Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009160.1 Hibiscus syriacus cultivar Beakdansim tig00112688_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: 458650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:396513 original size:129 final size:128
Alignment explanation
Indices: 396283--396566 Score: 469
Period size: 129 Copynumber: 2.2 Consensus size: 128
396273 ACGCGGTTCC
* *
396283 TACGTGATGAAGAAGTCTGGTCGTCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
1 TACGTGATGAAG-AGTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
* * *
396348 GTTATCTATGGTTGACATGGCTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGCTCA
65 GTTATCTATAGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGAGAATGACACGGCTCA
*
396412 TACGTGATGAAGAGTTCTGGCCATCTGAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
1 TACGTGATGAAGAG-TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
*
396477 GTTATCTATAGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGAGAATGATACGGCTCA
65 GTTATCTATAGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGAGAATGACACGGCTCA
*
396541 TACGTGATGAAGAGGGCTGGCCATCT
1 TACGTGATGAAGA-GTCTGGCCATCT
396567 TTAGGAGTTA
Statistics
Matches: 145, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 2 0.01
129 142 0.98
130 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (128 bp):
TACGTGATGAAGAGTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
TTATCTATAGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGAGAATGACACGGCTCA
Found at i:396619 original size:28 final size:28
Alignment explanation
Indices: 396579--396675 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
396569 AGGAGTTATG
* *
396579 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
396607 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
*
396635 GTTTCAAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTCAA-AAGAAACAGA-ATCAAAGAT--T-T
396666 GTTTCAAAAG
1 GTTTCAAAAG
396676 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.05
28 43 0.73
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:396672 original size:31 final size:28
Alignment explanation
Indices: 396599--396675 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 28
396589 AAACCAAATT
396599 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
396627 AAAGATTTGTTTCAAGAA-AAACA-AGCTC
1 AAAGATTTGTTTCAA-AAGAAACAGA-CTC
396655 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
396676 CAACTGTCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
27 1 0.02
28 29 0.67
29 2 0.05
30 3 0.07
31 8 0.19
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:397201 original size:15 final size:15
Alignment explanation
Indices: 397177--397220 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
397167 AAGATGATCT
*
397177 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
397192 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
397207 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
397221 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:397376 original size:40 final size:40
Alignment explanation
Indices: 397316--397395 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
397306 ATTTTAATAA
397316 AAACAATCTCAAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
397356 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
397396 CGAGAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:397449 original size:63 final size:63
Alignment explanation
Indices: 397377--397501 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 63
397367 AATGTGGGTA
* * *
397377 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
* * *
397439 TTTTCCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTT-CAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
397502 GGATCCCATC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 4 0.07
63 13 0.24
64 38 0.69
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:397761 original size:63 final size:63
Alignment explanation
Indices: 397646--397826 Score: 170
Period size: 64 Copynumber: 2.8 Consensus size: 63
397636 AAACAAACTC
* * * * * * *
397646 AAACATATTCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGA
1 AAACAGATTCAAAGATTTA-TTCAAAAGAAATTATCTTAAGAGAGAAAAAATT-ATGTTTCAA-A
397709 G
63 G
* *
397710 AAACAGATTCAAAGATTT-TTCCAAAAGAAATTATCTTAAGAGAGATAAAATTTTGTTTCCAAAG
1 AAACAGATTCAAAGATTTATT-CAAAAGAAATTATCTTAAGAGAGAAAAAATTATGTTT-CAAAG
* *
397774 AAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGAAAAAA
1 AAACAGATTCAAAGA--TTT-ATTCAAAAGAAATTATCTTAAGAGAGAAAAAA
397827 AAAATTTGTT
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
62 3 0.03
63 28 0.28
64 33 0.33
65 2 0.02
66 3 0.03
67 28 0.28
68 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (63 bp):
AAACAGATTCAAAGATTTATTCAAAAGAAATTATCTTAAGAGAGAAAAAATTATGTTTCAAAG
Found at i:397818 original size:67 final size:68
Alignment explanation
Indices: 397708--397876 Score: 238
