Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 127 of 199
Found at i:38461148 original size:40 final size:40
Alignment explanation
Indices: 38461028--38461301 Score: 352
Period size: 40 Copynumber: 6.9 Consensus size: 40
38461018 CTTCAAATTA
* * * * *
38461028 ACCAGAGTATAAACAGGGGCACATATCTGCATTCGGGGGT
1 ACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGT
* * *
38461068 ACCGAAGTACAAAC-GGGGCATGTATGTGCATTTAGGGGT
1 ACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGT
* **
38461107 ACCAAAGTACAAACAGGAGCACGTATGTGCATTCAAAGGT
1 ACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGT
* * *
38461147 ACCGAAGTACAAACAGGTGCACGTATGTGCATTCAGAGGT
1 ACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGT
* *
38461187 ACCAAAGTACAAACAAGGGCACGTAAGTGCATTCAGGGGT
1 ACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGT
* * *
38461227 ATCGAAGTACAAACAGGGGCACGTATGTACATTCAGGGGT
1 ACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGT
* *
38461267 ACCAAAGTACAAACATGAGCACGTATGTGCATTCA
1 ACCAAAGTACAAACAGGGGCACGTATGTGCATTCA
38461302 TACAATAATT
Statistics
Matches: 201, Mismatches: 32, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
39 33 0.16
40 168 0.84
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.19
Consensus pattern (40 bp):
ACCAAAGTACAAACAGGGGCACGTATGTGCATTCAGGGGT
Found at i:38461243 original size:20 final size:19
Alignment explanation
Indices: 38461191--38461281 Score: 56
Period size: 20 Copynumber: 4.6 Consensus size: 19
38461181 AGAGGTACCA
* *
38461191 AAGTACAAACAAGGGCACG
1 AAGTACAAACAGGGGTACG
* **
38461210 TAAGTGCATTCAGGGGTATCG
1 -AAGTACAAACAGGGGTA-CG
*
38461231 AAGTACAAACAGGGGCACG
1 AAGTACAAACAGGGGTACG
* ** *
38461250 TATGTACATTCAGGGGTACCA
1 -AAGTACAAACAGGGGTA-CG
38461271 AAGTACAAACA
1 AAGTACAAACA
38461282 TGAGCACGTA
Statistics
Matches: 51, Mismatches: 17, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
19 2 0.04
20 46 0.90
21 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.16
Consensus pattern (19 bp):
AAGTACAAACAGGGGTACG
Found at i:38461931 original size:24 final size:24
Alignment explanation
Indices: 38461873--38461931 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
38461863 ACCACGGAAG
* *
38461873 GAGATGAAGACGAAGACGAGGGTA
1 GAGATGAAGATGAAGACGAGGATA
* *
38461897 GAGATGAAGATGAAGATGAGGATC
1 GAGATGAAGATGAAGACGAGGATA
38461921 GAGATGAAGAT
1 GAGATGAAGAT
38461932 TAATACGGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.05, G:0.39, T:0.14
Consensus pattern (24 bp):
GAGATGAAGATGAAGACGAGGATA
Found at i:38466797 original size:16 final size:16
Alignment explanation
Indices: 38466776--38466818 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
38466766 TTGGCTCATT
*
38466776 GGAAAAGCTAGCTTAA
1 GGAAAAGCTAGCTCAA
*
38466792 GGAAAATCTAGCTCAA
1 GGAAAAGCTAGCTCAA
* *
38466808 CGAAAGGCTAG
1 GGAAAAGCTAG
38466819 ATTGTTCAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (16 bp):
GGAAAAGCTAGCTCAA
Found at i:38488275 original size:71 final size:71
Alignment explanation
Indices: 38488159--38488293 Score: 216
Period size: 71 Copynumber: 1.9 Consensus size: 71
38488149 GTGCTATCGT
* * * *
38488159 TACCTTGAGGACTTCTACCGAAACAACTCAAGTCAGTAGCCAAAGTTTAGCATCTCCTGCACTTA
1 TACCTTGAAGACTTCTACCGAAACAACTCAAGTCAGTAGCCAAAGTTCAGCATCCCCTACACTTA
38488224 TGCCTA
66 TGCCTA
* *
38488230 TACCTTGAAGACTTTTACCGAAACAAGTCAAGTCAGTAGCCAAAGTTCAGCATCCCCTACACTT
1 TACCTTGAAGACTTCTACCGAAACAACTCAAGTCAGTAGCCAAAGTTCAGCATCCCCTACACTT
38488294 CTACCAATAC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (71 bp):
TACCTTGAAGACTTCTACCGAAACAACTCAAGTCAGTAGCCAAAGTTCAGCATCCCCTACACTTA
TGCCTA
Found at i:38491960 original size:9 final size:9
Alignment explanation
Indices: 38491936--38491970 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
38491926 TTAATTATAA
*
38491936 TACTATTAT
1 TACTATTAC
*
38491945 TATTATTAC
1 TACTATTAC
38491954 TACTATTAC
1 TACTATTAC
38491963 TACTATTA
1 TACTATTA
38491971 TTATAGGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (9 bp):
TACTATTAC
Found at i:38497288 original size:32 final size:34
Alignment explanation
Indices: 38497249--38497312 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
38497239 TTCAGACTCA
* *
38497249 AAAAATAAAA-AAAAAGCA-AAAAAATCAAAGTC
1 AAAAATAAAAGAAAAAGAAGAAAAAATAAAAGTC
38497281 AAAAATAAAAGAAAAAGAAGAAAAAATAAAAG
1 AAAAATAAAAGAAAAAGAAGAAAAAATAAAAG
38497313 AAAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.36
33 7 0.25
34 11 0.39
ACGTcount: A:0.78, C:0.05, G:0.09, T:0.08
Consensus pattern (34 bp):
AAAAATAAAAGAAAAAGAAGAAAAAATAAAAGTC
Found at i:38499500 original size:50 final size:48
Alignment explanation
Indices: 38499435--38499718 Score: 144
Period size: 50 Copynumber: 5.7 Consensus size: 48
38499425 AATCTTACTA
* * *
38499435 TCCCTGGCAGTGCAGTGGAGCAAATTAAAGTCGTAACGGTGAATCTTGCC
1 TCCCTGACATTGCAGTGGAACAAATTAAAG-C-TAACGGTGAATCTTGCC
* * * *
38499485 TCCCTGACATTGCAGT-TAAAAAGATTAAAGCTACAACAGTGAATCTTACC
1 TCCCTGACATTGCAGTGGAACAA-ATTAAAGCT--AACGGTGAATCTTGCC
* * * *
38499535 TCCTCAGTCGA-TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCC
1 TCC-CTGAC-ATTGCAGTGGAACAAATTAAAG-C-TAACGGTGAATCTTGCC
* * * * * *
38499586 TCCCTGACATTGCGGT-TAAAAAGATTAAAGCTACAGCAGCGAATCTTACC
1 TCCCTGACATTGCAGTGGAACAA-ATTAAAGCTA-A-CGGTGAATCTTGCC
**** * * * * * *
38499636 TCCCTGGTGGTGCACTGGAACAGATTAAAGCCACGTCGGTGAATCTCGCT
1 TCCCTGACATTGCAGTGGAACAAATTAAAGCTA--ACGGTGAATCTTGCC
* *
38499686 TCCCTGACATTGCAGT-TAAAAAGATTAAAGCTA
1 TCCCTGACATTGCAGTGGAACAA-ATTAAAGCTA
38499719 CAACAGCGAA
Statistics
Matches: 168, Mismatches: 51, Indels: 30
0.67 0.20 0.12
Matches are distributed among these distances:
48 2 0.01
49 13 0.08
50 112 0.67
51 36 0.21
52 5 0.03
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (48 bp):
TCCCTGACATTGCAGTGGAACAAATTAAAGCTAACGGTGAATCTTGCC
Found at i:38499704 original size:100 final size:100
Alignment explanation
Indices: 38499424--38499783 Score: 479
Period size: 100 Copynumber: 3.6 Consensus size: 100
38499414 GTGAAATCAA
* ** * * * ** *
38499424 GAATCTTACTATCCCTGGCAGTGCAGTGGAGCAAATTAAAGTCGTAACGGTGAATCTTGCCTCCC
1 GAATCTTAC-CTCCCTGGTGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCCTCCC
*
38499489 TGACATTGCAGTTAAAAAGATTAAAGCTACAACAGT
65 TGACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * *
38499525 GAATCTTACCT-CCTCAGTCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCC
1 GAATCTTACCTCCCT-GGT-GGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCCTCC
* *
38499589 CTGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGC
64 CTGACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * *
38499626 GAATCTTACCTCCCTGGTGGTGCACTGGAACAGATTAAAGCCACGTCGGTGAATCTCGCTTCCCT
1 GAATCTTACCTCCCTGGTGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCCTCCCT
38499691 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
66 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
** * *
38499726 GAATCTTATTTCCCAGGTGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTG
1 GAATCTTACCTCCCTGGTGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTG
38499784 ATTAAAGCTA
Statistics
Matches: 227, Mismatches: 29, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
99 3 0.01
100 127 0.56
101 94 0.41
102 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (100 bp):
GAATCTTACCTCCCTGGTGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCCTCCCT
GACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
Found at i:38499730 original size:50 final size:50
Alignment explanation
Indices: 38499473--38499732 Score: 252
Period size: 50 Copynumber: 5.2 Consensus size: 50
38499463 AGTCGTAACG
38499473 GTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACA
1 GTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACA
* * * ** * * *
38499523 GTGAATCTTACCTCCTCAGTCGA-TGCAGTGGAACAGATTAAAGCCACAACG
1 GTGAATCTTGCCTCC-CTGAC-ATTGCAGTTAAAAAGATTAAAGCTACAACA
* *
38499574 GTGAATCTTGCCTCCCTGACATTGCGGTTAAAAAGATTAAAGCTACAGCA
1 GTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACA
* * **** * ** * * ** *
38499624 GCGAATCTTACCTCCCTGGTGGTGCACTGGAACAGATTAAAGCCACGTCG
1 GTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACA
* *
38499674 GTGAATCTCGCTTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACA
1 GTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACA
*
38499724 GCGAATCTT
1 GTGAATCTT
38499733 ATTTCCCAGG
Statistics
Matches: 156, Mismatches: 51, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
49 1 0.01
50 114 0.73
51 40 0.26
52 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (50 bp):
GTGAATCTTGCCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACA
Found at i:38499750 original size:50 final size:50
Alignment explanation
Indices: 38499495--38499782 Score: 200
Period size: 50 Copynumber: 5.7 Consensus size: 50
38499485 TCCCTGACAT
* * * *
38499495 TGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTACCT-CCTCAGTCGA
1 TGCAGTGAAAAAGATTAAAGCCACAACAGTGAATCTTACCTCCCT-GGT-GG
* * * * ****
38499546 TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGTGAATCTTACCTCCCTGGTGG
* * * * *
38499596 TGCGGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCTGGTGG
1 TGCAGTGAAAAAGATTAAAGCCACAACAGTGAATCTTACCTCCCTGGTGG
* * * ** * ** * ****
38499646 TGCACTGGAACAGATTAAAGCCACGTCGGTGAATCTCGCTTCCCTGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGTGAATCTTACCTCCCTGGTGG
* * * ** *
38499696 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTATTTCCCAGGTGG
1 TGCAGTGAAAAAGATTAAAGCCACAACAGTGAATCTTACCTCCCTGGTGG
* * *
38499746 TGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGTGAATCTT
38499783 GATTAAAGCT
Statistics
Matches: 172, Mismatches: 64, Indels: 3
0.72 0.27 0.01
Matches are distributed among these distances:
50 134 0.78
51 35 0.20
52 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (50 bp):
TGCAGTGAAAAAGATTAAAGCCACAACAGTGAATCTTACCTCCCTGGTGG
Found at i:38499804 original size:25 final size:25
Alignment explanation
Indices: 38499758--38499807 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38499748 CAGTGGAACA
* **
38499758 GATTAAAGCCACATCAGTGAATCTT
1 GATTAAAGCCACAACAACGAATCTT
*
38499783 GATTAAAGCTACAACAACGAATCTT
1 GATTAAAGCCACAACAACGAATCTT
38499808 ACTCCCTAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAACGAATCTT
Found at i:38499831 original size:75 final size:75
Alignment explanation
Indices: 38499708--38499858 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
38499698 CAGTTAAAAA
* * * *
38499708 GATTAAAGCTACAACAGCGAATCTTATTTCCCAGGTGGTGCAGTGGAACAGATTAAAGCCACATC
