Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 70 of 163
Found at i:23132935 original size:29 final size:29
Alignment explanation
Indices: 23132874--23132935 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
23132864 CAATTTCATT
*
23132874 TTTTTAAGAAAATTTTAAATATTTTTATT
1 TTTTTAAGAAAATTTTAAATATTTTTATA
23132903 TTTTTAA-AATAATTTTAAA-ATTTTTAATA
1 TTTTTAAGAA-AATTTTAAATATTTTT-ATA
23132932 TTTT
1 TTTT
23132936 CAACAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAATATTTTTATA
Found at i:23133055 original size:14 final size:15
Alignment explanation
Indices: 23133026--23133059 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
23133016 AAATTTTAAA
23133026 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
23133041 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
23133055 TTTTA
1 TTTTA
23133060 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:23136826 original size:126 final size:125
Alignment explanation
Indices: 23136602--23136883 Score: 392
Period size: 126 Copynumber: 2.2 Consensus size: 125
23136592 CATGAGGGCA
* * * *
23136602 CGATTTGACACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
** **
23136667 AAATCGCGTCCACGAGGGCGTGATTTCACAATTTCTTATCAT-ATAGCATCCTGGTATCAG
66 AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTATC-TGATAGCATCCTGGTAGAAG
23136727 CGATTTTATACTATTTGCTCATAAAACGTCAAAAAAAAATTATTT-CTGACATGACCAACTGT-G
1 CGATTTTATACTATTTGCTCA-AAAACGTCAAAAAAAAATTATTTCCT-ACATGACCAACTGTAG
* *
23136790 CCGAAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
64 -CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTATCTGATAGCATCCTGGTAGAAG
*
23136853 CGATTTTATACTATTTGAC-CAGAAACGTCAA
1 CGATTTTATACTATTTG-CTCAAAAACGTCAA
23136884 CTCGAAATAA
Statistics
Matches: 141, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
125 32 0.23
126 108 0.77
127 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (125 bp):
CGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTATCTGATAGCATCCTGGTAGAAG
Found at i:23142523 original size:32 final size:32
Alignment explanation
Indices: 23142487--23142550 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
23142477 ACTTTTTATC
23142487 TTCAAGTCTCTTCACATTACTAACTCTTCATA
1 TTCAAGTCTCTTCACATTACTAACTCTTCATA
* *
23142519 TTCAAGTCTCTTCACATTTCTAACTTTTCATA
1 TTCAAGTCTCTTCACATTACTAACTCTTCATA
23142551 ATTTATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.44
Consensus pattern (32 bp):
TTCAAGTCTCTTCACATTACTAACTCTTCATA
Found at i:23146920 original size:42 final size:41
Alignment explanation
Indices: 23146874--23146976 Score: 135
Period size: 39 Copynumber: 2.6 Consensus size: 41
23146864 TAACTCTTTA
*
23146874 TATAGGAGTTGTAAGTGACTATTCATCTACATCAC-TAAATGC
1 TATAGGAGTTGT--GTGACTATTCATCTACATAACTTAAATGC
*
23146916 TATAGGAG-T-TGTGACTATTCATTTACATAACTTAAATGC
1 TATAGGAGTTGTGTGACTATTCATCTACATAACTTAAATGC
23146955 TATAGGAG-T-TGTGACTATTCAT
1 TATAGGAGTTGTGTGACTATTCAT
23146977 GCATGAGTGT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
38 19 0.33
39 29 0.50
40 1 0.02
41 1 0.02
42 8 0.14
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (41 bp):
TATAGGAGTTGTGTGACTATTCATCTACATAACTTAAATGC
Found at i:23146943 original size:38 final size:39
Alignment explanation
Indices: 23146888--23146976 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 39
23146878 GGAGTTGTAA
*
23146888 GTGACTATTCATCTACATCAC-TAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATGCTATAGGAGTT
*
23146926 GTGACTATTCATTTACATAACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATGCTATAGGAGTT
23146965 GTGACTATTCAT
1 GTGACTATTCAT
23146977 GCATGAGTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 19 0.40
39 29 0.60
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (39 bp):
GTGACTATTCATCTACATAACTTAAATGCTATAGGAGTT
Found at i:23147034 original size:32 final size:32
Alignment explanation
Indices: 23146998--23147061 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
23146988 ACTTTTTATC
23146998 TTCAAGTCTCTTCACATTACTAACTCTTCATA
1 TTCAAGTCTCTTCACATTACTAACTCTTCATA
* *
23147030 TTCAAGTCTCTTCACATTTCTAACTTTTCATA
1 TTCAAGTCTCTTCACATTACTAACTCTTCATA
23147062 ATTTATTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.44
Consensus pattern (32 bp):
TTCAAGTCTCTTCACATTACTAACTCTTCATA
Found at i:23149986 original size:28 final size:27
Alignment explanation
Indices: 23149945--23149997 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
23149935 CAATGACAGA
* *
23149945 ATAGAACAATGTGGGCTTTAGCCCACT
1 ATAGAACAAGGTGGGCCTTAGCCCACT
23149972 ATAGAAACAAGGTGGGCCTTAGCCCA
1 ATAG-AACAAGGTGGGCCTTAGCCCA
23149998 ATACAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (27 bp):
ATAGAACAAGGTGGGCCTTAGCCCACT
Found at i:23150007 original size:28 final size:28
Alignment explanation
Indices: 23149949--23150009 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
23149939 GACAGAATAG
* * * * *
23149949 AACAATGTGGGCTTTAGCCCACTATAGA
1 AACAAGGTGGGCCTTAGCCCAATACAAA
23149977 AACAAGGTGGGCCTTAGCCCAATACAAA
1 AACAAGGTGGGCCTTAGCCCAATACAAA
23150005 AACAA
1 AACAA
23150010 TATGCAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (28 bp):
AACAAGGTGGGCCTTAGCCCAATACAAA
Found at i:23150204 original size:27 final size:27
Alignment explanation
Indices: 23150167--23150231 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
23150157 AGCAGAGCTG
23150167 CCAGT-ACAGTATATGTGGCAAAGCCA
1 CCAGTAACAGTATATGTGGCAAAGCCA
*
23150193 CCAGTAACAGTATATGTGGCAGAGCCA
1 CCAGTAACAGTATATGTGGCAAAGCCA
*
23150220 CCTGTAACAGTA
1 CCAGTAACAGTA
23150232 CTTTCTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 5 0.14
27 31 0.86
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCAAAGCCA
Found at i:23150464 original size:27 final size:27
Alignment explanation
Indices: 23150434--23150485 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
23150424 ACGGTCATTT
23150434 TACCCTATAAAGGTATTTCGGTAATCC
1 TACCCTATAAAGGTATTTCGGTAATCC
**
23150461 TACCCTATAGGGGTATTTCGGTAAT
1 TACCCTATAAAGGTATTTCGGTAAT
23150486 TTCACAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
TACCCTATAAAGGTATTTCGGTAATCC
Found at i:23153932 original size:36 final size:36
Alignment explanation
Indices: 23153887--23153966 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
23153877 GTGAACCATG
* *
23153887 TTAACTTGGTGAAT-TATATTATTATGGTGAACTGTA
1 TTAATTTGGTG-ATCTATATTAGTATGGTGAACTGTA
* *
23153923 TTTATTTGGTGATCTGTATTAGTATGGTGAACTGTA
1 TTAATTTGGTGATCTATATTAGTATGGTGAACTGTA
23153959 TTAATTTG
1 TTAATTTG
23153967 CCAAACTGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 2 0.05
36 36 0.95
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (36 bp):
TTAATTTGGTGATCTATATTAGTATGGTGAACTGTA
Found at i:23153957 original size:18 final size:17
Alignment explanation
Indices: 23153893--23153961 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 17
23153883 CATGTTAACT
* *
23153893 TGGTGAATTATATTATTA
1 TGGTGAACTGTATTA-TA
*
23153911 TGGTGAACTGTATTTATT
1 TGGTGAACTGTA-TTATA
*
23153929 TGGTGATCTGTATTAGTA
1 TGGTGAACTGTATTA-TA
23153947 TGGTGAACTGTATTA
1 TGGTGAACTGTATTA
23153962 ATTTGCCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.07
18 37 0.86
19 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.46
Consensus pattern (17 bp):
TGGTGAACTGTATTATA
Found at i:23155328 original size:20 final size:20
Alignment explanation
Indices: 23155303--23155341 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
23155293 GCATGAGATG
23155303 TAACATAGAATTTGGTTAAT
1 TAACATAGAATTTGGTTAAT
23155323 TAACATAGAATTTGGTTAA
1 TAACATAGAATTTGGTTAA
23155342 GTCATGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (20 bp):
TAACATAGAATTTGGTTAAT
Found at i:23155929 original size:15 final size:15
Alignment explanation
Indices: 23155905--23155938 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
23155895 GTGAAAATTT
23155905 CATG-CTTCAATCAC
1 CATGTCTTCAATCAC
23155919 CATGTCTTCAATCAC
1 CATGTCTTCAATCAC
23155934 CATGT
1 CATGT
23155939 TATCACTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.32
Consensus pattern (15 bp):
CATGTCTTCAATCAC
Found at i:23167131 original size:15 final size:15
Alignment explanation
Indices: 23167107--23167136 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23167097 AATTTCATTC
*
23167107 TTCAATCACCATGTT
1 TTCAAACACCATGTT
23167122 TTCAAACACCATGTT
1 TTCAAACACCATGTT
23167137 ATCACTTAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (15 bp):
TTCAAACACCATGTT
Found at i:23179058 original size:39 final size:39
Alignment explanation
Indices: 23178995--23179074 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
23178985 TCACATTACA
** *
23178995 CATACAATTACATAATGTTGAAGCACATATCGCAATACT
1 CATACAATTACATAACCTTCAAGCACATATCGCAATACT
* * *
23179034 CATATAATTACATAACCTTCAAGCATATATCGCAGTACT
1 CATACAATTACATAACCTTCAAGCACATATCGCAATACT
23179073 CA
1 CA
23179075 AAAACATGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.29
Consensus pattern (39 bp):
CATACAATTACATAACCTTCAAGCACATATCGCAATACT
Found at i:23180342 original size:21 final size:22
Alignment explanation
Indices: 23180307--23180357 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
23180297 GCTTTTATTC
* *
23180307 AAAACATGCGATTTAATGGCTA
1 AAAACATGCGATTTAAAGACTA
*
23180329 AAAACATG-GTTTTAAAGACTA
1 AAAACATGCGATTTAAAGACTA
23180350 AATAACAT
1 AA-AACAT
23180358 TTAAAACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (22 bp):
AAAACATGCGATTTAAAGACTA
Found at i:23183065 original size:34 final size:34
Alignment explanation
