Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 166 of 433
Found at i:51854187 original size:27 final size:27
Alignment explanation
Indices: 51854134--51854343 Score: 125
Period size: 27 Copynumber: 7.7 Consensus size: 27
51854124 TTTCATCCTA
* * * * *
51854134 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTCGGTAATTTTATAAAC
* *
51854161 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTATAAAC
* ** * *
51854188 CAATGGTATTTCTATAATTTTTAGAAAGT
1 CAAGGGTATTTCGGTAA-TTTTATAAA-C
* * * *
51854217 CAAGGGTATTTCTGTAATTGTGTAAAT
1 CAAGGGTATTTCGGTAATTTTATAAAC
* * * * *
51854244 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCGGTAATTTTATAAAC
** *
51854271 TGAGGGTATTTCGGTAATTTCATAAAC
1 CAAGGGTATTTCGGTAATTTTATAAAC
* *
51854298 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTCGGTAATTTTATAAAC
* * *
51854325 TAGGGGTATTTTGGTAATT
1 CAAGGGTATTTCGGTAATT
51854344 CTACCCTATA
Statistics
Matches: 142, Mismatches: 37, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.01
27 111 0.78
28 14 0.10
29 15 0.11
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTCGGTAATTTTATAAAC
Found at i:51854306 original size:54 final size:52
Alignment explanation
Indices: 51854163--51854343 Score: 166
Period size: 54 Copynumber: 3.3 Consensus size: 52
51854153 CTACAAACCA
* * * * *
51854163 AGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTTAGAAAGTCA
1 AGGGTATTTCGGTAA-TTTGTAAACCAGTGGTATTT-TGGTAA-TTTTACAAA-T-T
* ** *
51854219 AGGGTATTTCTGTAATTGTGTAAATTAGGGGTATTTTGGTAATTTTACAAATT
1 AGGGTATTTCGGTAATT-TGTAAACCAGTGGTATTTTGGTAATTTTACAAATT
* *
51854272 GAGGGTATTTCGGTAATTTCATAAACCAGTGGTATTTTGGTAATTTTACAAACT
1 -AGGGTATTTCGGTAATTT-GTAAACCAGTGGTATTTTGGTAATTTTACAAATT
*
51854326 AGGGGTATTTTGGTAATT
1 A-GGGTATTTCGGTAATT
51854344 CTACCCTATA
Statistics
Matches: 105, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
53 2 0.02
54 61 0.58
55 11 0.10
56 31 0.30
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (52 bp):
AGGGTATTTCGGTAATTTGTAAACCAGTGGTATTTTGGTAATTTTACAAATT
Found at i:51854396 original size:27 final size:27
Alignment explanation
Indices: 51854375--51854467 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
51854365 GTAATTTAAT
* *
51854375 AATCGAGGGATAAAACAATAATTTTGTA
1 AATCGAGGG-TAAAACAATAATTCTATA
* *
51854403 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAATAATTCTATA
*
51854430 AATCAAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACAATAATTCTATA
51854457 AATCGAGGGTA
1 AATCGAGGGTA
51854468 CTTTGGTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 50 0.85
28 9 0.15
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (27 bp):
AATCGAGGGTAAAACAATAATTCTATA
Found at i:51854421 original size:54 final size:54
Alignment explanation
Indices: 51854363--51854467 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 54
51854353 AGAGGTATTT
* * *
51854363 CAGTAATT-TA-ATAATCGAGGGATAAAACAATAATTTTGTAAATCGAGGGTAAAA
1 CAGTAATTCTATA-AATCAAGGG-TAAAACAATAATTCTATAAATCGAGGGTAAAA
*
51854417 CAGTAATTCTGTAAATCAAGGGTAAAACAATAATTCTATAAATCGAGGGTA
1 CAGTAATTCTATAAATCAAGGGTAAAACAATAATTCTATAAATCGAGGGTA
51854468 CTTTGGTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
54 35 0.78
55 9 0.20
56 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.28
Consensus pattern (54 bp):
CAGTAATTCTATAAATCAAGGGTAAAACAATAATTCTATAAATCGAGGGTAAAA
Found at i:51854477 original size:27 final size:27
Alignment explanation
Indices: 51854447--51854505 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
51854437 GGTAAAACAA
*
51854447 TAATTCTATAAATCGAGGGTACTTTGG
1 TAATTCTACAAATCGAGGGTACTTTGG
* * * *
51854474 TAATTTTACAAGTCGAGGGTATTTTTG
1 TAATTCTACAAATCGAGGGTACTTTGG
51854501 TAATT
1 TAATT
51854506 GGTAAACTAA
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:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
TAATTCTACAAATCGAGGGTACTTTGG
Found at i:51856872 original size:30 final size:31
Alignment explanation
Indices: 51856796--51856878 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
51856786 TTAGTCTCGA
* *
51856796 CATAT-ACTGGGCCAAAGCCTTTTTATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
51856826 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
51856857 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
51856879 ACTGTAAGCG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 18 0.36
31 32 0.64
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:51857132 original size:25 final size:25
Alignment explanation
Indices: 51857098--51857167 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
51857088 CTCTTTTAAT
* *
51857098 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
51857123 AACTGGGGCAAATCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
51857148 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
51857168 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:51858038 original size:27 final size:27
Alignment explanation
Indices: 51857979--51858053 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
51857969 CATATTCGTT
51857979 ATTTTACCATACAGGGGTATTACGGTC
1 ATTTTACCATACAGGGGTATTACGGTC
* *
51858006 ACTTTACCCTACAGGGGCT-TTACGGTC
1 ATTTTACCATACAGGGG-TATTACGGTC
* *
51858033 TTTTTACC-TATTAGGGGTATT
1 ATTTTACCATA-CAGGGGTATT
51858054 TTAGTCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.08
27 36 0.90
28 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (27 bp):
ATTTTACCATACAGGGGTATTACGGTC
Found at i:51858206 original size:27 final size:27
Alignment explanation
Indices: 51858091--51858260 Score: 94
Period size: 27 Copynumber: 6.2 Consensus size: 27
51858081 TTGGTAAATC
* * *
51858091 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAATCAGGGGTATTTCTGTAATTT
** * ** *
51858118 TGTAAACCAATGGTATTTCTATAATTTT
1 TACAAATCAGGGGTATTTCTGTAA-TTT
* * *
51858146 TAGAAAGTCAAGGGTATTTCTGTAATTG
1 TACAAA-TCAGGGGTATTTCTGTAATTT
**
51858174 TGTAAATCAGGGGTATTT-TGATAATTT
1 TACAAATCAGGGGTATTTCTG-TAATTT
* * *
51858201 TATAAAT-TGTGGGTATTTCTGTAATTG
1 TACAAATCAG-GGGTATTTCTGTAATTT
* * *
51858228 CACAAACCAGTGGTATTT-TGGTAATTT
1 TACAAATCAGGGGTATTTCT-GTAATTT
51858255 TACAAA
1 TACAAA
51858261 CTAAGGGTAT
Statistics
Matches: 111, Mismatches: 25, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
26 4 0.04
27 76 0.68
28 16 0.14
29 15 0.14
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
TACAAATCAGGGGTATTTCTGTAATTT
Found at i:51858261 original size:27 final size:27
Alignment explanation
Indices: 51858185--51858280 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
51858175 GTAAATCAGG
* * **
51858185 GGTATTTTGATAATTTTATAAA-TTGT
1 GGTATTTTGGTAATTTTACAAACAAGT
** *
51858211 GGGTATTTCT-GTAATTGCACAAACCAGT
1 -GGTATTT-TGGTAATTTTACAAACAAGT
51858239 GGTATTTTGGTAATTTTACAAACTAAG-
1 GGTATTTTGGTAATTTTACAAAC-AAGT
51858266 GGTATTTTGGTAATT
1 GGTATTTTGGTAATT
51858281 CTACCCTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
26 1 0.02
27 50 0.89
28 5 0.09
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACAAGT
Found at i:51858269 original size:54 final size:54
Alignment explanation
Indices: 51858091--51858280 Score: 186
Period size: 54 Copynumber: 3.5 Consensus size: 54
51858081 TTGGTAAATC
* * * *
51858091 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTT
1 TACAAACTAAGGGTATTTCTGTAATTGTGTAAACCAGTGGTATTT-TGATAA-TTT
* * * *
51858146 TAGAAAGTCAAGGGTATTTCTGTAATTGTGTAAATCAGGGGTATTTTGATAATTT
1 TACAAACT-AAGGGTATTTCTGTAATTGTGTAAACCAGTGGTATTTTGATAATTT
* * ** *** *
51858201 TATAAATTGTGGGTATTTCTGTAATTGCACAAACCAGTGGTATTTTGGTAATTT
1 TACAAACTAAGGGTATTTCTGTAATTGTGTAAACCAGTGGTATTTTGATAATTT
51858255 TACAAACTAAGGGTATTT-TGGTAATT
1 TACAAACTAAGGGTATTTCT-GTAATT
51858281 CTACCCTATA
Statistics
Matches: 110, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
53 1 0.01
54 58 0.53
55 15 0.14
56 36 0.33
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (54 bp):
TACAAACTAAGGGTATTTCTGTAATTGTGTAAACCAGTGGTATTTTGATAATTT
Found at i:51858414 original size:27 final size:27
Alignment explanation
Indices: 51858312--51858403 Score: 148
Period size: 27 Copynumber: 3.4 Consensus size: 27
51858302 ATAATTTCAC
* *
51858312 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTCTGTA
51858339 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTCTGTA
* *
51858366 AATCAAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAATAGTAATTCTGTA
51858393 AATCGAGGGTA
1 AATCGAGGGTA
51858404 CTTTGGTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATAGTAATTCTGTA
Found at i:51858665 original size:28 final size:28
Alignment explanation
Indices: 51858625--51858682 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
51858615 TGGGCTCATA
* * *
51858625 GGCCCATTGGGCCCACATGGCCCCTTTC
1 GGCCCACTAGGCCCACATGGCCCATTTC
51858653 GGCCCACTAGGCCCACATGGCCCATTTC
1 GGCCCACTAGGCCCACATGGCCCATTTC
51858681 GG
1 GG
51858683 TCCATCGCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.14, C:0.41, G:0.26, T:0.19
Consensus pattern (28 bp):
GGCCCACTAGGCCCACATGGCCCATTTC
Found at i:51860711 original size:28 final size:28
Alignment explanation
Indices: 51860671--51860826 Score: 126
Period size: 28 Copynumber: 5.6 Consensus size: 28
51860661 ATATATAAAT
51860671 GGCACTTAGTGTGCGAAGTATCGAGGAA
1 GGCACTTAGTGTGCGAAGTATCGAGGAA
* *
51860699 GGCACTTAGTGTGCGATA-CATCCA-GAA
1 GGCACTTAGTGTGCGA-AGTATCGAGGAA
*
51860726 TGACACTTAGTGTGCGAAGTATCGAGGATA
1 -GGCACTTAGTGTGCGAAGTATCGAGGA-A
* ** *
51860756 -GAACTTAGTGTGCGAAACATCTA-GAA
1 GGCACTTAGTGTGCGAAGTATCGAGGAA
* *
51860782 TGACACTTAGTGTGC-AAGGTATC-AGGTAT
