Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:5913 original size:56 final size:57
Alignment explanation
Indices: 5802--5928 Score: 156
Period size: 56 Copynumber: 2.2 Consensus size: 57
5792 ATTCTTGGGT
*
5802 AAAGTATAC-AAATGGTCCCGACTATAGAGTGTTACTTTGTTGAGTTCTTCGACTATTA
1 AAAGT-TACAAAATGGTCCCGACTATAGAGTGTTA-TTTGTTGAGTTCTTCAACTATTA
*
5860 GAAGTTACAAAATGGTCCCCGACTATAG-GATG-T-TTTGTTGAG-TCTTTCAACTATTA
1 AAAGTTACAAAATGGT-CCCGACTATAGAG-TGTTATTTGTTGAGTTC-TTCAACTATTA
5916 AAAGTTACAAAAT
1 AAAGTTACAAAAT
5929 AATCATTAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
55 2 0.03
56 31 0.50
57 3 0.05
58 13 0.21
59 13 0.21
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (57 bp):
AAAGTTACAAAATGGTCCCGACTATAGAGTGTTATTTGTTGAGTTCTTCAACTATTA
Found at i:12203 original size:35 final size:35
Alignment explanation
Indices: 12157--12223 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
12147 GAAAGATAGA
12157 CTCTCGATAAAGCTTATGTAGGGTCAGGGCTTAGT
1 CTCTCGATAAAGCTTATGTAGGGTCAGGGCTTAGT
*
12192 CTCTCGATAAAGCTTATGTCGGGTCAGGGCTT
1 CTCTCGATAAAGCTTATGTAGGGTCAGGGCTT
12224 GTGCATCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (35 bp):
CTCTCGATAAAGCTTATGTAGGGTCAGGGCTTAGT
Found at i:12469 original size:20 final size:20
Alignment explanation
Indices: 12441--12479 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12431 TCCGACACCA
12441 AAATGCAAAAAAAAAAAAGG
1 AAATGCAAAAAAAAAAAAGG
* *
12461 AAATTCAAATAAAAAAAAG
1 AAATGCAAAAAAAAAAAAG
12480 ACATCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (20 bp):
AAATGCAAAAAAAAAAAAGG
Found at i:31004 original size:2 final size:2
Alignment explanation
Indices: 30961--30989 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30951 ACACACGTGT
30961 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30990 GTACATGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31304 original size:2 final size:2
Alignment explanation
Indices: 31297--31325 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31287 TTAAGTAAAT
31297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31326 TAAGTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32132 original size:28 final size:27
Alignment explanation
Indices: 32101--32157 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
32091 ATAAAAAAAC
32101 AAACTTATTAATCTAATAATACATAATT
1 AAACTTATTAATCTAATAAT-CATAATT
* *
32129 AAACTTATTATTCTAATGATCATAATT
1 AAACTTATTAATCTAATAATCATAATT
32156 AA
1 AA
32158 CAATTCGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (27 bp):
AAACTTATTAATCTAATAATCATAATT
Found at i:32430 original size:28 final size:28
Alignment explanation
Indices: 32399--32461 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
32389 AACCAAATGT
* *
32399 AACTCGACTTTATATCAATACCAATTCA
1 AACTCAACTTCATATCAATACCAATTCA
*
32427 AACTCAACTTCATATCAATATCAATTCA
1 AACTCAACTTCATATCAATACCAATTCA
32455 AACTCAA
1 AACTCAA
32462 ATTAATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (28 bp):
AACTCAACTTCATATCAATACCAATTCA
Found at i:33799 original size:37 final size:38
Alignment explanation
Indices: 33749--33834 Score: 142
Period size: 37 Copynumber: 2.3 Consensus size: 38
33739 CCTAAACTCG
33749 AACCCGA-TCCGACCCGAATATCACACTTAAAAAACCC
1 AACCCGACTCCGACCCGAATATCACACTTAAAAAACCC
33786 AACCCGACT-CGACCCGAATATCACACTTAAAAAACCC
1 AACCCGACTCCGACCCGAATATCACACTTAAAAAACCC
*
33823 GACCCGAC-CCGA
1 AACCCGACTCCGA
33835 ATATATGAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
37 45 0.98
38 1 0.02
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (38 bp):
AACCCGACTCCGACCCGAATATCACACTTAAAAAACCC
Found at i:36825 original size:34 final size:35
Alignment explanation
Indices: 36770--36839 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
36760 ATCATCAATT
36770 TTCATTTATCCTTTTTGTTTCTCAACAAATCTCAG
1 TTCATTTATCCTTTTTGTTTCTCAACAAATCTCAG
36805 TTCATTTATCC-TTTTGTTTCTCAACAAATCTCAG
1 TTCATTTATCCTTTTTGTTTCTCAACAAATCTCAG
36839 T
1 T
36840 GCTTGAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 24 0.69
35 11 0.31
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (35 bp):
TTCATTTATCCTTTTTGTTTCTCAACAAATCTCAG
Found at i:37025 original size:29 final size:29
Alignment explanation
Indices: 36956--37011 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
36946 AAATTTTAAA
36956 TTGAA-CCTCAAACTTTAAAACATTCTAC
1 TTGAATCCTCAAACTTTAAAACATTCTAC
*
36984 TTGAATTCTCAAACTTTAAAACATTCTA
1 TTGAATCCTCAAACTTTAAAACATTCTA
37012 GTTACCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (29 bp):
TTGAATCCTCAAACTTTAAAACATTCTAC
Found at i:45633 original size:74 final size:75
Alignment explanation
Indices: 45540--45716 Score: 214
Period size: 74 Copynumber: 2.4 Consensus size: 75
45530 CTTTAGATTC
* * * *
45540 TTTTGTTTATGTGCTATGTTGATTAAACTT-ATAAAAAATACCATTGTCTGCTTGTATGCTACTA
1 TTTTGTTAATATGCTATGTTGATTAAACTTCATAAAAAATACCATTGTATACTTGTATGCTACTA
45604 AATTGAATTG
66 AATTGAATTG
* * * *
45614 TTTTGTTAATATGCTATGTTGATTAAA-TTCATAGAATATATCATTGTATATTTGTATGCTACTA
1 TTTTGTTAATATGCTATGTTGATTAAACTTCATAAAAAATACCATTGTATACTTGTATGCTACTA
* * *
45678 ATTTTAATTT
66 AATTGAATTG
** *
45688 TTTTGTTCGTATGCTATGTTGATTTAACT
1 TTTTGTTAATATGCTATGTTGATTAAACT
45717 ATTAGAAAGT
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
73 2 0.02
74 84 0.97
75 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (75 bp):
TTTTGTTAATATGCTATGTTGATTAAACTTCATAAAAAATACCATTGTATACTTGTATGCTACTA
AATTGAATTG
Found at i:58737 original size:189 final size:189
Alignment explanation
Indices: 58417--58773 Score: 696
Period size: 189 Copynumber: 1.9 Consensus size: 189
58407 ACAAAATAAT
* *
58417 AATATCTCTATGTGCTTTGTTCTTTCATGAAAAACTGGATATGTTACTATTTAAAGGGCTGCTCA
1 AATATCTCTATGTGCTTCGTTCTTTCATGAAAAACTGGATATGTTACTATTTAAAGGGATGCTCA
58482 CTATCACTTAGAAGTTTGACCCGTTGCTCTCCTTTAAATCTAAGCTCCTTCAACAAACCACTTAA
66 CTATCACTTAGAAGTTTGACCCGTTGCTCTCCTTTAAATCTAAGCTCCTTCAACAAACCACTTAA
58547 CAACACTATTTCTGATGTTGTCATTGTCATACTCCTATAGTCGGCCTCTGCAGAATCTG
131 CAACACTATTTCTGATGTTGTCATTGTCATACTCCTATAGTCGGCCTCTGCAGAATCTG
58606 AATATCTCTATGTGCTTCGTTCTTTCATGAAAAACTGGATATGTTACTATTTAAAGGGATGCTCA
1 AATATCTCTATGTGCTTCGTTCTTTCATGAAAAACTGGATATGTTACTATTTAAAGGGATGCTCA
58671 CTATCACTTAGAAGTTTGACCCGTTGCTCTCCTTTAAATCTAAGCTCCTTCAACAAACCACTTAA
66 CTATCACTTAGAAGTTTGACCCGTTGCTCTCCTTTAAATCTAAGCTCCTTCAACAAACCACTTAA
58736 CAACACTATTTCTGATGTTGTCATTGTCATACTCCTAT
131 CAACACTATTTCTGATGTTGTCATTGTCATACTCCTAT
58774 TGTCATTGTC
Statistics
Matches: 166, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 166 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (189 bp):
AATATCTCTATGTGCTTCGTTCTTTCATGAAAAACTGGATATGTTACTATTTAAAGGGATGCTCA
CTATCACTTAGAAGTTTGACCCGTTGCTCTCCTTTAAATCTAAGCTCCTTCAACAAACCACTTAA
CAACACTATTTCTGATGTTGTCATTGTCATACTCCTATAGTCGGCCTCTGCAGAATCTG
Found at i:60801 original size:2 final size:2
Alignment explanation
Indices: 60794--60818 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60784 TTCTCCCCCA
60794 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
60819 GCTTGACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:67408 original size:19 final size:18
Alignment explanation
Indices: 67375--67411 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
67365 CTAAATTATT
67375 AAATTATCTTATATTTTA
1 AAATTATCTTATATTTTA
*
67393 AAATTCTCTGTATATTTTA
1 AAATTATCT-TATATTTTA
67412 TATTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (18 bp):
AAATTATCTTATATTTTA
Found at i:77731 original size:19 final size:19
Alignment explanation
Indices: 77681--77722 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
77671 TATAGATTCA
*
77681 AATATTTAATCT--ATAAT
1 AATATTTAATTTAAATAAT
77698 AATATTTAATTTAAATAAT
1 AATATTTAATTTAAATAAT
77717 AATATT
1 AATATT
77723 ATCTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
19 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATTTAATTTAAATAAT
Found at i:80541 original size:17 final size:17
Alignment explanation
Indices: 80519--80554 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
80509 TTGTTATCTT
*
80519 TTAAATAATTTTCTTTA
1 TTAAATAATATTCTTTA
*
80536 TTAAATCATATTCTTTA
1 TTAAATAATATTCTTTA
80553 TT
1 TT
80555 TTAAATTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATAATATTCTTTA
Found at i:81777 original size:18 final size:18
Alignment explanation
Indices: 81754--81795 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
81744 AAAACATAAT
* *
81754 TTTATATTTTAAATAAAA
1 TTTATAATTAAAATAAAA
81772 TTTATAATTAAAATAAAA
1 TTTATAATTAAAATAAAA
81790 TATTAT
1 T-TTAT
81796 TAATAGAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTATAATTAAAATAAAA
Found at i:86678 original size:22 final size:22
Alignment explanation
Indices: 86650--86693 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
86640 CAATTTTGTT
86650 TCATTTATTTTACCAACAATGG
1 TCATTTATTTTACCAACAATGG
86672 TCATTTATTTTACCAACAATGG
1 TCATTTATTTTACCAACAATGG
86694 CATCTGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (22 bp):
TCATTTATTTTACCAACAATGG
Found at i:89762 original size:51 final size:52
Alignment explanation
Indices: 89702--89888 Score: 141
Period size: 52 Copynumber: 3.5 Consensus size: 52
89692 TTGCCTGCAC
*
89702 AAGAGGTAAT-GTACCTGTTTTATGATGAAATCTTAGTTTTTCCATGTAACT
1 AAGAGGTAATAATACCTGTTTTATGATGAAATCTTAGTTTTTCCATGTAACT
* *** * *
89753 AAGAGGTAATAATACCTGTTTTATTATCCTGACGGGGCCTTCGATCCTATATTGCC-TG-CAC-
1 AAGAGGTAATAATACCTGTTTTATGA---TGA---AATCTTAG-T--T-T-TT-CCATGTAACT
* * *
89814 AAGAGGTAAT-GTACCTGTTTTATGGTGAAATCTTAGTTTTTCCATATAACT
