Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 117 of 129
Found at i:21002138 original size:10 final size:9
Alignment explanation
Indices: 21002071--21002130 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 9
21002061 ACAACGCAAG
21002071 AAAAAAAAC
1 AAAAAAAAC
21002080 -AAAAAAAC
1 AAAAAAAAC
* * *
21002088 -AACACAAG
1 AAAAAAAAC
*
21002096 AAAAAAACC
1 AAAAAAAAC
21002105 AAAAAAAAC
1 AAAAAAAAC
21002114 AAAAAAACAC
1 AAAAAAA-AC
21002124 AAAAAAA
1 AAAAAAA
21002131 TAAAAAAAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
8 13 0.32
9 19 0.46
10 9 0.22
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:21002313 original size:6 final size:6
Alignment explanation
Indices: 21002302--21002336 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
21002292 TATCTTTGTC
21002302 ATTTTT ATTTTT ATTTTT A-TTTT ATTTTAT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT-T ATTTT
21002337 ATGTATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:21002337 original size:12 final size:12
Alignment explanation
Indices: 21002304--21002338 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
21002294 TCTTTGTCAT
21002304 TTTTAT-TTTTA
1 TTTTATATTTTA
21002315 TTTT-TATTTTA
1 TTTTATATTTTA
21002326 TTTTATATTTTA
1 TTTTATATTTTA
21002338 T
1 T
21002339 GTATATCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 13 0.59
12 8 0.36
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATATTTTA
Found at i:21002837 original size:25 final size:24
Alignment explanation
Indices: 21002781--21002837 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
21002771 GTTCTGGGAG
*
21002781 TGAGAAAAAATTTTTAGAAATTTT
1 TGAGAAAAAATTTTTAGAAATTTC
* * *
21002805 TGGCGAAAAATTTTTCTGGAAATTTC
1 T-GAGAAAAAATTTT-TAGAAATTTC
21002831 TGAGAAA
1 TGAGAAA
21002838 TTTCCAGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 16 0.62
26 9 0.35
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (24 bp):
TGAGAAAAAATTTTTAGAAATTTC
Found at i:21002992 original size:19 final size:20
Alignment explanation
Indices: 21002968--21003013 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
21002958 TCCGGCCAAC
*
21002968 TTCCGATGA-AATTTCCAGA
1 TTCCGACGACAATTTCCAGA
*
21002987 TTCCGACGACATTTTCCAGA
1 TTCCGACGACAATTTCCAGA
*
21003007 ATCCGAC
1 TTCCGAC
21003014 ACCGTTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCCGACGACAATTTCCAGA
Found at i:21005437 original size:60 final size:60
Alignment explanation
Indices: 21005363--21005571 Score: 284
Period size: 60 Copynumber: 3.5 Consensus size: 60
21005353 CTAAAAATAT
*
21005363 TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAAGG
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAAGG
* * * *
21005423 TTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAGAAATCAAAGTTTC-AAAAAAAAAGAG
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTCAAAAAAAAAAG-G
* *
21005484 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT-AAATTTCCAAAAAAAATA-T
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTT-CAAAAAAAAAAGG
21005542 TTTTG-GAGAAAAGTTGAAAGTATCAATTTT
1 TTTTGAG-GAAAAGTTGAAAGTATCAATTTT
21005572 TCCTACACAA
Statistics
Matches: 133, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.01
58 33 0.25
59 1 0.01
60 58 0.44
61 40 0.30
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (60 bp):
TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAAGG
Found at i:21006139 original size:19 final size:19
Alignment explanation
Indices: 21006115--21006157 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21006105 TGTGATTTTA
21006115 TTTTTT-TGGTTAATAATAT
1 TTTTTTATGGTTAA-AATAT
*
21006134 TTTTTTATGTTTAAAATAT
1 TTTTTTATGGTTAAAATAT
21006153 TTTTT
1 TTTTT
21006158 CTAAAACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTTTATGGTTAAAATAT
Found at i:21006258 original size:20 final size:20
Alignment explanation
Indices: 21006235--21006283 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
21006225 AATTTTACTT
*
21006235 TTTTTTTTTTATTTTTATCA
1 TTTTTTTTTTATTTTCATCA
* *
21006255 TTTTTTATTTATTTTCATTA
1 TTTTTTTTTTATTTTCATCA
21006275 TTATTTTTT
1 TT-TTTTTT
21006284 ATTGTAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTTTTATTTTCATCA
Found at i:21006272 original size:17 final size:16
Alignment explanation
Indices: 21006239--21006282 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
21006229 TTACTTTTTT
21006239 TTTTTTATTTTTATCA
1 TTTTTTATTTTTATCA
*
21006255 TTTTTTATTTATTTTCA
1 TTTTTTATTT-TTATCA
*
21006272 -TTATTATTTTT
1 TTTTTTATTTTT
21006283 TATTGTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 18 0.72
17 5 0.20
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTATTTTTATCA
Found at i:21008018 original size:2 final size:2
Alignment explanation
Indices: 21008006--21008038 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21007996 TTAAATTACT
*
21008006 TA TA TA GA 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
21008039 GATAATAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21008766 original size:28 final size:27
Alignment explanation
Indices: 21008734--21008787 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
21008724 TTTGGGGTCT
**
21008734 TTTTAAATTGTTCACTTAAATATTAAAA
1 TTTTAAATTAATCACTTAAAT-TTAAAA
*
21008762 TTTTAATTTAATCACTTAAATTTAAA
1 TTTTAAATTAATCACTTAAATTTAAA
21008788 TAAGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTAAATTAATCACTTAAATTTAAAA
Found at i:21009111 original size:28 final size:28
Alignment explanation
Indices: 21009079--21009137 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
21009069 TTGTTTATTT
21009079 ATTAATTTATTAATTTTTTATAAGTACG
1 ATTAATTTATTAATTTTTTATAAGTACG
21009107 ATTAATTTATTAATTTTTTATAAGTACG
1 ATTAATTTATTAATTTTTTATAAGTACG
21009135 ATT
1 ATT
21009138 GTTATTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (28 bp):
ATTAATTTATTAATTTTTTATAAGTACG
Found at i:21013395 original size:15 final size:14
Alignment explanation
Indices: 21013358--21013399 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
21013348 AACTTTAACA
*
21013358 TTATTATTGTATTT
1 TTATTATTTTATTT
21013372 TTATTATTTTATTT
1 TTATTATTTTATTT
*
21013386 TATGTTATTTTATT
1 T-TATTATTTTATT
21013400 GTAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTT
Found at i:21014069 original size:33 final size:33
Alignment explanation
Indices: 21014032--21014098 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
21014022 TTTTATGATG
21014032 TAAGTTTTTGTCAAATTTAATATGACAATATAA
1 TAAGTTTTTGTCAAATTTAATATGACAATATAA
21014065 TAAGTTTTTGTCAAATTTAATATGACAATATAA
1 TAAGTTTTTGTCAAATTTAATATGACAATATAA
21014098 T
1 T
21014099 GTTGTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (33 bp):
TAAGTTTTTGTCAAATTTAATATGACAATATAA
Found at i:21014103 original size:28 final size:30
Alignment explanation
Indices: 21014038--21014105 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 30
21014028 GATGTAAGTT
21014038 TTTGTCAAATTTAATATGACAATATAATAAG
1 TTTGTCAAATTTAATATGACAATATAAT-AG
21014069 TTTTTGTCAAATTTAATATGACAATATAAT-G
1 --TTTGTCAAATTTAATATGACAATATAATAG
21014100 -TTGTCA
1 TTTGTCA
21014106 TATTATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
28 6 0.17
31 1 0.03
33 28 0.80
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (30 bp):
TTTGTCAAATTTAATATGACAATATAATAG
Found at i:21015356 original size:27 final size:27
Alignment explanation
Indices: 21015321--21015376 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
21015311 TTTTCATTAA
21015321 TTTTTTCAATCACAGA-TACAATAATTT
1 TTTTTTCAATCACA-ATTACAATAATTT
*
21015348 TTTTTTCAATCATAATTACAATAATTT
1 TTTTTTCAATCACAATTACAATAATTT
21015375 TT
1 TT
21015377 ATTACTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTTTTCAATCACAATTACAATAATTT
Found at i:21017355 original size:4 final size:4
Alignment explanation
Indices: 21017292--21017336 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
21017282 ATTTTGTATT
*
21017292 TTTA TTT- TGTA TCTTA TTTA TTTA -TTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
21017337 GTTATTGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 5 0.14
4 28 0.78
5 3 0.08
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:21017420 original size:28 final size:24
Alignment explanation
Indices: 21017339--21017492 Score: 123
Period size: 24 Copynumber: 6.8 Consensus size: 24
21017329 TATTTATTGT
* *
21017339 TATTGTTA-TTATTTATTAATATA
1 TATTATTATTTATCTATTAATATA
21017362 TA-TATT-TTTATCTATTAATATA
1 TATTATTATTTATCTATTAATATA
*
21017384 TATTATTATTTATCTATTAATGTA
1 TATTATTATTTATCTATTAATATA
*
21017408 TATAAATT-TTTAT-TATTAACTAT-
1 TAT-TATTATTTATCTATTAA-TATA
* *
21017431 TATCTGTTATTTATCTATTAGTATA
1 TAT-TATTATTTATCTATTAATATA
* * *
21017456 TA-TA-TATGTATATA-T-ATTTA
1 TATTATTATTTATCTATTAATATA
21017476 T-TTATTATTTATCTATT
1 TATTATTATTTATCTATT
21017493 TTTTTTTCTT
Statistics
Matches: 104, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.06
21 9 0.09
22 28 0.27
23 18 0.17
24 33 0.32
25 10 0.10
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (24 bp):
TATTATTATTTATCTATTAATATA
Found at i:21018242 original size:3 final size:3
Alignment explanation
Indices: 21018234--21018314 Score: 87
Period size: 3 Copynumber: 27.3 Consensus size: 3
21018224 TAATTATTTA
*
21018234 ATT ATT ATT ATT -TCT -TT ATT ATT ATT ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
21018278 CTT ATT CTT ATT ATT ATT ATT AGT ATTT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT A
21018315 GAATTATTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.06
3 60 0.91
4 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:21018407 original size:16 final size:16
Alignment explanation
Indices: 21018387--21018427 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
21018377 TTTATAAACA
21018387 AAAAAAAATATTTTTT
1 AAAAAAAATATTTTTT
*
21018403 GAAAAAAATATTTTTT
1 AAAAAAAATATTTTTT
21018419 AAAAAAAAT
1 AAAAAAAAT
21018428 TGAAAGTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AAAAAAAATATTTTTT
