Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 120 of 311
Found at i:39932980 original size:93 final size:92
Alignment explanation
Indices: 39932716--39932980 Score: 377
Period size: 93 Copynumber: 2.8 Consensus size: 92
39932706 GGATATTTGA
* * **
39932716 GCATCTGAACTCGTTGAATTGAGTCCTAGTGCACTTATGGATGCGAACGTTCGAACTTGTTGAGT
1 GCATCTGAACTCGTTGAGTTGAGT-CTAGTTCACTTATGGATGCGAACGCCCGAACTTGTTGAGT
*
39932781 TGAGTCCGAGTTCATGAGATGTAACTAG
65 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * * *
39932809 GCATCTGAGCTCATTGAGTTGAGTCTGAGTTCGCTTATGGATGCGAATGCCCGAACTCGTTGAGT
1 GCATCTGAACTCGTTGAGTTGAGTCT-AGTTCACTTATGGATGCGAACGCCCGAACTTGTTGAGT
*
39932874 TGAGTCCGAGTTCGTGAGATGTAATTAG
65 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
39932902 GCATCCGAACTCGTTGAGTTGAGTCTAAGTTCACTTATGGATGCGAACGCCCGAGCTTATTGAGT
1 GCATCTGAACTCGTTGAGTTGAGTCT-AGTTCACTTATGGATGCGAACGCCCGAACTTGTTGAGT
39932967 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
39932981 CTTATGGGCG
Statistics
Matches: 151, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
92 2 0.01
93 149 0.99
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (92 bp):
GCATCTGAACTCGTTGAGTTGAGTCTAGTTCACTTATGGATGCGAACGCCCGAACTTGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39938599 original size:46 final size:46
Alignment explanation
Indices: 39938548--39938675 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
39938538 ATTTGAGCAT
* *
39938548 CCGAACTCGTTGAGTTGGGTCCGAGTTCGCTTATGGATGCGAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAAAGC
*
39938594 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAAAGC
* * *
39938640 CCGAGCTCATTGAGTTGAGTCTGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
39938676 GCGGGTTACA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAAAGC
Found at i:39939049 original size:25 final size:25
Alignment explanation
Indices: 39939021--39939071 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
39939011 TGAGAATGAT
*
39939021 TATCTATTGGAGTGGCTAATCGAGA
1 TATCCATTGGAGTGGCTAATCGAGA
39939046 TATCCATTGGAGTGGCTAATCGAGA
1 TATCCATTGGAGTGGCTAATCGAGA
39939071 T
1 T
39939072 TATATTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (25 bp):
TATCCATTGGAGTGGCTAATCGAGA
Found at i:39959480 original size:33 final size:33
Alignment explanation
Indices: 39959387--39959484 Score: 92
Period size: 34 Copynumber: 2.9 Consensus size: 33
39959377 GTTTTAGTTA
* * *
39959387 GGGCCTTAGCCCATTTCAGAATTAGAAACAGTGT
1 GGGCCTAAGCCCATTTCAGAATCAG-TACAGTGT
* * *
39959421 GGGCTTGAGCCCATTTCA-ATAACAGTATCAGTG-
1 GGGCCTAAGCCCATTTCAGA-ATCAGTA-CAGTGT
*
39959454 GGGCCTAAGCCCATTACAGAATCAGTACAGT
1 GGGCCTAAGCCCATTTCAGAATCAGTACAGT
39959485 ATGTAATCAG
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
32 4 0.08
33 23 0.44
34 25 0.48
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (33 bp):
GGGCCTAAGCCCATTTCAGAATCAGTACAGTGT
Found at i:39971952 original size:42 final size:42
Alignment explanation
Indices: 39971893--39971977 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
39971883 AATCTAAATT
39971893 ACATAGTGGAATAGAACCATACTTGTGGGCAAGCATGGGCTA
1 ACATAGTGGAATAGAACCATACTTGTGGGCAAGCATGGGCTA
39971935 ACATAGTGGAATAGAACCATACTTGTGGGCAAGCATGGGCTA
1 ACATAGTGGAATAGAACCATACTTGTGGGCAAGCATGGGCTA
39971977 A
1 A
39971978 GTAGGGGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (42 bp):
ACATAGTGGAATAGAACCATACTTGTGGGCAAGCATGGGCTA
Found at i:39972281 original size:12 final size:12
Alignment explanation
Indices: 39972264--39972293 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39972254 AAATTTGAAT
*
39972264 ATTATTTTTAGG
1 ATTATTGTTAGG
39972276 ATTATTGTTAGG
1 ATTATTGTTAGG
39972288 ATTATT
1 ATTATT
39972294 ATATTAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (12 bp):
ATTATTGTTAGG
Found at i:39975850 original size:43 final size:43
Alignment explanation
Indices: 39975789--39975872 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
39975779 TGTGATTTCG
*
39975789 ATATGTGTTTACGAGTAAGACC-CTGTCTGGGACAG-TGGCATCA
1 ATATGTGGTTACGAGTAAGACCAC-GTCTGGGAC-GTTGGCATCA
39975832 ATATGTGGTTAC-ATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATATGTGGTTACGA-GTAAGACCACGTCTGGGACGTTGGCAT
39975873 TGTACGATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 2 0.05
43 34 0.92
44 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (43 bp):
ATATGTGGTTACGAGTAAGACCACGTCTGGGACGTTGGCATCA
Found at i:39977237 original size:25 final size:25
Alignment explanation
Indices: 39977192--39977239 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
39977182 TGGTGCAATG
* *
39977192 TATTAAATATTTATATGTGATTACT
1 TATTAAATATATATATATGATTACT
39977217 TATTAAAT-TATATAATATGATTA
1 TATTAAATATATAT-ATATGATTA
39977240 AATGATTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (25 bp):
TATTAAATATATATATATGATTACT
Found at i:39979872 original size:18 final size:18
Alignment explanation
Indices: 39979849--39979885 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39979839 AACCTCAATG
39979849 TCATGGTTTCATATTCCA
1 TCATGGTTTCATATTCCA
39979867 TCATGGTTTCATATTCCA
1 TCATGGTTTCATATTCCA
39979885 T
1 T
39979886 ACATACATCA
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:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (18 bp):
TCATGGTTTCATATTCCA
Found at i:39983124 original size:41 final size:41
Alignment explanation
Indices: 39983043--39983226 Score: 181
Period size: 41 Copynumber: 4.5 Consensus size: 41
39983033 ACCTGATATA
* ** * *
39983043 ATACATCGGCACGAAGCCTGCTAGGCTTTAGGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCTCAAAGCCTAATAAT
*
39983084 ATACACCAGCACGAAGCCTGCTAGGCTCAAAGCCTAATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCTCAAAGCCTAATAAT
* * * *
39983125 ATACACCGGCTCAAAGCCTGCTAGACACAAAGCCTAATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCTCAAAGCCTAATAAT
* * * ** * * * *
39983166 CTTCATCGGCAAAAAGCCTGGTAAGCAT-AAGGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGC-TCAAAGCCTAATAAT
39983207 ATACACCGGCACGAAGCCTG
1 ATACACCGGCACGAAGCCTG
39983227 TTGTAACACC
Statistics
Matches: 115, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
41 115 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (41 bp):
ATACACCGGCACGAAGCCTGCTAGGCTCAAAGCCTAATAAT
Found at i:39984899 original size:27 final size:27
Alignment explanation
Indices: 39984868--39985062 Score: 277
Period size: 27 Copynumber: 7.2 Consensus size: 27
39984858 TAATTTACAA
*
39984868 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
39984895 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
39984922 AATT-CTTGAAATACCCCTGTAGGGTAG
1 AATTAC-TGAAATACCCCTGTAGGGTAG
39984949 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
39984976 AATTACCGAAATACCCTTATAGGGTAAG
1 AATTACTGAAATACCCCTGTAGGGT-AG
*
39985004 AA-TACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
39985030 AATTACTGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
39985057 AATTAC
1 AATTAC
39985063 CATTTTGCCC
Statistics
Matches: 153, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
26 5 0.03
27 143 0.93
28 5 0.03
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:39985629 original size:22 final size:22
Alignment explanation
Indices: 39985577--39985640 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
39985567 GCCAATTATT
* *
39985577 CTGATTATAGCTTTGCGCCAAC
1 CTGATTATGGCTTTGTGCCAAC
*
39985599 CT-ACATATGGCTTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
39985621 CTGATTATGG-TTGTGTGCCA
1 CTGATTATGGCTT-TGTGCCA
39985641 TTATTGTGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 3 0.09
22 31 0.89
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:39985682 original size:20 final size:20
Alignment explanation
Indices: 39985642--39985682 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39985632 TGTGTGCCAT
* *
39985642 TATTGTGGGCTTCGTATCGA
1 TATTGTAGGCTTCGTACCGA
*
39985662 TATTGTAGGCTTCGTGCCGA
1 TATTGTAGGCTTCGTACCGA
39985682 T
1 T
39985683 TATAGACCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (20 bp):
TATTGTAGGCTTCGTACCGA
Found at i:39985756 original size:27 final size:26
Alignment explanation
Indices: 39985726--39985807 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
39985716 ATTCTGTTAA
*
39985726 GTGGCTTTGCCACATTATCTGATTCTG
1 GTGGCTTTGCCACAATATCTG-TTCTG
39985753 GTGG-TTCTGCCACAATATCTGTATCTG
1 GTGGCTT-TGCCACAATATCTGT-TCTG
* * *
39985780 GTGACTCTGTCACAATATCTGTTCTG
1 GTGGCTTTGCCACAATATCTGTTCTG
39985806 GT
1 GT
39985808 AGCCAAGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.19
27 38 0.79
28 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (26 bp):
GTGGCTTTGCCACAATATCTGTTCTG
Found at i:39985933 original size:6 final size:6
Alignment explanation
Indices: 39985924--39985998 Score: 73
Period size: 6 Copynumber: 12.3 Consensus size: 6
39985914 TTGCATTCAC
* *
39985924 ATTCTG ATTCTG ATTCTG ATTCTG ATTCT- ATCACCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
39985973 ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
39985999 AATGTTTCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
5 3 0.05
6 48 0.86
7 3 0.05
8 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:39989055 original size:21 final size:22
Alignment explanation
Indices: 39989026--39989070 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
39989016 CAGACAGATT
39989026 ACCAGCCCA-ATCCAACCAACAC
1 ACCAGCCCATA-CCAACCAACAC
*
39989048 ACCA-CCCATACCAACCAGCAC
1 ACCAGCCCATACCAACCAACAC
39989069 AC
