Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 28
Found at i:2433722 original size:15 final size:16
Alignment explanation
Indices: 2433702--2433735 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2433692 CAAAAAAATT
2433702 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
2433717 TAATATAATAAACTTA
1 TAATATAATAAACTTA
2433733 TAA
1 TAA
2433736 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:2434019 original size:17 final size:17
Alignment explanation
Indices: 2433997--2434032 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2433987 TAAATTTTTT
2433997 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
2434014 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
2434031 AC
1 AC
2434033 AAACTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCTAACCCTAAACTA
Found at i:2434371 original size:22 final size:22
Alignment explanation
Indices: 2434340--2434393 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2434330 GGTGCATGGA
2434340 GCAGC-GGGAGCAGGCGAGCAT
1 GCAGCGGGGAGCAGGCGAGCAT
*
2434361 GCAGTGGGGAGCAGGCGAGCAT
1 GCAGCGGGGAGCAGGCGAGCAT
2434383 GCAGCGGGGAG
1 GCAGCGGGGAG
2434394 TAGGGCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.22, C:0.20, G:0.52, T:0.06
Consensus pattern (22 bp):
GCAGCGGGGAGCAGGCGAGCAT
Found at i:2434453 original size:29 final size:29
Alignment explanation
Indices: 2434421--2434520 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
2434411 TCGCGGGGCA
* *
2434421 TGCATGGCGACCTACCAT-GTCGCCTGGCG
1 TGCATGGCGACCT-CCATGGTCGCCCGGAG
*
2434450 TGCATGGCGACCTCCTTGGTCGCCCGGAG
1 TGCATGGCGACCTCCATGGTCGCCCGGAG
* *
2434479 TGCATGGCAACCTCCTTGGTCGCCCGGAG
1 TGCATGGCGACCTCCATGGTCGCCCGGAG
* *
2434508 GGCATGACGACCT
1 TGCATGGCGACCT
2434521 ATGTTTCGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
28 3 0.05
29 60 0.95
ACGTcount: A:0.14, C:0.34, G:0.32, T:0.20
Consensus pattern (29 bp):
TGCATGGCGACCTCCATGGTCGCCCGGAG
Found at i:2434567 original size:15 final size:15
Alignment explanation
Indices: 2434543--2434573 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2434533 GTGCATGTCC
2434543 CATGCAACGTTAATT
1 CATGCAACGTTAATT
*
2434558 CATGCGACGTTAATT
1 CATGCAACGTTAATT
2434573 C
1 C
2434574 GATTTTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (15 bp):
CATGCAACGTTAATT
Found at i:2435857 original size:14 final size:15
Alignment explanation
Indices: 2435838--2435868 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2435828 GGCCTACAAA
2435838 AAAATAAT-AATAAT
1 AAAATAATAAATAAT
2435852 AAAATAATAAATAAT
1 AAAATAATAAATAAT
2435867 AA
1 AA
2435869 TATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:2438070 original size:27 final size:27
Alignment explanation
Indices: 2438007--2438080 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
2437997 TACCCATATG
** *
2438007 GATGGAATACGGTGCATCATCTCAAAT
1 GATGGAATATTGTGCATCATCCCAAAT
*
2438034 GATGGAATATTGTGCATCATCCCGAAT
1 GATGGAATATTGTGCATCATCCCAAAT
*
2438061 GATGGAATATTATGCATCAT
1 GATGGAATATTGTGCATCAT
2438081 TTCGAAGGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (27 bp):
GATGGAATATTGTGCATCATCCCAAAT
Found at i:2438297 original size:31 final size:30
Alignment explanation
Indices: 2438262--2438322 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
2438252 CCAATTTGAC
*
2438262 CCGAATCGAAAATAATATGAACCGAAAACAA
1 CCGAATCGAAAATAACATGAACC-AAAACAA
*
2438293 CCGAATCGAAAATAACCTGAACCAAAACAA
1 CCGAATCGAAAATAACATGAACCAAAACAA
2438323 TACGAACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.54, C:0.23, G:0.11, T:0.11
Consensus pattern (30 bp):
CCGAATCGAAAATAACATGAACCAAAACAA
Found at i:2438933 original size:17 final size:17
Alignment explanation
Indices: 2438911--2438957 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2438901 TATAAACATC
*
2438911 TGTAACATTCAGTAACT
1 TGTAACATTCAATAACT
*
2438928 TGTAACATTTAATAACT
1 TGTAACATTCAATAACT
*
2438945 TGT-GCATTCAATA
1 TGTAACATTCAATA
2438958 CATGCATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (17 bp):
TGTAACATTCAATAACT
Found at i:2439096 original size:30 final size:30
Alignment explanation
Indices: 2439058--2439118 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
2439048 ATTTTACTTT
*
2439058 AACCATT-AATCTTTCAATT-TTATCAATCA
1 AACCATTAAATATTT-AATTGTTATCAATCA
*
2439087 AACCAATTAAATATTTAATTGTTGTCAATCA
1 AACC-ATTAAATATTTAATTGTTATCAATCA
2439118 A
1 A
2439119 GCCACTAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 7 0.26
31 16 0.59
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.39
Consensus pattern (30 bp):
AACCATTAAATATTTAATTGTTATCAATCA
Found at i:2441935 original size:20 final size:20
Alignment explanation
Indices: 2441910--2441948 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2441900 CAATAGTCAA
2441910 TAGTATCGAAACCCAGAGGC
1 TAGTATCGAAACCCAGAGGC
* *
2441930 TAGTATTGATACCCAGAGG
1 TAGTATCGAAACCCAGAGG
2441949 TCAATACCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (20 bp):
TAGTATCGAAACCCAGAGGC
Found at i:2443597 original size:18 final size:18
Alignment explanation
Indices: 2443574--2443615 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2443564 TAATTAAACT
*
2443574 TGTATTATCTTTTCTTCC-
1 TGTATTATCCTTT-TTCCA
*
2443592 TGTATTTTCCTTTTTCCA
1 TGTATTATCCTTTTTCCA
2443610 TGTATT
1 TGTATT
2443616 GTTCTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.62
Consensus pattern (18 bp):
TGTATTATCCTTTTTCCA
Found at i:2443939 original size:24 final size:24
Alignment explanation
Indices: 2443909--2444019 Score: 95
Period size: 23 Copynumber: 4.7 Consensus size: 24
2443899 AGTGTACAAA
*
2443909 GCACTAATACATGAGTGTGTATTT
1 GCACTAATACAGGAGTGTGTATTT
** *
2443933 GCACTAATACAGGAGTGCATAATT
1 GCACTAATACAGGAGTGTGTATTT
* * *
2443957 GCACT-ATAAAGGGGTGTGTATTC
1 GCACTAATACAGGAGTGTGTATTT
*
2443980 GCACTAATACA--AG-GTGCTCAATT
1 GCACTAATACAGGAGTGTG-T-ATTT
*
2444003 GCACTAATTCAGGAGTG
1 GCACTAATACAGGAGTG
2444020 CACAAAGGCA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
21 3 0.05
22 2 0.03
23 29 0.44
24 29 0.44
25 2 0.03
26 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (24 bp):
GCACTAATACAGGAGTGTGTATTT
Found at i:2443948 original size:47 final size:47
Alignment explanation
Indices: 2443889--2444008 Score: 111
Period size: 47 Copynumber: 2.6 Consensus size: 47
2443879 AATCAATGAT
* * * * *
2443889 ACTAATA-GGGAGTGTACAA-AGCACTAATACATGAGTGTGTATTTGC
1 ACTAATACAGGAGTGCACAATAGCACT-ATAAAGGAGTGTGTATTCGC
* * *
2443935 ACTAATACAGGAGTGCATAATTGCACTATAAAGGGGTGTGTATTCGC
1 ACTAATACAGGAGTGCACAATAGCACTATAAAGGAGTGTGTATTCGC
* * *
2443982 ACTAATACAAG-GTGCTCAATTGCACTA
1 ACTAATACAGGAGTGCACAATAGCACTA
2444009 ATTCAGGAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
46 21 0.34
47 35 0.57
48 5 0.08
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (47 bp):
ACTAATACAGGAGTGCACAATAGCACTATAAAGGAGTGTGTATTCGC
Found at i:2443995 original size:23 final size:22
Alignment explanation
Indices: 2443909--2444010 Score: 66
Period size: 24 Copynumber: 4.4 Consensus size: 22
2443899 AGTGTACAAA
*
2443909 GCACTAATACATGAGTGTGTATTT
1 GCACTAATACAAG-GTGTGTA-TT
*
2443933 GCACTAATAC-AGGAGTGCATAATT
1 GCACTAATACAAGGTGTG--T-ATT
2443957 GCACT-ATA-AAGGGGTGTGTATT
1 GCACTAATACAA--GGTGTGTATT
**
2443979 CGCACTAATACAAGGTGCTCAATT
1 -GCACTAATACAAGGTG-TGTATT
2444003 GCACTAAT
1 GCACTAAT
2444011 TCAGGAGTGC
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
22 7 0.11
23 23 0.37
24 25 0.40
25 8 0.13
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (22 bp):
GCACTAATACAAGGTGTGTATT
Found at i:2444030 original size:24 final size:24
Alignment explanation
Indices: 2444003--2444074 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
2443993 GTGCTCAATT
*
2444003 GCACTAATTCAGGAGTGCACAAAG
1 GCACTGATTCAGGAGTGCACAAAG
* *
2444027 GCACTGCTAT-AGGAGTGCACGAAG
1 GCACTGAT-TCAGGAGTGCACAAAG
* * *
2444051 GCACTGATACAAGAGTGAACAAAG
1 GCACTGATTCAGGAGTGCACAAAG
2444075 AACTGATAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.15
Consensus pattern (24 bp):
GCACTGATTCAGGAGTGCACAAAG
Found at i:2449267 original size:17 final size:17
Alignment explanation
Indices: 2449241--2449298 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
2449231 GCAAACATTA
* *
2449241 AATGAGCTAGTTTGATT
1 AATGAACTAGTTTAATT
2449258 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATT
* * *
2449275 AGTGAACTGACTTTATTT
1 AATGAACT-AGTTTAATT
2449293 AATGAA
1 AATGAA
2449299 GAGCATACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (17 bp):
AATGAACTAGTTTAATT
Found at i:2450555 original size:27 final size:27
Alignment explanation
Indices: 2450517--2450576 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
2450507 GAATAAATCT
* *
2450517 TCATTGGGCATGACTTTTGACTTAGCC
1 TCATGGGGCATGACTTTCGACTTAGCC
2450544 TCATGGGGCATGACTTTCGACTTAGCC
1 TCATGGGGCATGACTTTCGACTTAGCC
2450571 TCATGG
1 TCATGG
2450577 TATGTATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.33
Consensus pattern (27 bp):
TCATGGGGCATGACTTTCGACTTAGCC
Found at i:2459968 original size:18 final size:18
Alignment explanation
Indices: 2459937--2459980 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2459927 TCCCTTCATC
*
2459937 TTTATCATCTTTGTGATG
1 TTTATCATCCTTGTGATG
*
2459955 TTTATGATCCTTGTGATG
1 TTTATCATCCTTGTGATG
2459973 TTTATCAT
