Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008563.1 Hibiscus syriacus cultivar Beakdansim tig00111473_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: 653500
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 3
Found at i:324039 original size:5 final size:5
Alignment explanation
Indices: 324031--324064 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
324021 TAAAAGCAGA
*
324031 AAAAT AAAAT AAAAT AAAAT AAATAA AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAA
324065 GTCCAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:324051 original size:15 final size:16
Alignment explanation
Indices: 324031--324064 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
324021 TAAAAGCAGA
*
324031 AAAATAAA-ATAAAAT
1 AAAATAAATAAAAAAT
324046 AAAATAAATAAAAAAT
1 AAAATAAATAAAAAAT
324062 AAA
1 AAA
324065 GTCCAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAATAAAAAAT
Found at i:324149 original size:21 final size:23
Alignment explanation
Indices: 324105--324149 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
324095 TCCTGTAATT
*
324105 AATAATGAAAGATTAAGGACTAA
1 AATAATGAAAGATTAAGAACTAA
*
324128 AATAATGAAA-A-TCAGAACTAA
1 AATAATGAAAGATTAAGAACTAA
324149 A
1 A
324150 TCAAAACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 10 0.50
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (23 bp):
AATAATGAAAGATTAAGAACTAA
Found at i:325251 original size:3 final size:3
Alignment explanation
Indices: 325243--325313 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
325233 TGGGGCCTGC
325243 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
325291 AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
325314 GTTTTTGTAG
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:330956 original size:21 final size:20
Alignment explanation
Indices: 330928--330989 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
330918 ACCAGAACCC
*
330928 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGGATCGATTCCCT
* *
330947 CTGTGGGGGGAATCGGTTCCCT
1 CAG-GGGGGG-ATCGATTCCCT
330969 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGGATCGATTCCCT
330989 C
1 C
330990 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 15 0.43
22 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.23
Consensus pattern (20 bp):
CAGGGGGGGATCGATTCCCT
Found at i:341553 original size:13 final size:13
Alignment explanation
Indices: 341537--341561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
341527 CGACACTAAA
341537 TTTTTTCTATAAT
1 TTTTTTCTATAAT
341550 TTTTTTCTATAA
1 TTTTTTCTATAA
341562 ATAAATAATT
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):
TTTTTTCTATAAT
Found at i:347960 original size:31 final size:31
Alignment explanation
Indices: 347917--348000 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
347907 TAGTAAAGTA
*
347917 AGCCAAAAGCTCTTGTTCCCATTCATACCGG
1 AGCCAAATGCTCTTGTTCCCATTCATACCGG
* *
347948 AGCCAAATGCTCTTGTTCCCATTGATATCGG
1 AGCCAAATGCTCTTGTTCCCATTCATACCGG
*
347979 AGCCAAATGCTCTTGGTCCCAT
1 AGCCAAATGCTCTTGTTCCCAT
348001 CAATATCTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (31 bp):
AGCCAAATGCTCTTGTTCCCATTCATACCGG
Found at i:352897 original size:31 final size:31
Alignment explanation
Indices: 352859--352921 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
352849 TCAAATGATA
352859 ATTTTGTTACAAATCGATAATAGTAGTGACC
1 ATTTTGTTACAAATCGATAATAGTAGTGACC
* * *
352890 ATTTTGTTATAAATCGATAATATTATTGACC
1 ATTTTGTTACAAATCGATAATAGTAGTGACC
352921 A
1 A
352922 ATATATTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.40
Consensus pattern (31 bp):
ATTTTGTTACAAATCGATAATAGTAGTGACC
Found at i:357711 original size:3 final size:3
Alignment explanation
Indices: 357705--357758 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
357695 ATTATTTTTT
* * *
357705 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TTA TAA TTA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
357750 TAA TAA TAA
1 TAA TAA TAA
357759 AATGGGTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:358123 original size:124 final size:120
Alignment explanation
Indices: 357903--358186 Score: 353
Period size: 124 Copynumber: 2.4 Consensus size: 120
357893 ATTCTTCTCT
* * *
357903 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTGCTGG---GGATGATGTGGACCTATTTTCT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAGGATGATGTGAACCTATTCTCT
* * * *
357965 TCTATGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTC
65 TCTATAATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* *
358021 TTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCT-AATCTA-T
1 --T-T-CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATG-TGAACCTATT
* * *
358084 CTCTTTCTGTAATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
61 CTC-TTCTATAATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
*
358145 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
358187 AGCTAATCTA
Statistics
Matches: 144, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
120 40 0.28
121 6 0.04
122 33 0.23
123 3 0.02
124 61 0.42
125 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (120 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGTGAACCTATTCTCTT
CTATAATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
Found at i:358409 original size:225 final size:216
Alignment explanation
Indices: 358106--358507 Score: 633
Period size: 225 Copynumber: 1.8 Consensus size: 216
358096 TAGAATTATG
* *
358106 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
358171 GAACTTCCTCTGGAAAAGCTAATCTATCAAGTTATGGATTTGAGCAAAAGGTTGAACAAATTCTT
66 GAACTTCCTCTGGAAAAGCTAATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACAAATTCTT
358236 CTCATTATGAATTTCTTCTTATTCAGATGACGAGTTCTTATCATTATGAACTCTACCTGGCAATG
131 CTCATTATGAATTTCTTC-T-TTCAGATGA--A-TTCTTATCATTATGAACTCTACCTGGCAATG
358301 TTAATCCATCAAATAATGAATTTAAA
191 TTAATCCATCAAATAATGAATTTAAA
*
358327 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
* *
358392 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACAAAT
62 TTATGAACTTCCTCTGGAAAAGCTAATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACAAAT
*
358457 TCTTCTCATTATGAATTTCTTCTTTCAGATGAATTCTTCTCATTATGAACT
127 TCTTCTCATTATGAATTTCTTCTTTCAGATGAATTCTTATCATTATGAACT
358508 TCTTCTTCTT
Statistics
Matches: 167, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
220 17 0.10
221 30 0.18
223 9 0.05
224 7 0.04
225 104 0.62
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (216 bp):
CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCCTCTGGAAAAGCTAATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACAAATTCTT
CTCATTATGAATTTCTTCTTTCAGATGAATTCTTATCATTATGAACTCTACCTGGCAATGTTAAT
CCATCAAATAATGAATTTAAA
Found at i:358450 original size:113 final size:109
Alignment explanation
Indices: 358105--358508 Score: 526
Period size: 112 Copynumber: 3.7 Consensus size: 109
358095 ATAGAATTAT
** * *
358105 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
358170 TGAACTTCCTCTGGAAAAGCTAATCTATCAAGTTATGGATTTGA
66 TGAACTTACTCTGGAAAAGCTAATCCATCAAATAATGGATTTGA
* *
358214 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTATTCAGATGACGAGTTCTTATCA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGAT---GAGTTCTTCTCA
* * * * *
358279 TTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATAATGAATTTAA
63 TTATGAACT-TACTCTGGAAAAGCTAATCCATCAAATAATGGATTTGA
*
358326 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGAGTTCTTCTC
* * *
358391 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
62 ATTATGAACTTACTCTGGAAAAGCTAATCCATCAAATAATGGATTTGA
* *
358439 GCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAATTCTTCTCATTA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
358502 TGAACTT
66 TGAACTT
358509 CTTCTTCTTC
Statistics
Matches: 257, Mismatches: 29, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
107 28 0.11
108 1 0.00
109 46 0.18
110 5 0.02
111 1 0.00
112 80 0.31
113 80 0.31
114 1 0.00
115 5 0.02
116 10 0.04
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (109 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTACTCTGGAAAAGCTAATCCATCAAATAATGGATTTGA
Found at i:358478 original size:17 final size:16
Alignment explanation
Indices: 358454--358541 Score: 72
Period size: 17 Copynumber: 5.1 Consensus size: 16
358444 AAGTTGAACA
358454 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
*
358470 AATTTCTTCTTTCA-GATG
1 AA-TTCTTC--TCATTATG
358488 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
358504 AACTTCTTCTTC-TTCAGATG
1 AA-TTCTTC-TCATT---ATG
*
358524 AGTTCTTCTCATTATG
1 AATTCTTCTCATTATG
358540 AA
1 AA
358542 CTCGAACTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
15 3 0.05
16 11 0.19
17 20 0.34
18 9 0.16
19 11 0.19
20 4 0.07
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (16 bp):
AATTCTTCTCATTATG
Found at i:358497 original size:34 final size:36
Alignment explanation
Indices: 358454--358543 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
358444 AAGTTGAACA
*
358454 AATTCTTCTCATTATGAATTTCTTC-T-TTCAGATG
1 AATTCTTCTCATTATGAACTTCTTCTTCTTCAGATG
358488 AATTCTTCTCATTATGAACTTCTTCTTCTTCAGATG
1 AATTCTTCTCATTATGAACTTCTTCTTCTTCAGATG
*
358524 AGTTCTTCTCATTATGAACT
1 AATTCTTCTCATTATGAACT
358544 CGAACTGGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
34 24 0.46
35 1 0.02
36 27 0.52
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (36 bp):
AATTCTTCTCATTATGAACTTCTTCTTCTTCAGATG
Found at i:358524 original size:20 final size:20
Alignment explanation
Indices: 358473--358536 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 20
358463 CATTATGAAT
*
358473 TTCTTCTTTCAGATGAATTC
1 TTCTTCATTCAGATGAATTC
358493 TTC-TCATT---ATGAACTTC
1 TTCTTCATTCAGATGAA-TTC
*
358510 TTCTTC-TTCAGATGAGTTC
1 TTCTTCATTCAGATGAATTC
358529 TTC-TCATT
1 TTCTTCATT
358537 ATGAACTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 4 0.11
19 12 0.33
20 7 0.19
ACGTcount: A:0.19, C:0.22, G:0.09, T:0.50
Consensus pattern (20 bp):
TTCTTCATTCAGATGAATTC