Indices: 23183022--23183089 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
23183012 AGCAGAGATA
23183022 CTTACCTCATTCACTCGTTTAAATGTGGTGTCTT
1 CTTACCTCATTCACTCGTTTAAATGTGGTGTCTT
23183056 CTTACCTCATTCACTCGTTTAAATGTGGTGTCTT
1 CTTACCTCATTCACTCGTTTAAATGTGGTGTCTT
23183090 GTTGCAAGCT
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:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (34 bp):
CTTACCTCATTCACTCGTTTAAATGTGGTGTCTT
Found at i:23185024 original size:24 final size:24
Alignment explanation
Indices: 23184992--23185042 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
23184982 TTTAATCCTC
23184992 CTCCTCATTGCCCTAGCCGTTCAT
1 CTCCTCATTGCCCTAGCCGTTCAT
23185016 CTCCTCATTGCCCTAGCCGTTCAT
1 CTCCTCATTGCCCTAGCCGTTCAT
23185040 CTC
1 CTC
23185043 TCTCCCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.43, G:0.12, T:0.33
Consensus pattern (24 bp):
CTCCTCATTGCCCTAGCCGTTCAT
Found at i:23192140 original size:27 final size:27
Alignment explanation
Indices: 23192075--23192145 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
23192065 TCGCTCGAGG
* *
23192075 TGACTGTTATACTCCTATGGGATAAAA
1 TGACTGTTATACCCCTAAGGGATAAAA
* **
23192102 TGACCGAAATACCCCTACAGGG-TAAAA
1 TGACTGTTATACCCCTA-AGGGATAAAA
23192129 TGACTGTTATACCCCTA
1 TGACTGTTATACCCCTA
23192146 GGAATTGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (27 bp):
TGACTGTTATACCCCTAAGGGATAAAA
Found at i:23197422 original size:19 final size:19
Alignment explanation
Indices: 23197370--23197425 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
23197360 AAGAACCCTG
23197370 CCATATTTCGAGGTTATTC
1 CCATATTTCGAGGTTATTC
* **
23197389 CC--ACTTC--TTTTATTC
1 CCATATTTCGAGGTTATTC
23197404 CCATATTTCGAGGTTATTC
1 CCATATTTCGAGGTTATTC
23197423 CCA
1 CCA
23197426 CTTCTCTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
15 8 0.30
17 8 0.30
19 11 0.41
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.43
Consensus pattern (19 bp):
CCATATTTCGAGGTTATTC
Found at i:23197563 original size:16 final size:17
Alignment explanation
Indices: 23197522--23197564 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
23197512 TTCTTTCCAT
**
23197522 AGTTGTTCTTAATATAG
1 AGTTGTTCCGAATATAG
23197539 AGATTGTTCCGAATA-AG
1 AG-TTGTTCCGAATATAG
23197556 AGTTGTTCC
1 AGTTGTTCC
23197565 ATAGTGATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 6 0.26
18 10 0.43
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (17 bp):
AGTTGTTCCGAATATAG
Found at i:23197745 original size:16 final size:16
Alignment explanation
Indices: 23197704--23197748 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
23197694 TTCTAAATAA
* *
23197704 TAGTTGTTCTGAACAT
1 TAGTTGTTCTCAACAG
* *
23197720 TAGCTATTCTCAACAG
1 TAGTTGTTCTCAACAG
23197736 TAGTTGTTCTCAA
1 TAGTTGTTCTCAA
23197749 ATAACAACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (16 bp):
TAGTTGTTCTCAACAG
Found at i:23197854 original size:16 final size:16
Alignment explanation
Indices: 23197833--23197865 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
23197823 TCTTCGATCG
*
23197833 ACAACTGTTCTGAACA
1 ACAACTATTCTGAACA
23197849 ACAACTATTCTGAACA
1 ACAACTATTCTGAACA
23197865 A
1 A
23197866 GAGTTGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (16 bp):
ACAACTATTCTGAACA
Found at i:23199882 original size:12 final size:12
Alignment explanation
Indices: 23199865--23199890 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23199855 AGTTTGAGGA
23199865 TTGTTGTTATTG
1 TTGTTGTTATTG
23199877 TTGTTGTTATTG
1 TTGTTGTTATTG
23199889 TT
1 TT
23199891 CATCAACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (12 bp):
TTGTTGTTATTG
Found at i:23208406 original size:21 final size:21
Alignment explanation
Indices: 23208381--23208460 Score: 108
Period size: 21 Copynumber: 3.8 Consensus size: 21
23208371 ATGCCAACAA
23208381 AAGCTCATAAGAGCTGAAAAG
1 AAGCTCATAAGAGCTGAAAAG
* *
23208402 AAGCTCAAAAGAGCTGAACAG
1 AAGCTCATAAGAGCTGAAAAG
*
23208423 AAGCTCATAATAGCTGAACAA-
1 AAGCTCATAAGAGCTGAA-AAG
*
23208444 AAGCTCTTAAGAGCTGA
1 AAGCTCATAAGAGCTGA
23208461 TCCACCCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 50 0.98
22 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.16
Consensus pattern (21 bp):
AAGCTCATAAGAGCTGAAAAG
Found at i:23210834 original size:48 final size:46
Alignment explanation
Indices: 23210781--23210924 Score: 164
Period size: 46 Copynumber: 3.1 Consensus size: 46
23210771 ATTTGAGTTA
* * *
23210781 AACCTACATGAATGATGAATCATATTGTCTGGTCACCCGTTAAGGTTG
1 AACCTACATGAAT-ATG-ATAATAGTGTCTGTTCACCCGTTAAGGTTG
* * * *
23210829 AACCTACATGAATCTGATAATAGTGTCAGTTCACCCATTAAAGTTG
1 AACCTACATGAATATGATAATAGTGTCTGTTCACCCGTTAAGGTTG
* * *
23210875 AACCTACACGAATCA-GATAATAGTGCCTGTTCACCCGTTAGGGTTG
1 AACCTACATGAAT-ATGATAATAGTGTCTGTTCACCCGTTAAGGTTG
23210921 AACC
1 AACC
23210925 CAAACAACAA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
46 66 0.81
47 2 0.02
48 13 0.16
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (46 bp):
AACCTACATGAATATGATAATAGTGTCTGTTCACCCGTTAAGGTTG
Found at i:23214940 original size:3 final size:3
Alignment explanation
Indices: 23214932--23214962 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
23214922 ATGCTTTCTA
23214932 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
23214963 GTTAACAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23218786 original size:5 final size:5
Alignment explanation
Indices: 23218776--23218806 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
23218766 TGAGCATTCG
*
23218776 ATCGA ATCGA ATCGA ATTGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
23218807 AATTTTCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (5 bp):
ATCGA
Found at i:23218904 original size:5 final size:5
Alignment explanation
Indices: 23218896--23218921 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23218886 GAGATAGAAT
23218896 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
23218922 TGTTCGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:23219730 original size:9 final size:9
Alignment explanation
Indices: 23219716--23219752 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
23219706 TATAGTTTGA
23219716 TATTCGAAT
1 TATTCGAAT
23219725 TATTCGAAT
1 TATTCGAAT
*
23219734 TATTCGAGT
1 TATTCGAAT
23219743 TATTCGAAT
1 TATTCGAAT
23219752 T
1 T
23219753 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:23219822 original size:9 final size:9
Alignment explanation
Indices: 23219805--23219835 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
23219795 TCGAGTTGAT
23219805 TCGAATAAC
1 TCGAATAAC
*
23219814 TCGATTAAC
1 TCGAATAAC
23219823 TCGAATAAC
1 TCGAATAAC
23219832 TCGA
1 TCGA
23219836 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:23221612 original size:7 final size:7
Alignment explanation
Indices: 23221602--23221627 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23221592 ACAATTATAC
23221602 TTGAATT
1 TTGAATT
23221609 TTGAATT
1 TTGAATT
23221616 TTGAATT
1 TTGAATT
23221623 TTGAA
1 TTGAA
23221628 AAGTAGAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (7 bp):
TTGAATT
Found at i:23221878 original size:12 final size:12
Alignment explanation
Indices: 23221863--23221889 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23221853 TTCTAAATGT
23221863 TAATTCTAAGAC
1 TAATTCTAAGAC
23221875 TAATTCTAAGAC
1 TAATTCTAAGAC
23221887 TAA
1 TAA
23221890 GCATATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (12 bp):
TAATTCTAAGAC
Found at i:23224408 original size:23 final size:23
Alignment explanation
Indices: 23224378--23224433 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
23224368 AGACCCAAGA
*
23224378 TGAATTAATTCTGAATCCGTTTT
1 TGAATTAATTCTGAATCCGTTTG
*
23224401 TGAATTAATTTTGAATCCGTTTG
1 TGAATTAATTCTGAATCCGTTTG
23224424 TGAA-TAATTC
1 TGAATTAATTC
23224434 ACTTGTGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (23 bp):
TGAATTAATTCTGAATCCGTTTG
Found at i:23225260 original size:19 final size:19
Alignment explanation
Indices: 23225238--23225277 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23225228 ATTAATTTTG
* *
23225238 ATCAAGTAAATTTAAATTA
1 ATCAAATAAATTAAAATTA
*
23225257 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
23225276 AT
1 AT
23225278 ATGATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:23232448 original size:24 final size:24
Alignment explanation
Indices: 23232421--23232476 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
23232411 TTTCTTGAAA
**
23232421 AAATAATTTTGATTAAGTAAAATT
1 AAATAATTTAAATTAAGTAAAATT
*
23232445 AAATTAA-TTAAATTAATTAAAATT
1 AAA-TAATTTAAATTAAGTAAAATT
23232469 AATATAAT
1 AA-ATAAT
23232477 ATTTTTGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATAATTTAAATTAAGTAAAATT
Found at i:23232455 original size:9 final size:9
Alignment explanation
Indices: 23232441--23232471 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
23232431 GATTAAGTAA
23232441 AATTAAATT
1 AATTAAATT
23232450 AATTAAATT
1 AATTAAATT
23232459 AATTAAAATT
1 AATT-AAATT
23232469 AAT
1 AAT
23232472 ATAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:23232913 original size:37 final size:36
Alignment explanation
Indices: 23232862--23232937 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
23232852 ATTTCAAAGA
*
23232862 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATAT
*
23232898 TAATACTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATAT
23232935 TAA
1 TAA
23232938 AGTGATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATAT
