Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 18
Found at i:798473 original size:41 final size:41
Alignment explanation
Indices: 798422--798513 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
798412 AAATTGAAAT
* **
798422 GAACACGAACCGAATATAAAAACCTTAAAAAATAAATGAAC
1 GAACACGAACCGAACATAAAAACCTTAAAAAATAAACAAAC
* * *
798463 GAACATGAACCGAACATGAACACCTTAAAAAATAAACAAAC
1 GAACACGAACCGAACATAAAAACCTTAAAAAATAAACAAAC
798504 GAACACGAAC
1 GAACACGAAC
798514 ATAACCTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.12
Consensus pattern (41 bp):
GAACACGAACCGAACATAAAAACCTTAAAAAATAAACAAAC
Found at i:799557 original size:17 final size:17
Alignment explanation
Indices: 799537--799576 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
799527 CCAGAATTTT
799537 TCCTTCTTCCTCCTTCC
1 TCCTTCTTCCTCCTTCC
* *
799554 TCCTTCTTCCTTCTTCT
1 TCCTTCTTCCTCCTTCC
799571 TCCTTC
1 TCCTTC
799577 ATGCGTGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (17 bp):
TCCTTCTTCCTCCTTCC
Found at i:818576 original size:28 final size:30
Alignment explanation
Indices: 818545--818617 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 30
818535 GTTGTATCGT
818545 TTATACCACTGAACTTTAATTTT-G-TCAA
1 TTATACCACTGAACTTTAATTTTAGTTCAA
* * * *
818573 TTATAGCATTAAACTTTGATTTTAGTTTCAA
1 TTATACCACTGAACTTTAATTTTAG-TTCAA
818604 TTATACCACTGAAC
1 TTATACCACTGAAC
818618 CGTTAAATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
28 19 0.54
29 1 0.03
31 15 0.43
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (30 bp):
TTATACCACTGAACTTTAATTTTAGTTCAA
Found at i:818668 original size:19 final size:19
Alignment explanation
Indices: 818644--818683 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
818634 GCACGACGAT
* *
818644 GTGGCTGACGGCTGTCGAC
1 GTGGCTAACGACTGTCGAC
*
818663 GTGGCTAATGACTGTCGAC
1 GTGGCTAACGACTGTCGAC
818682 GT
1 GT
818684 AGACACCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (19 bp):
GTGGCTAACGACTGTCGAC
Found at i:834558 original size:18 final size:19
Alignment explanation
Indices: 834523--834559 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
834513 CACGGAATGT
834523 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
834543 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
834560 GGATTACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:835452 original size:21 final size:21
Alignment explanation
Indices: 835427--835494 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
835417 AATTATATTA
835427 AAATTTACATCATTCTAATGT
1 AAATTTACATCATTCTAATGT
* * *
835448 AAATTATTA-AGCCA-T-AAATAT
1 AAA-T-TTACA-TCATTCTAATGT
*
835469 TAATTTACATCATTCTAATGT
1 AAATTTACATCATTCTAATGT
835490 AAATT
1 AAATT
835495 ATTAAGCCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 17 0.52
22 3 0.09
23 5 0.15
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (21 bp):
AAATTTACATCATTCTAATGT
Found at i:835482 original size:42 final size:42
Alignment explanation
Indices: 835428--835513 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
835418 ATTATATTAA
835428 AATTTACATCATTCTAATGTAAATTATTAAGCCATAAATATT
1 AATTTACATCATTCTAATGTAAATTATTAAGCCATAAATATT
835470 AATTTACATCATTCTAATGTAAATTATTAAGCCATAAATATT
1 AATTTACATCATTCTAATGTAAATTATTAAGCCATAAATATT
835512 AA
1 AA
835514 GTATAATGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (42 bp):
AATTTACATCATTCTAATGTAAATTATTAAGCCATAAATATT
Found at i:836748 original size:22 final size:21
Alignment explanation
Indices: 836715--836766 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
836705 ATTATTACTT
* *
836715 TTAT-TTAATAATATTTACATA
1 TTATATTATTAATA-TTACAAA
836736 TTATATTATTAATATTACAAA
1 TTATATTATTAATATTACAAA
836757 TT-TATT-TTAA
1 TTATATTATTAA
836767 AAAAATACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 12 0.43
22 8 0.29
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATATTATTAATATTACAAA
Found at i:837289 original size:12 final size:12
Alignment explanation
Indices: 837272--837297 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
837262 GAGGTCCAAC
837272 GATTGAACCGGA
1 GATTGAACCGGA
837284 GATTGAACCGGA
1 GATTGAACCGGA
837296 GA
1 GA
837298 ACGAGTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (12 bp):
GATTGAACCGGA
Found at i:839312 original size:31 final size:31
Alignment explanation
Indices: 839277--839374 Score: 133
Period size: 31 Copynumber: 3.2 Consensus size: 31
839267 AGTTACGTCA
* *
839277 GGGACCATATTGCAAACAGACAAAATGTTGG
1 GGGACCATATTACAAACAGACTAAATGTTGG
*
839308 GGGACCATCTTACAAACAGACTAAATGTTGG
1 GGGACCATATTACAAACAGACTAAATGTTGG
* * *
839339 GGGACCATCTTACAAACAAACTAAATATTGG
1 GGGACCATATTACAAACAGACTAAATGTTGG
*
839370 AGGAC
1 GGGAC
839375 TGTATTGCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (31 bp):
GGGACCATATTACAAACAGACTAAATGTTGG
Found at i:840209 original size:19 final size:19
Alignment explanation
Indices: 840185--840221 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
840175 CATATGTTTT
*
840185 TGAAATAATTTACTAAAAA
1 TGAAATAATTTACCAAAAA
*
840204 TGAAATCATTTACCAAAA
1 TGAAATAATTTACCAAAA
840222 GTGGATAAAA
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:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (19 bp):
TGAAATAATTTACCAAAAA
Found at i:840844 original size:31 final size:31
Alignment explanation
Indices: 840806--840872 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
840796 CTTTTAAAAC
*
840806 TTGCAATACAGT-CTCTCAACATTTAATCTGT
1 TTGCAATACAGTCCTC-CAACATTTAATCCGT
** *
840837 TTGCAATATGGTCCTCCAACATTTAGTCCGT
1 TTGCAATACAGTCCTCCAACATTTAATCCGT
840868 TTGCA
1 TTGCA
840873 TTATGGTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.37
Consensus pattern (31 bp):
TTGCAATACAGTCCTCCAACATTTAATCCGT
Found at i:840878 original size:31 final size:31
Alignment explanation
Indices: 840822--840881 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
840812 TACAGTCTCT
*
840822 CAACATTTAATCTGTTTGCAATATGGTCCTC
1 CAACATTTAATCCGTTTGCAATATGGTCCTC
* *
840853 CAACATTTAGTCCGTTTGCATTATGGTCC
1 CAACATTTAATCCGTTTGCAATATGGTCC
840882 CCGACGTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (31 bp):
CAACATTTAATCCGTTTGCAATATGGTCCTC
Found at i:845415 original size:58 final size:60
Alignment explanation
Indices: 845285--845417 Score: 157
Period size: 58 Copynumber: 2.2 Consensus size: 60
845275 ATTTAAGGGT
* *
845285 AAAG-TACACAAATGATCCCTTGACTACAGGGTGTTGCTTTATTTAATCCCCTGACTATTA
1 AAAGTTACA-AAATGATCCCTTGACTACAAGGTGTTGCTTTAGTTAATCCCCTGACTATTA
* * * * *
845345 AAAGTTACAAAATGATCCC-TGACTATAATGTGTTGCTTT-GTTAGT-CCATCGACTGTTA
1 AAAGTTACAAAATGATCCCTTGACTACAAGGTGTTGCTTTAGTTAATCCCCT-GACTATTA
845403 AAAGTTACAAAATGA
1 AAAGTTACAAAATGA
845418 CCACTCGGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
57 3 0.05
58 26 0.41
59 17 0.27
60 14 0.22
61 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCCTTGACTACAAGGTGTTGCTTTAGTTAATCCCCTGACTATTA
Found at i:855841 original size:171 final size:166
Alignment explanation
Indices: 855513--855863 Score: 411
Period size: 171 Copynumber: 2.1 Consensus size: 166
855503 ATACATGAAT
* * * *
855513 CATGATAAATGCCACCATTCCTGAGATGCATAGAGAAATATAAACAAGGTTTCATGGCCCGTATT
1 CATGATAAAGGCCACCATTCCAGAGATACATAGAGAAATATAAACAAGGTTTCATGGCCCATATT
* *
855578 GTTAAAGCATGAAGAGTGATTGATATATGATCGAATTTACAAGATAGAGGAAACATCAGTCTCAA
66 GTTAAAGCACGAAGAGTGATTGATATACGATCGAATTTACAAGATAGAGGAAACATCAGTCTC-A
* * *
855643 GTGTCATTGGACTATTCATCGAAACATATCTTATTCTACTA
130 ----CATTAGACTATCCATCAAAACATATCTTATTCTACTA
* *
855684 CATGATAAAGGCCACCATTCCAGAGATACATAGAGAAATATGAACATGGTTTCATGGCCCATATT
1 CATGATAAAGGCCACCATTCCAGAGATACATAGAGAAATATAAACAAGGTTTCATGGCCCATATT
* * *
855749 GCTAAAAAGCTAAAGCACGAAGAGTGATTGCTATACGATCGAATTTACGAGATAGAGGAAACA-G
66 G-T-------TAAAGCACGAAGAGTGATTGATATACGATCGAATTTACAAGATAGAGGAAACATC
* *
855813 AGT-TC-CATTAGATTATCCGTCAAAACATATCTTATTCTACTA
123 AGTCTCACATTAGACTATCCATCAAAACATATCTTATTCTACTA
*
855855 CATGCTAAA
1 CATGATAAA
855864 AGCAATCGAT
Statistics
Matches: 155, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
171 100 0.65
172 1 0.01
177 2 0.01
178 3 0.02
179 49 0.32
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (166 bp):
