Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold415
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: 1242643
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 6 of 8
Found at i:864065 original size:18 final size:17
Alignment explanation
Indices: 864034--864084 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
864024 TGAAACTAGT
864034 TAAAAATA-AAATTAAA
1 TAAAAATATAAATTAAA
864050 TAAAAATATTAAATTAAA
1 TAAAAATA-TAAATTAAA
864068 TAAAAAT-TAAAATTAAA
1 TAAAAATAT-AAATTAAA
864085 ACTATTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.28
17 8 0.25
18 15 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAATATAAATTAAA
Found at i:864182 original size:15 final size:15
Alignment explanation
Indices: 864157--864192 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
864147 TAAAATTTGT
864157 AAAATTTTAT-AAGA
1 AAAATTTTATAAAGA
864171 AAAATCTTTATAAAGA
1 AAAAT-TTTATAAAGA
864187 AAAATT
1 AAAATT
864193 AACATATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 9 0.45
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAATTTTATAAAGA
Found at i:865214 original size:13 final size:13
Alignment explanation
Indices: 865196--865221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
865186 ACATTTTGGG
865196 ATGTATCGATACA
1 ATGTATCGATACA
865209 ATGTATCGATACA
1 ATGTATCGATACA
865222 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:865238 original size:32 final size:33
Alignment explanation
Indices: 865174--865241 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
865164 CGTTACAAGC
* *
865174 CAATGTATTGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGGATGTATCGATA
*
865207 CAATGTATCGATACATATTGTG-TGTATCGATA
1 CAATGTATCGATACATATTGGGATGTATCGATA
865239 CAA
1 CAA
865242 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATATTGGGATGTATCGATA
Found at i:865340 original size:13 final size:13
Alignment explanation
Indices: 865322--865346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
865312 ACATTTGGTC
865322 ATGTATCGATACA
1 ATGTATCGATACA
865335 ATGTATCGATAC
1 ATGTATCGATAC
865347 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:866710 original size:17 final size:17
Alignment explanation
Indices: 866688--866723 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
866678 AGTAAAAAAA
866688 TAGTATATACAATATAT
1 TAGTATATACAATATAT
866705 TAGTATATACAATATAT
1 TAGTATATACAATATAT
866722 TA
1 TA
866724 TCTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTATATACAATATAT
Found at i:868965 original size:25 final size:25
Alignment explanation
Indices: 868937--868985 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
868927 GATGGCCTTG
868937 TGCAATTTGCGAACATGCATAGGTT
1 TGCAATTTGCGAACATGCATAGGTT
* *
868962 TGCAATTTGTGAGCATGCATAGGT
1 TGCAATTTGCGAACATGCATAGGT
868986 ATATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (25 bp):
TGCAATTTGCGAACATGCATAGGTT
Found at i:876837 original size:18 final size:18
Alignment explanation
Indices: 876750--876843 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 18
876740 AGCCACCCTA
*
876750 TCTTCTTTCTTTTTTT-TT
1 TCTTC-TTCTTTTTTTCTC
876768 TCTTC-TCATTTTCCTTT-TC
1 TCTTCTTC-TTTT--TTTCTC
** *
876787 -CTTCTTCTTTCCTTCTT
1 TCTTCTTCTTTTTTTCTC
*
876804 TCTT-TTTTCTTTTTTCTC
1 TCTTCTTCT-TTTTTTCTC
876822 TCTTCTTCTTTTTTTCTC
1 TCTTCTTCTTTTTTTCTC
876840 TCTT
1 TCTT
876844 TCTTTTCTGG
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.07
17 8 0.14
18 38 0.64
19 9 0.15
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (18 bp):
TCTTCTTCTTTTTTTCTC
Found at i:876839 original size:16 final size:17
Alignment explanation
Indices: 876809--876849 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
876799 TTCTTTCTTT
876809 TTTCTTTTTTCTCTCT-
1 TTTCTTTTTTCTCTCTC
876825 TCTTCTTTTTT-TCTCTC
1 T-TTCTTTTTTCTCTCTC
876842 TTTCTTTT
1 TTTCTTTT
876850 CTGGTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTTTTCTCTCTC
Found at i:877014 original size:20 final size:20
Alignment explanation
Indices: 876991--877028 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
876981 AAATCTAAGG
*
876991 TTAGTTTTTTTTACATCTTT
1 TTAGATTTTTTTACATCTTT
*
877011 TTAGATTTTTTTAGATCT
1 TTAGATTTTTTTACATCT
877029 AAAAGAGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.66
Consensus pattern (20 bp):
TTAGATTTTTTTACATCTTT
Found at i:883518 original size:78 final size:78
Alignment explanation
Indices: 883382--884178 Score: 886
Period size: 78 Copynumber: 10.2 Consensus size: 78
883372 TGATTCAAAG
* * *
883382 GTTGCTGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAG
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
883447 TGATCACCTTGAT
66 TGATCACCTTGAT
* * * * * * * *
883460 GTTGCTGAGAAAACCTTACTCCACTCGTTGGAGATTGCACAGAGTTGGAGTGATCAGCCAGAAAC
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
* **
883525 AGAAAACCTTGAT
66 TGATCACCTTGAT
** * * *
883538 GTT-CTTGAGAAAGCCTCACTCCACCAATTTCAGATTGCAGAGAGTTTGATTTACCAGCCTGAAA
1 GTTGC-TGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAA
*
883602 CTGATCACCATGAT
65 CTGATCACCTTGAT
* * * * * * *
883616 GTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTGGGGGTT-ATCAGCCAGAAA
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGT-TGGATTGACCAGCCTGAAA
*
883680 CAGA-CTACCTTGAT
65 CTGATC-ACCTTGAT
* * *
883694 GTTGTTGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
883759 TGATCACCTTGAT
66 TGATCACCTTGAT
* * * * * *
883772 GTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGATCAGCCAGAAAC
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
*
883837 AGAGT-ACCTTGAT
66 TGA-TCACCTTGAT
* * * * *
883850 GTTGTTGTGAAAGCCTCACTCCACCCATTGCAGATAGCAGAGAGTTGGATTGACTAGCCTGAAAC
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
883915 TGATCACCTTGAT
66 TGATCACCTTGAT
* * * * * * *
883928 GTTGCTGAGAAAGCCTTACTCCACCAGTTGGAGATTGCACAGAGTTGGAGTGATCAGCCAGAAAC
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
*
883993 AGA-CTACCTTGAT
66 TGATC-ACCTTGAT
* * *
884006 GTTGCTGAGAGAGCCTCACTTCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGTCTGAAAC
1 GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
884071 TGATCACCTTGAT
66 TGATCACCTTGAT
* * * * * *
884084 GTTGCCGAGAAAGCCTCGGCACTCCACCCACTAG-AGATTGCAGAGAGTTGGATTGATCAACCAG
1 GTTGCTGAGAAAGCCT---CACTCCACCC-GTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTG
** * *
884148 ACTCTGACCAACTTGAT
62 AAACTGATCACCTTGAT
*
884165 GTTGATGAGAAAGC
1 GTTGCTGAGAAAGC
884179 TTGGGTACTC
Statistics
Matches: 589, Mismatches: 116, Indels: 25
0.81 0.16 0.03
Matches are distributed among these distances:
77 8 0.01
78 512 0.87
79 7 0.01
81 60 0.10
82 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (78 bp):
GTTGCTGAGAAAGCCTCACTCCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAC
TGATCACCTTGAT
Found at i:883672 original size:156 final size:156
Alignment explanation
Indices: 883387--884148 Score: 1184
Period size: 156 Copynumber: 4.9 Consensus size: 156
883377 CAAAGGTTGC
*
883387 TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAAGTGATC
1 TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAACTGATC
* *
883452 ACCTTGATGTTGCTGAGAAAACCTTACTCCACTCGTTGGAGATTGCACAGAGTTGGAGTGATCAG
66 ACCTTGATGTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGATCAG
**
883517 CCAGAAACAGAAAACCTTGATGTTCT
131 CCAGAAACAGACTACCTTGATGTTCT
* * * * *
883543 TGAGAAAGCCTCACTCCACCAATTTCAGATTGCAGAGAGTTTGATTTACCAGCCTGAAACTGATC
1 TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAACTGATC
* * * *
883608 ACCATGATGTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTGGGGGTTATCAG
66 ACCTTGATGTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGATCAG
*
883673 CCAGAAACAGACTACCTTGATGTTGT
131 CCAGAAACAGACTACCTTGATGTTCT
883699 TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAACTGATC
1 TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAACTGATC
883764 ACCTTGATGTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGATCAG
66 ACCTTGATGTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGATCAG
* *
883829 CCAGAAACAGAGTACCTTGATGTTGT
131 CCAGAAACAGACTACCTTGATGTTCT
* * * *
883855 TGTGAAAGCCTCACTCCACCCATTGCAGATAGCAGAGAGTTGGATTGACTAGCCTGAAACTGATC
1 TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAACTGATC
*
883920 ACCTTGATGTTGCTGAGAAAGCCTTACTCCACCAGTTGGAGATTGCACAGAGTTGGAGTGATCAG
66 ACCTTGATGTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGATCAG
883985 CCAGAAACAGACTACCTTGATGTTGC-
131 CCAGAAACAGACTACCTTGATGTT-CT
* * *
884011 TGAGAGAGCCTCACTTCACCCGTTGCAGATTGCAGAGAGTTGGATTGACCAGTCTGAAACTGATC
1 TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAACTGATC
* * ** * * *
884076 ACCTTGATGTTGCCGAGAAAGCCTCGGCACTCCACCCACTAGAGATTGCAGAGAGTTGGATTGAT
66 ACCTTGATGTTGCTGAGAAAGCCT---TACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGAT
*
884141 CAACCAGA
128 CAGCCAGA
884149 CTCTGACCAA
Statistics
Matches: 554, Mismatches: 48, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
156 516 0.93
159 38 0.07
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (156 bp):
TGAGAAAGCCTCACTTCACCCATTGCAGATTGCAGAGAGTTGGATTGACCAGCCTGAAACTGATC
ACCTTGATGTTGCTGAGAAAGCCTTACTCCACCCGTTGGAGATTGCACAGAGTTGGAGTGATCAG
CCAGAAACAGACTACCTTGATGTTCT
Found at i:885736 original size:10 final size:10
Alignment explanation
Indices: 885713--885748 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
885703 GATAAAATTT
885713 TTATAAAAAA
1 TTATAAAAAA
885723 -TATAAAAAA
1 TTATAAAAAA
885732 TTATAAAAAA
1 TTATAAAAAA
885742 TTTATAA
1 -TTATAA
885749 CTGAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 9 0.38
11 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:885771 original size:24 final size:23
Alignment explanation
Indices: 885730--885786 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
885720 AAATATAAAA
*
885730 AATTATAAAAAATTTATA-ACTG
1 AATTTTAAAAAATTTATATACTG
*
885752 AATTTTAAAAAATATATATATACTT
1 AATTTTAAAAAAT-T-TATATACTG
*
