Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 14 of 444
Found at i:4223805 original size:26 final size:28
Alignment explanation
Indices: 4223745--4223807 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 28
4223735 AATGTCAATG
4223745 GTCAAATTTAGCTCAAAATAGAAATAAA
1 GTCAAATTTAGCTCAAAATAGAAATAAA
4223773 GTCCAAATTTAGCTC-AAA-A-AAATAAA
1 GT-CAAATTTAGCTCAAAATAGAAATAAA
4223799 GATCAAATT
1 G-TCAAATT
4223808 GATTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 14 0.42
27 2 0.06
28 5 0.15
29 12 0.36
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (28 bp):
GTCAAATTTAGCTCAAAATAGAAATAAA
Found at i:4224350 original size:21 final size:21
Alignment explanation
Indices: 4224326--4224369 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4224316 TAAAAATTAA
* *
4224326 TTTATGGATTTTGATTGGATT
1 TTTATGGAATTTGATTCGATT
* *
4224347 TTTATTGAATTTGGTTCGATT
1 TTTATGGAATTTGATTCGATT
4224368 TT
1 TT
4224370 AATTTGGATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.59
Consensus pattern (21 bp):
TTTATGGAATTTGATTCGATT
Found at i:4224703 original size:39 final size:41
Alignment explanation
Indices: 4224621--4224709 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 41
4224611 TTTTTCAAAA
4224621 TTTTAAAAATAATATTTTAATATTTATTTCATAATTTTAAT
1 TTTTAAAAATAATATTTTAATATTTATTTCATAATTTTAAT
* * * * *
4224662 TTTTTAAAATACT-TTTTTATATTTTTTTGA-AATTTTAA-
1 TTTTAAAAATAATATTTTAATATTTATTTCATAATTTTAAT
4224700 TTTTAAAAAT
1 TTTTAAAAAT
4224710 TAATTAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 9 0.21
39 8 0.19
40 14 0.33
41 11 0.26
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (41 bp):
TTTTAAAAATAATATTTTAATATTTATTTCATAATTTTAAT
Found at i:4238154 original size:31 final size:31
Alignment explanation
Indices: 4238118--4238186 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
4238108 ATTTGATTAT
* *
4238118 TTTTAGTACTTGTACTTTTTGAATTGGTCAA
1 TTTTAGTACCTATACTTTTTGAATTGGTCAA
*
4238149 TTTTAGTCCCTATACTTTTTGAATTGGTCAA
1 TTTTAGTACCTATACTTTTTGAATTGGTCAA
4238180 TTTTAGT
1 TTTTAGT
4238187 CCCTGTTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (31 bp):
TTTTAGTACCTATACTTTTTGAATTGGTCAA
Found at i:4238187 original size:31 final size:31
Alignment explanation
Indices: 4238130--4238190 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
4238120 TTAGTACTTG
4238130 TACTTTTTGAATTGGTCAATTTTAGTCCCTA
1 TACTTTTTGAATTGGTCAATTTTAGTCCCTA
4238161 TACTTTTTGAATTGGTCAATTTTAGTCCCT
1 TACTTTTTGAATTGGTCAATTTTAGTCCCT
4238191 GTTGTGACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.49
Consensus pattern (31 bp):
TACTTTTTGAATTGGTCAATTTTAGTCCCTA
Found at i:4248109 original size:130 final size:137
Alignment explanation
Indices: 4247837--4248102 Score: 359
Period size: 130 Copynumber: 2.0 Consensus size: 137
4247827 TTATAATAAA
4247837 AAAAAAATGCTTAAGTTCTCCATTAAATATCCAATTTTCTACCCTTTTTTAAAGAAAGAAAAAGA
1 AAAAAAATGCTTAAGTTCTCCATTAAATATCCAATTTTCTACCCTTTTTT-AAGAAAGAAAAAGA
* * **
4247902 AACTATAAAATCAAGATTCAAGTATCATTTAGAAAATATTATTAAAACACGAAAATGAAACGAAC
65 AACTATAAAATCAAGATTCAAGCATCATTTAGAAAACACCATTAAAACACGAAAATGAAACGAAC
*
4247967 TCAATGCC
130 CCAATGCC
* *
4247975 AAAAAAA-GCTTACA-TTTTCCATTAAATATCCAATTTTCTA-GC-TTTTT-A-AAA-AAAAAG-
1 AAAAAAATGCTTA-AGTTCTCCATTAAATATCCAATTTTCTACCCTTTTTTAAGAAAGAAAAAGA
** * *
4248032 ATTTATAAAATCAAGATTCAAGCATCCTTTAGAAAACACCATTGAAACACGAAAATGAAACGAAC
65 AACTATAAAATCAAGATTCAAGCATCATTTAGAAAACACCATTAAAACACGAAAATGAAACGAAC
4248097 CCAATG
130 CCAATG
4248103 GGAAAAAGTG
Statistics
Matches: 116, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
130 62 0.53
131 6 0.05
132 3 0.03
133 1 0.01
135 5 0.04
136 1 0.01
137 30 0.26
138 8 0.07
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (137 bp):
AAAAAAATGCTTAAGTTCTCCATTAAATATCCAATTTTCTACCCTTTTTTAAGAAAGAAAAAGAA
ACTATAAAATCAAGATTCAAGCATCATTTAGAAAACACCATTAAAACACGAAAATGAAACGAACC
CAATGCC
Found at i:4262146 original size:19 final size:20
Alignment explanation
Indices: 4262124--4262162 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4262114 AACCACTGTC
*
4262124 ATCCATCGTAA-TAAAATTT
1 ATCCACCGTAATTAAAATTT
*
4262143 ATCCACCTTAATTAAAATTT
1 ATCCACCGTAATTAAAATTT
4262163 TTATTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (20 bp):
ATCCACCGTAATTAAAATTT
Found at i:4263613 original size:9 final size:9
Alignment explanation
Indices: 4263599--4263631 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4263589 ATTCGAGTTG
4263599 ACTCGAATA
1 ACTCGAATA
*
4263608 ACTCGATTA
1 ACTCGAATA
4263617 ACTCGAATA
1 ACTCGAATA
4263626 ACTCGA
1 ACTCGA
4263632 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:4263622 original size:18 final size:18
Alignment explanation
Indices: 4263599--4263633 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4263589 ATTCGAGTTG
4263599 ACTCGAATAACTCGATTA
1 ACTCGAATAACTCGATTA
4263617 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
4263634 CGTTTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:4264751 original size:28 final size:26
Alignment explanation
Indices: 4264708--4264776 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 26
4264698 CAGCTGAGCT
* *
4264708 AAACCATCATATCTTTTTAGTTCAAGTG
1 AAACCATGATAGCTTTTT--TTCAAGTG
4264736 AAACCATGATAGC-TTTTTTCAAGTG
1 AAACCATGATAGCTTTTTTTCAAGTG
*
4264761 AAACCATGGTAGCTTT
1 AAACCATGATAGCTTT
4264777 CTTGTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 20 0.54
26 2 0.05
27 4 0.11
28 11 0.30
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (26 bp):
AAACCATGATAGCTTTTTTTCAAGTG
Found at i:4264762 original size:25 final size:25
Alignment explanation
Indices: 4264728--4264776 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
4264718 ATCTTTTTAG
4264728 TTCAAGTGAAACCATGATAGCTTTT
1 TTCAAGTGAAACCATGATAGCTTTT
*
4264753 TTCAAGTGAAACCATGGTAGCTTT
1 TTCAAGTGAAACCATGATAGCTTT
4264777 CTTGTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (25 bp):
TTCAAGTGAAACCATGATAGCTTTT
Found at i:4265785 original size:24 final size:24
Alignment explanation
Indices: 4265753--4265798 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4265743 CAACGCACAA
*
4265753 GAATCAATTTT-TAACAATAAAAAT
1 GAATAAATTTTCTAACAA-AAAAAT
4265777 GAATAAATTTTCTAACAAAAAA
1 GAATAAATTTTCTAACAAAAAA
4265799 GTTAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAAATTTTCTAACAAAAAAAT
Found at i:4271103 original size:26 final size:26
Alignment explanation
Indices: 4271067--4271118 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4271057 GAACAAGTCT
4271067 AGTCAAACTAGTTTGTTATGGTTCAA
1 AGTCAAACTAGTTTGTTATGGTTCAA
4271093 AGTCAAACTAGTTTGTTATGGTTCAA
1 AGTCAAACTAGTTTGTTATGGTTCAA
4271119 TCTTTATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (26 bp):
AGTCAAACTAGTTTGTTATGGTTCAA
Found at i:4272210 original size:41 final size:41
Alignment explanation
Indices: 4272165--4272248 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
4272155 TCATATGATT
* *
4272165 TTGTTTTTGTAAAATCTGTCTTATATAAATTAATGGTTACG
1 TTGTTTCTATAAAATCTGTCTTATATAAATTAATGGTTACG
*
4272206 TTGTTTCTATAAAATCTGTCTTATATAAATTAATTGTTACG
1 TTGTTTCTATAAAATCTGTCTTATATAAATTAATGGTTACG
4272247 TT
1 TT
4272249 ATTTGTACAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (41 bp):
TTGTTTCTATAAAATCTGTCTTATATAAATTAATGGTTACG
Found at i:4275115 original size:18 final size:18
Alignment explanation
Indices: 4275079--4275141 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
4275069 AGCTGCGAGT
** *
4275079 TCATTCAAAGACACGAGC
1 TCATTCAAAGATGCAAGC
4275097 TCATTCAAAGATGCAAGC
1 TCATTCAAAGATGCAAGC
** * *
4275115 TCAACCCAAGTTGCAAGC
1 TCATTCAAAGATGCAAGC
4275133 TCA-TCAAAG
1 TCATTCAAAG
4275142 TGCGAGCTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 4 0.11
18 32 0.89
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (18 bp):
TCATTCAAAGATGCAAGC
Found at i:4281059 original size:20 final size:22
Alignment explanation
Indices: 4281017--4281058 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4281007 ATTTTTTAAA
4281017 AATATTTATATTATATTATTTT
1 AATATTTATATTATATTATTTT
4281039 AATATTTA-A-TATATTTATTT
1 AATATTTATATTATA-TTATTT
4281059 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTTATATTATATTATTTT
Found at i:4281074 original size:23 final size:25
Alignment explanation
Indices: 4281021--4281075 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
4281011 TTTAAAAATA
*
