 150 0.12
195 10 0.01
197 45 0.03
198 273 0.21
199 609 0.47
200 5 0.00
201 1 0.00
202 1 0.00
206 1 0.00
207 2 0.00
208 1 0.00
210 1 0.00
211 2 0.00
212 1 0.00
216 1 0.00
217 1 0.00
219 178 0.14
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (199 bp):
TTTAAAATTGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACA
ATATAACCGGTAGAAATATACCGATTTTATGAGAAAATAGGTCTACATAATGTATCGACACTTTA
TAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGA
TACA
Found at i:26123 original size:20 final size:20
Alignment explanation
Indices: 26098--26150 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
26088 CTATAATTAT
*
26098 AATGTAATATGTAAATTTAC
1 AATGTAATAGGTAAATTTAC
**
26118 AATGTAACCGGTAAATTTAC
1 AATGTAATAGGTAAATTTAC
*
26138 AATGTAATCGGTA
1 AATGTAATAGGTA
26151 GAAATATACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (20 bp):
AATGTAATAGGTAAATTTAC
Found at i:26278 original size:219 final size:219
Alignment explanation
Indices: 25899--26351 Score: 717
Period size: 219 Copynumber: 2.1 Consensus size: 219
25889 CTATAATTAT
** * *
25899 AATGTAATAGGTAAATTTAAAATATAACCGGTAGAAATATACCAATTTTATGAGAAAATATGTCT
1 AATGTAACCGGTAAATTTAAAATATAACCGGTAGAAATATACCAATTTTAGGAGAAAATAGGTCT
* *
25964 ACATAATGTATCGACACTTTCTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGA
66 ACATAATGTATCGACACTTTATAAATTTGTGTCAATACTTTTTGTCCAGAATGAATGCCCAACGA
* * * *
26029 GGTGTACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAATCTATAA
131 GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCACAAAAACATCGAAACCTATAA
*
26094 TTATAATGTAATATGTAAATTTAC
196 TTATAATGTAATAGGTAAATTTAC
* * * *
26118 AATGTAACCGGTAAATTTACAATGTAATCGGTAGAAATATACCGATTTTAGGAGAAAATAGGTCT
1 AATGTAACCGGTAAATTTAAAATATAACCGGTAGAAATATACCAATTTTAGGAGAAAATAGGTCT
* * *
26183 ATATAATGTATCGATACTTTATAAATTTGTGTCAATACTTTTTTTCCAGAATGAATGCCCAACGA
66 ACATAATGTATCGACACTTTATAAATTTGTGTCAATACTTTTTGTCCAGAATGAATGCCCAACGA
* *
26248 GGTGCACGTATAAAGTGTCGATACATTTAAAATTGTATCGATCACAAAAGCATCGAAACCTATAA
131 GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCACAAAAACATCGAAACCTATAA
26313 TTATAATGTAATAGGTAAATTTAC
196 TTATAATGTAATAGGTAAATTTAC
*
26337 AATATAACCGGTAAA
1 AATGTAACCGGTAAA
26352 ATATACCGGT
Statistics
Matches: 213, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
219 213 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (219 bp):
AATGTAACCGGTAAATTTAAAATATAACCGGTAGAAATATACCAATTTTAGGAGAAAATAGGTCT
ACATAATGTATCGACACTTTATAAATTTGTGTCAATACTTTTTGTCCAGAATGAATGCCCAACGA
GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCACAAAAACATCGAAACCTATAA
TTATAATGTAATAGGTAAATTTAC
Found at i:26893 original size:23 final size:23
Alignment explanation
Indices: 26845--26894 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
26835 ACATATTTTA
*
26845 TTATATAAACGTTAACTATTACG
1 TTATATAAACGTTAACTAATACG
* *
26868 TTATATAAGCGTT-ACTTAATATG
1 TTATATAAACGTTAAC-TAATACG
26891 TTAT
1 TTAT
26895 TGTGCTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (23 bp):
TTATATAAACGTTAACTAATACG
Found at i:26957 original size:23 final size:23
Alignment explanation
Indices: 26925--26972 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
26915 GTAATTAACT
* *
26925 TATTTTATTATATAAGTGTTATC
1 TATTTCATTATATAAGTGCTATC
26948 TATTTCATTATATAAGTGCTATC
1 TATTTCATTATATAAGTGCTATC
26971 TA
1 TA
26973 ATATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (23 bp):
TATTTCATTATATAAGTGCTATC
Found at i:26961 original size:87 final size:85
Alignment explanation
Indices: 26824--26993 Score: 216
Period size: 87 Copynumber: 2.0 Consensus size: 85
26814 AAATAACAAA
* *
26824 TTAAGTAATTAACATATTTTATTATATAAACGTTAACTATTACGTTATATAAGCGTTA-CTTAAT
1 TTAAGTAATTAACATATTTTATTATATAAACGTTAACTATTACATTATATAAGCGCTATC-TAAT
* *
