Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008552.1 Hibiscus syriacus cultivar Beakdansim tig00111447_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: 537591
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:8125 original size:18 final size:16
Alignment explanation
Indices: 8080--8138 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
8070 TCATGTTATA
8080 TCATTTAAGCATG-AGT
1 TCATTTAAGCATGCA-T
8096 TCATTTAAGCATGCAT
1 TCATTTAAGCATGCAT
8112 TGCATTTAAAGCAT-CTATT
1 T-CATTT-AAGCATGC-A-T
8131 TCATTTAA
1 TCATTTAA
8139 TAAAGTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 15 0.39
17 9 0.24
18 12 0.32
19 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (16 bp):
TCATTTAAGCATGCAT
Found at i:8165 original size:17 final size:17
Alignment explanation
Indices: 8145--8197 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
8135 TTAATAAAGT
8145 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
8162 TAGTTC-TTAAATCAAAC
1 TAGTTCATT-AATTAAAC
*
8179 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
8196 TA
1 TA
8198 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 2 0.06
17 27 0.87
18 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:12859 original size:18 final size:18
Alignment explanation
Indices: 12836--12870 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12826 TTGGTTTGCT
12836 TTTCTTTACCCTTGCTAC
1 TTTCTTTACCCTTGCTAC
12854 TTTCTTTACCCTTGCTA
1 TTTCTTTACCCTTGCTA
12871 GATTCGCCCA
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:0.11, C:0.31, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTCTTTACCCTTGCTAC
Found at i:15080 original size:12 final size:12
Alignment explanation
Indices: 15048--15087 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
15038 TCATCATCAA
*
15048 CATCATCAACATC
1 CATCATCAAGA-C
*
15061 CTTCATCAAGAC
1 CATCATCAAGAC
15073 CATCATCAAGAC
1 CATCATCAAGAC
15085 CAT
1 CAT
15088 AATTCCGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.23
Consensus pattern (12 bp):
CATCATCAAGAC
Found at i:15426 original size:11 final size:11
Alignment explanation
Indices: 15418--15453 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
15408 GAAAAAGACA
15418 AAAAGAAGAAG
1 AAAAGAAGAAG
15429 AAAAGAAGAAAG
1 AAAAGAAG-AAG
*
15441 AAAAGAAAAAG
1 AAAAGAAGAAG
15452 AA
1 AA
15454 TTCAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:15453 original size:18 final size:18
Alignment explanation
Indices: 15399--15453 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
15389 ATTGGAGTGC
15399 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
15416 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
*
15435 AGAAAGAAAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
15453 A
1 A
15454 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.09
18 20 0.61
19 7 0.21
20 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:23169 original size:18 final size:16
Alignment explanation
Indices: 23123--23182 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
23113 ATCATGCTAC
23123 TTCATTTAAGCATG-A
1 TTCATTTAAGCATGCA
23138 GTTCATTTAAGCATGCA
1 -TTCATTTAAGCATGCA
23155 TTGCATTTAAAGCAT-CTA
1 TT-CATTT-AAGCATGC-A
23173 TTTCATTTAA
1 -TTCATTTAA
23183 TAAAGTTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 16 0.41
17 9 0.23
18 12 0.31
19 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (16 bp):
TTCATTTAAGCATGCA
Found at i:23209 original size:17 final size:17
Alignment explanation
Indices: 23189--23241 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
23179 TTAATAAAGT
23189 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
23206 TAGTTCATAAATCAAAC
1 TAGTTCATTAATTAAAC
**
23223 TAGTTCATTTCTTAAAC
1 TAGTTCATTAATTAAAC
23240 TA
1 TA
23242 ACTCTTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:36065 original size:35 final size:37
Alignment explanation
Indices: 36019--36098 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
36009 TTTGAGAATT
*
36019 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
36054 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
36091 TGGTGATG
1 TGGTGATG
36099 GAAATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:40529 original size:35 final size:37
Alignment explanation
Indices: 40483--40562 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
40473 TTTGAGAATT
*
40483 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
40518 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
40555 TGGTGATG
1 TGGTGATG
40563 GAAATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:45015 original size:35 final size:37
Alignment explanation
Indices: 44961--45040 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
44951 TTTGAGAATT
*
44961 TGGTGATGATATAGACGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
* * *
44996 TGTTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
45033 TGGTGATG
1 TGGTGATG
45041 GAAATAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 19 0.50
36 4 0.11
37 15 0.39
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGACGTGATAATGGAAGATGGACTA
Found at i:49916 original size:24 final size:24
Alignment explanation
Indices: 49889--49940 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
49879 GACATGTCCT
* * *
49889 TTGACGTTCCAATAGCTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
49913 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
49937 TTGA
1 TTGA
49941 AGTGCCAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:53767 original size:15 final size:15
Alignment explanation
Indices: 53731--53760 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53721 GTGCTTCAAC
53731 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
53745 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
53760 T
1 T
53761 ATTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:56505 original size:35 final size:37
Alignment explanation
Indices: 56459--56538 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
56449 TTTTAGAATT
**
56459 TGGTGATGATATAGGCGTGAT-ATG-GTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGAAAGATGGACTA
*
56494 TGGTGATGATATAGGCGTGATAATGAAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGAAAGATGGACTA
56531 TGGTGATG
1 TGGTGATG
56539 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGAAAGATGGACTA
Found at i:61097 original size:11 final size:11
Alignment explanation
Indices: 61081--61105 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61071 ATTTTTTTTC
61081 AAAAAAACAAA
1 AAAAAAACAAA
61092 AAAAAAACAAA
1 AAAAAAACAAA
61103 AAA
1 AAA
61106 GGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:61113 original size:21 final size:21
Alignment explanation
Indices: 61089--61138 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
61079 TCAAAAAAAC
61089 AAAAAAAAAACAAAAAAGGAA
1 AAAAAAAAAACAAAAAAGGAA
* * *
61110 AAAAAACAAAGAAAAAAGGCA
1 AAAAAAAAAACAAAAAAGGAA
61131 AAAAAAAA
1 AAAAAAAA
61139 TGCCAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAGGAA
Found at i:61146 original size:21 final size:20
Alignment explanation
Indices: 61088--61155 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
61078 TTCAAAAAAA
*
61088 CAAAAAAAAAACAAAAAAGG
1 CAAAAAAAAAGCAAAAAAGG
*
61108 AAAAAAAACAAAG-AAAAAAGG
1 -CAAAAAA-AAAGCAAAAAAGG
*
61129 CAAAAAAAAATGCCAAAAAAGC
