Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 32 of 259
Found at i:9276946 original size:29 final size:29
Alignment explanation
Indices: 9276863--9276992 Score: 138
Period size: 29 Copynumber: 4.6 Consensus size: 29
9276853 ACCTCTACAT
* *
9276863 ACATGCATATGGCCCACTAGGCCCAA-TC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* * *
9276891 TCATTTATATGGCCCATTCGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* * * * *
9276920 ACGTTCTTATGGGCTATTAGGCGCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
9276949 ACATTCATATGGCCCATTAGGCCCAA-TC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* *
9276977 TCATTTATATGGCCCA
1 ACATTCATATGGCCCA
9276993 AATCACATTA
Statistics
Matches: 81, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
28 37 0.46
29 44 0.54
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAATTC
Found at i:9277003 original size:19 final size:19
Alignment explanation
Indices: 9276968--9277005 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9276958 TGGCCCATTA
*
9276968 GGCCCAATCTCATTTATAT
1 GGCCCAATCACATTTATAT
9276987 GGCCCAAATCACA-TTATAT
1 GGCCC-AATCACATTTATAT
9277006 TCATGCTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
GGCCCAATCACATTTATAT
Found at i:9277117 original size:19 final size:19
Alignment explanation
Indices: 9277071--9277108 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
9277061 TATGGCCCAA
* *
9277071 TAGCCCA-TCGGGCCTATT
1 TAGCCCATTCTGGCCAATT
9277089 TAGCCCATTCTGGCCAATT
1 TAGCCCATTCTGGCCAATT
9277108 T
1 T
9277109 GGCCTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (19 bp):
TAGCCCATTCTGGCCAATT
Found at i:9283585 original size:40 final size:40
Alignment explanation
Indices: 9283530--9283705 Score: 257
Period size: 40 Copynumber: 4.4 Consensus size: 40
9283520 GGATGATGTT
* *
9283530 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATC
9283570 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATC
**
9283610 CGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATC
* * *
9283650 CGGGCTAAGACCCGAAGGCATTTGCGCGAGTTG-CTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATC
*
9283690 C-GGCTAAATCCCGAAG
1 CGGGCTAAGTCCCGAAG
9283706 ATGCTTGGGT
Statistics
Matches: 124, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.10
40 109 0.88
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATC
Found at i:9290798 original size:40 final size:40
Alignment explanation
Indices: 9290743--9290920 Score: 252
Period size: 40 Copynumber: 4.5 Consensus size: 40
9290733 TCGGATGATG
* *
9290743 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATA
9290783 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATA
* **
9290823 TCCGGGCAAAGTCCCGAAGGCATTCATGCTAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATA
* * *
9290863 TCCGGGCTAAGACCCGAAGGCATTTGCGCGAGTTG-CTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATA
*
9290903 TCC-GGCTAAATCCCGAAG
1 TCCGGGCTAAGTCCCGAAG
9290921 ATGCTTGGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.10
40 109 0.88
41 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATA
Found at i:9294027 original size:28 final size:28
Alignment explanation
Indices: 9293995--9294116 Score: 131
Period size: 29 Copynumber: 4.3 Consensus size: 28
9293985 TACATAATGC
9293995 ATATGGCCCA-CTAGGCCCAATCTCATTT
1 ATATGGCCCATC-AGGCCCAATCTCATTT
* *
9294023 ATATGGCCCATCCGACCCAAT-TCATGTT
1 ATATGGCCCATCAGGCCCAATCTCAT-TT
* * * *
9294051 CTTATAGCCCATCAGGCCCAATTCACATTC
1 -ATATGGCCCATCAGGCCCAA-TCTCATTT
*
9294081 ATATGGCCCATTAGGCCCAATCTCATTT
1 ATATGGCCCATCAGGCCCAATCTCATTT
9294109 ATATGGCC
1 ATATGGCC
9294117 TAAATCACAT
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
27 4 0.05
28 33 0.43
29 34 0.45
30 2 0.03
31 3 0.04
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (28 bp):
ATATGGCCCATCAGGCCCAATCTCATTT
Found at i:9294243 original size:19 final size:19
Alignment explanation
Indices: 9294197--9294234 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
9294187 TATGGCCCAA
* *
9294197 TAGCCCA-TCGGGCCGATT
1 TAGCCCATTCTGGCCCATT
9294215 TAGCCCATTCTGGCCCATT
1 TAGCCCATTCTGGCCCATT
9294234 T
1 T
9294235 GGCCTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.34, G:0.21, T:0.29
Consensus pattern (19 bp):
TAGCCCATTCTGGCCCATT
Found at i:9296775 original size:46 final size:45
Alignment explanation
Indices: 9296614--9296784 Score: 181
Period size: 45 Copynumber: 3.7 Consensus size: 45
9296604 ACCCGCCCCT
* *
9296614 AAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCATCCA
1 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
9296658 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACATTTC-
1 -AAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCA-TCCA
*
9296708 -A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
9296751 GAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -AAGTGAACTCGGACTCAACTCAACGAGTTCGGA
9296785 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
42 4 0.04
43 3 0.03
44 1 0.01
45 31 0.30
46 29 0.28
47 28 0.27
48 2 0.02
50 2 0.02
51 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (45 bp):
AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:9296780 original size:93 final size:92
Alignment explanation
Indices: 9296618--9296787 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 92
9296608 GCCCCTAAGT
* * *
9296618 GAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCATCCATAAGTGAACTCGGACTCAACTCAAT
1 GAACTCGGACTCAACTCAACGAGCTCGGACTTCGCATCCAGAAGTGAACTCGGACTCAACTCAAC
9296683 GAGTTCGGATGCCTAGTTACATTTCAC
66 GAGTTCGGATGCCTAGTTACATTTCAC
*
9296710 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAGAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGAC-TTCGCATCCAGAAGTGAACTCGGACTCAACTCAA
9296775 CGAGTTCGGATGC
65 CGAGTTCGGATGC
9296788 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 28 0.38
93 45 0.62
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACTTCGCATCCAGAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCAC
Found at i:9301111 original size:15 final size:15
Alignment explanation
Indices: 9301091--9301120 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9301081 AAATCAAATC
9301091 TCAATAAAAAGGGAG
1 TCAATAAAAAGGGAG
*
9301106 TCAATAAACAGGGAG
1 TCAATAAAAAGGGAG
9301121 AAATTCTTAA
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:0.50, C:0.10, G:0.27, T:0.13
Consensus pattern (15 bp):
TCAATAAAAAGGGAG
Found at i:9302204 original size:6 final size:6
Alignment explanation
Indices: 9302188--9302222 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
9302178 TTAGAACATG
*
9302188 AAAAAT GAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
9302223 CAGAAGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:9308304 original size:27 final size:27
Alignment explanation
Indices: 9308266--9308329 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
9308256 TAATGCCTTG
9308266 TTGGTGTGTTTGGGAAGATATGA-TATA
1 TTGGTGTGTTTGGGAAGATAT-ATTATA
* *
9308293 TTGGTGTGTTTGGGAGGCTATATTATA
1 TTGGTGTGTTTGGGAAGATATATTATA
*
9308320 CTGGTGTGTT
1 TTGGTGTGTT
9308330 ATGGAGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (27 bp):
TTGGTGTGTTTGGGAAGATATATTATA
Found at i:9315759 original size:12 final size:12
Alignment explanation
Indices: 9315727--9315775 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
9315717 AACTATTTGG
9315727 CTATATCAACAA
1 CTATATCAACAA
9315739 CTATGA-C-A-AA
1 CTAT-ATCAACAA
9315749 C-ATATCAACAA
1 CTATATCAACAA
*
9315760 CTATATCAATAA
1 CTATATCAACAA
9315772 CTAT
1 CTAT
9315776 TTATACATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 18 0.58
13 1 0.03
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (12 bp):
CTATATCAACAA
Found at i:9316065 original size:17 final size:17
Alignment explanation
Indices: 9316043--9316075 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9316033 GGGGCTATAT
9316043 TAAATATAA-AAAATAAA
1 TAAATA-AATAAAATAAA
9316060 TAAATAAATAAAATAA
1 TAAATAAATAAAATAA
9316076 TTCGTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATAAATAAAATAAA
Found at i:9322124 original size:40 final size:40
Alignment explanation
Indices: 9322087--9322272 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
9322077 GCTACTCGTT
* *
9322087 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
9322127 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
9322167 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * * *
9322207 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
9322248 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9322273 CATCATTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 113 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9331633 original size:47 final size:46
Alignment explanation
Indices: 9331560--9331914 Score: 175
Period size: 47 Copynumber: 7.6 Consensus size: 46
9331550 TGATTTGTGT
*
9331560 GCCAGTGTAAGACATGTCTGGAACATGCTTTAGCCACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCTTTAGCCACATTATGAGA
* * * * * * *
9331606 GCCATTGTAAGACCATGTCTGGGACATGGC-ATCGGCATCCA-GACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCTTTAGCCA--CATTATGAGA
* * * *
9331654 GCTAGTGTAAGACATGTCTAGGACATGCTTCAGCCATATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCTTTAGCCACATTATGAGA
* * * * * * ** *
9331700 GCCAGTTTAAAACCATGTCTGGGACATGGC-ATCGACATAGAAATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCTTTAGCCACA-TTATGAGA
* * * * ** * *
9331748 GCCAGAGTAAGACATGTCTGGGACATGCATTGGCCTCGACAAAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCTTTAGCCAC-ATTATGAGA
* * * ** * * * *