1 AAGAGGTAATAATACCTGTTTTATGATGAAATCTTAGTTTTTCCATGTAACT
89865 AAGAGGTAATAATACCTGTTTTAT
1 AAGAGGTAATAATACCTGTTTTAT
89889 TATCCTGACG
Statistics
Matches: 102, Mismatches: 17, Indels: 33
0.67 0.11 0.22
Matches are distributed among these distances:
48 2 0.02
49 3 0.03
50 3 0.03
51 21 0.21
52 25 0.25
53 1 0.01
54 4 0.04
55 3 0.03
57 3 0.03
58 4 0.04
59 1 0.01
60 12 0.12
61 11 0.11
62 3 0.03
63 4 0.04
64 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (52 bp):
AAGAGGTAATAATACCTGTTTTATGATGAAATCTTAGTTTTTCCATGTAACT
Found at i:89876 original size:112 final size:112
Alignment explanation
Indices: 89663--89929 Score: 484
Period size: 112 Copynumber: 2.4 Consensus size: 112
89653 CCTGGTTTGG
*
89663 TTATTATCCTGA-TGGG-CTTCGATCCTATATTGCCTGCACAAGAGGTAATGTACCTGTTTTATG
1 TTATTATCCTGACGGGGCCTTCGATCCTATATTGCCTGCACAAGAGGTAATGTACCTGTTTTATG
*
89726 ATGAAATCTTAGTTTTTCCATGTAACTAAGAGGTAATAATACCTGTT
66 ATGAAATCTTAGTTTTTCCATATAACTAAGAGGTAATAATACCTGTT
89773 TTATTATCCTGACGGGGCCTTCGATCCTATATTGCCTGCACAAGAGGTAATGTACCTGTTTTATG
1 TTATTATCCTGACGGGGCCTTCGATCCTATATTGCCTGCACAAGAGGTAATGTACCTGTTTTATG
*
89838 GTGAAATCTTAGTTTTTCCATATAACTAAGAGGTAATAATACCTGTT
66 ATGAAATCTTAGTTTTTCCATATAACTAAGAGGTAATAATACCTGTT
*
89885 TTATTATCCTGACGGGGCCTTAGATCCTATATTGCCTGCACAAGA
1 TTATTATCCTGACGGGGCCTTCGATCCTATATTGCCTGCACAAGA
89930 CCTGCTTTAT
Statistics
Matches: 151, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
110 12 0.08
111 3 0.02
112 136 0.90
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (112 bp):
TTATTATCCTGACGGGGCCTTCGATCCTATATTGCCTGCACAAGAGGTAATGTACCTGTTTTATG
ATGAAATCTTAGTTTTTCCATATAACTAAGAGGTAATAATACCTGTT
Found at i:91580 original size:28 final size:28
Alignment explanation
Indices: 91540--91594 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
91530 TCCATTTACT
*
91540 TTATATTGCCGAGCTAGT-GCTTGAAAGA
1 TTATATTGCCGAGCCAGTAG-TTGAAAGA
*
91568 TTATATTGTCGAGCCAGTAGTTGAAAG
1 TTATATTGCCGAGCCAGTAGTTGAAAG
91595 CAACGGTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (28 bp):
TTATATTGCCGAGCCAGTAGTTGAAAGA
Found at i:92813 original size:145 final size:147
Alignment explanation
Indices: 92628--92913 Score: 434
Period size: 145 Copynumber: 2.0 Consensus size: 147
92618 AAACTATTTA
* *
92628 AATTAGAATAAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACA-AAACTCGAA
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTC-AA
*** *
92692 -AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCG-AATTTTTTTAGTAAACT
65 CAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTGAGTAAACT
92755 ATTTTATAAACTAAACTG
130 ATTTTATAAACTAAACTG
* * *
92773 AATTAGAATCAAATAATATTATAATATGCTAAATATTTATAATTAAATTTAAACAGAAATTCAAC
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAC
* * *
92838 AATTCAATTTAATTCGACTTGATTTAAATTTTATAAACTTAAATCGAAAAAATTTGAGTCAACTA
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTGAGTAAACTA
92903 TTTTATAAACT
131 TTTTATAAACT
92914 GAATTGAGTA
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
145 53 0.42
146 49 0.39
147 24 0.19
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (147 bp):
AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAC
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTGAGTAAACTA
TTTTATAAACTAAACTG
Found at i:93129 original size:35 final size:35
Alignment explanation
Indices: 93088--93164 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
93078 GGGTTGGGCA
** *
93088 GTAATTGAAGTATTTTGGAATTTGATG-TTTAGAAT
1 GTAATTGAAACATTTTGGAATTTG-GGATTTAGAAT
*
93123 GTAATTGAAACATTTTGGATTTTGGGATTTAGAAT
1 GTAATTGAAACATTTTGGAATTTGGGATTTAGAAT
93158 GTAATTG
1 GTAATTG
93165 GTGATGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.03
35 36 0.97
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.44
Consensus pattern (35 bp):
GTAATTGAAACATTTTGGAATTTGGGATTTAGAAT
Found at i:100459 original size:23 final size:23
Alignment explanation
Indices: 100429--100483 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
100419 CTGATCGTGT
100429 GATTTGCAGGTGATTTGAAAATG
1 GATTTGCAGGTGATTTGAAAATG
100452 GATTTGCAGGTGATTTGAAAATG
1 GATTTGCAGGTGATTTGAAAATG
*
100475 GTTTTGCAG
1 GATTTGCAG
100484 CCATTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.31, T:0.36
Consensus pattern (23 bp):
GATTTGCAGGTGATTTGAAAATG
Found at i:112560 original size:14 final size:14
Alignment explanation
Indices: 112543--112587 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
112533 TTGAATCTTA
*
112543 AAATTTAAAATATT
1 AAATCTAAAATATT
112557 AAATCT-AAATATT
1 AAATCTAAAATATT
112570 AAAATCTAAAAT-TT
1 -AAATCTAAAATATT
112584 AAAT
1 AAAT
112588 TCTTAAACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 11 0.39
14 13 0.46
15 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCTAAAATATT
Found at i:113759 original size:20 final size:20
Alignment explanation
Indices: 113734--113772 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
113724 TAATAATGGA
* *
113734 TTATAATTGTATTATTATAG
1 TTATAATTATATTACTATAG
113754 TTATAATTATATTACTATA
1 TTATAATTATATTACTATA
113773 AAATTATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
TTATAATTATATTACTATAG
Found at i:114194 original size:2 final size:2
Alignment explanation
Indices: 114187--114212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
114177 ATTCATGATA
114187 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
114213 CCCCTAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:132990 original size:16 final size:16
Alignment explanation
Indices: 132956--132998 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
132946 AAATATTTTT
* * *
132956 TTTCTAGTTTTCTATC
1 TTTCTAATTTTCAAAC
132972 TTTCTAATTTTCAAAC
1 TTTCTAATTTTCAAAC
*
132988 TTTCCAATTTT
1 TTTCTAATTTT
132999 GTTTCCACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTCTAATTTTCAAAC
Found at i:145501 original size:19 final size:19
Alignment explanation
Indices: 145477--145532 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
145467 GAACGCTGGA
145477 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
145496 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
145517 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
145533 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:145512 original size:11 final size:11
Alignment explanation
Indices: 145477--145525 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
145467 GAACGCTGGA
145477 AACCGGTTTTG
1 AACCGGTTTTG
145488 -ACCGG-TTT-
1 AACCGGTTTTG
145496 AACCGGTTTTG
1 AACCGGTTTTG
145507 AACCGGTTTTG
1 AACCGGTTTTG
145518 -ACCGGTTT
1 AACCGGTTT
145526 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:145528 original size:9 final size:10
Alignment explanation
Indices: 145478--145532 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
145468 AACGCTGGAA
145478 ACCGGTTTTG
1 ACCGGTTTTG
*
145488 ACCGG-TTTA
1 ACCGGTTTTG
145497 ACCGGTTTTG
1 ACCGGTTTTG
145507 AACCGGTTTTG
1 -ACCGGTTTTG
145518 ACCGG-TTTG
1 ACCGGTTTTG
145527 ACCGGT
1 ACCGGT
145533 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:145579 original size:18 final size:18
Alignment explanation
Indices: 145553--145591 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
145543 TTACCCGTTT
145553 ACCCAACCCGTTGACCCG
1 ACCCAACCCGTTGACCCG
* *
145571 ACCCGACCCGTTGACCTG
1 ACCCAACCCGTTGACCCG
145589 ACC
1 ACC
145592 GGTGCTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.49, G:0.18, T:0.13
Consensus pattern (18 bp):
ACCCAACCCGTTGACCCG
Found at i:145653 original size:29 final size:29
Alignment explanation
Indices: 145592--145667 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
145582 TGACCTGACC
* *** *
145592 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTATGGGAATTAATTCGAAATG
145621 GGTGCTATTATGGGAATTAATTCGAAATG
1 GGTGCTATTATGGGAATTAATTCGAAATG
* *
145650 GGTGCTATTTTGGTAATT
1 GGTGCTATTATGGGAATT
145668 TTTTTAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.22, C:0.08, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTATGGGAATTAATTCGAAATG
Found at i:152743 original size:19 final size:19
Alignment explanation
Indices: 152719--152774 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
152709 GAACGCTGGA
152719 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
152738 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
152759 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
152775 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:152754 original size:11 final size:11
Alignment explanation
Indices: 152719--152767 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
152709 GAACGCTGGA
152719 AACCGGTTTTG
1 AACCGGTTTTG
152730 -ACCGG-TTT-
1 AACCGGTTTTG
152738 AACCGGTTTTG
1 AACCGGTTTTG
152749 AACCGGTTTTG
1 AACCGGTTTTG
152760 -ACCGGTTT
1 AACCGGTTT
152768 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:152770 original size:9 final size:10
Alignment explanation
Indices: 152720--152774 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
152710 AACGCTGGAA
152720 ACCGGTTTTG
1 ACCGGTTTTG
*
152730 ACCGG-TTTA
1 ACCGGTTTTG
152739 ACCGGTTTTG
1 ACCGGTTTTG
152749 AACCGGTTTTG
1 -ACCGGTTTTG
152760 ACCGG-TTTG
1 ACCGGTTTTG
152769 ACCGGT
1 ACCGGT
152775 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:152818 original size:18 final size:18
Alignment explanation
Indices: 152795--152829 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
152785 TTACCCGTTT
152795 ACCCGACCCGTTGACCCA
1 ACCCGACCCGTTGACCCA
152813 ACCCGACCCGTTGACCC
