Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 77 of 345
Found at i:21136342 original size:21 final size:19
Alignment explanation
Indices: 21136308--21136369 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
21136298 TAAGTTATAT
21136308 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
21136330 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
21136352 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
21136370 GTAATTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:21136419 original size:21 final size:22
Alignment explanation
Indices: 21136393--21136434 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
21136383 AAAATATAGT
*
21136393 AAAATAAATAGTATA-AAAAAC
1 AAAATAAATAATATATAAAAAC
21136414 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATATAAAAA
21136435 TATAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAATAATATATAAAAAC
Found at i:21136784 original size:14 final size:14
Alignment explanation
Indices: 21136754--21136818 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
21136744 CAATTTTATA
21136754 AAAATATAT-AAA-
1 AAAATATATAAAAT
*
21136766 GAAATATATAAAAT
1 AAAATATATAAAAT
*
21136780 AAAATATATAATAT
1 AAAATATATAAAAT
* * *
21136794 AATATAATTTATAGAT
1 AAAAT-ATATA-AAAT
21136810 AAAATATAT
1 AAAATATAT
21136819 GATAAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 8 0.20
13 3 0.07
14 16 0.39
15 7 0.17
16 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AAAATATATAAAAT
Found at i:21139824 original size:15 final size:15
Alignment explanation
Indices: 21139789--21139821 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21139779 GTTAGGATTA
21139789 TTAGG-TTATTCGGG
1 TTAGGTTTATTCGGG
21139803 TTAGGTTTATT-GGG
1 TTAGGTTTATTCGGG
21139817 TTAGG
1 TTAGG
21139822 GTTAGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.15, C:0.03, G:0.36, T:0.45
Consensus pattern (15 bp):
TTAGGTTTATTCGGG
Found at i:21140903 original size:2 final size:2
Alignment explanation
Indices: 21140896--21140943 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
21140886 CAATTGTTGC
21140896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21140938 AT AT AT
1 AT AT AT
21140944 TATGTTTTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21145928 original size:26 final size:26
Alignment explanation
Indices: 21145899--21145964 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
21145889 CAAATATCCG
*
21145899 AAAACCAACCCCAATGGCCCAAACTT
1 AAAACCAAACCCAATGGCCCAAACTT
21145925 AAAACCAAACCCAATGGCCCAAACTT
1 AAAACCAAACCCAATGGCCCAAACTT
*
21145951 AAACCCAAACCCAA
1 AAAACCAAACCCAA
21145965 AAGTCCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.47, C:0.38, G:0.06, T:0.09
Consensus pattern (26 bp):
AAAACCAAACCCAATGGCCCAAACTT
Found at i:21145972 original size:26 final size:26
Alignment explanation
Indices: 21145899--21145973 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
21145889 CAAATATCCG
* **
21145899 AAAACCAACCCCAATGGCCCAAACTT
1 AAAACCAAACCCAAAAGCCCAAACTT
**
21145925 AAAACCAAACCCAATGGCCCAAACTT
1 AAAACCAAACCCAAAAGCCCAAACTT
* *
21145951 AAACCCAAACCCAAAAGTCCAAA
1 AAAACCAAACCCAAAAGCCCAAA
21145974 TACATAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.48, C:0.36, G:0.07, T:0.09
Consensus pattern (26 bp):
AAAACCAAACCCAAAAGCCCAAACTT
Found at i:21148005 original size:27 final size:28
Alignment explanation
Indices: 21147968--21148106 Score: 175
Period size: 27 Copynumber: 5.2 Consensus size: 28
21147958 AGCATGGCTG
* *
21147968 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
21147994 CCAGATACAGATA-ATCGTGGCAG-GCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
21148021 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
21148048 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
21148075 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
21148102 CCAGA
1 CCAGA
21148107 ACGCTTCCTC
Statistics
Matches: 104, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
26 19 0.18
27 79 0.76
28 6 0.06
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:21149758 original size:26 final size:25
Alignment explanation
Indices: 21149720--21149803 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
21149710 CATGAAATTC
*
21149720 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCTA
21149746 TTATCATAGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
21149772 TTATCATGGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
21149798 TTATCA
1 TTATCA
21149804 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
26 54 0.98
27 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCTA
Found at i:21152157 original size:128 final size:129
Alignment explanation
Indices: 21151982--21152241 Score: 398
Period size: 128 Copynumber: 2.0 Consensus size: 129
21151972 ATAAATTCTT
*
21151982 TTAAACGAATACGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTAGGTTGCA
1 TTAAACGAATA-GAGATTTGATATTTGGCAATTCGCGGAATCATGCCCTAACGTGCTAGGTTGCA
* *
21152047 ATTTCGTGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTT-TTAAAATCC
65 ATTTCGTGTTTGCTCAAAATAATCAAATATCACTTCAAAATTTCACTCATGT-TTATTAAAAACC
21152111 C
129 C
* * * *
21152112 TTAAACGAAT-GTGATTTGATATTTGGCAATTCGTGGAATCATGCCCTAACGTGTTGGGTTGCAA
1 TTAAACGAATAGAGATTTGATATTTGGCAATTCGCGGAATCATGCCCTAACGTGCTAGGTTGCAA
* * *
21152176 TTTCTTGTTTGCTTAAAATAATCAAATATCCCTTCAAAATTTCACTCATGTTTATTAAAAACCC
66 TTTCGTGTTTGCTCAAAATAATCAAATATCACTTCAAAATTTCACTCATGTTTATTAAAAACCC
21152240 TT
1 TT
21152242 CAAAAAGAAG
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
127 2 0.02
128 107 0.90
130 10 0.08
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (129 bp):
TTAAACGAATAGAGATTTGATATTTGGCAATTCGCGGAATCATGCCCTAACGTGCTAGGTTGCAA
TTTCGTGTTTGCTCAAAATAATCAAATATCACTTCAAAATTTCACTCATGTTTATTAAAAACCC
Found at i:21164135 original size:131 final size:131
Alignment explanation
Indices: 21163924--21164310 Score: 533
Period size: 132 Copynumber: 2.9 Consensus size: 131
21163914 CGAATCCTAC
* * * *
21163924 AGATCTTGTTTCCCTAAAGTTACAGTGAAGCAGATCGAAGATGGTGAATCTTGTCTTCCTGAAGT
1 AGATCTTGTTCCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGTCTTCCTGAAGT
* * * *
21163989 TGTAGTGAAGCAGATTTAAACCACTACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTT
66 TGCAGTGAAGAAGATTTAAGCCACTACCTAGCTCCCTAAAGTTGTAGCGGAGTAGGCTGAAATTT
21164054 T
131 T
* * *
21164055 AGATCTTGTTCCCCTGAAGTTGCAGTGAAGTAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGT
1 AGATCTTGTTCCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGTCTTCCTGAAGT
* * *
21164120 TACAGTGAAGAAGATTTAAGCCACCAACCTAGCTTCCTAAAGTTGTAGCGGAGTAGGCTGAAATT
66 TGCAGTGAAGAAGATTTAAGCCA-CTACCTAGCTCCCTAAAGTTGTAGCGGAGTAGGCTGAAATT
21164185 TT
130 TT
* * * * * *
21164187 AGATCTTG-TCTCCTTGAGGTTGCAGTGGAGCAGATCAAAGACGGTGAATCTAGTCTTCCTGAAA
1 AGATCTTGTTC-CCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGTCTTCCTGAAG
* *
21164251 TTGCAGTGAAGCAAGATTCAAGCCACTATCCTAGCTCCCTAAGGTTGTAGCGGAGTAGGC
65 TTGCAGTGAAG-AAGATTTAAGCCACTA-CCTAGCTCCCTAAAGTTGTAGCGGAGTAGGC
21164311 CGAAGATTGC
Statistics
Matches: 224, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
131 79 0.35
132 104 0.46
133 41 0.18
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (131 bp):
AGATCTTGTTCCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGTCTTCCTGAAGT
TGCAGTGAAGAAGATTTAAGCCACTACCTAGCTCCCTAAAGTTGTAGCGGAGTAGGCTGAAATTT
T
Found at i:21164785 original size:26 final size:26
Alignment explanation
Indices: 21164737--21164786 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
21164727 ACAAATATCC
**
21164737 TAAAACCAAACCCAATGGCCCAAACT
1 TAAAACCAAACCCAAAAGCCCAAACT
* *
21164763 TAAACCCAAACCCAAAAGTCCAAA
1 TAAAACCAAACCCAAAAGCCCAAA
21164787 TACATAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.50, C:0.34, G:0.06, T:0.10
Consensus pattern (26 bp):
TAAAACCAAACCCAAAAGCCCAAACT
Found at i:21167883 original size:128 final size:129
Alignment explanation
Indices: 21167729--21167983 Score: 381
Period size: 128 Copynumber: 2.0 Consensus size: 129
21167719 ACGAAGACGA
*
21167729 GATTTGACATTTGGCAATTCGCGGAATCGTGCCCTAATGTGCTAGGTTGCAATTTCGT-GTTTGC
1 GATTTGACATTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTAGGTTGCAATTTC-TCGTTTGC
* *
21167793 TCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTT-TTAAAATCCCTT-AAACGAATG
65 TCAAAATAATCAAATATCACTTCAAAATTTCACTCATGT-TTATTAAAAACCCTTAAAACGAATG
