Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001985.1 Hibiscus syriacus cultivar Beakdansim tig00004046_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: 712196
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:363335 original size:113 final size:113
Alignment explanation
Indices: 363137--363364 Score: 456
Period size: 113 Copynumber: 2.0 Consensus size: 113
363127 CAGTGAGTGT
363137 TCTCATCATACCATTTAGGGTAAGGGGGCTTCATTAGTTCCACAGGGTACGGTGACACTACATGA
1 TCTCATCATACCATTTAGGGTAAGGGGGCTTCATTAGTTCCACAGGGTACGGTGACACTACATGA
363202 GTGTCAAAAAGCTGTTGATATAATTTCTTGTATGACATGGAAATATGA
66 GTGTCAAAAAGCTGTTGATATAATTTCTTGTATGACATGGAAATATGA
363250 TCTCATCATACCATTTAGGGTAAGGGGGCTTCATTAGTTCCACAGGGTACGGTGACACTACATGA
1 TCTCATCATACCATTTAGGGTAAGGGGGCTTCATTAGTTCCACAGGGTACGGTGACACTACATGA
363315 GTGTCAAAAAGCTGTTGATATAATTTCTTGTATGACATGGAAATATGA
66 GTGTCAAAAAGCTGTTGATATAATTTCTTGTATGACATGGAAATATGA
363363 TC
1 TC
363365 GAATTGCTCA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 115 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (113 bp):
TCTCATCATACCATTTAGGGTAAGGGGGCTTCATTAGTTCCACAGGGTACGGTGACACTACATGA
GTGTCAAAAAGCTGTTGATATAATTTCTTGTATGACATGGAAATATGA
Found at i:367350 original size:36 final size:38
Alignment explanation
Indices: 367310--367404 Score: 104
Period size: 45 Copynumber: 2.4 Consensus size: 38
367300 AAGAATATTA
*
367310 AAGAAGCATTAAA-A-GAACATTGGATTATGGCTATGG
1 AAGAAGAATTAAATATGAACATTGGATTATGGCTATGG
367346 AAGAAGAATTAAATCAATTTGATGAACATTGGATTATGGCTATGG
1 AAGAAGAATT--A--AA--T-ATGAACATTGGATTATGGCTATGG
367391 AAGAAGAATTAAAT
1 AAGAAGAATTAAAT
367405 CAATTTGAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
36 9 0.18
38 1 0.02
39 1 0.02
40 2 0.04
41 2 0.04
43 1 0.02
44 1 0.02
45 32 0.65
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.27
Consensus pattern (38 bp):
AAGAAGAATTAAATATGAACATTGGATTATGGCTATGG
Found at i:367374 original size:45 final size:45
Alignment explanation
Indices: 367324--367412 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
367314 AGCATTAAAA
367324 GAACATTGGATTATGGCTATGGAAGAAGAATTAAATCAATTTGAT
1 GAACATTGGATTATGGCTATGGAAGAAGAATTAAATCAATTTGAT
367369 GAACATTGGATTATGGCTATGGAAGAAGAATTAAATCAATTTGA
1 GAACATTGGATTATGGCTATGGAAGAAGAATTAAATCAATTTGA
367413 GAGAAGTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (45 bp):
GAACATTGGATTATGGCTATGGAAGAAGAATTAAATCAATTTGAT
Found at i:378859 original size:19 final size:19
Alignment explanation
Indices: 378835--378875 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
378825 AAAATAGAAT
378835 AAAAGTGATA-TTTATACTA
1 AAAAGT-ATAGTTTATACTA
*
378854 AAAAGTATAGTTTATCCTA
1 AAAAGTATAGTTTATACTA
378873 AAA
1 AAA
378876 TCTAACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (19 bp):
AAAAGTATAGTTTATACTA
Found at i:389315 original size:18 final size:18
Alignment explanation
Indices: 389292--389328 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
389282 GTGTGGATAA
389292 GCAACTCACACTTGAAAT
1 GCAACTCACACTTGAAAT
389310 GCAACTCACACTTGAAAT
1 GCAACTCACACTTGAAAT
389328 G
1 G
389329 ACAAAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.22
Consensus pattern (18 bp):
GCAACTCACACTTGAAAT
Found at i:390583 original size:20 final size:20
Alignment explanation
Indices: 390560--390598 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
390550 TAAATTAAAT
390560 ATTAAATATG-ATCAGTTTTA
1 ATTAAATA-GAATCAGTTTTA
*
390580 ATTAGATAGAATCAGTTTT
1 ATTAAATAGAATCAGTTTT
390599 TATTCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (20 bp):
ATTAAATAGAATCAGTTTTA
Found at i:390635 original size:27 final size:27
Alignment explanation
Indices: 390605--390690 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
390595 TTTTTATTCT
390605 ATTAGTTATTAGATAGGATCATTTTTA
1 ATTAGTTATTAGATAGGATCATTTTTA
* * * * * *
390632 ATTAGATA-AAAATCA-GCT-TTTTATTCT
1 ATTAGTTATTAGAT-AGGATCATTT-TT-A
390659 ATTAGTTATTAGATAGGATCATTTTTA
1 ATTAGTTATTAGATAGGATCATTTTTA
390686 ATTAG
1 ATTAG
390691 ATAGAATCAT
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
25 3 0.07
26 7 0.17
27 21 0.51
28 7 0.17
29 3 0.07
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.47
Consensus pattern (27 bp):
ATTAGTTATTAGATAGGATCATTTTTA
Found at i:390667 original size:54 final size:53
Alignment explanation
Indices: 390559--390707 Score: 223
Period size: 54 Copynumber: 2.8 Consensus size: 53
390549 CTAAATTAAA
* * * *
390559 TATTAAATATGATCAGTTTTAATTAGAT-AGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAAAAATCAGTTTTTATTCTATTAGT
390611 TATTAGATAGGATCATTTTTAATTAGATAAAAATCAGCTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAAAAATCAG-TTTTTATTCTATTAGT
*
390665 TATTAGATAGGATCATTTTTAATTAGAT-AGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAAAAATCAGTTTTTATT
390708 TTGTTGCTAA
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
51 8 0.09
52 25 0.28
53 13 0.14
54 44 0.49
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAAAAATCAGTTTTTATTCTATTAGT
Found at i:390691 original size:20 final size:20
Alignment explanation
Indices: 390666--390705 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
390656 TCTATTAGTT
*
390666 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
390686 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
390706 TTTTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:395303 original size:20 final size:20
Alignment explanation
Indices: 395280--395424 Score: 63
Period size: 20 Copynumber: 8.0 Consensus size: 20
395270 TAAATTAAAT
395280 ATTAGATATG-ATCAGTTTTA
1 ATTAGATA-GAATCAGTTTTA
*
395300 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
395320 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
395332 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
*
395352 ATTAGATAGAATCAGCTTTTT
1 ATTAGATAGAATCAG-TTTTA
* *
395373 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
*
395385 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
*
395405 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
395425 TTTTGTTGCT
Statistics
Matches: 93, Mismatches: 14, Indels: 36
0.65 0.10 0.25
Matches are distributed among these distances:
12 6 0.06
13 4 0.04
14 2 0.02
15 4 0.04
16 4 0.04
17 6 0.06
18 1 0.01
19 6 0.06
20 53 0.57
21 7 0.08
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:395392 original size:53 final size:52
Alignment explanation
Indices: 395279--395426 Score: 253
Period size: 53 Copynumber: 2.8 Consensus size: 52
395269 CTAAATTAAA
* *
395279 TATTAGATATGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
395331 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGCTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
395384 TATTAGATAGAATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
395427 TTGTTGCTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 8 0.09
52 34 0.37
53 50 0.54
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:403068 original size:20 final size:20
Alignment explanation
Indices: 403043--403097 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
403033 CAGGTAAAAA
403043 TATGACAAAACCGGTTTAAT
1 TATGACAAAACCGGTTTAAT
403063 TATGACAAAACCGGTTTAAT
1 TATGACAAAACCGGTTTAAT
403083 TATGACAAAACCGGT
1 TATGACAAAACCGGT
403098 AAAACGCTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (20 bp):
TATGACAAAACCGGTTTAAT
Found at i:403391 original size:181 final size:181
Alignment explanation
Indices: 403084--403502 Score: 610
Period size: 181 Copynumber: 2.3 Consensus size: 181
403074 CGGTTTAATT
* * * * * *
403084 ATGACAAAACCGGTAAAACGCTACCGGATATGTTGAAAGTATCGATTAGATTGAA-ATAAGTATC
1 ATGACAAAACCGGTAAAACGCTACCAGATATATTGAAAGTGTTGA-TA-CTTTAATATAAGTATC
* *
403148 GACACTTTGGAATTTAAAAGAGAAGCATTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAAT
64 GACACTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAAAT
* *
403213 GTATTGATCCATAACAATATAACAGGTAAAAATAGGACAAAACC-GTCTTGAAA
129 GTATCGATCCATAACAATATAACAGGTAAAAATAGGACAAAACCAGTCTCG-AA
*
403266 AT-ACAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTTGATACTTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAACGCTACCAGATATATTGAAAGTGTTGATACTTTAATATAAGTATCGA
* * *
403330 CACTTTGAGAATTTAAAAGAGAAGTAGTAATAGTGTCTATAAAGTATCGATACTTTATAAAAATG
66 CACTTTG-GAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAAATG
** *
403395 TATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCAGTCTCGAA
130 TATCGATCCATAACAATATAACAGGTAAAAATAGGACAAAACCAGTCTCGAA
* *
403447 ATGACAAAACCGGTAAAACGCTACCAGATATATTGAAAGAGTTAATACTTTAATAT
1 ATGACAAAACCGGTAAAACGCTACCAGATATATTGAAAGTGTTGATACTTTAATAT
403503 GTACGCGTAA
Statistics
Matches: 213, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
179 4 0.02
180 20 0.09
181 132 0.62
182 57 0.27
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (181 bp):
ATGACAAAACCGGTAAAACGCTACCAGATATATTGAAAGTGTTGATACTTTAATATAAGTATCGA
CACTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAAATGT
ATCGATCCATAACAATATAACAGGTAAAAATAGGACAAAACCAGTCTCGAA
Found at i:405477 original size:22 final size:23
Alignment explanation
Indices: 405428--405482 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
405418 AACGTTTTTG
*
405428 TTTT-TTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAGAA
405450 TATTTATTATATAAAATGATA-AA
1 T-TTTATTATATAAAATGATAGAA
405473 TTTTATTATA
1 TTTTATTATA
405483 AATTCAGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 10 0.33
23 5 0.17
24 15 0.50
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAGAA
Found at i:405781 original size:15 final size:15
Alignment explanation
Indices: 405761--405790 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
405751 AGATGGTTAT
405761 AGGGGATAACGGTCA
1 AGGGGATAACGGTCA
*
405776 AGGGGATGACGGTCA
1 AGGGGATAACGGTCA
405791 GGAAAAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.43, T:0.13
Consensus pattern (15 bp):
AGGGGATAACGGTCA
Found at i:406710 original size:23 final size:23
Alignment explanation
Indices: 406680--406728 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
406670 AAAAGAAGAA
406680 AAATATATATAAATA-AAATAAAT
1 AAATATATATAAATATAAA-AAAT
*
406703 AAATATATATATATATAAAAAAT
1 AAATATATATAAATATAAAAAAT
406726 AAA
1 AAA
406729 AAAAATTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATATATATAAATATAAAAAAT
Found at i:406717 original size:31 final size:32
Alignment explanation
Indices: 406682--406789 Score: 103
Period size: 35 Copynumber: 3.2 Consensus size: 32
406672 AAGAAGAAAA
406682 ATATAT-ATAAATAAAATAAATAAATATATAT
1 ATATATAATAAATAAAATAAATAAATATATAT
* *
406713 ATATATAAAAAATAAAAAAAATTGTAAATATATAT
1 ATATATAATAAATAAAATAAA---TAAATATATAT
* *
406748 ATA-ATTAATAAAACTGATAATAAAAAAATATATAT
