Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 297 of 345
Found at i:89262476 original size:22 final size:22
Alignment explanation
Indices: 89262418--89262477 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
89262408 ATGATTAAAT
*
89262418 AATATAAATTAAAAATTAAAAT
1 AATATAAATTAAAAATTAAAAC
* * *
89262440 TATTTAATTTAAAAATTAAAAAC
1 AATATAAATTAAAAATT-AAAAC
89262463 AATATAAATTAAAAA
1 AATATAAATTAAAAA
89262478 AAATCAGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATATAAATTAAAAATTAAAAC
Found at i:89262877 original size:22 final size:22
Alignment explanation
Indices: 89262822--89262877 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
89262812 CCCCTGCCTT
*
89262822 CTTAACCCTTAATCCTAAAACC
1 CTTAACCCTTAATCATAAAACC
* *
89262844 C-CATCCCATTAACTCAT-AAACC
1 CTTAACCC-TTAA-TCATAAAACC
89262866 CTTAACCCTTAA
1 CTTAACCCTTAA
89262878 ATTTTAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.27
Consensus pattern (22 bp):
CTTAACCCTTAATCATAAAACC
Found at i:89262975 original size:22 final size:22
Alignment explanation
Indices: 89262946--89262994 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
89262936 ACTCAACCCT
*
89262946 TAAA-CCATAAACCATAATCCC
1 TAAACCCATAAACCATAATCCA
**
89262967 TAAACCCATAATTCATAATCCA
1 TAAACCCATAAACCATAATCCA
89262989 TAAACC
1 TAAACC
89262995 TTAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCCATAAACCATAATCCA
Found at i:89263021 original size:7 final size:7
Alignment explanation
Indices: 89262946--89263135 Score: 67
Period size: 7 Copynumber: 26.4 Consensus size: 7
89262936 ACTCAACCCT
89262946 TAAACCA
1 TAAACCA
89262953 TAAACCA
1 TAAACCA
* *
89262960 TAATCCC
1 TAAACCA
89262967 TAAACCCA
1 TAAA-CCA
**
89262975 TAATTCA
1 TAAACCA
*
89262982 TAATCCA
1 TAAACCA
*
89262989 TAAACCT
1 TAAACCA
**
89262996 TAAAATA
1 TAAACCA
*
89263003 TTAACTCA
1 TAAAC-CA
89263011 TAAACCA
1 TAAACCA
89263018 TAAACCCA
1 TAAA-CCA
* *
89263026 TAAATCT
1 TAAACCA
*
89263033 TAAACCC
1 TAAACCA
* * *
89263040 CAACCCT
1 TAAACCA
*
89263047 TAAACCC
1 TAAACCA
*
89263054 TAAACCCG
1 TAAA-CCA
*
89263062 TAATCCA
1 TAAACCA
*
89263069 TAAACCT
1 TAAACCA
**
89263076 TAAAATA
1 TAAACCA
*
89263083 TTAACTCA
1 TAAAC-CA
89263091 T-AACTCA
1 TAAAC-CA
*
89263098 TAAACCC
1 TAAACCA
*
89263105 TATACCA
1 TAAACCA
* *
89263112 TATACCC
1 TAAACCA
*
89263119 TAAACCT
1 TAAACCA
*
89263126 TAAACTA
1 TAAACCA
89263133 TAA
1 TAA
89263136 TGATAATTAA
Statistics
Matches: 132, Mismatches: 45, Indels: 12
0.70 0.24 0.06
Matches are distributed among these distances:
7 105 0.80
8 27 0.20
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.25
Consensus pattern (7 bp):
TAAACCA
Found at i:89263035 original size:29 final size:28
Alignment explanation
Indices: 89262951--89263035 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
89262941 ACCCTTAAAC
* * * *
89262951 CATAAACCATAATCCCTAAACCCATAATT
1 CATAAACCATAAACCCTAAA-TCTTAACT
* * *
89262980 CATAATCCATAAACCTTAAAATATTAACT
1 CATAAACCATAAACCCT-AAATCTTAACT
89263009 CATAAACCATAAACCCATAAATCTTAA
1 CATAAACCATAAACCC-TAAATCTTAA
89263036 ACCCCAACCC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 40 0.91
30 4 0.09
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (28 bp):
CATAAACCATAAACCCTAAATCTTAACT
Found at i:89263614 original size:40 final size:40
Alignment explanation
Indices: 89263561--89263658 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 40
89263551 GACGTTTTTT
* * * * * * *
89263561 AAAAAACGTCGCTAATGCTCGATCTATAGTGTCGTTTTTC
1 AAAAAGCGCCGCTAATGCTCAATATATAGCGGCGTTTTCC
* *
89263601 AAAAAGTGCCGCTAAAGCTCAATATATAGCGGCGTTTTCC
1 AAAAAGCGCCGCTAATGCTCAATATATAGCGGCGTTTTCC
89263641 AAAAAGCGCCGCTAATGC
1 AAAAAGCGCCGCTAATGC
89263659 CACTAAGGCT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (40 bp):
AAAAAGCGCCGCTAATGCTCAATATATAGCGGCGTTTTCC
Found at i:89263737 original size:154 final size:151
Alignment explanation
Indices: 89263439--89263731 Score: 365
Period size: 154 Copynumber: 1.9 Consensus size: 151
89263429 GTTTTTGTGG
* * * * * * *
89263439 CGTTTTTGAAAAAGCGCCGCTACAGCTCGATCTATAGAATCGTTTTTCAAAAAGTGCCGCTAATG
1 CGTTTTTCAAAAAGCGCCGCTAAAGCTCAATATATAGAAGCGTTTTCCAAAAAGCGCCGCTAATG
* * * *
89263504 CCACTAAGGCTAAAAATAAAAGACGGCGTGTTAATGAATTAATTTGTGACGTTTTTTAAAAAACG
66 CCACTAAGGCTAAAAATAAAAGACAGCGTGTTAATGAAATAATTTGCGACATTTTTT---AAACG
*
89263569 TCGCTAATGCTCGATCTATAGTGT
128 CCGCTAATGCTCGATCTATAGTGT
* **
89263593 CGTTTTTCAAAAAGTGCCGCTAAAGCTCAATATATAGCGGCGTTTTCCAAAAAGCGCCGCTAATG
1 CGTTTTTCAAAAAGCGCCGCTAAAGCTCAATATATAGAAGCGTTTTCCAAAAAGCGCCGCTAATG
* * *
89263658 CCACTAAGGCTCAACAAA-AAATGACAGCGTGTTGATGAAATAATTTGCGGCATTTTTT-AACGC
66 CCACTAAGGCT-AA-AAATAAAAGACAGCGTGTTAATGAAATAATTTGCGACATTTTTTAAACGC
89263721 CGCTAATGCTC
129 CGCTAATGCTC
89263732 ATCGATGGCG
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
151 15 0.13
154 66 0.55
155 35 0.29
156 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (151 bp):
CGTTTTTCAAAAAGCGCCGCTAAAGCTCAATATATAGAAGCGTTTTCCAAAAAGCGCCGCTAATG
CCACTAAGGCTAAAAATAAAAGACAGCGTGTTAATGAAATAATTTGCGACATTTTTTAAACGCCG
CTAATGCTCGATCTATAGTGT
Found at i:89263809 original size:40 final size:39
Alignment explanation
Indices: 89263765--89263900 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 39
89263755 AAACGTCGCT
* *
89263765 ATCTATAGTGGCGTTTTCCAAAAAGCGCCGCTAATGCTCG
1 ATCTATAGCGGCGTTTTCTAAAAA-CGCCGCTAATGCTCG
* *
89263805 ATCTATAGCGGCGCTTTTCTAAAAACGCCGTTAATGCTCA
1 ATCTATAGCGGCG-TTTTCTAAAAACGCCGCTAATGCTCG
* * *
89263845 ATCTATAGTGGCACTTTTATAAAAACGCCGCTAATGCTCG
1 ATCTATAGCGGC-GTTTTCTAAAAACGCCGCTAATGCTCG
*
89263885 ATTTATAGCGGCGTTT
1 ATCTATAGCGGCGTTT
89263901 GTTGCCAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.04
40 69 0.84
41 10 0.12
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (39 bp):
ATCTATAGCGGCGTTTTCTAAAAACGCCGCTAATGCTCG
Found at i:89265015 original size:26 final size:26
Alignment explanation
Indices: 89264979--89265028 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
89264969 TTCTTTAAAG
89264979 TTAACCCTATTCTGCTGTTTGACAAC
1 TTAACCCTATTCTGCTGTTTGACAAC
89265005 TTAACCCTATTCTGCTGTTTGACA
1 TTAACCCTATTCTGCTGTTTGACA
89265029 GCTTCGACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (26 bp):
TTAACCCTATTCTGCTGTTTGACAAC
Found at i:89271757 original size:53 final size:52
Alignment explanation
Indices: 89271678--89271794 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 52
89271668 AAAAGACATG
*
89271678 TAATTC-TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACC
1 TAATTCATTATCATGAAACATTTACCTAACCCATTATCATGAAACATTCACC
* * ** *
89271729 TAATTCATTATCATGGAATATTTTACCTAATTCATTATCATGGAACATTCACC
1 TAATTCATTATCATGAAACA-TTTACCTAACCCATTATCATGAAACATTCACC
**
89271782 TAACCCATTATCA
1 TAATTCATTATCA
89271795 ATTTGTACCA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 6 0.11
52 11 0.20
53 39 0.70
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (52 bp):
TAATTCATTATCATGAAACATTTACCTAACCCATTATCATGAAACATTCACC
Found at i:89271761 original size:27 final size:26
Alignment explanation
Indices: 89271678--89271794 Score: 146
Period size: 26 Copynumber: 4.5 Consensus size: 26
89271668 AAAAGACATG
89271678 TAATTC-TTATCATGAAACATTTACC
1 TAATTCATTATCATGAAACATTTACC
**
89271703 TAACCCATTATCATGAAACATTTACC
1 TAATTCATTATCATGAAACATTTACC
* *
89271729 TAATTCATTATCATGGAATATTTTACC
1 TAATTCATTATCATGAAACA-TTTACC
* *
89271756 TAATTCATTATCATGGAACATTCACC
1 TAATTCATTATCATGAAACATTTACC
**
89271782 TAACCCATTATCA
1 TAATTCATTATCA
89271795 ATTTGTACCA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
25 4 0.05
26 51 0.64
27 25 0.31
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (26 bp):
TAATTCATTATCATGAAACATTTACC
Found at i:89272349 original size:47 final size:48
Alignment explanation
Indices: 89272249--89272414 Score: 219
Period size: 48 Copynumber: 3.5 Consensus size: 48
89272239 GTTGAACCAG
*
89272249 ACATGGTCTTACACTGGCTCACATAATAATG-TCGATGCCATGTTCCAA
1 ACATGATCTTACACTGGCTCACATAATAATGCT-GATGCCATGTTCCAA
* * *
89272297 ACATGATCTTACACTGGCTCACATATTGA-GCTGATGCCATGTCCCAA
1 ACATGATCTTACACTGGCTCACATAATAATGCTGATGCCATGTTCCAA
* ** * *
89272344 ACATGATCTTACACTAGCTCTTATAACAATGCCGATGCCATGTTCCAA
1 ACATGATCTTACACTGGCTCACATAATAATGCTGATGCCATGTTCCAA
*
89272392 ACATGGTCTTACACTGGCTCACA
1 ACATGATCTTACACTGGCTCACA
89272415 CATAACCCTA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
47 38 0.38
48 62 0.62
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (48 bp):
ACATGATCTTACACTGGCTCACATAATAATGCTGATGCCATGTTCCAA
Found at i:89278528 original size:24 final size:24
Alignment explanation
Indices: 89278484--89278540 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
89278474 AAAATCTTAT
*
89278484 TTTATTTAATTTAATTATTTTTAA
1 TTTATTTTATTTAATTATTTTTAA
* *
89278508 TTTATTTTATATTACTT-TTTTTCA
1 TTTATTTTAT-TTAATTATTTTTAA
89278532 TTTAATTTT
1 TTT-ATTTT
89278541 GAGATTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATTTTATTTAATTATTTTTAA
Found at i:89280297 original size:40 final size:40
Alignment explanation
Indices: 89280231--89280397 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
89280221 AAATTGAATG
* * *
89280231 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
89280270 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
89280310 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
89280350 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