1 ACCCGACCCGTTGACCC
152830 GACCGGTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.51, G:0.17, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCA
Found at i:152895 original size:29 final size:29
Alignment explanation
Indices: 152834--152909 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
152824 TGACCCGACC
** *
152834 GGTGCTATTCTGGGAATTAATTCAGTTTT
1 GGTGCTATTCTGGGAATTAATTCAGAATG
152863 GGTGCTATTCTGGGAATTAATTC-GAAATG
1 GGTGCTATTCTGGGAATTAATTCAG-AATG
* *
152892 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
152910 TTTTAAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAGAATG
Found at i:158692 original size:11 final size:11
Alignment explanation
Indices: 158678--158733 Score: 52
Period size: 9 Copynumber: 5.5 Consensus size: 11
158668 ACCGGTAAAG
158678 AACCGGCTGAA
1 AACCGGCTGAA
158689 AACCGG--GAA
1 AACCGGCTGAA
*
158698 AACCGGGGTG--
1 AACC-GGCTGAA
158708 AACCGGCTGAA
1 AACCGGCTGAA
158719 AACCGGC--AA
1 AACCGGCTGAA
158728 AACCGG
1 AACCGG
158734 TTTGAACCAC
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 19 0.49
10 6 0.15
11 13 0.33
12 1 0.03
ACGTcount: A:0.36, C:0.27, G:0.32, T:0.05
Consensus pattern (11 bp):
AACCGGCTGAA
Found at i:158741 original size:30 final size:30
Alignment explanation
Indices: 158677--158733 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
158667 AACCGGTAAA
*
158677 GAACCGGCTGAAAACCGGGAAAACCGGGGT
1 GAACCGGCTGAAAACCGGCAAAACCGGGGT
158707 GAACCGGCTGAAAACCGGCAAAACCGG
1 GAACCGGCTGAAAACCGGCAAAACCGG
158734 TTTGAACCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.26, G:0.33, T:0.05
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAACCGGGGT
Found at i:158996 original size:24 final size:24
Alignment explanation
Indices: 158966--159021 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
158956 TAGAAATTCG
158966 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
158990 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
159014 ATTGAAGC
1 ATTGAAGC
159022 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:163098 original size:14 final size:15
Alignment explanation
Indices: 163063--163106 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
163053 CCTGATACCA
163063 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
163079 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
163093 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
163107 AAATCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:174002 original size:60 final size:60
Alignment explanation
Indices: 173921--174063 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
173911 GTTTGGGGAT
* * * * * ** * *
173921 CAATTTAGAATGAGGGACATAGTTTGGGTATGAAATT-GAATTTTTCAAACGTTTAATGAC
1 CAATTTAAAATGAGAGTCATAGTTTAGGAATGAAATTAGAACATTT-AAAAGTTTAAGGAC
* * *
173981 TAATTTAAAATGATAGTCATAGTTTATGAATGAAATTAGAACATTTAAAAGTTTAAGGAC
1 CAATTTAAAATGAGAGTCATAGTTTAGGAATGAAATTAGAACATTTAAAAGTTTAAGGAC
174041 CAATTTAAAATGAGAGTCATAGT
1 CAATTTAAAATGAGAGTCATAGT
174064 CTGAGGATAT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 62 0.91
61 6 0.09
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (60 bp):
CAATTTAAAATGAGAGTCATAGTTTAGGAATGAAATTAGAACATTTAAAAGTTTAAGGAC
Found at i:175615 original size:26 final size:26
Alignment explanation
Indices: 175584--175638 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
175574 AATAGTTTAA
175584 AAAATTAAGAATAATTGTCAGCATAT
1 AAAATTAAGAATAATTGTCAGCATAT
*
175610 AAAATTAAGAATGATTGTCAGCATAT
1 AAAATTAAGAATAATTGTCAGCATAT
175636 AAA
1 AAA
175639 TAATATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (26 bp):
AAAATTAAGAATAATTGTCAGCATAT
Found at i:178975 original size:40 final size:39
Alignment explanation
Indices: 178884--178994 Score: 147
Period size: 40 Copynumber: 2.9 Consensus size: 39
178874 TATTTTCAAC
* * *
178884 AAACATCTACCAAACTTTGTAAAACATTTTTC---AAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAAAAA
* *
178920 AAACATTTACTAAACTTTGAAAAATATTTTTCAAAAAAAA
1 AAACATTTACCAAACTTTGAAAAACATTTTTC-AAAAAAA
178960 AAACATTTACCAAACTTTGAAAAACATTTTTCAAA
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAA
178995 GTTGGTTGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
36 28 0.44
39 3 0.05
40 33 0.52
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.32
Consensus pattern (39 bp):
AAACATTTACCAAACTTTGAAAAACATTTTTCAAAAAAA
Found at i:178994 original size:21 final size:21
Alignment explanation
Indices: 178931--178994 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
178921 AACATTTACT
*
178931 AAACTTTGAAAAATATTTTTC
1 AAACTTTGAAAAACATTTTTC
*** **
178952 AAA--AAAAAAAACATTTACC
1 AAACTTTGAAAAACATTTTTC
178971 AAACTTTGAAAAACATTTTTC
1 AAACTTTGAAAAACATTTTTC
178992 AAA
1 AAA
178995 GTTGGTTGCC
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (21 bp):
AAACTTTGAAAAACATTTTTC
Found at i:183578 original size:36 final size:35
Alignment explanation
Indices: 183522--183591 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 35
183512 AACATCTACC
183522 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAT
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAT
* *
183557 AAACATTTATCAAACTTTGAAAAATATTTTTCAAA
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAA
183592 GTTAGTTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAT
Found at i:183609 original size:34 final size:34
Alignment explanation
Indices: 183531--183612 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 34
183521 CAAACTTTAC
*
183531 CAAACTTTGAAAAACATTTTTCAAATAAACATTTAT
1 CAAACTTTGAAAAACATTTTTCAAAT--ACAGTTAT
* * *
183567 CAAACTTTGAAAAATATTTTTCAAAGT-TAGTTGT
1 CAAACTTTGAAAAACATTTTTCAAA-TACAGTTAT
183601 CAAACTTTGAAA
1 CAAACTTTGAAA
183613 TTAACTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 16 0.39
36 24 0.59
37 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (34 bp):
CAAACTTTGAAAAACATTTTTCAAATACAGTTAT
Found at i:187125 original size:100 final size:100
Alignment explanation
Indices: 187003--187784 Score: 947
Period size: 100 Copynumber: 7.8 Consensus size: 100
186993 TATCGATAGT
* * *** * * *
187003 GTAATAATAATTATAACTTAACCGATTAAAATAAAATAGACACAACATATTACGTTAAAGTAACT
1 GTAA-AATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCT
* **
187068 ATCAATTTGTTTAAAAGTATAATAATAATGTAAACG
65 ACCGGTTTGTTTAAAAGTATAATAATAATGTAAACG
* * *
187104 GTAAAATAATTACAACTTAACCAATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGTTA
1 GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTA
* * *
187169 CCGATTTGTTTAAATGTATATTAATAATGTAAACG
66 CCGGTTTGTTTAAAAGTATAATAATAATGTAAACG
* ** * *
187204 GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGATGTTACCTATTACGTTAAAATAGCAA
1 GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTA
* **
187269 TCAATTTGTTTAAAAGTCATAATAATAATGTAAACG
66 CCGGTTTGTTTAAAAGT-ATAATAATAATGTAAACG
* ** * * * * * *
187305 GTAAAATATTTATAACTTAATGGGTTAAAATAAAATATGTGCATCCTATTAAGTTTAACTAGTTA
1 GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTA
* * *
187370 CCGGTTTGTTTAAAGGTATATTAATATTGTAAACG
66 CCGGTTTGTTTAAAAGTATAATAATAATGTAAACG
* * ** * *
187405 GTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGCGCTTCCTATTTCGTTAAATTAGCTA
1 GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTA
* * *
187470 -CGTGTTTGTTTAAAGGTAAAATAATAATTTAAACG
66 CCG-GTTTGTTTAAAAGTATAATAATAATGTAAACG
* * * *
187505 GTAAAATATTTACAACTTAAACGATTAAAATAAAATAGGCGCAACTTATTACGTTAAACTAGCCA
1 GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTA
* *
187570 CTGGTTTGTTTAAAAGTATAATAATAATGTAAATG
66 CCGGTTTGTTTAAAAGTATAATAATAATGTAAACG
*
187605 GTAAAATATTTACAACTTAACC-AGTTAAAATAAAATAGGTGCAACCTATTACGTTACACTAGCT
1 GTAAAATATTTACAACTTAACCGA-TTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCT
* *
187669 ACCGGTTTATTTAAAGGTATAATAATAATGTAAACG
65 ACCGGTTTGTTTAAAAGTATAATAATAATGTAAACG
* * * * **
187705 AGTAAAATAATTACAACTTAACCGGTTAAAATAGAATATGTGCAACCTATTATTTTAAACTAGCT
1 -GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCT
*
187770 ACCAGTTTGTTTAAA
65 ACCGGTTTGTTTAAA
187785 TATTTTTTTA
Statistics
Matches: 584, Mismatches: 91, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
99 3 0.01
100 426 0.73
101 155 0.27
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (100 bp):
GTAAAATATTTACAACTTAACCGATTAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTA
CCGGTTTGTTTAAAAGTATAATAATAATGTAAACG
Found at i:187462 original size:301 final size:300
Alignment explanation
Indices: 187073--187785 Score: 968
Period size: 301 Copynumber: 2.4 Consensus size: 300
187063 TAACTATCAA
* **
187073 TTTGTTTAAAAGTATAATAATAATGTAAACGGTAAAATAATTACAACTTAACCAATTAAAATAAA
1 TTTGTTTAAAGGTATAATAATAATGTAAACGGTAAAATAATTACAACTTAACCGGTTAAAATAAA
* * * *
187138 ATAGGTGCAACCTATTACGTTAAACTAGTTACCGATTTGTTTAAATGTATATTAATAATGTAAAC
66 ATAGGTGCAACCTATTTCGTTAAACTAGCTACCGATTTGTTTAAATGTAAAATAATAATGTAAAC
* * **
187203 GGTAAAATATTTACAACTTAACCGATTAAAATAAAATAGATGTTACCTATTACGTTAAAATAGCA
131 GGTAAAATATTTACAACTTAAACGATTAAAATAAAATAGACGCAACCTATTACGTTAAAATAGCA
* ***
187268 A-TCAATTTGTTTAAAAGTCATAATAATAATGTAAACGGTAAAATATTTATAACTTAATGGGTTA
196 ACT-AATTTGTTTAAAAGT-ATAATAATAATGTAAACGGTAAAATATTTACAACTTAACCAGTTA
* * *
187332 AAATAAAATATGTGCATCCTATTAAGTTTA-ACTAGTTACCGG
259 AAATAAAATAGGTGCAACCTATTAAG-TTACACTAGCTACCGG
* * *
187374 TTTGTTTAAAGGTATATTAATATTGTAAACGGTAAAATATTTACAACTTAACCGGTTAAAATAAA
1 TTTGTTTAAAGGTATAATAATAATGTAAACGGTAAAATAATTACAACTTAACCGGTTAAAATAAA
* ** * * * *
187439 ATAGGCGCTTCCTATTTCGTTAAATTAGCTA-CGTGTTTGTTTAAAGGTAAAATAATAATTTAAA