Found at i:358603 original size:143 final size:145
Alignment explanation
Indices: 358341--358622 Score: 388
Period size: 143 Copynumber: 1.9 Consensus size: 145
358331 AGGTTGAACA
****
358341 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAC
* * **
358406 TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGA
64 TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGA
*
358471 ATTTCTTCTTTCAGATG
129 ACTTCTTCTTTCAGATG
358488 AATTCTTCTCATTATGAA-CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 AATTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* * ** * * *
358551 GTAATGATGATCCATTGAATGATGAATTCAAGTAAAAAGTTGAACAAGTTCTTTTCATTATGAAC
66 GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAAC
358616 TTCTTCT
131 TTCTTCT
358623 GGAAAAGCTA
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
143 95 0.80
144 6 0.05
147 18 0.15
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (145 bp):
AATTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
GAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTTCAGATG
Found at i:359517 original size:115 final size:115
Alignment explanation
Indices: 359340--359999 Score: 1191
Period size: 115 Copynumber: 5.7 Consensus size: 115
359330 GATCATGCAG
* *
359340 TTCATCTTT-TAATTCCAATGATTGGTTCTGTGG-TTCCTACCGAAA-CAGATCAGATAACTCAA
1 TTCATCTTTCAAATT-CAATGATTGGTTCTGTGGTTTCATACC-AAACCAGATCAGATAACTCAA
*
359402 AGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCAAA
64 AGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
359454 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
*
359519 AACACTTCCAGAAGATGCTATTGGGTCTTCTTACTTCTACTATGATCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
359569 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
* *
359634 AACACTTCTAGAAGATGCTATTAGGTCTTCTTATTTCTACTATGATCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
* *
359684 TTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
*
359749 AACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
*
359799 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATTAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
359864 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
359914 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
359979 AACACTTCCAGAAGATGCTAT
66 AACACTTCCAGAAGATGCTAT
360000 GAGCACATTC
Statistics
Matches: 526, Mismatches: 17, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
114 30 0.06
115 496 0.94
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (115 bp):
TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
Found at i:360062 original size:93 final size:93
Alignment explanation
Indices: 359903--360193 Score: 476
Period size: 93 Copynumber: 3.1 Consensus size: 93
359893 CTTATTTCTA
* * * * * *
359903 CTATGATCACATTCATCTTTCAAATTCAATGATTGGTTCT-GTGGTTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCG-GGGTTCATATCAAACCAGATCA
359967 GATAACTCAAAGAACACTTCCAGAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
*
359996 CTATGAGCACATTCATATTTTAAATCCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAG
360061 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* *
360089 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGGGGTTTATATCAAACCTGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAG
360154 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
360182 ATATGAGCACAT
1 CTATGAGCACAT
360194 GACACTTGTT
Statistics
Matches: 186, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
93 185 0.99
94 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (93 bp):
CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:361213 original size:7 final size:7
Alignment explanation
Indices: 361201--361251 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
361191 CTTGACCCCC
361201 TTTTTCT
1 TTTTTCT
361208 TTTTTCT
1 TTTTTCT
*
361215 TTTCTCT
1 TTTTTCT
361222 TTTTTC-
1 TTTTTCT
361228 --TTTCT
1 TTTTTCT
*
361233 TTTTTAT
1 TTTTTCT
361240 TTTTTCT
1 TTTTTCT
361247 TTTTT
1 TTTTT
361252 TTCTTCAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
4 4 0.11
7 33 0.89
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:361224 original size:14 final size:14
Alignment explanation
Indices: 361200--361256 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
361190 TCTTGACCCC
361200 CTTTT-TCTTTTTT
1 CTTTTCTCTTTTTT
361213 CTTTTCTCTTTTTT
1 CTTTTCTCTTTTTT
361227 C-TTTCT-TTTTTAT
1 CTTTTCTCTTTTT-T
* *
361240 TTTTTCTTTTTTTT
1 CTTTTCTCTTTTTT
361254 CTT
1 CTT
361257 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.13
13 11 0.29
14 17 0.45
15 5 0.13
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTCTCTTTTTT
Found at i:361231 original size:25 final size:25
Alignment explanation
Indices: 361203--361251 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
361193 TGACCCCCTT
*
361203 TTTCTTTTTTCTTTTCTCTTTTTTC
1 TTTCTTTTTTATTTTCTCTTTTTTC
*
361228 TTTCTTTTTTATTTTTTCTTTTTT
1 TTTCTTTTTTATTTTCTCTTTTTT
361252 TTCTTCAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTCTTTTTTATTTTCTCTTTTTTC
Found at i:361233 original size:18 final size:18
Alignment explanation
Indices: 361210--361255 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
361200 CTTTTTCTTT
*
361210 TTTCTTTTCTCTTTTTTC
1 TTTCTTTTCTATTTTTTC
*
361228 TTTCTTTTTTATTTTTTC
1 TTTCTTTTCTATTTTTTC
*
361246 TTTTTTTTCT
1 TTTCTTTTCT
361256 TCAAGCATAA
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:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTCTTTTCTATTTTTTC
Found at i:368604 original size:15 final size:15
Alignment explanation
Indices: 368581--368612 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
368571 TGAAATGAAT
368581 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
368596 AATGTATGTATGCAA
1 AATGAATGTATGCAA
368611 AA
1 AA
368613 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:374091 original size:3 final size:3
Alignment explanation
Indices: 374085--374153 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
374075 ATTATTTTTT
* * *
374085 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
374130 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
374154 AATGGGTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:377895 original size:23 final size:23
Alignment explanation
Indices: 377845--377926 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
377835 TTGGTGCAGA
* *
377845 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCTTTGAAG
377865 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
377888 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
377911 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
377927 CACAGGGGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 8 0.14
21 9 0.16
22 1 0.02
23 39 0.68
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:377935 original size:21 final size:20
Alignment explanation
Indices: 377865--377948 Score: 69
Period size: 23 Copynumber: 3.9 Consensus size: 20
377855 CCCCCCTTGA
*
377865 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC---CAAG
*
377888 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC---CAAG
377911 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCA-AG
* *
377932 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
377949 TGGGGTTCTG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
20 1 0.02
21 17 0.30
23 39 0.68
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.17
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCAAG
Found at i:377935 original size:44 final size:42
Alignment explanation
Indices: 377845--377949 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 42
377835 TTGGTGCAGA
*
377845 GGGAATCGA-TCCCCCCTTGAGGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCCTTGAGGGAACCGATTCCCCC--TCAAG
* *
377888 GGGAACCGATTCCCCCTTTGAAGGGGAACCGATTCCCCC-CACAG
1 GGGAATCGATTCCCCCCTTG-A-GGGAACCGATTCCCCCTCA-AG
*
377932 GGGAATCGATACCCCCCT
1 GGGAATCGATTCCCCCCT
377950 GGGGTTCTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
43 9 0.17
44 26 0.50
45 1 0.02
46 16 0.31
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (42 bp):
GGGAATCGATTCCCCCCTTGAGGGAACCGATTCCCCCTCAAG
Found at i:379399 original size:13 final size:13
Alignment explanation
Indices: 379367--379419 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
379357 ACATAGTAAA
*
379367 ATGCACTCACCTAGT
1 ATGC-CTCA-CTATT
379382 ATGCCTCACTATT
1 ATGCCTCACTATT
379395 ATGCCTCACTATT
1 ATGCCTCACTATT
*
379408 ATGCCTTACTAT
1 ATGCCTCACTAT
379420 CGATATCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 28 0.78
14 4 0.11
15 4 0.11
ACGTcount: A:0.25, C:0.30, G:0.09, T:0.36
Consensus pattern (13 bp):
ATGCCTCACTATT
Found at i:381676 original size:25 final size:26
Alignment explanation
Indices: 381642--381694 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
381632 CCTTCCAAGG
*
381642 ATATATATAG-TTTTGAAAATATATA
1 ATATATATAGACTTTGAAAATATATA
381667 ATATATATAGACTTTGAAAATATATA
1 ATATATATAGACTTTGAAAATATATA
381693 AT
1 AT
381695 TTTTGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.42
Consensus pattern (26 bp):
ATATATATAGACTTTGAAAATATATA
Found at i:381749 original size:28 final size:27
Alignment explanation
Indices: 381716--381793 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 27
381706 CATTATACAG
381716 TAGTTTTTAAAATATAATATATATTATA
1 TAGTTTTTAAAATAT-ATATATATTATA
* * *
381744 TAGTTTTT--AATATATATGT-GTGTA
1 TAGTTTTTAAAATATATATATATTATA
381768 -A-TTTTTAAAATATATATATATTATA
1 TAGTTTTTAAAATATATATATATTATA
381793 T
1 T
381794 GTTATATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
22 5 0.12
23 1 0.03
24 13 0.32
25 8 0.20
26 5 0.12
28 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (27 bp):
TAGTTTTTAAAATATATATATATTATA
Found at i:381775 original size:22 final size:21
Alignment explanation
Indices: 381730--381788 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
381720 TTTTAAAATA
*
381730 TAATATATATTATATAGTTTT
1 TAATATATATTATATAATTTT
* *
381751 TAATATATATGTGTGTAATTTT