1 -GGCACTTAGTGTGCGAA-GTATCGAGG-AA
*
51860811 GGCACCTAGTGTGCGA
1 GGCACTTAGTGTGCGA
51860827 GACATTAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 21
0.72 0.12 0.15
Matches are distributed among these distances:
26 1 0.01
27 9 0.09
28 84 0.84
29 5 0.05
30 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAAGTATCGAGGAA
Found at i:51860762 original size:56 final size:56
Alignment explanation
Indices: 51860668--51860831 Score: 217
Period size: 56 Copynumber: 2.9 Consensus size: 56
51860658 TGGATATATA
* *
51860668 AATGGCACTTAGTGTGCGAAGTATCGAGGA-AGGCACTTAGTGTGCGATACATCCAG
1 AATGACACTTAGTGTGCGAAGTATCGAGGATA-GCACTTAGTGTGCGAAACATCCAG
* *
51860724 AATGACACTTAGTGTGCGAAGTATCGAGGATAGAACTTAGTGTGCGAAACATCTAG
1 AATGACACTTAGTGTGCGAAGTATCGAGGATAGCACTTAGTGTGCGAAACATCCAG
* * *
51860780 AATGACACTTAGTGTGC-AAGGTATC-AGGTATGGCACCTAGTGTGCGAGACAT
1 AATGACACTTAGTGTGCGAA-GTATCGAGG-ATAGCACTTAGTGTGCGAAACAT
51860832 TAAATATTCA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
55 5 0.05
56 91 0.94
57 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.24
Consensus pattern (56 bp):
AATGACACTTAGTGTGCGAAGTATCGAGGATAGCACTTAGTGTGCGAAACATCCAG
Found at i:51860938 original size:32 final size:32
Alignment explanation
Indices: 51860894--51861005 Score: 143
Period size: 32 Copynumber: 3.5 Consensus size: 32
51860884 ATAGTATAGA
**
51860894 TATGTACAAAAATTCACCCAAGATGGTACAGG
1 TATGTACAAAAATTCATACAAGATGGTACAGG
* ** * *
51860926 TATGTACGAAAATTTGTACAAGATGGTGCAAG
1 TATGTACAAAAATTCATACAAGATGGTACAGG
**
51860958 TATGTACGGAAATTCATACAAGATGGTACAGG
1 TATGTACAAAAATTCATACAAGATGGTACAGG
51860990 TATGTACAAAAATTCA
1 TATGTACAAAAATTCA
51861006 ATTGAGTATT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (32 bp):
TATGTACAAAAATTCATACAAGATGGTACAGG
Found at i:51861451 original size:21 final size:22
Alignment explanation
Indices: 51861409--51861454 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
51861399 GAATGCTTGG
* *
51861409 TTATTAGATGTTTTATGATAGA
1 TTATTAGATGTTTGAAGATAGA
*
51861431 TTATTA-ATGTTTGAAGCTAGA
1 TTATTAGATGTTTGAAGATAGA
51861452 TTA
1 TTA
51861455 ACAAGTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (22 bp):
TTATTAGATGTTTGAAGATAGA
Found at i:51861853 original size:28 final size:27
Alignment explanation
Indices: 51861811--51861908 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 27
51861801 GATCATATAA
51861811 ATGGCACTTAGTGTGCGTAGTACCGAGG
1 ATGGCACTTAGTGTGCG-AGTACCGAGG
* * * *
51861839 ATGGCACTTAATGTGTGA-TACATCCAGA
1 ATGGCACTTAGTGTGCGAGTAC--CGAGG
*
51861867 ATGGCACTTAGTGTGCGAAGTATCGAGG
1 ATGGCACTTAGTGTGCG-AGTACCGAGG
*
51861895 TTGGCACTTAGTGT
1 ATGGCACTTAGTGT
51861909 CCAAAACATC
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 49 0.88
29 1 0.02
30 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (27 bp):
ATGGCACTTAGTGTGCGAGTACCGAGG
Found at i:51861900 original size:56 final size:56
Alignment explanation
Indices: 51861810--51861937 Score: 166
Period size: 56 Copynumber: 2.3 Consensus size: 56
51861800 CGATCATATA
* *** *
51861810 AATGGCACTTAGTGTGCGTAGTACCGAGGATGGCACTTAATGTGTGATACATCCAG
1 AATGGCACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAG
* * *
51861866 AATGGCACTTAGTGTGCGAAGTATCGAGGTTGGCACTTAGTGTCCAAAACATCCAG
1 AATGGCACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAG
* *
51861922 AACGACACTTAGTGTG
1 AATGGCACTTAGTGTG
51861938 GGAGGTATTA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (56 bp):
AATGGCACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAG
Found at i:51861956 original size:56 final size:56
Alignment explanation
Indices: 51861815--51861964 Score: 149
Period size: 56 Copynumber: 2.7 Consensus size: 56
51861805 ATATAAATGG
* * * * * *** * * *
51861815 CACTTAGTGTGCGTAGTACCGAGGATGGCACTTAATGTGTGATACATCCAGAATGG
1 CACTTAGTGTGCGAAGTATCGAGGTTGGCACCTAGTGTCCAAAACATCCAGAACGA
*
51861871 CACTTAGTGTGCGAAGTATCGAGGTTGGCACTTAGTGTCCAAAACATCCAGAACGA
1 CACTTAGTGTGCGAAGTATCGAGGTTGGCACCTAGTGTCCAAAACATCCAGAACGA
* * *
51861927 CACTTAGTGTGGGAGGTAT-TAGGTATGGCACCTAGTGT
1 CACTTAGTGTGCGAAGTATCGAGGT-TGGCACCTAGTGT
51861965 GGAAGACATT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
55 4 0.05
56 75 0.95
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (56 bp):
CACTTAGTGTGCGAAGTATCGAGGTTGGCACCTAGTGTCCAAAACATCCAGAACGA
Found at i:51863381 original size:13 final size:13
Alignment explanation
Indices: 51863363--51863387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51863353 GCGTGTGGAT
51863363 GACACACGGGCTA
1 GACACACGGGCTA
51863376 GACACACGGGCT
1 GACACACGGGCT
51863388 TGTGGTCTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.32, G:0.32, T:0.08
Consensus pattern (13 bp):
GACACACGGGCTA
Found at i:51865198 original size:93 final size:93
Alignment explanation
Indices: 51865039--51865209 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
51865029 GCCCCAAAGT
* *
51865039 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCACATCCATAAATGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCAGGCATTCACATCCATAAATGAACTCGGACTCAACTCAA
51865104 CGAGTTCAGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* ** * *
51865132 GAACTCGGACTCAACTCAACAAGTTC-GGACATTTGCATCCATAAGTGAACTCGGACTCAGCTCA
1 GAACTCGGACTCAACTCAACAAGCTCAGG-CATTCACATCCATAAATGAACTCGGACTCAACTCA
*
51865196 ACGAGTTCGGATGC
65 ACGAGTTCAGATGC
51865210 TCAACCATCC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCAGGCATTCACATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:51870840 original size:21 final size:22
Alignment explanation
Indices: 51870798--51870843 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
51870788 GAATGCTTGG
* *
51870798 TTATTAGATGTTTTATGATAGA
1 TTATTAGATGTTTGAAGATAGA
*
51870820 TTATTA-ATGTTTGAAGCTAGA
1 TTATTAGATGTTTGAAGATAGA
51870841 TTA
1 TTA
51870844 ACAAGTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (22 bp):
TTATTAGATGTTTGAAGATAGA
Found at i:51871287 original size:28 final size:28
Alignment explanation
Indices: 51871207--51871297 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
51871197 TAAATGACAT
* *
51871207 TTAGTGTGCGTAGTACCGAGGATGGCAC
1 TTAGTGTGCGAAGTATCGAGGATGGCAC
* * * * *
51871235 TTAATGTGTGATA-CATCCAGAATGGCAC
1 TTAGTGTGCGA-AGTATCGAGGATGGCAC
51871263 TTAGTGTGCGAAGTATCGAGGATGGCAC
1 TTAGTGTGCGAAGTATCGAGGATGGCAC
51871291 TTAGTGT
1 TTAGTGT
51871298 CCAAAACATC
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
27 1 0.02
28 47 0.96
29 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (28 bp):
TTAGTGTGCGAAGTATCGAGGATGGCAC
Found at i:51871293 original size:56 final size:56
Alignment explanation
Indices: 51871202--51871326 Score: 160
Period size: 56 Copynumber: 2.2 Consensus size: 56
51871192 TCATATAAAT
* * *** * *
51871202 GACATTTAGTGTGCGTAGTACCGAGGATGGCACTTAATGTGTGATACATCCAGAAT
1 GACACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAGAAC
* * *
51871258 GGCACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTCCAAAACATCCAGAAC
1 GACACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAGAAC
51871314 GACACTTAGTGTG
1 GACACTTAGTGTG
51871327 GGAGGTATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (56 bp):
GACACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAGAAC
Found at i:51871344 original size:56 final size:56
Alignment explanation
Indices: 51871202--51871353 Score: 153
Period size: 56 Copynumber: 2.7 Consensus size: 56
51871192 TCATATAAAT
* * * * * *** * *
51871202 GACATTTAGTGTGCGTAGTACCGAGGATGGCACTTAATGTGTGATACATCCAGAAT
1 GACACTTAGTGTGCGAAGTATCGAGGATGGCACCTAGTGTCCAAAACATCCAGAAC
* *
51871258 GGCACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTCCAAAACATCCAGAAC
1 GACACTTAGTGTGCGAAGTATCGAGGATGGCACCTAGTGTCCAAAACATCCAGAAC
* * *
51871314 GACACTTAGTGTGGGAGGTAT-TAGGTATGGCACCTAGTGT
1 GACACTTAGTGTGCGAAGTATCGAGG-ATGGCACCTAGTGT
51871354 GGAAGACATT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
55 3 0.04
56 77 0.96
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (56 bp):
GACACTTAGTGTGCGAAGTATCGAGGATGGCACCTAGTGTCCAAAACATCCAGAAC
Found at i:51874561 original size:46 final size:46
Alignment explanation
Indices: 51874494--51874668 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
51874484 TGTAACCCGC
*
51874494 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
51874540 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
51874590 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
51874633 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
51874669 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.56
47 27 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:51874613 original size:93 final size:93
Alignment explanation
Indices: 51874501--51874672 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
51874491 CGCCCATAAG
* * *
51874501 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
51874566 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
51874594 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
51874659 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
51874673 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:51877311 original size:33 final size:34
Alignment explanation
Indices: 51877254--51877325 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
51877244 ATAGACCCAC
* * * * *
51877254 ACTGTTACTGCATAGGGATTAGGCCCAGACTG-T
1 ACTGTTAATGAATAGGGATCAGGCCAAGACCGTT
*
51877287 ACTGTTAATGAATAGGGCTCAGGCCAAGACCGTT
1 ACTGTTAATGAATAGGGATCAGGCCAAGACCGTT
51877321 ACTGT
1 ACTGT
