Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 43 of 292
Found at i:11897895 original size:178 final size:179
Alignment explanation
Indices: 11897601--11897923 Score: 483
Period size: 178 Copynumber: 1.8 Consensus size: 179
11897591 AATTTTATCT
*
11897601 GAAACTAGACTCATATATACTCTTACCATAAAATTTTCAAATTTTTGATTTAGCCAATTAGTACA
1 GAAACTAGACTCACATATACTCTTACCATAAAATTTTCAAATTTTTGATTTAGCCAATTAGTACA
* * ** * **
11897666 GTTTATTCATTAAATATAATCTTATTTCTTTGTCTGATAGTTCTGACCTCTCTTCACTAAAAATT
66 GTTTATTCATTAAATATAACCCTATTTCACTGTCTGACAGTTCCAACCTCTCTTCACTAAAAATT
11897731 ATTTAT-TTCATGGTAAGGGACTCAAAATTGAGAACCACTAATTTTCAAA
131 ATTTATCTT-ATGGTAAGGGACTCAAAATTGAGAACCACTAATTTTCAAA
* * *
11897780 GAAACTAGACTCACATATATTTTTACCATAAAATTTTCAGAATTTTT-A-TTATCCAATTAGTAC
1 GAAACTAGACTCACATATACTCTTACCATAAAATTTTCA-AATTTTTGATTTAGCCAATTAGTAC
*
11897843 ATTTTATTCATTAAATAT-ACCCTAGTTTCACTGTCTGACAGTTCCAACCTCTCTTCACTAAAAA
65 AGTTTATTCATTAAATATAACCCTA-TTTCACTGTCTGACAGTTCCAACCTCTCTTCACTAAAAA
11897907 TTATTTATCTTATGGTA
129 TTATTTATCTTATGGTA
11897924 CAGCCTTTGG
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
177 4 0.03
178 79 0.61
179 39 0.30
180 7 0.05
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.40
Consensus pattern (179 bp):
GAAACTAGACTCACATATACTCTTACCATAAAATTTTCAAATTTTTGATTTAGCCAATTAGTACA
GTTTATTCATTAAATATAACCCTATTTCACTGTCTGACAGTTCCAACCTCTCTTCACTAAAAATT
ATTTATCTTATGGTAAGGGACTCAAAATTGAGAACCACTAATTTTCAAA
Found at i:11900073 original size:50 final size:50
Alignment explanation
Indices: 11899854--11900234 Score: 307
Period size: 50 Copynumber: 7.6 Consensus size: 50
11899844 GGTACGCATT
** * * *
11899854 GTAGCCTGCACTTAGTACTACACATGTGAGTTATCCATCTGATACACGTA
1 GTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGATACACATA
* * * * * * * * * **
11899904 GTAGCCTACAATTAGTACTACACATGCGATCAAAGTTAACGGGTATGCATA
1 GTAGCCTGCACTTAGTACTACACATGTGACCTAA-CTATCTGATACACATA
* * * * * * * *
11899955 GTAGCCTGGACTTAGTACTAGACATGCGACCTATCAATCCGGTACACGTA
1 GTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGATACACATA
* * *
11900005 GT-GCCTGCACTTAATACTACACACGTGACCTAACCATCTGATACACATA
1 GTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGATACACATA
* ** * ** **
11900054 GTAGCCTGCACTTAGTACTACACACGTGATCGAAACTATCGGGGATGCATA
1 GTAGCCTGCACTTAGTACTACACATGTGA-CCTAACTATCTGATACACATA
* * * *
11900105 GTAGCCTACACTTAGTACTACACATGTGACCTAACAATCTAGA-ATACGTA
1 GTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCT-GATACACATA
* * * *
11900155 GTAGCCTGCACTTAGTACTACACACGTGACCTAAAACTGTCTTAAACACATA
1 GTAGCCTGCACTTAGTACTACACATGTGACCT--AACTATCTGATACACATA
*
11900207 GTAGCCTGCACATAGTACTACACATGTG
1 GTAGCCTGCACTTAGTACTACACATGTG
11900235 GTCTCCCAAT
Statistics
Matches: 258, Mismatches: 66, Indels: 12
0.77 0.20 0.04
Matches are distributed among these distances:
49 39 0.15
50 105 0.41
51 77 0.30
52 37 0.14
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (50 bp):
GTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCTGATACACATA
Found at i:11900130 original size:150 final size:151
Alignment explanation
Indices: 11899854--11900230 Score: 470
Period size: 150 Copynumber: 2.5 Consensus size: 151
11899844 GGTACGCATT
* ** * * * *
11899854 GTAGCCTGCACTTAGTACTACACATGTGAGTTATCCATCTGATACACGTAGTAGCCTACAATTAG
1 GTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACATAGTAGCCTGCACTTAG
* * * ** *
11899919 TACTACACATGCGATCAAAGTTAACGGGTATGCATAGTAGCCTGGACTTAGTACTAGACATGCGA
66 TACTACACACGCGATCAAAGCTAACGGGGATGCATAGTAGCCTACACTTAGTACTACACATGCGA
* * *
11899984 CCTATCAATCCGGTACACGTA
131 CCTAACAATCCAGAACACGTA
*
11900005 GT-GCCTGCACTTAATACTACACACGTGACCTAACCATCTGATACACATAGTAGCCTGCACTTAG
1 GTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACATAGTAGCCTGCACTTAG
* * *
11900069 TACTACACACGTGATCGAAA-CTATCGGGGATGCATAGTAGCCTACACTTAGTACTACACATGTG
66 TACTACACACGCGATC-AAAGCTAACGGGGATGCATAGTAGCCTACACTTAGTACTACACATGCG
* *
11900133 ACCTAACAATCTAGAATACGTA
130 ACCTAACAATCCAGAACACGTA
** * * *
11900155 GTAGCCTGCACTTAGTACTACACACGTGACCTAAAACTGTCTTAAACACATAGTAGCCTGCACAT
1 GTAGCCTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACACATAGTAGCCTGCACTT
11900220 AGTACTACACA
64 AGTACTACACA
11900231 TGTGGTCTCC
Statistics
Matches: 194, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
150 124 0.64
151 33 0.17
153 37 0.19
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (151 bp):
GTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACATAGTAGCCTGCACTTAG
TACTACACACGCGATCAAAGCTAACGGGGATGCATAGTAGCCTACACTTAGTACTACACATGCGA
CCTAACAATCCAGAACACGTA
Found at i:11900137 original size:101 final size:100
Alignment explanation
Indices: 11900003--11900183 Score: 283
Period size: 101 Copynumber: 1.8 Consensus size: 100
11899993 CCGGTACACG
* *
11900003 TAGTGCCTGCACTTAATACTACACACGTGACCTAACCATCT-GATACACATAGTAGCCTGCACTT
1 TAGTGCCTACACTTAATACTACACACGTGACCTAACAATCTAGA-ACACATAGTAGCCTGCACTT
11900067 AGTACTACACACGTGATCGAAACTATCGGGGATGCA
65 AGTACTACACACGTGATCGAAACTATCGGGGATGCA
* * * *
11900103 TAGTAGCCTACACTTAGTACTACACATGTGACCTAACAATCTAGAATACGTAGTAGCCTGCACTT
1 TAGT-GCCTACACTTAATACTACACACGTGACCTAACAATCTAGAACACATAGTAGCCTGCACTT
11900168 AGTACTACACACGTGA
65 AGTACTACACACGTGA
11900184 CCTAAAACTG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 67 0.92
102 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (100 bp):
TAGTGCCTACACTTAATACTACACACGTGACCTAACAATCTAGAACACATAGTAGCCTGCACTTA
GTACTACACACGTGATCGAAACTATCGGGGATGCA
Found at i:11900612 original size:19 final size:20
Alignment explanation
Indices: 11900584--11900630 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
11900574 AAGAACATGT
11900584 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
11900605 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
11900624 TATATAT
1 TATATAT
11900631 ACTTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:11918976 original size:29 final size:29
Alignment explanation
Indices: 11918944--11919003 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
11918934 TTATTTTATT
11918944 TTATTTGTATAATTTTCTCTTATTATTCA
1 TTATTTGTATAATTTTCTCTTATTATTCA
11918973 TTATTTGTATAATTTTCTCTTATTATTCA
1 TTATTTGTATAATTTTCTCTTATTATTCA
11919002 TT
1 TT
11919004 CATTCATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.63
Consensus pattern (29 bp):
TTATTTGTATAATTTTCTCTTATTATTCA
Found at i:11922106 original size:3 final size:3
Alignment explanation
Indices: 11922100--11922125 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11922090 TATGAGAAGA
11922100 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
11922126 ACCCCGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:11922670 original size:18 final size:17
Alignment explanation
Indices: 11922647--11922682 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
11922637 AGGTTAGTTT
*
11922647 AGTAAATTAGTAATTAAA
1 AGTAAATTA-AAATTAAA
11922665 AGTAAATTAAAATTAAA
1 AGTAAATTAAAATTAAA
11922682 A
1 A
11922683 CAAAGGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (17 bp):
AGTAAATTAAAATTAAA
Found at i:11923606 original size:30 final size:30
Alignment explanation
Indices: 11923567--11923626 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
11923557 TTCCCGAGCC
* *
11923567 TAGGTGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
11923597 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
11923627 CGTATTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:11933880 original size:39 final size:39
Alignment explanation
Indices: 11933776--11933880 Score: 122
Period size: 40 Copynumber: 2.7 Consensus size: 39
11933766 TTGATGACAA
* ** * * *
11933776 TTCGGCTATGTACAGCACTTAGTGTACGATTCGAGATAGC
1 TTCGGCTATCTATGGCACTTAGTGTGCGATTC-AAATAAC
*
11933816 TTCGGCTATGTATGGCACTTAGTGTGCGATT-AAATAAC
1 TTCGGCTATCTATGGCACTTAGTGTGCGATTCAAATAAC
11933854 TTCGGCTATCTATTGGCACTTAGTGTG
1 TTCGGCTATCTA-TGGCACTTAGTGTG
11933881 TGAGAATTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 16 0.28
39 14 0.24
40 28 0.48
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (39 bp):
TTCGGCTATCTATGGCACTTAGTGTGCGATTCAAATAAC
Found at i:11935520 original size:2 final size:2
Alignment explanation
Indices: 11935515--11935547 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11935505 GTATTATATA
11935515 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
11935548 TTTAGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11937830 original size:34 final size:34
Alignment explanation
Indices: 11937790--11937855 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
11937780 TAAGTCCAAG
11937790 ATTATTCTAATCCATTTTTTCTTTAGGTTTATCC
1 ATTATTCTAATCCATTTTTTCTTTAGGTTTATCC
* *
11937824 ATTATTCTAATCCCTTTTTTCTTTCGGTTTAT
1 ATTATTCTAATCCATTTTTTCTTTAGGTTTAT
11937856 TCGTGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (34 bp):
ATTATTCTAATCCATTTTTTCTTTAGGTTTATCC
Found at i:11939418 original size:44 final size:44
Alignment explanation
Indices: 11939357--11939669 Score: 213
Period size: 44 Copynumber: 6.8 Consensus size: 44
11939347 AATTTGTGCT
*
11939357 CCAGTGTAAGACGTGTCTGGGACATGCATCGGCTAAGAGTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTTGTG
* * * * * * * *
11939401 CTAGTGGAAGACATGTCTGGGACATGCATCAGCACAAATAAATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-G-GCTAA-GAGT-TGTG
*
11939449 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-AGAG-T-TGTG
* * *
11939497 CCAGAGTAA-ACATG-CATGGGACATGCATCGGCCTCAACAGAGAT-AG
1 CCAGTGTAAGACATGTC-TGGGACATGCATCGG-CT--A-AGAGTTGTG
* *
11939543 CCAGTGTGAGACATGTCTGGGACACGCATCGGCTAAGAGTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTTGTG
* * * * *
11939587 CTAGTGTAAGACATGTCTGGGACATTCATCAGC-AAGCATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTAAG-A-GT-T--GTG
*
11939635 CCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
