Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 44 of 132
Found at i:11922484 original size:204 final size:204
Alignment explanation
Indices: 11921836--11922846 Score: 1422
Period size: 204 Copynumber: 4.9 Consensus size: 204
11921826 TACCAACTCA
* * * * * *
11921836 ATGTGAACAAATCTTTGAACCCCAGCTTCCTGATGACATACTGAGAGGCAGGGCGAAGTAATAAA
1 ATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* *
11921901 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCTTGATGAGATACAGAG
65 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAG
* * * * * * * *
11921966 AAACGAATTGAAACAAGTGAGGCGGTCACCTTCCTGATGAGATACAGAGAAGTATACCAACTC--
130 AAGCG-ATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
* *
11922029 A---AGGCTCA
194 ACCCACGCTCG
* * * *
11922037 AAGTGAGCAAATCTTCGAACCCTAACTTCCTGATGAGATACAGAGAAGCAGATCGAAGCAATAAA
1 ATGTGAGCAAATCTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * *
11922102 ATGGTTAGCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTATAGAG
65 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAG
*
11922167 AAGCGGATTGAAACAAGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAA
130 AAGC-GATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
11922232 ACCCACGCTCG
194 ACCCACGCTCG
11922243 ATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
1 ATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
11922308 TGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTATAGAGA
66 TGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGA
* * *
11922373 AGCGATTGAAACAAGCGATACGATCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAAC
131 AGCGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
11922438 CCACGCTCG
196 CCACGCTCG
11922447 ATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
1 ATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
* *
11922512 TGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGA
66 TGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGA
*
11922577 AGCAGATTGAAACAAACGATGCGGTCATCTT-CTGATGAGATACTGAGAAGAAGACCAAATCAAA
131 AGC-GATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA
* *
11922641 CCAATGCTCG
195 CCCACGCTCG
** *
11922651 ATGTGAGCAAATCTTCGAACCCTTAGCTTTTTGATGAGATACTGAGAAGCAGGTCTAAGCAATAA
1 ATGTGAGCAAATCTTCGAACCC--AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
* * * * * *
11922716 AGTGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGA
64 AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA
* ** * * * * *
11922781 GAAGTGGATCAAAACAAGTGATGTGGTCATCTTCCTGATGAGATACAGAGAAGAAGGCCAAGTCA
129 GAAG-CGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCA
11922846 A
193 A
11922847 TGAAACCAGA
Statistics
Matches: 734, Mismatches: 64, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
200 3 0.00
201 163 0.22
202 1 0.00
203 1 0.00
204 259 0.35
205 130 0.18
206 148 0.20
207 29 0.04
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (204 bp):
ATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
TGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGA
AGCGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
CCACGCTCG
Found at i:11925034 original size:29 final size:28
Alignment explanation
Indices: 11924977--11925169 Score: 147
Period size: 29 Copynumber: 6.6 Consensus size: 28
11924967 AAGGGTCCTT
* * *
11924977 AAACTGTCAAAAAATTATATTTTGGCCCTG
1 AAACT-TCCAAAAATTACATTTT-ACCCTG
*
11925007 AAACTTCTAAAAATTACATTTGTACCCTCG
1 AAACTTCCAAAAATTACATTT-TACCCT-G
**
11925037 -AACTTCCAAAAATTACATTATTACCCCC
1 AAACTTCCAAAAATTACATT-TTACCCTG
* * *
11925065 AAAATTCCAAATATTCCATTTTTAACCCTG
1 AAACTTCCAAAAATTACA-TTTT-ACCCTG
**
11925095 AAACTTCCAAAAATTACATTTTGACCCCC
1 AAACTTCCAAAAATTACATTTT-ACCCTG
* **
11925124 AAACTTCC-AAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACA-TTTT-ACCCTG
*
11925153 AAACTTTCAAAAATTAC
1 AAACTTCCAAAAATTAC
11925170 CGTTTTACTC
Statistics
Matches: 134, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
28 8 0.06
29 90 0.67
30 36 0.27
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTACCCTG
Found at i:11925085 original size:58 final size:58
Alignment explanation
Indices: 11925016--11925169 Score: 190
Period size: 58 Copynumber: 2.7 Consensus size: 58
11925006 GAAACTTCTA
* *
11925016 AAAATTACATTTGT-ACCCTCGAACTTCCAAAAATTACATTATT-ACCCCCAAAATTCC
1 AAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTACATT-TTGACCCCCAAAATTCC
*
11925073 AAATATTCCATTTTTAACCCT-GAAACTTCCAAAAATTACATTTTGACCCCCAAACTTCC
1 AAA-ATTCCATTTTTAACCCTCG-AACTTCCAAAAATTACATTTTGACCCCCAAAATTCC
* * *
11925132 AAAATTCCATTTTTGACCC-CAAAACTTTCAAAAATTAC
1 AAAATTCCATTTTTAACCCTC-GAACTTCCAAAAATTAC
11925170 CGTTTTACTC
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
57 3 0.04
58 42 0.49
59 40 0.47
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.31
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTACATTTTGACCCCCAAAATTCC
Found at i:11925100 original size:59 final size:58
Alignment explanation
Indices: 11925037--11925169 Score: 196
Period size: 59 Copynumber: 2.3 Consensus size: 58
11925027 TGTACCCTCG
**
11925037 AACTTCCAAAAATTACATTATT-ACCCCCAAAATTCCAAATATTCCATTTTTAACCCTGA
1 AACTTCCAAAAATTACATT-TTGACCCCCAAAATTCCAAA-ATTCCATTTTTAACCCCAA
* *
11925096 AACTTCCAAAAATTACATTTTGACCCCCAAACTTCCAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTACATTTTGACCCCCAAAATTCCAAAATTCCATTTTTAACCCCAA
*
11925154 AACTTTCAAAAATTAC
1 AACTTCCAAAAATTAC
11925170 CGTTTTACTC
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
58 33 0.49
59 35 0.51
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.31
Consensus pattern (58 bp):
AACTTCCAAAAATTACATTTTGACCCCCAAAATTCCAAAATTCCATTTTTAACCCCAA
Found at i:11952739 original size:24 final size:24
Alignment explanation
Indices: 11952700--11952762 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
11952690 TAGAGTAACA
* *
11952700 AGAGTTTTACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
11952724 GGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
11952748 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
11952763 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:11969405 original size:22 final size:18
Alignment explanation
Indices: 11969380--11969424 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
11969370 CTCATTTTCC
11969380 TAAAATAGCCCAACACCCAAAA
1 TAAAATA-CCCAA-A-CC-AAA
11969402 TAAAATACCCAAACCAAA
1 TAAAATACCCAAACCAAA
11969420 TAAAA
1 TAAAA
11969425 CCCATACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 1 0.04
21 5 0.22
22 7 0.30
ACGTcount: A:0.60, C:0.27, G:0.02, T:0.11
Consensus pattern (18 bp):
TAAAATACCCAAACCAAA
Found at i:11990055 original size:22 final size:18
Alignment explanation
Indices: 11990027--11990071 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
11990017 CCCATTTTCC
11990027 TAAAATAGCCCAACACCCAAAA
1 TAAAATA-CCCAA-A-CC-AAA
11990049 TAAAATACCCAAACCAAA
1 TAAAATACCCAAACCAAA
11990067 TAAAA
1 TAAAA
11990072 CCCATACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 1 0.04
21 5 0.22
22 7 0.30
ACGTcount: A:0.60, C:0.27, G:0.02, T:0.11
Consensus pattern (18 bp):
TAAAATACCCAAACCAAA
Found at i:12008736 original size:30 final size:29
Alignment explanation
Indices: 12008672--12009065 Score: 205
Period size: 29 Copynumber: 13.6 Consensus size: 29
12008662 GATTAAATGC
* **
12008672 AATTTTTGGATGCCCGAGG-AAAAATGGT
1 AATTTTTGGAAGTTCGAGGTAAAAATGGT
*
12008700 AATTTTTAGGAAGTTCGAGGTCAAAAATTG-
1 AATTTTT-GGAAGTTCGAGGT-AAAAATGGT
*
12008730 AATTTTTGGACA-TTCGGGGGT-AAAATGGT
1 AATTTTTGGA-AGTTC-GAGGTAAAAATGGT
* * *
12008759 AATTTTGGGAAAGTTTGAGGTTAAAAATAG-
1 AATTTTTGG-AAGTTCGAGG-TAAAAATGGT
* *
12008789 AATTTTTGGAAGTTTGAGG-GAAAATGGT
1 AATTTTTGGAAGTTCGAGGTAAAAATGGT
* * *
12008817 AATTTTAGGAAAATT-GGGGTAAAAATGG-
1 AATTTTTGG-AAGTTCGAGGTAAAAATGGT
* * *
12008845 AATTTTTGGATGTTTGGGGGT-AAAATGGT
1 AATTTTTGGAAG-TTCGAGGTAAAAATGGT
* * * *
12008874 AATTTTGGGAAAGTTTGGGGTTAAAAA-CG-
1 AATTTTTGG-AAGTTCGAGG-TAAAAATGGT
* * *
12008903 AAATTTTGGAAGTCCAAGGT-AAAATGGT
1 AATTTTTGGAAGTTCGAGGTAAAAATGGT
* *
12008931 AGTTTTTAGGAAGTT-TAGGGTCAAAAATGG-
1 AATTTTT-GGAAGTTCGA-GGT-AAAAATGGT
*
12008961 AATTTTTGGACA-TTTGAGG-ATAAAATGGT
1 AATTTTTGGA-AGTTCGAGGTA-AAAATGGT
*
12008990 AATTTTGGGAAAGTTC-AGGGTCAAAAATGG-
1 AATTTTTGG-AAGTTCGA-GGT-AAAAATGGT
* * *
12009020 AATTTTTGGAAATTTAGGGGT-AAAATGGT
1 AATTTTTGG-AAGTTCGAGGTAAAAATGGT
12009049 AATTTTTGTGAAGTTCG
1 AATTTTTG-GAAGTTCG
12009066 TGATAATGTA
Statistics
Matches: 284, Mismatches: 45, Indels: 73
0.71 0.11 0.18
Matches are distributed among these distances:
26 4 0.01
27 10 0.04
28 67 0.24
29 113 0.40
30 58 0.20
31 31 0.11
32 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGAGGTAAAAATGGT
Found at i:12008763 original size:59 final size:58
Alignment explanation
Indices: 12008692--12009054 Score: 348
Period size: 59 Copynumber: 6.2 Consensus size: 58
12008682 TGCCCGAGGA
* * *
12008692 AAAATGGTAATTTTTAGG-AAGTTCGAGGTCAAAAATTGAATTTTTGGACATTCGGGGGT
1 AAAATGGTAA-TTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGA-ATTTGAGGGT
* * * *
12008751 AAAATGGTAATTTTGGGAAAGTTTGAGGTTAAAAATAGAATTTTTGGAAGTTTGAGGG-
1 AAAATGGTAATTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGAA-TTTGAGGGT
* * * *
12008809 AAAATGGTAATTTTAGGAAAATT-GGGGT-AAAAATGGAATTTTTGGATGTTTGGGGGT
1 AAAATGGTAATTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGA-ATTTGAGGGT
* * * * * * * ** *
12008866 AAAATGGTAATTTTGGGAAAGTTTGGGGTTAAAAA-CGAAATTTTGGAAGTCCAAGGT
1 AAAATGGTAATTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGAATTTGAGGGT
* * *
12008923 AAAATGGTAGTTTTTAGG-AAGTT-TAGGGTCAAAAATGGAATTTTTGGACATTTGAGGAT
1 AAAATGGTA-ATTTTAGGAAAGTTCGA-GGTCAAAAATGGAATTTTTGGA-ATTTGAGGGT
*
12008982 AAAATGGTAATTTTGGGAAAGTTC-AGGGTCAAAAATGGAATTTTTGGAAATTT-AGGGGT
1 AAAATGGTAATTTTAGGAAAGTTCGA-GGTCAAAAATGGAATTTTTGG-AATTTGA-GGGT
12009041 AAAATGGTAATTTT
1 AAAATGGTAATTTT
12009055 TGTGAAGTTC
Statistics
Matches: 253, Mismatches: 37, Indels: 28
0.80 0.12 0.09
Matches are distributed among these distances:
56 24 0.09
57 51 0.20
58 66 0.26
59 111 0.44
60 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGAATTTGAGGGT
Found at i:12011471 original size:49 final size:48
Alignment explanation
Indices: 12011411--12011529 Score: 134
Period size: 47 Copynumber: 2.5 Consensus size: 48
12011401 ATTTGGTCTA
* * * *
12011411 CTTCTCTGTATCTCATCAGGAAGATGACCGC-ATCACTTGTTTCAATCTG
1 CTTCTCAGTATCTCATCAGGAAGATAACC-CTATCA-TTGCTTCAACCTG
* * *
12011460 CTTCTCAGTATCTCATCAGG-AGATAACCCTTTTATTGCTTCGACCTG
1 CTTCTCAGTATCTCATCAGGAAGATAACCCTATCATTGCTTCAACCTG
*
12011507 CTTCTCAATATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
12011530 CTGGGGTTCG
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
47 30 0.50
48 11 0.18
49 19 0.32
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (48 bp):
CTTCTCAGTATCTCATCAGGAAGATAACCCTATCATTGCTTCAACCTG
Found at i:12016525 original size:29 final size:31
Alignment explanation
Indices: 12016455--12016527 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
12016445 TGCCAGGGGC
12016455 AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
1 AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
* *
12016486 AAAATTG-AATTTTT-GGACA-TTCGGGGTT-
1 AAAATGGTAATTTTTAGGA-AGTTCGAGGTTA
12016514 AAAATGGTAATTTT
1 AAAATGGTAATTTT
12016528 GGGAAAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 6 0.16
29 17 0.46
30 8 0.22
31 6 0.16
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (31 bp):
AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
Found at i:12016667 original size:58 final size:58
Alignment explanation
Indices: 12016455--12016863 Score: 367
Period size: 59 Copynumber: 7.1 Consensus size: 58
12016445 TGCCAGGGGC
* * * *
12016455 AAAATGGTAATTTTTAGG-AAG-TTCGAGGTTAAAAATTGAATTTTTGGACA-TTCG-GGGTT
1 AAAATGGTAA-TTTTGGGAAAGTTTAG-GGTCAAAAATGGAATTTTTGGA-AGTT-GAGGG-T
* * *
12016514 AAAATGGTAATTTTGGGAAAGTTTA-GG----ACATGGAATTTTTGGAAGTTTAAGAGT
1 AAAATGGTAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAG-TTGAGGGT
* * * ** *
12016568 AAAATGGTAATTTTAGGAAAGTAT-GGGTTAAAAATAAAATTTTTGGATGTTGAGGGT
1 AAAATGGTAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTGAGGGT
* *
12016625 AAAATGATAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTCTAAGGGT
1 AAAATGGTAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGT-TGAGGGT
* * * * *
12016684 AAAATGGTAATATTTGTG-AAGTTTGGGGTCAAAAATGGAATTTTTAGATATTTGGGGGT
1 AAAATGGTAAT-TTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTGAGGGT
* * * *
12016743 AAAATGGTAA-TTTGGGAAAGTTCAGGGTGAAAAATGGAATTTTTGGACATTTGGGGGT
1 AAAATGGTAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTGAGGGT
* * * * *
12016801 AGAATGGTAATTATGGGAAAGTTCAAGGTCAAAAATGGAATTTTTGGAAATTCGA-GGT
1 AAAATGGTAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTT-GAGGGT
12016859 AAAAT
1 AAAAT
12016864 ATGATTTTTG
Statistics
Matches: 291, Mismatches: 42, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
53 1 0.00
54 39 0.13
55 4 0.01
57 32 0.11
58 99 0.34
59 107 0.37
60 9 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTGAGGGT
Found at i:12016807 original size:117 final size:118
Alignment explanation
