Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 40
Found at i:3436152 original size:15 final size:15
Alignment explanation
Indices: 3436134--3436165 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3436124 ATTTTTTGCG
*
3436134 TTTGCATTTTTGCAT
1 TTTGCATCTTTGCAT
3436149 TTTGCATCTTTGCAT
1 TTTGCATCTTTGCAT
3436164 TT
1 TT
3436166 GTATTTTTAT
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:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTGCATCTTTGCAT
Found at i:3440090 original size:32 final size:32
Alignment explanation
Indices: 3440029--3440090 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
3440019 GTCAGACACA
* * *
3440029 AGAAGTATCTCTACGAGATGAGTATAACAACG
1 AGAAGTATCTCTACAAGATGAGCACAACAACG
3440061 AGAAGTATCTCTACAAGATGAGCACAACAA
1 AGAAGTATCTCTACAAGATGAGCACAACAA
3440091 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCACAACAACG
Found at i:3442463 original size:22 final size:22
Alignment explanation
Indices: 3442415--3442466 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3442405 CTACATCTTT
3442415 AAAGATGATAGATTCTCTCTCC
1 AAAGATGATAGATTCTCTCTCC
* * *
3442437 GAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTCTCC
3442459 AAAGATGA
1 AAAGATGA
3442467 AAGCTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTCTCC
Found at i:3443054 original size:113 final size:113
Alignment explanation
Indices: 3442841--3443610 Score: 1152
Period size: 113 Copynumber: 6.8 Consensus size: 113
3442831 CCATTACTCA
* *
3442841 ATGGATCAACA-TGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAGCATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
3442904 TTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTTAATTCATCACCCG
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
* *
3442953 ATGGATTAGCATTGCCAGAGAAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
3443018 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
*
3443066 ATGGATTAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
3443131 TTATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
* * * *
3443179 ATGGATTAGCATTGCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGACGAAGGAAGAGGAAGT
1 ATGGATCAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * ** * **
3443244 TCATAATGAGAAGAATTTGTTCAACATTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
3443292 ATGGATCAGCATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAGCATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * *
3443356 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTCG
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
* * * * * * *
3443405 ATAGATCAACTTTTCCAAAGAAAGTTCATAATGAGAAAAACTCATTTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * * *
3443470 TCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATTACTCA
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
* * * * *
3443518 ATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
3443582 TCATAATGAGAAGAACTTGTTCAACCTTT
66 TCATAATGAGAAGAACTTGTTCAACCTTT
3443611 ATTTGATTCT
Statistics
Matches: 609, Mismatches: 45, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
112 51 0.08
113 556 0.91
114 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
ATGGATCAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACCCG
Found at i:3443944 original size:3 final size:3
Alignment explanation
Indices: 3443936--3443984 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
3443926 TTGCTTATAT
*
3443936 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TG TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3443982 TTA
1 TTA
3443985 ATAAATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3444480 original size:26 final size:26
Alignment explanation
Indices: 3444445--3444500 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
3444435 ACCTATGCAA
3444445 CCTCCTTGGGACCGGTCTGAGAGCAT
1 CCTCCTTGGGACCGGTCTGAGAGCAT
3444471 CCTCCTTGGGACCGGTCTGAGAGCAT
1 CCTCCTTGGGACCGGTCTGAGAGCAT
3444497 CCTC
1 CCTC
3444501 GGTGGTGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.23
Consensus pattern (26 bp):
CCTCCTTGGGACCGGTCTGAGAGCAT
Found at i:3445490 original size:29 final size:30
Alignment explanation
Indices: 3445458--3445514 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
3445448 GGGCTGTAAA
3445458 TTTAATATTT-TATATTTTAATC-CTATTAT
1 TTTAAT-TTTATATATTTTAATCACTATTAT
* *
3445487 TTTAATTTTATATGTTTTAGTCACTATT
1 TTTAATTTTATATATTTTAATCACTATT
3445515 TAATTGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 16 0.67
30 5 0.21
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTAATTTTATATATTTTAATCACTATTAT
Found at i:3445615 original size:2 final size:2
Alignment explanation
Indices: 3445603--3445641 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3445593 TATATTAGTC
3445603 AT AT A- 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
3445642 TTGTTCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3448957 original size:74 final size:74
Alignment explanation
Indices: 3448836--3449166 Score: 531
Period size: 74 Copynumber: 4.5 Consensus size: 74
3448826 GTGAGGGATG
** * *
3448836 TTGATAATGCTCAATTAAG-TATTGAATAATGCTCATTCAACTAGCATTGTAAAAATGCTCAAAA
1 TTGATAATGCTCAATTTTGATAATG-ATCATGCTCATTCAACTAGCATTGTAAAAATGCTCAAAA
3448900 TTGTCATTTC
65 TTGTCATTTC
* * *
3448910 TTGATAATGCTTAATGTTGATAATGATCATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATCATGCTCATTCAACTAGCATTGTAAAAATGCTCAAAAT
3448975 TGTCATTTC
66 TGTCATTTC
* *
3448984 TTGATAATGTTCAATTTTGATAATGATCATGCTCATTCAACTAGCATTGTAAATATGCTCAAAAT
1 TTGATAATGCTCAATTTTGATAATGATCATGCTCATTCAACTAGCATTGTAAAAATGCTCAAAAT
3449049 TGTCATTTC
66 TGTCATTTC
*
3449058 TTGATAATGCTCAATTTTGATAATGATAATGCTCATTCAACTAGCATTGTAAAAATGCTCGAAAA
1 TTGATAATGCTCAATTTTGATAATGATCATGCTCATTCAACTAGCATTGTAAAAATGCTC-AAAA
3449123 -TGTCATTTC
65 TTGTCATTTC
*
3449132 TTGATAATGCTCAATTTTGGTAATGATCATGCTCA
1 TTGATAATGCTCAATTTTGATAATGATCATGCTCA
3449167 AATTAGGTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
74 232 0.97
75 8 0.03
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (74 bp):
TTGATAATGCTCAATTTTGATAATGATCATGCTCATTCAACTAGCATTGTAAAAATGCTCAAAAT
TGTCATTTC
Found at i:3455859 original size:18 final size:18
Alignment explanation
Indices: 3455836--3455871 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3455826 TATTGAGTTT
3455836 GTATATTAAT-ATTTTTTA
1 GTATA-TAATGATTTTTTA
3455854 GTATATAATGATTTTTTA
1 GTATATAATGATTTTTTA
3455872 CATTGAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
GTATATAATGATTTTTTA
Found at i:3465506 original size:21 final size:21
Alignment explanation
Indices: 3465480--3465543 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3465470 TTTTGGTGCA
*
3465480 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
3465501 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
3465522 GAAGAGGAACCGATTCCCCCCA
1 G-AG-GGAACCGATCCCCCCCA
3465544 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 2 0.06
23 15 0.43
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:3466280 original size:21 final size:21
Alignment explanation
Indices: 3466250--3466293 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3466240 AACCAAATCC
* *
3466250 TCCTCCAAATCCTCCTCCAAA
1 TCCTCAAAATCCTACTCCAAA
*
3466271 TCCTCAAAATCCTATTCCAAA
1 TCCTCAAAATCCTACTCCAAA
3466292 TC
1 TC
3466294 TTGATCCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (21 bp):
TCCTCAAAATCCTACTCCAAA
Found at i:3466293 original size:12 final size:12
Alignment explanation
Indices: 3466242--3466275 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3466232 TAGTCGTCAA
3466242 CCAAATCCTCCT
1 CCAAATCCTCCT
3466254 CCAAATCCTCCT
1 CCAAATCCTCCT
3466266 CCAAATCCTC
1 CCAAATCCTC
3466276 AAAATCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.50, G:0.00, T:0.24
Consensus pattern (12 bp):
CCAAATCCTCCT
Found at i:3467805 original size:41 final size:38
Alignment explanation
Indices: 3467760--3467845 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 38
3467750 AACAAAAAGG
*
3467760 GGGAGAAGTGTGTGCTTTAAGTGTGTTTTAAAATGATAAAT
1 GGGAGAAGTGTGTG-TTAAAGTGT-TTTT-AAATGATAAAT
3467801 GGGAGAA----GTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTGTGTTAAAGTGTTTTTAAATGATAAAT
3467835 GGGAGAAGTGT
1 GGGAGAAGTGT
3467846 TAAAGTAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
34 18 0.45
35 4 0.10
36 8 0.20
37 3 0.08
41 7 0.17
ACGTcount: A:0.34, C:0.01, G:0.31, T:0.34
Consensus pattern (38 bp):
GGGAGAAGTGTGTGTTAAAGTGTTTTTAAATGATAAAT
Found at i:3467828 original size:34 final size:34
Alignment explanation
Indices: 3467782--3467851 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
3467772 TGCTTTAAGT
3467782 GTGTTTTAAAATGATAAATGGGAGAAGTGTTAAA
1 GTGTTTTAAAATGATAAATGGGAGAAGTGTTAAA
*
3467816 GTGTTTTTAAATGATAAATGGGAGAAGTGTTAAA
1 GTGTTTTAAAATGATAAATGGGAGAAGTGTTAAA
3467850 GT
1 GT
3467852 AAGGGGGAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (34 bp):
GTGTTTTAAAATGATAAATGGGAGAAGTGTTAAA
