Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 15 of 433
Found at i:4074106 original size:131 final size:130
Alignment explanation
Indices: 4073882--4074394 Score: 677
Period size: 131 Copynumber: 3.9 Consensus size: 130
4073872 GAAAATTCAC
* * * * *
4073882 TAAAACAAAGGCGATACTCGATGTTTGGCAATTTGGGAATCGTGCCCTATCGTGCTGGGTTGCGA
1 TAAAACGAAGGCAATATTCGATGTTTGGCAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGCAA
* * * * * *
4073947 TTTCCTGTTTGTTCAAAACAATCGAATATTCCTATGGAATTTCACTCATGTTTTTAAAAATTATT
66 TTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTTTTTAAAAACTCTT
* * * *
4074012 TAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCA
1 TAAAACGAAGGCAATATTCGATGTTTGGCAATTCG-GGAATCGTGCCCTATCGTGCTGGGTTGCA
* * *
4074077 ATTTCTCGTTTGCTCAAAATAATCGAATATTCCTTTAGAATTTCATTCATGTTTTCTAAAAACTC
65 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTTTT-TAAAAACTC
4074142 TT
129 TT
* * * * *
4074144 TAAAACGAAGGAAATGTTCGATGTTTGACAATTCGAGGAGTCGTGCCCTATCGTGCTGGATTGCA
1 TAAAACGAAGGCAATATTCGATGTTTGGCAATTCG-GGAATCGTGCCCTATCGTGCTGGGTTGCA
* * *
4074209 ATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCGCTCATGTCTTTAAAAACTCT
65 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTTTTTAAAAACTCT
4074274 T
130 T
** * * * *
4074275 TAAAGTGAAGGCAATATTCGATGTTTGGAAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTTCG
1 TAAAACGAAGGCAATATTCGATGTTTGGCAATTC-GGGAATCGTGCCCTATCGTGCTGGGTTGCA
*
4074340 ATTTCCCGTTTGTTCAAAATAATCAAATATTCCTTT-GAAATTTCACTCATGTTTT
65 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAG-AATTTCACTCATGTTTT
4074395 CTAAGGCGAG
Statistics
Matches: 334, Mismatches: 45, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
130 31 0.09
131 187 0.56
132 116 0.35
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (130 bp):
TAAAACGAAGGCAATATTCGATGTTTGGCAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGCAA
TTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTTTTTAAAAACTCTT
Found at i:4074392 original size:263 final size:262
Alignment explanation
Indices: 4073899--4074398 Score: 714
Period size: 263 Copynumber: 1.9 Consensus size: 262
4073889 AAGGCGATAC
* * * * *
4073899 TCGATGTTTGGCAATTTGGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCCTGTTTGTTCAAA
1 TCGATGTTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGATTGCAATTTCCCGTTTGTTCAAA
* * * * * *
4073964 ACAATCGAATATTCCTATGGAATTTCACTCATGTTTTTAAAAATTATTTAAAACGAAGGCGATGT
66 ACAATCGAATATCCCTATAGAATTTCACTCATGTCTTTAAAAACTATTTAAAACGAAGGCAATAT
* * *
4074029 TCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGCTCAA
131 TCGATATTTGGAAATTCGCGGAATAGTGCCCTAACGTGCTGGGTTGCAATTTCCCGTTTGCTCAA
* *
4074094 AATAATCGAATATTCCTTTAGAATTTCATTCATGTTTTCTAAAAACTCTTTAAAACGAAGGAAAT
196 AATAATCAAATATTCCTTTAGAATTTCACTCATGTTTTCTAAAAACTCTTTAAAACGAAGGAAAT
4074159 GT
261 GT
*
4074161 TCGATGTTTGACAATTCGAGGAGTCGTGCCCTATCGTGCTGGATTGCAATTTCCCGTTTGTTCAA
1 TCGATGTTTGACAATTCG-GGAATCGTGCCCTATCGTGCTGGATTGCAATTTCCCGTTTGTTCAA
* * * * **
4074226 AATAATCGAATATCCCTTTAGAATTTCGCTCATGTCTTTAAAAACTCTTTAAAGTGAAGGCAATA
65 AACAATCGAATATCCCTATAGAATTTCACTCATGTCTTTAAAAACTATTTAAAACGAAGGCAATA
* * * * * *
4074291 TTCGATGTTTGGAAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTTCGATTTCCCGTTTGTTCA
130 TTCGATATTTGGAAATTCGCGGAATAGTGCCCTAACGTGCTGGGTTGCAATTTCCCGTTTGCTCA
4074356 AAATAATCAAATATTCCTTT-GAAATTTCACTCATGTTTTCTAA
195 AAATAATCAAATATTCCTTTAG-AATTTCACTCATGTTTTCTAA
4074399 GGCGAGGCAA
Statistics
Matches: 207, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
262 17 0.08
263 190 0.92
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (262 bp):
TCGATGTTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGATTGCAATTTCCCGTTTGTTCAAA
ACAATCGAATATCCCTATAGAATTTCACTCATGTCTTTAAAAACTATTTAAAACGAAGGCAATAT
TCGATATTTGGAAATTCGCGGAATAGTGCCCTAACGTGCTGGGTTGCAATTTCCCGTTTGCTCAA
AATAATCAAATATTCCTTTAGAATTTCACTCATGTTTTCTAAAAACTCTTTAAAACGAAGGAAAT
GT
Found at i:4075227 original size:15 final size:15
Alignment explanation
Indices: 4075207--4075242 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
4075197 TAAAAAGATA
4075207 AATAAACATAAAAGT
1 AATAAACATAAAAGT
*
4075222 AATAAACATAGAAGT
1 AATAAACATAAAAGT
4075237 AATAAA
1 AATAAA
4075243 TAAAGAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (15 bp):
AATAAACATAAAAGT
Found at i:4075249 original size:15 final size:15
Alignment explanation
Indices: 4075207--4075249 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4075197 TAAAAAGATA
4075207 AATAAACATAA-AAGT
1 AATAAACA-AAGAAGT
*
4075222 AATAAACATAGAAGT
1 AATAAACAAAGAAGT
*
4075237 AATAAATAAAGAA
1 AATAAACAAAGAA
4075250 TCTTCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (15 bp):
AATAAACAAAGAAGT
Found at i:4084736 original size:3 final size:3
Alignment explanation
Indices: 4084728--4084763 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4084718 TCAACATTGT
4084728 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4084764 AACCTTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4095210 original size:21 final size:22
Alignment explanation
Indices: 4095159--4095211 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
4095149 GACACATATG
4095159 CATGGTATAT-ATAAAAATGTA
1 CATGGTATATAATAAAAATGTA
* *
4095180 TA-AGTAATATAATAAAAAT-TA
1 CATGGT-ATATAATAAAAATGTA
4095201 CATGGTATATA
1 CATGGTATATA
4095212 TACATGTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (22 bp):
CATGGTATATAATAAAAATGTA
Found at i:4095992 original size:20 final size:20
Alignment explanation
Indices: 4095969--4096007 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4095959 ATATATTAGG
*
4095969 AACAATAATAATATATATAA
1 AACAATAATAAAATATATAA
*
4095989 AACAATTATAAAATATATA
1 AACAATAATAAAATATATA
4096008 TATATGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AACAATAATAAAATATATAA
Found at i:4096052 original size:22 final size:20
Alignment explanation
Indices: 4096027--4096069 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4096017 TATTAATCTA
4096027 AAAAAAATGCCTAAATAATAAT
1 AAAAAAATG-CTAAA-AATAAT
*
4096049 -AAAATATGCTAAAAATAAT
1 AAAAAAATGCTAAAAATAAT
4096068 AA
1 AA
4096070 TACAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
19 6 0.32
20 6 0.32
21 7 0.37
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAAAATGCTAAAAATAAT
Found at i:4097485 original size:41 final size:42
Alignment explanation
Indices: 4097428--4097545 Score: 184
Period size: 41 Copynumber: 2.8 Consensus size: 42
4097418 AGACACGTGA
*
4097428 CTTCAATCAATTCCACTGAAACTTCAAGGAGATCTATTGTAG
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTATTGTAG
* * * *
4097470 CTTTGCTTAA-TCCACTGAAACTTCAAGGAGATCTGTTGTAG
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTATTGTAG
4097511 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCT
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCT
4097546 GCTGTGGCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 37 0.55
42 30 0.45
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (42 bp):
CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTATTGTAG
Found at i:4097539 original size:42 final size:42
Alignment explanation
Indices: 4097428--4097555 Score: 186
Period size: 42 Copynumber: 3.1 Consensus size: 42
4097418 AGACACGTGA
* *
4097428 CTTCAATCAATTCCACTGAAACTTCAAGGAGATCTATTGTAG
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGTTGTAG
* * *
4097470 CTTTGCTTAA-TCCACTGAAACTTCAAGGAGATCTGTTGTAG
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGTTGTAG
* *
4097511 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTGG
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGTTGTAG
4097553 CTT
1 CTT
4097556 TTAGCTGCTC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
41 37 0.49
42 38 0.51
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGTTGTAG
Found at i:4097705 original size:42 final size:44
Alignment explanation
Indices: 4097598--4097717 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 44
4097588 TATTTGATTT
* * *
4097598 TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCA
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAACA
** * * *
4097642 TTGATCTGTTTCCCTACTGCTTAGGGGTTT-A-GATCTGTAAAC-
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCT-TGTAAACA
4097684 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
4097718 TTTGAAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 28 0.46
43 7 0.11
44 26 0.43
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (44 bp):
TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAACA
Found at i:4098270 original size:43 final size:44
Alignment explanation
Indices: 4098201--4098287 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
4098191 GGGAGACGAA
* * *
4098201 ATCTGTAATTTTCAGCCTATTACCCTATTGCTTAGGGGGTTAAG
1 ATCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGGTTAAG
* * *
4098245 ATCTGTAAATTT-AACCTGTTACCCTACTGCTTATGGGTTTAAG
1 ATCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGGTTAAG
4098288 GCTTGGTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 26 0.70
44 11 0.30