51877326 ATGCACTGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (34 bp):
ACTGTTAATGAATAGGGATCAGGCCAAGACCGTT
Found at i:51881085 original size:20 final size:20
Alignment explanation
Indices: 51881060--51881109 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
51881050 TTAGGGACAA
51881060 ATGAAAAATTCTGAAATTTT
1 ATGAAAAATTCTGAAATTTT
51881080 ATGAAAAATTCTGAAATTTT
1 ATGAAAAATTCTGAAATTTT
51881100 ATGAATAAAT
1 ATGAA-AAAT
51881110 GTGTTGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGAAAAATTCTGAAATTTT
Found at i:51882210 original size:57 final size:57
Alignment explanation
Indices: 51882141--51882249 Score: 209
Period size: 57 Copynumber: 1.9 Consensus size: 57
51882131 AAATAGGATA
*
51882141 GGTAAGTTTAGTTTCTGTTATATGAACTTACTAAGCATGTAATGCTTACTCTATTTT
1 GGTAAGTTTAGTTTCTGTTATACGAACTTACTAAGCATGTAATGCTTACTCTATTTT
51882198 GGTAAGTTTAGTTTCTGTTATACGAACTTACTAAGCATGTAATGCTTACTCT
1 GGTAAGTTTAGTTTCTGTTATACGAACTTACTAAGCATGTAATGCTTACTCT
51882250 GTTTATTTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (57 bp):
GGTAAGTTTAGTTTCTGTTATACGAACTTACTAAGCATGTAATGCTTACTCTATTTT
Found at i:51890254 original size:42 final size:42
Alignment explanation
Indices: 51890137--51890289 Score: 152
Period size: 42 Copynumber: 3.6 Consensus size: 42
51890127 TACCACAGTA
** * * *
51890137 ATGCCATATCCCAGATATGGTCTTTTAT-AGGATCTCATTTCA
1 ATGCCATATCCCAGATATGGTCTTACATGA-AATCTCATATCG
* * * *
51890179 ATGCCAATAGCCCAGCA-ATAGTCTTATACGAAATCTCATATCG
1 ATGCC-ATATCCCAG-ATATGGTCTTACATGAAATCTCATATCG
51890222 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCAT-ATCG
*
51890264 ATG-CATATCCTAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
51890290 CATAGTCTCG
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
41 23 0.24
42 36 0.38
43 33 0.35
44 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATATCG
Found at i:51892253 original size:29 final size:27
Alignment explanation
Indices: 51892219--51892321 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
51892209 TACTCAATCA
*
51892219 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
51892248 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
51892277 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
51892306 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
51892322 ATCTCGTCCC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:51899424 original size:24 final size:24
Alignment explanation
Indices: 51899108--51899422 Score: 558
Period size: 24 Copynumber: 13.1 Consensus size: 24
51899098 GCAAAGACCA
51899108 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
51899132 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
51899156 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
51899180 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
51899204 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
51899228 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
51899252 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
51899276 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
51899300 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
51899324 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
51899348 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
51899372 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
51899396 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
51899420 TAT
1 TAT
51899423 AGTCACATTC
Statistics
Matches: 281, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 281 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:51903531 original size:29 final size:27
Alignment explanation
Indices: 51903497--51903599 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
51903487 TACTCAATCA
*
51903497 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
51903526 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
51903555 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
51903584 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
51903600 ATCTCGTCCC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:51913051 original size:17 final size:18
Alignment explanation
Indices: 51913024--51913057 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
51913014 AATTAAATAT
51913024 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
*
51913042 ATGC-TATTAATTTATT
1 ATGCATATTAAATTATT
51913058 TAAACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:51913264 original size:16 final size:15
Alignment explanation
Indices: 51913239--51913272 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
51913229 AAAGTTGATG
*
51913239 ATAATTAATATATATT
1 ATAATAAATATA-ATT
51913255 ATAATAAATATAATT
1 ATAATAAATATAATT
51913270 ATA
1 ATA
51913273 TATTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:51916988 original size:6 final size:6
Alignment explanation
Indices: 51916977--51917163 Score: 170
Period size: 6 Copynumber: 30.8 Consensus size: 6
51916967 AACCAAAATG
* * *
51916977 AGAATC AGAATC AGAATC AGTAA-C AAAATC AGAATC AGAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* * *
51917025 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATT AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* *
51917074 AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT AGTAA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC
* *
51917122 AGAATC AGAATC AGAATT ACGTGA-C AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT
51917164 GTGAATGCAA
Statistics
Matches: 147, Mismatches: 20, Indels: 28
0.75 0.10 0.14
Matches are distributed among these distances:
5 10 0.07
6 125 0.85
7 10 0.07
8 2 0.01
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:51916992 original size:30 final size:30
Alignment explanation
Indices: 51916977--51917163 Score: 251
Period size: 30 Copynumber: 6.4 Consensus size: 30
51916967 AACCAAAATG
* *
51916977 AGAATCAGAATCAGAATCAGTAACAAAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
51917007 AGAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
51917037 AGAATCAGAATCAGAATTAGGT----G-A-C
1 AGAATCAGAATCAGAATTA-GTAACAGAATC
* *
51917062 AGAATTAGAATCAGAATCAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
51917092 AGAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
51917122 AGAATCAGAATCAGAATTACGTGACAGAATC
1 AGAATCAGAATCAGAATTA-GTAACAGAATC
51917153 AGAATCAGAAT
1 AGAATCAGAAT
51917164 GTGAATGCAA
Statistics
Matches: 138, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
24 2 0.01
25 18 0.13
26 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 91 0.66
31 23 0.17
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (30 bp):
AGAATCAGAATCAGAATTAGTAACAGAATC
Found at i:51917078 original size:85 final size:85
Alignment explanation
Indices: 51916977--51917163 Score: 347
Period size: 85 Copynumber: 2.2 Consensus size: 85
51916967 AACCAAAATG
51916977 AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
*
51917042 CAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATTACGTGAC
* *
51917062 AGAATTAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
51917127 CAGAATCAGAATTACGTGAC
66 CAGAATCAGAATTACGTGAC
51917147 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
51917164 GTGAATGCAA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 98 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (85 bp):
AGAATCAGAATCAGAATCAGTAACAAAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
CAGAATCAGAATTACGTGAC
Found at i:51917318 original size:27 final size:26
Alignment explanation
Indices: 51917281--51917346 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
51917271 AGCATGGCTG
*
51917281 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
51917307 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
51917334 CCAGAATCAGATA
1 CCAGAA-CAGATA
51917347 ATATGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:51917353 original size:27 final size:27
Alignment explanation
Indices: 51917299--51917354 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
51917289 GATATCGTGA
* * *
51917299 CAGAGTCACCAGATACAGATATTGTGG
1 CAGAGCCACCAGATACAGATAATATGG
51917326 CAGAGCCACCAGA-ATCAGATAATATGG
1 CAGAGCCACCAGATA-CAGATAATATGG
51917353 CA
1 CA
51917355 AACCCACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (27 bp):
CAGAGCCACCAGATACAGATAATATGG
Found at i:51917361 original size:27 final size:27
Alignment explanation
Indices: 51917305--51917362 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
51917295 GTGACAGAGT
* * * *
51917305 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATATGGCAAACC
51917332 CACCAGA-ATCAGATAATATGGCAAACC
1 CACCAGATA-CAGATAATATGGCAAACC
51917359 CACC
1 CACC
51917363 TAACAGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATATGGCAAACC
Found at i:51917567 original size:22 final size:22
Alignment explanation
Indices: 51917519--51917577 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
51917509 GTAAATACGT
*
51917519 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
51917541 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
51917563 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
51917578 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:51917704 original size:27 final size:26
Alignment explanation
Indices: 51917665--51917746 Score: 110
Period size: 27 Copynumber: 3.1 Consensus size: 26
51917655 TCGATCGGTC
*
51917665 AACAGATATTGTGACAGAGTCACCAG
1 AACAGATATTGTGACAGAGCCACCAG
*
51917691 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGACAGAGCCACCAG
* *
51917718 AACAGATATTTGTGTCATAGCCACCAG
1 AACAGATA-TTGTGACAGAGCCACCAG
51917745 AA
1 AA
51917747 TGCTTCCTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 42 0.84
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (26 bp):
AACAGATATTGTGACAGAGCCACCAG
Found at i:51917976 original size:27 final size:27
Alignment explanation
Indices: 51917946--51918141 Score: 239
Period size: 27 Copynumber: 7.3 Consensus size: 27
51917936 GGGGCAAAAT
* * *
51917946 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
51917973 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
51918000 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
51918027 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
51918054 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
51918081 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
51918108 AGAAATTTTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
51918135 AGTAATT
1 GGTAATT
51918142 TCACAATCAA
Statistics
Matches: 146, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:51918182 original size:27 final size:27
Alignment explanation
Indices: 51918146--51918636 Score: 601
Period size: 27 Copynumber: 18.2 Consensus size: 27
51918136 GTAATTTCAC
* *
51918146 AATCAAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
51918173 AATCGAGGGTAAAATGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
51918200 AA-CTGAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * * **
51918227 AATCAAGGGTAAAACAGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
51918254 AATCGAAGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** *
51918281 AATCGAGGGTAAAATAGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
51918308 AACCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
51918335 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
51918362 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
51918389 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
51918416 AA-CTGAAGGTAAAATGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* *
51918443 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
51918470 AATCGAGGGTAAAACAGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
51918497 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
51918524 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
51918551 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
51918578 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
51918605 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
51918632 AATCG
1 AATCG
51918637 GGAGTACTTT
Statistics
Matches: 403, Mismatches: 55, Indels: 12
0.86 0.12 0.03
Matches are distributed among these distances:
26 3 0.01
27 397 0.99
28 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:51928496 original size:31 final size:31
Alignment explanation
Indices: 51928461--51928519 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
51928451 ATGCCAATAG
* *
51928461 CCCAGCTATGGTCTTATACAAAATCTCATAT
1 CCCAGATATGGTCTTACACAAAATCTCATAT
51928492 CCCAGATATGGTCTTACACAAAATCTCA
1 CCCAGATATGGTCTTACACAAAATCTCA
51928520 CAATTATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (31 bp):
CCCAGATATGGTCTTACACAAAATCTCATAT
Found at i:51934338 original size:2 final size:2
Alignment explanation
Indices: 51934331--51934361 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51934321 TTTCAAATTT
51934331 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
51934362 TATGATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:51936710 original size:29 final size:28
Alignment explanation
Indices: 51936678--51936780 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
51936668 GTGACGAGAT
* *
51936678 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
51936707 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
51936736 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
51936765 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
51936781 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:51944460 original size:29 final size:29
Alignment explanation
Indices: 51944403--51944533 Score: 104
Period size: 29 Copynumber: 4.6 Consensus size: 29
51944393 AATTTAAGCC
* *** *
51944403 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACATAGTGCCATATTTTTCCAGCT
** *
51944432 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACATAGTGCCATATTTTTCCAGCT
* *
51944461 TGCACACATAGTGTCATA-TTTTCCAGCAT
1 CGCACACATAGTGCCATATTTTTCCAGC-T
* * * *
51944490 -GCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACATAGTGCCATATTTTTCCAGCT
*
51944518 CGCACACTTAGTGCCA
1 CGCACACATAGTGCCA
51944534 ATCTCGTCAC
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
28 23 0.28
29 59 0.72
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACATAGTGCCATATTTTTCCAGCT
Found at i:51944492 original size:28 final size:28
Alignment explanation
Indices: 51944441--51944533 Score: 114
Period size: 29 Copynumber: 3.2 Consensus size: 28
51944431 TCGCACACCC
* * *
51944441 AGTGCCGTATTTTTCCAGCTTGCACACAT
1 AGTGCCATA-TTTTCCAGCATGCACACTT
*
51944470 AGTGTCATATTTTCCAGCATGCACACTT
1 AGTGCCATATTTTCCAGCATGCACACTT
* *
51944498 AGTGCCTTATATTTCCAGCACGCACACTT
1 AGTGCCATAT-TTTCCAGCATGCACACTT
51944527 AGTGCCA
1 AGTGCCA
51944534 ATCTCGTCAC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 25 0.45
29 30 0.55
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (28 bp):
AGTGCCATATTTTCCAGCATGCACACTT
Found at i:51949782 original size:21 final size:20
Alignment explanation
Indices: 51949753--51949791 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
51949743 TCTTGAAACC
51949753 GGGCACACGCCCGTGTGGAA
1 GGGCACACGCCCGTGTGGAA
51949773 GGGCAACACGCCCGTGTGG
1 GGGC-ACACGCCCGTGTGG
51949792 TCATTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.18, C:0.31, G:0.41, T:0.10
Consensus pattern (20 bp):
GGGCACACGCCCGTGTGGAA
Found at i:51951125 original size:99 final size:96
Alignment explanation
Indices: 51950947--51951217 Score: 272
Period size: 99 Copynumber: 2.8 Consensus size: 96
51950937 AGGGTAAAAT
* * * *
51950947 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTCCTAT
1 GCCGAAGCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGCCGATGCCATGTCCTAG
51951012 ACATGGTCTTACACTGACTATCGAAACCGAG
66 ACATGGTCTTACACTGACTATCGAAACCGAG
* * *
51951043 GCCGAAGCCATGTCCTAGACATGGTGTTACACTAGCTC-TCACATATCCATGCCGATGCCATGTC
1 GCCGAAGCCATGTCCCAGACATGGTCTTACACTAGCTCATC-C--AT-CAAGCCGATGCCATGTC
* * *
51951107 CTAGACATGGTCTTACACTGAC-ACCTCTATA-C-AT
62 CTAGACATGGTCTTACACTGACTA--TCGAAACCGAG
* * * *
51951141 GCCGATGCCATGTCCCAGACATGGTCTTACA-TTGACACAT--ATCATAGCCGATG-CATGTCCC
1 GCCGAAGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCCATCA-AGCCGATGCCATGTCCT
*
51951202 AGACAT-GTCTTGCACT
64 AGACATGGTCTTACACT
51951218 AGCACACAAA
Statistics
Matches: 148, Mismatches: 18, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
92 9 0.06
93 15 0.10
94 9 0.06
95 2 0.01
96 35 0.24
97 2 0.01
98 34 0.23
99 38 0.26
100 4 0.03
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (96 bp):
GCCGAAGCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGCCGATGCCATGTCCTAG
ACATGGTCTTACACTGACTATCGAAACCGAG
Found at i:51955547 original size:34 final size:34
Alignment explanation
Indices: 51955487--51955552 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
51955477 ATTTCAAATA
* * *
51955487 GGGCCTTAACCCATTATAATATCAGTATCAGTGT
1 GGGCCTTAACCCATTACAAGATCAGTAACAGTGT
*
51955521 GGGCCTTAGCCCATTACAACGA-CAGTAACAGT
1 GGGCCTTAACCCATTACAA-GATCAGTAACAGT
51955553 ACAGAATGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (34 bp):
GGGCCTTAACCCATTACAAGATCAGTAACAGTGT
Found at i:51961530 original size:30 final size:31
Alignment explanation
Indices: 51961451--51961564 Score: 187
Period size: 31 Copynumber: 3.7 Consensus size: 31
51961441 TCAATCTCAG
**
51961451 CATAT-ACTGGGCCGAAGCCTTCACATTATT
1 CATATCACTGGGCCGAAGCCTTTTCATTATT
51961481 CATATCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTTCATTATT
*
51961512 CATATCACTGGG-CGAAGCCTTTTTATTATT
1 CATATCACTGGGCCGAAGCCTTTTCATTATT
51961542 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
51961565 ACTGTAACGA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
30 34 0.43
31 45 0.57
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATTATT
Found at i:51961799 original size:25 final size:25
Alignment explanation
Indices: 51961771--51961826 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
51961761 CTGGAGGCCT
*
51961771 AGCCTCTTTTAAT-AACTGGGGAAAA
1 AGCCT-TTTTAATAAACTAGGGAAAA
* *
51961796 AGCCATTTTTGATAAACTAGGGCAAA
1 AGCC-TTTTTAATAAACTAGGGAAAA
51961822 AGCCT
1 AGCCT
51961827 GTTTCGGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (25 bp):
AGCCTTTTTAATAAACTAGGGAAAA
Found at i:51961822 original size:26 final size:26
Alignment explanation
Indices: 51961784--51961845 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
51961774 CTCTTTTAAT
* * *
51961784 AACTGGGGAAAAAGCCAT-TTTTGATA
1 AACTAGGGCAAAAGCC-TGTTTCGATA
*
51961810 AACTAGGGCAAAAGCCTGTTTCGGTA
1 AACTAGGGCAAAAGCCTGTTTCGATA
51961836 AACTAGGGCA
1 AACTAGGGCA
51961846 TAGCCTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.03
26 30 0.97
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (26 bp):
AACTAGGGCAAAAGCCTGTTTCGATA
Found at i:51966731 original size:51 final size:51
Alignment explanation
Indices: 51966650--51966749 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 51
51966640 AGATATGTGG
* * * *
51966650 CATCGGAGCTCGTTGAGTGGTTCGAGTTCATAATGAATGCGATACATGTAA
