Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 50 of 91
Found at i:17408198 original size:17 final size:17
Alignment explanation
Indices: 17408172--17408204 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17408162 AAATATGCAC
17408172 ACACTAAGGGGGAGCAT
1 ACACTAAGGGGGAGCAT
*
17408189 ACACTTAGGGGGAGCA
1 ACACTAAGGGGGAGCA
17408205 ATCCTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.18, G:0.36, T:0.12
Consensus pattern (17 bp):
ACACTAAGGGGGAGCAT
Found at i:17409106 original size:33 final size:33
Alignment explanation
Indices: 17409068--17409165 Score: 83
Period size: 33 Copynumber: 2.9 Consensus size: 33
17409058 GAAAAGTTAG
17409068 TTGTTGGGTTTTGGTTGATCCCGTGAAAAACCA-
1 TTGTTGGGTTTTGGTTGA-CCCGTGAAAAACCAC
* * * * *
17409101 TTGTTGTAGGTTGTGGTTGAGCCTTGGAAAATCAC
1 TTGTTG--GGTTTTGGTTGACCCGTGAAAAACCAC
* *
17409136 TT-TGGGGTTTTAGTTGAGCCCGTGAAAAAC
1 TTGTTGGGTTTTGGTTGA-CCCGTGAAAAAC
17409166 TAGTGTAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
32 10 0.20
33 14 0.29
34 12 0.24
35 13 0.27
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (33 bp):
TTGTTGGGTTTTGGTTGACCCGTGAAAAACCAC
Found at i:17428658 original size:29 final size:29
Alignment explanation
Indices: 17428605--17428660 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
17428595 TTTGGTTCAA
* *
17428605 AATAAAAGTATAAGGGCTTAATTGAATAC
1 AATAAAAGTATAAAGACTTAATTGAATAC
17428634 AATAAAAGTATAAAGAC-TAATTTGAAT
1 AATAAAAGTATAAAGACTTAA-TTGAAT
17428661 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (29 bp):
AATAAAAGTATAAAGACTTAATTGAATAC
Found at i:17437068 original size:35 final size:36
Alignment explanation
Indices: 17437029--17437287 Score: 251
Period size: 35 Copynumber: 7.2 Consensus size: 36
17437019 ATTGTTTAAG
*
17437029 TTAATCAATTAGGCCCAATAACTTAATTAAACAA-T
1 TTAATCAATTAGGCCCAATAACTTAATTAAATAATT
* * * *
17437064 TTAATTAATTAAGCTCAATAATTTAATTAAATAATT
1 TTAATCAATTAGGCCCAATAACTTAATTAAATAATT
* * * *
17437100 TTAATCAATTAGGTCAAATGACTTAATTAAACAATT
1 TTAATCAATTAGGCCCAATAACTTAATTAAATAATT
* *
17437136 TTAATCAACTAGGCCCAATGACTTAATTAAATTAAATAATT
1 TTAATCAATTAGGCCCAAT-A---ACTT-AATTAAATAATT
* * *
17437177 TTAATCCATTAGGTCCAATGACTTAATTAAATAA-T
1 TTAATCAATTAGGCCCAATAACTTAATTAAATAATT
* *
17437212 TTAATTAATTAGGCCCAATGACTTAATTAAATAA-T
1 TTAATCAATTAGGCCCAATAACTTAATTAAATAATT
* * * *
17437247 TTAATTAATTAGG--C-ACAACTCAATTAAACAATT
1 TTAATCAATTAGGCCCAATAACTTAATTAAATAATT
17437280 TTAATCAA
1 TTAATCAA
17437288 GTGCTTGAGA
Statistics
Matches: 185, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
32 13 0.07
33 9 0.05
35 75 0.41
36 55 0.30
37 3 0.02
40 3 0.02
41 27 0.15
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (36 bp):
TTAATCAATTAGGCCCAATAACTTAATTAAATAATT
Found at i:17437110 original size:36 final size:35
Alignment explanation
Indices: 17437003--17437257 Score: 204
Period size: 35 Copynumber: 7.0 Consensus size: 35
17436993 AGTCCTTAAG
*** *
17437003 AAGCCCAATTAACTTAATTGTTTAAGTTAATCAATT
1 AAGCCCAA-TAACTTAATTAAATAATTTAATCAATT
* * *
17437039 AGGCCCAATAACTTAATTAAACAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAATAATTTAATCAATT
* *
17437074 AAGCTCAATAATTTAATTAAATAATTTTAATCAATT
1 AAGCCCAATAACTTAATTAAATAA-TTTAATCAATT
* * * * * *
17437110 AGGTCAAATGACTTAATTAAACAATTTTAATCAACT
1 AAGCCCAATAACTTAATTAAATAA-TTTAATCAATT
* * *
17437146 AGGCCCAATGACTTAATTAAATTAAATAATTTTAATCCATT
1 AAGCCCAAT-A---ACTT-AATTAAATAA-TTTAATCAATT
* * * *
17437187 AGGTCCAATGACTTAATTAAATAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAATAATTTAATCAATT
* * *
17437222 AGGCCCAATGACTTAATTAAATAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAATAATTTAATCAATT
17437257 A
1 A
17437258 GGCACAACTC
Statistics
Matches: 180, Mismatches: 33, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
35 85 0.47
36 62 0.34
37 3 0.02
40 3 0.02
41 27 0.15
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (35 bp):
AAGCCCAATAACTTAATTAAATAATTTAATCAATT
Found at i:17437188 original size:77 final size:76
Alignment explanation
Indices: 17437029--17437243 Score: 269
Period size: 77 Copynumber: 2.9 Consensus size: 76
17437019 ATTGTTTAAG
* * * * * * * *
17437029 TTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCTC-A--A--TAATTTA
1 TTAATCAATTAGGTCAAATGACTTAATTAAACAATTTAATCAACTAGGCCCAATGACTTAATTAA
17437089 ATTAAATAATT
66 ATTAAATAATT
17437100 TTAATCAATTAGGTCAAATGACTTAATTAAACAATTTTAATCAACTAGGCCCAATGACTTAATTA
1 TTAATCAATTAGGTCAAATGACTTAATTAAACAA-TTTAATCAACTAGGCCCAATGACTTAATTA
17437165 AATTAAATAATT
65 AATTAAATAATT
* * * * *
17437177 TTAATCCATTAGGTCCAATGACTTAATTAAATAATTTAATTAATTAGGCCCAATGACTTAATTAA
1 TTAATCAATTAGGTCAAATGACTTAATTAAACAATTTAATCAACTAGGCCCAATGACTTAATTAA
17437242 AT
66 AT
17437244 AATTTAATTA
Statistics
Matches: 125, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
71 31 0.25
72 13 0.10
73 1 0.01
75 1 0.01
76 31 0.25
77 48 0.38
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (76 bp):
TTAATCAATTAGGTCAAATGACTTAATTAAACAATTTAATCAACTAGGCCCAATGACTTAATTAA
ATTAAATAATT
Found at i:17443660 original size:20 final size:20
Alignment explanation
Indices: 17443635--17443710 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
17443625 CCTGGTTGCT
17443635 ATCTATCGATAGATGT-GTCC
1 ATCTATCGATAGATGTAG-CC
*
17443655 ATCTATCGATAGATTTAGCC
1 ATCTATCGATAGATGTAGCC
** *
17443675 ATCTAGGGATAGATCTAGCC
1 ATCTATCGATAGATGTAGCC
*
17443695 ATCTATCCATAGATGT
1 ATCTATCGATAGATGT
17443711 TCTTCAGTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 46 0.98
21 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (20 bp):
ATCTATCGATAGATGTAGCC
Found at i:17446060 original size:42 final size:42
Alignment explanation
Indices: 17446000--17446117 Score: 182
Period size: 42 Copynumber: 2.8 Consensus size: 42
17445990 GTGGACCCAG
**
17446000 CTATGTGCTAGTAGGAGTGCACCTAAGCCGTTGCTGACCCGA
1 CTATGTGCTAGTAGGAGTGCACAGAAGCCGTTGCTGACCCGA
* * *
17446042 CTATGTGCGAGTAAGAGTGCACAGAAGCCGTTGCTGACCCGG
1 CTATGTGCTAGTAGGAGTGCACAGAAGCCGTTGCTGACCCGA
*
17446084 CTATGTGCTAGTGGGAGTGCACAGAAGCCGTTGC
1 CTATGTGCTAGTAGGAGTGCACAGAAGCCGTTGC
17446118 ATATGAGATG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.22
Consensus pattern (42 bp):
CTATGTGCTAGTAGGAGTGCACAGAAGCCGTTGCTGACCCGA
Found at i:17448689 original size:87 final size:87
Alignment explanation
Indices: 17448537--17448703 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 87
17448527 CATGCTTCTG
* *
17448537 TGAGTGGCATATCAACCTCACCCATAATCTTTGAGTGATCCCACCCCACTCAAGAAAATAGTGAT
1 TGAGTGACATATCAACCTCACCCATAATCTTTGAGTGATCCCACCCCACTCAAGAAAATAATGAT
17448602 CAATC-CCCATTATCATCATTTC
66 CAA-CGCCCATTATCATCATTTC
* * * * * ***
17448624 TGAGTGACATATCAGCCTCACCCATAATCTTTTAGTGGTCCCACCCCACTTATGGGGATAATGAT
1 TGAGTGACATATCAACCTCACCCATAATCTTTGAGTGATCCCACCCCACTCAAGAAAATAATGAT
17448689 CAACGCCCATTATCA
66 CAACGCCCATTATCA
17448704 CATAGGATTC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
86 1 0.01
87 68 0.99
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (87 bp):
TGAGTGACATATCAACCTCACCCATAATCTTTGAGTGATCCCACCCCACTCAAGAAAATAATGAT
CAACGCCCATTATCATCATTTC
Found at i:17449013 original size:80 final size:80
Alignment explanation
Indices: 17448776--17448999 Score: 270
Period size: 80 Copynumber: 2.8 Consensus size: 80
17448766 TCTCATATTT
* ** * * ** * * *
17448776 AGCCCATAATGTATATGAAATTCTCAACACATACATCTTACAACATACATTTCACAATC-CTTTA
1 AGCCCATAGTGTGCATGATATTCTCAACACATACATCTCATGACATACATGTCATAATCTC-ATA
* * *
17448840 AATCATTCCCATGCTT
65 AATCATACACATGCTC
** *
17448856 AGCCCATAGTGTGCATGATATTCTCAACACATACATCTCATGGGATACATGTCATAATGTCATAA
1 AGCCCATAGTGTGCATGATATTCTCAACACATACATCTCATGACATACATGTCATAATCTCATAA
*
17448921 ATCATTCACATGCTC
66 ATCATACACATGCTC
*
17448936 AGCCCATAGTGTGCATGATATTCTTAACACATACATCTCATGACATACATGTCATAATCTCATA
1 AGCCCATAGTGTGCATGATATTCTCAACACATACATCTCATGACATACATGTCATAATCTCATA
17449000 GATGGAACTC
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 123 0.99
81 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (80 bp):
AGCCCATAGTGTGCATGATATTCTCAACACATACATCTCATGACATACATGTCATAATCTCATAA
ATCATACACATGCTC
Found at i:17450558 original size:2 final size:2
Alignment explanation
Indices: 17450553--17450580 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17450543 TATATATATA
17450553 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17450581 ATAGAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17466470 original size:45 final size:45
Alignment explanation
Indices: 17466395--17466744 Score: 399
Period size: 45 Copynumber: 7.8 Consensus size: 45
17466385 TGATATGGAA
* * ** * * *
17466395 ACTGCCAACGCCATCTCTTTCTTTGTCTTCTCAGATGAGCCATTC
1 ACTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
* * *
17466440 ACTGTCAAAGGCATCTCTTTCTTCATCTTCTCAGCCGAGATATTT
1 ACTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
*
17466485 AGTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
1 ACTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
* *
17466530 ACAGTCAAAGCCGTCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
1 ACTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
* *
17466575 ACTGTCAAAGCCGTCTCTTTCTTCATCTTCTCAGCCGAGCTATTT
1 ACTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
*
17466620 ACCGT---AG-CAGTCTCTTT-TCTCATCTTCTCAGCTGAGCTATTT
1 ACTGTCAAAGCCA-TCTCTTTCT-TCATCTTCTCAGCTGAGCTATTT
* * *
17466662 ACTGTC-ATGACCGTCTCTTTCTTCATCTTCTCAGCTGAGCTATCT
1 ACTGTCAAAG-CCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
* * * **
17466707 A-TGGTCACATCCATCTCTTTGTTTGTCTTCTCAGCTGA
1 ACT-GTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGA
17466745 ACTGTTCAGG
Statistics
Matches: 263, Mismatches: 33, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
41 2 0.01
42 35 0.13
44 2 0.01
45 222 0.84
46 2 0.01
ACGTcount: A:0.18, C:0.29, G:0.14, T:0.39
Consensus pattern (45 bp):
ACTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
Found at i:17466724 original size:132 final size:133
Alignment explanation
Indices: 17466408--17466741 Score: 410
Period size: 132 Copynumber: 2.5 Consensus size: 133
17466398 GCCAACGCCA
** * * *
17466408 TCTCTTTCTTTGTCTTCTCAGATGAGCCAT-TCACTGTCAAAGGCATCTCTTTCTTCATCTTCTC
