Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008193.1 Hibiscus syriacus cultivar Beakdansim tig00110812_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: 1025831
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 5
Found at i:148648 original size:21 final size:21
Alignment explanation
Indices: 148622--148671 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
148612 GGTGAACAGT
*
148622 CTATCGCAACGCCAATTCGGA
1 CTATCGCAACGCAAATTCGGA
*
148643 CTATCGCAACGCAAATTTGGA
1 CTATCGCAACGCAAATTCGGA
148664 CTATCGCA
1 CTATCGCA
148672 TTGCGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (21 bp):
CTATCGCAACGCAAATTCGGA
Found at i:148748 original size:19 final size:19
Alignment explanation
Indices: 148724--148760 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
148714 TGTGATACTG
*
148724 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
148743 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
148761 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:150581 original size:22 final size:22
Alignment explanation
Indices: 150549--150598 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
150539 ATTTAGTTGT
* *
150549 TATAACTCCTGAAATTATATCA
1 TATAACCCCTGAAATTAAATCA
*
150571 TATAACCCCTGGAATTAAATCA
1 TATAACCCCTGAAATTAAATCA
*
150593 AATAAC
1 TATAAC
150599 TCTTGTAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (22 bp):
TATAACCCCTGAAATTAAATCA
Found at i:156467 original size:22 final size:22
Alignment explanation
Indices: 156419--156472 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
156409 TTCAGCTATT
* *
156419 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
156441 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
156463 ATAACTCCTG
1 ATAACTCCTG
156473 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:162665 original size:24 final size:24
Alignment explanation
Indices: 162638--162695 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
162628 ATTTTCAACG
162638 TTTATGTTTAAAAATTTAATCATT
1 TTTATGTTTAAAAATTTAATCATT
* *
162662 TTTA-GTTTTAACAATTTAATTATT
1 TTTATG-TTTAAAAATTTAATCATT
162686 TTTAATGTTT
1 TTT-ATGTTT
162696 GTTTTTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 1 0.03
24 23 0.79
25 4 0.14
26 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (24 bp):
TTTATGTTTAAAAATTTAATCATT
Found at i:171736 original size:3 final size:3
Alignment explanation
Indices: 171711--171790 Score: 51
Period size: 3 Copynumber: 25.7 Consensus size: 3
171701 ATTTGTTTTA
*
171711 ATT ATT A-T ATT -TT AATT ATTT ATT ATTT ATT A-T ATTT AAT ATTT
1 ATT ATT ATT ATT ATT -ATT A-TT ATT A-TT ATT ATT A-TT ATT A-TT
*
171755 AAT ATT ATT AATT ATT ATT ATT ATT A-T ATTT ATT AT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT A-TT ATT AT
171791 AATATATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
2 8 0.13
3 37 0.60
4 17 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:171737 original size:7 final size:7
Alignment explanation
Indices: 171711--171790 Score: 62
Period size: 7 Copynumber: 11.7 Consensus size: 7
171701 ATTTGTTTTA
171711 ATTATTAT
1 ATTATT-T
*
171719 ATT-TTA
1 ATTATTT
171725 ATTATTT
1 ATTATTT
171732 ATTATTT
1 ATTATTT
171739 ATTATATTT
1 A-T-TATTT
*
171748 AATATTT
1 ATTATTT
*
171755 AATA-TT
1 ATTATTT
*
171761 ATTAATT
1 ATTATTT
171768 ATTA-TT
1 ATTATTT
171774 ATTA-TT
1 ATTATTT
171780 A-TATTT
1 ATTATTT
171786 ATTAT
1 ATTAT
171791 AATATATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
5 2 0.03
6 20 0.32
7 30 0.48
8 4 0.06
9 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATTATTT
Found at i:171746 original size:16 final size:16
Alignment explanation
Indices: 171727--171791 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
171717 ATATTTTAAT
171727 TATTTATTATTTATTA
1 TATTTATTATTTATTA
* *
171743 TATTTAATATTTAATA
1 TATTTATTATTTATTA
*
171759 TTATTAATTA-TTATTA
1 -TATTTATTATTTATTA
171775 T-TATTA-TATTTATTA
1 TAT-TTATTATTTATTA
171790 TA
1 TA
171792 ATATATTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 3 0.08
15 10 0.26
16 19 0.49
17 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATTATTTATTA
Found at i:171882 original size:16 final size:16
Alignment explanation
Indices: 171858--171939 Score: 72
Period size: 16 Copynumber: 5.6 Consensus size: 16
171848 TTCTATTTTA
*
171858 ATTACTATATTTATAT
1 ATTATTATATTTATAT
171874 ATTATTATATTTA-A-
1 ATTATTATATTTATAT
171888 ATTATT-TA-TTATAT
1 ATTATTATATTTATAT
*
171902 -TTA--ATAATTA-AT
1 ATTATTATATTTATAT
*
171914 ATTATTATATTTATTT
1 ATTATTATATTTATAT
*
171930 ATTATAATAT
1 ATTATTATAT
171940 GATTTTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
12 7 0.13
13 12 0.22
14 6 0.11
15 7 0.13
16 22 0.41
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:172380 original size:2 final size:2
Alignment explanation
Indices: 172373--172418 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
172363 TCTACCCTTT
172373 GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA G- GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
172413 GA GA GA
1 GA GA GA
172419 TATGTATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:172399 original size:21 final size:21
Alignment explanation
Indices: 172373--172418 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
172363 TCTACCCTTT
172373 GAGAGAGAGAGAGGAGAGAGA
1 GAGAGAGAGAGAGGAGAGAGA
172394 GAGAGAGAGAGAGGAGAGAGA
1 GAGAGAGAGAGAGGAGAGAGA
172415 GAGA
1 GAGA
172419 TATGTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (21 bp):
GAGAGAGAGAGAGGAGAGAGA
Found at i:174686 original size:57 final size:56
Alignment explanation
Indices: 174625--174733 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 56
174615 AATATTAAGA
*
174625 AATATATATATATATATAATAATAATA-AAATATAGTAAAAAATAAATAAAATAATTT
1 AATATATATATATATATAATAATAACATAAATA-A-TAAAAAATAAATAAAATAATTT
* *
174682 AATATATATATATATATAATAATAACATGAATAATAAAAAATGAATAAAATA
1 AATATATATATATATATAATAATAACATAAATAATAAAAAATAAATAAAATA
174734 TCCATATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
56 17 0.35
57 27 0.56
58 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (56 bp):
AATATATATATATATATAATAATAACATAAATAATAAAAAATAAATAAAATAATTT
Found at i:174688 original size:51 final size:55
Alignment explanation
Indices: 174628--174733 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 55
174618 ATTAAGAAAT
*
174628 ATATATATATATATAATAATAATAAAAT-ATAGTAAAAAATAAATAAAATAATTTA
1 ATATATATATATAT-ATAATAATAAAATAATAATAAAAAATAAATAAAATAATTTA
* *
174683 ATATATATATATATATAATAATAACATGAATAATAAAAAATGAATAAAATA
1 ATATATATATATATATAATAATAAAAT-AATAATAAAAAATAAATAAAATA
174734 TCCATATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
54 12 0.26
55 14 0.30
56 20 0.43
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (55 bp):
ATATATATATATATATAATAATAAAATAATAATAAAAAATAAATAAAATAATTTA
Found at i:174727 original size:14 final size:15
Alignment explanation
Indices: 174697--174733 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
174687 ATATATATAT
*
174697 ATAATAATAACATGA
1 ATAATAATAAAATGA
174712 ATAATAA-AAAATGA
1 ATAATAATAAAATGA
174726 ATAA-AATA
1 ATAATAATA
174734 TCCATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAATAATAAAATGA
Found at i:175141 original size:37 final size:37
Alignment explanation
Indices: 175091--175229 Score: 169
Period size: 37 Copynumber: 3.8 Consensus size: 37
175081 GTGCTTGTGG
* * * *
175091 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
* *
175128 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGT-T
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAAT-TCT
175165 ATCCTATTTTTAGGAGTTTGAATCCTA--A-AATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
* *
175199 ATCCTATTTTTAAGATTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
175230 GACGAAAAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 1 0.01
36 1 0.01
37 56 0.63
38 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
Found at i:175202 original size:34 final size:34
Alignment explanation
Indices: 175122--175225 Score: 147
Period size: 34 Copynumber: 3.0 Consensus size: 34
175112 ATCTTAGTAG
175122 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAGCAA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCT---AA
175159 AATGT-TATCCTATTTTTAGGAGTTTGAATCCTAA
1 AAT-TCTATCCTATTTTTAGGAGTTTGAATCCTAA
* *
175193 AATTCTATCCTATTTTTAAGATTTTGAATCCTA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTA
175226 GTAGGACGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
33 1 0.02
34 31 0.49
37 30 0.48
38 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (34 bp):
AATTCTATCCTATTTTTAGGAGTTTGAATCCTAA
Found at i:176082 original size:105 final size:105
Alignment explanation
Indices: 175775--176391 Score: 924
Period size: 105 Copynumber: 5.9 Consensus size: 105
175765 CATTGTTCCA
* * ** *
175775 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
175839 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
175881 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
175941 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
175981 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
176046 AGCGGTCCATTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
176086 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
176151 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
176191 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
176256 AGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
176296 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
*
176361 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTG
176392 TTGACGATAT
Statistics
Matches: 476, Mismatches: 27, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
100 85 0.18
101 1 0.00
102 7 0.01
104 5 0.01
105 305 0.64
106 72 0.15
