Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007963.1 Hibiscus syriacus cultivar Beakdansim tig00110392_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: 1627826
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:840455 original size:17 final size:18
Alignment explanation
Indices: 840438--840503 Score: 78
Period size: 18 Copynumber: 3.5 Consensus size: 18
840428 GCTATGTATA
840438 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* **
840456 TATATTTTATATGTTTTTAT
1 TATATTTT-T-TCTTAATAT
840476 ATATATTTTTTCTTAATAT
1 -TATATTTTTTCTTAATAT
840495 TATATTTTT
1 TATATTTTT
840504 ATTTTTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 17 0.44
19 7 0.18
20 7 0.18
21 8 0.21
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:840477 original size:39 final size:37
Alignment explanation
Indices: 840434--840541 Score: 136
Period size: 39 Copynumber: 3.0 Consensus size: 37
840424 ATTTGCTATG
840434 TATATATATTTTTTCTTAATATTATATTTTATATGTTTT
1 TATATATATTTTTTCTTAATATTATATTTT-TAT-TTTT
840473 TATATATATTTTTTCTTAATATTATATTTTTA-TTTT
1 TATATATATTTTTTCTTAATATTATATTTTTATTTTT
* *
840509 TAT-T-TA-TTTAT-ATATATATTATATTTTTATTTT
1 TATATATATTTTTTCTTA-ATATTATATTTTTATTTT
840542 ATTTTTTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
32 2 0.03
33 18 0.28
34 5 0.08
35 1 0.02
36 7 0.11
38 2 0.03
39 30 0.46
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.69
Consensus pattern (37 bp):
TATATATATTTTTTCTTAATATTATATTTTTATTTTT
Found at i:840545 original size:44 final size:43
Alignment explanation
Indices: 840492--840584 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 43
840482 TTTTTCTTAA
* *
840492 TATTATATTTTTATTTT-TATTTATTTATATATAT-AT-TATATTTT
1 TATTTTATTTTT-TTTTCTATTT-TTT-TA-ATATCATGTATATCTT
840536 TATTTTATTTTTTTTTCTATTTTTTTAATATCATGTATATCTT
1 TATTTTATTTTTTTTTCTATTTTTTTAATATCATGTATATCTT
840579 TATTTT
1 TATTTT
840585 TTACTTGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
41 4 0.09
42 4 0.09
43 20 0.45
44 16 0.36
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (43 bp):
TATTTTATTTTTTTTTCTATTTTTTTAATATCATGTATATCTT
Found at i:840583 original size:43 final size:44
Alignment explanation
Indices: 840455--840584 Score: 115
Period size: 46 Copynumber: 2.9 Consensus size: 44
840445 TTTCTTAATA
* * * * * *
840455 TTATATTTTATATGTTTTTATATATATTTTTTCTTAATATTATATTT
1 TTAT-TTTTATTTATTTATATATATATTATATCTT--TATTTTATTT
*
840502 TTATTTTTATTTATTTATATATATATTATATTTTTATTTTATTT
1 TTATTTTTATTTATTTATATATATATTATATCTTTATTTTATTT
840546 TT-TTTTCTATTT-TTT-TA-ATATCATGTATATCTTTATTTT
1 TTATTTT-TATTTATTTATATATAT-AT-TATATCTTTATTTT
840585 TTACTTGTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
41 4 0.06
42 4 0.06
43 20 0.28
44 16 0.22
46 24 0.33
47 4 0.06
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (44 bp):
TTATTTTTATTTATTTATATATATATTATATCTTTATTTTATTT
Found at i:840807 original size:26 final size:26
Alignment explanation
Indices: 840749--840811 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
840739 ATTCATTTTG
840749 TTTATTT-TTATTATTTTTTACGTGT
1 TTTATTTATTATTATTTTTTACGTGT
* * *
840774 TTT-GTTATTTTTCATTTTTT-CTTGT
1 TTTATTTATTATT-ATTTTTTACGTGT
840799 TTTATTTATTATT
1 TTTATTTATTATT
840812 CTCACGTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
24 2 0.07
25 14 0.47
26 14 0.47
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.75
Consensus pattern (26 bp):
TTTATTTATTATTATTTTTTACGTGT
Found at i:844741 original size:19 final size:19
Alignment explanation
Indices: 844717--844763 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
844707 ATAAACACAA
844717 TTTCATTTATTTAAACTCG
1 TTTCATTTATTTAAACTCG
844736 TTTCATTTATTTAAACTCG
1 TTTCATTTATTTAAACTCG
844755 TTTCATTTA
1 TTTCATTTA
844764 CAACTCTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTCATTTATTTAAACTCG
Found at i:859348 original size:80 final size:80
Alignment explanation
Indices: 859205--859353 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 80
859195 ACTATTGTTA
* ** ** *
859205 AATTACATTAGGTTAATATTTATTATTAAAGTTTATATTATTTAAGATTAGATATTTTTTATATG
1 AATTACATTAGGTTAATATTTATTATTAAAGTTTATATTAATTAAGATTAGATAGCTGATATATA
859270 TTAATATATTTAAAT
66 TTAATATATTTAAAT
* *
859285 AATTACATTAGGTTAATATTTATTATTAATGTTTATATTAAATTAA-ACTTTGA-AGCTGATATA
1 AATTACATTAGGTTAATATTTATTATTAAAGTTTATATT-AATTAAGA-TTAGATAGCTGATATA
859348 TATTAA
64 TATTAA
859354 AGGGGAAACG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
80 50 0.85
81 9 0.15
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.50
Consensus pattern (80 bp):
AATTACATTAGGTTAATATTTATTATTAAAGTTTATATTAATTAAGATTAGATAGCTGATATATA
TTAATATATTTAAAT
Found at i:865385 original size:25 final size:25
Alignment explanation
Indices: 865336--865409 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
865326 AATACAAGTG
* *
865336 AGAAAAAAATAAAGGCTTAGAAAAGCC
1 AGAATAAAA-AAA-GCTTAGCAAAGCC
*
865363 AGAATAAAAAAAGCTTAGCAAAGCT
1 AGAATAAAAAAAGCTTAGCAAAGCC
* * *
865388 AGAATGAGAATAGCTTAGCAAA
1 AGAATAAAAAAAGCTTAGCAAA
865410 CATATGAGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 30 0.73
26 3 0.07
27 8 0.20
ACGTcount: A:0.55, C:0.11, G:0.19, T:0.15
Consensus pattern (25 bp):
AGAATAAAAAAAGCTTAGCAAAGCC
Found at i:866575 original size:36 final size:36
Alignment explanation
Indices: 866532--866603 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
866522 AAAAACAAAA
866532 AAAAATTAGTTGATTAAATGGATTTAAATGTCTAAT
1 AAAAATTAGTTGATTAAATGGATTTAAATGTCTAAT
866568 AAAAATTAGTTGATTAAATGGATTTAAATGTCTAAT
1 AAAAATTAGTTGATTAAATGGATTTAAATGTCTAAT
866604 TGATAATCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (36 bp):
AAAAATTAGTTGATTAAATGGATTTAAATGTCTAAT
Found at i:877669 original size:17 final size:17
Alignment explanation
Indices: 877647--877681 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
877637 GAGGTGAAAA
877647 ACATATACTTATTTAGT
1 ACATATACTTATTTAGT
877664 ACATATACTTATTTAGT
1 ACATATACTTATTTAGT
877681 A
1 A
877682 GTAAGAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (17 bp):
ACATATACTTATTTAGT
Found at i:887192 original size:2 final size:2
Alignment explanation
Indices: 887187--887230 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
887177 ACACACATAC
* * *
887187 AT AT AT AT A- AT AT AT AT AC AC AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
887228 AT A
1 AT A
887231 CACAGTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:887715 original size:20 final size:20
Alignment explanation
Indices: 887621--887989 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
887611 GATTTTCCAT
* ** *
887621 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
887641 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
887661 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
887681 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
887701 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
887721 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
887741 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
887761 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
887781 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
887801 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
887821 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
887841 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
887861 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
887881 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
887901 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
887921 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
887941 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
887961 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
887981 AATCACAAC
1 AATCGCAAC
887990 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:888820 original size:19 final size:19
Alignment explanation
Indices: 888798--889066 Score: 300
Period size: 19 Copynumber: 15.4 Consensus size: 19
888788 CGGAAAATAC
*
888798 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
888817 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
888831 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
888851 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
888865 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
888884 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
888903 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
888917 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
888936 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
888955 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
888974 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
888988 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
889007 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
889026 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
889040 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
889059 AATCGCAA
1 AATCGCAA
889067 CGAAAGAATC
Statistics
Matches: 214, Mismatches: 10, Indels: 52
0.78 0.04 0.19
Matches are distributed among these distances:
14 48 0.22
15 2 0.01
16 16 0.07
17 14 0.07
18 3 0.01
19 118 0.55
20 13 0.06
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:888913 original size:52 final size:51
Alignment explanation
Indices: 888826--889078 Score: 293
Period size: 52 Copynumber: 4.9 Consensus size: 51
888816 AAATCCCAAC
888826 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAAT-CGAA
888879 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT-CGAA
* * * *
888931 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAATCGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATCGAA
* * *
888981 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA-CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATCGAA
*
889038 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGC
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGC
889079 GTTGCGATTT
Statistics
Matches: 177, Mismatches: 13, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
47 7 0.04
48 1 0.01
50 9 0.05
51 7 0.04
52 123 0.69
53 16 0.09
54 1 0.01
56 1 0.01
57 6 0.03
58 5 0.03
59 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (51 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATCGAA
Found at i:888949 original size:71 final size:71
Alignment explanation
Indices: 888865--889033 Score: 320
Period size: 71 Copynumber: 2.4 Consensus size: 71
888855 GCAACGAGAG
*
888865 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGA
888930 AATGAA
66 AATGAA
888936 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGA
*
889001 AATTAA
66 AATGAA
889007 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
889034 CGAAAGAATC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 96 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGA
AATGAA
Found at i:889045 original size:14 final size:14
Alignment explanation
Indices: 889026--889078 Score: 61
Period size: 14 Copynumber: 3.4 Consensus size: 14
889016 GCGAAATGAA
889026 AATCGCAACGAAAG
1 AATCGCAACGAAAG
889040 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
889057 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
889073 AATCGC
1 AATCGC
889079 GTTGCGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 14 0.41
16 6 0.18
17 6 0.18
19 8 0.24
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:889085 original size:33 final size:33
Alignment explanation
Indices: 888798--889078 Score: 217
Period size: 33 Copynumber: 8.2 Consensus size: 33
888788 CGGAAAATAC
* *
888798 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AAG
*
888831 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAAAG
888865 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
*
888901 AAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATG
1 --AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
888934 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 --AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
* *
888972 AAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 --AATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AG
889007 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
889040 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
889073 AATCGC
1 AATCGC
889079 GTTGCGATTT
Statistics
Matches: 217, Mismatches: 10, Indels: 42
0.81 0.04 0.16
Matches are distributed among these distances:
33 116 0.53
34 30 0.14
35 14 0.06
36 11 0.05
37 1 0.00
38 45 0.21
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:889101 original size:20 final size:20
Alignment explanation
Indices: 889076--889268 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
889066 ACGAAAGAAT
889076 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
889096 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
889118 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
889137 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
889157 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
889177 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
889197 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
889217 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
889237 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
889257 CGCGTTGCGATT
1 CGCGTTGCGATT
889269 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:889263 original size:60 final size:60
Alignment explanation
Indices: 889076--889268 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
889066 ACGAAAGAAT
**
889076 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
889137 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
889197 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
889257 CGCGTTGCGATT
1 CGCGTTGCGATT
889269 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:889349 original size:20 final size:20
Alignment explanation
Indices: 889324--889375 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
889314 AAGAATCGCG
*
889324 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
889344 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
889364 TTGCGATTCTGG
1 TTGCGATTCTGG
889376 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:891029 original size:34 final size:34
Alignment explanation
Indices: 890981--891080 Score: 155
Period size: 34 Copynumber: 2.9 Consensus size: 34
890971 ATAAGTGAGC
* *
890981 ACTTTCACCTCAAACCATCTTAATATCCTATGTT
1 ACTTCCACCTCAAACCATCTTAATACCCTATGTT
891015 ACTTCCACCTCAAACCATCTTAATACCCTATGTT
1 ACTTCCACCTCAAACCATCTTAATACCCTATGTT
* *
891049 AATTCCACCTCAAAACTATCTTAATACCCTAT
1 ACTTCCACCTC-AAACCATCTTAATACCCTAT
891081 ATACTCGGAG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 42 0.69
35 19 0.31
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (34 bp):
ACTTCCACCTCAAACCATCTTAATACCCTATGTT
Found at i:891192 original size:2 final size:2
Alignment explanation
Indices: 891185--891209 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
891175 CCACCAAGAA
891185 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
891210 AGGGATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:897862 original size:50 final size:49
Alignment explanation
Indices: 897808--898000 Score: 151
Period size: 49 Copynumber: 3.8 Consensus size: 49
897798 GCACCTAGCT
* * *
897808 GCAACAAGTACAGCCAGACAGGAATCAACAAGGATTCCCCAGACCATACA
1 GCAACAAGAACAACCAAACAGGAATCAACAAGGATTCCCCAGACCA-ACA
*
897858 GCAAC-AGCAA-AACCAAACTA-GAATCAACAAAGAATTCCCCAGGCAGACCAACA
1 GCAACAAG-AACAACCAAAC-AGGAATCAAC-AAGGATT-CCC---CAGACCAACA
* * * * * *
897911 ACAACAAAAACATCCAAACAGGAACCAACAGGGATTCCCCAGACAAACCA
1 GCAACAAGAACAACCAAACAGGAATCAACAAGGATTCCCCAGACCAA-CA
*
897961 GCAACAACAGATCAACCAAACA-GAATCAACAAAGGATTCC
1 GCAAC-A-AGAACAACCAAACAGGAATCAAC-AAGGATTCC
898001 TCAATCATTA
Statistics
Matches: 112, Mismatches: 17, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
49 23 0.21
50 19 0.17
51 11 0.10
52 22 0.20
53 15 0.13
54 22 0.20
ACGTcount: A:0.48, C:0.30, G:0.14, T:0.08
Consensus pattern (49 bp):
GCAACAAGAACAACCAAACAGGAATCAACAAGGATTCCCCAGACCAACA
Found at i:897966 original size:53 final size:50
Alignment explanation
Indices: 897825--898000 Score: 162
Period size: 53 Copynumber: 3.4 Consensus size: 50
897815 GTACAGCCAG
* *
897825 ACAGGAATCAACAAGGATTCCCCAGACCATA-CAGCAACAGC-AAAACCAA
1 ACAGGAATCAACAAGGATTCCCCAGA-CAAACCAGCAACAACAAAAACCAA
* * * *
897874 ACTA-GAATCAACAAAGAATTCCCCAGGCAGACCAACAACAACAAAAACATCCAA
1 AC-AGGAATCAAC-AAGGATTCCCCAGACAAACCAGCAACAAC-AAAA-A-CCAA
* * *
897928 ACAGGAACCAACAGGGATTCCCCAGACAAACCAGCAACAACAGATCAACCAA
1 ACAGGAATCAACAAGGATTCCCCAGACAAACCAGCAACAACA-A-AAACCAA
897980 ACA-GAATCAACAAAGGATTCC
1 ACAGGAATCAAC-AAGGATTCC
898001 TCAATCATTA
Statistics
Matches: 102, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
49 13 0.13
50 21 0.21
51 7 0.07
52 19 0.19
53 28 0.27
54 14 0.14
ACGTcount: A:0.48, C:0.30, G:0.13, T:0.09
Consensus pattern (50 bp):
ACAGGAATCAACAAGGATTCCCCAGACAAACCAGCAACAACAAAAACCAA
Found at i:904606 original size:162 final size:160
Alignment explanation
Indices: 904339--904639 Score: 397
Period size: 162 Copynumber: 1.9 Consensus size: 160
904329 CACATACTCA
* *
904339 ACCTAAATCCAAAAACGGGACAAACATCTTCTTTATCCATCTTAAATCTGAAATACATGACATGC
1 ACCTAAAACCAAAAACGGGACAAACATCTTCTTTATCCATCTTAAAGCTGAAATACATGACATGC
* ** * * *
904404 AAAGTATCACTTGATAATCAAAGGTTCTCATCTATTTATTTGGAATTTTATAACATGCATCTATT
66 AAAGTATCACTTGATAATAAAACCTTCTCATCAATTTATTTAGAA-TTTATAACATGC-CCTATT
*
904469 TCACTAGAAACATAATCTTCAACACATATTTG
129 TCACAAGAAACATAATCTTCAACACATATTTG
* ***
904501 ACCTAAAACCAAAATCGGGACAAGTTTCTTCTTTATCCATCTTAAGAGCTGAAATACA-GACATG
1 ACCTAAAACCAAAAACGGGACAAACATCTTCTTTATCCATCTTAA-AGCTGAAATACATGACATG
* * * * * *
904565 CAAAGTATTATTTGCTCATAAAACCTTCTCATCAATTTATTTAGAATTTATGATATGCCCTATTT
65 CAAAGTATCACTTGATAATAAAACCTTCTCATCAATTTATTTAGAATTTATAACATGCCCTATTT
904630 CACAAGAAAC
130 CACAAGAAAC
904640 GTAAATCAAT
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
160 15 0.13
161 10 0.08
162 83 0.70
163 11 0.09
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (160 bp):
ACCTAAAACCAAAAACGGGACAAACATCTTCTTTATCCATCTTAAAGCTGAAATACATGACATGC
AAAGTATCACTTGATAATAAAACCTTCTCATCAATTTATTTAGAATTTATAACATGCCCTATTTC
ACAAGAAACATAATCTTCAACACATATTTG
Found at i:907752 original size:15 final size:16
Alignment explanation
Indices: 907732--907770 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
907722 TTTTATTTCA
907732 GAATGATT-AAACGTT
1 GAATGATTCAAACGTT
*
907747 GAATGATTCAAATGTT
1 GAATGATTCAAACGTT
907763 GAATGATT
1 GAATGATT
907771 TAGAGACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (16 bp):
GAATGATTCAAACGTT
Found at i:915298 original size:30 final size:30
Alignment explanation
Indices: 915264--915329 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
915254 TTTCAAAACC
*
915264 ATACCTAAAGTTAGTTTTTATTTCATTTTA
1 ATACCCAAAGTTAGTTTTTATTTCATTTTA
** *
915294 ATACCCAACTTTAGTTTTTGTTTCATTTTA
1 ATACCCAAAGTTAGTTTTTATTTCATTTTA
*
915324 GTACCC
1 ATACCC
915330 TCATTCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.50
Consensus pattern (30 bp):
ATACCCAAAGTTAGTTTTTATTTCATTTTA
Found at i:915883 original size:20 final size:21
Alignment explanation
Indices: 915839--915883 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
915829 ATATTGAAAG
* *
915839 TTTAAGTACTAAAATAGATAG
1 TTTAAGTACTAAAATACATAA
*
915860 TTTAGGTACT-AAATACATAA
1 TTTAAGTACTAAAATACATAA
915880 TTTA
1 TTTA
915884 TCCTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (21 bp):
TTTAAGTACTAAAATACATAA
Found at i:920014 original size:2 final size:2
Alignment explanation
Indices: 920007--920033 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
919997 ACCCCCTAAA
920007 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
920034 AATCAAGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:921879 original size:14 final size:15