1 CATCCGAGCTCGTTGAGAGGTCCAAGTTCATAATGAATGCGATACATGTAA
* * * *
51966701 CATCCGAGCTCGTTGAGAGGTCCAAGTTCATTATGGATGTGTTACATGT
1 CATCCGAGCTCGTTGAGAGGTCCAAGTTCATAATGAATGCGATACATGT
51966750 TATAATGTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
CATCCGAGCTCGTTGAGAGGTCCAAGTTCATAATGAATGCGATACATGTAA
Found at i:51967722 original size:2 final size:2
Alignment explanation
Indices: 51967715--51967768 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
51967705 AGCATAGTTG
51967715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
51967757 AG AT AT AC AT AT
1 AT AT AT AT AT AT
51967769 TCGGCCATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:51968444 original size:29 final size:29
Alignment explanation
Indices: 51968409--51968482 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
51968399 GTTGTGAGAT
* *
51968409 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
51968438 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
51968467 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
51968483 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:51972614 original size:13 final size:13
Alignment explanation
Indices: 51972588--51972623 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
51972578 AAAAACAAAG
*
51972588 AGCCCAAGTATAA
1 AGCCCAAATATAA
*
51972601 AGCTCAAATATAA
1 AGCCCAAATATAA
51972614 AGCCCAAATA
1 AGCCCAAATA
51972624 CAATCTGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (13 bp):
AGCCCAAATATAA
Found at i:51977135 original size:5 final size:5
Alignment explanation
Indices: 51977127--51977153 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
51977117 TTGTTTTATT
51977127 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
51977154 AGAATAATTA
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:51988367 original size:27 final size:26
Alignment explanation
Indices: 51988319--51988370 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
51988309 GTGAGGCTGC
*
51988319 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
51988345 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
51988371 TTGCAGCAAG
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:51989057 original size:27 final size:27
Alignment explanation
Indices: 51988942--51989060 Score: 157
Period size: 27 Copynumber: 4.4 Consensus size: 27
51988932 GGGGAAAAAT
* * **
51988942 GGTAATTTTACCCCACAAGGGTATCGC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
51988969 GGTAATTTTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
51988996 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
51989023 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
51989050 GGTAATTCTAC
1 GGTAATTCTAC
51989061 AACTTATCCA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:51995033 original size:29 final size:28
Alignment explanation
Indices: 51994945--51995047 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 28
51994935 TACTCAATCA
** *
51994945 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-ACATTCAAGCT
* * * *
51994974 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATACA-TTCAAGCT
51995003 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCATACATT-CAAGCT
51995032 CGCACA-TTCAGTGCCA
1 CGCACACTT-AGTGCCA
51995048 ATCTCGTCCC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.07
29 57 0.93
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
CGCACACTTAGTGCCATACATTCAAGCT
Found at i:52003003 original size:29 final size:27
Alignment explanation
Indices: 52002969--52003071 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
52002959 TACTCAATCA
*
52002969 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
52002998 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
52003027 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
52003056 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
52003072 ATCTCGTCCC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:52005851 original size:40 final size:40
Alignment explanation
Indices: 52005796--52006020 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 40
52005786 TATTCGGATG
* * *
52005796 ATATCAGGGCTAAGTCCCGAAGGCATTTGTACGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
52005836 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52005876 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGGGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTACT
* * * * *
52005919 ATACCCGAGTTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52005959 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52005999 ATATCC-AGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
52006021 TACTTGGGTT
Statistics
Matches: 155, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
39 13 0.08
40 109 0.70
43 33 0.21
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52006039 original size:83 final size:80
Alignment explanation
Indices: 52005796--52006020 Score: 326
Period size: 83 Copynumber: 2.8 Consensus size: 80
52005786 TATTCGGATG
* * * *
52005796 ATATCAGGGCTAAGTCCCGAAGGCATTTGTACGAGTTCCTATATCCGGGTTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGAGTTAAGTCCCGAAGGCA
52005861 TTTGTGCTAGTGACT
66 TTTGTGCTAGTGACT
* * *
52005876 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGGGTAGTTGCTATACCCGAGTTAAGTCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTACTATATCCGAGTTAAGTCCCGAAG
52005941 GCATTTGTGCTAGTGACT
63 GCATTTGTGCTAGTGACT
* * *
52005959 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATATCC-AGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGAGTTAAGTCCCGAAGG
52006021 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
79 14 0.11
80 40 0.31
81 1 0.01
82 1 0.01
83 74 0.57
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGAGTTAAGTCCCGAAGGCA
TTTGTGCTAGTGACT
Found at i:52013671 original size:47 final size:49
Alignment explanation
Indices: 52013454--52013709 Score: 439
Period size: 49 Copynumber: 5.3 Consensus size: 49
52013444 GTATGAGGTA
52013454 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
52013503 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
52013552 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
52013601 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * *
52013648 TATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
52013695 TATAAATGTGATAAG
1 TATATATGTGATAAG
52013710 TCCCGAAGGG
Statistics
Matches: 199, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
47 56 0.28
48 5 0.03
49 138 0.69
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:52016123 original size:39 final size:40
Alignment explanation
Indices: 52016008--52016403 Score: 660
Period size: 39 Copynumber: 10.1 Consensus size: 40
52015998 AAGTCTCGAC
52016008 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52016047 GATGTATCTGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52016087 GATGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52016126 GATGTAT-CGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52016165 GATGTAT-CGGGCTAAGTCCTGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52016204 GATGTAT-CGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52016243 GATGTAT-CGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
52016282 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52016322 GATGTATCCGAGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * *
52016362 GATGTATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
52016402 GA
1 GA
52016404 CGTGTATTCG
Statistics
Matches: 341, Mismatches: 13, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
38 10 0.03
39 172 0.50
40 159 0.47
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:52020152 original size:47 final size:49
Alignment explanation
Indices: 52019935--52020190 Score: 439
Period size: 49 Copynumber: 5.3 Consensus size: 49
52019925 GTATGAGGTA
52019935 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
52019984 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
52020033 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
52020082 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * *
52020129 TATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
52020176 TATAAATGTGATAAG
1 TATATATGTGATAAG
52020191 TCCCGAAGGG
Statistics
Matches: 199, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
47 56 0.28
48 5 0.03
49 138 0.69
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:52024458 original size:40 final size:40
Alignment explanation
Indices: 52024403--52024626 Score: 317
Period size: 40 Copynumber: 5.6 Consensus size: 40
52024393 TATTCGGATG
*
52024403 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52024443 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52024483 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTACT
* *
52024526 ATA-CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52024565 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52024605 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
52024627 TACTTGGGTT
Statistics
Matches: 163, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
39 22 0.13
40 106 0.65
42 27 0.17
43 8 0.05
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52024563 original size:82 final size:80
Alignment explanation
Indices: 52024403--52024626 Score: 371
Period size: 82 Copynumber: 2.8 Consensus size: 80
52024393 TATTCGGATG
*
52024403 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCA
52024468 TTTGTGCTAGTGACT
