Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003407.1 Hibiscus syriacus cultivar Beakdansim tig00007179_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: 758105
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 4
Found at i:9808 original size:2 final size:2
Alignment explanation
Indices: 9801--9828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9791 TCCTATGTTC
9801 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
9829 GTATGTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10336 original size:21 final size:20
Alignment explanation
Indices: 10250--10407 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
10240 AAATGACCAA
**
10250 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
10269 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
10289 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
10309 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
10330 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
10351 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
10371 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
10392 AAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
10408 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:10400 original size:20 final size:20
Alignment explanation
Indices: 10375--10426 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
10365 GATTTTCAAG
* *
10375 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAACACAAA
*
10395 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACAAA
10415 AATCGCAACGCG
1 AATCGCAACGCG
10427 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.27, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAACACAAA
Found at i:10436 original size:20 final size:20
Alignment explanation
Indices: 10394--10623 Score: 250
Period size: 20 Copynumber: 11.5 Consensus size: 20
10384 GCGAATATAA
* *
10394 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
10414 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
10434 AAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
10454 AAATAGCAACGCGTATCAGT
1 AAATCGCAACGCGTATCCGT
10474 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
10494 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
10514 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
10534 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
10554 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
10574 AAATCGCAACG-ATAATCCAT
1 AAATCGCAACGCGT-ATCCGT
* * *
10594 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
10614 AAATCACAAC
1 AAATCGCAAC
10624 ACTGAAATTT
Statistics
Matches: 178, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:11354 original size:24 final size:24
Alignment explanation
Indices: 11315--11361 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11305 AAATTTGGTC
11315 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
11339 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
11362 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:13124 original size:23 final size:23
Alignment explanation
Indices: 13098--13142 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13088 CACCACAGCT
*
13098 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
13121 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
13143 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:13391 original size:149 final size:149
Alignment explanation
Indices: 13121--13425 Score: 574
Period size: 149 Copynumber: 2.0 Consensus size: 149
13111 CGAAGTGCCC
* * *
13121 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCCTAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
13186 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
13251 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
*
13270 CGTAGACTTGCACCGTAGTGCCATGTAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
13335 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
13400 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
13419 CGTAGAC
1 CGTAGAC
13426 CCTCGACTCT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:14952 original size:21 final size:21
Alignment explanation
Indices: 14928--14972 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
14918 TTCTTGTTCG
* *
14928 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
14949 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
14970 TTG
1 TTG
14973 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:18523 original size:149 final size:149
Alignment explanation
Indices: 18253--18557 Score: 556
Period size: 149 Copynumber: 2.0 Consensus size: 149
18243 CGAAGTTCCC
* * *
18253 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCCTAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
* *
18318 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGATTTCATACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
18383 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
*
18402 CGTAGACTTGCACCGTAGTGCCATGTAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
18467 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
18532 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
18551 CGTAGAC
1 CGTAGAC
18558 CCTCGACTCT
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:19031 original size:2 final size:2
Alignment explanation
Indices: 19024--19111 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
19014 TCTCTTAGAC
19024 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
19066 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
19108 AT AT
1 AT AT
19112 TCACATGTTC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20148 original size:21 final size:21
Alignment explanation
Indices: 20124--20168 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20114 TCTTGTTCGT
* *
20124 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
20145 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
20166 TTG
1 TTG
20169 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:21670 original size:33 final size:34
Alignment explanation
Indices: 21624--21866 Score: 147
Period size: 33 Copynumber: 6.9 Consensus size: 34
21614 ATTACAATCG
21624 CAATGAGAGAATCGCAATGCGAAATGAAAATCCCAA
1 CAATGA-A-AATCGCAATGCGAAATGAAAATCCCAA
*
21660 CAA-GAAAATCGCAATGCGGAAATGAAAATCGCAATA
1 CAATGAAAATCGCAATGC-GAAATGAAAATC-CCA-A
* * * * *
21696 CGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
1 C--AATGAAAATCGCAATGCGA-AAT-GAAAATCCCAA
* *
21733 -AATGAAAATCGCAATGTGAAATGAAAATCGCAA
1 CAATGAAAATCGCAATGCGAAATGAAAATCCCAA
* * *
21766 CGA-GAGAATCGCAATGCGAAATGAAAATCGCAA
1 CAATGAAAATCGCAATGCGAAATGAAAATCCCAA
* * * * **
21799 TGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGGA
1 --C--AATGAAAATCGCAATGCGA-AAT-GAAAATCCCAA
*
21838 -AATGAAAATCACAATGCGAAATGAAAATC
1 CAATGAAAATCGCAATGCGAAATGAAAATC
21867 GCATTGCGAT
Statistics
Matches: 160, Mismatches: 29, Indels: 39
0.70 0.13 0.17
Matches are distributed among these distances:
32 2 0.01
33 53 0.33
34 47 0.29
35 5 0.03
36 5 0.03
37 2 0.01
38 19 0.12
39 25 0.16
40 2 0.01
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (34 bp):
CAATGAAAATCGCAATGCGAAATGAAAATCCCAA
Found at i:21691 original size:53 final size:53
Alignment explanation
Indices: 21633--21869 Score: 404
Period size: 53 Copynumber: 4.5 Consensus size: 53
21623 GCAATGAGAG
* * *
21633 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
* *
21686 AATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
21739 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
21791 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
21844 AATCACAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
21870 TTGCGATTCT
Statistics
Matches: 173, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
52 50 0.29
53 123 0.71
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:21702 original size:19 final size:19
Alignment explanation
Indices: 21633--21875 Score: 247
Period size: 19 Copynumber: 13.7 Consensus size: 19
21623 GCAATGAGAG
21633 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21652 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
21666 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
21686 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21705 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
21719 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
21739 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21758 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
21772 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21791 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21810 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
21824 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
