Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 85 of 335
Found at i:28087753 original size:21 final size:21
Alignment explanation
Indices: 28087726--28087780 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
28087716 ATAGTGCTGA
* *
28087726 CGGTGAGATTAGTTACTGTAG
1 CGGTGAGATTAGATACTATAG
* *
28087747 TGGTGAGATTAAATACTATAG
1 CGGTGAGATTAGATACTATAG
28087768 CGGTGAGATTAGA
1 CGGTGAGATTAGA
28087781 AACAATGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (21 bp):
CGGTGAGATTAGATACTATAG
Found at i:28091255 original size:93 final size:93
Alignment explanation
Indices: 28091143--28091313 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
28091133 GCCCATAAGT
* *
28091143 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28091208 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
28091236 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28091301 CGAGTTCGGATGC
66 CGAGCTCGGATGC
28091314 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28091310 original size:46 final size:46
Alignment explanation
Indices: 28091135--28091310 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28091125 TGTAACCCGC
* * *
28091135 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
28091181 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
28091231 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
*
28091274 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
28091311 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
46 65 0.59
47 28 0.25
49 1 0.01
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:28093734 original size:30 final size:30
Alignment explanation
Indices: 28093690--28093778 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
28093680 CAAAGATAAC
28093690 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
28093719 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
28093749 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
28093779 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:28093738 original size:15 final size:15
Alignment explanation
Indices: 28093690--28093769 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
28093680 CAAAGATAAC
*
28093690 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28093704 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28093719 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
28093734 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
28093749 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
28093764 AAGAAA
1 AAGAAA
28093770 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28093778 original size:15 final size:15
Alignment explanation
Indices: 28093701--28093778 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
28093691 AGAAAACCGA
28093701 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
28093716 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
28093730 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
28093745 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
28093761 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28093776 ATA
1 ATA
28093779 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28096796 original size:46 final size:48
Alignment explanation
Indices: 28096674--28096803 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 48
28096664 TGTAACCCGC
*
28096674 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * *
28096724 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGA-C-ATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
28096767 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28096804 TGCTCAACCA
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
42 1 0.01
43 8 0.11
44 1 0.01
46 29 0.41
47 28 0.40
50 2 0.03
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:28096822 original size:46 final size:46
Alignment explanation
Indices: 28096679--28096822 Score: 122
Period size: 46 Copynumber: 3.1 Consensus size: 46
28096669 CCCGCCCATA
*
28096679 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC-CT
* * * *
28096728 --CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCCT
28096772 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
28096818 AGTGA
1 AGTGA
28096823 CATGTCACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
44 8 0.11
45 1 0.01
46 33 0.43
47 30 0.39
49 3 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:28103658 original size:24 final size:22
Alignment explanation
Indices: 28103631--28103675 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28103621 AGTGAACTCG
28103631 ATTGAGATGGAAACGGGAAGCTCT
1 ATTGAGAT-G-AACGGGAAGCTCT
*
28103655 ATTGAGCTGAACGGGAAGCTC
1 ATTGAGATGAACGGGAAGCTC
28103676 ATACGAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 1 0.05
24 7 0.35
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (22 bp):
ATTGAGATGAACGGGAAGCTCT
Found at i:28103683 original size:22 final size:22
Alignment explanation
Indices: 28103642--28103684 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28103632 TTGAGATGGA
*
28103642 AACGGGAAGCTCTATTGAGCTG
1 AACGGGAAGCTCTATCGAGCTG
28103664 AACGGGAAGCTC-ATACGAGCT
1 AACGGGAAGCTCTAT-CGAGCT
28103685 ATGGTGAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (22 bp):
AACGGGAAGCTCTATCGAGCTG
Found at i:28105942 original size:2 final size:2
Alignment explanation
Indices: 28105930--28105961 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
28105920 TTAATTATTA
28105930 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
28105962 AACTTATTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28108376 original size:52 final size:52
Alignment explanation
Indices: 28108301--28108406 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
28108291 AATTTGGGTA
28108301 TTCTTTCTCAAGTTTGCTGAGAGAGAAAGAAATGGCAGTAAGTTTTTTTTTC
1 TTCTTTCTCAAGTTTGCTGAGAGAGAAAGAAATGGCAGTAAGTTTTTTTTTC
28108353 TTCTTTCTCAAGTTTGCTGAGAGAGAAAGAAATGGCAGTAAGTTTTTTTTTC
1 TTCTTTCTCAAGTTTGCTGAGAGAGAAAGAAATGGCAGTAAGTTTTTTTTTC
28108405 TT
1 TT
28108407 TTAACTTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (52 bp):
TTCTTTCTCAAGTTTGCTGAGAGAGAAAGAAATGGCAGTAAGTTTTTTTTTC
Found at i:28111081 original size:32 final size:32
Alignment explanation
Indices: 28111045--28111178 Score: 196
Period size: 32 Copynumber: 4.2 Consensus size: 32
28111035 TACTTTTTTA
*
28111045 TATGATCTACTTTTTCATATGCAAAACTAATG
1 TATGATCTACTTTTTTATATGCAAAACTAATG
** *
28111077 TATGATCTACTTTTTTATATGTGAACCTAATG
1 TATGATCTACTTTTTTATATGCAAAACTAATG
*
28111109 TATGATATACTTTTTTATATGCAAAACTAATG
1 TATGATCTACTTTTTTATATGCAAAACTAATG
* * *
28111141 TATGATCTACTTTTTTATAGGTAAACCTAATG
1 TATGATCTACTTTTTTATATGCAAAACTAATG
28111173 TATGAT
1 TATGAT
28111179 ATTTTTTATG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 90 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (32 bp):
TATGATCTACTTTTTTATATGCAAAACTAATG
Found at i:28111146 original size:64 final size:64
Alignment explanation
Indices: 28111045--28111180 Score: 236
Period size: 64 Copynumber: 2.1 Consensus size: 64
28111035 TACTTTTTTA
* * *
28111045 TATGATCTACTTTTTCATATGCAAAACTAATGTATGATCTACTTTTTTATATGTGAACCTAATG
1 TATGATATACTTTTTCATATGCAAAACTAATGTATGATCTACTTTTTTATAGGTAAACCTAATG
*
28111109 TATGATATACTTTTTTATATGCAAAACTAATGTATGATCTACTTTTTTATAGGTAAACCTAATG
1 TATGATATACTTTTTCATATGCAAAACTAATGTATGATCTACTTTTTTATAGGTAAACCTAATG
28111173 TATGATAT
1 TATGATAT
28111181 TTTTTATGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (64 bp):
TATGATATACTTTTTCATATGCAAAACTAATGTATGATCTACTTTTTTATAGGTAAACCTAATG
Found at i:28113213 original size:21 final size:21
Alignment explanation
Indices: 28113187--28113260 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
28113177 CGCTGTTTCT
*
28113187 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
28113208 AATCTCACCGCTACAGTAACC
1 AATCTCACCGCTACAGTAACC
*
28113229 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
28113250 AATCTCACCGC
1 AATCTCACCGC
28113261 CACCGCTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.31, C:0.38, G:0.09, T:0.22
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:28114353 original size:25 final size:25
Alignment explanation
Indices: 28114324--28114374 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
28114314 CAAAGGAAAA
** *
28114324 TCCTAATCTAATTCCTAGTTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
28114349 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
28114374 T
1 T
28114375 TTATAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:28119023 original size:25 final size:25
Alignment explanation
Indices: 28118994--28119044 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
28118984 CAAAGGAAAA
**
28118994 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
28119019 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
28119044 T
1 T
28119045 TTATAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:28119798 original size:3 final size:3
Alignment explanation
Indices: 28119790--28119857 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
28119780 ATTTTCGGCA
* * *
28119790 AAG AAG AAG AAG AAA AAG AGAG AAG AAG -GG AAG AAG -GG AAG AAG
1 AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG
*
28119834 AA- AAG AAG AAG AAAG AAA AAG AAG
1 AAG AAG AAG AAG -AAG AAG AAG AAG
28119858 GAGAGGAGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28119815 original size:16 final size:15
Alignment explanation
Indices: 28119789--28119857 Score: 70
Period size: 16 Copynumber: 4.5 Consensus size: 15
28119779 CATTTTCGGC
28119789 AAAGAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
28119804 AAAGAGAGAAGAAGGGAA
1 AAAGA-AGAAGAA--GAA
* *
28119822 GAAG-GGAAGAAG-A
1 AAAGAAGAAGAAGAA
28119835 AAAGAAGAAGAAAGAA
1 AAAGAAGAAG-AAGAA
28119851 AAAGAAG
1 AAAGAAG
28119858 GAGAGGAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 4 0.09
14 5 0.11
15 8 0.18
16 21 0.48
18 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAGAAGAA
Found at i:28119833 original size:11 final size:11
Alignment explanation
Indices: 28119789--28119856 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
28119779 CATTTTCGGC
28119789 AAAGAAGAAGA
1 AAAGAAGAAGA
*
28119800 AGAAAAAGAGAGA
1 A-AAGAAGA-AGA
*
28119813 AGAAG-GGAAGA
1 A-AAGAAGAAGA
**
28119824 AGGGAAGAAGA
1 AAAGAAGAAGA
28119835 AAAGAAGAAG-
1 AAAGAAGAAGA
*
28119845 AAAGAAAAAGA
1 AAAGAAGAAGA
28119856 A
1 A
28119857 GGAGAGGAGG
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
10 10 0.23
11 19 0.43
12 8 0.18
13 7 0.16
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAGA
Found at i:28119943 original size:14 final size:14
Alignment explanation
Indices: 28119894--28119956 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
28119884 TGAGAGAAGA
28119894 AAAAAGAA--AAAG
1 AAAAAGAAGGAAAG
28119906 AAAAAGAGAAGGAGAAG
1 -AAAA-AGAAGGA-AAG
* * *
28119923 AAGAAGAGGGAAGG
1 AAAAAGAAGGAAAG
28119937 AAAAAGAAGGAAAG
1 AAAAAGAAGGAAAG
28119951 AAAAAG
1 AAAAAG
28119957 GTAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 4 0.10
14 23 0.57
15 6 0.15
16 4 0.10
17 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGGAAAG
Found at i:28119943 original size:17 final size:17
Alignment explanation
Indices: 28119899--28119956 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 17
28119889 GAAGAAAAAA
*
28119899 GAAAAAGAAAAAGAGAAG