1 TTTATCAT
2459981 TTTTATCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (18 bp):
TTTATCATCCTTGTGATG
Found at i:2461129 original size:25 final size:27
Alignment explanation
Indices: 2461090--2461139 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
2461080 AGGATTATTT
2461090 AAATAGTGTATATATATATATATTCAA
1 AAATAGTGTATATATATATATATTCAA
*
2461117 AAATAGT-TA-ATATATATTTATTC
1 AAATAGTGTATATATATATATATTC
2461140 TTTTAGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 2 0.09
27 7 0.32
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (27 bp):
AAATAGTGTATATATATATATATTCAA
Found at i:2474613 original size:20 final size:20
Alignment explanation
Indices: 2474584--2474625 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2474574 ATTCCACCAC
*
2474584 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2474604 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
2474624 AT
1 AT
2474626 AGGCTCTTAG
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:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2487890 original size:4 final size:4
Alignment explanation
Indices: 2487881--2487918 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
2487871 TGTAATAAAC
*
2487881 TTAT TTAT TTAAT TT-T TTAT TTAA TTAT TTAT TTAT TT
1 TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TT
2487919 TTTTTACACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:2487901 original size:12 final size:12
Alignment explanation
Indices: 2487884--2487921 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2487874 AATAAACTTA
2487884 TTTATTTAATTT
1 TTTATTTAATTT
*
2487896 TTTATTTAATTA
1 TTTATTTAATTT
2487908 TTTATTT-ATTT
1 TTTATTTAATTT
2487919 TTT
1 TTT
2487922 TTACACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTAATTT
Found at i:2488554 original size:14 final size:14
Alignment explanation
Indices: 2488535--2488564 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2488525 TAGGGGTATA
2488535 TTTTTAAAATTTAT
1 TTTTTAAAATTTAT
*
2488549 TTTTTAATATTTAT
1 TTTTTAAAATTTAT
2488563 TT
1 TT
2488565 ATTATTGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTAAAATTTAT
Found at i:2501572 original size:43 final size:43
Alignment explanation
Indices: 2501514--2501601 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
2501504 TTAATTTTTC
2501514 AAAAAATGTAATTCATTTTCTAGAATTCATTTTCAACCTATCA
1 AAAAAATGTAATTCATTTTCTAGAATTCATTTTCAACCTATCA
*
2501557 AAAAAATGTAATTCATTTTCTAGAATTTATTTTCAACCTATCA
1 AAAAAATGTAATTCATTTTCTAGAATTCATTTTCAACCTATCA
2501600 AA
1 AA
2501602 CAGACTTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.40
Consensus pattern (43 bp):
AAAAAATGTAATTCATTTTCTAGAATTCATTTTCAACCTATCA
Found at i:2520558 original size:21 final size:21
Alignment explanation
Indices: 2520528--2520709 Score: 90
Period size: 21 Copynumber: 8.6 Consensus size: 21
2520518 GATTTACATA
*
2520528 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
2520549 TTCGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** * *
2520570 TTAACGTTGCGA-A-TCTGGAAA
1 TTCGCGTTGCGATAGTC--CAAG
* ** *
2520591 CT-GATTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
2520611 TTCACGTTGCGATTTATTTCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
2520634 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
2520653 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
2520676 TT--CGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
2520697 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2520710 TTATTCCAAG
Statistics
Matches: 122, Mismatches: 26, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
19 9 0.07
20 11 0.09
21 77 0.63
22 2 0.02
23 23 0.19
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:2520651 original size:42 final size:42
Alignment explanation
Indices: 2520596--2520727 Score: 192
Period size: 42 Copynumber: 3.1 Consensus size: 42
2520586 GGAAACTGAT
* *
2520596 TTGCGATAGTCGAAGTTCACGTTGCGATTTATTTCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
2520638 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * * *
2520680 TTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCA
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
2520724 TTGC
1 TTGC
2520728 AATTTATTCC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 46 0.56
44 36 0.44
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:2520712 original size:44 final size:44
Alignment explanation
Indices: 2520608--2520751 Score: 188
Period size: 44 Copynumber: 3.4 Consensus size: 44
2520598 GCGATAGTCG
* * * *
2520608 AAGTTCACGTTGCGATTTATTTCAAATTCGTTGCGA--TAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCC
2520650 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCC
* * *
2520694 AAGTTCGCGTTGCGATTTATTCCAAGTTCATTGCAATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCC
*
2520738 AAATT--CGTTGCGAT
1 AAGTTCGCGTTGCGAT
2520752 AGTCCAAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 43 0.47
44 49 0.53
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (44 bp):
AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCC
Found at i:2520732 original size:21 final size:21
Alignment explanation
Indices: 2520615--2520751 Score: 152
Period size: 21 Copynumber: 6.4 Consensus size: 21
2520605 TCGAAGTTCA
*
2520615 CGTTGCGATTTATTTCAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
2520636 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
2520655 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
*
2520678 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
*
2520699 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATT
* *
2520722 CATTGCAATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
2520743 CGTTGCGAT
1 CGTTGCGAT
2520752 AGTCCAAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
19 7 0.07
21 61 0.63
23 29 0.30
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:2521647 original size:21 final size:20
Alignment explanation
Indices: 2521621--2521773 Score: 80
Period size: 21 Copynumber: 7.3 Consensus size: 20
2521611 ATTTTGGACT
2521621 ATCGCAACGAACTTGGAATA
1 ATCGCAACGAACTTGGAATA
* **
2521641 AGTCGCAACTTGAACTTCG-ACC
1 A-TCGCAAC--GAACTTGGAATA
2521663 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAAT-A
* *
2521684 ATCGCAACGCGAACTTCGACT-
1 ATCGCAA--CGAACTTGGAATA
* *
2521705 ATCGCAACGCGAATTTGAAATAA
1 ATCGCAA--CGAACTTGGAAT-A
*
2521728 ATCGCAACGCGAACTTGGACT-
1 ATCGCAA--CGAACTTGGAATA
* * *
2521749 ATTGCAACGAA-TTTGAAAA
1 ATCGCAACGAACTTGGAATA
2521768 ATCGCA
1 ATCGCA
2521774 TTGCGATAGT
Statistics
Matches: 103, Mismatches: 20, Indels: 21
0.72 0.14 0.15
Matches are distributed among these distances:
18 4 0.04
19 16 0.16
20 2 0.02
21 44 0.43
22 2 0.02
23 35 0.34
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAACTTGGAATA
Found at i:2521735 original size:23 final size:22
Alignment explanation
Indices: 2521678--2521740 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
2521668 AACGAACTTG
*
2521678 GAATAAATCGCAACGCGAACTTC
1 GAATAAATCGCAACGCGAA-TTT
*
2521701 GACT--ATCGCAACGCGAATTT
1 GAATAAATCGCAACGCGAATTT
2521721 GAAATAAATCGCAACGCGAA
1 G-AATAAATCGCAACGCGAA
2521741 CTTGGACTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.09
21 15 0.44
23 16 0.47
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (22 bp):
GAATAAATCGCAACGCGAATTT
Found at i:2521741 original size:44 final size:42
Alignment explanation
Indices: 2521617--2521773 Score: 201
Period size: 42 Copynumber: 3.7 Consensus size: 42
2521607 TGCGATTTTG
* **
2521617 GACTATCGCAACGAACTTGGAATAAGTCGCAACTTGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2521659 GACCATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
2521701 GACTATCGCAACGCGAATTTGAAATAAATCGCAACGCGAACTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* *
2521745 GACTATTGCAACGAA-TTTGAA-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
2521774 TTGCGATAGT
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 8 0.08
41 4 0.04
42 52 0.51
44 38 0.37
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:2521798 original size:21 final size:21
Alignment explanation
Indices: 2521769--2521821 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2521759 ATTTGAAAAA
*
2521769 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
2521790 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
*
2521811 TCGCGTAGCGA
1 TCGCGTTGCGA
2521822 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:2522817 original size:2 final size:2
Alignment explanation
Indices: 2522812--2522845 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2522802 CTCCCCCCCC
2522812 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2522846 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2537333 original size:43 final size:44
Alignment explanation
Indices: 2537263--2537887 Score: 268
Period size: 43 Copynumber: 14.5 Consensus size: 44
2537253 TTTTAATTTG
* * * * *
2537263 TTTTATGATTGA-GATCCCTAATTTTTTTAATCT-ATTTTTTTTA
1 TTTTATAATTGAGGCTCCC-AATTTTTTCAATCTCACTTTTTATA
2537306 CTTTTATAATTGAGGCTCCCAATTTTTTCAATCTCACTTTTTATA
1 -TTTTATAATTGAGGCTCCCAATTTTTTCAATCTCACTTTTTATA
* *
2537351 -TTTATAATTGAGGC-CCATAATTTTTTCAATCCCACTTTTTA-A
1 TTTTATAATTGAGGCTCC-CAATTTTTTCAATCTCACTTTTTATA
* * * ** * * *
