Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 65
Found at i:5359858 original size:21 final size:21
Alignment explanation
Indices: 5359829--5359887 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
5359819 AAAGTCCAAC
* *
5359829 CCCAGATCCAGAACCCGGAGG
1 CCCAGATCCAGAACCCGAAAG
* *
5359850 CCCATATCCAAAACCCGAAAG
1 CCCAGATCCAGAACCCGAAAG
5359871 CCCAGATCCAG-ACCCGA
1 CCCAGATCCAGAACCCGA
5359888 CCCAACACCC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.34, C:0.41, G:0.19, T:0.07
Consensus pattern (21 bp):
CCCAGATCCAGAACCCGAAAG
Found at i:5360509 original size:22 final size:22
Alignment explanation
Indices: 5360468--5360509 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5360458 GATCGATGGC
* *
5360468 CGAAATAGTGATCGGCGGTAGT
1 CGAAATAGTAACCGGCGGTAGT
*
5360490 CGAAATAGTAACCGGTGGTA
1 CGAAATAGTAACCGGCGGTA
5360510 ACCAGTCGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.21
Consensus pattern (22 bp):
CGAAATAGTAACCGGCGGTAGT
Found at i:5363343 original size:43 final size:44
Alignment explanation
Indices: 5363282--5363368 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
5363272 TGGCTTTAGA
* *
5363282 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
* *
5363325 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
5363369 TGATGCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:5363504 original size:20 final size:20
Alignment explanation
Indices: 5363447--5363504 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
5363437 CATACATGCA
* *
5363447 TTTGCATTTTGTATCTTTGTG
1 TTTGC-TTTTGTATTTTTATG
* * * *
5363468 TTTTCATTTATACTTTTATG
1 TTTGCTTTTGTATTTTTATG
5363488 TTTGCTTTTGTATTTTT
1 TTTGCTTTTGTATTTTT
5363505 TTTCATTTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTGCTTTTGTATTTTTATG
Found at i:5366303 original size:9 final size:9
Alignment explanation
Indices: 5366289--5366336 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
5366279 AAGATGAGAA
5366289 AAAAAAAAG
1 AAAAAAAAG
5366298 -AAAAAAAG
1 AAAAAAAAG
*
5366306 GAAAAAAAG
1 AAAAAAAAG
*
5366315 --AAAGAAG
1 AAAAAAAAG
5366322 AAAAAAAAG
1 AAAAAAAAG
5366331 AAAAAA
1 AAAAAA
5366337 TTGAATCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 6 0.18
8 8 0.24
9 20 0.59
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:5366327 original size:24 final size:22
Alignment explanation
Indices: 5366287--5366336 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
5366277 TGAAGATGAG
*
5366287 AAAAAAAAAAGAAAAAAAGGAA
1 AAAAAAAAAAGAAAAAAAAGAA
5366309 AAAAAGAAAGAAGAAAAAAAAGAA
1 AAAAA-AAA-AAGAAAAAAAAGAA
5366333 AAAA
1 AAAA
5366337 TTGAATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.20
23 3 0.12
24 17 0.68
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAAAAAGAA
Found at i:5366828 original size:32 final size:32
Alignment explanation
Indices: 5366788--5366854 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
5366778 AGAGTCTGGA
* *
5366788 AACAAGAAGTATTTCAACGAGATGACCATAAC
1 AACAAGAAGTATCTCAACGAGATAACCATAAC
* * *
5366820 AACAAGAAGTATCTCTACTAGATAAGCATAAC
1 AACAAGAAGTATCTCAACGAGATAACCATAAC
5366852 AAC
1 AAC
5366855 CATTTCTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (32 bp):
AACAAGAAGTATCTCAACGAGATAACCATAAC
Found at i:5370773 original size:22 final size:22
Alignment explanation
Indices: 5370748--5370799 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5370738 TACACTATTT
* *
5370748 AAAGATGATATATTCTCTTTTC
1 AAAGATGATAGAGTCTCTTTTC
5370770 AAAGATGATAGAGTCTCTTTTC
1 AAAGATGATAGAGTCTCTTTTC
5370792 AAAGATGA
1 AAAGATGA
5370800 ATACTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
AAAGATGATAGAGTCTCTTTTC
Found at i:5371775 original size:73 final size:73
Alignment explanation
Indices: 5371650--5371794 Score: 202
Period size: 73 Copynumber: 2.0 Consensus size: 73
5371640 TTTCAAATAG
* *
5371650 TAATTTATCTTACTTGAGATTATTTTTCTTAAAACTAAATGCATCTCGCTTGAGACAGTTTCACT
1 TAATTTATCTCACTTGAGATTATTTTTCTTAAAACTAAATGCATCTCACTTGAGACAGTTTCACT
*
5371715 CGAAACAC
66 AGAAACAC
* * ***
5371723 TAATTTATCTCACTTGATATTGTTTTTCTTAAAAC-AAGATTTGTCTCACTTGAGACAGTTTCAC
1 TAATTTATCTCACTTGAGATTATTTTTCTTAAAACTAA-ATGCATCTCACTTGAGACAGTTTCAC
5371787 TAGAAACA
65 TAGAAACA
5371795 GAAATTTCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 2 0.03
73 61 0.97
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (73 bp):
TAATTTATCTCACTTGAGATTATTTTTCTTAAAACTAAATGCATCTCACTTGAGACAGTTTCACT
AGAAACAC
Found at i:5371794 original size:36 final size:36
Alignment explanation
Indices: 5371692--5371794 Score: 93
Period size: 36 Copynumber: 2.8 Consensus size: 36
5371682 AACTAAATGC
* *
5371692 ATCTCGCTTGAGACAGTTTCACTCGAAACACTAATTT
1 ATCTCACTTGAGACAGTTTCACTAGAAACAC-AATTT
* ** **
5371729 ATCTCACTTGATATTGTTTTTCTTA-AAACA-AGATTT
1 ATCTCACTTGAGACAGTTTCAC-TAGAAACACA-ATTT
*
5371765 GTCTCACTTGAGACAGTTTCACTAGAAACA
1 ATCTCACTTGAGACAGTTTCACTAGAAACA
5371795 GAAATTTCCA
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
35 3 0.06
36 25 0.50
37 21 0.42
38 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (36 bp):
ATCTCACTTGAGACAGTTTCACTAGAAACACAATTT
Found at i:5371985 original size:122 final size:121
Alignment explanation
Indices: 5371816--5372503 Score: 839
Period size: 122 Copynumber: 5.7 Consensus size: 121
5371806 CACTCGATGG
* *
5371816 ACCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGGAGAAGTTCATA
1 ACCAACATTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
5371881 ACGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAAC
65 ATGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTAT-CCAAAAAGAGATAGATCAAC
*
5371939 ACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
* * * *** *
5372004 ATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTC-AT-C---ACTCGATGGAT----
65 ATGAGAAGAATTTGTTCAACCTTTTGCTCG-ATTCTATCCAAAAAGAGATAGATCAAC
* * * *
5372053 --CAGCATTTCCGGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAA
1 ACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
*
5372116 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAAC
66 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCCAA-AAAGAGATAGATCAAC
* * * *
5372173 ATCAAAATTT-CAGAAGTGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
5372237 TGAGAAAAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAAAGATAGATCAAC
66 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCCAA-AAAGAGATAGATCAAC
* * * *
5372294 ATCAAAATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAA
1 ACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* ** * * *
5372359 TAAGAAGAATTTGTTCAAGTTTTTGCAT-GACTCTATCACAAAAAGAGATATATCAGC
66 TGAGAAGAATTTGTTCAACCTTTTGC-TCGATTCTATC-CAAAAAGAGATAGATCAAC
*
5372416 ATCC-ACATTTCCAGAAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCA
1 A-CCAACATTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCA
*
5372479 TAATGAGAAGAATTTATTCAACCTT
63 TAATGAGAAGAATTTGTTCAACCTT
5372504 GCCTTAATTC
Statistics
Matches: 493, Mismatches: 52, Indels: 40
0.84 0.09 0.07
Matches are distributed among these distances:
110 4 0.01
111 46 0.09
112 40 0.08
116 7 0.01
118 7 0.01
121 115 0.23
122 139 0.28
123 128 0.26
124 7 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (121 bp):
ACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCCAAAAAGAGATAGATCAAC
Found at i:5372209 original size:121 final size:122
Alignment explanation
Indices: 5372057--5372503 Score: 659
Period size: 121 Copynumber: 3.7 Consensus size: 122
5372047 ATGGATCAGC
* *
5372057 ATTTCCGGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAATGAGAA
1 ATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
5372122 GAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAACATCAAA
66 GAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAACATCAAA
* * *
5372179 ATTT-CAGAAGTGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
1 ATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* *
5372243 AAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAAAGATAGATCAACATCAAA
66 GAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAACATCAAA
* * * *
5372300 ATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAATAAGAA
1 ATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
** * * * * *
5372365 GAATTTGTTCAAGTTTTTGCAT-GACTCTATCACAA-AAAGAGATATATCAGCATCCAC
66 GAATTTGTTCAACCTTTTGC-TCGATTCTATCA-AAGAAAGAGATAGATCAACATCAAA
5372422 ATTTCCAGAAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAG
1 ATTTCCAG-AAGAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAG
*
5372486 AAGAATTTATTCAACCTT
64 AAGAATTTGTTCAACCTT
5372504 GCCTTAATTC
Statistics
Matches: 294, Mismatches: 26, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
121 114 0.39
122 112 0.38
123 65 0.22
124 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (122 bp):
ATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
GAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAACATCAAA
Found at i:5372888 original size:3 final size:3
Alignment explanation
Indices: 5372880--5372913 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5372870 TTTGTCCCAT
*
5372880 TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5372914 AAAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:5373024 original size:21 final size:21
Alignment explanation
Indices: 5372971--5373046 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
5372961 GTCCAACAGT
*
5372971 AGATCCAGAACTCGGAGGCCC
1 AGATCCAGAACCCGGAGGCCC
* *
5372992 AAATCTAGAACCCGGAGGCCC
1 AGATCCAGAACCCGGAGGCCC
* * *
5373013 AGATCCAAAACCTGGAAGCCC
