Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 91
Found at i:926385 original size:19 final size:19
Alignment explanation
Indices: 926363--926400 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
926353 TGTGTCATTC
*
926363 TCCAGTAAGACGATCATCT
1 TCCAATAAGACGATCATCT
926382 TCCAATAAGACGATCATCT
1 TCCAATAAGACGATCATCT
926401 GCTTCGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCAATAAGACGATCATCT
Found at i:933256 original size:16 final size:15
Alignment explanation
Indices: 933199--933259 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 15
933189 TGAATTTTTG
*
933199 AAATATTAAAAAT-A
1 AAATAATAAAAATAA
933213 AAATAAATAAAATATAA
1 AAAT-AATAAAA-ATAA
933230 AATATTAATAAAAATAA
1 AA-A-TAATAAAAATAA
933247 AAAGTAATAAAAA
1 AAA-TAATAAAAA
933260 GTAATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 4 0.10
15 6 0.15
16 12 0.30
17 9 0.22
18 8 0.20
19 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
AAATAATAAAAATAA
Found at i:933268 original size:9 final size:10
Alignment explanation
Indices: 933242--933268 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
933232 TATTAATAAA
933242 AATAAAAAGT
1 AATAAAAAGT
933252 AATAAAAAGT
1 AATAAAAAGT
933262 AATAAAA
1 AATAAAA
933269 TATATTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (10 bp):
AATAAAAAGT
Found at i:933483 original size:13 final size:13
Alignment explanation
Indices: 933467--933504 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
933457 AAATGATGTA
933467 AAAAAGTATTTTT
1 AAAAAGTATTTTT
*
933480 -AAAAGTGTTTTT
1 AAAAAGTATTTTT
933492 AAAAAGTATTTTT
1 AAAAAGTATTTTT
933505 GAGAGGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (13 bp):
AAAAAGTATTTTT
Found at i:933495 original size:25 final size:23
Alignment explanation
Indices: 933467--933522 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
933457 AAATGATGTA
933467 AAAAAGTATTTTTAAAAGTGTTTTT
1 AAAAAGTATTTTTAAAAG-G-TTTT
* *
933492 AAAAAGTATTTTTGAGAGGTTTT
1 AAAAAGTATTTTTAAAAGGTTTT
933515 AAAAAGTA
1 AAAAAGTA
933523 AAAAGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 12 0.41
24 1 0.03
25 16 0.55
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (23 bp):
AAAAAGTATTTTTAAAAGGTTTT
Found at i:936309 original size:2 final size:2
Alignment explanation
Indices: 936302--936326 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
936292 ATTAATTTAT
936302 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
936327 TATTTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:936352 original size:2 final size:2
Alignment explanation
Indices: 936345--936387 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
936335 TAACTTCCGT
936345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
936386 TA
1 TA
936388 ATAGAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:937331 original size:15 final size:15
Alignment explanation
Indices: 937307--937340 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
937297 ATAAACGTAT
937307 TTTTAAAAAAAT-AA
1 TTTTAAAAAAATCAA
937321 TTTTAAGAAAAATCAA
1 TTTTAA-AAAAATCAA
937337 TTTT
1 TTTT
937341 TTAAGACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTTAAAAAAATCAA
Found at i:939226 original size:3 final size:3
Alignment explanation
Indices: 939218--939266 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
939208 CCTGCACACT
* *
939218 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA T-T TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
939265 TA
1 TA
939267 TTCTTTAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:939709 original size:136 final size:135
Alignment explanation
Indices: 939507--939986 Score: 657
Period size: 136 Copynumber: 3.6 Consensus size: 135
939497 ACTTGAAAGG
* *
939507 AACAAGTTCTTCTCATTATGAAC-T-TTC-TCC-TTT-AGGACGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTCA-GATGAGTTCTTCTCATTATGAACTC
* * *
939567 TTAATTGGAAATGTCAATCCCCCAAGTGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGAT
65 TCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGAT
939632 AGGTCA
130 AGGTCA
*
939638 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTGTCAGATGAGTTCTTCTTATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTT-TCAGATGAGTTCTTCTCATTATGAACTC
* * * *
939703 TCAATTGAAAATTTCAATCCCTCAAGTGAGGTGTCACTGATTTGAAATGCTGTGAATCGAGTGAT
65 TCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGAT
*
939768 AGGTCG
130 AGGTCA
* * *
939774 AACAAGCTTTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCT-TTTCAGATGAGTTCTTCTCATTATGAACTC
* ** **
939839 TTC-ACTGGAAATGTTGATCCCTCAAGTGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGA
65 -TCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGA
939903 TAGGTCA
129 TAGGTCA
* * * *
939910 AAAAAGCTCTTCTCATTATGAACTTCTTCTGCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCT-TTTCAGATGAGTTCTTCTCATTATGAACTC
*
939975 TCTATTGGAAAT
65 TCAATTGGAAAT
939987 ATTGGTTCAC
Statistics
Matches: 310, Mismatches: 30, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
131 22 0.07
132 1 0.00
133 3 0.01
134 3 0.01
135 4 0.01
136 272 0.88
137 5 0.02
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (135 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTCT
CAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATA
GGTCA
Found at i:940871 original size:7 final size:7
Alignment explanation
Indices: 940850--940907 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
940840 TCTCAAACCC
940850 TCATTTT
1 TCATTTT
940857 TC-TCTTT
1 TCAT-TTT
940864 TCATTTT
1 TCATTTT
*
940871 TTATTTCT
1 TCATTT-T
940879 T--TTTT
1 TCATTTT
940884 TCATTTTT
1 TCA-TTTT
940892 TCATTTTT
1 TCA-TTTT
940900 TCATTTT
1 TCATTTT
940907 T
1 T
940908 TTTCTTCAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
5 2 0.05
6 4 0.09
7 20 0.45
8 18 0.41
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (7 bp):
TCATTTT
Found at i:940872 original size:8 final size:8
Alignment explanation
Indices: 940861--940908 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
940851 CATTTTTCTC
940861 TTTTCATT
1 TTTTCATT
940869 TTTT-ATT
1 TTTTCATT
*
940876 TCTT---T
1 TTTTCATT
940881 TTTTCATT
1 TTTTCATT
940889 TTTTCATT
1 TTTTCATT
940897 TTTTCATT
1 TTTTCATT
940905 TTTT
1 TTTT
940909 TTCTTCAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
7 6 0.17
8 25 0.71
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCATT
Found at i:940882 original size:12 final size:13
Alignment explanation
Indices: 940850--940905 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 13
940840 TCTCAAACCC
*
940850 TCATTTTTCTCTTT
1 TCATTTTT-TCATT
940864 TCATTTTTT-ATT
1 TCATTTTTTCATT
*
940876 TCTTTTTTTCATTTTT
1 TCATTTTTTCA---TT
940892 TCATTTTTTCATT
1 TCATTTTTTCATT
940905 T
1 T
940906 TTTTTCTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
12 10 0.29
13 5 0.14
14 8 0.23
16 12 0.34
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (13 bp):
TCATTTTTTCATT
Found at i:952002 original size:15 final size:15
Alignment explanation
Indices: 951978--952011 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
951968 TAAAAACGTC
951978 TTTTAAAAAAAT-AA
1 TTTTAAAAAAATCAA
951992 TTTTAAGAAAAATCAA
1 TTTTAA-AAAAATCAA
952008 TTTT
1 TTTT
952012 TTAAGATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTTAAAAAAATCAA
Found at i:953874 original size:3 final size:3
Alignment explanation
Indices: 953866--953908 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
953856 ATTGGGCGCT
* *
953866 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
953909 TTCTTTAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:960967 original size:30 final size:30
Alignment explanation
Indices: 960859--960970 Score: 102
Period size: 30 Copynumber: 3.7 Consensus size: 30
960849 AACAAGGTTA
* * *
960859 TGTTCGTGTTAATTTAGTTAATTTTAAAGG
1 TGTTCGTGTTCATTTATTTATTTTTAAAGG
* * * *
960889 TGTTCGTGTTCGTTTA--AATTTTCAATATCG
1 TGTTCGTGTTCATTTATTTATTTTTAA-A-GG
* *
960919 TGTTCATGTTCATTTATTTATTTTTGAAGG
1 TGTTCGTGTTCATTTATTTATTTTTAAAGG
*
960949 TGTTCGTGTTCGTTTATTTATT
1 TGTTCGTGTTCATTTATTTATT
960971 GTTCACGTAC
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
28 6 0.09
29 1 0.02
30 50 0.78
31 1 0.02
32 6 0.09
ACGTcount: A:0.20, C:0.08, G:0.18, T:0.54
Consensus pattern (30 bp):
TGTTCGTGTTCATTTATTTATTTTTAAAGG
Found at i:961010 original size:12 final size:12
Alignment explanation
Indices: 960993--961037 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
960983 GTTCATTTAA
*
960993 TGTTCACGAATG
1 TGTTCATGAATG
** *
961005 TGTTCATTTATA
1 TGTTCATGAATG
961017 TGTTCATGAATG
1 TGTTCATGAATG
961029 TGTTCATGA
1 TGTTCATGA
961038 GCATGTTAGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (12 bp):
TGTTCATGAATG
Found at i:961027 original size:24 final size:23