1 GATTAAAGCTACAACAACGAATCTTATCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATC
38499773 AGTGAATCTT
66 AGTGAATCTT
*
38499783 GATTAAAGCTACAACAACGAATCTTA-CTCCCTAGGCGATGCAGTGGAACAGATTAAAGTCACAT
1 GATTAAAGCTACAACAACGAATCTTATCTCCC-AGGCGATGCAGTGGAACAGATTAAAGCCACAT
38499847 CAGTGAATCTT
65 CAGTGAATCTT
38499858 G
1 G
38499859 CTTCCCCAAC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 4 0.06
75 66 0.94
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (75 bp):
GATTAAAGCTACAACAACGAATCTTATCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATC
AGTGAATCTT
Found at i:38499855 original size:50 final size:49
Alignment explanation
Indices: 38499820--38500106 Score: 261
Period size: 50 Copynumber: 5.8 Consensus size: 49
38499810 TCCCTAGGCG
* * * *
38499820 ATGCAGTGGAACAGATTAAAGTCACATCAGTGAATCTTGCTTCCCCAAC
1 ATGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTACTTCCCCAAC
* * * * * *
38499869 ATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTACTTCTCTAGC
1 A-TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTACTTCCCCAAC
* * * * * *
38499919 GGTGCAGTGGAACAGATTAAAGCCATATCGGTGAATCTTGCTTCCCCAAC
1 -ATGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTACTTCCCCAAC
* * * ** *
38499969 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCAAATCTTAC-TCCCCAGGC
1 A-TGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTACTTCCCCA-AC
* * * * *
38500019 GATGCAGTGGAACAGATTAAAACCACATCGGTGAATCTTACTTCCCCGAC
1 -ATGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTACTTCCCCAAC
* *
38500069 ATGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
1 ATGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTT
38500107 GATTAAAGCT
Statistics
Matches: 183, Mismatches: 49, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
49 41 0.22
50 136 0.74
51 6 0.03
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (49 bp):
ATGCAGTGAAAAAGATTAAAGCCACATCAGTGAATCTTACTTCCCCAAC
Found at i:38499899 original size:175 final size:175
Alignment explanation
Indices: 38499608--38499958 Score: 517
Period size: 175 Copynumber: 2.0 Consensus size: 175
38499598 CGGTTAAAAA
* * * * *
38499608 GATTAAAGCTACAGCAGCGAATCTTACCTCCCTGGTGGTGCACTGGAACAGATTAAAGCCACGTC
1 GATTAAAGCTACAACAACGAATCTTACCTCCCTGGCGATGCACTGGAACAGATTAAAGCCACATC
* ** *
38499673 GGTGAATCTCGCTTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTATTTC
66 AGTGAATCTCGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTC
*
38499738 -CCAGGTGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTT
131 TCCA-GCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTT
* *
38499783 GATTAAAGCTACAACAACGAATCTTA-CTCCCTAGGCGATGCAGTGGAACAGATTAAAGTCACAT
1 GATTAAAGCTACAACAACGAATCTTACCTCCCT-GGCGATGCACTGGAACAGATTAAAGCCACAT
* *
38499847 CAGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTACTT
65 CAGTGAATCTCGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTT
* * *
38499912 CTCTAGCGGTGCAGTGGAACAGATTAAAGCCATATCGGTGAATCTT
130 CTCCAGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTT
38499958 G
1 G
38499959 CTTCCCCAAC
Statistics
Matches: 157, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
174 6 0.04
175 149 0.95
176 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (175 bp):
GATTAAAGCTACAACAACGAATCTTACCTCCCTGGCGATGCACTGGAACAGATTAAAGCCACATC
AGTGAATCTCGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTC
TCCAGCGGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTT
Found at i:38499956 original size:100 final size:100
Alignment explanation
Indices: 38499783--38500090 Score: 485
Period size: 100 Copynumber: 3.1 Consensus size: 100
38499773 AGTGAATCTT
* *
38499783 GATTAAAGCTACAACAACGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGTCACATC
1 GATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATC
*
38499848 AGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAA
66 GGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAA
* * * *
38499883 GATTAAAGCTACAACAGTGAATCTTACTTCTCTA-GCGGTGCAGTGGAACAGATTAAAGCCATAT
1 GATTAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACAT
38499947 CGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAA
65 CGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAA
* * *
38499983 GATTAAAGCTACAACAGCAAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAACCACATC
1 GATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATC
* *
38500048 GGTGAATCTTACTTCCCCGACA-TGCAGTTAAAAA
66 GGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAA
38500082 GATTAAAGC
1 GATTAAAGC
38500091 CACATCGGTG
Statistics
Matches: 190, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
99 25 0.13
100 160 0.84
101 5 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (100 bp):
GATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATC
GGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAA
Found at i:38500034 original size:275 final size:276
Alignment explanation
Indices: 38499507--38500057 Score: 818
Period size: 275 Copynumber: 2.0 Consensus size: 276
38499497 CAGTTAAAAA
** *
38499507 GATTAAAGCTACAACAGTGAATCTTACCTCCTCAGTCGATGCAGTGGAACAGATTAAAGCCACAA
1 GATTAAAGCTACAACAACGAATCTTACCTCCTCAGGCGATGCAGTGGAACAGATTAAAGCCACAA
* ** * *
38499572 CGGTGAATCTTGCCTCCCTGACATTGCGGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTACCT
66 CAGTGAATCTTGCCTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACCT
* * * **
38499637 CCCTGGTGGTGCACTGGAACAGATTAAAGCCACGTCGGTGAATCTCGCTTCCCTGACATTGCAGT
131 CCCTAGCGGTGCACTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTGCAGT
* * * * * *
38499702 TAAAAAGATTAAAGCTACAACAGCGAATCTTATTTCCCAGGTGGTGCAGTGGAACAGATTAAAGC
196 TAAAAAGATTAAAGCTACAACAGCAAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAAC
38499767 CACATCAGTGAATCTT
261 CACATCAGTGAATCTT
*
38499783 GATTAAAGCTACAACAACGAATCTTA-CTCC-CTAGGCGATGCAGTGGAACAGATTAAAGTCACA
1 GATTAAAGCTACAACAACGAATCTTACCTCCTC-AGGCGATGCAGTGGAACAGATTAAAGCCACA
* * * *
38499846 TCAGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTACT
65 ACAGTGAATCTTGCCTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACC
* * * *
38499911 TCTCTAGCGGTGCAGTGGAACAGATTAAAGCCATATCGGTGAATCTTGCTTCCCCAACATTGCAG
130 TCCCTAGCGGTGCACTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTGCAG
38499976 TTAAAAAGATTAAAGCTACAACAGCAAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAA
195 TTAAAAAGATTAAAGCTACAACAGCAAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAA
*
38500041 CCACATCGGTGAATCTT
260 CCACATCAGTGAATCTT
38500058 ACTTCCCCGA
Statistics
Matches: 245, Mismatches: 29, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
274 1 0.00
275 220 0.90
276 24 0.10
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (276 bp):
GATTAAAGCTACAACAACGAATCTTACCTCCTCAGGCGATGCAGTGGAACAGATTAAAGCCACAA
CAGTGAATCTTGCCTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACCT
CCCTAGCGGTGCACTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTGCAGT
TAAAAAGATTAAAGCTACAACAGCAAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAAC
CACATCAGTGAATCTT
Found at i:38500128 original size:25 final size:25
Alignment explanation
Indices: 38500082--38500131 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38500072 CAGTTAAAAA
* * *
38500082 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
38500107 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
38500132 ACTCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:38500162 original size:224 final size:225
Alignment explanation
Indices: 38499883--38500314 Score: 582
Period size: 224 Copynumber: 1.9 Consensus size: 225
38499873 CAGTTAAAAA
* * * * * *
38499883 GATTAAAGCTACAACAGTGAATCTTACTTCTCTAGCGGTGCAGTGGAACAGATTAAAGCCA-TAT
1 GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGTGGAACAGATTAAAGCCACAAT
*
38499947 CGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGCAAATCTTACTC
66 -GGTGAATCTTGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAACAGCAAATCTTACTC
* * * * *
38500012 CCCAGGCGATGCAGTGGAACAGATTAAAACCA-CATCGGTGAATCTTACTTCCCCGACAT-GCAG
130 CCCAAGCGATGCAGAGGAACAGATTAAAACCATAAT-GGCGAATCTTACTTCCCCGACATCACAG
*
38500075 TTAAAAAGATTAAAGCCACATCGGTGAATCTT
194 CTAAAAAGATTAAAGCCACATCGGTGAATCTT
*
38500107 GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGTGGAATAGATTAAAGCCACAAT
1 GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGTGGAACAGATTAAAGCCACAAT
** * * **
38500172 GGTGAATCTTGCTTCCCTGACATTACAGTTAAAAAGATTAAAGCTACAACGGCGAATCTTACTTT
66 GGTGAATCTTGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAACAGCAAATCTTACTCC
* * * * * *
38500237 CCAAGCGGTGTAGAGGAACAGATTGAAGCTATAATGGCGAATCTTACTTCCTCGACATCACAGCT
131 CCAAGCGATGCAGAGGAACAGATTAAAACCATAATGGCGAATCTTACTTCCCCGACATCACAGCT
*
38500302 AAACAGATTAAAG
196 AAAAAGATTAAAG
38500315 TTACGAGTTA
Statistics
Matches: 178, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
224 158 0.89
225 20 0.11
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (225 bp):
GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGTGGAACAGATTAAAGCCACAAT
GGTGAATCTTGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAACAGCAAATCTTACTCC
CCAAGCGATGCAGAGGAACAGATTAAAACCATAATGGCGAATCTTACTTCCCCGACATCACAGCT
AAAAAGATTAAAGCCACATCGGTGAATCTT
Found at i:38500280 original size:100 final size:100
Alignment explanation
Indices: 38500107--38500314 Score: 265
Period size: 100 Copynumber: 2.1 Consensus size: 100
38500097 GGTGAATCTT
* *
38500107 GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGTGGAATAGATTAAAGCCACAAT
1 GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGAGGAACAGATTAAAGCCACAAT
* * * *
38500172 GGTGAATCTTGCTTCC-CTGACATTACAGTTAAAAA
66 GGCGAATCTTACTTCCTC-GACATCACAGCTAAAAA
* ** * * * * *
38500207 GATTAAAGCTACAACGGCGAATCTTACTTTCCAAGCGGTGTAGAGGAACAGATTGAAGCTATAAT
1 GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGAGGAACAGATTAAAGCCACAAT
*
38500272 GGCGAATCTTACTTCCTCGACATCACAGCTAAACA
66 GGCGAATCTTACTTCCTCGACATCACAGCTAAAAA
38500307 GATTAAAG
1 GATTAAAG
38500315 TTACGAGTTA
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
100 91 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (100 bp):
GATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCAGTGCAGAGGAACAGATTAAAGCCACAAT
GGCGAATCTTACTTCCTCGACATCACAGCTAAAAA
Found at i:38501038 original size:16 final size:15
Alignment explanation
Indices: 38501019--38501053 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
38501009 TTTATATTAT
*
38501019 TTTTGTTTTCTTTTTC
1 TTTTGTTTTC-CTTTC
38501035 TTTTGTTTTCCTTTC
1 TTTTGTTTTCCTTTC
38501050 TTTT
1 TTTT
38501054 TTCATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTGTTTTCCTTTC
Found at i:38501708 original size:9 final size:9
Alignment explanation
Indices: 38501684--38501718 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
38501674 TAAATTATAA
*
38501684 TACTATTAT
1 TACTATTAC
*
38501693 TATTATTAC
1 TACTATTAC
38501702 TACTATTAC
1 TACTATTAC
38501711 TACTATTA
1 TACTATTA
38501719 TTATAGGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (9 bp):
TACTATTAC
Found at i:38509610 original size:27 final size:27
Alignment explanation
Indices: 38509579--38509773 Score: 119
Period size: 27 Copynumber: 7.3 Consensus size: 27
38509569 CCCAATATTT
* *
38509579 GTAAAATAATCGCAATACCCCTTTAGG
1 GTAAAATAATCGTAATACCCCTATAGG
* * *
38509606 GTAAAATGAA-CGTACTGCCCCTGTAGG
1 GTAAAAT-AATCGTAATACCCCTATAGG
* * *
38509633 GTAAAATAA-CTGAAAAACCCC-ATAAG
1 GTAAAATAATC-GTAATACCCCTATAGG
* * * *
38509659 GTAAAATAATTGTAATGCCCTTGTAGG
1 GTAAAATAATCGTAATACCCCTATAGG
* * * * ** *
38509686 GTAAAATGATTGAAAAACCCCCGTAGA
1 GTAAAATAATCGTAATACCCCTATAGG
* *
38509713 GTAAAATGATCGTAATGCCCCTATAGG
1 GTAAAATAATCGTAATACCCCTATAGG
* *
38509740 GTAAAATGACCGTAATA-CCCTCATAGG
1 GTAAAATAATCGTAATACCCCT-ATAGG
*
38509767 GTTAAAT
1 GTAAAAT
38509774 GACCAGAATA
Statistics
Matches: 129, Mismatches: 34, Indels: 10
0.75 0.20 0.06
Matches are distributed among these distances:
26 25 0.19
27 102 0.79
28 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24
Consensus pattern (27 bp):
GTAAAATAATCGTAATACCCCTATAGG
Found at i:38509653 original size:54 final size:53
Alignment explanation
Indices: 38509602--38509775 Score: 179
Period size: 54 Copynumber: 3.2 Consensus size: 53
38509592 AATACCCCTT
*
38509602 TAGGGTAAAATGAACGTACTGCCCCTGTAGGGTAAAATAACTGAAAAACCCCA
1 TAGGGTAAAATGAACGTAATGCCCCTGTAGGGTAAAATAACTGAAAAACCCCA
* * * * * *
38509655 TAAGGTAAAAT-AATTGTAATGCCCTTGTAGGGTAAAATGATTGAAAAACCCCCG
1 TAGGGTAAAATGAA-CGTAATGCCCCTGTAGGGTAAAATAACTGAAAAA-CCCCA
* * * * * * *
38509709 TAGAGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGACCGTAATACCCTCA
1 TAGGGTAAAATGAACGTAATGCCCCTGTAGGGTAAAATAACTGAAAAACCC-CA
*
38509763 TAGGGTTAAATGA
1 TAGGGTAAAATGA
38509776 CCAGAATACC
Statistics
Matches: 97, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
52 2 0.02
53 42 0.43
54 52 0.54
55 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (53 bp):
TAGGGTAAAATGAACGTAATGCCCCTGTAGGGTAAAATAACTGAAAAACCCCA
Found at i:38509684 original size:53 final size:54
Alignment explanation
Indices: 38509606--38509746 Score: 171
Period size: 53 Copynumber: 2.6 Consensus size: 54
38509596 CCCCTTTAGG
*
38509606 GTAAAATGAA-CGTACTGCCCCTGTAGGGTAAAATAACTGAAAAA-CCCCATA-A
1 GTAAAAT-AATCGTAATGCCCCTGTAGGGTAAAATAACTGAAAAACCCCCATAGA
* * * * *
38509658 GGTAAAATAATTGTAATGCCCTTGTAGGGTAAAATGATTGAAAAACCCCCGTAGA
1 -GTAAAATAATCGTAATGCCCCTGTAGGGTAAAATAACTGAAAAACCCCCATAGA
* *
38509713 GTAAAATGATCGTAATGCCCCTATAGGGTAAAAT
1 GTAAAATAATCGTAATGCCCCTGTAGGGTAAAAT
38509747 GACCGTAATA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
52 2 0.03
53 36 0.48
54 36 0.48
55 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (54 bp):
GTAAAATAATCGTAATGCCCCTGTAGGGTAAAATAACTGAAAAACCCCCATAGA
Found at i:38509774 original size:27 final size:27
Alignment explanation
Indices: 38509602--38509809 Score: 104
Period size: 27 Copynumber: 7.7 Consensus size: 27
38509592 AATACCCCTT
* * * *
38509602 TAGGGTAAAATGAACGTACTGCCC-CTG
1 TAGGGTAAAATGACCGTAATACCCTC-A
* * * *
38509629 TAGGGTAAAATAACTGAAAAACCC-CA
1 TAGGGTAAAATGACCGTAATACCCTCA
* * ** * **
38509655 TAAGGTAAAATAATTGTAATGCCCTTG
1 TAGGGTAAAATGACCGTAATACCCTCA
** * * * *
38509682 TAGGGTAAAATGATTGAAAAACCCCCG
1 TAGGGTAAAATGACCGTAATACCCTCA
* * *
38509709 TAGAGTAAAATGATCGTAATGCCC-CTA
1 TAGGGTAAAATGACCGTAATACCCTC-A
38509736 TAGGGTAAAATGACCGTAATACCCTCA
1 TAGGGTAAAATGACCGTAATACCCTCA
*
38509763 TAGGGTTAAATGACCAG-AATACCCCTGCA
1 TAGGGTAAAATGACC-GTAATA-CCCT-CA
38509792 -A-GGTAAAATGACCGTAAT
1 TAGGGTAAAATGACCGTAAT
38509810 GCCCATGGAG
Statistics
Matches: 141, Mismatches: 33, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
26 21 0.15
27 111 0.79
28 7 0.05
29 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (27 bp):
TAGGGTAAAATGACCGTAATACCCTCA
Found at i:38509823 original size:27 final size:26
Alignment explanation
Indices: 38509713--38509829 Score: 89
Period size: 27 Copynumber: 4.4 Consensus size: 26
38509703 CCCCCGTAGA
*
38509713 GTAAAATGATCGTAATGCCCCTAT-AGG
1 GTAAAATGACCGTAATG-CCC-ATGAGG
*
38509740 GTAAAATGACCGTAATACCCTCAT-AGG
1 GTAAAATGACCGTAAT-GCC-CATGAGG
* * * *
38509767 GTTAAATGACCAG-AATACCCCTGCAAG
1 GTAAAATGACC-GTAATGCCCATG-AGG
38509794 GTAAAATGACCGTAATGCCCATGGAGG
1 GTAAAATGACCGTAATGCCCAT-GAGG
38509821 GT-AAATGAC
1 GTAAAATGAC
38509830 TATTTTGCCT
Statistics
Matches: 73, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
25 2 0.03
26 10 0.14
27 58 0.79
28 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (26 bp):
GTAAAATGACCGTAATGCCCATGAGG
Found at i:38509883 original size:24 final size:24
Alignment explanation
Indices: 38509846--38509942 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
38509836 GCCTCTCAAG
* *
38509846 TGTAAATGATTGATTTGTTTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
38509870 TGTAAATGGCTGATTTGTCTATGA
1 TGTAAATGACTGATTTGTCTGTGA
*
38509894 TTTAAATGACTGATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
38509918 TTGGT--ATGATTGATTTGTCTGTGA
1 -T-GTAAATGACTGATTTGTCTGTGA
38509942 T
1 T
38509943 TTGTATAACT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
23 1 0.02
24 59 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:38510169 original size:32 final size:32
Alignment explanation
Indices: 38510128--38510266 Score: 138
Period size: 32 Copynumber: 4.4 Consensus size: 32
38510118 GTTGCGATGC
*
38510128 TACTGATGGCTTTGTGTCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
38510160 TACTGATGGCTTTTTACCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
38510192 TACTGATGG-TTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTT-TGTGCCGATCATATTACCGT
* * * * *
38510224 TACTGATGGATTTCTACCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
38510255 TACTTATGGCTT
1 TACTGATGGCTT
38510267 GTAGCCATTC
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
31 12 0.13
32 75 0.84
33 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:38510213 original size:64 final size:64
Alignment explanation
Indices: 38510128--38510252 Score: 171
Period size: 64 Copynumber: 2.0 Consensus size: 64
38510118 GTTGCGATGC
* * * * * *
38510128 TACTGATGGCTTTGTGTCGATCATATTACCGTTACTGATGGCTTTTTACCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATCACCGCTACTGATGGATTTCTACCAATCATATTACCAT
*
38510192 TACTGATGG-TTGTGTGCCGATCATATCACTGCTACTGATGGATTTCTACCAATCATATTAC
1 TACTGATGGCTT-TGTGCCGATCATATCACCGCTACTGATGGATTTCTACCAATCATATTAC
38510253 TGTACTTATG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
63 2 0.04
64 51 0.96
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (64 bp):
TACTGATGGCTTTGTGCCGATCATATCACCGCTACTGATGGATTTCTACCAATCATATTACCAT
Found at i:38510426 original size:37 final size:37
Alignment explanation
Indices: 38510376--38510464 Score: 178
Period size: 37 Copynumber: 2.4 Consensus size: 37
38510366 GTGCTGATAT
38510376 TGGTGTGTTGGTTGGGTGGGTCGATTTTATCCCCACA
1 TGGTGTGTTGGTTGGGTGGGTCGATTTTATCCCCACA
38510413 TGGTGTGTTGGTTGGGTGGGTCGATTTTATCCCCACA
1 TGGTGTGTTGGTTGGGTGGGTCGATTTTATCCCCACA
38510450 TGGTGTGTTGGTTGG
1 TGGTGTGTTGGTTGG
38510465 TACGGGTGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.09, C:0.13, G:0.38, T:0.39
Consensus pattern (37 bp):
TGGTGTGTTGGTTGGGTGGGTCGATTTTATCCCCACA
Found at i:38516021 original size:21 final size:20
Alignment explanation
Indices: 38515984--38516042 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
38515974 TAATTTTAAC
*
38515984 AAATGAAATGAAA-TCAACCT
1 AAATG-AATTAAATTCAACCT
*
38516004 AACATGAATTAAATTCAAGCT
1 AA-ATGAATTAAATTCAACCT
* *
38516025 AAATTATTTAAATT-AACC
1 AAATGAATTAAATTCAACC
38516043 ATTCCAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.09
20 18 0.56
21 11 0.34
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATGAATTAAATTCAACCT
Found at i:38518735 original size:3 final size:3
Alignment explanation
Indices: 38518727--38518751 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38518717 CTCTGTGGGA
38518727 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
38518752 TTGGATCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:38520373 original size:30 final size:30
Alignment explanation
Indices: 38520313--38520374 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
38520303 GCTTTTTGAA
* * *
38520313 AATATTTACAAAAAGAGTCATCTAATTTTT
1 AATATTTACAAAAAGAGTCACCAAAATTTT
38520343 AATATTTACAAAAAGAG-CAACCAAAATTTT
1 AATATTTACAAAAAGAGTC-ACCAAAATTTT
38520373 AA
1 AA
38520375 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGTCACCAAAATTTT
Found at i:38527300 original size:19 final size:19
Alignment explanation
Indices: 38527256--38527302 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
38527246 TTTCTTCAAA
38527256 TTTTCAATTTTTTATTGAT
1 TTTTCAATTTTTTATTGAT
** *
38527275 TCATCAATATTTTT-TTTAT
1 TTTTCAAT-TTTTTATTGAT
38527294 TTTTCAATT
1 TTTTCAATT
38527303 GGTTTCATCC
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTCAATTTTTTATTGAT
Found at i:38544362 original size:19 final size:19
Alignment explanation
Indices: 38544338--38544381 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
38544328 TAAAAGCAAC
38544338 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
38544357 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
38544376 ACAACA
1 ACAACA
38544382 AAAATAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:38547272 original size:96 final size:91
Alignment explanation
Indices: 38547007--38547406 Score: 619
Period size: 91 Copynumber: 4.4 Consensus size: 91
38546997 ATTAAAAATT
* * *
38547007 AATTAATATAATAGTACAACAGCATAAATTAAAC-AAAAAAAAGTATGTTAAGCTACATTTTAAA
1 AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAAAGTATGTTAAACCACAGTTTAAA
38547071 CTTTAAAGTTAGTTAATTGAAGCCTA
66 CTTTAAAGTTAGTTAATTGAAGCCTA
* * * * *
38547097 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTATTAAGCTATC-GTTTAA
1 AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAAAGTATGTTAAACCA-CAGTTTAA
38547161 ACTTTAAAGTTAGTTAATTGAAGCCTA
65 ACTTTAAAGTTAGTTAATTGAAGCCTA
38547188 AATTAATATAATAGTCCAAGTACAACAGCATAAATTAAAC-AAAAAAAAGTATGTTAAACCACAG
1 AATTAATAT-A-A-T---AGTACAACAGCATAAATTAAACAAAAAAAAAGTATGTTAAACCACAG
38547252 TTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
60 TTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
*
