Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 35 of 66
Found at i:12092966 original size:30 final size:30
Alignment explanation
Indices: 12092930--12092989 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
12092920 AGGATCGAAC
12092930 TTGTGAAGTAAAAATTTA-GGGGTAAATAAT
1 TTGTGAAGT-AAAATTTAGGGGGTAAATAAT
*
12092960 TTGTGAAGTAAAGTTTAGGGGGTAAATAAT
1 TTGTGAAGTAAAATTTAGGGGGTAAATAAT
12092990 AGCACTGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (30 bp):
TTGTGAAGTAAAATTTAGGGGGTAAATAAT
Found at i:12094498 original size:49 final size:48
Alignment explanation
Indices: 12094435--12095113 Score: 495
Period size: 49 Copynumber: 13.9 Consensus size: 48
12094425 GGTTCCAGAC
* * ** *
12094435 GATGATATGTTGTGAGATATATATGTTCCATCTATAGATGATTACAGAT
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATT-CGGAT
* * * *** * *
12094484 GTTGATATGATGTGAGGTATGTATTTTCTGCCCATAGATGATTCTAGAT
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATTC-GGAT
* ** * *
12094533 AATGATATGATGTGACTTATGTATGTTCCATCCGT-GAATGATTTTGGAC
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAG-ATGA-TTCGGAT
* * ** *
12094582 GATGATATGATATGAGATATGTATATTCCATTTGTAGATGATTAC-AACT
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATT-CGGA-T
*
12094631 GATGATATGATGTGAGATATGTATGTTGCATCCGTAGATGATTTCGGAT
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGA-TTCGGAT
* * * * * *
12094680 GATGATATGATCTGAGGTATGTATATTCCGTCCGTAGATGACTCTGGAC
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATTC-GGAT
** * * ** *
12094729 GATGATATGATGTGAGGCATGTATGTTGCGTTTGTAGATGATTTTGGAT
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGA-TTCGGAT
* * * * * * *
12094778 AATGATATGATATGAGACATGTATGTTCTATCTGTAGATGATTCTCGAC
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATTC-GGAT
* * **
12094827 GATGATATGATGTGAGATATGTATATTCCATCCGTGGATGGCTCTGGAT
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATTC-GGAT
* * * ** *
12094876 GATGATATGAAGTG-GATTAT-T-TGTTCCATCTGAAGACAATTCGGAAC
1 GATGATATGATGTGAGA-TATGTATGTTCCATCCGTAGATGATTCGG-AT
* * * * * *
12094923 GATTATATGATATTAGATATGTATGTTCTATCCATAGATGATTTCAGAT
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGA-TTCGGAT
* * *** * *
12094972 GATGATATGATGTGAGGTATGTATCTTTTGTCCATAGATGATTTCGGAC
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGA-TTCGGAT
** *
12095021 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATTCCAAAC
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATT-CGGAT
* * * * * *
12095070 AATGTTATGATGTGAGGTATGTATCTTCCGTCCGTGGATGATTC
1 GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATTC
12095114 CAAACGATGT
Statistics
Matches: 493, Mismatches: 119, Indels: 37
0.76 0.18 0.06
Matches are distributed among these distances:
46 2 0.00
47 27 0.05
48 18 0.04
49 435 0.88
50 11 0.02
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (48 bp):
GATGATATGATGTGAGATATGTATGTTCCATCCGTAGATGATTCGGAT
Found at i:12094574 original size:98 final size:98
Alignment explanation
Indices: 12094388--12095131 Score: 576
Period size: 98 Copynumber: 7.6 Consensus size: 98
12094378 ATTCTGGACA
* * * * *
12094388 ATGATATGATATGAGATATGTATATTCTGT-CATGGATGGTTCCAGACGATGATATGTTGTGAGA
1 ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATTCTAGACGATGATATGATGTGAGA
* ** * *
12094452 TATATATGTTCCATCTATAGATGATTACAGATG
66 TATGTATGTTCCATCCGTAGATGATTTCGGATG
* * * * * * ** **
12094485 TTGATATGATGTGAGGTATGTATTTTCTGCCCATAGATGATTCTAGATAATGATATGATGTGACT
1 ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATTCTAGACGATGATATGATGTGAGA
* *
12094550 TATGTATGTTCCATCCGT-GAATGATTTTGGACG
66 TATGTATGTTCCATCCGTAG-ATGATTTCGGATG
* ***
12094583 ATGATATGATATGAGATATGTATATTCCATTTGTAGATGATTAC-A-ACTGATGATATGATGTGA
1 ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATT-CTAGAC-GATGATATGATGTGA
*
12094646 GATATGTATGTTGCATCCGTAGATGATTTCGGATG
64 GATATGTATGTTCCATCCGTAGATGATTTCGGATG
* * * * * *
12094681 ATGATATGATCTGAGGTATGTATATTCCGTCCGTAGATGACTCTGGACGATGATATGATGTGAGG
1 ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATTCTAGACGATGATATGATGTGAGA
* * * ** * *
12094746 CATGTATGTTGCGTTTGTAGATGATTTTGGATA
66 TATGTATGTTCCATCCGTAGATGATTTCGGATG
* * ** ** *
12094779 ATGATATGATATGAGACATGTATGTTCTATCTGTAGATGATTCTCGACGATGATATGATGTGAGA
1 ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATTCTAGACGATGATATGATGTGAGA
* * **
12094844 TATGTATATTCCATCCGTGGATG-GCTCTGGATG
66 TATGTATGTTCCATCCGTAGATGATTTC-GGATG
* * * ** * * *
12094877 ATGATATGA-AGTG-GATTAT-T-TGTTCCATCTGA-AGACAATTC-GGAACGATTATATGATAT
1 ATGATATGATA-TGAGA-TATGTATATTCCGTC-CATAGATGATTCTAG-ACGATGATATGATGT
* * * *
12094936 TAGATATGTATGTTCTATCCATAGATGATTTCAGATG
62 GAGATATGTATGTTCCATCCGTAGATGATTTCGGATG
* * * ** *
12094973 ATGATATGATGTGAGGTATGTATCTTTTGTCCATAGATGATT-TCGGACGATGATATGATGTGAG
1 ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATTCT-AGACGATGATATGATGTGAG
* ** **
12095037 ATATGTATGTTCCATCCGTAGATGATTCCAAACA
65 ATATGTATGTTCCATCCGTAGATGATTTCGGATG
* * * * * * * * *
12095071 ATGTTATGATGTGAGGTATGTATCTTCCGTCCGTGGATGATTCCAAACGATGTTATGATGT
1 ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATTCTAGACGATGATATGATGT
12095132 TGTTTATGCA
Statistics
Matches: 510, Mismatches: 116, Indels: 41
0.76 0.17 0.06
Matches are distributed among these distances:
95 1 0.00
96 68 0.13
97 38 0.07
98 397 0.78
99 6 0.01
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
ATGATATGATATGAGATATGTATATTCCGTCCATAGATGATTCTAGACGATGATATGATGTGAGA
TATGTATGTTCCATCCGTAGATGATTTCGGATG
Found at i:12095128 original size:147 final size:147
Alignment explanation
Indices: 12094388--12095131 Score: 619
Period size: 147 Copynumber: 5.1 Consensus size: 147
12094378 ATTCTGGACA
* * * * * * * *
12094388 ATGATATGATATGAGATATGTATATTCTGT-CATGGATGGTTCCAGACGATGATATGTTGTGAGA
1 ATGATATGATGTGAGATATGTATATTCCGTCCGTAGATGATTTCGGACGATGATATGATGTGAGA
* * * * * * * **
12094452 TATATATGTTCCATCTATAGATGATTACAGATGTTGATATGATGTGAGGTATGTATTTTCTGCCC
66 TATGTATGTTCCATCTGTAGATGATTACAAACGATGATATGATGTGAGATATGTATGTTCTATCC
* * *
12094517 ATAGATGATTCTAGATA
131 GTAGATGATTCCAGATG
** * * * *
12094534 ATGATATGATGTGACTTATGTATGTTCCATCCGT-GAATGATTTTGGACGATGATATGATATGAG
1 ATGATATGATGTGAGATATGTATATTCCGTCCGTAG-ATGATTTCGGACGATGATATGATGTGAG
* *
12094598 ATATGTATATTCCATTTGTAGATGATTAC-AACTGATGATATGATGTGAGATATGTATGTTGC-A
65 ATATGTATGTTCCATCTGTAGATGATTACAAAC-GATGATATGATGTGAGATATGTATGTT-CTA
* *
12094661 TCCGTAGATGATTTCGGATG
128 TCCGTAGATGATTCCAGATG
* * *
12094681 ATGATATGATCTGAGGTATGTATATTCCGTCCGTAGATGA-CTCTGGACGATGATATGATGTGAG
1 ATGATATGATGTGAGATATGTATATTCCGTCCGTAGATGATTTC-GGACGATGATATGATGTGAG
** * * * **** ** * *
12094745 GCATGTATGTTGCGTTTGTAGATGATTTTGGATAATGATATGATATGAGACATGTATGTTCTATC
65 ATATGTATGTTCCATCTGTAGATGATTACAAACGATGATATGATGTGAGATATGTATGTTCTATC
* *
12094810 TGTAGATGATTCTC-GACG
130 CGTAGATGATTC-CAGATG
* * ** * *
12094828 ATGATATGATGTGAGATATGTATATTCCATCCGTGGATG-GCTCTGGATGATGATATGAAGTG-G
1 ATGATATGATGTGAGATATGTATATTCCGTCCGTAGATGATTTC-GGACGATGATATGATGTGAG
* ** * * * *
12094891 ATTAT-T-TGTTCCATCTGAAGACAATT-CGGAACGATTATATGATATTAGATATGTATGTTCTA
65 A-TATGTATGTTCCATCTGTAGATGATTAC-AAACGATGATATGATGTGAGATATGTATGTTCTA
* *
12094953 TCCATAGATGATTTCAGATG
128 TCCGTAGATGATTCCAGATG
* * ** *
12094973 ATGATATGATGTGAGGTATGTATCTTTTGTCCATAGATGATTTCGGACGATGATATGATGTGAGA
1 ATGATATGATGTGAGATATGTATATTCCGTCCGTAGATGATTTCGGACGATGATATGATGTGAGA
* * * * * * **
12095038 TATGTATGTTCCATCCGTAGATGATTCCAAACAATGTTATGATGTGAGGTATGTATCTTCCGTCC
66 TATGTATGTTCCATCTGTAGATGATTACAAACGATGATATGATGTGAGATATGTATGTTCTATCC
* * *
12095103 GTGGATGATTCCAAACG
131 GTAGATGATTCCAGATG
*
12095120 ATGTTATGATGT
1 ATGATATGATGT
12095132 TGTTTATGCA
Statistics
Matches: 472, Mismatches: 108, Indels: 35
0.77 0.18 0.06
Matches are distributed among these distances:
144 1 0.00
145 107 0.23
146 35 0.07
147 324 0.69
148 5 0.01
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (147 bp):
ATGATATGATGTGAGATATGTATATTCCGTCCGTAGATGATTTCGGACGATGATATGATGTGAGA
TATGTATGTTCCATCTGTAGATGATTACAAACGATGATATGATGTGAGATATGTATGTTCTATCC
GTAGATGATTCCAGATG
Found at i:12112129 original size:54 final size:54
Alignment explanation
Indices: 12112045--12112148 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
12112035 CCAGCAAACA
* *
12112045 TCCCATCTCACCCAACTCATGTGTAACCCACCACATCGTGTACATAGCCGGATG
1 TCCCATCTCACCCAACTCATGTGCAACCCACCACATCGTGCACATAGCCGGATG
* * *
12112099 TCCCATCTCATCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCG
1 TCCCATCTCACCCAACTCATGTGCAACCCACCACATCGTGCACATAGCCG
12112149 AACAGTATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.24, C:0.39, G:0.14, T:0.22
Consensus pattern (54 bp):
TCCCATCTCACCCAACTCATGTGCAACCCACCACATCGTGCACATAGCCGGATG
Found at i:12115777 original size:36 final size:37
Alignment explanation
Indices: 12115615--12115783 Score: 133
Period size: 36 Copynumber: 4.7 Consensus size: 37
12115605 TGTAACGTGC
*
12115615 ATGTGCGGTGTGGGAGTGCACATGACG-T-TGATAG-T
1 ATGTGCGGTGTGGGAGTGCACATGATGATAT-ATAGCT
* *
12115650 GGTGTGC--TGTGGGAGTGCACA-GACTGATGATATATGCC
1 -ATGTGCGGTGTGGGAGTGCACATGA-TGAT-ATATA-GCT
*
12115688 ATGTGCGGTGTGGGAGTGCATATGATGATAT-T-GCCT
1 ATGTGCGGTGTGGGAGTGCACATGATGATATATAG-CT
* ** *
12115724 -TGGGCAATGTGGGAGTGCACATGATGAT-TCTAGCT
1 ATGTGCGGTGTGGGAGTGCACATGATGATATATAGCT
*
12115759 ATGTGCTGTGTGGGAGTGCACATGA
1 ATGTGCGGTGTGGGAGTGCACATGA
12115784 GCTGGTGAGA
Statistics
Matches: 107, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
33 2 0.02
34 16 0.15
35 29 0.27
36 31 0.29
37 8 0.07
38 2 0.02
39 17 0.16
40 2 0.02
ACGTcount: A:0.21, C:0.13, G:0.37, T:0.29
Consensus pattern (37 bp):
ATGTGCGGTGTGGGAGTGCACATGATGATATATAGCT
Found at i:12119952 original size:35 final size:35
Alignment explanation
Indices: 12119908--12119978 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 35
12119898 TTTCACCAAG
*
12119908 CTTTTACAAT-GTCTTTTACC-AGACTCAACCAAAAC
1 CTTTCACAATGGT-TTTTACCAAGA-TCAACCAAAAC
12119943 CTTTCACAATGGTTTTTACCAAGATCAACCAAAAC
1 CTTTCACAATGGTTTTTACCAAGATCAACCAAAAC
