Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:3142508 original size:94 final size:93
Alignment explanation
Indices: 3142397--3142576 Score: 342
Period size: 94 Copynumber: 1.9 Consensus size: 93
3142387 AATTTATTTG
*
3142397 AACCGAATTTTTTCTTTAACATTAATCTAACCGAAATTATTTGACCGTTAATCGAACCGAAATTT
1 AACCGAATTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTT
3142462 ATTTGAAAATTATTAACCGAACCAAATT
66 ATTTGAAAATTATTAACCGAACCAAATT
3142490 AACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATT
1 AACCGAA-TTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATT
3142555 TATTTGAAAATTATTAACCGAA
65 TATTTGAAAATTATTAACCGAA
3142577 TTTTTTTCTT
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 7 0.08
94 78 0.92
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (93 bp):
AACCGAATTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTT
ATTTGAAAATTATTAACCGAACCAAATT
Found at i:3142544 original size:26 final size:26
Alignment explanation
Indices: 3142510--3142642 Score: 117
Period size: 26 Copynumber: 5.0 Consensus size: 26
3142500 TTTTCTTTAA
3142510 CATTAATCGAACCGAAATTATTTGAC
1 CATTAATCGAACCGAAATTATTTGAC
* *
3142536 CGTTAATCGAACCGAAATTTATTTGAA
1 CATTAATCGAACCGAAA-TTATTTGAC
* * * * *
3142563 AATT-AT-TAACCGAATTTTTTTCTTTAAC
1 CATTAATCGAACCGAA----ATTATTTGAC
3142591 CATTAATCGAACCGAAATTATTTGAC
1 CATTAATCGAACCGAAATTATTTGAC
* *
3142617 CGTTAATCGAACCCAAATTTATTTGA
1 CATTAATCGAACCGAAA-TTATTTGA
3142643 AAAATATTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
25 7 0.08
26 40 0.48
27 18 0.22
28 9 0.11
29 2 0.02
30 7 0.08
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (26 bp):
CATTAATCGAACCGAAATTATTTGAC
Found at i:3142608 original size:81 final size:80
Alignment explanation
Indices: 3142487--3142658 Score: 317
Period size: 81 Copynumber: 2.1 Consensus size: 80
3142477 ACCGAACCAA
*
3142487 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAA
1 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCCAA
*
3142552 ATTTATTTGAAAATT
66 ATTTATTTGAAAAAT
3142567 ATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCCA
1 ATTAACCGAATTTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCCA
3142632 AATTTATTTGAAAAAT
65 AATTTATTTGAAAAAT
3142648 ATTAACCGAAT
1 ATTAACCGAAT
3142659 AAAATAAATT
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
80 23 0.26
81 66 0.74
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (80 bp):
ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCCAA
ATTTATTTGAAAAAT
Found at i:3142934 original size:69 final size:66
Alignment explanation
Indices: 3142778--3142934 Score: 176
Period size: 66 Copynumber: 2.3 Consensus size: 66
3142768 TATTTGACCG
*
3142778 TTAATTGAA-TCGAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCCATAAC
1 TTAATTGAACT-GAAATTTATTTGAAAATTATTAACCGAATAAAACAAATTATTTTTTCCATAAC
*
3142842 CG
65 CA
** ** *
3142844 TTAATCAAACCAAAATTTATTTGAAAATTATTAACCGAATCGAATTAACCAAA-T-TTTTTTCTA
1 TTAATTGAACTGAAATTTATTTGAAAATTATTAACCGAAT--AA--AA-CAAATTATTTTTTCCA
3142907 TAACCA
61 TAACCA
3142913 TTAATTGAACTGAAATTTATTT
1 TTAATTGAACTGAAATTTATTT
3142935 AACCAAATAA
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
66 35 0.47
68 2 0.03
69 31 0.42
70 3 0.04
71 3 0.04
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (66 bp):
TTAATTGAACTGAAATTTATTTGAAAATTATTAACCGAATAAAACAAATTATTTTTTCCATAACC
A
Found at i:3145221 original size:18 final size:18
Alignment explanation
Indices: 3145198--3145233 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3145188 GTGTCCCAAA
*
3145198 TGTGGGGGTGGGGGTAGG
1 TGTGGGGGTGGGAGTAGG
3145216 TGTGGGGGTGGGAGTAGG
1 TGTGGGGGTGGGAGTAGG
3145234 AGCAAGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.69, T:0.22
Consensus pattern (18 bp):
TGTGGGGGTGGGAGTAGG
Found at i:3149836 original size:18 final size:17
Alignment explanation
Indices: 3149808--3149860 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
3149798 GTTCTTAAGG
3149808 AGTGGTCCTTCGGGACAT
1 AGTGGT-CTTCGGGACAT
* *
3149826 AGTGATTCTTCAGGACAT
1 AGTG-GTCTTCGGGACAT
3149844 AGTGGTCATTCGGGACA
1 AGTGGTC-TTCGGGACA
3149861 AATATTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.90