21167856 T
129 T
* * * *
21167857 GATTTGATATTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCT
1 GATTTGACATTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTAGGTTGCAATTTCTCGTTTGCT
* *
21167922 TAAAATAATCAAATATCCCTTCAAAATTTCACTCATGTTTATTAAAAACCCTTCAAAACGAA
66 CAAAATAATCAAATATCACTTCAAAATTTCACTCATGTTTATTAAAAACCCTT-AAAACGAA
21167984 GGCGACATTC
Statistics
Matches: 114, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
127 3 0.03
128 104 0.91
130 7 0.06
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (129 bp):
GATTTGACATTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTAGGTTGCAATTTCTCGTTTGCT
CAAAATAATCAAATATCACTTCAAAATTTCACTCATGTTTATTAAAAACCCTTAAAACGAATGT
Found at i:21174689 original size:6 final size:7
Alignment explanation
Indices: 21174674--21174698 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21174664 CAATAGTATG
21174674 AAAATAA
1 AAAATAA
21174681 AAAATAA
1 AAAATAA
21174688 AAAATAA
1 AAAATAA
21174695 AAAA
1 AAAA
21174699 GCAAATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:21175098 original size:23 final size:21
Alignment explanation
Indices: 21175071--21175120 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 21
21175061 AGTAATATAC
*
21175071 AAAATAATATACATTAATTTAA
1 AAAATAATATACATGAA-TTAA
21175093 ATAAATAATATACATGAATTAA
1 A-AAATAATATACATGAATTAA
21175115 AAAATA
1 AAAATA
21175121 GTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 6 0.23
23 15 0.58
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAATATACATGAATTAA
Found at i:21175150 original size:16 final size:17
Alignment explanation
Indices: 21175125--21175158 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21175115 AAAATAGTTT
21175125 AAAATAAATAATATATA
1 AAAATAAATAATATATA
*
21175142 AAAAT-AATAATGTATA
1 AAAATAAATAATATATA
21175158 A
1 A
21175159 GAGCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATAAATAATATATA
Found at i:21177036 original size:261 final size:261
Alignment explanation
Indices: 21176692--21177280 Score: 664
Period size: 261 Copynumber: 2.2 Consensus size: 261
21176682 TGAAAAAGCG
* * ** * *
21176692 CAACCCAGCACAATAGGGCACGATTCTCAAATCACCAAACATCGAACATCGCCTTCGTTTTGAAA
1 CAACCCAGCACGATAGGGCACGATTCTCGAATTGCCAAAAATCGAAAATCGCCTTCGTTTT-AAA
* *
21176757 GGTTTTTAATAAACATGAGTGAAAATCTAAAGGAATATTCGATTGTTTTGAGCAAACGAGAAATC
65 GGTTTTTAATAAACATGAGTGAAAATCTAAAGGAATATTCGATTATTTTAAGCAAACGAGAAATC
* ** * *
21176822 ACAACCCAGCACGATAGGGCATGATTCC-CGAATTGTCAAACACCGAATATTGTCTTCATTTTAA
130 ACAACCCAGCACGATAGGGCACGATTCCGCGAATTACCAAACACCGAATATCGTCTTC-GTTTAA
* ***
21176886 AGGA-TTTTAATAA-ACATGAGTGAAAATCTAAAGGAATATTCGATTGTTTTGAGCAAACGAGAA
194 AGGATTTTTAA-AAGACATGAGTGAAAATCTAAAGGAACATTCGATCACTTTGAGCAAACGAGAA
21176949 ATCA
258 ATCA
* * * * *
21176953 CAACCCAGCACGATAGGGCATGATTCTCGAATTGTCAAAAACCGAATATTGCCTTCGTTTTAAAG
1 CAACCCAGCACGATAGGGCACGATTCTCGAATTGCCAAAAATCGAAAATCGCCTTCGTTTTAAAG
* * * * * * * *
21177018 GATTTTTAGA-AGACATGAGTGAAATTTTGAAGGGATATTTGATTATTTTAAGCAAATGGGAAAT
66 G-TTTTTA-ATAAACATGAGTGAAAATCTAAAGGAATATTCGATTATTTTAAGCAAACGAGAAAT
** * * * *
21177082 TGCAACCCAGCACGTTAGGGCACGATTCCGCGAATTACCAAATATCGTATATCGTCTTCGTTTAA
129 CACAACCCAGCACGATAGGGCACGATTCCGCGAATTACCAAACACCGAATATCGTCTTCGTTTAA
* * * * * *
21177147 GGGATTTTTAAAAGACATGGGTGAAATTCTAAAGGGACCTTCGATCACTTTGAGCAAATGAGAAA
194 AGGATTTTTAAAAGACATGAGTGAAAATCTAAAGGAACATTCGATCACTTTGAGCAAACGAGAAA
**
21177212 TTG
259 TCA
* * * *
21177215 CAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAGAATCGAAAATCGCCTTCGTTTTAAA
1 CAACCCAGCACGATAGGGCACGATT-CTCGAATTGCCAAAAATCGAAAATCGCCTTCGTTTTAAA
21177280 G
65 G
21177281 AATTCTTAAT
Statistics
Matches: 270, Mismatches: 52, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
260 5 0.02
261 136 0.50
262 95 0.35
263 34 0.13
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (261 bp):
CAACCCAGCACGATAGGGCACGATTCTCGAATTGCCAAAAATCGAAAATCGCCTTCGTTTTAAAG
GTTTTTAATAAACATGAGTGAAAATCTAAAGGAATATTCGATTATTTTAAGCAAACGAGAAATCA
CAACCCAGCACGATAGGGCACGATTCCGCGAATTACCAAACACCGAATATCGTCTTCGTTTAAAG
GATTTTTAAAAGACATGAGTGAAAATCTAAAGGAACATTCGATCACTTTGAGCAAACGAGAAATC
A
Found at i:21177109 original size:131 final size:130
Alignment explanation
Indices: 21176642--21177289 Score: 647
Period size: 131 Copynumber: 5.0 Consensus size: 130
21176632 TAGAAAATAC
** * * * *
21176642 GAGTGAAATTCCGAAGGGATCTTCGATTATTTTG-GACAAATGAAAAAGCGCAACCCAGCACAAT
1 GAGTGAAATTCTAAAGGGATATTCGATTATTTTGAG-CAAATGAGAAATCGCAACCCAGCACGAT
* ** * * *
21176706 AGGGCACGATTCTCAAATCACCAAACATCGAACATCGCCTTCGTTTTGAAAGG-TTTTTAATAAA
65 AGGGCACGATTCTCGAATTGCCAAAAATCGAATATCGCCTTCGTTTT-AAAGGATTTTTAA-AGA
21176770 CAT
128 CAT
* * * * *
21176773 GAGTGAAAATCTAAAGGAATATTCGATTGTTTTGAGCAAACGAGAAATCACAACCCAGCACGATA
1 GAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAATGAGAAATCGCAACCCAGCACGATA
* * * * * * * * *
21176838 GGGCATGATTCCCGAATTGTCAAACACCGAATATTGTCTTCATTTTAAAGGA-TTTTAATAAACA
66 GGGCACGATTCTCGAATTGCCAAAAATCGAATATCGCCTTCGTTTTAAAGGATTTTTAA-AGACA
21176902 T
130 T
* * * * *
21176903 GAGTGAAAATCTAAAGGAATATTCGATTGTTTTGAGCAAACGAGAAATCACAACCCAGCACGATA
1 GAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAATGAGAAATCGCAACCCAGCACGATA
* * * *
21176968 GGGCATGATTCTCGAATTGTCAAAAACCGAATATTGCCTTCGTTTTAAAGGATTTTTAGAAGACA
66 GGGCACGATTCTCGAATTGCCAAAAATCGAATATCGCCTTCGTTTTAAAGGATTTTTA-AAGACA
21177033 T
130 T
* * * * * * *
21177034 GAGTGAAATTTTGAAGGGATATTTGATTATTTTAAGCAAATGGGAAATTGCAACCCAGCACGTTA
1 GAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAATGAGAAATCGCAACCCAGCACGATA
* * * * * *
21177099 GGGCACGATTCCGCGAATTACCAAATATCGTATATCGTCTTCG-TTTAAGGGATTTTTAAAAGAC
66 GGGCACGATT-CTCGAATTGCCAAAAATCGAATATCGCCTTCGTTTTAAAGGATTTTT-AAAGAC
21177163 AT
129 AT
* ** * * * * *
21177165 GGGTGAAATTCTAAAGGGACCTTCGATCACTTTGAGCAAATGAGAAATTGCAACCCAACACGTTA
1 GAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAATGAGAAATCGCAACCCAGCACGATA
* * * * *
21177230 GGGCACGATTCCACGAATTGCCAAGAATCGAAAATCGCCTTCGTTTTAAAGAATTCTTAA
66 GGGCACGATT-CTCGAATTGCCAAAAATCGAATATCGCCTTCGTTTTAAAGGATTTTTAA
21177290 TAATTGTGAA
Statistics
Matches: 440, Mismatches: 70, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
130 131 0.30
131 271 0.62
132 38 0.09
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (130 bp):
GAGTGAAATTCTAAAGGGATATTCGATTATTTTGAGCAAATGAGAAATCGCAACCCAGCACGATA
GGGCACGATTCTCGAATTGCCAAAAATCGAATATCGCCTTCGTTTTAAAGGATTTTTAAAGACAT
Found at i:21181402 original size:18 final size:19
Alignment explanation
Indices: 21181379--21181415 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21181369 ATTTTAAAAA
21181379 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
21181397 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
21181416 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:21181416 original size:18 final size:18
Alignment explanation
Indices: 21181379--21181431 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
21181369 ATTTTAAAAA
21181379 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAA-TTT
21181397 TATAAATATTTAGAATTT
1 TATAAATATTTAGAATTT
* *
21181415 TAAAAATTATTTTGAAT
1 TATAAA-TATTTAGAAT
21181432 ATTTGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
TATAAATATTTAGAATTT
Found at i:21181425 original size:19 final size:19
Alignment explanation
Indices: 21181385--21181446 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
21181375 AAAATATAAA
*
21181385 ATTTAGAATTTTTATAAA-T
1 ATTTAGAA-TTTTAAAAATT
21181404 ATTTAGAATTTTAAAAATT
1 ATTTAGAATTTTAAAAATT
* *
21181423 ATTTTGAATATTTGAAAATT
1 ATTTAGAAT-TTTAAAAATT
21181443 ATTT
1 ATTT
21181447 TTTTTTGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.21
19 17 0.45
20 13 0.34
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (19 bp):
ATTTAGAATTTTAAAAATT
Found at i:21181448 original size:21 final size:19
Alignment explanation
Indices: 21181394--21181447 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
21181384 AATTTAGAAT
* *
21181394 TTTTATAAA-TATTTAGAA
1 TTTTAAAAATTATTTTGAA
21181412 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
*
21181431 TATTTGAAAATTATTTT
1 T-TTTAAAAATTATTTT
21181448 TTTTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 8 0.26
19 9 0.29
20 14 0.45
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:21182787 original size:19 final size:19
Alignment explanation