66 TTTGTGCTAGTGACT
*
52024483 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCTATA-CCGGGCTAAGTCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTGCTATATCCGGGCTAAGTCCCGAAG
52024547 GCATTTGTGCTAGTGACT
63 GCATTTGTGCTAGTGACT
* *
52024565 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGG
52024627 TACTTGGGTT
Statistics
Matches: 135, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
79 25 0.19
80 34 0.25
82 67 0.50
83 9 0.07
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCTAGTGACT
Found at i:52028492 original size:12 final size:13
Alignment explanation
Indices: 52028475--52028507 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52028465 CTTAGTACTT
52028475 AATTCATAT-ACC
1 AATTCATATCACC
*
52028487 AATTCAAATCACC
1 AATTCATATCACC
52028500 AATTCATA
1 AATTCATA
52028508 ATCTAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (13 bp):
AATTCATATCACC
Found at i:52031045 original size:56 final size:57
Alignment explanation
Indices: 52030954--52031128 Score: 162
Period size: 56 Copynumber: 3.1 Consensus size: 57
52030944 TCTTACATGC
* * *
52030954 AATCACATATCAATGCCACTGT-TCCAAACAG-GGTCTTACTCAT-AAAAACATATCGG
1 AATCACATATCAATGCCAATGTAT-AAAAC-GTGGTCTTACTCATCAAAAACATATCAG
* * * * *
52031010 AATCACATATCTATGCCAATGTATAAAACGTGGTCTTACT-TTCACACATATATCAG
1 AATCACATATCAATGCCAATGTATAAAACGTGGTCTTACTCATCAAAAACATATCAG
* * * * * * *
52031066 AGTCACATATCGATGCCAATGCATAAAACGTGGTCTTACTC-GCACACATATATCAG
1 AATCACATATCAATGCCAATGTATAAAACGTGGTCTTACTCATCAAAAACATATCAG
52031122 AATCACA
1 AATCACA
52031129 AATACTTCCA
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
55 2 0.02
56 99 0.97
57 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (57 bp):
AATCACATATCAATGCCAATGTATAAAACGTGGTCTTACTCATCAAAAACATATCAG
Found at i:52037818 original size:26 final size:26
Alignment explanation
Indices: 52037761--52037832 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
52037751 CCTTTTTAAT
*
52037761 AACTGGGGCAAAGCCC-TTTTCGATT
1 AACTGGGGCAAAGCCCTTTTTCGATA
* *
52037786 AATTGGGGAAAAGCCCTTTTTCCG-TA
1 AACTGGGGCAAAGCCCTTTTT-CGATA
52037812 AACTGGGGCAAAGCCCTTTTT
1 AACTGGGGCAAAGCCCTTTTT
52037833 GCACTTCCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
25 14 0.35
26 24 0.60
27 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTTTCGATA
Found at i:52037904 original size:21 final size:21
Alignment explanation
Indices: 52037865--52037937 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
52037855 ACCCAACCCA
* *
52037865 TGCATATAATGAATATATCATG
1 TGCATATCAT-AACATATCATG
*
52037887 TGCATCTCATAACATATCATG
1 TGCATATCATAACATATCATG
**
52037908 TGCATATCATGTCATATCATG
1 TGCATATCATAACATATCATG
52037929 T-CATATCAT
1 TGCATATCAT
52037938 GTATATCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.18
21 29 0.64
22 8 0.18
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (21 bp):
TGCATATCATAACATATCATG
Found at i:52037923 original size:10 final size:10
Alignment explanation
Indices: 52037879--52037945 Score: 82
Period size: 10 Copynumber: 6.6 Consensus size: 10
52037869 TATAATGAAT
52037879 ATATCATGTGC
1 ATATCATGT-C
* **
52037890 ATCTCATAAC
1 ATATCATGTC
52037900 ATATCATGTGC
1 ATATCATGT-C
52037911 ATATCATGTC
1 ATATCATGTC
52037921 ATATCATGTC
1 ATATCATGTC
52037931 ATATCATGT-
1 ATATCATGTC
52037940 ATATCA
1 ATATCA
52037946 AAATCTCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
9 6 0.12
10 27 0.55
11 16 0.33
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (10 bp):
ATATCATGTC
Found at i:52040570 original size:28 final size:28
Alignment explanation
Indices: 52040505--52040605 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
52040495 ATAGTGAATC
*
52040505 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
52040534 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
52040562 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
52040592 CGCACACTTAGTGC
1 CGCACACTTAGTGC
52040606 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:52044222 original size:19 final size:19
Alignment explanation
Indices: 52044178--52044215 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52044168 CATCAGGCAA
*
52044178 AGGTAAATCGTGATTGAAT
1 AGGTAAATCATGATTGAAT
52044197 AGGTAAATCATGATTGAAT
1 AGGTAAATCATGATTGAAT
52044216 GTGTAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (19 bp):
AGGTAAATCATGATTGAAT
Found at i:52054766 original size:25 final size:25
Alignment explanation
Indices: 52054726--52054795 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
52054716 TCATGTACAT
* * **
52054726 GTATGCTTATACGAGCTGTGAATTG
1 GTATGCTCACACGAGCTGTGAATCA
* * * *
52054751 GTATGCTCTCATGAGCTATAAATCA
1 GTATGCTCACACGAGCTGTGAATCA
52054776 GTATGCTCACACGAGCTGTG
1 GTATGCTCACACGAGCTGTG
52054796 GGTTGGAACG
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCA
Found at i:52067122 original size:44 final size:44
Alignment explanation
Indices: 52067059--52067143 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
52067049 TATGTATGAG
* *
52067059 GCATCCAAGCTCGTTGAGTTGGTCTGAGCTCATTATGGATGTAA
1 GCATCCAAGCCCGTTGAGTTGGTCCGAGCTCATTATGGATGTAA
* *
52067103 GCATCCGAGCCCGTTGAGTTGGTCCGAGTTCATTATGGATG
1 GCATCCAAGCCCGTTGAGTTGGTCCGAGCTCATTATGGATG
52067144 CAATACATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (44 bp):
GCATCCAAGCCCGTTGAGTTGGTCCGAGCTCATTATGGATGTAA
Found at i:52071921 original size:20 final size:20
Alignment explanation
Indices: 52071898--52071962 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
52071888 CACTTACGTG
*
52071898 CCCCTATTTCCACTTCGGTA
1 CCCCTATTTGCACTTCGGTA
52071918 CCCCTGA-TTGCACTTAC-GTA
1 CCCCT-ATTTGCACTT-CGGTA
* * *
52071938 CCTCTGTTTGTACTTCGGTA
1 CCCCTATTTGCACTTCGGTA
52071958 CCCCT
1 CCCCT
52071963 TATTGTAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 1 0.03
20 33 0.92
21 2 0.06
ACGTcount: A:0.14, C:0.37, G:0.14, T:0.35
Consensus pattern (20 bp):
CCCCTATTTGCACTTCGGTA
Found at i:52071953 original size:40 final size:40
Alignment explanation
Indices: 52071883--52072092 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
52071873 ATTATTGAAC
* * **
52071883 GATTACACTTACGTGCCCCTATTTCCACTTCGGTACCCCT
1 GATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCT
* *
52071923 GATTGCACTTACGTACCTCTGTTTGTACTTCGGTACCCCT
1 GATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCT
* * * * * * *
52071963 TATTGTAGTTACGTTCCCCTGTTTGTACTTTGGTATCGCT
1 GATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCT
* *
52072003 GATTGCACTTACGTGCCCCTGCTTGTACTTCGGTACACCT
1 GATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCT
* * *
52072043 GATTGCACTTACGTGCCACTATTTGTACTTTGGTACCCCT
1 GATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCT
*
52072083 GGTTGCACTT
1 GATTGCACTT
52072093 CCATGCCACT
Statistics
Matches: 141, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 141 1.00
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (40 bp):
GATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCT
Found at i:52071968 original size:20 final size:20
Alignment explanation
Indices: 52071909--52072093 Score: 110
Period size: 20 Copynumber: 9.2 Consensus size: 20
52071899 CCCTATTTCC
*
52071909 ACTTCGGTACCCCTGATTGC
1 ACTTCGGTACCCCTGATTGT
* *
52071929 ACTTAC-GTACCTCTGTTTGT
1 ACTT-CGGTACCCCTGATTGT
*
52071949 ACTTCGGTACCCCTTATTGT
1 ACTTCGGTACCCCTGATTGT
* * *
52071969 AGTTAC-GTTCCCCTGTTTGT
1 ACTT-CGGTACCCCTGATTGT
* * * *
52071989 ACTTTGGTATCGCTGATTGC
1 ACTTCGGTACCCCTGATTGT
* *
52072009 ACTTAC-GTGCCCCTGCTTGT
1 ACTT-CGGTACCCCTGATTGT
* *
52072029 ACTTCGGTACACCTGATTGC
1 ACTTCGGTACCCCTGATTGT
* *
52072049 ACTTAC-GTGCCACT-ATTTGT
1 ACTT-CGGTACCCCTGA-TTGT
* * *
52072069 ACTTTGGTACCCCTGGTTGC
1 ACTTCGGTACCCCTGATTGT
52072089 ACTTC
1 ACTTC
52072094 CATGCCACTG
Statistics
Matches: 118, Mismatches: 37, Indels: 20
0.67 0.21 0.11
Matches are distributed among these distances:
19 3 0.03
20 112 0.95
21 3 0.03
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.38
Consensus pattern (20 bp):
ACTTCGGTACCCCTGATTGT
Found at i:52072117 original size:40 final size:40
Alignment explanation
Indices: 52072001--52072117 Score: 103
Period size: 40 Copynumber: 2.9 Consensus size: 40
52071991 TTTGGTATCG
* * *
52072001 CTGATTGCACTTACGTGCCCCT-GCTTGTACT-TCGGTACAC
1 CTGATTGCACTTACATGCCACTAG-TTATACTCT-GGTACAC
* * * * *
52072041 CTGATTGCACTTACGTGCCACTATTTGTACTTTGGTACCC
1 CTGATTGCACTTACATGCCACTAGTTATACTCTGGTACAC
* * *
52072081 CTGGTTGCACTTCCATGCCACTGGTTATACTCTGGTA
1 CTGATTGCACTTACATGCCACTAGTTATACTCTGGTA
52072118 ACTCTAAATC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 64 0.98
41 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (40 bp):
CTGATTGCACTTACATGCCACTAGTTATACTCTGGTACAC
Found at i:52074945 original size:31 final size:30
Alignment explanation
Indices: 52074889--52074946 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52074879 AAAATCATAT
52074889 TTTGGCAAAATAACATTTTTGCCCCTAAAA
1 TTTGGCAAAATAACATTTTTGCCCCTAAAA
* * *
52074919 TTTGTCAAAATTACACTTTTTTCCCCTA
1 TTTGGCAAAATAACA-TTTTTGCCCCTA
52074947 GGCTCATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTGGCAAAATAACATTTTTGCCCCTAAAA
Found at i:52084480 original size:25 final size:25
Alignment explanation
Indices: 52084427--52084480 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
52084417 AATTTTATTC
* *
52084427 AATTATCTAATTTTTCAATTTATTG
1 AATTATCTAATTTTTCAATTAATTA
52084452 AATTAT-TAATATTTT-ATATTAATTA
1 AATTATCTAAT-TTTTCA-ATTAATTA
52084477 AATT
1 AATT