9331795 GCCAGTGTAAGACGTGTCTAGGACATGCATCGGCTA-A-GA-GTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCTTTAGCCACATTATG-AGA
* * *
9331839 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CACGTATATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCTTTAGCCAC--AT-TATGAGA
9331887 GCCAGTGTAAGACCATGTCTGGGACATG
1 GCCAGTGTAAGA-CATGTCTGGGACATG
9331915 GCATCGACAA
Statistics
Matches: 229, Mismatches: 61, Indels: 35
0.70 0.19 0.11
Matches are distributed among these distances:
43 2 0.01
44 30 0.13
45 2 0.01
46 29 0.13
47 102 0.45
48 46 0.20
49 18 0.08
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCTTTAGCCACATTATGAGA
Found at i:9331724 original size:94 final size:92
Alignment explanation
Indices: 9331558--9331920 Score: 385
Period size: 94 Copynumber: 3.9 Consensus size: 92
9331548 GGTGATTTGT
* * * * *
9331558 GTGCCAGTGTAAGACATGTCTGGAACATGCTTTAGCCACATTATGAGAGCCATTGTAAGACCATG
1 GTGCTAGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCCAGTGTAAGACCATG
*
9331623 TCTGGGACATGGCATCGGCATCCAGACGA
66 TCTGGGACATGGCATCGGCAT-AAGA-GA
* * * *
9331652 GGGCTAGTGTAAGACATGTCTAGGACATGCTTCAGCCATATTATGAGAGCCAGTTTAAAACCATG
1 GTGCTAGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCCAGTGTAAGACCATG
* *
9331717 TCTGGGACATGGCATCGACATAGAAATGA
66 TCTGGGACATGGCATCGGCATA-AGA-GA
* * * ** * *
9331746 GTGCCAGAGTAAGACATGTCTGGGACATGCATT-GGCC-TCGACAAAGATAGCCAGTGTAAGA-C
1 GTGCTAGTGTAAGACATGTCTGGGACATGC-TTCAGCCAT--ATTATGAGAGCCAGTGTAAGACC
* * *
9331808 GTGTCTAGGACAT-GCATCGGC-TAAGAGTT
63 ATGTCTGGGACATGGCATCGGCATAAGAG-A
* *
9331837 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGTATATATGAGAGCCAGTGTAAGACCA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCTTCAGC-CATAT-TATGAGAGCCAGTGTAAGACCA
9331902 TGTCTGGGACATGGCATCG
64 TGTCTGGGACATGGCATCG
9331921 ACAATGTATC
Statistics
Matches: 219, Mismatches: 39, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
90 2 0.01
91 33 0.15
92 19 0.09
93 21 0.10
94 127 0.58
95 17 0.08
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (92 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGGCATAAGAGA
Found at i:9351806 original size:40 final size:40
Alignment explanation
Indices: 9351741--9351816 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
9351731 TGCGGTACCT
* *
9351741 TATGGTGTGTAGGGTTGGATAGGTCGATTATATCCCAATA
1 TATGGTGTGCAGGGATGGATAGGTCGATTATATCCCAATA
* * *
9351781 TATGGTGTGCAGGGATGGGTGGGTCGATTTTATCCC
1 TATGGTGTGCAGGGATGGATAGGTCGATTATATCCC
9351817 CACATGGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.34
Consensus pattern (40 bp):
TATGGTGTGCAGGGATGGATAGGTCGATTATATCCCAATA
Found at i:9356659 original size:51 final size:50
Alignment explanation
Indices: 9356587--9356738 Score: 176
Period size: 51 Copynumber: 3.1 Consensus size: 50
9356577 ACATGTAACA
*
9356587 CATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGCTACATGCATCG
1 CATCCATAATGAACTCGGACCACTCAACGAGCTCGGATG-TACATGCATCG
* *
9356638 CATCCATCATGAACACGGACCACTCAACGAGCTCGGATGT---T-CA---
1 CATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGTACATGCATCG
*
9356681 CATCCATAATGAACTCGGACCACT-AGACGAGCTCAGATGTTACATGCATCG
1 CATCCATAATGAACTCGGACCACTCA-ACGAGCTCGGATG-TACATGCATCG
*
9356732 TATCCAT
1 CATCCAT
9356739 CATGTTCATA
Statistics
Matches: 85, Mismatches: 7, Indels: 18
0.77 0.06 0.16
Matches are distributed among these distances:
42 1 0.01
43 34 0.40
44 1 0.01
46 2 0.02
47 2 0.02
48 2 0.02
50 1 0.01
51 42 0.49
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (50 bp):
CATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGTACATGCATCG
Found at i:9356700 original size:43 final size:42
Alignment explanation
Indices: 9356638--9356725 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 42
9356628 ACATGCATCG
* *
9356638 CATCCATCATGAACACGGACCACTCA-ACGAGCTCGGATGTTCA
1 CATCCATAATGAACACGGACCACT-AGACGAGCTCAGATGTT-A
*
9356681 CATCCATAATGAACTCGGACCACTAGACGAGCTCAGATGTTA
1 CATCCATAATGAACACGGACCACTAGACGAGCTCAGATGTTA
9356723 CAT
1 CAT
9356726 GCATCGTATC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (42 bp):
CATCCATAATGAACACGGACCACTAGACGAGCTCAGATGTTA
Found at i:9359277 original size:46 final size:46
Alignment explanation
Indices: 9359182--9359351 Score: 152
Period size: 46 Copynumber: 3.7 Consensus size: 46
9359172 CATCTTGTAA
* * *
9359182 CCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCCTGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCCTACGTCCTAAGG
* * *
9359228 CCGATGCATGTCTCAGACATGTCTTACACTAGCACT-CGT-TTCAATG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGC-CTACGTCCT-AAGG
* *
9359274 CCGATGCCATGTCCCAAACATGGTCTTACACTAG-CT-C-TCATAATGTGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCCTACGTCCTAA---GG
* *
9359322 CCGATGCATGTCCGAGACATGTTTTACACT
1 CCGATGCATGTCCCAGACATGTCTTACACT
9359352 GGCGCACATA
Statistics
Matches: 103, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
45 4 0.04
46 55 0.53
47 25 0.24
48 19 0.18
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCCTACGTCCTAAGG
Found at i:9359283 original size:138 final size:139
Alignment explanation
Indices: 9359050--9359354 Score: 323
Period size: 138 Copynumber: 2.2 Consensus size: 139
9359040 CAAGCAATGC
* * * *
9359050 CATGTCCCAGATATGGTCTTACACTAGCTTTCACATCTGGCTGATGTATGTCCCAAACATGTCTT
1 CATGTCCCAGACAT-GTCTTACACTGGCTTTCACATCTGGCCGATGCATGTCCCAAACATGTCTT
* * ** **
9359115 ACACTAGCACACATATCCGAGTCGAAGCCATGTCCCGGACATGGTCTTACACT-G-ACACATCTT
65 ACACTAGCACACATATCCAAGCCGAAGCCATGTCCCAAACATGGTCTTACACTAGCACACATAAT
9359178 GTAACCGATG
130 GTAACCGATG
* * *
9359188 CATGTCCCAGACATGTCTTACACTGGC-TT-ACGTCCTGAGGCCGATGCATGTCTCAGACATGTC
1 CATGTCCCAGACATGTCTTACACTGGCTTTCACAT-CT--GGCCGATGCATGTCCCAAACATGTC
* * * * * *
9359251 TTACACTAGCACTCGT-TTCAATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCAT
63 TTACACTAGCACACATATCCAA-GCCGAAGCCATGTCCCAAACATGGTCTTACACTAGCACACAT
**
9359315 AATGTGGCCGATG
127 AATGTAACCGATG
* *
9359328 CATGTCCGAGACATGTTTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
9359355 GCACATATCA
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
135 3 0.02
136 4 0.03
137 15 0.11
138 77 0.56
139 1 0.01
140 38 0.28
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (139 bp):
CATGTCCCAGACATGTCTTACACTGGCTTTCACATCTGGCCGATGCATGTCCCAAACATGTCTTA
CACTAGCACACATATCCAAGCCGAAGCCATGTCCCAAACATGGTCTTACACTAGCACACATAATG
TAACCGATG
Found at i:9359324 original size:94 final size:92
Alignment explanation
Indices: 9359092--9359351 Score: 234
Period size: 94 Copynumber: 2.8 Consensus size: 92
9359082 ACATCTGGCT
* ** * *
9359092 GATGTATGTCCCAAACATGTCTTACACTAGCACACAT-ATCCGA-GTCGAAGCCATGTCCCG-GA
1 GATGCATGTCCCAAACATGTCTTACACTAGCTTACATAAT--GAGGCCGATG-CATGT-CCGAGA
9359154 CATGGTCTTACACT-GACACATC-TTGT-AA--CC
62 CAT-GTCTTACACTAG-CAC-TCGTT-TCAATGCC
* * * **
9359184 GATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCCTGAGGCCGATGCATGTCTC-AGACAT
1 GATGCATGTCCCAAACATGTCTTACACTAGCTTACATAATGAGGCCGATGCATGTC-CGAGACAT
9359248 GTCTTACACTAGCACTCGTTTCAATGCC
65 GTCTTACACTAGCACTCGTTTCAATGCC
*
9359276 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCT-CATAATGTGGCCGATGCATGTCCGAGAC
1 GATG-CATGTCCCAAACAT-GTCTTACACTAGCT-TACATAATGAGGCCGATGCATGTCCGAGAC
*
9359340 ATGTTTTACACT
63 ATGTCTTACACT
9359352 GGCGCACATA
Statistics
Matches: 139, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
89 3 0.02
90 18 0.13
91 14 0.10
92 42 0.30
93 15 0.11
94 46 0.33
95 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (92 bp):
GATGCATGTCCCAAACATGTCTTACACTAGCTTACATAATGAGGCCGATGCATGTCCGAGACATG
TCTTACACTAGCACTCGTTTCAATGCC
Found at i:9362057 original size:51 final size:52
Alignment explanation
Indices: 9361976--9362082 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 52
9361966 CTACCTCATA
*
9361976 ACATGTAACACATCCATAATGAACTCGGACCACTCAACGAGCTCGGATGCT-
1 ACATGTAACACATCCATAATGAACTCGGACCACTCAACGAGCTCAGATGCTC
* * * * *
9362027 ACATGTATCGCATCCATCATGAACTTGGACCACTCAATGAGCTCAGATGCTC
1 ACATGTAACACATCCATAATGAACTCGGACCACTCAACGAGCTCAGATGCTC
9362079 ACAT
1 ACAT
9362083 CCATAATAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 45 0.92
52 4 0.08
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (52 bp):
ACATGTAACACATCCATAATGAACTCGGACCACTCAACGAGCTCAGATGCTC
Found at i:9362100 original size:43 final size:43
Alignment explanation
Indices: 9362037--9362118 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
9362027 ACATGTATCG
* * * *
9362037 CATCCATCATGAACTTGGACCACTCA-ATGAGCTCAGATGCTCA
1 CATCCATAATAAACTCGGACCACT-AGATGAACTCAGATGCTCA
9362080 CATCCATAATAAACTCGGACCACTAGATGAACTCAGATG
1 CATCCATAATAAACTCGGACCACTAGATGAACTCAGATG
9362119 TTACATGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (43 bp):
CATCCATAATAAACTCGGACCACTAGATGAACTCAGATGCTCA
Found at i:9370344 original size:40 final size:40
Alignment explanation
Indices: 9370298--9370375 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
9370288 GAAAAAATCA
* *
9370298 AATAGATGGAGTTTTAGCGGCGTTTTTAAAAAAATGCCTC
1 AATAGATCGAGCTTTAGCGGCGTTTTTAAAAAAATGCCTC
* *
9370338 AATAGATCGAGCTTTAGCGGCGTTTTTGAAAAAGTGCC
1 AATAGATCGAGCTTTAGCGGCGTTTTTAAAAAAATGCC
9370376 GCTAAAGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (40 bp):
AATAGATCGAGCTTTAGCGGCGTTTTTAAAAAAATGCCTC
Found at i:9370395 original size:40 final size:40
Alignment explanation
Indices: 9370311--9370411 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 40
9370301 AGATGGAGTT
* * *
9370311 TTAGCGGCGTTTTTAAAAAAATGCCTCAATAGATCGAGCT
1 TTAGCGGCGTTTTTAAAAAAATGCCGCAATAGATCGACCA
* * * *
9370351 TTAGCGGCGTTTTTGAAAAAGTGCCGCTAA-AGGTTGACCA
