Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 177 of 438
Found at i:54653354 original size:34 final size:34
Alignment explanation
Indices: 54653311--54653378 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
54653301 ATAATAATAA
54653311 TAATAATAATAATAATAACAACAACAACCAACAT
1 TAATAATAATAATAATAACAACAACAACCAACAT
54653345 TAATAATAATAATAATAACAACAACAACCAACAT
1 TAATAATAATAATAATAACAACAACAACCAACAT
54653379 ATTATTGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (34 bp):
TAATAATAATAATAATAACAACAACAACCAACAT
Found at i:54655250 original size:25 final size:25
Alignment explanation
Indices: 54655216--54655265 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
54655206 ATGAAAGTTT
54655216 GATGTATGATAAACATCTTTTACTA
1 GATGTATGATAAACATCTTTTACTA
54655241 GATGTATGATAAACATCTTTTACTA
1 GATGTATGATAAACATCTTTTACTA
54655266 AGTGGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
GATGTATGATAAACATCTTTTACTA
Found at i:54656276 original size:11 final size:11
Alignment explanation
Indices: 54656260--54656298 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
54656250 CTATGATACT
54656260 TGATTACATTA
1 TGATTACATTA
*
54656271 TGATTAACACT-
1 TGATT-ACATTA
54656282 TGATTACATTA
1 TGATTACATTA
54656293 TGATTA
1 TGATTA
54656299 ATATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 4 0.17
11 16 0.67
12 4 0.17
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (11 bp):
TGATTACATTA
Found at i:54656285 original size:22 final size:22
Alignment explanation
Indices: 54656257--54656299 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
54656247 TAACTATGAT
54656257 ACTTGATTACATTATGATTAAC
1 ACTTGATTACATTATGATTAAC
54656279 ACTTGATTACATTATGATTAA
1 ACTTGATTACATTATGATTAA
54656300 TATTATTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (22 bp):
ACTTGATTACATTATGATTAAC
Found at i:54658845 original size:40 final size:39
Alignment explanation
Indices: 54658790--54658977 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 39
54658780 TGAATGATAC
* * *
54658790 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-TTATAT
*
54658830 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
*
54658870 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * * *
54658910 CCGGGCTAAGACCCAAAGGCATTTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGT--TATAT
* *
54658950 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTTGTGC
54658978 TTGTGGTTAT
Statistics
Matches: 133, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 129 0.97
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:54658987 original size:80 final size:80
Alignment explanation
Indices: 54658790--54658990 Score: 251
Period size: 80 Copynumber: 2.5 Consensus size: 80
54658780 TGAATGATAC
* * * * *
54658790 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCAAAGGCATTCG
* *** *
54658855 TGCGAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * *
54658870 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCAAAGGCATTT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTGGTTATATCCGGGCTAAGACCCAAAGGCATTC
54658934 GTGCAAGTTACCAAAT
65 GTGCAAGTTACCAAAT
* *
54658950 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATC
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATC
54658991 TGGTTAAATT
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 2 0.02
80 97 0.95
81 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCAAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:54666879 original size:40 final size:38
Alignment explanation
Indices: 54666824--54666980 Score: 205
Period size: 40 Copynumber: 4.1 Consensus size: 38
54666814 TGAATGATAC
* *
54666824 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCA-TTGTGCTAGTG-TTATAT
*
54666864 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATT-GTGCTAG-TGTTATAT
54666904 CCGGGCTAAGACCCGAAGGCATTGTGC-A--GTTATAT
1 CCGGGCTAAGACCCGAAGGCATTGTGCTAGTGTTATAT
*
54666939 CCGGG-TAAGACCCGAAGGCATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTGTGCTAGT-GTTATAT
54666977 CCGG
1 CCGG
54666981 TTAAATTCCG
Statistics
Matches: 107, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
34 21 0.20
35 12 0.11
38 12 0.11
39 6 0.06
40 54 0.50
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (38 bp):
CCGGGCTAAGACCCGAAGGCATTGTGCTAGTGTTATAT
Found at i:54669400 original size:40 final size:39
Alignment explanation
Indices: 54669274--54669439 Score: 142
Period size: 40 Copynumber: 4.2 Consensus size: 39
54669264 CGGAATATAA
54669274 CCGGATATAATC-ACGT-GCACAAATGCC-TCGGGTCTTAGC
1 CCGGATATAA-CAAC-TAGCAC-AATGCCTTCGGGTCTTAGC
* * *
54669313 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCAC-AATGCCTTCGGGTCTTAGC
* * *
54669353 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTAGCACAA-TGCCTTCGGGTCTTAGC
*** * * *
54669393 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACAACTAGCACAA-TGCCTTCGGGTCTTAGC
54669432 CCGGATAT
1 CCGGATAT
54669440 CATTCAATTT
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.01
39 36 0.34
40 69 0.65
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACAACTAGCACAATGCCTTCGGGTCTTAGC
Found at i:54677320 original size:40 final size:40
Alignment explanation
Indices: 54677275--54677441 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
54677265 CGGAATATAA
54677275 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
54677315 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
54677355 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
54677395 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
54677434 CCGGATAT
1 CCGGATAT
54677442 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54678850 original size:11 final size:11
Alignment explanation
Indices: 54678834--54678864 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
54678824 ACCACTAGCA
54678834 AAACATGTTGG
1 AAACATGTTGG
54678845 AAACATGTTGG
1 AAACATGTTGG
54678856 AAACATGTT
1 AAACATGTT
54678865 CCCTTGCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.29
Consensus pattern (11 bp):
AAACATGTTGG
Found at i:54691761 original size:31 final size:31
Alignment explanation
Indices: 54691726--54691789 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
54691716 CCTTTGCATG
54691726 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
54691757 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
54691788 TT
1 TT
54691790 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:54692048 original size:23 final size:24
Alignment explanation
Indices: 54691981--54692146 Score: 239
Period size: 24 Copynumber: 7.0 Consensus size: 24
54691971 GCTTTATCAT
* *
54691981 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* * **
54692006 ATAACTGGGGCAAAATCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
54692030 ATAACT-GGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
54692052 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54692076 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54692100 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54692124 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54692147 TCACTTCCTC
Statistics
Matches: 131, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.05
23 29 0.22
24 85 0.65
25 11 0.08
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:54692221 original size:20 final size:20
Alignment explanation
Indices: 54692196--54692256 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
54692186 TTATGATTAC
54692196 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54692216 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54692236 TTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54692256 A
1 A
54692257 CCATATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54692227 original size:11 final size:11
Alignment explanation
Indices: 54692196--54692251 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54692186 TTATGATTAC
54692196 ATCATGTGCAT
1 ATCATGTGCAT
*
54692207 ATCA--TACAT
1 ATCATGTGCAT
54692216 ATCATGTGCAT
1 ATCATGTGCAT
*
54692227 ATCA--TACAT
1 ATCATGTGCAT
*
54692236 TTCATGTGCAT
1 ATCATGTGCAT
54692247 ATCAT
1 ATCAT
54692252 ACATACCATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:54693617 original size:27 final size:27
Alignment explanation
Indices: 54693586--54694141 Score: 690
Period size: 27 Copynumber: 20.6 Consensus size: 27
54693576 GGGTATTTTA
* *
54693586 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
54693613 ATAATTCTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
54693640 GTAATTCTATAAATCGAGGATAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
54693667 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
54693694 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
54693721 ATAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
54693748 GTAATTATGTAAAT-TAGGGGTAAAACA
1 GTAATTCTGTAAATCGA-GGGTAAAACG
* **
54693775 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
54693802 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
54693829 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
54693856 GTAATTTTACAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
54693883 GTAATTCTATAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
54693910 GTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54693937 ATAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
54693964 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
54693991 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
54694018 GTAATTTTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
54694045 GTAATTCTATAAATTGAGGGTAAAACT
1 GTAATTCTGTAAATCGAGGGTAAAACG
* ** *
54694072 GTAATTTTACAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
54694099 TTAATTCTATAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
54694126 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
54694142 GGAGTACTTT
Statistics
Matches: 464, Mismatches: 57, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.01
27 457 0.98
28 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:54697547 original size:15 final size:15
Alignment explanation
Indices: 54697527--54697556 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54697517 GTGTAATGCT
54697527 CCAAAAATCCCGAAA
1 CCAAAAATCCCGAAA
*
54697542 CCAAAAATCCTGAAA
1 CCAAAAATCCCGAAA
54697557 TCCTGAACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.30, G:0.07, T:0.10
Consensus pattern (15 bp):
CCAAAAATCCCGAAA
Found at i:54698948 original size:29 final size:29
Alignment explanation