885777 ATTTTTAAAA
1 AATTTTAAAA
885787 TTTTTATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.41
23 1 0.03
24 4 0.14
25 12 0.41
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
AATTTTAAAAAATTTATATACTG
Found at i:885994 original size:22 final size:22
Alignment explanation
Indices: 885969--886019 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
885959 GTAATAAGAA
885969 TTTAATTAATT-TTAAAATTAT-T
1 TTTAATT-ATTATT-AAATTATAT
885991 TTTAATTATTATTAAATTATAT
1 TTTAATTATTATTAAATTATAT
*
886013 TCTAATT
1 TTTAATT
886020 CAAGTACATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAATTATTATTAAATTATAT
Found at i:886300 original size:17 final size:17
Alignment explanation
Indices: 886275--886320 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
886265 AATATTAAAA
*
886275 AATATATTTTTTATTTT
1 AATAAATTTTTTATTTT
886292 AATAAATTTTTTTATTTT
1 AATAAA-TTTTTTATTTT
886310 --TAAATTTTTTA
1 AATAAATTTTTTA
886321 AAATAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 7 0.26
16 4 0.15
17 5 0.19
18 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATAAATTTTTTATTTT
Found at i:886313 original size:16 final size:17
Alignment explanation
Indices: 886281--886319 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
886271 AAAAAATATA
886281 TTTTTTATTTTAATAAAT
1 TTTTTTATTTT-ATAAAT
886299 TTTTTTATTTT-TAAAT
1 TTTTTTATTTTATAAAT
886315 TTTTT
1 TTTTT
886320 AAAATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.48
18 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTATTTTATAAAT
Found at i:887040 original size:16 final size:16
Alignment explanation
Indices: 887019--887049 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
887009 TTTCATTAGA
*
887019 TTTATATGTATATATG
1 TTTATATGTAAATATG
887035 TTTATATGTAAATAT
1 TTTATATGTAAATAT
887050 AAATTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
TTTATATGTAAATATG
Found at i:887067 original size:15 final size:16
Alignment explanation
Indices: 887047--887090 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
887037 TATATGTAAA
887047 TATAAAT-TTTAAAAT
1 TATAAATATTTAAAAT
*
887062 TATAAATATTTAATAT
1 TATAAATATTTAAAAT
887078 T-TAAATATTTAAA
1 TATAAATATTTAAA
887091 CATCAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAATATTTAAAAT
Found at i:887084 original size:8 final size:8
Alignment explanation
Indices: 887049--887090 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
887039 TATGTAAATA
887049 TAAAT-TT
1 TAAATATT
887056 TAAA-ATT
1 TAAATATT
887063 ATAAATATT
1 -TAAATATT
887072 T-AATATT
1 TAAATATT
887079 TAAATATT
1 TAAATATT
887087 TAAA
1 TAAA
887091 CATCAAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 13 0.42
8 15 0.48
9 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TAAATATT
Found at i:888844 original size:3 final size:3
Alignment explanation
Indices: 888836--888870 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
888826 AATGATATAT
888836 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
888871 TTATTCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:888954 original size:20 final size:20
Alignment explanation
Indices: 888926--888968 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
888916 TTTTAAATTC
888926 ATATTTATAT--TTAATTAT
1 ATATTTATATAATTAATTAT
*
888944 TTATTTATATAATTAATTAT
1 ATATTTATATAATTAATTAT
888964 ATATT
1 ATATT
888969 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTATATAATTAATTAT
Found at i:888958 original size:16 final size:16
Alignment explanation
Indices: 888927--888977 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
888917 TTTAAATTCA
888927 TATTTATATTTAATTATT
1 TATTTATA--TAATTATT
*
888945 TATTTATATAATTAAT
1 TATTTATATAATTATT
*
888961 TATATAT-TAAATTATT
1 TATTTATAT-AATTATT
888977 T
1 T
888978 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 20 0.69
18 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATATAATTATT
Found at i:889280 original size:2 final size:2
Alignment explanation
Indices: 889273--889321 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
889263 TTAAATTCAT
889273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
889315 TA TA TA T
1 TA TA TA T
889322 CTCGGCTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:889387 original size:13 final size:14
Alignment explanation
Indices: 889362--889390 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
889352 TATACATGGT
889362 AAAATAAAGAAGAA
1 AAAATAAAGAAGAA
889376 AAAATAAA-AAGAA
1 AAAATAAAGAAGAA
889389 AA
1 AA
889391 CGAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAATAAAGAAGAA
Found at i:890111 original size:16 final size:17
Alignment explanation
Indices: 890087--890120 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
890077 CTTCATATTA
890087 ATATAATAT-ATTTTTT
1 ATATAATATCATTTTTT
*
890103 ATATTATATCATTTTTT
1 ATATAATATCATTTTTT
890120 A
1 A
890121 AATTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATAATATCATTTTTT
Found at i:892859 original size:9 final size:9
Alignment explanation
Indices: 892819--892885 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
892809 TTATATTGAA
*
892819 AATTAAATT
1 AATTAATTT
892828 AATATAATTT
1 AAT-TAATTT
*
892838 -TTTAA-TT
1 AATTAATTT
892845 -ATTAATTT
1 AATTAATTT
*
892853 AATTAATTA
1 AATTAATTT
892862 AATTAATTT
1 AATTAATTT
*
892871 AAGTAATTT
1 AATTAATTT
892880 AATTAA
1 AATTAA
892886 ATTATTTAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
7 6 0.12
8 5 0.10
9 32 0.67
10 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:896689 original size:20 final size:19
Alignment explanation
Indices: 896662--896739 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 19
896652 GTAAAAAGAC
896662 AAAATGTATCGATACATTG
1 AAAATGTATCGATACATTG
*
896681 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
* *
896701 ATACATGTATCGATATATTG
1 A-AAATGTATCGATACATTG
*
896721 AAAAATGTATCAATACATT
1 -AAAATGTATCGATACATT
896740 TGGGTAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
19 2 0.04
20 45 0.92
21 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:902539 original size:21 final size:19
Alignment explanation
Indices: 902475--902546 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
902465 AGCGATACAT
*
902475 TGTATCGATACAACACTTA
1 TGTATCGATACAATACTTA
902494 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
* *
902513 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-ATACT-TA
902534 TGTATCGATACAA
1 TGTATCGATACAA
902547 ATTGTTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 30 0.64
20 4 0.09
21 13 0.28
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Found at i:902895 original size:21 final size:20
Alignment explanation
Indices: 902871--902941 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
902861 TAAGTTAACC
902871 AGGAACAGGCTATTGTCGACT
1 AGGAACAGGCT-TTGTCGACT
*
902892 AGGAACA-GATTTACGTCGACT
1 AGGAACAGGCTTT--GTCGACT
* *
902913 AAGAATAGGCTGTTGTCGACT
1 AGGAACAGGCT-TTGTCGACT
902934 AGGAACAG
1 AGGAACAG
902942 ATAAACAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 32 0.80
22 2 0.05
23 2 0.05
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (20 bp):
AGGAACAGGCTTTGTCGACT
Found at i:905523 original size:24 final size:24
Alignment explanation
Indices: 905496--905551 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
905486 GGTTTTGAGT
905496 CTTGGCTGAATGAGCAAAGGAAGG
1 CTTGGCTGAATGAGCAAAGGAAGG
*
905520 CTTGGCTGAATGAGCAAAGGGAGG
1 CTTGGCTGAATGAGCAAAGGAAGG
*
905544 CTTTGCTG
1 CTTGGCTG
905552 GATCAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.14, G:0.38, T:0.21
Consensus pattern (24 bp):
CTTGGCTGAATGAGCAAAGGAAGG
Found at i:906031 original size:43 final size:43
Alignment explanation
Indices: 905949--906074 Score: 164
Period size: 43 Copynumber: 2.9 Consensus size: 43
905939 ATTTAAGTAG
* * * *
905949 GCATGTATGCATGGCAACTTTA-TTGCTCGTTTGTATGCTTGCA
1 GCATCTATGCATGGTAAC-TTAGTTACTCGCTTGTATGCTTGCA
* *
905992 GCATCTATGCATGGTAACTTAGTTACTCGCTTGTGTGCTTGTA
1 GCATCTATGCATGGTAACTTAGTTACTCGCTTGTATGCTTGCA
* *
906035 GTATCTATGCGTGGTAACTTAGTTACTCGCTTGTATGCTT
1 GCATCTATGCATGGTAACTTAGTTACTCGCTTGTATGCTT
906075 TAGAAAAGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 3 0.04
43 70 0.96
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (43 bp):
GCATCTATGCATGGTAACTTAGTTACTCGCTTGTATGCTTGCA
Found at i:914177 original size:2 final size:2
Alignment explanation
Indices: 914170--914196 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
914160 AATGTATCAA
914170 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
914197 ATAAATGCTT
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:918778 original size:15 final size:17
Alignment explanation
Indices: 918739--918779 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
918729 ACCAGCATAT
918739 ATATATATATGATTTTA
1 ATATATATATGATTTTA
* *
918756 GTAAATATAT-A-TTTA
1 ATATATATATGATTTTA
918771 ATATATATA
1 ATATATATA
918780 CTAAAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 11 0.55
16 1 0.05
17 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
ATATATATATGATTTTA
Found at i:922559 original size:23 final size:23
Alignment explanation
Indices: 922508--922579 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
922498 AACATATTTC
922508 TTATATATTTCATAATAAAATAA
1 TTATATATTTCATAATAAAATAA
** *
922531 CAATATATTTCATCAATAATAT-A
1 TTATATATTTCAT-AATAAAATAA
*
922554 TTATAT-TCTTC--AATAGAATAA
1 TTATATAT-TTCATAATAAAATAA
922575 TTATA
1 TTATA
922580 AGTATGGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.15
21 6 0.15
22 1 0.03
23 19 0.49
24 7 0.18
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.43
Consensus pattern (23 bp):
TTATATATTTCATAATAAAATAA
Found at i:922760 original size:31 final size:31
Alignment explanation
Indices: 922722--922784 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
922712 TGTTTGGTTG
*
922722 TATTAACATATGTAAGATCAGAATATATGGA
1 TATTAACATATGCAAGATCAGAATATATGGA