1 AC
39989071 TATGTGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.40, C:0.51, G:0.04, T:0.04
Consensus pattern (22 bp):
ACCAGCCCATACCAACCAACAC
Found at i:39989632 original size:41 final size:40
Alignment explanation
Indices: 39989575--39989694 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 40
39989565 AAGTCACTGA
* *
39989575 TGGATCCACTGTCGTCAAGCAACCATGCAATCCTTAATCGG
1 TGGATCCAC-GTCGTCAAGCAACCATGCGATCCTCAATCGG
* **
39989616 TGGATCCACAGTCGTCAAACAACCACACGATCCTCAATCGG
1 TGGATCCAC-GTCGTCAAGCAACCATGCGATCCTCAATCGG
*
39989657 TGGATCCACGATTGTCAAGCAACCATGCGATCCTCAAT
1 TGGATCCACG-TCGTCAAGCAACCATGCGATCCTCAAT
39989695 TTCTTCCTCC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 1 0.01
41 67 0.99
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (40 bp):
TGGATCCACGTCGTCAAGCAACCATGCGATCCTCAATCGG
Found at i:39989975 original size:27 final size:27
Alignment explanation
Indices: 39989945--39989996 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39989935 GGGTGTTTTG
39989945 GTAAATCTACAAACCAAGGGTATTTCA
1 GTAAATCTACAAACCAAGGGTATTTCA
* * * *
39989972 GTAATTTTGCAAACCAATGGTATTT
1 GTAAATCTACAAACCAAGGGTATTT
39989997 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
GTAAATCTACAAACCAAGGGTATTTCA
Found at i:39990002 original size:27 final size:27
Alignment explanation
Indices: 39989954--39990328 Score: 223
Period size: 27 Copynumber: 13.9 Consensus size: 27
39989944 GGTAAATCTA
* * *
39989954 CAAACCAAGGGTATTTCAGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTC
* * * *
39989981 CAAACCAATGGTATTTTTGTAATTTTT
1 CAAATCAAGGGTATTTCTGTAATTTTC
* * *
39990008 AAAAGTCAAAGGTATTTCTGTAATTTTG
1 CAAA-TCAAGGGTATTTCTGTAATTTTC
*
39990036 TAAATC-AGGGCTATTTCTGTAATTTTC
1 CAAATCAAGGG-TATTTCTGTAATTTTC
*
39990063 CAAATCAAGGGTATTTCGGTAATTTTC
1 CAAATCAAGGGTATTTCTGTAATTTTC
* *
39990090 CAAATCGAGGGTATTTCGGTAATTTT-
1 CAAATCAAGGGTATTTCTGTAATTTTC
* ** *
39990116 AAAAGTTGAGGGTATTTC-GATAATTTTA
1 CAAA-TCAAGGGTATTTCTG-TAATTTTC
* *
39990144 CAAGATGAA-GGTATTTC-GATAATTTTA
1 CAA-ATCAAGGGTATTTCTG-TAATTTTC
* ** * *
39990171 TAGGTCGAGGGTATTTCGGTAA-TTTC
1 CAAATCAAGGGTATTTCTGTAATTTTC
* *
39990197 ACAAATCAGGGGTATTT-TGGTAATTTTA
1 -CAAATCAAGGGTATTTCT-GTAATTTTC
* *
39990225 CAAA-CTAGGGGTATTT-TGGTAATTTTT
1 CAAATC-AAGGGTATTTCT-GTAATTTTC
* * *
39990252 CTAATCGAGGGTATTT-TGGTAATTTTA
1 CAAATCAAGGGTATTTCT-GTAATTTTC
* * * *
39990279 TAAACCAAGGGTA-TTCAGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTC
* * *
39990305 TAAACCAAGGGTATTTCAGTAATT
1 CAAATCAAGGGTATTTCTGTAATT
39990329 CTACCTTATA
Statistics
Matches: 288, Mismatches: 44, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
26 36 0.12
27 216 0.75
28 35 0.12
29 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTGTAATTTTC
Found at i:39990095 original size:54 final size:54
Alignment explanation
Indices: 39989952--39990328 Score: 272
Period size: 54 Copynumber: 7.0 Consensus size: 54
39989942 TTGGTAAATC
* * * * * * *
39989952 TACAAACCAAGGGTATTTCAGTAATTTTGCAAACCAATGGTATTTTTGTAATTTT
1 TACAAATCAAGGGTATTTCGGTAATTTTCCAAATCGAGGGTATTTCTGTAA-TTT
* * **
39990007 TA-AAAGTCAAAGGTATTTCTGTAATTTTGTAAATC-AGGGCTATTTCTGTAATTT
1 TACAAA-TCAAGGGTATTTCGGTAATTTTCCAAATCGAGGG-TATTTCTGTAATTT
* *
39990061 TCCAAATCAAGGGTATTTCGGTAATTTTCCAAATCGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTCCAAATCGAGGGTATTTCTGTAATTT
** * * *
39990115 TA-AAAGTTGAGGGTATTTCGATAATTTTACAAGAT-GAAGGTATTTC-GATAATTT
1 TACAAA-TCAAGGGTATTTCGGTAATTTTCCAA-ATCGAGGGTATTTCTG-TAATTT
* ** *
39990169 TATAGGTCGAGGGTATTTCGGTAA-TTTCACAAATC-AGGGGTATTT-TGGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTC-CAAATCGA-GGGTATTTCT-GTAATTT
* * * *
39990223 TACAAA-CTAGGGGTATTTTGGTAATTTTTCTAATCGAGGGTATTT-TGGTAATTT
1 TACAAATC-AAGGGTATTTCGGTAATTTTCCAAATCGAGGGTATTTCT-GTAATTT
* * * ** * * *
39990277 TATAAACCAAGGGTA-TTCAGTAATTTTGTAAACCAAGGGTATTTCAGTAATT
1 TACAAATCAAGGGTATTTCGGTAATTTTCCAAATCGAGGGTATTTCTGTAATT
39990329 CTACCTTATA
Statistics
Matches: 261, Mismatches: 43, Indels: 38
0.76 0.13 0.11
Matches are distributed among these distances:
53 39 0.15
54 170 0.65
55 52 0.20
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTCGGTAATTTTCCAAATCGAGGGTATTTCTGTAATTT
Found at i:39990140 original size:81 final size:79
Alignment explanation
Indices: 39989961--39990328 Score: 291
Period size: 81 Copynumber: 4.6 Consensus size: 79
39989951 CTACAAACCA
* * * ** * * *
39989961 AGGGTATTTC-AGTAATTTTGCAAACCAATGGTATTTTTGTAATTTTTAAAAGTCAAAGGTATTT
1 AGGGTATTTCGA-TAATTTTACAAATCAAGGGTATTTCGGTAATTTTTCAAA-TCGAGGGTATTT
* *
39990025 CTGTAATTTTGTAAATC
64 CGGTAATTTT-AAAATC
* *
39990042 AGGGCTATTTCTG-TAATTTTCCAAATCAAGGGTATTTCGGTAATTTTCCAAATCGAGGGTATTT
1 AGGG-TATTTC-GATAATTTTACAAATCAAGGGTATTTCGGTAATTTTTCAAATCGAGGGTATTT
*
39990106 CGGTAATTTTAAAAGTTG
64 CGGTAATTTTAAAA--TC
* * **
39990124 AGGGTATTTCGATAATTTTACAAGATGAA-GGTATTTCGATAATTTTAT-AGGTCGAGGGTATTT
1 AGGGTATTTCGATAATTTTACAA-ATCAAGGGTATTTCGGTAATTTT-TCAAATCGAGGGTATTT
*
39990187 CGGTAATTTCACAAATC
64 CGGTAATTTTA-AAATC
* * * * *
39990204 AGGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTTCTAATCGAGGGTATTT
1 A-GGGTATTTCGATAATTTTACAAATC-AAGGGTATTTCGGTAATTTTTCAAATCGAGGGTATTT
* *
39990268 TGGTAATTTTATAAACC
64 CGGTAATTTTA-AAATC
** * *
39990285 AAGGGTA-TTC-AGTAATTTTGTAAACCAAGGGTATTTCAGTAATT
1 -AGGGTATTTCGA-TAATTTTACAAATCAAGGGTATTTCGGTAATT
39990329 CTACCTTATA
Statistics
Matches: 231, Mismatches: 40, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
80 36 0.16
81 144 0.62
82 51 0.22
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (79 bp):
AGGGTATTTCGATAATTTTACAAATCAAGGGTATTTCGGTAATTTTTCAAATCGAGGGTATTTCG
GTAATTTTAAAATC
Found at i:39990341 original size:26 final size:26
Alignment explanation
Indices: 39990312--39990392 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
39990302 TTGTAAACCA
* *
39990312 AGGGTATTTCAGTAATTCTACCTTAT
1 AGGGTATTTCAGTAATTCTACCCTAC
* *
39990338 AGGGCATTTTAGTAATTCTACCCTAC
1 AGGGTATTTCAGTAATTCTACCCTAC
* *
39990364 AGGGGTATTTCAGTAATACTAGCCTAC
1 A-GGGTATTTCAGTAATTCTACCCTAC
39990391 AG
1 AG
39990393 ATATGAGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 24 0.52
27 22 0.48
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
AGGGTATTTCAGTAATTCTACCCTAC
Found at i:39990389 original size:27 final size:26
Alignment explanation
Indices: 39990313--39990392 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 26
39990303 TGTAAACCAA
*
39990313 GGGTATTTCAGTAATTCTACCTTATA-
1 GGGTATTTCAGTAATTCTACC-TACAG
* *
39990339 GGGCATTTTAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTA-CCTACAG
*
39990366 GGGTATTTCAGTAATACTAGCCTACAG
1 GGGTATTTCAGTAATTCTA-CCTACAG
39990393 ATATGAGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.44
27 25 0.56
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
GGGTATTTCAGTAATTCTACCTACAG
Found at i:39991010 original size:15 final size:17
Alignment explanation
Indices: 39990990--39991021 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39990980 TCATTTCATT
39990990 TATAT-AAT-CATAAAA
1 TATATAAATGCATAAAA
39991005 TATATAAATGCATAAAA
1 TATATAAATGCATAAAA
39991022 AGATTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 3 0.20
17 7 0.47
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
TATATAAATGCATAAAA
Found at i:39991172 original size:17 final size:17
Alignment explanation
Indices: 39991150--39991188 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
39991140 AATTTAGATG
*
39991150 TAAAATATACTA-AAATA
1 TAAAATAAACTAGAAA-A
39991167 TAAAATAAACTAGAAAA
1 TAAAATAAACTAGAAAA
39991184 TAAAA
1 TAAAA
39991189 ATGGAGTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAAACTAGAAAA
Found at i:39991947 original size:36 final size:34
Alignment explanation
Indices: 39991907--39991980 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
39991897 AATGAAATTC
*
39991907 TAAATTATTAAATTAATAATTTATTTTAATTATACT
1 TAAATTATTAAATTAATAATTT-TTCTAATTA-ACT
* *
39991943 T-AA--ATTAAATTATTAATTTTTCTATTTAACT
1 TAAATTATTAAATTAATAATTTTTCTAATTAACT
39991974 TAAATTA
1 TAAATTA
39991981 AATAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
31 4 0.12
32 9 0.28
33 15 0.47
34 1 0.03
35 2 0.06
36 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (34 bp):
TAAATTATTAAATTAATAATTTTTCTAATTAACT
Found at i:39991978 original size:31 final size:33
Alignment explanation
Indices: 39991913--39992020 Score: 118
Period size: 31 Copynumber: 3.4 Consensus size: 33
39991903 ATTCTAAATT
*
39991913 ATTAAATTAATAATTTATTTTAATTATACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
* *
39991946 ATTAAATTATTAATTT-TTCTATTTA-ACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
** *
39991977 ATTAAA-TAATAATAAATTCTAAATATAC-TAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
39992008 ATATAAA-TAATAA
1 AT-TAAATTAATAA
39992021 CTAAATAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
30 6 0.09
31 24 0.38
32 19 0.30
33 15 0.23
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTAAATTAATAATTTATTCTAATTATACTTAA
Found at i:39992016 original size:26 final size:28
Alignment explanation
Indices: 39991979--39992047 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 28
39991969 TAACTTAAAT
*
39991979 TAAATAATAATAAAT-TCTAAAT-AT-AC
1 TAAATAA-AATAAATAACTAAATAATAAC
39992005 TAAATATAAAT-AATAACTAAATAATAAC
1 TAAATA-AAATAAATAACTAAATAATAAC
39992033 TAAATAGAAATAAAT
1 TAAATA-AAATAAAT
39992048 GTAACGGCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 3 0.08
26 15 0.42
27 3 0.08