Indices: 12016455--12016848 Score: 427
Period size: 117 Copynumber: 3.4 Consensus size: 118
12016445 TGCCAGGGGC
* * * * *
12016455 AAAATGGTAATTTTTAGG-AAGTTCGAGGTTAAAAATTGAATTTTTGGACATTCGGGGTTAAAAT
1 AAAATGGTAA-TTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGATATTTGGGGGTAAAAT
* *
12016519 GGTAATTTTGGGAAAGTTTA--G-G--ACATGGAATTTTTGGAAGTTTAAGAGT
65 GGTAATTTTGGGAAAGTTTAGGGTGAAAAATGGAATTTTTGGAAGTTTAAGGGT
* ** * *
12016568 AAAATGGTAATTTTAGGAAAGTAT-G-GGTTAAAAATAAAATTTTTGGAT-GTTGAGGGTAAAAT
1 AAAATGGTAATTTTAGGAAAGT-TCGAGGTCAAAAATGGAATTTTTGGATATTTGGGGGTAAAAT
* * *
12016630 GATAATTTTGGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTCTAAGGGT
65 GGTAATTTTGGGAAAGTTTAGGGTGAAAAATGGAATTTTTGGAAGTTTAAGGGT
* * *
12016684 AAAATGGTAATATTT-GTG-AAGTTTGGGGTCAAAAATGGAATTTTTAGATATTTGGGGGTAAAA
1 AAAATGGTAAT-TTTAG-GAAAGTTCGAGGTCAAAAATGGAATTTTTGGATATTTGGGGGTAAAA
* **
12016747 TGGTAA-TTTGGGAAAGTTCAGGGTGAAAAATGGAATTTTTGGACA-TTTGGGGGT
64 TGGTAATTTTGGGAAAGTTTAGGGTGAAAAATGGAATTTTTGGA-AGTTTAAGGGT
* * * *
12016801 AGAATGGTAATTATGGGAAAGTTCAAGGTCAAAAATGGAATTTTTGGA
1 AAAATGGTAATTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGA
12016849 AATTCGAGGT
Statistics
Matches: 236, Mismatches: 30, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
111 29 0.12
112 27 0.11
113 16 0.07
114 1 0.00
115 1 0.00
116 44 0.19
117 101 0.43
118 17 0.07
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (118 bp):
AAAATGGTAATTTTAGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGATATTTGGGGGTAAAATG
GTAATTTTGGGAAAGTTTAGGGTGAAAAATGGAATTTTTGGAAGTTTAAGGGT
Found at i:12016870 original size:27 final size:30
Alignment explanation
Indices: 12016822--12016902 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
12016812 TATGGGAAAG
12016822 TTCAA-GGTCAAAA-ATGGAATTTTTGG-AAA
1 TTCAAGGGTCAAAATAT-G-ATTTTTGGTAAA
* *
12016851 TTCGA-GGT-AAAATATGATTTTTGGTAAT
1 TTCAAGGGTCAAAATATGATTTTTGGTAAA
*
12016879 TTTAAGGGTCAAAATATGATTTTT
1 TTCAAGGGTCAAAATATGATTTTT
12016903 AGATAGTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 8 0.18
28 10 0.23
29 12 0.27
30 14 0.32
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.40
Consensus pattern (30 bp):
TTCAAGGGTCAAAATATGATTTTTGGTAAA
Found at i:12016874 original size:117 final size:116
Alignment explanation
Indices: 12016543--12016892 Score: 275
Period size: 117 Copynumber: 3.0 Consensus size: 116
12016533 AGTTTAGGAC
* * * * * * **
12016543 ATGGAATTTTTGGAAGTTTAAGAGTAAAATGGTAAT-TTTAGGAAAG-T-ATGGGTTAAAAATAA
1 ATGGAATTTTTGGAAGTCTAAGGGTAAAATGGTAATATAT-GGGAAGTTCA-AGGTCAAAAATGG
** * *
12016605 AATTTTTGGATGTTGAGGGTAAAATGAT-AATTTTGGGAAAGTTTAGGGTCAAAA
64 AATTTTTGGAAATTGA-GGTAAAAT-ATGATTTTTGGGAAAGTTCAGGGTCAAAA
* * ***
12016659 ATGGAATTTTTGGAAGTCTAAGGGTAAAATGGTAATATTTGTGAAGTTTGGGGTCAAAAATGGAA
1 ATGGAATTTTTGGAAGTCTAAGGGTAAAATGGTAATATATGGGAAGTTCAAGGTCAAAAATGGAA
* * * * * *
12016724 TTTTTAGATATTTGGGGGT-AAA-ATGGTAATTTGGGAAAGTTCAGGGTGAAAA
66 TTTTTGGA-AATT-GAGGTAAAATATGAT-TTTTGGGAAAGTTCAGGGTCAAAA
* ** *
12016776 ATGGAATTTTTGGACA-TTTGGGGGTAGAATGGTAAT-TATGGGAAAGTTCAAGGTCAAAAATGG
1 ATGGAATTTTTGGA-AGTCTAAGGGTAAAATGGTAATATATGGG-AAGTTCAAGGTCAAAAATGG
* ** *
12016839 AATTTTTGGAAATTCGAGGTAAAATATGATTTTTGGTAATTTTAAGGGTCAAAA
64 AATTTTTGGAAATT-GAGGTAAAATATGATTTTTGGGAAAGTTCAGGGTCAAAA
12016893 TATGATTTTT
Statistics
Matches: 186, Mismatches: 37, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
115 2 0.01
116 49 0.26
117 124 0.67
118 10 0.05
119 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (116 bp):
ATGGAATTTTTGGAAGTCTAAGGGTAAAATGGTAATATATGGGAAGTTCAAGGTCAAAAATGGAA
TTTTTGGAAATTGAGGTAAAATATGATTTTTGGGAAAGTTCAGGGTCAAAA
Found at i:12017978 original size:3 final size:3
Alignment explanation
Indices: 12017970--12018043 Score: 85
Period size: 3 Copynumber: 24.7 Consensus size: 3
12017960 TTCAACTGCC
* *
12017970 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * *
12018018 TTA AGA ATA GTA TTA GTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12018044 GATACTATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:12018237 original size:29 final size:28
Alignment explanation
Indices: 12018202--12018269 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
12018192 TTGTTTATTC
* *
12018202 AAATTTAGAATAATTTTAAAT-TTAAATAT
1 AAATTTAAAATAAATTT-AATCTTAAA-AT
12018231 AAATTTAAAATAAATTTAATCTTAAAAT
1 AAATTTAAAATAAATTTAATCTTAAAAT
12018259 AAATTTAAAAT
1 AAATTTAAAAT
12018270 GGATTTAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 16 0.44
29 20 0.56
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATTTAAAATAAATTTAATCTTAAAAT
Found at i:12018244 original size:17 final size:17
Alignment explanation
Indices: 12018224--12018263 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12018214 ATTTTAAATT
12018224 TAAATATAAAT-TTAAAA
1 TAAAT-TAAATCTTAAAA
*
12018241 TAAATTTAATCTTAAAA
1 TAAATTAAATCTTAAAA
12018258 TAAATT
1 TAAATT
12018264 TAAAATGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTAAATCTTAAAA
Found at i:12018269 original size:11 final size:12
Alignment explanation
Indices: 12018218--12018249 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12018208 AGAATAATTT
12018218 TAAATTTAAATA
1 TAAATTTAAATA
12018230 TAAATTTAAA-A
1 TAAATTTAAATA
12018241 TAAATTTAA
1 TAAATTTAA
12018250 TCTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:12019513 original size:173 final size:172
Alignment explanation
Indices: 12019224--12019566 Score: 517
Period size: 173 Copynumber: 2.0 Consensus size: 172
12019214 AATTAAATTA
* * *
12019224 AAATTTCCTTTATTGAAAAAATCATTGACCTAACTTAGTTACGAAAAGACACATATCATGCCAAG
1 AAATTTCCTTAATCGAAAAAAGCATTGACCTAACTTAGTTACGAAAAGACACATATCATGCCAAG
* *
12019289 AAATATCCTTCGAAGGACATGCACTATAATTTATAATATTTCGTAGCTCGTATACTAGCTAGTTT
66 AAATATCCTTCGAAGGACATGCACTATAATTTATAATAGTTAGTAGCTCGTATACTAGCTAGTTT
*
12019354 CATTTTGTGTTTTTTAGTACTTCGATGCTAGTCCGTTAGTTTC
131 CATTTTGTG-TTTTTAGTACTTCGATGCTAGTCCCTTAGTTTC
* * * *
12019397 AAATTTCCTTAATCGAAAAAAAGCCTTGACCTAACTTAGTTATGAAAAGACACATATCGTGCGAA
1 AAATTTCCTTAATCG-AAAAAAGCATTGACCTAACTTAGTTACGAAAAGACACATATCATGCCAA
* * * * *
12019462 -AAATATCCTTCGAAGGACATGCAGTATAATTTGTAATAGTTAGTTGCTCGTATACTAGTTGGTT
65 GAAATATCCTTCGAAGGACATGCACTATAATTTATAATAGTTAGTAGCTCGTATACTAGCTAGTT
*
12019526 TCGTTTTGTGTTTTTAGTACTTCGATGCTAGTCCCTTAGTT
130 TCATTTTGTGTTTTTAGTACTTCGATGCTAGTCCCTTAGTT
12019567 ATGACTTCTT
Statistics
Matches: 153, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
172 30 0.20
173 79 0.52
174 44 0.29
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (172 bp):
AAATTTCCTTAATCGAAAAAAGCATTGACCTAACTTAGTTACGAAAAGACACATATCATGCCAAG
AAATATCCTTCGAAGGACATGCACTATAATTTATAATAGTTAGTAGCTCGTATACTAGCTAGTTT
CATTTTGTGTTTTTAGTACTTCGATGCTAGTCCCTTAGTTTC
Found at i:12027406 original size:21 final size:20
Alignment explanation
Indices: 12027380--12027451 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
12027370 TTGACATTGT
12027380 TTAATTTTATGTCGAGTTAAA
1 TTAATTTTA-GTCGAGTTAAA
* **
12027401 TTAATTTTAGTCCA-TCT-GC
1 TTAATTTTAGTCGAGT-TAAA
*
12027420 TTAAATTTAAGTCGAGTTAAA
1 TT-AATTTTAGTCGAGTTAAA
12027441 TTAATTTTAGT
1 TTAATTTTAGT
12027452 TGTACGAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
19 3 0.08
20 24 0.62
21 12 0.31
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (20 bp):
TTAATTTTAGTCGAGTTAAA
Found at i:12035092 original size:6 final size:6
Alignment explanation
Indices: 12035072--12035127 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
12035062 ACCAGGCCCT
* * * *
12035072 TTTAAA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12035118 TTTAAA TTTA
1 TTTAAA TTTA
12035128 TTTTCAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.17
6 33 0.82
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:12035097 original size:17 final size:17
Alignment explanation
Indices: 12035072--12035127 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
12035062 ACCAGGCCCT
12035072 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
12035089 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
12035106 TTTGAATTTAAATTTAAA
1 TTTAAATTT-ATTTTAAA
12035124 TTTA
1 TTTA
12035128 TTTTCAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
17 23 0.70
18 10 0.30
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:12035115 original size:12 final size:11
Alignment explanation
Indices: 12035072--12035137 Score: 53
Period size: 12 Copynumber: 5.7 Consensus size: 11
12035062 ACCAGGCCCT
*
12035072 TTTAAATTTAT
1 TTTAAATTTAA
12035083 TTTAAATTTAGA
1 TTTAAATTTA-A
*
12035095 TTT-ATTTTAAA
1 TTTAAATTT-AA
*
12035106 TTTGAATTTAAA
1 TTTAAATTT-AA
*
12035118 TTTAAATTTAT
1 TTTAAATTTAA
12035129 TTTCAAATT
1 TTT-AAATT
12035138 AAAAAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 22 0.48
12 24 0.52
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:12036922 original size:29 final size:29
Alignment explanation
Indices: 12036879--12037047 Score: 125
Period size: 30 Copynumber: 5.8 Consensus size: 29
12036869 GAAGGTCCTT
*
12036879 AAACTGTCCAAAAATTATATTTTAGCCCCG
1 AAACT-TCCAAAAATTACATTTTAGCCCCG
*
12036909 AAACTTCTAAAAATTACATTTGTA-CCCCTG
1 AAACTTCCAAAAATTACATTT-TAGCCCC-G
12036939 -AACTTCCAAAAATTACATTTTTTA-CCCC-
1 AAACTTCCAAAAATTACA--TTTTAGCCCCG
* * * ** *
12036967 AGGACTTCTAGAAATCCCATTTTTGACCCCG
1 A-AACTTCCAAAAATTACATTTTAG-CCCCG
*
12036998 AAACCTCCAAAAATTACATTTTTAGCCCC-
1 AAACTTCCAAAAATTACA-TTTTAGCCCCG
* *
12037027 AAACTT-CTAAAATTCCATTTT
1 AAACTTCCAAAAATTACATTTT
12037048 TGACCTCAAA
Statistics
Matches: 110, Mismatches: 19, Indels: 23
0.72 0.12 0.15
Matches are distributed among these distances:
27 4 0.04
28 13 0.12
29 39 0.35
30 45 0.41
31 9 0.08
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTAGCCCCG
Found at i:12037033 original size:59 final size:58
Alignment explanation
Indices: 12036885--12037052 Score: 200
Period size: 59 Copynumber: 2.9 Consensus size: 58
12036875 CCTTAAACTG
* * * *
12036885 TCCAAAAATTATA-TTTTAGCCCCGAAACTTCTAAAAATTACATTTGT-ACCCCTGAACT
1 TCCAAAAATTACATTTTTAGCCCC-AAACTTCT-AAAATTCCATTTTTGACCCCTGAACC
* *
12036943 TCCAAAAATTACATTTTTTA-CCCCAGGACTTCTAGAAATCCCATTTTTGACCCC-GAAACC
1 TCCAAAAATTACA-TTTTTAGCCCCA-AACTTCTA-AAATTCCATTTTTGACCCCTG-AACC
12037003 TCCAAAAATTACATTTTTAGCCCCAAACTTCTAAAATTCCATTTTTGACC
1 TCCAAAAATTACATTTTTAGCCCCAAACTTCTAAAATTCCATTTTTGACC
12037053 TCAAAATTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
58 30 0.32
59 34 0.36
60 31 0.33
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTAGCCCCAAACTTCTAAAATTCCATTTTTGACCCCTGAACC
Found at i:12037245 original size:29 final size:29
Alignment explanation
Indices: 12037186--12037245 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
12037176 TTTTTTCCAT
*
12037186 AATTACCATTTTGCCCCCGAGAGTCCCAA
1 AATTACCATTTTGCCCCCGAGAGTCCAAA
*
12037215 AATTACCATTTTGTCCCCGAGTA-TCCAAA
1 AATTACCATTTTGCCCCCGAG-AGTCCAAA
12037244 AA
1 AA
12037246 GTCTCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.27
Consensus pattern (29 bp):
AATTACCATTTTGCCCCCGAGAGTCCAAA
Found at i:12062447 original size:23 final size:23
Alignment explanation
Indices: 12062417--12062478 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
12062407 TTAGAATTAT
*
12062417 TATGCGAAAATATGCAAATATGC
1 TATGCGAAAAAATGCAAATATGC
12062440 TATGCGAAAAAATGCAAATATGC
1 TATGCGAAAAAATGCAAATATGC
* *
12062463 AATGCAAAAAAATGCA
1 TATGCGAAAAAATGCA
12062479 TGTATGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (23 bp):
TATGCGAAAAAATGCAAATATGC
Found at i:12062484 original size:23 final size:23
Alignment explanation
Indices: 12062418--12062502 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
12062408 TAGAATTATT
* * * *
12062418 ATGCGAAAATATGCAAATATGCT
1 ATGCAAAAAAATGCATATATGCA
* *
12062441 ATGCGAAAAAATGCAAATATGCA
1 ATGCAAAAAAATGCATATATGCA
* *
12062464 ATGCAAAAAAATGCATGTATGTA
1 ATGCAAAAAAATGCATATATGCA
* *
12062487 ATGCAAGAAAAGGCAT
1 ATGCAAAAAAATGCAT
12062503 TGATTTTTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (23 bp):
ATGCAAAAAAATGCATATATGCA
Found at i:12069199 original size:39 final size:40
Alignment explanation
Indices: 12069146--12069223 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
12069136 AAGAGGTATG
*
12069146 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGCTGTCCA
1 TCCAATATGAAAAGGGTTATGACTCTTCAAAAGCTGTCCA
* *
12069186 TCCAATTTG-AAAGGGTTATGACTCTTCAAAAGGTGTCC
1 TCCAATATGAAAAGGGTTATGACTCTTCAAAAGCTGTCC
12069224 GTTGAGTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 27 0.77
40 8 0.23
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTATGACTCTTCAAAAGCTGTCCA
Found at i:12071131 original size:13 final size:13
Alignment explanation
Indices: 12071113--12071150 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
12071103 ATATTTTATC
*
12071113 ACTTTTATAGATG
1 ACTTTTCTAGATG
12071126 ACTTTTCTAGATG
1 ACTTTTCTAGATG
12071139 ACTTTTCTAGAT
1 ACTTTTCTAGAT
12071151 TTGCTTATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (13 bp):
ACTTTTCTAGATG
Found at i:12074158 original size:39 final size:40
Alignment explanation
Indices: 12074105--12074184 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
12074095 AAGAGTTATG
*
