Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 17 of 199
Found at i:5228138 original size:44 final size:44
Alignment explanation
Indices: 5228090--5228227 Score: 109
Period size: 44 Copynumber: 3.1 Consensus size: 44
5228080 CTGCTTCTCT
*
5228090 GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTATA
1 GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
* ** **** * * * * * *
5228134 GGAAGACAAAATCTTCAATCTTCAACCTACTCCACTG-CTGCT-CA
1 GGAAGATAAGGT-TGGTGTTTTCGATCTGCTTCACTGCCAG-TACA
*
5228178 GGAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
1 GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
5228222 GGAAGA
1 GGAAGA
5228228 CAAGATTTGT
Statistics
Matches: 62, Mismatches: 28, Indels: 8
0.63 0.29 0.08
Matches are distributed among these distances:
43 16 0.26
44 30 0.48
45 16 0.26
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
GGAAGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTACA
Found at i:5228305 original size:264 final size:264
Alignment explanation
Indices: 5227829--5228342 Score: 652
Period size: 264 Copynumber: 1.9 Consensus size: 264
5227819 AACTTCAGGG
* * * * *
5227829 AGATAAGGTTTGTGTTTTTAATTTGCTTCACTGTCAGTACAGGAAGACAAGATCTGCAATCTTCA
1 AGATAAGGTTGGTGTTTTCAATCTGCTTCACTGCCAGTACAGGAAGACAAAATCTGCAATCTTCA
* * * * * **
5227894 ACTTACTCCACTTCTGCTCAGAAAGATAAGGCTTGTGTTTTTGATCTGTTTCACTACCAGTGTAG
66 ACCTACTCCACTGCTGCTCAGAAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTACCAGTACAG
* * * * * * * ** *
5227959 GAAGATAAGACCTGCAATCTTTAACCTATTTCACTGCTACTTAAGGAGATAAGGCTTGTTATTTC
131 GAAGACAAGACCTGCAAACTTTAACCCACTCCACTACTACTCAAGGAGATAAGGCAGGTTACTTC
* * *
5228024 GATCTGTTTCACTGCCAATACAGGAAGACAAGATTTGCAATCTTCAACCTACTCCACTGCTTCTC
196 GATCTATTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTGCTTCTC
5228089 TGGA
261 TGGA
* * *
5228093 AGATAAGGTTGGTGTTTTCGATCTGCTTCACTGCCAGTATAGGAAGACAAAATCTTCAATCTTCA
1 AGATAAGGTTGGTGTTTTCAATCTGCTTCACTGCCAGTACAGGAAGACAAAATCTGCAATCTTCA
* *
5228158 ACCTACTCCACTGCTGCTCAGGAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAG
66 ACCTACTCCACTGCTGCTCAGAAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTACCAGTACAG
** * * *
5228223 GAAGACAAGATTTGTAAACTTTAACCCACTCCACTACTGCTCAGGGAGATAAGGCAGGTGT-CTT
131 GAAGACAAGACCTGCAAACTTTAACCCACTCCACTACTACTCAAGGAGATAAGGCAGGT-TACTT
** ** *
5228287 CGATCTATTTTGCTGCCAATACAGGAAGAAAAAATTTGTTATCTTCAACCTGCTCC
195 CGATCTATTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCC
5228343 GCTGTAAACT
Statistics
Matches: 209, Mismatches: 40, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
264 208 1.00
265 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (264 bp):
AGATAAGGTTGGTGTTTTCAATCTGCTTCACTGCCAGTACAGGAAGACAAAATCTGCAATCTTCA
ACCTACTCCACTGCTGCTCAGAAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTACCAGTACAG
GAAGACAAGACCTGCAAACTTTAACCCACTCCACTACTACTCAAGGAGATAAGGCAGGTTACTTC
GATCTATTTCACTGCCAATACAGGAAGAAAAAATTTGCAATCTTCAACCTACTCCACTGCTTCTC
TGGA
Found at i:5228497 original size:89 final size:89
Alignment explanation
Indices: 5228274--5228501 Score: 339
Period size: 89 Copynumber: 2.6 Consensus size: 89
5228264 CAGGGAGATA
* * * * *
5228274 AGGCAGGTGTCTTCGATCTATTTTGCTGCCAATACAGGAAGAAAAAATTTGTTATCTTCAACCTG
1 AGGCTGGTGTCTTCGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCAACCTG
* *
5228339 CTCCGCTGTAAACTCAGGGAGGCG
66 CTCCGCCGCAAACTCAGGGAGGCG
** * *
5228363 AGGCTGGTGTCTTCGATCTACTTCACTGCCAATGCAGGAAGACAAGATCTGTTATCTTCAACTTG
1 AGGCTGGTGTCTTCGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCAACCTG
5228428 CTCCGCCGCAAACTCAGGGAGGCG
66 CTCCGCCGCAAACTCAGGGAGGCG
* *
5228452 AGGCTGGTGTCTTTGATCTACTTTGCTGCCAATACAGGAATACAAGATCT
1 AGGCTGGTGTCTTCGATCTACTTTGCTGCCAATACAGGAAGACAAGATCT
5228502 ACCATAATGA
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 123 1.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (89 bp):
AGGCTGGTGTCTTCGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCAACCTG
CTCCGCCGCAAACTCAGGGAGGCG
Found at i:5229463 original size:5 final size:5
Alignment explanation
Indices: 5229448--5229513 Score: 59
Period size: 5 Copynumber: 13.4 Consensus size: 5
5229438 TTCGCCTTGG
* *
5229448 TCTTT TTTTT TCTTTT TCTTT T-TCT TCTTT TCTTT T-TTT T-TATT T-TTT
1 TCTTT TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT TCT-TT TCTTT
5229496 TCTTTT TCTTT TCTTT TC
1 TC-TTT TCTTT TCTTT TC
5229514 ATGAAACATT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 11 0.21
5 31 0.60
6 10 0.19
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:5229465 original size:6 final size:6
Alignment explanation
Indices: 5229450--5229512 Score: 69
Period size: 6 Copynumber: 10.5 Consensus size: 6
5229440 CGCCTTGGTC
*
5229450 TTTT-T TTTTCT TTTTCT TTTTCTT CTTTTCT TTTT-T TTTATTT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTC-T -TTTTCT TTTTCT TTT-TCT TTTTCT
5229499 TTTTC- TTTTCT TTT
1 TTTTCT TTTTCT TTT
5229513 CATGAAACAT
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
5 13 0.25
6 27 0.53
7 6 0.12
8 5 0.10
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:5229493 original size:29 final size:30
Alignment explanation
Indices: 5229448--5229512 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
5229438 TTCGCCTTGG
*
5229448 TCTTTTTTTTTC-TTTTTCTTTTTCTTCTTT
1 TCTTTTTTTTTCATTTTT-TTCTTCTTCTTT
*
5229478 TCTTTTTTTTT-ATTTTTTTCTTTTTCTTT
1 TCTTTTTTTTTCATTTTTTTCTTCTTCTTT
5229507 TCTTTT
1 TCTTTT
5229513 CATGAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.85
Consensus pattern (30 bp):
TCTTTTTTTTTCATTTTTTTCTTCTTCTTT
Found at i:5232199 original size:23 final size:23
Alignment explanation
Indices: 5232172--5232218 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5232162 AGAAAAGTGA
*
5232172 TTGTTTTTAATAAACAATTTGAT
1 TTGTTTTTAAGAAACAATTTGAT
*
5232195 TTGTTTTTAAGAAACGATTTGAT
1 TTGTTTTTAAGAAACAATTTGAT
5232218 T
1 T
5232219 ATATTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
TTGTTTTTAAGAAACAATTTGAT
Found at i:5234936 original size:10 final size:10
Alignment explanation
Indices: 5234921--5234945 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5234911 AATTGATCAT
5234921 AAGTAGGTAA
1 AAGTAGGTAA
5234931 AAGTAGGTAA
1 AAGTAGGTAA
5234941 AAGTA
1 AAGTA
5234946 TATAAAGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.20
Consensus pattern (10 bp):
AAGTAGGTAA
Found at i:5237575 original size:9 final size:9
Alignment explanation
Indices: 5237561--5237609 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
5237551 GTTAAACGGA
5237561 TCGAGTTAT
1 TCGAGTTAT
*
5237570 TCGAGTTAA
1 TCGAGTTAT
5237579 TCGAGTTAT
1 TCGAGTTAT
*
5237588 TCGAGTTAA
1 TCGAGTTAT
5237597 TCGAGTTAT
1 TCGAGTTAT
5237606 TCGA
1 TCGA
5237610 ATCAACTCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5237583 original size:18 final size:18
Alignment explanation
Indices: 5237560--5237609 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
5237550 AGTTAAACGG
5237560 ATCGAGTTATTCGAGTTA
1 ATCGAGTTATTCGAGTTA
5237578 ATCGAGTTATTCGAGTTA
1 ATCGAGTTATTCGAGTTA
5237596 ATCGAGTTATTCGA
1 ATCGAGTTATTCGA
5237610 ATCAACTCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (18 bp):
ATCGAGTTATTCGAGTTA
Found at i:5237679 original size:9 final size:9
Alignment explanation
Indices: 5237662--5237698 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5237652 TGAGTTTTCG
5237662 AATTCGAAT
1 AATTCGAAT
*
5237671 AACTCGAAT
1 AATTCGAAT
5237680 AATTCGAAT
1 AATTCGAAT
5237689 AATTCGAAT
1 AATTCGAAT
5237698 A
1 A
5237699 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5244112 original size:26 final size:27
Alignment explanation
Indices: 5244062--5244112 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
5244052 AGTTAATAAA
* *
5244062 TTCTCTCTGAGTTTTTTTTTCAAGAAT
1 TTCTCTCTGAGTTTCTTTTACAAGAAT
*
5244089 TTCTCT-TGAGTTTCTTTTAGAAGA
1 TTCTCTCTGAGTTTCTTTTACAAGA
5244113 GTTTTAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.53
Consensus pattern (27 bp):
TTCTCTCTGAGTTTCTTTTACAAGAAT
Found at i:5244352 original size:18 final size:18
Alignment explanation
Indices: 5244306--5244352 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5244296 ATTATTCTAA
*
5244306 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
5244323 TATTTTACTTATTTATTT
1 TATTTTATTTATTTATTT
5244341 TAATTTT-TTTAT
1 T-ATTTTATTTAT
5244353 CTGACTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:5247035 original size:45 final size:45
Alignment explanation
Indices: 5246984--5247115 Score: 151
Period size: 45 Copynumber: 3.0 Consensus size: 45
5246974 TACGTATACC
*
5246984 GGGTACCATTAATTATAAATGTGGTTGCTATGTGCTGATTCCACT
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
* * *
5247029 GGGTACCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACC
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
* * * * * * *
5247074 GAGTATCATTGACTATAAGGGTGG-TGCTGTGTGCAGA-TCCAC
1 GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCAC
5247116 CGTGTATCTA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
43 5 0.07
44 10 0.13
45 61 0.80
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (45 bp):
GGGTACCATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
Found at i:5249870 original size:19 final size:20
Alignment explanation
Indices: 5249828--5249870 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5249818 TCATACTTTC
* *
5249828 TATTCACATTTTCATATTCA
1 TATTCACATATTCAAATTCA
5249848 -ATTCACATATTCAAATT-A
1 TATTCACATATTCAAATTCA
5249866 TATTC
1 TATTC
5249871 CACAATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCACATATTCAAATTCA
Found at i:5250111 original size:42 final size:41
Alignment explanation
Indices: 5250052--5250196 Score: 109
Period size: 42 Copynumber: 3.5 Consensus size: 41
5250042 CAGAAGCAGT
*
5250052 ATACGGCACATAAAGTGCCTAAAACGACACACGTGGTGTCTA
1 ATACGACACATAAAGTGCCTAAAACGACACACGTGGTG-CTA
* * * ** * **
5250094 ATACGACACATATAGTGCCTGGTAAATGTA-TTA-GAAGCAG-T-
1 ATACGACACATAAAGTGCCT--AAAACG-ACACACG-TGGTGCTA
5250135 ATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTA
1 ATACGACACATAAAGTGCCTAAAACGACACACGTGGTG-CTA
* *
5250177 ATACGACGCATATAGTGCCT
1 ATACGACACATAAAGTGCCT
5250197 GATCGGCAAA
Statistics
