Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007803.1 Hibiscus syriacus cultivar Beakdansim tig00110121_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: 468357
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:17205 original size:13 final size:13
Alignment explanation
Indices: 17154--17199 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
17144 GTCATAAATC
17154 TATGACGCACATT
1 TATGACGCACATT
**
17167 TATGAAACACATT
1 TATGACGCACATT
17180 TATGACGCACATT
1 TATGACGCACATT
17193 TATGACG
1 TATGACG
17200 TTCATTGAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:23696 original size:14 final size:15
Alignment explanation
Indices: 23677--23705 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23667 TTGATTTTGA
23677 TATAATTAT-ATTAT
1 TATAATTATAATTAT
23691 TATAATTATAATTAT
1 TATAATTATAATTAT
23706 ATTATTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATAATTATAATTAT
Found at i:24237 original size:18 final size:18
Alignment explanation
Indices: 24214--24258 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
24204 TAAAGCCCTG
24214 ATTACAAGCC-GAAGCCCA
1 ATTACAA-CCTGAAGCCCA
24232 ATTACAACCTGAAGCCCA
1 ATTACAACCTGAAGCCCA
24250 ATTACAACC
1 ATTACAACC
24259 AACTCCCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.40, C:0.33, G:0.11, T:0.16
Consensus pattern (18 bp):
ATTACAACCTGAAGCCCA
Found at i:27077 original size:26 final size:26
Alignment explanation
Indices: 27041--27110 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
27031 GGTAGTCCAG
27041 TCAACAACTTCTAGAAGACAGTTC-AA
1 TCAACAACTTCTAGAAGACA-TTCTAA
* *
27067 TCAACAGCTTCTAGAAGACATTCTAG
1 TCAACAACTTCTAGAAGACATTCTAA
*
27093 TCAGCAACTTCTAGAAGA
1 TCAACAACTTCTAGAAGA
27111 TAGATGAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 3 0.08
26 36 0.92
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (26 bp):
TCAACAACTTCTAGAAGACATTCTAA
Found at i:27441 original size:21 final size:21
Alignment explanation
Indices: 27413--27456 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
27403 TTAATAAAAG
27413 TTTATTTCCTTC-TCA-TTATT
1 TTTATTT-CTTCTTCATTTATT
27433 TTTACTTTCTTCTTCATTTATT
1 TTTA-TTTCTTCTTCATTTATT
27455 TT
1 TT
27457 CCCATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 7 0.33
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTTCTTCTTCATTTATT
Found at i:28560 original size:19 final size:19
Alignment explanation
Indices: 28528--28583 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 19
28518 AGATATTTAG
* *
28528 TTAGTTAAGCTGTTGATAA
1 TTAGTTAGGTTGTTGATAA
28547 TTAGTTAGGTTGTTGTTGATAA
1 TTAGTTA-G--GTTGTTGATAA
28569 TTAGTTAGGTTGTTG
1 TTAGTTAGGTTGTTG
28584 TTGTTAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 14 0.44
21 1 0.03
22 17 0.53
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (19 bp):
TTAGTTAGGTTGTTGATAA
Found at i:28566 original size:22 final size:22
Alignment explanation
Indices: 28538--28604 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
28528 TTAGTTAAGC
28538 TGTTGATAATTAGTTAGGTTGT
1 TGTTGATAATTAGTTAGGTTGT
28560 TGTTGATAATTAGTTAGGTTGT
1 TGTTGATAATTAGTTAGGTTGT
* *
28582 TGTTGTTAATTAGTTAGTTTGT
1 TGTTGATAATTAGTTAGGTTGT
28604 T
1 T
28605 AGTGAGGCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (22 bp):
TGTTGATAATTAGTTAGGTTGT
Found at i:34324 original size:29 final size:29
Alignment explanation
Indices: 34292--34350 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
34282 CCTAAATTAA
34292 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
34321 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
34350 T
1 T
34351 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:38990 original size:29 final size:29
Alignment explanation
Indices: 38956--39014 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
38946 CCTAAATTAA
38956 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
38985 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
39014 T
1 T
39015 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:42158 original size:60 final size:60
Alignment explanation
Indices: 42065--42184 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
42055 ACACAGAATG
42065 TATGTAGTCAACTTTAAGCATTTTAAGGTGAAATGATCACGTGCCGAAGTTTTAATATAT
1 TATGTAGTCAACTTTAAGCATTTTAAGGTGAAATGATCACGTGCCGAAGTTTTAATATAT
42125 TATGTAGTCAACTTTAAGCATTTTAAGGTGAAATGATCACGTGCCGAAGTTTTAATATAT
1 TATGTAGTCAACTTTAAGCATTTTAAGGTGAAATGATCACGTGCCGAAGTTTTAATATAT
42185 GGCTAAAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (60 bp):
TATGTAGTCAACTTTAAGCATTTTAAGGTGAAATGATCACGTGCCGAAGTTTTAATATAT
Found at i:42295 original size:22 final size:22
Alignment explanation
Indices: 42253--42301 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
42243 TATCGGACAC
42253 ATTA-TTTTTTCTACCGATTTT
1 ATTATTTTTTTCTACCGATTTT
* * *
42274 GTTATTTTTTTCTACTGGTTTT
1 ATTATTTTTTTCTACCGATTTT
42296 ATTATT
1 ATTATT
42302 GTTGAGCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.16, C:0.10, G:0.08, T:0.65
Consensus pattern (22 bp):
ATTATTTTTTTCTACCGATTTT
Found at i:44740 original size:20 final size:20
Alignment explanation
Indices: 44715--44757 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
44705 TTTTCTCTTG
*
44715 AAAGCAAAATTG-GATTTTGA
1 AAAGCAAAA-TGAAATTTTGA
44735 AAAGCAAAATGAAATTTTGA
1 AAAGCAAAATGAAATTTTGA
44755 AAA
1 AAA
44758 ATAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (20 bp):
AAAGCAAAATGAAATTTTGA
Found at i:51283 original size:21 final size:21
Alignment explanation
Indices: 51252--51309 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
51242 TAAATATTAT
*
51252 AAAGGTAGTACCGATACTCATG
1 AAAGG-AGTACCGATACACATG
*
51274 AAAGGAGTACTGATACACATG
1 AAAGGAGTACCGATACACATG
*
51295 AAAGCAGTACCGATA
1 AAAGGAGTACCGATA
51310 TGCCCTGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (21 bp):
AAAGGAGTACCGATACACATG
Found at i:51837 original size:63 final size:63
Alignment explanation
Indices: 51759--51891 Score: 232
Period size: 63 Copynumber: 2.1 Consensus size: 63
51749 AAGTCATTTT
*
51759 GCAAATTGTTTCATCTTTATACTCCTTACTCTCTAAACT-AAAAAGTCAATTCACTCCCTCTTG
1 GCAAATTGTTTCATCTTTATACTCCTTACTCTCTAAACTCAAAAAGCCAATTCAC-CCCTCTTG
*
51822 GCAAATTGTTTCATCTTTATACTCCTTACTCTCTAAACTCAAAAAGCCATTTCACCCCTCTTG
1 GCAAATTGTTTCATCTTTATACTCCTTACTCTCTAAACTCAAAAAGCCAATTCACCCCTCTTG
51885 GCAAATT
1 GCAAATT
51892 ATCTAGTTGT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 54 0.81
64 13 0.19
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.37
Consensus pattern (63 bp):
GCAAATTGTTTCATCTTTATACTCCTTACTCTCTAAACTCAAAAAGCCAATTCACCCCTCTTG
Found at i:53068 original size:17 final size:16
Alignment explanation
Indices: 53025--53069 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
53015 TAAAATTATT
53025 ATATATTTTTA-AAAA
1 ATATATTTTTATAAAA
53040 ATATATTTTTTATTAAAA
1 ATATA-TTTTTA-TAAAA
*
53058 ATTTATTTTTAT
1 ATATATTTTTAT
53070 CTTTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 6 0.23
18 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATATTTTTATAAAA
Found at i:53885 original size:20 final size:22
Alignment explanation
Indices: 53848--53888 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53838 TTTCCTTTAA
*
53848 TTTATATAATAAATTTATAAAC
1 TTTATAAAATAAATTTATAAAC
53870 TTTATAAAAT-AA-TTATAAA
1 TTTATAAAATAAATTTATAAA
53889 TTATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTATAAAATAAATTTATAAAC
Found at i:68692 original size:22 final size:23
Alignment explanation
Indices: 68667--68710 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
68657 GTTTTTATAA
*
68667 AAGTT-TTCTCTTTTTTCTTTTT
1 AAGTTCTTCTCATTTTTCTTTTT
*
68689 AAGTTCTTTTCATTTTTCTTTT
1 AAGTTCTTCTCATTTTTCTTTT
68711 ATTTTTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (23 bp):
AAGTTCTTCTCATTTTTCTTTTT
Found at i:69349 original size:18 final size:19
Alignment explanation
Indices: 69314--69351 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
69304 CTCTCTTATT
*
69314 TTTATTTAAATTGCTTTTA
1 TTTATTTAAATCGCTTTTA
69333 TTTATTT-AATCGCTTTTA
1 TTTATTTAAATCGCTTTTA
69351 T
1 T
69352 CACTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTTAAATCGCTTTTA
Found at i:86258 original size:31 final size:31
Alignment explanation
Indices: 86223--86298 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
86213 ATATTTGTAC
* **
86223 AGTTTTGGTCACTTATGTTATCGTTTTATTA
1 AGTTTTGATCACTTACATTATCGTTTTATTA
* * * *
86254 AGTTTTGTTCACTTGCATTATTGTTTTATTT
1 AGTTTTGATCACTTACATTATCGTTTTATTA
86285 AGTTTTGATCACTT
1 AGTTTTGATCACTT
86299 GGAAATGAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.18, C:0.11, G:0.14, T:0.57
Consensus pattern (31 bp):
AGTTTTGATCACTTACATTATCGTTTTATTA
Found at i:86299 original size:31 final size:31
Alignment explanation
Indices: 86240--86299 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
86230 GTCACTTATG
*
86240 TTATCGTTTTATTAAGTTTTGTTCACTTGCA
1 TTATCGTTTTATTAAGTTTTGATCACTTGCA
* *
86271 TTATTGTTTTATTTAGTTTTGATCACTTG
1 TTATCGTTTTATTAAGTTTTGATCACTTG
86300 GAAATGAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.58
Consensus pattern (31 bp):
TTATCGTTTTATTAAGTTTTGATCACTTGCA
Found at i:87047 original size:29 final size:31
Alignment explanation
Indices: 87007--87078 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
86997 TTCAACGTCC
*
87007 AAGTGACCAAAACTT-ATAAAACGATAACAT
1 AAGTGACCAAAACTTAACAAAACGATAACAT
* *
87037 AA-TGACTAAAACTTAACAAAATGATAACAT
1 AAGTGACCAAAACTTAACAAAACGATAACAT
87067 AAGTGACCAAAA
1 AAGTGACCAAAA
87079 TGTACAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 11 0.31
30 17 0.47
31 8 0.22
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAACAAAACGATAACAT
Found at i:87550 original size:19 final size:20
Alignment explanation
Indices: 87502--87551 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
87492 CTATATTATC
*
87502 AATTATATATTAGTACAGTA
1 AATTATATATTAATACAGTA
*
87522 AA-TATTTATTAATACA-TA
1 AATTATATATTAATACAGTA
*
87540 AATTATGTATTA
1 AATTATATATTA
87552 TATATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 20 0.77
20 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (20 bp):
AATTATATATTAATACAGTA
Found at i:88469 original size:45 final size:45
Alignment explanation
Indices: 88418--88529 Score: 206
Period size: 45 Copynumber: 2.5 Consensus size: 45
88408 GGATGTCAAC
88418 TTCCATTATGTTAATTAAATGTTAGAAAAGTGCTATTATTTTCAT
1 TTCCATTATGTTAATTAAATGTTAGAAAAGTGCTATTATTTTCAT
**
88463 TTCCATTATGTTAATTAAATGTTAGTTAAGTGCTATTATTTTCAT
1 TTCCATTATGTTAATTAAATGTTAGAAAAGTGCTATTATTTTCAT