38547284 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCA-GTTAAACCACAGTTTAA
1 AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAAAGT-ATGTTAAACCACAGTTTAA
38547348 ACTTTAAAGTTAGTTAATTGAAGCCTA
65 ACTTTAAAGTTAGTTAATTGAAGCCTA
38547375 AATTAATATAATAGTACAACAGCATAAATTAA
1 AATTAATATAATAGTACAACAGCATAAATTAA
38547407 TTAATTGAAG
Statistics
Matches: 288, Mismatches: 11, Indels: 21
0.90 0.03 0.07
Matches are distributed among these distances:
90 54 0.19
91 145 0.50
92 3 0.01
93 2 0.01
94 2 0.01
95 2 0.01
96 59 0.20
97 21 0.07
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.30
Consensus pattern (91 bp):
AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAAAGTATGTTAAACCACAGTTTAAA
CTTTAAAGTTAGTTAATTGAAGCCTA
Found at i:38547326 original size:187 final size:187
Alignment explanation
Indices: 38547019--38547389 Score: 665
Period size: 187 Copynumber: 2.0 Consensus size: 187
38547009 TTAATATAAT
* * *
38547019 AGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAGCTACATTTTAAACTTTAAAGTTAGT
1 AGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAACCACAGTTTAAACTTTAAAGTTAGT
38547084 TAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTA-TTA
66 TAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTC-AGTTA
* *
38547148 AGCTATC-GTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTCCA
130 AACCA-CAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTCCA
38547206 AGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAACCACAGTTTAAACTTTAAAGTTAGT
1 AGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAACCACAGTTTAAACTTTAAAGTTAGT
38547271 TAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCAGTTAA
66 TAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCAGTTAA
38547336 ACCACAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGT
131 ACCACAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGT
38547390 ACAACAGCAT
Statistics
Matches: 177, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
186 2 0.01
187 175 0.99
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (187 bp):
AGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAACCACAGTTTAAACTTTAAAGTTAGT
TAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCAGTTAA
ACCACAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTCCA
Found at i:38547617 original size:19 final size:20
Alignment explanation
Indices: 38547595--38547640 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
38547585 TTTAATTTTT
38547595 ATTTA-TAATTTTATTCATC
1 ATTTAGTAATTTTATTCATC
*
38547614 ATTTAATGTTATTTTATTCATC
1 ATTT-A-GTAATTTTATTCATC
38547636 ATTTA
1 ATTTA
38547641 ATGTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 1 0.04
22 17 0.74
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTAGTAATTTTATTCATC
Found at i:38547630 original size:22 final size:22
Alignment explanation
Indices: 38547602--38547652 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
38547592 TTTATTTATA
38547602 ATTTTATTCATCATTTAATGTT
1 ATTTTATTCATCATTTAATGTT
38547624 ATTTTATTCATCATTTAATGTT
1 ATTTTATTCATCATTTAATGTT
38547646 ATTTTAT
1 ATTTTAT
38547653 CGAATTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (22 bp):
ATTTTATTCATCATTTAATGTT
Found at i:38547740 original size:17 final size:17
Alignment explanation
Indices: 38547718--38547769 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
38547708 TTTTCTCTAT
*
38547718 TAATATTACGTTATTAC
1 TAATATTACATTATTAC
*
38547735 TAATATTATATTATTAC
1 TAATATTACATTATTAC
38547752 TAATATTACATTATTAC
1 TAATATTACATTATTAC
38547769 T
1 T
38547770 TTGGGAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATATTACATTATTAC
Found at i:38548180 original size:19 final size:19
Alignment explanation
Indices: 38548156--38548217 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
38548146 GGAGAAGGAA
38548156 AATAGAGCGAAAATCATTC
1 AATAGAGCGAAAATCATTC
* *
38548175 AATAGAGCGAAACA-GATGC
1 AATAGAGCGAAA-ATCATTC
*
38548194 AAATAGAGCTAAAATCATTC
1 -AATAGAGCGAAAATCATTC
38548214 AATA
1 AATA
38548218 ATTCAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (19 bp):
AATAGAGCGAAAATCATTC
Found at i:38560996 original size:14 final size:13
Alignment explanation
Indices: 38560960--38560984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38560950 TAAACCGTTT
38560960 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
38560973 TTTTTCTTTTTT
1 TTTTTCTTTTTT
38560985 GCTTATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:38570447 original size:89 final size:89
Alignment explanation
Indices: 38570321--38570723 Score: 486
Period size: 89 Copynumber: 4.5 Consensus size: 89
38570311 CTAAAAACAA
* * * *
38570321 CAGACCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTGACCTCTTTGAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTGACCTCCTTGAGTT
* *
38570386 TGCAGCGGAGTAAACTGAAGATAG
66 TGCAGCGGAATAGACTGAAGATAG
* ** * * * *
38570410 CAGATCTTTTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACATTAGTCTAACCT-TTCTAAGT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTGACCTCCT-TGAGT
38570474 TTGCAGCGGAATAGACTGAAGATAG
65 TTGCAGCGGAATAGACTGAAGATAG
* * * *
38570499 CAGATCTTGTCTTCCTGTACTGGTAGCGAAGCAGATCAAAGACACCAGCCTGACCTCCCTGAGTT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTGACCTCCTTGAGTT
* *
38570564 TGCAGTGGAACAGACTGAAGATAG
66 TGCAGCGGAATAGACTGAAGATAG
38570588 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTCG-CCTCCTTGAGT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCT-GACCTCCTTGAGT
** * * *
38570652 TTGCAGCGGAGCAGACCGGAGATTG
65 TTGCAGCGGAATAGACTGAAGATAG
* * * * * * **
38570677 TAGATTTTGTCTTCTTGTACTGGCAGTGAAGTAGATTAAAGACACCA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCA
38570724 ATCCTATCTC
Statistics
Matches: 271, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
88 2 0.01
89 268 0.99
90 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (89 bp):
CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGCCTGACCTCCTTGAGTT
TGCAGCGGAATAGACTGAAGATAG
Found at i:38570665 original size:44 final size:43
Alignment explanation
Indices: 38570523--38570666 Score: 107
Period size: 44 Copynumber: 3.3 Consensus size: 43
38570513 CTGTACTGGT
*
38570523 AGCGAAGCAGATCAAAGACACCAGCCTGACCTCCCTGAGTTTGC
1 AGCGAAGCAGATCGAAGACACCAGCCTGACCT-CCTGAGTTTGC
* * * * * * *
38570567 AGTGGAA-CAGA-CTGAAGATAGCAGATCTTGTCTTCCTGTA-TTGGC
1 AG-CGAAGCAGATC-GAAGACACCAG--CCTGACCTCCTG-AGTTTGC
38570612 AGCGAAGCAGATCGAAGACACCAGCCTCG-CCTCCTTGAGTTTGC
1 AGCGAAGCAGATCGAAGACACCAGCCT-GACCTCC-TGAGTTTGC
*
38570656 AGCGGAGCAGA
1 AGCGAAGCAGA
38570667 CCGGAGATTG
Statistics
Matches: 75, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
43 8 0.11
44 34 0.45
45 26 0.35
46 7 0.09
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (43 bp):
AGCGAAGCAGATCGAAGACACCAGCCTGACCTCCTGAGTTTGC
Found at i:38570886 original size:99 final size:100
Alignment explanation
Indices: 38570753--38570960 Score: 301
Period size: 99 Copynumber: 2.1 Consensus size: 100
38570743 ATAGTGGAAT
* ** *
38570753 AGATTGAAGCTACAATGACGAATCTGACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCACAACAACGAATCTGACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAA
* * *
38570818 TGGTGAATCTTGCTTCCCCGACATTGCAATTAA-A
66 CGGTGAATCTAGCTTCCCCAACATTGCAATTAATA
* **
38570852 AGATTGAAGCCACAACAACGAATCTTACTTCCCTGGCAGTGCAGTGGAGTAGATTGAAGCTACAA
1 AGATTGAAGCCACAACAACGAATCTGACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAA
* *
38570917 CGGTGAATCTAGCTTCCCCAACATTGCAGTTAATT
66 CGGTGAATCTAGCTTCCCCAACATTGCAATTAATA
38570952 AGATTGAAG
1 AGATTGAAG
38570961 ATAGCAAATC
Statistics
Matches: 96, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 87 0.91
100 9 0.09
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (100 bp):
AGATTGAAGCCACAACAACGAATCTGACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAA
CGGTGAATCTAGCTTCCCCAACATTGCAATTAATA
Found at i:38570926 original size:50 final size:50
Alignment explanation
Indices: 38570745--38570918 Score: 188
Period size: 50 Copynumber: 3.5 Consensus size: 50
38570735 TTAGCATTAT
* * *
38570745 AGTGGAATAGATTGAAGCTACAATGACGAATCTGACTTCCCTGGCGGTGC
1 AGTGGAATAGATTGAAGCTACAACGACGAATCTTACTTCCCTGGCAGTGC
* * ** * * * *
38570795 AGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGC
1 AGTGGAATAGATTGAAGCTACAACGACGAATCTTACTTCCCTGGCAGTGC
* * * * *
38570845 AAT-TAAAAGATTGAAGCCACAACAACGAATCTTACTTCCCTGGCAGTGC
1 AGTGGAATAGATTGAAGCTACAACGACGAATCTTACTTCCCTGGCAGTGC
*
38570894 AGTGGAGTAGATTGAAGCTACAACG
1 AGTGGAATAGATTGAAGCTACAACG
38570919 GTGAATCTAG
Statistics
Matches: 96, Mismatches: 27, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
49 37 0.39
50 59 0.61
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (50 bp):
AGTGGAATAGATTGAAGCTACAACGACGAATCTTACTTCCCTGGCAGTGC
Found at i:38570945 original size:50 final size:50
Alignment explanation
Indices: 38570745--38570960 Score: 170
Period size: 50 Copynumber: 4.3 Consensus size: 50
38570735 TTAGCATTAT
* ** * * **
38570745 AGTGGAATAGATTGAAGCTACAATGACGAATCT-GACTTCCCTGGCGGTGC
1 AGTGGAATAGATTGAAGCTACAACGGTGAATCTAG-CTTCCCCGACATTGC
* * *
38570795 AGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGC
1 AGTGGAATAGATTGAAGCTACAACGGTGAATCTAGCTTCCCCGACATTGC
* * * * *** * * *
38570845 AAT-TAAAAGATTGAAGCCACAACAACGAATCTTA-CTTCCCTGGCAGTGC
1 AGTGGAATAGATTGAAGCTACAACGGTGAATC-TAGCTTCCCCGACATTGC
* *
38570894 AGTGGAGTAGATTGAAGCTACAACGGTGAATCTAGCTTCCCCAACATTGC
1 AGTGGAATAGATTGAAGCTACAACGGTGAATCTAGCTTCCCCGACATTGC
*
38570944 AGT-TAATTAGATTGAAG
1 AGTGGAA-TAGATTGAAG
38570961 ATAGCAAATC
Statistics
Matches: 128, Mismatches: 33, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
49 38 0.30
50 89 0.70
51 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (50 bp):
AGTGGAATAGATTGAAGCTACAACGGTGAATCTAGCTTCCCCGACATTGC
Found at i:38571119 original size:45 final size:44
Alignment explanation
Indices: 38571060--38571180 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 44
38571050 ATCGTATCAG
* *
38571060 GTCTTATC-CTCCTGAAGTTGAAGTGGGGCAGACTGAAGATAGCGA
1 GTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CGA
* * * *
38571105 GTCTTATCTCCCTGAAGTTGCAGAGGAGCAGATTGAAGCTACTA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACGA
* **
38571149 ATCCAATCTCCCTGAAGTTGCAGTGGAGCAGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
38571181 TTAAAACGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 30 0.46
45 34 0.52
46 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACGA
Found at i:38571603 original size:6 final size:6
Alignment explanation
Indices: 38571592--38571619 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38571582 AATAACCCAA