21844 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21863 AATCGCATTGCGA
1 AATCGCAATGCGA
21876 TTCTCTCGTT
Statistics
Matches: 187, Mismatches: 14, Indels: 46
0.76 0.06 0.19
Matches are distributed among these distances:
14 40 0.21
15 5 0.03
16 6 0.03
17 7 0.04
18 1 0.01
19 90 0.48
20 38 0.20
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:21776 original size:86 final size:84
Alignment explanation
Indices: 21600--21798 Score: 217
Period size: 86 Copynumber: 2.3 Consensus size: 84
21590 GCATTTGACT
* * * * *
21600 ATCGCAACACGGAAATTACAATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGA
1 ATCGCAATAC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAAAAGA
21665 AAATCGCAATGCGGAAATGAAA
65 AAATCGCAA-GCGG-AATGAAA
*
21687 ATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGTGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCG-AAATGAAAATCCCAA----A
*
21752 AATGAAAATCGCAA-C-G-A-GAGA
61 AA-GAAAATCGCAAGCGGAATGAAA
*
21773 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATACGAAATGAAAATCGCAA
21799 TGCGAAATGA
Statistics
Matches: 98, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
86 59 0.60
87 24 0.24
89 1 0.01
90 1 0.01
91 2 0.02
92 11 0.11
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (84 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAAAAGAA
AATCGCAAGCGGAATGAAA
Found at i:21819 original size:105 final size:106
Alignment explanation
Indices: 21633--21869 Score: 404
Period size: 105 Copynumber: 2.2 Consensus size: 106
21623 GCAATGAGAG
*
21633 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATACG
21698 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAA
* * * *
21739 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATACG
*
21803 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAA
*
21844 AATCACAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
21870 TTGCGATTCT
Statistics
Matches: 123, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
105 83 0.67
106 40 0.33
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATACG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAA
Found at i:22028 original size:14 final size:14
Alignment explanation
Indices: 22009--22045 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
21999 CATCAATTAC
22009 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
22023 ACAAATCATCTTTT
1 ACAAATCAACTTTT
22037 ACAAATCAA
1 ACAAATCAA
22046 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:23731 original size:21 final size:21
Alignment explanation
Indices: 23705--23747 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23695 ATTCTGGGTT
* *
23705 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
23726 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
23747 A
1 A
23748 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:23808 original size:66 final size:67
Alignment explanation
Indices: 23705--23877 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
23695 ATTCTGGGTT
* * * *
23705 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATG
23768 CTAG
64 CTAG
* * *
23772 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCT
*
23837 TG
66 AG
* *
23839 AGGGGAATCGATACCCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA-GGGGGGAACCGATACCCCC
23878 ATGAGAAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 2 0.02
66 26 0.28
67 47 0.51
68 18 0.19
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCT
AG
Found at i:24214 original size:29 final size:29
Alignment explanation
Indices: 24180--24251 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
24170 CATATTATGA
**
24180 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
24209 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
24238 TACATGACATGAAT
1 TACATGACATGAAT
24252 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:24306 original size:30 final size:31
Alignment explanation
Indices: 24266--24324 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
24256 AGAAAAGTTC
*
24266 TATGCACTATGTGATAAAGGTATGTAAATGA
1 TATGCACTATGTGATAAAGGTATGGAAATGA
*
24297 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAGGTATGGAAAT
24325 ACTATGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAGGTATGGAAATGA
Found at i:24618 original size:22 final size:22
Alignment explanation
Indices: 24544--24610 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
24534 TTATGGACAT
24544 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
24566 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
24588 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
24610 A
1 A
24611 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:26215 original size:19 final size:19
Alignment explanation
Indices: 26170--26328 Score: 148
Period size: 19 Copynumber: 8.6 Consensus size: 19
26160 TAGTTTACTT
* *
26170 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* *
26190 TCACAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
26209 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
* **
26228 TTGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
26247 TCGCAACGTGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
26266 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
26280 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
26299 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
26318 TCGCAATGCGA
1 TCGCAACGCGA
26329 TTTTGGTTTC
Statistics
Matches: 114, Mismatches: 20, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
14 8 0.07
16 5 0.04
17 4 0.04
19 86 0.75
20 11 0.10
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:26312 original size:52 final size:55
Alignment explanation
Indices: 26170--26323 Score: 170
Period size: 52 Copynumber: 2.8 Consensus size: 55
26160 TAGTTTACTT
* * * *
26170 TCGCAACACGAAACTTAAAATCACAACGCGAAATGAGAATCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAAAATCGCAAC-AG-AACCAAAA
* * *
26228 TTGCAACGCGAAACCAAAATCGCAACGTGAAATGAAAATCGCAAC-G-A-CAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
* **
26280 TCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA
26324 TGCGATTTTG
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
52 43 0.51
53 1 0.01
55 1 0.01
57 27 0.32
58 12 0.14
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (55 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAA
Found at i:26359 original size:14 final size:14
Alignment explanation
Indices: 26340--26398 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
26330 TTTGGTTTCG
26340 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
26354 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
26371 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
26387 CGTTGCGATTTT
1 CGTTGCGATTTT
26399 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:26366 original size:33 final size:33
Alignment explanation
Indices: 26324--26447 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
26314 AAAATCGCAA
*
26324 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
26357 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
26390 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
26423 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
26448 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:26378 original size:19 final size:18
Alignment explanation
Indices: 26324--26415 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
26314 AAAATCGCAA
26324 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
26343 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
26357 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
26376 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
26390 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
26409 TGCGATT
1 TGCGATT
26416 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:26425 original size:14 final size:14
Alignment explanation
Indices: 26373--26429 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
26363 TTTGGTTTCG
*
26373 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
26387 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
26406 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
26420 CGTTGCGATT
1 CGTTGCGATT
26430 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:26611 original size:83 final size:87
Alignment explanation
Indices: 26495--26767 Score: 324
Period size: 93 Copynumber: 3.1 Consensus size: 87
26485 ATGGATTGCA
* **
26495 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ACTTACAGTGAGATACACAGTTTAGCA
*
26554 GAATTGGCAGCAACCGACCAAAT
65 GAATTGGCAGCAACCGAACAAAT
*
26577 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
26642 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
*