11939670 AATATATCCC
Statistics
Matches: 211, Mismatches: 35, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
43 8 0.04
44 58 0.27
45 10 0.05
46 27 0.13
47 24 0.11
48 39 0.18
49 34 0.16
50 11 0.05
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (44 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTTGTG
Found at i:11939637 original size:92 final size:93
Alignment explanation
Indices: 11939357--11939669 Score: 356
Period size: 93 Copynumber: 3.4 Consensus size: 93
11939347 AATTTGTGCT
* *
11939357 CCAGTGTAAGA-CGTGTCTGGGACAT-GCATCGGCTAAGAGTTGTGCTAGTGGAAGACATGTCTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGTCTG
*
11939420 GGACATGCATCAGCACAAATAAATGAGAG
66 GGACATGCATCAGCA-ACATAAATGAGAG
* * *
11939449 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACAGAGATGAGTGCCAGAGTAA-ACATG-
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-AGAG-T-TGTGCTAGTGTAAGACATGT
* ** *
11939511 CATGGGACATGCATCGGCCTCA-ACAGA-GATAG
63 C-TGGGACATGCATCAGCAACATA-A-ATGAGAG
* *
11939543 CCAGTGTGAGA-CATGTCTGGGACA-CGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGTCTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGTCTG
* *
11939606 GGACATTCATCAGCAAGCATATATGAGAG
66 GGACATGCATCAGCAA-CATAAATGAGAG
*
11939635 CCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
11939670 AATATATCCC
Statistics
Matches: 181, Mismatches: 24, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
90 10 0.06
91 21 0.12
92 40 0.22
93 42 0.23
94 37 0.20
95 22 0.12
96 9 0.05
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (93 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGTCTG
GGACATGCATCAGCAACATAAATGAGAG
Found at i:11943760 original size:17 final size:17
Alignment explanation
Indices: 11943738--11943778 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
11943728 GTGCCAACAG
11943738 AGCTTTGAGAAATTAAA
1 AGCTTTGAGAAATTAAA
11943755 AGCTTTGAGAAATTAAA
1 AGCTTTGAGAAATTAAA
11943772 AGCTTTG
1 AGCTTTG
11943779 CCGACTGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (17 bp):
AGCTTTGAGAAATTAAA
Found at i:11946960 original size:48 final size:48
Alignment explanation
Indices: 11946906--11947168 Score: 204
Period size: 47 Copynumber: 5.5 Consensus size: 48
11946896 GTTGTGCTAA
*
11946906 TGTAAGACATGTCTGGTACATGCATCAGCACGCATAAATGAGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGAGAGCCAG
* * * * *
11946954 TGTAAGACCATGTCTAGGACATGGCATCAGTA--CAGAGATGAGTGCCAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCAGCACGCATAAATGAGAGCCAG
* * * * * *
11947002 AGTAAGACATGTCTAGGACATGCATCGGC-CTCA-ACAAAGATAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATA-AATGAGAGCCAG
* * * *
11947049 TGTAAGACGTGTCTGGGACATGCATC-G---GC-TAAGA-GTTGTGCTAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATAA-ATG-AGAGCCAG
* * * * *
11947093 TGTAAAACATGTTTGGGACATGCATCAACACGCATATATGAGAGCTAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGAGAGCCAG
11947141 TGTAAGACCATGTCTGGGACATGGCATC
1 TGTAAGA-CATGTCTGGGACAT-GCATC
11947169 GACAATATAT
Statistics
Matches: 169, Mismatches: 30, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
43 2 0.01
44 30 0.18
46 8 0.05
47 47 0.28
48 41 0.24
49 28 0.17
50 13 0.08
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.22
Consensus pattern (48 bp):
TGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGAGAGCCAG
Found at i:11950780 original size:22 final size:22
Alignment explanation
Indices: 11950755--11950796 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11950745 TATTTAACCG
11950755 AATTTTAATATATTTT-TATTAT
1 AATTTTAATA-ATTTTATATTAT
*
11950777 AATTTTATTAATTTTATATT
1 AATTTTAATAATTTTATATT
11950797 CATCCTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATTTTAATAATTTTATATTAT
Found at i:11955330 original size:53 final size:52
Alignment explanation
Indices: 11955250--11955404 Score: 150
Period size: 52 Copynumber: 3.0 Consensus size: 52
11955240 TACATATAAT
* * * *
11955250 ACCGATGCCATATCCCAGATATGGTCTTATAC-GGAATCACATTATCACATCAC
1 ACCGACGCCATAACCCAGCTATGGTCTTATACGGGAA-CAC-GTATCACATCAC
* * * **
11955303 ACCGACGTCATAGCCCAGCTATGGTCTTATACGGGAACACGTATCACGTTGC
1 ACCGACGCCATAACCCAGCTATGGTCTTATACGGGAACACGTATCACATCAC
* * * ** *
11955355 ACCGATGCCATAACCCAGCTATGGTTTTATACAGGTGCACATATCACATC
1 ACCGACGCCATAACCCAGCTATGGTCTTATACGGGAACACGTATCACATC
11955405 TTTTCCGTCA
Statistics
Matches: 83, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
52 48 0.58
53 31 0.37
54 4 0.05
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (52 bp):
ACCGACGCCATAACCCAGCTATGGTCTTATACGGGAACACGTATCACATCAC
Found at i:11955372 original size:52 final size:53
Alignment explanation
Indices: 11955250--11955386 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 53
11955240 TACATATAAT
* * *
11955250 ACCGATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATCAC
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACAGTATCACATCAC
* * * * **
11955303 ACCGACGTCATAGCCCAGCTATGGTCTTATACGGGAA-CAC-GTATCACGTTGC
1 ACCGATGCCATAACCCAGCTATGGTCTTATAC-GGAATCACAGTATCACATCAC
*
11955355 ACCGATGCCATAACCCAGCTATGGTTTTATAC
1 ACCGATGCCATAACCCAGCTATGGTCTTATAC
11955387 AGGTGCACAT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 36 0.51
53 31 0.44
54 4 0.06
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (53 bp):
ACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACAGTATCACATCAC
Found at i:11958069 original size:22 final size:22
Alignment explanation
Indices: 11958044--11958085 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11958034 TAGTTAAAGA
*
11958044 AAAAAACATT-TATTTTATTTTT
1 AAAAAA-ATTGTATTTAATTTTT
11958066 AAAAAAATTGTATTTAATTT
1 AAAAAAATTGTATTTAATTT
11958086 AATTTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAAAAATTGTATTTAATTTTT
Found at i:11959991 original size:25 final size:25
Alignment explanation
Indices: 11959957--11960020 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
11959947 GGCGCGACCC
11959957 ATTTTTTTAATAATATAATT-TATTT
1 ATTTTTTTAATAATATAATTAT-TTT
*
11959982 ATTTTTTT-A-AATATTATTATTTT
1 ATTTTTTTAATAATATAATTATTTT
11960005 ATTATATTTTAATAAT
1 ATT-T-TTTTAATAAT
11960021 TTTTAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 14 0.42
24 3 0.09
25 12 0.36
26 1 0.03
27 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTTTTTAATAATATAATTATTTT
Found at i:11959994 original size:26 final size:27
Alignment explanation
Indices: 11959957--11960014 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
11959947 GGCGCGACCC
11959957 ATTTTTTTAATAATA-TAATTTATT-T
1 ATTTTTTTAATAATATTAATTTATTAT
* *
11959982 ATTTTTTTAAATATTATTATTTTATTAT
1 ATTTTTTT-AATAATATTAATTTATTAT
11960010 ATTTT
1 ATTTT
11960015 AATAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.29
26 6 0.21
27 8 0.29
28 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTTTTAATAATATTAATTTATTAT
Found at i:11960256 original size:3 final size:3
Alignment explanation
Indices: 11960241--11960309 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
11960231 TGCAGCAGCA
* *
11960241 AAG AGAG AA- AAG AAG AAG AAG AAT AAG AAA AAG AAG AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
11960286 AAG GAG AAG GAG GAG AAAG AAG AA
1 AAG AAG AAG AAG AAG -AAG AAG AA
11960310 AAATGTTAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:11961397 original size:11 final size:11
Alignment explanation
Indices: 11961362--11961389 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
11961352 GAGAGTAAGA
11961362 AATTTTAATGT
1 AATTTTAATGT
11961373 AATTTTAATGT
1 AATTTTAATGT
11961384 AATTTT
1 AATTTT
11961390 GATATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTAATGT
Found at i:11963003 original size:6 final size:6
Alignment explanation
Indices: 11962994--11963042 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
11962984 TGCACCAGCT
* * * * *
11962994 CCAGAG CCAGAG CCAGAG CCAGAG CCGGAG GCAGTG CCGGAC CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
11963042 C
1 C
11963043 GGCGGCCAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.27, C:0.35, G:0.37, T:0.02
Consensus pattern (6 bp):
CCAGAG
Found at i:11963249 original size:33 final size:33
Alignment explanation
Indices: 11963178--11963253 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
11963168 CCACATCTGC
* *
11963178 ACTCTACTCCTCCTGGCTCATATCCACCATCGT
1 ACTCTACTCCTCCTGGCCCATATCCACCACCGT
* * *
11963211 ACTCTACTCTTCCTGGCCCATATCCAGCGCCGT
1 ACTCTACTCCTCCTGGCCCATATCCACCACCGT
*
11963244 TCTCTACTCC
1 ACTCTACTCC
11963254 ACCCGGCTCG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.16, C:0.43, G:0.11, T:0.30
Consensus pattern (33 bp):
ACTCTACTCCTCCTGGCCCATATCCACCACCGT
Found at i:11963811 original size:26 final size:27
Alignment explanation
Indices: 11963771--11963828 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
11963761 AAAAATTATT
11963771 AAAATATAATAAAATAATAATATTTAAA
1 AAAATATAATAAAATAATAATA-TTAAA
* *
11963799 AAAATA-AAT-AAATTATATTATTAAA
1 AAAATATAATAAAATAATAATATTAAA
11963824 AAAAT
1 AAAAT
11963829 GAGTCGCGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.36
26 9 0.32
27 3 0.11
28 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATATAATAAAATAATAATATTAAA
Found at i:11965814 original size:14 final size:14
Alignment explanation
Indices: 11965795--11965830 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
11965785 GATGTATGTA
11965795 AAAGCATGAAAATT
1 AAAGCATGAAAATT
11965809 AAAGCATGAAAATT
1 AAAGCATGAAAATT
11965823 AAAGCATG
1 AAAGCATG
11965831 TGTATCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (14 bp):
AAAGCATGAAAATT
Found at i:11973769 original size:96 final size:96
Alignment explanation
Indices: 11973597--11973784 Score: 297
Period size: 96 Copynumber: 2.0 Consensus size: 96