26888 ATGTTATTGTGCTTAATAATGT
65 ATATTATTGTACTT-ATAATGT
* ** * * *
26910 TTAATGTAATTAACTTATTTTATTATATAAGTGTTATCTATTTCATTATATAAGTGCTATCTAAT
1 TTAA-GTAATTAACATATTTTATTATATAAACGTTAACTATTACATTATATAAGCGCTATCTAAT
26975 ATATTATTGTACTTATAAT
65 ATATTATTGTACTTATAAT
26994 ATTTTCAGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
86 9 0.12
87 62 0.86
88 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (85 bp):
TTAAGTAATTAACATATTTTATTATATAAACGTTAACTATTACATTATATAAGCGCTATCTAATA
TATTATTGTACTTATAATGT
Found at i:26980 original size:23 final size:22
Alignment explanation
Indices: 26930--26981 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
26920 TAACTTATTT
* *
26930 TATTATATAAGTGTTATCTATT
1 TATTATATAAGTGCTATCTATA
26952 TCATTATATAAGTGCTATCTAATA
1 T-ATTATATAAGTGCTATCT-ATA
26976 TATTAT
1 TATTAT
26982 TGTACTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.85
24 3 0.12
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (22 bp):
TATTATATAAGTGCTATCTATA
Found at i:30841 original size:25 final size:24
Alignment explanation
Indices: 30809--30858 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 24
30799 ACTTGTGATA
30809 TAAAAATTATTTTTTTATTAAATAT
1 TAAAAATTA-TTTTTTATTAAATAT
30834 TAAAAATTATTTTTTATTAAATAT
1 TAAAAATTATTTTTTATTAAATAT
30858 T
1 T
30859 TTTAGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAAAATTATTTTTTATTAAATAT
Found at i:33201 original size:23 final size:24
Alignment explanation
Indices: 33157--33202 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33147 TATTTTATAA
*
33157 AATTTAATTGTTTAAAATATTTAC
1 AATTAAATTGTTTAAAATATTTAC
33181 AATTAAATT-TTTGAAAA-ATTTA
1 AATTAAATTGTTT-AAAATATTTA
33203 TCTATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
AATTAAATTGTTTAAAATATTTAC
Found at i:34205 original size:41 final size:42
Alignment explanation
Indices: 34142--34288 Score: 153
Period size: 41 Copynumber: 3.6 Consensus size: 42
34132 GACTTTTTGC
34142 GGCG-TTTTTATACAAACA-CCGCAATATGTGTAATA-TATAGT
1 GGCGTTTTTTA-ACAAA-AGCCGCAATATGTGTAATACTATAGT
* * * *
34183 GGCGTTTTTTAACAAAAGCCGCAAAATAT-TTATACTTTAGT
1 GGCGTTTTTTAACAAAAGCCGCAATATGTGTAATACTATAGT
* * *
34224 GGCGTTTTTGT-ACAAACGCCGCAATAGGTGTAA-ACTACAGT
1 GGCGTTTTT-TAACAAAAGCCGCAATATGTGTAATACTATAGT
*
34265 GGCGTTTTTTAACAAACGCCGCAA
1 GGCGTTTTTTAACAAAAGCCGCAA
34289 AATATTTGTA
Statistics
Matches: 89, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
40 6 0.07
41 74 0.83
42 9 0.10
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (42 bp):
GGCGTTTTTTAACAAAAGCCGCAATATGTGTAATACTATAGT
Found at i:34293 original size:82 final size:82
Alignment explanation
Indices: 34142--34295 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 82
34132 GACTTTTTGC
* *
34142 GGCGTTTTTATACAAACACCGCAATATGTGTAATATATAGTGGCGTTTTTTAACAAAAGCCGCAA
1 GGCGTTTTTATACAAACACCGCAATAGGTGTAATATACAGTGGCGTTTTTTAACAAAAGCCGCAA
34207 AATATTTATACTTTAGT
66 AATATTTATACTTTAGT
* * *
34224 GGCGTTTTTGTACAAACGCCGCAATAGGTGTAA-ACTACAGTGGCGTTTTTTAACAAACGCCGCA
1 GGCGTTTTTATACAAACACCGCAATAGGTGTAATA-TACAGTGGCGTTTTTTAACAAAAGCCGCA
34288 AAATATTT
65 AAATATTT
34296 GTAGTTTAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 1 0.02
82 65 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (82 bp):
GGCGTTTTTATACAAACACCGCAATAGGTGTAATATACAGTGGCGTTTTTTAACAAAAGCCGCAA
AATATTTATACTTTAGT
Found at i:34312 original size:82 final size:82
Alignment explanation
Indices: 34144--34312 Score: 232
Period size: 82 Copynumber: 2.1 Consensus size: 82
34134 CTTTTTGCGG
* *
34144 CGTTTTTATACAAACACCGCAATATGTGTAATATATAGTGGCGTTTTTTAACAAAAGCCGCAAAA
1 CGTTTTTATACAAACACCGCAATAGGTGTAATATACAGTGGCGTTTTTTAACAAAAGCCGCAAAA
** *
34209 TATTTATACTTTAGTGG
66 TATTTATACTTTAACGA
* * *