1 TAATATATAT-TATATAATTTT
*
381773 TAAAATATATATATAT
1 TAATATATAT-TATAT
381789 TATATGTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TAATATATATTATATAATTTT
Found at i:381853 original size:23 final size:23
Alignment explanation
Indices: 381800--381854 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
381790 ATATGTTATA
381800 TTATTTTATTATTTTTATTCATTC
1 TTATTTT-TTATTTTTATTCATTC
* * *
381824 TTTTTTTTTCTTTTTATTTACTT-
1 TTATTTTTTATTTTTATTCA-TTC
381847 TTATTTTT
1 TTATTTTT
381855 GTTTTAGGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (23 bp):
TTATTTTTTATTTTTATTCATTC
Found at i:393093 original size:21 final size:21
Alignment explanation
Indices: 393066--393192 Score: 123
Period size: 21 Copynumber: 5.9 Consensus size: 21
393056 GCATTATCGT
*
393066 AAGAGTATTTTGTGTACTTGG
1 AAGAGTACTTTGTGTACTTGG
* *
393087 AACAGTACTTTATGTACTATGG
1 AAGAGTACTTTGTGTACT-TGG
* *
393109 CAAGAGTACTTCGTGTACATGG
1 -AAGAGTACTTTGTGTACTTGG
393131 -AGTAGTACTTTGTGTACTATGG
1 AAG-AGTACTTTGTGTACT-TGG
*
393153 CAAGAGTACTGTGTGTACTT-G
1 -AAGAGTACTTTGTGTACTTGG
*
393174 TAGTAGTACTTTGTGTACT
1 AAG-AGTACTTTGTGTACT
393193 ATGGCACTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
20 4 0.05
21 43 0.49
22 10 0.11
23 28 0.32
24 2 0.02
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (21 bp):
AAGAGTACTTTGTGTACTTGG
Found at i:393138 original size:44 final size:43
Alignment explanation
Indices: 393066--393198 Score: 185
Period size: 44 Copynumber: 3.0 Consensus size: 43
393056 GCATTATCGT
* ** *
393066 AAGAGTATTTTGTGTACTTGGAACAGTACTTTATGTACTATGGC
1 AAGAGTA-CTTGTGTACTTGGAGTAGTACTTTGTGTACTATGGC
*
393110 AAGAGTACTTCGTGTACATGGAGTAGTACTTTGTGTACTATGGC
1 AAGAGTACTT-GTGTACTTGGAGTAGTACTTTGTGTACTATGGC
*
393154 AAGAGTACTGTGTGTACTTGTAGTAGTACTTTGTGTACTATGGC
1 AAGAGTACT-TGTGTACTTGGAGTAGTACTTTGTGTACTATGGC
393198 A
1 A
393199 CTTTGTGTGC
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 2 0.03
44 77 0.96
45 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (43 bp):
AAGAGTACTTGTGTACTTGGAGTAGTACTTTGTGTACTATGGC
Found at i:399517 original size:21 final size:21
Alignment explanation
Indices: 399491--399597 Score: 103
Period size: 21 Copynumber: 5.0 Consensus size: 21
399481 TATTTTCGTA
399491 AGAGTACTTTGTGTACT-TGG
1 AGAGTACTTTGTGTACTATGG
**
399511 AGCAGTACTTTGTGTACTATACA
1 AG-AGTACTTTGTGTACTAT-GG
*
399534 AGAGTACTTCT-TGAAC-ATGG
1 AGAGTACTT-TGTGTACTATGG
*
399554 AGTAGTACTTTGTGTATTATGG
1 AG-AGTACTTTGTGTACTATGG
399576 CAAGAGTACTTTGTGTACTATG
1 --AGAGTACTTTGTGTACTATG
399598 TCATTTTGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.07
21 27 0.39
22 16 0.23
23 20 0.29
24 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (21 bp):
AGAGTACTTTGTGTACTATGG
Found at i:399555 original size:43 final size:44
Alignment explanation
Indices: 399490--399590 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 44
399480 GTATTTTCGT
* *
399490 AAGAGTACTTTGTGTACTTGGAGCAGTACTTTGTGTACTAT-AC
1 AAGAGTACTTTGTGAACATGGAGCAGTACTTTGTGTACTATGAC
* * *
399533 AAGAGTACTTCT-TGAACATGGAGTAGTACTTTGTGTATTATGGC
1 AAGAGTACTT-TGTGAACATGGAGCAGTACTTTGTGTACTATGAC
399577 AAGAGTACTTTGTG
1 AAGAGTACTTTGTG
399591 TACTATGTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 36 0.72
44 14 0.28
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (44 bp):
AAGAGTACTTTGTGAACATGGAGCAGTACTTTGTGTACTATGAC
Found at i:400192 original size:13 final size:13
Alignment explanation
Indices: 400169--400200 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
400159 TTGAAGAATG
400169 TTTTA-TAAATTA
1 TTTTATTAAATTA
400181 TTTTATTAAATTA
1 TTTTATTAAATTA
400194 TTTTATT
1 TTTTATT
400201 TAAAGAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTATTAAATTA
Found at i:400435 original size:20 final size:20
Alignment explanation
Indices: 400390--400436 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
400380 ATGCCACTAA
*
400390 GATGTCAAAGTTATTGATAT
1 GATGTCAAAGTGATTGATAT
* *
400410 GGTGTCAATGTGATATGAT-T
1 GATGTCAAAGTGAT-TGATAT
400430 GATGTCA
1 GATGTCA
400437 CTCCTCACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (20 bp):
GATGTCAAAGTGATTGATAT
Found at i:408902 original size:2 final size:2
Alignment explanation
Indices: 408895--408928 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
408885 CAATACTAAC
408895 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
408929 TTATGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:409686 original size:45 final size:45
Alignment explanation
Indices: 409636--409786 Score: 232
Period size: 45 Copynumber: 3.4 Consensus size: 45
409626 CAAATAAGCT
* *
409636 TGGAATAAAAGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTA
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
409681 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTA
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
409726 TGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTCA
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
409771 TAGG-ATAAATGATAAG
1 T-GGAATAAATGGTAAG
409787 AAATTTTATA
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
45 96 0.98
46 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (45 bp):
TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
Found at i:411452 original size:31 final size:30
Alignment explanation
Indices: 411414--411472 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
411404 TTGCGACATG
411414 ATGTATGTATGATACGTG-TATATATATATGC
1 ATGTATGTAT-A-ACGTGTTATATATATATGC
*
411445 ATGTATGTATAATGTGTTATATATATAT
1 ATGTATGTATAACGTGTTATATATATAT
411473 ATATATCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 12 0.46
31 10 0.38
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (30 bp):
ATGTATGTATAACGTGTTATATATATATGC
Found at i:411530 original size:2 final size:2
Alignment explanation
Indices: 411523--411602 Score: 137
Period size: 2 Copynumber: 40.5 Consensus size: 2
411513 TTAAAAAGAA
411523 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
411565 AT AT AT AT AT AT AT AT AT AT AT -T A- AT ACT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A
411603 CTCATGCATA
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.03
2 71 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:412012 original size:2 final size:2
Alignment explanation
Indices: 412005--412040 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
411995 ACTTATTTGA
412005 AT AT AT AT AT -T 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
412041 ATTCAATCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:412266 original size:29 final size:30
Alignment explanation
Indices: 412227--412283 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
412217 AATGATTATG
*
412227 AATAAATTTA-TAATATAATTATTATAAAA
1 AATAAATTTATTAATATAATTATCATAAAA
*
412256 AATAAATTTATTAATTTAATTATCATAA
1 AATAAATTTATTAATATAATTATCATAA
412284 CTAACAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AATAAATTTATTAATATAATTATCATAAAA
Found at i:415016 original size:19 final size:20
Alignment explanation
Indices: 414977--415020 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
414967 CATTGAGTCT
414977 ATAAATATTAAAAATATAAA
1 ATAAATATTAAAAATATAAA
* *
414997 ATAAGTATTATAAA-ATAAA
1 ATAAATATTAAAAATATAAA
415016 ATAAA
1 ATAAA
415021 ATCAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
ATAAATATTAAAAATATAAA
Found at i:417710 original size:23 final size:22
Alignment explanation
Indices: 417652--417710 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
417642 AATCAACATA
*
417652 AGGGGTATCGGTACCTTTGGGAT
1 AGGGGTATC-GTACCTTTGGCAT
*
417675 A--GGTATCGATACCTCTTTGCAT
1 AGGGGTATCG-TACCT-TTGGCAT
417697 AGGGGTATCGTACC
1 AGGGGTATCGTACC
417711 CTATGGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 1 0.03
21 11 0.37
22 6 0.20
23 5 0.17
24 7 0.23
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.31
Consensus pattern (22 bp):
AGGGGTATCGTACCTTTGGCAT
Found at i:418120 original size:54 final size:54
Alignment explanation
Indices: 418061--418164 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
418051 CATTTTAGAA
418061 AATTTTAAGATTTTCTTTTGAAAAAA-CATATTTGAAAAATTTACTCCCACACCC
1 AATTTTAAGATTTTCTTTTGAAAAAATCAT-TTTGAAAAATTTACTCCCACACCC
418115 AATTTTAAGATTTTCTTTTGAAAAAATCATTTTGAAAAATTTACTCCCAC
1 AATTTTAAGATTTTCTTTTGAAAAAATCATTTTGAAAAATTTACTCCCAC
418165 TCCCCCATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 46 0.94
55 3 0.06
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.39
Consensus pattern (54 bp):
AATTTTAAGATTTTCTTTTGAAAAAATCATTTTGAAAAATTTACTCCCACACCC
Found at i:425933 original size:35 final size:37
Alignment explanation
Indices: 425862--425934 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
425852 GTTGGAAAAT
* *
425862 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
*
425899 ATTTATATAATTT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAAATT-AAAATCATAAA
425934 A
1 A
425935 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 13 0.41
36 7 0.22
37 12 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
Found at i:427471 original size:21 final size:22
Alignment explanation
Indices: 427445--427490 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
427435 TCAACATAAG
427445 AGGTATCGGTACCT-TTGGGAT
1 AGGTATCGGTACCTCTTGGGAT
*
427466 AGGTATCGGTACCTCTTTGGAT
1 AGGTATCGGTACCTCTTGGGAT
427488 AGG
1 AGG
427491 GGTATCAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (22 bp):
AGGTATCGGTACCTCTTGGGAT
Found at i:431370 original size:90 final size:88
Alignment explanation
Indices: 431218--431387 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 88
431208 ACACACCCTT
*
431218 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTAAAATTAATTAAATCTATATTTA
*
431283 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
*
431307 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTAAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTAAAATTAATTAAATCTATATTT
431372 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