Matches: 75, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
38 1 0.01
39 7 0.09
40 1 0.01
41 20 0.27
42 37 0.49
43 1 0.01
44 7 0.09
45 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (41 bp):
ATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCTA
Found at i:5250182 original size:83 final size:83
Alignment explanation
Indices: 5250043--5250197 Score: 283
Period size: 83 Copynumber: 1.9 Consensus size: 83
5250033 TCAATATATC
* *
5250043 AGAAGCAGTATACGGCACATAAAGTGCCTAAAACGACACACGTGGTGTCTAATACGACACATATA
1 AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACACATATA
5250108 GTGCCTGGTAAATGTATT
66 GTGCCTGGTAAATGTATT
*
5250126 AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACGCATATA
1 AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACACATATA
5250191 GTGCCTG
66 GTGCCTG
5250198 ATCGGCAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (83 bp):
AGAAGCAGTATACGACACATAAAGTGCCTAAAACGACACACGTGGTGCCTAATACGACACATATA
GTGCCTGGTAAATGTATT
Found at i:5250194 original size:21 final size:21
Alignment explanation
Indices: 5250135--5250196 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
5250125 TAGAAGCAGT
*
5250135 ATACGACACATAAAGTGCCTA
1 ATACGACACATATAGTGCCTA
* ** *
5250156 AAACGACACACGTGGTGCCTA
1 ATACGACACATATAGTGCCTA
*
5250177 ATACGACGCATATAGTGCCT
1 ATACGACACATATAGTGCCT
5250197 GATCGGCAAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTA
Found at i:5250397 original size:29 final size:29
Alignment explanation
Indices: 5250363--5250419 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5250353 ACTAATCAAT
*
5250363 ATTCAATTCAATATTAACACATATTTCTC
1 ATTCAATTCAATACTAACACATATTTCTC
5250392 ATTCAATTCAATACTAACACATATTTCT
1 ATTCAATTCAATACTAACACATATTTCT
5250420 GTAATACCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (29 bp):
ATTCAATTCAATACTAACACATATTTCTC
Found at i:5252547 original size:23 final size:24
Alignment explanation
Indices: 5252504--5252550 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5252494 CTTTTGAGTT
*
5252504 AATAAATTCTCTTGAGTTTTTTTC
1 AATAAATTCCCTTGAGTTTTTTTC
*
5252528 AATAATTTCCCTTGAGTTTTTTT
1 AATAAATTCCCTTGAGTTTTTTT
5252551 TAGAAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (24 bp):
AATAAATTCCCTTGAGTTTTTTTC
Found at i:5257842 original size:26 final size:27
Alignment explanation
Indices: 5257805--5257867 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
5257795 ATAAAAAATA
5257805 ACCAAAATATTAT-AACTTTTTTATTT
1 ACCAAAATATTATAAACTTTTTTATTT
* *
5257831 ACCCAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAACTTTTTTATTT
5257858 ACCAAAATAT
1 ACCAAAATAT
5257868 ACAAAAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (27 bp):
ACCAAAATATTATAAACTTTTTTATTT
Found at i:5257890 original size:17 final size:17
Alignment explanation
Indices: 5257860--5257893 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5257850 TTTTATTTAC
*
5257860 CAAAATATACAAAAAAA
1 CAAAAAATACAAAAAAA
*
5257877 CAAAAAATAGAAAAAAA
1 CAAAAAATACAAAAAAA
5257894 AACCTTCACC
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:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (17 bp):
CAAAAAATACAAAAAAA
Found at i:5258018 original size:27 final size:26
Alignment explanation
Indices: 5257924--5258026 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 26
5257914 CACCCTGGTC
*
5257924 GTGCCAAGATGATTGGCGGCACCAAAG
1 GTGCCAAG-TGATTGGCGGCACCAATG
* *
5257951 GTGCCAAAGTTATTGGCGGCACCGATG
1 GTGCC-AAGTGATTGGCGGCACCAATG
* * *
5257978 ATGTCAAGGAGATTGGCGGCACCAATG
1 GTGCCAA-GTGATTGGCGGCACCAATG
* *
5258005 GTGCCATACTGATTGGTGGCAC
1 GTGCCA-AGTGATTGGCGGCAC
5258027 TACTCGTGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
26 2 0.03
27 54 0.90
28 4 0.07
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.20
Consensus pattern (26 bp):
GTGCCAAGTGATTGGCGGCACCAATG
Found at i:5258252 original size:3 final size:3
Alignment explanation
Indices: 5258244--5258290 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
5258234 TTTTAGTTAG
*
5258244 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5258291 AGATGTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5259181 original size:18 final size:18
Alignment explanation
Indices: 5259139--5259181 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5259129 TTGATATAGT
* *
5259139 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
* *
5259157 TGCTGGCGAAGGAGAAGG
1 TGGTGGCGAAGAAGAAGG
5259175 TGGTGGC
1 TGGTGGC
5259182 AATCATTGGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.49, T:0.19
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:5264845 original size:28 final size:31
Alignment explanation
Indices: 5264795--5264861 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 31
5264785 AATTACATTT
5264795 TTTTCTTTTTTTTTCCTTCCTTC-CCTCTT-C
1 TTTTCTTTTTTTTTCCTTCCTTCTCCT-TTCC
5264825 TTCTTCTTTTTTTTT-C-T-CTTCTCCTTTCC
1 TT-TTCTTTTTTTTTCCTTCCTTCTCCTTTCC
5264854 TTTTCTTT
1 TTTTCTTT
5264862 CCTTCTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 12 0.35
29 7 0.21
30 3 0.09
31 12 0.35
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (31 bp):
TTTTCTTTTTTTTTCCTTCCTTCTCCTTTCC
Found at i:5264846 original size:18 final size:17
Alignment explanation
Indices: 5264825--5264974 Score: 79
Period size: 18 Copynumber: 8.2 Consensus size: 17
5264815 TTCCCTCTTC
5264825 TTCTTCTTTTTTTTTCT
1 TTCTTCTTTTTTTTTCT
* **
5264842 CTTCTCCTTTCCTTTTCT
1 -TTCTTCTTTTTTTTTCT
*
5264860 TTCCTTCTTTTTCTTTCTTTT
1 TT-CTTC-TTTT-TTT-TTCT
5264881 TTCTTCTCCTTTCCTCTTCTTCT
1 TTCTTCT--TTT--T-TT-TTCT
5264904 TTCTT-TTTTTTTTTCT
1 TTCTTCTTTTTTTTTCT
* **
5264920 CTTCTCCTTTCCTTTTCT
1 -TTCTTCTTTTTTTTTCT
*
5264938 TTCCTTCTTTTTCTTTCT
1 TT-CTTCTTTTTTTTTCT
* *
5264956 TTCTT-TCTTTCTTTCT
1 TTCTTCTTTTTTTTTCT
5264972 TTC
1 TTC
5264975 CCTCTCCTTC
Statistics
Matches: 105, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
16 17 0.16
17 13 0.12
18 40 0.38
19 4 0.04
20 9 0.09
21 8 0.08
22 3 0.03
23 11 0.10
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTCTTTTTTTTTCT
Found at i:5264850 original size:34 final size:34
Alignment explanation
Indices: 5264797--5264959 Score: 127
Period size: 37 Copynumber: 4.6 Consensus size: 34
5264787 TTACATTTTT
5264797 TTCTTTTTTTTTC-C-T-TCCTTCCCTCTTCTTC
1 TTCTTTTTTTTTCTCTTCTCCTTCCCTCTTCTTC
*
5264828 TTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTC
1 TTCTTTTTTTTTCTCTTCTCC-TTCC--CTC-TT-CTTC
* * *
5264867 TTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTC
1 TTCTT-TTT-TTTTCTCTTCTCCTTCCCTCTTCTTC
* *
5264903 TTTCTTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCC
1 -TTC--TTTTTTTTTCTCTTCTCCTTCCCTCTTC-TT-C
*
5264942 TTCTTTTTCTTTCT-TTCT
1 TTCTTTTTTTTTCTCTTCT
5264960 TTCTTTCTTT
Statistics
Matches: 108, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
31 13 0.12
32 1 0.01
33 1 0.01
34 3 0.03
35 8 0.07
36 14 0.13
37 27 0.25
38 12 0.11
39 11 0.10
40 6 0.06
41 12 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (34 bp):
TTCTTTTTTTTTCTCTTCTCCTTCCCTCTTCTTC
Found at i:5264876 original size:4 final size:4
Alignment explanation
Indices: 5264855--5264974 Score: 83
Period size: 4 Copynumber: 30.0 Consensus size: 4
5264845 CTCCTTTCCT
*
5264855 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * * *
5264900 -TTC TTTC TTTT TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC
5264947 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
5264975 CCTCTCCTTC
Statistics
Matches: 97, Mismatches: 6, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
3 16 0.16
4 62 0.64
5 11 0.11
6 8 0.08
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:5264929 original size:78 final size:74
Alignment explanation
Indices: 5264794--5264966 Score: 276
Period size: 78 Copynumber: 2.3 Consensus size: 74
5264784 AAATTACATT
*
5264794 TTTTTCTTT-TTTTTTCCTTCCTTCCCTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTT
1 TTTTTCTTTCTTTTTTCTTTCCTTCCCTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTT
5264858 CTTTCCTTC
66 CTTTCCTTC
*
5264867 TTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTTCTTTTTTTTTTTCTCTTCTCCTTTCC
1 TTTTTCTTTCTTTTTTCTT-TCCTTCCCTCTTCTTC-TTC--TTTTTTTTTCTCTTCTCCTTTCC
5264932 TTTTCTTTCCTTC
62 TTTTCTTTCCTTC
5264945 TTTTTCTTTCTTTCTTTCTTTC
1 TTTTTCTTTCTTT-TTTCTTTC
5264967 TTTCTTTCCC
Statistics
Matches: 92, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
73 9 0.10
74 8 0.09
75 15 0.16
76 3 0.03
78 51 0.55
79 6 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (74 bp):
TTTTTCTTTCTTTTTTCTTTCCTTCCCTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTT
CTTTCCTTC
Found at i:5264937 original size:30 final size:33
Alignment explanation
Indices: 5264863--5264940 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
5264853 CTTTTCTTTC
*
5264863 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCT
1 CTTCCTTTTCTTTCTTTTTTCTTCTCCTTTCCT
*
5264896 CTTCTTCTTTCTTT-TTTTTT-TTCT-CTTCTCCT
1 CTTCCT-TTTCTTTCTTTTTTCTTCTCCTT-TCCT
5264928 -TTCCTTTTCTTTC
1 CTTCCTTTTCTTTC
5264941 CTTCTTTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 7 0.17
31 7 0.17
32 8 0.20
33 12 0.29
34 7 0.17
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (33 bp):
CTTCCTTTTCTTTCTTTTTTCTTCTCCTTTCCT
Found at i:5264967 original size:30 final size:30
Alignment explanation
Indices: 5264794--5264970 Score: 93
Period size: 30 Copynumber: 5.9 Consensus size: 30
5264784 AAATTACATT
* * *
5264794 TTTTTCTTT-TTT-TTTCCTTCCTTCCCTC
1 TTTTTCTTTCTTTCTTTCTTTCTTTCCTTC
* *
5264822 TTCTTC-TTCTTT-TTTTTTCTCTTCTCCTTTC
1 TTTTTCTTTCTTTCTTTCTT-TCTT-TCC-TTC
* * *
5264853 CTTTTCTTTCCTTCTTTTTCTTTCTTT-TTTC
1 TTTTTCTTT-CTT-TCTTTCTTTCTTTCCTTC
* * *
5264884 TTCTCCTTTCCTCTTC-TTCTTTCTTT--TTT
1 TTTTTCTTT-CT-TTCTTTCTTTCTTTCCTTC
*
5264913 TTTTTCTCTTC-TCCTTTCCTTTTCTTTCCTTC
1 TTTTTCT-TTCTTTCTTT-C-TTTCTTTCCTTC
5264945 TTTTTCTTTCTTTCTTTCTTTCTTTC
1 TTTTTCTTTCTTTCTTTCTTTCTTTC
5264971 TTTCCCTCTC
Statistics
Matches: 114, Mismatches: 19, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
27 4 0.04
28 14 0.12
29 12 0.11
30 30 0.26
31 23 0.20
32 17 0.15
33 4 0.04
34 5 0.04
35 5 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (30 bp):
TTTTTCTTTCTTTCTTTCTTTCTTTCCTTC