Indices: 21182751--21182787 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21182741 TTTTGTTGTT
*
21182751 TTTCACTATTTTGCTACTG
1 TTTCACTATTATGCTACTG
*
21182770 TTTCACTATTATGTTACT
1 TTTCACTATTATGCTACT
21182788 ACTATTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTCACTATTATGCTACTG
Found at i:21187446 original size:15 final size:15
Alignment explanation
Indices: 21187426--21187457 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21187416 AGATTTCAAG
21187426 ATCGTCCCTACAATC
1 ATCGTCCCTACAATC
21187441 ATCGTCCCTACAATC
1 ATCGTCCCTACAATC
21187456 AT
1 AT
21187458 TCTCATAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.06, T:0.28
Consensus pattern (15 bp):
ATCGTCCCTACAATC
Found at i:21187733 original size:48 final size:48
Alignment explanation
Indices: 21187670--21188234 Score: 555
Period size: 48 Copynumber: 11.8 Consensus size: 48
21187660 TTGCCGATTA
* * ** * *
21187670 CATGTCCCAGACATGGTCTTACCCTAGCTCACATGTTGAGGCCGATAC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * * * **
21187718 CATGTCCCAAACATGGTCTTACACTAGCTCTCGTCTCAATGTTGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * * **
21187766 CATGTCCCAGACATGGTTTTACACTAGCTCTCGTCTCAATACCGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * * *** *
21187814 CATGTCCCAGACATGGTTTTACACTGGTTCTCATAAT-GTGGCTGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAACGCCGATGC
* *
21187862 CATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCTGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* ***
21187910 CATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTGGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAACGCCGATGC
*
21187958 CATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * *
21188006 CATGTCCAAGACATGGTCTTACACTGGCACACATATCAACACCGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * *
21188054 CATGTCCCATACATGGTCTTACACTAG-TATACATATCAACGCCGATAC
1 CATGTCCCAGACATGGTCTTACACTAGCT-CACATATCAACGCCGATGC
* * * * * * *
21188102 AATATTCCAGACATGGTCCTACACTGGCACACATATCAATGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * *** *
21188150 CATGT-CCAGTCATGGTCTTACACTTGCTCTCATAAT-GTGGTCGATGC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAACGCCGATGC
*
21188197 CATGTCCCAGACATGGTCTTACACTAGCACACATATCA
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATATCA
21188235 CCTAATTGTC
Statistics
Matches: 428, Mismatches: 80, Indels: 18
0.81 0.15 0.03
Matches are distributed among these distances:
47 41 0.10
48 384 0.90
49 3 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
Found at i:21191325 original size:13 final size:13
Alignment explanation
Indices: 21191307--21191334 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21191297 TTTTTATATT
21191307 CACATATGGTAAC
1 CACATATGGTAAC
21191320 CACATATGGTAAC
1 CACATATGGTAAC
21191333 CA
1 CA
21191335 AGGTCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (13 bp):
CACATATGGTAAC
Found at i:21192879 original size:13 final size:13
Alignment explanation
Indices: 21192861--21192886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21192851 ATTTTTCAAG
21192861 TCATTTTCATTTT
1 TCATTTTCATTTT
21192874 TCATTTTCATTTT
1 TCATTTTCATTTT
21192887 GAAGAAAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:21218367 original size:20 final size:20
Alignment explanation
Indices: 21218342--21218379 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21218332 ATGGCAAGGT
* *
21218342 TTGTCCCATCATAGACATCG
1 TTGTCCCACCAAAGACATCG
21218362 TTGTCCCACCAAAGACAT
1 TTGTCCCACCAAAGACAT
21218380 TCATTCCACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (20 bp):
TTGTCCCACCAAAGACATCG
Found at i:21225180 original size:19 final size:19
Alignment explanation
Indices: 21225156--21225192 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21225146 TTAGAAAAAA
21225156 TTTCATGT-TATAAGTAATG
1 TTTCATGTAT-TAAGTAATG
21225175 TTTCATGTATTAAGTAAT
1 TTTCATGTATTAAGTAAT
21225193 TATTCCACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (19 bp):
TTTCATGTATTAAGTAATG
Found at i:21226497 original size:15 final size:15
Alignment explanation
Indices: 21226442--21226498 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
21226432 TTTATACTAC
*
21226442 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
21226457 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
21226474 CATAAATATTTATTATT
1 -A-AAATATTTATTATT
21226491 AAAATATT
1 AAAATATT
21226499 AATATGGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:21226627 original size:22 final size:22
Alignment explanation
Indices: 21226593--21226634 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21226583 ATTAAAAAAA
21226593 TTATTAAAATAATAAATTATAT
1 TTATTAAAATAATAAATTATAT
* * *
21226615 TTATTATATTAATAATTTAT
1 TTATTAAAATAATAAATTAT
21226635 TATAAGACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTAAAATAATAAATTATAT
Found at i:21237806 original size:2 final size:2
Alignment explanation
Indices: 21237801--21237825 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21237791 ATATATTAAT
21237801 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21237826 GGACCAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21247034 original size:47 final size:47
Alignment explanation
Indices: 21246981--21247072 Score: 184
Period size: 47 Copynumber: 2.0 Consensus size: 47
21246971 ATTGTGAACT
21246981 AAATTTGTGTGTTTTATCTATATACCTATATATAAAAGGAATGTTCA
1 AAATTTGTGTGTTTTATCTATATACCTATATATAAAAGGAATGTTCA
21247028 AAATTTGTGTGTTTTATCTATATACCTATATATAAAAGGAATGTT
1 AAATTTGTGTGTTTTATCTATATACCTATATATAAAAGGAATGTT
21247073 GACCTTTACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (47 bp):
AAATTTGTGTGTTTTATCTATATACCTATATATAAAAGGAATGTTCA
Found at i:21248021 original size:6 final size:6
Alignment explanation
Indices: 21248007--21248051 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
21247997 TGCCTTCCAC
* *
21248007 CACCTT CACCCT CACCCT CATCCT CACCCT CACCCT CACCCT CAC
1 CACCCT CACCCT CACCCT CACCCT CACCCT CACCCT CACCCT CAC
21248052 GTGCAAGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.18, C:0.62, G:0.00, T:0.20
Consensus pattern (6 bp):
CACCCT
Found at i:21252039 original size:16 final size:16
Alignment explanation
Indices: 21252006--21252039 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21251996 TTGCACTGTT
* *
21252006 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
21252022 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
21252038 AA
1 AA
21252040 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:21256820 original size:16 final size:16
Alignment explanation
Indices: 21256787--21256820 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21256777 GGAGATTGTT
* *
21256787 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
21256803 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
21256819 AA
1 AA
21256821 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:21259987 original size:30 final size:29
Alignment explanation
Indices: 21259951--21260031 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 29
21259941 AATTTAACAT
21259951 AAACTTATAAAAGTTATAAAAAATTCATAA
1 AAACTTATAAAAGTTATAAAAAATT-ATAA
21259981 AAACTTATAAATAG-TATAAAAAATTATAA
1 AAACTTATAAA-AGTTATAAAAAATTATAA
* *
21260010 AAA-TTCTAATAAATTATAAAAA
1 AAACTTATAA-AAGTTATAAAAA
21260032 TAAAATGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
28 6 0.13
29 16 0.35
30 22 0.48
31 2 0.04
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (29 bp):
AAACTTATAAAAGTTATAAAAAATTATAA
Found at i:21259988 original size:21 final size:19
Alignment explanation
Indices: 21259957--21260032 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
21259947 ACATAAACTT
*
21259957 ATAAAAGTTATAAAAAATTC
1 ATAAAAATTAT-AAAAATTC
* *
21259977 ATAAAAACTTATAAATAGT-
1 ATAAAAA-TTATAAAAATTC
21259996 ATAAAAAATTATAAAAATTC
1 AT-AAAAATTATAAAAATTC
21260016 -TAATAAATTATAAAAAT
1 ATAA-AAATTATAAAAAT
21260033 AAAATGTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.04
19 25 0.53
20 16 0.34
21 4 0.09
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (19 bp):
ATAAAAATTATAAAAATTC
Found at i:21260032 original size:9 final size:9
Alignment explanation
Indices: 21259955--21260032 Score: 75
Period size: 10 Copynumber: 8.1 Consensus size: 9
21259945 TAACATAAAC
*
21259955 TTATAAAAG
1 TTATAAAAA
21259964 TTATAAAAAA
