Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 24 of 126
Found at i:5262697 original size:19 final size:19
Alignment explanation
Indices: 5262662--5262699 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5262652 TTCTATAACT
*
5262662 TAAAATAAAAATTTAATAA
1 TAAAATAAAAATATAATAA
5262681 TAAACATAAAAA-ATAATAA
1 TAAA-ATAAAAATATAATAA
5262700 AATGAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAATAAAAATATAATAA
Found at i:5265861 original size:4 final size:4
Alignment explanation
Indices: 5265852--5265878 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5265842 GTCATTTGTG
5265852 CATT CATT CATT CATT CATT CATT CAT
1 CATT CATT CATT CATT CATT CATT CAT
5265879 CTATTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:5266705 original size:9 final size:8
Alignment explanation
Indices: 5266684--5266709 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5266674 AAGAATGGGA
5266684 TAAAAAAT
1 TAAAAAAT
5266692 TAAAAAAT
1 TAAAAAAT
5266700 TAAAAAAT
1 TAAAAAAT
5266708 TA
1 TA
5266710 TGAATGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAAAAAT
Found at i:5268339 original size:30 final size:29
Alignment explanation
Indices: 5268294--5268353 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
5268284 GATAACAAGT
* **
5268294 TAAAAACAAAAACAAAAAAGGGGAAAAAA
1 TAAAAAAAAAAACAAAAAAGGAAAAAAAA
5268323 TAAAAAAAAAAGACAAAAAAGGAAAAAAAA
1 TAAAAAAAAAA-ACAAAAAAGGAAAAAAAA
5268353 T
1 T
5268354 TGATTATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (29 bp):
TAAAAAAAAAAACAAAAAAGGAAAAAAAA
Found at i:5268340 original size:29 final size:29
Alignment explanation
Indices: 5268294--5268351 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5268284 GATAACAAGT
* * *
5268294 TAAAAACAAAAACAAAAAAGGGGAAAAAA
1 TAAAAAAAAAAACAAAAAAAGGAAAAAAA
5268323 TAAAAAAAAAAGAC-AAAAAAGGAAAAAAA
1 TAAAAAAAAAA-ACAAAAAAAGGAAAAAAA
5268352 ATTGATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.03
Consensus pattern (29 bp):
TAAAAAAAAAAACAAAAAAAGGAAAAAAA
Found at i:5269064 original size:66 final size:66
Alignment explanation
Indices: 5268994--5269150 Score: 174
Period size: 66 Copynumber: 2.4 Consensus size: 66
5268984 TCAGTTTAAT
* * * * * * *
5268994 TGGCATTCAATGAAAGTTTAAACCTAGATTATTTGGCA-CCAATGAAAATTTTAGGCCAAGTTTG
1 TGGCATTCAATGAAAGTTTAAACCTACATTATCTGGCATCCAATGAAAACTTAAGCCCAA-CTTA
5269058 GC
65 GC
* * * *
5269060 TGGCACTCAATGAAAGTTTAAGCCCACATTATCTGGCATCCAGTGAAAACTTAAGCCCAACTTAG
1 TGGCATTCAATGAAAGTTTAAACCTACATTATCTGGCATCCAATGAAAACTTAAGCCCAACTTAG
5269125 C
66 C
* *
5269126 TGGTATCCAATGAAA-TTTAAACCTA
1 TGGCATTCAATGAAAGTTTAAACCTA
5269151 ACTTACCTGG
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
65 8 0.11
66 49 0.66
67 17 0.23
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (66 bp):
TGGCATTCAATGAAAGTTTAAACCTACATTATCTGGCATCCAATGAAAACTTAAGCCCAACTTAG
C
Found at i:5269107 original size:33 final size:32
Alignment explanation
Indices: 5268944--5269180 Score: 106
Period size: 33 Copynumber: 7.2 Consensus size: 32
5268934 TTATGAAAAG
* * *
5268944 ATTTAAGCCTAGCTTAGCTAGCA-CACAATGAA
1 ATTTAAGCCCAACTTAGCTGGCATC-CAATGAA
* ** ** *
5268976 ATTTAAGCTCAGTTTAATTGGCATTCAATGAA
1 ATTTAAGCCCAACTTAGCTGGCATCCAATGAA
* * **
5269008 AGTTTAAACCTAGA-TTATTTGGCA-CCAATGAAA
1 A-TTTAAGCCCA-ACTTAGCTGGCATCCAATG-AA
* * * *
5269041 ATTTTAGGCCAAGTTTGGCTGGCA-CTCAATGAA
1 ATTTAAGCCCAA-CTTAGCTGGCATC-CAATGAA
* *
5269074 AGTTTAAGCCC-ACATTATCTGGCATCCAGTGAAA
1 A-TTTAAGCCCAAC-TTAGCTGGCATCCAATG-AA
* *
5269108 ACTTAAGCCCAACTTAGCTGGTATCCAATGAA
1 ATTTAAGCCCAACTTAGCTGGCATCCAATGAA
* * * * * *
5269140 ATTTAAACCTAACTTACCTGGTATTCAATTAAA
1 ATTTAAGCCCAACTTAGCTGGCATCCAA-TGAA
5269173 ATTTAAGC
1 ATTTAAGC
5269181 TTAGATTAGC
Statistics
Matches: 155, Mismatches: 37, Indels: 25
0.71 0.17 0.12
Matches are distributed among these distances:
31 1 0.01
32 61 0.39
33 75 0.48
34 18 0.12
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (32 bp):
ATTTAAGCCCAACTTAGCTGGCATCCAATGAA
Found at i:5269310 original size:32 final size:32
Alignment explanation
Indices: 5269170--5269319 Score: 108
Period size: 33 Copynumber: 4.6 Consensus size: 32
5269160 GTATTCAATT
* *
5269170 AAAATTTAAG-CTTAGATTAGCTAACACCCAGTA
1 AAAATTTAAGTC-TAGATTAGCTGACACCTA-TA
* * **
5269203 AAAAGTTAAG-CTCAGTTTAGCT-AGCATTTAATA
1 AAAATTTAAGTCT-AGATTAGCTGA-CACCT-ATA
* * * * *
5269236 AAAATTTAAGCCCAGATTAGTTGACACTTAGTG
1 AAAATTTAAGTCTAGATTAGCTGACACCTA-TA
* *
5269269 AAAATTTAAGTCTAGTTTAGCTGATACCTATA