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (44 bp):
ATCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGGTTAAG
Found at i:4111157 original size:19 final size:21
Alignment explanation
Indices: 4111120--4111163 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4111110 ATTAATCTAA
4111120 AAAAAATGCTTAAATAATAAT
1 AAAAAATGCTTAAATAATAAT
* *
4111141 AAAATATGCTAAAAATAATAAT
1 AAAAAATGCT-TAAATAATAAT
4111163 A
1 A
4111164 CAAGAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAAATGCTTAAATAATAAT
Found at i:4116567 original size:21 final size:22
Alignment explanation
Indices: 4116536--4116576 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4116526 TTTACATTTT
*
4116536 TTAAAGTTAAAAGTCAAAACCA
1 TTAAAGTTAAAAGACAAAACCA
4116558 TTAAA-TTAAAAGACAAAAC
1 TTAAAGTTAAAAGACAAAAC
4116577 TATTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (22 bp):
TTAAAGTTAAAAGACAAAACCA
Found at i:4120820 original size:46 final size:44
Alignment explanation
Indices: 4120761--4120875 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
4120751 ACAGGACAGA
* *
4120761 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
4120807 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
4120851 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
4120876 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:4120856 original size:44 final size:45
Alignment explanation
Indices: 4120761--4120894 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
4120751 ACAGGACAGA
* *
4120761 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
4120807 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
4120851 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
4120895 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:4128190 original size:46 final size:44
Alignment explanation
Indices: 4128131--4128245 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
4128121 ACAGGACAGA
* *
4128131 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
4128177 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
4128221 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
4128246 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:4128226 original size:44 final size:45
Alignment explanation
Indices: 4128131--4128264 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
4128121 ACAGGACAGA
* *
4128131 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
4128177 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
4128221 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
4128265 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:4131952 original size:22 final size:22
Alignment explanation
Indices: 4131924--4131970 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
4131914 GTTTGACCCC
4131924 CTGCCAACCCCTGGATTCGTCT
1 CTGCCAACCCCTGGATTCGTCT
4131946 CTGCCAACCCCTGGATTCGTCT
1 CTGCCAACCCCTGGATTCGTCT
4131968 CTG
1 CTG
4131971 ACCACGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.13, C:0.40, G:0.19, T:0.28
Consensus pattern (22 bp):
CTGCCAACCCCTGGATTCGTCT
Found at i:4144177 original size:2 final size:2
Alignment explanation
Indices: 4144164--4144206 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4144154 ATCTATGCAC
*
4144164 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4144206 A
1 A
4144207 AGGTATCTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4144976 original size:39 final size:39
Alignment explanation
Indices: 4144920--4145051 Score: 203
Period size: 39 Copynumber: 3.4 Consensus size: 39
4144910 TGCATGGTAT
4144920 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTATGC
1 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTATGC
* *
4144959 TGGAAATATATCTGGACTTGAAGTCCGCAGGCTTTATGC
1 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTATGC
* * *
4144998 TGGAAATATATCCGGACTTAAAGTCCGCAGGC-TAAGTGC
1 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTA-TGC
4145037 TGGAAAAATATCCGG
1 TGGAAAAATATCCGG
4145052 GCTAAGAACC
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
38 2 0.02
39 84 0.98
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (39 bp):
TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTATGC
Found at i:4145065 original size:39 final size:39
Alignment explanation
Indices: 4144920--4145069 Score: 126
Period size: 39 Copynumber: 3.8 Consensus size: 39
4144910 TGCATGGTAT
* ** *
4144920 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTA-TGC
1 TGGAAAAATATCCGGACTTAAAACCCGCAGGC-TAAGTGC
* * * ** *
4144959 TGGAAATATATCTGGACTTGAAGTCCGCAGGCTTTA-TGC
1 TGGAAAAATATCCGGACTTAAAACCCGCAGGC-TAAGTGC
* **
4144998 TGGAAATATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
1 TGGAAAAATATCCGGACTTAAAACCCGCAGGCTAAGTGC
*
4145037 TGGAAAAATATCCGGGC-TAAGAACCCGCAGGCT
1 TGGAAAAATATCCGGACTTAA-AACCCGCAGGCT
4145070 CATGCTAGTA
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
38 5 0.05
39 95 0.95
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (39 bp):
TGGAAAAATATCCGGACTTAAAACCCGCAGGCTAAGTGC
Found at i:4145065 original size:78 final size:78
Alignment explanation
Indices: 4144920--4145069 Score: 196
Period size: 78 Copynumber: 1.9 Consensus size: 78
4144910 TGCATGGTAT
* * * * * *
4144920 TGGAAAAATATCCGGACTTGAAGTCCGCAGGCTTTATGCTGGAAATATATCTGGACTTGAAGTCC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTTAATGCTGGAAAAATATCCGGACTAGAAGCCC
4144985 GCAGGCTTTATGC
66 GCAGGCTTTATGC
* *
4144998 TGGAAATATATCCGGACTTAAAGTCCGCAGGC-TAAGTGCTGGAAAAATATCCGGGCTAAGAA-C
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTTAA-TGCTGGAAAAATATCCGGACT-AGAAGC
4145061 CCGCAGGCT
64 CCGCAGGCT
4145070 CATGCTAGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 2 0.03
78 57 0.92
79 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (78 bp):
TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTTAATGCTGGAAAAATATCCGGACTAGAAGCCC
GCAGGCTTTATGC
Found at i:4146596 original size:12 final size:12
Alignment explanation
Indices: 4146572--4146624 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
4146562 AATACATATG
*
4146572 TTTTTTA-TATA
1 TTTTTTATTCTA
4146583 TTTTTTATTCTA
1 TTTTTTATTCTA
*
4146595 TTTTTTATT-TT
1 TTTTTTATTCTA
*
4146606 TTTTCTTCTTCTA
1 TTTT-TTATTCTA
4146619 TTTTTT
1 TTTTTT
4146625 CATTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 12 0.34
12 18 0.51
13 5 0.14
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTATTCTA
Found at i:4146608 original size:8 final size:8
Alignment explanation
Indices: 4146595--4146641 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
4146585 TTTTATTCTA
4146595 TTTTTTAT
1 TTTTTTAT
4146603 TTTTTT-T
1 TTTTTTAT
*
4146610 CTTCTTCTAT
1 -TT-TTTTAT
*
4146620 TTTTTCAT
1 TTTTTTAT
4146628 TTTTTTAT
1 TTTTTTAT
4146636 TTTTTT
1 TTTTTT
4146642 TAAGAACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
7 1 0.03
8 25 0.78
9 5 0.16
10 1 0.03
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTAT
Found at i:4146617 original size:24 final size:23
Alignment explanation
Indices: 4146572--4146633 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
4146562 AATACATATG
* *
4146572 TTTTTTATATATTTTTTATTCTA
1 TTTTTTATTTTTTTTTTATTCTA
*
4146595 TTTTTTATTTTTTTTCTTCTTCTA
1 TTTTTTATTTTTTTT-TTATTCTA
4146619 TTTTTTCATTTTTTT
1 TTTTTT-ATTTTTTT
4146634 ATTTTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 13 0.38
24 13 0.38
25 8 0.24
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTATTTTTTTTTTATTCTA
Found at i:4147737 original size:14 final size:12
Alignment explanation
Indices: 4147707--4147741 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
4147697 ATAAAATTTG
4147707 AAATAAAAAGGA
1 AAATAAAAAGGA
4147719 AAATAATAAAGGAA
1 AAATAA-AAAGG-A
4147733 AAATAAAAA
1 AAATAAAAA
4147742 TAAAAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 8 0.38
14 7 0.33
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (12 bp):
AAATAAAAAGGA
Found at i:4147741 original size:20 final size:22
Alignment explanation
Indices: 4147718--4147759 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
4147708 AATAAAAAGG
*
4147718 AAAATAATAAA-G-GAAAAATA
1 AAAATAAAAAATGAGAAAAATA
4147738 AAAATAAAAAATGAGAAAAATA
1 AAAATAAAAAATGAGAAAAATA
4147760 GAACCGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAATAAAAAATGAGAAAAATA
Found at i:4150991 original size:4 final size:4
Alignment explanation
Indices: 4150982--4151016 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
4150972 AAGAAGATAA
4150982 AAAT AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
4151017 TAAACAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 4 0.14
4 25 0.86
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4150991 original size:10 final size:10
Alignment explanation
Indices: 4150978--4151020 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
4150968 AGAAAAGAAG
4150978 ATAAAAATAA
1 ATAAAAATAA
4150988 ATAAAAATAA
1 ATAAAAATAA
4150998 ATAAATAAATAA
1 AT-AA-AAATAA
*
4151010 ATAAATATAA
1 ATAAAAATAA
4151020 A
1 A
4151021 CAAATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 18 0.60
11 4 0.13