1 CAAAAAAAAA-G-CAAAAAAGG
61151 CAAAA
1 CAAAA
61156 TTTCAAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.08
20 7 0.18
21 14 0.36
22 15 0.38
ACGTcount: A:0.76, C:0.12, G:0.10, T:0.01
Consensus pattern (20 bp):
CAAAAAAAAAGCAAAAAAGG
Found at i:61146 original size:22 final size:22
Alignment explanation
Indices: 61080--61155 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 22
61070 TATTTTTTTT
*
61080 CAAAAAA-ACAAAAAAA-AAA-
1 CAAAAAAGGCAAAAAAACAAAG
*
61099 CAAAAAAGGAAAAAAAACAAAG
1 CAAAAAAGGCAAAAAAACAAAG
*
61121 -AAAAAAGGCAAAAAAA-AATG
1 CAAAAAAGGCAAAAAAACAAAG
*
61141 CCAAAAAAGCCAAAA
1 -CAAAAAAGGCAAAA
61156 TTTCAAAACA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.15
20 10 0.21
21 18 0.38
22 12 0.26
ACGTcount: A:0.78, C:0.12, G:0.09, T:0.01
Consensus pattern (22 bp):
CAAAAAAGGCAAAAAAACAAAG
Found at i:65463 original size:15 final size:16
Alignment explanation
Indices: 65432--65468 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
65422 CTTTATTATC
65432 TTATTTCATCTTCTGT
1 TTATTTCATCTTCTGT
*
65448 TTATTT-ATCTTTTGT
1 TTATTTCATCTTCTGT
65463 TTATTT
1 TTATTT
65469 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTCTGT
Found at i:66359 original size:17 final size:17
Alignment explanation
Indices: 66337--66386 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
66327 GTAGGAGTCT
66337 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
66354 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
*
66372 TTTT-TTTTTTTTGTT
1 TTTTCTTTTTCTTGTT
66387 ATAGCACTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.27
17 13 0.43
18 9 0.30
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:66807 original size:35 final size:37
Alignment explanation
Indices: 66761--66840 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
66751 TTTGAGAATT
*
66761 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
66796 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
66833 TGGTGATG
1 TGGTGATG
66841 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:87822 original size:19 final size:21
Alignment explanation
Indices: 87779--87830 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
87769 GAAAGCCCTT
87779 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
87800 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
87819 TGAATATACATG
1 TGAAAATACATG
87831 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:88756 original size:30 final size:31
Alignment explanation
Indices: 88715--88774 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
88705 ACATGCTGCC
**
88715 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
88746 ATGA-ATCTAAAACATATGTAATCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
88775 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:91181 original size:8 final size:8
Alignment explanation
Indices: 91170--91194 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
91160 TCTTTTTCTT
91170 TTCTTTTC
1 TTCTTTTC
91178 TTCTTTTC
1 TTCTTTTC
91186 TTCTTTTC
1 TTCTTTTC
91194 T
1 T
91195 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:93583 original size:25 final size:25
Alignment explanation
Indices: 93547--93609 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
93537 TATGCTTTGA
93547 TTAC-CGC-TTGATGTAAGGCGAAT
1 TTACACGCTTTGATGTAAGGCGAAT
93570 TTACACGCTTTGATGTAAGGCGAAT
1 TTACACGCTTTGATGTAAGGCGAAT
93595 TTACACGCTTTGATG
1 TTACACGCTTTGATG
93610 GAAGAGAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.11
24 3 0.08
25 31 0.82
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (25 bp):
TTACACGCTTTGATGTAAGGCGAAT
Found at i:94241 original size:19 final size:21
Alignment explanation
Indices: 94198--94249 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
94188 GAAACCCCTT
94198 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
94219 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
94238 TGAATATACATG
1 TGAAAATACATG
94250 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:95674 original size:90 final size:91
Alignment explanation
Indices: 95506--95678 Score: 260
Period size: 90 Copynumber: 1.9 Consensus size: 91
95496 CCGATTTGCC
* **
95506 TTGCATATGACCAGTCCCCATGTGCCTTGCATGAGGATCATTTAGGGGCCAAGATGAAGAGTTCT
1 TTGCATATGAACAGTCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGTTCT
95571 CTCCCTATTCGGCCAAGCCATGTGTT
66 CTCCCTATTCGGCCAAGCCATGTGTT
* * * *
95597 TTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCACCAAGATGAAGAGCTT-
1 TTGCATATGAACAGTCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAG-TTC
95660 TCTCCCTATTCGGCCAAGC
65 TCTCCCTATTCGGCCAAGC
95679 ATCATTTCCC
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
90 60 0.81
91 14 0.19
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (91 bp):
TTGCATATGAACAGTCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGTTCT
CTCCCTATTCGGCCAAGCCATGTGTT
Found at i:96945 original size:30 final size:31
Alignment explanation
Indices: 96904--96963 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
96894 ACATGCTGCC
**
96904 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
96935 ATGA-ATCTAAAACATATGTAATCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
96964 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:109536 original size:11 final size:14
Alignment explanation
Indices: 109491--109531 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
109481 ATAGGCGTGA
* *
109491 ATGGTGATAGAGA-
1 ATGGTGATGGAAAG
109504 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
109518 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
109532 GTGATATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:117565 original size:27 final size:27
Alignment explanation
Indices: 117531--117587 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
117521 TTTCTTTGCT
* *
117531 TTTCTTCTTTTTGAATGC-TGAATTTC
1 TTTCTTCTTTTGGAATGCTTCAATTTC
*
117557 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTGGAATGCTTCAATTTC
117585 TTT
1 TTT
117588 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 10 0.38
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (27 bp):
TTTCTTCTTTTGGAATGCTTCAATTTC
Found at i:122148 original size:3 final size:3
Alignment explanation
Indices: 122140--122202 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
122130 TTCGGGCTTG
* * *
122140 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA T-A TAA GAA T-A CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
122186 TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TA
122203 TTATTATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 3 0.06
3 47 0.94
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:122957 original size:42 final size:42
Alignment explanation
Indices: 122906--122987 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
122896 ATGGTCTTAT
* * **
122906 CATCTTGCTCGAAAGGCTTACAGATGACCTGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTACAGATGACCCAAAGGATTTAAG
*
122948 CATCATGCTCGAAAGACTTACTGATGACCCAAAGGATTTA
1 CATCATGCTCGAAAGACTTACAGATGACCCAAAGGATTTA
122988 CTTTCATCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCCAAAGGATTTAAG
Found at i:123133 original size:216 final size:218
Alignment explanation
Indices: 122858--123415 Score: 766
Period size: 226 Copynumber: 2.5 Consensus size: 218
122848 TAAATCTCAT