12119978 C
1 C
12119979 CAACAACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 28 0.85
36 5 0.15
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (35 bp):
CTTTCACAATGGTTTTTACCAAGATCAACCAAAAC
Found at i:12120940 original size:17 final size:17
Alignment explanation
Indices: 12120918--12120952 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12120908 GGAGGTTTTC
12120918 CTCCCCCTAAGTGTGTG
1 CTCCCCCTAAGTGTGTG
*
12120935 CTCCCCCTCAGTGTGTG
1 CTCCCCCTAAGTGTGTG
12120952 C
1 C
12120953 ATATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.40, G:0.23, T:0.29
Consensus pattern (17 bp):
CTCCCCCTAAGTGTGTG
Found at i:12127202 original size:63 final size:63
Alignment explanation
Indices: 12127103--12127276 Score: 240
Period size: 63 Copynumber: 2.8 Consensus size: 63
12127093 GGTACCATTG
* * ** * *
12127103 TGTGATAATTGTAATCATGCATGTGCAAAGTGGGCAGTGCACATGCTGGTTGAATGACAATGT
1 TGTGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGATTGAATGACAATGT
* * *
12127166 TGTGATAATTGTAACCGTGCATGTGTGGAGTGGGCAGTGCGCATACCGATTGAATGACAATGT
1 TGTGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGATTGAATGACAATGT
* **
12127229 CGTGATAATTACAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCG
1 TGTGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCG
12127277 GTAATGATGC
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 96 1.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (63 bp):
TGTGATAATTGTAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGATTGAATGACAATGT
Found at i:12137938 original size:27 final size:27
Alignment explanation
Indices: 12137908--12137959 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
12137898 AGTGTTGGGT
*
12137908 GGTG-TAAAATTACAATTTTGTCCCTAG
1 GGTGTTAAAATGACAATTTTG-CCCTAG
*
12137935 GGTGTTAAAATGACTATTTTGCCCT
1 GGTGTTAAAATGACAATTTTGCCCT
12137960 TTATGCTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (27 bp):
GGTGTTAAAATGACAATTTTGCCCTAG
Found at i:12141661 original size:40 final size:37
Alignment explanation
Indices: 12141613--12141715 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 37
12141603 ACCCGGCTCA
*
12141613 TGTACATCCCCCCACATCGTGCACA-TAGCCAAGACTATCG
1 TGTACATCCCCCCACATCGTGCACATTAG---AG-CCATCG
* * *
12141653 TGTGCATCCCCCCACATCATGCACAATTAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCAC-ATTAGAGCCATCG
12141691 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
12141716 CGAGCACTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.49
39 1 0.02
40 22 0.40
41 1 0.02
42 3 0.05
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.21
Consensus pattern (37 bp):
TGTACATCCCCCCACATCGTGCACATTAGAGCCATCG
Found at i:12143032 original size:18 final size:18
Alignment explanation
Indices: 12143009--12143047 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12142999 TAGGTGACAC
12143009 TTAGAATGGATGATGTGA
1 TTAGAATGGATGATGTGA
12143027 TTAGAATGGATGATGTGA
1 TTAGAATGGATGATGTGA
12143045 TTA
1 TTA
12143048 AGTCAAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (18 bp):
TTAGAATGGATGATGTGA
Found at i:12150347 original size:22 final size:22
Alignment explanation
Indices: 12150319--12150362 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12150309 TTAAAACAAC
12150319 TTTAAAACCAAAGGCTCTGATA
1 TTTAAAACCAAAGGCTCTGATA
12150341 TTTAAAACCAAAGGCTCTGATA
1 TTTAAAACCAAAGGCTCTGATA
12150363 CCAATCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (22 bp):
TTTAAAACCAAAGGCTCTGATA
Found at i:12152612 original size:11 final size:11
Alignment explanation
Indices: 12152584--12152628 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
12152574 CCTAGGGTTC
*
12152584 TTGTTCTTTC-
1 TTGTTCTTCCT
12152594 TT-TTCTTCCT
1 TTGTTCTTCCT
12152604 TTGTTCTTCCT
1 TTGTTCTTCCT
12152615 TTGGTT-TTCCT
1 TT-GTTCTTCCT
12152626 TTG
1 TTG
12152629 GCCGGCCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 6 0.19
10 5 0.16
11 17 0.55
12 3 0.10
ACGTcount: A:0.00, C:0.22, G:0.11, T:0.67
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:12152629 original size:11 final size:12
Alignment explanation
Indices: 12152596--12152629 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
12152586 GTTCTTTCTT
12152596 TTCTTCCTTT-G
1 TTCTTCCTTTGG
12152607 TTCTTCCTTTGG
1 TTCTTCCTTTGG
12152619 TT-TTCCTTTGG
1 TTCTTCCTTTGG
12152630 CCGGCCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.00, C:0.24, G:0.15, T:0.62
Consensus pattern (12 bp):
TTCTTCCTTTGG
Found at i:12162013 original size:26 final size:24
Alignment explanation
Indices: 12161972--12162019 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
12161962 TACTTTTATG
12161972 CTACAAAAATTATTTACGTAGAATT
1 CTACAAAAATTATTTACG-AGAATT
*
12161997 CTACAAAAATTGTTTTACGAGAA
1 CTACAAAAATT-ATTTACGAGAA
12162020 AATGGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (24 bp):
CTACAAAAATTATTTACGAGAATT
Found at i:12165603 original size:43 final size:43
Alignment explanation
Indices: 12165485--12165605 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
12165475 TCACTTGGCT
**
12165485 ATGTGCGAGTAGGG-GTGCGCATAAGCCGAG-GATGACCCGATT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCGACC
* * *
12165527 ATGTGCGAGTAAGGAGTGCGCATAACCCAGTGATGACCC-AGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCGA-CC
* * *
12165570 ATGTGCCAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
12165606 TGATGATGGG
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 15 0.23
43 50 0.77
ACGTcount: A:0.25, C:0.20, G:0.36, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCGACC
Found at i:12170092 original size:19 final size:19
Alignment explanation
Indices: 12170068--12170105 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12170058 CTGCCAAATC
*
12170068 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
12170087 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
12170106 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:12176610 original size:2 final size:2
Alignment explanation
Indices: 12176562--12176597 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12176552 AATTATTAAT
12176562 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12176598 CTTTGTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12181450 original size:42 final size:42
Alignment explanation
Indices: 12181383--12181466 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
12181373 GTAATGATAT
**
12181383 TGACCCGGCTATGTGAGAGTAGGAGTGTGCATAAGCCGATGC
1 TGACCCGGCTATGTGAGAGTAGGAGTGCACATAAGCCGATGC
* *
12181425 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGATGC
1 TGACCCGGCTATGTGAGAGTAGGAGTGCACATAAGCCGATGC
12181467 ATATGAGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.20
Consensus pattern (42 bp):
TGACCCGGCTATGTGAGAGTAGGAGTGCACATAAGCCGATGC
Found at i:12181512 original size:2 final size:2
Alignment explanation
Indices: 12181507--12181547 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12181497 ATGATGATTG
12181507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12181548 GACATATACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12185968 original size:24 final size:25
Alignment explanation
Indices: 12185941--12185996 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
12185931 ATGACAACTG
*
12185941 CGTATATCA-CTTGTGGCCTAGCCA
1 CGTATATCATCTCGTGGCCTAGCCA
*
12185965 CGTATATCATCTCGTGGCCTTGCCA
1 CGTATATCATCTCGTGGCCTAGCCA
*
12185990 TGTATAT
1 CGTATAT
12185997 ATCATAGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
CGTATATCATCTCGTGGCCTAGCCA
Found at i:12187236 original size:4 final size:4
Alignment explanation
Indices: 12187216--12187300 Score: 65
Period size: 4 Copynumber: 22.8 Consensus size: 4
12187206 TCATTTCTCA
* * * *
12187216 TTTC -TTC TTTC -TCC TTTC TTTC TTCC TTCC TTTC TTTC TTTC -TCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* * *
12187261 TTTC -TTC TTTC -TTC TTTC -TCC TTTC TTCC TTTC TCTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
12187301 GCTTCCAAGC
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
3 15 0.24
4 48 0.76
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:12187265 original size:7 final size:7
Alignment explanation
Indices: 12187209--12187300 Score: 76
Period size: 7 Copynumber: 12.4 Consensus size: 7
12187199 CGAACCTTCA
*
12187209 TTTCTCA
1 TTTCTCC
*
12187216 TTTCTTC
1 TTTCTCC
12187223 TTTCTCC
1 TTTCTCC
*
12187230 TTTCTTTC
1 TTTC-TCC
*
12187238 TTCCTTCC
1 TTTC-TCC
*
12187246 TTTCTTTC
1 TTTC-TCC
12187254 TTTCTCC
1 TTTCTCC
*
12187261 TTTCTTC
1 TTTCTCC
*
12187268 TTTCTTC
1 TTTCTCC
12187275 TTTCTCC
1 TTTCTCC
12187282 TTTCTTCC
1 TTTC-TCC
12187290 TTTCTCTC
1 TTTCTC-C
12187298 TTT
1 TTT
12187301 GCTTCCAAGC
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
7 42 0.59
8 29 0.41
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTCTCC
Found at i:12188514 original size:2 final size:2
Alignment explanation
Indices: 12188507--12188532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12188497 AACTTTGTAA
12188507 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
12188533 GTTTCATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12189088 original size:2 final size:2
Alignment explanation
Indices: 12189081--12189130 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
12189071 TATGATGTTG
12189081 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
12189124 AT GT AT A
1 AT AT AT A
12189131 CTATGTCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12189302 original size:54 final size:54
Alignment explanation
Indices: 12189236--12189401 Score: 271
Period size: 54 Copynumber: 3.1 Consensus size: 54
12189226 ATGGTGATAT
12189236 TGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGA-CTTGGGTGAGATGGGA
1 TGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGC-TGGGTGAGATGGGA
*
12189290 TGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTAGGTGAGATGGGA
1 TGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
