Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold132
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: 2008648
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 78371 characters in sequence are not A, C, G, or T
File 2 of 7
Found at i:352413 original size:32 final size:31
Alignment explanation
Indices: 352314--352424 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 31
352304 TTTGATCTTT
*
352314 TTTAA-CCTTTTTTAAACACTAAAT-AAAGCCC
1 TTTAATCCTTTTTT-AAC-CTTAATCAAAGCCC
* * * *
352345 TCTAATCCTTTTTTAACCCTAAACAAAACACC
1 TTTAATCCTTTTTTAACCTTAATCAAAGC-CC
*
352377 -TTAATCCTTTTTTAGACCTTAATCATAGCCC
1 TTTAATCCTTTTTTA-ACCTTAATCAAAGCCC
352408 TTTAATCCCTCTTTTTA
1 TTTAAT-CCT-TTTTTA
352425 TTCAAACACT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
30 3 0.05
31 26 0.41
32 25 0.40
33 3 0.05
34 6 0.10
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.40
Consensus pattern (31 bp):
TTTAATCCTTTTTTAACCTTAATCAAAGCCC
Found at i:352461 original size:32 final size:33
Alignment explanation
Indices: 352420--352481 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
352410 TAATCCCTCT
* *
352420 TTTTATTCAAACACTAAA-CTCTAACAAAACCC
1 TTTTATTCAAACACCAAATCCCTAACAAAACCC
* *
352452 TTTTCTTCAAACCCCAAATCCCTAACAAAA
1 TTTTATTCAAACACCAAATCCCTAACAAAA
352482 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 15 0.60
33 10 0.40
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (33 bp):
TTTTATTCAAACACCAAATCCCTAACAAAACCC
Found at i:352874 original size:17 final size:16
Alignment explanation
Indices: 352849--352892 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
352839 TCTTTTTCGA
*
352849 TTTTCTATTTGCATTTG
1 TTTTGTATTTG-ATTTG
*
352866 TTTTGTATTTGTTTTG
1 TTTTGTATTTGATTTG
352882 TATTTGTATTT
1 T-TTTGTATTT
352893 AGGTTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.11, C:0.05, G:0.14, T:0.70
Consensus pattern (16 bp):
TTTTGTATTTGATTTG
Found at i:352875 original size:11 final size:11
Alignment explanation
Indices: 352856--352888 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
352846 CGATTTTCTA
*
352856 TTTGCATTTGT
1 TTTGTATTTGT
352867 TTTGTATTTGT
1 TTTGTATTTGT
352878 TTTGTATTTGT
1 TTTGTATTTGT
352889 ATTTAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (11 bp):
TTTGTATTTGT
Found at i:352881 original size:5 final size:6
Alignment explanation
Indices: 352854--352892 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
352844 TTCGATTTTC
*
352854 TATTTG CATTTG T-TTTG TATTTG T-TTTG TATTTG TATTT
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTT
352893 AGGTTTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.13, C:0.03, G:0.15, T:0.69
Consensus pattern (6 bp):
TATTTG
Found at i:354625 original size:17 final size:16
Alignment explanation
Indices: 354590--354639 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
354580 TTAATTTTTT
*
354590 TTAAATATTAAATAAAA
1 TTAAAAATT-AATAAAA
354607 TTCAAAAAGTTAA-AAAA
1 TT-AAAAA-TTAATAAAA
354624 TTAAAAATTAATAAAA
1 TTAAAAATTAATAAAA
354640 AGCATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 8 0.28
18 6 0.21
19 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAATAAAA
Found at i:354640 original size:17 final size:16
Alignment explanation
Indices: 354590--354640 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
354580 TTAATTTTTT
*
354590 TTAAATATTAAATAAAA
1 TTAAAAATTAAA-AAAA
354607 TTCAAAAAGTT-AAAAAA
1 TT-AAAAA-TTAAAAAAA
354624 TTAAAAATTAATAAAAA
1 TTAAAAATTAA-AAAAA
354641 GCATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.07
16 6 0.21
17 13 0.45
18 6 0.21
19 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
TTAAAAATTAAAAAAA
Found at i:354778 original size:10 final size:10
Alignment explanation
Indices: 354763--354799 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
354753 TAGACTATAT
354763 AAAATTTTTA
1 AAAATTTTTA
*
354773 AAAATTATT-
1 AAAATTTTTA
354782 AAAATTTTTA
1 AAAATTTTTA
354792 AAAATTTT
1 AAAATTTT
354800 AATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:354785 original size:9 final size:9
Alignment explanation
Indices: 354762--354801 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
354752 TTAGACTATA
354762 TAAAATTTT
1 TAAAATTTT
*
354771 TAAAAATTAT
1 T-AAAATTTT
354781 TAAAATTTT
1 TAAAATTTT
*
354790 TAAAAATTT
1 TAAAATTTT
354799 TAA
1 TAA
354802 TAAAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAAAATTTT
Found at i:354786 original size:19 final size:18
Alignment explanation
Indices: 354762--354801 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
354752 TTAGACTATA
354762 TAAAATTTTTAAAAATTAT
1 TAAAATTTTTAAAAATT-T
354781 TAAAATTTTTAAAAATTT
1 TAAAATTTTTAAAAATTT
354799 TAA
1 TAA
354802 TAAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATTTTTAAAAATTT
Found at i:355049 original size:12 final size:12
Alignment explanation
Indices: 355032--355091 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
355022 TCTAGACTTA
355032 ATTTTTAAATGG
1 ATTTTTAAATGG
*
355044 ATTTTT--AT-T
1 ATTTTTAAATGG
* *
355053 AATTTTAAAT-T
1 ATTTTTAAATGG
*
355064 TTTTTTAAATGG
1 ATTTTTAAATGG
355076 ATTTTTAAATGG
1 ATTTTTAAATGG
355088 ATTT
1 ATTT
355092 AAAAATCCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 5 0.13
10 2 0.05
11 11 0.28
12 21 0.54
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (12 bp):
ATTTTTAAATGG
Found at i:359268 original size:13 final size:13
Alignment explanation
Indices: 359250--359301 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
359240 AGTCATTTTC
359250 TCAATAAGAAAGA
1 TCAATAAGAAAGA
*
359263 TCAATAAGAAA-T
1 TCAATAAGAAAGA
359275 TCCAA-ATA-AAAGA
1 T-CAATA-AGAAAGA
359288 TCAATAAGAAAGA
1 TCAATAAGAAAGA
359301 T
1 T
359302 ATTGTAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (13 bp):
TCAATAAGAAAGA
Found at i:359722 original size:18 final size:18
Alignment explanation
Indices: 359694--359738 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
359684 CGTTCGTTTC
*
359694 CAAAACATTATTC-ATTT
1 CAAAACGTTATTCAATTT
*
359711 ACAAATCGTTATTCAATTT
1 -CAAAACGTTATTCAATTT
359730 CAAAACGTT
1 CAAAACGTT
359739 TTCTTATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCAATTT
Found at i:362565 original size:11 final size:11
Alignment explanation
Indices: 362551--362594 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
362541 AGATAAATAT
362551 TATTTTATTAA
1 TATTTTATTAA
*
362562 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
362575 TATTTTATTAT
1 TATTTTATTAA
362586 TATTTTATT
1 TATTTTATT
362595 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:366074 original size:206 final size:204
Alignment explanation
Indices: 365621--366184 Score: 890
Period size: 206 Copynumber: 2.8 Consensus size: 204
365611 GGGGTGTTAC
* * *
365621 AGATATTGACTACACATGTTGAGAAATTATGTTAGAATATGACTAATCAAAGGAAATTGGTGAAT
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
* *
365686 TAAATTGTTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGTATGTAATGTGTGCTTT
66 GAAATTG-TTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGAATGTAATGTGTGCTTT
* * * *
365751 GAAAAATTTAAATTCCAAAAAG-----TCATTAAGAAATATTAATAAAAAATTCTAAATAAATGA
130 GAAAAATTCAAATTCCAAAAAGTCATTTCATTAAGAAAGATTAATAAAAAATTCCAAATAAAAGA
365811 TCAATAAGAA
195 TCAATAAGAA
*
365821 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATAACTAATCAAAGGAAATTGGTGAAT
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
365886 GAAATTG-TTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGAATGTAATGTGTGCTTTG
66 GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGAATGTAATGTGTGCTTTG
*
365950 AAAAATTCAAATTCCAAAAAGTCATTTTCTCATTAAGAAAGATTAATAAGAAATTCCAAATAAAA
131 AAAAATTCAAATTCCAAAAAGTCA--TT-TCATTAAGAAAGATTAATAAAAAATTCCAAATAAAA
366015 GATCAATAAGAA
193 GATCAATAAGAA
* *
366027 AGATATCGACTCCACATATTGAGAAATTATGTGAGAATATGACTAATCGAAA-GAAATTAGTGAA
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATC-AAAGGAAATTGGTGAA
*
366091 TGAAATTGTTTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCT
65 TGAAATTG--TTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGAATGTAATGTGTGCT
366156 TTGAAAAATTCAAATTCCAAAAAGTCATT
128 TTGAAAAATTCAAATTCCAAAAAGTCATT
366185 GTTGTACCAT
Statistics
Matches: 337, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
198 76 0.23
200 67 0.20
206 109 0.32
207 5 0.01
209 80 0.24
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (204 bp):
AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGAATGTAATGTGTGCTTTG
AAAAATTCAAATTCCAAAAAGTCATTTCATTAAGAAAGATTAATAAAAAATTCCAAATAAAAGAT
CAATAAGAA
Found at i:366250 original size:86 final size:85
Alignment explanation
Indices: 366133--366293 Score: 191
Period size: 85 Copynumber: 1.9 Consensus size: 85
366123 ATTATTTTAG
* * * *
366133 ATGCAATGGATGTAATGTGTGCTTTGAAAAATTCA-AATTCCAAAAAGTCATTGTTGTACCATTC
1 ATGCAATGGATGCAATGTCTACTTTGAAAAA-T-AGAATTCCAAAAAGACATTGTTGTACCATTC
*
366197 TATCACCAAAATGTTTCTAGGC
64 TATCACAAAAATGTTTCTAGGC
* * * **
366219 ATGCAATGGATGCATTGTCTACTTT-ATAAAATAGAATTCCAAAATGACATTTTTGTACTTTTCT
1 ATGCAATGGATGCAATGTCTACTTTGA-AAAATAGAATTCCAAAAAGACATTGTTGTACCATTCT
366283 ATCACAAAAAT
65 ATCACAAAAAT
366294 ATTCCAAGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
84 1 0.02
85 37 0.59
86 25 0.40
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (85 bp):
ATGCAATGGATGCAATGTCTACTTTGAAAAATAGAATTCCAAAAAGACATTGTTGTACCATTCTA