Period size: 70 Copynumber: 2.5 Consensus size: 68
397698 TCATTTTAAG
* * * *
397708 AGAAACAGATTCAAAGA--TTT-TTCCAAAAGAAATTATCTTAAGAGAG-ATAAAATTTTGTTTC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGAAAAAAAATTTGTTTC
397769 CAA
66 CAA
397772 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGAAAAAAAAAATTTGTT
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAG--AAAAAAAATTTGTT
*
397837 TCCGA
64 TCCAA
*
397842 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
397877 CAATCTCAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
64 16 0.17
66 3 0.03
67 25 0.27
70 49 0.53
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (68 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGAAAAAAAATTTGTTTC
CAA
Found at i:397905 original size:28 final size:28
Alignment explanation
Indices: 397841--397978 Score: 190
Period size: 28 Copynumber: 4.9 Consensus size: 28
397831 TTTGTTTCCG
397841 AAGAAACAAACTCAAAGATTTTTGTTTCAA
1 AAGAAACAAACTCAAAGA-TTTT-TTTCAA
*
397871 AAGAAACAATCTCAAAGATTTTTTTCAA
1 AAGAAACAAACTCAAAGATTTTTTTCAA
397899 AAGAAAC-AACTCAAAGATTTTTATTCAA
1 AAGAAACAAACTCAAAGATTTTT-TTCAA
*
397927 AATG-AACAAACTCAAATATTTTTTTCAA
1 AA-GAAACAAACTCAAAGATTTTTTTCAA
* *
397955 GAGGAACAAACTCAAAGATTTTTT
1 AAGAAACAAACTCAAAGATTTTTT
397979 CACAAAATTG
Statistics
Matches: 99, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
27 15 0.15
28 48 0.48
29 19 0.19
30 17 0.17
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (28 bp):
AAGAAACAAACTCAAAGATTTTTTTCAA
Found at i:398045 original size:52 final size:53
Alignment explanation
Indices: 397964--398067 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
397954 AGAGGAACAA
*
397964 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACCTTGTTTCAG
*
398017 ACTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACCTTGTTTCA
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACCTTGTTTCA
398068 AAATAAATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 40 0.82
53 9 0.18
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACCTTGTTTCAG
Found at i:398094 original size:28 final size:28
Alignment explanation
Indices: 398063--398157 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
398053 CAAAACCTTG
* *
398063 TTTCAAAATAAATAGACTCAAAGATTTT
1 TTTCAAAAGAAATAAACTCAAAGATTTT
*
398091 TTTCAAAAGAAATAAACTCAAATATTTT
1 TTTCAAAAGAAATAAACTCAAAGATTTT
* * *
398119 TTTCAAGAGGAACAAACTCAAAGA-TTT
1 TTTCAAAAGAAATAAACTCAAAGATTTT
*
398146 TTTCAAGAGAAA
1 TTTCAAAAGAAA
398158 CTGTCTCAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 14 0.24
28 45 0.76
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (28 bp):
TTTCAAAAGAAATAAACTCAAAGATTTT
Found at i:398484 original size:38 final size:35
Alignment explanation
Indices: 398393--398496 Score: 111
Period size: 38 Copynumber: 2.9 Consensus size: 35
398383 TATGAGAGAA
* *
398393 AATGATGTCTCAAGCGAGACAAAATTTGCTTTAAG
1 AATGTTGTCTCAAGCGAGACAAAATTTGTTTTAAG
* * **
398428 -ATATAGTCTCAAATGAGACAAAATTTGTTTTAAAGAG
1 AATGTTGTCTCAAGCGAGACAAAATTTGTTTT--A-AG
*
398465 AATGTTGTCTCAAGCGAGACAAAGTTTGTTTT
1 AATGTTGTCTCAAGCGAGACAAAATTTGTTTT
398497 TGAGAAACGA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
34 25 0.46
36 1 0.02
37 2 0.04
38 26 0.48
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (35 bp):
AATGTTGTCTCAAGCGAGACAAAATTTGTTTTAAG
Found at i:399172 original size:4 final size:4
Alignment explanation
Indices: 399163--399219 Score: 50
Period size: 4 Copynumber: 15.2 Consensus size: 4
399153 TTTTATGGAT
* * *
399163 TATG TATG TATG --TG TATA TATG TATG TATG TA-- TATA TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
399207 TATA TATG TATG T
1 TATG TATG TATG T
399220 TTTCTCGATC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
2 4 0.10
4 38 0.90
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:399186 original size:14 final size:14
Alignment explanation
Indices: 399167--399219 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
399157 ATGGATTATG
399167 TATGTATGTGTATA
1 TATGTATGTGTATA
* *
399181 TATGTATGTATGTA
1 TATGTATGTGTATA
*
399195 TATATATGCATGTATA
1 TATGTATG--TGTATA
399211 TATGTATGT
1 TATGTATGT
399220 TTTCTCGATC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 20 0.65
16 11 0.35
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (14 bp):
TATGTATGTGTATA
Found at i:399186 original size:18 final size:18
Alignment explanation
Indices: 399163--399209 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
399153 TTTTATGGAT
*
399163 TATGTATGTATGTGTATA
1 TATGTATGTATGTATATA
399181 TATGTATGTATGTATATA
1 TATGTATGTATGTATATA
*
399199 TATGCATGTAT
1 TATGTATGTAT
399210 ATATGTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (18 bp):
TATGTATGTATGTATATA
Found at i:400417 original size:12 final size:12
Alignment explanation
Indices: 400402--400446 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
400392 TGCTTTTTCC
400402 CTTTGATTTTTG
1 CTTTGATTTTTG
400414 CTTTGATTTTT-