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATCT-ACTGTCAAAGCCATCTCTTTCTTCATCTTCTC
**
17466472 AGCCGAGATATTTAGTGTCAAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACAGTCA
65 AGCCGAGATATTTACCGT--AAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACAGTCA
17466537 AAGCCG
128 AAGCCG
* *
17466543 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAAGCCGTCTCTTTCTTCATCTTCTCA
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATCTACTGTCAAAGCCATCTCTTTCTTCATCTTCTCA
* *
17466608 GCCGAGCTATTTACCGT-AG-CAGTCTCTTT-TCTCATCTTCTCAGCTGAGCTATTTACTGTC-A
66 GCCGAGATATTTACCGTAAGCCA-TCTCTTTCT-TCATCTTCTCAGCTGAGCTATTTACAGTCAA
*
17466669 TGACCG
129 AG-CCG
* * * **
17466675 TCTCTTTCTTCATCTTCTCAGCTGAGCTATCTA-TGGTCACATCCATCTCTTTGTTTGTCTTCTC
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATCTACT-GTCAAAGCCATCTCTTTCTTCATCTTCTC
17466739 AGC
65 AGC
17466742 TGAACTGTTC
Statistics
Matches: 176, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
131 6 0.03
132 98 0.56
135 71 0.40
136 1 0.01
ACGTcount: A:0.18, C:0.29, G:0.13, T:0.40
Consensus pattern (133 bp):
TCTCTTTCTTCATCTTCTCAGCTGAGCTATCTACTGTCAAAGCCATCTCTTTCTTCATCTTCTCA
GCCGAGATATTTACCGTAAGCCATCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACAGTCAAAG
CCG
Found at i:17469966 original size:87 final size:87
Alignment explanation
Indices: 17469820--17469994 Score: 296
Period size: 87 Copynumber: 2.0 Consensus size: 87
17469810 CATAAGACCC
* * * *
17469820 TGGAAACTCAGAACCAGAGTTTGCATCATTGGGTGGCATAGTTTGAGAACTAGCTCTGAATCTAA
1 TGGAAACACAAAAACAGAGTTTGCATCATTGGATGGCATAGTTTGAGAACTAGCTCTGAATCTAA
17469885 GATGGGACAATATATCACAAGT
66 GATGGGACAATATATCACAAGT
*
17469907 TGGAAACACAAAAACAGAGTTTGCATCATTGGATGGCGTAGTTTGAGAACTAGCTCTGAATCTAA
1 TGGAAACACAAAAACAGAGTTTGCATCATTGGATGGCATAGTTTGAGAACTAGCTCTGAATCTAA
*
17469972 GATGGGACAATATCTCACAAGT
66 GATGGGACAATATATCACAAGT
17469994 T
1 T
17469995 AATAAGCTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (87 bp):
TGGAAACACAAAAACAGAGTTTGCATCATTGGATGGCATAGTTTGAGAACTAGCTCTGAATCTAA
GATGGGACAATATATCACAAGT
Found at i:17475026 original size:56 final size:55
Alignment explanation
Indices: 17474951--17475062 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 55
17474941 CTCTTGAGGA
17474951 TCAAAGTCTTGAAAGAAAATTAGAGAAACCAGGCCTTCTTGAGCAAAACTTTCTT
1 TCAAAGTCTTGAAAGAAAATTAGAGAAACCAGGCCTTCTTGAGCAAAACTTTCTT
17475006 TNCAAAGTCTTGAAAGAAAATTAGAGAAACCAGGCCTTCTTGAGCAAAACTTTCTT
1 T-CAAAGTCTTGAAAGAAAATTAGAGAAACCAGGCCTTCTTGAGCAAAACTTTCTT
17475062 T
1 T
17475063 GTGCTTTCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 1 0.02
56 55 0.98
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (55 bp):
TCAAAGTCTTGAAAGAAAATTAGAGAAACCAGGCCTTCTTGAGCAAAACTTTCTT
Found at i:17477059 original size:71 final size:71
Alignment explanation
Indices: 17476873--17477063 Score: 233
Period size: 71 Copynumber: 2.7 Consensus size: 71
17476863 AGTAATCCTC
* * *
17476873 AAGGAAGGGTATCAATACCTAGCCAATAGAATGCCCTAAAAGGTATTCTATGTATAATGTATCAA
1 AAGGAAGGGTATCGATACCTAGCCAATAGAATGCCCTAAAAGGCATTTTATGTATAATGTATCAA
17476938 TATCTT
66 TATCTT
* * * * *
17476944 AAAGAACGGTATCGATACCTGGCCAATAGAATGCCTTAAGAGGCATTTTATGTATAATGTATCAA
1 AAGGAAGGGTATCGATACCTAGCCAATAGAATGCCCTAAAAGGCATTTTATGTATAATGTATCAA
17477009 TA-CTTT
66 TATC-TT
* * * * *
17477015 ATGGAAGGGTATCGATACCTAG-CAACCAAAATTCCCCAAAAGGCATTTT
1 AAGGAAGGGTATCGATACCTAGCCAA-TAGAATGCCCTAAAAGGCATTTT
17477064 GTATTAAAAG
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
70 4 0.04
71 96 0.96
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (71 bp):
AAGGAAGGGTATCGATACCTAGCCAATAGAATGCCCTAAAAGGCATTTTATGTATAATGTATCAA
TATCTT
Found at i:17482542 original size:43 final size:43
Alignment explanation
Indices: 17482427--17482545 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
17482417 CTCAGCTATA
* **
17482427 TGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCTGTTATG
1 TGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCCATG
* *
17482470 TGCGAGTAGAGAGTGCGCATAACCCGGTGATGACCCAGCCATG
1 TGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCCATG
* * *
17482513 TGCGAGTAGGGAGTACGCATGAGCTGGTGATGA
1 TGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
17482546 TGATGATGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.19
Consensus pattern (43 bp):
TGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCCATG
Found at i:17482896 original size:21 final size:22
Alignment explanation
Indices: 17482848--17482905 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
17482838 GGCCGAAAAC
*
17482848 TCGCTGCAGCGAGGATGCATTT
1 TCGCTGCAGCGAGAATGCATTT
*
17482870 TCGCTGCAGCGA-AATTCATTCT
1 TCGCTGCAGCGAGAATGCATT-T
*
17482892 T-GCTGCAGTGAGAA
1 TCGCTGCAGCGAGAA
17482906 ACTTTTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (22 bp):
TCGCTGCAGCGAGAATGCATTT
Found at i:17482994 original size:49 final size:49
Alignment explanation
Indices: 17482901--17482994 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
17482891 TTGCTGCAGT
* * * *
17482901 GAGAAACTTTTTGTTTTAGGGTTACAATTTCACTACAACGAGATTCAGC
1 GAGAAACATTCTGTTTTAGGGTCACAATTTCACTACAACAAGATTCAGC
* *
17482950 GAGAAACATTCTGTTTCT-GGGTCACAATTTCACTGCAGCAAGATT
1 GAGAAACATTCTGTTT-TAGGGTCACAATTTCACTACAACAAGATT
17482995 GAATCTCGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 37 0.97
50 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (49 bp):
GAGAAACATTCTGTTTTAGGGTCACAATTTCACTACAACAAGATTCAGC
Found at i:17495112 original size:591 final size:591
Alignment explanation
Indices: 17493923--17495063 Score: 1408
Period size: 591 Copynumber: 1.9 Consensus size: 591
17493913 ATTTAAAAAT
* *
17493923 TTTAAAAATAGTCATTGTTTTTTATAAAATTCAATCAAGTTTTTATATTTTTATTTTAAGGTAAA
1 TTTAAAAATAGTCATTGGTTTTTATAAAATTCAATCAAGTTTTTATATTTTTATTTTAAAGTAAA
* * * **
17493988 TAGGTAGACCCATATGACTAATACTTGATTAATTATTATTAATCGAAATATCACTTGTCATTTAA
66 TAGGTAGACCCA-ATGACTAATACTTGATTAATTATCATTAATCAAAATATAACTTACCATTTAA
* * * *
17494053 TACTCACATGATGCTGATGTGAAAGGTAAAAAATATCACTTGACATGTCATTATGCTACTTCAGC
130 TACTCACATGATACTAAAGTGAAAGGTAAAAAATATCACTTAACATGTCATTATGCTACTTCAGC
* * * * *
17494118 ATACTACATCAATATCACATAACATAGAATGATAAATAATATTTTGATTAATATTAATTAGTTAA
195 ATACTACATCAATATCACATAACATAAAATAATAAATAATATTTTGATTAACATTAATCAATTAA
* * ** * * *
17494183 TTATTACTAATAACGGTTTATTGGGTTTAAAATTAAAGTGTAAAGGGGCATTTGGTACTTCATTA
260 TGATTACTAATAAAGGTTTATTGGACTCAAAATTAAAGTATAAAAGGGCATTTGGTACTTCATTA
* * * **
17494248 ACGTTGCAACATTTGGTAATACATGAGAAAGTGGTGATTGTAGGGAATGTGATTATTAGGAACAT
325 ACATTGCAACATTTGATAATACATGAGAAAATGGTGATTGTAGGGAATGCAATTATTAGGAACAT
* * *
17494313 TACTTTATAATATTTGATTTGAAAAGAATAAGGCTAAAGAAGGTTAGGAAAATTTGGGGAAAAAA
390 TA--TTATAATATTTGATTTGAAAAGAATAAGGCCAAAGAAGGTCAAGAAAATTTGGGGAAAAAA
* * *
17494378 AAATTTCCCTTTGCAAAAGGAAACTTGCTTTCCCCTAGTGATGGAAGGGAATAACATTCCCTTTG
453 AAATTTCCCTTTGCAAAAGGAAACTTACTTTCCCCTAGTAATAGAAGGGAATAACATTCCCTTTG
** *** * *
17494443 CCCATTGTAATGTCATTACAATGGGAAGACTTTACCATTAAGTTTGATTGAACGTATTAATAAAA
518 CCCATTGTAATGTCATTACAATAAGAAGACTTTACCATT-AGTTTGACAAAACGAATGAATAAAA
17494508 GAATGACTTA
582 GAATGACTTA
* *
17494518 TTTAAAAATAGTCATTGGTTTTTATAAAATTCAATTAAGTTTTTGTATTTTTATTTTAAAGTAAA
1 TTTAAAAATAGTCATTGGTTTTTATAAAATTCAATCAAGTTTTTATATTTTTATTTTAAAGTAAA
*** *
17494583 TAGGTAGGTTC-AT-A-T-A-ACTTGATTAATTATCATTAATCAAAATATAATTTACCATTTTAA
66 TAGGTAGACCCAATGACTAATACTTGATTAATTATCATTAATCAAAATATAACTTACCA-TTTAA
* * * *
17494643 TACTCACATGATACTAAAGTGAAAAGGTGAAAAATGTCACTTAATATGTCATTATGCTACTT-TG
130 TACTCACATGATACTAAAGTG-AAAGGTAAAAAATATCACTTAACATGTCATTATGCTACTTCAG
** * * * *
17494707 ACATGTTATATCAATATCATATGACATAAAATAATAAATAATATTTTGATTAACATTAGTCAATT
194 -CATACTACATCAATATCACATAACATAAAATAATAAATAATATTTTGATTAACATTAATCAATT
* ** **
17494772 AATGATTAGTGGTAAAGGTTTATTGGACTCAAAATTAAAGTATAAAAGGGTGTTTGGTAC-TCTA
258 AATGATTACTAATAAAGGTTTATTGGACTCAAAATTAAAGTATAAAAGGGCATTTGGTACTTC-A
* *
17494836 TTAACATTGCAACATTTGATAATAGAT-AGGAAAATGGTGATTGTAGGGAATGCAATTATTTGGA
322 TTAACATTGCAACATTTGATAATACATGA-GAAAATGGTGATTGTAGGGAATGCAATTATTAGGA
* * * * * *
17494900 AGATTA-T-T-ATGTTTGATTTGAAAGGAATAAGGCCAATGAGGGTCAAGACAATTT-GGGAAAA
386 ACATTATTATAATATTTGATTTGAAAAGAATAAGGCCAAAGAAGGTCAAGAAAATTTGGGGAAAA
** ** *
17494961 AAAAATTTTTTTCTTTGCAAAAGGAAACTTACTTTCCCCTAGTAATAGAAGGGAATGGCATTCTC
451 AAAAA--TTTCCCTTTGCAAAAGGAAACTTACTTTCCCCTAGTAATAGAAGGGAATAACATTCCC
17495026 TTTGCCCATTGTAAT-TACATTACAATAAGAAGACTTTA
514 TTTGCCCATTGTAATGT-CATTACAATAAGAAGACTTTA
17495064 TCCTGTGTTT
Statistics
Matches: 468, Mismatches: 70, Indels: 24
0.83 0.12 0.04
Matches are distributed among these distances:
585 12 0.03
586 39 0.08
587 85 0.18
588 1 0.00
589 32 0.07
590 28 0.06
591 199 0.43
592 1 0.00
593 2 0.00
595 69 0.15
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (591 bp):
TTTAAAAATAGTCATTGGTTTTTATAAAATTCAATCAAGTTTTTATATTTTTATTTTAAAGTAAA
TAGGTAGACCCAATGACTAATACTTGATTAATTATCATTAATCAAAATATAACTTACCATTTAAT
ACTCACATGATACTAAAGTGAAAGGTAAAAAATATCACTTAACATGTCATTATGCTACTTCAGCA
TACTACATCAATATCACATAACATAAAATAATAAATAATATTTTGATTAACATTAATCAATTAAT
GATTACTAATAAAGGTTTATTGGACTCAAAATTAAAGTATAAAAGGGCATTTGGTACTTCATTAA
CATTGCAACATTTGATAATACATGAGAAAATGGTGATTGTAGGGAATGCAATTATTAGGAACATT
ATTATAATATTTGATTTGAAAAGAATAAGGCCAAAGAAGGTCAAGAAAATTTGGGGAAAAAAAAA
TTTCCCTTTGCAAAAGGAAACTTACTTTCCCCTAGTAATAGAAGGGAATAACATTCCCTTTGCCC
ATTGTAATGTCATTACAATAAGAAGACTTTACCATTAGTTTGACAAAACGAATGAATAAAAGAAT
GACTTA
Found at i:17504723 original size:20 final size:23
Alignment explanation
Indices: 17504684--17504725 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
17504674 CCCTTCATTG
17504684 ATTCTTCATGTTTGTCTCCCCTT
1 ATTCTTCATGTTTGTCTCCCCTT
17504707 ATTCTTC-TG-TT-TCTCCCCT
1 ATTCTTCATGTTTGTCTCCCCT
17504726 GATATCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 2 0.11
23 7 0.37
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.52
Consensus pattern (23 bp):
ATTCTTCATGTTTGTCTCCCCTT
Found at i:17507891 original size:87 final size:87
Alignment explanation
Indices: 17507745--17507990 Score: 429
Period size: 87 Copynumber: 2.8 Consensus size: 87
17507735 ACGCAGTGAA
*
17507745 GTCCTTTGTTGATATGTATTCATACAAATGTCATCTATCTCTACGGAAATAGATAATGAATATAT