1 GAAAAAG-AAGAGAGAAG
*
28119917 GAGAAGAAGAAGAGGGAAG
1 GA-AA-AAGAAGAGAGAAG
28119936 GAAAAAGAAG-GA-AA-
1 GAAAAAGAAGAGAGAAG
28119950 GAAAAAG
1 GAAAAAG
28119957 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 1 0.03
17 6 0.17
18 4 0.11
19 12 0.34
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAGAGAAG
Found at i:28120443 original size:30 final size:31
Alignment explanation
Indices: 28120403--28120461 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
28120393 TTTTGTTAAA
*
28120403 ATAATATAAAAAAATAAAATATGAAAATAGT
1 ATAATATAAAAAAATAAAATACGAAAATAGT
*
28120434 ATAAT-TAAAAAAATAAAATCCGAAAATA
1 ATAATATAAAAAAATAAAATACGAAAATA
28120462 AAAAAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (31 bp):
ATAATATAAAAAAATAAAATACGAAAATAGT
Found at i:28120553 original size:136 final size:133
Alignment explanation
Indices: 28120413--28120669 Score: 329
Period size: 136 Copynumber: 1.9 Consensus size: 133
28120403 ATAATATAAA
** * * *
28120413 AAAATAAAATATGAAAATAGTATAATTAAAAAAATAAAATCCGAAAATAAAAAAATACGAACAAG
1 AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACG-----AAAAAAATACGAACAAA
* **
28120478 GTGCCAAAGTCA-GGTTACTTATTAAATTAATATAAAAAA-ACTTAAATAATACATTTGAAAGAT
61 GTGCCAAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAAGAT
28120541 TTTATGCT
126 TTTATGCT
* * * * *
28120549 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
*
28120614 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
66 AAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
28120670 GCATTATGTA
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
131 25 0.24
132 24 0.23
133 20 0.19
136 36 0.34
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (133 bp):
AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
AAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAAGATTTTAT
GCT
Found at i:28120711 original size:145 final size:146
Alignment explanation
Indices: 28120549--28121455 Score: 961
Period size: 145 Copynumber: 6.1 Consensus size: 146
28120539 ATTTTATGCT
*
28120549 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
28120614 -AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATG
66 CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
28120678 TACTAAAATAATATAA
131 TACTAAAATAATATAA
*
28120694 AAAATAAAATACGAAAATAATATATTTT-AAAAATAATATACGGAAATAAAAAAATTACGAAGAA
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATAC-G----AAAAAAA-TACGAATAA
* * * * *
28120758 AGT-ATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAACAGTTAATTAATACAT
60 AGTGCTCAAAATCAGGGTTATTTA-TTAAAAA-----AATATAAA-AAATACTTAAATAATACAT
** * * *
28120822 TTG-AATTTTTTTTGCTAAAATAATATAA
118 TTGAAACATTATGTACTAAAATAATATAA
*
28120850 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* * *
28120915 -AAAATCAGGGATATTTATTGAAAAAATATAAAAAATACTAAAATAATACATTTGAAACATTATG
66 CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
*
28120979 TA-TAAAATAATACGAA
131 TACTAAAATAATA-TAA
* * *
28120995 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG-T
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
** *
28121058 CAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATATACATAATACATTTG
66 CAAAATCAGGGTTATTTATTAAA--AAAATATAAAAA-A--TAC-T--TA-A-ATAATACATTTG
* * *
28121123 AAACATTTTTTGCTAAAATAATATAAA
121 AAACATTATGTACTAAAATAATAT-AA
* *
28121150 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATAC--AAAAAATATGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* ** * *
28121213 -AAAATCAGAGTTATTTATT-AAAAAATATTTAAAATACTTAAATAATATATTTAAAACATTATG
66 CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
** * *
28121276 TACTGGAATAAGGGTTTTA
131 TACTAAAATAA---TATAA
* * *
28121295 AAATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAAAAAATA-GAA-AAAGTG
1 AAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTG
* ** * *
28121356 -TCAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTTACATAATACATTTAAAACATT
64 CTCAAAATCAGGGTTATTTATTAAAAAAATAT-AAAAAATACTTAAATAATACATTTGAAACATT
* *
28121420 -TTTGCTAAAATAATAT-A
128 ATGTACTAAAATAATATAA
*
28121437 AAAATAATATACGAAAATA
1 AAAATAAAATACGAAAATA
28121456 TTTTACTTAT
Statistics
Matches: 638, Mismatches: 82, Indels: 89
0.79 0.10 0.11
Matches are distributed among these distances:
140 10 0.02
141 2 0.00
142 5 0.01
143 29 0.05
144 82 0.13
145 120 0.19
146 41 0.06
147 53 0.08
148 3 0.00
149 11 0.02
150 35 0.05
151 40 0.06
152 9 0.01
153 3 0.00
154 56 0.09
155 52 0.08
156 55 0.09
157 32 0.05
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (146 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
TACTAAAATAATATAA
Found at i:28120855 original size:12 final size:13
Alignment explanation
Indices: 28120838--28120873 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
28120828 TTTTTTTGCT
28120838 AAAATAATATAA-
1 AAAATAATATAAG
*
28120850 AAAATAAAATAAG
1 AAAATAATATAAG
28120863 AAAATAATATA
1 AAAATAATATA
28120874 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAATAATATAAG
Found at i:28121373 original size:299 final size:293
Alignment explanation
Indices: 28120549--28121455 Score: 1098
Period size: 301 Copynumber: 3.1 Consensus size: 293
28120539 ATTTTATGCT
**
28120549 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATAC-AAAAAAATACGAATAAAGTGCT
*
28120614 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATGT
65 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
* *
28120679 ACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAATAATATACGGAAATAAA
130 ACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAAAAGATAC-G----AAA
* * *
28120744 AAAATTACGAAGAAAGTATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAACA-
190 AAAA-TACGAA-AAAGTGTCAAAATCAGGGTTATTTA-T--TAAA---TTAATATAAAAAAACAC
* **
28120808 GT---T-A-ATTAATACATTTGAATTTTTTTTGCTAAAATAATATAA
247 TTACATAATATTAATACATTTGAACATTTTTTGCTAAAATAATATAA
28120850 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATAC-AAAAAAATACGAATAAAGTGCT
* * *
28120915 AAAATCAGGGATATTTATTGAAAAAATATAAAAAATACTAAAATAATACATTTGAAACATTATGT
65 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
* *
28120980 A-TAAAATAATACGAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAA
130 ACTAAAATAATA-TAAAAAATAAAATACGAAAATAATATATTTTAAAAAA-AAGATACGAAAAAA
*
28121043 ATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATA
193 ATACG-AAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATAATA
28121108 TACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAA
257 T---TAATACATTTG-AACATTTTTTGCTAAAATAATAT-AA
* *
28121150 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATAC-AAAAAATATGAATAAAGTGCTA
1 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACAAAAAAATACGAATAAAGTGCTA
* ** * *
28121214 AAATCAGAGTTATTTATT-AAAAAATATTTAAAATACTTAAATAATATATTTAAAACATTATGTA
66 AAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
** * * * *
28121278 CTGGAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATATA-TTTAAAAAAAAGATACGAAAA
131 CTAAAATAA---TATAAAAAAT-AA-AATACGAAAATAATATATTTTAAAAAAAAGATACGAAAA
* *
28121342 AAATA-GAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTTAC-----
191 AAATACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATAAT
*
28121401 A-TAATACATTTAAAACA-TTTTTGCTAAAATAATAT-A
256 ATTAATACATTT-GAACATTTTTTGCTAAAATAATATAA
* *
28121437 AAAATAATATACGAAAATA
1 AAAATAAAATAAGAAAATA
28121456 TTTTACTTAT
Statistics
Matches: 544, Mismatches: 40, Indels: 58
0.85 0.06 0.09
Matches are distributed among these distances:
287 18 0.03
289 32 0.06
290 15 0.03
292 3 0.01
293 1 0.00
294 3 0.01
295 30 0.06
296 9 0.02
297 41 0.08
298 54 0.10
299 71 0.13
300 65 0.12
301 180 0.33
302 22 0.04
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (293 bp):
AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACAAAAAAATACGAATAAAGTGCTA
AAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
CTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAAAAGATACGAAAAAAATA
CGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATAATATTAA
TACATTTGAACATTTTTTGCTAAAATAATATAA
Found at i:28123416 original size:72 final size:72
Alignment explanation
Indices: 28123323--28123462 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
28123313 AGTCCGAGCA
* *
28123323 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTATCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCAGATTTGGCAGGCAATGACAATTTATCGG
28123388 GCTCGTC
66 GCTCGTC
* * * * *
28123395 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCAGATTTTGCGGGCAATGACAATTTCTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCAGATTTGGCAGGCAATGACAATTTATCGG
28123460 GCT
66 GCT
28123463 TATCGAGGGG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCAGATTTGGCAGGCAATGACAATTTATCGG
GCTCGTC
Found at i:28127875 original size:12 final size:11
Alignment explanation
Indices: 28127831--28127876 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 11
28127821 CCTTCTTTTT
28127831 TTCTTCTTCTCC
1 TTCTT-TTCTCC
28127843 TTCTTTTTCTTCC
1 TTC-TTTTC-TCC
28127856 TTCTTTTCTCC
1 TTCTTTTCTCC
28127867 TTTCTTTTCT
1 -TTCTTTTCT
28127877 TTTATTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.10
12 20 0.65
13 8 0.26
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TTCTTTTCTCC
Found at i:28127889 original size:25 final size:25
Alignment explanation
Indices: 28127827--28127893 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
28127817 TATACCTTCT
28127827 TTTTTTCTTCTTCTCC-TTCTTTTTC
1 TTTTTT-TTCTTCTCCTTTCTTTTTC
* *
28127852 TTCCTTCTT-TTCTCCTTTC-TTTTC
1 TT-TTTTTTCTTCTCCTTTCTTTTTC
28127876 TTTTATTTTCTTCTCCTT
1 TTTT-TTTTCTTCTCCTT
28127894 GCTGCTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 1 0.03
24 16 0.47
25 15 0.44
26 2 0.06
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTTTCTTCTCCTTTCTTTTTC
Found at i:28139053 original size:8 final size:8
Alignment explanation
Indices: 28139036--28139067 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
28139026 AATGATTCAC
28139036 AAAA-AAA
1 AAAAGAAA
28139043 AAAAG-AA
1 AAAAGAAA
28139050 AAAAGAAA
1 AAAAGAAA
28139058 AAAAGAAA
1 AAAAGAAA
28139066 AA
1 AA
28139068 GACAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 11 0.48
8 12 0.52
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:28139058 original size:15 final size:14
Alignment explanation
Indices: 28139036--28139067 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
28139026 AATGATTCAC
28139036 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
28139050 AAAAGAAAAAAAGAA
1 AAAA-AAAAAAAGAA
28139065 AAA
1 AAA
28139068 GACAAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:28139906 original size:16 final size:17
Alignment explanation
Indices: 28139871--28139920 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
28139861 TATTTTATAA
28139871 AAATATATATAAATATT
1 AAATATATATAAATATT
28139888 AAATATA-ATAAAT-TAT
1 AAATATATATAAATAT-T
*
28139904 AAAT-TTTATAAA-ATT
1 AAATATATATAAATATT
28139919 AA
1 AA
28139921 TAATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 5 0.17
16 17 0.59
17 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATATAAATATT
Found at i:28141014 original size:4 final size:4
Alignment explanation
Indices: 28141005--28141038 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
28140995 AGCCCAAAGT