Alignment explanation
Indices: 921848--921880 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
921838 TCCCCTCTAT
*
921848 TTTAATATTTTGTAA
1 TTTAATATTTTATAA
921863 TTTAATA-TTTATAA
1 TTTAATATTTTATAA
921877 TTTA
1 TTTA
921881 TCAAAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTAATATTTTATAA
Found at i:922269 original size:43 final size:42
Alignment explanation
Indices: 922237--922382 Score: 186
Period size: 43 Copynumber: 3.4 Consensus size: 42
922227 AATTTGCAGT
* *
922237 GTTTGTTCCAAAAACGCCGCTATAGATATCGACCTTTTTCGGC
1 GTTTGTTCCAAAAACACCGCTATAGATATCGACCTTTTGC-GC
* * *
922280 GTTTGTTCTAAAAATATCGCTATAGATATCGACCTTTTGCGAC
1 GTTTGTTCCAAAAACACCGCTATAGATATCGACCTTTTGCG-C
*
922323 GTTTGTTCCAAAAACACCGCAATAGATATCGACCTTTTGCGAC
1 GTTTGTTCCAAAAACACCGCTATAGATATCGACCTTTTGCG-C
* *
922366 -ATTGTTCTAAAAACACC
1 GTTTGTTCCAAAAACACC
922383 AAGATAGATC
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
42 16 0.18
43 75 0.82
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
GTTTGTTCCAAAAACACCGCTATAGATATCGACCTTTTGCGC
Found at i:923298 original size:39 final size:39
Alignment explanation
Indices: 923244--923759 Score: 438
Period size: 39 Copynumber: 13.6 Consensus size: 39
923234 ACTCTATCGG
* *
923244 CTCACTCGCCCGGGCACCATGGCCCATCCCCTTCACCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* * * * *
923283 CTCACTCTTCCGGGCACCATGGCTCAGCTCATTCCCCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* * * * * *
923322 CTCACTCTCCCGGGCACCTTGGTTTATCTCCTTCTCCAA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* * *
923361 GTCATTCTCCCGGACACCATGGCTCATCCCCTTCACCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
*
923400 CTCACTCTCTCGGGCACCATGGCTCATCCCCTTCACCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* * * *
923439 CTCACTCTCTCGGGCACCATGGCTCAGCTCATTC-CCTGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACC-GA
923478 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* * *
923517 CTCTCTCTCCCGAGCACCATGACTCATCCCCTTC-CCTGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACC-GA
* ** *
923556 GTCACTCTCCTAGGCACCATGG--C-T----TTCCCCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
*
923588 GTCACTC-CCCTGGGCACCATGG--C-T----TTC-CGCGA
1 CTCACTCTCCC-GGGCACCATGGCTCATCCCCTTCAC-CGA
* * *
923620 GTCACTCTCCCGGGCACCATGGCTCATCTCCTTCCCCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* * ** * * *
923659 GTCATTCTCCCATGAATCATGGCTCGTCCCCTTCACCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* * * * ** *
923698 CTCACTCTCTCGGGAACCATGACTCAACTTCTTCCCCGA
1 CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
* *
923737 GTCACTCTCCCGGGAACCATGGC
1 CTCACTCTCCCGGGCACCATGGC
923760 CATGTTGCCA
Statistics
Matches: 393, Mismatches: 69, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
31 3 0.01
32 48 0.12
33 5 0.01
34 1 0.00
35 1 0.00
36 1 0.00
37 1 0.00
38 4 0.01
39 326 0.83
40 3 0.01
ACGTcount: A:0.16, C:0.44, G:0.17, T:0.24
Consensus pattern (39 bp):
CTCACTCTCCCGGGCACCATGGCTCATCCCCTTCACCGA
Found at i:923590 original size:32 final size:32
Alignment explanation
Indices: 923548--923643 Score: 147
Period size: 32 Copynumber: 3.0 Consensus size: 32
923538 ACTCATCCCC
* *
923548 TTCCCTGAGTCACTCTCCTAGGCACCATGGCT
1 TTCCCCGAGTCACTCTCCTGGGCACCATGGCT
*
923580 TTCCCCGAGTCACTCCCCTGGGCACCATGGCT
1 TTCCCCGAGTCACTCTCCTGGGCACCATGGCT
* *
923612 TTCCGCGAGTCACTCTCCCGGGCACCATGGCT
1 TTCCCCGAGTCACTCTCCTGGGCACCATGGCT
923644 CATCTCCTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.14, C:0.41, G:0.22, T:0.24
Consensus pattern (32 bp):
TTCCCCGAGTCACTCTCCTGGGCACCATGGCT
Found at i:924905 original size:18 final size:18
Alignment explanation
Indices: 924882--924987 Score: 131
Period size: 18 Copynumber: 5.9 Consensus size: 18
924872 GCGTAGAATT
* *
924882 TGTCCCGTAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
924900 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
924918 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
*
924936 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
924954 TTTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
924972 TGCCCCAAAAGACCAC
1 TGTCCCGAAGGACCAC
924988 GTAGACCCTC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 75 1.00
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:924986 original size:36 final size:36
Alignment explanation
Indices: 924882--924973 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
924872 GCGTAGAATT
* *
924882 TGTCCCGTAGGACCACTGTGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCATTA
*
924918 TGTCCCGAAGGATCACTATGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCATTA
*
924954 TTTCCCGAAGGACCACTATG
1 TGTCCCGAAGGACCACTATG
924974 CCCCAAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (36 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCATTA
Found at i:930828 original size:188 final size:191
Alignment explanation
Indices: 930457--931036 Score: 525
Period size: 188 Copynumber: 3.1 Consensus size: 191
930447 GGGTGTTACA
* * * * *
930457 GTTATGAATATCTATAAGAAATTATG-TTGCGCCCAAGAATATTTTCG-GTTGCTAAGAAAGTAG
1 GTTATGAATATCTATAA-AAATTA-GATTGCACCCAATAATATTAT-GAGTCGC-AAGAAAGTAA
* * * * * *** *
930520 GTTACGATATGGAATGTTAATTTTATGTGTAATAAAT--T-TGGTTGA--G-CCTAAAATGTTAC
62 GTTACAATCTGAAATGCTAATTTGATGTGTAATAAATAATAAATTTGATTGTACTAAAATGTTAC
* * * * * * *
930579 CAGAGTTTAAGCTGATGAGGCCATAGACAATATCACGATAACAAAATAAGTTAACATCTAAAAAT
127 CATAGTTTAAGCTGACGAGACCTTAGACAATCTCATGATAACAAAATAAGTTAAAATCTAAAAAT
*** * *
930644 GTTATGAATATCTATAAGAAATTAGATTGTGTCCAATAATGTTATCGA-TCGC-A-AAA-TAGGT
1 GTTATGAATATCTATAA-AAATTAGATTGCACCCAATAATATTAT-GAGTCGCAAGAAAGTAAGT
* * *
930705 TGCGATCTGAAATGCTAATTTTATGTGTAATAAATAATAAATTTGATTGTACTAAAATGTTACCA
64 TACAATCTGAAATGCTAATTTGATGTGTAATAAATAATAAATTTGATTGTACTAAAATGTTACCA
* * *
930770 TAGTTTAAGTTGA-GCGACCTTAGACAATCTCATGATAACAAAATAAATTAAAATCTAAAAAT
129 TAGTTTAAGCTGACGAGACCTTAGACAATCTCATGATAACAAAATAAGTTAAAATCTAAAAAT
* *
930832 GTTATGAATATCTATTAAAAATTAGGTTGCACCCAATAATATTATTAGTCGCTAAGAAAGTAAGT
1 GTTATGAATATCTA-TAAAAATTAGATTGCACCCAATAATATTATGAGTCGC-AAGAAAGTAAGT
* * *
930897 TACAATTTGAAATGTTAATTTGATGTGTAATAAAT--TCAA-TTGA--GT-CTAAAATGTTACCA
64 TACAATCTGAAATGCTAATTTGATGTGTAATAAATAATAAATTTGATTGTACTAAAATGTTACCA
* * * * * *
930956 TAATTTTAAGCTGACGAGACCTTAGATATTCTCATGGA-AACTAAATATGTTAAAAGCTAAAAAT
129 T-AGTTTAAGCTGACGAGACCTTAGACAATCTCAT-GATAACAAAATAAGTTAAAATCTAAAAAT
* *
931020 GTTATAAATATATATAA
1 GTTATGAATATCTATAA
931037 TTAATTTGGT
Statistics
Matches: 329, Mismatches: 47, Indels: 34
0.80 0.11 0.08
Matches are distributed among these distances:
183 36 0.11
184 3 0.01
185 2 0.01
186 20 0.06
187 59 0.18
188 134 0.41
189 34 0.10
190 4 0.01
191 3 0.01
192 34 0.10
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (191 bp):
GTTATGAATATCTATAAAAATTAGATTGCACCCAATAATATTATGAGTCGCAAGAAAGTAAGTTA
CAATCTGAAATGCTAATTTGATGTGTAATAAATAATAAATTTGATTGTACTAAAATGTTACCATA
GTTTAAGCTGACGAGACCTTAGACAATCTCATGATAACAAAATAAGTTAAAATCTAAAAAT
Found at i:931822 original size:61 final size:61
Alignment explanation
Indices: 931748--931871 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
931738 ATTGATACTT
931748 AACATTTGTATTTATTCTATTTATAACCTCTTAAATGTAAAATATTTACACAAAAACAAAC
1 AACATTTGTATTTATTCTATTTATAACCTCTTAAATGTAAAATATTTACACAAAAACAAAC
*
931809 AACATTTGTATTTATTCTATTTATAACCTCTTAAATGTAAAATATTTACACAAAGACAAAC
1 AACATTTGTATTTATTCTATTTATAACCTCTTAAATGTAAAATATTTACACAAAAACAAAC
931870 AA
1 AA
931872 AGCCGACATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (61 bp):
AACATTTGTATTTATTCTATTTATAACCTCTTAAATGTAAAATATTTACACAAAAACAAAC
Found at i:936540 original size:41 final size:41
Alignment explanation
Indices: 936465--936568 Score: 185
Period size: 41 Copynumber: 2.6 Consensus size: 41
936455 TATTAGAGGT
936465 TTCAGCTCGCGGTATTGC--TTTTTTTTCTTCCCATTATTA
1 TTCAGCTCGCGGTATTGCTTTTTTTTTTCTTCCCATTATTA
936504 TTCAGCTCGCGGTATTGCTTTTTTTTTTCTTCCCATTATTA
1 TTCAGCTCGCGGTATTGCTTTTTTTTTTCTTCCCATTATTA
*
936545 TTCAGCTCGCTGTATTGCTTTTTT
1 TTCAGCTCGCGGTATTGCTTTTTT
936569 ATCCATTGTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
39 18 0.29
41 44 0.71
ACGTcount: A:0.12, C:0.22, G:0.13, T:0.53
Consensus pattern (41 bp):
TTCAGCTCGCGGTATTGCTTTTTTTTTTCTTCCCATTATTA
Found at i:943507 original size:32 final size:32
Alignment explanation
Indices: 943471--943542 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
943461 AAATGACGTT
*
943471 TTTATGAAATAAAGTGATAAATCATTGAAAAA
1 TTTATGAAATAAAGTGATAAATCAATGAAAAA
* *
943503 TTTATGAAATAAAGTGATATATCAATGAAAAG
1 TTTATGAAATAAAGTGATAAATCAATGAAAAA
943535 TTTATGAA
1 TTTATGAA
943543 GTGAAGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (32 bp):
TTTATGAAATAAAGTGATAAATCAATGAAAAA
Found at i:943676 original size:32 final size:32
Alignment explanation
Indices: 943640--943713 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
943630 CTCGTTTTTT
943640 AAAAGTTTTTGAAATGAAATGGTATATCATTG
1 AAAAGTTTTTGAAATGAAATGGTATATCATTG
* *
943672 AAAAGTTTTTGAAATGAAGTGGTATATCGTTG
1 AAAAGTTTTTGAAATGAAATGGTATATCATTG
*
943704 GAAAGTTTTT
1 AAAAGTTTTT
943714 ATGAAATTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (32 bp):
AAAAGTTTTTGAAATGAAATGGTATATCATTG
Found at i:952412 original size:15 final size:16
Alignment explanation
Indices: 952392--952422 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
952382 TATTTGTATA
952392 GTATTACT-AATAATT
1 GTATTACTAAATAATT
952407 GTATTACTAAATAATT
1 GTATTACTAAATAATT
952423 TTTTATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
GTATTACTAAATAATT
Found at i:960879 original size:21 final size:22
Alignment explanation
Indices: 960829--960881 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
960819 CAGGGCATTG
*
960829 CTTTAT-TTTTTTTATATTCGAA
1 CTTTATATATTTTTATATTC-AA
960851 -TTTA-ATATTTTTATATT-AA
1 CTTTATATATTTTTATATTCAA
960870 CTTTATATATTT
1 CTTTATATATTT