1 GTCCTTTGTTGATATGTATTCATACAAATGTCATCTATCTCTACGAAAATAGATAATGAATATAT
*
17507810 GTATATAGTGACACAATTATAC
66 GTATATAGCGACACAATTATAC
* *
17507832 GTCCTTTGTTGATATGTATTCATACAAATGTTATCTATCTCTACGAAAATAGATGATGAATATAT
1 GTCCTTTGTTGATATGTATTCATACAAATGTCATCTATCTCTACGAAAATAGATAATGAATATAT
17507897 GTATATAGCGACACAATTATAC
66 GTATATAGCGACACAATTATAC
* *
17507919 GTCCTTTGTTGATATATATTCATACAAATGTCATCTATCTCTACGAAAATAAATAATGAATATAT
1 GTCCTTTGTTGATATGTATTCATACAAATGTCATCTATCTCTACGAAAATAGATAATGAATATAT
*
17507984 ATATATA
66 GTATATA
17507991 TATATATATA
Statistics
Matches: 150, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 150 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (87 bp):
GTCCTTTGTTGATATGTATTCATACAAATGTCATCTATCTCTACGAAAATAGATAATGAATATAT
GTATATAGCGACACAATTATAC
Found at i:17507985 original size:2 final size:2
Alignment explanation
Indices: 17507978--17508016 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17507968 TAAATAATGA
17507978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17508017 GNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17509210 original size:14 final size:15
Alignment explanation
Indices: 17509178--17509215 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
17509168 ATATTTTATT
17509178 TTATAATTTAAACATTA
1 TTATAA-TTAAACA-TA
17509195 TTATAATTAAAC-TA
1 TTATAATTAAACATA
17509209 TTATAAT
1 TTATAAT
17509216 ATTAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
16 6 0.29
17 6 0.29
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATAATTAAACATA
Found at i:17509219 original size:16 final size:15
Alignment explanation
Indices: 17509178--17509220 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
17509168 ATATTTTATT
17509178 TTATAAT-TTAAACA
1 TTATAATATTAAACA
*
17509192 TTATTATAATTAAACTA
1 TTATAAT-ATTAAAC-A
17509209 TTATAATATTAA
1 TTATAATATTAA
17509221 TAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.25
16 11 0.46
17 7 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATAATATTAAACA
Found at i:17511407 original size:42 final size:42
Alignment explanation
Indices: 17511340--17511436 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
17511330 GTAATGATAT
17511340 TGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
1 TGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
* *
17511382 TGACTCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
1 TGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
17511424 TGACCCGGCTATG
1 TGACCCGGCTATG
17511437 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.21
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
Found at i:17515303 original size:21 final size:21
Alignment explanation
Indices: 17515261--17515303 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17515251 GTTTTATGGC
* *
17515261 ATGAATTTCGCTACAACGAGA
1 ATGAATCTCGCTACAACAAGA
* *
17515282 ATGAATCTCGCTGCAGCAAGA
1 ATGAATCTCGCTACAACAAGA
17515303 A
1 A
17515304 ACCTTCTGTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
ATGAATCTCGCTACAACAAGA
Found at i:17517448 original size:72 final size:71
Alignment explanation
Indices: 17517330--17517716 Score: 388
Period size: 71 Copynumber: 5.4 Consensus size: 71
17517320 TCTAATAATG
* * * * * *
17517330 GGATAGTGTTA-TTTCCCCTTCACTATCAAGGGAACACGATCTAGTGCGTTTAGCCACTAACCTT
1 GGATAGTGATATTTTCCCC-TCACTATCAAGGGAATATGGTCTAGTGCATTTAGCCACTGACCTT
*
17517394 ATTTACA-A
65 A-AT-CATA
* * * * * *
17517402 GGATAGTAATATTTTCCCTTCACTATCAAGGGAATATGGTCCAGTGCATTCAACCATTGACCTTA
1 GGATAGTGATATTTTCCCCTCACTATCAAGGGAATATGGTCTAGTGCATTTAGCCACTGACCTTA
17517467 ATCATA
66 ATCATA
* *
17517473 GGATAGTGATATTTTCCCCTCACTATCAAGGGAATATGGTCTAGTGCATTTAGCCATTGATCTTA
1 GGATAGTGATATTTTCCCCTCACTATCAAGGGAATATGGTCTAGTGCATTTAGCCACTGACCTTA
17517538 ATCATA
66 ATCATA
* * * *
17517544 GGATAGTGATATTTTCCCCTCGCTATCAAGGGAATATGGTTTAGTGCATTTAGCCACTTATCTTA
1 GGATAGTGATATTTTCCCCTCACTATCAAGGGAATATGGTCTAGTGCATTTAGCCACTGACCTTA
*
17517609 ATAATA
66 ATCATA
* * * * * * * * * * * *
17517615 GGATAATAATA-CTTCCCTTTCACTTTCAAGGGCATACGATCCAGTGTAATCAGCCTA-TGACCT
1 GGATAGTGATATTTTCCC-CTCACTATCAAGGGAATATGGTCTAGTGCATTTAGCC-ACTGACCT
*
17517678 TAATCATG
64 TAATCATA
17517686 GGATAGTGATA-TTTCCCCTTCACTATCAAGG
1 GGATAGTGATATTTTCCCC-TCACTATCAAGG
17517717 AAATTCCTCT
Statistics
Matches: 263, Mismatches: 47, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
70 7 0.03
71 203 0.77
72 47 0.18
73 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (71 bp):
GGATAGTGATATTTTCCCCTCACTATCAAGGGAATATGGTCTAGTGCATTTAGCCACTGACCTTA
ATCATA
Found at i:17517698 original size:213 final size:214
Alignment explanation
Indices: 17517330--17517716 Score: 507
Period size: 213 Copynumber: 1.8 Consensus size: 214
17517320 TCTAATAATG
* *
17517330 GGATAGTGTTATTTCCCCTTCACTATCAAGGGAACACGATCTAGTGCGTTTAGCCACTAACCTTA
1 GGATAGTGATATTTCCCCTTCACTATCAAGGGAACACGATCTAGTGCATTTAGCCACTAACCTTA
* * * * * *
17517395 TTTACAAGGATAGTAATATTTTCCCTTCACTATCAAGGGAATATGGTCCAGTGCATTCAACCATT
66 TATACAAGGATAATAATATCTTCCCTTCACTATCAAGGGAATACGATCCAGTGCAATCAACCATT
17517460 GACCTTAATCATAGGATAGTGATATTTTCCCC-TCACTATCAAGGGAATATGGTCTAGTGCATTT
131 GACCTTAATCATAGGATAGTGATA-TTTCCCCTTCACTATCAAGGGAATATGGTCTAGTGCATTT
17517524 AGCCATTGATCTTAATCATA
195 AGCCATTGATCTTAATCATA
* * * * * * *
17517544 GGATAGTGATATTTTCCCC-TCGCTATCAAGGGAATATGGTTTAGTGCATTTAGCCACTTATCTT
1 GGATAGTGATA-TTTCCCCTTCACTATCAAGGGAACACGATCTAGTGCATTTAGCCACTAACCTT
* * * *
17517608 A-ATA-ATAGGATAATAATA-CTTCCCTTTCACTTTCAAGGGCATACGATCCAGTGTAATCAGCC
65 ATATACA-AGGATAATAATATCTTCCC-TTCACTATCAAGGGAATACGATCCAGTGCAATCAACC
*
17517670 -TATGACCTTAATCATGGGATAGTGATATTTCCCCTTCACTATCAAGG
128 AT-TGACCTTAATCATAGGATAGTGATATTTCCCCTTCACTATCAAGG
17517717 AAATTCCTCT
Statistics
Matches: 148, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
212 14 0.09
213 79 0.53
214 48 0.32
215 7 0.05
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (214 bp):
GGATAGTGATATTTCCCCTTCACTATCAAGGGAACACGATCTAGTGCATTTAGCCACTAACCTTA
TATACAAGGATAATAATATCTTCCCTTCACTATCAAGGGAATACGATCCAGTGCAATCAACCATT
GACCTTAATCATAGGATAGTGATATTTCCCCTTCACTATCAAGGGAATATGGTCTAGTGCATTTA
GCCATTGATCTTAATCATA
Found at i:17520591 original size:16 final size:18
Alignment explanation
Indices: 17520556--17520597 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
17520546 TGATCTAAAC
*
17520556 AATTAAAATCAAATAATT
1 AATTAAACTCAAATAATT
17520574 AATTAAACT-AAA-AATT
1 AATTAAACTCAAATAATT
*
17520590 AACTAAAC
1 AATTAAAC
17520598 CTAATTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTAAACTCAAATAATT
Found at i:17529227 original size:19 final size:20
Alignment explanation
Indices: 17529200--17529245 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
17529190 AGGAGACAAG
*
17529200 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
17529219 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
17529238 ATAATATT
1 ATAATATT
17529246 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:17538933 original size:13 final size:13
Alignment explanation
Indices: 17538915--17538939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17538905 AGAGAAATTG
17538915 TGATTTTATAAAA
1 TGATTTTATAAAA
17538928 TGATTTTATAAA
1 TGATTTTATAAA
17538940 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17561411 original size:13 final size:14
Alignment explanation
Indices: 17561395--17561423 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17561385 TTATTTTTTA
17561395 TTTATTTA-TCATT
1 TTTATTTATTCATT
17561408 TTTATTTATTCATT
1 TTTATTTATTCATT
17561422 TT
1 TT
17561424 ATATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTATTCATT
Found at i:17565313 original size:18 final size:18
Alignment explanation
Indices: 17565290--17565327 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17565280 TGATGCCTTC
*
17565290 TTTTTTTCTTTCTTTCTT
1 TTTTTTTCTTTCTCTCTT
*
17565308 TTTTTTTTTTTCTCTCTT
1 TTTTTTTCTTTCTCTCTT
17565326 TT
1 TT
17565328 CCCATAAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTTTCTCTCTT
Found at i:17567587 original size:25 final size:25
Alignment explanation
Indices: 17567549--17567598 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17567539 GATAGAGTTT
** * *
17567549 GGGTTTTGGGAAAAGGGTTTGAGTG
1 GGGTTTTGAAAAAAGAGTTTCAGTG
17567574 GGGTTTTGAAAAAAGAGTTTCAGTG
1 GGGTTTTGAAAAAAGAGTTTCAGTG
17567599 TGGAAACCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.40, T:0.32
Consensus pattern (25 bp):
GGGTTTTGAAAAAAGAGTTTCAGTG
Found at i:17568703 original size:23 final size:23
Alignment explanation
Indices: 17568654--17568706 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
17568644 GTTTAGAGTT
* * * *
17568654 TGTGAAACGTCATGGTGGGAAGG
1 TGTGACACATCATGGTGAGAAGA
*
17568677 TGTGACACATCATGGTGAGAATA
1 TGTGACACATCATGGTGAGAAGA
17568700 TGTGACA
1 TGTGACA
17568707 TGTTAAGGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (23 bp):
TGTGACACATCATGGTGAGAAGA
Found at i:17568753 original size:23 final size:23
Alignment explanation
Indices: 17568724--17568784 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
17568714 GTTTAAAGTT
17568724 TGTGACAC-ACCATGGAGGGCATA
1 TGTGACACGA-CATGGAGGGCATA
* *
17568747 TGTGACACGACTTGGAGGGGATA
1 TGTGACACGACATGGAGGGCATA
*
17568770 TGTGAGACGACATGG
1 TGTGACACGACATGG
17568785 TGAGAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.20
Consensus pattern (23 bp):
TGTGACACGACATGGAGGGCATA
Found at i:17568793 original size:23 final size:23
Alignment explanation
Indices: 17568724--17568799 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
17568714 GTTTAAAGTT
* *
17568724 TGTGACAC-ACCATGGAGGGCATA
1 TGTGACACGA-CATGGAGAGAATA
* * *
17568747 TGTGACACGACTTGGAGGGGATA
1 TGTGACACGACATGGAGAGAATA
* *
17568770 TGTGAGACGACATGGTGAGAATA
1 TGTGACACGACATGGAGAGAATA
*
17568793 TATGACA
1 TGTGACA
17568800 TGTTAGTGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (23 bp):
TGTGACACGACATGGAGAGAATA
Found at i:17569345 original size:27 final size:27
Alignment explanation
Indices: 17569315--17569402 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
17569305 TATCTAAGGG
*
17569315 CAAAATGATAATTTTACCACTCGAGGA
1 CAAAATGATAATTTTGCCACTCGAGGA