26670 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
*
26735 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
26763 TTACT
1 TTACT
26768 AAGCAATCTA
Statistics
Matches: 173, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
82 7 0.04
83 31 0.18
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 128 0.74
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTTACAGTGAGATACACAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:26704 original size:93 final size:93
Alignment explanation
Indices: 26545--26767 Score: 428
Period size: 93 Copynumber: 2.4 Consensus size: 93
26535 TCAGGGTATT
*
26545 AGTTTAGCAGAATTGGCAGCAACCGACCAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
26610 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
26638 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
26703 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
26731 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
26768 AAGCAATCTA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 128 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:28486 original size:20 final size:20
Alignment explanation
Indices: 28454--28559 Score: 95
Period size: 19 Copynumber: 5.7 Consensus size: 20
28444 TTTTGGTTGA
28454 AATG-AAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
28473 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
28493 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
28512 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
28527 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
28546 AATGAAAATCGCAA
1 AATGAAAATCGCAA
28560 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 34 0.47
20 12 0.16
21 12 0.16
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:28505 original size:21 final size:21
Alignment explanation
Indices: 28452--28515 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
28442 TCTTTTGGTT
28452 GAAATG-AAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
28472 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
28492 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
28513 GAA
1 GAA
28516 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.11
20 13 0.36
21 19 0.53
ACGTcount: A:0.47, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:28595 original size:14 final size:14
Alignment explanation
Indices: 28576--28632 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
28566 TTTGGTTTCG
28576 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
28590 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
28609 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
28623 CGTTGCGATT
1 CGTTGCGATT
28633 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:28608 original size:33 final size:33
Alignment explanation
Indices: 28560--28639 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
28550 AAAATCGCAA
**
28560 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
28593 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
28626 TGCGATTTTCATTT
1 TGCGATTTTCATTT
28640 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:28645 original size:21 final size:21
Alignment explanation
Indices: 28620--28693 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
28610 GTTGCGATTC
28620 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
28641 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
28662 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
28683 TCTCGTTGCGA
1 TCTCGTTGCGA
28694 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:28815 original size:33 final size:33
Alignment explanation
Indices: 28773--28843 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
28763 AATACTAACT
28773 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
28806 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
28839 TGAAA
1 TGAAA
28844 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:29250 original size:20 final size:20
Alignment explanation
Indices: 29223--29415 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
29213 CTTTAAAAAT
*
29223 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
29243 CACGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
29263 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
29284 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
29304 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
29324 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
29344 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
29364 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
29384 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
29404 CGCGTTGCGATT
1 CGCGTTGCGATT
29416 CTGGAAAATC
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
20 132 0.89
21 17 0.11
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:38786 original size:2 final size:2
Alignment explanation
Indices: 38779--38812 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38769 TAACAGAATC
38779 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
38813 TTTTGAAAAT
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:48387 original size:16 final size:16
Alignment explanation
Indices: 48366--48410 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
48356 CAAGAGCTCC
48366 AGGGGTGACACTTTTG
1 AGGGGTGACACTTTTG
48382 AGGGGTGACACTTTTG
1 AGGGGTGACACTTTTG
*
48398 AGGGGTGGCACTT
1 AGGGGTGACACTT
48411 GTGGAAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.18, C:0.13, G:0.40, T:0.29
Consensus pattern (16 bp):
AGGGGTGACACTTTTG
Found at i:49196 original size:14 final size:14
Alignment explanation
Indices: 49161--49199 Score: 64
Period size: 12 Copynumber: 2.9 Consensus size: 14
49151 GCTGTAGAAA
49161 AAAATGTTAATTAT
1 AAAATGTTAATTAT
49175 AAAA--TTAATTAT
1 AAAATGTTAATTAT
49187 AAAATGTTAATTA
1 AAAATGTTAATTA
49200 AAATTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
AAAATGTTAATTAT
Found at i:62886 original size:2 final size:2
Alignment explanation
Indices: 62881--62914 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
62871 ACACACGCTC
62881 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
62915 GCATACATGT
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:63690 original size:3 final size:3
Alignment explanation
Indices: 63678--63708 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
63668 TATTAATCTA
63678 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
63709 AAATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:64955 original size:5 final size:5
Alignment explanation
Indices: 64951--65027 Score: 95
Period size: 5 Copynumber: 15.8 Consensus size: 5
64941 ATAATCTATT
* * *
64951 ATATT ATATC ATATC ATATC ATAGC ATACC ATATC ATATC ATATC A-ATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
* *
65000 ATTTC ATATC ATATT ATATC ATAT- ATAT
1 ATATC ATATC ATATC ATATC ATATC ATAT
65028 AATAAAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
4 8 0.13
5 55 0.87
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.42
Consensus pattern (5 bp):
ATATC
Found at i:69390 original size:21 final size:20
Alignment explanation
Indices: 69366--69404 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
69356 CATTAGAAAA
69366 AAATATTAAATAAAAATATAT
1 AAATATTAAA-AAAAATATAT
*
69387 AAATATTAAAAATAATAT
1 AAATATTAAAAAAAATAT
69405 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATTAAAAAAAATATAT
Found at i:81146 original size:16 final size:15
Alignment explanation
Indices: 81125--81157 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
81115 TTGTGAATTT
81125 TTTTAATTAATTTATA
1 TTTTAATTAATTT-TA
81141 TTTTAATTAATTTTA
1 TTTTAATTAATTTTA
81156 TT
1 TT
81158 CGGCCAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATTAATTTTA
Found at i:83414 original size:19 final size:19
Alignment explanation
Indices: 83390--83454 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
83380 TATACAAAAC
83390 TTTTATTGAATATAAACGA
1 TTTTATTGAATATAAACGA
*
83409 TTTTATTTATGAACATAAAC--
1 TTTTA--T-TGAATATAAACGA
*
83429 TTTTATTGAATATAAATGA
1 TTTTATTGAATATAAACGA
83448 TTTTATT
1 TTTTATT
83455 TGTGAACATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
17 9 0.24
18 1 0.03
19 12 0.32
20 5 0.13
21 1 0.03
22 10 0.26
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (19 bp):
TTTTATTGAATATAAACGA
Found at i:83421 original size:22 final size:22
Alignment explanation
Indices: 83391--83469 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
83381 ATACAAAACT
*
83391 TTTATTGAATATAAACGATTTTA
1 TTTA-TGAACATAAACGATTTTA
83414 TTTATGAACATAAAC--TTTTA
1 TTTATGAACATAAACGATTTTA
* *
83434 --T-TGAATATAAATGATTTTA
1 TTTATGAACATAAACGATTTTA
*
83453 TTTGTGAACATAAACGA
1 TTTATGAACATAAACGA
83470 ACAATACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