12074105 TCCAATATGAAAAGGGTTATGACTCTTTAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTATGACTCTTCAAAAGGTGTCCA
* *
12074145 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTATGACTCTTCAAAAGGTGTCCA
12074184 T
1 T
12074185 GGAGTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTATGACTCTTCAAAAGGTGTCCA
Found at i:12088158 original size:29 final size:29
Alignment explanation
Indices: 12088111--12088193 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
12088101 TGAAAGTTTC
** * *
12088111 GGGGTCAAAAATGGGATTTTTAGATTTTTG
1 GGGGT-AAAAATGTAATTTTTAGAATTTTA
*
12088141 GGGGTAAAAATGTAATTTTTGGAATTTTA
1 GGGGTAAAAATGTAATTTTTAGAATTTTA
* *
12088170 GGGGAAAAAATGTAAATTTTAGAA
1 GGGGTAAAAATGTAATTTTTAGAA
12088194 GTTTCGATGC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 40 0.89
30 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTAGAATTTTA
Found at i:12090094 original size:12 final size:12
Alignment explanation
Indices: 12090079--12090106 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12090069 AATTTGAAAA
12090079 TAAATTCAAATT
1 TAAATTCAAATT
12090091 TAAATTCAAATT
1 TAAATTCAAATT
12090103 TAAA
1 TAAA
12090107 ATAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATTCAAATT
Found at i:12094331 original size:6 final size:6
Alignment explanation
Indices: 12094294--12094363 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
12094284 CTAAATCCAT
* * *
12094294 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTATA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12094340 TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TT-TAAA TTTAAA T
12094364 AAATAAAGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 34 0.69
7 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:12094335 original size:13 final size:12
Alignment explanation
Indices: 12094312--12094343 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12094302 TATTTTAAGA
12094312 TTAAATTTAT-T
1 TTAAATTTATAT
12094323 TTAAATTTATAT
1 TTAAATTTATAT
12094335 TTAAATTTA
1 TTAAATTTA
12094344 AAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:12094336 original size:17 final size:18
Alignment explanation
Indices: 12094294--12094337 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12094284 CTAAATCCAT
12094294 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
12094312 -TTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
12094328 TTTATATTTA
1 TTTAAATTTA
12094338 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:12094345 original size:18 final size:17
Alignment explanation
Indices: 12094294--12094363 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
12094284 CTAAATCCAT
*
12094294 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTCTAA-A
*
12094312 -TTAAATTTATTTTAAA
1 TTTAAATTTATTCTAAA
12094328 TTT--A--TATT-TAAA
1 TTTAAATTTATTCTAAA
*
12094340 TTTAAAATTATTCTAAA
1 TTTAAATTTATTCTAAA
12094357 TTTAAAT
1 TTTAAAT
12094364 AAATAAAGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
12 7 0.16
13 4 0.09
14 1 0.02
15 1 0.02
16 5 0.11
17 27 0.60
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTCTAAA
Found at i:12094350 original size:29 final size:28
Alignment explanation
Indices: 12094292--12094360 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
12094282 AACTAAATCC
*
12094292 ATTTTAAATTTATTTTAAGATTAAATTT
1 ATTTTAAATTTATTTTAAGATTAAAATT
12094320 ATTTTAAATTTATATTTAA-ATTTAAAATT
1 ATTTTAAATTTAT-TTTAAGA-TTAAAATT
*
12094349 ATTCTAAATTTA
1 ATTTTAAATTTA
12094361 AATAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
ATTTTAAATTTATTTTAAGATTAAAATT
Found at i:12095745 original size:31 final size:31
Alignment explanation
Indices: 12095682--12095741 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
12095672 TGAACTATTT
*
12095682 AAAAATCATATTTTAACCCCTAAACTTTCCA
1 AAAAATCACATTTTAACCCCTAAACTTTCCA
* *
12095713 AAAAAT-ACATTTTCACCCCTGAACTTTCC
1 AAAAATCACATTTTAACCCCTAAACTTTCC
12095742 CAAATTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (31 bp):
AAAAATCACATTTTAACCCCTAAACTTTCCA
Found at i:12095804 original size:29 final size:28
Alignment explanation
Indices: 12095707--12096196 Score: 211
Period size: 29 Copynumber: 16.7 Consensus size: 28
12095697 ACCCCTAAAC
* *
12095707 TTTCCAAAAAATA-CATTTTCACCCCTGAA
1 TTTCCAAAAATTACCATTTT-ACCTC-GAA
* *
12095736 CTTTCCCAAATTTA-CATTATTACCCTCGAA
1 -TTTCCAAAAATTACCATT-TTA-CCTCGAA
* *
12095766 CTTCATAAAAATTACCATTTTACCTCGAA
1 TTTC-CAAAAATTACCATTTTACCTCGAA
*
12095795 TTTCCAAAAATT-CCATTTTTTACCCCGAA
1 TTTCCAAAAATTACCA--TTTTACCTCGAA
* * *
12095824 CTTTTCAAAAATTACCATTCTACCCCCGAA
1 -TTTCCAAAAATTACCATTTTA-CCTCGAA
12095854 TGTT-CAAAAATT-CCATTTTTCACC-CTGAA
1 T-TTCCAAAAATTACCA-TTTT-ACCTC-GAA
* * * * *
12095883 CTTCCCAAAATTATCATTTTACCCCAAGA
1 TTTCCAAAAATTACCATTTTACCTCGA-A
* *
12095912 CTTCC-AAAATT-CTATTTTTGAGCC-CGAA
1 TTTCCAAAAATTACCA-TTTT-A-CCTCGAA
* *
12095940 CTTTCCCAAAATTACCATTTTACTCCCGAA
1 -TTTCCAAAAATTACCATTTTAC-CTCGAA
* *
12095970 TGTCTAAAAATT-CCATTTTTGA-CTCTGAA
1 TTTCCAAAAATTACCA-TTTT-ACCTC-GAA
*
12095999 CTTCCCAAAAATTACCATTTTACCCTC-AGA
1 -TTTCCAAAAATTACCATTTTA-CCTCGA-A
** * *
12096029 CCTCTAAAAATT-CCATTTTTGACCTCAAA
1 TTTCCAAAAATTACCA-TTTT-ACCTCGAA
* **
12096058 CTTTCCCAAAATTACCATTTTACCCTTAAA
1 -TTTCCAAAAATTACCATTTTA-CCTCGAA
* *
12096088 CTTCCAAAAATT-CCATTTTTAACC-CTAAA
1 TTTCCAAAAATTACCA-TTTT-ACCTC-GAA
*
12096117 CTTTCCCAAAATTACCATTTTACCCTCGAA
1 -TTTCCAAAAATTACCATTTTA-CCTCGAA
* *
12096147 TATCCATAAATT-CCATTTTTAACCTCGAA
1 TTTCCAAAAATTACCA-TTTT-ACCTCGAA
*
12096176 CTTCCAAAAAATTACCATTTT
1 TTTCC-AAAAATTACCATTTT
12096197 TCCCCTGGCA
Statistics
Matches: 359, Mismatches: 51, Indels: 100
0.70 0.10 0.20
Matches are distributed among these distances:
27 4 0.01
28 43 0.12
29 151 0.42
30 131 0.36
31 30 0.08
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
TTTCCAAAAATTACCATTTTACCTCGAA
Found at i:12095806 original size:59 final size:59
Alignment explanation
Indices: 12095708--12096196 Score: 425
Period size: 59 Copynumber: 8.3 Consensus size: 59
12095698 CCCCTAAACT
* * * * *
12095708 TTCCAAAAAATA-CATTTTCACCC-CTGAACTTTCCCAAATTTACATTATT-ACCCTCGAAC
1 TTCCAAAAATTACCATTTT-ACCCTC-GAA-TTTCCAAAAATTCCATTTTTGACCCTCGAAC
* *
12095767 TTCATAAAAATTACCATTTTA-CCTCGAATTTCCAAAAATTCCATTTTTTACCC-CGAAC
1 TTC-CAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCTCGAAC
* * * *
12095825 TTTTCAAAAATTACCATTCTACCCCCGAATGTT-CAAAAATTCCATTTTTCACCCT-GAAC
1 -TTCCAAAAATTACCATTTTACCCTCGAAT-TTCCAAAAATTCCATTTTTGACCCTCGAAC
* * * * * *
12095884 TTCCCAAAATTATCATTTTACCC-CAAGACTTCC-AAAATTCTATTTTTGAGCC-CGAAC
1 TTCCAAAAATTACCATTTTACCCTCGA-ATTTCCAAAAATTCCATTTTTGACCCTCGAAC
* * * *
12095941 TTTCCCAAAATTACCATTTTACTCC-CGAATGTCTAAAAATTCCATTTTTGACTCT-GAAC
1 -TTCCAAAAATTACCATTTTAC-CCTCGAATTTCCAAAAATTCCATTTTTGACCCTCGAAC
** * *
12096000 TTCCCAAAAATTACCATTTTACCCTC-AGACCTCTAAAAATTCCATTTTTGA-CCTCAAAC
1 TT-CCAAAAATTACCATTTTACCCTCGA-ATTTCCAAAAATTCCATTTTTGACCCTCGAAC
* ** * * *
12096059 TTTCCCAAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACCCT-AAAC
1 -TTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCTCGAAC
* * * *
12096118 TTTCCCAAAATTACCATTTTACCCTCGAATATCCATAAATTCCATTTTT-AACCTCGAAC
1 -TTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCTCGAAC
12096177 TTCCAAAAAATTACCATTTT
1 TTCC-AAAAATTACCATTTT
12096197 TCCCCTGGCA
Statistics
Matches: 360, Mismatches: 46, Indels: 48
0.79 0.10 0.11
Matches are distributed among these distances:
57 24 0.07
58 95 0.26
59 218 0.61
60 17 0.05
61 6 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
TTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACCCTCGAAC
Found at i:12096079 original size:118 final size:116
Alignment explanation
Indices: 12095773--12096201 Score: 480
Period size: 118 Copynumber: 3.7 Consensus size: 116
12095763 GAACTTCATA
* * * *
12095773 AAAATTACCATTTTA-CCTCGAATTTCCAAAAATTCCATTTTTTACCCCGAACTTTTCAAAAATT
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAACTTTCCAAAAATT
* *
12095837 ACCATTCTACCCCCGAATGT-TCAAAAATTCCATTTTTCACCCTGAACTTCCC
66 ACCATTTTA-CCCCGAATGTCT-AAAAATTCCATTTTTAACCCTGAACTTCCC
* * * *
12095889 AAAATTATCATTTTACCC-CAAGACTTCC-AAAATTCTATTTTTGAGCC-CGAACTTTCCCAAAA
1 AAAATTACCATTTTACCCTCGA-ACTTCCAAAAATTCCATTTTTGA-CCTCGAACTTTCCAAAAA
* *
12095951 TTACCATTTTACTCCCGAATGTCTAAAAATTCCATTTTTGACTCTGAACTTCCC
64 TTACCATTTTAC-CCCGAATGTCTAAAAATTCCATTTTTAACCCTGAACTTCCC
* * * *
12096005 AAAAATTACCATTTTACCCTC-AGACCTCTAAAAATTCCATTTTTGACCTCAAACTTTCCCAAAA
1 -AAAATTACCATTTTACCCTCGA-ACTTCCAAAAATTCCATTTTTGACCTCGAACTTTCCAAAAA
** * *
12096069 TTACCATTTTACCCTTAAACT-TCCAAAAATTCCATTTTTAACCCTAAACTTTCCC
64 TTACCATTTTACCC-CGAA-TGTCTAAAAATTCCATTTTTAACCCTGAAC-TTCCC
* *
12096124 AAAATTACCATTTTACCCTCGAA-TATCCATAAATTCCATTTTTAACCTCGAAC-TTCCAAAAAA
1 AAAATTACCATTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGACCTCGAACTTTCC-AAAAA
*
12096187 TTACCATTTTTCCCC
64 TTACCATTTTACCCC
12096202 TGGCAGTAGA
Statistics
Matches: 269, Mismatches: 29, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
115 1 0.00
116 90 0.33
117 41 0.15
118 130 0.48
119 7 0.03
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (116 bp):
AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAACTTTCCAAAAATT
ACCATTTTACCCCGAATGTCTAAAAATTCCATTTTTAACCCTGAACTTCCC
Found at i:12100160 original size:23 final size:23
Alignment explanation
Indices: 12100134--12100195 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
12100124 ATTACATACA
* *
12100134 TGCATTTTTTCACATTGCATATT
1 TGCATATTTTCACATAGCATATT
*
12100157 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCACATAGCATATT
*
12100180 TGCATATTTTCGCATA
1 TGCATATTTTCACATA
12100196 ATAATTCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (23 bp):
TGCATATTTTCACATAGCATATT
Found at i:12104885 original size:29 final size:30
Alignment explanation
Indices: 12104835--12104914 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
12104825 AAAGGTCCCT
* * * *
12104835 AAACTGTCCAAAAATCATATTTTGA-CCCC
1 AAACTTTCCAAAAATTACATTTTAACCCCC
*
12104864 AAACTTTCCAAAAGTTACATTTTAACCCCC
1 AAACTTTCCAAAAATTACATTTTAACCCCC
*
12104894 AAACTTTCCAAAATTTACATT
1 AAACTTTCCAAAAATTACATT
12104915 ATCACTAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.45
30 24 0.55
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.31
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTAACCCCC
Found at i:12104962 original size:29 final size:29
Alignment explanation
Indices: 12104831--12105265 Score: 177
Period size: 29 Copynumber: 14.9 Consensus size: 29
12104821 CCCAAAAGGT
* * *
12104831 CCCTAAACTGTCCAAAAATCA-TATTTTGAC
1 CCCTAAA-TTTCCAAAAATTACCATTTT-AC
*
12104861 CCC-AAACTTTCCAAAAGTTA-CATTTTAAC
1 CCCTAAA-TTTCCAAAAATTACCATTTT-AC
* * *
12104890 CCCCAAACTTTCCAAAATTTA-CA--TTAT
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* * *
12104917 CACT-AACTTCAAAAAAATTACCATTTTAC
1 CCCTAAATTTC-CAAAAATTACCATTTTAC
*
12104946 CCCTAAATTTCCAAAAATT-CAATTTTTGA-
1 CCCTAAATTTCCAAAAATTACCA-TTTT-AC
* * *
12104975 CCCTGAACTTCCTAAAAACTACCATTTTAC
1 CCCTAAATTTCC-AAAAATTACCATTTTAC
** * * *
12105005 CCCCGAATGTCCTAAAATT-CAATTTTTTA-
1 CCCTAAATTTCCAAAAATTACCA--TTTTAC
** * *
12105034 CTTTGAACTTCCTAAAAATTACCATTTTAC
1 CCCTAAATTTCC-AAAAATTACCATTTTAC
* *
12105064 CCCTAAACTTCAAAAAATT-CCATTTTTGA-
1 CCCTAAATTTCCAAAAATTACCA-TTTT-AC
* *
12105093 CCCTGAACTTTCCCAAAATTACCATTTTAC
1 CCCT-AAATTTCCAAAAATTACCATTTTAC
* ** *
12105123 CCCCAAACATCTAAAAATT-CCATTTTTTAC
1 CCCTAAATTTCCAAAAATTACCA--TTTTAC
*
12105153 CCC-AAATTTTCCCAAAATTACCATTTTAC
1 CCCTAAA-TTTCCAAAAATTACCATTTTAC
* * * *
12105182 CCATAAACTTCTAAAAATT-CCTTTTTAAC
1 CCCTAAATTTCCAAAAATTACCATTTT-AC
* * * * *
12105211 CTCGAACTTTCCCAAAATTACCACTTTA-
1 CCCTAAATTTCCAAAAATTACCATTTTAC
* *
12105239 CCCTCGAATGTCCAAAAATT-CCATTTT
1 CCCT-AAATTTCCAAAAATTACCATTTT
12105266 TGACCTCGAA
Statistics
Matches: 303, Mismatches: 73, Indels: 60
0.69 0.17 0.14
Matches are distributed among these distances:
25 3 0.01
26 9 0.03
27 5 0.02
28 26 0.09
29 141 0.47
30 109 0.36
31 10 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTAAATTTCCAAAAATTACCATTTTAC
Found at i:12104992 original size:59 final size:58
Alignment explanation
Indices: 12104831--12105296 Score: 364
Period size: 59 Copynumber: 8.0 Consensus size: 58
12104821 CCCAAAAGGT
** *
12104831 CCCTAAACTGTCCAAAAA-T-CATATTTTGACCCCAAACTTTCCAAAAGTTA-CATTTTAAC
1 CCCTAAACT-TCCAAAAATTCCAT-TTTTGACCCTGAAC-TTCCAAAAATTACCATTTT-AC
* * * * * *
12104890 CCCCAAACTTTCCAAAATTTACA-TTAT--CACT-AACTTCAAAAAAATTACCATTTTAC
1 CCCTAAAC-TTCCAAAAATTCCATTTTTGACCCTGAACTTC-CAAAAATTACCATTTTAC
* * *
12104946 CCCTAAATTTCCAAAAATTCAATTTTTGACCCTGAACTTCCTAAAAACTACCATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAACTTCC-AAAAATTACCATTTTAC
** * * * **
12105005 CCCCGAA-TGTCCTAAAATTCAATTTTTTACTTTGAACTTCCTAAAAATTACCATTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTGACCCTGAACTTCC-AAAAATTACCATTTTAC
* *
12105064 CCCTAAACTTCAAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAAC-TTCCAAAAATTACCATTTTAC
* * * * ** * *
12105123 CCCCAAACATCTAAAAATTCCATTTTTTACCCCAAATTTTCCCAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAA-CTTCCAAAAATTACCATTTTAC
* * * * *