66 ATAGGTGCAACCTATTTCGTTAAACTAGCTACCG-ATTTGTTTAAATGTAAAATAATAATGTAAA
* * *
187503 CGGTAAAATATTTACAACTTAAACGATTAAAATAAAATAGGCGCAACTTATTACGTTAAACTAGC
130 CGGTAAAATATTTACAACTTAAACGATTAAAATAAAATAGACGCAACCTATTACGTTAAAATAGC
* ** *
187568 CACTGGTTTGTTTAAAAGTATAATAATAATGTAAATGGTAAAATATTTACAACTTAACCAGTTAA
195 AACTAATTTGTTTAAAAGTATAATAATAATGTAAACGGTAAAATATTTACAACTTAACCAGTTAA
*
187633 AATAAAATAGGTGCAACCTATTACGTTACACTAGCTACCGG
260 AATAAAATAGGTGCAACCTATTAAGTTACACTAGCTACCGG
* *
187674 TTTATTTAAAGGTATAATAATAATGTAAACGAGTAAAATAATTACAACTTAACCGGTTAAAATAG
1 TTTGTTTAAAGGTATAATAATAATGTAAACG-GTAAAATAATTACAACTTAACCGGTTAAAATAA
* *
187739 AATATGTGCAACCTATTAT-TTTAAACTAGCTACC-AGTTTGTTTAAAT
65 AATAGGTGCAACCTATT-TCGTTAAACTAGCTACCGA-TTTGTTTAAAT
187786 ATTTTTTTAT
Statistics
Matches: 356, Mismatches: 49, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
299 3 0.01
300 104 0.29
301 246 0.69
302 3 0.01
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (300 bp):
TTTGTTTAAAGGTATAATAATAATGTAAACGGTAAAATAATTACAACTTAACCGGTTAAAATAAA
ATAGGTGCAACCTATTTCGTTAAACTAGCTACCGATTTGTTTAAATGTAAAATAATAATGTAAAC
GGTAAAATATTTACAACTTAAACGATTAAAATAAAATAGACGCAACCTATTACGTTAAAATAGCA
ACTAATTTGTTTAAAAGTATAATAATAATGTAAACGGTAAAATATTTACAACTTAACCAGTTAAA
ATAAAATAGGTGCAACCTATTAAGTTACACTAGCTACCGG
Found at i:188090 original size:138 final size:134
Alignment explanation
Indices: 187814--188090 Score: 286
Period size: 138 Copynumber: 2.0 Consensus size: 134
187804 ATAATACATT
* * * * *
187814 ATTTTCAATTTTAATGTATTCAAACATATCTCTATACTATTATAACTGACAAAATTAATGCATCA
1 ATTTTCAATTTTAATGTACTCAAACATATCTCCATACTATTAAAACCGACAAAATGAATGCATCA
* * * ** *
187879 ATTATACTCAAACATTCGATACTTAAATTTCAATTCCAATTTCAATTTCAGACCCACTATTCATC
66 AGTATAATCAAACATTCAATACTTAAATTTCAATTCCAATTTCAATTTCAGACCCACTATAAATA
****
187944 TTTT
131 ACAA
187948 ATTTTCAATTTTAATGTACTCAAACATATCTCCATACTATTACAACCGACCGACAAAATGAATGC
1 ATTTTCAATTTTAATGTACTCAAACATATCTCCATACTATTA-AA---ACCGACAAAATGAATGC
* * * ** * * **
188013 AT-TAGTAGTAATCAAACATTTAATACTTAAATTTTAATTTTAATTTTAATTTGAGTTCCACTAT
62 ATCAAGTA-TAATCAAACATTCAATACTTAAATTTCAATTCCAATTTCAATTTCAGACCCACTAT
188077 AAATAACAA
126 AAATAACAA
188086 ATTTT
1 ATTTT
188091 GTGTTAAATG
Statistics
Matches: 114, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
134 40 0.35
135 1 0.01
137 3 0.03
138 70 0.61
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.39
Consensus pattern (134 bp):
ATTTTCAATTTTAATGTACTCAAACATATCTCCATACTATTAAAACCGACAAAATGAATGCATCA
AGTATAATCAAACATTCAATACTTAAATTTCAATTCCAATTTCAATTTCAGACCCACTATAAATA
ACAA
Found at i:188236 original size:33 final size:33
Alignment explanation
Indices: 188162--188242 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
188152 AAATGATACG
*
188162 GAGCAATCAACCAACAACTCATCAAAAAATCTT
1 GAGCAATCAACTAACAACTCATCAAAAAATCTT
** *
188195 GATTAATCAACTAACAATTCATCGAAAAAAT-TCT
1 GAGCAATCAACTAACAACTCATC-AAAAAATCT-T
188229 -AGCAATCAACTAAC
1 GAGCAATCAACTAAC
188243 CAATGTTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 32 0.80
34 8 0.20
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.22
Consensus pattern (33 bp):
GAGCAATCAACTAACAACTCATCAAAAAATCTT
Found at i:189255 original size:100 final size:100
Alignment explanation
Indices: 189068--189336 Score: 367
Period size: 100 Copynumber: 2.7 Consensus size: 100
189058 TCATAATAGA
* *
189068 TACCGGTTTGTTTAAATGTATAATATTAAAGTAAACGGTAAAATATTTAAAACTTAACCGGTTAA
1 TACCGGTTTGTTTAAATGTATAATATTAATGTAAACGGTAAAATATTTAAAACTTAACTGGTTAA
* * *
189133 AATAAAATAGGTGATACCTATTACGTTAAACTAGC
66 AATAAAACAGGCGATACCTATTACGTTAAACTACC
* * * * *
189168 TACCAGTTTGTTTAAAGGTATAATATCAATGTAAGCGGTAAAATATTTACAACTTAACTGGTTAA
1 TACCGGTTTGTTTAAATGTATAATATTAATGTAAACGGTAAAATATTTAAAACTTAACTGGTTAA
* * *
189233 AATAAAACATGCGCTACTTATTACGTTAAACTACC
66 AATAAAACAGGCGATACCTATTACGTTAAACTACC
* * * * * *
189268 TGCCGGTTTGTTTAAATGTATAATATTAATGTAAACAGTAAAATTTTTATAACTTAACTGCTTGA
1 TACCGGTTTGTTTAAATGTATAATATTAATGTAAACGGTAAAATATTTAAAACTTAACTGGTTAA
189333 AATA
66 AATA
189337 TTTTTTTTAA
Statistics
Matches: 146, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 146 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (100 bp):
TACCGGTTTGTTTAAATGTATAATATTAATGTAAACGGTAAAATATTTAAAACTTAACTGGTTAA
AATAAAACAGGCGATACCTATTACGTTAAACTACC
Found at i:191010 original size:21 final size:21
Alignment explanation
Indices: 190984--191024 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
190974 GGGTACCGAT
190984 ACACCAGGAGTGTGTCGGTTC
1 ACACCAGGAGTGTGTCGGTTC
191005 ACACCAGGAGTGTGTCGGTT
1 ACACCAGGAGTGTGTCGGTT
191025 TACTCCTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.24
Consensus pattern (21 bp):
ACACCAGGAGTGTGTCGGTTC
Found at i:192236 original size:19 final size:20
Alignment explanation
Indices: 192201--192242 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
192191 GGCTGAAATT
192201 ACTGTAGCAGTGTATCGATAC
1 ACTGTAGCAG-GTATCGATAC
192222 ACTGTAGCA-GTATCGATAC
1 ACTGTAGCAGGTATCGATAC
192241 AC
1 AC
192243 ATTTTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ACTGTAGCAGGTATCGATAC
Found at i:192310 original size:20 final size:20
Alignment explanation
Indices: 192282--192340 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
192272 TATTATTCAT
* * *
192282 TACTGTTTACACGGTATCGG
1 TACTATTTACACAGTATAGG
*
192302 TACTATTTACACAGTATATG
1 TACTATTTACACAGTATAGG
* *
192322 TACTATTCATACAGTATAG
1 TACTATTTACACAGTATAG
192341 TACCTATTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (20 bp):
TACTATTTACACAGTATAGG
Found at i:192347 original size:20 final size:20
Alignment explanation
Indices: 192301--192352 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
192291 CACGGTATCG
* *
192301 GTACTATTTACACAGTATAT
1 GTACTATTCATACAGTATAT
192321 GTACTATTCATACAGTATA-
1 GTACTATTCATACAGTATAT
192340 GTACCTATTCATA
1 GTA-CTATTCATA
192353 AAAACATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
GTACTATTCATACAGTATAT
Found at i:192779 original size:107 final size:106
Alignment explanation
Indices: 192525--192913 Score: 467
Period size: 108 Copynumber: 3.6 Consensus size: 106
192515 GTGTTACAGA
** * * * *
192525 TAACATTTTAGACGCTACCTAATATGCTGATAATAATAATAACAAAATAAGTAATTAACTTATTT
1 TAACATTTTAGGTGCTACATAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTT
* * * *
192590 TGTTATCGTCGAATTTTTAAGGCCCCGTA-AGCTTTAACTTTAG
66 TGTTATCGTCAAATTTTTAA-G-CTC-TATCGCTTAAACTTTAG
*
192633 TAACATTTTAGGTGCTACACAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTT
1 TAACATTTTAGGTGCTACATAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTT
* *
192698 TGTTATCGTCAAATTTCTAAGCTCATATCGCTTAAACTTTGG
66 TGTTATCGTCAAATTTTTAAGCTC-TATCGCTTAAACTTTAG
* *
192740 TAACATTTTAAGTGCTAAATAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTT
1 TAACATTTTAGGTGCTACATAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTT
* * * *
192805 TGTTATCGTCAGATTTTTAAGGTCTCATCAGCTTGAACTCTCA-
66 TGTTATCGTCAAATTTTTAAGCTCT-ATC-GCTTAAACT-TTAG
* * * * * * *
192848 TAATATATTAGGCGCTACCTAATCTGTTGATAATATTAATAACAAAATAAGTAATTTACTTATTT
1 TAACATTTTAGGTGCTACATAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTT
192913 T
66 T
192914 CTTACAATTT
Statistics
Matches: 245, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
106 5 0.02
107 98 0.40
108 141 0.58
109 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (106 bp):
TAACATTTTAGGTGCTACATAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTT
TGTTATCGTCAAATTTTTAAGCTCTATCGCTTAAACTTTAG
Found at i:193474 original size:60 final size:60
Alignment explanation
Indices: 193362--193474 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
193352 ATAGTAGACT
* * * *
193362 GACCATTTTGTAACTTTTAATAGTTGGGGGACTCAACCAAATAACACTCTATAGTTGAAA
1 GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACCAAATAACACCCTATAGTTGAAA
* *
193422 GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAA-TAAAGTATCACCCTATA
1 GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACCAAA-TAACACCCTATA
193475 ATCGGAGGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACCAAATAACACCCTATAGTTGAAA
Found at i:193486 original size:60 final size:60
Alignment explanation
Indices: 193362--193489 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
193352 ATAGTAGACT
* * * * * *
193362 GACCATTTTGTAACTTTTAATAGTTGGGGGACTCAACCAAATAACACTCTATAGTTGAAA
1 GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACCAAATAACACCCTATAATCGAAA
* * * *
193422 GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAA-TAAAGTATCACCCTATAATCGGAG
1 GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACCAAA-TAACACCCTATAATCGAAA
193482 GACCATTT
1 GACCATTT
193490 GTATACTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 3 0.05
60 54 0.95
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACCAAATAACACCCTATAATCGAAA
Found at i:193595 original size:36 final size:36
Alignment explanation
Indices: 193548--193620 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
193538 GTGTCAAGTC
193548 GAAGTTGACACCAACACCGTAAGGCTGAGAAGAAAA
1 GAAGTTGACACCAACACCGTAAGGCTGAGAAGAAAA
193584 GAAGTTGACACCAACACCGTAAGGCTGAGAAGAAAA
1 GAAGTTGACACCAACACCGTAAGGCTGAGAAGAAAA
193620 G
1 G
193621 CAACCCCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.11
Consensus pattern (36 bp):
GAAGTTGACACCAACACCGTAAGGCTGAGAAGAAAA
Found at i:198476 original size:23 final size:24
Alignment explanation
Indices: 198446--198498 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
198436 TGAAACGGAC
