Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008656.1 Hibiscus syriacus cultivar Beakdansim tig00111650_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: 2456495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:220981 original size:58 final size:58
Alignment explanation
Indices: 220891--221006 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
220881 ACACCAAAAT
* *
220891 CCCAAGGCATTTGAATTATAAAAAAAGACAAGTATTGGAATCAATGGGATTGGTTCAA
1 CCCAAGGCAATTGAATTATAAAAAAAGACAAGTATTGAAATCAATGGGATTGGTTCAA
* * *
220949 CCCAAGGCAATTGAATTATAAAGAAAGACAAGTATTGAAATCAATGGGGTTTGTTCAA
1 CCCAAGGCAATTGAATTATAAAAAAAGACAAGTATTGAAATCAATGGGATTGGTTCAA
221007 GTGGTAAGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (58 bp):
CCCAAGGCAATTGAATTATAAAAAAAGACAAGTATTGAAATCAATGGGATTGGTTCAA
Found at i:233021 original size:60 final size:60
Alignment explanation
Indices: 232927--233052 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 60
232917 AACATTAGGC
* *
232927 AACTATGACTATCATTCTAAATTAGTCTTCAAAC-TTTTGAATATTTCAATTTCATCCCCA
1 AACTATGACTATCATTATAAATTAGTCTTCAAACTTTTTGAACATTTCAATTTCAT-CCCA
*
232987 AACTATGAC-ATTCATTATAAATTAGTCCTT-AAACTTTTTGAACATTTCAATTTCATCTCA
1 AACTATGACTA-TCATTATAAATTAGT-CTTCAAACTTTTTGAACATTTCAATTTCATCCCA
233047 AACTAT
1 AACTAT
233053 ATGTATATAC
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
59 1 0.02
60 36 0.60
61 23 0.38
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (60 bp):
AACTATGACTATCATTATAAATTAGTCTTCAAACTTTTTGAACATTTCAATTTCATCCCA
Found at i:242931 original size:64 final size:63
Alignment explanation
Indices: 242809--243034 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 63
242799 ATTGTTTGAA
* ** **
242809 TGTGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAAT
1 TGTGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-AA-ACATCGAATGCAAT
242872 T
63 T
* *
242873 TGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATTGAATGCAATT
1 TGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT-AAACATCGAATGCAATT
* * * * ** * *
242937 GGTGCATCGATGCATAAGGAGTGAATCGATGCATCTCAACAATAATACAACATCGAATACATTT
1 TGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATA-AACATCGAATGCAATT
* * *
243001 TATGCATCGATGCATCAGTAGTGCATTGATGCAT
1 TGTGCATCGATGCATAAGTAGTGCATCGATGCAT
243035 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
63 1 0.01
64 129 0.96
65 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (63 bp):
TGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAACATCGAATGCAATT
Found at i:243729 original size:31 final size:31
Alignment explanation
Indices: 243691--243833 Score: 259
Period size: 31 Copynumber: 4.6 Consensus size: 31
243681 AGGGTCGAGG
243691 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
243722 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
243753 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
243784 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
243815 GTTTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
243834 AATCTATGGA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:247067 original size:45 final size:45
Alignment explanation
Indices: 247013--247115 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
247003 GCATTGGTAC
**
247013 TGCATCGATGCA-CTCTTTTAA-AATAAAGACATCAAATGCAATTCG
1 TGCATCGATGCATC-CCATTAATAATAAA-ACATCAAATGCAATTCG
* * * *
247058 TGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATTGG
1 TGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCG
247103 TGCATCGATGCAT
1 TGCATCGATGCAT
247116 AAGGAGTGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
45 45 0.90
46 5 0.10
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (45 bp):
TGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCG
Found at i:247128 original size:64 final size:64
Alignment explanation
Indices: 247057--247198 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 64
247047 AATGCAATTC
** * * * *
247057 GTGCATCGATGCATCCCATTAATAGTGA-AACATCGAATGCAATTGGTGCATCGATGCATAAGGA
1 GTGCATCGATGCATCCCAGCAATAAT-ACAACATCGAATACAATTGATGCACCGATGCATAAGGA
* * * * *
247121 GTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTTATGCACCGATGCATCAGTA
1 GTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTGATGCACCGATGCATAAGGA
247185 GTGCATCGATGCAT
1 GTGCATCGATGCAT
247199 ACCTTCATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
63 1 0.02
64 65 0.98
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (64 bp):
GTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTGATGCACCGATGCATAAGGA
Found at i:247892 original size:31 final size:31
Alignment explanation
Indices: 247854--248040 Score: 340
Period size: 31 Copynumber: 6.0 Consensus size: 31
247844 AGGGTCGAGG
247854 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
247885 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
247916 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
247947 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
247978 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
248009 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
248040 G
1 G
248041 GTCCTTCGGG
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 152 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:255651 original size:21 final size:21
Alignment explanation
Indices: 255625--255675 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
255615 AATCAAAAGA
255625 GGGGTATCGGTACCTATGAGC
1 GGGGTATCGGTACCTATGAGC
255646 GGGGTATCGGTACCTATGAGC
1 GGGGTATCGGTACCTATGAGC
*
255667 TGGGTATCG
1 GGGGTATCG
255676 ATACTACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.39, T:0.25
Consensus pattern (21 bp):
GGGGTATCGGTACCTATGAGC
Found at i:255963 original size:17 final size:18
Alignment explanation
Indices: 255943--255979 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
255933 TGATATTCGA
255943 ATAA-TTGAATCGAATAT
1 ATAATTTGAATCGAATAT
255960 ATAATTTTGAATCGAATAT
1 ATAA-TTTGAATCGAATAT
255979 A
1 A
255980 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
ATAATTTGAATCGAATAT
Found at i:260128 original size:6 final size:6
Alignment explanation
Indices: 260112--260148 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
260102 AAATCTCCTG
*
260112 CTCTCC TTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC C
260149 ATCCCTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTCTCC
Found at i:262895 original size:19 final size:19
Alignment explanation
Indices: 262871--262963 Score: 89
Period size: 19 Copynumber: 5.4 Consensus size: 19
262861 TAAGGTTAGT
262871 ATTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
**
262890 ATTGCGA--TTC-CCTCG-
1 ATTGCGATTTTCATTTCGC
262905 -TTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
*
262923 ATTGCGATTCTC--TT-G-
1 ATTGCGATTTTCATTTCGC
262938 -TTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
262956 ATTGCGAT
1 ATTGCGAT
262964 AGTAATTTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 16 0.28
16 9 0.16
17 9 0.16
19 24 0.41
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
ATTGCGATTTTCATTTCGC
Found at i:262914 original size:33 final size:33
Alignment explanation
Indices: 262872--262963 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
262862 AAGGTTAGTA
262872 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
* *
262905 TTGCGATTTTCATTTCGCATTGCGATTCTCTTG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
262938 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
262964 AGTAATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
Found at i:266265 original size:20 final size:21
Alignment explanation
Indices: 266240--266288 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
266230 TCCTAATTCA
*
266240 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
**
266260 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
266281 CAATGCGA
1 CAATGCGA
266289 TACTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:266310 original size:20 final size:20
Alignment explanation
Indices: 266277--266355 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
266267 AATTTGGAAA
* *
266277 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
266297 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
266318 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
266338 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
266356 AAATCACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:266673 original size:20 final size:20
Alignment explanation
Indices: 266578--266665 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
266568 CAACGGGGAA
*
266578 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
266598 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
266618 ATTGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
266638 ATCGTAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
266658 ATCGCAAC
1 ATCGCAAC
266666 TAGAAAATCG
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 5 0.10
20 41 0.80
21 5 0.10
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:266716 original size:14 final size:16
Alignment explanation
Indices: 266696--266769 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
266686 TGAAAATCGC
266696 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
266711 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
266728 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
266747 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
266763 -TTGCGAT
1 ATTGCGAT
266770 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:266733 original size:19 final size:19
Alignment explanation