2537393 CTTTATAATTGAGACACATAATTTTTT-ATTCTCACTTTCTA-C
1 TTTTATAATTGAGGCTCCCAATTTTTTCAATCTCACTTTTTATA
* * * ** *
2537435 CTTTATAATTGAAGC-CCTTAATTTTTTTTATCTCACTTTTTA-C
1 TTTTATAATTGAGGCTCC-CAATTTTTTCAATCTCACTTTTTATA
* * * * *
2537478 CTTTATAATTGAGGC-CTCTAATTTTTTTAATCCCACTTTTTA-C
1 TTTTATAATTGAGGCTC-CCAATTTTTTCAATCTCACTTTTTATA
* * * * *
2537521 CTTTATAATTGAGGC-CCCTAATTATTTCAATCTCACATTCTA-C
1 TTTTATAATTGAGGCTCCC-AATTTTTTCAATCTCACTTTTTATA
* * * * *
2537564 CTTTATAATTGAGGC-CCCTAATTATTTCAATCTCACATTCTA-C
1 TTTTATAATTGAGGCTCCC-AATTTTTTCAATCTCACTTTTTATA
* * * * * * * *
2537607 CTTTATAATTAAAGC-CTCTATTTTTTTTAATCTAACTTTTTACA
1 TTTTATAATTGAGGCTC-CCAATTTTTTCAATCTCACTTTTTATA
** * *
2537651 -TTTATAATTGAGGACT-TTAATTTTTTTCAATCCCACTTTTTA-C
1 TTTTATAATTGAGG-CTCCCAA-TTTTTTCAATCTCACTTTTTATA
* * * * * *
2537694 CTTTATAATTAAAGCTCCTAATTTTTTTTCAATATCACTTTTTA-C
1 TTTTATAATTGAGGCTCCCAA--TTTTTTCAATCTCACTTTTTATA
* * *** * *
2537739 TTTTATAATTAAAG-TCATTATTTTTT-AATCTCACTTTCTA-C
1 TTTTATAATTGAGGCTCCCAATTTTTTCAATCTCACTTTTTATA
* * *
2537780 CTTTATAAATTGA--C-CCCTATTTTTTTAATCTCAC-TTTTAT-
1 TTTTAT-AATTGAGGCTCCCAATTTTTTCAATCTCACTTTTTATA
* * * *
2537820 CTTTATAATTGAGGC-CTCTAATTTTTTCAATCT-AATTTTTTTA
1 TTTTATAATTGAGGCTC-CCAATTTTTTCAATCTCACTTTTTATA
*
2537863 CTTTTATAATTTAGGC-CCCTAATTT
1 -TTTTATAATTGAGGCTCCC-AATTT
2537888 AATCATTTTT
Statistics
Matches: 484, Mismatches: 69, Indels: 56
0.79 0.11 0.09
Matches are distributed among these distances:
39 6 0.01
40 19 0.04
41 30 0.06
42 66 0.14
43 233 0.48
44 83 0.17
45 47 0.10
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (44 bp):
TTTTATAATTGAGGCTCCCAATTTTTTCAATCTCACTTTTTATA
Found at i:2537417 original size:86 final size:85
Alignment explanation
Indices: 2537278--2537887 Score: 563
Period size: 86 Copynumber: 7.1 Consensus size: 85
2537268 TGATTGAGAT
* * * *
2537278 CCCTAATTTTTTTAATCT-ATTTTTTTTACTTTTATAATTGAGGCTCCCAATTTTTTCAATCTCA
1 CCCTAATTTTTTCAATCTCA-CTTTTTAAC-TTTATAATTGAGGC-CCTAATTTTTTCAATCTCA
** *
2537342 CTTTTTATATTTATAATTGAGGC
63 CTTTTTACCTTTATAATTGAAGC
* * * * *
2537365 CCATAATTTTTTCAATCCCACTTTTTAACTTTATAATTGAGACACATAATTTTTT-ATTCTCACT
1 CCCTAATTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGC-CCTAATTTTTTCAATCTCACT
*
2537429 TTCTACCTTTATAATTGAAGC
65 TTTTACCTTTATAATTGAAGC
* ** * * *
2537450 CCTTAATTTTTTTTATCTCACTTTTTACCTTTATAATTGAGGCCTCTAATTTTTTTAATCCCACT
1 CCCTAATTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGCC-CTAATTTTTTCAATCTCACT
*
2537515 TTTTACCTTTATAATTGAGGC
65 TTTTACCTTTATAATTGAAGC
* * * * * *
2537536 CCCTAATTATTTCAATCTCACATTCTACCTTTATAATTGAGGCCCCTAATTATTTCAATCTCACA
1 CCCTAATTTTTTCAATCTCACTTTTTAACTTTATAATTGAGG-CCCTAATTTTTTCAATCTCACT
* *
2537601 TTCTACCTTTATAATTAAAGC
65 TTTTACCTTTATAATTGAAGC
* * * * ** *
2537622 CTCTATTTTTTTTAATCTAACTTTTT-ACATTTATAATTGAGGACTTTAATTTTTTTCAATCCCA
1 CCCTAATTTTTTCAATCTCACTTTTTAAC-TTTATAATTGAGG-CCCTAA-TTTTTTCAATCTCA
*
2537686 CTTTTTACCTTTATAATTAAAGC
63 CTTTTTACCTTTATAATTGAAGC
* * * * * * *
2537709 TCCTAATTTTTTTTCAATATCACTTTTT-ACTTTTATAATTAAAGTCATTATTTTTT-AATCTCA
1 CCCTAA--TTTTTTCAATCTCACTTTTTAAC-TTTATAATTGAGGCCCTAATTTTTTCAATCTCA
*
2537772 CTTTCTACCTTTATAAATTG-A-C
63 CTTTTTACCTTTAT-AATTGAAGC
* * * *
2537794 CCCT-ATTTTTTTAATCTCAC-TTTTATCTTTATAATTGAGGCCTCTAATTTTTTCAATCTAATT
1 CCCTAATTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGCC-CTAATTTTTTCAATCTCA-C
* * *
2537857 TTTTTACTTTTATAATTTAGGC
64 TTTTTACCTTTATAATTGAAGC
2537879 CCCTAATTT
1 CCCTAATTT
2537888 AATCATTTTT
Statistics
Matches: 423, Mismatches: 84, Indels: 33
0.78 0.16 0.06
Matches are distributed among these distances:
81 16 0.04
82 22 0.05
83 10 0.02
84 13 0.03
85 81 0.19
86 178 0.42
87 70 0.17
88 3 0.01
89 30 0.07
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (85 bp):
CCCTAATTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGCCCTAATTTTTTCAATCTCACTT
TTTACCTTTATAATTGAAGC
Found at i:2537677 original size:214 final size:215
Alignment explanation
Indices: 2537300--2537873 Score: 619
Period size: 214 Copynumber: 2.7 Consensus size: 215
2537290 TAATCTATTT
* **
2537300 TTTTTACTTTTATAATTGAGGCTCCC-AATTTTTTCAATCTCACTTTTTATATTTATAATTGAGG
1 TTTTTACTTTTATAATTGAGGC-CCCTAA-TTTTTCAATCTCACTTTCTACCTTTATAATTGAGG
* * * * * * * *
2537364 CCCATAATTTTTTCAATCCCACTTTTTAACTTTATAATTGAGACAC-ATAATTTTTTATTCTCAC
64 CCCCTAATTTTTTCAATCTCAC-TTTTAACTTTATAATTAAGCCTCTAT-TTTTTTTAATCTAAC
* * * * * *
2537428 TTTCTACCTTTATAATTGAAGCCCTTAATTTTTTTT-ATCTCACTTTTTACCTTTATAATTGAGG
127 TTTTTACATTTATAATTGAAGACCTTAATTTTTTTTAATCCCACTTTTTACCTTTATAATTAAAG
*
2537492 C-CTCTAA-TTTTTTT-AATCCCAC
192 CTC-CTAATTTTTTTTCAATACCAC
* *
2537514 TTTTTACCTTTATAATTGAGGCCCCTAATTATTTCAATCTCACATTCTACCTTTATAATTGAGGC
1 TTTTTACTTTTATAATTGAGGCCCCTAATT-TTTCAATCTCACTTTCTACCTTTATAATTGAGGC
* * *
2537579 CCCTAATTATTTCAATCTCACATTCTACCTTTATAATTAAAGCCTCTATTTTTTTTAATCTAACT
65 CCCTAATTTTTTCAATCTCAC-TTTTAACTTTATAATT-AAGCCTCTATTTTTTTTAATCTAACT
* * *
2537644 TTTTACATTTATAATTGAGGACTTTAATTTTTTTCAATCCCACTTTTTACCTTTATAATTAAAGC
128 TTTTACATTTATAATTGAAGACCTTAATTTTTTTTAATCCCACTTTTTACCTTTATAATTAAAGC
*
2537709 TCCTAATTTTTTTTCAATATCAC
193 TCCTAATTTTTTTTCAATACCAC
* * * * * *
2537732 TTTTTACTTTTATAATTAAAG-TCATTATTTTTTAATCTCACTTTCTACCTTTATAAATTGA--C
1 TTTTTACTTTTATAATTGAGGCCCCTAATTTTTCAATCTCACTTTCTACCTTTAT-AATTGAGGC
* * * * * *
2537794 CCCT-ATTTTTTTAATCTCACTTTTATCTTTATAATTGAGGCCTCTAATTTTTTCAATCTAATTT
65 CCCTAATTTTTTCAATCTCACTTTTAACTTTATAATT-AAGCCTCTATTTTTTTTAATCTAA-CT
*
2537858 TTTTACTTTTATAATT
128 TTTTACATTTATAATT
2537874 TAGGCCCCTA
Statistics
Matches: 304, Mismatches: 46, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
213 40 0.13
214 115 0.38
215 51 0.17
216 55 0.18
217 19 0.06
218 24 0.08
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.50
Consensus pattern (215 bp):
TTTTTACTTTTATAATTGAGGCCCCTAATTTTTCAATCTCACTTTCTACCTTTATAATTGAGGCC
CCTAATTTTTTCAATCTCACTTTTAACTTTATAATTAAGCCTCTATTTTTTTTAATCTAACTTTT
TACATTTATAATTGAAGACCTTAATTTTTTTTAATCCCACTTTTTACCTTTATAATTAAAGCTCC
TAATTTTTTTTCAATACCAC
Found at i:2542444 original size:9 final size:9
Alignment explanation
Indices: 2542432--2542456 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2542422 GAATAAAATG
2542432 AAAATTTTT
1 AAAATTTTT
2542441 AAAATTTTT
1 AAAATTTTT
2542450 AAAATTT
1 AAAATTT
2542457 GGGGATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AAAATTTTT
Found at i:2543786 original size:16 final size:16
Alignment explanation
Indices: 2543765--2543806 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2543755 ATATGTGATC
2543765 TATATGAATACATGTA
1 TATATGAATACATGTA
* *
2543781 TATATGATTACATGTC
1 TATATGAATACATGTA
2543797 TATATGAATA
1 TATATGAATA
2543807 TCACAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (16 bp):
TATATGAATACATGTA
Found at i:2548487 original size:14 final size:14
Alignment explanation
Indices: 2548470--2548502 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2548460 ATTTCTATGT
*
2548470 AGGGAATTATTTGC
1 AGGGAATTATTTAC
2548484 AGGGAATTATTTAC
1 AGGGAATTATTTAC
2548498 AGGGA
1 AGGGA
2548503 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:2549572 original size:23 final size:23
Alignment explanation
Indices: 2549546--2549596 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
2549536 ATTTTCAAAT
*
2549546 AAAAATCATAATTGTTTTTTTT-
1 AAAAAACATAATTGTTTTTTTTC
* *
2549568 AAAAAACTTTATTGTTTTTTTTC
1 AAAAAACATAATTGTTTTTTTTC
2549591 AAAAAA
1 AAAAAA
2549597 AAATGGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (23 bp):
AAAAAACATAATTGTTTTTTTTC
Found at i:2550446 original size:24 final size:24
Alignment explanation
Indices: 2550414--2550500 Score: 165
Period size: 24 Copynumber: 3.6 Consensus size: 24
2550404 CTGAAACTGC
*
2550414 TTTGTGGAAACATTAACATCACAG
1 TTTGTGGAAACATTGACATCACAG
2550438 TTTGTGGAAACATTGACATCACAG
1 TTTGTGGAAACATTGACATCACAG
2550462 TTTGTGGAAACATTGACATCACAG
1 TTTGTGGAAACATTGACATCACAG
2550486 TTTGTGGAAACATTG
1 TTTGTGGAAACATTG
2550501 CTCTTCTTTG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (24 bp):
TTTGTGGAAACATTGACATCACAG
Found at i:2550932 original size:41 final size:41
Alignment explanation
Indices: 2550887--2550970 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
2550877 CAGAATAATT
* *
2550887 ATGTAATTTACCTTATTTATTACGAGAATGCAATATTTTCG
1 ATGTAATTTACCTTATTTAGTACGAAAATGCAATATTTTCG
* *
2550928 ATGTAATTTACCTTATTTAGTATGAAAATGTAATATTTTCG
1 ATGTAATTTACCTTATTTAGTACGAAAATGCAATATTTTCG
2550969 AT
1 AT
2550971 TTAAACTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (41 bp):
ATGTAATTTACCTTATTTAGTACGAAAATGCAATATTTTCG
Found at i:2552059 original size:3 final size:3
Alignment explanation
Indices: 2552051--2552098 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
2552041 TAATTTTTCC
* *
2552051 ATT ATT ATT ATT ATT ATT ATA AGT ATT ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2552098 A
1 A
2552099 ATAAATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2553167 original size:2 final size:2
Alignment explanation
Indices: 2553160--2553196 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2553150 TAGTCACTGC
2553160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2553197 TTAGGATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2553518 original size:2 final size:2
