Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021437.1 Corchorus olitorius cultivar O-4 contig21470, 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: 97919
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1527 original size:13 final size:13
Alignment explanation
Indices: 1502--1536 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
1492 TCCTTGCCCC
1502 GTTTTGACTGTTCG
1 GTTTTG-CTGTTCG
1516 GTTTTGCTGTTCG
1 GTTTTGCTGTTCG
1529 GTTTTGCT
1 GTTTTGCT
1537 TTCTGTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.03, C:0.14, G:0.29, T:0.54
Consensus pattern (13 bp):
GTTTTGCTGTTCG
Found at i:2387 original size:15 final size:15
Alignment explanation
Indices: 2367--2395 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2357 TAAAAGTACC
2367 TCCCATCCCGTCCCG
1 TCCCATCCCGTCCCG
2382 TCCCATCCCGTCCC
1 TCCCATCCCGTCCC
2396 TTACTGGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.62, G:0.10, T:0.21
Consensus pattern (15 bp):
TCCCATCCCGTCCCG
Found at i:3617 original size:20 final size:20
Alignment explanation
Indices: 3592--3632 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3582 AGCTGCAGCA
3592 CTTTCTTGTTACACTTCTCT
1 CTTTCTTGTTACACTTCTCT
3612 CTTTCTTGTTACACTTCTCT
1 CTTTCTTGTTACACTTCTCT
3632 C
1 C
3633 GAGCTCTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.32, G:0.05, T:0.54
Consensus pattern (20 bp):
CTTTCTTGTTACACTTCTCT
Found at i:5105 original size:82 final size:82
Alignment explanation
Indices: 4968--5128 Score: 295
Period size: 82 Copynumber: 2.0 Consensus size: 82
4958 TGATAAAGAA
*
4968 TAAACTGTAAGCATAATACAAATTAGGTTTTGTTATATGCTTCAGTGTATTAGAAATTATTAGTC
1 TAAACTGTAAGCATAATACAAATTAGGTTTTGTAATATGCTTCAGTGTATTAGAAATTATTAGTC
5033 AGTTTGTGTCTAAACTC
66 AGTTTGTGTCTAAACTC
*
5050 TAAACTGTAAGCATACTACAAATTAGGTTTTGTAATATGCTTCAGTGTATTAGAAATTATTAGTC
1 TAAACTGTAAGCATAATACAAATTAGGTTTTGTAATATGCTTCAGTGTATTAGAAATTATTAGTC
*
5115 GGTTTGTGTCTAAA
66 AGTTTGTGTCTAAA
5129 ATATGTTGCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (82 bp):
TAAACTGTAAGCATAATACAAATTAGGTTTTGTAATATGCTTCAGTGTATTAGAAATTATTAGTC
AGTTTGTGTCTAAACTC
Found at i:5917 original size:26 final size:25
Alignment explanation
Indices: 5888--5946 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
5878 TTTACTTCTA
*
5888 AATTTTTGGAGTTATTGAATTGGTAC
1 AATTTTTGGAGGTA-TGAATTGGTAC
*
5914 AATTTTTTTTGAGGTATGAATTGGTAC
1 AA--TTTTTGGAGGTATGAATTGGTAC
5941 AATTTT
1 AATTTT
5947 AATGATTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 4 0.14
26 2 0.07
27 13 0.45
28 10 0.34
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.49
Consensus pattern (25 bp):
AATTTTTGGAGGTATGAATTGGTAC
Found at i:6480 original size:24 final size:26
Alignment explanation
Indices: 6453--6518 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
6443 ATTCATTTTT
*
6453 TTTAAATAAAAATAATGA-TT-AAAA
1 TTTAAATAAAAATAATAATTTCAAAA
**
6477 TTTATTTAAAAATAA-AATTTCAAAA
1 TTTAAATAAAAATAATAATTTCAAAA
*
6502 -TTAAAAAAAAATAATAA
1 TTTAAATAAAAATAATAA
6519 CAAGCAACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.03
24 26 0.79
25 6 0.18
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
TTTAAATAAAAATAATAATTTCAAAA
Found at i:6711 original size:16 final size:15
Alignment explanation
Indices: 6690--6722 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
6680 TCAAACTCGA
6690 GAACCCGTCCGAACCC
1 GAACCCGTCC-AACCC
6706 GAACCCGTCCAACCC
1 GAACCCGTCCAACCC
6721 GA
1 GA
6723 TTTGACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.27, C:0.48, G:0.18, T:0.06
Consensus pattern (15 bp):
GAACCCGTCCAACCC
Found at i:6801 original size:16 final size:15
Alignment explanation
Indices: 6782--6841 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 15
6772 CGAACCTGAG
6782 ACCCGAATGACCCGTA
1 ACCCGAATGACCCG-A
6798 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCG-A
*
6814 ACCCGAGTGACCCGA
1 ACCCGAATGACCCGA
*
6829 GACCCAAATGACC
1 -ACCCGAATGACC
6842 TGTGACCCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 2 0.05
16 34 0.92
17 1 0.03
ACGTcount: A:0.33, C:0.38, G:0.20, T:0.08
Consensus pattern (15 bp):
ACCCGAATGACCCGA
Found at i:6846 original size:23 final size:23
Alignment explanation
Indices: 6820--6864 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6810 CGAAACCCGA
*
6820 GTGACCCGAGACCCAAATGACCT
1 GTGACCCAAGACCCAAATGACCT
*
6843 GTGACCCAAGACCCATATGACC
1 GTGACCCAAGACCCAAATGACC
6865 CGGATAACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.36, G:0.20, T:0.13
Consensus pattern (23 bp):
GTGACCCAAGACCCAAATGACCT
Found at i:7444 original size:42 final size:42
Alignment explanation
Indices: 7392--7473 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
7382 TGTTGACACA
*
7392 TACCCCACCTGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
*
7434 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAA
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAA
7474 TTAATATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (42 bp):
TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
Found at i:7708 original size:16 final size:16
Alignment explanation
Indices: 7689--7734 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
7679 AACCCGCCCA
7689 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* *
7705 ACCCGAAACCCGTATG
1 ACCCGAGACCCGAATG
*
7721 ACCCGTGACCCGAA