* *
17569342 CAAAATGGTAAGTTTGCCACTCGAGGA
1 CAAAATGATAATTTTGCCACTCGAGGA
*
17569369 CAAAATGATAATTTTGCCACTCGAGAA
1 CAAAATGATAATTTTGCCACTCGAGGA
*
17569396 TAAAATG
1 CAAAATG
17569403 GGAAGTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (27 bp):
CAAAATGATAATTTTGCCACTCGAGGA
Found at i:17574972 original size:28 final size:27
Alignment explanation
Indices: 17574927--17574979 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
17574917 ATGTCCTGGT
* * *
17574927 GGTGGAAAATTACGATTTTGCCCATGA
1 GGTGGAAAATGACCATTTTACCCATGA
17574954 GGTGGTAAAATGACCATTTTACCCAT
1 GGTGG-AAAATGACCATTTTACCCAT
17574980 ATACTCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATGACCATTTTACCCATGA
Found at i:17578338 original size:38 final size:39
Alignment explanation
Indices: 17578296--17578398 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 39
17578286 ATAGTGCCTG
17578296 TGTGCACGATGTGGGGGGATGTACACAATGGCACT-G-A
1 TGTGCACGATGTGGGGGGATGTACACAATGGCACTGGCA
* * **
17578333 TTGTGCACGATGTGGGGGGATGCACACGATGGTGCTGGCCA
1 -TGTGCACGATGTGGGGGGATGTACACAATGGCACTGG-CA
17578374 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
17578399 TGAGCCGGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
38 31 0.54
39 1 0.02
40 24 0.42
41 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.22
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGTACACAATGGCACTGGCA
Found at i:17578829 original size:60 final size:59
Alignment explanation
Indices: 17578729--17578889 Score: 171
Period size: 60 Copynumber: 2.7 Consensus size: 59
17578719 TTCTCGTTGT
* * * *
17578729 AGCGAAAAAGAAATCTCGCTACAGCAAAAAACTCTCTGTTTCATCAGTT-GAATTTCGCTGC
1 AGCGAGAAAG-AATCTCGCTACAGCAAAAACCT-TCTGTTT-ATCAGTTACAATTTCGCCGC
* * * **
17578790 AGCGAGAAAGAATCTTGCTACAGCAAGAAACCTTTTGTTTTTGGGTTACAATTTCGCCGC
1 AGCGAGAAAGAATCTCGCTACAGCAA-AAACCTTCTGTTTATCAGTTACAATTTCGCCGC
* *
17578850 AACGAGAAAGAATCTCGCTGCAGCGAAAAACCTTCTGTTT
1 AGCGAGAAAGAATCTCGCTACAGC-AAAAACCTTCTGTTT
17578890 TGGTCTCCTA
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.05
60 64 0.76
61 16 0.19
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (59 bp):
AGCGAGAAAGAATCTCGCTACAGCAAAAACCTTCTGTTTATCAGTTACAATTTCGCCGC
Found at i:17582870 original size:8 final size:8
Alignment explanation
Indices: 17582857--17582884 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
17582847 ATGGCTATAA
17582857 AAAAAATT
1 AAAAAATT
17582865 AAAAAATT
1 AAAAAATT
17582873 AAAAAATT
1 AAAAAATT
17582881 AAAA
1 AAAA
17582885 TTAACATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:17584906 original size:19 final size:20
Alignment explanation
Indices: 17584879--17584924 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
17584869 AAGAGACAAG
*
17584879 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
17584898 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
17584917 ATAATATT
1 ATAATATT
17584925 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:17588203 original size:104 final size:104
Alignment explanation
Indices: 17588010--17588209 Score: 224
Period size: 104 Copynumber: 1.9 Consensus size: 104
17588000 GACACAACTA
* * ** * *
17588010 TGACACGGCAGGGTTTAGAGTTTATGACACGTTATGGAGGGAATCTGTGGCACGGCAAGGTGAGA
1 TGACACGACAGGGTTTAGAGTTTATGACAAGCCATGGAGGGAATCTGTGACACGCCAAGGTGAGA
* *
17588075 ATGTGAGAAATGGCATGATTAGAATATGTGAAACGGTTG
66 ATGTGAGAAACGCCATGATTAGAATATGTGAAACGGTTG
* * * * *
17588114 TGACACGACAAGGG-TTAGAGTTTGTGACAAGCCATGGTGGGAATGTGTGACACGCCATGGTGGG
1 TGACACGAC-AGGGTTTAGAGTTTATGACAAGCCATGGAGGGAATCTGTGACACGCCAAGGTGAG
* * *
17588178 AATGTGTGACACGCCATG-TTGAGAATTTGTGA
65 AATGTGAGAAACGCCATGATT-AGAATATGTGA
17588210 CACAGCATGT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
103 2 0.03
104 72 0.92
105 4 0.05
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.25
Consensus pattern (104 bp):
TGACACGACAGGGTTTAGAGTTTATGACAAGCCATGGAGGGAATCTGTGACACGCCAAGGTGAGA
ATGTGAGAAACGCCATGATTAGAATATGTGAAACGGTTG
Found at i:17588218 original size:23 final size:24
Alignment explanation
Indices: 17588136--17588291 Score: 139
Period size: 23 Copynumber: 6.7 Consensus size: 24
17588126 GGTTAGAGTT
*
17588136 TGTGACA-AGCCATGGTGGGAATG
1 TGTGACACAGCCATGGTGAGAATG
*
17588159 TGTGACAC-GCCATGGTGGGAATG
1 TGTGACACAGCCATGGTGAGAATG
* *
17588182 TGTGACAC-GCCATGTTGAGAATT
1 TGTGACACAGCCATGGTGAGAATG
*
17588205 TGTGACACAG-CATGTTGA-AATCG
1 TGTGACACAGCCATGGTGAGAAT-G
* * *
17588228 TGTGAAACAG-CATGGTGAGATTT
1 TGTGACACAGCCATGGTGAGAATG
* *
17588251 TGTGACACAG-CATGGGGAGCATATA
1 TGTGACACAGCCATGGTGAG-A-ATG
17588276 TGTGACAC-GCCATGGT
1 TGTGACACAGCCATGGT
17588292 TTGAAATAGA
Statistics
Matches: 113, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.03
23 91 0.81
24 5 0.04
25 14 0.12
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (24 bp):
TGTGACACAGCCATGGTGAGAATG
Found at i:17593246 original size:35 final size:35
Alignment explanation
Indices: 17593196--17593425 Score: 217
Period size: 35 Copynumber: 6.5 Consensus size: 35
17593186 ATTAAGTTGT
* *
17593196 GCCTAATTAACTAAATTGTTTAATTAAATCATTGG
1 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
* *
17593231 GCCTAATTAATTAAATTATTTAATTAAGTCATTTG
1 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
*** * **
17593266 GCCTAATTAATTAAATTAAACAATTAAGTTGTTGG
1 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
* * * *
17593301 GCCTAATTGATTGAATTTGTTTAATTAACTCATTGG
1 GCCTAATTAATT-AAATTATTTAATTAAATCATTGG
* * * ** *
17593337 CCCTAGTTGAATAAAATTATTTAATTAAATTGTTAG
1 GCCTAATT-AATTAAATTATTTAATTAAATCATTGG
* * * *
17593373 GCTTAATTAATTAAATTATTTAATTAAGTTATTGA
1 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
*
17593408 GCCTAATTGATTAAATTA
1 GCCTAATTAATTAAATTA
17593426 AAAATTAAGT
Statistics
Matches: 154, Mismatches: 39, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
35 109 0.71
36 43 0.28
37 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (35 bp):
GCCTAATTAATTAAATTATTTAATTAAATCATTGG
Found at i:17593380 original size:107 final size:106
Alignment explanation
Indices: 17593196--17593424 Score: 289
Period size: 107 Copynumber: 2.2 Consensus size: 106
17593186 ATTAAGTTGT
* * * * *
17593196 GCCTAATTAACTAAA-TTGTTTAATTAAATCATTGGGCCTAATTAATTAAATTATTTAATTAAGT
1 GCCTAATTGATTAAATTTGTTTAATTAAATCATTGGCCCTAATTAATAAAATTATTTAATTAAAT
* * *
17593260 CATTTGGCCTAATTAATTAAATTAAACAATTAAGTTGTTGG
66 CATTAGGCCTAATTAATTAAATTAAACAATTAAGTTATTGA
* * *
17593301 GCCTAATTGATTGAATTTGTTTAATTAACTCATTGGCCCTAGTTGAATAAAATTATTTAATTAAA
1 GCCTAATTGATTAAATTTGTTTAATTAAATCATTGGCCCTAATT-AATAAAATTATTTAATTAAA
** * ***
17593366 TTGTTAGGCTTAATTAATTAAATTATTTAATTAAGTTATTGA
65 TCATTAGGCCTAATTAATTAAATTAAACAATTAAGTTATTGA
17593408 GCCTAATTGATTAAATT
1 GCCTAATTGATTAAATT
17593425 AAAAATTAAG
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
105 12 0.12
106 25 0.24
107 67 0.64
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (106 bp):
GCCTAATTGATTAAATTTGTTTAATTAAATCATTGGCCCTAATTAATAAAATTATTTAATTAAAT
CATTAGGCCTAATTAATTAAATTAAACAATTAAGTTATTGA
Found at i:17596092 original size:81 final size:81
Alignment explanation
Indices: 17595937--17596105 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 81
17595927 CAAAGGATGT
* * * * *
17595937 GAACCTTCAATTAGTTGATGCTGAAGGAGACCATGTTCCTCAAGCCGATGCAGTTGTCGATGCAT
1 GAACCTTCAATCAGTTGATGCTGAAGGAGACCATGTTCCTCAAGACGATGCAGTAGTCGAGGCAG
* *
17596002 CTGCGAGAGGGGAGGG
66 CTACAAGAGGGGAGGG
* * * *
17596018 GGACCTTCACTCAGTTGA-GACTGAAGGAGACCATGTTCCTCAAGATGATGCAGTAGTCGAGGTA
1 GAACCTTCAATCAGTTGATG-CTGAAGGAGACCATGTTCCTCAAGACGATGCAGTAGTCGAGGCA
*
17596082 GCTACAAGAGGGGATGG
65 GCTACAAGAGGGGAGGG
17596099 GAACCTT
1 GAACCTT
17596106 GCATCAATTC
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 73 0.99
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (81 bp):
GAACCTTCAATCAGTTGATGCTGAAGGAGACCATGTTCCTCAAGACGATGCAGTAGTCGAGGCAG
CTACAAGAGGGGAGGG
Found at i:17596937 original size:220 final size:220
Alignment explanation
Indices: 17596555--17596973 Score: 669
Period size: 220 Copynumber: 1.9 Consensus size: 220
17596545 TTCAACGTAC
** * *
17596555 TGTGTAAGTGAATGATAGGGTCGAAGTCCAAGTTGTACAACACCCGTGCATGCGTGGTTGATACA
1 TGTGTAAGCAAATGATAGGGTCGAAGTCCAAGTTATACAACACCCATGCATGCGTGGTTGATACA
*
17596620 ATATTCTTCATAAGTTTATTTGCACATTTTTCAACTATGAAAATACTAAAGTTTTGGATTGCATG
66 ATATTCTTCATAAATTTATTTGCACATTTTTCAACTATGAAAATACTAAAGTTTTGGATTGCATG
* * * *
17596685 CAGTGTAAGGTAATGTATAAATATTTCACAAGACACCA-TCTGTATGCTTTACATCACATATTCA
131 AAGTGTAAGCTAATGTATAAATATTTCACAAGACACCATTC-GTATGCTGTACATCACATATCCA
17596749 ACTGATTGACGCATGCCTCAGCATAT
195 ACTGATTGACGCATGCCTCAGCATAT
* * * *
17596775 TGTGTAAGCAAATGATAGGGTCGAAGTTCAAGTTATACAACATCCATGCATGTGTGGTTGATACG
1 TGTGTAAGCAAATGATAGGGTCGAAGTCCAAGTTATACAACACCCATGCATGCGTGGTTGATACA
* *
17596840 ATATTCTTCATAAATTTATTTGCACATTTTTTAATTATGAAAATACTAAAGTTTTGGATTGCATG
66 ATATTCTTCATAAATTTATTTGCACATTTTTCAACTATGAAAATACTAAAGTTTTGGATTGCATG
* *
17596905 AAGTGTAAGCTAATGTATAAGTATTTCACAAGACACCATTCGTATGCTGTACATCGCATATCCAA
131 AAGTGTAAGCTAATGTATAAATATTTCACAAGACACCATTCGTATGCTGTACATCACATATCCAA
17596970 CTGA
196 CTGA
17596974 AGATGGACAG
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
220 179 0.99
221 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (220 bp):
TGTGTAAGCAAATGATAGGGTCGAAGTCCAAGTTATACAACACCCATGCATGCGTGGTTGATACA
ATATTCTTCATAAATTTATTTGCACATTTTTCAACTATGAAAATACTAAAGTTTTGGATTGCATG
AAGTGTAAGCTAATGTATAAATATTTCACAAGACACCATTCGTATGCTGTACATCACATATCCAA
CTGATTGACGCATGCCTCAGCATAT
Found at i:17598086 original size:75 final size:75
Alignment explanation
Indices: 17597960--17598184 Score: 315
Period size: 75 Copynumber: 3.0 Consensus size: 75
17597950 TAAGCGTGGC
* * * *
17597960 GTGTCACCCCATAAGACTACAACCATTCAACGTGTCACCACAAGATATCATCGACATCTAACAAT
1 GTGTCA-CCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCATCGACATCTAACAAT
17598025 TGGGGCATGGT
65 TGGGGCATGGT
* * *
17598036 GTGTCACCCATACTACTGCAACCACTCAATGTGTCACCATAAGATGTCATCGACATCTAACAATT
1 GTGTCACCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCATCGACATCTAACAATT
**
17598101 GGGGTGTGGT
66 GGGGCATGGT
* * * *
17598111 GTGTCACCCTATAATATTGCAACCACTCAGCATGTCACCACAAGATGTCATTGACATCTAACAAT