1 ATATA-TAAT-AAA-T-AAAATAAATAAATATATAT
406783 ATATATA
1 ATATATA
406790 TATATATATA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
31 6 0.10
32 12 0.19
34 1 0.02
35 32 0.52
36 4 0.06
37 1 0.02
38 6 0.10
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (32 bp):
ATATATAATAAATAAAATAAATAAATATATAT
Found at i:406748 original size:35 final size:37
Alignment explanation
Indices: 406691--406795 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 37
406681 AATATATATA
*
406691 AATAAAATAA-ATAAATATATATATATATAAAA-AAT
1 AATAAAAAAATATAAATATATATATATATAAAACAAT
* * *
406726 AA-AAAAAATTGTAAATATATATATAATTAATAAAACTGAT
1 AATAAAAAAATATAAATATATATAT-A-T-ATAAAAC-AAT
*
406766 AATAAAAAAATATATATATATATATATATA
1 AATAAAAAAATATAAATATATATATATATA
406796 TATATCTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
34 5 0.09
35 15 0.27
36 1 0.02
37 1 0.02
38 9 0.16
39 1 0.02
40 5 0.09
41 19 0.34
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (37 bp):
AATAAAAAAATATAAATATATATATATATAAAACAAT
Found at i:406820 original size:2 final size:2
Alignment explanation
Indices: 406775--406800 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
406765 TAATAAAAAA
406775 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
406801 CTAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:408031 original size:33 final size:34
Alignment explanation
Indices: 407960--408041 Score: 121
Period size: 36 Copynumber: 2.4 Consensus size: 34
407950 AGGGTTTGGT
* *
407960 TTTCAAGAGAAACATTTTCAAAGGTTTTTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGG--TTTTTTTATG
407996 TTTCAAGAGAAACAATTTCAAAGG-TTTTTTATG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTTATG
408029 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
408042 TGTATTCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 21 0.48
36 23 0.52
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (34 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTTTTTATG
Found at i:408108 original size:36 final size:36
Alignment explanation
Indices: 408059--408168 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 36
408049 AAAGATTGAA
*
408059 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
408095 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
408129 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
408165 GTTT
1 GTTT
408169 AACGTAAAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
34 27 0.44
36 34 0.56
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:408141 original size:34 final size:35
Alignment explanation
Indices: 408068--408157 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 35
408058 AGTTTCAAGG
** * *
408068 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
408104 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
408138 GAAACTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
408158 GAGATTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 25 0.51
36 24 0.49
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:408218 original size:30 final size:30
Alignment explanation
Indices: 408182--408240 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
408172 GTAAAACATA
*
408182 TTCAAAGATTT-TGTTTCAA-AGGAAACTGTT
1 TTCAAAG-TTTATGCTTCAAGA-GAAACTGTT
408212 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGT
408241 CTCAAGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 22 0.85
31 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (30 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTT
Found at i:408273 original size:36 final size:36
Alignment explanation
Indices: 408226--408410 Score: 129
Period size: 36 Copynumber: 5.3 Consensus size: 36
408216 AAGTTTATGC
* *
408226 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* **
408262 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTAAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
408298 TTCAAAGGAAA-TGTTTTC-A-A-TG-----TTTATGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TGT
*
408327 TTCAAGAGAAACTGTCTCAA-AGGAGACAAAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGA-GAGACAAAA-TTTGT
** * * *
408364 TTCAAGGGAAACTACCCCAAGAGAGATAAAATTTAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
408400 TTCAAGGGAAA
1 TTCAAGGGAAA
408411 TGTTTTCAAT
Statistics
Matches: 113, Mismatches: 23, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
28 2 0.02
29 13 0.12
30 4 0.04
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.02
36 59 0.52
37 27 0.24
38 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:408339 original size:101 final size:102
Alignment explanation
Indices: 408195--408434 Score: 392
Period size: 102 Copynumber: 2.4 Consensus size: 102
408185 AAAGATTTTG
* * *
408195 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 TTTCAAAGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTT
* *
408259 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
65 TGTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
408297 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTT
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTT
* *
408362 GTTTCAAGGGAAACTACCCCAAGAGAGATAAAATTTA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
*
408399 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAG
408435 GGAGACAAAA
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
101 46 0.36
102 83 0.64
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (102 bp):
TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
Found at i:408375 original size:37 final size:36
Alignment explanation
Indices: 408324--408410 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 36
408314 TCAATGTTTA
* * *
408324 TGTTTCAAGAGAAACTGTCTCAAAG-GAGACAAAATTT
1 TGTTTCAAGGGAAACT-ACCCAAAGAGAGACAAAA-TT
* *
408361 TGTTTCAAGGGAAACTACCCCAAGAGAGATAAAATT
1 TGTTTCAAGGGAAACTACCCAAAGAGAGACAAAATT
*
408397 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
408411 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
36 20 0.47
37 23 0.53
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTACCCAAAGAGAGACAAAATT
Found at i:408439 original size:87 final size:87
Alignment explanation
Indices: 408343--408521 Score: 286
Period size: 87 Copynumber: 2.1 Consensus size: 87
408333 AGAAACTGTC
* * * *
408343 TCAAAGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGAGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGAGAAACTACCCCAAGAGAGATAAAATTCATTTCAAGGG
408408 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * **
408430 TCAAGGGAGACAAAATTTCGTTTCAAGAGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGAGAAACTACCCCAAGAGAGATAAAATTCATTTCAAGGG
408495 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
408517 TCAAG
1 TCAAG
408522 AGAAACTGTC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGAGAAACTACCCCAAGAGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:408621 original size:189 final size:188
Alignment explanation
Indices: 408242--408626 Score: 513
Period size: 189 Copynumber: 2.0 Consensus size: 188
408232 AGAAACTGTC
*
408242 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGGA
1 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGGA
* * **
408307 AATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAGGG
66 AATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTAGTTCCAAAAG
* * ** * *
408372 AAACTACCCCAAGAGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTT
131 AAAATACCCCAAGAGAGATAAAATTTATTTCAAGGAAAACATATTCAATATTTATGTT
** * * *
408430 TCAAGGGAGACAAAATTTCGTTTCAAGAGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTT-GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
* *
408495 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTAGTTCCAAAA
65 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTAGTTCCAAAA
** * * * *
408560 GAAAATGTCTCAAGGGAGATGAAA-TTAGTTTCAATGAAAACATATTCAAATATTT-TGTT
130 GAAAATACCCCAAGAGAGATAAAATTTA-TTTCAAGGAAAACATATTC-AATATTTATGTT
408619 TCAAGGGA
1 TCAAGGGA
408627 AACTTGGAAA
Statistics
Matches: 170, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
188 21 0.12
189 143 0.84
190 6 0.04
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (188 bp):
TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGGA
AATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTAGTTCCAAAAG
AAAATACCCCAAGAGAGATAAAATTTATTTCAAGGAAAACATATTCAATATTTATGTT
Found at i:409626 original size:32 final size:32
Alignment explanation
Indices: 409568--409656 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
409558 TTTGCATCAG
* * *
409568 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAACATTC
* *
409600 GATGTTGAATCTCAAAAAATGGCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTC
* *
409632 GATGTTAAATCTAAAAAAATGCCCC
1 GATGTTGAATCTCAAAAAATGCCCC
409657 CATTGTTCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 47 0.98
33 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTC
Found at i:410675 original size:69 final size:69
Alignment explanation
Indices: 410564--410701 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
410554 TGTCTCTCTC
* *
410564 TTGATGCTCCATGATCTTTGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATAATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
410629 TCAT
66 TCAT
* * *
410633 TTGATGCTCTATAATCTTCGAGT-GATGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAAT
1 TTGATGCTCCATAATCTTCGAGTGGA-GTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAAT
410697 CTCAT
65 CTCAT
410702 AGTTTGAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCCATAATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:410802 original size:25 final size:25
Alignment explanation
Indices: 410762--410823 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
410752 TCTTGTCTTC
*
410762 TTTTTCTC-TTTAATTT-TCTTTTGT
1 TTTTTCTCTTTTTATTTCTC-TTTGT
410786 TTTTTCTCTTTTTATTTCTCTTTGT
1 TTTTTCTCTTTTTATTTCTCTTTGT
410811 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
410824 CTCTTTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 8 0.23
25 25 0.71
26 2 0.06
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (25 bp):
TTTTTCTCTTTTTATTTCTCTTTGT
Found at i:410830 original size:15 final size:13
Alignment explanation
Indices: 410762--410821 Score: 72
Period size: 12 Copynumber: 4.8 Consensus size: 13
410752 TCTTGTCTTC
*
410762 TTTTTCTCTTT-A
1 TTTTTCTCTTTGT
*
410774 ATTTTCT-TTTGT
1 TTTTTCTCTTTGT
410786 TTTTTCTCTTT-T
1 TTTTTCTCTTTGT
*
410798 TATTTCTCTTTGT
1 TTTTTCTCTTTGT
410811 TTTTTCTCTTT
1 TTTTTCTCTTT
410822 TTCTCTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 3 0.08
12 23 0.57
13 14 0.35
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTCTCTTTGT
Found at i:413865 original size:21 final size:22
Alignment explanation
Indices: 413819--413862 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
413809 ATAAAAAGGT
* *
413819 AAGAAATAAATAAATTAAAATG
1 AAGAAATAAACAAATTAAAATA
413841 AAGAAA-AAACAAATT-AAATA
1 AAGAAATAAACAAATTAAAATA
413861 AA
1 AA
413863 AGATAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 8 0.40
22 6 0.30
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (22 bp):
AAGAAATAAACAAATTAAAATA
Found at i:413950 original size:25 final size:23
Alignment explanation
Indices: 413916--413990 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 23
413906 ATATGAAAAA
413916 ATAAAGAAAAAGAAGAAAAAAATAT
1 ATAAA-AAAAAGAA-AAAAAAATAT
413941 ATAAATAAAACA-AATAAATAAAATA-
1 ATAAA-AAAA-AGAA-AAA-AAAATAT
*
413966 AT-AAAAAAAGAAAAAATAATAT
1 ATAAAAAAAAGAAAAAAAAATAT
413988 ATA
1 ATA
413991 TATATAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
21 5 0.12
22 6 0.14
23 6 0.14
24 2 0.05
25 16 0.38
26 7 0.17
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (23 bp):
ATAAAAAAAAGAAAAAAAAATAT
Found at i:413959 original size:4 final size:4
Alignment explanation
Indices: 413935--414019 Score: 50
Period size: 4 Copynumber: 21.2 Consensus size: 4
413925 AAGAAGAAAA
* * * *
413935 AAAT ATAT AAAT AAAAC AAAT AAAT AAA- ATAAT AAAA AAAG AAA- AAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* * * *
413983 -AAT ATAT ATAT ATAAT AAAT AAAA AAAT AAAA AAAT A
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT A
414020 GTAAATATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
3 7 0.11
4 49 0.78
5 7 0.11
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:413980 original size:43 final size:44
Alignment explanation
Indices: 413911--414038 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 44
413901 AATAAATATG
*
413911 AAAAAATAAAGAAAAAGAAGAAAAAA-ATATATAAATAAAACAAATA
1 AAAAAAT-AA-AAAAA-AAGAAAAAATATATATATATAAAACAAATA
* *
413957 AATAAAATAATAAAAAAAGAAAAAATAATATATATATATAATAAATA
1 AA-AAAATAA-AAAAAAAGAAAAAAT-ATATATATATAAAACAAATA
* * *
414004 AAAAAATAAAAAAATAGTAAATATATATATATATA
1 AAAAAATAAAAAAAAAGAAAAAATATATATATATA
414039 TATATAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
44 11 0.15
45 21 0.29
46 16 0.22
47 24 0.33
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (44 bp):
AAAAAATAAAAAAAAAGAAAAAATATATATATATAAAACAAATA
Found at i:414017 original size:36 final size:35
Alignment explanation
Indices: 413952--414032 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
413942 TAAATAAAAC
* * *
413952 AAATAAATAAAAT-AATAAAAAAAGAAAAAATAAT
1 AAATATATATAATAAATAAAAAAAAAAAAAATAAT
* *
413986 ATATATATATAATAAATAAAAAAATAAAAAAATAGT
1 AAATATATATAATAAATAAAAAAA-AAAAAAATAAT
414022 AAATATATATA
1 AAATATATATA
414033 TATATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 10 0.26
35 10 0.26
36 19 0.49
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (35 bp):
AAATATATATAATAAATAAAAAAAAAAAAAATAAT
Found at i:414113 original size:21 final size:22
Alignment explanation
Indices: 414080--414122 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
414070 TAATATATAT
414080 ATATATAATCTAAAAATAAAAAA
1 ATATATAATCT-AAAATAAAAAA
*
414103 ATATAT-A-CTAAAGTAAAAAA
1 ATATATAATCTAAAATAAAAAA
414123 GAAAATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 1 0.05
23 6 0.32
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (22 bp):
ATATATAATCTAAAATAAAAAA
Found at i:421006 original size:3 final size:3
Alignment explanation
Indices: 420998--421061 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
420988 TTAATATATT
* * *
420998 TAA TAA TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
421046 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
421062 TAATTAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:421652 original size:24 final size:23
Alignment explanation
Indices: 421615--421661 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
421605 GTTGAACAAA
421615 TTCTTCTTATTATGAACTTCTTCT
1 TTCTTCTTATTATG-ACTTCTTCT
*
421639 TTCTTCTTCA-TATGAGTTCTTCT
1 TTCTTCTT-ATTATGACTTCTTCT
421662 CATTATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.57
Consensus pattern (23 bp):
TTCTTCTTATTATGACTTCTTCT
Found at i:421869 original size:113 final size:113
Alignment explanation
Indices: 421585--422383 Score: 1110
Period size: 113 Copynumber: 7.0 Consensus size: 113
421575 ATCTCCTTCT
* * * * *
421585 GTGATAGAATT-ATGCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCA
1 GTGATCGAATTCA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCA
* * * ** * * *
421649 TATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTT-CTCTGGAAAAGCTGATCCATCAA
* * * ** * *
421699 GTAAT-GGATTCATGTAAAAGGTTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTTC
1 GTGATCGAATTCA-GCAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTC
*
421763 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
64 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
* * * * **
421813 ATGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAG
1 GTGATCGAATTCAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAG
* * * *
421878 ATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGCGGATCCATCATT
66 ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA-A
* *
421927 TTGAT-GAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCA
1 GTGATCGAATTCA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCA
421991 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
*
422040 GTGA-CGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCA
1 GTGATCGAATTCAG-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCA
422104 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
422153 GTGA-CGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTC
1 GTGATCGAATTCAG-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCCTTCTTC
*
422216 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGTTGATCCATCAA
64 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
*
422266 GTGA-CGAATTCAGACAAAAGGTTGAACAAATTCTTCCCATTATGAA-TTTCTTCTTCCTTCTTC
1 GTGATCGAATTCAG-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCCTTCTTC
422329 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
64 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
*
422379 ATGAT
1 GTGAT
422384 AGATTTGAAT
Statistics
Matches: 632, Mismatches: 44, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
112 4 0.01
113 425 0.67
114 136 0.22
115 67 0.11
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
GTGATCGAATTCAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA
Found at i:423489 original size:82 final size:82
Alignment explanation
Indices: 423142--423733 Score: 1112
Period size: 82 Copynumber: 7.2 Consensus size: 82
423132 ACTCAAAGAA
423142 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGA
1 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATT-GTTCTGTCCAACCAGATCAGA
423207 TAACTCAAAGAACACTTC
65 TAACTCAAAGAACACTTC
*
423225 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTTCAACCAGATCAGA
1 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATT-GTTCTGTCCAACCAGATCAGA
423290 TAACTCAAAGAACACTTC
65 TAACTCAAAGAACACTTC
423308 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGA
1 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATT-GTTCTGTCCAACCAGATCAGA
423373 TAACTCAAAGAACACTTC
65 TAACTCAAAGAACACTTC
*
423391 CAGAAGATGCTATTGGCAAATTTATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
1 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
423456 AACTCAAAGAACACTTC
66 AACTCAAAGAACACTTC
423473 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
1 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
423538 AACTCAAAGAACACTTC
66 AACTCAAAGAACACTTC
*
423555 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTTTGTCCAACCAGATCAGAT
1 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
423620 AACTCAAAGAACACTTC
66 AACTCAAAGAACACTTC
*
423637 CAGAAGATGCTATTGGCAAATTTATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
1 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
423702 AACTCAAAGAACACTTC
66 AACTCAAAGAACACTTC
*
423719 TAGAAGATGCTATTG
1 CAGAAGATGCTATTG
423734 AGTCTCTTTC
Statistics
Matches: 501, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
82 295 0.59
83 206 0.41
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (82 bp):
CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGAT
AACTCAAAGAACACTTC
Found at i:424543 original size:16 final size:18
Alignment explanation
Indices: 424504--424550 Score: 71
Period size: 16 Copynumber: 2.7 Consensus size: 18
424494 TCATATATAA
424504 AAATAAATTGAATTTCTAC
1 AAATAAATTGAA-TTCTAC
424523 AAATAAATTGAA-TCT-C
1 AAATAAATTGAATTCTAC
424539 AAATAAATTGAA
1 AAATAAATTGAA
424551 CTTGAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.46
17 3 0.11
19 12 0.43
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (18 bp):
AAATAAATTGAATTCTAC
Found at i:424900 original size:14 final size:13
Alignment explanation
Indices: 424881--424937 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
424871 TGACCCCCCA
424881 TTTTTTCTT-TTTC
1 TTTTTT-TTCTTTC
*
424894 TTTTTTTTCTTCC
1 TTTTTTTTCTTTC
424907 TTTTTTTTTCTTTC
1 -TTTTTTTTCTTTC
424921 TTTTTTTTCTTTC
1 TTTTTTTTCTTTC
424934 TTTT
1 TTTT
424938 CTTCAAGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
12 2 0.05
13 26 0.65
14 12 0.30
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTTC
Found at i:424902 original size:9 final size:9
Alignment explanation
Indices: 424888--424940 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
424878 CCATTTTTTC
424888 TTTTTCTTT
1 TTTTTCTTT
*
424897 TTTTTCTTCC
1 TTTTTCTT-T
424907 TTTTT-TTT
1 TTTTTCTTT
*
424915 TCTTTCTTT
1 TTTTTCTTT
424924 TTTTTCTTT
1 TTTTTCTTT
*
424933 CTTTTCTT
1 TTTTTCTT
424941 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 4 0.11
9 28 0.76
10 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:424911 original size:27 final size:27
Alignment explanation
Indices: 424881--424937 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
424871 TGACCCCCCA
*
424881 TTTTTTCTT-TTTCTTTTTTTTCTTCC
1 TTTTTTTTTCTTTCTTTTTTTTCTTCC
*
424907 TTTTTTTTTCTTTCTTTTTTTTCTTTC
1 TTTTTTTTTCTTTCTTTTTTTTCTTCC
424934 TTTT
1 TTTT
424938 CTTCAAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTTTTTCTTTCTTTTTTTTCTTCC
Found at i:435589 original size:28 final size:28
Alignment explanation
Indices: 435558--435612 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
435548 TTACAAATAA
*
435558 AATAA-AACAATATAAATATTATGAAAAT
1 AATAAGAA-AATATAAAAATTATGAAAAT
* *
435586 AATAAGTAAATATAAAAATTTTGAAAA