Found at i:21019900 original size:26 final size:26
Alignment explanation
Indices: 21019871--21019928 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
21019861 ATTTTTTATT
21019871 AATTTTTTTCAATTACAGATACAATA
1 AATTTTTTTCAATTACAGATACAATA
* ** *
21019897 AATTTTTTTTAATTGTAGTTACAATA
1 AATTTTTTTCAATTACAGATACAATA
*
21019923 ACTTTT
1 AATTTT
21019929 GTTATTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (26 bp):
AATTTTTTTCAATTACAGATACAATA
Found at i:21021916 original size:31 final size:31
Alignment explanation
Indices: 21021857--21021916 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
21021847 TTTGTATCTT
* * *
21021857 ATTTATTTATTTATTTATTGTTATTATTATG
1 ATTTATTTATATATATATTATTATTATTATG
21021888 ATTTATTTATATATATA-TATTATCTATTA
1 ATTTATTTATATATATATTATTAT-TATTA
21021917 ATATATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (31 bp):
ATTTATTTATATATATATTATTATTATTATG
Found at i:21021939 original size:24 final size:23
Alignment explanation
Indices: 21021891--21022002 Score: 88
Period size: 24 Copynumber: 4.8 Consensus size: 23
21021881 TATTATGATT
*
21021891 TATTTATATATA-TATA-TTATC
1 TATTAATATATATTATATTTATC
21021912 TATTAATATATATTAGTATTTATC
1 TATTAATATATATTA-TATTTATC
* * *
21021936 TATTAATGTATATAAATTTTTAT-
1 TATTAATATATAT-TATATTTATC
*
21021959 TATTAACTAT-TATCTATTTTTTATC
1 TATTAA-TATATAT-TA-TATTTATC
*
21021984 TATTAGTATATATATATAT
1 TATTAATATATAT-TATAT
21022003 GTATATTTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
21 11 0.15
22 2 0.03
23 12 0.16
24 37 0.51
25 11 0.15
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (23 bp):
TATTAATATATATTATATTTATC
Found at i:21022406 original size:16 final size:19
Alignment explanation
Indices: 21022379--21022419 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 19
21022369 GAGTTCGAGT
21022379 AAAGAGAGGGAAGA-AGA-
1 AAAGAGAGGGAAGAGAGAG
21022396 AAAGA-AGGGAAGAGAGAG
1 AAAGAGAGGGAAGAGAGAG
21022414 AAAGAG
1 AAAGAG
21022420 TGAAGGGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (19 bp):
AAAGAGAGGGAAGAGAGAG
Found at i:21022718 original size:3 final size:3
Alignment explanation
Indices: 21022704--21022790 Score: 88
Period size: 3 Copynumber: 28.3 Consensus size: 3
21022694 TAATATATAT
21022704 TTA TTA TT- TTA TTA TTA TTA TTA TTTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * * *
21022748 TTA TTA TTA TTCC TTA TTC TTAA TTC TTA TTA GTA TTTA TTA T
1 TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TTA TTA -TTA TTA T
21022791 AATTTAATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.06
3 57 0.81
4 9 0.13
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:21022740 original size:30 final size:30
Alignment explanation
Indices: 21022704--21022790 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
21022694 TAATATATAT
*
21022704 TTATTATTTTATTATTATTATTATTTATTA
1 TTATTATTTTATTATTATTATTATTCATTA
* *
21022734 TTATTATATTATTATTATTATTATTCCTTA
1 TTATTATTTTATTATTATTATTATTCATTA
* *
21022764 TTCTTAATTCTTATTAGTATTTATTAT
1 TTATT-ATT-TTATTATTA-TTATTAT
21022791 AATTTAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.65
31 2 0.04
32 8 0.17
33 7 0.15
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.66
Consensus pattern (30 bp):
TTATTATTTTATTATTATTATTATTCATTA
Found at i:21023073 original size:58 final size:57
Alignment explanation
Indices: 21022997--21023177 Score: 202
Period size: 58 Copynumber: 3.1 Consensus size: 57
21022987 GTAATGCAAC
* * * * *
21022997 TTTTCCTTGAAAGTAATTTTGTAAATAAATATTTTTGAGGAAAAGGTAAAAATATCAA
1 TTTT-CTTGAAAATAATTTTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAA
* * *
21023055 TTTTAGTTGAAAATAATTTTTTTAAAAAAAATATTTTTGAGGGAAAAGTTGAAAGTACCAA
1 TTTT-CTTGAAAATAA-TTTTTT-AAAAAAATATTTTTGA-GGAAAAGTTGAAAATATCAA
*
21023116 TTTTCTT-AAAATAAATTTTTTAAAAAAATGTTTTTGAGGAAAAAGTTGAAAATATTCAA
1 TTTTCTTGAAAAT-AATTTTTTAAAAAAATATTTTTGAGG-AAAAGTTGAAAATA-TCAA
21023175 TTT
1 TTT
21023178 CCTCGAAATT
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
57 2 0.02
58 41 0.39
59 22 0.21
60 19 0.18
61 20 0.19
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (57 bp):
TTTTCTTGAAAATAATTTTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAA
Found at i:21031808 original size:7 final size:7
Alignment explanation
Indices: 21031796--21031851 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
21031786 TTATGTTATG
21031796 ATTTTTT
1 ATTTTTT
21031803 ATTTTTT
1 ATTTTTT
*
21031810 ATTATTT
1 ATTTTTT
*
21031817 ATTTGATCT
1 ATTT--TTT
* *
21031826 AATGTTT
1 ATTTTTT
21031833 ATTTTTT
1 ATTTTTT
21031840 A-TTTTT
1 ATTTTTT
21031846 ATTTTT
1 ATTTTT
21031852 ATAAATTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
6 6 0.16
7 28 0.74
9 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (7 bp):
ATTTTTT
Found at i:21031996 original size:15 final size:14
Alignment explanation
Indices: 21031959--21032000 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
21031949 AAATTTAACA
*
21031959 TTATTATTGTATTT
1 TTATTATTTTATTT
21031973 TTATTATTTTATTT
1 TTATTATTTTATTT
*
21031987 TATGTTATTTTATT
1 T-TATTATTTTATT
21032001 GTAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTT
Found at i:21033964 original size:19 final size:18
Alignment explanation
Indices: 21033912--21034108 Score: 95
Period size: 19 Copynumber: 10.6 Consensus size: 18
21033902 ATTTTGTATC
21033912 TTATTTATTTATTATTTA
1 TTATTTATTTATTATTTA
21033930 TTATTTATTTATTTATTTA
1 TTATTTATTTA-TTATTTA
*
21033949 TT-GTTATTGTTATTATTTA
1 TTATTTA-T-TTATTATTTA
* *
21033968 TTA-ATATATA-TATTT-
1 TTATTTATTTATTATTTA
* *
21033983 TTATCTATTAATATATATTA
1 TTATTTATTTAT-TAT-TTA
*
21034003 TTATTTATCTATTAATGTATA
1 TTATTTATTTATT-AT-T-TA
* * *
21034024 TAAATT-TTTATTATTAA
1 TTATTTATTTATTATTTA
* *
21034041 CTA-TTATCTATTATTTA
1 TTATTTATTTATTATTTA
*
21034058 TCTA-TTAGTATATATATGTATA
1 T-TATTTA-TTTAT-TAT-T-TA
21034080 TATATTTATTTATTATTTA
1 T-TATTTATTTATTATTTA
21034099 TCTA-TTATTT
1 T-TATTTATTT
21034109 TTTTTCTTTT
Statistics
Matches: 138, Mismatches: 23, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
15 3 0.02
16 11 0.08
17 13 0.09
18 30 0.22
19 35 0.25
20 24 0.17
21 10 0.07
22 9 0.07
23 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTTATTTATTATTTA
Found at i:21033969 original size:4 final size:4
Alignment explanation
Indices: 21033899--21033950 Score: 65
Period size: 4 Copynumber: 13.5 Consensus size: 4
21033889 ATTTCGTATT
*
21033899 TTTA TTT- TGTA TCTTA TTTA TTTA -TTA TTTA -TTA TTTA TTTA TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21033945 TTTA TT
1 TTTA TT
21033951 GTTATTGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 8 0.19
4 31 0.74
5 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:21034031 original size:48 final size:48
Alignment explanation
Indices: 21033961--21034073 Score: 153
Period size: 48 Copynumber: 2.4 Consensus size: 48
21033951 GTTATTGTTA
*
21033961 TTATTTATTAATATATAT--ATTTTTATCTATTAA-TATATAT-TATTAT
1 TTATCTATTAATATATATAAATTTTTAT-TATTAACTAT-TATCTATTAT
*
21034007 TTATCTATTAATGTATATAAATTTTTATTATTAACTATTATCTATTAT
1 TTATCTATTAATATATATAAATTTTTATTATTAACTATTATCTATTAT
*
21034055 TTATCTATTAGTATATATA
1 TTATCTATTAATATATATA
21034074 TGTATATATA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
46 16 0.27
47 9 0.15
48 34 0.58
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (48 bp):
TTATCTATTAATATATATAAATTTTTATTATTAACTATTATCTATTAT
Found at i:21034034 original size:28 final size:24
Alignment explanation
Indices: 21033912--21034072 Score: 126
Period size: 24 Copynumber: 6.9 Consensus size: 24
21033902 ATTTTGTATC
*
21033912 TTATTTATTTATT-AT-T-TATTA
1 TTATTTATCTATTAATATATATTA
* * * *
21033933 TTTATTTATTTATTTAT-TGTTATTG
1 -TTATTTATCTATTAATAT-ATATTA
*
21033958 TTA-TTATTTATTAATATATA-TA
1 TTATTTATCTATTAATATATATTA
21033980 TT-TTTATCTATTAATATATATTA
1 TTATTTATCTATTAATATATATTA
* *
21034003 TTATTTATCTATTAATGTATATAAA
1 TTATTTATCTATTAATATATAT-TA
21034028 TT-TTTAT-TATTAACTAT-TATCTA
1 TTATTTATCTATTAA-TATATAT-TA
*
21034051 TTATTTATCTATTAGTATATAT
1 TTATTTATCTATTAATATATAT
21034073 ATGTATATAT
Statistics
Matches: 116, Mismatches: 11, Indels: 21
0.78 0.07 0.14
Matches are distributed among these distances:
22 32 0.28
23 32 0.28
24 37 0.32
25 15 0.13
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATTTATCTATTAATATATATTA
Found at i:21034094 original size:48 final size:46
Alignment explanation
Indices: 21033912--21034096 Score: 139
Period size: 48 Copynumber: 4.0 Consensus size: 46
21033902 ATTTTGTATC
* * * *
21033912 TTATTTATTTATTA-TTTAT-TATTTATTTATTTATTTA-TTGTTATTG
1 TTATTTATCTATTAGTATATATA-TT-TTTA-TTATTTATTTATTATTA
* * * *
21033958 TTA-TTATTTATTAATATATATATTTTTATCTATTAATATA-TATTA
1 TTATTTATCTATTAGTATATATATTTTTAT-TATTTATTTATTATTA
* **
21034003 TTATTTATCTATTAATGTATATAAATTTTTATTA-TTAACTATTATCTA
1 TTATTTATCTATT-A-GTATATATATTTTTATTATTTATTTATTAT-TA
* *
21034051 TTATTTATCTATTAGTATATATATGTATATATATTTATTTATTATT
1 TTATTTATCTATTAGTATATATATTTTTAT-TATTTATTTATTATT
21034097 TATCTATTAT
Statistics
Matches: 112, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
44 1 0.01
45 26 0.23
46 35 0.31
47 12 0.11
48 38 0.34
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (46 bp):
TTATTTATCTATTAGTATATATATTTTTATTATTTATTTATTATTA
Found at i:21034560 original size:16 final size:16
Alignment explanation
Indices: 21034522--21034571 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
21034512 GGGTTTGAGT
21034522 AGAAAG-AGGGAAGAG
1 AGAAAGAAGGGAAGAG
21034537 -GAAAAGAAGGGAAGAG
1 AG-AAAGAAGGGAAGAG
*
21034553 AGAGAGAA-GGAATGAG
1 AGAAAGAAGGGAA-GAG
21034569 AGA
1 AGA
21034572 TCTGGTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 20 0.67
17 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (16 bp):
AGAAAGAAGGGAAGAG
Found at i:21034863 original size:3 final size:3
Alignment explanation
Indices: 21034849--21034937 Score: 87
Period size: 3 Copynumber: 30.3 Consensus size: 3