198446 ATAAAATTCTAGGAAG-TAAA-TT
1 ATAAAATTCTAGGAAGCTAAAGTT
* *
198468 GATAAAATTTTATGAAGCTAAAGTT
1 -ATAAAATTCTAGGAAGCTAAAGTT
198493 ATAAAA
1 ATAAAA
198499 CAAATTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 14 0.54
24 10 0.38
25 2 0.08
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (24 bp):
ATAAAATTCTAGGAAGCTAAAGTT
Found at i:209434 original size:23 final size:24
Alignment explanation
Indices: 209407--209456 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
209397 AAATTTTATA
*
209407 TTAGAATATAAA-CTTT-TAAAATT
1 TTAGAATA-AAATATTTATAAAATT
209430 TTAGAATAAAATATTTATAAAATT
1 TTAGAATAAAATATTTATAAAATT
209454 TTA
1 TTA
209457 AATTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 3 0.12
23 11 0.46
24 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (24 bp):
TTAGAATAAAATATTTATAAAATT
Found at i:209472 original size:31 final size:30
Alignment explanation
Indices: 209412--209489 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
209402 TTATATTAGA
*
209412 ATATAAACTTTTAAAATTTTAGAATAAAAT
1 ATATAAAATTTTAAAATTTTAGAATAAAAT
*
209442 ATTTATAAAATTTT-AAATTTT-TAATAAAAAT
1 A--TATAAAATTTTAAAATTTTAGAAT-AAAAT
*
209473 ATATATAATTTTAAAAT
1 ATATAAAATTTTAAAAT
209490 ATATTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 10 0.24
30 8 0.20
31 13 0.32
32 10 0.24
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
ATATAAAATTTTAAAATTTTAGAATAAAAT
Found at i:209490 original size:17 final size:18
Alignment explanation
Indices: 209468--209505 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
209458 ATTTTTAATA
209468 AAAATATA-TATAATTTT
1 AAAATATATTATAATTTT
*
209485 AAAATATATTTTAATTTT
1 AAAATATATTATAATTTT
209503 AAA
1 AAA
209506 TTTTTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATATTATAATTTT
Found at i:209992 original size:17 final size:17
Alignment explanation
Indices: 209952--209992 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
209942 TTTTTAAATC
*
209952 AATA-TTTATATTTTAA
1 AATATTTTAAATTTTAA
*
209968 TA-ATTTTAAATTTTAA
1 AATATTTTAAATTTTAA
209984 AATATTTTA
1 AATATTTTA
209993 TATCACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.65
17 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATTTTAAATTTTAA
Found at i:212509 original size:336 final size:337
Alignment explanation
Indices: 211896--212885 Score: 1871
Period size: 336 Copynumber: 3.0 Consensus size: 337
211886 AAGTTTATTA
211896 GTATTTATCATTAGGGTTAACTAAATTTGAGATTGTTTATTGATTTTGTTACTAAACTTTAAAAT
1 GTATTTATCATTAGGGTTAACTAAATTTGAGATTGTTTATTGATTTTGTTACTAAACTTTAAAAT
211961 ATTTCAATTTTAATATCAAAATTTCACATTATATTTTTGTCATTTAACCATTAACTTGTTAATAA
66 ATTTCAATTTTAATATCAAAATTTCACATTATATTTTTGTCATTTAACCATTAACTTGTTAATAA
212026 CTTGATGGTGTGATAATTTCTTCTTAG--TTTTTTTATAGAAAATCATCAACTCTTCATTGTCAG
131 CTTGATGGTGTGATAATTTCTTCTTAGTTTTTTTTTATAGAAAATCATCAACTCTTCATTGTCAG
212089 TCAACCATCGCTCGTCATTGATTGTTATTTGTGATAAGATCAATATCTAAACATTCATGTTTCAG
196 TCAACCATCGCTCGTCATTGATTGTTATTTGTGATAAGATCAATATCTAAACATTCATGTTTCAG
212154 TCATCATTATTCTTCATAGATTGGTTTTCTACAAAAACTACCAAAAATGATGAAGCCCCAATGTT
261 TCATCATTATT-TTCATAGATTGGTTTTCTACAAAAACTACCAAAAATGATGAAGCCCCAATGTT
212219 CTAATTATTATAT
325 CTAATTATTATAT
212232 GTATTTATCATTAGGGTTAACTAAATTTGAGATTGTTTATTGATTTTGTTACTAAACTTTAAAAT
1 GTATTTATCATTAGGGTTAACTAAATTTGAGATTGTTTATTGATTTTGTTACTAAACTTTAAAAT
212297 ATTTCAATTTTAATATCAAAATTTCACATTATATTTTTGTCATTTAACCATTAACTTGTTAATAA
66 ATTTCAATTTTAATATCAAAATTTCACATTATATTTTTGTCATTTAACCATTAACTTGTTAATAA
212362 CTTGATGGTGTGATAATTTCTTCTTAGTTTTTTTTTATAGAAAATCATCAACTCTTCATTGTCAG
131 CTTGATGGTGTGATAATTTCTTCTTAGTTTTTTTTTATAGAAAATCATCAACTCTTCATTGTCAG
212427 TCAACCATCGCTCGTCATTGATTGTTATTTGTGATAAGATCAATATCTAAACATTCATGTTTCAG
196 TCAACCATCGCTCGTCATTGATTGTTATTTGTGATAAGATCAATATCTAAACATTCATGTTTCAG
212492 -CATCATTATTTTCATAGATTGGTTTTCTACAAAAACTACCAAAAATGATGAAGCCCCAATGTTC
261 TCATCATTATTTTCATAGATTGGTTTTCTACAAAAACTACCAAAAATGATGAAGCCCCAATGTTC
212556 TAATTATTATAT
326 TAATTATTATAT
212568 GTATTTATCATTAGGGTTAACTAAATTTGAGATTGTTTATTGATTTTGTTACTAAACTTTAAAAT
1 GTATTTATCATTAGGGTTAACTAAATTTGAGATTGTTTATTGATTTTGTTACTAAACTTTAAAAT
212633 ATTTCAATTTTAATATCAAAATTTCACATTATATTTTTGTCATTT-ACCATTAACTTGTTAATAA
66 ATTTCAATTTTAATATCAAAATTTCACATTATATTTTTGTCATTTAACCATTAACTTGTTAATAA
212697 CTTGATGGTGTGATAATTTCTTCTTAGTTTTTTTTTATAGAAAA-CATC-ACTCTTCATTGTCA-
131 CTTGATGGTGTGATAATTTCTTCTTAGTTTTTTTTTATAGAAAATCATCAACTCTTCATTGTCAG
212759 TC-ACCATCGCTCGTCATTGATTGTTA-TTGTGATAAGATC-A-ATCTAAACATTCATGTTTCAG
196 TCAACCATCGCTCGTCATTGATTGTTATTTGTGATAAGATCAATATCTAAACATTCATGTTTCAG
*
212820 TCATCATTATCTTCATAGA-TGGTTTTCTACAAAAACTACC-AAAATGATGAAGCCCCAATGTTC
261 TCATCATTATTTTCATAGATTGGTTTTCTACAAAAACTACCAAAAATGATGAAGCCCCAATGTTC
212883 TAA
326 TAA
212886 AGCTTCTTCT
Statistics
Matches: 650, Mismatches: 1, Indels: 15
0.98 0.00 0.02
Matches are distributed among these distances:
327 26 0.04
328 42 0.06
329 18 0.03
330 13 0.02
331 24 0.04
332 2 0.00
333 14 0.02
334 4 0.01
335 63 0.10
336 333 0.51
337 10 0.02
338 101 0.16
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (337 bp):
GTATTTATCATTAGGGTTAACTAAATTTGAGATTGTTTATTGATTTTGTTACTAAACTTTAAAAT
ATTTCAATTTTAATATCAAAATTTCACATTATATTTTTGTCATTTAACCATTAACTTGTTAATAA
CTTGATGGTGTGATAATTTCTTCTTAGTTTTTTTTTATAGAAAATCATCAACTCTTCATTGTCAG
TCAACCATCGCTCGTCATTGATTGTTATTTGTGATAAGATCAATATCTAAACATTCATGTTTCAG
TCATCATTATTTTCATAGATTGGTTTTCTACAAAAACTACCAAAAATGATGAAGCCCCAATGTTC
TAATTATTATAT
Found at i:214432 original size:57 final size:59
Alignment explanation
Indices: 214371--214510 Score: 153
Period size: 57 Copynumber: 2.4 Consensus size: 59
214361 TATAGTTTGG
* ** *
214371 GATGAAATTGAAATGTTTAAAATTTTGGGGACCAATTTAGAA-AAT-GTCATAG-TTGAA
1 GATGAAATTGAAATGTTTAAAA-GTTGAAGACCAATTTAGAATAATAGTCATAGTTTAAA
* * * * *
214428 GATGAAAATG-AATATTCAAAAGTTGAAGACTAATTTAGAATGATAGTCATAGTTTAAA
1 GATGAAATTGAAATGTTTAAAAGTTGAAGACCAATTTAGAATAATAGTCATAGTTTAAA
*
214486 GATGAAATTAAAATGTTTAAAAGTT
1 GATGAAATTGAAATGTTTAAAAGTT
214511 TAGAGACTAC
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
55 15 0.23
56 11 0.17
57 16 0.24
58 12 0.18
59 12 0.18
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (59 bp):
GATGAAATTGAAATGTTTAAAAGTTGAAGACCAATTTAGAATAATAGTCATAGTTTAAA
Found at i:217915 original size:22 final size:22
Alignment explanation
Indices: 217887--217936 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
217877 AAGAGAATGT
217887 GGAATATTACCTTATTTCGTCC
1 GGAATATTACCTTATTTCGTCC
217909 GGAATATTACCTTATTTCGTCC
1 GGAATATTACCTTATTTCGTCC
217931 GGAATA
1 GGAATA
217937 ATACGTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (22 bp):
GGAATATTACCTTATTTCGTCC
Found at i:219488 original size:20 final size:21
Alignment explanation
Indices: 219447--219493 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
219437 AGCATTCACA
219447 TTAATAGTTGGAATATTTTTT
1 TTAATAGTTGGAATATTTTTT
219468 TTAATAGTTGGAATA-TTTTT
1 TTAATAGTTGGAATATTTTTT
219488 TTAATA
1 TTAATA
219494 AAGTCGCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (21 bp):
TTAATAGTTGGAATATTTTTT
Found at i:219984 original size:12 final size:12
Alignment explanation
Indices: 219967--220000 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
219957 AAAGGCAATT
219967 TAAAAAAAAAAC
1 TAAAAAAAAAAC
219979 TAAAAAAAGAAAC
1 TAAAAAAA-AAAC
219992 -AAAAAAAAA
1 TAAAAAAAAA
220001 GAAGAGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 15 0.71
13 4 0.19
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (12 bp):
TAAAAAAAAAAC
Found at i:220136 original size:22 final size:22
Alignment explanation
Indices: 220070--220136 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
220060 ATCAAAGAAT
220070 AAAAAGTTGATTTGATATATAG
1 AAAAAGTTGATTTGATATATAG
* ** * * *
220092 AAAACA-AT-ATAAGCTCTAAAG
1 AAAA-AGTTGATTTGATATATAG
220113 AAAAAGTTGATTTGATATATAG
1 AAAAAGTTGATTTGATATATAG
220135 AA
1 AA
220137 GAAAAAATTA
Statistics
Matches: 30, Mismatches: 12, Indels: 6
0.62 0.25 0.12
Matches are distributed among these distances:
20 1 0.03
21 13 0.43
22 15 0.50
23 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
AAAAAGTTGATTTGATATATAG
Found at i:229523 original size:37 final size:34
Alignment explanation
Indices: 229455--229519 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
229445 CCTTGGATGC
*
229455 TTTAATGTATCATCATCAGCACATTTTTTTTGTA
1 TTTAATGTATCATCATCAACACATTTTTTTTGTA
*
229489 TTTAATGTATCATCATCAACACTTTTTTTTT
1 TTTAATGTATCATCATCAACACATTTTTTTT
229520 TTTGCATGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.52
Consensus pattern (34 bp):
TTTAATGTATCATCATCAACACATTTTTTTTGTA
Found at i:230395 original size:23 final size:24
Alignment explanation
Indices: 230365--230411 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
230355 TTCGAATACA
230365 AAATAGAAAAATATAT-AAAGAGG
1 AAATAGAAAAATATATAAAAGAGG
230388 AAATAGAAAAATATATAAAAGAGG
1 AAATAGAAAAATATATAAAAGAGG
230412 TTAAAGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (24 bp):
AAATAGAAAAATATATAAAAGAGG
Found at i:236090 original size:28 final size:28
Alignment explanation
Indices: 236041--236117 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
236031 CTTTTTTTAA
*
236041 AAAATTTTATAA-TC-TTATTTATT-TTT
1 AAAATTTTATAATTCGTTA-TTATTATAT
236067 AAAATTTTATAAATTCGTTATTATTAATAT
1 AAAATTTTAT-AATTCGTTATTATT-ATAT
*
236097 AAAATTTT-TAATCCGTTATTA
1 AAAATTTTATAATTCGTTATTA
236118 ATTCACAGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 10 0.23
27 2 0.05
28 18 0.41
29 4 0.09
30 10 0.23