** * *
12189344 CATTCGGCTATCTGCACGATGTGGTGGGATGCACATGAGCTGGGTAAGATGGGA
1 TGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
12189398 TGTT
1 TGTT
12189402 TGCTGGAAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 102 0.99
55 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.39, T:0.27
Consensus pattern (54 bp):
TGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
Found at i:12193939 original size:63 final size:63
Alignment explanation
Indices: 12193851--12193994 Score: 171
Period size: 63 Copynumber: 2.3 Consensus size: 63
12193841 GCATGTGCAA
* * * * * *
12193851 AGTGGGTAGTGCACATGCTAGTTGAATGATGAGGTTTCGATAGTTACAACCATGCATGTACGG
1 AGTGGGCAATGCACATGCCAGTTGAATGACGAGGTTGCGATAATTACAACCATGCATGTACGG
* * * ** *
12193914 AGTGGGCAATGCACATGCCGGTTGAATGACGATGTTGCGATAATTACTACTGTGCATGTGCGG
1 AGTGGGCAATGCACATGCCAGTTGAATGACGAGGTTGCGATAATTACAACCATGCATGTACGG
*
12193977 AGTGGACAATGCACATGC
1 AGTGGGCAATGCACATGC
12193995 TGGTAATGAT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (63 bp):
AGTGGGCAATGCACATGCCAGTTGAATGACGAGGTTGCGATAATTACAACCATGCATGTACGG
Found at i:12201554 original size:63 final size:63
Alignment explanation
Indices: 12201450--12201611 Score: 236
Period size: 63 Copynumber: 2.6 Consensus size: 63
12201440 TAATGGATGT
* ** *
12201450 AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGATTGAATGATGAGGTTTTGATAGTTAC
1 AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGATTGAATGACGAGGTTGCGATAATTAC
* *
12201513 AACCGTGCATGTGCGGAGTGGGCAGTGCACAT-CCTGGTTGAATGACGATGTTGCGATAATTAC
1 AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCC-GATTGAATGACGAGGTTGCGATAATTAC
* *
12201576 AATCGTGCATGTGCGAAGTGGGCAGTGCACATGCCG
1 AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCG
12201612 GTAATGATGC
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
62 2 0.02
63 85 0.96
64 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (63 bp):
AACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGATTGAATGACGAGGTTGCGATAATTAC
Found at i:12205925 original size:37 final size:37
Alignment explanation
Indices: 12205884--12206004 Score: 172
Period size: 37 Copynumber: 3.3 Consensus size: 37
12205874 TGAGATTGGG
12205884 TGATGAT-ATTGAGGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATTGA-GTGTGCGAGTAGGGAGTGCACACA
* *
12205921 TGATGATGATTGAGTGTGCAAGTAAGGAGTGCACACA
1 TGATGATGATTGAGTGTGCGAGTAGGGAGTGCACACA
* * * *
12205958 TGACGATGATGGAGTGTGCGAGTAGGGAATGCATACA
1 TGATGATGATTGAGTGTGCGAGTAGGGAGTGCACACA
12205995 TGATGATGAT
1 TGATGATGAT
12206005 GTATGTATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 69 0.93
38 5 0.07
ACGTcount: A:0.30, C:0.10, G:0.36, T:0.25
Consensus pattern (37 bp):
TGATGATGATTGAGTGTGCGAGTAGGGAGTGCACACA
Found at i:12209719 original size:14 final size:14
Alignment explanation
Indices: 12209699--12209738 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
12209689 ATGTTTTCGA
12209699 AATGATGAATGTCT
1 AATGATGAATGTCT
* *
12209713 TATGATGAATATCT
1 AATGATGAATGTCT
12209727 AATGATGAATGT
1 AATGATGAATGT
12209739 TAAAGAAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (14 bp):
AATGATGAATGTCT
Found at i:12210660 original size:40 final size:40
Alignment explanation
Indices: 12210616--12210691 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
12210606 TTTCACAAAA
** *
12210616 ACTACCTTTTTGAGAAGAGCGAGCACAACCTCACAACATC
1 ACTACCTTTTCAAGAAGAGCAAGCACAACCTCACAACATC
* *
12210656 ACTACCTTTTCAAGAGGAGCAAGCACAACTTCACAA
1 ACTACCTTTTCAAGAAGAGCAAGCACAACCTCACAA
12210692 TGTCATTGCC
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:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (40 bp):
ACTACCTTTTCAAGAAGAGCAAGCACAACCTCACAACATC
Found at i:12212830 original size:25 final size:25
Alignment explanation
Indices: 12212771--12212830 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
12212761 ATGGTATCAA
* *
12212771 CCACGTGTATCAACCTGTGGCCTAG
1 CCACGTATATCAACCCGTGGCCTAG
* *
12212796 CCAC-TCATATCTACCCGTGGCCTTG
1 CCACGT-ATATCAACCCGTGGCCTAG
12212821 CCACGTATAT
1 CCACGTATAT
12212831 ATCACAGACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 27 0.93
26 1 0.03
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (25 bp):
CCACGTATATCAACCCGTGGCCTAG
Found at i:12215996 original size:42 final size:42
Alignment explanation
Indices: 12215937--12216102 Score: 219
Period size: 42 Copynumber: 4.0 Consensus size: 42
12215927 GTTGATGTGA
*
12215937 ACCTGGCTATGTGCGAGT-GAGAGTGCGCATAAGCCGTTGCTG
1 ACCTGGCTATGTGCGAGTAG-GAGTGCGCATAAGCCATTGCTG
12215979 ACCTGGCTATGTGCGAGTAGGAGTGCGCATAAGCCATTGCTG
1 ACCTGGCTATGTGCGAGTAGGAGTGCGCATAAGCCATTGCTG
* * * *
12216021 ATCTGGCTATGTGCGAATGGGAGTGC-CAATAAGCCATTGCTA
1 ACCTGGCTATGTGCGAGTAGGAGTGCGC-ATAAGCCATTGCTG
* * * *
12216063 ACCCGACTATGTGCGAGTAGGAGTGTGCATAAGCCGTTGC
1 ACCTGGCTATGTGCGAGTAGGAGTGCGCATAAGCCATTGC
12216103 ATATGAGCTA
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.01
42 106 0.97
43 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (42 bp):
ACCTGGCTATGTGCGAGTAGGAGTGCGCATAAGCCATTGCTG
Found at i:12219794 original size:40 final size:38
Alignment explanation
Indices: 12219709--12219793 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 38
12219699 TGAGGTTGGG
*
12219709 TGATGAT-ATTGAGGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATGGAGGTGTGCGAGTAGGGAGTGCACACA
*
12219746 TGACGATGATGGA-GTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATGGAGGTGTGCGAGTAGGGAGTGCACACA
12219783 TGATGATGATG
1 TGATGATGATG
12219794 ATGTATGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 40 0.91
38 4 0.09
ACGTcount: A:0.27, C:0.11, G:0.39, T:0.24
Consensus pattern (38 bp):
TGATGATGATGGAGGTGTGCGAGTAGGGAGTGCACACA
Found at i:12225217 original size:20 final size:20
Alignment explanation
Indices: 12225171--12225230 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
12225161 TATACCCATA
*
12225171 ATCATCATC-TCACCAAC-C
1 ATCATCATCATCACCAGCTC
*
12225189 ATTATCATCATCACCAGCTC
1 ATCATCATCATCACCAGCTC
12225209 ATCATCATCATCACCAGCTC
1 ATCATCATCATCACCAGCTC
12225229 AT
1 AT
12225231 GCGCACTCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 22 0.59
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.27
Consensus pattern (20 bp):
ATCATCATCATCACCAGCTC
Found at i:12225277 original size:43 final size:43
Alignment explanation
Indices: 12225229--12225338 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
12225219 TCACCAGCTC
* ** * *
12225229 ATGCGCACTCCCTACTTGCACATGGCTAGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATC-CTCGGCTT
*
12225272 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
12225315 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
12225339 GTCGAGTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 59 0.98
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
Found at i:12227440 original size:37 final size:37
Alignment explanation
Indices: 12227399--12227471 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
12227389 ATAATGTTGT
* **
12227399 ATGATGATAATGAGGTGTGCGAGTAGGGAGTGCACAC
1 ATGATGACAATGAAATGTGCGAGTAGGGAGTGCACAC
*
12227436 ATGATGACATTGAAATGTGCGAGTAGGGAGTGCACA
1 ATGATGACAATGAAATGTGCGAGTAGGGAGTGCACA
12227472 TATGGTGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.22
Consensus pattern (37 bp):
ATGATGACAATGAAATGTGCGAGTAGGGAGTGCACAC
Found at i:12227492 original size:37 final size:37
Alignment explanation
Indices: 12227414--12227508 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
12227404 GATAATGAGG
12227414 TGTGCGAGTAGGGAGTGCACACATGATGACATTGAAA
1 TGTGCGAGTAGGGAGTGCACACATGATGACATTGAAA
* * ***
12227451 TGTGCGAGTAGGGAGTGCACATATGGTGGA-ATTGCCT
1 TGTGCGAGTAGGGAGTGCACACATGAT-GACATTGAAA
*
12227488 TGTGCGTGTAGGGAGTGCACA
1 TGTGCGAGTAGGGAGTGCACA
12227509 AGAGCTGAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
37 49 0.96
38 2 0.04
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.24
Consensus pattern (37 bp):
TGTGCGAGTAGGGAGTGCACACATGATGACATTGAAA
Found at i:12231120 original size:36 final size:36
Alignment explanation
Indices: 12231061--12231156 Score: 147
Period size: 36 Copynumber: 2.6 Consensus size: 36
12231051 CATAGCCGAA
*
12231061 GTCATCATGTGCATCCCCCACATCGCGCACAACTAAT
1 GTCATCGTGTGC-TCCCCCACATCGCGCACAACTAAT
*
12231098 GTCATCGTGTGCTCCCCCACATCGCGCACAGCTAAT
1 GTCATCGTGTGCTCCCCCACATCGCGCACAACTAAT
* *
12231134 GCCATTGTGTGCTCCCCCACATC
1 GTCATCGTGTGCTCCCCCACATC
12231157 ATGCACAGGC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
36 44 0.80
37 11 0.20
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.23
Consensus pattern (36 bp):
GTCATCGTGTGCTCCCCCACATCGCGCACAACTAAT
Found at i:12232900 original size:25 final size:28
Alignment explanation
Indices: 12232872--12232930 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 28
12232862 TATCAACATG
12232872 TGGCCTAGCCA-CATATATCA-AG-CCA
1 TGGCCTAGCCAGCATATATCATAGACCA
* *
12232897 TGGCCTTGCCATGTATATATCATAGACCA
1 TGGCCTAGCCA-GCATATATCATAGACCA
12232926 TGGCC
1 TGGCC
12232931 CCAACCACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.36
27 8 0.29
28 2 0.07
29 8 0.29
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (28 bp):
TGGCCTAGCCAGCATATATCATAGACCA
Found at i:12234948 original size:55 final size:56
Alignment explanation
Indices: 12234889--12234994 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
12234879 GGCCGCCTAG
*
12234889 TGGAACCAATCACAACACATGCAC-AATTTTCCTTAGTTTTCATTTAGCCACCCTT
1 TGGAACCAATCACAACACATGAACAAATTTTCCTTAGTTTTCATTTAGCCACCCTT
* *
12234944 TGGAACCAATCACAACACATGAACAAATTTTCCTTTGTTTTCATTTGGCCA
1 TGGAACCAATCACAACACATGAACAAATTTTCCTTAGTTTTCATTTAGCCA
12234995 TTTTGCCAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 23 0.49
56 24 0.51
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.33
Consensus pattern (56 bp):
TGGAACCAATCACAACACATGAACAAATTTTCCTTAGTTTTCATTTAGCCACCCTT
Found at i:12235006 original size:55 final size:54
Alignment explanation
Indices: 12234892--12235008 Score: 155