1 AAAATTTAAGTCTAGATTAGCTGACACCTATA
5269301 AAAATTTAAGTCTAGATTA
1 AAAATTTAAGTCTAGATTA
5269320 ATTGGCATCT
Statistics
Matches: 92, Mismatches: 19, Indels: 13
0.74 0.15 0.10
Matches are distributed among these distances:
32 22 0.24
33 67 0.73
34 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (32 bp):
AAAATTTAAGTCTAGATTAGCTGACACCTATA
Found at i:5269553 original size:28 final size:26
Alignment explanation
Indices: 5269492--5269586 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 26
5269482 TCTTGGTTGT
* *
5269492 CATAAAA-GAAAAAAGAAAAAAAAAA
1 CATAAAACAAAAAAAAAAAAAAAAAA
* *
5269517 GATATAACAAGACGAAAAAAAAAAAAAAA
1 CATAAAACAA-A--AAAAAAAAAAAAAAA
5269546 CA-AAAACAAAAAAAAAAATAAAAAAA
1 CATAAAACAAAAAAAAAAA-AAAAAAA
* * *
5269572 GATAGAATAAAAAAA
1 CATAAAACAAAAAAA
5269587 TTCTTCTTAG
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
25 13 0.24
26 9 0.16
27 12 0.22
28 6 0.11
29 15 0.27
ACGTcount: A:0.81, C:0.05, G:0.07, T:0.06
Consensus pattern (26 bp):
CATAAAACAAAAAAAAAAAAAAAAAA
Found at i:5269586 original size:1 final size:1
Alignment explanation
Indices: 5269531--5269571 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
5269521 TAACAAGACG
* * *
5269531 AAAAAAAAAAAAAAACAAAAACAAAAAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5269572 GATAGAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.93, C:0.05, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:5269948 original size:11 final size:12
Alignment explanation
Indices: 5269932--5269964 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5269922 AATACAAAAA
5269932 ATAAAAAAT-AT
1 ATAAAAAATAAT
5269943 ATAAAAAATAGAT
1 ATAAAAAATA-AT
5269956 ATAAAAAAT
1 ATAAAAAAT
5269965 GGGTTTTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
13 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:5287286 original size:69 final size:70
Alignment explanation
Indices: 5287205--5287336 Score: 162
Period size: 69 Copynumber: 1.9 Consensus size: 70
5287195 TTTTTATATT
* *
5287205 TACTATGTTTTTTTGAATA-AAAATATAGTATTT-AAGTTCTCTTTTTTTTTTTTACTAATTTCT
1 TACTATGTTTTTTAGAATATAAAACATAGTATTTGAA-TTCT-TTTTTTTTTTTTACTAATTTCT
5287268 CACTTGA
64 CACTTGA
** * * *
5287275 TACTATG-TTTTTAGGCTATGAAACGTAGTATTTGAATTCTTTTTTTTTTTTTTCTAATTTCT
1 TACTATGTTTTTTAGAATATAAAACATAGTATTTGAATTCTTTTTTTTTTTTTACTAATTTCT
5287337 TACTCAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
69 29 0.55
70 22 0.42
71 2 0.04
ACGTcount: A:0.24, C:0.10, G:0.09, T:0.57
Consensus pattern (70 bp):
TACTATGTTTTTTAGAATATAAAACATAGTATTTGAATTCTTTTTTTTTTTTTACTAATTTCTCA
CTTGA
Found at i:5295897 original size:11 final size:12
Alignment explanation
Indices: 5295870--5295900 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5295860 ATCTAACAGT
5295870 AAAAATGATAAG
1 AAAAATGATAAG
*
5295882 AAAAATGATAGG
1 AAAAATGATAAG
5295894 AAAAATG
1 AAAAATG
5295901 TAAAAGTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (12 bp):
AAAAATGATAAG
Found at i:5302044 original size:12 final size:12
Alignment explanation
Indices: 5302027--5302057 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5302017 ATATTATCTC
*
5302027 AAAGTAAAACTT
1 AAAGTAAAACCT
5302039 AAAGTAAAACCT
1 AAAGTAAAACCT
5302051 AAAGTAA
1 AAAGTAA
5302058 TACCCTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (12 bp):
AAAGTAAAACCT
Found at i:5306027 original size:21 final size:22
Alignment explanation
Indices: 5305978--5306028 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 22
5305968 TAGGAATTTA
*
5305978 ATGATCAAACTTCAAATTAACT
1 ATGATCAAACGTCAAATTAACT
* *
5306000 AT-A-CAAACGTCTAATTCA-T
1 ATGATCAAACGTCAAATTAACT
5306019 ATGATCAAAC
1 ATGATCAAAC
5306029 CTTAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 3 0.12
20 13 0.54
21 6 0.25
22 2 0.08
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (22 bp):
ATGATCAAACGTCAAATTAACT
Found at i:5310035 original size:16 final size:19
Alignment explanation
Indices: 5310010--5310064 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
5310000 ATTTGTGTTG
*
5310010 AAAATATATTATGA-A-A-
1 AAAATTTATTATGACATAT
*
5310026 AAAATTTATTATTACATAT
1 AAAATTTATTATGACATAT
*
5310045 AAAATTTATTATCACATAT
1 AAAATTTATTATGACATAT
5310064 A
1 A
5310065 TTATATGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 12 0.36
17 1 0.03
18 1 0.03
19 19 0.58
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTTATTATGACATAT
Found at i:5310048 original size:19 final size:19
Alignment explanation