Found at i:3469235 original size:37 final size:37
Alignment explanation
Indices: 3469194--3469290 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 37
3469184 TCCTAATGTT
*
3469194 TTTATTAATTAATTTTCTTAATGTTTAATATT-TAATA
1 TTTATTATTTAATTTTCTTAATGTTTAAT-TTGTAATA
* * * * *
3469231 TTTA-TATTTAATTATTTTTATTATTTAGTTTGTAATG
1 TTTATTATTTAATT-TTCTTAATGTTTAATTTGTAATA
3469268 TTT-TTATTTAATTTTCTTAATGT
1 TTTATTATTTAATTTTCTTAATGT
3469291 ATTTATTGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
36 17 0.35
37 31 0.65
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (37 bp):
TTTATTATTTAATTTTCTTAATGTTTAATTTGTAATA
Found at i:3469252 original size:20 final size:20
Alignment explanation
Indices: 3469198--3469253 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
3469188 AATGTTTTTA
* * *
3469198 TTAATTAATTTTCTTAATGT
1 TTAATTATTTTTATTAATAT
* *
3469218 TTAA-TATTTAATATTTATAT
1 TTAATTATTT-TTATTAATAT
3469238 TTAATTATTTTTATTA
1 TTAATTATTTTTATTA
3469254 TTTAGTTTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 4 0.15
20 18 0.67
21 5 0.19
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATTATTTTTATTAATAT
Found at i:3473279 original size:20 final size:19
Alignment explanation
Indices: 3473254--3473295 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3473244 AAATATATTT
*
3473254 ATTAATTGTATTTTAATATA
1 ATTAATTGTAGTTT-ATATA
*
3473274 ATTAATTTTAGTTTATATA
1 ATTAATTGTAGTTTATATA
3473293 ATT
1 ATT
3473296 TTTAAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTAATTGTAGTTTATATA
Found at i:3499519 original size:12 final size:12
Alignment explanation
Indices: 3499498--3499523 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3499488 TTGAGGAATA
3499498 GGAGGAGGATTT
1 GGAGGAGGATTT
3499510 GGAGGAGGATTT
1 GGAGGAGGATTT
3499522 GG
1 GG
3499524 TTGACGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:3500230 original size:23 final size:22
Alignment explanation
Indices: 3500189--3500261 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
3500179 CAGAACCCCA
* *
3500189 GGGGGGGTATCGATTCCCTTAT
1 GGGGGGGAATCGGTTCCCTTAT
3500211 GGGGGGGAATCGGTTCCCCTTCA-
1 GGGGGGGAATCGGTT-CCCTT-AT
** * *
3500234 AAGGGGGAACCGGTTCCCTCAT
1 GGGGGGGAATCGGTTCCCTTAT
3500256 GGGGGG
1 GGGGGG
3500262 ATCGATTCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 1 0.03
22 21 0.52
23 17 0.43
24 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.41, T:0.22
Consensus pattern (22 bp):
GGGGGGGAATCGGTTCCCTTAT
Found at i:3510061 original size:21 final size:20
Alignment explanation
Indices: 3510037--3510111 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 20
3510027 AATATTTAAA
*
3510037 ATAATAATAAATTTAATACTT
1 ATAA-AATAAATTTAAGACTT
*
3510058 ATAAAAATAAATTTAAGATTT
1 AT-AAAATAAATTTAAGACTT
* *
3510079 TTAAAATAAATTTAA-AATT
1 ATAAAATAAATTTAAGACTT
* *
3510098 AAAAAATAATTTTA
1 ATAAAATAAATTTA
3510112 TCGAAACTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 14 0.30
20 13 0.28
21 17 0.37
22 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
ATAAAATAAATTTAAGACTT
Found at i:3510086 original size:20 final size:21
Alignment explanation
Indices: 3510037--3510111 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 21
3510027 AATATTTAAA
* *
3510037 ATAATAATAAATTTAATACTT
1 ATAAAAATAAATTTAAGACTT
3510058 ATAAAAATAAATTTAAGA-TT
1 ATAAAAATAAATTTAAGACTT
* * *
3510078 TTTAAAATAAATTTAA-AATT
1 ATAAAAATAAATTTAAGACTT
*
3510098 A-AAAAATAATTTTA
1 ATAAAAATAAATTTA
3510112 TCGAAACTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 12 0.26
20 18 0.39
21 16 0.35
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
ATAAAAATAAATTTAAGACTT
Found at i:3510930 original size:36 final size:36
Alignment explanation
Indices: 3510862--3510932 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
3510852 AACTTAGGTT
* *
3510862 CATAAGGAATTACCAGCTTGATTGGCGCTGAACCTG
1 CATAAGGAATTACCAGCTTGATCGGAGCTGAACCTG
*
3510898 CATAAGGAATTACCAGCTTGATCGGAGTTGAACCT
1 CATAAGGAATTACCAGCTTGATCGGAGCTGAACCT
3510933 ATATACTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (36 bp):
CATAAGGAATTACCAGCTTGATCGGAGCTGAACCTG
Found at i:3515405 original size:36 final size:36
Alignment explanation
Indices: 3515337--3515412 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
3515327 GCCTTAGGTC
* * * *
3515337 CATAAGGAATTACCAAATTGATCGGTGTTGAACCTG
1 CATAAGGAATTACCAAATTGATCAGAGCTGAACCTA
**
3515373 CATAAGGAATTACCAGCTTGATCAGAGCTGAACCTA
1 CATAAGGAATTACCAAATTGATCAGAGCTGAACCTA
3515409 CATA
1 CATA
3515413 CTCCCGAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (36 bp):
CATAAGGAATTACCAAATTGATCAGAGCTGAACCTA
Found at i:3517476 original size:10 final size:10
Alignment explanation
Indices: 3517461--3517488 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3517451 ATACGGTGGC
3517461 GCGTGACGGT
1 GCGTGACGGT
3517471 GCGTGACGGT
1 GCGTGACGGT
3517481 GCGTGACG
1 GCGTGACG
3517489 ACTGTGACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.21, G:0.50, T:0.18
Consensus pattern (10 bp):
GCGTGACGGT
Found at i:3519422 original size:41 final size:41
Alignment explanation
Indices: 3519371--3519580 Score: 339
Period size: 41 Copynumber: 5.1 Consensus size: 41
3519361 CGTTGCGGTT
*
3519371 ATAGTTTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCG
1 ATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCG
* *
3519412 ATAGTCTACAGTGTCGTTGCGGTTTTCCATTTTGCGTTGCG
1 ATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCG
* *
3519453 ATAGTCTACAGTGTCGTTGTGATTTTCCATTTCGTGTTGCG
1 ATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCG
* *
3519494 ATAGTCTACAATGTCGTTGCGATTTTCTATTTCGCGTTGCG
1 ATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCG
* *
3519535 ATAGTCTACAGTGTCGTCGTGATTTTCCATTTCGCGTTGCG
1 ATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCG
3519576 ATAGT
1 ATAGT
3519581 TTTAAAAATG
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 154 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.41
Consensus pattern (41 bp):
ATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCG
Found at i:3519542 original size:20 final size:20
Alignment explanation
Indices: 3519481--3519542 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
3519471 GTGATTTTCC
*
3519481 ATTTCGTGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCT
** **
3519501 ACAAT-GTCGTTGCGATTTTCT
1 A-TTTCG-CGTTGCGATAGTCT
3519522 ATTTCGCGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCT
3519542 A
1 A
3519543 CAGTGTCGTC
Statistics
Matches: 30, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTCGCGTTGCGATAGTCT
Found at i:3520385 original size:5 final size:5
Alignment explanation
Indices: 3520375--3520402 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3520365 CGCCGCCTTT
3520375 TCGTC TCGTC TCGTC TCGTC TCGTC TCG
1 TCGTC TCGTC TCGTC TCGTC TCGTC TCG
3520403 GGTCGTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.21, T:0.39
Consensus pattern (5 bp):
TCGTC
Found at i:3520408 original size:15 final size:15
Alignment explanation
Indices: 3520375--3520408 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3520365 CGCCGCCTTT
*
3520375 TCGTCTCGTCTCGTC
1 TCGTCTCGTCTCGGC
*
3520390 TCGTCTCGTCTCGGG
1 TCGTCTCGTCTCGGC
3520405 TCGT
1 TCGT
3520409 GGTCGTGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.38
Consensus pattern (15 bp):
TCGTCTCGTCTCGGC
Found at i:3520436 original size:27 final size:27
Alignment explanation
Indices: 3520406--3520458 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3520396 CGTCTCGGGT
3520406 CGTGGTCGTGGTCGTGGTAATACGTGC
1 CGTGGTCGTGGTCGTGGTAATACGTGC
3520433 CGTGGTCGTGGTCGTGGTAATACGTG
1 CGTGGTCGTGGTCGTGGTAATACGTG
3520459 TCTTCGACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.17, G:0.42, T:0.30
Consensus pattern (27 bp):
CGTGGTCGTGGTCGTGGTAATACGTGC
Found at i:3520561 original size:20 final size:20
Alignment explanation
Indices: 3520536--3520649 Score: 90
Period size: 20 Copynumber: 5.6 Consensus size: 20
3520526 TTTTAAAACT
3520536 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
3520556 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
3520577 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
3520597 ATCGCAACGAC-ACTATAGACT
1 ATCGCAACG-CGA-AATGGAAA
3520618 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
3520638 ACCGCAACGCGA
1 ATCGCAACGCGA
3520650 TTTTCAACTA
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
18 3 0.04
19 3 0.04
20 35 0.49
21 24 0.34
22 3 0.04
23 3 0.04
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:3520582 original size:21 final size:21
Alignment explanation
Indices: 3520556--3520626 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
3520546 GAAATGGAAA
3520556 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
3520577 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
*
3520597 ATCGCAACGACACTATAGACT
1 ATCGCAACGACACTGTAGACT
3520618 ATCGCAACG
1 ATCGCAACG
3520627 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 21 0.55