11973587 CTTTTTGCTT
*
11973597 CTCTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTGC
1 CTCTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTATCTGC
* * *
11973662 TCCATCGTTCCCTTCGATGACAGACTTGTTC
66 TCCATCATTCCCATCGATAACAGACTTGTTC
* *
11973693 CTCTTTGCCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCT-CTGTATCTG
1 CTCTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCT-TATCTG
*
11973757 CTCGATCATTCCCATCGATAACAGACTT
65 CTCCATCATTCCCATCGATAACAGACTT
11973785 CCTCGAACAC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 2 0.02
96 82 0.98
ACGTcount: A:0.13, C:0.34, G:0.18, T:0.36
Consensus pattern (96 bp):
CTCTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTATCTGC
TCCATCATTCCCATCGATAACAGACTTGTTC
Found at i:11980460 original size:2 final size:2
Alignment explanation
Indices: 11980455--11980485 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11980445 TTTCGGTTAC
11980455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11980486 AATACATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11981160 original size:3 final size:3
Alignment explanation
Indices: 11981152--11981366 Score: 120
Period size: 3 Copynumber: 72.3 Consensus size: 3
11981142 TTCTAAGACC
* *
11981152 ATT ATT ATT ACT ACTT CT- ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
11981197 ATT ATT ATT ATT ATT ATT ATGT -TT ATT TTT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * ** *
11981242 A-T AAT CTT ATTT ATG ACT ATT ATC ATT -TT TTT AAA ATT ATT GTT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * ** * * *
11981286 ACT AGT ATT CTT -TT ACC ATT -TA ATAC ATT ATT ATT ACT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT
* * *
11981331 ATT ATT ACT ATT -GT ATT ATT ACT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
11981367 CATTTTCTTT
Statistics
Matches: 157, Mismatches: 43, Indels: 24
0.70 0.19 0.11
Matches are distributed among these distances:
2 10 0.06
3 138 0.88
4 9 0.06
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:11981549 original size:3 final size:3
Alignment explanation
Indices: 11981528--11981708 Score: 133
Period size: 3 Copynumber: 60.7 Consensus size: 3
11981518 CAAACTTTAG
* * **
11981528 ATT ATTT ATT ATT -TGT ATT ATT -GT ATT ATT ACT ATTT ATT ATT ACC
1 ATT A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
* * *
11981574 ATT ATT ATT ACT ATT ACT ATT ACTT -TT ACTT -TT ATTT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT A-TT ATT ATT ATT
* * * *
11981620 A-T ATT ATT TTT ATT TTT ATT -TT A-T ATT ACT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
11981665 ATT ACT AAT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11981709 CGTTCTCATT
Statistics
Matches: 138, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
2 12 0.09
3 113 0.82
4 13 0.09
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12008221 original size:67 final size:65
Alignment explanation
Indices: 12008128--12008357 Score: 234
Period size: 64 Copynumber: 3.5 Consensus size: 65
12008118 CACTCATGTG
* * * * *
12008128 ACCTAGCCAC-TTTATCTCGTAGCTCTCTTGTTTACATGGTGTCCTTCACCTGGAA-CTACACAT
1 ACCTAGCTACATTTATCTCGTAGCTCTCTTGTCTACATGGTGT--TACACATAGAATC-ACACAT
12008191 GCA
63 GCA
* * *
12008194 ACCTAGCTACATTTATCTCGTAGCTCTCTTGTCTACATGGTG-TACACATAGTATCACCCATGCG
1 ACCTAGCTACATTTATCTCGTAGCTCTCTTGTCTACATGGTGTTACACATAGAATCACACATGCA
* * * * * *
12008258 ACCTAGCTACATATATCCCATAGCTCTCTTGTCTACATGGTG-TACACATAGTATCACCCATGCG
1 ACCTAGCTACATTTATCTCGTAGCTCTCTTGTCTACATGGTGTTACACATAGAATCACACATGCA
*
12008322 ACCTAGCTACATCATAATGTCTCGTAGCTCTCTTGT
1 ACCTAGCTACAT--T--TATCTCGTAGCTCTCTTGT
12008358 ACACATGATG
Statistics
Matches: 143, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
64 87 0.61
65 1 0.01
66 9 0.06
67 30 0.21
68 16 0.11
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (65 bp):
ACCTAGCTACATTTATCTCGTAGCTCTCTTGTCTACATGGTGTTACACATAGAATCACACATGCA
Found at i:12008289 original size:64 final size:64
Alignment explanation
Indices: 12008188--12008333 Score: 256
Period size: 64 Copynumber: 2.3 Consensus size: 64
12008178 TGGAACTACA
* * * *
12008188 CATGCAACCTAGCTACATTTATCTCGTAGCTCTCTTGTCTACATGGTGTACACATAGTATCACC
1 CATGCGACCTAGCTACATATATCCCATAGCTCTCTTGTCTACATGGTGTACACATAGTATCACC
12008252 CATGCGACCTAGCTACATATATCCCATAGCTCTCTTGTCTACATGGTGTACACATAGTATCACC
1 CATGCGACCTAGCTACATATATCCCATAGCTCTCTTGTCTACATGGTGTACACATAGTATCACC
12008316 CATGCGACCTAGCTACAT
1 CATGCGACCTAGCTACAT
12008334 CATAATGTCT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (64 bp):
CATGCGACCTAGCTACATATATCCCATAGCTCTCTTGTCTACATGGTGTACACATAGTATCACC
Found at i:12008393 original size:132 final size:127
Alignment explanation
Indices: 12008086--12008402 Score: 309
Period size: 132 Copynumber: 2.4 Consensus size: 127
12008076 CATAATTTTG
* * * * *
12008086 GCTCTCTTGTACACATGGTGAGCACTTAGTACCACTCATGTGACCTAGCCAC-TTTATCTCGTAG
1 GCTCTCTTGTACACATGGTGTGCAC-TAGTACCA-TCATGTGACCTAGCTACATATATCCCATAG
* * *
12008150 CTCTCTTGTTTACATGGTGTCCTTCACCTGGAACTACACATGCAACCTAGCTACATTTATCTCGT
64 CTCTCTTGTCTACATGGTG--CTACACATGGAACTACACATGCAACCTAGCTACATTTATCTCGT
12008215 A
127 A
* * * *
12008216 GCTCTCTTGT-CTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATATATCCCATA
1 GCTCTCTTGTAC-ACATGGTGTGCAC-TAGTACCA-TCATGTGACCTAGCTACATATATCCCATA
* * * * *
12008280 GCTCTCTTGTCTACATGGTG-TACACATAGTA-TCACCCATGCGACCTAGCTACATCATAATGTC
63 GCTCTCTTGTCTACATGGTGCTACACATGGAACT-ACACATGCAACCTAGCTACAT--T--TATC
12008343 TCGTA
123 TCGTA
* *
12008348 GCTCTCTTGTACACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA
1 GCTCTCTTGTACACATGGTGTGCACT-AGTACCAT-CATGTGACCTAGCTACATA
12008403 CCATTTGTAT
Statistics
Matches: 153, Mismatches: 24, Indels: 18
0.78 0.12 0.09
Matches are distributed among these distances:
127 1 0.01
128 26 0.17
129 1 0.01
130 44 0.29
131 28 0.18
132 52 0.34
133 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.31
Consensus pattern (127 bp):
GCTCTCTTGTACACATGGTGTGCACTAGTACCATCATGTGACCTAGCTACATATATCCCATAGCT
CTCTTGTCTACATGGTGCTACACATGGAACTACACATGCAACCTAGCTACATTTATCTCGTA
Found at i:12012816 original size:52 final size:51
Alignment explanation
Indices: 12012704--12012814 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
12012694 TACACTTTAG
* * *
12012704 AAAAAGAAGGGGCCAAGGTGAAAACCCGAAAAGGACGCTTTGAGACCTTCA
1 AAAAAAAAAGGGCCAAGGTGAAAACCCGAAAAGGACGCTTTAAGACCTTCA
** * *
12012755 AAAAAAAAAGGGCCAAGGTGAATTCCC-ACAAAGGGCGCTTTAAGACTTTCA
1 AAAAAAAAAGGGCCAAGGTGAAAACCCGA-AAAGGACGCTTTAAGACCTTCA
12012806 AAAAAAAAA
1 AAAAAAAAA
12012815 AGAAAATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (51 bp):
AAAAAAAAAGGGCCAAGGTGAAAACCCGAAAAGGACGCTTTAAGACCTTCA
Found at i:12022123 original size:24 final size:24
Alignment explanation
Indices: 12022094--12022144 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
12022084 TGTCACTACA
12022094 GAGTATGAGCATAGCGTACGCTTC
1 GAGTATGAGCATAGCGTACGCTTC
12022118 GAGTATGAGCATAGCGTACGCTTC
1 GAGTATGAGCATAGCGTACGCTTC
12022142 GAG
1 GAG
12022145 GATGGTCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (24 bp):
GAGTATGAGCATAGCGTACGCTTC
Found at i:12035434 original size:82 final size:82
Alignment explanation
Indices: 12035297--12035461 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
12035287 GTGAATGTTC
12035297 TAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAAAATGCCTAAGAGCACTCAAAAGTAGCCTTTT
1 TAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAAAATGCCTAAGAGCACTCAAAAGTAGCCTTTT
12035362 CCGAATAGGACTATACT
66 CCGAATAGGACTATACT
*
12035379 TAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAAAATGCCTAGGAGCACTCAAAAGTAGCCTTTT
1 TAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAAAATGCCTAAGAGCACTCAAAAGTAGCCTTTT
12035444 CCGAATAGGACTATACT
66 CCGAATAGGACTATACT
12035461 T
1 T
12035462 GGGCTCGACA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (82 bp):
TAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAAAATGCCTAAGAGCACTCAAAAGTAGCCTTTT
CCGAATAGGACTATACT
Found at i:12044213 original size:14 final size:13
Alignment explanation
Indices: 12044185--12044221 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
12044175 ATCTTGGAAT
12044185 ATTAAG-ACAATA
1 ATTAAGAACAATA
12044197 ATTAAGAACACATA
1 ATTAAGAACA-ATA
12044211 ATTAAGAACAA
1 ATTAAGAACAA
12044222 GTTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 13 0.57
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (13 bp):
ATTAAGAACAATA
Found at i:12045013 original size:44 final size:44
Alignment explanation
Indices: 12044965--12045229 Score: 146
Period size: 44 Copynumber: 6.0 Consensus size: 44
12044955 AGCCACCAGC
* *
12044965 CTTATC-TCTCTGAGGTAGCAAGGGAGTAGGCTGAAGATTGTAGT
1 CTTATCTTCT-TGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
12045009 CTTATCTTCTTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGAT
1 CTTATCTTCTTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
* * * * * * *
12045054 TTTGTCTCCTTGAGATAGC-AGTGGGGCAGA-TCGAAGACAATG-AAT
1 CTTATCTTCTTGAGGTAGCAAG-GGAGCAGACT-GAAG--ATTGTAGT
** * * * ** ***** *
12045099 CTTATCTTCCCGAGGCAGCAGGGGAGCAGATTTTAGCCACCAGC
1 CTTATCTTCTTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* * * *
12045143 CTTATC-TCTCTAAAGTAGCAAGGGAGTAGGCT-AGAGATTGTAGT
1 CTTATCTTCT-TGAGGTAGCAAGGGAGCAGACTGA-AGATTGTAGT
* * * *
12045187 CTTATTTTCCTGACGTAGCAAGGGAGCAGACTGAAGACTGTAG
1 CTTATCTTCTTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG
12045230 ATTTGTCTCC
Statistics
Matches: 159, Mismatches: 49, Indels: 26
0.68 0.21 0.11
Matches are distributed among these distances:
43 2 0.01
44 96 0.60
45 55 0.35
46 3 0.02
47 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (44 bp):
CTTATCTTCTTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
Found at i:12045231 original size:178 final size:177