431388 ATATTCGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 37 0.48
90 40 0.52
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTAAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:434295 original size:16 final size:15
Alignment explanation
Indices: 434258--434289 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
434248 TTTTTTACTG
*
434258 AACTCGATTCGAAAA
1 AACTCGACTCGAAAA
434273 AACTCGACTCGAAAA
1 AACTCGACTCGAAAA
434288 AA
1 AA
434290 TTTCGAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (15 bp):
AACTCGACTCGAAAA
Found at i:435137 original size:16 final size:16
Alignment explanation
Indices: 435116--435146 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
435106 TTACCGGATT
435116 AAAAACAGGTTTTTTA
1 AAAAACAGGTTTTTTA
*
435132 AAAAACCGGTTTTTT
1 AAAAACAGGTTTTTT
435147 TCAAACCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (16 bp):
AAAAACAGGTTTTTTA
Found at i:435454 original size:16 final size:16
Alignment explanation
Indices: 435424--435454 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
435414 ATGAAGCTTA
*
435424 GCTCGAACTCGAAAAG
1 GCTCGAACTCAAAAAG
435440 GCTCGAACTCAAAAA
1 GCTCGAACTCAAAAA
435455 TTTCAGGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (16 bp):
GCTCGAACTCAAAAAG
Found at i:435761 original size:37 final size:36
Alignment explanation
Indices: 435702--435775 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
435692 AAAGTTTACG
* *
435702 AAATATGATAACACATCTAAATTTATAAAAAGATGAC
1 AAATATGACAACACATCCAAATTTAT-AAAAGATGAC
* *
435739 AAATATGACAACATATCCAAATTTATACAAGATGAC
1 AAATATGACAACACATCCAAATTTATAAAAGATGAC
435775 A
1 A
435776 CTATTTTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.26
Consensus pattern (36 bp):
AAATATGACAACACATCCAAATTTATAAAAGATGAC
Found at i:439637 original size:14 final size:14
Alignment explanation
Indices: 439618--439647 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
439608 TATCAAATTA
*
439618 ATCATTTATATTTT
1 ATCATTTAAATTTT
439632 ATCATTTAAATTTT
1 ATCATTTAAATTTT
439646 AT
1 AT
439648 TTAAAAATTT
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:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
ATCATTTAAATTTT
Found at i:446241 original size:14 final size:15
Alignment explanation
Indices: 446215--446291 Score: 68
Period size: 14 Copynumber: 5.1 Consensus size: 15
446205 ACTGCACAAA
446215 AAAAT-TAATTAAAT
1 AAAATATAATTAAAT
* *
446229 AAAATATTATAAAAT
1 AAAATATAATTAAAT
446244 AAAA-ATAATTAAAT
1 AAAATATAATTAAAT
**
446258 AAAATACTAACAAAAT
1 AAAATA-TAATTAAAT
*
446274 ATTAAATATAATAAAAT
1 A--AAATATAATTAAAT
446291 A
1 A
446292 TACCTTAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
14 17 0.33
15 12 0.24
16 8 0.16
17 9 0.18
18 5 0.10
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATATAATTAAAT
Found at i:446285 original size:33 final size:30
Alignment explanation
Indices: 446215--446291 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
446205 ACTGCACAAA
* *
446215 AAAAT-TAATTAAATAAAATATTATAAAAT
1 AAAATATAATTAAATAAAATATAACAAAAT
446244 AAAA-ATAATTAAATAAAATACTAACAAAAT
1 AAAATATAATTAAATAAAATA-TAACAAAAT
*
446274 ATTAAATATAATAAAATA
1 A--AAATATAATTAAATA
446292 TACCTTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 19 0.47
30 8 0.20
32 3 0.08
33 10 0.25
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (30 bp):
AAAATATAATTAAATAAAATATAACAAAAT
Found at i:451786 original size:36 final size:36
Alignment explanation
Indices: 451734--451812 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
451724 ATGAGCTTCT
* *
451734 ATCAACAACTCATTCTTCAATTTCTCATCATCTAGA
1 ATCACCAACTCATTCTTCAATTTCTCATAATCTAGA
*
451770 ATCACCAACTCATTCTTCAATTTCTCATAATCTGGA
1 ATCACCAACTCATTCTTCAATTTCTCATAATCTAGA
451806 ATCACCA
1 ATCACCA
451813 GTCTCCATCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (36 bp):
ATCACCAACTCATTCTTCAATTTCTCATAATCTAGA
Found at i:461071 original size:32 final size:32
Alignment explanation
Indices: 461028--461107 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 32
461018 AACATAGTAA
* *
461028 ATTTAGTCAAAATAAAAATTTATGTCAAATTT
1 ATTTAGTCAAAATAAAAAATTATGACAAATTT
* * *
461060 ATTTTGTCAAAACAAAAAAATTCTGACAAATTT
1 ATTTAGTCAAAA-TAAAAAATTATGACAAATTT
*
461093 ATTTAATCAAAATAA
1 ATTTAGTCAAAATAA
461108 TATTTTATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 13 0.33
33 26 0.67
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (32 bp):
ATTTAGTCAAAATAAAAAATTATGACAAATTT
Found at i:461268 original size:88 final size:88
Alignment explanation
Indices: 461114--461289 Score: 280
Period size: 88 Copynumber: 2.0 Consensus size: 88
461104 ATAATATTTT
* *
461114 ATAACAAATATTAATTTCTTATCATAAAAAATTATGACAAGTAATATTCTTTCACAATAACAAAT
1 ATAACAAATATTAATTTCTCATCATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAAT
*
461179 TGCAACAAAATGATTTAGTCACA
66 TGCAACAAAATGATTTAGCCACA
* *
461202 ATAACAAATATTAATTTCTCATTATAAAAAATTGTGACAAATAATATTCTTTCACAATAACAAAT
1 ATAACAAATATTAATTTCTCATCATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAAT
* * *
461267 TGTAATAAAATTATTTAGCCACA
66 TGCAACAAAATGATTTAGCCACA
461290 GTAAAAAAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (88 bp):
ATAACAAATATTAATTTCTCATCATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAAT
TGCAACAAAATGATTTAGCCACA
Found at i:461283 original size:186 final size:186
Alignment explanation
Indices: 460899--461283 Score: 429
Period size: 186 Copynumber: 2.1 Consensus size: 186
460889 ACAACTTTTG
* * * *
460899 ACAAATTTATTTAGTCAGAATAACAATTTATAATAAATATTAATTCCTCAATATAAAAAATTATG
1 ACAAAATTATTTAATCAAAATAACAATTTATAACAAATATTAATTCCTCAATATAAAAAATTATG
* * * *
460964 ACAAATAATATTATTTCACAATAACAAATTGTAACAAATTTATTTAGTTACAATAACATAGTAAA
66 ACAAATAATATTATTTCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAACATAGTAAA
* * * * *
461029 TTTAGTCAAAATAAAAATTTATGTCAAATTTATTTTGTCAAAACAAAAAAATTCTG
131 TTTACTCAAAATAAAAAATTATGACAAATATATTTTGTCAAAACAAAAAAATTCTA
* * * * *
461085 ACAAATTTATTTAATCAAAATAATATTTTATAACAAATATTAATTTCT-TATCATAAAAAATTAT
1 ACAAAATTATTTAATCAAAATAACAATTTATAACAAATATTAATTCCTCAAT-ATAAAAAATTAT
* *
461149 GACAAGTAATATTCTTTCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAACAAATA-T
65 GACAAATAATATTATTTCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAAC--ATAGT
* ** * * * * *
461213 TAATTT-CTCATTATAAAAAATTGTGACAAATAATATTCTT-TCACAA-TAACAAATTGTA
128 AAATTTACTCAAAATAAAAAATTATGACAAAT-ATATT-TTGTCAAAACAAAAAAATTCTA
*
461271 ATAAAATTATTTA
1 ACAAAATTATTTA
461284 GCCACAGTAA
Statistics
Matches: 166, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
185 2 0.01
186 144 0.87
187 15 0.09
188 5 0.03
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (186 bp):
ACAAAATTATTTAATCAAAATAACAATTTATAACAAATATTAATTCCTCAATATAAAAAATTATG
ACAAATAATATTATTTCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAACATAGTAAA
TTTACTCAAAATAAAAAATTATGACAAATATATTTTGTCAAAACAAAAAAATTCTA
Found at i:469816 original size:20 final size:21
Alignment explanation
Indices: 469764--469817 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
469754 AAAAAATACT
469764 TGAGTATCGATACTGACCCTC
1 TGAGTATCGATACTGACCCTC
* *
469785 TAAGTATTGATACTGGACCC-C
1 TGAGTATCGATACT-GACCCTC
469806 -GAGTATCGATAC
1 TGAGTATCGATAC
469818 CCATTCATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (21 bp):
TGAGTATCGATACTGACCCTC
Found at i:477701 original size:21 final size:20
Alignment explanation
Indices: 477669--477720 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
477659 AAAATACTAT
*
477669 AGTATCGTTACTA-ACCCTCTG
1 AGTATCGATACTAGACCC-C-G
*
477690 AGTATTGATACTAGACCCCG
1 AGTATCGATACTAGACCCCG
477710 AGTATCGATAC
1 AGTATCGATAC
477721 CCACATAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 12 0.44
22 4 0.15
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTAGACCCCG
Found at i:485246 original size:18 final size:19
Alignment explanation
Indices: 485225--485260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
485215 AGAACCCCAG
485225 GGGGT-ATCGATTCCCCTA
1 GGGGTAATCGATTCCCCTA
*
485243 GGGGTAATCGGTTCCCCT
1 GGGGTAATCGATTCCCCT
485261 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (19 bp):
GGGGTAATCGATTCCCCTA
Found at i:485274 original size:23 final size:22
Alignment explanation
Indices: 485242--485291 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
485232 CGATTCCCCT
*
485242 AGGGGTAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTC-A
485265 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTCA
485287 AGGGG
1 AGGGG
485292 TATCGATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.20, C:0.24, G:0.34, T:0.22
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTCA
Found at i:492515 original size:29 final size:28
Alignment explanation
Indices: 492483--492560 Score: 111
Period size: 29 Copynumber: 2.8 Consensus size: 28
492473 CAAGATGGGG
* *
492483 ATATAATCTCATGCAGAATCAGGATAAGA
1 ATATAATCCCATGCAGAATCAGGACAA-A
*
492512 ATATAATCCCATGCAGAATAAGGACAAA
1 ATATAATCCCATGCAGAATCAGGACAAA
*
492540 ATATAATCCCATGCAAAATCA
1 ATATAATCCCATGCAGAATCA
492561 AACCAGGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 20 0.45
29 24 0.55
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (28 bp):
ATATAATCCCATGCAGAATCAGGACAAA
Found at i:493130 original size:6 final size:6
Alignment explanation
Indices: 493114--493148 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
493104 CAAAAAAATA
*
493114 TCAACAG TCAAAG TCAAAG TCAAAG TCAAAT TCAA
1 TCAA-AG TCAAAG TCAAAG TCAAAG TCAAAG TCAA
493149 TAGTTAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (6 bp):
TCAAAG
Found at i:493716 original size:25 final size:25
Alignment explanation
Indices: 493688--493738 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
493678 TACGATCACT
493688 CCATAGAACCATAACTATCATAATA
1 CCATAGAACCATAACTATCATAATA
*
493713 CCATAGAACCTTAACTATCATAATA
1 CCATAGAACCATAACTATCATAATA
493738 C
1 C
493739 GTTGGCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.25
Consensus pattern (25 bp):
CCATAGAACCATAACTATCATAATA
