Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 31
Found at i:5009251 original size:22 final size:23
Alignment explanation
Indices: 5009207--5009274 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
5009197 CAAAATATTA
* *
5009207 ATTATTAAAATAT-TAA-AATAT
1 ATTATTAATATTTATAATAATAT
5009228 ATTTATTAATATTTATAATAATAT
1 A-TTATTAATATTTATAATAATAT
* * *
5009252 AATATT-ATATTTTTAATATTAT
1 ATTATTAATATTTATAATAATAT
5009274 A
1 A
5009275 ATAAAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 25 0.64
23 7 0.18
24 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTATTAATATTTATAATAATAT
Found at i:5009275 original size:22 final size:23
Alignment explanation
Indices: 5009231--5009277 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5009221 AAAATATATT
5009231 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
5009254 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTATAATAATATAA
5009276 TA
1 TA
5009278 AAATATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:5009283 original size:22 final size:22
Alignment explanation
Indices: 5009235--5009301 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
5009225 TATATTTATT
* * *
5009235 AATATTTATAATAATATAATAT
1 AATATTTTTAATATTATAATAA
*
5009257 TATATTTTTAATATTATAATAA
1 AATATTTTTAATATTATAATAA
*
5009279 AATATTCAATT-ATATTATAATAA
1 AATATT--TTTAATATTATAATAA
5009302 TATAAGATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.62
23 12 0.32
24 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTTTTAATATTATAATAA
Found at i:5009291 original size:32 final size:33
Alignment explanation
Indices: 5009212--5009304 Score: 102
Period size: 32 Copynumber: 2.8 Consensus size: 33
5009202 TATTAATTAT
*
5009212 TAAAATATTAAAATATATTTATTAATATTTATAA
1 TAAAATATT-AATTATATTTATTAATATTTATAA
* *
5009246 TAATATAAT-ATTATATTT-TTAATA-TTATAA
1 TAAAATATTAATTATATTTATTAATATTTATAA
*
5009276 TAAAATATTCAATTATATTATAATAATAT
1 TAAAATATT-AATTATATT-TATTAATAT
5009305 AAGATATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
30 13 0.27
31 6 0.12
32 16 0.33
33 1 0.02
34 12 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (33 bp):
TAAAATATTAATTATATTTATTAATATTTATAA
Found at i:5009483 original size:23 final size:23
Alignment explanation
Indices: 5009457--5009501 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5009447 AATAATATTT
*
5009457 TAATAAAGATATTTAAAATATAC
1 TAATAAACATATTTAAAATATAC
* * *
5009480 TAATTAACATTTTTAAATTATA
1 TAATAAACATATTTAAAATATA
5009502 ATAGAACACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAACATATTTAAAATATAC
Found at i:5009655 original size:23 final size:26
Alignment explanation
Indices: 5009603--5009677 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 26
5009593 ATTATAAAAA
*
5009603 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATAT
5009630 TAATATTT-TAA-AAAT-AATTATAT
1 TAATATTTATAATAAATAAATTATAT
* *
5009653 TAAGT-TTTATGATAAACAATATTAT
1 TAA-TATTTATAATAAATAA-ATTAT
5009678 TTATTGTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 13 0.32
24 7 0.17
25 6 0.15
26 1 0.03
27 13 0.32
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATAT
Found at i:5009864 original size:50 final size:50
Alignment explanation
Indices: 5009767--5009871 Score: 117
Period size: 50 Copynumber: 2.1 Consensus size: 50
5009757 CAAACATCGT
***
5009767 AAAACATTTTCCAGAAAAATGTAATTCTTTTTCCTGGATAACATTTTCTAG
1 AAAACATTTTCCAGAAAAATGTAATTCTTTTTCCAAAATAACATTTTC-AG
* *
5009818 AAAACATTTTCCA-AAAAATGTAATT-TATTTTTCAAAAT-TCATTTTTCAG
1 AAAACATTTTCCAGAAAAATGTAATTCT-TTTTCCAAAATAACA-TTTTCAG
5009867 AAAAC
1 AAAAC
5009872 TAATTACACC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
49 10 0.21
50 24 0.51
51 13 0.28
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (50 bp):
AAAACATTTTCCAGAAAAATGTAATTCTTTTTCCAAAATAACATTTTCAG
Found at i:5012941 original size:25 final size:25
Alignment explanation
Indices: 5012913--5012961 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5012903 TCATCTTCAA
*
5012913 TCTCTTACATAATACACTCATTTCT
1 TCTCTTACACAATACACTCATTTCT
5012938 TCTCTTACACAATACACTCATTTC
1 TCTCTTACACAATACACTCATTTC
5012962 ATATTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.41
Consensus pattern (25 bp):
TCTCTTACACAATACACTCATTTCT
Found at i:5013798 original size:38 final size:38
Alignment explanation
Indices: 5013755--5013830 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5013745 TCAAGTGAAT
5013755 GTTTCCTTTCATTTTTTAAGTTGGTTTTAATTCTTGAG
1 GTTTCCTTTCATTTTTTAAGTTGGTTTTAATTCTTGAG
5013793 GTTTCCTTTCATTTTTTAAGTTGGTTTTAATTCTTGAG
1 GTTTCCTTTCATTTTTTAAGTTGGTTTTAATTCTTGAG
5013831 ATAATAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (38 bp):
GTTTCCTTTCATTTTTTAAGTTGGTTTTAATTCTTGAG
Found at i:5015302 original size:216 final size:218
Alignment explanation
Indices: 5015041--5015480 Score: 803
Period size: 224 Copynumber: 2.0 Consensus size: 218
5015031 TACATGATCT
5015041 ATGTGAAAAGAAGATATGAGATTACAAGTACAAGGGTATAAGTATGTGATGATTTGTGTGATTAT
1 ATGTGAAAAGAAGATATGAGATTACAAGTACAAGGGTATAAGTATGTGATGATTTGTGTGATTAT
5015106 ATGAATA-TG-TGATGAACATAAATGATAATGCCCATGTTATATGAAATGAGAGCTAGAGGTATA
66 ATGAATAGTGATGATGAACATAAATGATAATGCCCATGTTATATGAAATGAGAGCTAGAGGTATA
5015169 GTTGGCATGCCAAGAGTCGATGGTTCTACGTGGTCCTTCGGGACATATATGTAATCATTTGGAAC
131 GTTGGCATGCCAAGAGTCGATGGTTCTACGTGGTCCTTCGGGACATATATGTAATCATTTGGAAC
5015234 ATATATGCGGTACTTCGATACAC
196 ATATATGCGGTACTTCGATACAC
5015257 ATGTGAAAAGAAGATATGAGATTACAAGTACAAGGGTATAAGTATGTGATGATTTGTGTGATTAT
1 ATGTGAAAAGAAGATATGAGATTACAAGTACAAGGGTATAAGTATGTGATGATTTGTGTGATTAT
5015322 ATGAATATGTGAATAAATGATGAACATAAATGATAATGCCCATGTTATATGAAATGAGAGCTAGA
66 ATGAATA-GTG-----ATGATGAACATAAATGATAATGCCCATGTTATATGAAATGAGAGCTAGA
*
5015387 GGTATAGTTGGCATGCCAAGAGTCGATGGTTCTACGTGGTCCTTCGGGACATATATGTAATCCTT
125 GGTATAGTTGGCATGCCAAGAGTCGATGGTTCTACGTGGTCCTTCGGGACATATATGTAATCATT
5015452 TGGAACATATATGCGGTACTTCGATACAC
190 TGGAACATATATGCGGTACTTCGATACAC
5015481 CTATTTGGTC
Statistics
Matches: 215, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
216 72 0.33
218 2 0.01
224 141 0.66
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (218 bp):
ATGTGAAAAGAAGATATGAGATTACAAGTACAAGGGTATAAGTATGTGATGATTTGTGTGATTAT
ATGAATAGTGATGATGAACATAAATGATAATGCCCATGTTATATGAAATGAGAGCTAGAGGTATA
GTTGGCATGCCAAGAGTCGATGGTTCTACGTGGTCCTTCGGGACATATATGTAATCATTTGGAAC
ATATATGCGGTACTTCGATACAC
Found at i:5015729 original size:31 final size:31
Alignment explanation
Indices: 5015694--5015799 Score: 97
Period size: 31 Copynumber: 3.3 Consensus size: 31
5015684 TTAGGTCCAT
5015694 AAGGAATTACCAGTCAGTGCTGAACCTATAA
1 AAGGAATTACCAGTCAGTGCTGAACCTATAA
* *** *
5015725 AAGGAATTACCA-ACAGCAATTGAACCTGCCAAAA
1 AAGGAATTACCAGTCAG-TGCTGAACCT---ATAA
* *
5015759 ATAGGAATTACCAGTCAGTGCAGAACCTATAC
1 A-AGGAATTACCAGTCAGTGCTGAACCTATAA
5015791 AAGGAATTA
1 AAGGAATTA
5015800 TGTGCAACAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
30 3 0.05
31 27 0.47
32 3 0.05
34 4 0.07
35 17 0.30
36 3 0.05
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGTGCTGAACCTATAA
Found at i:5015815 original size:66 final size:66
Alignment explanation
Indices: 5015695--5015821 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
5015685 TAGGTCCATA
* * *
5015695 AGGAATTACCAGTCAGTGCTGAACCTATAAAAGGAATTACCAACAGCAATTGAACCTGCCAAAAA
1 AGGAATTACCAGTCAGTGCAGAACCTATAAAAGGAATTACCAACAACAACTGAACCTGCCAAAAA
5015760 T
66 T
* ****
5015761 AGGAATTACCAGTCAGTGCAGAACCTATACAAGGAATTATGTGCAACAACTGAACCTGCCA
1 AGGAATTACCAGTCAGTGCAGAACCTATAAAAGGAATTACCAACAACAACTGAACCTGCCA
5015822 GAGTCTTCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (66 bp):
AGGAATTACCAGTCAGTGCAGAACCTATAAAAGGAATTACCAACAACAACTGAACCTGCCAAAAA
T
Found at i:5017637 original size:30 final size:30
Alignment explanation
Indices: 5017601--5017671 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
5017591 TGACTTCTTG
5017601 GTCAAAGTCAACAATCAACGGGTTGACTCA
1 GTCAAAGTCAACAATCAACGGGTTGACTCA
** * *
5017631 GTCAAAGTCAACGGTCAATGGGTTGACTCG
1 GTCAAAGTCAACAATCAACGGGTTGACTCA
5017661 GTCAAAGTCAA
1 GTCAAAGTCAA
5017672 TGAGTTGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (30 bp):
GTCAAAGTCAACAATCAACGGGTTGACTCA
Found at i:5029122 original size:21 final size:22
Alignment explanation
Indices: 5029091--5029163 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
5029081 CTATCACCCA
5029091 TTTTCTCTCTCATTTTTTAACT
1 TTTTCTCTCTCATTTTTTAACT
* *
5029113 TTTTCTTCTCTTTCA-TTATTAATT
1 TTTTC-TCTC--TCATTTTTTAACT
* *
5029137 TTTTCTCTTTCA-TCTTTAACT
1 TTTTCTCTCTCATTTTTTAACT
5029158 TTTTCT
1 TTTTCT
5029164 TTTTCTCTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
21 15 0.36
22 5 0.12
23 7 0.17
24 12 0.29
25 3 0.07
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTCTCTCTCATTTTTTAACT
Found at i:5030051 original size:161 final size:162
Alignment explanation
Indices: 5029786--5030109 Score: 632
Period size: 161 Copynumber: 2.0 Consensus size: 162
5029776 GCCAAGTTGT
5029786 GGAACCATTTCCTTAAACACAAACTTATGCCTACATCTCACAATACGACAGTATCACTTTCTTGT
1 GGAACCATTTCCTTAAACACAAACTTATGCCTACATCTCACAATACGACAGTATCACTTTCTTGT
5029851 TTACAGCTTTTACACTCGATCATGGTATCCCGTCCTATTGATGTTGGTTGAATCATTGTTCATCA
66 TTACAGCTTTTACACTCGATCATGGTATCCCGTCCTATTGATGTTGGTTGAATCATTGTTCATCA
5029916 AGTTCAT-GAGTTTGGGTTAAAAGGCAAGTGC
131 AGTTCATAGAGTTTGGGTTAAAAGGCAAGTGC
5029947 GGAACCATTTCCTTAAACACAAACTTATGCCTACATCTCACAATACGACAGTATCACTTTCTTGT
1 GGAACCATTTCCTTAAACACAAACTTATGCCTACATCTCACAATACGACAGTATCACTTTCTTGT
5030012 TTACAGCTTTTACACTCGATCATGGTATCCCGTCCTATTGATGTTGGTTGAATCATTGTTCATCA
66 TTACAGCTTTTACACTCGATCATGGTATCCCGTCCTATTGATGTTGGTTGAATCATTGTTCATCA
5030077 AGTTCATGAGAGTTTGGGTTAAAAGGCAAGTGC
131 AGTTCAT-AGAGTTTGGGTTAAAAGGCAAGTGC
5030110 TTTAGTGTTT
Statistics