Alignment explanation
Indices: 12044926--12045335 Score: 615
Period size: 178 Copynumber: 2.3 Consensus size: 177
12044916 CAGTTTATCA
* * *
12044926 CTTCCCGAGGTACCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGGGAG
1 CTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAAGTAGCAAGGGAG
* * *
12044991 TAGGCTGAAGATTGTAGTCTTATCTTCTTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGATTT
66 TAGGCTGAAGATTGTAGTCTTATCTTCCTGACGTAGCAAGGGAGCAGACTGAAGACTGTAGA-TT
* *
12045056 TGTCTCCTTGAGATAGCAGTGGGGCAGATCGAAGACAATGAATCTTAT
130 TGTCTCCTCGAGATAGCAGTGGGGAAGATCGAAGACAATGAATCTTAT
*
12045104 CTTCCCGAGGCAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAAGTAGCAAGGGAG
1 CTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAAGTAGCAAGGGAG
*
12045169 TAGGCT-AGAGATTGTAGTCTTATTTTCCTGACGTAGCAAGGGAGCAGACTGAAGACTGTAGATT
66 TAGGCTGA-AGATTGTAGTCTTATCTTCCTGACGTAGCAAGGGAGCAGACTGAAGACTGTAGATT
* **
12045233 TGTCTCCTCGAGATAGTAGTGGGGAAGATCGAAGATGATGAATCTTAT
130 TGTCTCCTCGAGATAGCAGTGGGGAAGATCGAAGACAATGAATCTTAT
** * ** * *
12045281 CTTCTTGAGGTAGTAGGGGAGCAGATTAAAGTCACCAGCCTTATCTCCCTAAAGT
1 CTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAAGT
12045336 TGCAGTGGAG
Statistics
Matches: 210, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
177 93 0.44
178 117 0.56
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (177 bp):
CTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAAGTAGCAAGGGAG
TAGGCTGAAGATTGTAGTCTTATCTTCCTGACGTAGCAAGGGAGCAGACTGAAGACTGTAGATTT
GTCTCCTCGAGATAGCAGTGGGGAAGATCGAAGACAATGAATCTTAT
Found at i:12047951 original size:127 final size:129
Alignment explanation
Indices: 12047749--12047979 Score: 371
Period size: 127 Copynumber: 1.8 Consensus size: 129
12047739 CTTTCGAGAA
*
12047749 CAAGGCAATATTTTGTGTTTGGGAAATTCAAGAAATCGTGCCCTAACGTGCTGGGTTTCGATTGT
1 CAAGGCAATATTTCGTGTTTGGGAAATTCAAGAAATCGTGCCCTAACGTGCTGGGTTTCGATTGT
*
12047814 CCGTTCGACCAAATGACTGAATATCCTTTTTAAAATTTCATCTGTGTTTTCTTCAATTAATAAAG
66 CCGTTCGACCAAATAACTGAATATCC-TTTTAAAATTTCATCTGTGTTTTCTTCAATTAATAAAG
*
12047879 CAAGGCAAT-TTTCGTGTTT-GG-AATTCGAGAAATCGTGCCCTAACGTGCTGGGTTTCGATT-T
1 CAAGGCAATATTTCGTGTTTGGGAAATTCAAGAAATCGTGCCCTAACGTGCTGGGTTTCGATTGT
* *
12047940 ATCGTTTGACCAAATAACTGAATATCCTTTTAAAATTTCA
66 -CCGTTCGACCAAATAACTGAATATCCTTTTAAAATTTCA
12047980 CTTCACGAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
126 14 0.15
127 61 0.64
128 2 0.02
129 9 0.09
130 9 0.09
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (129 bp):
CAAGGCAATATTTCGTGTTTGGGAAATTCAAGAAATCGTGCCCTAACGTGCTGGGTTTCGATTGT
CCGTTCGACCAAATAACTGAATATCCTTTTAAAATTTCATCTGTGTTTTCTTCAATTAATAAAG
Found at i:12052439 original size:21 final size:22
Alignment explanation
Indices: 12052400--12052441 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
12052390 ATTCCTAAAA
12052400 TAGTTTATATTTAGAAAAATTT
1 TAGTTTATATTTAGAAAAATTT
*
12052422 TAGTTTAT-TTTAGGAAAATT
1 TAGTTTATATTTAGAAAAATT
12052442 GTACTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
TAGTTTATATTTAGAAAAATTT
Found at i:12055507 original size:40 final size:40
Alignment explanation
Indices: 12055452--12055559 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 40
12055442 GGAAATTATA
* *
12055452 CCGGGTTAAGACCCGAAGGCGATT-GTGCTAGTGGC-TAC-AT
1 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGT--CATACTAT
*
12055492 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATACTAT
*
12055532 CCGAGCTAAGACCCGAAGGCATTCGTGC
1 CCGGGCTAAGACCCGAAGGCATTCGTGC
12055560 ACGTATTATA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 5 0.08
40 55 0.90
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.20
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATACTAT
Found at i:12056623 original size:16 final size:17
Alignment explanation
Indices: 12056595--12056634 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
12056585 GTGCCAACAG
12056595 AGCTTTGAGAAATTAAA
1 AGCTTTGAGAAATTAAA
12056612 AGCTTT-AGAAATTAAA
1 AGCTTTGAGAAATTAAA
12056628 AGCTTTG
1 AGCTTTG
12056635 CCGACTGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.33
Consensus pattern (17 bp):
AGCTTTGAGAAATTAAA
Found at i:12059835 original size:48 final size:48
Alignment explanation
Indices: 12059781--12060043 Score: 204
Period size: 47 Copynumber: 5.5 Consensus size: 48
12059771 GTTGTGCTAA
*
12059781 TGTAAGACATGTCTGGTACATGCATCAGCACGCATAAATGAGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGAGAGCCAG
* * * * *
12059829 TGTAAGACCATGTCTAGGACATGGCATCAGTA--CAGAGATGAGTGCCAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCAGCACGCATAAATGAGAGCCAG
* * * * * *
12059877 AGTAAGACATGTCTAGGACATGCATCGGC-CTCA-ACAAAGATAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATA-AATGAGAGCCAG
* * * *
12059924 TGTAAGACGTGTCTGGGACATGCATC-G---GC-TAAGA-GTTGTGCTAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATAA-ATG-AGAGCCAG
* * * * *
12059968 TGTAAAACATGTTTGGGACATGCATCAACACGCATATATGAGAGCTAG
1 TGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGAGAGCCAG
12060016 TGTAAGACCATGTCTGGGACATGGCATC
1 TGTAAGA-CATGTCTGGGACAT-GCATC
12060044 GACAATATAT
Statistics
Matches: 169, Mismatches: 30, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
43 2 0.01
44 30 0.18
46 8 0.05
47 47 0.28
48 41 0.24
49 28 0.17
50 13 0.08
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.22
Consensus pattern (48 bp):
TGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGAGAGCCAG
Found at i:12067796 original size:7 final size:7
Alignment explanation
Indices: 12067769--12067817 Score: 73
Period size: 7 Copynumber: 6.9 Consensus size: 7
12067759 TGTGTTAAAA
12067769 TATATAT
1 TATATAT
12067776 TATAT-T
1 TATATAT
12067782 ATATTATAT
1 -TA-TATAT
12067791 TATATAT
1 TATATAT
12067798 TATATAT
1 TATATAT
12067805 TATATAT
1 TATATAT
12067812 TATATA
1 TATATA
12067818 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 1 0.03
7 32 0.82
8 5 0.13
9 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:12067816 original size:5 final size:5
Alignment explanation
Indices: 12067771--12067809 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
12067761 TGTTAAAATA
12067771 TATAT TATAT TATAT TATAT TATA- TAT-T ATATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT
12067810 ATTATATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.10
5 27 0.87
6 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:12069503 original size:23 final size:23
Alignment explanation
Indices: 12069473--12069559 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
12069463 GCTTTATCGA
* *
12069473 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
12069496 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
12069517 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
12069539 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
12069560 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:12070109 original size:36 final size:36
Alignment explanation
Indices: 12070007--12070110 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
12069997 TAAGGTATAA
* * *
12070007 AATAACTGATTATTACAGAATAATTGACTGTTACTG
1 AATAACTGATTATTACTGAATAATTGATTGTTACCG
* *
12070043 AATAACTGGTTATTACTGAATATTTGATTGTTACCG
1 AATAACTGATTATTACTGAATAATTGATTGTTACCG
* * * *
12070079 AATAACTGACTGTTACTGAATAAATAATTGTT
1 AATAACTGATTATTACTGAATAATTGATTGTT
12070111 CTGAGAGTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (36 bp):
AATAACTGATTATTACTGAATAATTGATTGTTACCG
Found at i:12070110 original size:18 final size:18
Alignment explanation
Indices: 12070007--12070114 Score: 101
Period size: 18 Copynumber: 6.1 Consensus size: 18
12069997 TAAGGTATAA
* *
12070007 AATAACTGATTATTACAG
1 AATAACTGATTGTTACTG
* *
12070025 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
12070043 AATAACTGGTTATTACTG
1 AATAACTGATTGTTACTG
** *
12070061 AATATTTGATTGTTACCG
1 AATAACTGATTGTTACTG
*
12070079 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
12070097 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
12070114 A
1 A
12070115 GAGTTAATGA
Statistics
Matches: 70, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
17 4 0.06
18 66 0.94
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:12072148 original size:16 final size:17
Alignment explanation
Indices: 12072117--12072150 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12072107 TACTATTGTT
12072117 TTCTGATTGATTTGATA
1 TTCTGATTGATTTGATA
*
12072134 TTCTTATTG-TTTGATA
1 TTCTGATTGATTTGATA
12072150 T
1 T
12072151 AATCTCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.59
Consensus pattern (17 bp):
TTCTGATTGATTTGATA
Found at i:12073075 original size:48 final size:49
Alignment explanation
Indices: 12073022--12073128 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 49
12073012 CCATTAAGCC
12073022 CCCCAAAAAACC-AAACCCAAGAAAAAAAAAAAG-AAAAAGAAAAACCTA
1 CCCCAAAAAACCTAAACCCAA-AAAAAAAAAAAGAAAAAAGAAAAACCTA
* *
12073070 CCCCAAAAAACCTAACCCCAAAAAAAAAAGAAGAAAAAAGAAAAACCTA
1 CCCCAAAAAACCTAAACCCAAAAAAAAAAAAAGAAAAAAGAAAAACCTA
* *
12073119 ACCAAAAAAA
1 CCCCAAAAAA
12073129 AAAGATAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
48 23 0.43
49 30 0.57
ACGTcount: A:0.68, C:0.23, G:0.06, T:0.03
Consensus pattern (49 bp):
CCCCAAAAAACCTAAACCCAAAAAAAAAAAAAGAAAAAAGAAAAACCTA
Found at i:12073079 original size:15 final size:15
Alignment explanation
Indices: 12073061--12073094 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12073051 AAAGAAAAAG
12073061 AAAAACCT-ACCCCA
1 AAAAACCTAACCCCA
12073075 AAAAACCTAACCCCA
1 AAAAACCTAACCCCA
12073090 AAAAA
1 AAAAA
12073095 AAAAGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.59, C:0.35, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAACCTAACCCCA
Found at i:12073124 original size:33 final size:34