89280390 ATATCCGG
1 ATATCCGG
89280398 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:89283527 original size:43 final size:43
Alignment explanation
Indices: 89283360--89283527 Score: 144
Period size: 43 Copynumber: 3.9 Consensus size: 43
89283350 ACATAAGCTC
* * * * *
89283360 ATACAATGTC-ATATCCCAGATATGGTCTTACATGTTATCAC-
1 ATACAATGCCAATATCCCAGACATGGTCTTACACGTAATCTCA
* * ** * *
89283401 ATATCGATGCCACTATCCCAGGTAGGGTCTTACACGAAATCAT-A
1 ATA-CAATGCCAATATCCCAGACATGGTCTTACACGTAATC-TCA
* * * *
89283445 ATACGATACCAATGTCCCAGACATGGTCTTACACATAATCTCA
1 ATACAATGCCAATATCCCAGACATGGTCTTACACGTAATCTCA
* *
89283488 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
1 ATACAATGCCAATATCCCAGACATGGTCTTACACGTAATC
89283528 ACAACTCGAT
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 3 0.03
42 6 0.06
43 89 0.88
44 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
ATACAATGCCAATATCCCAGACATGGTCTTACACGTAATCTCA
Found at i:89285650 original size:41 final size:41
Alignment explanation
Indices: 89285605--89285722 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
89285595 TGAAAGATAA
89285605 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
89285646 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89285676 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89285717 ATGTAG
1 ATGTAG
89285723 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:89285661 original size:71 final size:71
Alignment explanation
Indices: 89285573--89285736 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
89285563 GAGATGTATC
89285573 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89285638 AGGACA
66 AGGACA
89285644 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89285709 AGGACA
66 AGGACA
89285715 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
89285737 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:89292066 original size:41 final size:41
Alignment explanation
Indices: 89292021--89292138 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
89292011 TGAAAGATAA
89292021 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
89292062 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89292092 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89292133 ATGTAG
1 ATGTAG
89292139 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:89292077 original size:71 final size:71
Alignment explanation
Indices: 89291989--89292152 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
89291979 GAGATGTATC
89291989 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89292054 AGGACA
66 AGGACA
89292060 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89292125 AGGACA
66 AGGACA
89292131 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
89292153 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:89299395 original size:23 final size:23
Alignment explanation
Indices: 89299365--89299414 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
89299355 ACCCTATGCA
89299365 ATGCAACATA-ATATTATACATGG-
1 ATGCAACATACATA-TA-ACATGGC
89299388 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
89299411 ATGC
1 ATGC
89299415 TCAAATACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 16 0.64
24 3 0.12
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:89299567 original size:27 final size:27
Alignment explanation
Indices: 89299449--89299565 Score: 128
Period size: 27 Copynumber: 4.3 Consensus size: 27
89299439 GAACAAATCT
* ** * * *
89299449 GTCATTTTACCTTACCAAGGTATTACA
1 GTCATTTTACCCTATGAGGGTATTTCG
89299476 GTCATTTTACCCTAT-AGGGGTATTTCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* *
89299503 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
89299530 GTCATTTTATCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
89299557 GTCATTTTA
1 GTCATTTTA
89299566 TCATATAAGG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 76 0.99
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:89299587 original size:27 final size:27
Alignment explanation
Indices: 89299530--89299711 Score: 190
Period size: 27 Copynumber: 6.8 Consensus size: 27
89299520 GGGTATTTCG
* * *** *
89299530 GTCATTTTATCCTATGAGGGTATTTTG
1 GTCATTTTATCATATAAGGGTAAAATC
*
89299557 GTCATTTTATCATATAA-GGTCAAAATT
1 GTCATTTTATCATATAAGGGT-AAAATC
*
89299584 GTCATTTTATCAAATAAGGGT-AAATC
1 GTCATTTTATCATATAAGGGTAAAATC
* * *
89299610 GTTATTTTATCATATGAGGGCAAAATC
1 GTCATTTTATCATATAAGGGTAAAATC
89299637 GTCATTTTATCATATAAGGGTAAAATC
1 GTCATTTTATCATATAAGGGTAAAATC
*
89299664 GTCATTTTATCACATAAGGGTAAAA-C
1 GTCATTTTATCATATAAGGGTAAAATC
* * *
89299690 TTTCATTTTATCACATGAGGGT
1 -GTCATTTTATCATATAAGGGT
89299712 TCAGGTACGC
Statistics
Matches: 133, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 25 0.19
27 105 0.79
28 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (27 bp):
GTCATTTTATCATATAAGGGTAAAATC
Found at i:89299641 original size:80 final size:81
Alignment explanation
Indices: 89299557--89299710 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 81
89299547 GGGTATTTTG
* *
89299557 GTCATTTTATCATATAA-GGTCAAAATTGTCATTTTATCAAATAAGGGTAAATCGTT-ATTTTAT
1 GTCATTTTATCATATAAGGGT-AAAATCGTCATTTTATCAAATAAGGGTAAAACGTTCATTTTAT
*
89299620 CATATGAGGGCAAAATC
65 CACATGAGGGCAAAATC
* *
89299637 GTCATTTTATCATATAAGGGTAAAATCGTCATTTTATCACATAAGGGTAAAACTTTCATTTTATC
1 GTCATTTTATCATATAAGGGTAAAATCGTCATTTTATCAAATAAGGGTAAAACGTTCATTTTATC
89299702 ACATGAGGG
66 ACATGAGGG
89299711 TTCAGGTACG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 48 0.72
81 19 0.28
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (81 bp):
GTCATTTTATCATATAAGGGTAAAATCGTCATTTTATCAAATAAGGGTAAAACGTTCATTTTATC
ACATGAGGGCAAAATC
Found at i:89302159 original size:13 final size:13
Alignment explanation
Indices: 89302143--89302175 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
89302133 TTTAATTAAA
*
89302143 TTAGTTAATTAGT
1 TTAGATAATTAGT
89302156 TTAGATAATTAGT
1 TTAGATAATTAGT
89302169 TTA-ATAA
1 TTAGATAA
89302176 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:89302485 original size:12 final size:12
Alignment explanation
Indices: 89302468--89302520 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
89302458 TGGCACCAAC
89302468 TCCCTCCTAAAA
1 TCCCTCCTAAAA
* *
89302480 TCCCTCCTCATA
1 TCCCTCCTAAAA
* * *
89302492 TCTCTCCTCAAC
1 TCCCTCCTAAAA
*
89302504 TCCCTCCTACAA
1 TCCCTCCTAAAA
89302516 TCCCT
1 TCCCT
89302521 TCATGACCTA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.21, C:0.49, G:0.00, T:0.30
Consensus pattern (12 bp):
TCCCTCCTAAAA
Found at i:89306233 original size:30 final size:30
Alignment explanation
Indices: 89306182--89306238 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
89306172 ATGTATCATG
89306182 TATAAATTTATCAACTTTCACTTACTTTAA
1 TATAAATTTATCAACTTTCACTTACTTTAA
89306212 TATAAACTTT-TCAA-TTATCACTTACTT
1 TATAAA-TTTATCAACTT-TCACTTACTT
89306239 GCCAAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 2 0.08
30 20 0.80
31 3 0.12
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (30 bp):
TATAAATTTATCAACTTTCACTTACTTTAA
Found at i:89311978 original size:23 final size:23
Alignment explanation
Indices: 89311915--89312004 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
89311905 AAGCTCCTCT
*
89311915 TGAGCTGATGAACAGTAAGCT-CTA
1 TGAGCTGA--AACAGTAAGCTCCAA
*
89311939 TCAAGCTG-AACAGTAAGCTCCAA
1 T-GAGCTGAAACAGTAAGCTCCAA
* *
89311962 TGGGCTGAAACAATAAGCTCCAA
1 TGAGCTGAAACAGTAAGCTCCAA
*
89311985 TGAGCTAAAACAGTAAGCTC
1 TGAGCTGAAACAGTAAGCTC
89312005 TTACGAACTG
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
22 15 0.27
23 34 0.62
24 1 0.02
25 5 0.09
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCCAA
Found at i:89315093 original size:28 final size:29
Alignment explanation
Indices: 89315026--89315126 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
89315016 ATAGTGAATC
*
89315026 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
89315055 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
89315083 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
89315113 CGCACACTTAGTGC
1 CGCACACTTAGTGC
89315127 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:89322831 original size:26 final size:24
Alignment explanation
Indices: 89322801--89322857 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 24
89322791 GCCATAATTG
89322801 GTAAGCTCCT-TCTGAGCTGATGAACA
1 GTAAGCTCCTAT-TGAGCTGA--AACA
*
89322827 GTAAGCT-CTATTGAGCTGAATCA
1 GTAAGCTCCTATTGAGCTGAAACA
89322850 GTAAGCTC
1 GTAAGCTC
89322858 TATCATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 10 0.36
25 10 0.36
26 8 0.29
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
GTAAGCTCCTATTGAGCTGAAACA
Found at i:89322841 original size:25 final size:23
Alignment explanation
Indices: 89322813--89322860 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
89322803 AAGCTCCTTC
89322813 TGAGCTGATGAACAGTAAGCTCTAT
1 TGAGCTGA--AACAGTAAGCTCTAT
*
89322838 TGAGCTGAATCAGTAAGCTCTAT
1 TGAGCTGAAACAGTAAGCTCTAT
89322861 CATGTAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTAT
Found at i:89326786 original size:23 final size:23
Alignment explanation
Indices: 89326739--89326814 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
89326729 TTACATATCA
*
89326739 AGCTG-AACAGTAAGCTCCA-ATG
1 AGCTGAAACAGTAAGCT-CATACG
*
89326761 AGCTGAAACAGTAAGCTCTTACG
1 AGCTGAAACAGTAAGCTCATACG
* *