19 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (17 bp):
AGTGGTCTTCGGGACAT
Found at i:3152132 original size:33 final size:33
Alignment explanation
Indices: 3152090--3152156 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3152080 CCTAGTACAG
3152090 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
3152123 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
3152156 A
1 A
3152157 GCACTACAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:3153418 original size:68 final size:68
Alignment explanation
Indices: 3153338--3153477 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 68
3153328 GAACTAATAG
3153338 AATATAAAGACTTAGAATACAAGAATATGAGATAGAATATGTAACGAGAATATAGGGGTTAAATG
1 AATATAAAGACTTAGAATACAAGAATATGAGATAGAATATGTAACGAGAATATAGGGGTTAAATG
3153403 TTA
66 TTA
* *
3153406 AATATAAAGACTTAGAATACAATAATATGAGATAGAATATGTAACGAGAATATATGGGTTAAATG
1 AATATAAAGACTTAGAATACAAGAATATGAGATAGAATATGTAACGAGAATATAGGGGTTAAATG
3153471 TTA
66 TTA
3153474 AATA
1 AATA
3153478 GAAACATATG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (68 bp):
AATATAAAGACTTAGAATACAAGAATATGAGATAGAATATGTAACGAGAATATAGGGGTTAAATG
TTA
Found at i:3153445 original size:35 final size:35
Alignment explanation
Indices: 3153334--3153445 Score: 83
Period size: 35 Copynumber: 3.3 Consensus size: 35
3153324 AAATGAACTA
*
3153334 ATAGAATATAAAGACTTAGAATACAAGAATATGAG
1 ATAGAATATAAAGACTTAGAATACAATAATATGAG
** * * *
3153369 ATAGAATATGTA-AC-GAGAATATAGGGGTTAA-AT--G
1 ATAGAATATAAAGACTTAGAATACA----ATAATATGAG
*
3153403 TTA-AATATAAAGACTTAGAATACAATAATATGAG
1 ATAGAATATAAAGACTTAGAATACAATAATATGAG
3153437 ATAGAATAT
1 ATAGAATAT
3153446 GTAACGAGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 20
0.62 0.15 0.23
Matches are distributed among these distances:
31 3 0.06
32 2 0.04
33 13 0.24
34 10 0.19
35 22 0.41
36 2 0.04
37 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (35 bp):
ATAGAATATAAAGACTTAGAATACAATAATATGAG
Found at i:3155196 original size:42 final size:43
Alignment explanation
Indices: 3155084--3155198 Score: 207
Period size: 42 Copynumber: 2.7 Consensus size: 43
3155074 CCGAATTCTA
*
3155084 GTGTTTGTTTCACGTAATTCGTTTTCC-GAAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAATATTTTCCC
3155126 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAA-ATTTTCCC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAATATTTTCCC
3155168 GTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAA
3155199 TGTAATTCAT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
42 65 0.92
43 6 0.08
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (43 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAATATTTTCCC
Found at i:3155413 original size:21 final size:23
Alignment explanation
Indices: 3155387--3155436 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
3155377 TAATTATTAA
3155387 AATATTTAAAAT-ATATT-TATT
1 AATATTTAAAATAATATTATATT
*
3155408 AATATTTATAATAATATTATATT
1 AATATTTAAAATAATATTATATT
3155431 -ATATTT
1 AATATTT
3155437 TAATATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTAAAATAATATTATATT
Found at i:3155432 original size:26 final size:25
Alignment explanation
Indices: 3155370--3155432 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
3155360 CATTTTCATC
3155370 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATTAAAATATTT
*
3155394 AAAATA-TAT-TTATTAATAT-TTAT
1 AAAATATTATATTATTAAAATATT-T
3155417 AATAATATTATATTAT
1 AA-AATATTATATTAT
3155433 ATTTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.42
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATATTATATTATTAAAATATTT
Found at i:3155442 original size:30 final size:30
Alignment explanation
Indices: 3155406--3155472 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
3155396 AATATATTTA
*
3155406 TTAATATT-TATAATAAT-ATTATATTATATT
1 TTAATATTATATAA-AATAATCA-ATTATATT
3155436 TTAATATTATATAAAATAATCAATTATATT
1 TTAATATTATATAAAATAATCAATTATATT
*
3155466 ATAATAT
1 TTAATAT
3155473 AAGTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 25 0.76
31 8 0.24
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAATATTATATAAAATAATCAATTATATT
Found at i:3155447 original size:23 final size:23