17 9 0.20
18 1 0.02
19 5 0.11
20 5 0.11
21 1 0.02
22 21 0.46
23 4 0.09
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (22 bp):
TTTATGAACATAAACGATTTTA
Found at i:83440 original size:39 final size:39
Alignment explanation
Indices: 83386--83467 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
83376 AGTATATACA
83386 AAACTTTTATTGAATATAAACGATTTTATTTATGAACAT
1 AAACTTTTATTGAATATAAACGATTTTATTTATGAACAT
* *
83425 AAACTTTTATTGAATATAAATGATTTTATTTGTGAACAT
1 AAACTTTTATTGAATATAAACGATTTTATTTATGAACAT
83464 AAAC
1 AAAC
83468 GAACAATACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (39 bp):
AAACTTTTATTGAATATAAACGATTTTATTTATGAACAT
Found at i:83443 original size:17 final size:17
Alignment explanation
Indices: 83386--83444 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
83376 AGTATATACA
83386 AAACTTTTATTGAATAT
1 AAACTTTTATTGAATAT
*
83403 AAACGATTTTATTTATGAACAT
1 AAAC--TTTTA--T-TGAATAT
83425 AAACTTTTATTGAATAT
1 AAACTTTTATTGAATAT
83442 AAA
1 AAA
83445 TGATTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 13 0.37
18 1 0.03
19 5 0.14
20 5 0.14
21 1 0.03
22 10 0.29
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (17 bp):
AAACTTTTATTGAATAT
Found at i:94599 original size:73 final size:73
Alignment explanation
Indices: 94478--94644 Score: 266
Period size: 73 Copynumber: 2.3 Consensus size: 73
94468 AGATGACGAG
* * * *
94478 TTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGG
1 TTCTTCTCATTATGAACT-TTCTCTGGCAATGATAATCCATCAAATGATGAATTCAAACAAAAGG
94542 TTGAACAAA
65 TTGAACAAA
*
94551 TTCTTCTCATTATGAACTTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGCAATGATAATCCATCAAATGATGAATTCAAACAAAAGGT
94616 TGAACAAA
66 TGAACAAA
94624 TTCTTCTCATTATGAA-TTTCT
1 TTCTTCTCATTATGAACTTTCT
94645 TCTTCTTTAT
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
72 7 0.08
73 81 0.92
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (73 bp):
TTCTTCTCATTATGAACTTTCTCTGGCAATGATAATCCATCAAATGATGAATTCAAACAAAAGGT
TGAACAAA
Found at i:94749 original size:113 final size:112
Alignment explanation
Indices: 94551--95520 Score: 1245
Period size: 113 Copynumber: 8.7 Consensus size: 112
94541 GTTGAACAAA
* *
94551 TTCTTCTCATTATGAACTTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGT
1 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
*
94616 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTATTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTC-TTCTTCAGATGAG
*
94664 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGT
1 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
94729 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATGAG
*
94777 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGT
1 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
94842 TGAACAAATTCTTCTCATTATGAA---CTTCTTCTTC--C-------
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAG
* * * * * * * *
94877 TTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGT
1 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* *
94942 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAAGAG
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGAT---GAG
* * * * * **
94993 TTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAAC-CTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGG
95057 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAG
65 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTC-TTCTTCAGATGAG
95106 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
1 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* * * * *
95171 TAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAG
* * * **
95218 TTCTTCTCATTATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTTGAGCAAAAGGT
1 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* * * * *
95283 TAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAG
* * * * * *
95330 TTCTTCTCATTATGAA-CTTCCTCTGGAAAAGATAATTCATCAAGTAATGAATTCAGGGAAAAGG
1 TTCTTCTCATTATGAACCTT-CTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGG
*
95394 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAG
65 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAG
* * * * ** * *
95442 TTCTTCTCATTATGAA-C-TCTAACTGACACTGCTGATCCA-CCGGTGATGAATTTAAGCAAAAA
1 TTCTTCTCATTATGAACCTTCT--CTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAG
*
95504 GTTGAACAAGTTCTTCT
64 GTTGAACAAATTCTTCT
95521 TCTTCAAATG
Statistics
Matches: 767, Mismatches: 67, Indels: 48
0.87 0.08 0.05
Matches are distributed among these distances:
100 79 0.10
103 6 0.01
104 4 0.01
106 1 0.00
107 1 0.00
109 4 0.01
110 8 0.01
111 35 0.05
112 244 0.32
113 286 0.37
114 1 0.00
115 1 0.00
116 95 0.12
117 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (112 bp):
TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
TGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAG
Found at i:94954 original size:100 final size:100
Alignment explanation
Indices: 94777--94982 Score: 322
Period size: 100 Copynumber: 2.1 Consensus size: 100
94767 TTCAGATGAG
* * * *
94777 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGT
1 TTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAAACAAAAAGT
94842 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
* * * * *
94877 TTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGT
1 TTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAAACAAAAAGT
*
94942 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
66 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
94977 TTCTTC
1 TTCTTC
94983 AGATGAAGAG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (100 bp):
TTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAAACAAAAAGT
TGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
Found at i:95146 original size:329 final size:331
Alignment explanation
Indices: 94550--95458 Score: 1316
Period size: 329 Copynumber: 2.7 Consensus size: 331
94540 GGTTGAACAA
* * *
94550 ATTCTTCTCATTATGAACTTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGG
1 ATTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGG
* * * *
94615 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTATTCAGAT-GAGTTCTTCTCATTATGA
66 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
* * * *
94679 AC-CTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTC
131 ACTCTACTCTGGCAATGATAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATTCTTC
94743 TCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATG
196 TCATTATGAATTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATG
*
94808 ATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
260 ATAATCCATCAAGTGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTC
94873 -T-TC-C
325 TTCTCTC
* * * * *
94877 -TTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAAG
1 ATTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGG
94941 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAAGAGTTCTTCTCATTAT
66 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT--AGAGTTCTTCTCATTAT
* * * *
95006 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCT
129 GAACTCTACTCTGGCAATGATAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATTCT
95070 TCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAA
194 TCTCATTATGAATTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAA
* *
95135 TGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCT
258 TGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCT
95200 TCTTCCTCTTC
323 TCTT-CTC-TC
* *
95211 AGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTTGAGC
1 -----A-TTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGC
*
95276 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATA-AGTTCTTCTCA
60 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCA
* * * * * * * * *
95339 TTATGAACT-TCCTCTGGAAAAGATAATTCATCAAGTAATGAATTCAGGGAAAAGGTTGAACAAA
125 TTATGAACTCTACTCTGGCAATGATAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAA
*
95403 TTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
190 TTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
95459 TCTAACTGAC
Statistics
Matches: 520, Mismatches: 44, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
326 98 0.19
328 1 0.00
329 195 0.38
330 4 0.01
332 2 0.00
334 1 0.00
336 31 0.06
337 85 0.16
338 1 0.00
340 9 0.02
341 93 0.18
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (331 bp):
ATTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGG
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
ACTCTACTCTGGCAATGATAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATTCTTC
TCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGA
TAATCCATCAAGTGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCT
TCTCTC