Alignment explanation
Indices: 960964--961035 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
960954 GTGTTCGTTT
* * **
960964 ATTTATTGTTCACGTACATGTTC
1 ATTTAATGTTCACGAATGTGTTC
960987 ATTTAATGTTCACGAATGTGTTC
1 ATTTAATGTTCACGAATGTGTTC
*
961010 ATTTATATGTTCATGAATGTGTTC
1 ATTTA-ATGTTCACGAATGTGTTC
961034 AT
1 AT
961036 GAGCATGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 24 0.56
24 19 0.44
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (23 bp):
ATTTAATGTTCACGAATGTGTTC
Found at i:961043 original size:24 final size:24
Alignment explanation
Indices: 960982--961044 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
960972 TTCACGTACA
*
960982 TGTTCATTTA-ATGTTCACGAATG
1 TGTTCATTGACATGTTCACGAATG
* * *
961005 TGTTCATTTATATGTTCATGAATG
1 TGTTCATTGACATGTTCACGAATG
961029 TGTTCA-TGAGCATGTT
1 TGTTCATTGA-CATGTT
961045 AGTTTAGCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.34
24 23 0.66
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (24 bp):
TGTTCATTGACATGTTCACGAATG
Found at i:961073 original size:70 final size:70
Alignment explanation
Indices: 960988--961120 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 70
960978 TACATGTTCA
* * * *
960988 TTTAATGTTCACGAATGTGTTCATTTATATGTTCATGAATGTGTTCATGAGCATGTTAGTTTAGC
1 TTTAATGTTCACGAATGTGTTCATTTATATGTTCACGAAAGTGTTAATGAACATGTTAGTTTAGC
961053 TTTTG
66 TTTTG
* * *
961058 TTTAATGTTCGCGAATGTGTTCATTTATATGTTTACGAAAGTGTTAATGAACATGTTCGTTTA
1 TTTAATGTTCACGAATGTGTTCATTTATATGTTCACGAAAGTGTTAATGAACATGTTAGTTTA
961121 ACATTCATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (70 bp):
TTTAATGTTCACGAATGTGTTCATTTATATGTTCACGAAAGTGTTAATGAACATGTTAGTTTAGC
TTTTG
Found at i:961137 original size:70 final size:70
Alignment explanation
Indices: 960984--961137 Score: 200
Period size: 70 Copynumber: 2.2 Consensus size: 70
960974 CACGTACATG
* * * *
960984 TTCATTTAATGTTCACGAATGTGTTCATTTATATGTTCATGAATGTGTTCATGAGCATGTTAGTT
1 TTCATTTAATGTTCACGAATGTGTTCATTTATATGTTCACGAAAGTGTTAATGAACATGTTAGTT
* *
961049 TAGCT
66 TAACA
** * * *
961054 TTTGTTTAATGTTCGCGAATGTGTTCATTTATATGTTTACGAAAGTGTTAATGAACATGTTCGTT
1 TTCATTTAATGTTCACGAATGTGTTCATTTATATGTTCACGAAAGTGTTAATGAACATGTTAGTT
961119 TAACA
66 TAACA
*
961124 TTCATTTAGTGTTC
1 TTCATTTAATGTTC
961138 CTTTAGCGTT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (70 bp):
TTCATTTAATGTTCACGAATGTGTTCATTTATATGTTCACGAAAGTGTTAATGAACATGTTAGTT
TAACA
Found at i:971010 original size:36 final size:36
Alignment explanation
Indices: 970970--971041 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
970960 TCTTGAGGAA
970970 TCCACAACCAAATTACCGATATTGGAAATATCAAGG
1 TCCACAACCAAATTACCGATATTGGAAATATCAAGG
*
971006 TCCACAACCGAATTACCGATATTGGAAATATCAAGG
1 TCCACAACCAAATTACCGATATTGGAAATATCAAGG
971042 GAAACTCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.22
Consensus pattern (36 bp):
TCCACAACCAAATTACCGATATTGGAAATATCAAGG
Found at i:976326 original size:17 final size:17
Alignment explanation
Indices: 976304--976336 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
976294 AAATTACAAG
*
976304 GCAACAATAGGCAGCAA
1 GCAACAACAGGCAGCAA
976321 GCAACAACAGGCAGCA
1 GCAACAACAGGCAGCA
976337 TGCAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.27, G:0.24, T:0.03
Consensus pattern (17 bp):
GCAACAACAGGCAGCAA
Found at i:979043 original size:97 final size:98
Alignment explanation
Indices: 978868--979058 Score: 258
Period size: 97 Copynumber: 2.0 Consensus size: 98
978858 ATTATGCTAC
* *
978868 AAAGGAAACAAAGAAACACTAGCTACAAACAAAGGCATCTAACAACCTTATACAACCAATCCCAA
1 AAAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAACAACCCTATACAACCAATCCCAA
*
978933 TAAACAACCAACAACTACACAAATAAGGACTAT
66 TAAACAACCAACAACTACACAAACAAGGACTAT
* *** * *
978966 AAAGGAAACAAATAAACACTAGCTGTTAAC-AAGGCAACTAACGACCCTATACAACCATTCCCAA
1 AAAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAACAACCCTATACAACCAATCCCAA
* * * *
979030 TGAACATCTAACAACTATACAAACAAGGA
66 TAAACAACCAACAACTACACAAACAAGGA
979059 ATTATAACAA
Statistics
Matches: 80, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
97 54 0.68
98 26 0.32
ACGTcount: A:0.51, C:0.25, G:0.09, T:0.15
Consensus pattern (98 bp):
AAAGGAAACAAAGAAACACTAGCTACAAACAAAGGCAACTAACAACCCTATACAACCAATCCCAA
TAAACAACCAACAACTACACAAACAAGGACTAT
Found at i:979234 original size:15 final size:15
Alignment explanation
Indices: 979214--979244 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
979204 ATAATATTAA
979214 AATAAAAAATTAAAT
1 AATAAAAAATTAAAT
979229 AATAAAAAATTAAAT
1 AATAAAAAATTAAAT
979244 A
1 A
979245 TACCTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAAAATTAAAT
Found at i:979464 original size:30 final size:30
Alignment explanation
Indices: 979430--979493 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
979420 GTTCGGGTTC
*
979430 GGTTTGGATTTG-GCTTCAAGTTTGGGTTAG
1 GGTTTGGATTCGAG-TTCAAGTTTGGGTTAG
* * *
979460 GGTTTGGGTTCGAGTTCAGGTTTGGGTTTG
1 GGTTTGGATTCGAGTTCAAGTTTGGGTTAG
979490 GGTT
1 GGTT
979494 ATAGAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.09, C:0.06, G:0.41, T:0.44
Consensus pattern (30 bp):
GGTTTGGATTCGAGTTCAAGTTTGGGTTAG
Found at i:979491 original size:24 final size:23
Alignment explanation
Indices: 979413--979493 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 23
979403 TTTTTTCTTA
* *
979413 GGTTCGGGTTCGGGTTCGGTTTG
1 GGTTTGGGTTCGAGTTCGGTTTG
* * * * *
979436 GATTTGGCTTCAAGTTTGGGTTAG
1 GGTTTGGGTTCGAG-TTCGGTTTG
979460 GGTTTGGGTTCGAGTTCAGGTTTG
1 GGTTTGGGTTCGAGTTC-GGTTTG
979484 GGTTTGGGTT
1 GGTTTGGGTT
979494 ATAGAAGATG
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
23 11 0.25
24 33 0.75
ACGTcount: A:0.07, C:0.09, G:0.42, T:0.42
Consensus pattern (23 bp):
GGTTTGGGTTCGAGTTCGGTTTG
Found at i:980342 original size:36 final size:31
Alignment explanation
Indices: 980314--980620 Score: 123
Period size: 31 Copynumber: 9.7 Consensus size: 31
980304 TATAATTTTT
980314 AATTAATATTAATATAAAATATAGTTTATAA
1 AATTAATATTAATATAAAATATAGTTTATAA
* * *
980345 AATTAATATTAATAGAAACTATATTTTAT-A
1 AATTAATATTAATATAAAATATAGTTTATAA
* * * *
980375 AATTATATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAAATATAGTTTATAA
** * *
980411 AATTAATATTAATATAGTATATGGTTTATAG
1 AATTAATATTAATATAAAATATAGTTTATAA
*
980442 AA-T-ATAATTAATAT--TA-ATA--TTAT-A
1 AATTAAT-ATTAATATAAAATATAGTTTATAA
* * * *
980466 TACT-ATATTAATATAAACTATAGTTAAT-A
1 AATTAATATTAATATAAAATATAGTTTATAA
** * *
980495 TGTTAATATTAATGTAAACTATAGTTTATAA
1 AATTAATATTAATATAAAATATAGTTTATAA
* * *
980526 ACTATCTACTACATTAATACAAATTATAGTTTATAA
1 A--AT-TA--ATATTAATATAAAATATAGTTTATAA
* * * *
980562 ACTATATACTATATTAATATAAATTATAGTTAAGAT
1 A--AT-TA--ATATTAATATAAAATATAGTTTATAA
* * *
980598 AATTAACATGAATATAAATTATA
1 AATTAATATTAATATAAAATATA
980621 TAGTACATTA
Statistics
Matches: 217, Mismatches: 39, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
24 9 0.04
25 7 0.03
27 5 0.02
28 2 0.01
29 8 0.04
30 37 0.17
31 61 0.28
32 1 0.00
33 7 0.03
34 5 0.02
35 17 0.08
36 58 0.27
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATAGTTTATAA
Found at i:980473 original size:18 final size:16
Alignment explanation
Indices: 980452--980495 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
980442 AATATAATTA
980452 ATATTAATATTATATACT
1 ATATTAATATTA-A-ACT
980470 ATATTAATA-TAAACT
1 ATATTAATATTAAACT
980485 ATAGTTAATAT
1 ATA-TTAATAT
980496 GTTAATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 2 0.08
18 9 0.38
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATTAATATTAAACT
Found at i:980480 original size:15 final size:16
Alignment explanation
Indices: 980462--980495 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
980452 ATATTAATAT
*
980462 TATATACTATA-TTAA
1 TATAAACTATAGTTAA
980477 TATAAACTATAGTTAA
1 TATAAACTATAGTTAA
980493 TAT
1 TAT
980496 GTTAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
TATAAACTATAGTTAA
Found at i:980542 original size:84 final size:84
Alignment explanation
Indices: 980376--980567 Score: 193
Period size: 84 Copynumber: 2.3 Consensus size: 84
980366 TATTTTATAA
* * *
980376 ATTATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGTATATGGTTTATA
1 ATTATATACTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGAATATAGTTTATA
* *
980441 GAATATAATTAATATTAAT
66 GAATATAACTAACATTAAT
* *
980460 ATTATATACTATA-TTAATATAAACTATAGTTAATAT-GTTAATATTAATGTA-AACTATAGTTT
1 ATTATATACTATAGTT--TATAAACTATAGTTAATATAATTAATATTAATATAGAA-TATAGTTT
*
980522 ATA-AACTATCTACT-ACATTAAT
63 ATAGAA-TAT-AACTAACATTAAT
* *
980544 A-CA-A-ATTATAGTTTATAAACTATA
1 ATTATATACTATAGTTTATAAACTATA
980568 TACTATATTA
Statistics
Matches: 92, Mismatches: 10, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
80 11 0.12
81 5 0.05
82 3 0.03
83 6 0.07
84 46 0.50