922753 TATTAACATATGCAAGATCAGAATATATGGA
1 TATTAACATATGCAAGATCAGAATATATGGA
922784 T
1 T
922785 GAGTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (31 bp):
TATTAACATATGCAAGATCAGAATATATGGA
Found at i:923291 original size:21 final size:20
Alignment explanation
Indices: 923246--923298 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
923236 TAACATGATC
923246 AATTATT-ATATTTAATATGA
1 AATTATTAATA-TTAATATGA
*
923266 AATTATTAATATTAATATTA
1 AATTATTAATATTAATATGA
923286 ACATTATTAATAT
1 A-ATTATTAATAT
923299 ATTGTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AATTATTAATATTAATATGA
Found at i:923312 original size:21 final size:21
Alignment explanation
Indices: 923246--923298 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
923236 TAACATGATC
*
923246 AATTATT-ATATTTAATA-TGA
1 AATTATTAATA-TTAATATTAA
923266 AATTATTAATATTAATATTAA
1 AATTATTAATATTAATATTAA
*
923287 CATTATTAATAT
1 AATTATTAATAT
923299 ATTGTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATTATTAATATTAATATTAA
Found at i:927523 original size:18 final size:18
Alignment explanation
Indices: 927500--927535 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
927490 TTAATATTTT
927500 AAAA-TTTAATTTAAATAA
1 AAAATTTTAA-TTAAATAA
927518 AAAATTTTAATTAAATAA
1 AAAATTTTAATTAAATAA
927536 TACCTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTTTAATTAAATAA
Found at i:929926 original size:28 final size:27
Alignment explanation
Indices: 929867--929956 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
929857 CACCCATTTG
* *
929867 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
*
929894 TTTGTAAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
929922 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
929947 TTTGTCAAAA
1 TTTGTCAAAA
929957 TTTGTGGCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 11 0.21
26 3 0.06
27 18 0.35
28 20 0.38
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:931014 original size:19 final size:19
Alignment explanation
Indices: 930990--931027 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
930980 TTAATTAACC
*
930990 TTTTATATATGTATATATA
1 TTTTATATATATATATATA
931009 TTTTATATATATATATATA
1 TTTTATATATATATATATA
931028 ACAAGATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTATATATATATATATA
Found at i:931537 original size:28 final size:28
Alignment explanation
Indices: 931481--931537 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
931471 TAAAATTACT
* * *
931481 ATTTAATAATAAAAATATTTTTATTTAA
1 ATTTAATAATAAAAATATATTAATATAA
*
931509 ATTTAATTATAAAAATATATTAATATAA
1 ATTTAATAATAAAAATATATTAATATAA
931537 A
1 A
931538 AATAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTAATAATAAAAATATATTAATATAA
Found at i:931844 original size:20 final size:20
Alignment explanation
Indices: 931798--931846 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
931788 TATAAAAATA
* *
931798 AAATTAAAACACGTGACAAT
1 AAATTAAAACACATGACAAC
931818 AAGATTAAAACACAT-ACAAC
1 AA-ATTAAAACACATGACAAC
931838 ATAATTAAA
1 A-AATTAAA
931847 TACATAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.20
Consensus pattern (20 bp):
AAATTAAAACACATGACAAC
Found at i:935423 original size:13 final size:13
Alignment explanation
Indices: 935405--935431 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
935395 CTTCTCATGA
935405 GTCACATTCAATC
1 GTCACATTCAATC
935418 GTCACATTCAATC
1 GTCACATTCAATC
935431 G
1 G
935432 GTATCAATGA
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:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (13 bp):
GTCACATTCAATC
Found at i:936053 original size:21 final size:21
Alignment explanation
Indices: 936027--936068 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
936017 AAAAAATTAT
936027 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTATATA
936048 TTTTATAATTAAATTTATATA
1 TTTTATAATTAAATTTATATA
936069 AAAATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATTAAATTTATATA
Found at i:940689 original size:2 final size:2
Alignment explanation
Indices: 940678--940711 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
940668 AAATTAGTGC
940678 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
940712 TAAACTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:941689 original size:17 final size:17
Alignment explanation
Indices: 941669--941703 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
941659 TTAATATTTT
941669 AAAATTAAAATTAAATAA
1 AAAATT-AAATTAAATAA
*
941687 AAAATTTAATTAAATAA
1 AAAATTAAATTAAATAA
941704 TACCTCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTAAATTAAATAA
Found at i:952154 original size:21 final size:21
Alignment explanation
Indices: 952112--952170 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
952102 CTAAAATGCC
*
952112 TTTTTTTAAAT-TTTATAATTA
1 TTTTTTTATATATTT-TAATTA
*
952133 TTTTTTTATATATTTTAGTTA
1 TTTTTTTATATATTTTAATTA
* *
952154 TGTTTTTTTTTTATTTT
1 T-TTTTTTATATATTTT
952171 TTACAAGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTTTTATATATTTTAATTA
Found at i:952880 original size:22 final size:21
Alignment explanation
Indices: 952855--952895 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
952845 AATAAAAATT
952855 TATTTTCAT-ATTAATATTTATA
1 TATTTT-ATAATTAA-ATTTATA
952877 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
952896 AATTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:953466 original size:27 final size:27
Alignment explanation
Indices: 953401--953496 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 27
953391 CAAAAACCAC
* * *
953401 CCTTTGTGTTTGTCAACAATGGTGGTT
1 CCTTTTTGTTTGTCAAAAATGATGGTT
* * *
953428 ACTTTATATTTGTCAAAAATGATGGTT
1 CCTTTTTGTTTGTCAAAAATGATGGTT
* *
953455 CCTTTTTGTTTGTAAAAAATTATGG--
1 CCTTTTTGTTTGTCAAAAATGATGGTT
*
953480 -CTTATTGTTTGTCAAAA
1 CCTTTTTGTTTGTCAAAA
953497 TTGGTGGCTA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
24 15 0.26
27 42 0.74
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (27 bp):
CCTTTTTGTTTGTCAAAAATGATGGTT
Found at i:953496 original size:24 final size:25
Alignment explanation
Indices: 953436--953496 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
953426 TTACTTTATA
*
953436 TTTGTCAAAAATGATGGTTCCTTTTTG
1 TTTGTCAAAAATGATGG-T-CTTATTG
* *
953463 TTTGTAAAAAATTATGG-CTTATTG
1 TTTGTCAAAAATGATGGTCTTATTG
953487 TTTGTCAAAA
1 TTTGTCAAAA
953497 TTGGTGGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 15 0.50
27 15 0.50
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (25 bp):
TTTGTCAAAAATGATGGTCTTATTG
Found at i:953575 original size:13 final size:13
Alignment explanation
Indices: 953557--953592 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
953547 GAGGCTCCTT
*
953557 CATCCCTGTCAAG
1 CATCCCTCTCAAG
*
953570 CATCCCTCTTAAG
1 CATCCCTCTCAAG
953583 CATCCCTCTC
1 CATCCCTCTC
953593 TTGTATCCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.44, G:0.08, T:0.28
Consensus pattern (13 bp):
CATCCCTCTCAAG
Found at i:955752 original size:21 final size:21
Alignment explanation
Indices: 955726--955767 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
955716 AGCTACTGCC
*
955726 AAGGAAATGTATCGATACATT
1 AAGGAAATATATCGATACATT
955747 AAGGAAATATATCGATACATT
1 AAGGAAATATATCGATACATT
955768 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
AAGGAAATATATCGATACATT
Found at i:958201 original size:52 final size:53
Alignment explanation
Indices: 958144--958529 Score: 199
Period size: 52 Copynumber: 7.4 Consensus size: 53
958134 CAATTGTTCA
* *
958144 TAATCGGGGATACTCTAACCCCAATTTTATTTTC-AAAACACCAATTTTCCTC
1 TAATCGGGGATACTCCAACCCCAATTTTATTTCCAAAAACACCAATTTTCCTC
* * * *
958196 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 TAATCGGGGATACTCCAACCCCAATTTTATTTCCAAAAACACCAATTTTCCTC
* * * ** * * * *
958249 -AATTGAGGATACTTCAA--CC--TTGTTATTTCATCGGGGATACTCCAACCCCGTTACCTC
1 TAATCGGGGATACTCCAACCCCAATT-TTATTTC--C--AAAAACACCAA----TTTTCCTC
** ** * * * ***
958306 CGAT--GGGATACTCCAACCCCAGCTTTA-TTACTAAAATATTGA-TTT-CTC
1 TAATCGGGGATACTCCAACCCCAATTTTATTTCCAAAAACACCAATTTTCCTC
* * ** * * *
958354 ATAATCGAGGATACTCCAACCTCGGTTTTATTT-CTAAAACACTAATTTTCCAC
1 -TAATCGGGGATACTCCAACCCCAATTTTATTTCCAAAAACACCAATTTTCCTC
** * *
958407 -AATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCAATTTTATTTCCAAAAACACCAATTTTCCTC
* * * * *
958458 TAATCGGGGATAATCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 TAATCGGGGATACTCCAACCCCAATTTTATTTCCAAAAACACCAATTTTCCTC
*
958511 -AATCGAGGATACTCCAACC
1 TAATCGGGGATACTCCAACC
958530 TCGTTATTTC
Statistics
Matches: 254, Mismatches: 56, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
48 5 0.02
49 11 0.04
50 2 0.01
51 73 0.29
52 95 0.37
53 40 0.16
54 3 0.01
56 11 0.04
57 4 0.02
58 6 0.02
59 3 0.01
60 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (53 bp):
TAATCGGGGATACTCCAACCCCAATTTTATTTCCAAAAACACCAATTTTCCTC
Found at i:958373 original size:51 final size:51
Alignment explanation
Indices: 958311--958529 Score: 199
Period size: 51 Copynumber: 4.3 Consensus size: 51
958301 ACCTCCGATG
* * * * * *
958311 GGATACTCCAACCCCAGCTTTATTACTAAAATATTGA-TTTCTCATAATCGA
1 GGATACTCCAACCCCGGTTTTATTACTAAAACACTAATTTTC-CACAATCGA
* * *
958362 GGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTCCACAATCGG
1 GGATACTCCAACCCCGGTTTTATTACTAAAACACTAATTTTCCACAATCGA
* * ** *
958413 GGATACTCCAACCCCGGTTTTATT-TTCAAAACACCAATTTTCCTTTAATCGG
1 GGATACTCCAACCCCGGTTTTATTACT-AAAACACTAATTTTCC-ACAATCGA
* * * * * * *
958465 GGATAATCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGGTTTTA-TTACTAAAACACTAATTTTCCACAATCGA
958517 GGATACTCCAACC
1 GGATACTCCAACC
958530 TCGTTATTTC
Statistics
Matches: 138, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
50 1 0.01
51 75 0.54
52 45 0.33
53 17 0.12
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
GGATACTCCAACCCCGGTTTTATTACTAAAACACTAATTTTCCACAATCGA
Found at i:958610 original size:262 final size:262
Alignment explanation
Indices: 958145--958634 Score: 804