4281021 TTTATATTATATTATTTTAATATTT
1 TTTATATTATATTATATTAATATTT
** *
4281046 AATATATT-TATT-TATTAATTTTT
1 TTTATATTATATTATATTAATATTT
4281069 TTTATAT
1 TTTATAT
4281076 AGTCATCTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 14 0.58
24 4 0.17
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTATATTATATTATATTAATATTT
Found at i:4282407 original size:112 final size:112
Alignment explanation
Indices: 4282258--4282463 Score: 288
Period size: 112 Copynumber: 1.8 Consensus size: 112
4282248 AAAAAACGAC
* * * * * * **
4282258 AAAAATTTTATTTAATCTTTAAAAATTATAAAGATATAGTTTATTAAAATGGTGAAATTGTATTT
1 AAAAATTTGAGTTAATCTTTAAAAATTATAAAGATATAATCTATTAAAAAGGTAAAATTACATTT
*
4282323 TTTCTAT-AAAAAAATATACAATTTAATTCTAGCTCCCAAAAGTGAT
66 TTACTATCAAAAAAATATACAATTTAATTCTAGCTCCCAAAAGTGAT
*
4282369 AAAAATTTGAGTTAATCATTTAAAATTTATAAAGATATAATCTATTAAAAAGGTAAAATTACATT
1 AAAAATTTGAGTTAATC-TTTAAAAATTATAAAGATATAATCTATTAAAAAGGTAAAATTACATT
**
4282434 TTTACTATCGTAAAAATATACAATTTAATT
65 TTTACTATCAAAAAAATATACAATTTAATT
4282464 TCAGTCCCTT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
111 15 0.19
112 47 0.58
113 19 0.23
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (112 bp):
AAAAATTTGAGTTAATCTTTAAAAATTATAAAGATATAATCTATTAAAAAGGTAAAATTACATTT
TTACTATCAAAAAAATATACAATTTAATTCTAGCTCCCAAAAGTGAT
Found at i:4283330 original size:15 final size:13
Alignment explanation
Indices: 4283306--4283345 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
4283296 TGATTGTAAT
4283306 AGTTAGTAGTTAA
1 AGTTAGTAGTTAA
4283319 CAGTTAAGTAGTTAA
1 -AGTT-AGTAGTTAA
*
4283334 AATTAGTAGTTA
1 AGTTAGTAGTTA
4283346 GTAGTTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 7 0.29
15 9 0.38
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.38
Consensus pattern (13 bp):
AGTTAGTAGTTAA
Found at i:4287934 original size:29 final size:30
Alignment explanation
Indices: 4287901--4287961 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
4287891 AAAACGGTTG
4287901 TAACAATTAGTAGTTAACAGTT-ATGTAGT
1 TAACAATTAGTAGTTAACAGTTGATGTAGT
**
4287930 TAACAATTAGTAGTTAGTAGTTGATGTAGT
1 TAACAATTAGTAGTTAACAGTTGATGTAGT
4287960 TA
1 TA
4287962 GTCAACAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (30 bp):
TAACAATTAGTAGTTAACAGTTGATGTAGT
Found at i:4287944 original size:14 final size:14
Alignment explanation
Indices: 4287901--4287945 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
4287891 AAAACGGTTG
4287901 TAACAATTAGTAGT
1 TAACAATTAGTAGT
*
4287915 TAACAGTTATGTAGT
1 TAACAATTA-GTAGT
4287930 TAACAATTAGTAGT
1 TAACAATTAGTAGT
4287944 TA
1 TA
4287946 GTAGTTGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (14 bp):
TAACAATTAGTAGT
Found at i:4288729 original size:16 final size:15
Alignment explanation
Indices: 4288708--4288741 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
4288698 TATATATATA
4288708 TATATATAATAGTTTT
1 TATATATAATA-TTTT
*
4288724 TATATATATTATTTT
1 TATATATAATATTTT
4288739 TAT
1 TAT
4288742 TGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TATATATAATATTTT
Found at i:4298527 original size:21 final size:21
Alignment explanation
Indices: 4298501--4298541 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4298491 ATCTGCTCAA
* *
4298501 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
4298522 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
4298542 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:4303692 original size:3 final size:3
Alignment explanation
Indices: 4303684--4304283 Score: 142
Period size: 3 Copynumber: 202.3 Consensus size: 3
4303674 ATTGTTTATG
4303684 TTA TTA TTA TTA TTA TT- TATA CCTTA TTA TTA TTA GTTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA T-TA --TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * *
4303731 TTA TTT TTA TCTA ATA -TA TTA TCA TTA TCA TTA TTA TTA TT- TCA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
4303775 CTA TTG TAA CTTA ATA -TA TTA GTA TTG TTA TTT TTA TT- TTCA TCCTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T--TA
** ** *
4303822 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CCA CCA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * ** * ** * *
4303870 TTT TTA CCA TTA TTA TTA -TC TTA GCA TTA -AA CCCA TAAA TT- TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA
** * * *
4303914 -TA TCG TTA TCA TTA -TA TTA TATA TAA ATA -TA TT- TTA TGTA TATA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA T-TA
* ** * *
4303958 TTA TTA TT- TACA TTA TTA TTA TTA TTA CAA TTT TTA TT- TTCC TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* * * * * * * *
4304003 TT- TTA TTA CTA TTGA -CA TTA GTA CTA TTT TTA TTG CTA TTA CT-
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
4304046 TTA TTA CTA TTA CTA CTA ATA TCA CTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
4304094 CTA TTA TTA TTA TT- TTA TT- TTA CTA TCTA ATA -TA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * * * *
4304136 CCTT- TTA TTA TTA TTA CTA TTGT TTA TTA CTA CTA TTA TTA TCA -TA
1 --TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
4304182 TT- TTC TT- TTT TTA TTA CTA TTA CTA -TA TTA TTT TTA TTT TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * **
4304227 CTA TTA TTA TTA TCA TTA CTA TTA -TA TTA TTA GCA -TA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
4304271 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
4304284 CCTCATTAAC
Statistics
Matches: 425, Mismatches: 122, Indels: 100
0.66 0.19 0.15
Matches are distributed among these distances:
2 47 0.11
3 340 0.80
4 31 0.07
5 5 0.01
6 2 0.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:4304030 original size:26 final size:25
Alignment explanation
Indices: 4304001--4304056 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
4303991 TTATTTTCCT
4304001 TATTTTATTACTATTGACATTAGTAC
1 TATTTTATTACTATT-ACATTAGTAC
* * *
4304027 TATTTTTATTGCTATTACTTTATTAC
1 TA-TTTTATTACTATTACATTAGTAC
4304053 TATT
1 TATT
4304057 ACTACTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.08
26 12 0.46
27 12 0.46
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (25 bp):
TATTTTATTACTATTACATTAGTAC
Found at i:4304144 original size:52 final size:51
Alignment explanation
Indices: 4304077--4304258 Score: 130
Period size: 52 Copynumber: 3.5 Consensus size: 51
4304067 TCACTATTAT
4304077 TATTATTAT--TTTTATTACTATTATTATTATTTTATTTTACTATCTAATA
1 TATTATTATCCTTTTATTACTATTATTATTATTTTATTTTACTATCTAATA
* * * *
4304126 TATTATTATACCTTTTATTATTATTACTATT-GTTTATTACTACTAT-TATTATCA
1 TATTATTAT-CCTTTTATTACTATTATTATTATTTTATT-TTACTATCTA--AT-A
* **
4304180 TATT-TTCTTTTTTTATTACTATTACTATATTATTTTTATTTTTACTA-CT-AT-
1 TATTATTATCCTTTTATTACTATTA-T-TATTA-TTTTA-TTTTACTATCTAATA
* *
4304231 TATTATTATCATTACTATTA-TATTATTA
1 TATTATTATCCTT-TTATTACTATTATTA
4304259 GCATATTATT
Statistics
Matches: 103, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
49 9 0.09
50 2 0.02
51 13 0.13
52 46 0.45
53 12 0.12
54 9 0.09
56 10 0.10
57 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.01, T:0.62
Consensus pattern (51 bp):
TATTATTATCCTTTTATTACTATTATTATTATTTTATTTTACTATCTAATA
Found at i:4304217 original size:23 final size:24
Alignment explanation
Indices: 4304189--4304258 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 24
4304179 ATATTTTCTT
4304189 TTTTTATTACTATTACTA-TATTA
1 TTTTTATTACTATTACTATTATTA
** *
4304212 TTTTTATTTTTACTACTATTATTA
1 TTTTTATTACTATTACTATTATTA
* *
4304236 TTATCATTACTATTA-TATTATTA
1 TTTTTATTACTATTACTATTATTA
4304259 GCATATTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 23 0.61
24 15 0.39
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTTATTACTATTACTATTATTA
Found at i:4304420 original size:25 final size:24
Alignment explanation
Indices: 4304392--4304443 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
4304382 CCTTTTTTAC
*
4304392 TTATTCTCATTATTCTTATTTATTT
1 TTATTCTCATCATTCTTA-TTATTT
* * *
4304417 TTATTTTTATCATTTTTATTATTT
1 TTATTCTCATCATTCTTATTATTT
4304441 TTA
1 TTA
4304444 CCTATTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATTCTCATCATTCTTATTATTT
Found at i:4312829 original size:3 final size:3
Alignment explanation
Indices: 4312821--4313272 Score: 151
Period size: 3 Copynumber: 154.0 Consensus size: 3
4312811 ATTTTCATCC
4312821 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
4312869 TAT TAT TAC CAT TAT TAT TA- TCT TAG CAT TA- AACC CAT AAAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT
* ** * *
4312913 CA- TAT CGT TAT CAA TA- TAT TAT ATAT ATAT T-T TAT GTAT GTAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT -TAT -TAT TAT
* * * * *
4312959 TAT T-T ACAT TAT TAT TAT TAT TAC AAT TTT TAT T-T TCCT TAT T-T
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* * * * * * *
4313003 TAT TAC TAT TGA- CAT TAG TAC TAT TTT TAT TAC TAT TAC T-T TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
4313047 TAC TAT TAC TAC TAA TAT CAC TAT TAT TAT TAT T-T TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
4313094 TAT TAT T-T TAT T-T T-T TAC TAT CTAA TA- TAT TAT TA- TACCT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA--T TAT
* * * *
4313136 TAT TAT TAT TAC TAT TGTT TAT TAC TAT TAT TAT TAT CA- TAT T-T
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
4313180 TCT T-T TTT TAT TAC TAT TAC TA- TAT TAT TTT TAT TTT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
4313226 CAT CAC TAT TA- TAT TAT TAG CA- TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
4313270 TAT
1 TAT
4313273 CCTTATTAAC
Statistics
Matches: 329, Mismatches: 85, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
2 39 0.12
3 261 0.79
4 28 0.09
5 1 0.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:4313027 original size:26 final size:25
Alignment explanation
Indices: 4312998--4313092 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 25
4312988 TTATTTTCCT
4312998 TATTTTATTACTATTGACATTAGTAC
1 TATTTTATTACTATT-ACATTAGTAC
* *
4313024 TATTTTTATTACTATTACTTTATTAC
1 TA-TTTTATTACTATTACATTAGTAC
* * * * * *
4313050 TATTACTACTAATATCACTATTATTAT
1 TATT-TTATTACTATTAC-ATTAGTAC
4313077 TATTTTATTACTATTA
1 TATTTTATTACTATTA
4313093 TTATTATTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
25 2 0.04
26 29 0.54
27 23 0.43
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.55
Consensus pattern (25 bp):
TATTTTATTACTATTACATTAGTAC
Found at i:4313053 original size:20 final size:20
Alignment explanation
Indices: 4312997--4313105 Score: 89
Period size: 20 Copynumber: 5.5 Consensus size: 20
4312987 TTTATTTTCC
4312997 TTATTTTATTACTATTGAC-A
1 TTATTTTATTACTATT-ACTA
** **
4313017 TTAGTACTATTTTTATTACTA
1 TTA-TTTTATTACTATTACTA
*
4313038 TTACTTTATTACTATTACTA
1 TTATTTTATTACTATTACTA
* * * *
4313058 CTA--ATATCACTATTATTA
1 TTATTTTATTACTATTACTA
*
4313076 TTATTTTATTACTATTATTA
1 TTATTTTATTACTATTACTA
4313096 TTATTTTATT
1 TTATTTTATT
4313106 TTTTACTATC
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
18 14 0.20
20 42 0.61
21 13 0.19
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATTTTATTACTATTACTA
Found at i:4313158 original size:19 final size:19
Alignment explanation
Indices: 4313134--4313170 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4313124 TATTATACCT
*
4313134 TTTATTATTATTACTATTG
1 TTTATTACTATTACTATTG
*
4313153 TTTATTACTATTATTATT
1 TTTATTACTATTACTATT
4313171 ATCATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTATTACTATTACTATTG
Found at i:4313415 original size:16 final size:17
Alignment explanation
Indices: 4313389--4313431 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
4313379 ACTTATTCTC
*
4313389 ATTATTCTTAT-TTATTT
1 ATTATTTTTATCTT-TTT
4313406 -TTATTTTTATCTTTTT
1 ATTATTTTTATCTTTTT
4313422 ATTATTTTTA
1 ATTATTTTTA
4313432 CCTATTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTATTTTTATCTTTTT
Found at i:4316991 original size:18 final size:19
Alignment explanation
Indices: 4316956--4316991 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4316946 GTCTCCAAAC
*
4316956 CAAGTTCCTCCAAGGATGA
1 CAAGTTCCTCCAACGATGA
4316975 CAAGTTCC-CCAACGATG
1 CAAGTTCCTCCAACGATG
4316992 GTGGGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (19 bp):
CAAGTTCCTCCAACGATGA
Found at i:4321524 original size:12 final size:12
Alignment explanation
Indices: 4321509--4321539 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4321499 TTCTCTTTTA
4321509 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
4321521 TTTTTCTTTCTC
1 TTTTTCTTTCCC
4321533 TTTTTCT
1 TTTTTCT
4321540 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:4321936 original size:15 final size:14
Alignment explanation
Indices: 4321918--4321948 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4321908 TTAATTTATT
4321918 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
4321933 TAATAATAATCTAA
1 TAATAATAATCTAA
4321947 TA
1 TA
4321949 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:4321959 original size:21 final size:20
Alignment explanation
Indices: 4321935--4322003 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
4321925 AATGCTAATA
4321935 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
4321956 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
4321975 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
4321996 ATAATAAT
1 ATAATAAT
4322004 AATCATTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:4323634 original size:4 final size:4
Alignment explanation
Indices: 4323625--4323651 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4323615 ATTGTTAGTG
4323625 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
4323652 TTTGCTCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:4323823 original size:11 final size:11
Alignment explanation
Indices: 4323807--4323832 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4323797 TAAATCACCG
4323807 CTAAGCTTTAA
1 CTAAGCTTTAA
4323818 CTAAGCTTTAA
1 CTAAGCTTTAA
4323829 CTAA
1 CTAA
4323833 CGGTGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (11 bp):
CTAAGCTTTAA
Found at i:4329623 original size:14 final size:15
Alignment explanation
Indices: 4329604--4329635 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
4329594 TGTAAGAAAG
4329604 GAAAAAAAATTA-AA
1 GAAAAAAAATTATAA
4329618 GAAAAAAAATTATAA
1 GAAAAAAAATTATAA
4329633 GAA
1 GAA
4329636 TAGAAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (15 bp):
GAAAAAAAATTATAA
Found at i:4333523 original size:40 final size:40
Alignment explanation
Indices: 4333474--4333552 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
4333464 AGCTCATGCA
*
4333474 AATTCATGCACATAAGTTGT-CCGGGTAAAGTACGTGCAAG
1 AATTCATGCACATAAGTT-TCCCGAGTAAAGTACGTGCAAG
4333514 AATTCATGCACATAAGTTTCCCGAGTAAAGTACGTGCAA
1 AATTCATGCACATAAGTTTCCCGAGTAAAGTACGTGCAA
4333553 CTGAATATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (40 bp):
AATTCATGCACATAAGTTTCCCGAGTAAAGTACGTGCAAG
Found at i:4334691 original size:11 final size:11
Alignment explanation
Indices: 4334672--4334711 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4334662 TTTGTTAAGT
*
4334672 AATTTAAATTA
1 AATTAAAATTA
4334683 AATTAAAATTA
1 AATTAAAATTA
*
4334694 AATTAAAAATA
1 AATTAAAATTA
*
4334705 TATTAAA
1 AATTAAA
4334712 TATGGATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTAAAATTA
Found at i:4337471 original size:22 final size:21
Alignment explanation
Indices: 4337432--4337483 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
4337422 TTTTTATATA
*
4337432 TATTATTTTCATTTGCATC-T
1 TATTATTATCATTTGCATCTT
4337452 TACTTATTATCATTTTGCATCTT
1 TA-TTATTATCA-TTTGCATCTT
4337475 TATTATTAT
1 TATTATTAT
4337484 TATTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 8 0.29
22 15 0.54
23 3 0.11
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (21 bp):
TATTATTATCATTTGCATCTT
Found at i:4337480 original size:3 final size:3
Alignment explanation
Indices: 4337474--4337556 Score: 157
Period size: 3 Copynumber: 27.3 Consensus size: 3
4337464 TTTTGCATCT
4337474 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
4337520 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4337557 CATCATCTTA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4337644 original size:2 final size:2
Alignment explanation
Indices: 4337600--4337633 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4337590 TCGTTATCAT
4337600 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4337634 TAGGTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4337742 original size:20 final size:21
Alignment explanation
Indices: 4337714--4337752 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4337704 TCCTTTTTAT
*
4337714 TACTATTACTAC-ATTATTTC
1 TACTATTACAACTATTATTTC
*
4337734 TACTTTTACAACTATTATT
1 TACTATTACAACTATTATT
4337753 ATTATCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (21 bp):