85 21 0.23
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (84 bp):
ATTATATACTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGAATATAGTTTATA
GAATATAACTAACATTAAT
Found at i:980589 original size:15 final size:15
Alignment explanation
Indices: 980571--980621 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
980561 AACTATATAC
980571 TATATTAATATAAAT
1 TATATTAATATAAAT
*
980586 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
980601 TAACATGAATATAAAT
1 T-ATATTAATATAAAT
980617 TATAT
1 TATAT
980622 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:980796 original size:13 final size:13
Alignment explanation
Indices: 980774--980853 Score: 51
Period size: 13 Copynumber: 6.2 Consensus size: 13
980764 ATACATACAC
*
980774 TATAGGTTACATA
1 TATAGTTTACATA
980787 TATAGTTTACATA
1 TATAGTTTACATA
*
980800 TAAATAGATTGTATATA
1 T--ATAG-TT-TACATA
*
980817 TACA-TTTAC---
1 TATAGTTTACATA
*
980826 TATAGGTTACATA
1 TATAGTTTACATA
*
980839 TATAGCTTACATA
1 TATAGTTTACATA
980852 TA
1 TA
980854 AATTTATTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
12 2 0.04
13 29 0.56
15 6 0.12
16 2 0.04
17 6 0.12
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (13 bp):
TATAGTTTACATA
Found at i:980834 original size:52 final size:52
Alignment explanation
Indices: 980764--980954 Score: 238
Period size: 52 Copynumber: 3.6 Consensus size: 52
980754 TGTATACATA
* *
980764 ATACATACACTATAGGTTACATATATAGTTTACATATAAATAGATTGTATAT
1 ATACATATACTATAGGTTACATATATAGTTTACATATAAATACATTGTATAT
* * **
980816 ATACATTTACTATAGGTTACATATATAGCTTACATATAAATTTATTGTATAT
1 ATACATATACTATAGGTTACATATATAGTTTACATATAAATACATTGTATAT
* * * * *
980868 ATACATATACTATAGGTTATATATATAGTTTATATATACTATACATAGTTTATAC
1 ATACATATACTATAGGTTACATATATAGTTTACATATA-AATACAT--TGTATAT
* *
980923 ATACATGTACTATAAGTTACATATATAGTTTA
1 ATACATATACTATAGGTTACATATATAGTTTA
980955 TGTTGGATAT
Statistics
Matches: 119, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
52 81 0.68
53 4 0.03
55 34 0.29
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.42
Consensus pattern (52 bp):
ATACATATACTATAGGTTACATATATAGTTTACATATAAATACATTGTATAT
Found at i:980901 original size:11 final size:13
Alignment explanation
Indices: 980872--980905 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
980862 GTATATATAC
980872 ATATACTATAGGTT
1 ATATA-TATAGGTT
*
980886 ATATATATAGTTT
1 ATATATATAGGTT
980899 ATATATA
1 ATATATA
980906 CTATACATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (13 bp):
ATATATATAGGTT
Found at i:980910 original size:20 final size:20
Alignment explanation
Indices: 980887--980926 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
980877 CTATAGGTTA
* *
980887 TATATATAGTTTATATATAC
1 TATACATAGTTTATACATAC
980907 TATACATAGTTTATACATAC
1 TATACATAGTTTATACATAC
980927 ATGTACTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
TATACATAGTTTATACATAC
Found at i:981462 original size:22 final size:22
Alignment explanation
Indices: 981432--981473 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
981422 TTAGCTGTTA
* *
981432 TAACTCCTGAAATTATATCATG
1 TAACCCCTGAAATTAAATCATG
*
981454 TAACCCCTGGAATTAAATCA
1 TAACCCCTGAAATTAAATCA
981474 AATAACTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (22 bp):
TAACCCCTGAAATTAAATCATG
Found at i:981479 original size:22 final size:22
Alignment explanation
Indices: 981431--981479 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
981421 TTTAGCTGTT
* * *
981431 ATAACTCCTGAAATTATATCAT
1 ATAACCCCTGAAATTAAATCAA
* *
981453 GTAACCCCTGGAATTAAATCAA
1 ATAACCCCTGAAATTAAATCAA
981475 ATAAC
1 ATAAC
981480 TCATGTAACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (22 bp):
ATAACCCCTGAAATTAAATCAA
Found at i:982033 original size:16 final size:16
Alignment explanation
Indices: 982012--982042 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
982002 TACATATATA
982012 ATTTATATAAACTATT
1 ATTTATATAAACTATT
982028 ATTTATATAAACTAT
1 ATTTATATAAACTAT
982043 ATATCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTATATAAACTATT
Found at i:982133 original size:13 final size:13
Alignment explanation
Indices: 982101--982869 Score: 145
Period size: 13 Copynumber: 56.6 Consensus size: 13
982091 ATCAACTATT
*
982101 GTTTATAGACTATA
1 GTTTATATA-TATA
*
982115 GGTTATATATATA
1 GTTTATATATATA
*
982128 GTTTATATAAATTA
1 GTTTATATATA-TA
* *
982142 -TATATAAACTATA
1 GTTTATATA-TATA
*
982155 ATTTACATATATATA
1 GTTT--ATATATATA
982170 GTTTATA-ATA-A
1 GTTTATATATATA
* * *
982181 CTATATAGTTTATA
1 GTTTATA-TATATA
**
982195 -TAAACTATATATA
1 GTTTA-TATATATA
*
982208 GTTTATACATATGTA
1 GTTTAT--ATATATA
*
982223 GCTTATATATATA
1 GTTTATATATATA
982236 --TTATATATATA
1 GTTTATATATATA
982247 --TTATATATATA
1 GTTTATATATATA
982258 GTTTATATCTATATA
1 GTTTATA--TATATA
* *
982273 GTTGATTTATATA
1 GTTTATATATATA
* **
982286 ATTTATATACCTA
1 GTTTATATATATA
*
982299 GTTTATACATATGTA
1 GTTTAT--ATATATA
982314 GTTTATATAAACTATATA
1 G-TT-TAT--A-TATATA
*
982332 GTTCATACATATATA
1 GTT--TATATATATA
*
982347 GTTTATATTTACATGTATT
1 GTTTATA--T--A--TATA
982366 GTTTATATATATA
1 GTTTATATATATA
*
982379 GTTTAT-TAGTTTA
1 GTTTATATA-TATA
* *
982392 --TAATAACTACATA
1 GTTTAT-A-TATATA
* *
982405 GATTACATATATA
1 GTTTATATATATA
982418 GTTTATACATATATA
1 GTTTAT--ATATATA
*
982433 GTTTATGTATATA
1 GTTTATATATATA
982446 GTTTATAATAACCATATA
1 GTTTAT-AT----ATATA
982464 GTTTATATATATA
1 GTTTATATATATA
982477 GTTTATA-ATA-A
1 GTTTATATATATA
* * *
982488 CTATATA-ATTTA
1 GTTTATATATATA
982500 -TATTATATATATA
1 GT-TTATATATATA
* *
982513 ATTTATGTATAGT-
1 GTTTATATATA-TA
982526 GTTTCTATAAACTATATA
1 G-TT-TAT--A-TATATA
*
982544 CTTTATTACTTTATATA
1 GTTTA-TA---TATATA
982561 GTTTATATATATA
1 GTTTATATATATA
*
982574 ---TA-ATCTATA
1 GTTTATATATATA
* *
982583 GATTACATATATTA
1 GTTTATATATA-TA
* *
982597 G-TTATACATACA
1 GTTTATATATATA
*
982609 -TATATATATTATA
1 GTTTATATA-TATA
*
982622 -TTAATATAAATTATA
1 GTT--TATATA-TATA
*
982637 ATTTATA-A-ACTA
1 GTTTATATATA-TA
* *
982649 -TATACTTTATATA
1 GTTTA-TATATATA
*
982662 GTTTATACATATA
1 GTTTATATATATA
*
982675 GTTTATATACATA
1 GTTTATATATATA
* *
982688 CATATATATAATATA
1 -GTTTATAT-ATATA
*
982703 -TTAATATAAATTATA
1 GTT--TATATA-TATA
982718 GTTTATAAACTATATA
1 GTTTAT--A-TATATA
*
982734 -CTT-T-T-TATA
1 GTTTATATATATA
982743 GTTTATACATATATA
1 GTTTAT--ATATATA
982758 GTTTATATATATA
1 GTTTATATATATA
* *
982771 GTTCATATAAACATA
1 GTT--TATATATATA
982786 GTTTATATATATA
1 GTTTATATATATA
*
982799 GCTTATA-ATA-A
1 GTTTATATATATA
*
982810 --TTATATAGTTTA
1 GTTTATATA-TATA
* *
982822 -TAATATAAATATA
1 GT-TTATATATATA
982835 GTTTTTATATATATA
1 G--TTTATATATATA
982850 GTTTATATATA-A
1 GTTTATATATATA
*
982862 ATTTATAT
1 GTTTATAT
982870 TATGAGTGTT
Statistics
Matches: 565, Mismatches: 95, Indels: 192
0.66 0.11 0.23
Matches are distributed among these distances:
9 15 0.03
10 6 0.01
11 47 0.08
12 36 0.06
13 207 0.37
14 53 0.09
15 120 0.21
16 21 0.04
17 26 0.05
18 24 0.04
19 10 0.02
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (13 bp):
GTTTATATATATA
Found at i:982143 original size:20 final size:19
Alignment explanation
Indices: 982119--982214 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 19
982109 ACTATAGGTT
982119 ATATATATAGTTTATATAA
1 ATATATATAGTTTATATAA
* * * *
982138 ATTATATATAAACTATAATTTAC
1 A-TATATAT--AGT-TTATATAA
982161 ATATATATAGTTTATA-ATA
1 ATATATATAGTTTATATA-A
*
982180 A-CTATATAGTTTATATAA
1 ATATATATAGTTTATATAA
982198 ACTATATATAGTTTATA
1 A-TATATATAGTTTATA
982215 CATATGTAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
18 16 0.27
19 6 0.10
20 22 0.37
22 9 0.15
23 6 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATATATAGTTTATATAA
Found at i:982187 original size:18 final size:18
Alignment explanation
Indices: 982164--982205 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
982154 AATTTACATA
982164 TATATAGTTTATA-ATAAC
1 TATATAGTTTATATA-AAC
982182 TATATAGTTTATATAAAC
1 TATATAGTTTATATAAAC
982200 TATATA
1 TATATA
982206 TAGTTTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATAGTTTATATAAAC
Found at i:982196 original size:11 final size:11
Alignment explanation
Indices: 982182--982265 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
982172 TTATAATAAC
982182 TATATAGTTTA
1 TATATAGTTTA
**
982193 TATA-A-ACTA
1 TATATAGTTTA
982202 TATATAGTTTA
1 TATATAGTTTA
982213 TACATATGTAGCTTATA
1 T--ATA--TAG-TT-TA
982230 TATATA-TTATA
1 TATATAGTT-TA
982241 TATATA-TTATA
1 TATATAGTT-TA
982252 TATATAGTTTA
1 TATATAGTTTA
982263 TAT
1 TAT
982266 CTATATAGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
9 6 0.10
10 2 0.03
11 34 0.57
12 2 0.03
13 5 0.08
15 6 0.10
16 2 0.03
17 3 0.05
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:982197 original size:42 final size:40
Alignment explanation
