Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_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: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:2919198 original size:31 final size:31
Alignment explanation
Indices: 2919140--2919198 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2919130 AGTTGTATGG
* *
2919140 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
*
2919171 ATTATTTAAATCTCAGTATTGCGAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
2919199 CTTTTATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:2924611 original size:21 final size:21
Alignment explanation
Indices: 2924568--2924613 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2924558 TATAGAGCGA
*
2924568 TTTAGAGAGAGAATGAGAGTT
1 TTTAGAGAGAGAAGGAGAGTT
*
2924589 TTTAGAGAGAGAAAGGAGATTT
1 TTTAGAGAGAG-AAGGAGAGTT
2924611 TTT
1 TTT
2924614 TTTTGAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (21 bp):
TTTAGAGAGAGAAGGAGAGTT
Found at i:2925570 original size:48 final size:48
Alignment explanation
Indices: 2925495--2925588 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
2925485 AAATTACTTT
* *
2925495 GATGATCGAATGCAACACTCGTAAACTCGATCAAATGTGACACCCTTC
1 GATGATCGAATGCAACACTCGTAAACTCAATCAAATGAGACACCCTTC
* * * *
2925543 GATGATCGAATGCGACATTCGTGAACTCAATCGAATGAGACACCCT
1 GATGATCGAATGCAACACTCGTAAACTCAATCAAATGAGACACCCT
2925589 AAGTCGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (48 bp):
GATGATCGAATGCAACACTCGTAAACTCAATCAAATGAGACACCCTTC
Found at i:2925876 original size:16 final size:16
Alignment explanation
Indices: 2925855--2925896 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
2925845 AAATTTATAT
2925855 ATTTAATATAATTTTG
1 ATTTAATATAATTTTG
2925871 ATTTAATAGT-ATTTTG
1 ATTTAATA-TAATTTTG
2925887 ATTT-ATATAA
1 ATTTAATATAA
2925897 AAATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 4 0.17
16 18 0.75
17 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
ATTTAATATAATTTTG
Found at i:2927110 original size:10 final size:10
Alignment explanation
Indices: 2927095--2927122 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2927085 AAAAGGAAAA
2927095 AAATAAAATG
1 AAATAAAATG
2927105 AAATAAAATG
1 AAATAAAATG
2927115 AAATAAAA
1 AAATAAAA
2927123 AAGTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (10 bp):
AAATAAAATG
Found at i:2928134 original size:10 final size:10
Alignment explanation
Indices: 2928110--2928156 Score: 58
Period size: 11 Copynumber: 4.4 Consensus size: 10
2928100 CACCTACAAA
2928110 AATAAAAAAT
1 AATAAAAAAT
2928120 AAATAAAAAAT
1 -AATAAAAAAT
2928131 AATAATAATAAT
1 AATAA-AA-AAT
*
2928143 AATAAATAAT
1 AATAAAAAAT
2928153 AATA
1 AATA
2928157 GTAATAGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 12 0.36
11 13 0.39
12 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:2928136 original size:3 final size:3
Alignment explanation
Indices: 2928128--2928194 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
2928118 ATAAATAAAA
* * *
2928128 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AGT AAT AGT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2928174 AGT AAT AAT AAAT AAAT AAT A
1 AAT AAT AAT -AAT -AAT AAT A
2928195 TTTTTTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 44 0.81
4 10 0.19
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2938227 original size:12 final size:12
Alignment explanation
Indices: 2938212--2938268 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
2938202 CTTCAGCAAT
2938212 ATCCTCATCATC
1 ATCCTCATCATC
2938224 ATCCTCATCATC
1 ATCCTCATCATC
*
2938236 -TCC-C-TCGTC
1 ATCCTCATCATC
*
2938245 ATCATCATCATC
1 ATCCTCATCATC
*
2938257 ATCCCCATCATC
1 ATCCTCATCATC
2938269 TGCCATGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
9 4 0.11
10 3 0.08
11 4 0.11
12 26 0.70
ACGTcount: A:0.23, C:0.44, G:0.02, T:0.32
Consensus pattern (12 bp):
ATCCTCATCATC
Found at i:2938253 original size:33 final size:33
Alignment explanation
Indices: 2938216--2938290 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
2938206 AGCAATATCC
* *
2938216 TCATCATCATCCTCATCATCT-CCCTCGTCATCA
1 TCATCATCATCCCCATCATCTGCCAT-GTCATCA
2938249 TCATCATCATCCCCATCATCTGCCATGTCATCA
1 TCATCATCATCCCCATCATCTGCCATGTCATCA
*
2938282 TCTTCATCA
1 TCATCATCA
2938291 CCCATATCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.33
Consensus pattern (33 bp):
TCATCATCATCCCCATCATCTGCCATGTCATCA
Found at i:2946004 original size:3 final size:3
Alignment explanation
Indices: 2945996--2946048 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
2945986 ACCTCCTTGT
2945996 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2946044 TTA TT
1 TTA TT
2946049 GGTAAATAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2947912 original size:16 final size:15
Alignment explanation
Indices: 2947887--2947917 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2947877 TATATATTCG
2947887 ATAAATTTTAATTTA
1 ATAAATTTTAATTTA
2947902 ATAATATTTTAATTTA
1 ATAA-ATTTTAATTTA
2947918 TGTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAATTTTAATTTA
Found at i:2949055 original size:146 final size:146
Alignment explanation
Indices: 2948787--2949068 Score: 379
Period size: 146 Copynumber: 1.9 Consensus size: 146
2948777 CCTGATTTCA
* * *
2948787 TTATTTCTTCAATTCCTCCTTCATTTTAAGTCTATTTTTTTTACCAAATTTGAGTCACATGCTCC
1 TTATTTCTTCAATTCCTCATTCATTTTAAGTC--TTGTTTTTACCAAATTTGAGCCACATGCTCC
* * *
2948852 TAAACCATAGTAGAATACATGTGTAGTTTCAATCCCCTCTTTTTGTTAACAAATTTTTTATTTTT
64 TAAACCATAGTAGAATACATGTGTACTTTCAATCCCCTCTTATTGATAACAAATTTTTTATTTTT
2948917 CAATTTTTCATAATCACG
129 CAATTTTTCATAATCACG
* *
2948935 TTATTTCTTCAATTCGTCATTATATTTTAAGTC-TGTTTTTACCAAATTTGAGCCACATGCTCCT
1 TTATTTCTTCAATTCCTCATT-CATTTTAAGTCTTGTTTTTACCAAATTTGAGCCACATGCTCCT
* * * * * *
2948999 AAACTATAGTGGAATATATTTGTACTTTCAAT-TCCTCTTATTGATAACAATTTTTTTTATTTTT
65 AAACCATAGTAGAATACATGTGTACTTTCAATCCCCTCTTATTGATAACAA-ATTTTTTATTTTT
*
2949063 TAATTT
129 CAATTT
2949069 AGTCCTTCAA
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
145 15 0.13
146 73 0.62
148 19 0.16
149 10 0.09
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (146 bp):
TTATTTCTTCAATTCCTCATTCATTTTAAGTCTTGTTTTTACCAAATTTGAGCCACATGCTCCTA
AACCATAGTAGAATACATGTGTACTTTCAATCCCCTCTTATTGATAACAAATTTTTTATTTTTCA
ATTTTTCATAATCACG
Found at i:2951816 original size:16 final size:16
Alignment explanation
Indices: 2951795--2951825 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2951785 ATATAATCAA
2951795 ATATAAATTAATTCTT
1 ATATAAATTAATTCTT
2951811 ATATAAATTAATTCT
1 ATATAAATTAATTCT
2951826 CATTTGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAAATTAATTCTT
Found at i:2951848 original size:19 final size:19
Alignment explanation
Indices: 2951824--2951863 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2951814 TAAATTAATT
*
2951824 CTCATTTGCAAATCATATA
1 CTCATTTGCAAATCAGATA
*
2951843 CTCATTTTCAAATCAGATA
1 CTCATTTGCAAATCAGATA
2951862 CT
1 CT
2951864 ATGAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (19 bp):
CTCATTTGCAAATCAGATA
Found at i:2952105 original size:20 final size:20
Alignment explanation
Indices: 2952058--2952127 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
2952048 CCCAGTTTCT
*
2952058 AAATTCGCAACACGAATTTGT-
1 AAATTCGCAACACG-A-TAGTC
2952079 AAA-TCGCAACAC-ATAAGTC
1 AAATTCGCAACACGAT-AGTC
*
2952098 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACACGATAGTC
*
2952118 AAATTTGCAA
1 AAATTCGCAA
2952128 AGCGCGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 1 0.02
18 3 0.07
19 3 0.07
20 30 0.71
21 5 0.12
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACACGATAGTC
Found at i:2952216 original size:57 final size:57
Alignment explanation
Indices: 2952148--2952257 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
2952138 TTTTCGCAAA
**
2952148 ACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTGTAAATCGCGTTGCGATAGT
1 ACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTAAAAATCGCGTTGCGATAGT
* *
2952205 ACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTAAAAATCTCGTTGCGA
1 ACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTAAAAATCGCGTTGCGA
2952258 ATTTGTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (57 bp):
ACTGTTTACCTATATCGGTAATTAACGTTGCGAATTTAAAAATCGCGTTGCGATAGT
Found at i:2952267 original size:20 final size:20
Alignment explanation
Indices: 2952229--2952274 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2952219 TCGGTAATTA
2952229 GCGTTGCGAATTTAAAAATC
1 GCGTTGCGAATTTAAAAATC
* **
2952249 TCGTTGCGAATTTGTAAATC
1 GCGTTGCGAATTTAAAAATC
2952269 GCGTTG
1 GCGTTG
2952275 TGATAATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (20 bp):