TCACAAAAATGTTTCTAGGC
Found at i:378915 original size:27 final size:26
Alignment explanation
Indices: 378863--378916 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
378853 TAATTTTAAA
* *
378863 TTATTTTTAAAATACTTTTTTATGTT
1 TTATTTTTAAAATACATTTTGATGTT
* *
378889 TTATTTTTAAAATGCAATTTTGGTGTT
1 TTATTTTTAAAATAC-ATTTTGATGTT
378916 T
1 T
378917 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (26 bp):
TTATTTTTAAAATACATTTTGATGTT
Found at i:380716 original size:30 final size:32
Alignment explanation
Indices: 380653--380717 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
380643 ATAAAAATGG
380653 TGAAAATGGAGAAATGAAAAATCATTTGAAAA
1 TGAAAATGGAGAAATGAAAAATCATTTGAAAA
* *
380685 TGAAAATGGAGAAATG-GAAA-CATTTGGAAA
1 TGAAAATGGAGAAATGAAAAATCATTTGAAAA
380715 TGA
1 TGA
380718 TTATGGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 12 0.39
31 3 0.10
32 16 0.52
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (32 bp):
TGAAAATGGAGAAATGAAAAATCATTTGAAAA
Found at i:388176 original size:18 final size:18
Alignment explanation
Indices: 388153--388198 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
388143 TAAATAGTTT
388153 GAGTTATTCGAATTAATC
1 GAGTTATTCGAATTAATC
*
388171 GAGTTATTCAAATTAATC
1 GAGTTATTCGAATTAATC
*
388189 AAGTTATTCG
1 GAGTTATTCG
388199 GATCAACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (18 bp):
GAGTTATTCGAATTAATC
Found at i:390645 original size:6 final size:6
Alignment explanation
Indices: 390636--390669 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
390626 CATAATCCAA
390636 ATCATT ATCATT ATCATT ATCATT ATCATT ATCA
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCA
390670 AACCCATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (6 bp):
ATCATT
Found at i:393975 original size:62 final size:62
Alignment explanation
Indices: 393825--393988 Score: 222
Period size: 62 Copynumber: 2.6 Consensus size: 62
393815 ACACAATAAA
* * *
393825 TTACACGGCTTGGGCACACACCCGTGTCCCTAGCTGTGTGGTCTTGTACCAAAAATCGTGAG
1 TTACACGGCTTGGGCACACGCCCGTGTCCCTGGCCGTGTGGTCTTGTACCAAAAATCGTGAG
* * *
393887 TTACACGGCCTGGGCAAACGCCCGTGTCCCTGGCCGTGTGGTCTTGTACCACAAA-CAGTGAG
1 TTACACGGCTTGGGCACACGCCCGTGTCCCTGGCCGTGTGGTCTTGTACCAAAAATC-GTGAG
** * *
393949 TTACACGGCTTAAGCACACGCTCGTGTCTCTGGCCGTGTG
1 TTACACGGCTTGGGCACACGCCCGTGTCCCTGGCCGTGTG
393989 AACTCTTCAC
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
61 1 0.01
62 88 0.99
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.24
Consensus pattern (62 bp):
TTACACGGCTTGGGCACACGCCCGTGTCCCTGGCCGTGTGGTCTTGTACCAAAAATCGTGAG
Found at i:394979 original size:19 final size:19
Alignment explanation
Indices: 394955--394995 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
394945 GAGTCAAACA
394955 GATGCGGATACAGTCGTCG
1 GATGCGGATACAGTCGTCG
394974 GATGCGGATACAGTCGTCG
1 GATGCGGATACAGTCGTCG
394993 GAT
1 GAT
394996 TGATTCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (19 bp):
GATGCGGATACAGTCGTCG
Found at i:400901 original size:61 final size:62
Alignment explanation
Indices: 400836--400977 Score: 198
Period size: 62 Copynumber: 2.3 Consensus size: 62
400826 TTACATGGCT
* *
400836 TGGGCACACGCTCGTGTCCCTGGCCTGT-T-GTCTTGTACCACAAACAGTGAGTTACACAGCC
1 TGGGCACACGCTCGTGTCCCTAGCC-GTATGGTCTTGTACCACAAACAGTGAGCTACACAGCC
* * *
400897 TGGGCACACGCTTGTGTCCCTAGCCGTATGGTCTTGTACCACAAATAGTGAGCTACACGGCC
1 TGGGCACACGCTCGTGTCCCTAGCCGTATGGTCTTGTACCACAAACAGTGAGCTACACAGCC
* *
400959 TAGGCACACGCACGTGTCC
1 TGGGCACACGCTCGTGTCC
400978 TTGGATGTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
60 2 0.03
61 24 0.34
62 45 0.63
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.23
Consensus pattern (62 bp):
TGGGCACACGCTCGTGTCCCTAGCCGTATGGTCTTGTACCACAAACAGTGAGCTACACAGCC
Found at i:404104 original size:18 final size:20
Alignment explanation
Indices: 404075--404120 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
404065 TATGATTTAT
404075 AGGTTGAATTGAA-TACTTG
1 AGGTTGAATTGAAGTACTTG
404094 AGGTT-AATTGAAGTACTT-
1 AGGTTGAATTGAAGTACTTG
404112 A-GTTGAATT
1 AGGTTGAATT
404121 AAATTATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 12 0.48
19 10 0.40
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (20 bp):
AGGTTGAATTGAAGTACTTG
Found at i:405745 original size:54 final size:54
Alignment explanation
Indices: 405627--405749 Score: 149
Period size: 54 Copynumber: 2.3 Consensus size: 54
405617 TTATTTCAAT
* * *
405627 TCAGTGAGTTACACAGTCTAGCACACGGCCTGCGACACGACTGTGTGTCACAAA
1 TCAGAGAGTTACACGGTCTAGCACACGGCCTGCGACACGACTGTGTGACACAAA
* * * * *
405681 TTAGAAAGTTACACGGTCTGGCACATGGCCTGCGATACGACTGTGTGAC-CTAAA
1 TCAGAGAGTTACACGGTCTAGCACACGGCCTGCGACACGACTGTGTGACAC-AAA
*
405735 TCAGGGAGTTACACG
1 TCAGAGAGTTACACG
405750 ATTTAAGACA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.02
54 56 0.98
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (54 bp):
TCAGAGAGTTACACGGTCTAGCACACGGCCTGCGACACGACTGTGTGACACAAA
Found at i:407822 original size:3 final size:3
Alignment explanation
Indices: 407808--407869 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
407798 TTTTCTCTTA
* *
407808 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
407856 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
407870 CCTTATTCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:408026 original size:2 final size:2
Alignment explanation
Indices: 408021--408046 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
408011 ATATATTCAA
408021 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
408047 TCTCTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:412200 original size:21 final size:22
Alignment explanation
Indices: 412151--412200 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
412141 TAAAAATATT
* *
412151 TATAACATTATTTTTATGAATA
1 TATAATATTATATTTATGAATA
412173 -AGT-ATATTATATTTAT-AATA
1 TA-TAATATTATATTTATGAATA
412193 TATAATAT
1 TATAATAT
412201 ATACACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TATAATATTATATTTATGAATA
Found at i:413507 original size:33 final size:32
Alignment explanation
Indices: 413462--413621 Score: 140
Period size: 33 Copynumber: 4.8 Consensus size: 32
413452 ACATTCGTAG
* *
413462 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATCAGAA
* * *
413495 TACCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGCCATAGCCCAGCTATGGTCTTACAT-CAGA-A
* * * * * * *
413529 CTGCCATGGTCCAACCATGGTCTTACGTTCATAG
1 -TGCCATAGCCCAGCTATGGTCTTAC-ATCAGAA
* *
413563 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATCAGAA
413596 TGCCATAGCCCAGCTATGGTCTTACA
1 TGCCATAGCCCAGCTATGGTCTTACA
413622 CATAAACACT
Statistics
Matches: 97, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
32 5 0.05
33 67 0.69
34 2 0.02
35 22 0.23
36 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (32 bp):
TGCCATAGCCCAGCTATGGTCTTACATCAGAA
Found at i:413638 original size:101 final size:101
Alignment explanation
Indices: 413450--413689 Score: 426
Period size: 101 Copynumber: 2.4 Consensus size: 101
413440 AATTCGTCCT
* *
413450 TTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATACCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATACCATAGCCCAGCTATGGT
* *
413515 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
66 CTTACACATAAACACTACCATGGTCCAACCATGGTC
*
413551 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATACCATAGCCCAGCTATGGT
*
413616 CTTACACATAAACACTATCATGGTCCAACCATGGTC
66 CTTACACATAAACACTACCATGGTCCAACCATGGTC
413652 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
413690 CGTCAATTCA
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 133 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATACCATAGCCCAGCTATGGT
CTTACACATAAACACTACCATGGTCCAACCATGGTC
Found at i:422031 original size:22 final size:22
Alignment explanation
Indices: 422003--422046 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
421993 TAACATCAGC
422003 GCTTTCGGATATCACCTACGAT
1 GCTTTCGGATATCACCTACGAT
*
422025 GCTTTCGGATATCATCTACGAT
1 GCTTTCGGATATCACCTACGAT
422047 ATTTGTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (22 bp):
GCTTTCGGATATCACCTACGAT
Found at i:422457 original size:37 final size:38
Alignment explanation
Indices: 422400--422471 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
422390 CCGAATATAA
*
422400 TAAATATATATTTTTAA-TTTTTAATTTTAAAATACTT
1 TAAAAATATATTTTTAATTTTTTAATTTTAAAATACTT
* * *
422437 TAAAAATATTTTTTTTATTTTTTATTTTTAAAATA
1 TAAAAATATATTTTTAATTTTTTAATTTTAAAATA
422472 TTTTTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 14 0.47
38 16 0.53
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (38 bp):
TAAAAATATATTTTTAATTTTTTAATTTTAAAATACTT
Found at i:425347 original size:9 final size:9
Alignment explanation
Indices: 425330--425366 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
425320 TGAGTTTTCG
425330 AATTCGAAT
1 AATTCGAAT
*
425339 AACTCGAAT
1 AATTCGAAT
425348 AATTCGAAT
1 AATTCGAAT
425357 AATTCGAAT
1 AATTCGAAT
425366 A
1 A
425367 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:447804 original size:16 final size:16
Alignment explanation
Indices: 447783--447814 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
447773 GGTAAATTAC
447783 ACCAACAGTCAATCAA
1 ACCAACAGTCAATCAA
447799 ACCAACAGTCAATCAA
1 ACCAACAGTCAATCAA
447815 TTTTGAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.31, G:0.06, T:0.12