28 12 0.33
29 3 0.08
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (28 bp):
TAAATAAAATAAATAACTAAATAATAAC
Found at i:39992027 original size:11 final size:11
Alignment explanation
Indices: 39992011--39992038 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39992001 ATACTAAATA
39992011 TAAATAATAAC
1 TAAATAATAAC
39992022 TAAATAATAAC
1 TAAATAATAAC
39992033 TAAATA
1 TAAATA
39992039 GAAATAAATG
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:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAATAATAAC
Found at i:39993129 original size:19 final size:20
Alignment explanation
Indices: 39993105--39993142 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39993095 GGTACCACCA
39993105 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39993124 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39993143 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39993437 original size:46 final size:46
Alignment explanation
Indices: 39993370--39993491 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
39993360 CGCCCCTAAG
* * * *
39993370 TGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
* *
39993416 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
39993462 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
39993492 TGCTCAACCA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
Found at i:39993510 original size:46 final size:45
Alignment explanation
Indices: 39993368--39993510 Score: 128
Period size: 46 Copynumber: 3.1 Consensus size: 45
39993358 CCCGCCCCTA
* * ** *
39993368 AGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
* ** **
39993413 AAATGAACTCGGACTCAACTCAACGAGTTCGGACATT-TGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
*
39993459 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTC-ACCATCCT
39993506 AGTGA
1 AGTGA
39993511 CATGTCACTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
46 77 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCCT
Found at i:39993947 original size:30 final size:30
Alignment explanation
Indices: 39993913--39993972 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39993903 ATTTAATACG
39993913 AACTTTAAAAAAATTACACTTTTACCCCTA
1 AACTTTAAAAAAATTACACTTTTACCCCTA
*** * *
39993943 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTACCCCTA
39993973 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTACCCCTA
Found at i:39994807 original size:13 final size:13
Alignment explanation
Indices: 39994785--39994822 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
39994775 ATATTACAAT
39994785 AAAA-AATATATA
1 AAAATAATATATA
39994797 AAAATAATATATA
1 AAAATAATATATA
39994810 AATAGATAATATA
1 AA-A-ATAATATA
39994823 ATAATAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 1 0.04
15 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAATAATATATA
Found at i:39994808 original size:15 final size:16
Alignment explanation
Indices: 39994782--39994828 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
39994772 AGGATATTAC
39994782 AATAAA-AA-ATATAT
1 AATAAATAATATATAT
39994796 AA-AAATAATATATA-
1 AATAAATAATATATAT
*
39994810 AATAGATAATATA-AT
1 AATAAATAATATATAT
39994825 AATA
1 AATA
39994829 GATAGAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.11
14 7 0.25
15 18 0.64
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AATAAATAATATATAT
Found at i:39994823 original size:20 final size:19
Alignment explanation
Indices: 39994800--39994894 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 19
39994790 ATATATAAAA
39994800 ATAATATATAAATAGATAAT
1 ATAATATATAAATAGA-AAT
* *
39994820 ATAATA-ATAGATAGAATAAC
1 ATAATATATAAATAG-A-AAT
* *
39994840 AAAATAAATAATATAGAAAT
1 ATAATATATAA-ATAGAAAT
*
39994860 ATAGATTTATAAATCA-AAAT
1 ATA-ATATATAAAT-AGAAAT
*
39994880 ATATTAATATAAATA
1 ATAAT-ATATAAATA
39994895 TAAGAATATT
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
19 9 0.15
20 35 0.59
21 11 0.19
22 4 0.07
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAATATATAAATAGAAAT
Found at i:39994829 original size:15 final size:15
Alignment explanation
Indices: 39994789--39994832 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
39994779 TACAATAAAA
39994789 AATATATAAA-A-AT
1 AATATATAAATAGAT
39994802 AATATATAAATAGAT
1 AATATATAAATAGAT
39994817 AATATA-ATAATAGAT
1 AATATATA-AATAGAT
39994832 A
1 A
39994833 GAATAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.36
14 2 0.07
15 16 0.57
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
AATATATAAATAGAT
Found at i:39995395 original size:27 final size:28
Alignment explanation
Indices: 39995365--39995421 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
39995355 AAATGAATGG
*
39995365 AATAATTAGTTCTAGTTATTA-AATATA
1 AATAATTAGTTCTAGCTATTATAATATA
*
39995392 AATAATTAGTTCTAGCTATTATATTATA
1 AATAATTAGTTCTAGCTATTATAATATA
39995420 AA
1 AA
39995422 AAAATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (28 bp):
AATAATTAGTTCTAGCTATTATAATATA
Found at i:39997590 original size:71 final size:66
Alignment explanation
Indices: 39997511--39997651 Score: 183
Period size: 67 Copynumber: 2.1 Consensus size: 66
39997501 GCACTAGATG
* * *
39997511 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTAGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTAGCGAAGCCACCAGATTGCAGC-A
39997576 GGCTGC
61 GGCTGC
* * *
39997582 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCAGGCTG
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTAGCGAAGCCACCAGATTGCAGCAGGCTG
39997647 C
66 C
39997648 CAGA
1 CAGA
39997652 ACGCTTCCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
66 11 0.17
67 28 0.44
71 25 0.39
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (66 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTAGCGAAGCCACCAGATTGCAGCAGGCTG
C
Found at i:39997630 original size:27 final size:26
Alignment explanation
Indices: 39997582--39997633 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
39997572 GCGAGGCTGC
*
39997582 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
39997608 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
39997634 TTGCAGCAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40003229 original size:27 final size:26
Alignment explanation
Indices: 40003181--40003261 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
40003171 GCGAGGCTGC
*
40003181 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
40003208 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
40003234 CAAATATATATGTGGCGAAGCCACCAGA
1 C--AGATAT-TGTGACGAAGCCACCAGA
40003262 TTGCAGCAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.05
27 21 0.48
28 5 0.11
29 16 0.36
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40003341 original size:67 final size:68
Alignment explanation
Indices: 40003208--40003347 Score: 192
Period size: 67 Copynumber: 2.1 Consensus size: 68
40003198 TCACCAGATA
* * * *
40003208 CAGATATTGTGGCTAGGCCACCAGAACAAATATATATGTGGCGAAGCCACCAGATTGCAGCAAGG
1 CAGATATTGTGACTAAGCCACCAGAAC-AAGATATATGTGACGAAGCCACCAGATTGCAGCAAGG
40003273 CTGC
65 CTGC
* * * *
40003277 CAGATATTGTGACTAAGTCACCAGAAC-AGATATATGTGACGAGGCCACCATATTGCAGCGAGGC
1 CAGATATTGTGACTAAGCCACCAGAACAAGATATATGTGACGAAGCCACCAGATTGCAGCAAGGC
40003341 TGC
66 TGC
40003344 CAGA
1 CAGA
40003348 ACGCTTCCTC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 39 0.62
69 24 0.38
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (68 bp):
CAGATATTGTGACTAAGCCACCAGAACAAGATATATGTGACGAAGCCACCAGATTGCAGCAAGGC
TGC
Found at i:40005529 original size:30 final size:29
Alignment explanation
Indices: 40005486--40005546 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
40005476 TCAAGTAGCG
*
40005486 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTACTGCCA
40005515 AAGCTAGTTTAAATCGCACACTTACTGCCA
1 AAGCTAG-TTAAATCGCACACTTACTGCCA
40005545 AA
1 AA
40005547 ACTTCCGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTACTGCCA
Found at i:40012749 original size:30 final size:29
Alignment explanation
Indices: 40012701--40012761 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
40012691 CAAGTAGCCG
* *
40012701 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATAGCACACTTACTGCCA
40012730 AAGCTAGTTTAAATAGCACACTTACTGCCA
1 AAGCTAG-TTAAATAGCACACTTACTGCCA
40012760 AA
1 AA
40012762 ACTTCCGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATAGCACACTTACTGCCA
Found at i:40015669 original size:29 final size:29
Alignment explanation
Indices: 40015603--40015698 Score: 158
Period size: 29 Copynumber: 3.3 Consensus size: 29
40015593 AAGACTACAT
* *
40015603 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
40015631 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
40015660 ACATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
40015689 ACATTCATAT
1 ACATTCATAT
40015699 ACATGCTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 21 0.33
29 42 0.67
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:40025649 original size:48 final size:47
Alignment explanation
Indices: 40025578--40025861 Score: 214
Period size: 48 Copynumber: 5.9 Consensus size: 47
40025568 GACATTTGGG
* * * * *
40025578 TGATATGTGTGCCAGTATAAGACCACGTCAGGGAAATGGCATCGACCA
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGA-CA
* * *
40025626 TGATATGAGGGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGATGA
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGAA-ATGGCATCGA-CA
* * * *
40025674 TGTTGTGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACA
1 TGATATGAGAGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGACA
* * * * *
40025721 TTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 -TGATATGAGAGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGACA
* * * * * * *
40025769 TTGAGACGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATC-AGCC
1 -TGATATGAGAGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGA-CA
* * * * *
40025817 TCAACATGTGAACCAGTGTAAGACCATGT-TTGGAACATGGCATCG
1 T-GATATGAGAGCCAGTGTAAGACCATGTCTGGGAA-ATGGCATCG
40025862 GCAACTCACC
Statistics
Matches: 192, Mismatches: 37, Indels: 13
0.79 0.15 0.05
Matches are distributed among these distances:
47 10 0.05
48 178 0.93
49 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
TGATATGAGAGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGACA
Found at i:40025759 original size:96 final size:96
Alignment explanation
Indices: 40025595--40025861 Score: 294
Period size: 96 Copynumber: 2.8 Consensus size: 96
40025585 TGTGCCAGTA
* * * * *
40025595 TAAGACCACGTCAGGGAAATGGCATCGACCA-TGATATGAGGGCCAGTGTAAGACCATGTTTGGA
1 TAAGACCATGTCTGGGACATGGCATCGACCATTGATATGTGAGCCAGTGTAAGACCATGTTTGGA
**
40025659 ACATGGCATCG-A-TGATGTTGTGAGAGCTAGTG
66 ACATGGCATCGCATTGA-G--ACGAGAGCTAGTG
* * * *
40025691 TAAGACCATGTCTGGGACATGGCATCGA-CATTGATATGTGCGCTAGTGTAAGACCATGTCTGGG
1 TAAGACCATGTCTGGGACATGGCATCGACCATTGATATGTGAGCCAGTGTAAGACCATGTTTGGA
40025755 ACATGGCATCGGCATTGAGACGAGAGCTAGTG
66 ACATGGCATC-GCATTGAGACGAGAGCTAGTG
* * ** * *
40025787 TAAGACCATGTCTAGGACATGGTATC-AGCC-TCAACATGTGAACCAGTGTAAGACCATGTTTGG
1 TAAGACCATGTCTGGGACATGGCATCGA-CCATTGATATGTGAGCCAGTGTAAGACCATGTTTGG
40025850 AACATGGCATCG
65 AACATGGCATCG
40025862 GCAACTCACC
Statistics
Matches: 145, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
95 4 0.03
96 134 0.92
97 2 0.01
98 2 0.01
99 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (96 bp):
TAAGACCATGTCTGGGACATGGCATCGACCATTGATATGTGAGCCAGTGTAAGACCATGTTTGGA
ACATGGCATCGCATTGAGACGAGAGCTAGTG
Found at i:40029160 original size:42 final size:43
Alignment explanation
Indices: 40029098--40029213 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
40029088 CGATATGTGT
* *
40029098 TTTCGTGTATGACCACGTCTGGGACGTTGGCATC-GTATTTGA
1 TTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATATTTGA
** *
40029140 TTTCGTGTAAGACCTTGTCTGGGATAG-TGGCATCAATATTTGA
1 TTTCGTGTAAGACCACGTCTGGGA-CGTTGGCATCAATATTTGA
* * *
40029183 TTACATGTAAGACCACGTCTGGGACTTTGGC
1 TTTCGTGTAAGACCACGTCTGGGACGTTGGC
40029214 TTTGTATGAG
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 28 0.47
43 32 0.53
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (43 bp):
TTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATATTTGA
Found at i:40045583 original size:21 final size:20
Alignment explanation
Indices: 40045554--40045599 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
40045544 CGAAATACAA
40045554 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
40045575 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
40045595 T-AACC
1 TCAACC
40045600 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:40046447 original size:10 final size:10
Alignment explanation
Indices: 40046425--40046476 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
40046415 AATTCTGTCG
*
40046425 AAAA-TAATC
1 AAAATTAATT
*
40046434 AAAACTAATT
1 AAAATTAATT
*
40046444 AAAATTTATTAT
1 AAAA-TTAAT-T
40046456 AAAATTAATT
1 AAAATTAATT
40046466 AAAATTAATT
1 AAAATTAATT
40046476 A
1 A
40046477 CGTTAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 4 0.11
10 20 0.56
11 7 0.19
12 5 0.14
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTAATT
Found at i:40046464 original size:22 final size:22
Alignment explanation
Indices: 40046434--40046476 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40046424 GAAAATAATC
*
40046434 AAAACTAATTAAAATTTATTAT
1 AAAACTAATTAAAATTAATTAT
*
40046456 AAAATTAATTAAAATTAATTA
1 AAAACTAATTAAAATTAATTA
40046477 CGTTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAACTAATTAAAATTAATTAT
Found at i:40052485 original size:46 final size:46
Alignment explanation
Indices: 40052418--40052582 Score: 240
Period size: 46 Copynumber: 3.6 Consensus size: 46
40052408 TGTAACCCGC
* * * *
40052418 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACGTTCGCAT
* *
40052464 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGTCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACGTTCGCAT
* * *
40052510 CCATAAGTGAACTCAGACTCAGCTCAATGAGTTCGGATGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACGTTCGCAT
*
40052556 CCATAAGTGAACTCGAACTCAACTCAA
1 CCATAAGTGAACTCGGACTCAACTCAA
40052583 CAAGTTTAGA
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 106 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACGTTCGCAT
Found at i:40057673 original size:46 final size:46
Alignment explanation
Indices: 40057606--40057824 Score: 221
Period size: 46 Copynumber: 4.7 Consensus size: 46
40057596 TGTAACCTGC
*
40057606 CCATAAGA-GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAA-ATGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
40057652 CCATAAATGAACTTGGACTCAACTCAACGAGTTC-GG-ATTC-CTAGTT
1 CCATAAATGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGC-A--T
* ** * * **
40057698 ACATTTCACGAACTCGAACTCAACTCAACGAGTTCGTACGTTCGCAT
1 CCA-TAAATGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* * **
40057745 CCATAAGTGAACTCGGACTCAGCTCAACGAGTTCGGTTGTTCGCAT
1 CCATAAATGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
40057791 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC
1 CCATAAATGAACTCGGACTCAACTCAACGAGTTC
40057825 AGATGCCCAA
Statistics
Matches: 141, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
43 1 0.01
44 4 0.03
45 3 0.02
46 99 0.70
47 29 0.21
49 4 0.03
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (46 bp):
CCATAAATGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:40063260 original size:24 final size:24
Alignment explanation
Indices: 40063228--40063276 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40063218 TGCCATTATG
40063228 ACACGTTTCAGATAATGTGTAGCC
1 ACACGTTTCAGATAATGTGTAGCC
40063252 ACACGTTTCAGATAATGTGTAGCC
1 ACACGTTTCAGATAATGTGTAGCC
40063276 A
1 A
40063277 AGCTGGCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (24 bp):
ACACGTTTCAGATAATGTGTAGCC
Found at i:40065336 original size:22 final size:22
Alignment explanation
Indices: 40065311--40065353 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40065301 TAGCCCAACT
*
40065311 ATGGTCTTACACATA-TCTTACC
1 ATGGCCTTAC-CATAGTCTTACC
*
40065333 ATGGCCTTGCCATAGTCTTAC
1 ATGGCCTTACCATAGTCTTAC
40065354 ACATATCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (22 bp):
ATGGCCTTACCATAGTCTTACC
Found at i:40067284 original size:40 final size:40
Alignment explanation
Indices: 40067046--40067270 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
40067036 TTGAGTGATG
* * * *
40067046 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40067086 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40067126 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTAATAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40067165 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40067205 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40067246 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40067271 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40067293 original size:119 final size:119
Alignment explanation
Indices: 40067046--40067277 Score: 290
Period size: 119 Copynumber: 1.9 Consensus size: 119
40067036 TTGAGTGATG
* * *
40067046 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
* **
40067111 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTAATAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTAATAAA
* * * **
40067165 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
* *
40067228 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGT
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGT
40067278 AGCTATATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 3 0.03
119 67 0.70
120 26 0.27
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTAATAAA
Found at i:40080050 original size:42 final size:42
Alignment explanation
Indices: 40080002--40080184 Score: 219
Period size: 42 Copynumber: 4.4 Consensus size: 42
40079992 TCAAACTATA
*
40080002 TCTGGGATATGGCATCGTTATGAGAATTCATGTAAGACCATG
1 TCTGGGATATGGCATCGATATGAGAATTCATGTAAGACCATG
* * * *
40080044 TTTGGGACATGGCATCGATATGAGAATTCGTGTAAGACAATG
1 TCTGGGATATGGCATCGATATGAGAATTCATGTAAGACCATG
* *
40080086 TCTGGGACATGGCATCGATATGAGAATT-GTGTAAGACCATAG
1 TCTGGGATATGGCATCGATATGAGAATTCATGTAAGACCAT-G
* * *
40080128 -CTGGGCTATTGGCATCGATATGAG-ATCCCATGTAAGACCATA
1 TCTGGGATA-TGGCATCGATATGAGAAT-TCATGTAAGACCATG
*
40080170 TCTGGAATATGGCAT
1 TCTGGGATATGGCAT
40080185 TGGTATGATT
Statistics
Matches: 122, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
41 19 0.16
42 86 0.70
43 17 0.14
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (42 bp):
TCTGGGATATGGCATCGATATGAGAATTCATGTAAGACCATG
Found at i:40088214 original size:93 final size:93
Alignment explanation
Indices: 40088102--40088273 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
40088092 GCCCATAAGT
* * *
40088102 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
40088167 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
40088195 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