1 GTGTCACCC-ATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCATCGACATCTAACAAT
17598176 TGGGGCATG
65 TGGGGCATG
17598185 TGGTTGATGT
Statistics
Matches: 130, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
75 69 0.53
76 61 0.47
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (75 bp):
GTGTCACCCATAATACTGCAACCACTCAACGTGTCACCACAAGATGTCATCGACATCTAACAATT
GGGGCATGGT
Found at i:17598290 original size:37 final size:38
Alignment explanation
Indices: 17598249--17598322 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
17598239 ACACTTTTGC
*
17598249 ACATGGGTTGCT-ATCATGGCA-TTTATGGGTTCAAGTG
1 ACATGGATTGCTGA-CATGGCATTTTATGGGTTCAAGTG
*
17598286 ACATGGATTGCTGACGTGGCATTTTATGGGTTCAAGT
1 ACATGGATTGCTGACATGGCATTTTATGGGTTCAAGT
17598323 TGCCATGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 17 0.52
38 16 0.48
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (38 bp):
ACATGGATTGCTGACATGGCATTTTATGGGTTCAAGTG
Found at i:17598961 original size:41 final size:39
Alignment explanation
Indices: 17598910--17598991 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 39
17598900 ATTTACTAAT
** *
17598910 CAAAACTAAATACAAAATTTAAATAATCAAATAATATATCTA
1 CAAAACTAAATA-AAAAAATAAAGAATC--ATAATATATCTA
*
17598952 CAAAA-TAAATAAAAAAATAAAGACTCATAATATATCTA
1 CAAAACTAAATAAAAAAATAAAGAATCATAATATATCTA
17598990 CA
1 CA
17598992 CCACTCCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 14 0.39
40 11 0.31
41 6 0.17
42 5 0.14
ACGTcount: A:0.61, C:0.12, G:0.01, T:0.26
Consensus pattern (39 bp):
CAAAACTAAATAAAAAAATAAAGAATCATAATATATCTA
Found at i:17601984 original size:54 final size:54
Alignment explanation
Indices: 17601902--17602008 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
17601892 CTATAGTACG
* *
17601902 ATGACGATGGTGCTCAACAGAGAGTTGACAGAGCTGATACAATTCAGAGAGCTA
1 ATGACGATGGTGCTCAACAGAAACTTGACAGAGCTGATACAATTCAGAGAGCTA
* * *
17601956 ATGACGATGGTGTTCAACAGAAACTTGACAGAGCTGATACAGTTTAGAGAGCT
1 ATGACGATGGTGCTCAACAGAAACTTGACAGAGCTGATACAATTCAGAGAGCT
17602009 GAGAGAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (54 bp):
ATGACGATGGTGCTCAACAGAAACTTGACAGAGCTGATACAATTCAGAGAGCTA
Found at i:17604870 original size:2 final size:2
Alignment explanation
Indices: 17604863--17604896 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17604853 CACATGTCAC
17604863 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17604897 GAAGAGGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17609709 original size:13 final size:13
Alignment explanation
Indices: 17609682--17609722 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
17609672 ATTGATATAT
17609682 TATAATA-AATGA
1 TATAATATAATGA
*
17609694 TATAATATATTGA
1 TATAATATAATGA
*
17609707 TATAATATAATAA
1 TATAATATAATGA
17609720 TAT
1 TAT
17609723 TATTAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (13 bp):
TATAATATAATGA
Found at i:17619531 original size:178 final size:178
Alignment explanation
Indices: 17619217--17619551 Score: 460
Period size: 178 Copynumber: 1.9 Consensus size: 178
17619207 GAAGAATTGC
* * * *
17619217 TTTGAAATATCTTTGGATTAGTTCTTTGATTTACTTCTGAGTCATCCTATGAATTCACTGGTTAT
1 TTTGAAATATATTTGGATCAGTTCTTTGATTGACTTCTGAGTCATCCTATAAATTCACTGGTTAT
* * * * *
17619282 AGCAGTTATTAACAAGGCACAATATGCATAGATCTGCAATTCTAAGCAATAATTGGAATACAAAA
66 AGCAGTTATGAACAAGGCACAATATGCAGACATCTGCAATTCTAAGCAATAATTAGAAGACAAAA
*
17619347 ATGCAGTAAGATTATGTTCTGTTTCTAAGATTAAAAAATTGCAGTTCT
131 ATGCAGTAAGATTATATTCTGTTTCTAAGATTAAAAAATTGCAGTTCT
* *
17619395 TTTGTAATATATTTGGATCAGTTATTTTG-TTGACTTCTGAGTCATACC-ATAAATTCACTGGTT
1 TTTGAAATATATTTGGATCAGTT-CTTTGATTGACTTCTGAGTCAT-CCTATAAATTCACTGGTT
* * * *
17619458 ATAGTAGTTATGAAC-ATGCACAATATGCAGACATCTGCAATTCTAGGCAATAATTTATAAGACA
64 ATAGCAGTTATGAACAAGGCACAATATGCAGACATCTGCAATTCTAAGCAATAA-TTAGAAGACA
* *
17619522 AATATGCAGTAAGGTTATATTCTGTTTCTA
128 AAAATGCAGTAAGATTATATTCTGTTTCTA
17619552 GACAGAAGGG
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
177 34 0.25
178 96 0.71
179 6 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (178 bp):
TTTGAAATATATTTGGATCAGTTCTTTGATTGACTTCTGAGTCATCCTATAAATTCACTGGTTAT
AGCAGTTATGAACAAGGCACAATATGCAGACATCTGCAATTCTAAGCAATAATTAGAAGACAAAA
ATGCAGTAAGATTATATTCTGTTTCTAAGATTAAAAAATTGCAGTTCT
Found at i:17625507 original size:2 final size:2
Alignment explanation
Indices: 17625500--17625535 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
17625490 ATTTATCAAC
17625500 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17625536 TTGTTCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:17655678 original size:181 final size:181
Alignment explanation
Indices: 17655391--17655739 Score: 673
Period size: 181 Copynumber: 1.9 Consensus size: 181
17655381 TTTTCGCTTC
17655391 TTCTTCTTCTTCTTCTTCCATTAAAGTTAAGTTTGACAAAATTATCCAACTTCAAGAGATTTCAA
1 TTCTTCTTCTTCTTCTTCCATTAAAGTTAAGTTTGACAAAATTATCCAACTTCAAGAGATTTCAA
17655456 GATAATTTTTACTTGTACTCACAAATTATTTCTTTTTATATGAAAATATTTCTATTTTTTTATTG
66 GATAATTTTTACTTGTACTCACAAATTATTTCTTTTTATATGAAAATATTTCTATTTTTTTATTG
17655521 TATTAAATACTCTTTTATCTTTTGACTTGTATCCATACNTCTCTCTTTTTTT
131 TATTAAATACTCTTTTATCTTTTGACTTGTATCCATAC-TCTCTCTTTTTTT
*
17655573 TTCTTCTTCTTCTTCTTCCATTAAAGTTAAGTTTGACAAAATTATCCAA-TTCAAGATATTTCAA
1 TTCTTCTTCTTCTTCTTCCATTAAAGTTAAGTTTGACAAAATTATCCAACTTCAAGAGATTTCAA
17655637 GATAATTTTTACTTGTACTCACAAATTATTTCTTTTTATATGAAAATATTTCTATTTTTTTATTG
66 GATAATTTTTACTTGTACTCACAAATTATTTCTTTTTATATGAAAATATTTCTATTTTTTTATTG
17655702 TATTAAATACTCTTTTATCTTTTGACTTGTATCCATAC
131 TATTAAATACTCTTTTATCTTTTGACTTGTATCCATAC
17655740 AAATCTTTAA
Statistics
Matches: 166, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
181 117 0.70
182 49 0.30
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.50
Consensus pattern (181 bp):
TTCTTCTTCTTCTTCTTCCATTAAAGTTAAGTTTGACAAAATTATCCAACTTCAAGAGATTTCAA
GATAATTTTTACTTGTACTCACAAATTATTTCTTTTTATATGAAAATATTTCTATTTTTTTATTG
TATTAAATACTCTTTTATCTTTTGACTTGTATCCATACTCTCTCTTTTTTT
Found at i:17659500 original size:51 final size:51
Alignment explanation
Indices: 17659445--17659587 Score: 146
Period size: 51 Copynumber: 2.8 Consensus size: 51
17659435 ATGACAATTC
* * * * *
17659445 TTCCTGAGGGGATTTCACAAGGCTGGGAGATTTCATTTCGAATTG-CTGTAG
1 TTCCTGAGGGGATTTCACATGGCTGGAAGATTTCGTTTC-AAATGACTGCAG
* * * * *
17659496 TTCCTGAGAGGATTTAACATTG-TGAGCAGATTTCGTTTCAAATGACTGCCG
1 TTCCTGAGGGGATTTCACATGGCTG-GAAGATTTCGTTTCAAATGACTGCAG
* *
17659547 TTCCTGTGGGGATTTCACATGGCTAGAAGATTTCGTTTCAA
1 TTCCTGAGGGGATTTCACATGGCTGGAAGATTTCGTTTCAA
17659588 CTGGCAGTGA
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
50 6 0.08
51 67 0.91
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (51 bp):
TTCCTGAGGGGATTTCACATGGCTGGAAGATTTCGTTTCAAATGACTGCAG
Found at i:17661443 original size:27 final size:27
Alignment explanation
Indices: 17661412--17661473 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
17661402 TTTAAAAATT
* * *
17661412 TTTCAGAAAGATTTTTGACCGGTTCCA
1 TTTCAGAAAAAATTTTAACCGGTTCCA
*
17661439 TTTCAGAAAAAATTTTAACTGGTTCCA
1 TTTCAGAAAAAATTTTAACCGGTTCCA
17661466 TTTACAGA
1 TTT-CAGA
17661474 CCTCTAGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (27 bp):
TTTCAGAAAAAATTTTAACCGGTTCCA
Found at i:17672158 original size:20 final size:21
Alignment explanation
Indices: 17672120--17672159 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17672110 GGCTTAATTG
* *
17672120 TTTTTTTTATTTAGCTATATA
1 TTTTTTTAAGTTAGCTATATA
17672141 TTTTTTTAAGTTAG-TATAT
1 TTTTTTTAAGTTAGCTATAT
17672160 GACAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTTTAAGTTAGCTATATA
Found at i:17674999 original size:19 final size:19
Alignment explanation
Indices: 17674975--17675012 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17674965 CCATTTGACT
*
17674975 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
17674994 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
17675013 GGTTTGACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:17677556 original size:2 final size:2
Alignment explanation
Indices: 17677514--17677543 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17677504 NNNNNNNNNN
17677514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17677544 CCAGATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17686336 original size:22 final size:22
Alignment explanation
Indices: 17686293--17686336 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17686283 AGATTTGAAC
*
17686293 TTTTCTTTTATTCAACACATTT
1 TTTTCTTTTATTCAACAAATTT
*
17686315 TTTTCTTTTTTTTC-ACAAATTT
1 TTTTC-TTTTATTCAACAAATTT
17686337 AAAATTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTCTTTTATTCAACAAATTT
Found at i:17690349 original size:17 final size:17
Alignment explanation
Indices: 17690329--17690361 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17690319 ATAATAATAA
17690329 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
17690346 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
17690362 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:17695180 original size:42 final size:42
Alignment explanation
Indices: 17695133--17695219 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
17695123 CATATATGTA
17695133 GTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAG
1 GTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAG
*
17695175 GTCAGCAACGGCTTATGTGCACTCCTACTCGCACATAGCTAG
1 GTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAG
17695217 GTC
1 GTC
17695220 CACATCAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (42 bp):
GTCAGCAACGGCTTATGTGCACTCCCACTCGCACATAGCTAG
Found at i:17697896 original size:2 final size:2
Alignment explanation
Indices: 17697889--17697925 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
17697879 TGTTATGTTG
* *
17697889 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17697926 GGATATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17699905 original size:21 final size:21
Alignment explanation
Indices: 17699857--17699897 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17699847 TTTTAACGAG
* *
17699857 AAACCGTTGTGTAGTTGAGAC
1 AAACCCTTGTGCAGTTGAGAC
17699878 AAACCCTTGTGCAGTTGAGA