Period size: 55 Copynumber: 2.1 Consensus size: 54
12234882 CGCCTAGTGG
* *
12234892 AACCAATCACAACACATGCACAATTTTCCTTAGTTTTCATTTAGCCACCCTTTGG
1 AACCAATCACAACACATGAACAATTTTCCTTAGTTTTCATTTAGCCA-CCTTTGC
* * *
12234947 AACCAATCACAACACATGAACAAATTTTCCTTTGTTTTCATTTGGCCA-TTTTGCC
1 AACCAATCACAACACATGAAC-AATTTTCCTTAGTTTTCATTTAGCCACCTTTG-C
12235002 AACCAAT
1 AACCAAT
12235009 GGTTCTTCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 4 0.07
55 27 0.49
56 24 0.44
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (54 bp):
AACCAATCACAACACATGAACAATTTTCCTTAGTTTTCATTTAGCCACCTTTGC
Found at i:12235915 original size:11 final size:11
Alignment explanation
Indices: 12235901--12235931 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12235891 TTATAAAAAT
12235901 ATTATTATTTA
1 ATTATTATTTA
12235912 ATTATTATTTA
1 ATTATTATTTA
12235923 ATTATTATT
1 ATTATTATT
12235932 CCTTCACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTATTATTTA
Found at i:12238734 original size:43 final size:43
Alignment explanation
Indices: 12238664--12238782 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
12238654 GTAATTATGT
* *
12238664 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
12238707 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
12238750 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
12238783 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:12238792 original size:43 final size:43
Alignment explanation
Indices: 12238674--12238795 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
12238664 TGACTCGGCT
* **
12238674 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
12238717 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
12238760 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
12238796 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:12238806 original size:20 final size:20
Alignment explanation
Indices: 12238781--12238843 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
12238771 GGGAGTGCGC
12238781 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
12238801 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
12238821 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
12238840 ATGA
1 ATGA
12238844 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:12250155 original size:20 final size:20
Alignment explanation
Indices: 12250130--12250167 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12250120 GAAGAAGAAG
12250130 AAGCTGCTAGAAAAATGAAA
1 AAGCTGCTAGAAAAATGAAA
* *
12250150 AAGCTGCTGGAGAAATGA
1 AAGCTGCTAGAAAAATGA
12250168 GATATGTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.16
Consensus pattern (20 bp):
AAGCTGCTAGAAAAATGAAA
Found at i:12255440 original size:40 final size:37
Alignment explanation
Indices: 12255360--12255473 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 37
12255350 ATATGCATTA
*
12255360 ATCATCATGTGTGCACTCCCTACTTACACACTTCAAC
1 ATCATCATGTGTGCACTCCCTACTCACACACTTCAAC
* *
12255397 ATCATCATGTGTGCACTCCCTGCTCGCACAC-TCTAAC
1 ATCATCATGTGTGCACTCCCTACTCACACACTTC-AAC
**
12255434 ATCATCATGTGCACACTCCCTACTCACACACTTCAAC
1 ATCATCATGTGTGCACTCCCTACTCACACACTTCAAC
12255471 ATC
1 ATC
12255474 CTCACCCAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 2 0.03
37 64 0.94
38 2 0.03
ACGTcount: A:0.26, C:0.38, G:0.09, T:0.27
Consensus pattern (37 bp):
ATCATCATGTGTGCACTCCCTACTCACACACTTCAAC
Found at i:12257168 original size:42 final size:42
Alignment explanation
Indices: 12257116--12257233 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
12257106 GTGGACCCGG
*
12257116 CTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCTGACCCA-A
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGA-CCAGA
* * * *
12257158 CTATATGCGAGTGGGAGTGCACATAAGTCGTTGCTGACCAGG
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCAGA
*
12257200 CTATGTGCGAGTAGGAGTGCGCATAAGCCGTTGC
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
12257234 ATATGAGACG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
41 3 0.05
42 63 0.95
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (42 bp):
CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCAGA
Found at i:12264440 original size:31 final size:31
Alignment explanation
Indices: 12264216--12264443 Score: 228
Period size: 31 Copynumber: 7.4 Consensus size: 31
12264206 AACGTGTGAT
* *
12264216 AACATTTGACTTGATATGCATGGCGTGTCAC
1 AACATTTTACTTGTTATGCATGGCGTGTCAC
* * *
12264247 AACATTTTACTTGTTATTCGTGGCATGTCAC
1 AACATTTTACTTGTTATGCATGGCGTGTCAC
*
12264278 AACA-TTTATCTTGTTATGCATGGCGTATCAC
1 AACATTTTA-CTTGTTATGCATGGCGTGTCAC
* * **
12264309 AAC-GTTTATCTTGTTATGCATTGCGTGTCTT
1 AACATTTTA-CTTGTTATGCATGGCGTGTCAC
* * *
12264340 GACA-TTTATCTTGTTATGCATGGTGTGCCAC
1 AACATTTTA-CTTGTTATGCATGGCGTGTCAC
* * * *
12264371 CACATTTTACTTGTAATGCATGGTGTGTGAC
1 AACATTTTACTTGTTATGCATGGCGTGTCAC
* * *
12264402 AACATTTTACTTGATATGCACGGTGTGTCAC
1 AACATTTTACTTGTTATGCATGGCGTGTCAC
12264433 AACATTTTACT
1 AACATTTTACT
12264444 GTTTAAGGTT
Statistics
Matches: 165, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
30 4 0.02
31 157 0.95
32 4 0.02
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (31 bp):
AACATTTTACTTGTTATGCATGGCGTGTCAC
Found at i:12266136 original size:16 final size:15
Alignment explanation
Indices: 12266090--12266138 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
12266080 TTTTTTTCTG
*
12266090 TATACACAATATACTT
1 TATACACAAT-TATTT
12266106 TAT--ACAATTATTT
1 TATACACAATTATTT
12266119 TATACACAATTGATTT
1 TATACACAATT-ATTT
12266135 TATA
1 TATA
12266139 TCAAGAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 7 0.24
14 5 0.17
15 6 0.21
16 11 0.38
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (15 bp):
TATACACAATTATTT
Found at i:12266266 original size:31 final size:31
Alignment explanation
Indices: 12266228--12266395 Score: 162
Period size: 31 Copynumber: 5.4 Consensus size: 31
12266218 AATATGCTAC
12266228 CACTCAGCGTGTCCCCACATACATCTAGTTG
1 CACTCAGCGTGTCCCCACATACATCTAGTTG
* * * * * * *
12266259 CACTCAGCATGTGACGC-CATAAATAT-GCTA
1 CACTCAGCGTGT-CCCCACATACATCTAGTTG
* *
12266289 CAACTCAGCGTGTCCCCACATACATTTGGTTG
1 C-ACTCAGCGTGTCCCCACATACATCTAGTTG
* * *
12266321 CACTCAGCGTGTCACCC-CATAAATCTACTTC
1 CACTCAGCGTGTC-CCCACATACATCTAGTTG
* *
12266352 CGCTCAGCGTGTCCCCACATACATCTGGTTG
1 CACTCAGCGTGTCCCCACATACATCTAGTTG
12266383 CACTCAGCGTGTC
1 CACTCAGCGTGTC
12266396 ACGACGTTTA
Statistics
Matches: 106, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
30 8 0.08
31 90 0.85
32 8 0.08
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (31 bp):
CACTCAGCGTGTCCCCACATACATCTAGTTG
Found at i:12266281 original size:62 final size:62
Alignment explanation
Indices: 12266204--12266390 Score: 284
Period size: 62 Copynumber: 3.0 Consensus size: 62
12266194 AAGAAGTCAA
*
12266204 CATGTGACGCCATAAATATGCTACCACTCAGCGTGTCCCCACATACATCTAGTTGCACTCAG
1 CATGTGACGCCATAAATATGCTACCACTCAGCGTGTCCCCACATACATCTGGTTGCACTCAG
* *
12266266 CATGTGACGCCATAAATATGCTACAACTCAGCGTGTCCCCACATACATTTGGTTGCACTCAG
1 CATGTGACGCCATAAATATGCTACCACTCAGCGTGTCCCCACATACATCTGGTTGCACTCAG
* * * * * * *
12266328 CGTGTCACCCCATAAATCTACTTCCGCTCAGCGTGTCCCCACATACATCTGGTTGCACTCAG
1 CATGTGACGCCATAAATATGCTACCACTCAGCGTGTCCCCACATACATCTGGTTGCACTCAG
12266390 C
1 C
12266391 GTGTCACGAC
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 113 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (62 bp):
CATGTGACGCCATAAATATGCTACCACTCAGCGTGTCCCCACATACATCTGGTTGCACTCAG
Found at i:12266436 original size:31 final size:31
Alignment explanation
Indices: 12266389--12266783 Score: 314
Period size: 31 Copynumber: 12.7 Consensus size: 31
12266379 GTTGCACTCA
* *
12266389 GCGTGTCACGACGTTTAATTTGTTATGCATG
1 GCGTGTCACGACATTTAACTTGTTATGCATG
* **
12266420 GTGTGTCACGATGTTTAACTTGTTATGCATG
1 GCGTGTCACGACATTTAACTTGTTATGCATG
* * *
12266451 GCGGGTCA-GAACAATTTAA-TTGCTATACATG
1 GCGTGTCACG-AC-ATTTAACTTGTTATGCATG
* **
12266482 GCGTGTCATGACGGTTAACTTGTTATGCATG
1 GCGTGTCACGACATTTAACTTGTTATGCATG
* *
12266513 GCGGGTCA-GAACAATTTAA-TTTTTATGCATG
1 GCGTGTCACG-AC-ATTTAACTTGTTATGCATG
*
12266544 GCGTGTCACGACATTTAACTTCTTATGCATG
1 GCGTGTCACGACATTTAACTTGTTATGCATG
12266575 GCG-GATCA-GAACAATTTAA-TTGTTATGCATG
1 GCGTG-TCACG-AC-ATTTAACTTGTTATGCATG
*
12266606 GCGGGTCA-GAACAATTTAA-TTGTTATGCATG
1 GCGTGTCACG-AC-ATTTAACTTGTTATGCATG
* * * * *
12266637 GTGGGTCA-GAACAATTTTACTTGATATGCACG
1 GCGTGTCACG-AC-ATTTAACTTGTTATGCATG
*
12266669 GCGGGTCA-GAACAATTTAA-TTGTTATGCATG
1 GCGTGTCACG-AC-ATTTAACTTGTTATGCATG
*
12266700 GCGTGTCACGACATTTAACTTCTTATGCATG
1 GCGTGTCACGACATTTAACTTGTTATGCATG
* * *
12266731 GTGGGTCA-GAACAACTTAA-TTGTTATGCATG
1 GCGTGTCACG-AC-ATTTAACTTGTTATGCATG
* *
12266762 GCGTGTCATGACGTTTAACTTG
1 GCGTGTCACGACATTTAACTTG
12266784 CAGTAAGAAC
Statistics
Matches: 306, Mismatches: 39, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
30 25 0.08
31 229 0.75
32 52 0.17
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (31 bp):
GCGTGTCACGACATTTAACTTGTTATGCATG
Found at i:12266575 original size:93 final size:92
Alignment explanation
Indices: 12266389--12266779 Score: 379
Period size: 93 Copynumber: 4.2 Consensus size: 92
12266379 GTTGCACTCA
* * **
12266389 GCGTGTCACGACGTTTAATTTGTTATGCATGGTGTGTCACGA-TGTTTAACTTGTTATGCATGGC
1 GCGTGTCA-GACGTTTAA-TTGTTATGCATGGCGGGTCACGACAATTTAACTTGTTATGCATGGC
*
12266453 GGGTCAGAACAATTTAATTGC-TATACATG
64 GGGTCAGAACAATTTAATT-CTTATGCATG
* *
12266482 GCGTGTCATGACGGTTAACTTGTTATGCATGGCGGGTCA-GAACAATTTAA-TTTTTATGCATGG
1 GCGTGTCA-GACGTTTAA-TTGTTATGCATGGCGGGTCACG-ACAATTTAACTTGTTATGCATGG
*
12266545 CGTGTCACG-AC-ATTTAACTTCTTATGCATG
63 CGGGTCA-GAACAATTTAA-TTCTTATGCATG
*
12266575 GCG-GATCAGAACAATTTAATTGTTATGCATGGCGGGTCA-GAACAATTTAA-TTGTTATGCATG
1 GCGTG-TCAG-AC-GTTTAATTGTTATGCATGGCGGGTCACG-ACAATTTAACTTGTTATGCATG
* * ** *
12266637 GTGGGTCAGAACAATTTTACTTGATATGCACG
62 GCGGGTCAGAACAA-TTTAATTCTTATGCATG
* * * * *
12266669 GCGGGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACGAC-ATTTAACTTCTTATGCATGGT