1 CTTTGATTTTTG
400425 CTTTG-TTTTTG
1 CTTTGATTTTTG
400436 CTTTGATTTTT
1 CTTTGATTTTT
400447 TTCTCTCTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.16
11 10 0.32
12 16 0.52
ACGTcount: A:0.07, C:0.09, G:0.13, T:0.71
Consensus pattern (12 bp):
CTTTGATTTTTG
Found at i:400428 original size:11 final size:12
Alignment explanation
Indices: 400389--400446 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
400379 TCTTTTTGTT
*
400389 CTTTGCTTTTTCC
1 CTTTGATTTTT-C
*
400402 CTTTGATTTTTG
1 CTTTGATTTTTC
400414 CTTTGATTTTT-
1 CTTTGATTTTTC
*
400425 CTTTG-TTTTTG
1 CTTTGATTTTTC
400436 CTTTGATTTTT
1 CTTTGATTTTT
400447 TTCTCTCTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
10 5 0.12
11 10 0.24
12 16 0.39
13 10 0.24
ACGTcount: A:0.05, C:0.14, G:0.12, T:0.69
Consensus pattern (12 bp):
CTTTGATTTTTC
Found at i:400436 original size:22 final size:22
Alignment explanation
Indices: 400402--400504 Score: 84
Period size: 22 Copynumber: 4.5 Consensus size: 22
400392 TGCTTTTTCC
400402 CTTTGATTTTTGCTTTGATTTTT
1 CTTTG-TTTTTGCTTTGATTTTT
400425 CTTTGTTTTTGCTTTGA-TTTT
1 CTTTGTTTTTGCTTTGATTTTT
* * * *
400446 -TTTCTCTCTGCTCTTTGTTTTTT
1 CTTTGTTTTTG--CTTTGATTTTT
*
400469 CTTTGCTCTTTTCTCTTTGATTTTT
1 CTTTG-T-TTTT-GCTTTGATTTTT
*
400494 CCTTGTTTTTG
1 CTTTGTTTTTG
400505 ATTGGATCTT
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
20 7 0.11
21 4 0.06
22 17 0.27
23 13 0.21
24 4 0.06
25 15 0.24
26 2 0.03
ACGTcount: A:0.04, C:0.16, G:0.12, T:0.69
Consensus pattern (22 bp):
CTTTGTTTTTGCTTTGATTTTT
Found at i:400475 original size:18 final size:20
Alignment explanation
Indices: 400443--400479 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
400433 TTGCTTTGAT
400443 TTTTTTCTCTCTGCTCTTTG
1 TTTTTTCTCTCTGCTCTTTG
400463 TTTTTTCT-T-TGCTCTTT
1 TTTTTTCTCTCTGCTCTTT
400480 TCTCTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.00, C:0.22, G:0.08, T:0.70
Consensus pattern (20 bp):
TTTTTTCTCTCTGCTCTTTG
Found at i:401136 original size:26 final size:24
Alignment explanation
Indices: 401106--401176 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
401096 CAAGGTGGAA
401106 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
401130 AGGGAATGTTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
401152 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
401176 A
1 A
401177 TAAAATGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
20 12 0.32
22 5 0.14
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:401161 original size:20 final size:20
Alignment explanation
Indices: 401093--401167 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
401083 AAATACAGTG
*
401093 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
401112 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
401138 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
401158 TTTCAAGGTC
1 TTTCAAGGTC
401168 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:401184 original size:46 final size:45
Alignment explanation
Indices: 401091--401184 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
401081 ATAAATACAG
* **
401091 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAAAA
*
401136 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAAAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAAAA
401182 TGT
1 TGT
401185 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAAAA
Found at i:402421 original size:31 final size:32
Alignment explanation
Indices: 402365--402426 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
402355 TGACAAAATG
402365 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
402397 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
402427 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:406451 original size:3 final size:3
Alignment explanation
Indices: 406443--406496 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
406433 ATGTAAATTA
* * *
406443 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAC GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
406491 ATAT AA
1 A-AT AA
406497 AAAAAAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:408189 original size:18 final size:17
Alignment explanation
Indices: 408156--408189 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
408146 GAATAATTAA
408156 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
408173 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
408190 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:416102 original size:14 final size:14
Alignment explanation
Indices: 416083--416109 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
416073 TAGTTATCAA
416083 TAAAATAAACTAAG
1 TAAAATAAACTAAG
416097 TAAAATAAACTAA
1 TAAAATAAACTAA
416110 AATAATTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
TAAAATAAACTAAG
Found at i:416403 original size:18 final size:17
Alignment explanation
Indices: 416370--416403 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