* * ** *
122858 TTGAAAACATCCTGC-CCGAAGGTCTTATGGATGGCCTGATGGTCTTATCATCTTGCTCGAAAGG
1 TTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGG
122922 CTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCAAAGGATTT
66 CTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCAAAGGATTT
* * * *
122987 ACTTTCATCTC-G-ATTGCTATTTCAAGTGAAGCTTTCTAAAGCAAGACGTTGTTGATTCCAAAT
131 ACTTTAATCTCGGAATTACTATTTCAAGTGAAACTTTCTAAAGCAAGACATTGTTG-TTCCAAAT
* *
123050 GTCGTGAATCATGCAACAAAAATG
195 GTCATGAATCAAGCAACAAAAATG
123074 TTGAAAACATCCAGCACTGAA-GTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGG
1 TTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGG
* * ** *
123138 CTTACAGATGA-CTCGAAGGATTTAAGCATCATGTTCGAAATACTTACTGATGATTCGAAGGATT
66 CTTACAGATGACCT-GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCAAAGGATT
*
123202 TACTTTAATCTCGAGTGAGACAAATTACTATTTCAAGTGAAACTTTCTCAAGCAAGACATTGTTG
130 TACTTTAATCTC----G-G---AATTACTATTTCAAGTGAAACTTTCTAAAGCAAGACATTGTTG
* * *
123267 TTCGAAATGTCATGAATCAAGTAACGAAAATG
187 TTCCAAATGTCATGAATCAAGCAACAAAAATG
* ** *
123299 TTCAAAACATCCAGCACTGAAGGTCTTATGGATGGATCAAAGGTCTTATCATCTTGCTCAAAAGG
1 TTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGG
*
123364 CTTACAGATGACCTGAAGGATTTAAGCATAATGCTCGAAAGACTTACTGATG
66 CTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG
123416 GCCTGAAGGT
Statistics
Matches: 301, Mismatches: 27, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
215 2 0.01
216 121 0.40
217 4 0.01
222 1 0.00
225 47 0.16
226 124 0.41
227 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (218 bp):
TTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCAAAGGTCTTATCATCTTGCTCGAAAGG
CTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCAAAGGATTT
ACTTTAATCTCGGAATTACTATTTCAAGTGAAACTTTCTAAAGCAAGACATTGTTGTTCCAAATG
TCATGAATCAAGCAACAAAAATG
Found at i:125230 original size:90 final size:92
Alignment explanation
Indices: 125116--125284 Score: 256
Period size: 90 Copynumber: 1.9 Consensus size: 92
125106 TATTTGAAAC
*
125116 TTATCCATAAAGTAGGGGTTATTAACCAATTGCTCTAGAGGGACAGA-TCAAGCTTTATT-T-CA
1 TTATCCATAAAGTAGGGGTGATTAACCAATTGCTCTAGAGGGACA-ACTCAAGCTTTATTGTACA
*
125178 TATAATAGTATAATAGACTAGCTGAATA
65 TATAATAATATAATAGACTAGCTGAATA
* *
125206 TTATCCATAAAGCT-GGGGTGATTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATA
1 TTATCCATAAAG-TAGGGGTGATTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTACA
125270 TATAATAATATAATA
65 TATAATAATATAATA
125285 TGAGTATACG
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
89 1 0.01
90 53 0.75
91 2 0.03
92 15 0.21
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (92 bp):
TTATCCATAAAGTAGGGGTGATTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTACAT
ATAATAATATAATAGACTAGCTGAATA
Found at i:129470 original size:22 final size:22
Alignment explanation
Indices: 129428--129474 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
129418 TGCTGCAACA
* *
129428 AAAGAAACAAAAAGAGAAAAAG
1 AAAGAAAAAAAAAAAGAAAAAG
129450 AAAGAAAAAAAATAAAG-AAAAG
1 AAAGAAAAAAAA-AAAGAAAAAG
129472 AAA
1 AAA
129475 AAGACTCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAAAAAAAGAAAAAG
Found at i:137285 original size:14 final size:15
Alignment explanation
Indices: 137268--137304 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
137258 TGCTTTTCGA
137268 TTCTTCTTT-TTCTT
1 TTCTTCTTTGTTCTT
*
137282 TTCTT-TTTGTTTTT
1 TTCTTCTTTGTTCTT
137296 TTCTTCTTT
1 TTCTTCTTT
137305 CTTGTTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 14 0.70
15 3 0.15
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (15 bp):
TTCTTCTTTGTTCTT
Found at i:137295 original size:18 final size:18
Alignment explanation
Indices: 137268--137310 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
137258 TGCTTTTCGA
*
137268 TTCTTCTTTTTCTT-TTCT
1 TTCTTGTTTTT-TTCTTCT
137286 TT-TTGTTTTTTTCTTCT
1 TTCTTGTTTTTTTCTTCT
137303 TTCTTGTT
1 TTCTTGTT
137311 GCTTTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (18 bp):
TTCTTGTTTTTTTCTTCT
Found at i:137307 original size:21 final size:19
Alignment explanation
Indices: 137274--137317 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
137264 TCGATTCTTC
* *
137274 TTTTTCTTTTCTTTTTGTT
1 TTTTTCTTTTCTTGTTGCT
137293 TTTTTCTTCTTTCTTGTTGCT
1 TTTTTC-T-TTTCTTGTTGCT
137314 TTTT
1 TTTT
137318 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTGTTGCT
Found at i:142380 original size:21 final size:21
Alignment explanation
Indices: 142339--142399 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
142329 TGAAAATAAT
142339 TAAAATATCAAGGATTAAAATA
1 TAAAATATCAA-GATTAAAATA
*
142361 TAAAATATCAAGAATAAAATA
1 TAAAATATCAAGATTAAAATA
142382 TAAAATATCAAGATTAAA
1 TAAAATATCAAGATTAAA
142400 GGCCTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 26 0.70
22 11 0.30
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (21 bp):
TAAAATATCAAGATTAAAATA
Found at i:143548 original size:3 final size:3
Alignment explanation
Indices: 143540--143598 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
143530 TTCGGGCCTG
* * * *
143540 TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAT TAA TAA -AA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
143587 TAA TAA TAA TAA
1 TAA TAA TAA TAA
143599 AAAATAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:143817 original size:68 final size:68
Alignment explanation
Indices: 143725--143940 Score: 369
Period size: 68 Copynumber: 3.2 Consensus size: 68
143715 TACCAATTGT
*
143725 ACAGTTAGGCCTCAAATGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
143790 AGC
66 AGC
* *
143793 AGAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
143858 AGC
66 AGC
* *
143861 ACAGTTAGACCTCAAAGGTACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
*
143926 AGA
66 AGC
*
143929 ACATTTAGGCCT
1 ACAGTTAGGCCT
143941 ATTAATCCTT
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 138 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (68 bp):
ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
AGC
Found at i:153636 original size:13 final size:13
Alignment explanation
Indices: 153614--153643 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
153604 ACTAAACACC
153614 TTTC-ACATACCT
1 TTTCAACATACCT
153626 TTTCAACATACCT
1 TTTCAACATACCT
153639 TTTCA
1 TTTCA
153644 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:156968 original size:21 final size:21
Alignment explanation
Indices: 156929--156968 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
156919 ATACATTCAT
* *
156929 ATTAGCTCATAAACTTTATAC
1 ATTAGCTCACAAACATTATAC
*
156950 ATTAGCTCACACACATTAT
1 ATTAGCTCACAAACATTAT
156969 GAGATGATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACAAACATTATAC
Found at i:159006 original size:12 final size:12
Alignment explanation
Indices: 158991--159027 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
158981 TTTTGTTTTC
158991 AAAAAA-ACAAA
1 AAAAAAGACAAA
*
159002 AAAAAAGGCAAA
1 AAAAAAGACAAA
159014 AAAAAAGACAAA
1 AAAAAAGACAAA
159026 AA
1 AA
159028 GACAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAGACAAA
Found at i:159026 original size:20 final size:20
Alignment explanation
Indices: 158990--159034 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
158980 ATTTTGTTTT
*
158990 CAAAAAAACAAAAAAAAAGG
1 CAAAAAAACAAAAAAAAAGA