Alignment explanation
Indices: 3155387--3155447 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
3155377 TAATTATTAA
3155387 AATATTTA-AA-ATATATTTATT
1 AATATTTATAATATATATTTATT
3155408 AATATTTATAATA-ATATTATATT
1 AATATTTATAATATATATT-TATT
3155431 -ATATTT-TAATATTATAT
1 AATATTTATAATA-TATAT
3155448 AAAATAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 13 0.37
22 13 0.37
23 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTATAATATATATTTATT
Found at i:3155523 original size:30 final size:28
Alignment explanation
Indices: 3155418--3155558 Score: 98
Period size: 28 Copynumber: 5.0 Consensus size: 28
3155408 AATATTTATA
*
3155418 ATAATATTATATTATAT-TTTAATATTAT
1 ATAATATTAT-TTATATATTTAATAATAT
* * **
3155446 ATAAAATAATCAAT-TATATT-ATAATAT
1 ATAATATTATTTATATAT-TTAATAATAT
*
3155473 A-AGTATTTTATTT-TAT-TTTAATAATAT
1 ATA--ATATTATTTATATATTTAATAATAT
*
3155500 ATAATAAATTTTTTATATATTTAATAATGA-
1 ATAAT--ATTATTTATATATTTAATAAT-AT
3155530 ATAATATTATTTATATATTTCAATAATAT
1 ATAATATTATTTATATATTT-AATAATAT
3155559 TTTAGTAAAG
Statistics
Matches: 86, Mismatches: 13, Indels: 27
0.68 0.10 0.21
Matches are distributed among these distances:
26 6 0.07
27 20 0.23
28 36 0.42
29 9 0.10
30 14 0.16
31 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
ATAATATTATTTATATATTTAATAATAT
Found at i:3155780 original size:20 final size:20
Alignment explanation
Indices: 3155752--3155801 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3155742 TTTTCAGATG
*
3155752 TTTTCCAGAAATATAATTCA
1 TTTTTCAGAAATATAATTCA
*
3155772 TTTTTCAGAAATGTAATTCA
1 TTTTTCAGAAATATAATTCA
3155792 TTTTTCAGAA
1 TTTTTCAGAA
3155802 TTCAAATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTTTCAGAAATATAATTCA
Found at i:3155805 original size:14 final size:14
Alignment explanation
Indices: 3155784--3155869 Score: 66
Period size: 15 Copynumber: 5.9 Consensus size: 14
3155774 TTTCAGAAAT
3155784 GTAATTCATTTTTCA
1 GTAATTCA-TTTTCA
* *
3155799 G-AATTCAAATTCCA
1 GTAATTC-ATTTTCA
3155813 GTAATTCATTTTCA
1 GTAATTCATTTTCA
* *
3155827 GTAATTCAAATTCCA
1 GTAATTC-ATTTTCA
** *
3155842 GTAATTCAAACTCCA
1 GTAATTC-ATTTTCA
3155857 GTAATTCATTTTC
1 GTAATTCATTTTC
3155870 CGAAAACCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
14 25 0.43
15 33 0.57
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (14 bp):
GTAATTCATTTTCA
Found at i:3155809 original size:20 final size:20
Alignment explanation
Indices: 3155752--3155810 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
3155742 TTTTCAGATG
*
3155752 TTTTCCAGAAAT-ATAATTCA
1 TTTTTCAGAAATCA-AATTCA
**
3155772 TTTTTCAGAAATGTAATTCA
1 TTTTTCAGAAATCAAATTCA
*
3155792 TTTTTCAGAATTCAAATTC
1 TTTTTCAGAAATCAAATTC
3155811 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.44
Consensus pattern (20 bp):
TTTTTCAGAAATCAAATTCA
Found at i:3155820 original size:15 final size:15
Alignment explanation
Indices: 3155800--3155864 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
3155790 CATTTTTCAG
3155800 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
* *
3155815 AATTC-ATTTTCAGT
1 AATTCAAATTCCAGT
3155829 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
*
3155844 AATTCAAACTCCAGT
1 AATTCAAATTCCAGT
3155859 AATTCA
1 AATTCA
3155865 TTTTCCGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
14 12 0.27
15 32 0.73
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:3155820 original size:29 final size:29
Alignment explanation
Indices: 3155784--3155849 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
3155774 TTTCAGAAAT
3155784 GTAATTCATTTTTCAG-AATTCAAATTCCA
1 GTAATTCA-TTTTCAGTAATTCAAATTCCA
3155813 GTAATTCATTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCAGTAATTCAAATTCCA
3155842 GTAATTCA
1 GTAATTCA
3155850 AACTCCAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 7 0.19
29 29 0.81
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.41
Consensus pattern (29 bp):
GTAATTCATTTTCAGTAATTCAAATTCCA
Found at i:3160301 original size:424 final size:424
Alignment explanation
Indices: 3159513--3160361 Score: 1626
Period size: 424 Copynumber: 2.0 Consensus size: 424
3159503 CCCATGGCTG
3159513 ACTCACTGGAAAGCATTAGAGCATCTGCCTGCTGCCCTACTGCTTCAGAAACATCAGCAACTTCT