12105182 CCATAAACTTCTAAAAATTCC-TTTTT-AACCTCGAACTTTCCCAAAATTACCACTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCT-GAAC-TTCCAAAAATTACCATTTTAC
* *
12105239 CCCTCGAA-TGTCCAAAAATTCCATTTTTGA-CCTCGAACTTCCTAAAAGTTACCATTTT
1 CCCT-AAACT-TCCAAAAATTCCATTTTTGACCCT-GAACTTCC-AAAAATTACCATTTT
12105297 TCCTCGGGCA
Statistics
Matches: 333, Mismatches: 53, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
55 14 0.04
56 21 0.06
57 15 0.05
58 47 0.14
59 226 0.68
60 8 0.02
61 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTCCATTTTTGACCCTGAACTTCCAAAAATTACCATTTTAC
Found at i:12105067 original size:118 final size:117
Alignment explanation
Indices: 12104929--12105296 Score: 447
Period size: 118 Copynumber: 3.1 Consensus size: 117
12104919 CTAACTTCAA
* * *
12104929 AAAAATTACCATTTTACCCCTAAATTTCCAAAAATTCAATTTTTGACCCTGAAC-TTCCTAAAAA
1 AAAAATTACCATTTTACCCCTAAACTTCAAAAAATTC-ATTTTTGACCCTGAACTTTCC-CAAAA
* * * *
12104993 CTACCATTTTACCCCCGAATGTCCTAAAATTCAATTTTTTACTTTGAACTTCCT
64 TTACCATTTTACCCCCGAATGTCCTAAAATTCCATTTTTTACCTCGAACTTCCT
12105047 AAAAATTACCATTTTACCCCTAAACTTCAAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAAT
1 AAAAATTACCATTTTACCCCTAAACTTCAAAAAATT-CATTTTTGACCCTGAACTTTCCCAAAAT
* ** * * *
12105112 TACCATTTTACCCCCAAACAT-CTAAAAATTCCATTTTTTACCCCAAATTTTCC-
65 TACCATTTTACCCCCGAATGTCCT-AAAATTCCATTTTTTACCTCGAA-CTTCCT
* * * * *
12105165 CAAAATTACCATTTTACCCATAAACTTCTAAAAATTCCTTTTT-AACCTCGAACTTTCCCAAAAT
1 AAAAATTACCATTTTACCCCTAAACTTCAAAAAATTCATTTTTGACCCT-GAACTTTCCCAAAAT
* * * *
12105229 TACCACTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACCTCGAACTTCCT
65 TACCATTTTACCCCCGAATGTCCTAAAATTCCATTTTTTACCTCGAACTTCCT
*
12105282 AAAAGTTACCATTTT
1 AAAAATTACCATTTT
12105297 TCCTCGGGCA
Statistics
Matches: 213, Mismatches: 30, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
116 8 0.04
117 72 0.34
118 124 0.58
119 9 0.04
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCCTAAACTTCAAAAAATTCATTTTTGACCCTGAACTTTCCCAAAATT
ACCATTTTACCCCCGAATGTCCTAAAATTCCATTTTTTACCTCGAACTTCCT
Found at i:12105272 original size:29 final size:29
Alignment explanation
Indices: 12104929--12105316 Score: 166
Period size: 29 Copynumber: 13.2 Consensus size: 29
12104919 CTAACTTCAA
* * *
12104929 AAAAATTACCA-TTTTACCCCTAAATTTCC
1 AAAAATTACCATTTTTACCTC-GAACTTCC
*
12104958 AAAAATT-CAATTTTTGACC-CTGAACTTCC
1 AAAAATTACCATTTTT-ACCTC-GAACTTCC
* *
12104987 TAAAAACTACCA-TTTTACCCCCGAA-TGTCC
1 -AAAAATTACCATTTTTA-CCTCGAACT-TCC
* * * *
12105017 TAAAATT-CAATTTTTTACTTTGAACTTCC
1 AAAAATTACCA-TTTTTACCTCGAACTTCC
* * *
12105046 TAAAAATTACCA-TTTTACCCCTAAACTTCA
1 -AAAAATTACCATTTTTACCTC-GAACTTCC
12105076 AAAAATT-CCATTTTTGACC-CTGAACTTTCC
1 AAAAATTACCATTTTT-ACCTC-GAAC-TTCC
* * * * *
12105106 CAAAATTACCA-TTTTACCCCCAAACATCT
1 AAAAATTACCATTTTTA-CCTCGAACTTCC
* * *
12105135 AAAAATT-CCATTTTTTACCCCAAATTTTCC
1 AAAAATTACCA-TTTTTACCTCGAA-CTTCC
* * *
12105165 CAAAATTACCA-TTTTACC-CATAAACTTCT
1 AAAAATTACCATTTTTACCTC--GAACTTCC
12105194 AAAAATT-CC-TTTTTAACCTCGAACTTTCC
1 AAAAATTACCATTTTT-ACCTCGAAC-TTCC
* *
12105223 CAAAATTACCA-CTTTACCCTCGAA-TGTCC
1 AAAAATTACCATTTTTA-CCTCGAACT-TCC
12105252 AAAAATT-CCATTTTTGACCTCGAACTTCC
1 AAAAATTACCATTTTT-ACCTCGAACTTCC
* ** *
12105281 TAAAAGTTACCATTTTT-CCTCGGGCATCC
1 -AAAAATTACCATTTTTACCTCGAACTTCC
12105310 AAAAATT
1 AAAAATT
12105317 GCATTTAATC
Statistics
Matches: 278, Mismatches: 43, Indels: 77
0.70 0.11 0.19
Matches are distributed among these distances:
28 30 0.11
29 131 0.47
30 97 0.35
31 20 0.07
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAATTACCATTTTTACCTCGAACTTCC
Found at i:12116499 original size:30 final size:30
Alignment explanation
Indices: 12116378--12116507 Score: 88
Period size: 29 Copynumber: 4.4 Consensus size: 30
12116368 ATCCAAGAGT
* *
12116378 AAAATAGTAATTTTT-GAAAGTTTCGAGGTCT
1 AAAAT-GTAATTTTTAG-AAGTTTCGAGGGCA
** * * * *
12116409 AAAATGGGATTTTAAGATG-TTCGGGGGTA
1 AAAATGTAATTTTTAGAAGTTTCGAGGGCA
* * * *
12116438 AAAATGTATTTTTTGGAAATTTAG-GGGCA
1 AAAATGTAATTTTTAGAAGTTTCGAGGGCA
*
12116467 AAAATGTAATTTTTAGAAGTTTCGA-GGCC
1 AAAATGTAATTTTTAGAAGTTTCGAGGGCA
*
12116496 AAAATATAATTT
1 AAAATGTAATTT
12116508 CTGAACAGTT
Statistics
Matches: 73, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
29 56 0.77
30 11 0.15
31 6 0.08
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAGTTTCGAGGGCA
Found at i:12118168 original size:6 final size:6
Alignment explanation
Indices: 12118157--12118212 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
12118147 AATATGAAAA
* * * *
12118157 TAAATT TAAATT TAAATT CAAATT TAAA-A TAAATC TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
12118203 TAAATT TAAA
1 TAAATT TAAA
12118213 AGGGCTCGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 8 0.20
6 33 0.80
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:12118186 original size:29 final size:28
Alignment explanation
Indices: 12118153--12118213 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
12118143 TTTAAATATG
* *
12118153 AAAATAAATTTAAATTTAAATTCAAATTT
1 AAAATAAATCTAAATTTAAAAT-AAATTT
12118182 AAAATAAATCTAAATTTAAAATAAATTT
1 AAAATAAATCTAAATTTAAAATAAATTT
12118210 AAAA
1 AAAA
12118214 GGGCTCGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAATAAATCTAAATTTAAAATAAATTT
Found at i:12118196 original size:17 final size:16
Alignment explanation
Indices: 12118143--12118208 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 16
12118133 GCTTTTTTTT
*
12118143 TTTAAATATGAAAATAAA
1 TTTAAA-AT-AAATTAAA
*
12118161 TTTAAATTTAAATTCAAA
1 TTTAAA-ATAAATT-AAA
12118179 TTTAAAATAAATCTAAA
1 TTTAAAATAAAT-TAAA
12118196 TTTAAAATAAATT
1 TTTAAAATAAATT
12118209 TAAAAGGGCT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
16 1 0.02
17 24 0.56
18 18 0.42
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (16 bp):
TTTAAAATAAATTAAA
Found at i:12118212 original size:17 final size:17
Alignment explanation
Indices: 12118157--12118212 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
12118147 AATATGAAAA
*
12118157 TAAATTTAAATTTAAATT
1 TAAATTTAAA-ATAAATT
* *
12118175 CAAATTTAAAATAAATC
1 TAAATTTAAAATAAATT
12118192 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
12118209 TAAA
1 TAAA
12118213 AGGGCTCGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:12121843 original size:21 final size:21
Alignment explanation
Indices: 12121818--12121859 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12121808 ATTTGTACAA
12121818 AAACTTTTAAGGAATTGATAT
1 AAACTTTTAAGGAATTGATAT
12121839 AAACTTTTAAGGAATTGATAT
1 AAACTTTTAAGGAATTGATAT
12121860 TGTTTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (21 bp):
AAACTTTTAAGGAATTGATAT
Found at i:12122819 original size:13 final size:12
Alignment explanation
Indices: 12122796--12122827 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12122786 TATTTTAAGA
12122796 TTAAATTTAT-T
1 TTAAATTTATAT
12122807 TTAAATTTATAT
1 TTAAATTTATAT
12122819 TTAAATTTA
1 TTAAATTTA
12122828 AAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:12122820 original size:17 final size:18
Alignment explanation
Indices: 12122778--12122821 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12122768 CTAAATCCAT
12122778 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
12122796 -TTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
12122812 TTTATATTTA
1 TTTAAATTTA
12122822 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:12122834 original size:18 final size:17
Alignment explanation
Indices: 12122806--12122848 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
12122796 TTAAATTTAT
* *
12122806 TTTAAATTTATATTTAAA
1 TTTAAAATTAT-TCTAAA
12122824 TTTAAAATTATTCTAAA
1 TTTAAAATTATTCTAAA
*
12122841 TTTTAAAT
1 TTTAAAAT
12122849 AAACAAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATTATTCTAAA
Found at i:12122834 original size:29 final size:28
Alignment explanation
Indices: 12122776--12122843 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
12122766 AACTAAATCC
*
12122776 ATTTTAAATTTATTTTAAGATTAAATTT
1 ATTTTAAATTTATTTTAAGATTAAAATT
12122804 ATTTTAAATTTATATTTAA-ATTTAAAATT
1 ATTTTAAATTTAT-TTTAAGA-TTAAAATT
*
12122833 ATTCTAAATTT
1 ATTTTAAATTT
12122844 TAAATAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
ATTTTAAATTTATTTTAAGATTAAAATT
Found at i:12124079 original size:30 final size:29
Alignment explanation
Indices: 12124036--12124101 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
12124026 TGAACTGTCT
* * *
12124036 AAAAATCATATTTTGACCCTTAAACTTTCC
1 AAAAATTACATTTTGACCCCTAAACTTT-C
*
12124066 AAAAATTACATTTTGACCCCTGAACTTTC
1 AAAAATTACATTTTGACCCCTAAACTTTC
12124095 AAAAATT
1 AAAAATT
12124102 TAAGTTATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCTAAACTTTC
Found at i:12124215 original size:59 final size:58
Alignment explanation
Indices: 12124127--12124601 Score: 371
Period size: 59 Copynumber: 8.3 Consensus size: 58
12124117 GAACTTCACA
* * * *
12124127 AAAATTACCAGTTTACCTCGAATTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
1 AAAATTACCATTTTACCCCCAAATTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
* * * * * * *
12124185 ATAATTACCATTCTACCCCCAAATGTCCAAAAATTTCATTTTTTACCTTGAACTTGCCA
1 AAAATTACCATTTTACCCCCAAAT-TCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
* *
12124244 AAAATTACCATTTTACCCCCAGACTTCCAAAAATTCTA-TTTT-----TG-AC---CCC
1 AAAATTACCATTTTACCCCCA-AATTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
* * *
12124293 AAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACTCC-AAAC-TTCCC
1 AAAATTACCATTTTACCCCCAAAT-TCCAAAAATTCCATTTTTGAC-CCTGAACTTTCCC
***
12124351 AAATATTACCATTTTACCATTAAACTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
1 AAA-ATTACCATTTTACCCCCAAA-TTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
* * ** * **
12124411 AAAATTACCATTTTACCCTCAAACATCCAAAAATTTTATTTTTGACCC-CATACTTTCTT
1 AAAATTACCATTTTACCCCCAAA-TTCCAAAAATTCCATTTTTGACCCTGA-ACTTTCCC
* ** *
12124470 AAAATTATCATTTTACCCTTAAACTTCCAAAAATTCCA--TTT---CCTAAACTTTCCC
1 AAAATTACCATTTTACCCCCAAA-TTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
* * * * *
12124524 AAAATTACCATTTTAACCCCGAATATCCAAAAAATT-CATTTTT-AACCTCGATC-TTCCTA
1 AAAATTACCATTTTACCCCCAAAT-TCC-AAAAATTCCATTTTTGACCCT-GAACTTTCC-C
12124583 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
12124602 TGGCATCGAA
Statistics
Matches: 337, Mismatches: 53, Indels: 53
0.76 0.12 0.12
Matches are distributed among these distances:
48 2 0.01
49 33 0.10
50 4 0.01
52 2 0.01
53 3 0.01
54 31 0.09
55 8 0.02
56 5 0.01
57 3 0.01
58 38 0.11
59 197 0.58
60 11 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAATTCCAAAAATTCCATTTTTGACCCTGAACTTTCCC
Found at i:12124258 original size:29 final size:29
Alignment explanation
Indices: 12124116--12124278 Score: 95
Period size: 29 Copynumber: 5.6 Consensus size: 29
12124106 TTATTGTACT
* *
12124116 CGAACTT-CACAAAAATTACCAGTTTACCT
1 CGAACTTGC-CAAAAATTACCATTTTACCC
*
12124145 CGAA-TTTCCAAAAATT-CCATTTTTGACCC
1 CGAACTTGCCAAAAATTACCA-TTTT-ACCC
* * * * *
12124174 TGAACTTTCCCATAATTACCATTCTACCC
1 CGAACTTGCCAAAAATTACCATTTTACCC
* * * *
12124203 CCAA-ATGTCCAAAAATT-TCATTTTTTACCT
1 CGAACTTG-CCAAAAATTACCA--TTTTACCC
*
12124233 TGAACTTGCCAAAAATTACCATTTTACCC
1 CGAACTTGCCAAAAATTACCATTTTACCC
*
12124262 CCAGACTT-CCAAAAATT
1 CGA-ACTTGCCAAAAATT
12124279 CTATTTTTGA
Statistics
Matches: 101, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
27 3 0.03
28 16 0.16
29 41 0.41
30 34 0.34
31 7 0.07
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (29 bp):
CGAACTTGCCAAAAATTACCATTTTACCC
Found at i:12124325 original size:49 final size:49
Alignment explanation
Indices: 12124244--12124344 Score: 150
Period size: 49 Copynumber: 2.1 Consensus size: 49
12124234 GAACTTGCCA
* *
12124244 AAAATTACCATTTTACCCCCAGACTTCCAAAAATTCTATTTTTGACCCC
1 AAAATTACCATTTTACCCCCAGAATTCCAAAAATTCCATTTTTGACCCC
* *
12124293 AAAATTACCATTTTACCCCC-GAATGTCTAAAAATTCCATTTTTGACTCC
1 AAAATTACCATTTTACCCCCAGAAT-TCCAAAAATTCCATTTTTGACCCC
12124342 AAA
1 AAA
12124345 CTTCCCAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
48 3 0.06
49 44 0.94
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (49 bp):
AAAATTACCATTTTACCCCCAGAATTCCAAAAATTCCATTTTTGACCCC
Found at i:12124363 original size:31 final size:29
Alignment explanation
Indices: 12124322--12124537 Score: 100
Period size: 30 Copynumber: 7.5 Consensus size: 29
12124312 CGAATGTCTA
12124322 AAAATT-CCATTTTTGACTCCAAACTTCCC
1 AAAATTACCATTTTTGAC-CCAAACTTCCC
* *
12124351 AAATATTACCA-TTTT-ACCATTAAACTTCCA
1 AAA-ATTACCATTTTTGACC--CAAACTTCCC
*
12124381 AAAATT-CCATTTTTGACCCTGAACTTTCCC
1 AAAATTACCATTTTTGACCC-AAAC-TTCCC
* *
12124411 AAAATTACCA-TTTT-ACCCTCAAACATCCA
1 AAAATTACCATTTTTGA-CC-CAAACTTCCC
** * **
12124440 AAAATT-TTATTTTTGACCCCATACTTTCTT
1 AAAATTACCATTTTTGA-CCCAAAC-TTCCC
* *
12124470 AAAATTATCA-TTTT-ACCCTTAAACTTCCA
1 AAAATTACCATTTTTGACCC--AAACTTCCC
*
12124499 AAAATT-CCA--TTT--CCTAAACTTTCCC
1 AAAATTACCATTTTTGACCCAAAC-TTCCC
12124524 AAAATTACCATTTT
1 AAAATTACCATTTT
12124538 AACCCCGAAT
Statistics
Matches: 145, Mismatches: 21, Indels: 43
0.69 0.10 0.21
Matches are distributed among these distances:
24 4 0.03
25 10 0.07
26 5 0.03
27 3 0.02