Matches: 161, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
161 137 0.85
163 24 0.15
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (162 bp):
GGAACCATTTCCTTAAACACAAACTTATGCCTACATCTCACAATACGACAGTATCACTTTCTTGT
TTACAGCTTTTACACTCGATCATGGTATCCCGTCCTATTGATGTTGGTTGAATCATTGTTCATCA
AGTTCATAGAGTTTGGGTTAAAAGGCAAGTGC
Found at i:5035017 original size:2 final size:2
Alignment explanation
Indices: 5035010--5035046 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5035000 TAACAATTGC
5035010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5035047 CTATCATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5035374 original size:23 final size:23
Alignment explanation
Indices: 5035317--5035361 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5035307 CATGTAAAAT
*
5035317 TATCCCGAAGGACCACGTAGAAA
1 TATCCCGAAGGACCACATAGAAA
5035340 TATCCCGAAGGACCACATAGAA
1 TATCCCGAAGGACCACATAGAA
5035362 TTCTCCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (23 bp):
TATCCCGAAGGACCACATAGAAA
Found at i:5041038 original size:2 final size:2
Alignment explanation
Indices: 5041031--5041097 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
5041021 TCTTTTTAAC
5041031 AT AT AT AT 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
5041073 AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5041098 TATCCTTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5041336 original size:81 final size:81
Alignment explanation
Indices: 5041173--5041630 Score: 656
Period size: 81 Copynumber: 5.7 Consensus size: 81
5041163 ACAATAGTGT
* * * *
5041173 TTAA-CGTTCGTCTAACTGGCATAATTGACACATTTCTACCAA-TGCACAGTTAGGCCGTTATTC
1 TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAATTGCACAGTTAGGCCATTATTC
5041236 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
* *
5041252 TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAATTGCACAATTAGGCCATTTTTC
1 TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAATTGCACAGTTAGGCCATTATTC
5041317 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
* * *
5041333 TTAACCGTTCATCTAATTGGCATAATTGACATATTTCTGCCAATTACACAATTAGGCCATTATTC
1 TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAATTGCACAGTTAGGCCATTATTC
5041398 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
** ** * * *
5041414 TTAACCGTTCATCTAACTAACATAATTGACATATTTCTATCAATTCCATAGTTAGGCCATTTTTC
1 TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAATTGCACAGTTAGGCCATTATTC
5041479 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
** *
5041495 TTAA-CGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAGTTATGCCATTATTC
1 TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAATTGCACAGTTAGGCCATTATTC
*
5041559 TTTTACTCAACAGTAC
66 TTTTACTCAACGGTAC
* ** *
5041575 TTAACCGTTCATCTAACT-GCATAATTTACACCTTTCTGTC-ATATGCACAGTTAGGC
1 TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAAT-TGCACAGTTAGGC
5041631 TTCAAATGTA
Statistics
Matches: 343, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
79 6 0.02
80 136 0.40
81 201 0.59
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
TTAACCGTTCATCTAACTGGCATAATTGACATATTTCTGCCAATTGCACAGTTAGGCCATTATTC
TTTTACTCAACGGTAC
Found at i:5041687 original size:68 final size:68
Alignment explanation
Indices: 5041582--5041832 Score: 396
Period size: 68 Copynumber: 3.7 Consensus size: 68
5041572 TACTTAACCG
* * * *
5041582 TTCATCTAACT-GCATAATTTACACCTTTCTGTCATATGCACAGTTAGGCTTCAAATGTACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGTACTTAG
5041646 CAT
66 CAT
*
5041649 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATATGCACAGTTAGGCCTCAAAGGTACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGTACTTAG
*
5041714 CCT
66 CAT
* * *
5041717 TTCATCTAACTGACATAAATGACACCTTTCTGCCATATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGTACTTAG
5041782 CAT
66 CAT
* *
5041785 TTCATCTAACTGGCATAAATGACACATTTCTATCATATGCACAGTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAG
5041833 ACCTTTATTC
Statistics
Matches: 168, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 11 0.07
68 157 0.93
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGTACTTAG
CAT
Found at i:5042282 original size:58 final size:58
Alignment explanation
Indices: 5042212--5042378 Score: 235
Period size: 59 Copynumber: 2.9 Consensus size: 58
5042202 TCCCATACTG
** *
5042212 AAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACATTAGGTGCCCGATACAA
1 AAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCCCGATACAA
* **
5042270 AAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTATCAT-TTAGCACACGAAGTGCCCGATACAA
* ** *
5042329 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACATGAAGTGCC
1 AAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCC
5042379 ATTTGGTAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 47 0.48
59 51 0.52
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (58 bp):
AAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCCCGATACAA
Found at i:5042337 original size:59 final size:58
Alignment explanation
Indices: 5042206--5042378 Score: 238
Period size: 58 Copynumber: 3.0 Consensus size: 58
5042196 TATTTTTCCC
* ** *
5042206 ATACTGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACATTAGGTGCCCG
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCCCG
* *
5042264 ATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCT
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCAT-TTAGCACACGAAGTGCCCG
* * ** *
5042323 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTCACATGAAGTGCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCC
5042379 ATTTGGTAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 51 0.50
59 51 0.50
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (58 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACGAAGTGCCCG
Found at i:5043003 original size:19 final size:19
Alignment explanation
Indices: 5042962--5043003 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5042952 ATGCCAAATT
* *
5042962 GGTATCGGTACCATGATGA
1 GGTATCGATACCATGAAGA
5042981 GGTATCGATACCCATGAAG-
1 GGTATCGATA-CCATGAAGA
5043000 GGTA
1 GGTA
5043004 GTATCGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (19 bp):
GGTATCGATACCATGAAGA
Found at i:5043581 original size:21 final size:21
Alignment explanation
Indices: 5043555--5043604 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5043545 GTCGAGGGTT
5043555 TTATGTGGTCCTCCAGGACAA
1 TTATGTGGTCCTCCAGGACAA
* *
5043576 TTATGTGGTCCTTCGGGACAA
1 TTATGTGGTCCTCCAGGACAA
*
5043597 ATATGTGG
1 TTATGTGG
5043605 CACTTCGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (21 bp):
TTATGTGGTCCTCCAGGACAA
Found at i:5043610 original size:21 final size:21
Alignment explanation
Indices: 5043570--5043679 Score: 73
Period size: 21 Copynumber: 5.0 Consensus size: 21
5043560 TGGTCCTCCA
*
5043570 GGACAATTATGTGGTC-CTTCG
1 GGACAAATATGTGG-CACTTCG
5043591 GGACAAATATGTGGCACTTCG
1 GGACAAATATGTGGCACTTCG
* * *
5043612 GTG-CAACCCTATGTGGTATTTCG
1 G-GACAA--ATATGTGGCACTTCG
**
5043635 ATACAAACTTATGTGGTCA-TTCG
1 GGACAAA--TATGTGG-CACTTCG
*
5043658 GGACAATTATGTGGCACTTCG
1 GGACAAATATGTGGCACTTCG
5043679 G
1 G
5043680 TGCAAATTAC
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
20 3 0.04
21 34 0.49
22 1 0.01
23 30 0.43
24 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (21 bp):
GGACAAATATGTGGCACTTCG
Found at i:5043626 original size:23 final size:22
Alignment explanation
Indices: 5043598--5043684 Score: 72
Period size: 23 Copynumber: 3.9 Consensus size: 22
5043588 TCGGGACAAA
*
5043598 TATGTGGCACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAA-CT
* * * *
5043621 TATGTGGTATTTCGATACAAACT
1 TATGTGGCACTTCGGTGC-AACT
5043644 TATGTGGTCA-TTCGG-GACAA-T
1 TATGTGG-CACTTCGGTG-CAACT
5043665 TATGTGGCACTTCGGTGCAA
1 TATGTGGCACTTCGGTGCAA
5043685 ATTACGAGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
20 2 0.04
21 16 0.31
22 3 0.06
23 27 0.53
24 3 0.06
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAACT
Found at i:5044964 original size:29 final size:27
Alignment explanation
Indices: 5044912--5044967 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5044902 CTTTAATCAT
5044912 AATTATATAAAATATTTTTAAAAAATA
1 AATTATATAAAATATTTTTAAAAAATA
* *
5044939 AATTTTATAAAATATATATTTCAAAAATA
1 AATTATATAAAATAT-T-TTTAAAAAATA
5044968 CTTGATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 14 0.56
28 1 0.04
29 10 0.40
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
AATTATATAAAATATTTTTAAAAAATA
Found at i:5045357 original size:18 final size:18
Alignment explanation
Indices: 5045329--5045365 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5045319 GAATCGAAAA
5045329 AAATTTAAAATA-AATTT
1 AAATTTAAAATATAATTT
5045346 AAATTATAAAATATAATTT
1 AAATT-TAAAATATAATTT
5045365 A
1 A
5045366 TCAATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTTAAAATATAATTT
Found at i:5047867 original size:19 final size:19
Alignment explanation
Indices: 5047843--5047886 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
5047833 GAATCATGTG
5047843 TGCCCTAGGAAACTTTATA
1 TGCCCTAGGAAACTTTATA
*
5047862 TGCCCTAGGAAACTTTTTA
1 TGCCCTAGGAAACTTTATA
5047881 TGCCCT
1 TGCCCT
5047887 TTACAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (19 bp):
TGCCCTAGGAAACTTTATA
Found at i:5052138 original size:48 final size:48
Alignment explanation
Indices: 5052032--5052134 Score: 118
Period size: 48 Copynumber: 2.2 Consensus size: 48
5052022 AAACGGAGAT
* * * *
5052032 ATCATAAATCAAAACAGAATTCAGATAAGATATTATAAAATAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCATAAAAGAATCCAA
* * * * *
5052080 ATCAGAAATCAAAACAGAATTCAGGTTAGGTATCATAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCATAAAAGAATCCAA
5052128 ATC-GAAA
1 ATCAGAAA
