Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 24
Found at i:2237571 original size:14 final size:14
Alignment explanation
Indices: 2237554--2237630 Score: 102
Period size: 14 Copynumber: 5.5 Consensus size: 14
2237544 AAGACAAAAG
2237554 GAAAAAAAGAGAAA
1 GAAAAAAAGAGAAA
* *
2237568 GAAAAAAGGAAAAA
1 GAAAAAAAGAGAAA
*
2237582 GGAAAAAAGAGAAA
1 GAAAAAAAGAGAAA
2237596 GAAAAAAAGAGAAA
1 GAAAAAAAGAGAAA
*
2237610 -AGAAAAAAGAAAAA
1 GA-AAAAAAGAGAAA
2237624 GAAAAAA
1 GAAAAAA
2237631 GGGGGTCAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
13 1 0.02
14 52 0.96
15 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGAGAAA
Found at i:2238908 original size:113 final size:114
Alignment explanation
Indices: 2238638--2238950 Score: 511
Period size: 114 Copynumber: 2.7 Consensus size: 114
2238628 CCATGTGCTC
*** * * *
2238638 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAATATGAACCCCAAAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCCTAGAACCAAT
*
2238703 CATTAGATTTAAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
66 CATTAGATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
2238752 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCCTAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCCTAGAACCAAT
*
2238817 CATTAGATTTGAAAGATGAATTT-CTCATAGTAGAAATAAGGAGACCCA
66 CATTAGATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
2238865 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCCTCAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCCT-AGAACCAA
* * *
2238930 TCATTGGAATTGAAAGGTGAA
65 TCATTAGATTTGAAAGATGAA
2238951 CTACATGATC
Statistics
Matches: 187, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 80 0.43
114 107 0.57
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCCTAGAACCAAT
CATTAGATTTGAAAGATGAATTTGCTCATAGTAAAAATAAGGAGACCCA
Found at i:2240865 original size:54 final size:54
Alignment explanation
Indices: 2240783--2241002 Score: 370
Period size: 54 Copynumber: 4.1 Consensus size: 54
2240773 TAATGATAGA
2240783 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGT-TCTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGT-TGTCAAATGTTTTAC
2240837 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
2240891 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * * ***
2240945 GAACATCTGAGCAGAAGCCACAGGAAATGATGAATGCGCCATCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
2240999 GAAC
1 GAAC
2241003 CTGCTATTTT
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
54 158 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:2241418 original size:23 final size:22
Alignment explanation
Indices: 2241363--2241440 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
2241353 ATCTACATTC
*
2241363 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
* *
2241385 TTCAAAGATGATATATTCCCTTT
1 TTCAAAGATGATAGATTCTC-TT
*
2241408 TTAAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2241430 TTCAAAGATGA
1 TTCAAAGATGA
2241441 AAGCTTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 30 0.62
23 18 0.38
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2242037 original size:113 final size:113
Alignment explanation
Indices: 2241839--2242839 Score: 1309
Period size: 113 Copynumber: 9.0 Consensus size: 113
2241829 TAGCCAAGAT
*
2241839 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
2241904 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
2241952 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
2242017 AGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
2242065 TC--A---A--A----A---ATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
* *
2242116 AAGAAGGAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
2242165 TCAAATCCATCATTTGATGAATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
* * *
2242230 AAGAAGGAAAAAGAAATTCATAATAAGAAGAATTTGTT-AACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
2242278 TCAAATCCATCATTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
2242343 AGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTCAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
** * * * ** * ** * *
2242391 TTGAATTCATCA-TTCGATTGATCAACAGTGCCAGTTAGAGTTCATAATGAGAATAACTCATCTG
1 TCAAATCCATCACTT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * *
2242455 AAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * ** *
2242504 TTAAATTCATCACTCGGTGGATCAG-TAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCT-TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * *
2242568 AAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
2242617 TTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATTATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
2242682 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
2242730 TTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
** *
2242795 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
2242840 GCTAGATTAC
Statistics
Matches: 813, Mismatches: 53, Indels: 44
0.89 0.06 0.05
Matches are distributed among these distances:
99 14 0.02
100 78 0.10
102 2 0.00
105 1 0.00
106 1 0.00
107 1 0.00
108 1 0.00
111 2 0.00
112 71 0.09
113 555 0.68
114 87 0.11
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2243118 original size:24 final size:24
Alignment explanation
Indices: 2243077--2243125 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2243067 ATATTCTTTA
*
2243077 TATTATTATAATTATAATAATTAT
1 TATTATTATAATTATAATAAATAT
*
2243101 TATTATT-TTATTATTAATAAATAT
1 TATTATTATAATTA-TAATAAATAT
2243125 T
1 T
2243126 TTTACAGGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTATTATAATTATAATAAATAT
Found at i:2244649 original size:23 final size:22
Alignment explanation
Indices: 2244603--2244647 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2244593 ATATTATAAA
2244603 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
2244625 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
2244648 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:2246712 original size:24 final size:24
Alignment explanation
Indices: 2246650--2246705 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2246640 AACATCTATC
2246650 CGATAAAAAAGAAAGAAAATTAGA
1 CGATAAAAAAGAAAGAAAATTAGA
2246674 CGATAAAAAAGAAAGAAAATTAGA
1 CGATAAAAAAGAAAGAAAATTAGA
*
2246698 CGCTAAAA
1 CGATAAAA
2246706 CGAAAAGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.64, C:0.07, G:0.16, T:0.12
Consensus pattern (24 bp):
CGATAAAAAAGAAAGAAAATTAGA
Found at i:2250565 original size:28 final size:28
Alignment explanation
Indices: 2250522--2250578 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2250512 TTGTCGTTGC
* *
2250522 TTTCAAACACTGACTCGACGACATAATG
1 TTTCAAACACTAACTCAACGACATAATG
*
2250550 TTTCAAACACTAACTCAATGACATAATG
1 TTTCAAACACTAACTCAACGACATAATG
2250578 T
1 T
2250579 AAATAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (28 bp):
TTTCAAACACTAACTCAACGACATAATG
Found at i:2251236 original size:3 final size:3
Alignment explanation
Indices: 2251228--2251265 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2251218 TCCACCCGAG
2251228 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2251266 CAGTTTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:2259662 original size:188 final size:186
Alignment explanation
Indices: 2259430--2259800 Score: 715
Period size: 188 Copynumber: 2.0 Consensus size: 186
2259420 TTTATTTTGG
2259430 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
1 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
*
2259495 AACATACATGATGAGCACTTATGAGCAGAAGATGGTTCATGATGTATGGTAACAAGCATGGGTGA
66 AACATACATGATGAGCACTTATGAGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGTGA
2259560 TAGGAATTGGGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCATGA
131 TAGGAATT--GGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCATGA
2259618 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
1 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
2259683 AACATACATGATGAGCACTTATGAGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGTGA
66 AACATACATGATGAGCACTTATGAGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGTGA
2259748 TAGGAATTGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCA
131 TAGGAATTGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCA
2259801 ATCCAACGGT
Statistics
Matches: 182, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
186 45 0.25
188 137 0.75
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.30
Consensus pattern (186 bp):
ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
AACATACATGATGAGCACTTATGAGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGTGA
TAGGAATTGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCATGA
Found at i:2265208 original size:16 final size:17
Alignment explanation
Indices: 2265187--2265220 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2265177 ACTATTCATA
2265187 TGAATAGT-AAATTTTG
1 TGAATAGTAAAATTTTG
2265203 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
2265220 T
1 T
2265221 CGGCGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:2268737 original size:22 final size:23
Alignment explanation
Indices: 2268712--2268757 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
2268702 CGGTGATGAG
2268712 TTCGATTACCGG-TTTGGGACTA
1 TTCGATTACCGGTTTTGGGACTA