1 ACCCGAGACCCGAA
7735 ACCCGAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.30, C:0.39, G:0.22, T:0.09
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:7747 original size:23 final size:23
Alignment explanation
Indices: 7703--7747 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
7693 GAGACCCGAA
* *
7703 TGACCCGAAACCCGTATGACCCG
1 TGACCCGAAACCCGAATAACCCG
7726 TGACCCGAAACCCGAATAACCC
1 TGACCCGAAACCCGAATAACCC
7748 AAATCCAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.40, G:0.18, T:0.11
Consensus pattern (23 bp):
TGACCCGAAACCCGAATAACCCG
Found at i:8146 original size:44 final size:44
Alignment explanation
Indices: 8097--8260 Score: 276
Period size: 44 Copynumber: 3.7 Consensus size: 44
8087 GAACTTGATA
*
8097 ATTTGATTCAAGGGTCTTAGCGACTTGATTTTGAATTGATGAGG
1 ATTTGATTCAAGGGTCTTAGCGACTTGATCTTGAATTGATGAGG
*
8141 ATTTGATTCAAGGGTCTTGGCGACTTGATCTTGAATTGATGAGG
1 ATTTGATTCAAGGGTCTTAGCGACTTGATCTTGAATTGATGAGG
* *
8185 ATTTGACTCAAGGGTCTTGGCGACTTGATCTTGAATTG-TCGAGG
1 ATTTGATTCAAGGGTCTTAGCGACTTGATCTTGAATTGAT-GAGG
8229 ATTTGATTCAAGGGTCTTAGCGACTTGATCTT
1 ATTTGATTCAAGGGTCTTAGCGACTTGATCTT
8261 AAACGAACAA
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
43 1 0.01
44 113 0.99
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (44 bp):
ATTTGATTCAAGGGTCTTAGCGACTTGATCTTGAATTGATGAGG
Found at i:8450 original size:27 final size:28
Alignment explanation
Indices: 8383--8469 Score: 122
Period size: 27 Copynumber: 3.0 Consensus size: 28
8373 ATTCTTCAAG
*
8383 AATAATTCTCCAATAATTTTGGATCTTTTTTC
1 AATAATTCTCCAATAACTTTGGATC----TTC
8415 AATAATTCTCCAATAA-TTTGGATCTTC
1 AATAATTCTCCAATAACTTTGGATCTTC
8442 AATAATTCTCCAATAACTTTGGATCTTC
1 AATAATTCTCCAATAACTTTGGATCTTC
8470 TTTGATAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
27 19 0.35
28 11 0.20
31 8 0.15
32 16 0.30
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (28 bp):
AATAATTCTCCAATAACTTTGGATCTTC
Found at i:8481 original size:34 final size:32
Alignment explanation
Indices: 8383--8571 Score: 210
Period size: 34 Copynumber: 5.9 Consensus size: 32
8373 ATTCTTCAAG
* *
8383 AATAATTCTCCAATAATTTTGGATCTT-TTTT
1 AATAATTATCCAATAACTTTGGATCTTCTTTT
*
8414 CAATAATTCTCCAATAA-TTTGGATCTTC----
1 -AATAATTATCCAATAACTTTGGATCTTCTTTT
*
8442 AATAATTCTCCAATAACTTTGGATCTTCTTTGAT
1 AATAATTATCCAATAACTTTGGATCTTCTTT--T
* * *
8476 AATAATGATCCAATAACTTTGTATTTTCTTTGAT
1 AATAATTATCCAATAACTTTGGATCTTCTTT--T
*
8510 AATAATTATCCAATAACTTTGGATCTTCTTTC
1 AATAATTATCCAATAACTTTGGATCTTCTTTT
8542 AATAATTATCCAATAAACTTTGGATCTTCT
1 AATAATTATCCAAT-AACTTTGGATCTTCT
8572 CGAGACTTTG
Statistics
Matches: 140, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
27 16 0.11
28 11 0.08
31 10 0.07
32 30 0.21
33 15 0.11
34 58 0.41
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.44
Consensus pattern (32 bp):
AATAATTATCCAATAACTTTGGATCTTCTTTT
Found at i:9390 original size:60 final size:60
Alignment explanation
Indices: 9276--9395 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
9266 TATTTTTGTG
* * *
9276 CTCTAAATTTTGCCTAAGCTGTCATTTGCAGGATTTTCAACTTAGCAAATTTTTTTTTTC
1 CTCTAAATTTTACCTAAGCTGTCATTTACAGGATTTTCAACTTAACAAATTTTTTTTTTC
* * * **
9336 CTCTAACTTTTACCTCAGCTGTCCTTTACAGGATTTTCAACTTAACGATCTTTTTTTTTT
1 CTCTAAATTTTACCTAAGCTGTCATTTACAGGATTTTCAACTTAAC-AAATTTTTTTTTT
9396 TATTGTGTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 40 0.78
61 11 0.22
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (60 bp):
CTCTAAATTTTACCTAAGCTGTCATTTACAGGATTTTCAACTTAACAAATTTTTTTTTTC
Found at i:12161 original size:26 final size:25
Alignment explanation
Indices: 12127--12175 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
12117 GATTTTGAGT
* *
12127 TTTCCTCTCAAAATTCTCTTGTAAA
1 TTTCCTCTCAAAACTCACTTGTAAA
*
12152 TTTCCTTCTCGAAACTCACTTGTA
1 TTTCC-TCTCAAAACTCACTTGTA
12176 GTCAATAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.43
Consensus pattern (25 bp):
TTTCCTCTCAAAACTCACTTGTAAA
Found at i:14835 original size:25 final size:26
Alignment explanation
Indices: 14797--14849 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
14787 ATGTAATCTC
14797 TCATAGAAAGACAC-CTTTTCATGTT
1 TCATAGAAAGACACACTTTTCATGTT
* *
14822 TCATAGAAATACACATTTTTCATGTT
1 TCATAGAAAGACACACTTTTCATGTT
14848 TC
1 TC
14850 TGTAGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (26 bp):
TCATAGAAAGACACACTTTTCATGTT
Found at i:15813 original size:40 final size:39
Alignment explanation
Indices: 15712--15813 Score: 142
Period size: 37 Copynumber: 2.7 Consensus size: 39
15702 TTTGCATAGC
*
15712 ATGATTATTATAG---CATATATTATATGTTTCTATTATG
1 ATGATTATTATAGTTACATATA-TATATGTTTCTATCATG
15749 ATGATTATTATAGTTACAT-T-TATATGTTTCTATCATG
1 ATGATTATTATAGTTACATATATATATGTTTCTATCATG
15786 ATGATTATTATAGTTACATATAATATAT
1 ATGATTATTATAGTTACATAT-ATATAT
15814 ATTTAAGTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
37 48 0.83
38 1 0.02
39 1 0.02
40 8 0.14
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (39 bp):
ATGATTATTATAGTTACATATATATATGTTTCTATCATG
Found at i:16036 original size:57 final size:57
Alignment explanation
Indices: 15975--16087 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
15965 TGCGCCTTGC
*
15975 GCATCATTTTTCAGGGTAATTCGGTGTTAGTTTTGTGGAATTTCAGTTGATTATAAA
1 GCATCATTTTTCAGGGTAATTCGGTGTTAGTTTTGTGGAACTTCAGTTGATTATAAA