Consensus pattern (16 bp):
ACCAACAGTCAATCAA
Found at i:448031 original size:17 final size:17
Alignment explanation
Indices: 448009--448048 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
447999 TTAGAGAAGA
448009 AGAAGATGATGAGGAGG
1 AGAAGATGATGAGGAGG
*
448026 AGAAGATGATGATGAGG
1 AGAAGATGATGAGGAGG
448043 AGAAGA
1 AGAAGA
448049 AGAGGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.12
Consensus pattern (17 bp):
AGAAGATGATGAGGAGG
Found at i:448063 original size:20 final size:20
Alignment explanation
Indices: 448002--448051 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
447992 TTTAGGGTTA
448002 GAGAAGAAGAAGATGATGAG
1 GAGAAGAAGAAGATGATGAG
* *
448022 GAGGAGAAGATGATGATGAG
1 GAGAAGAAGAAGATGATGAG
448042 GAGAAGAAGA
1 GAGAAGAAGA
448052 GGAAGAAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.42, T:0.10
Consensus pattern (20 bp):
GAGAAGAAGAAGATGATGAG
Found at i:448757 original size:23 final size:24
Alignment explanation
Indices: 448718--448763 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
448708 AAAAAAAGAA
*
448718 ACATTTGTATTTCTCAATTCTCAC
1 ACATTTGTATTTCTCAATACTCAC
448742 ACATTTGT-TTTCTCAATACTCA
1 ACATTTGTATTTCTCAATACTCA
448764 TATGTTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.46
Consensus pattern (24 bp):
ACATTTGTATTTCTCAATACTCAC
Found at i:449199 original size:21 final size:22
Alignment explanation
Indices: 449173--449235 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 22
449163 ATCTTTTTGG
449173 TGAGTTGGGGCAGCTTGTTGA-
1 TGAGTTGGGGCAGCTTGTTGAC
*
449194 TGAGTTGGGGCAGCTTG-TAAC
1 TGAGTTGGGGCAGCTTGTTGAC
* *
449215 TGAGTTAGGGCAGCCTGTTGA
1 TGAGTTGGGGCAGCTTGTTGA
449236 GTTGGGGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.17, C:0.13, G:0.40, T:0.30
Consensus pattern (22 bp):
TGAGTTGGGGCAGCTTGTTGAC
Found at i:449284 original size:21 final size:21
Alignment explanation
Indices: 449233--449284 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
449223 GGCAGCCTGT
449233 TGAGTTGGGGTACTCTCTTGC
1 TGAGTTGGGGTACTCTCTTGC
* *
449254 TGATTTGGGGTAGC-CTGTTGC
1 TGAGTTGGGGTA-CTCTCTTGC
*
449275 TGAGTGGGGG
1 TGAGTTGGGG
449285 CAACCACTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.10, C:0.13, G:0.42, T:0.35
Consensus pattern (21 bp):
TGAGTTGGGGTACTCTCTTGC
Found at i:451620 original size:62 final size:62
Alignment explanation
Indices: 451554--451687 Score: 207
Period size: 62 Copynumber: 2.2 Consensus size: 62
451544 TTCTGTCAGT
451554 CAATAACCAATACAAAAATAATTTAATACAAACACAA-CAATTTAAGTCATGCACATGGCAGA
1 CAATAACCAATACAAAAATAATTTAATACAAACACAATC-ATTTAAGTCATGCACATGGCAGA
** * *
451616 CAATAACCAATACAAAAATAATTTAATACAAACACAATCATTTCTGTCATGCACATTGTAGA
1 CAATAACCAATACAAAAATAATTTAATACAAACACAATCATTTAAGTCATGCACATGGCAGA
*
451678 CAATAGCCAA
1 CAATAACCAA
451688 ACACTTTAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 65 0.98
63 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.23
Consensus pattern (62 bp):
CAATAACCAATACAAAAATAATTTAATACAAACACAATCATTTAAGTCATGCACATGGCAGA
Found at i:452011 original size:16 final size:17
Alignment explanation
Indices: 451992--452027 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
451982 AAATAACCCT
451992 AAATAACCCTAAATC-A
1 AAATAACCCTAAATCTA
452008 AAATAACCCTAAATCTA
1 AAATAACCCTAAATCTA
452025 AAA
1 AAA
452028 AATACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATAACCCTAAATCTA
Found at i:452260 original size:43 final size:42
Alignment explanation
Indices: 452174--452278 Score: 110
Period size: 43 Copynumber: 2.6 Consensus size: 42
452164 AAAAAAGATT
* *
452174 AATCATTTTCTAACCCTAAA-C--CCTATTAATCGATTATCA
1 AATCAATTTCTAACCCTAAACCAACCTATTAATCGATTACCA
* * *
452213 AATCAATTTCTAACCCTAAACCAACCTTCTTAATCGATTCCCG
1 AATCAATTTCTAACCCTAAACCAACC-TATTAATCGATTACCA
* *
452256 AATCAAATTCGAACCC-AAACCAA
1 AATCAATTTCTAACCCTAAACCAA
452279 TACAAATCAC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
39 19 0.35
40 1 0.02
42 9 0.16
43 26 0.47
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.29
Consensus pattern (42 bp):
AATCAATTTCTAACCCTAAACCAACCTATTAATCGATTACCA
Found at i:452314 original size:16 final size:17
Alignment explanation
Indices: 452293--452324 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
452283 AATCACAACT
452293 ATTTTTT-CCCAAATCG
1 ATTTTTTCCCCAAATCG
452309 ATTTTTTCCCCAAATC
1 ATTTTTTCCCCAAATC
452325 CCCTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTTTTTCCCCAAATCG
Found at i:453257 original size:29 final size:31
Alignment explanation
Indices: 453225--453288 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
453215 TTAATTTTAT
*
453225 TATTAAATTT-AAA-TAAAATAATGTATTTC
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
* *
453254 TATT--TTTTAAAAGGAAAATAATGTATTTT
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
453283 TATTAA
1 TATTAA
453289 TAACCAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.11
28 3 0.11
29 22 0.79
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (31 bp):
TATTAAATTTAAAAGGAAAATAATGTATTTC
Found at i:454164 original size:72 final size:71
Alignment explanation
Indices: 454032--454191 Score: 178
Period size: 72 Copynumber: 2.2 Consensus size: 71
454022 GGATTTCATG
** *
454032 ATCGATGGCTTGAGATCCAACATGAGTTGCAGATTCTCTGAAGCTTGCATGAGTAGCATCGAATC
1 ATCGATGGCTTGAGATCCAACAT-AGTTGCAGATTCTCTGAAAATTGCATGAGCAGCATCGAATC
**
454097 ATTGATT
65 ATACATT
* * ** * *
454104 ATCGATGGCTTGATATCCAGCACAT-GTTGCAGATTCTTTGAAAATTGTGTGAGCATCATCGATT
1 ATCGATGGCTTGAGATCCA--ACATAGTTGCAGATTCTCTGAAAATTGCATGAGCAGCATCGAAT
*
454168 TATACATT
64 CATACATT
454176 ATCGATGGCTTGAGAT
1 ATCGATGGCTTGAGAT
454192 TCGACACATG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
72 69 0.95
74 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (71 bp):
ATCGATGGCTTGAGATCCAACATAGTTGCAGATTCTCTGAAAATTGCATGAGCAGCATCGAATCA
TACATT
Found at i:455500 original size:9 final size:9
Alignment explanation
Indices: 455483--455512 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
455473 TGATACTTGG
*
455483 TTTGGAAAC
1 TTTGAAAAC
455492 TTTGAAAAC
1 TTTGAAAAC
455501 TTTGAAAAC
1 TTTGAAAAC
455510 TTT
1 TTT
455513 ACAATTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (9 bp):
TTTGAAAAC
Found at i:456178 original size:22 final size:22
Alignment explanation
Indices: 456152--456196 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
456142 AGATCAACAC
456152 AAATAT-AATCACATACATATCA
1 AAATATCAATCACA-ACATATCA
*
456174 AAATATCAATCTCAACATATCA
1 AAATATCAATCACAACATATCA
456196 A
1 A
456197 TCATCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATATCAATCACAACATATCA
Found at i:469428 original size:42 final size:42
Alignment explanation
Indices: 469375--469492 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
469365 TGATATGAGT
*
469375 TTCAGATTAACCCTTTTGGGTTTCAGTTTAGCTCTT-TTGAGC
1 TTCAGATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTT-AGC
* * * * * *
469417 TTTAGTTTAACCCTAATGGGCTTCAATTTAGCTATTCTTAGC
1 TTCAGATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
* *
469459 TTCAGATTAACCCTTATGGGTTTCCGTTCAGCTC
1 TTCAGATTAACCCTTATGGGTTTCAGTTTAGCTC
469493 CAATGAGTTC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 58 0.97
43 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.42
Consensus pattern (42 bp):
TTCAGATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
Found at i:486273 original size:19 final size:19
Alignment explanation
Indices: 486251--486293 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
486241 AAATTAATTT
*
486251 AAAATATAAAAAAATCATA
1 AAAATACAAAAAAATCATA
* * *
486270 AAAATGCAAAAAATTCCTA
1 AAAATACAAAAAAATCATA
486289 AAAAT
1 AAAAT
486294 TTCTTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATACAAAAAAATCATA
Found at i:488945 original size:57 final size:57
Alignment explanation
Indices: 488862--489005 Score: 267
Period size: 57 Copynumber: 2.6 Consensus size: 57
488852 AATACAAATA
488862 AATATAAT--AAA-TATATCCAATACAATAAATATTATTCTATTTATTTGTATTTTT
1 AATATAATAAAAATTATATCCAATACAATAAATATTATTCTATTTATTTGTATTTTT
488916 AATATAATAAAAATTATATCCAATACAATAAATATTATTCTATTTATTTGTATTTTT
1 AATATAATAAAAATTATATCCAATACAATAAATATTATTCTATTTATTTGTATTTTT
488973 AATATAATAAAAATTATATCCAATACAATAAAT
1 AATATAATAAAAATTATATCCAATACAATAAAT
489006 TTTTATTTTA
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
54 8 0.09
56 3 0.03
57 76 0.87
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (57 bp):
AATATAATAAAAATTATATCCAATACAATAAATATTATTCTATTTATTTGTATTTTT
Found at i:489111 original size:21 final size:22
Alignment explanation
Indices: 489057--489111 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
489047 ATATTCTGAG
489057 TTGACATTAT-TTCATATGAAAT
1 TTGA-ATTATATTCATATGAAAT
*
489079 TT-AATTATTATT-ATATGATAT
1 TTGAATTA-TATTCATATGAAAT
489100 TTGAATTATATT
1 TTGAATTATATT
489112 TTGAGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 16 0.55
22 9 0.31
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGAATTATATTCATATGAAAT
Found at i:489679 original size:19 final size:19
Alignment explanation
Indices: 489644--489694 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
489634 TCCTTAAATT
489644 AATTTTCTTTTAAATTTTAA
1 AATTTT-TTTTAAATTTTAA
*
489664 AATTTTTTTTACATTTTAA
1 AATTTTTTTTAAATTTTAA
*
489683 AATTATTTTTAA
1 AATTTTTTTTAA
489695 TAAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTTTTTAAATTTTAA
Found at i:492041 original size:49 final size:49
Alignment explanation
Indices: 491937--492067 Score: 145
Period size: 49 Copynumber: 2.7 Consensus size: 49
491927 AAAAGCTAGC
* * * *
491937 CCGTGTTGTCCACACGATCTACCCACATGGTTTGCACGATTTCACACAG
1 CCGTGTGGTCCACACGGTCTACCCACATGGTCTGCACAATTTCACACAG
** * * * *
491986 TTGTGTGGTCCACATGGGCTACCCACATGGTCTGCACAATTTTAGACAG
1 CCGTGTGGTCCACACGGTCTACCCACATGGTCTGCACAATTTCACACAG
* * *
492035 CCGTGTGGTCTACACGGTTTACCTACATGGTCT
1 CCGTGTGGTCCACACGGTCTACCCACATGGTCT
492068 ATATGATTTC
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (49 bp):
CCGTGTGGTCCACACGGTCTACCCACATGGTCTGCACAATTTCACACAG
Found at i:495677 original size:24 final size:25
Alignment explanation
Indices: 495647--495739 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
495637 GCCATATTGG
495647 GAAGCTC-CGAAGAGCCATTAA-CGA
1 GAAGCTCAC-AAGAGCCATTAATCGA
* * *
495671 GAAGCTCACAAGAGCCTTTAATTGG
1 GAAGCTCACAAGAGCCATTAATCGA
*
495696 GAAGCTCACAAAGAGCCATTTATCGA
1 GAAGCTCAC-AAGAGCCATTAATCGA
* * *
495722 GATGCTTATAAGAGCCAT
1 GAAGCTCACAAGAGCCAT
495740 GGTGTGTCTA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
24 18 0.32
25 20 0.36
26 18 0.32
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (25 bp):
GAAGCTCACAAGAGCCATTAATCGA
Found at i:500860 original size:16 final size:16
Alignment explanation
Indices: 500839--500870 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
500829 TGAAATGGTA
500839 AGTGTTCAATATGAAT
1 AGTGTTCAATATGAAT
500855 AGTGTTCAATATGAAT
1 AGTGTTCAATATGAAT
500871 TAAGATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
AGTGTTCAATATGAAT
Found at i:503484 original size:17 final size:17
Alignment explanation
Indices: 503462--503494 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
503452 TAAGTCAAAA
503462 TTGATAAGCATTGACTT
1 TTGATAAGCATTGACTT
503479 TTGATAAGCATTGACT
1 TTGATAAGCATTGACT
503495 ACGGAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (17 bp):
TTGATAAGCATTGACTT
Found at i:506371 original size:36 final size:36
Alignment explanation
Indices: 506327--506398 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
506317 AGTATAGCTT
*
506327 CACATCTTGGATTTCATTATCTC-AGTTTTCTTATCA
1 CACATCTTGGATTTCATTATCTCGA-TTTTCATATCA
506363 CACATCTTGGATTTCATTATCTCGATTTTCATATCA
1 CACATCTTGGATTTCATTATCTCGATTTTCATATCA
506399 TTCTTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (36 bp):
CACATCTTGGATTTCATTATCTCGATTTTCATATCA
Found at i:508474 original size:42 final size:43
Alignment explanation
Indices: 508365--508478 Score: 115
Period size: 43 Copynumber: 2.7 Consensus size: 43
508355 AGCTTGTACA
* * * * *
508365 ATGCCAACGTCGCAGACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATAACG
* * * *
508408 ATTCCACTGTCCCA-AGCAGGGTCTTACACGAAATCATAT-ACG
1 ATGCCAATGTCCCAGA-CATGGTCTTACACGAAATCAAATAACG
*
508450 ATGCCAATGTTCCAGACATGGTCTTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
508479 ATAAATCTCA
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
42 27 0.48
43 29 0.52
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATAACG
Found at i:519050 original size:42 final size:42
Alignment explanation
Indices: 518951--519111 Score: 146
Period size: 43 Copynumber: 3.8 Consensus size: 42
518941 AGCTCGTACA
* * * * * *
518951 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCAAATAATG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCATAT-ACG
*
518994 ATGCC-ACTGTCCCAGACAAGGTCTTACACGAAATCATATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCATATACG
* * * *
519036 ATGCCAATGTCCCAGACATGGTCTGACACGTAAATC-TCAAATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAATCAT-ATA-CG
* *
519080 ATGCCAACGTTCCAGACGTGGTCTTACACGAA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAA
519112 GTCACATATC
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 30 0.31
43 40 0.41
44 27 0.28
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCATATACG
Found at i:529976 original size:14 final size:14
Alignment explanation
Indices: 529957--529997 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
529947 TATTACCATA
529957 TAATTTTGGTTATC
1 TAATTTTGGTTATC
529971 TAATTTTGGTTATC
1 TAATTTTGGTTATC
529985 TAATTTTGGTTAT
1 TAATTTTGGTTAT
529998 AATGACATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.59
Consensus pattern (14 bp):
TAATTTTGGTTATC
Found at i:534437 original size:20 final size:19
Alignment explanation
Indices: 534404--534451 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
534394 TCGTATTCGT
* *
534404 ATTTT-ATTTTATTTTTAT
1 ATTTTAATTTAATTTTTAC
534422 ATTTTTAATTTAATTTTTAC
1 A-TTTTAATTTAATTTTTAC
534442 ATTTTAATTT
1 ATTTTAATTT
534452 TTCTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 12 0.46
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTAATTTAATTTTTAC
Found at i:534447 original size:14 final size:13
Alignment explanation
Indices: 534410--534453 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
534400 TCGTATTTTA
*
534410 TTTTATTTTTATAT
1 TTTTAATTTTA-AT
534424 TTTTAA-TTTAAT
1 TTTTAATTTTAAT
534436 TTTTACATTTTAAT
1 TTTTA-ATTTTAAT
534450 TTTT
1 TTTT
534454 CTTTTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 5 0.19
14 15 0.56
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:538288 original size:14 final size:14
Alignment explanation
Indices: 538264--538311 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
538254 CCCCACTGTC
538264 TATTCTTTTTATTTT
1 TATT-TTTTTATTTT
*
538279 TATTTTTTTATTAT
1 TATTTTTTTATTTT
*
538293 TATTATTTTATTATT
1 TATTTTTTTATT-TT
538308 TATT
1 TATT
538312 GTTATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTTTTATTTT
Found at i:538311 original size:21 final size:22
Alignment explanation
Indices: 538276--538318 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
538266 TTCTTTTTAT
*
538276 TTTTATTTTTTTATTATTATTA
1 TTTTATTTATTTATTATTATTA
*
538298 TTTTA-TTATTTATTGTTATTA
1 TTTTATTTATTTATTATTATTA
538319 AATCTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTATTTATTATTATTA
Found at i:538462 original size:3 final size:3
Alignment explanation
Indices: 538454--538532 Score: 54
Period size: 3 Copynumber: 26.0 Consensus size: 3
538444 TTTCATTTAG
* * *
538454 TAT TAT TAT TAT TAT TAT TTT TTT TCATT TAT TAT T-T TAT TAC T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TAT TAT TAT
* * * *
538499 TAT TAT TACT TAG TCT TAT TAC TAT TAT GAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
538533 GAGTCATATT
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
2 3 0.05
3 50 0.85
4 4 0.07
5 2 0.03
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:538479 original size:32 final size:32
Alignment explanation
Indices: 538441--538505 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
538431 CGTTTACTCA
538441 TTTTTTCATTTAGTATTATTATTA-TTATTATT
1 TTTTTTCATTTAGTATT-TTATTACTTATTATT
*
538473 TTTTTTCATTTATTATTTTATTACTTTATTATT
1 TTTTTTCATTTAGTATTTTATTAC-TTATTATT
538506 ACTTAGTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 6 0.20
32 16 0.53
33 8 0.27
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (32 bp):
TTTTTTCATTTAGTATTTTATTACTTATTATT
Found at i:538500 original size:16 final size:17
Alignment explanation
Indices: 538465--538505 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
538455 ATTATTATTA
* *
538465 TTATTATTTTTTTTCAT
1 TTATTATTTTATTACAT
538482 TTATTATTTTATTAC-T
1 TTATTATTTTATTACAT
538498 TTATTATT
1 TTATTATT
538506 ACTTAGTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTATTTTATTACAT
Found at i:538537 original size:24 final size:25
Alignment explanation
Indices: 538490--538548 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
538480 ATTTATTATT
* *
538490 TTATTACT-TTATTATTACTTAGTC
1 TTATTACTATTATGATTACTGAGTC
538514 TTATTACTATTATGATTA-TGAGTC
1 TTATTACTATTATGATTACTGAGTC
* *
538538 ATATTAGTATT
1 TTATTACTATT
538549 TCTATAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (25 bp):
TTATTACTATTATGATTACTGAGTC
Found at i:539918 original size:9 final size:9
Alignment explanation
Indices: 539904--539928 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
539894 AGCTCTATTT
539904 TTATTTTTA
1 TTATTTTTA
539913 TTATTTTTA
1 TTATTTTTA
539922 TTATTTT
1 TTATTTT
539929 AGTTGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATTTTTA
Found at i:546922 original size:18 final size:18
Alignment explanation
Indices: 546901--546939 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
546891 AATTCTGTAA
*
546901 TTAGTTTAAATTTGATCT
1 TTAGTTGAAATTTGATCT
*
546919 TTAGTTGAAATTTGATTT
1 TTAGTTGAAATTTGATCT
546937 TTA
1 TTA
546940 AATTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (18 bp):
TTAGTTGAAATTTGATCT
Found at i:551537 original size:15 final size:15
Alignment explanation
Indices: 551519--551561 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
551509 CTCTGCTTTG
551519 TTCTGTTCTGTTCTA
1 TTCTGTTCTGTTCTA
* *
551534 TTCTGCTCTGCTCTA
1 TTCTGTTCTGTTCTA
* *
551549 TTCAGTTCAGTTC
1 TTCTGTTCTGTTC
551562 AGTTCTATTC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.09, C:0.26, G:0.14, T:0.51
Consensus pattern (15 bp):
TTCTGTTCTGTTCTA
Found at i:551577 original size:15 final size:15
Alignment explanation
Indices: 551554--551583 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
551544 CTCTATTCAG
*
551554 TTCAGTTCAGTTCTA
1 TTCAATTCAGTTCTA