GCGTTGCGAATTTAAAAATC
Found at i:2952300 original size:77 final size:77
Alignment explanation
Indices: 2952173--2952566 Score: 707
Period size: 77 Copynumber: 5.1 Consensus size: 77
2952163 CGGTAATTAA
2952173 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
*
2952238 ATTTAAAAATCT
66 ATTTGAAAATCT
* *
2952250 CGTTGCGAATTTGTAAATCGCGTTGTGATAATACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
2952315 ATTTGAAAATCT
66 ATTTGAAAATCT
2952327 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
*
2952392 GTTTGAAAATCT
66 ATTTGAAAATCT
* *
2952404 CGTTGCGAAATTGTAAATCGCGTTGTGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
2952469 ATTTGAAAATCT
66 ATTTGAAAATCT
* *
2952481 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTGTACCTATGTCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
*
2952546 ATTTGAAAATCA
66 ATTTGAAAATCT
2952558 CGTTGCGAA
1 CGTTGCGAA
2952567 ATTACTGTTT
Statistics
Matches: 303, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 303 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (77 bp):
CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
ATTTGAAAATCT
Found at i:2952332 original size:20 final size:20
Alignment explanation
Indices: 2952306--2952354 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2952296 TCGGTAATTA
2952306 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
* *
2952326 TCGTTGCGAATTTGTAAATC
1 GCGTTGCGAATTTGAAAATC
2952346 GCGTTGCGA
1 GCGTTGCGA
2952355 TAGTACTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:2952421 original size:20 final size:20
Alignment explanation
Indices: 2952383--2952428 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2952373 TCGGTAATTA
**
2952383 GCGTTGCGAGTTTGAAAATC
1 GCGTTGCGAAATTGAAAATC
* *
2952403 TCGTTGCGAAATTGTAAATC
1 GCGTTGCGAAATTGAAAATC
2952423 GCGTTG
1 GCGTTG
2952429 TGATAGTACT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAAATTGAAAATC
Found at i:2952486 original size:20 final size:20
Alignment explanation
Indices: 2952460--2952508 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2952450 TCGGTAATTA
2952460 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
* *
2952480 TCGTTGCGAATTTGTAAATC
1 GCGTTGCGAATTTGAAAATC
2952500 GCGTTGCGA
1 GCGTTGCGA
2952509 TAGTACTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:2952573 original size:57 final size:57
Alignment explanation
Indices: 2952481--2952623 Score: 187
Period size: 57 Copynumber: 2.5 Consensus size: 57
2952471 TTGAAAATCT
* * * ** *
2952481 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTGTACCTATGTCGGTAATTAG
1 CGTTGCGAATTTGAAAATCACGTTGCGAAAGTACTGTGTACCTACATCGGTAATCAG
* *
2952538 CGTTGCGAATTTGAAAATCACGTTGCGAAATTACTGTTTACCTACATCGGTAATCAG
1 CGTTGCGAATTTGAAAATCACGTTGCGAAAGTACTGTGTACCTACATCGGTAATCAG
* *
2952595 TGTTGCGAATTTGGAAAACCACGTTGCGA
1 CGTTGCGAATTT-GAAAATCACGTTGCGA
2952624 TTTTGAAACC
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
57 60 0.80
58 15 0.20
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (57 bp):
CGTTGCGAATTTGAAAATCACGTTGCGAAAGTACTGTGTACCTACATCGGTAATCAG
Found at i:2954265 original size:40 final size:40
Alignment explanation
Indices: 2954214--2954294 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
2954204 ACATCAAATT
2954214 ATACTGATTAAAAATATCAATATAATATTTCTAACCTCAA
1 ATACTGATTAAAAATATCAATATAATATTTCTAACCTCAA
* *
2954254 ATACTGATTAAAAATATCAGTATAATATTTTTAACCTCAA
1 ATACTGATTAAAAATATCAATATAATATTTCTAACCTCAA
2954294 A
1 A
2954295 CTACATTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.36
Consensus pattern (40 bp):
ATACTGATTAAAAATATCAATATAATATTTCTAACCTCAA
Found at i:2961508 original size:23 final size:23
Alignment explanation
Indices: 2961436--2961509 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
2961426 GCCTGAGACC
2961436 TTATTTAAACGATATCAAGTTGT
1 TTATTTAAACGATATCAAGTTGT
* *
2961459 TTACTTAAACGATATCAAGCTGT
1 TTATTTAAACGATATCAAGTTGT
*
2961482 TTATTTAAACGATATCAAATTGT
1 TTATTTAAACGATATCAAGTTGT
2961505 TTATT
1 TTATT
2961510 ACTTGAACCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (23 bp):
TTATTTAAACGATATCAAGTTGT
Found at i:2977249 original size:21 final size:22
Alignment explanation
Indices: 2977203--2977251 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2977193 ATTTTTTTGG
*
2977203 GTCTTGCTTGGGATCTCCCGGC
1 GTCTTGCTTGGGATCTCCCAGC
* *
2977225 GTCTTGTTTGGGAT-TTCCAGC
1 GTCTTGCTTGGGATCTCCCAGC
2977246 GTCTTG
1 GTCTTG
2977252 AGGGTGTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.06, C:0.24, G:0.31, T:0.39
Consensus pattern (22 bp):
GTCTTGCTTGGGATCTCCCAGC
Found at i:2980956 original size:229 final size:228
Alignment explanation
Indices: 2980551--2980995 Score: 791
Period size: 229 Copynumber: 1.9 Consensus size: 228
2980541 GTAAATTATC
* * *
2980551 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
2980616 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
2980681 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 CGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
2980746 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTCAAAAAAGTATA
*
2980779 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
2980844 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
2980909 TCGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TCGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
2980974 GAAACATAAATTACATAACTTT
195 GAAACATAAATTACATAACTTT
2980996 TAAAGCAGTT
Statistics
Matches: 206, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
228 36 0.17
229 170 0.83
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
CGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:2981104 original size:19 final size:19
Alignment explanation
Indices: 2981050--2981108 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
2981040 TATATCGATC
* *
2981050 CAAAACGATATACCAGGTAA
1 CAAAATGATAAACC-GGTAA
2981070 -AAATATGATAAAACCGGTAA
1 CAAA-ATGAT-AAACCGGTAA
2981090 CAAAATGATAAACCGGTAA
1 CAAAATGATAAACCGGTAA
2981109 ATTTAAAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 13 0.38
20 14 0.41
21 7 0.21
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (19 bp):
CAAAATGATAAACCGGTAA
Found at i:2981254 original size:20 final size:19
Alignment explanation
Indices: 2981231--2981277 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2981221 CGATATAACA
2981231 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
2981251 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2981271 GGTAAAA
1 GGTAAAA
2981278 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2981279 original size:17 final size:18
Alignment explanation
Indices: 2981235--2981282 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
2981225 ATAACAGGTA
2981235 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
2981254 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
2981274 -AAAATGATA
1 AAAAATGATA
2981283 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:2982418 original size:184 final size:184
Alignment explanation
Indices: 2982109--2982636 Score: 948
Period size: 184 Copynumber: 2.9 Consensus size: 184
2982099 CTTTCAACAT
** * * * * *
2982109 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
*
2982174 GGTCTACAACCTATATCGGCACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
2982239 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
2982293 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
2982358 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
2982423 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
2982477 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
* * *
2982542 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2982607 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
2982637 GTAATTTGAA
Statistics
Matches: 332, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 332 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:2983167 original size:25 final size:25
Alignment explanation
Indices: 2983133--2983197 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
2983123 TTATCATTAA
2983133 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
2983158 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
2983183 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
2983198 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:2983514 original size:23 final size:23
Alignment explanation
Indices: 2983483--2983546 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2983473 ATAGGTAAAC
*
2983483 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2983506 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2983529 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2983547 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2983553 original size:23 final size:23
