Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008164.1 Hibiscus syriacus cultivar Beakdansim tig00110744_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: 2577652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:7156 original size:2 final size:2
Alignment explanation
Indices: 7149--7179 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7139 GATCCTGCCC
7149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7180 AAGTTTGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19148 original size:21 final size:21
Alignment explanation
Indices: 19118--19174 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
19108 GGGAGCGTGT
*
19118 GTGTACCGGTACACTCTCAAG
1 GTGTATCGGTACACTCTCAAG
19139 GTGTATCGGTACACTCTCAAG
1 GTGTATCGGTACACTCTCAAG
19160 GTGTATCGGTACACT
1 GTGTATCGGTACACT
19175 GTGTGTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
GTGTATCGGTACACTCTCAAG
Found at i:19599 original size:13 final size:13
Alignment explanation
Indices: 19581--19632 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 13
19571 TAAGATTTTC
19581 TTTGAAAATTATT
1 TTTGAAAATTATT
19594 TTTGAATAAAATTATT
1 TTTG---AAAATTATT
* *
19610 TTTG-AAATGAAT
1 TTTGAAAATTATT
19622 TTTGAAAATTA
1 TTTGAAAATTA
19633 CTCCCCCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 10 0.31
13 9 0.28
16 13 0.41
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (13 bp):
TTTGAAAATTATT
Found at i:19622 original size:16 final size:16
Alignment explanation
Indices: 19585--19615 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19575 ATTTTCTTTG
19585 AAAATTATTTTTGAAT
1 AAAATTATTTTTGAAT
19601 AAAATTATTTTTGAA
1 AAAATTATTTTTGAA
19616 ATGAATTTTG
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:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AAAATTATTTTTGAAT
Found at i:21356 original size:12 final size:12
Alignment explanation
Indices: 21339--21372 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
21329 AATGGGAAAT
*
21339 TTTTGAAAACTA
1 TTTTGAAAACAA
21351 TTTTGAAAACAA
1 TTTTGAAAACAA
21363 TGTTTGAAAA
1 T-TTTGAAAA
21373 ATTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (12 bp):
TTTTGAAAACAA
Found at i:21433 original size:18 final size:20
Alignment explanation
Indices: 21397--21437 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
21387 AGTTTTCATG
21397 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAATCA
21417 AAAACAACA-AA-TAAATCA
1 AAAACAACATAATTAAATCA
21435 AAA
1 AAA
21438 CATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAACAACATAATTAAATCA
Found at i:21917 original size:21 final size:21
Alignment explanation
Indices: 21888--21964 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
21878 CAAGGAATGC
*
21888 ATCGGTGCACTTTCATAGTGT
1 ATCGATGCACTTTCATAGTGT
* *
21909 ATCGATGCACATTT-AAAGGAATGC
1 ATCGATGCAC-TTTCATA-G--TGT
* *
21933 ATCGGTACACTTTCATAGTGT
1 ATCGATGCACTTTCATAGTGT
21954 ATCGATGCACT
1 ATCGATGCACT
21965 GTACACAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
21 22 0.52
22 4 0.10
23 4 0.10
24 12 0.29
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (21 bp):
ATCGATGCACTTTCATAGTGT
Found at i:21944 original size:45 final size:44
Alignment explanation
Indices: 21860--21963 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 44
21850 TACACTGGAG
* * *
21860 AGTGTATCGATACACATTCAAGGAATGCATCGGTGCACTTTCAT
1 AGTGTATCGATGCACATTAAAGGAATGCATCGGTACACTTTCAT
21904 AGTGTATCGATGCACATTTAAAGGAATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCACA-TTAAAGGAATGCATCGGTACACTTTCAT
21949 AGTGTATCGATGCAC
1 AGTGTATCGATGCAC
21964 TGTACACAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 15 0.27
45 41 0.73
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
AGTGTATCGATGCACATTAAAGGAATGCATCGGTACACTTTCAT
Found at i:31623 original size:22 final size:22
Alignment explanation
Indices: 31598--31647 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
31588 GACATAGTCA
31598 ACTTTCTTGTTAGTGGTATTGT
1 ACTTTCTTGTTAGTGGTATTGT
31620 ACTTTCTTGTTAGTGGTATTGT
1 ACTTTCTTGTTAGTGGTATTGT
31642 ACTTTC
1 ACTTTC
31648 AGATTAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (22 bp):
ACTTTCTTGTTAGTGGTATTGT
Found at i:37129 original size:27 final size:29
Alignment explanation
Indices: 37074--37129 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
37064 AAATCAACGC
* *
37074 TAGTATTTGCATTATTTATTTTTATTCGA
1 TAGTATTTGCATTATTTATTTTGACTCGA
*
37103 TAGT-TTTGCA-TATTTATTTTGCCTCGA
1 TAGTATTTGCATTATTTATTTTGACTCGA
37130 CCAAACTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 6 0.25
29 4 0.17
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.55
Consensus pattern (29 bp):
TAGTATTTGCATTATTTATTTTGACTCGA
Found at i:37398 original size:44 final size:44
Alignment explanation
Indices: 37335--37422 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
37325 CTTGCACAAA
37335 ATTGCTTGCCTTAACATATACATTTCCAAGCGATCAAGTTTTTT
1 ATTGCTTGCCTTAACATATACATTTCCAAGCGATCAAGTTTTTT
*
37379 ATTGCTTGCCTTAGCATATACATTTCCAAGCGATCAAGTTTTTT
1 ATTGCTTGCCTTAACATATACATTTCCAAGCGATCAAGTTTTTT
37423 CAAAAACTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.41
Consensus pattern (44 bp):
ATTGCTTGCCTTAACATATACATTTCCAAGCGATCAAGTTTTTT
Found at i:47543 original size:126 final size:126
Alignment explanation
Indices: 47316--47549 Score: 272
Period size: 126 Copynumber: 1.9 Consensus size: 126
47306 TACTTTTAGG
* * * *
47316 ATACATTATATGGAACATATATGATAATGGTGCCTGCACGTTTATGATGTTGGTGTGATGTATCC
1 ATACATTATATGGAACATATATGATAATGGTGCCTGCACCTATATGATGATGGTGCGATGTATCC
* * * * *
47381 TCATCGGTGGTACATTGATATTGTGTGTTTATAGTACTTGTACGTAATATGTGACACATGA
66 TCATCAGTGGTACAATGATATTGTGTGTCTACAGTACATGTACGTAATATGTGACACATGA
* * * * * * *
47442 ATACATTTTATGGCACGTCTATGATATTGGTGCCTGCACCTATGTGATGATGGTGCGATTTATTC
1 ATACATTATATGGAACATATATGATAATGGTGCCTGCACCTATATGATGATGGTGCGATGTA-TC
* * * *
47507 CTGATTATTGGTACAATGATGTTGTGT-TCTACAGTACATGTAC
65 CTCATCAGTGGTACAATGATATTGTGTGTCTACAGTACATGTAC
47550 ATTTACGATA
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
126 64 0.74
127 23 0.26
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (126 bp):
ATACATTATATGGAACATATATGATAATGGTGCCTGCACCTATATGATGATGGTGCGATGTATCC
TCATCAGTGGTACAATGATATTGTGTGTCTACAGTACATGTACGTAATATGTGACACATGA
Found at i:47607 original size:26 final size:26
Alignment explanation
Indices: 47558--47608 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
47548 ACATTTACGA
* *
47558 TACTGGCACTAAAAGTGTAATATGTT
1 TACTGGCACTAAAACTGCAATATGTT
* *
47584 TACTGGCAGTAAAACTGCATTATGT
1 TACTGGCACTAAAACTGCAATATGT
47609 GCATACTATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (26 bp):
TACTGGCACTAAAACTGCAATATGTT
Found at i:64585 original size:55 final size:55
Alignment explanation
Indices: 64475--64593 Score: 150
Period size: 55 Copynumber: 2.2 Consensus size: 55
64465 AAAGACATCT
* ** *
64475 GTGTGCTAAGTTAATAACAAAACAAAATATAAATAAATAAAATAATTACATCATA
1 GTGTGCTAAGTTAATAACAAAACAAAATAGAAATAAATAAAATAAAGACACCATA
* * * *
64530 GTGTGCTATGTTAATAATAAAACAAACTAGAAATACATAAAATAAAGACACCATA
1 GTGTGCTAAGTTAATAACAAAACAAAATAGAAATAAATAAAATAAAGACACCATA
64585 GCT-TGCTAA
1 G-TGTGCTAA
64594 TTGGGGAAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 53 0.98
56 1 0.02
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (55 bp):
GTGTGCTAAGTTAATAACAAAACAAAATAGAAATAAATAAAATAAAGACACCATA
Found at i:65076 original size:108 final size:108
Alignment explanation
Indices: 64887--65385 Score: 394
Period size: 108 Copynumber: 4.4 Consensus size: 108
64877 TTTTTAAAGG
* * * * ** * * *
64887 TGATGGGGCCTTAGAAATCTGATGATAATAAAATAGGTTAATTACTTGATTTGTTATCAATATTA
1 TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAATATTATCAACATAA
** * *
64952 TCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGT
66 TCAACATAACAAGTAGCGCCTAAAATGTTACCAAAGTTTAAGC
* * *
64995 TGATGGAGCCTTAAAAATCCGACGATAACAAAATAGGTTAATTAATTGAAACATTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAATATTATCAA-CATA
* * ***
65060 AT-AACATAACAAGTAGCGCTTATTTAATGTAATATGTAGCCCCTGTTTAAAGC
65 ATCAACATAACAAGTAGCGC----CTAA---AATGT-TA-CCAAAGTTT-AAGC
* * ** * * * *
65113 TGATGG-GACCTTAGAAATCCGATGATAACAAAATAGGTTAACTACTTGATTTGTTATTAATATT
1 TGATGGAG-CCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAATATTATCAACATA
* ** *
65177 ATCAATATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGC
65 ATCAACATAACAAGTAGCGCCTAAAATGTTACCAAAGTTTAAGC
* *
65221 TGATGGAGCCTTAGAAATCCGACTATAACAAAATAGGTTAATTACTGGAAATATTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAATATTATCAA-CATA
* * * *
65286 AT-AACATAACAAGTAGCGCTTATTTAATGTAATAGGTAGCACATGTTTAAAGC
65 ATCAACATAACAAGTAGCGC----CTAA---AAT-GTTACCA-AAGTTT-AAGC
*
65339 TGATGG-GACCTTAGAAATCCGACAATAACAAAATAGGTTAATTACTT
1 TGATGGAG-CCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTT
65386 AATTTTTTTT
Statistics
Matches: 304, Mismatches: 61, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
108 131 0.43
109 15 0.05
110 2 0.01
111 4 0.01
112 6 0.02
114 3 0.01
115 7 0.02
116 7 0.02
117 17 0.06
118 112 0.37
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (108 bp):
TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAATATTATCAACATAA
TCAACATAACAAGTAGCGCCTAAAATGTTACCAAAGTTTAAGC
Found at i:65199 original size:226 final size:226
Alignment explanation
Indices: 64802--65414 Score: 931