1 TTAGCGGCGTTTTTAAAAAAATGCCGC-AATAGATCGACCA
* *
9370391 TTAGCAGCGCTTTTTCAAAAA
1 TTAGCGGCG-TTTTTAAAAAA
9370412 CGCCACTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
40 38 0.76
41 12 0.24
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (40 bp):
TTAGCGGCGTTTTTAAAAAAATGCCGCAATAGATCGACCA
Found at i:9370698 original size:41 final size:41
Alignment explanation
Indices: 9370636--9370715 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
9370626 GCGCTTTCCT
*
9370636 AAAAACGCCGCAATAGCTCGCACT-TTAGAGGCATTTTTGTA
1 AAAAACGCCACAATAGCTCGCA-TATTAGAGGCATTTTTGTA
* * *
9370677 AAAAACGCCACTATAGGTCGCATAATTAGCGGCATTTTT
1 AAAAACGCCACAATAGCTCGCAT-ATTAGAGGCATTTTT
9370716 TTGTAAACGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.03
41 19 0.58
42 13 0.39
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (41 bp):
AAAAACGCCACAATAGCTCGCATATTAGAGGCATTTTTGTA
Found at i:9371468 original size:25 final size:24
Alignment explanation
Indices: 9371418--9371469 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
9371408 TAACTTATTT
**
9371418 TTTAAATGAATTTAAAATTTTCTA
1 TTTAAATGAATTTAAAATTTAATA
* *
9371442 TTTAAACTGATTTTTAAATTTAATA
1 TTTAAA-TGAATTTAAAATTTAATA
9371467 TTT
1 TTT
9371470 TTATAGGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTAAATGAATTTAAAATTTAATA
Found at i:9371504 original size:14 final size:13
Alignment explanation
Indices: 9371483--9371527 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
9371473 TAGGTTTAAG
9371483 GGTTATGATTTAT
1 GGTTATGATTTAT
9371496 GGTTGATGATTTAT
1 GGTT-ATGATTTAT
* *
9371510 GTTTTATGATTTAG
1 G-GTTATGATTTAT
9371524 GGTT
1 GGTT
9371528 TGAGGTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 6 0.22
14 19 0.70
15 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (13 bp):
GGTTATGATTTAT
Found at i:9371701 original size:14 final size:14
Alignment explanation
Indices: 9371684--9371713 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9371674 GTGTTTTAAA
9371684 GTTTATTATTTAGG
1 GTTTATTATTTAGG
9371698 GTTTATTATTTAGG
1 GTTTATTATTTAGG
9371712 GT
1 GT
9371714 CTAAGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (14 bp):
GTTTATTATTTAGG
Found at i:9371911 original size:7 final size:7
Alignment explanation
Indices: 9371888--9371946 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
9371878 GGTTAATTAA
9371888 GGTTTAG
1 GGTTTAG
**
9371895 GGGCTAG
1 GGTTTAG
*
9371902 GGTTTGG
1 GGTTTAG
9371909 GGTTTAG
1 GGTTTAG
*
9371916 GGTTTAT
1 GGTTTAG
*
9371923 AGTTTAG
1 GGTTTAG
*
9371930 GGTTTAT
1 GGTTTAG
*
9371937 GGTATAG
1 GGTTTAG
9371944 GGT
1 GGT
9371947 CAGGGTCTTA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.15, C:0.02, G:0.42, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:9372229 original size:14 final size:14
Alignment explanation
Indices: 9372210--9372243 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
9372200 CTTATGGTTT
*
9372210 GGGTTTGGGATTTG
1 GGGTTTGGGATTTA
9372224 GGGTTTGGGATTTA
1 GGGTTTGGGATTTA
9372238 GGGTTT
1 GGGTTT
9372244 AGTGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.44
Consensus pattern (14 bp):
GGGTTTGGGATTTA
Found at i:9373183 original size:24 final size:24
Alignment explanation
Indices: 9373153--9373198 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
9373143 GTCAGGTAAC
9373153 TTTAATTTCTAAGTCTCTGTTTCT
1 TTTAATTTCTAAGTCTCTGTTTCT
9373177 TTTAATTTCTAAGTCTCTGTTT
1 TTTAATTTCTAAGTCTCTGTTT
9373199 ACAAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (24 bp):
TTTAATTTCTAAGTCTCTGTTTCT
Found at i:9373979 original size:24 final size:23
Alignment explanation
Indices: 9373926--9373985 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
9373916 TGAAAATCGA
**
9373926 ATTATAATAATGTTATACTATCTT
1 ATTATAAT-ATGTTATAAAATCTT
*
9373950 ATTTATAATATGTTATGAAAATTTT
1 A-TTATAATATGTTAT-AAAATCTT
9373975 ATTATAATATG
1 ATTATAATATG
9373986 CTTTGGTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (23 bp):
ATTATAATATGTTATAAAATCTT
Found at i:9377485 original size:15 final size:15
Alignment explanation
Indices: 9377465--9377493 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9377455 GGAGTAGACC
9377465 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
9377480 AGGTACGTTTTATT
1 AGGTACGTTTTATT
9377494 TCAAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:9378494 original size:421 final size:420
Alignment explanation
Indices: 9377686--9378531 Score: 1536
Period size: 421 Copynumber: 2.0 Consensus size: 420
9377676 AGTATGAATT
*
9377686 AATTTTATTACCATATATGTAGCTTGCTTGTCCATTATGATTACAACAATAGCTGACCTTCTCTC
1 AATTTTATTACCATATATGTAGCTTGCTTGTCCATTATAATTACAACAATAGCTGACCTTCTCTC
*
9377751 CAACCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGTCTTA
66 CAACCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTA
* *
9377816 TATCAAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAA
131 TATCAAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACACCACGTATAATGAATCTTAA
*
9377881 AAAATTCAAAGAGACTTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTT
196 AAAATTCAAAGAAACTTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTT
*
9377946 CCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATTT
261 CCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGAAATTATTATATTCAAATTACTATTT
*
9378011 TTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTATTTTTATAAAAAAAAAAG
326 TTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTATTTGTAT--AAAAAAAAG
9378076 ATTTCAAAAAAAGTTCTATGGAGCTTATAAAC
389 ATTTCAAAAAAAGTTCTATGGAGCTTATAAAC
9378108 AATTTTATTACCATATATGTAGCTTGCTTGTCCATTATAATTACAACAATAGCTGACCTTCTCTC
1 AATTTTATTACCATATATGTAGCTTGCTTGTCCATTATAATTACAACAATAGCTGACCTTCTCTC
9378173 CAACCTTATTTTAAAT-TTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTA
66 CAACCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTA
*
9378237 TATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACACCACGTATAATGAATCTTAA
131 TATCAAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACACCACGTATAATGAATCTTAA
9378302 AAAATTCAAA-AAATCTTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATT
196 AAAATTCAAAGAAA-CTTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATT
9378366 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGAAATTATTATATTCAAATTACTATT
260 TCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGAAATTATTATATTCAAATTACTA--
9378431 TTTTTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTATTTGTAT-AAAAAAA
323 TTTTTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTATTTGTATAAAAAAAA
* *
9378495 GATTTCAAAAAAAGTTTTATGGAGCTTATAAAT
388 GATTTCAAAAAAAGTTCTATGGAGCTTATAAAC
9378528 AATT
1 AATT
9378532 CTATCGACCT
Statistics
Matches: 411, Mismatches: 10, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
420 44 0.11
421 231 0.56
422 80 0.19
423 56 0.14
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (420 bp):
AATTTTATTACCATATATGTAGCTTGCTTGTCCATTATAATTACAACAATAGCTGACCTTCTCTC
CAACCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTA
TATCAAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACACCACGTATAATGAATCTTAA
AAAATTCAAAGAAACTTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTT
CCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTGAAATTATTATATTCAAATTACTATTT
TTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTATTTGTATAAAAAAAAGAT
TTCAAAAAAAGTTCTATGGAGCTTATAAAC
Found at i:9378669 original size:53 final size:49
Alignment explanation
Indices: 9378580--9378684 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 49
9378570 GAAGTGCCAC
** *
9378580 TTATAAATAATTTTATCAATATAATAATATTGATCATTGTTTAAATATA
1 TTATAAATAATTTTATCAATATAATAATATTGATCATTACTTAAATAAA
* *
9378629 TTATAACTAATTTTTATCAAAATAGTATTAATATTGATCATTACTTAAATAAA
1 TTATAAATAA-TTTTATC--AATA-TAATAATATTGATCATTACTTAAATAAA
9378682 TTA
1 TTA
9378685 CATAACTCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 9 0.19
50 7 0.15
52 4 0.09
53 27 0.57
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (49 bp):
TTATAAATAATTTTATCAATATAATAATATTGATCATTACTTAAATAAA
Found at i:9383822 original size:37 final size:37
Alignment explanation
Indices: 9383771--9383887 Score: 171
Period size: 37 Copynumber: 3.2 Consensus size: 37
9383761 CTTATTACGA
* * *
9383771 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
* *
9383808 GGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
1 AGTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
* *
9383845 AGTCTTACCCGGACAAAATCCCCACATGTAGTCATCG
1 AGTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
9383882 AGTCTT
1 AGTCTT
9383888 TAGAGCTCGG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
Found at i:9384084 original size:47 final size:47
Alignment explanation
Indices: 9384006--9384173 Score: 246
Period size: 47 Copynumber: 3.6 Consensus size: 47
9383996 CCCTTCGGGA
* * * * * *
9384006 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
9384053 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9384100 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
9384147 CTTATCACACATATACACTTATCACAT
1 CTTATCACATATATACACTT-TCACAT
9384174 ATATACACTT
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 103 0.94
48 6 0.06
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:9384169 original size:17 final size:17
Alignment explanation
Indices: 9384147--9384183 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
9384137 GCCATTAGGC
9384147 CTTATCACACATATACA
1 CTTATCACACATATACA
*
9384164 CTTATCACATATATACA
1 CTTATCACACATATACA
9384181 CTT
1 CTT
9384184 TCTTGGCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (17 bp):