38571592 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
38571620 CAAGGCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:38573321 original size:26 final size:26
Alignment explanation
Indices: 38573255--38573313 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
38573245 CCTGAGGGCG
*
38573255 CGCTTTACTTACATGGACACAAAGCA
1 CGCTTTGCTTACATGGACACAAAGCA
**
38573281 CGCTTTGCTTACATGGACACAAAGTG
1 CGCTTTGCTTACATGGACACAAAGCA
38573307 CGCTTTG
1 CGCTTTG
38573314 TTGCCATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (26 bp):
CGCTTTGCTTACATGGACACAAAGCA
Found at i:38575485 original size:19 final size:19
Alignment explanation
Indices: 38575461--38575503 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
38575451 ATGTCATCAC
*
38575461 ATAAAATAACTTAAAAATT
1 ATAAAAGAACTTAAAAATT
*
38575480 ATAAAAGAATTTAAAAATT
1 ATAAAAGAACTTAAAAATT
38575499 ATAAA
1 ATAAA
38575504 TAAAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAAAGAACTTAAAAATT
Found at i:38583695 original size:20 final size:20
Alignment explanation
Indices: 38583670--38583712 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
38583660 TTATTTTCTT
*
38583670 TTTAAAATAT-TTTATTAAAA
1 TTTAAAATATATAT-TTAAAA
38583690 TTTAAAATATATATTTAAAA
1 TTTAAAATATATATTTAAAA
38583710 TTT
1 TTT
38583713 TAGAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAATATATATTTAAAA
Found at i:38585599 original size:2 final size:2
Alignment explanation
Indices: 38585592--38585634 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
38585582 TTACATGAGT
38585592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38585634 T
1 T
38585635 TAAAGATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38592805 original size:19 final size:20
Alignment explanation
Indices: 38592782--38592864 Score: 73
Period size: 25 Copynumber: 4.0 Consensus size: 20
38592772 AAAATTACAA
38592782 AAAAAATTTAAAATAATTT-T
1 AAAAAATTTAAAAT-ATTTAT
*
38592802 -AAAAATTCAAAATATTTAT
1 AAAAAATTTAAAATATTTAT
38592821 AAAAAATTCTAAAATTTATATTTAT
1 AAAAAATT-T-AAA---ATATTTAT
38592846 AAAAAATTATAAAAT-TTTA
1 AAAAAATT-TAAAATATTTA
38592865 ACAAAAGTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.08
19 13 0.25
20 11 0.21
21 2 0.04
22 3 0.06
24 3 0.06
25 17 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAATTTAAAATATTTAT
Found at i:38592841 original size:25 final size:25
Alignment explanation
Indices: 38592813--38592862 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
38592803 AAAATTCAAA
*
38592813 ATATTTATAAAAAATTCTAAAATTT
1 ATATTTATAAAAAATTATAAAATTT
38592838 ATATTTATAAAAAATTATAAAATTT
1 ATATTTATAAAAAATTATAAAATTT
38592863 TAACAAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTTATAAAAAATTATAAAATTT
Found at i:38599116 original size:29 final size:29
Alignment explanation
Indices: 38599043--38599118 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
38599033 TTCAGATTAC
* *
38599043 ATTTTAGTCACTTATATTTGAAATGTTAT
1 ATTTTAGTAACTTATGTTTGAAATGTTAT
* *
38599072 GTTTTAGTAATTTATGTTTGAAATGTTAT
1 ATTTTAGTAACTTATGTTTGAAATGTTAT
*
38599101 ATTTTAGTTACTTATGTT
1 ATTTTAGTAACTTATGTT
38599119 ATAGTATTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (29 bp):
ATTTTAGTAACTTATGTTTGAAATGTTAT
Found at i:38599205 original size:13 final size:13
Alignment explanation
Indices: 38599187--38599212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38599177 GCTGATGTGA
38599187 CAAACGAAAATTT
1 CAAACGAAAATTT
38599200 CAAACGAAAATTT
1 CAAACGAAAATTT
38599213 TAGGTCAAAT
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:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
CAAACGAAAATTT
Found at i:38602910 original size:40 final size:41
Alignment explanation
Indices: 38602837--38602956 Score: 106
Period size: 40 Copynumber: 2.9 Consensus size: 41
38602827 AAACTGTTCA
* *
38602837 TCCACGTCAGCAAATCGCGTCCTAGA-G-GG-CGCGATTT-GTG
1 TCCACGTAAGCAAATCGCG--CT-GACGTGGACGCGATTTCCTG
38602877 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATTTCCTG
1 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATTTCCTG
* ** *
38602918 -GCACGTACCCTGACATCGCGCTGACGTGGACGCGATTTC
1 TCCACGTAAGC--AAATCGCGCTGACGTGGACGCGATTTC
38602957 GCGGAAAATG
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
37 2 0.03
38 3 0.04
39 2 0.03
40 33 0.49
41 2 0.03
42 26 0.38
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (41 bp):
TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATTTCCTG
Found at i:38608684 original size:113 final size:114
Alignment explanation
Indices: 38608517--38608922 Score: 437
Period size: 113 Copynumber: 3.6 Consensus size: 114
38608507 GTTTATTTGT
* * * *
38608517 AAGCGCCGCAAAATACCTTAACCAAAACGTAGCGTTTGGTTTTGAGGTATATTAGAATTCGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAATTAGTGGC
*
38608582 GTTTACGATAAAACGACGCAAAAGAACATTACTAGCGGCGTATTACAAA
66 GTTTACGATAAAACGACGCAAAAGAACATTATTAGCGGCGTATTACAAA
* * * * **
38608631 AAGCGTCGC-AAATATCTTAATCAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTGTTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAATTAGTGGC
*** * * * * ***
38608695 GTTTTTAAAAAAACGTCGTAAAAGAACATTATTAGTGGCGT-TTATTTTTA
66 GTTTACGATAAAACGACGCAAAAGAACATTATTAGCGGCGTATTA--CAAA
* * *
38608745 AA-CGCCGCAAAATACCTTAACCAAAACGCAACGTTTGGTTTTGAGGTATATTAAAATTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAATTAGTGGC
* * *
38608809 GTTTACGATAAAACGCCGCTAAAGAACAGTATTAGCGGCGTATTACAAA
66 GTTTACGATAAAACGACGCAAAAGAACATTATTAGCGGCGTATTACAAA
* ** * * *
38608858 AAGCGCCAC-AAATATCAGT-ACTAAAACGCACCGTTTGGTGTTGAGG-AGGATTAGTATTAGTG
1 AAGCGCCGCAAAATA-CCTTAACCAAAACGCACCGTTTGGTTTTGAGGTA-GATTAGAATTAGTG
38608920 GCG
64 GCG
38608923 CTTATTGAAA
Statistics
Matches: 234, Mismatches: 51, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
112 4 0.02
113 130 0.56
114 97 0.41
115 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (114 bp):
AAGCGCCGCAAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAATTAGTGGC
GTTTACGATAAAACGACGCAAAAGAACATTATTAGCGGCGTATTACAAA
Found at i:38608822 original size:114 final size:114
Alignment explanation
Indices: 38608484--38608849 Score: 416
Period size: 114 Copynumber: 3.2 Consensus size: 114
38608474 AAAAAAATGC
* * * * * *
38608484 CGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGCAAAATACCTTAACCAAAACGTAG
1 CGTAAAAGAACATTATTAGCGGCGTTTATTTATAAACGCCGCAAAATACCTTAACCAAAACGCAA
*
38608549 CGTTTGGTTTTGAGGTATATTAGAATTCGTGGCGTTTACGATAAAACGA
66 CGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGATAAAACGA
* * * * * * *
38608598 CGCAAAAGAACATTACTAGCGGCG--TATTACAAAAAGCGTCGC-AAATATCTTAATCAAAACGC
1 CGTAAAAGAACATTATTAGCGGCGTTTATT-TATAAA-CGCCGCAAAATACCTTAACCAAAACGC
* * * ** *** * *
38608660 ACCGTTTGGTCTTGAGGTAGATTAGTGTTAGTGGCGTTTTTAAAAAAACGT
64 AACGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGATAAAACGA
* *
38608711 CGTAAAAGAACATTATTAGTGGCGTTTATTTTTAAACGCCGCAAAATACCTTAACCAAAACGCAA
1 CGTAAAAGAACATTATTAGCGGCGTTTATTTATAAACGCCGCAAAATACCTTAACCAAAACGCAA
* *
38608776 CGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGATAAAACGC
66 CGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGATAAAACGA
*
38608825 CGCT-AAAGAACAGTATTAGCGGCGT
1 CG-TAAAAGAACATTATTAGCGGCGT
38608850 ATTACAAAAA
Statistics
Matches: 201, Mismatches: 45, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
112 4 0.02
113 85 0.42
114 107 0.53
115 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (114 bp):
CGTAAAAGAACATTATTAGCGGCGTTTATTTATAAACGCCGCAAAATACCTTAACCAAAACGCAA
CGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGATAAAACGA
Found at i:38608856 original size:227 final size:227
Alignment explanation
Indices: 38608461--38608940 Score: 721
Period size: 227 Copynumber: 2.1 Consensus size: 227
38608451 CCCGAACAAG
* * *
38608461 TAGTGGCGTTTTAAAAAAAATGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAACGCCGC
* * * *
38608526 AAAATACCTTAACCAAAACGTAGCGTTTGGTTTTGAGGTATATTAGAATTCGTGGCGTTTACGAT
66 AAAATACCTTAACCAAAACGCAACGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
* * * *
38608591 AAAACGACGCAAAAGAACATTACTAGCGGCGTATTACAAAAAGCGTCGCAAATATC-TTAATCAA
131 AAAACGACGCAAAAGAACAGTACTAGCGGCGTATTACAAAAAGCGCCACAAATATCAGTAAT-AA
*
38608655 AACGCACCGTTTGGTCTTGAGGTA-GATTAGTGT
195 AACGCACCGTTTGGTCTTGAGG-AGGATTAGTAT
* * *
38608688 TAGTGGCGTTTTTAAAAAAACGTCGTAAAAGAACATTATTAGTGGCGTTTATTTTTAAACGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAACGCCGC
38608753 AAAATACCTTAACCAAAACGCAACGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
66 AAAATACCTTAACCAAAACGCAACGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
* * * *
38608818 AAAACGCCGCTAAAGAACAGTATTAGCGGCGTATTACAAAAAGCGCCACAAATATCAGTACTAAA
131 AAAACGACGCAAAAGAACAGTACTAGCGGCGTATTACAAAAAGCGCCACAAATATCAGTAATAAA
*
38608883 ACGCACCGTTTGGTGTTGAGGAGGATTAGTAT
196 ACGCACCGTTTGGTCTTGAGGAGGATTAGTAT
* *
38608915 TAGTGGCGCTTATTGAAAAAACGCCG
1 TAGTGGCG-TTTTTAAAAAAACGCCG
38608941 CCAAATATCG
Statistics
Matches: 227, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
226 1 0.00
227 209 0.92
228 17 0.07
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (227 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAACGCCGC
AAAATACCTTAACCAAAACGCAACGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
AAAACGACGCAAAAGAACAGTACTAGCGGCGTATTACAAAAAGCGCCACAAATATCAGTAATAAA
ACGCACCGTTTGGTCTTGAGGAGGATTAGTAT
Found at i:38611739 original size:9 final size:9
Alignment explanation
Indices: 38611721--38611795 Score: 79
Period size: 9 Copynumber: 8.8 Consensus size: 9
38611711 NNNNACATAA
*
38611721 TACATTACT
1 TACATAACT
38611730 TACATAACT
1 TACATAACT
*
38611739 TACATTACT
1 TACATAACT
38611748 TACAGT-ACT
1 TACA-TAACT
38611757 TACATAA--
1 TACATAACT
38611764 TACATAA--
1 TACATAACT
38611771 TACATAACT
1 TACATAACT
*
38611780 TAGATAACT
1 TACATAACT
38611789 TACATAA
1 TACATAA
38611796 TACATAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
7 14 0.24
8 1 0.02
9 42 0.72
10 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.35
Consensus pattern (9 bp):
TACATAACT
Found at i:38611781 original size:32 final size:33
Alignment explanation
Indices: 38611730--38611802 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
38611720 ATACATTACT
*
38611730 TACATAACTTACATTACTTACAGT-ACTTACATAA
1 TACATAAC-TACATAACTTACA-TAACTTACATAA
*
38611764 TACATAA-TACATAACTTAGATAACTTACATAA
1 TACATAACTACATAACTTACATAACTTACATAA
38611796 TACATAA
1 TACATAA
38611803 AAATATATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 1 0.03
32 28 0.78
34 7 0.19
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.33
Consensus pattern (33 bp):