88508 TTCCATTATGTTAATTAAATGT
1 TTCCATTATGTTAATTAAATGT
88530 CCATATAGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (45 bp):
TTCCATTATGTTAATTAAATGTTAGAAAAGTGCTATTATTTTCAT
Found at i:105737 original size:16 final size:16
Alignment explanation
Indices: 105718--105770 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
105708 TCTCACTTCT
105718 ATTCTCTCTCCTAGAC
1 ATTCTCTCTCCTAGAC
*
105734 ATTCTCTCTTCT----
1 ATTCTCTCTCCTAGAC
105746 ATTCTCTCTCCTAGAC
1 ATTCTCTCTCCTAGAC
105762 ATTCTCTCT
1 ATTCTCTCT
105771 TCTCACGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 11 0.35
16 20 0.65
ACGTcount: A:0.15, C:0.36, G:0.04, T:0.45
Consensus pattern (16 bp):
ATTCTCTCTCCTAGAC
Found at i:105739 original size:28 final size:28
Alignment explanation
Indices: 105708--105773 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
105698 TCTCTCTCAC
*
105708 TCTCACTTCTATTCTCTCTCCTAGACAT
1 TCTCTCTTCTATTCTCTCTCCTAGACAT
105736 TCTCTCTTCTATTCTCTCTCCTAGACAT
1 TCTCTCTTCTATTCTCTCTCCTAGACAT
105764 TCTCTCTTCT
1 TCTCTCTTCT
105774 CACGGATATG
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:0.14, C:0.36, G:0.03, T:0.47
Consensus pattern (28 bp):
TCTCTCTTCTATTCTCTCTCCTAGACAT
Found at i:120157 original size:21 final size:21
Alignment explanation
Indices: 120133--120179 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
120123 CGACGTCCGA
120133 CGTCCGCCGTCCTCCGACCAC
1 CGTCCGCCGTCCTCCGACCAC
*
120154 CGTCCGCCGTCTTCCGACCAC
1 CGTCCGCCGTCCTCCGACCAC
120175 CGTCC
1 CGTCC
120180 ACCGCCGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.55, G:0.19, T:0.17
Consensus pattern (21 bp):
CGTCCGCCGTCCTCCGACCAC
Found at i:123736 original size:76 final size:75
Alignment explanation
Indices: 123590--123818 Score: 264
Period size: 76 Copynumber: 3.0 Consensus size: 75
123580 TTCCAGATTA
* * * * *
123590 ATTCTAGTATGTTGGAATATATGTCAGAATTGAGCCTCTGACTGAATTTTTCC-TTTCCATGTAT
1 ATTCTAGTATGTAGAAATATCTGTAAGAATTGAGCCTCTGACTGAA-TTTTCCATTT-CATTTAT
*
123654 TCAGCCAAATGG
64 TGAGCCAAATGG
* *
123666 ATTCTAGTAGGTAGAAATATCTGTAAGAATTGAGCCTCAGACTGAATTTTCCATTTACATTTATT
1 ATTCTAGTATGTAGAAATATCTGTAAGAATTGAGCCTCTGACTGAATTTTCCATTT-CATTTATT
123731 GAGCCAAATGG
65 GAGCCAAATGG
* * * * * * *
123742 GTTCTAGTATTTAGAAATATCTG-ACAGAATTGAGTCTCTGACAGAATTTTTCATGTTTATTCAT
1 ATTCTAGTATGTAGAAATATCTGTA-AGAATTGAGCCTCTGACTGAATTTTCCAT-TTCATTTAT
123806 TGAGCCAAATGG
64 TGAGCCAAATGG
123818 A
1 A
123819 AAAAGGAAAT
Statistics
Matches: 131, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
75 7 0.05
76 122 0.93
77 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (75 bp):
ATTCTAGTATGTAGAAATATCTGTAAGAATTGAGCCTCTGACTGAATTTTCCATTTCATTTATTG
AGCCAAATGG
Found at i:132501 original size:35 final size:36
Alignment explanation
Indices: 132455--132529 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
132445 GATTTTGGAG
**
132455 TATGTAGGTTCAATTCC-ATCAAGCTGGTAATTACT
1 TATGTAGGTTCAACACCGATCAAGCTGGTAATTACT
* *
132490 TATGTAGGTTCAGCACCGATCAAGCTGGTAATTCCT
1 TATGTAGGTTCAACACCGATCAAGCTGGTAATTACT
132526 TATG
1 TATG
132530 GACCTAAGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
35 14 0.40
36 21 0.60
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (36 bp):
TATGTAGGTTCAACACCGATCAAGCTGGTAATTACT
Found at i:133943 original size:31 final size:31
Alignment explanation
Indices: 133845--133935 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
133835 CAATTTAAGG
133845 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
133876 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
133907 CAAAAT-GTTTTTAGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
133936 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:134141 original size:21 final size:21
Alignment explanation
Indices: 134115--134156 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
134105 ATTTGAATAT
*
134115 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
134136 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
134157 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:134478 original size:34 final size:32
Alignment explanation
Indices: 134439--134508 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
134429 TTTTGTAAAG
*
134439 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
134473 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
134505 GGGA
1 GGGA
134509 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:137171 original size:15 final size:16
Alignment explanation
Indices: 137148--137180 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
137138 CTTAAAGTTT
*
137148 GTACGTTGAATG-TAG
1 GTACATTGAATGCTAG
137163 GTACATTGAATGCTAG
1 GTACATTGAATGCTAG
137179 GT
1 GT
137181 TGCTGGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.09, G:0.30, T:0.33
Consensus pattern (16 bp):
GTACATTGAATGCTAG
Found at i:140333 original size:4 final size:4
Alignment explanation
Indices: 140324--140350 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
140314 GATGTTCAAC
140324 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
140351 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:141717 original size:2 final size:2
Alignment explanation
Indices: 141710--141738 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
141700 GTATGTTCTT
141710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
141739 TTTTGATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:145506 original size:36 final size:35
Alignment explanation
Indices: 145473--145540 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
145463 ACATATATGG
*
145473 TTTTTAAAACAATTTTTGAAAACATATAGTATATAA
1 TTTTTAAAACAA-TTTTGAAAACATATAATATATAA
* *
145509 TTTTTAAAATAATTTTGAAAACGTATAATATA
1 TTTTTAAAACAATTTTGAAAACATATAATATA
145541 GTTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (35 bp):
TTTTTAAAACAATTTTGAAAACATATAATATATAA
Found at i:145842 original size:26 final size:26
Alignment explanation
Indices: 145813--145871 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
145803 GTTCAAATCC
*
145813 AGTCCAAATAAATCGGTCAAGAGTAA
1 AGTCCAAATAAACCGGTCAAGAGTAA
*
145839 AGTCCAAATAAACCGGTCCAGAGTAA
1 AGTCCAAATAAACCGGTCAAGAGTAA
*
145865 AGCCCAA
1 AGTCCAA
145872 CAAAAGTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (26 bp):
AGTCCAAATAAACCGGTCAAGAGTAA
Found at i:146247 original size:16 final size:19
Alignment explanation
Indices: 146205--146247 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
146195 GACATGAGAA
146205 AAACCAAGCATTATCGAAT
1 AAACCAAGCATTATCGAAT
146224 -AA-CAAGCA-TA-C-AAT
1 AAACCAAGCATTATCGAAT
146238 AAACCAAGCA
1 AAACCAAGCA
146248 AAAAACAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.14
15 3 0.14
16 8 0.36
17 6 0.27
18 2 0.09
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.14
Consensus pattern (19 bp):
AAACCAAGCATTATCGAAT
Found at i:155754 original size:13 final size:13
Alignment explanation
Indices: 155738--155771 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
155728 TGCTTGTGAA
155738 CAAAATATTATTT
1 CAAAATATTATTT
*
155751 CAAAATATTTTTT
1 CAAAATATTATTT
*
155764 AAAAATAT
1 CAAAATAT
155772 GATCGTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (13 bp):
CAAAATATTATTT
Found at i:159608 original size:15 final size:15
Alignment explanation
Indices: 159588--159618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
159578 CAACAGATAG
159588 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
159603 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
159618 A
1 A
159619 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:176029 original size:13 final size:14
Alignment explanation
Indices: 175999--176031 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
175989 CAAGCACTAA
175999 AAAAGAAGAAACAG
1 AAAAGAAGAAACAG
176013 -AAAGAAGAAA-AG
1 AAAAGAAGAAACAG
176025 AAAAGAA
1 AAAAGAA
176032 ATTGCAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 16 0.89
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAACAG
Found at i:180223 original size:71 final size:72
Alignment explanation
Indices: 180140--180273 Score: 180
Period size: 72 Copynumber: 1.9 Consensus size: 72
180130 TTAAACTTTG
180140 AAAGTATGGATA-TTGTTTCACAAATACCGATACTTTCAAATTAAAAAAAAAAAGAAAAATGAGA
1 AAAGTATGGATATTTGTTTCACAAATACCGATACTTTCAAATTAAAAAAAAAAAGAAAAATGAGA
180204 AGGCTGC
66 AGGCTGC
* * * * * ** * *
180211 AAAGTATTGATATTTTTTTTACAAATATCGATACTTTCAAGTTTTAGAAAAAATGAAAAATGA
1 AAAGTATGGATATTTGTTTCACAAATACCGATACTTTCAAATTAAAAAAAAAAAGAAAAATGA
180274 TATTTTAACT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
71 11 0.21
72 42 0.79
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (72 bp):
AAAGTATGGATATTTGTTTCACAAATACCGATACTTTCAAATTAAAAAAAAAAAGAAAAATGAGA
AGGCTGC
Found at i:180670 original size:76 final size:74
Alignment explanation
Indices: 180418--180708 Score: 298
Period size: 76 Copynumber: 3.8 Consensus size: 74
180408 TTTATAATAA
* * * * * *** *
180418 AAAATATTAAAATTGCATATCGCAACCTACTTTCTTAGTAAACCTTAACATTCTTGGACACAATC
1 AAAATATTAACATT-CAAATCGCAA-CTA-TTTCTTAGTGAACCATGACATTCTTGGGTGCAACC
180483 CATTTTATTAAT
63 CATTTTATTAAT
* * * * *
180495 AAAAATATTAACATTTCAAATTGTAACATATTTCTTAGTGAACCAAGACATTTTTGGG-GCAACT
1 -AAAATATTAACA-TTCAAATCGCAAC-TATTTCTTAGTGAACCATGACATTCTTGGGTGCAACC
*
180559 CATTTGATTAA-
63 CATTTTATTAAT
* * *
180570 AAAATATTAACATTCTAGATCGCAACTCATTTATTAGTGAACCATGACATTCTTGGGTGTAACCC
1 AAAATATTAACATTC-AAATCGCAACT-ATTTCTTAGTGAACCATGACATTCTTGGGTGCAACCC
180635 ATTTTATTAAT
64 ATTTTATTAAT
* *
180646 AAAATATTAACATTCGAAATCGCAACTTATTTCTTAGTAAACCATGACATTCTTGGGTTCAAC
1 AAAATATTAACATTC-AAATCGCAAC-TATTTCTTAGTGAACCATGACATTCTTGGGTGCAAC
180709 TCTATTTCTT
Statistics
Matches: 177, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
73 4 0.02
74 45 0.25
75 14 0.08
76 68 0.38
77 24 0.14
78 20 0.11
79 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (74 bp):
AAAATATTAACATTCAAATCGCAACTATTTCTTAGTGAACCATGACATTCTTGGGTGCAACCCAT
TTTATTAAT
Found at i:189851 original size:20 final size:21
Alignment explanation
Indices: 189807--189851 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
189797 GATTTCTGGG
* *
189807 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
189828 CAAGGGGAACCGAT-CCCCTT
1 CAAGGGGAACCGATACCCATT
189848 CAAG
1 CAAG
189852 CGCCCTCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:190428 original size:23 final size:24
Alignment explanation
Indices: 190385--190431 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
190375 CTATGGCATG
*
190385 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