16032 GCATCATTTTTCAGGGTAATTCGGTGTTAGTTTTGTGGAACTTCAGTTGATTATAA
1 GCATCATTTTTCAGGGTAATTCGGTGTTAGTTTTGTGGAACTTCAGTTGATTATAA
16088 GCAAGTTGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.43
Consensus pattern (57 bp):
GCATCATTTTTCAGGGTAATTCGGTGTTAGTTTTGTGGAACTTCAGTTGATTATAAA
Found at i:19408 original size:21 final size:21
Alignment explanation
Indices: 19384--19426 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
19374 AATTAGAAAC
19384 ACTCAAAATAATAAAACAATT
1 ACTCAAAATAATAAAACAATT
*
19405 ACTCAAAATAATATAACAATT
1 ACTCAAAATAATAAAACAATT
19426 A
1 A
19427 AAAGGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
ACTCAAAATAATAAAACAATT
Found at i:20459 original size:13 final size:14
Alignment explanation
Indices: 20441--20469 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20431 ATGTCGGATT
20441 TTGTAGATATA-AG
1 TTGTAGATATAGAG
20454 TTGTAGATATAGAG
1 TTGTAGATATAGAG
20468 TT
1 TT
20470 CTGTCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (14 bp):
TTGTAGATATAGAG
Found at i:20780 original size:2 final size:2
Alignment explanation
Indices: 20729--20762 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20719 TGTGAATTGC
*
20729 AT AT AT AT GT A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20763 CATCATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23499 original size:32 final size:32
Alignment explanation
Indices: 23462--23620 Score: 135
Period size: 32 Copynumber: 5.3 Consensus size: 32
23452 ACAATCATGT
*
23462 ATCAATAACATAGGCTCACATTTAACAAATCA
1 ATCAATAACATAGACTCACATTTAACAAATCA
** * **
23494 ATCAATAACATA-AAACACA---ATC--ATGT
1 ATCAATAACATAGACTCACATTTAACAAATCA
23520 ATCAATAACATAGACTCACATTTAACAAATCA
1 ATCAATAACATAGACTCACATTTAACAAATCA
** * **
23552 ATCAATAACATA-AAACACA---ATC--ATGT
1 ATCAATAACATAGACTCACATTTAACAAATCA
23578 ATCAATAACATAGACTCACATTTAACAAATCA
1 ATCAATAACATAGACTCACATTTAACAAATCA
23610 ATCAATAACAT
1 ATCAATAACAT
23621 TTAGCAGTAT
Statistics
Matches: 94, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
26 28 0.30
27 10 0.11
28 4 0.04
30 4 0.04
31 9 0.10
32 39 0.41
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.25
Consensus pattern (32 bp):
ATCAATAACATAGACTCACATTTAACAAATCA
Found at i:23509 original size:58 final size:58
Alignment explanation
Indices: 23447--23620 Score: 339
Period size: 58 Copynumber: 3.0 Consensus size: 58
23437 ATCGTATATC
*
23447 AAAACACAATCATGTATCAATAACATAGGCTCACATTTAACAAATCAATCAATAACAT
1 AAAACACAATCATGTATCAATAACATAGACTCACATTTAACAAATCAATCAATAACAT
23505 AAAACACAATCATGTATCAATAACATAGACTCACATTTAACAAATCAATCAATAACAT
1 AAAACACAATCATGTATCAATAACATAGACTCACATTTAACAAATCAATCAATAACAT
23563 AAAACACAATCATGTATCAATAACATAGACTCACATTTAACAAATCAATCAATAACAT
1 AAAACACAATCATGTATCAATAACATAGACTCACATTTAACAAATCAATCAATAACAT
23621 TTAGCAGTAT
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 115 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.24
Consensus pattern (58 bp):
AAAACACAATCATGTATCAATAACATAGACTCACATTTAACAAATCAATCAATAACAT
Found at i:23524 original size:26 final size:26
Alignment explanation
Indices: 23494--23589 Score: 93
Period size: 26 Copynumber: 3.5 Consensus size: 26
23484 TAACAAATCA
23494 ATCAATAACATAAAACACAATCATGT
1 ATCAATAACATAAAACACAATCATGT
** * **
23520 ATCAATAACATAGACTCACATTTAACAAATCA
1 ATCAATAACATA-AAACACA---ATC--ATGT
23552 ATCAATAACATAAAACACAATCATGT
1 ATCAATAACATAAAACACAATCATGT
23578 ATCAATAACATA
1 ATCAATAACATA
23590 GACTCACATT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
26 26 0.48
27 5 0.09
28 2 0.04
30 2 0.04
31 5 0.09
32 14 0.26
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.24
Consensus pattern (26 bp):
ATCAATAACATAAAACACAATCATGT
Found at i:25226 original size:19 final size:19
Alignment explanation
Indices: 25181--25227 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
25171 TGGTTTGGTT
25181 AAAAAGACACAAAGAAAAGG
1 AAAAAGA-ACAAAGAAAAGG
**
25201 AGGAAGAACAAATGAAAA-G
1 AAAAAGAACAAA-GAAAAGG
25220 AAAAAGAA
1 AAAAAGAA
25228 AAAAATGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.02
Consensus pattern (19 bp):
AAAAAGAACAAAGAAAAGG
Found at i:26436 original size:16 final size:16
Alignment explanation
Indices: 26415--26456 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
26405 AAGTCAACGT
26415 CCCGAACCCGCCCGAG
1 CCCGAACCCGCCCGAG
26431 CCCGAACCCGCCCGAG
1 CCCGAACCCGCCCGAG
26447 CCCGAACCCG
1 CCCGAACCCG
26457 AAATTACCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.57, G:0.24, T:0.00
Consensus pattern (16 bp):
CCCGAACCCGCCCGAG
Found at i:26466 original size:16 final size:16
Alignment explanation
Indices: 26447--26489 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
26437 CCCGCCCGAG
*
26447 CCCGAACCCGAAATTA
1 CCCGAACCCGAAAATA
*
26463 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
26479 CCCGAACCCGA
1 CCCGAACCCGA
26490 GGCAGCTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.42, G:0.16, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:26506 original size:6 final size:6
Alignment explanation
Indices: 26497--26540 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
26487 CGAGGCAGCT
* *
26497 CGAGCC CGAGCC CGAGCC CGATCC CGA-CC CGAGCC CGAACC CGA
1 CGAGCC CGAGCC CGAGCC CGAGCC CGAGCC CGAGCC CGAGCC CGA
26541 AATAATTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.20, C:0.50, G:0.27, T:0.02