1 AAACCCTTGTGCAGTTGAGA
17699898 GGAACCCTCA
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:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
AAACCCTTGTGCAGTTGAGAC
Found at i:17704922 original size:151 final size:151
Alignment explanation
Indices: 17704645--17704949 Score: 486
Period size: 151 Copynumber: 2.0 Consensus size: 151
17704635 GCCGGTAGGG
* * * *
17704645 CTACTACAACCGTTACAGGAGCTCGAGTGGAAGTGGGAGCATGTTGTAATGGATTTTGTAACAAG
1 CTACTACAACCGTTACAGGAGCCCAAGTGAAAGTGGGAGCATGTTGCAATGGATTTTGTAACAAG
* *
17704710 CTTGCCTCGAACTAGTGGGGTTTATGACTCGATTTGGATTATAGTAGACCGATTGACGAAGTCAG
66 CTTGCCTCGAACTAGTGGGGGTTATGACTCGATTGGGATTATAGTAGACCGATTGACGAAGTCAG
17704775 CTCATTTTCTTCTAGTTAAGA
131 CTCATTTTCTTCTAGTTAAGA
* **
17704796 CTACTACAACCGTTACTA-GTGCCCAAGTGAAAGTGGGAGCATGTTGCAATGGATTTTGTAACGG
1 CTACTACAACCGTTAC-AGGAGCCCAAGTGAAAGTGGGAGCATGTTGCAATGGATTTTGTAACAA
* * *
17704860 GCTTGCCTTGAACTAGTGGGGGTTATGACTCGATTGGGATTATAGTAGACCGGTTGATGAAGTCA
65 GCTTGCCTCGAACTAGTGGGGGTTATGACTCGATTGGGATTATAGTAGACCGATTGACGAAGTCA
17704925 GCTCATTTTCTTCTAGTTAAGA
130 GCTCATTTTCTTCTAGTTAAGA
17704947 CTA
1 CTA
17704950 GTTACGGGGC
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
151 140 0.99
152 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (151 bp):
CTACTACAACCGTTACAGGAGCCCAAGTGAAAGTGGGAGCATGTTGCAATGGATTTTGTAACAAG
CTTGCCTCGAACTAGTGGGGGTTATGACTCGATTGGGATTATAGTAGACCGATTGACGAAGTCAG
CTCATTTTCTTCTAGTTAAGA
Found at i:17707774 original size:21 final size:21
Alignment explanation
Indices: 17707750--17707804 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
17707740 AGGTTTTAAC
17707750 GAGAAACCCTCGTGCAGTTGA
1 GAGAAACCCTCGTGCAGTTGA
* *
17707771 GAGAAACCCTTGTGTAGTTGA
1 GAGAAACCCTCGTGCAGTTGA
* *
17707792 GAAAAACCTTCGT
1 GAGAAACCCTCGT
17707805 ACAGATGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (21 bp):
GAGAAACCCTCGTGCAGTTGA
Found at i:17708710 original size:2 final size:2
Alignment explanation
Indices: 17708703--17708751 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
17708693 GTTATGTATG
17708703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17708745 TA TA TA T
1 TA TA TA T
17708752 TTATGCAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17709216 original size:19 final size:19
Alignment explanation
Indices: 17709192--17709249 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
17709182 GGTTTTAGTA
17709192 AGAAACCCTCGGCCAGCTG
1 AGAAACCCTCGGCCAGCTG
* *
17709211 AGAAACCCTCAGCCAGTTG
1 AGAAACCCTCGGCCAGCTG
17709230 AGAAACCCTCGGCCAGCTG
1 AGAAACCCTCGGCCAGCTG
17709249 A
1 A
17709250 TAATTTGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.29, C:0.34, G:0.24, T:0.12
Consensus pattern (19 bp):
AGAAACCCTCGGCCAGCTG
Found at i:17713026 original size:17 final size:17
Alignment explanation
Indices: 17713004--17713036 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17712994 ATAATAGTAA
17713004 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
17713021 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
17713037 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:17714651 original size:4 final size:4
Alignment explanation
Indices: 17714642--17714690 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
17714632 TGTGGCTTAT
* * * *
17714642 TATA TATA TATA TATA TATA TATA TATA AATA TTTA TATG TATT TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
17714690 T
1 T
17714691 GAATGATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (4 bp):
TATA
Found at i:17714653 original size:6 final size:6
Alignment explanation
Indices: 17714642--17714690 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
17714632 TGTGGCTTAT
* * * *
17714642 TATATA TATATA TATATA TATATA TATAAA TATTTA TATGTA TTTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
17714690 T
1 T
17714691 GAATGATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
TATATA
Found at i:17714657 original size:10 final size:10
Alignment explanation
Indices: 17714642--17714690 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
17714632 TGTGGCTTAT
17714642 TATATATATA
1 TATATATATA
17714652 TATATATATA
1 TATATATATA
*
17714662 TATATATAAA
1 TATATATATA
* *
17714672 TATTTATATG
1 TATATATATA
*
17714682 TATTTATAT
1 TATATATAT
17714691 GAATGATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
TATATATATA
Found at i:17723778 original size:2 final size:2
Alignment explanation
Indices: 17723771--17723823 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
17723761 AACCCATTTG
* *
17723771 AT AT AT AT AT AT AT AT A- AT TT AT TT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
17723811 GT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT
17723824 TTTTTTCTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:17724020 original size:70 final size:70
Alignment explanation
Indices: 17723945--17724105 Score: 211
Period size: 70 Copynumber: 2.3 Consensus size: 70
17723935 CTTTCCTTTT
* *
17723945 TCCCTCACATACCC-AGCAGCAAAA-CCTCTCATTTCTCTCTCTAAAACTAGTAGCAACAACTCC
1 TCCCTCACAAACCCGA-CAGCAAAATCC-CTCATTTCTCTCTCTAAAACTAGCAGCAACAACTCC
17724008 TCGTTT-C
64 TC-TTTCC
* * * *
17724015 TCCCTCACAAACTCGATAGCAAAATCCCTCATTTCTCTCTTTCAAACTAGCAGCAACAACTCCTC
1 TCCCTCACAAACCCGACAGCAAAATCCCTCATTTCTCTCTCTAAAACTAGCAGCAACAACTCCTC
17724080 TTTCC
66 TTTCC
*
17724085 TCCCTCACAAACTCGACAGCA
1 TCCCTCACAAACCCGACAGCA
17724106 CCAGCTCTTG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
69 3 0.04
70 75 0.93
71 3 0.04
ACGTcount: A:0.29, C:0.38, G:0.07, T:0.26
Consensus pattern (70 bp):
TCCCTCACAAACCCGACAGCAAAATCCCTCATTTCTCTCTCTAAAACTAGCAGCAACAACTCCTC
TTTCC
Found at i:17724096 original size:35 final size:35
Alignment explanation
Indices: 17723972--17724097 Score: 125
Period size: 35 Copynumber: 3.6 Consensus size: 35
17723962 AGCAAAACCT
*
17723972 CTCATTTCTCTCTCTA-AAACTAGTAGCAACAACTC
1 CTCATTTCTCCCTC-ACAAACTAGTAGCAACAACTC
* *
17724007 CTCGTTTCTCCCTCACAAACTCGATAGCAA-AA-TCC
1 CTCATTTCTCCCTCACAAACTAG-TAGCAACAACT-C
* ** *
17724042 CTCATTTCTCTCTTTCAAACTAGCAGCAACAACTC
1 CTCATTTCTCCCTCACAAACTAGTAGCAACAACTC
17724077 CTC-TTTCCTCCCTCACAAACT
1 CTCATTT-CTCCCTCACAAACT
17724098 CGACAGCACC
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
34 10 0.14
35 56 0.77
36 7 0.10
ACGTcount: A:0.28, C:0.37, G:0.06, T:0.30
Consensus pattern (35 bp):
CTCATTTCTCCCTCACAAACTAGTAGCAACAACTC
Found at i:17725019 original size:18 final size:19
Alignment explanation
Indices: 17724980--17725020 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17724970 TTAATATTTT
* *
17724980 AATATTATTTTATTTATAA
1 AATAATATTTTATCTATAA
17724999 AATAATATTTTATCT-TAA
1 AATAATATTTTATCTATAA
17725017 AATA
1 AATA
17725021 TTCTTCTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATATTTTATCTATAA
Found at i:17733134 original size:2 final size:2
Alignment explanation
Indices: 17733127--17733200 Score: 107
Period size: 2 Copynumber: 38.0 Consensus size: 2
17733117 NNNNNNNNNN
* *
17733127 AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT TT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
17733167 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17733201 TTCTATCGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
1 2 0.03
2 63 0.97
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (2 bp):
AT
Found at i:17733417 original size:70 final size:70
Alignment explanation
Indices: 17733337--17733470 Score: 223
Period size: 70 Copynumber: 1.9 Consensus size: 70
17733327 TACCTAGCAA
*
17733337 CAAAACCCCTCATTTCTGTCTCTAAAACCAGCAGCAACAACTCCTCTTTTCTCCCTCACAAACTT
1 CAAAACCCCTCATTTCTCTCTCTAAAACCAGCAGCAACAACTCCTCTTTTCTCCCTCACAAACTT
17733402 GATAG
66 GATAG
* * * *
17733407 CAAAATCCCTCCTTTCTCTCTCTCAAACTAGCAGCAACAACTCCTCTTTTCTCCCTCACAAACT
1 CAAAACCCCTCATTTCTCTCTCTAAAACCAGCAGCAACAACTCCTCTTTTCTCCCTCACAAACT
17733471 CAGCAGCACC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.28, C:0.38, G:0.05, T:0.28
Consensus pattern (70 bp):
CAAAACCCCTCATTTCTCTCTCTAAAACCAGCAGCAACAACTCCTCTTTTCTCCCTCACAAACTT
GATAG
Found at i:17733423 original size:35 final size:35
Alignment explanation
Indices: 17733361--17733478 Score: 141
Period size: 35 Copynumber: 3.3 Consensus size: 35
17733351 TCTGTCTCTA
*
17733361 AAACCAGCAGCAACAACTCCTCTTTTCTCCCTCAC
1 AAACTAGCAGCAACAACTCCTCTTTTCTCCCTCAC
* * * * *
17733396 AAACTTGATAGCAA-AA-TCCCTCCTTTCTCTCTCTC
1 AAACTAG-CAGCAACAACT-CCTCTTTTCTCCCTCAC
17733431 AAACTAGCAGCAACAACTCCTCTTTTCTCCCTCAC
1 AAACTAGCAGCAACAACTCCTCTTTTCTCCCTCAC
17733466 AAACTCAGCAGCA
1 AAACT-AGCAGCA
17733479 CCAGCTTTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
34 6 0.09
35 48 0.72
36 13 0.19
ACGTcount: A:0.30, C:0.38, G:0.07, T:0.25
Consensus pattern (35 bp):
AAACTAGCAGCAACAACTCCTCTTTTCTCCCTCAC
Found at i:17734883 original size:20 final size:22
Alignment explanation
Indices: 17734858--17734898 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
17734848 ATAATGGTAG
17734858 AATATAAATGA-AA-AAATAAA
1 AATATAAATGATAATAAATAAA
*
17734878 AATATACATGATAATAAATAA
1 AATATAAATGATAATAAATAA
17734899 TTGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AATATAAATGATAATAAATAAA
Found at i:17741530 original size:31 final size:31
Alignment explanation
Indices: 17741492--17741550 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
17741482 CAAGTTACCA
*
17741492 TATTTTTCTATGTGCACAATGTATGTAAGCG
1 TATTTTTCTATGAGCACAATGTATGTAAGCG
17741523 TATTTTTCTATGAGCACAATGTATGTAA
1 TATTTTTCTATGAGCACAATGTATGTAA
17741551 AGAAAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (31 bp):
TATTTTTCTATGAGCACAATGTATGTAAGCG
Found at i:17752693 original size:22 final size:22
Alignment explanation
Indices: 17752667--17752725 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
17752657 CGAGAGTTTC
17752667 TCGCTACAGCGAGAATCCATTT
1 TCGCTACAGCGAGAATCCATTT
* * * *
17752689 TCGCTGCAGTGAGAATTCGTTT
1 TCGCTACAGCGAGAATCCATTT
* *
17752711 TTGCTTCAGCGAGAA
1 TCGCTACAGCGAGAA
17752726 ACAGGGCTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (22 bp):
TCGCTACAGCGAGAATCCATTT
Found at i:17753044 original size:37 final size:37
Alignment explanation