21034839 TATACATTTA
21034849 ATT ATT -TT ATT ATT ATT ATT -TCT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
** * * *
21034892 ATT CGT ATT CTT ATT CTT ATT ATT ATT ATT AGT ATTT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
21034937 A
1 A
21034938 GAATTATTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 6 0.08
3 63 0.89
4 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:21036522 original size:26 final size:26
Alignment explanation
Indices: 21036485--21036540 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
21036475 TTTTTATTAA
*
21036485 TTTTTTTCAATTACAGATACAATAAT
1 TTTTTTTCAATTACAGATACAATAAC
* ** *
21036511 TTTTTTTTAATTGTAGTTACAATAAC
1 TTTTTTTCAATTACAGATACAATAAC
21036537 TTTT
1 TTTT
21036541 ATTATTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (26 bp):
TTTTTTTCAATTACAGATACAATAAC
Found at i:21038508 original size:23 final size:26
Alignment explanation
Indices: 21038478--21038525 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 26
21038468 TTATTTATTT
21038478 ATTTATTTAT-TAT-TAT-TATTATG
1 ATTTATTTATATATATATATATTATG
21038501 ATTTATTTATATATATATATATTAT
1 ATTTATTTATATATATATATATTAT
21038526 CTATTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.45
24 3 0.14
25 3 0.14
26 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTATTTATATATATATATATTATG
Found at i:21038525 original size:19 final size:18
Alignment explanation
Indices: 21038468--21038541 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 18
21038458 ATTTTGTATC
* *
21038468 TTATTTATTTATTTATTTA
1 TTATTTA-TTATATATATA
21038487 TTA-TTATTAT-TATGAT-
1 TTATTTATTATATAT-ATA
21038503 TTATTTATATATATATATA
1 TTATTTAT-TATATATATA
*
21038522 TTATCTATTA-ATATATA
1 TTATTTATTATATATATA
21038539 TTA
1 TTA
21038542 GTATTTATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
16 6 0.12
17 19 0.40
18 10 0.21
19 13 0.27
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (18 bp):
TTATTTATTATATATATA
Found at i:21038572 original size:24 final size:24
Alignment explanation
Indices: 21038504--21038579 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
21038494 TATTATGATT
* *
21038504 TATTTATATATATATATA-TTATC
1 TATTAATATATATAAATATTTATC
* *
21038527 TATTAATATATATTAGTATTTATC
1 TATTAATATATATAAATATTTATC
* *
21038551 TATTAATGTATATAAATTTTTAT-
1 TATTAATATATATAAATATTTATC
21038574 TATTAA
1 TATTAA
21038580 CTATTAACTA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 20 0.45
24 24 0.55
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (24 bp):
TATTAATATATATAAATATTTATC
Found at i:21039352 original size:3 final size:3
Alignment explanation
Indices: 21039339--21039420 Score: 103
Period size: 3 Copynumber: 27.0 Consensus size: 3
21039329 TTTATATATA
21039339 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
21039385 TCT TAT TCT TAT TCT TAT TAG TATT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
21039421 GAATTATTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.03
3 61 0.90
4 5 0.07
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:21039469 original size:15 final size:15
Alignment explanation
Indices: 21039449--21039487 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
21039439 TATTTTATCT
21039449 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
*
21039464 TTTATTTTAATTTTG
1 TTTATTTTAATTTTA
21039479 TTTATTTTA
1 TTTATTTTA
21039488 TGATTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:21039714 original size:58 final size:58
Alignment explanation
Indices: 21039619--21039861 Score: 260
Period size: 58 Copynumber: 4.2 Consensus size: 58
21039609 AAATTTAGGA
* * * * *
21039619 AAAAATTGAAAGTATCAATTTTCCTTGAAAGT-AATTTTGTAAAAAATATTTTTGAGG
1 AAAAGTTGAAAATATCAATTTTACTTGAAAATAAATTTTTTAAAAAATATTTTTGAGG
* * *
21039676 AAAAGGTAAAAATATCAATTTTAGTTGAAAATAAATTTTTTTAAAAAAATATTTTTGAGG
1 AAAAGTTGAAAATATCAATTTTACTTGAAAATAAA-TTTTTT-AAAAAATATTTTTGAGG
* * * * *
21039736 AAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAATTTTTTAAAAAATGTTTTTGAGG
1 AAAAGTTGAAAATATCAATTTTACTTGAAAATAAATTTTTTAAAAAATATTTTTGAGG
* * * * *
21039794 AAAAGTTGAAAATATCAATTTTCCTCGAAATTAAA-GTTTCAGAAAAATA-TTTTG-GG
1 AAAAGTTGAAAATATCAATTTTACTTGAAAATAAATTTTTTA-AAAAATATTTTTGAGG
21039850 AAAAAGTTGAAA
1 -AAAAGTTGAAA
21039862 GTACCAGTTT
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
56 2 0.01
57 45 0.29
58 53 0.34
59 11 0.07
60 45 0.29
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (58 bp):
AAAAGTTGAAAATATCAATTTTACTTGAAAATAAATTTTTTAAAAAATATTTTTGAGG
Found at i:21039736 original size:60 final size:58
Alignment explanation
Indices: 21039619--21039815 Score: 243
Period size: 60 Copynumber: 3.4 Consensus size: 58
21039609 AAATTTAGGA
* * * * * *
21039619 AAAAATTGAAAGTATCAATTTTCCTTGAAAGT-AATTTTGTAAAAAATATTTTTGAGG
1 AAAAGTTGAAAATATCAATTTTACTTAAAAATAAATTTTTTAAAAAATATTTTTGAGG
* * * *
21039676 AAAAGGTAAAAATATCAATTTTAGTTGAAAATAAATTTTTTTAAAAAAATATTTTTGAGG
1 AAAAGTTGAAAATATCAATTTTACTTAAAAATAAA-TTTTTT-AAAAAATATTTTTGAGG
* * * *
21039736 AAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAATTTTTTAAAAAATGTTTTTGAGG
1 AAAAGTTGAAAATATCAATTTTACTTAAAAATAAATTTTTTAAAAAATATTTTTGAGG
21039794 AAAAGTTGAAAATATCAATTTT
1 AAAAGTTGAAAATATCAATTTT
21039816 CCTCGAAATT
Statistics
Matches: 119, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
57 25 0.21
58 38 0.32
59 11 0.09
60 45 0.38
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (58 bp):
AAAAGTTGAAAATATCAATTTTACTTAAAAATAAATTTTTTAAAAAATATTTTTGAGG
Found at i:21043229 original size:15 final size:15
Alignment explanation
Indices: 21043209--21043239 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21043199 TTTGCATACA
*
21043209 TGCATTTTCATTCAT
1 TGCATTCTCATTCAT
21043224 TGCATTCTCATTCAT
1 TGCATTCTCATTCAT
21043239 T
1 T
21043240 ACACTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (15 bp):
TGCATTCTCATTCAT
Found at i:21050464 original size:11 final size:10
Alignment explanation
Indices: 21050449--21050506 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 10
21050439 TACTATGCTT
21050449 AAAAAAAAGA
1 AAAAAAAAGA
*
21050459 TAAAAAGAAAAA
1 -AAAAA-AAAGA
21050471 AAAAAGAAAGA
1 AAAAA-AAAGA
21050482 AAAAAAAATGA
1 AAAAAAAA-GA
*
21050493 AAAAAAATGA
1 AAAAAAAAGA
21050503 AAAA
1 AAAA
21050507 TGATGACTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.21
11 29 0.69
12 4 0.10
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.05
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:21050471 original size:15 final size:15
Alignment explanation
Indices: 21050462--21050499 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
21050452 AAAAAGATAA
21050462 AAAGAAAAAAAAAAG
1 AAAGAAAAAAAAAAG
*
21050477 AAAGAAAAAAAAATG
1 AAAGAAAAAAAAAAG
21050492 AAA-AAAAA
1 AAAGAAAAA
21050500 TGAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:21050473 original size:19 final size:18
Alignment explanation
Indices: 21050449--21050489 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
21050439 TACTATGCTT
21050449 AAAAAAAAGATAA-AAAGAA
1 AAAAAAAAGA-AAGAAA-AA
21050468 AAAAAAAAGAAAGAAAAA
1 AAAAAAAAGAAAGAAAAA
21050486 AAAA
1 AAAA
21050490 TGAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGAAAGAAAAA
Found at i:21050512 original size:10 final size:10
Alignment explanation
Indices: 21050482--21050506 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21050472 AAAAGAAAGA
21050482 AAAAAAAATG
1 AAAAAAAATG
21050492 AAAAAAAATG
1 AAAAAAAATG
21050502 AAAAA
1 AAAAA
21050507 TGATGACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:21051573 original size:44 final size:44
Alignment explanation
Indices: 21051525--21051874 Score: 248
Period size: 44 Copynumber: 8.2 Consensus size: 44
21051515 CTCTGATCAT
* **
21051525 AGGAGCTTTGTTTATTTTTCCAAAGTCATTGAGCCTCTGTTTAG
1 AGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTAATTAG
* * * * *
21051569 AGGAGTTTTGTTTATTTTTCAAAAGT-AGTTAAGCCTCTATTTAG
1 AGGAGCTTTATTTATTTTTCCAAAGTCA-TTGAGCCTCTAATTAG
* * *
21051613 AGGAGCTTTATTTATTTTTTCCAAAATCATTAAGCTTCTAATTAG
1 AGGAGCTTTATTTA-TTTTTCCAAAGTCATTGAGCCTCTAATTAG
*
21051658 AGGAGCCATTTA-TT-TTTTT-CAAAGTCATTGAGCCTCTGATTAG
1 AGGAG-C-TTTATTTATTTTTCCAAAGTCATTGAGCCTCTAATTAG
* * *
21051701 AGGAGC--AATTTA-CTTTCCAAAAGTCGTTGAGCCTCTAATT--
1 AGGAGCTTTATTTATTTTTCC-AAAGTCATTGAGCCTCTAATTAG
* ** *
21051741 A-GAG--TCATTTA-TTTTCCAAAGTTGTTGAGCCTTTAATTAG
1 AGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTAATTAG
* * * * * ** *
21051781 ATGAGC--CATTTA-TTTT-CAAGGTCGTGGAGCCTCTGTTTAA
1 AGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTAATTAG
* ** *
21051821 AGGAGCTTTGTTTATTTTTTTTAAAGTCATTGAGCCTCTACTTAG
1 AGGAGCTTTATTTA-TTTTTCCAAAGTCATTGAGCCTCTAATTAG
21051866 AGGAGCTTT
1 AGGAGCTTT
21051875 GATCAAAATT
Statistics
Matches: 248, Mismatches: 39, Indels: 37
0.77 0.12 0.11
Matches are distributed among these distances:
38 19 0.08
39 14 0.06
40 29 0.12
41 14 0.06
42 24 0.10
43 26 0.10
44 59 0.24
45 55 0.22
46 4 0.02
47 4 0.02
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (44 bp):
AGGAGCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTAATTAG
Found at i:21051686 original size:43 final size:43
Alignment explanation
Indices: 21051535--21051871 Score: 153
Period size: 45 Copynumber: 8.0 Consensus size: 43
21051525 AGGAGCTTTG
* * ** *
21051535 TTTA-TTTTTCCAAAGTCATTGAGCCTCTGTTTAGAGGAG--T
1 TTTATTTTTTTCAAAGTCATTAAGCCTCTAATTAGAGGAGCAA
* * *
21051575 TTTGTTTATTTTTCAAAAGT-AGTTAAGCCTCTATTTAGAGGAGCTTTA
1 TTT-ATT-TTTTTC-AAAGTCA-TTAAGCCTCTAATTAGAGGAGC--AA
* * * *
21051623 TTTATTTTTTCCAAAATCATTAAGCTTCTAATTAGAGGAGCCA
1 TTTATTTTTTTCAAAGTCATTAAGCCTCTAATTAGAGGAGCAA
* *
21051666 TTTATTTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCAA
1 TTTATTTTTTTCAAAGTCATTAAGCCTCTAATTAGAGGAGCAA
* * * * *
21051709 TTTA--CTTTCCAAAAGTCGTTGAGCCTCTAATTAGA-G-TC-A
1 TTTATTTTTTTC-AAAGTCATTAAGCCTCTAATTAGAGGAGCAA
* ** * * * *
21051748 TTTA--TTTTCCAAAGTTGTTGAGCCTTTAATTAGATGAGCCA