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:177147 original size:36 final size:35
Alignment explanation
Indices: 177093--177333 Score: 176
Period size: 36 Copynumber: 6.9 Consensus size: 35
177083 GATTTTTTGT
* *
177093 TTCAAGAGTAACTGTCTCAAGATAGACGAAAATTGA
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
*
177129 TTCAAGAGAAACTATCTCAAGAGAGACAAAACTT-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGA
* * * *
177164 GTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGT
1 -TT-CAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
* * ** *
177202 TTCAA-AGAAAACATAT-TC---A-A-A-TATTTTGT
1 TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTGA
* * * *
177231 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
*
177267 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
*
177302 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAA
177334 CTCTTCTAGT
Statistics
Matches: 166, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.10
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 12 0.07
36 98 0.59
37 28 0.17
38 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (35 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
Found at i:177355 original size:35 final size:36
Alignment explanation
Indices: 177231--177367 Score: 127
Period size: 36 Copynumber: 3.8 Consensus size: 36
177221 AATATTTTGT
* * * * **
177231 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTAC
* *
177267 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTAC
*
177303 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTAC
* * *
177337 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
177368 TCTTGTTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
34 5 0.06
35 23 0.26
36 58 0.67
37 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTAC
Found at i:178288 original size:22 final size:22
Alignment explanation
Indices: 178262--178316 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
178252 TTGTGTTTGG
178262 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
178284 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
178306 TCAAAGGTTTG
1 TCAAAGGTTTG
178317 ATGGGACAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:179016 original size:11 final size:10
Alignment explanation
Indices: 178992--179021 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
178982 CTTGTTTCTC
*
178992 TTTTTCTTTG
1 TTTTTTTTTG
179002 TTTTTTTTTG
1 TTTTTTTTTG
179012 TTTTTTTTTG
1 TTTTTTTTTG
179022 CTTCTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:180162 original size:8 final size:8
Alignment explanation
Indices: 180146--180184 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
180136 AATGTAGATG
180146 AAAATGCA
1 AAAATGCA
*
180154 AAAAGGCA
1 AAAATGCA
180162 AAAATGC-
1 AAAATGCA
180169 AAAATGCA
1 AAAATGCA
*
180177 AGAATGCA
1 AAAATGCA
180185 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:180172 original size:15 final size:15
Alignment explanation
Indices: 180146--180184 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
180136 AATGTAGATG
180146 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
180162 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
180177 AGAATGCA
1 AAAATGCA
180185 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:183241 original size:2 final size:2
Alignment explanation
Indices: 183234--183323 Score: 89
Period size: 2 Copynumber: 46.5 Consensus size: 2
183224 TATTAAAGAA
*
183234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
183275 AT AT AGT A- AA AA AT AA AT AA AA AT A- AT -T AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183315 AT AT AT AT A
1 AT AT AT AT A
183324 ACATGAATAA
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
1 4 0.05
2 71 0.92
3 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:183762 original size:37 final size:37
Alignment explanation
Indices: 183712--183850 Score: 160
Period size: 37 Copynumber: 3.8 Consensus size: 37
183702 GTGCTTGTGG
* * * *
183712 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
* *
183749 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGT-T
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAAT-TCT
183786 ATCCTATTTTTAGGAGTTTGAATCCTA--A-AATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
* * *
183820 ATCATATTTTTAAGAGTTTGAATCATAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
183851 GACGAAAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
33 1 0.01
34 28 0.32
35 1 0.01
36 1 0.01
37 56 0.64
38 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
Found at i:184650 original size:29 final size:30
Alignment explanation
Indices: 184608--184766 Score: 196
Period size: 36 Copynumber: 5.0 Consensus size: 30
184598 AAGGAAGGGT
184608 TTACAGATGCCATGATTCGAACCTATACC-
1 TTACAGATGCCATGATTCGAACCTATACCA
184637 TTACAGATGCCATGATTCGAACCTATACC-
1 TTACAGATGCCATGATTCGAACCTATACCA
184666 TTACAGATGCCATGATTCGAACCTATACCCAA
1 TTACAGATGCCATGATTCGAACCTATA-CC-A
184698 TGGTTTACAGATGCCATGATTCGAACCTATACCCAA
1 ----TTACAGATGCCATGATTCGAACCTATA-CC-A
184734 TGGTTTACAGATGCCATGATTCGAACCTATACC
1 ----TTACAGATGCCATGATTCGAACCTATACC
184767 CAATGGCTTC
Statistics
Matches: 123, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
29 56 0.46
30 2 0.02
35 2 0.02
36 63 0.51
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (30 bp):
TTACAGATGCCATGATTCGAACCTATACCA
Found at i:184713 original size:36 final size:36
Alignment explanation
Indices: 184666--184808 Score: 250
Period size: 36 Copynumber: 4.0 Consensus size: 36
184656 AACCTATACC
184666 TTACAGATGCCATGATTCGAACCTATACCCAATGGT
1 TTACAGATGCCATGATTCGAACCTATACCCAATGGT
184702 TTACAGATGCCATGATTCGAACCTATACCCAATGGT
1 TTACAGATGCCATGATTCGAACCTATACCCAATGGT
*
184738 TTACAGATGCCATGATTCGAACCTATACCCAATGGC
1 TTACAGATGCCATGATTCGAACCTATACCCAATGGT
* * *
184774 TTCCAGATGCCATGATTCGAAACAATACCCAATGG
1 TTACAGATGCCATGATTCGAACCTATACCCAATGG
184809 ATGTCACCTA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (36 bp):
TTACAGATGCCATGATTCGAACCTATACCCAATGGT
Found at i:198156 original size:12 final size:12
Alignment explanation
Indices: 198139--198163 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
198129 TGAAGCTCGG
198139 GTTTTCAAGATT
1 GTTTTCAAGATT
198151 GTTTTCAAGATT
1 GTTTTCAAGATT
198163 G
1 G
198164 AGAGAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (12 bp):
GTTTTCAAGATT
Found at i:203965 original size:20 final size:20
Alignment explanation
Indices: 203942--203983 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
203932 CAACACGAAC
* *
203942 TCCAATTTCGTAACACAGTT
1 TCCAAATTCGAAACACAGTT
*
203962 TCCAAATTCGAAACTCAGTT
1 TCCAAATTCGAAACACAGTT
203982 TC
1 TC
203984 TGAAATCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (20 bp):
TCCAAATTCGAAACACAGTT
Found at i:204014 original size:20 final size:21
Alignment explanation
Indices: 203980--204066 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
203970 CGAAACTCAG
203980 TTTCTGAAA-TCGCAACGCGAA
1 TTTCT-AAATTCGCAACGCGAA
**
204001 TTTCT-TTTTCGCAACGCAGAA
1 TTTCTAAATTCGCAACGC-GAA
*
204022 TTT-TAAATTCGCAACTCG-A
1 TTTCTAAATTCGCAACGCGAA
* *
204041 TTTCTGAATTCGCAACTCGAA
1 TTTCTAAATTCGCAACGCGAA
204062 TTTCT
1 TTTCT
204067 TTTCGGAACA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
19 4 0.07
20 25 0.45
21 26 0.47
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (21 bp):
TTTCTAAATTCGCAACGCGAA
Found at i:204115 original size:20 final size:20
Alignment explanation
Indices: 204092--204177 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
204082 TTCCTTTTCA
204092 CAACAAGATTTTCTAATTCG
1 CAACAAGATTTTCTAATTCG
* * *
204112 CAACACAAATTTTGT-TTTCG
1 CAACA-AGATTTTCTAATTCG
** *
204132 CAACTCGATTTTCAAATTCG
1 CAACAAGATTTTCTAATTCG
* *
204152 CAACACGAATTT-TAATTTCG
1 CAACAAGATTTTCTAA-TTCG
204172 CAACAA
1 CAACAA
204178 CTTTTATTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
19 7 0.14
20 36 0.72
21 7 0.14
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (20 bp):
CAACAAGATTTTCTAATTCG
Found at i:204164 original size:40 final size:40
Alignment explanation
Indices: 203989--204175 Score: 132
Period size: 40 Copynumber: 4.7 Consensus size: 40
203979 GTTTCTGAAA
* *
203989 TCGCAACGCGAATTTCT-TTTTCGCAACGCAGAATTTT-AAAT
1 TCGCAACACGAATTT-TGTTTTCGCAACTC-G-ATTTTCAAAT
* ** * **
204030 TCGCAACTCG-ATTTCTGAATTCGCAACTCGAATTTC-TTT
1 TCGCAACACGAATTT-TGTTTTCGCAACTCGATTTTCAAAT
* ** * ** *
204069 TCGGAACAC-AAGTTTCCTTTTCACAACAAGATTTTCTAAT
1 TCGCAACACGAA-TTTTGTTTTCGCAACTCGATTTTCAAAT
*
204109 TCGCAACACAAATTTTGTTTTCGCAACTCGATTTTCAAAT
1 TCGCAACACGAATTTTGTTTTCGCAACTCGATTTTCAAAT
**
204149 TCGCAACACGAATTTTAATTTCGCAAC
1 TCGCAACACGAATTTTGTTTTCGCAAC
204176 AACTTTTATT
Statistics
Matches: 111, Mismatches: 29, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
39 26 0.23
40 65 0.59
41 20 0.18
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (40 bp):
TCGCAACACGAATTTTGTTTTCGCAACTCGATTTTCAAAT
Found at i:205137 original size:24 final size:24
Alignment explanation
Indices: 205110--205163 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
205100 GTATTTGAAA
205110 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
205134 TTTGATCTTGGTTAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
205158 TTTGAT
1 TTTGAT
205164 GATGTTTCAG
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:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:207455 original size:6 final size:6
Alignment explanation
Indices: 207433--207496 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
207423 AAGAAAAAGG
* * * *
207433 AAATCA AAATCG CAATCA AAATCA AAATCG CAATCA AAATCA AAAT-A
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
207480 ACAATCA AAATCA AAAT
1 A-AATCA AAATCA AAAT
207497 AGCAATCACA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 2 0.04
6 44 0.92
7 2 0.04