Indices: 266692--266759 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
266682 GAAATGAAAA
266692 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
266708 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
266725 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
266744 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
266760 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:268398 original size:41 final size:42
Alignment explanation
Indices: 268344--268435 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
268334 CCTCTTCAAC
* *
268344 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
268385 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
268427 AATGACAGG
1 GATGACAGG
268436 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:268798 original size:20 final size:20
Alignment explanation
Indices: 268773--268811 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
268763 GAAGAATAGT
268773 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
268793 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
268812 ATGACTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:268822 original size:20 final size:20
Alignment explanation
Indices: 268779--268871 Score: 105
Period size: 20 Copynumber: 4.7 Consensus size: 20
268769 TAGTTTACTT
* * * *
268779 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
268799 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
268819 TCGCAATGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
268839 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
*
268859 TCGCAATGCGAAA
1 TCGCAACGCGAAA
268872 TGAAAATTGC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:268884 original size:39 final size:40
Alignment explanation
Indices: 268799--268923 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 40
268789 AAACTTACTT
**
268799 TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGAAAA
* *
268839 TCGCAACGCGGAAATGGCTATCGCAATGC-GAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGAAAA
* * *
268878 TTGCAA--CGACAA--A--ATCGCAATGC-AAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGAAAA
268911 TCGCAACGCGAAA
1 TCGCAACGCGAAA
268924 CACAAATCGC
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
33 24 0.33
35 4 0.06
37 4 0.06
39 13 0.18
40 27 0.38
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.15
Consensus pattern (40 bp):
TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGAAAA
Found at i:268971 original size:14 final size:14
Alignment explanation
Indices: 268952--269010 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
268942 TTTCATTTCG
268952 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
268966 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
*
268983 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
268999 CGTTGCGATTTT
1 CGTTGCGATTTT
269011 CATTTCGCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 18 0.46
15 3 0.08
16 4 0.10
17 5 0.13
18 3 0.08
19 6 0.15
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:268977 original size:33 final size:33
Alignment explanation
Indices: 268935--269026 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
268925 ACAAATCGCA
* *
268935 TTGCGATTTTCATTTCGCGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
268968 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
269001 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
269027 AGTCATTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:269034 original size:19 final size:19
Alignment explanation
Indices: 268930--269026 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
268920 GAAACACAAA
268930 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
268949 TCGCGTTGCGA-TTT--TT
1 TCGCATTGCGATTTTCATT
268965 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
268982 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
268998 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
269015 TCGCATTGCGAT
1 TCGCATTGCGAT
269027 AGTCATTTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
14 12 0.18
15 6 0.09
16 9 0.14
17 9 0.14
18 6 0.09
19 23 0.35
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:269609 original size:18 final size:18
Alignment explanation
Indices: 269586--269633 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
269576 CGGGTCGATC
269586 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
269604 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
269622 AGGTGACGGCTC
1 AGGTGATGGCTC
269634 CTGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.46, T:0.25
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:271576 original size:20 final size:20
Alignment explanation
Indices: 271503--271617 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
271493 GATTATGTAT
* *
271503 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * * *
271523 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGATAGTCAG
*
271543 TATCGAGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
271563 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
271584 TATCGCGTTGCGATAATCAG
1 TATCGCGTTGCGATAGTCAG
*
271604 TACCGCGTTGCGAT
1 TATCGCGTTGCGAT
271618 TATCCAAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.03
20 57 0.75
21 14 0.18
22 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:271604 original size:41 final size:41
Alignment explanation
Indices: 271483--271618 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
271473 CGCTTTGAAA
* * *
271483 ATCGCATTGCGATTATGTATTATCTCGTTGCGA-AAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAA-TCAGT
* * ** * * * *
271524 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAATCAGT
271564 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAATCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAATCAGT
*
271605 ACCGCGTTGCGATT
1 ATCGCGTTGCGATT
271619 ATCCAAATTC
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
40 29 0.40
41 44 0.60
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAATCAGT
Found at i:271679 original size:21 final size:21
Alignment explanation
Indices: 271611--271673 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
271601 CAGTACCGCG
* *
271611 TTGCGATTATCCAAATTCACA
1 TTGCGATTTTCCAAATTCGCA
271632 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
271653 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
271674 ACGCGAATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:271757 original size:41 final size:41
Alignment explanation
Indices: 271550--271759 Score: 133
Period size: 41 Copynumber: 5.1 Consensus size: 41
271540 AAGTATCGAG
* ** * *
271550 TTGCGATAGTCAGTATCGCGTTGCGATTTT-GTATTATCGCG
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCA
* * * * *
271591 TTGCGATAATCAGTACCGCGTTGCGATTATCCAAATTCACA
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
** *
271632 TTGCGATTTTCCA-AATTCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAAATTCGCA
** * * ****
271674 ACGCGAATACGT-A-AATCGCAATGCGAATTAGGAAAATT-GCA
1 TTGCG-ATA-GTCAGTATCGCATTGCG-ATTTTCCAAATTCGCA
*
271715 TTGCGATAGTCAGTATCGCATTGCGATTTTTCAAATTCGCA
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
271756 TTGC
1 TTGC
271760 AATTTACTTA
Statistics
Matches: 128, Mismatches: 32, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
39 2 0.02
40 12 0.09
41 71 0.55
42 40 0.31
43 2 0.02
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
Found at i:271774 original size:20 final size:20
Alignment explanation
Indices: 271749--271804 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
271739 GATTTTTCAA
271749 ATTCGCATTGCAATTTACTT
1 ATTCGCATTGCAATTTACTT
*
271769 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCAATTTACTT
271789 ATTCGCATTGCGAATT
1 ATTCGCATTGC-AATT
271805 GGGAAAATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCAATTTACTT
Found at i:271843 original size:21 final size:22
Alignment explanation
Indices: 271791--271843 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
271781 ATTTACTTAT
271791 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
271812 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
271833 TCGCATTGCGA
1 TCGCATTGCGA
271844 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:272107 original size:2 final size:2
Alignment explanation
Indices: 272102--272126 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
272092 TCTCTCTCTC
272102 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 T
272127 TAATGAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:274291 original size:21 final size:21
Alignment explanation
Indices: 274252--274329 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
274242 GAAGGTTAAG
* * *
274252 ACCTTTCGATGAAAGGACTTA
1 ACCTTTTGATTAAAAGACTTA
*
274273 ACATTTTGATTAAAAGACTTA
1 ACCTTTTGATTAAAAGACTTA
* * *
274294 TCCTTTTGA-TGAAAGAGCTTG
1 ACCTTTTGATTAAAAGA-CTTA
*
274315 ACCTTTTCATTAAAA
1 ACCTTTTGATTAAAA
274330 AAATTTAATA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
20 6 0.14
21 34 0.77
22 4 0.09
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (21 bp):
ACCTTTTGATTAAAAGACTTA
Found at i:278795 original size:22 final size:22
Alignment explanation
Indices: 278743--278803 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
278733 ATGAAATGTG
* *
278743 TCCCGAATGACCTCATG--TATG
1 TCCCGAAAGACCT-ATGTATATA
*
278764 TCCTGAAAGACCTATGTATATA
1 TCCCGAAAGACCTATGTATATA
278786 TCCCGAAAGACCTATGTA
1 TCCCGAAAGACCTATGTA
278804 ACCCTTGACT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.09
21 11 0.32
22 20 0.59
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (22 bp):