Consensus pattern (6 bp):
CGAGCC
Found at i:26529 original size:17 final size:18
Alignment explanation
Indices: 26479--26540 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 18
26469 CCCGAAAATA
*
26479 CCCGAACCCGAG-GC-AG
1 CCCGAACCCGAGCCCGAG
* *
26495 CTCGAGCCCGAGCCCGAG
1 CCCGAACCCGAGCCCGAG
*
26513 CCCGATCCCGA-CCCGAG
1 CCCGAACCCGAGCCCGAG
26530 CCCGAACCCGA
1 CCCGAACCCGA
26541 AATAATTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 10 0.26
17 17 0.45
18 11 0.29
ACGTcount: A:0.21, C:0.48, G:0.27, T:0.03
Consensus pattern (18 bp):
CCCGAACCCGAGCCCGAG
Found at i:27343 original size:8 final size:8
Alignment explanation
Indices: 27330--27363 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
27320 AATAATGTTA
27330 TATTATAT
1 TATTATAT
27338 TATTATAT
1 TATTATAT
27346 TATTATAT
1 TATTATAT
*
27354 CA-TATAT
1 TATTATAT
27361 TAT
1 TAT
27364 CAATAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:27512 original size:17 final size:18
Alignment explanation
Indices: 27492--27545 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 18
27482 AAATCAAACT
27492 CGAGCCCAAACCCG-ACC
1 CGAGCCCAAACCCGAACC
*
27509 CGAGCCCGAACCCGAACC
1 CGAGCCCAAACCCGAACC
27527 CGA---CATAACCCGAACC
1 CGAGCCCA-AACCCGAACC
27543 CGA
1 CGA
27546 AAATACCCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 1 0.03
16 13 0.39
17 13 0.39
18 6 0.18
ACGTcount: A:0.31, C:0.48, G:0.19, T:0.02
Consensus pattern (18 bp):
CGAGCCCAAACCCGAACC
Found at i:27538 original size:16 final size:16
Alignment explanation
Indices: 27518--27625 Score: 157
Period size: 16 Copynumber: 6.8 Consensus size: 16
27508 CCGAGCCCGA
*
27518 ACCCGAACCCG-ACAT
1 ACCCGAACCCGAAAAT
27533 AACCCGAACCCGAAAAT
1 -ACCCGAACCCGAAAAT
27550 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
27566 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
*
27582 ACCTGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
27598 ACCCGAACCCG-AAGT
1 ACCCGAACCCGAAAAT
27613 ACCCGAACCCGAA
1 ACCCGAACCCGAA
27626 CCCGCCCGAG
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
15 14 0.17
16 67 0.80
17 3 0.04
ACGTcount: A:0.40, C:0.39, G:0.15, T:0.06
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:32632 original size:22 final size:23
Alignment explanation
Indices: 32584--32636 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
32574 AATTGAAATC
*
32584 GAAAATTACAAGTAAAGAAATAA
1 GAAAATTACAAGGAAAGAAATAA
32607 -AAAATT-CAAGGAAAGAAA-AA
1 GAAAATTACAAGGAAAGAAATAA
32627 GGAAAATTAC
1 -GAAAATTAC
32637 GATTAGAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 11 0.42
22 12 0.46
23 1 0.04
ACGTcount: A:0.64, C:0.06, G:0.15, T:0.15
Consensus pattern (23 bp):
GAAAATTACAAGGAAAGAAATAA
Found at i:43012 original size:21 final size:21
Alignment explanation
Indices: 42982--43022 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42972 GAAAAAACCC
42982 TAGTACCACTTAG-ATCCAATT
1 TAGTACCACTT-GTATCCAATT
*
43003 TAGTATCACTTGTATCCAAT
1 TAGTACCACTTGTATCCAAT
43023 AGGGCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (21 bp):
TAGTACCACTTGTATCCAATT
Found at i:44935 original size:230 final size:230
Alignment explanation
Indices: 44527--44960 Score: 755
Period size: 230 Copynumber: 1.9 Consensus size: 230
44517 TGGCGCATCA
*
44527 GGAGTCGCCAAGCTGTCGCAACGTGCGGGTCCGGGGGACCCTGTCGCCGCCCACGACTTGGGGGA
1 GGAGTCGCCAAGCTGTCGCAACGTGCGGGTCCGGGGAACCCTGTCGCCGCCCACGACTTGGGGGA
*
44592 TCCCACCCCTATTGGAAATTTTGGGAGTCGCCACTAATCTTTTTTACCTAGGTGTGATTAGCCAC
66 TCCCACCCCTACTGGAAATTTTGGGAGTCGCCACTAATCTTTTTTACCTAGGTGTGATTAGCCAC
* *
44657 CTATCCATTTATTAAATCTAATATTAATCTAAGTTTGGCAAAGGTAACACTAAACCTAATAAAGT
131 CTATCCATTTATTAAATCTAATATTAAGCTAAGCTTGGCAAAGGTAACACTAAACCTAATAAAGT
*
44722 TTACTTAACTAGATATTTTGGGTTCGTTCCCCAGT
196 CTACTTAACTAGATATTTTGGGTTCGTTCCCCAGT
*
44757 GGAGTCGCCAAGCTGTCGCAACGTGCGGGTCCGGGGAACCCTGTTGCCGCCCACGACTTGGGGGA
1 GGAGTCGCCAAGCTGTCGCAACGTGCGGGTCCGGGGAACCCTGTCGCCGCCCACGACTTGGGGGA
* *
44822 TCCTACCCCTACTGG-AATTTCTGGGAGTCGCCACTATTCTTTTTTACCTAGGTGTGATTAGCCA
66 TCCCACCCCTACTGGAAATTT-TGGGAGTCGCCACTAATCTTTTTTACCTAGGTGTGATTAGCCA
*
44886 CCTATCCATTTATTAAATCTAATATTAAGCTAAGCTTGG-AAAGGGTAACATTAAACCTAATAAA
130 CCTATCCATTTATTAAATCTAATATTAAGCTAAGCTTGGCAAA-GGTAACACTAAACCTAATAAA
44950 GTCTACTTAAC
194 GTCTACTTAAC
44961 CAGAGATTCT
Statistics
Matches: 193, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
229 8 0.04
230 185 0.96
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (230 bp):
GGAGTCGCCAAGCTGTCGCAACGTGCGGGTCCGGGGAACCCTGTCGCCGCCCACGACTTGGGGGA
TCCCACCCCTACTGGAAATTTTGGGAGTCGCCACTAATCTTTTTTACCTAGGTGTGATTAGCCAC
CTATCCATTTATTAAATCTAATATTAAGCTAAGCTTGGCAAAGGTAACACTAAACCTAATAAAGT
CTACTTAACTAGATATTTTGGGTTCGTTCCCCAGT
Found at i:45431 original size:35 final size:34
Alignment explanation
Indices: 45312--45901 Score: 394
Period size: 35 Copynumber: 17.2 Consensus size: 34
45302 TTTTAATGTC
* *
45312 TTACTTAATTATCAC-GAATTAAGTTCTTTATTGACT
1 TTACTTAATTA-CCCTGAATTAAG-TCTTTACTGA-T
* ** * *
45348 CTACTTAATTACCCAAAATTAAGTTCCTTATTGACT
1 TTACTTAATTACCCTGAATTAAG-TCTTTACTGA-T
* *
45384 CTACTTAATTA-CCTCGAATTAAATCTTTGACTGAT
1 TTACTTAATTACCCT-GAATTAAGTCTTT-ACTGAT
* *
45419 TTACTTAATTACCCTAAATTAAGTCTTTACTAATT
1 TTACTTAATTACCCTGAATTAAGTCTTTACTGA-T
*
45454 TTAATTAATTACCCTGAATTAAGTCCTTTACTGAT
1 TTACTTAATTACCCTGAATTAAGT-CTTTACTGAT