1 AGATCCAGAACCCGGAGGCCC
5373034 AGATCCAG-ACCCG
1 AGATCCAGAACCCG
5373047 ACCCAACACC
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 4 0.09
21 41 0.91
ACGTcount: A:0.33, C:0.34, G:0.24, T:0.09
Consensus pattern (21 bp):
AGATCCAGAACCCGGAGGCCC
Found at i:5381556 original size:20 final size:20
Alignment explanation
Indices: 5381533--5381572 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5381523 AATCAACCAC
*
5381533 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
5381553 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
5381573 CTGGTCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:5391796 original size:20 final size:20
Alignment explanation
Indices: 5391773--5391815 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5391763 AATCCACCAC
*
5391773 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
5391793 ATGCACCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
5391813 ATG
1 ATG
5391816 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:5393294 original size:23 final size:23
Alignment explanation
Indices: 5393259--5393312 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5393249 AGTGTTATCA
* *
5393259 TAAAAAAACCCTAAAAGTATTTT
1 TAAAAAATCCCTAAAAGTATTTC
*
5393282 TAAAAAATTCCTAAAAGTATTTC
1 TAAAAAATCCCTAAAAGTATTTC
*
5393305 GAAAAAAT
1 TAAAAAAT
5393313 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.30
Consensus pattern (23 bp):
TAAAAAATCCCTAAAAGTATTTC
Found at i:5396819 original size:31 final size:32
Alignment explanation
Indices: 5396763--5396835 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
5396753 TAAGGTGACC
*
5396763 CTTGGGTAGG-CTCTGCGGCCTTGAG-ATTTT
1 CTTGGGTAGGCCTCTGCGGCCCTGAGAATTTT
*
5396793 CTTGGGTAGGCCTCTGTGGCCCTGAGAATTTT
1 CTTGGGTAGGCCTCTGCGGCCCTGAGAATTTT
5396825 CTTGGGTAGGC
1 CTTGGGTAGGC
5396836 TCGTAGGCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 10 0.26
31 13 0.33
32 16 0.41
ACGTcount: A:0.11, C:0.21, G:0.34, T:0.34
Consensus pattern (32 bp):
CTTGGGTAGGCCTCTGCGGCCCTGAGAATTTT
Found at i:5396845 original size:31 final size:29
Alignment explanation
Indices: 5396763--5396845 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 29
5396753 TAAGGTGACC
* *
5396763 CTTGGGTAGGCTCTGCGGCCTTGAGATTTT
1 CTTGGGTAGGCTC-GTGGCCCTGAGATTTT
5396793 CTTGGGTAGGCCTCTGTGGCCCTGAGAATTTT
1 CTTGGGTAGG-CTC-GTGGCCCTGAG-ATTTT
5396825 CTTGGGTAGGCTCGTAGGCCC
1 CTTGGGTAGGCTCGT-GGCCC
5396846 CAAGGTACTC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
30 12 0.25
31 21 0.44
32 15 0.31
ACGTcount: A:0.11, C:0.23, G:0.34, T:0.33
Consensus pattern (29 bp):
CTTGGGTAGGCTCGTGGCCCTGAGATTTT
Found at i:5402185 original size:2 final size:2
Alignment explanation
Indices: 5402174--5402204 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5402164 AGGAATCAAT
5402174 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5402205 ATAACTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5409346 original size:75 final size:75
Alignment explanation
Indices: 5409221--5409364 Score: 225
Period size: 75 Copynumber: 1.9 Consensus size: 75
5409211 CAACATCATG
* * * * *
5409221 TTGAGAGCAGCTTCCGTAGAAGACCTTCGAATTATGAAATGCCCTTTGTGAGACTCGATCCCTCG
1 TTGAGAACAGCTTCCGTAAAAGACCTTCGAATTATAAAATGCCATCTGTGAGACTCGATCCCTCG
5409286 ACCCTAAAAT
66 ACCCTAAAAT
* *
5409296 TTGAGAACAGCTTCCGTAAAAGACCTTCGAATTATAAAATGTCATCTGTGAGACTTGATCCCTCG
1 TTGAGAACAGCTTCCGTAAAAGACCTTCGAATTATAAAATGCCATCTGTGAGACTCGATCCCTCG
5409361 ACCC
66 ACCC
5409365 CAAGATTAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (75 bp):
TTGAGAACAGCTTCCGTAAAAGACCTTCGAATTATAAAATGCCATCTGTGAGACTCGATCCCTCG
ACCCTAAAAT
Found at i:5415050 original size:105 final size:108
Alignment explanation
Indices: 5414874--5415087 Score: 335
Period size: 105 Copynumber: 2.0 Consensus size: 108
5414864 AAGGTTGAAC
* * * *
5414874 AAGTTCTTCTCATTATGAACTTCTTCTCATTTTATTGGATGAGTTGTTCTCATTATGAACTCTTC
1 AAGTTCTTCTCATTACGAAC-TCTTCTCACTTTA-TGGACGAGTTCTTCTCATTATGAACTCTTC
*
5414939 TGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAAGGAAA
64 TGGAAATGTTGATTCACCTCCTTCTGCGGTGAATTTGAAAGGAAA
5414984 AAGTTCTTCTCATTACGAAC-CTTCTC-CTTTA-GGACGAGTTCTTCTCATTATGAACTCTTCTG
1 AAGTTCTTCTCATTACGAACTCTTCTCACTTTATGGACGAGTTCTTCTCATTATGAACTCTTCTG
*
5415046 GAAATGTTGATTCACCTCCTTCTGCGGTGGATTTGAAAGGAA
66 GAAATGTTGATTCACCTCCTTCTGCGGTGAATTTGAAAGGAA
5415088 CAGGCTCTTG
Statistics
Matches: 98, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
105 69 0.70
107 4 0.04
108 6 0.06
110 19 0.19
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (108 bp):
AAGTTCTTCTCATTACGAACTCTTCTCACTTTATGGACGAGTTCTTCTCATTATGAACTCTTCTG
GAAATGTTGATTCACCTCCTTCTGCGGTGAATTTGAAAGGAAA
Found at i:5416076 original size:37 final size:37
Alignment explanation
Indices: 5416035--5416144 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 37
5416025 CTTATCATCT
5416035 TGCTCGAATA-ACTTA-TAGATGACCTGAAGAATTTAAG
1 TGCTCGAA-AGACTTACT-GATGACCTGAAGAATTTAAG
*
5416072 TGCTCGAAAGACTTACTGATGACCTGAAGAATTTAATCATCA
1 TGCTCGAAAGACTTACTGATGACCTGAAGAATTT-A--A--G
* *
5416114 TGCTCAAAAGACTTACTGATGGCCTGAAGAA
1 TGCTCGAAAGACTTACTGATGACCTGAAGAA
5416145 CTTACTCATC
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
36 1 0.02
37 30 0.48
38 2 0.03
40 1 0.02
42 29 0.46
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (37 bp):
TGCTCGAAAGACTTACTGATGACCTGAAGAATTTAAG
Found at i:5416131 original size:42 final size:42
Alignment explanation
Indices: 5416072--5416172 Score: 166
Period size: 42 Copynumber: 2.4 Consensus size: 42
5416062 AGAATTTAAG
*
5416072 TGCTCGAAAGACTTACTGATGACCTGAAGAATTTAATCATCA
1 TGCTCGAAAGACTTACTGATGACCTGAAGAACTTAATCATCA
* * *
5416114 TGCTCAAAAGACTTACTGATGGCCTGAAGAACTTACTCATCA
1 TGCTCGAAAGACTTACTGATGACCTGAAGAACTTAATCATCA
5416156 TGCTCGAAAGACTTACT
1 TGCTCGAAAGACTTACT
5416173 TATCAAGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
TGCTCGAAAGACTTACTGATGACCTGAAGAACTTAATCATCA
Found at i:5416428 original size:53 final size:54
Alignment explanation
Indices: 5416214--5416463 Score: 222
Period size: 52 Copynumber: 4.6 Consensus size: 54
5416204 TTCTTAGTTG
* * * *
5416214 TCAAGGAACCCCTAAGAATTAGGCTTAGTTTCCTTTTAAAAACTCA-TTGAAAATCATCA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGTTT-C-TTT-AAAATTCATTTGAAAA--A-CA
* * *
5416273 TCAAGAAACCCCTAAAAATCAGGCTTAGTTT-TTAAAAACTCATTTG-AAAATA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAATTCATTTGAAAAACA
* * * * *
5416325 TCAAGAAATCCCTAAAAATTAGGCTTAATTTCTTTGAAATTAATTT-AAAAACA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAATTCATTTGAAAAACA
* * * * *
5416378 TTAAGAAACCCCT-AAAATTAGGCTTAGCTTCTTTCAAGTTCATTTGAAAAACA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAATTCATTTGAAAAACA
* * * *
5416431 CCGAGAAATCCCTGAAAATCAGGCTTAGTTTCT
1 TCAAGAAACCCCTAAAAATCAGGCTTAGTTTCT
5416464 AAAAGTCTTC
Statistics
Matches: 160, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
52 56 0.35
53 43 0.27
54 17 0.11
55 11 0.07
56 5 0.03
59 28 0.17
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (54 bp):
TCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAATTCATTTGAAAAACA
Found at i:5416793 original size:37 final size:36
Alignment explanation
Indices: 5416685--5416793 Score: 155
Period size: 36 Copynumber: 3.0 Consensus size: 36
5416675 AGAAAAAAAA
* * *
5416685 TGTCTCAAGCGAGACAAAGTCTGTTTTAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAAC
* *
5416721 TATCTCAAGGGAGACAAAATTTGTTTTAAGAGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAAC
*
5416757 TGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAAC
5416794 ATATTCAAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 49 0.77
37 15 0.23
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (36 bp):
TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAAC
Found at i:5416971 original size:37 final size:36
Alignment explanation
Indices: 5416930--5417019 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 36
5416920 GAGACGATGC
* * *
5416930 TTGTTTTGAGAGAAAAATATCTCAAGTAAAACAAAAT
1 TTGTTTT-AAAGAAAAATATCTCAAGCAAAACAAAAA
* * *
5416967 TTGTTTTAAAAGAAAAATGTCTCAAGCGAGACAAAAA
1 TTGTTTT-AAAGAAAAATATCTCAAGCAAAACAAAAA
*
5417004 TTGTTTTTAAGAAAAA
1 TTGTTTTAAAGAAAAA
5417020 CAACTTGGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 8 0.18
37 37 0.82
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (36 bp):
TTGTTTTAAAGAAAAATATCTCAAGCAAAACAAAAA
Found at i:5417951 original size:20 final size:22
Alignment explanation
Indices: 5417906--5417963 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
5417896 TGCATGGTAG
5417906 TGCATCGATGCACCTGTTAAAGAA
1 TGCATCGATGCA-CTGTT-AAGAA
5417930 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
5417950 TGCACCGATGCACT
1 TGCATCGATGCACT
5417964 TCAAGTGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 3 0.09
24 12 0.36
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:5419451 original size:15 final size:15
Alignment explanation
Indices: 5419431--5419463 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5419421 TTTTAAGAGA
5419431 AAAATGTCTCAAGTG
1 AAAATGTCTCAAGTG
5419446 AAAATGTCTCAAGTG
1 AAAATGTCTCAAGTG
5419461 AAA
1 AAA
5419464 CAAAATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (15 bp):
AAAATGTCTCAAGTG
Found at i:5419555 original size:37 final size:37
Alignment explanation
Indices: 5419512--5419664 Score: 121
Period size: 37 Copynumber: 4.4 Consensus size: 37
5419502 GTTCCAAAGG
5419512 AAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
1 AAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