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:207456 original size:18 final size:18
Alignment explanation
Indices: 207433--207504 Score: 117
Period size: 18 Copynumber: 4.0 Consensus size: 18
207423 AAGAAAAAGG
*
207433 AAATCAAAATCGCAATCA
1 AAATCAAAATAGCAATCA
*
207451 AAATCAAAATCGCAATCA
1 AAATCAAAATAGCAATCA
*
207469 AAATCAAAATAACAATCA
1 AAATCAAAATAGCAATCA
207487 AAATCAAAATAGCAATCA
1 AAATCAAAATAGCAATCA
207505 CAACCGGCTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (18 bp):
AAATCAAAATAGCAATCA
Found at i:207857 original size:49 final size:49
Alignment explanation
Indices: 207792--207886 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
207782 TGAAAATAAA
* *
207792 AATCGCAACGCAAATTTGACTTTCGCGTTGCGAATCTGACTTTCGCAAC
1 AATCGCAACGCAAATTTGACTTTCGCATTGCGAATCTGAATTTCGCAAC
* * * *
207841 AATCGTAACGCGAATTTGACTTTCGCATTGTGAATTTGAATTTCGC
1 AATCGCAACGCAAATTTGACTTTCGCATTGCGAATCTGAATTTCGC
207887 GTTACGAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (49 bp):
AATCGCAACGCAAATTTGACTTTCGCATTGCGAATCTGAATTTCGCAAC
Found at i:207895 original size:20 final size:20
Alignment explanation
Indices: 207851--207896 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
207841 AATCGTAACG
* *
207851 CGAATTTGACTTTCGCATTG
1 CGAATTTGAATTTCGCATTA
* *
207871 TGAATTTGAATTTCGCGTTA
1 CGAATTTGAATTTCGCATTA
207891 CGAATT
1 CGAATT
207897 CGATTTTCCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
CGAATTTGAATTTCGCATTA
Found at i:209430 original size:21 final size:21
Alignment explanation
Indices: 209404--209557 Score: 139
Period size: 21 Copynumber: 7.3 Consensus size: 21
209394 AGTATGCCAT
*
209404 GTGGATCCTGAACGGTGGGAG
1 GTGGATCCTGAACGATGGGAG
*
209425 GTGGATCCTGAACGGTGGGAG
1 GTGGATCCTGAACGATGGGAG
*
209446 GTGGATCCTGAACGATGGAAG
1 GTGGATCCTGAACGATGGGAG
* * *
209467 G-GGCCTCTTGAACTATGGGAG
1 GTGG-ATCCTGAACGATGGGAG
** * **
209488 GTGCCTCTTGAACGATGACAG
1 GTGGATCCTGAACGATGGGAG
* * *
209509 ATGAATCCTGAACAATGGGAG
1 GTGGATCCTGAACGATGGGAG
* * *
209530 GTGGATCCTAAACAATGGTAG
1 GTGGATCCTGAACGATGGGAG
209551 GTGGATC
1 GTGGATC
209558 GGGCTTTCTC
Statistics
Matches: 110, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 2 0.02
21 107 0.97
22 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.21
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:209941 original size:63 final size:64
Alignment explanation
Indices: 209874--210019 Score: 179
Period size: 63 Copynumber: 2.3 Consensus size: 64
209864 GTAACGTAGA
* * * *
209874 TACCTCACCACGTAAAGCACCATTGTCATCACGTAAAATAGCTACCTCACCACGTAAAG-ACCG
1 TACCTCATCACGTAAAGCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCG
** * ** * *
209937 TACCTCATCACGCCATGCACCATTGTTGTCACGTAAAGTACCGACCTCATCACGCAAAGCACCG
1 TACCTCATCACGTAAAGCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCG
210001 -ACCTCATCACGTAAAGCAC
1 TACCTCATCACGTAAAGCAC
210020 TGGCCTCATC
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 64 0.94
64 4 0.06
ACGTcount: A:0.32, C:0.35, G:0.14, T:0.19
Consensus pattern (64 bp):
TACCTCATCACGTAAAGCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCG
Found at i:209945 original size:42 final size:42
Alignment explanation
Indices: 209854--209948 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
209844 TAGAGCGGCT
**
209854 TCCTCATCACGTAACGTAGATACCTCACCACGTAAAGCACCA
1 TCCTCATCACGTAAAATAGATACCTCACCACGTAAAGCACCA
** * *
209896 TTGTCATCACGTAAAATAGCTACCTCACCACGTAAAG-ACCG
1 TCCTCATCACGTAAAATAGATACCTCACCACGTAAAGCACCA
209937 TACCTCATCACG
1 T-CCTCATCACG
209949 CCATGCACCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.09
42 40 0.91
ACGTcount: A:0.33, C:0.34, G:0.13, T:0.21
Consensus pattern (42 bp):
TCCTCATCACGTAAAATAGATACCTCACCACGTAAAGCACCA
Found at i:209989 original size:21 final size:21
Alignment explanation
Indices: 209965--210035 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
209955 ACCATTGTTG
*
209965 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
209986 TCACGCAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
210007 TCACGTAAAGCACTGGCCTCA
1 TCACGTAAAGCACCGACCTCA
*
210028 TCATGTAA
1 TCACGTAA
210036 CTCCCCTAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:210011 original size:42 final size:40
Alignment explanation
Indices: 209917--210030 Score: 102
Period size: 42 Copynumber: 2.7 Consensus size: 40
209907 TAAAATAGCT
* * *
209917 ACCTCACCACGTAAAGACCGTACCTCATCACGCCATGCACC
1 ACCTCATCACGTAAAGACCG-ACCTCATCACGCAAAGCACC
** **
209958 ATTGTTGTCACGTAAAGTACCGACCTCATCACGCAAAGCACC
1 A-CCTCATCACGTAAAG-ACCGACCTCATCACGCAAAGCACC
* *
210000 GACCTCATCACGTAAAGCACTGGCCTCATCA
1 -ACCTCATCACGTAAAG-ACCGACCTCATCA
210031 TGTAACTCCC
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
41 1 0.02
42 50 0.89
43 5 0.09
ACGTcount: A:0.30, C:0.37, G:0.15, T:0.18
Consensus pattern (40 bp):
ACCTCATCACGTAAAGACCGACCTCATCACGCAAAGCACC
Found at i:210211 original size:42 final size:42
Alignment explanation
Indices: 210150--210248 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
210140 ATGATGGAAT
* * *
210150 AGGTGATGGCTCTCAGTGTCTAGGTGTATAATCAGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCAGCTCGATC
* *
210192 AGGTGATGGCTCTCGGTGTCGAGTTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCAGCTCGATC
210234 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
210249 AAGTGGGGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.29
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCAGCTCGATC
Found at i:211838 original size:14 final size:15
Alignment explanation
Indices: 211819--211851 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
211809 TGCGAATTTC
211819 ATTTTCGCGTTGC-A
1 ATTTTCGCGTTGCGA
*
211833 ATTTTCGTGTTGCGA
1 ATTTTCGCGTTGCGA
211848 ATTT
1 ATTT
211852 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (15 bp):
ATTTTCGCGTTGCGA
Found at i:212388 original size:20 final size:20
Alignment explanation
Indices: 212363--212422 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
212353 TTCGAATTCA
212363 AAAATAAAATTCGCGTTGCG
1 AAAATAAAATTCGCGTTGCG
** *
212383 AAAAT-AAACGCGCTTTGCG
1 AAAATAAAATTCGCGTTGCG
*
212402 -AATTACAAATTCGCGTTGCG
1 AAAATA-AAATTCGCGTTGCG
212422 A
1 A
212423 TTTCAGAAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 3 0.10
19 11 0.37
20 16 0.53
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
AAAATAAAATTCGCGTTGCG
Found at i:212439 original size:20 final size:19
Alignment explanation
Indices: 212416--212462 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
212406 ACAAATTCGC
212416 GTTGCGATTTCAGAAACTGA
1 GTTGCGATTT-AGAAACTGA
* *
212436 GTTGCGAATTTGGAAACTGT
1 GTTGCG-ATTTAGAAACTGA
212456 GTTGCGA
1 GTTGCGA
212463 AATTGGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 19 0.79
21 4 0.17
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (19 bp):
GTTGCGATTTAGAAACTGA
Found at i:212463 original size:20 final size:20
Alignment explanation
Indices: 212428--212469 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
212418 TGCGATTTCA
*
212428 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
212448 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
212468 GA
1 GA
212470 GTTCGCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:213680 original size:42 final size:42
Alignment explanation
Indices: 213633--213873 Score: 183
Period size: 41 Copynumber: 5.8 Consensus size: 42
213623 AAAATGATAC
* *
213633 TTTAGCGGCGTTTTTTAAACAAACACCGTAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * *
213675 TTTAGCGGC-ATTTTT-AGCTAAAACGCCGCAATAGA-TATGT--
1 TTTAGCGGCGTTTTTTAAAC--AAACGCCGCAATAGAGT-GGTAA
* * *
213715 TTATAGTGGCGTTTTTTCAACAAACGCCACAATAGAGTGGTAA
1 TT-TAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * *
213758 TTTAGCGGCG-TTTTTACACAAACGCCGCGATAGTGTTGT--
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * * * **
213797 TTATAGTGGCGTTTGTTCAACAAACGACGCTATAGAGAAGTAA
1 TT-TAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * *
213840 TTTCGCGGCGTTTATCAAACAAACGCCGCAATAG
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAG
213874 TATTGTTTAT
Statistics
Matches: 153, Mismatches: 33, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
39 2 0.01
40 11 0.07
41 72 0.47
42 62 0.41
43 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
Found at i:213730 original size:41 final size:39
Alignment explanation
Indices: 213695--213949 Score: 133
Period size: 41 Copynumber: 6.3 Consensus size: 39
213685 TTTTTAGCTA
*
213695 AAACGCCGCAATAGATATGTTTATAGTGGCGTTTTTTCAAC
1 AAACGCCGCAATAGAT-TGTTTATAGTGGCGTTTTTAC-AC
* * *
213736 AAACGCCACAATAGAGTGGTAATT-TAGCGGCGTTTTTACAC
1 AAACGCCGCAATAGA-TTGT--TTATAGTGGCGTTTTTACAC
* *
213777 AAACGCCGCGATAGTGTTGTTTATAGTGGCGTTTGTT-CAAC
1 AAACGCCGCAATAG-ATTGTTTATAGTGGCGTTT-TTAC-AC
* * ** * * * *
213818 AAACGACGCTATAGAGAAGTAATT-TCGCGGCGTTTATCAAAC
1 AAACGCCGCAATAGA-TTGT--TTATAGTGGCGTTT-TTACAC
* * * *
213860 AAACGCCGCAATAGTATTGTTTATAGTGGCATTTGTGCAA
1 AAACGCCGCAATAG-ATTGTTTATAGTGGCGTTTTTACAC
* * * * *
213900 AAAAGCCGCAATATG-TTGTTTATCGTGACGTTTATATTA-
1 AAACGCCGCAATA-GATTGTTTATAGTGGCGTTTTTA-CAC
213939 AAACGCCGCAA
1 AAACGCCGCAA
213950 AAGGGTCAAT
Statistics
Matches: 160, Mismatches: 39, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
39 28 0.17
40 27 0.17
41 60 0.38
42 40 0.25
43 5 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (39 bp):
AAACGCCGCAATAGATTGTTTATAGTGGCGTTTTTACAC
Found at i:213809 original size:82 final size:81
Alignment explanation
Indices: 213639--213912 Score: 309
Period size: 83 Copynumber: 3.3 Consensus size: 81
213629 ATACTTTAGC
* * * *
213639 GGCGTTTTTTAAACAAACACCGTAATAGAGTGGTAATTTAGCGGCATTTTTAGCTA-AAACGCCG
1 GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTA-C-ACAAACGCCG
*
213703 CAATAGATATGTTTATAGT
64 CAATAG-TTTGTTTATAGT
* *