Period size: 262 Copynumber: 1.9 Consensus size: 262
958135 AATTGTTCAT
* *
958145 AATCGGGGATACTCTAACCCCAATTTTATTTTCAAAACACCAATTTTCCTCTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCCTCTAATCGGGGATAAT
* * *
958210 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTTCAACCTTGTTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
* * *
958275 TTCATCGGGGATACTCCAACCCCGTTACCTCCGATGGGATACTCCAACCCCAGCTTTATTACTAA
131 TTCATCGGGAATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCAGCTTTATTACTAA
958340 AATATTGATTTCTCATAATCGAGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTCC
196 AATATTGATTTCTCATAATCGAGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTCC
958405 AC
261 AC
** *
958407 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATAAT
1 AATCGGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCCTCTAATCGGGGATAAT
958472 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
* *
958537 TTCATCGGGAATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAA-CCCTGACTTTATT-TTC
131 TTCATCGGGAATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCAG-CTTTATTACT-
* * *
958600 AAAATATTGATTTCTCATAATTGGGGATGCTCCAA
194 AAAATATTGATTTCTCATAATCGAGGATACTCCAA
958635 GCCCGTTATT
Statistics
Matches: 210, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
261 5 0.02
262 205 0.98
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (262 bp):
AATCGGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCCTCTAATCGGGGATAAT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
TTCATCGGGAATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCAGCTTTATTACTAA
AATATTGATTTCTCATAATCGAGGATACTCCAACCTCGGTTTTATTTCTAAAACACTAATTTTCC
AC
Found at i:958674 original size:79 final size:78
Alignment explanation
Indices: 958540--958776 Score: 262
Period size: 79 Copynumber: 3.0 Consensus size: 78
958530 TCGTTATTTC
* ** *
958540 ATCGGGAATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCTGACTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCC-GATTTTATTTTCAAAAT
958605 ATTGATTTCTCATA
65 ATTGATTTCTCATA
* * * * *
958619 ATTGGGGATGCTCCAAGCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTTC-TAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAA-CCCGATTTTATTTTCAAAAT
* * *
958683 CATCGATTTTTCACA
65 -ATTGATTTCTCATA
* * *
958698 ATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCG-TTATTATCTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAA-CCCGATT-TTATTTTCAAAA
*
958762 TATTAAATTTCTCAT
64 TATT-GATTTCTCAT
958777 CGGGAAATAT
Statistics
Matches: 128, Mismatches: 25, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
78 5 0.04
79 110 0.86
80 13 0.10
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCGATTTTATTTTCAAAATA
TTGATTTCTCATA
Found at i:967989 original size:21 final size:21
Alignment explanation
Indices: 967959--968005 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
967949 GTCTTACCAA
967959 GACATACCTGGGTTAGACACC
1 GACATACCTGGGTTAGACACC
*
967980 GACATGCCTGGGTTAGACACC
1 GACATACCTGGGTTAGACACC
968001 GACAT
1 GACAT
968006 TGTGGTCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
GACATACCTGGGTTAGACACC
Found at i:971175 original size:1 final size:1
Alignment explanation
Indices: 971171--971246 Score: 71
Period size: 1 Copynumber: 76.0 Consensus size: 1
971161 TTCTTTTTTT
* * * * * * * *
971171 AAAAAAAAACAAAAAACAACAAAAAAACAAAAAAAAACAAAAAAACAAAAAAAACAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
971236 AGAAAAAAAAA
1 AAAAAAAAAAA
971247 GAATCTGCTT
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:971186 original size:10 final size:10
Alignment explanation
Indices: 971171--971246 Score: 88
Period size: 10 Copynumber: 7.8 Consensus size: 10
971161 TTCTTTTTTT
971171 AAAAAAAAAC
1 AAAAAAAAAC
*
971181 AAAAAACAAC
1 AAAAAAAAAC
971191 --AAAAAAAC
1 AAAAAAAAAC
971199 AAAAAAAAAC
1 AAAAAAAAAC
971209 AAAAAAACAA-
1 AAAAAAA-AAC
*
971219 AAAAAACAAC
1 AAAAAAAAAC
971229 AAAAAAAAGA-
1 AAAAAAAA-AC
971239 AAAAAAAA
1 AAAAAAAA
971247 GAATCTGCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.12
9 2 0.04
10 45 0.79
11 3 0.05
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:971196 original size:18 final size:18
Alignment explanation
Indices: 971173--971235 Score: 99
Period size: 18 Copynumber: 3.4 Consensus size: 18
971163 CTTTTTTTAA
971173 AAAAAAACAAAAAACAAC
1 AAAAAAACAAAAAACAAC
*
971191 AAAAAAACAAAAAAAAAC
1 AAAAAAACAAAAAACAAC
971209 AAAAAAACAAAAAAAACAAC
1 AAAAAAAC--AAAAAACAAC
971229 AAAAAAA
1 AAAAAAA
971236 AGAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 25 0.61
20 16 0.39
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAACAAC
Found at i:971213 original size:38 final size:39
Alignment explanation
Indices: 971171--971246 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
971161 TTCTTTTTTT
971171 AAAAAAA-AACAAAAAACAAC-AAAAAAACAAAAAAAAAC
1 AAAAAAACAA-AAAAAACAACAAAAAAAACAAAAAAAAAC
*
971209 AAAAAAACAAAAAAAACAACAAAAAAAAGAAAAAAAAA
1 AAAAAAACAAAAAAAACAACAAAAAAAACAAAAAAAAA
971247 GAATCTGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 17 0.49
39 18 0.51
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (39 bp):
AAAAAAACAAAAAAAACAACAAAAAAAACAAAAAAAAAC
Found at i:971241 original size:18 final size:18
Alignment explanation
Indices: 971172--971243 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 18
971162 TCTTTTTTTA
971172 AAAAAAAACAAAAAACAAC
1 AAAAAAAA-AAAAAACAAC
971191 AAAAAAACAAAAAAA-AAC
1 AAAAAAA-AAAAAAACAAC
971209 AAAAAAACAAAAAAAACAAC
1 -AAAAAA-AAAAAAAACAAC
971229 AAAAAAAAGAAAAAA
1 AAAAAAAA-AAAAAA
971244 AAAGAATCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.10
19 38 0.79
20 5 0.10
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAACAAC
Found at i:972396 original size:100 final size:100
Alignment explanation
Indices: 972214--972398 Score: 264
Period size: 100 Copynumber: 1.9 Consensus size: 100
972204 CCTTCCGCTT
* * *
972214 TTTAGTCCTCAAAGAGCATGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCA
1 TTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCA
* *
972279 GTCCTTAAAAAGTAGGACGCTCTCTCTTTTCGCCC
66 GTCCTCAAAAAGCAGGACGCTCTCTCTTTTCGCCC
* * * **
972314 TTTAGTCCTTAAAGAGCAAGACGCCTTCTCCTTTTAAAGTCCATACAAGTTGGTGGCACTTTTCA
1 TTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCA
972379 GTCCTCAAAGAA-CAGGACGC
66 GTCCTCAAA-AAGCAGGACGC
972399 CTTTCAAAGC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 72 0.97
101 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (100 bp):
TTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCA
GTCCTCAAAAAGCAGGACGCTCTCTCTTTTCGCCC
Found at i:972521 original size:116 final size:116
Alignment explanation
Indices: 972312--972791 Score: 620
Period size: 116 Copynumber: 4.2 Consensus size: 116
972302 CTCTTTTCGC
* * * * * *
972312 CCTTT-AGTCCTTAAAGAGCAAGACGCCTTCTCCTTTTAAAGTCCATACAAGTTGGTGGCACTTT
1 CCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
*
972376 TCAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
66 TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
972427 CCTTTCAGTCCTCAAAGAGTAGGACACCTTCTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTT
1 CCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
972492 TTAGTCCTCAAAGAGCAGGACGCCTTTCAACG-CCACACAAGTTGGTGGCA
66 TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* ** * * *
972542 CCTTTTAGTCCTCAAAGAGCAGGA-TGCTTTTTCTTTTCAAAGCCAACACAAGTTGGTGGCACCT
1 CCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCT
* * *
972606 TTCAGTCCCCAAAGACCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
65 TTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
972658 -TTTTCCAATCCTCAAAGAGCAGGACA-C--CT-C--TTAAAGCCCACACAAGTTGGTGGCACCT
1 CCTTT-CAGTCCTCAAAGAGCAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * *
972716 TTCAGTCCTCAAAGAGCAAGACGTCTTTCAAAGCCCACACGAGTTGGTGGCA
65 TTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
972768 CTTTTTAGTCCTCAAAAAGCAGGA
1 CCTTTCAGTCCTCAAAGAGCAGGA
972792 TGCACCTTAT
Statistics
Matches: 320, Mismatches: 39, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
110 87 0.27
111 6 0.02
113 1 0.00
114 10 0.03
115 100 0.31
116 116 0.36
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (116 bp):
CCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:972542 original size:54 final size:55
Alignment explanation
Indices: 972343--972791 Score: 512
Period size: 55 Copynumber: 8.0 Consensus size: 55
972333 GACGCCTTCT
* * * *
972343 CCTTTTAAAGTCCATACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAACAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGACG
* * *
972398 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
*
972453 CCTTCTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
1 CCTT-T-C----AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* *
972514 CCTTTCAACG-CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * * *
972568 CTTTTTCTTTTCAAAGCCAACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGACCAGGACA
1 C-----C-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* *
972629 CCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAATCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT--AGTCCTCAAAGAGCAGGACG
* *
972684 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * *
972739 TCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAAAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGA
972792 TGCACCTTAT
Statistics
Matches: 338, Mismatches: 36, Indels: 40
0.82 0.09 0.10
Matches are distributed among these distances:
53 3 0.01
54 45 0.13
55 180 0.53
56 8 0.02
57 4 0.01
59 2 0.01
60 8 0.02
61 88 0.26
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
Found at i:972654 original size:170 final size:167
Alignment explanation
Indices: 972347--972783 Score: 519
Period size: 170 Copynumber: 2.6 Consensus size: 167
972337 CCTTCTCCTT
* * * *