40088260 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
40088274 CAAATGTTCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:40088269 original size:46 final size:46
Alignment explanation
Indices: 40088094--40088269 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
40088084 TCTAACCCGC
* * *
40088094 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
40088140 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
40088186 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
40088233 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
40088270 TGCCCAAATG
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:40091408 original size:34 final size:34
Alignment explanation
Indices: 40091336--40091582 Score: 316
Period size: 34 Copynumber: 7.2 Consensus size: 34
40091326 TGTAAAATGT
* *
40091336 CATACCTACGTTTCATAACTCAGTATGGAAAATAC
1 CATACCTACGTATCATAGCTCAGTATGG-AAATAC
* * *
40091371 CATACCTATGTATCATAGCTCGGTATAGAAATAC
1 CATACCTACGTATCATAGCTCAGTATGGAAATAC
* * * *
40091405 CATACCTACATATTACAGCTCGGTATGGAAATAC
1 CATACCTACGTATCATAGCTCAGTATGGAAATAC
*
40091439 CATACCTACGTATGATAGCTCAGTATGGAAATAC
1 CATACCTACGTATCATAGCTCAGTATGGAAATAC
*
40091473 CATACTTACGTATCATAGCTCAGTATGGAAATAC
1 CATACCTACGTATCATAGCTCAGTATGGAAATAC
* * * *
40091507 AATACCTATGTATCATAGTTCAGTTTGGAAATAC
1 CATACCTACGTATCATAGCTCAGTATGGAAATAC
* *
40091541 GATACCTACATATCATAGCTC-GATATGGAAATAC
1 CATACCTACGTATCATAGCTCAG-TATGGAAATAC
40091575 CATACCTA
1 CATACCTA
40091583 TGCTTCACAT
Statistics
Matches: 184, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
33 1 0.01
34 160 0.87
35 23 0.12
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (34 bp):
CATACCTACGTATCATAGCTCAGTATGGAAATAC
Found at i:40102505 original size:15 final size:15
Alignment explanation
Indices: 40102466--40102506 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
40102456 CAAGGAAACC
40102466 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
40102481 -AGATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
40102496 GAATAAAGAAA
1 GAATAAAGAAA
40102507 CCCAATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.61, C:0.10, G:0.17, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:40109482 original size:42 final size:40
Alignment explanation
Indices: 40109423--40109544 Score: 100
Period size: 42 Copynumber: 2.9 Consensus size: 40
40109413 TTAGGGTTAC
* *
40109423 TGAGATTTTGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGA-TTCGTGTAAGACCATATCT-GGATATGGCATCAATA
* * * *
40109465 TGAGACTTCGTGTAAGACCGTAGCTGAGCTATTGCCATCAATA
1 TGAGA-TTCGTGTAAGACCATATCTG-GATA-TGGCATCAATA
** *
40109508 CAAGATTACATGTAAGACCATATCTGGGATATGGCAT
1 TGAGATT-CGTGTAAGACCATATCT-GGATATGGCAT
40109545 TGGTACGGTA
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
41 1 0.02
42 31 0.50
43 29 0.47
44 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (40 bp):
TGAGATTCGTGTAAGACCATATCTGGATATGGCATCAATA
Found at i:40118528 original size:23 final size:23
Alignment explanation
Indices: 40118502--40118552 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
40118492 AGTTATAGCT
40118502 TTCTAATCCATGAAGTACTCCTA
1 TTCTAATCCATGAAGTACTCCTA
40118525 TTCTAATCCATGAAGTACTCCTA
1 TTCTAATCCATGAAGTACTCCTA
40118548 TTCTA
1 TTCTA
40118553 GGGCTAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (23 bp):
TTCTAATCCATGAAGTACTCCTA
Found at i:40118784 original size:32 final size:32
Alignment explanation
Indices: 40118742--40118812 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
40118732 AAAACGATGC
* *
40118742 ATTAAGTGATTGAAGAACGGAAAGATCTCACCG
1 ATTAA-TGATTGAAGAACGAAAAGAGCTCACCG
40118775 ATTAATGATTGAAGAACGAAAAGAGCTCACCG
1 ATTAATGATTGAAGAACGAAAAGAGCTCACCG
40118807 ATTAAT
1 ATTAAT
40118813 CAAGAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.86
33 5 0.14
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (32 bp):
ATTAATGATTGAAGAACGAAAAGAGCTCACCG
Found at i:40124230 original size:30 final size:30
Alignment explanation
Indices: 40124194--40124253 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40124184 AAATTTGAAG
40124194 TTGAAAAAATTATTTTATTATTATTTTAGA
1 TTGAAAAAATTATTTTATTATTATTTTAGA
40124224 TTGAAAAAATTATTTTATTATTATTTTAGA
1 TTGAAAAAATTATTTTATTATTATTTTAGA
40124254 GTCATAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (30 bp):
TTGAAAAAATTATTTTATTATTATTTTAGA
Found at i:40125384 original size:27 final size:27
Alignment explanation
Indices: 40125336--40125494 Score: 193
Period size: 27 Copynumber: 5.9 Consensus size: 27
40125326 GCGAGGCTGC
* *
40125336 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
40125363 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
40125389 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
40125416 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
40125443 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
40125470 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
40125495 GACGCTTCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.09
27 102 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:40125429 original size:54 final size:54
Alignment explanation
Indices: 40125354--40125494 Score: 248
Period size: 54 Copynumber: 2.6 Consensus size: 54
40125344 GTGACGAAGT
*
40125354 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
40125408 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
40125462 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
40125495 GACGCTTCCT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:40125902 original size:8 final size:8
Alignment explanation
Indices: 40125886--40125915 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40125876 CTCAAAATAC
40125886 CGGCTTTT
1 CGGCTTTT
*
40125894 CGGCATTT
1 CGGCTTTT
40125902 CGGCTTTT
1 CGGCTTTT
40125910 CGGCTT
1 CGGCTT
40125916 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:40127130 original size:26 final size:26
Alignment explanation
Indices: 40127094--40127202 Score: 191
Period size: 26 Copynumber: 4.2 Consensus size: 26
40127084 ATGAAATGCC
*
40127094 TATCATGGAACATTTACCTAAACCAT
1 TATCATGGAACATTTACCTAACCCAT
40127120 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
* *
40127146 TATCATGGAATATTTACCTAATCCAT
1 TATCATGGAACATTTACCTAACCCAT
40127172 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
40127198 TATCA
1 TATCA
40127203 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:40128610 original size:46 final size:46
Alignment explanation
Indices: 40128472--40128647 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
40128462 TCATTTGTGT
* * *
40128472 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATT-ATA--A
1 GAGCTAGTGTAAGACATGTCTAGGACATGCATC-G--ACCTTGAGACGA
* *
40128518 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGACCTTGAGACGA
* * *
40128566 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGACGTA
1 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGACCTTGAGACG-A
* *
40128613 -AGTTAGTGTAAGACATGTCTAAGACATGCATCGAC
1 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGAC
40128648 TACAGGATGA
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
45 5 0.05
46 60 0.54
47 28 0.25
48 18 0.16
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTAGGACATGCATCGACCTTGAGACGA
Found at i:40128731 original size:140 final size:140
Alignment explanation
Indices: 40128476--40128734 Score: 319
Period size: 140 Copynumber: 1.9 Consensus size: 140
40128466 TTGTGTGAGC
** **
40128476 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATAAGAGCCAGTGTAAGACCATGTCTA
1 TAGTGTAAGACATGTCTAAGACATGCATCAGCCACAGGATAAGAGCCAGTGTAAGACCATGTCTA
* * *
40128541 GGACATGGCATCGACATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTG
66 GGACATGGCATCGACATTGAGACGAGAGCAAGTGTAAGACATGTCCGGGACATGCATCGGCCTTG
40128606 AGACGTAAGT
131 AGACGTAAGT
* * * *
40128616 TAGTGTAAGACATGTCTAAGACATGCATC-GACTACAGGATGATAGTCAGTGTAAGACCATGTCT
1 TAGTGTAAGACATGTCTAAGACATGCATCAG-CCACAGGATAAGAGCCAGTGTAAGACCATGTCT
* * * *
40128680 -GCGATATGGCATCGA-TTTGAGA-TATGAGCAAGTGTAAGACCATTTCCGGGACATG
65 AG-GACATGGCATCGACATTGAGACGA-GAGCAAGTGTAAGA-CATGTCCGGGACATG
40128735 GCATTGGCAC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
138 1 0.01
139 20 0.20
140 79 0.79
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (140 bp):
TAGTGTAAGACATGTCTAAGACATGCATCAGCCACAGGATAAGAGCCAGTGTAAGACCATGTCTA
GGACATGGCATCGACATTGAGACGAGAGCAAGTGTAAGACATGTCCGGGACATGCATCGGCCTTG
AGACGTAAGT
Found at i:40129774 original size:21 final size:21
Alignment explanation
Indices: 40129739--40129787 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
40129729 CGGCTATGGG
* *
40129739 ACACAGGCATGTTACCCTTCC
1 ACACGGGCGTGTTACCCTTCC
*
40129760 ATACGGGCGTGTTACCCTTCC
1 ACACGGGCGTGTTACCCTTCC
40129781 ACACGGG
1 ACACGGG
40129788 TGTGCCCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.22
Consensus pattern (21 bp):
ACACGGGCGTGTTACCCTTCC
Found at i:40132337 original size:22 final size:22
Alignment explanation
Indices: 40132305--40132353 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
40132295 GAGAGATTTC
* *
40132305 AAATACAAAAAAAGGAGCGAATTG
1 AAATA-AAAAAAA-AAGCAAATTG
40132329 AAATAAAAAAAAAAGCAAATTG
1 AAATAAAAAAAAAAGCAAATTG
40132351 AAA
1 AAA
40132354 GTTATTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 7 0.30
24 5 0.22
ACGTcount: A:0.67, C:0.06, G:0.14, T:0.12
Consensus pattern (22 bp):
AAATAAAAAAAAAAGCAAATTG
Found at i:40133459 original size:11 final size:11
Alignment explanation