CATGATAAAGGCCACCATTCCAGAGATACATAGAGAAATATAAACAAGGTTTCATGGCCCATATT
GTTAAAGCACGAAGAGTGATTGATATACGATCGAATTTACAAGATAGAGGAAACATCAGTCTCAC
ATTAGACTATCCATCAAAACATATCTTATTCTACTA
Found at i:856391 original size:16 final size:16
Alignment explanation
Indices: 856370--856411 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
856360 TTAAAAAATA
856370 GATTCAGGTTGGATCG
1 GATTCAGGTTGGATCG
856386 GATTCAGGTTGGATCG
1 GATTCAGGTTGGATCG
*
856402 GGTTCAGGTT
1 GATTCAGGTT
856412 TAGGGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.12, G:0.38, T:0.33
Consensus pattern (16 bp):
GATTCAGGTTGGATCG
Found at i:861548 original size:16 final size:17
Alignment explanation
Indices: 861527--861578 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
861517 TTTAAAATTT
861527 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
861543 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
861558 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
861575 AATT
1 AATT
861579 TATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:866421 original size:21 final size:21
Alignment explanation
Indices: 866395--866435 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
866385 CTCAATCGGC
866395 ATATCAA-CTTAAAACCAAATT
1 ATATCAATCTT-AAACCAAATT
*
866416 ATATCAATCTTTAACCAAAT
1 ATATCAATCTTAAACCAAAT
866436 GAATCTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (21 bp):
ATATCAATCTTAAACCAAATT
Found at i:869576 original size:28 final size:28
Alignment explanation
Indices: 869534--869590 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
869524 ATATCTATTT
*
869534 ACATTATGTCGTCAAGTTAGTGCTTGAA
1 ACATTATGTCATCAAGTTAGTGCTTGAA
*
869562 ACATTATGTCATCAAGTTAGTGTTTGAA
1 ACATTATGTCATCAAGTTAGTGCTTGAA
869590 A
1 A
869591 GCGACGGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (28 bp):
ACATTATGTCATCAAGTTAGTGCTTGAA
Found at i:870803 original size:2 final size:2
Alignment explanation
Indices: 870798--870828 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
870788 ATATAACTCA
870798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
870829 AATCGTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:896839 original size:19 final size:20
Alignment explanation
Indices: 896815--896856 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
896805 ATAATTATTT
896815 TTAATTTAA-TA-AAAAATTA
1 TTAATTTAATTATAAAAA-TA
896834 TTAATTTAATTATAAAAATA
1 TTAATTTAATTATAAAAATA
896854 TTA
1 TTA
896857 TTATGCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTTAATTATAAAAATA
Found at i:896856 original size:23 final size:24
Alignment explanation
Indices: 896807--896859 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
896797 ATTAATTTAT
896807 AATTATT--TTTAATTTAATAAAA
1 AATTATTAATTTAATTTAATAAAA
896829 AATTATTAATTTAA-TT-ATAAAA
1 AATTATTAATTTAATTTAATAAAA
896851 ATATTATTA
1 A-ATTATTA
896860 TGCAAACTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 14 0.50
23 9 0.32
24 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTATTAATTTAATTTAATAAAA
Found at i:896995 original size:4 final size:4
Alignment explanation
Indices: 896988--897051 Score: 83
Period size: 4 Copynumber: 15.5 Consensus size: 4
896978 TTTTTTTTAT
* *
896988 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
897036 AGTCC TATAC ATAC AT
1 A-TAC -ATAC ATAC AT
897052 TCTCATATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
4 47 0.90
5 4 0.08
6 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:902130 original size:7 final size:7
Alignment explanation
Indices: 902118--902142 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
902108 CATATCAAAT
902118 GTATCAC
1 GTATCAC
902125 GTATCAC
1 GTATCAC
902132 GTATCAC
1 GTATCAC
902139 GTAT
1 GTAT
902143 TGCATATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (7 bp):
GTATCAC
Found at i:902631 original size:20 final size:20
Alignment explanation
Indices: 902606--902660 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
902596 CGAAAATCCC
902606 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
902626 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
902646 ATGCATCGATGCACC
1 ATGCATCGATGCACC
902661 TTCAAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:905121 original size:20 final size:20
Alignment explanation
Indices: 905096--905152 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
905086 TTAGTTTACG
905096 GAATGTAAGATTA-TCAGTGA
1 GAATGTAAGATTACT-AGTGA
905116 GAATGTAAGATTACTAGTGA
1 GAATGTAAGATTACTAGTGA
*
905136 GACTGTAAGATTACTAG
1 GAATGTAAGATTACTAG
905153 GAAATATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (20 bp):
GAATGTAAGATTACTAGTGA
Found at i:907921 original size:29 final size:28
Alignment explanation
Indices: 907875--907931 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
907865 TAATGGAATG
907875 AAACGTTAATCACCAAACTGAAACAAAAT
1 AAACGTTAATCACCAAACTGAAA-AAAAT
* *
907904 AAACGTTAGAT-ACTAAACTGGAAAAAAT
1 AAACGTTA-ATCACCAAACTGAAAAAAAT
907932 TACATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 18 0.72
30 2 0.08
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (28 bp):
AAACGTTAATCACCAAACTGAAAAAAAT
Found at i:909008 original size:29 final size:29
Alignment explanation
Indices: 908966--909031 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
908956 ACCCGACCTA
*
908966 GTGATATTCTGGGAATTTTTGTGAAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
*
908995 GTGACATTCTGGGAATTTTTGTGGAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
909024 GTGACATT
1 GTGACATT
909032 TTGTGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.36
Consensus pattern (29 bp):
GTGACATTCTGGGAATTTTTGTGAAAAAG
Found at i:909050 original size:18 final size:19
Alignment explanation
Indices: 909011--909051 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
909001 TTCTGGGAAT
*
909011 TTTTGTGGAAAAGGTGACA
1 TTTTGTGGAAAAGATGACA
909030 TTTTGT-GAAAA-ATGACA
1 TTTTGTGGAAAAGATGACA
*
909047 ATTTG
1 TTTTG
909052 GAAATTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.45
18 5 0.25
19 6 0.30
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (19 bp):
TTTTGTGGAAAAGATGACA
Found at i:912460 original size:23 final size:23
Alignment explanation
Indices: 912434--912485 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
912424 ACTAAAAATT
912434 GAACATATAAATGAACGTTAAAC
1 GAACATATAAATGAACGTTAAAC
* ***
912457 GAACATGTTTGTGAACGTTAAAC
1 GAACATATAAATGAACGTTAAAC
912480 GAACAT
1 GAACAT
912486 GTTTGTGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (23 bp):
GAACATATAAATGAACGTTAAAC
Found at i:912486 original size:23 final size:23
Alignment explanation
Indices: 912445--912513 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
912435 AACATATAAA
912445 TGAACGTTAAACGAACATGTTTG
1 TGAACGTTAAACGAACATGTTTG
912468 TGAACGTTAAACGAACATGTTTG
1 TGAACGTTAAACGAACATGTTTG
* *
912491 TGAACATATAAACGAAAATGTTT
1 TGAACGT-TAAACGAACATGTTT
912514 ACGAACAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 29 0.67
24 14 0.33
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (23 bp):
TGAACGTTAAACGAACATGTTTG
Found at i:913243 original size:28 final size:28
Alignment explanation
Indices: 913198--913253 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
913188 TCAGTAAATC
* *
913198 AATTTCAGGTACCTAATTAGACCATAAA
1 AATTTCAGGTACCAAATTAAACCATAAA
* * *
913226 AATTTTAGGTATCAAATTAAACCTTAAA
1 AATTTCAGGTACCAAATTAAACCATAAA
913254 GCTAATTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (28 bp):
AATTTCAGGTACCAAATTAAACCATAAA
Found at i:924506 original size:60 final size:59
Alignment explanation
Indices: 924409--924550 Score: 178
Period size: 60 Copynumber: 2.4 Consensus size: 59
924399 TTTTTAGGGT
* * *
924409 AAAG-TACATAAATGGTTCTCGATTACAGGATGTTGCTTTATTGAGTCTCTCGACTATTA
1 AAAGTTACA-AAATGGTCCTCAATTACAGGATGTTGCTTTATTGAGTCCCTCGACTATTA
* *
924468 AAAGTTACAAAATGGTCCTTCAATTATAGGATGTTGCTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTACAAAATGGTCC-TCAATTACAGGATGTTGCTTTATTGAGTCCCTCGACTATTA
* * *
924528 AAAATTATAAAATGATCACTCAA
1 AAAGTTACAAAATGGTC-CTCAA
924551 CTATTTGTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 12 0.17