*
159010 CAAAAAAA-AAGACAAAAAGA
1 CAAAAAAACAA-AAAAAAAGA
159030 CAAAA
1 CAAAA
159035 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGA
Found at i:162296 original size:11 final size:11
Alignment explanation
Indices: 162282--162338 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
162272 AGGATGATTT
162282 AATGGTGATGA
1 AATGGTGATGA
162293 AATGGTGATGGA
1 AATGGTGAT-GA
162305 ATATGGTGATGA
1 A-ATGGTGATGA
* *
162317 TATAGGCG-TGA
1 AAT-GGTGATGA
162328 TAATGGTGATG
1 -AATGGTGATG
162339 GACAGATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 17 0.46
12 12 0.32
13 8 0.22
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.30
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:166733 original size:11 final size:11
Alignment explanation
Indices: 166719--166775 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
166709 AGGATGATTT
166719 AATGGTGATGA
1 AATGGTGATGA
166730 AATGGTGATGGA
1 AATGGTGAT-GA
166742 ATATGGTGATGA
1 A-ATGGTGATGA
* *
166754 TATAGGCG-TGA
1 AAT-GGTGATGA
166765 TAATGGTGATG
1 -AATGGTGATG
166776 GACAGATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 17 0.46
12 12 0.32
13 8 0.22
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.30
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:174588 original size:2 final size:2
Alignment explanation
Indices: 174581--174609 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
174571 CCTCTTTTTG
174581 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
174610 TTTTTGTTGT
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:178323 original size:20 final size:21
Alignment explanation
Indices: 178300--178344 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
178290 AAAAAACAAA
178300 AAAAAAAAGGC-AAAAAAA-CC
1 AAAAAAAA-GCTAAAAAAAGCC
*
178320 AAAAAAGAGCTAAAAAAAGCC
1 AAAAAAAAGCTAAAAAAAGCC
178341 AAAA
1 AAAA
178345 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 14 0.64
21 6 0.27
ACGTcount: A:0.73, C:0.13, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGCTAAAAAAAGCC
Found at i:196742 original size:35 final size:36
Alignment explanation
Indices: 196696--196774 Score: 115
Period size: 35 Copynumber: 2.2 Consensus size: 36
196686 TTTGAGAATT
**
196696 TGGTGATGATATAGGCATGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGAAGATGGACTA
* *
196731 TGGTGATGATATAGGCGTGATAATGAAGATGGATTA
1 TGGTGATGATATAGGCATGATAATGAAGATGGACTA
196767 TGGTGATG
1 TGGTGATG
196775 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 20 0.51
36 19 0.49
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGAAGATGGACTA
Found at i:201214 original size:35 final size:37
Alignment explanation
Indices: 201168--201246 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 37
201158 TTAAGAATTT
*
201168 GGTGATGATATAGGCGTGAT-ATGG-TGATGGACTAC
1 GGTGATGATATAGGCGTGATAATGGAAGATGGACTAC
* *
201203 GGTGATGATATAGGCGTGATAATGGAAGATGGATTAT
1 GGTGATGATATAGGCGTGATAATGGAAGATGGACTAC
201240 GGTGATG
1 GGTGATG
201247 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.29
Consensus pattern (37 bp):
GGTGATGATATAGGCGTGATAATGGAAGATGGACTAC
Found at i:204128 original size:24 final size:21
Alignment explanation
Indices: 204090--204135 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
204080 ATTGGCACAT
*
204090 TCTTTTGAATTTCAAGAGGTACA
1 TCTTTTGAATGTCAA-AGG-ACA
204113 TCTTTTGAAATGTCAAAGGACA
1 TCTTTTG-AATGTCAAAGGACA
204135 T
1 T
204136 GTCTTGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 10 0.48
24 7 0.33
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (21 bp):
TCTTTTGAATGTCAAAGGACA
Found at i:205507 original size:15 final size:15
Alignment explanation
Indices: 205487--205517 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
205477 CTTCTTTTTG
*
205487 TATTTTTGTTGTTGT
1 TATTTTGGTTGTTGT
205502 TATTTTGGTTGTTGT
1 TATTTTGGTTGTTGT
205517 T
1 T
205518 GCACATTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.23, T:0.71
Consensus pattern (15 bp):
TATTTTGGTTGTTGT
Found at i:210417 original size:15 final size:15
Alignment explanation
Indices: 210382--210410 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
210372 GTACTTCAAC
210382 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
210396 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
210411 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:211402 original size:91 final size:91
Alignment explanation
Indices: 211247--211429 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
211237 GGTAGTTGAT
*
211247 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
211312 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* * *
211338 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCATATTCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
* * **
211403 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGATCACATGCAAAACACATG
211429 G
1 G
211430 GTGTTCTAGG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
GGGGCTGATCACATGCAAAACACATG
Found at i:213040 original size:2 final size:2
Alignment explanation
Indices: 213033--213069 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
213023 ATCACCAACT
213033 TA TA TA TA 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 TA TA TA TA T
213070 TCTGCTACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:217507 original size:68 final size:67
Alignment explanation
Indices: 217293--217508 Score: 351
Period size: 68 Copynumber: 3.2 Consensus size: 67
217283 AAGGATTAAT
* *
217293 AGGCCTAAATGTTTTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGTCT
1 AGGCCTAACTGTTCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTG-CT
217358 TTG
65 TTG
* * *
217361 AGGTCTAACTATGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTTCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTG-CT
*
217426 TTA
65 TTG
217429 AGGCCTAACTGTTCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCAT
1 AGGCCTAACTGTTCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC-T
217494 TTG
65 TTG
217497 AGGCCTAACTGT
1 AGGCCTAACTGT
217509 GCAATTGGTA
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
67 1 0.01
68 135 0.99
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (67 bp):
AGGCCTAACTGTTCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCTT
TG
Found at i:217643 original size:3 final size:3
Alignment explanation
Indices: 217635--217754 Score: 174
Period size: 3 Copynumber: 41.0 Consensus size: 3
217625 ATTTTATTTT
* * * * *
217635 TTA TTA TTA TTA ATA TTA TTA TT- TTA TTA ATA TTA ATA CTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
217682 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
217728 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
217755 CAGGCCTGAA
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
2 6 0.06
3 100 0.94
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:219034 original size:21 final size:20
Alignment explanation
Indices: 219002--219040 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
218992 AATTAAGGCC
219002 TTTAATCTTGATATTTTATA
1 TTTAATCTTGATATTTTATA
219022 TTTAATCCTTGATATTTTA
1 TTTAAT-CTTGATATTTTA
219041 ATTATTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTAATCTTGATATTTTATA
Found at i:227561 original size:14 final size:14
Alignment explanation
Indices: 227542--227582 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