5052135 ATCAGATAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 4 0.09
48 42 0.91
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCATAAAAGAATCCAA
Found at i:5054405 original size:16 final size:17
Alignment explanation
Indices: 5054368--5054408 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5054358 TGTTCAACAG
5054368 TGGTCAACGGAGATCAA
1 TGGTCAACGGAGATCAA
*
5054385 CGGTCAACGTG-G-TCAA
1 TGGTCAACG-GAGATCAA
5054401 TGGTCAAC
1 TGGTCAAC
5054409 ACTCGGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 11 0.52
17 9 0.43
18 1 0.05
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (17 bp):
TGGTCAACGGAGATCAA
Found at i:5057922 original size:20 final size:21
Alignment explanation
Indices: 5057893--5057946 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 21
5057883 AGAACATATA
*
5057893 TTTAGGGTTTAGGGATTAAGG
1 TTTAAGGTTTAGGGATTAAGG
* * *
5057914 TTTAA-GTTTA-TGATTTAGT
1 TTTAAGGTTTAGGGATTAAGG
5057933 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
5057947 TTTACATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 11 0.42
20 10 0.38
21 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTAGGGATTAAGG
Found at i:5057950 original size:20 final size:20
Alignment explanation
Indices: 5057893--5057950 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
5057883 AGAACATATA
* *
5057893 TTTAGGGTTTAGGGATTAAGG
1 TTTAAGGTTTAGGG-TTTAGG
* * *
5057914 TTTAA-GTTTATGATTTAGT
1 TTTAAGGTTTAGGGTTTAGG
5057933 TTTAAGGTTTAGGGTTTA
1 TTTAAGGTTTAGGGTTTA
5057951 CATTCATAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 9 0.31
20 16 0.55
21 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (20 bp):
TTTAAGGTTTAGGGTTTAGG
Found at i:5057979 original size:15 final size:15
Alignment explanation
Indices: 5057959--5057991 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5057949 TACATTCATA
5057959 GTTT-AATATTTAAGG
1 GTTTAAATA-TTAAGG
5057974 GTTTAAATATTAAGG
1 GTTTAAATATTAAGG
5057989 GTT
1 GTT
5057992 AAGGTTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
GTTTAAATATTAAGG
Found at i:5062210 original size:28 final size:28
Alignment explanation
Indices: 5062176--5062229 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
5062166 AAAAAGGTAC
5062176 AGGGACTAAAGCATATATTAGTCATTAA
1 AGGGACTAAAGCATATATTAGTCATTAA
5062204 AGGGACTAAAGCATATATTAGTCATT
1 AGGGACTAAAGCATATATTAGTCATT
5062230 TAAAATAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (28 bp):
AGGGACTAAAGCATATATTAGTCATTAA
Found at i:5064476 original size:20 final size:20
Alignment explanation
Indices: 5064451--5064491 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5064441 AGCTGGTAGA
5064451 AAGTTTGACTTCCTGATAAC
1 AAGTTTGACTTCCTGATAAC
5064471 AAGTTTGACTTCCTGATAAC
1 AAGTTTGACTTCCTGATAAC
5064491 A
1 A
5064492 CATTTAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (20 bp):
AAGTTTGACTTCCTGATAAC
Found at i:5076492 original size:37 final size:37
Alignment explanation
Indices: 5076442--5076564 Score: 176
Period size: 37 Copynumber: 3.3 Consensus size: 37
5076432 TAAAACCAAG
*
5076442 AGTGAAACAAATCAATCTTAAGCCTTCACCGAATAGT
1 AGTGAAACAAATCAATCTTAAGCCTTCACCGAAGAGT
* * * *
5076479 AGTGAAGCAAATCAATCTTAAGCCTTCAACAAAGAAT
1 AGTGAAACAAATCAATCTTAAGCCTTCACCGAAGAGT
5076516 AGT-AAAGCAAATCAATCTTAAGCCTTCACCGAAGAGT
1 AGTGAAA-CAAATCAATCTTAAGCCTTCACCGAAGAGT
*
5076553 AATGAAACAAAT
1 AGTGAAACAAAT
5076565 TGATCTCGAG
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.03
37 69 0.93
38 3 0.04
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.22
Consensus pattern (37 bp):
AGTGAAACAAATCAATCTTAAGCCTTCACCGAAGAGT
Found at i:5076771 original size:9 final size:9
Alignment explanation
Indices: 5076747--5076784 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5076737 GGATATAATA
*
5076747 ATTATTATT
1 ATTAATATT
5076756 ATT-ATATT
1 ATTAATATT
5076764 ATTAATATT
1 ATTAATATT
*
5076773 ATTAATACT
1 ATTAATATT
5076782 ATT
1 ATT
5076785 TATTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATATT
Found at i:5077643 original size:21 final size:21
Alignment explanation
Indices: 5077619--5077668 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
5077609 CCATCACCAA
*
5077619 AAGAAAAATCAAATGATCCAG
1 AAGAAAAATCAAAGGATCCAG
5077640 AAGAAAAATCAAAGGATCCAG
1 AAGAAAAATCAAAGGATCCAG
*
5077661 AAAAAAAA
1 AAGAAAAA
5077669 AACTTCAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.10
Consensus pattern (21 bp):
AAGAAAAATCAAAGGATCCAG
Found at i:5081293 original size:48 final size:45
Alignment explanation
Indices: 5081183--5081295 Score: 113
Period size: 46 Copynumber: 2.5 Consensus size: 45
5081173 GTAACGATGC
5081183 AAATAAGCTTATGAGCTTATGGAATAATAGCAAATATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATAGCAAATATATTGAAAA
* * * * * * **
5081228 AAATAA--TAATAAGCTTATGGAATTTAAATTGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATAGCAAATATATTGAAAA
5081274 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTATGAGCTTATGG
5081296 GATGAAAGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
43 14 0.26
45 7 0.13
46 20 0.38
48 12 0.23
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATAGCAAATATATTGAAAA
Found at i:5082766 original size:21 final size:21
Alignment explanation
Indices: 5082734--5082774 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5082724 GAGAAATTAT
*
5082734 TTTAAATCTAAAAAT-TTAAA
1 TTTAAATATAAAAATATTAAA
5082754 TTTAAGATATAAAAATATTAA
1 TTTAA-ATATAAAAATATTAA
5082775 TTATGGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TTTAAATATAAAAATATTAAA
Found at i:5082776 original size:21 final size:20
Alignment explanation
Indices: 5082729--5082776 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
5082719 TTTTAGAGAA
* *
5082729 ATTATTTTAAATCTAAAAAT
1 ATTAATTTAAATATAAAAAT
5082749 -TTAAATTTAAGATATAAAAAT
1 ATT-AATTTAA-ATATAAAAAT
5082770 ATTAATT
1 ATTAATT
5082777 ATGGAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 2 0.09
20 6 0.26
21 13 0.57
22 2 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTAATTTAAATATAAAAAT
Found at i:5083436 original size:20 final size:22
Alignment explanation
Indices: 5083413--5083458 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
5083403 ATTTTTAGTA
5083413 ATTTAATTTTT-AT-TTTTGAT
1 ATTTAATTTTTAATGTTTTGAT
* *
5083433 ATTTATTTTTTAATGTTTTTAT
1 ATTTAATTTTTAATGTTTTGAT
5083455 ATTT
1 ATTT
5083459 TATAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (22 bp):
ATTTAATTTTTAATGTTTTGAT
Found at i:5084450 original size:18 final size:17
Alignment explanation
Indices: 5084429--5084529 Score: 57
Period size: 18 Copynumber: 5.9 Consensus size: 17
5084419 AAAAATATAT
5084429 ATATATATATATATATTA
1 ATATATATA-ATATATTA
* *
5084447 ATATTTCTAATA-ATATA
1 ATATATATAATATAT-TA
*
5084464 ATAT-TATAAT-TTTTA
1 ATATATATAATATATTA
* *
5084479 ATAT-TATAATAAAATA
1 ATATATATAATATATTA
* * *
5084495 ATAAATTATATTATAATA
1 ATATA-TATAATATATTA
*
5084513 ATATATGATATTATATT
1 ATATAT-ATAATATATT
5084530 TTTATTTTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
15 12 0.18
16 13 0.20
17 10 0.15
18 30 0.46
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (17 bp):
ATATATATAATATATTA
Found at i:5084465 original size:8 final size:8
Alignment explanation
Indices: 5084454--5084517 Score: 51
Period size: 8 Copynumber: 8.2 Consensus size: 8
5084444 TTAATATTTC
5084454 TAATAATA
1 TAATAATA
*
5084462 TAATATTA
1 TAATAATA
* *
5084470 TAAT-TTT
1 TAATAATA
*
5084477 TAATATTA
1 TAATAATA
*
5084485 TAATAAAA
1 TAATAATA
5084493 TAATAA-A
1 TAATAATA
* *
5084500 TTATATTA
1 TAATAATA
5084508 TAATAATA
1 TAATAATA
5084516 TA
1 TA
5084518 TGATATTATA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
7 11 0.24
8 34 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TAATAATA
Found at i:5084475 original size:23 final size:23
Alignment explanation
Indices: 5084435--5084489 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
5084425 ATATATATAT
5084435 ATATATATATTAATATTTCTAATA
1 ATATA-ATATTAATATTTCTAATA
*
5084459 ATATAATATT-ATAATTTTTAATA
1 ATATAATATTAAT-ATTTCTAATA
*
5084482 TTATAATA
1 ATATAATA
5084490 AAATAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 21 0.75
24 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATAATATTAATATTTCTAATA
Found at i:5084495 original size:23 final size:23
Alignment explanation
Indices: 5084449--5084513 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
5084439 ATATATTAAT
* * **
5084449 ATTTCTAATAATATAATATTATA
1 ATTTTTAATATTATAATAAAATA
5084472 ATTTTTAATATTATAATAAAATA
1 ATTTTTAATATTATAATAAAATA
**
5084495 ATAAATT-ATATTATAATAA
1 AT-TTTTAATATTATAATAA
5084514 TATATGATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTTAATATTATAATAAAATA
Found at i:5084558 original size:29 final size:29
Alignment explanation
Indices: 5084454--5084552 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
5084444 TTAATATTTC
* * *
5084454 TAATAATATAATATTATAATTTTTAATATTA
1 TAAT-ATATAATAATAT-ATTTTTATTATAA
* *
5084485 TAATA-A-AATAATA-AATTATATTATAA
1 TAATATATAATAATATATTTTTATTATAA
* * *
5084511 TAATATATGATATTATATTTTTATTTTAA
1 TAATATATAATAATATATTTTTATTATAA
5084540 TAATATATAATAA
1 TAATATATAATAA
5084553 ATTATTAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
26 14 0.26
27 1 0.02
28 11 0.21
29 22 0.42
30 1 0.02
31 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (29 bp):
TAATATATAATAATATATTTTTATTATAA
Found at i:5084572 original size:54 final size:53
Alignment explanation
Indices: 5084454--5084617 Score: 140
Period size: 53 Copynumber: 3.0 Consensus size: 53
5084444 TTAATATTTC
*
5084454 TAATAATATAATATTATAATTTTTAATATTATAATAA-A-ATAATAAATTATATTATAA
1 TAAT-ATATAATATTAT-ATTTTT-AT-TT-TAATAATATATAATAAATTAT-TAATAA
*
5084511 TAATATATGATATTATATTTTTATTTTAATAATATATAATAAATTATTAATAA