Indices: 5310026--5310064 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5310016 TATTATGAAA
*
5310026 AAAATTTATTATTACATAT
1 AAAATTTATTATCACATAT
5310045 AAAATTTATTATCACATAT
1 AAAATTTATTATCACATAT
5310064 A
1 A
5310065 TTATATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATTTATTATCACATAT
Found at i:5314737 original size:37 final size:36
Alignment explanation
Indices: 5314696--5314871 Score: 156
Period size: 37 Copynumber: 4.8 Consensus size: 36
5314686 TAAAATAGAG
* * *
5314696 CATACACTTCATTTCATGCACATATTAATAAATAATA
1 CATACA-TTCATCTCATGCACATCTTAATAGATAATA
* * *
5314733 CATACATTCTATCCCATGCACATTTTAATAGATGGA-A
1 CATACATTC-ATCTCATGCACATCTTAATAGAT-AATA
* * * ***
5314770 CATGCATTCCATATCATGTACATCTTAATAGATGGCA
1 CATACATT-CATCTCATGCACATCTTAATAGATAATA
*
5314807 CATACATTCATCTTATGCACATCTTAATAGATAATA
1 CATACATTCATCTCATGCACATCTTAATAGATAATA
* * *
5314843 TATGCATTCCATCTCATGCACATTTTAAT
1 CATACATT-CATCTCATGCACATCTTAAT
5314872 GGTGGTGTCA
Statistics
Matches: 112, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
36 32 0.29
37 78 0.70
38 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (36 bp):
CATACATTCATCTCATGCACATCTTAATAGATAATA
Found at i:5314848 original size:73 final size:74
Alignment explanation
Indices: 5314709--5314871 Score: 186
Period size: 73 Copynumber: 2.2 Consensus size: 74
5314699 ACACTTCATT
* * *** * *
5314709 TCATGCACATATTAATAAATAATACATACATTCTATCCCATGCACATTTTAATAGATGGAACATG
1 TCATGCACATCTTAATAGATGGCACATACATTCTATCCCATGCACATCTTAATAGATGAAACATG
5314774 CATTCCATA
66 CATTCCATA
* ** *
5314783 TCATGTACATCTTAATAGATGGCACATACATTC-ATCTTATGCACATCTTAATAGAT-AATATAT
1 TCATGCACATCTTAATAGATGGCACATACATTCTATCCCATGCACATCTTAATAGATGAA-ACAT
*
5314846 GCATTCCATC
65 GCATTCCATA
*
5314856 TCATGCACATTTTAAT
1 TCATGCACATCTTAAT
5314872 GGTGGTGTCA
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
72 1 0.01
73 46 0.62
74 27 0.36
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (74 bp):
TCATGCACATCTTAATAGATGGCACATACATTCTATCCCATGCACATCTTAATAGATGAAACATG
CATTCCATA
Found at i:5317234 original size:13 final size:13
Alignment explanation
Indices: 5317218--5317242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5317208 AATTAATTTC
5317218 CAAAAACAAAAAA
1 CAAAAACAAAAAA
5317231 CAAAAACAAAAA
1 CAAAAACAAAAA
5317243 TGCCTTGAAA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAACAAAAAA
Found at i:5318480 original size:28 final size:28
Alignment explanation
Indices: 5318417--5318480 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
5318407 ATCCACTCAA
5318417 AAAAAAAAGTGAAAAAAAAATGAGAAAG
1 AAAAAAAAGTGAAAAAAAAATGAGAAAG
* * *
5318445 TAAGAAAAGTG--AAAGAAATGAAGGAAAG
1 AAAAAAAAGTGAAAAAAAAATG-A-GAAAG
5318473 AAAAAAAA
1 AAAAAAAA
5318481 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 8 0.28
27 1 0.03
28 20 0.69
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (28 bp):
AAAAAAAAGTGAAAAAAAAATGAGAAAG
Found at i:5318510 original size:7 final size:7
Alignment explanation
Indices: 5318469--5318516 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
5318459 GAAATGAAGG
5318469 AAAGAAA
1 AAAGAAA
*
5318476 AAAAAAA
1 AAAGAAA
*
5318483 AAAAAAA
1 AAAGAAA
5318490 AAAGAAA
1 AAAGAAA
*
5318497 GAGAGAAA
1 -AAAGAAA
5318505 AAAGAAA
1 AAAGAAA
*
5318512 GAAGA
1 AAAGA
5318517 GGAAGAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:5322236 original size:140 final size:140
Alignment explanation
Indices: 5321943--5322238 Score: 314
Period size: 140 Copynumber: 2.1 Consensus size: 140
5321933 TTTTAAATAT
* * * *
5321943 TATTTCATAATTTTTGATGCATTAAAAACCCTGATTGCACCCTGGTAGGTGTGAAATTATCAAAA
1 TATTTCATAATTTTTGATACATTAAAAACCCTGATCGCACACTGGAAGGTGTGAAATTATCAAAA
* * *
5322008 TACCCTTAGTGGTATTTTCGTAATCTAACCTTTTCGAGGTTAGTTTTTAGTGAAATATAGATCAT
66 TACCCTTAGTGGTATTTTCGTAATCTAACATTTTCGAGGTTAGTTTTTAGCGAAACATAGATCAT
*
5322073 GGTTTTATAT
131 GGTTTTATAG
* ** *
5322083 TATTTCATGATTTTT-AGTACATTAAAAACTTTGATCGCACATTGGAAGGTGTGAAATTA-CTAA
1 TATTTCATAATTTTTGA-TACATTAAAAACCCTGATCGCACACTGGAAGGTGTGAAATTATC-AA
* * * * * *
5322146 AATACCCTTAG-GGTATTTTTGTAATTTGACATTTT-TATGTTGGTTTTTTA-CGAAACATTCCA
64 AATACCCTTAGTGGTATTTTCGTAATCTAACATTTTCGAGGTTAG-TTTTTAGCGAAACA-T--A
* *
5322208 TATCATGGTTTTATGG
125 GATCATGGTTTTATAG
*
5322224 TATTTCATATTTTTT
1 TATTTCATAATTTTT
5322239 TGTGTATTAA
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
138 10 0.08
139 29 0.23
140 62 0.48
141 27 0.21
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.44