Found at i:23232967 original size:59 final size:60
Alignment explanation
Indices: 23232891--23233005 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
23232881 TAATATTAAA
* * *
23232891 TTTAATTTAATACTTATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTGATTATCTT
1 TTTAATCTAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTATCTT
*
23232950 TTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTA
1 TTTAATCTAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTA
23233006 AGTTTAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 21 0.41
60 30 0.59
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (60 bp):
TTTAATCTAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTATCTT
Found at i:23235400 original size:20 final size:20
Alignment explanation
Indices: 23235372--23235432 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
23235362 AGTTTAATTA
23235372 AACTT-AATTAATCAAGGTT
1 AACTTAAATTAATCAAGGTT
23235391 AACTTAAATTAATCAAGGTT
1 AACTTAAATTAATCAAGGTT
*
23235411 AACTTAAATTAATCAAGTTT
1 AACTTAAATTAATCAAGGTT
23235431 AA
1 AA
23235433 TTATGATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 5 0.12
20 35 0.88
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (20 bp):
AACTTAAATTAATCAAGGTT
Found at i:23237651 original size:30 final size:30
Alignment explanation
Indices: 23237617--23237712 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
23237607 ATTTATCTCG
23237617 ATATTAATATGAGATA-TTACATTTAATTCA
1 ATATTAATATGAGATAGTTA-ATTTAATTCA
* * * **
23237647 ATATTTATCT-AGAAAGGTTTTTATTAATTCA
1 ATATTAATATGAGATA-GTTAAT-TTAATTCA
* * *
23237678 ATATTAATTTGAGATATTTAATTTAATTTA
1 ATATTAATATGAGATAGTTAATTTAATTCA
23237708 ATATT
1 ATATT
23237713 TATCTAGATA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
29 4 0.08
30 21 0.42
31 21 0.42
32 4 0.08
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (30 bp):
ATATTAATATGAGATAGTTAATTTAATTCA
Found at i:23237730 original size:61 final size:60
Alignment explanation
Indices: 23237617--23237734 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 60
23237607 ATTTATCTCG
23237617 ATATTAATATGAGATATTACATTTAATTCAATATTTATCTAGAAAGGTTTTTATTAATTCA
1 ATATTAATATGAGATATTACATTTAATTCAATATTTATCTAGAAA-GTTTTTATTAATTCA
* *
23237678 ATATTAATTTGAGATATTTA-ATTTAATTTAATATTTATCTAGATAA-TATTTTATTAA
1 ATATTAATATGAGATA-TTACATTTAATTCAATATTTATCTAGA-AAGT-TTTTATTAA
23237735 ATTAGTATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
60 1 0.02
61 46 0.88
62 5 0.10
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (60 bp):
ATATTAATATGAGATATTACATTTAATTCAATATTTATCTAGAAAGTTTTTATTAATTCA
Found at i:23237899 original size:26 final size:26
Alignment explanation
Indices: 23237847--23237897 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
23237837 AGTTGTAGAG
*
23237847 AGAAGATTCTCTACATAAATTATTTT
1 AGAAAATTCTCTACATAAATTATTTT
* *
23237873 AGAAAATT-TCTAGATATATTATTTT
1 AGAAAATTCTCTACATAAATTATTTT
23237898 TATTTACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (26 bp):
AGAAAATTCTCTACATAAATTATTTT
Found at i:23240157 original size:32 final size:32
Alignment explanation
Indices: 23240116--23240198 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
23240106 GTCCAGATTA
* *
23240116 GCCTTGCCCGTGTAGCCCATAAGCCCAATCTG
1 GCCTAGCCCGTGTGGCCCATAAGCCCAATCTG
* *
23240148 GCCTAGCCCGTGTGGCCCACACGCCCAATCTG
1 GCCTAGCCCGTGTGGCCCATAAGCCCAATCTG
*
23240180 G-CTAGCTCGTGTGGCCCAT
1 GCCTAGCCCGTGTGGCCCAT
23240199 TACACAGCCG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
31 16 0.36
32 29 0.64
ACGTcount: A:0.16, C:0.39, G:0.25, T:0.20
Consensus pattern (32 bp):
GCCTAGCCCGTGTGGCCCATAAGCCCAATCTG
Found at i:23244483 original size:45 final size:44
Alignment explanation
Indices: 23244408--23244539 Score: 142
Period size: 45 Copynumber: 3.0 Consensus size: 44
23244398 TACACGGTTG
* * * *
23244408 ATCAGCAGATAGC-ACCACCCTTATAGTCAATGATACTCGGTGGA
1 ATCAGCACATAGCAACCA-CCTTATAATCAATGATACCCGGTAGA
* *
23244452 ATTAGCACATAGCAACCACCTTCATAATCAAT-AGTACCCGATAGA
1 ATCAGCACATAGCAACCACCTT-ATAATCAATGA-TACCCGGTAGA
* *
23244497 ATCAGCACACAACAACCACCTTTATAATCAATGATACCCGGTA
1 ATCAGCACATAGCAACCACC-TTATAATCAATGATACCCGGTA
23244540 TACGTAGTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
44 16 0.22
45 54 0.74
46 3 0.04
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (44 bp):
ATCAGCACATAGCAACCACCTTATAATCAATGATACCCGGTAGA
Found at i:23244785 original size:20 final size:20
Alignment explanation
Indices: 23244757--23244817 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
23244747 CATTTAACTT
23244757 AATTAACACTCATATTATTC
1 AATTAACACTCATATTATTC
* *
23244777 AATTTACA--CAT-TTA-AC
1 AATTAACACTCATATTATTC
23244793 TAATTAACACTCATATTATTC
1 -AATTAACACTCATATTATTC
23244814 AATT
1 AATT
23244818 TAGTCCGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 1 0.03
17 10 0.31
18 3 0.09
19 3 0.09
20 14 0.44
21 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTAACACTCATATTATTC
Found at i:23244804 original size:37 final size:38
Alignment explanation
Indices: 23244744--23244819 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
23244734 ATTTATAATA
23244744 ACACATTTAACTTAATTAACACTCATATTATTCAATTT
1 ACACATTTAACTTAATTAACACTCATATTATTCAATTT
23244782 ACACATTTAAC-TAATTAACACTCATATTATTCAATTT
1 ACACATTTAACTTAATTAACACTCATATTATTCAATTT
23244819 A
1 A
23244820 GTCCGAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 27 0.71
38 11 0.29
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (38 bp):
ACACATTTAACTTAATTAACACTCATATTATTCAATTT
Found at i:23246375 original size:36 final size:36
Alignment explanation
Indices: 23246328--23246399 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
23246318 TTAGGGATCT
23246328 AAATTTCTTAAACTTCTAAAGTGGCACCATTTTACC
1 AAATTTCTTAAACTTCTAAAGTGGCACCATTTTACC
23246364 AAATTTCTTAAACTTCTAAAGTGGCACCATTTTACC
1 AAATTTCTTAAACTTCTAAAGTGGCACCATTTTACC
23246400 TCTTGGTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.36
Consensus pattern (36 bp):
AAATTTCTTAAACTTCTAAAGTGGCACCATTTTACC
Found at i:23246587 original size:20 final size:20
Alignment explanation
Indices: 23246555--23246592 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23246545 ATAAGTTTTG
23246555 AATTTCATTCAATTTAGTCT
1 AATTTCATTCAATTTAGTCT
23246575 AATTT-ATTACAATTTAGT
1 AATTTCATT-CAATTTAGT
23246593 TATTGACCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTCATTCAATTTAGTCT
Found at i:23248986 original size:36 final size:36
Alignment explanation
Indices: 23248946--23249029 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
23248936 AATTTCAAGG
* * *
23248946 TGGCTTTGTGGA-GAGATGTTGTTACAAATGAAATAT
1 TGGCTTTGTAGACG-GATGTTATTACAAATGAAATAA
* **
23248982 TGGCTTTGCAGACGGATGTTATTTGAAATGAAATAA
1 TGGCTTTGTAGACGGATGTTATTACAAATGAAATAA
23249018 TGGCTTTGTAGA
1 TGGCTTTGTAGA
23249030 GGTATGATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 39 0.98
37 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (36 bp):
TGGCTTTGTAGACGGATGTTATTACAAATGAAATAA
Found at i:23249252 original size:26 final size:26
Alignment explanation
Indices: 23249213--23249293 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
23249203 GTATAGTATA
* *
23249213 TGTGAACTAACTTTGAAAAGTATTTATG
1 TGTGAACT--CTTTGTAAAGTAATTATG
* * **
23249241 TGTGAGCTCTTTCTATGGTAATTATG
1 TGTGAACTCTTTGTAAAGTAATTATG
*
23249267 TGTGAACTCTTTGTAAA-TAGTTATG
1 TGTGAACTCTTTGTAAAGTAATTATG
23249292 TG
1 TG
23249294 CTTGCCAACT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
25 9 0.21
26 26 0.62
28 7 0.17
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (26 bp):
TGTGAACTCTTTGTAAAGTAATTATG
Found at i:23253323 original size:18 final size:18
Alignment explanation
Indices: 23253300--23253336 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
23253290 TAAAGGAAAG
23253300 GTTATGGTTATATGTAAA
1 GTTATGGTTATATGTAAA
23253318 GTTATGGTTATATGTAAA
1 GTTATGGTTATATGTAAA
23253336 G
1 G
23253337 GCACACTTCG
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:0.00, G:0.24, T:0.43
Consensus pattern (18 bp):
GTTATGGTTATATGTAAA
Found at i:23261084 original size:26 final size:27
Alignment explanation
Indices: 23261055--23261109 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
23261045 CCCAACAAAA
* *
23261055 TTTTGACAATTTTACCCTTGG-TAAAT
1 TTTTAACAATTTTACCCCTGGTTAAAT
*
23261081 TTTTAACGATTTTACCCCTGGTTAAAT
1 TTTTAACAATTTTACCCCTGGTTAAAT
23261108 TT
1 TT
23261110 CGAGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (27 bp):
TTTTAACAATTTTACCCCTGGTTAAAT
Found at i:23261293 original size:12 final size:12
Alignment explanation
Indices: 23261258--23261299 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
23261248 TGCAAATGGA
23261258 TCATTTCCATTT
1 TCATTTCCATTT
*
23261270 TCATTAT-AATTT
1 TCATT-TCCATTT
23261282 TCATTTCCATTT
1 TCATTTCCATTT
*
23261294 CCATTT
1 TCATTT
23261300 TTGGAACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:23281630 original size:5 final size:5
Alignment explanation
Indices: 23281620--23281644 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23281610 AAATGGGAAA
23281620 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
23281645 TTAATGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:23283655 original size:91 final size:88
Alignment explanation
Indices: 23283500--23283690 Score: 213
Period size: 91 Copynumber: 2.1 Consensus size: 88
23283490 CTCCAGTTTA
* * * * *
23283500 TGGATAAACCACCAGTGTTGCAGGTTAATACGCTGCCAGCAATTGTGAGTACACAACGGATTTGC
1 TGGATAAACCACAAGTGTTGCAAGTTAATACGCTGCCAACAATTGTGAATACACAACGAATTTGC