1 TTTATTTTTTTCAAAGTCATTAAGCCTCTAATTAGAGGAGCAA
* * ** ** * **
21051789 TTTA---TTTTCAAGGTCGTGGAGCCTCTGTTTAAAGGAGCTTTG
1 TTTATTTTTTTCAAAGTCATTAAGCCTCTAATTAGAGGAGC--AA
* * *
21051831 TTTATTTTTTTTAAAGTCATTGAGCCTCTACTTAGAGGAGC
1 TTTATTTTTTTCAAAGTCATTAAGCCTCTAATTAGAGGAGC
21051872 TTTGATCAAA
Statistics
Matches: 234, Mismatches: 44, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
38 22 0.09
39 11 0.05
40 30 0.13
41 10 0.04
42 27 0.12
43 48 0.21
44 24 0.10
45 51 0.22
46 6 0.03
47 2 0.01
48 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (43 bp):
TTTATTTTTTTCAAAGTCATTAAGCCTCTAATTAGAGGAGCAA
Found at i:21051736 original size:42 final size:41
Alignment explanation
Indices: 21051535--21051814 Score: 199
Period size: 43 Copynumber: 6.7 Consensus size: 41
21051525 AGGAGCTTTG
* ** ***
21051535 TTTATTTTTCCAAAGTCATTGAGCCTCTGTTTAGAGGAGTTTTG
1 TTTA-TTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAG--CCA
* * * * *
21051579 TTTATTTTTCAAAAGTAGTTAAGCCTCTATTTAGAGGAGCTTTA
1 TTTA-TTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAGC--CA
* * * *
21051623 TTTATTTTTTCCAAAATCATTAAGCTTCTAATTAGAGGAGCCA
1 TTTA--TTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAGCCA
* * * *
21051666 TTTATTTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCAA
1 TTTA--TTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAGCCA
* *
21051709 TTTACTTTCCAAAAGTCGTTGAGCCTCTAATT--A-GAGTCA
1 TTTATTTTCC-AAAGTCGTTGAGCCTCTAATTAGAGGAGCCA
* * *
21051748 TTTATTTTCCAAAGTTGTTGAGCCTTTAATTAGATGAGCCA
1 TTTATTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAGCCA
* *
21051789 TTTATTTT-CAAGGTCGTGGAGCCTCT
1 TTTATTTTCCAAAGTCGTTGAGCCTCT
21051815 GTTTAAAGGA
Statistics
Matches: 195, Mismatches: 34, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
38 19 0.10
39 13 0.07
40 16 0.08
41 17 0.09
42 19 0.10
43 42 0.22
44 39 0.20
45 30 0.15
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (41 bp):
TTTATTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAGCCA
Found at i:21051769 original size:80 final size:76
Alignment explanation
Indices: 21051669--21051814 Score: 175
Period size: 80 Copynumber: 1.9 Consensus size: 76
21051659 GGAGCCATTT
* *
21051669 ATTTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCAATTTACTTTCCAAAAGTCGTTGAGCC
1 ATTTTTTTCAAAGTCATTGAGCCTCTAATTAGAGGAGCAATTTA-TTTCC-AAAGTCGTGGAGCC
21051734 TCTAATTAGAGTC
64 TCTAATTAGAGTC
** * * * * *
21051747 ATTTATTTTCCAAAGTTGTTGAGCCTTTAATTAGATGAGCCATTTATTTTCAAGGTCGTGGAGCC
1 ATTT-TTTT-CAAAGTCATTGAGCCTCTAATTAGAGGAGCAATTTATTTCCAAAGTCGTGGAGCC
21051812 TCT
64 TCT
21051815 GTTTAAAGGA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
78 19 0.33
79 8 0.14
80 30 0.53
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (76 bp):
ATTTTTTTCAAAGTCATTGAGCCTCTAATTAGAGGAGCAATTTATTTCCAAAGTCGTGGAGCCTC
TAATTAGAGTC
Found at i:21052103 original size:10 final size:10
Alignment explanation
Indices: 21052069--21052242 Score: 67
Period size: 10 Copynumber: 17.2 Consensus size: 10
21052059 ATTTTGTATC
21052069 TTATTTA-T-
1 TTATTTATTA
*
21052077 TTATTTATTG
1 TTATTTATTA
21052087 TTA-TTATTA
1 TTATTTATTA
21052096 TTATTTATTGA
1 TTATTTATT-A
* *
21052107 TATATATATTT
1 T-TATTTATTA
*
21052118 TTATCTATTA
1 TTATTTATTA
* *
21052128 ATATATATTA
1 TTATTTATTA
21052138 TTATTTATCTA
1 TTATTTAT-TA
*
21052149 TTAATGTA-TA
1 TT-ATTTATTA
*
21052159 TAAATTT-TTA
1 T-TATTTATTA
** *
21052169 TTATCAACTA
1 TTATTTATTA
*
21052179 TTATCTATTA
1 TTATTTATTA
*
21052189 TTTATCTATTA
1 -TTATTTATTA
*
21052200 GTATATATATGTA
1 -T-TATTTAT-TA
21052213 -TATTTA-T-
1 TTATTTATTA
21052220 TTATTTATTA
1 TTATTTATTA
*
21052230 TTTATCTATTA
1 -TTATTTATTA
21052241 TT
1 TT
21052243 TTTTTCTTTT
Statistics
Matches: 127, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
8 14 0.11
9 12 0.09
10 55 0.43
11 27 0.21
12 17 0.13
13 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (10 bp):
TTATTTATTA
Found at i:21052160 original size:48 final size:46
Alignment explanation
Indices: 21052088--21052240 Score: 151
Period size: 48 Copynumber: 3.4 Consensus size: 46
21052078 TATTTATTGT
* *
21052088 TATTATTA-TTATTTATTGA-TATATATATTTTTATCTATTAATATA
1 TATTATTATTTATCTATTAAGTATATATATTTTTAT-TATTAATATA
* *
21052133 TATTATTATTTATCTATTAATGTATATAAATTTTTATTATCAACTAT-
1 TATTATTATTTATCTATTAA-GTATATATATTTTTATTATTAA-TATA
* * *
21052180 TATCTATTATTTATCTATT-AGTATATATA--TGTA-TATTTATTTA
1 TAT-TATTATTTATCTATTAAGTATATATATTTTTATTATTAATATA
21052223 T-TTATTATTTATCTATTA
1 TATTATTATTTATCTATTA
21052241 TTTTTTTCTT
Statistics
Matches: 92, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
41 15 0.16
42 3 0.03
43 5 0.05
44 3 0.03
45 8 0.09
46 17 0.18
47 9 0.10
48 32 0.35
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.59
Consensus pattern (46 bp):
TATTATTATTTATCTATTAAGTATATATATTTTTATTATTAATATA
Found at i:21052169 original size:28 final size:24
Alignment explanation
Indices: 21052088--21052243 Score: 119
Period size: 24 Copynumber: 6.5 Consensus size: 24
21052078 TATTTATTGT
* *
21052088 TATTATTA-TTATTTATTGATATA
1 TATTATTATTTATCTATTAATATA
21052111 TA-TATT-TTTATCTATTAATATA
1 TATTATTATTTATCTATTAATATA
*
21052133 TATTATTATTTATCTATTAATGTA
1 TATTATTATTTATCTATTAATATA
* *
21052157 TATAAATT-TTTAT-TATCAACTAT-
1 TAT-TATTATTTATCTATTAA-TATA
21052180 TATCTATTATTTATCTATTAGTATATA
1 TAT-TATTATTTATCTATTA--ATATA
* * *
21052207 TATGTA-TATTTATTTATTTATTATT
1 TAT-TATTATTTATCTA-TTAATATA
21052232 TATCTATTATTT
1 TAT-TATTATTT
21052244 TTTTCTTTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
22 19 0.18
23 17 0.16
24 30 0.28
25 15 0.14
26 17 0.16
27 9 0.08
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (24 bp):
TATTATTATTTATCTATTAATATA
Found at i:21052195 original size:11 final size:11
Alignment explanation
Indices: 21052179--21052243 Score: 64
Period size: 11 Copynumber: 6.2 Consensus size: 11
21052169 TTATCAACTA
21052179 TTATCTATTAT
1 TTATCTATTAT
21052190 TTATCTATTA-
1 TTATCTATTAT
* *
21052200 GTATATA-TAT
1 TTATCTATTAT
* *
21052210 GTATAT-TTAT
1 TTATCTATTAT
*
21052220 TTATTTATTAT
1 TTATCTATTAT
21052231 TTATCTATTAT
1 TTATCTATTAT
21052242 TT
1 TT
21052244 TTTTCTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
9 2 0.04
10 18 0.39
11 26 0.57
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (11 bp):
TTATCTATTAT
Found at i:21053035 original size:3 final size:3
Alignment explanation
Indices: 21053027--21053071 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
21053017 TTATTTCTTT
* *
21053027 TTA TTA TTA TTA TTC TTA TTA TTA TTA TTA GTA TTTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
21053072 GAATTATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:21053102 original size:11 final size:11
Alignment explanation
Indices: 21053086--21053119 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21053076 TATTTGGTAT
21053086 TCTTTATTTTA
1 TCTTTATTTTA
21053097 TCTTTATTTTTA
1 TCTTTA-TTTTA
21053109 T-TTTATTTTA
1 TCTTTATTTTA
21053119 T
1 T
21053120 GATTTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 10 0.45
12 6 0.27
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTATTTTA
Found at i:21053229 original size:16 final size:16
Alignment explanation
Indices: 21053189--21053234 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
21053179 TAAGGAAAAG
*
21053189 TTAAAAGTATCAAATTT
1 TTAAAA-TATAAAATTT
21053206 TCTAAAATATAAAATTT
1 T-TAAAATATAAAATTT
21053223 TTAAAATA-AAAA
1 TTAAAATATAAAA
21053235 AAATTTAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 4 0.15
16 7 0.26
17 11 0.41
18 5 0.19
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (16 bp):
TTAAAATATAAAATTT
Found at i:21053236 original size:17 final size:17
Alignment explanation
Indices: 21053200--21053235 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
21053190 TAAAAGTATC
*
21053200 AAATTTTCTAAAATATA
1 AAATTTTCTAAAATAAA
21053217 AAATTTT-TAAAATAAA
1 AAATTTTCTAAAATAAA
21053233 AAA
1 AAA
21053236 AATTTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTTCTAAAATAAA
Found at i:21053315 original size:118 final size:117
Alignment explanation
Indices: 21053175--21053508 Score: 360
Period size: 118 Copynumber: 2.8 Consensus size: 117
21053165 TGAAAAAGTG
* *
21053175 TTTTTAAGGAAAAGTTAAAAGTATCAAATTTTCTAAAATATAAAATTTTTAAAATAAAAAAA-AT
1 TTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTAAAA-AT-AAATTTTT--AATAAAAAAATAT
* *
21053239 TTAGGA-AAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AATTTTCTAAATAATA
62 TTAGGACAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCTAAAAAATA
* ** *
21053293 TTTTTGAGGAAAAGGTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTTTTAAAAAAATATTTT
1 TTTTTGAGGAAAAGTTAAAAGTATCAATTTTTC-TAAAAATAAATTTTTAATAAAAAAATATTTA
* * *
21053358 TGACGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTTAAAAAATA
65 GGAC-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCTAAAAAATA
* * * * * * *
21053412 TTTTTGACGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAA-AAAAATAT-TTTG
1 TTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCT-AAAAATAAATTTTTAATAAAAAAATATTT-
*
21053475 AGG--AAAAGTTGGAAGTA-CAAATTTTCCTTAAAAA
64 AGGACAAAAGTTGAAAGTATC-AATTTTCCTTAAAAA
21053509 AATATATTTT
Statistics
Matches: 183, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
114 1 0.01
115 35 0.19
116 6 0.03
117 11 0.06
118 71 0.39
119 59 0.32
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (117 bp):
TTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTAAAAATAAATTTTTAATAAAAAAATATTTAG
GACAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCTAAAAAATA
Found at i:21053316 original size:57 final size:58
Alignment explanation
Indices: 21053245--21053508 Score: 327
Period size: 58 Copynumber: 4.5 Consensus size: 58
21053235 AAATTTAGGA
* * * *
21053245 AAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AATTTTCTAAATAATATTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATATTTTTGACG
* * *