Found at i:505258 original size:12 final size:12
Alignment explanation
Indices: 505241--505265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
505231 CACCATAGTA
505241 AGTTTCCATTTT
1 AGTTTCCATTTT
505253 AGTTTCCATTTT
1 AGTTTCCATTTT
505265 A
1 A
505266 TTTTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (12 bp):
AGTTTCCATTTT
Found at i:506155 original size:22 final size:22
Alignment explanation
Indices: 506130--506177 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
506120 GGACATTCAC
* *
506130 ATAAAACAAAATAAATTGTTAT
1 ATAAAACAAAATAAATCGTTAA
*
506152 ATAAAACAAATTAAATCGTTAA
1 ATAAAACAAAATAAATCGTTAA
506174 ATAA
1 ATAA
506178 TATCAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (22 bp):
ATAAAACAAAATAAATCGTTAA
Found at i:507671 original size:37 final size:37
Alignment explanation
Indices: 507621--507694 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
507611 ATAGCTAGAA
507621 AGTAGAAGCCAACCCCCTGTTACAATTCTTTTCCCCC
1 AGTAGAAGCCAACCCCCTGTTACAATTCTTTTCCCCC
*
507658 AGTAGGAGCCAACCCCCTGTTACAATTCTTTTCCCCC
1 AGTAGAAGCCAACCCCCTGTTACAATTCTTTTCCCCC
507695 CCTTCTGTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.38, G:0.12, T:0.27
Consensus pattern (37 bp):
AGTAGAAGCCAACCCCCTGTTACAATTCTTTTCCCCC
Found at i:508185 original size:3 final size:3
Alignment explanation
Indices: 508177--508229 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
508167 CCTGCAAATG
* * *
508177 TAA TAA TAA TAA TAT TAA TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
508225 TAA TA
1 TAA TA
508230 TAAACTCGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:508681 original size:117 final size:118
Alignment explanation
Indices: 508469--508795 Score: 376
Period size: 117 Copynumber: 2.8 Consensus size: 118
508459 TACAGATGCA
* * * *
508469 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCATCTTTGGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
* * * * *
508534 GAACTCTCCACTGTAAATGTTGATCCACCTC-CT-TATGTGATGGAATCG-AATC
66 GAACTCTCCACTGAAAATATTGATCCACCTCAATCTACG-G-TGGAATCGAAACC
* * ** *
508586 AAGG-TGTAACAAGTTCTTCTCATTATGAACTTATCCACCCTCATTGGACGAGTTCTTCTCATTA
1 AAGGTTG-AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * * *
508650 TGAACTCTCCATTGAAAATATTGAGT-TACCTCAATCTACGGTGGACTTGAAACC
65 TGAACTCTCCACTGAAAATATTGA-TCCACCTCAATCTACGGTGGAATCGAAACC
* *
508704 AAGGTTGAACAAGTTCTTTTCATTATGAATTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
* **
508769 GAACTCTCCACTGGAAATGCTGATCCA
66 GAACTCTCCACTGAAAATATTGATCCA
508796 TCTCCTTCTG
Statistics
Matches: 173, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
116 2 0.01
117 85 0.49
118 81 0.47
119 5 0.03
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (118 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGAAAATATTGATCCACCTCAATCTACGGTGGAATCGAAACC
Found at i:508818 original size:118 final size:117
Alignment explanation
Indices: 508469--508819 Score: 386
Period size: 118 Copynumber: 3.0 Consensus size: 117
508459 TACAGATGCA
* * *
508469 AAGGTTGAACAAGTT-TTTCTCATTATGAACTTCTTCTTCATCTTTGGATGAGTTATTCTCATTA
1 AAGGTTGAACAAGTTCTTT-TCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * * * *
508533 TGAACTCTCCACTGTAAATGTTGATCCACCTCCTTATGTGATGGAATCG-AATC
65 TGAACTCTCCACTGAAAATGTTGATCCACCTCCTTCTGTGGT-GAATTGAAACC
* * * ** *
508586 AAGG-TGTAACAAGTTCTTCTCATTATGAACTTATCCACCCTCATTGGACGAGTTCTTCTCATTA
1 AAGGTTG-AACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * * ** ** *
508650 TGAACTCTCCATTGAAAATATTGAGT-TACCTCAATCTACGGTGGACTTGAAACC
65 TGAACTCTCCACTGAAAATGTTGA-TCCACCTCCTTCTGTGGT-GAATTGAAACC
*
508704 AAGGTTGAACAAGTTCTTTTCATTATGAATTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
* * *
508769 GAACTCTCCACTGGAAATGCTGATCCATCTCCTTCTGTGGTGAATTTGAAA
66 GAACTCTCCACTGAAAATGTTGATCCACCTCCTTCTGTGGTGAA-TTGAAA
508820 GGAACAAGTT
Statistics
Matches: 187, Mismatches: 40, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
116 2 0.01
117 87 0.47
118 96 0.51
119 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (117 bp):
AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGAAAATGTTGATCCACCTCCTTCTGTGGTGAATTGAAACC
Found at i:509058 original size:136 final size:136
Alignment explanation
Indices: 508821--509348 Score: 748
Period size: 136 Copynumber: 3.9 Consensus size: 136
508811 AATTTGAAAG
* * *
508821 GAACAAGTTCTTCTCATTATAAAC-T-TTCT-CCT-T-TAGGACGAGTTATTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
* * * * *
508881 CT--TTTGGAAATGTCAATCCCTCAAGCGATGTATCACTGATTTAAAATGTCGTGAATCGAGTGA
66 CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTATCACTGATTCAAAATATCATGAATCGAGTGA
508944 TAGGTC
131 TAGGTC
* *
508950 GAACAAGCTCTTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGACTTATTCTCATTATGAACC
1 GAACAAGCTCTTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
* * ** *
509015 CTTAATTGGAAATATCAATCCCTCAAGCGAGGTATCACTGATTTGAAAT-TCCGTGAATCGAGTG
66 CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTATCACTGATTCAAAATAT-CATGAATCGAGTG
509079 ATAGGTC
130 ATAGGTC
* * * * *
509086 AAACAAGCTCTTCTCATTATGAATTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
* * * * *
509151 CTCAATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTCAAAATACCACGAATCAAGTGA
66 CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTATCACTGATTCAAAATATCATGAATCGAGTGA
509216 TAGGTC
131 TAGGTC
*
509222 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
*
509287 CTCAATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCAAAATATCATGAATCGAG
66 CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTATCACTGATTCAAAATATCATGAATCGAG
509349 CAACGGAAAT
Statistics
Matches: 354, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
129 23 0.06
130 1 0.00
131 4 0.01
132 3 0.01
133 1 0.00
134 25 0.07
135 1 0.00
136 296 0.84
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTATCACTGATTCAAAATATCATGAATCGAGTGA
TAGGTC
Found at i:509449 original size:42 final size:42
Alignment explanation
Indices: 509389--509512 Score: 214
Period size: 42 Copynumber: 3.0 Consensus size: 42
509379 AAAGTATTAT
* *
509389 CATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAAG
*
509431 CATCATGCTCAAAAGACTTACTGATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAAG
509473 CATCATGCTCGAAAGACTTACTGATGA-CCGAAGGATTTAA
1 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAA
509513 AAATCAAGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 13 0.17
42 65 0.83
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAAG
Found at i:509656 original size:90 final size:90
Alignment explanation
Indices: 509503--509695 Score: 298
Period size: 90 Copynumber: 2.1 Consensus size: 90
509493 CTGATGACCG
* * * * *
509503 AAGGATTTAAAAATCAAGAAATCTCTAAAGGCTTAAGTTTTAAAATCTCATTTGAAAACATCCTG
1 AAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAAGTTTTAAAATCTCATTTGAAAACATCCTG
*
509568 CACTGAAGGTCTTATGGATGGTCCA
66 CACTGAAGGTCTTATGGATGGCCCA
509593 AAGGACTTACAAATCAAGAAACCCCCAAAGGCTT-AGTTTCTAAAATCTCATTTGAAAACATCCT
1 AAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAAGTTT-TAAAATCTCATTTGAAAACATCCT
*
509657 GCACTGAAGGTCTTATGGATGGCCCG
65 GCACTGAAGGTCTTATGGATGGCCCA
*
509683 AAGAACTTACAAA
1 AAGGACTTACAAA
509696 CCCTTGAAGG
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 5 0.05
90 89 0.95
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (90 bp):
AAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAAGTTTTAAAATCTCATTTGAAAACATCCTG
CACTGAAGGTCTTATGGATGGCCCA
Found at i:518409 original size:59 final size:62
Alignment explanation
Indices: 518320--518434 Score: 209
Period size: 59 Copynumber: 1.9 Consensus size: 62
518310 TAAATTTGGA
518320 AAATAACTAAATCAAGACAAACATAAAAGGCTAAATTAAAAATCATACCCTATATATAGCCG
1 AAATAACTAAATCAAGACAAACATAAAAGGCTAAATTAAAAATCATACCCTATATATAGCCG
518382 AAATAACT-AATCAAGAC-AACAT-AAAGGCTAAATTAAAAATCATACCCTATATA
1 AAATAACTAAATCAAGACAAACATAAAAGGCTAAATTAAAAATCATACCCTATATA
518435 GCCGTTTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
59 31 0.58
60 5 0.09
61 9 0.17
62 8 0.15
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.22
Consensus pattern (62 bp):
AAATAACTAAATCAAGACAAACATAAAAGGCTAAATTAAAAATCATACCCTATATATAGCCG
Found at i:518422 original size:29 final size:29
Alignment explanation
Indices: 518328--518423 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
518318 GAAAATAACT
518328 AAATCAAGACAAACATAAAAGGCTAAATTAA
1 AAATCAAGAC-AACAT-AAAGGCTAAATTAA
** * * * * *
518359 AAATCATACCCTATATATAGCCGAAA-TAA
1 AAATCA-AGACAACATAAAGGCTAAATTAA
*
518388 CTAATCAAGACAACATAAAGGCTAAATTAA
1 -AAATCAAGACAACATAAAGGCTAAATTAA
518418 AAATCA
1 AAATCA
518424 TACCCTATAT
Statistics
Matches: 46, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
29 20 0.43
30 15 0.33
31 9 0.20
32 2 0.04
ACGTcount: A:0.55, C:0.17, G:0.08, T:0.20
Consensus pattern (29 bp):
AAATCAAGACAACATAAAGGCTAAATTAA
Found at i:519421 original size:3 final size:3
Alignment explanation
Indices: 519413--519459 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
519403 CCTGTAAATG
* *
519413 TAA TAA TAA TAA TAT TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
519460 TAAACCCGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:522482 original size:29 final size:29
Alignment explanation
Indices: 522449--522534 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
522439 TAGGATGAGG
*
522449 ATATAATCTCATGAAGAATCAGGACATGT
1 ATATAATCTCATGAAGAATCAGGACATGA
* * *
522478 ATATAATCTCATGTAGAATCAAGACGTGA
1 ATATAATCTCATGAAGAATCAGGACATGA
*
522507 ATATAATCCCAT-ACAGAATCAGGACATG
1 ATATAATCTCATGA-AGAATCAGGACATG
522535 GATTACCTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (29 bp):
ATATAATCTCATGAAGAATCAGGACATGA
Found at i:522679 original size:41 final size:41
Alignment explanation
Indices: 522534--522667 Score: 205
Period size: 41 Copynumber: 3.3 Consensus size: 41
522524 ATCAGGACAT
* * * *
522534 GGATTACCTTCCATAGAGTATCCCATGTAGAAATAGGATGG
1 GGATTGCCATCCACAGAGTATCCCATGCAGAAATAGGATGG
*
522575 GGATTGCCATCCACAGAGTATCCCATGCAGAAATAGGACGG