* * *
5419549 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTA-AGA
1 AAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
* *** *
5419585 AAAA-----CAACT---TTGAAATTTGTGTTCCGAAG-G-
1 AAAATGTCTCAAGTGAAACAAAATTTG-GTT--TAAGAGA
*
5419615 AAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGA
1 AAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
5419652 AAAATGTCTCAAG
1 AAAATGTCTCAAG
5419665 CGAGACGACA
Statistics
Matches: 86, Mismatches: 16, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
28 7 0.08
29 2 0.02
30 4 0.05
31 6 0.07
35 7 0.08
36 8 0.09
37 45 0.52
38 7 0.08
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (37 bp):
AAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
Found at i:5419625 original size:103 final size:103
Alignment explanation
Indices: 5419446--5419670 Score: 414
Period size: 103 Copynumber: 2.2 Consensus size: 103
5419436 GTCTCAAGTG
*
5419446 AAAATGTCTCAAGTGAAACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCAAAG
1 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCAAAG
5419511 GAAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
66 GAAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
*
5419549 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAG
1 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCAAAG
*
5419614 GAAAATGTCTCAAGTGAAACAAAATTTGTTTTAAGAGA
66 GAAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
*
5419652 AAAATGTCTCAAGCGAGAC
1 AAAATGTCTCAAGTGAGAC
5419671 GACATTTTAT
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (103 bp):
AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCAAAG
GAAAATGTCTCAAGTGAAACAAAATTTGGTTTAAGAGA
Found at i:5427882 original size:47 final size:47
Alignment explanation
Indices: 5427831--5427925 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
5427821 ACTCGTACAA
* *
5427831 AGCATTAACGACACGTCAATCCGAACATAAAAAGCTTACATCACACT
1 AGCATTAACAACACGTCAATCCAAACATAAAAAGCTTACATCACACT
*
5427878 AGCATTAACAACACGTCAATCCAAACATAAAAATCTTACATCACACT
1 AGCATTAACAACACGTCAATCCAAACATAAAAAGCTTACATCACACT
5427925 A
1 A
5427926 ACAAATCAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.45, C:0.27, G:0.07, T:0.20
Consensus pattern (47 bp):
AGCATTAACAACACGTCAATCCAAACATAAAAAGCTTACATCACACT
Found at i:5431202 original size:116 final size:116
Alignment explanation
Indices: 5430993--5431255 Score: 508
Period size: 116 Copynumber: 2.3 Consensus size: 116
5430983 TGCTAGTCAT
5430993 GTAGCGAGCTTCATGCGACCTGACCGGCCAACGGCAACATACAGCTTGATCATTAAGTTTTTACC
1 GTAGCGAGCTTCATGCGACCTGACCGGCCAACGGCAACATACAGCTTGATCATTAAGTTTTTACC
*
5431058 ATAAGCTATTGGTTGCTAGTCATTTAGTAGTTATTCAGCATTAACTTGGGA
66 ATAAGCTATTGGTTGCTAGTCATGTAGTAGTTATTCAGCATTAACTTGGGA
*
5431109 GTAGCGAGCTTCATGCGACCTGACCGACCAACGGCAACATACAGCTTGATCATTAAGTTTTTACC
1 GTAGCGAGCTTCATGCGACCTGACCGGCCAACGGCAACATACAGCTTGATCATTAAGTTTTTACC
5431174 ATAAGCTATTGGTTGCTAGTCATGTAGTAGTTATTCAGCATTAACTTGGGA
66 ATAAGCTATTGGTTGCTAGTCATGTAGTAGTTATTCAGCATTAACTTGGGA
5431225 GTAGCGAGCTTCATGCGACCTGACCGGCCAA
1 GTAGCGAGCTTCATGCGACCTGACCGGCCAA
5431256 ACATGTAAAA
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 144 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (116 bp):
GTAGCGAGCTTCATGCGACCTGACCGGCCAACGGCAACATACAGCTTGATCATTAAGTTTTTACC
ATAAGCTATTGGTTGCTAGTCATGTAGTAGTTATTCAGCATTAACTTGGGA
Found at i:5432314 original size:3 final size:3
Alignment explanation
Indices: 5432306--5432343 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5432296 TATAAACTAA
5432306 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5432344 ATAAATACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5435183 original size:18 final size:18
Alignment explanation
Indices: 5435162--5435205 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5435152 AAATTATTTT
*
5435162 TAAAATAAAAGAT-TAGAA
1 TAAAATAAAAGATAAAG-A
5435180 TAAAATAAAAGATAAAGA
1 TAAAATAAAAGATAAAGA
5435198 TAAAATAA
1 TAAAATAA
5435206 TTAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
TAAAATAAAAGATAAAGA
Found at i:5436139 original size:23 final size:23
Alignment explanation
Indices: 5436067--5436139 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
5436057 GATAGTTCTT
*
5436067 AAAATATTTAAAATAAAATAATA
1 AAAATATTTAAAATAAAATACTA
* ** * * *
5436090 AAAAAAGATAAAATATAATTCTT
1 AAAATATTTAAAATAAAATACTA
* *
5436113 AAAATATTTAAACTAAAATCCTA
1 AAAATATTTAAAATAAAATACTA
5436136 AAAA
1 AAAA
5436140 CATGAGTTTG
Statistics
Matches: 36, Mismatches: 14, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.29
Consensus pattern (23 bp):
AAAATATTTAAAATAAAATACTA
Found at i:5441414 original size:16 final size:16
Alignment explanation
Indices: 5441395--5441425 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5441385 AAAATAAAAG
*
5441395 TAAAAATATAAACATA
1 TAAAAACATAAACATA
5441411 TAAAAACATAAACAT
1 TAAAAACATAAACAT
5441426 CTTTTTTTCA
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:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAACATAAACATA
Found at i:5441452 original size:19 final size:18
Alignment explanation
Indices: 5441428--5441490 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
5441418 ATAAACATCT
5441428 TTTTTTCAATCATTTTCTC
1 TTTTTTCAATC-TTTTCTC
** *
5441447 TTTTTTCTTTCTTTTCAC
1 TTTTTTCAATCTTTTCTC
* *
5441465 TTTTTTAAATTTTTTTCTTC
1 TTTTTTCAA-TCTTTTC-TC
5441485 TTTTTT
1 TTTTTT
5441491 TTCGTTTTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
18 12 0.35
19 15 0.44
20 7 0.21
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTCAATCTTTTCTC
Found at i:5442695 original size:6 final size:6
Alignment explanation
Indices: 5442684--5442708 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5442674 AATAAAAGAG
5442684 TTGGGA TTGGGA TTGGGA TTGGGA T
1 TTGGGA TTGGGA TTGGGA TTGGGA T
5442709 AGGTTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TTGGGA
Found at i:5445257 original size:21 final size:21
Alignment explanation
Indices: 5445231--5445272 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5445221 CCAGAATGGG
**
5445231 GGGAATCGGTACCCCTTCATA
1 GGGAATCGACACCCCTTCATA
5445252 GGGAATCGACACCCCTTCATA
1 GGGAATCGACACCCCTTCATA
5445273 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (21 bp):
GGGAATCGACACCCCTTCATA
Found at i:5445514 original size:29 final size:31
Alignment explanation
Indices: 5445482--5445541 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
5445472 AAATTTTGAA
*
5445482 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5445511 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5445542 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:5447243 original size:18 final size:18
Alignment explanation
Indices: 5447220--5447261 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5447210 ATTGTTTTTT
*
5447220 AAATAAAAGAT-TATAATA
1 AAATAAAAGATAAAT-ATA
5447238 AAATAAAAGATAAATATA
1 AAATAAAAGATAAATATA
5447256 AAATAA
1 AAATAA
5447262 TTAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAATATA
Found at i:5447299 original size:19 final size:18
Alignment explanation
Indices: 5447272--5447315 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
5447262 TTAATTAATT
*
5447272 AAATTAAATATAAGGATAA
1 AAATAAAATATAAGGAT-A
5447291 AAATAAAATATAAGGATA
1 AAATAAAATATAAGGATA
5447309 AAATAAA
1 AAATAAA
5447316 TAATTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (18 bp):
AAATAAAATATAAGGATA
Found at i:5453743 original size:5 final size:5
Alignment explanation
Indices: 5453733--5453758 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5453723 TATTATTATT
5453733 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
5453759 TTCTAAGTCA
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:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:5455541 original size:22 final size:22
Alignment explanation
Indices: 5455502--5455552 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
5455492 CTATCTAAAA
5455502 TTAAAAAAAATTAATAA-TTAT
1 TTAAAAAAAATTAATAATTTAT
* *
5455523 TTAAAAAATATATATTAATTTAT
1 TTAAAAAAAAT-TAATAATTTAT
5455546 TCTAAAA
1 T-TAAAA
5455553 TGTAATTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 5 0.20
23 5 0.20
24 5 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAAAAAAATTAATAATTTAT
Found at i:5457363 original size:18 final size:16
Alignment explanation
Indices: 5457340--5457380 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
5457330 TAAATTTATT
5457340 TATTTTTACTTTTTATAA
1 TATTTTTA-TTTTTA-AA
5457358 TATTTTTTATTTTTAAA
1 TA-TTTTTATTTTTAAA
5457375 TATTTT
1 TATTTT
5457381 AGATGATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 8 0.36
19 6 0.27
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTATTTTTAAA
Found at i:5457370 original size:24 final size:22
Alignment explanation
Indices: 5457313--5457370 Score: 55
Period size: 25 Copynumber: 2.5 Consensus size: 22
5457303 TTTATTTAAC
5457313 TTTTTT-TTTTAATTTCATAAA
1 TTTTTTATTTTAATTTCATAAA
* *
5457334 TTTATTTATTTTTACTTTTTATAATA
1 TTT-TTTA-TTTTA-ATTTCATAA-A
5457360 TTTTTTATTTT
1 TTTTTTATTTT
5457371 TAAATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 3 0.10
24 9 0.30
25 11 0.37
26 4 0.13
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTTATTTTAATTTCATAAA
Found at i:5457969 original size:17 final size:19
Alignment explanation
Indices: 5457935--5457973 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
5457925 AATTTATTTA
5457935 TTTTTATTTTTTATAATAT
1 TTTTTATTTTTTATAATAT
5457954 TTTTTA-TTTTTA-AATAT
1 TTTTTATTTTTTATAATAT
5457971 TTT
1 TTT