21053302 AAAAGGTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTTTTAAAAAAATATTTTTGACG
1 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA--TTTTCT-AAAAAATATTTTTGACG
*
21053363 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTTAAAAAATATTTTTGACG
1 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATATTTTTGACG
** * * * *
21053421 AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAAAAAAATA-TTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATATTTTTGACG
* *
21053478 AAAAGTTGGAAGTA-CAAATTTTCCTTAAAAA
1 AAAAGTTGAAAGTATC-AATTTTTCTTAAAAA
21053509 AATATATTTT
Statistics
Matches: 181, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
56 1 0.01
57 59 0.33
58 62 0.34
59 6 0.03
60 5 0.03
61 48 0.27
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (58 bp):
AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATATTTTTGACG
Found at i:21053340 original size:17 final size:16
Alignment explanation
Indices: 21053318--21053358 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
21053308 TAAAAGTATC
21053318 AATTTTTCTTAAAAATA
1 AATTTTTCTTAAAAA-A
*
21053335 AATTTTTTTTAAAAAA
1 AATTTTTCTTAAAAAA
21053351 ATATTTTT
1 A-ATTTTT
21053359 GACGAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTTTTCTTAAAAAA
Found at i:21053340 original size:58 final size:58
Alignment explanation
Indices: 21053175--21053508 Score: 338
Period size: 61 Copynumber: 5.7 Consensus size: 58
21053165 TGAAAAAGTG
* * * *
21053175 TTTTTAAGGAAAAGTTAAAAGTATCAAATTTTC-TAAAATATAAAATTTT-TAAAATAAAAAA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAA-AT-AAATTTTCT--AA-AAAATA
** * * *
21053236 AATTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AATTTTCTAAATAATA
1 TTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATA
* * *
21053293 TTTTTGAGGAAAAGGTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTTTTAAAAAAATA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA--TTTTCT-AAAAAATA
* *
21053354 TTTTTGACGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTTAAAAAATA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATA
* ** * * *
21053412 TTTTTGACGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAAAAAAATA
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATA
* *
21053470 -TTTTGAGGAAAAGTTGGAAGTA-CAAATTTTCCTTAAAAA
1 TTTTTGAGGAAAAGTTGAAAGTATC-AATTTTTCTTAAAAA
21053509 AATATATTTT
Statistics
Matches: 233, Mismatches: 31, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
56 1 0.00
57 66 0.28
58 67 0.29
59 12 0.05
60 9 0.04
61 74 0.32
62 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (58 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAAAATA
Found at i:21053408 original size:16 final size:17
Alignment explanation
Indices: 21053379--21053411 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21053369 TGAAAGTATC
*
21053379 AATTTTTCTTAAAAATA
1 AATTTTTCTAAAAAATA
21053396 AATTTTT-TAAAAAATA
1 AATTTTTCTAAAAAATA
21053412 TTTTTGACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTTCTAAAAAATA
Found at i:21054787 original size:26 final size:26
Alignment explanation
Indices: 21054745--21054794 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
21054735 AAGTAGTTAC
21054745 TGTAACTACAATTAAAAAAAAATTAT
1 TGTAACTACAATTAAAAAAAAATTAT
*
21054771 TGTAACTGC-ATTGAAAAAAAAATT
1 TGTAACTACAATT-AAAAAAAAATT
21054795 TAATAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (26 bp):
TGTAACTACAATTAAAAAAAAATTAT
Found at i:21059204 original size:18 final size:18
Alignment explanation
Indices: 21059140--21059207 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
21059130 TGAGGTGGCA
*
21059140 CTAACATGTC-GGTCGAC
1 CTAACATGTCAAGTCGAC
21059157 CTAACATGTCAAGTCAGTA-
1 CTAACATGTCAAGTC-G-AC
21059176 C-AA-ATGATCAAGTCGAC
1 CTAACATG-TCAAGTCGAC
21059193 CTAACATGTCAAGTC
1 CTAACATGTCAAGTC
21059208 AGTATAAAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 1 0.02
17 15 0.35
18 21 0.49
19 5 0.12
20 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (18 bp):
CTAACATGTCAAGTCGAC
Found at i:21059397 original size:233 final size:233
Alignment explanation
Indices: 21058990--21059420 Score: 826
Period size: 233 Copynumber: 1.8 Consensus size: 233
21058980 GATGGGCAAG
*
21058990 TCAGTAAAGATCAGGTCGGCAAAAAAGTAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
1 TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
21059055 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
66 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
21059120 AAGGTCGAGCTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
131 AAGGTCGAGCTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
21059185 AAGTCGACCTAACATGTCAAGTCAGTATAAAGGGATAA
196 AAGTCGACCTAACATGTCAAGTCAGTATAAAGGGATAA
21059223 TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
1 TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
*
21059288 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAGGGATAATTAGGA
66 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
* *
21059353 AAGGTTGAGTTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
131 AAGGTCGAGCTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
21059418 AAG
196 AAG
21059421 ATATCCCTGA
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 194 1.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (233 bp):
TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
AAGGTCGAGCTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
AAGTCGACCTAACATGTCAAGTCAGTATAAAGGGATAA
Found at i:21066538 original size:18 final size:19
Alignment explanation
Indices: 21066515--21066550 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21066505 GAAATTATCC
*
21066515 CATTTTTGTT-TTTATTTT
1 CATTTTTATTATTTATTTT
21066533 CATTTTTATTATTTATTT
1 CATTTTTATTATTTATTT
21066551 ATTTATTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (19 bp):
CATTTTTATTATTTATTTT
Found at i:21068206 original size:60 final size:61
Alignment explanation
Indices: 21068077--21068192 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 61
21068067 TTTCAAAAAC
* * *
21068077 AAAAAAA-AAAGAA-AAAAATTTTCTAAATAAGCTCAAATGGTAAAAAATTTAGAAATAAA
1 AAAAAAAGAAATAAGAAAAATTTTCTAAATAAGCCCAAATGGTAAAAAATTTAAAAATAAA
*
21068136 AAAAAAAGAAATAAGAAAAA-TTTCTAAATAAGCCCAAATGGTGAAAAATTTAAAAAT
1 AAAAAAAGAAATAAGAAAAATTTTCTAAATAAGCCCAAATGGTAAAAAATTTAAAAAT
21068193 TCTGAAAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 7 0.14
60 39 0.76
61 5 0.10
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (61 bp):
AAAAAAAGAAATAAGAAAAATTTTCTAAATAAGCCCAAATGGTAAAAAATTTAAAAATAAA
Found at i:21072861 original size:22 final size:21
Alignment explanation
Indices: 21072827--21072873 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
21072817 AGCCTGTGAG
21072827 TTATGATCGAAT-GATGAAAAT
1 TTATGATCGAATGGAT-AAAAT
21072848 ATTATGGATC-AATGGATAAAAT
1 -TTAT-GATCGAATGGATAAAAT
21072870 TTAT
1 TTAT
21072874 TCTAAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 7 0.30
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (21 bp):
TTATGATCGAATGGATAAAAT
Found at i:21073000 original size:63 final size:63
Alignment explanation
Indices: 21072879--21073003 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
21072869 TTTATTCTAA
* * *
21072879 AATGGCTAGTACTAAGAAACCTATAAGTGGTGACCCAGTGTTTGGTGACAAAAATTGTTTTGG
1 AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGTATGGGGACAAAAATTGTTTTGG
* * * *
21072942 AATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTG-ATGGAGGACGAAACTTGTTTTG
1 AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGTATGG-GGACAAAAATTGTTTTG
21073004 AAATTGTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 3 0.06
63 51 0.94
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (63 bp):
AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGTATGGGGACAAAAATTGTTTTGG
Found at i:21073020 original size:63 final size:63
Alignment explanation
Indices: 21072878--21073022 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
21072868 ATTTATTCTA
* * * * *
21072878 AAATGGCTAGTACTAAGAAACCTATAAGTGGTGACCCAGTGTTTGGTGACAAAAATTGTTTTG
1 AAATGGCTAATACTGAGAAACCTATAAGTAGTGACCCAGTGTATGGGGACAAAAATTGTTTTG
* * * * *
21072941 GAATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTG-ATGGAGGACGAAACTTGTTTTG
1 AAATGGCTAATACTGAGAAACCTATAAGTAGTGACCCAGTGTATGG-GGACAAAAATTGTTTTG
* * *
21073004 AAATTGTTAATGCTGAGAA
1 AAATGGCTAATACTGAGAA
21073023 GCTTATGAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
62 3 0.04
63 65 0.96
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (63 bp):
AAATGGCTAATACTGAGAAACCTATAAGTAGTGACCCAGTGTATGGGGACAAAAATTGTTTTG
Found at i:21073952 original size:42 final size:41
Alignment explanation
Indices: 21073884--21073964 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
21073874 CGAAGAGCAT
* * **
21073884 TTTATTTTTCTAAAGTTGCGGTGCCTCTGTTTAGAGGAGTA
1 TTTATTTTTCTAAAGTCGCGGAGCCTCTAATTAGAGGAGTA
**
21073925 TTTATTTTTCTTAAAGTCGTTGAGCCTCTAATTAGAGGAG
1 TTTATTTTTC-TAAAGTCGCGGAGCCTCTAATTAGAGGAG
21073965 CTTTGTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 10 0.30
42 23 0.70
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (41 bp):
TTTATTTTTCTAAAGTCGCGGAGCCTCTAATTAGAGGAGTA
Found at i:21080998 original size:19 final size:19
Alignment explanation
Indices: 21080974--21081016 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21080964 TGTGATTTTA
21080974 TTTTTT-TGGTTAATAATAT
1 TTTTTTATGGTTAA-AATAT
*
21080993 TTTTTTATGTTTAAAATAT
1 TTTTTTATGGTTAAAATAT
21081012 TTTTT
1 TTTTT
21081017 CTAAAACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTTTATGGTTAAAATAT
Found at i:21083972 original size:28 final size:28
Alignment explanation
Indices: 21083940--21083998 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
21083930 TTGTTTATTT
21083940 ATTAATTTATTAATTTTTTATAAGTACG
1 ATTAATTTATTAATTTTTTATAAGTACG
21083968 ATTAATTTATTAATTTTTTATAAGTACG
1 ATTAATTTATTAATTTTTTATAAGTACG
21083996 ATT