34226 CGTTTTTGTACAAACGCCGCAATAGGTGTAA-ACTACAGTGGCGTTTTTTAACAAACGCCGCAAA
1 CGTTTTTATACAAACACCGCAATAGGTGTAATA-TACAGTGGCGTTTTTTAACAAAAGCCGCAAA
* *
34290 ATATTTGTAGTTTAACGA
65 ATATTTATACTTTAACGA
34308 CGTTT
1 CGTTT
34313 CTTTTTAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
81 1 0.01
82 75 0.99
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (82 bp):
CGTTTTTATACAAACACCGCAATAGGTGTAATATACAGTGGCGTTTTTTAACAAAAGCCGCAAAA
TATTTATACTTTAACGA
Found at i:37344 original size:21 final size:20
Alignment explanation
Indices: 37303--37345 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
37293 TCATTAGTCT
37303 ATTTATGTTTCTTAACATCA
1 ATTTATGTTTCTTAACATCA
*
37323 ATTT-TGTTTTTTATACTATCA
1 ATTTATGTTTCTTA-AC-ATCA
37344 AT
1 AT
37346 ATTACTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTATGTTTCTTAACATCA
Found at i:38531 original size:43 final size:43
Alignment explanation
Indices: 38476--38855 Score: 593
Period size: 43 Copynumber: 8.9 Consensus size: 43
38466 TTTGTATAAA
* *
38476 AAAAACACCGCTATAGATCTCGACCTATTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
* * * * *
38519 AAAAACGTCGCTATAAATCTCAACCTATTGCGGTGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
*
38562 AAAAACGTCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
* *
38605 AAAAACGCCGCTATAGATCTCGACCTATTGAGGCATTTGTCCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
* **
38648 AAAAACGCCGCTATAGATCTCAACCTATTAAGGCGTTTGTCCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
*
38691 AAAAACGCCGC--TAGATCTCGACCTATTGCGGCGTTTCTCCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
*
38732 AAAAACGCCGCTATAGATCTCGACCTATTGCGGTGTTTGTCCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
*
38775 TAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
*
38818 AAAAACGCCGCTATAGATCTCAACCTATTGCGGCGTTT
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTT
38856 TTGTTCACAA
Statistics
Matches: 310, Mismatches: 25, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
41 37 0.12
43 273 0.88
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
Found at i:38772 original size:170 final size:171
Alignment explanation
Indices: 38476--38855 Score: 600
Period size: 170 Copynumber: 2.2 Consensus size: 171
38466 TTTGTATAAA
* * * *
38476 AAAAACACCGCTATAGATCTCGACCTATTGCGGCGTTTGTTCCAAAAACGTCGCTATAAATCTCA
1 AAAAACGCCGCTATAGATCTCAACCTATTGCGGCGTTTGTCCCAAAAACGCCGC-ATAAATCTCA
* * * *
38541 ACCTATTGCGGTGTTTGTTCCAAAAACGTCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCA
65 ACCTATTGCGGCGTTTCTCCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCA
38606 AAAACGCCGCTATAGATCTCGACCTATTGAGGCATTTGTCCC
130 AAAACGCCGCTATAGATCTCGACCTATTGAGGCATTTGTCCC
** * *
38648 AAAAACGCCGCTATAGATCTCAACCTATTAAGGCGTTTGTCCCAAAAACGCCGC-TAGATCTCGA
1 AAAAACGCCGCTATAGATCTCAACCTATTGCGGCGTTTGTCCCAAAAACGCCGCATAAATCTCAA
* *
38712 CCTATTGCGGCGTTTCTCCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGTGTTTGTCCCTA
66 CCTATTGCGGCGTTTCTCCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCAA
* *
38777 AAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCC
131 AAACGCCGCTATAGATCTCGACCTATTGAGGCATTTGTCCC
38818 AAAAACGCCGCTATAGATCTCAACCTATTGCGGCGTTT
1 AAAAACGCCGCTATAGATCTCAACCTATTGCGGCGTTT
38856 TTGTTCACAA
Statistics
Matches: 190, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
170 142 0.75
172 48 0.25
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (171 bp):
AAAAACGCCGCTATAGATCTCAACCTATTGCGGCGTTTGTCCCAAAAACGCCGCATAAATCTCAA
CCTATTGCGGCGTTTCTCCCAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCAA
AAACGCCGCTATAGATCTCGACCTATTGAGGCATTTGTCCC
Found at i:41878 original size:18 final size:18
Alignment explanation
Indices: 41833--41891 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