Consensus pattern (140 bp):
TATTTCATAATTTTTGATACATTAAAAACCCTGATCGCACACTGGAAGGTGTGAAATTATCAAAA
TACCCTTAGTGGTATTTTCGTAATCTAACATTTTCGAGGTTAGTTTTTAGCGAAACATAGATCAT
GGTTTTATAG
Found at i:5322258 original size:141 final size:138
Alignment explanation
Indices: 5321943--5322289 Score: 333
Period size: 141 Copynumber: 2.5 Consensus size: 138
5321933 TTTTAAATAT
* * * * *
5321943 TATTTCATAATTTTTGATGCATTAAAAACCCTGATTGCACCCTGGTAGGTGTGAAATTA-TCAAA
1 TATTTCATATTTTTTG-TGCATTAAAAACCTTGATCGCA-CTTGGAAGGTGTGAAATTACT-AAA
* * *
5322007 ATACCCTTAGTGGTATTTTCGTAATCTAACCTTTTCGAGGTTAGTTTTTAGTGAAATATAGATCA
63 ATACCCTTAGTGGTATTTTCGTAATCTAACATTTTCGAGGTTAGTTTTTAGCGAAACATAGATCA
*
5322072 TGGTTTTATAT
128 TGGTTTTATAG
* * *
5322083 TATTTCATGATTTTTAGTACATTAAAAACTTTGATCGCACATTGGAAGGTGTGAAATTACTAAAA
1 TATTTCAT-ATTTTTTGTGCATTAAAAACCTTGATCGCAC-TTGGAAGGTGTGAAATTACTAAAA
* * * * * * *
5322148 TACCCTTAG-GGTATTTTTGTAATTTGACATTTT-TATGTTGGTTTTTTA-CGAAACATTCCATA
64 TACCCTTAGTGGTATTTTCGTAATCTAACATTTTCGAGGTTAG-TTTTTAGCGAAACA-T--AGA
*
5322210 TCATGGTTTTATGG
125 TCATGGTTTTATAG
* * * * * *
5322224 TATTTCATATTTTTTTGTGTATTAAAAGCCTTGATCACATCTTGAAAAGTGTGAAATTTCTAAAA
1 TATTTCATA-TTTTTTGTGCATTAAAAACCTTGATCGCA-CTTGGAAGGTGTGAAATTACTAAAA
5322289 T
64 T
5322290 GACATATGCC
Statistics
Matches: 169, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
138 10 0.06
139 28 0.17
140 56 0.33
141 74 0.44
142 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (138 bp):
TATTTCATATTTTTTGTGCATTAAAAACCTTGATCGCACTTGGAAGGTGTGAAATTACTAAAATA
CCCTTAGTGGTATTTTCGTAATCTAACATTTTCGAGGTTAGTTTTTAGCGAAACATAGATCATGG
TTTTATAG
Found at i:5322498 original size:12 final size:12
Alignment explanation
Indices: 5322483--5322521 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
5322473 TTTTTTTAAA
5322483 AAAATGATGATG
1 AAAATGATGATG
5322495 AAAATGATGATG
1 AAAATGATGATG
5322507 -AAATGATGAATG
1 AAAATGATG-ATG
5322519 AAA
1 AAA
5322522 GAATGGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.32
12 15 0.60
13 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
AAAATGATGATG
Found at i:5323097 original size:49 final size:49
Alignment explanation
Indices: 5323042--5323459 Score: 301
Period size: 49 Copynumber: 8.6 Consensus size: 49
5323032 ACAACCTAAG
* * *
5323042 CTTTTTCAAAGTGAGTTTCTTAAAGTTCCCCGCTTATGTTTATAGGAGC
1 CTTTTTCAAAGTGAGATTCTTAAAGTTCCCTGCCTATGTTTATAGGAGC
* * * * * **
5323091 CCTTTTCAAAAG-AAAATT-TTAAAGTTCCTTGCCTATGCTTATAAAAGC
1 CTTTTTC-AAAGTGAGATTCTTAAAGTTCCCTGCCTATGTTTATAGGAGC
* * *
5323139 CTTTTTCAATGTGAGATTCTTAAAGTTCCCTACCTATGTTTATAAGAGC
1 CTTTTTCAAAGTGAGATTCTTAAAGTTCCCTGCCTATGTTTATAGGAGC
* * * * * *
5323188 TTTTTTCAACGTAAGA-TCTTTAAAATTCCCTGCCTATGTCTATAGGTGC
1 CTTTTTCAAAGTGAGATTC-TTAAAGTTCCCTGCCTATGTTTATAGGAGC
* * * * * *
5323237 TTTTTTCAAATTGAGATTTTTAAAGTTCCCTGCCCATATTTATAGGAAC
1 CTTTTTCAAAGTGAGATTCTTAAAGTTCCCTGCCTATGTTTATAGGAGC
* * * **
5323286 CTTTTTCAAAATGAGATTATTAAAGTTCCCTACCT-TGTTTATAATAGC
1 CTTTTTCAAAGTGAGATTCTTAAAGTTCCCTGCCTATGTTTATAGGAGC
* * * * * * **
5323334 CTTTTTCAAACTAAAATTTTTAAAGTTTCCT-CCTTATATTTATAAAAGC
1 CTTTTTCAAAGTGAGATTCTTAAAGTTCCCTGCC-TATGTTTATAGGAGC
*** * *** * *
5323383 C-TTTTCAAAAAAAGATTTTTAAAGTTATTTGCCTATGTTTAGAGGAGT
1 CTTTTTCAAAGTGAGATTCTTAAAGTTCCCTGCCTATGTTTATAGGAGC
* * *
5323431 ATTTTTCAAATTGAAAATT-TTAAAGTTCC
1 CTTTTTCAAAGTG-AGATTCTTAAAGTTCC
5323460 ATATCTATAC
Statistics
Matches: 289, Mismatches: 70, Indels: 20
0.76 0.18 0.05
Matches are distributed among these distances:
47 5 0.02
48 105 0.36
49 170 0.59
50 9 0.03
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (49 bp):
CTTTTTCAAAGTGAGATTCTTAAAGTTCCCTGCCTATGTTTATAGGAGC
Found at i:5323505 original size:48 final size:44
Alignment explanation
Indices: 5323448--5323553 Score: 137
Period size: 43 Copynumber: 2.4 Consensus size: 44
5323438 AAATTGAAAA
*
5323448 TTTTAAAGTTCCATATCTATACTTATAGGAGTCA-TTTCAGATAGAGAC
1 TTTTAAAGTTCC--AT-TATACTTATA-AAGT-ATTTTCAGATAGAGAC
5323496 TTTTAAAGTT-CATTATACTTATAAAGTATTTTCAGATAGAGAC
1 TTTTAAAGTTCCATTATACTTATAAAGTATTTTCAGATAGAGAC
5323539 TTTTAAAGTT-CATTA
1 TTTTAAAGTTCCATTA
5323554 CCTATGTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
42 1 0.02
43 32 0.57
44 10 0.18
45 2 0.04
47 1 0.02
48 10 0.18
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (44 bp):
TTTTAAAGTTCCATTATACTTATAAAGTATTTTCAGATAGAGAC
Found at i:5323534 original size:43 final size:44
Alignment explanation
Indices: 5323465--5323553 Score: 146