* * *
23283565 AGATAATAGTTGCCAGTATAAGTTG
66 AAATAAAAGCTGCCAG--TAAGTTG
* * * *
23283590 TGGATAAACCACAAGTTTTTGCAAGTTAATATGCTGCCAATAGTTGTGAATACACAAC-AACTTT
1 TGGATAAACCACAAG-TGTTGCAAGTTAATACGCTGCCAACAATTGTGAATACACAACGAA-TTT
*
23283654 GCAAATAAAAGCTGCCAGTAATTTG
64 GCAAATAAAAGCTGCCAGTAAGTTG
*
23283679 TGAATAAACCAC
1 TGGATAAACCAC
23283691 CAAACTTTGC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
89 17 0.20
90 15 0.18
91 53 0.62
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (88 bp):
TGGATAAACCACAAGTGTTGCAAGTTAATACGCTGCCAACAATTGTGAATACACAACGAATTTGC
AAATAAAAGCTGCCAGTAAGTTG
Found at i:23290232 original size:26 final size:25
Alignment explanation
Indices: 23290196--23290265 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 25
23290186 AAAAATAAAA
*
23290196 ATTTATCAAAATATTATAACTTTTTT
1 ATTTACCAAAATATTATAA-TTTTTT
23290222 ATTTACCAAAATATATATAATTTTTT
1 ATTTACCAAAATAT-TATAATTTTTT
23290248 ATTTACCAAAATA-TATAA
1 ATTTACCAAAATATTATAA
23290266 AAAAAAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
24 5 0.12
26 32 0.76
27 5 0.12
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTACCAAAATATTATAATTTTTT
Found at i:23290364 original size:27 final size:27
Alignment explanation
Indices: 23290334--23290427 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 27
23290324 CGCCATTGGG
* *
23290334 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
23290361 ATTGGCGGCATCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
* * *
23290388 ATTAGAGGCATCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
23290415 ATTGGCAGCACCA
1 ATTGGCGGCACCA
23290428 CTTAATAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:23290478 original size:4 final size:4
Alignment explanation
Indices: 23290469--23290602 Score: 86
Period size: 4 Copynumber: 33.0 Consensus size: 4
23290459 GAAGGAGAGG
* *
23290469 GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
*
23290517 GAAAA GGAAA G-GA GAAGA GAAA -AAGA GAAA GAAA G-AA G-AA G-AA
1 G-AAA -GAAA GAAA GAA-A GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
*
23290560 GAAAA GGAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 G-AAA -G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
23290603 AGGAAAGGAG
Statistics
Matches: 107, Mismatches: 8, Indels: 30
0.74 0.06 0.21
Matches are distributed among these distances:
3 20 0.19
4 57 0.53
5 23 0.21
6 7 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:23290498 original size:18 final size:18
Alignment explanation
Indices: 23290477--23290531 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
23290467 GGGAAAGAAA
23290477 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGGAGAG
*
23290495 GAAAGAAAGAAA-AAGAAG
1 GAAAGAAAGAAAGGAG-AG
23290513 GAAAGAAAAGGAAAGGAGA
1 GAAAG-AAA-GAAAGGAGA
23290532 AGAGAAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 2 0.06
18 19 0.61
19 3 0.10
20 5 0.16
21 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAAGGAGAG
Found at i:23290537 original size:18 final size:18
Alignment explanation
Indices: 23290516--23290621 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
23290506 AAAGAAGGAA
23290516 AGAAAAGGAAAGGAGAAG
1 AGAAAAGGAAAGGAGAAG
23290534 AGAAAAAGAGAAAGAAAGAAGAAG
1 AG-AAAAG-GAAAG---G-AGAAG
*
23290558 AAGAAAAGGAAAAGAGAAG
1 -AGAAAAGGAAAGGAGAAG
* *
23290577 A-AAAAAGAAAGAAAGAAGG
1 AGAAAAGGAAAG-GAGAA-G
23290596 AAAGAAAAGGAAAGGAGAAG
1 --AGAAAAGGAAAGGAGAAG
23290616 AGAAAA
1 AGAAAA
23290622 AAAGAAGAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
17 8 0.11
18 13 0.19
19 11 0.16
20 7 0.10
21 5 0.07
22 9 0.13
23 5 0.07
24 10 0.14
25 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AGAAAAGGAAAGGAGAAG
Found at i:23290546 original size:44 final size:43
Alignment explanation
Indices: 23290496--23290640 Score: 187
Period size: 43 Copynumber: 3.5 Consensus size: 43
23290486 AAAGGAGAGG
23290496 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
*
23290539 AAGAGAAAGAAAGAAGAA-G-AAGAAAAGGAAAAGAG-A-AGAAA
1 AA-AGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
23290580 AAAGAAAG--AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
* *
23290621 AAA-AGAAGAAGAAGAGGGAA
1 AAAGA-AAGAAAAAGAAGGAA
23290641 TGAAGGAAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
37 5 0.06
38 2 0.02
39 15 0.17
40 8 0.09
41 18 0.20
42 1 0.01
43 25 0.28
44 10 0.11
45 5 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (43 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
Found at i:23290582 original size:74 final size:70
Alignment explanation
Indices: 23290469--23290635 Score: 176
Period size: 74 Copynumber: 2.3 Consensus size: 70
23290459 GAAGGAGAGG
* * * *
23290469 GAAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAG-A-AAAGGAAAGGAGA
1 GAAAGAAAG-AAG-AAG-AAGAAAAGGAAAGAAAGAAAAAGAAAGAAAGAAGAAAGAAAAGGA-A
23290532 AGAGAAAAAGA
62 AG-G-AAAAGA
23290543 GAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGGAA
1 GAAAGAAAGAAGAAGAAGAAAAGG-AAAGA-AAG-AAAAAGAAAGAAAGAA-GAAAGAAAAGGAA
*
23290608 AGGAGAAGA
62 AGGAAAAGA
*
23290617 GAAAAAAAGAAGAAGAAGA
1 GAAAGAAAGAAGAAGAAGA
23290636 GGGAATGAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
71 7 0.09
72 8 0.10
73 6 0.07
74 45 0.56
75 2 0.02
76 3 0.04
77 10 0.12
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (70 bp):
GAAAGAAAGAAGAAGAAGAAAAGGAAAGAAAGAAAAAGAAAGAAAGAAGAAAGAAAAGGAAAGGA
AAAGA
Found at i:23293910 original size:3 final size:3
Alignment explanation
Indices: 23293902--23293963 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
23293892 NNNTCATACT
23293902 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
23293950 AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AA
23293964 TAATAATAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:23293968 original size:3 final size:3
Alignment explanation
Indices: 23293962--23294002 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
23293952 CAACAACAAC
*
23293962 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
23294003 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23294072 original size:19 final size:21
Alignment explanation
Indices: 23294048--23294086 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
23294038 ACTAAAACAA
*
23294048 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
23294067 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
23294087 ATCAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:23294279 original size:27 final size:27
Alignment explanation
Indices: 23294249--23294306 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
23294239 CCAAACAATA
*
23294249 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGCCAT
*
23294276 TGGCATCATTGGTGCCGCCAATGCCAT
1 TGGCACCATTGGTGCCGCCAATGCCAT
23294303 TGGC
1 TGGC
23294307 GTGACCAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGCCAT
Found at i:23294351 original size:14 final size:14
Alignment explanation
Indices: 23294332--23294359 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23294322 TCATATCGGT
23294332 CAGATTTTTTTTTG
1 CAGATTTTTTTTTG
23294346 CAGATTTTTTTTTG
1 CAGATTTTTTTTTG
23294360 TTTTTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (14 bp):
CAGATTTTTTTTTG
Found at i:23294402 original size:26 final size:28
Alignment explanation
Indices: 23294373--23294442 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
23294363 TTTTGTTTTT
23294373 TATATATTTTGGTAAAT-AAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
*
23294399 TATATTTTTTGGTAAATAAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
23294427 TA-ATATTTTGGTAAAT
1 TATATATTTTGGTAAAT
23294443 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.40
27 19 0.47
28 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAGTTA
Found at i:23296265 original size:22 final size:22
Alignment explanation
Indices: 23296234--23296283 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
23296224 CACAAATCGA
*
23296234 TTTTTTTTTC-TTTTGTTT-AGT
1 TTTTTTTTTCATTTT-TTTCAAT
23296255 TTTTTTGTTTCATTTTTTTCAAT
1 TTTTTT-TTTCATTTTTTTCAAT
23296278 TTTTTT
1 TTTTTT
23296284 ACTATCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 12 0.48
ACGTcount: A:0.08, C:0.06, G:0.06, T:0.80
Consensus pattern (22 bp):
TTTTTTTTTCATTTTTTTCAAT
Found at i:23296505 original size:9 final size:9
Alignment explanation
Indices: 23296486--23296522 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
23296476 TGAGTTTTCG
23296486 AATTCGAAT
1 AATTCGAAT
23296495 AACTT-GAAT
1 AA-TTCGAAT
23296504 AATTCGAAT
1 AATTCGAAT
23296513 AATTCGAAT
1 AATTCGAAT
23296522 A
1 A
23296523 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:23296720 original size:9 final size:9
Alignment explanation
Indices: 23296706--23296736 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
23296696 GTTAAACGAA
23296706 TCGAGTTAT
1 TCGAGTTAT
*
23296715 TCGAGTTAA
1 TCGAGTTAT
23296724 TCGAGTTAT
1 TCGAGTTAT
23296733 TCGA
1 TCGA
23296737 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:23296807 original size:9 final size:9
Alignment explanation
Indices: 23296789--23296826 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
23296779 TTGAGTTTTC
23296789 TAATTCGAA
1 TAATTCGAA
*
23296798 TAACTCGAA
1 TAATTCGAA
23296807 TAATTCGAA
1 TAATTCGAA
23296816 TAATTCGAA
1 TAATTCGAA
23296825 TA
1 TA
23296827 TCAAACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (9 bp):
TAATTCGAA
Found at i:23296889 original size:304 final size:304