1 AATAAGAAAATATAAAAATTATGAAAA
435613 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (28 bp):
AATAAGAAAATATAAAAATTATGAAAAT
Found at i:437743 original size:3 final size:3
Alignment explanation
Indices: 437735--437801 Score: 89
Period size: 3 Copynumber: 22.3 Consensus size: 3
437725 TTAATATATT
* * * *
437735 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
437783 TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
437802 TAATTAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:438608 original size:21 final size:21
Alignment explanation
Indices: 438582--438621 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
438572 AAGACTATTT
438582 TCATTTTT-TAATTTTGAAACA
1 TCATTTTTGT-ATTTTGAAACA
438603 TCATTTTTGTATTTTGAAA
1 TCATTTTTGTATTTTGAAA
438622 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTGTATTTTGAAACA
Found at i:439619 original size:37 final size:37
Alignment explanation
Indices: 439564--439638 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
439554 TTGTCTCTCA
*
439564 TTCACTCCACAATCTTGGATGAGT-AGAAGGTTTGATG
1 TTCACTCCACAATATTGGATGAGTGA-AAGGTTTGATG
439601 TTCACTCCACAATATTGGATGAGTGAAAGGTTTGATG
1 TTCACTCCACAATATTGGATGAGTGAAAGGTTTGATG
439638 T
1 T
439639 ATCCATCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (37 bp):
TTCACTCCACAATATTGGATGAGTGAAAGGTTTGATG
Found at i:443383 original size:23 final size:23
Alignment explanation
Indices: 443342--443399 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
443332 GCCTCGGGGA
*
443342 GGGTATCAGTA-CCATTCAAAGG
1 GGGTATCGGTACCCATTCAAAGG
443364 GGGTATCGGTACCCATTCAAAGG
1 GGGTATCGGTACCCATTCAAAGG
*
443387 GGGTATCGATACC
1 GGGTATCGGTACC
443400 TCCTGCGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGTATCGGTACCCATTCAAAGG
Found at i:444044 original size:34 final size:32
Alignment explanation
Indices: 443982--444051 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
443972 ACCTTACAAC
* *
443982 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
444014 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
444048 TCCC
1 TCCC
444052 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:444525 original size:21 final size:21
Alignment explanation
Indices: 444459--444557 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
444449 TCGAAATGGA
*
444459 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTACAGGG
* * * **
444479 GTACATCGATGTACTAGTGGTAG
1 GTGCATGGATGCACTACAGG--G
* *
444502 GTGCATGGATGGACTGCAGGG
1 GTGCATGGATGCACTACAGGG
444523 GTGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTACAGGG
444544 GTGCATGGA-GCACT
1 GTGCATGGATGCACT
444558 TTGACACCCT
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
20 18 0.29
21 29 0.47
23 15 0.24
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGG
Found at i:444810 original size:21 final size:21
Alignment explanation
Indices: 444781--444820 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
444771 ATGTTTAATG
444781 AAAAAGATACCAATTTTTAAC
1 AAAAAGATACCAATTTTTAAC
* *
444802 AAAATGATATCAATTTTTA
1 AAAAAGATACCAATTTTTA
444821 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAAGATACCAATTTTTAAC
Found at i:447933 original size:20 final size:20
Alignment explanation
Indices: 447904--447956 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
447894 GCAGCCTTGG
*
447904 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
447924 TGCATCGATGCATAGCAGGA
1 TGCATCGATGCACAGCAGGA
* *
447944 AGCATTGATGCAC
1 TGCATCGATGCAC
447957 TAATTGCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:451685 original size:22 final size:21
Alignment explanation
Indices: 451643--451682 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
451633 AAGACTATTT
451643 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
451664 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
451683 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:454072 original size:19 final size:19
Alignment explanation
Indices: 454048--454096 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
454038 AATGTAGGGT
454048 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
454067 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
454086 TAATTTTGTAT
1 TAATTTTGTAT
454097 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:454894 original size:201 final size:201
Alignment explanation
Indices: 454544--455091 Score: 857
Period size: 201 Copynumber: 2.7 Consensus size: 201
454534 AACATATGTA
* * * *
454544 TCGATACATTTACAAAAAGTATAGATCCCAAAATCATCGAAACTCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAACGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
* * * *
454609 AATTTTTCAATATAA-CTAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTAT
66 AATTTTTCAATGTAACCGA-TATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTAT
* * *
454673 CGACACTTTTGAAATTTGTGTCGATACGTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGCA
130 CAACACTTTTTAAATTTGTGTCGATACGTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCA
454738 TAAAGTG
195 TAAAGTG
*
454745 TCGATACATTTATAAAACGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAACGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
*
454810 AATTTTTCAATGTAACCGATATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATGTATC
66 AATTTTTCAATGTAACCGATATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTATC
* * *
454875 AACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCATGCAT
131 AACACTTTTTAAATTTGTGTCGATACGTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCAT
454940 AAAGTG
196 AAAGTG
*
454946 TCGATACATTTATAAAACATATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAACGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
* * * * *
455011 AATTTTTCAATGTAACCGGTATAAATATACCGGTTTTAAGAT-ACAATAGGTTTATATAATGTAT
66 AATTTTTCAATGTAACCGATATAAATATACCGGTTTTATG-TGAGAATAGGTCTACATAATGTAT
*
455075 CAACACATTTTAAATTT
130 CAACACTTTTTAAATTT
455092 ATGCTGATAC
Statistics
Matches: 319, Mismatches: 26, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
201 316 0.99
202 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (201 bp):
TCGATACATTTATAAAACGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
AATTTTTCAATGTAACCGATATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTATC
AACACTTTTTAAATTTGTGTCGATACGTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCAT
AAAGTG
Found at i:455428 original size:15 final size:15
Alignment explanation
Indices: 455408--455436 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
455398 GTCTTTCTCA
455408 AAGCTCTTCTCAACC
1 AAGCTCTTCTCAACC
455423 AAGCTCTTCTCAAC
1 AAGCTCTTCTCAAC
455437 GACAACCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGCTCTTCTCAACC
Found at i:456620 original size:12 final size:12
Alignment explanation
Indices: 456600--456633 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
456590 CAAGCGGTCA
* *
456600 ATGAAGATGACG
1 ATGATGATGAAG
456612 ATGATGATGAAG
1 ATGATGATGAAG
456624 ATGATGATGA
1 ATGATGATGA
456634 TGATCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.32, T:0.24
Consensus pattern (12 bp):
ATGATGATGAAG
Found at i:458049 original size:18 final size:18
Alignment explanation
Indices: 458023--458061 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
458013 TTTCATATGT
458023 AATTGGAGTTTAAATTTC
1 AATTGGAGTTTAAATTTC
* *
458041 AATTTGAGTTTGAATTTC
1 AATTGGAGTTTAAATTTC
458059 AAT
1 AAT
458062 ATAAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (18 bp):
AATTGGAGTTTAAATTTC
Found at i:459648 original size:199 final size:196
Alignment explanation
Indices: 459303--460486 Score: 1360
Period size: 198 Copynumber: 6.0 Consensus size: 196
459293 TTCAGTAATC
* * * *
459303 TCCAAAATGAATGCCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATTGAT
1 TCCAGAATGAATGCCTAAACGA-GTGCACGAATAAAGTGTCGATACATTTA-TAAAAGTATCGAT
* *
459368 CCCAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGG-AAAATA
64 CCCAAAAACATCGAA-AAGATAATTATAATGTAATAGGT-AATTTCCAATGTAACCGGTAGAA-A
* * * * **
459432 TATACCAGTTAATTAGAAAATAGGTCTACAAAATATATCGATACTT-TTTAAATTGTGTCGATAC
126 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAAATTGTGTCGATAC
459496 TTTTTG
191 TTTTTG
* *
459502 TCCAGAATGAATGACC-AACCGAGATGCACGAATAAAGTGTTGATACATTTATAACAAGTATCGA
1 TCCAGAATGAATG-CCTAAACGAG-TGCACGAATAAAGTGTCGATACATTTATAA-AAGTATCGA
*
459566 TCCCAAAAACATCCAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAA
63 TCCCAAAAACATCGAA-AAGATAATTATAATGTAATAGGT-AATTTCCAATGTAACCGGTAGAAA
* * * **
459631 TATACCGGTTAATTAGAAAATAGGTTTACATAATGTATCAACACTTTTTAAAATTGTGTCGATAC
126 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAAATTGTGTCGATAC
*
459696 GTTTTG
191 TTTTTG
* * *
459702 ACCAGAATGAATGTCC--AACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAACGTTTAGA
1 TCCAGAATGAATG-CCTAAACGA-GTGCACGAATAAAGTGTCGATACATTTATAAAA-GTATCGA
* * *
459765 TCCCAAAAA-A-C----TGATAAATATAATGTAATATGTAAATTTCCAATGTAACCGGTAGAAAT
63 TCCCAAAAACATCGAAAAGATAATTATAATGTAATAGGT-AATTTCCAATGTAACCGGTAGAAAT
* * * * *
459824 ATACCGGTTAATTAGAGAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTTGATATT
127 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAAATTGTGTCGATACT
459889 TTTTG
192 TTTTG
* * *
459894 TCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGATC
1 TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAA-AGTATCGATC
* * *
459958 CCAAAAACAT-TAAAACCGATAATTATAATGTAATAGGTAACTTCACAATGTAACCGATAGAAAT
65 CCAAAAACATCGAAAA--GATAATTATAATGTAATAGGTAATTTC-CAATGTAACCGGTAGAAAT
* * * * * * *
460022 ATACCGATTAATTAGAGAATATGCCTACATCATGTATTGACACTTGTGGAATTTGTGTCGATACT
127 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAAATTGTGTCGATACT
460087 TTTTG
192 TTTTG
* * *
460092 TCCAAAATGAATGCCTAAAGGAGTGCACGCATAAAGTGTCGATACATTTA-AAATTA-TATCGAT
1 TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAA--AGTATCGAT
* * * * * *
460155 CCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAACTATACAATGTACCCGGTAGAATT
64 CCCAAAAACATCGAAA-AGATAATTATAATGTAATAGGTAA-TTTCCAATGTAACCGGTAGAAAT
* * *
460220 ATACCGGTTAATTAGAAAATAGGTTTACATCATGTATCGACACTTGTGGAATTTGTGTCGATA-T
127 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAAATTGTGTCGATACT
460284 GTTTTG
192 -TTTTG
* * * * ** *
460290 TCCATAATGAATGCCTAAAAGAGTGCATGCATAAAGTGTTAATACATTTA-AAATTGTATCGATC
1 TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAA-AGTATCGATC
* **
460354 CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACTTTCCAATGTAACCACTAGAAATA
65 CCAAAAACATCGAAA-AGATAATTATAATGTAATAGGTAA-TTTCCAATGTAACCGGTAGAAATA
* * **
460419 TACCGGTTAATTAGAAAATAGATCTACATAATGTATCAACACTT-TTTAAAGTTGTGTCGATACT