Indices: 982119--982214 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 40
982109 ACTATAGGTT
*
982119 ATATATATAGTTTAT-ATAAATTATATATAAACTATAATTTAC
1 ATATATATAGTTTATAATAAACTATATATAAACTATAA---AC
**
982161 ATATATATAGTTTATAAT-AACTATATAGTTTA-TATAAAC
1 ATATATATAGTTTATAATAAACTATATA-TAAACTATAAAC
982200 -TATATATAGTTTATA
1 ATATATATAGTTTATA
982215 CATATGTAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
38 15 0.31
39 2 0.04
42 28 0.57
43 4 0.08
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (40 bp):
ATATATATAGTTTATAATAAACTATATATAAACTATAAAC
Found at i:982214 original size:18 final size:17
Alignment explanation
Indices: 982161--982264 Score: 63
Period size: 18 Copynumber: 5.9 Consensus size: 17
982151 TATAATTTAC
982161 ATATATATAGTTTAT-A
1 ATATATATAGTTTATAA
982177 ATAACTATATAGTTTATATAA
1 AT-A-TATATAG-TT-TATAA
982198 ACTATATATAGTTTAT--
1 A-TATATATAGTTTATAA
* * * *
982214 ACATATGTAGCTTATAT
1 ATATATATAGTTTATAA
* *
982231 ATATATTATA-TATATATT
1 ATATA-TATAGTTTATA-A
982249 ATATATATAGTTTATA
1 ATATATATAGTTTATA
982265 TCTATATAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
15 11 0.16
16 3 0.04
17 13 0.19
18 24 0.35
19 4 0.06
20 10 0.14
21 3 0.04
22 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (17 bp):
ATATATATAGTTTATAA
Found at i:982242 original size:9 final size:8
Alignment explanation
Indices: 982118--982272 Score: 54
Period size: 9 Copynumber: 19.2 Consensus size: 8
982108 GACTATAGGT
982118 TATATATA
1 TATATATA
*
982126 TAGTTTATA
1 TA-TATATA
*
982135 TAAAT-TA
1 TATATATA
*
982142 TATATAAA
1 TATATATA
*
982150 CTATA-ATT
1 -TATATATA
*
982158 TACATATA
1 TATATATA
*
982166 TATAGTTTA
1 TATA-TATA
982175 TA-ATA-A
1 TATATATA
*
982181 CTATATAGTT
1 -TATATA-TA
*
982191 TATATAAA
1 TATATATA
982199 CTATATATA
1 -TATATATA
* *
982208 GTTTATACA
1 -TATATATA
* **
982217 TATGTAGC
1 TATATATA
982225 T-TATATA
1 TATATATA
982232 TATAT-TA
1 TATATATA
982239 TATATATA
1 TATATATA
982247 T-TATATA
1 TATATATA
*
982254 TATAGTTTA
1 TATA-TATA
*
982263 TATCTATA
1 TATATATA
982271 TA
1 TA
982273 GTTGATTTAT
Statistics
Matches: 104, Mismatches: 29, Indels: 28
0.65 0.18 0.17
Matches are distributed among these distances:
6 1 0.01
7 30 0.29
8 32 0.31
9 41 0.39
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (8 bp):
TATATATA
Found at i:982285 original size:2 final size:2
Alignment explanation
Indices: 982118--982272 Score: 54
Period size: 2 Copynumber: 77.0 Consensus size: 2
982108 GACTATAGGT
* * * *
982118 TA TA TA TA TA GTT TA TA TA AA T- TA TA TA TA AA CTA TA -A TT TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
982160 CA TA TA TA TA GTT TA TA -A TA -A CTA TA TA GTT TA TA TA AA CTA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA
* * * **
982202 TA TA TA GTT TA TA CA TA TG TA GC T- TA TA TA TA TA T- 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
* *
982243 TA TA T- TA TA TA TA TA GTT TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
982273 GTTGATTTAT
Statistics
Matches: 109, Mismatches: 29, Indels: 30
0.65 0.17 0.18
Matches are distributed among these distances:
1 7 0.06
2 94 0.86
3 8 0.07
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:982390 original size:21 final size:20
Alignment explanation
Indices: 982336--982393 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
982326 TATATAGTTC
*
982336 ATACATATA-TAGTTTATAT
1 ATACATGTATTAGTTTATAT
*
982355 TTACATGTATT-GTTTATAT
1 ATACATGTATTAGTTTATAT
* *
982374 ATATAGTTTATTAGTTTATA
1 ATACA-TGTATTAGTTTATA
982394 ATAACTACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 18 0.58
20 6 0.19
21 7 0.23
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53
Consensus pattern (20 bp):
ATACATGTATTAGTTTATAT
Found at i:982423 original size:31 final size:30
Alignment explanation
Indices: 982385--982508 Score: 137
Period size: 31 Copynumber: 4.1 Consensus size: 30
982375 TATAGTTTAT
* *
982385 TAGTTTATAATAACTACATAGATTACATATA
1 TAGTTTATAATAACTA-ATAGTTTATATATA
*
982416 TAGTTTATACAT-A-T-ATAGTTTATGTATA
1 TAGTTTATA-ATAACTAATAGTTTATATATA
*
982444 TAGTTTATAATAACCATATAGTTTATATATA
1 TAGTTTATAATAACTA-ATAGTTTATATATA
*
982475 TAGTTTATAATAACTATATAATTTATATTATA
1 TAGTTTATAATAACTA-ATAGTTTATA-TATA
982507 TA
1 TA
982509 TATAATTTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.03
28 21 0.26
30 1 0.01
31 48 0.60
32 8 0.10
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (30 bp):
TAGTTTATAATAACTAATAGTTTATATATA
Found at i:982464 original size:18 final size:17
Alignment explanation
Indices: 982441--982501 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
982431 TAGTTTATGT
982441 ATATAGTTTATAATAACC
1 ATATAGTTTATAATAA-C
982459 ATATAGTTTAT-AT---
1 ATATAGTTTATAATAAC
982472 ATATAGTTTATAATAAC
1 ATATAGTTTATAATAAC
*
982489 TATATAATTTATA
1 -ATATAGTTTATA
982502 TTATATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 11 0.30
14 2 0.05
17 2 0.05
18 22 0.59
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (17 bp):
ATATAGTTTATAATAAC
Found at i:982510 original size:18 final size:18
Alignment explanation
Indices: 982466--982518 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
982456 ACCATATAGT
*
982466 TTATATATATAGTTTATA
1 TTATATATATAATTTATA
*
982484 ATA-ACTATATAATTTATA
1 TTATA-TATATAATTTATA
982502 TTATATATATAATTTAT
1 TTATATATATAATTTAT
982519 GTATAGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATATATATAATTTATA
Found at i:982512 original size:49 final size:48
Alignment explanation
Indices: 982459--982573 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 48
982449 TATAATAACC
*
982459 ATATAGTTTATATATATAGTTTATA-ATAACTATATAATTTATATTA-TAT
1 ATATAGTTTATATATATAGTTTATATA-AACTATAT-ACTT-TATTACTAT
* * * *
982508 ATATAATTTATGTATAGT-GTTTCTATAAACTATATACTTTATTACTTT
1 ATATAGTTTATATATA-TAGTTTATATAAACTATATACTTTATTACTAT
982556 ATATAGTTTATATATATA
1 ATATAGTTTATATATATA
982574 TAATCTATAG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
47 6 0.11
48 19 0.35
49 28 0.51
50 2 0.04
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.51
Consensus pattern (48 bp):
ATATAGTTTATATATATAGTTTATATAAACTATATACTTTATTACTAT
Found at i:982651 original size:81 final size:81
Alignment explanation
Indices: 982599--982766 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 81
982589 ATATATTAGT
*
982599 TATACATACATATATATATTATATTAATATAAATTATAATTTATAAACTATATACTTTATATAGT
1 TATACATACATATATATAATATATTAATATAAATTATAATTTATAAACTATATACTTTATATAGT
*
982664 TTATACATATAGTTTA
66 ATATACATATAGTTTA
* *
982680 TATACATACATATATATAATATATTAATATAAATTATAGTTTATAAACTATATACTTTTTATAGT
1 TATACATACATATATATAATATATTAATATAAATTATAATTTATAAACTATATACTTTATATAGT
*
982745 TTATACATATATAGTTTA
66 ATATAC--ATATAGTTTA
982763 TATA
1 TATA
982767 TATAGTTCAT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
81 68 0.83
83 14 0.17
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (81 bp):
TATACATACATATATATAATATATTAATATAAATTATAATTTATAAACTATATACTTTATATAGT
ATATACATATAGTTTA
Found at i:982805 original size:81 final size:80
Alignment explanation
Indices: 982599--982806 Score: 242
Period size: 81 Copynumber: 2.6 Consensus size: 80
982589 ATATATTAGT
** **
982599 TATACATACATATATATATTATATTAATATAAATTATAATTTATAAACTATATACTTTATATAGT
1 TATACATACATATATATAACATATT-ATATAAATTATAGCTTATAAACTATATACTTTATATAGT
982664 TTATACATATAGTTTA
65 TTATACATATAGTTTA
* * *
982680 TATACATACATATATATAATATATTAATATAAATTATAGTTTATAAACTATATACTTTTTATAGT
1 TATACATACATATATATAACATATT-ATATAAATTATAGCTTATAAACTATATACTTTATATAGT
982745 TTATACATATATAGTTTA
65 TTATAC--ATATAGTTTA
* ** *
982763 TATATATAGTTCATATA-AACATAGTT-TATATA-TATAGCTTATAA
1 TATACATACAT-ATATATAACATA-TTATATAAATTATAGCTTATAA
982807 TAATTATATA
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
81 79 0.69
82 5 0.04
83 23 0.20
84 7 0.06
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (80 bp):
TATACATACATATATATAACATATTATATAAATTATAGCTTATAAACTATATACTTTATATAGTT
TATACATATAGTTTA
Found at i:982833 original size:18 final size:17
Alignment explanation
Indices: 982789--982860 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 17
982779 AAACATAGTT
*
982789 TATATATATAGCTTATA
1 TATATATATAGTTTATA
982806 -ATAATTATATAGTTTATAA
1 TAT-A-TATATAGTTTAT-A
*
982825 TATAAATATAGTTT-T-
1 TATATATATAGTTTATA
982840 TATATATATAGTTTATA
1 TATATATATAGTTTATA
982857 TATA
1 TATA
982861 AATTTATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
15 13 0.28
16 3 0.07
17 6 0.13
18 20 0.43
19 2 0.04
20 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATATATAGTTTATA
Found at i:984626 original size:15 final size:16
Alignment explanation
Indices: 984606--984638 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
984596 CGATTATAAC
984606 TAAAATA-TCCAAAAT
1 TAAAATAGTCCAAAAT
*
984621 TAAAATAGTCCTAAAT