Alignment explanation
Indices: 23296335--23296942 Score: 1065
Period size: 304 Copynumber: 2.0 Consensus size: 304
23296325 GTCATGCGAT
* *
23296335 TAGGCGTGAGCAAAACTCGATTCGACTCGAAAAAATTGAAAAATAATTCGAATTTCAAGTTAAAC
1 TAGGCGTGAGCAAAACTCAATTCGACTCGAAAAAATCGAAAAATAATTCGAATTTCAAGTTAAAC
* *
23296400 GAATCGAGTTGTTCAAGTTAATCGAGTTATTCGAATCGACTCGAATTTTTTTTCGAATTTCGAGT
66 GAATCGAGTTATTCAAGTTAATCGAGTTATTCGAATCAACTCGAATTTTTTTTCGAATTTCGAGT
* *
23296465 TCGAATCGAGTTGAGTTTTCGAATTCGAATAACTTGAATAATTCGAATAATTCGAATATCAAACT
131 TCGAATCAAGTTGAGTTTTCGAATTCGAATAACTCGAATAATTCGAATAATTCGAATATCAAACT
*
23296530 ATAATATTTTACATTTTTACCCCAAACTCCCAAAGCTTTTTACTTTTCCCTCAAAACTTTTACTC
196 ATAATATTTTACATTTTTACCCCAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACTC
* * *
23296595 CTTCCTACTTTCCCCTCAAAACTTTTACTCCCCTCCCCTCCCAA
261 ATTCCCACTTTCCCCCCAAAACTTTTACTCCCCTCCCCTCCCAA
* *
23296639 TAGGGGTGAGCAAAACTCAATTCGACTCGAAAAAATCGAAAAA-AATTCGAATTTCGAGTTAAAC
1 TAGGCGTGAGCAAAACTCAATTCGACTCGAAAAAATCGAAAAATAATTCGAATTTCAAGTTAAAC
* *
23296703 GAATCGAGTTATTCGAGTTAATCGAGTTATTCGAATCAACTCGAATATTTTTTTTGAATTTCGAG
66 GAATCGAGTTATTCAAGTTAATCGAGTTATTCGAATCAACTCGAAT-TTTTTTTCGAATTTCGAG
*
23296768 TTCGAATCAAGTTGAGTTTTCTAATTCGAATAACTCGAATAATTCGAATAATTCGAATATCAAAC
130 TTCGAATCAAGTTGAGTTTTCGAATTCGAATAACTCGAATAATTCGAATAATTCGAATATCAAAC
23296833 TATAATATTTTACATTTTTACCCCAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACT
195 TATAATATTTTACATTTTTACCCCAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACT
23296898 CATTCCCACTTTCCCCCCAAAACTTTTACTCCCCTCCCCTCCCAA
260 CATTCCCACTTTCCCCCCAAAACTTTTACTCCCCTCCCCTCCCAA
23296943 CCCCCCAATC
Statistics
Matches: 288, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
303 63 0.22
304 225 0.78
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (304 bp):
TAGGCGTGAGCAAAACTCAATTCGACTCGAAAAAATCGAAAAATAATTCGAATTTCAAGTTAAAC
GAATCGAGTTATTCAAGTTAATCGAGTTATTCGAATCAACTCGAATTTTTTTTCGAATTTCGAGT
TCGAATCAAGTTGAGTTTTCGAATTCGAATAACTCGAATAATTCGAATAATTCGAATATCAAACT
ATAATATTTTACATTTTTACCCCAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACTC
ATTCCCACTTTCCCCCCAAAACTTTTACTCCCCTCCCCTCCCAA
Found at i:23297074 original size:30 final size:31
Alignment explanation
Indices: 23297040--23297099 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
23297030 AAACATTTTA
*
23297040 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
23297070 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
23297100 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:23298385 original size:5 final size:5
Alignment explanation
Indices: 23298375--23298401 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
23298365 GAAAATTTTT
23298375 ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG AT
23298402 CGAATGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:23302268 original size:16 final size:16
Alignment explanation
Indices: 23302247--23302277 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23302237 TTGAATTAAA
23302247 ATTTTAAAAAAATAAG
1 ATTTTAAAAAAATAAG
*
23302263 ATTTTATAAAAATAA
1 ATTTTAAAAAAATAA
23302278 CATATCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTTTAAAAAAATAAG
Found at i:23302820 original size:22 final size:22
Alignment explanation
Indices: 23302790--23302832 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23302780 ACACCAAAAC
* *
23302790 AGGCTTTTAGCGACGCTTTTTT
1 AGGCCTTTAGAGACGCTTTTTT
*
23302812 AGGCCTTTAGAGGCGCTTTTT
1 AGGCCTTTAGAGACGCTTTTT
23302833 AGCGCCGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGAGACGCTTTTTT
Found at i:23303109 original size:86 final size:86
Alignment explanation
Indices: 23302964--23303145 Score: 260
Period size: 86 Copynumber: 2.1 Consensus size: 86
23302954 TAAAGGTCAT
* * * *
23302964 GCCGCTAAAGACCATGACCTTTAGCGGCATTTTTATCACAAACGTCGCTAAAGACCAAGACCTTT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGTCGCTAAAGAACAAGACCTTT
*
23303029 AGCGGCACTTT-TACCACAAAC
66 AGCGGCACTTTCT-CCAAAAAC
* *
23303050 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG-CTGCTAAGGAACAAGACCTT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGTC-GCTAAAGAACAAGACCTT
23303114 TAGCGGCACTTTCTCCAAAAAC
65 TAGCGGCACTTTCTCCAAAAAC
*
23303136 GCCACTAAAG
1 GCCGCTAAAG
23303146 GTCACGAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
85 1 0.01
86 84 0.98
87 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (86 bp):
GCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGTCGCTAAAGAACAAGACCTTT
AGCGGCACTTTCTCCAAAAAC
Found at i:23303137 original size:43 final size:43
Alignment explanation
Indices: 23302967--23303125 Score: 239
Period size: 43 Copynumber: 3.7 Consensus size: 43
23302957 AGGTCATGCC
* * *
23302967 GCTAAAGACCATGACCTTTAGCGGCATTTTTATCACAAACG-T
1 GCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGCT
*
23303009 CGCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGCC
1 -GCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGCT
*
23303053 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCT
1 GCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGCT
* *
23303096 GCTAAGGAACAAGACCTTTAGCGGCACTTT
1 GCTAAAGACCAAGACCTTTAGCGGCACTTT
23303126 CTCCAAAAAC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (43 bp):
GCTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACGCT
Found at i:23303845 original size:23 final size:23
Alignment explanation
Indices: 23303810--23303928 Score: 75
Period size: 23 Copynumber: 5.2 Consensus size: 23
23303800 CAAGTTAAAT
23303810 TTAAACACT-TCAATTTGCAGCAC
1 TTAAACA-TATCAATTTGCAGCAC
* ** * *
23303833 TTTAACATATCAATTAACAACAT
1 TTAAACATATCAATTTGCAGCAC
* * *
23303856 TTATACACATCAA-TTACAGCGA-
1 TTAAACATATCAATTTGCAGC-AC
* * * *
23303878 TAAAACATCTCACTTTGTAGCAC
1 TTAAACATATCAATTTGCAGCAC
23303901 TTAAACACT-TCAATTTGCAGCAC
1 TTAAACA-TATCAATTTGCAGCAC
23303924 TTAAA
1 TTAAA
23303929 NNNNNNNNNN
Statistics
Matches: 71, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
22 15 0.21
23 55 0.77
24 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAACATATCAATTTGCAGCAC
Found at i:23304367 original size:72 final size:68
Alignment explanation
Indices: 23304076--23304795 Score: 668
Period size: 72 Copynumber: 10.2 Consensus size: 68
23304066 NNNTAGCAAC
* * * * * * * *
23304076 TAAACACTTCAATTTGTAGCACTTAAACACTTCAATTAACAACATTTATACACCTCAA-TTACAA
1 TAAACACTTAAATTTGCAGCAC-TAAATACTTCAATTTACAGCATTTAAACACTTCAATTTACAG
23304140 CGA-T
65 C-ATT
* * * ** * *
23304144 AAAACA-TCTCAATTTCCAGCAACTAAATACTTCAATTTGTAGCACTTAAACACTTCAATTTAAA
1 TAAACACT-TAAATTTGCAGC-ACTAAATACTTCAATTTACAGCATTTAAACACTTCAATTTACA
23304208 GCATT
64 GCATT
* * * * *
23304213 TAAACATTTAAATTTGCAGCACTTAA-ACATATCAATTAACAGCATTTATACACCTCAA-TTACA
1 TAAACACTTAAATTTGCAGCACTAAATAC-T-TCAATTTACAGCATTTAAACACTTCAATTTACA
23304276 GCGA-T
64 GC-ATT
* * * * * *
23304281 AAAACA-TCTCAATTTCCAACAACTAAATACTTCAATTTGCAGCACTTAAACAGTACTTCAATTT
1 TAAACACT-TAAATTTGCAGC-ACTAAATACTTCAATTTACAGCATTTAAAC---ACTTCAATTT
23304345 ACAGCATT
61 ACAGCATT
* * * * * * *
23304353 TAAACACTTAAATTTGCAGCAATTAAACACATCAATTAACAACATTTATACACCTCAA-TTACAG
1 TAAACACTTAAATTTGCAGC-ACTAAATACTTCAATTTACAGCATTTAAACACTTCAATTTACAG
23304417 CGA-T
65 C-ATT
* * * * * *
23304421 AAAACA-TCTCAATTTCCAACAACTAAATACTTCAATTTGCAGCACTTAAACAGTACTTCAATTT
1 TAAACACT-TAAATTTGCAGC-ACTAAATACTTCAATTTACAGCATTTAAAC---ACTTCAATTT
23304485 ACAGCATT
61 ACAGCATT
23304493 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTA
1 TAAACACTTAAATTTGCAGCAC-TAAA---TACTTCAATTTACAGCATTTAAACACTTCAATTTA
*
23304558 CAACATT
62 CAGCATT
23304565 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTA
1 TAAACACTTAAATTTGCAGCAC-TAAA---TACTTCAATTTACAGCATTTAAACACTTCAATTTA
*
23304630 CAACATT
62 CAGCATT
23304637 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTA
1 TAAACACTTAAATTTGCAGCAC-TAAA---TACTTCAATTTACAGCATTTAAACACTTCAATTTA
*
23304702 CAACATT
62 CAGCATT
23304709 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTA
1 TAAACACTTAAATTTGCAGCAC-TAAA---TACTTCAATTTACAGCATTTAAACACTTCAATTTA
*
23304774 CAACATT
62 CAGCATT
23304781 TAAACACTTAAATTT
1 TAAACACTTAAATTT
23304796 ACAAATCCAC
Statistics
Matches: 556, Mismatches: 67, Indels: 54
0.82 0.10 0.08
Matches are distributed among these distances:
67 5 0.01
68 131 0.24
69 58 0.10
70 3 0.01
71 16 0.03
72 319 0.57
73 2 0.00
75 22 0.04
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (68 bp):
TAAACACTTAAATTTGCAGCACTAAATACTTCAATTTACAGCATTTAAACACTTCAATTTACAGC
ATT
Found at i:23304653 original size:144 final size:138
Alignment explanation
Indices: 23304076--23304795 Score: 859
Period size: 144 Copynumber: 5.1 Consensus size: 138
23304066 NNNTAGCAAC
* * *
23304076 TAAACACTTCAATTTGTAGCACTTAAAC-ACTTCAATTAACAACATTTATACACCTCAATTACAA
1 TAAACACTTAAATTTGCAGCACTTAAACTACTTCAATTAACAGCATTTATACACCTCAATTACAA
*
23304140 CGATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGTAGCACTTAAACACTTCAATTT
66 CGATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTT
23304205 A-AAGCATT
131 ACAA-CATT
*
23304213 TAAACATTTAAATTTGCAGCACTTAAAC-A-TATCAATTAACAGCATTTATACACCTCAATTACA
1 TAAACACTTAAATTTGCAGCACTTAAACTACT-TCAATTAACAGCATTTATACACCTCAATTACA
* *
23304276 GCGATAAAACATCTCAATTTCCAACAACTAAATACTTCAATTTGCAGCACTTAAACAGTACTTCA
65 ACGATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAAC---ACTTCA
*
23304341 ATTTACAGCATT
127 ATTTACAACATT
* * * *
23304353 TAAACACTTAAATTTGCAGCAATTAAAC-ACATCAATTAACAACATTTATACACCTCAATTACAG
1 TAAACACTTAAATTTGCAGCACTTAAACTACTTCAATTAACAGCATTTATACACCTCAATTACAA
*
