Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 65 of 82
Found at i:23395947 original size:43 final size:44
Alignment explanation
Indices: 23395893--23395980 Score: 144
Period size: 43 Copynumber: 2.0 Consensus size: 44
23395883 CTAAGTTGGA
23395893 ATAAAAAGGAAAACCATAA-TCCATTTGGCATAT-AAACTAAGTC
1 ATAAAAAGGAAAACCATAATTCC-TTTGGCATATAAAACTAAGTC
*
23395936 ATAAAAAGGAAAACCATAATTCCTTTGGCATATAAAACTCAGTC
1 ATAAAAAGGAAAACCATAATTCCTTTGGCATATAAAACTAAGTC
23395980 A
1 A
23395981 CAACTTAGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 29 0.69
44 13 0.31
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (44 bp):
ATAAAAAGGAAAACCATAATTCCTTTGGCATATAAAACTAAGTC
Found at i:23422956 original size:18 final size:18
Alignment explanation
Indices: 23422933--23422972 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
23422923 TTTCTTTCTA
23422933 ATTTATTATTATTTTT-TT
1 ATTTATT-TTATTTTTATT
23422951 ATTTATTTTATTTTTATT
1 ATTTATTTTATTTTTATT
23422969 ATTT
1 ATTT
23422973 TTTAAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTATTTTATTTTTATT
Found at i:23422974 original size:15 final size:14
Alignment explanation
Indices: 23422934--23422975 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
23422924 TTCTTTCTAA
*
23422934 TTTATTATTATTTT
1 TTTATTATTTTTTT
*
23422948 TTTATTTATTTTATT
1 TTTA-TTATTTTTTT
23422963 TTTATTATTTTTT
1 TTTATTATTTTTT
23422976 AAACCAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTATTTTTTT
Found at i:23423326 original size:17 final size:18
Alignment explanation
Indices: 23423304--23423337 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23423294 TTTCTTTGGC
*
23423304 AATATATTTAA-TATTTT
1 AATATAATTAACTATTTT
23423321 AATATAATTAACTATTT
1 AATATAATTAACTATTT
23423338 CATTTAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATAATTAACTATTTT
Found at i:23430842 original size:58 final size:56
Alignment explanation
Indices: 23430777--23430890 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 56
23430767 AAGATATCCT
23430777 TCAAGTTTGATTGTAATTTGTAAAGGAGTT-TTTGGTGAAAGGGAGAAAAAGTGTTGCA
1 TCAAGTTTGATTGTAATTTGTAAAGGAGTTCTTT--T-AAAGGGAGAAAAAGTGTTGCA
*
23430835 TCAAGTTTGATTGTAATTTGTAAAGGAGTTCTTTTCAAGGGAGAAAAAGTGTTGCA
1 TCAAGTTTGATTGTAATTTGTAAAGGAGTTCTTTTAAAGGGAGAAAAAGTGTTGCA
23430891 AACAAATAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
56 20 0.37
57 1 0.02
58 30 0.56
59 3 0.06
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (56 bp):
TCAAGTTTGATTGTAATTTGTAAAGGAGTTCTTTTAAAGGGAGAAAAAGTGTTGCA
Found at i:23431619 original size:35 final size:34
Alignment explanation
Indices: 23431570--23431647 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 34
23431560 TCACGTGAAG
* * *
23431570 TAGTTGTTTTATGTGAAGTA-ATTGTCCACTTGTTT
1 TAGTTGTTTAATGTGAAATAGATT-T-CACTTATTT
23431605 TAGTTGTTTAATGTGAAATAGTATTTCACTTATTT
1 TAGTTGTTTAATGTGAAATAG-ATTTCACTTATTT
23431640 TAGTTGTT
1 TAGTTGTT
23431648 CTCATTATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 34 0.89
36 1 0.03
37 3 0.08
ACGTcount: A:0.23, C:0.06, G:0.18, T:0.53
Consensus pattern (34 bp):
TAGTTGTTTAATGTGAAATAGATTTCACTTATTT
Found at i:23435071 original size:54 final size:54
Alignment explanation
Indices: 23434970--23435078 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
23434960 CCAGTTATTC
*
23434970 GTCATTATCTTGGGCCCTTGAGAGTACATTTACATCACACATTACCAATGATTG
1 GTCATTATCTTGGGCCCTTGAGAGTACATTTACATCACACATGACCAATGATTG
* * * * *
23435024 GTCATTTTCTTGGGTCCTCT-AGAGTACATTTGCTTCA-AGCATGACCAATTATTG
1 GTCATTATCTTGGGCCCT-TGAGAGTACATTTACATCACA-CATGACCAATGATTG
23435078 G
1 G
23435079 CCATGCAGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 1 0.02
54 45 0.96
55 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (54 bp):
GTCATTATCTTGGGCCCTTGAGAGTACATTTACATCACACATGACCAATGATTG
Found at i:23448043 original size:4 final size:4
Alignment explanation
Indices: 23448034--23448064 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
23448024 TTTCCCTTTT
23448034 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
23448065 ACACTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:23449619 original size:2 final size:2
Alignment explanation
Indices: 23449612--23449636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23449602 TTATACATAC
23449612 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
23449637 ATTATTTTTT
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:23451307 original size:34 final size:33
Alignment explanation
Indices: 23451219--23451313 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 33
23451209 TTGGTTTTAA
*
23451219 CATGTAACATCTGATGCTGAAACTTTAATCTTGG
1 CATGTAACATCTG-TGCTGAAATTTTAATCTTGG
* *
23451253 CATATAACATCTAGTGCTGAAATTTTTATCTTGG
1 CATGTAACATCT-GTGCTGAAATTTTAATCTTGG
* * *
23451287 CATGTAATATCTGCTACTGAAGTTTTA
1 CATGTAACATCTG-TGCTGAAATTTTA
23451314 GTATGTAACA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 1 0.02
34 49 0.96
35 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
CATGTAACATCTGTGCTGAAATTTTAATCTTGG
Found at i:23451375 original size:123 final size:123
Alignment explanation
Indices: 23451221--23451449 Score: 264
Period size: 123 Copynumber: 1.9 Consensus size: 123
23451211 GGTTTTAACA
* * * * * * *
23451221 TGTAACATCTGATGCTGAAACTTTAATCTTGGCATATAACATCT-AGTGCTGAAA-TTTTTATCT
1 TGTAACATCTAATGATGAAACTTTAACCTTGGCATATAACATCTGA-TGAT-AAAGCTTTGACCT
* * *
23451284 TGGCATGTAATATCTGCTACTGAAGTTTTAGTATGTAACATTTCTGCTTTGGCTTTGGTG
64 TAGCATGTAACATCTGCTACTAAAGTTTTAGTATGTAACATTTCTGCTTTGGCTTTGGTG
** * * *
23451344 TGTAACATCTAATGATGAAGGTTTGACCTTGGTATATAATATCTGATGATAAAGCTTTGACCTTA
1 TGTAACATCTAATGATGAAACTTTAACCTTGGCATATAACATCTGATGATAAAGCTTTGACCTTA
* * *
23451409 GCATGTAACATTTGCTACTAAAGTTTTGGTGTGTAACATTT
66 GCATGTAACATCTGCTACTAAAGTTTTAGTATGTAACATTT
23451450 TTTGCTAAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
122 3 0.03
123 82 0.95
124 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (123 bp):
TGTAACATCTAATGATGAAACTTTAACCTTGGCATATAACATCTGATGATAAAGCTTTGACCTTA
GCATGTAACATCTGCTACTAAAGTTTTAGTATGTAACATTTCTGCTTTGGCTTTGGTG
Found at i:23451467 original size:22 final size:22
Alignment explanation
Indices: 23451439--23451493 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
23451429 AAGTTTTGGT
*
23451439 GTGTAACATTTTTTGCTAAAAC
1 GTGTAACATCTTTTGCTAAAAC
* *
23451461 GTGTAACATCTTTTGCTGAAGC
1 GTGTAACATCTTTTGCTAAAAC
23451483 GTGTAACATCT
1 GTGTAACATCT
23451494 GCTTAAGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (22 bp):
GTGTAACATCTTTTGCTAAAAC
Found at i:23451679 original size:29 final size:30
Alignment explanation
Indices: 23451621--23451680 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
23451611 TTTTTTAACT
* *
23451621 ATAACAATATTTTTTAAAATATAGCATGTA
1 ATAAAAATATTTTTTAAAATATACCATGTA
*
23451651 ATAAAAATATTTTTT-AAATATACCGTGTA
1 ATAAAAATATTTTTTAAAATATACCATGTA
23451680 A
1 A
23451681 CTTGTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (30 bp):
ATAAAAATATTTTTTAAAATATACCATGTA
Found at i:23452641 original size:22 final size:24
Alignment explanation
Indices: 23452607--23452651 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
23452597 AAGCTCGAGA
23452607 AGAAGAAGAGGAAGAA-AAAGGGAG
1 AGAAGAAGAGGAA-AATAAAGGGAG
23452631 AGAA-AAG-GGAAAATAAAGGGA
1 AGAAGAAGAGGAAAATAAAGGGA
23452652 AAAGGAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.10
22 11 0.55
23 3 0.15
24 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (24 bp):
AGAAGAAGAGGAAAATAAAGGGAG
Found at i:23459880 original size:12 final size:14
Alignment explanation
Indices: 23459852--23459878 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23459842 TAACAATAAG
23459852 AAAAAATTTAATAT
1 AAAAAATTTAATAT
23459866 AAAAAATTTAATA
1 AAAAAATTTAATA
23459879 AACATGAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAATTTAATAT
Found at i:23461518 original size:33 final size:33
Alignment explanation
Indices: 23461481--23461544 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
23461471 GAATCTACTC
23461481 ATCACAATAATTATCACATGTTTTTGTTAAATT
1 ATCACAATAATTATCACATGTTTTTGTTAAATT
23461514 ATCACAATAATTATCACATGTTTTTGTTAAA
1 ATCACAATAATTATCACATGTTTTTGTTAAA
23461545 ATAAGTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (33 bp):
ATCACAATAATTATCACATGTTTTTGTTAAATT
Found at i:23461570 original size:46 final size:46
Alignment explanation
Indices: 23461518--23461609 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
23461508 TAAATTATCA
* *
23461518 CAATAATTATCACATGTTTTTGTTAAAATAAGTATCATGTGCATCG
1 CAATAATTATCACATGTTTATCTTAAAATAAGTATCATGTGCATCG
*
23461564 CAATAATTATCACATGTTTATCTTAAATTAAGTATCATGTGCATCG
1 CAATAATTATCACATGTTTATCTTAAAATAAGTATCATGTGCATCG
23461610 ATCCTAGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (46 bp):
CAATAATTATCACATGTTTATCTTAAAATAAGTATCATGTGCATCG
Found at i:23463059 original size:18 final size:19