22 3 0.08
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:3520590 original size:41 final size:41
Alignment explanation
Indices: 3520533--3520674 Score: 216
Period size: 41 Copynumber: 3.5 Consensus size: 41
3520523 CATTTTTAAA
*
3520533 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTATAG
3520574 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTATAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTATAG
* * *
3520615 ACTATCGCAACGCGAAATGGAAAACCGCAACG-CGATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTAT-AG
3520656 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
3520675 CAGCGCGAAT
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
40 1 0.01
41 93 0.98
42 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTATAG
Found at i:3521751 original size:22 final size:21
Alignment explanation
Indices: 3521723--3521783 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
3521713 CTACGGTGAC
*
3521723 ATCCGTCTCCATCTCCGACGAA
1 ATCCGTC-CCATCTCCGACAAA
3521745 ATCCGTCCCCATCTCCGACAAA
1 ATCCGT-CCCATCTCCGACAAA
3521767 ATCCGTCCTCATCTCCG
1 ATCCGTCC-CATCTCCG
3521784 GTGAAACCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 2 0.06
22 33 0.92
23 1 0.03
ACGTcount: A:0.21, C:0.44, G:0.11, T:0.23
Consensus pattern (21 bp):
ATCCGTCCCATCTCCGACAAA
Found at i:3521886 original size:9 final size:9
Alignment explanation
Indices: 3521872--3521921 Score: 91
Period size: 9 Copynumber: 5.4 Consensus size: 9
3521862 GGTTAGTTTT
3521872 TTTTTTTAA
1 TTTTTTTAA
3521881 TTTTTTTAA
1 TTTTTTTAA
3521890 TTTTTTTTAA
1 -TTTTTTTAA
3521900 TTTTTTTAA
1 TTTTTTTAA
3521909 TTTTTTTAA
1 TTTTTTTAA
3521918 TTTT
1 TTTT
3521922 GAAATTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 31 0.77
10 9 0.22
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:3521895 original size:19 final size:19
Alignment explanation
Indices: 3521871--3521921 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
3521861 GGGTTAGTTT
3521871 TTTTTTTTAATTTTTTTAA
1 TTTTTTTTAATTTTTTTAA
3521890 TTTTTTTTAATTTTTTTAA
1 TTTTTTTTAATTTTTTTAA
3521909 -TTTTTTTAATTTT
1 TTTTTTTTAATTTT
3521922 GAAATTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 13 0.41
19 19 0.59
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTTAATTTTTTTAA
Found at i:3522225 original size:19 final size:19
Alignment explanation
Indices: 3522203--3522270 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
3522193 GCGGTTTTAG
*
3522203 TTTCACGTTGTGATTTTCA
1 TTTCGCGTTGTGATTTTCA
3522222 TTTCGCGTTGTGATTTTCA
1 TTTCGCGTTGTGATTTTCA
** *
3522241 TTTCGCGTTGCAATTTTTA
1 TTTCGCGTTGTGATTTTCA
3522260 TTTTCGCGTTG
1 -TTTCGCGTTG
3522271 CGCTTTTAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 34 0.77
20 10 0.23
ACGTcount: A:0.12, C:0.16, G:0.19, T:0.53
Consensus pattern (19 bp):
TTTCGCGTTGTGATTTTCA
Found at i:3522284 original size:20 final size:19
Alignment explanation
Indices: 3522197--3522284 Score: 77
Period size: 19 Copynumber: 4.5 Consensus size: 19
3522187 TGCAACGCGG
* * *
3522197 TTTTAGTTTCACGTTGTGA
1 TTTTAATTTCGCGTTGCGA
* *
3522216 TTTTCATTTCGCGTTGTGA
1 TTTTAATTTCGCGTTGCGA
* *
3522235 TTTTCATTTCGCGTTGCAA
1 TTTTAATTTCGCGTTGCGA
* *
3522254 TTTTTATTTTCGCGTTGCGC
1 -TTTTAATTTCGCGTTGCGA
3522274 TTTTAAGTTTC
1 TTTTAA-TTTC
3522285 AGAAGCTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
19 38 0.67
20 19 0.33
ACGTcount: A:0.12, C:0.16, G:0.18, T:0.53
Consensus pattern (19 bp):
TTTTAATTTCGCGTTGCGA
Found at i:3524395 original size:21 final size:21
Alignment explanation
Indices: 3524367--3524463 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
3524357 TTCACATGTC
*
3524367 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* * **
3524388 ATCATTCAAGAGGCCCTTATT
1 ATCGTTCAAGAGGCCCCTCCT
* *
3524409 ATCCTTCAAGAGGCCCCTCCC
1 ATCGTTCAAGAGGCCCCTCCT
* *
3524430 ACCGTTCAAGAGGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
3524450 CATCGTTCAAGAGG
1 -ATCGTTCAAGAGG
3524464 TCTCTCCCAC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:3524438 original size:42 final size:42
Alignment explanation
Indices: 3524365--3524483 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
3524355 GATTCACATG
* * * * *
3524365 TCATCGTTCAAGAGGCCTCTCCTATCATTCAAGAGGCCCTTA
1 TCATCCTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCCCCTA
* * *
3524407 TTATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCCTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCCCCTA
* * *
3524449 TCATCGTTCAAGAGGTCTCTCCCACCGTTCGAGAG
1 TCATCCTTCAAGAGGCCTCTCCCACCGTTCAAGAG
3524484 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.25
Consensus pattern (42 bp):
TCATCCTTCAAGAGGCCTCTCCCACCGTTCAAGAGGCCCCTA
Found at i:3524477 original size:21 final size:21
Alignment explanation
Indices: 3524369--3524483 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
3524359 CACATGTCAT
* * *
3524369 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
* * ***
3524390 CATTCAAGAGGCCCTTATTATC
1 CGTTCAAGAGGCCCCTCCCA-C
3524412 C-TTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
** *
3524432 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
3524453 CGTTCAAGAGGTCTCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
3524474 CGTTCGAGAG
1 CGTTCAAGAG
3524484 CCCGATTCAC
Statistics
Matches: 73, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 2 0.03
21 70 0.96
22 1 0.01
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:3525907 original size:64 final size:64
Alignment explanation
Indices: 3525829--3525977 Score: 244
Period size: 64 Copynumber: 2.3 Consensus size: 64
3525819 AAATTGATGT
*
3525829 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGTTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * ***
3525893 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
3525957 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
3525978 GTTTTAAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.29, C:0.01, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:3526312 original size:18 final size:18
Alignment explanation
Indices: 3526289--3526324 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3526279 AAGCCGGTTG
*
3526289 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3526307 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3526325 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3527517 original size:18 final size:18
Alignment explanation
Indices: 3527494--3527530 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3527484 CGAAATTTAT
3527494 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
3527512 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
3527530 A
1 A
3527531 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:3527941 original size:25 final size:25
Alignment explanation
Indices: 3527913--3527962 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3527903 CATTATTTTC
*
3527913 CAAATAATATACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
3527938 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
3527963 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:3528380 original size:18 final size:18
Alignment explanation
Indices: 3528357--3528392 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3528347 AAGCCGGTTG
3528357 TGATTGAGATTTTAATTT
1 TGATTGAGATTTTAATTT
* *
3528375 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTAATTT
3528393 CATTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTAATTT
Found at i:3530697 original size:24 final size:24
Alignment explanation
Indices: 3530663--3530716 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3530653 CTGAAAAATC
3530663 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3530687 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3530711 ATCAAA
1 ATCAAA
3530717 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3530730 original size:24 final size:24
Alignment explanation
Indices: 3530663--3530730 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3530653 CTGAAAAATC
* * *
3530663 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
3530687 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3530711 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3530731 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3531693 original size:21 final size:21
Alignment explanation
Indices: 3531589--3531723 Score: 93
Period size: 21 Copynumber: 6.7 Consensus size: 21
3531579 GCGATTTACT
** *
3531589 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTTGGG
* *
3531609 AAATCG-AAGTGCGAATTAGGA
1 AAATCGCAA-TGCGAATTTGGG
**
3531630 AAATCGCAATGC--A-TTACG
1 AAATCGCAATGCGAATTTGGG
* * **
3531648 TAATCGCATTGCG-ATTTACG
1 AAATCGCAATGCGAATTTGGG
* *
3531668 TAATCGCATTGCGAATTTGGG
1 AAATCGCAATGCGAATTTGGG
*
3531689 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTTGGG
3531710 AAATCGCAATGCGA
1 AAATCGCAATGCGA
3531724 TAGTCAGAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
18 11 0.12