Alignment explanation
Indices: 2983483--2983555 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2983473 ATAGGTAAAC
* **
2983483 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2983506 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2983529 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2983552 ATAT
1 ATAT
2983556 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2983857 original size:25 final size:25
Alignment explanation
Indices: 2983823--2983873 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2983813 ACAACAAATC
*
2983823 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
2983848 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
2983873 A
1 A
2983874 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:2984180 original size:18 final size:18
Alignment explanation
Indices: 2984159--2984195 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2984149 GTAATTGGAG
2984159 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2984177 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2984195 T
1 T
2984196 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2984203 original size:24 final size:24
Alignment explanation
Indices: 2984151--2984197 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2984141 TTTCATATGT
* *
2984151 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
2984175 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
2984198 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:2984535 original size:38 final size:39
Alignment explanation
Indices: 2984452--2984537 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
2984442 TCCGATGCTC
*
2984452 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
2984491 ATCAAAATCCAAATCTCATATGATGCCAAGC-AAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
2984529 ATCAAAATC
1 ATCAAAATC
2984538 TACAACTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 16 0.36
39 29 0.64
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:2984969 original size:23 final size:23
Alignment explanation
Indices: 2984938--2985001 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2984928 ATAGGTAAAC
*
2984938 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2984961 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2984984 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2985002 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2985008 original size:23 final size:23
Alignment explanation
Indices: 2984938--2985010 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2984928 ATAGGTAAAC
* **
2984938 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2984961 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2984984 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2985007 ATAT
1 ATAT
2985011 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2991531 original size:26 final size:26
Alignment explanation
Indices: 2991493--2991545 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
2991483 GTCGTTAATT
2991493 ATTTATTTATTTTTGTTTAGATAAAG
1 ATTTATTTATTTTTGTTTAGATAAAG
2991519 ATTTATTCT-TTTTTGTTTAGATAAAG
1 ATTTATT-TATTTTTGTTTAGATAAAG
2991545 A
1 A
2991546 GTTGTACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (26 bp):
ATTTATTTATTTTTGTTTAGATAAAG
Found at i:2993541 original size:23 final size:22
Alignment explanation
Indices: 2993480--2993542 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
2993470 ATAAAACTTT
2993480 AACT-TAAAAAAAATTAAGTTAA
1 AACTATAAAAAAAATTAA-TTAA
*
2993502 AACTAT--AAAACATTAATTAAA
1 AACTATAAAAAAAATTAATT-AA
2993523 AACTATAAAAAAAATTAATT
1 AACTATAAAAAAAATTAATT
2993543 GTACTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 2 0.06
21 17 0.49
22 4 0.11
23 12 0.34
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (22 bp):
AACTATAAAAAAAATTAATTAA
Found at i:2994887 original size:21 final size:22
Alignment explanation
Indices: 2994861--2994909 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
2994851 CCAACACCCT
*
2994861 CAAGACGCTGAAA-ATCCCAAA
1 CAAGACGCCGAAAGATCCCAAA
*
2994882 CAAGACGCCGAAAGATCCCAAG
1 CAAGACGCCGAAAGATCCCAAA
2994904 CAAGAC
1 CAAGAC
2994910 CCAAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.45, C:0.31, G:0.18, T:0.06
Consensus pattern (22 bp):
CAAGACGCCGAAAGATCCCAAA
Found at i:2994902 original size:22 final size:21
Alignment explanation
Indices: 2994861--2994918 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2994851 CCAACACCCT
*
2994861 CAAGACGCTGAAAATCCCAAA
1 CAAGACGCCGAAAATCCCAAA
*
2994882 CAAGACGCCGAAAGATCCCAAG
1 CAAGACGCCGAAA-ATCCCAAA
*
2994904 CAAGAC-CCAAAAATC
1 CAAGACGCCGAAAATC
2994919 AAGTTTTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 17 0.52
22 13 0.39
ACGTcount: A:0.47, C:0.31, G:0.16, T:0.07
Consensus pattern (21 bp):
CAAGACGCCGAAAATCCCAAA
Found at i:2995210 original size:15 final size:14
Alignment explanation
Indices: 2995192--2995221 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2995182 TTTTAAAAAA
2995192 TAATTTTTTTATTAT
1 TAATTTTTTT-TTAT
2995207 TAATTTTTTTTTAT
1 TAATTTTTTTTTAT
2995221 T
1 T
2995222 GTAAACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TAATTTTTTTTTAT
Found at i:2996533 original size:2 final size:2
Alignment explanation
Indices: 2996526--2996558 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2996516 ACGCTTGGTA
2996526 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2996559 ACACACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2997255 original size:60 final size:60
Alignment explanation
Indices: 2997110--2997255 Score: 170
Period size: 59 Copynumber: 2.5 Consensus size: 60
2997100 TAATTAGTCA
* * * * * **
2997110 AATGATCATTTTGTAACTTTTAATAGTCAGAGTACTCAATAAAGCAATGTCCTATAGTCG
1 AATGATCATTTTATAACTTTTAATAGTCAGAATACTCAACAAAACAACGTCCTATAACCG
** *
2997170 -GGGATCATTTTATAATTTTTAATAGTC-GAATGACTCAACAAAACAACGTCCTATAACCG
1 AATGATCATTTTATAACTTTTAATAGTCAGAAT-ACTCAACAAAACAACGTCCTATAACCG
*
2997229 AATGATCATTTTATAACATTTAATAGT
1 AATGATCATTTTATAACTTTTAATAGT
2997256 AAAAAATCTC
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
58 3 0.04
59 45 0.64
60 22 0.31
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (60 bp):
AATGATCATTTTATAACTTTTAATAGTCAGAATACTCAACAAAACAACGTCCTATAACCG
Found at i:2997285 original size:60 final size:61
Alignment explanation
Indices: 2997172--2997299 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 61
2997162 TATAGTCGGG
** * ** * *
2997172 GATCATTTTATAATTTTTAATAGTCGAATGACTCAACAAAACAACGTCCTATAACCG-AAT
1 GATCATTTTATAACATTTAATAGTCAAAAAACTCAACAAAACAACATCATATAACCGAAAT
* * *
2997232 GATCATTTTATAACATTTAATAGT-AAAAAATCTCAACTAAACAATATCATATAATCGAAAT
1 GATCATTTTATAACATTTAATAGTCAAAAAA-CTCAACAAAACAACATCATATAACCGAAAT
2997293 -ATCATTT
1 GATCATTT
2997300 ATGTATTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 3 0.05
60 50 0.89
61 3 0.05
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.34
Consensus pattern (61 bp):
GATCATTTTATAACATTTAATAGTCAAAAAACTCAACAAAACAACATCATATAACCGAAAT
Found at i:2999855 original size:44 final size:44
Alignment explanation
Indices: 2999767--2999855 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
2999757 AAGTAATGGA
* * *
2999767 GAAAACTGTAGGCACTTAAAAGTAGGCATGTAGACGAGCCGAAC
1 GAAAACTGTAGGCACCTAAAAGTAGGCATGTAAACGAACCGAAC
*
2999811 GAAAACTGTAGGCACCTAAAAGTAGGCATGTAAACGAACTGAAC
1 GAAAACTGTAGGCACCTAAAAGTAGGCATGTAAACGAACCGAAC
2999855 G
1 G
2999856 TTCAGCAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (44 bp):
GAAAACTGTAGGCACCTAAAAGTAGGCATGTAAACGAACCGAAC
Found at i:3000440 original size:99 final size:99
Alignment explanation
Indices: 3000331--3000531 Score: 314
Period size: 99 Copynumber: 2.0 Consensus size: 99
3000321 CGAACATGAA
*
3000331 AAAGAAATTCAATTTGTTTAGTTATTCT-TGTTTGTTCGTTTAAAGTTAAACGAACGAACATGAA
1 AAAGAAATTCAATTTGTTTAGTT-TTCTGTGTTTGTTCGTTTAAAGTTAAACGAACGAACATAAA
* * * *
3000395 CATACCCCCATTCGTGTTCGTTTATATGTCTACCT
65 CATACCCCCATTCATGTTCGTTTACAGGCCTACCT
* *
3000430 AAAGAAATTCAGTTTGTTTAGTTTTTTGTGTTTGTTCGTTTAAAGTTAAACGAACGAACATAAAC
1 AAAGAAATTCAATTTGTTTAGTTTTCTGTGTTTGTTCGTTTAAAGTTAAACGAACGAACATAAAC
*
3000495 ATACCCCCGTTCATGTTCGTTTACAGGCCTACCT
66 ATACCCCCATTCATGTTCGTTTACAGGCCTACCT
3000529 AAA
1 AAA
3000532 AGTATAACGG
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 3 0.03
99 90 0.97
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (99 bp):
AAAGAAATTCAATTTGTTTAGTTTTCTGTGTTTGTTCGTTTAAAGTTAAACGAACGAACATAAAC
ATACCCCCATTCATGTTCGTTTACAGGCCTACCT