TCCCGAAAGACCTATGTATATA
Found at i:280361 original size:3 final size:3
Alignment explanation
Indices: 280353--280380 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
280343 AAAAGATCAT
280353 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
280381 AACCCAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:283340 original size:22 final size:22
Alignment explanation
Indices: 283315--283356 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
283305 ATATGAAATT
283315 TGTCCCGAAAGACCTATGTATA
1 TGTCCCGAAAGACCTATGTATA
* * *
283337 TGTCCTGAAGGACCTGTGTA
1 TGTCCCGAAAGACCTATGTA
283357 ACCCTCGACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATGTATA
Found at i:290867 original size:18 final size:18
Alignment explanation
Indices: 290844--290890 Score: 71
Period size: 16 Copynumber: 2.7 Consensus size: 18
290834 TATATATAGT
290844 AATATATAGTATAATATA
1 AATATATAGTATAATATA
290862 AATATATA--ATAATATA
1 AATATATAGTATAATATA
*
290878 TATATATAGTATA
1 AATATATAGTATA
290891 TAGTTTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 15 0.58
18 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AATATATAGTATAATATA
Found at i:290909 original size:30 final size:30
Alignment explanation
Indices: 290875--290995 Score: 201
Period size: 30 Copynumber: 4.1 Consensus size: 30
290865 ATATAATAAT
*
290875 ATATATATATAGTATATAGTTTTTAGAAAA
1 ATATATATATAGTGTATAGTTTTTAGAAAA
*
290905 ATATATATATAGTGTATAGTTTTTAGAAAT
1 ATATATATATAGTGTATAGTTTTTAGAAAA
290935 ATATATATATAGTGTATAGTTTTTAGAAAA
1 ATATATATATAGTGTATAGTTTTTAGAAAA
*
290965 ATATATATAGA-T-TATAGTTTTTAGAAAA
1 ATATATATATAGTGTATAGTTTTTAGAAAA
290993 ATA
1 ATA
290996 ATACAAATAT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 19 0.22
29 1 0.01
30 67 0.77
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.44
Consensus pattern (30 bp):
ATATATATATAGTGTATAGTTTTTAGAAAA
Found at i:290910 original size:60 final size:60
Alignment explanation
Indices: 290844--290973 Score: 174
Period size: 60 Copynumber: 2.2 Consensus size: 60
290834 TATATATAGT
290844 AATATATAGTATAATATA-AATATATA-ATAATATATATATATAGTATATAGTTTTTAGAAA
1 AATATATA-TATAATATATAATATATAGA-AATATATATATATAGTATATAGTTTTTAGAAA
* * * * * *
290904 AATATATATATAGTGTATAGTTTTTAGAAATATATATATATAGTGTATAGTTTTTAGAAA
1 AATATATATATAATATATAATATATAGAAATATATATATATAGTATATAGTTTTTAGAAA
290964 AATATATATA
1 AATATATATA
290974 GATTATAGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 7 0.11
60 54 0.87
61 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (60 bp):
AATATATATATAATATATAATATATAGAAATATATATATATAGTATATAGTTTTTAGAAA
Found at i:290912 original size:2 final size:2
Alignment explanation
Indices: 290834--290892 Score: 54
Period size: 2 Copynumber: 30.0 Consensus size: 2
290824 TTACAATAAT
*
290834 TA TA TA TA GTA -A TA TA TA GTA TA -A TA TA AA TA TA TA -A TA -A
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
290874 TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA -TA TA TA
290893 GTTTTTAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
1 4 0.08
2 38 0.79
3 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (2 bp):
TA
Found at i:291180 original size:24 final size:24
Alignment explanation
Indices: 291152--291212 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
291142 AATAGTAGTT
291152 TTATTCGTTTTATCATTATCATTA
1 TTATTCGTTTTATCATTATCATTA
* * *
291176 TTATT-GTTTTTATTATTGTTATTA
1 TTATTCG-TTTTATCATTATCATTA
* *
291200 TTTTTCATTTTAT
1 TTATTCGTTTTAT
291213 TTATATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (24 bp):
TTATTCGTTTTATCATTATCATTA
Found at i:291188 original size:12 final size:12
Alignment explanation
Indices: 291172--291201 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
291162 TATCATTATC
291172 ATTATTATTGTT
1 ATTATTATTGTT
*
291184 TTTATTATTGTT
1 ATTATTATTGTT
291196 ATTATT
1 ATTATT
291202 TTTCATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:299097 original size:26 final size:25
Alignment explanation
Indices: 299040--299099 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
299030 CCAGAATAGC
*
299040 ACCGGTCAACGGTCAACGGGTCGGG
1 ACCGGTCAACGGTAAACGGGTCGGG
* * *
299065 TCGGGTCAACGGGTAAACGGGTCGTG
1 ACCGGTCAAC-GGTAAACGGGTCGGG
299091 ACCGGTCAA
1 ACCGGTCAA
299100 ACCGGTTCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (25 bp):
ACCGGTCAACGGTAAACGGGTCGGG
Found at i:299109 original size:10 final size:10
Alignment explanation
Indices: 299091--299126 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
299081 ACGGGTCGTG
299091 ACCGGTC-AA
1 ACCGGTCAAA
299100 ACCGGTTCAAA
1 ACCGG-TCAAA
299111 ACCGGTCAAA
1 ACCGGTCAAA
299121 ACCGGT
1 ACCGGT
299127 TTCCAGCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.20
10 13 0.52
11 7 0.28
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:306200 original size:13 final size:13
Alignment explanation
Indices: 306184--306216 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
306174 GTCAACGGGT
*
306184 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
306197 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
306210 CGGGTCG
1 CGGGTCG
306217 TGATCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:306239 original size:10 final size:10
Alignment explanation
Indices: 306221--306271 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
306211 GGGTCGTGAT
306221 CGGTC-AAAC
1 CGGTCAAAAC
306230 CGGTCAAAAC
1 CGGTCAAAAC
* *
306240 CGATTCAAAAT
1 CG-GTCAAAAC
*
306251 CGGT-TAAAC
1 CGGTCAAAAC
306260 CGGTCAAAAC
1 CGGTCAAAAC
306270 CG
1 CG
306272 ATTTCCAGCG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
9 12 0.36
10 13 0.39
11 8 0.24
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (10 bp):
CGGTCAAAAC
Found at i:308245 original size:24 final size:21
Alignment explanation
Indices: 308210--308252 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
308200 GGCTCATTCT
*
308210 TTTGAATTTCAAGAGGCACATCC
1 TTTGAATGTCAA-AGG-ACATCC
308233 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
308253 GTCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:317108 original size:15 final size:15
Alignment explanation
Indices: 317088--317116 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
317078 AAAGAGAGGA
317088 AAAAAGAAAAATAAG
1 AAAAAGAAAAATAAG
317103 AAAAAGAAAAATAA
1 AAAAAGAAAAATAA
317117 ATAAAGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAAGAAAAATAAG
Found at i:318425 original size:134 final size:134
Alignment explanation
Indices: 318180--318900 Score: 946
Period size: 134 Copynumber: 5.4 Consensus size: 134
318170 ATCTTCGAAA
*
318180 CAAATCACATTCGATTTAATCTTCCCTGAAGAGCAGTGGAGTGAATCAAAGTTTTCTCGAGTCTG
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGTGGAGTGAATCAAAGTTTTCTCGAGTCTG
* * * * * *
318245 ACATCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTTCAAATTTGATCTTCTTGAAGGGGAAT
66 ACATCCCCTAAAGAGTAGCGGAGCAGATTATTCTTCTTTCAGATTTGATCTTCCTGAAGAGCAGT
318310 GAAG
131 GAAG
*
318314 CAAATCACATTCGATTCAATCTTCCCTGAAGATCAGTGGAGTGAATCAAAGTTTTCTCGAGTCTG
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGTGGAGTGAATCAAAGTTTTCTCGAGTCTG
* *
318379 ACATCCCCTAAAGAGTAGCGGAGCAGATTATTCTTCCTTCAGATTTGATCTTCCTGAAGAGCAAT
66 ACATCCCCTAAAGAGTAGCGGAGCAGATTATTCTTCTTTCAGATTTGATCTTCCTGAAGAGCAGT
*
318444 GAAT
131 GAAG
* *
318448 CAAATCACATTCGATTCAATCTTCCCTAAAGAGGAGTGGAGTGAATCAAAGTTTTCTCGAGTCTG
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGTGGAGTGAATCAAAGTTTTCTCGAGTCTG
* * * * *
318513 ACTTCCCCTAAAGAGTAACGGAGCAGATTCTTCTTGTTTCAGATTTGATCTTCCTGAAAAGCAGT
66 ACATCCCCTAAAGAGTAGCGGAGCAGATTATTCTTCTTTCAGATTTGATCTTCCTGAAGAGCAGT
318578 GAAG
131 GAAG
* * * *
318582 CAAATCACATTCAATTCAATCTTCACTGAAGAG-TGATGGAGTGAATCAAAGTATTCTCGAGTCT
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAG-TGGAGTGAATCAAAGTTTTCTCGAGTCT
* * * *
318646 GACCTTCCCTAAAGAGTAGCAGAGCAGA-TATTTCTTCTTTCAGATTTAATCTTCCTGAAGAGCA
65 GACATCCCCTAAAGAGTAGCGGAGCAGATTA-TTCTTCTTTCAGATTTGATCTTCCTGAAGAGCA
318710 GTGAAG
129 GTGAAG
* * * * * * *
318716 TAAATCACATTCGATTCAATCTTCTCTGAAGAGCAGAGAAGTGGATCAAAGTTTTTCTTGAGCCT
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGTGGAGTGAATCAAAG-TTTTCTCGAGTCT
* * * * * * *
318781 AATC-TCCCCTAAAGTGTAGAGGAGCATATT-CTCTTTCTTTCAGATTTGATCTTTCTAAAGAGC
65 GA-CATCCCCTAAAGAGTAGCGGAGCAGATTATTC-TTCTTTCAGATTTGATCTTCCTGAAGAGC
318844 AGTGAAG
128 AGTGAAG
** * * * * *
318851 CAAATCATGTTAGATTCAATTTTCCCTGAAGAGTAGCGAAGTGAATCAAA
1 CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGTGGAGTGAATCAAA
318901 ATTATTTGAG
Statistics
Matches: 518, Mismatches: 62, Indels: 13
0.87 0.10 0.02
Matches are distributed among these distances:
133 2 0.00
134 409 0.79
135 105 0.20
136 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (134 bp):
CAAATCACATTCGATTCAATCTTCCCTGAAGAGCAGTGGAGTGAATCAAAGTTTTCTCGAGTCTG
ACATCCCCTAAAGAGTAGCGGAGCAGATTATTCTTCTTTCAGATTTGATCTTCCTGAAGAGCAGT
GAAG
Found at i:319331 original size:28 final size:28
Alignment explanation
Indices: 319300--319480 Score: 180
Period size: 28 Copynumber: 6.5 Consensus size: 28
319290 ATATATATAG
319300 TATATAGTATATAGTTTTTAGGAAAATA
1 TATATAGTATATAGTTTTTAGGAAAATA
319328 TATATAGTATATAGTTTTTA-GAAAA-A
1 TATATAGTATATAGTTTTTAGGAAAATA
* * * * *
319354 CA-A-A-TATATA-TATATA-GTATATA
1 TATATAGTATATAGTTTTTAGGAAAATA
319377 GTATATAGTATATAGTTTTTAGGAAAATA
1 -TATATAGTATATAGTTTTTAGGAAAATA
*
319406 TATATAGTATATAGTTTTTAGAAAAATATATA
1 TATATAGTATATAGTTTTTAG--GAA-A-ATA
* *
319438 TATATAGTATATAGGTTTTAGAAAAATAA
1 TATATAGTATATAGTTTTTAGGAAAAT-A
319467 TATATA-TATATAGT
1 TATATAGTATATAGT