19 4 0.04
20 28 0.29
21 50 0.53
22 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGG
Found at i:3534896 original size:59 final size:60
Alignment explanation
Indices: 3534810--3534927 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 60
3534800 CTTTTTTATG
* * * * *
3534810 TTATTGACTTGCACCGATATAAATATGTGTTAAATG-TTTTTGTCAAAATAAGGGAAATT
1 TTATTAACTTACACCGATATAAATATGTATTAAATGTTTTTTCTCAAAATAAGGAAAATT
* * * *
3534869 TTATTAACTTACACCGGTGTAAGTATGTATTATATGTTTTTTCTCAAAATAAGGAAAAT
1 TTATTAACTTACACCGATATAAATATGTATTAAATGTTTTTTCTCAAAATAAGGAAAAT
3534928 GGGTTTTGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 29 0.59
60 20 0.41
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (60 bp):
TTATTAACTTACACCGATATAAATATGTATTAAATGTTTTTTCTCAAAATAAGGAAAATT
Found at i:3539400 original size:33 final size:32
Alignment explanation
Indices: 3539350--3539415 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
3539340 AGCCCCGAAA
* *
3539350 TATATATTTTTTGTATGAGTTTTAAC-TTATTT
1 TATATATGTTTTGTATGA-TTTAAACATTATTT
3539382 TATACTATGTTTTGTATGATTTAAACATTATTT
1 TATA-TATGTTTTGTATGATTTAAACATTATTT
3539415 T
1 T
3539416 GGGAGCTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (32 bp):
TATATATGTTTTGTATGATTTAAACATTATTT
Found at i:3548392 original size:22 final size:22
Alignment explanation
Indices: 3548366--3548418 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
3548356 AAATATATTT
*
3548366 ATAAAAATATTATTTTTATTCA
1 ATAAAAATATTATTTTTATTAA
3548388 ATAAAAATATTATTTTTATTAA
1 ATAAAAATATTATTTTTATTAA
3548410 ATAAAAATA
1 ATAAAAATA
3548419 GAGATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAAAATATTATTTTTATTAA
Found at i:3549453 original size:485 final size:487
Alignment explanation
Indices: 3548534--3549502 Score: 1662
Period size: 485 Copynumber: 2.0 Consensus size: 487
3548524 CTTAAACTTT
3548534 AACCCGACCTAACCGAACATATTCTCTAAAAAAATCCAACCCTACGTGAACCTGAATTTTATTTT
1 AACCCGACCTAACCGAACATATTCTCTAAAAAAATCCAACCCTACGTGAACCTGAATTTTATTTT
* * * * *
3548599 AAAATACTCGACCCAGTTTGGTTGGGTCAGGTTATAACCTGTCGGACCCATTAAAACTCTATTTC
66 AAAAAACTCGACCCAATTAGGTTGGGTCAGGTCAGAACCTGTCGGACCCATTAAAACTCTATTTC
3548664 TTTAATTTTTTTTCATGATAAACTTTTATTTATTTGAGTAAACTACACTTTTAGTACATCAACCA
131 TTTAATTTTTTTTCATGATAAACTTTTATTTATTTGAGTAAACTACACTTTTAGTACATCAACCA
*
3548729 TCACTTTTGTTTCATTTTGGTCATTCAACTATTATTTTTTGGGTAAACTATGCATTTAGTATCTA
196 TCACTTTTGTTTCATTTTGGTCATTCAACTATTATTTTTTGGGTAAACTATGCATTTAGTACCTA
*
3548794 AACTATCCGTTTTAGTCCATTTCAGTACCTAAACTTTCATTTTTTAAAATATTAAACCTAATGTT
261 AACTATCCGTTTTAGTCCATTTCAGTACCTAAACTTTCAATTTTTAAAATATTAAACCTAATGTT
* *
3548859 TAGTTTTTGTTTCATTTCAGTACTCCGCCGTTAAAAATTTAATGCGTTTAGTACCTAAACTATTA
326 TAGTTTTTGTTTCATTTCAGTACTCCCCCGTTAAAAATTTAACGCGTTTAGTACCTAAACTATTA
3548924 ATTTTAGTCTGGTTTAGTACCTAAACTTTAAACTTT-AAAAAAAAATTAAAGTTAAATTTTGAAC
391 ATTTTAGTCTGGTTTAGTACCTAAACTTTAAACTTTAAAAAAAAAATTAAAGTTAAATTTTGAAC
3548988 GAGATACTAAAATGAAACAAAAACTAAACTCG
456 GAGATACTAAAATGAAACAAAAACTAAACTCG
* * * *
3549020 AACCTGACCTAACCCGAACATATTCTCTAAAAAAAT-TAACCCT-CTGTGAACCT-AGTTTTTTT
1 AACCCGACCTAA-CCGAACATATTCTCTAAAAAAATCCAACCCTAC-GTGAACCTGA-ATTTTAT
* *
3549082 TTTAAAAAAAC-CGACCCAATTAGGTTGGGTCAGGTCAGAACCTGTCGGACTCATTAAAATTCTA
63 TTT-AAAAAACTCGACCCAATTAGGTTGGGTCAGGTCAGAACCTGTCGGACCCATTAAAACTCTA
*
3549146 TTTCTTTAATTTTTTTT-ATGATAAACTTTTATTTATTTGTGTAAACTACACTTTTAGTACATCA
127 TTTCTTTAATTTTTTTTCATGATAAACTTTTATTTATTTGAGTAAACTACACTTTTAGTACATCA
*
3549210 ACCATCACTTTTGTTTCATTTTGGTCATTCAACTATTATTTTTTGGGTAAACTATGCATTTTGTA
192 ACCATCACTTTTGTTTCATTTTGGTCATTCAACTATTATTTTTTGGGTAAACTATGCATTTAGTA
*
3549275 CCTAAACTATCCGTTTTGGTCCATTTCAGTACCTAAACTTTCAATTTTTAAAATATTAAACCTAA
257 CCTAAACTATCCGTTTTAGTCCATTTCAGTACCTAAACTTTCAATTTTTAAAATATTAAACCTAA
3549340 TGTTTAGTTTTTGTTTCATTTCAGTACTCCCCCGTTAAAAATTTAACGCGTTTAGTACCTAAACT
322 TGTTTAGTTTTTGTTTCATTTCAGTACTCCCCCGTTAAAAATTTAACGCGTTTAGTACCTAAACT
* * *
3549405 ATTAATTTTAGTTTGGTTTAGTATCTAAACTTTAAACTTTTTAAAAAAAAATTAAAGTTAAATTT
387 ATTAATTTTAGTCTGGTTTAGTACCTAAACTTTAAAC-TTTAAAAAAAAAATTAAAGTTAAATTT
3549470 TGAACGAGATACTAAAATGAAACAAAAACTAAA
451 TGAACGAGATACTAAAATGAAACAAAAACTAAA
3549503 TTTTATGAAT
Statistics
Matches: 457, Mismatches: 20, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
485 272 0.60
486 100 0.22
487 85 0.19
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (487 bp):
AACCCGACCTAACCGAACATATTCTCTAAAAAAATCCAACCCTACGTGAACCTGAATTTTATTTT
AAAAAACTCGACCCAATTAGGTTGGGTCAGGTCAGAACCTGTCGGACCCATTAAAACTCTATTTC
TTTAATTTTTTTTCATGATAAACTTTTATTTATTTGAGTAAACTACACTTTTAGTACATCAACCA
TCACTTTTGTTTCATTTTGGTCATTCAACTATTATTTTTTGGGTAAACTATGCATTTAGTACCTA
AACTATCCGTTTTAGTCCATTTCAGTACCTAAACTTTCAATTTTTAAAATATTAAACCTAATGTT
TAGTTTTTGTTTCATTTCAGTACTCCCCCGTTAAAAATTTAACGCGTTTAGTACCTAAACTATTA
ATTTTAGTCTGGTTTAGTACCTAAACTTTAAACTTTAAAAAAAAAATTAAAGTTAAATTTTGAAC
GAGATACTAAAATGAAACAAAAACTAAACTCG
Found at i:3549933 original size:30 final size:29
Alignment explanation
Indices: 3549884--3549941 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
3549874 AAAATTTGTT
*
3549884 TTCACCCTCTAACATTTTATAAGTTCAAG
1 TTCACCCTCTAACATTTTATAAATTCAAG
3549913 TTCACCCTCCTGAA-ATTTTATAAATTCAA
1 TTCACCCT-CT-AACATTTTATAAATTCAA
3549942 ATTTATCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 16 0.62
31 2 0.08
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
TTCACCCTCTAACATTTTATAAATTCAAG
Found at i:3550589 original size:50 final size:48
Alignment explanation
Indices: 3550532--3550637 Score: 112
Period size: 48 Copynumber: 2.2 Consensus size: 48
3550522 TATTAAATAC
3550532 AATAAATAAT-ATT-ATTTATCA-TAAAACTTAATATTATTAT-TTTTAAA
1 AATAAA-AATAATTGATTTATCATTAAAA--TAATATTATTATATTTTAAA
* * * *
3550579 ATATTAAAATAATTGATTTATTATTAAAATATTATTTTTATATTTTAAA
1 A-ATAAAAATAATTGATTTATCATTAAAATAATATTATTATATTTTAAA
3550628 AATAAAAATA
1 AATAAAAATA
3550638 TTAATATTGG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
47 4 0.08
48 25 0.51
49 15 0.31
50 5 0.10
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (48 bp):
AATAAAAATAATTGATTTATCATTAAAATAATATTATTATATTTTAAA
Found at i:3550822 original size:19 final size:18
Alignment explanation
Indices: 3550752--3550988 Score: 67
Period size: 18 Copynumber: 13.0 Consensus size: 18
3550742 TTAAATATCT
*
3550752 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTA--ATA
3550771 TTATTATATTAATATTAAATA
1 TTATTA-A-TAATATT-AATA
* *
3550792 TATATAAATAATATTATTCA
1 T-TATTAATAATATTAAT-A
3550812 TTATTAATAAT-TTAATA
1 TTATTAATAATATTAATA
3550829 TTATTATTTCTATGAA-ATTAATA
1 TTATTA-----AT-AATATTAATA
* * * *
3550852 -AATAAATAATATAAATT
1 TTATTAATAATATTAATA
3550869 TTATTAATAATTTATTATATA
1 TTATTAATAA--TATTA-ATA
3550890 TTATTAA-AATA--AA-A
1 TTATTAATAATATTAATA
*
3550904 ATA-TAAT-ATATT-ATA
1 TTATTAATAATATTAATA
3550919 TTATT-ATAATA-TAATTGA
1 TTATTAATAATATTAA-T-A
* *
3550937 TTATT-TTATTA-TAATA
1 TTATTAATAATATTAATA
**
3550953 TTAAAATATAATATT-ATA
1 TTATTA-ATAATATTAATA
3550971 TTATTAGA-AATATTAATA
1 TTATTA-ATAATATTAATA
3550989 AATATATTTT
Statistics
Matches: 163, Mismatches: 24, Indels: 63
0.65 0.10 0.25
Matches are distributed among these distances:
13 6 0.04
14 4 0.02
15 7 0.04
16 12 0.07
17 22 0.13
18 41 0.25
19 18 0.11
20 16 0.10
21 13 0.08
22 15 0.09
23 9 0.06
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATTAATAATATTAATA
Found at i:3550833 original size:17 final size:17
Alignment explanation
Indices: 3550777--3550834 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
3550767 TAGATTATTA
*
3550777 TATTAAT-ATTAAATAT
1 TATTAATAATTTAATAT
* *
3550793 ATATAAATAATATTATTCAT
1 -TATTAATAAT-TTAAT-AT
3550813 TATTAATAATTTAATAT
1 TATTAATAATTTAATAT
3550830 TATTA
1 TATTA
3550835 TTTCTATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 13 0.39
18 6 0.18
19 12 0.36
20 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAATAATTTAATAT
Found at i:3550933 original size:23 final size:23
Alignment explanation
Indices: 3550903--3550969 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
3550893 TTAAAATAAA
3550903 AATATAATATATTATATTATTAT
1 AATATAATATATTATATTATTAT
*
3550926 AATATAAT-TGATTATTTTATTAT
1 AATATAATAT-ATTATATTATTAT
* *
3550949 AATATTAAAATATAATATTAT
1 AATA-TAATATATTATATTAT
3550970 ATTATTAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.03
23 24 0.65
24 11 0.30
25 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:3550947 original size:31 final size:29
Alignment explanation
Indices: 3550873--3550986 Score: 99
Period size: 29 Copynumber: 3.9 Consensus size: 29
3550863 TAAATTTTAT
*
3550873 TAATAATT-TATTA-TATATTATTAAAATAA
1 TAAT-ATTATATTATTATAATATTAAAAT-A
* * * *
3550902 AAATATAATA-TATTATATTATTATAATA
1 TAATATTATATTATTATAATATTAAAATA
*
3550930 TAATTGATTATTTTATTATAATATTAAAATA
1 TAA-T-ATTATATTATTATAATATTAAAATA
*
3550961 TAATATTATATTATTAGAAATATTAA
1 TAATATTATATTATTA-TAATATTAA
3550987 TAAATATATT
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
28 7 0.10
29 30 0.43
30 13 0.19
31 19 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TAATATTATATTATTATAATATTAAAATA