Alignment explanation
Indices: 23463036--23463071 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
23463026 CAATTTTAAA
23463036 ATTTTTTAATTT-ATATTT
1 ATTTTTTAATTTCATATTT
*
23463054 ATTTTTTATTTTCATATT
1 ATTTTTTAATTTCATATT
23463072 ATAAGTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTAATTTCATATTT
Found at i:23467222 original size:25 final size:26
Alignment explanation
Indices: 23467188--23467237 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
23467178 AACAACAATA
23467188 TTTTATAAAT-TAAAGTATAATAATT
1 TTTTATAAATATAAAGTATAATAATT
* *
23467213 TTTTTTAAATATAACGTATAATAAT
1 TTTTATAAATATAAAGTATAATAAT
23467238 AATATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (26 bp):
TTTTATAAATATAAAGTATAATAATT
Found at i:23467245 original size:29 final size:29
Alignment explanation
Indices: 23467184--23467276 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
23467174 AAGTAACAAC
*
23467184 AATATTTTATAAAT-TAAAGTATAATAAT
1 AATATTTTTTAAATATAAAGTATAATAAT
*
23467212 --T-TTTTTTAAATATAACGTATAATAAT
1 AATATTTTTTAAATATAAAGTATAATAAT
* * * * *
23467238 AATATTTTTTCAACATAATGTGTAACAAT
1 AATATTTTTTAAATATAAAGTATAATAAT
23467267 AATATTTTTT
1 AATATTTTTT
23467277 TCAACGTAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
25 9 0.17
26 14 0.26
28 1 0.02
29 30 0.56
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (29 bp):
AATATTTTTTAAATATAAAGTATAATAAT
Found at i:23467292 original size:30 final size:29
Alignment explanation
Indices: 23467206--23467292 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 29
23467196 ATTAAAGTAT
* * * * * *
23467206 AATAATTTTTTTTAAATATAACGTATAAT
1 AATAATATTTTTTCAACATAACATGTAAC
**
23467235 AATAATATTTTTTCAACATAATGTGTAAC
1 AATAATATTTTTTCAACATAACATGTAAC
* *
23467264 AATAATATTTTTTTCAACGTAGCATGTAA
1 AATAATA-TTTTTTCAACATAACATGTAA
23467293 TATGTTATTG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 30 0.64
30 17 0.36
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (29 bp):
AATAATATTTTTTCAACATAACATGTAAC
Found at i:23474331 original size:2 final size:2
Alignment explanation
Indices: 23474318--23474361 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
23474308 ACATACAGAC
*
23474318 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23474360 AT
1 AT
23474362 TTTATACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23475492 original size:17 final size:17
Alignment explanation
Indices: 23475467--23475512 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
23475457 AGAATCAATC
*
23475467 AAAAATATT-ATTTAATT
1 AAAATTATTAATTT-ATT
23475484 AAAATTATTAATTTATT
1 AAAATTATTAATTTATT
23475501 -AAA-TATTAATTT
1 AAAATTATTAATTT
23475513 CAAGAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
16 3 0.11
17 11 0.41
18 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATTATTAATTTATT
Found at i:23475509 original size:15 final size:17
Alignment explanation
Indices: 23475468--23475512 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
23475458 GAATCAATCA
23475468 AAAATATT-ATTTAATT
1 AAAATATTAATTTAATT
23475484 AAAATTATTAATTT-ATT
1 AAAA-TATTAATTTAATT
23475501 -AAATATTAATTT
1 AAAATATTAATTT
23475513 CAAGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.33
16 7 0.26
17 7 0.26
18 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAATATTAATTTAATT
Found at i:23476838 original size:29 final size:30
Alignment explanation
Indices: 23476805--23476904 Score: 120
Period size: 29 Copynumber: 3.4 Consensus size: 30
23476795 ATTTAAAAAA
23476805 ATTTAAAT-AAATTTTTATATTTTTATTAT
1 ATTTAAATCAAATTTTTATATTTTTATTAT
*
23476834 ATTT-AATCAAATTTTTATATTTTTATTTT
1 ATTTAAATCAAATTTTTATATTTTTATTAT
**
23476863 GAGCTAAAT-AAATTTTTTATATTTTT-TTAT
1 -ATTTAAATCAAA-TTTTTATATTTTTATTAT
23476893 -TTTAAATCAAAT
1 ATTTAAATCAAAT
23476905 AAATTTTCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
28 9 0.15
29 27 0.45
30 8 0.13
31 16 0.27
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (30 bp):
ATTTAAATCAAATTTTTATATTTTTATTAT
Found at i:23478712 original size:15 final size:15
Alignment explanation
Indices: 23478671--23478713 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
23478661 GAATATGAAA
*
23478671 TGATAAATAATATTT
1 TGATAAATAATAATT
23478686 TGACT-AATAATAATT
1 TGA-TAAATAATAATT
*
23478701 TGATAAAAAATAA
1 TGATAAATAATAA
23478714 AAATACACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (15 bp):
TGATAAATAATAATT
Found at i:23481145 original size:2 final size:2
Alignment explanation
Indices: 23481140--23481173 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
23481130 TGCCGTTGAT
23481140 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23481174 GTATTTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23486821 original size:13 final size:13
Alignment explanation
Indices: 23486803--23486828 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23486793 TGTACATGTT
23486803 TTTCATGTTAGGC
1 TTTCATGTTAGGC
23486816 TTTCATGTTAGGC
1 TTTCATGTTAGGC
23486829 AAAAATTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTCATGTTAGGC
Found at i:23499518 original size:10 final size:10
Alignment explanation
Indices: 23499505--23499545 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
23499495 AAATATATAA
*
23499505 AAAATTAATT
1 AAAATTATTT
23499515 AAAATT-TTT
1 AAAATTATTT
23499524 AAAATTATTT
1 AAAATTATTT
*
23499534 -AAATTTTTT
1 AAAATTATTT
23499543 AAA
1 AAA
23499546 GTATTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 16 0.59
10 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
AAAATTATTT
Found at i:23499539 original size:18 final size:19
Alignment explanation
Indices: 23499505--23499545 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
23499495 AAATATATAA
23499505 AAAATTAATTAAAATTTTT
1 AAAATTAATTAAAATTTTT
* *
23499524 AAAATTATTTAAATTTTTT
1 AAAATTAATTAAAATTTTT
23499543 AAA
1 AAA
23499546 GTATTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATTAATTAAAATTTTT
Found at i:23499550 original size:18 final size:17
Alignment explanation
Indices: 23499516--23499561 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
23499506 AAATTAATTA
* *
23499516 AAATTTTTAAAATTATTT
1 AAATTTTTTAAAGTA-TT
23499534 AAATTTTTTAAAGTATT
1 AAATTTTTTAAAGTATT
*
23499551 ATATTTTTTAA
1 AAATTTTTTAA
23499562 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AAATTTTTTAAAGTATT
Found at i:23510491 original size:26 final size:27
Alignment explanation
Indices: 23510451--23510502 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
23510441 GCTTGGAATG
*
23510451 CCCTTGGGCACTTCCATGATTCAAACA
1 CCCTTGGGCACTTCCACGATTCAAACA
* *
23510478 CCCTT-GGCATTTCCACGCTTCAAAC
1 CCCTTGGGCACTTCCACGATTCAAAC
23510503 GCCTCAGGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.23, C:0.37, G:0.13, T:0.27
Consensus pattern (27 bp):
CCCTTGGGCACTTCCACGATTCAAACA
Found at i:23513222 original size:17 final size:17
Alignment explanation
Indices: 23513200--23513249 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
23513190 ATTGTTTATG
23513200 AAGATAATTATA-ATTGA
1 AAGATAATTATATATT-A
*
23513217 AAGATAATCATATATTA
1 AAGATAATTATATATTA
* *
23513234 AAAATAATTAAATATT
1 AAGATAATTATATATT
23513250 TTATAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 25 0.89
18 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (17 bp):
AAGATAATTATATATTA
Found at i:23513540 original size:4 final size:4
Alignment explanation
Indices: 23513531--23513585 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
23513521 ATAAATTTAG
* * * * * *
23513531 ATAT ATAT ATAT ATAT ATTT ATAT ATAT GTAT TTAT GTAT GTAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
23513579 ATAT ATA
1 ATAT ATA
23513586 AGTTAGCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (4 bp):
ATAT
Found at i:23515421 original size:696 final size:696
Alignment explanation
Indices: 23514090--23516178 Score: 3874
Period size: 696 Copynumber: 3.0 Consensus size: 696
23514080 CTTCTATCGG
*
23514090 AACCTGTTATGGATAGGGTAATGAATATGTAGCGTTTAATGTCCAAATCTCATCATTGTCAGTTG
1 AACCTGTTACGGATAGGGTAATGAATATGTAGCGTTTAATGTCCAAATCTCATCATTGTCAGTTG
23514155 AAGCTGGACCGTGGCTGCCTCTTTATGAAGCAGAACGGTGTGGTCCTGTGTAAATGGTGCAGACC
66 AAGCTGGACCGTGGCTGCCTCTTTATGAAGCAGAACGGTGTGGTCCTGTGTAAATGGTGCAGACC
*
23514220 GCAAACCTCTCGCACCAAACTCTTTGAACAACTTCATTGCCAAATTTAATAGTTGATGCACCAAT
131 GCAAACCTCTCACACCAAACTCTTTGAACAACTTCATTGCCAAATTTAATAGTTGATGCACCAAT
* * *
23514285 AAGAAAGTGGAGAGACAGAGAGTATAATACAACGTAAATCTCATGGTTTTGAACACAATTTAAAG
196 AAGAAAGTGGAGAGACAGAGAGTATAATACAAGGTAAATCTCATAGTTTTGAACACGATTTAAAG
*
23514350 AAAACATGAGATTAGATAATTTTGAGTTTAATCTTAACGTGTTTCGTATTTAATCATTTTTAACA
261 AAGACATGAGATTAGATAATTTTGAGTTTAATCTTAACGTGTTTCGTATTTAATCATTTTTAACA
*
23514415 TGTTTAAGACACGAACATGTTAAACATGAATAATACGTTTAAAATACGTTTAGTTAATTGTATTA
326 TGTTTAAGACACGAACGTGTTAAACATGAATAATACGTTTAAAATACGTTTAGTTAATTGTATTA
*
23514480 TCGTGTTTAAACATGTATACGTGATACGTTTATCAACTTGTTAAAAATTAATAATCAAAAATTAT