1 ACTCACTGGAAAGCATTAGAGCATCTGCCTGCTGCCCTACTGCTTCAGAAACATCAGCAACTTCT
*
3159578 GCTCTGGTAGGTATGGGATATTCGATCATGGATTCAAGCAGCTGGGAGGCAACAACGACAGGCTT
66 GCTCTGGTAGGTATGGGATATTCGATCATGGATTCAAGCAGCTGGGAGGCAACAACGACAGGCTC
3159643 ATTCAGTTGCCTGCACAGTTGAGCAACCCTCTTTTGAACCGAAGGGACCTGTTCTATTGGTATCG
131 ATTCAGTTGCCTGCACAGTTGAGCAACCCTCTTTTGAACCGAAGGGACCTGTTCTATTGGTATCG
3159708 GTGAGCCTAGATCTCCCCTGGCTACCATAGCTCCATATGATGCCCTGATAATCTCTTCCAAATTT
196 GTGAGCCTAGATCTCCCCTGGCTACCATAGCTCCATATGATGCCCTGATAATCTCTTCCAAATTT
*
3159773 TTCAGAGAGTCGATACTCTCTATCTTGGCAATGACAGCAATTTGGCTGCAAAATTGAACCATCAG
261 TTCAGAGAGTCGATACTCTCTATCTTGGCAATGACAACAATTTGGCTGCAAAATTGAACCATCAG
*
3159838 AACATCTTACAGCTTCAATTTAATACAATAAAATGTTATACATGCATACCGTCCAGTTGATCGAG
326 AACATCTTACAGCTTCAATTTAATACAATAAAATGTTATACATGCATACCGTCCAGGTGATCGAG
3159903 CAGTGATATAACTCTTTAAAGTCTTAATAACTTC
391 CAGTGATATAACTCTTTAAAGTCTTAATAACTTC
* *
3159937 ACTCACTGGAAAGTATTAGAGCATCTGCCTGCTGCCCTACTGCTTCAGAAACATCGGCAACTTCT
1 ACTCACTGGAAAGCATTAGAGCATCTGCCTGCTGCCCTACTGCTTCAGAAACATCAGCAACTTCT
*
3160002 GCTCTGGTAGGTATGGGATATTCGATCATGGATTCAAGCAGCTGGGAGGCAACAATGACAGGCTC
66 GCTCTGGTAGGTATGGGATATTCGATCATGGATTCAAGCAGCTGGGAGGCAACAACGACAGGCTC
*
3160067 ATTCAGTTGCCTGCACAGTTGAGCAACCCTCTTTTGAACTGAAGGGACCTGTTCTATTGGTATCG
131 ATTCAGTTGCCTGCACAGTTGAGCAACCCTCTTTTGAACCGAAGGGACCTGTTCTATTGGTATCG
3160132 GTGAGCCTAGATCTCCCCTGGCTACCATAGCTCCATATGATGCCCTGATAATCTCTTCCAAATTT
196 GTGAGCCTAGATCTCCCCTGGCTACCATAGCTCCATATGATGCCCTGATAATCTCTTCCAAATTT
3160197 TTCAGAGAGTCGATACTCTCTATCTTGGCAATGACAACAATTTGGCTGCAAAATTGAACCATCAG
261 TTCAGAGAGTCGATACTCTCTATCTTGGCAATGACAACAATTTGGCTGCAAAATTGAACCATCAG
*
3160262 AACATCTTACAGCTTCAATTTAATACAATAAAATGTTATACATGCATACGGTCCAGGTGATCGAG
326 AACATCTTACAGCTTCAATTTAATACAATAAAATGTTATACATGCATACCGTCCAGGTGATCGAG
3160327 CAGTGATATAACTCTTTAAAGTCTTAATAACTTC
391 CAGTGATATAACTCTTTAAAGTCTTAATAACTTC
3160361 A
1 A
3160362 GCAGACCTCA
Statistics
Matches: 417, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
424 417 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (424 bp):
ACTCACTGGAAAGCATTAGAGCATCTGCCTGCTGCCCTACTGCTTCAGAAACATCAGCAACTTCT
GCTCTGGTAGGTATGGGATATTCGATCATGGATTCAAGCAGCTGGGAGGCAACAACGACAGGCTC
ATTCAGTTGCCTGCACAGTTGAGCAACCCTCTTTTGAACCGAAGGGACCTGTTCTATTGGTATCG
GTGAGCCTAGATCTCCCCTGGCTACCATAGCTCCATATGATGCCCTGATAATCTCTTCCAAATTT
TTCAGAGAGTCGATACTCTCTATCTTGGCAATGACAACAATTTGGCTGCAAAATTGAACCATCAG
AACATCTTACAGCTTCAATTTAATACAATAAAATGTTATACATGCATACCGTCCAGGTGATCGAG
CAGTGATATAACTCTTTAAAGTCTTAATAACTTC
Found at i:3165953 original size:2 final size:2
Alignment explanation
Indices: 3165946--3166034 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
3165936 ATCTAACTAG
3165946 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
3165988 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
3166030 AT AT A
1 AT AT A
3166035 ATTTTTATTT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3169094 original size:2 final size:2
Alignment explanation
Indices: 3169087--3169158 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
3169077 TATGGATTTG
3169087 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
3169129 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
3169159 CTTTCAAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3169681 original size:21 final size:21
Alignment explanation
Indices: 3169655--3169732 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 21
3169645 AAATTTTAAT
3169655 ATAATTTAAATAAAAGAAAAC
1 ATAATTTAAATAAAAGAAAAC
3169676 ATAATTTAAATAACATA-AAAAC
1 ATAATTTAAATAA-A-AGAAAAC
* *
3169698 TTTAGAGATTTAAATAAAAGGAAAC
1 ---ATA-ATTTAAATAAAAGAAAAC
3169723 ATAATTTAAA
1 ATAATTTAAA
3169733 AGCTTATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
21 20 0.43
22 8 0.17
23 1 0.02
24 1 0.02
25 7 0.15
26 10 0.21
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.28
Consensus pattern (21 bp):
ATAATTTAAATAAAAGAAAAC
Found at i:3174764 original size:40 final size:40
Alignment explanation
Indices: 3174709--3174788 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
3174699 AACAGTGCAC
3174709 GGCTTTGTGACTAAATTTCTATCAGAACACATTCCTAGAT