Period size: 226 Copynumber: 2.7 Consensus size: 226
64792 AACATAACCA
* * * * * *
64802 GTTAATTACTGAAAACATTATCAACCATAATAACATAACAAATAACGCTTATGTAACGTAATACG
1 GTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATACG
* * * * *
64867 TAGCACCTTCTTTTTAAAGGTGATGGGGCCTTAGAAATCTGATGATAATAAAATAGGTTAATTAC
66 TAGC-CC--CTGTTTAAAGCTGATGGGACCTTAGAAATCCGATGATAACAAAATAGGTTAATTAC
* * *
64932 TTGATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGTTG
128 TTGATTTGTTATTAATATTATCAATATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTG
64997 ATGGAGCCTTAAAAATCCGACGATAACAAAATAG
193 ATGGAGCCTTAAAAATCCGACGATAACAAAATAG
* *
65031 GTTAATTAATTGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATATG
1 GTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATACG
*
65096 TAGCCCCTGTTTAAAGCTGATGGGACCTTAGAAATCCGATGATAACAAAATAGGTTAACTACTTG
66 TAGCCCCTGTTTAAAGCTGATGGGACCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTG
65161 ATTTGTTATTAATATTATCAATATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATG
131 ATTTGTTATTAATATTATCAATATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATG
* *
65226 GAGCCTTAGAAATCCGACTATAACAAAATAG
196 GAGCCTTAAAAATCCGACGATAACAAAATAG
* * *
65257 GTTAATTACTGGAAATATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAGG
1 GTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATACG
* * ** *
65322 TAGCACATGTTTAAAGCTGATGGGACCTTAGAAATCCGACAATAACAAAATAGGTTAATTACTTA
66 TAGCCCCTGTTTAAAGCTGATGGGACCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTG
*
65387 ATTT-TTTTTCAATATTATCAATATATTA
131 ATTTGTTATT-AATATTATCAATATATTA
65415 CCGTGTACAT
Statistics
Matches: 353, Mismatches: 30, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
225 4 0.01
226 286 0.81
228 2 0.01
229 61 0.17
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (226 bp):
GTTAATTAATGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATACG
TAGCCCCTGTTTAAAGCTGATGGGACCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTG
ATTTGTTATTAATATTATCAATATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATG
GAGCCTTAAAAATCCGACGATAACAAAATAG
Found at i:65754 original size:51 final size:50
Alignment explanation
Indices: 65691--65817 Score: 166
Period size: 50 Copynumber: 2.5 Consensus size: 50
65681 TTAGCAGTAA
** *
65691 AGCGCG-CCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGAGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTG-GGTAT
* * *
65741 AGTGCGCCCCCTGCACCGCGTTATACGGTGAGCTGGCACCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGGGTAT
* *
65791 AGCGCGGCCCCTGCAGCGCGCTATACG
1 AGCGCGCCCCCTGCACCGCGCTATACG
65818 CCACGTAGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
50 33 0.50
51 33 0.50
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.18
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGGGTAT
Found at i:65816 original size:50 final size:51
Alignment explanation
Indices: 65691--65817 Score: 168
Period size: 51 Copynumber: 2.5 Consensus size: 51
65681 TTAGCAGTAA
** *
65691 AGCGC-GCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGAGGTAT
1 AGCGCGGCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGAGGTAT
* * * *
65741 AGTGCGCCCCCTGCACCGCGTTATACGGTGAGCTGGCACCACGTG-GGTAT
1 AGCGCGGCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGAGGTAT
*
65791 AGCGCGGCCCCTGCAGCGCGCTATACG
1 AGCGCGGCCCCTGCACCGCGCTATACG
65818 CCACGTAGGG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 32 0.49
51 33 0.51
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.18
Consensus pattern (51 bp):
AGCGCGGCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGAGGTAT
Found at i:70622 original size:110 final size:111
Alignment explanation
Indices: 70428--70648 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 111
70418 ATTACAAAAA
* *
70428 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
70493 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
70539 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
70603 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
70649 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 71 0.67
111 35 0.33
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:70801 original size:20 final size:19
Alignment explanation
Indices: 70773--70811 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
70763 CCTTAAAAAG
*
70773 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
70793 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
70812 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:71032 original size:51 final size:50
Alignment explanation
Indices: 70948--71050 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 50
70938 TGTAGGGGTT
* ** * *
70948 GCGCTATACCCACGTGGCGCTAGCTCACCGTATAGCGCGGTGCAGGGGGC
1 GCGCTATACCCACGTGGCGCCAAATCACCGTATAACGAGGTGCAGGGGGC
*
70998 GCGCTATACCCCACGTGGCGCCAAATCATCGTATAACGAGGTGCAGGGGGC
1 GCGCTATA-CCCACGTGGCGCCAAATCACCGTATAACGAGGTGCAGGGGGC
71049 GC
1 GC
71051 ACTTTACTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 8 0.17
51 38 0.83
ACGTcount: A:0.19, C:0.31, G:0.34, T:0.16
Consensus pattern (50 bp):
GCGCTATACCCACGTGGCGCCAAATCACCGTATAACGAGGTGCAGGGGGC
Found at i:71531 original size:171 final size:175
Alignment explanation
Indices: 71315--71690 Score: 417
Period size: 179 Copynumber: 2.1 Consensus size: 175
71305 AAAAGTATTG
* * **
71315 ATACATATATATAAAAGTATTGATACTTGTTATATACGCCTATTATCATTATATCGGTA-A-ACT
1 ATAC-TATA-ATAAAAGTATTGATACTTGTTATATACGCCTATTATCATTAAACCAATAGATACT
* * * * * * *
71378 TTTTATATTGTTAATTTACCTATTACTTTATAGTAATAG-GTTTC-AAATTCCAAGTATCGATAC
64 GTTTACATTATAAATTTACCTATTACTTTAAAATAAT-GCATTTCAAAATTCCAAGTATCGATAC
71441 TT-TGTACAT-TGTATCGATAC-TTTTGACGTGCAAATTGTTTGAGAAGC
128 TTGT-TACATGTGTATCGATACTTTTTG-CGTGCAAATTGTTTGAGAAGC
* * *
71488 ATACTATAATAAAATTATTGATACTT-TATGTTTACGCCTATTATCATTAAACCAATAGATTTTT
1 ATACTATAATAAAAGTATTGATACTTGT-TATATACGCCTATTATCATTAAACCAATAGA----T
* *
71552 ACTGTTTACATTATAAATTTACCTATTACTTTAAAATAATGCATTTCAAAATTCTAAGTATTGAT
61 ACTGTTTACATTATAAATTTACCTATTACTTTAAAATAATGCATTTCAAAATTCCAAGTATCGAT
* *
71617 ACTTGTTATATGTGTATCGATACTTTTTGCGTGCAAATTGTTTGAGATGC
126 ACTTGTTACATGTGTATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGC
** *
71667 ATACTGGAATAAAAGTATCGATAC
1 ATACTATAATAAAAGTATTGATAC
71691 ATAAAACATA
Statistics
Matches: 169, Mismatches: 22, Indels: 18
0.81 0.11 0.09
Matches are distributed among these distances:
170 1 0.01
171 40 0.24
172 5 0.03
173 4 0.02
176 1 0.01
177 38 0.22
178 23 0.14
179 52 0.31
180 5 0.03
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (175 bp):
ATACTATAATAAAAGTATTGATACTTGTTATATACGCCTATTATCATTAAACCAATAGATACTGT
TTACATTATAAATTTACCTATTACTTTAAAATAATGCATTTCAAAATTCCAAGTATCGATACTTG
TTACATGTGTATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGC
Found at i:76357 original size:21 final size:21
Alignment explanation
Indices: 76318--76357 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
76308 GAATTTCAAT
* *
76318 CAACATTCAGACCAGTCCAGC
1 CAACATTCAGAACAATCCAGC
*
76339 CAACATTCATAACAATCCA
1 CAACATTCAGAACAATCCA
76358 AGCAATGGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.35, G:0.07, T:0.17
Consensus pattern (21 bp):
CAACATTCAGAACAATCCAGC
Found at i:77122 original size:14 final size:14
Alignment explanation
Indices: 77103--77130 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
77093 TTGGGAAAAC
77103 AAAATAATTAAATT
1 AAAATAATTAAATT
77117 AAAATAATTAAATT
1 AAAATAATTAAATT
77131 TATGAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATAATTAAATT
Found at i:77856 original size:18 final size:18
Alignment explanation
Indices: 77833--77875 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
77823 AGAATCAATA
77833 AACTTAACAATTTCTCGT
1 AACTTAACAATTTCTCGT
77851 AACTTAACAATTTCTCGT
1 AACTTAACAATTTCTCGT
77869 AACTTAA
1 AACTTAA
77876 TAACAGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (18 bp):
AACTTAACAATTTCTCGT
Found at i:79374 original size:18 final size:18
Alignment explanation
Indices: 79348--79385 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
79338 CGAATAATTG
* *
79348 AATCTAATATAAAATTTT
1 AATCGAATATAAAATCTT
79366 AATCGAATATAAAATCTT
1 AATCGAATATAAAATCTT
79384 AA
1 AA
79386 AATTCATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (18 bp):
AATCGAATATAAAATCTT
Found at i:81859 original size:22 final size:21
Alignment explanation
Indices: 81831--81887 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
81821 ATACTATACT
81831 AGTAGTATCGATACCTAGCAAG
1 AGTAGTATCGATACCTAG-AAG
* *
81853 AGTAGTATCGGTA-CTAGATG
1 AGTAGTATCGATACCTAGAAG
**
81873 ACCAGTATCGATACC
1 AGTAGTATCGATACC
81888 AAGTGCACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 12 0.41
21 5 0.17
22 12 0.41
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (21 bp):
AGTAGTATCGATACCTAGAAG
Found at i:88773 original size:8 final size:8
Alignment explanation
Indices: 88751--88974 Score: 64
Period size: 8 Copynumber: 26.5 Consensus size: 8
88741 AATTGATAAT
*
88751 AAAAAACA
1 AAAAAATA
88759 AAAAAATA
1 AAAAAATA
88767 AAAAAATA
1 AAAAAATA
*
88775 ACAAAATA
1 AAAAAATA
88783 ACATATAAATGA
1 A-A-A-AAAT-A
88795 TAAAACATATA
1 -AAAA-A-ATA
88806 AAAAAAT-
1 AAAAAATA
88813 AAAAAAT-
1 AAAAAATA
88820 AAAAAATA
1 AAAAAATA
*
88828 AATAACAACA
1 AA-AA-AATA
* *
88838 TATAAATA
1 AAAAAATA
*