52084481 TTTGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTATCTAATTTTTCAATTAATTA
Found at i:52087353 original size:21 final size:20
Alignment explanation
Indices: 52087329--52087367 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52087319 AATTTTAGTT
52087329 AATTTATAATTATTTTTGATG
1 AATTT-TAATTATTTTTGATG
**
52087350 AATTTTGGTTATTTTTGA
1 AATTTTAATTATTTTTGA
52087368 CAGATTTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (20 bp):
AATTTTAATTATTTTTGATG
Found at i:52089444 original size:30 final size:30
Alignment explanation
Indices: 52089377--52089434 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
52089367 TATGTCTCAG
* *
52089377 CCGTGTGTGACACACAGCCATGCGACACGA
1 CCGTATGTGACACACAACCATGCGACACGA
*
52089407 CCGTATGTGACATACAACCATGCGACAC
1 CCGTATGTGACACACAACCATGCGACAC
52089435 AGCTGTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.16
Consensus pattern (30 bp):
CCGTATGTGACACACAACCATGCGACACGA
Found at i:52095585 original size:20 final size:21
Alignment explanation
Indices: 52095552--52095590 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
52095542 ATATGAGTAG
52095552 AAAATTTTATTGAA-AAGAAA
1 AAAATTTTATTGAATAAGAAA
52095572 AAAATATTTA-TGAATAAGA
1 AAAAT-TTTATTGAATAAGA
52095591 TGAATTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATTTTATTGAATAAGAAA
Found at i:52097296 original size:31 final size:31
Alignment explanation
Indices: 52097261--52097324 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
52097251 CCTTTTCATA
52097261 TTTCATATTTCATAACACTGGGCCAAAGCCT
1 TTTCATATTTCATAACACTGGGCCAAAGCCT
** *
52097292 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCAAAGCCT
52097323 TT
1 TT
52097325 CATTTAACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCAAAGCCT
Found at i:52097591 original size:26 final size:26
Alignment explanation
Indices: 52097535--52097696 Score: 242
Period size: 26 Copynumber: 6.3 Consensus size: 26
52097525 CTGGAGGCCT
*
52097535 AGCCTCTTTT-AAT-AACTGGGGTA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
*
52097559 AGCCCTTTTCAGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
52097585 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
52097611 AGCCTTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
52097637 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
52097663 AGCCCTTTTCAATAAACTGGGGCAT-
1 AGCCCTTTTCAATAAACTGGGGCATA
52097688 AGCCCTTTT
1 AGCCCTTTT
52097697 GCACTTCCTC
Statistics
Matches: 126, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
23 5 0.04
24 6 0.05
25 18 0.14
26 97 0.77
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:52097774 original size:20 final size:20
Alignment explanation
Indices: 52097749--52097820 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
52097739 TGATTACATT
*
52097749 ATGTGCATTTCATACATATC
1 ATGTGCATATCATACATATC
*
52097769 ATGTGCATATCATACATACC
1 ATGTGCATATCATACATATC
52097789 ATGTGCATATCATATCAT-TC
1 ATGTGCATATCATA-CATATC
52097809 ATGT--ATATCATA
1 ATGTGCATATCATA
52097821 TCCCACGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
18 8 0.17
20 37 0.77
21 3 0.06
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGTGCATATCATACATATC
Found at i:52101355 original size:48 final size:48
Alignment explanation
Indices: 52101279--52101540 Score: 278
Period size: 48 Copynumber: 5.7 Consensus size: 48
52101269 TACCACGGTT
* * *
52101279 ATACGTGTAACATGGTGCTAAGTGGATATACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACATATATTG
* *
52101327 ATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACATATATTG
* * *
52101375 ATTCAT-TAACGTAGTGCTAAGTGGATATACCACG-----GT-TA-TG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACATATATTG
* * * * *
52101415 ---CGTGTAACGTGATGCTAAGCGGATATACCATGATTACAAATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACATATATTG
* * *
52101460 ATACATGTAACGTGATGCTAAGTGGATATGCCACGGTTACATATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACATATATTG
* *
52101508 ATTCAT-TAACATGGTGCTAAGTGGATATACCAC
1 ATACATGTAACGTGGTGCTAAGTGGATATACCAC
52101541 AGTTAAACAT
Statistics
Matches: 177, Mismatches: 26, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.01
38 24 0.14
40 2 0.01
41 2 0.01
42 1 0.01
44 2 0.01
45 2 0.01
47 50 0.28
48 92 0.52
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACATATATTG
Found at i:52101487 original size:133 final size:133
Alignment explanation
Indices: 52101249--52101579 Score: 545
Period size: 133 Copynumber: 2.5 Consensus size: 133
52101239 GGAATGAAAA
*
52101249 AACGTGGTGCTAAGTGGATATACCACGGTTATACGTGTAACATGGTGCTAAGTGGATATACCACG
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACGTGTAACGTGGTGCTAAGTGGATATACCACG
* *
52101314 ATTACACATATTGATACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTC
66 ATTACAAATATTGATACATGTAACGTGATGCTAAGTGGATATGCCACGGTTACATATATTGATTC
52101379 ATT
131 ATT
* * * * *
52101382 AACGTAGTGCTAAGTGGATATACCACGGTTATGCGTGTAACGTGATGCTAAGCGGATATACCATG
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACGTGTAACGTGGTGCTAAGTGGATATACCACG
52101447 ATTACAAATATTGATACATGTAACGTGATGCTAAGTGGATATGCCACGGTTACATATATTGATTC
66 ATTACAAATATTGATACATGTAACGTGATGCTAAGTGGATATGCCACGGTTACATATATTGATTC
52101512 ATT
131 ATT
* * * * *
52101515 AACATGGTGCTAAGTGGATATACCACAGTTAAACATGTAACGTGGTGCTAAGTGGATATGCCACG
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACGTGTAACGTGGTGCTAAGTGGATATACCACG
52101580 GTTATACATG
Statistics
Matches: 180, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 180 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (133 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTATACGTGTAACGTGGTGCTAAGTGGATATACCACG
ATTACAAATATTGATACATGTAACGTGATGCTAAGTGGATATGCCACGGTTACATATATTGATTC
ATT
Found at i:52101570 original size:38 final size:38
Alignment explanation
Indices: 52101514--52101590 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
52101504 ATTGATTCAT
52101514 TAACATGGTGCTAAGTGGATATACCACAGTTAAACATG
1 TAACATGGTGCTAAGTGGATATACCACAGTTAAACATG
* * * *
52101552 TAACGTGGTGCTAAGTGGATATGCCACGGTTATACATG
1 TAACATGGTGCTAAGTGGATATACCACAGTTAAACATG
52101590 T
1 T
52101591 TAATTTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (38 bp):
TAACATGGTGCTAAGTGGATATACCACAGTTAAACATG
Found at i:52104861 original size:15 final size:15
Alignment explanation
Indices: 52104841--52104882 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
52104831 GCTGTAAATG
52104841 GGATTTCTTTATCAT
1 GGATTTCTTTATCAT
*
52104856 GGATTTCTTTATCTT
1 GGATTTCTTTATCAT
*
52104871 GGATTTCCTTAT
1 GGATTTCTTTAT
52104883 TCTGGGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
GGATTTCTTTATCAT
Found at i:52104892 original size:16 final size:15
Alignment explanation
Indices: 52104839--52104892 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
52104829 GTGCTGTAAA
52104839 TGGGATTTCTTTATC
1 TGGGATTTCTTTATC
52104854 AT-GGATTTCTTTATC
1 -TGGGATTTCTTTATC
* *
52104869 TTGGATTTCCTTATTC
1 TGGGATTTCTTTA-TC
52104885 TGGGATTT
1 TGGGATTT
52104893 TCCGTTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 1 0.03
15 23 0.68
16 10 0.29
ACGTcount: A:0.15, C:0.13, G:0.19, T:0.54
Consensus pattern (15 bp):
TGGGATTTCTTTATC
Found at i:52107742 original size:38 final size:38
Alignment explanation
Indices: 52107691--52107852 Score: 137
Period size: 38 Copynumber: 4.0 Consensus size: 38
52107681 ATTGATTCAT
*
52107691 TAACGTAGTGCTAAGTGGATATACCACGGTTAAACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
* *
52107729 TAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA-A-ACA-TG
* *
52107770 ATTCATTAATGTAGG-GCTAAGTGGATATACCATGGTTAAACATG
1 ------TAACGT-GGTGCTAAGTGGATATACCACGGTTAAACATG
* * * * *
52107814 TAATGTGGTGCTAACTGGATATGCCAGGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
52107852 T
1 T
52107853 TAATTTGAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
37 2 0.02
38 62 0.61
39 1 0.01
40 2 0.02
41 2 0.02
44 2 0.02
45 2 0.02
46 1 0.01
47 26 0.25
48 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
Found at i:52107789 original size:85 final size:85
Alignment explanation
Indices: 52107639--52107845 Score: 342
Period size: 85 Copynumber: 2.4 Consensus size: 85
52107629 ACATATTGAT
* * *
52107639 ACATGTAATGTGGTGCTAAGTGGATATGTCACGATTACATATATTGATTCATTAACGTAGTGCTA
1 ACATGTAATGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTAGGGCTA
52107704 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
* *
52107724 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAATGTAGGGCTA
1 ACATGTAATGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTAGGGCTA
*
52107789 AGTGGATATACCATGGTTAA
66 AGTGGATATACCACGGTTAA
* *
52107809 ACATGTAATGTGGTGCTAACTGGATATGCCAGGGTTA
1 ACATGTAATGTGGTGCTAAGTGGATATGCCACGGTTA
52107846 TACATGTTAA
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 113 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (85 bp):
ACATGTAATGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTAGGGCTA
AGTGGATATACCACGGTTAA
Found at i:52111760 original size:46 final size:47
Alignment explanation
Indices: 52111682--52111774 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 47
52111672 ATTGCACTAC
52111682 TGTATTTCTGTTACTGATACTGTCACTATATTGGGCTTAGGCCCACA
1 TGTATTTCTGTTACTGATACTGTCACTATATTGGGCTTAGGCCCACA
* * *
52111729 TGTA-TTCTGTTTCTGATTCTGAT-ACTGTATTGGGCTTAGGCCCACA
1 TGTATTTCTGTTACTGATACTG-TCACTATATTGGGCTTAGGCCCACA
52111775 CTGTTCTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 37 0.88
47 5 0.12
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (47 bp):