190409 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
190432 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:190679 original size:30 final size:31
Alignment explanation
Indices: 190641--190793 Score: 231
Period size: 30 Copynumber: 5.0 Consensus size: 31
190631 AGGGTCGAGG
190641 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
190672 G-TTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
190702 G-TTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
190732 GTTTA-CTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
190762 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
190793 G
1 G
190794 AATAAAGTGA
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 86 0.76
31 27 0.24
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:193883 original size:21 final size:21
Alignment explanation
Indices: 193857--193902 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
193847 GATTTCTGGG
* *
193857 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
193878 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
193899 CAAG
1 CAAG
193903 CGATAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:194540 original size:23 final size:24
Alignment explanation
Indices: 194497--194543 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
194487 ATATGGCATG
*
194497 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
194521 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
194544 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:194797 original size:31 final size:31
Alignment explanation
Indices: 194759--194945 Score: 277
Period size: 31 Copynumber: 6.0 Consensus size: 31
194749 AGGGTCGAGG
*
194759 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
194790 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
194821 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
194852 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
194883 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
194914 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
194945 G
1 G
194946 GTCCTTTGGG
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
31 143 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:206399 original size:16 final size:14
Alignment explanation
Indices: 206365--206401 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
206355 GGAAATTATC
*
206365 TTCTCTTTCTTCTT
1 TTCTCTCTCTTCTT
206379 TTCTCTCTCTTCTT
1 TTCTCTCTCTTCTT
206393 TTCTCTCTC
1 TTCTCTCTC
206402 CCACCATCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCTCTCTCTTCTT
Found at i:209890 original size:180 final size:179
Alignment explanation
Indices: 209583--210119 Score: 729
Period size: 180 Copynumber: 3.0 Consensus size: 179
209573 CCAACCAAAT
* * * * *
209583 TTTCTGCATAACATAGTAAATAACCATTATCATCTCCAAGTTCATTACCATCTTCTGCATAACCA
1 TTTCTGCATAACATAGTTAATAACCATTATTATTTCAAAGTTCATTATCATCTTCTGCATAACCA
* * *
209648 AGAACTTATCAGAAGGAAATAAACAACATACTTTGAACAGTAGAAGCATGCTTTGATGTTTTCTG
66 AGAACTTATCAGAA-GAAAAAAACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTG
* *
209713 ACAAGTTGCATTCTTGGGTAATGAGTGGTCATTGAGCAAACCCTTCTTAG
130 ACAACTTGCATTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
* *
209763 TTTCTGCATTACATAGTTAATAACCATTATTATTTCAAAGTTCATTATCATCTTCTTCATAACCA
1 TTTCTGCATAACATAGTTAATAACCATTATTATTTCAAAGTTCATTATCATCTTCTGCATAACCA
* *
209828 AGAACTCATCAGAAGAAAAAACACAACATACTTTGAACAGCAGAAGCATCCTTTGCTGTTTTCTG
66 AGAACTTATCAGAAGAAAAAA-ACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTG
*
209893 ACAACTTGCATTCTTGGGTAATGAGTGGTCATTGAGCAAGCTCTTCTTAG
130 ACAACTTGCATTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
* * * * * **
209943 TTTCTGCATAACATAGTTAATAACCTTTATTATTTCTAGGCTCATTATCATATTCTGCA-ATATT
1 TTTCTGCATAACATAGTTAATAACCATTATTATTTCAAAGTTCATTATCATCTTCTGCATA-ACC
* * * * * *
210007 AAGAACTTATCAGAAG--GAAAACGACATACTTCGAACAGCAGAAGCATCCTTTGGTTTTTTCAG
65 AAGAACTTATCAGAAGAAAAAAACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTG
* * * * *
210070 ACCACTTGCACTCTTGGGTGATGAGTGATCATTGTGCAAACTCTTCTTAG
130 ACAACTTGCATTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
210120 CTATGACTTT
Statistics
Matches: 318, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
177 82 0.26
178 3 0.01
179 7 0.02
180 226 0.71
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (179 bp):
TTTCTGCATAACATAGTTAATAACCATTATTATTTCAAAGTTCATTATCATCTTCTGCATAACCA
AGAACTTATCAGAAGAAAAAAACAACATACTTTGAACAGCAGAAGCATCCTTTGATGTTTTCTGA
CAACTTGCATTCTTGGGTAATGAGTGGTCATTGAGCAAACTCTTCTTAG
Found at i:214091 original size:51 final size:51
Alignment explanation
Indices: 214015--214115 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
214005 TAAGGAAAGG
* *
214015 ATAGGTTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
214066 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
214116 CTCCCCCTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:218215 original size:6 final size:6
Alignment explanation
Indices: 218204--218232 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
218194 TGTGTCCACA
218204 CTCACT CTCACT CTCACT CTCACT CTCAC
1 CTCACT CTCACT CTCACT CTCACT CTCAC
218233 ACAAGTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.52, G:0.00, T:0.31
Consensus pattern (6 bp):
CTCACT
Found at i:230328 original size:21 final size:19
Alignment explanation
Indices: 230275--230328 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
230265 CAATGGTAGG
* *
230275 GTCATGTTACTTTATTTTT
1 GTCATGTTCCTTTCTTTTT
230294 GTCATG--CCTTTCTTGTTT
1 GTCATGTTCCTTTCTT-TTT
230312 GTCATGTTCCATTTCTT
1 GTCATGTTCC-TTTCTT
230329 CTTTCTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 6 0.21
20 2 0.07
21 6 0.21
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (19 bp):
GTCATGTTCCTTTCTTTTT
Found at i:239911 original size:822 final size:821
Alignment explanation
Indices: 238329--239974 Score: 3094
Period size: 822 Copynumber: 2.0 Consensus size: 821
238319 TGTTTTCTGG
*
238329 ATTATTGTTCTGTGTTCGTTTTTCTGTTAGTTATTGGTAGATTGCACAACAATTATTATGTTATT
1 ATTATTGTTATGTGTTCGTTTTTCTGTTAGTTATTGGTAGATTGCACAACAATTATTATGTTATT
238394 ATCTATTAAATCATTTTTTCAATTGTATTTGATTTTGATATGGAATTCTTTAAAATAAGCTTGAT
66 ATCTATTAAATCATTTTTTCAATTGTATTTGATTTTGATATGGAATTCTTTAAAATAAGCTTGAT
** *
238459 TTTGGCATTTTTTTTCAAAAATCCAGGAATTATTGTTGATTGAAGTCATTTTTAGGTTTCTAGTT
131 TTTCCCATTTTGTTTCAAAAATCCAGGAATTATTGTTGATTGAAGTCATTTTTAGGTTTCTAGTT
* * *
238524 AGATATAGTTGTTGATATTAGTTGTTCTTGATCATATCTTGTTGAGAAGAAGTAGTGTTGATTAG
196 AGATATAGTTGTTGATATTAGTTGATCTTGATCATATCTTGTTGAGAAGAAGTAATGTTCATTAG
*
238589 ACCATAGGCTTAGAGAGTTGTTTCGGTAAGATTTTCGGTTCTTTCGCTCTGTTTTGGAAACTAAA
261 ACCATAAGCTTAGAGAGTTGTTTCGGTAAGATTTTCGGTTCTTTCGCTCTGTTTTGGAAACTAAA
*
238654 AATTATGCTTTGTTTTGGATATGTTCTTAATGTTTTGTTTTGTTTTCCAAGGTTTTTAATGTGTT
326 AATTATGCTTTGTTTTGGATAAGTTCTTAATGTTTTGTTTTGTTTTCCAAGGTTTTTAATGTGTT
238719 GAGAATTGAGGAAAGTTGGTACATCGTGTTTGGTGGTCATTTGCTAAGTGTTTGGAAGTGATTTC
391 GAGAATTGAGGAAAGTTGGTACATCGTGTTTGGTGGTCATTTGCTAAGTGTTTGGAAGTGATTTC
238784 GATTAGTGGACAACAAAGGTGAATGAATTTCATTCTTAAAGGATGAACATATTCAAAGGTAAAAA
456 GATTAGTGGACAACAAAGGTGAATGAATTTCATTCTTAAAGGATGAACATATTCAAAGGTAAAAA
* *
238849 AAGGTGTAGTTTAGAGTAATTATCTTGTCTTGAATTCTATTTTAAGTGAACTTATATTGATATAC
521 AAGGTGTAGTTTAGAGTAATTATCTTGGCTTGAATTCTATTTTAAGTGAACTTATATTGATACAC
238914 ATAATTAATTTTGGAATATGATATGAAATGATGATTTTGGTATATGCATTGTATATGTGATGTAT
586 ATAATTAATTTTGGAATATGATATGAAATGATGATTTTGGTATATGCATTGTATATGTGATGTAT
238979 AGTGGTTTTGAAAGTGTATGTATATGAATGTATTAACGATGAGTGGAACAACTTCACTATCCATG
651 AGTGGTTTTGAAAGTGTATGTATATGAATGTATTAACGATGAGTGGAACAACTTCACTATCCATG
*
239044 GATGAGTGAGAAACGTGTTGTCCATATAAGGTTGATCATGGCAACCATTTCTGATAAGTGTTTCA
716 GATGAGTGAGAAACGTGTTGTCCATATAAGATTGATCATGGCAACCATTTCTGATAAGTGTTTCA
239109 AAGTGTATTTTGGAAGTGTATATGTGTATAATTTATGCATC
781 AAGTGTATTTTGGAAGTGTATATGTGTATAATTTATGCATC
239150 ATTATTGTTATGTGTTCGTTTTTCTGTTAGTTATTGGTAGATTGCACAACAATTATTATGTTATT
1 ATTATTGTTATGTGTTCGTTTTTCTGTTAGTTATTGGTAGATTGCACAACAATTATTATGTTATT
239215 ATCTATTAAATCATTTTTTCAATTGTATTTGATTTTGATATGGAATTCTTTAAAATAAGCTTGAT
66 ATCTATTAAATCATTTTTTCAATTGTATTTGATTTTGATATGGAATTCTTTAAAATAAGCTTGA-
*
239280 TTTTCCCCTTTTGTTTCAAAAATCCAGGAATTATTGTTGATTGAAGTCATTTTTAGGTTTCTAGT
130 TTTTCCCATTTTGTTTCAAAAATCCAGGAATTATTGTTGATTGAAGTCATTTTTAGGTTTCTAGT
*
239345 TGGATATAGTTGTTGATATTAGTTGATCTTGATCATATCTTGTTGAGAAGAAGTAATGTTCATTA
195 TAGATATAGTTGTTGATATTAGTTGATCTTGATCATATCTTGTTGAGAAGAAGTAATGTTCATTA
*
239410 GATCATAAGCTTAGAGAGTTGTTTCGGTAAGATTTTCGGTTCTTTCGCTCTGTTTTGGAAACTAA
260 GACCATAAGCTTAGAGAGTTGTTTCGGTAAGATTTTCGGTTCTTTCGCTCTGTTTTGGAAACTAA
239475 AAATTATGCTTTGTTTTGGATAAGTTCTTAATGTTTTGTTTTGTTTTCCAAGGTTTTTAATGTGT
325 AAATTATGCTTTGTTTTGGATAAGTTCTTAATGTTTTGTTTTGTTTTCCAAGGTTTTTAATGTGT
* *
239540 TGAGAATTGAGGAAATTTGGTGCATCGTGTTTGGTGGTCATTTGCTAAGTGTTTGGAAGTGATTT
390 TGAGAATTGAGGAAAGTTGGTACATCGTGTTTGGTGGTCATTTGCTAAGTGTTTGGAAGTGATTT
239605 CGATTAGTGGACAACAAAGGTGAATGAATTTCATTCTTAAAGGATGAACATATTCAAAGGTAAAA
455 CGATTAGTGGACAACAAAGGTGAATGAATTTCATTCTTAAAGGATGAACATATTCAAAGGTAAAA
*
239670 AAAGGTTTAGTTTAGAGTAATTATCTTGGCTTGAATTCTATTTTAAGTGAACTTATATTGATACA
520 AAAGGTGTAGTTTAGAGTAATTATCTTGGCTTGAATTCTATTTTAAGTGAACTTATATTGATACA
* *
239735 CATAATTAATTTTGGAATATGATATGAAATGATGATTTTGGTATATGTATTGTATTTGTGATGTA
585 CATAATTAATTTTGGAATATGATATGAAATGATGATTTTGGTATATGCATTGTATATGTGATGTA
*
239800 TAGTGGTTTTGAAAGTGTATGTATATGAATGTATTAAGGATGAGTGGAACAACTTCACTATCCAT
650 TAGTGGTTTTGAAAGTGTATGTATATGAATGTATTAACGATGAGTGGAACAACTTCACTATCCAT
239865 GGATGAGTGAGAAACGTGTTGTCCATATAAGATTGATCATGGCAACCATTTCTGATAAGTGTTTC
715 GGATGAGTGAGAAACGTGTTGTCCATATAAGATTGATCATGGCAACCATTTCTGATAAGTGTTTC
239930 AAAGTGTATTTTGGAAGTGTATATGTGTATAATTTATGCATC
780 AAAGTGTATTTTGGAAGTGTATATGTGTATAATTTATGCATC
239972 ATT
1 ATT
239975 TGATAAGAAC
Statistics
Matches: 803, Mismatches: 21, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
821 128 0.16
822 675 0.84
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.43
Consensus pattern (821 bp):
ATTATTGTTATGTGTTCGTTTTTCTGTTAGTTATTGGTAGATTGCACAACAATTATTATGTTATT
ATCTATTAAATCATTTTTTCAATTGTATTTGATTTTGATATGGAATTCTTTAAAATAAGCTTGAT
TTTCCCATTTTGTTTCAAAAATCCAGGAATTATTGTTGATTGAAGTCATTTTTAGGTTTCTAGTT
AGATATAGTTGTTGATATTAGTTGATCTTGATCATATCTTGTTGAGAAGAAGTAATGTTCATTAG
ACCATAAGCTTAGAGAGTTGTTTCGGTAAGATTTTCGGTTCTTTCGCTCTGTTTTGGAAACTAAA
AATTATGCTTTGTTTTGGATAAGTTCTTAATGTTTTGTTTTGTTTTCCAAGGTTTTTAATGTGTT
GAGAATTGAGGAAAGTTGGTACATCGTGTTTGGTGGTCATTTGCTAAGTGTTTGGAAGTGATTTC
GATTAGTGGACAACAAAGGTGAATGAATTTCATTCTTAAAGGATGAACATATTCAAAGGTAAAAA