416360 TAATAATTAA
416370 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
416387 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
416404 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:421798 original size:34 final size:34
Alignment explanation
Indices: 421755--421823 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
421745 TGACCGATGA
*
421755 TACTAGACTTTTTAAGTCATCTTTTTGTATGCTC
1 TACTAGACTTTTTAAGTCATCTTTTTGCATGCTC
421789 TACTAGACTTTTTAAGTCATCTTTTTGCATGCTC
1 TACTAGACTTTTTAAGTCATCTTTTTGCATGCTC
421823 T
1 T
421824 TTCAGTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (34 bp):
TACTAGACTTTTTAAGTCATCTTTTTGCATGCTC
Found at i:426323 original size:4 final size:4
Alignment explanation
Indices: 426314--426342 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
426304 CTAAAAAGTC
426314 AAAG AAAG AAAG AAAG AAAG AAA- AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
426343 TGTTATACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:427059 original size:20 final size:21
Alignment explanation
Indices: 427028--427081 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
427018 GATTCTTGAC
427028 AATCGCAATGCGATTTT-CAT
1 AATCGCAATGCGATTTTCCAT
* *
427048 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTTCCAT
*
427069 AATCGCAACGCGA
1 AATCGCAATGCGA
427082 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
AATCGCAATGCGATTTTCCAT
Found at i:427094 original size:20 final size:20
Alignment explanation
Indices: 427069--427181 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
427059 GATTTTCCAT
* *
427069 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
427089 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
427109 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
427129 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
427149 TATCGCAACGCGTATC-CATA
1 AATCGCAACGCG-AACACATA
427169 AATCGCAACGCGA
1 AATCGCAACGCGA
427182 TTTTTAAAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 78 0.95
21 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:427132 original size:40 final size:39
Alignment explanation
Indices: 427065--427181 Score: 128
Period size: 40 Copynumber: 3.0 Consensus size: 39
427055 TTGCGATTTT
* ** *
427065 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
427103 CACATAAATCGCAACGCGTATCCGTAAATCGCAATGCGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * *
427144 CCGTATATCGCAACGCGTATCCATAAATCGCAACGCGA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
427182 TTTTTAAAGC
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
38 1 0.02
39 4 0.06
40 59 0.89
41 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:427598 original size:33 final size:33
Alignment explanation
Indices: 427559--427629 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
427549 TTCACTTAGA
* *
427559 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCATTGCAAT
* *
427592 TTTCATTTCGCGTTGCTATTCTCTCATTGCAAT
1 TTTCATTTCGCGTTACGATTCTCTCATTGCAAT
427625 TTTCA
1 TTTCA
427630 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCATTGCAAT
Found at i:427734 original size:21 final size:20
Alignment explanation
Indices: 427708--427814 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
427698 TGCAGAAGAG
427708 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
427729 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
427749 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
427771 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
427785 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
427804 TCGCAACGAGA
1 TCGCAACGAGA
427815 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:427788 original size:14 final size:14
Alignment explanation
Indices: 427769--427825 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
427759 GAAAAATGAA
427769 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
427783 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
427802 AATCGCAACGAGAG
1 AATCGCAACGAGAG
427816 AATCGCAACG
1 AATCGCAACG
427826 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:427800 original size:33 final size:33
Alignment explanation
Indices: 427762--427841 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
427752 GCAACGAGAA
427762 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
427795 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
427828 AAACCAAAATCGCA
1 AAATGAAAATCGCA
427842 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:427859 original size:19 final size:19
Alignment explanation
Indices: 427837--427964 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
427827 GAAACCAAAA
*
427837 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
427856 TCGCGTTGCGA--TTCA--
1 TCGCGTTGCGATTTTCATT
*
427871 -CTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
427889 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
427903 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