28141005 CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
28141039 AAAGAGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:28143100 original size:9 final size:9
Alignment explanation
Indices: 28143088--28143137 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
28143078 TTAAATATGT
28143088 TTTTATTAA
1 TTTTATTAA
28143097 TTTTA-TAA
1 TTTTATTAA
28143105 TTTT-TTAGA
1 TTTTATTA-A
* *
28143114 TTTTTTTAT
1 TTTTATTAA
*
28143123 TTTTATAAA
1 TTTTATTAA
28143132 TTTTAT
1 TTTTAT
28143138 AACTTGATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 9 0.26
9 22 0.65
10 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
TTTTATTAA
Found at i:28143202 original size:18 final size:20
Alignment explanation
Indices: 28143181--28143225 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
28143171 TTTTTAAATA
28143181 TTTAATA-ATTTGTAT-ATT
1 TTTAATATATTTGTATGATT
*
28143199 TTTAA-ATATTTTTATGATT
1 TTTAATATATTTGTATGATT
28143218 TTTAATAT
1 TTTAATAT
28143226 CTTTATAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.52
19 8 0.35
20 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTAATATATTTGTATGATT
Found at i:28143230 original size:18 final size:19
Alignment explanation
Indices: 28143196--28143231 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28143186 TAATTTGTAT
*
28143196 ATTTTTAAATATTTTTATG
1 ATTTTTAAATATCTTTATG
28143215 ATTTTT-AATATCTTTAT
1 ATTTTTAAATATCTTTAT
28143232 AGGAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTTTTAAATATCTTTATG
Found at i:28146797 original size:17 final size:17
Alignment explanation
Indices: 28146761--28146799 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28146751 GGAAAACAGT
*
28146761 TGAATTCTAATATTTAA
1 TGAATTCTAATATGTAA
* *
28146778 TGAATTTTAATATGTGA
1 TGAATTCTAATATGTAA
28146795 TGAAT
1 TGAAT
28146800 AATATTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (17 bp):
TGAATTCTAATATGTAA
Found at i:28157773 original size:17 final size:17
Alignment explanation
Indices: 28157751--28157784 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28157741 TTTGCTTATT
28157751 CACTTCCTTATCAGGGG
1 CACTTCCTTATCAGGGG
28157768 CACTTCCTTATCAGGGG
1 CACTTCCTTATCAGGGG
28157785 GGTGCCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (17 bp):
CACTTCCTTATCAGGGG
Found at i:28169960 original size:27 final size:27
Alignment explanation
Indices: 28169930--28169991 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
28169920 TTGTATTCAA
* *
28169930 TTTTTATACTTTAATTTTTAACATAAT
1 TTTTTATACTTTAATATTCAACATAAT
* * *
28169957 TTTTTATATTTTTATATTCGACATAAT
1 TTTTTATACTTTAATATTCAACATAAT
28169984 TTTTTATA
1 TTTTTATA
28169992 TTTTTATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTTATACTTTAATATTCAACATAAT
Found at i:28180186 original size:28 final size:28
Alignment explanation
Indices: 28180146--28180201 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28180136 AAAATCCAAG
28180146 TTTAGTTGTTGGCATCGTCAAACTCATT
1 TTTAGTTGTTGGCATCGTCAAACTCATT
*
28180174 TTTAGTTGTTGGCATCGTCAAAGTCATT
1 TTTAGTTGTTGGCATCGTCAAACTCATT
28180202 ACAATATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (28 bp):
TTTAGTTGTTGGCATCGTCAAACTCATT
Found at i:28180837 original size:24 final size:24
Alignment explanation
Indices: 28180810--28180865 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
28180800 TTTTCAAAAA
*
28180810 TAAAAAATTTTAATAAATCTTTTT
1 TAAAAAATTTTAATAAATATTTTT
*
28180834 TAAAAAAATTTAATAAATATTTTT
1 TAAAAAATTTTAATAAATATTTTT
28180858 TAAAAAAT
1 TAAAAAAT
28180866 AATGAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAAAAATTTTAATAAATATTTTT
Found at i:28182818 original size:25 final size:26
Alignment explanation
Indices: 28182790--28182849 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
28182780 ATTATTTTAC
28182790 TTATTTAAT-TTTTAAATA-ATATATT
1 TTATTTAATATTTTAAATATAT-TATT
*
28182815 TTA-TAAATATTTTAAATATATTATT
1 TTATTTAATATTTTAAATATATTATT
28182840 TACTATTTAA
1 T--TATTTAA
28182850 ACGAGAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 4 0.14
25 17 0.61
26 2 0.07
27 2 0.07
28 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTATTTAATATTTTAAATATATTATT
Found at i:28182824 original size:11 final size:12
Alignment explanation
Indices: 28182805--28182836 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28182795 TAATTTTTAA
28182805 ATAATATATTTT
1 ATAATATATTTT
28182817 ATAA-ATATTTT
1 ATAATATATTTT
28182828 A-AATATATT
1 ATAATATATT
28182837 ATTTACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 13 0.68
12 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATAATATATTTT
Found at i:28183207 original size:26 final size:26
Alignment explanation
Indices: 28183178--28183229 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28183168 GATTTTTCCC
28183178 ATAATCTTTTATTTGTTATTTTGAAT
1 ATAATCTTTTATTTGTTATTTTGAAT
28183204 ATAATCTTTTATTTGTTATTTTGAAT
1 ATAATCTTTTATTTGTTATTTTGAAT
28183230 GAAAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.62
Consensus pattern (26 bp):
ATAATCTTTTATTTGTTATTTTGAAT
Found at i:28185116 original size:31 final size:31
Alignment explanation
Indices: 28185081--28185147 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
28185071 AAAACAACTT
*
28185081 AATAGCCAAGTGACTTAAATAAAAACTTTTG
1 AATAGCCAAGTAACTTAAATAAAAACTTTTG
** *
28185112 AATAGTTAAGTAATTTAAATAAAAACTTTTG
1 AATAGCCAAGTAACTTAAATAAAAACTTTTG
28185143 AATAG
1 AATAG
28185148 TTCAATGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (31 bp):
AATAGCCAAGTAACTTAAATAAAAACTTTTG
Found at i:28191141 original size:17 final size:18
Alignment explanation
Indices: 28191106--28191143 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
28191096 AATTTAAAAA
*
28191106 TGAGTTCAGTTTTAATTT
1 TGAGTTCAGTTCTAATTT
*
28191124 TGAGTT-AGTTCTACTTT
1 TGAGTTCAGTTCTAATTT
28191141 TGA
1 TGA
28191144 AATACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.21, C:0.08, G:0.18, T:0.53
Consensus pattern (18 bp):
TGAGTTCAGTTCTAATTT
Found at i:28197735 original size:12 final size:12
Alignment explanation
Indices: 28197720--28197745 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28197710 ATAATATATT
28197720 TATTAATTAAAA
1 TATTAATTAAAA
28197732 TATTAATTAAAA
1 TATTAATTAAAA
28197744 TA
1 TA
28197746 AAAAACTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTAATTAAAA
Found at i:28201063 original size:21 final size:22
Alignment explanation
Indices: 28201030--28201070 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28201020 TGGGTAGTTG
*
28201030 TTATTAAACTGAGCAGAATACT
1 TTATGAAACTGAGCAGAATACT
*
28201052 TTATGAAA-TGAGCGGAATA
1 TTATGAAACTGAGCAGAATA
28201071 GCCGAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (22 bp):
TTATGAAACTGAGCAGAATACT
Found at i:28221939 original size:9 final size:9
Alignment explanation
Indices: 28221920--28221963 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
28221910 TAGTACTTAT
28221920 TTTTTTCTTC
1 TTTTTT-TTC
28221930 TTTTTTTTC
1 TTTTTTTTC
28221939 -TTTTTTTC
1 TTTTTTTTC
**
28221947 TTTTTTTGA
1 TTTTTTTTC
28221956 TTTTTTTT
1 TTTTTTTT
28221964 TAAATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 8 0.27
9 16 0.53
10 6 0.20
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:28221959 original size:17 final size:17
Alignment explanation
Indices: 28221921--28221962 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
28221911 AGTACTTATT
**
28221921 TTTTTCTTCTTTTTTTTC
1 TTTTT-TTCTTTTTTTGA
28221939 TTTTTTTCTTTTTTTGA
1 TTTTTTTCTTTTTTTGA
28221956 TTTTTTT
1 TTTTTTT
28221963 TTAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTGA
Found at i:28222250 original size:118 final size:117
Alignment explanation
Indices: 28222108--28222319 Score: 388
Period size: 118 Copynumber: 1.8 Consensus size: 117
28222098 TTTTACCCAA
28222108 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
1 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
*
28222173 TCAGTCACGATTTGAGCCATACTCATAACCTCGGCTAGTGGAGTTTTACTTGT
66 TCAGTCACGA-TTAAGCCATACTCATAACCTCGGCTAGTGGAGTTTTACTTGT
28222226 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
1 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
**
28222291 TCAGTCACGATTAAGCTGTACTCATAACC
66 TCAGTCACGATTAAGCCATACTCATAACC
28222320 ATGGAAAACA
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
117 16 0.18
118 75 0.82
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (117 bp):
CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
TCAGTCACGATTAAGCCATACTCATAACCTCGGCTAGTGGAGTTTTACTTGT
Found at i:28223156 original size:5 final size:5
Alignment explanation
Indices: 28223146--28223208 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
28223136 AATATTTAAC
* *
28223146 TAAAA TAAAA TAAAAA TAAAA GAAAA TAATAA -ATAA TAAAA TAAAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAA-AA TAAAA TAAAA T-AAAA
*
28223193 AAAAA TAAAAA TAAAA
1 TAAAA T-AAAA TAAAA
28223209 AGAAAGACTG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
4 2 0.04
5 29 0.62
6 16 0.34
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:28223181 original size:7 final size:6
Alignment explanation
Indices: 28223147--28223209 Score: 71
Period size: 6 Copynumber: 10.7 Consensus size: 6
28223137 ATATTTAACT
28223147 AAAAT- AAAATA AAAATA AAAGA-A AATAATA AATAAT- AAAATA AAAA-A
1 AAAATA AAAATA AAAATA AAA-ATA AA-AATA AA-AATA AAAATA AAAATA
28223194 AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAA
28223210 GAAAGACTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
5 13 0.25
6 30 0.58
7 9 0.17
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:28223189 original size:25 final size:22
Alignment explanation
Indices: 28223147--28223208 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 22
28223137 ATATTTAACT
28223147 AAAAT-AAAATAAAAATAAAAGAA
1 AAAATAAAAAT-AAAATAAAA-AA
28223170 AATAATAAATAATAAAATAAAAAA
1 AA-AATAAA-AATAAAATAAAAAA
28223194 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
28223209 AGAAAGACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 7 0.19
25 11 0.31
26 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAAAATAAAATAAAAAA
Found at i:28229570 original size:15 final size:15
Alignment explanation
Indices: 28229550--28229579 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28229540 ATAATCCTAA
*
28229550 TAATTATCTTAATAT
1 TAATTATCCTAATAT
28229565 TAATTATCCTAATAT
1 TAATTATCCTAATAT
28229580 AATAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:28237708 original size:16 final size:15
Alignment explanation
Indices: 28237687--28237729 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
28237677 TATTTTTTTA
28237687 TTTATTTAGTCTTATT
1 TTTATTTA-TCTTATT
*
28237703 TTTATTTTATTTTATT
1 TTTA-TTTATCTTATT
28237719 TTTATTT-TCTT
1 TTTATTTATCTT
28237730 TTAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 3 0.12
15 3 0.12
16 14 0.58
17 4 0.17
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTATTTATCTTATT
Found at i:28237709 original size:6 final size:6
Alignment explanation
Indices: 28237698--28237771 Score: 59
Period size: 6 Copynumber: 13.2 Consensus size: 6
28237688 TTATTTAGTC
* *
28237698 TTATTT TTA-TT TTA-TT TTATTT TTA-TT TTCTTT TAATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
* * * *
28237743 TCA-TT TCAATT TTATTA TTA-TT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT TTATTT T