88846 ACATAAA-A
1 A-AAAAATA
*
88854 AATAAATA
1 AAAAAATA
* *
88862 ATAACATA
1 AAAAAATA
88870 AAATAACATA
1 AAA-AA-ATA
*
88880 AATAACATA
1 AA-AAAATA
88889 CAAATAAATA
1 -AAA-AAATA
*
88899 AAAACA-A
1 AAAAAATA
**
88906 AAAGGAT-
1 AAAAAATA
*
88913 AACAAATA
1 AAAAAATA
*
88921 AAAAAA-C
1 AAAAAATA
*
88928 AAAATATA
1 AAAAAATA
88936 CAAAAACATA
1 -AAAAA-ATA
* *
88946 ATAACATA
1 AAAAAATA
*
88954 AAACAATA
1 AAAAAATA
*
88962 AAATAATTA
1 AAA-AAATA
88971 AAAA
1 AAAA
88975 CAGGAAAAAT
Statistics
Matches: 160, Mismatches: 33, Indels: 46
0.67 0.14 0.19
Matches are distributed among these distances:
7 33 0.21
8 59 0.37
9 30 0.19
10 25 0.16
11 8 0.05
12 4 0.03
13 1 0.01
ACGTcount: A:0.74, C:0.08, G:0.01, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:88816 original size:7 final size:7
Alignment explanation
Indices: 88748--88865 Score: 74
Period size: 7 Copynumber: 15.7 Consensus size: 7
88738 TTAAATTGAT
88748 AATAAAA
1 AATAAAA
*
88755 AACAAAAA
1 AA-TAAAA
88763 AATAAAAA
1 AAT-AAAA
88771 AATAACAA
1 AATAA-AA
*
88779 AATAACA
1 AATAAAA
* *
88786 TATAAAT
1 AATAAAA
*
88793 GATAAAA
1 AATAAAA
88800 CATATAAAAA
1 -A-AT-AAAA
88810 AATAAAA
1 AATAAAA
88817 AATAAAA
1 AATAAAA
*
88824 AATAAAT
1 AATAAAA
* *
88831 AACAACA
1 AATAAAA
*
88838 TATAAATA
1 AATAAA-A
88846 ACATAAAA
1 A-ATAAAA
*
88854 AATAAAT
1 AATAAAA
88861 AATAA
1 AATAA
88866 CATAAAATAA
Statistics
Matches: 85, Mismatches: 18, Indels: 16
0.71 0.15 0.13
Matches are distributed among these distances:
7 48 0.56
8 25 0.29
9 8 0.09
10 4 0.05
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.18
Consensus pattern (7 bp):
AATAAAA
Found at i:88864 original size:19 final size:19
Alignment explanation
Indices: 88811--88908 Score: 82
Period size: 19 Copynumber: 5.3 Consensus size: 19
88801 ATATAAAAAA
*
88811 ATAAAAAATAAAAAATAA-
1 ATAAAAAATAAATAATAAC
* *
88829 ATAACAACATATA-AATAAC
1 ATAA-AAAATAAATAATAAC
88848 ATAAAAAATAAATAATAAC
1 ATAAAAAATAAATAATAAC
88867 AT--AAAATAACATAAATAAC
1 ATAAAAAATAA-AT-AATAAC
* *
88886 AT-ACAAATAAATAAAAAC
1 ATAAAAAATAAATAATAAC
88904 A-AAAA
1 ATAAAA
88909 GGATAACAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
17 7 0.11
18 25 0.38
19 28 0.42
20 6 0.09
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.18
Consensus pattern (19 bp):
ATAAAAAATAAATAATAAC
Found at i:88865 original size:37 final size:37
Alignment explanation
Indices: 88794--88908 Score: 130
Period size: 37 Copynumber: 3.2 Consensus size: 37
88784 CATATAAATG
* *
88794 ATAAAACATATAAA-AAAATAAAAAATAAAAAATAA-
1 ATAAAACATATAAATAACATAAAAAATAAATAATAAC
88829 ATAACAACATATAAATAACATAAAAAATAAATAATAAC
1 ATAA-AACATATAAATAACATAAAAAATAAATAATAAC
* * * *
88867 ATAAAATAACATAAATAACAT-ACAAATAAATAAAAAC
1 ATAAAA-CATATAAATAACATAAAAAATAAATAATAAC
88904 A-AAAA
1 ATAAAA
88909 GGATAACAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
35 4 0.06
36 14 0.20
37 36 0.51
38 16 0.23
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (37 bp):
ATAAAACATATAAATAACATAAAAAATAAATAATAAC
Found at i:88873 original size:29 final size:30
Alignment explanation
Indices: 88811--88881 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
88801 ATATAAAAAA
88811 ATAAA-AA-ATAAAAAATAAATAACAACAT
1 ATAAATAACATAAAAAATAAATAACAACAT
*
88839 ATAAATAACATAAAAAATAAATAATAACAT
1 ATAAATAACATAAAAAATAAATAACAACAT
88869 A-AAATAACATAAA
1 ATAAATAACATAAA
88882 TAACATACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 5 0.12
29 14 0.35
30 21 0.52
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (30 bp):
ATAAATAACATAAAAAATAAATAACAACAT
Found at i:88915 original size:49 final size:50
Alignment explanation
Indices: 88835--88956 Score: 115
Period size: 49 Copynumber: 2.4 Consensus size: 50
88825 ATAAATAACA
* * *
88835 ACATATAAATAACATAAAAAATAAATAATAAC-ATAAAATAACATAAATA
1 ACATACAAATAACATAAAAAAAAAAGAATAACAATAAAATAACATAAATA
* *
88884 ACATACAAATAA-ATAAAAACAAAAAGGATAACAAATAAAAAAACA-AAATA
1 ACATACAAATAACATAAAAA-AAAAAGAATAAC-AATAAAATAACATAAATA
*
88934 TACAAAAACATAATAACATAAAA
1 -AC--ATACA-AATAACATAAAA
88957 CAATAAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
48 7 0.12
49 20 0.34
50 5 0.08
51 12 0.20
53 4 0.07
54 5 0.08
55 6 0.10
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.17
Consensus pattern (50 bp):
ACATACAAATAACATAAAAAAAAAAGAATAACAATAAAATAACATAAATA
Found at i:88920 original size:37 final size:37
Alignment explanation
Indices: 88841--88985 Score: 95
Period size: 37 Copynumber: 3.9 Consensus size: 37
88831 AACAACATAT
* *
88841 AAATAACATAAAAAATAAATAATAACATAAAATAACA
1 AAATAACATAAAAAATAAATAAAAACAAAAAATAACA
*
88878 TAAATAACAT-ACAAATAAATAAAAACAAAAAGGATAAC-
1 -AAATAACATAAAAAATAAATAAAAACAAAAA--ATAACA
* * * * *
88916 AAATAAAAAAACAAAATATACAAAAAC--ATAATAACA
1 AAATAACATAA-AAAATAAATAAAAACAAAAAATAACA
* * *
88952 TAA-AACA-ATAAAATAATTAAAAACAGGAAAAATA
1 AAATAACATAAAAAATAAATAAAAACA--AAAAATA
88986 GATAACAAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
33 12 0.15
34 1 0.01
35 8 0.10
36 2 0.02
37 32 0.39
38 10 0.12
39 17 0.21
ACGTcount: A:0.72, C:0.09, G:0.03, T:0.17
Consensus pattern (37 bp):
AAATAACATAAAAAATAAATAAAAACAAAAAATAACA
Found at i:88940 original size:15 final size:14
Alignment explanation
Indices: 88916--88959 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
88906 AAAGGATAAC
88916 AAATAA-AAAAACA
1 AAATAACAAAAACA
88929 AAATATACAAAAACA
1 AAATA-ACAAAAACA
*
88944 TAATAACATAAAACA
1 AAATAACA-AAAACA
88959 A
1 A
88960 TAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 17 0.65
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATAACAAAAACA
Found at i:89260 original size:21 final size:21
Alignment explanation
Indices: 89213--89262 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
89203 AAAAAATGTA
*
89213 AGGAGTCAAGAATAGAAGATG
1 AGGAGTCAAGAACAGAAGATG
* * * *
89234 ATGAGTCGAGAACAGTAGTTG
1 AGGAGTCAAGAACAGAAGATG
89255 AGGAGTCA
1 AGGAGTCA
89263 TCTAGAGTAG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.08, G:0.34, T:0.18
Consensus pattern (21 bp):
AGGAGTCAAGAACAGAAGATG
Found at i:89315 original size:21 final size:21
Alignment explanation
Indices: 89270--89317 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
89260 TCATCTAGAG
* * *
89270 TAGATGAGGAATAAATAATAG
1 TAGATGAGGAATAAAGAACAA
*
89291 TAGATGAGGAGTAAAGAACAA
1 TAGATGAGGAATAAAGAACAA
89312 TAGATG
1 TAGATG
89318 TCTAGATGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.27, T:0.21
Consensus pattern (21 bp):
TAGATGAGGAATAAAGAACAA
Found at i:89986 original size:11 final size:11
Alignment explanation
Indices: 89972--90026 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
89962 TATATAAACA
89972 ATATAGTTTAT
1 ATATAGTTTAT
*
89983 ATATAGTTCAT
1 ATATAGTTTAT
89994 ATATAGTTTAT
1 ATATAGTTTAT
**
90005 ATATA-AAT-T
1 ATATAGTTTAT
90014 ATATAGTTTAT
1 ATATAGTTTAT
90025 AT
1 AT
90027 TAATAAACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 28 0.78
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (11 bp):
ATATAGTTTAT
Found at i:89986 original size:22 final size:22
Alignment explanation
Indices: 89961--90052 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
89951 GTTATACATA
89961 ATATATAAACAATATAGTTTAT
1 ATATATAAACAATATAGTTTAT
*
89983 ATATAGT--TCATATATAG-TT-T
1 ATATA-TAAACA-ATATAGTTTAT
**
90003 ATATATAAATTATATAGTTTAT
1 ATATATAAACAATATAGTTTAT
* *
90025 AT-TAATAAACTATATA-TATAT
1 ATAT-ATAAACAATATAGTTTAT
90046 ATATATA
1 ATATATA
90053 TAATATGTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
19 1 0.02
20 12 0.21
21 16 0.29
22 26 0.46
23 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATATAAACAATATAGTTTAT
Found at i:89997 original size:2 final size:2
Alignment explanation
Indices: 89992--90148 Score: 58
Period size: 2 Copynumber: 83.0 Consensus size: 2
89982 TATATAGTTC
* * * *
89992 AT AT AT AGT TT AT AT AT AA AT -T AT AT AGT TT AT AT -T A- AT AA
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
90033 ACT AT AT AT AT AT AT AT AT AT A- AT AT GT A- AT -T AT AC AT -T
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
90072 AT ACT -T AT A- AT AT A- AGT AT AT CAT AT A- AT AC AT -T GT ACT
1 AT A-T AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT A-T
*
90111 -T AT A- AT AT AT AC A- AT AT -T 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
90149 TAAAATTGTT
Statistics
Matches: 116, Mismatches: 16, Indels: 46
0.65 0.09 0.26
Matches are distributed among these distances:
1 16 0.14
2 92 0.79
3 8 0.07
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:90358 original size:33 final size:33
Alignment explanation
Indices: 90320--90432 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 33
90310 GTCCTTAAAG
90320 TTATATTTGTATATGAAATTGGCCCATACTTAT
1 TTATATTTGTATATGAAATTGGCCCATACTTAT
* * * * * *
90353 TTATATTTTTGTGATTTACTTCAATTTAGTCCTTAC-AAT
1 TTATA--TTTGT-A--TA--TGAAATTGGCCCATACTTAT
*
90392 TTATATTTGTATATGAAATTGTCCCATACTTAT
1 TTATATTTGTATATGAAATTGGCCCATACTTAT
90425 TTATATTT
1 TTATATTT
90433 CGATTTGATC
Statistics
Matches: 59, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
32 10 0.17
33 15 0.25
34 2 0.03
35 5 0.08
36 2 0.03
37 5 0.08
38 2 0.03
39 7 0.12
40 11 0.19
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (33 bp):
TTATATTTGTATATGAAATTGGCCCATACTTAT
Found at i:91512 original size:47 final size:46
Alignment explanation