Found at i:3004869 original size:55 final size:55
Alignment explanation
Indices: 3004785--3004893 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
3004775 TCTCAAATGC
*
3004785 TGGACTTGTGTTCATGAAGTCGAATCTGAAGATCAAAACATGACATCATATACAG
1 TGGACTTGTGTTCATGAAGTCCAATCTGAAGATCAAAACATGACATCATATACAG
*
3004840 TGGACTTGTGTTCATGAAGTCCAATCTGAAGATCGAAACATGACATCATATACA
1 TGGACTTGTGTTCATGAAGTCCAATCTGAAGATCAAAACATGACATCATATACA
3004894 TTCGAGAGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (55 bp):
TGGACTTGTGTTCATGAAGTCCAATCTGAAGATCAAAACATGACATCATATACAG
Found at i:3012204 original size:15 final size:16
Alignment explanation
Indices: 3012176--3012214 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3012166 CAAATCTTAC
*
3012176 TTTATAAAATAATATA
1 TTTATAATATAATATA
3012192 TTTATAATA-AATATA
1 TTTATAATATAATATA
*
3012207 TTTTTAAT
1 TTTATAAT
3012215 TATGCTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTATAATATAATATA
Found at i:3014772 original size:43 final size:43
Alignment explanation
Indices: 3014663--3014780 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 43
3014653 GTAATCCAAG
* * *
3014663 CCGAAATTCAAAACCATCGAAATCTTTCTAACATATGCCTAAT
1 CCGAAATTCAAAACCATAGAAACCGTTCTAACATATGCCTAAT
* *
3014706 CCG-AATTCAAAACCATCA-AAACCGTTCTAACGTATGGCTAAT
1 CCGAAATTCAAAACCAT-AGAAACCGTTCTAACATATGCCTAAT
* *
3014748 CCGAAATTCGAAACTATAGAAACCGTTCTAACA
1 CCGAAATTCAAAACCATAGAAACCGTTCTAACA
3014781 GAAACCCAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 37 0.58
43 27 0.42
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (43 bp):
CCGAAATTCAAAACCATAGAAACCGTTCTAACATATGCCTAAT
Found at i:3015663 original size:35 final size:34
Alignment explanation
Indices: 3015624--3015701 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 34
3015614 ATTCCTTAAT
*
3015624 TTCATTCTAAACTCC-AAATTCCAAAGTAATTCAAA
1 TTCATTCTAAAC-CCTAAATTCCAAAATAATTC-AA
* *
3015659 TTCATTATAAACCCTAAATTCTAAAATAATTCAA
1 TTCATTCTAAACCCTAAATTCCAAAATAATTCAA
3015693 TTACATTCT
1 TT-CATTCT
3015702 CCCAAATTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.16
35 31 0.84
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TTCATTCTAAACCCTAAATTCCAAAATAATTCAA
Found at i:3016814 original size:35 final size:35
Alignment explanation
Indices: 3016765--3016877 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 35
3016755 AAAAAAGACA
* * *
3016765 GAAATTGAAGTATTTTAGAATTTGAGTTTTAGAAC
1 GAAATTGAATTATTTTGGAATTTGAGTTTTAGAAT
*
3016800 GTAATTGAATTATTTTGGAATTT-AGTGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGT-TTTAGAAT
* * *
3016835 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGTTTTAGAAT
3016870 GAAATTGA
1 GAAATTGA
3016878 TGATTGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.04
35 64 0.94
36 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (35 bp):
GAAATTGAATTATTTTGGAATTTGAGTTTTAGAAT
Found at i:3030895 original size:22 final size:20
Alignment explanation
Indices: 3030870--3030909 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3030860 TTACATTTCA
3030870 CAACACGAATTTGTCAAATTCG
1 CAACAC-AATTT-TCAAATTCG
*
3030892 CAACTCAATTTTCAAATT
1 CAACACAATTTTCAAATT
3030910 GTCGAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (20 bp):
CAACACAATTTTCAAATTCG
Found at i:3031022 original size:20 final size:20
Alignment explanation
Indices: 3030997--3031034 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3030987 TCGAGTTGCG
3030997 AAATTCACGCTGCGAAAACA
1 AAATTCACGCTGCGAAAACA
* *
3031017 AAATTCGCGTTGCGAAAA
1 AAATTCACGCTGCGAAAA
3031035 TTTCTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATTCACGCTGCGAAAACA
Found at i:3034128 original size:24 final size:24
Alignment explanation
Indices: 3034101--3034155 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
3034091 GGTGGAGGTG
3034101 GCCTCGGTGGATAGGCTTGATGTA
1 GCCTCGGTGGATAGGCTTGATGTA
* *
3034125 GCCTCGGTGGATAGGCTTGATTTG
1 GCCTCGGTGGATAGGCTTGATGTA
3034149 GCCTCGG
1 GCCTCGG
3034156 ATTTTGTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.20, G:0.38, T:0.29
Consensus pattern (24 bp):
GCCTCGGTGGATAGGCTTGATGTA
Found at i:3036442 original size:15 final size:14
Alignment explanation
Indices: 3036412--3036445 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3036402 GTGACATGTG
*
3036412 AATATGTGATATGA
1 AATATATGATATGA
3036426 AATATATGATAATGA
1 AATATATGAT-ATGA
3036441 AATAT
1 AATAT
3036446 GAGATTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (14 bp):
AATATATGATATGA
Found at i:3036657 original size:44 final size:44
Alignment explanation
Indices: 3036607--3036728 Score: 192
Period size: 44 Copynumber: 2.8 Consensus size: 44
3036597 AGGGTTCTAC
* *
3036607 GTGGTCCTTCGGGACATAGTGGTCATTTGA-GACATATGTTATAT
1 GTGGTCCTTCGGGACATAGTGGTC-TTTCAGGACATATGTGATAT
3036651 GTGGTCCTTCGGGACATAGTGGTCTTTCAGGACATATGTGATAT
1 GTGGTCCTTCGGGACATAGTGGTCTTTCAGGACATATGTGATAT
* *
3036695 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACATAGTGGTCTTTCAGGACA
3036729 AATTCTACGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
43 4 0.05
44 69 0.95
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (44 bp):
GTGGTCCTTCGGGACATAGTGGTCTTTCAGGACATATGTGATAT
Found at i:3036666 original size:26 final size:25
Alignment explanation
Indices: 3036637--3036712 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
3036627 GGTCATTTGA
3036637 GACATATGTTATATGTGGTCCTTCGG
1 GACATATG-TATATGTGGTCCTTCGG
* *
3036663 GAC------ATA-GTGGTCTTTCAG
1 GACATATGTATATGTGGTCCTTCGG
3036681 GACATATGTGATATGTGGTCCTTCGG
1 GACATATGT-ATATGTGGTCCTTCGG
3036707 GACATA
1 GACATA
3036713 GTGGTCCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
18 13 0.34
19 3 0.08
25 3 0.08
26 19 0.50
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (25 bp):
GACATATGTATATGTGGTCCTTCGG
Found at i:3036674 original size:18 final size:18
Alignment explanation
Indices: 3036651--3036728 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 18
3036641 TATGTTATAT
3036651 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
3036669 GTGGTCTTTCAGGACATA
1 GTGGTCCTTCGGGACATA
3036687 TGTGATATGTGGTCCTTCGGGACATA
1 ---G---T--GGTCCTTCGGGACATA
3036713 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
3036729 AATTCTACGC
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
18 30 0.62
20 1 0.02
21 1 0.02
23 1 0.02
24 1 0.02
26 14 0.29
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:3037151 original size:20 final size:20
Alignment explanation
Indices: 3037126--3037173 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3037116 AATAAGAGGA
3037126 GAAGAAAGAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
*
3037146 GAAGAAATAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
*
3037166 AAAGAAAG
1 GAAGAAAG
3037174 GAGAAGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (20 bp):
GAAGAAAGAAGAGAAAAGAG
Found at i:3039606 original size:14 final size:14
Alignment explanation
Indices: 3039587--3039613 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3039577 ACTTGATTTT
3039587 ATAATAATTTATGC
1 ATAATAATTTATGC
3039601 ATAATAATTTATG
1 ATAATAATTTATG
3039614 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
ATAATAATTTATGC
Found at i:3043516 original size:14 final size:15
Alignment explanation
Indices: 3043480--3043517 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3043470 GAAATCATTG
3043480 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
3043495 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
3043510 AAAAATTA
1 AAAAATTA
3043518 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:3043697 original size:19 final size:20
Alignment explanation
Indices: 3043673--3043783 Score: 95
Period size: 21 Copynumber: 5.6 Consensus size: 20
3043663 AACTAAAACC
3043673 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
3043692 TGTTGC-AAATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* * *
3043712 AGTTGTGAATTTGAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
3043731 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
* *
3043752 TGTTACGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
3043773 TGTTGC-AAATT
1 TGTTGCGAAATT
3043784 TGACTATCGC
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
18 5 0.06
19 24 0.31
20 20 0.26
21 28 0.36
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:3043722 original size:20 final size:19
Alignment explanation
Indices: 3043693--3043806 Score: 75
Period size: 21 Copynumber: 5.7 Consensus size: 19
3043683 TTAAATTCGT
* *
3043693 GTTGCAAATTCGAAAATCGA
1 GTTGCGAATTTGAAAATC-A
* *
3043713 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
*
3043732 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