391 TCGTGTTTAAACATGTATACGTGATACGTTTATCAACTTGTTAAAAATTAATAATCAAAAACTAT
* * *
23514545 TTTAATCTTACTTAAATAATTTTAGTTTGGATGTTTCGAATTGTTTATGGTTGATGATATAATTA
456 TTTAACCTTACTTAAATAATTTTAGTTTGGATGTTTCGAATTGTTCATAGTTGATGATATAATTA
* *
23514610 ATGATATGTACGTATTTAATCATGAATGAAAATTATAGATGATTTTAGGTATTATTAATATTTTC
521 ATGATATGTACGTATTTAATCATGAATGAAAATTATAGATGATTTTAGATATTATTAGTATTTTC
23514675 AGATTAGATGTTAATGATAGATTTTATCATATTATATGATAATGAATTTTATGTATGTTATTTAT
586 AGATTAGATGTTAATGATAGATTTTATCATATTATATGATAATGAATTTTATGTATGTTATTTAT
*
23514740 GTTAAATTTTATTATATTTGATATTAAGATTAGTTTGTTTTGATAT
651 GTTAAATTTTATTATATTTGATGTTAAGATTAGTTTGTTTTGATAT
*
23514786 AACCTGTTACGGATAGTGTAATGAATATGTAGCGTTTAATGTCCAAATCTCATCATTGTCAGTTG
1 AACCTGTTACGGATAGGGTAATGAATATGTAGCGTTTAATGTCCAAATCTCATCATTGTCAGTTG
23514851 AAGCTGGACCGTGGCTGCCTCTTTATGAAGCAGAACGGTGTGGTCCTGTGTAAATGGTGCAGACC
66 AAGCTGGACCGTGGCTGCCTCTTTATGAAGCAGAACGGTGTGGTCCTGTGTAAATGGTGCAGACC
23514916 GCAAACCTCTCACACCAAACTCTTTGAACAACTTCATTGCCAAATTTAATAGTTGATGCACCAAT
131 GCAAACCTCTCACACCAAACTCTTTGAACAACTTCATTGCCAAATTTAATAGTTGATGCACCAAT
* *
23514981 AAGAAAGTGGAGAGGCAGAGAGTATAATACAAGGTAAATCTCGTAGTTTTGAACACGATTTAAAG
196 AAGAAAGTGGAGAGACAGAGAGTATAATACAAGGTAAATCTCATAGTTTTGAACACGATTTAAAG
* * * *
23515046 ATGACATGAGATTAGATAATTTTGAGTTTAATCTTAACGTGTTTCATATTTAATTATTTTTAATA
261 AAGACATGAGATTAGATAATTTTGAGTTTAATCTTAACGTGTTTCGTATTTAATCATTTTTAACA
23515111 TGTTTAAGACACGAACGTGTTAAACATGAATAATACGTTTAAAATACGTTTAGTTAATTGTATTA
326 TGTTTAAGACACGAACGTGTTAAACATGAATAATACGTTTAAAATACGTTTAGTTAATTGTATTA
23515176 TCGTGTTTAAACATGTATACGTGATACGTTTATCAACTTGTTAAAAATTAATAATCAAAAACTAT
391 TCGTGTTTAAACATGTATACGTGATACGTTTATCAACTTGTTAAAAATTAATAATCAAAAACTAT
23515241 TTTAACCTTACTTAAATAATTTTAGTTTGGATGTTTCGAATTGTTCATAGTTGATGATATAATTA
456 TTTAACCTTACTTAAATAATTTTAGTTTGGATGTTTCGAATTGTTCATAGTTGATGATATAATTA
* *
23515306 ATGATATGTACATATTTAATCATGAATGAAAATTATAGAAGATTTTAGATATTATTAGTATTTTC
521 ATGATATGTACGTATTTAATCATGAATGAAAATTATAGATGATTTTAGATATTATTAGTATTTTC
23515371 AGATTAGATGTTAATGATAGATTTTATCATATTATATGATAATGAATTTTATGTATGTTATTTAT
586 AGATTAGATGTTAATGATAGATTTTATCATATTATATGATAATGAATTTTATGTATGTTATTTAT
23515436 GTTAAATTTTATTATATTTGATGTTAAGATTAGTTTGTTTTGATAT
651 GTTAAATTTTATTATATTTGATGTTAAGATTAGTTTGTTTTGATAT
23515482 AACCTGTTACGGATAGGGTAATGAATATGTAGCGTTTAATGTCCAAATCTCATCATTGTCAGTTG
1 AACCTGTTACGGATAGGGTAATGAATATGTAGCGTTTAATGTCCAAATCTCATCATTGTCAGTTG
23515547 AAGCTGGACCGTGGCTGCCTCTTTATGAAGCAGAACGGTGTGGTCCTGTGTAAATGGTGCAGACC
66 AAGCTGGACCGTGGCTGCCTCTTTATGAAGCAGAACGGTGTGGTCCTGTGTAAATGGTGCAGACC
23515612 GCAAACCTCTCACACCAAACTCTTTGAACAACTTCATTGCCAAATTTAATAGTTGATGCACCAAT
131 GCAAACCTCTCACACCAAACTCTTTGAACAACTTCATTGCCAAATTTAATAGTTGATGCACCAAT
*
23515677 AAGAAAGTGGAGAGACAAAGAGTATAATACAAGGTAAATCTCATAGTTTTGAACACGATTTAAAG
196 AAGAAAGTGGAGAGACAGAGAGTATAATACAAGGTAAATCTCATAGTTTTGAACACGATTTAAAG
*
23515742 AAGACATGAAATTAGATAATTTTGAGTTTAATCTTAACGTGTTTCGTATTTAATCATTTTTAACA
261 AAGACATGAGATTAGATAATTTTGAGTTTAATCTTAACGTGTTTCGTATTTAATCATTTTTAACA
* * * *
23515807 TGTTTAAGATACGAACGTGTTAAATATGAATAATATGTTTAATATACGTTTAGTTAATTGTATTA
326 TGTTTAAGACACGAACGTGTTAAACATGAATAATACGTTTAAAATACGTTTAGTTAATTGTATTA
23515872 TCGTGTTTAAACATGTATACGTGATACGTTTATCAACTTGTTAAAAATTAATAATCAAAAACTAT
391 TCGTGTTTAAACATGTATACGTGATACGTTTATCAACTTGTTAAAAATTAATAATCAAAAACTAT
*
23515937 TTTAACCTTACTTAAATAATTTTAGTTTGGATGTTTCAAATTGTTCATAGTTGATGATATAATTA
456 TTTAACCTTACTTAAATAATTTTAGTTTGGATGTTTCGAATTGTTCATAGTTGATGATATAATTA
23516002 ATGATATGTACGTATTTAATCATGAATGAAAATTATAGATGATTTTAGATATTATTAGTATTTT-
521 ATGATATGTACGTATTTAATCATGAATGAAAATTATAGATGATTTTAGATATTATTAGTATTTTC
* *
23516066 AGATTAGATGTTAATGATAGATTTTATCATATTATACGATAATGAATTTTATGTATGATATTTAT
586 AGATTAGATGTTAATGATAGATTTTATCATATTATATGATAATGAATTTTATGTATGTTATTTAT
*
23516131 GTTAAATTTTATTATATTTGATGTTAAGAGTAGTTTGTTTTGATAT
651 GTTAAATTTTATTATATTTGATGTTAAGATTAGTTTGTTTTGATAT
23516177 AA
1 AA
23516179 TTGTTTTTAT
Statistics
Matches: 1351, Mismatches: 42, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
695 110 0.08
696 1241 0.92
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (696 bp):
AACCTGTTACGGATAGGGTAATGAATATGTAGCGTTTAATGTCCAAATCTCATCATTGTCAGTTG
AAGCTGGACCGTGGCTGCCTCTTTATGAAGCAGAACGGTGTGGTCCTGTGTAAATGGTGCAGACC
GCAAACCTCTCACACCAAACTCTTTGAACAACTTCATTGCCAAATTTAATAGTTGATGCACCAAT
AAGAAAGTGGAGAGACAGAGAGTATAATACAAGGTAAATCTCATAGTTTTGAACACGATTTAAAG
AAGACATGAGATTAGATAATTTTGAGTTTAATCTTAACGTGTTTCGTATTTAATCATTTTTAACA
TGTTTAAGACACGAACGTGTTAAACATGAATAATACGTTTAAAATACGTTTAGTTAATTGTATTA
TCGTGTTTAAACATGTATACGTGATACGTTTATCAACTTGTTAAAAATTAATAATCAAAAACTAT
TTTAACCTTACTTAAATAATTTTAGTTTGGATGTTTCGAATTGTTCATAGTTGATGATATAATTA
ATGATATGTACGTATTTAATCATGAATGAAAATTATAGATGATTTTAGATATTATTAGTATTTTC
AGATTAGATGTTAATGATAGATTTTATCATATTATATGATAATGAATTTTATGTATGTTATTTAT
GTTAAATTTTATTATATTTGATGTTAAGATTAGTTTGTTTTGATAT
Found at i:23516442 original size:28 final size:28
Alignment explanation
Indices: 23516402--23516461 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
23516392 ATTTATATCG
*
23516402 TGTTTATATTTAATTTCGTGTCTAATCA
1 TGTTCATATTTAATTTCGTGTCTAATCA
*
23516430 TGTTCATATTTAATTTCGTGTCTAATTA
1 TGTTCATATTTAATTTCGTGTCTAATCA
23516458 TGTT
1 TGTT
23516462 TGACAAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (28 bp):
TGTTCATATTTAATTTCGTGTCTAATCA
Found at i:23522222 original size:15 final size:15
Alignment explanation
Indices: 23522202--23522233 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23522192 GTTAAATTCA
23522202 ATTAATAATAAAAAT
1 ATTAATAATAAAAAT
*
23522217 ATTAATAATAGAAAT
1 ATTAATAATAAAAAT
23522232 AT
1 AT
23522234 GAAACTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATTAATAATAAAAAT
Found at i:23522608 original size:50 final size:50
Alignment explanation
Indices: 23522554--23522664 Score: 186
Period size: 50 Copynumber: 2.2 Consensus size: 50
23522544 TTTATGTAAT
* *
23522554 ATAAAAAAGAAGAACATGGCAAATAGAAGGTAGACACCACATATTACATA
1 ATAAAAAAGAAGAACATGACAAATAGAAAGTAGACACCACATATTACATA
* *
23522604 ATAAAAAAGAAGAGCATGACAAATAGAAAGTAGATACCACATATTACATA
1 ATAAAAAAGAAGAACATGACAAATAGAAAGTAGACACCACATATTACATA
23522654 ATAAAAAAGAA
1 ATAAAAAAGAA
23522665 AGAAAAAGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (50 bp):
ATAAAAAAGAAGAACATGACAAATAGAAAGTAGACACCACATATTACATA
Found at i:23522752 original size:6 final size:6
Alignment explanation
Indices: 23522737--23522797 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
23522727 ACATATGAAC
*
23522737 AAAT-A AAATAA AAATAAA CAAATAAA CAAATAA AAATAA AAATAA TAATATA
1 AAATAA AAATAA AAAT-AA -AAAT-AA -AAATAA AAATAA AAATAA AAATA-A
*
23522789 AATTAA AAA
1 AAATAA AAA
23522798 AATTTAAAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
5 4 0.08
6 24 0.50
7 8 0.17
8 12 0.25
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:23522789 original size:28 final size:27
Alignment explanation
Indices: 23522726--23522790 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
23522716 AGAAACTTAT
*
23522726 AACATATGAACAAATAAAATAAAAATA
1 AACATATAAACAAATAAAATAAAAATA
*
23522753 AACAAATAAACAAATAAAAATAAAAATA
1 AACATATAAACAAAT-AAAATAAAAATA
23522781 ATA-ATATAAA
1 A-ACATATAAA
23522791 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.39
28 19 0.58
29 1 0.03
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (27 bp):
AACATATAAACAAATAAAATAAAAATA
Found at i:23529895 original size:4 final size:4
Alignment explanation
Indices: 23529886--23529959 Score: 94
Period size: 4 Copynumber: 18.5 Consensus size: 4
23529876 TGGATACAAG
* * *
23529886 CATA CATA CATA CATA CATA TACA TATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
23529934 CATA TACA TATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
23529960 CATATATATA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:23529910 original size:6 final size:6
Alignment explanation
Indices: 23529899--23530035 Score: 94
Period size: 6 Copynumber: 21.5 Consensus size: 6
23529889 ACATACATAC
* * *
23529899 ATACAT ATACAT ATACAT ACATACAT ACATAC ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT --ATACAT ATACAT ATACAT ATACAT ATACAT
* * * *
23529949 ACATACAT ACACATAT ATATAT ATACAT ATACAT ATATAT ATATGTAT
1 --ATACAT ATAC--AT ATACAT ATACAT ATACAT ATACAT ATA--CAT
** * * *
23529997 ATGTAT ATATAT ATACAT ATACAT ATATAT ATATAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
23530036 TATGTATATG
Statistics
Matches: 108, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
6 87 0.81
8 21 0.19
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.36
Consensus pattern (6 bp):
ATACAT
Found at i:23529914 original size:20 final size:20
Alignment explanation
Indices: 23529887--23529985 Score: 116
Period size: 20 Copynumber: 5.2 Consensus size: 20
23529877 GGATACAAGC
23529887 ATACATACATAC--ATACAT
1 ATACATACATACATATACAT
* * *
23529905 ATACAT--ATACATACATAC
1 ATACATACATACATATACAT