Found at i:3550969 original size:21 final size:23
Alignment explanation
Indices: 3550943--3550988 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
3550933 TTGATTATTT
3550943 TATTATAATATTA-AAATA-TAA
1 TATTATAATATTAGAAATATTAA
*
3550964 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAGAAATATTAA
3550987 TA
1 TA
3550989 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAATATTAGAAATATTAA
Found at i:3550989 original size:26 final size:24
Alignment explanation
Indices: 3550960--3551022 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
3550950 ATATTAAAAT
3550960 ATAATATTATATTATTAGAA-ATATTA
1 ATAATA-TATATT-TTA-AATATATTA
*
3550986 ATAA-ATATATTTTAAATATTTTA
1 ATAATATATATTTTAAATATATTA
3551009 ATAAT-TAATATTTT
1 ATAATAT-ATATTTT
3551023 GATTAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAATATATATTTTAAATATATTA
Found at i:3550996 original size:21 final size:21
Alignment explanation
Indices: 3550870--3551005 Score: 56
Period size: 21 Copynumber: 6.6 Consensus size: 21
3550860 ATATAAATTT
*
3550870 TATTAATAAT-TTATTAT-ATA
1 TATTAA-AATATTAATATAATA
**
3550890 TTATTAAAATAAAAATATAATA
1 -TATTAAAATATTAATATAATA
*
3550912 TATT---ATATTATTATAATA
1 TATTAAAATATTAATATAATA
* * * *
3550930 TAATT-GATTATT-TTATTATAA
1 T-ATTAAAATATTAATATAAT-A
*
3550951 TATTAAAATA-TAATATTATA
1 TATTAAAATATTAATATAATA
3550971 TTATTAGAAATATTAATA-AATA
1 -TATTA-AAATATTAATATAATA
*
3550993 TATTTTAAATATT
1 TA-TTAAAATATT
3551006 TTAATAATTA
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
18 12 0.13
19 3 0.03
20 14 0.16
21 43 0.48
22 13 0.14
23 5 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TATTAAAATATTAATATAATA
Found at i:3552064 original size:37 final size:36
Alignment explanation
Indices: 3552013--3552114 Score: 145
Period size: 35 Copynumber: 2.9 Consensus size: 36
3552003 ATATTCCAAC
* *
3552013 AAACATCTATCAAACTTTGAAAACCTACTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCTA-TTTTCAAAG
3552050 AAACATTTACCAAACTTTGAAAACC-ATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCTATTTTCAAAG
* *
3552085 AAATATTTACCAAACTTTTAAAA-CTATTTT
1 AAACATTTACCAAACTTTGAAAACCTATTTT
3552115 TTCAAAGTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 1 0.02
35 35 0.58
36 1 0.02
37 23 0.38
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCTATTTTCAAAG
Found at i:3556526 original size:37 final size:36
Alignment explanation
Indices: 3556484--3556592 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
3556474 ATATTTCAAC
* *
3556484 AAACATCTATCAAACTTTGAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
3556521 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
*
3556556 AAACATTTACCAAACTTTTAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
3556593 TTGGTTGCCA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 7 0.10
37 26 0.39
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:3556548 original size:21 final size:21
Alignment explanation
Indices: 3556524--3556584 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3556514 TTCAAAGAAA
3556524 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
3556545 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
*
3556559 CATTTACCAAACTTTTAAAAC
1 CATTTACCAAACTTTGAAAAC
3556580 CATTT
1 CATTT
3556585 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
20 7 0.23
21 10 0.33
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:3557113 original size:70 final size:69
Alignment explanation
Indices: 3557006--3557151 Score: 186
Period size: 70 Copynumber: 2.1 Consensus size: 69
3556996 CAAATTGAAA
* * * *
3557006 TATAAATAAGTATGAGCCAATTTTATATACAAATATAATTTTAATGACTAGATTGAAGTAAATTA
1 TATAAATAAGTATAAGCCAATTTCATATACAAATATAATTTTAAGGACTAAATTGAA-TAAA-TA
3557071 CAAAAT
64 CAAAAT
* * * *
3557077 TATAAATAAGTATAAG-CGATTTCATATATAAATATAATTTTAAGGATTAAATTGAATAAATATA
1 TATAAATAAGTATAAGCCAATTTCATATACAAATATAATTTTAAGGACTAAATTGAATAAATACA
3557141 AAAT
66 AAAT
*
3557145 TACAAAT
1 TATAAAT
3557152 TAAAATTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
68 13 0.20
69 4 0.06
70 34 0.52
71 15 0.23
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (69 bp):
TATAAATAAGTATAAGCCAATTTCATATACAAATATAATTTTAAGGACTAAATTGAATAAATACA
AAAT
Found at i:3557365 original size:2 final size:2
Alignment explanation
Indices: 3557360--3557516 Score: 110
Period size: 2 Copynumber: 80.0 Consensus size: 2
3557350 TAATGTACAC
* * * * *
3557360 TA TA TA TA TA TA TA TA -A TG T- TA TG CA TA CA T- TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
3557399 TA TA CT- TA TA TT TA TA CA TA TG TA TA TA TA -A AA GTA TC TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
** * * *
3557441 TA TA GG TA TG TA TA TA AA TA TA TA TA -A GTA TA AA 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
3557483 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
3557517 AATTTATGTT
Statistics
Matches: 118, Mismatches: 28, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
1 6 0.05
2 109 0.92
3 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3558157 original size:78 final size:78
Alignment explanation
Indices: 3558061--3558204 Score: 225
Period size: 78 Copynumber: 1.8 Consensus size: 78
3558051 TTATTAATTT
* * * *
3558061 AATTATTATAACTAACAATTTATATTAACTTTTAAAAGGTAATCATATTAATTATCATTGTTTAT
1 AATTATCACAACTAACAATTTATATTAACTTTTAAAAAGTAATCATATTAATTATCATAGTTTAT
3558126 TTAATTGACAAAA
66 TTAATTGACAAAA
* * *
3558139 AATTATCACAACTAACAATTTGTTTTAACTTTTAAAAAGTAATTATATTAATTATCATAGTTTAT
1 AATTATCACAACTAACAATTTATATTAACTTTTAAAAAGTAATCATATTAATTATCATAGTTTAT
3558204 T
66 T
3558205 ATAAATTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 59 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (78 bp):
AATTATCACAACTAACAATTTATATTAACTTTTAAAAAGTAATCATATTAATTATCATAGTTTAT
TTAATTGACAAAA
Found at i:3559822 original size:54 final size:54
Alignment explanation
Indices: 3559740--3559848 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
3559730 TAATGCTGGG
3559740 CAAGGCAAGCCAGTAGTTACTGTTGGGCACAGGTAATAAATGAGAGTCAGTGGA
1 CAAGGCAAGCCAGTAGTTACTGTTGGGCACAGGTAATAAATGAGAGTCAGTGGA
* *
3559794 CAAGGCAAGTCAGTAGTTACTGTTGGGCACATGTAATAAATGAGAGTCAGTGGA
1 CAAGGCAAGCCAGTAGTTACTGTTGGGCACAGGTAATAAATGAGAGTCAGTGGA
3559848 C
1 C
3559849 TTACAATGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (54 bp):
CAAGGCAAGCCAGTAGTTACTGTTGGGCACAGGTAATAAATGAGAGTCAGTGGA
Found at i:3564754 original size:32 final size:32
Alignment explanation
Indices: 3564657--3564757 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 32
3564647 CCAAAAAACC
* * *
3564657 TAGGT-ATACTCTCCATATATTCCTTAGAACA
1 TAGGTAATACTATCCATATGTTCCGTAGAACA
* * *
3564688 TAGGT-ATACTATCCATATGTCCCG-AAAGATA
1 TAGGTAATACTATCCATATGTTCCGTAGA-ACA
* *
3564719 TAGGTAATTCTGTCCATATGTTCCGTAGAACA
1 TAGGTAATACTATCCATATGTTCCGTAGAACA
3564751 TAGGTAA
1 TAGGTAA
3564758 ACCCTCGACT
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.04
31 27 0.48
32 25 0.45
33 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (32 bp):
TAGGTAATACTATCCATATGTTCCGTAGAACA
Found at i:3565855 original size:64 final size:64
Alignment explanation
Indices: 3565706--3565859 Score: 147
Period size: 64 Copynumber: 2.4 Consensus size: 64
3565696 TGAAAGTATG
* * ** * *
3565706 CATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGGATG
1 CATCGATGCACTACCTG-TGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAGATA
* * *
3565770 CATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-AGA
1 CATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGAGA
3565831 GTA
63 -TA
3565834 CATCGATGCACTACCTGTGCATCGAT
1 CATCGATGCACTACCTGTGCATCGAT
3565860 ACACCTTCAA
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
63 3 0.04
64 59 0.81
65 11 0.15
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
CATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAGATA
Found at i:3568914 original size:30 final size:30
Alignment explanation
Indices: 3568878--3569031 Score: 202
Period size: 30 Copynumber: 5.0 Consensus size: 30
3568868 CGTCAGCATT
*
3568878 GCATTTTTTATATGCGGCACTAACTTGTCA
1 GCATTTTTTATATGTGGCACTAACTTGTCA
* *
3568908 GCATTTTTTATATGCGGCACTAACTTATCA
1 GCATTTTTTATATGTGGCACTAACTTGTCA
** *
3568938 GCATTTTTTATATGTGATATTAACTTGTCA
1 GCATTTTTTATATGTGGCACTAACTTGTCA
*
3568968 GCATTTTTTTTATATGTGACACTAA-TCTGTCA
1 GCA--TTTTTTATATGTGGCACTAACT-TGTCA
3569000 GCATTTTTTTATATGTGGCACTAACTTGTCA
1 GCA-TTTTTTATATGTGGCACTAACTTGTCA
3569031 G
1 G
3569032 TGCCATATGA
Statistics
Matches: 111, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
30 57 0.51
31 27 0.24
32 27 0.24
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (30 bp):
GCATTTTTTATATGTGGCACTAACTTGTCA
Found at i:3569262 original size:25 final size:24
Alignment explanation
Indices: 3569234--3569282 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3569224 ACTCCCAAGA
**
3569234 AATTTAATTTTTACATAAAAATAAT
1 AATTTAATTTGAAC-TAAAAATAAT
*
3569259 AATTTGATTTGAACTAAAAATAAT