1 TAAAATAGTCCAAAAT
984637 TA
1 TA
984639 CTATTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAAATAGTCCAAAAT
Found at i:985160 original size:12 final size:12
Alignment explanation
Indices: 985130--985163 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
985120 ACTTTTCTTA
985130 ACTTTCATATTC
1 ACTTTCATATTC
*
985142 ACTTTTCATATTT
1 AC-TTTCATATTC
985155 ACTTTCATA
1 ACTTTCATA
985164 GCCAAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:987325 original size:20 final size:20
Alignment explanation
Indices: 987279--987377 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 20
987269 CCGTTAGACA
* *
987279 GGGGGAATCAGCACCCCCTTGG
1 GGGGGAATCTGTACCCCC-T-G
* *
987301 GGGGGAATTTGTTCCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
987321 GGGGGAATCGGTACCCCCT-
1 GGGGGAATCTGTACCCCCTG
*
987340 GGGGGAATCTATACCCCCTGG
1 GGGGGAATCTGTACCCCCT-G
*
987361 GGGGGAATCTATACCCC
1 GGGGGAATCTGTACCCC
987378 ATGGACATTC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
19 17 0.26
20 17 0.26
21 18 0.27
22 14 0.21
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.19
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:987370 original size:21 final size:20
Alignment explanation
Indices: 987300--987377 Score: 95
Period size: 19 Copynumber: 3.9 Consensus size: 20
987290 CACCCCCTTG
* * *
987300 GGGGGGAATTTGTTCCCCCT
1 GGGGGGAATCTATACCCCCT
**
987320 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCTATACCCCCT
987340 -GGGGGAATCTATACCCCCT
1 GGGGGGAATCTATACCCCCT
987359 GGGGGGGAATCTATACCCC
1 -GGGGGGAATCTATACCCC
987378 ATGGACATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
19 17 0.33
20 17 0.33
21 17 0.33
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTATACCCCCT
Found at i:987437 original size:20 final size:20
Alignment explanation
Indices: 987414--987454 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
987404 AAAACCTGCA
987414 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
987434 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
987454 G
1 G
987455 ACAATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.29, G:0.37, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:988911 original size:19 final size:20
Alignment explanation
Indices: 988868--988915 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
988858 TCTAAATCCT
*
988868 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
988888 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
988907 TTTTCAAAA
1 TTTTCAAAA
988916 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:990235 original size:20 final size:20
Alignment explanation
Indices: 990195--990270 Score: 107
Period size: 21 Copynumber: 3.7 Consensus size: 20
990185 TAGACAGGGA
* *
990195 GAATCAGTACCCCCTTAGGGG
1 GAATCTGTACCCCC-TGGGGG
*
990216 GAATCGGTACCCCCTGGGGG
1 GAATCTGTACCCCCTGGGGG
990236 GAATCTGTACCCCCTGGGTGG
1 GAATCTGTACCCCCTGGG-GG
990257 GAATCTGTACCCCC
1 GAATCTGTACCCCC
990271 CTGGACAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 22 0.43
21 29 0.57
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20
Consensus pattern (20 bp):
GAATCTGTACCCCCTGGGGG
Found at i:992204 original size:16 final size:16
Alignment explanation
Indices: 992172--992239 Score: 59
Period size: 16 Copynumber: 4.0 Consensus size: 16
992162 AGTTTAAAAT
992172 TAATGAAAATAAATAAA
1 TAAT-AAAATAAATAAA
992189 TAATAAAA-AAACTAAA
1 TAATAAAATAAA-TAAA
*
992205 TAA-AAAATAATTTGAATA
1 TAATAAAATAA-AT-AA-A
992223 TAAATAAAATAAATAAA
1 T-AATAAAATAAATAAA
992240 GTAGAAGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
15 7 0.17
16 14 0.33
17 7 0.17
18 4 0.10
19 3 0.07
20 7 0.17
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (16 bp):
TAATAAAATAAATAAA
Found at i:992206 original size:20 final size:19
Alignment explanation
Indices: 992177--992214 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
992167 AAAATTAATG
*
992177 AAAATAAATAAATAATAAA
1 AAAATAAATAAAAAATAAA
992196 AAAACTAAATAAAAAATAA
1 AAAA-TAAATAAAAAATAA
992215 TTTGAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAATAAATAAAAAATAAA
Found at i:994055 original size:27 final size:27
Alignment explanation
Indices: 994016--994072 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
994006 CTAAATGATA
* *
994016 CAAAAATCTAATAAACCAA-TATAAGTT
1 CAAAAACCAAATAAA-CAATTATAAGTT
* *
994043 CAAAAACCAAATATATAATTATAAGTT
1 CAAAAACCAAATAAACAATTATAAGTT
994070 CAA
1 CAA
994073 GCATTCAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (27 bp):
CAAAAACCAAATAAACAATTATAAGTT
Found at i:998888 original size:16 final size:16
Alignment explanation
Indices: 998867--998897 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
998857 AAAAGCATCA
*
998867 CAAATTTTATCTTTAT
1 CAAATTTTAGCTTTAT
998883 CAAATTTTAGCTTTA
1 CAAATTTTAGCTTTA
998898 GCAACCTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (16 bp):
CAAATTTTAGCTTTAT
Found at i:1006271 original size:20 final size:21
Alignment explanation
Indices: 1006246--1006285 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1006236 CTTTACATAA
1006246 TAGTATCAATACCAT-AGGCT
1 TAGTATCAATACCATCAGGCT
*
1006266 TAGTATCGATACCATCAGGC
1 TAGTATCAATACCATCAGGC
1006286 CCAATGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (21 bp):
TAGTATCAATACCATCAGGCT
Found at i:1013124 original size:10 final size:10
Alignment explanation
Indices: 1013109--1013146 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1013099 ATTTTTATGA
1013109 TTTAAAAGAT
1 TTTAAAAGAT
*
1013119 TTTAAAACAT
1 TTTAAAAGAT
*
1013129 TTTAAAATAT
1 TTTAAAAGAT
1013139 TTTAAAAG
1 TTTAAAAG
1013147 CTTCTCGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (10 bp):
TTTAAAAGAT
Found at i:1015064 original size:2 final size:2
Alignment explanation
Indices: 1015049--1015128 Score: 146
Period size: 2 Copynumber: 41.0 Consensus size: 2
1015039 ACGTTTAAAA
1015049 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1015089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1015129 CAAAGTAAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 74 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1016095 original size:20 final size:20
Alignment explanation
Indices: 1016070--1016140 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
1016060 GTTGAAGAGG
1016070 GTATCGATACTGTGTGGGTA
1 GTATCGATACTGTGTGGGTA
**
1016090 GTATCGATAC-CAG-GGGTGA
1 GTATCGATACTGTGTGGGT-A
1016109 GGGTATCGATACTGTGTGGGTA
1 --GTATCGATACTGTGTGGGTA
1016131 GTATCGATAC
1 GTATCGATAC
1016141 CAGGGGATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 4 0.10
19 2 0.05
20 20 0.48
21 10 0.24
22 2 0.05
23 4 0.10
ACGTcount: A:0.23, C:0.13, G:0.35, T:0.30
Consensus pattern (20 bp):
GTATCGATACTGTGTGGGTA
Found at i:1016123 original size:41 final size:40
Alignment explanation
Indices: 1016044--1016162 Score: 177
Period size: 41 Copynumber: 2.9 Consensus size: 40
1016034 AATTATTAAC
**
1016044 GGTAGTATCGATACCAGTTGAAGAGGGTATCGATACTGTGTG
1 GGTAGTATCGATACCAG--GGGGAGGGTATCGATACTGTGTG
1016086 GGTAGTATCGATACCAGGGGTGAGGGTATCGATACTGTGTG
1 GGTAGTATCGATACCAGGGG-GAGGGTATCGATACTGTGTG
*
1016127 GGTAGTATCGATACCA-GGGGATGGTATCGATACTGT
1 GGTAGTATCGATACCAGGGGGAGGGTATCGATACTGT
1016163 TTTTAAGATG
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
39 16 0.22
40 4 0.05
41 36 0.49
42 17 0.23
ACGTcount: A:0.24, C:0.13, G:0.35, T:0.28
Consensus pattern (40 bp):
GGTAGTATCGATACCAGGGGGAGGGTATCGATACTGTGTG
Found at i:1016155 original size:19 final size:19
Alignment explanation
Indices: 1016090--1016159 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
1016080 TGTGTGGGTA
*
1016090 GTATCGATACCAGGGGTGAGG
1 GTATCGATACCA-GGG-GATG
* * *
1016111 GTATCGATA-CTGTGTGGGTA
1 GTATCGATACCAG-G-GGATG
1016131 GTATCGATACCAGGGGATG
1 GTATCGATACCAGGGGATG
1016150 GTATCGATAC
1 GTATCGATAC
1016160 TGTTTTTAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 14 0.36
20 13 0.33
21 12 0.31
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (19 bp):
GTATCGATACCAGGGGATG
Found at i:1016217 original size:19 final size:21
Alignment explanation
Indices: 1016193--1016244 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1016183 ATGCCAGTTC
1016193 GGTATCGGTACCTTG-AG-GA
1 GGTATCGGTACCTTGAAGAGA
*
1016212 GGTATCGATACCCTTGAAGAGA
1 GGTATCGGTA-CCTTGAAGAGA
*
1016234 AGTATCGGTAC
1 GGTATCGGTAC
1016245 TGGAGGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 3 0.11
22 10 0.37
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (21 bp):
GGTATCGGTACCTTGAAGAGA
Found at i:1022872 original size:12 final size:12
Alignment explanation
Indices: 1022855--1022905 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1022845 TTCAAAGAGG
1022855 TTTTATATTTAA
1 TTTTATATTTAA
1022867 TTTTATA-TTATA
1 TTTTATATTTA-A
*