TACTATTACAACTATTATTTC
Found at i:4337920 original size:9 final size:9
Alignment explanation
Indices: 4337906--4337963 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
4337896 TCCTTTTTAC
4337906 TTATTCTTA
1 TTATTCTTA
4337915 TTATTCTTA
1 TTATTCTTA
4337924 TT-TAT-TT-
1 TTAT-TCTTA
4337931 TTATTCTTA
1 TTATTCTTA
* *
4337940 TCATTTTTA
1 TTATTCTTA
4337949 TTATTCTTA
1 TTATTCTTA
4337958 TCTATT
1 T-TATT
4337964 ATTTTCCTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
7 3 0.08
8 6 0.15
9 27 0.68
10 4 0.10
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTCTTA
Found at i:4337936 original size:16 final size:15
Alignment explanation
Indices: 4337915--4337950 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
4337905 CTTATTCTTA
*
4337915 TTATTCTTATTTATTT
1 TTATTCTTA-TCATTT
4337931 TTATTCTTATCATTT
1 TTATTCTTATCATTT
4337946 TTATT
1 TTATT
4337951 ATTCTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTCTTATCATTT
Found at i:4339373 original size:72 final size:72
Alignment explanation
Indices: 4339243--4339384 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 72
4339233 AGTAAGAAAA
* * * * * *
4339243 GATTTTTTGGCGTGATTTTTGAATGAATCACCCATGAATAAAGTTATTTTACCGCAATGAATAAG
1 GATTGTTTGACGTGATTTTTGAATGAATCACCCATGAAGAAAGTTATATTACCCCAATGAACAAG
4339308 CTAGAAG
66 CTAGAAG
* * * *
4339315 GATTGTTTGACGTGATTTTTGGATGAATC-CCTCGTGAAGAAAGTTATATTGCCCCAATGAGCAA
1 GATTGTTTGACGTGATTTTTGAATGAATCACC-CATGAAGAAAGTTATATTACCCCAATGAACAA
4339379 GCTAGA
65 GCTAGA
4339385 CGATATACAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 2 0.03
72 57 0.97
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (72 bp):
GATTGTTTGACGTGATTTTTGAATGAATCACCCATGAAGAAAGTTATATTACCCCAATGAACAAG
CTAGAAG
Found at i:4341453 original size:37 final size:37
Alignment explanation
Indices: 4341411--4341485 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
4341401 TTAATTAGTT
4341411 ATCCTATCAGATCTTCTCTAGAATTCAAATTCTACCC
1 ATCCTATCAGATCTTCTCTAGAATTCAAATTCTACCC
4341448 ATCCTATCAGATCTTCTCTAGAATTCAAATTCTACCC
1 ATCCTATCAGATCTTCTCTAGAATTCAAATTCTACCC
4341485 A
1 A
4341486 ACCTCCACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (37 bp):
ATCCTATCAGATCTTCTCTAGAATTCAAATTCTACCC
Found at i:4346716 original size:31 final size:29
Alignment explanation
Indices: 4346653--4346720 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
4346643 ATAATAGCAT
** *
4346653 AAGTGACT-AAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATGGCAAACAA
4346681 AAGTGACTAAAATGTAACATGAGGCAAACAA
1 AAGTGACTAAAATGTAACAT--GGCAAACAA
4346712 AAGTGACTA
1 AAGTGACTA
4346721 TTTTTGTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 8 0.24
29 11 0.32
31 15 0.44
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGGCAAACAA
Found at i:4373203 original size:30 final size:29
Alignment explanation
Indices: 4373167--4373289 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 29
4373157 AAGAAACATT
* * *
4373167 ATCAGAATTGGAACCAAAATGAGAATCAGA
1 ATCAGAATTGTAA-CAGAATCAGAATCAGA
* * *
4373197 ATCAGAATCAGTAACAGAATCAAAATCAAA
1 ATCAGAAT-TGTAACAGAATCAGAATCAGA
*
4373227 ATCAGTATTAGTAACAGAATCAGAATCAGA
1 ATCAGAATT-GTAACAGAATCAGAATCAGA
* *
4373257 ATCAGAATTAGGTGACAGAATTAGAATCAGA
1 ATCAGAATT--GTAACAGAATCAGAATCAGA
4373288 AT
1 AT
4373290 GTGAATGCAA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
30 53 0.70
31 23 0.30
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (29 bp):
ATCAGAATTGTAACAGAATCAGAATCAGA
Found at i:4373283 original size:6 final size:6
Alignment explanation
Indices: 4373188--4373264 Score: 86
Period size: 6 Copynumber: 12.8 Consensus size: 6
4373178 AACCAAAATG
* * * *
4373188 AGAATC AGAATC AGAATC AGTAA-C AGAATC AAAATC AAAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
4373236 AGTAA-C AGAATC AGAATC AGAATC AGAAT
1 AG-AATC AGAATC AGAATC AGAATC AGAAT
4373265 TAGGTGACAG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
5 4 0.07
6 54 0.89
7 3 0.05
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:4373289 original size:12 final size:12
Alignment explanation
Indices: 4373242--4373289 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
4373232 TATTAGTAAC
*
4373242 AGAATCAGAATC
1 AGAATCAGAATT
4373254 AGAATCAGAATT
1 AGAATCAGAATT
*
4373266 AG-GTGACAGAATT
1 AGAAT--CAGAATT
4373279 AGAATCAGAAT
1 AGAATCAGAAT
4373290 GTGAATGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.03
12 19 0.63
13 9 0.30
14 1 0.03
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (12 bp):
AGAATCAGAATT
Found at i:4373454 original size:27 final size:26
Alignment explanation
Indices: 4373410--4373492 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
4373400 TGGCTGCCAA
* * *
4373410 AACAGATATCGTGACAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
4373436 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
* *
4373463 AACAGATATTTGTGGCATAGCCACCGG
1 AACAGATA-TTGTGGCAGAGCCACCAG
4373490 AAC
1 AAC
4373493 GCTTCCTCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.16
27 42 0.84
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:4373812 original size:54 final size:54
Alignment explanation
Indices: 4373691--4373878 Score: 261
Period size: 54 Copynumber: 3.5 Consensus size: 54
4373681 GGGGTAAAAT
* * * *
4373691 GGTAATTTTACCCCACAAAGGTATCTCGATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
* *
4373745 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACGGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
* * * *
4373799 GGTAATTCTACCCTATAAGGGTATTT-TAGTAATTTTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGA-TAATTCTACCCTACAGGGGTATTTC
*
4373853 GGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
4373879 TAGTAATTTC
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
53 1 0.01
54 118 0.99
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
Found at i:4373886 original size:27 final size:27
Alignment explanation
Indices: 4373691--4373878 Score: 232
Period size: 27 Copynumber: 7.0 Consensus size: 27
4373681 GGGGTAAAAT
* * ** *
4373691 GGTAATTTTACCCCACAAAGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
4373718 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
4373745 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
4373772 GATAATTCTACCCTACGGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
4373799 GGTAATTCTACCCTATAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
4373826 AGTAATTTTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
4373853 GGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
4373879 TAGTAATTTC
Statistics
Matches: 136, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 136 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:4373921 original size:27 final size:27
Alignment explanation
Indices: 4373891--4374487 Score: 781
Period size: 27 Copynumber: 22.1 Consensus size: 27
4373881 GTAATTTCAC
* * *
4373891 AATCAAGGGTAAAATGATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
4373918 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
4373945 AATTGAGGGTAAACCAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** * **
4373972 AATTAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
4373999 AATCAAGGGTAAAACGGTAAATCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374026 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374053 AATTGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374080 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374107 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
4374134 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374161 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
**
4374188 AA-CTGAGGGTAAAACAATAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
4374215 AATCGAGGGTAAAACGGTAATTTTGTAA
1 AATCGAGGGTAAAACGGTAATTCTGT-A
*
4374243 AAT-GAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
4374269 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374296 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374323 AA-CTGAGGGTAAAACAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
4374350 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374377 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
4374404 AATCGAGGGTAAAACAGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
4374431 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