1 GCGTGTCAG-AC-GTTTAATTGTTATGCATGGCGGGTCACGACAATTTAACTTGTTATGCATGGC
* *
12266733 GGGTCAGAACAACTTAATTGTTATGCATG
64 GGGTCAGAACAATTTAATTCTTATGCATG
12266762 GCGTGTCATGACGTTTAA
1 GCGTGTCA-GACGTTTAA
12266780 CTTGCAGTAA
Statistics
Matches: 256, Mismatches: 27, Indels: 31
0.82 0.09 0.10
Matches are distributed among these distances:
92 16 0.06
93 150 0.59
94 84 0.33
95 6 0.02
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (92 bp):
GCGTGTCAGACGTTTAATTGTTATGCATGGCGGGTCACGACAATTTAACTTGTTATGCATGGCGG
GTCAGAACAATTTAATTCTTATGCATG
Found at i:12266710 original size:156 final size:155
Alignment explanation
Indices: 12266433--12266769 Score: 514
Period size: 156 Copynumber: 2.2 Consensus size: 155
12266423 TGTCACGATG
* *
12266433 TTTAACTTGTTATGCATGGCGGGTCAGAACAATTTAATTGCTATACATGGCGTGTCATGACGGTT
1 TTTAA-TTGTTATGCATGGCGGGTCAGAACAATTTAATTGCTATACATGGCGGGTCATGACAGTT
* * *
12266498 AACTTGTTATGCATGGCGGGTCAGAACAATTTAATTTTTATGCATGGCGTGTCACGACATTTAAC
65 AACTTGATATGCACGGCGGGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACGACATTTAAC
12266563 TTCTTATGCATGGCGGATCAGAACAA
130 TTCTTATGCATGGCGGATCAGAACAA
* * * *
12266589 TTTAATTGTTATGCATGGCGGGTCAGAACAATTTAATTGTTATGCATGGTGGGTCA-GAACAATT
1 TTTAATTGTTATGCATGGCGGGTCAGAACAATTTAATTGCTATACATGGCGGGTCATG-AC-AGT
*
12266653 TTACTTGATATGCACGGCGGGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACGACATTTAA
64 TAACTTGATATGCACGGCGGGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACGACATTTAA
* *
12266718 CTTCTTATGCATGGTGGGTCAGAACAA
129 CTTCTTATGCATGGCGGATCAGAACAA
* *
12266745 CTTAATTGTTATGCATGGCGTGTCA
1 TTTAATTGTTATGCATGGCGGGTCA
12266770 TGACGTTTAA
Statistics
Matches: 165, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
154 1 0.01
155 49 0.30
156 115 0.70
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (155 bp):
TTTAATTGTTATGCATGGCGGGTCAGAACAATTTAATTGCTATACATGGCGGGTCATGACAGTTA
ACTTGATATGCACGGCGGGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACGACATTTAACT
TCTTATGCATGGCGGATCAGAACAA
Found at i:12266782 original size:62 final size:63
Alignment explanation
Indices: 12266433--12266769 Score: 395
Period size: 62 Copynumber: 5.4 Consensus size: 63
12266423 TGTCACGATG
* * * *
12266433 TTTAACTTGTTATGCATGGCGGGTCAGAACAATTTAA-TTGCTATACATGGCGTGTCATG-AC-G
1 TTTAA-TTGTTATGCATGGCGGGTCAGAACAATTTAACTTGTTATGCATGGCGGGTCA-GAACAA
* * *
12266495 GTTAACTTGTTATGCATGGCGGGTCAGAACAATTTAA-TTTTTATGCATGGCGTGTCACG-AC-A
1 TTTAA-TTGTTATGCATGGCGGGTCAGAACAATTTAACTTGTTATGCATGGCGGGTCA-GAACAA
* *
12266557 TTTAACTTCTTATGCATGGCGGATCAGAACAATTTAA-TTGTTATGCATGGCGGGTCAGAACAA
1 TTTAA-TTGTTATGCATGGCGGGTCAGAACAATTTAACTTGTTATGCATGGCGGGTCAGAACAA
* * * *
12266620 TTTAATTGTTATGCATGGTGGGTCAGAACAATTTTACTTGATATGCACGGCGGGTCAGAACAA
1 TTTAATTGTTATGCATGGCGGGTCAGAACAATTTAACTTGTTATGCATGGCGGGTCAGAACAA
* * *
12266683 TTTAATTGTTATGCATGGCGTGTCACG-AC-ATTTAACTTCTTATGCATGGTGGGTCAGAACAA
1 TTTAATTGTTATGCATGGCGGGTCA-GAACAATTTAACTTGTTATGCATGGCGGGTCAGAACAA
* *
12266745 CTTAATTGTTATGCATGGCGTGTCA
1 TTTAATTGTTATGCATGGCGGGTCA
12266770 TGACGTTTAA
Statistics
Matches: 246, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
61 1 0.00
62 189 0.77
63 55 0.22
64 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (63 bp):
TTTAATTGTTATGCATGGCGGGTCAGAACAATTTAACTTGTTATGCATGGCGGGTCAGAACAA
Found at i:12270330 original size:23 final size:23
Alignment explanation
Indices: 12270298--12270374 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
12270288 AAATTTTGTA
* *
12270298 ACACGCCATGCATTAGTGTCGTG
1 ACACGCCATGCATCAGTGTCATG
*
12270321 ACACGTCATGCATCAGTGTCATG
1 ACACGCCATGCATCAGTGTCATG
*
12270344 ACACGCCATGCATCACTGTCATG
1 ACACGCCATGCATCAGTGTCATG
*
12270367 ACATGCCA
1 ACACGCCA
12270375 ATCACTGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (23 bp):
ACACGCCATGCATCAGTGTCATG
Found at i:12270380 original size:20 final size:21
Alignment explanation
Indices: 12270331--12270382 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
12270321 ACACGTCATG
*
12270331 CATCAGTGTCATGACACGCCA
1 CATCACTGTCATGACACGCCA
*
12270352 TGCATCACTGTCATGACATGCCA
1 --CATCACTGTCATGACACGCCA
12270375 -ATCACTGT
1 CATCACTGT
12270383 AATTACTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 8 0.30
23 19 0.70
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (21 bp):
CATCACTGTCATGACACGCCA
Found at i:12270480 original size:55 final size:56
Alignment explanation
Indices: 12270410--12270635 Score: 253
Period size: 55 Copynumber: 4.1 Consensus size: 56
12270400 ACCAATAGCA
* * * * *
12270410 GTGACATGCTAAAAACCCAAAAAACT-AGTTAACCCACAACACACCAGGAACAACC
1 GTGACACGCCAAAAACCCAAAAAACTCAGTTAACCCACGACACCCCAGGAACAGCC
* * * *
12270465 GTGACACTCCAAAAACCC-ATAAATTCAGTTAACCCATGACACCCCAGGAACAGCC
1 GTGACACGCCAAAAACCCAAAAAACTCAGTTAACCCACGACACCCCAGGAACAGCC
* * * * *
12270520 GTGACACGCC-AAAACCCCATAAATTCAGTTAACACATGACACCCCAGGAACAGCC
1 GTGACACGCCAAAAACCCAAAAAACTCAGTTAACCCACGACACCCCAGGAACAGCC
** * * *
12270575 GTGACACGATAACAACCCAAAAAACT-AGTTAACCCACTACACGCCAGGAACAGCC
1 GTGACACGCCAAAAACCCAAAAAACTCAGTTAACCCACGACACCCCAGGAACAGCC
12270630 GTGACA
1 GTGACA
12270636 TGCTAAAATA
Statistics
Matches: 147, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
54 12 0.08
55 124 0.84
56 11 0.07
ACGTcount: A:0.41, C:0.33, G:0.14, T:0.12
Consensus pattern (56 bp):
GTGACACGCCAAAAACCCAAAAAACTCAGTTAACCCACGACACCCCAGGAACAGCC
Found at i:12271431 original size:41 final size:41
Alignment explanation
Indices: 12271386--12271467 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
12271376 AAAGTGCTTT
**
12271386 TCAAACTTAAATGTAAATCTTTTTGAAAATGCACAAATTCA
1 TCAAACTTAAATGTAAATCTTTTTGAAAAAACACAAATTCA
12271427 TCAAACTTAAATGTAAATCTTTTTGAAAAAACACAAATTCA
1 TCAAACTTAAATGTAAATCTTTTTGAAAAAACACAAATTCA
12271468 GAGGGAGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (41 bp):
TCAAACTTAAATGTAAATCTTTTTGAAAAAACACAAATTCA
Found at i:12272336 original size:12 final size:12
Alignment explanation
Indices: 12272319--12272343 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12272309 AAGAATTGAC
12272319 ATCTCAAAATAG
1 ATCTCAAAATAG
12272331 ATCTCAAAATAG
1 ATCTCAAAATAG
12272343 A
1 A
12272344 AGAATCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
ATCTCAAAATAG
Found at i:12274937 original size:2 final size:2
Alignment explanation
Indices: 12274930--12274964 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12274920 AATAAAATAC
*
12274930 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12274965 CAAAAAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12276272 original size:7 final size:7
Alignment explanation
Indices: 12276262--12276304 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
12276252 ATCAACATCG
12276262 AACACCC
1 AACACCC
12276269 AACACCC
1 AACACCC
12276276 AACACCC
1 AACACCC
12276283 AACACCC
1 AACACCC
12276290 AACACCC
1 AACACCC
12276297 AACACCC
1 AACACCC
12276304 A
1 A
12276305 TCCCATCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
AACACCC
Found at i:12287220 original size:35 final size:35
Alignment explanation
Indices: 12287178--12287262 Score: 118
Period size: 35 Copynumber: 2.4 Consensus size: 35
12287168 TTCAATAGGG
12287178 TCAAGTGTAACCTTTACAACATACCTTTTGCAGAA
1 TCAAGTGTAACCTTTACAACATACCTTTTGCAGAA
* * *
12287213 TCAAGTGTAA-CTTCTACAACTTGCCTTTTGCAGGA
1 TCAAGTGTAACCTT-TACAACATACCTTTTGCAGAA
*
12287248 TCAGGTGTAACCTTT
1 TCAAGTGTAACCTTT
12287263 GCCAAGACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
34 3 0.07
35 38 0.86
36 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (35 bp):
TCAAGTGTAACCTTTACAACATACCTTTTGCAGAA
Found at i:12289535 original size:47 final size:46
Alignment explanation
Indices: 12289477--12289658 Score: 215
Period size: 47 Copynumber: 3.9 Consensus size: 46
12289467 AATAAATTGA
* *
12289477 AATGAACAAATAATAAATCAAAGTAAAGATATTTTCATAAATCAAGT
1 AATGAACAAATAATAAATCAAAGTAAA-ATATTTTCCTAAGTCAAGT
* * *
12289524 AATGAATAAATAATAAGTCAAAGTAAAAATATTTTCCTAGGTCAAGT
1 AATGAACAAATAATAAATCAAAGT-AAAATATTTTCCTAAGTCAAGT
* *
12289571 AATGAACAAATAATAAATCAAAGTAAACAAATTTTCCTATGTCAAGT
1 AATGAACAAATAATAAATCAAAGTAAA-ATATTTTCCTAAGTCAAGT
* *
12289618 GCAA-GCAA-AAATAATGAATCAAGGTAAAATATTTTCCTAAG
1 --AATG-AACAAATAATAAATCAAAGTAAAATATTTTCCTAAG
12289659 CTAAATGCAA
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
46 3 0.03
47 88 0.75
48 22 0.19
49 4 0.03
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.27
Consensus pattern (46 bp):
AATGAACAAATAATAAATCAAAGTAAAATATTTTCCTAAGTCAAGT
Found at i:12289554 original size:23 final size:23
Alignment explanation
Indices: 12289484--12289554 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
12289474 TGAAATGAAC
*
12289484 AAATAATAAATCAAAGTAAAGAT
1 AAATAATAAATCAAAGTAAAAAT
** * *
12289507 ATTTTCATAAATC-AAGTAATGAAT
1 A-AATAATAAATCAAAGTAA-AAAT
*
12289531 AAATAATAAGTCAAAGTAAAAAT
1 AAATAATAAATCAAAGTAAAAAT
12289554 A
1 A
12289555 TTTTCCTAGG
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (23 bp):
AAATAATAAATCAAAGTAAAAAT
Found at i:12289595 original size:94 final size:93
Alignment explanation
Indices: 12289477--12289656 Score: 240
Period size: 94 Copynumber: 1.9 Consensus size: 93
12289467 AATAAATTGA
* *
12289477 AATGAACAAATAATAAATCAAAGTAAAGATATTTTCATAAATCAAGT-AATG-AATAAATAAT-A
1 AATGAACAAATAATAAATCAAAGTAAACAAATTTTCATAAATCAAGTCAA-GCAA-AAATAATGA
12289539 AGTCAAAGTAAAAATATTTTCCTAGGTCAAGT
64 A-TCAAAGT-AAAATATTTTCCTAGGTCAAGT
* **
12289571 AATGAACAAATAATAAATCAAAGTAAACAAATTTTCCTATGTCAAGTGCAAGCAAAAATAATGAA
1 AATGAACAAATAATAAATCAAAGTAAACAAATTTTCATAAATCAAGT-CAAGCAAAAATAATGAA
*
12289636 TCAAGGTAAAATATTTTCCTA
65 TCAAAGTAAAATATTTTCCTA
12289657 AGCTAAATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
94 56 0.74
95 14 0.18
96 6 0.08
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (93 bp):
AATGAACAAATAATAAATCAAAGTAAACAAATTTTCATAAATCAAGTCAAGCAAAAATAATGAAT
CAAAGTAAAATATTTTCCTAGGTCAAGT
Found at i:12292061 original size:21 final size:20
Alignment explanation