227532 AAGACACTAC
227542 CTTTCCATCACCAT
1 CTTTCCATCACCAT
227556 CTTTCCATCACCAT
1 CTTTCCATCACCAT
* *
227570 -TCTCTATCACCAT
1 CTTTCCATCACCAT
227583 TCATGCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:227580 original size:13 final size:13
Alignment explanation
Indices: 227545--227584 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
227535 ACACTACCTT
*
227545 TCCATCACCATCTT
1 TCCATCACCAT-TC
227559 TCCATCACCATTC
1 TCCATCACCATTC
*
227572 TCTATCACCATTC
1 TCCATCACCATTC
227585 ATGCCTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (13 bp):
TCCATCACCATTC
Found at i:232331 original size:24 final size:25
Alignment explanation
Indices: 232280--232333 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
232270 AAATTAGAAA
**
232280 AAAAGCACTCAGAAAGAAGAAATTG
1 AAAAGCACTCAGAAAGAAGAAAAAG
232305 AAAA-CACTCA-AAAGAAGAAAAAAG
1 AAAAGCACTCAGAAAGAAG-AAAAAG
232329 AAAAG
1 AAAAG
232334 AAAAGTTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 7 0.28
24 14 0.56
25 4 0.16
ACGTcount: A:0.65, C:0.11, G:0.17, T:0.07
Consensus pattern (25 bp):
AAAAGCACTCAGAAAGAAGAAAAAG
Found at i:235107 original size:13 final size:12
Alignment explanation
Indices: 235088--235173 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
235078 TATAGGGCGT
235088 GATATGGTGATG
1 GATATGGTGATG
235100 GAATATGGTGAT-
1 G-ATATGGTGATG
*
235112 GATATAGG-CAT-
1 GATAT-GGTGATG
235123 GATAATGGTGATG
1 GAT-ATGGTGATG
235136 GACTATGGTGAT-
1 GA-TATGGTGATG
*
235148 GATATAGGCG-T-
1 GATAT-GGTGATG
235159 GATAATGGTGATG
1 GAT-ATGGTGATG
235172 GA
1 GA
235174 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:235174 original size:36 final size:36
Alignment explanation
Indices: 235069--235174 Score: 169
Period size: 36 Copynumber: 2.9 Consensus size: 36
235059 ATTTATAAGT
* *
235069 TGGTGATAATATAGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATA-GGCGTGATAATGGTGATGGACTA
*
235105 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
235141 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
235175 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 7 0.11
36 58 0.89
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:240762 original size:36 final size:36
Alignment explanation
Indices: 240684--240788 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
240674 ATTTATAAGT
* *
240684 TGGTGATAATATAGGCGTGATAA-GGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
240719 TGTTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
240755 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
240789 AATATCTTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:242479 original size:11 final size:13
Alignment explanation
Indices: 242447--242476 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
242437 TGGCCAAAGA
242447 TGAAAAGGTATGT
1 TGAAAAGGTATGT
242460 TGAAAAGGTATG-
1 TGAAAAGGTATGT
242472 TGAAA
1 TGAAA
242477 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:252395 original size:12 final size:10
Alignment explanation
Indices: 252363--252399 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
252353 AATTTTGGCT
252363 TTTTTTTG--
1 TTTTTTTGCC
252371 TTTTTTTGCC
1 TTTTTTTGCC
252381 TTTTTTTGCC
1 TTTTTTTGCC
252391 TCTTTTTTG
1 T-TTTTTTG
252400 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.31
10 11 0.42
11 7 0.27
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.76
Consensus pattern (10 bp):
TTTTTTTGCC
Found at i:256081 original size:39 final size:39
Alignment explanation
Indices: 256038--256116 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
256028 CTTATAAGAC
256038 TAAGAAGGAACCAATGCTATAAAGGAGCAAAGACCCATT
1 TAAGAAGGAACCAATGCTATAAAGGAGCAAAGACCCATT
*
256077 TAAGAAGGAACCAATGCTATAAAGGAGCAAGGACCCATT
1 TAAGAAGGAACCAATGCTATAAAGGAGCAAAGACCCATT
256116 T
1 T
256117 CTTATAAGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (39 bp):
TAAGAAGGAACCAATGCTATAAAGGAGCAAAGACCCATT
Found at i:260070 original size:24 final size:22
Alignment explanation
Indices: 260038--260084 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
260028 GATGTAGGAG
260038 TCTTTTTCTT-TTCTCTTTTATTT
1 TCTTTTTCTTGTT-TCTTTT-TTT
260061 TCTTCTTTCTTGTTTCTTTTTTT
1 TCTT-TTTCTTGTTTCTTTTTTT
260084 T
1 T
260085 GTAGCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.36
24 12 0.55
25 2 0.09
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (22 bp):
TCTTTTTCTTGTTTCTTTTTTT
Found at i:263740 original size:22 final size:22
Alignment explanation
Indices: 263710--263762 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
263700 TGAGCTGGAC
263710 TTTTGAGCTAGCTAGAGGTCTCA
1 TTTT-AGCTAGCTAGAGGTCTCA
263733 TTTTAGCTAGCTAGAGGTCTCA
1 TTTTAGCTAGCTAGAGGTCTCA
*
263755 TTTCAGCT
1 TTTTAGCT
263763 GGAGAGTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (22 bp):
TTTTAGCTAGCTAGAGGTCTCA
Found at i:264334 original size:20 final size:20
Alignment explanation
Indices: 264296--264338 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
264286 AAACATCATC
** *
264296 TATTTTCATTTTAAGACATG
1 TATTTTCATTAAAAAACATG
264316 TATTTTCATTAAAAAACATG
1 TATTTTCATTAAAAAACATG
264336 TAT
1 TAT
264339 CTAGCCGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
TATTTTCATTAAAAAACATG
Found at i:264677 original size:14 final size:14
Alignment explanation
Indices: 264658--264685 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
264648 AAGATAGTAC
264658 CTTTCCATCACCAT
1 CTTTCCATCACCAT
264672 CTTTCCATCACCAT
1 CTTTCCATCACCAT
264686 TTACGCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:264976 original size:17 final size:18
Alignment explanation
Indices: 264932--264976 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
264922 TAATCACACA
*
264932 ATTGAAA-AAAATAAATG
1 ATTGAAAGAAAATAAAGG
264949 ATT-AAATGAAAAT-AAGG
1 ATTGAAA-GAAAATAAAGG
264966 ATTGAAAGAAA
1 ATTGAAAGAAA
264977 TGGAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 13 0.54
18 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (18 bp):
ATTGAAAGAAAATAAAGG
Found at i:264991 original size:17 final size:15
Alignment explanation
Indices: 264966--265007 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
264956 GAAAATAAGG
264966 ATTGAAAGAAATGGAA
1 ATTGAAAGAAAT-GAA
264982 ATTGATAAGAAATGAA
1 ATTGA-AAGAAATGAA
*
264998 ATGGAAAGAA
1 ATTGAAAGAA
265008 TTGATACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (15 bp):
ATTGAAAGAAATGAA
Found at i:267710 original size:130 final size:129
Alignment explanation
Indices: 267456--267692 Score: 334
Period size: 129 Copynumber: 1.8 Consensus size: 129
267446 TCACACTTGA
267456 TGCATTTCCACCTTCATGAATCCATTTATGGCGTGTACATCATACAATAAGGCTAAAGGACTTGT
1 TGCATTTCCACCTTCATGAATCCATTTATGGCGTGTACATCATACAATAAGGCTAAAGGACTTGT
* * ** ** * * **
267521 TCACATTCAAGAGAGATGGATGCATTATTTTCAAACTCATTCACCAAATCCAAGTACATGAAGG
66 TCACATTCAACAGAAATGGAAACATTACCTCCAAACTCATGCACCAAATCCAACAACATGAAGG
267585 TGCATTTCCACCTTCATGAATCCATTTATGGCGTGTACAATCATACAATAAGGCTAAAGGACTTG
1 TGCATTTCCACCTTCATGAATCCATTTATGGCGTGTAC-ATCATACAATAAGGCTAAAGGACTTG
* *
267650 TTCACATTCAACATACAAT-GAAACATT-CCTCCAAATTCATGCA
65 TTCACATTCAACAGA-AATGGAAACATTACCTCCAAACTCATGCA
267693 AGGAAATGAA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
129 49 0.51
130 45 0.47
131 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (129 bp):