213722 GGCGTTTTTTCAACAAACGCCACAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGCCGCG
1 GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGCCGCA
213787 ATAGTGTTGTTTATAGT
66 ATAGT-TTGTTTATAGT
* * * ** * * *
213804 GGCGTTTGTTCAACAAACGACGCTATAGAGAAGTAATTTCGCGGCGTTTATCAAACAAACGCCGC
1 GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTT-TTACACAAACGCCGC
213869 AATAGTATTGTTTATAGT
65 AATAGT-TTGTTTATAGT
* * * *
213887 GGCATTTGTGCAA-AAAAGCCGCAATA
1 GGCGTTTTTTCAACAAACGCCGCAATA
213913 TGTTGTTTAT
Statistics
Matches: 165, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
81 2 0.01
82 76 0.46
83 87 0.53
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (81 bp):
GGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGCCGCA
ATAGTTTGTTTATAGT
Found at i:213895 original size:83 final size:82
Alignment explanation
Indices: 213695--213895 Score: 269
Period size: 82 Copynumber: 2.4 Consensus size: 82
213685 TTTTTAGCTA
* * **
213695 AAACGCCGCAATAG-ATATGTTTATAGTGGCGTTTTTTCAACAAACGCCACAATAGAGTGGTAAT
1 AAACGCCGCAATAGTAT-TGTTTATAGTGGCGTTTGTTCAACAAACGACACAATAGAGAAGTAAT
* *
213759 TTAGCGGCGTTTTTACAC
65 TTAGCGGCGTTTTCAAAC
* * * *
213777 AAACGCCGCGATAGTGTTGTTTATAGTGGCGTTTGTTCAACAAACGACGCTATAGAGAAGTAATT
1 AAACGCCGCAATAGTATTGTTTATAGTGGCGTTTGTTCAACAAACGACACAATAGAGAAGTAATT
*
213842 TCGCGGCGTTTATCAAAC
66 TAGCGGCGTTT-TCAAAC
*
213860 AAACGCCGCAATAGTATTGTTTATAGTGGCATTTGT
1 AAACGCCGCAATAGTATTGTTTATAGTGGCGTTTGT
213896 GCAAAAAAGC
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
82 65 0.63
83 38 0.37
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (82 bp):
AAACGCCGCAATAGTATTGTTTATAGTGGCGTTTGTTCAACAAACGACACAATAGAGAAGTAATT
TAGCGGCGTTTTCAAAC
Found at i:217937 original size:19 final size:19
Alignment explanation
Indices: 217900--217968 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
217890 TTTAAGTAGG
*
217900 TGCATCGATG--CTACTTA
1 TGCATCGATGCACTCCTTA
217917 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
217936 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
217955 TGCATCGATGCACT
1 TGCATCGATGCACT
217969 AATGCATTCG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
17 10 0.20
19 39 0.80
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:230744 original size:44 final size:44
Alignment explanation
Indices: 230644--230780 Score: 120
Period size: 45 Copynumber: 3.1 Consensus size: 44
230634 AAATATTAAC
* * * ** *
230644 ACCTATTGCGGCGTTTGTAT-CAAAAAACGCCGCTATGCACC-A
1 ACCTATAGCGGCGTTTGTATCCTAAAAACTCCGCTATATACCTG
* * *
230686 ACTTTTAACGGCGTTTGTATCCTAAAAACTCCGCTATATACCTG
1 ACCTATAGCGGCGTTTGTATCCTAAAAACTCCGCTATATACCTG
* *
230730 ACCTATAGCGGCGTTTTGTACCCTAAAAA-TGCCGCTAAATA-CTAG
1 ACCTATAGCGGCG-TTTGTATCCTAAAAACT-CCGCTATATACCT-G
230775 ACCTAT
1 ACCTAT
230781 TGCGACATTT
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
42 16 0.21
43 17 0.22
44 13 0.17
45 30 0.39
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
ACCTATAGCGGCGTTTGTATCCTAAAAACTCCGCTATATACCTG
Found at i:230757 original size:45 final size:44
Alignment explanation
Indices: 230604--230780 Score: 119
Period size: 45 Copynumber: 4.0 Consensus size: 44
230594 GTCAAATATT
* ** * * *
230604 TAGCGGCGTTTGTATCAGAAAAATGCCGCGAAATATTAACACCTA
1 TAGCGGCGTTTGTACCCTAAAAATGCCGCTAAATACT-AGACCTA
* * * * *** * * *
230649 TTGCGGCGTTTGTA-TCAAAAAACGCCGCTATGCACCA-ACTTT
1 TAGCGGCGTTTGTACCCTAAAAATGCCGCTAAATACTAGACCTA
* * *
230691 TAACGGCGTTTGTATCCTAAAAACT-CCGCTATATACCT-GACCTA
1 TAGCGGCGTTTGTACCCTAAAAA-TGCCGCTAAATA-CTAGACCTA
230735 TAGCGGCGTTTTGTACCCTAAAAATGCCGCTAAATACTAGACCTA
1 TAGCGGCG-TTTGTACCCTAAAAATGCCGCTAAATACTAGACCTA
230780 T
1 T
230781 TGCGACATTT
Statistics
Matches: 99, Mismatches: 26, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
42 15 0.15
43 15 0.15
44 26 0.26
45 43 0.43
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
TAGCGGCGTTTGTACCCTAAAAATGCCGCTAAATACTAGACCTA
Found at i:230869 original size:43 final size:40
Alignment explanation
Indices: 230753--230871 Score: 112
Period size: 43 Copynumber: 2.8 Consensus size: 40
230743 TTTTGTACCC
*
230753 TAAAAATGCCGCTAAATACTAGACCTATTGCGACATTTTCA
1 TAAAAATGCCGCTAAATA-TAAACCTATTGCGACATTTTCA
* * * * *
230794 TAAAAAAATACCGCGAAATATCAACACTTATTGCGACGTTTGTGA
1 T--AAAAATGCCGCTAAATAT-AA-ACCTATTGCGACATTT-TCA
230839 TAAAAATGCCGCTAAATATTGAAACCTATTGCG
1 TAAAAATGCCGCTAAATA-T-AAACCTATTGCG
230872 GTGTTTTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.02
42 1 0.02
43 40 0.65
44 17 0.27
45 3 0.05
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (40 bp):
TAAAAATGCCGCTAAATATAAACCTATTGCGACATTTTCA
Found at i:230893 original size:43 final size:43
Alignment explanation
Indices: 230804--230959 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 43
230794 TAAAAAAATA
* * * * * * *
230804 CCGCGAAATATCAACACTTATTGCGACGTTTGTGATAA-AAATG
1 CCGCTAAATATCGATACCTATTGCGGCGTTTGTTA-AACAAACG
* * *
230847 CCGCTAAATATTGAAACCTATTGCGGTGTTT-TTAAGACAAACG
1 CCGCTAAATATCGATACCTATTGCGGCGTTTGTTAA-ACAAACG
* * *
230890 CCGCTAAATATCGGTACCTATTGTGGCGTTTGTTAAACAAGCG
1 CCGCTAAATATCGATACCTATTGCGGCGTTTGTTAAACAAACG
* * *
230933 CCACTATATATCGTTACCTATTGCGGC
1 CCGCTAAATATCGATACCTATTGCGGC
230960 ATTTTTGGTT
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 83 0.91
44 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (43 bp):
CCGCTAAATATCGATACCTATTGCGGCGTTTGTTAAACAAACG
Found at i:231649 original size:94 final size:94
Alignment explanation
Indices: 231488--231746 Score: 369
Period size: 94 Copynumber: 2.7 Consensus size: 94
231478 TCTTACCATC
* *
231488 TGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTA-AGGGACAACTTAAGCTTTATT
1 TGAATCTTATCCATAAAGCTGGGGCG-TTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATT
*
231552 GTATATTATAATCACCTTTATCAGGCTAGA
65 GTATATCATAATCACCTTTATCAGGCTAGA
* *
231582 TGAATCTTATTCATAAAGCTGAGGCGTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATTG
1 TGAATCTTATCCATAAAGCTGGGGCGTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATTG
* *
231647 TATCTCATAATCACCTTTATCAGGCTAGC
66 TATATCATAATCACCTTTATCAGGCTAGA
* * * *
231676 TAAATCTTATCCATAAAG-TCGGGGCATTTAACCAATTGCTCTAGAGGGACATCTCAAGCTTTAT
1 TGAATCTTATCCATAAAGCT-GGGGC-GTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTAT
*
231740 TATATAT
64 TGTATAT
231747 AAATATAATT
Statistics
Matches: 147, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
93 17 0.12
94 90 0.61
95 40 0.27
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (94 bp):
TGAATCTTATCCATAAAGCTGGGGCGTTAACCAATTGCTCTAGAGGGACAACTTAAGCTTTATTG
TATATCATAATCACCTTTATCAGGCTAGA
Found at i:260309 original size:21 final size:20
Alignment explanation
Indices: 260279--260342 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
260269 ATATCCAGAA
260279 CCCTCGGGGGGTATCGATTC
1 CCCTCGGGGGGTATCGATTC
* *
260299 CCCTACGGGGGGAATCGGTTC
1 CCCT-CGGGGGGTATCGATTC
*
260320 CCCTTCAGGGGGTATCGATTC
1 CCC-TCGGGGGGTATCGATTC
260341 CC
1 CC
260343 TCTGCACCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 4 0.11
21 32 0.86
22 1 0.03
ACGTcount: A:0.12, C:0.31, G:0.33, T:0.23
Consensus pattern (20 bp):
CCCTCGGGGGGTATCGATTC
Found at i:261601 original size:44 final size:45
Alignment explanation
Indices: 261538--261623 Score: 156
Period size: 44 Copynumber: 1.9 Consensus size: 45
261528 GAACCAATAT
261538 TATCATCAACATAAATTTGAACTACTAAT-AATCTTTACCTTATA
1 TATCATCAACATAAATTTGAACTACTAATAAATCTTTACCTTATA
*
261582 TATCATCAACTTAAATTTGAACTACTAATAAATCTTTACCTT
1 TATCATCAACATAAATTTGAACTACTAATAAATCTTTACCTT
261624 TATGCTTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 28 0.70
45 12 0.30
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (45 bp):
TATCATCAACATAAATTTGAACTACTAATAAATCTTTACCTTATA
Found at i:267705 original size:187 final size:187
Alignment explanation
Indices: 267390--267763 Score: 748
Period size: 187 Copynumber: 2.0 Consensus size: 187
267380 CAAGCACTCG
267390 GGCTAGAATTAATCTCATTAGGCCCCAAGAATTAGAGACGATAACTGCATCTCCTTAGTAGGGTC
1 GGCTAGAATTAATCTCATTAGGCCCCAAGAATTAGAGACGATAACTGCATCTCCTTAGTAGGGTC
267455 CCTGTGACCCTTTTTCTCTATGTCCCTTTTTAAGTGTCTTATTGCATTTTCAGATAGAGCATTAC
66 CCTGTGACCCTTTTTCTCTATGTCCCTTTTTAAGTGTCTTATTGCATTTTCAGATAGAGCATTAC
267520 CTCCAAGTAGTCGAAACACAAGAAAAACTTTTTCGCCACCATTTAAAATCTTCTATT
131 CTCCAAGTAGTCGAAACACAAGAAAAACTTTTTCGCCACCATTTAAAATCTTCTATT
267577 GGCTAGAATTAATCTCATTAGGCCCCAAGAATTAGAGACGATAACTGCATCTCCTTAGTAGGGTC
1 GGCTAGAATTAATCTCATTAGGCCCCAAGAATTAGAGACGATAACTGCATCTCCTTAGTAGGGTC
267642 CCTGTGACCCTTTTTCTCTATGTCCCTTTTTAAGTGTCTTATTGCATTTTCAGATAGAGCATTAC
66 CCTGTGACCCTTTTTCTCTATGTCCCTTTTTAAGTGTCTTATTGCATTTTCAGATAGAGCATTAC
267707 CTCCAAGTAGTCGAAACACAAGAAAAACTTTTTCGCCACCATTTAAAATCTTCTATT
131 CTCCAAGTAGTCGAAACACAAGAAAAACTTTTTCGCCACCATTTAAAATCTTCTATT
267764 TCAACATTTT
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (187 bp):
GGCTAGAATTAATCTCATTAGGCCCCAAGAATTAGAGACGATAACTGCATCTCCTTAGTAGGGTC
CCTGTGACCCTTTTTCTCTATGTCCCTTTTTAAGTGTCTTATTGCATTTTCAGATAGAGCATTAC
CTCCAAGTAGTCGAAACACAAGAAAAACTTTTTCGCCACCATTTAAAATCTTCTATT
Found at i:268176 original size:42 final size:42
Alignment explanation
Indices: 268063--268176 Score: 174
Period size: 42 Copynumber: 2.7 Consensus size: 42
268053 TTCGGGAGGT
*
268063 GGAGACGCAGCAGGAGACTCCGCTGAAGGTTTCTCGACTGGC
1 GGAGACGCAGCAGGAGACTCCGCGGAAGGTTTCTCGACTGGC
* * *
268105 GGAGACGCAGAAGGAGACTCCGCGAAAGGTTTTTCGACTGGC
1 GGAGACGCAGCAGGAGACTCCGCGGAAGGTTTCTCGACTGGC
**
268147 GGAGACGCAGCAGGAGACTCTACGGAAGGT
1 GGAGACGCAGCAGGAGACTCCGCGGAAGGT
268177 GCCAGAGGTG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.25, C:0.23, G:0.37, T:0.15
Consensus pattern (42 bp):
GGAGACGCAGCAGGAGACTCCGCGGAAGGTTTCTCGACTGGC
Found at i:270165 original size:30 final size:30
Alignment explanation
Indices: 270125--270248 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
270115 CAGAAACTTG