1 TTAT-AAAAA
21259974 TTCATAAAAA
1 TT-ATAAAAA
*
21259984 CTTATAAATA
1 -TTATAAAAA
*
21259994 GTATAAAAAA
1 TTAT-AAAAA
21260004 TTATAAAAA
1 TTATAAAAA
*
21260013 TTCTAATAAA
1 TTATAA-AAA
21260023 TTATAAAAA
1 TTATAAAAA
21260032 T
1 T
21260033 AAAATGTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
9 21 0.37
10 32 0.56
11 4 0.07
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:21260179 original size:21 final size:22
Alignment explanation
Indices: 21260154--21260196 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21260144 TTATCCATAA
21260154 TTATAAA-ACTAATAAAAAAAT
1 TTATAAAGACTAATAAAAAAAT
*
21260175 TTATAAAGACTCATAAAAAAAT
1 TTATAAAGACTAATAAAAAAAT
21260197 CAAAACAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (22 bp):
TTATAAAGACTAATAAAAAAAT
Found at i:21260710 original size:18 final size:18
Alignment explanation
Indices: 21260646--21260732 Score: 65
Period size: 18 Copynumber: 4.9 Consensus size: 18
21260636 ATGACTTTCC
*
21260646 TTTTAT-AATTTTTA-AT
1 TTTTATAAAATTTTATAT
*
21260662 TTTT-TGAAA-TTTATAT
1 TTTTATAAAATTTTATAT
**
21260678 TATTTATAAGTTTTTATAT
1 T-TTTATAAAATTTTATAT
*
21260697 TTTTATAAAATTTTAAAT
1 TTTTATAAAATTTTATAT
*
21260715 ATTTTAAAAATATTTTAT
1 -TTTTATAAA-ATTTTAT
21260733 TAATTAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.09
16 9 0.16
17 3 0.05
18 16 0.29
19 16 0.29
20 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATAAAATTTTATAT
Found at i:21264359 original size:284 final size:284
Alignment explanation
Indices: 21263849--21264417 Score: 933
Period size: 284 Copynumber: 2.0 Consensus size: 284
21263839 TACTATAGTA
* *
21263849 TCTTATTCGTTGGTCTTAAATGGGAATAAAGGGGATACTTTTTTCCCTTCAAAGGGATTGAGACA
1 TCTTATTCGTTGGTCTTAAATGGGAATAAAGCGGATACTTTTTTCCCTTCAAAGGGATTAAGACA
* * *
21263914 AAGTGACCCGTTGAGTTTATTTTTATTCTTATTTTGTGGAGAAGGTCTTTCTAGCCTTATGAAGT
66 AAGTGACCCGTTGAGTCTACTCTTATTCTTATTTTGTGGAGAAGGTCTTTCTAGCCTTATGAAGT
21263979 TAGGGATACATGAAAAATTAATAAGAAGAGTTAAGGCAAGCAGAATGGGCCCTCAGATTTCTAGC
131 TAGGGATACATGAAAAATTAATAAGAAGAGTTAAGGCAAGCAGAATGGGCCCTCAGATTTCTAGC
* * *
21264044 ATACTTTTTGCAGATGATTGCATTTTATTTGGGACAGTAACGGAAAAAAATGCCACTTGTTTGAA
196 ATACTTCTTGCAGATGATTGCATTTTATTTGGGACAGCAACGGAAAAAAATACCACTTGTTTGAA
* *
21264109 ATATATACTACATGAATACGAAAT
261 ACAGATACTACATGAATACGAAAT
* *
21264133 TCTTATTCGTTGGTCTTAAATGGGAATAAAGCGGATACTTTTTTCCTTTCAAGGGGATTAAGACA
1 TCTTATTCGTTGGTCTTAAATGGGAATAAAGCGGATACTTTTTTCCCTTCAAAGGGATTAAGACA
** ** *
21264198 GGGTGACTTGTTGAGTCTACTCTTATTTTTATTTTGTGGAGAAGGTCTTTCTAGCCTTATGAAGT
66 AAGTGACCCGTTGAGTCTACTCTTATTCTTATTTTGTGGAGAAGGTCTTTCTAGCCTTATGAAGT
* * *
21264263 TAGGGATACATGAAAAATTAATGAGAAGAGTTAAGGTAAGTAGAA-GGGTCCCTCAGATTTCTAG
131 TAGGGATACATGAAAAATTAATAAGAAGAGTTAAGGCAAGCAGAATGGG-CCCTCAGATTTCTAG
*
21264327 CATACTTCTTGCAGATGATTGCATTTTATTTGGGACAGCAACGTAAAAAAATACCACTTGTTTGA
195 CATACTTCTTGCAGATGATTGCATTTTATTTGGGACAGCAACGGAAAAAAATACCACTTGTTTGA
21264392 AACAGATACTACATGAATACGAAAT
260 AACAGATACTACATGAATACGAAAT
21264417 T
1 T
21264418 TGTTCGGGTC
Statistics
Matches: 263, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
283 3 0.01
284 260 0.99
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (284 bp):
TCTTATTCGTTGGTCTTAAATGGGAATAAAGCGGATACTTTTTTCCCTTCAAAGGGATTAAGACA
AAGTGACCCGTTGAGTCTACTCTTATTCTTATTTTGTGGAGAAGGTCTTTCTAGCCTTATGAAGT
TAGGGATACATGAAAAATTAATAAGAAGAGTTAAGGCAAGCAGAATGGGCCCTCAGATTTCTAGC
ATACTTCTTGCAGATGATTGCATTTTATTTGGGACAGCAACGGAAAAAAATACCACTTGTTTGAA
ACAGATACTACATGAATACGAAAT
Found at i:21276665 original size:2 final size:2
Alignment explanation
Indices: 21276658--21276698 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
21276648 TAGATGATGT
21276658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21276699 TTGAACCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21279331 original size:2 final size:2
Alignment explanation
Indices: 21279324--21279348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21279314 TAAAATCTCT
21279324 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21279349 CCTAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21292609 original size:30 final size:30
Alignment explanation
Indices: 21292573--21292678 Score: 203
Period size: 30 Copynumber: 3.5 Consensus size: 30
21292563 ACTCGACACG
*
21292573 ATGTCAGCTTGTGTGAGCAATTCCACTAAA
1 ATGTCAGCTTGTGTGAGCAATTCCATTAAA
21292603 ATGTCAGCTTGTGTGAGCAATTCCATTAAA
1 ATGTCAGCTTGTGTGAGCAATTCCATTAAA
21292633 ATGTCAGCTTGTGTGAGCAATTCCATTAAA
1 ATGTCAGCTTGTGTGAGCAATTCCATTAAA
21292663 ATGTCAGCTTGTGTGA
1 ATGTCAGCTTGTGTGA
21292679 ACAAAACATT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (30 bp):
ATGTCAGCTTGTGTGAGCAATTCCATTAAA
Found at i:21295071 original size:19 final size:19
Alignment explanation
Indices: 21295047--21295085 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21295037 TAGGAAGGAG
21295047 AATTATTA-AGAAGCTTAGT
1 AATTATTAGAGAAG-TTAGT
21295066 AATTATTAGAGAAGTTAGT
1 AATTATTAGAGAAGTTAGT
21295085 A
1 A
21295086 TAAATAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (19 bp):
AATTATTAGAGAAGTTAGT
Found at i:21299916 original size:38 final size:38
Alignment explanation
Indices: 21299874--21299947 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
21299864 AAACACTACC
*
21299874 ATAAATATAATAAATATTTTATTATATTAAAAATAAAA
1 ATAAAAATAATAAATATTTTATTATATTAAAAATAAAA
* *
21299912 ATAAAAATAATAAATATTTTATTGTATTAAATATAA
1 ATAAAAATAATAAATATTTTATTATATTAAAAATAA
21299948 TTTTTATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (38 bp):
ATAAAAATAATAAATATTTTATTATATTAAAAATAAAA
Found at i:21300588 original size:2 final size:2
Alignment explanation
Indices: 21300583--21300617 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21300573 ATCTCTCATC
21300583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21300618 TTTTTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21301793 original size:19 final size:19
Alignment explanation
Indices: 21301769--21301807 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
21301759 CTTAACTAAT
21301769 GATAAGAATGAGCTTGTTG
1 GATAAGAATGAGCTTGTTG
21301788 GATAAGAATGAGCTTGTTG
1 GATAAGAATGAGCTTGTTG
21301807 G
1 G
21301808 TTTAGTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (19 bp):
GATAAGAATGAGCTTGTTG
Found at i:21307754 original size:18 final size:19
Alignment explanation
Indices: 21307718--21307756 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
21307708 TGGGGTGTGT
* *
21307718 AAGGGTGAGAAGAGGGGAG
1 AAGGGAGAGAAGAGAGGAG
21307737 AAGGGAGAG-AGAGAGGAG
1 AAGGGAGAGAAGAGAGGAG
21307755 AA
1 AA
21307757 AAATAGAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.03
Consensus pattern (19 bp):
AAGGGAGAGAAGAGAGGAG
Found at i:21307777 original size:7 final size:7
Alignment explanation
Indices: 21307763--21307796 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
21307753 AGAAAAATAG
21307763 AAGGAGA
1 AAGGAGA
*
21307770 ATGGAGA
1 AAGGAGA
21307777 AAGGAGA
1 AAGGAGA
21307784 AAGGAGA
1 AAGGAGA
21307791 AAGGAG
1 AAGGAG
21307797 TGGCCAAGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (7 bp):
AAGGAGA
Found at i:21319036 original size:21 final size:20
Alignment explanation
Indices: 21319012--21319050 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21319002 GAGTATTTTG
21319012 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
21319033 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
21319051 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:21319612 original size:42 final size:42
Alignment explanation
Indices: 21319551--21319631 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
21319541 TAATTATGGA
* * *
21319551 CACTTAGTGTGAGAAATCGAGATAGCTTTGGTTATATATTTG
1 CACTTAGTATGAGAAATCGAGATAGCTTCGGCTATATATTTG
* *
21319593 CACTTAGTATGCGAGATCGAGATAGCTTCGGCTATATAT
1 CACTTAGTATGAGAAATCGAGATAGCTTCGGCTATATAT
21319632 ATACATTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (42 bp):
CACTTAGTATGAGAAATCGAGATAGCTTCGGCTATATATTTG
Found at i:21326469 original size:21 final size:20
Alignment explanation
Indices: 21326445--21326483 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21326435 GAGTATTTTC
21326445 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
21326466 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
21326484 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:21334468 original size:19 final size:19