1 ATT
21083999 GTAATTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (28 bp):
ATTAATTTATTAATTTTTTATAAGTACG
Found at i:21084558 original size:230 final size:232
Alignment explanation
Indices: 21084261--21084730 Score: 601
Period size: 230 Copynumber: 2.0 Consensus size: 232
21084251 AAATTTTAAC
* * * *
21084261 AAATATCATATATAAGTTTAGTAAAAACAAATTTATATTTTTTTTATTTTTTGTATTGATACAAA
1 AAATACCATATACAAGTTTAGTAAAAAAAAATTTATA-TTTTTTTATTTTTTGTATTGACACAAA
* * * *
21084326 TTATGATATATAATTTTCGT-ATAAAGCATA-ATATTTATAAATACATAAATTATTAATATTTTA
65 TTATGATATATAATTTT-ATAATAAAACA-AGATATATATAAATACATAAATTATCAATATTTTA
* *** * * * *
21084389 CACAATACTAATACTTGAATTGTTAGTTCTGTATATA-TTTGATTTCATCCAACTTTGCATTTCT
128 AACAATACTAATACACAAATTGTCAATTCTATATATACATT-ATTTCATCCAACTTTGCATTTCT
* *
21084453 TTTGTATTTTTCACAAATA-TTATAATTTATTCCTTTTTCA
192 TTCGCATTTTTCACAAATATTTATAATTTATTCCTTTTTCA
*
21084493 AAATACCATATACGAGTTTAGTAAAAATAAAATTT-TA-TTTTTTATTTTTTGTATTGACACAAA
1 AAATACCATATACAAGTTTAGTAAAAA-AAAATTTATATTTTTTTATTTTTTGTATTGACACAAA
* * *
21084556 TTATTATATATAATTTTATAATAAAACAAGATATATATAAATATATGAATTATCAATATTTTAAA
65 TTATGATATATAATTTTATAATAAAACAAGATATATATAAATACATAAATTATCAATATTTTAAA
** *
21084621 CGTTACTAATACACAAATTGTCAATTCTATATATACATTATTTCATCTAACTTTGCATTTCTTTC
130 CAATACTAATACACAAATTGTCAATTCTATATATACATTATTTCATCCAACTTTGCATTTCTTTC
* *
21084686 GCATTTTTCACAAATATTTGTAATTTCTTCCTTTTTCA
195 GCATTTTTCACAAATATTTATAATTTATTCCTTTTTCA
*
21084724 AAGTACC
1 AAATACC
21084731 CTAGGGGACG
Statistics
Matches: 205, Mismatches: 28, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
229 2 0.01
230 144 0.70
231 27 0.13
232 26 0.13
233 6 0.03
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (232 bp):
AAATACCATATACAAGTTTAGTAAAAAAAAATTTATATTTTTTTATTTTTTGTATTGACACAAAT
TATGATATATAATTTTATAATAAAACAAGATATATATAAATACATAAATTATCAATATTTTAAAC
AATACTAATACACAAATTGTCAATTCTATATATACATTATTTCATCCAACTTTGCATTTCTTTCG
CATTTTTCACAAATATTTATAATTTATTCCTTTTTCA
Found at i:21088084 original size:37 final size:39
Alignment explanation
Indices: 21088010--21088101 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 39
21088000 TATATTGCAA
* * *
21088010 TTATTTTTTTTTATTT-TTTCATGTTATGTTATGATTTT
1 TTATTTTTTATTATTTATTTCATCTAATGTTATGATTTT
*
21088048 TTATTTTTTATTATTTATTTGATCTAATG-TAT-ATTTT
1 TTATTTTTTATTATTTATTTCATCTAATGTTATGATTTT
21088085 TTATTTTTTATT-TTTAT
1 TTATTTTTTATTATTTAT
21088102 AAATTACAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 5 0.10
37 17 0.35
38 18 0.37
39 9 0.18
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (39 bp):
TTATTTTTTATTATTTATTTCATCTAATGTTATGATTTT
Found at i:21088244 original size:15 final size:14
Alignment explanation
Indices: 21088207--21088248 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
21088197 AAATTTAACA
*
21088207 TTATTATTGTATTT
1 TTATTATTTTATTT
21088221 TTATTATTTTATTT
1 TTATTATTTTATTT
*
21088235 TATGTTATTTTATT
1 T-TATTATTTTATT
21088249 GTAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTT
Found at i:21088990 original size:20 final size:19
Alignment explanation
Indices: 21088953--21088990 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
21088943 TTGCACATGC
21088953 ATTTAATTAAATATTTAAT
1 ATTTAATTAAATATTTAAT
21088972 ATTTAAGTTGAAA-ATTTAA
1 ATTTAA-TT-AAATATTTAA
21088991 ATATCGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
ATTTAATTAAATATTTAAT
Found at i:21092943 original size:28 final size:28
Alignment explanation
Indices: 21092911--21092974 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
21092901 AAGTAATAAT
*
21092911 AAAAATTACTGTAGCTATAATTAAAAAA
1 AAAAATTACTGTAGCTACAATTAAAAAA
* * * *
21092939 AAAAATTATTGTAGCTGCGATTGAAAAA
1 AAAAATTACTGTAGCTACAATTAAAAAA
21092967 AAAAATTA
1 AAAAATTA
21092975 ATAAGAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (28 bp):
AAAAATTACTGTAGCTACAATTAAAAAA
Found at i:21096592 original size:26 final size:26
Alignment explanation
Indices: 21096554--21096614 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
21096544 CTAAGAGTTT
21096554 ATTAATTTATTTATCAATATTTTAACC
1 ATTAA-TTATTTATCAATATTTTAACC
*
21096581 ATTAATTATTTATCACTATTTTAACC
1 ATTAATTATTTATCAATATTTTAACC
*
21096607 -TTACTTAT
1 ATTAATTAT
21096615 AAGATAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 7 0.22
26 20 0.62
27 5 0.16
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTAATTATTTATCAATATTTTAACC
Found at i:21100687 original size:20 final size:20
Alignment explanation
Indices: 21100662--21100701 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21100652 GCTGCTGCTA
21100662 ATGAATAAATTCTGTAATTT
1 ATGAATAAATTCTGTAATTT
*
21100682 ATGAATAAATTTTGTAATTT
1 ATGAATAAATTCTGTAATTT
21100702 TTTGTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
ATGAATAAATTCTGTAATTT
Found at i:21105445 original size:12 final size:12
Alignment explanation
Indices: 21105428--21105468 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
21105418 ATATTTTTTT
21105428 TATTTTATTTAG
1 TATTTTATTTAG
21105440 TATTTTATTTATG
1 TATTTTATTTA-G
*
21105453 TA-CTT-TTTAG
1 TATTTTATTTAG
21105463 TATTTT
1 TATTTT
21105469 TGCATGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 3 0.12
11 6 0.24
12 13 0.52
13 3 0.12
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.68
Consensus pattern (12 bp):
TATTTTATTTAG
Found at i:21105679 original size:7 final size:7
Alignment explanation
Indices: 21105661--21105690 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
21105651 ATTTATTTTC
21105661 AAAACA-
1 AAAACAT
21105667 AAAACAT
1 AAAACAT
21105674 AAAACAT
1 AAAACAT
21105681 AAAACAT
1 AAAACAT
21105688 AAA
1 AAA
21105691 TAAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAACAT
Found at i:21105941 original size:46 final size:46
Alignment explanation
Indices: 21105879--21105977 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
21105869 TCAAAAACAA
* * *
21105879 AAAAAAAAGAAAAAATTTTCTAAATAAGCTCAGATGGTAGAAAATTT
1 AAAAATAA-AAAAAATTTTCTAAATAAGCCCAAATGGTAGAAAATTT
* * *
21105926 AGAAATAAAAAAAATTTTCTAAATAAGCCCAAATGGTGGAAATTTT
1 AAAAATAAAAAAAATTTTCTAAATAAGCCCAAATGGTAGAAAATTT
21105972 AAAAAT
1 AAAAAT
21105978 TCTGAAAAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 39 0.87
47 6 0.13
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (46 bp):
AAAAATAAAAAAAATTTTCTAAATAAGCCCAAATGGTAGAAAATTT
Found at i:21109983 original size:22 final size:21
Alignment explanation
Indices: 21109941--21109987 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
21109931 AGCCTGTGAG
21109941 TTATGATCGAATGATAAAAAT
1 TTATGATCGAATGATAAAAAT
21109962 ATTATAGATC-AATGGAT-AAAAT
1 -TTAT-GATCGAAT-GATAAAAAT
21109984 TTAT
1 TTAT
21109988 TTTGAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 7 0.30
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (21 bp):
TTATGATCGAATGATAAAAAT
Found at i:21110077 original size:63 final size:62
Alignment explanation
Indices: 21109979--21110097 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 62
21109969 ATCAATGGAT
* * *
21109979 AAAATTTATTTTGAAATGGCTAGTATTAAAAAACCTATAAGTGGTGACCTAGTGATGGTGAC
1 AAAATTTATTTTGAAATGGCTAGTACTAAAAAACCTATAAGTAGTGACCCAGTGATGGTGAC
* * * * *
21110041 AAAATTTGTTTTTGGAATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGAT
1 AAAATTT-ATTTTGAAATGGCTAGTACTAAAAAACCTATAAGTAGTGACCCAGTGAT
21110098 AAAGGACAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
62 7 0.15
63 41 0.85
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (62 bp):
AAAATTTATTTTGAAATGGCTAGTACTAAAAAACCTATAAGTAGTGACCCAGTGATGGTGAC
Found at i:21111079 original size:40 final size:40
Alignment explanation
Indices: 21111016--21111156 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
21111006 CATGATTGTC
* * *
21111016 AAAGAGTATTTTATTTTTTAAAGTTGTGGTGCCT-TATTT
1 AAAGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTT
* *
21111055 AAATGAGCATTTTATTTTCCAAAGTTGTGGTGCTTCTGTTT
1 AAA-GAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTT
* * **
21111096 AGAGGAGCAATTTATTTTTTCAAAGTCATGGTGCCTCTGTTT
1 A-AAGAGCATTTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTT
21111138 AGAAGAGCA-TTTATTTTTC
1 A-AAGAGCATTTTATTTTTC
21111157 TTAAAGTCGT
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
39 3 0.03
40 33 0.38
41 18 0.21
42 32 0.37
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (40 bp):
AAAGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTT
Found at i:21111113 original size:41 final size:41
Alignment explanation
Indices: 21111025--21111156 Score: 153
Period size: 42 Copynumber: 3.2 Consensus size: 41
21111015 CAAAGAGTAT
* * *
21111025 TTTATTTTTTAAAGTTGTGGTGCCT-TATTTA-AATGAGCAT
1 TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAA-GAGCAA
* * *
21111065 TTTATTTTCCAAAGTTGTGGTGCTTCTGTTTAGAGGAGCAA
1 TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAAGAGCAA
**
21111106 TTTATTTTTTCAAAGTCATGGTGCCTCTGTTTAGAAGAGC-A
1 TTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAAGAGCAA
21111147 TTTATTTTTC
1 TTTATTTTTC
21111157 TTAAAGTCGT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 28 0.36
41 19 0.24
42 31 0.40
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (41 bp):
TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAAGAGCAA
Found at i:21111135 original size:42 final size:42
Alignment explanation
Indices: 21111025--21111175 Score: 150
Period size: 42 Copynumber: 3.7 Consensus size: 42
21111015 CAAAGAGTAT
* * *
21111025 TTTATTTTTT-AAAGTTGTGGTGCCT-TATTTA-AATGAGCAT
1 TTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAA-GAGCAA
* * * *
21111065 TTTA-TTTTCCAAAGTTGTGGTGCTTCTGTTTAGAGGAGCAA
1 TTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAAGAGCAA
*
21111106 TTTATTTTTTCAAAGTCATGGTGCCTCTGTTTAGAAGAGC-A
1 TTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAAGAGCAA
* * *
21111147 TTTATTTTTCTTAAAGTCGTTGAGCCTCT
1 TTTATTTTT-TCAAAGTCGTGGTGCCTCT
21111176 AATTAGAAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 4 0.04