1 GGATTGCCATCCACAGAGTATCCCATGCAGAAATAGGATGG
*
522616 GGATTGCCATCCACAGTGTATCCCATGCAGAAATAGGATGG
1 GGATTGCCATCCACAGAGTATCCCATGCAGAAATAGGATGG
*
522657 GGATTACCATC
1 GGATTGCCATC
522668 TGTAGAATAT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (41 bp):
GGATTGCCATCCACAGAGTATCCCATGCAGAAATAGGATGG
Found at i:530595 original size:29 final size:29
Alignment explanation
Indices: 530522--530585 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
530512 AATTTGGTGA
*
530522 GCTAAAAGAATTAGTGACAACCAGAAAAT
1 GCTAATAGAATTAGTGACAACCAGAAAAT
* *
530551 GCTAATAGAATTAGTGACAAGCTGAAAAT
1 GCTAATAGAATTAGTGACAACCAGAAAAT
530580 GCTAAT
1 GCTAAT
530586 TGATGTAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (29 bp):
GCTAATAGAATTAGTGACAACCAGAAAAT
Found at i:531476 original size:17 final size:17
Alignment explanation
Indices: 531451--531509 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
531441 ATTAGACTAG
*
531451 CACTAAGTGTATAAGGA
1 CACTTAGTGTATAAGGA
* *
531468 CACTTAGTGCATATGG-
1 CACTTAGTGTATAAGGA
* *
531484 TACTATAGTGTGTAAGGA
1 CACT-TAGTGTATAAGGA
531502 CACTTAGT
1 CACTTAGT
531510 ATAACACTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 3 0.09
17 26 0.81
18 3 0.09
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (17 bp):
CACTTAGTGTATAAGGA
Found at i:534810 original size:45 final size:45
Alignment explanation
Indices: 534724--535193 Score: 660
Period size: 45 Copynumber: 10.4 Consensus size: 45
534714 TTCATATTTG
*
534724 TAATGCA-CCATTATGCATTTTAAACTATAGCATACTTTTCTGTTGA
1 TAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTTCTGTTGA
*
534770 TAATGCACCCATATGCATTTTAACTATAGCATACTTTTCTGTTGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
** * *
534815 TAATGCACCCATATGCATTTCAGTTATCGCTTACTTTTAC-GTTGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTT-CTGTTGA
*
534860 TAATGCACCCATATCCATTTCAACTATAGCATACTTTTCTGTTGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* *
534905 TAATGCACCCATATGCATTCCAACTATAGCATACTTTTATGTTGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
*
534950 TAATGCACCCATATGCATTTCAACTATAACATACTTTTCTGTTGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
534995 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* * * *
535040 AAATGCACCCATATGTATTTCAACTATCA-CATATTTTTATGTTGA
1 TAATGCACCCATATGCATTTCAACTAT-AGCATACTTTTCTGTTGA
* * *
535085 TAATGCACCCATATGCATTTAAATTATAGCATAATTTTCTGTTGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* * * * **
535130 TAATGCACCCATATGTATTTCAACTGTGGCAT-CCTTTCATGCCGA
1 TAATGCACCCATATGCATTTCAACTATAGCATACTTTTC-TGTTGA
535175 TAATGCACCCATATGCATT
1 TAATGCACCCATATGCATT
535194 ATTATTTTTC
Statistics
Matches: 380, Mismatches: 38, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
44 6 0.02
45 356 0.94
46 15 0.04
47 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (45 bp):
TAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
Found at i:541285 original size:45 final size:44
Alignment explanation
Indices: 541243--541797 Score: 663
Period size: 45 Copynumber: 12.4 Consensus size: 44
541233 TTCATGTTTG
*
541243 TAATGCA-CATTATGCATTTTCAACTATAGCATACTTTTATGTTGA
1 TAATGCACCA-TATGCA-TTTCAACTATAGCATACTTTTCTGTTGA
*
541288 TAATGCACCCATATGCGTTTCAACTATAGCATACTTTTCTGTTGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* *
541333 TAATGCACCCATATGCATTTCAACTATCGCATACTTTTATGTTGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* *
541378 TAATTCACCCATATGCATTTCAAGTATAGCATA-TTTTCCTGTTGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTT-CTGTTGA
*
541423 TAATGCAACCATATGCATTTCAACTATAGCATA-TTTCTCTATTGA
1 TAATGC-ACCATATGCATTTCAACTATAGCATACTTT-TCTGTTGA
* * *
541468 TAATGTACCCATATGCATTTCAACTATCGCATACTTTTATGTTGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* * *
541513 TAATGCACCCATATGTATTTCAACTATAACATACTTTTCTATTGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* *
541558 TAATGCACCCATATGCATTTCAATTGTAGCATACTTTTCTGTTGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* **
541603 TAATGCACCCATATGCATTTCAACTGTAGCAT--TTTTCTAATGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* *
541646 TAATGCACCCATATGCATTTCAACTATCGCATACTTTTATGTTGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* *
541691 TAATGCATCCATATGCATTTCAACTATATCATACTTTTCTGTTAA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
* * * * * **
541736 TACTGCACCCATATGCATTTCAACTGTGGCAT-CATTTCAGCCGA
1 TAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
*
541780 TAATGCATCATATGCATT
1 TAATGCACCATATGCATT
541798 ATTATTTTCA
Statistics
Matches: 449, Mismatches: 52, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
43 49 0.11
44 18 0.04
45 370 0.82
46 10 0.02
47 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (44 bp):
TAATGCACCATATGCATTTCAACTATAGCATACTTTTCTGTTGA
Found at i:541368 original size:90 final size:90
Alignment explanation
Indices: 541253--541760 Score: 736
Period size: 90 Copynumber: 5.7 Consensus size: 90
541243 TAATGCACAT
* * *
541253 TATGCATTTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATGCGTTTCAACTATAGC
1 TATGCA-TTTCAACTATAGCATACTTTTCTATTGATAATGCACCCATATGCATTTCAACTATAGC
541318 ATACTTTTCTGTTGATAATGCACCCA
65 ATACTTTTCTGTTGATAATGCACCCA
* * * * *
541344 TATGCATTTCAACTATCGCATACTTTTATGTTGATAATTCACCCATATGCATTTCAAGTATAGCA
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATGCACCCATATGCATTTCAACTATAGCA
*
541409 TA-TTTTCCTGTTGATAATGCAACCA
66 TACTTTT-CTGTTGATAATGCACCCA
* *
541434 TATGCATTTCAACTATAGCATA-TTTCTCTATTGATAATGTACCCATATGCATTTCAACTATCGC
1 TATGCATTTCAACTATAGCATACTTT-TCTATTGATAATGCACCCATATGCATTTCAACTATAGC
*
541498 ATACTTTTATGTTGATAATGCACCCA
65 ATACTTTTCTGTTGATAATGCACCCA
* * * *
541524 TATGTATTTCAACTATAACATACTTTTCTATTGATAATGCACCCATATGCATTTCAATTGTAGCA
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATGCACCCATATGCATTTCAACTATAGCA
541589 TACTTTTCTGTTGATAATGCACCCA
66 TACTTTTCTGTTGATAATGCACCCA
* * *
541614 TATGCATTTCAACTGTAGCAT--TTTTCTAATGATAATGCACCCATATGCATTTCAACTATCGCA
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATGCACCCATATGCATTTCAACTATAGCA
* *
541677 TACTTTTATGTTGATAATGCATCCA
66 TACTTTTCTGTTGATAATGCACCCA
* * * *
541702 TATGCATTTCAACTATATCATACTTTTCTGTTAATACTGCACCCATATGCATTTCAACT
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATGCACCCATATGCATTTCAACT
541761 GTGGCATCAT
Statistics
Matches: 375, Mismatches: 36, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
88 80 0.21
89 7 0.02
90 275 0.73
91 13 0.03
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (90 bp):
TATGCATTTCAACTATAGCATACTTTTCTATTGATAATGCACCCATATGCATTTCAACTATAGCA
TACTTTTCTGTTGATAATGCACCCA
Found at i:541468 original size:135 final size:135
Alignment explanation
Indices: 541253--541760 Score: 754
Period size: 135 Copynumber: 3.8 Consensus size: 135
541243 TAATGCACAT
*
541253 TATGCATTTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATGCGTTTCAACTATAGC
1 TATGCA-TTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGC
*
541318 ATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATCGCATACTTTTATGTTGATAATT
65 ATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATCGCATACTTTTATGTTGATAATG
541383 CACCCA
130 CACCCA
* * *
541389 TATGCATTTCAAGTATAGCATA-TTTTCCTGTTGATAATGCAACCATATGCATTTCAACTATAGC
1 TATGCATTTCAACTATAGCATACTTTT-ATGTTGATAATGCACCCATATGCATTTCAACTATAGC
* *
541453 ATA-TTTCTCTATTGATAATGTACCCATATGCATTTCAACTATCGCATACTTTTATGTTGATAAT
65 ATACTTT-TCTGTTGATAATGCACCCATATGCATTTCAACTATCGCATACTTTTATGTTGATAAT
541517 GCACCCA
129 GCACCCA
* * * * * *
541524 TATGTATTTCAACTATAACATACTTTTCTATTGATAATGCACCCATATGCATTTCAATTGTAGCA
1 TATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCA
* * * **
541589 TACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTGTAGCAT--TTTTCTAATGATAATGC
66 TACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATCGCATACTTTTATGTTGATAATGC
541652 ACCCA
131 ACCCA
* * *
541657 TATGCATTTCAACTATCGCATACTTTTATGTTGATAATGCATCCATATGCATTTCAACTATATCA
1 TATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCA
* *
541722 TACTTTTCTGTTAATACTGCACCCATATGCATTTCAACT
66 TACTTTTCTGTTGATAATGCACCCATATGCATTTCAACT
541761 GTGGCATCAT
Statistics
Matches: 336, Mismatches: 32, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
133 112 0.33
134 7 0.02
135 204 0.61
136 13 0.04
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (135 bp):
TATGCATTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCA
TACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATCGCATACTTTTATGTTGATAATGC
ACCCA
Found at i:559240 original size:18 final size:18
Alignment explanation
Indices: 559217--559259 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
559207 CTTTAGATTA
*
559217 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
559235 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
559253 TTTATTT
1 TTTATTT
559260 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:559475 original size:12 final size:11
Alignment explanation
Indices: 559453--559537 Score: 73
Period size: 12 Copynumber: 7.0 Consensus size: 11
559443 ATACCCCCAA
559453 ATTTTTATTTT
1 ATTTTTATTTT
559464 ATTTTATATTTTT
1 ATTTT-TA-TTTT
*
559477 AATTTTATTTT
1 ATTTTTATTTT
559488 CCCACTTATTT-TTTT
1 ---A-TT-TTTATTTT
559503 ATTTTTATTTTT
1 ATTTTTA-TTTT
559515 ATTTTTATTTTT
1 ATTTTTA-TTTT
559527 ATTTTTATTTT
1 ATTTTTATTTT
559538 CTCTTTAAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
10 3 0.05
11 15 0.24
12 28 0.44
13 8 0.13
14 1 0.02
15 5 0.08
16 3 0.05
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:559509 original size:6 final size:6
Alignment explanation
Indices: 559498--559537 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
559488 CCCACTTATT
559498 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
559538 CTCTTTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:559569 original size:18 final size:17
Alignment explanation
Indices: 559493--559571 Score: 70
Period size: 18 Copynumber: 4.5 Consensus size: 17
559483 ATTTTCCCAC
559493 TTATTTTTTTATTTTTA
1 TTATTTTTTTATTTTTA
*
559510 TTTTTATTTTTATTTTTA