Alignment explanation
Indices: 21334446--21334491 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21334436 AAATTCTCTT
*
21334446 AAATTAAAAAAAAAGTTAA
1 AAATCAAAAAAAAAGTTAA
* *
21334465 AAATCATAAAAAAATTTAA
1 AAATCAAAAAAAAAGTTAA
*
21334484 AATTCAAA
1 AAATCAAA
21334492 CTTTGCAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATCAAAAAAAAAGTTAA
Found at i:21334534 original size:12 final size:11
Alignment explanation
Indices: 21334498--21334539 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
21334488 CAAACTTTGC
21334498 AAAAAAA-TTT
1 AAAAAAATTTT
21334508 AAAAGATAATTTT
1 AAAA-A-AATTTT
21334521 AAAAAAATTATT
1 AAAAAAATT-TT
21334533 AAAAAAA
1 AAAAAAA
21334540 CTGAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.14
11 5 0.18
12 12 0.43
13 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAAAAATTTT
Found at i:21334829 original size:48 final size:48
Alignment explanation
Indices: 21334755--21334873 Score: 157
Period size: 48 Copynumber: 2.5 Consensus size: 48
21334745 ATACCCCAAT
* * * * *
21334755 CCACCAATAGTGAACCCACTAACACCATCGGTTTTACCACCTCCATCA
1 CCACCAATTGTGAACCCACCAACACCATCGATTCTACCACCACCATCA
**
21334803 CTTCCAATTGTGAACCCACCAACACCATCGATTCTACCACCACCATCA
1 CCACCAATTGTGAACCCACCAACACCATCGATTCTACCACCACCATCA
* *
21334851 CCACCTATTGTGAACCTACCAAC
1 CCACCAATTGTGAACCCACCAAC
21334874 GCCTCCTATC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.31, C:0.40, G:0.08, T:0.21
Consensus pattern (48 bp):
CCACCAATTGTGAACCCACCAACACCATCGATTCTACCACCACCATCA
Found at i:21337831 original size:16 final size:17
Alignment explanation
Indices: 21337800--21337833 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21337790 CTAAGATGTG
21337800 CAAAAATGCAATATATT
1 CAAAAATGCAATATATT
*
21337817 CAAATATGC-ATATATT
1 CAAAAATGCAATATATT
21337833 C
1 C
21337834 TATAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (17 bp):
CAAAAATGCAATATATT
Found at i:21344337 original size:25 final size:24
Alignment explanation
Indices: 21344286--21344333 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
21344276 AGGTTTCGTC
21344286 TTTCGTAGAAATGGGGGGTAAGGG
1 TTTCGTAGAAATGGGGGGTAAGGG
*
21344310 TTTCGTTGAAATGGGGGGTAAGGG
1 TTTCGTAGAAATGGGGGGTAAGGG
21344334 GTTTGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.46, T:0.27
Consensus pattern (24 bp):
TTTCGTAGAAATGGGGGGTAAGGG
Found at i:21344721 original size:9 final size:9
Alignment explanation
Indices: 21344696--21344741 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
21344686 TCGAAAAAAA
21344696 AATTCGAGTT
1 AATTCGA-TT
*
21344706 GATTCGATT
1 AATTCGATT
21344715 AATTCGATT
1 AATTCGATT
*
21344724 AACTCGATT
1 AATTCGATT
*
21344733 AACTCGATT
1 AATTCGATT
21344742 CGAATAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (9 bp):
AATTCGATT
Found at i:21345597 original size:30 final size:31
Alignment explanation
Indices: 21345558--21345616 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
21345548 GTAAATGCTC
* * *
21345558 AAAATTTGAAGGATTAA-AGTGTAAATATGA
1 AAAAATTGAAGGACTAATAGTGAAAATATGA
21345588 AAAAATTGAAGGACTAATAGTGAAAATAT
1 AAAAATTGAAGGACTAATAGTGAAAATAT
21345617 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.27
Consensus pattern (31 bp):
AAAAATTGAAGGACTAATAGTGAAAATATGA
Found at i:21349192 original size:2 final size:2
Alignment explanation
Indices: 21349185--21349226 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21349175 AGAATTCCAT
21349185 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
21349227 TCTTGATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:21353678 original size:21 final size:21
Alignment explanation
Indices: 21353652--21353703 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
21353642 CCCCCTCCAT
21353652 ATGGGCATGTG-GAGCCT-TCAC
1 ATGGGCATGTGTG-GCCTCT-AC
*
21353673 ATGGGCGTGTGTGGCCTCTAC
1 ATGGGCATGTGTGGCCTCTAC
21353694 ATGGGCATGT
1 ATGGGCATGT
21353704 AGACCCCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.15, C:0.21, G:0.37, T:0.27
Consensus pattern (21 bp):
ATGGGCATGTGTGGCCTCTAC
Found at i:21357378 original size:18 final size:18
Alignment explanation
Indices: 21357355--21357389 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21357345 TTTTTTTACT
21357355 AGTGGTTTATCCACAATG
1 AGTGGTTTATCCACAATG
21357373 AGTGGTTTATCCACAAT
1 AGTGGTTTATCCACAAT
21357390 ATGGTGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (18 bp):
AGTGGTTTATCCACAATG
Found at i:21371037 original size:26 final size:26
Alignment explanation
Indices: 21371000--21371083 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
21370990 TGATACAAAT
* * *
21371000 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
21371026 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
21371052 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
21371078 TGATAA
1 TGATAA
21371084 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:21374047 original size:22 final size:21
Alignment explanation
Indices: 21374009--21374052 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
21373999 TGACCTTGAA
*
21374009 TTATTATATTATGTAATGTATT
1 TTATTACATTATGTAAT-TATT
21374031 TTATTACATATAT-TAATTATT
1 TTATTACAT-TATGTAATTATT
21374052 T
1 T
21374053 CTAAAAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 12 0.60
23 3 0.15
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
TTATTACATTATGTAATTATT
Found at i:21376007 original size:17 final size:18
Alignment explanation
Indices: 21375985--21376018 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21375975 AAAAGAATTC
*
21375985 AAAATA-ATTTTTAAAAT
1 AAAATATATTTATAAAAT
21376002 AAAATATATTTATAAAA
1 AAAATATATTTATAAAA
21376019 ATTCCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATATTTATAAAAT
Found at i:21378799 original size:60 final size:59
Alignment explanation
Indices: 21378732--21378868 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 59
21378722 AACTATGTTA
*
21378732 ATATGGGCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTATGGCCCAGATTGATACTG
1 ATATGGGCAAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTATGGCCCAGATTAATACTG
* * *
21378792 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCAAGGCCCAATATACTCTGATA-TGTAAAGGGCTATGGCCCAGATTAATACTG
21378852 ATATGGGCTAAGGCCCA
1 ATATGGGC-AAGGCCCA
21378869 GTTAACACTG
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 1 0.01
60 52 0.76
61 15 0.22
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (59 bp):
ATATGGGCAAGGCCCAATATACTCTGATATGTAAAGGGCTATGGCCCAGATTAATACTG
Found at i:21382881 original size:21 final size:22
Alignment explanation
Indices: 21382851--21382891 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21382841 TTATATTTAT
*
21382851 GTTTTGAGGGTTT-GTTTTTGG
1 GTTTTCAGGGTTTAGTTTTTGG
21382872 GTTTTCAGGGTTTAGTTTTT
1 GTTTTCAGGGTTTAGTTTTT
21382892 ATCTTCATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.07, C:0.02, G:0.32, T:0.59
Consensus pattern (22 bp):
GTTTTCAGGGTTTAGTTTTTGG
Found at i:21388278 original size:23 final size:23
Alignment explanation
Indices: 21388237--21388283 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
21388227 AGGATTTATA
* *
21388237 ATATTTTGGATGTGTTTGGGCTGG
1 ATATTCTGGATGTATTTGGG-TGG
21388261 ATATTCTGG-TGTATTTGGGTGG
1 ATATTCTGGATGTATTTGGGTGG
21388283 A
1 A
21388284 ATCCGCGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 9 0.43
24 8 0.38
ACGTcount: A:0.15, C:0.04, G:0.36, T:0.45
Consensus pattern (23 bp):
ATATTCTGGATGTATTTGGGTGG
Found at i:21390847 original size:15 final size:17
Alignment explanation
Indices: 21390813--21390849 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
21390803 TCAAATCATA
21390813 ATAATTAACCAAATATT
1 ATAATTAACCAAATATT
*
21390830 ATAATT-ACCATA-ATT
1 ATAATTAACCAAATATT
21390845 ATAAT
1 ATAAT
21390850 AATGTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 5 0.26
17 6 0.32
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATTAACCAAATATT
Found at i:21390862 original size:38 final size:37
Alignment explanation
Indices: 21390820--21390926 Score: 99
Period size: 40 Copynumber: 2.8 Consensus size: 37
21390810 ATAATAATTA
* *
21390820 ACCAAATATTATAATTACCATAATTATAATAATGTTTG
1 ACCAAA-ATTATAATTACCATAATTATAATAATATTCG
* *
21390858 ACCAAAAAAATTACAATTA-CAGTGATTATAATAATATTCG
1 ACC---AAAATTATAATTACCA-TAATTATAATAATATTCG
* *