41823 ATATATATAA
* *
41833 TATAAAATTATATCTAAAC
1 TATATAATTAT-TATAAAC
41852 TATAT--TTATTATAAAC
1 TATATAATTATTATAAAC
41868 TATATAATTATTATAAAC
1 TATATAATTATTATAAAC
41886 TATATA
1 TATATA
41892 TAAATTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 11 0.31
17 4 0.11
18 17 0.47
19 4 0.11
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATAATTATTATAAAC
Found at i:41898 original size:18 final size:18
Alignment explanation
Indices: 41847--41990 Score: 70
Period size: 18 Copynumber: 8.1 Consensus size: 18
41837 AAATTATATC
*
41847 TAAACTATAT-T-TATTA
1 TAAACTATATATAAATTA
*
41863 TAAACTATATA-ATTATTA
1 TAAACTATATATA-AATTA
41881 TAAACTATATATAAATTA
1 TAAACTATATATAAATTA
* * *
41899 T--A-T-TATGTGCACTATA
1 TAAACTATATAT-AAAT-TA
41915 TAAACTATGTATATAAAATTA
1 TAAACTA--TATAT-AAATTA
* * *
41936 TAAAATATATTTATATTA
1 TAAACTATATATAAATTA
*
41954 TAAACTATATA-ATATTA
1 TAAACTATATATAAATTA
**
41971 TAAGTTATATATAAAATTA
1 TAAACTATATAT-AAATTA
41990 T
1 T
41991 GTTTATGTGA
Statistics
Matches: 98, Mismatches: 16, Indels: 25
0.71 0.12 0.18
Matches are distributed among these distances:
14 4 0.04
15 3 0.03
16 14 0.14
17 15 0.15
18 36 0.37
19 12 0.12
21 8 0.08
22 6 0.06
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAACTATATATAAATTA
Found at i:41962 original size:91 final size:92
Alignment explanation
Indices: 41832--42030 Score: 282
Period size: 91 Copynumber: 2.2 Consensus size: 92
41822 AATATATATA
41832 ATATAAAATTATATCTAAACTATATTTATTATAAACTATATAATTATTATAAACTATATAT-AAA
1 ATATAAAATTATA--TAAACTATATTTATTATAAACTATATAA-TATTATAAACTATATATAAAA
*
41896 TTAT-ATTATGTGCACTATATAAACTATGT
63 TTATGATTATGTGAACTATATAAACTATGT
**
41925 ATATAAAATTATA-AAA-TATATTTATATTATAAACTATATAATATTATAAGTTATATATAAAAT
1 ATATAAAATTATATAAACTATA-TT-TATTATAAACTATATAATATTATAAACTATATATAAAAT
*
41988 TATGTTTATGTGAACTATATAAACTATGT
64 TATGATTATGTGAACTATATAAACTATGT
42017 ATAT-AAATTATATA
1 ATATAAAATTATATA
42031 TGTATAAACT
Statistics
Matches: 97, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
89 4 0.04
90 20 0.21
91 32 0.33
92 28 0.29
93 13 0.13
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (92 bp):
ATATAAAATTATATAAACTATATTTATTATAAACTATATAATATTATAAACTATATATAAAATTA
TGATTATGTGAACTATATAAACTATGT
Found at i:41981 original size:17 final size:17
Alignment explanation
Indices: 41924--41973 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
41914 ATAAACTATG
*
41924 TATATAAAATTATAAAA
1 TATATAATATTATAAAA
* *
41941 TATATTTATATTATAAAC
1 TATA-TAATATTATAAAA
41959 TATATAATATTATAA
1 TATATAATATTATAA
41974 GTTATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATAATATTATAAAA
Found at i:42092 original size:2 final size:2
Alignment explanation
Indices: 42079--42144 Score: 52
Period size: 2 Copynumber: 34.0 Consensus size: 2
42069 ATTTATATTA
*
42079 AT AT AGT AT AT AT AT GT AT A- ACT A- AT AT A- AGT A- AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT
*
42118 AG A- 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
42145 TAAAGAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
1 5 0.09
2 44 0.83
3 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (2 bp):
AT
Found at i:42696 original size:16 final size:16
Alignment explanation
Indices: 42656--42709 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
42646 AATATTATAT
42656 AAATAAAAATCATAAA-A
1 AAATAAAAA-CA-AAACA
42673 AACA-AAAAACAAAACA
1 AA-ATAAAAACAAAACA
*
42689 AAATAAAAACAAAACC
1 AAATAAAAACAAAACA
42705 AAATA
1 AAATA
42710 TTTAAAACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 4 0.12
16 21 0.64
17 7 0.21
18 1 0.03
ACGTcount: A:0.78, C:0.13, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAAACA
Found at i:45224 original size:407 final size:407