4374458 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
4374485 AAT
1 AAT
4374488 TGGGAGTACT
Statistics
Matches: 509, Mismatches: 51, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
26 8 0.02
27 493 0.97
28 8 0.02
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:4375971 original size:10 final size:10
Alignment explanation
Indices: 4375956--4376016 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
4375946 TGTTAGTCCT
4375956 AATTATATAA
1 AATTATATAA
4375966 AATTATA-AA
1 AATTATATAA
4375975 AA-TAT-TAA
1 AATTATATAA
*
4375983 AA-AAT-TAA
1 AATTATATAA
*
4375991 AATTAAATATA
1 AATTATATA-A
*
4376002 AATTATAAAA
1 AATTATATAA
4376012 AATTA
1 AATTA
4376017 AAAATTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 14 0.33
9 5 0.12
10 15 0.36
11 8 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AATTATATAA
Found at i:4376021 original size:17 final size:17
Alignment explanation
Indices: 4375964--4376032 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
4375954 CTAATTATAT
4375964 AAAATTATAAAAATATTAA
1 AAAATTATAAAAA-ATT-A
4375983 AAAATTA-AAATTAAA-TA
1 AAAATTATAAA--AAATTA
*
4376000 TAAATTATAAAAAATTA
1 AAAATTATAAAAAATTA
* *
4376017 AAAATTTTTAAAAATT
1 AAAATTATAAAAAATT
4376033 TTTGTACCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.07
17 22 0.52
18 7 0.17
19 8 0.19
20 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTATAAAAAATTA
Found at i:4376032 original size:27 final size:28
Alignment explanation
Indices: 4375963--4376019 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
4375953 CCTAATTATA
4375963 TAAAATT--ATAAAAA-TATTAAAAAAT
1 TAAAATTAAATAAAAATTATTAAAAAAT
*
4375988 TAAAATTAAATATAAATTA-TAAAAAAT
1 TAAAATTAAATAAAAATTATTAAAAAAT
4376015 TAAAA
1 TAAAA
4376020 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 7 0.25
27 19 0.68
28 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAAATTAAATAAAAATTATTAAAAAAT
Found at i:4376073 original size:5 final size:5
Alignment explanation
Indices: 4376063--4376089 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4376053 TGAGCGTTTG
4376063 ATCGA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA AT
4376090 GAAAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATCGA
Found at i:4383464 original size:128 final size:130
Alignment explanation
Indices: 4383174--4383513 Score: 338
Period size: 128 Copynumber: 2.6 Consensus size: 130
4383164 TTAGTTCAAC
* *
4383174 GAAAAATCGAAACCCAGCACAGTAGGGCACAATTCCTCGAATTTCTAAACATTAAACATTGCCTT
1 GAAAAA-CGAAACCCAGCACAGTAGGGCACAATTCCTCGAATTTCCAAACA-TCAACATTGCCTT
4383239 GTTTTA-GAA-TTT--AAGAAACATGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAA
64 GTTTTAGGAATTTTCAAAGAAACATGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAA
*
4383300 CG
129 CA
* ** * * * * *
4383302 GGAAATTGCAACTCAGCACAATAGGGCACGATTCCCCGAATTTCCAAACATCGAACATTGCCTTC
1 GAAAAACGAAACCCAGCACAGTAGGGCACAATTCCTCGAATTTCCAAACATC-AACATTGCCTT-
* * ** *
4383367 GTTTTAAGGAATTTTCAAAG-TACA-GA-TGAAATT-TCAAGGAATATTTGATTA-TTTGGACAA
64 GTTTT-AGGAATTTTCAAAGAAACATGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAA
4383427 ACA
128 ACA
* * * * * *
4383430 GAAAAACGAAACCCAGCACGGTTGGGCACAATTCCTCGAGTTCCCAAAAATCAACTATTACCTTT
1 GAAAAACGAAACCCAGCACAGTAGGGCACAATTCCTCGAATTTCCAAACATCAAC-ATTGCC-TT
*
4383495 GTTTTAGTGAATCTTCAAA
64 GTTTTAG-GAATTTTCAAA
4383514 TAAAAAATTG
Statistics
Matches: 171, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
126 1 0.01
127 53 0.31
128 78 0.46
129 18 0.11
130 10 0.06
131 5 0.03
132 3 0.02
133 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (130 bp):
GAAAAACGAAACCCAGCACAGTAGGGCACAATTCCTCGAATTTCCAAACATCAACATTGCCTTGT
TTTAGGAATTTTCAAAGAAACATGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAACA
Found at i:4395342 original size:31 final size:32
Alignment explanation
Indices: 4395283--4395343 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
4395273 AACTACCTAG
* **
4395283 TTAGTCACTTAACTTTTTAAGGTGTTTTCATT
1 TTAGTCACCTAACTTTTTAAGGCATTTTCATT
4395315 TTAGTCACCTAAC-TTTTAAGGCATTTTCA
1 TTAGTCACCTAACTTTTTAAGGCATTTTCA
4395344 AGATCTGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (32 bp):
TTAGTCACCTAACTTTTTAAGGCATTTTCATT
Found at i:4396024 original size:36 final size:36
Alignment explanation
Indices: 4395977--4396051 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
4395967 AAGATGAGAG
4395977 AAGAAATTATTATCATAATTATATTTTCTAATTTGT
1 AAGAAATTATTATCATAATTATATTTTCTAATTTGT
4396013 AAGAAATTATTATCATAATTATATTTTCTAATTTGT
1 AAGAAATTATTATCATAATTATATTTTCTAATTTGT
4396049 AAG
1 AAG
4396052 TTTCTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (36 bp):
AAGAAATTATTATCATAATTATATTTTCTAATTTGT
Found at i:4415851 original size:40 final size:40
Alignment explanation
Indices: 4415807--4415885 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
4415797 GAAAATATAA
4415807 TTTTCTATTTCCAAAGTCATTATTGATAGCTGATGGATAT
1 TTTTCTATTTCCAAAGTCATTATTGATAGCTGATGGATAT
4415847 TTTTCTATTTCCAAAGTCATTATTGATAGCTGATGGATA
1 TTTTCTATTTCCAAAGTCATTATTGATAGCTGATGGATA
4415886 ATCAGATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (40 bp):
TTTTCTATTTCCAAAGTCATTATTGATAGCTGATGGATAT
Found at i:4416977 original size:20 final size:19
Alignment explanation
Indices: 4416948--4416985 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4416938 ATGAAGAAAT
4416948 TACTCGAAAAATGCTGTCA
1 TACTCGAAAAATGCTGTCA
4416967 TACTCGAAAAATGCTGTCA
1 TACTCGAAAAATGCTGTCA
4416986 GAATCAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
TACTCGAAAAATGCTGTCA
Found at i:4421590 original size:15 final size:15
Alignment explanation
Indices: 4421570--4421602 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4421560 TTTAGGATTC
4421570 TTTATTTGTGTTT-TT
1 TTTATTTGT-TTTATT
4421585 TTTATTTGTTTTATT
1 TTTATTTGTTTTATT
4421600 TTT
1 TTT
4421603 GGTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTATTTGTTTTATT
Found at i:4433206 original size:38 final size:39
Alignment explanation
Indices: 4433164--4433241 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
4433154 ATATATAGTA
4433164 AAATGATAATGGCAGACTTC-AAAGTAAACGCTGGATAG
1 AAATGATAATGGCAGACTTCAAAAGTAAACGCTGGATAG
*
4433202 AAATGATAATGGGAGACTTCAAAAAGTAAACGCTGGATAG
1 AAATGATAATGGCAGACTTC-AAAAGTAAACGCTGGATAG
4433242 TTTCAGTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 19 0.51
40 18 0.49
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.21
Consensus pattern (39 bp):
AAATGATAATGGCAGACTTCAAAAGTAAACGCTGGATAG
Found at i:4433858 original size:15 final size:15
Alignment explanation
Indices: 4433838--4433867 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4433828 CCATTGCCAA
*
4433838 AAAAATTTTAATATT
1 AAAAATTTAAATATT
4433853 AAAAATTTAAATATT
1 AAAAATTTAAATATT
4433868 TAGACATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAATTTAAATATT
Found at i:4434530 original size:22 final size:22
Alignment explanation
Indices: 4434488--4434530 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
4434478 AATACATGAT
* *
4434488 AAAATTATATTTTAATCTCTCA
1 AAAATTATAATTCAATCTCTCA
4434510 AAAATTTATAATTCAAT-TCTC
1 AAAA-TTATAATTCAATCTCTC
4434531 CCCTCCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATTATAATTCAATCTCTCA
Found at i:4435414 original size:61 final size:61
Alignment explanation
Indices: 4435363--4435486 Score: 178
Period size: 61 Copynumber: 2.0 Consensus size: 61
4435353 TTAATAGTTA
* * *
4435363 ATAATAAGTTAATTTATAAAATACTGAAACATAATAAATTAATTTAATATTTTTATTTAAT
1 ATAATAAGTTAATTTAGAAAATACTAAAACATAATAAATTAATTTAATATTTTTAGTTAAT
* * *
4435424 ATAATAAGTTAATTTAGAAAATATTAAAATATAATAAATTAATTTAGA-ATTTTTATTTAAT
1 ATAATAAGTTAATTTAGAAAATACTAAAACATAATAAATTAATTTA-ATATTTTTAGTTAAT
4435485 AT
1 AT
4435487 TTGAAATAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 57 0.98
62 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (61 bp):
ATAATAAGTTAATTTAGAAAATACTAAAACATAATAAATTAATTTAATATTTTTAGTTAAT
Found at i:4435457 original size:30 final size:30
Alignment explanation
Indices: 4435363--4435472 Score: 105
Period size: 30 Copynumber: 3.6 Consensus size: 30
4435353 TTAATAGTTA
* * * * *
4435363 ATAATAAGTTAATTTATAAAATACTGAAAC
1 ATAATAAATTAATTTAGAAAATATTAAAAT
* * * *
4435393 ATAATAAATTAATTTA-ATATTTTTATTTAAT
1 ATAATAAATTAATTTAGAAAATATTA--AAAT
*
4435424 ATAATAAGTTAATTTAGAAAATATTAAAAT
1 ATAATAAATTAATTTAGAAAATATTAAAAT