CTTATCACACATATACA
Found at i:9388478 original size:21 final size:21
Alignment explanation
Indices: 9388452--9388499 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
9388442 TCAACTTAGA
*
9388452 GCGGAGACAGCAGCGCGGGAG
1 GCGGAGACAGCAGCGAGGGAG
* *
9388473 GCGGAGGCAGCAGTGAGGGAG
1 GCGGAGACAGCAGCGAGGGAG
9388494 GCGGAG
1 GCGGAG
9388500 CAGAATAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.56, T:0.02
Consensus pattern (21 bp):
GCGGAGACAGCAGCGAGGGAG
Found at i:9388864 original size:43 final size:40
Alignment explanation
Indices: 9388793--9388940 Score: 147
Period size: 43 Copynumber: 3.5 Consensus size: 40
9388783 ACTGGGCAAA
* *
9388793 TTAGCGGCG-TTTTTCAAAAGCGCTACTAAAAGTGCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAGC-CCACTAAAAGT-CTGGTCT
*
9388834 TTAGCGGCGTTTTTTTAAAAAGCACCACTAAAAATCCTGGTCT
1 TTAGCGGCG-TTTTTTAAAAAGC-CCACTAAAAGT-CTGGTCT
* * *
9388877 TTAGCGGCGCTTTTATAAAAATG-CCGCTAAATGTCTGGTCT
1 TTAGCGGCG-TTTTTTAAAAA-GCCCACTAAAAGTCTGGTCT
*
9388918 TTAGTGGCGTTTTTTAAGAAAGC
1 TTAGCGGCGTTTTTTAA-AAAGC
9388941 GCCGCTAATT
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
40 8 0.09
41 27 0.30
42 8 0.09
43 46 0.51
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (40 bp):
TTAGCGGCGTTTTTTAAAAAGCCCACTAAAAGTCTGGTCT
Found at i:9391858 original size:11 final size:11
Alignment explanation
Indices: 9391842--9391869 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
9391832 AATTTGCGTG
9391842 TTATAAAAATA
1 TTATAAAAATA
9391853 TTATAAAAATA
1 TTATAAAAATA
9391864 TTATAA
1 TTATAA
9391870 TATACTCATA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TTATAAAAATA
Found at i:9397882 original size:14 final size:15
Alignment explanation
Indices: 9397863--9397896 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9397853 CATCCCACCT
9397863 TTATATA-ATTTTTA
1 TTATATATATTTTTA
*
9397877 TTATATATATTTTTG
1 TTATATATATTTTTA
9397892 TTATA
1 TTATA
9397897 AATCTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTATATATATTTTTA
Found at i:9402851 original size:35 final size:35
Alignment explanation
Indices: 9402812--9402891 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
9402802 CAAAATCAGT
*
9402812 CAGATGTAGAATCGGGCCTAAGCCCATCACAGATA
1 CAGATGCAGAATCGGGCCTAAGCCCATCACAGATA
* * * *
9402847 CAGATGCATACTTGGGCCTAAGCCCATCTCAGATA
1 CAGATGCAGAATCGGGCCTAAGCCCATCACAGATA
9402882 CAGATGCAGA
1 CAGATGCAGA
9402892 TATACAGATC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (35 bp):
CAGATGCAGAATCGGGCCTAAGCCCATCACAGATA
Found at i:9411268 original size:35 final size:35
Alignment explanation
Indices: 9411229--9411309 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
9411219 CAAAATCAGT
* *
9411229 CAGATGCAGATTCATGCCTAAGCCCATC-AAAGATA
1 CAGATGCAGATTCAGGCCTAAACCCATCTAAA-ATA
* ** *
9411264 CAGATGCATATTTGGGCCTAAACCCATCTCAAATA
1 CAGATGCAGATTCAGGCCTAAACCCATCTAAAATA
9411299 CAGATGCAGAT
1 CAGATGCAGAT
9411310 ATATAGATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (35 bp):
CAGATGCAGATTCAGGCCTAAACCCATCTAAAATA
Found at i:9421999 original size:10 final size:10
Alignment explanation
Indices: 9421984--9422023 Score: 55
Period size: 9 Copynumber: 3.9 Consensus size: 10
9421974 TAATTAGTTA
9421984 TTAAAAATTT
1 TTAAAAATTT
9421994 TT-AAAATTT
1 TTAAAAATTT
9422003 TTAAAAATTATT
1 TTAAAAA-T-TT
9422015 TTAAAAATT
1 TTAAAAATT
9422024 AAAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.33
10 7 0.26
11 2 0.07
12 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTAAAAATTT
Found at i:9422056 original size:16 final size:16
Alignment explanation
Indices: 9422012--9422066 Score: 69
Period size: 15 Copynumber: 3.6 Consensus size: 16
9422002 TTTAAAAATT
*
9422012 ATTTTAAAA-ATTAAA
1 ATTTTAAAATATTTAA
* *
9422027 AATATAAAAT-TTTAA
1 ATTTTAAAATATTTAA
9422042 ATTTTAAAATATTTAA
1 ATTTTAAAATATTTAA
9422058 ATTTTAAAA
1 ATTTTAAAA
9422067 AATTAATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTAAAATATTTAA
Found at i:9422800 original size:23 final size:22
Alignment explanation
Indices: 9422765--9422814 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 22
9422755 TTATAATTAA
9422765 AAAAATATAATTTTTAAAAAATTT
1 AAAAATATAATTTTT--AAAATTT
*
9422789 AAAATTAT-ATTTTTAAAATTT
1 AAAAATATAATTTTTAAAATTT
9422810 AAAAA
1 AAAAA
9422815 AGTGAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.46
23 6 0.25
24 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATATAATTTTTAAAATTT
Found at i:9422815 original size:23 final size:25
Alignment explanation
Indices: 9422761--9422815 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
9422751 AGGGTTATAA
9422761 TTAAAAAAATATAATTTTTAAAAAAT
1 TTAAAAAAATATAATTTTT-AAAAAT
*
9422787 TT--AAAATTAT-ATTTTT-AAAAT
1 TTAAAAAAATATAATTTTTAAAAAT
9422808 TTAAAAAA
1 TTAAAAAA
9422816 GTGAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 7 0.27
23 10 0.38
24 7 0.27
26 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAAAAAAATATAATTTTTAAAAAT
Found at i:9423439 original size:11 final size:11
Alignment explanation
Indices: 9423425--9423458 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
9423415 AAAATAAAAA
9423425 ATTAAAAATAT
1 ATTAAAAATAT
9423436 ATTAAAAATAT
1 ATTAAAAATAT
9423447 ATTAAAAATAT
1 ATTAAAAATAT
9423458 A
1 A
9423459 AAAAATTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTAAAAATAT
Found at i:9423655 original size:22 final size:23
Alignment explanation
Indices: 9423619--9423666 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
9423609 TTGAATTGAT
*
9423619 TTTTATATATTTTTAATATCTTTA
1 TTTTATATATTTTTAATA-ATTTA
9423643 TTTTA-AT-TTTTTAATAATTTA
1 TTTTATATATTTTTAATAATTTA
9423664 TTT
1 TTT
9423667 GCTTTGAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 2 0.09
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATATATTTTTAATAATTTA
Found at i:9423924 original size:25 final size:23
Alignment explanation
Indices: 9423895--9423954 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 23
9423885 TGATAAAATC
9423895 ATTTTTATTTTTTAAAATTTAAA
1 ATTTTTATTTTTTAAAATTTAAA
*
9423918 GAGTTTTTATTTTTTTAAATTTAAA
1 -A-TTTTTATTTTTTAAAATTTAAA
*
9423943 ATTTTCATTTTT
1 ATTTTTATTTTT
9423955 ATGTTCTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 10 0.30
24 2 0.06
25 21 0.64
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (23 bp):
ATTTTTATTTTTTAAAATTTAAA
Found at i:9428633 original size:46 final size:46
Alignment explanation
Indices: 9428566--9428740 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
9428556 TGTAACCCAC
* * *
9428566 CCATAAGCGAACTTGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
* * * *
9428612 CCATAAGTGAACTAGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCAT
* * * *
9428662 -C-TCA-CGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
*
9428705 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
9428741 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 2 0.02
46 60 0.57
47 26 0.25
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
Found at i:9428688 original size:93 final size:93
Alignment explanation
Indices: 9428573--9428744 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
9428563 CACCCATAAG
* * * * *
9428573 CGAACTTGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
9428638 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
9428666 CGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
9428731 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
9428745 TCAACCATCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:9428760 original size:46 final size:44
Alignment explanation
Indices: 9428617--9428760 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 44
9428607 TGCATCCATA
*
9428617 AGTGAACTAGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * * *
9428664 CA-CGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
9428710 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
9428756 AGTGA
1 AGTGA
9428761 CATGTCACTT
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.42
47 29 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:9430378 original size:20 final size:20
Alignment explanation
Indices: 9430353--9430400 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
9430343 TGCGCCTCCC
9430353 TCAGAATCGACTGCCTCAAA
1 TCAGAATCGACTGCCTCAAA
9430373 TCAGAATCGACTGCCTCAAA
1 TCAGAATCGACTGCCTCAAA
9430393 TCAGAATC
1 TCAGAATC
9430401 ATTTGGTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (20 bp):
TCAGAATCGACTGCCTCAAA
Found at i:9431909 original size:42 final size:42
Alignment explanation
Indices: 9431852--9432024 Score: 181
Period size: 42 Copynumber: 4.1 Consensus size: 42
9431842 ACATTAGGGT
* *
9431852 TATGAG-TTTTCGTGTAAGACCATATCTAGGATATGGCATCGT
1 TATGAGATTTT-GTGTAAGACCATATCTGGGATATGGCATCGA
*
9431894 TATGAGATTTTGTGTAAGACCATGAT-TGGGACATGGCATCGA
1 TATGAGATTTTGTGTAAGACCAT-ATCTGGGATATGGCATCGA
* * * *
9431936 TATGAGA-ATGGTGTAAGACCATAACTGGGCTATTGGCATCGA
1 TATGAGATTTTGTGTAAGACCATATCTGGGATA-TGGCATCGA
**** * *
9431978 TATGAGATCCCATGTAAGACCATATCTGGGATATGGTATTGA
1 TATGAGATTTTGTGTAAGACCATATCTGGGATATGGCATCGA
9432020 TATGA
1 TATGA
9432025 TCTATGTATA
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.01
41 18 0.16
42 66 0.60
43 25 0.23
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.31
Consensus pattern (42 bp):
TATGAGATTTTGTGTAAGACCATATCTGGGATATGGCATCGA
Found at i:9431994 original size:84 final size:83
Alignment explanation
Indices: 9431863--9432024 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 83
9431853 ATGAGTTTTC
* * ****
9431863 GTGTAAGACCATATCTAGGATATGGCATCGTTATGAGATTTTGTGTAAGACCATGAT-TGGGACA