89326784 AGCAGATATATCAGTAGGCTCATACG
1 AGCTGA-A-A-CAGTAAGCTCATACG
89326810 AGCTG
1 AGCTG
89326815 TGGTGAGTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 6 0.14
23 18 0.42
24 1 0.02
25 1 0.02
26 17 0.40
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (23 bp):
AGCTGAAACAGTAAGCTCATACG
Found at i:89329624 original size:46 final size:45
Alignment explanation
Indices: 89329574--89329696 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 45
89329564 GATGAGTGCT
89329574 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CAAGACGTAAG-C
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTACAAGACGT--GTC
* * * *
89329619 AAGTGTAAGATATGTCTGGGACATGCATCAG-CTACGAGATGTGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCCTACAAGACGTGTC
89329664 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
89329697 ACCTACACCC
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
44 10 0.15
45 16 0.24
46 40 0.61
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTACAAGACGTGTC
Found at i:89337362 original size:43 final size:43
Alignment explanation
Indices: 89337191--89337363 Score: 176
Period size: 43 Copynumber: 4.0 Consensus size: 43
89337181 ACATAGGATT
*
89337191 TCGATATGTG-TTATCATGTAAGACCATGTCTGGGACGTTGGCA
1 TCGATATTTGATT-TCATGTAAGACCATGTCTGGGACGTTGGCA
* * * *
89337234 TCGAT-TTGTGATTTACGTGTAAGACCATGTCTAGGACATTGGGA
1 TCGATATT-TGATTT-CATGTAAGACCATGTCTGGGACGTTGGCA
* * * *
89337278 TCG-TATATGATTTCGTGTAAGACCTTGTCTGAGACAG-TGGCA
1 TCGATATTTGATTTCATGTAAGACCATGTCTGGGAC-GTTGGCA
*
89337320 TCGATATTTGATTAT-ATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATTTGATT-TCATGTAAGACCATGTCTGGGACGTTGGCA
89337363 T
1 T
89337364 TGTACCAGCT
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
42 28 0.26
43 46 0.43
44 32 0.30
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
TCGATATTTGATTTCATGTAAGACCATGTCTGGGACGTTGGCA
Found at i:89338584 original size:2 final size:2
Alignment explanation
Indices: 89338569--89338614 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
89338559 AAATAATGTG
* * *
89338569 AT AT AT TT AG AT AT AT AT AT AT AT AT AT AT AT AT AT 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
89338611 AT AT
1 AT AT
89338615 GGCCAAGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89342589 original size:63 final size:63
Alignment explanation
Indices: 89342515--89342659 Score: 220
Period size: 63 Copynumber: 2.3 Consensus size: 63
89342505 ATGGGCTAAG
* * * *
89342515 GACACGGGCATGTGTCCAGATCGTGTAACTCACTGTTTGTGCATTAGAGTCATAC-AGTCCAAA
1 GACACGGGCATGTGTCCAGACCGTGTAACTCACTATTTGTGCATTAAAGTCAAACGAG-CCAAA
*
89342578 GACACGGGCATGTGTCCAAACCGTGTAACTCACTATTTGTGCATTAAAGTCAAACGAGCCAAA
1 GACACGGGCATGTGTCCAGACCGTGTAACTCACTATTTGTGCATTAAAGTCAAACGAGCCAAA
*
89342641 GACACAGGCATGTGTCCAG
1 GACACGGGCATGTGTCCAG
89342660 GCTGTATGAG
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
63 72 0.97
64 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (63 bp):
GACACGGGCATGTGTCCAGACCGTGTAACTCACTATTTGTGCATTAAAGTCAAACGAGCCAAA
Found at i:89344923 original size:22 final size:22
Alignment explanation
Indices: 89344895--89344937 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
89344885 TTTCACTATT
89344895 TTGCTACCATTTCATTATTATG
1 TTGCTACCATTTCATTATTATG
* * *
89344917 TTGCTACTATTTTATTGTTAT
1 TTGCTACCATTTCATTATTAT
89344938 TGCATAACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTCATTATTATG
Found at i:89345341 original size:20 final size:20
Alignment explanation
Indices: 89345316--89345355 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
89345306 AGCCCATGAG
89345316 CACATGTAGTCGAAATGGAA
1 CACATGTAGTCGAAATGGAA
89345336 CACATGTAGTCGAAATGGAA
1 CACATGTAGTCGAAATGGAA
89345356 GATATGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (20 bp):
CACATGTAGTCGAAATGGAA
Found at i:89345993 original size:21 final size:21
Alignment explanation
Indices: 89345967--89346008 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
89345957 AAATCATACC
89345967 CTTGCATTGAAGGATGGTATT
1 CTTGCATTGAAGGATGGTATT
89345988 CTTGCATTGAAGGATGGTATT
1 CTTGCATTGAAGGATGGTATT
89346009 TTGTAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (21 bp):
CTTGCATTGAAGGATGGTATT
Found at i:89348666 original size:168 final size:168
Alignment explanation
Indices: 89348388--89348889 Score: 679
Period size: 168 Copynumber: 3.0 Consensus size: 168
89348378 CTTTCGAGGC
* * *
89348388 TTAGAACATTGTGATTGCGGTTTCTTCTTCCTAGTTTCCTTGCATGGAGGAGTCTCATACAAGGT
1 TTAGAACATTGTGATTGTGATTTCTTCCTCCTAGTTTCCTTGCATGGAGGAGTCTCATACAAGG-
* * * *
89348453 TTTATCACAAACATCATCTTTAGCTTCTTCTTTGACGGGTTTTAGACTCACTTGATCTTCACTCT
65 TTTATCACAAACATCATCTTTAGCTTCTTCCTTGACGGGTTTTAGACACAATTGATCATCACTCT
* *
89348518 TGTTATCTTCAATATGGTTCTTGCATGGATATTCAACT-
130 TGTGATCTTCAATATGGCTCTTGCATGGATATTCAACTG
*
89348556 TTAGAACATTGTGATTGTGATTTATTCCTCCTAGCTTT-CTTGCATGGAGGAGTCTCATACAAGG
1 TTAGAACATTGTGATTGTGATTTCTTCCTCCTAG-TTTCCTTGCATGGAGGAGTCTCATACAAGG
* *
89348620 TTTCATCATAAACACCATCTTTAGCTTCTTCCTTGACGGGTTTTAGACACAATTGATCATCACTC
65 TTT-ATCACAAACATCATCTTTAGCTTCTTCCTTGACGGGTTTTAGACACAATTGATCATCACTC
* * **
89348685 TTAG-GATCTTCAATATAGCTCTTGCATAGATATTC-TGTG
129 TT-GTGATCTTCAATATGGCTCTTGCATGGATATTCAACTG
* * * * * * *
89348724 TTAGAACATAGTGGTCGTGATTTCTTCCTCTTAGTTTCCTTGCAAGAAGGAGTCCCATACAAGGG
1 TTAGAACATTGTGATTGTGATTTCTTCCTCCTAGTTTCCTTGCATGGAGGAGTCTCATACAA-GG
* ** *
89348789 TTTATCACAAACATCATCTTTAGGTTCTTCCTTGACAAGTTTTAGACACATTTGATCATCACTCT
65 TTTATCACAAACATCATCTTTAGCTTCTTCCTTGACGGGTTTTAGACACAATTGATCATCACTCT
*
89348854 TCTGATCTTCAATATGGCTCTTGCATGGATATTCAA
130 TGTGATCTTCAATATGGCTCTTGCATGGATATTCAA
89348890 TCTCTGATGC
Statistics
Matches: 292, Mismatches: 34, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
167 7 0.02
168 276 0.95
169 9 0.03
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.39
Consensus pattern (168 bp):
TTAGAACATTGTGATTGTGATTTCTTCCTCCTAGTTTCCTTGCATGGAGGAGTCTCATACAAGGT
TTATCACAAACATCATCTTTAGCTTCTTCCTTGACGGGTTTTAGACACAATTGATCATCACTCTT
GTGATCTTCAATATGGCTCTTGCATGGATATTCAACTG
Found at i:89351328 original size:20 final size:20
Alignment explanation
Indices: 89351296--89351337 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
89351286 TCATCTCGAA
89351296 CTGTATCCCTAATTCCTTATC
1 CTGTATCCCTAATTCC-TATC
89351317 CTGTAT-CCTAATTCCTATC
1 CTGTATCCCTAATTCCTATC
89351336 CT
1 CT
89351338 CTTGTACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.19, C:0.33, G:0.05, T:0.43
Consensus pattern (20 bp):
CTGTATCCCTAATTCCTATC
Found at i:89356736 original size:19 final size:17
Alignment explanation
Indices: 89356701--89356735 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
89356691 ACTTGAAAAT
89356701 TTTATGAAAAAAATATA
1 TTTATGAAAAAAATATA
* *
89356718 TTTATTAAAAAATTATA
1 TTTATGAAAAAAATATA
89356735 T
1 T
89356736 AAACATCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TTTATGAAAAAAATATA
Found at i:89363806 original size:22 final size:23
Alignment explanation
Indices: 89363776--89363833 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
89363766 AAGTCGAAAT
*
89363776 AGAATATAAAAATAATTTA-AAA
1 AGAAAATAAAAATAATTTATAAA
* *
89363798 AGAAAATAAACA-AATTTATAAT
1 AGAAAATAAAAATAATTTATAAA
*
89363820 ACAAAATATAAAAT
1 AGAAAATA-AAAAT
89363834 GAATAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 6 0.21
22 19 0.68
23 3 0.11
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (23 bp):
AGAAAATAAAAATAATTTATAAA
Found at i:89366200 original size:45 final size:45
Alignment explanation
Indices: 89366143--89366712 Score: 240
Period size: 45 Copynumber: 12.7 Consensus size: 45
89366133 TGATGGCTTT
* * * * *
89366143 AATCTGCTCCACTG-TAACTTTATGAAGATAAGATTTGCAGTTTTC
1 AATCTGCTCCACTGCT-ACTTCAGGAAGATAAGATCTACAGTCTTC
* *
89366188 GATCTGCTCCACTGCTACTTCAGGGAGATAAGATCTACAGTCTTC
1 AATCTGCTCCACTGCTACTTCAGGAAGATAAGATCTACAGTCTTC
* ** * *
89366233 AATCTGCTCCACTGCTACCTCA-GAGAGATAAGATCTGTAATATTC
1 AATCTGCTCCACTGCTACTTCAGGA-AGATAAGATCTACAGTCTTC
* ** * *** * * *
89366278 AATCTGCTCCACTGCTACCTCAGGGGGATAAG-GCTGGTGGCCTA
1 AATCTGCTCCACTGCTACTTCAGGAAGATAAGATCTACAGTCTTC
* * * *
89366322 AATCTGCTCCATTGCTACTTCATGAAGATAAGACTCGT-C-GTATTT
1 AATCTGCTCCACTGCTACTTCAGGAAGATAAGA-TC-TACAGTCTTC
* * * * * * * *
89366367 GATCTACTCCACTACTACTTCGGGGAGATAAAATCTACAATCTTT
1 AATCTGCTCCACTGCTACTTCAGGAAGATAAGATCTACAGTCTTC
* * * * *** * *
89366412 AATTTTCTCC-CTTGCTACTCCAAGG-AGATAAG-GCTGGTGGCTTA
1 AATCTGCTCCAC-TGCTACTTC-AGGAAGATAAGATCTACAGTCTTC
* * **
89366456 AATCTGCTCCATTGCTACTTCATGG-AGATAAAATTCT-TTGTCCTT-
1 AATCTGCTCCACTGCTACTTCA-GGAAGATAAGA-TCTACAGT-CTTC
* * *
89366501 GATCTGCTCCATTGCTACCTCATGG-AGATAAGATCTAC-GATCTTC
1 AATCTGCTCCACTGCTACTTCA-GGAAGATAAGATCTACAG-TCTTC
* * * *** *
89366546 AATATACTCCACTGCTACTTCAGGGAGATAAGA-CTGGTGGCTT-
1 AATCTGCTCCACTGCTACTTCAGGAAGATAAGATCTACAGTCTTC
* * * ** *
89366589 AGATTTGCTCCATTGCTGCTTCATGG-AGATAAGATTCT-TTGTCCTC
1 A-ATCTGCTCCACTGCTACTTCA-GGAAGATAAGA-TCTACAGTCTTC
* * * ** * *
89366635 AATCTACTCTATTGCTACCCCATGAAGATAAGATCTACAATCTTC
1 AATCTGCTCCACTGCTACTTCAGGAAGATAAGATCTACAGTCTTC
*
89366680 AATCTGCTCCACTGCTATTTCA-GAGAGATAAGA
1 AATCTGCTCCACTGCTACTTCAGGA-AGATAAGA
89366713 CTTGTGACTT
Statistics
Matches: 394, Mismatches: 103, Indels: 56
0.71 0.19 0.10
Matches are distributed among these distances:
43 3 0.01
44 110 0.28
45 267 0.68
46 13 0.03
