Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004338.1 Hibiscus syriacus cultivar Beakdansim tig00009508_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: 171413
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6177 original size:18 final size:18
Alignment explanation
Indices: 6154--6191 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6144 AACCAAATTC
6154 CTTCGCATATTCCCAATG
1 CTTCGCATATTCCCAATG
6172 CTTCGCATATTCCCAATG
1 CTTCGCATATTCCCAATG
6190 CT
1 CT
6192 AGTGCTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (18 bp):
CTTCGCATATTCCCAATG
Found at i:14623 original size:17 final size:17
Alignment explanation
Indices: 14601--14654 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
14591 ACTAATTATT
14601 AATAATAATTTAAATTA
1 AATAATAATTTAAATTA
* *
14618 AATAATAA-CTAAATATT
1 AATAATAATTTAAAT-TA
*
14635 ACTAATAATTTAAATTA
1 AATAATAATTTAAATTA
14652 AAT
1 AAT
14655 TAAAACGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 5 0.17
17 19 0.66
18 5 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATAATTTAAATTA
Found at i:14628 original size:34 final size:36
Alignment explanation
Indices: 14578--14654 Score: 122
Period size: 34 Copynumber: 2.2 Consensus size: 36
14568 ATAATCATGC
*
14578 ATTAAATGAATCAACTAATTATTAATAATAATTTAA
1 ATTAAATGAATCAACTAAATATTAATAATAATTTAA
*
14614 ATTAAAT-AAT-AACTAAATATTACTAATAATTTAA
1 ATTAAATGAATCAACTAAATATTAATAATAATTTAA
14648 ATTAAAT
1 ATTAAAT
14655 TAAAACGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 29 0.74
35 3 0.08
36 7 0.18
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (36 bp):
ATTAAATGAATCAACTAAATATTAATAATAATTTAA
Found at i:22185 original size:3 final size:3
Alignment explanation
Indices: 22177--22205 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
22167 CTTCACATTG
22177 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
22206 TCAATTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35982 original size:22 final size:22
Alignment explanation
Indices: 35939--35991 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
35929 CTAATAGTTA
35939 TAAATTAGTTAAAAACTTAAAGG
1 TAAATTA-TTAAAAACTTAAAGG
*
35962 TAAATTATTTAAAA-TTAAAAGG
1 TAAATTATTAAAAACTT-AAAGG
35984 TAAATTAT
1 TAAATTAT
35992 ATTAGTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 19 0.68
23 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (22 bp):
TAAATTATTAAAAACTTAAAGG
Found at i:36737 original size:22 final size:23
Alignment explanation
Indices: 36709--36760 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
36699 GATCAATGGT
36709 ATAATTTACCCATT-AA-TTTTAA
1 ATAATTTA-CCATTAAATTTTTAA
36731 ATAATTTACCATTAAATTTTTAA
1 ATAATTTACCATTAAATTTTTAA
*
36754 TTAATTT
1 ATAATTT
36761 TTAATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 10 0.37
23 12 0.44
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAATTTACCATTAAATTTTTAA
Found at i:48489 original size:22 final size:22
Alignment explanation
Indices: 48464--48532 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 22
48454 ATATATTTAT
*
48464 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAAAA
*
48486 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATA--ATATAAAA
*
48510 TAATCAATTATATAGTAATATAA
1 TAAT--ATT-TATAATAATATAA
48533 GATATTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 13 0.34
24 11 0.29
25 6 0.16
26 3 0.08
27 5 0.13
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (22 bp):
TAATATTTATAATAATATAAAA
Found at i:48512 original size:34 final size:34
Alignment explanation
Indices: 48436--48513 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 34
48426 CAAAATATTA
*
48436 ATTAT-TAAAAT-ATTTAAAATATATTTATTAAT
1 ATTATATAAAATAATATAAAATATATTTATTAAT
*
48468 ATT-TAT--AATAATATAATATAATATTT-TTAAT
1 ATTATATAAAATAATATAAAAT-ATATTTATTAAT
48499 ATTATATAAAATAAT
1 ATTATATAAAATAAT
48514 CAATTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 3 0.08
31 16 0.42
32 13 0.34
34 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTATATAAAATAATATAAAATATATTTATTAAT
Found at i:48588 original size:25 final size:26
Alignment explanation
Indices: 48542--48611 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
48532 AGATATTATA
*
48542 TTTTTAT-T-TTAATAATATAATAAT
1 TTTTTATATATTAATAATAGAATAAT
48566 TTTTTATATATTAATAAT-GAATAAT
1 TTTTTATATATTAATAATAGAATAAT
*
48591 ATTTTATATATTTAAATAATA
1 TTTTTATATA-TT-AATAATA
48612 TTTTAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 7 0.18
25 16 0.41
26 10 0.26