4435454 ATAATAAATTAATTTAGAA
1 ATAATAAATTAATTTAGAA
4435473 TTTTTATTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
29 4 0.06
30 36 0.57
31 17 0.27
32 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (30 bp):
ATAATAAATTAATTTAGAAAATATTAAAAT
Found at i:4442630 original size:21 final size:20
Alignment explanation
Indices: 4442606--4442648 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
4442596 GTTGATGAGG
4442606 AAAAGTAAATATAAATTATAA
1 AAAAGTAAATATAAATTA-AA
4442627 AAAAGTAAATATAAATTAAA
1 AAAAGTAAATATAAATTAAA
4442647 AA
1 AA
4442649 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAGTAAATATAAATTAAA
Found at i:4448326 original size:24 final size:26
Alignment explanation
Indices: 4448299--4448347 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
4448289 AGAAAGGAAT
4448299 AAAAGA-A-AAATAATTTTGAAACAC
1 AAAAGATAGAAATAATTTTGAAACAC
*
4448323 AAAAGATAGGGAATAATTTTGAAAC
1 AAAAGATA-GAAATAATTTTGAAAC
4448348 TCAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 1 0.05
27 14 0.67
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.22
Consensus pattern (26 bp):
AAAAGATAGAAATAATTTTGAAACAC
Found at i:4452919 original size:27 final size:27
Alignment explanation
Indices: 4452883--4452945 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
4452873 TAATTAATCT
* * * *
4452883 AAAAGTTATATTTCTTGGTTATTGGTA
1 AAAAATTATATTACTTGATTATTGATA
* *
4452910 AAAAATTATATTACTTGATTTTTTATA
1 AAAAATTATATTACTTGATTATTGATA
4452937 AAAAATTAT
1 AAAAATTAT
4452946 GACTATTCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.48
Consensus pattern (27 bp):
AAAAATTATATTACTTGATTATTGATA
Found at i:4455550 original size:22 final size:22
Alignment explanation
Indices: 4455511--4455565 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
4455501 TATCCAAATA
* *
4455511 ATAATAAT-ATAATGGTAGTAAC
1 ATAATAATGA-AATAGTAGCAAC
4455533 ATAATAATGAAATAGTAGCAAC
1 ATAATAATGAAATAGTAGCAAC
*
4455555 ACAATAA-GAAA
1 ATAATAATGAAA
4455566 ACAAGAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 24 0.83
23 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (22 bp):
ATAATAATGAAATAGTAGCAAC
Found at i:4466311 original size:35 final size:35
Alignment explanation
Indices: 4466265--4466370 Score: 185
Period size: 35 Copynumber: 3.0 Consensus size: 35
4466255 CACTTGCCTC
*
4466265 TTCCCACTCTCCCATGCTGTCTGCCACCAGCGCCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
4466300 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
* *
4466335 CTCCCACTCTCCCATGCTGTCTGCCGCCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
4466370 T
1 T
4466371 CACACACCCC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.15, C:0.49, G:0.13, T:0.23
Consensus pattern (35 bp):
TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
Found at i:4466812 original size:30 final size:30
Alignment explanation
Indices: 4466772--4466845 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 30
4466762 AAAGAGGGGA
*
4466772 AGCAAAAAAAAAA-TCCAGCAAAAA-TTCC
1 AGCAAAAAAAAAATTCCAGAAAAAATTTCC
4466800 AGCACCAAAAAAAAATTTCCAGAAAAAATTTCC
1 AGCA--AAAAAAAAA-TTCCAGAAAAAATTTCC
4466833 AGCAAAAAAAAAA
1 AGCAAAAAAAAAA
4466846 CCAAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 4 0.10
30 9 0.22
31 9 0.22
32 10 0.25
33 8 0.20
ACGTcount: A:0.62, C:0.19, G:0.07, T:0.12
Consensus pattern (30 bp):
AGCAAAAAAAAAATTCCAGAAAAAATTTCC
Found at i:4466821 original size:32 final size:31
Alignment explanation
Indices: 4466774--4466845 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
4466764 AGAGGGGAAG
*
4466774 CAAAAAAAAAATCCAGCAAAAA-TTCCAGCA
1 CAAAAAAAAAATCCAGAAAAAATTTCCAGCA
*
4466804 CCAAAAAAAAATTTCCAGAAAAAATTTCCAGCA
1 -CAAAAAAAAA-ATCCAGAAAAAATTTCCAGCA
4466837 -AAAAAAAAA
1 CAAAAAAAAA
4466846 CCAAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 19 0.51
32 10 0.27
33 8 0.22
ACGTcount: A:0.62, C:0.19, G:0.06, T:0.12
Consensus pattern (31 bp):
CAAAAAAAAAATCCAGAAAAAATTTCCAGCA
Found at i:4466827 original size:13 final size:14
Alignment explanation
Indices: 4466809--4466841 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
4466799 CAGCACCAAA
4466809 AAAAAATTTCCAG-
1 AAAAAATTTCCAGC
4466822 AAAAAATTTCCAGC
1 AAAAAATTTCCAGC
4466836 AAAAAA
1 AAAAAA
4466842 AAAACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAAAATTTCCAGC
Found at i:4467136 original size:11 final size:11
Alignment explanation
Indices: 4467107--4467155 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
4467097 CGACCGGATT
* *
4467107 TCCCTTCCCCC
1 TCCCTTCTCTC
4467118 TCCCTTCTCTC
1 TCCCTTCTCTC
4467129 TCCCTTCTCTC
1 TCCCTTCTCTC
4467140 TCCC-TCTCTC
1 TCCCTTCTCTC
*
4467150 TTCCTT
1 TCCCTT
4467156 TTTTTCTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (11 bp):
TCCCTTCTCTC
Found at i:4467745 original size:2 final size:2
Alignment explanation
Indices: 4467669--4467729 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
4467659 ATCATTTCTA
* * *
4467669 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT GT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4467709 AT AT AT AT AT -T AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4467730 GCCATTAGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4467910 original size:2 final size:2
Alignment explanation
Indices: 4467893--4467927 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4467883 GTGTATATTT
* *
4467893 TA TA TA CA TA TG 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 TA T
4467928 TTTGCACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4479252 original size:13 final size:13
Alignment explanation
Indices: 4479244--4479268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4479234 TAAAAAAAAG
4479244 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
4479257 AAAAGAAAAAGA
1 AAAAGAAAAAGA
4479269 GAGGGGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:4480445 original size:71 final size:71
Alignment explanation
Indices: 4480242--4480452 Score: 273
Period size: 72 Copynumber: 3.0 Consensus size: 71
4480232 CTTTTAATTT
* *
4480242 TTGTT-TTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAT
1 TTGTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTAT
*
4480306 TTTCAA
66 TTTTAA
* * ** * * ** *
4480312 TTTTTGTGTTTTAATTTCAACTCATATTGCGA-CAGATGAGTTGATCCTCAAGACACGTTGAGGT
1 TTGTTGT-TTTCAAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGACACGCTGAGGT
4480376 ATTTTTAA
64 ATTTTTAA
*
4480384 TTGTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTAT
1 TTGTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTAT
4480449 TTTT
66 TTTT
4480453 TAGTTTTAAA
Statistics
Matches: 115, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
70 4 0.03
71 52 0.45
72 59 0.51
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (71 bp):
TTGTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTAT
TTTTAA
Found at i:4480615 original size:72 final size:71
Alignment explanation
Indices: 4480494--4480688 Score: 239
Period size: 72 Copynumber: 2.7 Consensus size: 71
4480484 GAGTTAAGCC
* * ** *
4480494 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGA
4480558 TGAGGTA
65 TGAGGTA
**
4480565 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGA
1 TTTTCAATTTTTGT-TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGA
4480630 TGAGGTA
65 TGAGGTA
* * * * *
4480637 ATCTCAATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTTTCAATTTTTGTTT-TTAA-AATCAACTCATATTGCGAGAGGTGAGTTGA
4480689 ACCTTTTAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
71 6 0.06
72 69 0.65
73 31 0.29
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGAT
GAGGTA
Found at i:4480636 original size:260 final size:263
Alignment explanation
Indices: 4480138--4480688 Score: 950
Period size: 260 Copynumber: 2.1 Consensus size: 263
4480128 TCAAGGAAAG
4480138 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTTAGTTTTAAAT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTTAGTTTTAAAT
4480203 TGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTTCAAAATCAACTCATATT
66 TGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTTCAAAATCAACTCATATT
4480268 GCTAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAAC
131 GCTAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAAC
* * * * *
4480333 TCATATTGCGACAGATGAGTTGATCCTCAAGACACGTTGAGGTATTTTTAATTGT-TGTTT-TCA