1 TAATATATAATATTATATTTTTATTTTAATAATATATAATAAATTATTAATAA
* * *** *
5084564 -AATTTATATTATT-TATTAATTTCATAGAAATAATAT-TATTAAATTATTAATAA
1 TAATATATAATATTATATT--TTT-ATTTTAATAATATATAATAAATTATTAATAA
5084617 T
1 T
5084618 GAAGAATATT
Statistics
Matches: 92, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
51 4 0.04
52 16 0.17
53 27 0.29
54 24 0.26
55 6 0.07
56 11 0.12
57 4 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (53 bp):
TAATATATAATATTATATTTTTATTTTAATAATATATAATAAATTATTAATAA
Found at i:5084800 original size:28 final size:28
Alignment explanation
Indices: 5084747--5084825 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
5084737 ATACCAATAT
* *
5084747 TAATATTTTTATTAATAAAATTATAAAAA
1 TAATA-TTTTAATAATAAAATAATAAAAA
***
5084776 TAATATTTTAATAAT-AAATAAATAATTT
1 TAATATTTTAATAATAAAAT-AATAAAAA
*
5084804 TAATATTTTAAAAATAATAATA
1 TAATATTTTAATAATAA-AATA
5084826 TTAAGTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
27 4 0.10
28 27 0.66
29 7 0.17
30 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATATTTTAATAATAAAATAATAAAAA
Found at i:5084803 original size:20 final size:17
Alignment explanation
Indices: 5084769--5084808 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
5084759 TAATAAAATT
5084769 ATAAAAATAATATTTTA
1 ATAAAAATAATATTTTA
5084786 ATAATAAATAAATAATTTTA
1 ATAA-AAAT-AAT-ATTTTA
5084806 ATA
1 ATA
5084809 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 4 0.20
19 3 0.15
20 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAAATAATATTTTA
Found at i:5084815 original size:22 final size:21
Alignment explanation
Indices: 5084790--5084850 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
5084780 ATTTTAATAA
*
5084790 TAAATAAATAATTTTAATATTT
1 TAAATAAATAATATTAA-ATTT
* *
5084812 TAAAAATAATAATATTAAGTTT
1 TAAATA-AATAATATTAAATTT
*
5084834 TATGATAAATAATATTA
1 TA-AATAAATAATATTA
5084851 TTTATTGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TAAATAAATAATATTAAATTT
Found at i:5085506 original size:15 final size:15
Alignment explanation
Indices: 5085483--5085516 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5085473 TCATTATATT
5085483 TATTATTATATAAAA
1 TATTATTATATAAAA
* *
5085498 TATTTTTATTTAAAA
1 TATTATTATATAAAA
5085513 TATT
1 TATT
5085517 CTGTAGTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATTATATAAAA
Found at i:5085933 original size:18 final size:19
Alignment explanation
Indices: 5085889--5085934 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5085879 GCTGCTCCTC
* *
5085889 CTTCATCTTCTTCCTCAAA
1 CTTCATCATCTTCCTAAAA
*
5085908 -TTCTTCATCTTCC-AAAA
1 CTTCATCATCTTCCTAAAA
5085925 CTTCATCATC
1 CTTCATCATC
5085935 ATTTGGCTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (19 bp):
CTTCATCATCTTCCTAAAA
Found at i:5089108 original size:141 final size:138
Alignment explanation
Indices: 5088819--5089348 Score: 544
Period size: 141 Copynumber: 3.8 Consensus size: 138
5088809 AAAATATAGA
* * * * * * * * *
5088819 CTCTAATATTAAAACCTAGCGAATTTTAGCAATTTGTTGGATCAAATAATTAATATGGTA-CTCG
1 CTCTAATATT-AATCCTAACCAATTTTAACAAATTATTGAATCACATAATTAAT-TGGAACCTCG
* * ** * * * * *
5088883 AGCATGAAAGCGAGGACCAAACTAAAAGCTCTCTTAAGTTAAAGGACCAAAGGTTAAATTAATCT
64 AGCATAAAAGCGAGGACCAAATTAAAAATTCACCTAAATTAAAAGACTAAAGG-TAAATTAATCT
5088948 AAAAATGAAGG
128 AAAAATGAAGG
* * * *
5088959 TTTTAATATTAATACTAACCCATTTTAACAAATTATTGAATCGA-ATAATTAATTCGGAACCTCG
1 CTCTAATATTAATCCTAACCAATTTTAACAAATTATTGAATC-ACATAATTAATT-GGAACCTCG
* *
5089023 AGCATAAAAGCGAGGACCAAATTTAAAAATTCACCTAAATTAAATGACTAAAGGTAAATTTAATA
64 AGCATAAAAGCGAGGACCAAA-TTAAAAATTCACCTAAATTAAAAGACTAAAGGTAAA-TTAATC
5089088 TAAAAATGAAGG
127 TAAAAATGAAGG
* * ** *
5089100 CTCTAATATTAGTCCTAACCAATTTTAACAAATTATTGAATCATATAATTAATTCAAAACCTCCA
1 CTCTAATATTAATCCTAACCAATTTTAACAAATTATTGAATCACATAATTAATT-GGAACCTCGA
** ** * *
5089165 TAATAAAATTGAGAACCAAATTAAAAATTCGCCTAAATTAAAAGACTAAAAGGTGAAATTAATCT
65 GCATAAAAGCGAGGACCAAATTAAAAATTCACCTAAATTAAAAGACT-AAAGGT-AAATTAATCT
5089230 AAAAATGAAGG
128 AAAAATGAAGG
* * * *
5089241 CTCTAATATTAATCCTAACCAATTTTAGCAAATTATTGGATCACATAATTAAAATGGAATCTC-A
1 CTCTAATATTAATCCTAACCAATTTTAACAAATTATTGAATCACATAATT-AATTGGAACCTCGA
* * * *
5089305 TGCATAAATGTGATGACCAAATAAAAAATTCACCTAAATTAAAA
65 -GCATAAAAGCGAGGACCAAATTAAAAATTCACCTAAATTAAAA
5089349 AAGTTTAAGG
Statistics
Matches: 326, Mismatches: 54, Indels: 19
0.82 0.14 0.05
Matches are distributed among these distances:
138 1 0.00
139 35 0.11
140 64 0.20
141 220 0.67
142 6 0.02
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (138 bp):
CTCTAATATTAATCCTAACCAATTTTAACAAATTATTGAATCACATAATTAATTGGAACCTCGAG
CATAAAAGCGAGGACCAAATTAAAAATTCACCTAAATTAAAAGACTAAAGGTAAATTAATCTAAA
AATGAAGG
Found at i:5090602 original size:71 final size:73
Alignment explanation
Indices: 5090508--5090675 Score: 193
Period size: 71 Copynumber: 2.3 Consensus size: 73
5090498 ATCATCTTCA
*
5090508 TCAAC-TTTTCAATATATT-AAAGTATCGATCATCATCACATAACTATCGATATTTTAAATTTCA
1 TCAACTTTTTCAATAT-TTAAAAGTATCGATCATCACCACATAACTATCGATATTTTAAATTTCA
5090571 AT-TT-T-T
65 ATCTTATCT
** * * ** * *
5090577 ATCAGTTTTTTCAATATTTAAAAGTATTGATCATTACCGTATAAGTATCGATATTTTAACTTTCA
1 -TCAACTTTTTCAATATTTAAAAGTATCGATCATCACCACATAACTATCGATATTTTAAATTTCA
5090642 ATCTTATCT
65 ATCTTATCT
*
5090651 TCAACTTTTTAAATATTTAAAAGTA
1 TCAACTTTTTCAATATTTAAAAGTA
5090676 GGCTTAATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
70 5 0.06
71 50 0.62
72 2 0.02
73 23 0.28
74 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.45
Consensus pattern (73 bp):
TCAACTTTTTCAATATTTAAAAGTATCGATCATCACCACATAACTATCGATATTTTAAATTTCAA
TCTTATCT
Found at i:5091542 original size:188 final size:189
Alignment explanation
Indices: 5091219--5091586 Score: 440
Period size: 188 Copynumber: 2.0 Consensus size: 189
5091209 AGGTAACATT
* * ** *
5091219 TTAGGCGCAACAAATTTTATTAATAAAAAATATTAACATTCCATATCGTAATCTAACTTCTTAGT
1 TTAGGCGCAACAAATTTTATTAATAAAAAAAATTAACATTCCACATCACAACCTAACTTCTTAGT
* * * * * * * *
5091284 GAACCATTACATTGTTGGGCACAACTATATTTATTGTAAATATTCATAATGTTTATAGCTTTTTA
66 GAACCATTACATTCTTAGGCACAACCATATTTATTATAAATATCCATAATATTTATAACTTTTAA
* *
5091349 CTTATTTTCTTATATTGGG-AAAATCTA-AGGCTCCATCAGCTTAAACTCTAGTAAACTG
131 CTTATTTTCTTATAGTGGGAAAAATCTACA-GCTCCACCAGCTTAAACTCTAGTAAACTG
** **
5091407 TTAGGCGCAACCCATTTTATTAATAAAAAAAATTAATGTTCCACATCACAACCT-ACTTTCTTAG
1 TTAGGCGCAACAAATTTTATTAATAAAAAAAATTAACATTCCACATCACAACCTAAC-TTCTTAG
* * **
5091471 TGAACC-TTGACATTCTTAGGCGCAACCGTATTTATTATTGATATCCATAATATTT-TCAACTTT
65 TGAACCATT-ACATTCTTAGGCACAACCATATTTATTATAAATATCCATAATATTTAT-AACTTT
* *
5091534 TAACTTATTTTGTTATCGTGGGAAAAATCTACAGCTCCACCAGCTTAAACTCT
128 TAACTTATTTTCTTATAGTGGGAAAAATCTACAGCTCCACCAGCTTAAACTCT
5091587 GATAGCATTT
Statistics
Matches: 150, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
187 5 0.03
188 117 0.78
189 27 0.18
190 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (189 bp):
TTAGGCGCAACAAATTTTATTAATAAAAAAAATTAACATTCCACATCACAACCTAACTTCTTAGT
GAACCATTACATTCTTAGGCACAACCATATTTATTATAAATATCCATAATATTTATAACTTTTAA
CTTATTTTCTTATAGTGGGAAAAATCTACAGCTCCACCAGCTTAAACTCTAGTAAACTG
Found at i:5092378 original size:25 final size:25
Alignment explanation
Indices: 5092350--5092398 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5092340 ATATGAACAG
5092350 CCCTTGGTTTGAATGATTAAATCAA
1 CCCTTGGTTTGAATGATTAAATCAA
*
5092375 CCCTTGGTTTGGATGATTAAATCA
1 CCCTTGGTTTGAATGATTAAATCA
5092399 GCCTTGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (25 bp):
CCCTTGGTTTGAATGATTAAATCAA
Found at i:5092854 original size:18 final size:18
Alignment explanation
Indices: 5092812--5092857 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5092802 TAGTTTGATT
*
5092812 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
5092830 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
5092848 AATGAACTAA
1 AATGAACTAA
5092858 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:5096336 original size:18 final size:18
Alignment explanation
Indices: 5096312--5096358 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
5096302 GCTACCCAGT
5096312 GAGGAAGAAGTAGAGGCAA
1 GAGGAAGAAGTAGAGG-AA
5096331 -AGGAAGAAGTAGAGGAA
1 GAGGAAGAAGTAGAGGAA
5096348 GAGGAAGAAGT
1 GAGGAAGAAGT
5096359 CAATTAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.49, C:0.02, G:0.43, T:0.06
Consensus pattern (18 bp):
GAGGAAGAAGTAGAGGAA
Found at i:5101338 original size:18 final size:18
Alignment explanation
Indices: 5101312--5101382 Score: 106
Period size: 18 Copynumber: 3.8 Consensus size: 18
5101302 GGATTGTCAA
5101312 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
* *
5101330 TGGTTCTTCGGAACAATCAG
1 TGGTCCTTCGGGAC-AT-AG
5101350 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
5101368 TGGTCCTTCGGGACA
1 TGGTCCTTCGGGACA
5101383 AATATTCAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 29 0.62
19 4 0.09
20 14 0.30
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:5103013 original size:25 final size:25
Alignment explanation
Indices: 5102985--5103037 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
5102975 AGAATATGAA
5102985 CAGCCCTTGGTTTGAATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
*
5103010 CAGCCCTTGGTTTGGATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
5103035 CAG
1 CAG
5103038 ACTTGAATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (25 bp):
CAGCCCTTGGTTTGAATGATTAAAT
Found at i:5103553 original size:17 final size:17
Alignment explanation
Indices: 5103533--5103574 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
5103523 ACTACTTCCC
5103533 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
*
5103550 TAAATGCAATACATGCT
1 TAAATGAAATACATGCT
*
5103567 TTAATGAA
1 TAAATGAA
5103575 CAACATACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:5108966 original size:77 final size:77