319481 ATAGTTTAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 24
0.78 0.08 0.15
Matches are distributed among these distances:
22 7 0.05
23 7 0.05
24 2 0.02
25 2 0.02
26 3 0.02
27 11 0.09
28 54 0.42
29 13 0.10
30 5 0.04
31 1 0.01
32 23 0.18
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.42
Consensus pattern (28 bp):
TATATAGTATATAGTTTTTAGGAAAATA
Found at i:319332 original size:2 final size:2
Alignment explanation
Indices: 319165--319312 Score: 144
Period size: 2 Copynumber: 74.0 Consensus size: 2
319155 TTATAATAAT
*
319165 TA TA TA TA GTA -A TA TA TA -A TA TA -A TA TA AA TA TA TA -A TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
319204 -A TA TA TA TA TA GTA TA TA GTT TT TA GA AA AA CA AA 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
319247 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
319289 TA TA TA TA TA GTA TA TA GTA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA
319313 GTTTTTAGGA
Statistics
Matches: 127, Mismatches: 9, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
1 5 0.04
2 113 0.89
3 9 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:319339 original size:78 final size:78
Alignment explanation
Indices: 319250--319451 Score: 277
Period size: 78 Copynumber: 2.6 Consensus size: 78
319240 ATATATATAT
* * *
319250 ATATATATA-TATATA-TATATATATATATATATATATATATATA-TATATAGTATATAGTATAT
1 ATATATATAGTATATAGTTTATAAAAATATATATATATATATATAGTATATAGTATATAGTATAT
319312 AGTTTTTAGGAAA
66 AGTTTTTAGGAAA
* * *
319325 ATATATATAGTATATAGTTTTTAGAAAA-ACAAATATATATATATAGTATATAGTATATAGTATA
1 ATATATATAGTATATAGTTTATA-AAAATATATATATATATATATAGTATATAGTATATAGTATA
319389 TAGTTTTTAGGAAA
65 TAGTTTTTAGGAAA
*
319403 ATATATATAGTATATAGTTTTTAGAAAAATATATATATATAGTATATAG
1 ATATATATAGTATATAG--TTTATAAAAATATATATATATA-TATATAG
319452 GTTTTAGAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
75 9 0.08
76 6 0.06
77 19 0.17
78 51 0.47
79 4 0.04
80 13 0.12
81 7 0.06
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (78 bp):
ATATATATAGTATATAGTTTATAAAAATATATATATATATATATAGTATATAGTATATAGTATAT
AGTTTTTAGGAAA
Found at i:319449 original size:60 final size:61
Alignment explanation
Indices: 319371--319506 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 61
319361 ATATATATAG
* *
319371 TATATAGTATATAGTATATAGTTTTTAGGAAAAT-ATATATAGTATATAGT-T-TTTAGAAAAA
1 TATATA-TATATAGTATATAGGTTTTAGAAAAATAATATATA-TATATAGTATATTTA-AAAAA
*
319432 TATATATATATAGTATATAGGTTTTAGAAAAATAATATATATATATAGTATAGTTTAAAATA
1 TATATATATATAGTATATAGGTTTTAGAAAAATAATATATATATATAGTATA-TTTAAAAAA
319494 TATATA-ATATAGT
1 TATATATATATAGT
319507 TTTTTAATAT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
60 33 0.49
61 21 0.31
62 10 0.15
63 4 0.06
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (61 bp):
TATATATATATAGTATATAGGTTTTAGAAAAATAATATATATATATAGTATATTTAAAAAA
Found at i:319516 original size:13 final size:13
Alignment explanation
Indices: 319498--319522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319488 AAAATATATA
319498 TAATATAGTTTTT
1 TAATATAGTTTTT
319511 TAATATAGTTTT
1 TAATATAGTTTT
319523 AAAATATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TAATATAGTTTTT
Found at i:326374 original size:15 final size:14
Alignment explanation
Indices: 326350--326404 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
326340 ATTTTTATCA
326350 ATTTTA-TTTATTT
1 ATTTTATTTTATTT
326363 ATTTTATTTTTATGTT
1 ATTTTA-TTTTAT-TT
326379 CA-TTTATTTTATTT
1 -ATTTTATTTTATTT
*
326393 CTTTTAATTTTA
1 ATTTT-ATTTTA
326405 GGTACCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 6 0.17
14 5 0.14
15 17 0.49
16 6 0.17
17 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:326385 original size:21 final size:19
Alignment explanation
Indices: 326351--326392 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
326341 TTTTTATCAA
326351 TTTTATTTATTTATTTTAT
1 TTTTATTTATTTATTTTAT
326370 TTTTATGTTCATTTATTTTAT
1 TTTTAT-TT-ATTTATTTTAT
326391 TT
1 TT
326393 CTTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTTATTTATTTTAT
Found at i:326839 original size:18 final size:18
Alignment explanation
Indices: 326816--326851 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
326806 ATTTATGTTC
326816 CCTCTCTTATGTTTTTAT
1 CCTCTCTTATGTTTTTAT
326834 CCTCTCTTATGTTTTTAT
1 CCTCTCTTATGTTTTTAT
326852 TTATATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.06, T:0.61
Consensus pattern (18 bp):
CCTCTCTTATGTTTTTAT
Found at i:330388 original size:22 final size:22
Alignment explanation
Indices: 330335--330388 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
330325 TAGATATTAA
*
330335 AATTTTGTTTAATATGATTAGGT
1 AATTTT-TTTAATATGATTAGCT
* *
330358 CATTATTTTAATATG-TGTAGCT
1 AATTTTTTTAATATGAT-TAGCT
330380 AATTTTTTT
1 AATTTTTTT
330389 TTATTTAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 20 0.80
23 4 0.16
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.56
Consensus pattern (22 bp):
AATTTTTTTAATATGATTAGCT
Found at i:338837 original size:11 final size:11
Alignment explanation
Indices: 338821--338870 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
338811 ATTTTTTTTC
338821 AAAAAAAGGCA
1 AAAAAAAGGCA
338832 AAAAAAAGGCAA
1 AAAAAAAGGC-A
**
338844 AAAAAAAAACA
1 AAAAAAAGGCA
*
338855 AAAAAAAGCCA
1 AAAAAAAGGCA
338866 AAAAA
1 AAAAA
338871 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGCA
Found at i:338856 original size:23 final size:23
Alignment explanation
Indices: 338821--338870 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
338811 ATTTTTTTTC
** *
338821 AAAAAAAGGCAAAAAAAAGGCAA
1 AAAAAAAAACAAAAAAAAGCCAA
338844 AAAAAAAAACAAAAAAAAGCCAA
1 AAAAAAAAACAAAAAAAAGCCAA
338867 AAAA
1 AAAA
338871 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (23 bp):
AAAAAAAAACAAAAAAAAGCCAA
Found at i:347002 original size:40 final size:42
Alignment explanation
Indices: 346932--347019 Score: 144
Period size: 40 Copynumber: 2.1 Consensus size: 42
346922 GCAATGTACT
*
346932 TTTTAGTTTATATATATGATTTTTTTTCTGTTGTATTTATAG-
1 TTTTAGTTTATATATATGA-TTTTTCTCTGTTGTATTTATAGC
346974 TTTTAGTTTATATATATGA-TTTTCTCTGTTGTATTTATAGC
1 TTTTAGTTTATATATATGATTTTTCTCTGTTGTATTTATAGC
347015 TTTTA
1 TTTTA
347020 AAATAATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 20 0.45
41 5 0.11
42 19 0.43
ACGTcount: A:0.22, C:0.05, G:0.11, T:0.62
Consensus pattern (42 bp):
TTTTAGTTTATATATATGATTTTTCTCTGTTGTATTTATAGC
Found at i:347029 original size:40 final size:41
Alignment explanation
Indices: 346940--347030 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 41
346930 CTTTTTAGTT
* ***
346940 TATATATATGATTTTTTTTCTGTTGTATTTATAGTTTTAGTT
1 TATATATATGA-TTTTTCTCTGTTGTATTTATAGTTTTAAAA
346982 TATATATATGA-TTTTCTCTGTTGTATTTATAGCTTTTAAAA
1 TATATATATGATTTTTCTCTGTTGTATTTATAG-TTTTAAAA
347023 TA-ATATAT
1 TATATATAT
347031 TTTTCTTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
40 26 0.59
41 7 0.16
42 11 0.25
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.58
Consensus pattern (41 bp):
TATATATATGATTTTTCTCTGTTGTATTTATAGTTTTAAAA
Found at i:348109 original size:19 final size:19
Alignment explanation
Indices: 348085--348125 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
348075 GTACCGATTC
348085 ATAGTACTACAC-GATATGA
1 ATAGTACTACACTG-TATGA
*
348104 ATAGTACTATACTGTATGA
1 ATAGTACTACACTGTATGA
348123 ATA
1 ATA
348126 ATACCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (19 bp):
ATAGTACTACACTGTATGA
Found at i:354538 original size:23 final size:23
Alignment explanation
Indices: 354512--354575 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
354502 AGCTCATATA
*
354512 AATTGCACCGAAGTGTCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
354535 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
354558 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
354576 TATAAAATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:354584 original size:23 final size:23
Alignment explanation
Indices: 354506--354585 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
354496 CACCACAGCT
*
354506 CATATAAATTGCACCGAAGTGTCA
1 CATA-AAATTGCACCGAAGTGCCA
* * *
354530 CGTAGAATTGCACCGAAGTGCCG
1 CATAAAATTGCACCGAAGTGCCA
* * *
354553 CGTAGAATTGCACCGTAGTGCCA
1 CATAAAATTGCACCGAAGTGCCA
*
354576 TATAAAATTG
1 CATAAAATTG
354586 TCCATAAGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 44 0.94
24 3 0.06
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (23 bp):
CATAAAATTGCACCGAAGTGCCA
Found at i:357538 original size:81 final size:81
Alignment explanation
Indices: 357419--357999 Score: 715
Period size: 81 Copynumber: 7.2 Consensus size: 81
357409 TTATAATTCC
* ** * *
357419 TTTAGTCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTTGCATGATTGACACTTTTCTGCCT
1 TTTA-TCTTTTACTCAAAGATATTTAACCTTTCATCTAACTTGCATAATTGACACTTTTCTGCCA
357484 AATGCACAGCTAGGCCA
65 AATGCACAGCTAGGCCA
* * * * * *
357501 TTTATCTTTTACTCGACGATATTTAACCATTCATCTAACTGGCAAAATTGACACATTTCTGCCAA
1 TTTATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTTGCATAATTGACACTTTTCTGCCAA
*
357566 ATGCACAGCTAGGTCA
66 ATGCACAGCTAGGCCA
* * *
357582 TTTATCTTTTACTCAAAGATATTTAACCTTTCATCTAAC-TGACATAGTTGACACCTTTCTGTCA
1 TTTATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTTG-CATAATTGACACTTTTCTGCCA
*
357646 AATGCACAACTAGGCC-
65 AATGCACAGCTAGGCCA
* * * * * * *
357662 TTTAATCTTTTACTCAACGGTATTAAATCGTTCATCTAA-TTGGCATAATTGACACATTTCTACC
1 TTT-ATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTT-GCATAATTGACACTTTTCTGCC
357726 AAATGCACAGCTAGGCCA
64 AAATGCACAGCTAGGCCA
* * * * * *
357744 TTTATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAGTTGGCATTTTTCTGTCAA
1 TTTATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTTGCATAATTGACACTTTTCTGCCAA
357809 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * *
357825 TTTGTCTTTTACTCAATAG-TATTTAACCGTTCATCTAACTTGCATAATTGACACTTTGCTGCCA
1 TTTATCTTTTACTCAA-AGATATTTAACCTTTCATCTAACTTGCATAATTGACACTTTTCTGCCA
*
357889 AATACACAGCTAGGCCA
65 AATGCACAGCTAGGCCA
* * * *
357906 TTTATCTTTTACTCAATGGTATTTAACCATTCATCTAAC-TGCCATAATTGACA-TATTTCCGCC
1 TTTATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTTG-CATAATTGACACT-TTTCTGCC
*
357969 AAATGCACAGCTATGCCA
64 AAATGCACAGCTAGGCCA
357987 TTTATCTTTTACT
1 TTTATCTTTTACT
358000 ATTAAAATAG
Statistics
Matches: 430, Mismatches: 59, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
80 8 0.02
81 411 0.96
82 11 0.03
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (81 bp):
TTTATCTTTTACTCAAAGATATTTAACCTTTCATCTAACTTGCATAATTGACACTTTTCTGCCAA
ATGCACAGCTAGGCCA
Found at i:358229 original size:55 final size:53
Alignment explanation
Indices: 358156--358352 Score: 171
Period size: 55 Copynumber: 3.6 Consensus size: 53
358146 AAATTCACCT
* * * * *
358156 ACTTATTATGAACTTCTTATATTTGTACATATATCTCCCATATGGAAATTCATAC
1 ACTTAGTATGAATTTCTTAT-TTTGTACACATAT-TCCCATACGAAAATTCATAC
* * ** *
358211 ACTTAGTATGAATTTCTTAGTTCGTACACCGAGTTCCCTTAC-ATAAATTCATAC
1 ACTTAGTATGAATTTCTTATTTTGTACACATA-TTCCCATACGA-AAATTCATAC
* * * *
358265 AGTTAGTATGAATTTATTAGTTTTGCACACATAATGCCCATACGAAAATTCATAC
1 ACTTAGTATGAATTTCTTA-TTTTGTACACAT-ATTCCCATACGAAAATTCATAC
* * *
358320 AATTAGTATGAATTCCTTAGTTTTGCACACATA
1 ACTTAGTATGAATTTCTTA-TTTTGTACACATA
358353 GTGCCATTTG
Statistics
Matches: 115, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
54 42 0.37
55 71 0.62
56 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (53 bp):
ACTTAGTATGAATTTCTTATTTTGTACACATATTCCCATACGAAAATTCATAC
Found at i:358743 original size:19 final size:21
Alignment explanation
Indices: 358699--358749 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
358689 CCCCCACCAT
*
358699 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
358721 GGTATCGATACT-CTAT-TAC
1 GGTATCGATACTACTATATAC
*
358740 GGTACCGATA
1 GGTATCGATA
358750 ACATTTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
21 4 0.15
22 12 0.44
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Found at i:358797 original size:20 final size:21
Alignment explanation
Indices: 358772--358826 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
358762 TCTGTGATCA
358772 ATGGTATCGATACCATT-CTC
1 ATGGTATCGATACCATTCCTC
358792 ATGGTATCGATA-C-TTCCCTC
1 ATGGTATCGATACCATT-CCTC
*
358812 TTGGTATCGATACCA
1 ATGGTATCGATACCA
358827 CTAGAATCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.07
19 1 0.03
20 26 0.87
21 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (21 bp):
ATGGTATCGATACCATTCCTC
Found at i:367751 original size:24 final size:24
Alignment explanation
Indices: 367719--367782 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
367709 GAGTCGAGGG
* *
367719 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCGGTACTTCGAGACAAA
367743 TTCTACGCGGTACTTCGAGACAAA
1 TTCTACGCGGTACTTCGAGACAAA
* *
367767 TTCTACGTGGCACTTC
1 TTCTACGCGGTACTTC
367783 AGTGCAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (24 bp):
TTCTACGCGGTACTTCGAGACAAA
Found at i:370149 original size:21 final size:21
Alignment explanation
Indices: 370123--370177 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
370113 GATCTCCGGA
370123 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
*
370144 ATCGCAACGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
370165 ATCGCAATGCGAA
1 ATCGCAATGCGAA
370178 TATGTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (21 bp):
ATCGCAATGCGAACTTGGACT
Found at i:370216 original size:21 final size:21
Alignment explanation
Indices: 370186--370309 Score: 103
Period size: 21 Copynumber: 5.9 Consensus size: 21
370176 AATATGTAAA
* **
370186 TCGCAATGCGATAGTTGAAGT
1 TCGCATTGCGATAGTCCAAGT
370207 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
370228 TCGCATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
*
370251 TCG--TTGCGATAGTACAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
370270 TCGTATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
370293 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
370310 AATCGCAACG
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
19 17 0.20
21 47 0.55
23 21 0.25
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:370238 original size:42 final size:40
Alignment explanation
Indices: 370212--370305 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 40
370202 GAAGTTCGCA
*
370212 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTACAAGTTCGCATTGCGA--TATTCCAAATTCG
*
370254 TTGCGATAGTACAAGTTCGTATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTACAAGTTCGCATTGCGA--TATTCCAAATTCG
370296 TTGCGATAGT
1 TTGCGATAGT
370306 CCAAAATCGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTACAAGTTCGCATTGCGATATTCCAAATTCG
Found at i:370937 original size:6 final size:6
Alignment explanation
Indices: 370926--370950 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
370916 CTGTCTCGTC
370926 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
370951 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:371092 original size:42 final size:42
Alignment explanation
Indices: 371043--371265 Score: 313
Period size: 42 Copynumber: 5.3 Consensus size: 42
371033 TGCGATTTTG
* * *
371043 GACTATCGCAACGAATTTGGAATAAATTGCAATGCGATA-GTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGA-ACTTC
*
371085 GACTATCGCAACGAATTTGGAATAAATCGCAAAACCCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGC--AACGCGAACTTC
* * *
371129 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
371171 GACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
371213 GAATATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
371255 GACTATCGCAA
1 GACTATCGCAA
371266 TGCGAATATG
Statistics
Matches: 161, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 125 0.78
43 1 0.01
44 35 0.22
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:371262 original size:21 final size:20
Alignment explanation
Indices: 371121--371271 Score: 119
Period size: 21 Copynumber: 7.2 Consensus size: 20
371111 TCGCAAAACC
* * *
371121 CGAACTTCGACTATCACAA-
1 CGAACTTGGAATATCGCAAG
371140 CGAACTTGGAATAAATCGCAACG
1 CGAACTTGGAAT--ATCGCAA-G
*
371163 CGAACTTGGACTATCGCAA-
1 CGAACTTGGAATATCGCAAG
* *
371182 CAAATTTGGAATAAATCGCAACG
1 CGAACTTGGAAT--ATCGCAA-G
*
371205 CGAACTTCGAATATCGCAA-
1 CGAACTTGGAATATCGCAAG
371224 CGAACTTGGAATAAATCGCAACG
1 CGAACTTGGAAT--ATCGCAA-G
*
371247 CGAACTTGGACTATCGCAATG
1 CGAACTTGGAATATCGCAA-G
371268 CGAA
1 CGAA
371272 TATGTAAATC
Statistics
Matches: 107, Mismatches: 13, Indels: 22
0.75 0.09 0.15
Matches are distributed among these distances:
19 30 0.28
21 46 0.43
23 31 0.29
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
CGAACTTGGAATATCGCAAG
Found at i:372873 original size:2 final size:2
Alignment explanation
Indices: 372866--372895 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
372856 TAAATCTAAT
372866 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
372896 ATCAACCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:373009 original size:332 final size:318
Alignment explanation
Indices: 372409--373405 Score: 1467
Period size: 332 Copynumber: 3.1 Consensus size: 318
372399 ATTATAGCAA
* * *
372409 TTATTCATAAATTTGTTTGAAGAAATTACACTATAACCCTCGTGTCGAATCGGCTAGAGTTTTTT
1 TTATTCATAAATTTGTTTGAAG-AATTACACTATTACCCTCGTATCGAATCAGCTAGAGTTTTTT
* * *
372474 CACCCTCTCCCGAATCCGACTCGATCCGAACTCACTCCTTTATAAAATTCGACCTGAACCGATCT
65 CACCCTCTCCCGAATCC-A--CGATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCT
* * * *
372539 AAATCTAAATATATATTTTTTAAAATTCAATCCTAACAAATTGAATCAAATCAAAATCTATCAAT
127 AAATATAAATA-ATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAATCAAAATCTATCAAT
* * *
372604 TTCAAGTTAAATTATCACTCTTATAAATAACTACCGGAGAAAGAATATTCCTTTTCTTTTAAAAA
191 TTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTTTCTTCTAAAAA
*
372669 GCAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAC
256 GCAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAT
*
372732 TTATTCATAAATTTGTTTGAAGAAATTACACTATTACCCTCGTATCGAATCAGTTAGAGTTTTTT
1 TTATTCATAAATTTGTTTGAAG-AATTACACTATTACCCTCGTATCGAATCAGCTAGAGTTTTTT
*
372797 CACCCTCTCCCGAATCC-C-ATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGGTCTAAA
65 CACCCTCTCCCGAATCCACGATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCTAAA
* *
372860 TCTAATTATATATATATATATATATATATATATATAATCAACCCTATCTAATTGAATCAAATCAA
130 TATAA--ATA-AT-T-T-T-T-T-T-TA-A-A-AT--TCAACCCTATCAAATTGAATCAAATCAA
372925 AATCTATCAATTTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTT
180 AATCTATCAATTTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTT
* *
372990 TCTTCTAAAAAGTAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTTAATAAATA
245 TCTTCTAAAAAGCAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATA
373055 CAACAATAT
310 CAACAATAT
* * **
373064 TTATTCATAAATTTATTTGAAGAATTACACTATTACCCTCGTATTGAATTGGCTAGAGTTTTTTC
1 TTATTCATAAATTTGTTTGAAGAATTACACTATTACCCTCGTATCGAATCAGCTAGAGTTTTTTC
** * *
373129 ACCCTCTCCTTAATCCGATCTGATCTGACCTCACTCTTTTATAAAATTCTACCTGAGCCGATCTA
66 ACCCTCTCCCGAATCC-A-C-GATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCTA
*
373194 AATATAAATAATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAAACAAAATCTATCAATTT
128 AATATAAATAATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAATCAAAATCTATCAATTT
*