128 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAAA-TTGTGTCGATACT
460483 TTTT
192 TTTT
460487 TAAATTACGC
Statistics
Matches: 867, Mismatches: 91, Indels: 55
0.86 0.09 0.05
Matches are distributed among these distances:
191 19 0.02
192 143 0.16
193 4 0.00
197 11 0.01
198 446 0.51
199 202 0.23
200 42 0.05
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (196 bp):
TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAAAGTATCGATCC
CAAAAACATCGAAAAGATAATTATAATGTAATAGGTAATTTCCAATGTAACCGGTAGAAATATAC
CGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAAATTGTGTCGATACTTTTT
G
Found at i:460324 original size:396 final size:391
Alignment explanation
Indices: 459303--460486 Score: 1502
Period size: 396 Copynumber: 3.0 Consensus size: 391
459293 TTCAGTAATC
* *
459303 TCCAAAATGAATGCCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATTGAT
1 TCCAAAATGAATG-CCAAACGAGGTGCACGAATAAAGTGTCGATACATTTA-TAAAA-TATAGAT
*
459368 CCCAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGG-AAAAT
63 CCCAAAAA-ATCGAA-ACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAT
* ** * * ** *
459431 ATATACCAGTTAATTAGAAAATAGGTCTACAAAATATATCGATACTT-TTTAAATTGTGTCGATA
126 -TATACCGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATA
** *
459495 CTTTTTGTCCAGAATGAATGACC-AACCGAGATGCACGAATAAAGTGTTGATACATTTATAACA-
190 -TTTTTGTCCAGAATGAATG-CCTAAAAGAG-TGCACGCATAAAGTGTTGATACATTTA-AA-AT
* *
459558 AGTATCGATCCCAAAAACATCCAATAA--GATAATTATAATGTAATAGGTCAATTTCCAATGTAA
250 TGTATCGATCCCAAAAACAT-CAA-AACCGATAATTATAATGTAATAGGT-AACTTCCAATGTAA
* *
459621 CCGGTAGAAATATACCGGTTAATTAGAAAATAGGTTTACATAATGTATCAACACTTTTTAAAATT
312 CCGATAGAAATATACCGGTTAATTAGAAAATA-GTCTACATAATGTATCAACACTTTTTAAAATT
*
459686 GTGTCGATACGTTTTG
376 GTGTCGATACTTTTTG
* * *
459702 ACCAGAATGAATGTCC-AACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAACGTTTAGAT
1 TCCAAAATGAATG-CCAAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAA--TATAGAT
* * * * *
459766 CCC---AAA---AAACTGATAAATATAATGTAATATGTAAATTTCCAATGTAACCGGTAGAAATA
63 CCCAAAAAATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAATTA
* *
459825 TACCGGTTAATTAGAGAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTTGATATTT
128 TACCGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATA-TT
*
459890 TTTGTCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCG
192 TTTGTCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTTGATACATTTAAAATTGTATCG
*
459955 ATCCCAAAAACATTAAAACCGATAATTATAATGTAATAGGTAACTTCACAATGTAACCGATAGAA
257 ATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTC-CAATGTAACCGATAGAA
* * * * ** * ** *
460020 ATATACCGATTAATTAGAGAATATGCCTACATCATGTATTGACACTTGTGGAATTTGTGTCGATA
321 ATATACCGGTTAATTAGAAAATA-GTCTACATAATGTATCAACACTTTTTAAAATTGTGTCGATA
460085 CTTTTTG
385 CTTTTTG
* * *
460092 TCCAAAATGAATGCCTAAAGGA-GTGCACGCATAAAGTGTCGATACATTTA-AAATTATATCGAT
1 TCCAAAATGAATGCC-AAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAA--ATATAGAT
* * * *
460155 CCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAACTATACAATGTACCCGGTAGAATT
63 CCCAAAAA-ATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAATT
*
460220 ATACCGGTTAATTAGAAAATAGGTTTACATCATGTATCGACACTTGTGGAATTTGTGTCGATATG
127 ATACCGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATAT-
* * *
460285 TTTTGTCCATAATGAATGCCTAAAAGAGTGCATGCATAAAGTGTTAATACATTTAAAATTGTATC
191 TTTTGTCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTTGATACATTTAAAATTGTATC
*
460350 GATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACTTTCCAATGTAACC-ACTAG
256 GATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAC-TTCCAATGTAACCGA-TAG
*
460414 AAATATACCGGTTAATTAGAAAATAGATCTACATAATGTATCAACACTTTTTAAAGTTGTGTCGA
319 AAATATACCGGTTAATTAGAAAATAG-TCTACATAATGTATCAACACTTTTTAAAATTGTGTCGA
460479 TACTTTTT
383 TACTTTTT
460487 TAAATTACGC
Statistics
Matches: 684, Mismatches: 77, Indels: 51
0.84 0.09 0.06
Matches are distributed among these distances:
388 2 0.00
389 21 0.03
390 156 0.23
391 111 0.16
392 42 0.06
393 1 0.00
394 1 0.00
395 5 0.01
396 282 0.41
397 8 0.01
398 42 0.06
399 13 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (391 bp):
TCCAAAATGAATGCCAAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATATAGATCCC
AAAAAATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAATTATAC
CGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATATTTTTG
TCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTTGATACATTTAAAATTGTATCGATCC
CAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTCCAATGTAACCGATAGAAATATA
CCGGTTAATTAGAAAATAGTCTACATAATGTATCAACACTTTTTAAAATTGTGTCGATACTTTTT
G
Found at i:462082 original size:19 final size:19
Alignment explanation
Indices: 462055--462095 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
462045 AAATTTTATA
*
462055 TATATGATTCATAATTTTG
1 TATACGATTCATAATTTTG
*
462074 TATACGATTTATAATTTTG
1 TATACGATTCATAATTTTG
462093 TAT
1 TAT
462096 GTGAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (19 bp):
TATACGATTCATAATTTTG
Found at i:465184 original size:200 final size:199
Alignment explanation
Indices: 464814--465290 Score: 575
Period size: 200 Copynumber: 2.4 Consensus size: 199
464804 GTAAAAAGAT
* * *
464814 ATATCGATACATTT-TCTAAAAGTATCGACCCCAAAAACATCGAAACCAAAAATTATAATGTAAT
1 ATATCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* *** *
464878 AGGTAAATTAACAATATAACCGGTATAAATATACCAGTTAATTACAAAACAGGTAAACATAATGT
65 AGGTAAATTTACAATATAACAAATATAAATATACCAGTTAATGACAAAACAGGTAAACATAATGT
* * *
464943 ATCGACACTTGTGGAATTTGTGTCGATACTTATTATCCAGAATGAATGCCCAAACGAGGTGCACG
130 ATCGACACTTGTGAAATATGTGTCAATACTTATTATCCAGAATGAATGCCC-AACGAGGTGCACG
465008 CATAAA
194 CATAAA
* * * *
465014 ATGTCGATACATTTATTAAAAGTATCAATCCCAAAAACATCGAAACTGATAATTATGATGTAATA
1 ATATCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * * * * *
465079 GGTAAATTTACAGTGTAACAAATATAAATATACTGATTTTATGAGATAATAGGTCAACATAATGT
66 GGTAAATTTACAATATAACAAATATAAATATAC-CAGTTAATGACAAAACAGGTAAACATAATGT
* * * * * *
465144 ATCGACACTTTTTAAATATGTTTCAATA-TTTTTTTCCAGAATGAATGCCCAATGAGGTGCACGC
130 ATCGACACTTGTGAAATATGTGTCAATACTTATTATCCAGAATGAATGCCCAACGAGGTGCACGC
465208 ATAAA
195 ATAAA
* * * *
465213 GTATCAATACATTTA--AAATTGTATCGATCCCAAAAACATCGAAACCGATAGTTATAATGTAAT
1 ATATCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
*
465276 ATGTAAATTTACAAT
65 AGGTAAATTTACAAT
465291 GTTATCGGTA
Statistics
Matches: 234, Mismatches: 40, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
197 3 0.01
198 52 0.22
199 30 0.13
200 103 0.44
201 46 0.20
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (199 bp):
ATATCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATATAACAAATATAAATATACCAGTTAATGACAAAACAGGTAAACATAATGTA
TCGACACTTGTGAAATATGTGTCAATACTTATTATCCAGAATGAATGCCCAACGAGGTGCACGCA
TAAA
Found at i:465434 original size:23 final size:23
Alignment explanation
Indices: 465408--465470 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
465398 CGTTAAATGT
* *
465408 CTATTTTATTATATAATCGCTAC
1 CTATTATATTATATAAACGCTAC
465431 CTATTATATTATATAAACGCTAC
1 CTATTATATTATATAAACGCTAC
* * *
465454 TTAATATGTTAT-TAAAC
1 CTATTATATTATATAAAC
465471 TTGATGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (23 bp):
CTATTATATTATATAAACGCTAC
Found at i:465442 original size:85 final size:87
Alignment explanation
Indices: 465333--465492 Score: 252
Period size: 85 Copynumber: 1.9 Consensus size: 87
465323 AAATAAGTCA
* *
465333 ATATAAACGCTACCTATTACATTATATAAACGTTACCTAATATGTTATTATACTTGATAATA-TT
1 ATATAAACGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTAAACTTGATAATATTT
465397 TCG-TTAAATGTCTATTTTATT
66 TCGATTAAATGTCTATTTTATT
* * * *
465418 ATATAATCGCTACCTATTATATTATATAAACGCTACTTAATATGTTATTAAACTTGATGATATTT
1 ATATAAACGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTAAACTTGATAATATTT
465483 TCGATTAAAT
66 TCGATTAAAT
465493 AATATAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
85 56 0.84
86 5 0.07
87 6 0.09
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTAAACTTGATAATATTT
TCGATTAAATGTCTATTTTATT
Found at i:467188 original size:14 final size:14
Alignment explanation
Indices: 467169--467210 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
467159 ACCCGTCCCG
467169 CATCCGCCCGCCCA
1 CATCCGCCCGCCCA
467183 CATCCGCCCGCCCA
1 CATCCGCCCGCCCA
*
467197 CATCCGCCCACCCA
1 CATCCGCCCGCCCA
467211 GTTAAATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.17, C:0.64, G:0.12, T:0.07
Consensus pattern (14 bp):
CATCCGCCCGCCCA
Found at i:479389 original size:224 final size:224
Alignment explanation
Indices: 479000--479450 Score: 870
Period size: 224 Copynumber: 2.0 Consensus size: 224
478990 AAACGAATTT
479000 CTCACTATTGCCCACTTGGACTATAACAGGCTGCAAAACTTGGAACCAAATAATCTTCTTTAAAA
1 CTCACTATTGCCCACTTGGACTATAACAGGCTGCAAAACTTGGAACCAAATAATCTTCTTTAAAA
479065 TGATTATTCACCACCGATTTCCAAACCAAGAAGCTTAAGCTGGAATCTTGTTGTTAAACAATAAT
66 TGATTATTCACCACCGATTTCCAAACCAAGAAGCTTAAGCTGGAATCTTGTTGTTAAACAATAAT
479130 AAGGACAAGTCAAGATTGTACTTGTTGCAAATCATCTTCCTCCAAACGGACTTCTTATCATTAGC
131 AAGGACAAGTCAAGATTGTACTTGTTGCAAATCATCTTCCTCCAAACGGACTTCTTATCATTAGC
479195 -AACCTCCAAGACCATTTTCCTAAGAGAG
196 AAACCTCCAAGACCATTTTCCTAAGAGAG
479223 CTCACTATTGCCCACTTGGACTATAAACAGGCTGCAAAACTTGGAACCAAA-AATCTTCTTTAAA
1 CTCACTATTGCCCACTTGGACTAT-AACAGGCTGCAAAACTTGGAACCAAATAATCTTCTTTAAA
479287 ATGATTATTCACCACCGATTTCCAAAACCAAGAAGCTTAAGCTGGAATCTTGTTGTTAAACAATA
65 ATGATTATTCACCACCGATTTCC-AAACCAAGAAGCTTAAGCTGGAATCTTGTTGTTAAACAATA
479352 ATAAGGACAAGTCAAGATTGTACTTGTTGCAAATCATCTTCCTCCAAACGGACTTCTTATCATTA
129 ATAAGGACAAGTCAAGATTGTACTTGTTGCAAATCATCTTCCTCCAAACGGACTTCTTATCATTA
479417 GCAAACCTCCAAGACCATTTTCCTAAGAGAG
194 GCAAACCTCCAAGACCATTTTCCTAAGAGAG
479448 CTC
1 CTC
479451 TATTAATAAC
Statistics
Matches: 225, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
223 60 0.27
224 134 0.60
225 31 0.14
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (224 bp):
CTCACTATTGCCCACTTGGACTATAACAGGCTGCAAAACTTGGAACCAAATAATCTTCTTTAAAA
TGATTATTCACCACCGATTTCCAAACCAAGAAGCTTAAGCTGGAATCTTGTTGTTAAACAATAAT
AAGGACAAGTCAAGATTGTACTTGTTGCAAATCATCTTCCTCCAAACGGACTTCTTATCATTAGC
AAACCTCCAAGACCATTTTCCTAAGAGAG
Found at i:479954 original size:15 final size:17
Alignment explanation
Indices: 479917--479956 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
479907 GCCTCCAGCA
479917 AAAAGAACAAAACAACGC
1 AAAAGAACAAAACAAC-C
479935 AAAAGAACAAAAC-A-C
1 AAAAGAACAAAACAACC
479950 AAAAGAA
1 AAAAGAA
479957 AACCAACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
17 1 0.05
18 13 0.59
ACGTcount: A:0.72, C:0.17, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAGAACAAAACAACC
Found at i:481427 original size:16 final size:16
Alignment explanation