Alignment explanation
Indices: 5108786--5108949 Score: 265
Period size: 77 Copynumber: 2.1 Consensus size: 77
5108776 AACTCTGGTA
5108786 ACATTTTAGGCACAACCTAAAATGTTAATAATATTCATGACATTTACCATTTATAACTCATTTTC
1 ACATTTTAGGCACAACCTAAAATGTTAATAATATTCATGACATTTACCATTTATAACTCATTTTC
* * *
5108851 TTACCTTTTATT
66 TTACCGTTCATC
* * * *
5108863 ACATTTTAGGCACAACCTAAAATGTTAATTATATTCATTACATTTATCGTTTATAACTCATTTTC
1 ACATTTTAGGCACAACCTAAAATGTTAATAATATTCATGACATTTACCATTTATAACTCATTTTC
5108928 TTACCGTTCATC
66 TTACCGTTCATC
5108940 ACATTTTAGG
1 ACATTTTAGG
5108950 TTTAACTTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (77 bp):
ACATTTTAGGCACAACCTAAAATGTTAATAATATTCATGACATTTACCATTTATAACTCATTTTC
TTACCGTTCATC
Found at i:5110871 original size:20 final size:20
Alignment explanation
Indices: 5110831--5110873 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5110821 TCTTGAGACC
*
5110831 AAATTGGTCTCCATAATGAA
1 AAATTGGTCTCCATAACGAA
* *
5110851 AAATTGGTCTCTATACCGAA
1 AAATTGGTCTCCATAACGAA
5110871 AAA
1 AAA
5110874 GCGGGTATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (20 bp):
AAATTGGTCTCCATAACGAA
Found at i:5116674 original size:16 final size:16
Alignment explanation
Indices: 5116653--5116708 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
5116643 TTTACCCAAC
*
5116653 CTATACCTGACCTGAA
1 CTATACCCGACCTGAA
5116669 CTATACCCGATCC-GAA
1 CTATACCCGA-CCTGAA
*
5116685 CCATACCCGACCTGAA
1 CTATACCCGACCTGAA
5116701 CTATACCC
1 CTATACCC
5116709 AATCCAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.06
16 31 0.89
17 2 0.06
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (16 bp):
CTATACCCGACCTGAA
Found at i:5116697 original size:32 final size:33
Alignment explanation
Indices: 5116650--5116713 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
5116640 CGATTTACCC
* *
5116650 AACCTATACCTGACCTGAACTATACCCGATCCG
1 AACCTATACCCGACCTGAACTATACCCAATCCG
5116683 AACC-ATACCCGACCTGAACTATACCCAATCC
1 AACCTATACCCGACCTGAACTATACCCAATCC
5116714 AAAATTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.33, C:0.39, G:0.09, T:0.19
Consensus pattern (33 bp):
AACCTATACCCGACCTGAACTATACCCAATCCG
Found at i:5117010 original size:19 final size:20
Alignment explanation
Indices: 5116960--5117010 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
5116950 TAATAAATTG
5116960 ATTTA-AATAAAAT-TGATA
1 ATTTATAATAAAATATGATA
* *
5116978 ATTTATTA-AAAATATTAT-
1 ATTTATAATAAAATATGATA
5116996 ATTTATAATAAAATA
1 ATTTATAATAAAATA
5117011 ATAGAAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTATAATAAAATATGATA
Found at i:5121347 original size:2 final size:2
Alignment explanation
Indices: 5121340--5121396 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
5121330 TTTAATACAT
5121340 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
5121382 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5121397 TATTTAGCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5123662 original size:18 final size:18
Alignment explanation
Indices: 5123639--5123686 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
5123629 GTTACTGAGG
**
5123639 GATTCCTGACGTGGCAAA
1 GATTCCTGACGTGAAAAA
5123657 GATTCCTGACGTGAAAAA
1 GATTCCTGACGTGAAAAA
*
5123675 GATTCCTAACGT
1 GATTCCTGACGT
5123687 ATAAGCAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (18 bp):
GATTCCTGACGTGAAAAA
Found at i:5124470 original size:28 final size:28
Alignment explanation
Indices: 5124437--5124497 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
5124427 TTTTTAAAAT
* * *
5124437 AAAAAAGAAAACGGAGTTCGATTAACTA
1 AAAAAAGAAAACGCAATTCGAATAACTA
*
5124465 AAAAAAGAAAATGCAATTCGAATAACTA
1 AAAAAAGAAAACGCAATTCGAATAACTA
5124493 AAAAA
1 AAAAA
5124498 TTACAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (28 bp):
AAAAAAGAAAACGCAATTCGAATAACTA
Found at i:5126340 original size:4 final size:4
Alignment explanation
Indices: 5126331--5126602 Score: 132
Period size: 4 Copynumber: 68.8 Consensus size: 4
5126321 ATATCCCTTC
** * * **
5126331 AAAT AAAT AAAT AAAT AAAT TCA- AAAC AAAC AAAT AAAT TTA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
5126377 AACT AAAT AAAAA AAAT AAA- AAA- AATT AAAT AATT AAAT AAAT AAATTT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA--T
* * ** *
5126426 GAAAT AATT ACAT AAAT AAAT TTA- AAAT AAAT AAAT AAAT AAATTT GAGAT
1 -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA--T -AAAT
* * * * **
5126477 GAAT ATAT AAAT AAAT ATA- AAAT AAAT AAAT AAAT ACAT AAAT TCA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
** * * *
5126523 AAAT AAAT AAAT AAAT CCA- AAAT AAAT AAAC AAAT ATAT CAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* ** **
5126570 CAAT TTA- AAAT AAAT AAAT CCA- AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
5126603 AATTACCATC
Statistics
Matches: 194, Mismatches: 58, Indels: 32
0.68 0.20 0.11
Matches are distributed among these distances:
3 14 0.07
4 168 0.87
5 5 0.03
6 2 0.01
7 5 0.03
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:5126384 original size:19 final size:19
Alignment explanation
Indices: 5126335--5126588 Score: 133
Period size: 19 Copynumber: 13.6 Consensus size: 19
5126325 CCCTTCAAAT
*
5126335 AAATAAATAAATAAATTCA
1 AAATAAATAAATAAATTTA
* *
5126354 AAACAAACAAATAAATTTA
1 AAATAAATAAATAAATTTA
* *
5126373 AAATAACTAAATAAA--AA
1 AAATAAATAAATAAATTTA
*
5126390 AAAT-AA-AAA-AAATTAA
1 AAATAAATAAATAAATTTA
5126406 ATAATTAAATAAATAAATTTGAA
1 A-AA-TAAATAAATAAATTT--A
*
5126429 ATAATTACATAAATAAATTTAAAA
1 A-AA-TAAATAAATAAATTT---A
*
5126453 TAAATAAATAAATAAATTTG
1 -AAATAAATAAATAAATTTA
* * *
5126473 AGATGAATATATAAA--T-
1 AAATAAATAAATAAATTTA
*
5126489 AAATATA-AAATAAA--T-
1 AAATAAATAAATAAATTTA
* *
5126504 AAATAAATACATAAATTCA
1 AAATAAATAAATAAATTTA
**
5126523 AAATAAATAAATAAATCCA
1 AAATAAATAAATAAATTTA
*
5126542 AAATAAATAAACAAA--T-
1 AAATAAATAAATAAATTTA
* * *
5126558 ATATCAATAAATCAATTTA
1 AAATAAATAAATAAATTTA
5126577 AAATAAATAAAT
1 AAATAAATAAAT
5126589 CCAAAATAAA
Statistics
Matches: 184, Mismatches: 33, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
14 3 0.02
15 16 0.09
16 25 0.14
17 8 0.04
18 2 0.01
19 83 0.45
20 3 0.02
21 5 0.03
23 34 0.18
24 4 0.02
25 1 0.01
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATAAATAAATAAATTTA
Found at i:5126417 original size:50 final size:49
Alignment explanation
Indices: 5126362--5126604 Score: 168
Period size: 54 Copynumber: 4.8 Consensus size: 49
5126352 CAAAACAAAC
*
5126362 AAATAAATTTAAAATAACTAAATAAAAAAAATAAAAAAAATTAAATAATTAAAT
1 AAATAAATTTAAAATAAATAAATAAAAAAAATAAAAAAAA-T--A-AA-TAAAT
* * * * **
5126416 AAATAAATTTGAAATAATTACAT-AAATAAAT--TTAAAATAAATAAAT
1 AAATAAATTTAAAATAAATAAATAAAAAAAATAAAAAAAATAAATAAAT
* * * * * *
5126462 AAATAAATTTGAGATGAATATATAAATAAATATAAAATAAATAAATAAAT
1 AAATAAATTTAAAATAAATAAATAAA-AAAAATAAAAAAAATAAATAAAT
* * * * *
5126512 ACATAAATTCAAAATAAATAAATAAATCCAAAATAAATAAACAAATATATCAAT
1 AAATAAATTTAAAATAAATAAATAAA--AAAAAT-AA-AAA-AAATAAATAAAT
* *
5126566 AAATCAATTTAAAATAAATAAATCCAAAATAAATAAAAA
1 AAATAAATTTAAAATAAATAAAT--AAAAAAAATAAAAA
5126605 TTACCATCAA
Statistics
Matches: 147, Mismatches: 32, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
46 24 0.16
47 4 0.03
48 5 0.03
50 33 0.22
51 8 0.05
52 5 0.03
53 11 0.07
54 54 0.37
56 3 0.02
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (49 bp):
AAATAAATTTAAAATAAATAAATAAAAAAAATAAAAAAAATAAATAAAT
Found at i:5126430 original size:23 final size:23
Alignment explanation
Indices: 5126331--5126558 Score: 69
Period size: 23 Copynumber: 9.7 Consensus size: 23
5126321 ATATCCCTTC
5126331 AAATAAATAAATAAATAAA-TT-
1 AAATAAATAAATAAATAAATTTA
* * *
5126352 -CA-AAACAAACAAATAAATTTA
1 AAATAAATAAATAAATAAATTTA
* **
5126373 AAATAACTAAATAAA-AAAAATA
1 AAATAAATAAATAAATAAATTTA
* * *
5126395 AAAAAAATTAAATAATTAAATAAATA
1 AAATAAA-TAAATAAATAAAT--TTA
* * *
5126421 AATTTGAAATAATTACATAAA--TA
1 AA-AT-AAATAAATAAATAAATTTA
* *
5126444 AATTTAAAATAAATAAATAAATAAATTTG
1 AA-AT-AAATAAATAAAT--A--AATTTA
* * * *
5126473 AGATGAATATATAAATAAATATA
1 AAATAAATAAATAAATAAATTTA
*
5126496 AAATAAATAAATAAATACA--TA
1 AAATAAATAAATAAATAAATTTA
* **
5126517 AATTCAAAATAAATAAATAAATCCA
1 AAAT--AAATAAATAAATAAATTTA
*
5126542 AAATAAATAAACAAATA
1 AAATAAATAAATAAATA
5126559 TATCAATAAA
Statistics
Matches: 150, Mismatches: 37, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
19 13 0.09
20 3 0.02
21 5 0.03
22 11 0.07
23 77 0.51
24 3 0.02
25 6 0.04
26 5 0.03
27 21 0.14
28 4 0.03
29 2 0.01
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATAAATAAATAAATAAATTTA
Found at i:5126431 original size:46 final size:45
Alignment explanation
Indices: 5126381--5126537 Score: 145
Period size: 46 Copynumber: 3.3 Consensus size: 45
5126371 TAAAATAACT
* *
5126381 AAATAAAAAAAATAAAAAAAATTAAATAATTAAATAAATAAATTTG
1 AAAT-AAATAAATAAAAAAAATTAAATAAATAAATAAATAAATTTG
* * * *
5126427 AAATAATTACATAAATAAATTTAAAATAAATAAATAAATAAATTTGAG
1 AAATAAATAAATAAAAAAAATT-AAATAAATAAATAAATAAATTT--G
* * **
5126475 ATGAATATATAAATAAATATAAAA-TAAATAAATAAATACATAAATTCA
1 A--AATAAATAAATAAA-A-AAAATTAAATAAATAAATAAATAAATTTG
5126523 AAATAAATAAATAAA
1 AAATAAATAAATAAA
5126538 TCCAAAATAA
Statistics
Matches: 89, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
45 13 0.15
46 38 0.43
48 3 0.03
50 31 0.35
51 1 0.01
52 3 0.03
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (45 bp):
AAATAAATAAATAAAAAAAATTAAATAAATAAATAAATAAATTTG
Found at i:5126435 original size:31 final size:31
Alignment explanation
Indices: 5126338--5126518 Score: 85
Period size: 31 Copynumber: 5.5 Consensus size: 31
5126328 TTCAAATAAA
* * * *
5126338 TAAATAAATAAATTCAAAACAAACAAATAAATT
1 TAAATAAATAAA-T-AAAAAAAATAAAAAAAAT
*
5126371 TAAAATAACTAAATAAAAAAAATAAAAAAAAT