Period size: 43 Copynumber: 2.0 Consensus size: 44
5323455 GTTCCATATC
*
5323465 TATACTTATAGGAGTCATTTCAGATAGAGACTTTTAAAGTTCAT
1 TATACTTATAGAAGTCATTTCAGATAGAGACTTTTAAAGTTCAT
5323509 TATACTTATA-AAGT-ATTTTCAGATAGAGACTTTTAAAGTTCAT
1 TATACTTATAGAAGTCA-TTTCAGATAGAGACTTTTAAAGTTCAT
5323552 TA
1 TA
5323554 CCTATGTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
42 1 0.02
43 32 0.74
44 10 0.23
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (44 bp):
TATACTTATAGAAGTCATTTCAGATAGAGACTTTTAAAGTTCAT
Found at i:5323550 original size:21 final size:21
Alignment explanation
Indices: 5323483--5323550 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 21
5323473 TAGGAGTCAT
5323483 TTCAGATAGAGACTTTTAAAG
1 TTCAGATAGAGACTTTTAAAG
* * *
5323504 TTC--AT-TATACTTATAAAG
1 TTCAGATAGAGACTTTTAAAG
5323522 TATTTTCAGATAGAGACTTTTAAAG
1 ----TTCAGATAGAGACTTTTAAAG
5323547 TTCA
1 TTCA
5323551 TTACCTATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
18 10 0.29
19 2 0.06
21 7 0.21
22 3 0.09
24 2 0.06
25 10 0.29
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (21 bp):
TTCAGATAGAGACTTTTAAAG
Found at i:5323648 original size:23 final size:21
Alignment explanation
Indices: 5323615--5323656 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
5323605 TTTAGTTTTC
5323615 AAAAAATAAAAAAAAAAACAA
1 AAAAAATAAAAAAAAAAACAA
5323636 AAAAAATGAAAAAGAAAAAAC
1 AAAAAAT-AAAAA-AAAAAAC
5323657 CAACAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAAATAAAAAAAAAAACAA
Found at i:5324318 original size:99 final size:99
Alignment explanation
Indices: 5324209--5324406 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
5324199 GTGAAATTAC
*
5324209 CAAAGTACCTTTAAGGGTATTTTCATAATTTAATATTTTCGAGATTAGTTTTTTGTGAAACACTC
1 CAAAGTACCTTTAAGGGTATTTTCATAATTTAACATTTTCGAGATTAGTTTTTTGTGAAACACTC
5324274 TAGATTATGGTTTTATATTATTTCAATTTTGTAG
66 TAGATTATGGTTTTATATTATTTCAATTTTGTAG
*
5324308 CAAAGTACCTTTAAGGGTATTTTCATAATTTAACCTTTTCGAGATTAGTTTTTTGTGAAACACTC
1 CAAAGTACCTTTAAGGGTATTTTCATAATTTAACATTTTCGAGATTAGTTTTTTGTGAAACACTC
5324373 TAGATTATGGTTTTATATTATTTCAATTTTGTAG
66 TAGATTATGGTTTTATATTATTTCAATTTTGTAG
5324407 TGCCTTAAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (99 bp):
CAAAGTACCTTTAAGGGTATTTTCATAATTTAACATTTTCGAGATTAGTTTTTTGTGAAACACTC
TAGATTATGGTTTTATATTATTTCAATTTTGTAG
Found at i:5325145 original size:23 final size:23
Alignment explanation
Indices: 5325084--5325146 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
5325074 GTATAATTCT
5325084 TTTACCTTTGATTTTTCATAGCATA
1 TTTACCTTTGA-TTTTCATAGCA-A
* *
5325109 TTTACC-ATGTTTTTCATAGC-A
1 TTTACCTTTGATTTTCATAGCAA
5325130 TTTAGCCTTTGATTTTC
1 TTTA-CCTTTGATTTTC
5325147 TCATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 5 0.16
22 2 0.06
23 17 0.53
24 2 0.06
25 6 0.19
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (23 bp):
TTTACCTTTGATTTTCATAGCAA
Found at i:5326300 original size:17 final size:17
Alignment explanation
Indices: 5326278--5326325 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
5326268 CCCAAACTCT
5326278 AACCCAAACCTTAAACA
1 AACCCAAACCTTAAACA
5326295 AACCCAAACCTTAAACA
1 AACCCAAACCTTAAACA
5326312 AACCCAAACCTTAA
1 AACCCAAACCTTAA
5326326 CCTAGACCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.12
Consensus pattern (17 bp):
AACCCAAACCTTAAACA
Found at i:5326342 original size:20 final size:20
Alignment explanation
Indices: 5326317--5326360 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
5326307 AAACAAACCC
5326317 AAACCTTAACCTAGACCCTA
1 AAACCTTAACCTAGACCCTA
5326337 AAACCTTAACCTAGACCCTA
1 AAACCTTAACCTAGACCCTA
5326357 AAAC
1 AAAC
5326361 TATCCCAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.34, G:0.05, T:0.18
Consensus pattern (20 bp):
AAACCTTAACCTAGACCCTA
Found at i:5328008 original size:37 final size:37
Alignment explanation
Indices: 5327966--5328039 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
5327956 TAAAATTTTT
* *
5327966 TTGGTGTCGAAATCTGACATTTTC-TTAAAACTCTCTC
1 TTGGTGGCAAAATCTGAC-TTTTCATTAAAACTCTCTC
5328003 TTGGTGGCAAAATCTGACTTTTCATTAAAACTCTCTC
1 TTGGTGGCAAAATCTGACTTTTCATTAAAACTCTCTC
5328040 GATGATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 5 0.15
37 29 0.85
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTGGTGGCAAAATCTGACTTTTCATTAAAACTCTCTC
Found at i:5328051 original size:35 final size:35
Alignment explanation
Indices: 5327974--5328052 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 35