Alignment explanation
Indices: 44527--45751 Score: 1611
Period size: 407 Copynumber: 3.0 Consensus size: 407
44517 TTCGGTTAGT
* * * *
44527 AGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * * * ** * *
44592 TCGAAGGTCTCTGGCGACAAACAACCCTT-TCAGTCTTGGGTTATGCTATAAATGATATGCC-TT
66 TCGAAGGTCT-TTG-G-CAGATAGCCCTTCTC-GACTTAAGTTATGCTACAAATGATGTGCCGTT
* * * * * *
44655 AGAGCTGAGCGTAATCGAACTCGAAAGTCTTTTGCAGATAGCCCTTCTCGACTTAAACTATGCTG
127 -GAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTG
* *
44720 CAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGGCAGACAACCCTT
191 CAAATGATG-GCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTT
*
44785 CTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
255 CTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
*
44850 TGGTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGT
320 TGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGT
44915 AATCGAACTCGGGGGTCTTTGGC
385 AATCGAACTCGGGGGTCTTTGGC
*
44938 AGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
45003 TCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCGTTGAGC
66 TCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCGTTGAGC
*
45068 TGAGCATAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAAT
131 TGAGCATAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
* *
45133 GATGGCCGTTGAGCTGAGTGTAGTTGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTTCTAGAC
196 GATGGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTTCTAGAC
* *
45198 TTAAGTTGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGA
261 TTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
*
45263 CAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATACCCTCGAAGCTGAGTGTAATCGA
326 CAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
*
45328 ACTCGGGGGTATTTGGC
391 ACTCGGGGGTCTTTGGC
* *
45345 AAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * * *
45410 TCGAAGGTCTTTGGTAGATAGCCCTTCTCAAATTAAGTTATGTTGCAAATGATGTGCCGTTGAGC
66 TCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCGTTGAGC
* ** * * * *
45475 TGAGCATAGTCAAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
131 TGAGCATAGTCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGC
* * * * *
45540 AAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGG-TCTTTGGTGACAGATAACCCTT
192 AAATGAT-GGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTT
* * * * *** * * * **
45603 CTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCAAAGTTGAGTGTAATCGAACTCGGGGGTCT
255 CTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * * * * * * *
45668 TT-G-G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTG
319 TTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
* **
45729 TAGTCGAACTCGAAGGTCTTTGG
384 TAATCGAACTCGGGGGTCTTTGG
45752 TTGGCAATAC
Statistics
Matches: 723, Mismatches: 82, Indels: 21
0.88 0.10 0.03
Matches are distributed among these distances:
407 341 0.47
408 131 0.18
409 39 0.05
410 4 0.01
411 154 0.21
412 54 0.07
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (407 bp):
AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCGTTGAGC
TGAGCATAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
GATGGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTTCTAGAC
TTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
CAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
ACTCGGGGGTCTTTGGC
Found at i:45752 original size:328 final size:327
Alignment explanation
Indices: 44554--45751 Score: 1507
Period size: 328 Copynumber: 3.7 Consensus size: 327
44544 TTAAGCTATA
* * * * * *
44554 CTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTCTGGCGACAAACAACCC
1 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCC
* * * * * *