Alignment explanation
Indices: 12073075--12073141 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 34
12073065 ACCTACCCCA
12073075 AAAAACCTAACCCCAAAAAAAAAAGA-AGAAAAAAG
1 AAAAACCTAA-CCCAAAAAAAAAAGATA-AAAAAAG
12073110 AAAAACCTAA-CCAAAAAAAAAAGATAAAAAAA
1 AAAAACCTAACCCAAAAAAAAAAGATAAAAAAA
12073142 CCTAGCCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 20 0.65
34 1 0.03
35 10 0.32
ACGTcount: A:0.75, C:0.15, G:0.06, T:0.04
Consensus pattern (34 bp):
AAAAACCTAACCCAAAAAAAAAAGATAAAAAAAG
Found at i:12073677 original size:2 final size:2
Alignment explanation
Indices: 12073672--12073708 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
12073662 TAAATACTAT
* *
12073672 TA TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12073709 TTTAAATACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:12075334 original size:25 final size:25
Alignment explanation
Indices: 12075293--12075342 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
12075283 ATATTTCTTA
*
12075293 AAGATTCAGTTTGAAAAAAAAATTG
1 AAGATTCAGGTTGAAAAAAAAATTG
*
12075318 AAGA-TCAGGTTGAAAAAGAAATTG
1 AAGATTCAGGTTGAAAAAAAAATTG
12075342 A
1 A
12075343 GTTCTTGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (25 bp):
AAGATTCAGGTTGAAAAAAAAATTG
Found at i:12076001 original size:5 final size:5
Alignment explanation
Indices: 12075991--12076039 Score: 75
Period size: 5 Copynumber: 10.0 Consensus size: 5
12075981 TGTTAAAATA
12075991 TATAT TATAT TATAT TATAT TATAT TATAT TATA- TAT-T ATATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT
12076040 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.07
5 37 0.90
6 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:12076028 original size:7 final size:7
Alignment explanation
Indices: 12076001--12076040 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
12075991 TATATTATAT
12076001 TATATTA
1 TATATTA
12076008 TAT-TATA
1 TATAT-TA
12076015 TTATATTA
1 -TATATTA
12076023 TATATTA
1 TATATTA
12076030 TATATTA
1 TATATTA
12076037 TATA
1 TATA
12076041 AATAAGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 23 0.77
8 5 0.17
9 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:12076075 original size:14 final size:15
Alignment explanation
Indices: 12076058--12076095 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12076048 AAAGAAACAT
*
12076058 AAGAAACAAA-ATAG
1 AAGAAACAAACAGAG
12076072 AAGAAACGAAACAGAG
1 AAGAAAC-AAACAGAG
12076088 AAGAAACA
1 AAGAAACA
12076096 GGGGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.68, C:0.11, G:0.18, T:0.03
Consensus pattern (15 bp):
AAGAAACAAACAGAG
Found at i:12077345 original size:19 final size:15
Alignment explanation
Indices: 12077299--12077340 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
12077289 CGATGAATTT
12077299 ATTGAATTTATATTG
1 ATTGAATTTATATTG
12077314 ATTGAATTTATATTG
1 ATTGAATTTATATTG
12077329 ATTGAA-TTATAT
1 ATTGAATTTATAT
12077341 AATATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:12077743 original size:23 final size:23
Alignment explanation
Indices: 12077713--12077799 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
12077703 GCTTTATCGA
* * *
12077713 TCAGGCACTTTATGTGTCATATT
1 TCAGGCACCTCATGTGTCGTATT
*
12077736 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
12077757 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
12077779 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
12077800 ACTGATCAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
21 35 0.65
22 2 0.04
23 17 0.31
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:12078351 original size:36 final size:36
Alignment explanation
Indices: 12078249--12078352 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
12078239 TAAGGTATAA
* * *
12078249 AATAACTGATTATTACAGAATAATTGACTGTTACTG
1 AATAACTGATTATTACTGAATAATTGATTGTTACCG
* *
12078285 AATAACTGGTTATTACTGAATATTTGATTGTTACCG
1 AATAACTGATTATTACTGAATAATTGATTGTTACCG
* * * *
12078321 AATAACTGACTGTTACTGAATAAATAATTGTT
1 AATAACTGATTATTACTGAATAATTGATTGTT
12078353 CTGAGAGTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (36 bp):
AATAACTGATTATTACTGAATAATTGATTGTTACCG
Found at i:12078352 original size:18 final size:18
Alignment explanation
Indices: 12078249--12078356 Score: 101
Period size: 18 Copynumber: 6.1 Consensus size: 18
12078239 TAAGGTATAA
* *
12078249 AATAACTGATTATTACAG
1 AATAACTGATTGTTACTG
* *
12078267 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
12078285 AATAACTGGTTATTACTG
1 AATAACTGATTGTTACTG
** *
12078303 AATATTTGATTGTTACCG
1 AATAACTGATTGTTACTG
*
12078321 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
12078339 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
12078356 A
1 A
12078357 GAGTTAATGA
Statistics
Matches: 70, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
17 4 0.06
18 66 0.94
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:12079753 original size:53 final size:52
Alignment explanation
Indices: 12079673--12079827 Score: 168
Period size: 52 Copynumber: 3.0 Consensus size: 52
12079663 TACATATAAT
* * *
12079673 ACCGATGCCATATCCCAGATATGGTCTTATAC-GGAATCACATTATCACATCAC
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGGGAA-CAC-GTATCACATCAC
* * * **
12079726 ACCGACGCCATAGCCCAGCTATGGTCTTATACGGGAACACGTATCACGTTGC
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGGGAACACGTATCACATCAC
* * ** *
12079778 ACCGATGCCATAACCCAGCTATGGTTTTATACAGGTGCACATATCACATC
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGGGAACACGTATCACATC
12079828 TTTTCCGTCA
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
52 49 0.58
53 32 0.38
54 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (52 bp):
ACCGATGCCATAACCCAGCTATGGTCTTATACGGGAACACGTATCACATCAC
Found at i:12079795 original size:52 final size:53
Alignment explanation
Indices: 12079673--12079809 Score: 170
Period size: 52 Copynumber: 2.6 Consensus size: 53
12079663 TACATATAAT
* * *
12079673 ACCGATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATCAC
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACAGTATCACATCAC
* * * **
12079726 ACCGACGCCATAGCCCAGCTATGGTCTTATACGGGAA-CAC-GTATCACGTTGC
1 ACCGATGCCATAACCCAGCTATGGTCTTATAC-GGAATCACAGTATCACATCAC
*
12079778 ACCGATGCCATAACCCAGCTATGGTTTTATAC
1 ACCGATGCCATAACCCAGCTATGGTCTTATAC
12079810 AGGTGCACAT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 37 0.51
53 32 0.44
54 4 0.05
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (53 bp):
ACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACAGTATCACATCAC
Found at i:12082491 original size:22 final size:22
Alignment explanation
Indices: 12082466--12082507 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12082456 TAGTTAAAGA
*
12082466 AAAAAACATT-TATTTTATTTTT
1 AAAAAA-ATTGTATTTAATTTTT
12082488 AAAAAAATTGTATTTAATTT
1 AAAAAAATTGTATTTAATTT
12082508 AATTTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAAAAATTGTATTTAATTTTT
Found at i:12086121 original size:14 final size:14
Alignment explanation
Indices: 12086102--12086137 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
12086092 GATGTATGTA
12086102 AAAGCATGAAAATT
1 AAAGCATGAAAATT
12086116 AAAGCATGAAAATT
1 AAAGCATGAAAATT
12086130 AAAGCATG
1 AAAGCATG
12086138 TGTATCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (14 bp):
AAAGCATGAAAATT
Found at i:12094034 original size:23 final size:23
Alignment explanation
Indices: 12094008--12094082 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
12093998 AAGAAAGGAC
12094008 TAAGTGATCTACTACCGAAGGCA
1 TAAGTGATCTACTACCGAAGGCA
* ** *
12094031 TAAGGTG-TTTCAGGGACCAAAGG-A
1 TAA-GTGATCT-A-CTACCGAAGGCA
12094055 CTAAGTGATCTACTACCGAAGGCA
1 -TAAGTGATCTACTACCGAAGGCA
12094079 TAAG
1 TAAG
12094083 GTGTTTCAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
23 16 0.42
24 10 0.26
25 12 0.32
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (23 bp):
TAAGTGATCTACTACCGAAGGCA
Found at i:12094053 original size:25 final size:25
Alignment explanation
Indices: 12094025--12094098 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
12094015 TCTACTACCG
12094025 AAGGCATAAGGTGTTTCAGGGACCA
1 AAGGCATAAGGTGTTTCAGGGACCA
* ** *
12094050 AAGG-ACTAA-GTG-ATCTA-CTACCG
1 AAGGCA-TAAGGTGTTTC-AGGGACCA
12094073 AAGGCATAAGGTGTTTCAGGGACCA
1 AAGGCATAAGGTGTTTCAGGGACCA
12094098 A
1 A
12094099 CCTTGAACCT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
23 12 0.34
24 10 0.29
25 13 0.37
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (25 bp):
AAGGCATAAGGTGTTTCAGGGACCA
Found at i:12094072 original size:48 final size:48
Alignment explanation
Indices: 12094001--12094098 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
12093991 TGTTATGAAG
12094001 AAAGGACTAAGTGATCTACTACCGAAGGCATAAGGTGTTTCAGGGACC
1 AAAGGACTAAGTGATCTACTACCGAAGGCATAAGGTGTTTCAGGGACC
12094049 AAAGGACTAAGTGATCTACTACCGAAGGCATAAGGTGTTTCAGGGACC
1 AAAGGACTAAGTGATCTACTACCGAAGGCATAAGGTGTTTCAGGGACC
12094097 AA
1 AA
12094099 CCTTGAACCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (48 bp):
AAAGGACTAAGTGATCTACTACCGAAGGCATAAGGTGTTTCAGGGACC
Found at i:12097335 original size:12 final size:12
Alignment explanation
Indices: 12097317--12097351 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12097307 AGCACCTCTG
12097317 CCACCACCTGCT
1 CCACCACCTGCT
* *
12097329 CCTCCACTTGCT
1 CCACCACCTGCT
12097341 CCACCACCTGC
1 CCACCACCTGC
12097352 AAGATTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.14, C:0.57, G:0.09, T:0.20
Consensus pattern (12 bp):
CCACCACCTGCT
Found at i:12097606 original size:2 final size:2
Alignment explanation
Indices: 12097601--12097625 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12097591 TTTCGGTTAC