28 12 0.08
29 43 0.30
30 59 0.41
31 9 0.06
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTTGACCCAAACTTCCC
Found at i:12124378 original size:30 final size:28
Alignment explanation
Indices: 12124290--12124538 Score: 138
Period size: 29 Copynumber: 8.6 Consensus size: 28
12124280 TATTTTTGAC
**
12124290 CCCAAAATTACCATTTTACCCCCGAA-TGT
1 CCCAAAATTACCATTTTA-CCCTAAACT-T
**
12124319 CTAAAAATT-CCATTTTTGACTCC-AAACTT
1 CCCAAAATTACCA-TTTT-AC-CCTAAACTT
*
12124348 CCCAAATATTACCATTTTACCATTAAACTT
1 CCCAAA-ATTACCATTTTACC-CTAAACTT
* *
12124378 CCAAAAATT-CCATTTTTGACCCTGAACTTT
1 CCCAAAATTACCA-TTTT-ACCCTAAAC-TT
*
12124408 CCCAAAATTACCATTTTACCCTCAAACAT
1 CCCAAAATTACCATTTTACCCT-AAACTT
* ** * *
12124437 CCAAAAATT-TTATTTTTGACCCCATACTTT
1 CCCAAAATTACCA-TTTT-ACCCTAAAC-TT
** *
12124467 CTTAAAATTATCATTTTACCCTTAAACTT
1 CCCAAAATTACCATTTTACCC-TAAACTT
*
12124496 CCAAAAATT-CCA-TTT--CCTAAACTTT
1 CCCAAAATTACCATTTTACCCTAAAC-TT
12124521 CCCAAAATTACCATTTTA
1 CCCAAAATTACCATTTTA
12124539 ACCCCGAATA
Statistics
Matches: 171, Mismatches: 27, Indels: 45
0.70 0.11 0.19
Matches are distributed among these distances:
24 5 0.03
25 12 0.07
26 3 0.02
27 6 0.04
28 10 0.06
29 66 0.39
30 61 0.36
31 8 0.05
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (28 bp):
CCCAAAATTACCATTTTACCCTAAACTT
Found at i:12124442 original size:167 final size:166
Alignment explanation
Indices: 12124127--12124460 Score: 440
Period size: 167 Copynumber: 2.0 Consensus size: 166
12124117 GAACTTCACA
* * * *
12124127 AAAATTACCAGTTTACCTCGAATTTCCAAAAATTCCATTTTTGACCCTGAACTTTCCCATAATTA
1 AAAATTACCAGTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCCTAAACTTTCCCAAAATTA
* * * *
12124192 CCATTCTACCCCCAAATGTCCAAAAATTTCATTTTTTACCTTGAACTTGCCAAAAATTACCATTT
66 CCATTCTACCACCAAATGTCCAAAAATTCCATTTTTGACCCTGAACTTGCCAAAAATTACCATTT
* *
12124257 TACCCCCAGACTTCCAAAAATTCTATTTTTGACCCC
131 TACCCCCAAACATCCAAAAATTCTATTTTTGACCCC
* *
12124293 AAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACTCC-AAAC-TTCCCAAATA
1 AAAATTACCAGTTTA-CCCCGAATGTCCAAAAATTCCATTTTTGAC-CCTAAACTTTCCCAAA-A
* ** * *
12124356 TTACCATTTTACCATTAAACT-TCCAAAAATTCCATTTTTGACCCTGAACTTTCCCAAAATTACC
63 TTACCATTCTACCACCAAA-TGTCCAAAAATTCCATTTTTGACCCTGAACTTGCCAAAAATTACC
* *
12124420 ATTTTACCCTCAAACATCCAAAAATTTTATTTTTGACCCC
127 ATTTTACCCCCAAACATCCAAAAATTCTATTTTTGACCCC
12124460 A
1 A
12124461 TACTTTCTTA
Statistics
Matches: 145, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
166 21 0.14
167 121 0.83
168 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (166 bp):
AAAATTACCAGTTTACCCCGAATGTCCAAAAATTCCATTTTTGACCCTAAACTTTCCCAAAATTA
CCATTCTACCACCAAATGTCCAAAAATTCCATTTTTGACCCTGAACTTGCCAAAAATTACCATTT
TACCCCCAAACATCCAAAAATTCTATTTTTGACCCC
Found at i:12124528 original size:25 final size:25
Alignment explanation
Indices: 12124489--12124536 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
12124479 ATTTTACCCT
12124489 TAAACTTCCAAAAATT-CCATTTCC
1 TAAACTTCCAAAAATTACCATTTCC
*
12124513 TAAACTTTCCCAAAATTACCATTT
1 TAAAC-TTCCAAAAATTACCATTT
12124537 TAACCCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAACTTCCAAAAATTACCATTTCC
Found at i:12128557 original size:23 final size:23
Alignment explanation
Indices: 12128531--12128592 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
12128521 ATTATATACA
* *
12128531 TGCATTTTTTCGCATTGCATATT
1 TGCATATTTTCGCATAGCATATT
12128554 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCGCATAGCATATT
12128577 TGCATATTTTCGCATA
1 TGCATATTTTCGCATA
12128593 ATAATTCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (23 bp):
TGCATATTTTCGCATAGCATATT
Found at i:12137463 original size:18 final size:18
Alignment explanation
Indices: 12137440--12137485 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
12137430 CTAAACCCAT
*
12137440 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAAA
* *
12137458 TTTAAATATGTTTTAAAA
1 TTTAAATTTATTTTAAAA
12137476 TTTAAATTTA
1 TTTAAATTTA
12137486 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:12139505 original size:30 final size:30
Alignment explanation
Indices: 12139427--12139830 Score: 141
Period size: 30 Copynumber: 13.8 Consensus size: 30
12139417 AAAGGTCCCT
* * *
12139427 AAACTATCCAAAAATCATATTTTGACCCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
*
12139457 AAACTTTCCAAAAGTTACATTTTGACCCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * *
12139487 AAACTTTCCAAAATTTACA--TT-A-TCAC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * *
12139513 GAAC-TTCACAAAAATTACCATTTT-ATCCTC
1 AAACTTTC-CAAAAATTA-CATTTTGACCCCC
* * * *
12139543 AAA-TGTCCAAAAATTCCATTTTTTA-CCCT
1 AAACTTTCCAAAAATTACA-TTTTGACCCCC
* * **
12139572 AGAC-TTCCTAAAAACTACCATTTT-A-CCTT
1 AAACTTTCC-AAAAATTA-CATTTTGACCCCC
** * * *
12139601 GGAC-TTCCAAAAATTTCATTTTTAACCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* **
12139630 AAACTTTCCCAAAATTAGCATTTT-ACCCTT
1 AAACTTTCCAAAAATTA-CATTTTGACCCCC
* * * * *
12139660 AAA-ATTCCAAAAATTCCATTTTTAACCCT
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* * * *
12139689 GAACTTTCCCAAAATCACCAGTTT-ACCCCC
1 AAACTTTCCAAAAATTA-CATTTTGACCCCC
* * **
12139719 AAAC-TTCCAAAAATT-CTATTTTTAACATC
1 AAACTTTCCAAAAATTAC-ATTTTGACCCCC
* *
12139748 AAACTTTCCCAAAATTACCATTTT-ACCCCT
1 AAACTTTCCAAAAATTA-CATTTTGACCCCC
* * *
12139778 GAA-TGTCCAAAAATT-CAATTTTTGA-CCTC
1 AAACTTTCCAAAAATTAC-A-TTTTGACCCCC
12139807 AAAC-TTCCTAAAAATTACCATTTT
1 AAACTTTCC-AAAAATTA-CATTTT
12139831 TCCTCGGGCA
Statistics
Matches: 279, Mismatches: 65, Indels: 60
0.69 0.16 0.15
Matches are distributed among these distances:
25 3 0.01
26 13 0.05
27 11 0.04
28 22 0.08
29 90 0.32
30 119 0.43
31 19 0.07
32 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTGACCCCC
Found at i:12139553 original size:29 final size:28
Alignment explanation
Indices: 12139521--12139835 Score: 101
Period size: 29 Copynumber: 10.8 Consensus size: 28
12139511 ACGAACTTCA
12139521 CAAAAATTACCATTTTATCCTCAAATGTC
1 CAAAAATTACCATTTTATCCTCAAAT-TC
* *
12139550 CAAAAATT-CCATTTTTTACC-CTAGACTTC
1 CAAAAATTACCATTTTAT-CCTC-A-AATTC
* ** *
12139579 CTAAAAACTACCATTTTA-CCTTGGACTTC
1 C-AAAAATTACCATTTTATCC-TCAAATTC
* * *
12139608 CAAAAATT-TCATTTTTAACCCCAAACTTTC
1 CAAAAATTACCA-TTTTATCCTCAAA--TTC
* * * *
12139638 CCAAAATTAGCATTTTACCCTTAAAATTC
1 CAAAAATTACCATTTTATCC-TCAAATTC
* * *
12139667 CAAAAATT-CCATTTTTAACCCTGAACTTTC
1 CAAAAATTACCA-TTTT-ATCCTCAA-ATTC
* * * * *
12139697 CCAAAATCACCAGTTTACCCCCAAACTTC
1 CAAAAATTACCATTTTATCCTCAAA-TTC
* * *
12139726 CAAAAATT-CTATTTTTAACATCAAACTTTC
1 CAAAAATTACCA-TTTTATCCTCAAA--TTC
* * *
12139756 CCAAAATTACCATTTTA-CCCCTGAATGTC
1 CAAAAATTACCATTTTATCCTC-AAAT-TC
*
12139785 CAAAAATT-CAATTTT-TGACCTCAAACTTC
1 CAAAAATTACCATTTTAT--CCTCAAA-TTC
12139814 CTAAAAATTACCATTTT-TCCTC
1 C-AAAAATTACCATTTTATCCTC
12139836 GGGCATCCAA
Statistics
Matches: 212, Mismatches: 45, Indels: 58
0.67 0.14 0.18
Matches are distributed among these distances:
27 2 0.01
28 32 0.15
29 85 0.40
30 69 0.33
31 24 0.11
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
CAAAAATTACCATTTTATCCTCAAATTC
Found at i:12139591 original size:59 final size:57
Alignment explanation
Indices: 12139521--12139835 Score: 269
Period size: 59 Copynumber: 5.4 Consensus size: 57
12139511 ACGAACTTCA
* *
12139521 CAAAAATTACCATTTTATCCTCAAATGTCCAAAAATTCCATTTTTTACCCTAGAC-TTC
1 CAAAAATTACCATTTTA-CCTCAAAT-TCCAAAAATTCCATTTTTAACCCTAAACTTTC
* ** * * *
12139579 CTAAAAACTACCATTTTACCTTGGACTTCCAAAAATTTCATTTTTAACCCCAAACTTTC
1 C-AAAAATTACCATTTTACC-TCAAATTCCAAAAATTCCATTTTTAACCCTAAACTTTC
* * * *
12139638 CCAAAATTAGCATTTTACCCTTAAAATTCCAAAAATTCCATTTTTAACCCTGAACTTTC
1 CAAAAATTACCATTTTA-CC-TCAAATTCCAAAAATTCCATTTTTAACCCTAAACTTTC
* * * * * *
12139697 CCAAAATCACCAGTTTACCCCCAAACTTCCAAAAATTCTATTTTTAA-CATCAAACTTTC
1 CAAAAATTACCATTTTA-CCTCAAA-TTCCAAAAATTCCATTTTTAACCCT-AAACTTTC
* * * * *
12139756 CCAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCAATTTTTGA-CCTCAAAC-TTC
1 CAAAAATTACCATTTTACCTC-AAAT-TCCAAAAATTCCATTTTTAACCCT-AAACTTTC
*
12139814 CTAAAAATTACCATTTTTCCTC
1 C-AAAAATTACCATTTTACCTC
12139836 GGGCATCCAA
Statistics
Matches: 214, Mismatches: 34, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
58 54 0.25
59 160 0.75
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCTCAAATTCCAAAAATTCCATTTTTAACCCTAAACTTTC
Found at i:12139763 original size:118 final size:116
Alignment explanation
Indices: 12139523--12139826 Score: 330
Period size: 118 Copynumber: 2.6 Consensus size: 116
12139513 GAACTTCACA
* * *
12139523 AAAATTACCATTTTATCCTCAAATGTCCAAAAATTCCATTTTTTACCCTAGACTTCCTAAAAACT
1 AAAATTACCATTTTACCCT-AAATGTCCAAAAATTCCATTTTTAACCCTAGACTTCCCAAAAACT
* **** *
12139588 ACCATTTTACCTTGGACTTCCAAAAATTTCATTTTTAACCCCAAACTTTCCC
65 ACCAGTTTACCCCAAACTTCCAAAAATTTCATTTTTAACACCAAACTTTCCC
*
12139640 AAAATTAGCATTTTACCCTTAAAAT-TCCAAAAATTCCATTTTTAACCCT-GAACTTTCCCAAAA
1 AAAATTACCATTTTACCC-T-AAATGTCCAAAAATTCCATTTTTAACCCTAG-AC-TTCCCAAAA
* *
12139703 TC-ACCAGTTTACCCCCAAACTTCCAAAAA-TTCTATTTTTAACATCAAACTTTCCC
62 ACTACCAGTTTA-CCCCAAACTTCCAAAAATTTC-ATTTTTAACACCAAACTTTCCC
* * * * * *
12139758 AAAATTACCATTTTACCCCTGAATGTCCAAAAATTCAATTTTTGA-CCTCAAACTTCCTAAAAAT
1 AAAATTACCATTTTA-CCCTAAATGTCCAAAAATTCCATTTTTAACCCT-AGACTTCCCAAAAAC
12139822 TACCA
64 TACCA
12139827 TTTTTCCTCG
Statistics
Matches: 156, Mismatches: 21, Indels: 19
0.80 0.11 0.10
Matches are distributed among these distances:
116 1 0.01
117 66 0.42
118 86 0.55
119 3 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (116 bp):
AAAATTACCATTTTACCCTAAATGTCCAAAAATTCCATTTTTAACCCTAGACTTCCCAAAAACTA
CCAGTTTACCCCAAACTTCCAAAAATTTCATTTTTAACACCAAACTTTCCC
Found at i:12162342 original size:6 final size:6
Alignment explanation
Indices: 12162331--12162365 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
12162321 AACAACTTAT
*
12162331 AAATAA AAATAA AAAAAA AAATAA AAA-AA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
12162366 CAACTTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (6 bp):
AAATAA
Found at i:12162356 original size:11 final size:11
Alignment explanation
Indices: 12162335--12162365 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
12162325 ACTTATAAAT
12162335 AAAAATAAAAAA
1 AAAAAT-AAAAA
12162347 AAAAATAAAAA
1 AAAAATAAAAA
12162358 AAAAATAA
1 AAAAATAA
12162366 CAACTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:12175478 original size:24 final size:24
Alignment explanation
Indices: 12175446--12175492 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12175436 AGAAATAATC
*
12175446 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCCGTTTATTTG
12175470 TTTCAATTAAACTCCGTTTATTT
1 TTTCAATTAAACTCCGTTTATTT
12175493 ATTTGAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCCGTTTATTTG
Found at i:12175505 original size:24 final size:24
Alignment explanation
Indices: 12175446--12175507 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
12175436 AGAAATAATC
* * *
12175446 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATAAAACTCCGTTTATTTA
*
12175470 TTTCAATTAAACTCCGTTTATTTA
1 TTTCAATAAAACTCCGTTTATTTA
* *
12175494 TTTGAGTAAAACTC
1 TTTCAATAAAACTC
12175508 TTATTACTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTCAATAAAACTCCGTTTATTTA
Found at i:12205237 original size:29 final size:29
Alignment explanation
Indices: 12205203--12205393 Score: 123
Period size: 29 Copynumber: 6.7 Consensus size: 29
12205193 ACTTTTTGCC
*
12205203 AAAATTACCATTTTACCCTCAAACATCCA
1 AAAATTACCATTTTACCCTCAAACTTCCA
** * *
12205232 AAAATT-TTATTTTTGACCC-CATACTATCCT
1 AAAATTACCA-TTTT-ACCCTCAAACT-TCCA
*
12205262 AAAATTACCATTTTACCCTTAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCA
*
12205291 AAAATT-CCA-TTT--CCT-AAACTTTCCC
1 AAAATTACCATTTTACCCTCAAAC-TTCCA
* *
12205316 AAAACTACCATTTTAACCC-CGAA-TGTCCA
1 AAAATTACCATTTT-ACCCTCAAACT-TCCA
* **
12205345 AAAATT-CCATTTTTAACCTTGAACTTCCTA
1 AAAATTACCA-TTTTACCCTCAAACTTCC-A
*
12205375 AAAATTACCATTTTCCCCT
1 AAAATTACCATTTTACCCT
12205394 GGTATCGAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 35
0.70 0.11 0.20
Matches are distributed among these distances:
24 4 0.03
25 12 0.10
26 3 0.02
27 6 0.05
28 11 0.09
29 45 0.36
30 40 0.32
31 4 0.03
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCAAACTTCCA
Found at i:12205326 original size:26 final size:24
Alignment explanation
Indices: 12205281--12205328 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
12205271 ATTTTACCCT
*
12205281 TAAACTTCCAAAAATTCCATTTCC
1 TAAACTTCCAAAAATACCATTTCC
*
12205305 TAAACTTTCCCAAAACTACCATTT
1 TAAAC-TT-CCAAAAATACCATTT
12205329 TAACCCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 2 0.10
26 13 0.65
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAACTTCCAAAAATACCATTTCC
Found at i:12209162 original size:23 final size:23
Alignment explanation
Indices: 12209142--12209203 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
12209132 ATTACATACA
*
12209142 TGCATTTTTTCGCACT-GCATATT
1 TGCATATTTTCGCA-TAGCATATT
12209165 TGCATATTTTCGCATAGCATATT
1 TGCATATTTTCGCATAGCATATT
12209188 TGCATATTTTCGCATA
1 TGCATATTTTCGCATA
12209204 ATAATTCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (23 bp):