373259 CAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCTTTTTCTTCTAAAAAGC
193 CAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTTTCTTCTAAAAAGC
* *
373324 AAAAAATCAGGCGAAGAAAAATAGTTTACTCGTAATGTGGAGTCAATGAATACAACAATAT
258 AAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAT
*
373385 TTATTCATAATTTTGTTTGAA
1 TTATTCATAAATTTGTTTGAA
373406 TCTGTGGGGA
Statistics
Matches: 617, Mismatches: 38, Indels: 40
0.89 0.05 0.06
Matches are distributed among these distances:
318 46 0.07
319 1 0.00
320 6 0.01
321 179 0.29
322 1 0.00
323 81 0.13
324 2 0.00
325 2 0.00
326 3 0.00
327 3 0.00
328 2 0.00
329 2 0.00
330 3 0.00
331 54 0.09
332 180 0.29
333 2 0.00
334 4 0.01
336 46 0.07
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (318 bp):
TTATTCATAAATTTGTTTGAAGAATTACACTATTACCCTCGTATCGAATCAGCTAGAGTTTTTTC
ACCCTCTCCCGAATCCACGATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCTAAAT
ATAAATAATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAATCAAAATCTATCAATTTCAA
GTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTTTCTTCTAAAAAGCAAA
AAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAT
Found at i:373317 original size:321 final size:322
Alignment explanation
Indices: 372409--373405 Score: 1529
Period size: 321 Copynumber: 3.1 Consensus size: 322
372399 ATTATAGCAA
* *
372409 TTATTCATAAATTTGTTTGAAGAAATTACACTATAACCCTCGTGTCGAATCGGCTAGAGTTTTTT
1 TTATTCATAAATTTGTTTGAAGAAATTACACTATTACCCTCGTATCGAATCGGCTAGAGTTTTTT
* * *
372474 CACCCTCTCCCGAATCCGACTCGATCCGAACTCACTCCTTTATAAAATTCGACCTGAACCGATCT
66 CACCCTCTCCCGAATCCGACT-GATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCT
* * *
372539 AAATCTAAATATATATTTTTTAAAATTCAATCCTAACAAATTGAATCAAATCAAAATCTATCAAT
130 AAATCTAAATATATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAATCAAAATCTATCAAT
* * *
372604 TTCAAGTTAAATTATCACTCTTATAAATAACTACCGGAGAAAGAATATTCCTTTTCTTTTAAAAA
195 TTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTTTCTTCTAAAAA
*
372669 GCAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAC
260 GCAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAT
* *
372732 TTATTCATAAATTTGTTTGAAGAAATTACACTATTACCCTCGTATCGAATCAGTTAGAGTTTTTT
1 TTATTCATAAATTTGTTTGAAGAAATTACACTATTACCCTCGTATCGAATCGGCTAGAGTTTTTT
*
372797 CACCCTCTCCCGAATCC--C--ATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGGTCTA
66 CACCCTCTCCCGAATCCGACTGATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCTA
*
372858 AATCTAATTATATATATATATATATATATATATATATAATCAACCCTATCTAATTGAATCAAATC
131 AATCTAA--ATATAT-T-T-T-T-T-T-TA-A-A-AT--TCAACCCTATCAAATTGAATCAAATC
372923 AAAATCTATCAATTTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCAT
182 AAAATCTATCAATTTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCAT
* *
372988 TTTCTTCTAAAAAGTAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTTAATAAA
247 TTTCTTCTAAAAAGCAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAA
373053 TACAACAATAT
312 TACAACAATAT
* * *
373064 TTATTCATAAATTTATTTGAAG-AATTACACTATTACCCTCGTATTGAATTGGCTAGAGTTTTTT
1 TTATTCATAAATTTGTTTGAAGAAATTACACTATTACCCTCGTATCGAATCGGCTAGAGTTTTTT
** * *
373128 CACCCTCTCCTTAATCCGATCTGATCTGACCTCACTCTTTTATAAAATTCTACCTGAGCCGATCT
66 CACCCTCTCCCGAATCCGA-CTGATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCT
* *
373193 AAATATAAATA-ATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAAACAAAATCTATCAAT
130 AAATCTAAATATATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAATCAAAATCTATCAAT
*
373257 TTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCTTTTTCTTCTAAAAA
195 TTCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTTTCTTCTAAAAA
* *
373322 GCAAAAAATCAGGCGAAGAAAAATAGTTTACTCGTAATGTGGAGTCAATGAATACAACAATAT
260 GCAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAT
*
373385 TTATTCATAATTTTGTTTGAA
1 TTATTCATAAATTTGTTTGAA
373406 TCTGTGGGGA
Statistics
Matches: 617, Mismatches: 38, Indels: 40
0.89 0.05 0.06
Matches are distributed among these distances:
318 46 0.07
320 6 0.01
321 180 0.29
322 1 0.00
323 81 0.13
324 2 0.00
325 2 0.00
326 3 0.00
327 3 0.00
328 2 0.00
329 2 0.00
330 3 0.00
331 54 0.09
332 180 0.29
333 2 0.00
334 4 0.01
336 46 0.07
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (322 bp):
TTATTCATAAATTTGTTTGAAGAAATTACACTATTACCCTCGTATCGAATCGGCTAGAGTTTTTT
CACCCTCTCCCGAATCCGACTGATCCGACCTCACTCTTTTATAAAATTCTACCTGAACCGATCTA
AATCTAAATATATTTTTTTTAAAATTCAACCCTATCAAATTGAATCAAATCAAAATCTATCAATT
TCAAGTTAAATTATCACTCTTATAAATAACTATCGGAGAAAGAATATTCATTTTCTTCTAAAAAG
CAAAAAATCAGGCGAAGAAGAATAGTTTACTCGTAATGTGGAGTCAATAAATACAACAATAT
Found at i:376000 original size:43 final size:42
Alignment explanation
Indices: 375934--376071 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 42
375924 TCATGAGCCC
*
375934 TTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACA
1 TTTTGCGGCGTTTGT-TTCAAAAACGCCGCTATAGATATGACA
* * *
375977 TTTTGCGGCGTTTGTTTAAAAAAATGCCGCTATAGATATAACA
1 TTTTGCGGCGTTTGTTT-CAAAAACGCCGCTATAGATATGACA
* * *
376020 TTTTGC-GCGTTTG-TTCAAAAACACCGCTATAAAT-TGACC
1 TTTTGCGGCGTTTGTTTCAAAAACGCCGCTATAGATATGACA
376059 TTTTGCGGCGTTT
1 TTTTGCGGCGTTT
376072 CTTGACCTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
39 9 0.11
40 21 0.25
41 2 0.02
42 8 0.10
43 43 0.52
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (42 bp):
TTTTGCGGCGTTTGTTTCAAAAACGCCGCTATAGATATGACA
Found at i:376078 original size:20 final size:20
Alignment explanation
Indices: 376053--376091 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
376043 CCGCTATAAA
376053 TTGACCTTTTGCGGCGTTTC
1 TTGACCTTTTGCGGCGTTTC
376073 TTGACCTTTTGCGGCGTTT
1 TTGACCTTTTGCGGCGTTT
376092 GTTCCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.23, G:0.26, T:0.46
Consensus pattern (20 bp):
TTGACCTTTTGCGGCGTTTC
Found at i:381669 original size:3 final size:3
Alignment explanation
Indices: 381661--381707 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
381651 GAGTACAATT
381661 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
381708 TTGCAGCGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:391945 original size:20 final size:20
Alignment explanation
Indices: 391855--391946 Score: 51
Period size: 21 Copynumber: 4.5 Consensus size: 20
391845 CGTTTCAGCT
* *
391855 TAAAGGTTTCAAAACTTTTTA
1 TAAAGGTTTTAAAAC-CTTTA
* * *
391876 TAAGGGTCTTGAAACCTTTGA
1 TAAAGGTTTTAAAACCTTT-A
* * ** *
391897 TGACGGTTTTGTAACTTTTA
1 TAAAGGTTTTAAAACCTTTA
*
391917 T-AGGAGTTTTAAAACCTTTA
1 TAAAG-GTTTTAAAACCTTTA
391937 TAAAGGTTTT
1 TAAAGGTTTT
391947 GTCTAAGGAG
Statistics
Matches: 53, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.04
20 23 0.43
21 28 0.53
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (20 bp):
TAAAGGTTTTAAAACCTTTA
Found at i:392425 original size:2 final size:2
Alignment explanation
Indices: 392418--392469 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
392408 ATCTGCTTGC
392418 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
392460 AT AT AT AT AT
1 AT AT AT AT AT
392470 CCATGGGTAG
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:401694 original size:22 final size:22
Alignment explanation
Indices: 401648--401695 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
401638 ACTTTTTGGG
*
401648 TCAAAGTCAACGGTTAGACCAA
1 TCAAAGTCAACGGTCAGACCAA
* *
401670 TCAAAGTCAACGGTCATACCGA
1 TCAAAGTCAACGGTCAGACCAA
401692 TCAA
1 TCAA
401696 CGGGTCAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (22 bp):
TCAAAGTCAACGGTCAGACCAA
Found at i:410201 original size:21 final size:18
Alignment explanation
Indices: 410171--410213 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
410161 CGTCTTGTCG
410171 TTTTGTTTTTAGTTTAAATT
1 TTTTGTTTTT-GTTT-AATT
*
410191 TTTTGGTTTTTGTTTTATT
1 TTTT-GTTTTTGTTTAATT
410210 TTTT
1 TTTT
410214 ATTGTTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (18 bp):
TTTTGTTTTTGTTTAATT
Found at i:410220 original size:15 final size:15
Alignment explanation
Indices: 410200--410237 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
410190 TTTTTGGTTT
410200 TTGTTTTATTTTTTA
1 TTGTTTTATTTTTTA
*
410215 TTGTTTGA-TTTTTA
1 TTGTTTTATTTTTTA
410229 TT-TTTTATT
1 TTGTTTTATT
410238 ATCTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (15 bp):
TTGTTTTATTTTTTA
Found at i:410220 original size:21 final size:21
Alignment explanation
Indices: 410173--410237 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
410163 TCTTGTCGTT
* *
410173 TTGTTTTTAGTTTAAATTTTT-
1 TTGTTTTT-GTTTTATTTTTTA
*
410194 TGGTTTTTGTTTTATTTTTTA
1 TTGTTTTTGTTTTATTTTTTA
*
410215 TTGTTTGAT-TTTTATTTTTTA
1 TTGTTT-TTGTTTTATTTTTTA
410236 TT
1 TT
410238 ATCTTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (21 bp):
TTGTTTTTGTTTTATTTTTTA
Found at i:412042 original size:20 final size:21
Alignment explanation
Indices: 412017--412056 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
412007 CTTTGCATAG
412017 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
412037 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
412057 CCCAACAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:412131 original size:21 final size:21
Alignment explanation
Indices: 412102--412159 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
412092 AAACAAAGGT
*
412102 AGTATCGATACTCC-CTTTAGG
1 AGTACCGATAC-CCTCTTTAGG
412123 AGTACCGATACCCTCTTTAGG
1 AGTACCGATACCCTCTTTAGG
412144 AGTACCGATACCCTCT
1 AGTACCGATACCCTCT
412160 GTTCTAGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
AGTACCGATACCCTCTTTAGG
Found at i:415064 original size:94 final size:94
Alignment explanation
Indices: 414903--415084 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 94