960882 ATAAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.07
20 4 0.15
21 21 0.78
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (22 bp):
CTTTATATATTTTTATATTCAA
Found at i:963551 original size:16 final size:16
Alignment explanation
Indices: 963530--963562 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
963520 CACATTTATC
963530 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
963546 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
963562 A
1 A
963563 AAACCACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:965433 original size:24 final size:24
Alignment explanation
Indices: 965406--965454 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
965396 CAAAACACAA
*
965406 TAATTT-GAAAATTAACATTTTTTT
1 TAATTTCGAAAA-TAAAATTTTTTT
965430 TAATTTCGAAAATAAAATTTTTTT
1 TAATTTCGAAAATAAAATTTTTTT
965454 T
1 T
965455 GGAAAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATTTCGAAAATAAAATTTTTTT
Found at i:965662 original size:20 final size:20
Alignment explanation
Indices: 965625--965663 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
965615 AGATTGAGTG
* * *
965625 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
965645 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
965664 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:965892 original size:20 final size:20
Alignment explanation
Indices: 965863--965900 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
965853 CCCCTTCAAA
*
965863 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
965883 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
965901 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:971729 original size:25 final size:25
Alignment explanation
Indices: 971701--971750 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
971691 AAAATGTTTT
971701 CAACACAAATGTACAAACATACATA
1 CAACACAAATGTACAAACATACATA
971726 CAACACAAATGTACAAACATACATA
1 CAACACAAATGTACAAACATACATA
971751 TAAAATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.04, T:0.16
Consensus pattern (25 bp):
CAACACAAATGTACAAACATACATA
Found at i:974294 original size:83 final size:82
Alignment explanation
Indices: 974135--974364 Score: 290
Period size: 83 Copynumber: 2.8 Consensus size: 82
974125 GAGTTTTAGT
*
974135 CCAACTAAAACTCTTTTAATATCT-AA---AAATAGATAATAATATCTTTTAAATTTAAAATATT
1 CCAACTAAAACTCTTTTAATATCTAAATTTAAATACATAATAATATCTTTTAAATTT-AAATATT
** * *
974196 AAATGTGAGAGTTTTACA
65 AAACCTAAGAATTTTACA
* * * *
974214 CTAACTAAAACTCTTTTAATATTTAAATTTAAACACATTATAATATCTTTTAAATTTATAATATT
1 CCAACTAAAACTCTTTTAATATCTAAATTTAAATACATAATAATATCTTTTAAATTTA-AATATT
*
974279 AAACCTAAGAATTTTACT
65 AAACCTAAGAATTTTACA
* *
974297 CCAACCAAAACTCTTTTAATATCTAAATTTAAATATATAATAATAT-TGTTTAAATTTAAATATT
1 CCAACTAAAACTCTTTTAATATCTAAATTTAAATACATAATAATATCT-TTTAAATTTAAATATT
974361 AAAC
65 AAAC
974365 ATATATTTCC
Statistics
Matches: 129, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
79 22 0.17
80 2 0.02
82 12 0.09
83 93 0.72
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.40
Consensus pattern (82 bp):
CCAACTAAAACTCTTTTAATATCTAAATTTAAATACATAATAATATCTTTTAAATTTAAATATTA
AACCTAAGAATTTTACA
Found at i:976336 original size:35 final size:36
Alignment explanation
Indices: 976276--976345 Score: 115
Period size: 38 Copynumber: 1.9 Consensus size: 36
976266 TGAAGGTGAA
976276 ATAAAATAATAAAATTTTGCCATTAAAATATAAAAACT
1 ATAAAATAATAAAATTTT--CATTAAAATATAAAAACT
976314 ATAAAATAATAAAATTTT-ATTAAAATATAAAA
1 ATAAAATAATAAAATTTTCATTAAAATATAAAA
976346 TAATAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 14 0.44
38 18 0.56
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (36 bp):
ATAAAATAATAAAATTTTCATTAAAATATAAAAACT
Found at i:976344 original size:26 final size:27
Alignment explanation
Indices: 976308--976384 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 27
976298 TTAAAATATA
976308 AAAACTATAAAATAATAAAATTTT-ATT
1 AAAA-TATAAAATAATAAAATTTTCATT
976335 AAAATATAAAATAATAAAATTTTGCCATT
1 AAAATATAAAATAATAAAATTTT--CATT
976364 AAAATAATAAAATAATAAAAT
1 AAAAT-ATAAAATAATAAAAT
976385 GACACGTGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
26 19 0.41
27 4 0.09
29 8 0.17
30 15 0.33
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (27 bp):
AAAATATAAAATAATAAAATTTTCATT
Found at i:977181 original size:17 final size:17
Alignment explanation
Indices: 977147--977200 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
977137 ATCGGACAAA
* *
977147 TTTATTATTTTAGAGAG
1 TTTATTAATTTAAAGAG
**
977164 TTTATTAATTTACCGAG
1 TTTATTAATTTAAAGAG
977181 --TATTAATTTAAAGAG
1 TTTATTAATTTAAAGAG
977196 TTTAT
1 TTTAT
977201 ATTGTATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTAAAGAG
Found at i:984463 original size:114 final size:114
Alignment explanation
Indices: 984259--984492 Score: 414
Period size: 114 Copynumber: 2.1 Consensus size: 114
984249 GCGTGTTAAT
*
984259 AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAGCAGAAACGAAAATCTTCCTGC
1 AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAGCAGAAACAAAAATCTTCCTGC
* * * *
984324 TACAAGAATTAGTCTTCCTGTTCCTCGCAAGGGACTGAATTCGGTGTTA
66 TACAAGAATTACTCTTCCTGCTCCTCCCAAGGGACTGAATTCGGTATTA
*
984373 AGTTCTGATAATTCGTTTGAGGAAAGGACCATTCAAGCATCTAGCAGAAACAAAAATCTTCCTGC
1 AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAGCAGAAACAAAAATCTTCCTGC
984438 TACAAGAATTACTCTTCCTGCTCCTCCCAAGGGACTGAATTCGGTATTA
66 TACAAGAATTACTCTTCCTGCTCCTCCCAAGGGACTGAATTCGGTATTA
984487 AGTTCT
1 AGTTCT
984493 TTTTCTGGTG
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (114 bp):
AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAGCAGAAACAAAAATCTTCCTGC
TACAAGAATTACTCTTCCTGCTCCTCCCAAGGGACTGAATTCGGTATTA
Found at i:985603 original size:114 final size:114
Alignment explanation
Indices: 985435--985714 Score: 337
Period size: 114 Copynumber: 2.5 Consensus size: 114
985425 CAATGCATCA
* * *
985435 TCAACAACAACTAGCATTGCTAGCACATCAACAGTCCCTTCTGATGGCTGCTGCAGCTAAATCTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAAGCTG
* ** * * *
985500 CTCCTATAAATACTCAACA-GTCACCATCCAACGGCGCAATCATACCCTC
66 CTCCTAGAAATACTCAACATG-CACCATCCAACACCACAAGCATACCCAC
* * * * * *
985549 TCAACAACAGCTAGCTTTGCTAGCACAGCAACAATCTCTTCTCATAGCTGCTGCAGCTAAAGGTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAAGCTG
* * * * * * *
985614 CTCCTGGAAATTCTCAGCATGCTCCGTCTACCACCACAAGCATACCCAC
66 CTCCTAGAAATACTCAACATGCACCATCCAACACCACAAGCATACCCAC
*
985663 TCAACAACAACTAGCTTTGTTAGCACATCAACAGTCCCTTCTCATGGCTGCT
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCT
985715 CCTGAAAATA
Statistics
Matches: 137, Mismatches: 28, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
114 136 0.99
115 1 0.01
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (114 bp):
TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAAGCTG
CTCCTAGAAATACTCAACATGCACCATCCAACACCACAAGCATACCCAC
Found at i:990342 original size:4 final size:4
Alignment explanation
Indices: 990333--990360 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
990323 CAAGTAACCA
990333 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
990361 CCAATCAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:990623 original size:27 final size:27
Alignment explanation
Indices: 990604--990672 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
990594 CAACAGGTGT
990604 TACAGAAACCATTGCACCAATAGGAGC
1 TACAGAAACCATTGCACCAATAGGAGC
990631 TACAGAAACCATTGCACCAATAGGAGC
1 TACAGAAACCATTGCACCAATAGGAGC
990658 TACAGAAACCATTGC
1 TACAGAAACCATTGC
990673 TTGTTCTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (27 bp):
TACAGAAACCATTGCACCAATAGGAGC
Found at i:991006 original size:33 final size:33
Alignment explanation
Indices: 990969--991085 Score: 171
Period size: 33 Copynumber: 3.5 Consensus size: 33
990959 CTAATGACGA
*
990969 GGCAAGAAGCTACTCAGCGTCGACTAAGGAGGT
1 GGCAAGTAGCTACTCAGCGTCGACTAAGGAGGT
*
991002 GGCAAGTAGCTACTCAGTGTCGACTAAGGAGGT
1 GGCAAGTAGCTACTCAGCGTCGACTAAGGAGGT
* * * *
991035 GGCAAGTAGCTATTCAGGGTCGACTAAGGAAGA
1 GGCAAGTAGCTACTCAGCGTCGACTAAGGAGGT
*
991068 GGGAAGTAGCTACTCAGC
1 GGCAAGTAGCTACTCAGC
991086 ATCTGGTTCC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.18
Consensus pattern (33 bp):
GGCAAGTAGCTACTCAGCGTCGACTAAGGAGGT
Found at i:991718 original size:60 final size:58
Alignment explanation
Indices: 991625--991981 Score: 319
Period size: 57 Copynumber: 6.1 Consensus size: 58
991615 CAACTTTGGG
* * **
991625 GCAAAAAGAACAGGAGAATGTCACATTACGGGAACAATTACGACAGTGTGAGGAAAAAAT
1 GCAAAAAGAACAGGAAAATGT-ACA-TACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * * * *
991685 GCAAAAGGAACAGAAAAATGATACATTACGGGAACAATTACAACAGTACGACGCAAAGAT
1 GCAAAAAGAACAGGAAAATG-TACA-TACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * **
991745 GC-AAAAGAACTGGAAAATGT-CATACGGGAACAATTACAACGGTACGAGGGGAAAAT
1 GCAAAAAGAACAGGAAAATGTACATACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * * * * * * * *
991801 GCAGAAGGAACAGGAAAACG-CCACACGGGAACAATTACAACTGTATGAGGCAAATAT
1 GCAAAAAGAACAGGAAAATGTACATACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * * * * *
991858 TCAAAAAGAACAGGAAAATCATTCATTTCGGGAACAATTAAAACAGTACGGGGAAAAGAA-
1 GCAAAAAGAACAGGAAAAT-GTACA-TACGGGAACAATTACAACAGTACGAGGAAAA-AAT
* * * *
991918 GCAAAAAGAACTGGAAAATG-CCATACGGGAACAATTACAACAGTACGAGGCAAAGAT
1 GCAAAAAGAACAGGAAAATGTACATACGGGAACAATTACAACAGTACGAGGAAAAAAT
*
991975 GAAAAAA
1 GCAAAAA
991982 ATGGAGGAGA
Statistics
Matches: 238, Mismatches: 51, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
56 32 0.13
57 93 0.39
58 3 0.01
59 16 0.07
60 92 0.39
61 2 0.01
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.14
Consensus pattern (58 bp):
GCAAAAAGAACAGGAAAATGTACATACGGGAACAATTACAACAGTACGAGGAAAAAAT
Found at i:991981 original size:117 final size:113
Alignment explanation
Indices: 991627--991980 Score: 343
Period size: 117 Copynumber: 3.0 Consensus size: 113
991617 ACTTTGGGGC
* ** **