Indices: 54698900--54699043 Score: 175
Period size: 29 Copynumber: 5.0 Consensus size: 29
54698890 GTGAGCATGA
* * *
54698900 ATATGAATGTGA-CTGGGCCTAACGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
54698928 AAATAAATGTGATTTGGGCCTATTGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
54698957 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
54698986 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* * * *
54699015 ATATGAATATGA-TTGAGCTTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
54699043 A
1 A
54699044 GATACAGGTA
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 25 0.25
29 75 0.75
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:54702238 original size:42 final size:42
Alignment explanation
Indices: 54702167--54702281 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
54702157 CGTATCAATG
* * * * * *
54702167 CCATATCTCAAATATGGTCTTACATGAAAT-ATCATATCGACG
1 CCATATCTCAGACATGGTCTTATACGAAATCA-CATACCGACA
* * *
54702209 CCATGTCTCGGACATGGTCTTATACGAAATCACATACCGATA
1 CCATATCTCAGACATGGTCTTATACGAAATCACATACCGACA
* *
54702251 CCATATCTCAGATATGGTCTTATACGGAATC
1 CCATATCTCAGACATGGTCTTATACGAAATC
54702282 TCGGTAGCCC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
42 58 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
CCATATCTCAGACATGGTCTTATACGAAATCACATACCGACA
Found at i:54706392 original size:27 final size:27
Alignment explanation
Indices: 54706350--54706480 Score: 163
Period size: 27 Copynumber: 4.9 Consensus size: 27
54706340 TACATCACCT
* * * *
54706350 AGGGCAAAATAATCATCTTACCATATA
1 AGGGCAAAACAGTCATTTTACCACATA
*
54706377 AGGGCAAAACAGTCATTTTACCATATA
1 AGGGCAAAACAGTCATTTTACCACATA
* *
54706404 AAGGCAAAAAAGTCATTTTACCACATA
1 AGGGCAAAACAGTCATTTTACCACATA
* * *
54706431 AGGGTAAAACAATCATTTTACCACGTA
1 AGGGCAAAACAGTCATTTTACCACATA
*
54706458 AGGGCAAAATAGTCATTTTACCA
1 AGGGCAAAACAGTCATTTTACCA
54706481 ATTAGGGGTC
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (27 bp):
AGGGCAAAACAGTCATTTTACCACATA
Found at i:54710683 original size:48 final size:48
Alignment explanation
Indices: 54710612--54710745 Score: 187
Period size: 48 Copynumber: 2.8 Consensus size: 48
54710602 AATATCGATA
* * * *
54710612 CCAATGCCATATCCCAAATATGGTCTTACATGAGATCAAATATTAATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAAATATTAATG
* * * *
54710660 CCAATGCCATGTCCTAGACATGGTCTTACATGGGATCATATTTTGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAAATATTAATG
*
54710708 CCAATGCCATGTCCCAGGCATGGTCTTACATGGGATCA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCA
54710746 CATGTACTGC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (48 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAAATATTAATG
Found at i:54713648 original size:24 final size:24
Alignment explanation
Indices: 54713621--54713803 Score: 312
Period size: 24 Copynumber: 7.6 Consensus size: 24
54713611 CTTATTATGT
* * *
54713621 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
54713645 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54713669 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54713693 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54713717 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54713741 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
54713765 TCGTACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
54713789 TCGCACACATAGTGC
1 TCGCACACATAGTGC
54713804 ATTTGAGATA
Statistics
Matches: 153, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 153 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:54713655 original size:48 final size:47
Alignment explanation
Indices: 54713599--54713803 Score: 284
Period size: 48 Copynumber: 4.3 Consensus size: 47
54713589 GCCGAATGTG
* ** * * *
54713599 GCACACATAGTGCTTATTATGTTCGCACACATAGAGCTATAGCAAATC
1 GCACACATAGTGCTTAGTA-AATCGCACACATAGTGCCATAGTAAATC
54713647 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCT-TAGTAAATCGCACACATAGTGCCATAGTAAATC
*
54713695 GCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATCGCACACATAGTGCCATAGTAAATC
* * *
54713743 GCACACATAGTGCCATAGTAAATCGTACACATAGTGCCATAGTGAATC
1 GCACACATAGTG-CTTAGTAAATCGCACACATAGTGCCATAGTAAATC
54713791 GCACACATAGTGC
1 GCACACATAGTGC
54713804 ATTTGAGATA
Statistics
Matches: 146, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
47 1 0.01
48 140 0.96
49 5 0.03
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (47 bp):
GCACACATAGTGCTTAGTAAATCGCACACATAGTGCCATAGTAAATC
Found at i:54721520 original size:24 final size:24
Alignment explanation
Indices: 54721493--54721699 Score: 369
Period size: 24 Copynumber: 8.6 Consensus size: 24
54721483 CTTATTATGT
* * *
54721493 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
54721517 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54721541 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54721565 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54721589 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54721613 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
54721637 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
54721661 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
54721685 TCGCACACATAGTGC
1 TCGCACACATAGTGC
54721700 ATTTGAGATA
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 179 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:54726391 original size:40 final size:40
Alignment explanation
Indices: 54726345--54726568 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
54726335 CTTGCACAAG
* * *
54726345 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
54726385 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
54726425 GCCTTCGGGT-TTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
54726464 GCCTTCGGGTCTTAGCCCGGATATAGTAACTCA-CACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACT-AGCACAAAT
* * * *
54726504 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
* *
54726545 GCCTTCGGGACTTAGCCTGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
54726569 CATTCGAATA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 38 0.24
40 93 0.59
41 27 0.17
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:54726439 original size:79 final size:80
Alignment explanation
Indices: 54726345--54726568 Score: 290
Period size: 79 Copynumber: 2.8 Consensus size: 80
54726335 CTTGCACAAG
* * *
54726345 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
**
54726410 GTCGCT-AGCACAAAT
66 GTAACTCA-CACAAAT
* * *
54726425 GCCTTCGGGT-TTAGCCCGGATATAATCGCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
*
54726489 GTAACTCACACGAAT
66 GTAACTCACACAAAT
* * * * *
54726504 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGCCTTCGGGACTTAGCCTGGATAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
54726569 CATTCGAATA
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
79 67 0.54
80 25 0.20
81 32 0.26
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GTAACTCACACAAAT
Found at i:54726529 original size:119 final size:120
Alignment explanation
Indices: 54726309--54726568 Score: 316
Period size: 119 Copynumber: 2.2 Consensus size: 120
54726299 CTCAAGTAAT
* * * *
54726309 CTTCGGGATTTAG-CCGGATATAACTACTTGCACAAGGCCTTCGGGTCTTAGCCCGGATGTGGTC
1 CTTCGGGATTTAGCCCGGATATAACTACTAGCACAAGGCCTTCGGGTCTTAGCCCGGATATAGTA
* * *
54726373 ACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGC
66 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACCTAGCACAAAAGC
* *
54726427 CTTCGGG-TTTAGCCCGGATATAA-TCGCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGATTTAGCCCGGATATAACT-ACTAGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATAG
* * *
54726490 TAACTCA-CACGAATGCCTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGC
64 TAACT-AGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTCACCTAGCACAAAAGC
* *
54726547 CTTCGGGACTTAGCCTGGATAT
1 CTTCGGGATTTAGCCCGGATAT
54726569 CATTCGAATA
Statistics
Matches: 121, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
117 6 0.05
118 26 0.21
119 57 0.47
120 20 0.17
121 12 0.10
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (120 bp):
CTTCGGGATTTAGCCCGGATATAACTACTAGCACAAGGCCTTCGGGTCTTAGCCCGGATATAGTA
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACCTAGCACAAAAGC
Found at i:54730013 original size:38 final size:40
Alignment explanation
Indices: 54729924--54730074 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
54729914 GGATATAGCG
* * * * * **
54729924 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGACCGGATATGGTA
* *
54729964 GCTCGCACAAATGCCTTCGGGACTTA-ACCGGATTTGG-A
1 ACTCGCACAAATGCCTTCGGGACTTAGACCGGATATGGTA
* *
54730002 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGACCGGATATGGTA
* *
54730042 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGACCGGA
54730075 CATCATTCGA
Statistics
Matches: 91, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
37 3 0.03
38 22 0.24
39 15 0.16
40 40 0.44
41 11 0.12
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGACCGGATATGGTA
Found at i:54730786 original size:2 final size:2
Alignment explanation
Indices: 54730779--54730804 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54730769 ATGTGCAAAC
54730779 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
54730805 GCTAGAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54737793 original size:40 final size:40
Alignment explanation
Indices: 54737747--54737970 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
54737737 CTTGCACAAG
* * *
54737747 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
54737787 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
54737827 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
54737867 GCCTTCGGGTCTTAGCCCGGATATAG-CAACT-GCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
54737906 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
54737947 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
54737971 CATTCGAATA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 32 0.20
40 101 0.64
41 26 0.16
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:54737842 original size:80 final size:79
Alignment explanation
Indices: 54737711--54737970 Score: 310
Period size: 80 Copynumber: 3.3 Consensus size: 79
54737701 CTCAAGTAAT
* * * * * *
54737711 CTTCGGGATTTAG-CCGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAAC-TGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
54737774 CACTAGCATAAATGC
65 CACTAGCACAAATGC
* * *