5457974 AGATGATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 6 0.30
19 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTTTATAATAT
Found at i:5458164 original size:593 final size:593
Alignment explanation
Indices: 5457037--5458225 Score: 2333
Period size: 593 Copynumber: 2.0 Consensus size: 593
5457027 TACCGAATAA
5457037 ATCCAGTAATTTGGCACACACTCAGTATCTGTAATATTTGGAAGACTTCGATGTATGTTGTAATA
1 ATCCAGTAATTTGGCACACACTCAGTATCTGTAATATTTGGAAGACTTCGATGTATGTTGTAATA
5457102 CCAGGTGGAGCTTGGTGATTTTAGTCTTTCTGTACTTGGAGCTTTACAAGGCTACAATTGTCCAG
66 CCAGGTGGAGCTTGGTGATTTTAGTCTTTCTGTACTTGGAGCTTTACAAGGCTACAATTGTCCAG
5457167 CCGAGTCAAAAAGCCGATGTAGCAGGTTGTCTGATACTACTATAGTCATGTGCTTGATATAGCTT
131 CCGAGTCAAAAAGCCGATGTAGCAGGTTGTCTGATACTACTATAGTCATGTGCTTGATATAGCTT
5457232 TCTATTTTTTACGCCAATTACACCAGCCCTCGTTGAGTTTTCGCTGGCTACAAGTTAATTGTTTA
196 TCTATTTTTTACGCCAATTACACCAGCCCTCGTTGAGTTTTCGCTGGCTACAAGTTAATTGTTTA
*
5457297 ACTTCATTTATTTAACTTTTTTTTTTAATTTCATAAATTTATTTATTTTTACTTTTTATAATATT
261 ACTTCATTTATTTAACCTTTTTTTTTAATTTCATAAATTTATTTATTTTTACTTTTTATAATATT
5457362 TTTTATTTTTAAATATTTTAGATGATGTAATAAAATATCGGAGACAAAGTTGGCAGGTGCCACTG
326 TTTTATTTTTAAATATTTTAGATGATGTAATAAAATATCGGAGACAAAGTTGGCAGGTGCCACTG
5457427 CACAAGGCATACGGATGAGGATCAACATCGTCAGTTGATATGCAGTATGACAAACAAAATTATTA
391 CACAAGGCATACGGATGAGGATCAACATCGTCAGTTGATATGCAGTATGACAAACAAAATTATTA
5457492 TTATTATTTCGAATCTTTTTAACTTTATATATACTAACTTTGATATTTAATTTTACAGTTCTCTT
456 TTATTATTTCGAATCTTTTTAACTTTATATATACTAACTTTGATATTTAATTTTACAGTTCTCTT
5457557 GGCTTCCATATATCGATGAGGAGATCAACTAATTATTATCGGGGCAAGTTTTGAAGGGTCCCACC
521 GGCTTCCATATATCGATGAGGAGATCAACTAATTATTATCGGGGCAAGTTTTGAAGGGTCCCACC
5457622 TATAGTGT
586 TATAGTGT
5457630 ATCCAGTAATTTGGCACACACTCAGTATCTGTAATATTTGGAAGACTTCGATGTATGTTGTAATA
1 ATCCAGTAATTTGGCACACACTCAGTATCTGTAATATTTGGAAGACTTCGATGTATGTTGTAATA
5457695 CCAGGTGGAGCTTGGTGATTTTAGTCTTTCTGTACTTGGAGCTTTACAAGGCTACAATTGTCCAG
66 CCAGGTGGAGCTTGGTGATTTTAGTCTTTCTGTACTTGGAGCTTTACAAGGCTACAATTGTCCAG
*
5457760 CCGAGTCAAAAAGCCGATGTAGCAGGTTGTCTGATACTACTATAGTCCTGTGCTTGATATAGCTT
131 CCGAGTCAAAAAGCCGATGTAGCAGGTTGTCTGATACTACTATAGTCATGTGCTTGATATAGCTT
5457825 TCTATTTTTTACGCCAATTACACCAGCCCTCGTTGAGTTTTCGCTGGCTACAAGTTAATTGTTTA
196 TCTATTTTTTACGCCAATTACACCAGCCCTCGTTGAGTTTTCGCTGGCTACAAGTTAATTGTTTA
*
5457890 ACTTCATTTATTTAACCTTTTTTTTTAATTTCATAAATTTATTTATTTTTATTTTTTATAATATT
261 ACTTCATTTATTTAACCTTTTTTTTTAATTTCATAAATTTATTTATTTTTACTTTTTATAATATT
*
5457955 TTTTATTTTTAAATATTTTAGATGATGTAATAAAATATCGGAGACGAAGTTGGCAGGTGCCACTG
326 TTTTATTTTTAAATATTTTAGATGATGTAATAAAATATCGGAGACAAAGTTGGCAGGTGCCACTG
*
5458020 CACAAGGCATACGGATGAGGATCAACATCGTCGGTTGATATGCAGTATGACAAACAAAATTATTA
391 CACAAGGCATACGGATGAGGATCAACATCGTCAGTTGATATGCAGTATGACAAACAAAATTATTA
5458085 TTATTATTTCGAATCTTTTTAACTTTATATATACTAACTTTGATATTTAATTTTACAGTTCTCTT
456 TTATTATTTCGAATCTTTTTAACTTTATATATACTAACTTTGATATTTAATTTTACAGTTCTCTT
5458150 GGCTTCCATATATCGATGAGGAGATCAACTAATTATTATCGGGGCAAGTTTTGAAGGGTCCCACC
521 GGCTTCCATATATCGATGAGGAGATCAACTAATTATTATCGGGGCAAGTTTTGAAGGGTCCCACC
5458215 TATAGTGT
586 TATAGTGT
5458223 ATC
1 ATC
5458226 GTGACACCAT
Statistics
Matches: 591, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
593 591 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (593 bp):
ATCCAGTAATTTGGCACACACTCAGTATCTGTAATATTTGGAAGACTTCGATGTATGTTGTAATA
CCAGGTGGAGCTTGGTGATTTTAGTCTTTCTGTACTTGGAGCTTTACAAGGCTACAATTGTCCAG
CCGAGTCAAAAAGCCGATGTAGCAGGTTGTCTGATACTACTATAGTCATGTGCTTGATATAGCTT
TCTATTTTTTACGCCAATTACACCAGCCCTCGTTGAGTTTTCGCTGGCTACAAGTTAATTGTTTA
ACTTCATTTATTTAACCTTTTTTTTTAATTTCATAAATTTATTTATTTTTACTTTTTATAATATT
TTTTATTTTTAAATATTTTAGATGATGTAATAAAATATCGGAGACAAAGTTGGCAGGTGCCACTG
CACAAGGCATACGGATGAGGATCAACATCGTCAGTTGATATGCAGTATGACAAACAAAATTATTA
TTATTATTTCGAATCTTTTTAACTTTATATATACTAACTTTGATATTTAATTTTACAGTTCTCTT
GGCTTCCATATATCGATGAGGAGATCAACTAATTATTATCGGGGCAAGTTTTGAAGGGTCCCACC
TATAGTGT
Found at i:5459300 original size:20 final size:19
Alignment explanation
Indices: 5459264--5459301 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5459254 GAGTTCCGCC
5459264 TAAATTTTTTTAAATTTTA
1 TAAATTTTTTTAAATTTTA
*
5459283 TAAATTTTATTTATATTTT
1 TAAATTTT-TTTAAATTTT
5459302 TAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TAAATTTTTTTAAATTTTA
Found at i:5459804 original size:13 final size:13
Alignment explanation
Indices: 5459786--5459811 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5459776 GAGCTGTTCA
5459786 AACCTTTTGAGCG
1 AACCTTTTGAGCG
5459799 AACCTTTTGAGCG
1 AACCTTTTGAGCG
5459812 CGATCACGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
AACCTTTTGAGCG
Found at i:5463601 original size:4 final size:4
Alignment explanation
Indices: 5463592--5463618 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5463582 AAGAGAGGAA
5463592 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
5463619 GGTTAGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5465072 original size:36 final size:36
Alignment explanation
Indices: 5465012--5465275 Score: 182
Period size: 36 Copynumber: 7.0 Consensus size: 36
5465002 AAGCATTTTC
5465012 AAAA-TATATATTATATATTT-AAAAATGTTTTCAAAA
1 AAAATTATATA-TATAT-TTTCAAAAATGTTTTCAAAA
* *
5465048 AAAATTATATAGT-TATTTTCAAAAATATTTTAAAAA
1 AAAATTATATA-TATATTTTCAAAAATGTTTTCAAAA
5465084 AAAACTATATAGTATATATTTGTTTTC-AAAATGTTTTCAAAA
1 AAAA-T-TATA-TATATA----TTTTCAAAAATGTTTTCAAAA
* * *
5465126 CTATATAATATATATATTTTCAAAAATGTTTTCAAAA
1 -AAAATTATATATATATTTTCAAAAATGTTTTCAAAA
* * * *
5465163 ACTATATAATATATATGTTTTAAAAAATGTTTTCAAAA
1 A--AAATTATATATATATTTTCAAAAATGTTTTCAAAA
**
5465201 ACTA-TATATTATATATTTTC-AAAATGTTTTTTCAAAA
1 AAAATTATA-TATATATTTTCAAAAATG--TTTTCAAAA
* *
5465238 AAAACCATATATTATATCATTTTC-AAAATGATTTCAAA
1 AAAA--TTATA-TATAT-ATTTTCAAAAATGTTTTCAAA
5465276 CTATATAATA
Statistics
Matches: 189, Mismatches: 18, Indels: 39
0.77 0.07 0.16
Matches are distributed among these distances:
35 12 0.06
36 41 0.22
37 34 0.18
38 39 0.21
39 11 0.06
40 16 0.08
41 15 0.08
42 14 0.07
43 7 0.04
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAATTATATATATATTTTCAAAAATGTTTTCAAAA
Found at i:5465129 original size:38 final size:37
Alignment explanation
Indices: 5465083--5465290 Score: 214
Period size: 38 Copynumber: 5.5 Consensus size: 37
5465073 TATTTTAAAA
*
5465083 AAAAACTATATAGTATATATTTGTTTTCAAAATGTTTTC
1 AAAAACTATATA--ATATATATGTTTTCAAAATGTTTTC
*
5465122 -AAAACTATATAATATATATATTTTCAAAAATGTTTTC
1 AAAAACTATATAATATATATGTTTTC-AAAATGTTTTC
*
5465159 AAAAACTATATAATATATATGTTTTAAAAAATGTTTTC
1 AAAAACTATATAATATATATGTTTT-CAAAATGTTTTC
*
5465197 AAAAACTATAT-AT-TATATATTTTCAAAATGTTTTTTC
1 AAAAACTATATAATATATATGTTTTCAAAATG--TTTTC
* * *
5465234 AAAAAAAACCATAT-AT-TATATCATTTTCAAAATGATTTC
1 ---AAAAACTATATAATATATAT-GTTTTCAAAATGTTTTC
5465273 --AAACTATATAATATATAT
1 AAAAACTATATAATATATAT
5465291 ATATAATAAT
Statistics
Matches: 149, Mismatches: 9, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
34 8 0.05
35 8 0.05
36 26 0.17
37 18 0.12
38 56 0.38
39 4 0.03
40 17 0.11
41 12 0.08
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAAACTATATAATATATATGTTTTCAAAATGTTTTC
Found at i:5465290 original size:41 final size:39
Alignment explanation
Indices: 5465012--5465275 Score: 176
Period size: 38 Copynumber: 7.0 Consensus size: 39
5465002 AAGCATTTTC
*
5465012 AAAA-TATATATTATATA-TTTAAAAATGT-TTTCAAAA
1 AAAACTATATATTATATATTTTCAAAATGTATTTCAAAA
* *
5465048 AAAA-T-TATA-TAGT-TATTTTCAAAA-ATATTTTAAAAA
1 AAAACTATATATTA-TATATTTTCAAAATGTA-TTTCAAAA
*
5465084 AAAACTATATAGTATATATTTGTTTTCAAAATGT-TTTC----
1 AAAACTATATA-T-TATA--TATTTTCAAAATGTATTTCAAAA
5465122 AAAACTATATAATATATATATTTTCAAAAATGT-TTTC---A
1 AAAACTATAT-AT-TATATATTTTC-AAAATGTATTTCAAAA
* *
5465160 AAAACTATATAATATATATGTTTTAAAAAATGT-TTTC---A
1 AAAACTATAT-AT-TATATATTTT-CAAAATGTATTTCAAAA
*
5465198 AAAACTATATATTATATATTTTCAAAATGTTTTTTCAAAA
1 AAAACTATATATTATATATTTTCAAAATG-TATTTCAAAA
*
5465238 AAAACCATATATTATATCATTTTCAAAATG-ATTTCAAA
1 AAAACTATATATTATAT-ATTTTCAAAATGTATTTCAAA
5465276 CTATATAATA
Statistics
Matches: 192, Mismatches: 13, Indels: 43
0.77 0.05 0.17
Matches are distributed among these distances:
34 5 0.03
35 18 0.09
36 32 0.17
37 18 0.09
38 65 0.34
39 8 0.04
40 18 0.09
41 14 0.07
42 3 0.02
43 10 0.05
44 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (39 bp):
AAAACTATATATTATATATTTTCAAAATGTATTTCAAAA
Found at i:5466036 original size:84 final size:84
Alignment explanation
Indices: 5465845--5466307 Score: 475
Period size: 84 Copynumber: 5.5 Consensus size: 84
5465835 GAACTCGACA
* * * * * * *
5465845 CTTTTATTGACATATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTCT-AAGTT
1 CTTTTGTTGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAA--TGATATGCCT-TGGAGCT
* * *
5465909 GAGTGTAATCGAACTCGAAAGT
63 GAGCGTAGTCGAACTCGAAGGT
* * * * * *
5465931 CTTTTGTTGGA-ATATAACCCTTTTTGCCTTGAGTTATGCTACAAATGATATGCCTTGGAGCTGA
1 CTTTTGTT-GACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGA
5465995 GCGTAGTCGAACTCGAAGGT
65 GCGTAGTCGAACTCGAAGGT
* * * * * *
5466015 CTTTTGATGACAGATAGCCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCTTTCGAGCTGAG
1 CTTTTGTTGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
5466080 CGTAGTC-AATCTCGAAGGT
66 CGTAGTCGAA-CTCGAAGGT
* * * * *
5466099 CTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAA
1 CTTTTGTTGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
*
5466164 CGTAGTCGAATTCGAAGGT
66 CGTAGTCGAACTCGAAGGT
* * * * *
5466183 CTTTTGGTGGCAAATAGCCCTTCTAGCATTGAGCTATGCTACAAATGATGTGCCTTGGAGCTGAG
1 CTTTTGTTGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
* * *