23304417 CGATAAAACATCTCAATTTCCAACAACTAAATACTTCAATTTGCAGCACTTAAACAGTACTTCAA
66 CGATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAAC---ACTTCAA
*
23304482 TTTACAGCATT
128 TTTACAACATT
* * *
23304493 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTA
1 TAAACACTTAAATTTGCAGCACTTAAA-C-TACTTCAATTAACAGCATTTATACACCTCAA-TTA
* * * * *
23304558 CAAC-ATTTAAACA-CTTAAATTTGCAGC-ACTTAAACCGTACTTCAATTTACAGCATTTAAACA
63 CAACGA-TAAAACATC-TCAATTTCCAGCAAC-TAAA---TACTTCAATTTGCAGCACTTAAACA
23304620 CTTCAATTTACAACATT
122 CTTCAATTTACAACATT
* * *
23304637 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTA
1 TAAACACTTAAATTTGCAGCACTTAAA-C-TACTTCAATTAACAGCATTTATACACCTCAA-TTA
* * * * *
23304702 CAAC-ATTTAAACA-CTTAAATTTGCAGC-ACTTAAACCGTACTTCAATTTACAGCATTTAAACA
63 CAACGA-TAAAACATC-TCAATTTCCAGCAAC-TAAA---TACTTCAATTTGCAGCACTTAAACA
23304764 CTTCAATTTACAACATT
122 CTTCAATTTACAACATT
23304781 TAAACACTTAAATTT
1 TAAACACTTAAATTT
23304796 ACAAATCCAC
Statistics
Matches: 541, Mismatches: 26, Indels: 25
0.91 0.04 0.04
Matches are distributed among these distances:
136 1 0.00
137 110 0.20
140 176 0.33
141 2 0.00
143 29 0.05
144 201 0.37
147 22 0.04
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (138 bp):
TAAACACTTAAATTTGCAGCACTTAAACTACTTCAATTAACAGCATTTATACACCTCAATTACAA
CGATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAACACTTCAATTT
ACAACATT
Found at i:23304744 original size:49 final size:46
Alignment explanation
Indices: 23304076--23304798 Score: 500
Period size: 49 Copynumber: 15.4 Consensus size: 46
23304066 NNNTAGCAAC
** * * * *
23304076 TAAACACTTCAATTTGTAGCACTTAAACACTTCAATTAACAACATT
1 TAAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
* * * * *
23304122 TATACACCTCAA-TTACAACGA-TAAAACA-TCTCAATTTCCAGCAAC-
1 TAAACACTTCAATTTACAGC-ATTTAAACACT-TCAATTTACAGC-ACT
* ** * * *
23304167 TAAATACTTCAATTTGTAGCACTTAAACACTTCAATTTAAAGCATT
1 TAAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
* * * * * *
23304213 TAAACATTTAAATTTGCAGCACTTAAACA-TATCAATTAACAGCATT
1 TAAACACTTCAATTTACAGCATTTAAACACT-TCAATTTACAGCACT
* * * * *
23304259 TATACACCTCAA-TTACAGCGA-TAAAACA-TCTCAATTTCCAACAAC-
1 TAAACACTTCAATTTACAGC-ATTTAAACACT-TCAATTTACAGC-ACT
* * * *
23304304 TAAATACTTCAATTTGCAGCACTTAAACAGTACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAGCATTTAAAC---ACTTCAATTTACAGCACT
* * * * * * *
23304353 TAAACACTTAAATTTGCAGCAATTAAACACATCAATTAACAACATT
1 TAAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
* * * * *
23304399 TATACACCTCAA-TTACAGCGA-TAAAACA-TCTCAATTTCCAACAAC-
1 TAAACACTTCAATTTACAGC-ATTTAAACACT-TCAATTTACAGC-ACT
* * * *
23304444 TAAATACTTCAATTTGCAGCACTTAAACAGTACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAGCATTTAAAC---ACTTCAATTTACAGCACT
* * * *
23304493 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAGCATTTAAA-C--ACTTCAATTTACAGCACT
* * *
23304542 TAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
* *
23304588 TAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTACAACATT
1 TAAA-C--ACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
* * * *
23304637 TAAACACTTAAATTTGCAGCACTTAAACCGTACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAGCATTTAAA-C--ACTTCAATTTACAGCACT
* * *
23304686 TAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
* *
23304732 TAAACCGTACTTCAATTTACAGCATTTAAACACTTCAATTTACAACATT
1 TAAA-C--ACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
*
23304781 TAAACACTTAAATTTACA
1 TAAACACTTCAATTTACA
23304799 AATCCACCAT
Statistics
Matches: 541, Mismatches: 99, Indels: 74
0.76 0.14 0.10
Matches are distributed among these distances:
44 1 0.00
45 95 0.18
46 197 0.36
47 4 0.01
48 6 0.01
49 235 0.43
50 3 0.01
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.32
Consensus pattern (46 bp):
TAAACACTTCAATTTACAGCATTTAAACACTTCAATTTACAGCACT
Found at i:23304799 original size:23 final size:23
Alignment explanation
Indices: 23304076--23304798 Score: 566
Period size: 23 Copynumber: 30.8 Consensus size: 23
23304066 NNNTAGCAAC
** *
23304076 TAAACACTTCAATTTGTAGCACT
1 TAAACACTTCAATTTACAGCATT
* *
23304099 TAAACACTTCAATTAACAACATT
1 TAAACACTTCAATTTACAGCATT
* * *
23304122 TATACACCTCAA-TTACAACGA-T
1 TAAACACTTCAATTTACAGC-ATT
* * **
23304144 AAAACA-TCTCAATTTCCAGCAAC
1 TAAACACT-TCAATTTACAGCATT
* ** *
23304167 TAAATACTTCAATTTGTAGCACT
1 TAAACACTTCAATTTACAGCATT
*
23304190 TAAACACTTCAATTTAAAGCATT
1 TAAACACTTCAATTTACAGCATT
* * * *
23304213 TAAACATTTAAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
*
23304236 TAAACA-TATCAATTAACAGCATT
1 TAAACACT-TCAATTTACAGCATT
* *
23304259 TATACACCTCAA-TTACAGCGA-T
1 TAAACACTTCAATTTACAGC-ATT
* * * **
23304281 AAAACA-TCTCAATTTCCAACAAC
1 TAAACACT-TCAATTTACAGCATT
* * *
23304304 TAAATACTTCAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
23304327 TAAACAGTACTTCAATTTACAGCATT
1 TAAAC---ACTTCAATTTACAGCATT
* * *
23304353 TAAACACTTAAATTTGCAGCAAT
1 TAAACACTTCAATTTACAGCATT
* * *
23304376 TAAACACATCAATTAACAACATT
1 TAAACACTTCAATTTACAGCATT
* *
23304399 TATACACCTCAA-TTACAGCGA-T
1 TAAACACTTCAATTTACAGC-ATT
* * * **
23304421 AAAACA-TCTCAATTTCCAACAAC
1 TAAACACT-TCAATTTACAGCATT
* * *
23304444 TAAATACTTCAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
23304467 TAAACAGTACTTCAATTTACAGCATT
1 TAAAC---ACTTCAATTTACAGCATT
* * *
23304493 TAAACACTTAAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
23304516 TAAACCGTACTTCAATTTACAGCATT
1 TAAA-C--ACTTCAATTTACAGCATT
*
23304542 TAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTACAGCATT
* * *
23304565 TAAACACTTAAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
23304588 TAAACCGTACTTCAATTTACAGCATT
1 TAAA-C--ACTTCAATTTACAGCATT
*
23304614 TAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTACAGCATT
* * *
23304637 TAAACACTTAAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
23304660 TAAACCGTACTTCAATTTACAGCATT
1 TAAA-C--ACTTCAATTTACAGCATT
*
23304686 TAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTACAGCATT
* * *
23304709 TAAACACTTAAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
23304732 TAAACCGTACTTCAATTTACAGCATT
1 TAAA-C--ACTTCAATTTACAGCATT
*
23304758 TAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTACAGCATT
*
23304781 TAAACACTTAAATTTACA
1 TAAACACTTCAATTTACA
23304799 AATCCACCAT
Statistics
Matches: 554, Mismatches: 111, Indels: 70
0.75 0.15 0.10
Matches are distributed among these distances:
22 48 0.09
23 377 0.68
24 7 0.01
25 4 0.01
26 118 0.21
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.32
Consensus pattern (23 bp):
TAAACACTTCAATTTACAGCATT
Found at i:23306446 original size:38 final size:38
Alignment explanation
Indices: 23306404--23306479 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
23306394 TAAACAAAGT
23306404 CTACATCTATATAAATCAATACTATTACATTCCATCCA
1 CTACATCTATATAAATCAATACTATTACATTCCATCCA
23306442 CTACATCTATATAAATCAATACTATTACATTCCATCCA
1 CTACATCTATATAAATCAATACTATTACATTCCATCCA
23306480 TGTAATGGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (38 bp):
CTACATCTATATAAATCAATACTATTACATTCCATCCA
Found at i:23307980 original size:41 final size:41
Alignment explanation
Indices: 23307918--23308153 Score: 359
Period size: 41 Copynumber: 5.8 Consensus size: 41
23307908 TCAATTTTGG
* *
23307918 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACATGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGC
23307959 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGAC-CGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGC
* *
23307999 ATTAGCGGTGCTTTTTCAAAAACGCCGCTAAAGACATGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGC
* * *
23308040 ATTAGCGGCGCTTTTTCAAAAATGTCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGC
* * *
23308081 ATTAGCGGCGTTTTTTC-AAAACGCCACTAAAGACCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGC
*
23308121 ATTAGCGGCGCTTTTTCAAAAACACCGCTAAAG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG
23308154 CCTCGAAAGG
Statistics
Matches: 177, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 74 0.42
41 103 0.58
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGC
Found at i:23308014 original size:81 final size:82
Alignment explanation
Indices: 23307918--23308153 Score: 377
Period size: 81 Copynumber: 2.9 Consensus size: 82
23307908 TCAATTTTGG
23307918 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACATGAGCATTAGCGGCGCTTTTTCAAAAACG
1 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACATGAGCATTAGCGGCGCTTTTTCAAAAACG
23307983 CCGCTAAAGA-CCGAGC
66 CCGCTAAAGACCCGAGC
* * *
23307999 ATTAGCGGTGCTTTTTCAAAAACGCCGCTAAAGACATGAGCATTAGCGGCGCTTTTTCAAAAATG
1 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACATGAGCATTAGCGGCGCTTTTTCAAAAACG
*
23308064 TCGCTAAAGACCCGAGC
66 CCGCTAAAGACCCGAGC
* * ** *
23308081 ATTAGCGGCG-TTTTTTCAAAACGCCACTAAAGACCCGAGCATTAGCGGCGCTTTTTCAAAAACA
1 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACATGAGCATTAGCGGCGCTTTTTCAAAAACG
23308145 CCGCTAAAG
66 CCGCTAAAG
23308154 CCTCGAAAGG
Statistics
Matches: 141, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
81 126 0.89
82 15 0.11
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (82 bp):
ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACATGAGCATTAGCGGCGCTTTTTCAAAAACG
CCGCTAAAGACCCGAGC
Found at i:23308135 original size:122 final size:122
Alignment explanation
Indices: 23307918--23308153 Score: 375
Period size: 122 Copynumber: 1.9 Consensus size: 122
23307908 TCAATTTTGG
* *