Indices: 91428--91577 Score: 175
Period size: 43 Copynumber: 3.3 Consensus size: 46
91418 AGTTCTATTT
* * * *
91428 AATATATACATA-ACATATATA-ATATATAATTTCGAAAACATTTCTG
1 AATATATATATATATATATATATA-ATATAGTTTTGAAAACATTT-TG
91474 AATATATATATATATATATATATAATATAGTTTTGAAAACATTTT-
1 AATATATATATATATATATATATAATATAGTTTTGAAAACATTTTG
* *
91519 -AGA-ATATATATATATATATATAATATAGTTTTAAAAACATTTTTG
1 AATATATATATATATATATATATAATATAGTTTTGAAAACA-TTTTG
*
91564 AAAATATATATATA
1 AATATATATATATA
91578 GTTTTAAAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
43 35 0.38
44 6 0.07
46 14 0.15
47 35 0.38
48 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (46 bp):
AATATATATATATATATATATATAATATAGTTTTGAAAACATTTTG
Found at i:91530 original size:37 final size:37
Alignment explanation
Indices: 91487--91662 Score: 170
Period size: 37 Copynumber: 4.7 Consensus size: 37
91477 ATATATATAT
* *
91487 ATATATATATAATATAGTTTTGAAAACATTTTAGAATATATA
1 ATATATATATAATATAGTTTTAAAAACATTTT----TAGA-A
91529 TATATATATATAATATAGTTTTAAAAACATTTTT-G-A
1 -ATATATATATAATATAGTTTTAAAAACATTTTTAGAA
*
91565 A-A-ATATAT-ATATAGTTTTAAAAACATTTTTCAAAA
1 ATATATATATAATATAGTTTTAAAAACATTTTT-AGAA
*
91600 ATATATATA-ATATATAGTTTT-AAAACATTTTTTTGAA
1 ATATATATATA-ATATAGTTTTAAAAACA-TTTTTAGAA
91637 ATATATATGAT-ATATAGTTTTAAAAA
1 ATATATAT-ATAATATAGTTTTAAAAA
91663 ATGATTTATA
Statistics
Matches: 117, Mismatches: 5, Indels: 27
0.79 0.03 0.18
Matches are distributed among these distances:
32 22 0.19
33 6 0.05
34 1 0.01
35 3 0.03
36 2 0.02
37 31 0.26
38 20 0.17
39 1 0.01
43 31 0.26
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATATATATAATATAGTTTTAAAAACATTTTTAGAA
Found at i:92202 original size:17 final size:19
Alignment explanation
Indices: 92182--92216 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
92172 ACCAAACTAC
92182 CAAAGC-AAC-CAAGCAAA
1 CAAAGCAAACACAAGCAAA
92199 CAAAGCAAACACAAGCAA
1 CAAAGCAAACACAAGCAA
92217 TCGAAACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.60, C:0.29, G:0.11, T:0.00
Consensus pattern (19 bp):
CAAAGCAAACACAAGCAAA
Found at i:93230 original size:12 final size:12
Alignment explanation
Indices: 93213--93239 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
93203 GAATTGAATT
93213 TTTAAATTTCAA
1 TTTAAATTTCAA
93225 TTTAAATTTCAA
1 TTTAAATTTCAA
93237 TTT
1 TTT
93240 TCGCAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:93747 original size:68 final size:68
Alignment explanation
Indices: 93638--93769 Score: 246
Period size: 68 Copynumber: 1.9 Consensus size: 68
93628 ATAGTTTTGT
*
93638 GTGAATTTATTCTCTGTATAGACATTAGGGAATATATCCTCTCGAGTTTAACTTAGTCCACATGT
1 GTGAATTTATTCTCTGTATAGACATAAGGGAATATATCCTCTCGAGTTTAACTTAGTCCACATGT
93703 TAC
66 TAC
*
93706 GTGAATTTATTCTCTGTATAGACATAAGGGAATGTATCCTCTCGAGTTTAACTTAGTCCACATG
1 GTGAATTTATTCTCTGTATAGACATAAGGGAATATATCCTCTCGAGTTTAACTTAGTCCACATG
93770 AGCTTGTAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (68 bp):
GTGAATTTATTCTCTGTATAGACATAAGGGAATATATCCTCTCGAGTTTAACTTAGTCCACATGT
TAC
Found at i:94136 original size:16 final size:15
Alignment explanation
Indices: 94093--94136 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
94083 TCTCACTAAC
*
94093 TTTTTTTCCTTTTAT
1 TTTTTTTCATTTTAT
*
94108 TTTTGTTTTATTTTAT
1 TTTT-TTTCATTTTAT
94124 TTTTTTATCATTT
1 TTTTTT-TCATTT
94137 ACATCATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTCATTTTAT
Found at i:95331 original size:19 final size:19
Alignment explanation
Indices: 95307--95358 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
95297 TGCTTTTTAG
95307 AATTTATAATTTAATCATT
1 AATTTATAATTTAATCATT
* * * *
95326 AATTTAGAATGTAAACTTT
1 AATTTATAATTTAATCATT
*
95345 AATTT-TTATTTAAT
1 AATTTATAATTTAAT
95359 TTACTCCTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (19 bp):
AATTTATAATTTAATCATT
Found at i:96338 original size:17 final size:17
Alignment explanation
Indices: 96318--96351 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
96308 ATACTATTCA
96318 ATTAGGCATATTTTCTT
1 ATTAGGCATATTTTCTT
* *
96335 ATTAGTCATCTTTTCTT
1 ATTAGGCATATTTTCTT
96352 TGAACGACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTAGGCATATTTTCTT
Found at i:97189 original size:13 final size:13
Alignment explanation
Indices: 97171--97231 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
97161 TGCGTCATAA
**
97171 ATTTATGATGCGC
1 ATTTATGACACGC
97184 ATTTATGACACGC
1 ATTTATGACACGC
*
97197 ATTTATGACACAC
1 ATTTATGACACGC
**
97210 ATTTATGATGCGC
1 ATTTATGACACGC
97223 ATTTATGAC
1 ATTTATGAC
97232 GTTCATTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:113387 original size:18 final size:18
Alignment explanation
Indices: 113364--113415 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
113354 GAGGGTCTAC
*
113364 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGGACACA
*
113382 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCAGGACACA
113400 GTGGTCCTTCAGGACA
1 GTGGTCCTTCAGGACA
113416 AATTCTACGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (18 bp):
GTGGTCCTTCAGGACACA
Found at i:113612 original size:7 final size:7
Alignment explanation
Indices: 113573--113609 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
113563 GTGAAATGGT
113573 ATATGTG
1 ATATGTG
113580 ATATGTG
1 ATATGTG
113587 ATATGTG
1 ATATGTG
113594 ATATGT-
1 ATATGTG
*
113600 ATAAGTG
1 ATATGTG
113607 ATA
1 ATA
113610 AGTTAGGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (7 bp):
ATATGTG
Found at i:118774 original size:43 final size:43
Alignment explanation
Indices: 118726--118808 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
118716 TTTTAATTTC
*
118726 ACTTTCTACATTAATAATTGAG-GTCCTTAATTTTTTCAATCCT
1 ACTTTCTACATTAATAATTGAGACTCC-TAATTTTTTCAATCCT
*
118769 ACTTTCTACATTTATAATTGAGACTCCTAATTTTTTCAAT
1 ACTTTCTACATTAATAATTGAGACTCCTAATTTTTTCAAT
118809 TTCATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 34 0.92
44 3 0.08
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (43 bp):
ACTTTCTACATTAATAATTGAGACTCCTAATTTTTTCAATCCT
Found at i:119625 original size:9 final size:8
Alignment explanation
Indices: 119609--119685 Score: 79
Period size: 9 Copynumber: 9.5 Consensus size: 8
119599 TTGTCTGTTT
119609 TTATTAT-
1 TTATTATA
*
119616 TAATTATA
1 TTATTATA
119624 TTATT-TA
1 TTATTATA
119631 TTATTATTA
1 TTATTA-TA
119640 TTATTATTA
1 TTATTA-TA
119649 TTATTATTA
1 TTATTA-TA
119658 TTATTATA
1 TTATTATA
*
119666 TTA-CATA
1 TTATTATA
119673 TTTATTATA
1 -TTATTATA
119682 TTAT
1 TTAT
119686 ATTTGCATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
7 16 0.26
8 16 0.26
9 29 0.48
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATTATA
Found at i:119627 original size:12 final size:11
Alignment explanation
Indices: 119609--119688 Score: 78
Period size: 12 Copynumber: 7.2 Consensus size: 11
119599 TTGTCTGTTT
119609 TTATTATTA-A
1 TTATTATTATA
119619 TTA-TATTATTTA
1 TTATTATTA--TA
119631 TTATTATTATTA
1 TTATTATTA-TA
119643 TTATTATTATTA
1 TTATTATTA-TA
119655 TTATTATTATA
1 TTATTATTATA
*
119666 TTACATATT-TA
1 TTA-TTATTATA
119677 TTA-TATTATA
1 TTATTATTATA
119687 TT
1 TT
119689 TGCATTTACA
Statistics
Matches: 63, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
9 9 0.14
10 7 0.11
11 10 0.16
12 32 0.51
13 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATTATTATA
Found at i:119680 original size:3 final size:3
Alignment explanation
Indices: 119609--119668 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
119599 TTGTCTGTTT
119609 TTA TTA TTAA TTA -TA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
119655 TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA
119669 CATATTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:121077 original size:20 final size:20
Alignment explanation
Indices: 121054--121119 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
121044 TTGTAAATCC
121054 TTCGGGTCATCTGTAAGTCT
1 TTCGGGTCATCTGTAAGTCT
* * * *
121074 TTCGAG-CATGATGCTTAAATCC
1 TTCGGGTCAT-CTG--TAAGTCT
*
121096 TTCGGGTCATCTGTCAGTCT
1 TTCGGGTCATCTGTAAGTCT
121116 TTCG
1 TTCG
121120 AGCTAGGTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
22 12 0.36
23 3 0.09
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
TTCGGGTCATCTGTAAGTCT
Found at i:125413 original size:65 final size:65
Alignment explanation
Indices: 125306--125438 Score: 171
Period size: 65 Copynumber: 2.0 Consensus size: 65
125296 AACCTTGTTC
* * *
125306 GAGATCTGATTAGATGTGGAGATGTGAAACGAATTAGAATAAATCCTTTTTGTGA-GTTATTTCA
1 GAGATCTGATTAGATGTGGAGATATGAAACGAACTAGAATAAATCCTTCTTGTGATG-TATTTCA
125370 A
65 A
* * * *
125371 GAGATCTGATTAGATGTGGAG-TCATGAAAGGGACTAGGATAAATCCTTCTTGTGATGTGTTTCA
1 GAGATCTGATTAGATGTGGAGAT-ATGAAACGAACTAGAATAAATCCTTCTTGTGATGTATTTCA
125435 A
65 A
125436 GAG
1 GAG
125439 TTAAATCAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 1 0.02
65 57 0.97
66 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (65 bp):
GAGATCTGATTAGATGTGGAGATATGAAACGAACTAGAATAAATCCTTCTTGTGATGTATTTCAA
Found at i:125541 original size:22 final size:22
Alignment explanation
Indices: 125516--125564 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
125506 ATTATGAAAG
*
125516 GATGATAGATTCTCTTTTCAAA
1 GATGATAAATTCTCTTTTCAAA
125538 GATGATAAATTCTCTTTTCAAA
1 GATGATAAATTCTCTTTTCAAA
125560 GATGA
1 GATGA
125565 AAGCTTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