* *
3043751 GTGTTACGAATTTGAAATTCA
1 --GTTGCGAATTTGAAAATCA
* ** *
3043772 GTGTTGCAAATTTGACTATCGC
1 --GTTGCGAATTTGAAAATC-A
3043794 GTTGCGAATTTGA
1 GTTGCGAATTTGA
3043807 CTTATGTGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 19 0.24
20 26 0.33
21 33 0.42
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAAATCA
Found at i:3043762 original size:21 final size:21
Alignment explanation
Indices: 3043673--3043964 Score: 151
Period size: 20 Copynumber: 14.6 Consensus size: 21
3043663 AACTAAAACC
*
3043673 TGTTGCGAAATT-AAATTC-G
1 TGTTGCGAATTTGAAATTCAG
* * *
3043692 TGTTGCAAATTCGAAAATC-G
1 TGTTGCGAATTTGAAATTCAG
* *
3043712 AGTTGTGAATTTGAAATTCA-
1 TGTTGCGAATTTGAAATTCAG
3043732 -GTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCAG
*
3043752 TGTTACGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCAG
* *
3043773 TGTTGCAAATTTG-ACTATC-G
1 TGTTGCGAATTTGAAAT-TCAG
* *
3043793 CGTTGCGAATTTG-ACTT-ATG
1 TGTTGCGAATTTGAAATTCA-G
3043813 TGTTGCG-ATTT-ACAGATTC-G
1 TGTTGCGAATTTGA-A-ATTCAG
* * **
3043833 CGTTGCGAATTTG-ACTTTTG
1 TGTTGCGAATTTGAAATTCAG
* *
3043853 TGTTACGAATTTG-ACTATC-G
1 TGTTGCGAATTTGAAAT-TCAG
* * *
3043873 CGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTCAG
*
3043893 TGTTGCGAATTTG-ACTTCAG
1 TGTTGCGAATTTGAAATTCAG
3043913 TGTTGCG-ATTT-ACAGATTC-G
1 TGTTGCGAATTTGA-A-ATTCAG
* *
3043933 CGTTGCGAATTTGAGA-TC-G
1 TGTTGCGAATTTGAAATTCAG
*
3043952 CGTTGCGAATTTG
1 TGTTGCGAATTTG
3043965 TTGGTCATTT
Statistics
Matches: 221, Mismatches: 31, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
19 56 0.25
20 118 0.53
21 46 0.21
22 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (21 bp):
TGTTGCGAATTTGAAATTCAG
Found at i:3043807 original size:20 final size:20
Alignment explanation
Indices: 3043774--3043964 Score: 164
Period size: 20 Copynumber: 9.6 Consensus size: 20
3043764 GAAATTCAGT
*
3043774 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
3043794 GTTGCGAATTTGACTTAT-GT
1 GTTGCGAATTTGAC-TATCGC
*
3043814 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
* * *
3043834 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
*
3043854 GTTACGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
3043874 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
3043894 GTTGCGAATTTGACT-TCAGT
1 GTTGCGAATTTGACTATC-GC
*
3043914 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
*
3043934 GTTGCGAATTTGA-GATCGC
1 GTTGCGAATTTGACTATCGC
3043953 GTTGCGAATTTG
1 GTTGCGAATTTG
3043965 TTGGTCATTT
Statistics
Matches: 142, Mismatches: 18, Indels: 23
0.78 0.10 0.13
Matches are distributed among these distances:
18 5 0.04
19 27 0.19
20 94 0.66
21 13 0.09
22 3 0.02
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:3043878 original size:60 final size:60
Alignment explanation
Indices: 3043732--3043964 Score: 185
Period size: 60 Copynumber: 3.9 Consensus size: 60
3043722 TTGAAATTCA
* * * * * * * * *
3043732 GTTGCGAATTTGAAAT-TCAGTGTTACGAATTTGAAATTCAGTGTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACATATC-GCGTTGCGAATTT-AGATTC-GCGTTGCGAATTTGACTTTAGT
* * *
3043794 GTTGCGAATTTGACTTAT-GTGTTGCG-ATTTACAGATTCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACATATCGCGTTGCGAATTT--AGATTCGCGTTGCGAATTTGACTTTAGT
* * *
3043854 GTTACGAATTTGAC-TATCGCGTTGCGAATTT-GACTTCTGTGTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACATATCGCGTTGCGAATTTAGA-TTC-GCGTTGCGAATTTGACTTTAGT
*
3043914 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGAGA-TCGCGTTGCGAATTTG
1 GTTGCGAATTTGACATA-TCGCGTTGCGAATTT-AGATTCGCGTTGCGAATTTG
3043965 TTGGTCATTT
Statistics
Matches: 143, Mismatches: 18, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
58 4 0.03
59 24 0.17
60 82 0.57
61 16 0.11
62 16 0.11
63 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGACATATCGCGTTGCGAATTTAGATTCGCGTTGCGAATTTGACTTTAGT
Found at i:3051012 original size:21 final size:21
Alignment explanation
Indices: 3050986--3051025 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3050976 TCCGAGGCGC
3050986 AAAACGTTTATGGCACATAAG
1 AAAACGTTTATGGCACATAAG
3051007 AAAACGTTTATGGCACATA
1 AAAACGTTTATGGCACATA
3051026 TCTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
AAAACGTTTATGGCACATAAG
Found at i:3051323 original size:20 final size:20
Alignment explanation
Indices: 3051298--3051340 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3051288 TCTAAGAGCC
3051298 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
3051318 CATTTAGGAGCATATAGTTG
1 CATTTAGAACCATATAGATG
3051338 CAT
1 CAT
3051341 GTGGTAGAAT
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:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:3053874 original size:14 final size:15
Alignment explanation
Indices: 3053838--3053875 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3053828 GAAATCATTG
3053838 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
3053853 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
3053868 AAAAATTA
1 AAAAATTA
3053876 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:3054055 original size:19 final size:20
Alignment explanation
Indices: 3054031--3054141 Score: 95
Period size: 21 Copynumber: 5.6 Consensus size: 20
3054021 AACTAAAACC
3054031 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
3054050 TGTTGC-AAATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* * *
3054070 AGTTGTGAATTTGAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
3054089 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
* *
3054110 TGTTACGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
3054131 TGTTGC-AAATT
1 TGTTGCGAAATT
3054142 TGACTATCGC
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
18 5 0.06
19 24 0.31
20 20 0.26
21 28 0.36
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:3054080 original size:20 final size:19
Alignment explanation
Indices: 3054051--3054164 Score: 75
Period size: 21 Copynumber: 5.7 Consensus size: 19
3054041 TTAAATTCGT
* *
3054051 GTTGCAAATTCGAAAATCGA
1 GTTGCGAATTTGAAAATC-A
* *
3054071 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
*
3054090 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
* *
3054109 GTGTTACGAATTTGAAATTCA
1 --GTTGCGAATTTGAAAATCA
* ** *
3054130 GTGTTGCAAATTTGACTATCGC
1 --GTTGCGAATTTGAAAATC-A
3054152 GTTGCGAATTTGA
1 GTTGCGAATTTGA
3054165 CTTATGTGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 19 0.24
20 26 0.33
21 33 0.42
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAAATCA
Found at i:3054120 original size:21 final size:21
Alignment explanation
Indices: 3054031--3054322 Score: 151
Period size: 20 Copynumber: 14.6 Consensus size: 21
3054021 AACTAAAACC
*
3054031 TGTTGCGAAATT-AAATTC-G
1 TGTTGCGAATTTGAAATTCAG
* * *
3054050 TGTTGCAAATTCGAAAATC-G
1 TGTTGCGAATTTGAAATTCAG
* *
3054070 AGTTGTGAATTTGAAATTCA-
1 TGTTGCGAATTTGAAATTCAG
3054090 -GTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCAG
*
3054110 TGTTACGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCAG
* *
3054131 TGTTGCAAATTTG-ACTATC-G
1 TGTTGCGAATTTGAAAT-TCAG
* *
3054151 CGTTGCGAATTTG-ACTT-ATG
1 TGTTGCGAATTTGAAATTCA-G
3054171 TGTTGCG-ATTT-ACAGATTC-G
1 TGTTGCGAATTTGA-A-ATTCAG
* * **
3054191 CGTTGCGAATTTG-ACTTTTG
1 TGTTGCGAATTTGAAATTCAG
* *
3054211 TGTTACGAATTTG-ACTATC-G
1 TGTTGCGAATTTGAAAT-TCAG
* * *
3054231 CGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTCAG
*
3054251 TGTTGCGAATTTG-ACTTCAG
1 TGTTGCGAATTTGAAATTCAG
3054271 TGTTGCG-ATTT-ACAGATTC-G
1 TGTTGCGAATTTGA-A-ATTCAG
* *
3054291 CGTTGCGAATTTGAGA-TC-G
1 TGTTGCGAATTTGAAATTCAG
*
3054310 CGTTGCGAATTTG
1 TGTTGCGAATTTG
3054323 TTGGTCATTT
Statistics
Matches: 221, Mismatches: 31, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
19 56 0.25
20 118 0.53
21 46 0.21
22 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (21 bp):
TGTTGCGAATTTGAAATTCAG
Found at i:3054165 original size:20 final size:20
Alignment explanation
Indices: 3054132--3054322 Score: 164
Period size: 20 Copynumber: 9.6 Consensus size: 20
3054122 GAAATTCAGT
*
3054132 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
3054152 GTTGCGAATTTGACTTAT-GT
1 GTTGCGAATTTGAC-TATCGC
*
3054172 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
* * *
3054192 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
*
3054212 GTTACGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
3054232 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
3054252 GTTGCGAATTTGACT-TCAGT
1 GTTGCGAATTTGACTATC-GC
*
3054272 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
*
3054292 GTTGCGAATTTGA-GATCGC
1 GTTGCGAATTTGACTATCGC
3054311 GTTGCGAATTTG
1 GTTGCGAATTTG
3054323 TTGGTCATTT