60 59 0.82
61 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCCTCAATTACAGGATGTTGCTTTATTGAGTCCCTCGACTATTA
Found at i:924894 original size:60 final size:60
Alignment explanation
Indices: 924772--924885 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
924762 ATTTTATAGT
* * *
924772 TTTTAATAGTCGAGAGACTCAACAAAATAACACCATATAGTTAGAAGACTATTTTATGAC
1 TTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAGTCAGAAGACCATTTTATGAC
* * * * *
924832 TTTTAATAGTCGAGGGACTCAACAAAGCAACACCCTGTAGTCAGAGGACCATTT
1 TTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAGTCAGAAGACCATTT
924886 GTGTACTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (60 bp):
TTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAGTCAGAAGACCATTTTATGAC
Found at i:929903 original size:15 final size:15
Alignment explanation
Indices: 929885--929916 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
929875 TGTTTGATAA
929885 TTGAAAAATATTTTT
1 TTGAAAAATATTTTT
929900 TTGAAAAATATTTTT
1 TTGAAAAATATTTTT
929915 TT
1 TT
929917 TATGTGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
TTGAAAAATATTTTT
Found at i:930168 original size:15 final size:17
Alignment explanation
Indices: 930148--930179 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
930138 AATATTATAT
930148 ATAATA-TA-ATTTTTA
1 ATAATATTATATTTTTA
930163 ATAATATTATATTTTTA
1 ATAATATTATATTTTTA
930180 GTATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAATATTATATTTTTA
Found at i:930186 original size:14 final size:16
Alignment explanation
Indices: 930167--930199 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
930157 TTTTTAATAA
930167 TATTATA-T-TTTTAG
1 TATTATATTATTTTAG
930181 TATTATATTATTTTAG
1 TATTATATTATTTTAG
930197 TAT
1 TAT
930200 AAAGTATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 1 0.06
16 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATTATATTATTTTAG
Found at i:933934 original size:31 final size:31
Alignment explanation
Indices: 933899--933968 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
933889 CTTTTAAAAC
* * * *
933899 TTGCAATGCAGTCCCTTAATATTTAGTCTGT
1 TTGCAATACAGTCCCTCAACATTTAGTCCGT
**
933930 TTGCAATATGGTCCCTCAACATTTAGTCCGT
1 TTGCAATACAGTCCCTCAACATTTAGTCCGT
933961 TTGCAATA
1 TTGCAATA
933969 TGGTCCCCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (31 bp):
TTGCAATACAGTCCCTCAACATTTAGTCCGT
Found at i:933969 original size:31 final size:31
Alignment explanation
Indices: 933909--933975 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
933899 TTGCAATGCA
* * *
933909 GTCCCTTAATATTTAGTCTGTTTGCAATATG
1 GTCCCTCAACATTTAGTCCGTTTGCAATATG
933940 GTCCCTCAACATTTAGTCCGTTTGCAATATG
1 GTCCCTCAACATTTAGTCCGTTTGCAATATG
933971 GTCCC
1 GTCCC
933976 CGACGTAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (31 bp):
GTCCCTCAACATTTAGTCCGTTTGCAATATG
Found at i:935902 original size:31 final size:31
Alignment explanation
Indices: 935864--935940 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
935854 AGTTACGTCG
* *
935864 GGGACCATATTGCAAACAGACTAAATGTTGA
1 GGGACCATATTGCAAACAAACTAAATATTGA
*
935895 GGGACCATATTGCAAATAAACTAAATATTGA
1 GGGACCATATTGCAAACAAACTAAATATTGA
**
935926 GGGACTGTATTGCAA
1 GGGACCATATTGCAA
935941 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
GGGACCATATTGCAAACAAACTAAATATTGA
Found at i:936175 original size:20 final size:21
Alignment explanation
Indices: 936146--936185 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
936136 GTTTATAGTT
936146 ACAATCAAAT-TTTAATTTTA
1 ACAATCAAATATTTAATTTTA
*
936166 ACAATTAAATCATTTAATTT
1 ACAATCAAAT-ATTTAATTT
936186 ATTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
ACAATCAAATATTTAATTTTA
Found at i:943519 original size:24 final size:25
Alignment explanation
Indices: 943488--943539 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
943478 TCGTAATTTA
*
943488 TTATGAG-AAAAAATAATCTCTAAC
1 TTATGAGAAAAAAACAATCTCTAAC
*
943512 TTATGAGAAAAAAACAATCTTTAAC
1 TTATGAGAAAAAAACAATCTCTAAC
943537 TTA
1 TTA
943540 GAAAAACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.31
Consensus pattern (25 bp):
TTATGAGAAAAAAACAATCTCTAAC
Found at i:957483 original size:2 final size:2
Alignment explanation
Indices: 957476--957503 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
957466 AGTTTTATCA
957476 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
957504 TTTGAAGTTA
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:957597 original size:24 final size:25
Alignment explanation
Indices: 957558--957605 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
957548 AAATATAATA
957558 AAATCTTTTTCAAACACGTTAAATC
1 AAATCTTTTTCAAACACGTTAAATC
*
957583 AAATCTTTTTC-AACATGTTAAAT
1 AAATCTTTTTCAAACACGTTAAAT
957606 ATTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATCTTTTTCAAACACGTTAAATC
Found at i:959335 original size:60 final size:60
Alignment explanation
Indices: 959189--959335 Score: 181
Period size: 60 Copynumber: 2.5 Consensus size: 60
959179 GAACATATGA
* * * * *
959189 ATAGTCAGGTGACCATTTTGTAACATTTAATAGTCGAGGGACTCAATAAAGCAATACCCT
1 ATAGTCAGGGGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACCCT
* * * *
959249 ATAG-CTGAGGGACCATTTTGTAACTTTTAATAGTTGAGTGACTCAACAAAATAACACCCT
1 ATAGTCAG-GGGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACCCT
959309 ATAGTCAGGGGACCATTTGTGT-ACTTT
1 ATAGTCAGGGGACCATTT-TGTAACTTT
959336 ACCCTTAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.03
60 67 0.91
61 5 0.07
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (60 bp):
ATAGTCAGGGGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACCCT
Found at i:961324 original size:60 final size:61
Alignment explanation
Indices: 961210--961345 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 61
961200 ATAGTCGGGT
* * * ** **
961210 GATCATTTTGTAACTTTTAATAATTAGGGGGACTCAACAAAGTAACATTCTATAATTGGGA
1 GATCATTTTGTAACTTTTAATAATCAGGAGGACTCAACAAAGCAACACCCTATAATCAGGA
* * *
961271 GATCATTTTGTAACTTTTGATAGTCA-GATGACTCAACAAAGCAACACCCTATAATCAGGA
1 GATCATTTTGTAACTTTTAATAATCAGGAGGACTCAACAAAGCAACACCCTATAATCAGGA
*
961331 GACCATTTGTGTAAC
1 GATCATTT-TGTAAC
961346 ATCATCAATA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 34 0.54
61 29 0.46
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (61 bp):
GATCATTTTGTAACTTTTAATAATCAGGAGGACTCAACAAAGCAACACCCTATAATCAGGA
Found at i:970884 original size:11 final size:11
Alignment explanation
Indices: 970868--970892 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
970858 TATATATATT
970868 ATTATAGTAGA
1 ATTATAGTAGA
970879 ATTATAGTAGA
1 ATTATAGTAGA
970890 ATT
1 ATT
970893 CAACTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (11 bp):
ATTATAGTAGA
Found at i:971615 original size:19 final size:19
Alignment explanation
Indices: 971591--971633 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
971581 AATACATTTA
971591 AAACATCAAATAAGTCCTT
1 AAACATCAAATAAGTCCTT
971610 AAACATCAAATAAGTCCTT
1 AAACATCAAATAAGTCCTT
971629 AAACA
1 AAACA
971634 ATGATTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (19 bp):
AAACATCAAATAAGTCCTT
Found at i:974726 original size:29 final size:30
Alignment explanation
Indices: 974676--974732 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
974666 TATTTTGAGT
* *
974676 AACGAAATGAAACGTTAGACACCAAACTGA
1 AACGAAATGAAACATTAAACACCAAACTGA
*
974706 AACGAAAT-AAACATTAAACACTAAACT
1 AACGAAATGAAACATTAAACACCAAACT
974733 AAAAAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.54, C:0.19, G:0.11, T:0.16
Consensus pattern (30 bp):
AACGAAATGAAACATTAAACACCAAACTGA
Found at i:974919 original size:28 final size:28
Alignment explanation
Indices: 974879--974933 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
974869 TCTTTTCCTT
974879 CTCAATCTCTCACCATTCAAATTTAAAC
1 CTCAATCTCTCACCATTCAAATTTAAAC
974907 CTCAATCTCTCACCATTCAAATTTAAA
1 CTCAATCTCTCACCATTCAAATTTAAA
974934 AGAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (28 bp):
CTCAATCTCTCACCATTCAAATTTAAAC
Found at i:977811 original size:21 final size:21
Alignment explanation
Indices: 977785--977963 Score: 238
Period size: 21 Copynumber: 8.6 Consensus size: 21
977775 GTTTCCAGAT
* *