414893 TACCGATGAG
* * *
414903 GTAGTATCGATACTATGGTAAGGGTATCGATACCAGGTAACATCAGACCTAATTTTGGTATCGAT
1 GTAGTATCAATACTATGGTAAGGGTATCGATACCAAGCAACATCAGACCTAATTTTGGTATCGAT
* * *
414968 ACCATAGGGGGTATCGGTACCATAATATA
66 ACCAGAAGGGGTATCGATACCATAATATA
* * * *
414997 GTAGTATCAATACTATGGTGAGGGTATCGATACCAAGCCACATC-GAATCTAATTTTGGTATTGA
1 GTAGTATCAATACTATGGTAAGGGTATCGATACCAAGCAACATCAG-ACCTAATTTTGGTATCGA
*
415061 TACCAGAAGGGTTATCGATACCAT
65 TACCAGAAGGGGTATCGATACCAT
415085 GGTAGGGCTA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 75 0.99
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (94 bp):
GTAGTATCAATACTATGGTAAGGGTATCGATACCAAGCAACATCAGACCTAATTTTGGTATCGAT
ACCAGAAGGGGTATCGATACCATAATATA
Found at i:415101 original size:20 final size:20
Alignment explanation
Indices: 415068--415141 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
415058 TGATACCAGA
* *
415068 AGGGTTATCGATACCATGGT
1 AGGGCTATCAATACCATGGT
* *
415088 AGGGCTATTAATACCATGAT
1 AGGGCTATCAATACCATGGT
* *
415108 AGGGGTATCGATACCATGGT
1 AGGGCTATCAATACCATGGT
* *
415128 AGGGGTATCGATAC
1 AGGGCTATCAATAC
415142 TAAATAGCCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (20 bp):
AGGGCTATCAATACCATGGT
Found at i:415118 original size:40 final size:38
Alignment explanation
Indices: 415055--415131 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 38
415045 CTAATTTTGG
* *
415055 TATTGATACCAGAAGGGTTATCGATACCATGGTAGGGC
1 TATTAATACCAGAAGGGGTATCGATACCATGGTAGGGC
415093 TATTAATACCATGATAGGGGTATCGATACCATGGTAGGG
1 TATTAATACCA-GA-AGGGGTATCGATACCATGGTAGGG
415132 GTATCGATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 10 0.29
39 2 0.06
40 23 0.66
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (38 bp):
TATTAATACCAGAAGGGGTATCGATACCATGGTAGGGC
Found at i:415539 original size:59 final size:59
Alignment explanation
Indices: 415462--416008 Score: 837
Period size: 59 Copynumber: 9.3 Consensus size: 59
415452 TGATTACCAA
415462 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
* * * * * *
415521 ATGGTAAGGAATTCATACTATGTGTATAAATTTCCATATAGGGTACTTCGTGTGTTAAC
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
* *
415580 ATGATAATAAATTCATACTAAGTGTATGAATTTTCATATAGGGCACTTCGTGTGCTAAC
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
* * *
415639 ATGATAAGGAATTCATACTAAGAGCATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
* * *
415698 ATGATAAGAAATTCATACTAAGTGTATGAATTTCTATATAGGGAACTTCATGTGCTAAC
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
* *
415757 ATGATAAGGAATTCATACTAAGTGTATGAATTTTCATATAGGGCACTTCGTGTGCTAAC
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
415816 ATGATAAGAAATTCATACTAA-TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
* ** * * *
415874 ATGATAAGGAATTCATACTAAGTGTATGAATTTCTGTATACGGCACTTCATGTGCTAAA
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
* * * *
415933 ATGCTAAGGAATTCATACTAAGTGTATGAATTTCCATATTGGGCACCTT-GTGTGCTAAA
1 ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA-CTTCGTGTGCTAAC
415992 ATGATAAGAAATTCATA
1 ATGATAAGAAATTCATA
416009 AATGGTAAGA
Statistics
Matches: 440, Mismatches: 46, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
58 56 0.13
59 381 0.87
60 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (59 bp):
ATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAC
Found at i:416017 original size:18 final size:18
Alignment explanation
Indices: 415990--416026 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
415980 TTGTGTGCTA
415990 AAATGATAAGAAATTCAT
1 AAATGATAAGAAATTCAT
*
416008 AAATGGTAAGAAATTCAT
1 AAATGATAAGAAATTCAT
416026 A
1 A
416027 CTAAGTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (18 bp):
AAATGATAAGAAATTCAT
Found at i:417723 original size:16 final size:17
Alignment explanation
Indices: 417691--417723 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
417681 ATTAAATTTT
417691 CTTTTAAAATGAAAAAA
1 CTTTTAAAATGAAAAAA
417708 CTTTTAAAAT-AAAAAA
1 CTTTTAAAATGAAAAAA
417724 GGACGTTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (17 bp):
CTTTTAAAATGAAAAAA
Found at i:418727 original size:20 final size:21
Alignment explanation
Indices: 418690--418731 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
418680 AAACCATTCA
* *
418690 GGGGGTATCTGTTCCCCTTTG
1 GGGGGAATCGGTTCCCCTTTG
418711 GGGGGAATCGGTT-CCCTTTG
1 GGGGGAATCGGTTCCCCTTTG
418731 G
1 G
418732 CCAATCTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.07, C:0.21, G:0.38, T:0.33
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTTTG
Found at i:419377 original size:16 final size:16
Alignment explanation
Indices: 419356--419388 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
419346 AATATCTAAA
*
419356 ACAAATTTAAACATCC
1 ACAAATTCAAACATCC
419372 ACAAATTCAAACATCC
1 ACAAATTCAAACATCC
419388 A
1 A
419389 TAAGCATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (16 bp):
ACAAATTCAAACATCC
Found at i:428436 original size:16 final size:17
Alignment explanation
Indices: 428404--428436 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
428394 ATTAAATTTT
428404 CTTTTAAAATGAAAAAA
1 CTTTTAAAATGAAAAAA
428421 CTTTTAAAAT-AAAAAA
1 CTTTTAAAATGAAAAAA
428437 GGACGTTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (17 bp):
CTTTTAAAATGAAAAAA
Found at i:430088 original size:16 final size:16
Alignment explanation
Indices: 430067--430099 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
430057 AATATCTAAA
*
430067 ACAAATTTAAACATCC
1 ACAAATTCAAACATCC
430083 ACAAATTCAAACATCC
1 ACAAATTCAAACATCC
430099 A
1 A
430100 TAAGCATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (16 bp):
ACAAATTCAAACATCC
Found at i:433506 original size:23 final size:22
Alignment explanation
Indices: 433471--433519 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
433461 TTCCCTAAAA
*
433471 GGGGAAACGGTTCCCATTCAAAG
1 GGGGAAACAGTTCCCATTC-AAG
* *
433494 GGGGAATCAGTTCCCTTTCAAG
1 GGGGAAACAGTTCCCATTCAAG
433516 GGGG
1 GGGG
433520 TATCGATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.20
Consensus pattern (22 bp):
GGGGAAACAGTTCCCATTCAAG
Found at i:433529 original size:22 final size:21
Alignment explanation
Indices: 433450--433529 Score: 56
Period size: 23 Copynumber: 3.7 Consensus size: 21
433440 AGACCCCGTG
* *
433450 GGGGGTATCGATTCCC-TAAA
1 GGGGGAATCGATTCCCTTCAA
* * *
433470 AGGGGAAACGGTTCCCATTCAAA
1 GGGGGAATCGATTCCC-TTC-AA
433493 GGGGGAATC-AGTTCCCTTTCAA
1 GGGGGAATCGA-TTCCC-TTCAA
*
433515 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
433530 TTCTACACTA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
20 12 0.27
22 15 0.33
23 18 0.40
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTCAA
Found at i:439395 original size:20 final size:21
Alignment explanation
Indices: 439358--439400 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
439348 AAACCATTCA
* *
439358 GGGGGTATCGGTTCCCCTTTG
1 GGGGGAATCGGTTCCCCTCTG
439379 GGGGGAATCGGTT-CCCTCTG
1 GGGGGAATCGGTTCCCCTCTG
439399 GG
1 GG
439401 TAATCTGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.07, C:0.23, G:0.42, T:0.28
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCTG
Found at i:449515 original size:54 final size:56
Alignment explanation
Indices: 449409--449536 Score: 199
Period size: 54 Copynumber: 2.3 Consensus size: 56
449399 ACTTGGGTCG
449409 AGACATT-GTGCAAGTGTCCGACAAAGAGGTTCAAGACAGAGGATCGGGCTTGCCA
1 AGACATTGGTGCAAGTGTCCGACAAAGAGGTTCAAGACAGAGGATCGGGCTTGCCA
* * * *
449464 AGACATTGGTGCAAGTGTCCGACAATGA-G-TCAAGATAGAGTATCGGGCTTGCTA
1 AGACATTGGTGCAAGTGTCCGACAAAGAGGTTCAAGACAGAGGATCGGGCTTGCCA
449518 AGACATTGGTGCAAGTGTC
1 AGACATTGGTGCAAGTGTC
449537 TGAAAGGGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
54 41 0.60
55 8 0.12
56 19 0.28
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (56 bp):
AGACATTGGTGCAAGTGTCCGACAAAGAGGTTCAAGACAGAGGATCGGGCTTGCCA
Found at i:458421 original size:15 final size:15
Alignment explanation
Indices: 458397--458427 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
458387 AAGGAAGAAG
*
458397 AAGATTAAGAAAAGA
1 AAGATGAAGAAAAGA
458412 AAGATGAAGAAAAGA
1 AAGATGAAGAAAAGA
458427 A
1 A
458428 TTAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.10
Consensus pattern (15 bp):
AAGATGAAGAAAAGA
Found at i:462071 original size:19 final size:19
Alignment explanation
Indices: 462044--462112 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
462034 CCTCTGGTAC
*
462044 ATGTCAATTTCTAGGAAAT
1 ATGTTAATTTCTAGGAAAT
462063 ATGTTAATTTCTAGGAAAT
1 ATGTTAATTTCTAGGAAAT
462082 ATGTTAATTTCTAGGAAAT
1 ATGTTAATTTCTAGGAAAT
462101 ATGTTAATTTCT
1 ATGTTAATTTCT
462113 TGATTTTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (19 bp):
ATGTTAATTTCTAGGAAAT
Found at i:490368 original size:19 final size:19
Alignment explanation
Indices: 490343--490391 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
490333 GGGGAAAATA
490343 TTCTTTTTACTTTA-TTCC
1 TTCTTTTTACTTTATTTCC
*
490361 -TCTCTTTTATTTTATTTCC
1 TTCT-TTTTACTTTATTTCC
*
490380 TTATTTTTACTT
1 TTCTTTTTACTT
490392 CTCTCTCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.12
18 9 0.36
19 11 0.44
20 2 0.08
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (19 bp):
TTCTTTTTACTTTATTTCC
Found at i:533532 original size:22 final size:22
Alignment explanation
Indices: 533507--533557 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
533497 GGTTTCTATA
533507 CTTTAGAATATAATGCTATTTT
1 CTTTAGAATATAATGCTATTTT
533529 CTTTAGAATATAATGCTATTTT
1 CTTTAGAATATAATGCTATTTT
533551 CTTTAGA
1 CTTTAGA
533558 TGACATGCGT