Found at i:5265051 original size:27 final size:27
Alignment explanation
Indices: 5265013--5265064 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5265003 TATTATAACA
* * *
5265013 TTGGTGCCGCCAATGACTTTGGCACCT
1 TTGGTGCAGCCAATCACCTTGGCACCT
5265040 TTGGTGCAGCCAATCACCTTGGCAC
1 TTGGTGCAGCCAATCACCTTGGCAC
5265065 GACCAGGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.25, T:0.27
Consensus pattern (27 bp):
TTGGTGCAGCCAATCACCTTGGCACCT
Found at i:5265152 original size:25 final size:27
Alignment explanation
Indices: 5265123--5265185 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 27
5265113 TGTTTTTGGT
5265123 ATATTTTGGTAAAT-AAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
5265148 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAAGTTATA
5265176 ATATTTTGGT
1 ATATTTTGGT
5265186 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.40
27 6 0.17
28 15 0.43
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:5265361 original size:24 final size:24
Alignment explanation
Indices: 5265332--5265379 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5265322 AATAAAAAAT
5265332 AATATTATTCTAAAGATCTTATAA
1 AATATTATTCTAAAGATCTTATAA
5265356 AATATTATTCTAAAGATCTTATAA
1 AATATTATTCTAAAGATCTTATAA
5265380 TAGTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
AATATTATTCTAAAGATCTTATAA
Found at i:5276891 original size:17 final size:17
Alignment explanation
Indices: 5276869--5276902 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5276859 AGAGTTGAAA
5276869 ACAAAACTCAAAAATTG
1 ACAAAACTCAAAAATTG
* *
5276886 ACAAAATTCTAAAATTG
1 ACAAAACTCAAAAATTG
5276903 TTCATTAACC
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:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
ACAAAACTCAAAAATTG
Found at i:5281994 original size:25 final size:25
Alignment explanation
Indices: 5281966--5282033 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
5281956 CATGTAATTA
* *
5281966 GGAAGCTCTTCTGAGCCATGTAACG
1 GGAAGCTCTTCTGAGCCATATAAAG
* * **
5281991 GGAAGCTCATGTGAGCTGTATAAAG
1 GGAAGCTCTTCTGAGCCATATAAAG
5282016 GGAAGCTCTTGC-GAGCCA
1 GGAAGCTCTT-CTGAGCCA
5282034 GTTATCGAGA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (25 bp):
GGAAGCTCTTCTGAGCCATATAAAG
Found at i:5282168 original size:25 final size:25
Alignment explanation
Indices: 5282140--5282223 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 25
5282130 CATTAATCGA
*
5282140 GAAGCTCATGAGAGCCAATTATCAG
1 GAAGCTCATGAGAGCCAAATATCAG
* * * *
5282165 GAAGCTCGTAAGGGCCAAATAACAG
1 GAAGCTCATGAGAGCCAAATATCAG
* *
5282190 GAAGCTCGTGAGAGCCAAATATCGG
1 GAAGCTCATGAGAGCCAAATATCAG
*
5282215 GACGCTCAT
1 GAAGCTCAT
5282224 AAGATCTGTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAAATATCAG
Found at i:5282563 original size:61 final size:61
Alignment explanation
Indices: 5282487--5282609 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
5282477 ACTAATCCGA
5282487 TACTTTTTCTTTTCCTCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAAT
1 TACTTTTTCTTTTCCTCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAAT
5282548 TACTTTTTCTTTTCCTCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAAT
1 TACTTTTTCTTTTCCTCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAAT
5282609 T
1 T
5282610 TTAACTTAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (61 bp):
TACTTTTTCTTTTCCTCAATCCAATTCCGTACTAGGTCTATCTAGATCTATACAAATGAAT
Found at i:5288271 original size:25 final size:25
Alignment explanation
Indices: 5288217--5288271 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
5288207 AAACATTAAA
*
5288217 TTTAATTTAATATTAAGATAATGAC
1 TTTAATTTAATATTAAGAAAATGAC
*
5288242 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATGAC
5288266 TATTAA
1 T-TTAA
5288272 GACAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATGAC
Found at i:5288298 original size:17 final size:18
Alignment explanation
Indices: 5288276--5288310 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5288266 TATTAAGACA
5288276 AATATTAAACTA-AATTT
1 AATATTAAACTATAATTT
5288293 AATATTAAACTATAATTT
1 AATATTAAACTATAATTT
5288311 GAGGTCAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATTAAACTATAATTT
Found at i:5292173 original size:21 final size:21
Alignment explanation
Indices: 5292149--5292196 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5292139 TTTAATCACC
* *
5292149 GAAAATGCAGTAATGCTGTCT
1 GAAAACGCAGTAATACTGTCT
* *
5292170 GAAAACGTAGTAATACTGTTT
1 GAAAACGCAGTAATACTGTCT
5292191 GAAAAC
1 GAAAAC
5292197 ACTTCCTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (21 bp):
GAAAACGCAGTAATACTGTCT
Found at i:5297417 original size:27 final size:27
Alignment explanation
Indices: 5297386--5297446 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
5297376 CTAGTTTATG
*
5297386 AATTTATACATTAATAAT-ATATATAAT
1 AATTTATACAATAA-AATAATATATAAT
* * *
5297413 AATTTCTTCAATAAACTAATATATAAT
1 AATTTATACAATAAAATAATATATAAT
5297440 AATTTAT
1 AATTTAT
5297447 TTATTTACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTTATACAATAAAATAATATATAAT
Found at i:5304374 original size:16 final size:16
Alignment explanation
Indices: 5304353--5304386 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5304343 CTATTCATGC
*
5304353 AAAATATAAAAGATAG
1 AAAATACAAAAGATAG
5304369 AAAATACAAAAGATAG
1 AAAATACAAAAGATAG
5304385 AA
1 AA
5304387 TAGTGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAATACAAAAGATAG
Found at i:5306235 original size:40 final size:39
Alignment explanation
Indices: 5306187--5306282 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
5306177 GAAATTGAGA
5306187 TTGA-TACTGAATTGAATTATGGAA-TACTGAATATTGTTT
1 TTGAGTACTGAATTGAATTAT-GAAGTACTGAATATTG-TT
5306226 TTGAGTACTGAATTGAATTATGAAGTTACTGAATATTGTT
1 TTGAGTACTGAATTGAATTATGAAG-TACTGAATATTGTT
* * *
5306266 ATGTGTACTGCATTGAA
1 TTGAGTACTGAATTGAA
5306283 CTGTGAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
39 7 0.14
40 32 0.63
41 12 0.24
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (39 bp):
TTGAGTACTGAATTGAATTATGAAGTACTGAATATTGTT
Found at i:5306267 original size:21 final size:20
Alignment explanation
Indices: 5306197--5306275 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 20
5306187 TTGATACTGA
*
5306197 ATTGAATTATGGAATACTGAAT
1 ATTG-ATTAT-GAGTACTGAAT
* *
5306219 ATTGTTTTTGAGTACTG-A-
1 ATTGATTATGAGTACTGAAT
5306237 ATTGAATTATGAAGTTACTGAAT
1 ATTG-ATTATG-AG-TACTGAAT
*
5306260 ATTG-TTATGTGTACTG
1 ATTGATTATGAGTACTG
5306276 CATTGAACTG
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
18 4 0.09
19 10 0.22
20 10 0.22
21 13 0.28
22 5 0.11
23 4 0.09
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (20 bp):
ATTGATTATGAGTACTGAAT
Found at i:5306592 original size:6 final size:6
Alignment explanation
Indices: 5306581--5306625 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
5306571 GTTTGTTGAA
** *
5306581 TACTGT TACTGT TACTGT TACTAC TACCGT TACTGAT TACTGT TA
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT TA
5306626 AGGTGTTGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:5306600 original size:45 final size:45
Alignment explanation
Indices: 5306497--5306601 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
5306487 TAATGCCGAC
* * *
5306497 TACTGTTACTATTACCGATTCGACACTTTGTGTGTTGAATATTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTTGAATACTGT
** * *
5306542 TACCATTATTGTTACAGATTC-AGCACTTTGTTTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGA-CACTTTGTGTGTTGAATACTGT
5306587 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
5306602 TACTACCGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 48 0.98
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGACACTTTGTGTGTTGAATACTGT
Found at i:5314895 original size:14 final size:14
Alignment explanation
Indices: 5314878--5314911 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5314868 AATTTATAGC
5314878 TAAAAATAAAATAT
1 TAAAAATAAAATAT
* *
5314892 TAAATATTAAATAT
1 TAAAAATAAAATAT
5314906 TAAAAA
1 TAAAAA
5314912 ATAATATGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAATAAAATAT
Found at i:5314910 original size:27 final size:27
Alignment explanation
Indices: 5314880--5314961 Score: 62
Period size: 27 Copynumber: 2.9 Consensus size: 27
5314870 TTTATAGCTA
5314880 AAAATAAAATATTAAATATTAAATATT
1 AAAATAAAATATTAAATATTAAATATT
*
5314907 AAAA-AATAATATGTGATAATATTTAAA-GTT
1 AAAATAA-AATAT-T-A-AATA-TTAAATATT
**
5314937 AAAAT-AAATAACAATATATTAAATA
1 AAAATAAAATATTAA-ATATTAAATA
5314962 ATAATTCCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
26 8 0.19
27 13 0.30
28 1 0.02
29 5 0.12
30 11 0.26
31 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (27 bp):
AAAATAAAATATTAAATATTAAATATT
Found at i:5317198 original size:22 final size:22
Alignment explanation
Indices: 5317173--5317264 Score: 87
Period size: 22 Copynumber: 4.0 Consensus size: 22
5317163 TGCACTAATG
*
5317173 AACAGATAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
*
5317195 AACAGAGAGCAC-AGAATTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
5317217 AACAGAGAGCACTGACGTGCTAAA
1 AACAGAGAGCACTAAAGTGCT--A
* *
5317241 AATCAGAGAGCACTGATGTGCTA
1 AA-CAGAGAGCACTAAAGTGCTA
5317264 A
1 A
5317265 TAATCAGAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.02
22 35 0.59
23 2 0.03
24 3 0.05
25 18 0.31
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:5317250 original size:25 final size:25
Alignment explanation
Indices: 5317219--5317277 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
5317209 AATTGCTAAA
5317219 CAGAGAGCACTGACGTGCTAAAAAT
1 CAGAGAGCACTGACGTGCTAAAAAT
* *
5317244 CAGAGAGCACTGATGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAAAAAT
5317269 CAGAGAGCA
1 CAGAGAGCA
5317278 TGCTAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACTGACGTGCTAAAAAT
Found at i:5317418 original size:2 final size:2
Alignment explanation
Indices: 5317411--5317476 Score: 86
Period size: 2 Copynumber: 34.0 Consensus size: 2
5317401 ACATTTACAC
5317411 AT AT AT AT AT -T CAT A- AT AT AT AT AT AT -T CAT A- 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
5317451 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
5317477 TCCAATTCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.07