27 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
TTTTTATATATTAATAATAGAATAAT
Found at i:48613 original size:75 final size:77
Alignment explanation
Indices: 48445--48614 Score: 169
Period size: 75 Copynumber: 2.2 Consensus size: 77
48435 AATTATTAAA
*
48445 ATATTTAAA-ATATATTTATTAATATTTATAATAATATAATATAATATTTTTAATATTATATAAA
1 ATATTTAAATAGATATTTATTAATATTTATAATAATATAATATAATATTTTTAATATTATATAAA
48509 ATAATCAATTAT
66 ATAATCAATTAT
* **
48521 ATA-GTAATATAAGATATTATATTTTTATTT-TAATAATAT-A-ATAAT-TTTTTATATATTA-A
1 ATATTTAA-AT-AGATATT-TATTAATATTTATAATAATATAATATAATATTTTTA-ATATTATA
*
48580 TAATGAATAAT-ATTTTAT
62 TAA--AATAATCA-ATTAT
48598 ATATTTAAATA-ATATTT
1 ATATTTAAATAGATATTT
48615 TAATAAAGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
74 1 0.01
75 18 0.23
76 17 0.22
77 16 0.20
78 18 0.23
79 9 0.11
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (77 bp):
ATATTTAAATAGATATTTATTAATATTTATAATAATATAATATAATATTTTTAATATTATATAAA
ATAATCAATTAT
Found at i:48948 original size:14 final size:15
Alignment explanation
Indices: 48927--48999 Score: 78
Period size: 15 Copynumber: 4.9 Consensus size: 15
48917 TTCTAAAAAT
48927 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
48942 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
48956 GTAATTCATTTTCTA
1 GTAATTCATTTTCCA
*
48971 GTAATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
*
48986 GTAATTTATTTTCC
1 GTAATTCATTTTCC
49000 GAAAAACCAG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
14 16 0.35
15 26 0.57
16 4 0.09
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:48979 original size:30 final size:29
Alignment explanation
Indices: 48927--48999 Score: 110
Period size: 30 Copynumber: 2.5 Consensus size: 29
48917 TTCTAAAAAT
48927 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
* *
48956 GTAATTCATTTTCTAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
*
48986 GTAATTTATTTTCC
1 GTAATTCATTTTCC
49000 GAAAAACCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:58170 original size:20 final size:20
Alignment explanation
Indices: 58145--58187 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
58135 CTGTTTAAGT
*
58145 CATTTAGGATCACATAGATG
1 CATTTAGGAGCACATAGATG
* *
58165 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCACATAGATG
58185 CAT
1 CAT
58188 GTGGTGAAAT
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:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGAGCACATAGATG
Found at i:59641 original size:337 final size:337
Alignment explanation
Indices: 59026--59703 Score: 1347
Period size: 337 Copynumber: 2.0 Consensus size: 337
59016 ATTCCTTAGG
59026 AGATTACTTAAGGTTTGAGAGAATATCTAGGTAGAGTATCATTAGTGTTCGAGAGAAACTAGGGA
1 AGATTACTTAAGGTTTGAGAGAATATCTAGGTAGAGTATCATTAGTGTTCGAGAGAAACTAGGGA
59091 GGAACCACATAAGCAAGGGGTTCTAGATAATAACTATGCCTAATCCACCTTAGAGATAAGGCTAT
66 GGAACCACATAAGCAAGGGGTTCTAGATAATAACTATGCCTAATCCACCTTAGAGATAAGGCTAT
59156 GATTTCATTCTACTAAAAGGAGTTGTGCATGAGCGATAGGTTAGATGTTAATGTTGCCGCAAAAA
131 GATTTCATTCTACTAAAAGGAGTTGTGCATGAGCGATAGGTTAGATGTTAATGTTGCCGCAAAAA
59221 GGTATTACAGAGACATATCATGTTATCTGGACCAATAGGATCACTGCAGGGGCTTACGCCAACCG
196 GGTATTACAGAGACATATCATGTTATCTGGACCAATAGGATCACTGCAGGGGCTTACGCCAACCG
59286 ATTTTGCCAGGGCATCTTAAATCTATCGAGTCCCTTACTAGAGATAGCATAGGGCACCATAGTAA
261 ATTTTGCCAGGGCATCTTAAATCTATCGAGTCCCTTACTAGAGATAGCATAGGGCACCATAGTAA
59351 ACTTTGTCGGAC
326 ACTTTGTCGGAC
*
59363 AGATTACTTAAGGTTTGAGAGAATATCTTGGTAGAGTATCATTAGTGTTCGAGAGAAACTAGGGA
1 AGATTACTTAAGGTTTGAGAGAATATCTAGGTAGAGTATCATTAGTGTTCGAGAGAAACTAGGGA
59428 GGAACCACATAAGCAAGGGGTTCTAGATAATAACTATGCCTAATCCACCTTAGAGATAAGGCTAT
66 GGAACCACATAAGCAAGGGGTTCTAGATAATAACTATGCCTAATCCACCTTAGAGATAAGGCTAT
59493 GATTTCATTCTACTAAAAGGAGTTGTGCATGAGCGATAGGTTAGATGTTAATGTTGCCGCAAAAA
131 GATTTCATTCTACTAAAAGGAGTTGTGCATGAGCGATAGGTTAGATGTTAATGTTGCCGCAAAAA
59558 GGTATTACAGAGACATATCATGTTATCTGGACCAATAGGATCACTGCAGGGGCTTACGCCAACCG
196 GGTATTACAGAGACATATCATGTTATCTGGACCAATAGGATCACTGCAGGGGCTTACGCCAACCG
59623 ATTTTGCCAGGGCATCTTAAATCTATCGAGTCCCTTACTAGAGATAGCATAGGGCACCATAGTAA
261 ATTTTGCCAGGGCATCTTAAATCTATCGAGTCCCTTACTAGAGATAGCATAGGGCACCATAGTAA
59688 ACTTTGTCGGAC
326 ACTTTGTCGGAC
59700 AGAT
1 AGAT
59704 AAGACATAGA
Statistics
Matches: 340, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
337 340 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (337 bp):
AGATTACTTAAGGTTTGAGAGAATATCTAGGTAGAGTATCATTAGTGTTCGAGAGAAACTAGGGA
GGAACCACATAAGCAAGGGGTTCTAGATAATAACTATGCCTAATCCACCTTAGAGATAAGGCTAT