1 GGCTTTGTGACTAAATTTCTATCAGAACACATTCCTAGAT
3174749 GGCTTTGTGACTAAATTTCTATCAGAACACATTCCTAGAT
1 GGCTTTGTGACTAAATTTCTATCAGAACACATTCCTAGAT
3174789 AACTTTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (40 bp):
GGCTTTGTGACTAAATTTCTATCAGAACACATTCCTAGAT
Found at i:3178198 original size:22 final size:22
Alignment explanation
Indices: 3178172--3178216 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3178162 GAAATCGACT
*
3178172 ATATTTGTAATTTTAGTTT-TAA
1 ATATTTATAATTTTA-TTTGTAA
3178194 ATATTTATAATTTTATTTGTAA
1 ATATTTATAATTTTATTTGTAA
3178216 A
1 A
3178217 AAATAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (22 bp):
ATATTTATAATTTTATTTGTAA
Found at i:3178371 original size:20 final size:21
Alignment explanation
Indices: 3178334--3178373 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3178324 ATCATAAAAT
3178334 TTAAAATATTATATATTATTC
1 TTAAAATATTATATATTATTC
*
3178355 TTAAACTATTA-ATATTATT
1 TTAAAATATTATATATTATT
3178374 TTATTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAATATTATATATTATTC
Found at i:3194818 original size:2 final size:2
Alignment explanation
Indices: 3194811--3194866 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
3194801 ATAACAAATA
3194811 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3194851 AT A- AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3194867 CCACTTTATG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3194830 original size:17 final size:16
Alignment explanation
Indices: 3194811--3194866 Score: 84
Period size: 15 Copynumber: 3.8 Consensus size: 16
3194801 ATAACAAATA
3194811 ATATATATATATATAT
1 ATATATATATATATAT
3194827 A-ATATATATATATAT
1 ATATATATATATATAT
3194842 ATATA-ATATATA-AT
1 ATATATATATATATAT
3194856 A-ATATATATAT
1 ATATATATATAT
3194867 CCACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.08
14 9 0.24
15 22 0.58
16 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATATATATATATAT
Found at i:3194835 original size:19 final size:19
Alignment explanation
Indices: 3194811--3194865 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
3194801 ATAACAAATA
3194811 ATATATATATATATATAAT
1 ATATATATATATATATAAT
3194830 ATATATATATATATATAAT
1 ATATATATATATATATAAT
3194849 ATATA-ATAATATATATA
1 ATATATAT-ATATATATA
3194866 TCCACTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 2 0.06
19 33 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATATATATATATAAT
Found at i:3196908 original size:18 final size:19
Alignment explanation
Indices: 3196870--3196913 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3196860 ACTAATTAAT
3196870 TTTTAATTAATTAAAATAA
1 TTTTAATTAATTAAAATAA
**
3196889 TTTTAATTAATT-GGATAA
1 TTTTAATTAATTAAAATAA
3196907 TTTTAAT
1 TTTTAAT
3196914 GGTTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTTAATTAATTAAAATAA
Found at i:3203863 original size:21 final size:20
Alignment explanation
Indices: 3203810--3203871 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
3203800 AATAAAAATC
3203810 AATAAATT-TTAG-AATAAT
1 AATAAATTATTAGTAATAAT
*
3203828 AATAAATGTA-CAGTAGATAAT
1 AATAAAT-TATTAGTA-ATAAT
3203849 AATAAATTATTAGTAATAGAT
1 AATAAATTATTAGTAATA-AT
3203870 AA
1 AA
3203872 CTTGTTAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 7 0.19
19 3 0.08
20 6 0.17
21 20 0.56
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.34
Consensus pattern (20 bp):
AATAAATTATTAGTAATAAT
Found at i:3222933 original size:12 final size:12
Alignment explanation
Indices: 3222916--3222940 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3222906 ATCTAATTGA
3222916 AAATAGATAGAT
1 AAATAGATAGAT
3222928 AAATAGATAGAT
1 AAATAGATAGAT
3222940 A
1 A
3222941 GAAGGATATT
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:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AAATAGATAGAT
Found at i:3227511 original size:29 final size:30
Alignment explanation
Indices: 3227447--3227518 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
3227437 GGTTCTTCGG
* * *
3227447 GACCTATGGACAGTTGTCGAGGTTCTTTAT
1 GACCTCTGGATAGTTGTCGAGGGTCTTTAT
*
3227477 GACCTCTGGATAGTTGTCG-GGGTCTTTGT
1 GACCTCTGGATAGTTGTCGAGGGTCTTTAT
3227506 GACCTCTGGATAG
1 GACCTCTGGATAG