TGCATTTCCACCTTCATGAATCCATTTATGGCGTGTACATCATACAATAAGGCTAAAGGACTTGT
TCACATTCAACAGAAATGGAAACATTACCTCCAAACTCATGCACCAAATCCAACAACATGAAGG
Found at i:282791 original size:20 final size:20
Alignment explanation
Indices: 282766--282805 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
282756 ACCTTTCATC
282766 ATTTGAGCTACTTCTCATGT
1 ATTTGAGCTACTTCTCATGT
282786 ATTTGAGCTACTTCTCATGT
1 ATTTGAGCTACTTCTCATGT
282806 GCTTGAGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTTGAGCTACTTCTCATGT
Found at i:282811 original size:20 final size:20
Alignment explanation
Indices: 282768--282814 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
282758 CTTTCATCAT
*
282768 TTGAGCTACTTCTCATGTAT
1 TTGAGCTACTTCTCATGTAC
*
282788 TTGAGCTACTTCTCATGTGC
1 TTGAGCTACTTCTCATGTAC
282808 TTGAGCT
1 TTGAGCT
282815 GAAGATAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (20 bp):
TTGAGCTACTTCTCATGTAC
Found at i:283335 original size:33 final size:33
Alignment explanation
Indices: 283293--283361 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
283283 GTTGATGAAT
*
283293 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
283326 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
283359 GAA
1 GAA
283362 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:283402 original size:36 final size:36
Alignment explanation
Indices: 283332--283444 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
283322 AATGGAAGGA
* * *
283332 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
283367 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
283403 TGATGATATAGGCGTCATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
283439 TGATGA
1 TGATGA
283445 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:287360 original size:22 final size:20
Alignment explanation
Indices: 287317--287361 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
287307 TGTAGGAGTC
* *
287317 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGCTT
287337 TTTTTCTTCTTTCTTGTTGCTT
1 TTTTTC-T-TTTCTTGTTGCTT
287359 TTT
1 TTT
287362 GTTGTAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGCTT
Found at i:287744 original size:33 final size:33
Alignment explanation
Indices: 287702--287770 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
287692 GTTGATGAAT
*
287702 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGG-CATGAAATGGTAATG
* *
287735 GAAGGATGATGTTATTGGCATGATATGGTAATG
1 GAAGGATGATGTTAATGGCATGAAATGGTAATG
287768 GAA
1 GAA
287771 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.35, C:0.01, G:0.33, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCATGAAATGGTAATG
Found at i:287805 original size:36 final size:36
Alignment explanation
Indices: 287741--287853 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
287731 AATGGAAGGA
* * * *
287741 TGATGTTATTGGCATGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
287776 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
287812 TGATGATATAGGCGTCATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
287848 TGATGA
1 TGATGA
287854 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 15 0.22
36 54 0.78
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:291236 original size:36 final size:36
Alignment explanation
Indices: 291183--291295 Score: 149
Period size: 36 Copynumber: 3.2 Consensus size: 36
291173 GATACTATTT
291183 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
** *
291219 TCATCACCATAGCCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
291255 TCATCACCATATTCCAT-TACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCT-CCATTATCACGCCTATA
*
291290 ACATCA
1 TCATCA
291296 TCCTTCCTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
35 17 0.25
36 51 0.75
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCTCCATTATCACGCCTATA
Found at i:292876 original size:11 final size:11
Alignment explanation
Indices: 292843--292931 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 11
292833 ACAATCTGTC
292843 CATCACCATTAT
1 CATCACCA-TAT
*
292855 CA-CGCCTATAT
1 CATCACC-ATAT
292866 CATCACCATATT
1 CATCACCATA-T
292878 CCATCACCATAT
1 -CATCACCATAT
*
292890 CA-CACCAATAA
1 CATCACC-ATAT
292901 CATCATCC-T-T
1 CATCA-CCATAT
* *
292911 CCATTACCATTT
1 -CATCACCATAT
292923 CATCACCAT
1 CATCACCAT
292932 TAAATCATCC
Statistics
Matches: 61, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
10 6 0.10
11 32 0.52
12 11 0.18
13 12 0.20
ACGTcount: A:0.33, C:0.37, G:0.01, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:292920 original size:33 final size:33
Alignment explanation
Indices: 292876--292944 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
292866 CATCACCATA
292876 TTCCATCACCATATCA-CACCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
292909 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
292942 TTC
1 TTC
292945 ATTCATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:295383 original size:19 final size:20
Alignment explanation
Indices: 295356--295397 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
295346 TATTTTTTTC
295356 AAAAAAAAAAAAG-G-CAAA
1 AAAAAAAAAAAAGAGCCAAA
295374 AAAAACAAAAAAAGAGCCAAA
1 AAAAA-AAAAAAAGAGCCAAA
295395 AAA
1 AAA
295398 TCCAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 1 0.05
21 7 0.33
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAGAGCCAAA
Found at i:302801 original size:20 final size:21
Alignment explanation
Indices: 302764--302804 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
302754 TTTTTTGCCT
302764 TTTTTTTTTTTGCCTTTTTTG
1 TTTTTTTTTTTGCCTTTTTTG
*
302785 TTTTTTTTTTTG-TTTTTTTG
1 TTTTTTTTTTTGCCTTTTTTG
302805 AAGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTTTGCCTTTTTTG
Found at i:302803 original size:15 final size:15
Alignment explanation
Indices: 302737--302790 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
302727 AAATTTTGGC
*
302737 TTTTTTGGCTCTTTTT
1 TTTTTTTGC-CTTTTT
302753 TTTTTTTGCCTTTTT
1 TTTTTTTGCCTTTTT
302768 TTTTTTTGCCTTTTT
1 TTTTTTTGCCTTTTT
302783 TGTTTTTT
1 T-TTTTTT
302791 TTTTTGTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
15 22 0.61
16 14 0.39
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (15 bp):
TTTTTTTGCCTTTTT
Found at i:304447 original size:11 final size:11
Alignment explanation
Indices: 304423--304470 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
304413 TATTTTTTTC
*
304423 AAAAAA-AAAC
1 AAAAAACAAAA
304433 AAAAAACAAAA
1 AAAAAACAAAA
*
304444 AAAAAGGCAAAA
1 AAAAA-ACAAAA
304456 AAAAAACAAAA
1 AAAAAACAAAA
304467 AAAA
1 AAAA
304471 GAGCCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 6 0.18
11 17 0.52
12 10 0.30
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:304463 original size:23 final size:24
Alignment explanation
Indices: 304428--304483 Score: 87
Period size: 23 Copynumber: 2.3 Consensus size: 24
304418 TTTTCAAAAA
*
304428 AAAACAAAAAACAAAAAAAA-AGGC
1 AAAA-AAAAAACAAAAAAAAGAGCC
304452 AAAAAAAAAACAAAAAAAAGAGCC
1 AAAAAAAAAACAAAAAAAAGAGCC
304476 AAAAAAAA
1 AAAAAAAA
304484 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAACAAAAAAAAGAGCC
Found at i:304479 original size:11 final size:11
Alignment explanation
Indices: 304441--304490 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
304431 ACAAAAAACA
*
304441 AAAAAAAAGGCA