Alignment explanation
Indices: 2553511--2553550 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2553501 CATATTAGTC
2553511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2553551 TTGTTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2561136 original size:76 final size:74
Alignment explanation
Indices: 2561005--2561147 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 74
2560995 CTACAGTGCA
* *
2561005 TGATGTTTTCAAAACATTCGGGTCATCCATAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACATTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAA-CCTT
2561070 CGGGAGCTTTT
64 CGGGAGCTTTT
* ** *
2561081 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACATTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCG
2561146 GG
66 GG
2561148 TCATCCATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 49 0.80
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (74 bp):
TGATATTTTCAAAACATTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCG
GGAGCTTTT
Found at i:2561150 original size:45 final size:45
Alignment explanation
Indices: 2561081--2561184 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
2561071 GGGAGCTTTT
* **
2561081 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
2561126 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
*
2561171 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
2561185 AGCCTTCAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
Found at i:2561201 original size:121 final size:121
Alignment explanation
Indices: 2560987--2561500 Score: 852
Period size: 121 Copynumber: 4.3 Consensus size: 121
2560977 TTCCCACATT
* *
2560987 TGTAAGACCTACAGTGCATGATGTTTTCAAAACATTCGGGTCATCCATAAGACCTATAGTGCAGG
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGG
*
2561052 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
66 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
2561108 TGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGG
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGG
* **
2561173 ATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATA-TTT-AAAGCCTTTAGGTCATC
66 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
* * *
2561227 TGTAAGACCTACAATGCATGATGTTTTCAATACCTTCGGGTCATCCATAAGACCTACAGTGCATG
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGG
* * *
2561292 ATGTTTTCAAAAATCCTTCGAGAGCTTTTTGATATTTTCAAGGCCTTCGGGTCATC
66 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
* *
2561348 TGTAAGACCTACAATGCATGTTGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGG
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGG
* * *
2561413 ATGTTTTCAAAAAGCCTTCGGGAGCGTTTTGATGTTTTCAAAGCCTTCGGGTCATA
66 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
*
2561469 TGTAAGACCTACAGTGCAGGATGTTTTCAAAA
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAA
2561501 AGCCTCCAGG
Statistics
Matches: 364, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
119 107 0.29
120 6 0.02
121 251 0.69
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (121 bp):
TGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGG
ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATC
Found at i:2561390 original size:45 final size:45
Alignment explanation
Indices: 2561326--2561434 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
2561316 CTTTTTGATA
** ** * *
2561326 TTTTCAAGGCCTTCGGGTCATCTGTAAGACCTACAATGCATGTTG
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTACAATGCAGGATG
*
2561371 TTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTACAATGCAGGATG
2561416 TTTTCAAAAAGCCTTCGGG
1 TTTTC-AAAA-CCTTCGGG
2561435 AGCGTTTTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 43 0.78
46 4 0.07
47 8 0.15
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCCATAAGACCTACAATGCAGGATG
Found at i:2561410 original size:240 final size:242
Alignment explanation
Indices: 2560987--2561500 Score: 852
Period size: 240 Copynumber: 2.1 Consensus size: 242
2560977 TTCCCACATT
*
2560987 TGTAAGACCTACAGTGCATGATGTTTTCAAAACATTCGGGTCATCCATAAGACCTATAGTGCAGG
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAACATTCGGGTCATCCATAAGACCTACAGTGCAGG
*
2561052 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGACC
66 ATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGACC
*
2561117 TACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCA
131 TACAATGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCA
* * *
2561182 AAAAGCCTTCAGGAGCTTTTTGAT-ATTT-AAAGCCTTTAGGTCATC
196 AAAAGCCTTCAGGAGCGTTTTGATGATTTCAAAGCCTTCAGGTCATA
* * * *
2561227 TGTAAGACCTACAATGCATGATGTTTTCAATACCTTCGGGTCATCCATAAGACCTACAGTGCATG
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAACATTCGGGTCATCCATAAGACCTACAGTGCAGG
* **
2561292 ATGTTTTCAAAAATCCTTCGAGAGCTTTTTGATATTTTCAAGGCCTTCGGGTCATCTGTAAGACC
66 ATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGACC
*
2561357 TACAATGCATGTTGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCA
131 TACAATGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCA
* * *
2561422 AAAAGCCTTCGGGAGCGTTTTGATGTTTTCAAAGCCTTCGGGTCATA
196 AAAAGCCTTCAGGAGCGTTTTGATGATTTCAAAGCCTTCAGGTCATA
*
2561469 TGTAAGACCTACAGTGCAGGATGTTTTCAAAA
1 TGTAAGACCTACAGTGCATGATGTTTTCAAAA
2561501 AGCCTCCAGG
Statistics
Matches: 252, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
240 206 0.82
241 3 0.01
242 43 0.17
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (242 bp):
TGTAAGACCTACAGTGCATGATGTTTTCAAAACATTCGGGTCATCCATAAGACCTACAGTGCAGG
ATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGACC
TACAATGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCA
AAAAGCCTTCAGGAGCGTTTTGATGATTTCAAAGCCTTCAGGTCATA
Found at i:2561449 original size:76 final size:76
Alignment explanation
Indices: 2561369--2561582 Score: 319
Period size: 76 Copynumber: 2.9 Consensus size: 76
2561359 CAATGCATGT
* **
2561369 TGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG
1 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG
2561434 GAGCGTTTTGA
66 GAGCGTTTTGA
* * *
2561445 TGTTTTCAAAGCCTTCGGGTCATATGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTCCAG
1 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG
*
2561510 GAGCTTTTTGA
66 GAGCGTTTTGA
* *
2561521 T-ATTT-AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAA-CCTTCGG
1 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG
2561582 G
66 G
2561583 TCATCCATAA
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
72 6 0.05
73 4 0.03
74 43 0.34
75 3 0.02
76 70 0.56
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (76 bp):
TGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG
GAGCGTTTTGA
Found at i:2561594 original size:45 final size:47
Alignment explanation
Indices: 2561526--2561629 Score: 167
Period size: 45 Copynumber: 2.3 Consensus size: 47
2561516 TTTGATATTT
** *
2561526 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTC-A
1 AAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAA
2561572 AAA-CCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAA
1 AAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAA
2561618 AAAGCCTTCGGG
1 AAAGCCTTCGGG
2561630 AGCTTTTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
45 38 0.72
46 7 0.13
47 8 0.15
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAA
Found at i:2561594 original size:119 final size:121
Alignment explanation
Indices: 2561442--2561686 Score: 395
Period size: 119 Copynumber: 2.0 Consensus size: 121
2561432 GGGAGCGTTT
* **
2561442 TGATGTTTTCAAAGCCTTCGGGTCATATGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTC
1 TGATGTTTTCAAAACCTTCGGGTCATACATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTC
*
2561507 CAGGAGCTTTTTGAT-ATTT-AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
66 CAGGAGCTTTTTGATGATTTCAAAGCCTTCAGGTCATCTGTAAGACCTACAGTGCA
* *
2561561 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATACATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTC
* *
2561626 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGACCTACAGTGCA
66 CAGGAGCTTTTTGATGATTTCAAAGCCTTCAGGTCATCTGTAAGACCTACAGTGCA
*
2561682 AGATG
1 TGATG
2561687 ATAAGACATC
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
119 74 0.64
120 3 0.03
121 38 0.33
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATACATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTC
CAGGAGCTTTTTGATGATTTCAAAGCCTTCAGGTCATCTGTAAGACCTACAGTGCA
Found at i:2561606 original size:195 final size:197
Alignment explanation
Indices: 2561245--2561686 Score: 730
Period size: 195 Copynumber: 2.3 Consensus size: 197
2561235 CTACAATGCA
** * *
2561245 TGATGTTTTCAATA-CCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAATCCT
1 TGATGTTTTCAA-AGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCT
* * *
2561309 TCGAGAGCTTTTTGATATTTTCAAGGCCTTCGGGTCATCTGTAAGACCTACAATGCATGTTGTTT
65 CCGAGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCATGATGTTT
2561374 TCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCG
130 TCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCG
2561439 TTT
195 TTT
* *
2561442 TGATGTTTTCAAAGCCTTCGGGTCATATGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTC
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTC
*