2268734 TTCGATTACCGGTTTTGGGACTA
1 TTCGATTACCGGTTTTGGGACTA
2268757 T
1 T
2268758 GAAAATCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (23 bp):
TTCGATTACCGGTTTTGGGACTA
Found at i:2272803 original size:28 final size:28
Alignment explanation
Indices: 2272763--2272819 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2272753 GTGGGTGTCG
2272763 GTATGAATATGTTTCTCATATTGATGAT
1 GTATGAATATGTTTCTCATATTGATGAT
2272791 GTATGAATATGTTTCTCATATTGATGAT
1 GTATGAATATGTTTCTCATATTGATGAT
2272819 G
1 G
2272820 CAGACACACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (28 bp):
GTATGAATATGTTTCTCATATTGATGAT
Found at i:2274173 original size:10 final size:10
Alignment explanation
Indices: 2274158--2274186 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2274148 TAGATATTGG
2274158 AAAATTTCCC
1 AAAATTTCCC
2274168 AAAATTTCCC
1 AAAATTTCCC
2274178 AAAATTTCC
1 AAAATTTCC
2274187 GAGTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTCCC
Found at i:2274957 original size:36 final size:37
Alignment explanation
Indices: 2274910--2274979 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
2274900 AAAAATAGGG
* * *
2274910 TCGGGTCAGATTTGGGTGAAG-ATATATATTTTCAGA
1 TCGGGTCAGATTCGGGAGAAGAATACATATTTTCAGA
2274946 TCGGGTCAGATTCGGGAGAAGAATACATATTTTC
1 TCGGGTCAGATTCGGGAGAAGAATACATATTTTC
2274980 GGGTTGACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 19 0.63
37 11 0.37
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (37 bp):
TCGGGTCAGATTCGGGAGAAGAATACATATTTTCAGA
Found at i:2277246 original size:2 final size:2
Alignment explanation
Indices: 2277239--2277265 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2277229 AATAATAAAT
2277239 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2277266 TTAAGTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2278278 original size:5 final size:5
Alignment explanation
Indices: 2278268--2278296 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2278258 CTTGCTTATC
2278268 TCGTT TCGTT TCGTT TCGTT TCGTT TCGT
1 TCGTT TCGTT TCGTT TCGTT TCGTT TCGT
2278297 GTATTCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.59
Consensus pattern (5 bp):
TCGTT
Found at i:2282082 original size:26 final size:25
Alignment explanation
Indices: 2282053--2282121 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 25
2282043 TCCCGGTTCT
2282053 ATTATTTTTTTATTATAATAATTATA
1 ATTATTTTTTTATTATAATAATTA-A
* *
2282079 ATTATAATTATTTTATTATTATTATTAA
1 ATTAT--TT-TTTTATTATAATAATTAA
*
2282107 ATAATTTTATTTATT
1 ATTATTTT-TTTATT
2282122 TTACAGGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.03
26 13 0.36
28 7 0.19
29 15 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTATTTTTTTATTATAATAATTAA
Found at i:2282753 original size:10 final size:10
Alignment explanation
Indices: 2282738--2282771 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2282728 TAGAGCTCTG
2282738 TTTTGGGGTA
1 TTTTGGGGTA
2282748 TTTTGGGG--
1 TTTTGGGGTA
2282756 TTTTGGGGTA
1 TTTTGGGGTA
2282766 TTTTGG
1 TTTTGG
2282772 TGTTTTTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (10 bp):
TTTTGGGGTA
Found at i:2282760 original size:18 final size:18
Alignment explanation
Indices: 2282737--2282777 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2282727 TTAGAGCTCT
2282737 GTTTTGGGGTATTTTGGG
1 GTTTTGGGGTATTTTGGG
*
2282755 GTTTTGGGGTATTTTGGT
1 GTTTTGGGGTATTTTGGG
2282773 GTTTT
1 GTTTT
2282778 TCGGCCACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.05, C:0.00, G:0.39, T:0.56
Consensus pattern (18 bp):
GTTTTGGGGTATTTTGGG
Found at i:2284071 original size:124 final size:124
Alignment explanation
Indices: 2283850--2284076 Score: 314
Period size: 124 Copynumber: 1.8 Consensus size: 124
2283840 TATTTTAAGA
* ** *
2283850 AAATATTTTAGTTATTTATTTATTTTTTAATGTTGAAGGAAAGAGCTGTCTTAAAGCAACTAGAA
1 AAATATTTTAGTTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAACTAGAA
**
2283915 GCCCTTTTCTAAATATTTTTAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
66 GCCCTTTTCTAAATATTTCCAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
* * * *
2283974 AAATGTTTTAGTTATTTATTTATTTTTTTAATATCAAAGAAAAGAGTTGTCTT-AAGTTACCTAG
1 AAATATTTTAGTTATTTATTTA-TTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAG-CAACTAG
* *
2284038 AAGCCCTTTTCT-GATATTTCCAAGTAAATAAATATCTTA
64 AAGCCCTTTTCTAAATATTTCCAAATAAATAAATATCTTA
2284077 TTTATAAATA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
124 47 0.53
125 42 0.47
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (124 bp):
AAATATTTTAGTTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAACTAGAA
GCCCTTTTCTAAATATTTCCAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
Found at i:2286259 original size:14 final size:14
Alignment explanation
Indices: 2286221--2286274 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
2286211 ATTTTAAATA
*
2286221 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
2286235 TTTTACATTTGCAT
1 ATTTACATTTGCAT
2286249 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
2286264 CTTTGCATTTG
1 ATTTACATTTG
2286275 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:2289809 original size:4 final size:4
Alignment explanation
Indices: 2289800--2289867 Score: 52
Period size: 4 Copynumber: 16.8 Consensus size: 4
2289790 CTCATCCAGC
*
2289800 AAAG AAAG AAA- AAAG AAA- AATCCAG CAAAG AAAG AAAA AAAG AAA-
1 AAAG AAAG AAAG AAAG AAAG AA---AG -AAAG AAAG AAAG AAAG AAAG
* *
2289845 AAAA AAAG AAAA AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAA
2289868 AAAAAGAAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
3 8 0.15
4 39 0.75
5 2 0.04
6 1 0.02
8 2 0.04
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:2289823 original size:26 final size:27
Alignment explanation
Indices: 2289793--2289846 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
2289783 TCATATACTC
2289793 ATCCAGCAAAGAAAG-AAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAAGAAAA
2289819 ATCCAGCAAAGAAAGAAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAAGAAAA
2289846 A
1 A
2289847 AAAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (27 bp):
ATCCAGCAAAGAAAGAAAAAAAGAAAA
Found at i:2289852 original size:19 final size:19
Alignment explanation
Indices: 2289830--2289888 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 19
2289820 TCCAGCAAAG
2289830 AAAGAAAAAAAGAAAAAAA
1 AAAGAAAAAAAGAAAAAAA
2289849 AAAGAAAAAAAGAAAGAAAAA
1 AAAGAAAAAAAG-AA-AAAAA
2289870 AAAGAAGGAAAAAGAAAAA
1 AAAGAA--AAAAAGAAAAA
2289889 GGGGAGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.33
20 2 0.06
21 14 0.39
22 2 0.06
23 6 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAAAGAAAAAAA
Found at i:2289858 original size:13 final size:14
Alignment explanation
Indices: 2289830--2289889 Score: 63
Period size: 13 Copynumber: 4.3 Consensus size: 14
2289820 TCCAGCAAAG
2289830 AAAGAAAAAAAGAA
1 AAAGAAAAAAAGAA
2289844 AAA-AAAAAGAA-AA
1 AAAGAAAAA-AAGAA
*
2289857 AAAGAAAGAAA-AA
1 AAAGAAAAAAAGAA
2289870 AAAGAAGGAAAAAGAA
1 AAAGAA--AAAAAGAA
2289886 AAAG
1 AAAG
2289890 GGGAGAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 20 0.51
14 9 0.23
15 4 0.10
16 6 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:2289861 original size:31 final size:31
Alignment explanation
Indices: 2289826--2289888 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
2289816 AAAATCCAGC
2289826 AAAGAAAG-AAAAAAAGAAAAAAAAAAGAAAA
1 AAAGAAAGAAAAAAAAG-AAAAAAAAAGAAAA
**
2289857 AAAGAAAGAAAAAAAAGAAGGAAAAAGAAAA
1 AAAGAAAGAAAAAAAAGAAAAAAAAAGAAAA
2289888 A
1 A
2289889 GGGGAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (31 bp):
AAAGAAAGAAAAAAAAGAAAAAAAAAGAAAA
Found at i:2289864 original size:23 final size:23
Alignment explanation
Indices: 2289826--2289886 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2289816 AAAATCCAGC
2289826 AAAGAAAGAAAA-AAAGAAAAAAA
1 AAAGAAA-AAAAGAAAGAAAAAAA
2289849 AAAGAAAAAAAGAAAGAAAAAAA
1 AAAGAAAAAAAGAAAGAAAAAAA
*
2289872 AGAAG-GAAAAAGAAA
1 A-AAGAAAAAAAGAAA
2289887 AAGGGGAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
22 4 0.11
23 28 0.80
24 3 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAAGAAAGAAAAAAA
Found at i:2289890 original size:13 final size:11
Alignment explanation
Indices: 2289826--2289889 Score: 83
Period size: 12 Copynumber: 5.4 Consensus size: 11
2289816 AAAATCCAGC
2289826 AAAGAAAGAAAA
1 AAAGAAA-AAAA
2289838 AAAGAAAAAAA
1 AAAGAAAAAAA
2289849 AAAGAAAAAAA
1 AAAGAAAAAAA
2289860 GAAAGAAAAAAA
1 -AAAGAAAAAAA
2289872 AGAAGGAAAAAGAA
1 A-AA-GAAAAA-AA
2289886 AAAG
1 AAAG
2289890 GGGAGAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
11 16 0.33
12 21 0.44
13 8 0.17
14 3 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:2295104 original size:112 final size:113
Alignment explanation
Indices: 2294902--2296134 Score: 1528
Period size: 112 Copynumber: 10.9 Consensus size: 113
2294892 GCAAAGATTT
* * ** *
2294902 AAATCCATCACTTGATGGACCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCGTCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2294966 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
2295014 AAATTCATCACTTGATGGACCACCATTTCCAGAGAAAGTTCATAATGAGAAGAAATTATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2295079 -AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-C-TTTCCT-
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