23307918 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGACATGAGCATTAGCGGCGCTTTTTCAAAAACG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGCATTAGCGGCGCTTTTTCAAAAACG
* * *
23307983 CCGCTAAAGACCGAGCATTAGCGGTGCTTTTTCAAAAACGCCGCTAAAGACATGAGC
66 CCACTAAAGACCGAGCATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGACATGAGC
* * * *
23308040 ATTAGCGGCGCTTTTTCAAAAATGTCGCTAAAGACCCGAGCATTAGCGGCGTTTTTTC-AAAACG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGCATTAGCGGCGCTTTTTCAAAAACG
23308104 CCACTAAAGACCCGAGCATTAGCGGCGCTTTTTCAAAAACACCGCTAAAG
66 CCACTAAAGA-CCGAGCATTAGCGGCGCTTTTTCAAAAACACCGCTAAAG
23308154 CCTCGAAAGG
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
121 15 0.14
122 89 0.86
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (122 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACGAGCATTAGCGGCGCTTTTTCAAAAACG
CCACTAAAGACCGAGCATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGACATGAGC
Found at i:23308341 original size:40 final size:38
Alignment explanation
Indices: 23308213--23308343 Score: 102
Period size: 40 Copynumber: 3.3 Consensus size: 38
23308203 TTTCTCAAAA
* * *
23308213 AAACGCCGCTAATGCTCATTTTTCA-CGGCGCTTTCCTGG
1 AAACGCCGCTAATGCTCATTTTT-AGCGGCGTTTTACT-T
* * * * *
23308252 AAGCGCCGTTAATGCTCGATCTTTAGCGGCATTTTACGT
1 AAACGCCGCTAATGCTC-ATTTTTAGCGGCGTTTTACTT
* **
23308291 AAAGCACCGCTAATGCTCAATTTTTAGCGGCGTTTTTTTT
1 AAA-CGCCGCTAATGCTC-ATTTTTAGCGGCGTTTTACTT
23308331 CAAACGCCGCTAA
1 -AAACGCCGCTAA
23308344 AAGTCTGTTT
Statistics
Matches: 70, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
39 18 0.26
40 49 0.70
41 3 0.04
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (38 bp):
AAACGCCGCTAATGCTCATTTTTAGCGGCGTTTTACTT
Found at i:23311197 original size:20 final size:19
Alignment explanation
Indices: 23311142--23311212 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
23311132 TAAACACAAG
* *
23311142 AAGTATCGATAATTATTCTC
1 AAGTATCGAT-ATTTTTCTA
* * *
23311162 AAGTATCGGTGGTTTTACTA
1 AAGTATCGAT-ATTTTTCTA
23311182 AAGTATCGATATTTTT-TA
1 AAGTATCGATATTTTTCTA
23311200 ACTAGTATCGATA
1 A--AGTATCGATA
23311213 CCAAATTGCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 3 0.08
19 4 0.10
20 33 0.82
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (19 bp):
AAGTATCGATATTTTTCTA
Found at i:23313106 original size:15 final size:14
Alignment explanation
Indices: 23313085--23313120 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
23313075 ATAATCTTTA
*
23313085 ATAATTATCTTAAT
1 ATAATTATCCTAAT
23313099 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
23313114 ATAATTA
1 ATAATTA
23313121 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:23314733 original size:12 final size:12
Alignment explanation
Indices: 23314716--23314785 Score: 63
Period size: 12 Copynumber: 5.5 Consensus size: 12
23314706 CCAAATAAGT
23314716 AATAAATAATAA
1 AATAAATAATAA
23314728 AATAAAGTAAT-A
1 AATAAA-TAATAA
*
23314740 AATAAAGTAAAGAA
1 AATAAA-T-AATAA
23314754 AATAAAATAAT-A
1 AAT-AAATAATAA
23314766 AATAAATAAATAA
1 AATAAAT-AATAA
23314779 TAATAAA
1 -AATAAA
23314786 ATAAAAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
11 4 0.08
12 22 0.45
13 9 0.18
14 11 0.22
15 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:23314743 original size:4 final size:4
Alignment explanation
Indices: 23314716--23314790 Score: 52
Period size: 4 Copynumber: 18.5 Consensus size: 4
23314706 CCAAATAAGT
*
23314716 AATA AAT- AATAA AATA AAGT- AATA AATA AAGTA AAGAA AATA AA-A
1 AATA AATA AAT-A AATA AA-TA AATA AATA AA-TA AA-TA AATA AATA
23314761 TAATA AATA AATA AAT- AAT- AATAA AATA AA
1 -AATA AATA AATA AATA AATA AAT-A AATA AA
23314791 AATAAAAATT
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
3 11 0.18
4 33 0.55
5 16 0.27
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:23314758 original size:26 final size:25
Alignment explanation
Indices: 23314708--23314796 Score: 103
Period size: 26 Copynumber: 3.6 Consensus size: 25
23314698 ATTAATATCC
*
23314708 AAATAAGT-AATAAAT-AATAAAATA
1 AAATAA-TAAATAAATAAAGAAAATA
*
23314732 AAGTAATAAATAAAGTAAAGAAAATA
1 AAATAATAAATAAA-TAAAGAAAATA
*
23314758 AAATAATAAATAAATAAATAATAATA
1 AAATAATAAATAAATAAAGAA-AATA
23314784 AAATAA-AAATAAA
1 AAATAATAAATAAA
23314797 AATTGGGTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
23 1 0.02
24 11 0.19
25 14 0.25
26 31 0.54
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (25 bp):
AAATAATAAATAAATAAAGAAAATA
Found at i:23321192 original size:15 final size:15
Alignment explanation
Indices: 23321172--23321209 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
23321162 AAATAATCAT
*
23321172 TAATAATTATCTTAA
1 TAATAATTATCCTAA
23321187 TAATAATTATCCTAA
1 TAATAATTATCCTAA
23321202 T-ATAATTA
1 TAATAATTA
23321210 AAATAGAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAATTATCCTAA
Found at i:23332571 original size:260 final size:260
Alignment explanation
Indices: 23332108--23332630 Score: 958
Period size: 260 Copynumber: 2.0 Consensus size: 260
23332098 CAAAAGTTCT
23332108 ACTACAAGCAGTTTAACATAAATATTGATATGGTACATACTAAGCACATCAAGTATGTTTACTAT
1 ACTACAAGCAGTTTAACATAAATATTGATATGGTACATACTAAGCACATCAAGTATGTTTACTAT
* *
23332173 GATCATTTACACGAGTGCATATTTATATTTATTCTGTGCTTTTTGGCATTCCAATAAATGATTAA
66 GATCACTTACACGACTGCATATTTATATTTA-TCTGTGCTTTTTGGCATTCCAATAAATGATTAA
23332238 TGAGCGACTTAAAAACTAATATTTACTTTGAGGTCCATGTTAGTCATCGTCTCTTTGGTTTTTTG
130 TGAGCGACTTAAAAACTAATATTTACTTTGAGGTCCATGTTAGTCATCGTCTCTTTGGTTTTTTG
*
23332303 CTAGCATAAATATTAAAGGACTGGCACCTTTAAGGAAACACAAGTTCCCCACCAGTAGGCTATTA
195 CTAGCATAAATATCAAAGGACTGGCACC-TTAAGGAAACACAAGTTCCCCACCAGTAGGCTATTA
23332368 AA
259 AA
* *
23332370 ACTACAAGCAGTTTAACATAAATATTGATATGGTACATACTAAGCCCATGAAGTATGTTTACTAT
1 ACTACAAGCAGTTTAACATAAATATTGATATGGTACATACTAAGCACATCAAGTATGTTTACTAT
*
23332435 GATCACTTACATGACTGCATATTTATATTTA-CTGTGCTTTTTGGCATTCCAATAAATGATTAAT
66 GATCACTTACACGACTGCATATTTATATTTATCTGTGCTTTTTGGCATTCCAATAAATGATTAAT
*
23332499 GAGCGACTTAAAAACTAATATTTACTTTGAGGTCCATGTTAGTCATTGTCTCTTTGGTTTTTTGC
131 GAGCGACTTAAAAACTAATATTTACTTTGAGGTCCATGTTAGTCATCGTCTCTTTGGTTTTTTGC
23332564 TAGCATAAATATCAAAGGACTGGCACCTTAAGGAAACACAAGTTCCCCACCAGTAGGCTATTAAA
196 TAGCATAAATATCAAAGGACTGGCACCTTAAGGAAACACAAGTTCCCCACCAGTAGGCTATTAAA
23332629 AC
1 AC
23332631 CATCCATCAC
Statistics
Matches: 254, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
259 40 0.16
260 123 0.48
262 91 0.36
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (260 bp):
ACTACAAGCAGTTTAACATAAATATTGATATGGTACATACTAAGCACATCAAGTATGTTTACTAT
GATCACTTACACGACTGCATATTTATATTTATCTGTGCTTTTTGGCATTCCAATAAATGATTAAT
GAGCGACTTAAAAACTAATATTTACTTTGAGGTCCATGTTAGTCATCGTCTCTTTGGTTTTTTGC
TAGCATAAATATCAAAGGACTGGCACCTTAAGGAAACACAAGTTCCCCACCAGTAGGCTATTAAA
Found at i:23340815 original size:24 final size:24
Alignment explanation
Indices: 23340752--23340803 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
23340742 TTTCTAGAAG
* * *
23340752 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
23340776 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
23340800 ATTT
1 ATTT
23340804 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:23345182 original size:24 final size:24
Alignment explanation
Indices: 23345119--23345170 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
23345109 TTTCTAGAAG
* * *
23345119 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
23345143 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
23345167 ATTT
1 ATTT
23345171 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:23350305 original size:18 final size:18
Alignment explanation
Indices: 23350282--23350323 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
23350272 CTACTAAAAA
23350282 TCACAAGAAAACAATCAT
1 TCACAAGAAAACAATCAT
*
23350300 TCACAAGAAAGCAATCAT
1 TCACAAGAAAACAATCAT
*
23350318 GCACAA
1 TCACAA
23350324 AAGAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.24, G:0.10, T:0.14
Consensus pattern (18 bp):
TCACAAGAAAACAATCAT
Found at i:23353256 original size:12 final size:12
Alignment explanation
Indices: 23353239--23353264 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23353229 TAAGACATTT
23353239 AGGACCAGCACC
1 AGGACCAGCACC
23353251 AGGACCAGCACC
1 AGGACCAGCACC
23353263 AG
1 AG
23353265 AAACATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.38, G:0.27, T:0.00
Consensus pattern (12 bp):
AGGACCAGCACC
Found at i:23360453 original size:14 final size:15
Alignment explanation
Indices: 23360424--23360453 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23360414 TGTGAAGAAA
23360424 TATTTTTCTTCTCCT
1 TATTTTTCTTCTCCT
23360439 TATTTTTCTTC-CCT
1 TATTTTTCTTCTCCT
23360453 T
1 T
23360454 GGTTGAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTCTTCTCCT
Found at i:23361247 original size:48 final size:48
Alignment explanation
Indices: 23361152--23361250 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 48
23361142 AAAGTGGAAG
* * *
23361152 TATGTGGCAGTTTATCTGCATTAATGTGACATTGTTCACGATTTTGAT
1 TATGTGGCAGTATATCTGCATTAATGTGACATTGTCCACGATATTGAT
* * *
23361200 TATGTGGCAGTATATCTGCGATT-TTGGTGTC-TTGTCCATGATATTGAT
1 TATGTGGCAGTATATCTGC-ATTAAT-GTGACATTGTCCACGATATTGAT
23361248 TAT
1 TAT
23361251 TAGTAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
48 36 0.84
49 7 0.16
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.44
Consensus pattern (48 bp):
TATGTGGCAGTATATCTGCATTAATGTGACATTGTCCACGATATTGAT
Found at i:23362191 original size:21 final size:22
Alignment explanation
Indices: 23362167--23362213 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