2 52 0.90
3 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5322731 original size:15 final size:15
Alignment explanation
Indices: 5322711--5322742 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5322701 CATTTCACTA
*
5322711 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
5322726 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
5322741 TT
1 TT
5322743 TGCATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:5335257 original size:28 final size:28
Alignment explanation
Indices: 5335190--5335257 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
5335180 AGCACGATTC
*
5335190 AAGTTCAAGTACCAATTAGGTCAAAAAAA
1 AAGTT-AAGTACAAATTAGGTCAAAAAAA
**
5335219 AAGTTGGGTACAAATTAGGTCAAAAAAA
1 AAGTTAAGTACAAATTAGGTCAAAAAAA
**
5335247 ATTTTAAGTAC
1 AAGTTAAGTAC
5335258 CAAGTAAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (28 bp):
AAGTTAAGTACAAATTAGGTCAAAAAAA
Found at i:5335387 original size:26 final size:26
Alignment explanation
Indices: 5335349--5335399 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5335339 TTTGCTAGAA
5335349 TAAACAAAATTGTGCTAATTTTATTT
1 TAAACAAAATTGTGCTAATTTTATTT
*
5335375 TAAA-AAAAGTTGTGTTAATTTTATT
1 TAAACAAAA-TTGTGCTAATTTTATT
5335400 GATTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (26 bp):
TAAACAAAATTGTGCTAATTTTATTT
Found at i:5335599 original size:23 final size:22
Alignment explanation
Indices: 5335548--5335600 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
5335538 TGATATGTTG
5335548 AATATGTTAAAAATGTGTTATTT
1 AATAT-TTAAAAATGTGTTATTT
* *
5335571 ATTATTTAAAAAT-TTTCTATTAT
1 AATATTTAAAAATGTGT-TATT-T
5335594 AATATTT
1 AATATTT
5335601 GAATCGATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 12 0.48
23 11 0.44
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
AATATTTAAAAATGTGTTATTT
Found at i:5338759 original size:20 final size:19
Alignment explanation
Indices: 5338734--5338773 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5338724 TTTGTTTTCA
*
5338734 TTTTATTTATAGTTCATTTG
1 TTTTATGTATA-TTCATTTG
*
5338754 TTTTATGTATATTGATTTG
1 TTTTATGTATATTCATTTG
5338773 T
1 T
5338774 GCATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (19 bp):
TTTTATGTATATTCATTTG
Found at i:5339615 original size:21 final size:23
Alignment explanation
Indices: 5339586--5339630 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
5339576 GCGGGTCCTT
*
5339586 AACTCATTTTTAAATTTAC-TCA
1 AACTCATTTTTAAATGTACATCA
5339608 AACT-ATTTTTAAATGTACATCA
1 AACTCATTTTTAAATGTACATCA
5339630 A
1 A
5339631 TAAAAATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (23 bp):
AACTCATTTTTAAATGTACATCA
Found at i:5343730 original size:11 final size:11
Alignment explanation
Indices: 5343683--5343730 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
5343673 GTTTTCTCCC
*
5343683 TATTTTGTTAC
1 TATTTTGTTAT
* *
5343694 CATTTTATTAT
1 TATTTTGTTAT
* *
5343705 TATGTTGCTAT
1 TATTTTGTTAT
5343716 TATTTTGTTAT
1 TATTTTGTTAT
5343727 TATT
1 TATT
5343731 GTTCGGATAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:5345350 original size:18 final size:18
Alignment explanation
Indices: 5345317--5345374 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
5345307 ATTCTTCTGT
*
5345317 TAATGTTATAATATATTATT
1 TAAT-TTAT-ATATATTATA
*
5345337 TTATTTATATATATTATA
1 TAATTTATATATATTATA
*
5345355 TAATTTATA-ATAATATA
1 TAATTTATATATATTATA
5345372 TAA
1 TAA
5345375 ATAAACATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.29
18 17 0.50
19 4 0.12
20 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTTATATATATTATA
Found at i:5348897 original size:22 final size:22
Alignment explanation
Indices: 5348871--5348915 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5348861 GAAAAAAGAA
*
5348871 AACATTGACGTAAAAGAGTGGG
1 AACATTAACGTAAAAGAGTGGG
5348893 AACATTAACGTAAAAGAGTGGG
1 AACATTAACGTAAAAGAGTGGG
5348915 A
1 A
5348916 GACCCAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.29, T:0.18
Consensus pattern (22 bp):
AACATTAACGTAAAAGAGTGGG
Found at i:5351234 original size:9 final size:9
Alignment explanation
Indices: 5351220--5351247 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5351210 TAAGTTTTCG
5351220 AATTCGAAT
1 AATTCGAAT
5351229 AATTCGAAT
1 AATTCGAAT
5351238 AATTCGAAT
1 AATTCGAAT
5351247 A
1 A
5351248 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5352425 original size:23 final size:23
Alignment explanation
Indices: 5352397--5352443 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5352387 TAATGTTAGA
5352397 AAGTGGATCCCTATTTATAGTTC
1 AAGTGGATCCCTATTTATAGTTC
5352420 AAGTGGATCCCTATTTATAGTTC
1 AAGTGGATCCCTATTTATAGTTC
5352443 A
1 A
5352444 GACTTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (23 bp):
AAGTGGATCCCTATTTATAGTTC
Found at i:5352590 original size:21 final size:21
Alignment explanation
Indices: 5352564--5352623 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
5352554 AAAAACAAGT
5352564 TTTTAGCGGCGTTTTTTATGC
1 TTTTAGCGGCGTTTTTTATGC
5352585 TTTTAGCGGCGTTTTTTATGC
1 TTTTAGCGGCGTTTTTTATGC
*
5352606 TTTTAGCGGCGCTTTTTA
1 TTTTAGCGGCGTTTTTTA
5352624 ACGCCGCTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.52
Consensus pattern (21 bp):
TTTTAGCGGCGTTTTTTATGC
Found at i:5352774 original size:43 final size:42
Alignment explanation
Indices: 5352704--5352970 Score: 324
Period size: 43 Copynumber: 6.3 Consensus size: 42
5352694 TTTTAGAAAT
*
5352704 AAACGCCGCTATAGATCATGACATTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGAC-TTTAGCGGCGCTTTTCCCAC
* * *
5352747 AAACGACGCTATAGATCAGGAGCTTTAGCGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAAGA-CTTTAGCGGCGCTTTTCCCAC
*
5352789 AAACGTCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGA-CTTTAGCGGCGCTTTTCCCAC
* * * *
5352832 AAACTCCGCCATAGATC-AGAACCTTTAGCGGTGCTTTT-ACAC
1 AAACGCCGCTATAGATCAAG-A-CTTTAGCGGCGCTTTTCCCAC
* * *
5352874 AAACGCCGCTATAGCTCAAGATCTTTAGCGACGCTTATCCCAC
1 AAACGCCGCTATAGATCAAGA-CTTTAGCGGCGCTTTTCCCAC
* *
5352917 AAACGCCGCTATAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGAC-TTTAGCGGCGCTTTTCCCAC
5352960 AAACGCCGCTA
1 AAACGCCGCTA
5352971 AAAACATATA
Statistics
Matches: 194, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
42 72 0.37
43 121 0.62
44 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAAGACTTTAGCGGCGCTTTTCCCAC
Found at i:5352847 original size:85 final size:84
Alignment explanation
Indices: 5352704--5352970 Score: 363
Period size: 85 Copynumber: 3.1 Consensus size: 84
5352694 TTTTAGAAAT
* * *
5352704 AAACGCCGCTATAGATCATGACATTTAGCGGCGCTTTTCCCACAAACGACGCTATAGATCAGGAG
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGA-
5352769 CTTTAGCGGCGCTTTTACAC
65 CTTTAGCGGCGCTTTTACAC
* * * *
5352789 AAACGTCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACTCCGCCATAGATCAGAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGA-
*
5352854 CTTTAGCGGTGCTTTTACAC
65 CTTTAGCGGCGCTTTTACAC
* * * * * *
5352874 AAACGCCGCTATAGCTCAAGATCTTTAGCGACGCTTATCCCACAAACGCCGCTATAGGTCATGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
*
5352939 TTTTAGCGGCGCTTTTCCCAC
66 -TTTAGCGGCGCTTTT-ACAC
5352960 AAACGCCGCTA
1 AAACGCCGCTA
5352971 AAAACATATA
Statistics
Matches: 159, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 144 0.91
86 14 0.09
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (84 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
TTTAGCGGCGCTTTTACAC
Found at i:5352920 original size:128 final size:128
Alignment explanation
Indices: 5352704--5352968 Score: 354
Period size: 128 Copynumber: 2.1 Consensus size: 128
5352694 TTTTAGAAAT
* * *
5352704 AAACGCCGCTATAGATCATGACATTTAGCGGCGCTTTTCCCACAAACGACGCTATAGATCAGGAG
1 AAACGCCGCCATAGATCATGACATTTAGCGGCGCTTTTCACACAAACGACGCTATAGATCAAGAG
* * *
5352769 CTTTAGCGGCGCTTTTACACAAACGTCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
66 CTTTAGCGACGCTTTCACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
5352832 AAACTCCGCCATAGATCA-GAACCTTTAGCGGTGCTTTT-ACACAAACGCCGCTATAGCTCAAGA
1 AAACGCCGCCATAGATCATG-ACATTTAGCGGCGCTTTTCACACAAACGACGCTATAGATCAAGA
* * * * *
5352895 TCTTTAGCGACGCTTATCCCACAAACGCCGCTATAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
65 GCTTTAGCGACGCTT-TCACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
5352960 AAACGCCGC
1 AAACGCCGC
5352969 TAAAAACATA
Statistics
Matches: 118, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
127 35 0.30
128 83 0.70
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (128 bp):
AAACGCCGCCATAGATCATGACATTTAGCGGCGCTTTTCACACAAACGACGCTATAGATCAAGAG
CTTTAGCGACGCTTTCACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:5353199 original size:9 final size:9
Alignment explanation
Indices: 5353185--5353210 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5353175 AATAAATATC
5353185 ATGCTTATA
1 ATGCTTATA
5353194 ATGCTTATA
1 ATGCTTATA
5353203 ATGCTTAT
1 ATGCTTAT
5353211 TGAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (9 bp):
ATGCTTATA
Found at i:5356561 original size:24 final size:25
Alignment explanation
Indices: 5356516--5356562 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5356506 CGCTATTGCT
5356516 TATGCAAAAAATTATTTCATTTTAC
1 TATGCAAAAAATTATTTCATTTTAC
* *
5356541 TATGCTAAAAATT-TTTTATTTT
1 TATGCAAAAAATTATTTCATTTT
5356563 GTTTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (25 bp):
TATGCAAAAAATTATTTCATTTTAC
Found at i:5357434 original size:21 final size:22
Alignment explanation
Indices: 5357410--5357464 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
5357400 GACCCCGAAT
*
5357410 CTCTAAACCTTAAATCACTAA-
1 CTCTAAACCTTAAACCACTAAC
* **
5357431 CTCTTAACCCCAAACCACTAAC
1 CTCTAAACCTTAAACCACTAAC
5357453 CTCTAAACCTTA
1 CTCTAAACCTTA
5357465 TTTAATATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.25
Consensus pattern (22 bp):
CTCTAAACCTTAAACCACTAAC
Found at i:5357540 original size:7 final size:7
Alignment explanation
Indices: 5357528--5357564 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
5357518 GACCCCAAAT
5357528 CCCTAAC
1 CCCTAAC
5357535 CCCTAAC
1 CCCTAAC
5357542 CCCTAAC
1 CCCTAAC
5357549 CCCTAAC
1 CCCTAAC
5357556 CCCTAAC
1 CCCTAAC
5357563 CC
1 CC