1022879 TTTGAT-TTTAA
1 TTTTATATTTAA
1022890 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1022902 TTTT
1 TTTT
1022906 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1022909 original size:14 final size:14
Alignment explanation
Indices: 1022890--1022938 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
1022880 TTGATTTTAA
1022890 TTTTAATATTAATT
1 TTTTAATATTAATT
1022904 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
1022914 ATTAAATATTAATT
1 TTTTAATATTAATT
1022928 TTTTAATATTA
1 TTTTAATATTA
1022939 TATTATAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 6 0.22
13 1 0.04
14 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:1023013 original size:19 final size:18
Alignment explanation
Indices: 1022969--1023027 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
1022959 ATATCATATA
*
1022969 AATTATTTTATATATTATT
1 AATTATTTTATTTATT-TT
*
1022988 AA-AATTTATATTTATTTT
1 AATTATTT-TATTTATTTT
1023006 AATTATTTTTATTTAATTTT
1 AATTA-TTTTATTT-ATTTT
1023026 AA
1 AA
1023028 ATATAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 8 0.24
19 15 0.45
20 10 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATTTTATTTATTTT
Found at i:1023510 original size:31 final size:31
Alignment explanation
Indices: 1023475--1023534 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1023465 TAGTTGTATG
* *
1023475 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
1023506 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
1023535 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:1035123 original size:24 final size:24
Alignment explanation
Indices: 1035096--1035183 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
1035086 ATTTGAATTT
1035096 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
1035120 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
1035144 TGATCTGTTACTTGA-TTTGATTTC
1 TGATCTGATACTTGACATGGA-TTC
*
1035168 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
1035184 CTGATTTATG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.07
24 51 0.91
25 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1035188 original size:24 final size:24
Alignment explanation
Indices: 1035092--1035190 Score: 98
Period size: 24 Copynumber: 4.2 Consensus size: 24
1035082 TTCGATTTGA
*
1035092 ATTT-TGATCTGATA-TCTGACATGG
1 ATTTCTGATCTGATACT-TGAC-TTG
1035116 A-TTCTGATCTGATACTTGACTTGG
1 ATTTCTGATCTGATACTTGACTT-G
* *
1035140 A-TTCTGATCTGTTACTTGATTTG
1 ATTTCTGATCTGATACTTGACTTG
* *
1035163 ATTTCTGATATGATACTTGACCTG
1 ATTTCTGATCTGATACTTGACTTG
1035187 ATTT
1 ATTT
1035191 ATGTTTTGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
23 5 0.08
24 58 0.91
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (24 bp):
ATTTCTGATCTGATACTTGACTTG
Found at i:1038887 original size:23 final size:24
Alignment explanation
Indices: 1038852--1038917 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
1038842 ATTTATCTTT
1038852 TAAATTTTA-TAAAAAT-TATATA
1 TAAATTTTATTAAAAATATATATA
1038874 TAAATTTTATTAAAAAGTATATATA
1 TAAATTTTATTAAAAA-TATATATA
* *
1038899 TATATATATATTAAAAATA
1 TAAAT-TTTATTAAAAATA
1038918 ATAAAGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 9 0.24
23 6 0.16
24 1 0.03
25 12 0.32
26 10 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAATTTTATTAAAAATATATATA
Found at i:1041678 original size:22 final size:22
Alignment explanation
Indices: 1041626--1041678 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1041616 TCAGGAGTTA
** *
1041626 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTACATGATATAATTC
*
1041648 CAAGG-GTTACATGATATAATTT
1 C-AGGAGTTACATGATATAATTC
1041670 CAGGAGTTA
1 CAGGAGTTA
1041679 TAACAGCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTC
Found at i:1047224 original size:10 final size:10
Alignment explanation
Indices: 1047211--1047244 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1047201 CGTCTCGTCT
*
1047211 CGGCTCGGCA
1 CGGCACGGCA
1047221 CGGCACGGCA
1 CGGCACGGCA
*
1047231 CGGCACGGCT
1 CGGCACGGCA
1047241 CGGC
1 CGGC
1047245 TCGTGGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.12, C:0.41, G:0.41, T:0.06
Consensus pattern (10 bp):
CGGCACGGCA
Found at i:1047229 original size:15 final size:15
Alignment explanation
Indices: 1047211--1047247 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1047201 CGTCTCGTCT
1047211 CGGCTCGGCACGGCA
1 CGGCTCGGCACGGCA
* *
1047226 CGGCACGGCACGGCT
1 CGGCTCGGCACGGCA
1047241 CGGCTCG
1 CGGCTCG
1047248 TGGTCGTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.41, G:0.41, T:0.08
Consensus pattern (15 bp):
CGGCTCGGCACGGCA
Found at i:1047558 original size:22 final size:22
Alignment explanation
Indices: 1047506--1047558 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1047496 TCAAGAGTTA
** *
1047506 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTACATGATATAATTC
*
1047528 CAAGG-GTTACATGATATAATTT
1 C-AGGAGTTACATGATATAATTC
1047550 CAGGAGTTA
1 CAGGAGTTA
1047559 TAACAGCTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTC
Found at i:1048383 original size:19 final size:20
Alignment explanation
Indices: 1048338--1048383 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1048328 TAAATATCAT
1048338 TTTTTATGTTTATAAAATAA
1 TTTTTATGTTTATAAAATAA
*
1048358 TTGTTATGTTTA-AAAA-AGA
1 TTTTTATGTTTATAAAATA-A
1048377 TTTTTAT
1 TTTTTAT
1048384 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (20 bp):
TTTTTATGTTTATAAAATAA
Found at i:1050062 original size:23 final size:23
Alignment explanation
Indices: 1050031--1050092 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1050021 ACAGGTAAAA
*
1050031 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
1050054 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
**
1050077 ATATAATAAAATAGGT
1 ATATAATGTAATAGGT
1050093 TAATTACTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1050145 original size:87 final size:87
Alignment explanation
Indices: 1050042--1050272 Score: 383
Period size: 87 Copynumber: 2.7 Consensus size: 87
1050032 TATGATGTAA
1050042 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT-GAAAA
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAG-AAA
*
1050106 CATTATCAAGCACAATAATATAT
65 CATTATCAAGCACAATAACATAT
* * *
1050129 TAGGTAACGCTTATATAATTTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAT
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
1050194 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* * *
1050216 TAGGTAGCGCTTATATAACGTAATAGGTAACACTTATATAATAAAATAGGTTAATTA
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA
1050273 TTTAATTTGT
Statistics
Matches: 134, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
87 133 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (87 bp):
TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
ATTATCAAGCACAATAACATAT
Found at i:1050146 original size:23 final size:23
Alignment explanation
Indices: 1050120--1050179 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1050110 ATCAAGCACA
*
1050120 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
1050143 ATAATTTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
*
1050166 ATAATAAAATAGGT
1 ATAATATAATAGGT
1050180 TAATTACTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:1050242 original size:23 final size:23
Alignment explanation
Indices: 1050207--1050266 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1050197 ATCAAGCACA
* * *
1050207 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACACTTAT
*
1050230 ATAACGTAATAGGTAACACTTAT
1 ATAACATAATAGGTAACACTTAT
* *
1050253 ATAATAAAATAGGT
1 ATAACATAATAGGT
1050267 TAATTATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAACACTTAT
Found at i:1050590 original size:14 final size:14
Alignment explanation
Indices: 1050571--1050615 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1050561 TATTAGAATA
*
1050571 ATTTATTTAATATT
1 ATTTATTAAATATT
1050585 ATTTATGTAAATATT
1 ATTTAT-TAAATATT
1050600 A-TTATTAAAATATT
1 ATTTATT-AAATATT
1050614 AT
1 AT
1050616 ATCTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:1050629 original size:28 final size:28
Alignment explanation
Indices: 1050543--1050666 Score: 81
Period size: 28 Copynumber: 4.7 Consensus size: 28
1050533 TAGCAAAATA
*
1050543 ATAATATTATTTTTAAAATATTA-GA--
1 ATAATATTATTATTAAAATATTATGATT
*
1050568 ATAAT-TTA-T-TT--AATATTATTTATGT
1 ATAATATTATTATTAAAATATTA-TGAT-T
1050593 A-AATATTATTATTAAAATATTAT-ATCT
1 ATAATATTATTATTAAAATATTATGAT-T
* * * *
1050620 ATAATTTTATAAATAAAAAATTATGATT
1 ATAATATTATTATTAAAATATTATGATT
*
1050648 ATTATATT-TTATTAAAATA
1 ATAATATTATTATTAAAATA
1050667 AAATTATTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.09
22 3 0.04
23 1 0.01
24 6 0.08
25 9 0.12
26 1 0.01