TACATAACTACATAACTTACATAACTTACATAA
Found at i:38621559 original size:21 final size:21
Alignment explanation
Indices: 38621533--38621582 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
38621523 CTACAACTTA
*
38621533 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
38621554 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
38621575 AAGCAGAG
1 AAGCAGAG
38621583 AGGCCAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:38622016 original size:42 final size:42
Alignment explanation
Indices: 38621941--38622176 Score: 346
Period size: 42 Copynumber: 5.6 Consensus size: 42
38621931 AATTCCCAAA
* * *
38621941 AACATGGTCTTTAGAGGTGTTTTTTTTTTAAGCGCCGCTAAAG
1 AACATGGTCTTTAGCGGCG-TTTTTTTCTAAGCGCCGCTAAAG
* *
38621984 AACATTGTCTGTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAG
*
38622026 AACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAG
* *
38622068 AACATGGTCTTTAGAGGTGTTTTTTTTCTAAGCGCCGCTAAAG
1 AACATGGTCTTTAGCGGCG-TTTTTTTCTAAGCGCCGCTAAAG
* * *
38622111 AACATGTTCTTTAGCGGTGTTTTTTTCTAAGCGCCACTAAAG
1 AACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAG
*
38622153 AACATGGTCTTTAGCGGCATTTTT
1 AACATGGTCTTTAGCGGCGTTTTT
38622177 GTTTGTAAAC
Statistics
Matches: 177, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
42 122 0.69
43 55 0.31
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (42 bp):
AACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAG
Found at i:38622093 original size:85 final size:84
Alignment explanation
Indices: 38621941--38622176 Score: 355
Period size: 85 Copynumber: 2.8 Consensus size: 84
38621931 AATTCCCAAA
* * * *
38621941 AACATGGTCTTTAGAGGTGTTTTTTTTTTAAGCGCCGCTAAAGAACATTGTCTGTAGCGGCGTTT
1 AACATGGTCTTTAGAGGTG-TTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTT
38622006 TTTTCTAAGCGCCGCTAAAG
65 TTTTCTAAGCGCCGCTAAAG
* *
38622026 AACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGTGTTTT
1 AACATGGTCTTTAGAGGTGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCG-TTT
38622091 TTTTCTAAGCGCCGCTAAAG
65 TTTTCTAAGCGCCGCTAAAG
* * * * *
38622111 AACATGTTCTTTAGCGGTGTTTTTTTCTAAGCGCCACTAAAGAACATGGTCTTTAGCGGCATTTT
1 AACATGGTCTTTAGAGGTGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTT
38622176 T
66 T
38622177 GTTTGTAAAC
Statistics
Matches: 137, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
84 42 0.31
85 95 0.69
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (84 bp):
AACATGGTCTTTAGAGGTGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTT
TTTCTAAGCGCCGCTAAAG
Found at i:38622141 original size:127 final size:127
Alignment explanation
Indices: 38621941--38622176 Score: 402
Period size: 127 Copynumber: 1.9 Consensus size: 127
38621931 AATTCCCAAA
*
38621941 AACATGGTCTTTAGAGGTGTTTTTTTTTTAAGCGCCGCTAAAGAACATTGTCTGTAGCGGCGTTT
1 AACATGGTCTTTAGAGGTGTTTTTTTTCTAAGCGCCGCTAAAGAACATTGTCTGTAGCGGCGTTT
* *
38622006 TTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAG
66 TTTTCTAAGCGCCACTAAAGAACATGGTCTTTAGAGGCATTTTTTTCTAAGCGCCGCTAAAG
* *
38622068 AACATGGTCTTTAGAGGTGTTTTTTTTCTAAGCGCCGCTAAAGAACA-TGTTCTTTAGCGGTGTT
1 AACATGGTCTTTAGAGGTGTTTTTTTTCTAAGCGCCGCTAAAGAACATTG-TCTGTAGCGGCGTT
*
38622132 TTTTTCTAAGCGCCACTAAAGAACATGGTCTTTAGCGGCATTTTT
65 TTTTTCTAAGCGCCACTAAAGAACATGGTCTTTAGAGGCATTTTT
38622177 GTTTGTAAAC
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 2 0.02
127 100 0.98
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (127 bp):
AACATGGTCTTTAGAGGTGTTTTTTTTCTAAGCGCCGCTAAAGAACATTGTCTGTAGCGGCGTTT
TTTTCTAAGCGCCACTAAAGAACATGGTCTTTAGAGGCATTTTTTTCTAAGCGCCGCTAAAG
Found at i:38629565 original size:22 final size:22
Alignment explanation
Indices: 38629533--38629587 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
38629523 TTCAAATTTA
*
38629533 TATTTTGTTTACAAG-TCCAGTTG
1 TATTTT-TTTA-AAGATCCAATTG
* *
38629556 TGTTTTTTTAAAGATTCAATTG
1 TATTTTTTTAAAGATCCAATTG
38629578 TATTTTTTTA
1 TATTTTTTTA
38629588 TAATAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.11
22 19 0.70
23 5 0.19
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.56
Consensus pattern (22 bp):
TATTTTTTTAAAGATCCAATTG
Found at i:38632520 original size:19 final size:20
Alignment explanation
Indices: 38632487--38632540 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
38632477 TAATTTTTAT
*
38632487 TAAAAATTAGAAAAAGATTA
1 TAAAAATTAGAAAAAAATTA
*
38632507 TAAAAATT-GTAAAAAATTA
1 TAAAAATTAGAAAAAAATTA
38632526 TAAAATATGTAGAAA
1 TAAAA-AT-TAGAAA
38632541 TATAGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 14 0.50
20 10 0.36
21 1 0.04
22 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
TAAAAATTAGAAAAAAATTA
Found at i:38632807 original size:19 final size:22
Alignment explanation
Indices: 38632774--38632818 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
38632764 CGGTTAAAGG
38632774 TTTTTTGATGCATTTTAT-AAA
1 TTTTTTGATGCATTTTATAAAA
38632795 TTTTTT-ATG-ATTTTATAAAA
1 TTTTTTGATGCATTTTATAAAA
38632815 TTTT
1 TTTT
38632819 ATATTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 10 0.43
21 6 0.26
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTTTTGATGCATTTTATAAAA
Found at i:38632815 original size:20 final size:21
Alignment explanation
Indices: 38632774--38632818 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
38632764 CGGTTAAAGG
38632774 TTTTTTGATGCATTTTATAAA
1 TTTTTTGATGCATTTTATAAA
38632795 TTTTTT-ATG-ATTTTATAAA
1 TTTTTTGATGCATTTTATAAA
*
38632814 ATTTT
1 TTTTT
38632819 ATATTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.61
20 3 0.13
21 6 0.26
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTTTTGATGCATTTTATAAA
Found at i:38632882 original size:10 final size:9
Alignment explanation
Indices: 38632844--38632913 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 9
38632834 TTTTTATATA
38632844 TATAATTTT
1 TATAATTTT
*
38632853 T-TATTTTT
1 TATAATTTT
*
38632861 TATTAAAGTTT
1 TA-T-AATTTT
*
38632872 AATAATTTT
1 TATAATTTT
38632881 TATAA-TTT
1 TATAATTTT
38632889 TATAGATTTT
1 TATA-ATTTT
38632899 TAT--TTTT
1 TATAATTTT
38632906 TATAATTT
1 TATAATTT
38632914 ATTTGTCACA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
7 7 0.15
8 14 0.29
9 14 0.29
10 8 0.17
11 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TATAATTTT
Found at i:38633851 original size:24 final size:24
Alignment explanation
Indices: 38633824--38633890 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 24
38633814 GATGTTTATC
* *
38633824 TATAGAATTTTAATAAATGA-AAAA
1 TATACAATATTAATAAAT-ATAAAA
*
38633848 TATACAATATTATTAAATATAAAA
1 TATACAATATTAATAAATATAAAA
* *
38633872 TA-AAAATAAT-ATAAATATA
1 TATACAATATTAATAAATATA
38633891 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 8 0.22
23 7 0.19
24 21 0.58
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (24 bp):
TATACAATATTAATAAATATAAAA
Found at i:38633898 original size:34 final size:33
Alignment explanation
Indices: 38633846--38633909 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
38633836 ATAAATGAAA
* *
38633846 AATATACAATATTATTAAATATAAAATAAAAAT
1 AATATAAAATATTATTAAAAATAAAATAAAAAT
* *
38633879 AATATAAATATATTTTTAAAAATAATATAAA
1 AATATAAA-ATATTATTAAAAATAAAATAAA
38633910 CAGATCCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.27
34 19 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (33 bp):
AATATAAAATATTATTAAAAATAAAATAAAAAT
Found at i:38646287 original size:13 final size:12
Alignment explanation
Indices: 38646259--38646305 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
38646249 AGATATAAGT
*
38646259 TTGATTAAAAAC
1 TTGATGAAAAAC
38646271 TTGATGAAAACAC
1 TTGATGAAAA-AC
*
38646284 TTGATGAAAGAC
1 TTGATGAAAAAC
*
38646296 TTTATGAAAA
1 TTGATGAAAA
38646306 GCTTAAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.30
Consensus pattern (12 bp):
TTGATGAAAAAC
Found at i:38647237 original size:37 final size:35
Alignment explanation
Indices: 38647196--38647273 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 35
38647186 AGAAGTACTA
*
38647196 TTTGTTCTTTTGTTTTCTTTTCTTTTTTCTTTCT-TTT
1 TTTGTTCTTTTGTTTT-TTTT-TGTTTTC-TTCTATTT
38647233 TTTGTT-TTTTGTTTTTTTTTGTTTTCTTCTATTT
1 TTTGTTCTTTTGTTTTTTTTTGTTTTCTTCTATTT
38647267 TTT-TTCT
1 TTTGTTCT
38647274 GCTTTCCAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 6 0.16
34 13 0.34
35 4 0.11
36 9 0.24
37 6 0.16
ACGTcount: A:0.01, C:0.10, G:0.06, T:0.82
Consensus pattern (35 bp):
TTTGTTCTTTTGTTTTTTTTTGTTTTCTTCTATTT
Found at i:38647240 original size:19 final size:18
Alignment explanation
Indices: 38647208--38647271 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 18
38647198 TGTTCTTTTG
* *
38647208 TTTTCTTTTCTTTTTTCT
1 TTTTTTTTTGTTTTTTCT
*
38647226 TTCTTTTTTTGTTTTTT-G
1 TT-TTTTTTTGTTTTTTCT
38647244 TTTTTTTTTGTTTTCTTCT
1 TTTTTTTTTGTTTT-TTCT
38647263 ATTTTTTTT
1 -TTTTTTTT
38647272 CTGCTTTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 12 0.32
18 6 0.16
19 12 0.32
20 8 0.21
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTCT
Found at i:38647244 original size:36 final size:37
Alignment explanation
Indices: 38647196--38647271 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
38647186 AGAAGTACTA
*
38647196 TTTGTTCTTTTGTTTTCTTTTCTTTT-TTCTTTCTTTT
1 TTTGTTCTTTTGTTTTCTTTTCTTTTCTTCTAT-TTTT
* *
38647233 TTTGTT-TTTTGTTTTTTTTTGTTTTCTTCTATTTTT
1 TTTGTTCTTTTGTTTTCTTTTCTTTTCTTCTATTTTT
38647269 TTT
1 TTT
38647272 CTGCTTTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 24 0.69
37 11 0.31
ACGTcount: A:0.01, C:0.09, G:0.07, T:0.83
Consensus pattern (37 bp):
TTTGTTCTTTTGTTTTCTTTTCTTTTCTTCTATTTTT
Found at i:38647709 original size:28 final size:28
Alignment explanation
Indices: 38647657--38647715 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
38647647 GTCTACCTGC
* *
38647657 AAAATAAAATAAAATAGAAGGAAAAAGA
1 AAAATAAAATAAAATAAAAGAAAAAAGA
* *
38647685 AAAATAAAATAAAATAAAATAAAAAATA
1 AAAATAAAATAAAATAAAAGAAAAAAGA
38647713 AAA
1 AAA
38647716 TATGCAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (28 bp):
AAAATAAAATAAAATAAAAGAAAAAAGA
Found at i:38647717 original size:5 final size:5
Alignment explanation
Indices: 38647657--38647708 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
38647647 GTCTACCTGC
* * * *
38647657 AAAAT AAAAT AAAAT AGAAG GAAA- AAGA- AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
38647705 AAAA
1 AAAA
38647709 AATAAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
4 5 0.13
5 34 0.87
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:38652684 original size:12 final size:12
Alignment explanation
Indices: 38652663--38652807 Score: 80
Period size: 12 Copynumber: 11.6 Consensus size: 12