*
45489 TTACTTAATTACCCTGAATTTA--C-TTA---A-
1 TTACTTAATTACCCTGAATTAAGTCTTTACTGAT
* * ** * * *
45516 TTACCCTGAATTAAGTCCTTTATT--G-ATTTACTTAA
1 TTA--CTTAATT-A-CCCTGAATTAAGTCTTTACTGAT
* * * *
45551 TTACCCTGAATTA---AG---T---CCTTAACTGAT
1 TTA--CTTAATTACCCTGAATTAAGTCTTTACTGAT
* *
45578 TTATTTAATTACCCTGAATTATGTCTTTGACTGATT
1 TTACTTAATTACCCTGAATTAAGTCTTT-ACTGA-T
*
45614 TTACTTAATTACCCTAAATTAAGTCTTTACTGATT
1 TTACTTAATTACCCTGAATTAAGTCTTTACTGA-T
* **
45649 TTACTTAATTACCCTGAATTAAGTCTATGTTGATT
1 TTACTTAATTACCCTGAATTAAGTCTTTACTGA-T
** *
45684 TTACTTAATTTTCCTGAATTAAGTCTTTGACTGGT
1 TTACTTAATTACCCTGAATTAAGTCTTT-ACTGAT
* *
45719 TTACTTAATTACCCTAAATTAAGTCTTGACTGATT
1 TTACTTAATTACCCTGAATTAAGTCTTTACTGA-T
* * *
45754 TTACTCAATTTCCCTGAATTAAGTCTTAACTGAT
1 TTACTTAATTACCCTGAATTAAGTCTTTACTGAT
* *
45788 TATACTTAATTTCCCTGAATTAAGTCTTTGACTGGT
1 T-TACTTAATTACCCTGAATTAAGTCTTT-ACTGAT
* *
45824 TTACTTAATTTCCCTGAATTAAGTCTTTGATTGATT
1 TTACTTAATTACCCTGAATTAAGTCTTT-ACTGA-T
* * *
45860 TTAATTAATTTCCCTGAATTAAGTCTTTGCTGATT
1 TTACTTAATTACCCTGAATTAAGTCTTTACTGA-T
45895 TTACTTA
1 TTACTTA
45902 GGTTCTGTTT
Statistics
Matches: 456, Mismatches: 65, Indels: 67
0.78 0.11 0.11
Matches are distributed among these distances:
25 6 0.01
27 13 0.03
28 2 0.00
29 6 0.01
30 1 0.00
31 13 0.03
32 1 0.00
34 15 0.03
35 276 0.61
36 123 0.27
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (34 bp):
TTACTTAATTACCCTGAATTAAGTCTTTACTGAT
Found at i:45511 original size:19 final size:19
Alignment explanation
Indices: 45487--45527 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
45477 TCCTTTACTG
45487 ATTTACTTAATTACCCTGA
1 ATTTACTTAATTACCCTGA
45506 ATTTACTTAATTACCCTGA
1 ATTTACTTAATTACCCTGA
45525 ATT
1 ATT
45528 AAGTCCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTTACTTAATTACCCTGA
Found at i:45533 original size:54 final size:54
Alignment explanation
Indices: 45453--45562 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
45443 CTTTACTAAT
45453 TTTAATTAATTACCCTGAATTAAGTCCTTTACTGATTTACTTAATTACCCTGAA
1 TTTAATTAATTACCCTGAATTAAGTCCTTTACTGATTTACTTAATTACCCTGAA
* *
45507 TTTACTTAATTACCCTGAATTAAGTCCTTTATTGATTTACTTAATTACCCTGAA
1 TTTAATTAATTACCCTGAATTAAGTCCTTTACTGATTTACTTAATTACCCTGAA
45561 TT
1 TT
45563 AAGTCCTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (54 bp):
TTTAATTAATTACCCTGAATTAAGTCCTTTACTGATTTACTTAATTACCCTGAA
Found at i:45544 original size:124 final size:125
Alignment explanation
Indices: 45385--45633 Score: 355
Period size: 124 Copynumber: 2.0 Consensus size: 125
45375 TTATTGACTC
*
45385 TACTTAATTACCTCGAATTAAATCTTTGACTGATTTACTTAATTACCCTAAATTAAGT-CTTTAC
1 TACTTAATTACCTCGAATTAAATCTTTGACTGATTTACTTAATTACCCTAAATTAAGTCCTTAAC
*
45449 TAATTTTAATTAATTACCCTGAATTAAGTCCTTT-ACTGA-TTTACTTAATTACCCTGAATT
66 TAA-TTTAATTAATTACCCTGAATTAAGT-CTTTGACTGATTTTACTTAATTACCCTAAATT
* * *
45509 TACTTAATTACC-CTGAATTAAGTCCTTT-ATTGATTTACTTAATTACCCTGAATTAAGTCCTTA
1 TACTTAATTACCTC-GAATTAAAT-CTTTGACTGATTTACTTAATTACCCTAAATTAAGTCCTTA
* * *
45572 ACTGATTTATTTAATTACCCTGAATTATGTCTTTGACTGATTTTACTTAATTACCCTAAATT
64 ACTAATTTAATTAATTACCCTGAATTAAGTCTTTGACTGATTTTACTTAATTACCCTAAATT
45634 AAGTCTTTAC
Statistics
Matches: 112, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
123 5 0.04
124 76 0.68
125 31 0.28
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (125 bp):
TACTTAATTACCTCGAATTAAATCTTTGACTGATTTACTTAATTACCCTAAATTAAGTCCTTAAC
TAATTTAATTAATTACCCTGAATTAAGTCTTTGACTGATTTTACTTAATTACCCTAAATT
Found at i:45568 original size:89 final size:89
Alignment explanation
Indices: 45417--45597 Score: 292
Period size: 89 Copynumber: 2.0 Consensus size: 89
45407 TCTTTGACTG
45417 ATTTACTTAATTACCCTAAATTAAGTCTTTACTAATTTTAATTAATTACCCTGAATTAAGTCCTT
1 ATTTACTTAATTACCCTAAATTAAGTCTTTACTAATTTTAATTAATTACCCTGAATTAAGTCCTT
*
45482 TACTGATTTACTTAATTACCCTGA
66 AACTGATTTACTTAATTACCCTGA
* * * *
45506 ATTTACTTAATTACCCTGAATTAAGTCCTTTATTGA-TTTACTTAATTACCCTGAATTAAGTCCT
1 ATTTACTTAATTACCCTAAATTAAGT-CTTTACTAATTTTAATTAATTACCCTGAATTAAGTCCT
*
45570 TAACTGATTTATTTAATTACCCTGA
65 TAACTGATTTACTTAATTACCCTGA
45595 ATT
1 ATT
45598 ATGTCTTTGA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
89 78 0.92
90 7 0.08
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (89 bp):
ATTTACTTAATTACCCTAAATTAAGTCTTTACTAATTTTAATTAATTACCCTGAATTAAGTCCTT
AACTGATTTACTTAATTACCCTGA
Found at i:45586 original size:70 final size:70
Alignment explanation
Indices: 45506--45901 Score: 485
Period size: 70 Copynumber: 5.6 Consensus size: 70
45496 ATTACCCTGA
* *
45506 ATTTACTTAATTACCCTGAATTAAGTCCTTTATTGA-TTTACTTAATTACCCTGAATTAAGTCCT
1 ATTTACTTAATTACCCTGAATTAAGT-CTTTACTGATTTTACTTAATTTCCCTGAATTAAGTCCT
45570 TAACTG
65 TAACTG
* * * *
45576 ATTTATTTAATTACCCTGAATTATGTCTTTGACTGATTTTACTTAATTACCCTAAATTAAGT-CT
1 ATTTACTTAATTACCCTGAATTAAGTCTTT-ACTGATTTTACTTAATTTCCCTGAATTAAGTCCT
*
45640 TTACTG
65 TAACTG
* ** * *
45646 ATTTTACTTAATTACCCTGAATTAAGTCTATGTTGATTTTACTTAATTTTCCTGAATTAAGTCTT
1 A-TTTACTTAATTACCCTGAATTAAGTCTTTACTGATTTTACTTAATTTCCCTGAATTAAGTCCT
*
45711 TGACTG
65 TAACTG
* * * *
45717 GTTTACTTAATTACCCTAAATTAAGTCTTGACTGATTTTACTCAATTTCCCTGAATTAAGT-CTT
1 ATTTACTTAATTACCCTGAATTAAGTCTTTACTGATTTTACTTAATTTCCCTGAATTAAGTCCTT
45781 AACTG
66 AACTG
* * *
45786 ATTATACTTAATTTCCCTGAATTAAGTCTTTGACTG-GTTTACTTAATTTCCCTGAATTAAGTCT