Indices: 481385--481453 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 16
481375 GTTTAGAACT
* *
481385 GAATTACTGTAGCCGG
1 GAATTACTGTAACCGA
481401 GAA-TA--GTAACCGA
1 GAATTACTGTAACCGA
*
481414 GAATTACTGTAACCGG
1 GAATTACTGTAACCGA
*
481430 GAA-TA--ATAACCGA
1 GAATTACTGTAACCGA
481443 GAATTACTGTA
1 GAATTACTGTA
481454 GCCAGGAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
13 18 0.44
14 4 0.10
15 4 0.10
16 15 0.37
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (16 bp):
GAATTACTGTAACCGA
Found at i:481429 original size:29 final size:29
Alignment explanation
Indices: 481385--481470 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
481375 GTTTAGAACT
481385 GAATTACTGTAGCCGGGAATAGTAACCGA
1 GAATTACTGTAGCCGGGAATAGTAACCGA
* *
481414 GAATTACTGTAACCGGGAATAATAACCGA
1 GAATTACTGTAGCCGGGAATAGTAACCGA
*
481443 GAATTACTGTAGCCAGGAATAGTAACCG
1 GAATTACTGTAGCCGGGAATAGTAACCG
481471 TCGACGGTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.21
Consensus pattern (29 bp):
GAATTACTGTAGCCGGGAATAGTAACCGA
Found at i:486779 original size:20 final size:20
Alignment explanation
Indices: 486754--486800 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
486744 GTTAGCTAAG
486754 GTTGTTAGTCAGGTAGTTTA
1 GTTGTTAGTCAGGTAGTTTA
486774 GTTGTTAGTCAGGTAGTTTA
1 GTTGTTAGTCAGGTAGTTTA
486794 GTTGTTA
1 GTTGTTA
486801 AAAGCAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.47
Consensus pattern (20 bp):
GTTGTTAGTCAGGTAGTTTA
Found at i:496217 original size:73 final size:72
Alignment explanation
Indices: 496084--496219 Score: 164
Period size: 73 Copynumber: 1.9 Consensus size: 72
496074 GAGTTGGGCA
* * * **
496084 GTGCTCGACTCGTACTCGTTAAAAAAATTTGCTCCTCGACTCGACTAATTGCTCGTTAAGCTCGT
1 GTGCTCGACTCGTACTCGTTAAAAAAAATTGCTCATCAACTCGACTAATTGCTCACTAAGCTCGT
496149 TAAAATT
66 TAAAATT
* * * * **
496156 GTGCTCGGCTCGTGCTCGTTAAAAAAAAATTGTTGATCAACTCGACTCGTTGCTCACTAAGCTC
1 GTGCTCGACTCGTACTCGTT-AAAAAAAATTGCTCATCAACTCGACTAATTGCTCACTAAGCTC
496220 ACTAAAAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
72 18 0.35
73 34 0.65
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (72 bp):
GTGCTCGACTCGTACTCGTTAAAAAAAATTGCTCATCAACTCGACTAATTGCTCACTAAGCTCGT
TAAAATT
Found at i:498443 original size:16 final size:16
Alignment explanation
Indices: 498410--498444 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
498400 TTGAGTCGAA
* *
498410 CTCGAGTATTATTGAG
1 CTCGAGTATTACTAAG
498426 CTCGAGTATTACTAAG
1 CTCGAGTATTACTAAG
498442 CTC
1 CTC
498445 TATTCAGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (16 bp):
CTCGAGTATTACTAAG
Found at i:499002 original size:11 final size:11
Alignment explanation
Indices: 498988--499015 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
498978 ATTTTGAGTA
498988 TATTTTATATT
1 TATTTTATATT
498999 TATTTTATATT
1 TATTTTATATT
499010 TATTTT
1 TATTTT
499016 TTGAGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TATTTTATATT
Found at i:499052 original size:35 final size:35
Alignment explanation
Indices: 498979--499052 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
498969 TTAATTTTTA
* ** *
498979 TTTTGAGTATATTTTATATTTATTTTATATTTATT
1 TTTTGAGTATATTTTATATTTAATTTATAAATAAT
499014 TTTTGAGTAT-TTTTATATTTTAAATTTA-AAATAAT
1 TTTTGAGTATATTTTATA-TTT-AATTTATAAATAAT
499049 TTTT
1 TTTT
499053 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 7 0.21
35 21 0.64
36 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (35 bp):
TTTTGAGTATATTTTATATTTAATTTATAAATAAT
Found at i:501044 original size:32 final size:32
Alignment explanation
Indices: 501003--501064 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
500993 GACAAATCGA
* *
501003 AACAGATCATAGTTTAGAGGAAGCGAATGGGT
1 AACAGATCATAGTTTACAGGAAACGAATGGGT
501035 AACAGATCATAGTTTACAGGAAACGAATGG
1 AACAGATCATAGTTTACAGGAAACGAATGG
501065 CTTACCAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.21
Consensus pattern (32 bp):
AACAGATCATAGTTTACAGGAAACGAATGGGT
Found at i:505941 original size:21 final size:21
Alignment explanation
Indices: 505917--505966 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
505907 TTGCGATATA
* * *
505917 GATCCAAGGTTTTCATTTGAT
1 GATCCAAGGTATTCAGTCGAT
505938 GATCCAAGGTATTCAGTCGAT
1 GATCCAAGGTATTCAGTCGAT
*
505959 GAGCCAAG
1 GATCCAAG
505967 AGCTTCCTGG
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:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (21 bp):
GATCCAAGGTATTCAGTCGAT
Found at i:508371 original size:21 final size:21
Alignment explanation
Indices: 508330--508395 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
508320 GTAAAATAAA
* *
508330 TAAAT-AAATTATATATTAAAG
1 TAAATAAAATAATA-ATAAAAG
508351 TAAATAAAATAATAATAAAAG
1 TAAATAAAATAATAATAAAAG
*
508372 AAAATAAAATGAAT-A-AAAAG
1 TAAATAAAAT-AATAATAAAAG
508392 TAAA
1 TAAA
508396 AGGGTTAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 8 0.21
21 21 0.54
22 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (21 bp):
TAAATAAAATAATAATAAAAG
Found at i:510012 original size:102 final size:98
Alignment explanation
Indices: 509869--510181 Score: 290
Period size: 103 Copynumber: 3.1 Consensus size: 98
509859 AACAATAATA
*
509869 ATATA-TTTAAAAAATATTTTCCAAAAATCTATATAAC-ATATATTTTTAAAAGTATTTTAAAAT
1 ATATATTTTCAAAAATATTTT--AAAAAT-TATAT-ACTATATATTTTTAAAA-TATTTTAAAAT
*
509932 TATATATTATATATTTTTGAAAAAAAATGTTTTCAAAATT
61 TATATATTATATATTTTT--AAAAAAATGTTTTAAAAATT
* *
509972 ATATAGTTTTCAAAAATATTTTTAAAATTATATACTATATAATTTTTCAAAATGATTTCAAAATT
1 ATATA-TTTTCAAAAATATTTTAAAAATTATATACTATAT-ATTTTT-AAAAT-ATTTTAAAATT
* * ** * * *
510037 ATATAATATATATGTTTTCAAAATGTTTTTTTAAACTAT
62 ATATATTATATAT-TTTTAAAAAAATGTTTTAAAAAT-T
* * * * * *
510076 ATATATTTTC-AAAATGTTTTAAAAACTATATAATATATATTTTCAAAAATGTTTTAAAAACTAT
1 ATATATTTTCAAAAATATTTTAAAAATTATATACTATATATTTT-TAAAATATTTT-AAAATTAT
** *
510140 ATATTATATATTTTTTCAAAAATGTTTTAAAAACT
64 ATATTATATATTTTTAAAAAAATGTTTTAAAAATT
510175 ATATATT
1 ATATATT
510182 ATATTTATTT
Statistics
Matches: 173, Mismatches: 27, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
99 8 0.05
100 18 0.10
101 29 0.17
102 33 0.19
103 35 0.20
104 32 0.18
105 18 0.10
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (98 bp):
ATATATTTTCAAAAATATTTTAAAAATTATATACTATATATTTTTAAAATATTTTAAAATTATAT
ATTATATATTTTTAAAAAAATGTTTTAAAAATT
Found at i:510020 original size:37 final size:36
Alignment explanation
Indices: 509971--510264 Score: 275
Period size: 36 Copynumber: 8.2 Consensus size: 36
509961 TTTTCAAAAT
* * * *
509971 TATATAGTTTTCAAAAATATTTTTAAAATTATATACTA
1 TATATA-TTTTC-AAAATGTTTTAAAAACTATATAATA
* * *
510009 TATA-ATTTTTCAAAATGATTTCAAAATTATATAATA
1 TATATA-TTTTCAAAATGTTTTAAAAACTATATAATA
* *
510045 TATATGTTTTCAAAATGTTTT------TTTA-AACTA
1 TATATATTTTCAAAATGTTTTAAAAACTATATAA-TA
510075 TATATATTTTCAAAATGTTTTAAAAACTATAT-A-A
1 TATATATTTTCAAAATGTTTTAAAAACTATATAATA
*
510109 TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
1 TATATATTTTC-AAAATGTTTTAAAAACTATATAATA
* *
510146 TATATTTTTTCAAAAATGTTTTAAAAACTATATATTA
1 TATATATTTTC-AAAATGTTTTAAAAACTATATAATA
* *
510183 TATTTATTTTCAAAATGTTTTAAAAACTATACAATA
1 TATATATTTTCAAAATGTTTTAAAAACTATATAATA
* * * *
510219 TATAAATGTTTTCAAACATATTTTCAAAACTATATATTA
1 TAT--ATATTTTCAAA-ATGTTTTAAAAACTATATAATA
510258 TATATAT
1 TATATAT
510265 GTTTTTTAAA
Statistics
Matches: 218, Mismatches: 23, Indels: 31
0.80 0.08 0.11
Matches are distributed among these distances:
29 2 0.01
30 25 0.11
34 12 0.06
35 21 0.10
36 69 0.32
37 55 0.25
38 13 0.06
39 21 0.10
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATATTTTCAAAATGTTTTAAAAACTATATAATA
Found at i:510024 original size:36 final size:36
Alignment explanation
Indices: 509971--510306 Score: 230
Period size: 37 Copynumber: 9.2 Consensus size: 36
509961 TTTTCAAAAT
* *
509971 TATATAGTTTTCAAAAATATTTTTAAAATTATATACTA
1 TATATA-TTTTC-AAAATATTTTTAAAACTATATAATA
* *
510009 TATA-ATTTTTCAAAATGA-TTTCAAAATTATATAATA
1 TATATA-TTTTCAAAAT-ATTTTTAAAACTATATAATA
* *
510045 TATATGTTTTCAAAATGTTTTT-----T-TA-AACTA
1 TATATATTTTCAAAATATTTTTAAAACTATATAA-TA
* *
510075 TATATATTTTCAAAATGTTTTAAAAACTATAT-A-A
1 TATATATTTTCAAAATATTTTTAAAACTATATAATA
*
510109 TATATATTTTCAAAA-ATGTTTTAAAAACTATATATTA
1 TATATATTTTCAAAATAT-TTTT-AAAACTATATAATA
* *
510146 TATATTTTTTCAAAA-ATGTTTTAAAAACTATATATTA
1 TATATATTTTCAAAATAT-TTTT-AAAACTATATAATA
* * * *
510183 TATTTATTTTCAAAATGTTTTAAAAACTATACAATA
1 TATATATTTTCAAAATATTTTTAAAACTATATAATA
* *
510219 TATAAATGTTTTCAAACATATTTTCAAAACTATATATTATA
1 TAT--ATATTTTCAAA-ATATTTTTAAAACTATATA--ATA
* * * *
510260 TATATGTTTTTTAAAAAATATTTTCAAACTATATTTAATA
1 TATAT-ATTTTCAAAATAT-TTTTAAAACTATA--TAATA
510300 TATATAT
1 TATATAT
510307 ATATATATAT
Statistics
Matches: 244, Mismatches: 29, Indels: 49
0.76 0.09 0.15
Matches are distributed among these distances:
29 2 0.01
30 24 0.10
31 1 0.00
33 1 0.00
34 19 0.08
35 11 0.05
36 56 0.23
37 60 0.25
38 14 0.06
39 22 0.09
40 26 0.11
41 6 0.02
42 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATATTTTCAAAATATTTTTAAAACTATATAATA
Found at i:510090 original size:66 final size:65
Alignment explanation
Indices: 510005--510213 Score: 219
Period size: 66 Copynumber: 3.1 Consensus size: 65
509995 AAAATTATAT
* * *
510005 ACTATATA-ATTTTTCAAAATGATTTCAAAATTATATAATATATATGTTTTC-AAAATGTTTTTT
1 ACTATATATATTTTTCAAAATGATTTAAAAACTATATAATATATA--TTTTCAAAAATG-TTTTA
*
510068 TAA
63 AAA
*
510071 ACTATATATA-TTTTCAAAATGTTTTAAAAACTATATAATATATATTTTCAAAAATGTTTTAAAA
1 ACTATATATATTTTTCAAAATGATTTAAAAACTATATAATATATATTTTCAAAAATGTTTTAAAA
* *
510135 ACTATATATTATATATTTTTTCAAAAATGTTTTAAAAACTATATATTATATTTATTTTC-AAAAT
1 AC----TA-TATATA-TTTTTC-AAAATGATTTAAAAACTATATA--ATATATATTTTCAAAAAT
510199 GTTTTAAAA
57 GTTTTAAAA
510208 ACTATA
1 ACTATA
510214 CAATATATAA
Statistics
Matches: 125, Mismatches: 6, Indels: 22
0.82 0.04 0.14
Matches are distributed among these distances:
64 13 0.10
65 6 0.05
66 39 0.31
67 1 0.01
68 4 0.03
69 8 0.06
71 5 0.04
72 22 0.18
73 16 0.13
74 11 0.09
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (65 bp):
ACTATATATATTTTTCAAAATGATTTAAAAACTATATAATATATATTTTCAAAAATGTTTTAAAA
Found at i:510304 original size:2 final size:2
Alignment explanation
Indices: 510297--510338 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
510287 ACTATATTTA
510297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
510339 GATAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:517301 original size:32 final size:32
Alignment explanation
Indices: 517263--517329 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
517253 ATCCCTCTTG
*
517263 CTTATGGCTTAGTTGTGAATTTCATCCCTCAA
1 CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
*