1 GTGTAAGACCATAACTAGGATATGGCATCGATATGAGATCCCATGTAAGACCAT-ATCTGGGACA
9431927 TGGCATCGATATGAGAATG
65 TGGCATCGATATGAGAATG
* * *
9431946 GTGTAAGACCATAACTGGGCTATTGGCATCGATATGAGATCCCATGTAAGACCATATCTGGGATA
1 GTGTAAGACCATAACTAGGATA-TGGCATCGATATGAGATCCCATGTAAGACCATATCTGGGACA
* *
9432011 TGGTATTGATATGA
65 TGGCATCGATATGA
9432025 TCTATGTATA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
83 21 0.32
84 45 0.68
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (83 bp):
GTGTAAGACCATAACTAGGATATGGCATCGATATGAGATCCCATGTAAGACCATATCTGGGACAT
GGCATCGATATGAGAATG
Found at i:9439503 original size:42 final size:42
Alignment explanation
Indices: 9439456--9439608 Score: 166
Period size: 42 Copynumber: 3.6 Consensus size: 42
9439446 TAAGTTTATG
* ** *
9439456 TGTAAGACCATATTTGGGATATGGCATCTTTATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATATCA
* * * *
9439498 TGTAAGACCATGTCTAGGACATGGCATCGATATGAGA-ATCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATATCA
* **
9439539 TGTAAGACCATAGCTAGGG-TATTGGCATCGATATGAGATCCCA
1 TGTAAGACCATATCT-GGGATA-TGGCATCGATATGAGATATCA
*
9439582 TGTAAGCCCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
9439609 TGGAATGATT
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 16 0.18
42 58 0.64
43 16 0.18
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATATCA
Found at i:9439575 original size:84 final size:83
Alignment explanation
Indices: 9439455--9439608 Score: 193
Period size: 84 Copynumber: 1.8 Consensus size: 83
9439445 ATAAGTTTAT
* * ** ** *
9439455 GTGTAAGACCATATTTGGGATATGGCATCTTTATGAGATTTCATGTAAGACCATGTCTAGGACAT
1 GTGTAAGACCATACTAGGGATATGGCATCGATATGAGATCCCATGTAAGACCATATCTAGGACAT
9439520 GGCATCGATATGAGAATC
66 GGCATCGATATGAGAATC
* * *
9439538 GTGTAAGACCATAGCTAGGG-TATTGGCATCGATATGAGATCCCATGTAAGCCCATATCTGGGAT
1 GTGTAAGACCATA-CTAGGGATA-TGGCATCGATATGAGATCCCATGTAAGACCATATCTAGGAC
9439602 ATGGCAT
64 ATGGCAT
9439609 TGGAATGATT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
83 15 0.25
84 44 0.75
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (83 bp):
GTGTAAGACCATACTAGGGATATGGCATCGATATGAGATCCCATGTAAGACCATATCTAGGACAT
GGCATCGATATGAGAATC
Found at i:9444372 original size:20 final size:22
Alignment explanation
Indices: 9444333--9444377 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
9444323 CTGACAATAC
*
9444333 TTTGATAAAATCATGTTCAGTTA
1 TTTGATAAAATCA-GTTCAGGTA
9444356 TTTGAT-AAATC-GTTCAGGTA
1 TTTGATAAAATCAGTTCAGGTA
9444376 TT
1 TT
9444378 GTAAAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (22 bp):
TTTGATAAAATCAGTTCAGGTA
Found at i:9444520 original size:13 final size:13
Alignment explanation
Indices: 9444504--9444529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9444494 ATTTTCCAAA
9444504 AAAACCATTTGTT
1 AAAACCATTTGTT
9444517 AAAACCATTTGTT
1 AAAACCATTTGTT
9444530 TGCGTAATGT
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:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:9445417 original size:31 final size:32
Alignment explanation
Indices: 9445379--9445454 Score: 127
Period size: 31 Copynumber: 2.4 Consensus size: 32
9445369 CACACGTCCC
*
9445379 TGTGGCCCATACGCCCAAATTGG-CTTGCCCG
1 TGTGGCCCACACGCCCAAATTGGCCTTGCCCG
*
9445410 TGTGGCCCACATGCCCAAATTGGCCTTGCCCG
1 TGTGGCCCACACGCCCAAATTGGCCTTGCCCG
9445442 TGTGGCCCACACG
1 TGTGGCCCACACG
9445455 GCTTAGCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 21 0.51
32 20 0.49
ACGTcount: A:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (32 bp):
TGTGGCCCACACGCCCAAATTGGCCTTGCCCG
Found at i:9449033 original size:11 final size:12
Alignment explanation
Indices: 9449017--9449045 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
9449007 AATTTGTGAG
9449017 TTATAAAAA-TA
1 TTATAAAAAGTA
9449028 TTATAAAAAGTA
1 TTATAAAAAGTA
9449040 TTATAA
1 TTATAA
9449046 TATACTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
TTATAAAAAGTA
Found at i:9450001 original size:19 final size:19
Alignment explanation
Indices: 9449979--9450025 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
9449969 ACTCGTTTTA
*
9449979 AATTTTTTATTAT-AATGAT
1 AATTTTTTATAATAAAT-AT
9449998 AATTTTTTATAATAAATAT
1 AATTTTTTATAATAAATAT
9450017 ATATTTTTT
1 A-ATTTTTT
9450026 TAAATGATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTTTATAATAAATAT
Found at i:9457399 original size:29 final size:31
Alignment explanation
Indices: 9457350--9457408 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
9457340 AATGTGTATC
* *
9457350 TATTTATTTGATGGATGAAAT-T-GAGATAG
1 TATTTATTTAATAGATGAAATGTGGAGATAG
9457379 TATTTATTATAATAGAT-AAATGTGGAGATA
1 TATTTATT-TAATAGATGAAATGTGGAGATA
9457409 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 12 0.48
30 7 0.28
31 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (31 bp):
TATTTATTTAATAGATGAAATGTGGAGATAG
Found at i:9468125 original size:57 final size:58
Alignment explanation
Indices: 9468013--9468126 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
9468003 GAAATGGTGA
* * **
9468013 AAATGGAGAAACGGGAAACATTTGGAAATGATTATGGTTTTCTCCAACATGAAAATGG
1 AAATGGAGAAACGGGAAACATTTGGAAATGAATATGGTTTTCTCCAAAACCAAAATGG
* *
9468071 AAATGGAGAAA-TGGAATCATTTGGAAATGAATATGGTTTTCTCCAAAACCAAAATG
1 AAATGGAGAAACGGGAAACATTTGGAAATGAATATGGTTTTCTCCAAAACCAAAATG
9468127 AAAAAGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 39 0.78
58 11 0.22
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (58 bp):
AAATGGAGAAACGGGAAACATTTGGAAATGAATATGGTTTTCTCCAAAACCAAAATGG
Found at i:9471480 original size:26 final size:26
Alignment explanation
Indices: 9471451--9471503 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9471441 GTGAATTCCA
9471451 AAACATAATGAGTACATAGAAGTCTT
1 AAACATAATGAGTACATAGAAGTCTT
9471477 AAACATAATGAGTACATAGAAGTCTT
1 AAACATAATGAGTACATAGAAGTCTT
9471503 A
1 A
9471504 CTCTTAAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.26
Consensus pattern (26 bp):
AAACATAATGAGTACATAGAAGTCTT
Found at i:9480638 original size:20 final size:20
Alignment explanation
Indices: 9480615--9480705 Score: 76
Period size: 21 Copynumber: 4.5 Consensus size: 20
9480605 TTAATACTTG
9480615 TAAGGATTTATCAATATTTC
1 TAAGGATTTATCAATATTTC
* *
9480635 TAA-GATTTTTGCCAATATTCC
1 TAAGGATTTAT--CAATATTTC
* * *
9480656 TAAGGCTTTACCAAAATTTC
1 TAAGGATTTATCAATATTTC
* *
9480676 TAAAGGATTTAACAATGTTTC
1 T-AAGGATTTATCAATATTTC
*
9480697 TAAAGATTT
1 TAAGGATTT
9480706 CCCTTGGTGC
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
19 6 0.11
20 18 0.33
21 27 0.49
22 4 0.07
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
TAAGGATTTATCAATATTTC
Found at i:9488078 original size:17 final size:20
Alignment explanation
Indices: 9488056--9488098 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
9488046 TTGTATTTAT
9488056 TATTTAA-AA-TTT-TGATG
1 TATTTAATAAGTTTATGATG
*
9488073 TATTTAATAAGTTTATGTTG
1 TATTTAATAAGTTTATGATG
9488093 TATTTA
1 TATTTA
9488099 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 3 0.14
20 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (20 bp):
TATTTAATAAGTTTATGATG
Found at i:9502294 original size:10 final size:10
Alignment explanation
Indices: 9502281--9502317 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
9502271 TAACAATTTG
9502281 TAAAAATTAT
1 TAAAAATTAT
*
9502291 TAAAAATTAC
1 TAAAAATTAT
9502301 TAAAAATTAT
1 TAAAAATTAT
*
9502311 AAAAAAT
1 TAAAAAT
9502318 AAATTTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:9502345 original size:24 final size:25
Alignment explanation
Indices: 9502291--9502352 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
9502281 TAAAAATTAT
*
9502291 TAAAAATTACTAAAAATTATAAAAA
1 TAAAAATTACTAAAAATAATAAAAA
* **
9502316 -ATAAATTTGTAAAAA-AATAAAAA
1 TAAAAATTACTAAAAATAATAAAAA
9502339 TAAAAATTA-TAAAA
1 TAAAAATTACTAAAA
9502353 TTCAAGGAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
TAAAAATTACTAAAAATAATAAAAA
Found at i:9503454 original size:21 final size:21
Alignment explanation
Indices: 9503428--9503479 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
9503418 AAAAAAGTTC
9503428 AACTATCCAAAAAGAATATGA
1 AACTATCCAAAAAGAATATGA
9503449 AACTATCCAAAAAGAATATGA
1 AACTATCCAAAAAGAATATGA
9503470 AACTATCCAA
1 AACTATCCAA
9503480 TTATTAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (21 bp):
AACTATCCAAAAAGAATATGA
Found at i:9504211 original size:171 final size:171
Alignment explanation
Indices: 9503926--9504258 Score: 506
Period size: 171 Copynumber: 1.9 Consensus size: 171
9503916 TCATACCATA
*
9503926 ATCCCAAGAGCAATACAATGACATGAAATCAATCTCCCTACCAAATGAAAACTAGAGGTGCTATA
1 ATCCCAAGAACAATACAATGACATGAAATCAATCTCCCTACCAAATGAAAACTAGAGGTGCTATA
* * *
9503991 GACCCTGTTACACTAACCTCAATAAAAAACACTTTTTTAAGTGAAATTTCTCCACACCAAGATGG
66 GACCCTATTACACTAACCCCAATAAAAAACACTTCTTTAAGTGAAATTTCTCCACACCAAGATGG
*
9504056 CTCAATTGAATTATTATTCAATAGGCCACCCAAAACATGAC
131 CTCAATTGAATTAATATTCAATAGGCCACCCAAAACATGAC
* *
9504097 ATCCCAAGAACAATGCAATGACATGAAATCAATCTCCTTACCAAATGAAAACTAGAAGGTGCT-T
1 ATCCCAAGAACAATACAATGACATGAAATCAATCTCCCTACCAAATGAAAACTAG-AGGTGCTAT
* * * * * *
9504161 AGCCCCTATTGCACTAACCCCAATTAGAAACACTTCTTTAAGTGAAATTTCTCGACATCAAGATG
65 AGACCCTATTACACTAACCCCAATAAAAAACACTTCTTTAAGTGAAATTTCTCCACACCAAGATG
* * *
9504226 GCTTAGTTGAATTAATATTTAATAGGCCACCCA
130 GCTCAATTGAATTAATATTCAATAGGCCACCCA
9504259 GAATGACCCC
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
171 138 0.95
172 7 0.05
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (171 bp):
ATCCCAAGAACAATACAATGACATGAAATCAATCTCCCTACCAAATGAAAACTAGAGGTGCTATA
GACCCTATTACACTAACCCCAATAAAAAACACTTCTTTAAGTGAAATTTCTCCACACCAAGATGG