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (28 bp):
AAAATTTTATAATTCGTTATTATTATAT
Found at i:236093 original size:25 final size:26
Alignment explanation
Indices: 236041--236093 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
236031 CTTTTTTTAA
* * *
236041 AAAATTTTATAATCTTATTTATTTTT
1 AAAATTTTATAATATTAGTTATTATT
*
236067 AAAATTTTATAA-ATTCGTTATTATT
1 AAAATTTTATAATATTAGTTATTATT
236092 AA
1 AA
236094 TATAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (26 bp):
AAAATTTTATAATATTAGTTATTATT
Found at i:240493 original size:27 final size:28
Alignment explanation
Indices: 240462--240518 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
240452 AAAAAAATAA
*
240462 GGCCTTAATTATAAATATATAAATT-AG
1 GGCCTTAATTATAAATATAAAAATTGAG
240489 GGCCTTAATTATAAATATAAAAATTGAG
1 GGCCTTAATTATAAATATAAAAATTGAG
240517 GG
1 GG
240519 ACTGAGCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (28 bp):
GGCCTTAATTATAAATATAAAAATTGAG
Found at i:247803 original size:9 final size:9
Alignment explanation
Indices: 247785--247819 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
247775 GCTGGCTATA
*
247785 CTTCCCTCT
1 CTTCCATCT
247794 CTTCCATCT
1 CTTCCATCT
247803 CTTCCATCT
1 CTTCCATCT
247812 CTT-CATCT
1 CTTCCATCT
247820 GACCTCGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 5 0.20
9 20 0.80
ACGTcount: A:0.09, C:0.46, G:0.00, T:0.46
Consensus pattern (9 bp):
CTTCCATCT
Found at i:253706 original size:12 final size:12
Alignment explanation
Indices: 253677--253761 Score: 50
Period size: 12 Copynumber: 7.0 Consensus size: 12
253667 AAATTTATTT
253677 TATAAA-TAT-A
1 TATAAATTATAA
*
253687 TATTAATTATAA
1 TATAAATTATAA
253699 TATAAATTATAA
1 TATAAATTATAA
* *
253711 -AGTATATTTTTAA
1 TA-TA-AATTATAA
* * *
253724 TATCATTTAAAA
1 TATAAATTATAA
*
253736 TATATTATTTATAA
1 TATA--AATTATAA
253750 TATAAATTATAA
1 TATAAATTATAA
253762 AAGTTCAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 5 0.09
11 4 0.07
12 30 0.52
13 7 0.12
14 12 0.21
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (12 bp):
TATAAATTATAA
Found at i:259193 original size:29 final size:30
Alignment explanation
Indices: 259146--259206 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
259136 TTTTGGTTCT
**
259146 TAAACTTTTCAAAGTTTATACTTTAGCCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
* *
259176 TAAAC-TTTCAAAACTTATATTTTAGTCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
259205 TA
1 TA
259207 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTTTAGCCAC
Found at i:259311 original size:22 final size:21
Alignment explanation
Indices: 259277--259320 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
259267 AGTAAGCCCC
*
259277 CAAATTAATTATTTTATCTTCA
1 CAAATTAATTA-TTTATATTCA
259299 CAAATT-ATCTATTTATATTCA
1 CAAATTAAT-TATTTATATTCA
259320 C
1 C
259321 TTTAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (21 bp):
CAAATTAATTATTTATATTCA
Found at i:260378 original size:10 final size:10
Alignment explanation
Indices: 260365--260390 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
260355 AAAAATACTA
260365 AAAAAATTAC
1 AAAAAATTAC
260375 AAAAAATTAC
1 AAAAAATTAC
260385 AAAAAA
1 AAAAAA
260391 ATTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTAC
Found at i:260381 original size:21 final size:21
Alignment explanation
Indices: 260355--260394 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
260345 AATTAAATAT
260355 AAAAA-TACTAAAAAAATTACA
1 AAAAATTAC-AAAAAAATTACA
260376 AAAAATTACAAAAAAATTA
1 AAAAATTACAAAAAAATTA
260395 AAATATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAATTACAAAAAAATTACA
Found at i:260393 original size:11 final size:11
Alignment explanation
Indices: 260355--260394 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
260345 AATTAAATAT
260355 AAAAA-TACTAA
1 AAAAATTAC-AA
260366 AAAAATTAC-A
1 AAAAATTACAA
260376 AAAAATTACAA
1 AAAAATTACAA
260387 AAAAATTA
1 AAAAATTA
260395 AAATATACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 14 0.52
12 3 0.11
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAATTACAA
Found at i:266634 original size:36 final size:37
Alignment explanation
Indices: 266594--266667 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
266584 CACTTGATTA
266594 TTATTTCTTTTCACTTTGATCATCGA-TTTTTAATTT
1 TTATTTCTTTTCACTTTGATCATCGATTTTTTAATTT
*
266630 TTATTTCTTTTCACTTTGATCGTCGATTTTTTAATTT
1 TTATTTCTTTTCACTTTGATCATCGATTTTTTAATTT
266667 T
1 T
266668 ATCAATCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 25 0.69
37 11 0.31
ACGTcount: A:0.18, C:0.14, G:0.07, T:0.62
Consensus pattern (37 bp):
TTATTTCTTTTCACTTTGATCATCGATTTTTTAATTT
Found at i:272181 original size:3 final size:3
Alignment explanation
Indices: 272173--272239 Score: 109
Period size: 3 Copynumber: 22.0 Consensus size: 3
272163 AATTATTTTT
272173 TAA TAA TAA TAA TATA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
272218 TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA
272240 ATAAAAAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.03
3 53 0.87
4 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:272540 original size:17 final size:17
Alignment explanation
Indices: 272483--272541 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
272473 TTGAACAAGC
*
272483 TCTTTTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
272500 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
272519 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
272536 TCTTCT
1 TCTTCT
272542 GGAAATGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.06
17 15 0.45
18 4 0.12
19 10 0.30
20 2 0.06
ACGTcount: A:0.15, C:0.22, G:0.12, T:0.51
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:272622 original size:120 final size:121
Alignment explanation
Indices: 272442--272774 Score: 324
Period size: 113 Copynumber: 2.8 Consensus size: 121
272432 GATGACAATT
* * *
272442 TATCTCCTTCTGTGATGTAATCTAGCAAAGGTTGAACAAGCTCTTTTCATTGTGAA-CTTCTTC-
1 TATCTCCTTCTGTGATGTAATCTAGCAAAGGTCGAACAAGCTCTTCTCATTATGAATCTTCTTCT
*
272505 TTCTTCAGATGAGTTCTTCTCATTGTGAACT-TCTTCTGGAAATGCTGATGATGATA
66 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTC-TCTGGAAATGCTGATGATGATA
*
272561 TATCTCCTTCTGTGATAG-AGTC-ATGCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTT
1 TATCTCCTTCTGTGAT-GTAATCTA-GC-AAAGGTCGAACAAGCTCTTCTCATTATGAA--TCTT
272624 CTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAA-----A-G-T--T-
61 CTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATGATGATA
* * * * * * * *
272675 GA--TCCATCGAGTGATG-AATTTGAGCGAAAAGTTGAACAAGTTCATCTCATTATGAACTTCTT
1 TATCTCCTTC-TGTGATGTAATCT-AGC-AAAGGTCGAACAAGCTCTTCTCATTATGAA--TCTT
272737 CTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
61 CTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
272775 TTCACTGGGG
Statistics
Matches: 188, Mismatches: 15, Indels: 28
0.81 0.06 0.12
Matches are distributed among these distances:
112 8 0.04
113 77 0.41
114 2 0.01
115 1 0.01
117 1 0.01
118 2 0.01
119 22 0.12
120 28 0.15
123 7 0.04
124 38 0.20
125 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (121 bp):
TATCTCCTTCTGTGATGTAATCTAGCAAAGGTCGAACAAGCTCTTCTCATTATGAATCTTCTTCT
TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATGATGATA
Found at i:272727 original size:113 final size:113
Alignment explanation
Indices: 272586--273377 Score: 1079
Period size: 113 Copynumber: 7.0 Consensus size: 113
272576 TAGAGTCATG
* ** *
272586 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
272651 TTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTTGAG
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
* * *
272699 CGAAAA-GTTGAACAAGTTCATCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * **
272763 ATTATGAACTCTTTCACTGGGGATGCTGATCCATCAAATGATGAATTCAAA
65 ATTATGAACT-TTT-TCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
272814 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * * **
272879 TTATGAACTCTTTCACTGGGGATGCTGATCCATCAAATAATGAATTCAAA
66 TTATGAACT-TTT-TCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
*
272929 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * **
272994 TTATGAACTTTTTCTGGAAAAGCTGATCTATCAAGTGACGAATTCAAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
* * *
273042 CAAAAGGTTGAACAATTTCTTCTCATTATGAATTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
273107 TTATGAACTTTTTCTGGAAAAACTGATCCATCAAATGATGGATTTGAG
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
* *
273155 CAAAAGGTTGAACAAATTCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
273220 TTATAAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
* * *
273268 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TT-TTTTTCCTTCTTTAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
273331 TTATGAACTTTTTCTGAAAAAGCTGATCCATCAAGTGATG-ATTTGAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
273378 TCTTTGAAAT
Statistics
Matches: 623, Mismatches: 52, Indels: 11
0.91 0.08 0.02
Matches are distributed among these distances:
110 6 0.01
111 63 0.10
112 2 0.00
113 335 0.54
114 12 0.02
115 205 0.33
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAA
Found at i:272863 original size:228 final size:226
Alignment explanation
Indices: 272586--273376 Score: 1086
Period size: 228 Copynumber: 3.5 Consensus size: 226
272576 TAGAGTCATG
* ** *
272586 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
272651 TTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTTGAGCGAAAA-GTTGAACAAG