2561507 C-AGGAGCTTTTTGATA-TTT-AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTT
66 CGA-GAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCATGATGTTT
*
2561569 TCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCT
130 TCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCG
2561634 TTT
195 TTT
*
2561637 TGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGACCTACAGTGCAAGATG
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATG
2561687 ATAAGACATC
Statistics
Matches: 230, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
195 154 0.67
196 5 0.02
197 71 0.31
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (197 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTC
CGAGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCATGATGTTTT
CAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCGT
TT
Found at i:2561734 original size:20 final size:20
Alignment explanation
Indices: 2561687--2561736 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2561677 GTGCAAGATG
*
2561687 ATAAGACATCAGGACCATCC
1 ATAAGACCTCAGGACCATCC
2561707 ATAAGACCTCAGGACCATCC
1 ATAAGACCTCAGGACCATCC
2561727 ATAAGACCTC
1 ATAAGACCTC
2561737 CAGAGCAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (20 bp):
ATAAGACCTCAGGACCATCC
Found at i:2562014 original size:3 final size:3
Alignment explanation
Indices: 2562006--2562056 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
2561996 TAATTTTTCC
* * *
2562006 ATT ATT ATT ATT ATT ATA AGT ATT ATT ATT TTT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2562053 ATT A
1 ATT A
2562057 ATAATAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2563250 original size:13 final size:13
Alignment explanation
Indices: 2563232--2563256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2563222 ATTTTTATAT
2563232 ATTTTACAATTTG
1 ATTTTACAATTTG
2563245 ATTTTACAATTT
1 ATTTTACAATTT
2563257 TAATTTCTTT
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:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTTACAATTTG
Found at i:2566992 original size:25 final size:23
Alignment explanation
Indices: 2566954--2567001 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
2566944 ATTATCTTCC
2566954 TATTAATTAATTTTGAATAGATTGA
1 TATTAATTAATTTT-AAT-GATTGA
* *
2566979 TATTGATTATTTTTAATGATTGA
1 TATTAATTAATTTTAATGATTGA
2567002 AAATCATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 3 0.14
25 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (23 bp):
TATTAATTAATTTTAATGATTGA
Found at i:2568824 original size:3 final size:3
Alignment explanation
Indices: 2568816--2568847 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2568806 ATGAATGAAA
2568816 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2568848 TAAATGTTTA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2573002 original size:2 final size:2
Alignment explanation
Indices: 2572995--2573033 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2572985 AAATTAAAAT
2572995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2573034 TAAGAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2583359 original size:27 final size:27
Alignment explanation
Indices: 2583293--2583360 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
2583283 CGATTTGATG
2583293 GTATCGACACTTGACCATGTAGTATTA
1 GTATCGACACTTGACCATGTAGTATTA
* * *
2583320 GTGTCAACACTTGACCGTGTAGTATTA
1 GTATCGACACTTGACCATGTAGTATTA
* *
2583347 GTATTGACCCTTGA
1 GTATCGACACTTGA
2583361 GTATCGATAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (27 bp):
GTATCGACACTTGACCATGTAGTATTA
Found at i:2602486 original size:25 final size:25
Alignment explanation
Indices: 2602448--2602515 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
2602438 ATAAAGCTCC
*
2602448 AAGGAG-TGGCAAGCTAGGCGCCGG
1 AAGGAGCTAGCAAGCTAGGCGCCGG
2602472 AAGGAGCTAGCAAGCTAGGCGCCGG
1 AAGGAGCTAGCAAGCTAGGCGCCGG
2602497 AAGGAGCTAGCAAGCTAGG
1 AAGGAGCTAGCAAGCTAGG
2602516 TGGTTCGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 6 0.14
25 36 0.86
ACGTcount: A:0.29, C:0.21, G:0.41, T:0.09
Consensus pattern (25 bp):
AAGGAGCTAGCAAGCTAGGCGCCGG
Found at i:2621169 original size:2 final size:2
Alignment explanation
Indices: 2621157--2621187 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2621147 ACCCTTGTAC
2621157 AT AT A- 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
2621188 GACTTGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2622876 original size:73 final size:73
Alignment explanation
Indices: 2622785--2622927 Score: 234
Period size: 73 Copynumber: 2.0 Consensus size: 73
2622775 TAGTTCCATA
* * **
2622785 TGTTTCCTCATGTTGAGGTTTCTCTATACTTCTTTGTATTTTTCAAA-GAAAAATATGAATAATA
1 TGTTCCCTCATGTTGAGGTTTCTCTATACTTCTTTATATTTTTCAAATG-AAAATAAAAATAATA
2622849 TAATATGTG
65 TAATATGTG
2622858 TGTTCCCTCATGTTGAGGTTTCTCTATACTTCTTTATATTTTTCAAATGAAAATAAAAATAATAT
1 TGTTCCCTCATGTTGAGGTTTCTCTATACTTCTTTATATTTTTCAAATGAAAATAAAAATAATAT
2622923 AATAT
66 AATAT
2622928 TTAAATAGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
73 64 0.98
74 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (73 bp):
TGTTCCCTCATGTTGAGGTTTCTCTATACTTCTTTATATTTTTCAAATGAAAATAAAAATAATAT
AATATGTG
Found at i:2625280 original size:2 final size:2
Alignment explanation
Indices: 2625268--2625309 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
2625258 CAAATTACAC
* * *
2625268 AG AG AG CG AG AG AA AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2625310 GGAAGAGGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2628304 original size:14 final size:14
Alignment explanation
Indices: 2628285--2628325 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
2628275 AGAAATGGGT
2628285 GAGAGAAAAGTAGA
1 GAGAGAAAAGTAGA
2628299 GAGAGAAAAGTAGA
1 GAGAGAAAAGTAGA
2628313 GAGAGAAAA-TAGA
1 GAGAGAAAAGTAGA
2628326 TTCCGATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (14 bp):
GAGAGAAAAGTAGA
Found at i:2636990 original size:11 final size:11
Alignment explanation
Indices: 2636976--2637012 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2636966 TTTTAAGTAT
2636976 ATATTAATAAA
1 ATATTAATAAA
2636987 ATATTAATAAA
1 ATATTAATAAA
* *
2636998 ATAATAAAAAA
1 ATATTAATAAA
2637009 ATAT
1 ATAT
2637013 AATGTCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATTAATAAA
Found at i:2642739 original size:21 final size:22
Alignment explanation
Indices: 2642714--2642758 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
2642704 AAGAACGTTA
2642714 CTCGACTATAATTGAAG-AATT
1 CTCGACTATAATTGAAGAAATT
*
2642735 CTCGATTATAATTGAAGAAATT
1 CTCGACTATAATTGAAGAAATT
2642757 CT
1 CT
2642759 GGTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
CTCGACTATAATTGAAGAAATT
Found at i:2643834 original size:2 final size:2
Alignment explanation
Indices: 2643827--2643852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2643817 GTTACCTTTA
2643827 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
2643853 TTAAAATAGA
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:2645486 original size:20 final size:20
Alignment explanation
Indices: 2645437--2645479 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2645427 TTACCTTGGG
**
2645437 TATCGATACTACAAGAACAA
1 TATCGATACTGTAAGAACAA
2645457 TATCGATACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
2645477 TAT
1 TAT
2645480 TGGTACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (20 bp):
TATCGATACTGTAAGAACAA
Found at i:2647572 original size:25 final size:25
Alignment explanation
Indices: 2647538--2647588 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2647528 ATCCATTACC
2647538 TTAGCTCCACACTAAGAATTTCTAA
1 TTAGCTCCACACTAAGAATTTCTAA
2647563 TTAGCTCCACACTAAGAATTTCTAA
1 TTAGCTCCACACTAAGAATTTCTAA
2647588 T
1 T
2647589 AAATTCACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (25 bp):
TTAGCTCCACACTAAGAATTTCTAA
Found at i:2649603 original size:26 final size:26
Alignment explanation
Indices: 2649574--2649644 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
2649564 ATTATTATAA
*
2649574 TATATTAAAATTAATAATAAATTTTT
1 TATATTAAAATTAATAATAAATTTAT
* *
2649600 TATAAT-AAA-TAAT-ATTAA-TTAT
1 TATATTAAAATTAATAATAAATTTAT
2649622 TATATTCAATAATT-ATAATAAAT
1 TATATT-AA-AATTAATAATAAAT
2649645 CATTTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 11
0.68 0.10 0.22
Matches are distributed among these distances:
22 8 0.24
23 4 0.12
24 5 0.15
25 7 0.21
26 10 0.29
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATTAAAATTAATAATAAATTTAT
Found at i:2653276 original size:137 final size:137
Alignment explanation
Indices: 2652823--2654093 Score: 1573
Period size: 137 Copynumber: 9.3 Consensus size: 137
2652813 TTCCATTATT
* * * * *
2652823 CATGTTATCATTGTCCTATTATGTGAGTCAAGTCCCCCGGGGCACTATTCATGCTA-GTACCTAT
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCACTATTCATG-TATG-CCCTAT
* * * *
2652887 TATGTTTGAGGGGACGCAGCAAAGTGGTGAAAGTG-AGTTTCCGGGGGCGCGCATTCTATTATTT
64 TATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCA-TTTCCGGGGGCGCGCCTTCCATTATTT
* * *
2652951 TATAAGATAA
128 TGTCAGAGAA
* * * * * *
2652961 TATGTTATTATTGCCCTATTATGTCACTAATGTCCCCTGGGGCACTATTCATATATTCCCTATTA
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCACTATTCATGTATGCCCTATTA
* * *
2653026 TGTTTGAGGGGACGCAACAAAGTGGTGAAAGCACGTTTTCGGGGG-GCGCCTTCCATTATTTTGT