5327964 TTTTGGTGTC
* *
5327974 GAAATCTGACATTTTCTTAAAACTCTCTCTTGGTG
1 GAAATCTGACATTTTCTTAAAACTCTCTCATGATG
5328009 GCAAAATCTGAC-TTTTCATTAAAACTCTCTCGATGAT-
1 G--AAATCTGACATTTTC-TTAAAACTCTCTC-ATGATG
5328046 GAAATCT
1 GAAATCT
5328053 TACCTCTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
35 7 0.18
36 5 0.13
37 23 0.61
38 3 0.08
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (35 bp):
GAAATCTGACATTTTCTTAAAACTCTCTCATGATG
Found at i:5328656 original size:17 final size:16
Alignment explanation
Indices: 5328621--5328675 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
5328611 CTTTGAAAGT
5328621 AAAAAAACAAAAACA-A
1 AAAAAAAC-AAAACATA
5328637 AAACAAAACAAAACATA
1 AAA-AAAACAAAACATA
* *
5328654 AAAAAGAATAAAAAATA
1 AAAAA-AACAAAACATA
5328671 AAAAA
1 AAAAA
5328676 CAAACAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 11 0.32
17 23 0.68
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05
Consensus pattern (16 bp):
AAAAAAACAAAACATA
Found at i:5331032 original size:21 final size:21
Alignment explanation
Indices: 5331007--5331047 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5330997 ACCATAAACC
* *
5331007 AAAACTTTAACCCCAAACCTT
1 AAAACTATAAACCCAAACCTT
*
5331028 AAAACTATAAACCCTAACCT
1 AAAACTATAAACCCAAACCT
5331048 AGACCTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAACTATAAACCCAAACCTT
Found at i:5337238 original size:32 final size:33
Alignment explanation
Indices: 5337202--5337268 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
5337192 AAGTAAATAA
*
5337202 TAGTAACA-TGTGTATACTAAACATTTTTCATG
1 TAGTAACATTGTGTATACTAAAAATTTTTCATG
5337234 TAGTAACATTTGTGTATACTAAAAATTTTTCATG
1 TAGTAACA-TTGTGTATACTAAAAATTTTTCATG
5337268 T
1 T
5337269 TACATAAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 8 0.25
34 24 0.75
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (33 bp):
TAGTAACATTGTGTATACTAAAAATTTTTCATG
Found at i:5338176 original size:29 final size:30
Alignment explanation
Indices: 5338131--5338190 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
5338121 AATGTAATAA
5338131 TTTTTTTTATATGATATTATAAA-AATAAAT
1 TTTTTTTTATATGATATTATAAACAA-AAAT
*
5338161 TTTTTTCTTA-AT-ATATTTTAAACAAAAAT
1 TTTTTT-TTATATGATATTATAAACAAAAAT
5338190 T
1 T
5338191 ACATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 14 0.52
30 10 0.37
31 3 0.11
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (30 bp):
TTTTTTTTATATGATATTATAAACAAAAAT
Found at i:5338365 original size:71 final size:72
Alignment explanation
Indices: 5338247--5338386 Score: 228
Period size: 71 Copynumber: 1.9 Consensus size: 72
5338237 AAAAGCATAA
5338247 TATTTGTTAAAAATATGAAAAAAAAATTACTTTTCATAATTCAACAAAAACAATGTTTTTAAGAT
1 TATTTGTTAAAAATATG-AAAAAAAATTACTTTTCATAATTCAACAAAAACAATGTTTTTAAGAT
5338312 AAAATTGT
65 AAAATTGT
* * * *
5338320 TATTTGTTAAAAATATG-AAATAAATTATTTTTCATAATTTAACAAAAACAATGTTTTTAGGATA
1 TATTTGTTAAAAATATGAAAAAAAATTACTTTTCATAATTCAACAAAAACAATGTTTTTAAGATA
5338384 AAA
66 AAA
5338387 AAATGTAATC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 46 0.73
73 17 0.27
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (72 bp):
TATTTGTTAAAAATATGAAAAAAAATTACTTTTCATAATTCAACAAAAACAATGTTTTTAAGATA
AAATTGT
Found at i:5340683 original size:9 final size:9
Alignment explanation
Indices: 5340665--5340698 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5340655 GAATATGCAT
*
5340665 AAAAAGAAA
1 AAAAATAAA
5340674 AAAAATAAA
1 AAAAATAAA
5340683 AAAAGATAAA
1 AAAA-ATAAA
5340693 AAAAAT
1 AAAAAT
5340699 CTATTAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (9 bp):
AAAAATAAA
Found at i:5342024 original size:35 final size:35
Alignment explanation
Indices: 5341982--5342055 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
5341972 TTATAATGAC
* *
5341982 TTTTATTT-TTAAAA-ATTTCTTTTTTTATTTTTATT
1 TTTTATTTATAAAAAGATTT-TTTATTT-TTTTTATT
5342017 TTTTATTTACTAAAAAGATTTTTTATTTTTTTTATT
1 TTTTATTTA-TAAAAAGATTTTTTATTTTTTTTATT
5342053 TTT
1 TTT
5342056 ATACACTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 8 0.24
36 11 0.32
37 11 0.32
38 4 0.12
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (35 bp):
TTTTATTTATAAAAAGATTTTTTATTTTTTTTATT
Found at i:5342118 original size:25 final size:24
Alignment explanation
Indices: 5342072--5342121 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5342062 TTGTTTTGAA
*
5342072 AACTTATTTAAAAAGATTTTTTTT
1 AACTTATTTAAAAAGATATTTTTT
* *
5342096 AACTTATTTGAAAAGGTCATTTTTT