GATGATAAATTCTCTTTTCAAA
Found at i:126185 original size:20 final size:20
Alignment explanation
Indices: 126162--126227 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
126152 TTGTAAATCC
126162 TTCGGGTCATCTGTAAGTCT
1 TTCGGGTCATCTGTAAGTCT
* * * *
126182 TTCGAG-CATGATGCTTAAATCC
1 TTCGGGTCAT-CTG--TAAGTCT
*
126204 TTCGGGTCATCTGTCAGTCT
1 TTCGGGTCATCTGTAAGTCT
126224 TTCG
1 TTCG
126228 AGCTAGGTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
22 12 0.36
23 3 0.09
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
TTCGGGTCATCTGTAAGTCT
Found at i:126723 original size:12 final size:11
Alignment explanation
Indices: 126696--126755 Score: 61
Period size: 12 Copynumber: 5.4 Consensus size: 11
126686 TGTCCGTTTT
*
126696 TATTATTAACTA
1 TATTATT-ATTA
126708 TATTATTATTA
1 TATTATTATTA
126719 TTATTATTATTA
1 -TATTATTATTA
*
126731 TATTACATATT-
1 TATTA-TTATTA
126742 TATTA-TATTA
1 TATTATTATTA
126752 TATT
1 TATT
126756 TGCATTTACA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 4 0.09
10 4 0.09
11 13 0.30
12 22 0.51
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTATTA
Found at i:126747 original size:3 final size:3
Alignment explanation
Indices: 126695--126735 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
126685 TTGTCCGTTT
*
126695 TTA TTA TTAA CTA -TA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
126736 CATATTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
2 4 0.12
3 28 0.82
4 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:128083 original size:18 final size:17
Alignment explanation
Indices: 128052--128089 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
128042 ATTTTAAGAC
*
128052 TAATTATAATATTAGTA
1 TAATTATAATATTAGGA
128069 TAATTATATATATTAGGA
1 TAATTATA-ATATTAGGA
128087 TAA
1 TAA
128090 CTTTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TAATTATAATATTAGGA
Found at i:131111 original size:25 final size:24
Alignment explanation
Indices: 131077--131127 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
131067 ATATTTGTAA
131077 GAGTTGCCCCCTAAAGTATTTTTC
1 GAGTTGCCCCCTAAAGTATTTTTC
131101 GAGTTGCCCCCTAAAGTATTTTTC
1 GAGTTGCCCCCTAAAGTATTTTTC
131125 GAG
1 GAG
131128 ACGTTTTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (24 bp):
GAGTTGCCCCCTAAAGTATTTTTC
Found at i:149992 original size:20 final size:19
Alignment explanation
Indices: 149968--150029 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
149958 AAAGAAGGGG
149968 AGAAGAAAGAAGAGAAAAGA
1 AGAAGAAAGAAGA-AAAAGA
* *
149988 GGAAGAAAGAAAAAAAAAGA
1 AGAAGAAAG-AAGAAAAAGA
* *
150008 AAAAAAAAGAAGAAAAAGA
1 AGAAGAAAGAAGAAAAAGA
150027 AGA
1 AGA
150030 GAATAATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 11 0.32
20 20 0.59
21 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AGAAGAAAGAAGAAAAAGA
Found at i:149996 original size:10 final size:10
Alignment explanation
Indices: 149968--150029 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
149958 AAAGAAGGGG
149968 AGAAGAAAGA
1 AGAAGAAAGA
149978 AG-AGAAAAGA
1 AGAAG-AAAGA
*
149988 GGAAGAAAGA
1 AGAAGAAAGA
* *
149998 AAAAAAAAGA
1 AGAAGAAAGA
* *
150008 AAAAAAAAGA
1 AGAAGAAAGA
150018 AGAA-AAAGA
1 AGAAGAAAGA
150027 AGA
1 AGA
150030 GAATAATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
9 10 0.22
10 33 0.73
11 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (10 bp):
AGAAGAAAGA
Found at i:150015 original size:13 final size:13
Alignment explanation
Indices: 149990--150024 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
149980 AGAAAAGAGG
149990 AAGAAAGAAAAAAA
1 AAGAAA-AAAAAAA
*
150004 AAGAAAAAAAAAG
1 AAGAAAAAAAAAA
150017 AAGAAAAA
1 AAGAAAAA
150025 GAAGAGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAAA
Found at i:150402 original size:18 final size:17
Alignment explanation
Indices: 150369--150402 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
150359 TTATTTTTTG
*
150369 ATTAAATTAATGTTTAT
1 ATTAAATTAATCTTTAT
150386 ATTAAATGTAATCTTTA
1 ATTAAAT-TAATCTTTA
150403 AATTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTAAATTAATCTTTAT
Found at i:151497 original size:20 final size:20
Alignment explanation
Indices: 151474--151647 Score: 96
Period size: 20 Copynumber: 8.7 Consensus size: 20
151464 AAAATGCAGA
151474 AATTATTATAAAATAAAGTT
1 AATTATTATAAAATAAAGTT
* *
151494 AATTACTAT---AT--A-TA
1 AATTATTATAAAATAAAGTT
*
151508 AATTATTATAAAATCAAGTT
1 AATTATTATAAAATAAAGTT
*
151528 AATTATTATAAAATCAAATATATACAT
1 AATTATTATAAAAT--AA-A-GT---T
*
151555 AAATTATTATAAAATCAAGTT
1 -AATTATTATAAAATAAAGTT
*
151576 AATTATTATAAAATTAAA-TC
1 AATTATTATAAAA-TAAAGTT
* * *
151596 AATTA-TATACATATACA-TG
1 AATTATTATA-AAATAAAGTT
*
151615 AATTATTATAAAATCAAGTT
1 AATTATTATAAAATAAAGTT
*
151635 AGTTATTATAAAA
1 AATTATTATAAAA
151648 AATTCAAATG
Statistics
Matches: 118, Mismatches: 18, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
17 4 0.03
19 18 0.15
20 61 0.52
21 4 0.03
22 1 0.01
23 1 0.01
24 2 0.02
25 1 0.01
26 1 0.01
27 1 0.01
28 14 0.12
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.39
Consensus pattern (20 bp):
AATTATTATAAAATAAAGTT
Found at i:151511 original size:34 final size:34
Alignment explanation
Indices: 151473--151537 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
151463 AAAAATGCAG
151473 AAATTATTATAAAATAAAGTTAATTACTATATAT
1 AAATTATTATAAAATAAAGTTAATTACTATATAT
* *
151507 AAATTATTATAAAATCAAGTTAATTATTATA
1 AAATTATTATAAAATAAAGTTAATTACTATA
151538 AAATCAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (34 bp):
AAATTATTATAAAATAAAGTTAATTACTATATAT
Found at i:151562 original size:48 final size:48
Alignment explanation
Indices: 151500--151594 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
151490 AGTTAATTAC
*
151500 TATATATAAATTATTATAAAATCAAGTTAATTATTATAAAATCAAATA
1 TATACATAAATTATTATAAAATCAAGTTAATTATTATAAAATCAAATA
*
151548 TATACATAAATTATTATAAAATCAAGTTAATTATTATAAAATTAAAT
1 TATACATAAATTATTATAAAATCAAGTTAATTATTATAAAATCAAAT
151595 CAATTATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (48 bp):
TATACATAAATTATTATAAAATCAAGTTAATTATTATAAAATCAAATA
Found at i:153038 original size:2 final size:2
Alignment explanation
Indices: 153031--153059 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
153021 TCATAAATTT
153031 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
153060 GATTGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:154844 original size:23 final size:24
Alignment explanation
Indices: 154813--154868 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
154803 ATCTCCGTTC
154813 ACACGTTTTTTCCCAA-CAATGCCA
1 ACAC-TTTTTTCCCAATCAATGCCA
*
154837 ACAC-TTTTTCCTAATCAATGCCA
1 ACACTTTTTTCCCAATCAATGCCA
154860 ACACTTTTT
1 ACACTTTTT
154869 CCTACAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 9 0.31
23 12 0.41
24 8 0.28
ACGTcount: A:0.29, C:0.30, G:0.05, T:0.36
Consensus pattern (24 bp):
ACACTTTTTTCCCAATCAATGCCA
Found at i:154869 original size:23 final size:22
Alignment explanation
Indices: 154819--154876 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 22
154809 GTTCACACGT
*
154819 TTTTTCCCAACAATGCCAACAC
1 TTTTTCCTAACAATGCCAACAC
154841 TTTTTCCTAATCAATGCCAACAC
1 TTTTTCCTAA-CAATGCCAACAC
154864 TTTTTCCT-ACAAT
1 TTTTTCCTAACAAT
154877 AAAATATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 4 0.12
22 10 0.29
23 20 0.59
ACGTcount: A:0.29, C:0.31, G:0.03, T:0.36
Consensus pattern (22 bp):
TTTTTCCTAACAATGCCAACAC
Found at i:165375 original size:37 final size:37
Alignment explanation
Indices: 165329--165440 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
165319 AATATAACGT
* *
165329 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
165366 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
165403 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
165440 T
1 T
165441 CCACAAGCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:166033 original size:44 final size:43
Alignment explanation
Indices: 165985--166084 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 43
165975 TTAGATTACA
165985 TATATATATATATATG-TTAAT-TTTTATTATCTGTTTTATTAATT
1 TATATATATATATATGTTTAATATTTT-TTATCT-TTTTATTAA-T
* * *
166029 TATATATATATATATGTTTACTATTTTTTATGTTTTTATTTAT
1 TATATATATATATATGTTTAATATTTTTTATCTTTTTATTAAT
166072 TATATATATATAT
1 TATATATATATAT
166085 TTATTATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
43 14 0.27
44 24 0.47
45 9 0.18
46 4 0.08
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (43 bp):
TATATATATATATATGTTTAATATTTTTTATCTTTTTATTAAT
Found at i:166197 original size:23 final size:23
Alignment explanation
Indices: 166148--166197 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
166138 TGTTTTCTTC
* **
166148 TTTTTTCTTTATTTTTTTAATAT
1 TTTTTTATTTATTTTACTAATAT
166171 TTTTTTATTTATTTTACTAACTAT
1 TTTTTTATTTATTTTACTAA-TAT
166195 TTT
1 TTT
166198 ATATTTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTATTTATTTTACTAATAT
Found at i:169293 original size:13 final size:13
Alignment explanation
Indices: 169262--169310 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
169252 CAATCAGAAC
*
169262 AAAAATAGAAAAT
1 AAAAAGAGAAAAT
169275 --AAAGAGAAAAT
1 AAAAAGAGAAAAT
169286 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
169298 AACAAAG-GAAAAT
1 AA-AAAGAGAAAAT
169311 TGAAGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.32