66 TGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTGT
2653090 CAGAGAA
131 CAGAGAA
* * * *
2653097 TATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGTACTATTCATGTATGCCTTGTTA
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCACTATTCATGTATGCCCTATTA
* * * *
2653162 TGTTTGAGGGGACGCAACAAAGTGGTTAAAGCACATTTTCGGGGGCGCACCTTCCATTATTTTGT
66 TGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTGT
2653227 CAGAGAA
131 CAGAGAA
* * *
2653234 CATGTTATCATTGCCCTATTATGTCACTCATGTTCCCTGGGGTACTATTCATGTATGCCCTATTA
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCACTATTCATGTATGCCCTATTA
* * ** * * * *
2653299 TGTTTGAGGGGACGCAGCAAAGTGGTGAAAGTGTGTTTCCGAGTGCGCGTCTTCCATTATTTTAT
66 TGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTGT
*
2653364 CAGACAA
131 CAGAGAA
* * * * *
2653371 CATTTTATCATTGACTTATTATGTCACTCATGTCCCCCGGGGCACTATTCATATATGCGCTATTA
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCACTATTCATGTATGCCCTATTA
* * * * *
2653436 TGTTTGAGGGGACGCAACAAATTGGTGAAAACACATTTCCGAGTGCGCGCCTTCCATTATTTTGT
66 TGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTGT
2653501 CAGAGAA
131 CAGAGAA
*
2653508 CATGTTATCATTGCCTTATTATGTCACTCATGTCCCCCGGGGGCACTATTCATGTATGCCCTATT
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCC-GGGGCACTATTCATGTATGCCCTATT
* * * * *
2653573 ATGTTTGAGGGGACGCAGCAAAGTGGTGAAAGTGCGTTTCC-GGGGTGCACCTTCCATTATTTTG
65 ATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTG
*
2653637 TCAGAAAA
130 TCAGAGAA
* * * *** * *
2653645 CATGTTATCATTGTCCTATTATGTCACTTACGTCCTTTGGGGGAACTATTTATGTATGCCCTATT
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCC-CCCGGGGCACTATTCATGTATGCCCTATT
* * * * * *
2653710 ATGTTTGAAGGGATGCAGCAAAGTAGTGAAAGCGCATTTCCGGGGGCGTGCCTTCCATTATTTTT
65 ATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTG
2653775 TCAGAGAA
130 TCAGAGAA
* *
2653783 CATGTTATCATTGCCCTATTATGTCACTCGTGTCCCCCGGTGGCACTATTCATATATGCCCTATT
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGG-GGCACTATTCATGTATGCCCTATT
* * * *
2653848 ATGTTTGAGGGGACACAACAAAGTGGTGAAAGCGCGTTTCCGGGGGAGCGCCTTTCATTATTTTG
65 ATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTG
*
2653913 TCAGAAAA
130 TCAGAGAA
* * * * *
2653921 CATGTTATCATTGCCTTATTATATCACTCATGTCCCCCGGCGGCACTATTCATATATGCCATATC
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGG-GGCACTATTCATGTATGCCCTATT
* * * * *
2653986 ATGTTTGAGGGGATGCAATAAAGTGGTGAAAGCGCATTT-C-AGGGTGCGCCTTCCATTATTATG
65 ATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTG
*
2654049 TCAAAGAA
130 TCAGAGAA
* * * * * *
2654057 TATGTTATAATTTCCCTATTACGTGAGTCATGTCCCC
1 CATGTTATCATTGCCCTATTATGTCACTCATGTCCCC
2654094 TGAGACGAAG
Statistics
Matches: 979, Mismatches: 147, Indels: 16
0.86 0.13 0.01
Matches are distributed among these distances:
136 175 0.18
137 467 0.48
138 337 0.34
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (137 bp):
CATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCACTATTCATGTATGCCCTATTA
TGTTTGAGGGGACGCAACAAAGTGGTGAAAGCGCATTTCCGGGGGCGCGCCTTCCATTATTTTGT
CAGAGAA
Found at i:2654263 original size:23 final size:23
Alignment explanation
Indices: 2654237--2654289 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2654227 TAAAGTTTGA
*
2654237 ATAAATTGAATAAAATGTTAAG-G
1 ATAAATTGAAT-AAATGTGAAGTG
2654260 ATAAATTGAATAAATGTGAAGTG
1 ATAAATTGAATAAATGTGAAGTG
2654283 ATAAATT
1 ATAAATT
2654290 TAACATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAAATTGAATAAATGTGAAGTG
Found at i:2654869 original size:219 final size:219
Alignment explanation
Indices: 2654471--2654901 Score: 765
Period size: 219 Copynumber: 2.0 Consensus size: 219
2654461 CAAGTTAATG
2654471 TAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGAATACAATTTTA
1 TAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGAATACAATTTTA
2654536 AATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTATTTTAAAAACATTTAACAAACATTTAA
66 AATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTATTTTAAAAACATTTAACAAACATTTAA
*
2654601 TGTTAAATTTGAATAAAAAATAACATTAAAAATATTTTGTAACAACCATTAAACATTTAAATAAC
131 TGTTAAATTTGAATAAAAAATAACATTAAAAATATTTTCTAACAACCATTAAACATTTAAATAAC
*
2654666 ATTACAAAATTACATAATGTACTT
196 ATTACAAAAGTACATAATGTACTT
* * *
2654690 TAATTTCAATTTAAGTATTGTTAACTATAATTGGAATATAACTTTGAATTTCGAATACAATTTTA
1 TAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGAATACAATTTTA
*
2654755 AATTTCAATTGGAATATTAAGTTGAATTTGAATTTGTATTTTAAAAACATTTAACAAACATTTAA
66 AATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTATTTTAAAAACATTTAACAAACATTTAA
* * *
2654820 TGTTAATTTTGAA-CAAAAATAACATTAAAAATATTGTTCTAATAACCATTAAACATTTAAATAA
131 TGTTAAATTTGAATAAAAAATAACATTAAAAATATT-TTCTAACAACCATTAAACATTTAAATAA
2654884 CATTACAAAAGTACATAA
195 CATTACAAAAGTACATAA
2654902 ATTTCTGAAA
Statistics
Matches: 202, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
218 21 0.10
219 181 0.90
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (219 bp):
TAATTTCAATTTAAGTACTGTGAACTATAATTGGAATATAACTTTAAATTTCGAATACAATTTTA
AATTTCAATTGGAATATTAAGTTCAATTTGAATTTGTATTTTAAAAACATTTAACAAACATTTAA
TGTTAAATTTGAATAAAAAATAACATTAAAAATATTTTCTAACAACCATTAAACATTTAAATAAC
ATTACAAAAGTACATAATGTACTT
Found at i:2655374 original size:42 final size:42
Alignment explanation
Indices: 2655328--2655415 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
2655318 GGCATGTAAC
*
2655328 CTGGTGAGCTAGGAATGTAACCCTACGAAAATGGCATA-TGAA
1 CTGGTGAGCTAGGAATATAACCCTACGAAAATGGCA-ACTGAA
* * * * * *
2655370 CTGGTGGGCTTGGCATATACCCCTACGGAGATGGCAACTGAA
1 CTGGTGAGCTAGGAATATAACCCTACGAAAATGGCAACTGAA
2655412 CTGG
1 CTGG
2655416 AGGGCTGAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (42 bp):
CTGGTGAGCTAGGAATATAACCCTACGAAAATGGCAACTGAA
Found at i:2655421 original size:42 final size:42
Alignment explanation
Indices: 2655348--2655435 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
2655338 AGGAATGTAA
*
2655348 CCCTACGAAAATGGCATATGAACTGGTGGGCTTG-GCATATAC
1 CCCTACGAAAATGGCATATGAACTGGAGGGC-TGAGCATATAC
* * *
2655390 CCCTACGGAGATGGCA-ACTGAACTGGAGGGCTGAGCATGTAC
1 CCCTACGAAAATGGCATA-TGAACTGGAGGGCTGAGCATATAC
2655432 CCCT
1 CCCT
2655436 GTGGCATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
41 3 0.08
42 37 0.93
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.20
Consensus pattern (42 bp):
CCCTACGAAAATGGCATATGAACTGGAGGGCTGAGCATATAC
Found at i:2656997 original size:22 final size:22
Alignment explanation
Indices: 2656971--2657040 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
2656961 AAAATTTATA
* *
2656971 ATTAATATAAATTCATGATAAAT
1 ATTAA-ATAAATTAATAATAAAT
*
2656994 -TTAAATTAAAATAATAATAAAT
1 ATTAAA-TAAATTAATAATAAAT
2657016 ATTAACATAAATTAA-AA-AAAT
1 ATTAA-ATAAATTAATAATAAAT
2657037 ATTA
1 ATTA
2657041 TCATATCACT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 9 0.22
22 19 0.47
23 11 0.28
24 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (22 bp):
ATTAAATAAATTAATAATAAAT
Found at i:2657536 original size:60 final size:60
Alignment explanation
Indices: 2657442--2657554 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
2657432 TTAATGGAAG
* *
2657442 GCGCGTCCCCGGGGACGCGCCTTACCCCCGTGGCATCTGACTCAGCAAAAACCCGTGAAA
1 GCGCGTCCCCGGAGACGCGCCTTACCCCCGTGGCATCCGACTCAGCAAAAACCCGTGAAA
*
2657502 GCGCGTCCCCGGAGATGCGCCTTACCCACC-TGGCATCCGACTCAGCAAAAACC
1 GCGCGTCCCCGGAGACGCGCCTTACCC-CCGTGGCATCCGACTCAGCAAAAACC
2657555 TAGGTAAAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.22, C:0.40, G:0.25, T:0.13
Consensus pattern (60 bp):
GCGCGTCCCCGGAGACGCGCCTTACCCCCGTGGCATCCGACTCAGCAAAAACCCGTGAAA
Found at i:2658244 original size:12 final size:12
Alignment explanation
Indices: 2658227--2658266 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2658217 ACCGAAACTC
* *
2658227 ATGTATGTATGT
1 ATGTATATATAT
2658239 ATGTATATATAT
1 ATGTATATATAT
*
2658251 ATGTATATGTAT
1 ATGTATATATAT
2658263 ATGT
1 ATGT
2658267 GTGTCAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:2658632 original size:2 final size:2
Alignment explanation
Indices: 2658625--2658677 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2658615 AATCCGCCAT
2658625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2658667 TA TA TA TA TA T
1 TA TA TA TA TA T
2658678 GCCTATATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2663028 original size:24 final size:24
Alignment explanation
Indices: 2663001--2663046 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2662991 TAATATAATT
* *
2663001 ATATCTAATATAAATTTAAATAAA
1 ATATCAAATAAAAATTTAAATAAA
2663025 ATATCAAATAAAAATTTAAATA
1 ATATCAAATAAAAATTTAAATA
2663047 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATCAAATAAAAATTTAAATAAA
Found at i:2663112 original size:26 final size:22
Alignment explanation
Indices: 2663053--2663104 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2663043 AATATATTTT
* *
2663053 TTAATATTATATGATAAATATGA
1 TTAA-ATTATTTGATAAATATAA
2663076 TTAAATTATTTGATAAATATAA
1 TTAAATTATTTGATAAATATAA
2663098 TTGAAAT
1 TT-AAAT
2663105 GTGAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (22 bp):
TTAAATTATTTGATAAATATAA
Found at i:2663604 original size:2 final size:2
Alignment explanation
Indices: 2663597--2663624 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2663587 AGAATCTATC