44619 TT-TCAGTCTTGGGTTATGCTATAAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCGAAAGT
66 TTCT-AGCCTTGAGTTATGCTGTAAATGATATGCCTCAAAGCTGAGCGTAATCGAACTCGAAGGT
* *
44683 CTTTTGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTA
130 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTA
* * *
44748 GTCGAACTCAAAGGTCTTTTATTGGCAGACAACCCTTCT-AGACTTAAGTTGTGCTGCAAATGAT
195 GTCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCA-ACTTAAGTTATGCTGCAAATGAT
* * * * * *
44812 ATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTGACATATAACCCTTCTAGCCT
255 GTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACT
* *
44875 TGAGTTATG
319 TAAGTTGTG
* * * * * ** * *
44884 CTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CAGATAGCC
1 CTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACC
* * * * * * * *** *
44946 CTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
65 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTCAAAGCTGAGCGTAATCGAACTCGAAGGT
* * *
45011 CTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCGTTGAGCTGAGCATA
130 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTA
* * *
45076 GTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATG-GCC
195 GTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCC
* * *
45140 GTTGAGCTGAGTGTAGTTGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
260 GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
45205 GTG
325 GTG
* *
45208 CTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGACAAATAACCC
1 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCC
* * * **
45273 TTCTAGCCTTGAGTTATGCTGTAAATGATATACCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT
66 TTCTAGCCTTGAGTTATGCTGTAAATGATAT-GCCTCAAAGCTGAGCGTAATCGAACTCGAAGGT
* * *
45338 ATTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCC-TTGGAGCTGAGCGT
130 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGT
* * * *
45402 AGTCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCAAATTAAGTTATGTTGCAAATGATGTGC
194 AGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGC
* * *
45467 CGTTGAGCTGAGCATAGTCAAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGT
259 CGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGT
45532 TGTG
324 TGTG
* *
45536 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCC
1 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCC
* * **
45601 TTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCAAAGTTGAGTGTAATCGAACTCGGGGGT
66 TTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCTCAAAGCTGAGCGTAATCGAACTCGAAGGT
* *
45666 CTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGTGT
130 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGT
45730 AGTCGAACTCGAAGGTCTTTGG
194 AGTCGAACTCGAAGGTCTTTGG
45752 TTGGCAATAC
Statistics
Matches: 752, Mismatches: 104, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
323 57 0.08
324 81 0.11
325 2 0.00
326 34 0.05
327 136 0.18
328 400 0.53
329 2 0.00
330 13 0.02
331 27 0.04
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (327 bp):
CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCC
TTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTCAAAGCTGAGCGTAATCGAACTCGAAGGTC
TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCG
TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
TG
Found at i:51878 original size:19 final size:19
Alignment explanation
Indices: 51839--51878 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51829 TGAGATTTGG
* *
51839 TTGAAAAAAATACTTTATA
1 TTGAAAAAAATACATCATA
*
51858 TTGAAAAAAATACATCCTA
1 TTGAAAAAAATACATCATA
51877 TT
1 TT
51879 CTGAGTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (19 bp):
TTGAAAAAAATACATCATA