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:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (22 bp):
CTTTAGAATATAATGCTATTTT
Found at i:535715 original size:142 final size:141
Alignment explanation
Indices: 535484--535765 Score: 519
Period size: 142 Copynumber: 2.0 Consensus size: 141
535474 TGTCGGAATA
*
535484 GAGTACAAAAAGAAGATTGATTATAACATTTTATAAATTAAATATATATATAAACTTAATCGGGT
1 GAGTACAAAAAGAAGATTGATTATAACATTTTATAAATTAAATATATATATAAACTTAACCGGGT
*
535549 ACTCGGGTAACTGAATATCCAGAAAAATCAATTTTTGTGACCCGAGCCCGACCTGGAAAGTGTCG
66 ACTCGGGTAACTGAATATCCAGAAAAATCAATTTTTGTGACCCGAGCCCGACCCGGAAAGTGTC-
535614 GGTCGGTTACCC
130 GGTCGGTTACCC
535626 GAGTACAAAAAGAAGATTGATTATAACATTTTATAAATTAAATATATATATAAACTTAACCGGGT
1 GAGTACAAAAAGAAGATTGATTATAACATTTTATAAATTAAATATATATATAAACTTAACCGGGT
* *
535691 ACTTGGGTAACTGAGTATCCAGAAAAATCAATTTTTGTGACCCGAGCCCGACCCGGAAAGTGTCG
66 ACTCGGGTAACTGAATATCCAGAAAAATCAATTTTTGTGACCCGAGCCCGACCCGGAAAGTGTCG
535756 GTCGGTTACC
131 GTCGGTTACC
535766 TGACCCGGAC
Statistics
Matches: 136, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
141 11 0.08
142 125 0.92
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (141 bp):
GAGTACAAAAAGAAGATTGATTATAACATTTTATAAATTAAATATATATATAAACTTAACCGGGT
ACTCGGGTAACTGAATATCCAGAAAAATCAATTTTTGTGACCCGAGCCCGACCCGGAAAGTGTCG
GTCGGTTACCC
Found at i:536189 original size:52 final size:52
Alignment explanation
Indices: 536111--536214 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
536101 TGCACCATCT
*
536111 TTCCTCAAATAAATGAATCTTCAGTTTCTAAC-ATTCGATTGAGGAATTTCAA
1 TTCCTCAAATAAATGAATCTTCAGTTTCTAACAATT-GATTGAGAAATTTCAA
*
536163 TTCCTCAAATAAATGAATCTTCAGTTTCTATCAATTGATTGAGAAATTTCAA
1 TTCCTCAAATAAATGAATCTTCAGTTTCTAACAATTGATTGAGAAATTTCAA
536215 GATTCATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 46 0.94
53 3 0.06
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (52 bp):
TTCCTCAAATAAATGAATCTTCAGTTTCTAACAATTGATTGAGAAATTTCAA
Found at i:539542 original size:19 final size:18
Alignment explanation
Indices: 539520--539570 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
539510 AGTATCGCTC
**
539520 AAAATAGTAGTATAAGCAT
1 AAAATAGTAG-ATAAAAAT
539539 AAAATA-TCAGATAAAAAT
1 AAAATAGT-AGATAAAAAT
*
539557 AAAATAGTAAATAA
1 AAAATAGTAGATAA
539571 TCAACATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.24
Consensus pattern (18 bp):
AAAATAGTAGATAAAAAT
Found at i:540446 original size:13 final size:13
Alignment explanation
Indices: 540428--540452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
540418 AAAACAAGTA
540428 AAACAATCATATG
1 AAACAATCATATG
540441 AAACAATCATAT
1 AAACAATCATAT
540453 ATCACACAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (13 bp):
AAACAATCATATG
Found at i:540633 original size:27 final size:27
Alignment explanation
Indices: 540603--540674 Score: 117
Period size: 27 Copynumber: 2.6 Consensus size: 27
540593 TATTCATAAG
540603 GTTCACGGATCATACGAGTAATCACTA
1 GTTCACGGATCATACGAGTAATCACTA
540630 GTTCACGGATCATACGAGTAATCACTA
1 GTTCACGGATCATACGAGTAATCACTA
* *
540657 GCTCACGGTATCAAACGA
1 GTTCACGG-ATCATACGA
540675 ATCAAGAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 34 0.81
28 8 0.19
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (27 bp):
GTTCACGGATCATACGAGTAATCACTA
Found at i:541028 original size:15 final size:15
Alignment explanation
Indices: 541010--541050 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
541000 ACTCAATTCA
*
541010 AGTTGACTCAGGATT
1 AGTTGACTCAGGATG
*
541025 AGTTGACTTAGGATG
1 AGTTGACTCAGGATG
*
541040 AGTTTACTCAG
1 AGTTGACTCAG
541051 TTTGGACTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (15 bp):
AGTTGACTCAGGATG
Found at i:553459 original size:20 final size:20
Alignment explanation
Indices: 553417--553461 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
553407 AGAAATAGAG
*
553417 GAAAAGAGAAAAAAGAAAAT
1 GAAAAGAGAAAAAACAAAAT
*
553437 GAAAA-AGAAAAAACCAAAGT
1 GAAAAGAGAAAAAA-CAAAAT
553457 GAAAA
1 GAAAA
553462 CCCGAAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.04
Consensus pattern (20 bp):
GAAAAGAGAAAAAACAAAAT
Found at i:553580 original size:13 final size:13
Alignment explanation
Indices: 553562--553586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553552 TTCCAAACAT
553562 GAGATGAAACCAA
1 GAGATGAAACCAA
553575 GAGATGAAACCA
1 GAGATGAAACCA
553587 TGAGTTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (13 bp):
GAGATGAAACCAA
Found at i:558953 original size:2 final size:2
Alignment explanation
Indices: 558946--558973 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
558936 TTTTGAACAT
558946 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
558974 ATCCCCTCAT
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):
TA
Found at i:559162 original size:81 final size:81
Alignment explanation
Indices: 559023--559674 Score: 905
Period size: 81 Copynumber: 8.0 Consensus size: 81
559013 CACTATAATT
* * * * * *
559023 CCTTTATTCTTTTAGTCCATGGTATTTAACCGTTCATTTAAATAGCATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
559088 CAAATGTAAAGTTAGG
66 CAAATGCAAAGTTAGG
* *
559104 CCTATATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTCGCATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
559169 CAAATGCACAGTTAGG
66 CAAATGCAAAGTTAGG
* *
559185 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACGGGCATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
559250 CAAATGCACAA-TTAGG
66 CAAATGCA-AAGTTAGG
* * * *
559266 CCTTTATTCTTTTACTCAATGGTATTTAATCGTTCATCTAACTGGCATAATTGACACGTTTCTAT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
559331 CAAATGCATAA-TTAGG
66 CAAATGCA-AAGTTAGG
* * * **
559347 CCTTTATTCTTTTACTCCACAGTATTTAACCGTTCATCTAAATAACATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
* *
559412 CAAATGTACAGTTAGG
66 CAAATGCAAAGTTAGG
* * * * * * *
559428 CCTTTATTCGTTTACTCAACGGTATTTAATCGTTCCTCTAACTGACATAATTTATACCTTTCTCT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
559493 CAAATGCACAGTTAGG
66 CAAATGCAAAGTTAGG
* * *
559509 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGAATAATTGACACCTTTATGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
559574 CAAGTGCACAA-TTAGG
66 CAAATGCA-AAGTTAGG
* * *
559590 CCTTTATTCTTTTACTCAACGGTATTTAATCATTCATCTAACTGACATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
559655 CAAATGCACAGTTAGG
66 CAAATGCAAAGTTAGG
559671 CCTT
1 CCTT
559675 AAAGGCACTC
Statistics
Matches: 504, Mismatches: 63, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
80 2 0.00
81 500 0.99
82 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (81 bp):
CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
CAAATGCAAAGTTAGG
Found at i:559733 original size:68 final size:68
Alignment explanation
Indices: 559622--560012 Score: 525
Period size: 68 Copynumber: 5.8 Consensus size: 68
559612 TATTTAATCA
* * * ** * *
559622 TTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTAAAGGCACTCAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
559687 CCT
66 CCT
* * * * * *
559690 TTCATCTAACTGGCATAAATTATACCTTTCTGTCATTTTCACAGTTAGGCCTCAAAGGCAGTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
559755 CCT
66 CCT
* *** * *
559758 TTCATCGAACCAACATAAATGAAACCTTTCTATAATTTGCACAGTTAGGCCTCAAAGGCACTCAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
559823 CCT
66 CCT
* *
559826 TTCATCTAACTGGCATAAATGACATCTTTCTATCATTTACACAGTTAGGCCTCAAAGGCACAT-A
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCAC-TCA
559890 GCCT
65 GCCT
* *
559894 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
559959 CCT
66 CCT
* * *
559962 TTCATCTAACT-GCATAAATGACACCATTCTGTCATTTGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCT
560013 ATAATCTTTT
Statistics
Matches: 285, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
67 38 0.13
68 246 0.86
69 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
CCT
Found at i:561738 original size:81 final size:81
Alignment explanation
Indices: 561628--562097 Score: 380
Period size: 81 Copynumber: 5.8 Consensus size: 81
561618 CATAGCTAGT
* ** * * *
561628 CCATTATTCTTTTACTTAACAGTGCTTAACCATTCAGT-TAACCAGCACAATTCACACTTTTCTG
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCA-TATAACTAGCATAATTGACACTTTTCTG
*
561692 TGAATTGCACTGTTAGG
65 TAAATTGCACTGTTAGG
* * * *
561709 CCATTATCCTTTTACTCAACAGTATTTAACCATTCATATAACTTGCATAATTGTCACCTTTCTGT
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATATAACTAGCATAATTGACACTTTTCTGT
561774 CAAATT-CA-TAGTTAGG
66 -AAATTGCACT-GTTAGG
* * ** * * * *
561790 CCTTTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAGCTGGCATTATTGACACTTTTCTGT
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATATAACTAGCATAATTGACACTTTTCTGT
**
561855 CAAA-TGCACAATTAGG
66 -AAATTGCACTGTTAGG
* * * * * * * * *
561871 CCTTTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGAAACCTTTATGT
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATATAACTAGCATAATTGACACTTTTCTGT
***
561936 CAAA-TGCACAACTAGG
66 -AAATTGCACTGTTAGG
* ** * * *
561952 CC-TTGATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGAGACATTTT-T
1 CCATT-ATTCTTTTACTCAACAGTATTTAACCATTCATATAACTAGCATAATTGACAC-TTTTCT
* * *
562015 GTCAAGTGCACAGTTAGG
64 GTAAATTGCACTGTTAGG
* * * * * *
562033 CCTTTATTCTTTTACTCATC-GATATTTAATCATTCATCTAACTGGCATAATTGACACATTTCTG
1 CCATTATTCTTTTACTCAACAG-TATTTAACCATTCATATAACTAGCATAATTGACACTTTTCTG
562097 T
65 T
562098 CAAAAACACA
Statistics
Matches: 333, Mismatches: 45, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
80 11 0.03
81 313 0.94
82 9 0.03
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACAGTATTTAACCATTCATATAACTAGCATAATTGACACTTTTCTGT
AAATTGCACTGTTAGG
Done.