991627 AAAAAGAACAGGAGAATGTCACATTACGGGAACAATTACGACAGTGTGA-GGAAAAAATGCAAAA
1 AAAAAGAACAGGAAAATGT--CA-TACGGGAACAATTAAAACAGTACGAGGGAAAAAA-GCAAAA
* * * * *
991691 GGAACAGAAAAATGATACATTACGGGAACAATTACAACAGTACGACGCAAAGATG
62 AGAACAGGAAAACG--CCA-TACGGGAACAATTACAACAGTACGAGGCAAAGATG
* * * * * * * *
991746 CAAAAGAACTGGAAAATGTCATACGGGAACAATTACAACGGTACGAGGGGAAAATGCAGAAGGAA
1 AAAAAGAACAGGAAAATGTCATACGGGAACAATTAAAACAGTACGAGGGAAAAAAGCAAAAAGAA
* * * * *
991811 CAGGAAAACGCCACACGGGAACAATTACAACTGTATGAGGCAAATATTC
66 CAGGAAAACGCCATACGGGAACAATTACAACAGTACGAGGCAAAGA-TG
* *
991860 AAAAAGAACAGGAAAATCATTCATTTCGGGAACAATTAAAACAGTACG-GGGAAAAGAAGCAAAA
1 AAAAAGAACAGGAAAAT--GTCA-TACGGGAACAATTAAAACAGTACGAGGGAAAA-AAGCAAAA
* *
991924 AGAACTGGAAAATGCCATACGGGAACAATTACAACAGTACGAGGCAAAGATG
62 AGAACAGGAAAACGCCATACGGGAACAATTACAACAGTACGAGGCAAAGATG
991976 AAAAA
1 AAAAA
991981 AATGGAGGAG
Statistics
Matches: 193, Mismatches: 36, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
113 28 0.15
114 18 0.09
116 53 0.27
117 78 0.40
119 16 0.08
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.14
Consensus pattern (113 bp):
AAAAAGAACAGGAAAATGTCATACGGGAACAATTAAAACAGTACGAGGGAAAAAAGCAAAAAGAA
CAGGAAAACGCCATACGGGAACAATTACAACAGTACGAGGCAAAGATG
Found at i:993886 original size:19 final size:19
Alignment explanation
Indices: 993864--993900 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
993854 TTTATTTAAT
*
993864 TTTTTCATGTCTATTTTTA
1 TTTTTAATGTCTATTTTTA
*
993883 TTTTTAATTTCTATTTTT
1 TTTTTAATGTCTATTTTT
993901 CCCCTTGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTTTAATGTCTATTTTTA
Found at i:1004960 original size:16 final size:17
Alignment explanation
Indices: 1004936--1004971 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1004926 AATGTTAAAC
*
1004936 TATGTTCAATTT-ATGT
1 TATGATCAATTTGATGT
1004952 TATGATCAATTTGATGT
1 TATGATCAATTTGATGT
1004969 TAT
1 TAT
1004972 ATACTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.53
Consensus pattern (17 bp):
TATGATCAATTTGATGT
Found at i:1007534 original size:32 final size:36
Alignment explanation
Indices: 1007468--1007534 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
1007458 CAAAATTATT
1007468 AAATATTGACATACATTATATAAATAAATTAAATAAA
1 AAATATTGACATA-ATTATATAAATAAATTAAATAAA
1007505 AAATATTGACAT-ATTA-A-AAA-AAATTAAATA
1 AAATATTGACATAATTATATAAATAAATTAAATA
1007535 TAGGATCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 10 0.33
33 3 0.10
34 1 0.03
35 4 0.13
37 12 0.40
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (36 bp):
AAATATTGACATAATTATATAAATAAATTAAATAAA
Found at i:1009972 original size:33 final size:33
Alignment explanation
Indices: 1009930--1009996 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1009920 ACTCGGCTTT
1009930 TAAATGTTCTTCCTTCCCTATAAATAACAACCC
1 TAAATGTTCTTCCTTCCCTATAAATAACAACCC
*
1009963 TAAATGTTCTTCCTTCCTTATAAATAACAACCC
1 TAAATGTTCTTCCTTCCCTATAAATAACAACCC
1009996 T
1 T
1009997 CTTAATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (33 bp):
TAAATGTTCTTCCTTCCCTATAAATAACAACCC
Found at i:1015557 original size:23 final size:24
Alignment explanation
Indices: 1015531--1015575 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1015521 TGTATTATAG
1015531 ACTTGTA-TATCTGCTGTTCTGTC
1 ACTTGTATTATCTGCTGTTCTGTC
*
1015554 ACTTGTATTTTCTGCTGTTCTG
1 ACTTGTATTATCTGCTGTTCTG
1015576 CCTGCTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (24 bp):
ACTTGTATTATCTGCTGTTCTGTC
Found at i:1022673 original size:237 final size:240
Alignment explanation
Indices: 1022257--1022735 Score: 903
Period size: 237 Copynumber: 2.0 Consensus size: 240
1022247 CTGAAGTGCT
1022257 TTCCACCTTGTTTATCATTTAAAAAAATTTGCTTTGAGAAATATATGTGCAGGTTTGTAGGACAT
1 TTCCACCTTGTTTATCATTTAAAAAAATTTGCTTTGAGAAATATATGTGCAGGTTTGTAGGACAT
1022322 AACTACATAAGTATTTCCTTCAATATCATGCGAGGGAATAGTTCATAACTGAAAGAGCTGCAAGA
66 AACTACATAAGTATTTCCTTCAATATCATGCGAGGGAATAGTTCATAACTGAAAGAGCTGCAAGA
*
1022387 AACTTTATGTTCTTGATCAATCATGTGTTTGATTGGTGTTATTCTGTTATACTATCTTGC-ATTT
131 AACTTTATGTTCTTGATCAATCATGTGTTTGATTGGTGTTATGCTGTTATACTATCTTGCAATTT
1022451 CATTTAGTGTACGGAAAAG-A-T-TAATGTATTCAGTTTTCGATC
196 CATTTAGTGTACGGAAAAGTATTATAATGTATTCAGTTTTCGATC
1022493 TTCCACCTTGTTTATCATTTAAAAAAATTTGCTTCTGAGAAATATATGTGCAGGTTTGTAGGACA
1 TTCCACCTTGTTTATCATTTAAAAAAATTTGCTT-TGAGAAATATATGTGCAGGTTTGTAGGACA
1022558 TAACTACATAAGTATTTCCTTCAATATCATGCGAGGGAATAGTTCATAACTGAAAGAGCTGCAAG
65 TAACTACATAAGTATTTCCTTCAATATCATGCGAGGGAATAGTTCATAACTGAAAGAGCTGCAAG
1022623 AAACTTTATGTTCTTGATCAATCATGTGTTTGATTGGTGTTATGCTGTTATACTATCTTGCAATT
130 AAACTTTATGTTCTTGATCAATCATGTGTTTGATTGGTGTTATGCTGTTATACTATCTTGCAATT
1022688 TCATTTAGTGTACGGAAAAGTATTAATAATGTATTCAGTTTTCGATC
195 TCATTTAGTGTACGGAAAAGTATT-ATAATGTATTCAGTTTTCGATC
1022735 T
1 T
1022736 CGATATTCTA
Statistics
Matches: 236, Mismatches: 1, Indels: 6
0.97 0.00 0.02
Matches are distributed among these distances:
236 34 0.14
237 155 0.66
238 23 0.10
239 1 0.00
240 1 0.00
242 22 0.09
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (240 bp):
TTCCACCTTGTTTATCATTTAAAAAAATTTGCTTTGAGAAATATATGTGCAGGTTTGTAGGACAT
AACTACATAAGTATTTCCTTCAATATCATGCGAGGGAATAGTTCATAACTGAAAGAGCTGCAAGA
AACTTTATGTTCTTGATCAATCATGTGTTTGATTGGTGTTATGCTGTTATACTATCTTGCAATTT
CATTTAGTGTACGGAAAAGTATTATAATGTATTCAGTTTTCGATC
Found at i:1023982 original size:27 final size:26
Alignment explanation
Indices: 1023952--1024043 Score: 94
Period size: 27 Copynumber: 3.3 Consensus size: 26
1023942 CTCCGAGTCT
1023952 CGTGCTGCACCACCTTATCCCGATCCC
1 CGTGCTGCACCACCTT-TCCCGATCCC
* *
1023979 CGTGCTGCACCACCGCTCCTTCCTGATCCT
1 CGTGCTGCACCA-C-CT--TTCCCGATCCC
*
1024009 CATGCTGCACCACCTTCTCCCGATCCC
1 CGTGCTGCACCACCTT-TCCCGATCCC
*
1024036 TGTGCTGC
1 CGTGCTGC
1024044 CACCCGCTCC
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.02
27 26 0.49
28 3 0.06
29 3 0.06
30 19 0.36
31 1 0.02
ACGTcount: A:0.12, C:0.47, G:0.16, T:0.25
Consensus pattern (26 bp):
CGTGCTGCACCACCTTTCCCGATCCC
Found at i:1024207 original size:33 final size:30
Alignment explanation
Indices: 1023981--1024253 Score: 228
Period size: 30 Copynumber: 9.2 Consensus size: 30
1023971 CCGATCCCCG
1023981 TGCTGCACCACCG-CTCCTTCCTGATCCTCA
1 TGCTGCACCACCGCCTCC-TCCTGATCCTCA
* *
1024011 TGCTGCACCA---CCTTCTCCCGATCC-C-
1 TGCTGCACCACCGCCTCCTCCTGATCCTCA
* * * *
1024036 TG-TGCTGCCACC-CGCTCCCACCCGATCCCCA
1 TGCTGC-ACCACCGC-CT-CCTCCTGATCCTCA
* *
1024067 TGCTGCGCCACCG-CTCCCACCTGATCCTCA
1 TGCTGCACCACCGCCT-CCTCCTGATCCTCA
*
1024097 TGCCGCACCACCGCCTCCTCCTGATCCTCA
1 TGCTGCACCACCGCCTCCTCCTGATCCTCA
*
1024127 TGCTGCACCACCGCCTCCTCCTGATTCTCA
1 TGCTGCACCACCGCCTCCTCCTGATCCTCA
*
1024157 TGCTGCACCACTGCCT-C-CC-GATCCTCA
1 TGCTGCACCACCGCCTCCTCCTGATCCTCA
* *
1024184 TGCTGCACCTCCTCCTCCTCCTCCTGATCCTCA
1 TGCTGCA---CCACCGCCTCCTCCTGATCCTCA
* * * * *
1024217 TGCTGCACCATCGACTCCTGCTGTTCCTCG
1 TGCTGCACCACCGCCTCCTCCTGATCCTCA
1024247 TGCTGCA
1 TGCTGCA
1024254 TTTGTTCATT
Statistics
Matches: 202, Mismatches: 24, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.01
25 5 0.02
26 1 0.00
27 23 0.11
28 7 0.03
29 10 0.05
30 122 0.60
31 11 0.05
32 5 0.02
33 15 0.07
ACGTcount: A:0.12, C:0.49, G:0.15, T:0.24
Consensus pattern (30 bp):
TGCTGCACCACCGCCTCCTCCTGATCCTCA
Found at i:1025162 original size:2 final size:2
Alignment explanation
Indices: 1025155--1025180 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1025145 AGGCCATCCA
1025155 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
1025181 CTTTTATTGT
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:1033570 original size:34 final size:34
Alignment explanation
Indices: 1033532--1033607 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 34
1033522 TAGGCCCTTC
1033532 GGCCCTAAGATATATATTCTTAGGTAGGC-CTCAT
1 GGCCCTAAGATATATA-TCTTAGGTAGGCTCTCAT
* * *
1033566 GGCCCCAA-A-ATCTATCTTGGGTAGGCTCTCAT
1 GGCCCTAAGATATATATCTTAGGTAGGCTCTCAT
1033598 -GCCCTAAGAT
1 GGCCCTAAGAT
1033608 GTTCCCTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
31 17 0.49
32 10 0.29
33 1 0.03
34 7 0.20
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (34 bp):
GGCCCTAAGATATATATCTTAGGTAGGCTCTCAT
Found at i:1036612 original size:21 final size:21
Alignment explanation
Indices: 1036588--1036638 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1036578 TGTTTTTGGT
1036588 TTGCAAAACTTTAAGTTCGCA
1 TTGCAAAACTTTAAGTTCGCA
*
1036609 TTGCGAAACTTTAAGTTCGCA
1 TTGCAAAACTTTAAGTTCGCA
1036630 TTGCGAAAA
1 TTGC-AAAA
1036639 TAGACATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (21 bp):
TTGCAAAACTTTAAGTTCGCA
Found at i:1036750 original size:21 final size:21
Alignment explanation
Indices: 1036726--1036770 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1036716 GCGAATTTAG
*
1036726 AAATTTACGTTGCAAAAAATA
1 AAATTCACGTTGCAAAAAATA
* *
1036747 AAA-TCGCGTTGCGAAAAATA
1 AAATTCACGTTGCAAAAAATA
1036767 AAAT
1 AAAT
1036771 CGCATTGCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (21 bp):
AAATTCACGTTGCAAAAAATA
Found at i:1036779 original size:20 final size:20
Alignment explanation
Indices: 1036735--1036781 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1036725 GAAATTTACG
* *
1036735 TTGCAAAAAATAAAATCGCG
1 TTGCGAAAAATAAAATCGCA
1036755 TTGCGAAAAATAAAATCGCA
1 TTGCGAAAAATAAAATCGCA
1036775 TTGCGAA
1 TTGCGAA
1036782 TTCGAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (20 bp):
TTGCGAAAAATAAAATCGCA
Found at i:1037013 original size:28 final size:28
Alignment explanation
Indices: 1036973--1037035 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1036963 ATATAATCCA
*
1036973 CATTCCCCATTTGATTGGCTGAGAATGT
1 CATTCCCCATTTGATTGGCCGAGAATGT
**
1037001 CATTCCCTGTTTGATTGGCCGAGAATGT
1 CATTCCCCATTTGATTGGCCGAGAATGT
1037029 CATTCCC
1 CATTCCC
1037036 GGGAATCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (28 bp):
CATTCCCCATTTGATTGGCCGAGAATGT
Found at i:1037251 original size:36 final size:36
Alignment explanation