GATTTCATTCTACTAAAAGGAGTTGTGCATGAGCGATAGGTTAGATGTTAATGTTGCCGCAAAAA
GGTATTACAGAGACATATCATGTTATCTGGACCAATAGGATCACTGCAGGGGCTTACGCCAACCG
ATTTTGCCAGGGCATCTTAAATCTATCGAGTCCCTTACTAGAGATAGCATAGGGCACCATAGTAA
ACTTTGTCGGAC
Found at i:61883 original size:21 final size:21
Alignment explanation
Indices: 61841--61893 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
61831 ATTCTGACTA
61841 TCGCATTGCGATATCCCAAAT
1 TCGCATTGCGATATCCCAAAT
* * * *
61862 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATATCCCAAAT
*
61883 TCGCAATGCGA
1 TCGCATTGCGA
61894 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATATCCCAAAT
Found at i:61908 original size:20 final size:20
Alignment explanation
Indices: 61883--61994 Score: 152
Period size: 20 Copynumber: 5.5 Consensus size: 20
61873 TTTTCCTAAT
61883 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
61903 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
61924 TCGCAATGCGATTTCGTAAA
1 TCGCAATGCGAATACGTAAA
*
61944 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
61964 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
61984 TCGCAATGCGA
1 TCGCAATGCGA
61995 TTTACATAGT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 64 0.81
21 15 0.19
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:61958 original size:61 final size:60
Alignment explanation
Indices: 61868--61997 Score: 179
Period size: 61 Copynumber: 2.1 Consensus size: 60
61858 AAATTCGCGT
* **
61868 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAA
1 TGCGA-TTTCCTAAATCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAATCGCAA
* * * *
61930 TGCGATTTCGTAAATCGCAATGTGAATACGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTCCTAAATCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAATCGCAA
61990 TGCGATTT
1 TGCGATTT
61998 ACATAGTGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 19 0.31
61 37 0.61
62 5 0.08
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
TGCGATTTCCTAAATCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAATCGCAA
Found at i:62197 original size:22 final size:22
Alignment explanation
Indices: 62172--62237 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
62162 GGCGATATCC
62172 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
62194 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
62216 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
62238 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:62662 original size:20 final size:19
Alignment explanation
Indices: 62576--62678 Score: 81
Period size: 20 Copynumber: 5.5 Consensus size: 19
62566 CGATTATGTC
62576 GTTGCGATTTTCATTTCGT
1 GTTGCGATTTTCATTTCGT
*
62595 GTTGCGA--TTC--TT-GC
1 GTTGCGATTTTCATTTCGT
** * *
62609 GTTGCGATAGTCAAATTCGC
1 GTTGCGATTTTC-ATTTCGT
**
62629 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCA-TTTCGT
62649 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCA-TTTCGT
62669 GTTGCGATTT
1 GTTGCGATTT
62679 AAAGTTTCAG
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.11
15 2 0.03
16 2 0.03
17 3 0.04
19 10 0.14
20 46 0.65
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.46
Consensus pattern (19 bp):
GTTGCGATTTTCATTTCGT
Found at i:62686 original size:20 final size:20
Alignment explanation
Indices: 62643--62686 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
62633 CGATAGTCAT
** *
62643 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
62663 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
62683 TTTC
1 TTTC
62687 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:64564 original size:20 final size:20
Alignment explanation
Indices: 64539--64590 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
64529 AGAATAGTTT
*
64539 ACTATCGCAATGCGAAAATA
1 ACTATCGCAACGCGAAAATA
*
64559 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATA
64579 ACTATCGCAACG
1 ACTATCGCAACG
64591 AGAGAATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATA
Found at i:64654 original size:20 final size:20
Alignment explanation
Indices: 64629--64675 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
64619 CAACAACAAA
64629 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
64649 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
64669 ATCGCAA
1 ATCGCAA
64676 CGAAAGAATC
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:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:64656 original size:53 final size:53
Alignment explanation
Indices: 64599--64713 Score: 126
Period size: 53 Copynumber: 2.2 Consensus size: 53