12 7 0.23
13 14 0.45
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:169499 original size:68 final size:69
Alignment explanation
Indices: 169382--169518 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 69
169372 GATTCAAACT
* *
169382 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGAT-ATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACCGAACCACTCCACTCGAAGATCATAGAGCA
169446 TCAA
66 TCAA
*
169450 ATGAGATTGATCAAGCACAATCATTTCTGAATCACCGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACCGAACCACTCCACTCGAAGATCATAGAGCA
169515 TCAA
66 TCAA
169519 GAGAGAGACA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 53 0.82
69 12 0.18
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACCGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:170475 original size:32 final size:32
Alignment explanation
Indices: 170439--170545 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
170429 GGAACACTGA
*
170439 GGGCATCTTTGAAGATTCAACATCAAAT-TCTG
1 GGGCATCTTTGTAGATTCAACATCAAATAT-TG
* * * *
170471 GGGCATTTTTTTAGATTTAACATCAAATGTTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
* * * * *
170503 GGCCATTTTTTTAGATTCATCATCGAATATTG
1 GGGCATCTTTGTAGATTCAACATCAAATATTG
170535 GGGCATCTTTG
1 GGGCATCTTTG
170546 GGAATTCAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
32 61 0.98
33 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (32 bp):
GGGCATCTTTGTAGATTCAACATCAAATATTG
Found at i:171796 original size:37 final size:37
Alignment explanation
Indices: 171746--171852 Score: 175
Period size: 34 Copynumber: 3.0 Consensus size: 37
171736 TTTCCAAGTT
171746 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
* *
171783 TTGTCTCTCTTGAGATAGTTTCCCTTG--A-AAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
171817 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
171853 ATTTGAATCT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
34 31 0.48
35 1 0.02
36 1 0.02
37 31 0.48
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
Found at i:171941 original size:21 final size:21
Alignment explanation
Indices: 171917--171957 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
171907 TGGAACTAAG
171917 TTTTGTCTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAAACAAA
*
171938 TTTTGTCTCTCTTGAGACAA
1 TTTTGTCTCTCTTGAAACAA
171958 TTTCTCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTTGTCTCTCTTGAAACAAA
Found at i:172046 original size:35 final size:34
Alignment explanation
Indices: 171958--172073 Score: 205
Period size: 34 Copynumber: 3.4 Consensus size: 34
171948 CTTGAGACAA
171958 TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
171992 TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
* *
172026 TTTCTCTTAAAACACAAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACAC-AAAAAAACCTTTGAAATTG
172061 TTTCTCTTGAAAC
1 TTTCTCTTGAAAC
172074 CCAAGACATT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
34 48 0.62
35 30 0.38
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (34 bp):
TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
Found at i:172709 original size:36 final size:36
Alignment explanation
Indices: 172663--172771 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
172653 AACATAACGT
* *
172663 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGG
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGG
172699 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGG
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGG
*
172735 -ATGAAGTTCTACTATGATTCAAACTCCTAAAAATAGG
1 TA-G-AGTTTTACTATGATTCAAACTCCTAAAAATAGG
172772 ATCCACAAGC
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 1 0.01
36 35 0.51
37 32 0.47
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (36 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGG
Found at i:172757 original size:37 final size:37
Alignment explanation
Indices: 172671--172773 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
172661 GTTAGAATTT
* *
172671 TACTAGGATTCAAACTCCTAAAAATAGG-TAGAGTTT
1 TACTATGATTCAAACTCCTAAAAATAGGATAGAGTTC
172707 TACTATGATTCAAACTCCTAAAAATAGGAT-GAAGTTC
1 TACTATGATTCAAACTCCTAAAAATAGGATAG-AGTTC
172744 TACTATGATTCAAACTCCTAAAAATAGGAT
1 TACTATGATTCAAACTCCTAAAAATAGGAT
172774 CCACAAGCAT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
36 28 0.44
37 35 0.56
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (37 bp):
TACTATGATTCAAACTCCTAAAAATAGGATAGAGTTC
Found at i:173397 original size:42 final size:42
Alignment explanation
Indices: 173351--173458 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 42
173341 TATTATCTGT
173351 TTTATTAATTTATATATATATTTAC--TATTTTTTA-TGTTTTTA
1 TTTATT-ATTTATATATATATTTACATTA-TTTTTACT-TTTTTA
* *
173393 TTTATTATATATATATATATATACATTATTTTTACTTTTTTA
1 TTTATTATTTATATATATATTTACATTATTTTTACTTTTTTA
* *
173435 TTTATTTGTTTTATTTATATATTT
1 TTTA-TT-ATTTATATATATATTT
173459 TTTTCTTCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
41 16 0.29
42 22 0.40
43 5 0.09
44 12 0.22
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (42 bp):
TTTATTATTTATATATATATTTACATTATTTTTACTTTTTTA
Found at i:173457 original size:17 final size:16
Alignment explanation
Indices: 173431--173499 Score: 52
Period size: 17 Copynumber: 4.3 Consensus size: 16
173421 TTTTTACTTT
*
173431 TTTATTTATTTGTTTTA
1 TTTATATATTT-TTTTA
*
173448 TTTATATATTTTTTTC
1 TTTATATATTTTTTTA
* * * *
173464 TTCTTTTTCTTTATTT-
1 TT-TATATATTTTTTTA
173480 TTTA-ATATTTTTTTA
1 TTTATATATTTTTTTA
173495 TTTAT
1 TTTAT
173500 TTTACTTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
14 7 0.18
15 5 0.13
16 8 0.21
17 19 0.49
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTATATATTTTTTTA
Found at i:173492 original size:22 final size:23
Alignment explanation
Indices: 173467--173514 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
173457 TTTTTTCTTC
*
173467 TTTTTCTTTATTTT-TTAATATT
1 TTTTTATTTATTTTATTAATATT
173489 TTTTTATTTATTTTACTTAATATT
1 TTTTTATTTATTTTA-TTAATATT
173513 TT
1 TT
173515 ATATTTGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTATTTATTTTATTAATATT
Found at i:173519 original size:31 final size:29
Alignment explanation
Indices: 173419--173520 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 29
173409 ATATATACAT
*
173419 TATTTT-TACTTTTTTATTTATTTGT-TT-
1 TATTTTATATTTTTTTATTTATTT-TCTTA
*
173446 TATTTATATATTTTTTTCTTCT-TTTTCTTTA
1 TATTT-TATATTTTTTTATT-TATTTTC-TTA
*
173477 TTTTTTAATATTTTTTTATTTATTTTACTTAA
1 TATTTT-ATATTTTTTTATTTATTTT-CTT-A
173509 TATTTTATATTT
1 TATTTTATATTT
173521 GCTTTCTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
27 5 0.08
28 2 0.03
29 13 0.22
30 5 0.08
31 28 0.47
32 7 0.12
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.75
Consensus pattern (29 bp):
TATTTTATATTTTTTTATTTATTTTCTTA
Found at i:173590 original size:31 final size:32
Alignment explanation
Indices: 173542--173601 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
173532 CTTATCTTTT
*
173542 ATTTAATTTGTTTTTTCTT-CATTTTAATTTA
1 ATTTAATTTATTTTTTCTTACATTTTAATTTA
*
173573 ATTT-ATTTATTTATTTCTTACCTTTTAAT
1 ATTTAATTTATTT-TTTCTTACATTTTAAT
173602 CTAACACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 10 0.40
32 8 0.32
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (32 bp):
ATTTAATTTATTTTTTCTTACATTTTAATTTA
Found at i:180433 original size:20 final size:20
Alignment explanation
Indices: 180390--180458 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
180380 CCGACTTTAA
*
180390 CTTTCTTCTCTTCTTCTTCTTT
1 CTTTCTCCT-TTC-TCTTCTTT
*
180412 CTTTCTCCTTTCTCTTCGTT
1 CTTTCTCCTTTCTCTTCTTT
* *
180432 CTTCCTCTTTTCTCTTCTTT
1 CTTTCTCCTTTCTCTTCTTT
180452 C-TTCTCC
1 CTTTCTCC
180459 CCTTCTTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 4 0.10
20 25 0.62
21 3 0.08
22 8 0.20
ACGTcount: A:0.00, C:0.36, G:0.01, T:0.62
Consensus pattern (20 bp):
CTTTCTCCTTTCTCTTCTTT
Found at i:180761 original size:14 final size:14
Alignment explanation
Indices: 180742--180776 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
180732 CAACGCATGG
180742 TGGCATGCAGG-GAC
1 TGGCATGCAGGAG-C
180756 TGGCATGCAGGAGC
1 TGGCATGCAGGAGC
180770 TGGCATG
1 TGGCATG
180777 GAAAGTCGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 19 0.95
15 1 0.05
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.17
Consensus pattern (14 bp):
TGGCATGCAGGAGC
Found at i:182609 original size:1 final size:1
Alignment explanation
Indices: 182603--182628 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
182593 TAACCAAATT
182603 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
182629 CAAATAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:184546 original size:100 final size:101
Alignment explanation
Indices: 184373--184558 Score: 347
Period size: 100 Copynumber: 1.9 Consensus size: 101
184363 GTGGCAACAA
* *
184373 TAGTGGCGTTTTTTTGAAAAAACGTCGTAATAGGTCCATCTATAGTGGTGTTTATTGGAAAAACG
1 TAGTGGCGTTTTTTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAACG
184438 CCACTATATATATACTTTTTTGGCCCTGCACAATAC
66 CCACTATATATATACTTTTTTGGCCCTGCACAATAC
184474 TAGTGGCG-TTTTTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAACG
1 TAGTGGCGTTTTTTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAACG
184538 CCACTATATATATACTTTTTT
66 CCACTATATATATACTTTTTT
184559 AGTCCCATTT