2663597 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
2663625 GTATGTATAA
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:2670201 original size:15 final size:15
Alignment explanation
Indices: 2670177--2670217 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2670167 ACATGCATTC
*
2670177 ATAAGTCATCAATTT
1 ATAAGCCATCAATTT
2670192 ATAAGCCATCAATTT
1 ATAAGCCATCAATTT
2670207 ATAAGCCATCA
1 ATAAGCCATCA
2670218 TATTCTGACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (15 bp):
ATAAGCCATCAATTT
Found at i:2680971 original size:18 final size:18
Alignment explanation
Indices: 2680948--2680993 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2680938 TTTTTTATTT
*
2680948 ATTTTATTTTGGCCATGA
1 ATTTTAATTTGGCCATGA
*
2680966 ATTTTAATTTGGTCATGA
1 ATTTTAATTTGGCCATGA
2680984 ATTTTAATTT
1 ATTTTAATTT
2680994 AGTCCCCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (18 bp):
ATTTTAATTTGGCCATGA
Found at i:2682406 original size:13 final size:14
Alignment explanation
Indices: 2682388--2682427 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2682378 ATGACTTTTG
2682388 GGTCAAAGTCAA-T
1 GGTCAAAGTCAACT
*
2682401 GGTCAAAGTAAACT
1 GGTCAAAGTCAACT
2682415 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
2682428 GGATCGGACG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (14 bp):
GGTCAAAGTCAACT
Found at i:2682419 original size:14 final size:13
Alignment explanation
Indices: 2682388--2682423 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2682378 ATGACTTTTG
*
2682388 GGTCAAAGTCAAT
1 GGTCAAAGTAAAT
2682401 GGTCAAAGTAAACT
1 GGTCAAAGTAAA-T
2682415 GGTCAAAGT
1 GGTCAAAGT
2682424 CAACGGATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (13 bp):
GGTCAAAGTAAAT
Found at i:2684819 original size:13 final size:14
Alignment explanation
Indices: 2684785--2684817 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2684775 GAAGTTTATT
2684785 AATTTTAAAATAAA
1 AATTTTAAAATAAA
*
2684799 AATTTTAAGATAAA
1 AATTTTAAAATAAA
2684813 AATTT
1 AATTT
2684818 AAATCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
AATTTTAAAATAAA
Found at i:2690257 original size:17 final size:18
Alignment explanation
Indices: 2690212--2690258 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2690202 TGACGTATAT
2690212 AATATTTAAATAATAATAA
1 AATATTTAAA-AATAATAA
* *
2690231 GA-ATTGAAAAATAA-AA
1 AATATTTAAAAATAATAA
2690247 AATATTTAAAAA
1 AATATTTAAAAA
2690259 GTATATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.13
17 13 0.57
18 6 0.26
19 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
AATATTTAAAAATAATAA
Found at i:2690471 original size:30 final size:29
Alignment explanation
Indices: 2690435--2690504 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
2690425 TGGTTCATAA
2690435 ATATTTTTTAAAATTTA-ACATTTATCATTT
1 ATATTTTTTAAAATTTATA-ATTT-TCATTT
* * *
2690465 ATATTTTTCAAATTTTATAATTTTTATTT
1 ATATTTTTTAAAATTTATAATTTTCATTT
2690494 A-ATTTTTTAAA
1 ATATTTTTTAAA
2690505 TTCTTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.26
29 6 0.17
30 19 0.54
31 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATTTTTTAAAATTTATAATTTTCATTT
Found at i:2690539 original size:10 final size:10
Alignment explanation
Indices: 2690524--2690548 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2690514 AATAATTTTA
2690524 TTTTAATAAT
1 TTTTAATAAT
2690534 TTTTAATAAT
1 TTTTAATAAT
2690544 TTTTA
1 TTTTA
2690549 TTATATTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:2695272 original size:94 final size:94
Alignment explanation
Indices: 2695111--2695305 Score: 372
Period size: 94 Copynumber: 2.1 Consensus size: 94
2695101 ATAGTAAAGA
*
2695111 TGGAAGGATTGAAGGGTATTATGGTCTTTTCAGTTTAAAGGATATTTTATCTCCTTTATTAAGAG
1 TGGAAGCATTGAAGGGTATTATGGTCTTTTCAGTTTAAAGGATATTTTATCTCCTTTATTAAGAG
2695176 ATAAGTACGTGGGATTTGGGAGAGTTATC
66 ATAAGTACGTGGGATTTGGGAGAGTTATC
*
2695205 TGGAAGCATTGAAGGGTATTATGGTCTTTTCAGTTTAAATGATATTTTATCTCCTTTATTAAGAG
1 TGGAAGCATTGAAGGGTATTATGGTCTTTTCAGTTTAAAGGATATTTTATCTCCTTTATTAAGAG
2695270 ATAAGTACGTGGGATTTGGGAGAGTTATC
66 ATAAGTACGTGGGATTTGGGAGAGTTATC
2695299 TGGAAGC
1 TGGAAGC
2695306 TTATTTTCTC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 99 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (94 bp):
TGGAAGCATTGAAGGGTATTATGGTCTTTTCAGTTTAAAGGATATTTTATCTCCTTTATTAAGAG
ATAAGTACGTGGGATTTGGGAGAGTTATC
Found at i:2696215 original size:20 final size:20
Alignment explanation
Indices: 2696190--2696229 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2696180 TGTATTCATG
2696190 TAGATATCGATCGAAAACAA
1 TAGATATCGATCGAAAACAA
2696210 TAGATATCGATCGAAAACAA
1 TAGATATCGATCGAAAACAA
2696230 AGTCCCGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (20 bp):
TAGATATCGATCGAAAACAA
Found at i:2698664 original size:40 final size:40
Alignment explanation
Indices: 2698581--2698657 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
2698571 TAAAAAGTAG
2698581 TTTTGCTTTGAATAGGATCTACTGGATCTATATTTTTCTA
1 TTTTGCTTTGAATAGGATCTACTGGATCTATATTTTTCTA
* * * *
2698621 TTTTGCTTTGAGTAGGATTTATTGGATCTGTATTTTT
1 TTTTGCTTTGAATAGGATCTACTGGATCTATATTTTT
2698658 TCATTTTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.19, C:0.09, G:0.18, T:0.53
Consensus pattern (40 bp):
TTTTGCTTTGAATAGGATCTACTGGATCTATATTTTTCTA
Found at i:2702246 original size:4 final size:4
Alignment explanation
Indices: 2702239--2702265 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2702229 ACTATGTATG
2702239 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
2702266 ATATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2704034 original size:8 final size:7
Alignment explanation
Indices: 2704012--2704070 Score: 66
Period size: 8 Copynumber: 7.9 Consensus size: 7
2704002 TAAATTGGAA
2704012 AAAAAAG
1 AAAAAAG
2704019 -AAAAAG
1 AAAAAAG
2704025 AAAAATAG
1 AAAAA-AG
2704033 AAAAAAG
1 AAAAAAG
2704040 AATAAAAG
1 AA-AAAAG
2704048 AACAAAAG
1 AA-AAAAG
2704056 AAAGAAGAG
1 AAA-AA-AG
2704065 AAAAAA
1 AAAAAA
2704071 ATAAGGTGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
6 6 0.13
7 10 0.22
8 25 0.54
9 5 0.11
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:2704983 original size:41 final size:41
Alignment explanation
Indices: 2704870--2705029 Score: 160
Period size: 43 Copynumber: 3.8 Consensus size: 41
2704860 CGAATGGGCC
*
2704870 ATCCACGATTTCAACTCCACGAC-AGAGGATATCGTACCCAT
1 ATCCACGATTTCAACTCCACGACGA-AGGATATCGTGCCCAT
* * *
2704911 AAATCCACGATTTCAACTCCACAACGGAGGATATTGTGCCCAT
1 --ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCAT
* * * *
2704954 TTCCATGATTTCAACTTCACGACGAAGGATATCGTGCCAACT
1 ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCA-T
* * * *
2704996 CTACATTGATTTCAACTTCACGACGAAGGATATC
1 ATCCA-CGATTTCAACTCCACGACGAAGGATATC
2705030 CAATTCAAAG
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 33 0.33
42 4 0.04
43 64 0.63
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (41 bp):
ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCAT
Found at i:2705896 original size:12 final size:12
Alignment explanation
Indices: 2705858--2705957 Score: 72
Period size: 12 Copynumber: 8.5 Consensus size: 12
2705848 TCAATGTTAT
2705858 TATATTATATAA
1 TATATTATATAA
2705870 TATA-TAT-T--
1 TATATTATATAA
2705878 TATATTATA-AA
1 TATATTATATAA
2705889 TCATATTATATAA
1 T-ATATTATATAA
*
2705902 TATATTCATCT-A
1 TATATT-ATATAA
*
2705914 TAT-TTATGATTATT
1 TATATTAT-A-TA-A
2705928 TATATTATA-AA
1 TATATTATATAA
2705939 TCATATTATATAA
1 T-ATATTATATAA
2705952 TATATT
1 TATATT
2705958 CATCTATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 28
0.69 0.04 0.27
Matches are distributed among these distances:
8 4 0.06
9 3 0.04
10 3 0.04
11 7 0.10
12 36 0.51
13 9 0.13
14 4 0.06
15 4 0.06
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TATATTATATAA
Found at i:2705937 original size:50 final size:50
Alignment explanation
Indices: 2705874--2705980 Score: 214
Period size: 50 Copynumber: 2.1 Consensus size: 50
2705864 ATATAATATA
2705874 TATTTATATTATAAATCATATTATATAATATATTCATCTATATTTATGAT
1 TATTTATATTATAAATCATATTATATAATATATTCATCTATATTTATGAT
2705924 TATTTATATTATAAATCATATTATATAATATATTCATCTATATTTATGAT
1 TATTTATATTATAAATCATATTATATAATATATTCATCTATATTTATGAT
2705974 TATTTAT
1 TATTTAT
2705981 TTACATTCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (50 bp):
TATTTATATTATAAATCATATTATATAATATATTCATCTATATTTATGAT
Found at i:2707022 original size:19 final size:19
Alignment explanation
Indices: 2706998--2707035 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2706988 TCAATCCTTG
*
2706998 AATTTTGACCTTAAATTCT
1 AATTTTGACCTCAAATTCT
*
2707017 AATTTTTACCTCAAATTCT
1 AATTTTGACCTCAAATTCT
2707036 CCTTAATTTA
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:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (19 bp):
AATTTTGACCTCAAATTCT
Found at i:2707139 original size:40 final size:45
Alignment explanation
Indices: 2707103--2707185 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
2707093 AATTATTTTC
*
2707103 ATTTTTTT-TT-TTATTTATT-TAT-T-TTTACATTTTTATTACTA
1 ATTTTTTTATTATTACTTATTATATATATTT-CATTTTTATTACTA
2707144 ATTTTTTTATTATTACTTATTATATATATTTCATTTTTATTA
1 ATTTTTTTATTATTACTTATTATATATATTTCATTTTTATTA
2707186 TTTTTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 8 0.22