47 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (45 bp):
AATCTGCTCCACTGCTACTTCAGGAAGATAAGATCTACAGTCTTC
Found at i:89366338 original size:134 final size:135
Alignment explanation
Indices: 89366189--89366860 Score: 561
Period size: 134 Copynumber: 5.0 Consensus size: 135
89366179 GCAGTTTTCG
* * * *
89366189 ATCTGCTCCACTGCTACTTCAGGGAGATAAGA-TCTACAGTCTTCAATCTGCTCCACTGCTACCT
1 ATCTGCTCCATTGCTACTTCATGGAGATAAGATTCT-CTGTCTTCAATCTACTCCACTGCTACCT
** * *
89366253 CA-GAGAGATAAGATCTGTAATATTCAATCTGCTCCACTGCTACCTCAGGGGGATAAGGCTGGTG
65 CATGAGAGATAAGATCTACAATCTTCAATCTGCTCCACTGCTACCTCAGGGAGATAAGGCTGGTG
*
89366317 GCCTAA
130 GCTTAA
* * * ** * *
89366323 ATCTGCTCCATTGCTACTTCATGAAGATAAGACTCGTC-GTATTTGATCTACTCCACTACTACTT
1 ATCTGCTCCATTGCTACTTCATGGAGATAAGATTC-TCTGTCTTCAATCTACTCCACTGCTACCT
* * * * * * *
89366387 C-GGGGAGATAAAATCTACAATCTTTAATTTTCTCC-CTTGCTA-CTCCAAGGAGATAAGGCTGG
65 CATGAGAGATAAGATCTACAATCTTCAATCTGCTCCAC-TGCTACCT-CAGGGAGATAAGGCTGG
89366449 TGGCTTAA
128 TGGCTTAA
* * * * *
89366457 ATCTGCTCCATTGCTACTTCATGGAGATAAAATTCTTTGTCCTT-GATCTGCTCCATTGCTACCT
1 ATCTGCTCCATTGCTACTTCATGGAGATAAGATTCTCTGT-CTTCAATCTACTCCACTGCTACCT
* * * * *
89366521 CATG-GAGATAAGATCTACGATCTTCAATATACTCCACTGCTACTTCAGGGAGATAAGACTGGTG
65 CATGAGAGATAAGATCTACAATCTTCAATCTGCTCCACTGCTACCTCAGGGAGATAAGGCTGGTG
*
89366585 GCTTAG
130 GCTTAA
* * * * * * *
89366591 ATTTGCTCCATTGCTGCTTCATGGAGATAAGATTCTTTGTCCTCAATCTACTCTATTGCTACCCC
1 ATCTGCTCCATTGCTACTTCATGGAGATAAGATTCTCTGTCTTCAATCTACTCCACTGCTACCTC
** * * * *
89366656 ATGA-AGATAAGATCTACAATCTTCAATCTGCTCCACTGCTATTTCAGAGAGATAAGACTTGTGA
66 ATGAGAGATAAGATCTACAATCTTCAATCTGCTCCACTGCTACCTCAGGGAGATAAGGCTGGTGG
89366720 CTTAA
131 CTTAA
* * * * * *
89366725 ATCTTCTTC--T-CTACTATC-TCGGAAAGATAAGATTCGTC-ATCTTCGAA-CTGCTTCACTAC
1 ATCTGCTCCATTGCTACT-TCAT-GG--AGATAAGATTC-TCTGTCTTC-AATCTACTCCACTGC
* * * ** ** *
89366784 TA-CTTAAG-GAGATAAAATCCGCAATCTTCAGCCTGCTCCACTGTTA-CTCAGGGAGATAAGGC
60 TACCTCATGAGAGATAAGATCTACAATCTTCAATCTGCTCCACTGCTACCTCAGGGAGATAAGGC
*
89366846 TAGTGGCTTAA
125 TGGTGGCTTAA
89366857 ATCT
1 ATCT
89366861 ACTTCTCCAC
Statistics
Matches: 438, Mismatches: 81, Indels: 40
0.78 0.14 0.07
Matches are distributed among these distances:
131 5 0.01
132 31 0.07
133 40 0.09
134 350 0.80
135 11 0.03
136 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (135 bp):
ATCTGCTCCATTGCTACTTCATGGAGATAAGATTCTCTGTCTTCAATCTACTCCACTGCTACCTC
ATGAGAGATAAGATCTACAATCTTCAATCTGCTCCACTGCTACCTCAGGGAGATAAGGCTGGTGG
CTTAA
Found at i:89366600 original size:89 final size:88
Alignment explanation
Indices: 89366189--89366696 Score: 291
Period size: 89 Copynumber: 5.7 Consensus size: 88
89366179 GCAGTTTTCG
* * * *
89366189 ATCTGCTCCACTGCTACTTCAGGGAGATAAGATCTACAGTCTTCAATCTGCTCCACTGCTACCTC
1 ATCTACTCCACTGCTACTTCAGGGAGATAAGATCTACTGGCTT-AATCTGCTCCATTGCTACCTC
*
89366254 A-GAGAGATAAGATCT-GTAATATTCA
65 ATG-GAGATAAGATCTCG--ATCTTCA
* * * * ** * *
89366279 ATCTGCTCCACTGCTACCTCAGGGGGATAAG-GCTGGTGGCCTAAATCTGCTCCATTGCTACTTC
1 ATCTACTCCACTGCTACTTCAGGGAGATAAGATCTACTGG-CTTAATCTGCTCCATTGCTACCTC
* *
89366343 ATGAAGATAAGACTCGTCGTAT-TT-G
65 ATGGAGATAAGA-TC-TCG-ATCTTCA
* * * *** * * *
89366368 ATCTACTCCACTACTACTTCGGGGAGATAAAATCTACAATCTTTAATTTTCTCCCTTGCTA-CTC
1 ATCTACTCCACTGCTACTTCAGGGAGATAAGATCTACTGGC-TTAATCTGCTCCATTGCTACCT-
* * * *
89366432 CAAGGAGATAAG-GCT-GGTGGCTTAA
64 CATGGAGATAAGATCTCGAT--CTTCA
* * * * * * *
89366457 ATCTGCTCCATTGCTACTTCATGGAGATAAAATTCT-TTGTCCTTGATCTGCTCCATTGCTACCT
1 ATCTACTCCACTGCTACTTCAGGGAGATAAGA-TCTACTG-GCTTAATCTGCTCCATTGCTACCT
89366521 CATGGAGATAAGATCTACGATCTTCA
64 CATGGAGATAAGATCT-CGATCTTCA
* ** * * *
89366547 ATATACTCCACTGCTACTTCAGGGAGATAAGA-CTGGTGGCTTAGATTTGCTCCATTGCTGCTTC
1 ATCTACTCCACTGCTACTTCAGGGAGATAAGATCTACTGGCTTA-ATCTGCTCCATTGCTACCTC
* *
89366611 ATGGAGATAAGATTCTTTG-TCCTCA
65 ATGGAGATAAGA-TC-TCGATCTTCA
* * ** * * *** *
89366636 ATCTACTCTATTGCTACCCCATGAAGATAAGATCTACAATCTTCAATCTGCTCCACTGCTA
1 ATCTACTCCACTGCTACTTCAGGGAGATAAGATCTACTGGCTT-AATCTGCTCCATTGCTA
89366697 TTTCAGAGAG
Statistics
Matches: 314, Mismatches: 80, Indels: 48
0.71 0.18 0.11
Matches are distributed among these distances:
85 1 0.00
86 1 0.00
87 1 0.00
88 8 0.03
89 172 0.55
90 123 0.39
91 5 0.02
92 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (88 bp):
ATCTACTCCACTGCTACTTCAGGGAGATAAGATCTACTGGCTTAATCTGCTCCATTGCTACCTCA
TGGAGATAAGATCTCGATCTTCA
Found at i:89366884 original size:132 final size:133
Alignment explanation
Indices: 89366672--89366930 Score: 324
Period size: 132 Copynumber: 2.0 Consensus size: 133
89366662 ATAAGATCTA
* * * * *
89366672 CAATCTTCAATCTGCTCCACTGCTATTTCAGAGAGATAAGACTTGTGACTTAAATCTTCTTCTCT
1 CAATCTTCAACCTGCTCCACTGCTATCTCAGAGAGATAAGACTAGTGACTTAAATCTACTTCTCC
* *
89366737 ACTATCTCGGAAAGATAAGATTCGTCATCTTCGAACTGCTTCACTACTACTTAAGGAGATAAAAT
66 ACTACCTCGGAAAGATAAGATTCGTCATCTTCGAACTGCTCCACTACTACTTAAGGAGATAAAAT
89366802 CCG
131 CCG
* * * * *
89366805 CAATCTTCAGCCTGCTCCACTGTTA-CTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCTCC
1 CAATCTTCAACCTGCTCCACTGCTATCTCAGAGAGATAAGACTAGTGACTTAAATCTACTTCTCC
* * ** * * *
89366869 ACTACCT-TGAGAAGATAAGATTCGTCGTCTTCGATTTTCTCCACTACTGCTTAGGGAGATAA
66 ACTACCTCGGA-AAGATAAGATTCGTCATCTTCGAACTGCTCCACTACTACTTAAGGAGATAA
89366931 GATTCATGAA
Statistics
Matches: 106, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
131 2 0.02
132 82 0.77
133 22 0.21
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (133 bp):
CAATCTTCAACCTGCTCCACTGCTATCTCAGAGAGATAAGACTAGTGACTTAAATCTACTTCTCC
ACTACCTCGGAAAGATAAGATTCGTCATCTTCGAACTGCTCCACTACTACTTAAGGAGATAAAAT
CCG
Found at i:89369206 original size:25 final size:25
Alignment explanation
Indices: 89369178--89369227 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
89369168 CTGATCCTTC
89369178 CTCTTTTTATACAGGATCTCTCCGT
1 CTCTTTTTATACAGGATCTCTCCGT
89369203 CTCTTTTTATACAGGATCTCTCCGT
1 CTCTTTTTATACAGGATCTCTCCGT
89369228 TTAAGACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (25 bp):
CTCTTTTTATACAGGATCTCTCCGT
Found at i:89371626 original size:21 final size:22
Alignment explanation
Indices: 89371600--89371647 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
89371590 ACTAAAAACA
89371600 AGAATAAAAG-AATATTTGCTC
1 AGAATAAAAGAAATATTTGCTC
89371621 AGAATAAAAGAAATATTTGCTC
1 AGAATAAAAGAAATATTTGCTC
89371643 AGAAT
1 AGAAT
89371648 GAGACGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AGAATAAAAGAAATATTTGCTC
Found at i:89376275 original size:42 final size:43
Alignment explanation
Indices: 89376194--89376288 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 43
89376184 TCCTAGACGT
* * **
89376194 GGTCTTACATGTAATTCAGTATCGATGCCTCTGTCCCAGACAG
1 GGTCTTACACGTAAATCAGTATCGATGCCGATGTCCCAGACAG
* *
89376237 GGTCTTACACG-AAATCAG-ATACGATGCCGATGTGCCAGACAT
1 GGTCTTACACGTAAATCAGTAT-CGATGCCGATGTCCCAGACAG
89376279 GGTCTTACAC
1 GGTCTTACAC
89376289 TACATCTCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.04
42 33 0.73
43 10 0.22
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAGTATCGATGCCGATGTCCCAGACAG
Found at i:89379684 original size:41 final size:41
Alignment explanation
Indices: 89379627--89379707 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
89379617 GATAATGAAG
89379627 TAAAGCTGTATATTCTTCTACAGTAGGAACCAAATCTACCT
1 TAAAGCTGTATATTCTTCTACAGTAGGAACCAAATCTACCT
89379668 TAAAGCTGTATATTCTTCTACAGTAGGAACCAAATCTACC
1 TAAAGCTGTATATTCTTCTACAGTAGGAACCAAATCTACC
89379708 CTCCCAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (41 bp):
TAAAGCTGTATATTCTTCTACAGTAGGAACCAAATCTACCT
Found at i:89381771 original size:20 final size:22
Alignment explanation
Indices: 89381748--89381788 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
89381738 TATCACAAAA
89381748 TTTAAAAT-AAT-ATATATAAG
1 TTTAAAATAAATAATATATAAG
89381768 TTTAAAATAAATAATATATAA
1 TTTAAAATAAATAATATATAA
89381789 AATAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATAATATATAAG
Found at i:89382158 original size:17 final size:19
Alignment explanation
Indices: 89382136--89382178 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 19
89382126 ATAATAGAAG
89382136 TAATAATGAAAAATA-AA-
1 TAATAATGAAAAATATAAC
89382153 TAATAATGAAAAATATAAC
1 TAATAATGAAAAATATAAC
89382172 TAATAAT
1 TAATAAT
89382179 ATTACAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 15 0.62
18 2 0.08
19 7 0.29
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (19 bp):
TAATAATGAAAAATATAAC
Found at i:89383730 original size:19 final size:18
Alignment explanation
Indices: 89383706--89383751 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
89383696 TAAATACAAG
* *
89383706 TAAAAATTATTGATTAGAA
1 TAAAAATAACTGATTA-AA
*
89383725 TAAAAACAACTGATTAAA
1 TAAAAATAACTGATTAAA
89383743 TAAAAATAA
1 TAAAAATAA
89383752 ATAAATCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (18 bp):
TAAAAATAACTGATTAAA
Found at i:89384839 original size:25 final size:24
Alignment explanation
Indices: 89384792--89384848 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
89384782 ATTAATTATT
89384792 AATATAATTTATTTTCAAGTTAATA
1 AATATAATTTATTTTCAAGTTAA-A
* *
89384817 AATATAAGTTTATTTT-TATTTAAA
1 AATATAA-TTTATTTTCAAGTTAAA
89384841 AATA-AATT
1 AATATAATT
89384849 AGTAAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 5 0.17
25 12 0.41
26 8 0.28
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
AATATAATTTATTTTCAAGTTAAA
Found at i:89386444 original size:28 final size:28