977785 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
977806 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
977827 TCACAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
977847 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
977868 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
977889 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
977910 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
977931 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
977952 TCGCAATGCGAA
1 TCGCAATGCGAA
977964 TATGTAAATC
Statistics
Matches: 137, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 17 0.12
21 119 0.87
22 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:977880 original size:83 final size:83
Alignment explanation
Indices: 977785--977963 Score: 290
Period size: 83 Copynumber: 2.1 Consensus size: 83
977775 GTTTCCAGAT
977785 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCACAATGCGAATATGT-A-AAT
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCACAATGCG-ATA-GTCACAAT
977848 CGCAATGCGAACTTGGACTA
64 CGCAATGCGAACTTGGACTA
* *
977868 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGACTATC
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCACAATGCGATAGTC-ACAATC
977933 GCAATGCGAACTTGGACTA
65 GCAATGCGAACTTGGACTA
*
977952 TCGCAATGCGAA
1 TCGCAACGCGAA
977964 TATGTAAATC
Statistics
Matches: 90, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
81 2 0.02
82 3 0.03
83 52 0.58
84 33 0.37
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (83 bp):
TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCACAATGCGATAGTCACAATCG
CAATGCGAACTTGGACTA
Found at i:977997 original size:41 final size:41
Alignment explanation
Indices: 977972--978088 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 41
977962 AATATGTAAA
*
977972 TCGCAATGCGATAGTCGAAGTTCGCATTGCGATTTACATAT
1 TCGCAATGCGATAGTCGAAGTTCGCAATGCGATTTACATAT
* * ** * *
978013 TCGCATTGTGATAGTCGAAGTTCGCGTTGCGATTTTCCAAAT
1 TCGCAATGCGATAGTCGAAGTTCGCAATGCGA-TTTACATAT
* * **
978055 TCG--TTGCGATAGTCGAAGTTTGCGTTGCGATTTA
1 TCGCAATGCGATAGTCGAAGTTCGCAATGCGATTTA
978089 TTCCAAATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.04
40 25 0.37
41 29 0.43
42 10 0.15
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
TCGCAATGCGATAGTCGAAGTTCGCAATGCGATTTACATAT
Found at i:978002 original size:21 final size:21
Alignment explanation
Indices: 977972--978085 Score: 85
Period size: 21 Copynumber: 5.6 Consensus size: 21
977962 AATATGTAAA
*
977972 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
977993 TCGCATTGCGAT-TTAC-ATA-T
1 TCGCATTGCGATAGT-CGA-AGT
*
978013 TCGCATTGTGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* ** * *
978034 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATAGTCGAAGT
978055 TCG--TTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
978074 TTGCGTTGCGAT
1 TCGCATTGCGAT
978086 TTATTCCAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
19 14 0.20
20 16 0.23
21 41 0.58
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:978094 original size:42 final size:42
Alignment explanation
Indices: 977978--978110 Score: 168
Period size: 42 Copynumber: 3.2 Consensus size: 42
977968 TAAATCGCAA
* *
977978 TGCGATAGTCGAAGTTCGCATTGCGATTTA---CATATTCGCAT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG--T
*
978019 TGTGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
*
978059 TGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
*
978101 TGTGATAGTC
1 TGCGATAGTC
978111 CAAAATCGCA
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
40 27 0.33
41 26 0.32
42 28 0.35
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
Found at i:978101 original size:21 final size:20
Alignment explanation
Indices: 978037--978102 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
978027 TCGAAGTTCG
978037 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
978056 CGTTGCGA-TAGTCGAAGTTT
1 CGTTGCGATTATTCCAA-ATT
978076 GCGTTGCGATTTATTCCAAATT
1 -CGTTGCGA-TTATTCCAAATT
978098 CGTTG
1 CGTTG
978103 TGATAGTCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 12 0.33
20 2 0.06
21 13 0.36
22 2 0.06
23 6 0.17
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:978114 original size:19 final size:19
Alignment explanation
Indices: 978037--978114 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
978027 TCGAAGTTCG
**
978037 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
* *
978056 CGTTGCGATAGTCGAAGTTT
1 CGTTGCGATAGTCCAA-ATT
*
978076 GCGTTGCGATTTATTCCAAATT
1 -CGTTGCGA--TAGTCCAAATT
*
978098 CGTTGTGATAGTCCAAA
1 CGTTGCGATAGTCCAAA
978115 ATCGCAACGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
19 21 0.46
20 2 0.04
21 15 0.33
22 2 0.04
23 6 0.13
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:978227 original size:5 final size:5
Alignment explanation
Indices: 978207--978245 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
978197 CGTATTATCA
*
978207 CGACC GCGACC GGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGA
978246 GACGAGACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.21, C:0.54, G:0.26, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:978918 original size:21 final size:21
Alignment explanation
Indices: 978894--979002 Score: 132
Period size: 21 Copynumber: 5.3 Consensus size: 21
978884 TTTGAAATAA
*
978894 ATCGCAACGCGAACTTCTACT
1 ATCGCAACGCGAACTTCGACT
* * **
978915 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
978934 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
978955 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
978976 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
978997 ATCGCA
1 ATCGCA
979003 TTGCGATTTA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.19
21 58 0.81
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:978929 original size:42 final size:41
Alignment explanation
Indices: 978869--979002 Score: 166
Period size: 42 Copynumber: 3.2 Consensus size: 41
978859 TGCGATTTTG
978869 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTG-AATAAATCGCAACGCGAACTTC
* *
978911 TACTATCGCAACGAATTTGGA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTC
* * *
978951 GACTATCGCAATGCGAACTTGGACT--ATCGCAACACGAACTTC
1 GACTATCGCAA--CGAA-TTTGAATAAATCGCAACGCGAACTTC
978993 GACTATCGCA
1 GACTATCGCA
979003 TTGCGATTTA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
40 29 0.36
41 1 0.01
42 48 0.59
43 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (41 bp):
GACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTC
Found at i:979043 original size:21 final size:21
Alignment explanation
Indices: 979017--979125 Score: 116
Period size: 21 Copynumber: 5.2 Consensus size: 21
979007 GATTTACATA
979017 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
979038 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
979058 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
979079 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
979100 TTAGCATTGTGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
979121 TTCGC
1 TTCGC
979126 GCTGCGAATC
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.23
21 55 0.75
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:979043 original size:62 final size:62
Alignment explanation
Indices: 978977--979101 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
978967 ACTTGGACTA
*
978977 TCGCAACACGA-ACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCAACACGATA-GTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
***
979039 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCAACACGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
979101 T
1 T
979102 AGCATTGTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 57 0.98
63 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (62 bp):
TCGCAACACGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:979107 original size:62 final size:62
Alignment explanation
Indices: 978991--979118 Score: 238
Period size: 62 Copynumber: 2.1 Consensus size: 62
978981 AACACGAACT
*
978991 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTAGCATTGCGATAG
*
979053 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTAGCATTGTGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTAGCATTGCGATAG
979115 TCGA
1 TCGA
979119 AGTTCGCGCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (62 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTAGCATTGCGATAG
Found at i:979308 original size:27 final size:29
Alignment explanation
Indices: 979278--979347 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
979268 TTATTTTCTC
*
979278 TTTAATTTATTTA-AT-TATATATATTAG
1 TTTAATTTATATATATATATATATATTAG
979305 TTTAAATTTTATATATATATATATATATTAG
1 TTT-AA-TTTATATATATATATATATATTAG
*
979336 TTTAAATTATAT
1 TTTAATTTATAT
979348 TTTTATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 13 0.35
30 4 0.11
31 15 0.41
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTAATTTATATATATATATATATATTAG
Found at i:980497 original size:205 final size:207
Alignment explanation
Indices: 980123--980507 Score: 551
Period size: 205 Copynumber: 1.9 Consensus size: 207
980113 CAGATTTATC
* * * * *
980123 TGTATCTATTTTTTGTTCGAGTCTTTTGGTTGAGTTTTTAACTTTTTCTATGTATGGTTCTTATA
1 TGTATCTATTTTTTGTTCGAATATTTTGGTTGAGTTTTTAACTTTTTCTACGTATGATCCTTATA
* * ** *
980188 TGATCTAAAATGATTAGTTTCAATGTTATAAGAAAATGTTCATATTATGGAGTTTATGATGATAG
66 TGATATAAAATGATTAGTTTCAATGTTATAAGAAAATGTTCAAAACATGGAGTTTATGATGATAA
* *
980253 TTGTAAATCATTATTGTAATTTTAAATATTTTTAAATATATATATATATAATCGAATATACGTCA
131 TTGTAAATCATTATTGTAATTTTAAACATTTTCAAATATATATATATATAATCGAATATACGTCA
980318 TCCGAAAATATT
196 TCCGAAAATATT
* * * *
980330 TGTATCTATTTTTTGTTTGAATATTTTGGTTGATTTTTTAACTTTTTC-CCGTATGATCCTTGTA
1 TGTATCTATTTTTTGTTCGAATATTTTGGTTGAGTTTTTAACTTTTTCTACGTATGATCCTTATA
* * * *
980394 TGATATAAAATGATTAGTTTTAATGTTATAGGAAATAT-TT-AAAACGTGTAGTTTATGATGATA
66 TGATATAAAATGATTAGTTTCAATGTTATAAGAAA-ATGTTCAAAACATGGAGTTTATGATGATA
*
980457 ATTGTAAATTATTATTGTAATTTTAAACATTTTCAAATATATATATATATA
130 ATTGTAAATCATTATTGTAATTTTAAACATTTTCAAATATATATATATATA
980508 TATATATATA
Statistics
Matches: 156, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
205 65 0.42
206 45 0.29
207 46 0.29
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (207 bp):
TGTATCTATTTTTTGTTCGAATATTTTGGTTGAGTTTTTAACTTTTTCTACGTATGATCCTTATA
TGATATAAAATGATTAGTTTCAATGTTATAAGAAAATGTTCAAAACATGGAGTTTATGATGATAA
TTGTAAATCATTATTGTAATTTTAAACATTTTCAAATATATATATATATAATCGAATATACGTCA
TCCGAAAATATT
Found at i:980500 original size:2 final size:2
Alignment explanation
Indices: 980493--980527 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
980483 ACATTTTCAA
980493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
980528 ACAAATGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:986852 original size:29 final size:27
Alignment explanation
Indices: 986795--986854 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
986785 CAACCCCCTA
*
986795 AAATTTTATAAGTTCTCCCCATACTTG
1 AAATTTTATAAGTTCTCCCCATACATG
*
986822 AAATTTTATAAGTTCTCTCCTCCTACATG
1 AAATTTTATAAGTTCTC-CC-CATACATG
986851 AAAT
1 AAAT
986855 CTTGCGTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 17 0.59
28 2 0.07
29 10 0.34
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.40
Consensus pattern (27 bp):
AAATTTTATAAGTTCTCCCCATACATG
Found at i:992559 original size:5 final size:5
Alignment explanation
Indices: 992551--992580 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
992541 AGAAAGAAAA
992551 GAGTT GAGTT GAGTT GAGTT GAGTT GAGTT
1 GAGTT GAGTT GAGTT GAGTT GAGTT GAGTT
992581 CAAGAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GAGTT
Found at i:994755 original size:60 final size:60
Alignment explanation
Indices: 994620--994793 Score: 158
Period size: 60 Copynumber: 2.9 Consensus size: 60
994610 GTTCTCAAGA
* * * *
994620 TATGACCCTCATTT-TAAATCAGTCCCTAAACTTTTGAATTTTTCAATTTCAT-CCTCAAAC
1 TATGACTCTC-TTTCTAAATCAGTCCTTAAACTTTTGAAATTCT-AATTTCATCCCTCAAAC
* * * *
994680 TATGGCTCCCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCCT-AAA-
1 TATGACTCTCTTTCTAAATCAGTCCTTAAACTTTTGAA-ATTCTAATTTCATCCCTCAAAC
* * * * *
994739 TCATGACTCTCTTTCTAAATCGGTCATCAAACTTTTGAATATTCCAAATTCATCC
1 T-ATGACTCTCTTTCTAAATCAGTCCTTAAACTTTTGAA-ATTCTAATTTCATCC
994794 AAATATGTAA
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
59 3 0.03
60 83 0.90
61 6 0.07
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.39
Consensus pattern (60 bp):
TATGACTCTCTTTCTAAATCAGTCCTTAAACTTTTGAAATTCTAATTTCATCCCTCAAAC
Found at i:995075 original size:59 final size:60
Alignment explanation
Indices: 994948--995090 Score: 171
Period size: 59 Copynumber: 2.4 Consensus size: 60
994938 AACATTTATG
* ** * * *
994948 GACCAATTTAGAATGATAGTCATAGTTTAGGGATGAAATTGGAAAGCTAAAAAGTTTGAG
1 GACCAATTTAGAATGATAGTCATAGTTTAGGGATGAAACTAAAAAACTAAAAAGTTTAAA
* * * *
995008 GACTAATTTAGAATTATAGTCATA-TTTAGGGATGAAACTAAAAAATTTAAAAGTTTAAA
1 GACCAATTTAGAATGATAGTCATAGTTTAGGGATGAAACTAAAAAACTAAAAAGTTTAAA
* *
995067 GACCAATTTAAAATGAGAGTCATA
1 GACCAATTTAGAATGATAGTCATA
995091 CTTTGAGGAT
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 47 0.68
60 22 0.32
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (60 bp):
GACCAATTTAGAATGATAGTCATAGTTTAGGGATGAAACTAAAAAACTAAAAAGTTTAAA
Found at i:995319 original size:2 final size:2
Alignment explanation
Indices: 995314--995355 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
995304 TAATTTACAT
995314 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
995356 CTTTGACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:995698 original size:2 final size:2
Alignment explanation
Indices: 995691--995715 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
995681 CGATTTTTAA
995691 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
995716 GCACGCATAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:998674 original size:228 final size:228
Alignment explanation
Indices: 998278--998767 Score: 883
Period size: 228 Copynumber: 2.1 Consensus size: 228
998268 TATTGTAAAT
* * *
998278 TATATATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTT
1 TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATT
998343 TAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT
66 TAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT
*
998408 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AA
131 ATTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAA
998472 ATTGAAACATAAATTACATAACTTTCAAAAAAG
196 ATTGAAACATAAATTACATAACTTTCAAAAAAG
998505 TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATAT
1 TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATAT
* * *
998570 TTGGTTAATATTGTTAAATTTAAATTTTAAATAATATTTTATAAAATATCAAAACAATCAAATAA
65 TTAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA
*
998635 TATTTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATA
130 TATTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATA
*
998700 AATTGAAACATAAATTACATAACTTTCAAAGAAG
195 AATTGAAACATAAATTACATAACTTTCAAAAAAG
998734 TATATATCATTTTTATAAAAGTGTCCATACTTAT
1 TATATATCATTTTTATAAAAGTGTCCATACTTAT
998768 AAAAGTAGGT
Statistics
Matches: 252, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
227 40 0.16
228 144 0.57
229 68 0.27
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (228 bp):
TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATT
TAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT
ATTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAA
ATTGAAACATAAATTACATAACTTTCAAAAAAG
Found at i:999069 original size:20 final size:19
Alignment explanation
Indices: 999046--999092 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
999036 CGATATACCA
999046 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
999066 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
999086 GGTAAAA
1 GGTAAAA
999093 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:999188 original size:181 final size:182
Alignment explanation
Indices: 998834--999306 Score: 689
Period size: 181 Copynumber: 2.6 Consensus size: 182
998824 GATCCAAATT
* * * *
998834 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * * *
998898 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATATGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
998963 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
999016 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
999081 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
999145 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * * *
999197 AAAAATATATCGATCCACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
999262 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
999307 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 166 0.63
182 97 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:999275 original size:17 final size:19
Alignment explanation
Indices: 999236--999278 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
999226 AAGTAAAAAT
999236 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
999256 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
999273 ATGATA
1 ATGATA
999279 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1001528 original size:21 final size:21
Alignment explanation
Indices: 1001501--1001565 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1001491 AAGACAATCA
*
1001501 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
1001522 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1001543 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1001564 AG
1 AG
1001566 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1001641 original size:33 final size:33
Alignment explanation
Indices: 1001599--1001664 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1001589 AAATAGATGG
*
1001599 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1001632 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1001665 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1004539 original size:25 final size:25
Alignment explanation
Indices: 1004505--1004574 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
1004495 AAATTCGCAG
1004505 TACATATTTAGGTATGTACAATAAC
1 TACATATTTAGGTATGTACAATAAC
****
1004530 TACATATTTAGGTATGTTTGTTAAC
1 TACATATTTAGGTATGTACAATAAC
*
1004555 TACATATTTAGGTATATACA
1 TACATATTTAGGTATGTACA
1004575 TCTTTTGAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (25 bp):
TACATATTTAGGTATGTACAATAAC
Found at i:1004903 original size:22 final size:22
Alignment explanation
Indices: 1004858--1004903 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1004848 ATTACATAAC
*
1004858 TTTTAAAAAAAGTATCGATCCT
1 TTTTAAAAAAAGTATCGAACCT
*
1004880 TTTTATAAAAAGTAT-GAACACT
1 TTTTAAAAAAAGTATCGAAC-CT
1004902 TT
1 TT
1004904 CAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTAAAAAAAGTATCGAACCT
Found at i:1004952 original size:23 final size:23
Alignment explanation
Indices: 1004921--1004993 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1004911 ATAGGTAAAC
*
1004921 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1004944 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1004967 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1004990 ATAT
1 ATAT
1004994 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1005442 original size:18 final size:18
Alignment explanation
Indices: 1005421--1005457 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1005411 GTAATTGGAG
1005421 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1005439 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1005457 T
1 T
1005458 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1005465 original size:24 final size:24
Alignment explanation
Indices: 1005413--1005459 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1005403 TTTCATATGT
* *
1005413 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1005437 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1005460 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1005770 original size:34 final size:34
Alignment explanation
Indices: 1005732--1005797 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1005722 AAATCCAAAG
*
1005732 CTCATATGGTGCCAAGCAAAAGGAAATCAAAAAT
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
1005766 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1005798 TCTACAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (34 bp):
CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
Found at i:1006256 original size:23 final size:23
Alignment explanation
Indices: 1006226--1006293 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1006216 TAAACATGTG
1006226 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1006249 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1006272 ATGTAATAGGTAGTGGTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1006294 TGTAAAGTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1006497 original size:30 final size:29
Alignment explanation
Indices: 1006438--1006504 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1006428 GTTACGATAT
* *
1006438 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
1006468 ATATTTTATAAAATATAAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
1006498 ATTTTTT
1 ATATTTT
1006505 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:1009192 original size:260 final size:261
Alignment explanation
Indices: 1008707--1009228 Score: 947
Period size: 260 Copynumber: 2.0 Consensus size: 261
1008697 ACAGTTTTGG
* * *
1008707 CATTCCAATAGCATGAAAAATGAAAAAGATCTATTGTATTTTTTCGTCTTTCACATTATTGTGTT
1 CATTCCAATAGCATGAAAAATGAAAAAGATCTATTGTATTTTTGCGTCTTTCACATTAATGTGTC
* * *
1008772 GATCACATTATCTCAAAAAATAATTTCGATAACACCTTACAAGAGTCAATTATTTTTTTCAACAC
66 GATCACATCATCTCAAAAAATAACTTCGATAACACCTCACAAGAGTCAATTATTTTTTTCAACAC
*
1008837 CCCACACGAGCAATTCAGTCCAAGTATGTTAGTTGAAATCACTACTTAATTTCTGGGTAAACATG
131 CCCACACGAGCAATTCAGCCCAAGTATGTTAGTTGAAATCACTACTTAATTTCTGGGTAAACATG
*
1008902 CATTTGGTACTTGAACTTTGTATTAACATTCAATTTGGCACTTAATTTTTATTTTCAATTAGGTA
196 CATTTGGTACTTGAACTTAGTATTAACATTCAATTTGGCACTTAATTTTTATTTTCAATTAGGTA
1008967 A
261 A
*
1008968 CATTCCAATAGCGTGAAAAATGAAAAAGATCTATTGTATTTTTGCGTCTTTCACATTAATGTGTC
1 CATTCCAATAGCATGAAAAATGAAAAAGATCTATTGTATTTTTGCGTCTTTCACATTAATGTGTC
*
1009033 GATCACATCATCTCAAAAAATAACTTCGATAAGACCTCACAAGAGTCAATTA-TTTTTTCAACAC
66 GATCACATCATCTCAAAAAATAACTTCGATAACACCTCACAAGAGTCAATTATTTTTTTCAACAC
1009097 CCCACACGAGCAATTCAGCCCAAGTATGTTAGTTGAAATCACTACTTAATTTCTGGGTAAACATG
131 CCCACACGAGCAATTCAGCCCAAGTATGTTAGTTGAAATCACTACTTAATTTCTGGGTAAACATG
1009162 CATTTGGTACTTGAACTTAGTATTAACATTCAATTTGGCACTTAATTTTTATTTTCAATTAGGTA
196 CATTTGGTACTTGAACTTAGTATTAACATTCAATTTGGCACTTAATTTTTATTTTCAATTAGGTA
1009227 A
261 A
1009228 C
1 C
1009229 GTTTTGGTTC
Statistics
Matches: 251, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
260 142 0.57
261 109 0.43
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (261 bp):
CATTCCAATAGCATGAAAAATGAAAAAGATCTATTGTATTTTTGCGTCTTTCACATTAATGTGTC
GATCACATCATCTCAAAAAATAACTTCGATAACACCTCACAAGAGTCAATTATTTTTTTCAACAC
CCCACACGAGCAATTCAGCCCAAGTATGTTAGTTGAAATCACTACTTAATTTCTGGGTAAACATG
CATTTGGTACTTGAACTTAGTATTAACATTCAATTTGGCACTTAATTTTTATTTTCAATTAGGTA
A
Found at i:1009947 original size:59 final size:60
Alignment explanation
Indices: 1009841--1009985 Score: 147
Period size: 59 Copynumber: 2.4 Consensus size: 60
1009831 ACTTTTAAAT
* *
1009841 ATTTCAATTTCATCCTTAAACTATGAT--TATCATTCTAAATTTATCCTCAAACTT-TTGAACA
1 ATTTCAATTTCATCC-CAAACTAT-ATCCT-TCATTCTAAATTTATCCTCAAAATTGTT-AACA
* * * *
1009902 ATTT-ATTTTCATCCCAAACTATATCCTTCATTCTCAA-TTAGTCCTCAAAATTGTTCACC
1 ATTTCAATTTCATCCCAAACTATATCCTTCATTCTAAATTTA-TCCTCAAAATTGTTAACA
*
1009961 ATTTCAATTTCATCCCAAATTATAT
1 ATTTCAATTTCATCCCAAACTATAT
1009986 GTATATACTA
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
58 5 0.07
59 32 0.45
60 30 0.42
61 4 0.06
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (60 bp):
ATTTCAATTTCATCCCAAACTATATCCTTCATTCTAAATTTATCCTCAAAATTGTTAACA
Found at i:1010988 original size:96 final size:96
Alignment explanation
Indices: 1010824--1011013 Score: 335
Period size: 96 Copynumber: 2.0 Consensus size: 96
1010814 TCTTATACCC
* * *
1010824 AAACCTTAAATTCTAAATCATAAACAATAATAAATATTTTAAACGTTGATGCAATTGAGCAATTT
1 AAACCATAAATTCTAAATCATAAACAATAATAAATATTTTAAACATTGATACAATTGAGCAATTT