54737789 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTTTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACT-GCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
*
54737853 TCGCTAGCACAAATGC
64 TCACTAGCACAAATGC
* * * * *
54737869 CTTCGGGTCTTAGCCCGGATATAGCAACTGCACGAATGCCTTCGGATCTTAGTCCGGTTATAGTC
1 CTTCGGGACTTAGCCCGGATATAGCAACTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTC
*
54737934 ACCTAGCACAAAAGC
66 A-CTAGCACAAATGC
54737949 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
54737971 CATTCGAATA
Statistics
Matches: 155, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
78 13 0.08
79 45 0.29
80 97 0.63
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTC
ACTAGCACAAATGC
Found at i:54737953 original size:120 final size:119
Alignment explanation
Indices: 54737711--54737970 Score: 323
Period size: 120 Copynumber: 2.2 Consensus size: 119
54737701 CTCAAGTAAT
* * *
54737711 CTTCGGGATTTAG-CCGGATATAACTACTTGCACAAGGCCTTCGGGTCTTAGCCCGGATGTGGTC
1 CTTCGGGATTTAGCCCGGATATAACTACTAGCACAAGGCCTTCGGGTCTTAGCCCGGATATAGTC
* * *
54737775 ACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
66 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCCCTAGCACAAAAGC
* * *
54737829 CTTCGGGTTTTAGCCCGGATATAA-TCGCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGATTTAGCCCGGATATAACT-ACTAGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATAG
* * *
54737893 -CAACT-GCACGAATGCCTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGC
64 TC-ACTAGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTC-CCTAGCACAAAAGC
*
54737949 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGATTTAGCCCGGATAT
54737971 CATTCGAATA
Statistics
Matches: 122, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
118 16 0.13
119 45 0.37
120 61 0.50
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (119 bp):
CTTCGGGATTTAGCCCGGATATAACTACTAGCACAAGGCCTTCGGGTCTTAGCCCGGATATAGTC
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCCCTAGCACAAAAGC
Found at i:54741552 original size:226 final size:226
Alignment explanation
Indices: 54741154--54741590 Score: 784
Period size: 226 Copynumber: 1.9 Consensus size: 226
54741144 GTGTTTATCA
* *
54741154 ATGATATCCTGATTTATTCTCGTGACGAGTCTGAACATGCCGATAATCTGAGGACTGTTTTGCAA
1 ATGATATCCTGATTTATTCTCGTGACGAGTCTGAACATACCGATAATCTGAGGACTATTTTGCAA
*
54741219 ACCTTGAGAGATAGGTAGTTGTATGCTAAGTTTAGCAAAAGTGAGTTCTGGCTTAGAGAAGTCAG
66 ACCTTGAGAGATAGGTAGTTGTATGCTAAGTTTAGCAAAAGGGAGTTCTGGCTTAGAGAAGTCAG
*
54741284 ATTTTTATGGCATATTGTGTCGGGGGAAGGGATCCAAGTTGATCCGAGTAAGATTTCAACCATTG
131 ATTTTTAGGGCATATTGTGTCGGGGGAAGGGATCCAAGTTGATCCGAGTAAGATTTCAACCATTG
54741349 TTGATTGGAAACCACTATCCGAAGTTAGAAG
196 TTGATTGGAAACCACTATCCGAAGTTAGAAG
*
54741380 ATGATATCCTGATTTATTCTCGTGACGAGTCTGAACATACCGATCATCTGAGGACTATTTTGCAA
1 ATGATATCCTGATTTATTCTCGTGACGAGTCTGAACATACCGATAATCTGAGGACTATTTTGCAA
* *
54741445 ACCTTGAGAGATAGGTGGTTGTATGCTAAGTTTAGCAAAAGGGATTTCTGGCTTAGAGAAGTCAG
66 ACCTTGAGAGATAGGTAGTTGTATGCTAAGTTTAGCAAAAGGGAGTTCTGGCTTAGAGAAGTCAG
* **
54741510 ATTTTTAGGGCATATTGTGTCGGGGGAAGGGATCCGAGTTGATCCGAGTAAGATTTCGGCCATTG
131 ATTTTTAGGGCATATTGTGTCGGGGGAAGGGATCCAAGTTGATCCGAGTAAGATTTCAACCATTG
54741575 TTGATTGGAAACCACT
196 TTGATTGGAAACCACT
54741591 GAGAAACGTA
Statistics
Matches: 201, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
226 201 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (226 bp):
ATGATATCCTGATTTATTCTCGTGACGAGTCTGAACATACCGATAATCTGAGGACTATTTTGCAA
ACCTTGAGAGATAGGTAGTTGTATGCTAAGTTTAGCAAAAGGGAGTTCTGGCTTAGAGAAGTCAG
ATTTTTAGGGCATATTGTGTCGGGGGAAGGGATCCAAGTTGATCCGAGTAAGATTTCAACCATTG
TTGATTGGAAACCACTATCCGAAGTTAGAAG
Found at i:54744625 original size:42 final size:42
Alignment explanation
Indices: 54744514--54744660 Score: 170
Period size: 43 Copynumber: 3.5 Consensus size: 42
54744504 TTCTGAGATG
* * *
54744514 TGATATCGTGTAAGACCATGTCTGGGACATTGGTATCG-ATC
1 TGATATCATGTAAGACCATGTCTGGGACATTGGCATCGTATA
* *
54744555 TGAGATTACATGTAAGACCATGTTTGGGACATTGGCATCGTATA
1 TGATA-T-CATGTAAGACCATGTCTGGGACATTGGCATCGTATA
* * * * *
54744599 TGATTTCGTGTAAGACCTTGTCTGGGACAGTGGCATCGATATT
1 TGATATCATGTAAGACCATGTCTGGGACATTGGCATCG-TATA
54744642 TGATATCATGTAAGACCAT
1 TGATATCATGTAAGACCAT
54744661 ATCTAGCATA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
41 4 0.05
42 29 0.33
43 49 0.56
44 5 0.06
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (42 bp):
TGATATCATGTAAGACCATGTCTGGGACATTGGCATCGTATA
Found at i:54748295 original size:94 final size:94
Alignment explanation
Indices: 54748184--54748372 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 94
54748174 TGTCTTCAAT
*
54748184 TTTAAGCTATGCTTATGAATTTATGACAACACATAAGTAAACTATGTTATGTCAATGGTATTTAT
1 TTTAAGCTATGCCTATGAATTTATGACAACACATAAGTAAACTATGTTATGTCAATGGTATTTAT
*
54748249 ATATATGATTATGTGGCTAATTATTTGCA
66 ATATATGATTATATGGCTAATTATTTGCA
54748278 TTTAAGCTATGCCTATGAATTTATGACAACACATAAGTAAACTATGTTATGTCAATGGTATTTAT
1 TTTAAGCTATGCCTATGAATTTATGACAACACATAAGTAAACTATGTTATGTCAATGGTATTTAT
*
54748343 ATATATGATTATATTGCTAATTATTTGCA
66 ATATATGATTATATGGCTAATTATTTGCA
54748372 T
1 T
54748373 GTGAACTTAT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (94 bp):
TTTAAGCTATGCCTATGAATTTATGACAACACATAAGTAAACTATGTTATGTCAATGGTATTTAT
ATATATGATTATATGGCTAATTATTTGCA
Found at i:54750638 original size:37 final size:37
Alignment explanation
Indices: 54750585--54750722 Score: 222
Period size: 37 Copynumber: 3.7 Consensus size: 37
54750575 CGAATAGTCC
* * *
54750585 CCACACGTAGTTATCAGGTCTTACCCGTACAAAATCT
1 CCACACGTAGTCATCAGGTCTTACCCGAACATAATCT
*
54750622 CCACACGTAGTCATCAGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCAGGTCTTACCCGAACATAATCT
*
54750659 CCACACGTAGTCATCGGGTCTTACCCGAACATAATCT
1 CCACACGTAGTCATCAGGTCTTACCCGAACATAATCT
*
54750696 CCACACGTAGTCATCGGGTCTTACCCG
1 CCACACGTAGTCATCAGGTCTTACCCG
54750723 GAATATATTT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.25
Consensus pattern (37 bp):
CCACACGTAGTCATCAGGTCTTACCCGAACATAATCT
Found at i:54750923 original size:48 final size:48
Alignment explanation
Indices: 54750865--54750975 Score: 195
Period size: 48 Copynumber: 2.3 Consensus size: 48
54750855 ATATACACAC
*
54750865 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
54750913 ATCTCATACATACTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
54750961 ATCTCATATATATTT
1 ATCTCATACATATTT
54750976 ATCTTGTACA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:54763952 original size:46 final size:45
Alignment explanation
Indices: 54763899--54764073 Score: 199
Period size: 46 Copynumber: 3.8 Consensus size: 45
54763889 TGGTTGAGCA
*
54763899 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGC-AACG
*** * * *
54763945 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGTATGC-A-ACG
*
54763992 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGC-AACG
* * *
54764038 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG
54764074 GGCGGGTTAC
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
46 70 0.65
47 37 0.35
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGCAACG
Found at i:54764055 original size:93 final size:93
Alignment explanation
Indices: 54763896--54764067 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
54763886 GGATGGTTGA
* * *
54763896 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
54763961 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
54763989 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
54764054 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
54764068 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:54772109 original size:29 final size:29
Alignment explanation
Indices: 54772019--54772207 Score: 229
Period size: 29 Copynumber: 6.5 Consensus size: 29
54772009 ACTCGATTTC
* * **
54772019 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
54772048 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
54772076 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
*
54772106 GCACACTTAGTGCCATATATTTCTAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54772135 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54772164 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
54772193 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
54772208 ATCTCGTCAC
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
28 2 0.01
29 135 0.98
30 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:54780089 original size:49 final size:49
Alignment explanation
Indices: 54780030--54780528 Score: 839
Period size: 49 Copynumber: 10.3 Consensus size: 49
54780020 GTATGAGATA
*
54780030 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54780079 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54780128 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54780177 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
54780226 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54780275 TATATATGTGATATGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* *
54780324 TATATATGTGATATGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54780373 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAG-AAG-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54780420 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * * * * *
54780467 TATATATGTGATAGGGCCGAATGGCCAAAGTGATGGATGTGGAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
54780514 TATAAATGTGATAAG
1 TATATATGTGATAAG
54780529 TCCCGAAGGG
Statistics
Matches: 434, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 99 0.23
48 5 0.01
49 330 0.76
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:54782754 original size:55 final size:53
Alignment explanation
Indices: 54782687--54782941 Score: 261
Period size: 55 Copynumber: 4.8 Consensus size: 53
54782677 ATTAGGGTTT
*
54782687 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAAT-GGTAA-GTTTCTAAGGC
* * * * * *
54782742 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTTTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT--TCTAAGGC
* * * * *
54782797 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTAGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTC-TAAGGC
*
54782850 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTCTAAGGC
** * *
54782899 AAGGATACCACATAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG
54782942 GTACCCGTGT
Statistics
Matches: 168, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
49 39 0.23
52 7 0.04
53 41 0.24
54 8 0.05
55 69 0.41
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTCTAAGGC
Found at i:54782893 original size:108 final size:110
Alignment explanation
Indices: 54782694--54782894 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
54782684 TTTAAGGATA
* *
54782694 CCATGTAAGACCATGCCAAGGCATGGCAATGGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATGAGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
54782759 CCATGTCAAGACATGGCATTGATAAGTTACTTTAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTTTAAGGCAAAGGTC
* * *
54782804 CCATGTAAGACCATGCCAAGGCATGGC-ATTAGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATGAGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
54782866 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
54782895 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.58
109 5 0.06
110 27 0.33
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATGAGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTTTAAGGCAAAGGTC
Found at i:54783045 original size:23 final size:24
Alignment explanation
Indices: 54783015--54783059 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
54783005 AAGGTAAGGT
*
54783015 AAGGTAAGACGAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
54783038 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
54783060 CAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:54783159 original size:16 final size:16
Alignment explanation
Indices: 54783138--54783168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54783128 ATAAATTTGA
54783138 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
54783154 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
54783169 AGTGAAGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:54790339 original size:55 final size:53
Alignment explanation
Indices: 54790252--54790485 Score: 255
Period size: 55 Copynumber: 4.4 Consensus size: 53
54790242 ATTAGGGTTT
*
54790252 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * * *
54790307 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* * * *
54790362 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTAGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* *
54790415 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
*
54790464 AAGGATACCACGTAAGACCATG
1 AAGGATACCATGTAAGACCATG
54790486 AAAAGTCATA
Statistics
Matches: 151, Mismatches: 22, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
49 21 0.14
52 7 0.05
53 41 0.27
54 11 0.07
55 67 0.44
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:54790458 original size:108 final size:110
Alignment explanation
Indices: 54790259--54790459 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
54790249 TTTAAGGATA
* *
54790259 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTAGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
54790324 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
54790369 CCATGTAAGACCATGCCAAGGCATGGC-ATTAGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTAGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
54790431 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
54790460 TCAAAAGGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.57
109 6 0.07
110 27 0.32
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTAGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:54790601 original size:23 final size:24
Alignment explanation
Indices: 54790575--54790619 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
54790565 AAGGTAAGGT
*
54790575 AAGGTAAGACGAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
54790598 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
54790620 CAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:54790719 original size:16 final size:16
Alignment explanation
Indices: 54790698--54790728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54790688 ATAAATTTGA
54790698 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
54790714 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
54790729 AGTGAATAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:54805586 original size:79 final size:80
Alignment explanation
Indices: 54805426--54805592 Score: 212
Period size: 79 Copynumber: 2.1 Consensus size: 80
54805416 CATTTGAATG
* * * **
54805426 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTGACCATATCCGGGCTAAGACCCGAAGGCA
*
54805491 TTCGTGCGAGTTGTT
66 TTCGTGCGAGTGGTT
* * *
54805506 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCA-ATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTGACCATATCCGGGCTAAGACCCGAAGGC-
**
54805570 ATT-GTGCTTGTGGTT
65 ATTCGTGCGAGTGGTT
54805585 ATATCCGG
1 ATATCCGG
54805593 TTAAATCCCG
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
79 38 0.51
80 37 0.49
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTGACCATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTGGTT
Found at i:54805606 original size:39 final size:40
Alignment explanation
Indices: 54805426--54805592 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
54805416 CATTTGAATG
* * *
54805426 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
54805466 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * **
54805506 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * *
54805546 A-ATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
54805585 ATATCCGG
1 ATATCCGG
54805593 TTAAATCCCG
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.33
40 67 0.63
41 5 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:54813706 original size:39 final size:40
Alignment explanation
Indices: 54813531--54813692 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
54813521 TTGAATGATA
* * *
54813531 CCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
54813570 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * **
54813610 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCA-AT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
54813649 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
54813689 CCGG
1 CCGG
54813693 TTAAATCCCG
Statistics
Matches: 102, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
39 45 0.44
40 52 0.51
41 5 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:54821109 original size:27 final size:28
Alignment explanation
Indices: 54821052--54821121 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54821042 AAATTTGTAC
**
54821052 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
54821080 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
54821107 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
54821122 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:54821130 original size:27 final size:27
Alignment explanation
Indices: 54821052--54821133 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
54821042 AAATTTGTAC
* *
54821052 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
54821080 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
54821107 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
54821134 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:54823198 original size:2 final size:2
Alignment explanation
Indices: 54823191--54823222 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54823181 ATGTGCAAAC
54823191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54823223 GCTAGAGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54830819 original size:18 final size:18
Alignment explanation
Indices: 54830771--54830821 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
54830761 GTGTTGAGAT
*
54830771 ATTTTGAAAACAAGTATC
1 ATTTTGAAAACACGTATC
54830789 ATTTTGAAAACACGTATC
1 ATTTTGAAAACACGTATC
54830807 ATTTTGAAAACACGT
1 ATTTTGAAAACACGT
54830822 CCTAAGTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (18 bp):
ATTTTGAAAACACGTATC
Found at i:54831228 original size:31 final size:31
Alignment explanation
Indices: 54831187--54831250 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
54831177 CCTTTTCATA
* *
54831187 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCAGAACACTGGGCCGAAGCCT
**
54831218 TTTCAAATTTCAGATTACTGGGCCGAAGCCT
1 TTTCAAATTTCAGAACACTGGGCCGAAGCCT
54831249 TT
1 TT
54831251 ACGGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (31 bp):
TTTCAAATTTCAGAACACTGGGCCGAAGCCT
Found at i:54831486 original size:25 final size:24
Alignment explanation
Indices: 54831444--54831539 Score: 124
Period size: 25 Copynumber: 4.0 Consensus size: 24
54831434 ACTTTATCAT
*
54831444 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
54831469 ATAACTGGGGCAAAAGCCCTTTTTG
1 ATAACTGGGGCATAAGCCC-TTTTA
54831494 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
54831517 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54831540 TCACTTCCTC
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
23 22 0.35
24 7 0.11
25 34 0.54
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:54831524 original size:23 final size:23
Alignment explanation
Indices: 54831465--54831538 Score: 112
Period size: 23 Copynumber: 3.1 Consensus size: 23
54831455 CCTAGCCTCT
*
54831465 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
54831488 TTTTTGATAACTGGGGCATAAGCCC
1 --TTTAATAACTGGGGCATAAGCCC
54831513 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54831536 TTT
1 TTT
54831539 TTCACTTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 25 0.54
25 21 0.46
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:54831612 original size:9 final size:9
Alignment explanation
Indices: 54831598--54831654 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
54831588 ATCTCGTGTG
54831598 CATATCATA
1 CATATCATA
*
54831607 CATATCATGTG
1 CATATCA--TA
54831618 CATATCATA
1 CATATCATA
* *
54831627 CATGTCATGTG
1 CATATCA--TA
54831638 CATATCATA
1 CATATCATA
54831647 CATATCAT
1 CATATCAT
54831655 GTTTACCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:54831617 original size:20 final size:20
Alignment explanation
Indices: 54831594--54831656 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
54831584 GAACATCTCG
54831594 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
54831614 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
54831634 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
54831654 TGT
1 TGT
54831657 TTACCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:54832923 original size:27 final size:27
Alignment explanation
Indices: 54832893--54832964 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
54832883 TACCATACAG
* **
54832893 GGGTATTTTGGTAGTTTTACAAATTAA