2295123 GAATTCATCACTTGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
2295188 AAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * ** * * **
2295235 TAATTCATTACCCGATGGATTAGCATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
2295299 AAGGAAGAAGAAGTTCATAATGAGAAGAACTAGTTTAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
2295347 AAATTCATCACTTGATGGACCACCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2295412 -AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACATTTTGC-C
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
2295458 TGAATTCATCACTTGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAA
1 -AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
2295523 GAAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* ** * * *
2295571 TAATTCATCACCCGATGGATTAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
2295636 AAGGAAGATGAAGTTCATAATGCGAAGAACTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* ** *
2295684 AAATCCATCACTTGATGGATCAACATTTCCAGA-AGTGTTCATAATGATAAGAACTCATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2295748 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
2295796 GAATTTATCACTTGATAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2295861 -AGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC-C
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
2295907 TGAATTCATCACTTGATGAATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA
1 -AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
2295972 G-AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTGTTTGACTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC--T-TTTG-CTC
** ** * * ** **
2296024 TATCACA-GAAGGAGATAGATCAACATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCA
1 -A--A-ATTCATCA-CTTGAT--GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
*
2296087 TCTGAAGAAGG-AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
59 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
2296135 GCCTTAATTT
Statistics
Matches: 975, Mismatches: 121, Indels: 44
0.86 0.11 0.04
Matches are distributed among these distances:
109 89 0.09
110 9 0.01
111 40 0.04
112 594 0.61
113 148 0.15
114 1 0.00
115 4 0.00
116 1 0.00
117 2 0.00
118 1 0.00
119 4 0.00
120 5 0.01
121 61 0.06
122 16 0.02
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:2295825 original size:449 final size:447
Alignment explanation
Indices: 2294902--2296134 Score: 1726
Period size: 449 Copynumber: 2.7 Consensus size: 447
2294892 GCAAAGATTT
* ** **
2294902 AAATCCATCACTTGATGGACCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCGTCTGAAG
1 AAATTCATCACTTGATGGACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
* * * *
2294966 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG-CTCAAATTCATCACTTGAT
66 -AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCT-GAATTCATCACTTGAT
** * * * *
2295030 GGACCACCATTTCCAGAGAAAGTTCATAATGAGAAGAAATTATCTGAAGAGGAAGAAGAAATTCA
129 GGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCA
** * * *
2295095 TAATGAGAAGAATTTGTTCAA-C-TTTCCTGAATTCATCACTTGATGGATTAACTTTTCCAGAGG
194 TAATGAGAAGAATTTGTTCAACCTTTTCCTGAATTCATCACCCGATGGATTAACATTGCCAGAGA
*
2295158 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTTGTTC
259 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
** * * * *
2295223 AACCTTTTGCTTTAATTCATTACCCGATGGATTAGCATTTCCAGAAGTGTTCATAATGAGAAGAA
324 AACCTTTTGCTCAAATCCATCACCCGATGGATCAACATTTCCAGAAGTGTTCATAATGAGAAGAA
2295288 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTAGTTTAACCTTTTGCTC
389 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTAGTTTAACCTTTTGCTC
*
2295347 AAATTCATCACTTGATGGACCACCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
1 AAATTCATCACTTGATGGACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
*
2295412 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACATTTTGCCTGAATTCATCACTTGATGG
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGG
* *
2295477 ATTAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
131 ATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
* * *
2295541 AATGAGAAGAATTTGTTCAACCTTTTGCTTTAATTCATCACCCGATGGATTAGCATTGCCAGAGA
195 AATGAGAAGAATTTGTTCAACCTTTT-CCTGAATTCATCACCCGATGGATTAACATTGCCAGAGA
* *
2295606 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGATGAAGTTCATAATGCGAAGAACTTGTT
259 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTT
** *
2295671 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGAAGTGTTCATAATGATAAGA
323 CAACCTTTTGCTCAAATCCATCACCCGATGGATCAACATTTCCAGAAGTGTTCATAATGAGAAGA
*
2295736 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTC
388 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTAGTTTAACCTTTTGCTC
* * * * *
2295796 GAATTTATCACTTGATAGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAAAG
1 AAATTCATCACTTGATGGACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
* *
2295861 AGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGA
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGG
2295926 ATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
131 ATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * * ** *
2295991 ATAAGAAGAATTTGTTCAACCTTTGT-TTG-ACTCTATCACAGAAGGAGATAGATCAACATCAAC
196 ATGAGAAGAATTTGTTCAACCTTT-TCCTGAATTC-ATCAC-----CCGATGGAT-----T-AAC
* ** *
2296054 ATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCATAATGAGA
248 ATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGA
*
2296118 AGAATTTGTTCAACCTT
313 AGAACTTGTTCAACCTT
2296135 GCCTTAATTT
Statistics
Matches: 702, Mismatches: 65, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
445 160 0.23
446 33 0.05
447 6 0.01
448 74 0.11
449 345 0.49
450 1 0.00
453 6 0.01
457 33 0.05
458 34 0.05
459 10 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (447 bp):
AAATTCATCACTTGATGGACCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGG
ATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTTCCTGAATTCATCACCCGATGGATTAACATTGCCAGAGAAA
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTGCTCAAATCCATCACCCGATGGATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACT
CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTAGTTTAACCTTTTGCTC
Found at i:2296453 original size:3 final size:3
Alignment explanation
Indices: 2296439--2296490 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
2296429 ATCCCGGTTC
* * * * *
2296439 TAT TAT TTT TAT TAT AAT AAT TAT AAT TAT AAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2296486 TAT TA
1 TAT TA
2296491 AATAATTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2297753 original size:124 final size:123
Alignment explanation
Indices: 2297557--2297782 Score: 290
Period size: 124 Copynumber: 1.8 Consensus size: 123
2297547 TATTTTAAGA
* * ** * *
2297557 AAATATTTTTGTTATTTATTTATTTTTTAATGTTGAAGGAAAGAGCTGTCTTAAAGCAACTAGAA
1 AAATATTTTAGTTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAACTAAAA
* **
2297622 GCCCTTTTCTAAATATTTTTAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
66 ACCCTTTTCT-AATATTTCCAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
* * * * *
2297681 AAATGTTTTAGTTATTTATTTATTTTTTAATATCAAAGAAAAGAGTTGTCTTAAGGTACCTAAAA
1 AAATATTTTAGTTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAACTAAAA
* * *
2297746 ACTCTTTTCTGATATTTCCAAGTAAATAAATATCTTA
66 ACCCTTTTCTAATATTTCCAAATAAATAAATATCTTA
2297783 TTTATAAATA
Statistics
Matches: 85, Mismatches: 17, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
123 23 0.27
124 62 0.73
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (123 bp):
AAATATTTTAGTTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCAACTAAAA
ACCCTTTTCTAATATTTCCAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
Found at i:2302573 original size:40 final size:40
Alignment explanation
Indices: 2302499--2302606 Score: 94
Period size: 40 Copynumber: 2.7 Consensus size: 40
2302489 TTGCACAATC
* *
2302499 GCGACATTTA-TAATAAAACGCCACT-AAGGTACATCACTATG
1 GCGACGTTTATTAA-AAAA-GCCACTAAATG-ACATCACTATG
* * *
2302540 GCGATGTTTATTAAAAAAGCCACTAAATGACATCTCTATT
1 GCGACGTTTATTAAAAAAGCCACTAAATGACATCACTATG
* * * *
2302580 GCGGCGTTTGTTAAAAACGCCAGTAAA
1 GCGACGTTTATTAAAAAAGCCACTAAA
2302607 GTACTACTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 37 0.67
41 15 0.27
42 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (40 bp):
GCGACGTTTATTAAAAAAGCCACTAAATGACATCACTATG
Found at i:2302648 original size:41 final size:41
Alignment explanation
Indices: 2302551--2302767 Score: 146
Period size: 41 Copynumber: 5.4 Consensus size: 41
2302541 CGATGTTTAT
*
2302551 TAAAAAAGCCACTAAA-TGAC-ATCTCTATTGCGGCGTTTGT-
1 TAAAAACGCCACTAAAGT-ACTA-CTCTATTGCGGCGTTTGTA
* *
2302591 TAAAAACGCCAGTAAAGTACTACTCTGTTGCGGCGTTTGTA
1 TAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* ** * * * * *
2302632 TACAAACGCCACTAAAGTAAGAGTATTTTGCAGCATTTG-A
1 TAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* * * *
2302672 TCAAAAAATGTCGCT--A--ACAACTCTATTGCGGCGTTTGT-
1 T--AAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* * *
2302710 TGAAAAACGCTACTAAAGTACTACTCTGTTGTGGCGTTTGTA
1 T-AAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* *
2302752 TACAAATGCCACTAAA
1 TAAAAACGCCACTAAA
2302768 ATAAGAGTAT
Statistics
Matches: 132, Mismatches: 34, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