1 T-AAATAAATAAATAAAAAAAATAAAAAAAAT
* * * ** *
5126403 TAAATAATTAAATAAATAAATTTGAAATAAT
1 TAAATAAATAAATAAAAAAAATAAAAAAAAT
* *
5126434 TACATAAATAAATTTAAAATAAATAAATAAATAAATT
1 TAAATAAATAAA--TAAAAAAAAT-AA-AAA-AAA-T
* * * * *
5126471 TGAGATGAATATATAAATAAATATAAAATAAA-
1 T-AAATAAATAAATAAA-AAAAATAAAAAAAAT
*
5126503 TAAATAAATACATAAA
1 TAAATAAATAAATAAA
5126519 TTCAAAATAA
Statistics
Matches: 111, Mismatches: 28, Indels: 20
0.70 0.18 0.13
Matches are distributed among these distances:
31 46 0.41
32 16 0.14
33 9 0.08
34 13 0.12
35 5 0.05
36 8 0.07
37 6 0.05
38 8 0.07
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (31 bp):
TAAATAAATAAATAAAAAAAATAAAAAAAAT
Found at i:5132445 original size:14 final size:15
Alignment explanation
Indices: 5132417--5132445 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5132407 AAATAAACTC
5132417 AACAGCCATAAAATG
1 AACAGCCATAAAATG
5132432 AACAGCCA-AAAATG
1 AACAGCCATAAAATG
5132446 GTACACAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (15 bp):
AACAGCCATAAAATG
Found at i:5138417 original size:81 final size:81
Alignment explanation
Indices: 5138268--5138439 Score: 211
Period size: 81 Copynumber: 2.1 Consensus size: 81
5138258 ACTTGTCTTT
* ** * * * * *
5138268 TGAATAAACACAAATGCATGTGAGCCTTTGATGGATGTTTGATCCAATGGTCCCAAGAGGATTCC
1 TGAAGAAACACAAATGCACATGAGCATTTGATGGAAGTTTGATCCAACGATCCCAAGAGGATGCC
*
5138333 ACTTTATCAATCCATA
66 ACTTCATCAATCCATA
* * *
5138349 TGAAGAAACACAAATGCACATGAGGCATTT-ATGGAAGTTTGATCCAACGATCTCAAGATGATGG
1 TGAAGAAACACAAATGCACATGA-GCATTTGATGGAAGTTTGATCCAACGATCCCAAGAGGATGC
*
5138413 CACTTCATCAATCCATT
65 CACTTCATCAATCCATA
5138430 TGAAGAAACA
1 TGAAGAAACA
5138440 TAAACACATC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 72 0.94
82 5 0.06
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (81 bp):
TGAAGAAACACAAATGCACATGAGCATTTGATGGAAGTTTGATCCAACGATCCCAAGAGGATGCC
ACTTCATCAATCCATA
Found at i:5138853 original size:20 final size:20
Alignment explanation
Indices: 5138828--5138872 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
5138818 TGTCGCCCAC
5138828 CACCACCCACCGTTGTCCAT
1 CACCACCCACCGTTGTCCAT
5138848 CACCACCCACCGTTGTCCAT
1 CACCACCCACCGTTGTCCAT
5138868 CACCA
1 CACCA
5138873 TTGCCAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.51, G:0.09, T:0.18
Consensus pattern (20 bp):
CACCACCCACCGTTGTCCAT
Found at i:5143286 original size:20 final size:23
Alignment explanation
Indices: 5143245--5143286 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5143235 ATGGTTTTCA
5143245 TGATTACTGGTATATTGATACAC
1 TGATTACTGGTATATTGATACAC
5143268 TGATTA-TGGTAT-TTG-TACA
1 TGATTACTGGTATATTGATACA
5143287 TGTGATTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 6 0.32
23 6 0.32
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (23 bp):
TGATTACTGGTATATTGATACAC
Found at i:5144226 original size:16 final size:17
Alignment explanation
Indices: 5144193--5144226 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5144183 ACCTTATGTT
*
5144193 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
5144210 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
5144226 T
1 T
5144227 AATAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:5147908 original size:2 final size:2
Alignment explanation
Indices: 5147901--5147932 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5147891 TTTACATGAC
5147901 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
5147933 GGGACATGAT
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:5155635 original size:2 final size:2
Alignment explanation
Indices: 5155628--5155679 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
5155618 TATATTTTAT
5155628 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
5155670 TA TA T- TA TA T
1 TA TA TA TA TA T
5155680 TTTATTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5155730 original size:9 final size:9
Alignment explanation
Indices: 5155718--5155917 Score: 78
Period size: 9 Copynumber: 21.9 Consensus size: 9
5155708 TTATCTCTTT
5155718 TTTTATTTA
1 TTTTATTTA
*
5155727 TTTTA-TCA
1 TTTTATTTA
5155735 TTTTATTTTA
1 TTTTA-TTTA
5155745 TTCTTA--T-
1 TT-TTATTTA
5155752 TTTTATTTA
1 TTTTATTTA
5155761 -TTTATTTA
1 TTTTATTTA
* *
5155769 TTATATGTA
1 TTTTATTTA
*
5155778 TATTA-TTA
1 TTTTATTTA
5155786 TTTTATTTA
1 TTTTATTTA
5155795 TTTCTATTT-
1 TTT-TATTTA
*
5155804 TCGTTTATTTTTCC
1 T--TTTA--TTT-A
*
5155818 TTTTATTTC
1 TTTTATTTA
5155827 TTTTATTT-
1 TTTTATTTA
*
5155835 TTTCTCTTTA
1 TTT-TATTTA
*
5155845 TTTTTTTTA
1 TTTTATTTA
*
5155854 TTTTTTTTA
1 TTTTATTTA
* *
5155863 TCTCATTT-
1 TTTTATTTA
*
5155871 CTTTATTTCA
1 TTTTATTT-A
*
5155881 TTTGTTTTTTA
1 -TT-TTATTTA
* *
5155892 TTTTCTTTG
1 TTTTATTTA
5155901 TTTTATTT-
1 TTTTATTTA
5155909 TCTTTATTT
1 T-TTTATTT
5155918 TCATTATTTT
Statistics
Matches: 148, Mismatches: 21, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
6 3 0.02
7 2 0.01
8 32 0.22
9 72 0.49
10 19 0.13
11 7 0.05
12 12 0.08
14 1 0.01
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:5155730 original size:22 final size:20
Alignment explanation
Indices: 5155705--5155863 Score: 79
Period size: 22 Copynumber: 7.3 Consensus size: 20
5155695 GTCTTTGCCT
5155705 TTTTTATCTCTTTTTTTATTTA
1 TTTTTAT-T-TTTTTTTATTTA
*
5155727 TTTTATCATTTTATTTTATTCTTA
1 TTTT-T-ATTTTTTTTTA-T-TTA
5155751 TTTTTATTTATTTATTTATTATA
1 TTTTTATTT-TTT-TTTATT-TA
* * *
5155774 TGTATATTATTATTTTATTTA
1 TTTTTATT-TTTTTTTATTTA
* ** *
5155795 TTTCTATTTTCGTTTATTTT
1 TTTTTATTTTTTTTTATTTA
* *
5155815 TCCTTTTATTTCTTTTATTTTTTC
1 T--TTTTATTT-TTTT-TTATTTA
*
5155839 TCTTTA-TTTTTTTTATTT-
1 TTTTTATTTTTTTTTATTTA
5155857 TTTTTAT
1 TTTTTAT
5155864 CTCATTTCTT
Statistics
Matches: 106, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 14 0.13
21 10 0.09
22 33 0.31
23 19 0.18
24 20 0.19
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTTTTTTATTTA
Found at i:5155732 original size:21 final size:21
Alignment explanation
Indices: 5155706--5155857 Score: 57
Period size: 21 Copynumber: 7.2 Consensus size: 21
5155696 TCTTTGCCTT
5155706 TTTTATCTCTTTTTTTATTTA
1 TTTTATCTCTTTTTTTATTTA
5155727 TTTTATCAT-TTTATTTTATTCT-
1 TTTTATC-TCTTT-TTTTATT-TA
* *
5155749 TATTT-T-TATTTATTTATTTA
1 T-TTTATCTCTTTTTTTATTTA
* * * * *
5155769 TTATATGTATATTATTATTT-
1 TTTTATCTCTTTTTTTATTTA
* * **
5155789 TATTTATTTCTATTTTCGTTTA
1 T-TTTATCTCTTTTTTTATTTA
*
5155811 TTTT-TC-CTTTTATTTCTTTTA
1 TTTTATCTCTTTT-TTT-ATTTA
* *
5155832 TTTTTTCTCTTTATTTTTTTTA
1 TTTTATCTCTTT-TTTTATTTA
5155854 TTTT
1 TTTT
5155858 TTTTATCTCA
Statistics
Matches: 101, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
19 7 0.07
20 13 0.13
21 47 0.47
22 22 0.22
23 11 0.11
24 1 0.01
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.74
Consensus pattern (21 bp):
TTTTATCTCTTTTTTTATTTA
Found at i:5155740 original size:17 final size:16
Alignment explanation
Indices: 5155718--5155836 Score: 75
Period size: 17 Copynumber: 7.2 Consensus size: 16
5155708 TTATCTCTTT
5155718 TTTTATTTATTTTATCA
1 TTTTATTTATTTTAT-A
5155735 TTTTATTTTATTCTTAT-
1 TTTTA-TTTATT-TTATA
*
5155752 TTTTATTTATTTATTTA
1 TTTTATTTATTT-TATA
* * *
5155769 TTATATGTATATTATTA
1 TTTTATTTATTTTA-TA
5155786 TTTTATTTATTTCTAT-
1 TTTTATTTATTT-TATA
** *
5155802 TTTCGTTTATTTT-TCC
1 TTTTATTTATTTTAT-A
*
5155818 TTTTATTTCTTTTAT-
1 TTTTATTTATTTTATA
5155833 TTTT
1 TTTT
5155837 TCTCTTTATT
Statistics
Matches: 80, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
14 1 0.01
15 6 0.08
16 29 0.36
17 32 0.40
18 8 0.10
19 4 0.05
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTATTTATTTTATA
Found at i:5155742 original size:5 final size:5
Alignment explanation
Indices: 5155718--5155918 Score: 65
Period size: 5 Copynumber: 41.8 Consensus size: 5
5155708 TTATCTCTTT
*
5155718 TTTTA -TTTA TTTTA --TCA TTTTA TTTTA TTCTTA TTTT- TATTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA T-TTTA TTTTA
* * * *
5155765 -TTTA TTATA TGTATA TTATTA TTTTA -TTTA TTTCTA TTTTC GTTTA
1 TTTTA TTTTA T-TTTA TT-TTA TTTTA TTTTA TTT-TA TTTTA TTTTA
* * * *
5155811 TTTTTCC TTTTA -TTTC TTTTA TTTT- TTCT- CTTTA TTTT- TTTTA TTTT-
1 -TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * * * * * *
5155858 TTTTA TCTCA -TTT- CTTTA TTTCA TTTGTT TTTTA TTTT- CTTTG TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA
*
5155906 TTTT- CTTTA TTTT
1 TTTTA TTTTA TTTT
5155919 CATTATTTTC
Statistics
Matches: 144, Mismatches: 30, Indels: 44
0.66 0.14 0.20
Matches are distributed among these distances:
3 2 0.01
4 43 0.30
5 70 0.49
6 29 0.20
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:5155755 original size:34 final size:35
Alignment explanation
Indices: 5155706--5155802 Score: 103
Period size: 34 Copynumber: 2.8 Consensus size: 35
5155696 TCTTTGCCTT
*
5155706 TTTTATCTCTT-TTTTTATTTATTTTA-TCATTTTA
1 TTTTAT-TCTTATTTTTATTTATTTTATTCATTATA
*
5155740 TTTTATTCTTATTTTTATTTA-TTTATTTATTATA
1 TTTTATTCTTATTTTTATTTATTTTATTCATTATA
* *
5155774 TGTATATTATTA-TTTTATTTATTTCTATT
1 T-TTTATTCTTATTTTTATTTATTT-TATT
5155803 TTCGTTTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
33 8 0.15
34 32 0.59
35 10 0.19
36 4 0.07
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (35 bp):
TTTTATTCTTATTTTTATTTATTTTATTCATTATA
Found at i:5155769 original size:46 final size:46
Alignment explanation
Indices: 5155705--5155792 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
5155695 GTCTTTGCCT
* * *
5155705 TTTTTATCTCTTTTTTTATT-TATTTTATCATT-TTATTTTATTCTTA
1 TTTTTATCTATTTATTTATTATA-TGTAT-ATTATTATTTTATTCTTA
*
5155751 TTTTTATTTATTTATTTATTATATGTATATTATTATTTTATT
1 TTTTTATCTATTTATTTATTATATGTATATTATTATTTTATT
5155793 TATTTCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.08
46 31 0.86
47 2 0.06
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.73