1 AATTTAATTTGAACTAAAAATAAT
3569283 TATAGCAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (24 bp):
AATTTAATTTGAACTAAAAATAAT
Found at i:3570303 original size:33 final size:33
Alignment explanation
Indices: 3570249--3570317 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
3570239 TAATTGCAAG
*
3570249 TATTATAAATATTTTTATAAAATATATTAATTAA
1 TATTATAAATATTATTATAAAATATATTAA-TAA
*
3570283 TATTAT-AATATTAATT-TAAAATATATTGATAA
1 TATTATAAATATT-ATTATAAAATATATTAATAA
3570315 TAT
1 TAT
3570318 AAATTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 6 0.19
33 18 0.56
34 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
TATTATAAATATTATTATAAAATATATTAATAA
Found at i:3570322 original size:24 final size:25
Alignment explanation
Indices: 3570264--3570336 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 25
3570254 TAAATATTTT
* *
3570264 TATAAAATATATTAATTAATATTATAA
1 TATAAATTATAATAA-T-ATATTATAA
*
3570291 TATTAATT-TAA-AATATATTGATAA
1 TATAAATTATAATAATATATT-ATAA
3570315 TATAAATTATAATAATAT-TTAT
1 TATAAATTATAATAATATATTAT
3570337 TGTAACCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 5 0.13
24 14 0.36
25 7 0.18
26 7 0.18
27 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
TATAAATTATAATAATATATTATAA
Found at i:3571263 original size:23 final size:23
Alignment explanation
Indices: 3571233--3571278 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3571223 ATATATAATA
3571233 GTAATAAAAATACTTAGTACTAT
1 GTAATAAAAATACTTAGTACTAT
3571256 GTAATAAAAATACTTAGTACTAT
1 GTAATAAAAATACTTAGTACTAT
3571279 TTTCATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (23 bp):
GTAATAAAAATACTTAGTACTAT
Found at i:3572882 original size:3 final size:3
Alignment explanation
Indices: 3572863--3572908 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
3572853 AACTTGAAAA
*
3572863 AAT AAT AA- AAG AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3572909 GAACAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3576260 original size:16 final size:16
Alignment explanation
Indices: 3576241--3576296 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
3576231 TAAAAAAAAT
3576241 TAATTAAGTAAATTAA
1 TAATTAAGTAAATTAA
* *
3576257 TAATTATATTAAA-AAA
1 TAATTA-AGTAAATTAA
3576273 TAATTACCAAGTAAATTAA
1 TAATT---AAGTAAATTAA
3576292 TAATT
1 TAATT
3576297 TTATTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
16 13 0.42
17 5 0.16
18 5 0.16
19 8 0.26
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (16 bp):
TAATTAAGTAAATTAA
Found at i:3576285 original size:35 final size:35
Alignment explanation
Indices: 3576229--3576311 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 35
3576219 CCTGATTAAA
**
3576229 ATTAAAAAAAATTAATTAAGTAAATTAATAATTAT
1 ATTAAAAAAAATTAACCAAGTAAATTAATAATTAT
*
3576264 ATTAAAAAATAATT-ACCAAGTAAATTAATAATTTT
1 ATTAAAAAA-AATTAACCAAGTAAATTAATAATTAT
3576299 ATTAAAAATAAAT
1 ATTAAAAA-AAAT
3576312 AAATTGCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 38 0.88
36 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (35 bp):
ATTAAAAAAAATTAACCAAGTAAATTAATAATTAT
Found at i:3579363 original size:62 final size:61
Alignment explanation
Indices: 3579244--3579367 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 61
3579234 ACGTTAAGAT
3579244 GTATCTGGACTGATTTCCAGCTTTGTACAAGGGGACAAGCTGTTAATATCAGGAGTTACAG
1 GTATCTGGACTGATTTCCAGCTTTGTACAAGGGGACAAGCTGTTAATATCAGGAGTTACAG
3579305 GTATCTGGACTGATTTCCAGCTTTGTACAAAGGGGACAAGCTGTTAATATCAGGAGTTACAG
1 GTATCTGGACTGATTTCCAGCTTTGTAC-AAGGGGACAAGCTGTTAATATCAGGAGTTACAG
3579367 G
1 G
3579368 AGTTACATGA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 28 0.45
62 34 0.55
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (61 bp):
GTATCTGGACTGATTTCCAGCTTTGTACAAGGGGACAAGCTGTTAATATCAGGAGTTACAG
Found at i:3581321 original size:41 final size:41
Alignment explanation
Indices: 3581261--3581378 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
3581251 AATAGTGGCA
*
3581261 TTTA-AAAAAATGCCA-CTAAATATCATTACCTTTAGCGGCG
1 TTTATAAAAAATG-CAGCTAAATATCATTACCTTTAGCGACG
*
3581301 TTTATAAAAAATGTAGCTAAATATCATTACCTTTAGCGACG
1 TTTATAAAAAATGCAGCTAAATATCATTACCTTTAGCGACG
* * * * *
3581342 TTTGTAAAAAATGCCGCTAAAAAGCATAACCTTTAGC
1 TTTATAAAAAATGCAGCTAAATATCATTACCTTTAGC
3581379 AGATTTTGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 5 0.07
41 63 0.93
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (41 bp):
TTTATAAAAAATGCAGCTAAATATCATTACCTTTAGCGACG
Found at i:3582927 original size:21 final size:21
Alignment explanation
Indices: 3582901--3582952 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
3582891 GTATATTTTT
3582901 AATATTATAA-AATTATTTTAA
1 AATATTATAATAATT-TTTTAA
3582922 AATATT-TAATTAATTTTTTAA
1 AATATTATAA-TAATTTTTTAA
3582943 ATCATATTAT
1 A--ATATTAT
3582953 TCATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 3 0.12
21 13 0.50
22 4 0.15
23 5 0.19
24 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTATAATAATTTTTTAA
Found at i:3582967 original size:23 final size:21
Alignment explanation
Indices: 3582934--3582999 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 21
3582924 TATTTAATTA
*
3582934 ATTT-TTTAAATCATATTATT
1 ATTTATTTAAATAATATTATT
3582954 CATTTATTTCAAATAATATTAATT
1 -ATTTATTT-AAATAATATT-ATT
3582978 ATTTATTTGAAATAATATTATT
1 ATTTATTT-AAATAATATTATT
3583000 TTAAAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.10
22 6 0.15
23 27 0.68
24 3 0.08
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTATTTAAATAATATTATT
Found at i:3582997 original size:19 final size:19
Alignment explanation
Indices: 3582975--3583032 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 19
3582965 AATAATATTA
*
3582975 ATTATTTATTTGAAATAAT
1 ATTATTTATTTAAAATAAT
3582994 ATTA--T-TTTAAAAT-AT
1 ATTATTTATTTAAAATAAT
*
3583009 A-TATTTAATTTTAAATAAT
1 ATTATTT-ATTTAAAATAAT
3583028 ATTAT
1 ATTAT
3583033 ACGAAACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
14 2 0.06
15 3 0.10
16 8 0.26
17 1 0.03
18 7 0.23
19 7 0.23
20 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTATTTATTTAAAATAAT
Found at i:3583012 original size:17 final size:15
Alignment explanation
Indices: 3582980--3583032 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
3582970 TATTAATTAT
*
3582980 TTATTTGAAATAATA
1 TTATTTTAAATAATA
3582995 TTATTTTAAAATATATA
1 TTATTTT-AAATA-ATA
3583012 TTTAATTTTAAATAATA
1 -TT-ATTTTAAATAATA
3583029 TTAT
1 TTAT
3583033 ACGAAACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 8 0.24
16 7 0.21
17 6 0.18
18 7 0.21
19 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TTATTTTAAATAATA
Found at i:3594997 original size:12 final size:12
Alignment explanation
Indices: 3594980--3595004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3594970 ATTGCATCTA
3594980 AACAAACAAAAC
1 AACAAACAAAAC
3594992 AACAAACAAAAC
1 AACAAACAAAAC
3595004 A
1 A
3595005 CACTTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (12 bp):
AACAAACAAAAC
Found at i:3596159 original size:5 final size:5
Alignment explanation
Indices: 3596119--3596175 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
3596109 AAGGAATAAA
* * *
3596119 AAAAT AAAGAT AAAAT AGAAT AAGAT AAATAA AAAAT AAAA- AAAAT AACAAT
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AA-AAT
3596171 AAAAT
1 AAAAT
3596176 GAATAAACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 4 0.10
5 24 0.57
6 14 0.33
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3596172 original size:31 final size:32
Alignment explanation
Indices: 3596117--3596182 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
3596107 GAAAGGAATA
* *
3596117 AAAAAATAAAGATAAAATAGAATAAGATAAAT
1 AAAAAATAAAGATAAAATACAATAAAATAAAT
*
3596149 AAAAAATAAA-A-AAAATAACAATAAAATGAAT
1 AAAAAATAAAGATAAAAT-ACAATAAAATAAAT
3596180 AAA
1 AAA
3596183 CAAAACGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
31 15 0.50
32 10 0.33
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (32 bp):
AAAAAATAAAGATAAAATACAATAAAATAAAT
Found at i:3596277 original size:2 final size:2
Alignment explanation
Indices: 3596270--3596324 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
3596260 ATAAATATTA
* *
3596270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3596312 AT AT A- AT A- AT AT A
1 AT AT AT AT AT AT AT A
3596325 AATAAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3598235 original size:111 final size:111
Alignment explanation
Indices: 3598090--3598297 Score: 301
Period size: 111 Copynumber: 1.9 Consensus size: 111
3598080 AACTGGGAAA
* **
3598090 TTGTTTGTTGACAGCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGATGTCTCGAGTCTAATA
1 TTGTTTGTTGACAACCAGCCGCCCCTCCGCTGTGAAGTTGAGCTTGTGATGTCTCGAGTCTAATA
3598155 -TCTTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAG
66 TTC-TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAG
* * * ** *
3598201 TTGTTTGTTGACAATCAGTCGCCCCTCCGTTGTGAAGTTGAGCTTGTTTTGTCTTGAGTCTAATA
1 TTGTTTGTTGACAACCAGCCGCCCCTCCGCTGTGAAGTTGAGCTTGTGATGTCTCGAGTCTAATA