1 TTATT-TTTTTATTTTTA
* *
559528 TT-TTTATTTTCTCTTTAA
1 TTATTT-TTTTAT-TTTTA
**
559546 ACATTTTTTTATATTTTA
1 TTATTTTTTTAT-TTTTA
559564 TTATTTTT
1 TTATTTTT
559572 CTTTTTTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
16 1 0.02
17 11 0.23
18 33 0.69
19 3 0.06
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTTTTATTTTTA
Found at i:567160 original size:123 final size:123
Alignment explanation
Indices: 566931--567160 Score: 320
Period size: 123 Copynumber: 1.9 Consensus size: 123
566921 AGAACCAATG
* * * * * *
566931 CAATTTTCAAGATTGGATTTCAACTTCACAGCGAAGGACATCCAATTCAAAGCTCAACTTCACAG
1 CAATTTACAAGATTGAATTTCAACTTCACAACGAAGCACATCAAATTCAAAGCTCAACTTCACAA
*
566996 CGAATGAGCCATCCATAATTGCAACTTCACAGCGAAAGATATTAATCTCAAAGTGATT
66 CGAATGAGCCATCCATAATTGCAACTTCACAACGAAAGATATTAATCTCAAAGTGATT
* *
567054 CAATTTACAAGATTGAATTTCAACTTCACAACGAAGCATATCAAATTTAAAGCTCAACTTCACAA
1 CAATTTACAAGATTGAATTTCAACTTCACAACGAAGCACATCAAATTCAAAGCTCAACTTCACAA
* * *
567119 CGAATGAGCCA-CC-TACGATTTCGACTTCACAACGAAGGATAT
66 CGAATGAGCCATCCATA--ATTGCAACTTCACAACGAAAGATAT
567161 CGTACCCAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
121 2 0.02
122 2 0.02
123 89 0.96
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (123 bp):
CAATTTACAAGATTGAATTTCAACTTCACAACGAAGCACATCAAATTCAAAGCTCAACTTCACAA
CGAATGAGCCATCCATAATTGCAACTTCACAACGAAAGATATTAATCTCAAAGTGATT
Found at i:568078 original size:85 final size:85
Alignment explanation
Indices: 567916--568078 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 85
567906 TTTTATCTTT
* **
567916 GTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTATGATATTATTTTAAATATTATT
1 GTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTAAAAATATTATTTTAAATATTATT
**
567981 TTATTTTATTTTTGTTTTAG
66 TTAGCTTATTTTTGTTTTAG
* * *
568001 GTATTTTAGTTTAAATA-ATTTTAAGTGTTTTAATTAGGA-TAAAAATATTATTTTAGAA-ATTA
1 GTATTTTAGTTTAAATAGATGTT-AGTATTTCAATTAGGATTAAAAATATTATTTTA-AATATTA
*
568063 TCTTTAGCTTGTTTTT
64 T-TTTAGCTTATTTTT
568079 AGGAATTTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
84 22 0.33
85 44 0.67
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (85 bp):
GTATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTAAAAATATTATTTTAAATATTATT
TTAGCTTATTTTTGTTTTAG
Found at i:568606 original size:18 final size:18
Alignment explanation
Indices: 568583--568625 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
568573 CTTTAGATTA
*
568583 TTTATTTAATAATTTTCT
1 TTTATTTAATAATTATCT
**
568601 TTTATTTAATTCTTATCT
1 TTTATTTAATAATTATCT
568619 TTTATTT
1 TTTATTT
568626 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATAATTATCT
Found at i:568840 original size:14 final size:13
Alignment explanation
Indices: 568818--568871 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 13
568808 ATACCCCCCA
568818 TTTTTATTTTATT
1 TTTTTATTTTATT
568831 TTTTTAATTTTATT
1 TTTTT-ATTTTATT
* *
568845 TTTTCACTTCT-TT
1 TTTTTA-TTTTATT
568858 TTTTT-TTTTATT
1 TTTTTATTTTATT
568870 TT
1 TT
568872 CTCTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 3 0.09
12 4 0.12
13 12 0.35
14 15 0.44
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:568959 original size:33 final size:34
Alignment explanation
Indices: 568858--568962 Score: 88
Period size: 40 Copynumber: 2.9 Consensus size: 34
568848 TCACTTCTTT
* * *
568858 TTTTTTTTTATTTTCTCTTTTAACATTTTTTATA
1 TTTTATTTTATTTTTTCTTTTAACATTTTTTACA
* *
568892 TTTTATTATTTTTCTTTTCTGAAATTTAATATTTTCTT-CA
1 TTTTATT-TTATT-TTTTCT----TTTAACATTTT-TTACA
568932 -TTTATTTTATTTTTTCTTTTAACATTTTTTA
1 TTTTATTTTATTTTTTCTTTTAACATTTTTTA
568963 TATAACATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
32 2 0.04
33 10 0.18
34 6 0.11
35 4 0.07
36 5 0.09
37 6 0.11
38 4 0.07
39 6 0.11
40 11 0.20
41 2 0.04
ACGTcount: A:0.20, C:0.09, G:0.01, T:0.70
Consensus pattern (34 bp):
TTTTATTTTATTTTTTCTTTTAACATTTTTTACA
Found at i:570485 original size:29 final size:31
Alignment explanation
Indices: 570428--570487 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
570418 CAATTTATGG
*
570428 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
570459 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
570488 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:570494 original size:31 final size:32
Alignment explanation
Indices: 570419--570495 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 32
570409 TCGATATAAC
*
570419 AATTTATGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAT--CAAAATGGTATTTGGACTTGAATTG
570453 AATTTA-CAAAAT-GTATTTGGACTT-AATTG
1 AATTTATCAAAATGGTATTTGGACTTGAATTG
570482 AATTTATTCAAAAT
1 AATTTA-TCAAAAT
570496 TTACAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 11 0.28
30 11 0.28
31 12 0.30
34 6 0.15
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (32 bp):
AATTTATCAAAATGGTATTTGGACTTGAATTG
Found at i:572100 original size:24 final size:24
Alignment explanation
Indices: 572067--572124 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
572057 AATACACTTA
*
572067 AACCTTATCTCAAGATATAGATAC
1 AACCTCATCTCAAGATATAGATAC
572091 AACCTCATCTCAAGATATAGATAC
1 AACCTCATCTCAAGATATAGATAC
*
572115 AACCCCATCT
1 AACCTCATCT
572125 TAATATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.26
Consensus pattern (24 bp):
AACCTCATCTCAAGATATAGATAC
Found at i:575732 original size:3 final size:3
Alignment explanation
Indices: 575691--575715 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
575681 TCTTAATTAT
575691 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
575716 CCCCTAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:576227 original size:45 final size:45
Alignment explanation
Indices: 576128--576245 Score: 119
Period size: 45 Copynumber: 2.5 Consensus size: 45
576118 TGAAAAGTTG
* * **
576128 ACTCCTCTCCACAAGAAAGTCAAGTTGAGAATGTCATCACTAAAATGTTA
1 ACTCCTCTCCACGAGAAAGTCAA--T-A-AA-GTCATCACCAAAAAATTA
* * *
576178 ACTCCTCTCCACGATAAATTCAATAAAGTCATCACCAAAAAATTG
1 ACTCCTCTCCACGAGAAAGTCAATAAAGTCATCACCAAAAAATTA
*
576223 ACTCCTCTTCACGAGAAAGTCAA
1 ACTCCTCTCCACGAGAAAGTCAA
576246 GAATGATATC
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
45 34 0.59
46 2 0.03
47 1 0.02
48 1 0.02
50 20 0.34
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (45 bp):
ACTCCTCTCCACGAGAAAGTCAATAAAGTCATCACCAAAAAATTA
Found at i:576257 original size:45 final size:45
Alignment explanation
Indices: 576208--576381 Score: 206
Period size: 45 Copynumber: 3.9 Consensus size: 45
576198 CAATAAAGTC
* * **
576208 ATCACCAAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGAT
1 ATCACTAAAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGAT
* *
576253 ATCACTGAAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGAC
1 ATCACTAAAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGAT
* * * *
576298 ATCACTAAAAGGTTGACTTCTCTT-TTGGAGAAAGTCAAGAATTAT
1 ATCACTAAAAGATTGACTCCTCTTCGT-GAGAAAGTCAAGAATGAT
* * * *
576343 ATTACTAAAAGGTTGATTCCTCTTCGTAAGAAAGTCAAG
1 ATCACTAAAAGATTGACTCCTCTTCGTGAGAAAGTCAAG
576382 TCGAGGTGTC
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.01
45 108 0.98
46 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (45 bp):
ATCACTAAAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGAT
Found at i:576301 original size:90 final size:90
Alignment explanation
Indices: 576207--576381 Score: 233
Period size: 90 Copynumber: 1.9 Consensus size: 90
576197 TCAATAAAGT
*
576207 CATCACCAAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGATATCACTGAAAGATTGACTC
1 CATCACCAAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGATATCACTAAAAGATTGACTC
*
576272 CTCTTCGTGAGAAAGTCAAGAATGA
66 CTCTTCGTAAGAAAGTCAAGAATGA
* ** * *** * * * *
576297 CATCACTAAAAGGTTGACTTCTCTTTTGGAGAAAGTCAAGAATTATATTACTAAAAGGTTGATTC
1 CATCACCAAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGATATCACTAAAAGATTGACTC
576362 CTCTTCGTAAGAAAGTCAAG
66 CTCTTCGTAAGAAAGTCAAG
576382 TCGAGGTGTC
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (90 bp):
CATCACCAAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGATATCACTAAAAGATTGACTC
CTCTTCGTAAGAAAGTCAAGAATGA
Found at i:576483 original size:36 final size:36
Alignment explanation
Indices: 576423--576502 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
576413 GACTAAATTG
* * *
576423 AATTTATTGAGAAACGATCGT-AAAAAGGACTCAAACA
1 AATTT-TTGAAAAACGATCCTAAAAAAGG-CTAAAACA
* *
576460 AATTTTTGAAAAATGATCCTAAAAAAGGCTAAAATA
1 AATTTTTGAAAAACGATCCTAAAAAAGGCTAAAACA
576496 AATTTTT
1 AATTTTT
576503 AGACGAGCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 25 0.68
37 12 0.32
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (36 bp):
AATTTTTGAAAAACGATCCTAAAAAAGGCTAAAACA
Found at i:578532 original size:105 final size:105
Alignment explanation
Indices: 578331--578539 Score: 237
Period size: 105 Copynumber: 2.0 Consensus size: 105
578321 ATTCAATTTA
* * *
578331 ATTTGCCTTTGTTTGGCTAGCTGAAGAAACCTATCCCATAAAGCCAAGGCTTTTAACCAATTGCT
1 ATTTGCCTTTATTCGGCTAGCTGAAGAAACCTATCCCATAAAGCCAAGACTTTTAACCAATTGCT
* * * *
578396 TTAGAGGAATAGCTCAGCGTTATTGTATGTATATGTATAGT
66 TTAGAGGAATAACTCA-CATTATTATATGTATATATATAGT
* * * * *
578437 ATTTGCCTTTATTCGGCTAGCTTAAGGAATCTAT-CCATAAAGCCACGACTTTTAACCAATTTCT
1 ATTTGCCTTTATTCGGCTAGCTGAAGAAACCTATCCCATAAAGCCAAGACTTTTAACCAATTGCT
578501 TTAGTTAGAAGAATAACTCA-ATT-TTAT-TGTATATATATA
66 TTAG--AG--GAATAACTCACATTATTATATGTATATATATA
578540 ATTACATTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
105 42 0.48
106 32 0.37
107 4 0.05
109 9 0.10
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (105 bp):
ATTTGCCTTTATTCGGCTAGCTGAAGAAACCTATCCCATAAAGCCAAGACTTTTAACCAATTGCT
TTAGAGGAATAACTCACATTATTATATGTATATATATAGT
Found at i:587656 original size:24 final size:24
Alignment explanation
Indices: 587624--587672 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
587614 ATATTAGTAC
*
587624 CTCCTGTATTAGTGCATTCATGCA
1 CTCCTGTATTAGTGCAATCATGCA
*
587648 CTCCTGTATTAGTGCAATCTTGCA
1 CTCCTGTATTAGTGCAATCATGCA
587672 C
1 C
587673 ACTAGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (24 bp):