TGCATATTTTCGCATAGCATATT
Found at i:12215334 original size:209 final size:208
Alignment explanation
Indices: 12214961--12215623 Score: 871
Period size: 209 Copynumber: 3.2 Consensus size: 208
12214951 TATCCAAAAT
* * *
12214961 ATAAAGCAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCTGTCTTCCTGATGAGACA
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
* * *
12215026 TAGAGAAGTAGATCAAAGCAAGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAA
66 CAGAGAAGTAGATCAAA-CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* ** * *
12215091 ATCAATAAAATCAGGCTCAAAGTGAG-AGAATCTTCGAACCCCAGCTTCCTAATGAGATATTGAG
130 ATCAATGAAGCCAAGCTCAAAGTGAGCA-AATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
*
12215155 AAGCAGGTCGAAGAA
194 AAGCAGGTCGAAGCA
* * *
12215170 ATAAAGCAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTTTAATGAGACA
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
* * * *
12215235 CAGAGAAGTGGATCAAACTAAGCGAAGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGGCCAA
66 CAGAGAAGTAGATCAAAC-AAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* * * *
12215300 ATCAATGAAGCCAAGCTCAAAATGAGCAAATCTTCGAACCTCAACTTCTTGATGAGATATTGAGA
130 ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
12215365 AGCAGGTCGAAGCA
195 AGCAGGTCGAAGCA
** * * * * * * *
12215379 ATAAAATGGTTAGCTTCCAGATGAGATACTA-AGAAGTGGACCAAATTCGCCTTTCTGATGAGAT
1 ATAAAACAGTTACCTTCCTGATGAGATAC-AGAGAAGTGAACCAGATCCGTCTTTCTGATGAGAC
* * * **
12215443 ACAGAGAAGCAGATTGAAACAAGTGATGTTGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCA
65 ACAGAGAAGTAGA-TCAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCA
* *
12215508 AATCAATGAAGCCAAGCTCAAAGTAAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
129 AATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
*
12215573 AAGCAGGTTGAAGCA
194 AAGCAGGTCGAAGCA
** * *
12215588 ATAAAATGGTTATCTTCCTGATGAGATACTGAGAAG
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAG
12215624 CGGATTGAAA
Statistics
Matches: 397, Mismatches: 52, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
208 1 0.00
209 389 0.98
210 7 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (208 bp):
ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
CAGAGAAGTAGATCAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAA
TCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAA
GCAGGTCGAAGCA
Found at i:12215663 original size:49 final size:49
Alignment explanation
Indices: 12215553--12215721 Score: 234
Period size: 49 Copynumber: 3.5 Consensus size: 49
12215543 CGAACCCCAG
* * * *** *
12215553 CTTCCTGATGAGATATTGAGAAGCAGG-TTGAAGCAA-TAAAATGGTTAT
1 CTTCCTGATGAGATACTGAGAAGC-GGATTGAAACAAGTGATGCGGTCAT
12215601 CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
1 CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
*
12215650 CTTCCTGATGAGATACTAAGAAGCGGATTGAAACAAGTGATGCGGTCAT
1 CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
*
12215699 CTTCCTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
12215722 TAGACCAAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
47 2 0.02
48 31 0.28
49 76 0.70
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (49 bp):
CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
Found at i:12216101 original size:6 final size:6
Alignment explanation
Indices: 12216037--12216084 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
12216027 CTAAACCCAT
** * *
12216037 TTTAAA TTTATT TTTAAA TTTAAA TTTAAA TTTATA TTTATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12216085 AATATTCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:12218063 original size:29 final size:29
Alignment explanation
Indices: 12218013--12218069 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
12218003 AAAGGTCCTT
*
12218013 AAACTATCCAAAAATCATATTTTGACCCA
1 AAACTATCCAAAAATCACATTTTGACCCA
* * *
12218042 AAACTTTCCAAAAGTTACATTTTGACCC
1 AAACTATCCAAAAATCACATTTTGACCC
12218070 CCAAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (29 bp):
AAACTATCCAAAAATCACATTTTGACCCA
Found at i:12218208 original size:59 final size:59
Alignment explanation
Indices: 12218097--12218542 Score: 451
Period size: 59 Copynumber: 7.6 Consensus size: 59
12218087 ACGAACTTCA
* * * *
12218097 CAAAATTACCATTTTACCC-CTAATTTCCAAAAATCCCATTTTTGACCCTAAACTTTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * * *
12218155 CAAAATTACCATTTTATCCTCAAATATCAAAAAATTTCATTTTTAACCCTAAAC-TTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * *** * ** *
12218213 TAAAAACTACCATTTTA-CCTTGGACGTCCAAAAATTCTGTTTTTAACCCCAAACTTTCC
1 -CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * *
12218272 CAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACTCTAAAC-TTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* *
12218330 CAAAAATTACCATTTTATCCAT-AAACT-TCCAAAAATTCCATTTTTAACCCTGAACTTTCC
1 C-AAAATTACCATTTTA-CCCTCAAA-TGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * ** * * *
12218390 CAAAATCACCATTTTACCCCCAAACATCAAAAAATTCCATTTTT-ACCCCAAATTTTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * * *
12218448 TAAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCTATTTTTAA-CCTCGAACTTTTC
1 CAAAATTACCATTTTACCCTCAAA-TGTCCAAAAATTCCATTTTTAACCCT-AAACTTTCC
* * *
12218507 CAAAATTACCAATTTACCCCCGAATGTCCAAAAATT
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATT
12218543 TAATTTTTGA
Statistics
Matches: 318, Mismatches: 56, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
58 121 0.38
59 188 0.59
60 9 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
Found at i:12218313 original size:117 final size:118
Alignment explanation
Indices: 12218098--12218580 Score: 528
Period size: 117 Copynumber: 4.1 Consensus size: 118
12218088 CGAACTTCAC
* * * * * *
12218098 AAAATTACCATTTTACCC-CTAATTTCCAAAAATCCCATTTTTGACCCTAAACTTTCCCAAAATT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
* * * *
12218162 ACCATTTTATCCTCAAATATCAAAAAATTTCATTTTTAACCCTAAACTTCCTA
66 ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAACTTCCTA
* *** * *
12218215 AAAACTACCATTTTA-CCTTGGACGTCCAAAAATTCTGTTTTTAACCCCAAACTTTCCCAAAATT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
* * * * * *
12218279 ACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACTCTAAACTTCCCA
66 ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAACTTCCTA
* * **
12218332 AAAATTACCATTTTATCCAT-AAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCCAAAAT
1 AAAATTACCATTTTA-CCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAAT
* * * *
12218396 CACCATTTTACCCCCAAACATCAAAAAATTCCATTTTT-ACCCCAAATTTTCCT-
65 TACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAA-CTTCCTA
* * *
12218449 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCTCGAACTTTTCCAAAATT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
* * * * ** *
12218514 ACCAATTTACCCCCGAATGTCCAAAAATTTAATTTTTGA-CCTCGAACTTCCTA
66 ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCT-AAACTTCCTA
*
12218567 AAGATTACCATTTT
1 AAAATTACCATTTT
12218581 TCCTCGGGCA
Statistics
Matches: 303, Mismatches: 55, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
116 5 0.02
117 207 0.68
118 89 0.29
119 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (118 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAACTTCCTA
Found at i:12218497 original size:29 final size:29
Alignment explanation
Indices: 12218121--12218581 Score: 202
Period size: 29 Copynumber: 15.7 Consensus size: 29
12218111 TACCCCTAAT
* *
12218121 TTCCAAAAATCCCATTTTTGACC-CTAAAC
1 TTCCAAAAATTCCATTTTTAACCTC-AAAC
* *
12218150 TTTCCCAAAATTACCA-TTTTATCCTCAAA-
1 -TTCCAAAAATT-CCATTTTTAACCTCAAAC
* *
12218179 TATCAAAAAATTTCATTTTTAACC-CTAAAC
1 T-TCCAAAAATTCCATTTTTAACCTC-AAAC
* ***
12218209 TTCCTAAAAACTACCA-TTTT-ACCTTGGAC
1 TTCC-AAAAA-TTCCATTTTTAACCTCAAAC
* ** *
12218238 GTCCAAAAATTCTGTTTTTAACCCCAAAC
1 TTCCAAAAATTCCATTTTTAACCTCAAAC
* * *
12218267 TTTCCCAAAATTACCA-TTTTACCCTCGAA-
1 -TTCCAAAAATT-CCATTTTTAACCTCAAAC
*
12218296 TGTCCAAAAATTCCATTTTTGA-CTCTAAAC
1 T-TCCAAAAATTCCATTTTTAACCTC-AAAC
*
12218326 TTCCCAAAAATTACCA-TTTTATCCAT-AAAC
1 TT-CCAAAAATT-CCATTTTTAACC-TCAAAC
*
12218356 TTCCAAAAATTCCATTTTTAACC-CTGAAC
1 TTCCAAAAATTCCATTTTTAACCTC-AAAC
* * * *
12218385 TTTCCCAAAATCACCA-TTTTACCCCCAAAC
1 -TTCCAAAAAT-TCCATTTTTAACCTCAAAC
* * * *
12218415 ATCAAAAAATTCCATTTTT-ACCCCAAATT
1 TTCCAAAAATTCCATTTTTAACCTCAAA-C
* *
12218444 TTCCTAAAATTACCA-TTTTACCCTCAAAC
1 TTCCAAAAATT-CCATTTTTAACCTCAAAC
* *
12218473 TTCCAAAAATTCTATTTTTAACCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCAAAC
* * * *
12218502 TTTTCC-AAAATTACCA-ATTTACCCCCGAA-
1 --TTCCAAAAATT-CCATTTTTAACCTCAAAC
** * *
12218531 TGTCCAAAAATTTAATTTTTGACCTCGAAC
1 T-TCCAAAAATTCCATTTTTAACCTCAAAC
*
12218561 TTCCTAAAGATTACCATTTTT
1 TTCC-AAAAATT-CCATTTTT
12218582 CCTCGGGCAT
Statistics
Matches: 320, Mismatches: 70, Indels: 81
0.68 0.15 0.17
Matches are distributed among these distances:
27 3 0.01
28 39 0.12
29 131 0.41
30 118 0.37
31 28 0.09
32 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTAACCTCAAAC
Found at i:12218579 original size:176 final size:174
Alignment explanation
Indices: 12218097--12218580 Score: 532
Period size: 176 Copynumber: 2.8 Consensus size: 174
12218087 ACGAACTTCA
* *
12218097 CAAAATTACCATTTTACCC-CTAATTTCCAAAAATCCCATTTTTGACC-CTAAACTTTCCCAAAA
1 CAAAATTACCATTTTACCCTC-AAATTCCAAAAATTCCATTTTTGACCTCTAAACTTTCCCAAAA
* * * *
12218160 TTACCATTTTATCCTCAAATATCAAAAAATTTCATTTTTAACCCTAAACTTCCTAAAAACTACCA
65 TTACCATTTTATCCACAAAT-TCCAAAAATTTCATTTTTAACCCTGAACTTCCT-AAAATTACCA
**** * * **
12218225 TTTTACCTTGGACGTCCAAAAATTCTGTTTTTAACCCCAAACTTTCC
128 TTTTACCCCAAACATCAAAAAATTCCATTTTTAACCCCAAACTTTCC
*
12218272 CAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA-CTCTAAAC-TTCCCAAAA
1 CAAAATTACCATTTTACCCTCAAAT-TCCAAAAATTCCATTTTTGACCTCTAAACTTTCCC-AAA
* * * *
12218335 ATTACCATTTTATCCATAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCCAAAATCACC
64 ATTACCATTTTATCCACAAA-TTCCAAAAATTTCATTTTTAACCCTGAAC-TTCCTAAAATTACC
*
12218400 ATTTTACCCCCAAACATCAAAAAATTCCATTTTT-ACCCCAAATTTTCC
127 ATTTTA-CCCCAAACATCAAAAAATTCCATTTTTAACCCCAAACTTTCC
* * * * *
12218448 TAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCTC-GAACTTTTCCAAAA
1 CAAAATTACCATTTTACCCTCAAA-TTCCAAAAATTCCATTTTTGACCTCTAAACTTTCCCAAAA
* * * * * *
12218512 TTACCAATTTACCCCCGAATGTCCAAAAATTTAATTTTTGA-CCTCGAACTTCCTAAAGATTACC
65 TTACCATTTTATCCACAAAT-TCCAAAAATTTCATTTTTAACCCT-GAACTTCCTAAA-ATTACC
12218576 ATTTT
127 ATTTT
12218581 TCCTCGGGCA
Statistics
Matches: 260, Mismatches: 36, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
175 38 0.15
176 190 0.73
177 32 0.12
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (174 bp):
CAAAATTACCATTTTACCCTCAAATTCCAAAAATTCCATTTTTGACCTCTAAACTTTCCCAAAAT
TACCATTTTATCCACAAATTCCAAAAATTTCATTTTTAACCCTGAACTTCCTAAAATTACCATTT
TACCCCAAACATCAAAAAATTCCATTTTTAACCCCAAACTTTCC
Found at i:12232031 original size:209 final size:208
Alignment explanation
Indices: 12231658--12232320 Score: 871
Period size: 209 Copynumber: 3.2 Consensus size: 208
12231648 TATCCAAAAT
* * *
12231658 ATAAAGCAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCTGTCTTCCTGATGAGACA
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
* * *
12231723 TAGAGAAGTAGATCAAAGCAAGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAA
66 CAGAGAAGTAGATCAAA-CAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* ** * *
12231788 ATCAATAAAATCAGGCTCAAAGTGAG-AGAATCTTCGAACCCCAGCTTCCTAATGAGATATTGAG
130 ATCAATGAAGCCAAGCTCAAAGTGAGCA-AATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
*
12231852 AAGCAGGTCGAAGAA
194 AAGCAGGTCGAAGCA
* * *
12231867 ATAAAGCAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTTTAATGAGACA
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
* * * *
12231932 CAGAGAAGTGGATCAAACTAAGCGAAGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGGCCAA
66 CAGAGAAGTAGATCAAAC-AAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
* * * *
12231997 ATCAATGAAGCCAAGCTCAAAATGAGCAAATCTTCGAACCTCAACTTCTTGATGAGATATTGAGA
130 ATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGA
12232062 AGCAGGTCGAAGCA
195 AGCAGGTCGAAGCA
** * * * * * * *
12232076 ATAAAATGGTTAGCTTCCAGATGAGATACTA-AGAAGTGGACCAAATTCGCCTTTCTGATGAGAT
1 ATAAAACAGTTACCTTCCTGATGAGATAC-AGAGAAGTGAACCAGATCCGTCTTTCTGATGAGAC
* * * **
12232140 ACAGAGAAGCAGATTGAAACAAGTGATGTTGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCA
65 ACAGAGAAGTAGA-TCAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCA
* *
12232205 AATCAATGAAGCCAAGCTCAAAGTAAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
129 AATCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
*
12232270 AAGCAGGTTGAAGCA
194 AAGCAGGTCGAAGCA
** * *
12232285 ATAAAATGGTTATCTTCCTGATGAGATACTGAGAAG
1 ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAG
12232321 CGGATTGAAA
Statistics
Matches: 397, Mismatches: 52, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
208 1 0.00
209 389 0.98
210 7 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (208 bp):
ATAAAACAGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGACA
CAGAGAAGTAGATCAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAA
TCAATGAAGCCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAA
GCAGGTCGAAGCA
Found at i:12232360 original size:49 final size:49
Alignment explanation
Indices: 12232250--12232418 Score: 234
Period size: 49 Copynumber: 3.5 Consensus size: 49
12232240 CGAACCCCAG
* * * *** *
12232250 CTTCCTGATGAGATATTGAGAAGCAGG-TTGAAGCAA-TAAAATGGTTAT
1 CTTCCTGATGAGATACTGAGAAGC-GGATTGAAACAAGTGATGCGGTCAT
12232298 CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
1 CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
*
12232347 CTTCCTGATGAGATACTAAGAAGCGGATTGAAACAAGTGATGCGGTCAT
1 CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
*
12232396 CTTCCTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
12232419 TAGACCAAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
47 2 0.02
48 31 0.28
49 76 0.70
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (49 bp):
CTTCCTGATGAGATACTGAGAAGCGGATTGAAACAAGTGATGCGGTCAT
Found at i:12232798 original size:6 final size:6
Alignment explanation
Indices: 12232734--12232781 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
12232724 CTAAACCCAT
** * *
12232734 TTTAAA TTTATT TTTAAA TTTAAA TTTAAA TTTATA TTTATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12232782 AATATTCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:12234760 original size:29 final size:29
Alignment explanation
Indices: 12234710--12234766 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
12234700 AAAGGTCCTT
*
12234710 AAACTATCCAAAAATCATATTTTGACCCA
1 AAACTATCCAAAAATCACATTTTGACCCA
* * *
12234739 AAACTTTCCAAAAGTTACATTTTGACCC
1 AAACTATCCAAAAATCACATTTTGACCC
12234767 CCAAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (29 bp):
AAACTATCCAAAAATCACATTTTGACCCA
Found at i:12234905 original size:59 final size:59
Alignment explanation
Indices: 12234794--12235239 Score: 451
Period size: 59 Copynumber: 7.6 Consensus size: 59
12234784 ACGAACTTCA
* * * *
12234794 CAAAATTACCATTTTACCC-CTAATTTCCAAAAATCCCATTTTTGACCCTAAACTTTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * * *
12234852 CAAAATTACCATTTTATCCTCAAATATCAAAAAATTTCATTTTTAACCCTAAAC-TTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * *** * ** *
12234910 TAAAAACTACCATTTTA-CCTTGGACGTCCAAAAATTCTGTTTTTAACCCCAAACTTTCC
1 -CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * *
12234969 CAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACTCTAAAC-TTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* *
12235027 CAAAAATTACCATTTTATCCAT-AAACT-TCCAAAAATTCCATTTTTAACCCTGAACTTTCC
1 C-AAAATTACCATTTTA-CCCTCAAA-TGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * ** * * *
12235087 CAAAATCACCATTTTACCCCCAAACATCAAAAAATTCCATTTTT-ACCCCAAATTTTCC
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
* * * *
12235145 TAAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCTATTTTTAA-CCTCGAACTTTTC
1 CAAAATTACCATTTTACCCTCAAA-TGTCCAAAAATTCCATTTTTAACCCT-AAACTTTCC
* * *
12235204 CAAAATTACCAATTTACCCCCGAATGTCCAAAAATT
1 CAAAATTACCATTTTACCCTCAAATGTCCAAAAATT
12235240 TAATTTTTGA
Statistics
Matches: 318, Mismatches: 56, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
58 121 0.38
59 188 0.59
60 9 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCCATTTTTAACCCTAAACTTTCC
Found at i:12235010 original size:117 final size:118
Alignment explanation
Indices: 12234795--12235277 Score: 528
Period size: 117 Copynumber: 4.1 Consensus size: 118
12234785 CGAACTTCAC
* * * * * *
12234795 AAAATTACCATTTTACCC-CTAATTTCCAAAAATCCCATTTTTGACCCTAAACTTTCCCAAAATT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
* * * *
12234859 ACCATTTTATCCTCAAATATCAAAAAATTTCATTTTTAACCCTAAACTTCCTA
66 ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAACTTCCTA
* *** * *
12234912 AAAACTACCATTTTA-CCTTGGACGTCCAAAAATTCTGTTTTTAACCCCAAACTTTCCCAAAATT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
* * * * * *
12234976 ACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGACTCTAAACTTCCCA
66 ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAACTTCCTA
* * **
12235029 AAAATTACCATTTTATCCAT-AAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCCAAAAT
1 AAAATTACCATTTTA-CCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAAT
* * * *
12235093 CACCATTTTACCCCCAAACATCAAAAAATTCCATTTTT-ACCCCAAATTTTCCT-
65 TACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAA-CTTCCTA
* * *
12235146 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCTCGAACTTTTCCAAAATT
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
* * * * ** *
12235211 ACCAATTTACCCCCGAATGTCCAAAAATTTAATTTTTGA-CCTCGAACTTCCTA
66 ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCT-AAACTTCCTA
*
12235264 AAGATTACCATTTT
1 AAAATTACCATTTT
12235278 TCCTCGGGCA
Statistics
Matches: 303, Mismatches: 55, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
116 5 0.02
117 207 0.68
118 89 0.29
119 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (118 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATT
ACCATTTTACCCCCAAATATCAAAAAATTCCATTTTTGACCCTAAACTTCCTA
Found at i:12235194 original size:29 final size:29
Alignment explanation
Indices: 12234818--12235278 Score: 202
Period size: 29 Copynumber: 15.7 Consensus size: 29
12234808 TACCCCTAAT
* *
12234818 TTCCAAAAATCCCATTTTTGACC-CTAAAC
1 TTCCAAAAATTCCATTTTTAACCTC-AAAC
* *
12234847 TTTCCCAAAATTACCA-TTTTATCCTCAAA-
1 -TTCCAAAAATT-CCATTTTTAACCTCAAAC
* *
12234876 TATCAAAAAATTTCATTTTTAACC-CTAAAC
1 T-TCCAAAAATTCCATTTTTAACCTC-AAAC
* ***
12234906 TTCCTAAAAACTACCA-TTTT-ACCTTGGAC
1 TTCC-AAAAA-TTCCATTTTTAACCTCAAAC
* ** *
12234935 GTCCAAAAATTCTGTTTTTAACCCCAAAC
1 TTCCAAAAATTCCATTTTTAACCTCAAAC
* * *
12234964 TTTCCCAAAATTACCA-TTTTACCCTCGAA-
1 -TTCCAAAAATT-CCATTTTTAACCTCAAAC
*
12234993 TGTCCAAAAATTCCATTTTTGA-CTCTAAAC
1 T-TCCAAAAATTCCATTTTTAACCTC-AAAC
*
12235023 TTCCCAAAAATTACCA-TTTTATCCAT-AAAC
1 TT-CCAAAAATT-CCATTTTTAACC-TCAAAC
*
12235053 TTCCAAAAATTCCATTTTTAACC-CTGAAC
1 TTCCAAAAATTCCATTTTTAACCTC-AAAC
* * * *
12235082 TTTCCCAAAATCACCA-TTTTACCCCCAAAC
1 -TTCCAAAAAT-TCCATTTTTAACCTCAAAC
* * * *
12235112 ATCAAAAAATTCCATTTTT-ACCCCAAATT
1 TTCCAAAAATTCCATTTTTAACCTCAAA-C
* *
12235141 TTCCTAAAATTACCA-TTTTACCCTCAAAC
1 TTCCAAAAATT-CCATTTTTAACCTCAAAC
* *
12235170 TTCCAAAAATTCTATTTTTAACCTCGAAC
1 TTCCAAAAATTCCATTTTTAACCTCAAAC
* * * *
12235199 TTTTCC-AAAATTACCA-ATTTACCCCCGAA-
1 --TTCCAAAAATT-CCATTTTTAACCTCAAAC
** * *
12235228 TGTCCAAAAATTTAATTTTTGACCTCGAAC
1 T-TCCAAAAATTCCATTTTTAACCTCAAAC
*
12235258 TTCCTAAAGATTACCATTTTT
1 TTCC-AAAAATT-CCATTTTT
12235279 CCTCGGGCAT
Statistics
Matches: 320, Mismatches: 70, Indels: 81
0.68 0.15 0.17
Matches are distributed among these distances:
27 3 0.01
28 39 0.12
29 131 0.41
30 118 0.37
31 28 0.09
32 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTAACCTCAAAC
Found at i:12235276 original size:176 final size:174
Alignment explanation
Indices: 12234794--12235277 Score: 532
Period size: 176 Copynumber: 2.8 Consensus size: 174
12234784 ACGAACTTCA
* *
12234794 CAAAATTACCATTTTACCC-CTAATTTCCAAAAATCCCATTTTTGACC-CTAAACTTTCCCAAAA
1 CAAAATTACCATTTTACCCTC-AAATTCCAAAAATTCCATTTTTGACCTCTAAACTTTCCCAAAA
* * * *
12234857 TTACCATTTTATCCTCAAATATCAAAAAATTTCATTTTTAACCCTAAACTTCCTAAAAACTACCA
65 TTACCATTTTATCCACAAAT-TCCAAAAATTTCATTTTTAACCCTGAACTTCCT-AAAATTACCA
**** * * **
12234922 TTTTACCTTGGACGTCCAAAAATTCTGTTTTTAACCCCAAACTTTCC
128 TTTTACCCCAAACATCAAAAAATTCCATTTTTAACCCCAAACTTTCC
*
12234969 CAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTGA-CTCTAAAC-TTCCCAAAA
1 CAAAATTACCATTTTACCCTCAAAT-TCCAAAAATTCCATTTTTGACCTCTAAACTTTCCC-AAA
* * * *
12235032 ATTACCATTTTATCCATAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCCAAAATCACC
64 ATTACCATTTTATCCACAAA-TTCCAAAAATTTCATTTTTAACCCTGAAC-TTCCTAAAATTACC
*
12235097 ATTTTACCCCCAAACATCAAAAAATTCCATTTTT-ACCCCAAATTTTCC
127 ATTTTA-CCCCAAACATCAAAAAATTCCATTTTTAACCCCAAACTTTCC
* * * * *
12235145 TAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAACCTC-GAACTTTTCCAAAA
1 CAAAATTACCATTTTACCCTCAAA-TTCCAAAAATTCCATTTTTGACCTCTAAACTTTCCCAAAA
* * * * * *
12235209 TTACCAATTTACCCCCGAATGTCCAAAAATTTAATTTTTGA-CCTCGAACTTCCTAAAGATTACC
65 TTACCATTTTATCCACAAAT-TCCAAAAATTTCATTTTTAACCCT-GAACTTCCTAAA-ATTACC
12235273 ATTTT
127 ATTTT
12235278 TCCTCGGGCA
Statistics
Matches: 260, Mismatches: 36, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
175 38 0.15
176 190 0.73
177 32 0.12
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (174 bp):
CAAAATTACCATTTTACCCTCAAATTCCAAAAATTCCATTTTTGACCTCTAAACTTTCCCAAAAT
TACCATTTTATCCACAAATTCCAAAAATTTCATTTTTAACCCTGAACTTCCTAAAATTACCATTT
TACCCCAAACATCAAAAAATTCCATTTTTAACCCCAAACTTTCC
Found at i:12240568 original size:258 final size:258
Alignment explanation
Indices: 12240099--12240617 Score: 876
Period size: 258 Copynumber: 2.0 Consensus size: 258
12240089 AAACTTTTCC
* *
12240099 CAACGCAAAAAGTTCGCTGCAACACTTGTTAGAGAAACTCCCTGTCTCGAAAATACTCGTGAAAG
1 CAACGCAAAAAGTTCGCTGCAACACTTCTTAGAGAAACTCCCTGTCTCAAAAATACTCGTGAAAG
*
12240164 TTTCTTGAACACAGGGCCAACCCATTTTAGTTTCATAATTATTTTCCTTAATAATCTGGTAGTTC
66 TTTCTTGAACACAGGGCCAACCCATTTTAGTTTCACAATTATTTTCCTTAATAATCTGGTAGTTC
*
12240229 TCCTTCGTAGCCATTACTACCACGCAAGTTAAGAATTAAACCACTAGGACGGAATAAACATTAAG
131 TCCTTCGTAGCCATTACTACCACGCAAGTTAAGAATAAAACCACTAGGACGGAATAAACATTAAG
* * * *
12240294 GCTTGCCATATTGTGTGAATTTGATGTTTCTACTTGAATTTTGTTCGTAAATTTAATTTCGAA
196 GCCTGCCATATTGTGTGAATTTGATGTTTCTACTTGAATTTGGTTCATAAAATTAATTTCGAA
* * *
12240357 CAACGCAACAAGTTCGCTGCAACACTTCTTAGAGATACTTCCTGTCTCAAAAATACTCGTGAAAG
1 CAACGCAAAAAGTTCGCTGCAACACTTCTTAGAGAAACTCCCTGTCTCAAAAATACTCGTGAAAG
* *
12240422 TTTCTTGAACACAGGGCCAACCCATTTTATTTTCACAATTATTTTCCTTAATAATCTGGTCGTTC
66 TTTCTTGAACACAGGGCCAACCCATTTTAGTTTCACAATTATTTTCCTTAATAATCTGGTAGTTC
* * *
12240487 TCCTTCGTAGCCATTACTGCCAGGCAAGTTACGAATAAAACCACTAGGACGGAATAAACATTAAG
131 TCCTTCGTAGCCATTACTACCACGCAAGTTAAGAATAAAACCACTAGGACGGAATAAACATTAAG
* *
12240552 GCCTGCCATGTTGTGTGAATTTGATGTTTCTACTTGAATTTGGTTCATAAAATTAATTTGGAA
196 GCCTGCCATATTGTGTGAATTTGATGTTTCTACTTGAATTTGGTTCATAAAATTAATTTCGAA
12240615 CAA
1 CAA
12240618 TATTAGAAGG
Statistics
Matches: 243, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
258 243 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (258 bp):
CAACGCAAAAAGTTCGCTGCAACACTTCTTAGAGAAACTCCCTGTCTCAAAAATACTCGTGAAAG
TTTCTTGAACACAGGGCCAACCCATTTTAGTTTCACAATTATTTTCCTTAATAATCTGGTAGTTC
TCCTTCGTAGCCATTACTACCACGCAAGTTAAGAATAAAACCACTAGGACGGAATAAACATTAAG
GCCTGCCATATTGTGTGAATTTGATGTTTCTACTTGAATTTGGTTCATAAAATTAATTTCGAA
Found at i:12275358 original size:29 final size:29
Alignment explanation
Indices: 12275326--12275391 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
12275316 AAAATGAGAC
12275326 TTTTTGGA-TACCCGAGGATAAAATGGTAA
1 TTTTTGGACT-CCCGAGGATAAAATGGTAA
* * * *
12275355 TTTTGGGACTCTCGGGGGTAAAATGGTAA
1 TTTTTGGACTCCCGAGGATAAAATGGTAA
12275384 TTTTTGGA
1 TTTTTGGA
12275392 AAAATCGGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.29, T:0.35
Consensus pattern (29 bp):
TTTTTGGACTCCCGAGGATAAAATGGTAA
Found at i:12275400 original size:30 final size:29
Alignment explanation
Indices: 12275344--12275400 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
12275334 TACCCGAGGA
* ***
12275344 TAAAATGGTAATTTTGGGACTCTCGGGGG
1 TAAAATGGTAATTTTGGAAAAATCGGGGG
12275373 TAAAATGGTAATTTTTGGAAAAATCGGG
1 TAAAATGGTAA-TTTTGGAAAAATCGGG
12275401 ATCAAAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 11 0.48
30 12 0.52
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (29 bp):
TAAAATGGTAATTTTGGAAAAATCGGGGG
Found at i:12275416 original size:59 final size:59
Alignment explanation
Indices: 12275353--12275509 Score: 167
Period size: 59 Copynumber: 2.7 Consensus size: 59
12275343 ATAAAATGGT
12275353 AATTTTGGGACTCTCGGGGGTAAAATGGTAATTTTTGGAAA-AATCGGGATCAAAAACAG
1 AATTTTGGGACT-TCGGGGGTAAAATGGTAATTTTTGGAAAGAATCGGGATCAAAAACAG
* * * ** * **
12275412 AATTTTTGGACATTCGGGAGTAAAACGGTAATTTTT-GAAAGTTTCGGGGTCAAAAATGG
1 AATTTTGGGAC-TTCGGGGGTAAAATGGTAATTTTTGGAAAGAATCGGGATCAAAAACAG
* * *
12275471 AATTTTGGAAGTTTGGGGGTAAAAAT-GTAATTTTTGGAA
1 AATTTTGGGACTTCGGGGGT-AAAATGGTAATTTTTGGAA
12275510 GTTTTAGGGT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
58 20 0.25
59 59 0.74
60 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (59 bp):
AATTTTGGGACTTCGGGGGTAAAATGGTAATTTTTGGAAAGAATCGGGATCAAAAACAG
Found at i:12275444 original size:29 final size:29
Alignment explanation
Indices: 12275344--12275448 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 29
12275334 TACCCGAGGA
* * *
12275344 TAAAATGGTAATTTTGGGAC-TCTCGGGGG
1 TAAAACGGTAATTTTTGGACAT-TCGGGAG
* * *
12275373 TAAAATGGTAATTTTTGGAAAAATCGGGA-
1 TAAAACGGTAATTTTTGG-ACATTCGGGAG
*
12275402 TCAAAAACAG-AATTTTTGGACATTCGGGAG
1 T--AAAACGGTAATTTTTGGACATTCGGGAG
12275432 TAAAACGGTAATTTTTG
1 TAAAACGGTAATTTTTG
12275449 AAAGTTTCGG
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.10
29 34 0.56
30 16 0.26
31 5 0.08
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (29 bp):
TAAAACGGTAATTTTTGGACATTCGGGAG
Found at i:12275505 original size:58 final size:56
Alignment explanation
Indices: 12275345--12275569 Score: 177