Indices: 1037204--1037298 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
1037194 CAAAAGTTTG
* * * *
1037204 TTCCGATTCAAGTCGAACGGAGGGAAGCATCTGCAT
1 TTCCGATTCAAGTCGAACGGAAGAAAGCATCGGCAC
1037240 TTCCGATTCAAGTCGAACGGAAGAAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGAAAGCATCGGCAC
*
1037276 TTCCGATTCAAGTCAAACGGAAG
1 TTCCGATTCAAGTCGAACGGAAG
1037299 GATGTGTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGAAAGCATCGGCAC
Found at i:1039706 original size:20 final size:20
Alignment explanation
Indices: 1039683--1039725 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1039673 TTAAAATCGT
*
1039683 AACGTAAATTTGTAAATCAC
1 AACGCAAATTTGTAAATCAC
* *
1039703 AACGCGAATTTGTAAATCGC
1 AACGCAAATTTGTAAATCAC
1039723 AAC
1 AAC
1039726 ACAGTTTCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (20 bp):
AACGCAAATTTGTAAATCAC
Found at i:1039762 original size:22 final size:21
Alignment explanation
Indices: 1039719--1039785 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1039709 AATTTGTAAA
* *
1039719 TCGCAACACAGTTTC-CAAAT
1 TCGCAACGCAATTTCACAAAT
1039739 TCGCAACGCGAATTTCACAAAT
1 TCGCAACGC-AATTTCACAAAT
* * * *
1039761 TCCCAACTCAGTTTCAGAAAT
1 TCGCAACGCAATTTCACAAAT
1039782 TCGC
1 TCGC
1039786 GTTGTAATAG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 8 0.21
21 18 0.47
22 12 0.32
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (21 bp):
TCGCAACGCAATTTCACAAAT
Found at i:1039849 original size:20 final size:20
Alignment explanation
Indices: 1039824--1039869 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1039814 GTAATTAGCG
1039824 TTGCGAATTTAAAAATCGCA
1 TTGCGAATTTAAAAATCGCA
1039844 TTGCGAATTTAAAAATCGCA
1 TTGCGAATTTAAAAATCGCA
1039864 TTGCGA
1 TTGCGA
1039870 TATCACTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTAAAAATCGCA
Found at i:1039885 original size:20 final size:20
Alignment explanation
Indices: 1039862--1039976 Score: 180
Period size: 20 Copynumber: 5.8 Consensus size: 20
1039852 TTAAAAATCG
1039862 CATTGCGATA-TCACTGTTCA
1 CATTGCGATAGT-ACTGTTCA
1039882 CATTGCGATA-TCACTGTTCA
1 CATTGCGATAGT-ACTGTTCA
1039902 CATTGCGATAGTACTGTTCA
1 CATTGCGATAGTACTGTTCA
*
1039922 CATTGTGATAGTACTGTTCA
1 CATTGCGATAGTACTGTTCA
1039942 CATTGCGATAGTACTGTTCA
1 CATTGCGATAGTACTGTTCA
*
1039962 CATTACGATAGTACT
1 CATTGCGATAGTACT
1039977 TATATAGGTA
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
20 90 0.99
21 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTCA
Found at i:1040034 original size:20 final size:20
Alignment explanation
Indices: 1040011--1040051 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1040001 TTTGAAAATC
*
1040011 ACATTGCGATAGTATTGTTT
1 ACATTGCGATAGTACTGTTT
1040031 ACATTGCGATAGTACTGTTT
1 ACATTGCGATAGTACTGTTT
1040051 A
1 A
1040052 TACCATTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (20 bp):
ACATTGCGATAGTACTGTTT
Found at i:1040170 original size:19 final size:20
Alignment explanation
Indices: 1040146--1040188 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1040136 CGGTGTTAGT
1040146 GAACC-GCTTTGAACCGTTC
1 GAACCGGCTTTGAACCGTTC
*
1040165 GAACCGGCTTTGAATCGTTC
1 GAACCGGCTTTGAACCGTTC
1040185 GAAC
1 GAAC
1040189 AGGACCGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (20 bp):
GAACCGGCTTTGAACCGTTC
Found at i:1040241 original size:13 final size:13
Alignment explanation
Indices: 1040223--1040256 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
1040213 ACCTAAATTT
1040223 TTTAATTTTTTTA
1 TTTAATTTTTTTA
1040236 TTTAA--TTTTTA
1 TTTAATTTTTTTA
1040247 TTTAATTTTT
1 TTTAATTTTT
1040257 AAAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTAATTTTTTTA
Found at i:1040244 original size:11 final size:11
Alignment explanation
Indices: 1040230--1040257 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1040220 TTTTTTAATT
1040230 TTTTTATTTAA
1 TTTTTATTTAA
1040241 TTTTTATTTAA
1 TTTTTATTTAA
1040252 TTTTTA
1 TTTTTA
1040258 AAATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTATTTAA
Found at i:1040680 original size:31 final size:31
Alignment explanation
Indices: 1040645--1040729 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
1040635 TGATTACTTT
1040645 TTAATTTAATCTTTAAATTTTAA-ATAAAATA
1 TTAATTTAAT-TTTAAATTTTAAGATAAAATA
* ** *
1040676 TTAATATTAATTCTAGTTTTTAAGATAAGATA
1 TTAAT-TTAATTTTAAATTTTAAGATAAAATA
* *
1040708 TAAATTTAATATTTTAATTTTA
1 TTAATTTAAT-TTTAAATTTTA
1040730 TATTTTGATA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
31 19 0.45
32 23 0.55
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (31 bp):
TTAATTTAATTTTAAATTTTAAGATAAAATA
Found at i:1040977 original size:21 final size:22
Alignment explanation
Indices: 1040943--1040988 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1040933 TCAGAAATAT
* *
1040943 TAAAAAATATTAATATTTTAGG
1 TAAAAAATAATAATATTTTAAG
*
1040965 TAAAAAA-AATAATGTTTTAAG
1 TAAAAAATAATAATATTTTAAG
1040986 TAA
1 TAA
1040989 TTTTTTAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
TAAAAAATAATAATATTTTAAG
Found at i:1042969 original size:228 final size:227
Alignment explanation
Indices: 1042334--1043630 Score: 1652
Period size: 228 Copynumber: 5.7 Consensus size: 227
1042324 TTCAAAATAG
* * * * * * * * * *
1042334 ATGCAAATTTTCGTCAAGACGCTCACTGGCAAGACCATCACCCTT-GAGGTGGAAAGTTCTGATA
1 ATGCAGATTTTTGTGAAGACACTCACCGGGAAGACCATCA-CCTTGGAGGTTGAAAGCTCCGACA
* * * * * * * * *
1042398 CCATTGATAATGTAAAGGCCAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAACAGCGGCTT
65 CAATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGG-TT
* * * * * *
1042463 -ATTTTTGCTGGTAAACAGCTGGAGGATGGCCGGACCCTT-GCTGACTACAACATCCAGAAGGAA
129 GATTTTTGCTGGTAAGCAACT-GAGGATGGCCGCA-CCTTGGCTGACTATAACATCCAAAAGGAG
* * * ** *
1042526 TCCACACTCCACTTGGTTCTTCGAT-TGAGGGGTGGT
192 TCCACCCTCCACTTGGTGCTCCG-TCTTCGTGGTGGT
* * * * * * * * * * * *
1042562 ATGCAAATCTTTGTTAAGACCCTCACCGGAAAGACCATTACATTGGAGGTGGAGAGTTCAGATAC
1 ATGCAGATTTTTGTGAAGACACTCACCGGGAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
* *
1042627 AATTGACAATGTCAAGGCAAAGATTCAGGACAAGGAAGGTAT-CCCCCAGACCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
1042691 TTTTTGCTGGTAAGCAACTAGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
131 TTTTTGCTGGTAAGCAACT-GAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
1042756 ACCCTCCA-TCTGGTGCTCCGTCTTCGTGGTGGT
195 ACCCTCCACT-TGGTGCTCCGTCTTCGTGGTGGT
* *
1042789 ATGCAGATTTTTGTGAAGACACTTACCGGGAAGACCATCACCTTGGAAGTTGAAAGCTCCGACAC
1 ATGCAGATTTTTGTGAAGACACTCACCGGGAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
* *
1042854 AATTGACAATGTGAAGGCCAAGATTCAGGACAAGGAGGGTATCCCTCCAGACCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
* *
1042919 TTTTTGCTGGTAAGCAATTGGAGGATGGCCGCACTTTGGCTGACTATAACATCCAAAAGGAGTCC
131 TTTTTGCTGGTAAGCAACT-GAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
*
1042984 ACCCTACACTTGGTGCTCCGTCTTCGTGGTGGT
195 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
* *
1043017 ATGCAGATTTTTGTGAAGACACTAACCGGGAAGACCATCACCTTGGAAGTTGAAAGCTCCGACAC
1 ATGCAGATTTTTGTGAAGACACTCACCGGGAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
*
1043082 GATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
* * * *
1043147 TCTTTGCTGGGAAGCAACTAGAGGATGGGCGCACCTTGGCCGACTATAACATCCAAAAGGAGTCC
131 TTTTTGCTGGTAAGCAACT-GAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
1043212 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
195 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
* * * * * *
1043245 ATGCAGATTTTCGTGAAGACACTTACCGGAAAGACCATCACCCTGGAGGTAGAAAGTTCCGACAC
1 ATGCAGATTTTTGTGAAGACACTCACCGGGAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
* * * *
1043310 AATCGATAATGTCAAGGCCAAAATTCAGGACAAGGAGGGTATCCCGCCAGACCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
* *
1043375 TTTTTGCTGGTAAGCAACTTGAGGATGGGCGCACCTTGGCCGACTATAACATCCAAAAGGAGTCC
131 TTTTTGCTGGTAAGCAAC-TGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
*
1043440 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGG
195 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
* * * * * * * *
1043473 ATGCAAATTTTCGTGAAGACCCTCACCGGGAAAACCATCACCCTAGAGGTTGAGAGCTCGGACAC
1 ATGCAGATTTTTGTGAAGACACTCACCGGGAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
* * * * * * *
1043538 GATTGATAATGTCAAGGCCAAGATTCAGGATAAGGAAGGAATCCCCCCGGATCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
* *
1043603 TCTTTGCTGGGAAGCAACTTGAGGATGG
131 TTTTTGCTGGTAAGCAAC-TGAGGATGG
1043631 GAGGACCCTT
Statistics
Matches: 957, Mismatches: 104, Indels: 16
0.89 0.10 0.01
Matches are distributed among these distances:
226 8 0.01
227 185 0.19
228 762 0.80
229 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (227 bp):
ATGCAGATTTTTGTGAAGACACTCACCGGGAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
TTTTTGCTGGTAAGCAACTGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCCA
CCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
Found at i:1044254 original size:29 final size:30
Alignment explanation
Indices: 1044192--1044263 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1044182 TTTTAAAATA
* * * *
1044192 ATTTAAATTCGTTTAAATTTGTAGTATTGT
1 ATTTATATTTGTTTAAATTTGTAGTACTAT
*
1044222 ATTTGTATTTGTTTAAATTT-TAGTACTAT
1 ATTTATATTTGTTTAAATTTGTAGTACTAT
1044251 ATTTATATTTGTT
1 ATTTATATTTGTT
1044264 CATATGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (30 bp):
ATTTATATTTGTTTAAATTTGTAGTACTAT
Found at i:1044344 original size:23 final size:23
Alignment explanation
Indices: 1044318--1044368 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1044308 AGTATATTCG
* *
1044318 TTTAATGTTTATGAATATCTTTA
1 TTTAATGTTTATAAATATATTTA
*
1044341 TTTAATGTTTGTAAATATATTTA
1 TTTAATGTTTATAAATATATTTA
1044364 TTTAA
1 TTTAA
1044369 CGTCTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (23 bp):
TTTAATGTTTATAAATATATTTA
Found at i:1045346 original size:23 final size:23
Alignment explanation