Alignment explanation
Indices: 89386409--89386467 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
89386399 GTTGATAAAG
89386409 TTCAAAACAAAGCCACCAAACCCAAGTT
1 TTCAAAACAAAGCCACCAAACCCAAGTT
89386437 TTCAAAACAAAGCCACCAAACCCAAGTT
1 TTCAAAACAAAGCCACCAAACCCAAGTT
89386465 TTC
1 TTC
89386468 TTAATCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.44, C:0.32, G:0.07, T:0.17
Consensus pattern (28 bp):
TTCAAAACAAAGCCACCAAACCCAAGTT
Found at i:89393373 original size:42 final size:42
Alignment explanation
Indices: 89393326--89393437 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
89393316 GAGTATGCAC
* * * *
89393326 AGGTGTTTTTAACCTTTCATCCTTTTTACTTGGTGTATTTACT
1 AGGTGTTTTTAACCTTTCATCCCTTTTACTAGGGGTATGTA-T
*
89393369 -GGTGTTTTTAACCTTTCATCCCTTATACTAGGGGTATGTAT
1 AGGTGTTTTTAACCTTTCATCCCTTTTACTAGGGGTATGTAT
89393410 AGGTGTTTTTAACCTTTCATCCCTTTTA
1 AGGTGTTTTTAACCTTTCATCCCTTTTA
89393438 GAAGGCGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 61 0.98
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (42 bp):
AGGTGTTTTTAACCTTTCATCCCTTTTACTAGGGGTATGTAT
Found at i:89400236 original size:126 final size:126
Alignment explanation
Indices: 89400018--89400319 Score: 478
Period size: 126 Copynumber: 2.4 Consensus size: 126
89400008 ATTAATTACC
*
89400018 AAAAAAAGCTCCCACGTGGACGCTCTTTTGCTATAGTAGTATCTGAAAAAATAATTTTGAGAAGA
1 AAAAAAA-CTCCTACGTGGACGCTCTTTTGCTATAGTAGTATCTGAAAAAATAATTTTGAGAAGA
* * * * * *
89400083 TGTTTCTGAATAAATAGTGTCAAAAACGTTTCAAGAATGATACACTGTCAGTAAAATTATGG
65 TGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAAAAGGATACACTGTCAGCAAAATTATGG
*
89400145 AAAAAAACTCCTACGTGGACGCTCTTTTGCTATAGTAGTATCTGAAAAAATAATTTTGATAAGAT
1 AAAAAAACTCCTACGTGGACGCTCTTTTGCTATAGTAGTATCTGAAAAAATAATTTTGAGAAGAT
*
89400210 GTTTCTAAACAAATAGTGTCAAAAACGCTTCAAAAAGGATGCACTGTCAGCAAAATTATGG
66 GTTTCTAAACAAATAGTGTCAAAAACGCTTCAAAAAGGATACACTGTCAGCAAAATTATGG
* ** *
89400271 AAAAAAGCTCCTGTGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAA
1 AAAAAAACTCCTACGTGGACGCTCTTTTGCTATAGTAGTATCTGAAAAA
89400320 GCCTTAGACT
Statistics
Matches: 162, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
126 155 0.96
127 7 0.04
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (126 bp):
AAAAAAACTCCTACGTGGACGCTCTTTTGCTATAGTAGTATCTGAAAAAATAATTTTGAGAAGAT
GTTTCTAAACAAATAGTGTCAAAAACGCTTCAAAAAGGATACACTGTCAGCAAAATTATGG
Found at i:89401928 original size:49 final size:49
Alignment explanation
Indices: 89401869--89402093 Score: 256
Period size: 49 Copynumber: 4.5 Consensus size: 49
89401859 TGAATACATG
* *
89401869 TGTGTAGTACTAAGTGCAGGCTACTACGTGTTCCGGATTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGGTCACA
* * * * *
89401918 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC--AATGACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CGGATTG--TT-GGTCACA
* * * * * *
89401969 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGT-TGGTCACA
* *
89402019 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATTATTGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGGTCACA
89402068 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
89402094 TGCGTATCAG
Statistics
Matches: 148, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
48 3 0.02
49 62 0.42
50 46 0.31
51 35 0.24
52 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGGTCACA
Found at i:89402094 original size:99 final size:100
Alignment explanation
Indices: 89401869--89402105 Score: 311
Period size: 99 Copynumber: 2.4 Consensus size: 100
89401859 TGAATACATG
* * * * *
89401869 TGTGTAGTACTAAGTGCAGGCTACTACGTGT-TCCGGATTGTTGGTCGCATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTAT-CAGATGGTAGGTCACATGTGTAGTACTAAGT
* *
89401933 GCAGGCTACTATGCGTACTCAATGACTTCGATCACG
65 GCAGGCTACTACGCGTACTCAATGACTTCGATCACA
*
89401969 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTGAGGTCACGTGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGT-AGGTCACATGTGTAGTACTAAGT
* * *
89402034 GCAGGCTACTACGTGTAC-CGAATTA-TT-GGTCACA
65 GCAGGCTACTACGCGTACTC-AATGACTTCGATCACA
*
89402068 TGTGTAGTACTAAGTGCAGGCTACTATGCGTATCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGAT
89402106 AGCTTCGGCT
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
99 42 0.34
100 39 0.32
101 41 0.34
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (100 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTAGGTCACATGTGTAGTACTAAGTG
CAGGCTACTACGCGTACTCAATGACTTCGATCACA
Found at i:89406122 original size:13 final size:13
Alignment explanation
Indices: 89406104--89406128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89406094 TGAAACTATA
89406104 TAAAAAAATAAAT
1 TAAAAAAATAAAT
89406117 TAAAAAAATAAA
1 TAAAAAAATAAA
89406129 AATATTGGCT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAAATAAAT
Found at i:89406257 original size:15 final size:17
Alignment explanation
Indices: 89406228--89406264 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
89406218 TAATTGAAAC
89406228 TATATAAAATAAATAAA
1 TATATAAAATAAATAAA
89406245 TATA-AAAAT-AATAAA
1 TATATAAAATAAATAAA
*
89406260 AATAT
1 TATAT
89406265 TGGCTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TATATAAAATAAATAAA
Found at i:89406335 original size:131 final size:130
Alignment explanation
Indices: 89405994--89406379 Score: 690
Period size: 131 Copynumber: 3.0 Consensus size: 130
89405984 ACATTTATTT
* * *
89405994 TAATAAAATTATTGGCTAATTTAAATA-AACATTTATTGTATTAAAATTAAAAAAAGTAAAGTAC
1 TAATAAAAATATTGGCTAATTTAAA-AGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTAC
89406058 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAAATAAAT-TAAAA
65 AATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAAATAAATATAAAA
89406122 A
130 A
89406123 -AATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
1 TAATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
89406187 ATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAATAAATAAATATAAAA
66 ATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAA-AAATAAATATAAAA
89406252 A
130 A
89406253 TAATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
1 TAATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
*
89406318 ATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATAT-AAAAATTAAATATAAA
66 ATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAAATAAATATAAA
89406380 TTTAAAAGAA
Statistics
Matches: 249, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
127 1 0.00
128 109 0.44
129 20 0.08
130 9 0.04
131 110 0.44
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (130 bp):
TAATAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACA
ATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAAATAAATATAAAAA
Found at i:89406345 original size:55 final size:55
Alignment explanation
Indices: 89406275--89406455 Score: 203
Period size: 55 Copynumber: 3.3 Consensus size: 55
89406265 TGGCTAATTT
89406275 AAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTA
1 AAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTA
* * * * ** *
89406330 AAAACAACTTTTATTTT-AT-TAATTGAAACTA-TATAA--A-AATTAAATATAAATTT
1 AAAAGAACATTTATTTTAATAAAATTAAAAAAAGTA-AAGTACAATTAAA-AT--ATTA
89406383 AAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTA
1 AAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTA
* *
89406438 AAAATAACTTTTATTTTA
1 AAAAGAACATTTATTTTA
89406456 TTATATGAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 20
0.74 0.12 0.15
Matches are distributed among these distances:
50 7 0.07
51 3 0.03
52 2 0.02
53 28 0.28
54 4 0.04
55 44 0.44
56 2 0.02
57 3 0.03
58 7 0.07
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (55 bp):
AAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTA
Found at i:89406389 original size:108 final size:108
Alignment explanation
Indices: 89406270--89406476 Score: 389
Period size: 108 Copynumber: 1.9 Consensus size: 108
89406260 AATATTGGCT
89406270 AATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTAAAAAC
1 AATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTAAAAAC
89406335 AACTTTTATTTTATTA-ATTGAAACTATATAAAAATTAAATATA
66 AACTTTTATTTTATTATA-TGAAACTATATAAAAATTAAATATA
*
89406378 AATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTAAAAAT
1 AATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTAAAAAC
89406443 AACTTTTATTTTATTATATGAAACTATATAAAAA
66 AACTTTTATTTTATTATATGAAACTATATAAAAA
89406477 AGTTTCTACA
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
108 96 0.99
109 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (108 bp):
AATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAGTAAAGTACAATTAAAATATTAAAAAC
AACTTTTATTTTATTATATGAAACTATATAAAAATTAAATATA
Found at i:89407532 original size:7 final size:7
Alignment explanation
Indices: 89407520--89407558 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
89407510 TTATATAAGT
89407520 AATACTA
1 AATACTA
89407527 AATACTA
1 AATACTA
89407534 AATACTA
1 AATACTA
*
89407541 AATATTA
1 AATACTA
89407548 AATACTA
1 AATACTA
89407555 AATA
1 AATA
89407559 AAAAATGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (7 bp):
AATACTA
Found at i:89407564 original size:14 final size:14
Alignment explanation
Indices: 89407520--89407564 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
89407510 TTATATAAGT
*
89407520 AATACTAAATACTA
1 AATACTAAATAATA
*
89407534 AATACTAAATATTA
1 AATACTAAATAATA