64589 CGAGAGAATT
* **
64599 GCAATGCGAA-ATGAAAATCGCAAC-AACAAAATCGCAATGCGAAAATGACTATC
1 GCAATGCGAATATGAAAATCGCAACGAA-AAAATCGCAATACG-AAATGAAAATC
* ** *
64652 GCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATACGAAATGAAAATC
1 GCAATGCGAATATGAAAATCGCAACGAAAAAATCGCAATACGAAATGAAAATC
*
64705 GCATTGCGA
1 GCAATGCGA
64714 TTCTCTCGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
53 27 0.52
54 23 0.44
55 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.17
Consensus pattern (53 bp):
GCAATGCGAATATGAAAATCGCAACGAAAAAATCGCAATACGAAATGAAAATC
Found at i:64690 original size:87 final size:87
Alignment explanation
Indices: 64542--64707 Score: 269
Period size: 87 Copynumber: 1.9 Consensus size: 87
64532 ATAGTTTACT
* * *
64542 ATCGCAATGCGAAAATAACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATTGCAATGCG
1 ATCGCAATGCGAAAATAACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATACG
64607 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
* * **
64629 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATACG
1 ATCGCAATGCGAAAATAACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATACG
64694 AAATGAAAATCGCA
66 AAATGAAAATCGCA
64708 TTGCGATTCT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (87 bp):
ATCGCAATGCGAAAATAACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATACG
AAATGAAAATCGCAACAACAAA
Found at i:64765 original size:20 final size:20
Alignment explanation
Indices: 64720--64768 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
64710 GCGATTCTCT
*
64720 CGTTGTGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTTG
* *
64740 CATTGCGATAGTC-ATTTTCG
1 CGTTGCGATAGTCAAATTT-G
64760 CGTTGCGAT
1 CGTTGCGAT
64769 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTTG
Found at i:64799 original size:33 final size:34
Alignment explanation
Indices: 64742--64838 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
64732 CAAATTTGCA
* *
64742 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
** * *
64776 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
64809 TTGCGATAGTCATTTTCGCGTTGCGATTTT
1 TTGCGATAGTCATTTTCGCGTTGCGATTTT
64839 AAGTTTCAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
Found at i:66825 original size:14 final size:14
Alignment explanation
Indices: 66806--66841 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
66796 ATTGTTTAAT
66806 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
66820 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
66834 TGATTTGT
1 TGATTTGT
66842 TTAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:67009 original size:33 final size:34
Alignment explanation
Indices: 66947--67010 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
66937 AAAACAGACT
** *
66947 ATCGCAACGCGGAAATGACTATCGTAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
*
66981 ATCGCAATGC-GAAATGAAAATCGCAACGAG
1 ATCGCAACGCGGAAATGAAAATCGCAACGAG
67011 TTCGCGTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 17 0.65
34 9 0.35
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
Found at i:67072 original size:33 final size:33
Alignment explanation
Indices: 67016--67099 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
67006 ACGAGTTCGC
67016 GTTGCGATTTTCATTTTCGCATTGCGATTCACTA
1 GTTGCGATTTTCA-TTTCGCATTGCGATTCACTA
* *
67050 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCACTA
**
67083 GTTGCGATAGTCATTTC
1 GTTGCGATTTTCATTTC
67100 CGTGTTGCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.72
34 13 0.28
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCACTA
Found at i:67108 original size:20 final size:20
Alignment explanation
Indices: 67083--67130 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
67073 CGATTCTCTC
*
67083 GTTGCGATAGTCAT-TTCCGT
1 GTTGCGATAGTCATATT-CGA
67103 GTTGCGATAGTCATATTCGA
1 GTTGCGATAGTCATATTCGA
67123 GTTGCGAT
1 GTTGCGAT
67131 TTCCGTGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATATTCGA
Found at i:70483 original size:20 final size:20
Alignment explanation
Indices: 70458--70504 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
70448 AAATTCAGTA
*
70458 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
70478 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
70498 TTGCGAT
1 TTGCGAT
70505 TTACGTATTC
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:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:70514 original size:20 final size:20
Alignment explanation