5466248 TGTAATCGAACTCGAATGT
66 CGTAGTCGAACTCGAAGGT
* * * * *
5466267 ATTTGGCTGACAAATAACCCTTCTCA-CCTTGAGTTATGCTG
1 CTTTTGTTGACAAATAGCCCTTCT-AGCCTTGAGCTATGCTG
5466308 TCAATAGTTT
Statistics
Matches: 318, Mismatches: 53, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
83 5 0.02
84 272 0.86
85 3 0.01
86 36 0.11
87 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (84 bp):
CTTTTGTTGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
CGTAGTCGAACTCGAAGGT
Found at i:5466137 original size:168 final size:167
Alignment explanation
Indices: 5465852--5466306 Score: 556
Period size: 168 Copynumber: 2.7 Consensus size: 167
5465842 ACACTTTTAT
* * * * * * *
5465852 TGACATATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTAAGTTGAGTGTAA
1 TGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAA--TGATGTGCTTC-GAGCTGAGTGTAA
* * *
5465917 TCGAACTCGAAAGTCTTTTGTTGG-AATATAACCCTTTTTGCCTTGAGTTATGCTACAAATGATA
63 TCGAACTCGAAAGTCTTTGGTTGGCAA-ATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATA
*
5465981 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGA
127 TGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGA
* * * *
5466022 TGACAGATAGCCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCTTTCGAGCTGAGCGTAGTC
1 TGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGC-TTCGAGCTGAGTGTAATC
* * * *
5466087 -AATCTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATG
65 GAA-CTCGAAAGTCTTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATG
* *
5466151 CCTTGGAGCTGAACGTAGTCGAATTCGAAGGTCTTTTGG
129 CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGA
* * * *
5466190 TGGCAAATAGCCCTTCTAGCATTGAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGTGTAATC
1 TGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTG-CTTCGAGCTGAGTGTAATC
* * * *
5466255 GAACTCGAATGTATTTGGCTGACAAATAACCCTTCTCA-CCTTGAGTTATGCT
65 GAACTCGAAAGTCTTTGGTTGGCAAATAACCCTTCT-AGCCTTGAGTTATGCT
5466307 GTCAATAGTT
Statistics
Matches: 245, Mismatches: 34, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
167 2 0.01
168 202 0.82
169 7 0.03
170 34 0.14
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (167 bp):
TGACAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCTTCGAGCTGAGTGTAATCG
AACTCGAAAGTCTTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCC
TTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGA
Found at i:5467657 original size:95 final size:94
Alignment explanation
Indices: 5467479--5467674 Score: 275
Period size: 95 Copynumber: 2.1 Consensus size: 94
5467469 GGACAACTCA
* * * * * * *
5467479 ATATGTAAACACCTTTATCAGGTTAGCTAAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTG
1 ATATATAATCACCTTTATCAAGCTAGCTAAATATTATCCATAAAGCCGAGGCGTTTAACCAATTA
5467544 CCTTAGAGGGACAACTCAAGCTTTATTGT
66 CCTTAGAGGGACAACTCAAGCTTTATTGT
* *
5467573 ATAGTATAATCACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGAGGCTTTTAACCAATT
1 ATA-TATAATCACCTTTATCAAGCTAGCTAAATATTATCCATAAAGCCGAGGCGTTTAACCAATT
* * *
5467638 ACTTTAGAGGGATAGCTCAAGCTTTATTGT
65 ACCTTAGAGGGACAACTCAAGCTTTATTGT
5467668 ATATATA
1 ATATATA
5467675 TGATATTATA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 7 0.08
95 82 0.92
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (94 bp):
ATATATAATCACCTTTATCAAGCTAGCTAAATATTATCCATAAAGCCGAGGCGTTTAACCAATTA
CCTTAGAGGGACAACTCAAGCTTTATTGT
Found at i:5471535 original size:4 final size:4
Alignment explanation
Indices: 5471526--5471587 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
5471516 AGACCTGATC
* *
5471526 AAAT AAAT AAA- AAAT AAAT ATATAT TAAT AAA- CAAT AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT AAAT AAAT
*
5471573 AAA- AAAT AAAA AAAT
1 AAAT AAAT AAAT AAAT
5471588 CATTTTTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
3 11 0.24
4 31 0.67
5 2 0.04
6 2 0.04
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:5471542 original size:11 final size:11
Alignment explanation
Indices: 5471526--5471575 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
5471516 AGACCTGATC
5471526 AAATAAATAAA
1 AAATAAATAAA
*
5471537 AAATAAAT-AT
1 AAATAAATAAA
* *
5471547 ATATTAATAAA
1 AAATAAATAAA
*
5471558 CAATAAATAAA
1 AAATAAATAAA
5471569 AAATAAA
1 AAATAAA
5471576 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:5471575 original size:18 final size:17
Alignment explanation
Indices: 5471552--5471586 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5471542 AATATATATT
*
5471552 AATAAACAATAAATAAAA
1 AATAAAAAATAAA-AAAA
5471570 AATAAAAAATAAAAAAA
1 AATAAAAAATAAAAAAA
5471587 TCATTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AATAAAAAATAAAAAAA
Found at i:5471702 original size:34 final size:34
Alignment explanation
Indices: 5471659--5471787 Score: 88
Period size: 34 Copynumber: 3.7 Consensus size: 34
5471649 TGTTTTCCAA
5471659 AAAATTATTTTTTAAAACTATATATA-ATATTTTC
1 AAAA-TATTTTTTAAAACTATATATAGATATTTTC
* *
5471693 AAAAGTA--TTTTCAAACTATATATTATATATATTT-
1 AAAA-TATTTTTTAAAACTATATA-TAGATAT-TTTC
* ** *
5471727 AAAA-ATGTTTTCAAAAAAATTATATAGTTATTTTC
1 AAAATAT-TTTTTAAAACTA-TATATAGATATTTTC
5471762 AAAAATATTTTTTAAAAAACTATATA
1 -AAAATATTTTTT--AAAACTATATA
5471788 GTATATATAT
Statistics
Matches: 72, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
32 15 0.21
33 2 0.03
34 17 0.24
35 15 0.21
36 12 0.17
37 6 0.08
38 5 0.07
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (34 bp):
AAAATATTTTTTAAAACTATATATAGATATTTTC
Found at i:5471865 original size:26 final size:26
Alignment explanation
Indices: 5471766--5471985 Score: 367
Period size: 26 Copynumber: 8.5 Consensus size: 26
5471756 ATTTTCAAAA
* *
5471766 ATATTTTTTAAAAAACTATATAGTATAT
1 ATATGTTTTCAAAAACTATATA--ATAT
5471794 ATATGTTTTC-AAAACTATATAATAT
1 ATATGTTTTCAAAAACTATATAATAT
5471819 ATATGTTTTC-AAAACTATATAATAT
1 ATATGTTTTCAAAAACTATATAATAT
5471844 ATATGTTTTCAAAAACTATATAATAT
1 ATATGTTTTCAAAAACTATATAATAT
5471870 ATATGTTTTCAAAAACTATATAATAT
1 ATATGTTTTCAAAAACTATATAATAT
5471896 ATATGTTTTCAAAAACTATATAATAT
1 ATATGTTTTCAAAAACTATATAATAT
5471922 ATATGTTTTCAAAAACTATATAATAT
1 ATATGTTTTCAAAAACTATATAATAT
5471948 ATATGTTTTCAAAAACTATAT-AT-T
1 ATATGTTTTCAAAAACTATATAATAT
*
5471972 ATATATTTTCAAAA
1 ATATGTTTTCAAAA
5471986 TGTTTTTTTC
Statistics
Matches: 188, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
24 14 0.07
25 41 0.22
26 114 0.61
27 11 0.06
28 8 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATGTTTTCAAAAACTATATAATAT
Found at i:5472009 original size:39 final size:39
Alignment explanation
Indices: 5471953--5472027 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
5471943 AATATATATG
*
5471953 TTTTCAAAAACTATATATTATAT-ATTTTCAAAATGTTT
1 TTTTCAAAAACCATATATTATATAATTTTCAAAATGTTT
5471991 TTTTCAAAAAACCATATATTATATAATTTTCAAAATG
1 TTTTC-AAAAACCATATATTATATAATTTTCAAAATG
5472028 ATTTCAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 5 0.15
39 17 0.50
40 12 0.35
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (39 bp):
TTTTCAAAAACCATATATTATATAATTTTCAAAATGTTT
Found at i:5482009 original size:19 final size:19
Alignment explanation
Indices: 5481981--5482031 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
5481971 ATGTTAATAA
5481981 AAAATATTAATTTTT-AAT
1 AAAATATTAATTTTTAAAT
* *
5481999 ATAAATCTTAAATTTTAAAT
1 A-AAATATTAATTTTTAAAT
5482019 AAAATATTAATTT
1 AAAATATTAATTT
5482032 AACTCCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 1 0.04
19 22 0.81
20 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTAATTTTTAAAT
Found at i:5482029 original size:31 final size:31
Alignment explanation
Indices: 5481994--5482056 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5481984 ATATTAATTT
*
5481994 TTAATATAAATCTTAAATTTTAAATAAAATA
1 TTAATATAAATCCTAAATTTTAAATAAAATA
* * * *
5482025 TTAATTTAACTCCTAAATTTTAGATAAGATA
1 TTAATATAAATCCTAAATTTTAAATAAAATA
5482056 T
1 T
5482057 CAATTTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (31 bp):
TTAATATAAATCCTAAATTTTAAATAAAATA
Found at i:5482078 original size:31 final size:31
Alignment explanation
Indices: 5482006--5482096 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
5481996 AATATAAATC
* * *
5482006 TTAAATTTTAAATAAAATATTAATTTAACTC
1 TTAAATTTTAGATAAAATATCAATTTAACTA
* * *
5482037 CTAAATTTTAGATAAGATATCAATTTAATTA
1 TTAAATTTTAGATAAAATATCAATTTAACTA
* * * *
5482068 TTAAAATTTAGAGAAACTATCAATATAAC
1 TTAAATTTTAGATAAAATATCAATTTAAC
5482097 CCTGGAACTC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (31 bp):
TTAAATTTTAGATAAAATATCAATTTAACTA
Found at i:5482461 original size:21 final size:21
Alignment explanation
Indices: 5482412--5482452 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5482402 TCTAAATTCG
5482412 CAACGCGAACTTCGACTATCA
1 CAACGCGAACTTCGACTATCA
*
5482433 CAACGCGAACTTGGACTATC
1 CAACGCGAACTTCGACTATC
5482453 GCATTGCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCA
Found at i:5482564 original size:13 final size:13
Alignment explanation
Indices: 5482548--5482575 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5482538 TGTCGAAGAC
5482548 ACGTATTACCACG
1 ACGTATTACCACG
5482561 ACGTATTACCACG
1 ACGTATTACCACG
5482574 AC
1 AC
5482576 CACGACCACG
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:0.32, C:0.32, G:0.14, T:0.21
Consensus pattern (13 bp):
ACGTATTACCACG
Found at i:5482579 original size:6 final size:6
Alignment explanation
Indices: 5482568--5482606 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
5482558 ACGACGTATT
5482568 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
5482607 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5483126 original size:6 final size:6