23529923 ATACATACATACATATACAT
1 ATACATACATACATATACAT
*
23529943 ATACATACATACATACACAT
1 ATACATACATACATATACAT
* *
23529963 ATATATATATACATATACAT
1 ATACATACATACATATACAT
23529983 ATA
1 ATA
23529986 TATATATGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
16 4 0.06
18 15 0.22
20 48 0.72
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (20 bp):
ATACATACATACATATACAT
Found at i:23529915 original size:24 final size:24
Alignment explanation
Indices: 23529887--23529991 Score: 120
Period size: 26 Copynumber: 4.1 Consensus size: 24
23529877 GGATACAAGC
23529887 ATACATACATACATACATATACAT
1 ATACATACATACATACATATACAT
23529911 ATACATACATACATACATACATACAT
1 ATACATACATACATACAT--ATACAT
*
23529937 ATACATATACATACATACATACACAT
1 ATAC--ATACATACATACATATACAT
* * *
23529963 ATATATATATACATATACATATATAT
1 ATACATACATAC--ATACATATACAT
23529989 ATA
1 ATA
23529992 TGTATATGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
24 25 0.36
26 31 0.44
28 14 0.20
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.31
Consensus pattern (24 bp):
ATACATACATACATACATATACAT
Found at i:23529915 original size:32 final size:32
Alignment explanation
Indices: 23529886--23529983 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
23529876 TGGATACAAG
23529886 CATACATACATACATACATATACATATACATA
1 CATACATACATACATACATATACATATACATA
23529918 CATACATACATACATACATATACATATACATA
1 CATACATACATACATACATATACATATACATA
* *
23529950 CATACATACACATATATATATATACATATACATA
1 CATACAT--ACATACATACATATACATATACATA
23529984 TATATATATG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 39 0.63
34 23 0.37
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (32 bp):
CATACATACATACATACATATACATATACATA
Found at i:23529968 original size:2 final size:2
Alignment explanation
Indices: 23529961--23530060 Score: 128
Period size: 2 Copynumber: 50.0 Consensus size: 2
23529951 ATACATACAC
* * * *
23529961 AT AT AT AT AT AT AC AT AT AC AT AT AT AT AT AT GT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
23530003 AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
23530045 GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
23530061 GTTTGCAAGG
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:23529986 original size:20 final size:20
Alignment explanation
Indices: 23529903--23530057 Score: 143
Period size: 20 Copynumber: 7.8 Consensus size: 20
23529893 ACATACATAC
* * * *
23529903 ATATACATATACATACATAC
1 ATATATATATACATATACAT
* *
23529923 ATACATACATACATATACAT
1 ATATATATATACATATACAT
* * *
23529943 ATACATACATACATACACAT
1 ATATATATATACATATACAT
23529963 ATATATATATACATATACAT
1 ATATATATATACATATACAT
* **
23529983 ATATATATAT--GTATATGT
1 ATATATATATACATATACAT
23530001 ATATATATATACATATACAT
1 ATATATATATACATATACAT
* **
23530021 ATATATATATATATATATGT
1 ATATATATATACATATACAT
* *
23530041 ATATGTATATATATATA
1 ATATATATATACATATA
23530058 TATGTTTGCA
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.13
20 98 0.87
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.39
Consensus pattern (20 bp):
ATATATATATACATATACAT
Found at i:23535682 original size:62 final size:62
Alignment explanation
Indices: 23535616--23535739 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
23535606 GGAAAATTGC
*
23535616 CAAGCCCATTAACCAAAATATTCCAAGCACTTGGTCCTCAAGCCAATGAAGATAAATATATA
1 CAAGCCCATTAACCAAAATATTCCAAGCACTTGGTCCTCAAACCAATGAAGATAAATATATA
*
23535678 CAAGCCCATTAACCAAAATATTCCAAGCACTTGGTCCTCAAACCAATGAAGATACATATATA
1 CAAGCCCATTAACCAAAATATTCCAAGCACTTGGTCCTCAAACCAATGAAGATAAATATATA
23535740 TATGGAGAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (62 bp):
CAAGCCCATTAACCAAAATATTCCAAGCACTTGGTCCTCAAACCAATGAAGATAAATATATA
Found at i:23538966 original size:4 final size:4
Alignment explanation
Indices: 23538957--23538982 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
23538947 GATATACTAT
23538957 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
23538983 TCACAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:23540534 original size:15 final size:15
Alignment explanation
Indices: 23540512--23540541 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
23540502 TTTCTGAAGC
23540512 TTTTTTTTTTAAAAT
1 TTTTTTTTTTAAAAT
23540527 TTTATTTTTTTAAAA
1 TTT-TTTTTTTAAAA
23540542 AAAAGTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 3 0.21
16 11 0.79
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTTTTTTAAAAT
Found at i:23549461 original size:36 final size:36
Alignment explanation
Indices: 23549414--23549482 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
23549404 GACAACCGAC
23549414 GGAACTGAGACCTGGGAATTCATCCAACTCTTCACT
1 GGAACTGAGACCTGGGAATTCATCCAACTCTTCACT
23549450 GGAACTGAGACCTGGGAATTCATCCAACTCTTC
1 GGAACTGAGACCTGGGAATTCATCCAACTCTTC
23549483 GCTGAAACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (36 bp):
GGAACTGAGACCTGGGAATTCATCCAACTCTTCACT
Found at i:23550523 original size:24 final size:24
Alignment explanation
Indices: 23550494--23550542 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
23550484 CCAAGCCCTC
23550494 CAACACTTGTTCATCATTGAACCT
1 CAACACTTGTTCATCATTGAACCT
23550518 CAACACTTGTTCATCATTGAACCT
1 CAACACTTGTTCATCATTGAACCT
23550542 C
1 C
23550543 GTACTAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (24 bp):
CAACACTTGTTCATCATTGAACCT
Found at i:23550731 original size:57 final size:57
Alignment explanation
Indices: 23550662--23550781 Score: 222
Period size: 57 Copynumber: 2.1 Consensus size: 57
23550652 CGTCCTGGCC
* *
23550662 GAAGCACTGATCACTGGAGTAAGACTGCAAGTCGTCCAACACTTCTGTATCATAGTT
1 GAAGCTCTGATCACTGGAGTAAGACTGCAAGTCGTCCAACACTTCTCTATCATAGTT
23550719 GAAGCTCTGATCACTGGAGTAAGACTGCAAGTCGTCCAACACTTCTCTATCATAGTT
1 GAAGCTCTGATCACTGGAGTAAGACTGCAAGTCGTCCAACACTTCTCTATCATAGTT
23550776 GAAGCT
1 GAAGCT
23550782 TCTATAGCTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (57 bp):
GAAGCTCTGATCACTGGAGTAAGACTGCAAGTCGTCCAACACTTCTCTATCATAGTT
Found at i:23553520 original size:143 final size:144
Alignment explanation
Indices: 23553250--23553537 Score: 458
Period size: 143 Copynumber: 2.0 Consensus size: 144
23553240 CCTCAATTAA
* *
23553250 AGGTCACGTTCTTTTATGAACTTTGCTGGATTAAAATATACAACCCTTAAACGCTGTTTGGGTTG
1 AGGTCACGTTCTTTTATGAACTTTACTGGATTAAAATATACAACCCTTAAACGCGGTTTGGGTTG
*
23553315 TTTCATTGAGTTTAAGGTGTTTTGCTTTTCGGTATGCACATGCGTCCCTTGAAGGTCGCGTATGG
66 TTTCACTGAGTTTAAGGTGTTTTGCTTTTCGGTATGCACATGCGTCCCTTGAAGGTCGCGTATGG
23553380 GTTGTTTTATTTGG
131 GTTGTTTTATTTGG
* * *
23553394 AGGTCACGTTC-TTTATGAACTTTATTGGATTAAAATATGCAACCCTTAAACGCGGTTTTGGTTG
1 AGGTCACGTTCTTTTATGAACTTTACTGGATTAAAATATACAACCCTTAAACGCGGTTTGGGTTG
*
23553458 TTTCACTGTA-TTTAAGG-GTTTTTGCTTTTCGGTATGCATATGCAG-CCCTTGAAGGTCGCGTA
66 TTTCACTG-AGTTTAAGGTG-TTTTGCTTTTCGGTATGCACATGC-GTCCCTTGAAGGTCGCGTA
23553520 TGGGTTGTTTTATTTGG
128 TGGGTTGTTTTATTTGG
23553537 A
1 A
23553538 TTGTCAATAA
Statistics
Matches: 134, Mismatches: 7, Indels: 7
0.91 0.05 0.05
Matches are distributed among these distances:
142 1 0.01
143 120 0.90
144 13 0.10
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (144 bp):
AGGTCACGTTCTTTTATGAACTTTACTGGATTAAAATATACAACCCTTAAACGCGGTTTGGGTTG
TTTCACTGAGTTTAAGGTGTTTTGCTTTTCGGTATGCACATGCGTCCCTTGAAGGTCGCGTATGG
GTTGTTTTATTTGG
Found at i:23554861 original size:44 final size:44
Alignment explanation
Indices: 23554813--23554901 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
23554803 TTCAAAAGAA
23554813 TAATTTTTTCTTCAATGGTTAATGTACAATGATCTCTTATACAC
1 TAATTTTTTCTTCAATGGTTAATGTACAATGATCTCTTATACAC
23554857 TAATTTTTTCTTCAATGGTTAATGTACAATGATCTCTTATACAC
1 TAATTTTTTCTTCAATGGTTAATGTACAATGATCTCTTATACAC
23554901 T
1 T
23554902 TTTAATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (44 bp):
TAATTTTTTCTTCAATGGTTAATGTACAATGATCTCTTATACAC
Found at i:23555679 original size:16 final size:15
Alignment explanation
Indices: 23555658--23555707 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
23555648 TTTAAGAAGA
23555658 TAAAATTATAAATTTT
1 TAAAATTATAAA-TTT
*
23555674 TAAAATTA-AAA--A
1 TAAAATTATAAATTT
23555686 TAAAATTATAAATATT
1 TAAAATTATAAAT-TT
23555702 TAAAAT
1 TAAAAT
23555708 AAAACAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.29
13 3 0.11
15 3 0.11
16 14 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATTATAAATTT
Found at i:23555692 original size:28 final size:29
Alignment explanation
Indices: 23555657--23555732 Score: 109
Period size: 28 Copynumber: 2.6 Consensus size: 29
23555647 ATTTAAGAAG
*
23555657 ATAAAATTATAAATTTTTAAAATTAAA-A
1 ATAAAATTATAAATTTTTAAAATAAAACA
*
23555685 ATAAAATTATAAATATTTAAAATAAAACA
1 ATAAAATTATAAATTTTTAAAATAAAACA
*
23555714 AAAAAATTTATAAATTTTT
1 ATAAAA-TTATAAATTTTT
23555733 GAAACTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 25 0.60
29 6 0.14
30 11 0.26
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAAAATTATAAATTTTTAAAATAAAACA
Found at i:23557813 original size:79 final size:80