5357565 ATAAACATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.27, C:0.59, G:0.00, T:0.14
Consensus pattern (7 bp):
CCCTAAC
Found at i:5357552 original size:21 final size:21
Alignment explanation
Indices: 5357519--5357564 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5357509 CCCTAACCCG
*
5357519 ACCCCAAATCCCTAACCCCTA
1 ACCCCAAACCCCTAACCCCTA
*
5357540 ACCCCTAACCCCTAACCCCTA
1 ACCCCAAACCCCTAACCCCTA
5357561 ACCC
1 ACCC
5357565 ATAAACATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.57, G:0.00, T:0.13
Consensus pattern (21 bp):
ACCCCAAACCCCTAACCCCTA
Found at i:5357672 original size:14 final size:14
Alignment explanation
Indices: 5357643--5357689 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5357633 TAAATCTATA
*
5357643 AACCCTAAATCCCT
1 AACCCTTAATCCCT
* *
5357657 AACTCTTAATCTCT
1 AACCCTTAATCCCT
*
5357671 AACCCTTAACCCCT
1 AACCCTTAATCCCT
5357685 AACCC
1 AACCC
5357690 ATAAACCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCCTTAATCCCT
Found at i:5357681 original size:118 final size:114
Alignment explanation
Indices: 5357344--5357682 Score: 350
Period size: 110 Copynumber: 2.9 Consensus size: 114
5357334 ATATAAGACC
* * * *
5357344 TTATTTAACATATAAATTAAAAAATACTAATTAATCTAAACCTTAAACCCTAA-CTCGACCCCGA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACCT-GACCCCAA
* * * *
5357408 ATCTCTAAACCTTAAATCACTAACTCTTAACCCCAAACCACTAACCTCTAAACC
65 ATCTCTAAACCCTAAATCCCTAACTCTTAA--CCTAACC-CTAACC-CTAAACA
** *
5357462 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATTATAAACCCTAACCCGACCCCAAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACCTGACCCCAAA
* * *
5357527 TCCCTAACCCCT-AACCCCTAAC-C----CCTAACCCCTAACCCATAAACA
66 TCTCTAAACCCTAAATCCCTAACTCTTAACCTAA-CCCTAACCC-TAAACA
* * * ** *
5357572 TTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTAAACCCTAACCTAATACTAAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACCTGACCCCAAA
*
5357637 TCTATAAACCCTAAATCCCTAACTCTTAATCTCTAACCCTTAACCC
66 TCTCTAAACCCTAAATCCCTAACTCTTAA-C-CTAACCC-TAACCC
5357683 CTAACCCATA
Statistics
Matches: 182, Mismatches: 27, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
109 1 0.01
110 80 0.44
111 11 0.06
112 1 0.01
116 1 0.01
117 12 0.07
118 75 0.41
119 1 0.01
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.27
Consensus pattern (114 bp):
TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACCTGACCCCAAA
TCTCTAAACCCTAAATCCCTAACTCTTAACCTAACCCTAACCCTAAACA
Found at i:5358147 original size:41 final size:41
Alignment explanation
Indices: 5358102--5358257 Score: 240
Period size: 41 Copynumber: 3.8 Consensus size: 41
5358092 AAATGTTTTT
* *
5358102 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
5358143 GCGGCGCTTTCTAAAAAATGCCGCTAAATATATGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
5358184 GCGGCGCTTTCTCAAAATCGCCGCTAAAGATCTAAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
5358225 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCT
5358258 AAAAGGTACA
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:5358341 original size:40 final size:40
Alignment explanation
Indices: 5358291--5358425 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
5358281 GGGCTTAGAC
* *
5358291 TTTTT-GCGGCGTTTTTCCAAAAAACGCCGCTAATGCT-AA
1 TTTTTAGCGGCG-TTTTACAAAAAACGCCGCTAATGCTCGA
* ***
5358330 TTTTTAGCGGCGCTTTACTGGAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTACAAAAAACGCCGCTAATGCTCGA
* ** *
5358370 TCTTTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTACAAAAAACGCCGCTAATGCTCGA
*
5358410 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
5358426 TTATCCAAAC
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
39 25 0.31
40 55 0.69
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTACAAAAAACGCCGCTAATGCTCGA
Found at i:5359955 original size:3 final size:3
Alignment explanation
Indices: 5359941--5359973 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5359931 CGCATGTATG
*
5359941 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5359974 CATAGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5361556 original size:44 final size:44
Alignment explanation
Indices: 5361515--5362620 Score: 334
Period size: 44 Copynumber: 25.2 Consensus size: 44
5361505 ACCATCTTTG
*
5361515 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* ** * * *
5361559 ATCTATTCCACTGTTGCCTAGGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * *
5361602 ATGTACTCCACTGTAAC--CTCAGGGAGGA-AAAATCTGTCATCTTCG
1 ATCTACTCCAC--T-ACTGCTTAGGGA-GATAAGATCTGTAATCTTCA
* *
5361647 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* ** * * *
5361691 ATCTATTCCACTGTTGCCTAGGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * *
5361734 ATGTACTCCACTGTAAC--CTTAGGGAGGTAAAATCCGCT-ATCTTCG
1 ATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATCTG-TAATCTTCA
** *
5361779 ATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* * ** * * *
5361823 ATCTATTTCACTGTTGCCTAGGGAGATAGAAATACTG---GCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATA-AGAT-CTGTAATCTTCA
* * * * * ** *
5361866 ATGTACTCCACTGTAAC--CTCAGGGAGGTAAAATCCGCCATCTTCG
1 ATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* * *
5361911 ATCTGCTCCTCTACTGCTTATGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* ** ** * *
5361955 ATCTATTCCACTGTTGCCCAGGGAGATAAAATTACTG---GCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGA-T-CTGTAATCTTCA
* * * * * ** *
5361998 ATGTACTCCACTGTAAC--CTCAGAGAGGTAAAATCTGCCATCTTCG
1 ATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* *
5362043 ATCTGCTCCACTACTTCTTAGGGAGATAAGA-CTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* ** * * * *
5362086 ATCTATTCCACTGTTGCCTAGGGAGAT-AGA-AT-TACTGGCTTCT
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * ** * *
5362129 ATGTACTCCACTGTAAC--CTTAGGGAGGTAAAATCCGCCACCTTCG
1 ATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* *
5362174 ATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* ** ** * *
5362218 ATCTATTCCACTGTTGCCCAGGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * * *
5362261 ATGTACTCCACTGTAAC--CTCAGGGAGGTAAAATCCGCT-ATCTTCG
1 ATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATCTG-TAATCTTCA
* *
5362306 ATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* * ** * * *
5362350 ATCTATTCCACTGCTGCCCAAGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * * * * ** *
5362393 ATGTACTCCATTA-TAACCTCAGGAAGGTAAAATCTGCCATCTTCG
1 ATCTACTCCACTACT--GCTTAGGGAGATAAGATCTGTAATCTTCA
* * *
5362438 ATCTGCTCCACTTCTGCTTATGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
* * ** * * *
5362482 ATCTATTCCACTGCTGCCCAGGGATAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCA
* * * * * * ** *
5362525 ATGTACTCCACTGTA-TCCTCAGGGAGGTAAAATCCGCCATCTTCG
1 ATCTACTCCAC--TACTGCTTAGGGAGATAAGATCTGTAATCTTCA
** * *
5362570 ATCTGTTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCG
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
5362614 ATCTACT
1 ATCTACT
5362621 TCACGCCAAT
Statistics
Matches: 738, Mismatches: 242, Indels: 164
0.65 0.21 0.14
Matches are distributed among these distances:
41 18 0.02
42 27 0.04
43 171 0.23
44 379 0.51
45 126 0.17
46 9 0.01
47 6 0.01
48 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
Found at i:5361616 original size:132 final size:132
Alignment explanation
Indices: 5361462--5362618 Score: 1911
Period size: 132 Copynumber: 8.8 Consensus size: 132
5361452 GAGATAGGAT
* ** *
5361462 TGGCTTCAATGTACTCTACTGTAACCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
*
5361527 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5361592 AC
131 AC
* * *
5361594 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCTGTCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* *
5361659 ACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5361724 AC
131 AC
* * *
5361726 TGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCTATCTTCGATCTGTTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* * * *
5361791 ACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTTCACTGTTGCCTAGGGAGATAGAAAT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5361856 AC
131 AC
*
5361858 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCTCT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* *
5361923 ACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAAAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5361988 AC
131 AC
* *
5361990 TGGCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* *
5362055 ACTTCTTAGGGAGATAAGA-CTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5362119 AC
131 AC
* * *
5362121 TGGCTTCTATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCCACCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
*
5362186 ACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5362251 AC
131 AC
*
5362253 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* * *
5362318 ACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5362383 AC
131 AC
* * * *
5362385 TGGCTTCAATGTACTCCATTATAACCTCAGGAAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* * * *
5362450 TCTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGATATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
5362515 AC
131 AC
* *
5362517 TGGCTTCAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
* *
5362582 ACTGCTTAAGGAGATAAGATCTGTAATCTTCGATCTA
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
5362619 CTTCACGCCA
Statistics
Matches: 960, Mismatches: 64, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
131 122 0.13
132 838 0.87
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATT
AC
Found at i:5361637 original size:88 final size:89
Alignment explanation
Indices: 5361534--5362449 Score: 368
Period size: 88 Copynumber: 10.4 Consensus size: 89
5361524 ACTACTGCTT
* * *
5361534 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAAT-TACTGGC
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAGC
*
5361598 TTCAATGTACTCCACTGTAACCTC
66 TTCAATCTACTCCACTGTAACCTC
* * * ** *
5361622 AGGGAGGA-AAAATCTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATA-AGATCTA-TA
1 AGGGA-GATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-
* * **