* *
3598266 TTCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
66 TTCTTCGCTGTGAAGTTGAAATTGACTCTGAA
3598298 ATTGGGAAAC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 83 0.98
112 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (111 bp):
TTGTTTGTTGACAACCAGCCGCCCCTCCGCTGTGAAGTTGAGCTTGTGATGTCTCGAGTCTAATA
TTCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAG
Found at i:3599401 original size:15 final size:16
Alignment explanation
Indices: 3599381--3599410 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3599371 ACCCACATTT
3599381 TCTTTTT-CTTTTTTC
1 TCTTTTTACTTTTTTC
3599396 TCTTTTTACTTTTTT
1 TCTTTTTACTTTTTT
3599411 TTAATTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTTTTACTTTTTTC
Found at i:3599491 original size:18 final size:18
Alignment explanation
Indices: 3599448--3599493 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
3599438 CACTCTAAAC
3599448 GTTTTTTC--TCTTTTTT
1 GTTTTTTCTTTCTTTTTT
*
3599464 G-TTCTT-TTTCTTTTTT
1 GTTTTTTCTTTCTTTTTT
3599480 GTTTTTTCTTTCTT
1 GTTTTTTCTTTCTT
3599494 CGACTTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 4 0.17
16 10 0.42
17 4 0.17
18 6 0.25
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (18 bp):
GTTTTTTCTTTCTTTTTT
Found at i:3607405 original size:20 final size:20
Alignment explanation
Indices: 3607380--3607418 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3607370 GGCATCTAGC
*
3607380 TTCCACTGATAACGTTCAGG
1 TTCCACTGATAACATTCAGG
3607400 TTCCACTGATAACATTCAG
1 TTCCACTGATAACATTCAG
3607419 CTTCAAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (20 bp):
TTCCACTGATAACATTCAGG
Found at i:3612392 original size:34 final size:32
Alignment explanation
Indices: 3612317--3612393 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 32
3612307 CCCAAAAAAG
3612317 TATATAAT-TAAATATAAATACATTTTAAATTT
1 TATA-AATATAAATATAAATACATTTTAAATTT
* *
3612349 TATTAAATATAAATTATTAATATATTTT-AATTT
1 TA-TAAATATAAA-TATAAATACATTTTAAATTT
3612382 ATATAGAATATA
1 -TATA-AATATA
3612394 TCAACAACGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
32 5 0.13
33 13 0.34
34 20 0.53
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (32 bp):
TATAAATATAAATATAAATACATTTTAAATTT
Found at i:3613993 original size:100 final size:99
Alignment explanation
Indices: 3613871--3614058 Score: 279
Period size: 100 Copynumber: 1.9 Consensus size: 99
3613861 ATAAACCCTA
** * * *
3613871 AAATTTTAAATAATTATAAACCCCAAATTCTAATCCTAAATTGATACTATAAATTTTAAATG-TA
1 AAATTTTAAATAAACATAAACCCCAAATTCTAATCCTAAACTGATACCATAAATCTTAAA-GATA
* *
3613935 AGTCCTGATTTTCAAATCCTAAAATCTTAAATGCT
65 AATCCTGATTTTCAAAGCCTAAAATCTTAAATGCT
*
3613970 AAATTTTAAATAAAACATAAACCCCAAATTCTAATCCTAAACTGATACCCTAAATCTTAAAGATA
1 AAATTTTAAAT-AAACATAAACCCCAAATTCTAATCCTAAACTGATACCATAAATCTTAAAGATA
3614035 AATCCTGATTTTCAAAGCCTAAAA
65 AATCCTGATTTTCAAAGCCTAAAA
3614059 CCCGAAATCT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
99 12 0.15
100 67 0.85
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.33
Consensus pattern (99 bp):
AAATTTTAAATAAACATAAACCCCAAATTCTAATCCTAAACTGATACCATAAATCTTAAAGATAA
ATCCTGATTTTCAAAGCCTAAAATCTTAAATGCT
Found at i:3614531 original size:15 final size:15
Alignment explanation
Indices: 3614490--3614555 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
3614480 TTCTGAAAAA
* *
3614490 TGAATTACAGCAATT
1 TGAATTACTGAAATT
*
3614505 TAAATTACTGAAATT
1 TGAATTACTGAAATT
* **
3614520 TGAATTATTGAAAAA
1 TGAATTACTGAAATT
*
3614535 TGAATTACTGGAATT
1 TGAATTACTGAAATT
3614550 TGAATT
1 TGAATT
3614556 CTGGAAAATG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:3614541 original size:30 final size:29
Alignment explanation
Indices: 3614507--3614571 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
3614497 CAGCAATTTA
*
3614507 AATTACTGAAATTTGAATTATTGAAAAATG
1 AATTACTGAAATTTGAATT-CTGAAAAATG
* *
3614537 AATTACTGGAATTTGAATTCTGGAAAATG
1 AATTACTGAAATTTGAATTCTGAAAAATG
3614566 AATTAC
1 AATTAC
3614572 ATTTCTGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.35
Consensus pattern (29 bp):
AATTACTGAAATTTGAATTCTGAAAAATG
Found at i:3614567 original size:14 final size:15
Alignment explanation
Indices: 3614507--3614571 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
3614497 CAGCAATTTA
*
3614507 AATTACT-GAAATTTG
1 AATTACTGGAAA-ATG
* *
3614522 AATTATTGAAAAATG
1 AATTACTGGAAAATG
**
3614537 AATTACTGGAATTTG
1 AATTACTGGAAAATG
3614552 AATT-CTGGAAAATG
1 AATTACTGGAAAATG
3614566 AATTAC
1 AATTAC
3614572 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 12 0.31
15 24 0.62
16 3 0.08
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.35
Consensus pattern (15 bp):
AATTACTGGAAAATG
Found at i:3615008 original size:24 final size:26
Alignment explanation
Indices: 3614981--3615166 Score: 74
Period size: 28 Copynumber: 7.1 Consensus size: 26
3614971 TTAGATTATT
3614981 ATATTA-A-TATTAAATATATAAATA
1 ATATTATATTATTAAATATATAAATA
*
3615005 ATATTATTCATTATTAAATATATAAAAA
1 ATATTA-T-ATTATTAAATATATAAATA
3615033 ATTTATTATATATTTATTAAA-ATA-AAA-A
1 A--TA-T-TATA-TTATTAAATATATAAATA
* *
3615061 ATA-TATA-TCTTATATTATTATAATATA
1 ATATTATATTATTA-AATA-TATAA-ATA
*
3615088 ATTGATTATTTTATTATAATAT-TAAA-A
1 A-T-ATTATATTATTA-AATATATAAATA
* *
3615115 ATAATATAATTATTATAA-ATATTAATA
1 ATATTAT-ATTATTA-AATATATAAATA
* *
3615142 A-A-TATATT-TTAAATATTTTAATA
1 ATATTATATTATTAAATATATAAATA
3615165 AT
1 AT
3615167 TAATATTTTG
Statistics
Matches: 128, Mismatches: 10, Indels: 48
0.69 0.05 0.26
Matches are distributed among these distances:
21 4 0.03
22 3 0.02
23 17 0.13
24 11 0.09
25 11 0.09
26 17 0.13
27 7 0.05
28 21 0.16
29 7 0.05
30 10 0.08
31 18 0.14
32 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATTATATTATTAAATATATAAATA
Found at i:3615040 original size:30 final size:29
Alignment explanation
Indices: 3614988--3615066 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 29
3614978 ATTATATTAA
*
3614988 TATTAAATATATAAATAATATTAT-TCA-T
1 TATTAAATATATAAAAAATATTATAT-ATT
3615016 TATTAAATATATAAAAAATTTATTATATATT
1 TATTAAATATATAAAAAA--TATTATATATT
3615047 TATTAAA-ATA-AAAAATATAT
1 TATTAAATATATAAAAA-ATAT
3615067 ATCTTATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
28 20 0.44
29 5 0.11
30 11 0.24
31 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
TATTAAATATATAAAAAATATTATATATT
Found at i:3615134 original size:18 final size:18
Alignment explanation
Indices: 3615080--3615135 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
3615070 TTATATTATT
*
3615080 ATAATATAATTGATTAT-T
1 ATAATATAATT-ATTATAA
* * *
3615098 TTATTATAA-TATTAAAA
1 ATAATATAATTATTATAA
3615115 ATAATATAATTATTATAA
1 ATAATATAATTATTATAA
3615133 ATA
1 ATA
3615136 TTAATAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 4 0.14
17 8 0.28
18 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAATATAATTATTATAA
Found at i:3615149 original size:21 final size:21
Alignment explanation
Indices: 3615102--3615158 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3615092 ATTATTTTAT
3615102 TATAA-TATTA-AAA-A-TAA
1 TATAATTATTATAAATATTAA
3615119 TATAATTATTATAAATATTAA
1 TATAATTATTATAAATATTAA
*
3615140 TA-AATATATTTTAAATATT
1 TATAAT-TATTATAAATATT
3615159 TTAATAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 3 0.09
20 4 0.12
21 17 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAATTATTATAAATATTAA
Found at i:3615308 original size:27 final size:27
Alignment explanation
Indices: 3615278--3615329 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3615268 ATGATTTACG
* *
3615278 GAAAATTAGACCGTAAGTCATTTTCCA
1 GAAAATCAAACCGTAAGTCATTTTCCA
*
3615305 GAAAATCAAACTGTAAGTCATTTTC
1 GAAAATCAAACCGTAAGTCATTTTC
3615330 AAAAAAACGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (27 bp):
GAAAATCAAACCGTAAGTCATTTTCCA
Found at i:3615460 original size:42 final size:39
Alignment explanation
Indices: 3615399--3615531 Score: 144
Period size: 42 Copynumber: 3.3 Consensus size: 39
3615389 TTCCTCCAAC
* * *
3615399 CAAACACCGGAACATATTTTCTGAAAAATGAATTATGTGAAA
1 CAAACACGGGAA-ATATTTTCCGAAAAACGAATTA--TGAAA
*
3615441 CAAACACGGGAAATCATTTTCCGGAAAACGAATTA--AAA
1 CAAACACGGGAAAT-ATTTTCCGAAAAACGAATTATGAAA
*
3615479 CAAACACGAGAAAATATTTTCCGAAAAACGAATTACATGAAA
1 CAAACACG-GGAAATATTTTCCGAAAAACGAATT--ATGAAA
3615521 CAAACACGGGA
1 CAAACACGGGA
3615532 TTTCGAGGAA
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
38 29 0.37
39 5 0.06
40 1 0.01
41 4 0.05
42 39 0.50
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (39 bp):
CAAACACGGGAAATATTTTCCGAAAAACGAATTATGAAA
Found at i:3615522 original size:38 final size:38
Alignment explanation
Indices: 3615438--3615513 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
3615428 GAATTATGTG
* *
3615438 AAACAAACACGGGAAATCATTTTCCGGAAAACGAATTA
1 AAACAAACACGGAAAATCATTTTCCGAAAAACGAATTA
3615476 AAACAAACACGAGAAAAT-ATTTTCCGAAAAACGAATTA
1 AAACAAACACG-GAAAATCATTTTCCGAAAAACGAATTA
3615514 CATGAAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 30 0.86
39 5 0.14