Alignment explanation
Indices: 23557652--23557817 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 80
23557642 ATAACATTTC
* * * *
23557652 CATAAATCATCATCATACTTAGCCCATAGTGTATATGACTATCTTAACACATACATCTCATGGAA
1 CATAAATCATCAACATACTTAGCCCATAGTGTACATGACTATATTAACACATACATCTCAAGGAA
*
23557717 TACATTTCATAACCT
66 TACATATCATAACCT
* * * * *
23557732 CATAAATCA-CTAACATGCTTAGCCCATATTGTACATGA-TGTATTAGCACATACATCTCAAGGC
1 CATAAATCATC-AACATACTTAGCCCATAGTGTACATGACTATATTAACACATACATCTCAAGGA
*
23557795 ATACATGAT-ATAATCT
65 ATACAT-ATCATAACCT
23557811 CATAAAT
1 CATAAAT
23557818 GGAACTCATG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
79 40 0.55
80 33 0.45
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.31
Consensus pattern (80 bp):
CATAAATCATCAACATACTTAGCCCATAGTGTACATGACTATATTAACACATACATCTCAAGGAA
TACATATCATAACCT
Found at i:23560380 original size:21 final size:21
Alignment explanation
Indices: 23560356--23560396 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23560346 TAACAGTCAA
*
23560356 ATTAAAGTAAATAAATAAAAT
1 ATTAAAATAAATAAATAAAAT
* *
23560377 ATTAAAATAACTCAATAAAA
1 ATTAAAATAAATAAATAAAA
23560397 ATAAACTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
ATTAAAATAAATAAATAAAAT
Found at i:23563197 original size:18 final size:18
Alignment explanation
Indices: 23563149--23563197 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
23563139 GACAGGAAAG
* **
23563149 TTAGGATTTTTTTTGGTT
1 TTAGGGTTTTTTTTACTT
23563167 TTAGGG--TTTTTTACTT
1 TTAGGGTTTTTTTTACTT
23563183 TTAGGGTTTTTTTTA
1 TTAGGGTTTTTTTTA
23563198 AGGTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 14 0.54
18 12 0.46
ACGTcount: A:0.12, C:0.02, G:0.20, T:0.65
Consensus pattern (18 bp):
TTAGGGTTTTTTTTACTT
Found at i:23563202 original size:12 final size:12
Alignment explanation
Indices: 23563181--23563210 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23563171 GGTTTTTTAC
*
23563181 TTTTAGGGTTTT
1 TTTTAAGGTTTT
23563193 TTTTAAGGTTTT
1 TTTTAAGGTTTT
23563205 TTTTAA
1 TTTTAA
23563211 ATTCGGCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (12 bp):
TTTTAAGGTTTT
Found at i:23566912 original size:41 final size:41
Alignment explanation
Indices: 23566867--23566946 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
23566857 AATCTTTACA
*
23566867 ATGATTTAATCAGTTTTG-GATTTAAACCCTAAATCAAACAC
1 ATGATTTAATCAATTTTGAG-TTTAAACCCTAAATCAAACAC
23566908 ATGATTTAATCAATTTTGAGTTTAAACCCTAAATCAAAC
1 ATGATTTAATCAATTTTGAGTTTAAACCCTAAATCAAAC
23566947 GATTTAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (41 bp):
ATGATTTAATCAATTTTGAGTTTAAACCCTAAATCAAACAC
Found at i:23577443 original size:22 final size:22
Alignment explanation
Indices: 23577415--23577461 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
23577405 ATTTAAAAAA
23577415 AAAAAGAATT-AGTATATTTATT
1 AAAAAGAATTCA-TATATTTATT
23577437 AAAAAGAATTCATATATTTATT
1 AAAAAGAATTCATATATTTATT
23577459 AAA
1 AAA
23577462 TTTTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
AAAAAGAATTCATATATTTATT
Found at i:23578355 original size:21 final size:21
Alignment explanation
Indices: 23578325--23578404 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
23578315 TATAAAAATA
23578325 TGTTACACGTCATGATTAGGT
1 TGTTACACGTCATGATTAGGT
* * **
23578346 TGTTATACGTCATG-TGCAAAAAT
1 TGTTACACGTCATGAT---TAGGT
*
23578369 ATGTTACACGTTATGATTAGGT
1 -TGTTACACGTCATGATTAGGT
*
23578391 TGTTATACGTCATG
1 TGTTACACGTCATG
23578405 TGCAAAAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
20 1 0.02
21 25 0.58
22 2 0.05
23 2 0.05
24 12 0.28
25 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (21 bp):
TGTTACACGTCATGATTAGGT
Found at i:23578356 original size:45 final size:45
Alignment explanation
Indices: 23578301--23578607 Score: 226
Period size: 45 Copynumber: 6.8 Consensus size: 45
23578291 CACGCTATGA
* *
23578301 TGTTACACGTCATGTATAAAAATATGTTACACGTCATGATTAGGT
1 TGTTACACGTCATGTACAAAAATATGTGACACGTCATGATTAGGT
* * * *
23578346 TGTTATACGTCATGTGCAAAAATATGTTACACGTTATGATTAGGT
1 TGTTACACGTCATGTACAAAAATATGTGACACGTCATGATTAGGT
* * * *
23578391 TGTTATACGTCATGTGCAAAAATATGTGACACATCATGATTAAGT
1 TGTTACACGTCATGTACAAAAATATGTGACACGTCATGATTAGGT
** * * ** ***
23578436 TGTTACACACCATGTACAGAAACATGTGACACGTCATGTACAAAAACA
1 TGTTACACGTCATGTACAAAAATATGTGACACGTCATG---ATTAGGT
* * * ** * * *
23578484 TATAACACGTCATGGT---TAGGT-TGTTACACGCCATGATTAGAT
1 TGTTACACGTCAT-GTACAAAAATATGTGACACGTCATGATTAGGT
* * **
23578526 TGTTACACGTCATGTGCAAAAATATGTGACACGTCATGGTTAACT
1 TGTTACACGTCATGTACAAAAATATGTGACACGTCATGATTAGGT
* * * * *
23578571 TATTACACATCATGTACAGAAACATGTGACATGTCAT
1 TGTTACACGTCATGTACAAAAATATGTGACACGTCAT
23578608 ATACAAAAAC
Statistics
Matches: 204, Mismatches: 50, Indels: 16
0.76 0.19 0.06
Matches are distributed among these distances:
41 2 0.01
42 13 0.06
44 2 0.01
45 172 0.84
46 1 0.00
48 12 0.06
49 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (45 bp):
TGTTACACGTCATGTACAAAAATATGTGACACGTCATGATTAGGT
Found at i:23578518 original size:21 final size:21
Alignment explanation
Indices: 23578488--23578539 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
23578478 AAAACATATA
* *
23578488 ACACGTCATGGTTAGGTTGTT
1 ACACGTCATGATTAGATTGTT
*
23578509 ACACGCCATGATTAGATTGTT
1 ACACGTCATGATTAGATTGTT
23578530 ACACGTCATG
1 ACACGTCATG
23578540 TGCAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
ACACGTCATGATTAGATTGTT
Found at i:23578543 original size:135 final size:135
Alignment explanation
Indices: 23578370--23578653 Score: 433
Period size: 135 Copynumber: 2.1 Consensus size: 135
23578360 TGCAAAAATA
* * * *
23578370 TGTTACACGTTATGATTAGGTTGTTATACGTCATGTGCAAAAATATGTGACACATCATGATTAAG
1 TGTTACACGTCATGATTAGATTGTTACACGTCATGTGCAAAAATATGTGACACATCATGATTAAC
* * *
23578435 TTGTTACACACCATGTACAGAAACATGTGACACGTCATGTACAAAAACATATAACACGTCATGGT
66 TTATTACACACCATGTACAGAAACATGTGACACGTCATATACAAAAACATATAACACGTAATGGT
*
23578500 TAGGT
131 TAGAT
* * *
23578505 TGTTACACGCCATGATTAGATTGTTACACGTCATGTGCAAAAATATGTGACACGTCATGGTTAAC
1 TGTTACACGTCATGATTAGATTGTTACACGTCATGTGCAAAAATATGTGACACATCATGATTAAC
* * *
23578570 TTATTACACATCATGTACAGAAACATGTGACATGTCATATACAAAAACATGTAACACGTAATGGT
66 TTATTACACACCATGTACAGAAACATGTGACACGTCATATACAAAAACATATAACACGTAATGGT
23578635 TAGAT
131 TAGAT
*
23578640 TATTACACGTCATG
1 TGTTACACGTCATG
23578654 TTAAAAAAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
135 133 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (135 bp):
TGTTACACGTCATGATTAGATTGTTACACGTCATGTGCAAAAATATGTGACACATCATGATTAAC
TTATTACACACCATGTACAGAAACATGTGACACGTCATATACAAAAACATATAACACGTAATGGT
TAGAT
Found at i:23578645 original size:69 final size:69
Alignment explanation
Indices: 23578397--23578711 Score: 255
Period size: 69 Copynumber: 4.5 Consensus size: 69
23578387 AGGTTGTTAT
* * * * * *
23578397 ACGTCATGTGCAAAAATATGTGACACATCATGATTA-AGTTGTTACACACCATGTACAGAAACAT
1 ACGTCATGTACAAAAACATGTAACACGTCATGGTTAGA-TTATTACACACCATGTACAGAAACAT
23578461 GTGAC
65 GTGAC
* * * * * *
23578466 ACGTCATGTACAAAAACATATAACACGTCATGGTTAGGTTGTTACACGCCATG-ATTAG--A-TT
1 ACGTCATGTACAAAAACATGTAACACGTCATGGTTAGATTATTACACACCATGTA-CAGAAACAT
*
23578527 GTTAC
65 GTGAC
* * * *
23578532 ACGTCATGTGCAAAAATATGTGACACGTCATGGTTA-ACTTATTACACATCATGTACAGAAACAT
1 ACGTCATGTACAAAAACATGTAACACGTCATGGTTAGA-TTATTACACACCATGTACAGAAACAT
23578596 GTGAC
65 GTGAC
* * * ** * * *
23578601 ATGTCATATACAAAAACATGTAACACGTAATGGTTAGATTATTACACGTCATGTTAAAAAAAATA
1 ACGTCATGTACAAAAACATGTAACACGTCATGGTTAGATTATTACACACCATG-T-ACAGAAACA
23578666 TTGTTGTTAC
64 -TG-TG--AC
* * *
23578676 ACATCATGTACAAAAACATGTTACACGTCATAGTTA
1 ACGTCATGTACAAAAACATGTAACACGTCATGGTTA
23578712 AAAAAGGTGG
Statistics
Matches: 194, Mismatches: 38, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
66 51 0.26
67 2 0.01
68 2 0.01
69 95 0.49
70 2 0.01
71 6 0.03
72 2 0.01
73 2 0.01
75 32 0.16
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (69 bp):
ACGTCATGTACAAAAACATGTAACACGTCATGGTTAGATTATTACACACCATGTACAGAAACATG
TGAC
Found at i:23578758 original size:32 final size:32
Alignment explanation
Indices: 23578721--23578784 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
23578711 AAAAAAGGTG
23578721 GTTACACGCCATGTTGAAAAAAAAATATTGTT
1 GTTACACGCCATGTTGAAAAAAAAATATTGTT
* * *
23578753 GTTACACGTCATGTTGAAAAAATATTATTGTT
1 GTTACACGCCATGTTGAAAAAAAAATATTGTT
23578785 ATACGTCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (32 bp):
GTTACACGCCATGTTGAAAAAAAAATATTGTT
Found at i:23578772 original size:29 final size:28
Alignment explanation
Indices: 23578642--23578815 Score: 114
Period size: 29 Copynumber: 6.2 Consensus size: 28
23578632 GGTTAGATTA
23578642 TTACACGTCATGTTAAAAAAAATATTGTTG
1 TTACACGTCATGTT--AAAAAATATTGTTG
* *
23578672 TTACACATCATG-TACAAAAACA----TG
1 TTACACGTCATGTTA-AAAAATATTGTTG
* *
23578696 TTACACGTCATAGTT-AAAAA-A-GGTGG
1 TTACACGTCAT-GTTAAAAAATATTGTTG
*