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
100 75 0.90
101 8 0.10
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (101 bp):
TAGTGGCGTTTTTTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAACG
CCACTATATATATACTTTTTTGGCCCTGCACAATAC
Found at i:185918 original size:37 final size:37
Alignment explanation
Indices: 185856--185960 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
185846 CCTTTTCTTC
* *
185856 CTACTAGAATTCAAACTCCTGAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
185893 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
185930 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
185961 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:186574 original size:2 final size:2
Alignment explanation
Indices: 186567--186641 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
186557 GTATTATTAC
186567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
186609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
186642 TGTAATTATC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:186804 original size:33 final size:31
Alignment explanation
Indices: 186723--186811 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 31
186713 TATAAGCCAA
186723 TTATCATTATATGTATATTTTTATATTTGGTTT
1 TTAT-ATTATAT-TATATTTTTATATTTGGTTT
* * *
186756 ATATATT-TATT-TATTTTTGTTTTTGGTTTTT
1 TTATATTATATTATATTTTTATATTTGG--TTT
*
186787 TTATATTATATTATATTTTGATATT
1 TTATATTATATTATATTTTTATATT
186812 ACTATTATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
29 13 0.29
30 1 0.02
31 12 0.27
32 7 0.16
33 12 0.27
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.67
Consensus pattern (31 bp):
TTATATTATATTATATTTTTATATTTGGTTT
Found at i:186810 original size:18 final size:19
Alignment explanation
Indices: 186784--186819 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
186774 GTTTTTGGTT
*
186784 TTTTTATATTA-TATTATA
1 TTTTGATATTACTATTATA
186802 TTTTGATATTACTATTAT
1 TTTTGATATTACTATTAT
186820 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTGATATTACTATTATA
Found at i:186863 original size:2 final size:2
Alignment explanation
Indices: 186856--186884 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
186846 TTTACTCATT
186856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
186885 TAATATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:191418 original size:9 final size:8
Alignment explanation
Indices: 191391--191461 Score: 65
Period size: 8 Copynumber: 8.8 Consensus size: 8
191381 AGATCCTATC
*
191391 AAGAACAA
1 AAGAAAAA
*
191399 AA-AAGAA
1 AAGAAAAA
191406 AAGAAGAAA
1 AAGAA-AAA
*
191415 AAGAAGAA
1 AAGAAAAA
*
191423 AA-AAACA
1 AAGAAAAA
191430 AAGAAAAA
1 AAGAAAAA
191438 AGAGAAACAA
1 A-AGAAA-AA
191448 AAGAAAAA
1 AAGAAAAA
191456 AAGAAA
1 AAGAAA
191462 GAACAAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 11 0.21
8 21 0.40
9 17 0.33
10 3 0.06
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:191427 original size:12 final size:12
Alignment explanation
Indices: 191391--191483 Score: 56
Period size: 12 Copynumber: 7.9 Consensus size: 12
191381 AGATCCTATC
*
191391 AAGAACAAAAAA
1 AAGAAGAAAAAA
*
191403 GAA-AAGAAGAAA
1 -AAGAAGAAAAAA
191415 AAGAAGAAAAAA
1 AAGAAGAAAAAA
191427 ACA-AAG--AAAA
1 A-AGAAGAAAAAA
*
191437 AAG-AGAAACAA
1 AAGAAGAAAAAA
191448 AAGAA-AAAAAGA
1 AAGAAGAAAAA-A
*
191460 AAGAACAAAAATCA
1 AAGAAGAAAAA--A
191474 AA-AAGAAAAA
1 AAGAAGAAAAA
191484 GGGACAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
9 3 0.05
10 5 0.08
11 12 0.19
12 26 0.41
13 15 0.23
14 3 0.05
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (12 bp):
AAGAAGAAAAAA
Found at i:191435 original size:21 final size:19
Alignment explanation
Indices: 191391--191483 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
191381 AGATCCTATC
* * *
191391 AAGAACAAAA-AAGAAAAG
1 AAGAAAAAAAGAAAAAAAA
191409 AAGAAAAAGAAGAAAAAAACA
1 AAGAAAAA-AAGAAAAAAA-A
* *
191430 AAG-AAAAAAGAGAAACAA
1 AAGAAAAAAAGAAAAAAAA
191448 AAGAAAAAAAGAAAGAACAAA
1 AAGAAAAAAAGAAA-AA-AAA
**
191469 AA-TCAAAAAGAAAAA
1 AAGAAAAAAAGAAAAA
191484 GGGACAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
18 11 0.18
19 21 0.35
20 21 0.35
21 7 0.12
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (19 bp):
AAGAAAAAAAGAAAAAAAA
Found at i:191452 original size:30 final size:32
Alignment explanation
Indices: 191394--191469 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 32
191384 TCCTATCAAG
* *
191394 AACAAAAAAGAAAAGAAGAAAAAGAAGAAAAA
1 AACAAAGAACAAAAGAAGAAAAAGAAGAAAAA
191426 AACAAAGAA-AAAAG-AGAAACAA-AAGAAAAA
1 AACAAAGAACAAAAGAAGAAA-AAGAAGAAAAA
*
191456 AAGAAAGAACAAAA
1 AACAAAGAACAAAA
191470 ATCAAAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 21 0.52
31 11 0.28
32 8 0.20
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.00
Consensus pattern (32 bp):
AACAAAGAACAAAAGAAGAAAAAGAAGAAAAA
Found at i:193298 original size:106 final size:106
Alignment explanation
Indices: 193113--194093 Score: 1395
Period size: 106 Copynumber: 9.3 Consensus size: 106
193103 AAACAACTTC
* *
193113 CCAATTTCAACTTTACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
193178 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
*
193219 CCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
193284 GGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTTAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
* *
193325 CCAATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAATGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
193390 GGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
193431 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
193496 GGGACTGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
* * * * *
193537 CCAATTTCAACTTCACAACAAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
** *
193602 GGGATGGCTGGTTGTCAA-CAACAATTTCCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
* * * * *
193642 CGAGTTTCAACTTCGCAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGTA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
193707 GGGACTGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
*
193748 CCAATTTCAACTT-ACAGTGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
** *
193812 GGGACTACTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
* * * **
193853 CCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCCCAACTTCACGACGA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGA
* * * *
193917 AGGGGCGGCTGATTGTCAA-CAA-AATTT--C-ATTT-AGAG
65 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
* * * * * * *
193953 TCAATTTCAACTTCACAACGAAGGATATTGGAATCGAGACAACACAAGTTCAACTTCACAATGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * ** *
194018 GGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
** *
194059 CCAATTTCAACTTCACAATGGAGGATATTGGACTC
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTC
194094 GTACAATGCT
Statistics
Matches: 785, Mismatches: 80, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
100 73 0.09
101 7 0.01
102 6 0.01
104 5 0.01
105 195 0.25
106 499 0.64
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
Found at i:194831 original size:35 final size:36
Alignment explanation
Indices: 194777--194876 Score: 121
Period size: 37 Copynumber: 2.8 Consensus size: 36
194767 CCTTTTCGTC
*
194777 CTACTAGAATTCAAACTCCTAAAAATA-ATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGATAGAATT
* * *
194812 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATA-GATAGAATT
* * *
194849 CTACTATGATTTAAACTCCTAAAGATAG
1 CTACTAGGATTCAAACTCCTAAAAATAG
194877 GATCCACAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
35 24 0.44
36 1 0.02
37 29 0.54
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAAATAGATAGAATT
Found at i:195419 original size:18 final size:18
Alignment explanation
Indices: 195398--195444 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
195388 ATTCATTTGG
195398 TTATTTTTTA-ATACTATA
1 TTATTTTTTATATA-TATA
*
195416 TTATTATTTATATATATA
1 TTATTTTTTATATATATA
195434 TATACTTTTTT
1 T-TA-TTTTTT
195445 TAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 14 0.58
19 5 0.21
20 5 0.21
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTTTTTATATATATA
Found at i:195671 original size:12 final size:11
Alignment explanation
Indices: 195631--195686 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 11
195621 TTTGGTTTTT
195631 TTATATTA-TA
1 TTATATTATTA
*
195641 TTATATTATTT
1 TTATATTATTA
195652 TTCATATTATTA
1 TT-ATATTATTA
*
195664 -T-TATTATTG
1 TTATATTATTA
195673 TTATGATTATTA
1 TTAT-ATTATTA
195685 TT
1 TT
195687 TTTCTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 7 0.19
10 9 0.24
11 5 0.14
12 16 0.43
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (11 bp):
TTATATTATTA
Found at i:195744 original size:12 final size:13
Alignment explanation
Indices: 195723--195803 Score: 53
Period size: 12 Copynumber: 6.4 Consensus size: 13
195713 TATATATTAA
195723 TATTTCATTTATT
1 TATTTCATTTATT
195736 TATTT-ATTTATT
1 TATTTCATTTATT
* *
195748 T-TTCCTTTTATT
1 TATTTCATTTATT
* *
195760 TATTTTTACTTATT
1 TA-TTTCATTTATT
* *
195774 TTTATTC-TTCATT
1 TAT-TTCATTTATT
195787 T-TTTCATTTATT
1 TATTTCATTTATT
*
195799 CATTT
1 TATTT
195804 TTCCCTTCTA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
11 5 0.10