*
89407548 AATACTAAATAAAA
1 AATACTAAATAATA
89407562 AAT
1 AAT
89407565 GATTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (14 bp):
AATACTAAATAATA
Found at i:89407564 original size:21 final size:21
Alignment explanation
Indices: 89407520--89407569 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
89407510 TTATATAAGT
* **
89407520 AATACTAAATACTAAATACTA
1 AATATTAAATACTAAATAAAA
89407541 AATATTAAATACTAAATAAAA
1 AATATTAAATACTAAATAAAA
89407562 AATGATTA
1 AAT-ATTA
89407570 TTTTATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (21 bp):
AATATTAAATACTAAATAAAA
Found at i:89408742 original size:11 final size:12
Alignment explanation
Indices: 89408722--89408776 Score: 75
Period size: 11 Copynumber: 5.0 Consensus size: 12
89408712 AAAAATTGAA
89408722 AATTT-TGAGAG
1 AATTTGTGAGAG
89408733 AATTTG-GAGAG
1 AATTTGTGAGAG
89408744 AA-TTGTGAGAG
1 AATTTGTGAGAG
89408755 AA-TTGTGAGAG
1 AATTTGTGAGAG
89408766 -ATTTGTGAGAG
1 AATTTGTGAGAG
89408777 GACTATTGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.10
11 37 0.90
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (12 bp):
AATTTGTGAGAG
Found at i:89410113 original size:18 final size:17
Alignment explanation
Indices: 89410090--89410172 Score: 66
Period size: 18 Copynumber: 4.8 Consensus size: 17
89410080 TACATGTGTA
89410090 ATAATATTATACATATAT
1 ATAATATTATA-ATATAT
* *
89410108 ATAATAATATACATAATAC
1 ATAATATTATA-AT-ATAT
89410127 ATAATATT-TAAGT-T-T
1 ATAATATTATAA-TATAT
89410142 A-AATATTATAATATATT
1 ATAATATTATAATATA-T
*
89410159 ATATTATTATAATA
1 ATAATATTATAATA
89410173 ATAAATTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
14 7 0.13
15 5 0.09
16 1 0.02
17 3 0.06
18 27 0.51
19 10 0.19
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
ATAATATTATAATATAT
Found at i:89410216 original size:6 final size:6
Alignment explanation
Indices: 89410191--89410273 Score: 51
Period size: 6 Copynumber: 13.0 Consensus size: 6
89410181 AAGAATAAAC
* * * *
89410191 AAAGAA AATAAAA GAAAGAA AAAGAA AAAGAA CAGATGAA ATAG-A AAGGAGA
1 AAAGAA AA-AGAA -AAAGAA AAAGAA AAAGAA -A-AAGAA AAAGAA AAAGA-A
* *
89410243 AAAGAA GAAAGAA AAAGAG AAACAA AAAGAA
1 AAAGAA -AAAGAA AAAGAA AAAGAA AAAGAA
89410274 GGAGAATTAG
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
5 3 0.05
6 30 0.52
7 19 0.33
8 6 0.10
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:89410252 original size:21 final size:20
Alignment explanation
Indices: 89410191--89410260 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
89410181 AAGAATAAAC
*
89410191 AAAG-AAAATAAAAGAAAGAA
1 AAAGAAAAAGAAAAG-AAGAA
* *
89410211 AAAGAAAAAGAACAGATGAA
1 AAAGAAAAAGAAAAGAAGAA
* *
89410231 ATAGAAAGGAGAAAAGAAG--
1 AAAGAAA-AAGAAAAGAAGAA
89410250 AAAGAAAAAGA
1 AAAGAAAAAGA
89410261 GAAACAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
18 3 0.08
19 6 0.15
20 14 0.36
21 16 0.41
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAGAAAAGAAGAA
Found at i:89414250 original size:27 final size:26
Alignment explanation
Indices: 89414220--89414281 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
89414210 AGATAATTAA
89414220 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
89414247 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
89414274 AATAAAAT
1 AATAAAAT
89414282 GGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:89414854 original size:10 final size:9
Alignment explanation
Indices: 89414839--89414863 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
89414829 ATTAATATGA
89414839 TTTTTTTTC
1 TTTTTTTTC
89414848 TTTTTTTTC
1 TTTTTTTTC
89414857 TTTTTTT
1 TTTTTTT
89414864 ATAGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:89415868 original size:15 final size:15
Alignment explanation
Indices: 89415848--89415895 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
89415838 TTAATATCTG
*
89415848 AAAATAATAAATAAT
1 AAAATAATAAATAAA
89415863 AAAATAATAAGATAAA
1 AAAATAATAA-ATAAA
89415879 ATAAATAA-AAATAAA
1 A-AAATAATAAATAAA
89415894 AA
1 AA
89415896 TTGGGTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 7 0.23
17 6 0.20
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAA
Found at i:89420761 original size:18 final size:18
Alignment explanation
Indices: 89420738--89420775 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
89420728 TTTATAGTGC
89420738 TAGGGAGATAGTCTAATT
1 TAGGGAGATAGTCTAATT
89420756 TAGGGAGATAGTCTAATT
1 TAGGGAGATAGTCTAATT
89420774 TA
1 TA
89420776 ACTTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (18 bp):
TAGGGAGATAGTCTAATT
Found at i:89420831 original size:20 final size:20
Alignment explanation
Indices: 89420789--89420836 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
89420779 TAAATTCTAA
*
89420789 AAAGATAAATACAATTAACT
1 AAAGATAAATACAAATAACT
*
89420809 AAAGATAAATA-AAGATAATT
1 AAAGATAAATACAA-ATAACT
89420829 AAA-ATAAA
1 AAAGATAAA
89420837 ATTCTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAGATAAATACAAATAACT
Found at i:89431573 original size:5 final size:5
Alignment explanation
Indices: 89431563--89431611 Score: 80
Period size: 5 Copynumber: 9.6 Consensus size: 5
89431553 CATAATTCAT
*
89431563 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTT AATATC AAT
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC AAT-TC AAT
89431612 ACTCACCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTC
Found at i:89432490 original size:17 final size:19
Alignment explanation
Indices: 89432468--89432505 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
89432458 CAAGAATTAC
89432468 TTATCG-ATGT-TCAAGAT
1 TTATCGAATGTATCAAGAT
*
89432485 TTATCGAATTTATCAAGAT
1 TTATCGAATGTATCAAGAT
89432504 TT
1 TT
89432506 TCAAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (19 bp):
TTATCGAATGTATCAAGAT
Found at i:89432763 original size:23 final size:22
Alignment explanation
Indices: 89432721--89432763 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
89432711 AAATTTTATG
*
89432721 AAAAAGAAAAAGATATATTTAA
1 AAAAAGAAAAAGATAAATTTAA
89432743 AAAAAGAGAGAAA-ATAAATTT
1 AAAAAGA-A-AAAGATAAATTT
89432764 TAAATAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 8 0.44
24 3 0.17
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (22 bp):
AAAAAGAAAAAGATAAATTTAA
Found at i:89434769 original size:107 final size:108
Alignment explanation
Indices: 89434639--89434853 Score: 387
Period size: 107 Copynumber: 2.0 Consensus size: 108
89434629 AAAACACGTC
89434639 AAAAATTTTATCAGAGTAATTAACAAAAAATTTAATACAATTTTGTTAGAAATTTTATTATTTAA
1 AAAAATTTTATCAGAGTAATTAACAAAAAATTTAATACAATTTTGTTAGAAATTTTATTATTTAA
*
89434704 AACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAATA
66 AACTTATTCCAACTTAACATATCATTATTTTGTTAAACTAATA
*
89434747 AAAAATTTTAT-AGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTTAA
1 AAAAATTTTATCAGAGTAATTAACAAAAAATTTAATACAATTTTGTTAGAAATTTTATTATTTAA
* *
89434811 AATTTATTCTAACTTAACATATCATTATTTTGTTAAACTAATA
66 AACTTATTCCAACTTAACATATCATTATTTTGTTAAACTAATA
89434854 TTTTGTTTAA
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 92 0.89
108 11 0.11
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (108 bp):
AAAAATTTTATCAGAGTAATTAACAAAAAATTTAATACAATTTTGTTAGAAATTTTATTATTTAA
AACTTATTCCAACTTAACATATCATTATTTTGTTAAACTAATA
Found at i:89436199 original size:23 final size:24
Alignment explanation
Indices: 89436164--89436212 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
89436154 TAAATATTTT
*
89436164 AATTAATTCATTTAT-AATTTTAA
1 AATTAATTAATTTATAAATTTTAA
*
89436187 AATTATTTAATTTATCAAATTTTAA
1 AATTAATTAATTTAT-AAATTTTAA
89436212 A
1 A
89436213 CCTACGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTAATTAATTTATAAATTTTAA
Found at i:89438186 original size:2 final size:2
Alignment explanation
Indices: 89438181--89438212 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
89438171 GTGAAAGTCG
89438181 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89438213 TCTGAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:89438729 original size:39 final size:39
Alignment explanation
Indices: 89438675--89438790 Score: 214
Period size: 39 Copynumber: 3.0 Consensus size: 39
89438665 GATATTGATG
89438675 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
89438714 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
**
89438753 TATATCCGGACTTAATGTCCGCAGGCTATGTGCTGGAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
89438791 ATATGTCTGG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:89438814 original size:39 final size:39
Alignment explanation
Indices: 89438675--89438870 Score: 202
Period size: 39 Copynumber: 5.0 Consensus size: 39
89438665 GATATTGATG
**
89438675 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAT
**
89438714 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAT
* *
89438753 TATATCCGGACTTAATGTCCGCAGGCTATGTGCTGGAAA
1 TATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAT
* * * * *
89438792 TATGTCTGGGC-TAAAGTCCCGCAGGCT-TCGAGCTGGTAT
1 TATATCCGGACTTAAAGT-CCGCAGGCTAT-GTGCTGGAAT
** *
89438831 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGGTAAT
1 TATATCCGGACTTAAAGT-CCGCAGGCTATGTGCTGG-AAT
89438870 T
1 T
89438871 GGTTTCAAGT
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
38 16 0.12
39 121 0.88
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (39 bp):
TATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAT
Found at i:89439991 original size:28 final size:28
Alignment explanation
Indices: 89439959--89440016 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
89439949 GGGATAACAG
89439959 AGCTATAAAGAAAAAAGAAGAAAATGAA
1 AGCTATAAAGAAAAAAGAAGAAAATGAA
89439987 AGCTATAAAGAAAAAAGAAGAAAATGAA
1 AGCTATAAAGAAAAAAGAAGAAAATGAA
89440015 AG
1 AG
89440017 GACATGAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.67, C:0.03, G:0.19, T:0.10
Consensus pattern (28 bp):
AGCTATAAAGAAAAAAGAAGAAAATGAA
Found at i:89440707 original size:2 final size:2
Alignment explanation
Indices: 89440700--89440725 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89440690 GTAATTGTTA
89440700 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
89440726 TCTAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89441492 original size:56 final size:56
Alignment explanation
Indices: 89441430--89441543 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
89441420 GGTAAGAAAC
89441430 TAACCCAATACAGTTTTTACGTTTCTAATTTATACCATTTATGCATTTTGCTTACA
1 TAACCCAATACAGTTTTTACGTTTCTAATTTATACCATTTATGCATTTTGCTTACA
89441486 TAACCCAATACAGTTTTTACGTTTCTAATTTATACCATTTATGCATTTTGCTTACA
1 TAACCCAATACAGTTTTTACGTTTCTAATTTATACCATTTATGCATTTTGCTTACA
89441542 TA
1 TA
89441544 TTCCAAGGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (56 bp):
TAACCCAATACAGTTTTTACGTTTCTAATTTATACCATTTATGCATTTTGCTTACA
Found at i:89443239 original size:40 final size:40
Alignment explanation
Indices: 89443202--89443387 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
89443192 GCTACTCGTT
*
89443202 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
89443242 CAGATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
89443282 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
89443322 CGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
89443363 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
89443388 CATCATTCGA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:89451273 original size:40 final size:40
Alignment explanation
Indices: 89451236--89451421 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
89451226 GCTACTCGTT
*
89451236 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
89451276 CAGATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
89451316 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
89451356 CGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
89451397 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
89451422 CATCATTCGA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:89466777 original size:10 final size:10
Alignment explanation
Indices: 89466762--89466789 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
89466752 TTCATCAATG
89466762 GAAACTTTTA
1 GAAACTTTTA
89466772 GAAACTTTTA
1 GAAACTTTTA
89466782 GAAACTTT
1 GAAACTTT
89466790 AATAGTTTTA
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:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (10 bp):
GAAACTTTTA
Found at i:89484680 original size:40 final size:40
Alignment explanation
Indices: 89484631--89484741 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
89484621 TATATACAGG
* *
89484631 TGACACTTAGTGTACGATTCGAGATAGCTTCGGCTATATA
1 TGACACTTAGTGTACGATTCAAAATAGCTTCGGCTATATA
* *
89484671 T-AGCACTTAGTGTGCGATTCAAAATAGCTTCGGCTATATG
1 TGA-CACTTAGTGTACGATTCAAAATAGCTTCGGCTATATA
*
89484711 TGACACTTAGTGTGCTAGATT-AAAATAGCTT
1 TGACACTTAGTGTAC--GATTCAAAATAGCTT
89484742 AGACTATGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
39 1 0.02
40 47 0.75
41 11 0.17
42 4 0.06
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (40 bp):
TGACACTTAGTGTACGATTCAAAATAGCTTCGGCTATATA
Found at i:89486678 original size:22 final size:22
Alignment explanation
Indices: 89486652--89486715 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
89486642 GTTGGGAGTT
*
89486652 AATTGGATTGATTTAACCTTTC
1 AATTGGATTGATTTGACCTTTC
89486674 AATTGGATTGATTTGACCTTTC
1 AATTGGATTGATTTGACCTTTC
89486696 AATTGGATTGATTTGACCTT
1 AATTGGATTGATTTGACCTT
89486716 CTCCATGACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (22 bp):
AATTGGATTGATTTGACCTTTC
Found at i:89494069 original size:46 final size:46
Alignment explanation
Indices: 89494019--89494194 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
89494009 TGGTTGAGCA
89494019 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89494065 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
89494110 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89494158 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89494195 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:89494175 original size:93 final size:93
Alignment explanation
Indices: 89494016--89494187 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
89494006 GGATGGTTGA
* *
89494016 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89494081 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
89494109 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89494174 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
89494188 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:89501589 original size:46 final size:46
Alignment explanation
Indices: 89501539--89501714 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
89501529 TGGTTGAGCA
89501539 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89501585 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
89501630 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89501678 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89501715 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:89501695 original size:93 final size:93
Alignment explanation
Indices: 89501536--89501707 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
89501526 GGATGGTTGA
* *
89501536 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89501601 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
89501629 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89501694 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
89501708 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:89507912 original size:29 final size:29
Alignment explanation
Indices: 89507821--89507981 Score: 182
Period size: 29 Copynumber: 5.6 Consensus size: 29
89507811 TACTCGATTT
* *
89507821 CGCACACTTAGTGCCAT-TCGATTT-AAGCC
1 CGCACACTTAGTGCCATAT--ATTTCCAGCA
* *** * *
89507850 CGCACACATAGTGCCATAGCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
** *
89507879 CGCACACCCAGTGCCGTATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
89507908 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
89507937 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
89507966 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
89507982 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.02
29 109 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:89515135 original size:29 final size:29
Alignment explanation
Indices: 89515044--89515204 Score: 182
Period size: 29 Copynumber: 5.6 Consensus size: 29
89515034 TACTCGATTT
* *
89515044 CGCACACTTAGTGCCAT-TCGATTT-AAGCC
1 CGCACACTTAGTGCCATAT--ATTTCCAGCA
* *** * *
89515073 CGCACACATAGTGCCATAGCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
** *
89515102 CGCACACCCAGTGCCGTATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
89515131 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
89515160 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
89515189 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
89515205 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.02
29 109 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:89519423 original size:43 final size:43
Alignment explanation
Indices: 89519342--89519466 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 43
89519332 GTACAACGAA
* * *
89519342 AACGTCCCAGACGTGGTCTTACATGTAATAACATATCGATG-C
1 AACGTCCCAGACGTGGTCTTACACGAAATCACATATCGATGTC
* * *
89519384 CACTGTCCCAGACAG-GGTCTTACACAAAATCACAAATCGATGTC
1 AAC-GTCCCAGAC-GTGGTCTTACACGAAATCACATATCGATGTC
*
89519428 AACATCCCAGACGTGGTCTTACACGAAATCACATATCGA
1 AACGTCCCAGACGTGGTCTTACACGAAATCACATATCGA
89519467 AATCCTATGT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
42 3 0.04
43 62 0.90
44 4 0.06
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
AACGTCCCAGACGTGGTCTTACACGAAATCACATATCGATGTC
Found at i:89530993 original size:28 final size:28
Alignment explanation
Indices: 89530924--89531024 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
89530914 GACAAGATTG
* * * *
89530924 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
89530954 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
89530982 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
89531011 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
89531025 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:89538550 original size:93 final size:93
Alignment explanation
Indices: 89538442--89538612 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
89538432 GCCCCTAAGT
* * *
89538442 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89538507 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
89538535 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89538600 CGAGTTCGGATGC
66 CGAGTTCGGATGC
89538613 TCAACCATTC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:89538609 original size:46 final size:46