38652653 AGATATAAGT
*
38652663 TTGATTAAAAAC
1 TTGATGAAAAAC
38652675 TTGATGAAAACAC
1 TTGATGAAAA-AC
38652688 TTGATGAAAACAC
1 TTGATGAAAA-AC
*
38652701 TTGATGAAAGAC
1 TTGATGAAAAAC
* *
38652713 TTTATGAAAAGC
1 TTGATGAAAAAC
*
38652725 TT-A-AAAAGAAC
1 TTGATGAAA-AAC
*
38652736 TTGATGCAAAAC
1 TTGATGAAAAAC
* *
38652748 TTAATAAAAAAAAC
1 TTGAT--GAAAAAC
*
38652762 TTGGTAATTAAAAAC
1 TT-G--ATGAAAAAC
* **
38652777 TTGATTAATGAC
1 TTGATGAAAAAC
38652789 TTGATTG-AAAAC
1 TTGA-TGAAAAAC
38652801 TTGATGA
1 TTGATGA
38652808 TTAAATGAAC
Statistics
Matches: 103, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
10 3 0.03
11 7 0.07
12 48 0.47
13 27 0.26
14 8 0.08
15 8 0.08
17 2 0.02
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (12 bp):
TTGATGAAAAAC
Found at i:38652714 original size:25 final size:25
Alignment explanation
Indices: 38652663--38652722 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
38652653 AGATATAAGT
*
38652663 TTGATTAAAAACTTGATGAAAACAC
1 TTGATGAAAAACTTGATGAAAACAC
*
38652688 TTGATGAAAACACTTGATG-AAAGAC
1 TTGATGAAAA-ACTTGATGAAAACAC
*
38652713 TTTATGAAAA
1 TTGATGAAAA
38652723 GCTTAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 23 0.74
26 8 0.26
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (25 bp):
TTGATGAAAAACTTGATGAAAACAC
Found at i:38652723 original size:13 final size:13
Alignment explanation
Indices: 38652663--38652722 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
38652653 AGATATAAGT
*
38652663 TTGATTAAAA-AC
1 TTGATGAAAACAC
38652675 TTGATGAAAACAC
1 TTGATGAAAACAC
38652688 TTGATGAAAACAC
1 TTGATGAAAACAC
*
38652701 TTGATG-AAAGAC
1 TTGATGAAAACAC
*
38652713 TTTATGAAAA
1 TTGATGAAAA
38652723 GCTTAAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
12 19 0.44
13 24 0.56
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (13 bp):
TTGATGAAAACAC
Found at i:38652750 original size:23 final size:22
Alignment explanation
Indices: 38652707--38652751 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
38652697 ACACTTGATG
*
38652707 AAAGACTTTATGAAAAGCTTAA
1 AAAGACTTGATGAAAAGCTTAA
38652729 AAAGAACTTGATGCAAAA-CTTAA
1 AAAG-ACTTGATG-AAAAGCTTAA
38652752 TAAAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (22 bp):
AAAGACTTGATGAAAAGCTTAA
Found at i:38654452 original size:10 final size:10
Alignment explanation
Indices: 38654437--38654461 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38654427 ATTAAATAAT
38654437 AATCACCAAA
1 AATCACCAAA
38654447 AATCACCAAA
1 AATCACCAAA
38654457 AATCA
1 AATCA
38654462 TATTACGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (10 bp):
AATCACCAAA
Found at i:38663483 original size:23 final size:23
Alignment explanation
Indices: 38663457--38663533 Score: 91
Period size: 23 Copynumber: 3.2 Consensus size: 23
38663447 AGTGCCACAT
38663457 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
* *
38663480 TGATATGTATGTAGCGGTAGCTACCAC
1 TG--A--TATGTAGCCGAAGCTACCAC
*
38663507 TGAAATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
38663530 TGAT
1 TGAT
38663534 CAACTGGTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 22 0.50
25 2 0.05
27 20 0.45
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAC
Found at i:38663490 original size:27 final size:25
Alignment explanation
Indices: 38663459--38663533 Score: 100
Period size: 27 Copynumber: 3.0 Consensus size: 25
38663449 TGCCACATTG
38663459 ATATGTAGCCGAAGCTACCACTGAT
1 ATATGTAGCCGAAGCTACCACTGAT
* *
38663484 ATGTATGTAGCGGTAGCTACCACTGA-
1 A--TATGTAGCCGAAGCTACCACTGAT
38663510 A-ATGTAGCCGAAGCTACCACTGAT
1 ATATGTAGCCGAAGCTACCACTGAT
38663534 CAACTGGTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 20 0.47
25 1 0.02
26 1 0.02
27 21 0.49
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (25 bp):
ATATGTAGCCGAAGCTACCACTGAT
Found at i:38665370 original size:23 final size:23
Alignment explanation
Indices: 38665341--38665462 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
38665331 AGTGTTATTG
38665341 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
38665364 TTTAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
38665387 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
38665410 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
38665433 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
38665456 ATCAGTG
1 ATCAGTG
38665463 TGGCACTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:38665393 original size:46 final size:46
Alignment explanation
Indices: 38665341--38665462 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
38665331 AGTGTTATTG
*
38665341 ATCAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
38665387 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
38665433 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
38665463 TGGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:38674790 original size:15 final size:15
Alignment explanation
Indices: 38674770--38674798 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38674760 ATTAACCGAA
38674770 TATAATAATTATAAT
1 TATAATAATTATAAT
38674785 TATAATAATTATAA
1 TATAATAATTATAA
38674799 CAATATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATAATTATAAT
Found at i:38683929 original size:34 final size:34
Alignment explanation
Indices: 38683891--38683965 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
38683881 ATCTGCAAAA
** **
38683891 CGATACAATTTGCTAGATTATACTATCCGCCAGG
1 CGATACAATCCGCTAGACGATACTATCCGCCAGG
* * *
38683925 CGATATAGTCCGCTAGACGATACTATCCGTCAGG
1 CGATACAATCCGCTAGACGATACTATCCGCCAGG
38683959 CGATACA
1 CGATACA
38683966 GCTCACCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (34 bp):
CGATACAATCCGCTAGACGATACTATCCGCCAGG
Found at i:38683953 original size:17 final size:17
Alignment explanation
Indices: 38683910--38683964 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
38683900 TTGCTAGATT
*
38683910 ATACTATCCGCCAGGCG
1 ATACTATCCGCCAGACG
*
38683927 ATA-TAGTCCGCTAGACG
1 ATACTA-TCCGCCAGACG
* *
38683944 ATACTATCCGTCAGGCG
1 ATACTATCCGCCAGACG
38683961 ATAC
1 ATAC
38683965 AGCTCACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 2 0.06
17 27 0.87
18 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (17 bp):
ATACTATCCGCCAGACG
Found at i:38697820 original size:17 final size:19
Alignment explanation
Indices: 38697788--38697825 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38697778 TGGCACTCTC
*
38697788 TTATTTTTCATTTAAT-TT
1 TTATTTTTCATCTAATATT
38697806 TTATTTTT-ATCTAATATT
1 TTATTTTTCATCTAATATT
38697824 TT
1 TT
38697826 TCATTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTTCATCTAATATT
Found at i:38699820 original size:43 final size:43
Alignment explanation
Indices: 38699772--38699857 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
38699762 AGGTTGATGT
38699772 TAGCTACGGATTAACACGAAGCATATAACACTATCAATAATCA
1 TAGCTACGGATTAACACGAAGCATATAACACTATCAATAATCA
* *
38699815 TAGCTATGGATTAACACGAAGCTTATAACACTATCAATAATCA
1 TAGCTACGGATTAACACGAAGCATATAACACTATCAATAATCA
38699858 ACCAATTCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.26
Consensus pattern (43 bp):
TAGCTACGGATTAACACGAAGCATATAACACTATCAATAATCA
Found at i:38700947 original size:26 final size:26
Alignment explanation
Indices: 38700907--38700960 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
38700897 TATAACCCAT
38700907 AAATTAAAATATATTAAAATATTGATA
1 AAATTAAAATATATTAAAAT-TTGATA
*
38700934 AAATTAAAAGTAT-TT-AAATTTTATA
1 AAATTAAAA-TATATTAAAATTTGATA
38700959 AA
1 AA
38700961 TGTCACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 11 0.44
28 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
AAATTAAAATATATTAAAATTTGATA
Found at i:38701088 original size:38 final size:39
Alignment explanation
Indices: 38701046--38701144 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 39
38701036 ATATATATAT
38701046 ATATATATGATAAGTTAACAAAACA-ATTTATCTACTCA
1 ATATATATGATAAGTTAACAAAACATATTTATCTACTCA
* ** *
38701084 ATATATAT-ATTA-TATAA-ATTACATTATTTATCTATTCA
1 ATATATATGATAAGT-TAACAAAACA-TATTTATCTACTCA
* *
38701122 ATATATATGTTAAGTTCACAAAA
1 ATATATATGATAAGTTAACAAAA
38701145 AAAAAAATTG
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
36 5 0.11
37 6 0.13
38 28 0.61
39 4 0.09
40 3 0.07
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (39 bp):
ATATATATGATAAGTTAACAAAACATATTTATCTACTCA
Found at i:38704577 original size:16 final size:17
Alignment explanation
Indices: 38704550--38704584 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38704540 AGAGAGTTGA
38704550 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
38704567 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
38704583 GA
1 GA
38704585 ATGAAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:38708589 original size:17 final size:17
Alignment explanation
Indices: 38708567--38708605 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
38708557 GAATGAAAAA
*
38708567 TAAACTTCTAATTTAAT
1 TAAACTTCTAATTTAAC
38708584 TAAACTTCTAATTTAAC
1 TAAACTTCTAATTTAAC
38708601 TAAAC
1 TAAAC
38708606 AAGAAGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAACTTCTAATTTAAC
Found at i:38709484 original size:30 final size:30
Alignment explanation
Indices: 38709438--38709561 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
38709428 TTTTATTATG
*
38709438 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
38709469 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
38709499 CCAATATTTGATACCAATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
38709529 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
38709559 CCA
1 CCA
38709562 TAAATATAGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 79 0.92
31 7 0.08
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:38709493 original size:15 final size:15
Alignment explanation
Indices: 38709448--38709555 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
38709438 CCAATATCTC
38709448 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
38709463 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
38709478 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
38709493 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
*
38709508 GATACCAATATCTTT
1 GATACCCATATCTTT
** * *
38709523 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
38709538 GATACCCATATCTTT
1 GATACCCATATCTTT
38709553 GAT
1 GAT
38709556 TTTCCATAAA
Statistics
Matches: 66, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
14 11 0.17
15 43 0.65
16 12 0.18
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:38714183 original size:30 final size:30
Alignment explanation