Indices: 1045320--1045366 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1045310 TAGAAGAGAA
1045320 TAAAATATTTTAGTGATGAATGG
1 TAAAATATTTTAGTGATGAATGG
*
1045343 TAAAATGTTTTAGTGATGAATGG
1 TAAAATATTTTAGTGATGAATGG
1045366 T
1 T
1045367 GTAATTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.40
Consensus pattern (23 bp):
TAAAATATTTTAGTGATGAATGG
Found at i:1052974 original size:10 final size:10
Alignment explanation
Indices: 1052959--1052994 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
1052949 CCATACTCTC
1052959 AACTCAGTTT
1 AACTCAGTTT
1052969 AACTCAGTTT
1 AACTCAGTTT
*
1052979 AATTCAGTTT
1 AACTCAGTTT
1052989 AACTCA
1 AACTCA
1052995 TTTGTAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (10 bp):
AACTCAGTTT
Found at i:1055229 original size:22 final size:24
Alignment explanation
Indices: 1055183--1055237 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
1055173 CATCAAATTT
1055183 ATAA-ATAATGTTTTTATAATCAA
1 ATAATATAATGTTTTTATAATCAA
*
1055206 ATATTATAAT-TTTATTA-AAT-AA
1 ATAATATAATGTTT-TTATAATCAA
1055228 ATAATATAAT
1 ATAATATAAT
1055238 ATAATGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.39
23 9 0.32
24 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
ATAATATAATGTTTTTATAATCAA
Found at i:1073450 original size:18 final size:17
Alignment explanation
Indices: 1073366--1073467 Score: 75
Period size: 18 Copynumber: 5.7 Consensus size: 17
1073356 AACTTAATGG
1073366 AATAATATAATTTAATA
1 AATAATATAATTTAATA
*
1073383 TATCAA-ATAATTCTTAATA
1 AAT-AATATAA-T-TTAATA
* *
1073402 AAT-ATATATATAATATTA
1 AATAATATA-AT-TTAATA
*
1073420 AATTATAATAATTTAATGA
1 AATAAT-ATAATTTAAT-A
1073439 AATAATATAATTTAATA
1 AATAATATAATTTAATA
1073456 GAATAA-ATAATT
1 -AATAATATAATT
1073468 CTTAATTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
17 14 0.21
18 32 0.47
19 19 0.28
20 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AATAATATAATTTAATA
Found at i:1079733 original size:28 final size:28
Alignment explanation
Indices: 1079702--1079767 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
1079692 AAAAATCGGG
*
1079702 TTCGGGTC-GAGTTTTTTTAAGTTTGATA
1 TTCGGGTCGGA-TTTTTTTAAGTGTGATA
1079730 TTCGGGTCGGATTTTTTTAAGTGTGATA
1 TTCGGGTCGGATTTTTTTAAGTGTGATA
*
1079758 TTCTGGTCGG
1 TTCGGGTCGG
1079768 GTGAAACTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.15, C:0.09, G:0.29, T:0.47
Consensus pattern (28 bp):
TTCGGGTCGGATTTTTTTAAGTGTGATA
Found at i:1080459 original size:22 final size:22
Alignment explanation
Indices: 1080417--1080493 Score: 97
Period size: 21 Copynumber: 3.6 Consensus size: 22
1080407 ATTCTGACTA
*
1080417 TCGCATTGCGA-TTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAAT
* *
1080438 TCGCGTTGCGGTTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
1080459 TCGCAATGCGATTTTCCT-AAT
1 TCGCATTGCGATTTTCCTAAAT
1080480 TCGCATTGCGATTT
1 TCGCATTGCGATTT
1080494 ACATAGCGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.04
21 37 0.79
22 8 0.17
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:1081056 original size:20 final size:19
Alignment explanation
Indices: 1081027--1081098 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1081017 TTCTAAACTT
*
1081027 AAAATTGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
1081047 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
1081067 ACTATCACAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
1081088 AAAATCGCAAC
1 AAAATCGCAAC
1081099 GAGAGAATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:1081087 original size:21 final size:21
Alignment explanation
Indices: 1081042--1081105 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1081032 TGCAACATGA
*
1081042 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCACAACGA-GAG
**
1081062 AAATGACTATCACAACGAGAG
1 AAATGAAAATCACAACGAGAG
*
1081083 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCACAACGAGAG
1081104 AA
1 AA
1081106 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCACAACGAGAG
Found at i:1081119 original size:33 final size:33
Alignment explanation
Indices: 1081082--1081162 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
1081072 CACAACGAGA
1081082 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
1081115 GAAATGAAAATCGCAACGATATAATTGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1081148 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1081163 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1081228 original size:20 final size:20
Alignment explanation
Indices: 1081163--1081251 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
1081153 CAAAATCGCA
1081163 TTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCCGCG
*
1081182 TTGCGA--TT-A--T-CTCG
1 TTGCGATTTTCATTTCCGCG
**
1081196 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCCGCG
*
1081216 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTC-CGCG
1081236 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1081252 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 10 0.18
20 28 0.50
21 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCG
Found at i:1083163 original size:94 final size:94
Alignment explanation
Indices: 1083054--1083403 Score: 603
Period size: 94 Copynumber: 3.7 Consensus size: 94
1083044 CGGCTGCTGC
*
1083054 CTAAACTGTGTATTCTTTAACATTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
1083119 GTAAATTTGTTCGGTTGCTGCCAATTCTG
66 GTAAATTTGTTCGGTTGCTGCCAATTCTG
*
1083148 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTTTTTGTCTTTGTTTTGTCTTTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
* *
1083213 GTAAATTTGTTCGGTTGCTGCTAATTCAG
66 GTAAATTTGTTCGGTTGCTGCCAATTCTG
*
1083242 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
* * *
1083307 GTAAATTTGTTCGTTTACTGTCAATTCTG
66 GTAAATTTGTTCGGTTGCTGCCAATTCTG
* *
1083336 CTAAACTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-AA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
1083400 GTAA
66 GTAA
1083404 TGCAATCCAT
Statistics
Matches: 242, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
93 6 0.02
94 236 0.98
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
GTAAATTTGTTCGGTTGCTGCCAATTCTG
Found at i:1083378 original size:188 final size:179
Alignment explanation
Indices: 1082944--1083403 Score: 678
Period size: 188 Copynumber: 2.5 Consensus size: 179
1082934 TAGATTGCTT
* * *
1082944 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1083005 ATTTGTCTTT-TGTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCTAAACTGTGTATTC
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCTAAACTGTGTATTC
* *
1083069 TTTAACATTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
1083118 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* * *
1083183 TTTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCTAATTCAGCTAAAC
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTC-G--GCTGC---TGC--CTAAAC
1083248 TGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
122 TGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
* * * * *
1083306 AGTAAATTTGTTCGTTTACTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1083371 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
1083404 TGCAATCCAT
Statistics
Matches: 257, Mismatches: 15, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
174 34 0.13
176 3 0.01
177 2 0.01
178 28 0.11
179 15 0.06
180 13 0.05
181 1 0.00
183 5 0.02
186 2 0.01
187 6 0.02
188 148 0.58
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (179 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCTAAACTGTGTATTC
TTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
Found at i:1083510 original size:20 final size:19
Alignment explanation
Indices: 1083485--1083605 Score: 161
Period size: 20 Copynumber: 6.2 Consensus size: 19
1083475 TCTTTTGGTT
*
1083485 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
1083504 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
1083524 GAAACGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1083543 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1083562 GAAACCAAAAAACGCAACGC
1 GAAA-TGAAAATCGCAACGC
*
1083582 GAAATCAAAAATCGCAACGC
1 GAAAT-GAAAATCGCAACGC
1083602 GAAA
1 GAAA
1083606 CTATAATCGC
Statistics
Matches: 91, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
19 40 0.44
20 51 0.56
ACGTcount: A:0.50, C:0.22, G:0.20, T:0.07
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1083533 original size:39 final size:38
Alignment explanation
Indices: 1083485--1083615 Score: 172
Period size: 39 Copynumber: 3.4 Consensus size: 38
1083475 TCTTTTGGTT
* *
1083485 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
1083524 GAAACGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGCGAAATGAAAATCGCAACGC
* * *
1083562 GAAACCAAAAAACGCAACGCGAAATCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGCGAAAT-GAAAATCGCAACGC
* *
1083602 GAAACTATAATCGC
1 GAAACGAAAATCGC
1083616 GTTGCGATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
38 21 0.26
39 44 0.54
40 17 0.21
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.09
Consensus pattern (38 bp):
GAAACGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1083550 original size:58 final size:59
Alignment explanation
Indices: 1083485--1083605 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 59
1083475 TCTTTTGGTT
** * *
1083485 GAAATGAAAATCGCAACGAGAGAA-TGAAAATCGCAACGCGAAA-CGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGA-AACCAAAAAACGCAACGCGAAATCAAAAATCGCAACGC
*
1083543 GAAATGAAAATCGCAACGCGAAACCAAAAAACGCAACGCGAAATCAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAACCAAAAAACGCAACGCGAAATCAAAAATCGCAACGC
1083602 GAAA
1 GAAA
1083606 CTATAATCGC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
57 2 0.04
58 36 0.64
59 18 0.32
ACGTcount: A:0.50, C:0.22, G:0.20, T:0.07
Consensus pattern (59 bp):
GAAATGAAAATCGCAACGAGAAACCAAAAAACGCAACGCGAAATCAAAAATCGCAACGC