427923 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
427943 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
427963 TC
1 TC
427965 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.22
16 7 0.08
17 7 0.08
19 21 0.24
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:427878 original size:14 final size:14
Alignment explanation
Indices: 427859--427915 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
427849 TTTCATTTCG
427859 CGTTGCGATTCACT
1 CGTTGCGATTCACT
*
427873 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTCA---CT
*
427892 CGTTGCGATTCTCT
1 CGTTGCGATTCACT
427906 CGTTGCGATT
1 CGTTGCGATT
427916 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 4 0.11
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCACT
Found at i:427884 original size:33 final size:33
Alignment explanation
Indices: 427842--427923 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
427832 CAAAATCGCA
427842 TTGCGATTTTCATTTCGCGTTGCGATTCACTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCACTCG
*
427875 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCACTCG
427908 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
427924 TCTCGTTGCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCACTCG
Found at i:427926 original size:21 final size:21
Alignment explanation
Indices: 427900--427964 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
427890 CGCGTTGCGA
427900 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
427921 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
427941 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
427962 TTC
1 TTC
427965 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:427961 original size:20 final size:20
Alignment explanation
Indices: 427899--427962 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
427889 TCGCGTTGCG
427899 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
427919 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
427940 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
427960 ATT
1 ATT
427963 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:430063 original size:92 final size:93
Alignment explanation
Indices: 429887--430190 Score: 548
Period size: 92 Copynumber: 3.3 Consensus size: 93
429877 TAGATTGCTT
*
429887 AGTAAATTTATTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
429950 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
429978 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
430043 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
430070 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
430135 TTTGTCTTTGTTTTGTCTTTTGGTTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGG-TTGAA
430164 AGTAAATTTG-TC-GTTGCTGCC-ATTCTG
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTG
430191 AAACTAATAC
Statistics
Matches: 208, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
91 30 0.14
92 120 0.58
93 43 0.21
94 15 0.07
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:430377 original size:19 final size:19
Alignment explanation
Indices: 430353--430411 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
430343 GCAACGACAG
430353 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
430372 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
430386 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
430405 AATCGCA
1 AATCGCA
430412 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:430379 original size:33 final size:33
Alignment explanation
Indices: 430289--430411 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
430279 TAGTTTACTT
* * *
430289 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
430323 TCGCAACGCG-AATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
430355 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
430388 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
430412 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
32 27 0.33
33 45 0.56
34 9 0.11
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:430388 original size:14 final size:14
Alignment explanation
Indices: 430305--430395 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
430295 CACGAAACTT
*
430305 AAAATCGCAACGAG
1 AAAATCGCAACGAC
* *
430319 AGAATCGCAACGCGAATG
1 AAAATCGCAA--CG-A-C
430337 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
430351 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
430370 AAAATCGCAACGAC
1 AAAATCGCAACGAC
430384 AAAATCGCAACG
1 AAAATCGCAACG
430396 CGAAACCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 31 0.49
15 2 0.03
16 6 0.10
17 3 0.05
18 11 0.17
19 10 0.16
ACGTcount: A:0.46, C:0.26, G:0.20, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:430467 original size:19 final size:19
Alignment explanation
Indices: 430443--430578 Score: 140
Period size: 19 Copynumber: 7.4 Consensus size: 19
430433 GCGATTCTCT
430443 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