Consensus pattern (46 bp):
TTTTTATCTATTTATTTATTATATGTATATTATTATTTTATTCTTA
Found at i:5155784 original size:38 final size:37
Alignment explanation
Indices: 5155715--5155797 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
5155705 TTTTTATCTC
* * *
5155715 TTTT-TTTATTTATTTTATCATTTTATTTTATTCTTAT
1 TTTTATTTATTTATTTTATCATTGTATATTATTATT-T
*
5155752 TTTTATTTATTTA-TTTATTATATGTATATTATTATTT
1 TTTTATTTATTTATTTTATCAT-TGTATATTATTATTT
5155789 TATTTATTT
1 T-TTTATTT
5155798 CTATTTTCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 13 0.33
38 26 0.67
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.73
Consensus pattern (37 bp):
TTTTATTTATTTATTTTATCATTGTATATTATTATTT
Found at i:5155846 original size:13 final size:12
Alignment explanation
Indices: 5155801--5155850 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
5155791 TTTATTTCTA
*
5155801 TTTTCGTTTATT
1 TTTTCTTTTATT
*
5155813 TTTCCTTTTA--
1 TTTTCTTTTATT
5155823 -TTTCTTTTATT
1 TTTTCTTTTATT
5155834 TTTTCTCTTTATT
1 TTTTCT-TTTATT
5155847 TTTT
1 TTTT
5155851 TTATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 8 0.26
12 13 0.42
13 10 0.32
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTATT
Found at i:5155893 original size:16 final size:16
Alignment explanation
Indices: 5155872--5155928 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 16
5155862 ATCTCATTTC
5155872 TTTA-TTTCATTTGTTT
1 TTTATTTTC-TTTGTTT
5155888 TTTATTTTCTTTG--T
1 TTTATTTTCTTTGTTT
*
5155902 TTTATTTTCTTTATTT
1 TTTATTTTCTTTGTTT
5155918 TCATTATTTTC
1 T--TTATTTTC
5155929 ATTAGCTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 13 0.37
16 10 0.29
17 4 0.11
18 8 0.23
ACGTcount: A:0.12, C:0.09, G:0.04, T:0.75
Consensus pattern (16 bp):
TTTATTTTCTTTGTTT
Found at i:5155906 original size:14 final size:14
Alignment explanation
Indices: 5155818--5155918 Score: 61
Period size: 14 Copynumber: 7.3 Consensus size: 14
5155808 TTATTTTTCC
5155818 TTTTA-TTTCTTTTA
1 TTTTATTTTC-TTTA
*
5155832 TTTT-TTCTCTTTA
1 TTTTATTTTCTTTA
* *
5155845 TTTT-TTTTATTTT
1 TTTTATTTTCTTTA
5155858 TTTTATCTCATTTCTTTA
1 TTTTA--T--TTTCTTTA
* *
5155876 TTTCA-TTT-GTT-
1 TTTTATTTTCTTTA
*
5155887 TTTTATTTTCTTTG
1 TTTTATTTTCTTTA
5155901 TTTTATTTTCTTTA
1 TTTTATTTTCTTTA
5155915 TTTT
1 TTTT
5155919 CATTATTTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
11 4 0.06
12 5 0.07
13 23 0.34
14 24 0.36
16 1 0.01
18 10 0.15
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTATTTTCTTTA
Found at i:5155929 original size:9 final size:9
Alignment explanation
Indices: 5155903--5155932 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5155893 TTTCTTTGTT
*
5155903 TTATTTTCT
1 TTATTTTCA
5155912 TTATTTTCA
1 TTATTTTCA
5155921 TTATTTTCA
1 TTATTTTCA
5155930 TTA
1 TTA
5155933 GCTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (9 bp):
TTATTTTCA
Found at i:5165645 original size:12 final size:12
Alignment explanation
Indices: 5165624--5165654 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5165614 GTTTGCTTAC
*
5165624 CAAACCTCGGTA
1 CAAACTTCGGTA
5165636 CAAACTTCGGTA
1 CAAACTTCGGTA
5165648 CAAACTT
1 CAAACTT
5165655 TGACTGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (12 bp):
CAAACTTCGGTA
Found at i:5165928 original size:93 final size:93
Alignment explanation
Indices: 5165769--5165955 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
5165759 GATTCAGTAT
5165769 GGGTGTAATCCCTATATGATCAACTGAACCTGATAGATTAAAAGAGTTTGAAAGCCATTCATCAT
1 GGGTGTAATCCCTATATGATCAACTGAACCTGATAGATTAAAAGAGTTTGAAAGCCATTCATCAT
5165834 GGTCAAATCTATCAAAGACGAATGATTG
66 GGTCAAATCTATCAAAGACGAATGATTG
5165862 GGGTGTAATCCCTATATGATCAACTGAACCTGATAGATTAAAAGAGTTTGAAAGCCATTCATCAT
1 GGGTGTAATCCCTATATGATCAACTGAACCTGATAGATTAAAAGAGTTTGAAAGCCATTCATCAT
5165927 GGTCAAATCTATCAAAGACGAATGATTG
66 GGTCAAATCTATCAAAGACGAATGATTG
5165955 G
1 G
5165956 AGCACATAAC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (93 bp):
GGGTGTAATCCCTATATGATCAACTGAACCTGATAGATTAAAAGAGTTTGAAAGCCATTCATCAT
GGTCAAATCTATCAAAGACGAATGATTG
Found at i:5166236 original size:15 final size:15
Alignment explanation
Indices: 5166216--5166249 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5166206 CCTAGGTCGA
5166216 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
* *
5166231 AAAAGAGAAAAAGAG
1 AAAAGAAAAAAAAAG
5166246 AAAA
1 AAAA
5166250 AACATTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:5166309 original size:60 final size:60
Alignment explanation
Indices: 5166226--5166362 Score: 186
Period size: 60 Copynumber: 2.2 Consensus size: 60
5166216 AAAAGAAAAA
*
5166226 AAAAGAAAAGAGAAAAAGAGAAAAAACATTTAGGGCGAAAACCCGAAAGGGCGCCCCTAAATT
1 AAAA-AAAAGA-AAAAAGAGAAAAAACATTTAGGGCGAAAACCCGAAAGGGC-ACCCTAAATT
* * * *
5166289 -AAAAAAAGAAAAAAGAGAAAAAACGTTTAGGGTGAAAACTCGAAAGGGCACCCTAATTT
1 AAAAAAAAGAAAAAAGAGAAAAAACATTTAGGGCGAAAACCCGAAAGGGCACCCTAAATT
5166348 GAAAAAAAAGAAAAA
1 -AAAAAAAAGAAAAA
5166363 GAAAAAGAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 8 0.12
60 37 0.55
61 19 0.28
62 3 0.04
ACGTcount: A:0.56, C:0.12, G:0.20, T:0.11
Consensus pattern (60 bp):
AAAAAAAAGAAAAAAGAGAAAAAACATTTAGGGCGAAAACCCGAAAGGGCACCCTAAATT
Found at i:5167284 original size:60 final size:60
Alignment explanation
Indices: 5167214--5167505 Score: 309
Period size: 60 Copynumber: 4.7 Consensus size: 60
5167204 CACAAGATTT
*
5167214 GATTTCAACTTCACAACGAAGGATATCCAACTTAAAGTCAATTCGGTGAAACAATACTTG
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTCGGTGAAACAATACTTG
* * *
5167274 GATTTCAACTTCACAACGAAGGATATCTAACTCAAAGCCAATTTGGTGAAACAATACAACACAAG
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTCGGTGAAACAAT-----AC---
5167339 ATTG
58 -TTG
* * * * *
5167343 AATTTCAACTTCACAACAAAGGATATCCAACTTAAAGTCAATTCGGTGAAGCAGTACTTG
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTCGGTGAAACAATACTTG
* * *
5167403 GATTTCAACTTCACAACAAAGGATATCCAACTCAAAG-CAGATTTGGTGAACCACAAGA-TTG
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCA-ATTCGGTGAA--ACAATACTTG
* * **
5167464 GATTTCAACTTTACAAAGAAATATATCCAACTCAAAGCTCAA
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAG-TCAA
5167506 CTTCACAACG
Statistics
Matches: 195, Mismatches: 23, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
59 2 0.01
60 98 0.50
61 35 0.18
62 4 0.02
63 2 0.01
64 2 0.01
65 2 0.01
69 50 0.26
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (60 bp):
GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTCGGTGAAACAATACTTG
Found at i:5167435 original size:129 final size:129
Alignment explanation
Indices: 5167203--5167452 Score: 423
Period size: 129 Copynumber: 1.9 Consensus size: 129
5167193 GATGCAACTT
*
5167203 ACACAAGATTTGATTTCAACTTCACAACGAAGGATATCCAACTTAAAGTCAATTCGGTGAAACAA
1 ACACAAGATTTGATTTCAACTTCACAACAAAGGATATCCAACTTAAAGTCAATTCGGTGAAACAA
* *
5167268 TACTTGGATTTCAACTTCACAACGAAGGATATCTAACTCAAAGCCA-ATTTGGTGAAACAATACA
66 TACTTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAG-CAGATTTGGTGAAACAATACA
*
5167332 ACACAAGA-TTGAATTTCAACTTCACAACAAAGGATATCCAACTTAAAGTCAATTCGGTGAAGCA
1 ACACAAGATTTG-ATTTCAACTTCACAACAAAGGATATCCAACTTAAAGTCAATTCGGTGAAACA
*
5167396 GTACTTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCAGATTTGGTGAA
65 ATACTTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCAGATTTGGTGAA
5167453 CCACAAGATT
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
128 5 0.04
129 109 0.96
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (129 bp):
ACACAAGATTTGATTTCAACTTCACAACAAAGGATATCCAACTTAAAGTCAATTCGGTGAAACAA
TACTTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCAGATTTGGTGAAACAATACA
Found at i:5168261 original size:2 final size:2
Alignment explanation
Indices: 5168254--5168314 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
5168244 TACATTTACA
5168254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5168295 A- AT AA AC AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5168315 TTATTATTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5169514 original size:5 final size:5
Alignment explanation
Indices: 5169506--5169642 Score: 54
Period size: 5 Copynumber: 26.8 Consensus size: 5
5169496 TATTTTATCC
* * *
5169506 TTTTA TTTTA TTATTG TTTT- TATTTA -TTTA -TTTA TTATA TGTATA
1 TTTTA TTTTA TT-TTA TTTTA T-TTTA TTTTA TTTTA TTTTA T-TTTA
* * *
5169551 TTATTA TTTT- CTTTA TTTTATA TTTTCC TTTTT TTTTA TTTTTA TTTCT-
1 TT-TTA TTTTA TTTTA -TTT-TA TTTT-A TTTTA TTTTA -TTTTA TTT-TA
* * *
5169600 TTTATT TTTTA TCTTA TTTTA -TTTA TTTTA -TTTA CTTTA TTTT
1 TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5169643 TTTCTGTTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
4 20 0.19
5 51 0.49
6 31 0.30
7 2 0.02
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:5169515 original size:18 final size:20
Alignment explanation
Indices: 5169478--5169517 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5169468 CTTTGCCTTT
5169478 TTTTATCTCCTTTATATTTA
1 TTTTATCTCCTTTATATTTA
*
5169498 TTTTATC-CTTTTAT-TTTA
1 TTTTATCTCCTTTATATTTA
5169516 TT
1 TT
5169518 ATTGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATCTCCTTTATATTTA
Found at i:5169568 original size:9 final size:9
Alignment explanation
Indices: 5169492--5169738 Score: 121
Period size: 9 Copynumber: 28.1 Consensus size: 9
5169482 ATCTCCTTTA
5169492 TATTTATTT
1 TATTTATTT
**
5169501 TA-TCCTTT
1 TATTTATTT
*
5169509 TATTT-TAT
1 TATTTATTT
5169517 TATTGT-TTT
1 TATT-TATTT
5169526 TATTTA-TT
1 TATTTATTT
*
5169534 TATTTATTA
1 TATTTATTT
* *
5169543 TATGTATAT
1 TATTTATTT
5169552 TA-TTATTT
1 TATTTATTT
*
5169560 TCTTTATTT
1 TATTTATTT
5169569 TA--TATTT
1 TATTTATTT
**
5169576 TCCTT-TTT
1 TATTTATTT
5169584 T-TTTATTTT
1 TATTTA-TTT
*
5169593 TATTTCTTT
1 TATTTATTT
5169602 TA-TT-TTT
1 TATTTATTT
5169609 TATCTTATTT