12 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:4151010 original size:22 final size:22
Alignment explanation
Indices: 4150982--4151026 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4150972 AAGAAGATAA
*
4150982 AAATAAATAAAAATAAATAAAT
1 AAATAAATAAAAATAAACAAAT
*
4151004 AAATAAATAAATATAAACAAAT
1 AAATAAATAAAAATAAACAAAT
4151026 A
1 A
4151027 TATATATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AAATAAATAAAAATAAACAAAT
Found at i:4151031 original size:14 final size:14
Alignment explanation
Indices: 4150982--4151032 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
4150972 AAGAAGATAA
* *
4150982 AAATAAATAAAAAT
1 AAATAAATATAAAC
*
4150996 AAAT-AA-ATAAAT
1 AAATAAATATAAAC
4151008 AAATAAATATAAAC
1 AAATAAATATAAAC
*
4151022 AAATATATATA
1 AAATAAATATA
4151033 TAGTAATGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 9 0.28
13 4 0.12
14 19 0.59
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAAATATAAAC
Found at i:4158553 original size:25 final size:25
Alignment explanation
Indices: 4158525--4158572 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4158515 AGGAAGAGCA
*
4158525 TGCCAAAAGGTAGACACAGAAAACG
1 TGCCAAAAGGCAGACACAGAAAACG
* *
4158550 TGCCATAAGGCAGACAGAGAAAA
1 TGCCAAAAGGCAGACACAGAAAA
4158573 TATATTATGA
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:0.48, C:0.19, G:0.25, T:0.08
Consensus pattern (25 bp):
TGCCAAAAGGCAGACACAGAAAACG
Found at i:4163598 original size:6 final size:6
Alignment explanation
Indices: 4163589--4163627 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
4163579 AGAGAGATAT
* *
4163589 GAAGTA GAAGGA GAAGGA GAAGGA GAAGGA GAGGGA GAA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAA
4163628 TAAGAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (6 bp):
GAAGGA
Found at i:4163633 original size:18 final size:18
Alignment explanation
Indices: 4163589--4163634 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
4163579 AGAGAGATAT
*
4163589 GAAGTAGAAGGAGAAGGA
1 GAAGAAGAAGGAGAAGGA
* *
4163607 GAAGGAGAAGGAGAGGGA
1 GAAGAAGAAGGAGAAGGA
*
4163625 GAATAAGAAG
1 GAAGAAGAAG
4163635 AAGGGGAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.46, T:0.04
Consensus pattern (18 bp):
GAAGAAGAAGGAGAAGGA
Found at i:4163638 original size:21 final size:21
Alignment explanation
Indices: 4163612--4163658 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4163602 AAGGAGAAGG
4163612 AGAAGGAG-AGGGAGAATAAGA
1 AGAAGGAGAAGGG-GAATAAGA
* *
4163633 AGAAGGGGAAGGGGAATAGGA
1 AGAAGGAGAAGGGGAATAAGA
4163654 AGAAG
1 AGAAG
4163659 AGGAAGAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (21 bp):
AGAAGGAGAAGGGGAATAAGA
Found at i:4163643 original size:6 final size:6
Alignment explanation
Indices: 4163629--4163701 Score: 89
Period size: 6 Copynumber: 12.7 Consensus size: 6
4163619 GAGGGAGAAT
* * * *
4163629 AAGAAG AAGGGG AAGGGG AATAGG AAGA-- A-GAGG AAGAGG AAGAGG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG
4163674 AAGAGG AAGAGG AAGAGG AAGAGG AAGA
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGA
4163702 AGCACTTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 1 0.02
6 55 0.93
ACGTcount: A:0.51, C:0.00, G:0.48, T:0.01
Consensus pattern (6 bp):
AAGAGG
Found at i:4168099 original size:2 final size:2
Alignment explanation
Indices: 4168092--4168154 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
4168082 ACTCCAAGAT
4168092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4168134 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
4168155 CAGTTGATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4174768 original size:54 final size:53
Alignment explanation
Indices: 4174687--4174794 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 53
4174677 CGCACTAAAC
4174687 TTTCAATAGGTAAATTGTTTTATAAACTCTCCTTATTTATTATTTTCTTTTAT
1 TTTCAATAGGTAAATTGTTTTATAAACTCTCCTTATTTATTATTTTCTTTTAT
4174740 TTTCAATAGGGTAAATTGTTTTATAAACTCTCCTTATTTATTATTTTCTTTTAT
1 TTTCAATA-GGTAAATTGTTTTATAAACTCTCCTTATTTATTATTTTCTTTTAT
4174794 T
1 T
4174795 CTCCTTTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 8 0.15
54 46 0.85
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.56
Consensus pattern (53 bp):
TTTCAATAGGTAAATTGTTTTATAAACTCTCCTTATTTATTATTTTCTTTTAT
Found at i:4177122 original size:29 final size:29
Alignment explanation
Indices: 4177056--4177124 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
4177046 ATTTAGTTTT
* * *
4177056 ATATTTTTATAATGTTATTAATTAATTTA
1 ATATGTTTATAATGTAATTAATTAATTAA
* *
4177085 ATATTTTTATAATGTAATTAATTAGTTCAA
1 ATATGTTTATAATGTAATTAATTAATT-AA
4177115 ATA-GTTTATA
1 ATATGTTTATA
4177125 TTTTCAGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (29 bp):
ATATGTTTATAATGTAATTAATTAATTAA
Found at i:4180788 original size:72 final size:72
Alignment explanation
Indices: 4180707--4180851 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
4180697 CACCTAGGGG
4180707 AGATGAACCCTATGATGAATTTTGTCATTTGATTTTTATTTTATGTAATAAATACTTAGTTTCTT
1 AGATGAACCCTATGATGAATTTTGTCATTTGATTTTTATTTTATGTAATAAATACTTAGTTTCTT
4180772 GTTCTCA
66 GTTCTCA
4180779 AGATGAACCCTATGATGAATTTTGTCATTTGATTTTTATTTTATGTAATAAATACTTAGTTTCTT
1 AGATGAACCCTATGATGAATTTTGTCATTTGATTTTTATTTTATGTAATAAATACTTAGTTTCTT
4180844 GTTCTCA
66 GTTCTCA
4180851 A
1 A
4180852 TTATGTGTGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (72 bp):
AGATGAACCCTATGATGAATTTTGTCATTTGATTTTTATTTTATGTAATAAATACTTAGTTTCTT
GTTCTCA
Found at i:4180908 original size:91 final size:91
Alignment explanation
Indices: 4180805--4180979 Score: 323
Period size: 91 Copynumber: 1.9 Consensus size: 91
4180795 GAATTTTGTC
* *
4180805 ATTTGATTTTTATTTTATGTAATAAATACTTAGTTTCTTGTTCTCAATTATGTGTGCTTAATTCT
1 ATTTGATTTTTATTTTACGTAATAAATACTTAGTTTCTTGTTCCCAATTATGTGTGCTTAATTCT
*
4180870 TGGTTTAATTTTTTTAGAGCTCTGTG
66 TGGTTTAATTTTTCTAGAGCTCTGTG
4180896 ATTTGATTTTTATTTTACGTAATAAATACTTAGTTTCTTGTTCCCAATTATGTGTGCTTAATTCT
1 ATTTGATTTTTATTTTACGTAATAAATACTTAGTTTCTTGTTCCCAATTATGTGTGCTTAATTCT
4180961 TGGTTTAATTTTTCTAGAG
66 TGGTTTAATTTTTCTAGAG
4180980 TATTGATCTA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.54
Consensus pattern (91 bp):
ATTTGATTTTTATTTTACGTAATAAATACTTAGTTTCTTGTTCCCAATTATGTGTGCTTAATTCT
TGGTTTAATTTTTCTAGAGCTCTGTG
Found at i:4183755 original size:3 final size:3
Alignment explanation
Indices: 4183749--4183777 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4183739 TAAAAGTATG
4183749 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4183778 TCTACAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4183912 original size:29 final size:28
Alignment explanation
Indices: 4183859--4183913 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
4183849 AAAATAATGA
*
4183859 TATGTACAAAAATATATATATATATACG
1 TATGTACAAAAATATACATATATATACG
4183887 TATGTACATAAAATATACACTA-ATATA
1 TATGTACA-AAAATATACA-TATATATA
4183914 ATAATAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 14 0.58
30 2 0.08
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (28 bp):
TATGTACAAAAATATACATATATATACG
Found at i:4184050 original size:2 final size:2
Alignment explanation
Indices: 4183983--4184035 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
4183973 ATGGTATTTA
* *
4183983 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A- AT AGT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
4184025 A- AT A- AT AT AT A
1 AT AT AT AT AT AT A
4184036 CATAAGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.88
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4184619 original size:36 final size:33
Alignment explanation
Indices: 4184570--4184663 Score: 143
Period size: 36 Copynumber: 2.8 Consensus size: 33
4184560 GGCTAGGGTT
4184570 TTTTTTTTTTTTGGGTTAGGTTTTCTCTTTTCTTC
1 TTTTTTTTTTTTGGGTTAGGTTTT-TCTTTT-TTC
4184605 TTCTTTTTTTTTTGGGTTAGGTTTTTCTTTTTTC
1 TT-TTTTTTTTTTGGGTTAGGTTTTTCTTTTTTC
**
4184639 TTTTTTTTTTGGGGGTTAGGTTTTT
1 TTTTTTTTTTTTGGGTTAGGTTTTT
4184664 TGGGGGGCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
33 21 0.38
34 5 0.09
35 8 0.14
36 22 0.39
ACGTcount: A:0.03, C:0.07, G:0.18, T:0.71
Consensus pattern (33 bp):
TTTTTTTTTTTTGGGTTAGGTTTTTCTTTTTTC
Found at i:4185524 original size:30 final size:30
Alignment explanation
Indices: 4185488--4185549 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
4185478 TTTTGAAAAA
4185488 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
4185518 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
4185548 CA
1 CA
4185550 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:4185666 original size:14 final size:14
Alignment explanation
Indices: 4185643--4185677 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4185633 TGAGTTGATT
4185643 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
4185656 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
4185670 TTTGAAAA
1 TTTGAAAA
4185678 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:4185864 original size:77 final size:75
Alignment explanation
Indices: 4185656--4186223 Score: 432
Period size: 77 Copynumber: 7.3 Consensus size: 75
4185646 GAAAACAGAA