CTCAATTGAATTAATATTCAATAGGCCACCCAAAACATGAC
Found at i:9506408 original size:13 final size:13
Alignment explanation
Indices: 9506390--9506415 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9506380 AGCAACACGG
9506390 TGCTTAGTAAGTT
1 TGCTTAGTAAGTT
9506403 TGCTTAGTAAGTT
1 TGCTTAGTAAGTT
9506416 CATTCGAAAA
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TGCTTAGTAAGTT
Found at i:9507186 original size:18 final size:18
Alignment explanation
Indices: 9507163--9507225 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
9507153 GGTGCCAACT
9507163 ATAAAAAATAATATTTTA
1 ATAAAAAATAATATTTTA
*
9507181 AT-AAAAATCAATAAATTTA
1 ATAAAAAAT-AAT-ATTTTA
*
9507200 A-AAATAATAATATTTTA
1 ATAAAAAATAATATTTTA
9507217 ATATAAAAA
1 ATA-AAAAA
9507226 GGGATGATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 12 0.33
18 9 0.25
19 15 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAAATAATATTTTA
Found at i:9507208 original size:15 final size:17
Alignment explanation
Indices: 9507182--9507214 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9507172 AATATTTTAA
9507182 TAAAAATCAATAA-ATT
1 TAAAAATCAATAATATT
9507198 TAAAAAT-AATAATATT
1 TAAAAATCAATAATATT
9507214 T
1 T
9507215 TAATATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATCAATAATATT
Found at i:9510167 original size:18 final size:18
Alignment explanation
Indices: 9510144--9510178 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9510134 TATTTCAATC
9510144 AATATAATAATAAATATT
1 AATATAATAATAAATATT
*
9510162 AATATAATAATTAATAT
1 AATATAATAATAAATAT
9510179 ATTATGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAATAATAAATATT
Found at i:9511640 original size:28 final size:28
Alignment explanation
Indices: 9511600--9511656 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
9511590 ATTAATTTCA
9511600 AGATCATTTATTTTATGTTATTCTTAAC
1 AGATCATTTATTTTATGTTATTCTTAAC
9511628 AGATCATTTATTTTATGTTATTCTTAAC
1 AGATCATTTATTTTATGTTATTCTTAAC
9511656 A
1 A
9511657 AACCATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (28 bp):
AGATCATTTATTTTATGTTATTCTTAAC
Found at i:9512104 original size:13 final size:14
Alignment explanation
Indices: 9512086--9512117 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
9512076 GTCATATCTG
9512086 ATTATTATT-TTTC
1 ATTATTATTCTTTC
9512099 ATTATTATTCTTTC
1 ATTATTATTCTTTC
9512113 ATTAT
1 ATTAT
9512118 ATGTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTATTCTTTC
Found at i:9515306 original size:43 final size:43
Alignment explanation
Indices: 9515222--9515350 Score: 147
Period size: 43 Copynumber: 3.0 Consensus size: 43
9515212 ATTTGCGGCA
** * * *
9515222 TTGTGAGAAAAGGGCCGAT-AAAG-CATGACTTTTAGCAGCGT
1 TTGTGAGAAAAGCACCGCTAAAAGTCATGGCTTTTAGCGGCGT
*
9515263 TTGTTG-GAAAAGCACCGCTAAAGGTCATGGCTTTTAGCGGCGT
1 TTG-TGAGAAAAGCACCGCTAAAAGTCATGGCTTTTAGCGGCGT
* * *
9515306 TTGTGAGGAAAGCGCCGCTAAAATTCATGGCTTTTAGCGGCGT
1 TTGTGAGAAAAGCACCGCTAAAAGTCATGGCTTTTAGCGGCGT
9515349 TT
1 TT
9515351 TTTTCACAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 13 0.18
42 7 0.09
43 54 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (43 bp):
TTGTGAGAAAAGCACCGCTAAAAGTCATGGCTTTTAGCGGCGT
Found at i:9516212 original size:13 final size:14
Alignment explanation
Indices: 9516186--9516214 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9516176 ACTAACGACG
9516186 AATTAAACCATTAT
1 AATTAAACCATTAT
9516200 AATTAAA-CATTAT
1 AATTAAACCATTAT
9516213 AA
1 AA
9516215 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:9521395 original size:18 final size:18
Alignment explanation
Indices: 9521333--9521444 Score: 52
Period size: 18 Copynumber: 6.3 Consensus size: 18
9521323 TATGTATTAC
* * *
9521333 GTAAGTTAAGTAAGCTTT
1 GTAAGTTATGTAAGATAT
*
9521351 GTAAGTTATGTTATGATAT
1 GTAAGTTATG-TAAGATAT
* * *
9521370 G-CATTTATGTAAGGTAT
1 GTAAGTTATGTAAGATAT
*
9521387 GTAAGTTATGATATGATAT
1 GTAAGTTATG-TAAGATAT
* * *
9521406 AT-ATTTATGT-A-TTAT
1 GTAAGTTATGTAAGATAT
* *
9521421 GTAAGTTGTGTAAGTTAT
1 GTAAGTTATGTAAGATAT
9521439 GATAAG
1 G-TAAG
9521445 ATATATATTT
Statistics
Matches: 68, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
15 4 0.06
16 6 0.09
17 9 0.13
18 32 0.47
19 17 0.25
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (18 bp):
GTAAGTTATGTAAGATAT
Found at i:9521477 original size:44 final size:43
Alignment explanation
Indices: 9521374--9521501 Score: 204
Period size: 44 Copynumber: 3.0 Consensus size: 43
9521364 TGATATGCAT
* *
9521374 TTATGTAAGGTATGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGTA
*
9521417 TTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTGGA-GTA
1 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTT--ATGTA
9521461 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATG
1 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATG
9521502 AAATATATTT
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
42 1 0.01
43 36 0.46
44 40 0.51
45 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (43 bp):
TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGTA
Found at i:9521521 original size:56 final size:56
Alignment explanation
Indices: 9521458--9521592 Score: 225
Period size: 56 Copynumber: 2.4 Consensus size: 56
9521448 TATATTTGGA
9521458 GTATTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGAAATATATTTAT
1 GTATTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGAAATATATTTAT
* * *
9521514 GTATTATGTTATTTGTGTAAGTTATGATATGATATATATTTATGATATATATTTAT
1 GTATTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGAAATATATTTAT
* *
9521570 GTAATATGTAAGTTTTGTAAGTT
1 GTATTATGTAAGTTGTGTAAGTT
9521593 TTGTAAGTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.50
Consensus pattern (56 bp):
GTATTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATGAAATATATTTAT
Found at i:9521576 original size:11 final size:13
Alignment explanation
Indices: 9521485--9521570 Score: 68
Period size: 13 Copynumber: 6.3 Consensus size: 13
9521475 TAAGTTATGA
9521485 TATGATATATATT
1 TATGATATATATT
*
9521498 TATGAAATATATT
1 TATGATATATATT
*
9521511 TATGTATTATGTTATT
1 TATG-A-TAT-ATATT
* *
9521527 TGTG-TA-AGTTATGA
1 TATGATATA--TAT-T
9521541 TATGATATATATT
1 TATGATATATATT
9521554 TATGATATATATT
1 TATGATATATATT
9521567 TATG
1 TATG
9521571 TAATATGTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
13 38 0.67
14 7 0.12
15 4 0.07
16 8 0.14
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (13 bp):
TATGATATATATT
Found at i:9521590 original size:9 final size:9
Alignment explanation
Indices: 9521576--9521601 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9521566 TTATGTAATA
9521576 TGTAAGTTT
1 TGTAAGTTT
9521585 TGTAAGTTT
1 TGTAAGTTT
9521594 TGTAAGTT
1 TGTAAGTT
9521602 ATTATATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (9 bp):
TGTAAGTTT
Found at i:9521616 original size:65 final size:69
Alignment explanation
Indices: 9521485--9521616 Score: 175
Period size: 65 Copynumber: 2.0 Consensus size: 69
9521475 TAAGTTATGA
* * *
9521485 TATGATATATATTTATGAAATATATTTATGTATTATGTTATTTGTGTAAGTTATGATATGATATA
1 TATGATATATATTTATGAAATATATGTAAGTATTATGTAATTTGTGTAAGTTATGATATGATATA
9521550 TATT
66 TATT
* *
9521554 TATGATATATATTTATG-TA-ATATGTAAGT-TT-TGTAAGTTT-TGTAAGTTATTATATGATAT
1 TATGATATATATTTATGAAATATATGTAAGTATTATGTAA-TTTGTGTAAGTTATGATATGATAT
9521614 ATA
65 ATA
9521617 ATAAACATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
65 26 0.46
66 5 0.09
67 8 0.14
68 1 0.02
69 17 0.30
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (69 bp):
TATGATATATATTTATGAAATATATGTAAGTATTATGTAATTTGTGTAAGTTATGATATGATATA
TATT
Found at i:9521766 original size:15 final size:15
Alignment explanation
Indices: 9521746--9521774 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9521736 TTGTGTCCTG
9521746 ATTAATCCAAAATAA
1 ATTAATCCAAAATAA
9521761 ATTAATCCAAAATA
1 ATTAATCCAAAATA
9521775 TGTAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAATCCAAAATAA
Found at i:9524958 original size:59 final size:60
Alignment explanation
Indices: 9524854--9524975 Score: 158
Period size: 59 Copynumber: 2.0 Consensus size: 60
9524844 GGGGAAAAAA
* * * * *
9524854 GGGTAATTATTTTAGGGTTTCGAATTAAGGGAAAAGGGGGGAAATAAACTAGGGAGAAGG
1 GGGTAATTATTTTAGGGATTCGAATGAAGGGAAAAGGAGGAAAATAAACCAGGGAGAAGG
* *
9524914 GGGTGATTATTTTAGGGATTC-AGA-GAAGGGAAAATGAGGAAAATAAACCAGGGAGAAGG
1 GGGTAATTATTTTAGGGATTCGA-ATGAAGGGAAAAGGAGGAAAATAAACCAGGGAGAAGG
9524973 GGG
1 GGG
9524976 GAAATGAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 34 0.63
60 20 0.37
ACGTcount: A:0.38, C:0.04, G:0.38, T:0.20
Consensus pattern (60 bp):
GGGTAATTATTTTAGGGATTCGAATGAAGGGAAAAGGAGGAAAATAAACCAGGGAGAAGG
Found at i:9525256 original size:106 final size:105
Alignment explanation
Indices: 9525053--9525457 Score: 325
Period size: 116 Copynumber: 3.6 Consensus size: 105
9525043 TAACATTTGC
9525053 GGCGTTTTCTCCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACATAAACGCCACTAAA
1 GGCGTTTTCTCCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACATAAACGCCACTAAA
*
9525118 AATCAAACAAAACGACGATATAAACAGAATAAACTTTAGT
66 AATCAAAAAAAACGACGATATAAACAGAATAAACTTTAGT
* * * * *
9525158 GGCGTTTTTTCCCTAGCGCCGCTAATGGCAAATCAATTGCGGCG-TTTAACCCTAAAATGCCACT
1 GGCGTTTTCT-CCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAA-CAT-AAACGCCACT
*
9525222 AAAAATCCAAAAAAGTAACGGCGTTTTCATATAAACAGAAT-AACATTTAGT
63 AAAAAT-CAAAAAA--AACGACG-----ATATAAACAGAATAAAC-TTTAGT
* * * * *
9525273 GGCATTTTATCTCCAAGCGCCGCTAAAGGCGAAA-CTATTGCGGCGTTTTACCCTAAAACGCCAC
1 GGC-GTTT-TCTCCTAGCGCCGCTAAAGGC-AAACCAATTGCGGCGTTTTAACAT-AAACGCCAC