28237772 GAAAGATATA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
5 23 0.42
6 32 0.58
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:28237712 original size:5 final size:5
Alignment explanation
Indices: 28237702--28237771 Score: 68
Period size: 5 Copynumber: 12.8 Consensus size: 5
28237692 TTAGTCTTAT
* *
28237702 TTTTA TTTTA TTTTA TTTTTA TTTTC TTTTAA TTTTTA TTTTCA TTTCAA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT-A -TTTTA TTTT-A TTT-TA
28237752 TTTTA TTATTA TTTTA TTTT
1 TTTTA TT-TTA TTTTA TTTT
28237772 GAAAGATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 32 0.58
6 19 0.35
7 4 0.07
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:28237714 original size:11 final size:11
Alignment explanation
Indices: 28237698--28237771 Score: 71
Period size: 11 Copynumber: 6.6 Consensus size: 11
28237688 TTATTTAGTC
28237698 TTATTTTTATT
1 TTATTTTTATT
28237709 TTA-TTTTATTT
1 TTATTTTTA-TT
28237720 TTATTTTCT-TT
1 TTATTTT-TATT
*
28237731 TAATTTTTATT
1 TTATTTTTATT
**
28237742 TTCATTTCAATT
1 TT-ATTTTTATT
*
28237754 TTATTATTATT
1 TTATTTTTATT
28237765 TTATTTT
1 TTATTTT
28237772 GAAAGATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
10 6 0.12
11 31 0.62
12 12 0.24
13 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:28237721 original size:17 final size:16
Alignment explanation
Indices: 28237698--28237771 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 16
28237688 TTATTTAGTC
28237698 TTATTTTTATTTTATT
1 TTATTTTTATTTTATT
*
28237714 TTATTTTTATTTTCTT
1 TTATTTTTATTTTATT
28237730 TTAATTTTTATTTTCATT
1 TT-ATTTTTATTTT-ATT
* *
28237748 TCAATTTTATTATTATT
1 TTATTTTTATT-TTATT
28237765 TTATTTT
1 TTATTTT
28237772 GAAAGATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
16 17 0.35
17 27 0.55
18 5 0.10
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTTATTTTATT
Found at i:28243511 original size:3 final size:3
Alignment explanation
Indices: 28243505--28243623 Score: 75
Period size: 3 Copynumber: 41.0 Consensus size: 3
28243495 GTAAAAAAAC
* * * *
28243505 ATA ATA ATA AT- ATA ATA GTA ATA ATA AT- ATA ATA AAA ATA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** * * * * * * *
28243551 ATA GCA ATA A-A ATA ATA GTT ATA AAA ATA ATA CTA ATA GTA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
28243598 ATA ATA AT- ACA ATA GTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
28243624 GTAGTAGTAA
Statistics
Matches: 88, Mismatches: 24, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
2 7 0.08
3 81 0.92
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28243528 original size:20 final size:20
Alignment explanation
Indices: 28243505--28243623 Score: 94
Period size: 23 Copynumber: 5.5 Consensus size: 20
28243495 GTAAAAAAAC
28243505 ATAATAATAATATAATAGTA
1 ATAATAATAATATAATAGTA
*
28243525 ATAATAATATAATAAAAATAGTA
1 ATAAT-A-ATAAT-ATAATAGTA
* * *
28243548 GTAATAGCAATAAAATAATAGTT
1 ATAAT---AATAATATAATAGTA
*
28243571 ATAAAAATAATACTAATAGTA
1 ATAATAATAATA-TAATAGTA
*
28243592 GTAGTAATAATAATACAATAGTA
1 --A-TAATAATAATATAATAGTA
28243615 ATAATAATA
1 ATAATAATA
28243624 GTAGTAGTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
20 19 0.24
21 9 0.12
22 5 0.06
23 30 0.38
24 14 0.18
25 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (20 bp):
ATAATAATAATATAATAGTA
Found at i:28244374 original size:9 final size:9
Alignment explanation
Indices: 28244337--28244384 Score: 53
Period size: 10 Copynumber: 5.0 Consensus size: 9
28244327 AAATAGATTC
28244337 GAAAAGAAAA
1 GAAAA-AAAA
28244347 GAAATAAAATA
1 GAAA-AAAA-A
28244358 -AAATAAAAA
1 GAAA-AAAAA
28244367 GAAAAAAAA
1 GAAAAAAAA
28244376 GAAAAAAAA
1 GAAAAAAAA
28244385 TAAATAACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 15 0.43
10 18 0.51
11 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.06
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:28245368 original size:182 final size:182
Alignment explanation
Indices: 28245042--28245546 Score: 746
Period size: 182 Copynumber: 2.8 Consensus size: 182
28245032 GTTTGTAGTT
* * * * * *
28245042 TTCATCCTGCTCCACTGCAACTTTAGGAAGATAAAGTTTGTTATGATCTGCTCTA-TAGCAACTT
1 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACT-GCAACTT
*
28245106 CAGAGAGATAAGATCTGTTTATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGG
65 CAGAGAGATAAGATCTGTTTATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA
28245171 TTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTGAC
130 TTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTGAC
*
28245224 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGTAACTTC
1 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTC
* * * * *
28245289 AGAGAGATAAGATTTATTTATTTATAGCTTCAATCTATTCTACTGCAACTTCAGGGAAATAAGAT
66 AGAGAGATAAGATCTGTTTATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGAT
* * * *
28245354 TTGCTGTTTTCAGTCTGCTCCACTGCATCTTCAGGGAGATAAGACTAGTGAC
131 TTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTGAC
* * *
28245406 TTCAA-CTGCTCCTCTGTAACTTCAGAGAGGTAAGGTTTGTTTTGATCTGCTCTACTGCAACTTC
1 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTC
* * * **
28245470 AGATAGATAAGATCTGTTTATTCATAGCTTTAATATGTTCCACTAAAACTTCAGGGAAATAAGAT
66 AGAGAGATAAGATCTGTTTATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGAT
28245535 TTG-TAATCTTCA
131 TTGCT-ATCTTCA
28245547 TCTTGTTGCC
Statistics
Matches: 288, Mismatches: 33, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
180 1 0.00
181 118 0.41
182 168 0.58
183 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (182 bp):
TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTC
AGAGAGATAAGATCTGTTTATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGAT
TTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTGAC
Found at i:28245396 original size:45 final size:44
Alignment explanation
Indices: 28245138--28245482 Score: 200
Period size: 45 Copynumber: 7.8 Consensus size: 44
28245128 TTATAGCTTT
* * * * *
28245138 AATCTGTTCCACTGCAACTTCAGGGAAATAAGGTTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGTTTTC
* * * * **
28245183 AGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTGACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGTTTTC
* * *
28245227 AACCTGCTCCTCTGCAACTTCAGGGAGATAAG-GTT-TGTTTT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGTTTTC
* * * * * *
28245268 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATTTATTTATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG----ATTTGTGT-T---TTC
** * *
28245320 AATCTATTCTACTGCAACTTCAGGGAAATAAGATTTGCTGTTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGTTTTC
* * * * **
28245365 AGTCTGCTCCACTGCATCTTCAGGGAGATAAGACTAGTGACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGTTTTC
* * * * *
28245409 AA-CTGCTCCTCTGTAACTTCAGAGAGGTAAG-GTT-TGTTTT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGTTTTC
* * **
28245449 GATCTGCTCTACTGCAACTTCAGATAGATAAGAT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
28245483 CTGTTTATTC
Statistics
Matches: 226, Mismatches: 60, Indels: 31
0.71 0.19 0.10
Matches are distributed among these distances:
40 1 0.00
41 54 0.24
42 5 0.02
43 25 0.11
44 39 0.17
45 62 0.27
46 2 0.01
47 2 0.01
48 6 0.03
49 2 0.01
51 2 0.01
52 26 0.12
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGTTTTC
Found at i:28245680 original size:88 final size:88
Alignment explanation
Indices: 28245522--28246320 Score: 1037
Period size: 88 Copynumber: 9.1 Consensus size: 88
28245512 CTAAAACTTC
* * * * * * * *
28245522 AGGGAAATAAGATTTGTAATCTTCATCTTGTTGCCCTACTGCTTAGGGGATTAAGACTCATTGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
*
28245587 TTCGATCTACTCCACAACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * *
28245610 AGGGAGATAAGATTTGTAAT-TTCCAGCCTGTTGCCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 AGGGAGATAAGATCTGTAATCTT-CAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGT
* *
28245674 CGTCGATCTACCCCACTACTGCTT
65 CTTCGATCTACTCCACTACTGCTT
* * *
28245698 AGGGAGATAAGATATGTAATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
* ***
28245763 TTCAATCCGTTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * * *
28245786 AGGGAGATAAGATCTGTAATCTGCAGCCTGTTTCCCAACTACTTA-GGGGTTAAGGCTCATCGTT
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
28245850 TTCGATCTACTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* ** * *
28245873 AAGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTTTTGCTTAGGAGGTTAAGGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
**
28245938 TTCGATCCGCTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * * * *
28245961 AGGGAGATAAGATCTGTAATCTTTACCCTGTTTCCCTACTACTTAGGGGGTTAAAGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
28246026 TTCGATCT-CTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * * *
28246048 ATGGAGATAAGATCCGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGTGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
* *
28246113 TTTGATCTACTCCATTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * * ** * *
28246136 AGAGAGATGAGATCTGTAATCTTCAGCTTGTTTCCCTACTATTTAAGGGGTTAAGGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
* * *
28246201 TTCGATCTGCTGCACTACTGTTT
66 TTCGATCTACTCCACTACTGCTT
* * * * * *
28246224 AGGGAGATAAGGTCTGTAATCTTCAGTCTGTTTCCCAACTGCTTAAGAGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
28246289 TTCGATCTACTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
28246312 AGGGAGATA
1 AGGGAGATA
28246321 GGATGGTGGC
Statistics
Matches: 616, Mismatches: 91, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
87 154 0.25
88 460 0.75
89 2 0.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (88 bp):
AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
TTCGATCTACTCCACTACTGCTT
Found at i:28245898 original size:175 final size:176
Alignment explanation
Indices: 28245522--28246320 Score: 1057
Period size: 175 Copynumber: 4.6 Consensus size: 176
28245512 CTAAAACTTC
* * * * * * *
28245522 AGGGAAATAAGATTTGTAATCTTCATCTTGTTGCCCTACTGCTTAGG-GGATTAAGACTCATTGT
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGAGG-TTAAGGCTCATCGT
* * *
28245586 CTTCGATCTACTCCACAACTGCTTAGGGAGATAAGATTTGTAAT-TTCCAGCCTGTTGCCCTACT
65 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT-CAGCCTGTTTCCCTACT
* * * *
28245650 GCTTAGGGGGTTAAGGCTCACCGTCGTCGATCTACCCCACTACTGCTT
129 ACTTAGGGGGTTAAGGCTCATCGTCTTCGATCTACTCCACTACTGCTT
* * * *
28245698 AGGGAGATAAGATATGTAATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTCATCGTC
* *** * *
28245763 TTCAATCCGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTGCAGCCTGTTTCCCAACTAC
66 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTAC
*
28245828 TTA-GGGGTTAAGGCTCATCGTTTTCGATCTACTCCACTACTGCTT
131 TTAGGGGGTTAAGGCTCATCGTCTTCGATCTACTCCACTACTGCTT
* ** *
28245873 AAGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTTTTGCTTAGGAGGTTAAGGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTCATCGTC
** * *
28245938 TTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTACCCTGTTTCCCTACTAC
66 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTAC
* *
28246003 TTAGGGGGTTAAAGCTCGTCGTCTTCGATCT-CTCCACTACTGCTT
131 TTAGGGGGTTAAGGCTCATCGTCTTCGATCTACTCCACTACTGCTT
* * * *
28246048 ATGGAGATAAGATCCGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGTGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTCATCGTC
* * * * * *
28246113 TTTGATCTACTCCATTACTGCTTAGAGAGATGAGATCTGTAATCTTCAGCTTGTTTCCCTACTAT
66 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTAC
* * * * *
28246178 TTAAGGGGTTAAGGCTCGTCGTCTTCGATCTGCTGCACTACTGTTT
131 TTAGGGGGTTAAGGCTCATCGTCTTCGATCTACTCCACTACTGCTT
* * * * *
28246224 AGGGAGATAAGGTCTGTAATCTTCAGTCTGTTTCCCAACTGCTTAAGAGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTCATCGTC
28246289 TTCGATCTACTCCACTACTGCTTAGGGAGATA
66 TTCGATCTACTCCACTACTGCTTAGGGAGATA
28246321 GGATGGTGGC
Statistics
Matches: 549, Mismatches: 70, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
175 315 0.57
176 231 0.42
177 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (176 bp):
AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTCATCGTC
TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTAC
TTAGGGGGTTAAGGCTCATCGTCTTCGATCTACTCCACTACTGCTT
Found at i:28246102 original size:263 final size:261
Alignment explanation
Indices: 28245522--28246320 Score: 1057
Period size: 263 Copynumber: 3.0 Consensus size: 261
28245512 CTAAAACTTC
* * * * * * * *
28245522 AGGGAAATAAGATTTGTAATCTTCATCTTGTTGCCCTACTGCTTAGGGGATTAAGACTCATTGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGG-TTAAGGCTCATCGTT
* * * *
28245587 TTCGATCTACTCCACAACTGCTTAGGGAGATAAGATTTGTAAT-TTCCAGCCTGTTGCCCTACTG
65 TTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTT-CAGCCTGTTTCCCTACTG
** * * * *
28245651 CTTAGGGGGTTAAGGCTCACCGTCGTCGATCTACCCCACTACTGCTTAGGGAGATAAGATATGTA
129 CTTA-GGGGTTAAGGCTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
*
28245716 ATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCGTCGTCTTCAATC-CGTTCCACTA
193 ATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCGTCGTCTTCGATCTC--TCCACTA
28245780 CTGCTT
256 CTGCTT
* * *
28245786 AGGGAGATAAGATCTGTAATCTGCAGCCTGTTTCCCAACTACTTAGGGGTTAAGGCTCATCGTTT
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGTTAAGGCTCATCGTTT
**
28245851 TCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTTTTGCT
66 TCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCT
*
28245916 TAGGAGGTTAAGGCTCGTCGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
131 TAGG-GGTTAAGGCTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
* * *
28245981 CTTTACCCTGTTTCCCTACTACTTAGGGGGTTAAAGCTCGTCGTCTTCGATCTCTCCACTACTGC
195 CTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCGTCGTCTTCGATCTCTCCACTACTGC
28246046 TT
260 TT
* * *
28246048 ATGGAGATAAGATCCGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGTGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGG-GGTTAAGGCTCATCGT-
* * *
28246113 TTT-GATCTACTCCATTACTGCTT-AGAGAGATGAGATCTGTAATCTTCAGCTTGTTTCCCTACT
64 TTTCGATCTACTCCACTACTGCTTAAG-GAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACT
** * * *
28246176 ATTTAAGGGGTTAAGGCTCGTCGTCTTCGATCTGCTGCACTACTGTTTAGGGAGATAAGGTCTGT
128 GCTT-AGGGGTTAAGGCTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
* * * * * **
28246241 AATCTTCAGTCTGTTTCCCAACTGCTTAAGAGGTTAAGGCTCACCGTCTTCGATCTACTCCACTA
192 AATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCGTCGTCTTCGATCT-CTCCACTA
28246306 CTGCTT
256 CTGCTT
28246312 AGGGAGATA
1 AGGGAGATA
28246321 GGATGGTGGC
Statistics
Matches: 471, Mismatches: 56, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
262 59 0.13
263 340 0.72
264 72 0.15
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (261 bp):
AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGTTAAGGCTCATCGTTT
TCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCT
TAGGGGTTAAGGCTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
TTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCGTCGTCTTCGATCTCTCCACTACTGCT
T
Found at i:28246235 original size:44 final size:44
Alignment explanation
Indices: 28245557--28246408 Score: 240
Period size: 44 Copynumber: 19.5 Consensus size: 44
28245547 TCTTGTTGCC
* * * *
28245557 CTACTGCTTAGGG-GATTAAGACTCATTGTCTTCGATCTACTCCA
1 CTACTGCTTAGGGAGA-TAAGGCTCGTCGTCTTCGATCTGCTCCA
* ** * ** * * *
28245601 CAACTGCTTAGGGAGATAAGATTTGTAAT-TTCCAGCCTGTTGCC-
1 CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCGA-TCTGCT-CCA
* * ** * * *
28245645 CTACTGCTTAGGGGGTTAAGGCTCACCGTCGTCGATCTACCCCA
1 CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
* * ** * *
28245689 CTACTGCTTAGGGAGATAA-GATATGTAATCTTC-AGCCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGGCT-CGTCGTCTTCGA-TCTG-CTCCA
* * * * * *
28245733 CTACTACTTAGGGGGTTAAGGCTCGTCGTCTTCAATCCGTTCCA
1 CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
* ** * * *
28245777 CTACTGCTTAGGGAGATAA-GATCTGTAATCTGC-AGCCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGGCTC-GTCGTCTTCGA-TCTG-CTCCA
* * * * * *
28245821 CAACTACTTAGGG-GTTAAGGCTCATCGTTTTCGATCTACTCCA
1 CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
* * ** * *
28245864 CTACTGCTTAAGGAGATAA-GATCTGTAATCTTC-AGCCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGGCTC-GTCGTCTTCGA-TCTG-CTCCA
** * *
28245908 CTTTTGCTTA-GGAGGTTAAGGCTCGTCGTCTTCGATCCGCTCCA
1 CTACTGCTTAGGGA-GATAAGGCTCGTCGTCTTCGATCTGCTCCA
* ** * * *
28245952 CTACTGCTTAGGGAGATAA-GATCTGTAATCTT-TACCCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGGCTC-GTCGTCTTCGA-TCTG-CTCCA
* * * *
28245996 CTACTACTTAGGGGGTTAAAGCTCGTCGTCTTCGATCT-CTCCA
1 CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
* * ** * *
28246039 CTACTGCTTATGGAGATAA-GATCCGTAATCTTC-AGCCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGGCT-CGTCGTCTTCGA-TCTG-CTCCA
* ** * *
28246083 CTACTGCTTAGGTG-GTTAAGGCTCACCGTCTTTGATCTACTCCA
1 CTACTGCTTAGG-GAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
* * * * ** * *
28246127 TTACTGCTTAGAGAGATGA-GATCTGTAATCTTC-AGCTTGTTTCC-
1 CTACTGCTTAGGGAGATAAGGCTC-GTCGTCTTCGATC-TG-CTCCA
** * *
28246171 CTACTATTTAAGGG-GTTAAGGCTCGTCGTCTTCGATCTGCTGCA
1 CTACTGCTT-AGGGAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
* ** *
28246215 CTACTGTTTAGGGAGATAAGG-TCTGTAATCTTC-AGTCTGTTTCC-
1 CTACTGCTTAGGGAGATAAGGCTC-GTCGTCTTCGA-TCTG-CTCCA
* * * ** *
28246259 CAACTGCTTA-AGAGGTTAAGGCTCACCGTCTTCGATCTACTCCA
1 CTACTGCTTAGGGA-GATAAGGCTCGTCGTCTTCGATCTGCTCCA
* * *
28246303 CTACTGCTTAGGGAGAT-AGGATGGT-GGCTT-GAATCTGCTCCA
1 CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCG-ATCTGCTCCA
** * * * * * *
28246345 CTACTGCTTAGGGAGATAAGATTCGCCATTTTTGATCTACTTCA
1 CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
28246389 CTACTGCTTAGGGAGATAAG
1 CTACTGCTTAGGGAGATAAG
28246409 ATCTATAAAT
Statistics
Matches: 559, Mismatches: 188, Indels: 122
0.64 0.22 0.14
Matches are distributed among these distances:
41 1 0.00
42 39 0.07
43 107 0.19
44 353 0.63
45 59 0.11
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGGCTCGTCGTCTTCGATCTGCTCCA
Found at i:28251600 original size:21 final size:20
Alignment explanation
Indices: 28251560--28251597 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28251550 CAAAGCAGTA
28251560 ACGAAAATAGGAACAAAATG
1 ACGAAAATAGGAACAAAATG
* *
28251580 ACGAAAATCGTAACAAAA
1 ACGAAAATAGGAACAAAA
28251598 ATGGATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.11
Consensus pattern (20 bp):
ACGAAAATAGGAACAAAATG
Found at i:28252759 original size:15 final size:15
Alignment explanation
Indices: 28252719--28252761 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
28252709 ATTTTAAAAA
*
28252719 AATGATAGTAATAGT
1 AATGATAATAATAGT
* *
28252734 AATGATTATAATATT
1 AATGATAATAATAGT
*
28252749 AATGGTAATAATA
1 AATGATAATAATA
28252762 CAAGTAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (15 bp):
AATGATAATAATAGT
Found at i:28252894 original size:3 final size:3
Alignment explanation
Indices: 28252881--28253013 Score: 94
Period size: 3 Copynumber: 45.3 Consensus size: 3
28252871 AATAGGTAAA
*
28252881 AAT ATAT AAT AAT AAT AAT -AT AAT AGT AAT AAT AAT -AT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * * * * *
28252925 AAT AGC AGT AAC AGT AAT AA- AAT AAT AGT TAT AAA AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
28252972 AGT AGT AAT AAT AAT AAT -AC AAT AAT AAT AGT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28253014 TTGAATTAAT
Statistics
Matches: 101, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
2 7 0.07
3 91 0.90
4 3 0.03
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28252912 original size:23 final size:24
Alignment explanation
Indices: 28252886--28253039 Score: 136
Period size: 23 Copynumber: 6.4 Consensus size: 24
28252876 GTAAAAATAT
28252886 ATAATAATAATAAT-ATAATAGTA
1 ATAATAATAATAATAATAATAGTA
*
28252909 ATAATAAT-ATAATAATAATAGCA
1 ATAATAATAATAATAATAATAGTA
* * * *
28252932 GTAACAGTAATAA-AATAATAGTT
1 ATAATAATAATAATAATAATAGTA
* * *
28252955 ATAAAAATAATACTAATAGTAGTA
1 ATAATAATAATAATAATAATAGTA
28252979 ATAATAATAATACAATAATAATAGTA
1 ATAATAATAAT--AATAATAATAGTA
* * *
28253005 GTAATAATATTGAATTAATTAAT-TTA
1 ATAATAATAAT-AA-TAA-TAATAGTA
28253031 ATAATAATA
1 ATAATAATA
28253040 GCAAAAATAA
Statistics
Matches: 104, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
22 5 0.05
23 38 0.37
24 22 0.21
25 2 0.02
26 33 0.32
27 4 0.04
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (24 bp):
ATAATAATAATAATAATAATAGTA
Found at i:28253807 original size:25 final size:23
Alignment explanation
Indices: 28253778--28253827 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 23
28253768 AATAGATTAG
*
28253778 AAAAGAAAAGAAAGAAAATAAAATA
1 AAAAGAAAAAAAAG-AAA-AAAATA
28253803 AAAAGAAAAAAAAGAAAAAAATA
1 AAAAGAAAAAAAAGAAAAAAATA
28253826 AA
1 AA
28253828 TAACAGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.33
24 3 0.12
25 13 0.54
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (23 bp):
AAAAGAAAAAAAAGAAAAAAATA
Found at i:28253808 original size:20 final size:20
Alignment explanation
Indices: 28253783--28253820 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28253773 ATTAGAAAAG
* *
28253783 AAAAGAAAGAAAATAAAATA
1 AAAAGAAAAAAAAGAAAATA
28253803 AAAAGAAAAAAAAGAAAA
1 AAAAGAAAAAAAAGAAAA
28253821 AAATAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAAAAGAAAATA
Found at i:28253809 original size:16 final size:15
Alignment explanation
Indices: 28253776--28253821 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
28253766 TAAATAGATT
28253776 AGAAAAGAAAAG--AA
1 AGAAAA-AAAAGAAAA
*
28253790 AGAAAATAAAATAAAA
1 AGAAAA-AAAAGAAAA
28253806 AGAAAAAAAAGAAAA
1 AGAAAAAAAAGAAAA
28253821 A
1 A
28253822 AATAAATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.37
15 9 0.33
16 8 0.30
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (15 bp):
AGAAAAAAAAGAAAA
Found at i:28260778 original size:26 final size:24
Alignment explanation
Indices: 28260749--28260803 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 24
28260739 GGACTCACCA
*
28260749 CAGCTTGTATGAGCTTACTGATATAT
1 CAGCTTGTAAGAGCTTACTG-T-TAT
28260775 CAGCTTGTAAGAGCTTACTGTTAT
1 CAGCTTGTAAGAGCTTACTGTTAT
28260799 CAGCT
1 CAGCT
28260804 CAATAGAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 8 0.29
25 1 0.04
26 19 0.68
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (24 bp):
CAGCTTGTAAGAGCTTACTGTTAT
Found at i:28260811 original size:24 final size:24
Alignment explanation
Indices: 28260784--28260853 Score: 97
Period size: 23 Copynumber: 2.9 Consensus size: 24
28260774 TCAGCTTGTA