** * *
4185656 TTTGAAAAACAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCACATCTCGCAAT
1 TTTG-AAAACAGAAATTGAAAATACCTCAGGC--GTGACCCGAGGCTCAACTCACCTCTCGCAAT
*
4185720 GTGAGTTGATTTT
63 ATGAGTTGATTTT
* * * * * *
4185733 TTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAA
1 TTTG-AAAACAGAAATTG--AAAATACCTCAG-GCGTGACCCGAGGCTCAACTCACCTCTCGCAA
4185798 TATGAGTTGATTTT
62 TATGAGTTGATTTT
* * *
4185812 TTTGAAAGATAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATA
1 TTTGAAA-ACAGAAATTGAAAATACCTCAG-GCGTGACCCGAGGCTCAACTCACCTCTCGCAATA
*
4185877 TAAGTTGATTTT
64 TGAGTTGATTTT
* * * ** **
4185889 TTTGAAAACAAAAATTGAAAATACCTCA-ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTGAAAACAGAAATTGAAAATACCTCAGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
*
4185953 AGTTGA--AT
66 AGTTGATTTT
* *
4185961 TTTGAAAACAGAAATTGAAATTACCTCA-GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAACAGAAATTGAAAATACCTCAGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
4186025 AGTTGATTTTTT
66 AGTTGA--TTTT
* ** * *** *
4186037 TTTGAAAGGCAGAAATTGAAAAATGGAAAT-TGAAAAT-ACCTCGGCGTGTGATCTGAAGCTCAA
1 TTTGAAA-ACAGAAATTG-AAAAT--ACCTCAG-GCGTGA-C-C--CGAG-G--C------TCAA
* *
4186100 CTCACCTCTCGCAATACGAGTTGACTTT
48 CTCACCTCTCGCAATATGAGTTGATTTT
* * * * **
4186128 TTTGACAATAGAAATTGAAATTACCTCA-GCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAACAGAAATTGAAAATACCTCAGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
4186192 AGTTGATTTT
66 AGTTGATTTT
*
4186202 TTTGAAAGGCAGAAATTGAAAA
1 TTTGAAA-ACAGAAATTGAAAA
4186224 ACGGAAATTG
Statistics
Matches: 389, Mismatches: 71, Indels: 64
0.74 0.14 0.12
Matches are distributed among these distances:
72 64 0.16
74 69 0.18
75 11 0.03
76 27 0.07
77 82 0.21
78 7 0.02
79 62 0.16
80 4 0.01
81 2 0.01
82 2 0.01
83 2 0.01
84 3 0.01
85 1 0.00
86 2 0.01
87 3 0.01
89 4 0.01
90 8 0.02
91 9 0.02
93 27 0.07
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (75 bp):
TTTGAAAACAGAAATTGAAAATACCTCAGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:4185994 original size:72 final size:73
Alignment explanation
Indices: 4185695--4186223 Score: 441
Period size: 74 Copynumber: 6.8 Consensus size: 73
4185685 ACATGTGACC
* * * *
4185695 CGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTG--AAAATAC
* *
4185760 CTCAGTGTGTGAT
62 CTCAGCGTGT-CT
* *
4185773 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATACC
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
4185838 TCAGCGCGTGAGC-
63 TCA--GCGTG-TCT
* * *
4185851 CAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAAAAATTGAAAATACCTC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTC
*
4185916 AACGTGTCT
65 AGCGTGTCT
* ** * *
4185925 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
*
4185989 GCGTGTCC
66 GCGTGTCT
*
4185997 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAATG
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAA-ACAGAAATTG----A--
** ** *
4186062 GAAATTGAAAATACCTCGGCGTGTGAT
56 -AAA-T--ACCT-CAGC---GTGT-CT
* * * * *
4186089 CTGAAGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTTTGACAATAGAAATTGAAATTACCT
1 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCT
4186154 CAGCGTGTCT
64 CAGCGTGTCT
* *
4186164 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAGAAATTGAAAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAA
4186224 ACGGAAATTG
Statistics
Matches: 367, Mismatches: 56, Indels: 59
0.76 0.12 0.12
Matches are distributed among these distances:
72 64 0.17
73 1 0.00
74 73 0.20
75 12 0.03
76 31 0.08
77 61 0.17
78 5 0.01
79 53 0.14
80 2 0.01
81 1 0.00
82 1 0.00
83 2 0.01
84 2 0.01
85 1 0.00
86 1 0.00
87 2 0.01
88 2 0.01
90 8 0.02
91 13 0.04
92 1 0.00
93 31 0.08
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (73 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA
GCGTGTCT
Found at i:4186352 original size:74 final size:75
Alignment explanation
Indices: 4186227--4186369 Score: 225
Period size: 74 Copynumber: 1.9 Consensus size: 75
4186217 TTGAAAAACG
* *
4186227 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTT
4186292 TTTTGACAACT
65 TTTTGACAACT
* * *
4186303 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
4186367 TTT
66 TTT
4186370 TTAAAGACAG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 40 0.65
76 22 0.35
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
TTTGACAACT
Found at i:4186369 original size:76 final size:75
Alignment explanation
Indices: 4186227--4186389 Score: 213
Period size: 76 Copynumber: 2.1 Consensus size: 75
4186217 TTGAAAAACG
* *
4186227 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTT
* *
4186292 TTTTGACA-ACT
65 TTTT-AAAGACA
* * *
4186303 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGA--TT
4186367 TTTTTAAAGACA
64 TTTTTAAAGACA
4186379 GAAATTGAAAA
1 GAAATTGAAAA
4186390 ACGGAAATTG
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
74 33 0.43
75 2 0.03
76 41 0.54
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
TTTAAAGACA
Found at i:4186458 original size:166 final size:166
Alignment explanation
Indices: 4185900--4186458 Score: 860
Period size: 165 Copynumber: 3.4 Consensus size: 166
4185890 TTGAAAACAA
** * ** * *
4185900 AAATTGAAAATACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--AT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
* * *
4185961 TTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
66 TTTGACAACTGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
4186026 GTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAATGG
131 GTTGATTTTTTTTT-AAAGGCAGAAATTGAAAAACGG
* * *
4186063 AAATTGAAAATACCTCGGCGTGTGATCTGAAGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
*
4186128 TTTGACAA-TAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
66 TTTGACAACT-GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
4186192 AGTTGA-TTTTTTTGAAAGGCAGAAATTGAAAAACGG
130 AGTTGATTTTTTTTTAAAGGCAGAAATTGAAAAACGG
* *
4186228 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
4186293 TTTGACAACTGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
66 TTTGACAACTGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
4186358 GTTGATTTTTTTTTAAAGACAGAAATTGAAAAACGG
131 GTTGATTTTTTTTTAAAGGCAGAAATTGAAAAACGG
* * *
4186394 AAATTGAAAATACCTCGGCGTGCGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
4186459 GAAAAAGTAG
Statistics
Matches: 361, Mismatches: 28, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
163 21 0.06
165 178 0.49
166 96 0.27
167 66 0.18
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (166 bp):
AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
TTTGACAACTGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTTTAAAGGCAGAAATTGAAAAACGG
Found at i:4186573 original size:73 final size:72
Alignment explanation
Indices: 4186481--4186670 Score: 256
Period size: 72 Copynumber: 2.6 Consensus size: 72
4186471 ATTAAAAGGT
* * * * * *
4186481 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGAAAAACAAAAATTGAAAATACCTCAGCGTGC
*
4186546 CCTGAGGC
65 CCCGAGGC
**
4186554 TCAACTCACCTCTCGCAATATGAGTTGAAATT-AAAACACAAAAATTGAAAATACCTCAGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA-ACAAAAATTGAAAATACCTCAGCGTGC
4186618 CCCGAGGC
65 CCCGAGGC
* *
4186626 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAAT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAT
4186671 AAAAAGGCTT
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
71 3 0.03
72 68 0.67
73 31 0.30
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (72 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAAATACCTCAGCGTGCC
CCGAGGC
Found at i:4186801 original size:114 final size:116
Alignment explanation
Indices: 4186601--4186904 Score: 535
Period size: 114 Copynumber: 2.6 Consensus size: 116
4186591 ACAAAAATTG
*
4186601 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACC
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
*
4186666 AAAATAAAAAGGCTTAACTCACCTCTCGC-ATATGAGTCAA-TTAAAACTA
66 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACTA
4186715 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
4186780 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACTA
66 AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACTA
*
4186831 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCA-CAATATGAGTTGATTTTG-AAAAC
1 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCT-AGCAATATGAGTTGATTTTGAAAAAC
*
4186894 AACAATTAAAA
65 AAAAATTAAAA
4186905 ATACCTCAAC
Statistics
Matches: 183, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
114 92 0.50
115 26 0.14
116 64 0.35
117 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (116 bp):
AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACA
AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACTA
Found at i:4195433 original size:3 final size:3
Alignment explanation
Indices: 4195427--4195461 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4195417 TAAAAGTATG
4195427 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4195462 TCTACAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4195742 original size:2 final size:2