37 8 0.06
38 15 0.11
39 1 0.01
40 36 0.27
41 63 0.48
42 9 0.07
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (41 bp):
TAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
Found at i:2302733 original size:120 final size:117
Alignment explanation
Indices: 2302573--2302806 Score: 362
Period size: 120 Copynumber: 2.0 Consensus size: 117
2302563 TAAATGACAT
*
2302573 CTCTATTGCGGCGTTTGTTAAAAACGCCAGTAAAGTACTACTCTGTTGCGGCGTTTGTATACAAA
1 CTCTATTGCGGCGTTTGTTAAAAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTGTATACAAA
* *
2302638 CGCCACTAAAGTAAGAGTATTTTGCAGCA-TTTGATCAAAAAATGTCGCTAACAA
66 CGCCACTAAAATAAGAGTATTTTGCAG-AGTTTGAT-AAAAAA-GCCGCTAACAA
* *
2302692 CTCTATTGCGGCGTTTGTTGAAAAACGCTACTAAAGTACTACTCTGTTGTGGCGTTTGTATACAA
1 CTCTATTGCGGCGTTTGTT-AAAAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTGTATACAA
* *
2302757 ATGCCACTAAAATAAGAGTATTTTGTAGAGTTTGATAAAAAAGCCGCTAA
65 ACGCCACTAAAATAAGAGTATTTTGCAGAGTTTGATAAAAAAGCCGCTAA
2302807 AAATAATGCT
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
118 7 0.07
119 26 0.25
120 73 0.69
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (117 bp):
CTCTATTGCGGCGTTTGTTAAAAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTGTATACAAA
CGCCACTAAAATAAGAGTATTTTGCAGAGTTTGATAAAAAAGCCGCTAACAA
Found at i:2302920 original size:42 final size:42
Alignment explanation
Indices: 2302874--2303002 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 42
2302864 TAACTGTTGT
2302874 GGCATTTGTTGTAAAAACGCTACTATATATAAACCCTATTGC
1 GGCATTTGTTGTAAAAACGCTACTATATATAAACCCTATTGC
* * * * * *
2302916 GGCATTT-TTATAAAAACGCTGCTA-A-AGTACTA-TCTGTTAC
1 GGCATTTGTTGTAAAAACGCTACTATATA-TA-AACCCTATTGC
* * *
2302956 GACGTTTGTTGAAAAAACG-TCACTATATATAAACCCTATTGC
1 GGCATTTGTTGTAAAAACGCT-ACTATATATAAACCCTATTGC
2302998 GGCAT
1 GGCAT
2303003 ATTGAATGGA
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
39 1 0.02
40 14 0.22
41 29 0.46
42 18 0.29
43 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (42 bp):
GGCATTTGTTGTAAAAACGCTACTATATATAAACCCTATTGC
Found at i:2305246 original size:23 final size:23
Alignment explanation
Indices: 2305220--2305280 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2305210 CTCATATAAA
*
2305220 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
2305243 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
2305266 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
2305281 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:2305467 original size:103 final size:103
Alignment explanation
Indices: 2305296--2305616 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
2305286 TAATGTCCAT
* * *
2305296 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
2305361 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2305399 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
2305464 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2305502 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
2305567 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2305605 AAGGACCACATA
1 AAGGACCACATA
2305617 GACCCTCGAC
Statistics
Matches: 214, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 214 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2306826 original size:21 final size:21
Alignment explanation
Indices: 2306800--2306843 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2306790 ATTTTATTCG
* *
2306800 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
2306821 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
2306842 CT
1 CT
2306844 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:2312136 original size:30 final size:30
Alignment explanation
Indices: 2312086--2312142 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2312076 TATTCAAACT
* *
2312086 GGTTTTGCCGATTTTTAGCCGGTTCATCCC
1 GGTTTTACCGATTTTCAGCCGGTTCATCCC
*
2312116 GGTTTTACCGGTTTTCAGCCGGTTCAT
1 GGTTTTACCGATTTTCAGCCGGTTCAT
2312143 TACCAAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (30 bp):
GGTTTTACCGATTTTCAGCCGGTTCATCCC
Found at i:2317444 original size:29 final size:28
Alignment explanation
Indices: 2317412--2317479 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
2317402 AAGAAGGAGG
*
2317412 GAAGAAAAAGGAAGAAAGAAAGTAAAAAT
1 GAAGAAAAAGG-AGAAAGAAAGAAAAAAT
*
2317441 GAAGAGAAATGGAGAAAGAAAGAAAAAAT
1 GAAGA-AAAAGGAGAAAGAAAGAAAAAAT
*
2317470 CAGAGAAAAA
1 GA-AGAAAAA
2317480 ACCCCAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.06
Consensus pattern (28 bp):
GAAGAAAAAGGAGAAAGAAAGAAAAAAT
Found at i:2317775 original size:21 final size:20
Alignment explanation
Indices: 2317749--2317933 Score: 84
Period size: 21 Copynumber: 8.9 Consensus size: 20
2317739 CGCAAATCAG
2317749 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* *
2317770 TTTCCAATTTCGCATTACGAT
1 TTTCCAA-TTCGCAATGCGAT
*
2317791 TTTCCCAATTCGCAATGCGAA
1 TTT-CCAATTCGCAATGCGAT
**** *
2317812 TAAGTAAATCGCAATGCGAAT
1 TTTCCAATTCGCAATGCG-AT
*** *
2317833 TTGGAAAATCGCAATGCGAT
1 TTTCCAATTCGCAATGCGAT
** * * *
2317853 ACT-GACTATCGCAATGCAAT
1 TTTCCAAT-TCGCAATGCGAT
*
2317873 TTTCCTAATTCGCATTGCGAT
1 TTTCC-AATTCGCAATGCGAT
* ** **
2317894 TTACGTATTCGCGTTGCGAT
1 TTTCCAATTCGCAATGCGAT
*
2317914 TTTCATAATTCGCAATGCGA
1 TTTC-CAATTCGCAATGCGA
2317934 ATACGTAAAT
Statistics
Matches: 121, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 43 0.36
21 71 0.59
22 6 0.05
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:2317948 original size:20 final size:20
Alignment explanation
Indices: 2317923--2318034 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
2317913 TTTTCATAAT
2317923 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
2317943 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2317963 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
2317984 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
2318004 TTGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
2318024 TCGCAATGCGA
1 TCGCAATGCGA
2318035 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 56 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2317954 original size:41 final size:41
Alignment explanation
Indices: 2317787--2318042 Score: 152
Period size: 41 Copynumber: 6.3 Consensus size: 41
2317777 TTTCGCATTA
** *
2317787 CGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATG
1 CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATG
** * *
2317828 CGAATTTGGA-AAATCGCAATGCG-ATAC-TGACTATCGCAATG
1 CG-ATTTTCATAATTCGCAATGCGAATACGT-A-AATCGCAATG
* * * * * **
2317869 CAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGTTG
1 CGATTTTCATAATTCGCAATGCGA-ATACGTAAATCGCAATG
*
2317910 CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACG
1 CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATG
* * * *
2317951 CGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATG
1 CGATTTTCA-TAATTCGCAATGCGAA-TACGTAAATCGCAATG
* * * * *
2317992 CGA-ATACGTAAATT-GCAATGCGAAT-CTTACTATCGCAATG
1 CGATTTTCAT-AATTCGCAATGCGAATACGTA-AATCGCAATG
*
2318032 CGATTTACATA
1 CGATTTTCATA
2318043 GCGCCATTCG
Statistics
Matches: 161, Mismatches: 40, Indels: 29
0.70 0.17 0.13
Matches are distributed among these distances:
39 5 0.03
40 42 0.26
41 102 0.63
42 8 0.05
43 3 0.02
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATG
Found at i:2318702 original size:20 final size:19
Alignment explanation
Indices: 2318613--2318725 Score: 101
Period size: 20 Copynumber: 6.1 Consensus size: 19
2318603 GAAACCAAAA
*
2318613 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
** *
2318632 TCGCGTTGCGATAGTCACT
1 TCGCGTTGCGATTTTCATT
2318651 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2318665 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2318684 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
2318704 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2318724 TC
1 TC
2318726 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 2 0.03
19 29 0.38
20 32 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2322297 original size:14 final size:14
Alignment explanation
Indices: 2322278--2322313 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2322268 ATTGTTTAAT
2322278 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2322292 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2322306 TGATTTGT
1 TGATTTGT
2322314 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2322442 original size:19 final size:19
Alignment explanation
Indices: 2322420--2322537 Score: 96
Period size: 19 Copynumber: 6.7 Consensus size: 19
2322410 AAAAATTACT
2322420 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2322439 ATCGCAA--CG--AT-ATA
1 ATCGCAATGCGAAATGAAA
2322453 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2322472 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
2322486 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2322505 ATCGCAACGTGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
*
2322524 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2322538 CTAAATTCGC
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
14 19 0.24
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 46 0.57
20 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2322462 original size:33 final size:33
Alignment explanation