Indices: 38714137--38714260 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
38714127 TTTTATTATG
*
38714137 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
38714168 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
38714198 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
38714228 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
38714258 CCA
1 CCA
38714261 TAAATATAGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:38714192 original size:15 final size:15
Alignment explanation
Indices: 38714147--38714254 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
38714137 CCAATATCTC
38714147 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
38714162 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
38714177 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
38714192 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
38714207 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
38714222 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
38714237 GATACCCATATCTTT
1 GATACCCATATCTTT
38714252 GAT
1 GAT
38714255 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:38714553 original size:21 final size:21
Alignment explanation
Indices: 38714527--38714566 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38714517 GTTTTGTTTA
38714527 TTTATTCATTTAGTTTTTACT
1 TTTATTCATTTAGTTTTTACT
* *
38714548 TTTATTCTTTTATTTTTTA
1 TTTATTCATTTAGTTTTTA
38714567 AAACTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTATTCATTTAGTTTTTACT
Found at i:38715217 original size:24 final size:24
Alignment explanation
Indices: 38715185--38715238 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
38715175 CGGATTTCCC
*
38715185 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAACCTTCAAGGTTCAAT
38715209 CCACTGTAACCTTCAAGGTTCAAT
1 CCACTGTAACCTTCAAGGTTCAAT
38715233 CCACTG
1 CCACTG
38715239 CACCTTTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30
Consensus pattern (24 bp):
CCACTGTAACCTTCAAGGTTCAAT
Found at i:38716195 original size:6 final size:6
Alignment explanation
Indices: 38716184--38716245 Score: 67
Period size: 6 Copynumber: 10.7 Consensus size: 6
38716174 CTCTCCTCTT
* * *
38716184 TTTTTC TTTTTC TTTTTC -TTTTC TTCTTC TTCTT- TATTTC TTTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC
38716231 TTTTTC TTTTT- TTTT
1 TTTTTC TTTTTC TTTT
38716246 AAATATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
5 12 0.24
6 31 0.63
7 6 0.12
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:38716199 original size:14 final size:14
Alignment explanation
Indices: 38716180--38716235 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
38716170 TGGCCTCTCC
38716180 TCTTTTT-TTCTTTT
1 TCTTTTTCTT-TTTT
*
38716194 TCTTTTTCTTTTCT
1 TCTTTTTCTTTTTT
* *
38716208 TCTTCTTCTTTATT
1 TCTTTTTCTTTTTT
38716222 TCTTTCTTCTTTTT
1 TCTTT-TTCTTTTT
38716236 CTTTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 25 0.74
15 9 0.26
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:38716229 original size:21 final size:22
Alignment explanation
Indices: 38716180--38716239 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
38716170 TGGCCTCTCC
* *
38716180 TCTTTTTTTCTTTTTC-TT-TT
1 TCTTTTCTTCTTCTTCTTTATT
38716200 TCTTTTCTTCTTCTTCTTTATT
1 TCTTTTCTTCTTCTTCTTTATT
*
38716222 TC-TTTCTTCTTTTTCTTT
1 TCTTTTCTTCTTCTTCTTT
38716240 TTTTTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.40
21 17 0.49
22 4 0.11
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TCTTTTCTTCTTCTTCTTTATT
Found at i:38716346 original size:14 final size:15
Alignment explanation
Indices: 38716323--38716355 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
38716313 ATCAACGCTT
38716323 TTCCAGATAAGG-CC
1 TTCCAGATAAGGTCC
*
38716337 TTCCATATAAGGTCC
1 TTCCAGATAAGGTCC
38716352 TTCC
1 TTCC
38716356 TAGTTTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (15 bp):
TTCCAGATAAGGTCC
Found at i:38720831 original size:74 final size:74
Alignment explanation
Indices: 38720703--38720847 Score: 238
Period size: 74 Copynumber: 2.0 Consensus size: 74
38720693 TCTCGGATTT
* * *
38720703 AAAAAATGGATCATGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTTCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATCTCCGAGATCGTTTAAAA
38720768 CTTGAGAAG
66 CTTGAGAAG
*
38720777 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATGCT-CGAGATCGTTTAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAAT-CTCCGAGATCGTTTAAA
38720841 ACTTGAG
65 ACTTGAG
38720848 TTTGAAAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
74 65 0.98
75 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (74 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATCTCCGAGATCGTTTAAAA
CTTGAGAAG
Found at i:38721266 original size:42 final size:41
Alignment explanation
Indices: 38721206--38721300 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
38721196 AAGATGAATA
* * *
38721206 AAATTATAAAATGC-AAAAAGATATATGCATGTACATATATAT
1 AAATTATAAAATACAAAAAAAATATAAGCATGT--ATATATAT
*
38721248 AAATTATAAGATATA-AAAAAAAATATAAGTATGTATATATAT
1 AAATTATAA-A-ATACAAAAAAAATATAAGCATGTATATATAT
38721290 AAATTATAAAA
1 AAATTATAAAA
38721301 AATATGTACG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
40 1 0.02
41 1 0.02
42 26 0.57
43 1 0.02
44 17 0.37
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (41 bp):
AAATTATAAAATACAAAAAAAATATAAGCATGTATATATAT
Found at i:38721448 original size:18 final size:18
Alignment explanation
Indices: 38721427--38721473 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
38721417 ACGATAATTC
* *
38721427 TAATAGTAACATTAAAAA
1 TAATAATAACAGTAAAAA
*
38721445 TAATAATAATAGTAAAAA
1 TAATAATAACAGTAAAAA
*
38721463 TAATGATAACA
1 TAATAATAACA
38721474 CTATTAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (18 bp):
TAATAATAACAGTAAAAA
Found at i:38723301 original size:16 final size:17
Alignment explanation
Indices: 38723271--38723305 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38723261 AAATGGGTAA
*
38723271 TATGTATTTTAAATAAT
1 TATGTATGTTAAATAAT
38723288 TATGTATGTT-AATAAT
1 TATGTATGTTAAATAAT
38723304 TA
1 TA
38723306 CAGATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (17 bp):
TATGTATGTTAAATAAT
Found at i:38732358 original size:16 final size:16
Alignment explanation
Indices: 38732320--38732361 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38732310 GAAATAAAAA
*
38732320 AGAAAATAAATAATTT
1 AGAAAATAAATAATAT
38732336 A-AAAATAAA-AATGAT
1 AGAAAATAAATAAT-AT
38732351 AGAAAATAAAT
1 AGAAAATAAAT
38732362 TTTTTTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (16 bp):
AGAAAATAAATAATAT
Found at i:38737821 original size:31 final size:31
Alignment explanation
Indices: 38737783--38737851 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
38737773 TGGCCTCAAT
38737783 TAAAATTT-CAAAATTTAAAAAGTAC-AGAGAC
1 TAAAATTTAC-AAATTTAAAAAGTACAAG-GAC
* *
38737814 TAAAATTTACCAATTTAAAAAGTATAAGGAC
1 TAAAATTTACAAATTTAAAAAGTACAAGGAC
38737845 TAAAATT
1 TAAAATT
38737852 GATCAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (31 bp):
TAAAATTTACAAATTTAAAAAGTACAAGGAC
Found at i:38739427 original size:34 final size:35
Alignment explanation
Indices: 38739383--38739449 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
38739373 CAGTAAAATA
*
38739383 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
38739417 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
38739450 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:38741794 original size:18 final size:18
Alignment explanation
Indices: 38741773--38741809 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38741763 AATCATTCCA
* *
38741773 CATCACTTATAATCATTT
1 CATCACTTACAACCATTT
38741791 CATCACTTACAACCATTT
1 CATCACTTACAACCATTT
38741809 C
1 C
38741810 GAAACATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.38
Consensus pattern (18 bp):
CATCACTTACAACCATTT
Found at i:38756039 original size:86 final size:85
Alignment explanation
Indices: 38755840--38756163 Score: 259
Period size: 86 Copynumber: 3.8 Consensus size: 85
38755830 TTATATCATT
* * * *
38755840 AAATCAAAATAAAATCTATTAAACGGCGGGAATAAATCCCGAAACCGA-ATTATTT-TA-TT-AC
1 AAATC-AAATAAAAT-TATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTACATTTAAT
*
38755901 GTCT-TTGTTTGGAAACAAAA-C
64 TTCTCTT-TTTGGAAACAAAATC
** * *
38755922 AATATTGAATAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTA-ATTTAAT
1 AA-ATCAAATAAA-ATTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTACATTTAAT
* *
38755986 TTCTCATTTTTAGCAACAAAATC
64 TTCTC-TTTTTGGAAACAAAATC
* * ** *
38756009 AAATCAAATAAAACTTATTAAACGGCGGGAATCAATCCCAAAATGGATTTTATTTACCTTTAATT
1 AAATCAAATAAAA-TTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTACATTTAATT
* *
38756074 TC-CTGTTTGGAAATAAAATC
65 TCTCTTTTTGGAAACAAAATC
* * * ** * *
38756094 AAAATAATGGAATAAAATCAGTTGAACAACGGGAATAAATCCCGAAACAGGTTTTATTTACTTTT
1 -AAATCA---AATAAAATTA-TTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTACATTT
38756159 AATTT
61 AATTT
38756164 TGAAAACAAA
Statistics
Matches: 192, Mismatches: 34, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
82 38 0.20
83 10 0.05
84 2 0.01
85 17 0.09
86 62 0.32
87 14 0.07
88 2 0.01
89 47 0.24
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (85 bp):
AAATCAAATAAAATTATTAAACGGCGGGAATAAATCCCGAAACAGATTTTATTTACATTTAATTT
CTCTTTTTGGAAACAAAATC
Found at i:38759756 original size:22 final size:23
Alignment explanation
Indices: 38759729--38759808 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 23
38759719 AACTAATGAA
38759729 CAGAGAGCACTAAAGTGCTATA-
1 CAGAGAGCACTAAAGTGCTATAT
*
38759751 CAGAGAGCAC-AGATGTGCTA-AT
1 CAGAGAGCACTA-AAGTGCTATAT
*
38759773 CGGAGAGCACTAACA-TGCTAATAAT
1 CAGAGAGCACTAA-AGTGCT-AT-AT
38759798 CAGAGAGCACT
1 CAGAGAGCACT
38759809 GATGTCCTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.04
22 31 0.66
23 2 0.04
25 12 0.26
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (23 bp):
CAGAGAGCACTAAAGTGCTATAT
Found at i:38759792 original size:44 final size:47
Alignment explanation
Indices: 38759731--38759819 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
38759721 CTAATGAACA
*
38759731 GAGAGCACTAAAGTGCT-AT-A-CAGAGAGCACAGATGTGCTAATCG
1 GAGAGCACTAAAGTGCTAATAATCAGAGAGCACAGATGTCCTAATCG
*
38759775 GAGAGCACTAACA-TGCTAATAATCAGAGAGCACTGATGTCCTAAT
1 GAGAGCACTAA-AGTGCTAATAATCAGAGAGCACAGATGTCCTAAT
38759820 AATCAGAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 15 0.38
45 3 0.08
46 1 0.03
47 20 0.51
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (47 bp):
GAGAGCACTAAAGTGCTAATAATCAGAGAGCACAGATGTCCTAATCG
Done.