430462 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTGGTTTCG
**
430476 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
430494 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
430513 CGTTGCGATTTTGGTTTCT
1 CGTTGCGATTTTGGTTTCG
* **
430532 CGTTGCGATTCTCATTTCG
1 CGTTGCGATTTTGGTTTCG
*
430551 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
430571 TGTTGCGA
1 CGTTGCGA
430579 AAGTAAACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.02
14 8 0.08
16 2 0.02
18 9 0.09
19 63 0.66
20 12 0.12
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:430481 original size:14 final size:14
Alignment explanation
Indices: 430429--430485 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
430419 TTTCAGTTCG
*
430429 CGTTGCGATTCTCT
1 CGTTGCGATTCTGT
*
430443 CGTTGCGATTTTGGTTT
1 CGTTGCGATTCT-G--T
430460 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTGT
430476 CGTTGCGATT
1 CGTTGCGATT
430486 TCATTTCGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 21 0.60
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.21, G:0.28, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:430503 original size:51 final size:54
Alignment explanation
Indices: 430443--430578 Score: 188
Period size: 51 Copynumber: 2.5 Consensus size: 54
430433 GCGATTCTCT
430443 CGTTGCGATTTTGGTTTCGCGTTGCGATTCT-G-TCGTTGCGATT-TCATTTCG
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATTTCG
*
430494 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATTTCG
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGG--T-TCGTTGCGATTCTCATTTCG
* *
430551 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTT-GGTTTCGCGTTGCGA
430579 AAGTAAACTA
Statistics
Matches: 75, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
51 30 0.40
52 1 0.01
56 11 0.15
57 20 0.27
58 13 0.17
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (54 bp):
CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATTTCG
Found at i:430550 original size:38 final size:36
Alignment explanation
Indices: 430407--430578 Score: 144
Period size: 33 Copynumber: 4.8 Consensus size: 36
430397 GAAACCAAAA
* *
430407 TCGCATTGCGATTTTCAG-TTCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTT-GGTTTCGCGTTGCGATTTCTT
* *
430440 TCTCGTTGCGATTTTGGTTTCGCGTTGCGA-TTCTG
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTCTT
** *
430475 T--CGTTGCGA-TTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGA-TTT-CTT
*
430510 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATT-TC-TT
* *
430548 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTT-GGTTTCGCGTTGCGA
430579 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
32 17 0.15
33 36 0.32
34 2 0.02
35 3 0.03
37 10 0.09
38 33 0.29
39 12 0.11
ACGTcount: A:0.09, C:0.20, G:0.26, T:0.45
Consensus pattern (36 bp):
TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTCTT
Found at i:432340 original size:14 final size:14
Alignment explanation
Indices: 432321--432356 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
432311 ATTGTTTAAT
432321 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
432335 TGATTTTTAAAAGT
1 TGATTTGTAAAAGA
432349 TGATTTGT
1 TGATTTGT
432357 GTAATTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:432468 original size:19 final size:19
Alignment explanation
Indices: 432444--432531 Score: 98
Period size: 19 Copynumber: 4.8 Consensus size: 19
432434 GCATTATGTT
432444 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
432463 GAAATGAAAATCG-AA-AC
1 GAAATGAAAATCGCAATGC
*
432480 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
432496 GAAATG-AAATCGCAATGC
1 GAAATGAAAATCGCAATGC
432514 GGAAATGAAAAATCGCAA
1 -GAAATG-AAAATCGCAA
432532 CGAGAGAATC
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
14 7 0.12
15 3 0.05
16 2 0.04
17 2 0.04
18 14 0.25
19 20 0.35
21 9 0.16
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:432541 original size:53 final size:52
Alignment explanation
Indices: 432444--432550 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 52
432434 GCATTATGTT
432444 GAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAGAATCGCAATGC
*
432496 GAAATG-AAATCGCAATGCGGAAATGAAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC-GAAATG-AAAATCGAAACGAGAGAATCGCAATGC
432549 GA
1 GA
432551 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
51 12 0.23
52 12 0.23
53 28 0.54
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAGAATCGCAATGC
Found at i:432568 original size:19 final size:19
Alignment explanation
Indices: 432540--432782 Score: 265
Period size: 19 Copynumber: 13.7 Consensus size: 19
432530 AACGAGAGAA
*
432540 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
432559 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
432578 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
432595 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
432612 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