Indices: 70491--70584 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
70481 CGATAGTCAG
*
70491 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
70511 ATTCGCATTGCGACTTACGT
1 ATTCGCATTGCGATTTACGT
*
70531 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
70551 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
70571 AATCGCAATGCGAT
1 ATTCGCATTGCGAT
70585 AGTCAGAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:70602 original size:60 final size:60
Alignment explanation
Indices: 70459--70603 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 60
70449 AATTCAGTAT
* * * *
70459 TGCGATAGTCAGAATCTCGTTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCAT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGATTCGCATTGCGATTTACGTAATCGCAA
* * * **
70519 TGCGACT--T-ACGTATTCGCATTGCGAT-TTACTTATTCGCATTGCGATTTACGTAATCGCAA
1 TGCGA-TAGTCA-G-AATCGCGTTGCGATAGT-CAGATTCGCATTGCGATTTACGTAATCGCAA
70579 TGCGATAGTCAGAATCGCGTTGCGA
1 TGCGATAGTCAGAATCGCGTTGCGA
70604 ATCTAGAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
58 1 0.01
59 4 0.06
60 58 0.87
61 3 0.04
62 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (60 bp):
TGCGATAGTCAGAATCGCGTTGCGATAGTCAGATTCGCATTGCGATTTACGTAATCGCAA
Found at i:75929 original size:51 final size:50
Alignment explanation
Indices: 75838--75954 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 50
75828 GTAGTAAAGC
* * * *
75838 GCGCCCCCTG-ACCCGCACTATATGTTGATTTGGCGCCACGTGGGGTATAGA
1 GCGCCCCCTGCA-CCGCACTATATGTTGACTGGGCGACACGT-GGCTATAGA
** *
75889 GCGCCCCCTGCACCGCACTATATGTTGACTGGGTTACACGTGGCTATAGC
1 GCGCCCCCTGCACCGCACTATATGTTGACTGGGCGACACGTGGCTATAGA
*
75939 GCGCCCCCTGCTCCGC
1 GCGCCCCCTGCACCGC
75955 GTTATACCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 22 0.39
51 34 0.60
52 1 0.02
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.22
Consensus pattern (50 bp):
GCGCCCCCTGCACCGCACTATATGTTGACTGGGCGACACGTGGCTATAGA
Found at i:76145 original size:12 final size:10
Alignment explanation
Indices: 76127--76160 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
76117 CGTTTAAGGT
*
76127 ATATTTTATA
1 ATATTTTTTA
76137 ATATTTTTTA
1 ATATTTTTTA
76147 ATA-TTTTTA
1 ATATTTTTTA
76156 ATATT
1 ATATT
76161 ATGTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATATTTTTTA
Found at i:76155 original size:9 final size:9
Alignment explanation
Indices: 76127--76160 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
76117 CGTTTAAGGT
76127 ATATTTTATA
1 ATATTTT-TA
76137 ATATTTTTTA
1 ATA-TTTTTA
76147 ATATTTTTA
1 ATATTTTTA
76156 ATATT
1 ATATT
76161 ATGTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 11 0.48
10 8 0.35
11 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATATTTTTA
Found at i:76203 original size:17 final size:18
Alignment explanation
Indices: 76166--76205 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
76156 ATATTATGTA
*
76166 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
76184 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
76201 TTTAC
1 TTTAC
76206 CAATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:78456 original size:26 final size:24
Alignment explanation
Indices: 78384--78456 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
78374 TTATATTTGC
78384 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
78409 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
78432 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
78457 GTTGGGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:92223 original size:3 final size:3
Alignment explanation
Indices: 92215--92239 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
92205 GACAATGGGA
92215 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
92240 GAACACGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:94228 original size:7 final size:7
Alignment explanation
Indices: 94218--94261 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
94208 CCTTGCTCCC
94218 CCCTTAA
1 CCCTTAA
94225 CCCTTAA
1 CCCTTAA
94232 CCCTTAA
1 CCCTTAA
94239 CCCTTAA
1 CCCTTAA
94246 CCCTTAA
1 CCCTTAA
94253 CCCTTAA
1 CCCTTAA
94260 CC
1 CC
94262 AGCTGTTCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.27
Consensus pattern (7 bp):
CCCTTAA
Found at i:102264 original size:2 final size:2
Alignment explanation
Indices: 102216--102244 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
102206 TGTCTTGCTT
102216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
102245 TTGTCTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104790 original size:25 final size:25