21390898 ATCCTAAATTATAATTACAATAATTATAA
1 A-CCAAAATTATAATTACCATAATTATAA
21390927 CAAGGATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
38 22 0.40
39 3 0.05
40 25 0.45
41 5 0.09
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.36
Consensus pattern (37 bp):
ACCAAAATTATAATTACCATAATTATAATAATATTCG
Found at i:21392506 original size:47 final size:47
Alignment explanation
Indices: 21392397--21392507 Score: 129
Period size: 47 Copynumber: 2.4 Consensus size: 47
21392387 CCAGGATAAG
* *
21392397 CACATAGTGTTTCATCGGAACAAATCTGAAACTTTAACATTATAGTA
1 CACATAGTGTCTCATCGGAACAAATCTGAAACTTTAACAGTATAGTA
* * *
21392444 CACAAAGT-ACTTCATCGGAACAAATCT-AGAACTTTAACAGTAGTCG-A
1 CACATAGTGTC-TCATCGGAACAAATCTGA-AACTTTAACAGTA-TAGTA
21392491 CACATAGTGTCTCATCG
1 CACATAGTGTCTCATCG
21392508 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
46 1 0.02
47 49 0.92
48 3 0.06
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (47 bp):
CACATAGTGTCTCATCGGAACAAATCTGAAACTTTAACAGTATAGTA
Found at i:21393374 original size:13 final size:13
Alignment explanation
Indices: 21393356--21393388 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
21393346 TCTATATTCA
21393356 ATATAATAATATT
1 ATATAATAATATT
21393369 ATATAATAATATT
1 ATATAATAATATT
21393382 A-ATAATA
1 ATATAATA
21393389 TAATATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAATAATATT
Found at i:21394540 original size:2 final size:2
Alignment explanation
Indices: 21394524--21394559 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
21394514 TCAAGTAATC
*
21394524 TA TA AA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21394560 CGTGAGAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21400438 original size:51 final size:50
Alignment explanation
Indices: 21400279--21400435 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
21400269 ACTTCTGATC
* *
21400279 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
21400330 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
21400380 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
21400431 AGTGA
1 AGTGA
21400436 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:21401994 original size:20 final size:18
Alignment explanation
Indices: 21401969--21402005 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
21401959 ATTGCTAAGT
21401969 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
21401989 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
21402006 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:21405129 original size:46 final size:45
Alignment explanation
Indices: 21405027--21405193 Score: 185
Period size: 46 Copynumber: 3.6 Consensus size: 45
21405017 GAGATTTGTG
* * * * *
21405027 TGCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGA
1 TGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGA
* *
21405074 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
1 -TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
* *
21405120 TAGCCAGTGTCAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-
1 T-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGA
*
21405165 TGCTAGTGTAAGACATGTCTGGGACATGC
1 TGCCAGTGTAAGACATGTCTGGGACATGC
21405194 GTCAGCACGG
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
44 26 0.25
45 3 0.03
46 52 0.50
47 12 0.12
48 11 0.11
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (45 bp):
TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:21405188 original size:44 final size:44
Alignment explanation
Indices: 21405076--21405236 Score: 184
Period size: 46 Copynumber: 3.6 Consensus size: 44
21405066 TGAGACGAGG
*
21405076 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAT
1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-T
* *
21405121 AGCCAGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
1 -GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
* *
21405166 GCTAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTAC-G--AGATGT
*
21405212 G-TCAGTGTAAGACCTGTCTGGGACA
1 GCT-AGTGTAAGACATGTCTGGGACA
21405237 CGGCATCGAC
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
43 2 0.02
44 32 0.31
45 4 0.04
46 64 0.63
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
Found at i:21408038 original size:20 final size:18
Alignment explanation
Indices: 21408013--21408049 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
21408003 ATTGCTAAGT
21408013 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
21408033 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
21408050 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:21411168 original size:46 final size:45
Alignment explanation
Indices: 21411066--21411232 Score: 185
Period size: 46 Copynumber: 3.6 Consensus size: 45
21411056 GAGATTTGTG
* * * * *
21411066 TGCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGA
1 TGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGA
* *
21411113 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
1 -TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
* *
21411159 TAGCCAGTGTCAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-
1 T-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGA
*
21411204 TGCTAGTGTAAGACATGTCTGGGACATGC
1 TGCCAGTGTAAGACATGTCTGGGACATGC
21411233 GTCAGCACGG
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
44 26 0.25
45 3 0.03
46 52 0.50
47 12 0.12
48 11 0.11
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (45 bp):
TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:21411227 original size:44 final size:44
Alignment explanation
Indices: 21411115--21411275 Score: 184
Period size: 46 Copynumber: 3.6 Consensus size: 44
21411105 TGAGACGAGG
*
21411115 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAT
1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-T
* *
21411160 AGCCAGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
1 -GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
* *
21411205 GCTAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTAC-G--AGATGT
*
21411251 G-TCAGTGTAAGACCTGTCTGGGACA
1 GCT-AGTGTAAGACATGTCTGGGACA
21411276 CGGCATCGAC
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
43 2 0.02
44 32 0.31
45 4 0.04
46 64 0.63
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
Found at i:21414051 original size:20 final size:18
Alignment explanation
Indices: 21414026--21414062 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
21414016 ATTGCTAAGT
21414026 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
21414046 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
21414063 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:21418386 original size:23 final size:25
Alignment explanation
Indices: 21418338--21418393 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
21418328 TTTACCCTAC
21418338 TTTTA-TATTATATATTGAAAATTTA
1 TTTTATTA-TATATATTGAAAATTTA
*
21418363 TTTTATTATATATATT-AATA-TTA
1 TTTTATTATATATATTGAAAATTTA
21418386 -TTTATTAT
1 TTTTATTAT
21418394 CTATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.28
23 3 0.10
24 3 0.10
25 13 0.45
26 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTATTATATATATTGAAAATTTA
Found at i:21424600 original size:19 final size:19
Alignment explanation
Indices: 21424558--21424600 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
21424548 AATTGGATTT
* *
21424558 GAAAATTGGACTCAATATC
1 GAAAATTGAACTCAATAAC
*
21424577 GAAAATTGAACTCGATAAC
1 GAAAATTGAACTCAATAAC
*
21424596 TAAAA
1 GAAAA
21424601 CCCAAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (19 bp):
GAAAATTGAACTCAATAAC
Found at i:21425752 original size:18 final size:18
Alignment explanation
Indices: 21425729--21425769 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
21425719 GCTTGTAGGA
21425729 CCAAACGGGCATATGGGC
1 CCAAACGGGCATATGGGC
*
21425747 CCAAACGGGCATGTGGGC
1 CCAAACGGGCATATGGGC
21425765 CCAAA
1 CCAAA
21425770 TTTTAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.32, T:0.10
Consensus pattern (18 bp):
CCAAACGGGCATATGGGC
Found at i:21430859 original size:15 final size:15
Alignment explanation
Indices: 21430806--21430849 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
21430796 TGCTATAAAT
21430806 TGGATTTCTTTATCA
1 TGGATTTCTTTATCA
*
21430821 TGGATTTCTTTATCT
1 TGGATTTCTTTATCA
21430836 TGGATTTCTTTATC
1 TGGATTTCTTTATC