Alignment explanation
Indices: 5483105--5483165 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
5483095 TCTCGTCTCG
5483105 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
5483151 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
5483166 AATACGTGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.18
6 45 0.82
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:5484166 original size:12 final size:13
Alignment explanation
Indices: 5484149--5484177 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5484139 TGTGTTATCA
5484149 TTTTGTTTTTTT-
1 TTTTGTTTTTTTG
5484161 TTTTGTTTTTTTG
1 TTTTGTTTTTTTG
5484174 TTTT
1 TTTT
5484178 TAACTTCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTGTTTTTTTG
Found at i:5485527 original size:31 final size:30
Alignment explanation
Indices: 5485480--5485554 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
5485470 TAAGCACTAT
* *
5485480 ACGAACACTAACACCTTAAAAAAATAAATAA
1 ACGAACACAAATACCTT-AAAAAATAAATAA
** * *
5485511 GTGAACATAAATACCTTCAAAAATAAATAA
1 ACGAACACAAATACCTTAAAAAATAAATAA
5485541 ACGAACACAAATAC
1 ACGAACACAAATAC
5485555 AACACTAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 23 0.66
31 12 0.34
ACGTcount: A:0.59, C:0.19, G:0.05, T:0.17
Consensus pattern (30 bp):
ACGAACACAAATACCTTAAAAAATAAATAA
Found at i:5488028 original size:22 final size:24
Alignment explanation
Indices: 5487985--5488043 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
5487975 ATTTAAATAC
5487985 CAAAAAAA-TAA-ACTAAATAAAT
1 CAAAAAAATTAATACTAAATAAAT
*
5488007 -AAAAAAATTAATAGTAAA-AAAT
1 CAAAAAAATTAATACTAAATAAAT
5488029 CAAAATAATATTAAT
1 CAAAA-AA-ATTAAT
5488044 TAATTTACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 9 0.29
24 2 0.06
25 6 0.19
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (24 bp):
CAAAAAAATTAATACTAAATAAAT
Found at i:5488425 original size:19 final size:19
Alignment explanation
Indices: 5488403--5488468 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
5488393 TATTTATATA
5488403 TTATTATATTTTTAATTAT
1 TTATTATATTTTTAATTAT
* *
5488422 TTATTATATTTGT-ATTAA
1 TTATTATATTTTTAATTAT
*
5488440 TTATTAT-TGTTTTATTTAT
1 TTATTATAT-TTTTAATTAT
5488459 TTATT-TATTT
1 TTATTATATTT
5488469 ATTATAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.03
18 17 0.44
19 21 0.54
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTATTATATTTTTAATTAT
Found at i:5488556 original size:20 final size:20
Alignment explanation
Indices: 5488542--5488622 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
5488532 AATTTCTATT
5488542 TTAATTATTATATTTATATA
1 TTAATTATTATATTTATATA
* *
5488562 TTATTTATTATATTGA-ATAA
1 TTAATTATTATATTTATAT-A
*
5488582 TTAA-TATTATTACTTAT-TA
1 TTAATTATTA-TATTTATATA
* *
5488601 TT-ATTCTTATATTTATTTA
1 TTAATTATTATATTTATATA
5488620 TTA
1 TTA
5488623 TAATATATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 7 0.15
19 18 0.38
20 23 0.48
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (20 bp):
TTAATTATTATATTTATATA
Found at i:5489248 original size:28 final size:27
Alignment explanation
Indices: 5489217--5489313 Score: 70
Period size: 28 Copynumber: 3.4 Consensus size: 27
5489207 AAAAAAATTT
5489217 AAATAATTTAACTATCTATTTTGACATA
1 AAATAATTTAACTATCTATTTTGACA-A
* * *
5489245 AAATACTTTAAGTA-CTTATTTTTTAACAA
1 AAATAATTTAACTATC-TA--TTTTGACAA
* * *
5489274 AAATAATTTTAATTATTTATTTTGATTAA
1 AAATAA-TTTAACTATCTATTTTGA-CAA
*
5489303 AAATATTTTAA
1 AAATAATTTAA
5489314 ATACTTAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.02
28 24 0.44
29 13 0.24
30 16 0.30
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (27 bp):
AAATAATTTAACTATCTATTTTGACAA
Found at i:5489277 original size:29 final size:31
Alignment explanation
Indices: 5489235--5489296 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
5489225 TAACTATCTA
*
5489235 TTTTGACATAAAAT-ACTTTAAGTACTTATT
1 TTTTAACATAAAATAACTTTAAGTACTTATT
* * *
5489265 TTTTAACA-AAAATAATTTTAATTATTTATT
1 TTTTAACATAAAATAACTTTAAGTACTTATT
5489295 TT
1 TT
5489297 GATTAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTTAACATAAAATAACTTTAAGTACTTATT
Found at i:5499426 original size:35 final size:35
Alignment explanation
Indices: 5499379--5499464 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
5499369 AAAACAGTCA
* * *
5499379 TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCTAAATTCCAAAATAAT
* * *
5499414 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCTAAATTCCAAAATAAT
*
5499449 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
5499465 ATACTTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCTAAATTCCAAAATAAT
Found at i:5499458 original size:21 final size:21
Alignment explanation
Indices: 5499433--5499475 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5499423 TTCTAAACCC
5499433 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
5499454 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
5499475 T
1 T
5499476 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:5499629 original size:14 final size:16
Alignment explanation
Indices: 5499593--5499629 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5499583 TATTAATGTA
5499593 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
5499610 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
5499625 T-AATA
1 TGAATA
5499630 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:5500296 original size:130 final size:130
Alignment explanation
Indices: 5500093--5500340 Score: 417
Period size: 130 Copynumber: 1.9 Consensus size: 130
5500083 AATTTTCTTC
* * *
5500093 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
5500158 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
5500223 TAATTA-GATGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGA
1 TAATTAGGA-GGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGA
5500287 TCCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
65 TCCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
5500341 TATATAAATA
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
129 2 0.02
130 108 0.98
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:5505658 original size:16 final size:16
Alignment explanation
Indices: 5505637--5505667 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5505627 TTGAATTGAA
5505637 ATAGGTAATTTCTGGG
1 ATAGGTAATTTCTGGG
5505653 ATAGGTAATTTCTGG
1 ATAGGTAATTTCTGG
5505668 ATAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (16 bp):
ATAGGTAATTTCTGGG
Found at i:5506052 original size:23 final size:22
Alignment explanation
Indices: 5506007--5506087 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
5505997 CGGTCCTTCA
* * * *
5506007 GGACAATTCTACCTGGTCCTTC
1 GGACATTTCTACGTAGTCATTC
*
5506029 GAGATATTTCTACGTAGTCATTC
1 G-GACATTTCTACGTAGTCATTC
* * *
5506052 GGAACATATCTATGTAGTCCTTC
1 GG-ACATTTCTACGTAGTCATTC
5506075 GGGACATTTCTAC
1 -GGACATTTCTAC
5506088 ATAGCACTTC
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
22 2 0.04
23 41 0.91
24 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (22 bp):
GGACATTTCTACGTAGTCATTC
Found at i:5512817 original size:45 final size:45
Alignment explanation
Indices: 5512765--5512865 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
5512755 TATATTTTAT
* *
5512765 GCTATATGATATTAACCTATATGATTACATGAAAATGA-GATATAA
1 GCTATATGACATTAACCTACATGATTACATGAAAAT-ATGATATAA
* * * *
5512810 TCTATATGGCATTGACCTACGTGATTACATGAAAATATGATATAA
1 GCTATATGACATTAACCTACATGATTACATGAAAATATGATATAA
*
5512855 GCTATGTGACA
1 GCTATATGACA
5512866 ATGATCTATG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (45 bp):
GCTATATGACATTAACCTACATGATTACATGAAAATATGATATAA
Found at i:5512879 original size:45 final size:45
Alignment explanation
Indices: 5512779--5512912 Score: 128
Period size: 45 Copynumber: 3.0 Consensus size: 45
5512769 TATGATATTA
* * * * *
5512779 ACCTATATGATTACATGAAAATGA-GATATAATCTATATGGCATTG
1 ACCTATGTGATTACATGAAAAT-ATGATATAAGCTATGTGACAATG
*
5512824 ACCTACGTGATTACATGAAAATATGATATAAGCTATGTGACAATG
1 ACCTATGTGATTACATGAAAATATGATATAAGCTATGTGACAATG
* * *** * *
5512869 ATCTATGTGATTATATGTCTATGTGATATTAGCTATGTGA-AATG
1 ACCTATGTGATTACATGAAAATATGATATAAGCTATGTGACAATG
5512913 TTATAAATGA
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
44 5 0.07
45 69 0.93
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (45 bp):
ACCTATGTGATTACATGAAAATATGATATAAGCTATGTGACAATG
Found at i:5513037 original size:46 final size:46
Alignment explanation
Indices: 5512985--5513082 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
5512975 GAGTCGAGGG
* *
5512985 TTCTACGCGGTCCTTTGGGATAAT-TCTACGTGGTCCTTTGGGACAT
1 TTCTACGCGGTCCTTCGGGA-AATATCTACGTGGTCCTTCGGGACAT
* * *
5513031 TTCTACGCGGTCCTTCGGGACATATCTATGTGGTCCTTCGGGGCAT
1 TTCTACGCGGTCCTTCGGGAAATATCTACGTGGTCCTTCGGGACAT
5513077 TTCTAC
1 TTCTAC
5513083 ATGGCACTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 2 0.04
46 44 0.96
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGGGAAATATCTACGTGGTCCTTCGGGACAT
Found at i:5513069 original size:23 final size:23
Alignment explanation
Indices: 5512985--5513082 Score: 115
Period size: 23 Copynumber: 4.3 Consensus size: 23
5512975 GAGTCGAGGG
* * * *
5512985 TTCTACGCGGTCCTTTGGGATAA
1 TTCTACGTGGTCCTTCGGGACAT
*
5513008 TTCTACGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
5513031 TTCTACGCGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * *
5513054 ATCTATGTGGTCCTTCGGGGCAT
1 TTCTACGTGGTCCTTCGGGACAT
5513077 TTCTAC
1 TTCTAC