Alignment explanation
Indices: 4195675--4195727 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
4195665 GTATTTAAAA
* *
4195675 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A- AT AGT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
4195717 A- AT A- AT AT AT A
1 AT AT AT AT AT AT A
4195728 CATAAGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.88
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4196299 original size:18 final size:18
Alignment explanation
Indices: 4196272--4196333 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
4196262 TTTTTTTATT
*
4196272 TTTTTATTTTGGGTTAGG
1 TTTTTCTTTTGGGTTAGG
*** *
4196290 TTTTTCTTTTTTCTT--C
1 TTTTTCTTTTGGGTTAGG
*
4196306 TTTTTTTTTTGGGTTAGG
1 TTTTTCTTTTGGGTTAGG
4196324 TTTTTCTTTT
1 TTTTTCTTTT
4196334 TTCTTTTTTT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
16 11 0.35
18 20 0.65
ACGTcount: A:0.05, C:0.06, G:0.16, T:0.73
Consensus pattern (18 bp):
TTTTTCTTTTGGGTTAGG
Found at i:4196310 original size:34 final size:32
Alignment explanation
Indices: 4196263--4196359 Score: 151
Period size: 34 Copynumber: 3.0 Consensus size: 32
4196253 TGGCTAGGGT
*
4196263 TTTTTTATTTTTTTATTTTGGGTTAGGTTTTTC
1 TTTTTTCTTTTTTT-TTTTGGGTTAGGTTTTTC
4196296 TTTTTTCTTCTTTTTTTTTTGGGTTAGGTTTTTC
1 TTTTTTC-T-TTTTTTTTTTGGGTTAGGTTTTTC
4196330 TTTTTTC-TTTTTTTTTTGGGTTAGGTTTTT
1 TTTTTTCTTTTTTTTTTTGGGTTAGGTTTTT
4196360 TTTGGAGAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
31 23 0.38
33 6 0.10
34 26 0.43
35 6 0.10
ACGTcount: A:0.05, C:0.05, G:0.15, T:0.74
Consensus pattern (32 bp):
TTTTTTCTTTTTTTTTTTGGGTTAGGTTTTTC
Found at i:4196341 original size:31 final size:33
Alignment explanation
Indices: 4196271--4196359 Score: 146
Period size: 31 Copynumber: 2.7 Consensus size: 33
4196261 GTTTTTTTAT
4196271 TTTTTTATTTTGGGTTAGGTTTTTCTTTTTTCTTC
1 TTTTTT-TTTTGGGTTAGGTTTTTC-TTTTTCTTC
4196306 TTTTTTTTTTGGGTTAGGTTTTTC-TTTT-TTC
1 TTTTTTTTTTGGGTTAGGTTTTTCTTTTTCTTC
4196337 TTTTTTTTTTGGGTTAGGTTTTT
1 TTTTTTTTTTGGGTTAGGTTTTT
4196360 TTTGGAGAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.48
32 4 0.07
34 18 0.33
35 6 0.11
ACGTcount: A:0.04, C:0.06, G:0.17, T:0.73
Consensus pattern (33 bp):
TTTTTTTTTTGGGTTAGGTTTTTCTTTTTCTTC
Found at i:4196362 original size:34 final size:33
Alignment explanation
Indices: 4196262--4196362 Score: 145
Period size: 31 Copynumber: 3.1 Consensus size: 33
4196252 GTGGCTAGGG
* *
4196262 TTTTTTTATT-TTTTTATTTTGGGTTAGGTTTT
1 TTTTTTTCTTCTTTTTTTTTTGGGTTAGGTTTT
4196294 TCTTTTTTCTTCTTTTTTTTTTGGGTTAGG-TTT
1 T-TTTTTTCTTCTTTTTTTTTTGGGTTAGGTTTT
*
4196327 TTCTTTT-TTCTTTTTTTTTTGGGTTAGGTTTT
1 TTTTTTTCTTCTTTTTTTTTTGGGTTAGGTTTT
4196359 TTTT
1 TTTT
4196363 GGAGAGGGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
31 21 0.34
32 12 0.19
33 12 0.19
34 17 0.27
ACGTcount: A:0.05, C:0.05, G:0.15, T:0.75
Consensus pattern (33 bp):
TTTTTTTCTTCTTTTTTTTTTGGGTTAGGTTTT
Found at i:4197032 original size:15 final size:16
Alignment explanation
Indices: 4197010--4197061 Score: 72
Period size: 15 Copynumber: 3.3 Consensus size: 16
4197000 AATAAATAGT
4197010 TAATAATAAAATGATA
1 TAATAATAAAATGATA
*
4197026 TAA-AATAAAATAATA
1 TAATAATAAAATGATA
4197041 -AATAATAAAAATGATA
1 TAATAAT-AAAATGATA
4197057 TAATA
1 TAATA
4197062 TATATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 2 0.06
15 14 0.45
16 11 0.35
17 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (16 bp):
TAATAATAAAATGATA
Found at i:4197126 original size:17 final size:17
Alignment explanation
Indices: 4197083--4197128 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
4197073 ACATATATAA
*
4197083 ATATAATAAAATGAATT
1 ATATAATAAAATAAATT
4197100 ATA-AAGTAAAA-AAATAT
1 ATATAA-TAAAATAAAT-T
4197117 ATATAATAAAAT
1 ATATAATAAAAT
4197129 TTATAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 5 0.21
17 17 0.71
18 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
ATATAATAAAATAAATT
Found at i:4198778 original size:41 final size:41
Alignment explanation
Indices: 4198707--4198844 Score: 222
Period size: 41 Copynumber: 3.3 Consensus size: 41
4198697 AAACTTAGGA
*
4198707 ACGCCAAATCTGTTATCTTCGATCTGCTCTCTGGCAATACAGAG
1 ACGCCAAATCTG-T-T-TTCGATCTGCTCTCTGACAATACAGAG
*
4198751 ATGCCAAATCTGTTTTCGATCTGCTCTCTGACAATACAGAG
1 ACGCCAAATCTGTTTTCGATCTGCTCTCTGACAATACAGAG
*
4198792 ACGCCAAATCTATTTTCGATCTGCTCTCTGACAATACAGAG
1 ACGCCAAATCTGTTTTCGATCTGCTCTCTGACAATACAGAG
4198833 ACGCCAAATCTG
1 ACGCCAAATCTG
4198845 CTATCTTCGA
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
41 76 0.85
42 1 0.01
43 1 0.01
44 11 0.12
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (41 bp):
ACGCCAAATCTGTTTTCGATCTGCTCTCTGACAATACAGAG
Found at i:4199106 original size:220 final size:220
Alignment explanation
Indices: 4198848--4199281 Score: 661
Period size: 220 Copynumber: 2.0 Consensus size: 220
4198838 AAATCTGCTA
* * * * *
4198848 TCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAATCATCTTGGATTTGCTTCAATGCAAAAA
1 TCTTCGATCTGCCCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTACTTCAATGCAAAAA
* ** ** *
4198913 CATCTGAAGGTTAGATCTGTTATGTCTTCGATCTGCCCTCCGTTGAATATGGAGATGCCAAATCT
66 CATCCGAAGGTTAGATCTACTATGTCTTCGATCTGCCCTCCGTCAAATATGAAGATGCCAAATCT
*
4198978 GTTTCTTCAATTTGCTCTCTGACAATACAGAGATCCCAAATCATCTTGGATCTACTTTAGCGTAA
131 GTTTCTTCAATTTGCTCTCTGACAATACAGAGATCCCAAATCATCTTGGATCTACTTCAGCGTAA
4199043 ACACCTGAAGGTCAGATCTATTATG
196 ACACCTGAAGGTCAGATCTATTATG
* **
4199068 TCTTCGATCTGCCCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTACTTCGATGTGAAAA
1 TCTTCGATCTGCCCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTACTTCAATGCAAAAA
*
4199133 CATCCGAAGGTTAGATCTACTATGTCTTCGATCTGCTCTCCGTCAAATATGAAGATGCCAAATCT
66 CATCCGAAGGTTAGATCTACTATGTCTTCGATCTGCCCTCCGTCAAATATGAAGATGCCAAATCT
* * * ** *
4199198 GTTTCTTCGATTTTCTTTCTGACAATACAGAGATGTCAAATCATCTTGGATCTGCTTCAGCGTAA
131 GTTTCTTCAATTTGCTCTCTGACAATACAGAGATCCCAAATCATCTTGGATCTACTTCAGCGTAA
*
4199263 ACACCTGAGGGTCAGATCT
196 ACACCTGAAGGTCAGATCT
4199282 GCTATGCTTT
Statistics
Matches: 191, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
220 191 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (220 bp):
TCTTCGATCTGCCCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTACTTCAATGCAAAAA
CATCCGAAGGTTAGATCTACTATGTCTTCGATCTGCCCTCCGTCAAATATGAAGATGCCAAATCT
GTTTCTTCAATTTGCTCTCTGACAATACAGAGATCCCAAATCATCTTGGATCTACTTCAGCGTAA
ACACCTGAAGGTCAGATCTATTATG
Found at i:4211128 original size:15 final size:16
Alignment explanation
Indices: 4211106--4211157 Score: 72
Period size: 15 Copynumber: 3.3 Consensus size: 16
4211096 AATAAATAGT
4211106 TAATAATAAAATGATA
1 TAATAATAAAATGATA
*
4211122 TAA-AATAAAATAATA
1 TAATAATAAAATGATA
4211137 -AATAATAAAAATGATA
1 TAATAAT-AAAATGATA
4211153 TAATA
1 TAATA
4211158 TATATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 2 0.06
15 14 0.45
16 11 0.35
17 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (16 bp):
TAATAATAAAATGATA
Found at i:4211155 original size:26 final size:25
Alignment explanation
Indices: 4211126--4211190 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
4211116 ATGATATAAA
4211126 ATAAAATAATAAATAATAAAAATGAT
1 ATAAAATAATAAATAATAAAAAT-AT
* ** *
4211152 ATAATAT-ATATAATAATTTACATAT
1 ATAAAATAATA-AATAATAAAAATAT
4211177 ATAAATATAATAAA
1 ATAAA-ATAATAAA
4211191 ATGAATTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 9 0.29
26 19 0.61
27 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAAAATAATAAATAATAAAAATAT
Found at i:4211224 original size:17 final size:17
Alignment explanation
Indices: 4211181--4211226 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
4211171 ACATATATAA
*
4211181 ATATAATAAAATGAATT
1 ATATAATAAAATAAATT
4211198 ATA-AAGTAAAA-AAATAT
1 ATATAA-TAAAATAAAT-T
4211215 ATATAATAAAAT
1 ATATAATAAAAT
4211227 TTATAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 5 0.21
17 17 0.71
18 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
ATATAATAAAATAAATT
Found at i:4211254 original size:30 final size:32
Alignment explanation
Indices: 4211179--4211256 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 32
4211169 TTACATATAT
*
4211179 AAATATAATAAAAT-GAA-TTATAAAGTAAAA
1 AAATATAATAAAATAAAATTTATAAAGTAAAA
* *
4211209 AAATAT-ATATAATAAAATTTAT-AAG-AAAC
1 AAATATAATAAAATAAAATTTATAAAGTAAAA
*
4211238 ACATATAATAAAATAAAAT
1 AAATATAATAAAATAAAAT
4211257 AATATATGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 14 0.35
30 22 0.55
31 4 0.10
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (32 bp):
AAATATAATAAAATAAAATTTATAAAGTAAAA
Found at i:4215290 original size:3 final size:3
Alignment explanation
Indices: 4215284--4215334 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
4215274 TATGAACTAT
4215284 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4215332 ATA
1 ATA
4215335 TAAGAACATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4215401 original size:26 final size:24
Alignment explanation
Indices: 4215362--4215415 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
4215352 AATATTATAC
4215362 AAAATATTAAAATAATCTGATATAAA