21430850 CTGGGCTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (15 bp):
TGGATTTCTTTATCA
Found at i:21437235 original size:17 final size:16
Alignment explanation
Indices: 21437208--21437244 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
21437198 GATAATATTT
21437208 TTTAATGAATTTAATA
1 TTTAATGAATTTAATA
21437224 TTTAATTGAATTTAATA
1 TTTAA-TGAATTTAATA
21437241 TTTA
1 TTTA
21437245 TCTAGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TTTAATGAATTTAATA
Found at i:21437318 original size:42 final size:42
Alignment explanation
Indices: 21437221--21437318 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
21437211 AATGAATTTA
* * *
21437221 ATATTTAATTGAATTTAATATTTATCTAGATATTAATATATT
1 ATATTTAATTTAATTCAATATTTATCTAGATAATAATATATT
* * *
21437263 ATATTTAATTTAATTCAATATTTATTTAGATAATATTTTATT
1 ATATTTAATTTAATTCAATATTTATCTAGATAATAATATATT
21437305 A-ATTTAATATTAAT
1 ATATTTAAT-TTAAT
21437319 GTGATTAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 7 0.14
42 42 0.86
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (42 bp):
ATATTTAATTTAATTCAATATTTATCTAGATAATAATATATT
Found at i:21444370 original size:21 final size:21
Alignment explanation
Indices: 21444344--21444401 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
21444334 GGTGGATTAG
*
21444344 CTCTTACAAGCTTCTGTTCAA
1 CTCTTACGAGCTTCTGTTCAA
* *
21444365 CTCTTACGAGCTTCTATTCAG
1 CTCTTACGAGCTTCTGTTCAA
21444386 CT-TT-CGAGCTTCTGTT
1 CTCTTACGAGCTTCTGTT
21444402 GGCGTATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.33
20 2 0.06
21 20 0.61
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.41
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTCAA
Found at i:21457035 original size:2 final size:2
Alignment explanation
Indices: 21457028--21457055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21457018 GTATTAAATA
21457028 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21457056 GGTACTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21461295 original size:9 final size:9
Alignment explanation
Indices: 21461277--21461398 Score: 63
Period size: 9 Copynumber: 12.7 Consensus size: 9
21461267 GTGGTAATTT
21461277 TTTTTAATAA
1 TTTTT-ATAA
21461287 TTTTTATAA
1 TTTTTATAA
*
21461296 TTTTCTCT-A
1 TTTT-TATAA
*
21461305 TTTTTTTAA
1 TTTTTATAA
* *
21461314 -GTTTCTAA
1 TTTTTATAA
21461322 TTTTTATAATA
1 TTTTTAT-A-A
21461333 TTTTTATAA
1 TTTTTATAA
21461342 TTTTCTA-AA
1 TTTT-TATAA
21461351 CTTTTTTATAA
1 --TTTTTATAA
21461362 TACTTTTATAA
1 T--TTTTATAA
*
21461373 TTTCTAGTAA
1 TTTTTA-TAA
21461383 TTATTT-TAA
1 TT-TTTATAA
21461392 TATTTTA
1 T-TTTTA
21461399 ATACTCTATA
Statistics
Matches: 89, Mismatches: 8, Indels: 30
0.70 0.06 0.24
Matches are distributed among these distances:
8 8 0.09
9 37 0.42
10 19 0.21
11 25 0.28
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:21461337 original size:11 final size:11
Alignment explanation
Indices: 21461321--21461373 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
21461311 TAAGTTTCTA
21461321 ATTTTTATAAT
1 ATTTTTATAAT
21461332 ATTTTTATAAT
1 ATTTTTATAAT
*
21461343 -TTTCTA-AACT
1 ATTTTTATAA-T
21461353 -TTTTTATAAT
1 ATTTTTATAAT
*
21461363 ACTTTTATAAT
1 ATTTTTATAAT
21461374 TTCTAGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.06
10 12 0.33
11 22 0.61
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTTTATAAT
Found at i:21461344 original size:20 final size:19
Alignment explanation
Indices: 21461276--21461375 Score: 73
Period size: 20 Copynumber: 5.2 Consensus size: 19
21461266 AGTGGTAATT
21461276 TTTTTTAATAATTTTTATAA
1 TTTTTT-ATAATTTTTATAA
* * *
21461296 TTTTCTCT-ATTTTTTTAA
1 TTTTTTATAATTTTTATAA
* *
21461314 --GTTTCTAATTTTTATAA
1 TTTTTTATAATTTTTATAA
21461331 TATTTTTATAATTTTCTA-AA
1 T-TTTTTATAATTTT-TATAA
21461351 CTTTTTTATAATACTTTTATAA
1 -TTTTTTATAAT--TTTTATAA
21461373 TTT
1 TTT
21461376 CTAGTAATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
16 4 0.06
17 9 0.14
18 9 0.14
19 1 0.02
20 27 0.43
21 8 0.13
22 5 0.08
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTTTATAATTTTTATAA
Found at i:21462755 original size:25 final size:27
Alignment explanation
Indices: 21462727--21462776 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
21462717 TATTATTGCA
21462727 ATATTTAAAT-ATTTAAA-AAAATAAT
1 ATATTTAAATAATTTAAATAAAATAAT
*
21462752 ATATTTTAATAATTTAAATAAAATA
1 ATATTTAAATAATTTAAATAAAATA
21462777 CTTACACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTTAAATAATTTAAATAAAATAAT
Found at i:21465511 original size:43 final size:43
Alignment explanation
Indices: 21465463--21465603 Score: 176
Period size: 43 Copynumber: 3.3 Consensus size: 43
21465453 TATCCCAGAT
* *
21465463 ATGGTCTTACATGTTATCACATATTGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGTAATCACATATTGATGCCAATGTCCTAGAC
* ** ** * *
21465506 ATGGTCTTACACGAAATCACATAACGATATCAATGTCCCAAAC
1 ATGGTCTTACACGTAATCACATATTGATGCCAATGTCCTAGAC
21465549 ATGGTCTTACACGTAATCACA-ATATGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGTAATCACATAT-TGATGCCAATGTCCTAGAC
*
21465592 ATGGTTTTACAC
1 ATGGTCTTACAC
21465604 AAAATCATGT
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 1 0.01
43 79 0.99
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACATATTGATGCCAATGTCCTAGAC
Found at i:21469483 original size:23 final size:26
Alignment explanation
Indices: 21469436--21469487 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
21469426 GTAGAGTCCC
21469436 AGTAGGAGTGTAATTCTTCTACCACT
1 AGTAGGAGTGTAATTCTTCTACCACT
*
21469462 AGTAGGAGTGTAATTCTTCCACCACT
1 AGTAGGAGTGTAATTCTTCTACCACT
21469488 CAACCATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (26 bp):
AGTAGGAGTGTAATTCTTCTACCACT
Found at i:21473212 original size:24 final size:23
Alignment explanation
Indices: 21473181--21473236 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
21473171 TATTATTTTA
21473181 TTATATTTATACTATAA-TCTAAAT
1 TTATATTTATA-TA-AATTCTAAAT
21473205 TTATATTTATATAAATTCTAAAT
1 TTATATTTATATAAATTCTAAAT
*
21473228 CTACTATTT
1 TTA-TATTT
21473237 CTATTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 11 0.38
24 16 0.55
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATATTTATATAAATTCTAAAT
Found at i:21473215 original size:30 final size:30
Alignment explanation
Indices: 21473181--21473248 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
21473171 TATTATTTTA
21473181 TTATATTTATACTATAATCTA-AATTTATAT
1 TTATATTTATACTA-AATCTACAATTTATAT
** * * *
21473211 TTATATAAATTCTAAATCTACTATTTCTAT
1 TTATATTTATACTAAATCTACAATTTATAT
21473241 TTATATTT
1 TTATATTT
21473249 TCAATAACAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (30 bp):
TTATATTTATACTAAATCTACAATTTATAT
Found at i:21473457 original size:15 final size:15
Alignment explanation
Indices: 21473437--21473466 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21473427 TGTTTCATAA
21473437 ATTAAAAAAATAAGT
1 ATTAAAAAAATAAGT
*
21473452 ATTAAAAAATTAAGT
1 ATTAAAAAAATAAGT
21473467 GTCGAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
ATTAAAAAAATAAGT
Found at i:21476536 original size:23 final size:22
Alignment explanation
Indices: 21476506--21476549 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
21476496 TTTGACAGAC
*
21476506 CTAACCCATTTAGCTAGACAAT
1 CTAACCCATTTAGCTAAACAAT
21476528 CTAAGCCCATTTAGCTAAACAA
1 CTAA-CCCATTTAGCTAAACAA
21476550 CAAAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (22 bp):
CTAACCCATTTAGCTAAACAAT
Found at i:21477278 original size:2 final size:2
Alignment explanation
Indices: 21477271--21477305 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21477261 TATAATTCCT
21477271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21477306 TTGTAATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21483528 original size:18 final size:18
Alignment explanation
Indices: 21483505--21483539 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21483495 TATACCAAAT
21483505 AATAATATATAACAAAAA
1 AATAATATATAACAAAAA
21483523 AATAATATATAACAAAA
1 AATAATATATAACAAAA
21483540 TTATTATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
AATAATATATAACAAAAA
Found at i:21483540 original size:15 final size:16
Alignment explanation
Indices: 21483495--21483539 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
21483485 GTATTTATAC
*
21483495 TATACCAAATAATAATA
1 TATAACAAA-AATAATA
21483512 TATAACAAAAAAATAATA
1 TATAAC--AAAAATAATA