1 ATT-TACTTAATTACCCTGAATTAAGTCTTT-ACTGATTTTACTTAATTTCCCTGAATTAAGTCC
* *
45850 TTGATTG
64 TTAACTG
* * *
45857 ATTTTAATTAATTTCCCTGAATTAAGTCTTTGCTGATTTTACTTA
1 A-TTTACTTAATTACCCTGAATTAAGTCTTTACTGATTTTACTTA
45902 GGTTCTGTTT
Statistics
Matches: 280, Mismatches: 37, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
69 12 0.04
70 166 0.59
71 100 0.36
72 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (70 bp):
ATTTACTTAATTACCCTGAATTAAGTCTTTACTGATTTTACTTAATTTCCCTGAATTAAGTCCTT
AACTG
Found at i:45741 original size:105 final size:105
Alignment explanation
Indices: 45507--45901 Score: 544
Period size: 105 Copynumber: 3.7 Consensus size: 105
45497 TTACCCTGAA
* *
45507 TTTACTTAATTACCCTGAATTAAGTCCTTTATTGA-TTTACTTAATTACCCTGAATTAAGTCCTT
1 TTTACTTAATTACCCTAAATTAAGT-CTTTACTGATTTTACTTAATTACCCTGAATTAAGT-CTT
* * * *
45571 AACTGA-TTTATTTAATTACCCTGAATTATGTCTTTGACTGAT
64 AACTGATTTTACTTAATTTCCCTGAATTAAGTCTTTGACTG-G
45613 TTTACTTAATTACCCTAAATTAAGTCTTTACTGATTTTACTTAATTACCCTGAATTAAGTC-TAT
1 TTTACTTAATTACCCTAAATTAAGTCTTTACTGATTTTACTTAATTACCCTGAATTAAGTCTTA-
** *
45677 GTTGATTTTACTTAATTTTCCTGAATTAAGTCTTTGACTGG
65 ACTGATTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGG
* * *
45718 TTTACTTAATTACCCTAAATTAAGTCTTGACTGATTTTACTCAATTTCCCTGAATTAAGTCTTAA
1 TTTACTTAATTACCCTAAATTAAGTCTTTACTGATTTTACTTAATTACCCTGAATTAAGTCTTAA
*
45783 CTGATTATACTTAATTTCCCTGAATTAAGTCTTTGACTGG
66 CTGATTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGG
* * * * * *
45823 TTTACTTAATTTCCCTGAATTAAGTCTTTGATTGATTTTAATTAATTTCCCTGAATTAAGTCTTT
1 TTTACTTAATTACCCTAAATTAAGTCTTT-ACTGATTTTACTTAATTACCCTGAATTAAGTCTTA
*
45888 GCTGATTTTACTTA
65 ACTGATTTTACTTA
45902 GGTTCTGTTT
Statistics
Matches: 259, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
104 2 0.01
105 133 0.51
106 124 0.48
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (105 bp):
TTTACTTAATTACCCTAAATTAAGTCTTTACTGATTTTACTTAATTACCCTGAATTAAGTCTTAA
CTGATTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGG
Found at i:45959 original size:15 final size:15
Alignment explanation
Indices: 45919--45953 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
45909 TTTGATAAAA
45919 CTGAAA-ATTAAGTG
1 CTGAAAGATTAAGTG
45933 CTGAAAGATTAAGTG
1 CTGAAAGATTAAGTG
*
45948 TTGAAA
1 CTGAAA
45954 TTTTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (15 bp):
CTGAAAGATTAAGTG
Found at i:46896 original size:35 final size:36
Alignment explanation
Indices: 46848--47754 Score: 1148
Period size: 35 Copynumber: 25.8 Consensus size: 36
46838 CAAACAGACC
*
46848 CTTAATTTA-CCTGAATTAAGTCTTTGACTG-GTTTA
1 CTTAA-TTACCCTGAATTAAGTCTTTGACTGATTTTA
*
46883 CTTAATTACCCTGAATTAAGTCTTTGACTG-GTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
*
46918 CTTAATTACCCTGAATTAAGT-TTTTACTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* * *
46953 CTTAATTACCCAGAATTAAGTCCTTT-CCAGA-TTTA
1 CTTAATTACCCTGAATTAAGT-CTTTGACTGATTTTA
46988 CTTAATTACCCTGAATTAAGTCTTTGACT--TGTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGAT-TTTA
* *
47023 CTTAATTACCCTGAATTAAATCTTTGACTGCTTTT-
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
*
47058 CTTAATTACCCTGAATTAAGTCTTT-ACTGAGTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
47093 CTTAATTACCCTGAATTAAGTCCTTT-ACTGA-TTTA
1 CTTAATTACCCTGAATTAAGT-CTTTGACTGATTTTA
* *
47128 CTTAATTACCCTAAATTAAGTCCTTGACTGA-TTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
*
47163 -TATAATTACCCTGAATTTTAGTCTTTGACTGATTTTA
1 CT-TAATTACCCTGAA-TTAAGTCTTTGACTGATTTTA
*
47200 CTTAATTACCCTAAATTAAGTCTTTG-CTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* * *
47235 CTTAATTACCTTGAATTGAGTCTTTG-TTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* * * *
47270 CATAATTTCGCTGAATTAAGTCTTTGACTG-GTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
*
47305 CTTAATTACCCTAAATTAAGTC-TTGACTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* *
47340 CTTAATTTCTCTGAATTAAGTC-TTGACTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* * * *
47375 CTTAATTTCCCTGAATTAAGTCTTTAACCG-GTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* *
47410 CTTAATTTCCCTGAATTAAGTCTTTG-TTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
*
47445 CTTAATTTCCCTGAATTAAGT-TTTGACTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* *
47480 CTTAATTTCCCTGAATTAGGTCTTTG-CTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* * *
47515 CTTAATTTCCCTGAATTTAGTCTTTGACT-AGTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* *
47550 CTTTATTACGCTGAATTAAGTCTTTGACTG-TTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
*
47585 CTTAATTACCCTGAATTAAGTCTTTGGCTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
47621 CTTAATTACCCTGAATTAAGTCTTTGACTGA-TTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* * *
47656 CTTAATTACCCTGAATCAAGTCTTTGATTGCTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
* * *
47692 CTTAATTGCCTTGAATTAAGTATTTGACTG-TGTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGAT-TTTA
* *
47728 CTTAATTTCCTTGAATTAAGTCTTTGA
1 CTTAATTACCCTGAATTAAGTCTTTGA
47755 TTACTTTTAC
Statistics
Matches: 775, Mismatches: 70, Indels: 53
0.86 0.08 0.06
Matches are distributed among these distances:
34 37 0.05
35 572 0.74
36 145 0.19
37 20 0.03
38 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (36 bp):
CTTAATTACCCTGAATTAAGTCTTTGACTGATTTTA