1 AAAAAAAA-GCC
* *
304453 AAAAAAAAACA
1 AAAAAAAAGCC
304464 AAAAAAAGAGCC
1 AAAAAAA-AGCC
304476 AAAAAAAAGCC
1 AAAAAAAAGCC
304487 AAAA
1 AAAA
304491 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 17 0.50
12 17 0.50
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGCC
Found at i:304484 original size:13 final size:12
Alignment explanation
Indices: 304427--304483 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
304417 TTTTTCAAAA
*
304427 AAAAACAAAAAAC
1 AAAAA-AAAAGAC
*
304440 AAAAAAAAAGGC
1 AAAAAAAAAGAC
304452 AAAAAAAAA-AC
1 AAAAAAAAAGAC
*
304463 AAAAAAAAGAGCC
1 AAAAAAAA-AGAC
304476 AAAAAAAA
1 AAAAAAAA
304484 GCCAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 9 0.24
12 15 0.39
13 14 0.37
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAC
Found at i:311260 original size:33 final size:33
Alignment explanation
Indices: 311181--311284 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
311171 ATACAATCTG
* *
311181 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
311217 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
311250 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
311283 TC
1 TC
311285 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:315388 original size:36 final size:36
Alignment explanation
Indices: 315336--315448 Score: 158
Period size: 36 Copynumber: 3.2 Consensus size: 36
315326 GATACTATTT
315336 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
315372 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
315408 TCATCACCATATTCCAT-TACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCT-CCATTATCACGCCTATA
*
315443 ACATCA
1 TCATCA
315449 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
35 17 0.24
36 53 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCTCCATTATCACGCCTATA
Found at i:315461 original size:33 final size:33
Alignment explanation
Indices: 315384--315487 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
315374 ATCACCATAG
* * *
315384 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATTACCA-TATCACGCCAATAACATCATCC---T
315420 TCCATTACCATATCACGCCAATAACATCATCCT
1 TCCATTACCATATCACGCCAATAACATCATCCT
* * *
315453 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATTACCATATCA-CGCCAATAACATCATCCT
315486 TC
1 TC
315488 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 25 0.42
34 7 0.12
35 17 0.28
36 11 0.18
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.32
Consensus pattern (33 bp):
TCCATTACCATATCACGCCAATAACATCATCCT
Found at i:318673 original size:22 final size:21
Alignment explanation
Indices: 318632--318675 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
318622 CAACATCTCC
*
318632 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
318653 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
318675 A
1 A
318676 TTCCGTAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:325308 original size:19 final size:20
Alignment explanation
Indices: 325284--325334 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
325274 CGGCCAAGAG
* *
325284 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
325303 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
325323 CATGTATTTTCA
1 CATGTATTTTCA
325335 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:329429 original size:36 final size:36
Alignment explanation
Indices: 329377--329489 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
329367 GATACTATTT
*
329377 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
329413 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
329449 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
329484 ACATCA
1 TCATCA
329490 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:329432 original size:13 final size:11
Alignment explanation
Indices: 329377--329475 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
329367 GATACTATTT
329377 TCATCACCATAA
1 TCATCACCAT-A
*
329389 TCCATCTCCATTA
1 T-CATCACCA-TA
*
329402 TCA-CGCCTATA
1 TCATCACC-ATA
329413 TCATCACCATA
1 TCATCACCATA
329424 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
329438 TCA-CGCCTATA
1 TCATCACC-ATA
329449 TCATCACCATA
1 TCATCACCATA
329460 TTCCATCACCATA
1 -T-CATCACCATA
329473 TCA
1 TCA
329476 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:329504 original size:33 final size:33
Alignment explanation
Indices: 329389--329528 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
329379 ATCACCATAA
* * *
329389 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
329423 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
329461 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
329494 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
329527 TC
1 TC
329529 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:333347 original size:34 final size:34
Alignment explanation
Indices: 333304--333410 Score: 146
Period size: 34 Copynumber: 3.1 Consensus size: 34
333294 ATACTATTTT
*
333304 CATCACCATAATCCATCTCCATTATCACGCTATA
1 CATCACCATAATCCATCACCATTATCACGCTATA
*
333338 CATCACCATAGTCCATCACCATTATCACGCCTATA
1 CATCACCATAATCCATCACCATTATCACG-CTATA
* *
333373 TCATCACCATATTCCATCACCA-TATCACGCCA-A
1 -CATCACCATAATCCATCACCATTATCACGCTATA
333406 CATCA
1 CATCA
333411 TCCTTCCATT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 5 0.07
33 1 0.01
34 29 0.43
35 12 0.18
36 20 0.30
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.26
Consensus pattern (34 bp):
CATCACCATAATCCATCACCATTATCACGCTATA
Found at i:333356 original size:13 final size:11
Alignment explanation
Indices: 333303--333399 Score: 58
Period size: 13 Copynumber: 8.3 Consensus size: 11
333293 GATACTATTT
333303 TCATCACCATAA
1 TCATCACCAT-A
*
333315 TCCATCTCCAT-
1 T-CATCACCATA
333326 T-ATCACGC-TA
1 TCATCAC-CATA
333336 TACATCACCATA
1 T-CATCACCATA
333348 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
333362 TCA-CGCCTATA
1 TCATCACC-ATA
333373 TCATCACCATA
1 TCATCACCATA
333384 TTCCATCACCATA
1 -T-CATCACCATA
333397 TCA
1 TCA
333400 CGCCAACATC
Statistics
Matches: 68, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
11 15 0.22
12 16 0.24
13 28 0.41
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:333858 original size:70 final size:71
Alignment explanation
Indices: 333744--333885 Score: 261
Period size: 70 Copynumber: 2.0 Consensus size: 71
333734 CAAAGCAACA
333744 TATCTGTGATTCAAAAGACATCACTTTTGGCAATCCAAAAGATATGAACAGGGAGTATACCTTTA
1 TATCTGTGATTCAAAAGACATCACTTTTGGCAATCCAAAAGATATGAACAGGGAGTATACCTTTA
333809 ACTTTC
66 ACTTTC
333815 TATCTTGTGATTC-AAAGACATCAC-TTTGGCAATCCAAAAGATATGAACAGGGAGTATACCTTT
1 TATC-TGTGATTCAAAAGACATCACTTTTGGCAATCCAAAAGATATGAACAGGGAGTATACCTTT
333878 AACTTTC
65 AACTTTC
333885 T
1 T
333886 CATGATTAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
70 47 0.67
71 15 0.21
72 8 0.11
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (71 bp):
TATCTGTGATTCAAAAGACATCACTTTTGGCAATCCAAAAGATATGAACAGGGAGTATACCTTTA
ACTTTC
Found at i:335354 original size:19 final size:20
Alignment explanation
Indices: 335330--335380 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
335320 TCGGCAAGAG
* *
335330 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
335349 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
335369 CATGTATTTTCA
1 CATGTATTTTCA