5361684 ATCTTCAATCTATTCCACTGTTGCCT-
63 AGCTTCAATCTACTCCACTGTAACCTC
* * * ** * * **
5361710 AGGGAGATAGAATTACTG---GCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCT
1 AGGGAGATA-AAAT-CTGTAATCTTCAATCTACTCCACTGTTGCC-TAGGGAGATAGAATCTACT
* * ** *
5361772 ATCTTCGATCTGTTCCAC--T-ACTGCTT
63 AGCTTCAATCTACTCCACTGTAAC--CTC
* * * * * *
5361798 AGGGAGATAAGATCTGTAATCTTTAATCTATTTCACTGTTGCCTAGGGAGATAGAA-ATACTGGC
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAGC
*
5361862 TTCAATGTACTCCACTGTAACCTC
66 TTCAATCTACTCCACTGTAACCTC
* * ** * * * ** * * *
5361886 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCTCTACTGCTTATGGAGATA-AGATCT-GTAA
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-A
* * **
5361949 TCTTCAATCTATTCCACTGTTGCC-C
64 GCTTCAATCTACTCCACTGTAACCTC
* * ** * * * * *
5361974 AGGGAGATAAAATTACTG---GCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCC
1 AGGGAGATAAAA-T-CTGTAATCTTCAATCTACTCCACTGTTGCCT-AGGGAGATAGAATCTACT
* * * *
5362036 ATCTTCGATCTGCTCCAC--T-ACTTCTT
63 AGCTTCAATCTACTCCACTGTAAC--CTC
* * *
5362062 AGGGAGATAAGA-CTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAAT-TACTGGC
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAGC
* * *
5362125 TTCTATGTACTCCACTGTAACCTT
66 TTCAATCTACTCCACTGTAACCTC
* * ** * * * ** * * *
5362149 AGGGAGGTAAAATCCGCCACCTTCGATCTGCTCCACTACTGCTTATGGAGATA-AGATCT-GTAA
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGA-ATCTACT-A
* * **
5362212 TCTTCAATCTATTCCACTGTTGCC-C
64 GCTTCAATCTACTCCACTGTAACCTC
* * * ** * * **
5362237 AGGGAGATAGAATTACTG---GCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCT
1 AGGGAGATA-AAAT-CTGTAATCTTCAATCTACTCCACTGTTGCCT-AGGGAGATAGAATCTACT
* * * *
5362299 ATCTTCGATCTGCTCCAC--T-ACTGCTT
63 AGCTTCAATCTACTCCACTGTAAC--CTC
* * * * * * *
5362325 ATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAAT-TACTGGC
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAGC
* * *
5362389 TTCAATGTACTCCATTATAACCTC
66 TTCAATCTACTCCACTGTAACCTC
* * ** * *
5362413 AGGAAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACT
5362450 TCTGCTTATG
Statistics
Matches: 588, Mismatches: 186, Indels: 108
0.67 0.21 0.12
Matches are distributed among these distances:
85 6 0.01
86 24 0.04
87 110 0.19
88 323 0.55
89 114 0.19
90 11 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
AGGGAGATAAAATCTGTAATCTTCAATCTACTCCACTGTTGCCTAGGGAGATAGAATCTACTAGC
TTCAATCTACTCCACTGTAACCTC
Found at i:5362457 original size:527 final size:528
Alignment explanation
Indices: 5361462--5362618 Score: 1974
Period size: 527 Copynumber: 2.2 Consensus size: 528
5361452 GAGATAGGAT
* * *
5361462 TGGCTTCAATGTACTCTACTGTAACCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
5361527 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
* * *
5361592 ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCTGTCATCTTCGATCTGCTCCA
131 ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCCGCCACCTTCGATCTGCTCCA
*
5361657 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAA
196 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
* *
5361722 TTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCTATCTTCGATCTGTTC
261 TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
* * * * *
5361787 CACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTTCACTGTTGCCTAGGGAGATAG
326 CACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
* *
5361852 AAATACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGC
391 AAATACTGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGC
* *
5361917 TCCTCTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGAT
456 TCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGAT
5361982 AAAATTAC
521 AAAATTAC
*
5361990 TGGCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
*
5362055 ACTTCTTAGGGAGATAAGA-CTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
* * *
5362119 ACTGGCTTCTATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCCACCTTCGATCTGCTCCA
131 ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCCGCCACCTTCGATCTGCTCCA
* *
5362184 CTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
196 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
5362249 TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
261 TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
*
5362314 CACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
326 CACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
* * *
5362379 AATTACTGGCTTCAATGTACTCCATTATAACCTCAGGAAGGTAAAATCTGCCATCTTCGATCTGC
391 AAATACTGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGC
* *
5362444 TCCACTTCTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGATAT
456 TCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGAT
*
5362509 AGAATTAC
521 AAAATTAC
* * *
5362517 TGGCTTCAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACT
1 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
* *
5362582 ACTGCTTAAGGAGATAAGATCTGTAATCTTCGATCTA
66 ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
5362619 CTTCACGCCA
Statistics
Matches: 589, Mismatches: 39, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
527 494 0.84
528 95 0.16
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (528 bp):
TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT
ACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATT
ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGAAAAATCCGCCACCTTCGATCTGCTCCA
CTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAA
TTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAG
AAATACTGGCTTCAATGTACTCCACTATAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGC
TCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGAT
AAAATTAC
Found at i:5362755 original size:89 final size:87
Alignment explanation
Indices: 5362635--5362878 Score: 308
Period size: 89 Copynumber: 2.7 Consensus size: 87
5362625 GCCAATACAT
* * *
5362635 GAAGACAAGATCTACTATCTTTGATCCACTTCATGCCAATATATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATC-CTGATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTCTT
5362700 CAATCTACTCCACCACCAGTATGG
65 C-ATCTACTCCACCACCAGTATGG
* * * * *
5362724 GGAGACAAGATCTGTTGTCCCTGATCTACTTCATGCCAATATATAAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGCTAT-CCTGATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTC-T
* *
5362789 TCATCTACTTCGCCACCAGTATGG
64 TCATCTACTCCACCACCAGTATGG
* * * * *
5362813 GAAGATAAGATCTGCTATCTTCGATCTACTTTATGCCAATACATGAAGACAGGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCCT-GATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTCTT
5362878 C
65 C
5362879 CTAGCCTACT
Statistics
Matches: 132, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
88 5 0.04
89 123 0.93
90 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (87 bp):
GAAGACAAGATCTGCTATCCTGATCTACTTCATGCCAATATATGAAGACAAGATCTGCTTTCTTC
ATCTACTCCACCACCAGTATGG
Found at i:5362871 original size:44 final size:44
Alignment explanation
Indices: 5362597--5362878 Score: 219
Period size: 44 Copynumber: 6.4 Consensus size: 44
5362587 TTAAGGAGAT
*
5362597 AAGATCTG-TAATCTTCGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCTGCT-ATCTTCGATCTACTTCACGCCAATATATGAAGAC
* * * *
5362641 AAGATCTACTATCTTTGATCCACTTCATGCCAATATATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACGCCAATATATGAAGAC
* * * * * ** *
5362685 AAGATCTGCTTTCTTCAATCTACTCCACCACCAGTATGGGGAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA-CGCCAATATATGAAGAC
* * * * *
5362730 AAGATCTGTTGTC-CCTGATCTACTTCATGCCAATATATAAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCACGCCAATATATGAAGAC
* * * * * ** *
5362774 AAGATCTGTTTTCTTTC-ATCTACTTCGCCACCAGTATGGGAAGAT
1 AAGATCTGCTATC-TTCGATCTACTTC-ACGCCAATATATGAAGAC
* * *
5362819 AAGATCTGCTATCTTCGATCTACTTTATGCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACGCCAATATATGAAGAC
* *
5362863 AGGATCTGCTTTCTTC
1 AAGATCTGCTATCTTC
5362879 CTAGCCTACT
Statistics
Matches: 179, Mismatches: 52, Indels: 14
0.73 0.21 0.06
Matches are distributed among these distances:
44 117 0.65
45 61 0.34
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (44 bp):
AAGATCTGCTATCTTCGATCTACTTCACGCCAATATATGAAGAC
Found at i:5364081 original size:14 final size:13
Alignment explanation
Indices: 5364057--5364087 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
5364047 CCATTTTACG
5364057 TTTTCATTTTTCA
1 TTTTCATTTTTCA
5364070 TTTTCATCTTTTCA
1 TTTTCAT-TTTTCA
5364084 TTTT
1 TTTT
5364088 TTCATCTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:5364091 original size:16 final size:16
Alignment explanation
Indices: 5364057--5364104 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
5364047 CCATTTTACG
5364057 TTTTCAT-TTTTCA--
1 TTTTCATCTTTTCATT
5364070 TTTTCATCTTTTCATT
1 TTTTCATCTTTTCATT
**
5364086 TTTTCATCTCGTCATT
1 TTTTCATCTTTTCATT
5364102 TTT
1 TTT
5364105 CCGACTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
16 17 0.57
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTCATCTTTTCATT
Found at i:5365023 original size:18 final size:18
Alignment explanation
Indices: 5364997--5365036 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5364987 TGGTTTGGCA
*
5364997 GAAAGAATCCAAAAGAAT
1 GAAACAATCCAAAAGAAT
**
5365015 GAAACAATCGTAAAGAAT
1 GAAACAATCCAAAAGAAT
5365033 GAAA
1 GAAA
5365037 GAACATTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.12
Consensus pattern (18 bp):
GAAACAATCCAAAAGAAT
Found at i:5366636 original size:18 final size:18
Alignment explanation
Indices: 5366615--5366656 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5366605 TATACATTAC
5366615 ATATATTTTATCTA-ATAT
1 ATATATTTTAT-TATATAT
*
5366633 ATATAATTTATTATATAT
1 ATATATTTTATTATATAT
5366651 ATATAT
1 ATATAT
5366657 GCATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTTTATTATATAT
Found at i:5366834 original size:24 final size:27
Alignment explanation
Indices: 5366807--5366858 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5366797 TTTCTTTTTT
5366807 TATGTTCA-T-TTATGTATTT-GTTTA
1 TATGTTCATTCTTATGTATTTAGTTTA
*
5366831 TATGTTCATTCTTATGTTTTTAGTTTA
1 TATGTTCATTCTTATGTATTTAGTTTA
5366858 T
1 T
5366859 TTATTTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 1 0.04