Found at i:95291 original size:112 final size:112
Alignment explanation
Indices: 94877--95520 Score: 826
Period size: 112 Copynumber: 5.7 Consensus size: 112
94867 TTCTTCTTCC
* * * * *
94877 TTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGGT
94942 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAAGAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGAT--A-AG
* * * * * * *
94993 TTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACT-TTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGG
* * * *
95057 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAG
65 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAG
* * *
95106 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGGT
*
95171 TAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
* *
95218 TTCTTCTCATTATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTTGAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGGT
*
95283 TAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
* * * * * * *
95330 TTCTTCTCATTATGAACTTCCTCTGGAAAAGATAATTCATCAAGTAATGAATTCAGGGAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGGT
* * *
95395 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
* ** * * * ** *
95442 TTCTTCTCATTATGAACTCTAACT-GACACTGCTGATCCA-CCGGTGATGAATTTAAGCAAAAAG
1 TTCTTCTCATTATGAACTTTCTCTGGA-AATGATAATCCATCAAGTGATGAATTTAAGCAAAAGG
95505 TTGAACAAGTTCTTCT
65 TTGAACAAGTTCTTCT
95521 TCTTCAAATG
Statistics
Matches: 465, Mismatches: 59, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
111 34 0.07
112 246 0.53
113 87 0.19
116 96 0.21
117 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTTAAGCAAAAGGT
TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
Found at i:95960 original size:22 final size:22
Alignment explanation
Indices: 95935--95989 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
95925 CATAAAGTTT
*
95935 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
95957 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
95979 TCATCTTTGAA
1 TCATCTTTGAA
95990 GAGTGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:98664 original size:81 final size:82
Alignment explanation
Indices: 98522--98783 Score: 447
Period size: 82 Copynumber: 3.2 Consensus size: 82
98512 CTTATTTCTA
*
98522 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTT-TG-CCAAACCAGATCAGATAACTCAA
98586 AGAACACTTCCAGAAGATG
64 AGAACACTTCCAGAAGATG
* *
98605 CTATGAACAAATTCATC-TCTAAATTCAATGATTGGTTTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTGCCAAACCAGATCAGATAACTCAAAG
98669 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
*
98686 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTGCCAAACCAGATCAGATAACTCAAAG
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTGCCAAACCAGATCAGATAACTCAAAG
98751 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
*
98768 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
98784 TTGTTCCATT
Statistics
Matches: 171, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
80 2 0.01
81 55 0.32
82 98 0.57
83 16 0.09
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (82 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTGCCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATG
Found at i:103001 original size:26 final size:26
Alignment explanation
Indices: 102972--103028 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
102962 ATGTAATTAT
*
102972 GTAAAAATGAAAATGTAAATACAAAC
1 GTAAAAATGAAAATGCAAATACAAAC
* * *
102998 GTAAAAATGCAAATGCAAATTCAAAT
1 GTAAAAATGAAAATGCAAATACAAAC
103024 GTAAA
1 GTAAA
103029 TATGTGAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (26 bp):
GTAAAAATGAAAATGCAAATACAAAC
Found at i:103122 original size:7 final size:7
Alignment explanation
Indices: 103088--103129 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
103078 ATAAAAGTAT
103088 AAATGCA
1 AAATGCA
* *
103095 CAATGAA
1 AAATGCA
103102 AAATGCA
1 AAATGCA
103109 AAGATGCA
1 AA-ATGCA
103117 AAATGC-
1 AAATGCA
103123 AAATGCA
1 AAATGCA
103130 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:106646 original size:3 final size:3
Alignment explanation
Indices: 106638--106735 Score: 99
Period size: 3 Copynumber: 31.7 Consensus size: 3
106628 GGCCCGTTTG
* * *
106638 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* * *
106685 TTA TAA TTA TAA TAAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
106731 TAA TA
1 TAA TA
106736 TTTAAATGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.03
3 67 0.85
4 10 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:106722 original size:31 final size:30
Alignment explanation
Indices: 106639--106735 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 30
106629 GCCCGTTTGT
106639 AATAATAAT-TAATAATAAT-ATTAGTAATA
1 AATAATAATATAATAATAATAATTA-TAATA
* * *
106668 AATAATAAAATTAGTAATTATAATTATAATA
1 AATAATAATA-TAATAATAATAATTATAATA
*
106699 AATAATAATTATAATAATAATAATAATAAT-
1 AATAATAA-TATAATAATAATAATTATAATA
106729 AATAATA
1 AATAATA
106736 TTTAAATGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
29 8 0.14
30 7 0.12
31 37 0.65
32 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
AATAATAATATAATAATAATAATTATAATA
Found at i:120289 original size:12 final size:12
Alignment explanation
Indices: 120272--120299 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
120262 CCACCCACCG
120272 CCGCAACCTCCA
1 CCGCAACCTCCA
120284 CCGCAACCTCCA
1 CCGCAACCTCCA
120296 CCGC
1 CCGC
120300 CACTACCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.61, G:0.11, T:0.07
Consensus pattern (12 bp):
CCGCAACCTCCA
Found at i:122438 original size:18 final size:17
Alignment explanation
Indices: 122411--122445 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
122401 TCACAGGTTG
*
122411 AAGTCCCATAACATAATT
1 AAGTCACATAACA-AATT
122429 AAGTCACATAACAAATT
1 AAGTCACATAACAAATT
122446 CTTGGTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (17 bp):
AAGTCACATAACAAATT
Found at i:132981 original size:13 final size:13
Alignment explanation
Indices: 132963--132999 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
132953 AATTCATAAC
132963 AATTAAATATTTT
1 AATTAAATATTTT
132976 AATTAAATATTTT
1 AATTAAATATTTT
132989 AATTAAATATT
1 AATTAAATATT
133000 AAATTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTAAATATTTT
Found at i:138799 original size:17 final size:17
Alignment explanation
Indices: 138785--138832 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
138775 TAAAAATATT
138785 TAATAAAATAAAATAGA
1 TAATAAAATAAAATAGA
*
138802 TAATAAAAAAATAATAG-
1 TAATAAAATAA-AATAGA
*
138819 TAGTAAAGATAAAA
1 TAATAAA-ATAAAA
138833 AGAGGGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (17 bp):
TAATAAAATAAAATAGA
Found at i:139546 original size:63 final size:63
Alignment explanation
Indices: 139479--139647 Score: 234
Period size: 63 Copynumber: 2.7 Consensus size: 63
139469 TAAAACATCT
* * *
139479 TAAATCCTAATTAAAACACTTAAA-CTATTTAAACTAAAATACCTAAAA-AATAATATAATATTC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA-AA-ATAATATCC
* *
139542 TAAATCCTAACTAAAATACTAAAACCTATTTAAATTAAAATACCTAAAACAAAAATAATATCC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAATATCC
* * *
139605 TAAAACTTAATTAAAATACTAAAACCTAATTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
139648 AAAGATAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 67 0.71
64 25 0.27
65 2 0.02
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (63 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAATATCC
Found at i:139569 original size:19 final size:19
Alignment explanation
Indices: 139513--139638 Score: 72
Period size: 19 Copynumber: 6.2 Consensus size: 19
139503 CTATTTAAAC
**
139513 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * * *
139533 ATAATATTCTAAATCCTAAC
1 -TAAAATACTAAAACCTAAT
139553 TAAAATACTAAAACCTATTTAAAT
1 TAAAATACTAAAACC----T-AAT
** *
139577 TAAAATACCTAAAACAAAAA
1 TAAAATA-CTAAAACCTAAT
* * *
139597 TAATATCCTAAAACTTAAT
1 TAAAATACTAAAACCTAAT
139616 TAAAATACTAAAACCTAAT
1 TAAAATACTAAAACCTAAT
139635 TAAA
1 TAAA
139639 CTAAAATACA
Statistics
Matches: 78, Mismatches: 21, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
19 41 0.53
20 15 0.19
21 5 0.06
23 1 0.01
24 9 0.12
25 7 0.09
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:139663 original size:63 final size:63
Alignment explanation
Indices: 139452--139663 Score: 225
Period size: 63 Copynumber: 3.3 Consensus size: 63
139442 TATAGCCTTC
* * * * * * * *
139452 AAATTCCTAAAAAAAGCTAAAACATCTTAAATCCTAATTAAAACACTTAAA-CTATTTAAACTA
1 AAATACCTAAAAAAA-ATATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTA
* * * *
139515 AAATACCTAAAAAATAATATAATATTCTAAATCCTAACTAAAATACTAAAACCTATTTAAATTA