Indices: 12292021--12292069 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
12292011 TTCTGTGTAA
* **
12292021 AATCTATCGATAGATTGGACC
1 AATCTATCGATAAAGAGGA-C
12292042 AATCTATCGATAAAGAGGAC
1 AATCTATCGATAAAGAGGAC
*
12292062 AATTTATC
1 AATCTATC
12292070 AATACATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
AATCTATCGATAAAGAGGAC
Found at i:12299005 original size:70 final size:69
Alignment explanation
Indices: 12298868--12299024 Score: 174
Period size: 70 Copynumber: 2.2 Consensus size: 69
12298858 TTGATGTTGG
* * * * * *
12298868 GGTAAGAATACCACAAGACCAAGATGAGTGAATATGCACATTCTTGTCCTTTTCTAAAGCTCGGT
1 GGTAAGAATACCACAGGACCAAGATGAGTGAATATACACATTCTTATCCGTTTCTAAACCTCAGT
12298933 GTGAA
66 GTG-A
* * *
12298938 GGTAAAAATACCACAGGACCAAGATGGGTGAATGTAC-CTATTCTTATCCGTTTCTAAATCCT-A
1 GGTAAGAATACCACAGGACCAAGATGAGTGAATATACAC-ATTCTTATCCGTTTCTAAA-CCTCA
*
12299001 GTGTGG
64 GTGTGA
12299007 GAGTAAGAATACCACAGG
1 G-GTAAGAATACCACAGG
12299025 GTTTTATTGG
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
69 2 0.03
70 69 0.95
71 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (69 bp):
GGTAAGAATACCACAGGACCAAGATGAGTGAATATACACATTCTTATCCGTTTCTAAACCTCAGT
GTGA
Found at i:12301265 original size:15 final size:17
Alignment explanation
Indices: 12301232--12301274 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
12301222 CTATTTTGTG
12301232 TTAACATTATAACAATTA
1 TTAAC-TTATAACAATTA
12301250 -TAACTTATAA-AATTA
1 TTAACTTATAACAATTA
12301265 TTAA-TTATAA
1 TTAACTTATAA
12301275 TATATATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAACTTATAACAATTA
Found at i:12301537 original size:17 final size:17
Alignment explanation
Indices: 12301511--12301555 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
12301501 ATATATACAC
12301511 TAAA-ATACTTTAAATA
1 TAAATATACTTTAAATA
*
12301527 TATATATACTTTAAATA
1 TAAATATACTTTAAATA
12301544 TAAATATA-TTTA
1 TAAATATACTTTA
12301556 CTTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATACTTTAAATA
Found at i:12301601 original size:15 final size:16
Alignment explanation
Indices: 12301570--12301612 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
12301560 TTATTTTATG
12301570 TTAACATTATAAAAATTA
1 TTAAC-TTAT-AAAATTA
12301588 -TAACTTATAAAATTA
1 TTAACTTATAAAATTA
12301603 TTAA-TTATAA
1 TTAACTTATAA
12301613 TATATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAACTTATAAAATTA
Found at i:12310690 original size:13 final size:13
Alignment explanation
Indices: 12310672--12310696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12310662 TTTCAGAAAA
12310672 TTTATAAAATCAT
1 TTTATAAAATCAT
12310685 TTTATAAAATCA
1 TTTATAAAATCA
12310697 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:12312093 original size:19 final size:19
Alignment explanation
Indices: 12312069--12312106 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12312059 CTGCCAAACC
*
12312069 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
12312088 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
12312107 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:12315763 original size:12 final size:12
Alignment explanation
Indices: 12315748--12315785 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
12315738 ATGATTTTCC
*
12315748 CTTCTCTTTTTT
1 CTTCTCTGTTTT
12315760 CTTCTCTGTTTT
1 CTTCTCTGTTTT
*
12315772 CTTCTATGTTTT
1 CTTCTCTGTTTT
12315784 CT
1 CT
12315786 GTTCTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.24, G:0.05, T:0.68
Consensus pattern (12 bp):
CTTCTCTGTTTT
Found at i:12315799 original size:24 final size:24
Alignment explanation
Indices: 12315742--12315800 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
12315732 TCTTAGATGA
* * *
12315742 TTTTCCCTTCTCTTTTTTCTTCTC
1 TTTTTCCTTCTATGTTTTCTTCTC
12315766 TGTTTT-CTTCTATGTTTTCTGT-TC
1 T-TTTTCCTTCTATGTTTTCT-TCTC
12315790 TTTTTCCTTCT
1 TTTTTCCTTCT
12315801 GCGATTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 4 0.14
24 21 0.72
25 4 0.14
ACGTcount: A:0.02, C:0.25, G:0.05, T:0.68
Consensus pattern (24 bp):
TTTTTCCTTCTATGTTTTCTTCTC
Found at i:12316304 original size:21 final size:21
Alignment explanation
Indices: 12316264--12316305 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12316254 AGACAGAATG
* * *
12316264 CTCTTAGTTGATTAAGTGCCT
1 CTCTTAGTCGACTAAATGCCT
12316285 CTCTTAGTCGACTAAATGCCT
1 CTCTTAGTCGACTAAATGCCT
12316306 ATTGTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (21 bp):
CTCTTAGTCGACTAAATGCCT
Found at i:12321416 original size:11 final size:11
Alignment explanation
Indices: 12321396--12321462 Score: 118
Period size: 11 Copynumber: 6.2 Consensus size: 11
12321386 AACGGTGAAA
12321396 TTCA-CAAGCT
1 TTCACCAAGCT
12321406 TTCACCAAGCT
1 TTCACCAAGCT
*
12321417 TTCACTAAGCT
1 TTCACCAAGCT
12321428 TTCACCAAGCT
1 TTCACCAAGCT
12321439 TTCACCAAGCT
1 TTCACCAAGCT
12321450 TTCACCAAGCT
1 TTCACCAAGCT
12321461 TT
1 TT
12321463 TATAATGGCT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
10 4 0.07
11 50 0.93
ACGTcount: A:0.27, C:0.33, G:0.09, T:0.31
Consensus pattern (11 bp):
TTCACCAAGCT
Found at i:12324225 original size:21 final size:21
Alignment explanation
Indices: 12324183--12324225 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12324173 TAAGTCATGT
*
12324183 GTTGCTTAAACTAGTTCCCAA
1 GTTGCTTAAACTAGTGCCCAA
*
12324204 GTTGCTT-AACTAGATGCTCAA
1 GTTGCTTAAACTAG-TGCCCAA
12324225 G
1 G
12324226 GTTCTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
GTTGCTTAAACTAGTGCCCAA
Found at i:12325329 original size:25 final size:25
Alignment explanation
Indices: 12325296--12325355 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
12325286 GTGGTGGCAA
*
12325296 CCACGTATATCAA-CTCGTGGCCTTG
1 CCACGTATAACAACCT-GTGGCCTTG
12325321 CCACGTATAACAACCTGTGGCCTTG
1 CCACGTATAACAACCTGTGGCCTTG
*
12325346 CCACATATAA
1 CCACGTATAA
12325356 TCACAAACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (25 bp):
CCACGTATAACAACCTGTGGCCTTG
Found at i:12328256 original size:21 final size:21
Alignment explanation
Indices: 12328206--12328256 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
12328196 AGAACCCTAG
*
12328206 GTGGAAAAATTCAAGGGAAAA
1 GTGGAAAAATTCAAGGAAAAA
12328227 GTGTG-AAAATTCAAGGAAACAA
1 GTG-GAAAAATTCAAGGAAA-AA
12328249 G-GGAAAAA
1 GTGGAAAAA
12328257 AAGGTAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.53, C:0.06, G:0.27, T:0.14
Consensus pattern (21 bp):
GTGGAAAAATTCAAGGAAAAA
Found at i:12332577 original size:2 final size:2
Alignment explanation
Indices: 12332538--12332569 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12332528 TATTATGTTG
*
12332538 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12332570 GAATATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12332686 original size:37 final size:37
Alignment explanation
Indices: 12332621--12332787 Score: 261
Period size: 37 Copynumber: 4.6 Consensus size: 37
12332611 GTTGAAGTGT
*
12332621 GGGAGTCCACACA-GATGATGTTGAAGTGTGCGAGTA
1 GGGAGTGCACACATGATGATGTTGAAGTGTGCGAGTA
12332657 GGGAGTGCACACATGATGATGTT-AGAGTGTGCGAGTA
1 GGGAGTGCACACATGATGATGTTGA-AGTGTGCGAGTA
*
12332694 -AGAGTGCACACATGATGATGTTGAAGTGTGCGAGTA
1 GGGAGTGCACACATGATGATGTTGAAGTGTGCGAGTA
12332730 GGGAGTGCACACATGATGATGTT-AGAGTGTGCGAGTA
1 GGGAGTGCACACATGATGATGTTGA-AGTGTGCGAGTA
*
12332767 AGGAGTGCACACATGATGATG
1 GGGAGTGCACACATGATGATG
12332788 ATATTGCATT
Statistics
Matches: 122, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
36 47 0.39
37 75 0.61
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.23
Consensus pattern (37 bp):
GGGAGTGCACACATGATGATGTTGAAGTGTGCGAGTA
Found at i:12332714 original size:73 final size:74
Alignment explanation
Indices: 12332622--12332787 Score: 309
Period size: 73 Copynumber: 2.3 Consensus size: 74
12332612 TTGAAGTGTG
*
12332622 GGAGTCCACACA-GATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAGAGTG
1 GGAGTGCACACATGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAGAGTG
12332686 TGCGAGTAA
66 TGCGAGTAA
12332695 -GAGTGCACACATGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAGAGTG
1 GGAGTGCACACATGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAGAGTG
12332759 TGCGAGTAA
66 TGCGAGTAA
12332768 GGAGTGCACACATGATGATG
1 GGAGTGCACACATGATGATG
12332788 ATATTGCATT
Statistics
Matches: 90, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
72 10 0.11
73 61 0.68
74 19 0.21
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.23
Consensus pattern (74 bp):
GGAGTGCACACATGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGATGATGTTAGAGTG
TGCGAGTAA
Found at i:12382750 original size:19 final size:20
Alignment explanation
Indices: 12382721--12382760 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
12382711 TCACTTATAA
12382721 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
12382741 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
12382760 A
1 A
12382761 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:12395782 original size:4 final size:4
Alignment explanation
Indices: 12395773--12395809 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
12395763 TTAATAATTT
12395773 AATA AATA AATA AAT- AA-A AATA AATA AATA CAATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA -AATA AA
12395810 AAAAGGTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 4 0.13
4 22 0.73
5 4 0.13
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:12395795 original size:14 final size:14
Alignment explanation
Indices: 12395776--12395802 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12395766 ATAATTTAAT
12395776 AAATAAATAAATAA
1 AAATAAATAAATAA
12395790 AAATAAATAAATA
1 AAATAAATAAATA
12395803 CAATAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:12395796 original size:18 final size:19
Alignment explanation
Indices: 12395773--12395811 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
12395763 TTAATAATTT
12395773 AATAAATAAATA-AATAAA
1 AATAAATAAATACAATAAA
12395791 AATAAATAAATACAATAAA
1 AATAAATAAATACAATAAA
12395810 AA
1 AA