551569 TTCAATTCAGTTCTA
1 TTCAATTCAGTTCTA
551584 CTTGAGTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (15 bp):
TTCAATTCAGTTCTA
Found at i:552123 original size:17 final size:18
Alignment explanation
Indices: 552090--552124 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
552080 AAAAGTCTAC
552090 ATAAAATAAAATATAAAT
1 ATAAAATAAAATATAAAT
*
552108 ATAAAA-AAATTATAAAT
1 ATAAAATAAAATATAAAT
552125 TATGCTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAATAAAATATAAAT
Found at i:558917 original size:32 final size:32
Alignment explanation
Indices: 558876--559087 Score: 237
Period size: 32 Copynumber: 6.7 Consensus size: 32
558866 CAATATATAA
**
558876 ATACATATACAATTCAATTCGGCAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATAGAAGT
* *
558908 ATACCTATACAA-TCAATTCGGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATAGAAGT
* * * *
558939 ATATATATACAATTCAAATCAGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATAGAAGT
* **
558971 ATATATATACAATTCAATTCGGCAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATAGAAGT
* * *
559003 ATACCTATACAATTCAAATCGGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATAGAAGT
* * **
559035 ATATATATACAATTCAATTCGGCAGTAGGTGT
1 ATACATATACAATTCAATTCGGCAATAGAAGT
* *
559067 ATACCTATAAAATTCAATTCG
1 ATACATATACAATTCAATTCG
559088 ACAGTATATA
Statistics
Matches: 150, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
31 26 0.17
32 124 0.83
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (32 bp):
ATACATATACAATTCAATTCGGCAATAGAAGT
Found at i:558982 original size:95 final size:96
Alignment explanation
Indices: 558857--559051 Score: 331
Period size: 95 Copynumber: 2.0 Consensus size: 96
558847 AATGCTCAAA
*
558857 TCAAATTAGCAATATATAAATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAA-T
1 TCAAATCAGCAATATATAAATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAATT
*
558921 CAATTCGGCAATATAAGTATATATATACAAT
66 CAAATCGGCAATATAAGTATATATATACAAT
* *
558952 TCAAATCAGCAATATA-AGTATATATATACAATTCAATTCGGCAATAGGTGTATACCTATACAAT
1 TCAAATCAGCAATATATA-AATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAAT
559016 TCAAATCGGCAATATAAGTATATATATACAAT
65 TCAAATCGGCAATATAAGTATATATATACAAT
559048 TCAA
1 TCAA
559052 TTCGGCAGTA
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
94 1 0.01
95 58 0.62
96 35 0.37
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (96 bp):
TCAAATCAGCAATATATAAATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAATT
CAAATCGGCAATATAAGTATATATATACAAT
Found at i:559018 original size:64 final size:64
Alignment explanation
Indices: 558876--559083 Score: 274
Period size: 64 Copynumber: 3.3 Consensus size: 64
558866 CAATATATAA
* *** ** ***
558876 ATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAA-TCAATTCGGCAATATAAGT
1 ATACATATACAATTCAAATCGGCAATATAAGTATATATATACAATTCAATTCGGCAATAGGTGT
* *
558939 ATATATATACAATTCAAATCAGCAATATAAGTATATATATACAATTCAATTCGGCAATAGGTGT
1 ATACATATACAATTCAAATCGGCAATATAAGTATATATATACAATTCAATTCGGCAATAGGTGT
* *
559003 ATACCTATACAATTCAAATCGGCAATATAAGTATATATATACAATTCAATTCGGCAGTAGGTGT
1 ATACATATACAATTCAAATCGGCAATATAAGTATATATATACAATTCAATTCGGCAATAGGTGT
* *
559067 ATACCTATAAAATTCAA
1 ATACATATACAATTCAA
559084 TTCGACAGTA
Statistics
Matches: 128, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 36 0.28
64 92 0.72
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (64 bp):
ATACATATACAATTCAAATCGGCAATATAAGTATATATATACAATTCAATTCGGCAATAGGTGT
Found at i:559081 original size:96 final size:95
Alignment explanation
Indices: 558876--559087 Score: 325
Period size: 96 Copynumber: 2.2 Consensus size: 95
558866 CAATATATAA
*
558876 ATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAATCAATTCGGCAATATAAGTAT
1 ATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAATCAAATCGGCAATATAAGTAT
*
558941 ATATATACAATTCAAATCAGCAATATAAGT
66 ATATATACAATTCAAATCAGCAATAGAAGT
*
558971 ATATATATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAAATCGGCAATATAAGTA
1 ATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAA-TCAAATCGGCAATATAAGTA
* * * **
559036 TATATATACAATTCAATTCGGCAGTAGGTGT
65 TATATATACAATTCAAATCAGCAATAGAAGT
* *
559067 ATACCTATAAAATTCAATTCG
1 ATACATATACAATTCAATTCG
559088 ACAGTATATA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 43 0.41
96 62 0.59
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (95 bp):
ATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAATCAAATCGGCAATATAAGTAT
ATATATACAATTCAAATCAGCAATAGAAGT
Found at i:573231 original size:61 final size:61
Alignment explanation
Indices: 573136--573264 Score: 231
Period size: 61 Copynumber: 2.1 Consensus size: 61
573126 GTATAGTTCC
**
573136 ATACTTTGTGATTTTGCTATTTCGGTTTTATTATGATTCTATGTGATTATTTGAAAGAGAT
1 ATACTTTGTGATTTCACTATTTCGGTTTTATTATGATTCTATGTGATTATTTGAAAGAGAT
573197 ATACTTTGTGATTTCACTATTTCGGTTTTATTATGATTCTATGTGATTATTTGAAAGAGAT
1 ATACTTTGTGATTTCACTATTTCGGTTTTATTATGATTCTATGTGATTATTTGAAAGAGAT
*
573258 ATTCTTT
1 ATACTTT
573265 TGACGGAGAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (61 bp):
ATACTTTGTGATTTCACTATTTCGGTTTTATTATGATTCTATGTGATTATTTGAAAGAGAT
Found at i:577100 original size:43 final size:43
Alignment explanation
Indices: 577005--577150 Score: 154
Period size: 43 Copynumber: 3.4 Consensus size: 43
576995 GGGTTAACGA
* * *
577005 GATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATGAT
1 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATG-T
*
577048 -AATTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATGT
1 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATGT
* * * * *
577090 GATTTTGTGTAATACCATGGCT-TGACTATTGGCATCGATACGT
1 GATTTCGTGTAAGACCATGTCTGGGAC-ATTGGCATCGATATGT
* *
577133 GATTACATGTAAGACCAT
1 GATTTCGTGTAAGACCAT
577151 ATCTTGGATA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 27 0.31
43 59 0.69
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATGT
Found at i:579980 original size:23 final size:23
Alignment explanation
Indices: 579954--580003 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
579944 ATTAGTGCCA
*
579954 CACTAATATGTAGCCGAAGCTAC
1 CACTAAAATGTAGCCGAAGCTAC
*
579977 CACTAAAATGTAGCTGAAGCTAC
1 CACTAAAATGTAGCCGAAGCTAC
580000 CACT
1 CACT
580004 GATCAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (23 bp):
CACTAAAATGTAGCCGAAGCTAC
Found at i:587429 original size:23 final size:23
Alignment explanation
Indices: 587403--587461 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
587393 ATAAGTGCCA
587403 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
* **
587426 CACTGATATGTAGTCGTAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
587449 CACTGAGATGTAG
1 CACTGATATGTAG
587462 TCGTAGCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:587462 original size:23 final size:23
Alignment explanation
Indices: 587420--587477 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
587410 ATGTAGCCAA
*
587420 AGCTACCACTGATATGTAGTCGT
1 AGCTACCACTGAGATGTAGTCGT
587443 AGCTACCACTGAGATGTAGTCGT
1 AGCTACCACTGAGATGTAGTCGT
*
587466 AGCTACCGCTGA
1 AGCTACCACTGA
587478 AATCACACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (23 bp):
AGCTACCACTGAGATGTAGTCGT
Found at i:589771 original size:26 final size:26
Alignment explanation
Indices: 589740--589806 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
589730 CATTTCGACC
**
589740 CATAGCTCGTGTGAGAAGGCTTATTT
1 CATAGCTCGTGTGAGAAGGCCCATTT
* *
589766 CATAGCTTGTGTGAGCAGGCCCATTT
1 CATAGCTCGTGTGAGAAGGCCCATTT
* *
589792 TACAGCTCGTGTGAG
1 CATAGCTCGTGTGAG
589807 CAATGATGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (26 bp):
CATAGCTCGTGTGAGAAGGCCCATTT
Found at i:593005 original size:28 final size:28
Alignment explanation
Indices: 592967--593045 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
592957 GTGAGCAGCC
** *
592967 CAAATATCACAGGTTGTGTGAGCAAATT
1 CAAATATCACAACTTGTGTGAGCAAACT
592995 CAAATATCACAACTTGTGTGAGCAAACT
1 CAAATATCACAACTTGTGTGAGCAAACT
* * *
593023 CAAATATCATAACTCGTATGAGC
1 CAAATATCACAACTTGTGTGAGC
593046 CAATCGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (28 bp):
CAAATATCACAACTTGTGTGAGCAAACT
Found at i:593876 original size:16 final size:15
Alignment explanation
Indices: 593855--593884 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
593845 AATTAAATAC
593855 AACAACATTCATTAAT
1 AACAACATT-ATTAAT
593871 AACAACATTATTAA
1 AACAACATTATTAA
593885 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
AACAACATTATTAAT
Found at i:594247 original size:18 final size:19
Alignment explanation
Indices: 594224--594263 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
594214 AGTAGCATTC
594224 AAAACATTATATCAAAA-A
1 AAAACATTATATCAAAAGA
594242 AAAACATTATATCAAAAGA
1 AAAACATTATATCAAAAGA
594261 AAA
1 AAA
594264 TTAAGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.20
Consensus pattern (19 bp):
AAAACATTATATCAAAAGA
Found at i:594502 original size:15 final size:15
Alignment explanation
Indices: 594482--594513 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
594472 GTATATAAAA
594482 AACTAAATTTGAATG
1 AACTAAATTTGAATG
594497 AACTAAATTTGAATG
1 AACTAAATTTGAATG
594512 AA
1 AA
594514 ATTTTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (15 bp):
AACTAAATTTGAATG
Found at i:596413 original size:49 final size:49
Alignment explanation
Indices: 596357--596493 Score: 213