196 TCATATTGCGACAGATGAGTTGAGCCTCAAGACACGATGAGGTAATCTCAATT-TCTGTTTGTCA
4480396 A-AA
260 AGAA
*
4480399 TCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTTAGTTTTAAAT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTTAGTTTTAAAT
*
4480464 TGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTTCAAAATCAACTCATATT
66 TGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTTCAAAATCAACTCATATT
*
4480528 GCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAAC
131 GCTAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAAC
* *
4480593 TCATATTGCGAGAGGTGAGTTGAGCCTC-AGAACACGATGAGGTAATCTCAATTTCTGTTTGTCA
196 TCATATTGCGACAGATGAGTTGAGCCTCAAG-ACACGATGAGGTAATCTCAATTTCTGTTTGTCA
4480657 AGAA
260 AGAA
*
4480661 TCAACTCATATTGCGAGAGGTGGGTTGA
1 TCAACTCATATTGCGAGAGGTGAGTTGA
4480689 ACCTTTTAAT
Statistics
Matches: 274, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
259 3 0.01
260 134 0.49
261 109 0.40
262 28 0.10
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (263 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTTAGTTTTAAAT
TGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTTCAAAATCAACTCATATT
GCTAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAAC
TCATATTGCGACAGATGAGTTGAGCCTCAAGACACGATGAGGTAATCTCAATTTCTGTTTGTCAA
GAA
Found at i:4480785 original size:14 final size:13
Alignment explanation
Indices: 4480766--4480801 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
4480756 TGTCGAGGTA
4480766 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
4480779 TTTTTCAAATTCTG
1 -TTTTCAAAATCTG
4480793 TTTTCAAAA
1 TTTTCAAAA
4480802 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:4480860 original size:88 final size:86
Alignment explanation
Indices: 4480706--4480874 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 86
4480696 AATTTCTACT
* * * *
4480706 TTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTC
1 TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTTTC
4480771 AAAATCTGTTTTTCAAATTCTG
66 AAAATCTG-TTTTCAAATTCTG
* *
4480793 TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTG-CTGAGCTATTT
1 TTTTC-AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTC-GAGCTATTT
**
4480857 TCAATTTCTGTTTTCAAA
64 TCAAAATCTGTTTTCAAA
4480875 AAATTTCAAC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
87 14 0.19
88 58 0.81
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (86 bp):
TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTTTC
AAAATCTGTTTTCAAATTCTG
Found at i:4480927 original size:30 final size:30
Alignment explanation
Indices: 4480891--4480952 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
4480881 CAACTCATAT
4480891 TGCGAGAGATGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGATGAGTTGAGTC-TTTTAATTTC
*
4480921 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGATGAGTTGAGTCTTTTAATTTC
4480951 TG
1 TG
4480953 TTCTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (30 bp):
TGCGAGAGATGAGTTGAGTCTTTTAATTTC
Found at i:4481798 original size:22 final size:20
Alignment explanation
Indices: 4481773--4481847 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
4481763 TTAAGCCCCC
4481773 AAAAAAACCTAACCCAAAAAAA
1 AAAAAAACCTAA--CAAAAAAA
*** * *
4481795 AAAAAAAAAAAAGAAAAAAG
1 AAAAAAACCTAACAAAAAAA
4481815 AAAAAAACCTAACAAAAAAA
1 AAAAAAACCTAACAAAAAAA
4481835 ACTAAAAAACCTA
1 A--AAAAAACCTA
4481848 GCCACCTAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 22 0.54
22 19 0.46
ACGTcount: A:0.77, C:0.15, G:0.03, T:0.05
Consensus pattern (20 bp):
AAAAAAACCTAACAAAAAAA
Found at i:4481835 original size:1 final size:1
Alignment explanation
Indices: 4481788--4481821 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
4481778 AACCTAACCC
* *
4481788 AAAAAAAAAAAAAAAAAAAGAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4481822 CCTAACAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:4481890 original size:12 final size:12
Alignment explanation
Indices: 4481873--4481914 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
4481863 TCCCACTTGC
4481873 CCCATTTTTCCT
1 CCCATTTTTCCT
4481885 CCCATTTTTCCT
1 CCCATTTTTCCT
4481897 CCCATTTTTCCT
1 CCCATTTTTCCT
4481909 CCCATT
1 CCCATT
4481915 GTCTACCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.48
Consensus pattern (12 bp):
CCCATTTTTCCT
Found at i:4482371 original size:29 final size:29
Alignment explanation
Indices: 4482315--4482371 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4482305 TCTCTTTTTT
* *
4482315 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
4482344 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
4482372 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:4482632 original size:11 final size:11
Alignment explanation
Indices: 4482614--4482643 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4482604 GTGTATATTG
4482614 TATATATTATA
1 TATATATTATA
*
4482625 TTTATATTATA
1 TATATATTATA
4482636 TATATATT
1 TATATATT
4482644 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:4487314 original size:18 final size:18
Alignment explanation
Indices: 4487293--4487327 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4487283 AAAAGGAAAC
*
4487293 ATATAAGGGTTAGGATAT
1 ATATAAGGGCTAGGATAT
4487311 ATATAAGGGCTAGGATA
1 ATATAAGGGCTAGGATA
4487328 CGCACCTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.29
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAT
Found at i:4487964 original size:7 final size:7
Alignment explanation
Indices: 4487954--4487983 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4487944 TTATATACAT
4487954 AATACTA
1 AATACTA
4487961 AATACTA
1 AATACTA
4487968 AATACTA
1 AATACTA
*
4487975 AATATTA
1 AATACTA
4487982 AA
1 AA
4487984 CGACTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:4506073 original size:15 final size:15
Alignment explanation
Indices: 4506053--4506082 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4506043 TTGGTAGAGC
*
4506053 TTTGCTGTCTGTTTA
1 TTTGCTGACTGTTTA
4506068 TTTGCTGACTGTTTA
1 TTTGCTGACTGTTTA
4506083 AAGGTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (15 bp):
TTTGCTGACTGTTTA
Found at i:4510295 original size:2 final size:2
Alignment explanation
Indices: 4510288--4510312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4510278 AACACCATAC
4510288 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4510313 CCTTACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4514814 original size:21 final size:21
Alignment explanation
Indices: 4514790--4514831 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4514780 TTTTCAAATT
* **
4514790 TTTTACTTATTTTTTTATGTA
1 TTTTAATTATTTAGTTATGTA
4514811 TTTTAATTATTTAGTTATGTA
1 TTTTAATTATTTAGTTATGTA
4514832 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTAATTATTTAGTTATGTA
Found at i:4516340 original size:177 final size:176
Alignment explanation
Indices: 4516041--4516383 Score: 530
Period size: 177 Copynumber: 1.9 Consensus size: 176
4516031 TAGTTGGGAT
*
4516041 GTGAAAGTTTCATATTTGAGAAAAAAATACAATGGGTAATAAATAATTATGTATAAGCCCGTAGG
1 GTGAAAGTTTCATATTTGAGAAAAAAATACAATGGGTAATAAATAATTATGTATAAGCCCATAGG
* *
4516106 AAGGGCCTACTTACATAATGTAAAAACTAATTGAATTTATCAGTAAAATTGTATTTGTCATGCAT
66 AAGGGCCTACTTACATAATGTAAAAACTAATTGAATTTATCAATAAAATTATATTTGTCATGCAT
* * *
4516171 GTAAATTTTTGTA-CTGGTCAAATATCTCTATTATATCTATCTAAAC
131 GTAAATTTTAG-AGCTGATCAAATATCTCTATCATATCTATCTAAAC
* *
4516217 GTGAAAGTTTCATATTTGAGAAAAAAATAACTAA-GGGTAATAAATAATTATGTATAAGTCTATA
1 GTGAAAGTTTCATATTTGAGAAAAAAAT-AC-AATGGGTAATAAATAATTATGTATAAGCCCATA
* *
4516281 GGAGGGGTCC-ACTTACATAATGTAAAAACTAATTGAATTTATCAATATAATTATATTTGTCATG
64 GGAAGGG-CCTACTTACATAATGTAAAAACTAATTGAATTTATCAATAAAATTATATTTGTCATG
*
4516345 CATGTAAATTTTAGAGTTGATCAAATATCTCTATCATAT
128 CATGTAAATTTTAGAGCTGATCAAATATCTCTATCATAT
4516384 TGAATACTCT
Statistics
Matches: 152, Mismatches: 11, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
176 29 0.19
177 119 0.78
178 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (176 bp):
GTGAAAGTTTCATATTTGAGAAAAAAATACAATGGGTAATAAATAATTATGTATAAGCCCATAGG
AAGGGCCTACTTACATAATGTAAAAACTAATTGAATTTATCAATAAAATTATATTTGTCATGCAT
GTAAATTTTAGAGCTGATCAAATATCTCTATCATATCTATCTAAAC
Found at i:4519014 original size:4 final size:4
Alignment explanation
Indices: 4519005--4519061 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
4518995 CATTCCCCCA