*
28260784 AGAGCTTACTGTTATCAGCTCAAT
1 AGAGCTTACTGTTATCAACTCAAT
*
28260808 AGAGCTTACCGTT-TCAACTCAAT
1 AGAGCTTACTGTTATCAACTCAAT
*
28260831 AGAGCTTATTGTTTATCAACTCA
1 AGAGCTTACTG-TTATCAACTCA
28260854 GGAGGAGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 18 0.45
24 14 0.35
25 8 0.20
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (24 bp):
AGAGCTTACTGTTATCAACTCAAT
Found at i:28269421 original size:46 final size:46
Alignment explanation
Indices: 28269322--28269447 Score: 164
Period size: 46 Copynumber: 2.7 Consensus size: 46
28269312 GAGTCATCCA
* * * *
28269322 AACTCGTTGAGTTGCGTTCTGAGTTCACCTATGGATGCAAGCATCCG
1 AACTCGTTGAGTTGTGTTCCGAGTTCA-TTATGGATGCAAGCACCCG
*
28269369 AACTCGTTGAGTTGTGTTCCAAGTTCATTATGGATGCGAA-CACCCG
1 AACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGC-AAGCACCCG
* *
28269415 AGCTCGTTGAGTTGTGTTTCGAGTTCATTATGG
1 AACTCGTTGAGTTGTGTTCCGAGTTCATTATGG
28269448 GTGAGATTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
46 44 0.63
47 26 0.37
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (46 bp):
AACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGCAAGCACCCG
Found at i:28280633 original size:23 final size:24
Alignment explanation
Indices: 28280577--28280633 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
28280567 GATTTTTAAT
*
28280577 TAAATAAAATATTTAAAATTAAGAT
1 TAAATAAAA-ATTTAAAATTAAGAA
* *
28280602 TCAAT-AAAATTTAAATTTAA-AA
1 TAAATAAAAATTTAAAATTAAGAA
28280624 TAAATAAAAA
1 TAAATAAAAA
28280634 ATCATCTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 5 0.19
23 15 0.56
24 3 0.11
25 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAATAAAAATTTAAAATTAAGAA
Found at i:28291373 original size:20 final size:22
Alignment explanation
Indices: 28291333--28291374 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
28291323 ATTGTTAATA
*
28291333 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
28291355 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
28291375 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:28291475 original size:15 final size:15
Alignment explanation
Indices: 28291455--28291511 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
28291445 ATTCAATATT
28291455 AATATTTTAATAATA
1 AATATTTTAATAATA
*
28291470 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
28291489 AATATATTAATAATA
1 AATATTTTAATAATA
*
28291504 AATGTTTT
1 AATATTTT
28291512 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:28291914 original size:32 final size:34
Alignment explanation
Indices: 28291878--28291949 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
28291868 AACTTTTATG
*
28291878 AAATATTTTTA-AGAAA-T-CTACCAAACACCAAA
1 AAATATTTTTACACAAATTCCT-CCAAACACCAAA
*
28291910 AAATA-TTTTACACAAATTCCTCCAAACACCAGA
1 AAATATTTTTACACAAATTCCTCCAAACACCAAA
28291943 AAATATT
1 AAATATT
28291950 AGCTTTTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 5 0.15
32 9 0.26
33 17 0.50
34 3 0.09
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (34 bp):
AAATATTTTTACACAAATTCCTCCAAACACCAAA
Found at i:28291989 original size:14 final size:14
Alignment explanation
Indices: 28291967--28292005 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
28291957 CCAGAAAAGT
*
28291967 AAATTATTTTCCAG
1 AAATCATTTTCCAG
*
28291981 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
28291995 AATTCATTTTC
1 AAATCATTTTC
28292006 AGTGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.44
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:28298414 original size:25 final size:24
Alignment explanation
Indices: 28298339--28298513 Score: 182
Period size: 25 Copynumber: 7.4 Consensus size: 24
28298329 CACTAATGAA
*
28298339 CAGAGAGCACTGAAGTGCT-ATA-
1 CAGAGAGCACTGACGTGCTAATAT
** *
28298361 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
28298383 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
* *
28298408 CAGAGAGCACTGGCGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTAAT-AT
*
28298433 CAGAGAGCACTGGCGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
** *
28298458 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
28298480 CAGAGAGCACTGACGTGCTAATATT
1 CAGAGAGCACTGACGTGCTAATA-T
28298505 CAGAGAGCA
1 CAGAGAGCA
28298514 TGCTGAAGTC
Statistics
Matches: 128, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
21 1 0.01
22 51 0.40
23 2 0.02
24 4 0.03
25 68 0.53
26 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTAATAT
Found at i:28298444 original size:50 final size:47
Alignment explanation
Indices: 28298339--28298513 Score: 223
Period size: 47 Copynumber: 3.7 Consensus size: 47
28298329 CACTAATGAA
* *
28298339 CAGAGAGCACTGAAGTGCT--ATA-CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAACGTGCTAAT
***
28298383 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTGGCGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAACGTGC---TAAT
* *
28298433 CAGAGAGCACTGGCGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAACGTGCTAAT
28298480 CAGAGAGCACTGACGTGCT-AATATTCAGAGAGCA
1 CAGAGAGCACTGACGTGCTAAATA-TCAGAGAGCA
28298514 TGCTGAAGTC
Statistics
Matches: 113, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
44 18 0.16
46 7 0.06
47 46 0.41
50 42 0.37
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (47 bp):
CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAACGTGCTAAT
Found at i:28298477 original size:97 final size:94
Alignment explanation
Indices: 28298339--28298513 Score: 289
Period size: 97 Copynumber: 1.8 Consensus size: 94
28298329 CACTAATGAA
28298339 CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
1 CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
28298404 -ATATCAGAGAGCACTGGCGTGCTAGTAAT
66 TAT-TCAGAGAGCACTGGCGTGCTAGTAAT
**
28298433 CAGAGAGCACTGGCGTGCTAAATATCAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGC
1 CAGAGAGCACTGAAGTGCT--ATA-CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGC
28298498 TAATATTCAGAGAGCA
63 TAATATTCAGAGAGCA
28298514 TGCTGAAGTC
Statistics
Matches: 75, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
94 17 0.23
96 3 0.04
97 53 0.71
98 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (94 bp):
CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
TATTCAGAGAGCACTGGCGTGCTAGTAAT
Found at i:28303127 original size:13 final size:14
Alignment explanation
Indices: 28303091--28303128 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
28303081 ATATTTTATG
*
28303091 ATATATTTTATATT
1 ATATAGTTTATATT
28303105 ATAATAGTTTATATT
1 AT-ATAGTTTATATT
28303120 AT-TAGTTTA
1 ATATAGTTTA
28303129 CTAAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 2 0.09
15 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
ATATAGTTTATATT
Found at i:28306805 original size:52 final size:49
Alignment explanation
Indices: 28306625--28306814 Score: 187
Period size: 47 Copynumber: 3.9 Consensus size: 49
28306615 ACATAGTCAT
* ** * *
28306625 ATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-ATCAC
1 ATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
* * *
28306673 ATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAGCAC
1 ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
*
28306720 ATATCACA--CCGATGCCATATCCC-GAATATGGTCTTATACGGAAGCAC
1 ATATCACACTCCGATGCCATAGCCCAG-ATATGGTCTTATACGGAAGCAC
* *
28306767 ATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 ATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
28306815 ATCACATTTC
Statistics
Matches: 119, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
46 26 0.22
47 53 0.45
48 8 0.07
49 1 0.01
52 30 0.25
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
ATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAGCAC
Found at i:28319754 original size:83 final size:81
Alignment explanation
Indices: 28319662--28319880 Score: 281
Period size: 75 Copynumber: 2.7 Consensus size: 81
28319652 GCAGCTACAT
*
28319662 CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTGTCCGAATATATACATACATA
1 CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTTTCC-AATATATACATA-ATA
*
28319727 CATACATATATTATGCTA
64 CATACATATATAATGCTA
* * *
28319745 CATCACTACCTAAAAGCTTCACTAATAACCCTTCATGGCGGATTTTCC--TA-AT--AT-GTACA
1 CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTTTCCAATATATACATAATACA
28319804 TACATATATAATGCTA
66 TACATATATAATGCTA
* * *
28319820 CATCACTACCTAAAAGCTTCTCTGATAA-CTCTTCATGGAGGATTTTCCTAAAATATACATA
1 CATCACTACCTAAAAGCTTCACTGATAACCT-TTCATGGCGGATTTTCC-AATATATACATA
28319881 TCTATTTGGT
Statistics
Matches: 118, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
74 1 0.01
75 61 0.52
77 2 0.02
78 1 0.01
79 4 0.03
80 2 0.02
81 2 0.02
83 45 0.38
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (81 bp):
CATCACTACCTAAAAGCTTCACTGATAACCTTTCATGGCGGATTTTCCAATATATACATAATACA
TACATATATAATGCTA
Found at i:28321008 original size:17 final size:19
Alignment explanation
Indices: 28320964--28321010 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28320954 TAGTTGAATC
28320964 AATTTTCTTTATTTTTTAAA
1 AATTTT-TTTATTTTTTAAA
* *
28320984 AATATTTTTA-TTTTT-AT
1 AATTTTTTTATTTTTTAAA
28321001 AATTTTTTTA
1 AATTTTTTTA
28321011 AACTTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 5 0.21
19 4 0.17
20 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTTTTTTATTTTTTAAA
Found at i:28330467 original size:38 final size:38
Alignment explanation
Indices: 28330416--28330526 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 38
28330406 TTTCAAATTA
* *
28330416 ACATGTATAACCATGGCATATCCATTTAACACCACGTT
1 ACATGTTTAACCATGGTATATCCATTTAACACCACGTT
*
28330454 ACATGTTTAACCATGGTATATCCACTTAACACCACGTT
1 ACATGTTTAACCATGGTATATCCATTTAACACCACGTT
* * *
28330492 ACATGTTTAATCGTGGTATATCCATTTAGCACCAC
1 ACATGTTTAACCATGGTATATCCATTTAACACCAC
28330527 ATTAATGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (38 bp):
ACATGTTTAACCATGGTATATCCATTTAACACCACGTT
Found at i:28330608 original size:48 final size:48
Alignment explanation
Indices: 28330494--28330632 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 48
28330484 ACCACGTTAC
* * * * *
28330494 ATGTTTAATCGTGGTATATCCATTTAGCACCACATTA-ATGAATTAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
* * *
28330541 ATATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
28330589 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTAT
28330633 AACCATGGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 31 0.39
48 49 0.61
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (48 bp):
ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
Found at i:28333195 original size:42 final size:42
Alignment explanation
Indices: 28333128--28333326 Score: 227
Period size: 42 Copynumber: 4.7 Consensus size: 42
28333118 GTACATCATT
* * **
28333128 AACAGAAGCTCATAAGAGCTGAACAGAAGCTTGTAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
* * * *
28333170 AACAGAAGCTTGTAAAAGCTTAACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
*
28333212 AATAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
* * * * *
28333254 AACAGAAGCTCGTCATAGCTGAATAGAAACTTATAAGAGTTT
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
* * *
28333296 AACAGAAACTCTCGAAAGAGCTAAACAGAAA
1 AACAG-AA-GCTCGTAAGAGCTGAACAGAAA
28333327 GTAAAATATG
Statistics
Matches: 130, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 112 0.86