* ** * * *
9525337 TAAGAATCGAATAAAACTACATCGTTTTGATATAAACAAAATAACCATTAGT
62 TAAAAATC-AA-AAAA--A-A-CG--ACGATATAAACAGAATAAACTTTAGT
* * * * *
9525389 GGCGTTTATAC-CCTAGCGCCACTAAA-TCAAACCTATTGTGGCGTTTTAACCAAAAACGCCACT
1 GGCGTTT-T-CTCCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAA-CATAAACGCCACT
9525452 AAAAAT
63 AAAAAT
9525458 TCATGAAAAC
Statistics
Matches: 244, Mismatches: 30, Indels: 43
0.77 0.09 0.14
Matches are distributed among these distances:
105 14 0.06
106 33 0.14
107 15 0.06
108 6 0.02
110 6 0.02
113 3 0.01
114 34 0.14
115 42 0.17
116 70 0.29
117 17 0.07
118 1 0.00
119 2 0.01
121 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (105 bp):
GGCGTTTTCTCCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACATAAACGCCACTAAA
AATCAAAAAAAACGACGATATAAACAGAATAAACTTTAGT
Found at i:9525326 original size:116 final size:112
Alignment explanation
Indices: 9525063--9525576 Score: 494
Period size: 114 Copynumber: 4.6 Consensus size: 112
9525053 GGCGTTTTCT
* * *
9525063 CCTAGCGCCGCTAAAGGCAAACCAATTGCGGCGTTTTAACAT-AAACGCCACTAAAAAT-CAAAC
1 CCTAGCGCCGCTAAA-GCAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAAA
** * * * * *
9525126 AA--AA-CG--ACGATATAAACAGAATAAACTTTAGTGGCGTTTTTTC
65 AACTAACCGTTTTGATATAAACAAAATAACCATTAGTGGCATTTTATC
* * * *
9525169 CCTAGCGCCGCTAATGGCAAATCAATTGCGGCG-TTTAACCCTAAAATGCCACTAAAAATCCAAA
1 CCTAGCGCCGCTAA-AGCAAACCTATTGCGGCGTTTTAA-CCTAAAACGCCACTAAAAATCCAAA
* * *
9525233 AAAGTAACGGCGTTTTCATATAAACAGAATAA-CATTTAGTGGCATTTTATC
64 AAACTAAC--CGTTTTGATATAAACAAAATAACCA-TTAGTGGCATTTTATC
* * * *
9525284 TCCAAGCGCCGCTAAAGGCGAAA-CTATTGCGGCGTTTTACCCTAAAACGCCACTAAGAATCGAA
1 -CCTAGCGCCGCTAAA-GC-AAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAA
* *
9525348 TAAAACTACATCGTTTTGATATAAACAAAATAACCATTAGTGGC-GTTTATAC
63 -AAAACTA-ACCGTTTTGATATAAACAAAATAACCATTAGTGGCATTTTAT-C
* * * * * *
9525400 CCTAGCGCCACTAAATCAAACCTATTGTGGCGTTTTAACCAAAAACGCCACTAAAAATTCATGAA
1 CCTAGCGCCGCTAAAGCAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCA-AAA
* *
9525465 AACTACACCGTTTTGATATAAACAAAATAACCATTAGAGGCA-TTTATAA
65 AACTA-ACCGTTTTGATATAAACAAAATAACCATTAGTGGCATTTTAT-C
* * * *
9525514 CCTTGCGCCGATAAATCAATCCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAA
1 CCTAGCGCCGCTAAAGCAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAA
9525577 GAAAACGGTG
Statistics
Matches: 341, Mismatches: 44, Indels: 39
0.80 0.10 0.09
Matches are distributed among these distances:
105 5 0.01
106 32 0.09
107 15 0.04
108 6 0.02
110 2 0.01
113 6 0.02
114 137 0.40
115 47 0.14
116 75 0.22
117 15 0.04
118 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (112 bp):
CCTAGCGCCGCTAAAGCAAACCTATTGCGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAAAA
ACTAACCGTTTTGATATAAACAAAATAACCATTAGTGGCATTTTATC
Found at i:9526058 original size:22 final size:23
Alignment explanation
Indices: 9526031--9526083 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
9526021 CTTAATCTCC
9526031 AACCCTTAAA-CCATACA-CCATA
1 AACCCTTAAACCCATA-ATCCATA
9526053 AACCC-TAAACCCATAATCCATA
1 AACCCTTAAACCCATAATCCATA
9526075 AA-CCTTAAA
1 AACCCTTAAA
9526084 ATAGTAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (23 bp):
AACCCTTAAACCCATAATCCATA
Found at i:9526127 original size:14 final size:14
Alignment explanation
Indices: 9526102--9526146 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
9526092 TCATACACTT
*
9526102 TAAACACTAAACCA
1 TAAACCCTAAACCA
*
9526116 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
9526130 TAAACCCTAAACTA
1 TAAACCCTAAACCA
9526144 TAA
1 TAA
9526147 TGATAAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:9526135 original size:7 final size:7
Alignment explanation
Indices: 9526037--9526146 Score: 55
Period size: 7 Copynumber: 15.4 Consensus size: 7
9526027 CTCCAACCCT
9526037 TAAACCA
1 TAAACCA
*
9526044 TACACCA
1 TAAACCA
*
9526051 TAAACCC
1 TAAACCA
9526058 TAAACCCA
1 TAAA-CCA
*
9526066 TAATCCA
1 TAAACCA
*
9526073 TAAACCT
1 TAAACCA
9526080 TAAA--A
1 TAAACCA
9526085 TAGTAACTCA
1 TA--AAC-CA
* **
9526095 TACACTT
1 TAAACCA
9526102 TAAA-CA
1 TAAACCA
9526108 CTAAACCA
1 -TAAACCA
* *
9526116 TATACCC
1 TAAACCA
9526123 TAAACCA
1 TAAACCA
*
9526130 TAAACCC
1 TAAACCA
*
9526137 TAAACTA
1 TAAACCA
9526144 TAA
1 TAA
9526147 TGATAAATAG
Statistics
Matches: 74, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
5 2 0.03
7 60 0.81
8 9 0.12
10 3 0.04
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:9526459 original size:7 final size:7
Alignment explanation
Indices: 9526449--9526515 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
9526439 TTAAACCCTT
9526449 AACCCCA
1 AACCCCA
9526456 AACCCCA
1 AACCCCA
9526463 AACCCCA
1 AACCCCA
9526470 AACCCCA
1 AACCCCA
* *
9526477 AATCTCA
1 AACCCCA
*
9526484 AATCCCA
1 AACCCCA
* *
9526491 AATCCTA
1 AACCCCA
*
9526498 AACCACA
1 AACCCCA
*
9526505 AATCCCA
1 AACCCCA
9526512 AACC
1 AACC
9526516 ATAAATCTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.45, C:0.46, G:0.00, T:0.09
Consensus pattern (7 bp):
AACCCCA
Found at i:9526485 original size:21 final size:21
Alignment explanation
Indices: 9526449--9526515 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
9526439 TTAAACCCTT
* *
9526449 AACCCCAAACCCCAAACCCCA
1 AACCCCAAACCTCAAATCCCA
*
9526470 AACCCCAAATCTCAAATCCCA
1 AACCCCAAACCTCAAATCCCA
* * *
9526491 AATCCTAAACCACAAATCCCA
1 AACCCCAAACCTCAAATCCCA
9526512 AACC
1 AACC
9526516 ATAAATCTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.45, C:0.46, G:0.00, T:0.09
Consensus pattern (21 bp):
AACCCCAAACCTCAAATCCCA
Found at i:9527471 original size:278 final size:278
Alignment explanation
Indices: 9526974--9527528 Score: 1065
Period size: 278 Copynumber: 2.0 Consensus size: 278
9526964 ATAATTAATT
*
9526974 ATAGGGTCTAGGATTTAATTATTGAATATGATTCACTTGAGATTCACATACTATATACCCATGGC
1 ATAGGGTCTAGGATTTAATTATTGAATATGATTCACTTGAGATTAACATACTATATACCCATGGC
9527039 CATTAAACTTAAACCATAAAACCCTAAACCATAGACCTTAAACCTTTAATATTAAACCTTAAACC
66 CATTAAACTTAAACCATAAAACCCTAAACCATAGACCTTAAACCTTTAATATTAAACCTTAAACC
9527104 CAAAAATAAATTTAATCAATATTAAGTATTGCTTCCATAATTTATTATGAACATAAGCTTTTACA
131 CAAAAATAAATTTAATCAATATTAAGTATTGCTTCCATAATTTATTATGAACATAAGCTTTTACA
*
9527169 TTAATATCTATGTATATACACATCAACATCCATATGATGTTTTTTGGGGTTTAGAGTTTTAAATG
196 TTAATATCTATGTATATACACATCAACATCCATATGATGTTTTTTGGGGTTTAGAGTTTTAAAGG
9527234 TTATAGTTTAGTGTTTAG
261 TTATAGTTTAGTGTTTAG
*
9527252 ATAGGGTTTAGGATTTAATTATTGAATATGATTCACTTGAGATTAACATACTATATACCCATGGC
1 ATAGGGTCTAGGATTTAATTATTGAATATGATTCACTTGAGATTAACATACTATATACCCATGGC
9527317 CATTAAACTTAAACCATAAAACCCTAAACCATAGACCTTAAACCTTTAATATTAAACCTTAAACC
66 CATTAAACTTAAACCATAAAACCCTAAACCATAGACCTTAAACCTTTAATATTAAACCTTAAACC
9527382 CAAAAATAAATTTAATCAATATTAAGTATTGCTTCCATAATTTATTATGAACATAAGCTTTTACA
131 CAAAAATAAATTTAATCAATATTAAGTATTGCTTCCATAATTTATTATGAACATAAGCTTTTACA
*
9527447 TTAATATTTATGTATATACACATCAACATCCATATGATGTTTTTTGGGGTTTAGAGTTTTAAAGG
196 TTAATATCTATGTATATACACATCAACATCCATATGATGTTTTTTGGGGTTTAGAGTTTTAAAGG
*
9527512 TTGTAGTTTAGTGTTTA
261 TTATAGTTTAGTGTTTA
9527529 AGGTTTAAGG
Statistics
Matches: 272, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
278 272 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (278 bp):
ATAGGGTCTAGGATTTAATTATTGAATATGATTCACTTGAGATTAACATACTATATACCCATGGC
CATTAAACTTAAACCATAAAACCCTAAACCATAGACCTTAAACCTTTAATATTAAACCTTAAACC
CAAAAATAAATTTAATCAATATTAAGTATTGCTTCCATAATTTATTATGAACATAAGCTTTTACA
TTAATATCTATGTATATACACATCAACATCCATATGATGTTTTTTGGGGTTTAGAGTTTTAAAGG
TTATAGTTTAGTGTTTAG
Found at i:9527541 original size:28 final size:29
Alignment explanation
Indices: 9527495--9527556 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
9527485 GTTTTTTGGG
* * *
9527495 GTTTAGAGTTTTAAAGGTTGTAGTTTAGT
1 GTTTAGAGGTTTAAAGGTTATAGATTAGT
*
9527524 GTTTA-AGGTTTAAGGGTTATAGATTAGT
1 GTTTAGAGGTTTAAAGGTTATAGATTAGT
9527552 GTTTA
1 GTTTA
9527557 TGTTTTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (29 bp):
GTTTAGAGGTTTAAAGGTTATAGATTAGT
Found at i:9527732 original size:40 final size:41
Alignment explanation
Indices: 9527596--9527752 Score: 201
Period size: 41 Copynumber: 3.9 Consensus size: 41
9527586 TTATATGACA
* **
9527596 TTTAGCGGCGTTTTACCGAAAGCGCTGCTAATGCTTTGGTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTTTGGTT
* * * *
9527637 TTTAGCAGCGTTTTA-CAGAAAGCGCCGCTAATTCTTTAGTT
1 TTTAGCGGCGTTTTACCA-AAAGCGCCACTAATGCTTTGGTT
* * *
9527678 TTTAGCGGCATTTTACCAAAAGCACCACTAATGC-CTGGTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTTTGGTT
9527718 TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCT
1 TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCT
9527753 CTAGCTTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 37 0.37
41 60 0.61
42 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTTTGGTT
Found at i:9527743 original size:81 final size:82
Alignment explanation
Indices: 9527596--9527764 Score: 216
Period size: 81 Copynumber: 2.1 Consensus size: 82
9527586 TTATATGACA
* * * ** *
9527596 TTTAGCGGCGTTTTACCGAAAGCGCTGCTAATGCTTTGGTTTTTAGCAGCGTTTTACAGAAAGCG
1 TTTAGCGGCATTTTACCAAAAGCACCACTAATGCTCTGGTTTTTAGCAGCGTTTTACAGAAAGCG
* * * *
9527661 CCGCTAATTCTTTAGTT
66 CCACTAATGCTCTAGCT
*
9527678 TTTAGCGGCATTTTACCAAAAGCACCACTAATGC-CTGGTTTTTAGCGGCGTTTTACCA-AAAGC
1 TTTAGCGGCATTTTACCAAAAGCACCACTAATGCTCTGGTTTTTAGCAGCGTTTTA-CAGAAAGC
9527741 GCCACTAATGCTCTAGCT
65 GCCACTAATGCTCTAGCT
9527759 TTTAGC
1 TTTAGC
9527765 AACGTTTTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
81 44 0.59
82 31 0.41
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (82 bp):