Found at i:1083639 original size:19 final size:19
Alignment explanation
Indices: 1083612--1083718 Score: 89
Period size: 19 Copynumber: 5.8 Consensus size: 19
1083602 GAAACTATAA
1083612 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1083631 ACGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1083645 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1083664 TCGCGTTACGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
**
1083683 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
1083704 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1083719 AAGTTCCAGA
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
14 8 0.12
16 3 0.05
17 3 0.05
19 38 0.58
21 14 0.21
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1084198 original size:42 final size:42
Alignment explanation
Indices: 1084119--1084207 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
1084109 GACTCGCCTG
* * * *
1084119 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
* * * * *
1084161 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAAAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
1084203 TCATC
1 TCATC
1084208 GTTGAAGAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
Found at i:1085609 original size:14 final size:14
Alignment explanation
Indices: 1085590--1085625 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1085580 ATTGTTTAAT
1085590 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1085604 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1085618 TGATTTGT
1 TGATTTGT
1085626 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1085787 original size:19 final size:19
Alignment explanation
Indices: 1085763--1085801 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1085753 GCAACGAGAG
*
1085763 AATCGCAACGCGAAACTAA
1 AATCGCAACACGAAACTAA
1085782 AATCGCAACACGAAACTAA
1 AATCGCAACACGAAACTAA
1085801 A
1 A
1085802 TTCGTGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.26, G:0.13, T:0.10
Consensus pattern (19 bp):
AATCGCAACACGAAACTAA
Found at i:1085850 original size:33 final size:33
Alignment explanation
Indices: 1085807--1085932 Score: 207
Period size: 33 Copynumber: 3.8 Consensus size: 33
1085797 CTAAATTCGT
* * *
1085807 GTTGCGATTTTCATTTCGCTTTGTGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
1085840 GTTGCAATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
1085873 GTTGCGATTTTTATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1085906 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
1085933 AGTCATTTCC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:1085898 original size:19 final size:19
Alignment explanation
Indices: 1085874--1085932 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
1085864 GATTCTCTCG
1085874 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTTATTTCGCA
* *
1085893 TTGCGA---TTCTCTCG--
1 TTGCGATTTTTATTTCGCA
*
1085907 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTTATTTCGCA
1085926 TTGCGAT
1 TTGCGAT
1085933 AGTCATTTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 6 0.20
16 6 0.20
17 5 0.17
19 13 0.43
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTTATTTCGCA
Found at i:1085951 original size:20 final size:19
Alignment explanation
Indices: 1085905--1085959 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1085895 GCGATTCTCT
**
1085905 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1085924 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1085944 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
1085960 AAGATGATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1089357 original size:20 final size:20
Alignment explanation
Indices: 1089342--1089429 Score: 124
Period size: 20 Copynumber: 4.3 Consensus size: 20
1089332 AGAATCTCGT
1089342 TGCGATTTACTAAATCGCAA
1 TGCGATTTACTAAATCGCAA
1089362 TGCGATTTACTAAATCGCAA
1 TGCGATTTACTAAATCGCAA
1089382 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTAC-TAAATCGCAA
* **
1089402 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTA-CTAAATCGCAA
1089423 TGCGATT
1 TGCGATT
1089430 ATTGCAATGC
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.06
20 40 0.65
21 18 0.29
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (20 bp):
TGCGATTTACTAAATCGCAA
Found at i:1089417 original size:21 final size:21
Alignment explanation
Indices: 1089353--1089479 Score: 110
Period size: 21 Copynumber: 6.5 Consensus size: 21
1089343 GCGATTTACT
* **
1089353 AAATCGCAATGCGATTTA-CT
1 AAATCGCAATGCGAATTAGGA
* *
1089373 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
1089393 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
1089414 AAATCGCAATGCG-ATT----
1 AAATCGCAATGCGAATTAGGA
*
1089430 --ATTGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
1089449 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
1089470 AAATCGCAAT
1 AAATCGCAAT
1089480 ACGATAGTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
14 10 0.11
15 3 0.03
19 3 0.03
20 30 0.34
21 42 0.48
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:1089465 original size:56 final size:55
Alignment explanation
Indices: 1089378--1089484 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 55
1089368 TTACTAAATC
* * *
1089378 GCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTATT
1 GCAATGCGATTACGAAAATCGCAACGCGAATTAGGAAAATCGCAATACGATTATT
* * *
1089433 GCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAATACGAT
1 GCAATGCG-ATTACGAAAATCGCAACGCGAATTAGGAAAATCGCAATACGAT
1089485 AGTTAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
55 8 0.18
56 37 0.82
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.22
Consensus pattern (55 bp):
GCAATGCGATTACGAAAATCGCAACGCGAATTAGGAAAATCGCAATACGATTATT
Found at i:1097166 original size:21 final size:21
Alignment explanation
Indices: 1097140--1097196 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1097130 AAAATTTAAA
*
1097140 AGTTTAGATACTAAAATTGAT
1 AGTTTAGATACTAAAACTGAT
1097161 AGTTTAGATACTAAAACTGAT
1 AGTTTAGATACTAAAACTGAT
*
1097182 AGTTTAAATACTAAA
1 AGTTTAGATACTAAA
1097197 CACGTAGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (21 bp):
AGTTTAGATACTAAAACTGAT
Found at i:1106067 original size:18 final size:19
Alignment explanation
Indices: 1106030--1106067 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1106020 ATTTACAATT
1106030 AAATTTAAATAGAAACTCGA
1 AAATTTAAATAG-AACTCGA
*
1106050 AAATTTGAATAG-ACTCGA
1 AAATTTAAATAGAACTCGA
1106068 CTCGGCTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (19 bp):
AAATTTAAATAGAACTCGA
Found at i:1106405 original size:20 final size:18
Alignment explanation
Indices: 1106373--1106427 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
1106363 GAAATAATTT
*
1106373 ATTTAATAAAAAATATTA
1 ATTTAATAAAAAATATGA
1106391 ATTTTAATAAAAAAAATATGA
1 A-TTTAAT--AAAAAATATGA
*
1106412 ACTTAATTAAAAAATA
1 ATTTAA-TAAAAAATA
1106428 ATATATAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 4 0.13
21 12 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
ATTTAATAAAAAATATGA
Found at i:1106406 original size:21 final size:21
Alignment explanation
Indices: 1106375--1106431 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
1106365 AATAATTTAT
* *
1106375 TTAATAAAAAATATTAATTTTAA
1 TTAA-AAAAAATATGAA-CTTAA
1106398 -TAAAAAAAATATGAACTTAA
1 TTAAAAAAAATATGAACTTAA
1106418 TTAAAAAATAATAT
1 TTAAAAAA-AATAT
1106432 ATAGATAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.13
21 18 0.60
22 8 0.27
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
TTAAAAAAAATATGAACTTAA
Found at i:1107566 original size:28 final size:25
Alignment explanation
Indices: 1107521--1107589 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 25
1107511 AATTGATCAG
* *
1107521 ATATTTTAAAAGTTAATATT-TTATA
1 ATATTTTAATATTTAATATTATT-TA
1107546 ATCATTTTATATCATTTAATATTATTTA
1 AT-ATTTTA-AT-ATTTAATATTATTTA
1107574 ATATTTTAATATTTAA
1 ATATTTTAATATTTAA
1107590 CGAAGATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 8 0.21
26 8 0.21
27 7 0.18
28 13 0.34
29 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (25 bp):
ATATTTTAATATTTAATATTATTTA
Found at i:1107581 original size:18 final size:18
Alignment explanation
Indices: 1107533--1107586 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1107523 ATTTTAAAAG
*
1107533 TTAATATTTT-ATAATCAT
1 TTAATATTTTAAT-ATTAT
*
1107551 TTTATATCATTTAATATTAT
1 TTAATAT--TTTAATATTAT
1107571 TTAATATTTTAATATT
1 TTAATATTTTAATATT
1107587 TAACGAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 15 0.50
20 13 0.43
21 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTTAATATTAT
Found at i:1112185 original size:58 final size:58
Alignment explanation
Indices: 1112115--1112226 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
1112105 GTCCTCGTGC
* *
1112115 AACTATAACAAACACCAGTGTTCTATACTATAACTACTCAAACTTGGGATGAATGCCA
1 AACTATAACAAACACCAGTGTTCTATACTACAACCACTCAAACTTGGGATGAATGCCA
*
1112173 AACTATAACAAACACCAGTGTTCTATACTACGACCACTCAAACTTGGGATGAAT
1 AACTATAACAAACACCAGTGTTCTATACTACAACCACTCAAACTTGGGATGAAT
1112227 ACCGGATAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (58 bp):
AACTATAACAAACACCAGTGTTCTATACTACAACCACTCAAACTTGGGATGAATGCCA
Found at i:1118844 original size:2 final size:2
Alignment explanation
Indices: 1118837--1118868 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1118827 ACCGAAAATA
1118837 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
1118869 TAATATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1119660 original size:20 final size:20
Alignment explanation
Indices: 1119635--1119687 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1119625 AAAATTAAAG
1119635 TTTAATATTATAATTGAAAA
1 TTTAATATTATAATTGAAAA
1119655 TTTAATATTATAATTGAAAA
1 TTTAATATTATAATTGAAAA
1119675 TTTAATATTATAA
1 TTTAATATTATAA
1119688 ACAATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TTTAATATTATAATTGAAAA
Done.