1010889 CTAGGACTAACAATAGGGACAAAAATGATTA
66 CTAGGACTAACAATAGGGACAAAAATGATTA
*
1010920 AAACCATAAATTCTAAATCTTAAACAATAATAAATATTTTAAACATTGATACAATTGAGCAATTT
1 AAACCATAAATTCTAAATCATAAACAATAATAAATATTTTAAACATTGATACAATTGAGCAATTT
*
1010985 CTAGGACTAACGATAGGGACAAAAATGAT
66 CTAGGACTAACAATAGGGACAAAAATGAT
1011014 AAATTGAGTC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (96 bp):
AAACCATAAATTCTAAATCATAAACAATAATAAATATTTTAAACATTGATACAATTGAGCAATTT
CTAGGACTAACAATAGGGACAAAAATGATTA
Found at i:1025358 original size:29 final size:29
Alignment explanation
Indices: 1025316--1025390 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
1025306 AACCCAACCA
**
1025316 TAGGTCGCCATGCACTCCCAGCGACCTTC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
1025345 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
1025374 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
1025391 GGGGAGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.39, G:0.27, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:1025399 original size:29 final size:29
Alignment explanation
Indices: 1025346--1025404 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1025336 GCGACCTTCT
*
1025346 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGAGACCAAGG
* **
1025375 AGGTCGCCATGCACTCGGGGAGACCAAGG
1 AGGTCGCCATGCACGCCCGGAGACCAAGG
1025404 A
1 A
1025405 TTCATGCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.32, G:0.36, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGAGACCAAGG
Found at i:1025652 original size:29 final size:29
Alignment explanation
Indices: 1025619--1025703 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
1025609 AGCAGGGGAT
* * **
1025619 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
1025648 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
1025677 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
1025704 GCCACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:1026541 original size:18 final size:17
Alignment explanation
Indices: 1026502--1026548 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1026492 AACAGGTATG
*
1026502 TATTTTTCTT-AAAAAT
1 TATTTTTTTTAAAAAAT
1026518 TAATTTTTTTTAAAATAAT
1 T-ATTTTTTTTAAAA-AAT
*
1026537 TATTTATTTTAA
1 TATTTTTTTTAA
1026549 TGATTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 8 0.31
18 13 0.50
19 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTTTTAAAAAAT
Found at i:1030093 original size:17 final size:18
Alignment explanation
Indices: 1030056--1030096 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1030046 CTATTATGTA
*
1030056 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1030074 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1030091 TTTACT
1 TTTACT
1030097 AATATGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1030352 original size:111 final size:111
Alignment explanation
Indices: 1030170--1030379 Score: 393
Period size: 111 Copynumber: 1.9 Consensus size: 111
1030160 ATCTCTACTC
*
1030170 TTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAATAATTAGTTGAT
1 TTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGAT
*
1030235 TTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCGACAA
66 TTATTTAATACATGATTATTAGATTAAGAATTAAATATCTCGACAA
*
1030281 TTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGAT
1 TTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGAT
1030346 TTATTTAATACATGATTATTAGATTAAGAATTAA
66 TTATTTAATACATGATTATTAGATTAAGAATTAA
1030380 TTTTTGTAAT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 96 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (111 bp):
TTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGAT
TTATTTAATACATGATTATTAGATTAAGAATTAAATATCTCGACAA
Found at i:1032507 original size:35 final size:33
Alignment explanation
Indices: 1032468--1032552 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
1032458 TTATTTCAGT
1032468 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
* *
1032503 TAATTTGGTTATCATTTATCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
1032538 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1032553 TAAATACCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:1038987 original size:20 final size:20
Alignment explanation
Indices: 1038959--1039052 Score: 64
Period size: 20 Copynumber: 4.3 Consensus size: 20
1038949 ACTAATGGAA
1038959 GAAGAAGAAATTGA-TTTATG
1 GAAGAAGAAA-TGAGTTTATG
*
1038979 GAAGGAGAAATGAGTTTATG
1 GAAGAAGAAATGAGTTTATG
* *
1038999 TATAAGAAAAAAAAATGAGTTTATG
1 -----GAAGAAGAAATGAGTTTATG
*
1039024 GAAGAAGAAGAGATGAGTTTATA
1 GAAGAAG-A-A-ATGAGTTTATG
1039047 GAAGAA
1 GAAGAA
1039053 AAAAATAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
19 3 0.05
20 20 0.34
21 1 0.02
22 1 0.02
23 16 0.28
25 17 0.29
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (20 bp):
GAAGAAGAAATGAGTTTATG
Found at i:1039039 original size:23 final size:23
Alignment explanation
Indices: 1038953--1039105 Score: 120
Period size: 23 Copynumber: 6.7 Consensus size: 23
1038943 TCTCAGACTA
1038953 ATGGAAGAAGAAGAAATTGA-TTT
1 ATGGAAGAAGAAGAAA-TGAGTTT
1038976 ATGGAAG--G-AGAAATGAGTTT
1 ATGGAAGAAGAAGAAATGAGTTT
* * *
1038996 ATGTATAAGAAAAAAAAATGAGTTT
1 ATG--GAAGAAGAAGAAATGAGTTT
*
1039021 ATGGAAGAAGAAGAGATGAGTTT
1 ATGGAAGAAGAAGAAATGAGTTT
* *
1039044 ATAGAAGAA-AA-AAATAAAATGTTT
1 ATGGAAGAAGAAGAAAT--GA-GTTT
* * * *
1039068 ATGGAATAAAAAGAAACGTGTTT
1 ATGGAAGAAGAAGAAATGAGTTT
1039091 ATGGAAGAAGAAGAA
1 ATGGAAGAAGAAGAA
1039106 TGATTCATAA
Statistics
Matches: 102, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.03
20 11 0.11
21 4 0.04
22 5 0.05
23 49 0.48
24 11 0.11
25 16 0.16
26 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.25, T:0.24
Consensus pattern (23 bp):
ATGGAAGAAGAAGAAATGAGTTT
Found at i:1041029 original size:25 final size:25
Alignment explanation
Indices: 1040993--1041068 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 25
1040983 AAGAGTCGAG
*
1040993 ATTTCTATGTGGTCATTCGGGACAA
1 ATTTCTACGTGGTCATTCGGGACAA
*
1041018 ATTTCTACGTGGTCTTTCGGGACAA
1 ATTTCTACGTGGTCATTCGGGACAA
* * * *
1041043 A-TTCTACGCGGTTATTCAGAACAA
1 ATTTCTACGTGGTCATTCGGGACAA
1041067 AT
1 AT
1041069 CTATGTGGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 19 0.44
25 24 0.56
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (25 bp):
ATTTCTACGTGGTCATTCGGGACAA
Found at i:1052169 original size:19 final size:19
Alignment explanation
Indices: 1052145--1052182 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1052135 GACACAACTG
1052145 CCCTCGAGGATATTAGCAA
1 CCCTCGAGGATATTAGCAA
1052164 CCCTCGAGGATATTAGCAA
1 CCCTCGAGGATATTAGCAA
1052183 AGCTTATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (19 bp):
CCCTCGAGGATATTAGCAA
Found at i:1056193 original size:18 final size:19
Alignment explanation
Indices: 1056172--1056209 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1056162 TAAAAATACA
1056172 AAAAAATATA-ATTATAAT
1 AAAAAATATATATTATAAT
*
1056190 -AAAAATATATTTTATAAT
1 AAAAAATATATATTATAAT
1056208 AA
1 AA
1056210 CTCACCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.53
18 7 0.41
19 1 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAATATATATTATAAT
Found at i:1056810 original size:60 final size:60
Alignment explanation
Indices: 1056709--1056870 Score: 202
Period size: 60 Copynumber: 2.7 Consensus size: 60
1056699 AAATATGATT
* **
1056709 CTCATTCTAAATTGGTCCTTAAACCTTTGATTATT-TCAATTTCATCCTCAAACTATAATA
1 CTCATTCTAAATTGGTCCTTAAACTTTTGAACATTCT-AATTTCATCCTCAAACTATAATA
* * * *
1056769 CTCATTATAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCTCAAACTATGATC
1 CTCATTCTAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCTCAAACTATAATA
** *
1056829 CTCATTCTAAATTGGTCCGCAAACTTTTAAATCATTC-AATTT
1 CTCATTCTAAATTGGTCCTTAAACTTTTGAA-CATTCTAATTT
1056871 TATTCCCAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
60 82 0.93
61 6 0.07
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.41
Consensus pattern (60 bp):
CTCATTCTAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCTCAAACTATAATA
Found at i:1057435 original size:31 final size:31