Indices: 2322420--2322513 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2322410 AAAAATTACT
* *
2322420 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2322453 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2322486 ATCGCAATACGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2322514 TGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2322538 original size:19 final size:19
Alignment explanation
Indices: 2322502--2322547 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2322492 ATACGAAATG
*
2322502 AAAATCGCAACGTGAAACT
1 AAAATCGCAACGCGAAACT
2322521 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
2322540 AAATTCGC
1 AAAATCGC
2322548 GTTACGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:2322574 original size:19 final size:18
Alignment explanation
Indices: 2322552--2322673 Score: 88
Period size: 19 Copynumber: 7.2 Consensus size: 18
2322542 ATTCGCGTTA
2322552 CGATTTTCATTTCGCTTTG
1 CGATTTTCATTTCGC-TTG
**
2322571 CGA--TTC-CCTCG-TTG
1 CGATTTTCATTTCGCTTG
2322585 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGC-TTG
*
2322604 CGA--TTC-TCTCG-TTG
1 CGATTTTCATTTCGCTTG
2322618 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGC-TTG
*
2322637 CGA--TT-ATCTCG-TTG
1 CGATTTTCATTTCGCTTG
2322651 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGC-TTG
2322670 CGAT
1 CGAT
2322674 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 8, Indels: 30
0.68 0.07 0.25
Matches are distributed among these distances:
14 18 0.22
16 20 0.25
17 20 0.25
19 22 0.28
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (18 bp):
CGATTTTCATTTCGCTTG
Found at i:2322594 original size:33 final size:33
Alignment explanation
Indices: 2322547--2322673 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
2322537 ACTAAATTCG
* * *
2322547 CGTTACGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2322580 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
2322613 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2322646 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2322674 AGTAATTTCC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2322620 original size:14 final size:14
Alignment explanation
Indices: 2322568--2322655 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
2322558 TCATTTCGCT
*
2322568 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
2322582 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2322599 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
2322615 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
2322632 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
2322648 TTGCGATT
1 TTGCGATT
2322656 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2325233 original size:24 final size:24
Alignment explanation
Indices: 2325199--2325252 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2325189 CTGAAACAAC
*
2325199 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
2325223 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2325247 ATCAAA
1 ATCAAA
2325253 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2326672 original size:20 final size:20
Alignment explanation
Indices: 2326624--2326682 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2326614 AATAGTTTCT
* *
2326624 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
2326644 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
2326664 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
2326683 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:2326972 original size:22 final size:22
Alignment explanation
Indices: 2326945--2326988 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2326935 GATGGAGATA
2326945 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2326967 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2326989 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2327206 original size:20 final size:20
Alignment explanation
Indices: 2327181--2327223 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2327171 GTATTATCTC
* *
2327181 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTAAGTATCGA
*
2327201 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTAAGTATCGA
2327221 GTT
1 GTT
2327224 ACGATTTTGT
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:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (20 bp):
GTTGCGAAAGTAAGTATCGA
Found at i:2327262 original size:21 final size:21
Alignment explanation
Indices: 2327238--2327310 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
2327228 TTTTGTATTA
* *
2327238 TCGCGTTGCAATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
2327259 TCGCATTCCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
2327280 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
2327300 TCGCATTGCGA
1 TCGCATTGCGA
2327311 ATTGGGAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 17 0.38
21 28 0.62
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2327410 original size:20 final size:20
Alignment explanation
Indices: 2327387--2327432 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2327377 GGAAACTGAT
*
2327387 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
2327407 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
2327426 TTGCGAT
1 TTGCGAT
2327433 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:2335821 original size:103 final size:104
Alignment explanation
Indices: 2335617--2335824 Score: 382
Period size: 105 Copynumber: 2.0 Consensus size: 104
2335607 GCACCCTCCC
*
2335617 AGTTTGTGCATATGATTGAAATAATATATATTATGGTTATCTCTTGGGACTTTTAGTAAAGAGAA
1 AGTTTGTGCATATGATTAAAATAATATATATTATGGTTATCTCTTGGGACTTTTAGTAAAGAG-A
2335682 AGGGAAAAAAGGTGCCATATCAGATTCTAAAGAATCTTCT
65 AGGGAAAAAAGGTGCCATATCAGATTCTAAAGAATCTTCT
2335722 AGTTTGTGCATATGATTAAAATAATATATATTATGGTTATCTCTTGGGACTTTTAGTAAAGAG-A
1 AGTTTGTGCATATGATTAAAATAATATATATTATGGTTATCTCTTGGGACTTTTAGTAAAGAGAA
*
2335786 GGGAAAAAAGGTGTCATATCAGATTCTAAAGAATCTTCT
66 GGGAAAAAAGGTGCCATATCAGATTCTAAAGAATCTTCT
2335825 GCTGTTGTTT
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
103 39 0.39
105 62 0.61
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (104 bp):
AGTTTGTGCATATGATTAAAATAATATATATTATGGTTATCTCTTGGGACTTTTAGTAAAGAGAA
GGGAAAAAAGGTGCCATATCAGATTCTAAAGAATCTTCT
Found at i:2339693 original size:29 final size:29
Alignment explanation
Indices: 2339604--2339693 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
2339594 AAATTATAAG
*
2339604 AATAAGCTCC-TAATAATAAATACTAAAAA
1 AATAAGC-CCGTAATAATAAATATTAAAAA
*
2339633 AATAAGCTCGTAATAATAAATATTGAGGAAAA
1 AATAAGCCCGTAATAATAAATATT-A--AAAA
* *
2339665 AATGAA-CCCTTAATAATAAGTATTAAAAA
1 AAT-AAGCCCGTAATAATAAATATTAAAAA
2339694 TAATTTGACC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 24 0.47
30 1 0.02
31 1 0.02
32 22 0.43
33 2 0.04
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.26
Consensus pattern (29 bp):
AATAAGCCCGTAATAATAAATATTAAAAA
Found at i:2340264 original size:21 final size:21
Alignment explanation
Indices: 2340239--2340279 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2340229 GTAAATCACA
*
2340239 TTGCGATTTTCTAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
2340260 TTGCGATTTTCCAAATTCGC
1 TTGCGATTTTCCAAATTCGC
2340280 AACGCGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:2340286 original size:21 final size:21
Alignment explanation
Indices: 2340241--2340286 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2340231 AAATCACATT
* ***
2340241 GCGATTTTCTAAATTCGCGTT
1 GCGATTTTCCAAATTCGCAAC
2340262 GCGATTTTCCAAATTCGCAAC
1 GCGATTTTCCAAATTCGCAAC
2340283 GCGA
1 GCGA
2340287 ATATATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
GCGATTTTCCAAATTCGCAAC
Found at i:2340315 original size:40 final size:40
Alignment explanation
Indices: 2340271--2340383 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 40
2340261 TGCGATTTTC
* *
2340271 CAAATTCGCAACGCGAATA-TATAAA-TCGTAACACAGAAGT
1 CAAATTCGCAACGCG-ATAGT-TAAATTCGCAACACAAAAGT
*
2340311 CAAATACGCAACGCGATAGTTAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGTTAAATTCGCAACACAAAAGT
*
2340351 CAAATTCGCAACGCGGA-ATTTCAAATTCGCAAC
1 CAAATTCGCAACGC-GATAGTT-AAATTCGCAAC
2340384 GCGGAATTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
39 7 0.11
40 44 0.69
41 13 0.20
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTTAAATTCGCAACACAAAAGT
Found at i:2340340 original size:20 final size:20
Alignment explanation
Indices: 2340306--2340404 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
2340296 TCGTAACACA
* *
2340306 GAAGTCAAATACGCAACGC-
1 GAAGTTAAATTCGCAACGCG
* *
2340325 GATAGTTAAATTCGCAACACA
1 GA-AGTTAAATTCGCAACGCG
* *
2340346 AAAGTCAAATTCGCAACGCG
1 GAAGTTAAATTCGCAACGCG
*
2340366 GAATTTCAAATTCGCAACGCG
1 GAAGTT-AAATTCGCAACGCG
*
2340387 GAATTTCAAATTCGCAAC
1 GAAGTT-AAATTCGCAAC
2340405 TGAATTTCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.03
20 32 0.48
21 33 0.49
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
GAAGTTAAATTCGCAACGCG
Found at i:2340376 original size:21 final size:21
Alignment explanation
Indices: 2340350--2340423 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
2340340 AACACAAAAG
2340350 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAACGCGGAATT
2340371 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAACGCGGAATT
*