CTCCTGTATTAGTGCAATCATGCA
Found at i:594849 original size:77 final size:79
Alignment explanation
Indices: 594763--594909 Score: 192
Period size: 77 Copynumber: 1.9 Consensus size: 79
594753 ATAAAAAATC
* **
594763 TTATTTAATTAATTC-AAATTAAATATCCATT-AAAGACTTATAATCTGAATTATAATC-TTTAA
1 TTATTTAATT-ATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTATAATCTTTTAA
594825 CGTTTATTTAAACTT
65 CGTTTATTTAAACTT
* * * * *
594840 TTATTTAATTATTCTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTATATTCTTTTAAT
1 TTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTATAATCTTTTAAC
594905 GTTTA
66 GTTTA
594910 CTTATTATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
76 4 0.07
77 24 0.41
78 21 0.36
79 10 0.17
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.46
Consensus pattern (79 bp):
TTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTATAATCTTTTAAC
GTTTATTTAAACTT
Found at i:598071 original size:20 final size:20
Alignment explanation
Indices: 598046--598086 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
598036 TTGTTACTCT
598046 TGGAGAATTCGCCAATTAAA
1 TGGAGAATTCGCCAATTAAA
*
598066 TGGAGAATTCTCCAATTAAA
1 TGGAGAATTCGCCAATTAAA
598086 T
1 T
598087 AACTTTCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (20 bp):
TGGAGAATTCGCCAATTAAA
Found at i:598864 original size:19 final size:18
Alignment explanation
Indices: 598840--598930 Score: 85
Period size: 19 Copynumber: 4.8 Consensus size: 18
598830 AATGACCAAT
598840 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAA-A
**
598859 AAAATCGCAACGCGATTTA
1 AAAATCGCAACGCGA-AAA
* *
598878 GAAATCGCAACGTTGAAAA
1 AAAATCGCAACG-CGAAAA
*
598897 AAAATCGCAACG-GTCAAAG
1 AAAATCGCAACGCG--AAAA
598916 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
598931 TATTCCAAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 54 0.92
20 3 0.05
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAA
Found at i:598921 original size:38 final size:39
Alignment explanation
Indices: 598840--599054 Score: 143
Period size: 42 Copynumber: 5.4 Consensus size: 39
598830 AATGACCAAT
**
598840 AAAATCGCAACGCGAAATAAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAAATAAAAATCGCAACGCGATAAAG
*
598879 -AAATCGCAACGTTGAAA-AAAAATCGCAACG-G-TCAAAG
1 AAAATCGCAACG-CGAAATAAAAATCGCAACGCGAT-AAAG
* * * *
598916 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGA-AAT--AAAAATCGCAACGCGATAAAG
* ** ** **
598958 AGAATCGCAACGCGATCTTCCAAGGATCGCAACGCGATTCAG
1 AAAATCGCAACGCGA-AAT--AAAAATCGCAACGCGATAAAG
* * **
599000 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATAAAG
599040 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
599055 TTCCAAGAAT
Statistics
Matches: 150, Mismatches: 16, Indels: 18
0.82 0.09 0.10
Matches are distributed among these distances:
36 1 0.01
37 5 0.03
38 36 0.24
39 4 0.03
40 38 0.25
41 11 0.07
42 54 0.36
43 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (39 bp):
AAAATCGCAACGCGAAATAAAAATCGCAACGCGATAAAG
Found at i:598963 original size:20 final size:21
Alignment explanation
Indices: 598918--599077 Score: 190
Period size: 20 Copynumber: 7.8 Consensus size: 21
598908 GGTCAAAGAA
598918 AATCGCAACGCGATATTCCA-AG
1 AATCGCAACGCG--ATTCCAGAG
* *
598940 AATCGCAATGCGATT-AAGAG
1 AATCGCAACGCGATTCCAGAG
598960 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGA--TTCCAGAG
* *
598982 GATCGCAACGCGATT-CAGAA
1 AATCGCAACGCGATTCCAGAG
599002 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATTCCAGAG
*
599022 AATCGCAACGCGATT-CAGAA
1 AATCGCAACGCGATTCCAGAG
599042 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATTCCAGAG
599062 AATCGCAACGCGATTC
1 AATCGCAACGCGATTC
599078 AGAAAATGAG
Statistics
Matches: 120, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
19 5 0.04
20 83 0.69
21 4 0.03
22 27 0.22
23 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.17
Consensus pattern (21 bp):
AATCGCAACGCGATTCCAGAG
Found at i:599030 original size:40 final size:40
Alignment explanation
Indices: 598914--599084 Score: 270
Period size: 40 Copynumber: 4.2 Consensus size: 40
598904 CAACGGTCAA
* *
598914 AGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTA
1 AGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTC
* *
598956 AGAGAATCGCAACGCGATCTTCCAAGGATCGCAACGCGATTC
1 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTC
598998 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
599038 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
599078 AGAAAAT
1 AGAAAAT
599085 GAGTAAATTC
Statistics
Matches: 121, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
40 70 0.58
42 51 0.42
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.16
Consensus pattern (40 bp):
AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
Found at i:599194 original size:6 final size:6
Alignment explanation
Indices: 599183--599245 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
599173 ACGTATTACC
599183 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
599231 ACCACG ACCACG ACC
1 ACCACG ACCACG ACC
599246 CGAGACGAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:599748 original size:6 final size:6
Alignment explanation
Indices: 599728--599792 Score: 95
Period size: 6 Copynumber: 11.7 Consensus size: 6
599718 TCGTCTCGTC
599728 TGGTCG TGG--G TGGTCG TGGTCG TGGTCG TGGTCG T-G--G TGGTCG
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG
599771 TGGTCG TGGTCG TGGTCG TGGT
1 TGGTCG TGGTCG TGGTCG TGGT
599793 AATACGTGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.04
4 5 0.09
5 1 0.02
6 46 0.85
ACGTcount: A:0.00, C:0.14, G:0.52, T:0.34
Consensus pattern (6 bp):
TGGTCG
Found at i:599769 original size:21 final size:21
Alignment explanation
Indices: 599728--599786 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
599718 TCGTCTCGTC
* *
599728 TGGTCGTGGGTGGTCGTGGTCG
1 TGGTCGT-GGTCGTGGTGGTCG
599750 TGGTCGTGGTCGTGGTGGTCG
1 TGGTCGTGGTCGTGGTGGTCG
599771 TGGTCGTGGTCGTGGT
1 TGGTCGTGGTCGTGGT
599787 CGTGGTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.00, C:0.14, G:0.53, T:0.34
Consensus pattern (21 bp):
TGGTCGTGGTCGTGGTGGTCG
Found at i:599771 original size:27 final size:27
Alignment explanation
Indices: 599728--599792 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
599718 TCGTCTCGTC
599728 TGGTCGTGGGTGGTCGTGGTCGTGGTCG
1 TGGTCGT-GGTGGTCGTGGTCGTGGTCG
599756 TGGTCGTGGTGGTCGTGGTCGTGGTCG
1 TGGTCGTGGTGGTCGTGGTCGTGGTCG
599783 TGGTCGTGGT
1 TGGTCGTGGT
599793 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 30 0.81
28 7 0.19
ACGTcount: A:0.00, C:0.14, G:0.52, T:0.34
Consensus pattern (27 bp):
TGGTCGTGGTGGTCGTGGTCGTGGTCG
Found at i:599913 original size:20 final size:20
Alignment explanation
Indices: 599888--600145 Score: 229
Period size: 20 Copynumber: 13.2 Consensus size: 20
599878 AATTTACTCA
599888 TTTCTTAATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
599908 TTTCTTGGAATCGCGTTGCGAT
1 TTTCTT--AATCGCGTTGCGAT
599930 TTTCTTAA-CGCGTTGCGA-
1 TTTCTTAATCGCGTTGCGAT
599948 -TT-TTAATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
*
599966 TTTCTGAATCGCGTTGCGA-
1 TTTCTTAATCGCGTTGCGAT
*
599985 -TTCTTGGATCGCGTTGCGAT
1 TTTCTT-AATCGCGTTGCGAT
600005 TTTC-T--TCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGAT
* *
600022 TCTCTTAATCGCATTGCGAT
1 TTTCTTAATCGCGTTGCGAT
***
600042 TCTTGGAATATCGCGTTGCGAT
1 T-TTCTTA-ATCGCGTTGCGAT
*
600064 TTTCTT--TTGACCGTTGCGAT
1 TTTCTTAATCG--CGTTGCGAT
* *
600084 TTTCTT-TTCAACGTTGCGAT
1 TTTCTTAATC-GCGTTGCGAT
*
600104 TTTCTAAATCGCGTTGCGA-
1 TTTCTTAATCGCGTTGCGAT
*
600123 TTT-TTATTTCGCGTTGCGAT
1 TTTCTTA-ATCGCGTTGCGAT
600143 TTT
1 TTT
600146 GTTGGTCATT
Statistics
Matches: 196, Mismatches: 21, Indels: 42
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.02
17 27 0.14
18 9 0.05
19 38 0.19
20 75 0.38
21 10 0.05
22 33 0.17
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCTTAATCGCGTTGCGAT
Found at i:599998 original size:56 final size:56
Alignment explanation
Indices: 599892--600066 Score: 219
Period size: 56 Copynumber: 3.0 Consensus size: 56
599882 TACTCATTTC
*
599892 TTAATCGCGTTGCGATTTTCTTGGAATCGCGTTGCGATTTTCTT--AACGCGTTGCGATT
1 TTAATCGCGTTGCGATTTTC-T-GAATCGCGTTGCGA--TTCTTGGATCGCGTTGCGATT
599950 TTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGATCGCGTTGCGATT
1 TTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGATCGCGTTGCGATT
** * * *
600006 TTCTTCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATT
1 TTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG---ATCGCGTTGCGATT
600065 TT
1 TT
600067 CTTTTGACCG
Statistics
Matches: 106, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
54 5 0.05
56 64 0.60
57 1 0.01
58 20 0.19
59 16 0.15
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (56 bp):
TTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGATCGCGTTGCGATT
Found at i:600138 original size:138 final size:133
Alignment explanation
Indices: 599890--600145 Score: 336
Period size: 138 Copynumber: 1.9 Consensus size: 133
599880 TTTACTCATT
*
599890 TCTTAATCGCGTTGCGATTTTCTTGGAATCGCGTTGCGATTTTCTTAACGCGTTGCGATTTTAAT
1 TCTTAATCGCATTGCGA-TTTCTTGGAATCGCGTTGCGATTTTCTTAACGCGTTGCGATTTTAAT
* * *
599955 CGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGATCGCGTTGCGATTTTCTTCGCGTTGCG
65 CACGTTGCGATTTTCTAAATCGCGTTGCGATTCTTAGATCGCGTTGCGATTTTCTTCGCGTTGCG
600020 ATTC
130 ATTC
*
600024 TCTTAATCGCATTGCGA-TTCTTGGAATATCGCGTTGCGATTTTCTTTTGAC-CGTTGCGATTTT
1 TCTTAATCGCATTGCGATTTCTTGG-A-ATCGCGTTGCGATTTTC--TTAACGCGTTGCGA-TTT
** * **
600087 CTTTTCAACGTTGCGATTTTCTAAATCGCGTTGCGATTTTTATTTCGCGTTGCGATTTT
61 -TAATC-ACGTTGCGATTTTCTAAATCGCGTTGCGATTCTTAGATCGCGTTGCGATTTT
600146 GTTGGTCATT
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
132 7 0.07
133 1 0.01
134 33 0.31
135 8 0.08
136 7 0.07
137 3 0.03
138 46 0.44
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (133 bp):
TCTTAATCGCATTGCGATTTCTTGGAATCGCGTTGCGATTTTCTTAACGCGTTGCGATTTTAATC
ACGTTGCGATTTTCTAAATCGCGTTGCGATTCTTAGATCGCGTTGCGATTTTCTTCGCGTTGCGA
TTC
Done.