517295 CTTATGGCTAAGTTGTGAATTTCATCCCTCGA
1 CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
517327 CTT
1 CTT
517330 CCCAAATGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.40
Consensus pattern (32 bp):
CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
Found at i:522431 original size:17 final size:17
Alignment explanation
Indices: 522405--522447 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
522395 GCAGCAAATT
*
522405 ATCATTCCGGCATCAGA
1 ATCATCCCGGCATCAGA
522422 ATCATCCCGGCATCAGA
1 ATCATCCCGGCATCAGA
522439 ATCATCCCG
1 ATCATCCCG
522448 AAAACCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.21
Consensus pattern (17 bp):
ATCATCCCGGCATCAGA
Found at i:528320 original size:343 final size:343
Alignment explanation
Indices: 527694--528379 Score: 1354
Period size: 343 Copynumber: 2.0 Consensus size: 343
527684 ATAACCTTAC
527694 AGTTAGTTCATCACTGGAAAATGTTTCTGCAACGTATTTGCTATAGTAAACATTTGGTAAAAAAA
1 AGTTAGTTCATCACTGGAAAATGTTTCTGCAACGTATTTGCTATAGTAAACATTTGGTAAAAAAA
527759 TTCAGCTGATTTGGCTATGAACTTTTAATTGAGAATGAACTTATGCAAAAACCAGTATTTGTACA
66 TTCAGCTGATTTGGCTATGAACTTTTAATTGAGAATGAACTTATGCAAAAACCAGTATTTGTACA
*
527824 GCCTCGTTAGTCGCTTGAACATTATTCTTCTATGTTCTGTCAACTACAAAATGATTTGAATCAAA
131 GCCTCGTTAGTCGCTTGAACATTATTCCTCTATGTTCTGTCAACTACAAAATGATTTGAATCAAA
527889 TAAAAAGAAAAGGAAATAATCTCCTAAGCAATACGACGCCCAACTCAAGTGCTCAATCTTCTTAA
196 TAAAAAGAAAAGGAAATAATCTCCTAAGCAATACGACGCCCAACTCAAGTGCTCAATCTTCTTAA
527954 GATGCAAACGGGACTTAGAATAAGCTTCCATGGAATATCATTCAAAAGCGCTGCCATAAACACAT
261 GATGCAAACGGGACTTAGAATAAGCTTCCATGGAATATCATTCAAAAGCGCTGCCATAAACACAT
528019 TAGCTAACAAATTAATGA
326 TAGCTAACAAATTAATGA
528037 AGTTAGTTCATCACTGGAAAATGTTTCTGCAACGTATTTGCTATAGTAAACATTTGGTAAAAAAA
1 AGTTAGTTCATCACTGGAAAATGTTTCTGCAACGTATTTGCTATAGTAAACATTTGGTAAAAAAA
528102 TTCAGCTGATTTGGCTATGAACTTTTAATTGAGAATGAACTTATGCAAAAACCAGTATTTGTACA
66 TTCAGCTGATTTGGCTATGAACTTTTAATTGAGAATGAACTTATGCAAAAACCAGTATTTGTACA
528167 GCCTCGTTAGTCGCTTGAACATTATTCCTCTATGTTCTGTCAACTACAAAATGATTTGAATCAAA
131 GCCTCGTTAGTCGCTTGAACATTATTCCTCTATGTTCTGTCAACTACAAAATGATTTGAATCAAA
528232 TAAAAAGAAAAGGAAATAATCTCCTAAGCAATACGACGCCCAACTCAAGTGCTCAATCTTCTTAA
196 TAAAAAGAAAAGGAAATAATCTCCTAAGCAATACGACGCCCAACTCAAGTGCTCAATCTTCTTAA
*
528297 GATGCAAACGGGACTTGGAATAAGCTTCCATGGAATATCATTCAAAAGCGCTGCCATAAACACAT
261 GATGCAAACGGGACTTAGAATAAGCTTCCATGGAATATCATTCAAAAGCGCTGCCATAAACACAT
528362 TAGCTAACAAATTAATGA
326 TAGCTAACAAATTAATGA
528380 TCATAACTGC
Statistics
Matches: 341, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
343 341 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (343 bp):
AGTTAGTTCATCACTGGAAAATGTTTCTGCAACGTATTTGCTATAGTAAACATTTGGTAAAAAAA
TTCAGCTGATTTGGCTATGAACTTTTAATTGAGAATGAACTTATGCAAAAACCAGTATTTGTACA
GCCTCGTTAGTCGCTTGAACATTATTCCTCTATGTTCTGTCAACTACAAAATGATTTGAATCAAA
TAAAAAGAAAAGGAAATAATCTCCTAAGCAATACGACGCCCAACTCAAGTGCTCAATCTTCTTAA
GATGCAAACGGGACTTAGAATAAGCTTCCATGGAATATCATTCAAAAGCGCTGCCATAAACACAT
TAGCTAACAAATTAATGA
Found at i:530362 original size:26 final size:26
Alignment explanation
Indices: 530326--530376 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
530316 GAAGTGCTAG
*
530326 TACACATAAGGTTGTGCCCACCATAA
1 TACACATAAGGTCGTGCCCACCATAA
530352 TACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
530377 TGCACTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (26 bp):
TACACATAAGGTCGTGCCCACCATAA
Found at i:531459 original size:81 final size:81
Alignment explanation
Indices: 531349--531569 Score: 329
Period size: 81 Copynumber: 2.7 Consensus size: 81
531339 CCCAAAGGCA
* * * * *
531349 TTTAATCTTTCATCTAAGTTGCATGATTGACA-CTTGTCTGCCAAATGCACAGCTAGTCCATTTA
1 TTTAATCATTCATCTAACTGGCATAATTGACACCTT-TCTGCCAAATGCACAGCTAGGCCATTTA
531413 TCTTTTACTCAACGATC
65 TCTTTTACTCAACGATC
*
531430 TTTAATCATTCATATAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTAT
1 TTTAATCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTAT
*
531495 CTTTTACTCAACGGTC
66 CTTTTACTCAACGATC
* *
531511 TTTAA-CTGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC
1 TTTAATC-ATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCC
531570 TCAAAGGCAC
Statistics
Matches: 128, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
80 1 0.01
81 124 0.97
82 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (81 bp):
TTTAATCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTAT
CTTTTACTCAACGATC
Found at i:538961 original size:22 final size:22
Alignment explanation
Indices: 538931--538983 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
538921 AAATTGAAAT
*
538931 TTTCTTTTTCAATACTTTCAAA
1 TTTCATTTTCAATACTTTCAAA
538953 TTTCATTTTCAATACTTTCAAA
1 TTTCATTTTCAATACTTTCAAA
538975 TTTCATTTT
1 TTTCATTTT
538984 TGAGAGTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTCATTTTCAATACTTTCAAA
Found at i:541613 original size:16 final size:16
Alignment explanation
Indices: 541578--541626 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
541568 AGCATTTAAG
541578 TTCAAACATCCAAAACAAA
1 TTCAAACATCC---ACAAA
541597 TTCAAACATCCACAAA
1 TTCAAACATCCACAAA
* *
541613 TTTAAACATTCACA
1 TTCAAACATCCACA
541627 TACATCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 17 0.61
19 11 0.39
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (16 bp):
TTCAAACATCCACAAA
Found at i:543638 original size:23 final size:23
Alignment explanation
Indices: 543577--543639 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
543567 ATCCTCATGT
* *
543577 GGGGGTATCGATACCCATTCAAA
1 GGGGGTATCGATACCTATGCAAA
*
543600 GAGGGTATCGATACCTATGCAAA
1 GGGGGTATCGATACCTATGCAAA
543623 GGGGGTATCGATACCTA
1 GGGGGTATCGATACCTA
543640 GCGCTTAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGGGTATCGATACCTATGCAAA
Found at i:547472 original size:22 final size:21
Alignment explanation
Indices: 547430--547469 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
547420 AAGACTATTT
547430 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
547451 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
547470 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:549480 original size:20 final size:20
Alignment explanation
Indices: 549455--549495 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
549445 ATCTTATTTA
*
549455 GGGGTATCGGTACCCTCTGG
1 GGGGTATCGGTACCCTATGG
549475 GGGGTATCGGTACCCTATGG
1 GGGGTATCGGTACCCTATGG
549495 G
1 G
549496 ATATCTGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.22, G:0.41, T:0.24
Consensus pattern (20 bp):
GGGGTATCGGTACCCTATGG
Found at i:553671 original size:29 final size:28
Alignment explanation
Indices: 553629--553693 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 28
553619 AATCGATCTT
*
553629 ACCACCAATTATTTTTTGTCTCAATTCG
1 ACCACCAACTATTTTTTGTCTCAATTCG
* *
553657 GCCACCGAACTATTTTTTGTCTTAATTCG
1 ACCACC-AACTATTTTTTGTCTCAATTCG
553686 ACCACCAA
1 ACCACCAA
553694 ACCTTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (28 bp):
ACCACCAACTATTTTTTGTCTCAATTCG
Found at i:554008 original size:28 final size:28
Alignment explanation
Indices: 553965--554030 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
553955 TGTCACCACC
*
553965 CCGATTGAAATGAAAAATTGAAGAACAG
1 CCGATTGAAATAAAAAATTGAAGAACAG
553993 CCGATTGAAATAAAAAATTGAAGAACAG
1 CCGATTGAAATAAAAAATTGAAGAACAG
554021 CCGATTGAAA
1 CCGATTGAAA
554031 AAATTGAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.50, C:0.12, G:0.20, T:0.18
Consensus pattern (28 bp):
CCGATTGAAATAAAAAATTGAAGAACAG
Found at i:554032 original size:24 final size:25
Alignment explanation
Indices: 553977--554042 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 25
553967 GATTGAAATG
553977 AAAAATTGAAGAACAGCCGATTGAAATA
1 AAAAATTGAAGAACAGCCGATTG--A-A
554005 AAAAATTGAAGAACAGCCGATTG-A
1 AAAAATTGAAGAACAGCCGATTGAA
554029 AAAAATTGAAGAAC
1 AAAAATTGAAGAAC
554043 CAATTTGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 15 0.39
28 23 0.61
ACGTcount: A:0.55, C:0.11, G:0.18, T:0.17
Consensus pattern (25 bp):
AAAAATTGAAGAACAGCCGATTGAA
Found at i:554518 original size:26 final size:26
Alignment explanation
Indices: 554461--554619 Score: 106
Period size: 26 Copynumber: 6.0 Consensus size: 26
554451 TTTTCTTTAA
** * *
554461 CATTAATCGAAATGAAATTATTTAAT
1 CATTAATCGAACCGAAATTATTTGAC
*
554487 CGTTAATCGAACCGAAATTATTTGAC
1 CATTAATCGAACCGAAATTATTTGAC
* * *
554513 CTTTAATCGAGCCGAAATTTATTTGAA
1 CATTAATCGAACCGAAA-TTATTTGAC
* * * * * *
554540 AATT-AT-TAACCGAATGTTTTTCTTTAAT
1 CATTAATCGAACCGAA----ATTATTTGAC
*
554568 CATTAATCGAACCGAAATTATTTTAC
1 CATTAATCGAACCGAAATTATTTGAC
*
554594 CGTTAATCGAACCGAAATTTATTTGA
1 CATTAATCGAACCGAAA-TTATTTGA
554620 AAATTATTAA
Statistics
Matches: 101, Mismatches: 24, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
25 6 0.06
26 60 0.59
27 17 0.17
28 9 0.09
29 2 0.02
30 7 0.07
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (26 bp):
CATTAATCGAACCGAAATTATTTGAC
Found at i:554579 original size:81 final size:81
Alignment explanation
Indices: 554481--554672 Score: 312
Period size: 81 Copynumber: 2.4 Consensus size: 81
554471 AATGAAATTA
* * *
554481 TTTAATCGTTAATCGAACCGAAATTATTTGACCTTTAATCGAGCCGAAATTTATTTGAAAATTAT
1 TTTAATCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTAT
554546 TAACCGAATGTTTTTC
66 TAACCGAATGTTTTTC
*
554562 TTTAATCATTAATCGAACCGAAATTATTTTACCGTTAATCGAACCGAAATTTATTTGAAAATTAT
1 TTTAATCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTAT
*
554627 TAACCGAATTTTTTTC
66 TAACCGAATGTTTTTC
* *
554643 TTTAAGCATTAATCGAACCCAAATTTATTT
1 TTTAATCATTAATCGAACCGAAA-TTATTT
554673 TATTCGATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
81 97 0.94
82 6 0.06
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (81 bp):
TTTAATCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTAT
TAACCGAATGTTTTTC
Found at i:554738 original size:26 final size:27
Alignment explanation
Indices: 554690--554740 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
554680 TTAATAATTT
*
554690 TCAAATAAATTTCGTTTCAATTAACGG
1 TCAAATAAATTTCGGTTCAATTAACGG
*
554717 TCAAAT-AATTTCGGTTCTATTAAC
1 TCAAATAAATTTCGGTTCAATTAAC
554741 AGTTAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (27 bp):
TCAAATAAATTTCGGTTCAATTAACGG
Found at i:554828 original size:26 final size:27
Alignment explanation
Indices: 554792--554843 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
554782 AATAATTTTC
554792 AAATAAATTTTGATTCGATTAACGGTT
1 AAATAAATTTTGATTCGATTAACGGTT
*
554819 AAAT-AATTTTGGTTCGATTAACGGT
1 AAATAAATTTTGATTCGATTAACGGT
554844 CATTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (27 bp):
AAATAAATTTTGATTCGATTAACGGTT
Found at i:556961 original size:15 final size:15
Alignment explanation