* *
270125 AGGACCAAAATAGCAAAAGCAAAAACCTAA
1 AGGACAAAAATAGCAAAAACAAAAACCTAA
* *
270155 AGGACAAAAATAGCAAAAACATAAACTTAA
1 AGGACAAAAATAGCAAAAACAAAAACCTAA
* * *
270185 AGGACTAAAATAGCACAAAA-AGAAACTTAA
1 AGGACAAAAATAGCA-AAAACAAAAACCTAA
* * * * **
270215 AAGACTAAAATAACACAAACAAAAATTTAA
1 AGGACAAAAATAGCAAAAACAAAAACCTAA
270245 AGGA
1 AGGA
270249 TTGAATAATA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
29 3 0.04
30 73 0.91
31 4 0.05
ACGTcount: A:0.62, C:0.15, G:0.11, T:0.12
Consensus pattern (30 bp):
AGGACAAAAATAGCAAAAACAAAAACCTAA
Found at i:270199 original size:60 final size:60
Alignment explanation
Indices: 270125--270248 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
270115 CAGAAACTTG
* * *
270125 AGGACCAAAATAGCA-AAAGCAA-AAACCTAAAGGACAAAAATAGCAAAAACATAAACTTAA
1 AGGACCAAAATAGCACAAA--AAGAAACCTAAAAGACAAAAATAACAAAAACAAAAACTTAA
* * * * *
270185 AGGACTAAAATAGCACAAAAAGAAACTTAAAAGACTAAAATAACACAAACAAAAATTTAA
1 AGGACCAAAATAGCACAAAAAGAAACCTAAAAGACAAAAATAACAAAAACAAAAACTTAA
270245 AGGA
1 AGGA
270249 TTGAATAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.04
60 49 0.91
61 3 0.06
ACGTcount: A:0.62, C:0.15, G:0.11, T:0.12
Consensus pattern (60 bp):
AGGACCAAAATAGCACAAAAAGAAACCTAAAAGACAAAAATAACAAAAACAAAAACTTAA
Found at i:273327 original size:20 final size:20
Alignment explanation
Indices: 273269--273321 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
273259 GTAATCCTAT
*
273269 CACTGGTAATCTTTTATTCC
1 CACTGATAATCTTTTATTCC
273289 CACTGATAATCTTTTATTCC
1 CACTGATAATCTTTTATTCC
273309 CACTGATAATCTT
1 CACTGATAATCTT
273322 ACATTCTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.43
Consensus pattern (20 bp):
CACTGATAATCTTTTATTCC
Found at i:274093 original size:3 final size:3
Alignment explanation
Indices: 274085--274126 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
274075 TGTAAAACAA
274085 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT -AT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
274127 TATTTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:277708 original size:13 final size:13
Alignment explanation
Indices: 277680--277745 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
277670 AAAATAAAAA
277680 AAATATAATATTAT
1 AAATAT-ATATTAT
*
277694 AAATATATTTTAT
1 AAATATATATTAT
*
277707 AAATTTATATTAT
1 AAATATATATTAT
**
277720 ATTTGATATA-T-T
1 AAAT-ATATATTAT
277732 AAATA-ATATTAT
1 AAATATATATTAT
277744 AA
1 AA
277746 TGTGAAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 3 0.07
11 2 0.05
12 6 0.15
13 20 0.49
14 10 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
AAATATATATTAT
Found at i:277768 original size:2 final size:2
Alignment explanation
Indices: 277763--277800 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
277753 AAAATATGAA
277763 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
277801 GATTAGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:285232 original size:15 final size:15
Alignment explanation
Indices: 285208--285237 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
285198 CCGTAGGACC
285208 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
285223 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
285238 GCCATTATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:285369 original size:29 final size:29
Alignment explanation
Indices: 285326--285493 Score: 311
Period size: 29 Copynumber: 5.8 Consensus size: 29
285316 TTTTATATGT
285326 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
285354 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
285383 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
285412 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
285441 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
285470 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
285494 ATATCACATA
Statistics
Matches: 136, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
28 7 0.05
29 124 0.91
30 5 0.04
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:292332 original size:29 final size:29
Alignment explanation
Indices: 292296--292427 Score: 237
Period size: 29 Copynumber: 4.5 Consensus size: 29
292286 TGTTCACGTA
292296 CTCATGTCATTTCTCTTGTGATCATGTAG
1 CTCATGTCATTTCTCTTGTGATCATGTAG
* *
292325 TTTATGTCATTTCTCTTGTGATCATGTAG
1 CTCATGTCATTTCTCTTGTGATCATGTAG
292354 CTCATGTCATTTCTCTTGTGATCATGTAG
1 CTCATGTCATTTCTCTTGTGATCATGTAG
292383 CTCATGTCATTTCTCTTGTGATCATGTAG
1 CTCATGTCATTTCTCTTGTGATCATGTAG
292412 CTCATGTCATGTTCTC
1 CTCATGTCAT-TTCTC
292428 ATATCACATA
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 93 0.95
30 5 0.05
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (29 bp):
CTCATGTCATTTCTCTTGTGATCATGTAG
Found at i:294230 original size:30 final size:30
Alignment explanation
Indices: 294194--294257 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
294184 GAAGAACCTG
* *
294194 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
294224 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
294254 TCCA
1 TCCA
294258 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:295024 original size:64 final size:62
Alignment explanation
Indices: 294936--295142 Score: 199
Period size: 64 Copynumber: 3.2 Consensus size: 62
294926 CAATGAAGGT
* *
294936 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATTAATGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCAT-AAATGCATTCGATGTTTCCTTATTAA-GAG
* * * *
295000 ATGCATCGATGCA-TACCTTATGCATCGATGCACTAATTGCATTTGATG-TTCTATTATTAAAAG
1 ATGCATCGATGCACTA-CTTATGCATCGATGCA-TAAATGCATTCGATGTTTC-CTTATTAAGA-
295063 G
62 G
* * *
295064 ATGCATCGATGCATTA-TCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTT-TTAA-AG
1 ATGCATCGATGCACTACT-TATGCATCGATGCAT-AAATGCATTCGATGTT-TCCTTATTAAGA-
295126 G
62 G
295127 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
295143 TATGAATGTG
Statistics
Matches: 121, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
63 11 0.09
64 103 0.85
65 6 0.05
66 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATGCATTCGATGTTTCCTTATTAAGAG
Found at i:299148 original size:20 final size:20
Alignment explanation
Indices: 299112--299149 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
299102 GTTACACCTA
*
299112 AAATGTTATAAAGATAAAAG
1 AAATGTTATAAAAATAAAAG
299132 AAAT-TTATAAATAATAAA
1 AAATGTTATAAA-AATAAA
299150 TGTTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAATGTTATAAAAATAAAAG
Found at i:299364 original size:41 final size:41
Alignment explanation
Indices: 299319--299444 Score: 109
Period size: 37 Copynumber: 3.2 Consensus size: 41
299309 AATAAGAAAC
*
299319 GGGTTGCGATCTGGAATGTTAATATTTTTATTTAATAAAAT
1 GGGTTGCGATCTAGAATGTTAATATTTTTATTTAATAAAAT
*** * * * * *
299360 GGGTTGCCCCCAAGAATGTT-AT-TGTTCA-CTAA-GAAAT
1 GGGTTGCGATCTAGAATGTTAATATTTTTATTTAATAAAAT
* * *
299397 AGTTTGCGATCTAGAATGTTAATATTTTT-TTAAATAAAAT
1 GGGTTGCGATCTAGAATGTTAATATTTTTATTTAATAAAAT
299437 GGGTTGCG
1 GGGTTGCG
299445 CCCAGGAATA
Statistics
Matches: 59, Mismatches: 22, Indels: 9
0.66 0.24 0.10
Matches are distributed among these distances:
37 18 0.31
38 5 0.08
39 9 0.15
40 12 0.20
41 15 0.25
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (41 bp):
GGGTTGCGATCTAGAATGTTAATATTTTTATTTAATAAAAT
Found at i:299473 original size:77 final size:77
Alignment explanation
Indices: 299296--299703 Score: 448
Period size: 77 Copynumber: 5.3 Consensus size: 77
299286 TGCGCTTAAA
* * ** *
299296 AATGTCATGGTTCAATAAGAAACGGGTTGCGATCTGGAATGTTAATATTTTTATTTAATAAAATG
1 AATGTCATGATTCACTAAGAAATAGTTTGCGATCTGGAATGTTAATATTTTTA-TTAATAAAATG
*
299361 GGTTGCCCCCAAG
65 GGTTGCGCCCAAG
* *
299374 AATGTTATTG-TTCACTAAGAAATAGTTTGCGATCTAGAATGTTAATATTTTT-TTAAATAAAAT
1 AATGTCA-TGATTCACTAAGAAATAGTTTGCGATCTGGAATGTTAATATTTTTATT-AATAAAAT
*
299437 GGGTTGCGCCCAGG
64 GGGTTGCGCCCAAG
* * * *
299451 AATATCATAATTCACTAAGAAATAAG-TTACGATCTGGAATGTTAATATTTTTATAAATAAAATG
1 AATGTCATGATTCACTAAGAAAT-AGTTTGCGATCTGGAATGTTAATATTTTTATTAATAAAATG
* *
299515 AGTTGCACCCAAG
65 GGTTGCGCCCAAG
* * * * * *
299528 AATGTCATGATTCACTAAGAAATCGGTTACAATTTGGAATGTTAATATTTTTATTTATAAAATGA
1 AATGTCATGATTCACTAAGAAATAGTTTGCGATCTGGAATGTTAATATTTTTATTAATAAAATG-
299593 GG-TGCGCCCAAG
65 GGTTGCGCCCAAG
* * * *
299605 AATGTCATGGTTCACTAATAAATA-TGTTGCGATATGGAATGTTAATATTTTTATTAATAAAATA
1 AATGTCATGATTCACTAAGAAATAGT-TTGCGATCTGGAATGTTAATATTTTTATTAATAAAATG
** *
299669 GGTTGTACACAAG
65 GGTTGCGCCCAAG
* * *
299682 AATGCCATGGTTTACTAAGAAA
1 AATGTCATGATTCACTAAGAAA
299704 GCAAGTTGAT
Statistics
Matches: 280, Mismatches: 41, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
76 6 0.02
77 225 0.80
78 47 0.17
79 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (77 bp):
AATGTCATGATTCACTAAGAAATAGTTTGCGATCTGGAATGTTAATATTTTTATTAATAAAATGG
GTTGCGCCCAAG
Found at i:300279 original size:20 final size:20
Alignment explanation
Indices: 300254--300292 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
300244 CATTTAAATT
*
300254 TAAAAGTATCGATACTTTTC
1 TAAAAGTATCAATACTTTTC
300274 TAAAAGTATCAATACTTTT
1 TAAAAGTATCAATACTTTT
300293 AAATTCAAAA
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:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (20 bp):
TAAAAGTATCAATACTTTTC
Found at i:300878 original size:15 final size:15
Alignment explanation
Indices: 300858--300890 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
300848 GGTGAATTAT
*
300858 TTTGAATTTAGATAA
1 TTTGAATTTAAATAA
300873 TTTGAATTTAAATAA
1 TTTGAATTTAAATAA
300888 TTT
1 TTT
300891 TAATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (15 bp):
TTTGAATTTAAATAA
Found at i:302512 original size:227 final size:228
Alignment explanation
Indices: 302109--302841 Score: 760
Period size: 227 Copynumber: 3.2 Consensus size: 228
302099 AAGTTGTTTC
* * * * *
302109 CCAGCAAAGATCAACCTCTGTTAGTCTGGCAGGATTCCCTCCTTAT-CTGGATCTTAGCCTTAAC