Alignment explanation
Indices: 104761--104813 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
104751 ACAACTTATA
* *
104761 GATAAGACCTCTAATAGGCTTATGT
1 GATAAAACCTCTAACAGGCTTATGT
* * *
104786 GATAAAACTTCTAACATGTTTATGT
1 GATAAAACCTCTAACAGGCTTATGT
104811 GAT
1 GAT
104814 GTGTCCGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (25 bp):
GATAAAACCTCTAACAGGCTTATGT
Found at i:112838 original size:7 final size:7
Alignment explanation
Indices: 112826--112861 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
112816 CTTTCTTCTT
112826 CAGATTC
1 CAGATTC
112833 CAGATTC
1 CAGATTC
112840 CAGATTC
1 CAGATTC
112847 CAGATTC
1 CAGATTC
112854 CAGATTC
1 CAGATTC
112861 C
1 C
112862 TTCTTCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (7 bp):
CAGATTC
Found at i:113710 original size:2 final size:2
Alignment explanation
Indices: 113703--113748 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
113693 ACCATATAAG
113703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113745 AT AT
1 AT AT
113749 TCATATTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120240 original size:6 final size:6
Alignment explanation
Indices: 120229--120526 Score: 578
Period size: 6 Copynumber: 49.7 Consensus size: 6
120219 ACAGCATTAC
120229 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
120277 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
120325 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
* *
120373 ATATGT ATATGT ATATGT ATATAT ATATGT ATATAT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
120421 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
120469 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
120517 ATATGT ATAT
1 ATATGT ATAT
120527 TATTTTATAA
Statistics
Matches: 288, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 288 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:120688 original size:5 final size:5
Alignment explanation
Indices: 120673--120703 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
120663 AAAGTCACAG
120673 GAAAA GAAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA G-AAAA GAAAA GAAAA GAAAA GAAAA
120704 AAACAGGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:126772 original size:3 final size:3
Alignment explanation
Indices: 126759--126829 Score: 124
Period size: 3 Copynumber: 23.0 Consensus size: 3
126749 GTAATATTTA
126759 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
126805 AAT AAAT AAT AAT AAT AAT AAT AAT
1 AAT -AAT AAT AAT AAT AAT AAT AAT
126830 TTAAAATGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 60 0.91
4 6 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:127089 original size:76 final size:76
Alignment explanation
Indices: 126998--127595 Score: 1081
Period size: 76 Copynumber: 7.9 Consensus size: 76
126988 ACCCTGAGGG
126998 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACT-ATAGGGCTTACAGA
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA-AGGGCTTACAGA
*
127062 TGACCCGAAGGT
65 TGACCCGAAGGA
127074 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
127139 GACCCGAAGGA
66 GACCCGAAGGA
*
127150 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
127215 GACCCGAAGGA
66 GACCCGAAGGA
*
127226 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATTATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
*
127291 GACCCGAAGGC
66 GACCCGAAGGA
* *
127302 TTTGACAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
127367 GACCCGAAGGA
66 GACCCGAAGGA
* * *
127378 TTTGACAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAAGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
127443 GACCCGAAGGA
66 GACCCGAAGGA
*
127454 TTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
127519 GACCCGAAGGA
66 GACCCGAAGGA
*
127530 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
127595 G
66 G
127596 TGGGAAATAG
Statistics
Matches: 503, Mismatches: 18, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
76 502 1.00
77 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
GACCCGAAGGA
Found at i:128342 original size:22 final size:22
Alignment explanation
Indices: 128265--128341 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
128255 CATAAAGCTT
128265 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * * *
128287 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* **
128309 TCATCTCTGAAGTGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
128331 TCATCTTTGAA
1 TCATCTTTGAA