Statistics
Matches: 142, Mismatches: 18, Indels: 23
0.78 0.10 0.13
Matches are distributed among these distances:
18 5 0.04
19 27 0.19
20 94 0.66
21 13 0.09
22 3 0.02
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:3054236 original size:60 final size:60
Alignment explanation
Indices: 3054090--3054322 Score: 185
Period size: 60 Copynumber: 3.9 Consensus size: 60
3054080 TTGAAATTCA
* * * * * * * * *
3054090 GTTGCGAATTTGAAAT-TCAGTGTTACGAATTTGAAATTCAGTGTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACATATC-GCGTTGCGAATTT-AGATTC-GCGTTGCGAATTTGACTTTAGT
* * *
3054152 GTTGCGAATTTGACTTAT-GTGTTGCG-ATTTACAGATTCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACATATCGCGTTGCGAATTT--AGATTCGCGTTGCGAATTTGACTTTAGT
* * *
3054212 GTTACGAATTTGAC-TATCGCGTTGCGAATTT-GACTTCTGTGTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACATATCGCGTTGCGAATTTAGA-TTC-GCGTTGCGAATTTGACTTTAGT
*
3054272 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGAGA-TCGCGTTGCGAATTTG
1 GTTGCGAATTTGACATA-TCGCGTTGCGAATTT-AGATTCGCGTTGCGAATTTG
3054323 TTGGTCATTT
Statistics
Matches: 143, Mismatches: 18, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
58 4 0.03
59 24 0.17
60 82 0.57
61 16 0.11
62 16 0.11
63 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGACATATCGCGTTGCGAATTTAGATTCGCGTTGCGAATTTGACTTTAGT
Found at i:3061370 original size:21 final size:21
Alignment explanation
Indices: 3061344--3061383 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3061334 TCCGAGGCGC
3061344 AAAACGTTTATGGCACATAAG
1 AAAACGTTTATGGCACATAAG
3061365 AAAACGTTTATGGCACATA
1 AAAACGTTTATGGCACATA
3061384 TCTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
AAAACGTTTATGGCACATAAG
Found at i:3061681 original size:20 final size:20
Alignment explanation
Indices: 3061656--3061698 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3061646 TCTAAGAGCC
3061656 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
3061676 CATTTAGGAGCATATAGTTG
1 CATTTAGAACCATATAGATG
3061696 CAT
1 CAT
3061699 GTGGTAGAAT
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:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:3063989 original size:20 final size:20
Alignment explanation
Indices: 3063964--3064007 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3063954 CATCTGACTG
3063964 TTCACCCA-ACATCATGTCTC
1 TTCACCCAGA-ATCATGTCTC
* *
3063984 TTCACCGAGAGTCATGTCTC
1 TTCACCCAGAATCATGTCTC
3064004 TTCA
1 TTCA
3064008 TCAAAGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.32
Consensus pattern (20 bp):
TTCACCCAGAATCATGTCTC
Found at i:3064017 original size:20 final size:20
Alignment explanation
Indices: 3063975--3064017 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3063965 TCACCCAACA
**
3063975 TCATGTCTCTTCACCGAGAG
1 TCATGTCTCTTCACAAAGAG
3063995 TCATGTCTCTTCATCAAAG-G
1 TCATGTCTCTTCA-CAAAGAG
3064015 TCA
1 TCA
3064018 CCTTCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (20 bp):
TCATGTCTCTTCACAAAGAG
Found at i:3065208 original size:20 final size:20
Alignment explanation
Indices: 3065183--3065226 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3065173 CATCTGACTG
3065183 TTCACCCA-ACATCATGTCTC
1 TTCACCCAGA-ATCATGTCTC
* *
3065203 TTCACCGAGAGTCATGTCTC
1 TTCACCCAGAATCATGTCTC
3065223 TTCA
1 TTCA
3065227 TCAAAGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.32
Consensus pattern (20 bp):
TTCACCCAGAATCATGTCTC
Found at i:3065236 original size:20 final size:20
Alignment explanation
Indices: 3065194--3065236 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3065184 TCACCCAACA
**
3065194 TCATGTCTCTTCACCGAGAG
1 TCATGTCTCTTCACAAAGAG
3065214 TCATGTCTCTTCATCAAAG-G
1 TCATGTCTCTTCA-CAAAGAG
3065234 TCA
1 TCA
3065237 CCTTCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (20 bp):
TCATGTCTCTTCACAAAGAG
Found at i:3068922 original size:21 final size:21
Alignment explanation
Indices: 3068896--3068939 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3068886 TTATTTCTTT
3068896 ATTTCATCTTCACCATACTTA
1 ATTTCATCTTCACCATACTTA
3068917 ATTTCATCTTCACCATACTTA
1 ATTTCATCTTCACCATACTTA
3068938 AT
1 AT
3068940 CAAATCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTCATCTTCACCATACTTA
Found at i:3070938 original size:13 final size:14
Alignment explanation
Indices: 3070922--3070958 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
3070912 TTTTTATTTT
3070922 TTATTATTAATA-A
1 TTATTATTAATATA
3070935 TTATTATTAA-ATA
1 TTATTATTAATATA
3070948 TTATTATTAAT
1 TTATTATTAAT
3070959 TTTACATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTATTAATATA
Found at i:3071491 original size:22 final size:20
Alignment explanation
Indices: 3071461--3071501 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
3071451 AACATAAATC
*
3071461 AAGGGAACGAAACCAGAAAAAA
1 AAGGAAACGAAA--AGAAAAAA
3071483 AAGGAAACGAAAAGAAAAA
1 AAGGAAACGAAAAGAAAAA
3071502 GACAGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.10, G:0.22, T:0.00
Consensus pattern (20 bp):
AAGGAAACGAAAAGAAAAAA
Found at i:3085613 original size:135 final size:129
Alignment explanation
Indices: 3085326--3085634 Score: 354
Period size: 135 Copynumber: 2.3 Consensus size: 129
3085316 TCAACATCAG
* ** * * *
3085326 CTGACCAGATCTCCTCATCACGTAGGAGCAACGTCAACATTAGATAACCAGCCGTCCTCATTACG
1 CTGACCAGATATCCTCATCACGTAGGAGC-GTGTCACCCTTAGATAACCAGCCGTCCTCATCACG
* *
3085391 TAGGAACTATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGTAGGAGCAGTGTCATCCC
65 TAGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
* *
3085456 CTGACTAGATATCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGCCGTCCTCATCGCG
1 CTGACCAGATATCCTCATCACGTAGGAG-CGTGTCACCCTTAGATAACCAGCCGTCCTCATCACG
* *
3085521 TAGGAACCGA-GTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGCATGAGTC-GTG
65 TAGGAA-CGATGTTATCA--C-T-ATAAA-ATGGCCAAGAACTCTTCATCACGCAGGAG-CAGTG
3085584 TCAT-CC
123 TCATCCC
* * * *
3085590 TTCGACCAGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGA
1 CT-GACCAGATATCCTCATCACGTA-GGAGCGTGTCACCCTTAGA
3085635 CGACCCGAAC
Statistics
Matches: 152, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
130 68 0.45
131 3 0.02
132 1 0.01
133 1 0.01
134 7 0.05
135 69 0.45
136 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (129 bp):
CTGACCAGATATCCTCATCACGTAGGAGCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGT
AGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
Found at i:3085652 original size:43 final size:40
Alignment explanation
Indices: 3085557--3085660 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
3085547 AAGATGGCCA
* ** *
3085557 AGAACTCTTCATCACGCATGAGTCGTGTCATCCTTCGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
** *
3085597 AGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTT---CGACC
*
3085640 CGAACTCTTCATCACGTATGA
1 AGAACTCTTCATCACGTATGA
3085661 GCAGTGTCGT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
40 28 0.56
43 22 0.44
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
Found at i:3085847 original size:13 final size:13
Alignment explanation
Indices: 3085838--3085875 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3085828 TTTTTATTTT
3085838 TTATTATT-ATTAA
1 TTATTATTAATT-A
*
3085851 TTATTATTAACTA
1 TTATTATTAATTA
3085864 TTATTATTAATT
1 TTATTATTAATT
3085876 TTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:3085856 original size:10 final size:10
Alignment explanation
Indices: 3085840--3085869 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3085830 TTTATTTTTT
3085840 ATTATTATTA
1 ATTATTATTA
3085850 ATTATTATTA
1 ATTATTATTA
*
3085860 ACTATTATTA
1 ATTATTATTA
3085870 TTAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:3086407 original size:22 final size:20
Alignment explanation
Indices: 3086377--3086417 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
3086367 AACATAAATC
*
3086377 AAGGGAACGAAACCAGAAAAAA
1 AAGGAAACGAAA--AGAAAAAA
3086399 AAGGAAACGAAAAGAAAAA
1 AAGGAAACGAAAAGAAAAA
3086418 GACAGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.10, G:0.22, T:0.00
Consensus pattern (20 bp):
AAGGAAACGAAAAGAAAAAA
Found at i:3090666 original size:36 final size:35
Alignment explanation
Indices: 3090621--3090691 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
3090611 AACATCTACC
*
3090621 AAACTTTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
3090656 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
3090692 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:3090690 original size:21 final size:21
Alignment explanation
Indices: 3090630--3090690 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
3090620 CAAACTTTAC
*
3090630 CAAACTTTGAAAAATATTTTT