Alignment explanation
Indices: 89538437--89538609 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
89538427 AACCCGCCCC
* * *
89538437 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
89538483 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
89538531 TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
89538576 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
89538610 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:89541282 original size:25 final size:24
Alignment explanation
Indices: 89541254--89541305 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
89541244 GCAAAATCTC
*
89541254 GAGCCATATAACAGGATGCTCATGT
1 GAGCCATATAACAGGAAGCTCAT-T
* *
89541279 GAGCCATGTAATAGGAAGCTCATT
1 GAGCCATATAACAGGAAGCTCATT
89541303 GAG
1 GAG
89541306 TTTAACAGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (24 bp):
GAGCCATATAACAGGAAGCTCATT
Found at i:89541928 original size:21 final size:21
Alignment explanation
Indices: 89541900--89541949 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
89541890 GATCTATACG
*
89541900 AGTA-AATTTAAAATCAATTT
1 AGTACAATTTAAAATCAATTC
* *
89541920 AGTACAATTTATACTCAATTC
1 AGTACAATTTAAAATCAATTC
*
89541941 AGTCCAATT
1 AGTACAATT
89541950 CATATCTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (21 bp):
AGTACAATTTAAAATCAATTC
Found at i:89543873 original size:22 final size:20
Alignment explanation
Indices: 89543847--89543887 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
89543837 TAAATGAAAT
89543847 AAAAGAAACAAAAGCATAAAAC
1 AAAAGAAAC-AAAGC-TAAAAC
89543869 AAAAGAAACAAAGCTAAAA
1 AAAAGAAACAAAGCTAAAA
89543888 AGAAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.73, C:0.12, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAAGAAACAAAGCTAAAAC
Found at i:89544335 original size:17 final size:18
Alignment explanation
Indices: 89544313--89544346 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
89544303 TCAATGAGTT
89544313 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
89544330 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
89544347 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:89544852 original size:21 final size:21
Alignment explanation
Indices: 89544802--89544863 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
89544792 GGCTTTATTG
* *
89544802 ATCAGGCACTTTATGTGTCAT
1 ATCAGGCACCTTGTGTGTCAT
*
89544823 ATTTGAGGCACCTTGTGTGTCAT
1 A--TCAGGCACCTTGTGTGTCAT
*
89544846 ATCAGGCACCTCGTGTGT
1 ATCAGGCACCTTGTGTGT
89544864 TGTTTCATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.47
23 18 0.53
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (21 bp):
ATCAGGCACCTTGTGTGTCAT
Found at i:89554479 original size:35 final size:35
Alignment explanation
Indices: 89554422--89554495 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
89554412 TAATTACTTT
* *
89554422 TTATTAAAGTAAAAATATATTTATTATTTATTATAA
1 TTATTAAAGTAAAAATATATTTATTAATTA-AATAA
*
89554458 TTATT-AAGTTAAAATATATTTATTAATTAAATAA
1 TTATTAAAGTAAAAATATATTTATTAATTAAATAA
89554492 TTAT
1 TTAT
89554496 ATTGTAAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 8 0.23
35 22 0.63
36 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (35 bp):
TTATTAAAGTAAAAATATATTTATTAATTAAATAA
Found at i:89554678 original size:16 final size:16
Alignment explanation
Indices: 89554640--89554681 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
89554630 GTATTATTAT
89554640 TATT-ATTATTAATTTA
1 TATTAATTA-TAATTTA
*
89554656 T-TAAATTATAATTTA
1 TATTAATTATAATTTA
89554671 TATTAATTATA
1 TATTAATTATA
89554682 TTACGAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAATTATAATTTA
Found at i:89554921 original size:22 final size:20
Alignment explanation
Indices: 89554894--89554934 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
89554884 TAAATGAAAT
89554894 AAAAGAAACAAAAGCATAAAAC
1 AAAAGAAAC-AAAGC-TAAAAC
89554916 AAAAGAAACAAAGCTAAAA
1 AAAAGAAACAAAGCTAAAA
89554935 AGAAATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.73, C:0.12, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAAGAAACAAAGCTAAAAC
Found at i:89555385 original size:17 final size:18
Alignment explanation
Indices: 89555363--89555396 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
89555353 TAAATGAGTT
89555363 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
89555380 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
89555397 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:89564433 original size:41 final size:41
Alignment explanation
Indices: 89564387--89564482 Score: 149
Period size: 41 Copynumber: 2.3 Consensus size: 41
89564377 CAAAGCTTGG
*
89564387 TAGGCACAAAGCCTGAATCAATACACCGGCAC-AAAACCTGC
1 TAGGCACAAAGCCTGAATCAATACACCAGCACTAAAA-CTGC
*
89564428 TAGGCACAAAGCCTGAATCAATATACCAGCACTAAAACTGC
1 TAGGCACAAAGCCTGAATCAATACACCAGCACTAAAACTGC
*
89564469 TAGGTACAAAGCCT
1 TAGGCACAAAGCCT
89564483 AAATTGCTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 47 0.92
42 4 0.08
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.16
Consensus pattern (41 bp):
TAGGCACAAAGCCTGAATCAATACACCAGCACTAAAACTGC
Found at i:89578354 original size:19 final size:19
Alignment explanation
Indices: 89578321--89578367 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
89578311 TTTCATAGTT
*
89578321 TATTATTATTATTTTATTCA
1 TATTATT-TTATTTTATTAA
89578341 T-TTATTTTATTTTTATTAA
1 TATTATTTTA-TTTTATTAA
89578360 TATTATTT
1 TATTATTT
89578368 GTGTTTAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
20 7 0.29
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTATTTTATTTTATTAA
Found at i:89587498 original size:40 final size:40
Alignment explanation
Indices: 89587432--89587598 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
89587422 AAATTGAATG
* * *
89587432 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
89587471 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
89587511 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
89587551 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
89587591 ATATCCGG
1 ATATCCGG
89587599 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:89593088 original size:40 final size:40
Alignment explanation
Indices: 89593022--89593188 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
89593012 AAATTGAATG
* * *
89593022 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
89593061 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
89593101 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
89593141 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
89593181 ATATCCGG
1 ATATCCGG
89593189 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:89595051 original size:40 final size:39
Alignment explanation
Indices: 89594945--89595052 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
89594935 TGCTGGAAAT
* * *
89594945 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* * *
89594985 TATATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
*
89595025 TCTATCCGGGCTAAGACCCGAAGGCATT
1 TATATCCGGGCTAAGACCCGAAGGCATT
89595053 TGGCACGTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
39 3 0.05
40 56 0.95
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:89602968 original size:40 final size:40
Alignment explanation
Indices: 89602902--89603068 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
89602892 AAATTGAATG
* * *
89602902 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
89602941 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
89602981 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
89603021 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
89603061 ATATCCGG
1 ATATCCGG
89603069 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:89608853 original size:46 final size:46
Alignment explanation
Indices: 89608803--89608978 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
89608793 TGGTTGAGCA
89608803 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89608849 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
89608894 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89608942 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89608979 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:89608959 original size:93 final size:93
Alignment explanation
Indices: 89608800--89608971 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
89608790 GGATGGTTGA
* *
89608800 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89608865 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
89608893 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89608958 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
89608972 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:89631801 original size:40 final size:39
Alignment explanation
Indices: 89631756--89631963 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
89631746 CGGAATACAA
*
89631756 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
** *
89631796 CCGGATATAACGTCTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
89631836 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
89631876 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
89631916 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
89631956 CCGGATAT
1 CCGGATAT
89631964 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Done.