1 AACTTATTTAAAAAGAT-ATTTTTT
5342121 A
1 A
5342122 TATATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
AACTTATTTAAAAAGATATTTTTT
Found at i:5342172 original size:19 final size:19
Alignment explanation
Indices: 5342150--5342195 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5342140 AAACAAAAAT
*
5342150 AATTTTTACAAAATAATA-A
1 AATTTTTA-AAAATAAAACA
5342169 AATTTCTTAAAAATAAAACA
1 AATTT-TTAAAAATAAAACA
5342189 AATTTTT
1 AATTTTT
5342196 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTTTAAAAATAAAACA
Found at i:5342193 original size:20 final size:19
Alignment explanation
Indices: 5342139--5342195 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
5342129 TTATTTTTTT
*
5342139 AAAACAAAAATAATTTTTAC
1 AAAATAAAAA-AATTTTTAC
*
5342159 AAAATAATAAAATTTCTTA-
1 AAAATAAAAAAATTT-TTAC
5342178 AAAATAAAACAAATTTTT
1 AAAATAAAA-AAATTTTT
5342196 TTTAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATAAAAAAATTTTTAC
Found at i:5343062 original size:3 final size:3
Alignment explanation
Indices: 5343056--5343163 Score: 118
Period size: 3 Copynumber: 37.7 Consensus size: 3
5343046 AAAAGAAGAA
5343056 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
5343104 AAT GAT AAT GAT -AT TAT AAT -AT TAT AAT AAT -AT TAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
5343148 -AT AAC AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AA
5343164 AACACGATCC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
2 10 0.11
3 81 0.89
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5347152 original size:19 final size:21
Alignment explanation
Indices: 5347107--5347152 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
5347097 TATTAAAATA
*
5347107 TAAAATATATATTTAATTTAAT
1 TAAAATATATAATT-ATTTAAT
5347129 T-AAATATATAATT-TTT-AT
1 TAAAATATATAATTATTTAAT
5347147 TAAAAT
1 TAAAAT
5347153 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 3 0.14
19 7 0.32
21 11 0.50
22 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAATATATAATTATTTAAT
Found at i:5347200 original size:19 final size:19
Alignment explanation
Indices: 5347158--5347203 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
5347148 AAAATTTTAA
5347158 ATTATATTATTATGATTTTT
1 ATTATATTATTAT-ATTTTT
5347178 -TTATATTATTAT-TTTTGT
1 ATTATATTATTATATTTT-T
5347196 ATTATATT
1 ATTATATT
5347204 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.17
18 1 0.04
19 19 0.79
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTATATTATTATATTTTT
Found at i:5347203 original size:16 final size:17
Alignment explanation
Indices: 5347162--5347200 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
5347152 TTTTAAATTA
* *
5347162 TATTATTATGATTTTTT
1 TATTATTATTATTTTTG
5347179 TA-TATTATTATTTTTG
1 TATTATTATTATTTTTG
5347195 TATTAT
1 TATTAT
5347201 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TATTATTATTATTTTTG
Found at i:5348264 original size:19 final size:20
Alignment explanation
Indices: 5348219--5348265 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5348209 AAGTTTTTCA
*
5348219 AAAAATGTATAAAATGAATC
1 AAAAATTTATAAAATGAATC
*
5348239 AATAAATTTA-AAAATGATTC
1 AA-AAATTTATAAAATGAATC
5348259 AAAAATT
1 AAAAATT
5348266 GATGTCACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 13 0.54
21 6 0.25
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (20 bp):
AAAAATTTATAAAATGAATC
Found at i:5348685 original size:14 final size:14
Alignment explanation
Indices: 5348662--5348693 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5348652 TTCCAGAATT
5348662 GTGATAGGTGATTA
1 GTGATAGGTGATTA
*
5348676 GTGATTGGTGATTA
1 GTGATAGGTGATTA
5348690 GTGA
1 GTGA
5348694 GCGAAGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (14 bp):
GTGATAGGTGATTA
Found at i:5351298 original size:20 final size:20
Alignment explanation
Indices: 5351275--5351382 Score: 103
Period size: 20 Copynumber: 5.4 Consensus size: 20
5351265 AACAATATAT
* *
5351275 TAATTATGCAAATATATTAA
1 TAATCATGCAAATATATAAA
* *
5351295 TAATCATGCAATTA-ACAAA
1 TAATCATGCAAATATATAAA
* *
5351314 TAATTATGCAATTAATATTAAA
1 TAATCATGCAAAT-ATA-TAAA
**
5351336 -AATCATGCAAGCATATAAA
1 TAATCATGCAAATATATAAA
*
5351355 TAATCATGCAAGTATATAAA
1 TAATCATGCAAATATATAAA
5351375 TAATCATG
1 TAATCATG
5351383 AAGATAATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
19 19 0.26
20 42 0.57
21 10 0.14
22 3 0.04
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.32
Consensus pattern (20 bp):