Indices: 556941--556973 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
556931 CTTGTCTGTA
556941 TTTTGGACA-TTCTAT
1 TTTTGGA-ATTTCTAT
556956 TTTTGGAATTTCTAT
1 TTTTGGAATTTCTAT
556971 TTT
1 TTT
556974 AGTCCTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTTGGAATTTCTAT
Found at i:557421 original size:2 final size:2
Alignment explanation
Indices: 557414--557450 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
557404 TACGTACGTG
*
557414 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
557451 GAATTTTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:558348 original size:16 final size:16
Alignment explanation
Indices: 558311--558351 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
558301 AAAAATGAAG
*
558311 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
558327 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
558342 AATAAATAAA
1 AATAAATAAA
558352 TAAATAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:558356 original size:12 final size:13
Alignment explanation
Indices: 558287--558366 Score: 51
Period size: 13 Copynumber: 6.4 Consensus size: 13
558277 TCAGAGGGGA
*
558287 AAATGAATAAATG
1 AAATAAATAAATG
*
558300 AAA-AAATGAA-G
1 AAATAAATAAATG
* * *
558311 AATAAAAATAAGTA
1 AA-ATAAATAAATG
* *
558325 AAAAAAATAAAAG
1 AAATAAATAAATG
*
558338 GAA-AAATAAAT-
1 AAATAAATAAATG
558349 AAATAAATAAATG
1 AAATAAATAAATG
558362 AAATA
1 AAATA
558367 TTATATATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
11 5 0.10
12 21 0.41
13 23 0.45
14 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (13 bp):
AAATAAATAAATG
Found at i:558375 original size:2 final size:2
Alignment explanation
Indices: 558364--558403 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
558354 AATAAATGAA
558364 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
558404 ATGAGTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:558468 original size:18 final size:18
Alignment explanation
Indices: 558420--558473 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 18
558410 AAAATAGAAA
558420 AATAATAATCATAACAATAAT
1 AATAATAAT-ATAA-AAT-AT
558441 AATAATAATATGAAAATAT
1 AATAATAATAT-AAAATAT
558460 AAT-ATAATATAAAA
1 AATAATAATATAAAA
558474 AAACCAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.12
18 7 0.22
19 5 0.16
20 5 0.16
21 11 0.34
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAATAATATAAAATAT
Found at i:558474 original size:18 final size:20
Alignment explanation
Indices: 558420--558474 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
558410 AAAATAGAAA
*
558420 AATAATAATCATAACAATAAT
1 AATAATAAT-ATAAAAATAAT
*
558441 AATAATAATATGAAAAT-AT
1 AATAATAATATAAAAATAAT
558460 AAT-ATAATATAAAAA
1 AATAATAATATAAAAA
558475 AACCAAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.35
19 5 0.16
20 6 0.19
21 9 0.29
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAATAATATAAAAATAAT
Found at i:558672 original size:21 final size:21
Alignment explanation
Indices: 558648--558704 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
558638 TATAAGTAAA
*
558648 ATATTT-AAAATATATATATAT
1 ATATTTAAAAATA-ATAAATAT
*
558669 ATATATAAAAATAATAAATAT
1 ATATTTAAAAATAATAAATAT
*
558690 AGTATTAAAAAATAA
1 A-TATTTAAAAATAA
558705 CCAAATGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAAAAATAATAAATAT
Found at i:559274 original size:37 final size:37
Alignment explanation
Indices: 559233--559329 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
559223 GGATCTTATC
* * * *
559233 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTATATCATATT
* * * *
559270 TTTAGGAGTTTGAATCCTAGCAAAATTATATTATATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTATATCATATT
559307 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
559330 GACGAAAAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTATATCATATT
Found at i:561209 original size:106 final size:106
Alignment explanation
Indices: 560060--561190 Score: 1620
Period size: 106 Copynumber: 10.7 Consensus size: 106
560050 GCATTGTTCC
* * ** * * *
560060 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTAACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* * * *
560124 ACCAGCCGTCCCTTCGTTGT-AAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
560165 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * *
560224 TCAACCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
560266 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATT-AGGAAATTATTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTGTTGACA
*
560329 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
560371 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
560436 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
560477 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
560542 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
560583 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
560648 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
560689 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
560754 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
560795 GAGTCCAATAACCTTCG-TAGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* *
560859 ACCATCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
560901 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTAAGTAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
560966 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
561007 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
561072 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
561113 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
561178 CCAGTGGTCCCTT
66 CCAGCGGTCCCTT
561191 TATTGTGAAT
Statistics
Matches: 935, Mismatches: 76, Indels: 29
0.90 0.07 0.03
Matches are distributed among these distances:
98 2 0.00
99 23 0.02
100 53 0.06
101 8 0.01
102 1 0.00
104 6 0.01
105 39 0.04
106 800 0.86
107 3 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:561621 original size:30 final size:32
Alignment explanation
Indices: 561585--561645 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
561575 TTGCATTAGG
561585 ATGTTGAATC-CAAAAATGCCCC-AATATTTT
1 ATGTTGAATCTCAAAAATGCCCCAAATATTTT
*
561615 ATGTTGAATCTTCAAAGATGCCCCAAATATT
1 ATGTTGAATC-TCAAAAATGCCCCAAATATT
561646 CCTCATTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.37
32 11 0.41
33 6 0.22
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (32 bp):
ATGTTGAATCTCAAAAATGCCCCAAATATTTT
Found at i:561826 original size:24 final size:24
Alignment explanation
Indices: 561798--561858 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
561788 AATATCAATA
561798 AAGAGTTTTGAAAGATGTTTAATC
1 AAGAGTTTTGAAAGATGTTTAATC
*
561822 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTTGAAAGATGTTTAATC
*
561846 AAAAGTTTTGAAA
1 AAGAGTTTTGAAA
561859 ATATTGTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (24 bp):
AAGAGTTTTGAAAGATGTTTAATC
Found at i:562075 original size:22 final size:22
Alignment explanation
Indices: 562050--562125 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
562040 TTATGTTTGG
562050 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
562072 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
562094 TCATAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
562116 TCAATGGTTT
1 TCAAAGGTTT
562126 AATGAGGCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:567410 original size:2 final size:2
Alignment explanation
Indices: 567399--567432 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
567389 TAAATAAGAA
567399 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
567433 AATGAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:568305 original size:37 final size:37
Alignment explanation
Indices: 568259--568360 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
568249 CTTGTGGATC
* * * *
568259 CTATCTTTAGGAGTTTAAATCATAGTAGAACTCTA-T
1 CTATTTTTAGGAGTTTGAATCCTAGTAGAACTATATT
* * *
568295 CATATTTTTAGGAGTTTGAATCCTAGCAAAATTATATT
1 C-TATTTTTAGGAGTTTGAATCCTAGTAGAACTATATT
568333 CTATTTTTAGGAGTTTGAATCCTAGTAG
1 CTATTTTTAGGAGTTTGAATCCTAGTAG
568361 GACGAAAATG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
36 1 0.02
37 52 0.95
38 2 0.04
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTGAATCCTAGTAGAACTATATT
Found at i:569671 original size:21 final size:21
Alignment explanation
Indices: 569646--569686 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
569636 TTTAATAAAA
569646 AATTAACTATTTTAAATCTAT
1 AATTAACTATTTTAAATCTAT
* *
569667 AATTAACTTTTTTTAATCTA
1 AATTAACTATTTTAAATCTA
569687 AAGAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTAACTATTTTAAATCTAT
Found at i:570751 original size:21 final size:21
Alignment explanation
Indices: 570726--570769 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
570716 TTTATATTTT
570726 TAATATAACTTCTTAAATTCA
1 TAATATAACTTCTTAAATTCA
570747 TAATATAACTTCTTAAATTCA
1 TAATATAACTTCTTAAATTCA
570768 TA
1 TA
570770 CTCTGACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATAACTTCTTAAATTCA
Found at i:579892 original size:207 final size:210
Alignment explanation
Indices: 579550--579967 Score: 806
Period size: 208 Copynumber: 2.0 Consensus size: 210
579540 TAAAAATATT
579550 AAAAAAATTCAATCGCACAGTGACACATGTCACAATAAGATTGAAGATTAAATTTATTGAATTAA
1 AAAAAAATTCAATCGCACAGTGACACATGTCACAATAAGATTGAAGATTAAATTTATTGAATTAA
579615 ATAAAAGTTAGGACCAAATTAATAGAATGTGTAAGTAATGAGGACTAAATATATAATTATACAAA
66 ATAAAAGTTAGGACCAAATTAATAGAATGTGTAAGTAATGAGGACTAAATATATAATTATACAAA
*
579680 TTTTATT-ACTGCGACATCATCTCCTCCGTTAATATTTAACGACGGGTGGCTTGATTGATAATAT
131 TTTTATTAACTGCGACATCATCTCCTCCGTTAATATTTAACGACGGGTGGCTTGATTGACAATAT
579744 TTAAATAGTTAGGTG
196 TTAAATAGTTAGGTG
579759 AAAAAAATTCAATCGCACAGTGACACATGTCACAATAAGATTGAAGATT-AATTTATTGAATTAA
1 AAAAAAATTCAATCGCACAGTGACACATGTCACAATAAGATTGAAGATTAAATTTATTGAATTAA
579823 AT-AAAGTTAGGACCAAATTAATAGAATGTGTAAGTAATGAGGACTAAATATATAATTATACAAA
66 ATAAAAGTTAGGACCAAATTAATAGAATGTGTAAGTAATGAGGACTAAATATATAATTATACAAA
579887 TTTTATTAACTGCGACATCATCTCCTCCGTTAATATTTAACGACGGGTGGCTTGATTGACAATAT
131 TTTTATTAACTGCGACATCATCTCCTCCGTTAATATTTAACGACGGGTGGCTTGATTGACAATAT
579952 TTAAATAGTTAGGTG
196 TTAAATAGTTAGGTG
579967 A
1 A
579968 CCCAATTGAC
Statistics
Matches: 207, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
207 69 0.33
208 89 0.43
209 49 0.24
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (210 bp):
AAAAAAATTCAATCGCACAGTGACACATGTCACAATAAGATTGAAGATTAAATTTATTGAATTAA
ATAAAAGTTAGGACCAAATTAATAGAATGTGTAAGTAATGAGGACTAAATATATAATTATACAAA
TTTTATTAACTGCGACATCATCTCCTCCGTTAATATTTAACGACGGGTGGCTTGATTGACAATAT
TTAAATAGTTAGGTG
Done.