2340392 TCAAATTCGCAA--CTGAATT
1 TCAAATTCGCAACGCGGAATT
2340411 TCAAATTCGCAAC
1 TCAAATTCGCAAC
2340424 TAGATTTTCG
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.35
21 33 0.65
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (21 bp):
TCAAATTCGCAACGCGGAATT
Found at i:2340437 original size:20 final size:19
Alignment explanation
Indices: 2340350--2340443 Score: 107
Period size: 21 Copynumber: 4.7 Consensus size: 19
2340340 AACACAAAAG
*
2340350 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
*
2340371 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
2340392 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
2340411 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
*
2340431 TCGAATTCGCAAC
1 TCAAATTCGCAAC
2340444 ATGTTTTAGT
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
19 20 0.29
20 16 0.23
21 33 0.48
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:2341254 original size:12 final size:12
Alignment explanation
Indices: 2341233--2341266 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2341223 ACCACATTTC
*
2341233 CAATACCAAACA
1 CAATATCAAACA
2341245 CAATATCAAACA
1 CAATATCAAACA
*
2341257 CAATCTCAAA
1 CAATATCAAA
2341267 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2343721 original size:18 final size:18
Alignment explanation
Indices: 2343698--2343733 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2343688 AAGCAAAAGG
*
2343698 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2343716 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2343734 CAACCGGCTT
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:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2344040 original size:20 final size:20
Alignment explanation
Indices: 2344015--2344057 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2344005 GATCAATGCG
2344015 AAAGTCAAATTCGCAACGCA
1 AAAGTCAAATTCGCAACGCA
*
2344035 AAAGTCAAATTTGCAACGCA
1 AAAGTCAAATTCGCAACGCA
2344055 AAA
1 AAA
2344058 TCGTAAACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (20 bp):
AAAGTCAAATTCGCAACGCA
Found at i:2344132 original size:22 final size:20
Alignment explanation
Indices: 2344079--2344133 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 20
2344069 AAGTCGCAAC
2344079 GCGAATTTGA-CTTTCGCGTT
1 GCGAATTT-ACCTTTCGCGTT
2344099 GCGAATTTACCTTTCGCGTT
1 GCGAATTTACCTTTCGCGTT
2344119 GCGAAAGTTTACCTT
1 GCG-AA-TTTACCTT
2344134 CAACAAGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.03
20 21 0.66
21 2 0.06
22 8 0.25
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
GCGAATTTACCTTTCGCGTT
Found at i:2344232 original size:25 final size:25
Alignment explanation
Indices: 2344194--2344243 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2344184 AAATCAATTA
*
2344194 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2344219 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2344244 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:2345477 original size:64 final size:64
Alignment explanation
Indices: 2345403--2345523 Score: 242
Period size: 64 Copynumber: 1.9 Consensus size: 64
2345393 TGATGCTTGG
2345403 GTAGTTGTTCTCTTGCTTCTTCAAGTGTCCTTAGCTTGTATTTATAGCTTGGAATGTTGATGTT
1 GTAGTTGTTCTCTTGCTTCTTCAAGTGTCCTTAGCTTGTATTTATAGCTTGGAATGTTGATGTT
2345467 GTAGTTGTTCTCTTGCTTCTTCAAGTGTCCTTAGCTTGTATTTATAGCTTGGAATGT
1 GTAGTTGTTCTCTTGCTTCTTCAAGTGTCCTTAGCTTGTATTTATAGCTTGGAATGT
2345524 GTTTGATGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.16, C:0.15, G:0.21, T:0.48
Consensus pattern (64 bp):
GTAGTTGTTCTCTTGCTTCTTCAAGTGTCCTTAGCTTGTATTTATAGCTTGGAATGTTGATGTT
Found at i:2345595 original size:20 final size:20
Alignment explanation
Indices: 2345563--2345612 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2345553 ATGTTGCGAT
* *
2345563 CAACGCAAAAGTCAAATTTG
1 CAACGCGAAAGTCAAATTCG
*
2345583 CAATGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
2345603 CAACGCGAAA
1 CAACGCGAAA
2345613 TAAGCGTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:2345835 original size:66 final size:64
Alignment explanation
Indices: 2345764--2345903 Score: 217
Period size: 66 Copynumber: 2.2 Consensus size: 64
2345754 GATTTAAAAC
* **
2345764 AACAAATTAAATTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTGCACATCAAATT
1 AACAAATCAAATTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTCCCACATC-AATT
2345829 A
64 A
* *
2345830 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTCCCTCATCAATTA
1 AACAAATCAAATTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTCCCACATCAATTA
2345894 AACAAATCAA
1 AACAAATCAA
2345904 CTTTCAATGT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
64 15 0.22
65 22 0.32
66 32 0.46
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAAATTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTCCCACATCAATTA
Found at i:2347131 original size:22 final size:23
Alignment explanation
Indices: 2347104--2347165 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
2347094 CAGCTCGTAT
2347104 AATGCACCGAAGTGCCACGTAG-
1 AATGCACCGAAGTGCCACGTAGA
* * *
2347126 ATTGCACCGTAGTGCCGCGTAGA
1 AATGCACCGAAGTGCCACGTAGA
2347149 AATGCACCGAAGTGCCA
1 AATGCACCGAAGTGCCA
2347166 TATAATGTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
AATGCACCGAAGTGCCACGTAGA
Found at i:2347451 original size:64 final size:64
Alignment explanation
Indices: 2347350--2347498 Score: 264
Period size: 64 Copynumber: 2.3 Consensus size: 64
2347340 CATTATCATT
2347350 TATGTCATTTCACATGTTCACATATTCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAACA
1 TATGTCATTTCACATGTTCACATATTCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAACA
2347414 TATGTCATTTCACATGTTCACATATTCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAACA
1 TATGTCATTTCACATGTTCACATATTCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAACA
*
2347478 TA-GCTCATTATCACATTTTCA
1 TATG-TCATT-TCACATGTTCA
2347499 TATAATCACA
Statistics
Matches: 82, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
63 1 0.01
64 71 0.87
65 10 0.12
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (64 bp):
TATGTCATTTCACATGTTCACATATTCATATTACCTGGGCACGTAGTCTCATAGTTTTTGAACA
Found at i:2349887 original size:21 final size:20
Alignment explanation
Indices: 2349848--2349885 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2349838 AGTATGTCCA
2349848 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
2349868 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
2349886 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:2352392 original size:21 final size:21
Alignment explanation
Indices: 2352368--2352466 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
2352358 GCGGGTGGGA
*
2352368 CCTCTTGAATGATGATAGGGG
1 CCTCTTGAATGATGAGAGGGG
* * *
2352389 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAGGGG
*
2352410 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
* *
2352431 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAATGATGA-GAGGGG
2352452 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
2352467 TAGGTGCATC
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.25
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:2352422 original size:42 final size:42
Alignment explanation
Indices: 2352368--2352470 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
2352358 GCGGGTGGGA
* * *
2352368 CCTCTTGAATGATGATAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGCG
* *
2352410 CTTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGATAGGGGCCTCTTGAACGATAGGAGGCG
2352452 CCTCTTGAATGATGATAGG
1 CCTCTTGAATGATGATAGG
2352471 TGCATCAAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 1 0.02
42 50 0.96
43 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CCTCTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGCG
Found at i:2352662 original size:100 final size:100
Alignment explanation
Indices: 2352489--2352688 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
2352479 GCTTCTTCTT
2352489 ACGGAGTCTTGGCACTAGTGGGGTGAACGGAGACGTAATGGCACGTGCACGACATCTGATGCGTG
1 ACGGAGTCTTGGCACTAGTGGGGTGAACGGAGACGTAATGGCACGTGCACGACATCTGATGCGTG
2352554 AACCCCGTCGTGCAAGAAAAACCCGACGTAAAGCA
66 AACCCCGTCGTGCAAGAAAAACCCGACGTAAAGCA
2352589 ACGGAGTCTTGGCACTAGTGGGGTGAACGGAGACGTAATGGCACGTGCACGACATCTGATGCGTG
1 ACGGAGTCTTGGCACTAGTGGGGTGAACGGAGACGTAATGGCACGTGCACGACATCTGATGCGTG
2352654 AACCCCGTCGTGCAAGAAAAACCCGACGTAAAGCA
66 AACCCCGTCGTGCAAGAAAAACCCGACGTAAAGCA
2352689 TCTACCTTGT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.29, C:0.24, G:0.31, T:0.16
Consensus pattern (100 bp):
ACGGAGTCTTGGCACTAGTGGGGTGAACGGAGACGTAATGGCACGTGCACGACATCTGATGCGTG
AACCCCGTCGTGCAAGAAAAACCCGACGTAAAGCA
Found at i:2353475 original size:24 final size:24
Alignment explanation
Indices: 2353448--2353554 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
2353438 AAACGGAGAT
*
2353448 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
2353472 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
2353496 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
2353520 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
2353544 ATCAGAAATCA
1 ATCAGAAATCA
2353555 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:2353554 original size:48 final size:48
Alignment explanation
Indices: 2353448--2353556 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