43 2 0.02
44 16 0.12
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.20
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
Found at i:28333279 original size:63 final size:63
Alignment explanation
Indices: 28333126--28333306 Score: 202
Period size: 63 Copynumber: 2.9 Consensus size: 63
28333116 GAGTACATCA
* * **
28333126 TTAACAGAAGCTCATAAGAGCTGAACAGAAGCTTGTAAGAGTTGAACAGAAGCTTGTAAAAGC
1 TTAACAGAAGCTCATAAGAGCTGAATAGAAGCTTGTAAGAGTTGAACAGAAACTCATAAAAGC
* * * * * *
28333189 TTAACAGAAACTCATAAGAGTTAAATAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAG-
1 TTAACAGAAGCTCATAAGAGCTGAATAGAAGCTTGTAAGAGTTGAACAGAAACTCATAAAAGC
* * * * * *
28333251 TTGAACAGAAGCTCGTCATAGCTGAATAGAAACTTATAAGAGTTTAACAGAAACTC
1 TT-AACAGAAGCTCATAAGAGCTGAATAGAAGCTTGTAAGAGTTGAACAGAAACTC
28333307 TCGAAAGAGC
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
62 2 0.02
63 94 0.98
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (63 bp):
TTAACAGAAGCTCATAAGAGCTGAATAGAAGCTTGTAAGAGTTGAACAGAAACTCATAAAAGC
Found at i:28333305 original size:21 final size:21
Alignment explanation
Indices: 28333128--28333302 Score: 152
Period size: 21 Copynumber: 8.3 Consensus size: 21
28333118 GTACATCATT
28333128 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
** *
28333149 AACAGAAGCTTGTAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
** * *
28333170 AACAGAAGCTTGTAAAAGCTT
1 AACAGAAGCTCATAAGAGCTG
* * *
28333191 AACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGCTG
* *
28333212 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
28333233 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
* * *
28333254 AACAGAAGCTCGTCATAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * * * *
28333275 AATAGAAACTTATAAGAGTTT
1 AACAGAAGCTCATAAGAGCTG
28333296 AACAGAA
1 AACAGAA
28333303 ACTCTCGAAA
Statistics
Matches: 119, Mismatches: 35, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 119 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:28335607 original size:44 final size:43
Alignment explanation
Indices: 28335531--28335641 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 43
28335521 CTCCAGTCCG
* *
28335531 CTCCACTGCAACTTCAAGGAGATGAGGCTTGTAATTTTAACCTA
1 CTCCACTACAACTTC-AGGAGATGAGGCTTGTAATTTCAACCTA
* * * *
28335575 CTCTACTACAACTTCAGGAAGATGAGGTTTGTAATTTCGACCTG
1 CTCCACTACAACTTCAGG-AGATGAGGCTTGTAATTTCAACCTA
*
28335619 CTCCACTGCAACTTCAGAGAGAT
1 CTCCACTACAACTTCAG-GAGAT
28335642 AAGATCTGCG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
43 3 0.05
44 53 0.93
45 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
CTCCACTACAACTTCAGGAGATGAGGCTTGTAATTTCAACCTA
Found at i:28335740 original size:45 final size:45
Alignment explanation
Indices: 28335616--28336154 Score: 235
Period size: 45 Copynumber: 11.7 Consensus size: 45
28335606 TAATTTCGAC
* * *
28335616 CTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCGATTCATAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGC---T-ATA--TTCAGT
* * *
28335667 CTGTTCCACTGCAACTTCAGGAAAATAAGATTTGCTATATTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
** * *
28335712 CTGCTCCACTGCAACTTCAGGGAGATAAGGCTTG-T-T-TTGA-C
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
* * * *
28335753 CTGCTCTACTGCAACTTCAGAGAGATAGGATCTG-TA-ATTGACAGCTTCGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATT--CA-----G-T
* * *
28335804 CTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
* * * ** * *
28335849 CTGCTCCACTACGACTTCAGAGAGATAAGGCTTG-T-T-TTGA-C
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
* * * * ** *
28335890 CTGCTCTACTGCAACTTTAGAGAGATAGGATCTGTAATTTATAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-T--GCTATA--TTCAGT
* * * *
28335941 CTGTTTCACTGTAACTTCAGGGAAATAAGATTTGCTATATTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
** ** * *
28335986 CTGCTCCACTGCGGCTTCAGGGAGATAAGGCTTG-T-T-TTGA-C
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
* * * * * **
28336027 CTGCACTACTGCAACTTTAGAGAGATAGGATCTGTAATTTATAGCTTC-GAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-T--GCTATA--TTCAG-T
* * * * *
28336078 CTGTTCCGCTGCAACTTCAGGGAAATAAAATTTGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
* *
28336123 CTGCTCCACTGCGACTTTAGGGAGATAAGATT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATT
28336155 GATGACTTTA
Statistics
Matches: 356, Mismatches: 97, Indels: 76
0.67 0.18 0.14
Matches are distributed among these distances:
41 75 0.21
42 13 0.04
43 5 0.01
44 4 0.01
45 122 0.34
46 4 0.01
47 12 0.03
48 1 0.00
49 2 0.01
50 7 0.02
51 106 0.30
52 2 0.01
53 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATATTCAGT
Found at i:28335769 original size:41 final size:42
Alignment explanation
Indices: 28335712--28335916 Score: 146
Period size: 41 Copynumber: 4.6 Consensus size: 42
28335702 TATATTCAGT
* *
28335712 CTGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT-TTTGAC
1 CTGCTCTACTGCAACTTCAGAGAGATAAGGCTTGTATTTGAC
* *
28335753 CTGCTCTACTGCAACTTCAGAGAGAT-AGGATCTGTAATTGAC
1 CTGCTCTACTGCAACTTCAGAGAGATAAGGCT-TGTATTTGAC
* * ** * *
28335795 AGCTTCGATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGT
1 --C-T-G--C---TCTACTGCAACTTCAGAGAGATAAGGCTTG-TAT-TTGA-C
* * *
28335849 CTGCTCCACTACGACTTCAGAGAGATAAGGCTTGT-TTTGAC
1 CTGCTCTACTGCAACTTCAGAGAGATAAGGCTTGTATTTGAC
*
28335890 CTGCTCTACTGCAACTTTAGAGAGATA
1 CTGCTCTACTGCAACTTCAGAGAGATA
28335917 GGATCTGTAA
Statistics
Matches: 125, Mismatches: 24, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
40 4 0.03
41 50 0.40
42 8 0.06
43 1 0.01
44 2 0.02
45 24 0.19
46 1 0.01
48 2 0.02
50 1 0.01
51 23 0.18
52 6 0.05
53 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
CTGCTCTACTGCAACTTCAGAGAGATAAGGCTTGTATTTGAC
Found at i:28335785 original size:137 final size:137
Alignment explanation
Indices: 28335585--28336151 Score: 864
Period size: 137 Copynumber: 4.1 Consensus size: 137
28335575 CTCTACTACA
* * * * *
28335585 ACTTCAGGAAGATGAGGTTTGTAATTTCGACCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG
1 ACTTCAGGGAGATAAGGCTTGT--TTT-GACCTGCTCTACTGCAACTTCAGAGAGATAGGATCTG
** * *
28335650 CGATTCATAGCTTCAATCTGTTCCACTGCAACTTCAGGAAAATAAGATTTGCTATATTCAGTCTG
63 TAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTG
*
28335715 CTCCACTGCA
128 CTCCACTGCG
28335725 ACTTCAGGGAGATAAGGCTTGTTTTGACCTGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAA
1 ACTTCAGGGAGATAAGGCTTGTTTTGACCTGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAA
* * * *
28335790 TTGACAGCTTCGATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGCTC
66 TTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGCTC
*
28335855 CACTACG
131 CACTGCG
* *
28335862 ACTTCAGAGAGATAAGGCTTGTTTTGACCTGCTCTACTGCAACTTTAGAGAGATAGGATCTGTAA
1 ACTTCAGGGAGATAAGGCTTGTTTTGACCTGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAA
* *
28335927 TTTATAGCTTCAATCTGTTTCACTGTAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGCTC
66 TTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGCTC
28335992 CACTGCG
131 CACTGCG
* * *
28335999 GCTTCAGGGAGATAAGGCTTGTTTTGACCTGCACTACTGCAACTTTAGAGAGATAGGATCTGTAA
1 ACTTCAGGGAGATAAGGCTTGTTTTGACCTGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAA
* * * *
28336064 TTTATAGCTTCGATCTGTTCCGCTGCAACTTCAGGGAAATAAAATTTGCTATCTTCAGTCTGCTC
66 TTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGCTC
28336129 CACTGCG
131 CACTGCG
*
28336136 ACTTTAGGGAGATAAG
1 ACTTCAGGGAGATAAG
28336152 ATTGATGACT
Statistics
Matches: 393, Mismatches: 34, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
137 371 0.94
138 3 0.01
140 19 0.05
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (137 bp):
ACTTCAGGGAGATAAGGCTTGTTTTGACCTGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAA
TTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATATTCAGTCTGCTC
CACTGCG
Found at i:28343957 original size:84 final size:83
Alignment explanation
Indices: 28343851--28344017 Score: 194
Period size: 84 Copynumber: 2.0 Consensus size: 83
28343841 GGGCCTGATT
* * * * *
28343851 GTAACGGATGGCATTCGCGTGTGTAG-CTCCGGTTGCGTTTGAGCATTCGTCGAGGTGAAACCAT
1 GTAACGGATGGCATTCGCGTGTGT-GTCTCAGGTTGCGTTTAAGCATTCGCCAAGGTAAAACCA-
*
28343915 GGGGGTAAAGAGGATCTTCA
64 GAGGGTAAAGAGGATCTTCA
* * * * *
28343935 GTAACGGATGGC-CTCTGCGTGTGTGTCTTATGTTGCGTTTAAGCATTTGCCAAGGTAAAACTAG
1 GTAACGGATGGCATTC-GCGTGTGTGTCTCAGGTTGCGTTTAAGCATTCGCCAAGGTAAAACCAG
28343999 AGGGTAAAGAGGATCTTCA
65 AGGGTAAAGAGGATCTTCA
28344018 TTGTTATTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
83 22 0.31
84 48 0.69
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (83 bp):
GTAACGGATGGCATTCGCGTGTGTGTCTCAGGTTGCGTTTAAGCATTCGCCAAGGTAAAACCAGA
GGGTAAAGAGGATCTTCA
Found at i:28349226 original size:46 final size:44
Alignment explanation
Indices: 28349167--28349281 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
28349157 ACAGGACAGA
* *
28349167 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
28349213 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
28349257 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
28349282 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:28349262 original size:44 final size:45
Alignment explanation
Indices: 28349167--28349300 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
28349157 ACAGGACAGA
* *
28349167 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
28349213 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
28349257 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
28349301 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:28351393 original size:2 final size:2
Alignment explanation
Indices: 28351386--28351422 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28351376 TTCCCAAAGC
*
28351386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28351423 GATTTGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:28354559 original size:43 final size:43
Alignment explanation
Indices: 28354511--28354597 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
28354501 GGCCCTTAAT
*
28354511 CATTTCTTAA-CTACTTAACTATTATAATTAATAACCCAATAAC
1 CATTTCTTAATC-ACTTAACTATTATAATTAACAACCCAATAAC
* * *
28354554 CATTTCTTAATCATTTAATTATTATAATTAACAACTCAATAAC
1 CATTTCTTAATCACTTAACTATTATAATTAACAACCCAATAAC
28354597 C
1 C
28354598 CACTAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (43 bp):
CATTTCTTAATCACTTAACTATTATAATTAACAACCCAATAAC
Found at i:28357413 original size:24 final size:24
Alignment explanation
Indices: 28357385--28357432 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28357375 AGAAGTAGAA
28357385 GATTATTTTAAAATTATAAATACT
1 GATTATTTTAAAATTATAAATACT
28357409 GATTATTTTAAAATTATAAATACT
1 GATTATTTTAAAATTATAAATACT
28357433 TTCTTTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
GATTATTTTAAAATTATAAATACT
Found at i:28357511 original size:35 final size:36
Alignment explanation
Indices: 28357472--28357542 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
28357462 ATTATAATAC
28357472 ATACTTTTAATTTTAAAT-AAAAATATAGATTATAT
1 ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
28357507 ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
1 ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
28357543 GAACTTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (36 bp):
ATACTTTTAATTTTAAATAAAAAATATAGATTATAT