4519005 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4519053 TATG TATG T
1 TATG TATG T
4519062 TATATCCCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:4520948 original size:46 final size:46
Alignment explanation
Indices: 4520892--4521067 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
4520882 TATTTGGGCA
*
4520892 TCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4520938 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
4520983 CATCTGAGCTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4521031 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4521068 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.56
47 27 0.25
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4521047 original size:93 final size:93
Alignment explanation
Indices: 4520888--4521060 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
4520878 GGGATATTTG
* * *
4520888 GGCATCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCATTGAG
4520953 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
4520981 GGCATCTGAGCTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCATTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCATTGAG
4521046 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
4521061 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:4522677 original size:4 final size:4
Alignment explanation
Indices: 4522668--4522693 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4522658 TTTCACAACA
4522668 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
4522694 TTCTATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4523708 original size:21 final size:21
Alignment explanation
Indices: 4523675--4523714 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4523665 TAATGGAAAA
*
4523675 TAAAAGAAAATAAAGGAAAGT
1 TAAAAGAAAATAAAAGAAAGT
* *
4523696 TAAAATAACATAAAAGAAA
1 TAAAAGAAAATAAAAGAAA
4523715 AAAATTACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (21 bp):
TAAAAGAAAATAAAAGAAAGT
Found at i:4523717 original size:17 final size:18
Alignment explanation
Indices: 4523697--4523735 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4523687 AAGGAAAGTT
*
4523697 AAAATAACATAAAAGAAA
1 AAAATAACATAAAACAAA
* *
4523715 AAAATTACTTAAAACAAA
1 AAAATAACATAAAACAAA
4523733 AAA
1 AAA
4523736 TATGAGGACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAATAACATAAAACAAA
Found at i:4526279 original size:30 final size:31
Alignment explanation
Indices: 4526217--4526281 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
4526207 TGGTGAAGTG
*
4526217 AGAAATTTGATAGGAGAAAATTTTTTGTTTT
1 AGAAATTTGATAGGAGAAAATTTTTTGATTT
4526248 AGAAATTTGATAGGAGAAAATTTTTT-ATTT
1 AGAAATTTGATAGGAGAAAATTTTTTGATTT
4526278 AGAA
1 AGAA
4526282 TTTTTTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (31 bp):
AGAAATTTGATAGGAGAAAATTTTTTGATTT
Found at i:4526358 original size:29 final size:28
Alignment explanation
Indices: 4526310--4526367 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
4526300 ATTTTAAATT
*
4526310 AATAATAAAATTATATTTTAATCTTTTAA
1 AATAATAAAATTATAATTTAAT-TTTTAA
4526339 AATAATAAAAATT-TAATTTAATTTTTAA
1 AATAAT-AAAATTATAATTTAATTTTTAA
4526367 A
1 A
4526368 GAATATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.26
29 14 0.52
30 6 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AATAATAAAATTATAATTTAATTTTTAA
Found at i:4526392 original size:16 final size:16
Alignment explanation
Indices: 4526371--4526403 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4526361 TTTTAAAGAA
4526371 TATT-AAATATATAAAT
1 TATTAAAATA-ATAAAT
4526387 TATTAAAATAATAAAT
1 TATTAAAATAATAAAT
4526403 T
1 T
4526404 TATATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAAAATAATAAAT
Found at i:4535819 original size:15 final size:15
Alignment explanation
Indices: 4535795--4535825 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4535785 ATAGAATTTT
*
4535795 TAAAATTTATTTGAA
1 TAAAAATTATTTGAA
4535810 TAAAAATTATTTGAA
1 TAAAAATTATTTGAA
4535825 T
1 T
4535826 TGCACTCTTC
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:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
TAAAAATTATTTGAA
Found at i:4541652 original size:25 final size:23
Alignment explanation
Indices: 4541576--4541652 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 23
4541566 TTTATTTATT
*
4541576 TATTCATTT-TTTTAAAAATTGTTA
1 TATT-ATTTATTTTAAATATT-TTA
* *
4541600 TTATTATTCATTTTAAGT-TTTTA
1 -TATTATTTATTTTAAATATTTTA
4541623 TATTATTTATTTTAAATCATTTTA
1 TATTATTTATTTTAAAT-ATTTTA
4541647 TCATTA
1 T-ATTA
4541653 CTCTTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 15 0.35
23 3 0.07
24 11 0.26
25 14 0.33
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (23 bp):
TATTATTTATTTTAAATATTTTA
Found at i:4541739 original size:29 final size:27
Alignment explanation
Indices: 4541672--4541744 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 27
4541662 ACGTATTATG
**
4541672 TATTTTAA-AC-TATTATAAATTTAAA
1 TATTTTAATACATATTATTCATTTAAA
4541697 TATTTTACAT--ATATTATTCATTTCAAA
1 TATTTTA-ATACATATTATTCATTT-AAA
4541724 CTATTTTAATACATATTATTC
1 -TATTTTAATACATATTATTC
4541745 TGAATTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 7 0.18
26 11 0.28
27 5 0.13
28 7 0.18
29 9 0.23
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTTTAATACATATTATTCATTTAAA
Found at i:4542104 original size:15 final size:16
Alignment explanation
Indices: 4542086--4542125 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
4542076 TTTAAGTTGC
*
4542086 ATTATTTTAT-TTTTA
1 ATTATTTTATGTATTA
*
4542101 ATTATTTTGTGTATTA
1 ATTATTTTATGTATTA
4542117 ATTATTTTA
1 ATTATTTTA
4542126 AATTGTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
ATTATTTTATGTATTA
Found at i:4543571 original size:19 final size:20
Alignment explanation
Indices: 4543549--4543586 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4543539 AAAATAATAA
*
4543549 TATATAA-AAAATATATACG
1 TATATAACAAAACATATACG
4543568 TATATAACAAAACATATAC
1 TATATAACAAAACATATAC
4543587 TACGGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.29
Consensus pattern (20 bp):
TATATAACAAAACATATACG
Found at i:4543813 original size:8 final size:8
Alignment explanation
Indices: 4543800--4543837 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
4543790 CTATACGTAA
*
4543800 ATATATAT
1 ATATATAC
4543808 ATATATAC
1 ATATATAC
4543816 ATATATAC
1 ATATATAC
*
4543824 ATA-AAAC
1 ATATATAC
4543831 ATATATA
1 ATATATA
4543838 AACATTGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATATAC
Found at i:4543974 original size:3 final size:3
Alignment explanation
Indices: 4543966--4544010 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4543956 ACAAAAGCAC
4543966 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4544011 TGAAAATAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4545947 original size:107 final size:109
Alignment explanation
Indices: 4545757--4546010 Score: 476
Period size: 107 Copynumber: 2.3 Consensus size: 109
4545747 ATGTGACCCG
4545757 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
4545822 ACCTCTCGCAATATGAGTTGA-TTTTTG-AAAACAGAAATTAAA
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAA
*
4545864 AGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
4545929 ACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAA
66 ACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTAAA
4545974 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
4546011 TTTTTTGAAG
Statistics
Matches: 142, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
107 85 0.60
109 6 0.04
110 51 0.36
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (109 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAA
Found at i:4546012 original size:56 final size:54
Alignment explanation
Indices: 4545757--4546010 Score: 474
Period size: 54 Copynumber: 4.7 Consensus size: 54
4545747 ATGTGACCCG
4545757 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
4545811 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
*
4545864 AGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
4545918 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAA
4545974 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
4546011 TTTTTTGAAG
Statistics
Matches: 195, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
53 52 0.27
54 89 0.46
56 54 0.28
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
Done.