2353438 AAACGGAGAT
* * * *
2353448 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
2353496 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2353544 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2353557 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:2356025 original size:14 final size:15
Alignment explanation
Indices: 2355998--2356030 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2355988 GGTCAACTCT
2355998 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
2356013 GGTCAAC-GTCAACG
1 GGTCAACGGTCAACG
2356027 GGTC
1 GGTC
2356031 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:2356042 original size:24 final size:24
Alignment explanation
Indices: 2356011--2356072 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 24
2356001 CAACGGTCAA
2356011 CGGGTCAACGTC-AACGGGTCGGGT
1 CGGGTCAACGTCGAAC-GGTCGGGT
2356035 CGGGTCAACGGTCGGTAAACGGTCGGGT
1 CGGGTCAAC-GTC-G--AACGGTCGGGT
2356063 CGGGTCAACG
1 CGGGTCAACG
2356073 GGTCGGGTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
24 9 0.27
25 3 0.09
27 1 0.03
28 17 0.52
29 3 0.09
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (24 bp):
CGGGTCAACGTCGAACGGTCGGGT
Found at i:2356043 original size:18 final size:17
Alignment explanation
Indices: 2356020--2356085 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 17
2356010 ACGGGTCAAC
2356020 GTCAACGGGTCGGGTCGG
1 GTCAAC-GGTCGGGTCGG
2356038 GTCAA----C-GGTC-G
1 GTCAACGGTCGGGTCGG
*
2356049 GTAAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
2356066 GTCAACGGGTCGGGTCGG
1 GTCAAC-GGTCGGGTCGG
2356084 GT
1 GT
2356086 TGTGACCGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
11 5 0.13
12 4 0.10
13 1 0.03
15 1 0.03
16 4 0.10
17 6 0.15
18 18 0.46
ACGTcount: A:0.14, C:0.21, G:0.47, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:2356104 original size:9 final size:9
Alignment explanation
Indices: 2356090--2356135 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
2356080 TCGGGTTGTG
2356090 ACCGGTCAA
1 ACCGGTCAA
2356099 ACCGGTCAAA
1 ACCGGTC-AA
* *
2356109 ACAGTTCCAA
1 ACCGGT-CAA
2356119 ACCGGTCAA
1 ACCGGTCAA
2356128 ACCGGTCA
1 ACCGGTCA
2356136 CTTTTCCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 18 0.58
10 12 0.39
11 1 0.03
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.13
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2358026 original size:2 final size:2
Alignment explanation
Indices: 2358014--2358054 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2358004 CTTTTAAAAC
2358014 AT AT AT A- AT AT AT AT AT AT A- 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
2358054 A
1 A
2358055 CCCCATCCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2358032 original size:13 final size:13
Alignment explanation
Indices: 2358014--2358054 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
2358004 CTTTTAAAAC
2358014 ATATATAATATAT
1 ATATATAATATAT
2358027 ATATATAATATAT
1 ATATATAATATAT
2358040 ATATAT-ATATAT
1 ATATATAATATAT
2358052 ATA
1 ATA
2358055 CCCCATCCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:2358319 original size:48 final size:48
Alignment explanation
Indices: 2358214--2358321 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
2358204 AAACGGAGAT
* * *
2358214 ATCAGAAATCA-AACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
2358261 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2358309 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2358322 TAAAATATTC
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
47 8 0.17
48 40 0.83
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:2360779 original size:17 final size:17
Alignment explanation
Indices: 2360757--2360840 Score: 94
Period size: 17 Copynumber: 5.3 Consensus size: 17
2360747 CAACGGTCAA
2360757 CGGGTCAACGGTCGGGT
1 CGGGTCAACGGTCGGGT
2360774 CGGGTCAACGGGTCGGGT
1 CGGGTCAAC-GGTCGGGT
2360792 CGGGTCAA----C-GGT
1 CGGGTCAACGGTCGGGT
2360804 C-GGT-AACGGTCGGGT
1 CGGGTCAACGGTCGGGT
2360819 CGGGTC-ACGGGTCGGGT
1 CGGGTCAAC-GGTCGGGT
2360836 CGGGT
1 CGGGT
2360841 TGTGACCGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
10 2 0.03
11 3 0.05
12 4 0.07
13 1 0.02
14 1 0.02
15 4 0.07
16 5 0.09
17 22 0.38
18 16 0.28
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
CGGGTCAACGGTCGGGT
Found at i:2361899 original size:21 final size:21
Alignment explanation
Indices: 2361871--2361920 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2361861 ACCATTATCT
*
2361871 TCACGTAAAGTACTAACCTCA
1 TCACGTAAAGCACTAACCTCA
* *
2361892 TGACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACTAACCTCA
2361913 TCACGTAA
1 TCACGTAA
2361921 CTCCTCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACTAACCTCA
Found at i:2364237 original size:20 final size:20
Alignment explanation
Indices: 2364208--2364289 Score: 121
Period size: 20 Copynumber: 4.1 Consensus size: 20
2364198 TAATATTGTG
*
2364208 TTTCGCGTTGCGAATTTGAC
1 TTTCGTGTTGCGAATTTGAC
*
2364228 TTTCGTGTTGCGAATTTGGC
1 TTTCGTGTTGCGAATTTGAC
*
2364248 TATCGTGTTGCGAATTTGAC
1 TTTCGTGTTGCGAATTTGAC
2364268 TTAT-GTGTTGCGAATTTGAC
1 TT-TCGTGTTGCGAATTTGAC
2364288 TT
1 TT
2364290 CTGTATTGCG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 55 0.98
21 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.44
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTGAC
Found at i:2364298 original size:20 final size:20
Alignment explanation
Indices: 2364214--2364300 Score: 115
Period size: 20 Copynumber: 4.3 Consensus size: 20
2364204 TGTGTTTCGC
2364214 GTTGCGAATTTGACTT-TCGT
1 GTTGCGAATTTGACTTCT-GT
*
2364234 GTTGCGAATTTGGCTATC-GT
1 GTTGCGAATTTGACT-TCTGT
*
2364254 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTCTGT
2364274 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
2364294 ATTGCGA
1 GTTGCGA
2364301 TTTACAGATT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.02
20 57 0.97
21 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:2364299 original size:40 final size:40
Alignment explanation
Indices: 2364215--2364326 Score: 124
Period size: 40 Copynumber: 2.8 Consensus size: 40
2364205 GTGTTTCGCG
* *
2364215 TTGCGAATTTGACTTTCGTGTTGCGAATTTGGCTATCGTG
1 TTGCGAATTTGACTTTCGTGTTGCGAATTTGACTATCGTA
2364255 TTGCGAATTTGACTTAT-GTGTTGCGAATTTGACT-TCTGTA
1 TTGCGAATTTGACTT-TCGTGTTGCGAATTTGACTATC-GTA
* *
2364295 TTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGA
1 TTGCGAATTTGAC--TTTCGTGTTGCGAATTTGA
2364327 AAAAGCGCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
38 2 0.03
39 7 0.11
40 53 0.84
41 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (40 bp):
TTGCGAATTTGACTTTCGTGTTGCGAATTTGACTATCGTA
Found at i:2365014 original size:31 final size:31
Alignment explanation
Indices: 2364977--2365054 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
2364967 AAAAAATTTC
2364977 TTGTTCGTGTTCGTTCGTTAAAAAATGTAGT
1 TTGTTCGTGTTCGTTCGTTAAAAAATGTAGT
*
2365008 TTGTTCGTGTTCGTTCGTTAAGAAATGTAGT
1 TTGTTCGTGTTCGTTCGTTAAAAAATGTAGT
2365039 TTGTTCGTGTTCGTTC
1 TTGTTCGTGTTCGTTC
2365055 ATGTTCGTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.47
Consensus pattern (31 bp):
TTGTTCGTGTTCGTTCGTTAAAAAATGTAGT
Found at i:2365096 original size:14 final size:14
Alignment explanation
Indices: 2365077--2365108 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2365067 TTAAATGATA
2365077 AACGAACACAAATG
1 AACGAACACAAATG
*
2365091 AACGAACATAAATG
1 AACGAACACAAATG
2365105 AACG
1 AACG
2365109 GATGTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:2365303 original size:16 final size:17
Alignment explanation
Indices: 2365282--2365319 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2365272 TTGAGTTTTT
*
2365282 TTATTTGTA-TTTAAAA
1 TTATTTGAATTTTAAAA
2365298 TTATTTGAATTTTAAAA
1 TTATTTGAATTTTAAAA
2365315 -TATTT
1 TTATTT
2365320 ATGGGTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
TTATTTGAATTTTAAAA
Found at i:2365426 original size:10 final size:10
Alignment explanation
Indices: 2365409--2365438 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2365399 CACATAAGCG
2365409 AACGAACATA
1 AACGAACATA
*
2365419 AGCGAACATA
1 AACGAACATA
2365429 AACGAACATA
1 AACGAACATA
2365439 TTATCGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (10 bp):
AACGAACATA
Found at i:2365671 original size:2 final size:2
Alignment explanation
Indices: 2365664--2365700 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2365654 ATTATAAGTA
2365664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2365701 CTTAGAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2366392 original size:218 final size:211
Alignment explanation
Indices: 2366019--2366448 Score: 761
Period size: 218 Copynumber: 2.0 Consensus size: 211
2366009 ACTATTTTTT
* **
2366019 AGTTTTTCACTCATCTAACGATTAGAAATCTATGTAAAACTAAAATTTTTTTTTAAAAAATGTAA
1 AGTTTTTCACTCATCTAACGATTAGAAATCTATGTAAAACTAAAATTTCTTTAAAAAAAATGTAA
*
2366084 GTGGATCCTATATATGGGGGGGGATCAATCAATAAATTAAGTGAAGTTTAACTCCTTTACAAAGT
66 GTGGATCCTATATATGGGGGGGGATCAATCAATAAATTAAATGAAGTTTAACTCCTTTACAAAGT
2366149 TGGTTTACATAAGTTGAATATAAGGAGGTACATGAGGATGTTGATGAGAAGATGGCAGTGGTTGA
131 TGGTTTACATAAGTTGAATATAAGGAGGTACATGAGGATGTTGATGAGAAGATGGCAGTGGTTGA
2366214 GGATTCAATTGATGAA
196 GGATTCAATTGATGAA
2366230 AGTTTTTCACTCATCTAACGATTAGAAATCTATGTAAAACTAAAATTTCTTTAAAAAAAATGTAA