AAGGTGTAGTTTAGAGTAATTATCTTGGCTTGAATTCTATTTTAAGTGAACTTATATTGATACAC
ATAATTAATTTTGGAATATGATATGAAATGATGATTTTGGTATATGCATTGTATATGTGATGTAT
AGTGGTTTTGAAAGTGTATGTATATGAATGTATTAACGATGAGTGGAACAACTTCACTATCCATG
GATGAGTGAGAAACGTGTTGTCCATATAAGATTGATCATGGCAACCATTTCTGATAAGTGTTTCA
AAGTGTATTTTGGAAGTGTATATGTGTATAATTTATGCATC
Found at i:244846 original size:2 final size:2
Alignment explanation
Indices: 244841--244890 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
244831 ACACACACAC
244841 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
244883 AT AT AT AT
1 AT AT AT AT
244891 GTTTAGGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247229 original size:26 final size:26
Alignment explanation
Indices: 247198--247247 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
247188 CTAACGTGGT
*
247198 AGTTTCTAGAAGGTCTAGTCAGCGGC
1 AGTTTCTAGAAGATCTAGTCAGCGGC
*
247224 AGTTTCTAGAAGATCTAGTTAGCG
1 AGTTTCTAGAAGATCTAGTCAGCG
247248 CGCCTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (26 bp):
AGTTTCTAGAAGATCTAGTCAGCGGC
Found at i:254903 original size:2 final size:2
Alignment explanation
Indices: 254896--254974 Score: 126
Period size: 2 Copynumber: 40.0 Consensus size: 2
254886 TCTATACATC
254896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
254938 TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
254975 ATAAAAATAA
Statistics
Matches: 73, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
1 2 0.03
2 69 0.95
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:254987 original size:23 final size:22
Alignment explanation
Indices: 254961--255032 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
254951 ATATATAATG
254961 ATATAAGATATATAATAAAAATA
1 ATAT-AGATATATAATAAAAATA
*
254984 ATATA-ATATA-AATAAAAAGGA
1 ATATAGATATATAATAAAAA-TA
*
255005 ATATAG-TAAATAAATAAAAATA
1 ATATAGATATAT-AATAAAAATA
255027 TATATA
1 -ATATA
255033 ATTAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
20 8 0.20
21 14 0.34
22 2 0.05
23 17 0.41
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
ATATAGATATATAATAAAAATA
Found at i:254992 original size:19 final size:19
Alignment explanation
Indices: 254970--255048 Score: 72
Period size: 19 Copynumber: 4.0 Consensus size: 19
254960 GATATAAGAT
254970 ATATAATAAAAATAATATA
1 ATATAATAAAAATAATATA
*
254989 ATATAAATAAAAAGGAATATA
1 ATAT-AATAAAAA-TAATATA
* *
255010 GTA-AATAAATAAAAATAT-
1 ATATAATAAA-AATAATATA
255028 ATATAATTAAAAATATATATA
1 ATATAA-TAAAAATA-ATATA
255049 TAGGGGACGA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
18 2 0.04
19 20 0.42
20 18 0.38
21 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
ATATAATAAAAATAATATA
Found at i:255038 original size:16 final size:16
Alignment explanation
Indices: 254901--255048 Score: 73
Period size: 16 Copynumber: 8.6 Consensus size: 16
254891 ACATCTATAT
* * *
254901 ATATATATATATATAT
1 ATATATATAAATAAAA
* * *
254917 ATATATATATATATAT
1 ATATATATAAATAAAA
* * *
254933 ATATATATATATATAT
1 ATATATATAAATAAAA
*
254949 ATATATATAATGATATAAG
1 ATATATATAA--ATA-AAA
*
254968 ATATATAATAAA-AATA
1 ATATAT-ATAAATAAAA
254984 ATATAATATAAATAAAAAGGA
1 ATAT-ATATAAAT--AAA--A
255005 ATATAGTAAATAAATAAAA
1 ATATA-T--ATAAATAAAA
*
255024 ATATATATAATTAAAA
1 ATATATATAAATAAAA
255040 ATATATATA
1 ATATATATA
255049 TAGGGGACGA
Statistics
Matches: 112, Mismatches: 7, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
16 69 0.62
17 3 0.03
18 5 0.04
19 15 0.13
20 5 0.04
21 9 0.08
23 6 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATATATAAATAAAA
Found at i:256187 original size:85 final size:83
Alignment explanation
Indices: 256045--256273 Score: 219
Period size: 85 Copynumber: 2.7 Consensus size: 83
256035 AGTGTGATTG
* * * * * ** * * *
256045 ATGTGTCATCGAGCTGAATGGAATCAAACTCGAAAATTTTTGTTGACAGATAGCCCTTCTTGCCT
1 ATGTGTCTTGGAGATGAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTTGCCT
*
256110 TAACCTATGCTGTAAATT
66 TAACCTATGCTATAAATT
* * *
256128 -TGATTTACCTCT-GAGTTGAATGTAATCGAACTCGAAGGTCTTTGATGATAGATAACCCTTCTT
1 ATG-TGT--CT-TGGAGATGAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTT
* **
256191 GCCTTGAGTTATGCTATAAATT
62 GCCTTAACCTATGCTATAAATT
** * *
256213 ATGTGTCTTGGAGATGAGCGTAGTCGAACTCCAAGGTCTTTGTTGATAGATAACCCTTCTT
1 ATGTGTCTTGGAGATGAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTT
256274 TGAGTTGGAT
Statistics
Matches: 118, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
82 3 0.03
83 49 0.42
85 63 0.53
86 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (83 bp):
ATGTGTCTTGGAGATGAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTTGCCT
TAACCTATGCTATAAATT
Found at i:256660 original size:110 final size:110
Alignment explanation
Indices: 256509--256712 Score: 291
Period size: 110 Copynumber: 1.9 Consensus size: 110
256499 TGGGAAATTG
* * * *
256509 TTTGTTGACAGCCAATCGCCCCTTCGCTGTGAAATTGAGCTTGTGTTGTCTCGAGTTCAATATCA
1 TTTGTTGACAACCAATCACCCCTTCGCTGTGAAATTGAGCTTGTGTTATCTCGAGTCCAATATCA
*
256574 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAGACTGAAAAGTTA
66 TTCGCTGTGAAGTTAAAATTGACTCTGAATGAGACTGAAAAGTTA
* * * * * *
256619 TTTGTTGACAATCAGTCACCCCTTCGTTGTGAAGTTGAGCTTGTGTTATCTTGAGTCCAATATCT
1 TTTGTTGACAACCAATCACCCCTTCGCTGTGAAATTGAGCTTGTGTTATCTCGAGTCCAATATCA
* *
256684 TTCGTTGTGAAGTTAAAATTGGCTCTGAA
66 TTCGCTGTGAAGTTAAAATTGACTCTGAA
256713 ACTGGGAAGC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 81 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAACCAATCACCCCTTCGCTGTGAAATTGAGCTTGTGTTATCTCGAGTCCAATATCA
TTCGCTGTGAAGTTAAAATTGACTCTGAATGAGACTGAAAAGTTA
Found at i:257545 original size:67 final size:65
Alignment explanation
Indices: 257446--257749 Score: 223
Period size: 65 Copynumber: 4.5 Consensus size: 65
257436 ATGAAAACGA
* **
257446 TCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAA
1 TCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGAGAAA
257511 CTG
63 CTG
* * *
257514 TCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGATACTG
1 TCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTG
* ** * ** * * *
257579 TCTCAAGAGAGACAAAATTTGTTACAAGAGAAACTGTCTCAAGAGAGACAAA-ACTTAGTTCCAA
1 TCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-ATTCAAAGATTTTGTTTCAA
*
257643 AAGAAACTG
57 GAGAAACTG
** ** *** * * * * *
257652 TCTCAAGGGAGATGAAATTTGTTGCAAATAAAACATATTCAAATAATTTGTTTCAAGGGAAACTG
1 TCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTG
* *
257717 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
257750 CTGTCTCAAG
Statistics
Matches: 184, Mismatches: 42, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
64 5 0.03
65 85 0.46
66 4 0.02
67 25 0.14
68 16 0.09
70 1 0.01
72 1 0.01
73 42 0.23
74 5 0.03
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (65 bp):
TCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTG
Found at i:257597 original size:65 final size:67
Alignment explanation
Indices: 257446--257601 Score: 226
Period size: 65 Copynumber: 2.3 Consensus size: 67
257436 ATGAAAACGA
* **
257446 TCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAA
1 TCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAA
257511 CTG
65 CTG
* * *
257514 TCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGATAC
1 TCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAAC
257577 TG
66 TG
*
257579 TCTCAAGAGAGACAAAATTTGTT
1 TCTCAAGGGAGACAAAATTTGTT
257602 ACAAGAGAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
65 37 0.46
66 3 0.04
67 25 0.31
68 16 0.20
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (67 bp):
TCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAAC
TG
Found at i:257615 original size:36 final size:36
Alignment explanation
Indices: 257560--257785 Score: 182
Period size: 36 Copynumber: 6.4 Consensus size: 36
257550 ATTCAAAGAT
* *
257560 TTTGTTTCAAGGGATACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
257596 TTTGTTACAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * **
257632 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
257669 TTTGTTGCAA-ATAAAACATAT-TC-----A-A-ATAA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACAAAA
*
257698 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * **
257734 TTTGTTTCAAGGGAAACTGTCTCAAGATAGATGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
257770 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
257786 TGTTTTAAAT
Statistics
Matches: 154, Mismatches: 24, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
30 1 0.01
31 1 0.01
34 1 0.01
35 2 0.01
36 98 0.64
37 32 0.21
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:257657 original size:37 final size:36
Alignment explanation
Indices: 257575--257663 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 36
257565 TTCAAGGGAT
* *
257575 ACTGTCTCAAGAGAGACAAAATTTGTTACAAGAGAA
1 ACTGTCTCAAGAGAGACAAAATTAGTTACAAAAGAA
*
257611 ACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAA
1 ACTGTCTCAAGAGAGACAAAA-TTAGTTACAAAAGAA
*
257648 ACTGTCTCAAGGGAGA
1 ACTGTCTCAAGAGAGA
257664 TGAAATTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
36 21 0.44
37 27 0.56
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (36 bp):
ACTGTCTCAAGAGAGACAAAATTAGTTACAAAAGAA
Found at i:257670 original size:138 final size:138
Alignment explanation
Indices: 257506--257760 Score: 375
Period size: 138 Copynumber: 1.8 Consensus size: 138
257496 GTGTTTCAAG
** ** * * *
257506 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTGCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
*
257571 GGATACTGTCTCAAGAGAGACAAAATTTGTTACAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTACAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
257636 GTTCCAAA
131 GTTCCAAA
** * * *
257644 AGAAACTGTCTCAAGGGAGATGAAATTTGTTGCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTGCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
257709 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTACAAGAGAAACTGTCTCAAGA
257761 TAGATGAAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 102 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTGCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTACAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:257805 original size:101 final size:101
Alignment explanation
Indices: 257594--257872 Score: 290
Period size: 101 Copynumber: 2.7 Consensus size: 101
257584 AGAGAGACAA
* * * *
257594 AATTTGTTACAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAG
* * *
257659 GGAGATGAAATTTGTTGCAAATAAAACATATTCAAAT