1 CAAACTTTGAAAAACATTTTT
**
3090651 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
3090666 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
3090687 CAAA
1 CAAA
3090691 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 11 0.38
17 1 0.03
19 1 0.03
21 16 0.55
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:3101053 original size:42 final size:41
Alignment explanation
Indices: 3100967--3101173 Score: 220
Period size: 42 Copynumber: 4.9 Consensus size: 41
3100957 CTATACACCA
* *
3100967 GTAAGGCTTAACCTGTGCACA-AAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAA-CAAAGGGA-CCT-GGGAAACT
* * *
3101011 GTAAGGTTTATCCTTACACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
* *
3101053 GTAAGGTTTACCCTTGCACACAACAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
* *
3101095 GTAAGGCTTACCTTCGTACACAGCAAAGGGACCCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAACAAAGGGA-CCTGGGAAACT
*
3101138 GTAAGGCTTACCTTTGCACACAACAAAGGGGCCTGG
1 GTAAGGCTTACC-TTGCACACAACAAAGGGACCTGG
3101174 TAATACTTCC
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
41 4 0.03
42 73 0.52
43 47 0.33
44 17 0.12
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAACAAAGGGACCTGGGAAACT
Found at i:3101149 original size:85 final size:84
Alignment explanation
Indices: 3100967--3101176 Score: 266
Period size: 85 Copynumber: 2.5 Consensus size: 84
3100957 CTATACACCA
* * * *
3100967 GTAAGGCTTAACCTGTGCACA-AAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTTACAC
1 GTAAGGCTTACCCT-TGCACACAA-CAAAGGGA-CCT-GGTAAACTGTAAGGCTTATCCTTACAC
3101030 ACAGCAAAGGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
*
3101053 GTAAGGTTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTA-CCTT-CGTACAC
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTATCCTTAC--ACAC
3101116 AGCAAAGGGACCCTGGGAAACT
64 AGCAAAGGGA-CCTGGGAAACT
* *
3101138 GTAAGGCTTACCTTTGCACACAACAAAGGGGCCTGGTAA
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAA
3101177 TACTTCCTTC
Statistics
Matches: 111, Mismatches: 8, Indels: 11
0.85 0.06 0.08
Matches are distributed among these distances:
82 1 0.01
83 4 0.04
84 30 0.27
85 59 0.53
86 17 0.15
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTATCCTTACACACAG
CAAAGGGACCTGGGAAACT
Found at i:3102142 original size:29 final size:29
Alignment explanation
Indices: 3102101--3102176 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
3102091 ATTTTTTTAA
* *
3102101 AATTACAAAAATAGCACCATTTTCAAAAT
1 AATTACCAAAATAGCACCATTTCCAAAAT
* *
3102130 AATTACCAGAATAGCACCATTTCCCAAAT
1 AATTACCAAAATAGCACCATTTCCAAAAT
*
3102159 AATTACCAAAATATCACC
1 AATTACCAAAATAGCACC
3102177 CGGTCAACGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (29 bp):
AATTACCAAAATAGCACCATTTCCAAAAT
Found at i:3108334 original size:43 final size:42
Alignment explanation
Indices: 3108271--3108430 Score: 128
Period size: 42 Copynumber: 3.8 Consensus size: 42
3108261 CTATACACCA
* *
3108271 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGAAAAACT
1 GTAAGGTTTAACCT-TGCACAAAGCAAATGGA-CCT-GAAAAACT
* * **
3108315 GTAAGGTTTATCCTTGCACACAGCAAATGGACCTGGGAAACT
1 GTAAGGTTTAACCTTGCACAAAGCAAATGGACCTGAAAAACT
* * * **
3108357 GTAAGGTTTACCCTTACACACAA-CAAAGGGACCTGGTAAACT
1 GTAAGGTTTAACCTTGCACA-AAGCAAATGGACCTGAAAAACT
* * *
3108399 GTAAGGCTT-ACCTTCGCACACAGCAAAGGGAC
1 GTAAGGTTTAACCTT-GCACAAAGCAAATGGAC
3108431 TTGGGAAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
41 5 0.05
42 62 0.64
43 15 0.15
44 15 0.15
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
GTAAGGTTTAACCTTGCACAAAGCAAATGGACCTGAAAAACT
Found at i:3108357 original size:42 final size:42
Alignment explanation
Indices: 3108310--3108476 Score: 212
Period size: 42 Copynumber: 4.0 Consensus size: 42
3108300 GAGCCTAGAA
* * *
3108310 AAACTGTAAGGTTTATCCTT-GCACACAGCAAATGGACCTGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGGG
* * *
3108352 AAACTGTAAGGTTTACCCTT-ACACACAACAAAGGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGGG
* *
3108394 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACTTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
* *
3108436 AAATTGTAAGGCTTACCTTCGTACACAACAAAGGGACCTGG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGG
3108477 TAATACTTCC
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 4 0.04
42 106 0.96
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
Found at i:3108418 original size:84 final size:83
Alignment explanation
Indices: 3108310--3108479 Score: 245
Period size: 84 Copynumber: 2.0 Consensus size: 83
3108300 GAGCCTAGAA
* * *
3108310 AAACTGTAAGGTTTATCCTTGCACACAGCAAATGGACCTGGGAAACTGTAAGGTTTACCCTTAC-
1 AAACTGTAAGGCTTATCCTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTA-CCTT-CG
3108374 ACACAACAAAGGGACCTGGT
64 ACACAACAAAGGGACCTGGT
* *
3108394 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACTTGGGAAATTGTAAGGCTTACCTTCGT
1 AAACTGTAAGGCTTATCCTT-GCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTCG-
3108458 ACACAACAAAGGGACCTGGT
64 ACACAACAAAGGGACCTGGT
3108478 AA
1 AA
3108480 TACTTCCTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
82 1 0.01
83 8 0.10
84 69 0.88
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (83 bp):
AAACTGTAAGGCTTATCCTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTCGAC
ACAACAAAGGGACCTGGT
Found at i:3109452 original size:29 final size:29
Alignment explanation
Indices: 3109414--3109595 Score: 97
Period size: 29 Copynumber: 6.4 Consensus size: 29
3109404 TTTTTTTAAC
* * ** *
3109414 ATTACGAAAATAGCACCATTTTGTAATTA
1 ATTACCAAAATAACACCATTTTCAAAATA
*
3109443 ATTACCAAAATAACATCATTTTCAAAATA
1 ATTACCAAAATAACACCATTTTCAAAATA
* ** *
3109472 ATTACTAAAATATTACTC-TTTAT-AAAATT
1 ATTACCAAAATAACAC-CATTT-TCAAAATA
* * *** * *
3109501 TTTA-CGAAAT--TGTCATTTTTAAAAAA
1 ATTACCAAAATAACACCATTTTCAAAATA
*
3109527 ATTACAAAAATAACATCC-TTTTCAAAATA
1 ATTACCAAAATAACA-CCATTTTCAAAATA
* * * *
3109556 ATTACCATAATAGCACCATTTACCAAATA
1 ATTACCAAAATAACACCATTTTCAAAATA
3109585 ATTACCAAAAT
1 ATTACCAAAAT
3109596 GTCATCTGGT
Statistics
Matches: 112, Mismatches: 32, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
25 2 0.02
26 11 0.10
27 4 0.04
28 6 0.05
29 86 0.77
30 3 0.03
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (29 bp):
ATTACCAAAATAACACCATTTTCAAAATA
Found at i:3109599 original size:84 final size:84
Alignment explanation
Indices: 3109442--3109600 Score: 194
Period size: 84 Copynumber: 1.9 Consensus size: 84
3109432 TTTTGTAATT
* * ** * ** *
3109442 AATTACCAAAATAACATCATTTTCAAAATAATTACTAAAATATTACTCTTTATAAAATTTTTACG
1 AATTACAAAAATAACATCATTTTCAAAATAATTACCAAAATAGCACTCTTTACAAAATAATTACC
*
3109507 AAATTGTCATTTTTAAAAA
66 AAAATGTCATTTTTAAAAA
* * *
3109526 AATTACAAAAATAACATCCTTTTCAAAATAATTACCATAATAGCAC-CATTTACCAAATAATTAC
1 AATTACAAAAATAACATCATTTTCAAAATAATTACCAAAATAGCACTC-TTTACAAAATAATTAC
3109590 CAAAATGTCAT
65 CAAAATGTCAT
3109601 CTGGTCAACG
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
83 1 0.02
84 61 0.98
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.35
Consensus pattern (84 bp):
AATTACAAAAATAACATCATTTTCAAAATAATTACCAAAATAGCACTCTTTACAAAATAATTACC
AAAATGTCATTTTTAAAAA
Found at i:3109644 original size:17 final size:18
Alignment explanation
Indices: 3109622--3109662 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
3109612 TCAACGAGTC
3109622 AGTCAACGGGTC-GGTCG
1 AGTCAACGGGTCAGGTCG
3109639 AGTCAACGGGTCAGGTCG
1 AGTCAACGGGTCAGGTCG
*
3109657 GGTCAA
1 AGTCAA
3109663 AACTGGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (18 bp):
AGTCAACGGGTCAGGTCG
Found at i:3112540 original size:15 final size:15
Alignment explanation
Indices: 3112522--3112566 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
3112512 TTCTTTAATA
3112522 ATAAAATATATTATT
1 ATAAAATATATTATT
3112537 ATAAAATATATTATT
1 ATAAAATATATTATT
*
3112552 TTAAAATATTATTAT
1 ATAAAATA-TATTAT
3112567 ATTCAAGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAAAATATATTATT
Found at i:3113104 original size:35 final size:35
Alignment explanation
Indices: 3113056--3113135 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
3113046 AACAGAGTCA
* *
3113056 TCAATTACATTCTAAACC-CTATATTCCAAAATACT
1 TCAATTACATTCTAAACCTC-AAATTCCAAAACACT
*
3113091 TTAATTACATTCTAAACCTCAAATTCCAAAACACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAACACT
3113126 TCAATTACAT
1 TCAATTACAT
3113136 ACCCAACCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 39 0.98
36 1 0.03
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAACACT
Found at i:3113149 original size:35 final size:35
Alignment explanation
Indices: 3113056--3113151 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