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.18
Consensus pattern (38 bp):
AAACAAACACGGAAAATCATTTTCCGAAAAACGAATTA
Found at i:3615881 original size:13 final size:15
Alignment explanation
Indices: 3615851--3615888 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3615841 TAAATTGTAT
3615851 AAAATATATATTTAA
1 AAAATATATATTTAA
*
3615866 AAAATA-ATTTTTAA
1 AAAATATATATTTAA
*
3615880 AATATATAT
1 AAAATATAT
3615889 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATATATATTTAA
Found at i:3618858 original size:72 final size:71
Alignment explanation
Indices: 3618724--3618975 Score: 247
Period size: 72 Copynumber: 3.5 Consensus size: 71
3618714 TAAATATAGT
* * * * *
3618724 TTTTGAGAATATATAATATATAATTTTTGAAAACGTATTTTTTAAAACATATATAATATAGTTTT
1 TTTTGAAAACATATAATATATAATTTTTTAAAA--TAGTTTTAAAAACATATAT-ATATAGTTTT
*
3618789 TTGAAATGG
63 TTAAAATGG
* *
3618798 TTTTGAAAGCGTATAATATATAATTTTTTAAAATAGTTTTAAAAACATATAGTATATAG-TTTTT
1 TTTTGAAAACATATAATATATAATTTTTTAAAATAGTTTTAAAAACATATA-TATATAGTTTTTT
*
3618862 AAAACGG
65 AAAATGG
* * * * * *
3618869 TTTTGAAAACAAATATTATATATTTTTTTTGAAAT-GATTTTGAAAACGTATAATATATAGTTTT
1 TTTTGAAAACATATAATATATA-ATTTTTTAAAATAG-TTTTAAAAACATAT-ATATATAGTTTT
*
3618933 TTAAAAATGA
63 TT-AAAATGG
* **
3618943 TTCTGAAAACATATAATATATGGTTTTTTAAAA
1 TTTTGAAAACATATAATATATAATTTTTTAAAA
3618976 AACAGTTTTG
Statistics
Matches: 147, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
71 29 0.20
72 51 0.35
73 16 0.11
74 51 0.35
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (71 bp):
TTTTGAAAACATATAATATATAATTTTTTAAAATAGTTTTAAAAACATATATATATAGTTTTTTA
AAATGG
Found at i:3618910 original size:37 final size:36
Alignment explanation
Indices: 3618724--3619035 Score: 216
Period size: 37 Copynumber: 8.4 Consensus size: 36
3618714 TAAATATAGT
* * * * *
3618724 TTTTGAGAATATATAATATATAATTTTTGAAAACGTA
1 TTTTGAAAACATATAATATATATTTTTTTAAAATG-A
* * * *
3618761 TTTTTTAAAACATAT-ATAATATAGTTTTTTGAAATGG
1 -TTTTGAAAACATATAAT-ATATATTTTTTTAAAATGA
* * *
3618798 TTTTGAAAGCGTATAATATATAATTTTTTAAAAT-A
1 TTTTGAAAACATATAATATATATTTTTTTAAAATGA
* * * * *
3618833 GTTTTAAAAACATATAGTATATA-GTTTTTAAAACGG
1 -TTTTGAAAACATATAATATATATTTTTTTAAAATGA
* * *
3618869 TTTTGAAAACAAATATTATATATTTTTTTTGAAATGA
1 TTTTGAAAACATATAATATATA-TTTTTTTAAAATGA
* *
3618906 TTTTGAAAACGTATAATATATAGTTTTTTAAAAATGA
1 TTTTGAAAACATATAATATATA-TTTTTTTAAAATGA
* * * **
3618943 TTCTGAAAACATATAATATATGGTTTTTTAAAAAACA
1 TTTTGAAAACATATAATATAT-ATTTTTTTAAAATGA
* * *
3618980 GTTTTGAAAACGCATATTATATATATATATTTTAAAAACGA
1 -TTTTGAAAA--CATA-TA-ATATATATTTTTTTAAAATGA
3619021 TTTTCGAAAACATAT
1 TTTT-GAAAACATAT
3619036 TATTATTATT
Statistics
Matches: 217, Mismatches: 44, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
35 28 0.13
36 44 0.20
37 75 0.35
38 34 0.16
39 4 0.02
40 8 0.04
41 18 0.08
42 6 0.03
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATATTTTTTTAAAATGA
Found at i:3619041 original size:3 final size:3
Alignment explanation
Indices: 3619033--3619090 Score: 84
Period size: 3 Copynumber: 19.3 Consensus size: 3
3619023 TTCGAAAACA
3619033 TAT TAT TAT TAT TAT TAT TAT TA- TACT TAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
3619077 TAT TATT TAT TAT T
1 TAT TA-T TAT TAT T
3619091 TATTTTAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 42 0.82
4 5 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3619094 original size:26 final size:29
Alignment explanation
Indices: 3619035--3619091 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3619025 CGAAAACATA
3619035 TTATTATTATTATTATTATTATACTTATT
1 TTATTATTATTATTATTATTATACTTATT
3619064 TTATTATTATTATTATTATT-TA-TTATT
1 TTATTATTATTATTATTATTATACTTATT
3619091 T
1 T
3619092 ATTTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 6 0.21
28 2 0.07
29 20 0.71
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TTATTATTATTATTATTATTATACTTATT
Found at i:3619147 original size:18 final size:18
Alignment explanation
Indices: 3619124--3619173 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
3619114 GCAGGATCCA
*
3619124 AGTCCAATATTCCAACCG
1 AGTCCAACATTCCAACCG
3619142 AGTCCAACATTCCAACCG
1 AGTCCAACATTCCAACCG
* *
3619160 GGTCCAACAATCCA
1 AGTCCAACATTCCA
3619174 GCAAAAGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.18
Consensus pattern (18 bp):
AGTCCAACATTCCAACCG
Found at i:3619264 original size:20 final size:20
Alignment explanation
Indices: 3619239--3619283 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3619229 AGACCGATGC
3619239 GGGTGGCCCGATCCGATCCA
1 GGGTGGCCCGATCCGATCCA
*
3619259 GGGTGGCCCGATTCGATCCA
1 GGGTGGCCCGATCCGATCCA
3619279 GGGTG
1 GGGTG
3619284 TCACATTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (20 bp):
GGGTGGCCCGATCCGATCCA
Found at i:3622538 original size:22 final size:20
Alignment explanation
Indices: 3622506--3622557 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
3622496 TAACCCTATA
*
3622506 TGTGTGTGTGCGCGCGTGTG
1 TGTGTGTGTGCGCGCGTGAG
*
3622526 TGTGTGTACGTGCGTGCGTGAG
1 TGTGTGT--GTGCGCGCGTGAG
*
3622548 TCTGTGTGTG
1 TGTGTGTGTG
3622558 TGAATTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.04, C:0.13, G:0.46, T:0.37
Consensus pattern (20 bp):
TGTGTGTGTGCGCGCGTGAG
Found at i:3622540 original size:18 final size:18
Alignment explanation
Indices: 3622506--3622541 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3622496 TAACCCTATA
*
3622506 TGTGTGTGTGCGCGCGTG
1 TGTGTGTGTACGCGCGTG
*
3622524 TGTGTGTGTACGTGCGTG
1 TGTGTGTGTACGCGCGTG
3622542 CGTGAGTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.14, G:0.47, T:0.36
Consensus pattern (18 bp):
TGTGTGTGTACGCGCGTG
Found at i:3622650 original size:53 final size:53
Alignment explanation
Indices: 3622570--3622672 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
3622560 AATTTATCAA
** * *
3622570 AATTTATCAAATGACATCGGTGGTAAAAAAATGTTATTCTCACTAGAGATATG
1 AATTTATCAAATGACATCAATGATAAAAAAATGTTATTATCACTAGAGATATG
*
3622623 AATTTATCAAGTGACATCAATGATAAAAAAATGTTATTATCACTAGAGAT
1 AATTTATCAAATGACATCAATGATAAAAAAATGTTATTATCACTAGAGAT
3622673 TTTAAATTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (53 bp):
AATTTATCAAATGACATCAATGATAAAAAAATGTTATTATCACTAGAGATATG
Found at i:3627391 original size:19 final size:19
Alignment explanation
Indices: 3627367--3627419 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
3627357 GAATGCACTT
3627367 CATGCATCAATGCACATAC
1 CATGCATCAATGCACATAC
3627386 CATGCATCAATGCACATAC
1 CATGCATCAATGCACATAC
*
3627405 CATGCATCGATGCAC
1 CATGCATCAATGCAC
3627420 TGAGGATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.21
Consensus pattern (19 bp):
CATGCATCAATGCACATAC
Found at i:3627506 original size:65 final size:65
Alignment explanation
Indices: 3627387--3627530 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 65
3627377 TGCACATACC
* * * * *
3627387 ATGCATCAATGCACATACCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACAGACCATGCATCGATGCACTCAGGATATTATCAAAACATCGAATGCATTTG
* * *
3627452 ATGCATCGATGCACAAGACCATGCATCGATGCACTCTGGCTATT-TCAAAGCATCGAATGCATTT
1 ATGCATCGATGCAC-AGACCATGCATCGATGCACTCAGGATATTATCAAAACATCGAATGCATTT
*
3627516 T
65 G
* *
3627517 ACGCATCGGTGCAC
1 ATGCATCGATGCAC
3627531 TCTTAGTGCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
65 43 0.64
66 24 0.36
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (65 bp):
ATGCATCGATGCACAGACCATGCATCGATGCACTCAGGATATTATCAAAACATCGAATGCATTTG
Found at i:3635391 original size:12 final size:13
Alignment explanation
Indices: 3635374--3635408 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3635364 TAAGGGGGAG
3635374 TAATTTCAAAA-T
1 TAATTTCAAAACT
3635386 TAATTTCAAAACT
1 TAATTTCAAAACT
*
3635399 TATTTTCAAA
1 TAATTTCAAA
3635409 GAAAATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATTTCAAAACT
Found at i:3635824 original size:65 final size:65
Alignment explanation
Indices: 3635755--3635915 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 65
3635745 AATTAAATTG
* * * *
3635755 AACATCGAATGCATTTCATGCAAT-GATGCAC-ATACCATGCATCGATGCACTGAGGATTTTATG
1 AACATCGAATGCATTTCATGC-ATCGATGCACAAGACCATGCATCGATGCACTCAGGATATT-TC
3635818 AA
64 AA
* * ** *
3635820 AACATCGAATGCATTTGATTCATCGATGCACAAGACTGTGCATCGATGCACTCAGGCTATTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACCATGCATCGATGCACTCAGGATATTTCAA
* * *
3635885 AACATTGGATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
3635916 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 2 0.02
65 56 0.69
66 23 0.28
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGACCATGCATCGATGCACTCAGGATATTTCAA
Found at i:3636004 original size:21 final size:21
Alignment explanation
Indices: 3635974--3636028 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3635964 TTTACACTTG
*
3635974 ATGCACCGATGCACCTAGGGT
1 ATGCATCGATGCACCTAGGGT
3635995 ATGCATCGATGCACCTAGGGT
1 ATGCATCGATGCACCTAGGGT
3636016 ATGCATCGATGCA
1 ATGCATCGATGCA
3636029 TGAGACACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGCATCGATGCACCTAGGGT
Done.