26 9 0.38
27 6 0.25
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.63
Consensus pattern (27 bp):
TATGTTCATTCTTATGTATTTAGTTTA
Found at i:5367152 original size:109 final size:108
Alignment explanation
Indices: 5366981--5367286 Score: 444
Period size: 109 Copynumber: 2.8 Consensus size: 108
5366971 TCAAAAAAGG
*
5366981 AAAATATTTCAAAATAAGGTAATGTTTT---TTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAAT-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
5367043 GGTTTCGATTTCTCGTTCGACCAAATAACTTAA-TATCCTTTTCA
65 GGTTTCGATTTCTCGTTCAACCAAATAAC-TAAGTATCCTTTTCA
* *
5367087 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTG
* *
5367152 GGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTCA
65 GGTTTCGA--TTTCTCGTTCAACCAAATAACTAAGTATCCTTTTCA
* *
5367198 AAAA-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTGG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
5367262 GTTTCGATTTCTCG-TCTAACCAAAT
66 GTTTCGATTTCTCGTTC-AACCAAAT
5367287 TGACAAATAT
Statistics
Matches: 181, Mismatches: 11, Indels: 15
0.87 0.05 0.07
Matches are distributed among these distances:
105 21 0.12
106 7 0.04
107 15 0.08
108 14 0.08
109 48 0.27
110 42 0.23
111 34 0.19
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (108 bp):
AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCAACCAAATAACTAAGTATCCTTTTCA
Found at i:5369320 original size:19 final size:20
Alignment explanation
Indices: 5369296--5369334 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5369286 AACTGTGTTT
* *
5369296 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
5369315 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
5369335 GTGTGAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:5372529 original size:14 final size:15
Alignment explanation
Indices: 5372493--5372531 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5372483 CCAAAAAAGT
5372493 AAGTCATTTTCCAGA
1 AAGTCATTTTCCAGA
*
5372508 AA-TTATTTTCC-GA
1 AAGTCATTTTCCAGA
5372521 AAGTCATTTTC
1 AAGTCATTTTC
5372532 AGTGAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 4 0.19
14 15 0.71
15 2 0.10
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (15 bp):
AAGTCATTTTCCAGA
Found at i:5372943 original size:14 final size:14
Alignment explanation
Indices: 5372924--5372971 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
5372914 AGGATGTTTC
*
5372924 TTTTGATTTGTATG
1 TTTTGATTTGAATG
5372938 TTTTGATTTGAATG
1 TTTTGATTTGAATG
*
5372952 TTTTTGTTTTGAAGTG
1 -TTTTGATTTGAA-TG
5372968 TTTT
1 TTTT
5372972 TTAATTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 13 0.43
15 15 0.50
16 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (14 bp):
TTTTGATTTGAATG
Found at i:5372971 original size:16 final size:15
Alignment explanation
Indices: 5372924--5372972 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
5372914 AGGATGTTTC
*
5372924 TTTTGATTTGTATG-
1 TTTTGATTTGAATGT
5372938 TTTTGATTTGAATGT
1 TTTTGATTTGAATGT
*
5372953 TTTTGTTTTGAAGTGT
1 TTTTGATTTGAA-TGT
5372969 TTTT
1 TTTT
5372973 TAATTGTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 13 0.42
15 11 0.35
16 7 0.23
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.65
Consensus pattern (15 bp):
TTTTGATTTGAATGT
Found at i:5373731 original size:29 final size:31
Alignment explanation
Indices: 5373682--5373741 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
5373672 GGCTACACAC
*
5373682 GAACTTTGATTCTATGTGCAATGTTATACAT
1 GAACTTTAATTCTATGTGCAATGTTATACAT
*
5373713 GAACTTTAATT-T-TGTGCAATTTTATACAT
1 GAACTTTAATTCTATGTGCAATGTTATACAT
5373742 TAAATGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 1 0.04
31 10 0.37
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (31 bp):
GAACTTTAATTCTATGTGCAATGTTATACAT
Found at i:5377661 original size:14 final size:14
Alignment explanation
Indices: 5377644--5377673 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5377634 AAATTTTTTA
5377644 TTTCTTATTTCTTT
1 TTTCTTATTTCTTT
*
5377658 TTTCTTTTTTCTTT
1 TTTCTTATTTCTTT
5377672 TT
1 TT
5377674 CTTCTTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTTATTTCTTT
Found at i:5377827 original size:28 final size:28
Alignment explanation
Indices: 5377795--5377854 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
5377785 TTCTATTCTC
*
5377795 TCTTTCTTTTCTCT-TCTCTCTTCTTTTT
1 TCTTTCTTTTCTCTCT-TCTCTTCTCTTT
*
5377823 TCTTTTTTTTCTCTCTTCTCTTCTCTTT
1 TCTTTCTTTTCTCTCTTCTCTTCTCTTT
5377851 TCTT
1 TCTT
5377855 GTTTCTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (28 bp):
TCTTTCTTTTCTCTCTTCTCTTCTCTTT
Found at i:5378289 original size:29 final size:28
Alignment explanation
Indices: 5378238--5378355 Score: 119
Period size: 28 Copynumber: 4.1 Consensus size: 28
5378228 TAGAGGACGC
** *
5378238 AAAAATTCTAAGGTTGAATTGTAATTTTA
1 AAAAATT-TAAGGTCAAAATGTAATTTTA
*
5378267 GGAAAATTTAAGGTCAAAATGTAATTTTA
1 -AAAAATTTAAGGTCAAAATGTAATTTTA
** *
5378296 AAAAATTGGAGGTCAAAATATAATTTTA
1 AAAAATTTAAGGTCAAAATGTAATTTTA
* *
5378324 AAAAAATTAGGGGTCAAAATGTAAATTTTA
1 AAAAATTTA-AGGTCAAAATGT-AATTTTA
5378354 AA
1 AA
5378356 TTTTATATAT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
28 30 0.41
29 28 0.38
30 15 0.21
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.34
Consensus pattern (28 bp):
AAAAATTTAAGGTCAAAATGTAATTTTA
Found at i:5378309 original size:28 final size:28
Alignment explanation
Indices: 5378257--5378355 Score: 119
Period size: 29 Copynumber: 3.4 Consensus size: 28
5378247 AAGGTTGAAT
* **
5378257 TGTAATTTTAGGAAAATTTAAGGTCAAAA
1 TGTAATTTTA-AAAAATTGGAGGTCAAAA
5378286 TGTAATTTTAAAAAATTGGAGGTCAAAA
1 TGTAATTTTAAAAAATTGGAGGTCAAAA
*
5378314 TATAATTTTAAAAAAATTAGG-GGTCAAAA
1 TGTAATTTT-AAAAAATT-GGAGGTCAAAA
5378343 TGTAAATTTTAAA
1 TGT-AATTTTAAA
5378356 TTTTATATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 23 0.37
29 31 0.50
30 8 0.13
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.34
Consensus pattern (28 bp):
TGTAATTTTAAAAAATTGGAGGTCAAAA
Found at i:5378393 original size:14 final size:15
Alignment explanation
Indices: 5378358--5378398 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
5378348 ATTTTAAATT
*
5378358 TTATATATTTTTCTGA
1 TTAT-TATTATTCTGA
5378374 TTATTATTATTCTG-
1 TTATTATTATTCTGA
5378388 TTATTATTATT
1 TTATTATTATT
5378399 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 9 0.38
16 4 0.17
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (15 bp):
TTATTATTATTCTGA
Found at i:5389697 original size:34 final size:35
Alignment explanation
Indices: 5389642--5389708 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5389632 CAAACACCAG
*
5389642 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
5389677 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5389709 TATTTTATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5391435 original size:15 final size:17
Alignment explanation
Indices: 5391415--5391458 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
5391405 AGGGCCCGAG
5391415 GTGGCCCAAACCT-A-T
1 GTGGCCCAAACCTAACT
5391430 GTGGCCCAAACCTAACT
1 GTGGCCCAAACCTAACT
*
5391447 GAGGCCCAAACC
1 GTGGCCCAAACC
5391459 AAACAGAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 13 0.50
16 1 0.04
17 12 0.46
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (17 bp):
GTGGCCCAAACCTAACT
Found at i:5391454 original size:17 final size:17
Alignment explanation
Indices: 5391417--5391473 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
5391407 GGCCCGAGGT
*
5391417 GGCCCAAACCT-A-TGT
1 GGCCCAAACCTAACTGA
5391432 GGCCCAAACCTAACTGA
1 GGCCCAAACCTAACTGA
* *
5391449 GGCCCAAACCAAACAGA
1 GGCCCAAACCTAACTGA
*
5391466 AGCCCAAA
1 GGCCCAAA
5391474 GCAGATTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
15 11 0.31
16 1 0.03
17 24 0.67
ACGTcount: A:0.39, C:0.35, G:0.18, T:0.09
Consensus pattern (17 bp):
GGCCCAAACCTAACTGA
Found at i:5395854 original size:114 final size:114
Alignment explanation
Indices: 5395654--5395883 Score: 424
Period size: 114 Copynumber: 2.0 Consensus size: 114
5395644 ATCGGTTTAA
*
5395654 AGAAGCTGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
1 AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
5395719 ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
66 ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
5395768 AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
1 AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
* * *
5395833 ATAAATGGAGTGAAAAAGTATAAACAAAACAAATCTTCCTTAAAGAATC
66 ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
5395882 AG
1 AG
5395884 TCACAAGATG
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (114 bp):
AGAAGCAGCTCTATGGGGTTGAATTGACCTCCCAGGAAAGTCACCCATGCCCTAGGGGAATTGTA
ATAAAAGAAGTGAAAAAGTATAAACAAAACAAATCTTCCCTAAAGAATC
Found at i:5407338 original size:516 final size:506
Alignment explanation
Indices: 5406294--5407363 Score: 1551
Period size: 516 Copynumber: 2.1 Consensus size: 506
5406284 AACGGATTCC
* *
5406294 ATAGCTACAAAATCTAGAATCTAATTGTGCCAACGGAAAGATAGAAAGCCATTGAATCGAAAAAC
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGCCATTGAATCGAAAAAC
* **
5406359 CCAGATATCTTCATTCACTTACGTTTCATGAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGA
66 CCAGAAATCTTCATTCACTTACGTTTCAACAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGA
* * *
5406424 CATTAACTGGAGAAAATTCCTTAAATAATAACCATACTTGTAGTCAACACCCTAATAAACAAGGG
131 CACTAACTGGAGAAAATTCCTTAAATAATAACCATACTTGTAATCAACACCCTAATAAACAAGAG
5406489 AACAAGAAATAACATTTCTACTTACGTATAATTATAACATTCAAAAGCTTTAGAAAATGAGATGG
196 AACAAGAAATAACATTTCTACTTAC--ATAA-TATAACATTCAAAAGCTTTAGAAAATGAGATGG
*
5406554 TTGCCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCATTTGACATTA
258 TTGCCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTCCAGAATCATTTGACATTA
* *
5406619 AATACAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACAGAACCTAATTATTATATAT
323 AATACAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACACAACCTAATTATTATACAT
* * *
5406684 CATAACAAACCAACCAAATTTTCCAAAAGAAGTTATCAACTACACGTGGCAAGTTTGCAAGTTAG
388 CATAACAAACCAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGTTTGCAAGTTAG
* *
5406749 AATCAGGCATGAGCTAACTAAACTGGTACAATGAAACGGATTCCATTTTTGTTA