1 GGGTATTTTGGTAATTTTACAAACCAA
** *
54832920 GGGTATTGCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
54832947 GGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTT
54832965 GTAAATCGAG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:54832976 original size:27 final size:27
Alignment explanation
Indices: 54832956--54833352 Score: 476
Period size: 27 Copynumber: 14.7 Consensus size: 27
54832946 AGGGTATTTT
*
54832956 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
54832983 AGTAATTCTGTAAATCAAGGGTGAACC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
54833010 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
54833037 GGTAATTTTGTAAATTGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
54833064 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
54833091 -GATAATTATGTAAATCGAGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * * *
54833118 GGTAATTATGTAAATTGGGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
54833145 GGTAATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
54833172 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
54833199 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
54833226 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
54833253 GGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
54833280 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
54833307 AATAATTCTATAAA-CTGAAGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
54833334 GGTAATTCTGTAAATCGAG
1 AGTAATTCTGTAAATCGAG
54833353 AGTACTTTGG
Statistics
Matches: 322, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.01
27 316 0.98
28 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:54846226 original size:9 final size:9
Alignment explanation
Indices: 54846208--54846244 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
54846198 TATAGTTTGA
54846208 TATTCGAAT
1 TATTCGAAT
*
54846217 TATTCAAAT
1 TATTCGAAT
*
54846226 TATTCGAGT
1 TATTCGAAT
54846235 TATTCGAAT
1 TATTCGAAT
54846244 T
1 T
54846245 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54846316 original size:9 final size:9
Alignment explanation
Indices: 54846284--54846317 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
54846274 TTTGAAAAAA
54846284 TCGAGTTAAC
1 TCGA-TTAAC
*
54846294 TCGAATAAC
1 TCGATTAAC
54846303 TCGATTAAC
1 TCGATTAAC
54846312 TCGATT
1 TCGATT
54846318 CGTTTGACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (9 bp):
TCGATTAAC
Found at i:54853655 original size:40 final size:39
Alignment explanation
Indices: 54853586--54853751 Score: 260
Period size: 40 Copynumber: 4.2 Consensus size: 39
54853576 AACCCAAGTA
* * *
54853586 CCTTCGAGATTTAGCTGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCTGGATATAGTAACTCGCACAAATG
54853625 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CTGGATATAGTAACTCGCACAAATG
*
54853665 CCTTCGGAACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCT-GGATATAGTAACTCGCACAAATG
*
54853705 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CTGGATATAGTAACTCGCACAAATG
54853745 CCTTCGG
1 CCTTCGG
54853752 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 14 0.12
40 103 0.87
41 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCTGGATATAGTAACTCGCACAAATG
Found at i:54853718 original size:80 final size:79
Alignment explanation
Indices: 54853596--54853758 Score: 290
Period size: 80 Copynumber: 2.1 Consensus size: 79
54853586 CCTTCGAGAT
*
54853596 TTAGCTGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCTGGATATAGTAACTCGCACA
1 TTAGCTGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
54853661 AATGCCTTCGGAAC
66 AATGCCTTCGGAAC
*
54853675 TTAGCTCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
1 TTAGCT-GGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
*
54853740 AAATGCCTTCGGATC
65 AAATGCCTTCGGAAC
54853755 TTAG
1 TTAG
54853759 TCCGGTTATC
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 6 0.08
80 74 0.93
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (79 bp):
TTAGCTGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
AATGCCTTCGGAAC
Found at i:54861787 original size:78 final size:77
Alignment explanation
Indices: 54861658--54861819 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 77
54861648 AACCCAAGTA
*
54861658 CCTTCGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 CCTTC-GACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
54861723 ACTCGCACAAATG
65 ACTCGCACAAATG
*
54861736 CCTTCGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 CCTTCGACTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
54861801 ACTCGCACAAATG
65 ACTCGCACAAATG
54861814 CCTTCG
1 CCTTCG
54861820 GATCTTAGTC
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
77 6 0.07
78 75 0.93
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (77 bp):
CCTTCGACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
CTCGCACAAATG
Found at i:54861827 original size:40 final size:39
Alignment explanation
Indices: 54861658--54861832 Score: 282
Period size: 40 Copynumber: 4.5 Consensus size: 39
54861648 AACCCAAGTA
* *
54861658 CCTTCGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54861696 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
54861736 CCTTC-GACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54861774 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54861814 CCTTCGGATCTTAGTCCGG
1 CCTTCGGA-CTTAGCCCGG
54861833 TTATCATCCG
Statistics
Matches: 129, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
38 43 0.33
39 10 0.08
40 76 0.59
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54864950 original size:29 final size:29
Alignment explanation
Indices: 54864918--54864990 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
54864908 CTTCGAGCTC
* *
54864918 GCACACCCAGTGCCGTATTTTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
54864947 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
54864976 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
54864991 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:54866206 original size:24 final size:24
Alignment explanation
Indices: 54866165--54866220 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
54866155 TTTTTTTCCT
54866165 TTTCTTTGTTTTTCTTCATATTCTC
1 TTTCTTTGTTTTTCTTCAT-TTCTC
* *
54866190 TTTCTTT-TTTTTTTTCATTTCTT
1 TTTCTTTGTTTTTCTTCATTTCTC
54866213 TATTCTTT
1 T-TTCTTT
54866221 CTACATAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 16 0.57
25 7 0.25
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTCTTTGTTTTTCTTCATTTCTC
Found at i:54872806 original size:29 final size:29
Alignment explanation
Indices: 54872774--54872846 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
54872764 CTTCGAGCTC
* *
54872774 GCACACCCAGTGCCGTATTTTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
54872803 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
54872832 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
54872847 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:54873768 original size:7 final size:7
Alignment explanation
Indices: 54873756--54873784 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
54873746 TCACCACCAC
54873756 AACATCA
1 AACATCA
54873763 AACATCA
1 AACATCA
54873770 AACATCA
1 AACATCA
54873777 AACATCA
1 AACATCA
54873784 A
1 A
54873785 TGATACCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (7 bp):
AACATCA
Found at i:54874070 original size:24 final size:24
Alignment explanation
Indices: 54874029--54874084 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
54874019 TTTTTTTCCT
54874029 TTTCTTTGTTTTTCTTCATATTCTC
1 TTTCTTTGTTTTTCTTCAT-TTCTC
* *
54874054 TTTCTTT-TTTTTTTTCATTTCTT
1 TTTCTTTGTTTTTCTTCATTTCTC
54874077 TATTCTTT
1 T-TTCTTT
54874085 CTACATAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 16 0.57
25 7 0.25
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTCTTTGTTTTTCTTCATTTCTC
Found at i:54883938 original size:20 final size:20
Alignment explanation
Indices: 54883893--54883952 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
54883883 ATAAATATGG
*
54883893 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
54883913 -ATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
54883932 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
54883952 T
1 T
54883953 GTAATCATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.47
20 20 0.53
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:54883966 original size:20 final size:19
Alignment explanation
Indices: 54883894--54883955 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
54883884 TAAATATGGT
*
54883894 ATGTATGAGATGCACATGA
1 ATGTATGATATGCACATGA
54883913 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
54883932 TATGTATGATATGCACATG-
1 -ATGTATGATATGCACATGA
54883951 ATGTA
1 ATGTA
54883956 ATCATAATGC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 5 0.12
19 18 0.44
20 18 0.44
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (19 bp):
ATGTATGATATGCACATGA
Found at i:54884028 original size:24 final size:24
Alignment explanation
Indices: 54884001--54884143 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
54883991 GAGGAAGTGA
54884001 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
54884025 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
54884049 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
54884072 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
54884096 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
54884120 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54884144 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:54884094 original size:47 final size:47
Alignment explanation
Indices: 54884001--54884143 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
54883991 GAGGAAGTGA
54884001 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
54884049 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
54884096 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
54884144 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:54884117 original size:71 final size:72
Alignment explanation
Indices: 54884001--54884144 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
54883991 GAGGAAGTGA
*
54884001 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
54884064 CCAGTTAT
65 CCAGTTAT
** * *
54884072 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
54884137 CAGTTAT
66 CAGTTAT
54884144 A
1 A
54884145 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:54884370 original size:31 final size:31