65 AGAGATGAAATTTATTGCAAAGAAAACATATTCAAAT
* *
257696 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGA
* * * * ** *
257761 TAGATGAAATTTATTTCAAGGGAAATGT-TTTAAAT
66 GAGATGAAATTTATTGCAAAGAAAACATATTCAAAT
** * * * * * *
257796 GTTTATGTTTCAAAAGAAACTGTCTCAAGGGAGAGAATATTTTGTTTCAAGTGAAACTATCTCAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATTTGTTTCAAGAGAAACTGTCTCAA
* *
257861 GCGAGATAAAAT
64 GAGAGATGAAAT
257873 CTTCTTTTTA
Statistics
Matches: 147, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
100 8 0.05
101 70 0.48
102 69 0.47
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGA
GAGATGAAATTTATTGCAAAGAAAACATATTCAAAT
Found at i:259567 original size:26 final size:25
Alignment explanation
Indices: 259525--259584 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
259515 TTTTTCTTCA
* *
259525 ATTTTC-CTTTGTTTTTTCTCTTTTT
1 ATTTTCTCTTTGCTTTTTCTC-TCTT
*
259550 ATTTTCTCTTTGCTTTTTTTCTCTT
1 ATTTTCTCTTTGCTTTTTCTCTCTT
259575 -TTTTCTCTTT
1 ATTTTCTCTTT
259585 TTGTTCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 12 0.39
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (25 bp):
ATTTTCTCTTTGCTTTTTCTCTCTT
Found at i:259569 original size:15 final size:13
Alignment explanation
Indices: 259526--259578 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
259516 TTTTCTTCAA
*
259526 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
259538 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
259551 TTTTCTCTTTGCTTT
1 TTTTCTCTTT--TTT
259566 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
259579 CTCTTTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 5 0.14
13 18 0.51
15 12 0.34
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:259573 original size:28 final size:25
Alignment explanation
Indices: 259525--259577 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 25
259515 TTTTTCTTCA
259525 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
259550 ATTTTCTCTTTGCTTTTTTTCTCTTTTT
1 ATTTTC-CTTTG--TTTTTTCTCTTTTT
259578 TCTCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
28 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:262567 original size:7 final size:7
Alignment explanation
Indices: 262557--262581 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
262547 AAAAATAATA
262557 AATATGT
1 AATATGT
262564 AATATGT
1 AATATGT
262571 AATATGT
1 AATATGT
262578 AATA
1 AATA
262582 CTAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (7 bp):
AATATGT
Found at i:262652 original size:18 final size:19
Alignment explanation
Indices: 262625--262673 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
262615 AGATATTAAG
262625 AAAA-AAAATAATAG-AAA
1 AAAATAAAATAATAGTAAA
262642 AAAATAAAATAA-AGTAAA
1 AAAATAAAATAATAGTAAA
* *
262660 AATATAATATAATA
1 AAAATAAAATAATA
262674 TATATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 20 0.74
19 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAATAAAATAATAGTAAA
Found at i:262722 original size:2 final size:2
Alignment explanation
Indices: 262715--262739 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
262705 AATATTAAGA
262715 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 A
262740 AACGTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:262877 original size:23 final size:23
Alignment explanation
Indices: 262834--262907 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
262824 ATGATATAAG
* *
262834 ATATATATAATAAAAATAATATA
1 ATATAAATAATAAAAAGAATATA
262857 ATATAAATAA-AAAAAGGAATATA
1 ATATAAATAATAAAAA-GAATATA
* *
262880 GTA-AAAAAATAAATAA-AATATA
1 ATATAAATAATAAA-AAGAATATA
262902 AT-TAAA
1 ATATAAA
262908 ATATATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 20 0.48
23 20 0.48
24 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
ATATAAATAATAAAAAGAATATA
Found at i:264392 original size:46 final size:46
Alignment explanation
Indices: 264339--264446 Score: 144
Period size: 46 Copynumber: 2.3 Consensus size: 46
264329 TTATTGGTTG
* *
264339 CATCCTTTCATGCCAATTATTCAACGTTAAGCATTTTCATTTATGA
1 CATCCTTTCATGCCAATAATACAACGTTAAGCATTTTCATTTATGA
* * * * * *
264385 TATCCTTTCATACCGATAATACACCGTTATGCATTTTCATTTATGG
1 CATCCTTTCATGCCAATAATACAACGTTAAGCATTTTCATTTATGA
264431 CATCCTTTCATGCCAA
1 CATCCTTTCATGCCAA
264447 AGGCATTTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (46 bp):
CATCCTTTCATGCCAATAATACAACGTTAAGCATTTTCATTTATGA
Found at i:264544 original size:81 final size:81
Alignment explanation
Indices: 264444--264640 Score: 288
Period size: 81 Copynumber: 2.4 Consensus size: 81
264434 CCTTTCATGC
* * **
264444 CAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTTGCATTATTGACACCTTTCTACCAAATGCACAGCCAGG
264509 CAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* * * ** *
264525 TAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCCATG
1 CAAAGGTATTTAACCTTTCATCTAACTTGCATTATTGACACCTTTCTACCAAATGCACAGCCAGG
264590 CAATTAATCTTTTACT
66 CAATTAATCTTTTACT
264606 CAAAGGTATTTAACCTTTCATCTAAC-TGCCATTAT
1 CAAAGGTATTTAACCTTTCATCTAACTTG-CATTAT
264641 GTATACCTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 101 0.99
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTTGCATTATTGACACCTTTCTACCAAATGCACAGCCAGG
CAATTAATCTTTTACT
Found at i:264648 original size:27 final size:27
Alignment explanation
Indices: 264618--264678 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
264608 AAGGTATTTA
*
264618 ACCTTTCATCTAACTGCCATTA-TGTAT
1 ACCTTTCATCTAACTGCAATTATTG-AT
*
264645 ACCTTTCATCTAACTGGAATTATTGAT
1 ACCTTTCATCTAACTGCAATTATTGAT
264672 ACCTTTC
1 ACCTTTC
264679 TATCAAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (27 bp):
ACCTTTCATCTAACTGCAATTATTGAT
Found at i:264726 original size:108 final size:108
Alignment explanation
Indices: 264537--264741 Score: 320
Period size: 108 Copynumber: 1.9 Consensus size: 108
264527 AAGGTATTTA
* * * * *
264537 ACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCCATGCAATTAATCTTT
1 ACCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAACCAGGCAATTAATATTT
264602 TACTCAAAGGTATTTAACCTTTCATCTAACTGCCATTATGTAT
66 TACTCAAAGGTATTTAACCTTTCATCTAACTGCCATTATGTAT
* * *
264645 ACCTTTCATCTAACTGGAATTATTGATACCTTTCTATCAAATGCACAACTAGGCAATTAATATTT
1 ACCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAACCAGGCAATTAATATTT
* *
264710 TACTTAGAGGTATTTAACCTTTCATCTAACTG
66 TACTCAAAGGTATTTAACCTTTCATCTAACTG
264742 TCAGGATTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 87 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (108 bp):
ACCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAACCAGGCAATTAATATTT
TACTCAAAGGTATTTAACCTTTCATCTAACTGCCATTATGTAT
Found at i:264784 original size:81 final size:81
Alignment explanation
Indices: 264645--265105 Score: 642
Period size: 80 Copynumber: 5.7 Consensus size: 81
264635 CATTATGTAT
* * * * *
264645 ACCTTTCATCTAACTGGAATTATTGATACCTTTCTATCAAATGCACAACTAGGCAATTAATATTT
1 ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATATTT
* *
264710 TACTTAGAGGTATTTA
66 TACTCAAAGGTATTTA
* * * * * * *
264726 ACCTTTCATCTAACTGTCAGGATTAACACCTTTTTGTCAAATACATAGCTAGGTAATTAATATTT
1 ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATATTT
264791 TACTCAAAGGTATTTA
66 TACTCAAAGGTATTTA
* * * * *
264807 ACCTTTCATCTAACTGGCATGACTGACACCTTTATGTCAAATGCACAACTAAGTAATTAAT-TTT
1 ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATATTT
*
264871 TACTCAAAGGTAATTA
66 TACTCAAAGGTATTTA
*
264887 GCCTTTCATCTAACTGGCATGATTGACACCTTTCTGT-AGAA-GCACAGCTAGGCAATTAATATT
1 ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCA-AATGCACAGCTAGGCAATTAATATT
* *
264950 TTGCTCAAAGATATTTA
65 TTACTCAAAGGTATTTA
*
264967 ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACATCTAGGC-ATTAATATTT
1 ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATATTT
*
265031 TACTCAAAGCTATTTA
66 TACTCAAAGGTATTTA
* *
265047 ACCTTTCATCTAACTGTCATGATTGACACCTTTCTATCAAATGCACAGCTAGGCAATTA
1 ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTA
265106 GTCTTTTATT
Statistics
Matches: 335, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
79 17 0.05
80 183 0.55
81 135 0.40
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (81 bp):
ACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATATTT
TACTCAAAGGTATTTA
Found at i:264786 original size:189 final size:189
Alignment explanation
Indices: 264456--264822 Score: 554
Period size: 189 Copynumber: 1.9 Consensus size: 189
264446 AAGGCATTTA
* * * ** *
264456 ACCTTTCATCTAACTTGCATTATTGGCACCTTTCTACCAAATGCACAGTTAGGCAATTAATCTTT
1 ACCTTTCATCTAACTGGAATTATTGACACCTTTCTACCAAATGCACAACTAGGCAATTAATATTT
* * *
264521 TACTTAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGC
66 TACTTAAAGGTATTTAACCTTTCATCTAACTGGCAGAATTAACACCTTTCTGTCAAATACACAGC
* *
264586 CATGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCCATTATGTAT
131 CAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCCATTATGTAT
* *
264645 ACCTTTCATCTAACTGGAATTATTGATACCTTTCTATCAAATGCACAACTAGGCAATTAATATTT
1 ACCTTTCATCTAACTGGAATTATTGACACCTTTCTACCAAATGCACAACTAGGCAATTAATATTT
* * * * *
264710 TACTTAGAGGTATTTAACCTTTCATCTAACTGTCAGGATTAACACCTTTTTGTCAAATACATAGC
66 TACTTAAAGGTATTTAACCTTTCATCTAACTGGCAGAATTAACACCTTTCTGTCAAATACACAGC
* *
264775 TAGGTAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTG
131 CAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTG
264823 GCATGACTGA
Statistics
Matches: 158, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
189 158 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (189 bp):
ACCTTTCATCTAACTGGAATTATTGACACCTTTCTACCAAATGCACAACTAGGCAATTAATATTT
TACTTAAAGGTATTTAACCTTTCATCTAACTGGCAGAATTAACACCTTTCTGTCAAATACACAGC
CAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCCATTATGTAT
Found at i:271775 original size:30 final size:30
Alignment explanation
Indices: 271738--271807 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
271728 AGAGTCAATA
*
271738 CGTTGACTTTAACCGAGTTAACCAGGTGA-
1 CGTTGACTTTAACCGAGTCAACCAGGTGAT
* *
271767 CTGTTGACTTTAACCGAGTCAACCCGTTGAT
1 C-GTTGACTTTAACCGAGTCAACCAGGTGAT
271798 CGTTGACTTT
1 CGTTGACTTT
271808 GATTAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.03
30 34 0.94
31 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (30 bp):
CGTTGACTTTAACCGAGTCAACCAGGTGAT
Found at i:274283 original size:21 final size:21
Alignment explanation
Indices: 274257--274314 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
274247 TCCGAGTTAC
* *
274257 CCGCGACTGTCGCAATAGCGT
1 CCGCGACAGCCGCAATAGCGT
*
274278 CCGCGACAGCCGCAATAGCGC