1 AAAATATTAAAATAA--TGATATAAA
* * *
4215388 AAAATTTTACAATAATGATTTAAA
1 AAAATATTAAAATAATGATATAAA
4215412 AAAA
1 AAAA
4215416 CAAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
26 13 0.52
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATATTAAAATAATGATATAAA
Found at i:4226699 original size:22 final size:21
Alignment explanation
Indices: 4226644--4226700 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
4226634 TCTAATTTAC
*
4226644 AATTTTTATCAAATTAATTTT
1 AATTTTTATTAAATTAATTTT
*
4226665 TATTTTTAATTAAATTAAATTATT
1 AATTTTT-ATTAAATT-AATT-TT
4226689 AATTTTT-TTAAA
1 AATTTTTATTAAA
4226701 AAAGTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 6 0.20
22 12 0.40
23 4 0.13
24 8 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTTTATTAAATTAATTTT
Found at i:4226733 original size:12 final size:12
Alignment explanation
Indices: 4226716--4226745 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4226706 TAAATCTGAT
4226716 TTAATAAAAATA
1 TTAATAAAAATA
4226728 TTAATAAAAATA
1 TTAATAAAAATA
*
4226740 TAAATA
1 TTAATA
4226746 TTATAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:4227513 original size:4 final size:4
Alignment explanation
Indices: 4227504--4227529 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4227494 ATTTAAAATA
4227504 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
4227530 TCACTAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:4231504 original size:43 final size:43
Alignment explanation
Indices: 4231452--4231537 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
4231442 TTGTTATTAC
4231452 TTTAATGGAATTAGAATTG-GGTTAAGAAATTAATTTATTTAAT
1 TTTAATGGAATTAGAA-TGAGGTTAAGAAATTAATTTATTTAAT
4231495 TTTAATGGAATTAGAATGAGGTTAAGAAATTAATTTATTTAAT
1 TTTAATGGAATTAGAATGAGGTTAAGAAATTAATTTATTTAAT
4231538 CTAATTAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 2 0.05
43 40 0.95
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (43 bp):
TTTAATGGAATTAGAATGAGGTTAAGAAATTAATTTATTTAAT
Found at i:4231544 original size:37 final size:40
Alignment explanation
Indices: 4231453--4231548 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 40
4231443 TGTTATTACT
4231453 TTAATGGAATTAGAATTGGGTTAAGAAATTAATTTATTTAA
1 TTAAT-GAATTAGAATTGGGTTAAGAAATTAATTTATTTAA
4231494 TTTTAATGGAATTAGAA-TGAGGTTAAGAAATTAATTTATTTAA
1 --TTAAT-GAATTAGAATTG-GGTTAAGAAATTAATTTATTTAA
*
4231537 TCTAATTAATTA
1 T-TAATGAATTA
4231549 AATAATATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
41 6 0.12
42 6 0.12
43 38 0.76
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.43
Consensus pattern (40 bp):
TTAATGAATTAGAATTGGGTTAAGAAATTAATTTATTTAA
Found at i:4235395 original size:15 final size:15
Alignment explanation
Indices: 4235376--4235425 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
4235366 TTTGAATTGT
*
4235376 TGTATTATATGTTTT
1 TGTATTATATGTTTA
4235391 TGTA-TATAATGTTTA
1 TGTATTAT-ATGTTTA
4235406 T-TATTATTAT-TTTA
1 TGTATTA-TATGTTTA
4235420 TGTATT
1 TGTATT
4235426 TTCTTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 10 0.33
15 19 0.63
16 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (15 bp):
TGTATTATATGTTTA
Found at i:4235754 original size:13 final size:13
Alignment explanation
Indices: 4235736--4235760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4235726 TTTGTATATA
4235736 TATTATTTTCATT
1 TATTATTTTCATT
4235749 TATTATTTTCAT
1 TATTATTTTCAT
4235761 ATAGATACGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTTCATT
Found at i:4237600 original size:53 final size:53
Alignment explanation
Indices: 4237519--4237669 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
4237509 CTTACACGGT
* *
4237519 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
4237574 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
4237627 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
4237670 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:4245116 original size:53 final size:53
Alignment explanation
Indices: 4245035--4245185 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
4245025 CTTACACGGT
* *
4245035 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
4245090 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
4245143 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
4245186 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:4246999 original size:28 final size:24
Alignment explanation
Indices: 4246945--4246995 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
4246935 GCACTTTAAA
4246945 TTTTCCAACTTGTTGTATCAAGTG
1 TTTTCCAACTTGTTGTATCAAGTG
4246969 TTTTCCTAACTTGTTGTCAT-AAGTG
1 TTTTCC-AACTTGTTGT-ATCAAGTG
4246994 TT
1 TT
4246996 GTTTAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (24 bp):
TTTTCCAACTTGTTGTATCAAGTG
Found at i:4257372 original size:106 final size:107
Alignment explanation
Indices: 4257187--4257463 Score: 335
Period size: 106 Copynumber: 2.6 Consensus size: 107
4257177 CAATGAAGAT
* * * * *
4257187 GCATCCATTGTGTCTCTACATCTAGTTAGTGGAGACGCATTTACGTGACTA-TATAGCTCAATCT
1 GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGAC-ACTATAGCTCAGTCT
* * *
4257251 ATGGTGATGCGAGACATGCATCTTCACT-G-TGTCAGTAGAGAA
65 ATGGTGACGCGAGACATGCATCTTCA-TAGATATCAATAGAGAA
* ** *
4257293 GCATCCACTGTGTCTCTACCTCTAGTTAGTTAAGACGCATGTATGCGACGCTATAGCTCAGTCTA
1 GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGACACTATAGCTCAGTCTA
*
4257358 TGGTGACGCGAGACATGCATCTTCATAAGCATATCAATAGAGAC
66 TGGTGACGCGAGACATGCATCTTCAT-AG-ATATCAATAGAGAA
* * * * *
4257402 GTATCCATTGTGTCTCTACCTTTAGTTAGTGGGGACACATGTGTGCGACACTATAGCTCAGT
1 GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGACACTATAGCTCAGT
4257464 TTGTAGAGAC
Statistics
Matches: 144, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
105 1 0.01
106 79 0.55
107 1 0.01
109 63 0.44
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (107 bp):
GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGACACTATAGCTCAGTCTA
TGGTGACGCGAGACATGCATCTTCATAGATATCAATAGAGAA
Found at i:4258408 original size:22 final size:23
Alignment explanation
Indices: 4258377--4258437 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
4258367 TATGCACTAT
4258377 TAAACAGAGAGCACTAAA-GTGC
1 TAAACAGAGAGCACTAAATGTGC
* *
4258399 TATACGGAGAGCAC-AAATGTGC
1 TAAACAGAGAGCACTAAATGTGC
4258421 TAAACAGAGAGCACTAA
1 TAAACAGAGAGCACTAA
4258438 TATACTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 28 0.85
23 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (23 bp):
TAAACAGAGAGCACTAAATGTGC
Found at i:4258445 original size:22 final size:22
Alignment explanation
Indices: 4258377--4258445 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
4258367 TATGCACTAT
4258377 TAAACAGAGAGCACTAA-AGTGC
1 TAAACAGAGAGCACTAATA-TGC
* * * *
4258399 TATACGGAGAGCACAAATGTGC
1 TAAACAGAGAGCACTAATATGC
*
4258421 TAAACAGAGAGCACTAATATAC
1 TAAACAGAGAGCACTAATATGC
4258443 TAA
1 TAA
4258446 TAATCTAAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (22 bp):
TAAACAGAGAGCACTAATATGC
Found at i:4261417 original size:11 final size:11
Alignment explanation
Indices: 4261401--4261453 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
4261391 TTTAATCACT
4261401 TTAATATTAAA
1 TTAATATTAAA
4261412 TTAATA-TAATA
1 TTAATATTAA-A
* *
4261423 TAAATATTAAG
1 TTAATATTAAA
4261434 TTAATATTAAA
1 TTAATATTAAA
4261445 TTAA-ATTAA
1 TTAATATTAA
4261454 TATTTACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 8 0.22
11 25 0.69
12 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:4262071 original size:22 final size:21
Alignment explanation
Indices: 4262028--4262072 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4262018 ATTTTACTTT
*
4262028 ATCAAAATAATTTTTTCAAAA
1 ATCAAAATAATTTTTTAAAAA
*
4262049 ATCAAATTAATTTTTTAAGAAA
1 ATCAAAATAATTTTTTAA-AAA
4262071 AT
1 AT
4262073 TCTTTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (21 bp):
ATCAAAATAATTTTTTAAAAA
Found at i:4267063 original size:45 final size:41
Alignment explanation
Indices: 4267006--4267102 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 41
4266996 TTAGACAACA
* **
4267006 AAGAATCGATTCAAAGAAGCAAATAATTGATTTAAAATAACAAT
1 AAGAATCGATTCAAAGAAGCAAAGAATCAATTT--AA-AACAAT
4267050 AATGAATCGATTCAAAGAAGCAAAGAATCAATTTAAAACAAT
1 AA-GAATCGATTCAAAGAAGCAAAGAATCAATTTAAAACAAT
4267092 AAGAATCGATT
1 AAGAATCGATT
4267103 TAAAATAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 9 0.18
42 8 0.16
43 2 0.04
44 2 0.04
45 28 0.57
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (41 bp):
AAGAATCGATTCAAAGAAGCAAAGAATCAATTTAAAACAAT
Found at i:4267121 original size:21 final size:20
Alignment explanation
Indices: 4266988--4267123 Score: 85
Period size: 21 Copynumber: 6.5 Consensus size: 20
4266978 CATGAAGTTT
* * *
4266988 GAATCGAGTTAGACAACAAA
1 GAATCGATTTAAAAAACAAA
* *
4267008 GAATCGATTCAAAGAAGCAAA
1 GAATCGATTTAAA-AAACAAA
* *
4267029 TAATTGATTTAAAATAACAATAA
1 GAATCGATTTAAAA-AAC-A-AA
* *
4267052 TGAATCGATTCAAAGAAGCAAA
1 -GAATCGATTTAAA-AAACAAA
* *
4267074 GAATCAATTTAAAACAA-TAA
1 GAATCGATTTAAAA-AACAAA
4267094 GAATCGATTTAAAATAACAAA
1 GAATCGATTTAAAA-AACAAA
*
4267115 CAATCGATT