3227519 ATCATTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.35
Consensus pattern (30 bp):
GACCTCTGGATAGTTGTCGAGGGTCTTTAT
Found at i:3229779 original size:31 final size:31
Alignment explanation
Indices: 3229741--3229805 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3229731 AGAGTCGAGG
*
3229741 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
3229772 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
3229803 GTT
1 GTT
3229806 GCTGAGGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:3229852 original size:28 final size:30
Alignment explanation
Indices: 3229791--3229861 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
3229781 GGTTCTTCGG
* *
3229791 GACCTATGGACAGTTGCTGAGGTTCTTTAT
1 GACCTATGGATAGTTGCCGAGGTTCTTTAT
* *
3229821 GACCTATGGATAGTTTCCG-GG-TCTTTGT
1 GACCTATGGATAGTTGCCGAGGTTCTTTAT
*
3229849 GACCTTTGGATAG
1 GACCTATGGATAG
3229862 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 18 0.50
29 2 0.06
30 16 0.44
ACGTcount: A:0.18, C:0.17, G:0.28, T:0.37
Consensus pattern (30 bp):
GACCTATGGATAGTTGCCGAGGTTCTTTAT
Found at i:3232737 original size:20 final size:20
Alignment explanation
Indices: 3232708--3232752 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3232698 CACATGTTAA
*
3232708 AGAATGCATCGATTCACTGT
1 AGAATACATCGATTCACTGT
3232728 AGAATACATCGATTCACTGT
1 AGAATACATCGATTCACTGT
3232748 AGAAT
1 AGAAT
3232753 GCATAGATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
AGAATACATCGATTCACTGT
Found at i:3233747 original size:31 final size:31
Alignment explanation
Indices: 3233709--3233769 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3233699 GAGTCGAGGG
*
3233709 TTTACCTATG-TCTTTCGAGACATATGGACAA
1 TTTACCTAGGTTC-TTCGAGACATATGGACAA
* *
3233740 TTTACCTAGGTTCTTCGGGACCTATGGACA
1 TTTACCTAGGTTCTTCGAGACATATGGACA
3233770 GTTGCGAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (31 bp):
TTTACCTAGGTTCTTCGAGACATATGGACAA
Found at i:3233783 original size:29 final size:29
Alignment explanation
Indices: 3233747--3233803 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
3233737 CAATTTACCT
*
3233747 AGGTTCTTCGGGACCTATGGACAGTTGCG
1 AGGTTCTTCAGGACCTATGGACAGTTGCG
* * *
3233776 AGGTTCTTTATGACCTATGGATAGTTGC
1 AGGTTCTTCAGGACCTATGGACAGTTGC
3233804 CGGGGTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (29 bp):
AGGTTCTTCAGGACCTATGGACAGTTGCG
Found at i:3233812 original size:29 final size:29
Alignment explanation
Indices: 3233758--3233828 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
3233748 GGTTCTTCGG
* *
3233758 GACCTATGGACAGTTGCGAGGTTCTTTAT
1 GACCTATGGATAGTTGCGAGGGTCTTTAT
*
3233787 GACCTATGGATAGTTGCCG-GGGTCTTTGT
1 GACCTATGGATAGTTG-CGAGGGTCTTTAT
*
3233816 GACCTCTGGATAG
1 GACCTATGGATAG
3233829 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.32
Consensus pattern (29 bp):
GACCTATGGATAGTTGCGAGGGTCTTTAT
Found at i:3235809 original size:13 final size:14
Alignment explanation
Indices: 3235791--3235826 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3235781 TTTACGCAGG
*
3235791 GATTTATTTTC-GA
1 GATTTATTTGCGGA
3235804 GATTTATTTGCGGA
1 GATTTATTTGCGGA
3235818 GATTTATTT
1 GATTTATTT
3235827 ATATACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (14 bp):
GATTTATTTGCGGA
Found at i:3237637 original size:76 final size:77
Alignment explanation
Indices: 3237465--3237653 Score: 267
Period size: 77 Copynumber: 2.5 Consensus size: 77
3237455 CAAAGCCAAA
* * * **
3237465 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
3237530 TTTGGCCCTGAG
66 TTTGGCCCTGAG
* *
3237542 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACTGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
3237607 TTT-GCTCC-GAG
66 TTTGGC-CCTGAG
*
3237618 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCTCCCA
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCC-CCCA
3237654 AGGGGGTACA
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
75 4 0.04
76 34 0.34
77 63 0.62
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCTGAG
Found at i:3243510 original size:21 final size:21
Alignment explanation
Indices: 3243484--3243523 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3243474 CCCCCTTTGA
*