Alignment explanation
Indices: 54884335--54884398 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
54884325 CGTTTACAGT
54884335 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
54884366 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54884397 AA
1 AA
54884399 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54890849 original size:25 final size:25
Alignment explanation
Indices: 54890820--54890867 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54890810 TTATAATATG
* * *
54890820 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
54890845 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
54890868 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:54890970 original size:20 final size:20
Alignment explanation
Indices: 54890910--54890970 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
54890900 ATAAATATGG
*
54890910 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
54890930 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
54890950 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
54890970 T
1 T
54890971 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:54891047 original size:24 final size:24
Alignment explanation
Indices: 54891020--54891138 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
54891010 GAGGAAGTGA
54891020 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54891044 AAAAGGGCTTATGCCTCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
54891067 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
54891091 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54891115 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54891139 ATGATAAAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 22 0.26
24 52 0.61
25 11 0.13
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:54891089 original size:47 final size:48
Alignment explanation
Indices: 54891020--54891138 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
54891010 GAGGAAGTGA
*
54891020 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCTCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
* *
54891067 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
*
54891115 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54891139 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:54891365 original size:31 final size:31
Alignment explanation
Indices: 54891330--54891393 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
54891320 CGTTTACAGT
54891330 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
54891361 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54891392 AA
1 AA
54891394 TAAGAAAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54892923 original size:27 final size:27
Alignment explanation
Indices: 54892889--54893088 Score: 247
Period size: 27 Copynumber: 7.4 Consensus size: 27
54892879 TGGATAAGTT
*
54892889 GTAGAATTACCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
54892916 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** * *
54892943 GTAGAATTATTGAAATACCCTTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
54892970 GTAGAATTACCGAAAAACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* **
54892997 ATAGAATTACCGAAATACCTTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
54893024 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** * * *
54893051 GTAGAATTATTGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
54893078 GTAAAATTACC
1 GTAGAATTACC
54893089 ATTTTGCCCC
Statistics
Matches: 146, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:54893887 original size:27 final size:26
Alignment explanation
Indices: 54893847--54893905 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
54893837 TATATATATC
*
54893847 TATCTGTTCTGGTGGCCTAGCCACAA
1 TATCTGTTCTGGTGACCTAGCCACAA
* * *
54893873 TATCTGTATCTGGTGACTTCGTCACAA
1 TATCTGT-TCTGGTGACCTAGCCACAA
54893900 TATCTG
1 TATCTG
54893906 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (26 bp):
TATCTGTTCTGGTGACCTAGCCACAA
Found at i:54899242 original size:14 final size:16
Alignment explanation
Indices: 54899218--54899250 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
54899208 ATTTTCTGTG
54899218 TTTATTATGTGTGA-A
1 TTTATTATGTGTGAGA
54899233 TTTA-TATGTGTGAGA
1 TTTATTATGTGTGAGA
54899248 TTT
1 TTT
54899251 TCGTGATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (16 bp):
TTTATTATGTGTGAGA
Found at i:54913127 original size:56 final size:56
Alignment explanation
Indices: 54913041--54913176 Score: 254
Period size: 56 Copynumber: 2.4 Consensus size: 56
54913031 ACCATGGCAT
*
54913041 TGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTC
1 TGATATATGTGTGCGAGTAAGACCAAGTTTAATACGTTGGCATCGATATGTGACTC
54913097 TGATATATGTGTGCGAGTAAGACCAAGTTTAATACGTTGGCATCGATATGTGACTC
1 TGATATATGTGTGCGAGTAAGACCAAGTTTAATACGTTGGCATCGATATGTGACTC
*
54913153 CGATATATGTGTGCGAGTAAGACC
1 TGATATATGTGTGCGAGTAAGACC
54913177 CTGTCTGGGA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
56 78 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (56 bp):
TGATATATGTGTGCGAGTAAGACCAAGTTTAATACGTTGGCATCGATATGTGACTC
Found at i:54916859 original size:31 final size:31
Alignment explanation
Indices: 54916824--54916887 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
54916814 CTTTTTCATG
*
54916824 TTTCATATTCCATAACACTAGGCTGAAGCCT
1 TTTCATATTCCATAACACTAGGCCGAAGCCT
* ** *
54916855 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTAGGCCGAAGCCT
54916886 TT
1 TT
54916888 ACTGTAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTCCATAACACTAGGCCGAAGCCT
Found at i:54917130 original size:24 final size:24
Alignment explanation
Indices: 54917079--54917221 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
54917069 GCTTTATCAT
*
54917079 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
54917104 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
54917128 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
54917151 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
54917175 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
54917199 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54917222 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:54917158 original size:47 final size:48
Alignment explanation
Indices: 54917079--54917220 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
54917069 GCTTTATCAT
* *
54917079 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
54917128 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
54917175 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
54917221 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:54917179 original size:71 final size:72
Alignment explanation
Indices: 54917078--54917221 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
54917068 TGCTTTATCA
*
54917078 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
54917143 GCCCTTT
66 GCCCTTT
* * **
54917150 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
54917213 AGCCCTTT
65 AGCCCTTT
54917221 T
1 T
54917222 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:54917296 original size:20 final size:20
Alignment explanation
Indices: 54917271--54917331 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
54917261 TTACGATTAC
54917271 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54917291 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
54917311 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
54917331 A
1 A
54917332 CCATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54918725 original size:27 final size:27
Alignment explanation
Indices: 54918692--54919003 Score: 184
Period size: 27 Copynumber: 11.6 Consensus size: 27
54918682 TTGGTAAATC
*
54918692 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
** * *
54918719 TGTAAACCAATGGTATTTCTA-TAATTTT
1 TACAAATCAAGGGTATTTC-AGTAA-TTT
* * *
54918747 TAGAAAGTCAAGGGTATTTCTGTAACTT
1 TACAAA-TCAAGGGTATTTCAGTAATTT
** * **
54918775 TGTAAATCAGGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
** *
54918802 TACAAATTGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * **
54918829 CACAAA-CCAGTGGTATTTTGGTAATTT
1 TACAAATCAAG-GGTATTTCAGTAATTT
* **
54918856 TACAAA-CTAGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
** *
54918882 TACAAATTGAGGGTATTTCTGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * *
54918909 TACAAACCAAGGGTATTTTAGCAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* *
54918936 TACAGA-CTAGGGTA-TTCTAGTAATTT
1 TACAAATCAAGGGTATTTC-AGTAATTT
** * *** *
54918962 TGTAAATCGAGGGTAAAACAGTAATTC
1 TACAAATCAAGGGTATTTCAGTAATTT
**
54918989 TGTAAATCAAGGGTA
1 TACAAATCAAGGGTA
54919004 AAACGGTAAT
Statistics
Matches: 227, Mismatches: 49, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
25 2 0.01
26 41 0.18
27 155 0.68
28 15 0.07
29 14 0.06
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCAGTAATTT
Found at i:54918885 original size:80 final size:80
Alignment explanation
Indices: 54918785--54918976 Score: 278
Period size: 80 Copynumber: 2.4 Consensus size: 80
54918775 TGTAAATCAG
*
54918785 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATTTTA
*
54918849 GTAATTTTACAAACTA
65 GCAATTTTACAAACTA
* *
54918865 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTTTAG
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG
*
54918930 CAATTTTACAGACTA
66 CAATTTTACAAACTA
* * ** *
54918945 GGGTATTCTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTA
54918977 AAACAGTAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 99 0.98
81 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG
CAATTTTACAAACTA
Found at i:54918976 original size:53 final size:54
Alignment explanation
Indices: 54918692--54918962 Score: 164
Period size: 53 Copynumber: 5.0 Consensus size: 54
54918682 TTGGTAAATC
* * ** ** * *
54918692 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCTATAATTTT
1 TACAAACCAAGGGTATTTTAGCAATTTTACAAACTGAGGGTATTTCTGTAA-TTT
* * * * *
54918747 TAGAAAGTCAAGGGTATTTCT-GTAACTTTGTA-AATCAG-GGGTATTT-TGGTAATTT
1 TACAAA-CCAAGGGTATTT-TAGCAA-TTT-TACAAACTGAGGGTATTTCT-GTAATTT
*** ** * * *
54918802 TACAAATTGAGGGTATTTCGGTAATTTCACAAAC-CAGTGGTATTT-TGGTAATTT
1 TACAAACCAAGGGTATTTTAGCAATTTTACAAACTGAG-GGTATTTCT-GTAATTT
* * * *
54918856 TACAAA-CTAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTT
1 TACAAACCAAGGGTATTTTAGCAATTTTACAAACTGAGGGTATTTCTGTAATTT
*
54918909 TACAAACCAAGGGTATTTTAGCAATTTTACAGACT-AGGGTA-TTCTAGTAATTT