Period size: 58 Copynumber: 3.9 Consensus size: 56
12275335 ACCCGAGGAT
* ** *
12275345 AAAATGGTAATTTTGGGACTCTCGGGGGTAAAATGGTAATTTTTGGAAA-AATCGGGATCA
1 AAAATGG-AATTTT-GGAAT-TCGGGGGTAAAAT-GTAATTTTT-GAAAGTTTCGGGGTCA
** * *
12275405 AAAACAGAATTTTTGGACATTCGGGAGTAAAACGGTAATTTTTGAAAGTTTCGGGGTCA
1 AAAATGGAA-TTTTGGA-ATTCGGGGGTAAAA-TGTAATTTTTGAAAGTTTCGGGGTCA
* * **
12275464 AAAATGGAATTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTC-
1 AAAATGGAATTTTGGAA-TTCGGGGGT-AAAATGTAATTTTTGAAAGTTTCGGGGTCA
* * * *
12275521 AAAATGGAATATTTGAAATTTTGGGGG-CAAATGTAATTTTTGGAAGTTT
1 AAAATGGAAT-TTTGGAA-TTCGGGGGTAAAATGTAATTTTTGAAAGTTT
12275570 GAGGGTACAA
Statistics
Matches: 139, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
56 21 0.15
57 11 0.08
58 53 0.38
59 44 0.32
60 10 0.07
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (56 bp):
AAAATGGAATTTTGGAATTCGGGGGTAAAATGTAATTTTTGAAAGTTTCGGGGTCA
Found at i:12275596 original size:29 final size:29
Alignment explanation
Indices: 12275439--12275603 Score: 142
Period size: 29 Copynumber: 5.8 Consensus size: 29
12275429 GAGTAAAACG
*
12275439 GTAATTTTTGAAAGTTTCG-GGGTCAAAAAT
1 GTAATTTTTGAAAGTTT-GAGGGT-ACAAAT
* * * *
12275469 GGAA-TTTTGGAAGTTTGGGGGTAAAAAT
1 GTAATTTTTGAAAGTTTGAGGGTACAAAT
* *
12275497 GTAATTTTTGGAAGTTTTAGGGT-CAAAAT
1 GTAATTTTTGAAAGTTTGAGGGTAC-AAAT
* * * *
12275526 GGAATATTTGAAATTTTG-GGG-GCAAAT
1 GTAATTTTTGAAAGTTTGAGGGTACAAAT
*
12275553 GTAATTTTTGGAAGTTTGAGGGTACAAAT
1 GTAATTTTTGAAAGTTTGAGGGTACAAAT
* *
12275582 GTAATTTTTCAAAGTTTTAGGG
1 GTAATTTTTGAAAGTTTGAGGG
12275604 CCAAAATATA
Statistics
Matches: 110, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
27 18 0.16
28 17 0.15
29 72 0.65
30 3 0.03
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.38
Consensus pattern (29 bp):
GTAATTTTTGAAAGTTTGAGGGTACAAAT
Found at i:12275610 original size:29 final size:28
Alignment explanation
Indices: 12275439--12275628 Score: 134
Period size: 29 Copynumber: 6.6 Consensus size: 28
12275429 GAGTAAAACG
**
12275439 GTAATTTTTGAAAGTTTCGGGGTCAAAAAT
1 GTAATTTTTGAAAGTTTTAGGG-C-AAAAT
* * ** *
12275469 GGAA-TTTTGGAAGTTTGGGGGTAAAAAT
1 GTAATTTTTGAAAGTTTTAGGG-CAAAAT
*
12275497 GTAATTTTTGGAAGTTTTAGGGTCAAAAT
1 GTAATTTTTGAAAGTTTTAGGG-CAAAAT
* * *
12275526 GGAATATTTGAAA-TTTTGGGGGC-AAAT
1 GTAATTTTTGAAAGTTTT-AGGGCAAAAT
* * *
12275553 GTAATTTTTGGAAGTTTGAGGGTACAAAT
1 GTAATTTTTGAAAGTTTTAGGGCA-AAAT
*
12275582 GTAATTTTTCAAAGTTTTAGGGCCAAAAT
1 GTAATTTTTGAAAGTTTTAGGG-CAAAAT
* *
12275611 ATAATTTCTTGACAGTTT
1 GTAATTT-TTGAAAGTTT
12275629 AAGGACCTTT
Statistics
Matches: 128, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
27 17 0.13
28 16 0.12
29 83 0.65
30 12 0.09
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (28 bp):
GTAATTTTTGAAAGTTTTAGGGCAAAAT
Found at i:12277315 original size:23 final size:24
Alignment explanation
Indices: 12277282--12277327 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12277272 CTTTTTTTTA
* *
12277282 AAATTTGAAAATTAATTTAAATTC
1 AAATTTGAAAATAAATCTAAATTC
12277306 AAATTT-AAAATAAATCTAAATT
1 AAATTTGAAAATAAATCTAAATT
12277328 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATTTGAAAATAAATCTAAATTC
Found at i:12277319 original size:17 final size:18
Alignment explanation
Indices: 12277299--12277342 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
12277289 AAAATTAATT
12277299 TAAATTC-AAATTTAAAA
1 TAAATTCTAAATTTAAAA
12277316 TAAA-TCTAAATTTAAAA
1 TAAATTCTAAATTTAAAA
12277333 TAAATT-TAAA
1 TAAATTCTAAA
12277343 AGGGCTCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTCTAAATTTAAAA
Found at i:12278309 original size:134 final size:133
Alignment explanation
Indices: 12278067--12278356 Score: 517
Period size: 134 Copynumber: 2.2 Consensus size: 133
12278057 ACTTGGTCTT
*
12278067 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTCTTTATACCTCATC
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTCTCTATACCTCATC
*
12278132 AGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTCCTTCGAC
66 AGGAAGACAAATTTGGTCCACTTCTCAGTATATCATCAAGAAGCTAACCATTTTATTCCTTCGAC
12278197 CAG
131 CAG
12278200 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAAT-CGCTTCTCTATACCTCAT
* * *
12278265 CAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCTAACCATTTTATTGCTTCGA
65 CAGGAAGACAAATTTGGTCCACTTCTCAGTATATCATCAAGAAGCTAACCATTTTATTCCTTCGA
*
12278330 CCTG
130 CCAG
12278334 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
12278357 TTAGGGTTCG
Statistics
Matches: 150, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
133 46 0.31
134 104 0.69
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.32
Consensus pattern (133 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCGCTTCTCTATACCTCATC
AGGAAGACAAATTTGGTCCACTTCTCAGTATATCATCAAGAAGCTAACCATTTTATTCCTTCGAC
CAG
Found at i:12278553 original size:201 final size:194
Alignment explanation
Indices: 12278200--12278628 Score: 615
Period size: 201 Copynumber: 2.2 Consensus size: 194
12278190 CTTCGACCAG
* *
12278200 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTATACCTCAT
*
12278265 CAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCTAACCATTTTATTACTTCGA
* * * * *
12278330 CCTGCTTCTCAGTATCTCATCAGGAAGTTAGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTT
131 CCTACCTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGATCTGCTCAC----A---TTGAGTT
12278395 GGTATA
189 GGTATA
* * * * * *
12278401 CTTCTCTGTATCTCATCATGAAGGTGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTATACCTCAT
* * *
12278466 CAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGC
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCTAACCATTTTATTACTTCGA
* * *
12278531 CCTACCTCTTAGTATGTCATCAGGAAGCTAGGGTTCAAAGATCTGTTCACATTGAGTTGGTATA
131 CCTACCTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGATCTGCTCACATTGAGTTGGTATA
12278595 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTC
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTC
12278629 TCTATTTGTG
Statistics
Matches: 205, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
194 44 0.21
197 1 0.00
201 160 0.78
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (194 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTATACCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCTAACCATTTTATTACTTCGA
CCTACCTCTCAGTATCTCATCAGGAAGCTAGGGTTCAAAGATCTGCTCACATTGAGTTGGTATA
Found at i:12279125 original size:49 final size:48
Alignment explanation
Indices: 12278985--12279125 Score: 131
Period size: 49 Copynumber: 2.9 Consensus size: 48
12278975 TCCCTTCAAA
* * * *
12278985 TCTTCGTGGTACTGGATCTACTGTCACAGCTTAGATCTTTCTCTTCCTG
1 TCTTCGTGGTACTGGATCCACCGTCACGGCTTAGATCTTTC-CTTCATG
* * * * * *
12279034 TCTTTGTAGTACTAGG-TCCATCATCGCGGCTTAGATATTTTCCTTCATG
1 TCTTCGTGGTACT-GGATCCACCGTCACGGCTTAGAT-CTTTCCTTCATG
* *
12279083 TCTTCGTGGTACTGGATCCGCCGTTACGGCTTTAGATCTTTCC
1 TCTTCGTGGTACTGGATCCACCGTCACGGC-TTAGATCTTTCC
12279126 CGTCGTGTCT
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
48 2 0.03
49 56 0.80
50 12 0.17
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.40
Consensus pattern (48 bp):
TCTTCGTGGTACTGGATCCACCGTCACGGCTTAGATCTTTCCTTCATG
Found at i:12285171 original size:29 final size:29
Alignment explanation
Indices: 12285139--12285200 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
12285129 AAAATGAGAC
12285139 TTTTTAGA-TACTC-GAGGGCAAAATGGTAA
1 TTTTTAGACT-CTCGGA-GGCAAAATGGTAA
* *
12285168 TTTTTGGACTCTCGGAGGTAAAATGGTAA
1 TTTTTAGACTCTCGGAGGCAAAATGGTAA
12285197 TTTT
1 TTTT
12285201 GGAAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (29 bp):
TTTTTAGACTCTCGGAGGCAAAATGGTAA
Found at i:12285382 original size:199 final size:200
Alignment explanation
Indices: 12285042--12285408 Score: 718
Period size: 199 Copynumber: 1.8 Consensus size: 200
12285032 ATGGTAAGCA
12285042 AAAATCAAAAATATAAAATACGAGTGCATAATAATTAAAGGTAAATGCTAATATTGATGAGGAAG
1 AAAATCAAAAATATAAAATACGAGTGCATAATAATTAAAGGTAAATGCTAATATTGATGAGGAAG
12285107 AAAAATGATGCAATCAGGGTTAAAAATGAGACTTTTTAGATACTCGAGGGCAAAATGGTAATTTT
66 AAAAATGATGCAATCAGGGTTAAAAATGAGACTTTTTAGATACTCGAGGGCAAAATGGTAATTTT
*
12285172 TGGACTCTCGGAGGTAAAATGGTAA-TTTTGGAAAAATTTTGGGGTTAAAAATGATATTTTAGAC
131 TGGACTCTCGGAGGTAAAATGGAAATTTTTGGAAAAATTTTGGGGTTAAAAATGATATTTTAGAC
12285236 ATTCG
196 ATTCG
12285241 AAAATCAAAAATATAAAATACGAGTGCATAATAATTAAAGGTAAATGCTAATATTGATGAGGAAG
1 AAAATCAAAAATATAAAATACGAGTGCATAATAATTAAAGGTAAATGCTAATATTGATGAGGAAG
12285306 AAAAATGATGCAATCAGGGTTAAAAATGAGACTTTTTAGATACTCGAGGGCAAAATGGTAATTTT
66 AAAAATGATGCAATCAGGGTTAAAAATGAGACTTTTTAGATACTCGAGGGCAAAATGGTAATTTT
12285371 TGGACTCTCGGAGGTAAAATGGAAATTTTTGGAAAAAT
131 TGGACTCTCGGAGGTAAAATGGAAATTTTTGGAAAAAT
12285409 CGGGATCAAA
Statistics
Matches: 166, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
199 154 0.93
200 12 0.07
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.29
Consensus pattern (200 bp):
AAAATCAAAAATATAAAATACGAGTGCATAATAATTAAAGGTAAATGCTAATATTGATGAGGAAG
AAAAATGATGCAATCAGGGTTAAAAATGAGACTTTTTAGATACTCGAGGGCAAAATGGTAATTTT
TGGACTCTCGGAGGTAAAATGGAAATTTTTGGAAAAATTTTGGGGTTAAAAATGATATTTTAGAC
ATTCG
Found at i:12285516 original size:29 final size:29
Alignment explanation
Indices: 12285467--12285550 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
12285457 TTTGAAAGTT
**
12285467 TCGA-GGTCAAAAATGGGATTTTTAGATTC
1 TCGAGGGT-AAAAATGTAATTTTTAGATTC
* *
12285496 TCGAGGGTAAAAATGTAATTTTTGGAATTT
1 TCGAGGGTAAAAATGTAATTTTTAG-ATTC
* * *
12285526 TAG-GGGCAAAAATGTAAATTTTAGA
1 TCGAGGGTAAAAATGTAATTTTTAGA
12285551 AGTTTCGATG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
28 1 0.02
29 36 0.80
30 8 0.18
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.35
Consensus pattern (29 bp):
TCGAGGGTAAAAATGTAATTTTTAGATTC
Found at i:12287446 original size:11 final size:11
Alignment explanation
Indices: 12287445--12287478 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12287435 AAAATAAATT
*
12287445 TAAATTTAAAT
1 TAAATTTAAAA
12287456 TCAAATTTAAAA
1 T-AAATTTAAAA
12287468 TAAATTTAAAA
1 TAAATTTAAAA
12287479 GGGCCCGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:12287450 original size:6 final size:6
Alignment explanation
Indices: 12287439--12287477 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
12287429 AATTTTAAAA
* *
12287439 TAAATT TAAATT TAAATT CAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
12287478 AGGGCCCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:12287451 original size:18 final size:18
Alignment explanation
Indices: 12287432--12287466 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12287422 TTTTTAAAAT
12287432 TTTAAAAT-AAATTTAAA
1 TTTAAAATCAAATTTAAA
*
12287449 TTTAAATTCAAATTTAAA
1 TTTAAAATCAAATTTAAA
12287467 ATAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAAATCAAATTTAAA
Found at i:12288601 original size:6 final size:6
Alignment explanation
Indices: 12288564--12288633 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
12288554 CTAAATCCAT
* * *
12288564 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTATA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12288610 TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TT-TAAA TTTAAA T
12288634 AAACAAAGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 34 0.69
7 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:12288605 original size:13 final size:12
Alignment explanation
Indices: 12288582--12288613 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
12288572 TATTTTAAGA
12288582 TTAAATTTAT-T
1 TTAAATTTATAT
12288593 TTAAATTTATAT
1 TTAAATTTATAT
12288605 TTAAATTTA
1 TTAAATTTA
12288614 AAATTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:12288606 original size:17 final size:18
Alignment explanation
Indices: 12288564--12288607 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12288554 CTAAATCCAT
12288564 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
12288582 -TTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
12288598 TTTATATTTA
1 TTTAAATTTA
12288608 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:12288615 original size:18 final size:17
Alignment explanation
Indices: 12288564--12288633 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
12288554 CTAAATCCAT
*
12288564 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTCTAA-A
*
12288582 -TTAAATTTATTTTAAA
1 TTTAAATTTATTCTAAA
12288598 TTT--A--TATT-TAAA
1 TTTAAATTTATTCTAAA
*
12288610 TTTAAAATTATTCTAAA
1 TTTAAATTTATTCTAAA
12288627 TTTAAAT
1 TTTAAAT
12288634 AAACAAAGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
12 7 0.16
13 4 0.09
14 1 0.02
15 1 0.02
16 5 0.11
17 27 0.60
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTCTAAA
Found at i:12288620 original size:29 final size:28
Alignment explanation
Indices: 12288562--12288630 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
12288552 AACTAAATCC
*
12288562 ATTTTAAATTTATTTTAAGATTAAATTT
1 ATTTTAAATTTATTTTAAGATTAAAATT
12288590 ATTTTAAATTTATATTTAA-ATTTAAAATT
1 ATTTTAAATTTAT-TTTAAGA-TTAAAATT
*
12288619 ATTCTAAATTTA
1 ATTTTAAATTTA
12288631 AATAAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
ATTTTAAATTTATTTTAAGATTAAAATT
Done.