3243484 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3243505 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3243524 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3245481 original size:9 final size:8
Alignment explanation
Indices: 3245459--3245509 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
3245449 TGTTTCAACA
3245459 TTTTGGAT
1 TTTTGGAT
3245467 ATTTTGGAT
1 -TTTTGGAT
3245476 TGTTT-GAT
1 T-TTTGGAT
3245484 TTTGTGGAT
1 TTT-TGGAT
*
3245493 TGTTGGA-
1 TTTTGGAT
3245500 TTTTGGAT
1 TTTTGGAT
3245508 TT
1 TT
3245510 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:3245493 original size:17 final size:17
Alignment explanation
Indices: 3245461--3245504 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3245451 TTTCAACATT
3245461 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
3245478 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
3245495 TTGGATTTTG
1 TTGGATTTTG
3245505 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:3246594 original size:15 final size:15
Alignment explanation
Indices: 3246571--3246648 Score: 138
Period size: 15 Copynumber: 5.2 Consensus size: 15
3246561 CGTAGGACTC
*
3246571 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
3246586 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
3246601 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
3246616 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
*
3246631 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
3246646 CTA
1 CTA
3246649 TTTTACCCTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.14
Consensus pattern (15 bp):
CTACGTCCCGAAGGA
Found at i:3246778 original size:29 final size:29
Alignment explanation
Indices: 3246743--3246806 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
3246733 TCATGTACTT
*
3246743 ATGTCATTTCTCTTGTGATCATGTAGCCC
1 ATGTCATTTCTCTTATGATCATGTAGCCC
*
3246772 ATGTCATTTCTCTTATGATCATGTAGCTC
1 ATGTCATTTCTCTTATGATCATGTAGCCC
3246801 ATGTCA
1 ATGTCA
3246807 CTTCATATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (29 bp):
ATGTCATTTCTCTTATGATCATGTAGCCC
Found at i:3246839 original size:12 final size:12
Alignment explanation
Indices: 3246822--3246869 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
3246812 TATCATGTTC
3246822 TCATATCACATG
1 TCATATCACATG
*
3246834 TCATATCACATA
1 TCATATCACATG
*
3246846 TTATATCACATAG
1 TCATATCACAT-G
3246859 -CATATCACATG
1 TCATATCACATG
3246870 AACATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 1 0.03
12 30 0.97
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:3258128 original size:26 final size:27
Alignment explanation
Indices: 3258092--3258144 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
3258082 CAGAGGAAAC
3258092 AAAGCATG-AAAAAAATGAAACAAAAA
1 AAAGCATGAAAAAAAATGAAACAAAAA
3258118 AAAGCATGAAAAAAAATGAAACAAAAA
1 AAAGCATGAAAAAAAATGAAACAAAAA
3258145 TGCATCAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.74, C:0.08, G:0.11, T:0.08
Consensus pattern (27 bp):
AAAGCATGAAAAAAAATGAAACAAAAA
Found at i:3260109 original size:27 final size:27
Alignment explanation
Indices: 3260078--3260142 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
3260068 AAACAGTGTT
3260078 GAATGATTCAGCACAAAAGTACATTCG
1 GAATGATTCAGCACAAAAGTACATTCG
*
3260105 GAATGATTCAGCACAGAAGTACATTCG
1 GAATGATTCAGCACAAAAGTACATTCG
3260132 GAATGATTCAG
1 GAATGATTCAG
3260143 AGTCATTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (27 bp):
GAATGATTCAGCACAAAAGTACATTCG
Found at i:3261768 original size:21 final size:22
Alignment explanation
Indices: 3261732--3261775 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3261722 TAATTTATCA
* *
3261732 ATTTATTTTATGATTATTTTTT
1 ATTTAATTTATGATTATATTTT
3261754 ATTTAATTT-TGATTATATTTT
1 ATTTAATTTATGATTATATTTT
3261775 A
1 A
3261776 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
ATTTAATTTATGATTATATTTT
Found at i:3262078 original size:52 final size:52
Alignment explanation
Indices: 3262005--3262117 Score: 201
Period size: 52 Copynumber: 2.2 Consensus size: 52
3261995 TATATGATAT
3262005 AAAATTAAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAA
1 AAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AA