12097601 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12097626 AATACATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12098303 original size:3 final size:3
Alignment explanation
Indices: 12098295--12098512 Score: 162
Period size: 3 Copynumber: 73.7 Consensus size: 3
12098285 TTCTAATACC
* *
12098295 ATT ATT ATT ACT ACTT CT- ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12098340 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATGT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
* * * * * * *
12098385 ATT TTT ATT AAT ATT ATT ATT A-T AAT CTT ATTT ATG ACT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
* ** * * ** * *
12098430 ATT -TT TTT AAA ATT ATT GTT ACT ATT ATT ATT -TT ACC ATT -TA ATAC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * *
12098476 ATT ATT ATT ACT ATT -GT ATT ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12098513 CACATTTACT
Statistics
Matches: 165, Mismatches: 39, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
2 10 0.06
3 148 0.90
4 7 0.04
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:12098683 original size:3 final size:3
Alignment explanation
Indices: 12098662--12098842 Score: 133
Period size: 3 Copynumber: 60.7 Consensus size: 3
12098652 CAAACTTTAG
* * **
12098662 ATT ATTT ATT ATT -TGT ATT ATT -GT ATT ATT ACT ATTT ATT ATT ACC
1 ATT A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
* * *
12098708 ATT ATT ATT ACT ATT ACT ATT ACTT -TT ACTT -TT ATTT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT A-TT ATT ATT ATT
* * * *
12098754 A-T ATT ATT TTT ATT TTT ATT -TT A-T ATT ACT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
12098799 ATT ACT AAT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12098843 CGTTCTCATT
Statistics
Matches: 138, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
2 12 0.09
3 113 0.82
4 13 0.09
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12114995 original size:40 final size:39
Alignment explanation
Indices: 12114853--12114996 Score: 143
Period size: 40 Copynumber: 3.7 Consensus size: 39
12114843 AATTGAATGA
* * ** *
12114853 TATCCGGGCTAAG-CCCGAAGACATTATGCTG-GAAATTA
1 TATCCGGGCTAAGACCCGAAGGCATTGTGC-GAGTCATTC
* * *
12114891 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGT--CATTC
12114932 -ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTCATTC
12114971 TATCCGGGCTAAGACCCGAAGGCATT
1 TATCCGGGCTAAGACCCGAAGGCATT
12114997 TGCACGTATT
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
38 13 0.15
39 13 0.15
40 60 0.69
41 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTCATTC
Found at i:12122868 original size:40 final size:41
Alignment explanation
Indices: 12122818--12122925 Score: 136
Period size: 40 Copynumber: 2.7 Consensus size: 41
12122808 GGAAATTATA
* *
12122818 CCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGGC-TAC-AT
1 CCGGGCTAAGACCCGAAGGCAATTCGTGCGAGT--CATACTAT
*
12122858 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCAATTCGTGCGAGTCATACTAT
12122898 CCGGGCTAAGACCCGAAGGC-ATTCGTGC
1 CCGGGCTAAGACCCGAAGGCAATTCGTGC
12122926 ACGGTATATC
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
38 1 0.02
39 5 0.08
40 56 0.90
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.20
Consensus pattern (41 bp):
CCGGGCTAAGACCCGAAGGCAATTCGTGCGAGTCATACTAT
Found at i:12129858 original size:17 final size:17
Alignment explanation
Indices: 12129823--12129855 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12129813 TTAAGATAAG
*
12129823 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
12129840 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
12129856 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:12130649 original size:36 final size:36
Alignment explanation
Indices: 12130602--12130675 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
12130592 CAGTTTGAAC
12130602 TTAGATAATCAATGAACTAATA-TTTCATTATCACAA
1 TTAGATAATCAATGAACTAATATTTTC-TTATCACAA
12130638 TTAGATAATCAATGAACTAATATTTTCTTATCACAA
1 TTAGATAATCAATGAACTAATATTTTCTTATCACAA
12130674 TT
1 TT
12130676 TCGCTATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 33 0.89
37 4 0.11
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (36 bp):
TTAGATAATCAATGAACTAATATTTTCTTATCACAA
Found at i:12135760 original size:22 final size:22
Alignment explanation
Indices: 12135732--12135776 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
12135722 CCAAGGATGC
*
12135732 TCCCAATGATGATTATTTTATT
1 TCCCAATGATGATTACTTTATT
12135754 TCCCAATGATGATTACTTTATT
1 TCCCAATGATGATTACTTTATT
12135776 T
1 T
12135777 ACTTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.49
Consensus pattern (22 bp):
TCCCAATGATGATTACTTTATT
Found at i:12141524 original size:61 final size:62
Alignment explanation
Indices: 12141449--12141570 Score: 167
Period size: 64 Copynumber: 2.0 Consensus size: 62
12141439 TTATCAATGT
* **
12141449 TTTAAATATTTTTCAT-ATATATATAATCTCA-TTTTTATTTTTTTGGTAAATTATATATCCA
1 TTTAAATATTTTTCATAATATATATAATCT-ATTTTTTATTTTCTTAATAAATTATATATCCA
*
12141510 TTTAAATATTTTTCATAGATATTTATAATCTATTTTTTTATTTTCTTAATAAATTATATAT
1 TTTAAATATTTTTCATA-ATATATATAATCTA-TTTTTTATTTTCTTAATAAATTATATAT
12141571 TATTTTGATA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
61 16 0.30
62 1 0.02
63 12 0.23
64 24 0.45
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (62 bp):
TTTAAATATTTTTCATAATATATATAATCTATTTTTTATTTTCTTAATAAATTATATATCCA
Found at i:12141574 original size:23 final size:23
Alignment explanation
Indices: 12141547--12141594 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12141537 ATCTATTTTT
*
12141547 TTATTTTCTTAATAAA-TTATATA
1 TTATTTTCATAA-AAACTTATATA
*
12141570 TTATTTTGATAAAAACTTATATA
1 TTATTTTCATAAAAACTTATATA
12141593 TT
1 TT
12141595 TTATGTGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTATTTTCATAAAAACTTATATA
Found at i:12142374 original size:3 final size:3
Alignment explanation
Indices: 12142360--12142400 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
12142350 ATAGTTTACC
*
12142360 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12142401 ACTACTGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12144608 original size:45 final size:45
Alignment explanation
Indices: 12144540--12144715 Score: 254
Period size: 45 Copynumber: 4.0 Consensus size: 45
12144530 AATATCGTAT
**
12144540 GATACTAATCGGGCCTTTAAGCCTAGCAGGCTATAATGCCGGTGA
1 GATACTAATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
*
12144585 GATACTAATCGGGCCCTT-GAGCCTAGCAGGTTATAATGCCGGTGA
1 GATACTAATCGGG-CCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
12144630 GATACTAATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
1 GATACTAATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
* *
12144675 AATGA-T-ATCGGG-CTTCGAGCCTAGCAGGCAAT-ATGCCGGTG
1 GAT-ACTAATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTG
12144716 GATGAATTCA
Statistics
Matches: 123, Mismatches: 5, Indels: 9
0.90 0.04 0.07
Matches are distributed among these distances:
42 9 0.07
43 19 0.15
44 10 0.08
45 80 0.65
46 5 0.04
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (45 bp):
GATACTAATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
Found at i:12149757 original size:20 final size:20
Alignment explanation
Indices: 12149719--12149757 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12149709 CGTTTCTCTA
*
12149719 ACCATAAACATGCATAATAT
1 ACCATAAACATGCAAAATAT
12149739 ACCATTAAACAT-CAAAATA
1 ACCA-TAAACATGCAAAATA
12149758 CACAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.23
Consensus pattern (20 bp):
ACCATAAACATGCAAAATAT
Found at i:12153403 original size:12 final size:12
Alignment explanation
Indices: 12153381--12153436 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
12153371 AAGTCTAAGA
*
12153381 AAATAACAATAG
1 AAATAAAAATAG
*
12153393 ACATAAAAATAG
1 AAATAAAAATAG
* *
12153405 AAATAAAACTAAA
1 AAATAAAAAT-AG
12153418 AAATAAAAATA-
1 AAATAAAAATAG
12153429 AAATAAAA
1 AAATAAAA
12153437 TAAATGGACT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
11 8 0.22
12 19 0.51
13 10 0.27
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (12 bp):
AAATAAAAATAG
Found at i:12153417 original size:18 final size:17
Alignment explanation
Indices: 12153380--12153440 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 17
12153370 GAAGTCTAAG
* *
12153380 AAAATAACAATAGACATA
1 AAAATAAAAATA-AAATA
*
12153398 AAAATAGAAATAAAACTAA
1 AAAATAAAAATAAAA-T-A
12153417 AAAATAAAAATAAAAT-
1 AAAATAAAAATAAAATA
12153433 AAAATAAA
1 AAAATAAA
12153441 TGGACTCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 8 0.22
17 2 0.05
18 12 0.32
19 15 0.41
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:12153421 original size:19 final size:18
Alignment explanation
Indices: 12153397--12153436 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
12153387 CAATAGACAT
*
12153397 AAAAATAGAAATAAAACTA
1 AAAAATAAAAATAAAA-TA
12153416 AAAAATAAAAATAAAATA
1 AAAAATAAAAATAAAATA
12153434 AAA
1 AAA
12153437 TAAATGGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAATAAAATA
Found at i:12155440 original size:40 final size:40
Alignment explanation
Indices: 12155237--12155440 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
12155227 CGGAGTTTAA
** *
12155237 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12155277 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12155317 CC-GATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
12155356 CCGGATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
12155396 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12155436 CCGGA
1 CCGGA
12155441 CATCATTCGA
Statistics
Matches: 146, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
38 3 0.02
39 32 0.22
40 100 0.68
41 11 0.08