23578722 TTACACGCCATGTTGAAAAAAAAATATTGTTG
1 TTACACGTCATGTT----AAAAAATATTGTTG
*
23578754 TTACACGTCATGTTGAAAAAATATTATTG
1 TTACACGTCATGTT-AAAAAATATTGTTG
* * * *
23578783 TTATACGTCATATTCAAAAACATT-TTG
1 TTACACGTCATGTTAAAAAATATTGTTG
23578810 TTACAC
1 TTACAC
23578816 TTTAATGTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
23 1 0.01
24 17 0.15
25 4 0.03
26 12 0.10
27 9 0.08
28 14 0.12
29 26 0.22
30 16 0.14
31 1 0.01
32 16 0.14
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (28 bp):
TTACACGTCATGTTAAAAAATATTGTTG
Found at i:23579495 original size:16 final size:17
Alignment explanation
Indices: 23579469--23579501 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23579459 TTCCTCATAA
*
23579469 TTTTCTCTTATTTATTT
1 TTTTCTCTTATTAATTT
23579486 TTTTCT-TTATTAATTT
1 TTTTCTCTTATTAATTT
23579502 AAAAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCTCTTATTAATTT
Found at i:23580407 original size:13 final size:13
Alignment explanation
Indices: 23580378--23580420 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
23580368 ATTTTACCTT
**
23580378 TAAAAAATTATGT
1 TAAAAAATTATAA
23580391 TAAAAAATTATAA
1 TAAAAAATTATAA
* *
23580404 TAAAATATTAAAA
1 TAAAAAATTATAA
23580417 TAAA
1 TAAA
23580421 TATATAACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TAAAAAATTATAA
Found at i:23593921 original size:2 final size:2
Alignment explanation
Indices: 23593914--23593944 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23593904 CTTACATTTA
23593914 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
23593945 ATCAACTGTA
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:23604141 original size:229 final size:230
Alignment explanation
Indices: 23603736--23604191 Score: 655
Period size: 229 Copynumber: 2.0 Consensus size: 230
23603726 ATGAAGCATT
** **
23603736 ATTAGTCAATCACAACCATGCTGTAGTGATACTAGTTTCAAACATCAATAATTGAGCTGTGTTGG
1 ATTAGTCAATCACAACCATGCCATAGTGATACTAGTTTCAAACATCAATAATTGAGCTGCATT-G
* * *
23603801 GCTGAGATTCAACAACTAAGCTCCAAGAAATTAAATCAAGGAAGAACACAAATGAGGCACAAAGC
65 ACTGAGATTCAACAACTAAGCTCCAAGAAATGAAATCAAGGAAGAACACAAATGAGGCACAAAGA
* *
23603866 TGGTAAGGAGATTCCTTAAATTTGAAGGAGGTGCTGTGTCGAAGTTATTGTCTTTTATTTGCTAA
130 TGGTAAGGAGATTCCTTAAATTTGAAGGAGGTGCTATGTCGAAGTTATTCTCTTTTATTTGCTAA
* *
23603931 ATATAATGAGCATAGCACTACTGTCTCGATTAGTCA
195 AGATAATGAGCATAACACTACTGTCTCGATTAGTCA
* * *
23603967 ATTAGTCAATCATAACTATGCCATAGTGATACTAGTTTCAAATATCAATAATTGAGCTGCATT-A
1 ATTAGTCAATCACAACCATGCCATAGTGATACTAGTTTCAAACATCAATAATTGAGCTGCATTGA
* * * * **
23604031 CTGAGATTCAACAATTTAGCTCCAAGAAATGAAATC-AGTTAAGAACACAGATGAGGCACTGAGA
66 CTGAGATTCAACAACTAAGCTCCAAGAAATGAAATCAAG-GAAGAACACAAATGAGGCACAAAGA
* *
23604095 TGGTAAGGAGATTCCTTAAATTTGAAGGAGGTGCTATGTTGAAGTTATTCTGTTTTATTTGCTAA
130 TGGTAAGGAGATTCCTTAAATTTGAAGGAGGTGCTATGTCGAAGTTATTCTCTTTTATTTGCTAA
* * *
23604160 AGATGATGAGCATAACACTACTTTCTGGATTA
195 AGATAATGAGCATAACACTACTGTCTCGATTA
23604192 AGCTGGTCAT
Statistics
Matches: 199, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
228 2 0.01
229 141 0.71
231 56 0.28
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (230 bp):
ATTAGTCAATCACAACCATGCCATAGTGATACTAGTTTCAAACATCAATAATTGAGCTGCATTGA
CTGAGATTCAACAACTAAGCTCCAAGAAATGAAATCAAGGAAGAACACAAATGAGGCACAAAGAT
GGTAAGGAGATTCCTTAAATTTGAAGGAGGTGCTATGTCGAAGTTATTCTCTTTTATTTGCTAAA
GATAATGAGCATAACACTACTGTCTCGATTAGTCA
Found at i:23623304 original size:23 final size:23
Alignment explanation
Indices: 23623270--23623316 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
23623260 GCATCGAGCC
*
23623270 GGCCATGTTCAAATGGCGTGAGA
1 GGCCATGATCAAATGGCGTGAGA
23623293 GGCCATGATCAAATGGCGTGAGA
1 GGCCATGATCAAATGGCGTGAGA
23623316 G
1 G
23623317 AGAGAGAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.36, T:0.19
Consensus pattern (23 bp):
GGCCATGATCAAATGGCGTGAGA
Found at i:23625174 original size:15 final size:15
Alignment explanation
Indices: 23625124--23625174 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
23625114 CGTCATAGTG
23625124 ATTAAATTGAACAAA
1 ATTAAATTGAACAAA
* * *
23625139 AATATA-TAATACAAGA
1 ATTAAATTGA-ACAA-A
23625155 ATTAAATTGAACAAA
1 ATTAAATTGAACAAA
23625170 ATTAA
1 ATTAA
23625175 GATGTTGAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 2 0.07
15 14 0.52
16 9 0.33
17 2 0.07
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (15 bp):
ATTAAATTGAACAAA
Found at i:23626107 original size:108 final size:109
Alignment explanation
Indices: 23625959--23626169 Score: 352
Period size: 108 Copynumber: 1.9 Consensus size: 109
23625949 TATAAGAAAT
* *
23625959 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTACAAAAGAATGTGTAT
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTAAATAATTACAAAAGAATATGTAT
* * * *
23626024 TTGTAAATTGTGGAAGTTGTAACTAAATCAACATATTTTGTTAA
66 TTATAAATTATGAAAGTTGTAACTAAATCAACAAATTTTGTTAA
*
23626068 TTTGAGTAAATTTAAATAAAAA-GTAAATTGGGTAAGAGTTAAATAATTTCAAAAGAATATGTAT
1 TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTAAATAATTACAAAAGAATATGTAT
23626132 TTATAAATTATGAAAGTTGTAACTAAATCAACAAATTT
66 TTATAAATTATGAAAGTTGTAACTAAATCAACAAATTT
23626170 AGTCATTTTG
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 73 0.77
109 22 0.23
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.36
Consensus pattern (109 bp):
TTTGAGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTAAATAATTACAAAAGAATATGTAT
TTATAAATTATGAAAGTTGTAACTAAATCAACAAATTTTGTTAA
Found at i:23626827 original size:31 final size:29
Alignment explanation
Indices: 23626792--23626863 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
23626782 AGGAAAGGAT
23626792 TAAATTGATATAATTTTTAAAATAAAATAAC
1 TAAATTGATATAA-TTTT-AAATAAAATAAC
* * *
23626823 TAAATT-ATTTTAATTTTAAATATAATAAT
1 TAAATTGA-TATAATTTTAAATAAAATAAC
23626852 TAAATTGA-ATAA
1 TAAATTGATATAA
23626864 AATTAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.09
29 16 0.46
30 6 0.17
31 10 0.29
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAATTGATATAATTTTAAATAAAATAAC
Found at i:23627851 original size:20 final size:20
Alignment explanation
Indices: 23627828--23627867 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23627818 AAACAGAATA
23627828 GGAAAACAAGAAAGAGAAAT
1 GGAAAACAAGAAAGAGAAAT
* *
23627848 GGAAAGCAATAAAGAGAAAT
1 GGAAAACAAGAAAGAGAAAT
23627868 TAGTGGACGA
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:0.62, C:0.05, G:0.25, T:0.07
Consensus pattern (20 bp):
GGAAAACAAGAAAGAGAAAT
Found at i:23638023 original size:2 final size:2
Alignment explanation
Indices: 23638016--23638044 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23638006 AAATTCTTTC
23638016 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
23638045 TAAACTTTAA
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:23643668 original size:54 final size:53
Alignment explanation
Indices: 23643582--23643684 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 53
23643572 TTCATAACCC
*
23643582 ACTATCACTCCGAGAGAGAGAGAGAGAGAGAGAGTATAGTGTGGCTTTTNCCTA
1 ACTATCACTACGAGAGAGAGAGAGAGAGAGAGAGTATAGTGTGGCTTTT-CCTA
23643636 ACTA-CACTACGACGAGAGAGAGAGAGAGAGAGAGTATAGTGTGGCTTTT
1 ACTATCACTACGA-GAGAGAGAGAGAGAGAGAGAGTATAGTGTGGCTTTT
23643685 TTCTGATACA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 7 0.15
54 40 0.85
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.21
Consensus pattern (53 bp):
ACTATCACTACGAGAGAGAGAGAGAGAGAGAGAGTATAGTGTGGCTTTTCCTA
Found at i:23672288 original size:17 final size:19
Alignment explanation
Indices: 23672255--23672292 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
23672245 TATAACAATC
23672255 AATATTTTTATTTAAAAAT
1 AATATTTTTATTTAAAAAT
23672274 AATA-TTTTA-TTAAAAAT
1 AATATTTTTATTTAAAAAT
23672291 AA
1 AA
23672293 AGTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 5 0.26
19 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTTTTATTTAAAAAT
Found at i:23673951 original size:30 final size:31
Alignment explanation
Indices: 23673882--23673951 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
23673872 AAATGGCTAA
*
23673882 ATTATTTTGTATTAAAATAATAATAATTTAT
1 ATTATTTTTTATTAAAATAATAATAATTTAT
* * *
23673913 A-TAGTTTTTTATTTAATTAATAA-AATTTTT
1 ATTA-TTTTTTATTAAAATAATAATAATTTAT
23673943 ATTATTTTT
1 ATTATTTTT
23673952 GTTTCCCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
ATTATTTTTTATTAAAATAATAATAATTTAT
Found at i:23682138 original size:23 final size:24
Alignment explanation
Indices: 23682112--23682156 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
23682102 AAACACATTG
**
23682112 AAAATCTT-AAATCATTGAAAACT
1 AAAATCTTCAAAGAATTGAAAACT
23682135 AAAATCTTCAAAGAATTGAAAA
1 AAAATCTTCAAAGAATTGAAAA
23682157 TTTCAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (24 bp):
AAAATCTTCAAAGAATTGAAAACT
Found at i:23692046 original size:28 final size:28
Alignment explanation
Indices: 23692015--23692077 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