3262058 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
3262110 AAAATTAA
1 AAAATTAA
3262118 CATTAAAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 30 0.51
53 29 0.49
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (52 bp):
AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
Found at i:3262094 original size:28 final size:24
Alignment explanation
Indices: 3262005--3262117 Score: 111
Period size: 28 Copynumber: 4.3 Consensus size: 24
3261995 TATATGATAT
3262005 AAAATTAAATATCTATAATATAATATT-A
1 AAAATT-AATAT-T-TAAT-TAAT-TTAA
*
3262033 AAAATTAATATTTAATTTATTTAAA
1 AAAATTAATATTTAATTAATTT-AA
3262058 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATAT-T-TAAT-TAAT-TTAA
*
3262086 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTTAA
3262110 AAAATTAA
1 AAAATTAA
3262118 CATTAAAATT
Statistics
Matches: 76, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
23 2 0.03
24 15 0.20
25 19 0.25
26 6 0.08
27 10 0.13
28 22 0.29
29 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAATTAATATTTAATTAATTTAA
Found at i:3262127 original size:25 final size:24
Alignment explanation
Indices: 3262032--3262117 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 24
3262022 ATATAATATT
3262032 AAAAATTAATATTTAATTTATTTAA
1 AAAAATTAATATTTAATTTATTT-A
*
3262057 AAAAATTAATATCTATAATATAATATTA
1 AAAAATTAATAT-T-TAAT-TTAT-TTA
3262085 AAAAATTAATATTTAATTTATTTA
1 AAAAATTAATATTTAATTTATTTA
3262109 AAAAATTAA
1 AAAAATTAA
3262118 CATTAAAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
24 12 0.22
25 15 0.27
26 5 0.09
27 5 0.09
28 16 0.29
29 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAATTAATATTTAATTTATTTA
Found at i:3262155 original size:12 final size:12
Alignment explanation
Indices: 3262110--3262161 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
3262100 ATTTATTTAA
3262110 AAAATTAACAT-T
1 AAAATTAA-ATAT
3262122 AAAATTAAA-AT
1 AAAATTAAATAT
*
3262133 CAAA-TATAATAT
1 AAAATTA-AATAT
3262145 AAAATTAAATAT
1 AAAATTAAATAT
3262157 AAAAT
1 AAAAT
3262162 CTCTTTGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 2 0.06
11 7 0.21
12 23 0.68
13 2 0.06
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:3266336 original size:20 final size:20
Alignment explanation
Indices: 3266313--3266355 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3266303 AATCCACCAC
*
3266313 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
3266333 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
3266353 ATG
1 ATG
3266356 GGCTCTTAGA
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:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:3295944 original size:35 final size:35
Alignment explanation
Indices: 3295905--3296018 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 35
3295895 CAACTTTAAA
* *
3295905 AAAAATGGTTTTCAAAGTTTGGCAAATGTTTCTTT
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTATTT
*
3295940 AAAAATGGTTTTTAAAGTTTGGTAAATGTTTATTT
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTATTT
* * * *
3295975 GAAAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTG
1 -AAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTATTT
3296012 AAAAATG
1 AAAAATG
3296019 ATAATGGGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 33 0.48
36 12 0.17
37 24 0.35
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (35 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTATTT
Found at i:3296017 original size:36 final size:35
Alignment explanation
Indices: 3295905--3296018 Score: 140
Period size: 36 Copynumber: 3.2 Consensus size: 35
3295895 CAACTTTAAA
* * *
3295905 AAAAATGGTTTTCAAAGTTTGGCAAATGTTTCTTT
1 AAAAATGTTTTTCAAAGTTTGGTAAATGTTTCTTG
*
3295940 AAAAATGGTTTTT-AAAGTTTGGTAAATGTTTATTTG
1 AAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT-CTTG
* *
3295976 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTG
1 AAAAAT-GTTTTTCAAAGTTTGGTAAATGTTTCTTG
3296012 AAAAATG
1 AAAAATG
3296019 ATAATGGGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 24 0.35
36 28 0.41
37 17 0.25
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (35 bp):
AAAAATGTTTTTCAAAGTTTGGTAAATGTTTCTTG
Done.