453 AATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
* *
5406803 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCATTGAATCGTAAAAC
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGCCATTGAATCGAAAAAC
* *
5406868 CCAGAAATCTTCATTCACTTAGGTTT-AACAGTAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
66 CCAGAAATCTTCATTCACTTACGTTTCAACAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGA
**
5406932 CACTGGCTGGAGAAAATTCCTTAAATAATGATCATGTATGGCACATGTTACTTGTAATCAACACC
131 CACTAACTGGAGAAAATTCCTTAAAT-A--AT-A---A---C-CA---TACTTGTAATCAACACC
* *
5406997 CTAATAAACAAGAGAACAAGAAATATCATTTCTACTTA-A-GA-ATAACATTCAAAAGCTTTAGA
182 CTAATAAACAAGAGAACAAGAAATAACATTTCTACTTACATAATATAACATTCAAAAGCTTTAGA
* ** *
5407059 AAATGAGATGGTTGCCCGATGCTAGATTGCATCAGAACTTTCAACGCAGTTCCACTTCCAGAATC
247 AAATGAGATGGTTGCCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTCCAGAATC
* * * *
5407124 TTTTGACATTAAATACAGTGGTTGATTGTTAATGCAATGATTCGCAATAAACCAACACAATCTAA
312 ATTTGACATTAAATACAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACACAACCTAA
** * *
5407189 TTATTATACATCATAATGAACTAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAGGT
377 TTATTATACATCATAACAAACCAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGT
* * *
5407254 TTGCCAAGTTAGAAT-ATGGCAAGAGCTAACTAAACTGGTTCAAAGAAATGGCTTCCATTTTTGT
442 TTG-CAAGTTAGAATCA-GGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGT
5407318 TA
505 TA
*
5407320 ATAGCTACAAAA-CTAGAATCTAATTGCAG-CAATGGAAAGATAAA
1 ATAGCTACAAAATCTAGAATCTAATTG-TGCCAATGGAAAGATAAA
5407364 CAAAGAAAAG
Statistics
Matches: 504, Mismatches: 40, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
508 58 0.12
509 86 0.17
511 2 0.00
512 1 0.00
515 1 0.00
516 231 0.46
517 68 0.13
518 2 0.00
519 3 0.01
522 52 0.10
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (506 bp):
ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGCCATTGAATCGAAAAAC
CCAGAAATCTTCATTCACTTACGTTTCAACAGTAGCCAAAGGGCACTTCTTACAACTTTTCGTGA
CACTAACTGGAGAAAATTCCTTAAATAATAACCATACTTGTAATCAACACCCTAATAAACAAGAG
AACAAGAAATAACATTTCTACTTACATAATATAACATTCAAAAGCTTTAGAAAATGAGATGGTTG
CCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTCCAGAATCATTTGACATTAAAT
ACAATGGTTGATTGTTAATGCAATGATTCACAATAAACCAACACAACCTAATTATTATACATCAT
AACAAACCAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGTTTGCAAGTTAGAAT
CAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
Found at i:5407415 original size:38 final size:38
Alignment explanation
Indices: 5407364--5407440 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
5407354 GAAAGATAAA
5407364 CAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAAT
1 CAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAAT
5407402 CAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAAT
1 CAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAAT
5407440 C
1 C
5407441 TAGAATCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (38 bp):
CAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAAT
Found at i:5407485 original size:108 final size:108
Alignment explanation
Indices: 5407293--5407510 Score: 341
Period size: 108 Copynumber: 2.0 Consensus size: 108
5407283 CTAAACTGGT
* *
5407293 TCAAAGAAATGGCTTCCATTTTTGTTAATAGCTACAAAACTAGAATCTAATTGCAGCAATGGAAA
1 TCAAAGAAAAGGATTCCATTTTTGTTAATAGCTACAAAACTAGAATCTAATTGCAGCAATGGAAA
*
5407358 GATAAACAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAA
66 GATAAACAAAGAAAAGGATTCCATTTTGTTCATAGCTACAAAA
* *
5407401 TCAAAGAAAAGGATTCCA-TTTTGTTGATAGCTACAAAATCTAGAATCTAATTG-TGTCAATGGA
1 TCAAAGAAAAGGATTCCATTTTTGTTAATAGCTACAAAA-CTAGAATCTAATTGCAG-CAATGGA
* *
5407464 AAGATGAACAAAGAAACGGATTCCATTTTGTTCATAGCTACAAAA
64 AAGATAAACAAAGAAAAGGATTCCATTTTGTTCATAGCTACAAAA
5407509 TC
1 TC
5407511 TAGAATCTAA
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
107 20 0.20
108 81 0.80
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (108 bp):
TCAAAGAAAAGGATTCCATTTTTGTTAATAGCTACAAAACTAGAATCTAATTGCAGCAATGGAAA
GATAAACAAAGAAAAGGATTCCATTTTGTTCATAGCTACAAAA
Found at i:5407486 original size:70 final size:70
Alignment explanation
Indices: 5407402--5407538 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
5407392 GCTACAAAAT
* *
5407402 CAAAGAAAAGGATTCCATTTTGTTGATAGCTACAAAATCTAGAATCTAATTGTGTCAATGGAAAG
1 CAAAGAAAAGGATTCCATTTTGTTCATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
5407467 ATGAA
66 ATGAA
*
5407472 CAAAGAAACGGATTCCATTTTGTTCATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
1 CAAAGAAAAGGATTCCATTTTGTTCATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
5407537 AT
66 AT
5407539 AAGAAGTCAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (70 bp):
CAAAGAAAAGGATTCCATTTTGTTCATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAG
ATGAA
Found at i:5410143 original size:21 final size:21
Alignment explanation
Indices: 5410117--5410164 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
5410107 GTTTCTAATT
*
5410117 TCACCGCTACAGTATCCAATC
1 TCACCGCTACAGTAACCAATC
*
5410138 TCACCGCTACAGTAACTAATC
1 TCACCGCTACAGTAACCAATC
5410159 TCACCG
1 TCACCG
5410165 GAGGTAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.23
Consensus pattern (21 bp):
TCACCGCTACAGTAACCAATC
Found at i:5416536 original size:32 final size:31
Alignment explanation
Indices: 5416476--5416536 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
5416466 TCATGCTTGT
* *
5416476 AATATAATTTTTACAGGTTAAACTTGTATAA
1 AATATAATTTTTACAAGTTAAACATGTATAA
5416507 AATATAACTTTTTA-AAGTTAAAACATGTAT
1 AATATAA-TTTTTACAAGTT-AAACATGTAT
5416537 GAGTGTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (31 bp):
AATATAATTTTTACAAGTTAAACATGTATAA
Found at i:5419877 original size:2 final size:2
Alignment explanation
Indices: 5419870--5419896 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5419860 TACAATCCTC
5419870 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
5419897 AGTAAGTTAC
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:5423380 original size:3 final size:3
Alignment explanation
Indices: 5423372--5423417 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
5423362 TCTTCTGCAA
* * * *
5423372 CAT CAT CAT CAT CAT CAT CAT CTT CAT AAT CAC CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5423418 TTCTGTACTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:5429757 original size:43 final size:43
Alignment explanation
Indices: 5429709--5429861 Score: 209
Period size: 43 Copynumber: 3.6 Consensus size: 43
5429699 GGTTTTGTGC
*
5429709 AAGACCATGTCTGGGACATTGGCATCGATATAAGATTACGTGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACGTGT
*
5429752 AAGACCATGTCCGGGACATTGGCATCGATATGAGATTACGTGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACGTGT
* * * * * *
5429795 AAGACCCTGTCTAGGACAGTGGCATCGATATGTGATAACATGT
1 AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACGTGT
* *
5429838 AAGACCATATCTGGGATA-TGGCAT
1 AAGACCATGTCTGGGACATTGGCAT
5429862 TGTATGTGAT
Statistics
Matches: 97, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 6 0.06
43 91 0.94
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
AAGACCATGTCTGGGACATTGGCATCGATATGAGATTACGTGT
Found at i:5432002 original size:25 final size:25
Alignment explanation
Indices: 5431968--5432016 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
5431958 TCCCATAACT
5431968 CATCATGTATCATGCAAACACAACC
1 CATCATGTATCATGCAAACACAACC
5431993 CATCATGTATCATGCAAACACAAC
1 CATCATGTATCATGCAAACACAAC
5432017 TCACATCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.20
Consensus pattern (25 bp):
CATCATGTATCATGCAAACACAACC
Found at i:5434027 original size:23 final size:23
Alignment explanation
Indices: 5434001--5434053 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
5433991 TACTAAATAA
* *
5434001 ATTAATAACAAT-AAAATAATAT
1 ATTAATAAAAATCAAAATAAAAT
*
5434023 CATTAA-AAAAATCAAATTAAAAT
1 -ATTAATAAAAATCAAAATAAAAT
5434046 ATTAATAA
1 ATTAATAA
5434054 GCTAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAATAAAAATCAAAATAAAAT
Found at i:5435219 original size:13 final size:13
Alignment explanation
Indices: 5435201--5435227 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5435191 CTTTCTTCTC
5435201 TAAAATGATGATA
1 TAAAATGATGATA
5435214 TAAAATGATGATA
1 TAAAATGATGATA
5435227 T
1 T
5435228 TTTCTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (13 bp):
TAAAATGATGATA
Found at i:5436675 original size:47 final size:47
Alignment explanation
Indices: 5436617--5436706 Score: 180
Period size: 47 Copynumber: 1.9 Consensus size: 47
5436607 TTTATTTTAA
5436617 TGTGGTACATATTTTATGTGTTATTAATTAGTTCAAACCGTATTTTT
1 TGTGGTACATATTTTATGTGTTATTAATTAGTTCAAACCGTATTTTT
5436664 TGTGGTACATATTTTATGTGTTATTAATTAGTTCAAACCGTAT
1 TGTGGTACATATTTTATGTGTTATTAATTAGTTCAAACCGTAT
5436707 CTTTGTTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.49
Consensus pattern (47 bp):
TGTGGTACATATTTTATGTGTTATTAATTAGTTCAAACCGTATTTTT
Found at i:5442799 original size:26 final size:27
Alignment explanation
Indices: 5442742--5442817 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
5442732 GAAGCTCCGG
* * *
5442742 AGAGCTTTTAATCAGAAAGCTCA-CAA
1 AGAGCCTTTAATCGGGAAGCTCATCAA
*
5442768 AGAGCCTTTAATCGGGAAGCTCATGAA
1 AGAGCCTTTAATCGGGAAGCTCATCAA
* *
5442795 A-AGCC-ATATATCGGGACGCTCAT
1 AGAGCCTTTA-ATCGGGAAGCTCAT
5442818 AAGAGTTGCG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 37 0.88
27 3 0.07
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (27 bp):
AGAGCCTTTAATCGGGAAGCTCATCAA
Found at i:5444352 original size:34 final size:35
Alignment explanation
Indices: 5444308--5444374 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5444298 CAGTAAAATA
*
5444308 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
5444342 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
5444375 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:5445122 original size:11 final size:11
Alignment explanation
Indices: 5445106--5445130 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5445096 GAATTTACGG
5445106 TAGAAATTGAA
1 TAGAAATTGAA
5445117 TAGAAATTGAA
1 TAGAAATTGAA
5445128 TAG
1 TAG
5445131 GAAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (11 bp):
TAGAAATTGAA
Done.