335381 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:337568 original size:19 final size:18
Alignment explanation
Indices: 337546--337599 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
337536 TTCTTTTGAA
337546 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
337564 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
*
337583 GTCTTTTTC-TTTCTTTT
1 TTCTTTTTCTTTTCTTTT
337600 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.22
18 10 0.31
19 15 0.47
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:337570 original size:13 final size:13
Alignment explanation
Indices: 337552--337599 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
337542 TGAATTCTTT
337552 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
337565 TTCTTTTCTTCTTC
1 TTCTTTTCTT-TTC
*
337579 TT-TTGTCTTTTTC
1 TTCTTTTC-TTTTC
337592 TTTCTTTT
1 -TTCTTTT
337600 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 17 0.59
14 9 0.31
15 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:341267 original size:13 final size:11
Alignment explanation
Indices: 341226--341310 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
341216 ACAATCTGTC
341226 CATCACCATTAT
1 CATCACCA-TAT
*
341238 CATGC-CTATAT
1 CAT-CACCATAT
341249 CATCACCATAGT
1 CATCACCATA-T
341261 CCATCACCATTAT
1 -CATCACCA-TAT
*
341274 CA-CGCCTATAT
1 CATCACC-ATAT
341285 CATCACCATATT
1 CATCACCATA-T
341297 CCATCACCATAT
1 -CATCACCATAT
341309 CA
1 CA
341311 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:341270 original size:36 final size:36
Alignment explanation
Indices: 341223--341327 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
341213 GATACAATCT
*
341223 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
341259 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
341295 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
341328 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:341795 original size:14 final size:15
Alignment explanation
Indices: 341761--341807 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
341751 AATTTGGAGT
341761 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
341776 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
341790 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
341807 G
1 G
341808 TGAAGCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:349274 original size:90 final size:91
Alignment explanation
Indices: 349158--349339 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
349148 GAGAAATGAT
* *
349158 GCTTGGCCGAATAGGGAGAGAGCTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCACCTAAATAAACCACATGCAAGGCACATG
*
349222 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * *
349248 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCACCTAAATAAACCACATGCAAGGCACATG
* **
349313 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
349339 G
1 G
349340 GTGTTCTAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 58 0.72
91 23 0.28
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCACCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:356868 original size:20 final size:20
Alignment explanation
Indices: 356843--356891 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
356833 GATGAAGTAT
356843 GGTAATGGAAGTAGAATGAA
1 GGTAATGGAAGTAGAATGAA
356863 GGTAATGGAAGTAGAATGAA
1 GGTAATGGAAGTAGAATGAA
356883 GGTAATGGA
1 GGTAATGGA
356892 GATGAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (20 bp):
GGTAATGGAAGTAGAATGAA
Found at i:358073 original size:30 final size:31
Alignment explanation
Indices: 358021--358080 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
358011 CTTAGCTTTA
**
358021 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
358051 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
358081 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:364875 original size:19 final size:20
Alignment explanation
Indices: 364851--364901 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
364841 CGGCCAAGAG
* *
364851 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
364870 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
364890 CATGTATTTTCA
1 CATGTATTTTCA
364902 AAGAGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:365647 original size:8 final size:8
Alignment explanation
Indices: 365602--365660 Score: 57
Period size: 8 Copynumber: 6.9 Consensus size: 8
365592 TTGGAGTGCA
365602 AAAAGAAAG
1 AAAAG-AAG
365611 AAAAGACA-
1 AAAAGA-AG
365619 AAAAGAAG
1 AAAAGAAG
*
365627 AGAAAAATCAG
1 A-AAAGA--AG
365638 AAAAGAAG
1 AAAAGAAG
365646 AAAAGAAG
1 AAAAGAAG
365654 AAAAGAA
1 AAAAGAA
365661 AAGAAAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
7 1 0.02
8 25 0.58
9 10 0.23
10 4 0.09
11 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:365670 original size:27 final size:26
Alignment explanation
Indices: 365602--365667 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
365592 TTGGAGTGCA
365602 AAAAG-AAAGAAAAGACAAAAAGAAG
1 AAAAGAAAAGAAAAGACAAAAAGAAG
*
365627 AGAAA-AATCAGAAAAGA-AGAAAAGAAG
1 A-AAAGAA-AAGAAAAGACA-AAAAGAAG
365654 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
365668 AGAGAAGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
25 1 0.03
26 14 0.41
27 19 0.56
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAGAAAAGACAAAAAGAAG
Found at i:368101 original size:30 final size:31
Alignment explanation
Indices: 368049--368108 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
368039 CTTAGCTTTA
**
368049 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
368079 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
368109 GGCAACATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:369042 original size:19 final size:20
Alignment explanation
Indices: 369018--369068 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
369008 CGGCCAAGAG
* *
369018 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
369037 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
369057 CATGTATTTTCA
1 CATGTATTTTCA
369069 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:376578 original size:36 final size:36
Alignment explanation
Indices: 376528--376632 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
376518 GATACAATAT
*
376528 GTCCATCACCATTATCACGCCTAAATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
376564 GTCCATCACTATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
376600 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
376633 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 21 0.33
36 43 0.67
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:377043 original size:30 final size:30
Alignment explanation
Indices: 377009--377065 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
376999 CATGTGCTGC
* *
377009 AAGAAAAGCAACAAA-AAGAGAAAAAGAAAG
1 AAGAAAAACAA-AAAGAAAAGAAAAAGAAAG
377039 AAGAAAAACAAAAAGAAAAGAAAAAGA
1 AAGAAAAACAAAAAGAAAAGAAAAAGA
377066 CTCCTACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (30 bp):
AAGAAAAACAAAAAGAAAAGAAAAAGAAAG
Found at i:377063 original size:6 final size:6
Alignment explanation
Indices: 377022--377065 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
377012 AAAAGCAACA
*
377022 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
377066 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Done.