21483530 TATAACAAAA
1 TATAACAAAA
21483540 TTATTATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.16
17 5 0.20
18 13 0.52
19 3 0.12
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (16 bp):
TATAACAAAAATAATA
Found at i:21500681 original size:2 final size:2
Alignment explanation
Indices: 21500674--21500714 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
21500664 TGACAACACA
21500674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21500715 CTTGTTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21501016 original size:26 final size:26
Alignment explanation
Indices: 21500968--21501017 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
21500958 TAAATGTGTT
*
21500968 AACTATGATAATTAATTCTTAAAAAA
1 AACTATGATAATTAATGCTTAAAAAA
21500994 AACTATGATAATTAA-GCTATAAAA
1 AACTATGATAATTAATGCT-TAAAA
21501018 CAAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (26 bp):
AACTATGATAATTAATGCTTAAAAAA
Found at i:21504887 original size:18 final size:19
Alignment explanation
Indices: 21504843--21504894 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
21504833 AATTATTCAC
*
21504843 AAATTTAAAAAAAATCTAA
1 AAATTTATAAAAAATCTAA
* * *
21504862 AAACTTATAAAAACT-TAT
1 AAATTTATAAAAAATCTAA
21504880 AAATTTATAAAAAAT
1 AAATTTATAAAAAAT
21504895 TCAAAACTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATTTATAAAAAATCTAA
Found at i:21505282 original size:20 final size:20
Alignment explanation
Indices: 21505257--21505303 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
21505247 ATATTTTTTA
21505257 TTTTTTTAA-ATTAT-TATAT
1 TTTTTTTAACATTATATA-AT
*
21505276 TTATTTTCAACATTATATAAT
1 TT-TTTTTAACATTATATAAT
21505297 TTTTTTT
1 TTTTTTT
21505304 CTTTGTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 9 0.39
22 2 0.09
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTTTAACATTATATAAT
Found at i:21505303 original size:21 final size:20
Alignment explanation
Indices: 21505257--21505304 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
21505247 ATATTTTTTA
21505257 TTTTTTT-AAATTATTATAT
1 TTTTTTTCAAATTATTATAT
*
21505276 TTATTTTCAACATTA-TATAAT
1 TTTTTTTCAA-ATTATTAT-AT
21505297 TTTTTTTC
1 TTTTTTTC
21505305 TTTGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 13 0.54
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTTCAAATTATTATAT
Found at i:21508515 original size:44 final size:44
Alignment explanation
Indices: 21508452--21508541 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
21508442 TTATGATTTT
21508452 TTTAAAAGGAAAAATCCTTTTTGATCACTTAATTTTGAGAATTC
1 TTTAAAAGGAAAAATCCTTTTTGATCACTTAATTTTGAGAATTC
21508496 TTTAAAAGGAAAAATCCTTTTTGATCACTTAATTTTGAGAATTC
1 TTTAAAAGGAAAAATCCTTTTTGATCACTTAATTTTGAGAATTC
21508540 TT
1 TT
21508542 ACTTTTATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (44 bp):
TTTAAAAGGAAAAATCCTTTTTGATCACTTAATTTTGAGAATTC
Found at i:21512407 original size:22 final size:22
Alignment explanation
Indices: 21512379--21512428 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
21512369 TCTTTGTAAT
*
21512379 CTATCATGGAATATTTCAATTC
1 CTATCATGGAATATTTCAATAC
21512401 CTATCATGGAATATTTCAATAC
1 CTATCATGGAATATTTCAATAC
21512423 CTATCA
1 CTATCA
21512429 CATAGGATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (22 bp):
CTATCATGGAATATTTCAATAC
Found at i:21514147 original size:32 final size:32
Alignment explanation
Indices: 21514075--21514151 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
21514065 AAAAGGAAAA
* * *
21514075 GTACACTATATGTGTACACTTGAGAAGGTTAT
1 GTACACTTTGTGTGTACACTTGAGAAGGTTAG
*
21514107 GTACACTTTGTGTGTACACTTG-GAAATGTTAG
1 GTACACTTTGTGTGTACACTTGAG-AAGGTTAG
*
21514139 GTATACTTTGTGT
1 GTACACTTTGTGT
21514152 ATACCATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (32 bp):
GTACACTTTGTGTGTACACTTGAGAAGGTTAG
Found at i:21514178 original size:33 final size:33
Alignment explanation
Indices: 21514137--21514213 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
21514127 TGGAAATGTT
*
21514137 AGGTATACTTTGTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTATATACCATATGAAAAGGAA
21514170 AGGTATACTTTGTATATACCATATGAAAAGGAA
1 AGGTATACTTTGTATATACCATATGAAAAGGAA
*
21514203 ATGTATACTTT
1 AGGTATACTTT
21514214 ATGTGTTCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (33 bp):
AGGTATACTTTGTATATACCATATGAAAAGGAA
Found at i:21520062 original size:23 final size:24
Alignment explanation
Indices: 21520030--21520075 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
21520020 GATGTGTATA
*
21520030 AAAACTTTATGTAAAAAATAAATG
1 AAAACTTTATATAAAAAATAAATG
*
21520054 AAAA-TTTATATAAAAATTAAAT
1 AAAACTTTATATAAAAAATAAAT
21520076 ATGCTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAACTTTATATAAAAAATAAATG
Found at i:21527025 original size:13 final size:12
Alignment explanation
Indices: 21527007--21527102 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 12
21526997 AATAATCAAT
*
21527007 ATATATAGTAACA
1 ATATATAATAA-A
21527020 ATATATAATAAA
1 ATATATAATAAA
*
21527032 ATATA-AATAGA
1 ATATATAATAAA
* *
21527043 ATAAATAACATATA
1 ATATAT-A-ATAAA
*
21527057 ATA-AAAATATAA
1 ATATATAATA-AA
21527069 A-ATATAATAAA
1 ATATATAATAAA
*
21527080 ATTTATAA-AAA
1 ATATATAATAAA
21527091 ATGTATATAATA
1 A--TATATAATA
21527103 TTATAAATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
11 20 0.31
12 19 0.29
13 18 0.28
14 8 0.12
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:21527045 original size:23 final size:23
Alignment explanation
Indices: 21527019--21527081 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 23
21527009 ATATAGTAAC
*
21527019 AATATATAATAAAATATAAATAG
1 AATATATAATAAAATAAAAATAG
* * *
21527042 AATAAATAACATATAATAAAAATAT
1 AATATAT-A-ATAAAATAAAAATAG
*
21527067 AAAATATAATAAAAT
1 AATATATAATAAAAT
21527082 TTATAAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
23 12 0.39
24 2 0.06
25 17 0.55
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AATATATAATAAAATAAAAATAG
Found at i:21527056 original size:45 final size:43
Alignment explanation
Indices: 21526985--21527081 Score: 101
Period size: 43 Copynumber: 2.3 Consensus size: 43
21526975 TTCACATATA
* * * *
21526985 AAAATAT-AGTAGAATAATCAATATATATAGTAACAATATATAAT
1 AAAATATAAATAGAATAATCAACATATA-A-TAAAAATATAAAAT
21527029 AAAATATAAATAGAATAAAT-AACATATAATAAAAATATAAAAT
1 AAAATATAAATAGAAT-AATCAACATATAATAAAAATATAAAAT
*
21527072 ATAATA-AAAT
1 AAAATATAAAT
21527082 TTATAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
42 4 0.09
43 17 0.37
44 8 0.17
45 14 0.30
46 3 0.07
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (43 bp):
AAAATATAAATAGAATAATCAACATATAATAAAAATATAAAAT
Found at i:21527073 original size:18 final size:17
Alignment explanation
Indices: 21527026--21527080 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 17
21527016 AACAATATAT
21527026 AATAAAATATAAATAGAATA
1 AATAAAATAT-AATA-AA-A
*
21527046 AATAACATATAATAAAA
1 AATAAAATATAATAAAA
21527063 ATATAAAATATAATAAAA
1 A-ATAAAATATAATAAAA
21527081 TTTATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 2 0.06
18 17 0.53
19 4 0.12
20 9 0.28
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AATAAAATATAATAAAA
Found at i:21527087 original size:30 final size:31
Alignment explanation
Indices: 21527009--21527091 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 31
21526999 TAATCAATAT
*
21527009 ATATAGTAACAATATATAAT-AAAATAT-AA
1 ATATAATAACAATATATAATAAAAATATAAA
* * *
21527038 ATAGAATAAATAACATATAATAAAAATATAAA
1 ATATAAT-AACAATATATAATAAAAATATAAA
*
21527070 ATATAATAA-AATTTATAA-AAAA
1 ATATAATAACAATATATAATAAAA
21527092 TGTATATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 9 0.20
30 18 0.41
31 9 0.20
32 8 0.18
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (31 bp):
ATATAATAACAATATATAATAAAAATATAAA
Found at i:21527089 original size:9 final size:10
Alignment explanation
Indices: 21527047--21527109 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
21527037 AATAGAATAA
* *
21527047 ATAACATATA
1 ATAAAATATT
21527057 ATAAAA-A-T
1 ATAAAATATT
*
21527065 ATAAAATATA
1 ATAAAATATT
21527075 ATAAAAT-TT
1 ATAAAATATT
*
21527084 ATAAAAAATGT
1 ATAAAATAT-T
*
21527095 ATATAATATT
1 ATAAAATATT
21527105 ATAAA
1 ATAAA
21527110 TAATGAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
8 6 0.15
9 9 0.22
10 18 0.44
11 8 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
ATAAAATATT
Done.