40 18 0.20
41 24 0.26
42 46 0.50
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (42 bp):
TTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAAGAGCAA
Found at i:21112378 original size:13 final size:12
Alignment explanation
Indices: 21112349--21112389 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
21112339 TGGTTTTTTT
21112349 TATTTTATTTAG
1 TATTTTATTTAG
21112361 TATTTTATTTATG
1 TATTTTATTTA-G
21112374 TA-TTT-TTTAG
1 TATTTTATTTAG
21112384 TATTTT
1 TATTTT
21112390 TGCATGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
12 14 0.52
13 3 0.11
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (12 bp):
TATTTTATTTAG
Found at i:21112732 original size:197 final size:193
Alignment explanation
Indices: 21112408--21112785 Score: 476
Period size: 197 Copynumber: 1.9 Consensus size: 193
21112398 TAAATTTAGA
** * **
21112408 AAAAAAAATAAAAAAATAAAAAAATTTTAGAATAAATATTAATTATCCAATGATGAAATTTATAA
1 AAAAAAAATAAAAAAATAAAAAAATTTTAGAATAAATACAAATTACCCAAAAATGAAATTTATAA
* * *
21112473 AAATTTCAAATAGTAAATTTTTATAAAATTCTTAGATGAGAAATTTTGTCTAAATTTGTCCCAAA
66 AAATTTCAAATAGTAAAGTTTTAAAAAATTCTTAGATGAGAAATTTTCTCTAAATTTGTCCCAAA
* **
21112538 TTGTGGAATAATTTAGATAG-AATTTCAATAGCAATAATTAATATTTATTTTCCAAAAAAAAAAA
131 ATGTGGAATAATTTAGA-AGAAATTTCAATAAAAATAATT-ATATTT-TTTTCCAAAAAAAAAAA
21112602 C
193 C
* * *
21112603 AAAATAAATAAATAAATAAATAAAAATTTTAGAA-AAATACAAATTACCCAAAAATGAGATTCT-
1 AAAAAAAATAAAAAAAT-AA-AAAAATTTTAGAATAAATACAAATTACCCAAAAATGAAATT-TA
* * * * *
21112666 TAGAAATTTTAAATTGTAAAGTTTTAAAGAAA-TCTTTAGGTGAGAAATTTTCTTTAAATTTGTC
63 TAAAAATTTCAAATAGTAAAGTTTTAAA-AAATTC-TTAGATGAGAAATTTTCTCTAAATTTGTC
*
21112730 CCAAAATGTGGAATAATTTAGAAGAAATTTCAATAAAAATAATTGTATTTTTTTCC
126 CCAAAATGTGGAATAATTTAGAAGAAATTTCAATAAAAATAATTATATTTTTTTCC
21112786 CAATAAAATT
Statistics
Matches: 157, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
195 21 0.13
196 55 0.35
197 81 0.52
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (193 bp):
AAAAAAAATAAAAAAATAAAAAAATTTTAGAATAAATACAAATTACCCAAAAATGAAATTTATAA
AAATTTCAAATAGTAAAGTTTTAAAAAATTCTTAGATGAGAAATTTTCTCTAAATTTGTCCCAAA
ATGTGGAATAATTTAGAAGAAATTTCAATAAAAATAATTATATTTTTTTCCAAAAAAAAAAAC
Found at i:21113061 original size:56 final size:55
Alignment explanation
Indices: 21112988--21113122 Score: 173
Period size: 56 Copynumber: 2.4 Consensus size: 55
21112978 AGGAAAAAGA
* * *
21112988 ATTTCTAAATAAGCCCAAATGGTGAAAATTTTAAAAATTTAAAAAAAAAAGAAAAT
1 ATTTCTAATTGAGCCCAAATGGTGAAAAATTTAAAAATTTAAAAAAAAAA-AAAAT
** *
21113044 ATTTCTAGATTGA-CCCAAATGGTGAAAAATTTAAAAATTTTGAAAAAGAAAAAAT
1 ATTTCTA-ATTGAGCCCAAATGGTGAAAAATTTAAAAATTTAAAAAAAAAAAAAAT
* *
21113099 ATTTCTAATTTAGCCAAAATGGTG
1 ATTTCTAATTGAGCCCAAATGGTG
21113123 GAATAATTAG
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
54 4 0.06
55 22 0.32
56 40 0.58
57 3 0.04
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (55 bp):
ATTTCTAATTGAGCCCAAATGGTGAAAAATTTAAAAATTTAAAAAAAAAAAAAAT
Found at i:21115916 original size:26 final size:26
Alignment explanation
Indices: 21115878--21115938 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
21115868 CTAAGAGTTT
21115878 ATTAATTTATTTATCAATATTTTAACC
1 ATTAA-TTATTTATCAATATTTTAACC
*
21115905 ATTAATTATTTATCACTATTTTAACC
1 ATTAATTATTTATCAATATTTTAACC
*
21115931 -TTACTTAT
1 ATTAATTAT
21115939 AAGATAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 7 0.22
26 20 0.62
27 5 0.16
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTAATTATTTATCAATATTTTAACC
Found at i:21119972 original size:20 final size:20
Alignment explanation
Indices: 21119947--21119986 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21119937 GCTGCTGCTA
21119947 ATGAAT-AAATTCTGTAATTT
1 ATGAATAAAATT-TGTAATTT
21119967 ATGAATAAAATTTGTAATTT
1 ATGAATAAAATTTGTAATTT
21119987 TTTGTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (20 bp):
ATGAATAAAATTTGTAATTT
Found at i:21123802 original size:18 final size:19
Alignment explanation
Indices: 21123779--21123814 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21123769 CAAATTGGCC
*
21123779 CATTTTTGTT-TTTATTTT
1 CATTTTTATTATTTATTTT
21123797 CATTTTTATTATTTATTT
1 CATTTTTATTATTTATTT
21123815 ATTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (19 bp):
CATTTTTATTATTTATTTT
Found at i:21124681 original size:12 final size:12
Alignment explanation
Indices: 21124639--21124680 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
21124629 GATATTTTTT
21124639 TATTTTATTTAG
1 TATTTTATTTAG
21124651 TATTTTATTTATG
1 TATTTTATTTA-G
21124664 TATTTT-TTTAG
1 TATTTTATTTAG
21124675 TATTTT
1 TATTTT
21124681 TGCATGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.24
12 15 0.52
13 7 0.24
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (12 bp):
TATTTTATTTAG
Found at i:21125042 original size:195 final size:194
Alignment explanation
Indices: 21124701--21125055 Score: 492
Period size: 195 Copynumber: 1.8 Consensus size: 194
21124691 AATTTAAAAA
**
21124701 AAATAAAAAAAAATTTTGAAAATAAATATTAATTATCCAATGATGGAATTTATAAAAATTTCAAA
1 AAATAAAAAAAAATTTTGAAAATAAATAAAAATTATCCAATGATGGAATTTATAAAAATTTCAAA
*
21124766 TGATAAATTTTTATAAAATTTCTAGGTGAGAAATTTTATCTAAATTTGTCCCAAATTGTGGAATA
66 TGATAAATTTCTATAAAATTTCTAGGTGAGAAATTTTATCTAAATTTGTCCCAAATTGTGGAATA
21124831 ATTTAGATAGAATTTCAATAACAATAAATAATATTTATTTTCAAAACAAAAACATAAAACATAAA
131 ATTTAGATAGAATTTCAATAA-AA-AAATAATATTTATTTTCAAAACAAAAACATAAAACATAAA
21124896 T
194 T
* * *
21124897 AAATAAATAAAAATTTTG-AAA-AAATAAAAATTA-CCTAATGAT-GAGATTTTTAGAAATTTCA
1 AAATAAAAAAAAATTTTGAAAATAAATAAAAATTATCC-AATGATGGA-ATTTATAAAAATTTCA
* * *
21124958 AATGGTAAAGTTTCTA-AGAAATCTT-TAGGTGAGAAATTTT-TTTAAAATTTGTTCCAAATTGT
64 AATGATAAA-TTTCTATA-AAAT-TTCTAGGTGAGAAATTTTATCT-AAATTTGTCCCAAATTGT
21125020 GGAATAATTTAGAT-GAAATTTCAATAAAAAAATAAT
125 GGAATAATTTAGATAG-AATTTCAATAAAAAAATAAT
21125056 TGTCATATTA
Statistics
Matches: 143, Mismatches: 9, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
193 11 0.08
194 44 0.31
195 69 0.48
196 19 0.13
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (194 bp):
AAATAAAAAAAAATTTTGAAAATAAATAAAAATTATCCAATGATGGAATTTATAAAAATTTCAAA
TGATAAATTTCTATAAAATTTCTAGGTGAGAAATTTTATCTAAATTTGTCCCAAATTGTGGAATA
ATTTAGATAGAATTTCAATAAAAAAATAATATTTATTTTCAAAACAAAAACATAAAACATAAAT
Found at i:21125160 original size:47 final size:47
Alignment explanation
Indices: 21125084--21125184 Score: 139
Period size: 47 Copynumber: 2.1 Consensus size: 47
21125074 TCAAAAACAA
* * *
21125084 AAAAAAAAAGAAAAAATTTTCTAAATAAGCTCAGATGGTAGAAAATTT
1 AAAAATAAA-AAAAAATTTTCTAAATAAGCCCAAATGGTAGAAAATTT
* * *
21125132 AGAAATAAAAAAAAATTTTCTAAATAAGCCCAAATGGTGGAAATTTT
1 AAAAATAAAAAAAAATTTTCTAAATAAGCCCAAATGGTAGAAAATTT
21125179 AAAAAT
1 AAAAAT
21125185 TATGAAAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 39 0.85
48 7 0.15
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (47 bp):
AAAAATAAAAAAAAATTTTCTAAATAAGCCCAAATGGTAGAAAATTT
Found at i:21129197 original size:22 final size:21
Alignment explanation
Indices: 21129155--21129201 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
21129145 AGCCTGTGAG
21129155 TTATGATCGAATGATAAAAAT
1 TTATGATCGAATGATAAAAAT
21129176 ATTATAGATC-AATGGAT-AAAAT
1 -TTAT-GATCGAAT-GATAAAAAT
21129198 TTAT
1 TTAT
21129202 TTTGAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 7 0.30
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (21 bp):
TTATGATCGAATGATAAAAAT
Found at i:21129292 original size:63 final size:63
Alignment explanation
Indices: 21129193--21129335 Score: 180
Period size: 63 Copynumber: 2.3 Consensus size: 63
21129183 ATCAATGGAT
* * * * * **
21129193 AAAATTTATTTTGAAATGGCTAGTATTAAGAAACCTATAAGTGGTGACCTAGTGAT-GGGTGAC
1 AAAATTTGTTTTGGAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATAAAG-GAC
* *
21129256 AAAATTTGTTTTGGAATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATAAAGGAC
1 AAAATTTGTTTTGGAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATAAAGGAC
*
21129319 AAAACTTGTTTTGGAAT
1 AAAATTTGTTTTGGAAT
21129336 TGTTAATGCT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
63 68 0.99
64 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (63 bp):
AAAATTTGTTTTGGAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATAAAGGAC
Found at i:21129373 original size:63 final size:63
Alignment explanation
Indices: 21129201--21129377 Score: 144
Period size: 63 Copynumber: 2.8 Consensus size: 63
21129191 ATAAAATTTA
* * * * * * ** *
21129201 TTTTGAAATGGCTAGTATTAAGAAACCTAT-AAGTGGTGACCTAGTGAT-GGGTGACAAAATTTG
1 TTTTGGAATGGCTAATACTGAGAAACCTATGAA-TAGTGACCAAGTGATAAAG-GACAAAACTTG
* * *
21129264 TTTTGGAATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATAAAGGACAAAACTTG
1 TTTTGGAATGGCTAATACTGAGAAACCTATGAATAGTGACCAAGTGATAAAGGACAAAACTTG
* * * * * *
21129327 TTTTGGAATTGTTAATGCTGAGAAGCTTATGAAT-GATGATCAAGTGATAAA
1 TTTTGGAATGGCTAATACTGAGAAACCTATGAATAG-TGACCAAGTGATAAA
21129378 AATAAGGATC
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
62 1 0.01
63 90 0.97
64 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (63 bp):
TTTTGGAATGGCTAATACTGAGAAACCTATGAATAGTGACCAAGTGATAAAGGACAAAACTTG
Found at i:21130292 original size:41 final size:42
Alignment explanation
Indices: 21130204--21130342 Score: 160
Period size: 42 Copynumber: 3.4 Consensus size: 42
21130194 ATGATTGTCA
* * *
21130204 AAGAGTATTTTATTTTTCTAAAGTTGTGGTGCCT-TATTTA-
1 AAGAGCATTTTATTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
*
21130244 AATGAGCATTTTA-TTTTCCAAAGTTGTGGTGCTTCTGTTTAG
1 AA-GAGCATTTTATTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
* * * **
21130286 AGGAGCAATTTATTTTTTCAAAGTCATGGTGCCTCTGTTTAG
1 AAGAGCATTTTATTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
21130328 AAGAGCA-TTTATTTT
1 AAGAGCATTTTATTTT
21130343 CTTAAAGTCG
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
40 21 0.25
41 31 0.37
42 32 0.38
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.45
Consensus pattern (42 bp):
AAGAGCATTTTATTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
Found at i:21130323 original size:42 final size:41
Alignment explanation
Indices: 21130212--21130362 Score: 146
Period size: 41 Copynumber: 3.7 Consensus size: 41
21130202 CAAAGAGTAT
* * *
21130212 TTTATTTTTCTAAAGTTGTGGTGCCT-TATTTA-AATGAGCAT
1 TTTATTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAA-GAGCAA
* * * *
21130253 TTTATTTTCCAAAGTTGTGGTGCTTCTGTTTAGAGGAGCAA
1 TTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAAGAGCAA
*
21130294 TTTATTTTTTCAAAGTCATGGTGCCTCTGTTTAGAAGAGC-A
1 TTTA-TTTTTCAAAGTCGTGGTGCCTCTGTTTAGAAGAGCAA
* * *
21130335 TTTATTTTCTTAAAGTCGTTGAGCCTCT
1 TTTATTTT-TCAAAGTCGTGGTGCCTCT
21130363 AATTAGAAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 18 0.20
41 43 0.47
42 31 0.34
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (41 bp):
TTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAAGAGCAA
Found at i:21131585 original size:11 final size:11
Alignment explanation
Indices: 21131529--21131586 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
21131519 GCCACTTTTA
*
21131529 TTTTTTGGT-T
1 TTTTTTAGTAT
21131539 TTTTTTA-T-T
1 TTTTTTAGTAT
*
21131548 TTATTTAGTAT
1 TTTTTTAGTAT
*
21131559 TTTATTTATATAT
1 TTT-TTTA-GTAT
21131572 TTTTTTAGTAT
1 TTTTTTAGTAT
21131583 TTTT
1 TTTT
21131587 GCATGATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 8 0.21
10 7 0.18
11 10 0.26
12 8 0.21
13 6 0.15
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTTTTAGTAT
Found at i:21131586 original size:12 final size:12
Alignment explanation
Indices: 21131544--21131585 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
21131534 TGGTTTTTTT
21131544 TATTTTATTTAG
1 TATTTTATTTAG
21131556 TATTTTATTTA-
1 TATTTTATTTAG
*
21131567 TATATTTTTTTAG
1 TAT-TTTATTTAG
21131580 TATTTT
1 TATTTT
21131586 TGCATGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (12 bp):
TATTTTATTTAG
Found at i:21132276 original size:57 final size:55
Alignment explanation
Indices: 21132185--21132321 Score: 159
Period size: 55 Copynumber: 2.4 Consensus size: 55
21132175 AGGAAAAAGA
* * *
21132185 ATTTCTAAATAAGCCCAAATTGGTGAAAATTTTAAAAATTTCAAAAAAAAAAGAAAAT
1 ATTTCTAATTGAGCCCAAA-TGGTGAAAAATTTAAAAATTT--AAAAAAAAAGAAAAT
** *
21132243 ATTTCTAGATTGA-CCCAAATGGTGAAAAATTTAAAAATTTTGAAAAAGAGAAAAT
1 ATTTCTA-ATTGAGCCCAAATGGTGAAAAATTTAAAAATTTAAAAAAAAAGAAAAT
* *
21132298 ATTTCTAATTTAGCCAAAATGGTG
1 ATTTCTAATTGAGCCCAAATGGTG
21132322 GTGGAATAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
54 4 0.06
55 29 0.42
57 20 0.29
58 13 0.19
59 3 0.04
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (55 bp):
ATTTCTAATTGAGCCCAAATGGTGAAAAATTTAAAAATTTAAAAAAAAAGAAAAT
Found at i:21134910 original size:18 final size:18
Alignment explanation
Indices: 21134873--21134919 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
21134863 TAATATGAAT
* *
21134873 TATAATATATAATTTTTA
1 TATAATATATAATATATA
*
21134891 TATAAGATATAATATATA
1 TATAATATATAATATATA
21134909 TA-AATATATAA
1 TATAATATATAA
21134920 ATTATCAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TATAATATATAATATATA
Found at i:21134929 original size:15 final size:17
Alignment explanation
Indices: 21134876--21134932 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
21134866 TATGAATTAT
* *
21134876 AATATATAATTTTTATA
1 AATATATAATATATATA
*
21134893 TAAGATATAATATATATA
1 -AATATATAATATATATA
*
21134911 AATATATAA-AT-TATC
1 AATATATAATATATATA
21134926 AATATAT
1 AATATAT
21134933 TACATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 10 0.29
16 2 0.06
17 8 0.24
18 14 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AATATATAATATATATA
Found at i:21138749 original size:31 final size:29
Alignment explanation
Indices: 21138708--21138773 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
21138698 AAAATAAAAA
* *
21138708 ATATATTTTTTATAT-TAATATGAATTATAAT
1 ATATAATTTTTATATAAAATAT-AA-TAT-AT
21138739 ATATAATTTTTATATAAAATATAATATAT
1 ATATAATTTTTATATAAAATATAATATAT
21138768 ATATAA
1 ATATAA
21138774 AATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.25
30 3 0.09
31 16 0.50
32 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
ATATAATTTTTATATAAAATATAATATAT
Found at i:21138754 original size:18 final size:18
Alignment explanation
Indices: 21138733--21138779 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
21138723 TAATATGAAT
* * *
21138733 TATAATATATAATTTTTA
1 TATAAAATATAATATATA
21138751 TATAAAATATAATATATA
1 TATAAAATATAATATATA
21138769 TATAAAATATA
1 TATAAAATATA
21138780 TAAATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAATATAATATATA
Found at i:21140813 original size:4 final size:4
Alignment explanation
Indices: 21140806--21140853 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
21140796 CAAGTAGATA
* * *
21140806 AAAT AAAT GAAT AAAT AAAT AAGT AAATT AAAC AAAT AAAT AAGAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AA-AT AA
21140854 GTATATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
4 28 0.78
5 8 0.22
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:21153821 original size:27 final size:26
Alignment explanation
Indices: 21153791--21153847 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
21153781 AAAAAAAAAC
*
21153791 AAAACAAAACCAAGTCCAAAAATCCTAA
1 AAAACAAAACAAAG-CCAAAAATCC-AA
* *
21153819 AAAACAAAATAAAGCCAAAAATTCAA
1 AAAACAAAACAAAGCCAAAAATCCAA
21153845 AAA
1 AAA
21153848 CCCTTTGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 9 0.35
28 12 0.46
ACGTcount: A:0.67, C:0.19, G:0.04, T:0.11
Consensus pattern (26 bp):
AAAACAAAACAAAGCCAAAAATCCAA
Found at i:21160016 original size:35 final size:37
Alignment explanation
Indices: 21159970--21160041 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 37
21159960 CATAAAAACT
* *
21159970 CCTCTAAATAGAGGCTTAAC-AC-TTTGAAAATATAA
1 CCTCTAAATAGAGGCTCAACAACTTTTAAAAATATAA
*
21160005 CCTCTCAATAGAGGCTCAACAACTTTTAAAAATATAA
1 CCTCTAAATAGAGGCTCAACAACTTTTAAAAATATAA
21160042 AAATTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 18 0.56
36 2 0.06
37 12 0.38
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (37 bp):
CCTCTAAATAGAGGCTCAACAACTTTTAAAAATATAA
Found at i:21160130 original size:39 final size:38
Alignment explanation
Indices: 21160078--21160288 Score: 194
Period size: 39 Copynumber: 5.4 Consensus size: 38
21160068 CAAAGGCTCA
*
21160078 ACAACTTGAAAAATAAAGGGCTCTTCCTAACAGAGGCAC
1 ACAACTTTAAAAATAAA-GGCTCTTCCTAACAGAGGCAC
* *
21160117 ACATCTTTAAAAAT-AAGAC-CTTCTCTATAACAGAGGCAC
1 ACAACTTTAAAAATAAAGGCTCTTC-C--TAACAGAGGCAC
* * * * * *
21160156 ACAACTTTTAAAAATAAAGGTTCCTCATGATAGAGGCAT
1 ACAAC-TTTAAAAATAAAGGCTCTTCCTAACAGAGGCAC
* * *
21160195 ACAACTTT-AAAATAAGGGCTCTTCTTAACAGAAGCAC
1 ACAACTTTAAAAATAAAGGCTCTTCCTAACAGAGGCAC
* ** *
21160232 ACAACTTTTAAAAATAAAAGGCTCCTATTAATAGAGGCAC
1 ACAAC-TTTAAAAAT-AAAGGCTCTTCCTAACAGAGGCAC
21160272 ACAACTTTAAAAATAAA
1 ACAACTTTAAAAATAAA
21160289 TAAACACCCA
Statistics
Matches: 139, Mismatches: 24, Indels: 19
0.76 0.13 0.10
Matches are distributed among these distances:
36 4 0.03
37 29 0.21
38 11 0.08
39 56 0.40
40 33 0.24
41 3 0.02
42 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (38 bp):
ACAACTTTAAAAATAAAGGCTCTTCCTAACAGAGGCAC
Found at i:21160213 original size:115 final size:117
Alignment explanation
Indices: 21160078--21160288 Score: 297
Period size: 115 Copynumber: 1.8 Consensus size: 117
21160068 CAAAGGCTCA
* * *
21160078 ACAACTTGAAAAATAAAGGGCTCTTCCTAACAGAGGCACACATC-TTTAAAAATAAGA-CCTTCT
1 ACAACTTGAAAAATAAAGGGCTCTTCCTAACAGAAGCACACAACTTTTAAAAATAAAAGCC-TC-
21160141 CTA-TAACAGAGGCACACAACTTTTAAAAATAAAGGTTCCTCATGATAGAGGCAT
64 CTATTAACAGAGGCACACAAC-TTTAAAAATAAAGGTTCCTCATGATAGAGGCAT
* * *
21160195 ACAACTT-TAAAAT-AAGGGCTCTTCTTAACAGAAGCACACAACTTTTAAAAATAAAAGGCTCCT
1 ACAACTTGAAAAATAAAGGGCTCTTCCTAACAGAAGCACACAACTTTTAAAAATAAAAGCCTCCT
*
21160258 ATTAATAGAGGCACACAACTTTAAAAATAAA
66 ATTAACAGAGGCACACAACTTTAAAAATAAA
21160289 TAAACACCCA
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
115 41 0.49
116 35 0.42
117 8 0.10
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (117 bp):
ACAACTTGAAAAATAAAGGGCTCTTCCTAACAGAAGCACACAACTTTTAAAAATAAAAGCCTCCT
ATTAACAGAGGCACACAACTTTAAAAATAAAGGTTCCTCATGATAGAGGCAT
Found at i:21160276 original size:77 final size:77
Alignment explanation
Indices: 21160078--21160283 Score: 231
Period size: 77 Copynumber: 2.7 Consensus size: 77
21160068 CAAAGGCTCA
* * * * * *
21160078 ACAAC-TTGAAAAATAAAGGGCTCTTCCTAACAGAGGCACACATCTTTAAAAATAAGACCTTCTC
1 ACAACTTTTAAAAATAAAAGGCTCCT-ATAATAGAGGCACACAACTTT-AAAATAAGACCTTCTC
*
21160142 TATAACAGAGGCAC
64 TATAACAGAAGCAC
* * * **
21160156 ACAACTTTTAAAAAT-AAAGGTTCCTCATGATAGAGGCATACAACTTTAAAATAAGGGC-TCTTC
1 ACAACTTTTAAAAATAAAAGGCTCCT-ATAATAGAGGCACACAACTTTAAAATAAGACCTTC-TC
21160219 T-TAACAGAAGCAC
64 TATAACAGAAGCAC
21160232 ACAACTTTTAAAAATAAAAGGCTCCTATTAATAGAGGCACACAACTTTAAAA
1 ACAACTTTTAAAAATAAAAGGCTCCTA-TAATAGAGGCACACAACTTTAAAA
21160284 ATAAATAAAC
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
76 29 0.27
77 43 0.39
78 29 0.27
79 8 0.07
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (77 bp):
ACAACTTTTAAAAATAAAAGGCTCCTATAATAGAGGCACACAACTTTAAAATAAGACCTTCTCTA
TAACAGAAGCAC
Found at i:21171715 original size:6 final size:6
Alignment explanation
Indices: 21171699--21171809 Score: 66
Period size: 6 Copynumber: 17.5 Consensus size: 6
21171689 ATATGCATGT
* *
21171699 AAATGAA AAATAA AAAT-A AAATAA GCAAATTAAA AAATAA AAACAA AAACAA
1 AAAT-AA AAATAA AAATAA AAATAA --AAA-T-AA AAATAA AAATAA AAATAA
* * *
21171751 AAATAA AACTAA AACTAA AAA-ATA AAAT-G AAATAA AAATATCA AAATTAA
1 AAATAA AAATAA AAATAA AAATA-A AAATAA AAATAA AAATA--A AAA-TAA
*
21171801 AAAGAA AAA
1 AAATAA AAA
21171810 AGAAAAAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
5 10 0.12
6 52 0.60
7 9 0.10
8 10 0.12
9 3 0.03
10 2 0.02
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (6 bp):
AAATAA
Done.