23692005 ACTTATAATT
*
23692015 ATAAAAT-ATACAAA-TAATCTAAATATAA
1 ATAAAATAATACAAATTAATAT-AA-ATAA
*
23692043 ATAAATTAATACAAATTAATATAAATAA
1 ATAAAATAATACAAATTAATATAAATAA
23692071 ATAAAAT
1 ATAAAAT
23692078 TTATTAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 16 0.53
29 9 0.30
30 5 0.17
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (28 bp):
ATAAAATAATACAAATTAATATAAATAA
Found at i:23692191 original size:2 final size:2
Alignment explanation
Indices: 23692184--23692229 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
23692174 TTTTCCCCCT
23692184 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
23692226 TA TA
1 TA TA
23692230 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23692269 original size:2 final size:2
Alignment explanation
Indices: 23692257--23692301 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
23692247 NNNNNNNNCT
23692257 TA TA T- TA TA TA TA TA TA TA TA TA TA -A TCA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
23692298 TA TA
1 TA TA
23692302 AACCTTTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23721738 original size:27 final size:27
Alignment explanation
Indices: 23721699--23721754 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
23721689 TAATAATATT
* *
23721699 TAAATTATCAATTAATAATATTTTAAA
1 TAAATTATAAATTAATAATATTTAAAA
*
23721726 TAAATTATAAATTATTAATATTTAAAA
1 TAAATTATAAATTAATAATATTTAAAA
23721753 TA
1 TA
23721755 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAATTATAAATTAATAATATTTAAAA
Found at i:23721756 original size:22 final size:22
Alignment explanation
Indices: 23721689--23721767 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
23721679 GTAAATGAAA
* *
23721689 TAATAATATTTAAATTATCAAT
1 TAATAATATTTAAAATATAAAT
23721711 TAATAATATTTTAAATAAATTATAAAT
1 TAATAATA-TTT--A-AAA-TATAAAT
* *
23721738 TATTAATATTTAAAATATAAAA
1 TAATAATATTTAAAATATAAAT
*
23721760 TAAAAATA
1 TAATAATA
23721768 AATAATCATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
22 20 0.43
23 6 0.13
24 1 0.02
25 1 0.02
26 5 0.11
27 13 0.28
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAATATTTAAAATATAAAT
Found at i:23721762 original size:27 final size:27
Alignment explanation
Indices: 23721699--23721763 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
23721689 TAATAATATT
* * *
23721699 TAAATTATCAATTAATAATATTTTAAA
1 TAAATAATAAATTAATAATATTTAAAA
* *
23721726 TAAATTATAAATTATTAATATTTAAAA
1 TAAATAATAAATTAATAATATTTAAAA
23721753 TATAA-AATAAA
1 TA-AATAATAAA
23721764 AATAAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATAATAAATTAATAATATTTAAAA
Found at i:23722344 original size:21 final size:21
Alignment explanation
Indices: 23722320--23722359 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
23722310 ACTTTAAGCA
23722320 ATTAAAATAATAA-ATAATAAT
1 ATTAAAA-AATAATATAATAAT
23722341 ATTAAAAAATAATATAATA
1 ATTAAAAAATAATATAATA
23722360 TTTTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAAAAATAATATAATAAT
Found at i:23731598 original size:44 final size:44
Alignment explanation
Indices: 23731535--23731622 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
23731525 CTAACCGTTT
23731535 TCCCTTAAACTTGTTGGTTGGATAGACCATTGGACGGATATTTA
1 TCCCTTAAACTTGTTGGTTGGATAGACCATTGGACGGATATTTA
23731579 TCCCTTAAACTTGTTGGTTGGATAGACCATTGGACGGATATTTA
1 TCCCTTAAACTTGTTGGTTGGATAGACCATTGGACGGATATTTA
23731623 CAGACAAGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (44 bp):
TCCCTTAAACTTGTTGGTTGGATAGACCATTGGACGGATATTTA
Found at i:23732555 original size:20 final size:19
Alignment explanation
Indices: 23732544--23732582 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
23732534 AAAATATAAG
23732544 AAAGAGAGAGAAATAAACAA
1 AAAGAGAGA-AAATAAACAA
23732564 AAAGAGAGCAAAATAAACA
1 AAAGAGAG-AAAATAAACA
23732583 GACGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.69, C:0.08, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAGAGAGAAAATAAACAA
Found at i:23736370 original size:49 final size:49
Alignment explanation
Indices: 23736317--23736418 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
23736307 TAATCTCCTA
23736317 ATAACTTTCGTCCACTACATTAAATTAAAAAGTATTTGATGAGTCCCAT
1 ATAACTTTCGTCCACTACATTAAATTAAAAAGTATTTGATGAGTCCCAT
* * *
23736366 ATAACTTTGGTCCACTACATTAAATTAAAAAGTCTTTGATGAGTGCCAT
1 ATAACTTTCGTCCACTACATTAAATTAAAAAGTATTTGATGAGTCCCAT
23736415 ATAA
1 ATAA
23736419 TTTTATTTCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (49 bp):
ATAACTTTCGTCCACTACATTAAATTAAAAAGTATTTGATGAGTCCCAT
Found at i:23740931 original size:16 final size:15
Alignment explanation
Indices: 23740896--23740935 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
23740886 TATTGTCTCA
* *
23740896 TTTAATAAATAAATT
1 TTTAAAAAATAAAAT
23740911 TTTAAAAAATAAAAAT
1 TTTAAAAAAT-AAAAT
23740927 TTTAAAAAA
1 TTTAAAAAA
23740936 CAAATACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAAAATAAAAT
Found at i:23756179 original size:4 final size:4
Alignment explanation
Indices: 23756170--23756200 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
23756160 TTGCAACTAT
23756170 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
23756201 TATATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:23760277 original size:56 final size:56
Alignment explanation
Indices: 23760186--23760303 Score: 148
Period size: 56 Copynumber: 2.1 Consensus size: 56
23760176 GCATCGCCCT
* * * *
23760186 CCCTCAAGGGAGTGCATCAACGACGCTCGCCTAGGGAATGCAGATTTGGCCGCGCC
1 CCCTCAAGGGAGTGCAGCAACAACGCTCGCCTAGGGAACGCAGATTTGGCCACGCC
* * * *
23760242 CCCTCAGGGGAGTGCAGCAATAATGCT-GCCTTAGGGAACGCAGATTTGGCCACGCT
1 CCCTCAAGGGAGTGCAGCAACAACGCTCGCC-TAGGGAACGCAGATTTGGCCACGCC
23760298 CCCTCA
1 CCCTCA
23760304 CGGTAATGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 3 0.06
56 50 0.94
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (56 bp):
CCCTCAAGGGAGTGCAGCAACAACGCTCGCCTAGGGAACGCAGATTTGGCCACGCC
Found at i:23761568 original size:19 final size:17
Alignment explanation
Indices: 23761544--23761578 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
23761534 TTACTAATTG
23761544 ATATATATTATTATATATA
1 ATATATA-TA-TATATATA
23761563 ATATATATATATATAT
1 ATATATATATATATAT
23761579 TTGAGACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:23762034 original size:13 final size:13
Alignment explanation
Indices: 23762016--23762045 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23762006 TTGTCACATT
23762016 TGAATATACAATG
1 TGAATATACAATG
*
23762029 TGAATATGCAATG
1 TGAATATACAATG
23762042 TGAA
1 TGAA
23762046 ACCAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
TGAATATACAATG
Found at i:23763747 original size:17 final size:17
Alignment explanation
Indices: 23763725--23763757 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23763715 TAACCCTTAA
23763725 TTAAA-TATTTATAAAAG
1 TTAAATTATTTA-AAAAG
23763742 TTAAATTATTTAAAAA
1 TTAAATTATTTAAAAA
23763758 AATTCAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATTATTTAAAAAG
Found at i:23763766 original size:19 final size:18
Alignment explanation
Indices: 23763723--23763766 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
23763713 ATTAACCCTT
*
23763723 AATTAAA-TATTTATAAA
1 AATTAAATTATTTAAAAA
*
23763740 AGTTAAATTATTTAAAAA
1 AATTAAATTATTTAAAAA
23763758 AATTCAAAT
1 AATT-AAAT
23763767 AAATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTAAATTATTTAAAAA
Found at i:23764057 original size:31 final size:30
Alignment explanation
Indices: 23764022--23764084 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
23764012 AATTATTAAT
* *
23764022 TATAAAAACTTATTTGACGAAAAAATAAAAA
1 TATAAAAACGTATTTAAC-AAAAAATAAAAA
* **
23764053 TATAAGAACGTATTTAACTCAAAATAAAAA
1 TATAAAAACGTATTTAACAAAAAATAAAAA
23764083 TA
1 TA
23764085 CAAGACTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (30 bp):
TATAAAAACGTATTTAACAAAAAATAAAAA
Found at i:23764120 original size:28 final size:28
Alignment explanation
Indices: 23764045--23764128 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
23764035 TTGACGAAAA
* * * *
23764045 AATAAAAATATAAGAACGTATTTAACTCAA
1 AATAAAAATACAAG-ACTTATTTAAAT-AT
23764075 AATAAAAATACAAGACTTGA-TTAAATAT
1 AATAAAAATACAAGACTT-ATTTAAATAT
*
23764103 AATAAAAATATATA-ACTTATTTAAAT
1 AATAAAAATACA-AGACTTATTTAAAT
23764129 TATCTTAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.02
28 22 0.48
29 9 0.20
30 14 0.30
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (28 bp):
AATAAAAATACAAGACTTATTTAAATAT
Found at i:23771065 original size:23 final size:23
Alignment explanation
Indices: 23771034--23771083 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
23771024 TATTAAAAAT
* *
23771034 AAATTAAAAGAGAAAAAAATGAA
1 AAATGAAAAGAGAAAAAAATAAA
* *
23771057 AAATGAAAATAGAGAAAAATAAA
1 AAATGAAAAGAGAAAAAAATAAA
23771080 AAAT
1 AAAT
23771084 TATTAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (23 bp):