Found at i:28358882 original size:126 final size:125
Alignment explanation
Indices: 28358655--28358938 Score: 390
Period size: 126 Copynumber: 2.3 Consensus size: 125
28358645 TTTTAATTAA
*
28358655 TTATATTTCGAAAATATGATTAAATTTATCACACAAATTTCAAAAATTAAAAATATAAAATTACC
1 TTATATTTCGAAAATATGATTAAATTTATCACACAAATTTAAAAAATTAAAAATATAAAATTACC
* * *
28358720 ATCATACTATTAAGAACATTAAAAATCGGAATTAAATTTTATTTTAATTAATATTTATCT
66 ATCATACTATTAAGAACATTAAAAATCGCAACTAAATTTTATTTCAATTAATATTTATCT
* * * *
28358780 TTATACTTCGAAAATAGGATTAAATTTATCACACAATTTTTAAAAAAGTT-AAAATGTAAAATTA
1 TTATATTTCGAAAATATGATTAAATTTATCACACAA-ATTTAAAAAA-TTAAAAATATAAAATTA
* * * * * * *
28358844 CCATCTTACTATTAATAATATTAAAAATTGCCACTAAATTTTATTTCCATTAATATTTGTCT
64 CCATCATACTATTAAGAACATTAAAAATCGCAACTAAATTTTATTTCAATTAATATTTATCT
* *
28358906 TTATATTTCGAAAATATAATTAAATTTGTCACA
1 TTATATTTCGAAAATATGATTAAATTTATCACA
28358939 ATTTTATATT
Statistics
Matches: 138, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
125 34 0.25
126 102 0.74
127 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (125 bp):
TTATATTTCGAAAATATGATTAAATTTATCACACAAATTTAAAAAATTAAAAATATAAAATTACC
ATCATACTATTAAGAACATTAAAAATCGCAACTAAATTTTATTTCAATTAATATTTATCT
Found at i:28360780 original size:6 final size:6
Alignment explanation
Indices: 28360771--28360801 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28360761 TTTTTTTTTT
*
28360771 AATATG AATATG GATATG AATATG AATATG A
1 AATATG AATATG AATATG AATATG AATATG A
28360802 TATTTTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (6 bp):
AATATG
Found at i:28360794 original size:18 final size:17
Alignment explanation
Indices: 28360771--28360804 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28360761 TTTTTTTTTT
28360771 AATATGAATATGGATATG
1 AATATGAATAT-GATATG
28360789 AATATGAATATGATAT
1 AATATGAATATGATAT
28360805 TTTGGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (17 bp):
AATATGAATATGATATG
Found at i:28380339 original size:12 final size:12
Alignment explanation
Indices: 28380322--28380346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28380312 GAACTTAAGG
28380322 AAAAAAAACAAA
1 AAAAAAAACAAA
28380334 AAAAAAAACAAA
1 AAAAAAAACAAA
28380346 A
1 A
28380347 TCGCTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:28385957 original size:16 final size:17
Alignment explanation
Indices: 28385936--28385970 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
28385926 AAAAATTGTT
28385936 TTACTTTTC-TATATTA
1 TTACTTTTCATATATTA
28385952 TTACTTTTCATATATTA
1 TTACTTTTCATATATTA
28385969 TT
1 TT
28385971 TCATGTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (17 bp):
TTACTTTTCATATATTA
Found at i:28386021 original size:12 final size:13
Alignment explanation
Indices: 28385999--28386032 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28385989 ATATATTTTC
28385999 ATTATTTTATATT
1 ATTATTTTATATT
28386012 ATTATTTATATATAT
1 ATTATTT-TATAT-T
28386027 ATTATT
1 ATTATT
28386033 ATCCTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 5 0.26
15 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTATTTTATATT
Found at i:28386050 original size:21 final size:17
Alignment explanation
Indices: 28386000--28386034 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28385990 TATATTTTCA
*
28386000 TTATTTTATATTATTAT
1 TTATATTATATTATTAT
28386017 TTATATATATATTATTAT
1 TTATAT-TATATTATTAT
28386035 CCTTAACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATTATATTATTAT
Found at i:28398385 original size:206 final size:206
Alignment explanation
Indices: 28398023--28399190 Score: 1733
Period size: 206 Copynumber: 5.7 Consensus size: 206
28398013 ACAGATCTGG
*
28398023 CTGAAGCAAGATCCAAGAT-AGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGC
1 CTGAAGC-AGATCCAAGATGA-TTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGC
* *
28398087 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATTTCTGTATTGTTA
64 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
* * * *
28398152 GAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGGTACATAGCAGATTTGGTCT
129 GAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGCCT
28398217 TCAGATGTTTATA
194 TCAGATGTTTATA
* *
28398230 CTGAAGTAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* * *
28398295 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTACTGTTAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* *
28398360 GAACAAATCAAATTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGCCTTC
131 GAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGCCTTC
28398425 AGATGTTTATA
196 AGATGTTTATA
* * * * *
28398436 CTGAAACAGATCCAAGATGATTTGGCATCTTTGTGTTTACAAGAAACAAATCAAAGACATAGAC-
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAG-CT
** * *
28398500 GATTTGGCTTTCATATGTTTGCGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
28398565 AGAACAAATTGAAGTCT-GCATCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
130 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGCCTT
* *
28398629 CAGATGATTAGA
195 CAGATGTTTATA
* * * *
28398641 CTGAAGCAGATCCAAGATAATTTGGCATCCTTGTGTTTACAAGGAACAAAT-TAAAATCATAGCT
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA-CATAGCT
* *
28398705 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTCGGCATCTCTGTATTGTCAA
65 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
*
28398770 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATGCATAGCAGATCTAGCCTT
130 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGCCTT
28398835 CAGATGTTTATA
195 CAGATGTTTATA
* *
28398847 CTGAAGCAGATCCAAGATGATTTGGCATCGTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* *
28398912 ATTTGGCCTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * *
28398977 GAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
131 GAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGCCTTC
* *
28399042 AGATGATTAGA
196 AGATGTTTATA
* * * * *
28399053 CTGAAGCAGATCAAATATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* ** * *
28399118 ATTTGGTTTTTGCGTGCTTACGCTGAAGTAAA--T---ATGATTTGGCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
28399178 GAACAAATCGAAG
131 GAACAAATCGAAG
28399191 AAGCAGATTT
Statistics
Matches: 874, Mismatches: 81, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
201 39 0.04
204 5 0.01
205 180 0.21
206 640 0.73
207 10 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (206 bp):
CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGCCTTC
AGATGTTTATA
Found at i:28398794 original size:411 final size:412
Alignment explanation
Indices: 28398031--28399190 Score: 1780
Period size: 411 Copynumber: 2.8 Consensus size: 412
28398021 GGCTGAAGCA
* *
28398031 AGATCCAAGAT-AGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGG
1 AGATCCAAGATGA-TTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGG
* *
28398095 CTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATTTCTGTATTGTTAGAGAACAA
65 CTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
** * * *
28398160 ATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGGTACATAGCAGATTTGGTCTTCAGATGT
130 ATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCAGATGA
* *
28398225 TTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACAT
195 TTAGACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACAT
* *
28398290 AGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTACTG
260 AGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTG
* * *
28398355 TTAGAGAACAAATCAAATTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAG
325 TCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAG
28398420 CCTTCAGATGTTTATACTGAAAC
390 CCTTCAGATGTTTATACTGAAAC
* * *
28398443 AGATCCAAGATGATTTGGCATCTTTGTGTTTACAAGAAACAAATCAAAGACATAGAC-GATTTGG
1 AGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAG-CTGATTTGG
** * *
28398507 CTTTCATATGTTTGCGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
65 CTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA
* * *
28398572 ATTGAAGTCT-GCATCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCAGATGA
130 ATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCAGATGA
** * * *
28398636 TTAGACTGAAGCAGATCCAAGATAATTTGGCATCCTTGTGTTTACAAGGAACAAAT-TAAAATCA
195 TTAGACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA-CA
*
28398700 TAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTCGGCATCTCTGTATT
259 TAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATT
* *
28398765 GTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATGCATAGCAGATCTA
324 GTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTA
*
28398830 GCCTTCAGATGTTTATACTGAAGC
389 GCCTTCAGATGTTTATACTGAAAC
*
28398854 AGATCCAAGATGATTTGGCATCGTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGC
1 AGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGC
* *
28398919 CTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTCAGAGAACAAA
66 TTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
* **
28398984 TCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTCAGATGAT
131 TCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCAGATGAT
* * * *
28399049 TAGACTGAAGCAGATCAAATATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATA
196 TAGACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATA
* ** * *
28399114 GCTGATTTGGTTTTTGCGTGCTTACGCTGAAGTAAA--T---ATGATTTGGCATCTCTGTATTGT
261 GCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGT
28399174 CAGAGAACAAATCGAAG
326 CAGAGAACAAATCGAAG
28399191 AAGCAGATTT
Statistics
Matches: 676, Mismatches: 66, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
407 38 0.06
410 5 0.01
411 372 0.55
412 256 0.38
413 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (412 bp):
AGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGC
TTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
TCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCAGATGAT
TAGACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATA
GCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGT
CAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGATACATAGCAGATCTAGC
CTTCAGATGTTTATACTGAAAC
Found at i:28401015 original size:16 final size:17
Alignment explanation
Indices: 28400994--28401028 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
28400984 AAAAATTGTT
28400994 TTACTTTTC-TATATTA
1 TTACTTTTCATATATTA
28401010 TTACTTTTCATATATTA
1 TTACTTTTCATATATTA
28401027 TT
1 TT
28401029 TCATGTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (17 bp):
TTACTTTTCATATATTA
Found at i:28401079 original size:12 final size:13
Alignment explanation
Indices: 28401057--28401090 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28401047 ATATATTTTC
28401057 ATTATTTTATATT
1 ATTATTTTATATT
28401070 ATTATTTATATATAT
1 ATTATTT-TATAT-T
28401085 ATTATT
1 ATTATT
28401091 ATCCTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 5 0.26
15 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTATTTTATATT
Found at i:28401108 original size:21 final size:17
Alignment explanation
Indices: 28401058--28401092 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28401048 TATATTTTCA
*
28401058 TTATTTTATATTATTAT
1 TTATATTATATTATTAT
28401075 TTATATATATATTATTAT
1 TTATAT-TATATTATTAT
28401093 CCTTAACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATTATATTATTAT
Done.