432631 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
432647 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
432664 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
432683 TCCGCTTTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
432700 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
432717 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
432736 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
432754 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
432770 TCGCATTGCGATT
1 TCGCATTGCGATT
432783 CTCTCGTTGC
Statistics
Matches: 191, Mismatches: 10, Indels: 46
0.77 0.04 0.19
Matches are distributed among these distances:
14 28 0.15
16 20 0.10
17 20 0.10
18 8 0.04
19 81 0.42
20 34 0.18
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:432609 original size:53 final size:53
Alignment explanation
Indices: 432546--432782 Score: 431
Period size: 53 Copynumber: 4.5 Consensus size: 53
432536 AGAATCGCAA
432546 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
432599 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
432651 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCTTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* *
432704 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
432757 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
432783 CTCTCGTTGC
Statistics
Matches: 178, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
52 52 0.29
53 126 0.71
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:432666 original size:105 final size:106
Alignment explanation
Indices: 432546--432782 Score: 431
Period size: 105 Copynumber: 2.2 Consensus size: 106
432536 AGAATCGCAA
432546 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
432611 TTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
432651 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCTTTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
* *
432716 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
432757 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
432783 CTCTCGTTGC
Statistics
Matches: 127, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 85 0.67
106 42 0.33
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (106 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:432779 original size:86 final size:84
Alignment explanation
Indices: 432617--432796 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
432607 TCATTTCGCA
432617 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTCG-ATTGCGATTTTCAT
*
432682 TTCCGCTTTGCGATTCTCTCG
64 TTCCGCATTGCGATTCTCTCG
* *
432703 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC-TT-G-TTGGGATTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATTCGATTGCGATTT
432765 TCATTT-CGCATTGCGATTCTCTCG
60 TCATTTCCGCATTGCGATTCTCTCG
432789 TTGCGATT
1 TTGCGATT
432797 GTAATTTCCG
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 50 0.59
87 14 0.16
88 3 0.04
89 3 0.04
90 4 0.05
92 11 0.13
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.47
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTCGATTGCGATTTTCATTT
CCGCATTGCGATTCTCTCG
Found at i:432780 original size:33 final size:33
Alignment explanation
Indices: 432546--432796 Score: 193
Period size: 33 Copynumber: 7.2 Consensus size: 33
432536 AGAATCGCAA
*
432546 TGCGATTTTCATTTCGCATTGCGATTTTCAT-T
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
* * * *
432578 TCCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTC--TT-G--T
* *
432618 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
*
432651 TGCGATTTTCATTTCGCATTGCGATTTTCAT-T
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
* * * * *
432683 TCCGCTTTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTTTC-ATT-TCGCATTGCGATTTTC--TT-G--T
432723 TGCGATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCTTGT
* * *
432757 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
432790 TGCGATT
1 TGCGATT
432797 GTAATTTCCG
Statistics
Matches: 171, Mismatches: 29, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
32 14 0.08
33 59 0.35
34 42 0.25
35 1 0.01
36 4 0.02
37 2 0.01
38 14 0.08
39 20 0.12
40 15 0.09
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
Found at i:432811 original size:53 final size:53
Alignment explanation
Indices: 432546--432815 Score: 279
Period size: 53 Copynumber: 5.1 Consensus size: 53
432536 AGAATCGCAA
* *
432546 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GT
* *
432599 TGCGATTTTCATTTCGCATTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GT
* * *
432651 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCTTTGCGA-TTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GT
* * * *
432704 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCGTGT
* * *
432757 TGGGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGT
1 TGCGATTTTCATTTCGCATTGCGATT-T-TCAGTTCCGCATTGCAATTTCCGTGT