23362157 AAGCCAATAG
23362167 TTTTAAAATATTT-TTT-AAAAA
1 TTTTAAAAT-TTTATTTCAAAAA
* *
23362188 TTTTGAAATTTTATTTCAACAA
1 TTTTAAAATTTTATTTCAAAAA
23362210 TTTT
1 TTTT
23362214 CATGGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 11 0.50
22 8 0.36
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTAAAATTTTATTTCAAAAA
Found at i:23363429 original size:20 final size:20
Alignment explanation
Indices: 23363404--23363458 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
23363394 TTGTACAGGA
23363404 TTGCACTTCGATGCTTCTGT
1 TTGCACTTCGATGCTTCTGT
*
23363424 TTGCACTTC-AGTGCCTCTGT
1 TTGCACTTCGA-TGCTTCTGT
* *
23363444 TAGCATTTCGATGCT
1 TTGCACTTCGATGCT
23363459 CTTTGGTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCACTTCGATGCTTCTGT
Found at i:23381875 original size:2 final size:2
Alignment explanation
Indices: 23381868--23381896 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23381858 TGCTTTTACA
23381868 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 A
23381897 AGCAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23382314 original size:12 final size:12
Alignment explanation
Indices: 23382297--23382336 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
23382287 TGTCAAGGAT
*
23382297 AGGGGAAGGGGA
1 AGGGGAAGGGAA
23382309 AGGGGAAGGGAA
1 AGGGGAAGGGAA
* *
23382321 AGGGAAAAGGAA
1 AGGGGAAGGGAA
23382333 AGGG
1 AGGG
23382337 AAGATCGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
AGGGGAAGGGAA
Found at i:23382323 original size:18 final size:18
Alignment explanation
Indices: 23382291--23382338 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
23382281 ATCATGTGTC
* * *
23382291 AAGGATAGGGGAAGGGGA
1 AAGGAAAGGGAAAGGGAA
* *
23382309 AGGGGAAGGGAAAGGGAA
1 AAGGAAAGGGAAAGGGAA
23382327 AAGGAAAGGGAA
1 AAGGAAAGGGAA
23382339 GATCGGTGTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.52, T:0.02
Consensus pattern (18 bp):
AAGGAAAGGGAAAGGGAA
Found at i:23388379 original size:67 final size:67
Alignment explanation
Indices: 23388271--23388396 Score: 182
Period size: 67 Copynumber: 1.9 Consensus size: 67
23388261 GAACTCAAAG
*
23388271 ATTTATACACAATAAAATTTGTGAACTCAAAGTTTCCATAAACTTACTCG-TAAATCAAATCCTT
1 ATTTATACACAATAAAATTTGTGAACTAAAAGTTTCCATAAACTTAC-CGTTAAATCAAATCCTT
23388335 ATA
65 ATA
* * * * *
23388338 ATTTATACATAATAAGATTTGTGAACTAAAATTTTTCATAAATTTACCGTTAAATCAAA
1 ATTTATACACAATAAAATTTGTGAACTAAAAGTTTCCATAAACTTACCGTTAAATCAAA
23388397 ACTAAATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 2 0.04
67 50 0.96
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (67 bp):
ATTTATACACAATAAAATTTGTGAACTAAAAGTTTCCATAAACTTACCGTTAAATCAAATCCTTA
TA
Found at i:23388835 original size:15 final size:13
Alignment explanation
Indices: 23388794--23388836 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 13
23388784 TGGTCCTTTA
23388794 GAATAATTTTTTTT
1 GAATAA-TTTTTTT
23388808 GACATAATTTTTTT
1 GA-ATAATTTTTTT
23388822 GAATATATTGTTTTT
1 GAATA-ATT-TTTTT
23388837 CACTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.12
14 14 0.54
15 9 0.35
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (13 bp):
GAATAATTTTTTT
Found at i:23389404 original size:26 final size:27
Alignment explanation
Indices: 23389357--23389411 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
23389347 GTCTGTGTGG
*
23389357 TAGGTGCCACTAGTGACTCCTACCTGA
1 TAGGCGCCACTAGTGACTCCTACCTGA
23389384 TAGGCGCCACT-GTGACTCCTACCTGA
1 TAGGCGCCACTAGTGACTCCTACCTGA
23389410 TA
1 TA
23389412 AGCGGCACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (27 bp):
TAGGCGCCACTAGTGACTCCTACCTGA
Found at i:23393405 original size:43 final size:41
Alignment explanation
Indices: 23393339--23393538 Score: 177
Period size: 43 Copynumber: 4.7 Consensus size: 41
23393329 TAAATTTAGT
* * *
23393339 GATATGGGGAATCAACACATAGCAACCCCTTTCACAATCAAA
1 GATACGGGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAA
* * * * * **
23393381 GGTACGGTGAAATCAGCACTTAGCAACCATCTTTATATTCAGT
1 GATACGG-GGAATCAGCACTTAGCAACC-CCTTTACAATCAAA
* *
23393424 GATACTGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
1 GATACGGGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAA
* * *
23393466 TATAAGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATA
1 GATACGG-GGAATCAGCACTTAGCAACC-CCTTTACAATCAA-A
* *
23393510 -ATTCGGGGAATCAGCACTCAGCAACCCCT
1 GATACGGGGAATCAGCACTTAGCAACCCCT
23393539 AGGGGAATCT
Statistics
Matches: 125, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
41 7 0.06
42 51 0.41
43 57 0.46
44 10 0.08
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (41 bp):
GATACGGGGAATCAGCACTTAGCAACCCCTTTACAATCAAA
Found at i:23393440 original size:42 final size:41
Alignment explanation
Indices: 23393313--23393535 Score: 168
Period size: 43 Copynumber: 5.3 Consensus size: 41
23393303 GTGGATTCAA
* * * *
23393313 CACTTAGCAACCACC-TTA-AATTTAGTGATATGGGGAATCAA
1 CACTTAGCAACCACCTTTACAA-TCAAT-ATACGGGGAATCAG
* *
23393354 CACATAGCAACC-CCTTTCACAATCAA-AGGTACGGTGAAATCAG
1 CACTTAGCAACCACCTTT-ACAATCAATA--TACGG-GGAATCAG
* * * * *
23393397 CACTTAGCAACCATCTTTATATTCAGTGATACTGGGAATCAG
1 CACTTAGCAACCACCTTTACAATCAAT-ATACGGGGAATCAG
* *
23393439 CACATAGCAACC-CCTTTCACAATCAAATATAAGGTGGAATCAG
1 CACTTAGCAACCACCTTT-ACAATC-AATATACGG-GGAATCAG
* *
23393482 CACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATCAG
1 CACTTAGCAACCACCTTTACAATCAAT-ATACGGGGAATCAG
*
23393524 CACTCAGCAACC
1 CACTTAGCAACC
23393536 CCTAGGGGAA
Statistics
Matches: 143, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
40 3 0.02
41 17 0.12
42 55 0.38
43 58 0.41
44 9 0.06
45 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
CACTTAGCAACCACCTTTACAATCAATATACGGGGAATCAG
Found at i:23393443 original size:85 final size:84
Alignment explanation
Indices: 23393313--23393538 Score: 278
Period size: 85 Copynumber: 2.7 Consensus size: 84
23393303 GTGGATTCAA
* * *
23393313 CACTTAGCAACCACCTTAAATTTAGTGATA-TGGGGAATCAACACATAGCAACCCCTTTCACAAT
1 CACTTAGCAACCACTTTAAATTCAGTGATACT-GGGAATCAGCACATAGCAACCCCTTTCACAAT
* *
23393377 CAAAGGTACGGTGAAATCAG
65 CAAAGATAAGGTGAAATCAG
*
23393397 CACTTAGCAACCATCTTTATATTCAGTGATACTGGGAATCAGCACATAGCAACCCCTTTCACAAT
1 CACTTAGCAACCA-CTTTAAATTCAGTGATACTGGGAATCAGCACATAGCAACCCCTTTCACAAT
* *
23393462 CAAATATAAGGTGGAATCAG
65 CAAAGATAAGGTGAAATCAG
* * * *
23393482 CACTTAGCAACCACCTTTAGAA-TCAATAATTCGGGGAATCAGCAC-TCAGCAACCCCT
1 CACTTAGCAACCA-CTTTA-AATTCAGTGATACTGGGAATCAGCACAT-AGCAACCCCT
23393539 AGGGGAATCT
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
84 14 0.11
85 108 0.87
86 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.23
Consensus pattern (84 bp):
CACTTAGCAACCACTTTAAATTCAGTGATACTGGGAATCAGCACATAGCAACCCCTTTCACAATC
AAAGATAAGGTGAAATCAG
Found at i:23400302 original size:77 final size:75
Alignment explanation
Indices: 23400066--23400295 Score: 311
Period size: 75 Copynumber: 3.1 Consensus size: 75
23400056 TTACGTAAAT
* * * * * * *
23400066 AATAAAAAGTTTATTATTTAAATTGTAAAAAATCC-TAAAATTAATAACTGAAATAG-AGAAAAA
1 AATACAAAGTTGACTATTTAAATTGAAAAAAAACCATAAAATTAATAACTAAAATGGCA-AAAAA
23400129 GTCATTACATA
65 GTCATTACATA
*
23400140 AATACAAAGTTGACTATTTAAATTGAAAAAAAACCATCAAATTAATAACTAAAATGGCAAAAAAG
1 AATACAAAGTTGACTATTTAAATTGAAAAAAAACCATAAAATTAATAACTAAAATGGCAAAAAAG
*
23400205 TCATTACACA
66 TCATTACATA
* *
23400215 AATACAAAGTTGACTATTTAAATTGCAAAAAAAACCCATAAAATTAAGAACTTAAATGGCAAAAA
1 AATACAAAGTTGACTATTTAAATTG-AAAAAAAA-CCATAAAATTAATAACTAAAATGGCAAAAA
*
23400280 AGTCATTATATA
64 AGTCATTACATA
23400292 AATA
1 AATA
23400296 TGAAGTTATT
Statistics
Matches: 138, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
74 30 0.22
75 58 0.42
76 9 0.07
77 41 0.30
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.27
Consensus pattern (75 bp):
AATACAAAGTTGACTATTTAAATTGAAAAAAAACCATAAAATTAATAACTAAAATGGCAAAAAAG
TCATTACATA
Found at i:23400546 original size:33 final size:33
Alignment explanation
Indices: 23400509--23400649 Score: 165
Period size: 33 Copynumber: 4.3 Consensus size: 33
23400499 AGAGTACAGT
* * *
23400509 GGTGGATATGGGCCAGGAAGAGTGGAGTATGGC
1 GGTGGATACGGGCCGGGAGGAGTGGAGTATGGC
*
23400542 GGTGGATACAGGCCGGGAGGAGTGGAGTATGGC
1 GGTGGATACGGGCCGGGAGGAGTGGAGTATGGC
* * *
23400575 AGTGGATACGGGCCGGGAGGAGTGAAGTATGGT
1 GGTGGATACGGGCCGGGAGGAGTGGAGTATGGC
** * * * *
23400608 GGTGGATACGAACTGGAAGGAGTGGAGTATTGA
1 GGTGGATACGGGCCGGGAGGAGTGGAGTATGGC
23400641 GGTGGATAC
1 GGTGGATAC
23400650 AAGACGGGAT
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 92 1.00
ACGTcount: A:0.25, C:0.09, G:0.48, T:0.18
Consensus pattern (33 bp):
GGTGGATACGGGCCGGGAGGAGTGGAGTATGGC
Found at i:23401258 original size:13 final size:13
Alignment explanation
Indices: 23401240--23401267 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23401230 ACAAAATTGG
23401240 AAAGATGAAAAAT
1 AAAGATGAAAAAT
23401253 AAAGATGAAAAAT
1 AAAGATGAAAAAT
23401266 AA
1 AA
23401268 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGATGAAAAAT
Found at i:23402455 original size:24 final size:24
Alignment explanation
Indices: 23402422--23402483 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
23402412 TGGCTCTTTG
*
23402422 GAGCTACCCGTTATTGGCTCGCAT
1 GAGCTTCCCGTTATTGGCTCGCAT
* **
23402446 GAGTTTCCCGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGCAT
23402470 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
23402484 ATTTCCCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 3 0.10
24 25 0.81
25 3 0.10
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGCAT
Done.