AAATGAAAAGAGAAAAAAATAAA
Found at i:23775950 original size:45 final size:45
Alignment explanation
Indices: 23775899--23776136 Score: 287
Period size: 45 Copynumber: 5.3 Consensus size: 45
23775889 CTTAATGAAA
** * *
23775899 TTACACGTTATGTACAAAAATATGTGACAAGCGATGGTTAGGTTG
1 TTACACGCCATGTACAAAAACATGTGACAAGCCATGGTTAGGTTG
23775944 TTACACGCCATGTACAAAAACATGTGACAAGCCATGGTTAGGTTG
1 TTACACGCCATGTACAAAAACATGTGACAAGCCATGGTTAGGTTG
* ** * *
23775989 TTACACGTCATGTACATTAACATGTGACAAGCCATGATTAAGTTG
1 TTACACGCCATGTACAAAAACATGTGACAAGCCATGGTTAGGTTG
* * * * *
23776034 TTATACGCAATGTACAAAAACATGTGATAAGCTATGGTTAGGTTA
1 TTACACGCCATGTACAAAAACATGTGACAAGCCATGGTTAGGTTG
* * * * * *
23776079 TTATACCCCATGTGCAAAAACATATGACAAGTCATGGTTAGGTTA
1 TTACACGCCATGTACAAAAACATGTGACAAGCCATGGTTAGGTTG
*
23776124 TTACACGCAATGT
1 TTACACGCCATGT
23776137 TGAAAAAAAA
Statistics
Matches: 164, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 164 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (45 bp):
TTACACGCCATGTACAAAAACATGTGACAAGCCATGGTTAGGTTG
Found at i:23776168 original size:52 final size:52
Alignment explanation
Indices: 23776112--23776213 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
23776102 ATGACAAGTC
*
23776112 ATGGTTAGGTTATTACACGCAATGTTGAAAAAAAATATTATTGTTACACGAT
1 ATGGTTAGGTTATTACACGCAATGTTGAAAAAAAATACTATTGTTACACGAT
* *
23776164 ATGGTTAGGTTGTTACACGCCATGTTGAAAAAAAATACTATTGTTACACG
1 ATGGTTAGGTTATTACACGCAATGTTGAAAAAAAATACTATTGTTACACG
23776214 TCATGTATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (52 bp):
ATGGTTAGGTTATTACACGCAATGTTGAAAAAAAATACTATTGTTACACGAT
Found at i:23776238 original size:26 final size:26
Alignment explanation
Indices: 23776207--23776267 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 26
23776197 AATACTATTG
*
23776207 TTACACGTCAT-GTATAAAAACATGTTA
1 TTACACGTCATGGT-TAAAAA-AGGTTA
23776234 -TACAC--CATGGTTAAAAAAGGTTA
1 TTACACGTCATGGTTAAAAAAGGTTA
23776257 TTACACGTCAT
1 TTACACGTCAT
23776268 ATTGAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
23 5 0.17
24 14 0.48
25 2 0.07
26 8 0.28
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (26 bp):
TTACACGTCATGGTTAAAAAAGGTTA
Found at i:23776313 original size:27 final size:29
Alignment explanation
Indices: 23776257--23776318 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
23776247 AAAAAGGTTA
* *
23776257 TTACACGTCATATTGAAAAAATATTGTTG
1 TTACACGGCATATTGAAAAAACATTGTTG
*
23776286 TTACACGGCATATT-CAAAAACATT-TTG
1 TTACACGGCATATTGAAAAAACATTGTTG
23776313 TTACAC
1 TTACAC
23776319 TTTAATACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 9 0.30
28 8 0.27
29 13 0.43
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (29 bp):
TTACACGGCATATTGAAAAAACATTGTTG
Found at i:23776729 original size:23 final size:23
Alignment explanation
Indices: 23776697--23776742 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
23776687 CTTGGTGTCT
*
23776697 TGAAAGCGTAAGAAAAAGAAATC
1 TGAAAACGTAAGAAAAAGAAATC
* *
23776720 TGAAAACGTAAGAGAGAGAAATC
1 TGAAAACGTAAGAAAAAGAAATC
23776743 AGAAGCATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.54, C:0.09, G:0.24, T:0.13
Consensus pattern (23 bp):
TGAAAACGTAAGAAAAAGAAATC
Found at i:23778122 original size:132 final size:132
Alignment explanation
Indices: 23777921--23778185 Score: 514
Period size: 132 Copynumber: 2.0 Consensus size: 132
23777911 TTTGAGTTTT
23777921 TTTCTTTTAAAAAAATTATGACATGCTTGAAGTCTTGGTTTGACCCACTTTCATTAACTTTAGAA
1 TTTCTTTTAAAAAAATTATGACATGCTTGAAGTCTTGGTTTGACCCACTTTCATTAACTTTAGAA
23777986 TAAATTAATTATTTAGTCATTTAAATTTTTAAATTTTTTATTTTTCGTTATTTAGTTTTGGAAAT
66 TAAATTAATTATTTAGTCATTTAAATTTTTAAATTTTTTATTTTTCGTTATTTAGTTTTGGAAAT
23778051 AA
131 AA
23778053 TNTTCTTTT-AAAAAATTATGACATGCTTGAAGTCTTGGTTTGACCCACTTTCATTAACTTTAGA
1 T-TTCTTTTAAAAAAATTATGACATGCTTGAAGTCTTGGTTTGACCCACTTTCATTAACTTTAGA
23778117 ATAAATTAATTATTTAGTCATTTAAATTTTTAAATTTTTTATTTTTCGTTATTTAGTTTTGGAAA
65 ATAAATTAATTATTTAGTCATTTAAATTTTTAAATTTTTTATTTTTCGTTATTTAGTTTTGGAAA
23778182 TAA
130 TAA
23778185 T
1 T
23778186 GTATTGTTCA
Statistics
Matches: 132, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
132 125 0.95
133 7 0.05
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (132 bp):
TTTCTTTTAAAAAAATTATGACATGCTTGAAGTCTTGGTTTGACCCACTTTCATTAACTTTAGAA
TAAATTAATTATTTAGTCATTTAAATTTTTAAATTTTTTATTTTTCGTTATTTAGTTTTGGAAAT
AA
Found at i:23778775 original size:21 final size:17
Alignment explanation
Indices: 23778728--23778761 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
23778718 TTTCTGACTT
23778728 CTTTTTCTTTCTTCTTC
1 CTTTTTCTTTCTTCTTC
23778745 CTTTTTCTTTCTTCTTC
1 CTTTTTCTTTCTTCTTC
23778762 TCTTACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
CTTTTTCTTTCTTCTTC
Found at i:23779156 original size:19 final size:20
Alignment explanation
Indices: 23779101--23779158 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
23779091 ATTAAAATTT
*
23779101 AGTTATTTTTAATTGTTTTTAC
1 AGTTA-TTTTAATT-TTATTAC
* * *
23779123 AATTAGTTTATTTTTATTA-
1 AGTTATTTTAATTTTATTAC
23779142 AGTTATTTTAATTTTAT
1 AGTTATTTTAATTTTAT
23779159 GTTTATTTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 14 0.48
20 5 0.17
21 6 0.21
22 4 0.14
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.64
Consensus pattern (20 bp):
AGTTATTTTAATTTTATTAC
Found at i:23780157 original size:15 final size:15
Alignment explanation
Indices: 23780130--23780170 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
23780120 AATTTTATGT
23780130 ATGTTATTTATATTAA
1 ATGTTA-TTATATTAA
* *
23780146 ATTTTATTATATTTA
1 ATGTTATTATATTAA
23780161 ATGTTATTAT
1 ATGTTATTAT
23780171 TATTTTGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
ATGTTATTATATTAA
Found at i:23780181 original size:14 final size:14
Alignment explanation
Indices: 23780149--23780190 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
23780139 ATATTAAATT
23780149 TTATTA-TATTTAATG
1 TTATTATTATTT--TG
23780164 TTATTATTATTTTG
1 TTATTATTATTTTG
*
23780178 TTATAATTATTTT
1 TTATTATTATTTT
23780191 AATAATATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 14 0.56
15 6 0.24
16 5 0.20
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TTATTATTATTTTG
Found at i:23784111 original size:22 final size:22
Alignment explanation
Indices: 23784085--23784128 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
23784075 AATAAAAATC
* *
23784085 ATATTAACATTTTATTAATAAA
1 ATATTAACATTGTAATAATAAA
23784107 ATATTAACATTGTAATAATAAA
1 ATATTAACATTGTAATAATAAA
23784129 TTACTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATTAACATTGTAATAATAAA
Found at i:23784294 original size:22 final size:23
Alignment explanation
Indices: 23784264--23784312 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
23784254 TATTAAAAAT
* *
23784264 AAATTAAAAGAGA-AAAAATGAA
1 AAATGAAAAGAGATAAAAATAAA
*
23784286 AAATGAAAATAGATAAAAATAAA
1 AAATGAAAAGAGATAAAAATAAA
23784309 AAAT
1 AAAT
23784313 TATAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.16
Consensus pattern (23 bp):
AAATGAAAAGAGATAAAAATAAA
Found at i:23784410 original size:27 final size:27
Alignment explanation
Indices: 23784380--23784457 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 27
23784370 CAAAATAGAG
23784380 AAAAAATAAATATTAATATTAATATTT
1 AAAAAATAAATATTAATATTAATATTT
*
23784407 AAAAAAT-CA-ATT--T-TTAATATTT
1 AAAAAATAAATATTAATATTAATATTT
* * *
23784429 TAACAATAACATATTAA-ATTATTATTT
1 AAAAAATAA-ATATTAATATTAATATTT
23784456 AA
1 AA
23784458 TAATTACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
22 14 0.36
23 1 0.03
24 1 0.03
25 6 0.15
26 1 0.03
27 16 0.41
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAAATAAATATTAATATTAATATTT
Found at i:23791473 original size:3 final size:3
Alignment explanation
Indices: 23791460--23791497 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
23791450 ATTTATTTAT
*
23791460 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23791498 TTAATAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:23794809 original size:15 final size:15
Alignment explanation
Indices: 23794797--23794839 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
23794787 CCTAGGAGGT
23794797 GCAGCTCTTGGAGAA
1 GCAGCTCTTGGAGAA
*
23794812 GGAGCTCTTGGAGAA
1 GCAGCTCTTGGAGAA
*
23794827 GCAGCTCGTGGAG
1 GCAGCTCTTGGAG
23794840 GTGGAGGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.40, T:0.19
Consensus pattern (15 bp):
GCAGCTCTTGGAGAA
Found at i:23794895 original size:15 final size:15
Alignment explanation
Indices: 23794875--23794921 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
23794865 TTGTGGAGGG
*
23794875 GAAGCAGCTCTAGGA
1 GAAGCAGCCCTAGGA
*
23794890 GAAGCAGCCCTCGGA
1 GAAGCAGCCCTAGGA
*
23794905 GAAGCAACCCTAGGA
1 GAAGCAGCCCTAGGA
23794920 GA
1 GA
23794922 GGCAATCCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.32, T:0.09
Consensus pattern (15 bp):
GAAGCAGCCCTAGGA
Done.