TTTAGCGGCATTTTACCAAAAGCACCACTAATGCTCTGGTTTTTAGCAGCGTTTTACAGAAAGCG
CCACTAATGCTCTAGCT
Found at i:9528957 original size:7 final size:7
Alignment explanation
Indices: 9528947--9528993 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
9528937 TTAAACCATA
9528947 AACCCCT
1 AACCCCT
9528954 AACCCCT
1 AACCCCT
*
9528961 AACCACT
1 AACCCCT
9528968 AACCCCT
1 AACCCCT
* *
9528975 AATCCTT
1 AACCCCT
9528982 AACCCCT
1 AACCCCT
9528989 AACCC
1 AACCC
9528994 TTAAATCTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCCCT
Found at i:9528971 original size:21 final size:21
Alignment explanation
Indices: 9528930--9528993 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
9528920 ACCTTAGACT
9528930 CTAACCCTTAAACCA-TAAACCC
1 CTAACCCTT-AACCACT-AACCC
*
9528952 CTAACCCCTAACCACTAACCC
1 CTAACCCTTAACCACTAACCC
* *
9528973 CTAATCCTTAACCCCTAACCC
1 CTAACCCTTAACCACTAACCC
9528994 TTAAATCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 28 0.76
22 9 0.24
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (21 bp):
CTAACCCTTAACCACTAACCC
Found at i:9528995 original size:14 final size:14
Alignment explanation
Indices: 9528930--9528997 Score: 75
Period size: 14 Copynumber: 4.8 Consensus size: 14
9528920 ACCTTAGACT
*
9528930 CTAACCCTTAAACC
1 CTAACCCTTAACCC
* *
9528944 ATAAACCCCTAACCC
1 CT-AACCCTTAACCC
9528959 CTAACCAC-TAACCC
1 CTAACC-CTTAACCC
*
9528973 CTAATCCTTAACCC
1 CTAACCCTTAACCC
9528987 CTAACCCTTAA
1 CTAACCCTTAA
9528998 ATCTTAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
13 1 0.02
14 32 0.71
15 12 0.27
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:9529003 original size:21 final size:21
Alignment explanation
Indices: 9528930--9529004 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
9528920 ACCTTAGACT
*
9528930 CTAACCCTTAAACCA-TAAACCC
1 CTAAACCTT-AACCACT-AACCC
* *
9528952 CTAACCCCTAACCACTAACCC
1 CTAAACCTTAACCACTAACCC
* *
9528973 CTAATCCTTAACCCCTAACCC
1 CTAAACCTTAACCACTAACCC
* *
9528994 TTAAATCTTAA
1 CTAAACCTTAA
9529005 ACTATAACTG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 36 0.80
22 9 0.20
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAAACCTTAACCACTAACCC
Found at i:9533248 original size:29 final size:30
Alignment explanation
Indices: 9533198--9533271 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
9533188 TATAGACTAC
*
9533198 TAAAATAATA-AATTTATATTTTTATTATCA
1 TAAAA-AATATAATTTATATTTTAATTATCA
* **
9533228 TAAAAAATATAATTTA-ATTTTAATTTTTT
1 TAAAAAATATAATTTATATTTTAATTATCA
*
9533257 TAAAAAATTTAATTT
1 TAAAAAATATAATTT
9533272 TACCTCTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 27 0.71
30 11 0.29
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TAAAAAATATAATTTATATTTTAATTATCA
Found at i:9533939 original size:29 final size:29
Alignment explanation
Indices: 9533900--9533963 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
9533890 ATTTATAATT
* *
9533900 TTAATAAATTATAAAATTTTTATAAACAA
1 TTAAAAAATTATAAAATTTTTATAAAAAA
*
9533929 TTAAAAAATTATATAATTTTTATAAAAAA
1 TTAAAAAATTATAAAATTTTTATAAAAAA
*
9533958 ATAAAA
1 TTAAAA
9533964 CCCTATAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TTAAAAAATTATAAAATTTTTATAAAAAA
Found at i:9533970 original size:29 final size:29
Alignment explanation
Indices: 9533909--9533972 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
9533899 TTTAATAAAT
* * *
9533909 TATAAAATTTTTATAAACAATTAAAAAAT
1 TATAAAATTTTTATAAAAAAATAAAAAAC
* **
9533938 TATATAATTTTTATAAAAAAATAAAACCC
1 TATAAAATTTTTATAAAAAAATAAAAAAC
9533967 TATAAA
1 TATAAA
9533973 GCAGAAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (29 bp):
TATAAAATTTTTATAAAAAAATAAAAAAC
Found at i:9534604 original size:20 final size:21
Alignment explanation
Indices: 9534575--9534616 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
9534565 TTATATTTTT
9534575 AAGAAAATATAAA-AAAATTA
1 AAGAAAATATAAAGAAAATTA
*
9534595 AAGAATATATAAAGAAAATTA
1 AAGAAAATATAAAGAAAATTA
9534616 A
1 A
9534617 TAATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AAGAAAATATAAAGAAAATTA
Found at i:9534609 original size:11 final size:11
Alignment explanation
Indices: 9534575--9534613 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
9534565 TTATATTTTT
9534575 AAGAAAATATA
1 AAGAAAATATA
9534586 AA-AAAAT-TA
1 AAGAAAATATA
*
9534595 AAGAATATATA
1 AAGAAAATATA
9534606 AAGAAAAT
1 AAGAAAAT
9534614 TAATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 4 0.17
10 9 0.38
11 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (11 bp):
AAGAAAATATA
Found at i:9535804 original size:18 final size:18
Alignment explanation
Indices: 9535777--9535813 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9535767 GTTTGATAAA
*
9535777 TTATTAAAAATTTTCATT
1 TTATTAAAAATTTTAATT
*
9535795 TTATTGAAAATTTTAATT
1 TTATTAAAAATTTTAATT
9535813 T
1 T
9535814 GATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTATTAAAAATTTTAATT
Found at i:9541907 original size:48 final size:48
Alignment explanation
Indices: 9541716--9541897 Score: 222
Period size: 48 Copynumber: 3.8 Consensus size: 48
9541706 GAGTTTTGAA
* *
9541716 ATCCCGTATAAGACCATATCTGGGATATGGCATCGACATCAATATGAG
1 ATCCCATATAAGACCATATCTGGGATATGACATCGACATCAATATGAG
* * * * * *
9541764 ATCCCTTGTAAGACCGTATCTGGGATATGACAT-AAGCATCGACATGAG
1 ATCCCATATAAGACCATATCTGGGATATGACATCGA-CATCAATATGAG
* *
9541812 ATCCCATGTAAGACCATATCTGGGATATGACATCGGCATCAATATGAG
1 ATCCCATATAAGACCATATCTGGGATATGACATCGACATCAATATGAG
* * * *
9541860 GTCCCATATAAGACCATGTCTGGGACATGGCATCGACA
1 ATCCCATATAAGACCATATCTGGGATATGACATCGACA
9541898 CTATTATGAG
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
47 1 0.01
48 112 0.99
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (48 bp):
ATCCCATATAAGACCATATCTGGGATATGACATCGACATCAATATGAG
Found at i:9547357 original size:18 final size:19
Alignment explanation
Indices: 9547334--9547371 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9547324 CCAAATGTAC
9547334 TTTTCATATACA-CATATA
1 TTTTCATATACATCATATA
*
9547352 TTTTCATTTACATCATATA
1 TTTTCATATACATCATATA
9547371 T
1 T
9547372 AATTTGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTCATATACATCATATA
Found at i:9547626 original size:41 final size:42
Alignment explanation
Indices: 9547558--9547668 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 42
9547548 TCTTACATGC
* * * *
9547558 AATCACATATTGATGCCACTGTCCCAGACAGGGTCTTAAACG-
1 AATCAAATATCGATGCCAATGTCCCAGAC-GGATCTTAAACGT
* * *
9547600 AATCAAATA-CGATGCCAATGTACCAGACTGATCTTATACGT
1 AATCAAATATCGATGCCAATGTCCCAGACGGATCTTAAACGT
* *
9547641 AATCACATATCGATGCCAACGTCCCAGA
1 AATCAAATATCGATGCCAATGTCCCAGA
9547669 TGTGGTCTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 9 0.16
41 24 0.42
42 24 0.42
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (42 bp):
AATCAAATATCGATGCCAATGTCCCAGACGGATCTTAAACGT
Found at i:9547668 original size:42 final size:42
Alignment explanation
Indices: 9547558--9547668 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
9547548 TCTTACATGC
* *
9547558 AATCACATATTGATGCC-ACTGTCCCAGACAGGGTCTTAAACG
1 AATCACATATCGATGCCAAC-GTCCCAGACAGGATCTTAAACG
* * * * *
9547600 AATCAAATA-CGATGCCAATGTACCAGAC-TGATCTTATACG
1 AATCACATATCGATGCCAACGTCCCAGACAGGATCTTAAACG
9547640 TAATCACATATCGATGCCAACGTCCCAGA
1 -AATCACATATCGATGCCAACGTCCCAGA
9547669 TGTGGTCTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
40 9 0.16
41 22 0.39
42 25 0.45
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (42 bp):
AATCACATATCGATGCCAACGTCCCAGACAGGATCTTAAACG
Found at i:9548609 original size:16 final size:15
Alignment explanation
Indices: 9548588--9548625 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
9548578 TTATAATAAC
*
9548588 ATATTTAACATTTTAT
1 ATATTTAAC-CTTTAT
9548604 ATATTTAACCTTTAT
1 ATATTTAACCTTTAT
9548619 A-ATTTAA
1 ATATTTAA
9548626 TAACTAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTAACCTTTAT
Found at i:9552766 original size:48 final size:48
Alignment explanation
Indices: 9552706--9552879 Score: 206
Period size: 48 Copynumber: 3.6 Consensus size: 48
9552696 AAATCCTGTA
* *
9552706 TAAGACCATATCTGGGATATGGCATCGGCATCAATATGAGATCCCTTG
1 TAAGACCATATCTGGGATATGGCATCGGCATCGATATGAGATCCCATG
* ** *
9552754 TAAGACCGTATCTGGGATATGATATAC-GCATCGACATGAGATCCCATG
1 TAAGACCATATCTGGGATATGGCAT-CGGCATCGATATGAGATCCCATG
* * * *
9552802 TAAGACCATATCTGGGATATGGCATTGGCATCGATATGAGGTCCCGTA
1 TAAGACCATATCTGGGATATGGCATCGGCATCGATATGAGATCCCATG
* * * *
9552850 CAAGACCATGTTTGGGACATGGCATCGGCA
1 TAAGACCATATCTGGGATATGGCATCGGCA
9552880 CTGTTATGAG
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
48 104 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (48 bp):
TAAGACCATATCTGGGATATGGCATCGGCATCGATATGAGATCCCATG
Found at i:9564362 original size:40 final size:40
Alignment explanation
Indices: 9564288--9564512 Score: 285
Period size: 40 Copynumber: 5.6 Consensus size: 40
9564278 AACCCAAGTA
* * * * *
9564288 CCTTCGGGATTTAG-CCAGATATAG-CTACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTC-AATAGCACAAATG
*
9564327 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
9564367 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
9564407 CCTTCGGGACTTAGCCCGGATATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TA---GCACAAATG
* * *
9564450 CCTTCGGGACTTCGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
9564490 CCTTCGGGACTTAGCCAGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
9564513 CATTCGAATA
Statistics
Matches: 165, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
39 14 0.08
40 114 0.69
41 1 0.01
43 34 0.21
44 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Done.