1 TACAAACCAAGGGTATTTTAGCAATTTTACAAACTGAGGGTATTTCT-GTAATTT
54918962 T
1 T
54918963 GTAAATCGAG
Statistics
Matches: 176, Mismatches: 27, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
52 5 0.03
53 63 0.36
54 62 0.35
55 14 0.08
56 25 0.14
57 6 0.03
58 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (54 bp):
TACAAACCAAGGGTATTTTAGCAATTTTACAAACTGAGGGTATTTCTGTAATTT
Found at i:54919000 original size:80 final size:80
Alignment explanation
Indices: 54918785--54919003 Score: 199
Period size: 80 Copynumber: 2.7 Consensus size: 80
54918775 TGTAAATCAG
* * * *** *
54918785 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATT-TCACAAACC-AGTGGTATTTT
1 GGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCT-ACAAACCAAG-GGTATTTT
* *
54918848 GGTAATTTTACAAACTA
64 AGCAATTTTACAAACTA
* * * *** * *
54918865 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTTTAG
1 GGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTACAAACCAAGGGTATTTTAG
*
54918930 CAATTTTACAGACTA
66 CAATTTTACAAACTA
** ** *
54918945 GGGTATTCTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTA
1 GGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTACAAACCAAGGGTA
54919004 AAACGGTAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
80 117 0.98
81 3 0.03
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (80 bp):
GGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTACAAACCAAGGGTATTTTAG
CAATTTTACAAACTA
Found at i:54919004 original size:27 final size:27
Alignment explanation
Indices: 54918955--54919090 Score: 200
Period size: 27 Copynumber: 5.0 Consensus size: 27
54918945 GGGTATTCTA
* *
54918955 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54918982 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
54919009 GTAATTCTATAAATCAAAGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54919036 GTACTTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54919063 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
54919090 G
1 G
54919091 GGGTAAAATG
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:54919086 original size:38 final size:38
Alignment explanation
Indices: 54919044--54919122 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
54919034 CGGTACTTCT
* * *
54919044 GTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGG
1 GTAAAACGAGGGTAAAACGGTAATTATGTAAATCGAGG
* * *
54919082 GTAAAACGGGGGTAAAATGGTAATTATGTAAATCGGGG
1 GTAAAACGAGGGTAAAACGGTAATTATGTAAATCGAGG
54919120 GTA
1 GTA
54919123 CTTTGGTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.08, G:0.33, T:0.24
Consensus pattern (38 bp):
GTAAAACGAGGGTAAAACGGTAATTATGTAAATCGAGG
Found at i:54919149 original size:27 final size:27
Alignment explanation
Indices: 54919119--54919194 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
54919109 GTAAATCGGG
* *
54919119 GGTACTTTGGTAATTTTACAAGTCGAA
1 GGTACTTTAGTAATTTTACAAATCGAA
* *
54919146 GGTACTTCAGTAATTTTACAAATCGAG
1 GGTACTTTAGTAATTTTACAAATCGAA
*
54919173 GGTA-TTTCAGTATTTTTACAAA
1 GGTACTTT-AGTAATTTTACAAA
54919195 CTAAGCGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (27 bp):
GGTACTTTAGTAATTTTACAAATCGAA
Found at i:54919224 original size:28 final size:27
Alignment explanation
Indices: 54919128--54919226 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
54919118 GGGTACTTTG
* * *
54919128 GTAATTTTACAAGTCGAAG-GTACTTCA
1 GTAATTTTACAA-ACTAAGCGTATTTCA
* *
54919155 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGCGTATTTCA
* *
54919182 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGCGTATTTCA
*
54919209 GTAATTTTAGTAAACTAA
1 GTAATTTTA-CAAACTAA
54919227 AGTATTCTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
26 2 0.03
27 48 0.83
28 8 0.14
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGCGTATTTCA
Found at i:54922248 original size:47 final size:48
Alignment explanation
Indices: 54922169--54922334 Score: 248
Period size: 47 Copynumber: 3.5 Consensus size: 48
54922159 GCTTTATCAT
* * **
54922169 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTG
54922218 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTG
*
54922265 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTG
54922313 ATAACT-GGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54922335 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
47 60 0.54
48 39 0.35
49 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTG
Found at i:54922269 original size:71 final size:71
Alignment explanation
Indices: 54922168--54922334 Score: 248
Period size: 71 Copynumber: 2.3 Consensus size: 71
54922158 TGCTTTATCA
*
54922168 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
54922232 AGCCCTTT
64 AGCCCTTT
* * **
54922240 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
54922305 CCCTTT
66 CCCTTT
54922311 TGATAACT-GGGCATAAGCCCTTTT
1 T-ATAACTGGGGCATAAGCCCTTTT
54922335 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
71 69 0.78
72 19 0.22
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (71 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
CCCTTT
Found at i:54922335 original size:24 final size:24
Alignment explanation
Indices: 54922169--54922334 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
54922159 GCTTTATCAT
* *
54922169 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* **
54922194 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
54922218 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
54922241 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54922265 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54922289 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54922313 ATAACT-GGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54922335 TCACTTCCTC
Statistics
Matches: 134, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
23 39 0.29
24 83 0.62
25 12 0.09
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:54922409 original size:20 final size:20
Alignment explanation
Indices: 54922384--54922450 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
54922374 TTATGATTAC
54922384 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54922404 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
54922424 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
*
54922444 ACCATGT
1 ATCATGT
54922451 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54924329 original size:187 final size:189
Alignment explanation
Indices: 54923996--54924472 Score: 655
Period size: 187 Copynumber: 2.5 Consensus size: 189
54923986 ATTACTGAAA
* ***
54923996 TACCCTCGACTTGTAAAATTACCAAAGTACTCC-CGATTTACAGAATTACCGTTTTACCCTCAGT
1 TACCCTCGATTTGTAAAATTACCATTTTAC-CCTCGATTTACAGAATTACCGTTTTACCCTCAGT
* *
54924060 TTACAGAATTACTATTTTACCCTCGA-TT-TACAATTACCGTTTTACCCTCAGTTTACAGAATTA
65 TTACAGAATTACTATTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCAATTTACAGAATTA
*** * *
54924123 TTGTTTTACCCTTGATTTACAGAATTA-CTGTTTTACCCTCGATTTATAGAATTACCGTTT
130 CCATTTTACCCTCGATTTACAGAATTATC-GTTTTACCCTCGATTTACAGAATTACCGTTT
*
54924183 TACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTT
1 TACCCTCGATTTGTAAAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTT
* *
54924248 TACAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCC-CTAATTTACATAATTA
66 TACAGAATTACTATTTTACCCTCGATTTATAAAATTACCGTTTTACCCTC-AATTTACAGAATTA
*
54924312 CCATTTT-CCC-CGATTTACATAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTT
130 CCATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTT
** * * * *
54924370 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCT-TGAT
1 TACCCTCGATTTGTAAAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAG-T
* *
54924434 TTACAGAATTACTGTTTTACCCTCGATTTACAAAATTAC
65 TTACAGAATTACTATTTTACCCTCGATTTATAAAATTAC
54924473 TAAAATACCC
Statistics
Matches: 260, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
186 3 0.01
187 216 0.83
188 7 0.03
189 34 0.13
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (189 bp):
TACCCTCGATTTGTAAAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAGTT
TACAGAATTACTATTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCAATTTACAGAATTAC
CATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTT
Found at i:54924473 original size:27 final size:27
Alignment explanation
Indices: 54924029--54924472 Score: 580
Period size: 27 Copynumber: 16.6 Consensus size: 27
54924019 AAAGTACTCC
54924029 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54924056 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
54924083 CGATTTAC--AATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54924108 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
54924135 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
54924162 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
54924189 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
54924216 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54924243 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
54924270 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
54924296 CTAATTTACATAATTACCATTTT-CCC-
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
54924322 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
54924349 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
54924376 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54924403 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54924430 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
54924457 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
54924473 TAAAATACCC
Statistics
Matches: 368, Mismatches: 38, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
24 1 0.00
25 39 0.11
26 10 0.03
27 315 0.86
28 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:54924509 original size:81 final size:81
Alignment explanation
Indices: 54923993--54924516 Score: 314
Period size: 81 Copynumber: 6.5 Consensus size: 81
54923983 CCAATTACTG
* * * *
54923993 AAATACCCTCGACTTGTAAAATTACC-AAAGTACTCC-CGATTTACAGAATTACCGTTTTACCCT
1 AAATACCCTCGATTTATAGAATTACCGCAA-TAC-CCTCGATTTACAGAATTACCGTTTTACCCT
* *
54924056 C-AGTTTACAGAATTACTA
64 CGA-TTTACAAAATTACCA
*** * *** ** *
54924074 TTTTACCCTCGA-TT-TACAATTACCGTTTTACCCTC-AGTTTACAGAATTATTGTTTTACCCTT
1 AAATACCCTCGATTTATAGAATTACCGCAATACCCTCGA-TTTACAGAATTACCGTTTTACCCTC
* **
54924136 GATTTACAGAATTACTG
65 GATTTACAAAATTACCA
*** *** ** *
54924153 TTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCG
1 AAATACCCTCGATTTATAGAATTACCGCAATACCCTCGATTTACAGAATTACCGTTTTACCCTCG
* *