Indices: 17752996--17753077 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
17752986 AATGCAATAT
17752996 CATCATCATGTGTGCACTCCCTACTCGAACAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCGAACACTTC-AA
* * *
17753033 CATCATTATGTGTGCACTCCCTACTTGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGAACACTTCAA
17753070 CATCATCA
1 CATCATCA
17753078 CACAACATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 38 0.95
38 2 0.05
ACGTcount: A:0.27, C:0.34, G:0.10, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGAACACTTCAA
Found at i:17756056 original size:40 final size:40
Alignment explanation
Indices: 17755998--17756076 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
17755988 TTGTGAAAGA
* *
17755998 CACCAATCGTGGCGAGGTTGGAAACCCCACTAAGGTGAAT
1 CACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAAT
* *
17756038 CACCAATCTTGGCAAGGTTGAAAACCCCACTAAGTTGAA
1 CACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAA
17756077 AAATAGCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (40 bp):
CACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAAT
Found at i:17758697 original size:2 final size:2
Alignment explanation
Indices: 17758690--17758826 Score: 166
Period size: 2 Copynumber: 64.0 Consensus size: 2
17758680 TTGGACATGT
17758690 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
17758732 AG AG AG AG AG AG AG AG AG AG TAG TAG TACG TAG TAG TAG TAG TAN
1 AG AG AG AG AG AG AG AG AG AG -AG -AG -A-G -AG -AG -AG -AG -AG
**
17758777 NN AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17758819 AG AG AG AG
1 AG AG AG AG
17758827 TGATTTCCCT
Statistics
Matches: 129, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
2 107 0.83
3 19 0.15
4 3 0.02
ACGTcount: A:0.46, C:0.01, G:0.45, T:0.06
Consensus pattern (2 bp):
AG
Found at i:17760369 original size:38 final size:39
Alignment explanation
Indices: 17760327--17760429 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 39
17760317 ATAGTGCCCG
* *
17760327 TGTGCACGATGTGGGCGGATGTACACGATGGCATT-GAC-
1 TGTGCACGATGTGGGCGGATGCACACGATGAC-TTCGACA
* *
17760365 TGTGCACGATGCGGGGGGATGCACACGATGACTTCGACTA
1 TGTGCACGATGTGGGCGGATGCACACGATGACTTCGAC-A
* *
17760405 TGTGCACGATGTGCGAGGATGCACA
1 TGTGCACGATGTGGGCGGATGCACA
17760430 TGAGCTAGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.04
38 31 0.56
40 22 0.40
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.21
Consensus pattern (39 bp):
TGTGCACGATGTGGGCGGATGCACACGATGACTTCGACA
Found at i:17762130 original size:37 final size:38
Alignment explanation
Indices: 17762087--17762198 Score: 174
Period size: 37 Copynumber: 3.0 Consensus size: 38
17762077 TGAGGATGTT
*
17762087 GAAGTGTGCGAGTAGGGAGTGCATACATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
** *
17762125 G-AGTGTGCGAGTAAAGAGTGCACACATGATGATG-TT
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
17762161 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
1 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
17762199 TTGCATTGAG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 2 0.03
37 61 0.94
38 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.23
Consensus pattern (38 bp):
GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGATA
Found at i:17768099 original size:13 final size:13
Alignment explanation
Indices: 17768081--17768110 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17768071 ATGATAGAGT
*
17768081 GTGCGAGTAGGGA
1 GTGCGAGTACGGA
17768094 GTGCGAGTACGGA
1 GTGCGAGTACGGA
17768107 GTGC
1 GTGC
17768111 ACACATGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.50, T:0.17
Consensus pattern (13 bp):
GTGCGAGTACGGA
Found at i:17768099 original size:50 final size:50
Alignment explanation
Indices: 17768044--17768147 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 50
17768034 ATGTTGAAGT
*
17768044 GTGCGAGTAGGGAGTGCACACATGATGATGATAGAGTGTGCGAGTAGGGA
1 GTGCGAGTACGGAGTGCACACATGATGATGATAGAGTGTGCGAGTAGGGA
*
17768094 GTGCGAGTACGGAGTGCACACATGATGATGATAGAGTGTTCGAGTAGGGA
1 GTGCGAGTACGGAGTGCACACATGATGATGATAGAGTGTGCGAGTAGGGA
17768144 GTGC
1 GTGC
17768148 ACACATGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.27, C:0.12, G:0.40, T:0.21
Consensus pattern (50 bp):
GTGCGAGTACGGAGTGCACACATGATGATGATAGAGTGTGCGAGTAGGGA
Found at i:17768145 original size:37 final size:39
Alignment explanation
Indices: 17768097--17768200 Score: 144
Period size: 37 Copynumber: 2.8 Consensus size: 39
17768087 GTAGGGAGTG
*
17768097 CGAGTACGGAGTGCACACATGATGATGATAG-AGTGT-T
1 CGAGTAGGGAGTGCACACATGATGATGATAGAAGTGTAT
*
17768134 CGAGTAGGGAGTGCACACATGATGATG-TTGAAGTGTAT
1 CGAGTAGGGAGTGCACACATGATGATGATAGAAGTGTAT
* *
17768172 -GAGTAGGGAGTGCACAAATGATAATGATA
1 CGAGTAGGGAGTGCACACATGATGATGATA
17768201 TTGCATTGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
36 2 0.03
37 55 0.93
38 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.24
Consensus pattern (39 bp):
CGAGTAGGGAGTGCACACATGATGATGATAGAAGTGTAT
Found at i:17770186 original size:40 final size:40
Alignment explanation
Indices: 17770131--17770209 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
17770121 CTCTGAAAGA
* *
17770131 CACCAATCGTGGCAAGGTTGGAAAC-CTTACTAAGGTGAAT
1 CACCAATCGTGGCAAGGTTGAAAACTC-CACTAAGGTGAAT
*
17770171 CACCAATCTTGGCAAGGTTGAAAACTCCACTAAGGTGAA
1 CACCAATCGTGGCAAGGTTGAAAACTCCACTAAGGTGAA
17770210 AAATAGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (40 bp):
CACCAATCGTGGCAAGGTTGAAAACTCCACTAAGGTGAAT
Found at i:17779739 original size:38 final size:40
Alignment explanation
Indices: 17779639--17779741 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 40
17779629 ACCCGGCTCA
*
17779639 TGTACATCCCCCCACATCGTGCAC-ATAGCTGGCACCATTG
1 TGTACATCCCCCCACATCGTGCACAATAGCTGG-ACCATCG
* *
17779679 TGTGCATCCCCCCACATTGTGCACAATTAG-T-G-CCATCG
1 TGTACATCCCCCCACATCGTGCACAA-TAGCTGGACCATCG
17779717 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
17779742 CAGGCACTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 28 0.50
40 23 0.41
41 2 0.04
42 3 0.05
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACAATAGCTGGACCATCG
Found at i:17784375 original size:13 final size:13
Alignment explanation
Indices: 17784357--17784382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17784347 ATGTTTATAT
17784357 GTATATATGTGAA
1 GTATATATGTGAA
17784370 GTATATATGTGAA
1 GTATATATGTGAA
17784383 TCGTGTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GTATATATGTGAA
Found at i:17805061 original size:21 final size:21
Alignment explanation
Indices: 17805037--17805080 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17805027 CATGCAATTT
* *
17805037 ATGACAAAGACTGATGCCTTC
1 ATGACAAAGACTAATGCCATC
*
17805058 ATGACAAGGACTAATGCCATC
1 ATGACAAAGACTAATGCCATC
17805079 AT
1 AT
17805081 TCAAAGTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (21 bp):
ATGACAAAGACTAATGCCATC
Found at i:17805594 original size:19 final size:18
Alignment explanation
Indices: 17805560--17805596 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17805550 TTCGAAACTC
17805560 TTATTTTTTTAGTTATTT
1 TTATTTTTTTAGTTATTT
*
17805578 TTATTTTATTTATTTATTT
1 TTATTTT-TTTAGTTATTT
17805597 ATTTTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
TTATTTTTTTAGTTATTT
Found at i:17806425 original size:19 final size:19
Alignment explanation
Indices: 17806403--17806441 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17806393 ACAAGTGGAA
17806403 AATTTTAGAACAAAATAAT
1 AATTTTAGAACAAAATAAT
* * *
17806422 AATTTTTGGATAAAATAAT
1 AATTTTAGAACAAAATAAT
17806441 A
1 A
17806442 TTAAAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (19 bp):
AATTTTAGAACAAAATAAT
Found at i:17807546 original size:21 final size:24
Alignment explanation
Indices: 17807507--17807550 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
17807497 TAGAAATAAA
17807507 GAAGAAGAGAAAGGAAGAAAGGAG
1 GAAGAAGAGAAAGGAAGAAAGGAG
17807531 GAAGAAGA-AAA-G-AGAAAGGA
1 GAAGAAGAGAAAGGAAGAAAGGA
17807551 AGGTTTGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 3 0.15
24 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (24 bp):
GAAGAAGAGAAAGGAAGAAAGGAG
Found at i:17810670 original size:3 final size:3
Alignment explanation
Indices: 17810656--17810687 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
17810646 ACTTTATCTC
*
17810656 TAG TAA TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
17810688 ACTATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:17821670 original size:28 final size:29
Alignment explanation
Indices: 17821629--17821688 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
17821619 GTCTATGGGC
*
17821629 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
17821657 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
17821687 AA
1 AA
17821689 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:17830314 original size:73 final size:73
Alignment explanation
Indices: 17830175--17830356 Score: 176
Period size: 73 Copynumber: 2.5 Consensus size: 73
17830165 GATAGAATGA
* * *
17830175 TCTTAGTCGACTAACTGCGC-TCTTAGTCGACAAAGTTGTCTCTATCTTCTGATCCTAATTTTTA
1 TCTTAGTCGACTAACTTC-CTTCTTAGTCGACTAAGTTGTCTCTATCTTCTGATCCTAATTTCTA
*
17830239 GCAGTGAGC
65 GCAGTAAGC
* * *
17830248 TCTTAGTCGACTAACTTCCTTCTTAGTCGATTAAGTTGTTTCTGTC-T-TGAAGTCC-AGATTTC
1 TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTCTCTATCTTCTG-A-TCCTA-ATTTC
17830310 TAGCAGTAAGC
63 TAGCAGTAAGC
* * ** *
17830321 TTTTAATC-AGCTAACTTAGTTCTTGGTCGACTAAGT
1 TCTTAGTCGA-CTAACTTCCTTCTTAGTCGACTAAGT
17830357 CTTCTCTGTC
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
71 2 0.02
72 5 0.05
73 84 0.92
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (73 bp):
TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTCTCTATCTTCTGATCCTAATTTCTAG
CAGTAAGC
Found at i:17832957 original size:23 final size:21
Alignment explanation
Indices: 17832913--17832963 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
17832903 ATGACGTGCT
*
17832913 AGAGAAAGAGAAAAAGAGAGA
1 AGAGAAAGAGAAAAAAAGAGA
17832934 AGAAGAAA-AGAAAGAAAAGTAGA
1 AG-AGAAAGAGAAA-AAAAG-AGA
17832957 AGAGAAA
1 AGAGAAA
17832964 CGCTGGTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.27