TGTATTTCTGTTACTGATACTGTCACTATATTGGGCTTAGGCCCACA
Found at i:52120011 original size:29 final size:29
Alignment explanation
Indices: 52119977--52120108 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
52119967 TACTCGATTT
** * *
52119977 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
52120006 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
52120035 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
52120064 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52120093 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
52120109 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:52125531 original size:40 final size:40
Alignment explanation
Indices: 52125486--52125651 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
52125476 CGGAATATAA
52125486 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
52125526 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
52125566 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
52125606 CCGGATATAATTTC-CGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
52125644 CCGGATAT
1 CCGGATAT
52125652 CATTCAATTT
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
38 13 0.12
39 16 0.15
40 77 0.73
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:52126471 original size:17 final size:19
Alignment explanation
Indices: 52126448--52126493 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
52126438 AAGAAGCATG
52126448 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
52126466 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
52126484 AATCATGCTC
1 AATCATGCTC
52126494 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:52133089 original size:40 final size:40
Alignment explanation
Indices: 52133044--52133210 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
52133034 CGGAATATAA
52133044 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
52133084 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
52133124 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
52133164 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
52133203 CCGGATAT
1 CCGGATAT
52133211 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:52133194 original size:80 final size:79
Alignment explanation
Indices: 52133044--52133210 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
52133034 CGGAATATAA
* *
52133044 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
52133109 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
52133124 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
52133186 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
52133203 CCGGATAT
1 CCGGATAT
52133211 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:52134059 original size:17 final size:19
Alignment explanation
Indices: 52134036--52134081 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
52134026 AAGAAGCATG
52134036 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
52134054 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
52134072 AATCATGCTC
1 AATCATGCTC
52134082 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:52134539 original size:29 final size:29
Alignment explanation
Indices: 52134497--52134568 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
52134487 GGGTGTCACA
*
52134497 CACACTTAGTGCCATATATTTCCAGCATG
1 CACACTTAGTGCCATATATTTCCAGCACG
52134526 CACACTTAGTGCCATATATTTCCAGCACG
1 CACACTTAGTGCCATATATTTCCAGCACG
52134555 CACACTTAGTGCCA
1 CACACTTAGTGCCA
52134569 ATCTCGTCAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (29 bp):
CACACTTAGTGCCATATATTTCCAGCACG
Found at i:52140189 original size:42 final size:42
Alignment explanation
Indices: 52140069--52140233 Score: 131
Period size: 42 Copynumber: 3.9 Consensus size: 42
52140059 AATCATACCA
* * **** *
52140069 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCATGTCG
1 ATGCCATATCCCAGACATGGCCTTACACAAAATCTCATATCG
* * * * *
52140111 ATGCCAATAACCTAG-CTATAGCCTTACAC-GATTCTCATATCG
1 ATGCC-ATATCCCAGAC-ATGGCCTTACACAAAATCTCATATCG
52140153 ATGCCATATCCCAGACATGGCCTTACACAAAATCTCATAAT-G
1 ATGCCATATCCCAGACATGGCCTTACACAAAATCTCAT-ATCG
** *
52140195 ATGCCATATCCCAGTTATGGTCTTACACATAAA-CTCATA
1 ATGCCATATCCCAGACATGGCCTTACACA-AAATCTCATA
52140234 ACCCTAATGT
Statistics
Matches: 100, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
41 19 0.19
42 60 0.60
43 21 0.21
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGCCTTACACAAAATCTCATATCG
Found at i:52143728 original size:48 final size:48
Alignment explanation
Indices: 52143652--52143834 Score: 162
Period size: 48 Copynumber: 3.9 Consensus size: 48
52143642 TAGGGTTATG
* * * *
52143652 TGTGATCCCATGAAAGACTATGTATGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATA
* *
52143700 TGTGATCTCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATA
* * * * * * **
52143748 TGAGA-CATCGTGTAAGACCATAGCTGGG-C-T---ATCGGCTTCGACC
1 TGTGATC-CCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATA
* * *
52143791 TGTGATCCCATGTAAGACCACATCTGGGATATGGAATTGGCATC
1 TGTGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATC
52143835 TTACTATGTG
Statistics
Matches: 106, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 30 0.28
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 72 0.68
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATA
Found at i:52148946 original size:13 final size:13
Alignment explanation
Indices: 52148928--52148957 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52148918 TATTCGGTAG
52148928 TACAAAGTGTAAT
1 TACAAAGTGTAAT
*
52148941 TACAAATTGTAAT
1 TACAAAGTGTAAT
52148954 TACA
1 TACA
52148958 CAGTTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (13 bp):
TACAAAGTGTAAT
Found at i:52150009 original size:18 final size:18
Alignment explanation
Indices: 52149986--52150020 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52149976 GTAAATTAAT
52149986 TTTATAATATACTTTTTA
1 TTTATAATATACTTTTTA
52150004 TTTATAATATACTTTTT
1 TTTATAATATACTTTTT
52150021 TACCACGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATAATATACTTTTTA
Found at i:52155705 original size:26 final size:26
Alignment explanation
Indices: 52155676--52155783 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
52155666 TGAAATGCCC
*
52155676 ATCATGGAACATTTACCTAAATCATT
1 ATCATGGAACATTTACCTAAACCATT
*
52155702 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
52155728 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
52155754 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
52155780 ATCA
1 ATCA
52155784 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:52155754 original size:52 final size:52
Alignment explanation
Indices: 52155676--52155783 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 52
52155666 TGAAATGCCC
52155676 ATCATGGAACATTTACCTAAATCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAATCATTATCATGGAACATTTACCTAACCCATT
*
52155728 ATCATGGAATATTTACCT-AATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAAT-CATTATCATGGAACATTTACCTAACCCATT
52155780 ATCA
1 ATCA
52155784 ATTTGTACCA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
51 3 0.06
52 51 0.94
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAATCATTATCATGGAACATTTACCTAACCCATT
Found at i:52157503 original size:24 final size:24
Alignment explanation
Indices: 52157415--52157561 Score: 156
Period size: 24 Copynumber: 6.2 Consensus size: 24
52157405 AGCTTCTCCT
* * **
52157415 GAGCTAATGAATAGTAAGCTCTTTT
1 GAGCTAA-GAACAATAAGCTCTTAC
* * *
52157440 GAGCTGA-AACAGTAAGCTCTGAC
1 GAGCTAAGAACAATAAGCTCTTAC
* * *
52157463 AAGCT--GAACAGTAAGCTCATAC
1 GAGCTAAGAACAATAAGCTCTTAC
* *
52157485 GAGCTGAGAATAATAAGCTCTTAC
1 GAGCTAAGAACAATAAGCTCTTAC
52157509 GAGCTAAGAACAATAAGCTCTTAC
1 GAGCTAAGAACAATAAGCTCTTAC
52157533 GAGCTAAGAACAATAAGCTCTTAC
1 GAGCTAAGAACAATAAGCTCTTAC
52157557 GAGCT
1 GAGCT
52157562 GATATATTGG
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.17
23 16 0.15
24 65 0.62
25 6 0.06
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (24 bp):
GAGCTAAGAACAATAAGCTCTTAC
Found at i:52157560 original size:72 final size:69
Alignment explanation
Indices: 52157423--52157563 Score: 174
Period size: 72 Copynumber: 2.0 Consensus size: 69
52157413 CTGAGCTAAT
* ** * * *
52157423 GAATAGTAAGCTCTTTTGAGCTGAAACAGTAAGCTCTGACAAGCTGAACAGTAAGCTCATACGAG
1 GAATAATAAGCTCTTACGAGCTAAAACAATAAGCTCTGACAAGCTGAACAATAAGCTCATACGAG
52157488 CTGA
66 CTGA
* * *
52157492 GAATAATAAGCTCTTACGAGCTAAGAACAATAAGCTCTTACGAGCTAAGAACAATAAGCTCTTAC
1 GAATAATAAGCTCTTACGAGCTAA-AACAATAAGCTCTGACAAGCT--GAACAATAAGCTCATAC
52157557 GAGCTGA
63 GAGCTGA
52157564 TATATTGGTA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
69 20 0.33
70 18 0.30
72 22 0.37
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (69 bp):
GAATAATAAGCTCTTACGAGCTAAAACAATAAGCTCTGACAAGCTGAACAATAAGCTCATACGAG
CTGA
Found at i:52169064 original size:3 final size:3
Alignment explanation
Indices: 52169056--52169082 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52169046 GCAGATCTGA
52169056 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
52169083 AATTTAATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:52179022 original size:20 final size:21
Alignment explanation
Indices: 52178984--52179022 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
52178974 TTCAACTAGG
* *
52178984 ATTATAATTAATCACATTAAT
1 ATTATAATTAATAAAATTAAT
52179005 ATTAT-ATTAATAAAATTA
1 ATTATAATTAATAAAATTA
52179023 TCTAGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTATAATTAATAAAATTAAT
Done.