Period size: 49 Copynumber: 2.8 Consensus size: 49
596347 TTTTTTCTCA
* *
596357 ATGCCATAGTCCAACTATGGTCTTACACGTAATCACATAACATATACCG
1 ATGCCATAGACCAGCTATGGTCTTACACGTAATCACATAACATATACCG
* *
596406 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATTCCG
1 ATGCCATAGACCAGCTATGGTCTTACACGTAATCACATAACATATACCG
*
596455 ATGCCATA-ACCTAGCTATGGTCTTACACGGAATCACATA
1 ATGCCATAGACC-AGCTATGGTCTTACACGTAATCACATA
596494 TCACTTATTG
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 2 0.02
49 80 0.98
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (49 bp):
ATGCCATAGACCAGCTATGGTCTTACACGTAATCACATAACATATACCG
Found at i:597701 original size:23 final size:23
Alignment explanation
Indices: 597675--597770 Score: 102
Period size: 23 Copynumber: 4.2 Consensus size: 23
597665 ATAAGTGCCA
*
597675 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
* * ** *
597698 CACTAATACGTAAATGTAGCTAC
1 CACTGATATGTAACCGAAGCTAC
* * *
597721 CATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
*
597744 CACTGATATGTAACCGTAGCTAC
1 CACTGATATGTAACCGAAGCTAC
597767 CACT
1 CACT
597771 AATCAATAAC
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAACCGAAGCTAC
Found at i:598036 original size:18 final size:20
Alignment explanation
Indices: 597999--598040 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
597989 ATTTTCCTTC
*
597999 CACATTTAATAATAATAATT
1 CACATATAATAATAATAATT
598019 CACATATAA-AAT-ATAATT
1 CACATATAATAATAATAATT
598037 CACA
1 CACA
598041 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 8 0.38
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (20 bp):
CACATATAATAATAATAATT
Found at i:599450 original size:11 final size:11
Alignment explanation
Indices: 599436--599461 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
599426 TATTTTTTTA
599436 TTTTAAAATAC
1 TTTTAAAATAC
599447 TTTTAAAATAC
1 TTTTAAAATAC
599458 TTTT
1 TTTT
599462 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:599462 original size:38 final size:37
Alignment explanation
Indices: 599415--599532 Score: 115
Period size: 38 Copynumber: 3.3 Consensus size: 37
599405 GCCCGAATAT
*
599415 AATAATTTTTTTATTTTTTTATTTTAAAATACTTTTAA
1 AATACTTTTTTTATTTTTTTATTTTAAAATA-TTTTAA
** *
599453 AATACTTTTTTTAAATTTTTA-ATT----T-TTTTAA
1 AATACTTTTTTTATTTTTTTATTTTAAAATATTTTAA
*
599484 AATAC-TTTTTAATTTTTTTAATTTTAAAATATTTTTAA
1 AATACTTTTTTTATTTTTTT-ATTTTAAAATA-TTTTAA
599522 AATACTTTTTT
1 AATACTTTTTT
599533 AAATTTTTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
30 11 0.17
31 12 0.19
32 2 0.03
33 1 0.02
36 1 0.02
37 2 0.03
38 29 0.46
39 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (37 bp):
AATACTTTTTTTATTTTTTTATTTTAAAATATTTTAA
Found at i:599480 original size:9 final size:9
Alignment explanation
Indices: 599458--599508 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
599448 TTTAAAATAC
599458 TTTTTTTAA
1 TTTTTTTAA
*
599467 -ATTTTTAA
1 TTTTTTTAA
599475 TTTTTTTAAAA
1 TTTTTTT--AA
*
599486 TACTTTTTAA
1 T-TTTTTTAA
599496 TTTTTTTAA
1 TTTTTTTAA
599505 TTTT
1 TTTT
599509 AAAATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 7 0.21
9 16 0.47
10 3 0.09
11 3 0.09
12 5 0.15
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:599502 original size:30 final size:30
Alignment explanation
Indices: 599447--599508 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 30
599437 TTTAAAATAC
599447 TTTTAAAATACTTTTTTTAAATTTTTAATTT
1 TTTTAAAATAC-TTTTTTAAATTTTTAATTT
*
599478 TTTTAAAATAC-TTTTTAATTTTTTTAATTT
1 TTTTAAAATACTTTTTTAA-ATTTTTAATTT
599508 T
1 T
599509 AAAATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.24
30 11 0.38
31 11 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTAAAATACTTTTTTAAATTTTTAATTT
Found at i:599582 original size:26 final size:25
Alignment explanation
Indices: 599532--599582 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
599522 AATACTTTTT
**
599532 TAAATTTTTGTTTTAATTTTCAAAA
1 TAAATTTTTGTTTTAATTTAAAAAA
599557 TAAATTTTTGGTATTT-ATTTAAAAAA
1 TAAATTTTT-GT-TTTAATTTAAAAAA
599583 CGGGCTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 9 0.41
26 10 0.45
27 3 0.14
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (25 bp):
TAAATTTTTGTTTTAATTTAAAAAA
Found at i:602276 original size:18 final size:17
Alignment explanation
Indices: 602250--602283 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
602240 GCGCCGCGCT
602250 CCTCCCACGCGCGCCTG
1 CCTCCCACGCGCGCCTG
*
602267 CCTCCTCACGTGCGCCT
1 CCTCC-CACGCGCGCCT
602284 CCGTACCCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.56, G:0.21, T:0.18
Consensus pattern (17 bp):
CCTCCCACGCGCGCCTG
Found at i:609163 original size:27 final size:26
Alignment explanation
Indices: 609126--609176 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
609116 AAAAAGGAGC
**
609126 AAAAGAAAAAAATCAAAATCAAAACA
1 AAAAGAAAAAAAGAAAAATCAAAACA
609152 AAAAGAAGAAAAAGAAAAATCAAAA
1 AAAAGAA-AAAAAGAAAAATCAAAA
609177 ATCAAGGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAAAGAAAAATCAAAACA
Found at i:609218 original size:15 final size:13
Alignment explanation
Indices: 609186--609235 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
609176 AATCAAGGTC
*
609186 AAAATGAAAATGAA
1 AAAAAGAAAA-GAA
* *
609200 AAAGAGAGAAGAA
1 AAAAAGAAAAGAA
609213 AAAAAGAAAAG-A
1 AAAAAGAAAAGAA
609225 AAAAAGAAAAG
1 AAAAAGAAAAG
609236 GAGAGCTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 12 0.39
13 12 0.39
14 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:611458 original size:87 final size:88
Alignment explanation
Indices: 611312--611707 Score: 516
Period size: 87 Copynumber: 4.5 Consensus size: 88
611302 CAGATCAGTG
* *
611312 AAGATAGCAAATCTTGCCTTCCTGCATTTACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAGACAAAGCCTTGCCTCC
* *
611376 ATCGGTTGCATTGGAGCTGGTTA
66 ATCGGTTGCAGTGGAGCAGGTTA
* * * *
611399 AAGATAGCAGATCTTGTCTTCCTGCATTGATAGCAAAGCAGATCGAAA-ACAAAGCCTTGCCTCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAGACAAAGCCTTGCCTCC
611463 ATCGGTTGCAGTGGAGCAGGTTA
66 ATCGGTTGCAGTGGAGCAGGTTA
* * *
611486 AAGATAGCAGATCTTGCCTTCCTGCACT-ACAGCGAAGCAGATCG-AAGATACCAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAGACA-AAGCCTTGCCTC
* * *
611549 CCTCGGTTGTAGTGGAGTAGGTTA
65 CATCGGTTGCAGTGGAGCAGGTTA
* * **
611573 AAGATATCAGATCTTGCCCTCCTGCGCTGACAGCGAAGCAGATC-AAAGACACCAA-CCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAGACA--AAGCCTTGCCT
* *
611636 CCCTCGGTTGCAGTGGAGCAGGTTG
64 CCATCGGTTGCAGTGGAGCAGGTTA
* * *
611661 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAAATCGAA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA
611708 GATTAGAAGT
Statistics
Matches: 270, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
85 2 0.01
86 16 0.06
87 161 0.60
88 87 0.32
89 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (88 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAGACAAAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCAGGTTA
Found at i:611577 original size:43 final size:43
Alignment explanation
Indices: 611451--611666 Score: 132
Period size: 44 Copynumber: 5.0 Consensus size: 43
611441 TCGAAAACAA
** *
611451 AGCCTTGCCTCAATCGGTTGCAGTGGAGCAGGTTAAAGATAGC
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATACC
* * ** * * * * **
611494 AGATCTTGCCTTCCT-GCACTACAGCGAAGCAGATCGAAGATACC
1 AG-CCTTGCCTCCCTCG-GTTGCAGTGGAGCAGGTTAAAGATACC
* * *
611538 AGCCTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTAAAGATATC
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATACC
* * * * * * *
611581 AGATCTTGCC-CTCCT-GCGCTGACAGCGAAGCAGATCAAAGACACC
1 AG-CCTTGCCTC-CCTCG-GTTG-CAGTGGAGCAGGTTAAAGATACC
* *
611626 AACCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATA
611667 GCAGATCTTG
Statistics
Matches: 119, Mismatches: 45, Indels: 18
0.65 0.25 0.10
Matches are distributed among these distances:
43 48 0.40
44 53 0.45
45 18 0.15
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (43 bp):
AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATACC
Found at i:611994 original size:44 final size:44
Alignment explanation
Indices: 611926--612019 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
611916 TAGATCGCAT
*
611926 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
* *
611970 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
*
612014 CGGATT
1 CAGATT
612020 AAAATAAAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
Found at i:612007 original size:98 final size:97
Alignment explanation
Indices: 611828--612009 Score: 224
Period size: 98 Copynumber: 1.9 Consensus size: 97
611818 TGTAAGGAAG
* * * * *
611828 CAGATTGAAGCCAGTAATCCTATCTCCCTGATATTACAGCGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCT
*
611893 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
* * **
611926 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAAG-AATCC
611990 TATCTCCCTG-AGATTACAGT
64 TATCTCCCTGAAG-TTACAGT
612010 GGAGCGGATT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 4 0.06
98 64 0.90
99 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (97 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAGAATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:612084 original size:142 final size:142
Alignment explanation
Indices: 611826--612095 Score: 504
Period size: 142 Copynumber: 1.9 Consensus size: 142
611816 AGTGTAAGGA
*