972347 TTAAAGTCCATACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCC
1 TTAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCA
* **
972411 ACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACACCTTCTCCTTTTAAAGCCCACAC
65 ACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGACCAGGACACCTTCTCC---TAAAGCCCACAC
* * *
972476 GAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGACGCCT-
127 AAGTTGGTGGCA--TTTTCAATCCTCAAAGAGCAGGACACCTC
* *
972517 TTCAA-CGCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCA
1 TTAAAGC-CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGC-----C-TTTCA
972581 AAGCCAACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGACCAGGACACCTT-T-C-AAAGCCCA
59 AAGCCAACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGACCAGGACACCTTCTCCTAAAGCCCA
972643 CACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTC
124 CACAAGTTGGTGGCATTTT-CAATCCTCAAAGAGCAGGACACCTC
* * * *
972688 TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGTCTTTCAAAGCCCA
1 TTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCAA
* * * *
972753 CACGAGTTGGTGGCACTTTTTAGTCCTCAAA
66 CACAAGTTGGTGGCACCTTTCAGTCCCCAAA
972784 AAGCAGGATG
Statistics
Matches: 233, Mismatches: 22, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
165 38 0.16
166 1 0.00
168 4 0.02
170 83 0.36
171 50 0.21
172 1 0.00
174 1 0.00
175 2 0.01
176 53 0.23
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (167 bp):
TTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCAA
CACAAGTTGGTGGCACCTTTCAGTCCCCAAAGACCAGGACACCTTCTCCTAAAGCCCACACAAGT
TGGTGGCATTTTCAATCCTCAAAGAGCAGGACACCTC
Found at i:973590 original size:19 final size:19
Alignment explanation
Indices: 973566--973627 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
973556 TTTTGAATTT
973566 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
*
973585 CAAACAGAAAATT-TATCGATA
1 CAAACAG---TTTGTATCGATA
*
973606 CACA-AGTGTTGTATCGATA
1 CAAACAGT-TTGTATCGATA
973625 CAA
1 CAA
973628 TGTATCGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 2 0.06
19 17 0.50
20 2 0.06
21 11 0.32
22 2 0.06
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:973633 original size:13 final size:13
Alignment explanation
Indices: 973615--973639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
973605 ACACAAGTGT
973615 TGTATCGATACAA
1 TGTATCGATACAA
973628 TGTATCGATACA
1 TGTATCGATACA
973640 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:973639 original size:32 final size:32
Alignment explanation
Indices: 973598--973666 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
973588 ACAGAAAATT
973598 TATCGATACACAAGTGTTGTATCGATACAATG
1 TATCGATACACAAGTGTTGTATCGATACAATG
* * *
973630 TATCGATACATAAGTTTTGTATCGATGCAATG
1 TATCGATACACAAGTGTTGTATCGATACAATG
973662 TATCG
1 TATCG
973667 CTATGAAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (32 bp):
TATCGATACACAAGTGTTGTATCGATACAATG
Found at i:973708 original size:13 final size:13
Alignment explanation
Indices: 973690--973715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
973680 GCCAAGGAAA
973690 TGTATCGATACAT
1 TGTATCGATACAT
973703 TGTATCGATACAT
1 TGTATCGATACAT
973716 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:976139 original size:52 final size:52
Alignment explanation
Indices: 976077--976565 Score: 404
Period size: 52 Copynumber: 9.4 Consensus size: 52
976067 CAATTGTTCA
*
976077 TAATCGGGGATACTCCAACCCCGATTTTATATTC-AAAACACCAAATTTCCTC
1 TAATCGGGGATACTCCAACCCCGATTTTAT-TTCTAAAACACCAATTTTCCTC
* * * *
976129 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 TAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTCCTC
** * * ***** * * * *
976182 -AATCGATGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTC
1 TAATCGGGGATACTCCAACCCCG--ATTTTATTTCTAAAACACCAA----TTTTCCTC
** ** * * ***
976239 CGAT--GGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGA-TTT-CTC
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCTC
* * *
976287 ATAATCGGGGATACTCCAACCCC-AGTTTTATTTCTAAAACACTAATTTTTCAC
1 -TAATCGGGGATACTCCAACCCCGA-TTTTATTTCTAAAACACCAATTTTCCTC
* * *
976340 -AATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCTC
* * *
976391 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACTAATTTTCC-A
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCTC
* * *
976442 TAATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCTC
** * * *
976494 TAATCGGGGATACTCCAACTTCGATTTTATTTTCAAAAACACCAATTTT-TTA
1 TAATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACCAATTTTCCTC
*
976546 TAATCGAGGATACTCCAACC
1 TAATCGGGGATACTCCAACC
976566 TCGTTATTTC
Statistics
Matches: 345, Mismatches: 73, Indels: 38
0.76 0.16 0.08
Matches are distributed among these distances:
48 3 0.01
49 4 0.01
51 123 0.36
52 141 0.41
53 41 0.12
54 13 0.04
56 14 0.04
57 4 0.01
58 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (52 bp):
TAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCTC
Found at i:976305 original size:51 final size:51
Alignment explanation
Indices: 976243--976565 Score: 387
Period size: 51 Copynumber: 6.3 Consensus size: 51
976233 TACCTCCGAT
* * * * *
976243 GGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGA-TTTCTCATAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTC-CATAATCG
* * *
976294 GGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTTCACAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCATAATCG
* * *
976345 GGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTTTAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC-ATAATCG
* *
976397 GGGATACTCCAACTCCGATTTTATTTCTAAAACACTAATTTTCCATAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCATAATCG
* * *
976448 GGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTTTAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCC-ATAATCG
** * * * **
976500 GGGATACTCCAACTTCGATTTTATTTTCAAAAACACCAATTTTTTATAATCG
1 GGGATACTCCAACCCCGGTTTTA-TTTCTAAAACACTAATTTTCCATAATCG
*
976552 AGGATACTCCAACC
1 GGGATACTCCAACC
976566 TCGTTATTTC
Statistics
Matches: 234, Mismatches: 34, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
51 125 0.53
52 92 0.39
53 17 0.07
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (51 bp):
GGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCATAATCG
Found at i:976424 original size:103 final size:103
Alignment explanation
Indices: 976288--976565 Score: 459
Period size: 103 Copynumber: 2.7 Consensus size: 103
976278 TGATTTCTCA
* *
976288 TAATCGGGGATACTCCAAC-CCCAGTTTTATTTCTAAAACACTAATTTTTCACAATCGGGGATAC
1 TAATCGGGGATACTCCAACTCCGA-TTTTATTTCTAAAACACTAATTTTTCATAATCGGGGATAC
976352 TCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTT
65 TCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTT
*
976391 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACTAATTTTCCATAATCGGGGATACT
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACTAATTTTTCATAATCGGGGATACT
976456 CCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTT
66 CCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTT
* * * * *
976494 TAATCGGGGATACTCCAACTTCGATTTTATTTTCAAAAACACCAATTTTTTATAATCGAGGATAC
1 TAATCGGGGATACTCCAACTCCGATTTTA-TTTCTAAAACACTAATTTTTCATAATCGGGGATAC
976559 TCCAACC
65 TCCAACC
976566 TCGTTATTTC
Statistics
Matches: 164, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 124 0.76
104 40 0.24
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (103 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACTAATTTTTCATAATCGGGGATACT
CCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTT
Found at i:976572 original size:26 final size:27
Alignment explanation
Indices: 976546--976599 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
976536 CAATTTTTTA
*
976546 TAATCGAGGATACTCCAACCTCGTTATT
1 TAATCGAGGATACTCCAACCCCGTTA-T
* *
976574 TCATCGGGGATACTCCAACCCCGTTA
1 TAATCGAGGATACTCCAACCCCGTTA
976600 CCTCCGAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (27 bp):
TAATCGAGGATACTCCAACCCCGTTAT
Found at i:976710 original size:79 final size:78
Alignment explanation
Indices: 976576--976812 Score: 251
Period size: 79 Copynumber: 3.0 Consensus size: 78
976566 TCGTTATTTC
** *
976576 ATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC-GTTTTATTTTCAAAAT
976641 ATTGATTTCTCATA
65 ATTGATTTCTCATA
* * * * ** *
976655 ATTGGGGATGCTCCAAGCCTGTTATTTCCGAGGGGATACTCCAATTCCGATTTTATTTTC-TAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG-TTTTATTTTCAAAAT
* * *
976719 CATCGATTTTTCACA
65 -ATTGATTTCTCATA
* * * * *
976734 ATCGGTGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTT-TTATTTTCAAAAT
*
976799 ATTAAATTTCTCAT
65 ATT-GATTTCTCAT
976813 CGAAAAATAT
Statistics
Matches: 124, Mismatches: 29, Indels: 9
0.77 0.18 0.06
Matches are distributed among these distances:
78 6 0.05
79 108 0.87
80 10 0.08
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTTTATTTTCAAAATA
TTGATTTCTCATA
Found at i:982229 original size:52 final size:52
Alignment explanation
Indices: 982148--982268 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
982138 TGAAAAGTTA
*
982148 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
982200 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
982252 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
982269 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:982281 original size:52 final size:51
Alignment explanation
Indices: 982148--982288 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
982138 TGAAAAGTTA
982148 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
982200 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
982252 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
982289 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:982295 original size:13 final size:13
Alignment explanation
Indices: 982277--982301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
982267 CAAAGATCAG
982277 TGTATCGATACAA
1 TGTATCGATACAA
982290 TGTATCGATACA