1 CCGCGACAGCCGCAATAGCGT
* *
274299 CCACGACGGCCGCAAT
1 CCGCGACAGCCGCAAT
274315 CACGGTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.40, G:0.28, T:0.10
Consensus pattern (21 bp):
CCGCGACAGCCGCAATAGCGT
Found at i:279064 original size:3 final size:3
Alignment explanation
Indices: 279056--279118 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
279046 TTTTTATTTT
* * *
279056 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TAA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
279104 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
279119 AATAATAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:284461 original size:15 final size:15
Alignment explanation
Indices: 284443--284474 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
284433 GGATCATACC
284443 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
284458 TTTTGCATACATTCA
1 TTTTGCATACATGCA
284473 TT
1 TT
284475 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:287042 original size:161 final size:165
Alignment explanation
Indices: 286777--287104 Score: 619
Period size: 161 Copynumber: 2.0 Consensus size: 165
286767 ATACCCCAAA
286777 AGGTATTTGATGATGAATCCCCTCCAGTATTCAATGAGCCTGTAACAGAAAAACAAGCTCAAGAA
1 AGGTATTTGATGATGAATCCCCTCCAGTATTCAATGAGCCTGTAACAGAAAAACAAGCTCAAGAA
286842 TTTTTGAAATTCCTGAAACATAGTGAGTATAGTGTGGTTGAA-AACTACACAAACAACAAGCGAG
66 TTTTTGAAATTCCTGAAACATAGTGAGTATAGTGTGGTTGAACAACTACACAAACAACAAGCGAG
286906 AA-TTCTATTCTTGATCTA-T-TGAATTCAGAAGC
131 AATTTCTATTCTTGATCTATTATGAATTCAGAAGC
286938 AGGTATTTGATGATGAATCCCCTCCAGTATTCAATGAGCCTGTAACAGAAAAACAAGCTCAAGAA
1 AGGTATTTGATGATGAATCCCCTCCAGTATTCAATGAGCCTGTAACAGAAAAACAAGCTCAAGAA
287003 TTTTTGAAATTCCTGAAACATAGTGAGTATAGTGTGGTTGAACAACTACACAAACAACAAGCGAG
66 TTTTTGAAATTCCTGAAACATAGTGAGTATAGTGTGGTTGAACAACTACACAAACAACAAGCGAG
287068 AATTTCTATTCTTGATCTATTGATGAATTCAGAAGC
131 AATTTCTATTCTTGATCTATT-ATGAATTCAGAAGC
287104 A
1 A
287105 CATAAAAATG
Statistics
Matches: 162, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
161 107 0.66
162 24 0.15
163 16 0.10
164 1 0.01
166 14 0.09
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (165 bp):
AGGTATTTGATGATGAATCCCCTCCAGTATTCAATGAGCCTGTAACAGAAAAACAAGCTCAAGAA
TTTTTGAAATTCCTGAAACATAGTGAGTATAGTGTGGTTGAACAACTACACAAACAACAAGCGAG
AATTTCTATTCTTGATCTATTATGAATTCAGAAGC
Found at i:291924 original size:14 final size:13
Alignment explanation
Indices: 291908--291963 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
291898 TTGCTTGAAG
291908 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
*
291921 GAAAAAAAAGAAA
1 AAAAAAAAAGAAA
291934 AAAAATAAAA-AAA
1 AAAAA-AAAAGAAA
291947 AAAGAGAAAAAGAAA
1 AAA-A-AAAAAGAAA
291962 AA
1 AA
291964 GGGTCAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 22 0.59
14 9 0.24
15 6 0.16
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:291937 original size:22 final size:22
Alignment explanation
Indices: 291905--291957 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
291895 TATTTGCTTG
291905 AAGA-AAAAAAAAGAAAGAAAAA
1 AAGAGAAAAAAAAGAAA-AAAAA
*
291927 AA-AGAAAAAAAATAAAAAAAA
1 AAGAGAAAAAAAAGAAAAAAAA
291948 AAGAGAAAAA
1 AAGAGAAAAA
291958 GAAAAAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (22 bp):
AAGAGAAAAAAAAGAAAAAAAA
Found at i:293275 original size:91 final size:92
Alignment explanation
Indices: 292938--293286 Score: 549
Period size: 93 Copynumber: 3.9 Consensus size: 92
292928 TAGTATCTTT
* *
292938 TGGAAGTGTTCTTTGAGTTATATGATCTGGTTTGGTATGAACCTCAAAAAACCAATCATTGAATT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAA-CTCAAAAAACCAATCATTGAATT
293003 TGGAAGATGAATGTGCTCATAGCATTTTC
65 TGGAAGATGAATGTGCTCATAGCA-TTTC
293032 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACTCAAAAAACCAATCATTGAATTT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACTCAAAAAACCAATCATTGAATTT
293097 GGAAGATGAATGTGCTCAT---A--TC
66 GGAAGATGAATGTGCTCATAGCATTTC
*
293119 TGGAAGTGTTCTCTTTGAGTTATC---TCTGGTTTGGTATGAACCTC-AAAAACC-ATCATTGAA
1 TGGAAGTG-T-TCTTTGAGTTATCTGATCTGGTTTGATATGAA-CTCAAAAAACCAATCATTGAA
293179 TTTGGAAGATGAATGTGCTCATAGCATTTC
63 TTTGGAAGATGAATGTGCTCATAGCATTTC
293209 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAC-CAAAAAACCAATCATTGAATTT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACTCAAAAAACCAATCATTGAATTT
293273 GGAAGATGAATGTG
66 GGAAGATGAATGTG
293287 GTATGAACCT
Statistics
Matches: 238, Mismatches: 4, Indels: 29
0.88 0.01 0.11
Matches are distributed among these distances:
85 31 0.13
86 22 0.09
87 13 0.05
88 15 0.06
89 15 0.06
90 19 0.08
91 41 0.17
93 43 0.18
94 39 0.16
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (92 bp):
TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACTCAAAAAACCAATCATTGAATTT
GGAAGATGAATGTGCTCATAGCATTTC
Found at i:293320 original size:45 final size:44
Alignment explanation
Indices: 293244--293331 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 44
293234 TCTGGTTTGA
293244 TATGAACCAAAAAACCAATCATTGAATTTGGAAGATGAATGTGG
1 TATGAACCAAAAAACCAATCATTGAATTTGGAAGATGAATGTGG
293288 TATGAACCTCAAAAAACCAATCATTG-ATTTGGAAGATGAATGTG
1 TATGAA-C-CAAAAAACCAATCATTGAATTTGGAAGATGAATGTG
293332 CTCATAGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
44 6 0.14
45 19 0.45
46 17 0.40
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (44 bp):
TATGAACCAAAAAACCAATCATTGAATTTGGAAGATGAATGTGG
Found at i:294500 original size:223 final size:226
Alignment explanation
Indices: 294200--294871 Score: 924
Period size: 223 Copynumber: 3.0 Consensus size: 226
294190 GCAAAGATTA
*
294200 AAATCCATCACTTGATGGATTAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATCCATCAC-TGATGGA-TAGCATTTCCAGAGAGAGTTCATAATGAGAAGAAC-CGTCATCTG
294265 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTG
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTG
294330 ATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACGTCAT-TGAAGAAGGAAGAAGAAT
128 ATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACGTCATCTGAAGAAGGAAGAAGAA-
294394 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
192 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
294429 AAATCCATCACTGATGGATCAGC-TTTCCAGAGAAAG-TCATAATGAGAAGAA-C-TCATCTGAA
1 AAATCCATCACTGATGGAT-AGCATTTCCAGAGAGAGTTCATAATGAGAAGAACCGTCATCTGAA
294490 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGAT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGAT
*
294555 GG--TAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAG
130 GGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--CGTCATCTGAAGAAGGAAGAAGAAT
* *
294618 TCAT-ATGAGAAGAATTTGTTCAACCTTTTGTTT
193 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
294651 AAATTCATCATTTGATGGATTGACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATCCATCA-CTGATGGATAG-CATTTCCAGAG-AGAGTTCATAATGAGAAGAAC-CGTCATCT
* * *
294715 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TCTCAAATCCATCACT
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT-TTAAATTCATCATT
* * * * * *
294779 TAATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAAC-TCATCTGAAGAA-GAAGAAG
126 TGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACGTCATCTGAAGAAGGAAGAAG
* * **
294841 --TTCACAATAAGAAGAGCTTGTTCAACCTTTT
190 AATTCATAATGAGAAGAATTTGTTCAACCTTTT
294872 ACATAATTTT
Statistics
Matches: 403, Mismatches: 23, Indels: 38
0.87 0.05 0.08
Matches are distributed among these distances:
221 34 0.08
222 37 0.09
223 96 0.24
224 30 0.07
225 37 0.09
226 22 0.05
227 27 0.07
228 81 0.20
229 11 0.03
230 27 0.07
231 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (226 bp):
AAATCCATCACTGATGGATAGCATTTCCAGAGAGAGTTCATAATGAGAAGAACCGTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATG
GATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACGTCATCTGAAGAAGGAAGAAGAATTCA
TAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:294835 original size:116 final size:115
Alignment explanation
Indices: 294200--294871 Score: 841
Period size: 116 Copynumber: 6.0 Consensus size: 115
294190 GCAAAGATTA
* * *
294200 AAATCCATCACTTGATGGATTAGCTTTTCCAGAG-AGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATCCATCACTTGATGGA-TAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCT
294264 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * *
294316 AAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--CGTCAT-TG
1 AAATCCATCACTTGATGGA-TAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
* * *
294378 AAGAAGGAAGAAGAATTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* *
294429 AAATCCATCAC-TGATGGATCAGC-TTTCCAGAG-AAAG-TCATAATGAGAAGAA--C-TCATCT
1 AAATCCATCACTTGATGGAT-AGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCT
294487 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * *
294539 AAATTCATCATTTGATGG-TAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGA
1 AAATCCATCACTTGATGGATAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGA
294603 AGAAGGAAGAAGAAG-TCAT-ATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * *
294651 AAATTCATCATTTGATGGATTGACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATCCATCACTTGATGGATAG-CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
*
294716 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TCTC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT-TT
* * * *
294767 AAATCCATCACTTAATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCT
1 AAATCCATCACTTGATGGAT-AGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCT
* * **
294828 ---GAA-GAAGAAGAAGTTCACAATAAGAAGAGCTTGTTCAACCTTTT
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
294872 ACATAATTTT
Statistics
Matches: 503, Mismatches: 35, Indels: 43
0.87 0.06 0.07
Matches are distributed among these distances:
109 44 0.09
110 88 0.17
111 31 0.06
112 57 0.11
113 71 0.14
114 88 0.17
115 6 0.01
116 116 0.23
117 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (115 bp):
AAATCCATCACTTGATGGATAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
Found at i:295112 original size:3 final size:3
Alignment explanation
Indices: 295106--295132 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
295096 ACATTTTTAT
295106 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
295133 AATAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:303191 original size:64 final size:65
Alignment explanation
Indices: 303041--303202 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
303031 AATTAAATTG
* * *
303041 AACATCGAATGCATTTCATGGATCGATGCACTTACCATGCACCGATACACTAAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATACACTAAGGATTTTATGAA
* * ** *
303106 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGCACCGATACACTAAGGAT-TTTATG
303169 -A
64 AA
*
303170 AACATCGAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
303203 TTAGTGCACC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 32 0.38
65 50 0.59
66 3 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATACACTAAGGATTTTATGAA
Found at i:309045 original size:24 final size:23
Alignment explanation
Indices: 309018--309098 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
309008 ACACTTAACA
309018 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCC-TTGAAT
* *
309042 GTGCATCGATTCAT--CATG-AT
1 GTGCATCGATGCATCCCTTGAAT
*
309062 GATGCACCGATGCA-CGCCTTGAAT
1 G-TGCATCGATGCATC-CCTTGAAT
309086 GTGCATCGATGCA
1 GTGCATCGATGCA
309099 CGGGGTTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.07
21 12 0.26
22 1 0.02
23 14 0.30
24 16 0.35
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCATCCCTTGAAT
Found at i:311842 original size:65 final size:64
Alignment explanation
Indices: 311773--311956 Score: 196
Period size: 65 Copynumber: 2.9 Consensus size: 64
311763 AATTAAATTG
* *
311773 AACATTGAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTAAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTT-T-A
311837 A
64 A
* * * ** *
311838 AACATCGAATGCATTTGACGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGCACTTA-CCATGCACCGATGCACTAAGGATATTTTAA
* * *
311902 AACATCAAATGCACTTGATGCATCGATGCACTCTTA--GTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTGATGCATCGATGCA--CTTACCATGCACCGATGCACTAAGG
311957 GTCCAACGGT
Statistics
Matches: 98, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
64 45 0.46
65 48 0.49
66 4 0.04
67 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTTTAA
Found at i:311932 original size:17 final size:19
Alignment explanation
Indices: 311910--311952 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
311900 AAAACATCAA
*
311910 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
311927 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
311946 ATGCACT
1 ATGCACT
311953 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:311948 original size:64 final size:64
Alignment explanation
Indices: 311780--311956 Score: 175
Period size: 64 Copynumber: 2.7 Consensus size: 64
311770 TTGAACATTG
* *
311780 AATGCATTTCATGCATCGATGCA-CTTACCATGCACCGATGCACTAAGGATTTTATGAAAACATC
1 AATGCATTTGATGCATCGATGCACCTTA--GTGCACCGATGCACTAAGGATTTTATGAAAACATC
*
311844 G
64 A
* * ** *
311845 AATGCATTTGACGCATCGATGCACC--AGCCATGCATCGATGCACTCTGGCTATTT-T-AAAACA
1 AATGCATTTGATGCATCGATGCACCTTAG---TGCACCGATGCACTAAGGAT-TTTATGAAAACA
311906 TCA
62 TCA
*
311909 AATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACTAAGG
1 AATGCATTTGATGCATCGATGCAC-CTTAGTGCACCGATGCACTAAGG
311957 GTCCAACGGT
Statistics
Matches: 91, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
64 46 0.51
65 39 0.43
66 4 0.04
67 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (64 bp):
AATGCATTTGATGCATCGATGCACCTTAGTGCACCGATGCACTAAGGATTTTATGAAAACATCA
Found at i:317421 original size:26 final size:26
Alignment explanation
Indices: 317382--317432 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
317372 CTGAGCTAAT
*
317382 CATGCTAGGCTTATGCTTGTCATTAC
1 CATGCTAGGATTATGCTTGTCATTAC
*
317408 CATGTTAGGATTATGCTTGTCATTA
1 CATGCTAGGATTATGCTTGTCATTA
317433 TTCGTAGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (26 bp):
CATGCTAGGATTATGCTTGTCATTAC
Found at i:318368 original size:21 final size:19
Alignment explanation
Indices: 318344--318389 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
318334 TAATGTTTGA
318344 AATTATTAAAGATGTTGGGT-T
1 AATTATTAAA-AT-TT-GGTAT
318365 AATT-TTAAAATTTGGTAT
1 AATTATTAAAATTTGGTAT
318383 AATTATT
1 AATTATT
318390 GTTATTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 4 0.17
20 5 0.22
21 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (19 bp):
AATTATTAAAATTTGGTAT
Found at i:320888 original size:1 final size:1
Alignment explanation
Indices: 320873--320906 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
320863 TATTTCCCAC
* *
320873 TTTTTGTTTTGTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
320907 GCTGATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:322749 original size:25 final size:26
Alignment explanation
Indices: 322707--322760 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
322697 TCTTAATTTA
322707 TTATGAGAAAAAACATAATCTCTAAC
1 TTATGAGAAAAAACATAATCTCTAAC
*
322733 TTATGAGAAAAAA-ATAATCTTTAAC
1 TTATGAGAAAAAACATAATCTCTAAC
322758 TTA
1 TTA
322761 GAAAAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (26 bp):
TTATGAGAAAAAACATAATCTCTAAC
Found at i:333114 original size:20 final size:20
Alignment explanation
Indices: 333040--333119 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
333030 TTTAATTAAA
*
333040 AATTAAAATTTTAAATTATTT
1 AATTAAAA-TATAAATTATTT
*
333061 -A--AAAATATAGAACTTTTTT
1 AATTAAAATATA-AA-TTATTT
* *
333080 CATTATAAAT-CAAATTATTT
1 AATTA-AAATATAAATTATTT
333100 AATTAAAATATAAATTATTT
1 AATTAAAATATAAATTATTT
333120 TAACTTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
17 3 0.07
18 6 0.13
19 9 0.20
20 20 0.43
21 2 0.04
22 2 0.04
23 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (20 bp):
AATTAAAATATAAATTATTT
Found at i:333179 original size:22 final size:23
Alignment explanation
Indices: 333136--333183 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
333126 TATTTTATAT
333136 TTTTAAAAATAAATATTAAATTA
1 TTTTAAAAATAAATATTAAATTA
*
333159 TTTTAAAAATAAA-ATTGAATTA
1 TTTTAAAAATAAATATTAAATTA
333181 TTT
1 TTT
333184 ATTTATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTTAAAAATAAATATTAAATTA
Found at i:333893 original size:151 final size:152
Alignment explanation
Indices: 333619--333920 Score: 588
Period size: 151 Copynumber: 2.0 Consensus size: 152
333609 TTGAGTTCAT
333619 TTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACACATGTCAC
1 TTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACACATGTCAC
333684 TATCTTATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAAA
66 TATCTTATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAAA
333749 AAATATTAAAAA-GCATTACGC
131 AAATATTAAAAATGCATTACGC
*
333770 TTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCGTGGTGACACATGTCAC
1 TTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACACATGTCAC
333835 TATCTTATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAAA
66 TATCTTATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAAA
333900 AAATATTAAAAATGCATTACG
131 AAATATTAAAAATGCATTACG
333921 TTGTACGACA
Statistics
Matches: 149, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
151 141 0.95
152 8 0.05
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (152 bp):
TTTATTATTCCAATGGACCCTATTGGTTAATTATTTTATTTCAATAGCATGGTGACACATGTCAC
TATCTTATTGGTTAATTAAAAATAATTAAGATATCTTATTTGATTGTTGACGTGGAATTTGAAAA
AAATATTAAAAATGCATTACGC
Found at i:337560 original size:20 final size:21
Alignment explanation
Indices: 337524--337566 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
337514 TTATAAACTC
*
337524 GTACCTTCAATATAAAATTAT
1 GTACCTTCAACATAAAATTAT
337545 GTACCTT-AACATAAAATTAT
1 GTACCTTCAACATAAAATTAT
337565 GT
1 GT
337567 GTATGTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (21 bp):
GTACCTTCAACATAAAATTAT
Found at i:344959 original size:110 final size:108
Alignment explanation
Indices: 344759--344983 Score: 378
Period size: 110 Copynumber: 2.1 Consensus size: 108
344749 CTCCCTATTG
* * * *
344759 CTTCCACGATCGTGTCTGCCCCCTATATCTTCAGAGTGTATAAGACCCACAATCTTCATCAATCG
1 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCAACAATCTTCAACAATCG
*
344824 CGTCTGCCCCCTATTTCTTCTGAGAGTATAAGACTCGAACAAT
66 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
*
344867 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAAACAATCTTCAACGAT
1 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-C-AACAATCTTCAACAAT
344932 CGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
64 CGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
344977 CTTCAAC
1 CTTCAAC
344984 AAATGGGTTC
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 44 0.40
109 1 0.01
110 64 0.59
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (108 bp):
CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCAACAATCTTCAACAATCG
CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
Found at i:345006 original size:55 final size:55
Alignment explanation
Indices: 344759--344983 Score: 337
Period size: 55 Copynumber: 4.1 Consensus size: 55
344749 CTCCCTATTG
* * * * *
344759 CTTCCACGATCGTGTCTGCCCCCTATATCTTCAGAGTGTATAAGAC-C-CACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
* * *
344812 CTTCATCAATCGCGTCTGCCCCCTATTTCTTCTGAGAGTATAAGACTCGAACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
* * *
344867 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAAACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
344922 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
344977 CTTCAAC
1 CTTCAAC
344984 AAATGGGTTC
Statistics
Matches: 153, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 39 0.25
54 1 0.01
55 113 0.74
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
Found at i:345162 original size:51 final size:51
Alignment explanation
Indices: 344942--345493 Score: 563
Period size: 51 Copynumber: 10.5 Consensus size: 51
344932 CGCGTCTGCC
* * * * *
344942 CCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCACT
1 CCCTCTTTCTTTAGGGAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCT
* * * *
344997 CCCTATTTCTCTAGGGAGTATGGAACTCAGACATATTCTTCAAACGGGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTC-GA-ACA-TCTTCAAACGGGTTCGCT
* * *
345051 CCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGAGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCT
* * *
345104 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTTGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
* *
345155 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
*
345206 CCCTCTTTCTTTAGGGAGTATAGAACTCAAACATCTTC-AACTGGGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAAC-GGGTTCGCT
* * * **
345257 CCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCT
** * **
345311 CATTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
* * * * * * *
345362 CCTTCTTTCATTAAGGAGTAT-GAAACTCGGATATCTTCATACGCGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAG-AACTCGAACATCTTCAAACGGGTTCGCT