54924218 ATTTACAGAATTACCG
66 ATTTACAAAATTACCA
*** * ***** *
54924234 TTTTACCCTC-AGTTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCC-C
1 AAATACCCTCGA-TTTATAGAATTACCGCAATACCCTCGATTTACAGAATTACCGTTTTACCCTC
* *
54924297 TAATTTACATAATTACC-
65 -GATTTACAAAATTACCA
** * * * * ***
54924314 ATTTTCCC-CGATTTACATAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCG
1 AAATACCCTCGATTTATAGAATTACCGCAATACCCTCGATTTACAGAATTACCGTTTTACCCTCG
*
54924378 ATTTACAGAATTACCA
66 ATTTACAAAATTACCA
*** * *** * *
54924394 TTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCG
1 AAATACCCTCGATTTATAGAATTACCGCAATACCCTCGATTTACAGAATTACCGTTTTACCCTCG
*
54924459 ATTTACAAAATTACTA
66 ATTTACAAAATTACCA
* * * *
54924475 AAATACCCTTGGTTTGT-GAAATTACCGCAATACCCTCAATTT
1 AAATACCCTCGATTTATAG-AATTACCGCAATACCCTCGATTT
54924517 GTAAAACTAC
Statistics
Matches: 372, Mismatches: 57, Indels: 28
0.81 0.12 0.06
Matches are distributed among these distances:
78 3 0.01
79 121 0.33
80 22 0.06
81 225 0.60
82 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (81 bp):
AAATACCCTCGATTTATAGAATTACCGCAATACCCTCGATTTACAGAATTACCGTTTTACCCTCG
ATTTACAAAATTACCA
Found at i:54925741 original size:25 final size:25
Alignment explanation
Indices: 54925712--54925759 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54925702 TTATAATATG
* * *
54925712 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
54925737 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
54925760 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:54925843 original size:11 final size:11
Alignment explanation
Indices: 54925807--54925862 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54925797 CATGGTATGT
54925807 ATGATATGCAC
1 ATGATATGCAC
* *
54925818 ATGACATG--T
1 ATGATATGCAC
54925827 ATGATATGCAC
1 ATGATATGCAC
*
54925838 ATGATATG--T
1 ATGATATGCAC
54925847 ATGATATGCAC
1 ATGATATGCAC
54925858 ATGAT
1 ATGAT
54925863 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:54925862 original size:20 final size:20
Alignment explanation
Indices: 54925796--54925862 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
54925786 ATTTTGATAA
*
54925796 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
54925816 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
54925836 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
54925856 ACATGAT
1 ACATGAT
54925863 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:54925967 original size:24 final size:23
Alignment explanation
Indices: 54925912--54926077 Score: 219
Period size: 24 Copynumber: 7.0 Consensus size: 23
54925902 GAGGAAGTGA
54925912 AAAAGGGCTTATG-CCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
54925934 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
54925957 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
54925981 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
54926005 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
54926028 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
54926053 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54926077 A
1 A
54926078 TGATAAAGCA
Statistics
Matches: 129, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
22 12 0.09
23 30 0.23
24 76 0.59
25 11 0.09
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:54926010 original size:47 final size:46
Alignment explanation
Indices: 54925913--54926077 Score: 217
Period size: 47 Copynumber: 3.5 Consensus size: 46
54925903 AGGAAGTGAA
* *
54925913 AAAGGGCTTATG-CCCAGTTATTAAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT-T
*
54925959 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
*
54926006 AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
*
54926053 AAAAGAGGC-TAGGCCTCCAGTTATA
1 -AAAG-GGCTTATGCC-CCAGTTATA
54926078 TGATAAAGCA
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
46 12 0.11
47 53 0.50
48 31 0.29
49 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:54926027 original size:71 final size:71
Alignment explanation
Indices: 54925912--54926076 Score: 253
Period size: 71 Copynumber: 2.3 Consensus size: 71
54925902 GAGGAAGTGA
* *
54925912 AAAAGGGCTTATG-CCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
54925976 GTTATC
66 GTTATC
*
54925982 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
*
54926047 GTTATT
66 GTTATC
*
54926053 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTACGCC-CCAGTTAT
54926077 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
70 12 0.14
71 64 0.74
72 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
GTTATC
Found at i:54926303 original size:31 final size:31
Alignment explanation
Indices: 54926268--54926331 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
54926258 CGTTTACAGT
*
54926268 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
54926299 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54926330 AA
1 AA
54926332 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54929245 original size:80 final size:80
Alignment explanation
Indices: 54929155--54929600 Score: 530
Period size: 80 Copynumber: 5.6 Consensus size: 80
54929145 AAAGTACTCC
54929155 CGATTTACAGAATTACCGTTTTACCCTC-AGTTTACAGAATTACTATTTACCCTCGATTTACAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACTATTTACCCTCGATTTACAGA
54929219 ATTACCGTTTTACCCT
65 ATTACCGTTTTACCCT
** * * * *
54929235 C-AGTTTACAGAATTATTGTTTTACCCTTGATTTATAGAATTACTGTTTTACCCTCGATTTATAG
1 CGA-TTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACT-ATTTACCCTCGATTTACAG
54929299 AATTACCGTTTTACCCT
64 AATTACCGTTTTACCCT
** *
54929316 CGATTTGTAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGT-TTTACCCTC-AGTTTACA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTA-C-TATTTACCCTCGA-TTTACA
**
54929379 GAATTACTATTTTA-CCT
63 GAATTACCGTTTTACCCT
* * * * *
54929396 CGATTTATAGAATTACCGTTTTACCC-CTAATTTACATAATTACCATTTTACCC-CGATTTACAT
1 CGATTTACAGAATTACCGTTTTACCCTC-GATTTACAGAATTACTA-TTTACCCTCGATTTACAG
*
54929459 AATTATCGTTTTACCCT
64 AATTACCGTTTTACCCT
* * *
54929476 CGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTA-CCTCGATTTATAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTA-TTTACCCTCGATTTACAGA
*
54929540 ATTACTGTTTTACCCT
65 ATTACCGTTTTACCCT
* * * *
54929556 TGATTTACAGAATTACTGTTTTACCCTTGATTTACAAAATTACTA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTA
54929601 AAATACCCTT
Statistics
Matches: 313, Mismatches: 39, Indels: 28
0.82 0.10 0.07
Matches are distributed among these distances:
79 22 0.07
80 193 0.62
81 95 0.30
82 2 0.01
83 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (80 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTACCCTCGATTTACAGAA
TTACCGTTTTACCCT
Found at i:54929599 original size:27 final size:27
Alignment explanation
Indices: 54929155--54929598 Score: 555
Period size: 27 Copynumber: 16.6 Consensus size: 27
54929145 AAAGTACTCC
54929155 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
54929182 C-AGTTTACAGAATTA-C-TATTTACCCT
1 CGA-TTTACAGAATTACCGT-TTTACCCT
54929208 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54929235 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* * *
54929262 TGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
54929289 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
54929316 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
54929343 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54929370 C-AGTTTACAGAATTACTATTTTA-CCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
54929396 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
54929422 CTAATTTACATAATTACCATTTTACCC-
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
54929449 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
54929476 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54929503 CGATTTATAGAATTACCATTTTA-CCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54929529 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54929556 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54929583 TGATTTACAAAATTAC
1 CGATTTACAGAATTAC
54929599 TAAAATACCC
Statistics
Matches: 371, Mismatches: 33, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
25 1 0.00
26 93 0.25
27 275 0.74
28 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:54929607 original size:27 final size:27
Alignment explanation
Indices: 54929550--54929611 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
54929540 ATTACTGTTT
* ****
54929550 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGATTTACAAAATTACTAAAA
54929577 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
54929604 TACCCTTG
1 TACCCTTG
54929612 GTTTGTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTAAAA
Found at i:54929611 original size:54 final size:54
Alignment explanation
Indices: 54929155--54929598 Score: 555
Period size: 53 Copynumber: 8.3 Consensus size: 54
54929145 AAAGTACTCC
54929155 CGATTTACAGAATTACCGTTTTACCCTC-AGTTTACAGAATTA-C-TATTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACCGT-TTTACCCT
**
54929208 CGATTTACAGAATTACCGTTTTACCCTC-AGTTTACAGAATTATTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
* * * *
54929262 TGATTTATAGAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
** *
54929316 CGATTTGTAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
** *
54929370 C-AGTTTACAGAATTACTATTTTA-CCTCGATTTATAGAATTACCGTTTTACCC-
1 CGA-TTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * * * *
54929422 CTAATTTACATAATTACCATTTTACCC-CGATTTACATAATTATCGTTTTACCCT
1 C-GATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* *
54929476 CGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTA-CCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * * *
54929529 CGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* *
54929583 TGATTTACAAAATTAC
1 CGATTTACAGAATTAC
54929599 TAAAATACCC
Statistics
Matches: 342, Mismatches: 39, Indels: 19
0.86 0.10 0.05
Matches are distributed among these distances:
52 1 0.00
53 181 0.53
54 158 0.46
55 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (54 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
Found at i:54930885 original size:25 final size:25
Alignment explanation
Indices: 54930839--54930886 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
54930829 TTATAACATG
* * * *
54930839 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCACTAGGTA
54930864 AAAATGACCATTATACCACTAGG
1 AAAATGACCATTATACCACTAGG
54930887 GTTTGTGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCACTAGGTA
Done.