1 AAATACCTAAAAAA-AATATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTA
* *
139579 AAATACCTAAAACAAAA-ATAATATCCTAAAACTTAATTAAAATACTAAAACCTAATTAAACTA
1 AAATACCTAAAA-AAAATATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTA
139642 AAATA-C-AAAGATAAAATATAAT
1 AAATACCTAAA-A-AAAATATAAT
139664 GTTTAAAACA
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
61 3 0.02
62 6 0.05
63 90 0.71
64 26 0.20
65 2 0.02
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.28
Consensus pattern (63 bp):
AAATACCTAAAAAAAATATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTA
Found at i:142015 original size:103 final size:103
Alignment explanation
Indices: 141844--142164 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
141834 TAATGTCCAT
* *
141844 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
141909 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
141947 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
*
142012 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
142050 AATGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
142115 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
142153 AAGGACCACATA
1 AAGGACCACATA
142165 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:143037 original size:64 final size:64
Alignment explanation
Indices: 142883--143039 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 64
142873 TAATGAAGGT
** * ** *
142883 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACCAATGCATCGATGCATAAAATGTATTCGATGTTTGTTTATTAAAGAG
* * * * *
142947 ATGCATCGATGCA-TGCCTTATACATCGATGCACT-AATTGTATTCGATGTTT-TTATTTTCAAA
1 ATGCATCGATGCACTACC-AATGCATCGATGCA-TAAAATGTATTCGATGTTTGTT-TATT-AAA
143009 GAG
62 GAG
143012 -TGCATCGATGCACTACCAATGCATCGAT
1 ATGCATCGATGCACTACCAATGCATCGAT
143040 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
63 4 0.05
64 64 0.85
65 7 0.09
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACCAATGCATCGATGCATAAAATGTATTCGATGTTTGTTTATTAAAGAG
Found at i:143100 original size:21 final size:21
Alignment explanation
Indices: 143074--143129 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
143064 TTAACATTGA
143074 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
143095 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
*
143116 TGCATTGATGCACT
1 TGCATCGATGCACT
143130 CTGCCCAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
TGCATCGATGCACTATGAATG
Found at i:144317 original size:5 final size:5
Alignment explanation
Indices: 144309--144358 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
144299 TAAGCATCTG
** *
144309 ATAAA ATAAA ATAAA AT-AA ATGGA ATGAA AT-AA ATAAA ATAAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA
144358 A
1 A
144359 CGAAATGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 8 0.20
5 27 0.68
6 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:147306 original size:18 final size:18
Alignment explanation
Indices: 147285--147327 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
147275 GTGATTTTTA
*
147285 AAATAAAAGATAAGAATG
1 AAATAAAAGAAAAGAATG
* *
147303 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATG
147321 AAATAAA
1 AAATAAA
147328 TAAATTAAAG
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:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATG
Found at i:148009 original size:19 final size:19
Alignment explanation
Indices: 147981--148078 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 19
147971 ATATAATATT
*
147981 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
148000 CTAAAACCTATTTAAATTAAAATA
1 CTAAAACC----T-AATTAAAATA
** * ** *
148024 CCTAAAACAAAAATAATGTC
1 -CTAAAACCTAATTAAAATA
*
148044 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
148063 CTAAAACCTAATTAAA
1 CTAAAACCTAATTAAA
148079 TTAAAATACA
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
19 35 0.59
20 6 0.10
23 1 0.02
24 10 0.17
25 7 0.12
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:148062 original size:63 final size:65
Alignment explanation
Indices: 147910--148087 Score: 218
Period size: 63 Copynumber: 2.8 Consensus size: 65
147900 AACAAGCTAA
* * ** * *
147910 AATATCTTAAATCCTAATTAAAACGCTTAAAA-CTATTTAAACTAGAATACCTAAAAAAATAATA
1 AATATCCTAAAACCTAATTAAAATAC-TAAAACCTATTTAAATTAAAATACCTAAAAAAATAATA
147974 T
65 T
* * *
147975 AATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAATTAAAATACCTAAAACAA-AA-AT
1 AATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAATTAAAATACCTAAAAAAATAATAT
* * *
148038 AATGTCCTAAAACTTAATTAAAATACTAAAACCTAATTAAATTAAAATAC
1 AATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAATTAAAATAC
148088 AAAGATAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
63 47 0.47
64 7 0.07
65 46 0.46
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (65 bp):
AATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAATTAAAATACCTAAAAAAATAATAT
Found at i:163503 original size:29 final size:29
Alignment explanation
Indices: 163424--163505 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
163414 CTTCCCAGCA
* * *
163424 TAGGTCGCCATGC-C-CTCGGGTGACCTTG
1 TAGGTCGCCATGCACGCT-GGGCGACATGG
**
163452 TAGGTCGCCATGCACGCCAGGCGACATGG
1 TAGGTCGCCATGCACGCTGGGCGACATGG
163481 TAGGTCGCCATGCACGCTGGGCGAC
1 TAGGTCGCCATGCACGCTGGGCGAC
163506 CTTGTCATGC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 13 0.29
29 31 0.69
30 1 0.02
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCTGGGCGACATGG
Found at i:163546 original size:22 final size:23
Alignment explanation
Indices: 163515--163558 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
163505 CCTTGTCATG
* *
163515 CGCCTTGCTCCTCGCTGCATGCT
1 CGCCTTGCTCCCCACTGCATGCT
163538 CGCC-TGCTCCCCACTGCATGC
1 CGCCTTGCTCCCCACTGCATGC
163559 AGGCGACCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.07, C:0.48, G:0.20, T:0.25
Consensus pattern (23 bp):
CGCCTTGCTCCCCACTGCATGCT
Found at i:163650 original size:31 final size:31
Alignment explanation
Indices: 163589--163650 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
163579 CATGGCGCAT
*
163589 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAACTCGTA
* *
163620 GCAAAGCTTCATCCTCTCGCCACAATTCGTA
1 GCAAAGCTTCATCCTCTCACCACAACTCGTA
163651 TAGAACACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAACTCGTA
Found at i:169935 original size:21 final size:21
Alignment explanation
Indices: 169882--169925 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
169872 TCCTTACACT
*
169882 TCAATACTATAAATCATCATA
1 TCAACACTATAAATCATCATA
*
169903 TCAACACTATAAATTATCATA
1 TCAACACTATAAATCATCATA
169924 TC
1 TC
169926 CACGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (21 bp):
TCAACACTATAAATCATCATA
Found at i:177961 original size:2 final size:2
Alignment explanation
Indices: 177915--177948 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
177905 AATACCCATT
177915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
177949 CTCTCACATA
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):
TA
Found at i:183389 original size:201 final size:201
Alignment explanation
Indices: 183044--183445 Score: 804
Period size: 201 Copynumber: 2.0 Consensus size: 201
183034 TTTGACTCCA
183044 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTTAGAGCATCTGTTGAATC
1 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTTAGAGCATCTGTTGAATC
183109 TTTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTTCACAGAATTTATCGAATTCTCTT
66 TTTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTTCACAGAATTTATCGAATTCTCTT
183174 TAGCATTTGGGCATTGAAGACAGTACACACACACACACGTGTATATAATGTGTGTACCAAAGTTG
131 TAGCATTTGGGCATTGAAGACAGTACACACACACACACGTGTATATAATGTGTGTACCAAAGTTG
183239 GGGTGG
196 GGGTGG
183245 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTTAGAGCATCTGTTGAATC
1 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTTAGAGCATCTGTTGAATC
183310 TTTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTTCACAGAATTTATCGAATTCTCTT
66 TTTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTTCACAGAATTTATCGAATTCTCTT
183375 TAGCATTTGGGCATTGAAGACAGTACACACACACACACGTGTATATAATGTGTGTACCAAAGTTG
131 TAGCATTTGGGCATTGAAGACAGTACACACACACACACGTGTATATAATGTGTGTACCAAAGTTG
183440 GGGTGG
196 GGGTGG
183446 CCGCAGATAA
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 201 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (201 bp):
TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTTAGAGCATCTGTTGAATC
TTTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTTCACAGAATTTATCGAATTCTCTT
TAGCATTTGGGCATTGAAGACAGTACACACACACACACGTGTATATAATGTGTGTACCAAAGTTG
GGGTGG
Found at i:186008 original size:24 final size:24
Alignment explanation
Indices: 185976--186021 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
185966 CAATTGCTCC