Indices: 40133418--40133459 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
40133408 ATTTAGAGTA
40133418 TTATTAT-TATT
1 TTATTATCTA-T
*
40133429 TTATTATTTAT
1 TTATTATCTAT
40133440 TTATATATCTAT
1 TTAT-TATCTAT
40133452 TTATTATC
1 TTATTATC
40133460 CTTTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 16 0.57
12 12 0.43
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATCTAT
Found at i:40136194 original size:19 final size:19
Alignment explanation
Indices: 40136170--40136213 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
40136160 TGCCTCTTTT
* *
40136170 TGCATT-CATTTTATGCATC
1 TGCATTGCATTGTAT-CATA
40136189 TGCATTGCATTGTATCATA
1 TGCATTGCATTGTATCATA
40136208 TGCATT
1 TGCATT
40136214 AAATTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (19 bp):
TGCATTGCATTGTATCATA
Found at i:40138712 original size:8 final size:9
Alignment explanation
Indices: 40138698--40138733 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
40138688 AGAGGTAGCA
40138698 AAAAAAAAC
1 AAAAAAAAC
40138707 AAAAAAAAC
1 AAAAAAAAC
*
40138716 AAAAAAAAT
1 AAAAAAAAC
40138725 ATAAAAAAA
1 A-AAAAAAA
40138734 GATTGTGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.89, C:0.06, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:40138720 original size:19 final size:20
Alignment explanation
Indices: 40138696--40138733 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40138686 GCAGAGGTAG
40138696 CAAAAAAAA-ACAAAAAAAA
1 CAAAAAAAATACAAAAAAAA
*
40138715 CAAAAAAAATATAAAAAAA
1 CAAAAAAAATACAAAAAAA
40138734 GATTGTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.87, C:0.08, G:0.00, T:0.05
Consensus pattern (20 bp):
CAAAAAAAATACAAAAAAAA
Found at i:40139665 original size:53 final size:53
Alignment explanation
Indices: 40139585--40139687 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
40139575 TGGGCTATGC
*
40139585 TCCCAATCAAGTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCAT
1 TCCCAATAAAGTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCAT
*
40139638 TCCCAATAAATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATT
1 TCCCAATAAAGTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATT
40139688 TGTTTCGAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.49
Consensus pattern (53 bp):
TCCCAATAAAGTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCAT
Found at i:40139685 original size:27 final size:27
Alignment explanation
Indices: 40139602--40139687 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
40139592 CAAGTTCCTT
40139602 CTTATTACATTTGCTATCTTTGATTAA
1 CTTATTACATTTGCTATCTTTGATTAA
** ** **
40139629 CTTATT-CATTCCCAATAAATTTCCTT--
1 CTTATTACATTTGC--TATCTTTGATTAA
40139655 CTTATTACATTTGCTATCTTTGATTAA
1 CTTATTACATTTGCTATCTTTGATTAA
40139682 CTTATT
1 CTTATT
40139688 TGTTTCGAGC
Statistics
Matches: 42, Mismatches: 12, Indels: 10
0.66 0.19 0.16
Matches are distributed among these distances:
25 7 0.17
26 11 0.26
27 17 0.40
28 7 0.17
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.51
Consensus pattern (27 bp):
CTTATTACATTTGCTATCTTTGATTAA
Found at i:40140170 original size:46 final size:46
Alignment explanation
Indices: 40140120--40140218 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
40140110 AATCATATGG
40140120 CCCTGAGCTCCAATGGGATGGATTGAAGAGGATACAAATCCT-ATAC
1 CCCTGAGCTCCAATGGGATGGATTGAAGAGGATACAAAT-CTGATAC
* * * * *
40140166 CCCTGAGTTGCAGTGGGATGGATTGGAGATGATACAAATCTGATAC
1 CCCTGAGCTCCAATGGGATGGATTGAAGAGGATACAAATCTGATAC
*
40140212 CCTTGAG
1 CCCTGAG
40140219 TTGCAGTGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 2 0.04
46 44 0.96
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (46 bp):
CCCTGAGCTCCAATGGGATGGATTGAAGAGGATACAAATCTGATAC
Found at i:40140219 original size:46 final size:46
Alignment explanation
Indices: 40140133--40140240 Score: 155
Period size: 46 Copynumber: 2.3 Consensus size: 46
40140123 TGAGCTCCAA
40140133 TGGGATGGATTGAAGAGGATACAAATCCTATACCCCTGAGTTGCAG
1 TGGGATGGATTGAAGAGGATACAAATCCTATACCCCTGAGTTGCAG
* * *
40140179 TGGGATGGATTGGAGATGATACAAAT-CTGATACCCTTGAGTTGCAG
1 TGGGATGGATTGAAGAGGATACAAATCCT-ATACCCCTGAGTTGCAG
* *
40140225 TGAGATGGATGGAAGA
1 TGGGATGGATTGAAGA
40140241 AACCAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 2 0.04
46 53 0.96
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (46 bp):
TGGGATGGATTGAAGAGGATACAAATCCTATACCCCTGAGTTGCAG
Found at i:40140745 original size:89 final size:89
Alignment explanation
Indices: 40140591--40141165 Score: 395
Period size: 89 Copynumber: 6.5 Consensus size: 89
40140581 AGTGAATCCA
* * * **
40140591 CAAATCTCATCTCCCTGAAG-TAGCAGTGGAGCAGACTGAAGTTGA--AGATGTTATCTCCTTGA
1 CAAATCTCATCTTCCTGAAGTTA-CAGTGGAGCAGATTGAAG-TCACTAG-CCTTATCTCCTTGA
*
40140653 AGTTGTAGTGGAGTAGATCAAATATGG
63 AGTTGCAGTGGAGTAGATCAAATATGG
* * * * * *
40140680 CAAATCTTATCTTCCTGAAGTTACAGTGAAACAGATTGAAGCCACCAGCCTTATCTCCTTAAAGT
1 CAAATCTCATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGTCACTAGCCTTATCTCCTTGAAGT
* * * * * *
40140745 TGTAGCGGAGCAAACTGAAGATA--A
66 TGCAGTGGAGTAGA-TCAA-ATATGG
* * * * * * * *
40140769 AAAATCTCATCTCCCTAAAGTAACAGTGGAGCATATTGAAGTTA-AAGATCTTATCTCCTTGAAG
1 CAAATCTCATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGTCACTAG-CCTTATCTCCTTGAAG
40140833 TTGCAGTGGAGTAGATCAAATATGG
65 TTGCAGTGGAGTAGATCAAATATGG
* * * * * * * *
40140858 CGAATCCCATCTTCTTGAAGTTGCAGCGAAGCAGATTAAAGCCACTAGCCTTATC-CCTCTGAAG
1 CAAATCTCATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGTCACTAGCCTTATCTCCT-TGAAG
* * * *
40140922 TTGCAGAGGAGCAGA-CTAAAGATAG
65 TTGCAGTGGAGTAGATC-AAATATGG
* * * *
40140947 CAAATCTCATCCTCCTGAAG-TAGCAGTGGAGCATATTGAAGT--TTAAGAACTTAT-TCCTTGA
1 CAAATCTCATCTTCCTGAAGTTA-CAGTGGAGCAGATTGAAGTCACT-AG-CCTTATCTCCTTGA
*
40141008 AGTTGCAGTGGAGTAGATCAATTATGG
63 AGTTGCAGTGGAGTAGATCAAATATGG
** * * * * * *
40141035 TGAATCTTTATCTTCCTAAAGTTACAGTGGAACAGATTGAAGTCACTAGCTTTATCTCCCTAAAG
1 CAAATC-TCATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGTCACTAGCCTTATCTCCTTGAAG
** * ** *
40141100 TAACAGCGGAACAGACTGAAGATA--G
65 TTGCAGTGGAGTAGA-TCAA-ATATGG
* *
40141125 CAAATCTCATTTTCCTGAAGTTGCAGTGGAGCAGATTGAAG
1 CAAATCTCATCTTCCTGAAGTTACAGTGGAGCAGATTGAAG
40141166 CTATAAGTTA
Statistics
Matches: 366, Mismatches: 97, Indels: 46
0.72 0.19 0.09
Matches are distributed among these distances:
87 4 0.01
88 40 0.11
89 278 0.76
90 35 0.10
91 7 0.02
92 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (89 bp):
CAAATCTCATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGTCACTAGCCTTATCTCCTTGAAGT
TGCAGTGGAGTAGATCAAATATGG
Found at i:40140902 original size:178 final size:177
Alignment explanation
Indices: 40140591--40141165 Score: 733
Period size: 178 Copynumber: 3.2 Consensus size: 177
40140581 AGTGAATCCA
* * *
40140591 CAAATCTCATCTCCCTGAAGTAGCAGTGGAGCAGACTGAAGTTGAAGATGTTATCTCCTTGAAGT
1 CAAATCTCATCTCCCTGAAGTAGCAGTGGAGCAGATTGAAGTTAAAGATCTTATCTCCTTGAAGT
* * *
40140656 TGTAGTGGAGTAGATCAAATATGGCAAATCTTATCTTCCTGAAGTTACAGTGAAACAGATTGAAG
66 TGCAGTGGAGTAGATCAAATATGGCGAATCTTATCTTCCTGAAGTTACAGCG-AACAGATTGAAG
* * * *
40140721 CCACCAGCCTTATCTCCTTAAAGTTGTAGCGGAGCAAACTGAAGATAA
130 CCACTAGCCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGATAG
* * * *
40140769 AAAATCTCATCTCCCTAAAGTAACAGTGGAGCATATTGAAGTTAAAGATCTTATCTCCTTGAAGT
1 CAAATCTCATCTCCCTGAAGTAGCAGTGGAGCAGATTGAAGTTAAAGATCTTATCTCCTTGAAGT
** * * *
40140834 TGCAGTGGAGTAGATCAAATATGGCGAATCCCATCTTCTTGAAGTTGCAGCGAAGCAGATTAAAG
66 TGCAGTGGAGTAGATCAAATATGGCGAATCTTATCTTCCTGAAGTTACAGCGAA-CAGATTGAAG
* * *
40140899 CCACTAGCCTTATC-CCTCTGAAGTTGCAGAGGAGCAGACTAAAGATAG
130 CCACTAGCCTTATCTCCT-TAAAGTTGCAGCGGAGCAGACTGAAGATAG
* * *
40140947 CAAATCTCATC-CTCCTGAAGTAGCAGTGGAGCATATTGAAGTTTAAGAACTTAT-TCCTTGAAG
1 CAAATCTCATCTC-CCTGAAGTAGCAGTGGAGCAGATTGAAGTTAAAGATCTTATCTCCTTGAAG
* * * *
40141010 TTGCAGTGGAGTAGATCAATTATGGTGAATCTTTATCTTCCTAAAGTTACAGTGGAACAGATTGA
65 TTGCAGTGGAGTAGATCAAATATGGCGAATC-TTATCTTCCTGAAGTTACAG-CGAACAGATTGA
* * * ** *
40141075 AGTCACTAGCTTTATCTCCCTAAAGTAACAGCGGAACAGACTGAAGATAG
128 AGCCACTAGCCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGATAG
* * *
40141125 CAAATCTCATTTTCCTGAAGTTGCAGTGGAGCAGATTGAAG
1 CAAATCTCATCTCCCTGAAGTAGCAGTGGAGCAGATTGAAG
40141166 CTATAAGTTA
Statistics
Matches: 341, Mismatches: 49, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
177 44 0.13
178 292 0.86
179 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (177 bp):
CAAATCTCATCTCCCTGAAGTAGCAGTGGAGCAGATTGAAGTTAAAGATCTTATCTCCTTGAAGT
TGCAGTGGAGTAGATCAAATATGGCGAATCTTATCTTCCTGAAGTTACAGCGAACAGATTGAAGC
CACTAGCCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGATAG
Found at i:40142986 original size:11 final size:11
Alignment explanation
Indices: 40142945--40142986 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
40142935 TAGAGTATTA
40142945 TTATTAT-TATT
1 TTATTATCTA-T
*
40142956 TTATTATTTAT
1 TTATTATCTAT
40142967 TTATATATCTAT
1 TTAT-TATCTAT
40142979 TTATTATC
1 TTATTATC
40142987 CTTTTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 16 0.57
12 12 0.43
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATCTAT
Found at i:40143104 original size:16 final size:16
Alignment explanation
Indices: 40143052--40143105 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
40143042 TATATTGTTA
40143052 TTATTA-TTAT-TACT
1 TTATTATTTATGTACT
*
40143066 ATTATTATTTATTGT-CA
1 -TTATTATTTA-TGTACT
*
40143083 TCATTATTTATGTACT
1 TTATTATTTATGTACT
40143099 TTATTAT
1 TTATTAT