432810 TGCGAT
1 TGCGAT
432816 AGTCAAATGC
Statistics
Matches: 199, Mismatches: 13, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
52 51 0.26
53 138 0.69
54 8 0.04
55 2 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCGTGT
Found at i:434341 original size:21 final size:21
Alignment explanation
Indices: 434315--434359 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
434305 GATTTCTGGG
* *
434315 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
434336 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
434357 CAA
1 CAA
434360 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:434998 original size:23 final size:24
Alignment explanation
Indices: 434955--435001 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
434945 ATATGGCATG
*
434955 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
434979 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
435002 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:435216 original size:31 final size:31
Alignment explanation
Indices: 435178--435333 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
435168 AGGGTCGAGG
435178 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
435209 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
435240 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
435271 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
435302 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
435333 G
1 G
435334 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:438390 original size:20 final size:20
Alignment explanation
Indices: 438362--438590 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
438352 AAATTTCAGT
* * *
438362 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
438382 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
438402 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
438422 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
438442 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
438462 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
438482 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
438502 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
438522 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
438542 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
438562 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
438582 GTTGCGATT
1 GTTGCGATT
438591 ATGGAAAATC
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:438608 original size:21 final size:20
Alignment explanation
Indices: 438584--438631 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
438574 ATATTCGCGT
438584 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
438605 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
438625 TGCGATT
1 TGCGATT
438632 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:441531 original size:15 final size:15
Alignment explanation
Indices: 441511--441543 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
441501 AAATCAGAGG
441511 GGGGCCTAGGGCTCA
1 GGGGCCTAGGGCTCA
441526 GGGGCCTAGGGCTCA
1 GGGGCCTAGGGCTCA
441541 GGG
1 GGG
441544 ACCTTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.52, T:0.12
Consensus pattern (15 bp):
GGGGCCTAGGGCTCA
Found at i:446576 original size:16 final size:17
Alignment explanation
Indices: 446536--446583 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
446526 TATTTATGAG
446536 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
446554 CGAATTGAAATCTGT-A
1 GGAATTGGAATCTGTAA
446570 GGAATTGGAATCTG
1 GGAATTGGAATCTG
446584 AATCTGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
18 13 0.50
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:447293 original size:98 final size:96
Alignment explanation
Indices: 447117--447309 Score: 237
Period size: 97 Copynumber: 2.0 Consensus size: 96
447107 CCTAAACCTG
*
447117 AACCCGACCCGAATATCACACTTAAAAAACCCAACCCGACCCGTACCCAAAATTTAAAAAAAATC
1 AACCCGACCCGAATATCACACTTAAAAAACCCAACCCGACCCGTACCCAAAATTTAAAAAAAACC
* *
447182 CGACCCAATCCCGAATTTTTTTTTAAAAAAAA
66 CGACCCAACCCCGAA-ATTTTTTTAAAAAAAA
* * * * * *
447214 AACCCGACCCGAATATCACACTTACAAAAACTCGACCCTATCCGAATA-TCAAACTTT-AAAAAA
1 AACCCGACCCGAATATCACACTTA-AAAAACCCAACCCGACCCG--TACCCAAAATTTAAAAAAA
* *
447277 CCCCGACCCGACCCCGAAATTTTTTTAAAAAAA
63 ACCCGACCCAACCCCGAAATTTTTTTAAAAAAA
447310 TCCTACCCGA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
97 38 0.46
98 35 0.43
99 7 0.09
100 2 0.02
ACGTcount: A:0.43, C:0.31, G:0.07, T:0.20
Consensus pattern (96 bp):
AACCCGACCCGAATATCACACTTAAAAAACCCAACCCGACCCGTACCCAAAATTTAAAAAAAACC
CGACCCAACCCCGAAATTTTTTTAAAAAAAA
Found at i:450957 original size:2 final size:2
Alignment explanation
Indices: 450950--450980 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
450940 TCTCTGTCTT
450950 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 T
450981 GAATTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.