12395812 AAGGTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (19 bp):
AATAAATAAATACAATAAA
Found at i:12399045 original size:40 final size:38
Alignment explanation
Indices: 12398953--12399055 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
12398943 ATAGTGCCCG
* * *
12398953 TGTGCACGATGTGGGGGAATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTGAT
* *
12398991 TGTGCACGATGTGGGGGGATGCACACGATGACTCTGGCT
1 TGTGCACGATGTGGGGGGATGCACACGATGACACT-GAT
12399030 ATGTGCACGATGTGGGGGGATGCACA
1 -TGTGCACGATGTGGGGGGATGCACA
12399056 TAAGTTGGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 31 0.53
39 2 0.03
40 25 0.43
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.22
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACACTGAT
Found at i:12411211 original size:2 final size:2
Alignment explanation
Indices: 12411204--12411259 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
12411194 AAAGGCCTAG
12411204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12411246 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
12411260 NNNNNNNNNN
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12422335 original size:23 final size:24
Alignment explanation
Indices: 12422295--12422344 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
12422285 TAAGTAGACC
*
12422295 TAAGGCGTAAATGAATGATGAAAA
1 TAAGGCGTAAATGAATGAAGAAAA
*
12422319 TAAGG-GTAAAATG-ATGAAGCAAA
1 TAAGGCGT-AAATGAATGAAGAAAA
12422342 TAA
1 TAA
12422345 AAATAATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.52, C:0.04, G:0.24, T:0.20
Consensus pattern (24 bp):
TAAGGCGTAAATGAATGAAGAAAA
Found at i:12423455 original size:83 final size:85
Alignment explanation
Indices: 12423354--12423511 Score: 241
Period size: 83 Copynumber: 1.9 Consensus size: 85
12423344 TTTAGTGATA
* * *
12423354 ATGATGACCCAACTATGTGC-ATGTGGGAGTGCACATGAGCTAATGATGACCCAGC-ATGTGCGT
1 ATGATGACCCAACTATGTGCGGTGT-GGAATGCACATGAGCTAATGATGACCCAGCTATGTGCGA
12423417 GT-GGGAGTGCGTATGAGTTG
65 GTGGGGAGTGCGTATGAGTTG
* *
12423437 ATGATGACCCAGCTATGTGCGGTGTGGAATGCACATGAGCTGATGATGACCCAGCTATGTGCGAG
1 ATGATGACCCAACTATGTGCGGTGTGGAATGCACATGAGCTAATGATGACCCAGCTATGTGCGAG
12423502 TGGGGAGTGC
66 TGGGGAGTGC
12423512 ACATGAGCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 47 0.70
84 12 0.18
85 8 0.12
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (85 bp):
ATGATGACCCAACTATGTGCGGTGTGGAATGCACATGAGCTAATGATGACCCAGCTATGTGCGAG
TGGGGAGTGCGTATGAGTTG
Found at i:12423475 original size:42 final size:42
Alignment explanation
Indices: 12423352--12423527 Score: 239
Period size: 42 Copynumber: 4.2 Consensus size: 42
12423342 TTTTTAGTGA
* *
12423352 TAATGATGACCCAACTATGTGCATGTGGGAGTGCACATGAGC
1 TAATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGC
** *
12423394 TAATGATGACCCAGC-ATGTGCGTGTGGGAGTGCGTATGAGT
1 TAATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGC
* *
12423435 TGATGATGACCCAGCTATGTGCG-GTGTGGAATGCACATGAGC
1 TAATGATGACCCAGCTATGTGCGTGTG-GGAGTGCACATGAGC
* *
12423477 TGATGATGACCCAGCTATGTGCGAGTGGGGAGTGCACATGAGC
1 TAATGATGACCCAGCTATGTGCGTGT-GGGAGTGCACATGAGC
12423520 TAATGATG
1 TAATGATG
12423528 GTGGGATGGT
Statistics
Matches: 118, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
41 39 0.33
42 55 0.47
43 23 0.19
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (42 bp):
TAATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGC
Found at i:12423920 original size:40 final size:40
Alignment explanation
Indices: 12423862--12423952 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
12423852 TTATTCTCCC
12423862 TGCAGCAAGAAACATTCTGTTTCT-GCTGCCTGTAA-CTCGT
1 TGCAGCAAGAAACATTCTGTTT-TGGCTGCCTG-AATCTCGT
* *
12423902 TGCAGCGAGAAACTTTCTGTTTTGGCTGCCTGAATCTCGT
1 TGCAGCAAGAAACATTCTGTTTTGGCTGCCTGAATCTCGT
12423942 TGCAGCAAGAA
1 TGCAGCAAGAA
12423953 TGCTTTCTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 3 0.07
40 43 0.93
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (40 bp):
TGCAGCAAGAAACATTCTGTTTTGGCTGCCTGAATCTCGT
Found at i:12430472 original size:74 final size:75
Alignment explanation
Indices: 12430373--12430526 Score: 240
Period size: 74 Copynumber: 2.0 Consensus size: 75
12430363 CACATAACGG
* *
12430373 TGATGGGGTTGTGGTGTGCGATGTGGGAGCACATACGATGATGAT-ATTTGCCATGTGCGGTGTG
1 TGATGGGGTTGTGGTGTGCGATGTGGGAGCACACACGATGATGATAATATGCCATGTGCGGTGTG
12430437 GGAGTGCACA
66 GGAGTGCACA
*
12430447 TGATGGGGTTGTGGTGTGC-AGTGTGGGAGTACACACGATGATGATGACATATGCCATGTGCGGT
1 TGATGGGGTTGTGGTGTGCGA-TGTGGGAGCACACACGATGATGAT-A-ATATGCCATGTGCGGT
12430511 GTGGGAGTGCACA
63 GTGGGAGTGCACA
12430524 TGA
1 TGA
12430527 GGATATTAGC
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
73 1 0.01
74 41 0.56
77 31 0.42
ACGTcount: A:0.20, C:0.12, G:0.40, T:0.27
Consensus pattern (75 bp):
TGATGGGGTTGTGGTGTGCGATGTGGGAGCACACACGATGATGATAATATGCCATGTGCGGTGTG
GGAGTGCACA
Found at i:12432486 original size:73 final size:73
Alignment explanation
Indices: 12432392--12432606 Score: 256
Period size: 73 Copynumber: 2.9 Consensus size: 73
12432382 AAGATGGTCA
* * *
12432392 GTTCAGAAACAGAGACAACTTAATCGACTAAGAAACATTGTTAGTCGACTAAGAGCTTACTGCCA
1 GTTCAGAAACAAAGACGACTTAATTGACTAAGAAACATTGTTAGTCGACTAAGAGCTTACTGCCA
*
12432457 GAAACTGG
66 GAAACTGC
* * *
12432465 GTTCAGAAACAAAGACGACTTAATTGACTAAG-AA-GTTCAGTTAGTCGATTAAGAGCCTACTGC
1 GTTCAGAAACAAAGACGACTTAATTGACTAAGAAACATT--GTTAGTCGACTAAGAGCTTACTGC
12432528 CAGAAACTGC
64 CAGAAACTGC
* * * * * * *
12432538 GTTCAAAAACATAGATGATTTAATTGACTAAGAAGCATAGTTAGTCGACTAAGAGCATT-CTGTC
1 GTTCAGAAACAAAGACGACTTAATTGACTAAGAAACATTGTTAGTCGACTAAGAGC-TTACTGCC
12432602 AGAAA
65 AGAAA
12432607 ATTTGAATTT
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
71 2 0.02
72 2 0.02
73 113 0.94
74 2 0.02
75 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (73 bp):
GTTCAGAAACAAAGACGACTTAATTGACTAAGAAACATTGTTAGTCGACTAAGAGCTTACTGCCA
GAAACTGC
Found at i:12442307 original size:20 final size:16
Alignment explanation
Indices: 12442269--12442300 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12442259 GATATTGAGC
12442269 TTGCATTTATTTATAT
1 TTGCATTTATTTATAT
12442285 TTGCATTTATTTATAT
1 TTGCATTTATTTATAT
12442301 ACTTTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TTGCATTTATTTATAT
Found at i:12468971 original size:15 final size:15
Alignment explanation
Indices: 12468947--12468979 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12468937 AATCAAAAAC
12468947 AAAACAAGAGC-AGA
1 AAAACAAGAGCAAGA
12468961 AAAATCAAGAGCAAGA
1 AAAA-CAAGAGCAAGA
12468977 AAA
1 AAA
12468980 GTGTTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.67, C:0.12, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAACAAGAGCAAGA
Found at i:12481391 original size:23 final size:23
Alignment explanation
Indices: 12481361--12481409 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
12481351 CAATTAATAT
*
12481361 CTATCTCTACCCTAGTAAACATG
1 CTATCTCTACCCTAATAAACATG
12481384 CTATCTCTACCCTAATAAACATG
1 CTATCTCTACCCTAATAAACATG
12481407 CTA
1 CTA
12481410 GAATGATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (23 bp):
CTATCTCTACCCTAATAAACATG
Found at i:12482976 original size:31 final size:31
Alignment explanation
Indices: 12482941--12483004 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
12482931 AAAGAACTTG
12482941 ATGATATTTCTTGTCAACAAAATAATGATAA
1 ATGATATTTCTTGTCAACAAAATAATGATAA
12482972 ATGATATTTCTTGTCAACAAAATAATGATAA
1 ATGATATTTCTTGTCAACAAAATAATGATAA
12483003 AT
1 AT
12483005 TGCACTAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (31 bp):
ATGATATTTCTTGTCAACAAAATAATGATAA
Found at i:12485943 original size:18 final size:18
Alignment explanation
Indices: 12485920--12485956 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12485910 ACTTGTCTAC
12485920 TAGCACTTCAAAACTCGG
1 TAGCACTTCAAAACTCGG
12485938 TAGCACTTCAAAACTCGG
1 TAGCACTTCAAAACTCGG
12485956 T
1 T
12485957 CTAGGCAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (18 bp):
TAGCACTTCAAAACTCGG
Found at i:12497597 original size:2 final size:2
Alignment explanation
Indices: 12497586--12497634 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
12497576 ACATAAAAGA
12497586 AT AT -T AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12497625 AT AT AT AT AT
1 AT AT AT AT AT
12497635 TGACATTAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12498978 original size:7 final size:7
Alignment explanation
Indices: 12498966--12498997 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
12498956 ATGACATATA
12498966 TATAATC
1 TATAATC
12498973 TATAATC
1 TATAATC
12498980 TATAATC
1 TATAATC
*
12498987 TATAATA
1 TATAATC
12498994 TATA
1 TATA
12498998 TAAAAGTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAATC
Found at i:12498985 original size:14 final size:14
Alignment explanation
Indices: 12498963--12498997 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12498953 CTGATGACAT
12498963 ATATATAATCTATA
1 ATATATAATCTATA
*
12498977 ATCTATAATCTATA
1 ATATATAATCTATA
12498991 ATATATA
1 ATATATA
12498998 TAAAAGTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATAATCTATA
Found at i:12499710 original size:335 final size:335
Alignment explanation
Indices: 12499100--12499711 Score: 885
Period size: 335 Copynumber: 1.8 Consensus size: 335
12499090 TTTTTTATTG
* ** *
12499100 AATTAATTTTTTTTACACCTTATGTAAAAAATAAATTATTTTTTATATTTGAAAGGTTTTTTTTA
1 AATTAATTTTTTTTACACCTTATGTAAAAAATAAATTACTTTCAACATTTGAAAGGTTTTTTTTA
** * * * *
12499165 TTTTTTTTATTTATTTTAATAAAAAATATTTAAAAATAATAAATTTTAATTTTTAGTGTTTAGAA
66 TTACTTTTATTTATTTTAATAAAAAATATTTAAAAACAATAAATTTTAACTTTTAATGCTTAGAA
* *
12499230 GATAGATTCATTTAATATTTATCAATTATAATTTAATATTATTTTTTGTTTATATTTTCTTATTC
131 GATAGATTCATTTAATATTTATCAATTATAATTTAATATTATTTTTTGTCTATATTCTCTTATTC
* * *
12499295 TGTATGAACCTAAATCTATAGTATATAGATATCTCTTTTATACTTAAATGTTTAAATTTCAATAA
196 TCTATCAACCTAAATCTATAATATATAGATATCTCTTTTATACTTAAATGTTTAAATTTCAATAA
*
12499360 ATATCCATACAATTCATCATATAAAAGTAAAATAATTGATTAGGTCAATTAATTGATATTTGTCA