1 TGTATCGATACA
982302 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:982382 original size:33 final size:33
Alignment explanation
Indices: 982340--982409 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
982330 GGCAGTAGCT
982340 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
982373 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
982406 TACA
1 TACA
982410 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:982383 original size:13 final size:13
Alignment explanation
Indices: 982365--982389 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
982355 CAAAAAAATA
982365 TGTATCGATACAT
1 TGTATCGATACAT
982378 TGTATCGATACA
1 TGTATCGATACA
982390 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:983320 original size:67 final size:68
Alignment explanation
Indices: 983198--983324 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
983188 ATTGGGTTTT
* * *
983198 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGATGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGATGATG
983263 AGA
66 AGA
* * ** *
983266 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGCTATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
983325 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGATGATG
AGA
Found at i:983401 original size:49 final size:49
Alignment explanation
Indices: 983328--984176 Score: 1104
Period size: 49 Copynumber: 17.9 Consensus size: 49
983318 AAGATGAGAA
* *
983328 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
983378 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
983427 TAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
983476 AAAGGTGCCAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 -AA------AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
983532 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
983581 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
983630 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
983673 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
983722 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
983765 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
983814 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
983857 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
983906 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
983949 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
983998 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
984041 AAAGCTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
984090 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
984133 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
984177 GAAGGGTTGC
Statistics
Matches: 707, Mismatches: 53, Indels: 83
0.84 0.06 0.10
Matches are distributed among these distances:
43 233 0.33
44 6 0.01
48 6 0.01
49 408 0.58
50 6 0.01
55 2 0.00
56 46 0.07
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:983703 original size:92 final size:92
Alignment explanation
Indices: 983485--984176 Score: 1294
Period size: 92 Copynumber: 7.5 Consensus size: 92
983475 TAAAGGTGCC
983485 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
*
983550 ATTCAAGGCCAGCTACATTGGACTTAAAGATGA
66 ATTCAAGGCCAGCTATATTGGACTT----A--A
983583 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
983648 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
983675 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
983740 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
983767 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
983832 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
983859 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
983924 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
983951 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
984016 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
*
984043 AGCTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
984108 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
* *
984135 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTATATTGGGCTTA
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
984177 GAAGGGTTGC
Statistics
Matches: 589, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
92 499 0.85
94 1 0.00
98 89 0.15
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (92 bp):
AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
ATTCAAGGCCAGCTATATTGGACTTAA
Found at i:984225 original size:34 final size:34
Alignment explanation
Indices: 984176--984314 Score: 209
Period size: 34 Copynumber: 4.2 Consensus size: 34
984166 TATTGGGCTT
984176 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
984209 AGAAGGGTTTGCCACCGCCTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
984243 AAGAA-GG-TTGCCACCGAC-T-TGTGGACTTTAG
1 -AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
984274 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
984308 A-AAGGGT
1 AGAAGGGT
984315 GAAAGATGCC
Statistics
Matches: 96, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
30 4 0.04
31 13 0.14
32 12 0.12
33 24 0.25
34 39 0.41
35 4 0.04
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (34 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:984273 original size:65 final size:65
Alignment explanation
Indices: 984169--984314 Score: 226
Period size: 65 Copynumber: 2.2 Consensus size: 65
984159 CCAGCTATAT
* *
984169 TGGGC-TTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGCCTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGACTTTAGAGAAGGGTTTGCCACCGACTTGTG
984233 TGGGCTTTAGAAGAAGGTTGCCACCGAC-T-TGTGGACTTTAGAGAAGGGTTTGCCACCGACTTG
1 TGGGCTTTAGAAG--GGTTGCCACCGACTTGTGTGGACTTTAGAGAAGGGTTTGCCACCGACTTG
984296 TG
64 TG
984298 TGGGCTTTAGAAAGGGT
1 TGGGCTTTAG-AAGGGT
984315 GAAAGATGCC
Statistics
Matches: 76, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
64 8 0.11
65 51 0.67
66 4 0.05
67 13 0.17
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.28
Consensus pattern (65 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGACTTTAGAGAAGGGTTTGCCACCGACTTGTG
Found at i:984661 original size:35 final size:34
Alignment explanation
Indices: 984296--985054 Score: 939
Period size: 34 Copynumber: 22.3 Consensus size: 34
984286 CACCGACTTG
* *
984296 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGT
1 TGTGGGCTTTA-AAA-GG-AAAAGAGTGCCACGGAGT
* * **
984332 TGTGGAC-TTAAAAAGAATAAG-GTGCCACAAAGT
1 TGTGGGCTTTAAAAGGAA-AAGAGTGCCACGGAGT
984365 TGTGGGCTTTAAAAAGGAAAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGG---AAAAGAGTGCCACGGAGT
* *
984403 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGAAGT
1 TGTGGGCTTTAAAAGG-AAAAGAGTGCCACGGAGT
*
984437 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGG-AAAAGAGTGCCACGGAGT
*
984471 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGG-AAAAGAGTGCCACGGAGT
984505 TGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAGAGTGCCACGGAGT
* *
984538 TGTGGGC-TTAGAAGGAAAAAGAATGCCACGGAGT
1 TGTGGGCTTTAAAAGG-AAAAGAGTGCCACGGAGT
*
984572 TGTGGGC-TTAGAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAGAGTGCCACGGAGT
984605 TGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAGAGTGCCACGGAGT
984638 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAGAGTGCCACGGAGT
*
984673 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGG-AAAAGAGTGCCACGGAGT
984707 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAGAGTGCCACGGAGT
984742 TGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAGAGTGCCACGGAGT
984775 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAGAGTGCCACGGAGT
*
984810 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGG-AAAAGAGTGCCACGGAGT
984844 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAGAGTGCCACGGAGT
984879 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAGAGTGCCACGGAGT
*
984914 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGG-AAAAGAGTGCCACGGAGT
* *
984948 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGTAAT
1 TGTGGGCTTT-AAAAGGAAAAGAGTGCCACGGAGT
* * *
984983 TGTGGACTTT--GA-GACAAA-A-TGCCACTGAGT
1 TGTGGGCTTTAAAAGGA-AAAGAGTGCCACGGAGT
* * *
985013 CGTGGACTTT-AAAGGAAAAGA-TGCCACTGAGT
1 TGTGGGCTTTAAAAGGAAAAGAGTGCCACGGAGT
* *
985045 CGTGGACTTT
1 TGTGGGCTTT
985055 GAGCAGAGAT
Statistics
Matches: 663, Mismatches: 31, Indels: 62
0.88 0.04 0.08
Matches are distributed among these distances:
30 17 0.03
31 7 0.01
32 31 0.05
33 153 0.23
34 216 0.33
35 189 0.29
36 26 0.04
37 5 0.01
38 19 0.03
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (34 bp):
TGTGGGCTTTAAAAGGAAAAGAGTGCCACGGAGT
Found at i:984934 original size:69 final size:68
Alignment explanation
Indices: 984296--985056 Score: 971
Period size: 69 Copynumber: 11.2 Consensus size: 68
984286 CACCGACTTG
* * * * *
984296 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAATAAG-GTGCCA
1 TGTGGGCTTT-GAAAAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA-AAGAGTGCCA
**
984359 CAAAGT
63 CGGAGT
* *
984365 TGTGGGCTTTAAAAAGGAAAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCC
1 TGTGGGCTTTGAAAAGG---AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAGAGTGCC
*
984430 ACGAAGT
62 ACGGAGT
* *
984437 TGTGGGC-TT-AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCAC
1 TGTGGGCTTTGAAAAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAGAGTGCCAC
984500 GGAGT
64 GGAGT
* *
984505 TGTGGGCTTT--AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAATGCCACG
1 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAGAGTGCCACG
984568 GAGT
65 GAGT
* *
984572 TGTGGGC-TT-AGAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGG
1 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACGG
984635 AGT
66 AGT
*
984638 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACG
1 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAGAGTGCCACG
984703 GAGT
65 GAGT
*
984707 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGG
1 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACGG
984772 AGT
66 AGT
*
984775 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACG
1 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAGAGTGCCACG
984840 GAGT
65 GAGT
984844 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAGAGTGCCAC
1 TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAAAAGAGTGCCAC
984909 GGAGT
64 GGAGT
*
984914 TGTGGGC-TT-AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAGAGTGCCA
1 TGTGGGCTTTGAAAAGG-AAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAAAAGAGTGCCA
* *
984977 CGTAAT
63 CGGAGT
* * * * * *
984983 TGTGGACTTTG---A-GACAAA-A-TGCCACTGAGTCGTGGACTTTAAAGGAAAAGA-TGCCACT
1 TGTGGGCTTTGAAAAGGA-AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACG
985041 GAGT
65 GAGT
* *
985045 CGTGGACTTTGA
1 TGTGGGCTTTGA
985057 GCAGAGATTG
Statistics
Matches: 637, Mismatches: 37, Indels: 42
0.89 0.05 0.06
Matches are distributed among these distances:
62 18 0.03
63 11 0.02
64 2 0.00
65 15 0.02
66 28 0.04
67 99 0.16
68 176 0.28
69 197 0.31
70 39 0.06
71 32 0.05
72 20 0.03
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (68 bp):
TGTGGGCTTTGAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACGG
AGT
Found at i:985072 original size:31 final size:31
Alignment explanation
Indices: 984984--985147 Score: 235
Period size: 31 Copynumber: 5.3 Consensus size: 31
984974 CCACGTAATT
*
984984 GTGGACTTTGAGACA-A-AATGCCACTGAGTC
1 GTGGACTTTGAG-CAGAGATTGCCACTGAGTC
* * *
985014 GTGGACTTTAAAGGAAAAGA-TGCCACTGAGTC
1 GTGGACTTT-GA-GCAGAGATTGCCACTGAGTC
985046 GTGGACTTTGAGCAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGCAGAGATTGCCACTGAGTC
*
985077 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGCAGAGATTGCCACTGAGTC
985108 GTGGACTTTGAGCAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGCAGAGATTGCCACTGAGTC
985139 GTGGACTTT
1 GTGGACTTT
985148 AAAAAGGTAT
Statistics
Matches: 122, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
30 14 0.11
31 84 0.69
32 23 0.19
33 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (31 bp):
GTGGACTTTGAGCAGAGATTGCCACTGAGTC
Found at i:986093 original size:11 final size:11
Alignment explanation
Indices: 986077--986106 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
986067 GGGGTTGTTC
986077 TTTTTTTTCTT
1 TTTTTTTTCTT
*
986088 TTTTTTTTGTT
1 TTTTTTTTCTT
986099 TTTTTTTT
1 TTTTTTTT
986107 TTTGGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.93
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:986103 original size:14 final size:14
Alignment explanation
Indices: 986077--986110 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
986067 GGGGTTGTTC
986077 TTTTTT-TTCTTTT
1 TTTTTTGTTCTTTT
*
986090 TTTTTTGTTTTTTT
1 TTTTTTGTTCTTTT
986104 TTTTTTG
1 TTTTTTG
986111 GAAAAGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (14 bp):
TTTTTTGTTCTTTT
Found at i:986362 original size:12 final size:12
Alignment explanation
Indices: 986347--986414 Score: 66
Period size: 12 Copynumber: 5.6 Consensus size: 12
986337 GACTTTGCAC
*
986347 TTTTTTTCTGTG
1 TTTTTTTGTGTG
* *
986359 TTTTTTTTTTTG
1 TTTTTTTGTGTG
*
986371 TTTTTTTGT-TT
1 TTTTTTTGTGTG
986382 TTTTTTTGTGTG
1 TTTTTTTGTGTG
*
986394 TTTTTTTTGTTTG
1 -TTTTTTTGTGTG
986407 TTTGTTTT
1 TTT-TTTT
986415 TTTTTTCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
11 10 0.21
12 22 0.47
13 15 0.32
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84
Consensus pattern (12 bp):
TTTTTTTGTGTG
Found at i:986365 original size:13 final size:12
Alignment explanation
Indices: 986347--986403 Score: 66
Period size: 11 Copynumber: 4.9 Consensus size: 12
986337 GACTTTGCAC
*
986347 TTTTTTTCTGTG
1 TTTTTTTTTGTG
986359 TTTTTTTTT-T-
1 TTTTTTTTTGTG
*
986369 TGTTTTTTTGT-
1 TTTTTTTTTGTG
986380 TTTTTTTTTGTG
1 TTTTTTTTTGTG
986392 TGTTTTTTTTGT
1 T-TTTTTTTTGT
986404 TTGTTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
10 8 0.21
11 12 0.31
12 9 0.23
13 10 0.26
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGTG
Found at i:986408 original size:13 final size:13
Alignment explanation
Indices: 986347--986415 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
986337 GACTTTGCAC
* *
986347 TTTTTTTCTGTGT
1 TTTTTTTGTTTGT
986360 TTTTTTT-TTTG-
1 TTTTTTTGTTTGT
986371 TTTTTTTG-TT-T
1 TTTTTTTGTTTGT
*
986382 TTTTTTTGTGTGT
1 TTTTTTTGTTTGT
986395 TTTTTTTGTTTGT
1 TTTTTTTGTTTGT
986408 TTGTTTTT
1 TT-TTTTT
986416 TTTTTCATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
11 17 0.35
12 4 0.08
13 22 0.46
14 5 0.10
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.84
Consensus pattern (13 bp):
TTTTTTTGTTTGT
Found at i:986419 original size:33 final size:33
Alignment explanation
Indices: 986347--986420 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 33
986337 GACTTTGCAC
* * *
986347 TTTTTTTCTGTGTTTTTTTTTTTGTTTTTTTGT
1 TTTTTTTTTGTGTTGTTTTTTTTGTTTGTTTGT
986380 TTTTTTTTTGTG-TGTTTTTTTTGTTTGTTTGT
1 TTTTTTTTTGTGTTGTTTTTTTTGTTTGTTTGT
986412 TTTTTTTTT
1 TTTTTTTTT
986421 CATCACCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 27 0.71
33 11 0.29
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (33 bp):
TTTTTTTTTGTGTTGTTTTTTTTGTTTGTTTGT
Found at i:986433 original size:1 final size:1
Alignment explanation
Indices: 986359--986420 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
986349 TTTTTCTGTG
* * * * * * * *
986359 TTTTTTTTTTTGTTTTTTTGTTTTTTTTTTGTGTGTTTTTTTTGTTTGTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
986421 CATCACCTTT
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:993366 original size:52 final size:52
Alignment explanation
Indices: 993285--993405 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
993275 TGAAAAGTTA
*
993285 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
993337 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
993389 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
993406 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:993418 original size:52 final size:51
Alignment explanation
Indices: 993285--993425 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
993275 TGAAAAGTTA
993285 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
993337 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
993389 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
993426 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:993432 original size:13 final size:13
Alignment explanation
Indices: 993414--993438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
993404 CAAAGATCAG
993414 TGTATCGATACAA
1 TGTATCGATACAA
993427 TGTATCGATACA
1 TGTATCGATACA
993439 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:993519 original size:33 final size:33
Alignment explanation
Indices: 993477--993546 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
993467 GGCAGTAGCT
993477 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
993510 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
993543 TACA
1 TACA
993547 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:993520 original size:13 final size:13
Alignment explanation
Indices: 993502--993526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
993492 CAAAAAAATA
993502 TGTATCGATACAT
1 TGTATCGATACAT
993515 TGTATCGATACA
1 TGTATCGATACA
993527 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:994457 original size:67 final size:68
Alignment explanation
Indices: 994335--994461 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
994325 ATTGGGTTTT
* * *
994335 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGATGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGATGATG
994400 AGA
66 AGA
* * ** *
994403 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGCTATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
994462 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGATGATG
AGA
Found at i:994538 original size:49 final size:49
Alignment explanation
Indices: 994465--995313 Score: 1104
Period size: 49 Copynumber: 17.9 Consensus size: 49
994455 AAGATGAGAA
* *
994465 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
994515 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
994564 TAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
994613 AAAGGTGCCAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 -AA------AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
994669 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
994718 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
994767 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
994810 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
994859 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
994902 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
994951 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
994994 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
995043 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
995086 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
995135 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
995178 AAAGCTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
995227 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
995270 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
995314 GAAGGGTTGC
Statistics
Matches: 707, Mismatches: 53, Indels: 83
0.84 0.06 0.10
Matches are distributed among these distances:
43 233 0.33
44 6 0.01
48 6 0.01
49 408 0.58
50 6 0.01
55 2 0.00
56 46 0.07
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:994840 original size:92 final size:92
Alignment explanation
Indices: 994622--995313 Score: 1294
Period size: 92 Copynumber: 7.5 Consensus size: 92
994612 TAAAGGTGCC
994622 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
*
994687 ATTCAAGGCCAGCTACATTGGACTTAAAGATGA
66 ATTCAAGGCCAGCTATATTGGACTT----A--A