42 2 0.06
43 8 0.22
44 3 0.08
45 12 0.33
46 3 0.08
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (45 bp):
ATTTTTTTATTATTACTTATTATATATATTTCATTTTTATTACTA
Found at i:2707156 original size:3 final size:3
Alignment explanation
Indices: 2707150--2707239 Score: 54
Period size: 3 Copynumber: 31.7 Consensus size: 3
2707140 ACTAATTTTT
* *
2707150 TTA TTA TTA CTTA TTA -TA TATA TT- TCA TTT TTA TTA TT- TT- TTA
1 TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
2707193 -TA TACA TTA TTA TT- TTA TTA -TA TTTA TTA TTA TT- TTA TT- TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
2707235 TTA TT
1 TTA TT
2707240 TTTTATTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
2 17 0.25
3 42 0.61
4 10 0.14
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2707240 original size:52 final size:55
Alignment explanation
Indices: 2707132--2707246 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 55
2707122 TATTTTTACA
*
2707132 TTTTTATTACTAATTTTTTTATTATTACTTATTATATATATTTCATTTTTATTAT
1 TTTTTATTACTAATTATTTTATTATTACTTATTATATATATTTCATTTTTATTAT
* *
2707187 TTTTTATATACATTATTATTTTATTA-TATTTATTAT-TAT-TTT-A-TTTTATTAT
1 TTTTTAT-TAC-TAATTATTTTATTATTACTTATTATATATATTTCATTTTTATTAT
2707239 TTTTTATT
1 TTTTTATT
2707247 TTTTTTGCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
51 1 0.02
52 16 0.29
53 1 0.02
54 3 0.05
55 10 0.18
56 12 0.22
57 12 0.22
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (55 bp):
TTTTTATTACTAATTATTTTATTATTACTTATTATATATATTTCATTTTTATTAT
Found at i:2707248 original size:20 final size:20
Alignment explanation
Indices: 2707134--2707236 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
2707124 TTTTTACATT
* *
2707134 TTTATTACTAATTT-TTTTA
1 TTTATTATTATTTTATTTTA
2707153 -TTATTACTTATTATATATATTTCA
1 TTTATTA-TTATT-T-TAT-TTT-A
*
2707177 TTT-TTATTATTTT-TTATA
1 TTTATTATTATTTTATTTTA
** *
2707195 TACATTATTATTTTATTATA
1 TTTATTATTATTTTATTTTA
2707215 TTTATTATTATTTTATTTTA
1 TTTATTATTATTTTATTTTA
2707235 TT
1 TT
2707237 ATTTTTTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
18 8 0.12
19 15 0.22
20 26 0.39
21 2 0.03
22 2 0.03
23 8 0.12
24 4 0.06
25 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTATTATTTTATTTTA
Found at i:2707261 original size:25 final size:25
Alignment explanation
Indices: 2707202--2707251 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
2707192 ATATACATTA
2707202 TTATTTTATTATATTTATTATTATT
1 TTATTTTATTATATTTATTATTATT
*
2707227 TTATTTTATTAT-TTT-TTATTTTT
1 TTATTTTATTATATTTATTATTATT
2707250 TT
1 TT
2707252 TGCTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.38
24 3 0.12
25 12 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (25 bp):
TTATTTTATTATATTTATTATTATT
Found at i:2707356 original size:9 final size:9
Alignment explanation
Indices: 2707349--2707436 Score: 78
Period size: 9 Copynumber: 9.9 Consensus size: 9
2707339 TTTCGTTTTG
2707349 TTTATTT-T
1 TTTATTTAT
2707357 ATTTATTTAT
1 -TTTATTTAT
2707367 TTTATTTA-
1 TTTATTTAT
*
2707375 CTTATTTA-
1 TTTATTTAT
2707383 TTTATTT-T
1 TTTATTTAT
2707391 ATTTATTTAT
1 -TTTATTTAT
2707401 TTTATTTA-
1 TTTATTTAT
2707409 TTTATTTTCAT
1 TTTA-TTT-AT
* *
2707420 TTTGTTTGT
1 TTTATTTAT
2707429 TTTATTTA
1 TTTATTTA
2707437 CCTGTTATCT
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
8 17 0.26
9 40 0.61
10 6 0.09
11 3 0.05
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2707363 original size:4 final size:4
Alignment explanation
Indices: 2707349--2707415 Score: 89
Period size: 4 Copynumber: 15.8 Consensus size: 4
2707339 TTTCGTTTTG
*
2707349 TTTA TTTTA TTTA TTTA TTTTA TTTA CTTA TTTA TTTA TTTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
2707400 TTTTA TTTA TTTA TTT
1 -TTTA TTTA TTTA TTT
2707416 TCATTTTGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
4 41 0.72
5 16 0.28
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2707367 original size:13 final size:13
Alignment explanation
Indices: 2707349--2707436 Score: 99
Period size: 13 Copynumber: 6.6 Consensus size: 13
2707339 TTTCGTTTTG
2707349 TTTATTTTATTTA-
1 TTTA-TTTATTTAT
2707362 TTTATTTTATTTA-
1 TTTA-TTTATTTAT
*
2707375 CTTATTTATTTAT
1 TTTATTTATTTAT
2707388 TTTATTTATTTAT
1 TTTATTTATTTAT
2707401 TTTATTTATTTAT
1 TTTATTTATTTAT
* *
2707414 TTTCATTTTGTTTGT
1 TTT-A-TTTATTTAT
2707429 TTTATTTA
1 TTTATTTA
2707437 CCTGTTATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
12 8 0.12
13 47 0.70
14 2 0.03
15 10 0.15
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:2707379 original size:17 final size:18
Alignment explanation
Indices: 2707349--2707415 Score: 104
Period size: 17 Copynumber: 3.9 Consensus size: 18
2707339 TTTCGTTTTG
2707349 TTTATTTTATTTATTTAT
1 TTTATTTTATTTATTTAT
*
2707367 TTTA-TTTACTTATTTA-
1 TTTATTTTATTTATTTAT
2707383 TTTATTTTATTTATTTAT
1 TTTATTTTATTTATTTAT
2707401 TTTA-TTTATTTATTT
1 TTTATTTTATTTATTT
2707416 TCATTTTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
16 4 0.09
17 33 0.73
18 8 0.18
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTATTTATTTAT
Found at i:2707903 original size:20 final size:20
Alignment explanation
Indices: 2707878--2707916 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2707868 CGACAATATT
2707878 TTATTT-TATTTCTTCATTAA
1 TTATTTGTATTTC-TCATTAA
*
2707898 TTATTTGTTTTTCTCATTA
1 TTATTTGTATTTCTCATTA
2707917 GATATACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (20 bp):
TTATTTGTATTTCTCATTAA
Found at i:2712256 original size:13 final size:13
Alignment explanation
Indices: 2712240--2712270 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2712230 TTTGTGTGTC
*
2712240 ACATTTATGACTT
1 ACATTTACGACTT
2712253 ACATTTACGACTT
1 ACATTTACGACTT
2712266 ACATT
1 ACATT
2712271 GCGTGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (13 bp):
ACATTTACGACTT
Found at i:2726602 original size:7 final size:7
Alignment explanation
Indices: 2726590--2726640 Score: 95
Period size: 7 Copynumber: 7.4 Consensus size: 7
2726580 GTCAAAGGAA
2726590 GTCAACG
1 GTCAACG
2726597 GTCAACG
1 GTCAACG
2726604 GTCAACG
1 GTCAACG
2726611 GTCAACG
1 GTCAACG
2726618 GTC-ACG
1 GTCAACG
2726624 GTCAACG
1 GTCAACG
2726631 GTCAACG
1 GTCAACG
2726638 GTC
1 GTC
2726641 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.14
7 37 0.86
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2726647 original size:5 final size:5
Alignment explanation
Indices: 2726637--2726669 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
2726627 AACGGTCAAC
2726637 GGTCG GGTCG GGTCG GGTC- GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
2726670 AGACCGGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.21, G:0.58, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:2726659 original size:14 final size:15
Alignment explanation
Indices: 2726637--2726669 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2726627 AACGGTCAAC
2726637 GGTCGGGTCGGGTCG
1 GGTCGGGTCGGGTCG
2726652 GGTC-GGTCGGGTCG
1 GGTCGGGTCGGGTCG
2726666 GGTC
1 GGTC
2726670 AGACCGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.00, C:0.21, G:0.58, T:0.21
Consensus pattern (15 bp):
GGTCGGGTCGGGTCG
Found at i:2726661 original size:9 final size:9
Alignment explanation
Indices: 2726636--2726666 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2726626 CAACGGTCAA
2726636 CGGTCGGGT
1 CGGTCGGGT
2726645 CGGGTCGGGT
1 C-GGTCGGGT
2726655 CGGTCGGGT
1 CGGTCGGGT
2726664 CGG
1 CGG
2726667 GTCAGACCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.00, C:0.23, G:0.58, T:0.19
Consensus pattern (9 bp):
CGGTCGGGT
Found at i:2726677 original size:19 final size:19
Alignment explanation
Indices: 2726636--2726678 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2726626 CAACGGTCAA
* **
2726636 CGGTCGGGTCGGGTCGGGT
1 CGGTCGGGTCGGGTCAGAC
2726655 CGGTCGGGTCGGGTCAGAC
1 CGGTCGGGTCGGGTCAGAC
2726674 CGGTC
1 CGGTC
2726679 AAACCGGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.05, C:0.26, G:0.51, T:0.19
Consensus pattern (19 bp):
CGGTCGGGTCGGGTCAGAC
Found at i:2726690 original size:19 final size:19
Alignment explanation
Indices: 2726668--2726746 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
2726658 TCGGGTCGGG
2726668 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
2726687 TCAGACCGATCAAACCAGT
1 TCAGACCGGTCAAACCGGT
2726706 TC-GAACCGGTCAGAACCGGT
1 TCAG-ACCGGTCA-AACCGGT
* *
2726726 TAAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
2726746 T
1 T
2726747 TCCAGCCCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
18 1 0.02
19 26 0.52
20 15 0.30
21 8 0.16
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2726743 original size:9 final size:9
Alignment explanation
Indices: 2726666--2726745 Score: 61
Period size: 9 Copynumber: 8.3 Consensus size: 9
2726656 GGTCGGGTCG
*
2726666 GGTCAGACC
1 GGTCAAACC
2726675 GGTCAAACC
1 GGTCAAACC
*
2726684 GGTTCAGACC
1 GG-TCAAACC
*
2726694 GATCAAACC
1 GGTCAAACC
* *
2726703 AGTTCGAACC
1 -GGTCAAACC
2726713 GGTCAGAACC
1 GGTCA-AACC
*
2726723 GGTTAAAAACC
1 GG-T-CAAACC
2726734 GGTCAAACC
1 GGTCAAACC
2726743 GGT
1 GGT
2726746 TTCCAGCCCT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
9 27 0.48
10 21 0.38
11 7 0.12
12 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Done.