1 CCAGCAAAGATCAACCTCTGCTGGTCTGGCGGGATTCCCTCCTTGTCCTGAATCTTAGCCTTAAC
* * * * * * *
302173 ATTATCAATTGTGTCTGAGCTCTCGACTTCCAGGGTTATGGTCTTTCC-GGTCAGGGT-TTTCAC
66 ATTGTCAATAGTATCTGAACTCTCCACTTCCAGGGTGATGGTCTTTCCTGATCAGGGTCTTT-AC
* * * * * * *
302236 AAAAATCTGCATCCCACCAC-GAAGGT-GAAGCACTAAGTGGAGGGTGGACTCCTTTTGGATGTT
130 AAAAATCTACATTCCACCTCTCAA--TCGAAGGACCAAGTGGAGTGTGGACTCCTTTTGGATGTT
* *
302299 GTAATCAGCCAATGTGCAGCCATCCTCGAGTTTCTTA
193 ATAGTCAGCCAA-GTGCAGCCATCCTCGAGTTTCTTA
* * * *
302336 CCAGCAAAGATTAACCTCTGCTGGTCTGG-GGGATACCCTCCTTGTCCTGAATCTCAGCCTTGAC
1 CCAGCAAAGATCAACCTCTGCTGGTCTGGCGGGATTCCCTCCTTGTCCTGAATCTTAGCCTTAAC
* * *
302400 AATGTCAATAGTATCTGAACTCTCCACTTCCAGGGTGATGGAC-TTCCTGCTCAGGGTCTTTACA
66 ATTGTCAATAGTATCTGAACTCTCCACTTCCAGGGTGATGGTCTTTCCTGATCAGGGTCTTTACA
* *
302464 AAAATCTCCATTCCACCTCTCAATCGAAGGACCAAGTGGAGTGTGGACTCCTGCTT-GATGTTAT
131 AAAATCTACATTCCACCTCTCAATCGAAGGACCAAGTGGAGTGTGGACTCCT-TTTGGATGTTAT
* * *
302528 AGTCAG-CAAGAGTACGACCATCCTCGAGTTGCTTA
195 AGTCAGCCAAGTGCA-G-CCATCCTCGAGTTTCTTA
* * * *
302563 CCAGCAAAGATCAATCTCTGCTGGTCTGG-GGGA-T---TCCTTGTCTTGAATCTTGGCCTTCAC
1 CCAGCAAAGATCAACCTCTGCTGGTCTGGCGGGATTCCCTCCTTGTCCTGAATCTTAGCCTTAAC
* * * ** * *
302623 ATTGTCGATAGTATCAGAACTCTCCACCTCCAATGTGATGGTCTTTCCT-ATGAGGGTCTTAACA
66 ATTGTCAATAGTATCTGAACTCTCCACTTCCAGGGTGATGGTCTTTCCTGATCAGGGTCTTTACA
* * *
302687 AAAATTTACATTCCACCTCTTAATCGAAGGACCAAGTGGAGTGTGGATTCCTTTTGGATGTTATA
131 AAAATCTACATTCCACCTCTCAATCGAAGGACCAAGTGGAGTGTGGACTCCTTTTGGATGTTATA
* * * * *
302752 GTCAGCCAGAGTACGGCCATCCTCCAACTGT-TTA
196 GTCAGCCA-AGTGCAGCCATCCT-CGAGTTTCTTA
* * * * *
302786 CCAGCAAAGATCAACCTCTGTTGGTCTGGTGGGATTCCTTCTTTGTCTTGAATCTT
1 CCAGCAAAGATCAACCTCTGCTGGTCTGGCGGGATTCCCTCCTTGTCCTGAATCTT
302842 GACCTTTGCA
Statistics
Matches: 424, Mismatches: 64, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
222 2 0.00
223 169 0.40
224 15 0.04
225 6 0.01
226 22 0.05
227 187 0.44
228 23 0.05
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (228 bp):
CCAGCAAAGATCAACCTCTGCTGGTCTGGCGGGATTCCCTCCTTGTCCTGAATCTTAGCCTTAAC
ATTGTCAATAGTATCTGAACTCTCCACTTCCAGGGTGATGGTCTTTCCTGATCAGGGTCTTTACA
AAAATCTACATTCCACCTCTCAATCGAAGGACCAAGTGGAGTGTGGACTCCTTTTGGATGTTATA
GTCAGCCAAGTGCAGCCATCCTCGAGTTTCTTA
Found at i:302702 original size:223 final size:224
Alignment explanation
Indices: 302192--302895 Score: 699
Period size: 223 Copynumber: 3.1 Consensus size: 224
302182 TGTGTCTGAG
* * * * * * * * * *
302192 CTCTCGACTTCCAGGGTTATGGTCTTTCC-GGTCAGGGTTTTCACAAAAATCTGCATCCCACCAC
1 CTCTCCACCTCCAAGGTGATGGTCTTTCCTGATCAGGGTCTTAACAAAAATCTACATTCCACCTC
* * * * * * * * *
302256 -GAAGGT-GAAGCACTAAGTGGAGGGTGGACTCCTTTTGGATGTTGTAATCAGCCAA-TGTGC-A
66 TCAA--TCGAAGGACCAAGTGGAGTGTGGACTCCTCTTGGATGTTATAGTCAG-CAAGAGTACGA
* *
302317 GCCATCCTCGAGTTTCTTACCAGCAAAGATTAACCTCTGCTGGTCTGGGGGATACCCTCCTTGTC
128 -CCATCCTCGAGTTGCTTACCAGCAAAGATCAACCTCTGCTGGTCTGGGGGAT----TCCTTGTC
* ** * * * *
302382 CTGAATCTCAGCCTTGACAATGTCAATAGTATCTGAA
188 TTGAATCTTGGCCTTCACATTGTCGATAGTATCAGAA
* * * * * *
302419 CTCTCCACTTCCAGGGTGATGGAC-TTCCTGCTCAGGGTCTTTACAAAAATCTCCATTCCACCTC
1 CTCTCCACCTCCAAGGTGATGGTCTTTCCTGATCAGGGTCTTAACAAAAATCTACATTCCACCTC
302483 TCAATCGAAGGACCAAGTGGAGTGTGGACTCCTGCTT-GATGTTATAGTCAGCAAGAGTACGACC
66 TCAATCGAAGGACCAAGTGGAGTGTGGACTCCT-CTTGGATGTTATAGTCAGCAAGAGTACGACC
*
302547 ATCCTCGAGTTGCTTACCAGCAAAGATCAATCTCTGCTGGTCTGGGGGATTCCTTGTCTTGAATC
130 ATCCTCGAGTTGCTTACCAGCAAAGATCAACCTCTGCTGGTCTGGGGGATTCCTTGTCTTGAATC
302612 TTGGCCTTCACATTGTCGATAGTATCAGAA
195 TTGGCCTTCACATTGTCGATAGTATCAGAA
* * *
302642 CTCTCCACCTCCAATGTGATGGTCTTTCCT-ATGAGGGTCTTAACAAAAATTTACATTCCACCTC
1 CTCTCCACCTCCAAGGTGATGGTCTTTCCTGATCAGGGTCTTAACAAAAATCTACATTCCACCTC
* * * * *
302706 TTAATCGAAGGACCAAGTGGAGTGTGGATTCCTTTTGGATGTTATAGTCAGCCAGAGTACGGCCA
66 TCAATCGAAGGACCAAGTGGAGTGTGGACTCCTCTTGGATGTTATAGTCAGCAAGAGTACGACCA
* ** * *
302771 TCCTCCAACTGTTTACCAGCAAAGATCAACCTCTGTTGGTCTGGTGGGATTCCTTCTTTGTCTTG
131 TCCTCGAGTTGCTTACCAGCAAAGATCAACCTCTGCTGGTCTGG-GGGATT-C--C-TTGTCTTG
* ** * *
302836 AATCTTGACCTTTGCATAGTCGATGGTATCCA-AA
191 AATCTTGGCCTTCACATTGTCGATAGTAT-CAGAA
* *
302870 TTTTCCACCT-CAAGGGTGATGGTCTT
1 CTCTCCACCTCCAA-GGTGATGGTCTT
302896 ATCAGTGAGG
Statistics
Matches: 406, Mismatches: 56, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
222 2 0.00
223 182 0.45
224 11 0.03
225 1 0.00
226 8 0.02
227 142 0.35
228 58 0.14
229 2 0.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (224 bp):
CTCTCCACCTCCAAGGTGATGGTCTTTCCTGATCAGGGTCTTAACAAAAATCTACATTCCACCTC
TCAATCGAAGGACCAAGTGGAGTGTGGACTCCTCTTGGATGTTATAGTCAGCAAGAGTACGACCA
TCCTCGAGTTGCTTACCAGCAAAGATCAACCTCTGCTGGTCTGGGGGATTCCTTGTCTTGAATCT
TGGCCTTCACATTGTCGATAGTATCAGAA
Found at i:303898 original size:14 final size:14
Alignment explanation
Indices: 303875--303914 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
303865 TTCGATAATA
303875 CGTTCGTTTATATT
1 CGTTCGTTTATATT
* *
303889 CGTTCATTTATGTT
1 CGTTCGTTTATATT
303903 CGTTCGTTTATA
1 CGTTCGTTTATA
303915 GTCACCATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (14 bp):
CGTTCGTTTATATT
Found at i:304131 original size:24 final size:24
Alignment explanation
Indices: 304104--304167 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
304094 ACGTTAGTTT
*
304104 GTTTATGTTCGTTTATATTCGTTC
1 GTTTGTGTTCGTTTATATTCGTTC
*
304128 GTTTGTGTTCGTTTACATTCGTTC
1 GTTTGTGTTCGTTTATATTCGTTC
* *
304152 ATTTGTGTTTGTTTAT
1 GTTTGTGTTCGTTTAT
304168 CATTTAAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (24 bp):
GTTTGTGTTCGTTTATATTCGTTC
Found at i:311001 original size:24 final size:24
Alignment explanation
Indices: 310950--311001 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
310940 AGCGTCTCAC
* * *
310950 CCCTCTTGTTTCAGAGCCTTCTAT
1 CCCTCTCGTTTCACAGCCTTCTAA
310974 CCCTCTCGTTTCACAGCCTAT-TAA
1 CCCTCTCGTTTCACAGCCT-TCTAA
310998 CCCT
1 CCCT
311002 TTCTTCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.15, C:0.38, G:0.10, T:0.37
Consensus pattern (24 bp):
CCCTCTCGTTTCACAGCCTTCTAA
Found at i:312948 original size:13 final size:14
Alignment explanation
Indices: 312923--312974 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
312913 AAAAAAATGT
312923 AATTTATTTTTCAG
1 AATTTATTTTTCAG
*
312937 TATTTA-TTTTCAAG
1 AATTTATTTTTC-AG
*
312951 AATTTATTTTTCGG
1 AATTTATTTTTCAG
312965 AATTTATTTT
1 AATTTATTTT
312975 CAGTAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 5 0.15
14 23 0.70
15 5 0.15
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.60
Consensus pattern (14 bp):
AATTTATTTTTCAG
Found at i:312955 original size:28 final size:28
Alignment explanation
Indices: 312923--312976 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
312913 AAAAAAATGT
*
312923 AATTTATTTTTCAGTATTTATTTTCAAG
1 AATTTATTTTTCAGAATTTATTTTCAAG
*
312951 AATTTATTTTTCGGAATTTATTTTCA
1 AATTTATTTTTCAGAATTTATTTTCA
312977 GTAAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (28 bp):
AATTTATTTTTCAGAATTTATTTTCAAG
Found at i:313429 original size:3 final size:3
Alignment explanation
Indices: 313421--313452 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
313411 ATTATAAACT
313421 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
313453 TACAAAGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:314603 original size:11 final size:11
Alignment explanation
Indices: 314579--314608 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
314569 TGGTGGACTA
314579 AATTTATA-TT
1 AATTTATATTT
314589 AATTTATATTT
1 AATTTATATTT
314600 AATTTATAT
1 AATTTATAT
314609 GTGTCACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTATATTT
Found at i:314931 original size:29 final size:29
Alignment explanation
Indices: 314883--314975 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
314873 TATTATTATC
*
314883 TTAACTTTTAAATGAAGAATAAAATATATTT
1 TTAA-TTTAAAAT-AAGAATAAAATATATTT
* *
314914 TTAATTTAAAATAAGAATAAAATAAAATT
1 TTAATTTAAAATAAGAATAAAATATATTT
* ** * *
314943 TTAAGTGGAGATAAGAATAAACTATATATT
1 TTAATTTAAAATAAGAATAAAATATAT-TT
314973 TTA
1 TTA
314976 TATTAAATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
29 35 0.69
30 12 0.24
31 4 0.08
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (29 bp):
TTAATTTAAAATAAGAATAAAATATATTT
Found at i:315090 original size:31 final size:30
Alignment explanation
Indices: 315055--315145 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
315045 TGATAATGAT
* *
315055 AAAATATATATTTTTATAA-TAAAATAAAAAC
1 AAAATATATA--TTAATAAGTAAAACAAAAAC
315086 AAAATATATATTAATAAGTTAAAACAAAAAC
1 AAAATATATATTAATAAG-TAAAACAAAAAC
*
315117 AAAATATAT-TAAATAAGTTAAAACAAAAA
1 AAAATATATATTAATAAG-TAAAACAAAAA
315146 ATAAAAGACA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
29 6 0.11
30 19 0.35
31 30 0.55
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAATATATATTAATAAGTAAAACAAAAAC
Found at i:315102 original size:29 final size:31
Alignment explanation
Indices: 315055--315145 Score: 100
Period size: 30 Copynumber: 3.0 Consensus size: 31
315045 TGATAATGAT
* *
315055 AAAATATATATTTTTATAA-TAAAATAAAAAC
1 AAAATATATA-TTTAATAAGTAAAACAAAAAC
315086 AAAATATATA-TTAATAAGTTAAAACAAAAAC
1 AAAATATATATTTAATAAG-TAAAACAAAAAC
*
315117 -AAA-ATATATTAAATAAGTTAAAACAAAAA
1 AAAATATATATTTAATAAG-TAAAACAAAAA
315146 ATAAAAGACA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
29 11 0.20
30 22 0.41
31 21 0.39
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (31 bp):
AAAATATATATTTAATAAGTAAAACAAAAAC
Found at i:315146 original size:31 final size:31
Alignment explanation
Indices: 315074--315145 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
315064 ATTTTTATAA
* *
315074 TAAAATAAAAACAAAATATATATTAATAAGT
1 TAAAACAAAAACAAAATATATATAAATAAGT
315105 TAAAACAAAAACAAAATATAT-TAAATAAGT
1 TAAAACAAAAACAAAATATATATAAATAAGT
315135 TAAAACAAAAA
1 TAAAACAAAAA