* *
345413 CCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAACGGGTTCGCT
1 CCCTCTTTCTTTAGGGAGTATAGAACTCGA-ACA--TCTTCAAACGGGTTCGCT
* *
345466 CCCTCTTTCTCTAGGGAGTATGGAACTC
1 CCCTCTTTCTTTAGGGAGTATAGAACTC
345494 AAATAATCTT
Statistics
Matches: 430, Mismatches: 52, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
50 4 0.01
51 219 0.51
52 5 0.01
53 95 0.22
54 74 0.17
55 24 0.06
56 4 0.01
57 5 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (51 bp):
CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
Found at i:345345 original size:207 final size:208
Alignment explanation
Indices: 344957--345504 Score: 739
Period size: 207 Copynumber: 2.6 Consensus size: 208
344947 TTTCTTCAGA
* * *
344957 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCACTCCCTATTTCTCTAGGGAGTATGGA
1 GAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
345021 ACTCAGACATATTCTTCAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATC
61 ACTCA-A-ACATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAAATC
* * *
345086 -TCTTCAAACGAGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGT
124 TTCTTCAAACGAGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGT
* *
345150 TTGCTCCTTCTTTCTTTAAG
189 TCGCTCCTTCTTTCATTAAG
* *
345170 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCA
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
345235 AACA-TCTTC-AACTGGGTTCGCTCCCTCTTTCT-TCAGGGAGTATAGAACTCAAAAATCTTCTT
66 AACATTCTTCAAAC-GGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCAAAAATCTTCTT
** *
345297 CTTACGGGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
129 CAAACGAGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
345362 CCTTCTTTCATTAAG
194 CCTTCTTTCATTAAG
* * * *
345377 GAGTAT-GAAACTCGGATATCTTCATACGCGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 GAGTATAG-AACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
* *
345441 AGACATCTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAATAATCTTC
65 AAACAT-TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAA-AATCTTC
345505 ATTTGCTTCA
Statistics
Matches: 300, Mismatches: 25, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
205 4 0.01
206 45 0.15
207 138 0.46
208 1 0.00
209 80 0.27
210 11 0.04
212 5 0.02
213 15 0.05
214 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (208 bp):
GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
AACATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCA
AACGAGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCC
TTCTTTCATTAAG
Found at i:345357 original size:156 final size:153
Alignment explanation
Indices: 345033--345466 Score: 543
Period size: 156 Copynumber: 2.8 Consensus size: 153
345023 TCAGACATAT
* *
345033 TCTTCAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGAG
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACA--TCTTC-AACGAG
* * * * * *
345098 TTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC-GAA-CATCTTCAAACGGGTTTGCTCCTTCT
63 TTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAATC-TCTTCAAACGGGTTCGCTCATTCT
* *
345161 TTCTTTAAGGAGTATAGAACTCGAACA
127 CTCTTTAAAGAGTATAGAACTCGAACA
* *
345188 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAAACATCTTCAACTGGGTT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAC-GAGTT
**
345253 CGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCATTCTC
65 CGCTCCCTCTTTCTTCAGGGAGTATAGAACTC-AAAATC-TCTTCAAACGGGTTCGCTCATTCTC
345318 TCTTTAAAGAGTATAGAACTCGAACA
128 TCTTTAAAGAGTATAGAACTCGAACA
* * * * * *
345344 TCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTAT-GAAACTCGGATATCTTCATACGCGT
1 TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAG-AACTCGAACATCTTCA-ACGAGT
* *
345408 TCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAGACATCTCTTCAAACGGGTTCGCTC
64 TCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCA-AAATCTCTTCAAACGGGTTCGCTC
345467 CCTCTTTCTC
Statistics
Matches: 245, Mismatches: 26, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
152 3 0.01
153 38 0.16
155 71 0.29
156 131 0.53
157 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (153 bp):
TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAACGAGTTC
GCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAATCTCTTCAAACGGGTTCGCTCATTCTCTCT
TTAAAGAGTATAGAACTCGAACA
Found at i:345503 original size:156 final size:152
Alignment explanation
Indices: 344983--345505 Score: 532
Period size: 156 Copynumber: 3.3 Consensus size: 152
344973 CAATCTTCAA
* * * * * *
344983 CAAATGGGTTCACTCCCTATTTCTCTAGGGAGTATGGAACTCAGACATATTCTTCAAACGGGTTC
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCA-A-A-AATCTTCAAACGGGTTC
* * *
345048 GCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGAGTTCGCTCCTTCTTTC
63 GCTCCCTCTTTCT-TAGGGAGTATAGAACTCG-A-ATATCTTC-AACGAGTTCGCTCCCTCTTTC
*
345113 TTTAAGGAGTATAGAACTC-GAA-CATCTT
124 -TTAGGGAGTATAGAACTCAGAATCATCTT
* * * * *
345141 CAAACGGGTTTGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCAAAAATCTTCAAACGGGTTCGCT
* * *
345206 CCCTCTTTCTTTAGGGAGTATAGAACTCAAACATCTTCAACTGGGTTCGCTCCCTCTTTCTTCAG
66 CCCTCTTTC-TTAGGGAGTATAGAACTCGAATATCTTCAAC-GAGTTCGCTCCCTCTTTCTT-AG
* *
345271 GGAGTATAGAACTCAAAAATCTTCTT
128 GGAGTATAGAACTC-AGAATCATCTT
** ** * * * * *
345297 CTTACGGGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCAAAAATCTTCAAACGGGTTCGCT
* * * *
345362 CCTTCTTTCATTAAGGAGTAT-GAAACTCGGATATCTTCATACGCGTTCGCTCCCTCTTTCTCTA
66 CCCTCTTTC-TTAGGGAGTATAG-AACTCGAATATCTTCA-ACGAGTTCGCTCCCTCTTTCT-TA
*
345426 GGGAGTATGGAACTCAGACATC-TCTT
127 GGGAGTATAGAACTCAGA-ATCATCTT
* *
345452 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAATAATCTTCA
1 CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCAAA-AATCTTCA
345506 TTTGCTTCAC
Statistics
Matches: 308, Mismatches: 46, Indels: 24
0.81 0.12 0.06
Matches are distributed among these distances:
152 5 0.02
153 37 0.12
154 1 0.00
155 87 0.28
156 140 0.45
157 4 0.01
158 34 0.11
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (152 bp):
CAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCAAAAATCTTCAAACGGGTTCGCT
CCCTCTTTCTTAGGGAGTATAGAACTCGAATATCTTCAACGAGTTCGCTCCCTCTTTCTTAGGGA
GTATAGAACTCAGAATCATCTT
Found at i:345933 original size:36 final size:36
Alignment explanation
Indices: 345875--346140 Score: 329
Period size: 36 Copynumber: 7.4 Consensus size: 36
345865 ACTCTTCTGA
* * **
345875 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * * *
345912 GAAGACTTAATATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
345948 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
345984 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
346020 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
346056 GAAGGCTTAGGATGGTTTGCTTCACTATTCTCCAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
346092 GAAGGCTTCAGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
346128 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
346141 TGACTTTGCT
Statistics
Matches: 203, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
35 2 0.01
36 188 0.93
37 13 0.06
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:348884 original size:43 final size:44
Alignment explanation
Indices: 348821--348920 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 44
348811 TTTTCTTTCA
* *
348821 TTCTTTTTTCTTTTTTCATTTTCAATTTTTCTC-TTTCTTTTC-CT
1 TTCTATTTTC-TTTTTCA-TTTCAATTTTTATCTTTTCTTTTCTCT
* *
348865 TTTTATTTTCTTTTTCATTTCATTTTTTATCTTTTCTTTTCTCT
1 TTCTATTTTCTTTTTCATTTCAATTTTTATCTTTTCTTTTCTCT
348909 TTCTATATTTCT
1 TTCTAT-TTTCT
348921 CTTCTTTCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
42 12 0.25
43 16 0.33
44 15 0.31
45 5 0.10
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (44 bp):
TTCTATTTTCTTTTTCATTTCAATTTTTATCTTTTCTTTTCTCT
Found at i:351235 original size:6 final size:6
Alignment explanation
Indices: 351214--351248 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
351204 AAACAAATAC
351214 ATGC-A ATGCAAA ATGCAA ATGCAA ATGCAA ATGCA
1 ATGCAA ATGC-AA ATGCAA ATGCAA ATGCAA ATGCA
351249 CGAGGTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.14
6 19 0.68
7 5 0.18
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGCAA
Found at i:358250 original size:24 final size:25
Alignment explanation
Indices: 358213--358259 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
358203 CTATTCTTTC
**
358213 GCTTCAATTTAAC-TCAAATTTTAG
1 GCTTCAATCGAACTTCAAATTTTAG
*
358237 GCTTCAATCGAACTTCTAATTTT
1 GCTTCAATCGAACTTCAAATTTT
358260 TTTTTGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (25 bp):
GCTTCAATCGAACTTCAAATTTTAG
Found at i:359808 original size:15 final size:16
Alignment explanation
Indices: 359776--359808 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
359766 TTTGATTGTG
359776 TTATATCTTTAAATTTT
1 TTATATCTTT-AATTTT
359793 TTATATCTTT-ATTTT
1 TTATATCTTTAATTTT
359808 T
1 T
359809 AAAGAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATATCTTTAATTTT
Found at i:360080 original size:31 final size:31
Alignment explanation
Indices: 360042--360153 Score: 125
Period size: 31 Copynumber: 3.6 Consensus size: 31
360032 CTTTGGTTAG
*
360042 ATTTAAGGATTAAATTAATATTTTATCTAAA
1 ATTTAAAGATTAAATTAATATTTTATCTAAA
* * * * *
360073 ATTTAAGGATCAAATTGACATTTTATCAAAA
1 ATTTAAAGATTAAATTAATATTTTATCTAAA
* ** *
360104 ATTCAAAGATTAGCTTAATATTTTATATGAAA
1 ATTTAAAGATTAAATTAATATTTTATCT-AAA
360136 ATTTAAAGATTAAATTAA
1 ATTTAAAGATTAAATTAA
360154 GAATGAACTT
Statistics
Matches: 64, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
31 46 0.72
32 18 0.28
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (31 bp):
ATTTAAAGATTAAATTAATATTTTATCTAAA
Found at i:362557 original size:2 final size:2
Alignment explanation
Indices: 362550--362575 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
362540 GCTAACAAAT
362550 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
362576 AATGAAGCTA
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):
TA
Found at i:368365 original size:45 final size:45
Alignment explanation
Indices: 368301--368427 Score: 254
Period size: 45 Copynumber: 2.8 Consensus size: 45
368291 GCCCATATAC
368301 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
368346 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
368391 TTATTATGTTCATTATATTGCACGTCAATTACAATTA
1 TTATTATGTTCATTATATTGCACGTCAATTACAATTA
368428 TATTGCAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (45 bp):
TTATTATGTTCATTATATTGCACGTCAATTACAATTAGTGTTAGT
Done.