1 TAT-TTATTT
5169619 TATTTATTT
1 TATTTATTT
*
5169628 TATTTACTT
1 TATTTATTT
*
5169637 TATTTTTTT
1 TATTTATTT
*
5169646 CTGTTTATTT
1 -TATTTATTT
5169656 T-TTTATTT
1 TATTTATTT
* *
5169664 TCTTTATCT
1 TATTTATTT
*
5169673 CATTT-TTT
1 TATTTATTT
*
5169681 TATCTCATTT
1 TAT-TTATTT
*
5169691 GT-TTTTTTAT
1 -TATTTATT-T
*
5169701 TATTT-TCCT
1 TATTTAT-TT
5169710 TATTT-TCCTT
1 TATTTAT--TT
5169720 TATTTATTT
1 TATTTATTT
5169729 TATTTATTT
1 TATTTATTT
5169738 T
1 T
5169739 GATTACCTTT
Statistics
Matches: 184, Mismatches: 31, Indels: 46
0.70 0.12 0.18
Matches are distributed among these distances:
7 13 0.07
8 44 0.24
9 94 0.51
10 31 0.17
11 2 0.01
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTTATTT
Found at i:5169571 original size:17 final size:17
Alignment explanation
Indices: 5169492--5169670 Score: 109
Period size: 17 Copynumber: 10.4 Consensus size: 17
5169482 ATCTCCTTTA
**
5169492 TATTTATTTTATCCTTT
1 TATTTATTTTATTATTT
* *
5169509 TATTT-TATTATTGTTTT
1 TATTTATTTTATT-ATTT
*
5169526 TATTTA-TTTATTTATTA
1 TATTTATTTTA-TTATTT
* *
5169543 TATGTATATTATTATTT
1 TATTTATTTTATTATTT
*
5169560 TCTTTATTTTA-TATTT
1 TATTTATTTTATTATTT
*
5169576 TCCTTT-TTTT-TTATTTT
1 T-ATTTATTTTATTA-TTT
*
5169593 TATTTCTTTTATT-TTT
1 TATTTATTTTATTATTT
5169609 TATCTTATTTTATTTATTT
1 TAT-TTATTTTA-TTATTT
* *
5169628 TATTTACTTTATTTTTTT
1 TATTTATTTTA-TTATTT
* *
5169646 CTGTTTATTTTTTTATTT
1 -TATTTATTTTATTATTT
*
5169664 TCTTTAT
1 TATTTAT
5169671 CTCATTTTTT
Statistics
Matches: 128, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
16 26 0.20
17 61 0.48
18 27 0.21
19 14 0.11
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.75
Consensus pattern (17 bp):
TATTTATTTTATTATTT
Found at i:5169572 original size:22 final size:21
Alignment explanation
Indices: 5169551--5169738 Score: 85
Period size: 23 Copynumber: 8.9 Consensus size: 21
5169541 TATATGTATA
5169551 TTATTATTTTCTTTATTTTA-
1 TTATTATTTTCTTTATTTTAT
5169571 -TATT-TTCCTT-TTT-TTTTAT
1 TTATTATT--TTCTTTATTTTAT
5169590 TT-TTA-TTTCTTTTATTTT-T
1 TTATTATTTTC-TTTATTTTAT
* *
5169609 TATCTTATTTTATTTATTTTAT
1 T-TATTATTTTCTTTATTTTAT
*
5169631 TTACTTTATTTT-TTTCTGTTTATT
1 TTA--TTATTTTCTTTAT-TTTA-T
* * *
5169655 TTTTTATTTTCTTTATCTCAT
1 TTATTATTTTCTTTATTTTAT
*
5169676 TT-TT-TTATCTCATTTGTTTT-T
1 TTATTATT-T-TC-TTTATTTTAT
* *
5169697 TTATTATTTTCCTTATTTTCCT
1 TTATTATTTTCTTTATTTT-AT
*
5169719 TTATTTATTTTATTTATTTT
1 TTA-TTATTTTCTTTATTTT
5169739 GATTACCTTT
Statistics
Matches: 129, Mismatches: 14, Indels: 47
0.68 0.07 0.25
Matches are distributed among these distances:
17 2 0.02
18 7 0.05
19 17 0.13
20 17 0.13
21 22 0.17
22 30 0.23
23 31 0.24
24 3 0.02
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.76
Consensus pattern (21 bp):
TTATTATTTTCTTTATTTTAT
Found at i:5169617 original size:59 final size:59
Alignment explanation
Indices: 5169554--5169683 Score: 151
Period size: 58 Copynumber: 2.2 Consensus size: 59
5169544 ATGTATATTA
* *
5169554 TTATTTTCTTTATTTTATATTTTCCTT-TTTTTTTATTTTTATTTCTTTTA-TTT-TTTATC
1 TTATTTT-TTTATTTT-TATTTACCTTATTTTTTTATGTTTATTT-TTTTATTTTCTTTATC
* *
5169613 TTATTTTATTTA-TTTTATTTACTTTATTTTTTTCTGTTTATTTTTTTATTTTCTTTATC
1 TTATTTT-TTTATTTTTATTTACCTTATTTTTTTATGTTTATTTTTTTATTTTCTTTATC
*
5169672 TCATTTTTTTAT
1 TTATTTTTTTAT
5169684 CTCATTTGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
57 13 0.21
58 25 0.41
59 23 0.38
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.77
Consensus pattern (59 bp):
TTATTTTTTTATTTTTATTTACCTTATTTTTTTATGTTTATTTTTTTATTTTCTTTATC
Found at i:5169684 original size:13 final size:13
Alignment explanation
Indices: 5169660--5169695 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
5169650 TTATTTTTTT
5169660 ATTTTCTTTATCTC
1 ATTTT-TTTATCTC
5169674 ATTTTTTTATCTC
1 ATTTTTTTATCTC
5169687 ATTTGTTTT
1 ATTT-TTTT
5169696 TTTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (13 bp):
ATTTTTTTATCTC
Found at i:5170735 original size:2 final size:2
Alignment explanation
Indices: 5170728--5170759 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5170718 GTTACAAATA
5170728 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5170760 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5173098 original size:197 final size:199
Alignment explanation
Indices: 5172642--5173109 Score: 547
Period size: 200 Copynumber: 2.4 Consensus size: 199
5172632 TGTTGGAATT
* * * * * *
5172642 TATCATTCAGTTGAGGCCAATATCGACACATACAAGATATTGTAAGCGGGTTAAAAATCGCGTTA
1 TATCTTTCAATTGAGGCTAATATCGACACATATAAGACATTGTAAGTGGGTTAAAAATCGCGTTA
* *
5172707 AAAATGGTTTCAAAACTTGTTTTGCTAATGAAGCAAGAGCTAAAATGGGATTGATAGGCATATTC
66 AAAATGGTTCCAAAACTTGTTTTGATAATGAAGCAAGAGCTAAAATGGGATTGATAGGCATATTC
* * ** *
5172772 GAAGGGTATTTTTGGGTAGTTAATTTGAAATTTTTCGTAATTTATAAGTTTAGAGGTGTAGTATT
131 GAAGGGTATTTTTAGGAAGTTAAGATGAAATTTTTCGTAATTTATAAGATTAGAGGTGTAGTA-T
5172837 GTAAC
195 GTAAC
* * * *
5172842 TATCTTTCAATTGAGGGTAATATCGGCACATATAAGACATTGTAAGTGGGTTAAAAATCGCATTC
1 TATCTTTCAATTGAGGCTAATATCGACACATATAAGACATTGTAAGTGGGTTAAAAATCGCGTTA
* * * *
5172907 AAAATGGTTCCAAAGCTTGGTTTT-ATGAATGAAG-AAGAAGCTAAAAT-GGCTTGATAGGCTTG
66 AAAATGGTTCCAAAACTT-GTTTTGAT-AATGAAGCAAG-AGCTAAAATGGGATTGATAGGCATA
* **
5172969 TTCG-GGGAGTATTTTTAGGAAGTTAAGATG-AATTTTTTTTAATTTATAAGATTAGAGGTGTAG
128 TTCGAAGG-GTATTTTTAGGAAGTTAAGATGAAATTTTTCGTAATTTATAAGATTAGAGGTGTAG
5173032 TA-GT-AC
192 TATGTAAC
* * * * *
5173038 TTATGTTTCAATTGATGCTAGTATCGACACATATGAGACATTCTAAGT-GGTGTAAAAATCGCGT
1 -TATCTTTCAATTGAGGCTAATATCGACACATATAAGACATTGTAAGTGGGT-TAAAAATCGCGT
*
5173102 TGAAAATG
64 TAAAAATG
5173110 ATTCGAAACA
Statistics
Matches: 229, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
196 5 0.02
197 60 0.26
199 34 0.15
200 109 0.48
201 21 0.09
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.34
Consensus pattern (199 bp):
TATCTTTCAATTGAGGCTAATATCGACACATATAAGACATTGTAAGTGGGTTAAAAATCGCGTTA
AAAATGGTTCCAAAACTTGTTTTGATAATGAAGCAAGAGCTAAAATGGGATTGATAGGCATATTC
GAAGGGTATTTTTAGGAAGTTAAGATGAAATTTTTCGTAATTTATAAGATTAGAGGTGTAGTATG
TAAC
Found at i:5174915 original size:20 final size:19
Alignment explanation
Indices: 5174887--5174940 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
5174877 CTATTCGTCC
* *
5174887 AAAAGCATGTCTTTTCACTT
1 AAAACCATGTATTTTC-CTT
*
5174907 AAAACCATGTATTTTCGTT
1 AAAACCATGTATTTTCCTT
*
5174926 AAAACC-TATATTTTC
1 AAAACCATGTATTTTC
5174941 AATGGGTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 8 0.27
19 8 0.27
20 14 0.47
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (19 bp):
AAAACCATGTATTTTCCTT
Found at i:5174939 original size:18 final size:19
Alignment explanation
Indices: 5174905--5174940 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5174895 GTCTTTTCAC
*
5174905 TTAAAACCATGTATTTTCG
1 TTAAAACCATATATTTTCG
5174924 TTAAAACC-TATATTTTC
1 TTAAAACCATATATTTTC
5174941 AATGGGTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (19 bp):
TTAAAACCATATATTTTCG
Found at i:5176877 original size:30 final size:30
Alignment explanation
Indices: 5176842--5176911 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
5176832 AATGAACATG
* *
5176842 TTCAAAAAGAAGAGTATGAGAGTGAAATAA
1 TTCAAAAAGAAGAGTATGAGAATGAAAGAA
*
5176872 TTCAAAAAGAAGAGTGTGAGAATGAAAGAA
1 TTCAAAAAGAAGAGTATGAGAATGAAAGAA
5176902 TTCAAAAAGA
1 TTCAAAAAGA
5176912 GCATGGGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (30 bp):
TTCAAAAAGAAGAGTATGAGAATGAAAGAA
Found at i:5180406 original size:17 final size:17
Alignment explanation
Indices: 5180359--5180406 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
5180349 GAAGGACGAC
* *
5180359 TTAAACAAATTTATAAT
1 TTAAAAAAATTAATAAT
**
5180376 TTAAAGTTAATTAATAAT
1 TTAAA-AAAATTAATAAT
5180394 TTAAAAAAATTAA
1 TTAAAAAAATTAA
5180407 CATTATATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAAAAAATTAATAAT
Found at i:5181304 original size:30 final size:30
Alignment explanation
Indices: 5181229--5181316 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
5181219 ATGAATCAAT
* * *
5181229 CTATCTTCACCATCATCAACATCACCATCA
1 CTATCATCAACATCATCAATATCACCATCA
* ** * * *
5181259 CTATCATTAGTATCATTAATATCACTATCG
1 CTATCATCAACATCATCAATATCACCATCA
*
5181289 CTATCATCAACATCATCATTATCACCAT
1 CTATCATCAACATCATCAATATCACCAT
5181317 GAACATCACT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (30 bp):
CTATCATCAACATCATCAATATCACCATCA
Found at i:5181305 original size:3 final size:3
Alignment explanation
Indices: 5181291--5181383 Score: 62
Period size: 3 Copynumber: 31.0 Consensus size: 3
5181281 CACTATCGCT
* * * * * * *
5181291 ATC ATC AAC ATC ATC ATT ATC ACC ATG AAC ATC A-C TACC ATC ACC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC -ATC ATC ATC
* * * * *
5181336 ACC ACC ATC ATC ATC ATT ATC ATC ATC ATT ATC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
5181384 GCTATCTACA
Statistics
Matches: 69, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
2 1 0.01
3 67 0.97
4 1 0.01
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:5181383 original size:12 final size:12
Alignment explanation
Indices: 5181342--5181376 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
5181332 CACCACCACC
5181342 ATCATCATCATT
1 ATCATCATCATT
5181354 ATCATCATCATT
1 ATCATCATCATT
5181366 ATCATCATCAT
1 ATCATCATCAT
5181377 CGTCATCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCATCATCATT
Found at i:5184931 original size:25 final size:25
Alignment explanation
Indices: 5184892--5184941 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5184882 AACCCAAAAC
5184892 TTTGAAAATCCTAATTTCAACCCCT
1 TTTGAAAATCCTAATTTCAACCCCT
5184917 TTTGAAAA-CCTTAATTTCAACCCCT
1 TTTGAAAATCC-TAATTTCAACCCCT
5184942 AAACTTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (25 bp):
TTTGAAAATCCTAATTTCAACCCCT
Done.