5513083 ATGGCACTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:5513093 original size:46 final size:47
Alignment explanation
Indices: 5512985--5513107 Score: 121
Period size: 46 Copynumber: 2.7 Consensus size: 47
5512975 GAGTCGAGGG
* * * *
5512985 TTCTACGCGGTCCTTTGG-G-ATAATTCTACGTGGTCCTTTGGGACAT
1 TTCTACACGGTCCTTCGGTGCAT-ATTCTATGTGGTCCTTCGGGACAT
* *
5513031 TTCTACGCGGTCCTTCGG-GACATA-TCTATGTGGTCCTTCGGGGCAT
1 TTCTACACGGTCCTTCGGTG-CATATTCTATGTGGTCCTTCGGGACAT
*
5513077 TTCTACATGG-CACTTCGGTGCATATTCTATG
1 TTCTACACGGTC-CTTCGGTGCATATTCTATG
5513108 CGACACTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
45 1 0.02
46 55 0.83
47 8 0.12
48 2 0.03
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (47 bp):
TTCTACACGGTCCTTCGGTGCATATTCTATGTGGTCCTTCGGGACAT
Found at i:5513728 original size:16 final size:16
Alignment explanation
Indices: 5513703--5513733 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5513693 TTTTCAACTA
*
5513703 TATTTTAAAAGTAAAC
1 TATTTAAAAAGTAAAC
5513719 TATTTAAAAAGTAAA
1 TATTTAAAAAGTAAA
5513734 TGTGATACCT
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:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
TATTTAAAAAGTAAAC
Found at i:5517620 original size:2 final size:2
Alignment explanation
Indices: 5517615--5517649 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5517605 TACGTGTGTG
5517615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5517650 TACTATATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5517700 original size:12 final size:13
Alignment explanation
Indices: 5517683--5517754 Score: 73
Period size: 12 Copynumber: 5.8 Consensus size: 13
5517673 TCTTTTGTCT
5517683 TTATTATTATA-A
1 TTATTATTATATA
*
5517695 TTATTATTGTATA
1 TTATTATTATATA
5517708 TATATT-TTATATA
1 T-TATTATTATATA
5517721 TTTATTATTATAT-
1 -TTATTATTATATA
*
5517734 TTATTA-TATATT
1 TTATTATTATATA
5517746 TTATT-TTAT
1 TTATTATTAT
5517755 TTTATTGCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
11 5 0.10
12 24 0.46
13 12 0.23
14 11 0.21
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (13 bp):
TTATTATTATATA
Found at i:5517725 original size:27 final size:25
Alignment explanation
Indices: 5517684--5517754 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
5517674 CTTTTGTCTT
*
5517684 TATTAT-TATAATTATTATTGTATATA
1 TATTATATATATTTATTA-T-TATATA
* *
5517710 TATTTTATATATTTATTATTATATT
1 TATTATATATATTTATTATTATATA
5517735 TATTATATAT-TTTATT-TTAT
1 TATTATATATATTTATTATTAT
5517755 TTTATTGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 4 0.10
24 6 0.15
25 14 0.35
26 6 0.15
27 10 0.25
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (25 bp):
TATTATATATATTTATTATTATATA
Found at i:5517944 original size:23 final size:23
Alignment explanation
Indices: 5517905--5517951 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5517895 TGCAGTAATT
*
5517905 TTTATTTTACTTTCTTTATTTTA
1 TTTATTTTACTTACTTTATTTTA
*
5517928 TTTACTTTTAC-TACTTTTTTTTA
1 TTTA-TTTTACTTACTTTATTTTA
5517951 T
1 T
5517952 CTAACCTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTATTTTACTTACTTTATTTTA
Found at i:5521955 original size:13 final size:13
Alignment explanation
Indices: 5521937--5521971 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
5521927 CCAGGAGAGT
5521937 CTATCTGGTTCAG
1 CTATCTGGTTCAG
5521950 CTATCTGGTTCAG
1 CTATCTGGTTCAG
5521963 CTATCTGGT
1 CTATCTGGT
5521972 GATACAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (13 bp):
CTATCTGGTTCAG
Found at i:5528350 original size:13 final size:13
Alignment explanation
Indices: 5528332--5528372 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5528322 TAAGTCGAAG
5528332 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
5528345 AAG-AAAAGAACAA
1 AAGAAAAAGAA-AA
5528358 AA-AAAAAGAGAAA
1 AAGAAAAAGA-AAA
5528371 AA
1 AA
5528373 TGTTTAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.28
13 17 0.68
14 1 0.04
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:5528362 original size:18 final size:18
Alignment explanation
Indices: 5528332--5528366 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5528322 TAAGTCGAAG
5528332 AAGAAAAAGAAAAAAGAA
1 AAGAAAAAGAAAAAAGAA
5528350 AAGAACAAA-AAAAAAGA
1 AAGAA-AAAGAAAAAAGA
5528367 GAAAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAAAAAAGAA
Found at i:5528372 original size:21 final size:21
Alignment explanation
Indices: 5528329--5528371 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5528319 TCCTAAGTCG
*
5528329 AAGAAGAAAAAGAAAAAAGAA
1 AAGAACAAAAAGAAAAAAGAA
*
5528350 AAGAACAAAAA-AAAAGAGAA
1 AAGAACAAAAAGAAAAAAGAA
5528370 AA
1 AA
5528372 ATGTTTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (21 bp):
AAGAACAAAAAGAAAAAAGAA
Found at i:5529196 original size:118 final size:118
Alignment explanation
Indices: 5528995--5529539 Score: 457
Period size: 118 Copynumber: 4.4 Consensus size: 118
5528985 ACAAGATTGG
*
5528995 ATTTCAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCAC
1 ATTTCAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAAGGGGCCATCCAC
* * *
5529060 GATTCCAACTTCACGACGAAGGATATCGTGCCCACCAACAACATTTAGATTAA
66 GATTCCAACTTCACGACGAAGGATATCATGCCCACCAACAACATTCAAATTAA
* * * * *
5529113 ATTTCAACTTCACAACGAAAGATATACAATTCAAGGCTCAATTTCACAAAGAAGGGGCCATCTAC
1 ATTTCAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAAGGGGCCATCCAC
* * * **
5529178 GATTTCAACTTCACGACGAAGGATATCATGCCCATCAGCAACATTCAAATTGG
66 GATTCCAACTTCACGACGAAGGATATCATGCCCACCAACAACATTCAAATTAA
*
5529231 ATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACAATTCAAGGCTCAACTTCACAAC
1 ATTTCAACTTCACAATGAAGGATATCCAATTCAAGGCTCAAC---T------TC-A---CA-AA-
* * * * * ** *
5529296 GAAAGGGTCATCCACAATTTCAACTTCACAACGAAGGATATTGTGTCCACCAACAACACTCATCC
51 GAAGGGGCCATCCACGATTCCAACTTCACGACGAAGGATATCATGCCCACCAACAACA-T--T-C
* **
5529361 TTAGATTGG
112 --AAATTAA
* * * * * *
5529370 ATTTCAACTTCACGACGATGGATATCCAATTCAAGGATCAACTTCACAACGAAGAGGCCATCCAC
1 ATTTCAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAAGGGGCCATCCAC
* * * * * *
5529435 GATTTCAACTTCACGATGAAGGATATCGTACCCA-TAACCAA-ATTACTCAAGATTGGA
66 GATTCCAACTTCACGACGAAGGATATCATGCCCACCAA-CAACA-T--TCAA-ATT-AA
* *
5529492 TTTTCAACTTCACGATGAAGGATATCCAATTCCAA-GCTCAACTTCACA
1 ATTTCAACTTCACAATGAAGGATATCCAATT-CAAGGCTCAACTTCACA
5529540 GCGAATGAGC
Statistics
Matches: 349, Mismatches: 53, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
118 141 0.40
120 1 0.00
121 4 0.01
122 42 0.12
123 8 0.02
124 43 0.12
125 1 0.00
126 2 0.01
127 2 0.01
128 1 0.00
129 1 0.00
130 2 0.01
131 2 0.01
132 2 0.01
133 48 0.14
134 1 0.00
136 2 0.01
137 1 0.00
139 45 0.13
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (118 bp):
ATTTCAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAAGGGGCCATCCAC
GATTCCAACTTCACGACGAAGGATATCATGCCCACCAACAACATTCAAATTAA
Found at i:5529275 original size:15 final size:15
Alignment explanation
Indices: 5529257--5529287 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5529247 GAAGGATATC
5529257 CAATTCAAGGCTCAA
1 CAATTCAAGGCTCAA
5529272 CAATTCAAGGCTCAA
1 CAATTCAAGGCTCAA
5529287 C
1 C
5529288 TTCACAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (15 bp):
CAATTCAAGGCTCAA
Found at i:5529642 original size:261 final size:254
Alignment explanation
Indices: 5529023--5529729 Score: 679
Period size: 261 Copynumber: 2.8 Consensus size: 254
5529013 AGGATATCCA
* *** * * * * * *
5529023 ATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTCCAACTTCACGACGAAGGATATCG
1 ATTCAAGGATCAACTTCACAACGAAACAGTCATACACAATTTCAACTTCACAACGAAGGATATTG
* ** * * *
5529088 TG-CC-C-ACCAACA-ACAT--TTAGATTAAATTTCAACTTCACAACGAAAGATATACAATTCAA
66 TGACCACAAACAACACACATCCTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAA
* * * *
5529147 GGCTCAATTTCACAAAGAAGGGGCCATCTACGATTTCAACTTCACGACGAAGGATATCATGCCCA
131 GGCTCAACTTCAC-AAGAA-GGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTACCCA
* *
5529212 TCAGCAACATTCAAATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAAC
194 TAACCAACATTCAAATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAAC
* ** *
5529273 AATTCAAGGCTCAACTTCACAACGAAAGGGTCATCCACAATTTCAACTTCACAACGAAGGATATT
1 -ATTCAAGGATCAACTTCACAACGAAACAGTCATACACAATTTCAACTTCACAACGAAGGATATT
* * * *
5529338 GTGTCCACCAACAACACTCATCCTTAGATTGGATTTCAACTTCACGACGATGGATATCCAATTCA
65 GTGACCACAAACAACACACATCCTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCA
* *
5529403 AGGATCAACTTCACAACGAAGAGGCCATCCACGATTTCAACTTCACGATGAAGGATATCGTACCC
130 AGGCTCAACTTCACAA-GAAG-GGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTACCC
5529468 ATAACCAA-ATTACTCAAGATTGGATTTTCAACTTCACGATGAAGGATATCCAATTCCAA-GCTC
193 ATAACCAACA-T--TCAA-ATTGGA-TTTCAACTTCACGATGAAGGATATCCAATT-CAAGGCTC
5529531 AAC
252 AAC
* * *** * ** **
5529534 -TTCACAGCGAATGAGCTTTC-C-A-GTTTCATTCATAGTCAATTTCAACTTCACGGCGAAGGAT
1 ATTCA-AG-G-ATCAAC-TTCACAACGAAACAGTCATACACAATTTCAACTTCACAACGAAGGAT
* * *
5529595 ATTG-GACTCA-AAACAACACAACTTACAC-TAGATTGGATTTTAACTTCACGATGAAGGATATC
62 ATTGTGAC-CACAAACAACAC-ACAT-C-CTTAGATTGGATTTCAACTTCACGACGAAGGATATC
* * *
5529657 CAATTCAAGGCTCAACTTCACAGAGAAGGAGCCACCCTACGATTTCAACTTCACAACGAATGATA
123 CAATTCAAGGCTCAACTTCACA-AGAAGG-GCCATCC-ACGATTTCAACTTCACGACGAAGGATA
5529722 TCGTACCC
185 TCGTACCC
5529730 TAAAGATTGA
Statistics
Matches: 383, Mismatches: 48, Indels: 39
0.81 0.10 0.08
Matches are distributed among these distances:
251 61 0.16
252 2 0.01
253 1 0.00
254 6 0.02
255 3 0.01
256 4 0.01
257 97 0.25
259 18 0.05
260 45 0.12
261 102 0.27
262 41 0.11
263 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (254 bp):