185976 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
186000 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
186022 TTCTACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:191127 original size:24 final size:24
Alignment explanation
Indices: 191095--191140 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
191085 CAATTGCTCC
191095 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
191119 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
191141 TTCTACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:193249 original size:17 final size:18
Alignment explanation
Indices: 193226--193266 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
193216 AATCTTTTTT
193226 TATTTAA-T-AAAAATAA
1 TATTTAATTGAAAAATAA
193242 TGATTTAATTGAAAAATAA
1 T-ATTTAATTGAAAAATAA
193261 TATTTA
1 TATTTA
193267 TAGTAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 6 0.27
18 6 0.27
19 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TATTTAATTGAAAAATAA
Found at i:195044 original size:3 final size:3
Alignment explanation
Indices: 195036--195060 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
195026 GTGGCTTAGT
195036 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
195061 ATTTTGTATT
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:201187 original size:15 final size:16
Alignment explanation
Indices: 201163--201203 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
201153 CTTTCGATAA
201163 CCTC-TTCTTCCTCTT
1 CCTCGTTCTTCCTCTT
*
201178 -CTCGTTCTTCTTCTT
1 CCTCGTTCTTCCTCTT
*
201193 CCTTGTTCTTC
1 CCTCGTTCTTC
201204 TTCTCTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.00, C:0.39, G:0.05, T:0.56
Consensus pattern (16 bp):
CCTCGTTCTTCCTCTT
Found at i:201202 original size:16 final size:15
Alignment explanation
Indices: 201167--201207 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
201157 CGATAACCTC
*
201167 TTCTTCCTCTTCTCG
1 TTCTTCTTCTTCTCG
*
201182 TTCTTCTTCTTCCTTG
1 TTCTTCTTCTT-CTCG
201198 TTCTTCTTCT
1 TTCTTCTTCT
201208 CTCCAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.00, C:0.34, G:0.05, T:0.61
Consensus pattern (15 bp):
TTCTTCTTCTTCTCG
Found at i:207659 original size:26 final size:27
Alignment explanation
Indices: 207592--207663 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
207582 TGTAGATATT
*
207592 TTATAATTTTAATTATATATAATCGAA
1 TTATAATTTTAATTATATGTAATCGAA
* *
207619 TTA-AATTTT-A--A-ATGTAAT-TAC
1 TTATAATTTTAATTATATGTAATCGAA
207640 TTATAATTTTAATTATATGTAATC
1 TTATAATTTTAATTATATGTAATC
207664 AGTCAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
21 4 0.11
22 12 0.33
23 2 0.06
25 2 0.06
26 13 0.36
27 3 0.08
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (27 bp):
TTATAATTTTAATTATATGTAATCGAA
Found at i:215714 original size:2 final size:2
Alignment explanation
Indices: 215709--215735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
215699 ACACACACAC
215709 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
215736 AAAAAGACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:220870 original size:14 final size:14
Alignment explanation
Indices: 220851--220878 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
220841 GGGCAAGGAG
220851 GGTATTGTCTATAA
1 GGTATTGTCTATAA
220865 GGTATTGTCTATAA
1 GGTATTGTCTATAA
220879 TACTCCTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
GGTATTGTCTATAA
Found at i:227594 original size:17 final size:17
Alignment explanation
Indices: 227553--227597 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
227543 CTCTACTTGA
227553 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
227570 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
227587 TTAAATATTTA
1 TTAAATATTTA
227598 TTTTTACATA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:242761 original size:64 final size:62
Alignment explanation
Indices: 242693--242900 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 62
242683 TGCACTAAGA
*
242693 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGTATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGG-TG
* * *
242757 GTGCATCGATGCATTAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATAC-CAGAGTGCATCGATGCATGGT-
*
242821 T
62 G
* * *
242822 GTGCATCGATGCATGAAATGCATTCAATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATGG--
242885 TG
61 TG
*
242887 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
242901 CACTTTGAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.39
65 65 0.54
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGTG
Found at i:252646 original size:17 final size:17
Alignment explanation
Indices: 252613--252646 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
252603 TTGAATATTT
* *
252613 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
252630 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
252647 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:258927 original size:22 final size:21
Alignment explanation
Indices: 258886--258932 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
258876 GAGCTTATTT
*
258886 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
258907 TCATTTTT-ATATTTTAAAA-A
1 TCATTTTTCA-ATTTTAAAACA
258927 -CATTTT
1 TCATTTT
258933 CTCATAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:264345 original size:31 final size:31
Alignment explanation
Indices: 264307--264462 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
264297 AGGGTCGAGG
*
264307 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
264338 GTTTACCTATGTTCTTCGGGACATATAGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
264369 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
264400 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
264431 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
264462 G
1 G
264463 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:264968 original size:21 final size:21
Alignment explanation
Indices: 264943--264985 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
264933 AAAGAATATA
264943 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
264964 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
264985 T
1 T
264986 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:268734 original size:31 final size:31
Alignment explanation
Indices: 268696--268851 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
268686 AGGGTCGAGG
268696 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
268727 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
268758 GTTTACCTATGTTCTTCGGGACATGTGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
268789 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
268820 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
268851 G
1 G
268852 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:269355 original size:21 final size:21
Alignment explanation
Indices: 269330--269372 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
269320 AAAGAATATA
269330 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
269351 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
269372 T
1 T
269373 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:269672 original size:24 final size:24
Alignment explanation
Indices: 269645--269690 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
269635 TCATATAAAT
269645 TGCACCAAAGTGCCACGTAGAATA
1 TGCACCAAAGTGCCACGTAGAATA
***
269669 TGCATTGAAGTGCCACGTAGAA
1 TGCACCAAAGTGCCACGTAGAA
269691 ATGTCCCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (24 bp):
TGCACCAAAGTGCCACGTAGAATA
Found at i:269707 original size:23 final size:23
Alignment explanation
Indices: 269681--269772 Score: 89
Period size: 23 Copynumber: 4.1 Consensus size: 23
269671 CATTGAAGTG
269681 CCACGTAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCGAAGGA
* *
269704 CCAC--ATAAATGTCCCGAATGA
1 CCACGTAGAAATGTCCCGAAGGA
** * *
269725 CCGTGTAAAAATGTCCCAAAGGA
1 CCACGTAGAAATGTCCCGAAGGA
* * *
269748 CCACGTAGAATTGTCTCGAATGA
1 CCACGTAGAAATGTCCCGAAGGA
269771 CC
1 CC
269773 GTATAGAACC
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
21 17 0.32
23 36 0.68
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCGAAGGA
Found at i:271204 original size:30 final size:30
Alignment explanation
Indices: 271170--271226 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
271160 ATATAATACG
271170 CAAAGAATAAATTTTAAATTCATTTTCCCC
1 CAAAGAATAAATTTTAAATTCATTTTCCCC
271200 CAAAGAATAAATTTTAAATTCATTTTC
1 CAAAGAATAAATTTTAAATTCATTTTC
271227 TTGACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.39
Consensus pattern (30 bp):
CAAAGAATAAATTTTAAATTCATTTTCCCC
Found at i:291164 original size:23 final size:24
Alignment explanation