Found at i:53040 original size:45 final size:45
Alignment explanation
Indices: 52976--53065 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
52966 TTTCAATTAC
*
52976 AGTGTTTTACTATATGGAAGGAGTAATATTGGTGTCTTTAATTTG
1 AGTGTTTTACTATATGGAAGGAGTAACATTGGTGTCTTTAATTTG
* *
53021 AGTGTTTTAGTATATGGAAGGGGTAACATTGGTGTCTTTAATTTG
1 AGTGTTTTACTATATGGAAGGAGTAACATTGGTGTCTTTAATTTG
53066 TTCGATGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.26, C:0.04, G:0.27, T:0.43
Consensus pattern (45 bp):
AGTGTTTTACTATATGGAAGGAGTAACATTGGTGTCTTTAATTTG
Found at i:56707 original size:19 final size:19
Alignment explanation
Indices: 56683--56719 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56673 CTCCTCTATC
*
56683 ATGAAAACACTTTTTTTTT
1 ATGAAAACAATTTTTTTTT
56702 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTTTTTTT
56720 AATTACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (19 bp):
ATGAAAACAATTTTTTTTT
Found at i:58435 original size:5 final size:6
Alignment explanation
Indices: 58373--58412 Score: 53
Period size: 6 Copynumber: 6.2 Consensus size: 6
58363 AAAATTAATG
58373 TAAAAA TTAAAAA TAATAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA -TAAAAA T-A-AAAA TAAAAA TAAAAA TAAAAA T
58413 TAAATTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 18 0.58
7 8 0.26
8 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
TAAAAA
Found at i:65327 original size:41 final size:41
Alignment explanation
Indices: 65028--65351 Score: 418
Period size: 41 Copynumber: 7.9 Consensus size: 41
65018 TTTTCGTTTG
* *
65028 TTCAAGATCAAGCCATCGAGAGCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
65069 TTCAAGATTGAGTCATCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
65110 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
65151 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
65192 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * * *
65233 TTCAAGAACAGGTCATCTAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * *
65277 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
65318 TTCAAGACCAAGTCATTCG-G-CCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
65352 CAAATCAAAC
Statistics
Matches: 252, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
40 12 0.05
41 201 0.80
42 4 0.02
43 1 0.00
44 34 0.13
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:67928 original size:16 final size:16
Alignment explanation
Indices: 67904--67938 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
67894 ACAATCCAGA
67904 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
*
67920 AAGCGGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
67936 AAG
1 AAG
67939 TATTTTCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.29, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:68091 original size:41 final size:41
Alignment explanation
Indices: 68034--68316 Score: 390
Period size: 41 Copynumber: 6.9 Consensus size: 41
68024 TTTTCGTTTG
68034 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
68075 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
68116 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
68157 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * *
68198 TTCAAGAACAGGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * *
68242 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
68283 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
68317 CAAATCAAAC
Statistics
Matches: 217, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
40 14 0.06
41 164 0.76
42 4 0.02
43 1 0.00
44 34 0.16
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:74934 original size:123 final size:124
Alignment explanation
Indices: 74714--74939 Score: 382
Period size: 123 Copynumber: 1.8 Consensus size: 124
74704 AGCAGCACTT
* *
74714 CCCAGCAGCGTTTCTCGACACAAGTGCCTCCTTCTTGGTGGAATGACACGTCAACAGCGTTGCAC
1 CCCAGCAGCGTGTCTCGACACAAGTGCCTCCTTCTTGGTGGAATGACACGTCAACAACGTTGCAC
*
74779 CAGGTTAGCCATGCAGCTGACCTCGTTTGTTGATGAAGAACAGGACTTCGATCGAAGTG
66 CAGGTTAGCCATGCAGCTGACCTCCTTTGTTGATGAAGAACAGGACTTCGATCGAAGTG
* *
74838 CCCAGCAGCGTGTCTCGACAGAAGTGTCTCCTTCTTGGTGGAATGA-ACGTCAACAACGTTGCAC
1 CCCAGCAGCGTGTCTCGACACAAGTGCCTCCTTCTTGGTGGAATGACACGTCAACAACGTTGCAC
**
74902 CAGGTTAGCCATGTTGCTGACCTCCTTTGTTGATGAAG
66 CAGGTTAGCCATGCAGCTGACCTCCTTTGTTGATGAAG
74940 GATAAGACTG
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
123 52 0.55
124 43 0.45
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (124 bp):
CCCAGCAGCGTGTCTCGACACAAGTGCCTCCTTCTTGGTGGAATGACACGTCAACAACGTTGCAC
CAGGTTAGCCATGCAGCTGACCTCCTTTGTTGATGAAGAACAGGACTTCGATCGAAGTG
Found at i:75167 original size:18 final size:18
Alignment explanation
Indices: 75141--75179 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
75131 GTAAATTTAA
*
75141 TAATAATAAGGGAAATAG
1 TAATAATAAAGGAAATAG
*
75159 TAATTATAAAGGAAATAG
1 TAATAATAAAGGAAATAG
75177 TAA
1 TAA
75180 GAGAGGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (18 bp):
TAATAATAAAGGAAATAG
Found at i:75379 original size:2 final size:2
Alignment explanation
Indices: 75361--75395 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
75351 TGAGGGCTTT
*
75361 AG AG TAG AG AG AA AG AG AG AG AG AG AG AG AG AG AG
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
75396 TAGTGGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:78846 original size:22 final size:22