611826 AGCAGATTGAAGCCAGTAATCCTATCTCCCTGATATTACAGCGGAGCGGATTAAAATAAAGGATC
1 AGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGCGGAGCGGATTAAAATAAAGGATC
*
611891 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCTAGAAATCTTATCTCCCTG
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTG
611956 AGATTACAGCGG
131 AGATTACAGCGG
* *
611968 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATC
1 AGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGCGGAGCGGATTAAAATAAAGGATC
612033 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCC
66 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCC
612096 AAGCGATATA
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 124 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (142 bp):
AGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGCGGAGCGGATTAAAATAAAGGATC
TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTG
AGATTACAGCGG
Found at i:612159 original size:50 final size:50
Alignment explanation
Indices: 612105--612337 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
612095 CAAGCGATAT
* * * * **
612105 AGTGGAATAGATTAAAGCTACAACAGCGAATCTTACCT-CCTAGGCGGTGC
1 AGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCT-GACATTGC
* *
612155 AGTGGAGCAGATTAAAGCCACAACAGTGAATCTTGCCTCCCTGACATTGC
1 AGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCTGACATTGC
* * *
612205 AGTGGAGCAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGC
1 AGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCTGACATTGC
* * *
612255 AGTGGAACAGATTAAAGCCACAACAGCGAATCATGCTTCCCCGACATTGC
1 AGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCTGACATTGC
** * **
612305 AGTTAAAAAGATTAAAGCCACAATGGCGAATCT
1 AGTGGAACAGATTAAAGCCACAACAGCGAATCT
612338 AACTTTCCAA
Statistics
Matches: 161, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
50 158 0.98
51 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (50 bp):
AGTGGAACAGATTAAAGCCACAACAGCGAATCTTGCCTCCCTGACATTGC
Found at i:613759 original size:23 final size:23
Alignment explanation
Indices: 613733--613777 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
613723 CACGCATTTT
*
613733 TTTATATAGTATAGACATATTCC
1 TTTATATAATATAGACATATTCC
* *
613756 TTTATATAATATATATATATTC
1 TTTATATAATATAGACATATTC
613778 TTAAACTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTATATAATATAGACATATTCC
Found at i:627061 original size:54 final size:54
Alignment explanation
Indices: 626974--627098 Score: 223
Period size: 54 Copynumber: 2.3 Consensus size: 54
626964 ACCACGGTCT
*
626974 CGGGTGCGGGTGCTTCAACCGGTGGGTCGGCCTTCTCTTCTTCCCTGACTTCAA
1 CGGGTGCGGGTGCTTCAACCGGTGGGTCAGCCTTCTCTTCTTCCCTGACTTCAA
* *
627028 CGGGTGCGGGTGCTTCAATCGGTGGGTCAGCCTTCTCTTCTTCCTTGACTTCAA
1 CGGGTGCGGGTGCTTCAACCGGTGGGTCAGCCTTCTCTTCTTCCCTGACTTCAA
627082 CGGGTGCGGGTGCTTCA
1 CGGGTGCGGGTGCTTCA
627099 GTTTCGACTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.10, C:0.29, G:0.31, T:0.30
Consensus pattern (54 bp):
CGGGTGCGGGTGCTTCAACCGGTGGGTCAGCCTTCTCTTCTTCCCTGACTTCAA
Found at i:638129 original size:24 final size:25
Alignment explanation
Indices: 638102--638151 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
638092 ACTAGTCATA
*
638102 GAGAGAATTGAGGAG-GGATATTTG
1 GAGAGAATTGAGGAGAGAATATTTG
*
638126 GAGAGATTTGAGGAGAGAATATTTG
1 GAGAGAATTGAGGAGAGAATATTTG
638151 G
1 G
638152 GATTTGGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (25 bp):
GAGAGAATTGAGGAGAGAATATTTG
Found at i:639081 original size:27 final size:27
Alignment explanation
Indices: 638821--639070 Score: 293
Period size: 27 Copynumber: 9.3 Consensus size: 27
638811 AGAGATCGAT
* * *
638821 AAATGATCAAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
638848 AAATGACTGAAATACCCCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** **
638875 AAATGACCGAAATACCCCTGTAAAGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** *
638902 AAATGATCGAAATACCTTCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
**
638929 AAATGACCGAAATACCCTTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
638956 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
638983 AAATTATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
639010 AAATGACCGAAATACTCTCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
**
639037 AAATGACTAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
639064 AAATGAC
1 AAATGAC
639071 TATTATACCC
Statistics
Matches: 188, Mismatches: 35, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 188 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:639081 original size:81 final size:81
Alignment explanation
Indices: 638821--639069 Score: 327
Period size: 81 Copynumber: 3.1 Consensus size: 81
638811 AGAGATCGAT
* * * * *
638821 AAATGATCAAAATACCCCCATAGGATAAAATGACTGAAATACCCCCGTAGGGTAAAATGACCGAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCGAA
** **
638886 ATACCCCTGTAAAGTA
66 ATACCCCCATAGGGTA
** * * *
638902 AAATGATCGAAATACCTTCATAAGGTAAAATGACCGAAATACCCTTATAGGGTAGAATGACCGAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCGAA
638967 ATACCCCCATAGGGTA
66 ATACCCCCATAGGGTA
* * * **
638983 AAATTATCGAAATACCCCCATAGGGTAAAATGACCGAAATACTCTCATAGGATAAAATGACTAAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCGAA
639048 ATACCCCCATAGGGTA
66 ATACCCCCATAGGGTA
639064 AAATGA
1 AAATGA
639070 CTATTATACC
Statistics
Matches: 143, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 143 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (81 bp):
AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCGAA
ATACCCCCATAGGGTA
Found at i:643728 original size:35 final size:35
Alignment explanation
Indices: 643689--643760 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
643679 TTTAGAAATA
643689 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
1 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
*
643724 TCTCGCCTGCTTAGATAAGGAGTCAAAAGATATGG
1 TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
643759 TC
1 TC
643761 ATGCTGTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (35 bp):
TCTCGCCTGCTTAGATAAAGAGTCAAAAGATATGG
Found at i:649415 original size:21 final size:21
Alignment explanation
Indices: 649391--649434 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
649381 CACCCAAACA
649391 CTTAGCGGAGAATTTACCAAT
1 CTTAGCGGAGAATTTACCAAT
649412 CTTAGCGGAGAATTTACCAAT
1 CTTAGCGGAGAATTTACCAAT
649433 CT
1 CT
649435 CATCCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (21 bp):
CTTAGCGGAGAATTTACCAAT
Found at i:667563 original size:76 final size:75
Alignment explanation
Indices: 667428--667788 Score: 283
Period size: 76 Copynumber: 4.8 Consensus size: 75
667418 CCACACCACA
* * * * * * *
667428 TGGTAGAGCCTACTCCCTTAGGAGGGGAGACCATCAAGCCAAACAATTTGACTATCATCTCTTAT
1 TGGTAGAGCCTACTCCTTTA--A-AGGATACCATCAAGCTAAACAAATTGACTCTCATCTCTTTT
*
667493 GCTATCATGCCATG
63 GCT-TCATACCATG
* * *
667507 TGGTAGAGTCTACTCCTTTAAAGGATACCATCAAGCTAAACAAATTGTCTCTCATCTATTTTGCT
1 TGGTAGAGCCTACTCCTTTAAAGGATACCATCAAGCTAAACAAATTGACTCTCATCTCTTTTGCT
* *
667572 CTCATATCAAG
66 -TCATACCATG
* * *
667583 TGGTAGAGCCTACTCCCTTAAAGGATACCATCAAGCTAAAAAAATTGGCTCTCATCTCTTTTGCT
1 TGGTAGAGCCTACTCCTTTAAAGGATACCATCAAGCTAAACAAATTGACTCTCATCTCTTTTGCT
* * *
667648 CCTATTCCATA
66 TC-ATACCATG
* * * * * *
667659 TGGTAAAGCCTAGTCCTTCAAAGGATATCATCAA-TTCAAACAAATGTG-CTCTC-T-TTTATTT
1 TGGTAGAGCCTACTCCTTTAAAGGATACCATCAAGCT-AAACAAAT-TGACTCTCATCTCT-TTT
*
667720 GCATCA-A--AT-
63 GCTTCATACCATG
* * * * * *
667729 T-GTAAAGCCTAATCC-TTAAAGTATACCATAAAGCTAAACAAATTGGCTCTCATTTCTTTT
1 TGGTAGAGCCTACTCCTTTAAAGGATACCATCAAGCTAAACAAATTGACTCTCATCTCTTTT
667789 TACCCTATAC
Statistics
Matches: 232, Mismatches: 42, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
67 2 0.01
68 26 0.11
69 18 0.08
70 3 0.01
71 2 0.01
74 3 0.01
75 9 0.04
76 148 0.64
77 3 0.01
79 18 0.08
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (75 bp):
TGGTAGAGCCTACTCCTTTAAAGGATACCATCAAGCTAAACAAATTGACTCTCATCTCTTTTGCT
TCATACCATG
Found at i:667682 original size:152 final size:145
Alignment explanation
Indices: 667427--667821 Score: 359
Period size: 152 Copynumber: 2.7 Consensus size: 145
667417 CCCACACCAC
* * * * * * *
667427 ATGGTAGAGCCTACTCCCTTAGGAGGGGAGACCATCAAGCCAAACAATTTGACTATCATCTCTTA
1 ATGGTAGAGCCTACTCCCTTA--A-AGGATACCATCAAGCTAAACAAATTGGCTCTCATCTCTTT
* * * * * *
667492 TGCT-ATCATGCCATGTGGTAGAGTCTACTCCTTTAAAGGATACCATCAAGCT-AAACAAAT-TG
63 TGCTCCT-ATACCATGTGGTAAAGCCTAGTCCTTCAAAGGATACCATCAA-CTCAAACAAATGTG
667554 TCTCTCATCTATTTTGCTCTCATATCAA
126 -CTCTCATCTA-TTTG----C--ATCAA
* *
667582 GTGGTAGAGCCTACTCCCTTAAAGGATACCATCAAGCTAAAAAAATTGGCTCTCATCTCTTTTGC
1 ATGGTAGAGCCTACTCCCTTAAAGGATACCATCAAGCTAAACAAATTGGCTCTCATCTCTTTTGC
* * * *
667647 TCCTATTCCATATGGTAAAGCCTAGTCCTTCAAAGGATATCATCAATTCAAACAAATGTGCTCTC
66 TCCTATACCATGTGGTAAAGCCTAGTCCTTCAAAGGATACCATCAACTCAAACAAATGTGCTCTC
* *
667712 TTTTATTTGCATCAA
131 ATCTATTTGCATCAA
* * * * * * *
667727 ATTGTAAAGCCTAAT-CCTTAAAGTATACCATAAAGCTAAACAAATTGGCTCTCATTTCTTTTTA
1 ATGGTAGAGCCTACTCCCTTAAAGGATACCATCAAGCTAAACAAATTGGCTCTCATCTC-TTTTG
*
667791 C-CCTATACCACGTGGTAAAGCCTAGTTCCTT
65 CTCCTATACCATGTGGTAAAGCCTAG-TCCTT
667822 AGGGATACCA
Statistics
Matches: 203, Mismatches: 32, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
144 60 0.30
145 26 0.13
147 1 0.00
151 5 0.02
152 87 0.43
153 4 0.02
155 20 0.10
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (145 bp):