27 14 0.18
28 26 0.34
29 9 0.12
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (28 bp):
ATAATATTATTATTAAAATATTATGATT
Found at i:1051184 original size:2 final size:2
Alignment explanation
Indices: 1051177--1051201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1051167 CATTCAAATA
1051177 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1051202 ATTACAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1051274 original size:30 final size:30
Alignment explanation
Indices: 1051199--1051274 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 30
1051189 ATATATATAT
*
1051199 ATAATTACAATATAATTTTAAAAAATAATC
1 ATAATTACAATATAATTATAAAAAATAATC
* *
1051229 ATAA-T---A-A-AGTGATAAAAAATAATC
1 ATAATTACAATATAATTATAAAAAATAATC
1051253 ATAATTACAATATAATTATAAA
1 ATAATTACAATATAATTATAAA
1051275 CATCAAATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
24 18 0.51
25 2 0.06
26 1 0.03
28 1 0.03
29 2 0.06
30 11 0.31
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (30 bp):
ATAATTACAATATAATTATAAAAAATAATC
Found at i:1051310 original size:24 final size:25
Alignment explanation
Indices: 1051283--1051351 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
1051273 AACATCAAAT
1051283 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
*
1051307 ACAA-AATAATAATATTATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
1051330 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
1051352 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 23 0.59
25 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:1051401 original size:28 final size:28
Alignment explanation
Indices: 1051367--1051438 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
1051357 ATTTATGTCG
1051367 ATATTATTATTAAAATATTATATCTATA
1 ATATTATTATTAAAATATTATATCTATA
* * * * * * *
1051395 ATTTTATAAATAAAAAATTATGTTTATT
1 ATATTATTATTAAAATATTATATCTATA
1051423 ATATT-TTATTAAAATA
1 ATATTATTATTAAAATA
1051439 AAATTATTAT
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
27 8 0.24
28 25 0.76
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATATTATTATTAAAATATTATATCTATA
Found at i:1052021 original size:198 final size:199
Alignment explanation
Indices: 1051564--1052243 Score: 922
Period size: 198 Copynumber: 3.4 Consensus size: 199
1051554 CATATATGTT
* * * * *
1051564 ACATCAAAACCGATAATTATAATGTAATAGATAAAGTTACAATGTAACCAGTATAAATATACCGA
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGA
* * * * *** *
1051629 TTTTATGAGAGAATAAGTCTACATACTGTATCGACACAAATTTAA-AAAGTGTCGATACATTTTG
66 TTTTATGAGAAAATAGGTCTACATAATGTATCGACAC-ATTTTAAGTTTGTGTCGATAC-TTTTT
*
1051693 TCCAGAATGAATG-CCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCTAT
129 TCCAGAATGAATGTCC-AACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGAT
1051757 CCCAAAA
193 CCCAAAA
* * * *
1051764 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATATCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGA
* *
1051829 TTTTATGAGAAAATATGTCTATATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
66 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
* * *
1051894 TAGAATGAATGTCCAACGAGTTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
131 CAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
1051959 AAAA
196 AAAA
* * * *
1051963 A-ATCCAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCGGTAGAAATATACCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGA
* *
1052027 TTTTATGAGAAAATAGGTCTACATAATGTATTGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
66 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
* *
1052092 CGGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATCGATCC
131 CAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC
1052155 CAAAA
195 CAAAA
* * * * * *
1052160 ATATCGAAACTGATAATTATAATGTAATATGTAAATTTGCAATGTTA-CCAGTATAAATATATCG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG-TACCCAGTAGAAATATACCG
* *
1052224 ATTTTATGATAGAATAGGTC
65 ATTTTATGAGAAAATAGGTC
1052244 AATATAAGCG
Statistics
Matches: 429, Mismatches: 46, Indels: 12
0.88 0.09 0.02
Matches are distributed among these distances:
196 3 0.01
197 16 0.04
198 232 0.54
199 77 0.18
200 101 0.24
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGA
TTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
CAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
AAAA
Found at i:1052346 original size:87 final size:87
Alignment explanation
Indices: 1052245--1052434 Score: 310
Period size: 87 Copynumber: 2.2 Consensus size: 87
1052235 GAATAGGTCA
* * *
1052245 ATATAAGCGCTACCTATTACATTATATAAGCGCTATCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATGTTT
1052310 -TCAGTAATTAACATATTTTATT
66 CT-AGTAATTAACATATTTTATT
* *
1052332 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATGTTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATGTTT
*
1052397 CTAGTAATTAACCTATTTTATT
66 CTAGTAATTAACATATTTTATT
1052419 ATATAAGCGCTACCTA
1 ATATAAGCGCTACCTA
1052435 ATTTGTTATT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 95 0.99
88 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATGTTT
CTAGTAATTAACATATTTTATT
Found at i:1052379 original size:23 final size:23
Alignment explanation
Indices: 1052329--1052373 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1052319 AACATATTTT
* *
1052329 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
1052352 ATTATATAAACGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
1052374 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:1056497 original size:41 final size:41
Alignment explanation
Indices: 1056420--1056502 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
1056410 ACAATAAACT
** *
1056420 AACACAAGATGTGAAAAATAAAAATATTACATAAGAGAATC
1 AACACAAGATGTGAAAAATAAAAATACCACACAAGAGAATC
** * * *
1056461 AACACAAGATGTTTATATTAAAAATACCACACAAGAGTATC
1 AACACAAGATGTGAAAAATAAAAATACCACACAAGAGAATC
1056502 A
1 A
1056503 TATTCAACAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (41 bp):
AACACAAGATGTGAAAAATAAAAATACCACACAAGAGAATC
Found at i:1061008 original size:20 final size:20
Alignment explanation
Indices: 1060967--1061025 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1060957 AAGTTACAAT
*
1060967 ATTTAACTTTT-GTATTTGAA
1 ATTTAACTTTTAGAATTT-AA
1060987 ATTTAACTTTTAGAATTTAA
1 ATTTAACTTTTAGAATTTAA
* * *
1061007 ATTAAATTTTTAGCATTTA
1 ATTTAACTTTTAGAATTTA
1061026 TTTGTTATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTTAACTTTTAGAATTTAA
Found at i:1062226 original size:20 final size:21
Alignment explanation
Indices: 1062201--1062240 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1062191 CTCTGTATAG
1062201 TAGTATCGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
1062221 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
1062241 CCCAAATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:1064808 original size:23 final size:23
Alignment explanation
Indices: 1064770--1064849 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
1064760 ATCTTATATA
* *
1064770 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGTAATTCTACGCG
*
1064793 GTACTTCGGTGTAATTCTACGCG
1 GCACTTCGGTGTAATTCTACGCG
* *
1064816 GCAGTTCGGTGTAATTCTACGTG
1 GCACTTCGGTGTAATTCTACGCG
1064839 GCACTTCGGTG
1 GCACTTCGGTG
1064850 CATTTATACG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.30
Consensus pattern (23 bp):
GCACTTCGGTGTAATTCTACGCG
Found at i:1067140 original size:24 final size:20
Alignment explanation
Indices: 1067108--1067165 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1067098 GCATAGGTAG
*
1067108 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TG-T-A-GAA
*
1067132 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
1067152 TGCATCGATGCACT
1 TGCATCGATGCACT
1067166 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1067857 original size:2 final size:2
Alignment explanation
Indices: 1067850--1067898 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1067840 AATAGAAGTA
1067850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1067891 AT AT AT AT
1 AT AT AT AT
1067899 GTTTATAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1068727 original size:23 final size:23
Alignment explanation
Indices: 1068653--1068720 Score: 127
Period size: 23 Copynumber: 3.0 Consensus size: 23
1068643 AATCTTATAT
1068653 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
1068676 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
*
1068699 GGCACTACGGTGCAATTCTACG
1 GGCACTACGGTGCATTTCTACG
1068721 TGACACTTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:1068738 original size:46 final size:46
Alignment explanation
Indices: 1068653--1068743 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
1068643 AATCTTATAT
* * * * *