Found at i:52281 original size:40 final size:41
Alignment explanation
Indices: 52236--52333 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
52226 ACAATAGTTA
* * *
52236 ATATATGTAACTTATAGTGTGTGTATACATATAATGTAAAC
1 ATATATGTAACTTATAGTATATATATACATATAATGTAAAC
* *
52277 -TATATAGTGAC-TATAGTATATATATACATGTAATGTAAAC
1 ATATAT-GTAACTTATAGTATATATATACATATAATGTAAAC
52317 TATATATGTAACTTATA
1 -ATATATGTAACTTATA
52334 TGTAAGTACA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
40 30 0.64
41 8 0.17
42 9 0.19
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (41 bp):
ATATATGTAACTTATAGTATATATATACATATAATGTAAAC
Found at i:52320 original size:20 final size:20
Alignment explanation
Indices: 52259--52322 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
52249 ATAGTGTGTG
*
52259 TATACATATAATGTAAACTA
1 TATACATGTAATGTAAACTA
* *
52279 TATA-GTG-ACTATAGTATA-TA
1 TATACATGTA--AT-GTAAACTA
52299 TATACATGTAATGTAAACTA
1 TATACATGTAATGTAAACTA
52319 TATA
1 TATA
52323 TGTAACTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
18 1 0.03
19 5 0.15
20 20 0.61
21 6 0.18
22 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (20 bp):
TATACATGTAATGTAAACTA
Found at i:52367 original size:2 final size:2
Alignment explanation
Indices: 52360--52385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52350 TTAAACTATG
52360 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
52386 AATCATAAAG
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):
TA
Found at i:54050 original size:14 final size:14
Alignment explanation
Indices: 54033--54079 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
54023 ATATATTATT
54033 TATATAAATTAAAC
1 TATATAAATTAAAC
54047 TATAT-AATT----
1 TATATAAATTAAAC
54056 TATATAAATTAAAC
1 TATATAAATTAAAC
*
54070 TATATTAATT
1 TATATAAATT
54080 TTCTTTGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:54056 original size:23 final size:23
Alignment explanation
Indices: 54024--54080 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
54014 ACTTTTATTA
*
54024 TATATTATTTATATAAATTAAAC
1 TATATAATTTATATAAATTAAAC
54047 TATATAATTTATATAAATTAAAC
1 TATATAATTTATATAAATTAAAC
54070 TATATTAATTT
1 TATA-TAATTT
54081 TCTTTGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 26 0.81
24 6 0.19
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATAATTTATATAAATTAAAC
Found at i:54123 original size:25 final size:22
Alignment explanation
Indices: 54094--54156 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 22
54084 TTGCATTATT
54094 AATAATTTTATCTAATTTACATTTA
1 AATAATTTTAT-TAATTT-CA-TTA
*
54119 AATAATTTTATTAATTTTATTA
1 AATAATTTTATTAATTTCATTA
54141 AATAATTTTATATAAT
1 AATAATTTTAT-TAAT
54157 AGGTCTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 14 0.39
23 5 0.14
24 6 0.17
25 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
AATAATTTTATTAATTTCATTA
Found at i:54348 original size:15 final size:15
Alignment explanation
Indices: 54330--54380 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
54320 CGGATCATTT
* *
54330 ACAGTCATGTTAAAA
1 ACAGTCAGGTTGAAA
54345 ACAGGTCAGGTTGAAA
1 ACA-GTCAGGTTGAAA
54361 ACAAGTCAGGTTGAAA
1 AC-AGTCAGGTTGAAA
54377 ACAG
1 ACAG
54381 GTCGGGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 5 0.16
16 26 0.81
17 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.20
Consensus pattern (15 bp):
ACAGTCAGGTTGAAA
Found at i:54361 original size:16 final size:16
Alignment explanation
Indices: 54342--54383 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
54332 AGTCATGTTA
54342 AAAACAGGTCAGGTTG
1 AAAACAGGTCAGGTTG
*
54358 AAAACAAGTCAGGTTG
1 AAAACAGGTCAGGTTG
54374 AAAACAGGTC
1 AAAACAGGTC
54384 GGGTAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (16 bp):
AAAACAGGTCAGGTTG
Done.