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12157899 original size:40 final size:40
Alignment explanation
Indices: 12157816--12157968 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
12157806 TCGAATGATG
* *
12157816 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
12157856 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
12157896 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
12157937 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
12157969 CGCTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:12165918 original size:40 final size:40
Alignment explanation
Indices: 12165835--12165987 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
12165825 TCGAATGATG
* *
12165835 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
12165875 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
12165915 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
12165956 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
12165988 CGCTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:12174503 original size:40 final size:40
Alignment explanation
Indices: 12174466--12174651 Score: 245
Period size: 40 Copynumber: 4.7 Consensus size: 40
12174456 GCTACTCGTT
*
12174466 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
12174506 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
12174546 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
12174586 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
12174627 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12174652 CATCATTCGA
Statistics
Matches: 134, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
39 3 0.02
40 118 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:12176886 original size:23 final size:23
Alignment explanation
Indices: 12176843--12176886 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12176833 CCAATTCAAC
*
12176843 ATATTTTCAAGATAAATTCATGT
1 ATATTTTCAAGATAAAGTCATGT
*
12176866 ATATTTAT-AAGATAACGTCAT
1 ATATTT-TCAAGATAAAGTCAT
12176887 CACATACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
ATATTTTCAAGATAAAGTCATGT
Found at i:12184712 original size:22 final size:23
Alignment explanation
Indices: 12184687--12184732 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12184677 CAACCAAACC
12184687 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
12184709 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
12184732 A
1 A
12184733 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:12184738 original size:23 final size:23
Alignment explanation
Indices: 12184694--12184738 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12184684 ACCAATTCAA
*
12184694 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
12184717 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
12184739 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:12189469 original size:25 final size:25
Alignment explanation
Indices: 12189435--12189484 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12189425 TGGAAGAAAA
12189435 CTCAAGCATTCCAGAACTATATAGT
1 CTCAAGCATTCCAGAACTATATAGT
12189460 CTCAAGCATTCCAGAACTATATAGT
1 CTCAAGCATTCCAGAACTATATAGT
12189485 GAAACTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (25 bp):
CTCAAGCATTCCAGAACTATATAGT
Found at i:12189788 original size:3 final size:3
Alignment explanation
Indices: 12189774--12189836 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
12189764 AGACAATTCA
* *
12189774 AAT AACT AAT AAT AAG AAT AAT AAT AAAT AAT AAAT AA- AAA AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT
*
12189821 -AT ACT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
12189837 ATAAGGATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.08
3 37 0.74
4 9 0.18
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:12189805 original size:22 final size:21
Alignment explanation
Indices: 12189774--12189833 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
12189764 AGACAATTCA
*
12189774 AATAACTAATAATAAGAATAAT
1 AATAACTAATAATAA-AAAAAT
*
12189796 AATAAATAATAAATAAAAAAAT
1 AATAACTAAT-AATAAAAAAAT
12189818 AATATACTAATAATAA
1 AATA-ACTAATAATAA
12189834 TAAATAAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAACTAATAATAAAAAAAT
Found at i:12191398 original size:42 final size:42
Alignment explanation
Indices: 12191339--12191420 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
12191329 TACTCGCTTC
*
12191339 TGATTTTGTGACACATCTCTGAATTACTTGATCTGCACATTT
1 TGATTTTCTGACACATCTCTGAATTACTTGATCTGCACATTT
*
12191381 TGATTTTCTGATACATCTCTGAATTACTTGATCTGCACAT
1 TGATTTTCTGACACATCTCTGAATTACTTGATCTGCACAT
12191421 ACACAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (42 bp):
TGATTTTCTGACACATCTCTGAATTACTTGATCTGCACATTT
Found at i:12195984 original size:28 final size:28
Alignment explanation
Indices: 12195919--12196019 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
12195909 ATAGTGAATC
*
12195919 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
*
12195948 CGAACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
12195976 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
12196006 CGCACACTTAGTGC
1 CGCACACTTAGTGC
12196020 CAATCTTGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.06
28 22 0.35
29 17 0.27
30 19 0.31
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:12202537 original size:5 final size:5
Alignment explanation
Indices: 12202527--12202570 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
12202517 ATTTATCCAT
* * *
12202527 TTTTA TTTTA TTTTA TTTTA TTTTA TATT- TTTTG TTTTA ATTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
12202571 AATTTTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:12202564 original size:19 final size:19
Alignment explanation
Indices: 12202527--12202576 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
12202517 ATTTATCCAT
*
12202527 TTTTATTTTATTTTATTTTA
1 TTTTATATT-TTTTATTTTA
*
12202547 TTTTATATTTTTTGTTTTA
1 TTTTATATTTTTTATTTTA
* *
12202566 ATTTAAATTTT
1 TTTTATATTTT
12202577 CTTTTGTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATATTTTTTATTTTA
Found at i:12206933 original size:30 final size:29
Alignment explanation
Indices: 12206839--12206940 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
12206829 TATAGTGAAT
* * *
12206839 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
12206868 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
12206896 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
12206926 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
12206941 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:12226077 original size:30 final size:29
Alignment explanation
Indices: 12225983--12226084 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
12225973 TATAGTGAAT
* * *
12225983 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
12226012 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
12226040 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
12226070 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
12226085 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:12238092 original size:13 final size:13
Alignment explanation
Indices: 12238074--12238099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12238064 TTCAAACTAC
12238074 TTTTTATTTTTTA
1 TTTTTATTTTTTA
12238087 TTTTTATTTTTTA
1 TTTTTATTTTTTA
12238100 GCAGATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:12239923 original size:11 final size:11
Alignment explanation
Indices: 12239907--12239931 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12239897 TAGAAGACCG
12239907 AAATGAGCCAA
1 AAATGAGCCAA
12239918 AAATGAGCCAA
1 AAATGAGCCAA
12239929 AAA
1 AAA
12239932 AGGGACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (11 bp):
AAATGAGCCAA
Found at i:12244419 original size:40 final size:40
Alignment explanation
Indices: 12244338--12244558 Score: 277
Period size: 40 Copynumber: 5.6 Consensus size: 40
12244328 AAACCAAGTA
** * *
12244338 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
12244377 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
12244417 CCTTCGGGACTTAGCTCGGTTATAGTAACTCGTACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
12244457 CCTTCGGGATTTGGCCCGGTTATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
12244497 CCTTCGGGACTTGGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
12244537 TCTTCCGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
12244559 CAATCCGAAT
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
39 25 0.16
40 135 0.84
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:12247288 original size:39 final size:38
Alignment explanation
Indices: 12247222--12247309 Score: 104
Period size: 39 Copynumber: 2.3 Consensus size: 38
12247212 TCACATTACC
*
12247222 ACTTGGTGTGTAGGGCTGGAAAAGTCGATTTTATCCCAT
1 ACTTGGTGTGTAGGACTGGAAAAGTCGATTTTATCCC-T
**** *
12247261 ACTTGGTGTGTAGGACTGGGTGGGTCGATTTTATCTCT
1 ACTTGGTGTGTAGGACTGGAAAAGTCGATTTTATCCCT
*
12247299 ACATGGTGTGT
1 ACTTGGTGTGT
12247310 TGGGTTGGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 11 0.26
39 31 0.74
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (38 bp):
ACTTGGTGTGTAGGACTGGAAAAGTCGATTTTATCCCT
Found at i:12253954 original size:29 final size:29
Alignment explanation
Indices: 12253915--12253993 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
12253905 CTTAATAATC
*
12253915 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
12253945 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
12253974 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
12253994 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:12257283 original size:30 final size:30
Alignment explanation
Indices: 12257247--12257319 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