128342 GAGTGTAGAT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:128776 original size:54 final size:54
Alignment explanation
Indices: 128697--128807 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 54
128687 GAATAGCAGA
*** *
128697 TTCGTAAAACATTTAACAGTGCATTCATCCTTTCCTGTGGTTTCTGCTCAGATG
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATG
* **
128751 TTCGTAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGATG
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATG
128805 TTC
1 TTC
128808 TCATTCATTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (54 bp):
TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATG
Found at i:131182 original size:93 final size:92
Alignment explanation
Indices: 131022--131304 Score: 408
Period size: 93 Copynumber: 3.1 Consensus size: 92
131012 CTTATTTCTA
* * * * *
131022 CTATGAGCAAAATTCATCTTTCAAATCCAATGATTGATT-T-TAGAATTCATACCAAATCATATC
1 CTATGAGC-ACATTCATCTTCCAAATTCAATGATTGATTCTGT-G-GTTCATACCAAACCATATC
*
131085 AGATAATTCAAAGAACACTTCCAGAAGATG
63 AGATAACTCAAAGAACACTTCCAGAAGATG
*
131115 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTCCATACCAAACCATATTAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTT-CATACCAAACCATATCAG
*
131180 ATAACTCAAAGAACACTTCCAAAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
* * * *
131208 CTATGAGCACATTCATCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTCATACCAAACCATATCAGA
131273 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
131300 CTATG
1 CTATG
131305 GGTCTCCTTA
Statistics
Matches: 173, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
92 77 0.45
93 95 0.55
94 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (92 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTCATACCAAACCATATCAGA
TAACTCAAAGAACACTTCCAGAAGATG
Found at i:133577 original size:21 final size:21
Alignment explanation
Indices: 133535--133577 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
133525 TTTCTGGGCT
* *
133535 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
133556 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
133577 A
1 A
133578 ACGAGTAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:134133 original size:2 final size:2
Alignment explanation
Indices: 134126--134219 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
134116 ACATGTTACA
134126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134210 AT AT AT AT AT
1 AT AT AT AT AT
134220 GAGTTGTGTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134632 original size:30 final size:30
Alignment explanation
Indices: 134598--134814 Score: 434
Period size: 30 Copynumber: 7.2 Consensus size: 30
134588 TCTGGGCCTA
134598 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
134628 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
134658 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
134688 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
134718 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
134748 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
134778 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
134808 TGGATAG
1 TGGATAG
134815 GTCCTTCGGA
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 187 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:138056 original size:21 final size:21
Alignment explanation
Indices: 138014--138056 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
138004 TTTCTGGGCT
* *
138014 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
138035 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
138056 A
1 A
138057 ACGAGTAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:138606 original size:2 final size:2
Alignment explanation
Indices: 138599--138650 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
138589 GACATGTACA
138599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
138641 AT AT AT AT AT
1 AT AT AT AT AT
138651 TATGAGTTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:139066 original size:30 final size:30
Alignment explanation
Indices: 139032--139188 Score: 314
Period size: 30 Copynumber: 5.2 Consensus size: 30
139022 TCGGGGCCTA
139032 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
139062 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
139092 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
139122 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
139152 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
139182 TGGATAG