40143106 AAATTGTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 9 0.29
16 19 0.61
17 2 0.06
18 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (16 bp):
TTATTATTTATGTACT
Found at i:40148005 original size:68 final size:68
Alignment explanation
Indices: 40147896--40148033 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
40147886 ACCCGATGAA
*
40147896 TGCCTAAAATGTGCTATATCTTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGCTAATTTC
1 TGCCTAAAATGTGCTATATCTTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGCTAATTTA
40147961 TGT
66 TGT
40147964 TGCCTAAAATGTGCTATATCTTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGCTAATTTA
1 TGCCTAAAATGTGCTATATCTTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGCTAATTTA
40148029 TGT
66 TGT
40148032 TG
1 TG
40148034 TGCCCAGAGA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (68 bp):
TGCCTAAAATGTGCTATATCTTTGCTACGTGATTCTGCCTACTATTGGTGGAATACGCTAATTTA
TGT
Found at i:40153095 original size:40 final size:40
Alignment explanation
Indices: 40153058--40153203 Score: 231
Period size: 40 Copynumber: 3.7 Consensus size: 40
40153048 TGAGGAATTG
40153058 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
40153098 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
* * * * *
40153138 TATCCGGGCTTAAAGACCTGCAGGCTTTGTGCTAGAATGC
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
*
40153178 TATCCGGGC-TAGAGACCCGCAGGCTA
1 TATCCGGGCTTAAAGACCCGCAGGCTA
40153204 CGAGCTGGTA
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 14 0.14
40 84 0.86
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATGT
Found at i:40154624 original size:20 final size:22
Alignment explanation
Indices: 40154584--40154625 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
40154574 ATTACTAATA
*
40154584 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
40154606 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
40154626 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:40154713 original size:15 final size:15
Alignment explanation
Indices: 40154681--40154751 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
40154671 TATTATTCAC
*
40154681 ATATTATTAA-AATTA
1 ATATT-TTAATAATAA
40154696 ATATTTTAATAATAA
1 ATATTTTAATAATAA
*
40154711 ATATTTATTACAATTATAA
1 ATA-TT-TT--AATAATAA
*
40154730 ATATATTAATAATAA
1 ATATTTTAATAATAA
40154745 ATATTTT
1 ATATTTT
40154752 GTAGTACAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 4 0.09
15 25 0.54
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTTTAATAATAA
Found at i:40155780 original size:24 final size:24
Alignment explanation
Indices: 40155745--40155807 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 24
40155735 TTAATGATTT
* *
40155745 AAAAAGAT-TAAATGATACTTAGA
1 AAAAAAATATAAATAATACTTAGA
40155768 AAAAAAATATAAATTTAATACTTAGA
1 AAAAAAATATAAA--TAATACTTAGA
40155794 AAAAAAATATAAAT
1 AAAAAAATATAAAT
40155808 TTATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 7 0.20
24 5 0.14
26 23 0.66
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (24 bp):
AAAAAAATATAAATAATACTTAGA
Found at i:40155809 original size:26 final size:26
Alignment explanation
Indices: 40155759--40155810 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
40155749 AGATTAAATG
40155759 ATACTTAGAAAAAAAATATAAATTTA
1 ATACTTAGAAAAAAAATATAAATTTA
40155785 ATACTTAGAAAAAAAATATAAATTTA
1 ATACTTAGAAAAAAAATATAAATTTA
40155811 TTTTTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (26 bp):
ATACTTAGAAAAAAAATATAAATTTA
Found at i:40156681 original size:13 final size:13
Alignment explanation
Indices: 40156642--40156685 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
40156632 ACTCTTCCAC
40156642 AAGAAAACTC-AA
1 AAGAAAACTCAAA
* *
40156654 AAGAAATTCTTAAA
1 AAGAAA-ACTCAAA
40156668 AAGAAAACTCAAA
1 AAGAAAACTCAAA
40156681 AAGAA
1 AAGAA
40156686 TTTATTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 6 0.23
13 12 0.46
14 8 0.31
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.14
Consensus pattern (13 bp):
AAGAAAACTCAAA
Found at i:40156693 original size:27 final size:26
Alignment explanation
Indices: 40156642--40156693 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
40156632 ACTCTTCCAC
*
40156642 AAGAAAACTCAAAAGAAATTCTTAAA
1 AAGAAAACTCAAAAGAAATTATTAAA
*
40156668 AAGAAAACTCAAAAAGAATTTATTAA
1 AAGAAAACTC-AAAAGAAATTATTAA
40156694 TTAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.21
Consensus pattern (26 bp):
AAGAAAACTCAAAAGAAATTATTAAA
Found at i:40162745 original size:17 final size:18
Alignment explanation
Indices: 40162720--40162756 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40162710 AAATTAAAAC
40162720 AAAATTTAAATAATAATT
1 AAAATTTAAATAATAATT
*
40162738 AAAA-TTAAATATTAATT
1 AAAATTTAAATAATAATT
40162755 AA
1 AA
40162757 CACATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTTAAATAATAATT
Found at i:40169185 original size:21 final size:23
Alignment explanation
Indices: 40169161--40169202 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
40169151 ATATTTTAAG
*
40169161 GTGTAATGAT-GATGG-TTAAAA
1 GTGTAAAGATGGATGGCTTAAAA
40169182 GTGTAAAGATGGATGGCTTAA
1 GTGTAAAGATGGATGGCTTAA
40169203 GGACTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (23 bp):
GTGTAAAGATGGATGGCTTAAAA
Found at i:40181436 original size:11 final size:11
Alignment explanation
Indices: 40181420--40181444 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40181410 TTAAATTTAG
40181420 AAATAAAATAA
1 AAATAAAATAA
40181431 AAATAAAATAA
1 AAATAAAATAA
40181442 AAA
1 AAA
40181445 CCAAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:40193940 original size:23 final size:23
Alignment explanation
Indices: 40193914--40193961 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40193904 ATCCAATTAA
40193914 AATAACCAATAGTTTGTAAAATG
1 AATAACCAATAGTTTGTAAAATG
40193937 AATAACCAATAGTTTGTAAAATG
1 AATAACCAATAGTTTGTAAAATG
40193960 AA
1 AA
40193962 CTTAAGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (23 bp):
AATAACCAATAGTTTGTAAAATG
Found at i:40196895 original size:48 final size:48
Alignment explanation
Indices: 40196824--40196953 Score: 199
Period size: 48 Copynumber: 2.7 Consensus size: 48
40196814 TAGGGGATAC
* *
40196824 ATTGATTTGACTTCGAGCCATGATATCAGCACTTCGGGTGCGAGCTTT
1 ATTGATTTGACTTAGGGCCATGATATCAGCACTTCGGGTGCGAGCTTT
40196872 ATTGATTTGACTTAGGGCCATGATATC-GACACTTCGGGTGCGAGCTTT
1 ATTGATTTGACTTAGGGCCATGATATCAG-CACTTCGGGTGCGAGCTTT
* * *
40196920 ATTGATTTGGCTTTGGGCCATGATATTAGCACTT
1 ATTGATTTGACTTAGGGCCATGATATCAGCACTT
40196954 AGTGTACGAG
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
47 1 0.01
48 73 0.97
49 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (48 bp):
ATTGATTTGACTTAGGGCCATGATATCAGCACTTCGGGTGCGAGCTTT
Found at i:40202728 original size:43 final size:42
Alignment explanation
Indices: 40202632--40202754 Score: 122
Period size: 43 Copynumber: 2.9 Consensus size: 42
40202622 GACTTATGAC
* * *
40202632 TTACGTGTAAGACCATGTCTGGGACGTTGGCATCGTATCTGA
1 TTACATGTAAGACCATGTCTAGGACGTTGACATCGTATCTGA
* * * *
40202674 TTTCATGTAAGACCCTGTCTAGGACAG-TGACATTGATATTTGA
1 TTACATGTAAGACCATGTCTAGGAC-GTTGACATCG-TATCTGA
* * * *
40202717 TTACATGTAAGACCACGTCTGGGACGTTGGCATTGTAT
1 TTACATGTAAGACCATGTCTAGGACGTTGACATCGTAT
40202755 GGTCTTTCTG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 31 0.47
43 35 0.53
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTAGGACGTTGACATCGTATCTGA
Found at i:40217115 original size:26 final size:26
Alignment explanation
Indices: 40217079--40217177 Score: 146
Period size: 26 Copynumber: 3.8 Consensus size: 26
40217069 CGTCAGAAAA
*
40217079 TGGAAGCCTTTGTGGCGTATCTGAAG
1 TGGAAGCCTTTGTGGTGTATCTGAAG
40217105 TGGAAGCCTTTGTGGTGTATCTGAAG
1 TGGAAGCCTTTGTGGTGTATCTGAAG
* * *
40217131 TGGAAGCTTTTGTGGTGTAACTGAAA
1 TGGAAGCCTTTGTGGTGTATCTGAAG
*
40217157 TGGAAGCCTTCGTGGTG-ATCT
1 TGGAAGCCTTTGTGGTGTATCT
40217178 ATGGAAAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
25 3 0.05
26 63 0.95
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (26 bp):
TGGAAGCCTTTGTGGTGTATCTGAAG
Found at i:40217316 original size:27 final size:27
Alignment explanation
Indices: 40217269--40217327 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
40217259 CTAGAAAGGG
** *
40217269 AAGAATGGTAAATGTGACAAACTCTAA
1 AAGAATGGTAAAAATGACAAACGCTAA
* *
40217296 AAGAATGGTAAAAATGGCAAACGCTGA
1 AAGAATGGTAAAAATGACAAACGCTAA
40217323 AAGAA
1 AAGAA
40217328 CAATCCGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17
Consensus pattern (27 bp):
AAGAATGGTAAAAATGACAAACGCTAA
Found at i:40218709 original size:70 final size:69
Alignment explanation
Indices: 40218623--40218779 Score: 228
Period size: 70 Copynumber: 2.3 Consensus size: 69
40218613 TCTTCACTAT
* *
40218623 TTAAAAAGTTAATTTTAATCCTACACTGACTAGAAAACACTCTCATAGCTCACTTAT-TCACTAT
1 TTAAAAAGTTAATTTTAATCCTAAACTGACTAGAAAACACTCCCATAGCTCACTT-TCTCACTAT
40218687 TTTTA
65 TTTTA
* * *
40218692 TTAAAAAAGTTAATTTTAATCTTAAATTGACTAGAAAATACTCCCATAGCTCACTTTCTCACTAT
1 TT-AAAAAGTTAATTTTAATCCTAAACTGACTAGAAAACACTCCCATAGCTCACTTTCTCACTAT
*
40218757 TTTAA
65 TTTTA
40218762 TTAAAAA-TTAATTTTAAT
1 TTAAAAAGTTAATTTTAAT
40218780 GTTAATTTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
68 11 0.14
69 8 0.10
70 61 0.76
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (69 bp):
TTAAAAAGTTAATTTTAATCCTAAACTGACTAGAAAACACTCCCATAGCTCACTTTCTCACTATT
TTTA
Found at i:40220069 original size:20 final size:20
Alignment explanation