3113046 AACAGAGTCA
* * * * *
3113056 TCAATTACATTCTAAACCCTATATTCCAAAATACT
1 TCAATTACATACCAAACCCCAAATTCCAAAACACT
* * * *
3113091 TTAATTACATTCTAAACCTCAAATTCCAAAACACT
1 TCAATTACATACCAAACCCCAAATTCCAAAACACT
*
3113126 TCAATTACATACCCAACCCCAAATTC
1 TCAATTACATACCAAACCCCAAATTC
3113152 ATAATATATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.30
Consensus pattern (35 bp):
TCAATTACATACCAAACCCCAAATTCCAAAACACT
Found at i:3113933 original size:149 final size:148
Alignment explanation
Indices: 3113634--3113922 Score: 481
Period size: 149 Copynumber: 1.9 Consensus size: 148
3113624 AAACTATTTA
*
3113634 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAGTATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
*
3113699 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGATTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACT
3113764 ATTTTATAAAATAAACTG
131 ATTTTATAAAATAAACTG
* *
3113782 AATTAGAATCAAATAATATTAAATA-TATGATAAATATTTTTAATTAAATTTAAACAGAAACTCG
1 AATTAGAATCAAATAATATT--ATAGTATGATAAATATTTATAATTAAATTTAAACAGAAACTCA
* * * *
3113846 AAAATTCAATTCAATTTGACTTGATTTAAATTTTGTAAACTCAAATCGAAAACATTTTGAGTCAA
64 AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAA
3113911 CTATTTTATAAA
129 CTATTTTATAAA
3113923 CTGAATTGAA
Statistics
Matches: 131, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
148 20 0.15
149 108 0.82
150 3 0.02
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAGTATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACT
ATTTTATAAAATAAACTG
Found at i:3114133 original size:35 final size:35
Alignment explanation
Indices: 3114094--3114173 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
3114084 GGGGTTGGGT
*
3114094 ATGTAATTGAAGTATTTTGGAATTT-GAGGTTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTAG-GGTTTAAA
*
3114129 ATGTAATTGAATTATTTTGGAATTTAGGGTTTAAA
1 ATGTAATTGAAGTATTTTGGAATTTAGGGTTTAAA
*
3114164 ATATAATTGA
1 ATGTAATTGA
3114174 TGATTGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGAATTTAGGGTTTAAA
Found at i:3116044 original size:24 final size:26
Alignment explanation
Indices: 3115993--3116044 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
3115983 CGTTCGTGAA
* * *
3115993 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTAATATT
3116019 CGTTC-ATT-TATGTTCATTAATATT
1 CGTTCGATTATATGTTCATTAATATT
3116043 CG
1 CG
3116045 AACAGAAGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.52
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTAATATT
Found at i:3122145 original size:31 final size:31
Alignment explanation
Indices: 3122074--3122151 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
3122064 CTTTTAAAAC
* **
3122074 TTGCAATATAATCCCCCAACATTTAGTCTGT
1 TTGCAATATGATCCCCCAACATTTAGTCCAT
* *
3122105 TTGCAATATGATCCCTCAATATTTAGTCCAT
1 TTGCAATATGATCCCCCAACATTTAGTCCAT
*
3122136 TTGCAATATGGTCCCC
1 TTGCAATATGATCCCC
3122152 GACGTAACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (31 bp):
TTGCAATATGATCCCCCAACATTTAGTCCAT
Found at i:3122234 original size:29 final size:29
Alignment explanation
Indices: 3122187--3122259 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
3122177 GCAAATGGAC
*
3122187 TAAATGTT-GGGGACTGTATTGCAAGTTT
1 TAAAAGTTGGGGGACTGTATTGCAAGTTT
3122215 TAAAAGTTGGGGGACTGTATTGCAAGTTT
1 TAAAAGTTGGGGGACTGTATTGCAAGTTT
*
3122244 TAAAAGTTGGGTGACT
1 TAAAAGTTGGGGGACT
3122260 TAAATGAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.27, C:0.07, G:0.30, T:0.36
Consensus pattern (29 bp):
TAAAAGTTGGGGGACTGTATTGCAAGTTT
Found at i:3122274 original size:29 final size:29
Alignment explanation
Indices: 3122187--3122274 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
3122177 GCAAATGGAC
* * * *
3122187 TAAATGTT-GGGGACTGTATTGCAAGTTT
1 TAAAAGTTGGGGGACTGTAATGAAAGCTT
* * *
3122215 TAAAAGTTGGGGGACTGTATTGCAAGTTT
1 TAAAAGTTGGGGGACTGTAATGAAAGCTT
*
3122244 TAAAAGTTGGGTGACT-TAAATGAAAGCTT
1 TAAAAGTTGGGGGACTGT-AATGAAAGCTT
3122273 TA
1 TA
3122275 GAAAAGTTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 8 0.15
29 45 0.85
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (29 bp):
TAAAAGTTGGGGGACTGTAATGAAAGCTT
Found at i:3123508 original size:31 final size:31
Alignment explanation
Indices: 3123435--3123512 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
3123425 CAATTACGTC
3123435 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACGGACTAAATGTTG
*
3123466 AGTGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACGGACTAAATGTTG
* **
3123497 GGGGATTATATTGCAA
1 AGGGACCATATTGCAA
3123513 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.26
Consensus pattern (31 bp):
AGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:3124826 original size:13 final size:14
Alignment explanation
Indices: 3124794--3124835 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 14
3124784 TGCATACAGC
3124794 ATAAGTATATACTTAT
1 ATAAGTATATA--TAT
3124810 ATAAGTATATA-AT
1 ATAAGTATATATAT
3124823 ATAAGTATATATA
1 ATAAGTATATATA
3124836 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 1 0.04
16 11 0.44
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (14 bp):
ATAAGTATATATAT
Found at i:3127287 original size:2 final size:2
Alignment explanation
Indices: 3127280--3127308 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3127270 TCGCATATGT
3127280 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3127309 CAAATACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3128954 original size:15 final size:16
Alignment explanation
Indices: 3128924--3128956 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3128914 ACTAAAATAC
3128924 TAAAACAAAGATAAAA
1 TAAAACAAAGATAAAA
*
3128940 TAAAATAAA-ATAAAA
1 TAAAACAAAGATAAAA
3128955 TA
1 TA
3128957 TTTAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
TAAAACAAAGATAAAA
Found at i:3131116 original size:74 final size:75
Alignment explanation
Indices: 3130935--3131141 Score: 258
Period size: 75 Copynumber: 2.8 Consensus size: 75
3130925 CAAAGCCAAA
** * **
3130935 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGGT
1 AATTCCAGA-TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
3130999 TTGGCTCTGAG
65 TTGGCTCCGAG
*
3131010 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
3131074 TTTGTTCCGAG
65 TTGGCTCCGAG
* * *
3131085 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
3131142 TGTACAACGG
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
74 21 0.18
75 87 0.76
76 7 0.06
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (75 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:3136984 original size:21 final size:21
Alignment explanation
Indices: 3136958--3136997 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3136948 CCTCCTTTGA
*
3136958 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3136979 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3136998 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3139771 original size:75 final size:75
Alignment explanation
Indices: 3139598--3139808 Score: 239
Period size: 75 Copynumber: 2.8 Consensus size: 75
3139588 CAATTCAAAG
* **
3139598 CCAAAAATTCCA-AATTGCTCATAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCT
1 CCAAGAATTCCAGAA-TGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCT
* **
3139661 GAATGGTTTGGCT
63 AAACAGTTTGGCT
*
3139674 CCAAGATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAA
* *
3139739 CAGTTTTGTT
66 CAGTTTGGCT
* * * * *
3139749 CCGAGAATTCCAGTATGCTCGGAGGGAACCGATACCCCCCA-AGGGGGTACCGATTCCCCC
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCC
3139809 TTGTACAACG
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
74 21 0.18
75 61 0.52
76 33 0.28
77 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.20
Consensus pattern (75 bp):
CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAA
CAGTTTGGCT
Found at i:3141156 original size:5 final size:5
Alignment explanation
Indices: 3141148--3141187 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
3141138 TAAGCATATG
* * *
3141148 ATAAA ATAAA ATAAA ATAAA ATAAA CTTAA ATGAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
3141188 GCGTGCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:3144169 original size:18 final size:18
Alignment explanation
Indices: 3144148--3144190 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3144138 GTTGTTTTTA
*
3144148 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
3144166 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
*
3144184 AATTAAA
1 AAATAAA
3144191 TAAATTTAAA
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:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Done.