12257237 TAGGCTGCAT
12257247 GGGCGTGTGGGTCACACGGGTGAACCACAC
1 GGGCGTGTGGGTCACACGGGTGAACCACAC
12257277 GGGCGTGTGGGTCACACGGGTGAACCACAC
1 GGGCGTGTGGGTCACACGGGTGAACCACAC
* *
12257307 GAGCGTGTAGGTC
1 GGGCGTGTGGGTC
12257320 TTGGGCCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.19, C:0.25, G:0.41, T:0.15
Consensus pattern (30 bp):
GGGCGTGTGGGTCACACGGGTGAACCACAC
Found at i:12269979 original size:124 final size:125
Alignment explanation
Indices: 12269574--12270039 Score: 821
Period size: 125 Copynumber: 3.8 Consensus size: 125
12269564 AATTATGTGG
* * * *
12269574 AATGAAATATGGATGTGTACTGATTATTGAT-T-TATGTGTGTATGAGCAATTGAATGATACTCG
1 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
12269637 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
66 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
*
12269697 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTAAATGATACCCG
1 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
*
12269762 GGTTAAGTCCCGAATGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
66 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
12269822 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATA-CCG
1 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
12269886 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
66 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
*
12269946 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATATCCG
1 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
* * *
12270011 GGCTAAGTCCCGAAGACGTTTATGCTAGT
66 GGTTAAGTCCCGAAGGCGATTATGCTAGT
12270040 AATTATATCC
Statistics
Matches: 329, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
123 29 0.09
124 124 0.38
125 176 0.53
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (125 bp):
AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
Found at i:12270020 original size:249 final size:248
Alignment explanation
Indices: 12269574--12270039 Score: 828
Period size: 249 Copynumber: 1.9 Consensus size: 248
12269564 AATTATGTGG
* * *
12269574 AATGAAATATGGATGTGTACTGATTATTGATTTATGTGTGTATGAGCAATTGAATGATACTCGGG
1 AATGAAACATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACTCGGG
12269639 TTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAAAATGAAA
66 TTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAAAATGAAA
*
12269704 CATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTAAATGATACCCGGGTTAAG
131 CATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTAAATGATACCCGGGCTAAG
12269769 TCCCGAATG-CGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
196 TCCCGAA-GACGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
12269822 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATAC-CG
1 AATGAAACATGGATGTGTAATGATTATTGAT-T-TATGTGTGCATGAGCAATTGAATGATACTCG
12269886 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAAAATGA
64 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAAAATGA
* *
12269951 AACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATATCCGGGCTA
129 AACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTAAATGATACCCGGGCTA
*
12270016 AGTCCCGAAGACGTTTATGCTAGT
194 AGTCCCGAAGACGATTATGCTAGT
12270040 AATTATATCC
Statistics
Matches: 208, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
248 30 0.14
249 151 0.73
250 27 0.13
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (248 bp):
AATGAAACATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACTCGGG
TTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAAAATGAAA
CATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTAAATGATACCCGGGCTAAG
TCCCGAAGACGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
Found at i:12270139 original size:80 final size:80
Alignment explanation
Indices: 12270046--12270211 Score: 323
Period size: 80 Copynumber: 2.1 Consensus size: 80
12270036 TAGTAATTAT
12270046 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
12270111 CGTGCATGTGGTTAA
66 CGTGCATGTGGTTAA
12270126 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
*
12270191 CGTGCATGTGGTTAT
66 CGTGCATGTGGTTAA
12270206 ATCCGG
1 ATCCGG
12270212 TTGTATTCCG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (80 bp):
ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
CGTGCATGTGGTTAA
Found at i:12270211 original size:40 final size:40
Alignment explanation
Indices: 12270006--12270188 Score: 217
Period size: 40 Copynumber: 4.6 Consensus size: 40
12269996 ATTGAATGAT
* * ** * * *
12270006 ATCCGGGCTAAGTCCCGAAGACGTTTATGCTAGTAATTAT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
* *
12270046 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
* *
12270086 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-ATGTGGTTAA
1 ATCCGGGCTAAGACCCGAAGGCAATT-GTGCTA-GTGATTAC
* *
12270126 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
12270166 ATCCGGGCTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
12270189 TTCGTGCATG
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
39 4 0.03
40 113 0.93
41 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
Found at i:12277308 original size:125 final size:125
Alignment explanation
Indices: 12277088--12277429 Score: 589
Period size: 125 Copynumber: 2.8 Consensus size: 125
12277078 AATTATGTGG
* * * *
12277088 AATGAAATATGGATGTGTACTGATTATTGAT-T-TATGTGTGTATGAGCAATTGAATGATACTCG
1 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
12277151 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
66 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
*
12277211 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTAAATGATACCCG
1 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
12277276 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
66 GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
*
12277336 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATATCCG
1 AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
* * *
12277401 GGCTAAGTCCCGAAGACGTTTATGCTAGT
66 GGTTAAGTCCCGAAGGCGATTATGCTAGT
12277430 AATTATATCC
Statistics
Matches: 207, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
123 29 0.14
124 1 0.00
125 177 0.86
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (125 bp):
AATGAAACATGGATGTGTAATGATTATTGATGTATATGTGTGCATGAGCAATTGAATGATACCCG
GGTTAAGTCCCGAAGGCGATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGAA
Found at i:12277535 original size:80 final size:80
Alignment explanation
Indices: 12277436--12277601 Score: 305
Period size: 80 Copynumber: 2.1 Consensus size: 80
12277426 TAGTAATTAT
* *
12277436 ATCCGGGTTAAGACTCGAAGGCAATTGTGCTAGTGACTACATCTGGGCTAAGACCCGAAGGCATT
1 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
12277501 CGTGCATGTGGTTAA
66 CGTGCATGTGGTTAA
12277516 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
*
12277581 CGTGCATGTGGTTAT
66 CGTGCATGTGGTTAA
12277596 ATCCGG
1 ATCCGG
12277602 TTGTATTCCG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTACATCCGGGCTAAGACCCGAAGGCATT
CGTGCATGTGGTTAA
Found at i:12277601 original size:40 final size:40
Alignment explanation
Indices: 12277396--12277578 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 40
12277386 ATTGAATGAT
* * ** * * *
12277396 ATCCGGGCTAAGTCCCGAAGACGTTTATGCTAGTAATTAT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
* * *
12277436 ATCCGGGTTAAGACTCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
* * *
12277476 ATCTGGGCTAAGACCCGAAGGC-ATTCGTGC-ATGTGGTTAA
1 ATCCGGGCTAAGACCCGAAGGCAATT-GTGCTA-GTGATTAC
* *
12277516 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
12277556 ATCCGGGCTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
12277579 TTCGTGCATG
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 4 0.03
40 109 0.93
41 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAC
Found at i:12279552 original size:24 final size:24
Alignment explanation
Indices: 12279475--12279552 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
12279465 TTTTAAATTA
* **
12279475 TTTTACATATTATTTCCTTTAAGT
1 TTTTACATATTATATATTTTAAGT
* * **
12279499 TTTTATGTACATTATATATTTTAAAC
1 TTTTA--CATATTATATATTTTAAGT
12279525 TTTTACATATTATATATTTTAAGT
1 TTTTACATATTATATATTTTAAGT
12279549 TTTT
1 TTTT
12279553 TTTTTTTACA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
24 24 0.59
26 17 0.41
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTTACATATTATATATTTTAAGT
Found at i:12279554 original size:26 final size:26
Alignment explanation
Indices: 12279458--12279554 Score: 76
Period size: 26 Copynumber: 3.8 Consensus size: 26
12279448 TGTTTCATTA
* *
12279458 TATATTATTTTAAATTATTTTACATAT
1 TATA-TATTTTAAGTTTTTTTACATAT
* **
12279485 TATTTCCTTTAAGTTTTTATGTAC--AT
1 TATATATTTTAAGTTTTT-T-TACATAT
**
12279511 TATATATTTTAA--ACTTTTACATAT
1 TATATATTTTAAGTTTTTTTACATAT
12279535 TATATATTTTAAGTTTTTTT
1 TATATATTTTAAGTTTTTTT
12279555 TTTTTACATA
Statistics
Matches: 52, Mismatches: 12, Indels: 13
0.68 0.16 0.17
Matches are distributed among these distances:
22 3 0.06
23 1 0.02
24 16 0.31
26 25 0.48
27 4 0.08
28 3 0.06
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (26 bp):
TATATATTTTAAGTTTTTTTACATAT
Found at i:12279636 original size:26 final size:25
Alignment explanation
Indices: 12279570--12279656 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 25
12279560 ACATATTATG
** *
12279570 TATTTTATATGTTATTCATGTTAAT
1 TATTTTATATAATATTCATTTTAAT
* *
12279595 TTTTTTATATAGTATTCATTTTAAAT
1 TATTTTATATAATATTCATTTT-AAT
*
12279621 TGTTTTA-ATACATATT-ATTTTGAAT
1 TATTTTATATA-ATATTCATTTT-AAT
12279646 TATTTTATATA
1 TATTTTATATA
12279657 TTAATTACTT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
25 35 0.69
26 16 0.31
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (25 bp):
TATTTTATATAATATTCATTTTAAT
Done.