1068653 GGCACTACGGTGCATTTCTACGCGGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCAATTCTACGCGACACTACGATACATTTATACGC
* *
1068699 GGCACTACGGTGCAATTCTACGTGACACTTCGATACATTTATACG
1 GGCACTACGGTGCAATTCTACGCGACACTACGATACATTTATACG
1068744 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.27
Consensus pattern (46 bp):
GGCACTACGGTGCAATTCTACGCGACACTACGATACATTTATACGC
Found at i:1074870 original size:23 final size:23
Alignment explanation
Indices: 1074838--1074896 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1074828 ATGTTATATA
*
1074838 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* *
1074861 GCACTTCGGTGCAATTTTACGTG
1 GCACTTCGGTGCAATTCTACGCG
1074884 GCACTTCGGTGCA
1 GCACTTCGGTGCA
1074897 TTTATACGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:1074904 original size:23 final size:22
Alignment explanation
Indices: 1074838--1074904 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
1074828 ATGTTATATA
* *
1074838 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGC-ATTTTACGCG
*
1074861 GCACTTCGGTGCAATTTTACGTG
1 GCACTTCGGTGC-ATTTTACGCG
1074884 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTT-TACG
1074905 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.10
23 36 0.90
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
GCACTTCGGTGCATTTTACGCG
Found at i:1076377 original size:19 final size:18
Alignment explanation
Indices: 1076353--1076403 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
1076343 TGAAAATGAT
*
1076353 TTGATTTTGAAAGTCAAA
1 TTGATTTTGAAAATCAAA
1076371 GTTGATTTTGAAAATCAAA
1 -TTGATTTTGAAAATCAAA
*
1076390 ATGAATTTTGAAAA
1 TTG-ATTTTGAAAA
1076404 ATGATTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 2 0.07
19 27 0.93
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (18 bp):
TTGATTTTGAAAATCAAA
Found at i:1077963 original size:20 final size:21
Alignment explanation
Indices: 1077938--1077978 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1077928 ACTCTGTATA
1077938 ATAGTATCGATACCA-TAGGC
1 ATAGTATCGATACCATTAGGC
1077958 ATAGTATCGATACCATTAGGC
1 ATAGTATCGATACCATTAGGC
1077979 CCTAACGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (21 bp):
ATAGTATCGATACCATTAGGC
Found at i:1080038 original size:29 final size:29
Alignment explanation
Indices: 1080006--1080064 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1079996 ACATCCTTCA
*
1080006 AGAAGTCACGATATATTGATATTATTTTT
1 AGAAGTCACGACATATTGATATTATTTTT
1080035 AGAAGTCACGACATATTGATATTATTTTT
1 AGAAGTCACGACATATTGATATTATTTTT
1080064 A
1 A
1080065 ACAAGACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (29 bp):
AGAAGTCACGACATATTGATATTATTTTT
Found at i:1080778 original size:13 final size:13
Alignment explanation
Indices: 1080760--1080786 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1080750 TCTGACACGT
1080760 GGGGTATAGCGCG
1 GGGGTATAGCGCG
1080773 GGGGTATAGCGCG
1 GGGGTATAGCGCG
1080786 G
1 G
1080787 TGCAGGGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (13 bp):
GGGGTATAGCGCG
Found at i:1080890 original size:10 final size:10
Alignment explanation
Indices: 1080875--1080907 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1080865 TTTATCACAC
1080875 CAAATTCTCT
1 CAAATTCTCT
1080885 CAAATTCTCT
1 CAAATTCTCT
1080895 -AAATTTCTCT
1 CAAA-TTCTCT
1080905 CAA
1 CAA
1080908 CTACTCTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.14
10 16 0.76
11 2 0.10
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1081186 original size:111 final size:111
Alignment explanation
Indices: 1081041--1081373 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
1081031 TGGAAATCAT
* *
1081041 ATATCTCTACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1081106 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1081152 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1081217 TAATTAGTTAATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1081263 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1081328 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1081374 TTTTTGTAAT
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1083273 original size:6 final size:6
Alignment explanation
Indices: 1083250--1083303 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
1083240 TACTCAGGAC
* * *
1083250 GACGAC GACGAC GACGAT GACGAT G--G-T GACGAA GACGAT GACGAT
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT
*
1083295 GATGAT GAC
1 GACGAT GAC
1083304 AGAAATGAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
5 1 0.03
6 36 0.90
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.13
Consensus pattern (6 bp):
GACGAT
Found at i:1083280 original size:21 final size:21
Alignment explanation
Indices: 1083256--1083295 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1083246 GGACGACGAC
*
1083256 GACGACGACGATGACGATGGT
1 GACGAAGACGATGACGATGGT
1083277 GACGAAGACGATGACGATG
1 GACGAAGACGATGACGATG
1083296 ATGATGACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.38, T:0.12
Consensus pattern (21 bp):
GACGAAGACGATGACGATGGT
Found at i:1083554 original size:35 final size:33
Alignment explanation
Indices: 1083515--1083599 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
1083505 ATATTTCAGT
1083515 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
1083550 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
1083585 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1083600 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:1087071 original size:20 final size:20
Alignment explanation
Indices: 1087046--1087083 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1087036 TGATCCGCGT
*
1087046 TATACCCCTACGTGACGTGC
1 TATACCCCTACGTAACGTGC
1087066 TATACCCCTACGTAACGT
1 TATACCCCTACGTAACGT
1087084 ATAGCGCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (20 bp):
TATACCCCTACGTAACGTGC
Found at i:1090970 original size:8 final size:8
Alignment explanation
Indices: 1090957--1090997 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1090947 CTCATTTTCA
1090957 GAGAATTT
1 GAGAATTT
1090965 GAGAATTT
1 GAGAATTT
*
1090973 -AGAGTTT
1 GAGAATTT
*
1090980 GGGAATTT
1 GAGAATTT
1090988 GAGAATTT
1 GAGAATTT
1090996 GA
1 GA
1090998 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1091301 original size:128 final size:128
Alignment explanation
Indices: 1091068--1092723 Score: 2836
Period size: 128 Copynumber: 12.9 Consensus size: 128
1091058 TAATCAGAGT
*
1091068 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1091133 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
1091196 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1091261 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1091324 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1091389 CATTGCCCTATTATGTTACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
1091452 TC-AGGGGACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1091516 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1091580 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1091645 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* ***
1091708 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1091772 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1091836 ACTATTCACATGAATGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1091901 CATTGCCCTATTATGTCACTTATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
1091964 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1092028 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1092092 ACTATTCACATGAAGGAGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1092157 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
1092220 TC-AGGGGACATGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1092284 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
1092348 ACTATTCACATGAAGGCGTGTTCCCGGGGGCCCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1092413 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACAATAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * * *
1092476 TC-AGGGGACATGAAGGCGCATTCCCGGGGGGGGGGGGCCTTCCATTATTTCGTCAGAGAATATG
1 ACTA-TTCACATGAAGGCGCGTTCCC---GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATG
*
1092540 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCGGTACCTATTATT
62 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
1092605 TC
127 TC
* *
1092607 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1092672 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
1092724 AATCAGGTAA
Statistics
Matches: 1439, Mismatches: 76, Indels: 26
0.93 0.05 0.02
Matches are distributed among these distances:
127 5 0.00
128 1314 0.91
129 4 0.00
131 115 0.08
132 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Done.