261 ACATCCATACAATTCATCATATAAAAGTAAAATAATTGATTAGGTCAATTAATTGATATTTGTCA
12499425 TTCTTAATTA
326 TTCTTAATTA
* * * *
12499435 AATTAATTTTTTTTACACCTTATGTCAAAACTACATTGCTTTCAACATTT-AAAGGGTTTTCTTT
1 AATTAATTTTTTTTACACCTTATGTAAAAAATAAATTACTTTCAACATTTGAAA-GGTTTT-TTT
*
12499499 T-TTACTTTTATTTATTTTAGTATAAAAA-ATTTAAAAACAAT-AATTTCTAACTTTTAATGCTT
64 TATTACTTTTATTTATTTTAATA-AAAAATATTTAAAAACAATAAATTT-TAACTTTTAATGCTT
*
12499561 ATAAGATAGATTCATTTAATATTTATCAATTATAATTTAATATTATTTTTTGTCTATATTCTCTT
127 AGAAGATAGATTCATTTAATATTTATCAATTATAATTTAATATTATTTTTTGTCTATATTCTCTT
* * * *
12499626 ATTCTCTATCAACCTGAATCTATAATATATAGATATCTTTTTTGTA-TATGAATGTTTAAA-TTC
192 ATTCTCTATCAACCTAAATCTATAATATATAGATATCTCTTTTATACT-TAAATGTTTAAATTTC
*
12499689 TAATAAACATCCATCCAATTCAT
256 -AATAAACATCCATACAATTCAT
12499712 TGAACAAAAT
Statistics
Matches: 244, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
334 12 0.05
335 223 0.91
336 9 0.04
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (335 bp):
AATTAATTTTTTTTACACCTTATGTAAAAAATAAATTACTTTCAACATTTGAAAGGTTTTTTTTA
TTACTTTTATTTATTTTAATAAAAAATATTTAAAAACAATAAATTTTAACTTTTAATGCTTAGAA
GATAGATTCATTTAATATTTATCAATTATAATTTAATATTATTTTTTGTCTATATTCTCTTATTC
TCTATCAACCTAAATCTATAATATATAGATATCTCTTTTATACTTAAATGTTTAAATTTCAATAA
ACATCCATACAATTCATCATATAAAAGTAAAATAATTGATTAGGTCAATTAATTGATATTTGTCA
TTCTTAATTA
Found at i:12503154 original size:231 final size:231
Alignment explanation
Indices: 12502723--12503184 Score: 786
Period size: 231 Copynumber: 2.0 Consensus size: 231
12502713 TAAAAGTAAG
12502723 ATGTTTCAATTTCTTTCAATTTTTTTCAATTAAGTCTTCAATTGAATGACAAATGTCAATTCAAT
1 ATGTTTCAATTTCTTTCAATTTTTTTCAATTAAGTCTTCAATTGAATGACAAATGTCAATTCAAT
*
12502788 TAGAACTCCTTTTTATTTTTTTGACCTTTTGTTTTCCATTGAATTAATTTTTTTTACACTTATGC
66 TAGAACTCCTTTTTATTTTTTTGACCTTTCGTTTTCCATTGAATTAATTTTTTTTACACTTATGC
* *
12502853 CAAAAATAAGTTGTTTTTTATATTTGAAGGTTTTTTTTGTTTTTTACTTTTATTTATTTTAATAA
131 CAAAAATAAGTTGTTTTTGACATTTGAAGGTTTTTTTTGTTTTTTACTTTTATTTATTTTAATAA
12502918 AAAAATACTTAAAAACAATAATTTCTAACTTTTAAT
196 AAAAATACTTAAAAACAATAATTTCTAACTTTTAAT
* * * *
12502954 ATGTTTCAATTTCTTTCAATTTTTTTCAATTGAGTTTTCAATTGAATGTCAAGTGTC-ATTCAAT
1 ATGTTTCAATTTCTTTCAATTTTTTTCAATTAAGTCTTCAATTGAATGACAAATGTCAATTCAAT
*
12503018 TAGAACTCC-TTTTATTTTTTTGACCTTTCGTTTTCTATTGAATTAATTTTTTTTACACTTTATG
66 TAGAACTCCTTTTTATTTTTTTGACCTTTCGTTTTCCATTGAATTAATTTTTTTTACAC-TTATG
* *
12503082 TCAAAAATAAGTTGTTTTTGACATTTGAAAGGTTTTTTTTTTTTTTTTACTTTTATTTATTTTAA
130 CCAAAAATAAGTTGTTTTTGACATTTG-AAGG-TTTTTTTTGTTTTTTACTTTTATTTATTTTAA
12503147 T-AAAAAATACTTAAAAACAATAATTTCTAACTTTTAAT
193 TAAAAAAATACTTAAAAACAATAATTTCTAACTTTTAAT
12503185 GCTTAGAAGA
Statistics
Matches: 218, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
229 47 0.22
230 45 0.21
231 94 0.43
232 32 0.15
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (231 bp):
ATGTTTCAATTTCTTTCAATTTTTTTCAATTAAGTCTTCAATTGAATGACAAATGTCAATTCAAT
TAGAACTCCTTTTTATTTTTTTGACCTTTCGTTTTCCATTGAATTAATTTTTTTTACACTTATGC
CAAAAATAAGTTGTTTTTGACATTTGAAGGTTTTTTTTGTTTTTTACTTTTATTTATTTTAATAA
AAAAATACTTAAAAACAATAATTTCTAACTTTTAAT
Found at i:12516651 original size:52 final size:52
Alignment explanation
Indices: 12516589--12516700 Score: 197
Period size: 52 Copynumber: 2.2 Consensus size: 52
12516579 TCTTTGCTGT
* *
12516589 AGCGAGAAACAGGGCTGGTTTGTGCCTCCACCAGCCGAGAGTTTCTCCCTGC
1 AGCGAGAAACAGGGCTGGTTTGTGCCCCCACCACCCGAGAGTTTCTCCCTGC
*
12516641 AGCGAGAAACAGGGCTGGTTTGTGCCCCCACCACCCGAGAGTTTCTCGCTGC
1 AGCGAGAAACAGGGCTGGTTTGTGCCCCCACCACCCGAGAGTTTCTCCCTGC
12516693 AGCGAGAA
1 AGCGAGAA
12516701 TGCAGCGAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.21, C:0.30, G:0.29, T:0.19
Consensus pattern (52 bp):
AGCGAGAAACAGGGCTGGTTTGTGCCCCCACCACCCGAGAGTTTCTCCCTGC
Found at i:12519984 original size:34 final size:34
Alignment explanation
Indices: 12519946--12520022 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
12519936 TGGGATTATA
* *
12519946 ATTGAGTTGAGCATCTGAGAACATATATCTAAAT
1 ATTGAGTTGAGCATCCGAGAACATATATCCAAAT
*
12519980 ATTGAGGTGAGCATCCGAGAACATATATCCAAAT
1 ATTGAGTTGAGCATCCGAGAACATATATCCAAAT
12520014 ATTGGAGTT
1 ATT-GAGTT
12520023 CATAATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (34 bp):
ATTGAGTTGAGCATCCGAGAACATATATCCAAAT
Found at i:12520476 original size:31 final size:31
Alignment explanation
Indices: 12520352--12520504 Score: 116
Period size: 31 Copynumber: 4.9 Consensus size: 31
12520342 AAGTTGAAAC
** *
12520352 ACCAAAGTCGAGGCAAATACCCAATCCAAAG
1 ACCAAAGTCGAAACAAATACCAAATCCAAAG
* *
12520383 ATCAAAGTC-AAGACGAATACCAAATCCAAATG
1 ACCAAAGTCGAA-ACAAATACCAAATCCAAA-G
* * * * *
12520415 -CTAAAATTGAAACAAATAGCAAA-CTTAAAG
1 ACCAAAGTCGAAACAAATACCAAATC-CAAAG
*
12520445 ACCAAGGTCGAAAC-AATATCCAAATCCAAAG
1 ACCAAAGTCGAAACAAATA-CCAAATCCAAAG
* **
12520476 ACTAAAGTCTTAACAAATACCAAATCCAA
1 ACCAAAGTCGAAACAAATACCAAATCCAA
12520505 TGTTCAAAGT
Statistics
Matches: 92, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
30 7 0.08
31 77 0.84
32 8 0.09
ACGTcount: A:0.50, C:0.23, G:0.11, T:0.16
Consensus pattern (31 bp):
ACCAAAGTCGAAACAAATACCAAATCCAAAG
Found at i:12533054 original size:31 final size:31
Alignment explanation
Indices: 12533016--12533076 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
12533006 TGAAGAAAGA
12533016 TTCATTAAGTTTTTGCTCTAATACTGGCTAT
1 TTCATTAAGTTTTTGCTCTAATACTGGCTAT
*
12533047 TTCATTAAGTTTTTGCTCTAATCCTGGCTA
1 TTCATTAAGTTTTTGCTCTAATACTGGCTA
12533077 CGCATGGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (31 bp):
TTCATTAAGTTTTTGCTCTAATACTGGCTAT
Found at i:12544540 original size:48 final size:47
Alignment explanation
Indices: 12544481--12544626 Score: 202
Period size: 48 Copynumber: 3.0 Consensus size: 47
12544471 ACGAAAGGTT
* *
12544481 ATCAATATCCAAGTAGCATCCATCAGTAGTTAATACTAACAGAATGTC
1 ATCAATATCCAAGTA-CAACCATCAATAGTTAATACTAACAGAATGTC
*
12544529 ATCAATATCCAAGTACTAACCATCAATAGTTAATACTAACAAAATGTC
1 ATCAATATCCAAGTAC-AACCATCAATAGTTAATACTAACAGAATGTC
* * * *
12544577 ATCAATATCAAAGTACCAAACATCAACAGTTAATACTAACAGAATTTC
1 ATCAATATCCAAGTA-CAACCATCAATAGTTAATACTAACAGAATGTC
12544625 AT
1 AT
12544627 AAACAATTAA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 1 0.01
48 86 0.98
49 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27
Consensus pattern (47 bp):
ATCAATATCCAAGTACAACCATCAATAGTTAATACTAACAGAATGTC
Found at i:12546042 original size:62 final size:62
Alignment explanation
Indices: 12545945--12546068 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
12545935 ATGCAATAAA
*
12545945 ATGGTGTAAGATCCTAGTTCGAGAACTCTTGATGAAGCTTGCATAACTCCTGGAGGAGTACC
1 ATGGTGTAAGATCCTAGTTCGAGAACTCTTGATGAAGCTTGCATAACTCCTGGAGGAATACC
* * *
12546007 ATGGTGTAAGATCCTAGTTCGAGGACTCTTGATGAAGCTTGCATATCTCTTGGAGGAATACC
1 ATGGTGTAAGATCCTAGTTCGAGAACTCTTGATGAAGCTTGCATAACTCCTGGAGGAATACC
12546069 TTTCCTTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (62 bp):
ATGGTGTAAGATCCTAGTTCGAGAACTCTTGATGAAGCTTGCATAACTCCTGGAGGAATACC
Found at i:12548873 original size:31 final size:31
Alignment explanation
Indices: 12548835--12548902 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
12548825 CCAATAATCT
12548835 GCTCTTATGGGTGGTCTTTGACATATTTCCA
1 GCTCTTATGGGTGGTCTTTGACATATTTCCA
12548866 GCTCTTATGGGTGGTCTTTGACATATTTCCA
1 GCTCTTATGGGTGGTCTTTGACATATTTCCA
12548897 GCTCTT
1 GCTCTT
12548903 TGGAAGATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.43
Consensus pattern (31 bp):
GCTCTTATGGGTGGTCTTTGACATATTTCCA
Found at i:12557458 original size:2 final size:2
Alignment explanation
Indices: 12557451--12557492 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
12557441 ATGTTGATAC
12557451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
12557493 GTACTGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12557626 original size:35 final size:35
Alignment explanation
Indices: 12557587--12557665 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
12557577 AGTGTGGACA
* * *
12557587 ATGATATTGAAGTGTGTGAGTAGGGAGTGCACACG
1 ATGATATTGAAATGTGCGAATAGGGAGTGCACACG
* * *
12557622 ATGATATAGAAATGTGCGAATAGGTAGTGCACATG
1 ATGATATTGAAATGTGCGAATAGGGAGTGCACACG
12557657 ATGATATTG
1 ATGATATTG
12557666 CCTTGTGCGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.28
Consensus pattern (35 bp):
ATGATATTGAAATGTGCGAATAGGGAGTGCACACG
Found at i:12557673 original size:35 final size:36
Alignment explanation
Indices: 12557610--12557690 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 36
12557600 GTGTGAGTAG
*
12557610 GGAGTGCACACGATGATATAGAAATGTGCG-A-ATA
1 GGAGTGCACATGATGATATAGAAATGTGCGTACATA
* ***
12557644 GGTAGTGCACATGATGATATTGCCTTGTGCGTACA-A
1 GG-AGTGCACATGATGATATAGAAATGTGCGTACATA
12557680 GGAGTGCACAT
1 GGAGTGCACAT
12557691 TGGCTAAGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.05
35 32 0.82
36 4 0.10
37 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.25
Consensus pattern (36 bp):
GGAGTGCACATGATGATATAGAAATGTGCGTACATA
Found at i:12572403 original size:20 final size:20
Alignment explanation
Indices: 12572379--12572422 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
12572369 TATATAAATG
12572379 AAAAATATACATTTC-ATATCT
1 AAAAATA-A-ATTTCGATATCT
*
12572400 AAAAATAAATTTCGGTATCT
1 AAAAATAAATTTCGATATCT
12572420 AAA
1 AAA
12572423 TCATCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAATAAATTTCGATATCT
Found at i:12579119 original size:43 final size:43
Alignment explanation
Indices: 12579048--12579166 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
12579038 GTAATGACAT
* * * *
12579048 TGACTCGGTTATGTGCGAGTAGGAAGTGCGCATAAGTCGAG-GA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACTAG-GTGA
12579091 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACTAGGTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACTAGGTGA
* **
12579134 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCAT
12579167 GAGCTGGTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (43 bp):
TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACTAGGTGA
Done.