Alignment explanation
Indices: 78821--78871 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
78811 CTCTCATCTC
*
78821 TTTTCTTGTGAAGATTT-T-ATT
1 TTTTCTT-TGAAAATTTCTAATT
*
78842 TTTTTTTTGAAAATTTCTAATT
1 TTTTCTTTGAAAATTTCTAATT
78864 TTTTCTTT
1 TTTTCTTT
78872 TTTTTTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 7 0.28
22 10 0.40
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.67
Consensus pattern (22 bp):
TTTTCTTTGAAAATTTCTAATT
Found at i:78852 original size:20 final size:23
Alignment explanation
Indices: 78821--78872 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 23
78811 CTCTCATCTC
* *
78821 TTTTCTTGTGAAGATTT-T-ATT
1 TTTTCTTTTGAAAATTTCTAATT
78842 TTTT-TTTTGAAAATTTCTAATT
1 TTTTCTTTTGAAAATTTCTAATT
78864 TTTTCTTTT
1 TTTTCTTTT
78873 TTTTTTTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 10 0.38
21 5 0.19
22 7 0.27
23 4 0.15
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTTCTTTTGAAAATTTCTAATT
Found at i:79782 original size:22 final size:22
Alignment explanation
Indices: 79757--79798 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
79747 ATGCTATTTC
**
79757 TATAAGAATTTCAAACTTAAAA
1 TATAAGAAAATCAAACTTAAAA
79779 TATAAGAAAATCAAACTTAA
1 TATAAGAAAATCAAACTTAA
79799 CATGATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (22 bp):
TATAAGAAAATCAAACTTAAAA
Found at i:80179 original size:32 final size:32
Alignment explanation
Indices: 80143--80203 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
80133 TGCAAAACAA
80143 CATAAACCCATTCGATTTCCCCCTTTCCAAAC
1 CATAAACCCATTCGATTTCCCCCTTTCCAAAC
* *
80175 CATAAAGCCATTTGATTTCCCCCTTTCCA
1 CATAAACCCATTCGATTTCCCCCTTTCCA
80204 CAATCCCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.38, G:0.05, T:0.31
Consensus pattern (32 bp):
CATAAACCCATTCGATTTCCCCCTTTCCAAAC
Found at i:81137 original size:21 final size:19
Alignment explanation
Indices: 81094--81149 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
81084 GTTTAGTAAT
81094 TGTACAGATGAGATTACAC
1 TGTACAGATGAGATTACAC
* *
81113 TGTACAGATTAGATTAGGTAC
1 TGTACAGATGAGATTA--CAC
81134 TGTACAGATGAGATTA
1 TGTACAGATGAGATTA
81150 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (19 bp):
TGTACAGATGAGATTACAC
Found at i:87017 original size:96 final size:96
Alignment explanation
Indices: 86891--87282 Score: 631
Period size: 96 Copynumber: 4.1 Consensus size: 96
86881 AATAATACCT
* * *
86891 TGATGATGGGTAATATATCATAACAAGGAAGACTAGGTGAGAGCTATATACCGCTCAAACACCGG
1 TGATGATGAGTAAAATATCATAACAAGGAAGACTAGGTGAGAGCTATATACCGCTCAATCACCGG
*
86956 TGGCTTGATGATGCCTCGCCACATCTTGTAA
66 CGGCTTGATGATGCCTCGCCACATCTTGTAA
*
86987 TGATGGTGAGTAAAATATCATAACAAGGAAGACTAGGTGAGAGCTATATACCGCTCAATCACCGG
1 TGATGATGAGTAAAATATCATAACAAGGAAGACTAGGTGAGAGCTATATACCGCTCAATCACCGG
87052 CGGCTTGATGATGCCTCGCCACATCTTGTAA
66 CGGCTTGATGATGCCTCGCCACATCTTGTAA
* * * * *
87083 TGATGGTGAGTAAAATATCATAACAATGAAGACTAGGTGAAAGCTATATACCACTCAATCACCAG
1 TGATGATGAGTAAAATATCATAACAAGGAAGACTAGGTGAGAGCTATATACCGCTCAATCACCGG
* *
87148 CGGCTTGATGATGCCTCACCACATTTTGTAA
66 CGGCTTGATGATGCCTCGCCACATCTTGTAA
* * * *
87179 TGATGATGAGTAACATATCATAACAACGAAGACTAGGTGAGAGCTATATACTGCTCAATCATCGG
1 TGATGATGAGTAAAATATCATAACAAGGAAGACTAGGTGAGAGCTATATACCGCTCAATCACCGG
*
87244 CGGCTTGATGATGCCTCGCCACATCTTGTAC
66 CGGCTTGATGATGCCTCGCCACATCTTGTAA
87275 TGATGATG
1 TGATGATG
87283 GACTAAGCCA
Statistics
Matches: 274, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 274 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (96 bp):
TGATGATGAGTAAAATATCATAACAAGGAAGACTAGGTGAGAGCTATATACCGCTCAATCACCGG
CGGCTTGATGATGCCTCGCCACATCTTGTAA
Found at i:87351 original size:46 final size:46
Alignment explanation
Indices: 87298--87385 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
87288 AGCCATCTTT
87298 TGGCTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGAGCTG
1 TGGCTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGAGCTG
*
87344 TGGCTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAGATGA
1 TGGCTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGA
87386 ACCATGACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (46 bp):
TGGCTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGAGCTG
Found at i:87397 original size:46 final size:46
Alignment explanation
Indices: 87301--87397 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
87291 CATCTTTTGG
* ** *
87301 CTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGAGCTGTGG
1 CTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGAACCATGA
*
87347 CTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAGATGAACCATGA
1 CTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGAACCATGA
87393 CTTGA
1 CTTGA
87398 TGAAAAACCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (46 bp):
CTTGAAGAAGCCTTTGCCACATAGTGGACCTTGAAATGAACCATGA
Found at i:96002 original size:30 final size:30
Alignment explanation
Indices: 95968--96039 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
95958 GTACCCGGGA
95968 GGTCCATATACTATAGGAAATGTTAATTTT
1 GGTCCATATACTATAGGAAATGTTAATTTT
* *
95998 GGTCCTTATACTATAGGAAATGTTGATTTT
1 GGTCCATATACTATAGGAAATGTTAATTTT
*
96028 GGTCCCTATACT
1 GGTCCATATACT
96040 TTTTTTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (30 bp):
GGTCCATATACTATAGGAAATGTTAATTTT
Done.