66 TTATGAACTCTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAGC-AAAAGGTTGAACAAA
* * *
272715 TTCATCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCAC
130 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTT-TC
** *
272780 TGGGGATGCTGATCCATCAAATGATGAATTCAAA
193 TGGAAAAGCTGATCCATCAAATGATGAATTCAAA
272814 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * * ** *
272879 TTATGAACTCTTTCACTGGGGATGCTGATCCATCAAATAATGAATTCAAACAAAAGGTTGAACAA
66 TTATGAACTC--TCTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAGCAAAAGGTTGAACAA
*
272944 ATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCT
129 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCT
* * *
273009 GGAAAAGCTGATCTATCAAGTGACGAATTCAAA
194 GGAAAAGCTGATCCATCAAATGATGAATTCAAA
* * *
273042 CAAAAGGTTGAACAATTTCTTCTCATTATGAATTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
273107 TTATGAACTTTTTCTGGAAAAACTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTCTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAGCAAAAGGTTGAACAAAT
* * *
273172 TCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTTTTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
* ** *
273237 AAAAGCTGATCCATCAAATGATGGATTTGAG
196 AAAAGCTGATCCATCAAATGATGAATTCAAA
* * *
273268 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TT-TTTTTCCTTCTTTAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
273331 TTATGAACTTTTTCTGAAAAAGCTGATCCATCAAGTGATG-ATTTGA
66 TTATGAACTCTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTGA
273377 ATCTTTGAAA
Statistics
Matches: 502, Mismatches: 58, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
223 6 0.01
224 64 0.13
225 2 0.00
226 160 0.32
228 171 0.34
229 7 0.01
230 92 0.18
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (226 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTGAGCAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
AAAAGCTGATCCATCAAATGATGAATTCAAA
Found at i:273806 original size:22 final size:24
Alignment explanation
Indices: 273764--273820 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
273754 CATAAAGCTT
273764 TCATCTTTGAAAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAGAATCTA
273788 TCATCTTT-AAAA-AGAGAATCTA
1 TCATCTTTGAAAAGAGAGAATCTA
273810 TCATCTTTGAA
1 TCATCTTTGAA
273821 GAGTGTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.56
23 6 0.19
24 8 0.25
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (24 bp):
TCATCTTTGAAAAGAGAGAATCTA
Found at i:276551 original size:114 final size:114
Alignment explanation
Indices: 276351--276573 Score: 365
Period size: 114 Copynumber: 2.0 Consensus size: 114
276341 CATGCAGTTC
* * * * *
276351 ATCTTTCAATTCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
*
276416 TTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTA
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTA
* *
276465 ATCTTTCAAATCCAATGATTGGTTTTGAGGTTCATATCAAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
*
276530 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
276574 CATGGCACTT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
ATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTA
Found at i:278711 original size:7 final size:7
Alignment explanation
Indices: 278685--278755 Score: 56
Period size: 7 Copynumber: 9.6 Consensus size: 7
278675 AATTTCTCCC
278685 CTTTTTT
1 CTTTTTT
278692 -TTTTTT
1 CTTTTTT
278698 -TTTTTT
1 CTTTTTT
278704 CTTTTTT
1 CTTTTTT
278711 CTCATTTTT
1 CT--TTTTT
*
278720 CATTTTT
1 CTTTTTT
278727 CATTTTTCAT
1 C-TTTTT--T
*
278737 TTTTTTT
1 CTTTTTT
278744 CTTTTTT
1 CTTTTTT
278751 GCTTT
1 -CTTT
278756 CTTTATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
6 12 0.23
7 21 0.40
8 8 0.15
9 11 0.21
10 1 0.02
ACGTcount: A:0.06, C:0.13, G:0.01, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:278725 original size:6 final size:7
Alignment explanation
Indices: 278707--278740 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
278697 TTTTTTTCTT
278707 TTTTCTCA
1 TTTT-TCA
278715 TTTTTCA
1 TTTTTCA
278722 TTTTTCA
1 TTTTTCA
278729 TTTTTCA
1 TTTTTCA
278736 TTTTT
1 TTTTT
278741 TTTCTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:282410 original size:14 final size:14
Alignment explanation
Indices: 282372--282425 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
282362 CATAAAAATA
* *
282372 CAAATGCAAAGATG
1 CAAATGTAAATATG
282386 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
282401 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
282415 TAAATGTAAAT
1 CAAATGTAAAT
282426 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:286210 original size:3 final size:3
Alignment explanation
Indices: 286202--286242 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
286192 AATTATTTTT
* *
286202 TAA TAA TAA TAA TAA TAA T-A TTA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
286243 ATAAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:290212 original size:12 final size:12
Alignment explanation
Indices: 290195--290219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
290185 TCAATTTAAA
290195 TAAAATAAAATT
1 TAAAATAAAATT
290207 TAAAATAAAATT
1 TAAAATAAAATT
290219 T
1 T
290220 GATAATTTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATAAAATT
Found at i:294062 original size:31 final size:30
Alignment explanation
Indices: 293988--294067 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
293978 AATTCTACAC
* **
293988 TTTTCTAGAGTTCTCCGAAAATGCTCTAGAA
1 TTTTCTAGACTTCTCC-AAAAAACTCTAGAA
** *
294019 AATTCTACACTTCTCCAAAAAACTCTAGAA
1 TTTTCTAGACTTCTCCAAAAAACTCTAGAA
294049 TTTTCTAGAACTTCTCCAA
1 TTTTCTAG-ACTTCTCCAA
294068 TTAAGGAGAG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.34
Consensus pattern (30 bp):
TTTTCTAGACTTCTCCAAAAAACTCTAGAA
Found at i:295502 original size:95 final size:95
Alignment explanation
Indices: 295329--295551 Score: 265
Period size: 95 Copynumber: 2.3 Consensus size: 95
295319 TAGCGACGAG
** *
295329 GTAGTATCGATACCATGGTAAGGGCATCGATACCAGATAATATCGAACCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGATATCGATACCAGACAATATCGAACCTAATTTTGGTATCGAT
* *
295394 ACCAGAAGAGGGTATCGGTA-CAATAATATA
66 ACCAGAAGAGGGTATCGATATC-ATAATAGA
* *
295424 GTAGTATCGATACCATGGTAAGGATATCGATACCATG-CCATATCGAATCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGGTAAGGATATCGATACCA-GACAATATCGAACCTAATTTTGGTATCGA
* * * *
295488 TATC-GAAAGGGGGTATCGATATCATAGTAGG
65 TACCAG-AAGAGGGTATCGATATCATAATAGA
* *
295519 GTAGTATCGATACCATTGTCA-GAGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGA-TATCGATAC
295552 TGAAGAACCA
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
94 3 0.03
95 106 0.95
96 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGATATCGATACCAGACAATATCGAACCTAATTTTGGTATCGAT
ACCAGAAGAGGGTATCGATATCATAATAGA
Found at i:295951 original size:59 final size:59
Alignment explanation
Indices: 295888--296024 Score: 202
Period size: 59 Copynumber: 2.3 Consensus size: 59
295878 GCACTAAGTA
* *
295888 TGCTAAAATGTTAAGAAATACATACTAAGTGTATGAATTTCTGTATAGGGTACTTCATG
1 TGCTAAAATGTTAAGAAATACATACTAAGTGTATGAATTTCAGTATAGGGCACTTCATG
* * **
295947 TGCTAAAATGTTAAGAACTTCATACTAAGTGTATGAATTTCAGTATAGGGCACTTTGTG
1 TGCTAAAATGTTAAGAAATACATACTAAGTGTATGAATTTCAGTATAGGGCACTTCATG
* *
296006 TGCTAAAATGATACGAAAT
1 TGCTAAAATGTTAAGAAAT
296025 TTGTAACATC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (59 bp):
TGCTAAAATGTTAAGAAATACATACTAAGTGTATGAATTTCAGTATAGGGCACTTCATG
Found at i:298465 original size:59 final size:59
Alignment explanation
Indices: 298392--298520 Score: 199
Period size: 59 Copynumber: 2.2 Consensus size: 59
298382 GGGTGTTACA
*
298392 AAATTCATACTAAGTGTATGAATTTCAGTATAGGGCA-CTTCGTGTGCTAAAAT-ATTAAG
1 AAATTCATACTAAGTGTATGAATTTCAGTATAGGACACCTT-GTGTGCTAAAATGA-TAAG
* *
298451 AAATTCATACTAAGTGTATGAATTTCCGTATTGGACACCTTGTGTGCTAAAATGATAAG
1 AAATTCATACTAAGTGTATGAATTTCAGTATAGGACACCTTGTGTGCTAAAATGATAAG
298510 AAATTCATACT
1 AAATTCATACT
298521 GAGAAATAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
59 61 0.94
60 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (59 bp):
AAATTCATACTAAGTGTATGAATTTCAGTATAGGACACCTTGTGTGCTAAAATGATAAG
Found at i:312814 original size:60 final size:60
Alignment explanation
Indices: 312737--312900 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 60
312727 ATATTTTGGT
* * * **
312737 ACATGAACTAGACATCTTTTCCTAAGTTAATACCTAAAGAATTTTTGCTCCCAAGTTAGC
1 ACATGAACTAGGCATCTTCTCCCAAGTTGGTACCTAAAGAATTTTTGCTCCCAAGTTAGC
* * * * * *
312797 ACCTGAACTAGGCATCTTCTCCCAAGTTGGTACTTGAAGAACTTTTGCTCCCAAGTTGGT
1 ACATGAACTAGGCATCTTCTCCCAAGTTGGTACCTAAAGAATTTTTGCTCCCAAGTTAGC
*
312857 ATATGAACTAGGCATCTTCTCCCAAGTTGGTACCTAAAGAATTT
1 ACATGAACTAGGCATCTTCTCCCAAGTTGGTACCTAAAGAATTT
312901 AGGAAAAGAT
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 88 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (60 bp):
ACATGAACTAGGCATCTTCTCCCAAGTTGGTACCTAAAGAATTTTTGCTCCCAAGTTAGC
Found at i:312822 original size:31 final size:31
Alignment explanation
Indices: 312784--312889 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 31
312774 AGAATTTTTG
* * *
312784 CTCCCAAGTTAGCACCTGAACTAGGCATCTT
1 CTCCCAAGTTGGTACATGAACTAGGCATCTT
* * * *
312815 CTCCCAAGTTGGTACTTGAA-GA-AC-TTTT
1 CTCCCAAGTTGGTACATGAACTAGGCATCTT
*
312843 GCTCCCAAGTTGGTATATGAACTAGGCATCTT
1 -CTCCCAAGTTGGTACATGAACTAGGCATCTT
312875 CTCCCAAGTTGGTAC
1 CTCCCAAGTTGGTAC
312890 CTAAAGAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.05
29 19 0.32