22 14 0.54
23 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (21 bp):
AGAGAAAGAGAAAAAAAGAGA
Found at i:17834446 original size:29 final size:29
Alignment explanation
Indices: 17834404--17834468 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
17834394 TTGGGTGAGA
*
17834404 TGGGATGTCCGGCTATGTGGACGATGTGG
1 TGGGATGTCCGGCTATGTGCACGATGTGG
17834433 TGGGATGTCCGGCTATGTGCACGATGTGG
1 TGGGATGTCCGGCTATGTGCACGATGTGG
*
17834462 TAGGATG
1 TGGGATG
17834469 CACATGAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.15, C:0.14, G:0.43, T:0.28
Consensus pattern (29 bp):
TGGGATGTCCGGCTATGTGCACGATGTGG
Found at i:17838540 original size:220 final size:220
Alignment explanation
Indices: 17838158--17839044 Score: 1774
Period size: 220 Copynumber: 4.0 Consensus size: 220
17838148 GCATTTTTTG
17838158 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
1 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
17838223 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
66 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
17838288 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
131 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
17838353 TAAAAATGCACTTTTTACATCCATT
196 TAAAAATGCACTTTTTACATCCATT
17838378 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
1 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
17838443 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
66 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
17838508 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
131 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
17838573 TAAAAATGCACTTTTTACATCCATT
196 TAAAAATGCACTTTTTACATCCATT
17838598 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
1 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
17838663 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
66 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
17838728 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
131 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
17838793 TAAAAATGCACTTTTTACATCCATT
196 TAAAAATGCACTTTTTACATCCATT
17838818 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
1 TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
17838883 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
66 TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
17838948 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
131 CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
17839013 TAAAAATGCACTTTTTACATCCATT
196 TAAAAATGCACTTTTTACATCCATT
17839038 TAAAATA
1 TAAAATA
17839045 ATTTGAAGTT
Statistics
Matches: 667, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 667 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (220 bp):
TAAAATAGTGTTGTATCAATGCTTCCTCTACTATATCATTTCTCAACTAAAAACCTAGAGAGTCT
TTCATACCAAGCTCTTGGAGCTTGTTTTAGTCCATACAAAGCCTTATGAAGTTTGAACACATAAT
CTGGTTTTTCATAATCCTCAAATTAGGGGGGTTGTTCAACATATATTTCCTCTTAATAAACCATT
TAAAAATGCACTTTTTACATCCATT
Found at i:17842961 original size:35 final size:34
Alignment explanation
Indices: 17842916--17842985 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 34
17842906 TTTCACTAAG
*
17842916 CTTTTACAATGGCTTTTACCA-GACTCAGCCAAAA
1 CTTTTACAATGGCTTTTACCAGGA-TCAACCAAAA
*
17842950 CTTTTCACAATGGTTTTTACCAGGATCAACCAAAA
1 CTTTT-ACAATGGCTTTTACCAGGATCAACCAAAA
17842985 C
1 C
17842986 CCAACAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 5 0.16
35 25 0.78
36 2 0.06
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (34 bp):
CTTTTACAATGGCTTTTACCAGGATCAACCAAAA
Found at i:17844116 original size:2 final size:2
Alignment explanation
Indices: 17844109--17844142 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17844099 TTGATCTCTT
17844109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17844143 NCATCCTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17844215 original size:2 final size:2
Alignment explanation
Indices: 17844208--17844241 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17844198 TTGATCTCCT
17844208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17844242 CTATCAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17844216 original size:99 final size:98
Alignment explanation
Indices: 17844045--17844242 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 98
17844035 CTCCGAGGCT
*
17844045 CATCCTAACAACATAGGCATAGTGACCTTGGTGTTAGGGGGTTGTGACACCATTTTGATCTCTTT
1 CATCCTAACAACATAGGCATAGTGACCTTGGTGTTAGGGGGTTGTGACACCATTTTGATCTCCTT
17844110 ATATATATATATATATATATATATATATATATA
66 ATATATATATATATATATATATATATATATATA
17844143 NCATCCTAACAACATAGGCATAGTGACCTTGGTGTTAGGGGGTTGTGACACCATTTTGATCTCCT
1 -CATCCTAACAACATAGGCATAGTGACCTTGGTGTTAGGGGGTTGTGACACCATTTTGATCTCCT
17844208 TATATATATATATATATATATATATATATATATA
65 TATATATATATATATATATATATATATATATATA
17844242 C
1 C
17844243 TATCAATAAG
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
98 1 0.01
99 97 0.99
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (98 bp):
CATCCTAACAACATAGGCATAGTGACCTTGGTGTTAGGGGGTTGTGACACCATTTTGATCTCCTT
ATATATATATATATATATATATATATATATATA
Found at i:17844305 original size:18 final size:18
Alignment explanation
Indices: 17844282--17844327 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
17844272 ACAAAAATCA
*
17844282 GAAAATAAAAATACAATT
1 GAAAATAAAAATACAAGT
**
17844300 GAAAATAAAAATGTAAGT
1 GAAAATAAAAATACAAGT
17844318 GAAAATAAAA
1 GAAAATAAAA
17844328 GTAAAATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (18 bp):
GAAAATAAAAATACAAGT
Found at i:17845912 original size:43 final size:43
Alignment explanation
Indices: 17845846--17845969 Score: 189
Period size: 43 Copynumber: 2.9 Consensus size: 43
17845836 CCACACTTAG
*
17845846 CTCATGTGCACTCCCTAC-TCGCACATAG-TAGGGTCATCATCAA
1 CTCATGTGCACTCCC-ACACCGCACATAGCT-GGGTCATCATCAA
*
17845889 CTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCATCAG
1 CTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCATCAA
*
17845932 CTCATGTGCACTCCCACACTGCACATAGCTGGGTCATC
1 CTCATGTGCACTCCCACACCGCACATAGCTGGGTCATC
17845970 TTTATCACAC
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
42 2 0.03
43 73 0.96
44 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.23
Consensus pattern (43 bp):
CTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCATCAA
Found at i:17848073 original size:23 final size:23
Alignment explanation
Indices: 17848041--17848086 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17848031 AATAAAGTTA
*
17848041 GCTAATACAAACCTGATTGAAGG
1 GCTAACACAAACCTGATTGAAGG
* *
17848064 GCTAACACAAACTTTATTGAAGG
1 GCTAACACAAACCTGATTGAAGG
17848087 ACTTTTCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (23 bp):
GCTAACACAAACCTGATTGAAGG
Found at i:17850645 original size:10 final size:9
Alignment explanation
Indices: 17850584--17850644 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 9
17850574 AAGTTGGGAG
17850584 AAGAAAGAA
1 AAGAAAGAA
17850593 GCAAGAAGAGAA
1 --AAGAA-AGAA
17850605 AAGAAATGAA
1 AAGAAA-GAA
17850615 AAGAAA-ACA
1 AAGAAAGA-A
*
17850624 AGGAAAGAA
1 AAGAAAGAA
17850633 AATGAAAGAA
1 AA-GAAAGAA
17850643 AA
1 AA
17850645 TTATCTTTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
8 1 0.02
9 9 0.21
10 24 0.56
11 5 0.12
12 4 0.09
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.03
Consensus pattern (9 bp):
AAGAAAGAA
Found at i:17855526 original size:37 final size:37
Alignment explanation
Indices: 17855446--17855529 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
17855436 TTGACACATA
*** *
17855446 CATGATTTGAACCTCTATCGATCACTTTGGTGTCGTG
1 CATGATTTGAACCTCTATCGATCACTTCAATCTCGTG
* *
17855483 CGTGATTTGAACCTCTATCGGTCACTTCAATACT-GTG
1 CATGATTTGAACCTCTATCGATCACTTCAAT-CTCGTG
17855520 CATGATTTGA
1 CATGATTTGA
17855530 CTCTTTGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 38 0.97
38 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (37 bp):
CATGATTTGAACCTCTATCGATCACTTCAATCTCGTG
Found at i:17857961 original size:190 final size:189
Alignment explanation
Indices: 17857633--17858000 Score: 655
Period size: 190 Copynumber: 1.9 Consensus size: 189
17857623 TAACCCCCAA
17857633 ACTACTTTTGCCAATTATAAACTAGGGCTAATTGTACTAACAACCATCACTTTTTTTTTTCTTTT
1 ACTACTTTTGCCAATTATAAACTAGGGCTAATTGTACTAACAACCATCACTTTTTTTTTTCTTTT
* *
17857698 TTTTCACCTTTCTCTCTCAATTTATCTTTAAGCTCAAACCATTCTTTAGAAAGATTAAAATACTT
66 TTTTCACCTTTCTCTCTCAATTTATCTTTAAGCTCAAACAATTCCTTAGAAAGATTAAAATACTT
* *
17857763 AGAGGGTGAAAGGTTCAAAATGCTGGACTTAATTAAACAGGCCAAGGCTAATATAACTG
131 AAAGGGTGAAAGGTTCAAAATGCTGGACTTAAATAAACAGGCCAAGGCTAATATAACTG
17857822 NACTACTTTTGCCAATTATAAACTAGGGCTAATTGTACTAACAACCATCACTTTTTTTTTTCTTT
1 -ACTACTTTTGCCAATTATAAACTAGGGCTAATTGTACTAACAACCATCACTTTTTTTTTTCTTT
17857887 TTTTTCACCTTTCTCTCTCAATTTATCTTTAAGCTCAAACAATTCCTTAGAAAGATTAAAATACT
65 TTTTTCACCTTTCTCTCTCAATTTATCTTTAAGCTCAAACAATTCCTTAGAAAGATTAAAATACT
* * * *
17857952 TAAAGGGTGAAAGGTTCAAATTGCTGGATTTAAATAGACAGGTCAAGGC
130 TAAAGGGTGAAAGGTTCAAAATGCTGGACTTAAATAAACAGGCCAAGGC
17858001 CAACACAAGT
Statistics
Matches: 170, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 170 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (189 bp):
ACTACTTTTGCCAATTATAAACTAGGGCTAATTGTACTAACAACCATCACTTTTTTTTTTCTTTT
TTTTCACCTTTCTCTCTCAATTTATCTTTAAGCTCAAACAATTCCTTAGAAAGATTAAAATACTT
AAAGGGTGAAAGGTTCAAAATGCTGGACTTAAATAAACAGGCCAAGGCTAATATAACTG
Found at i:17859711 original size:21 final size:20
Alignment explanation
Indices: 17859685--17859724 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17859675 AAAAACTAAT
17859685 AAATAATAAAAAAATTAAAAG
1 AAATAA-AAAAAAATTAAAAG
* *
17859706 AAATAACATAAAATTAAAA
1 AAATAAAAAAAAATTAAAA
17859725 TAACTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATAAAAAAAAATTAAAAG
Found at i:17859720 original size:20 final size:20
Alignment explanation
Indices: 17859695--17859738 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
17859685 AAATAATAAA
17859695 AAAATTAAAAGAAATAACAT
1 AAAATTAAAAGAAATAACAT
* * *
17859715 AAAATTAAAATAACTAACTT
1 AAAATTAAAAGAAATAACAT
17859735 AAAA
1 AAAA
17859739 GTAACCTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATTAAAAGAAATAACAT
Done.