315146 ATAAAAGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (31 bp):
TAAAACAAAAACAAAATATATATAAATAAGT
Found at i:321975 original size:20 final size:20
Alignment explanation
Indices: 321950--322028 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
321940 TTTTGGTGCA
321950 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
* * **
321970 GAGGGAACCGATTCTCCCTTT
1 GAGGGAATCGATAC-CCCCAT
*
321991 GAAGGGAA-CGATTCCCCCA-
1 G-AGGGAATCGATACCCCCAT
*
322010 CAGGGGAATCGATACCCCC
1 GA-GGGAATCGATACCCCC
322029 CTGGGGTTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
18 1 0.02
19 5 0.11
20 24 0.51
21 11 0.23
22 6 0.13
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:322667 original size:265 final size:272
Alignment explanation
Indices: 322174--322711 Score: 1002
Period size: 265 Copynumber: 2.0 Consensus size: 272
322164 ATATCTTCTA
322174 ACCTCTAGCATCATTAAAATCTTGCAAACAACATCAAAATCCACTCAATCTCATCTTTCAAGGTA
1 ACCTCTAGCATCATTAAAATCTTGCAAACAACATCAAAATCCACTCAATCTCATCTTTCAAGGTA
322239 AATTTTTCTAAATTCTCTATTTCATTGATTTTGAACATAGGACTTGTTTTAATTAGTTCTAGAAA
66 AATTTTTCTAAATTCTCTATTTCATTGATTTTGAACATAGGACTTGTTTTAATTAGTTCTAGAAA
322304 GAAATAGTGATCGGGCATTGATTGCTTAATGATTAGAAACTAGATATTACAACTAATTTCATCAA
131 GAAATAGTGATCGGGCATTGATTGCTTAATGATTAGAAACTAGATATTACAACTAATTTCATCAA
322369 AAACACAAGAATTTTTCCAAAAATTTTGAAAATTTTGAAAT-AAAAAATTA-TTTTCAAATTA-T
196 AAACACAAGAATTTTTCCAAAAATTTTGAAAATTTTGAAATAAAAAAATTATTTTTCAAATTATT
322431 ATGTTTTAATTG
261 ATGTTTTAATTG
322443 ACCTACTAGCATCATT-AAATCTTGCAAACAACATCAAAATCCACTCAATCTCATCTTTCAAGGT
1 ACCT-CTAGCATCATTAAAATCTTGCAAACAACATCAAAATCCACTCAATCTCATCTTTCAAGGT
*
322507 -AATTTTTCTAAATTCTCTATTTCATTGA-TTTG-ATATAGGACTT-TTTTAATTAGTTCTAGAA
65 AAATTTTTCTAAATTCTCTATTTCATTGATTTTGAACATAGGACTTGTTTTAATTAGTTCTAGAA
322568 AGAAATAGTGATCGGGCATTGATTGCTTAATGATTAGAAACTAGATATTACAACTAATTTCATCA
130 AGAAATAGTGATCGGGCATTGATTGCTTAATGATTAGAAACTAGATATTACAACTAATTTCATCA
322633 AAAACACAAGAATTTTTCCAAAAATTTTGAAAATTTTGAAATAAAAAAATTATTTTTCAAATTAT
195 AAAACACAAGAATTTTTCCAAAAATTTTGAAAATTTTGAAATAAAAAAATTATTTTTCAAATTAT
322698 TATGTTTTAATTG
260 TATGTTTTAATTG
322711 A
1 A
322712 ATTATGTTGT
Statistics
Matches: 264, Mismatches: 1, Indels: 9
0.96 0.00 0.03
Matches are distributed among these distances:
265 125 0.47
266 19 0.07
267 15 0.06
268 42 0.16
269 52 0.20
270 11 0.04
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Consensus pattern (272 bp):
ACCTCTAGCATCATTAAAATCTTGCAAACAACATCAAAATCCACTCAATCTCATCTTTCAAGGTA
AATTTTTCTAAATTCTCTATTTCATTGATTTTGAACATAGGACTTGTTTTAATTAGTTCTAGAAA
GAAATAGTGATCGGGCATTGATTGCTTAATGATTAGAAACTAGATATTACAACTAATTTCATCAA
AAACACAAGAATTTTTCCAAAAATTTTGAAAATTTTGAAATAAAAAAATTATTTTTCAAATTATT
ATGTTTTAATTG
Found at i:330397 original size:16 final size:18
Alignment explanation
Indices: 330362--330399 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
330352 TTTTTAGTGA
*
330362 TTTAGGGTTTTATATGGG
1 TTTAGGGTTTGATATGGG
330380 TTTAGGG-TTGAT-TGGG
1 TTTAGGGTTTGATATGGG
330396 TTTA
1 TTTA
330400 TTTTAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (18 bp):
TTTAGGGTTTGATATGGG
Found at i:339638 original size:165 final size:167
Alignment explanation
Indices: 339440--339772 Score: 652
Period size: 165 Copynumber: 2.0 Consensus size: 167
339430 GGCTGGCAAG
339440 CTAGCAAAAGAGGGGATCGGGTGACGATTTTGTCTGTTTCAGTTGGTGTTTGTTTCTGAGCTAAG
1 CTAGCAAAAGAGGGGATCGGGTGACGATTTTGTCTGTTTCAGTTGGTGTTTGTTTCTGAGCTAAG
339505 AAGCTAGAGGAGTGTGTGAGATCTTATATTGTATGTAAAAGTGTTTTTAAGTCTTATGTAA-TTG
66 AAGCTAGAGGAGTGTGTGAGATCTTATATTGTATGTAAAAGTGTTTTTAAGTCTTATGTAACTTG
339569 GCTATCATTAATAAATTGA-GTACTCTTTTCCTCCTT
131 GCTATCATTAATAAATTGAGGTACTCTTTTCCTCCTT
339605 CTAGCAAAAGAGGGGATCGGGTGACGATTTTGTCTGTTTCAGTTGGTGTTTGTTTCTGAGCTAAG
1 CTAGCAAAAGAGGGGATCGGGTGACGATTTTGTCTGTTTCAGTTGGTGTTTGTTTCTGAGCTAAG
339670 AAGCTAGAGGAGTGTGTGAGATCTTATATTGTATGTAAAAGTGTTTTTAAGTCTTATGTAACTTG
66 AAGCTAGAGGAGTGTGTGAGATCTTATATTGTATGTAAAAGTGTTTTTAAGTCTTATGTAACTTG
339735 GCTATCATTAATAAATTGAGGTACTCTTTTCCTCCTT
131 GCTATCATTAATAAATTGAGGTACTCTTTTCCTCCTT
339772 C
1 C
339773 CGCTAGTTGG
Statistics
Matches: 166, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
165 126 0.76
166 22 0.13
167 18 0.11
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (167 bp):
CTAGCAAAAGAGGGGATCGGGTGACGATTTTGTCTGTTTCAGTTGGTGTTTGTTTCTGAGCTAAG
AAGCTAGAGGAGTGTGTGAGATCTTATATTGTATGTAAAAGTGTTTTTAAGTCTTATGTAACTTG
GCTATCATTAATAAATTGAGGTACTCTTTTCCTCCTT
Found at i:341295 original size:45 final size:45
Alignment explanation
Indices: 341244--341336 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
341234 TTGAAGAGTG
341244 ATCTGTGAAGTATATTGTTTCTAACTATTTGTTTTGCTTGAAGTA
1 ATCTGTGAAGTATATTGTTTCTAACTATTTGTTTTGCTTGAAGTA
341289 ATCTGTGAAGTATATTGTTTCTAACTATTTGTTTTGCTTGAAGTA
1 ATCTGTGAAGTATATTGTTTCTAACTATTTGTTTTGCTTGAAGTA
341334 ATC
1 ATC
341337 GTATCTGGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (45 bp):
ATCTGTGAAGTATATTGTTTCTAACTATTTGTTTTGCTTGAAGTA
Found at i:349159 original size:54 final size:54
Alignment explanation
Indices: 349094--349404 Score: 226
Period size: 54 Copynumber: 5.7 Consensus size: 54
349084 GAGGACTGAG
** * * * *
349094 AAGGTGGTTCGGCACTAGGATCAGGGGAAGGTGGTTCGGCATGAGGATCGGGAA
1 AAGGTGGTTCGGCAGGAGGATCAGGAGAAGGTGGTGCAGCATGAGGATCAGGAA
* *
349148 AAGGTGATTCGGCAGGAGTATCAGGAGAAGGCGGTGGTGCAGCATGAGGATCAGGAA
1 AAGGTGGTTCGGCAGGAGGATCAGGAGAA---GGTGGTGCAGCATGAGGATCAGGAA
* * * * **
349205 AATGTGGTGCGGTAGGAGGATCAGGAGAAGGTGGTGCAGCATAAGGATCAGGTG
1 AAGGTGGTTCGGCAGGAGGATCAGGAGAAGGTGGTGCAGCATGAGGATCAGGAA
*** * * * * ** **
349259 AAGGTGGTGAAGCACGAGGATCGGGAAAAGGTGGTGTAGCACAAGGATCAGGTG
1 AAGGTGGTTCGGCAGGAGGATCAGGAGAAGGTGGTGCAGCATGAGGATCAGGAA
*** * * * * * **
349313 AAGGTGACGCGGCACGAGGATCGGGTGAAGGTGGTGCAGCATTAGGATGAGGCG
1 AAGGTGGTTCGGCAGGAGGATCAGGAGAAGGTGGTGCAGCATGAGGATCAGGAA
* * ** **
349367 ACGATGGAACGGCACAAGGATCAGGAGAAGGTGGTGCA
1 AAGGTGGTTCGGCAGGAGGATCAGGAGAAGGTGGTGCA
349405 ACACGAGACT
Statistics
Matches: 210, Mismatches: 44, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
54 164 0.78
57 46 0.22
ACGTcount: A:0.28, C:0.13, G:0.43, T:0.16
Consensus pattern (54 bp):
AAGGTGGTTCGGCAGGAGGATCAGGAGAAGGTGGTGCAGCATGAGGATCAGGAA
Found at i:349203 original size:30 final size:27
Alignment explanation
Indices: 349091--349404 Score: 198
Period size: 27 Copynumber: 11.5 Consensus size: 27
349081 CAGGAGGACT
* *
349091 GAGAAGGTGGTTCGGCACT-AGGATCAG
1 GAGAAGGTGGTGCAGCA-TGAGGATCAG
* * * *
349118 GGGAAGGTGGTTCGGCATGAGGATCGG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
* * * * * *
349145 GAAAAGGTGATTCGGCAGGAGTATCAG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
349172 GAGAAGGCGGTGGTGCAGCATGAGGATCAG
1 GAGAA---GGTGGTGCAGCATGAGGATCAG
* * * * *
349202 GAAAATGTGGTGCGGTAGGAGGATCAG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
*
349229 GAGAAGGTGGTGCAGCATAAGGATCAG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
* * * *
349256 GTGAAGGTGGTGAAGCACGAGGATCGG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
* * **
349283 GAAAAGGTGGTGTAGCACAAGGATCAG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
* ** * * *
349310 GTGAAGGTGACGCGGCACGAGGATCGG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
* * *
349337 GTGAAGGTGGTGCAGCATTAGGATGAG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
* * * ** * **
349364 GCGACGATGGAACGGCACAAGGATCAG
1 GAGAAGGTGGTGCAGCATGAGGATCAG
349391 GAGAAGGTGGTGCA
1 GAGAAGGTGGTGCA
349405 ACACGAGACT
Statistics
Matches: 218, Mismatches: 65, Indels: 8
0.75 0.22 0.03
Matches are distributed among these distances:
26 1 0.00
27 196 0.90
30 21 0.10
ACGTcount: A:0.28, C:0.12, G:0.44, T:0.16
Consensus pattern (27 bp):
GAGAAGGTGGTGCAGCATGAGGATCAG
Found at i:350765 original size:152 final size:152
Alignment explanation
Indices: 350489--350792 Score: 608
Period size: 152 Copynumber: 2.0 Consensus size: 152
350479 AGTAGGTGCC
350489 ATCTTCAATAAAGTTTGGAGGAGTTCGATGGGAAGCTCATTTGCTGATTTCAGAAGAACAGGTTA
1 ATCTTCAATAAAGTTTGGAGGAGTTCGATGGGAAGCTCATTTGCTGATTTCAGAAGAACAGGTTA
350554 GAATATCGATATTGAAAGCTGAACAAACCAGTAATGCTTTTCCAAATAACAATGAAATTGCAAGA
66 GAATATCGATATTGAAAGCTGAACAAACCAGTAATGCTTTTCCAAATAACAATGAAATTGCAAGA
350619 TGGATTAACAGCATAAAGCCAA
131 TGGATTAACAGCATAAAGCCAA
350641 ATCTTCAATAAAGTTTGGAGGAGTTCGATGGGAAGCTCATTTGCTGATTTCAGAAGAACAGGTTA
1 ATCTTCAATAAAGTTTGGAGGAGTTCGATGGGAAGCTCATTTGCTGATTTCAGAAGAACAGGTTA
350706 GAATATCGATATTGAAAGCTGAACAAACCAGTAATGCTTTTCCAAATAACAATGAAATTGCAAGA
66 GAATATCGATATTGAAAGCTGAACAAACCAGTAATGCTTTTCCAAATAACAATGAAATTGCAAGA
350771 TGGATTAACAGCATAAAGCCAA
131 TGGATTAACAGCATAAAGCCAA
350793 TCAAACACAT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (152 bp):
ATCTTCAATAAAGTTTGGAGGAGTTCGATGGGAAGCTCATTTGCTGATTTCAGAAGAACAGGTTA
GAATATCGATATTGAAAGCTGAACAAACCAGTAATGCTTTTCCAAATAACAATGAAATTGCAAGA
TGGATTAACAGCATAAAGCCAA
Found at i:351536 original size:30 final size:30
Alignment explanation
Indices: 351502--351560 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
351492 CTTGGAGCAC
351502 CACCACCTTTTGGAGGAGGTGGAGGAGGAG
1 CACCACCTTTTGGAGGAGGTGGAGGAGGAG
*
351532 CACCACCTTTTGGAGGAGGTGGTGGAGGA
1 CACCACCTTTTGGAGGAGGTGGAGGAGGA
351561 CCTGGTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.42, T:0.19
Consensus pattern (30 bp):
CACCACCTTTTGGAGGAGGTGGAGGAGGAG
Found at i:356804 original size:19 final size:19
Alignment explanation
Indices: 356780--356816 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
356770 ATGACCAACA
*
356780 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
356799 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
356817 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:356894 original size:21 final size:21
Alignment explanation
Indices: 356842--356895 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