12 21 0.42
13 14 0.28
14 10 0.20
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTCATTTATT
Found at i:195757 original size:16 final size:16
Alignment explanation
Indices: 195738--195779 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
195728 CATTTATTTA
*
195738 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
195754 TTTATTTATTTTTACT
1 TTTATTTATTTTTACT
195770 TATT-TTTATT
1 T-TTATTTATT
195780 CTTCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:199477 original size:43 final size:43
Alignment explanation
Indices: 199350--199600 Score: 141
Period size: 43 Copynumber: 5.8 Consensus size: 43
199340 CTAAAGTTCG
* * *** * *
199350 CGGCGTTTGTTAACGAAAAACGCCACAATAGGTAACAATATATAG
1 CGGCGTTTGTTAA--ACAAACGCCGCAATAGGTGTTAATATTTAA
*
199395 CGGCGTTTGTTCAACAAACGCCGCAATAGGTGTTAATATTTAA
1 CGGCGTTTGTTAAACAAACGCCGCAATAGGTGTTAATATTTAA
* * * *
199438 CGGCGTTTG-TAAGACAAACGCCGTAATAGGTTTTGATATTTAG
1 CGGCGTTTGTTAA-ACAAACGCCGCAATAGGTGTTAATATTTAA
* * * * * * * *
199481 TGACGTTTTTTCCAA-AAATGCCGCAATAGGTGTTGAGATTTAG
1 CGGCGTTTGTT-AAACAAACGCCGCAATAGGTGTTAATATTTAA
* ** * * * * * *
199524 CGGCATTT-TTCTCACAAATGCCGTAATAAGTGTTGAGATTTAG
1 CGGCGTTTGTT-AAACAAACGCCGCAATAGGTGTTAATATTTAA
* *
199567 CGGCGTTT-TTATTACAAATGCCGCAATAGGTGTT
1 CGGCGTTTGTTA-AACAAACGCCGCAATAGGTGTT
199601 GAGATTCAGT
Statistics
Matches: 168, Mismatches: 33, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
42 6 0.04
43 147 0.88
44 2 0.01
45 13 0.08
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (43 bp):
CGGCGTTTGTTAAACAAACGCCGCAATAGGTGTTAATATTTAA
Found at i:199601 original size:43 final size:43
Alignment explanation
Indices: 199392--199748 Score: 360
Period size: 43 Copynumber: 8.3 Consensus size: 43
199382 TAACAATATA
* * * *
199392 TAGCGGCGTTTGTTC-AACAAACGCCGCAATAGGTGTTAATATT
1 TAGCGGCGTTT-TTCTCACAAATGCCGCAATAGGTGTTGAGATT
* * *** * * * *
199435 TAACGGCGTTTGTAAGACAAACGCCGTAATAGGTTTTGATATT
1 TAGCGGCGTTTTTCTCACAAATGCCGCAATAGGTGTTGAGATT
* * *
199478 TAGTGACGTTTTT-TCCAAAAATGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCT-CACAAATGCCGCAATAGGTGTTGAGATT
* * *
199521 TAGCGGCATTTTTCTCACAAATGCCGTAATAAGTGTTGAGATT
1 TAGCGGCGTTTTTCTCACAAATGCCGCAATAGGTGTTGAGATT
* *
199564 TAGCGGCGTTTTTATTACAAATGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCTCACAAATGCCGCAATAGGTGTTGAGATT
* * * * *
199607 CAGTGGCTTTTTTCTCACAAACGTCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCTCACAAATGCCGCAATAGGTGTTGAGATT
** *
199650 TAGCGGCGTTTTTCTTTCAAACT-CCGCAATAAGTGTTGAGATT
1 TAGCGGCGTTTTTCTCACAAA-TGCCGCAATAGGTGTTGAGATT
* * *
199693 TAGCGGCGGTTTTCTCACAAATGCTGCAATAGGTGTTGAGCTT
1 TAGCGGCGTTTTTCTCACAAATGCCGCAATAGGTGTTGAGATT
* *
199736 TTGCGGTGTTTTT
1 TAGCGGCGTTTTT
199749 TTGATACAAA
Statistics
Matches: 256, Mismatches: 53, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
42 2 0.01
43 253 0.99
44 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
TAGCGGCGTTTTTCTCACAAATGCCGCAATAGGTGTTGAGATT
Found at i:199799 original size:43 final size:40
Alignment explanation
Indices: 199751--199866 Score: 115
Period size: 43 Copynumber: 2.8 Consensus size: 40
199741 GTGTTTTTTT
*
199751 GATACAAACGTCGCTAAAGGTCTGGTATATAGCAATGTTTTAG
1 GATACAAACGCCGCTAAAGGTCTGGTATATAGC-A--TTTTAG
* * *
199794 GATACAAACCCCGCTAAAGATCTAGTGTATAGTGGCATTTTAG
1 GATACAAACGCCGCTAAAGGTCT-G-GTATA-TAGCATTTTAG
* * *
199837 GATACAAATGCCGCTAAATGTATGGTATAT
1 GATACAAACGCCGCTAAAGGTCTGGTATAT
199867 TGCGGCGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
40 1 0.02
41 5 0.08
42 1 0.02
43 44 0.72
44 1 0.02
45 6 0.10
46 3 0.05
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (40 bp):
GATACAAACGCCGCTAAAGGTCTGGTATATAGCATTTTAG
Found at i:200678 original size:23 final size:22
Alignment explanation
Indices: 200616--200725 Score: 118
Period size: 22 Copynumber: 5.0 Consensus size: 22
200606 CTGTTAGACA
* *
200616 GGGGGGAATCGGTACCCCCTAG
1 GGGGGGAATCTGTACCCCCTGG
200638 GGGGGGAATC-GTTACCCCCTGG
1 GGGGGGAATCTG-TACCCCCTGG
* *
200660 GGGGTGAATTTGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCTGG
*
200682 GGGAGGGAATCTGTACCCTCT--
1 GGG-GGGAATCTGTACCCCCTGG
* *
200703 GGGGGGAATCTATACCCCTTGG
1 GGGGGGAATCTGTACCCCCTGG
200725 G
1 G
200726 CAATCTGATT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
20 14 0.19
21 4 0.05
22 41 0.55
23 15 0.20
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (22 bp):
GGGGGGAATCTGTACCCCCTGG
Found at i:204100 original size:21 final size:21
Alignment explanation
Indices: 204075--204141 Score: 102
Period size: 20 Copynumber: 3.3 Consensus size: 21
204065 CCGTTAGACA
204075 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
* *
204096 GGGGGAATCTGTTCCCCCT-G
1 GGGGGAATCGGTACCCCCTGG
204116 GGGGGAATCGGTA-CCCCTGG
1 GGGGGAATCGGTACCCCCTGG
204136 GGGGGA
1 GGGGGA
204142 TCTAGACCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 5 0.12
20 19 0.46
21 17 0.41
ACGTcount: A:0.13, C:0.25, G:0.45, T:0.16
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:204151 original size:19 final size:19
Alignment explanation
Indices: 204075--204139 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 19
204065 CCGTTAGACA
*
204075 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCAGTA-CCCCT-G
* *
204096 GGGGGAATCTGTTCCCCCTG
1 GGGGGAATCAG-TACCCCTG
*
204116 GGGGGAATCGGTACCCCTG
1 GGGGGAATCAGTACCCCTG
204135 GGGGG
1 GGGGG
204140 GATCTAGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.31
20 11 0.28
21 15 0.38
22 1 0.03
ACGTcount: A:0.12, C:0.26, G:0.45, T:0.17
Consensus pattern (19 bp):
GGGGGAATCAGTACCCCTG
Found at i:204152 original size:20 final size:20
Alignment explanation
Indices: 204075--204155 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 20
204065 CCGTTAGACA
* *
204075 GGGGGAATCGGTACCCCCTG
1 GGGGGGATCTGTACCCCCTG
*
204095 GGGGGGAATCTGTTCCCCCTG
1 GGGGGG-ATCTGTACCCCCTG
* *
204116 GGGGGAATCGGTA-CCCCTG
1 GGGGGGATCTGTACCCCCTG
204135 GGGGGGATCTAG-ACCCCCTG
1 GGGGGGATCT-GTACCCCCTG
204155 G
1 G
204156 ACAATCTGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
19 15 0.30
20 18 0.36
21 17 0.34
ACGTcount: A:0.14, C:0.28, G:0.41, T:0.17
Consensus pattern (20 bp):
GGGGGGATCTGTACCCCCTG
Found at i:204706 original size:21 final size:21
Alignment explanation
Indices: 204682--204742 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
204672 GTACTGCCGC
*
204682 TGCTTCTCTTTCTGCTTCCGA
1 TGCTACTCTTTCTGCTTCCGA
** * * *
204703 TGCTACTCTGGCTACTTCTGC
1 TGCTACTCTTTCTGCTTCCGA
*
204724 TGCTGCTCTTTCTGCTTCC
1 TGCTACTCTTTCTGCTTCC
204743 CTTGCTTCAT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.05, C:0.34, G:0.16, T:0.44
Consensus pattern (21 bp):
TGCTACTCTTTCTGCTTCCGA
Found at i:213299 original size:42 final size:42
Alignment explanation
Indices: 213235--213353 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 42
213225 AAGGGACACA
* *
213235 CTATTGTGGAGTTTATTACAAAAATGA-CACTAAATTACAACT
1 CTATTGCGGAGTTTATTACAAAAA-CACCACTAAATTACAACT
* *
213277 CTATTGCGGCGTTTATGT-CAAAAACACCACTAAATTATAACT
1 CTATTGCGGAGTTTAT-TACAAAAACACCACTAAATTACAACT
* * * ** *
213319 TTATAGCGGTGTTTGGTA-ACAAACACCACTAAATT
1 CTATTGCGGAGTTTATTACAAAAACACCACTAAATT
213354 TAGAGTATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 18 0.28
42 45 0.70
43 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (42 bp):
CTATTGCGGAGTTTATTACAAAAACACCACTAAATTACAACT
Found at i:213348 original size:41 final size:42
Alignment explanation
Indices: 213262--213353 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
213252 ACAAAAATGA
* *
213262 CACTAAATTACAACTCTATTGCGGCGTTTATGTCAAAAACAC
1 CACTAAATTACAACTCTATAGCGGCGTTTAGGTCAAAAACAC
* * *
213304 CACTAAATTATAACTTTATAGCGGTGTTT-GGT-AACAAACAC
1 CACTAAATTACAACTCTATAGCGGCGTTTAGGTCAA-AAACAC
213345 CACTAAATT
1 CACTAAATT
213354 TAGAGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
40 2 0.05
41 17 0.39
42 25 0.57
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (42 bp):
CACTAAATTACAACTCTATAGCGGCGTTTAGGTCAAAAACAC
Found at i:213574 original size:133 final size:134
Alignment explanation
Indices: 213270--213595 Score: 415
Period size: 134 Copynumber: 2.4 Consensus size: 134
213260 GACACTAAAT
* * * * *
213270 TACAACTCTATTGCGGCGTTTATGTCAAAAACACCACTAAATTATAACTTTATAGCGGTGTTTGG
1 TACAACTCTATTGCGGCGTTTATGTAAAAAACGCCACTAAAGTATAACTTTTTAGCGGCGTTTGG
* * * * * *
213335 TAACAAACACCACTAAATTTAGAGTATTTTACGTCGTTTGCTTAAAAAACGTCGTTATAAATGAC
66 TAACAAACACCACTAAATTTAGAATATTTTACGGCATTTGATTAAAAAACGCCGCTATAAATGAC
213400 AATA
131 AATA
213404 TACAACTCTATTGCGGCGTTTATGTAAAAAACGCCACTAAAGTATAACTTTTTAGCGGCGTTTGG
1 TACAACTCTATTGCGGCGTTTATGTAAAAAACGCCACTAAAGTATAACTTTTTAGCGGCGTTTGG
** * *
213469 TAACAAATGCCCCT-AATTTAAGAATATTTTATGGCATTTGATT-AAAAACGCCGCTATAAATGA
66 TAACAAACACCACTAAATTT-AGAATATTTTACGGCATTTGATTAAAAAACGCCGCTATAAATGA
213532 CAATA
130 CAATA
* * * * * * *
213537 TACAAC-CATTTTGCGGCGTTTGTTTGAAAAATGCCACTAAAGTATTACTCTTTAGCGGC
1 TACAACTC-TATTGCGGCGTTTATGTAAAAAACGCCACTAAAGTATAACTTTTTAGCGGC
213596 ATTTTTTTGA
Statistics
Matches: 168, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
132 1 0.01
133 78 0.46
134 89 0.53
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (134 bp):
TACAACTCTATTGCGGCGTTTATGTAAAAAACGCCACTAAAGTATAACTTTTTAGCGGCGTTTGG
TAACAAACACCACTAAATTTAGAATATTTTACGGCATTTGATTAAAAAACGCCGCTATAAATGAC
AATA
Done.