ATGGTAGAGCCTACTCCCTTAAAGGATACCATCAAGCTAAACAAATTGGCTCTCATCTCTTTTGC
TCCTATACCATGTGGTAAAGCCTAGTCCTTCAAAGGATACCATCAACTCAAACAAATGTGCTCTC
ATCTATTTGCATCAA
Found at i:667831 original size:75 final size:75
Alignment explanation
Indices: 667751--667890 Score: 167
Period size: 75 Copynumber: 1.9 Consensus size: 75
667741 TCCTTAAAGT
* * *
667751 ATACCATAAAG-CTAAACAAATTGGCTCTCATTTCTTTTTAC-CCTATACCACGTGGTAAAGCCT
1 ATACCATAAAGTC-AAACAAATTGGCTCTCAGTTC-TTCTACTCCCATACCACGTGGTAAAGCCT
667814 AGTTCCTTAGGG
64 AGTTCCTTAGGG
* * * * * *
667826 ATACCATTAAGTCAATCAACTTGTCTTTCAGTTCTTCTACTCCCATACCACGTGGTAGAGCCTAG
1 ATACCATAAAGTCAAACAAATTGGCTCTCAGTTCTTCTACTCCCATACCACGTGGTAAAGCCTAG
667891 CCTCTCAGGG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
74 5 0.09
75 48 0.89
76 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (75 bp):
ATACCATAAAGTCAAACAAATTGGCTCTCAGTTCTTCTACTCCCATACCACGTGGTAAAGCCTAG
TTCCTTAGGG
Found at i:670527 original size:21 final size:21
Alignment explanation
Indices: 670482--670529 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
670472 TTTAAAATCT
*
670482 AAAAAATAAAATACTATTTAA
1 AAAAAATAAAATACTATATAA
670503 AAAAAATAAAAGTA-TA-ATAA
1 AAAAAATAAAA-TACTATATAA
*
670523 CAAAAAT
1 AAAAAAT
670530 CGAAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 13 0.54
22 2 0.08
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAAAATAAAATACTATATAA
Found at i:672085 original size:12 final size:12
Alignment explanation
Indices: 672068--672093 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
672058 AATATTTGTC
672068 TTAATTAAAAAA
1 TTAATTAAAAAA
672080 TTAATTAAAAAA
1 TTAATTAAAAAA
672092 TT
1 TT
672094 TTGAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAATTAAAAAA
Found at i:674031 original size:512 final size:513
Alignment explanation
Indices: 672829--674223 Score: 2558
Period size: 512 Copynumber: 2.7 Consensus size: 513
672819 TTCATATTTT
672829 ACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTT
1 ACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTT
*
672894 TATTACTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGT
66 TCTTACTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGT
* *
672959 GAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCCGACATTATGCTGTGAAGTATG
131 GAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATG
*
673024 TGATTGTGATATGTGTTAAATATAAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTACGAT
196 TGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTACGAT
*
673089 CTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAATACTCACCTTTGTGTTTTATG
261 CTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATG
*
673154 ATTTGGGCGAAAGGCCCTAGGACAGGTTAGGAGAAATAATATGCCTCGTCTATTAGTAACTTGAG
326 ATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATGCCTCGTCTATTAGTAACTTGAG
*
673219 TATATTTGTGAAGTTGTGAACTTAACAGAGTCGTCTACAGGCAAAAAAAAAAAAGGAAAAGCGAA
391 TATATTTGTGAAGTTGTGAACCTAACAGAGTCGTCTACAGGC--AAAAAAAAAAGGAAAAGCGAA
673284 GCTTTTTTAAAGCTTTCAATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCGA
454 GCTTTTTTAAAGCTTTCAATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCGA
673344 ACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTT
1 ACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTT
*
673409 TCTTACTTTAACTTTCATATTTTGTGATAAATTCTTATGTTATGTTATAAGGAGTTCACACATGT
66 TCTTACTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGT
* *
673474 GAACCATAGTTTGCATATGTAGTTTAGACGAGTATAGGATCGCAGACATTATACTGCGAAGTATG
131 GAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATG
673539 TGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTACGAT
196 TGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTACGAT
*
673604 CTTTGAAACAATTGGAAATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATG
261 CTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATG
* *
673669 ATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATGCTTCGTTTATTAGTAACTTGAG
326 ATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATGCCTCGTCTATTAGTAACTTGAG
* *
673734 TATATTTGTGAAGTTGTGAACCTAATAGAGTCGTCTACAGGC-AAAAAAAAGGGAAAAGCGAAGC
391 TATATTTGTGAAGTTGTGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAAGGAAAAGCGAAGC
* *
673798 TTTTTTAAAGCTTTCAATACACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGTGA
456 TTTTTTAAAGCTTTCAATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCGA
* * *
673856 ACCATTGTGTTAAACGAGATCTTAGGTTGGTGTAAAACACCTAATCTAAGTCCTGGGTGTAAGTT
1 ACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTT
* *
673921 TCTTGCTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCAGACATGT
66 TCTTACTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGT
673986 GAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATG
131 GAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATG
*
674051 TGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCTATTTCGGTACTACGAT
196 TGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTACGAT
674116 CTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATG
261 CTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATG
674181 ATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATG
326 ATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATG
674224 TCCCGAGTTT
Statistics
Matches: 853, Mismatches: 27, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
512 435 0.51
515 418 0.49
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (513 bp):
ACCATTGTGTTAAACGAGAGCTTAGGTTGGTCTAAAACACCTAATCTAAGTCCCGGGTGTAAGTT
TCTTACTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCACACATGT
GAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGAAGTATG
TGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCTATTTTGGTACTACGAT
CTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGTTTTATG
ATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATGCCTCGTCTATTAGTAACTTGAG
TATATTTGTGAAGTTGTGAACCTAACAGAGTCGTCTACAGGCAAAAAAAAAAGGAAAAGCGAAGC
TTTTTTAAAGCTTTCAATAAACTAGTGAGTGTTTTGGGGTTGCTGCTAGTATGAGCGA
Found at i:674492 original size:318 final size:318
Alignment explanation
Indices: 673915--674541 Score: 1211
Period size: 318 Copynumber: 2.0 Consensus size: 318
673905 GTCCTGGGTG
* *
673915 TAAGTTTCTTGCTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCAG
1 TAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCAC
673980 ACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGA
66 ACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGA
*
674045 AGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCTATTTCGGTAC
131 AGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCCATTTCGGTAC
674110 TACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGT
196 TACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGT
674175 TTTATGATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATGTCCCGAGTT
261 TTTATGATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATGTCCCGAGTT
674233 TAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATGT-TTGTGTTATGTTATAAGGAGTTCA
1 TAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAAT-TCTTGTGTTATGTTATAAGGAGTTCA
674297 CACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCG
65 CACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCG
674362 AAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCCATTTCGGTA
130 AAGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCCATTTCGGTA
674427 CTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTG
195 CTACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTG
674492 TTTTATGATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATG
260 TTTTATGATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATG
674542 CTTCGTCTAT
Statistics
Matches: 305, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
318 304 1.00
319 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.37
Consensus pattern (318 bp):
TAAGTTTCTTACTTTAACTTTCATATTTTGTGATAAATTCTTGTGTTATGTTATAAGGAGTTCAC
ACATGTGAACCATAGTTTGCATATGTAGTTTAGCCGAGTATAGGATCGCAGACATTATGCTGCGA
AGTATGTGATTGTGATATGTGTTAAATATGAAAATTAATATCTGTAATTGTGGCCATTTCGGTAC
TACGATCTTTGAAACAATTGGATATTGTTGGCATGCCATAGGATTGTGAGTACTCACCTTTGTGT
TTTATGATTTGGGCGAAAGTCCCTAGGACAGGTTAGGAGAAATAATATGTCCCGAGTT
Found at i:674876 original size:7 final size:7
Alignment explanation
Indices: 674866--674927 Score: 65
Period size: 7 Copynumber: 8.9 Consensus size: 7
674856 CCCAAATCCT
674866 TAAACCC
1 TAAACCC
674873 TAAACCC
1 TAAACCC
674880 -AAACCC
1 TAAACCC
*
674886 CAAACCC
1 TAAACCC
*
674893 TTAAACCT
1 -TAAACCC
*
674901 TAAACCT
1 TAAACCC
674908 TAAA-CC
1 TAAACCC
674914 TCAAACCC
1 T-AAACCC
674922 TAAACC
1 TAAACC
674928 TTGAGGTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
6 8 0.17
7 32 0.67
8 8 0.17
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:674896 original size:28 final size:29
Alignment explanation
Indices: 674856--674927 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
674846 AGTATAGGAT
*
674856 CCCAAATCCTTAAACCCTAAACC-CAAAC
1 CCCAAACCCTTAAACCCTAAACCTCAAAC
* *
674884 CCCAAACCCTTAAACCTTAAACCTTAAAC
1 CCCAAACCCTTAAACCCTAAACCTCAAAC
*
674913 CTCAAACCC-TAAACC
1 CCCAAACCCTTAAACC
674928 TTGAGGTTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 27 0.69
29 12 0.31
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (29 bp):
CCCAAACCCTTAAACCCTAAACCTCAAAC
Done.