356832 GTTTCCAGAT
*
356842 TCGCAACGCAATAATACAAAA
1 TCGCAACGCGATAATACAAAA
356863 TCGCAACGCGATAATACAAAA
1 TCGCAACGCGATAATACAAAA
* *
356884 TCGTAATGCGAT
1 TCGCAACGCGAT
356896 TTTCAAAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGATAATACAAAA
Found at i:357558 original size:20 final size:20
Alignment explanation
Indices: 357478--357575 Score: 99
Period size: 20 Copynumber: 5.0 Consensus size: 20
357468 GTTTGTTGCG
*
357478 ATTTTCTCGTTGCGATTTTC
1 ATTTTCGCGTTGCGATTTTC
**
357498 A-TTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATTTTC
** **
357517 AAATTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATTTTC
*
357537 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGCGTTGCGATTTTC
* *
357557 ATTTTCGTGTTGCTATTTT
1 ATTTTCGCGTTGCGATTTT
357576 AAGTTTCAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
19 16 0.24
20 51 0.76
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.48
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATTTTC
Found at i:357582 original size:20 final size:20
Alignment explanation
Indices: 357539--357582 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
357529 CGATAGTCAT
* *
357539 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
*
357559 TTTCGTGTTGCTATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
357579 TTTC
1 TTTC
357583 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:359462 original size:20 final size:20
Alignment explanation
Indices: 359435--359503 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
359425 GAAACTTAAA
359435 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
359455 ATCACAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
359475 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
359495 ATCGCAACG
1 ATCGCAACG
359504 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:359545 original size:33 final size:34
Alignment explanation
Indices: 359495--359570 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
359485 GAATTTGACT
* *
359495 ATCGCAACGGGATAATCGCAATGC-GAAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCAAAAATAAAA
* *
359528 ATCGCAACGTGAAAATCGCAATGCAAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCAAAAATAAAA
359562 ATCGCAACG
1 ATCGCAACG
359571 CGAATTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCAAAAATAAAA
Found at i:359674 original size:20 final size:20
Alignment explanation
Indices: 359619--359686 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
359609 CGATTATCTT
*
359619 GTTGCGATAGTCAAATT-CGC
1 GTTGCGATAGTC-ATTTCCGC
*
359639 ATTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
* *
359659 GTTGCGATAGTTATTTTCGC
1 GTTGCGATAGTCATTTCCGC
359679 GTTGCGAT
1 GTTGCGAT
359687 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.07
20 39 0.93
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:359696 original size:20 final size:20
Alignment explanation
Indices: 359673--359716 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
359663 CGATAGTTAT
359673 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
359693 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
359713 TTTC
1 TTTC
359717 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:360270 original size:42 final size:42
Alignment explanation
Indices: 360224--360318 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
360214 TCTCCTATCG
*
360224 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCACTCAAGAGGT-CCCTCCCACCA
* * *
360266 TTCAAGAGGCCCCTGTCATCATTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCCACCA
360308 TTCAAGAGGCC
1 TTCAAGAGGCC
360319 GATTCACACG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 46 0.96
43 2 0.04
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCCACCA
Found at i:360288 original size:21 final size:21
Alignment explanation
Indices: 360199--360318 Score: 114
Period size: 21 Copynumber: 5.7 Consensus size: 21
360189 CTCACCTGTT
* *
360199 ATCATTCAAGAGGCCTCTCCT
1 ATCATTCAAGAGGCCCCTCCC
* **
360220 ATCGTTCAAGAGGCCCCTATC
1 ATCATTCAAGAGGCCCCTCCC
** *
360241 ATCCCTCAAGAGTCCCCTCCC
1 ATCATTCAAGAGGCCCCTCCC
* **
360262 ACCATTCAAGAGGCCCCTGTC
1 ATCATTCAAGAGGCCCCTCCC
* *
360283 ATCATTGAAGAGGTCCCTCCC
1 ATCATTCAAGAGGCCCCTCCC
*
360304 ACCATTCAAGAGGCC
1 ATCATTCAAGAGGCC
360319 GATTCACACG
Statistics
Matches: 75, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.22
Consensus pattern (21 bp):
ATCATTCAAGAGGCCCCTCCC
Found at i:361683 original size:14 final size:14
Alignment explanation
Indices: 361664--361700 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
361654 TTGCTTGTAA
361664 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
361678 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
361692 TTGATTTGT
1 TTGATTTGT
361701 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:361845 original size:20 final size:20
Alignment explanation
Indices: 361820--361897 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
361810 ATGTACATTT
*
361820 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
361840 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
361860 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
361880 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
361898 TTCGCGTTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:361864 original size:40 final size:40
Alignment explanation
Indices: 361820--361897 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
361810 ATGTACATTT
* *
361820 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGCAACGCGAAAGTCAAAA
*
361860 TCGCAATGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
361898 TTCGCGTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAAAA
Found at i:361970 original size:20 final size:20
Alignment explanation
Indices: 361936--362052 Score: 162
Period size: 20 Copynumber: 5.8 Consensus size: 20
361926 GCGATTTTCT
*
361936 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* * * *
361956 CATTGTGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
361976 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
361996 TGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
362016 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
362036 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
362053 GAATGTGTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:364274 original size:12 final size:13
Alignment explanation
Indices: 364244--364275 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
364234 CCCGTGGCAT
364244 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
364257 TTTCTTCGGGGA-
1 TTTCTTCGGGGAC
364269 TTTCTTC
1 TTTCTTC
364276 TTTTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.06, C:0.22, G:0.25, T:0.47
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:364509 original size:23 final size:24
Alignment explanation
Indices: 364457--364509 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
364447 ATGAAACATC
364457 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
364481 ATCAAAGTCCGGGTATTGACC-AG
1 ATCAAAATCCGAGTATTGACCAAG
364504 ATCAAA
1 ATCAAA
364510 TTTGATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:364981 original size:17 final size:17
Alignment explanation
Indices: 364959--364993 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
364949 GGATGGGGAT
364959 ATGTCGTTGGATATAGG
1 ATGTCGTTGGATATAGG
364976 ATGTCGTTGGATATAGG
1 ATGTCGTTGGATATAGG
364993 A
1 A
364994 ACGGATGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.34, T:0.34
Consensus pattern (17 bp):
ATGTCGTTGGATATAGG
Found at i:365199 original size:20 final size:21
Alignment explanation
Indices: 365176--365230 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
365166 CGATTTTGCT
*
365176 AAATCGC-ATGCGAATTTTGA
1 AAATCGCAATGCGAATTTGGA
*
365196 AAATCGCAACGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
365217 AAATCGCAATGCGA
1 AAATCGCAATGCGA
365231 TAGTCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 7 0.23
21 24 0.77
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:365288 original size:20 final size:19
Alignment explanation
Indices: 365265--365310 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
365255 GGAAACTGAT
* *
365265 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
365285 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
365304 TTGCGAT
1 TTGCGAT
365311 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:365300 original size:19 final size:19
Alignment explanation
Indices: 365276--365312 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
365266 TGCGATACTG
*
365276 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
365295 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
365313 TGTTGGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:365802 original size:103 final size:104
Alignment explanation
Indices: 365676--365882 Score: 350
Period size: 105 Copynumber: 2.0 Consensus size: 104
365666 ATCTTTTTTG
365676 GAACTAACCATGCCCATAGCGAGTTCTGTTAATATATATTTTTTAATTTTAAAAAATATAAAAT-
1 GAACTAACCATGCCCATAGCGAGTTCTGTTAATATATA-TTTTTAATTTT-AAAAATATAAAATA
365740 A-T-T-ATTATTTAAAAAAACATTGAGGCTTGTCATGCTTA
64 ATTATAATTATTTAAAAAAACATTGAGGCTTGTCATGCTTA
365778 GAACTAACCATGCCGCATAGCGAGTTCTGTTAATATATATTTTTAATTTTAAAAATATAAAATAA
1 GAACTAACCATGCC-CATAGCGAGTTCTGTTAATATATATTTTTAATTTTAAAAATATAAAATAA
*
365843 TTATAATTATTTAAAAAAGCATTGAGGCTTGTCATGCTTA
65 TTATAATTATTTAAAAAAACATTGAGGCTTGTCATGCTTA
365883 CATGGTGAGT
Statistics
Matches: 99, Mismatches: 1, Indels: 7
0.93 0.01 0.07
Matches are distributed among these distances:
101 13 0.13
102 26 0.26
103 25 0.25
104 1 0.01
105 34 0.34
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (104 bp):
GAACTAACCATGCCCATAGCGAGTTCTGTTAATATATATTTTTAATTTTAAAAATATAAAATAAT
TATAATTATTTAAAAAAACATTGAGGCTTGTCATGCTTA
Done.