30 2 0.03
31 32 0.54
32 3 0.05
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (31 bp):
CTCCCAAGTTGGTACATGAACTAGGCATCTT
Found at i:326609 original size:15 final size:17
Alignment explanation
Indices: 326577--326610 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
326567 TTTTATTTAA
326577 AAATTAGATATACAAAT
1 AAATTAGATATACAAAT
326594 AAATTA-ATAT-CAAAT
1 AAATTAGATATACAAAT
326609 AA
1 AA
326611 TTTACAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATTAGATATACAAAT
Found at i:328386 original size:2 final size:2
Alignment explanation
Indices: 328379--328424 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
328369 TTGCTGAGCA
328379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
328421 AT AT
1 AT AT
328425 TTGATTATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:330325 original size:72 final size:71
Alignment explanation
Indices: 330170--330325 Score: 163
Period size: 71 Copynumber: 2.2 Consensus size: 71
330160 TTTCCTAGTA
* * ** *
330170 TAATTATTTTTTAAGACACTTTCATTTTTAAAATTAATAGAATTAAGTCTTAATTCCAAATTTAT
1 TAATTATTTTTTAAGACACTCTAAAATTTAAAATTAATAGAATTAACTCTTAATTCCAAATTTAT
*
330235 CTGATT
66 ATGATT
* ***
330241 TAATTATATTTTAAGACA-TCTAAAATTTAAAATTAAT-GAAATTGAACTCTTAATCTTTTAATT
1 TAATTATTTTTTAAGACACTCTAAAATTTAAAATTAATAG-AATT-AACTCTTAAT-TCCAAATT
* *
330304 TTTATGGTT
63 TATATGATT
330313 TAATTATTTTTTA
1 TAATTATTTTTTA
330326 GGATTTTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
69 1 0.01
70 19 0.28
71 26 0.38
72 23 0.33
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (71 bp):
TAATTATTTTTTAAGACACTCTAAAATTTAAAATTAATAGAATTAACTCTTAATTCCAAATTTAT
ATGATT
Found at i:331774 original size:25 final size:26
Alignment explanation
Indices: 331708--331777 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
331698 GTCATGTTTT
*
331708 TAAGTACTTAATTTTTTTTATTAAAA
1 TAAGTATTTAATTTTTTTTATTAAAA
331734 TAAGTATTTAATTTTTTTTATTAAAA
1 TAAGTATTTAATTTTTTTTATTAAAA
331760 TAAGTATTTAATTTTTTT
1 TAAGTATTTAATTTTTTT
331778 GGAAAAATAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (26 bp):
TAAGTATTTAATTTTTTTTATTAAAA
Found at i:331784 original size:25 final size:25
Alignment explanation
Indices: 331708--331795 Score: 115
Period size: 26 Copynumber: 3.4 Consensus size: 25
331698 GTCATGTTTT
*
331708 TAAGTACTTAATTTTTTTTATTAAAA
1 TAAGTATTTAATTTTTTTTA-TAAAA
331734 TAAGTATTTAATTTTTTTTATTAAAA
1 TAAGTATTTAATTTTTTTTA-TAAAA
*
331760 TAAGTATTTAATTTTTTTGGA-AAAA
1 TAAGTATTTAATTTTTTT-TATAAAA
*
331785 TAGGTATTTAA
1 TAAGTATTTAA
331796 AATATTTTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
25 14 0.24
26 43 0.74
27 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (25 bp):
TAAGTATTTAATTTTTTTTATAAAA
Found at i:336915 original size:11 final size:11
Alignment explanation
Indices: 336899--336924 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
336889 TAGGTAGTCT
336899 ATTTTGACAAA
1 ATTTTGACAAA
336910 ATTTTGACAAA
1 ATTTTGACAAA
336921 ATTT
1 ATTT
336925 GAATCACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (11 bp):
ATTTTGACAAA
Found at i:338559 original size:36 final size:35
Alignment explanation
Indices: 338478--338612 Score: 189
Period size: 35 Copynumber: 3.8 Consensus size: 35
338468 AGATGAACAA
* * **
338478 TTGAATCGAAAGTGCCGATGTTTCCTACCGTTCAC
1 TTGAATCGAAAGTGCCAATGCTTCCTTTCGTTCAC
*
338513 TTGAATCGAAAGTGCCAATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCAATGCTTCCTTTCGTTC-AC
* * *
338549 TTGATTCGAAAGTGTCGATGCTTCCTTTCGTTCAC
1 TTGAATCGAAAGTGCCAATGCTTCCTTTCGTTCAC
338584 TTGAATCGAAAGTGCCAATGCTTCCTTTC
1 TTGAATCGAAAGTGCCAATGCTTCCTTTC
338613 TTTCTTCTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 56 0.64
36 31 0.36
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCAATGCTTCCTTTCGTTCAC
Found at i:338599 original size:71 final size:71
Alignment explanation
Indices: 338478--338625 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
338468 AGATGAACAA
* *
338478 TTGAATCGAAAGTGCCGATGTTTCCTACCGTTCACTTGAATCGAAAGTGCCAATGCTTCCTTTCG
1 TTGATTCGAAAGTGCCGATGCTTCCTACCGTTCACTTGAATCGAAAGTGCCAATGCTTCCTTTCG
338543 TTCTTC
66 TTCTTC
* ** *
338549 TTGATTCGAAAGTGTCGATGCTTCCTTTCGTTCACTTGAATCGAAAGTGCCAATGCTTCCTTTCT
1 TTGATTCGAAAGTGCCGATGCTTCCTACCGTTCACTTGAATCGAAAGTGCCAATGCTTCCTTTCG
338614 TTCTTC
66 TTCTTC
338620 TT-ATTC
1 TTGATTC
338626 ACCTTCATTT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 4 0.06
71 67 0.94
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (71 bp):
TTGATTCGAAAGTGCCGATGCTTCCTACCGTTCACTTGAATCGAAAGTGCCAATGCTTCCTTTCG
TTCTTC
Found at i:341864 original size:22 final size:23
Alignment explanation
Indices: 341813--341865 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
341803 TGTTTGTGTT
* * **
341813 TGTTTATTTATTGTTCGTGAACA
1 TGTTCATTTAGTGTTCACGAACA
341836 TGTTCATTTAGTGTTCACGAAC-
1 TGTTCATTTAGTGTTCACGAACA
341858 TGTTCATT
1 TGTTCATT
341866 AAGCGTTCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (23 bp):
TGTTCATTTAGTGTTCACGAACA
Found at i:341873 original size:22 final size:23
Alignment explanation
Indices: 341831--341873 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
341821 TATTGTTCGT
* *
341831 GAACATGTTCATTTAGTGTTCAC
1 GAACATGTTCATTAAGCGTTCAC
341854 GAAC-TGTTCATTAAGCGTTC
1 GAACATGTTCATTAAGCGTTC
341874 GTTTAGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (23 bp):
GAACATGTTCATTAAGCGTTCAC
Found at i:342763 original size:37 final size:37
Alignment explanation
Indices: 342687--342763 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
342677 TTTTTATATT
*
342687 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * * *
342724 TTTAATTTTTTAAAGAAAA-TATTTAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
342761 TTT
1 TTT
342764 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:346498 original size:35 final size:36
Alignment explanation
Indices: 346436--346506 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 36
346426 TATGTGCAGG
346436 GGGAACAGATTCCCCCCTGGGGTGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGTGTATCGATTCCCC
346472 GGGAACAGATT-CCCCCTGAGGG-GTATCGATTCCCC
1 GGGAACAGATTCCCCCCTG-GGGTGTATCGATTCCCC
346507 CATAAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 20 0.59
36 14 0.41
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCTGGGGTGTATCGATTCCCC
Found at i:354915 original size:34 final size:35
Alignment explanation
Indices: 354860--354928 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
354850 TATGTGCAGG
354860 GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
354895 GGGAACAGATT-CCCCCTGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
354929 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 23 0.68
35 11 0.32
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCTGGGGGTATCGATTCCCC
Found at i:360762 original size:2 final size:2
Alignment explanation
Indices: 360755--360795 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
360745 ACCCATACAA
360755 AT AT 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 AT AT A
360796 ATCATTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:361105 original size:60 final size:61
Alignment explanation
Indices: 361007--361222 Score: 191
Period size: 55 Copynumber: 3.6 Consensus size: 61
360997 TTTTTTATAT
* * * *
361007 ATCGAGCTAAGTTTAAAAATATTTCAA-TTCAAGTTTTTTT-GAGCTCGAGTTTGAACTTCA
1 ATCGAGCTAAATCT-AAAATATTTCAAGTTAAAGTTTTTTTCAAGCTCGAGTTTGAACTTCA
* * *
361067 ATTGAGCTAAATCTTAAAATGTTTCAAGTTAAAG-TTTTTTCAAGCTCGAGTTTGAGCTTCA
1 ATCGAGCTAAATC-TAAAATATTTCAAGTTAAAGTTTTTTTCAAGCTCGAGTTTGAACTTCA
* * * *
361128 ATCGAGCTAAATCTAAGAATATTTC------AAG-TTTTTCCGAGCTTGAGTTTGAGCTTCA
1 ATCGAGCTAAATCTAA-AATATTTCAAGTTAAAGTTTTTTTCAAGCTCGAGTTTGAACTTCA
* * *
361183 ATCGAGTTAAGTCTAAAAATATTTCAAGTTCAAAATTTTT
1 ATCGAGCTAAATCT-AAAATATTTCAAGTT-AAAGTTTTT
361223 CGAGCCAGAG
Statistics
Matches: 128, Mismatches: 15, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
55 47 0.37
56 2 0.02
60 30 0.23
61 43 0.34
62 2 0.02
63 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (61 bp):
ATCGAGCTAAATCTAAAATATTTCAAGTTAAAGTTTTTTTCAAGCTCGAGTTTGAACTTCA
Found at i:361114 original size:61 final size:60
Alignment explanation
Indices: 361007--361222 Score: 203
Period size: 61 Copynumber: 3.6 Consensus size: 60
360997 TTTTTTATAT
* * * **
361007 ATCGAGCTAAGTTTAAAAATATTTCAA-TTCAAGTTTTTTTGAGCTCGAGTTTGAACTTCA
1 ATCGAGCTAAATCT-AAAATATTTCAAGTTAAAGTTTTTTCAAGCTCGAGTTTGAACTTCA
* * *
361067 ATTGAGCTAAATCTTAAAATGTTTCAAGTTAAAGTTTTTTCAAGCTCGAGTTTGAGCTTCA
1 ATCGAGCTAAATC-TAAAATATTTCAAGTTAAAGTTTTTTCAAGCTCGAGTTTGAACTTCA
* * * *
361128 ATCGAGCTAAATCTAAGAATATTTC------AAGTTTTTCCGAGCTTGAGTTTGAGCTTCA
1 ATCGAGCTAAATCTAA-AATATTTCAAGTTAAAGTTTTTTCAAGCTCGAGTTTGAACTTCA
* * *
361183 ATCGAGTTAAGTCTAAAAATATTTCAAGTTCAAAATTTTT
1 ATCGAGCTAAATCT-AAAATATTTCAAGTT-AAAGTTTTT
361223 CGAGCCAGAG
Statistics
Matches: 129, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
55 47 0.36
56 2 0.02
60 24 0.19
61 49 0.38
62 7 0.05
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (60 bp):
ATCGAGCTAAATCTAAAATATTTCAAGTTAAAGTTTTTTCAAGCTCGAGTTTGAACTTCA
Found at i:368121 original size:13 final size:14
Alignment explanation
Indices: 368092--368122 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
368082 TTTTAGACTA
368092 ATATTAGCCGCCCC
1 ATATTAGCCGCCCC
368106 ATATTAGCCG-CCC
1 ATATTAGCCGCCCC
368119 ATAT
1 ATAT
368123 GCTAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (14 bp):
ATATTAGCCGCCCC
Done.