ATTCAAGGATCAACTTCACAACGAAACAGTCATACACAATTTCAACTTCACAACGAAGGATATTG
TGACCACAAACAACACACATCCTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAA
GGCTCAACTTCACAAGAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTACCCATA
ACCAACATTCAAATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAAC
Found at i:5531777 original size:20 final size:19
Alignment explanation
Indices: 5531754--5531791 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5531744 TTCCTTTTTG
5531754 CTTTTTTATGATTATTATTA
1 CTTTTTTATGATT-TTATTA
*
5531774 CTTTTTTATTATTTTATT
1 CTTTTTTATGATTTTATT
5531792 CTATTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (19 bp):
CTTTTTTATGATTTTATTA
Found at i:5531968 original size:14 final size:14
Alignment explanation
Indices: 5531939--5531992 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
5531929 ATTAATGTTG
*
5531939 TATATATATT-TTA
1 TATATTTATTATTA
5531952 TATATTTATTATTA
1 TATATTTATTATTA
*
5531966 TATATTTATTATTT
1 TATATTTATTATTA
* *
5531980 TATTTTTTTTATT
1 TATATTTATTATT
5531993 TTTTTTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
13 9 0.25
14 27 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATTTATTATTA
Found at i:5531993 original size:14 final size:14
Alignment explanation
Indices: 5531945--5531998 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
5531935 GTTGTATATA
5531945 TATTTTATATATTTAT
1 TATTTTAT-T-TTTAT
* *
5531961 TATTATATATTTAT
1 TATTTTATTTTTAT
*
5531975 TATTTTATTTTTTT
1 TATTTTATTTTTAT
5531989 TATTTT-TTTT
1 TATTTTATTTT
5531999 ACATTTTCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
13 4 0.12
14 22 0.67
16 7 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTATTTTTAT
Found at i:5532298 original size:35 final size:35
Alignment explanation
Indices: 5532242--5532321 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
5532232 CTGTTGAAAC
* * *
5532242 ACAAACACCATATCCGGACTAAGGGAGTCGAGACTA
1 ACAAAC-CCAGATCCGAACTAAGGGAGTCGAGACGA
5532278 ACAAACCCAGATCCGAACTAAGGGAGTCGAGACGA
1 ACAAACCCAGATCCGAACTAAGGGAGTCGAGACGA
5532313 ACAAACCCA
1 ACAAACCCA
5532322 TCCCATTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 35 0.85
36 6 0.15
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (35 bp):
ACAAACCCAGATCCGAACTAAGGGAGTCGAGACGA
Found at i:5532462 original size:32 final size:32
Alignment explanation
Indices: 5532421--5532484 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
5532411 ATAAGAGAAG
5532421 GAAAAAGGATAAATTACACCAT-AGGTCATTAA
1 GAAAAAGGATAAATTACACCATGA-GTCATTAA
5532453 GAAAAAGGATAAATTACACCATGAGTCATTAA
1 GAAAAAGGATAAATTACACCATGAGTCATTAA
5532485 ACTTTACTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (32 bp):
GAAAAAGGATAAATTACACCATGAGTCATTAA
Found at i:5537729 original size:17 final size:17
Alignment explanation
Indices: 5537707--5537743 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5537697 TAATAAACTA
*
5537707 ATGATAATTAAATTATT
1 ATGATAATTAAATTAAT
5537724 ATGATAATTAAATTAAT
1 ATGATAATTAAATTAAT
5537741 ATG
1 ATG
5537744 GTTACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (17 bp):
ATGATAATTAAATTAAT
Found at i:5537827 original size:51 final size:51
Alignment explanation
Indices: 5537715--5537811 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
5537705 TAATGATAAT
* *
5537715 TAAATTATTATGATAATTAAATTAATATGGTTACTTTTTGAAATTTTATCA
1 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTGAAAATTTATCA
5537766 TAAATTATTATGATAATTAAATTAATATGATTAC-TTTT-AAAATTTA
1 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTGAAAATTTA
5537812 GTTTTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 7 0.16
50 4 0.09
51 33 0.75
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (51 bp):
TAAATTATTATGATAATTAAATTAATATGATTACTTTTTGAAAATTTATCA
Found at i:5538519 original size:3 final size:3
Alignment explanation
Indices: 5538511--5538566 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
5538501 TTGTTTTTAA
* *
5538511 TAT TAT TAT TAA TA- TAT TAT TA- TAA TAT TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
5538556 TAT TAT TAT TA
1 TAT TAT TAT TA
5538567 AATAATTACA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5538566 original size:26 final size:28
Alignment explanation
Indices: 5538513--5538566 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5538503 GTTTTTAATA
5538513 TTATTATTAATATATTATTATAATATTAT
1 TTATTATTAATATATTATTAT-ATATTAT
5538542 TTATTATT-ATATATTATTAT-TATTA
1 TTATTATTAATATATTATTATATATTA
5538567 AATAATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTATTATTAATATATTATTATATATTAT
Found at i:5539914 original size:3 final size:3
Alignment explanation
Indices: 5539906--5539935 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5539896 TTTACTTTTA
*
5539906 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5539936 TAGCCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5539974 original size:22 final size:22
Alignment explanation
Indices: 5539943--5539988 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5539933 ATTTAGCCAT
5539943 AAATATATATATATTTATATAAA
1 AAATATATATATATTT-TATAAA
* *
5539966 AAATA-ATATTTATTTTATTAA
1 AAATATATATATATTTTATAAA
5539987 AA
1 AA
5539989 TCTTATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATATATATATTTTATAAA
Found at i:5540225 original size:120 final size:117
Alignment explanation
Indices: 5540021--5540253 Score: 274
Period size: 120 Copynumber: 2.0 Consensus size: 117
5540011 TATTTTAATC
* * *
5540021 TTGTTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAATAACTGAATGTCCAT
1 TTGTTTTAATATTTATTTATTTTTCAATATGAAGAAAGAGCAGTCTTAAACAACTGAATGTCCAT
*
5540086 TTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAT
66 TTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATATATTAT
* * * * *
5540138 TTGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAATAGCTGTCTTAAGGCACCTAGAA-G
1 TTGTTTTAA-TATTTATTTATTTTTCAATAT-GAAG-AAAGAGCAGTCTTAA-ACAACT-GAATG
* * **
5540202 TCC-TTTTTTGATATTTCTGAATAAATAAATATTTTATTTATAAATATATATA
61 TCCATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATA
5540254 AATTAATATA
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
117 9 0.09
118 20 0.21
119 12 0.12
120 46 0.47
121 7 0.07
122 3 0.03
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.48
Consensus pattern (117 bp):
TTGTTTTAATATTTATTTATTTTTCAATATGAAGAAAGAGCAGTCTTAAACAACTGAATGTCCAT
TTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATATTAT
Found at i:5540837 original size:33 final size:33
Alignment explanation
Indices: 5540761--5540844 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
5540751 TTTCAAATTT
* *
5540761 TTTATATATA-TACTTA--TTATTTTCATAGTA
1 TTTATATATATTATTTATTTTATTTCCATAGTA
5540791 TTTATATATATTATTTCATTTTATTTCCA-AGTA
1 TTTATATATATTATTT-ATTTTATTTCCATAGTA
*
5540824 TTT-TATTTCATTATTTATTTT
1 TTTATATAT-ATTATTTATTTT
5540845 TCTGTCAGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 10 0.22
31 4 0.09
32 10 0.22
33 14 0.30
34 8 0.17
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (33 bp):
TTTATATATATTATTTATTTTATTTCCATAGTA
Found at i:5542368 original size:15 final size:15
Alignment explanation
Indices: 5542348--5542386 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
5542338 ACTCACCATT
5542348 GAAAGAATTTCTGGA
1 GAAAGAATTTCTGGA
*
5542363 GAAAGAATTTTTGGA
1 GAAAGAATTTCTGGA
*
5542378 GCAAGAATT
1 GAAAGAATT
5542387 GCCGAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (15 bp):
GAAAGAATTTCTGGA
Found at i:5544107 original size:14 final size:14
Alignment explanation
Indices: 5544088--5544117 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5544078 ATCAATACCT
5544088 TTTGCATACATGCA
1 TTTGCATACATGCA
*
5544102 TTTGCATACATTCA
1 TTTGCATACATGCA
5544116 TT
1 TT
5544118 ATTGCATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (14 bp):
TTTGCATACATGCA
Found at i:5547880 original size:8 final size:9
Alignment explanation
Indices: 5547853--5547883 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5547843 AAATGGCAAT
5547853 CATTCTTTA
1 CATTCTTTA
5547862 CATTCTTTA
1 CATTCTTTA
5547871 CATT-TTTA
1 CATTCTTTA
5547879 CATTC
1 CATTC
5547884 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:5551371 original size:9 final size:9
Alignment explanation
Indices: 5551359--5551409 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
5551349 AGAAAAAATG
5551359 AAAAAGAAAA
1 AAAAAG-AAA
5551369 AAAAAGAAA
1 AAAAAGAAA
5551378 AAAAAG--A
1 AAAAAGAAA
*
5551385 AAAAGGAAA
1 AAAAAGAAA
5551394 AAAGAAGAAA
1 AAA-AAGAAA
5551404 ATAAAA
1 A-AAAA
5551410 AAAGAGGGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
7 6 0.17
9 13 0.37
10 14 0.40
11 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:5551374 original size:10 final size:10
Alignment explanation
Indices: 5551359--5551388 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5551349 AGAAAAAATG
5551359 AAAAAGAAAA
1 AAAAAGAAAA
5551369 AAAAAG-AAA
1 AAAAAGAAAA
5551378 AAAAAGAAAA
1 AAAAAGAAAA
5551388 A
1 A
5551389 GGAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:5551379 original size:25 final size:26
Alignment explanation
Indices: 5551351--5551409 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
5551341 ATGCTTGAAG
*
5551351 AAAAAATGAAAAA-GAAAAAAAAAGA
1 AAAAAAAGAAAAAGGAAAAAAAAAGA
*
5551376 AAAAAAAGAAAAAGGAAAAAAGAAGA
1 AAAAAAAGAAAAAGGAAAAAAAAAGA
5551402 AAATAAAA
1 AAA-AAAA
5551410 AAAGAGGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 12 0.40
26 14 0.47
27 4 0.13
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (26 bp):
AAAAAAAGAAAAAGGAAAAAAAAAGA
Done.