1 GAATCGATT
4267124 CAAATAAGCA
Statistics
Matches: 87, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
20 29 0.33
21 39 0.45
22 3 0.03
23 3 0.03
24 12 0.14
25 1 0.01
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (20 bp):
GAATCGATTTAAAAAACAAA
Found at i:4268607 original size:17 final size:17
Alignment explanation
Indices: 4268585--4268641 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
4268575 ACGTATGAGA
4268585 AAAACAAAAAACGTGGG
1 AAAACAAAAAACGTGGG
* * *
4268602 AAAAC-AAAATC--AGA
1 AAAACAAAAAACGTGGG
4268616 AAAACAAAAAACGTGGG
1 AAAACAAAAAACGTGGG
4268633 AAAACAAAA
1 AAAACAAAA
4268642 TCAAGAAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 5 0.16
17 15 0.48
ACGTcount: A:0.67, C:0.12, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAACAAAAAACGTGGG
Found at i:4268620 original size:31 final size:32
Alignment explanation
Indices: 4268582--4268650 Score: 131
Period size: 31 Copynumber: 2.2 Consensus size: 32
4268572 ATTACGTATG
4268582 AGAAAAACAAAAAACGTGGGAAAACAAAATC-
1 AGAAAAACAAAAAACGTGGGAAAACAAAATCA
4268613 AGAAAAACAAAAAACGTGGGAAAACAAAATCA
1 AGAAAAACAAAAAACGTGGGAAAACAAAATCA
4268645 AGAAAA
1 AGAAAA
4268651 CACCCAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 31 0.84
32 6 0.16
ACGTcount: A:0.67, C:0.12, G:0.16, T:0.06
Consensus pattern (32 bp):
AGAAAAACAAAAAACGTGGGAAAACAAAATCA
Found at i:4273650 original size:15 final size:15
Alignment explanation
Indices: 4273630--4273659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4273620 CTTAATTTAG
*
4273630 TTAACTCGGTAGTCA
1 TTAACTCGGGAGTCA
4273645 TTAACTCGGGAGTCA
1 TTAACTCGGGAGTCA
4273660 AATTGTAGAA
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:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (15 bp):
TTAACTCGGGAGTCA
Found at i:4275856 original size:16 final size:18
Alignment explanation
Indices: 4275821--4275857 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
4275811 TACATAACAT
*
4275821 ATATTAATATATATAATA
1 ATATTAATATATAAAATA
4275839 ATATTAA-A-ATAAAATA
1 ATATTAATATATAAAATA
4275855 ATA
1 ATA
4275858 AGTGATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATTAATATATAAAATA
Found at i:4276274 original size:19 final size:19
Alignment explanation
Indices: 4276250--4276286 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4276240 TATAAATAAT
*
4276250 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
4276269 AATGATATTAGAAATATA
1 AATGATATTAGAAATATA
4276287 TATAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:4276384 original size:24 final size:24
Alignment explanation
Indices: 4276343--4276398 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
4276333 ACACAATAAT
*
4276343 ATATATAACATACAATAT-TGAAAA
1 ATATAT-ACATACAATATACGAAAA
4276367 CATATATACATA-ATATATACGAAAA
1 -ATATATACATACA-ATATACGAAAA
4276392 ATATATA
1 ATATATA
4276399 GATATACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
25 11 0.39
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
ATATATACATACAATATACGAAAA
Found at i:4276423 original size:30 final size:30
Alignment explanation
Indices: 4276370--4276444 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
4276360 TTGAAAACAT
*
4276370 ATATACATAATATATACGAAAAATATATAG
1 ATATACATAATATATACGAAAAATATATAC
** *
4276400 ATATACATAATATAATA-TTAAAATATTTAC
1 ATATACATAATAT-ATACGAAAAATATATAC
4276430 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
4276445 TAGGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 26 0.67
31 11 0.28
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATACATAATATATACGAAAAATATATAC
Found at i:4278481 original size:13 final size:13
Alignment explanation
Indices: 4278453--4278487 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
4278443 TGAGTTGACT
4278453 TTTGAAAACAGAA
1 TTTGAAAACAGAA
*
4278466 TTTGCAAAACAGAT
1 TTTG-AAAACAGAA
4278480 TTTGAAAA
1 TTTGAAAA
4278488 TACCTCGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAGAA
Found at i:4278613 original size:89 final size:88
Alignment explanation
Indices: 4278396--4278728 Score: 315
Period size: 89 Copynumber: 3.8 Consensus size: 88
4278386 GAAATTGAAA
* * ** ** *
4278396 AAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCATTTCTCGCAATATGAGTTGACTTTTGAAAA
1 AAAATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* * * *
4278461 CA-GAATTTGCAAAACAGATTTTG
65 CATAAATTTGAAAAAAACATTTTG
* *
4278484 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
4278549 GCATAAATTT-AAAAAAACATTAATTG
65 -CATAAATTTGAAAAAAACATT--TTG
* *
4278575 AAAATATCTCAGC-GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 AAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
* *
4278639 CATAAA-TTGAACAGAA-A--TTG
65 CATAAATTTGAAAAAAACATTTTG
* * ** * ** *
4278659 AAAATACCTCAAC-GTGTCTTGAGGCTCAATTCATTTCTCGCAATATGAGTTGAGTTTTG-AAAC
1 AAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAC
*
4278722 AAAAATT
66 ATAAATT
4278729 AACAATACCT
Statistics
Matches: 208, Mismatches: 30, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
82 8 0.04
83 1 0.00
84 53 0.25
88 58 0.28
89 65 0.31
90 9 0.04
91 14 0.07
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (88 bp):
AAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAC
ATAAATTTGAAAAAAACATTTTG
Found at i:4278769 original size:71 final size:71
Alignment explanation
Indices: 4278648--4278787 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 71
4278638 ACATAAATTG
* ** * **
4278648 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAATTCATTTCTCGCAATATGAGTTGAG
1 AACAAAAATTGAAAATACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAG
4278713 TTTTGA
66 TTTTGA
*
4278719 AACAAAAATT-AACAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAAAAATTGAA-AATACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
4278783 TTTTT
65 GTTTT
4278788 TTGAAAAGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 2 0.03
71 58 0.97
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (71 bp):
AACAAAAATTGAAAATACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAG
TTTTGA
Found at i:4278875 original size:92 final size:91
Alignment explanation
Indices: 4278750--4278972 Score: 297
Period size: 90 Copynumber: 2.5 Consensus size: 91
4278740 AGCGTGTCCC
* **
4278750 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTAAAAAACATTA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTAAAAAACAGAA
* * *
4278815 ATTGAAAATACCTCGGCATGTGATCTT
66 ATTGAAAACACCTCGACATGTGA-CCT
* * * * * *
4278842 GAGGCTAAATTCACCTCTAGCAATATGAATTGA--TTTTTGAAAAACATAAATTGAAAAATAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTAAAAAACAGAA
*
4278905 ATTGTAAACACCTCGACATGTGACCT
66 ATTGAAAACACCTCGACATGTGACCT
*
4278931 GAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
4278973 TGAATAGAAA
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
89 30 0.27
90 45 0.41
91 7 0.06
92 29 0.26
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (91 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTAAAAAACAGAA
ATTGAAAACACCTCGACATGTGACCT
Found at i:4279023 original size:75 final size:76
Alignment explanation
Indices: 4278892--4279123 Score: 321
Period size: 74 Copynumber: 3.1 Consensus size: 76
4278882 AAAACATAAA
* *
4278892 TTGAAAAATAGAAATTGTAAAC-ACCTCGACATGTGACCTGAGGTTCAACTCACCTCTCGCAATA
1 TTGAAAAATAGAAATTGAAAACTACCTC-A-ATGTGTCCTGAGGTTCAACTCACCTCTCGCAATA
4278956 TGAGTTGATTTTT
64 TGAGTTGATTTTT
** *
4278969 TTGATGAATAGAAATT-AAAACTACCTCAATGTGTCCTAAGGTTCAACTCACCTCTCGCAATATG
1 TTGAAAAATAGAAATTGAAAACTACCTCAATGTGTCCTGAGGTTCAACTCACCTCTCGCAATATG
4279033 AGTTGATTTTT
66 AGTTGATTTTT
* * * *
4279044 TTGAAAAAATAG--ATTGAAAA-TACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATAT
1 TTG-AAAAATAGAAATTGAAAACTACCTCAATGTGTCCTGAGGTTCAACTCACCTCTCGCAATAT
4279106 GAGTTGATTTTT
65 GAGTTGATTTTT
4279118 TTGAAA
1 TTGAAA
4279124 CAGAAATAAA
Statistics
Matches: 140, Mismatches: 12, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
73 3 0.02
74 55 0.39
75 52 0.37
76 11 0.08
77 19 0.14
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (76 bp):
TTGAAAAATAGAAATTGAAAACTACCTCAATGTGTCCTGAGGTTCAACTCACCTCTCGCAATATG
AGTTGATTTTT
Found at i:4291542 original size:9 final size:9
Alignment explanation
Indices: 4291528--4291562 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4291518 ACATTAAAAT
4291528 ATATATATA
1 ATATATATA
*
4291537 ATATATAAA
1 ATATATATA
*
4291546 ATACATATA
1 ATATATATA
4291555 ATATATAT
1 ATATATAT
4291563 TAGAAATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATATATA
Found at i:4294266 original size:26 final size:26
Alignment explanation
Indices: 4294230--4294313 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
4294220 CATGAAATTC
4294230 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
4294256 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
4294282 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
4294308 TTATCA
1 TTATCA
4294314 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:4294653 original size:19 final size:19
Alignment explanation
Indices: 4294629--4294665 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4294619 TATATATAAT