1 TGGATAG
139189 GTCCTTCGGA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 127 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:140586 original size:17 final size:16
Alignment explanation
Indices: 140564--140596 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
140554 CTTGATTCAA
140564 TTTTCCTTTTTCTTTTT
1 TTTTCCTTTTT-TTTTT
140581 TTTTCCTTTTTTTTTT
1 TTTTCCTTTTTTTTTT
140597 CTTCTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCCTTTTTTTTTT
Found at i:147523 original size:3 final size:3
Alignment explanation
Indices: 147510--147570 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
147500 GTAATATTTA
* * * *
147510 AAT AAT AAAT AAT ATT ACT ATT ATT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
147556 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
147571 TTAAAATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:149495 original size:17 final size:17
Alignment explanation
Indices: 149470--149506 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
149460 CACGGTATTT
*
149470 TTATTAAATTAAAGTAA
1 TTATAAAATTAAAGTAA
149487 TTATAAAATTAAAGTAA
1 TTATAAAATTAAAGTAA
149504 TTA
1 TTA
149507 AAGTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TTATAAAATTAAAGTAA
Found at i:151944 original size:18 final size:18
Alignment explanation
Indices: 151897--151945 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
151887 CACACTCATA
* *
151897 TTTTAAAAAAAATATATT
1 TTTTAAAAATATTATATT
*
151915 TTTTAAATAATATTTTATT
1 TTTTAAA-AATATTATATT
151934 TTTTAAAAATAT
1 TTTTAAAAATAT
151946 AAACGTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAAAAATATTATATT
Found at i:157218 original size:2 final size:2
Alignment explanation
Indices: 157211--157236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
157201 ATTTACTATC
157211 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
157237 TGATTAAGTT
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:162585 original size:30 final size:30
Alignment explanation
Indices: 162549--162606 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
162539 AGTGCTCCAT
*
162549 AGGTCGCTGTGTGCTCCTGAAGACCTATGG
1 AGGTCGCTGTATGCTCCTGAAGACCTATGG
162579 AGGTCGCTGTATGCTCCTGAAGACCTAT
1 AGGTCGCTGTATGCTCCTGAAGACCTAT
162607 AGTGGTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (30 bp):
AGGTCGCTGTATGCTCCTGAAGACCTATGG
Found at i:166253 original size:14 final size:14
Alignment explanation
Indices: 166234--166264 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
166224 AAAGTAAACC
166234 AAATTGAAAAATAG
1 AAATTGAAAAATAG
166248 AAATTGAAAAATAG
1 AAATTGAAAAATAG
166262 AAA
1 AAA
166265 ATTTATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (14 bp):
AAATTGAAAAATAG
Found at i:166803 original size:7 final size:8
Alignment explanation
Indices: 166775--166846 Score: 62
Period size: 7 Copynumber: 9.1 Consensus size: 8
166765 AGTTTATTAT
166775 AAAATATTA
1 AAAATA-TA
*
166784 AAAGTAATA
1 AAAAT-ATA
166793 AAAAT-TA
1 AAAATATA
166800 AAAAT-TA
1 AAAATATA
166807 AAAATATA
1 AAAATATA
*
166815 ATAATATA
1 AAAATATA
*
166823 AAATAAATA
1 AAA-ATATA
166832 AAAA-AT-
1 AAAATATA
166838 AAAATATA
1 AAAATATA
166846 A
1 A
166847 TCAATTAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
6 4 0.08
7 18 0.34
8 13 0.25
9 17 0.32
10 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (8 bp):
AAAATATA
Found at i:166824 original size:23 final size:22
Alignment explanation
Indices: 166772--166846 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 22
166762 ATAAGTTTAT
*
166772 TATAAAATATTAAAAGTAATAAAA
1 TATAAAA-ATTAAAAAT-ATAAAA
166796 -ATTAAAAATTAAAAATATAATAA
1 TA-TAAAAATTAAAAATATAA-AA
*
166819 TATAAAATAAATAAAAA-ATAAAA
1 TAT-AAA-AATTAAAAATATAAAA
166842 TATAA
1 TATAA
166847 TCAATTAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
22 6 0.14
23 17 0.39
24 13 0.30
25 8 0.18
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (22 bp):
TATAAAAATTAAAAATATAAAA
Found at i:169745 original size:28 final size:29
Alignment explanation
Indices: 169677--169750 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 29
169667 AATATTGAAT
* * *
169677 ACTTTAAATATCTATTTTGACCAAAGAAAT
1 ACTTTAAGTACCTATTTTGACC-AAGAAAA
*
169707 ATTTTAAGTACCTATTTTGACC-AGAAAA
1 ACTTTAAGTACCTATTTTGACCAAGAAAA
* *
169735 ACTTTAGGTACTTATT
1 ACTTTAAGTACCTATT
169751 GCGATAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 18 0.49
30 19 0.51
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (29 bp):
ACTTTAAGTACCTATTTTGACCAAGAAAA
Done.