1 AGTTTTTCACTCATCTAACGATTAGAAATCTATGTAAAACTAAAATTTCTTTAAAAAAAATGTAA
2366295 GTGGATCCTATATATGTGTGTGGGGGGGGGATCAATCAATAAATTAAATGAAGTTTAACTCCTTT
66 GTGGATCCTATATA------T-GGGGGGGGATCAATCAATAAATTAAATGAAGTTTAACTCCTTT
2366360 ACAAAGTTGGTTTACATAAGTTGAATATAAGGAGGTACATGAGGATGTTGATGAGAAGATGGCAG
124 ACAAAGTTGGTTTACATAAGTTGAATATAAGGAGGTACATGAGGATGTTGATGAGAAGATGGCAG
2366425 TGGTTGAGGATTCAATTGATGAA
189 TGGTTGAGGATTCAATTGATGAA
2366448 A
1 A
2366449 TTTGCAACAT
Statistics
Matches: 208, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
211 76 0.37
217 1 0.00
218 131 0.63
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (211 bp):
AGTTTTTCACTCATCTAACGATTAGAAATCTATGTAAAACTAAAATTTCTTTAAAAAAAATGTAA
GTGGATCCTATATATGGGGGGGGATCAATCAATAAATTAAATGAAGTTTAACTCCTTTACAAAGT
TGGTTTACATAAGTTGAATATAAGGAGGTACATGAGGATGTTGATGAGAAGATGGCAGTGGTTGA
GGATTCAATTGATGAA
Found at i:2367043 original size:83 final size:83
Alignment explanation
Indices: 2366904--2367069 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
2366894 CTCTGTGATA
2366904 AGTAGGACACAATCCACCATTTAACCATATCTTCAAGGACTCTCCAACCATGACTATGAAAGAGT
1 AGTAGGACACAATCCACCATTTAACCATATCTTCAAGGACTCTCCAACCATGACTATGAAAGAGT
2366969 TGGGCGAGGGTTCAACGT
66 TGGGCGAGGGTTCAACGT
2366987 AGTAGGACACAATCCACCATTTAACCATATCTTCAAGGACTCTCCAACCATGACTATGAAAGAGT
1 AGTAGGACACAATCCACCATTTAACCATATCTTCAAGGACTCTCCAACCATGACTATGAAAGAGT
2367052 TGGGCGAGGGTTCAACGT
66 TGGGCGAGGGTTCAACGT
2367070 TGATCCACTC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (83 bp):
AGTAGGACACAATCCACCATTTAACCATATCTTCAAGGACTCTCCAACCATGACTATGAAAGAGT
TGGGCGAGGGTTCAACGT
Found at i:2367806 original size:22 final size:22
Alignment explanation
Indices: 2367778--2367848 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
2367768 AATCCGATCA
2367778 TAATTTTTTTTATAGAAACAAC
1 TAATTTTTTTTATAGAAACAAC
* * **
2367800 TAATTTTATTCA-A-AATAGGA-
1 TAATTTTTTTTATAGAA-ACAAC
2367820 TAATTTTTTTTATAGAAACAAC
1 TAATTTTTTTTATAGAAACAAC
2367842 TAATTTT
1 TAATTTT
2367849 ATTCAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 12 0.32
21 6 0.16
22 19 0.51
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (22 bp):
TAATTTTTTTTATAGAAACAAC
Found at i:2367836 original size:42 final size:42
Alignment explanation
Indices: 2367777--2367861 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
2367767 AAATCCGATC
2367777 ATAATTTTTTTTATAGAAACAACTAATTTTATTCAAAATAGG
1 ATAATTTTTTTTATAGAAACAACTAATTTTATTCAAAATAGG
2367819 ATAATTTTTTTTATAGAAACAACTAATTTTATTCAAAATAGG
1 ATAATTTTTTTTATAGAAACAACTAATTTTATTCAAAATAGG
2367861 A
1 A
2367862 AATATTCCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (42 bp):
ATAATTTTTTTTATAGAAACAACTAATTTTATTCAAAATAGG
Found at i:2368310 original size:23 final size:23
Alignment explanation
Indices: 2368284--2368328 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2368274 CATGCCAAAA
2368284 GAAAACGAGTAATAAATGCAGAT
1 GAAAACGAGTAATAAATGCAGAT
* * *
2368307 GAAAACGTGTCATACATGCAGA
1 GAAAACGAGTAATAAATGCAGA
2368329 ATTATTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.18
Consensus pattern (23 bp):
GAAAACGAGTAATAAATGCAGAT
Found at i:2368626 original size:17 final size:18
Alignment explanation
Indices: 2368601--2368638 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2368591 AATCTGAAAA
2368601 TTTATAATTATTATATAT
1 TTTATAATTATTATATAT
* *
2368619 TTTA-AATTTTTATGTAT
1 TTTATAATTATTATATAT
2368636 TTT
1 TTT
2368639 TTATTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTATAATTATTATATAT
Found at i:2368689 original size:25 final size:26
Alignment explanation
Indices: 2368652--2368709 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
2368642 TTTAAGATCT
**
2368652 ATTTTTTTCTTCTT-GGATTTTATAA
1 ATTTTTTTCTTCTTAAAATTTTATAA
2368677 ATTTATTTT-TTCTTAAAATTTTATAA
1 ATTT-TTTTCTTCTTAAAATTTTATAA
2368703 ATTTTTT
1 ATTTTTT
2368710 AAATTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (26 bp):
ATTTTTTTCTTCTTAAAATTTTATAA
Found at i:2370468 original size:34 final size:34
Alignment explanation
Indices: 2370425--2370508 Score: 150
Period size: 34 Copynumber: 2.5 Consensus size: 34
2370415 CCCGACCCGC
2370425 AAATATTATATATATAATTAATATAAAAAATATA
1 AAATATTATATATATAATTAATATAAAAAATATA
*
2370459 AAATATTATATATATAATTAATATAAAATATATA
1 AAATATTATATATATAATTAATATAAAAAATATA
*
2370493 AAATATTATATGTATA
1 AAATATTATATATATA
2370509 TATAATCGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (34 bp):
AAATATTATATATATAATTAATATAAAAAATATA
Found at i:2370491 original size:9 final size:9
Alignment explanation
Indices: 2370445--2370498 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
2370435 TATATAATTA
*
2370445 ATATAAAAA
1 ATATAAAAT
2370454 ATATAAAAT
1 ATATAAAAT
*
2370463 AT-T-ATAT
1 ATATAAAAT
*
2370470 ATAT-AATT
1 ATATAAAAT
2370478 AATATAAAAT
1 -ATATAAAAT
2370488 ATATAAAAT
1 ATATAAAAT
2370497 AT
1 AT
2370499 TATATGTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 5 0.14
8 4 0.11
9 25 0.68
10 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
ATATAAAAT
Found at i:2377075 original size:13 final size:13
Alignment explanation
Indices: 2377057--2377081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2377047 TGATATAAAT
2377057 ATTAAATTCATCA
1 ATTAAATTCATCA
2377070 ATTAAATTCATC
1 ATTAAATTCATC
2377082 TTTTTTTCAA
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAAATTCATCA
Found at i:2380778 original size:13 final size:14
Alignment explanation
Indices: 2380762--2380796 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2380752 TTACATTAGG
*
2380762 TTAATATTTATT-A
1 TTAAGATTTATTAA
2380775 TTAAGATTTATTAA
1 TTAAGATTTATTAA
2380789 TTAAGATT
1 TTAAGATT
2380797 AGATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (14 bp):
TTAAGATTTATTAA
Found at i:2386963 original size:2 final size:2
Alignment explanation
Indices: 2386956--2386990 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2386946 ATGAATACAA
2386956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2386991 AAAGAAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2387388 original size:23 final size:23
Alignment explanation
Indices: 2387359--2387417 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
2387349 CTCGGATGTC
* *
2387359 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATGCCCTCACATAGCTCG
2387382 CTCGGATGCCCTCACATAGCTCG
1 CTCGGATGCCCTCACATAGCTCG
* *
2387405 TTCGGATGGCCTC
1 CTCGGATGCCCTC
2387418 GGATGCTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.14, C:0.37, G:0.24, T:0.25
Consensus pattern (23 bp):
CTCGGATGCCCTCACATAGCTCG
Found at i:2387431 original size:20 final size:20
Alignment explanation
Indices: 2387406--2387459 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2387396 CATAGCTCGT
2387406 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
* *
2387426 TCGGATGGCATCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
2387446 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
2387460 TCGGATGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:2387465 original size:14 final size:14
Alignment explanation
Indices: 2387446--2387473 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2387436 TCGGATGCTT
2387446 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
2387460 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
2387474 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:2387476 original size:10 final size:10
Alignment explanation
Indices: 2387406--2387459 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
2387396 CATAGCTCGT
2387406 TCGGATGGCC
1 TCGGATGGCC
2387416 TCGGAT-GCTC
1 TCGGATGGC-C
*
2387426 TCGGATGGCA
1 TCGGATGGCC
*
2387436 TCGGAT-GCTT
1 TCGGATGGC-C
2387446 TCGGATGGCC
1 TCGGATGGCC
2387456 TCGG
1 TCGG
2387460 TCGGATGGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.11
10 29 0.78
11 4 0.11
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:2387814 original size:29 final size:28
Alignment explanation
Indices: 2387772--2387853 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 28
2387762 AACACCCCAC
2387772 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGC-CGGATGCCATGGCGACCTCCA
2387801 AGGTCGTCCGGATGCCATGGCGACCTCCA
1 AGGTCG-CCGGATGCCATGGCGACCTCCA
2387830 AGGTCGCCCGGATGCCATGGCGAC
1 AGGTCG-CCGGATGCCATGGCGAC
2387854 TAGGGTTGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 50 0.98
30 1 0.02
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (28 bp):
AGGTCGCCGGATGCCATGGCGACCTCCA
Found at i:2388025 original size:15 final size:15
Alignment explanation
Indices: 2388007--2388062 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2387997 TAACCGGTTT
2388007 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2388022 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
2388039 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2388054 CGATTTTAA
1 CGGTTTTAA
2388063 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:2388035 original size:17 final size:17
Alignment explanation
Indices: 2388010--2388060 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2388000 CCGGTTTCGG
2388010 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
2388027 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
2388042 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
2388059 TT
1 TT
2388061 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Done.