*
4294629 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
4294648 AATGATATTAGAAATATA
1 AATGATATTAGAAATATA
4294666 TATAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:4294763 original size:24 final size:24
Alignment explanation
Indices: 4294722--4294777 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
4294712 ACACAATAAT
*
4294722 ATATATAACATACAATAT-TGAAAA
1 ATATAT-ACATACAATATACGAAAA
4294746 CATATATACATA-ATATATACGAAAA
1 -ATATATACATACA-ATATACGAAAA
4294771 ATATATA
1 ATATATA
4294778 GATATACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
25 11 0.39
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
ATATATACATACAATATACGAAAA
Found at i:4294802 original size:30 final size:30
Alignment explanation
Indices: 4294749--4294823 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
4294739 TTGAAAACAT
*
4294749 ATATACATAATATATACGAAAAATATATAG
1 ATATACATAATATATACGAAAAATATATAC
** *
4294779 ATATACATAATATAATA-TTAAAATATTTAC
1 ATATACATAATAT-ATACGAAAAATATATAC
4294809 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
4294824 TAGGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 26 0.67
31 11 0.28
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATACATAATATATACGAAAAATATATAC
Found at i:4294888 original size:25 final size:24
Alignment explanation
Indices: 4294861--4294906 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
4294851 CTACATAAGT
4294861 ATATACATAAATATAT-TAAAAAC
1 ATATACATAAATATATATAAAAAC
*
4294884 ATATACATATATATATATAAAAA
1 ATATACATAAATATATATAAAAA
4294907 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATACATAAATATATATAAAAAC
Found at i:4294913 original size:31 final size:32
Alignment explanation
Indices: 4294860--4294929 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 32
4294850 GCTACATAAG
*
4294860 TATATACATAAATATATTAAAAACATATACA-TA
1 TATATATATAAATATA-TAAAAA-ATATACACTA
4294893 TATATATATAAA-A-ATAAAAAATATACACTA
1 TATATATATAAATATATAAAAAATATACACTA
4294923 -ATATATA
1 TATATATA
4294930 GTAATCATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 14 0.40
30 8 0.23
31 1 0.03
32 1 0.03
33 11 0.31
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (32 bp):
TATATATATAAATATATAAAAAATATACACTA
Found at i:4295535 original size:36 final size:37
Alignment explanation
Indices: 4295483--4295553 Score: 135
Period size: 36 Copynumber: 1.9 Consensus size: 37
4295473 GCCGGGTCAA
4295483 TAAACGGCCAACCCCAAAACGACGTCGTTTTGGGGTT
1 TAAACGGCCAACCCCAAAACGACGTCGTTTTGGGGTT
4295520 TAAA-GGCCAACCCCAAAACGACGTCGTTTTGGGG
1 TAAACGGCCAACCCCAAAACGACGTCGTTTTGGGG
4295554 GGCTATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 30 0.88
37 4 0.12
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (37 bp):
TAAACGGCCAACCCCAAAACGACGTCGTTTTGGGGTT
Found at i:4296392 original size:24 final size:20
Alignment explanation
Indices: 4296346--4296412 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 20
4296336 CTTTCTTTCC
*
4296346 TTCTTTTCTTCTCTGTTTTCAT
1 TTCTTTTGTT-TCT-TTTTCAT
4296368 TTCATATTCTGTTTCCTTTTTCAT
1 TTC-T-TT-TGTTT-CTTTTTCAT
4296392 TTCTTTTGTTTCTTTTT-AT
1 TTCTTTTGTTTCTTTTTCAT
4296411 TT
1 TT
4296413 ATTATAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
19 4 0.10
20 6 0.15
21 5 0.12
22 5 0.12
23 2 0.05
24 13 0.32
25 5 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.70
Consensus pattern (20 bp):
TTCTTTTGTTTCTTTTTCAT
Found at i:4299352 original size:44 final size:44
Alignment explanation
Indices: 4299302--4299385 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
4299292 AAATAAAAAG
4299302 AAAATCTAATAAAATTTGAGAATAATTTAT-TATAGGATGATCCT
1 AAAATCTAATAAAATTTGAGAATAATTTATAT-TAGGATGATCCT
4299346 AAAATCTAATAAAATTTGAGAATAATTTATATTAGGATGA
1 AAAATCTAATAAAATTTGAGAATAATTTATATTAGGATGA
4299386 AATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (44 bp):
AAAATCTAATAAAATTTGAGAATAATTTATATTAGGATGATCCT
Found at i:4300562 original size:29 final size:29
Alignment explanation
Indices: 4300523--4300593 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
4300513 TACACTAATA
*
4300523 GTCACCTAACTATTAGTAAATTTCTTTTT
1 GTCACCCAACTATTAGTAAATTTCTTTTT
* * * *
4300552 GTCATCCAACTAGTAGTTAATTTTTTTTT
1 GTCACCCAACTATTAGTAAATTTCTTTTT
4300581 GTCACCCAACTAT
1 GTCACCCAACTAT
4300594 GAACGGTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (29 bp):
GTCACCCAACTATTAGTAAATTTCTTTTT
Found at i:4303100 original size:20 final size:21
Alignment explanation
Indices: 4303075--4303117 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
4303065 TTTATTTTCC
*
4303075 TATTAAAATTTTATTAT-TTT
1 TATTAAAATATTATTATCTTT
4303095 TATTAAAATATTATTATCTTT
1 TATTAAAATATTATTATCTTT
4303116 TA
1 TA
4303118 CAAGAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTAAAATATTATTATCTTT
Found at i:4303209 original size:29 final size:29
Alignment explanation
Indices: 4303131--4303271 Score: 198
Period size: 29 Copynumber: 4.9 Consensus size: 29
4303121 GAAATTCATG
*
4303131 ATAATAATTATTTTAAAATTTATGAG-T-
1 ATAATAATTATTTTAAAATTTAAGAGATC
*
4303158 -TAATAAATCTATTTTAAAATTTAAGAGATG
1 ATAAT-AAT-TATTTTAAAATTTAAGAGATC
*
4303188 ATAATAATTATTTTAAACTTTAAGAGATC
1 ATAATAATTATTTTAAAATTTAAGAGATC
*
4303217 ATAATAATTATTTTAAACTTTAAGAGATC
1 ATAATAATTATTTTAAAATTTAAGAGATC
*
4303246 ATAATAATTATTTTAAATTTTAAGAG
1 ATAATAATTATTTTAAAATTTAAGAG
4303272 GGAATTATGA
Statistics
Matches: 105, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.04
27 3 0.03
28 17 0.16
29 74 0.70
30 3 0.03
31 4 0.04
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (29 bp):
ATAATAATTATTTTAAAATTTAAGAGATC
Found at i:4308240 original size:19 final size:20
Alignment explanation
Indices: 4308207--4308246 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
4308197 ATATATATAT
4308207 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
4308226 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
4308246 A
1 A
4308247 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:4308513 original size:18 final size:17
Alignment explanation
Indices: 4308490--4308535 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
4308480 AGAGGTTAGG
*
4308490 TTTTTTTCTTTTTCTTCA
1 TTTTTTTATTTTT-TTCA
*
4308508 TTTTTTTATTTTTTTTA
1 TTTTTTTATTTTTTTCA
4308525 -TTTTTTATTTT
1 TTTTTTTATTTT
4308536 GGGTTGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 3 0.12
18 12 0.46
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTATTTTTTTCA
Found at i:4312221 original size:16 final size:16
Alignment explanation
Indices: 4312200--4312239 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4312190 TGAATTACTT
4312200 ATTACAG-CTCTATTCA
1 ATTACAGTCT-TATTCA
*
4312216 ATTACAGTCTTATTCC
1 ATTACAGTCTTATTCA
4312232 ATTACAGT
1 ATTACAGT
4312240 GAACCAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTACAGTCTTATTCA
Found at i:4316599 original size:3 final size:3
Alignment explanation
Indices: 4316591--4316657 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
4316581 TGAATTTCTA
4316591 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4316639 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
4316658 TATAGTAGTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4316834 original size:14 final size:14
Alignment explanation
Indices: 4316815--4316844 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4316805 ATTTATATTC
4316815 TATATGTATATATA
1 TATATGTATATATA
*
4316829 TATATGTTTATATA
1 TATATGTATATATA
4316843 TA
1 TA
4316845 GTGTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (14 bp):
TATATGTATATATA
Found at i:4316876 original size:136 final size:134
Alignment explanation
Indices: 4316636--4316883 Score: 306
Period size: 134 Copynumber: 1.8 Consensus size: 134
4316626 TTATTATTAT
* * * * * *
4316636 TATTATTATTATTATTATTATTTATAGTAGTGTATATTTTTATTATCTATGTATATGTATATGCA
1 TATTATTACTATTATTATTATTGATAGTAGTGTATATTTATATTATATATGTATATATATATACA
4316701 TTTATTATAGTATTATTTTAATTACTTTATCATTTTATTA-TATTATATTGTTCTTTTTTGTATT
66 TTTATTATAGTATTATTTTAATTACTTTATCATTTTATTATTATTATATTGTTCTTTTTTGTATT
4316765 TCAA
131 TCAA
* *
4316769 TATTATTACTATTATTATTA-TGATACGTTAGTGTGTATTTATATTCTATATGTATATATATATA
1 TATTATTACTATTATTATTATTGATA-G-TAGTGTATATTTATATTATATATGTATATATATATA
** * *
4316833 TGTTTATATATAGTGTTATTTTTATTTACTTTA-C-TTTAATATTATTATTAT
64 CATTTAT-TATAGTATTA-TTTTAATTACTTTATCATTT--TATTATTATTAT
4316884 TATTATGTAC
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
132 4 0.04
133 20 0.21
134 38 0.40
135 10 0.10
136 18 0.19
137 6 0.06
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.59
Consensus pattern (134 bp):
TATTATTACTATTATTATTATTGATAGTAGTGTATATTTATATTATATATGTATATATATATACA
TTTATTATAGTATTATTTTAATTACTTTATCATTTTATTATTATTATATTGTTCTTTTTTGTATT
TCAA
Found at i:4317282 original size:12 final size:12
Alignment explanation
Indices: 4317254--4317282 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4317244 AAAAAAAATC
4317254 AAAAA-AAAGAA
1 AAAAACAAAGAA
4317265 AAAAACAAAGAA
1 AAAAACAAAGAA
4317277 AAAAAC
1 AAAAAC
4317283 CTAATCTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAACAAAGAA
Done.