Indices: 40220046--40220099 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
40220036 ACAACTCCAC
*
40220046 TTCTATCCATACATGTTAAG
1 TTCTACCCATACATGTTAAG
* * *
40220066 TTCTACCCATACAAGTTTAT
1 TTCTACCCATACATGTTAAG
40220086 TTCTACCCATACAT
1 TTCTACCCATACAT
40220100 CTTGTAAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.39
Consensus pattern (20 bp):
TTCTACCCATACATGTTAAG
Found at i:40220090 original size:40 final size:42
Alignment explanation
Indices: 40220046--40220127 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
40220036 ACAACTCCAC
*
40220046 TTCTATCCATACAT-GT-TAAGTTCTACCCATACAAGTTTAT
1 TTCTACCCATACATCGTGTAAGTTCTACCCATACAAGTTTAT
* * **
40220086 TTCTACCCATACATCTTGTAAGTTGTACCGGTACAAGTTTAT
1 TTCTACCCATACATCGTGTAAGTTCTACCCATACAAGTTTAT
40220128 CTGCAATGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 13 0.37
41 1 0.03
42 21 0.60
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (42 bp):
TTCTACCCATACATCGTGTAAGTTCTACCCATACAAGTTTAT
Found at i:40239796 original size:15 final size:16
Alignment explanation
Indices: 40239776--40239811 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
40239766 TTGCTTATCA
40239776 ATTTTTC-GGATTTTC
1 ATTTTTCGGGATTTTC
40239791 ATTTTTCTGGGATTTTC
1 ATTTTTC-GGGATTTTC
40239808 ATTT
1 ATTT
40239812 GCTCTTAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
17 12 0.63
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (16 bp):
ATTTTTCGGGATTTTC
Found at i:40245392 original size:26 final size:26
Alignment explanation
Indices: 40245351--40245428 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
40245341 ATTAATAAGA
*
40245351 TATGATTA-GCACTTCGGTGCGATAT
1 TATGATTATGCACTTCGGTGCAATAT
40245376 TATGATTATGCACTTCGGTGCAATAT
1 TATGATTATGCACTTCGGTGCAATAT
* * * *
40245402 TGTGATTATGCATTTCAGTGCATTAT
1 TATGATTATGCACTTCGGTGCAATAT
40245428 T
1 T
40245429 GTTAATTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 8 0.17
26 39 0.83
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (26 bp):
TATGATTATGCACTTCGGTGCAATAT
Found at i:40267632 original size:42 final size:42
Alignment explanation
Indices: 40267577--40267780 Score: 192
Period size: 42 Copynumber: 4.8 Consensus size: 42
40267567 GGGTTATGTC
* *
40267577 TGATTTCGTGTAAGACAATATCTGGGATATGGCATCGATATG
1 TGATATCGTGTAAGACCATATCTGGGATATGGCATCGATATG
* * * * *
40267619 TGATTTTGTGTAAGACCATTTCTGGGACACGGCATCGATATG
1 TGATATCGTGTAAGACCATATCTGGGATATGGCATCGATATG
* * * * * *
40267661 AGACATCGTGTAAGACCATGTCTGGTACATGGCATCGATATA
1 TGATATCGTGTAAGACCATATCTGGGATATGGCATCGATATG
** * * * *
40267703 AAACATCGTGTAAGACCGTAGCTGGGCTATCGGCATCGATATG
1 TGATATCGTGTAAGACCATATCTGGGATAT-GGCATCGATATG
** * *
40267746 TGATCCCATGTAAGACCATATCTAGGATATGGCAT
1 TGATATCGTGTAAGACCATATCTGGGATATGGCAT
40267781 TGGCATCTTA
Statistics
Matches: 130, Mismatches: 31, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
42 99 0.76
43 31 0.24
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (42 bp):
TGATATCGTGTAAGACCATATCTGGGATATGGCATCGATATG
Found at i:40270937 original size:42 final size:42
Alignment explanation
Indices: 40270870--40270989 Score: 188
Period size: 42 Copynumber: 2.9 Consensus size: 42
40270860 ACCATACCAT
* *
40270870 TTCCATATCCCAGATATGGTATTACATGTAATCTCATATTGA
1 TTCCATATCCCAGATATGGTCTTACATGTAATCTCATATAGA
* *
40270912 TGT-CATATCCCAGATATGGTCTTACACGTAGTCTCATATAGA
1 T-TCCATATCCCAGATATGGTCTTACATGTAATCTCATATAGA
40270954 TTCCATATCCCAGATATGGTCTTACATGTAATCTCA
1 TTCCATATCCCAGATATGGTCTTACATGTAATCTCA
40270990 GTAACCCTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.97
43 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (42 bp):
TTCCATATCCCAGATATGGTCTTACATGTAATCTCATATAGA
Found at i:40272784 original size:13 final size:13
Alignment explanation
Indices: 40272766--40272795 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40272756 TAATCTGTTA
40272766 TTTTTGTATCTAT
1 TTTTTGTATCTAT
40272779 TTTTTGTATCTAT
1 TTTTTGTATCTAT
40272792 TTTT
1 TTTT
40272796 GGGTGGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (13 bp):
TTTTTGTATCTAT
Found at i:40284056 original size:34 final size:34
Alignment explanation
Indices: 40284018--40284085 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
40284008 TATTAAATTA
40284018 ATGAATGGACTAAAATTGTAAATATGTGAAAAGT
1 ATGAATGGACTAAAATTGTAAATATGTGAAAAGT
40284052 ATGAATGGACTAAAATTGTAAATATGTGAAAAGT
1 ATGAATGGACTAAAATTGTAAATATGTGAAAAGT
40284086 TTTGTGGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (34 bp):
ATGAATGGACTAAAATTGTAAATATGTGAAAAGT
Found at i:40287112 original size:24 final size:24
Alignment explanation
Indices: 40287084--40287137 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
40287074 ACCTTCCATT
*
40287084 TTTCATCTTCTTTAACTTTTCACA
1 TTTCATCTTCTTTAACTCTTCACA
* *
40287108 TTTCATTTTCTTTAACTCTTCACC
1 TTTCATCTTCTTTAACTCTTCACA
40287132 TTTCAT
1 TTTCAT
40287138 GTGTTTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTCATCTTCTTTAACTCTTCACA
Found at i:40289064 original size:20 final size:20
Alignment explanation
Indices: 40289052--40289092 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
40289042 AATAATTTTC
40289052 AAAATTTTCAAATATTTATA
1 AAAATTTTCAAATATTTATA
*
40289072 AAAATTTT-AGATATTTA-A
1 AAAATTTTCAAATATTTATA
40289090 AAA
1 AAA
40289093 TATATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAATTTTCAAATATTTATA
Found at i:40289074 original size:19 final size:18
Alignment explanation
Indices: 40289052--40289149 Score: 56
Period size: 19 Copynumber: 5.1 Consensus size: 18
40289042 AATAATTTTC
40289052 AAAATTTTCAAATATTTATA
1 AAAATTTT-AAATATTTA-A
*
40289072 AAAATTTTAGATATTT-A
1 AAAATTTTAAATATTTAA
* *
40289089 AAAATATATAATTTATTTAAA
1 AAAAT-TTTAA-ATATTT-AA
* *
40289110 AAAATTCTAAAGAATATATAA
1 AAAATT-T-TA-AATATTTAA
40289131 AGAAATTTTAAAT-TTTAA
1 A-AAATTTTAAATATTTAA
40289149 A
1 A
40289150 TTTTTTTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
17 6 0.10
18 8 0.13
19 15 0.25
20 10 0.17
21 10 0.17
22 10 0.17
23 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (18 bp):
AAAATTTTAAATATTTAA
Found at i:40292637 original size:45 final size:45
Alignment explanation
Indices: 40292564--40292806 Score: 209
Period size: 45 Copynumber: 5.4 Consensus size: 45
40292554 CCTGCATTAG
* * * *
40292564 GGAAACATCTTGTTTCCTCTGTCCATATCCTGTTGCTAGCATCAA
1 GGAAACTTCTTGTTTCCTATATCTATATCCTGTTGCTAGCATCAA
*
40292609 GGAAACTTCTTATTTCCTATATCTATATCCTGTTGCTAGCATCAA
1 GGAAACTTCTTGTTTCCTATATCTATATCCTGTTGCTAGCATCAA
* * ** * *
40292654 CGAAACTTCTTGTTTCCTATATCTACATCCTGTTTATGGCACCAA
1 GGAAACTTCTTGTTTCCTATATCTATATCCTGTTGCTAGCATCAA
* * * * * * ** *
40292699 GGAAACTCCTTGTTTCCTGTATCCATAGCATGTTTCCGGC-TCCAT
1 GGAAACTTCTTGTTTCCTATATCTATATCCTGTTGCTAGCAT-CAA
* * * * ** * *
40292744 GGAAACTTCTTGTTTCCTTTATCCATAGCCTGTTTCCGGCTTCAT
1 GGAAACTTCTTGTTTCCTATATCTATATCCTGTTGCTAGCATCAA
*
40292789 GGAAACTTCTCGTTTCCT
1 GGAAACTTCTTGTTTCCT
40292807 GCACCTGTAG
Statistics
Matches: 169, Mismatches: 27, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
45 168 0.99
46 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (45 bp):
GGAAACTTCTTGTTTCCTATATCTATATCCTGTTGCTAGCATCAA
Found at i:40294397 original size:8 final size:8
Alignment explanation
Indices: 40294384--40294413 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
40294374 AGTCTTATTC
40294384 AAAAAAAG
1 AAAAAAAG
40294392 AAAAAAAG
1 AAAAAAAG
40294400 -AAAAAAG
1 AAAAAAAG
40294407 AAAAAAA
1 AAAAAAA
40294414 AAGGAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:40294405 original size:15 final size:15
Alignment explanation
Indices: 40294385--40294413 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40294375 GTCTTATTCA
40294385 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
40294400 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
40294414 AAGGAAGTTA
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:40294684 original size:28 final size:28
Alignment explanation
Indices: 40294652--40294709 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
40294642 TTGATTTAGA
40294652 AATACATTATTCAGAAATTAGGAAGATG
1 AATACATTATTCAGAAATTAGGAAGATG
40294680 AATACATTATTCAGAAATTAGGAAGATG
1 AATACATTATTCAGAAATTAGGAAGATG
40294708 AA
1 AA
40294710 CATATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (28 bp):
AATACATTATTCAGAAATTAGGAAGATG
Found at i:40296804 original size:41 final size:42
Alignment explanation
Indices: 40296759--40296850 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
40296749 ACGACCAAAG
40296759 CACATGCCCATGGGACA-GCCGTGTGTCAGACACGGCCTAGA
1 CACATGCCCATGGGACAGGCCGTGTGTCAGACACGGCCTAGA
*
40296800 CACATGCCCATGGGACAGGCCGTGTGTCAGACATGGCCTAGA
1 CACATGCCCATGGGACAGGCCGTGTGTCAGACACGGCCTAGA
40296842 CACATGCCC
1 CACATGCCC
40296851 GTGTGTCTAC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 17 0.35
42 32 0.65
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (42 bp):
CACATGCCCATGGGACAGGCCGTGTGTCAGACACGGCCTAGA
Found at i:40306796 original size:36 final size:36
Alignment explanation
Indices: 40306739--40306825 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
40306729 ACATCAATAT
* * *
40306739 TCCAACCAAAACACACCAGATGCTCATAAGAGTTAA
1 TCCATCCAAAACACAACAGATGCTCATAAGAGCTAA
* * *
40306775 TCCATCCGAAACACAATAGATGTTCATAAGAGCTAA
1 TCCATCCAAAACACAACAGATGCTCATAAGAGCTAA
40306811 TCCATCCAAAACACA
1 TCCATCCAAAACACA
40306826 CCAATGGCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.44, C:0.28, G:0.10, T:0.18
Consensus pattern (36 bp):
TCCATCCAAAACACAACAGATGCTCATAAGAGCTAA
Done.