Alignment explanation
Indices: 1057400--1057472 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
1057390 AAATGTATCA
1057400 TTGCCCCCTAACATATGTCATTTATACCAAG
1 TTGCCCCCTAACATATGTCATTTATACCAAG
1057431 TTGCCCCCTAACATATGTCATTTATACCAAG
1 TTGCCCCCTAACATATGTCATTTATACCAAG
1057462 TTGCCCCCTAA
1 TTGCCCCCTAA
1057473 AGTATTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (31 bp):
TTGCCCCCTAACATATGTCATTTATACCAAG
Found at i:1059504 original size:21 final size:22
Alignment explanation
Indices: 1059480--1059521 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1059470 GTAATATAAA
1059480 ATAATAATTAATTAA-AATTAT
1 ATAATAATTAATTAATAATTAT
*
1059501 ATAATATTTAATTAATAATTA
1 ATAATAATTAATTAATAATTA
1059522 AATGATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATAATTAATTAATAATTAT
Found at i:1064018 original size:16 final size:17
Alignment explanation
Indices: 1063968--1064018 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
1063958 TAAAAAAATA
1063968 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1063985 GA-TT-AAA-TTAAGAGT
1 AATTTGAAAGTT-AGAGT
1064000 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1064016 AAT
1 AAT
1064019 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 10 0.36
17 5 0.18
18 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1064290 original size:33 final size:33
Alignment explanation
Indices: 1064225--1064291 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1064215 ATACTAAAAT
* * *
1064225 AAAATAAAAATTAAATATTAGATATGATTTAAA
1 AAAATAAAAATTAAATATTAGAAACGAATTAAA
*
1064258 AAAATAAAAATTTAGATATTA-AAACGAATTAAA
1 AAAATAAAAA-TTAAATATTAGAAACGAATTAAA
1064291 A
1 A
1064292 TTGATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (33 bp):
AAAATAAAAATTAAATATTAGAAACGAATTAAA
Found at i:1072385 original size:27 final size:27
Alignment explanation
Indices: 1072355--1072412 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1072345 CCATCATTTG
**
1072355 AGATGATGCATCGTATTCCATCCTTCA
1 AGATGATGCATAATATTCCATCCTTCA
* * *
1072382 AGATGATGTATAATATTTCATCCTTCG
1 AGATGATGCATAATATTCCATCCTTCA
1072409 AGAT
1 AGAT
1072413 CATACACATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (27 bp):
AGATGATGCATAATATTCCATCCTTCA
Found at i:1073251 original size:46 final size:46
Alignment explanation
Indices: 1073077--1073253 Score: 138
Period size: 46 Copynumber: 3.8 Consensus size: 46
1073067 AAATTAAACT
* * * * **
1073077 TTACCATTCTATAAGGATACACCAGCTTGTAATTTGGTAATTAAAA
1 TTACCATCCAATAAGGATACACCAGCCTGTAATTCGGTAATTGGAA
* * * * * * *
1073123 TTACCATCAAATAAGGATGCATCAACCTGTATTTCGATAATTGGGA
1 TTACCATCCAATAAGGATACACCAGCCTGTAATTCGGTAATTGGAA
* * *** * * * *
1073169 TTACTATCCAATGAGGATTTTCCGGCCTGCATTTCGGTGATTGGAA
1 TTACCATCCAATAAGGATACACCAGCCTGTAATTCGGTAATTGGAA
* *
1073215 TTACCATCCAATAAGGATACAACAGCATGTAATTCGGTA
1 TTACCATCCAATAAGGATACACCAGCCTGTAATTCGGTA
1073254 TTGTTACTCT
Statistics
Matches: 94, Mismatches: 37, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
46 94 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (46 bp):
TTACCATCCAATAAGGATACACCAGCCTGTAATTCGGTAATTGGAA
Found at i:1073804 original size:15 final size:16
Alignment explanation
Indices: 1073776--1073809 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1073766 TGAGACATTA
*
1073776 CCCGTCCCCGCATCCG
1 CCCGTCCCCACATCCG
1073792 CCCG-CCCCACATCCG
1 CCCGTCCCCACATCCG
1073807 CCC
1 CCC
1073810 ACCCAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.09, C:0.68, G:0.15, T:0.09
Consensus pattern (16 bp):
CCCGTCCCCACATCCG
Found at i:1083024 original size:22 final size:22
Alignment explanation
Indices: 1082996--1083046 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1082986 CTATTAATTA
1082996 TGTTTATTGATTTTAGATGTTT
1 TGTTTATTGATTTTAGATGTTT
1083018 TGTTTATTGATTTTAGATGTTT
1 TGTTTATTGATTTTAGATGTTT
1083040 TGTTTAT
1 TGTTTAT
1083047 AATAAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (22 bp):
TGTTTATTGATTTTAGATGTTT
Found at i:1085030 original size:22 final size:21
Alignment explanation
Indices: 1084991--1085034 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1084981 CATTTACAAA
*
1084991 TAAATAATTAACCGACTGCAAT
1 TAAATAATTAACCAACTG-AAT
* *
1085013 TAAATATTTCACCAACTGAAT
1 TAAATAATTAACCAACTGAAT
1085034 T
1 T
1085035 TGCACATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (21 bp):
TAAATAATTAACCAACTGAAT
Found at i:1089061 original size:2 final size:2
Alignment explanation
Indices: 1089056--1089116 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
1089046 GCGCAAAGTT
*
1089056 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1089096 AA AA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
1089117 GTTATAAACA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1101242 original size:12 final size:12
Alignment explanation
Indices: 1101211--1101235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1101201 ACTTGAAAGT
1101211 AAAAAAAGAAAA
1 AAAAAAAGAAAA
1101223 AAAAAAAGAAAA
1 AAAAAAAGAAAA
1101235 A
1 A
1101236 GGAAAAGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:1101473 original size:17 final size:18
Alignment explanation
Indices: 1101436--1101473 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1101426 TTATTATTAT
*
1101436 TAAAATATAAGAATAATA
1 TAAAATATAAGAATAAAA
*
1101454 TAAAAT-TAATAATAAAA
1 TAAAATATAAGAATAAAA
1101471 TAA
1 TAA
1101474 TATTTTCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAATATAAGAATAAAA
Found at i:1102749 original size:27 final size:26
Alignment explanation
Indices: 1102719--1102773 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
1102709 GGCTGATAGT
*
1102719 TGATTTCAGTAGTTGGTTTGATCTAAC
1 TGATTTCAGTAGTTGATTTGAT-TAAC
* *
1102746 TGATTTGATTAGTTGATTTGATTAAC
1 TGATTTCAGTAGTTGATTTGATTAAC
1102772 TG
1 TG
1102774 TTTATATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (26 bp):
TGATTTCAGTAGTTGATTTGATTAAC
Found at i:1102764 original size:13 final size:13
Alignment explanation
Indices: 1102715--1102769 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1102705 TGATGGCTGA
* *
1102715 TAGTTGATTTCAG
1 TAGTTGATTTGAT
*
1102728 TAGTTGGTTTGAT
1 TAGTTGATTTGAT
**
1102741 CTAACTGATTTGAT
1 -TAGTTGATTTGAT
1102755 TAGTTGATTTGAT
1 TAGTTGATTTGAT
1102768 TA
1 TA
1102770 ACTGTTTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (13 bp):
TAGTTGATTTGAT
Found at i:1107668 original size:12 final size:11
Alignment explanation
Indices: 1107635--1107673 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
1107625 AATATGCTCT
1107635 ATTTTGTTTT-
1 ATTTTGTTTTG
*
1107645 AATTTGTTTTG
1 ATTTTGTTTTG
1107656 ATTTTGATTTTG
1 ATTTTG-TTTTG
1107668 ATTTTG
1 ATTTTG
1107674 GCTTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 5 0.20
12 11 0.44
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (11 bp):
ATTTTGTTTTG
Found at i:1107721 original size:23 final size:23
Alignment explanation
Indices: 1107695--1107743 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1107685 TTATGATCCA
* *
1107695 AACTTTACTAATTTCTAACAACT
1 AACTTTACTAACTTATAACAACT
* *
1107718 AACTTTTCTAACTTATAACTACT
1 AACTTTACTAACTTATAACAACT
1107741 AAC
1 AAC
1107744 CACTAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTTACTAACTTATAACAACT
Found at i:1108302 original size:26 final size:26
Alignment explanation
Indices: 1108273--1108331 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
1108263 AATTTGAGAT
1108273 ATTTCTTATTTTGAATAAAATTAATA
1 ATTTCTTATTTTGAATAAAATTAATA
1108299 ATTTCTTATTTTGAATAAAATTAATA
1 ATTTCTTATTTTGAATAAAATTAATA
1108325 ATTTCTT
1 ATTTCTT
1108332 TTAAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (26 bp):
ATTTCTTATTTTGAATAAAATTAATA
Found at i:1109092 original size:25 final size:25
Alignment explanation
Indices: 1109064--1109113 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1109054 TAAATATGAG
1109064 AGTGCAATGCCTCTCCCATATTTTT
1 AGTGCAATGCCTCTCCCATATTTTT
1109089 AGTGCAATGCCTCTCCCATATTTTT
1 AGTGCAATGCCTCTCCCATATTTTT
1109114 TTTCACCAAT
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:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (25 bp):
AGTGCAATGCCTCTCCCATATTTTT
Done.