994720 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
994785 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
994812 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
994877 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
994904 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
994969 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
994996 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
995061 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
995088 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
995153 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
*
995180 AGCTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
995245 ATTCAAGGCCAGCTATATTGGACTTAA
66 ATTCAAGGCCAGCTATATTGGACTTAA
* *
995272 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTATATTGGGCTTA
1 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
995314 GAAGGGTTGC
Statistics
Matches: 589, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
92 499 0.85
94 1 0.00
98 89 0.15
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (92 bp):
AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTG
ATTCAAGGCCAGCTATATTGGACTTAA
Found at i:995362 original size:34 final size:34
Alignment explanation
Indices: 995313--995451 Score: 200
Period size: 34 Copynumber: 4.2 Consensus size: 34
995303 TATTGGGCTT
995313 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
995346 AGAAGGGTTTGCCACCGCCTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
995380 AAGAA-GG-TTGCCACCGAC-T-TGTGGACTTTAG
1 -AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
995411 AGAAGGGTTTGCCACCGACTTATGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
995445 A-AAGGGT
1 AGAAGGGT
995452 GAAAGATGCC
Statistics
Matches: 96, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
30 4 0.04
31 13 0.14
32 12 0.12
33 24 0.25
34 39 0.41
35 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (34 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:995410 original size:65 final size:65
Alignment explanation
Indices: 995306--995451 Score: 217
Period size: 65 Copynumber: 2.2 Consensus size: 65
995296 CCAGCTATAT
* * *
995306 TGGGC-TTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGCCTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGACTTTAGAGAAGGGTTTGCCACCGACTTATG
995370 TGGGCTTTAGAAGAAGGTTGCCACCGAC-T-TGTGGACTTTAGAGAAGGGTTTGCCACCGACTTA
1 TGGGCTTTAGAAG--GGTTGCCACCGACTTGTGTGGACTTTAGAGAAGGGTTTGCCACCGACTTA
995433 TG
64 TG
995435 TGGGCTTTAGAAAGGGT
1 TGGGCTTTAG-AAGGGT
995452 GAAAGATGCC
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
64 8 0.11
65 50 0.67
66 4 0.05
67 13 0.17
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (65 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGACTTTAGAGAAGGGTTTGCCACCGACTTATG
Found at i:996436 original size:27 final size:26
Alignment explanation
Indices: 996406--996497 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 26
996396 ACCATTTGTG
996406 TTTGTCAACAATGGTGGTTACTTTATA
1 TTTGTCAA-AATGGTGGTTACTTTATA
* * * *
996433 TTTGTCAAAAATGATGGTTCCTTTTTG
1 TTTGTC-AAAATGGTGGTTACTTTATA
* * *
996460 TTTGTCAAAATTGGTGGCTAATTTTTA
1 TTTGTCAAAA-TGGTGGTTACTTTATA
996487 -TTGT-AAAATGG
1 TTTGTCAAAATGG
996498 GGGAGGATGG
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.06
25 4 0.07
26 8 0.15
27 37 0.69
28 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (26 bp):
TTTGTCAAAATGGTGGTTACTTTATA
Found at i:996548 original size:13 final size:13
Alignment explanation
Indices: 996530--996578 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
996520 GAGGCTCCTT
996530 CATCCCTCTCAAG
1 CATCCCTCTCAAG
*
996543 CATCCCTCTTAAG
1 CATCCCTCTCAAG
*
996556 CATCTCTCTCAAG
1 CATCCCTCTCAAG
*
996569 CATCCTTCTC
1 CATCCCTCTC
996579 TTGTATCCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.20, C:0.43, G:0.06, T:0.31
Consensus pattern (13 bp):
CATCCCTCTCAAG
Found at i:996590 original size:26 final size:25
Alignment explanation
Indices: 996530--996590 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
996520 GAGGCTCCTT
996530 CATCCCTCTCAAGCATCCCTCTTAAG
1 CATCCCTCTCAAGCATCCCTCTT-AG
*
996556 CATCTCTCTCAAGCATCCTTCTCTT-G
1 CATCCCTCTCAAGCATCC--CTCTTAG
*
996582 TATCCCTCT
1 CATCCCTCT
996591 TCAATTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 25 0.83
28 5 0.17
ACGTcount: A:0.18, C:0.41, G:0.07, T:0.34
Consensus pattern (25 bp):
CATCCCTCTCAAGCATCCCTCTTAG
Found at i:997417 original size:2 final size:2
Alignment explanation
Indices: 997404--997433 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
997394 CAATTAAGTC
*
997404 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
997434 CCTTACCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:999157 original size:16 final size:16
Alignment explanation
Indices: 999136--999169 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
999126 AATATTTAGC
999136 ATATAATAGAATTAAA
1 ATATAATAGAATTAAA
**
999152 ATATAATTTAATTAAA
1 ATATAATAGAATTAAA
999168 AT
1 AT
999170 TTAAGTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATAATAGAATTAAA
Found at i:1001976 original size:24 final size:26
Alignment explanation
Indices: 1001916--1001979 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
1001906 AAGCCACCCT
* * *
1001916 TTGTTTGTCAAAAATGGTAGTTACTT
1 TTGTTTGTCAAAAATGGTAGTGAATG
1001942 TGTGTTTGTCAAAAATGGT-G-GAATG
1 T-TGTTTGTCAAAAATGGTAGTGAATG
1001967 TTGTTTGTCAAAA
1 TTGTTTGTCAAAA
1001980 TTTGTGCCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.35
25 3 0.09
26 2 0.06
27 17 0.50
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.42
Consensus pattern (26 bp):
TTGTTTGTCAAAAATGGTAGTGAATG
Found at i:1002064 original size:13 final size:13
Alignment explanation
Indices: 1002042--1002075 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1002032 GGCTCCCTCC
*
1002042 TCCCTCTCAAGTA
1 TCCCTCTCAAGCA
*
1002055 TCCTTCTCAAGCA
1 TCCCTCTCAAGCA
1002068 TCCCTCTC
1 TCCCTCTC
1002076 TTGTATCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.44, G:0.06, T:0.32
Consensus pattern (13 bp):
TCCCTCTCAAGCA
Found at i:1006476 original size:24 final size:26
Alignment explanation
Indices: 1006421--1006484 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
1006411 AAGCCACTCT
* *
1006421 TTGTTTGTCAAAAATGGTGGTTACTT
1 TTGTTTGTCAAAAATGGTGGTCACTG
1006447 TGTGTTTGTCAAAAATGGTGG-CA-TG
1 T-TGTTTGTCAAAAATGGTGGTCACTG
1006472 TTGTTTGTCAAAA
1 TTGTTTGTCAAAA
1006485 TTTGTGGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 12 0.34
25 2 0.06
26 2 0.06
27 19 0.54
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (26 bp):
TTGTTTGTCAAAAATGGTGGTCACTG
Found at i:1006565 original size:13 final size:13
Alignment explanation
Indices: 1006547--1006580 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1006537 GGCTCCCTCC
1006547 TCCCTCTCAAGCA
1 TCCCTCTCAAGCA
1006560 TCCCTCTCAAGCA
1 TCCCTCTCAAGCA
*
1006573 TCCTTCTC
1 TCCCTCTC
1006581 TTGTATCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.47, G:0.06, T:0.29
Consensus pattern (13 bp):
TCCCTCTCAAGCA
Found at i:1007310 original size:27 final size:27
Alignment explanation
Indices: 1007278--1007365 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
1007268 TTACTATAAT
1007278 ATTAAAAATGAATAATATAGTTATGAA
1 ATTAAAAATGAATAATATAGTTATGAA
* * *
1007305 ATT-AAAATCAATTATATAGCATAT-AA
1 ATTAAAAATGAATAATATAG-TTATGAA
* * * *
1007331 TATTAAGAATGAATAAGATAGTTGTGAG
1 -ATTAAAAATGAATAATATAGTTATGAA
1007359 ATTAAAA
1 ATTAAAA
1007366 TCAGTTTTAT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
26 16 0.35
27 17 0.37
28 13 0.28
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (27 bp):
ATTAAAAATGAATAATATAGTTATGAA
Found at i:1007321 original size:26 final size:26
Alignment explanation
Indices: 1007282--1007368 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
1007272 TATAATATTA
*
1007282 AAAATGAATAATATAGTTATGAAATT
1 AAAATCAATAATATAGTTATGAAATT
* *
1007308 AAAATCAATTATATAGCATAT-AATATT
1 AAAATCAATAATATAG-TTATGAA-ATT
* * * *
1007335 AAGAATGAATAAGATAGTTGTGAGATT
1 AA-AATCAATAATATAGTTATGAAATT
1007362 AAAATCA
1 AAAATCA
1007369 GTTTTATAGC
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
26 20 0.43
27 15 0.32
28 12 0.26
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (26 bp):
AAAATCAATAATATAGTTATGAAATT
Found at i:1007363 original size:54 final size:54
Alignment explanation
Indices: 1007272--1007380 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
1007262 GATTAGTTAC
*
1007272 TATAATATTAAAAATGAATAATATAGTTATGAAATTAAAATCAATTATATAGCA
1 TATAATATTAAAAATGAATAAGATAGTTATGAAATTAAAATCAATTATATAGCA
* * * * *
1007326 TATAATATTAAGAATGAATAAGATAGTTGTGAGATTAAAATCAGTTTTATAGCA
1 TATAATATTAAAAATGAATAAGATAGTTATGAAATTAAAATCAATTATATAGCA
1007380 T
1 T
1007381 GTATTTGGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.36
Consensus pattern (54 bp):
TATAATATTAAAAATGAATAAGATAGTTATGAAATTAAAATCAATTATATAGCA
Found at i:1007704 original size:35 final size:36
Alignment explanation
Indices: 1007652--1007740 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 36
1007642 TTCATTAGGT
1007652 AATAATAAAATTAATATAT-T-TATT-ATATTATTATAC
1 AATAATAAAA--AATATATATCTATTGAT-TTATTATAC
* *
1007688 AA-AA-AAAAAAGTATATATCTGTTGATTTATTATAT
1 AATAATAAAAAA-TATATATCTATTGATTTATTATAC
1007723 AATAATAAAAAATATATA
1 AATAATAAAAAATATATA
1007741 ATAAAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
32 2 0.04
33 5 0.11
34 5 0.11
35 15 0.33
36 12 0.27
37 6 0.13
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (36 bp):
AATAATAAAAAATATATATCTATTGATTTATTATAC
Found at i:1007738 original size:17 final size:16
Alignment explanation
Indices: 1007718--1007750 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1007708 GTTGATTTAT
1007718 TATATAATAATAAAAAA
1 TATATAATAA-AAAAAA
1007735 TATATAATAAAAAAAA
1 TATATAATAAAAAAAA
1007751 CAAAAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TATATAATAAAAAAAA
Done.