Indices: 291138--291200 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
291128 ATAATATGTT
291138 TTCGTCCCCTAAATATTTT-TAAG
1 TTCGTCCCCTAAATATTTTATAAG
**
291161 TTCGTTCTGCTAAA-ATTTTATAAG
1 TTCG-TCCCCTAAATATTTTATAAG
*
291185 TTCGTCCCCTTAATAT
1 TTCGTCCCCTAAATAT
291201 AAAATCTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (24 bp):
TTCGTCCCCTAAATATTTTATAAG
Found at i:296865 original size:20 final size:20
Alignment explanation
Indices: 296840--296932 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
296830 TTTTCCCAAT
296840 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
296860 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
296880 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
296901 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
296922 TCGCAATGCGA
1 TCGCAATGCGA
296933 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:296882 original size:41 final size:41
Alignment explanation
Indices: 296837--296932 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
296827 CGATTTTCCC
296837 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
296878 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
296919 AAATCGCAATGCGA
1 AATTCGCAATGCGA
296933 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:296886 original size:21 final size:20
Alignment explanation
Indices: 296840--296932 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
296830 TTTTCCCAAT
*
296840 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
296860 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
296880 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
296901 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
296922 TCGCAATGCGA
1 TCGCAATGCGA
296933 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:296945 original size:41 final size:41
Alignment explanation
Indices: 296859--296993 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
296849 GAATAAGTAA
* * *
296859 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
296900 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
296941 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
296982 TTCGCAACGCGA
1 ATCGCAACGCGA
296994 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:296946 original size:20 final size:20
Alignment explanation
Indices: 296921--297014 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
296911 AATTGGGAAA
*
296921 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
296941 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
296962 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
296982 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
297002 TTCGCAACGCGAT
1 ATCGCAACGCGAT
297015 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:297572 original size:19 final size:19
Alignment explanation
Indices: 297535--297600 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
297525 TTCGAGAATG
*
297535 AAATCGCAAAGCGGAAATAA
1 AAATCGCAACGC-GAAATAA
**
297555 CTATCGCAACGCGAAATAA
1 AAATCGCAACGCGAAATAA
**
297574 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAATAA
297593 AAATCGCA
1 AAATCGCA
297601 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.77
20 9 0.23
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (19 bp):
AAATCGCAACGCGAAATAA
Found at i:297618 original size:19 final size:19
Alignment explanation
Indices: 297596--297646 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
297586 GAAACCAAAA
*
297596 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
297615 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
297634 TCGCGTTGCGATT
1 TCGCGTTGCGATT
297647 CTCTCGTCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:297666 original size:33 final size:33
Alignment explanation
Indices: 297629--297716 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
297619 GTTGCGATTT
*
297629 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
297662 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
297695 TCATTTCCGCGTTGCAATTCTC
1 TCATTT-CGCGTTGCGATTCTC
297717 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:299800 original size:42 final size:42
Alignment explanation
Indices: 299740--299862 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
299730 GCCCGACTCG
* * *
299740 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
299782 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
299824 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
299863 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:299820 original size:21 final size:21
Alignment explanation
Indices: 299796--299862 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
299786 TCATTCCTCG
299796 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
299817 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
299838 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
299859 AGAG
1 AGAG
299863 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:301239 original size:14 final size:14
Alignment explanation
Indices: 301220--301255 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
301210 ATTGTTTAAT
301220 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
301234 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
301248 TGATTTGT
1 TGATTTGT
301256 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:301480 original size:33 final size:33
Alignment explanation
Indices: 301438--301531 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
301428 ATTAAATTCG
*
301438 CGTTGCGATTTTCATTTCACATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
301471 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
301504 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
301532 AGTAATTTCT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:301497 original size:19 final size:19
Alignment explanation
Indices: 301434--301531 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
301424 CGAAATTAAA
*
301434 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
301453 TTCACATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
301469 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
301486 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
301502 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
301519 TTCGCATTGCGAT
1 TTCGCATTGCGAT
301532 AGTAATTTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 12 0.20
16 12 0.20
17 13 0.22
19 23 0.38
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:303798 original size:42 final size:42
Alignment explanation
Indices: 303738--303821 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
303728 GCCCGACTCG
* * *
303738 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
303780 CCTATCATTCCTCGAGAGTCCTCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
303822 ACTGTCACCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:304092 original size:12 final size:12
Alignment explanation
Indices: 304075--304099 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
304065 TCTTCGGGGA
304075 CTTTTTCTTCTT
1 CTTTTTCTTCTT
304087 CTTTTTCTTCTT
1 CTTTTTCTTCTT
304099 C
1 C
304100 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:305876 original size:14 final size:14
Alignment explanation
Indices: 305857--305893 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
305847 CATCAATTAA
305857 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
305871 ACAAATCATCTTTT
1 ACAAATCAACATTT
305885 ACAAATCAA
1 ACAAATCAA
305894 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:306284 original size:20 final size:20
Alignment explanation
Indices: 306259--306315 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
306249 TTCATTTGAC
*
306259 TATCGCAATGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
306279 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
* *
306299 TATCACAACGAGAAAAT
1 TATCGCAACGCGAAAAT
306316 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGT
Found at i:306358 original size:14 final size:14
Alignment explanation
Indices: 306339--306392 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
306329 GAAAATCGCA
306339 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
306353 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
306370 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
306386 TTGCGAT
1 TTGCGAT
306393 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:306358 original size:33 final size:33
Alignment explanation
Indices: 306321--306391 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
306311 AAAATCGCAA
306321 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
306354 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
306387 TGCGA
1 TGCGA
306392 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Done.