TAATCATGCAAATATATAAA
Found at i:5351304 original size:40 final size:40
Alignment explanation
Indices: 5351260--5351382 Score: 124
Period size: 40 Copynumber: 3.1 Consensus size: 40
5351250 AAAATAAATT
*
5351260 ATGCAAACAATATATTAATTATGCAAATATATTAATAATC
1 ATGCAAACAATATAATAATTATGCAAATATATTAATAATC
** * * *
5351300 ATGCAATTAACA-AATAATTATGCAATTAATATTAAAAATC
1 ATGCAAACAATATAATAATTATGCAAAT-ATATTAATAATC
* * * *
5351340 ATGCAAGC-ATATAAATAATCATGCAAGTATATAAATAATC
1 ATGCAAACAATAT-AATAATTATGCAAATATATTAATAATC
5351380 ATG
1 ATG
5351383 AAGATAATTA
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
39 15 0.22
40 39 0.58
41 13 0.19
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (40 bp):
ATGCAAACAATATAATAATTATGCAAATATATTAATAATC
Found at i:5351585 original size:10 final size:10
Alignment explanation
Indices: 5351572--5351601 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5351562 CAAAATAAAA
5351572 AAATCAAATT
1 AAATCAAATT
*
5351582 AAATCAAATC
1 AAATCAAATT
5351592 AAATCAAATT
1 AAATCAAATT
5351602 TGAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATCAAATT
Found at i:5360925 original size:90 final size:90
Alignment explanation
Indices: 5360804--5360978 Score: 280
Period size: 90 Copynumber: 1.9 Consensus size: 90
5360794 TGAAAAGCCT
* * * *
5360804 ATAGATTAGCCCTGTTATAGGATTGATCAATTCTTCATGTAGCATTTTTTTAAATGAATTCTGAA
1 ATAGATTAGCCCTATTACAGGATTGATCAATTCTTCAGGTAGCATTTTTTTAAACGAATTCT-AA
5360869 A-GAATTATATGCAAAATGATAACCA
65 AGGAATTATATGCAAAATGATAACCA
*
5360894 ATAGATTAGTCCTATTACAGGATTGATCAATTCTTCAGGTAGCATTTTTTTAAACGAATTCTAAA
1 ATAGATTAGCCCTATTACAGGATTGATCAATTCTTCAGGTAGCATTTTTTTAAACGAATTCTAAA
*
5360959 GGAATTTTATGCAAAATGAT
66 GGAATTATATGCAAAATGAT
5360979 CATTCCAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 3 0.04
90 75 0.96
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (90 bp):
ATAGATTAGCCCTATTACAGGATTGATCAATTCTTCAGGTAGCATTTTTTTAAACGAATTCTAAA
GGAATTATATGCAAAATGATAACCA
Found at i:5361763 original size:32 final size:32
Alignment explanation
Indices: 5361726--5361789 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
5361716 ATTATATCTG
* * *
5361726 GTCTACTTGAAGTATGATATAACATTGAGCCA
1 GTCTACTTGAAATAAGATATAACATTAAGCCA
*
5361758 GTCTACTTGAAATAAGATATAGCATTAAGCCA
1 GTCTACTTGAAATAAGATATAACATTAAGCCA
5361790 ATCATAAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (32 bp):
GTCTACTTGAAATAAGATATAACATTAAGCCA
Found at i:5367947 original size:21 final size:22
Alignment explanation
Indices: 5367910--5367950 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5367900 GTTACACCCT
*
5367910 TTTGATCATTTGACTTTTAACC
1 TTTGATCATTAGACTTTTAACC
5367932 TTTGATC-TTAGACTTTTAA
1 TTTGATCATTAGACTTTTAA
5367951 TTTTGACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (22 bp):
TTTGATCATTAGACTTTTAACC
Found at i:5376001 original size:19 final size:19
Alignment explanation
Indices: 5375977--5376020 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
5375967 CATAAAGATT
5375977 AAGGATTATAGGTGTAAAG
1 AAGGATTATAGGTGTAAAG
5375996 AAGGATTATAGGTGTAAAG
1 AAGGATTATAGGTGTAAAG
5376015 AAGGAT
1 AAGGAT
5376021 AAGTTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (19 bp):
AAGGATTATAGGTGTAAAG
Found at i:5377107 original size:16 final size:16
Alignment explanation
Indices: 5377088--5377126 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
5377078 ATCATAATCA
5377088 AATCATGCAATCATGT
1 AATCATGCAATCATGT
5377104 AATCATGCAATCATGT
1 AATCATGCAATCATGT
5377120 AATCATG
1 AATCATG
5377127 TAAATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (16 bp):
AATCATGCAATCATGT
Found at i:5377127 original size:8 final size:8
Alignment explanation
Indices: 5377088--5377129 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
5377078 ATCATAATCA
*
5377088 AATCATGC
1 AATCATGT
5377096 AATCATGT
1 AATCATGT
*
5377104 AATCATGC
1 AATCATGT
5377112 AATCATGT
1 AATCATGT
5377120 AATCATGT
1 AATCATGT
5377128 AA
1 AA
5377130 ATATCATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (8 bp):
AATCATGT
Found at i:5377324 original size:20 final size:20
Alignment explanation
Indices: 5377236--5377346 Score: 95
Period size: 20 Copynumber: 5.5 Consensus size: 20
5377226 AAAACCAAAA
5377236 AAATAAATCATGCAAAGAATAT
1 AAAT-AATCATGC-AAGAATAT
* * **
5377258 -AATAATTATACAATTA-AT
1 AAATAATCATGCAAGAATAT
*
5377276 AAATAATCATGCAATTAATATT
1 AAATAATCATGCAA-GAATA-T
*
5377298 AAA-AATCATGCAAGCATAT
1 AAATAATCATGCAAGAATAT
5377317 AAATAATCATGCAAGTAA-AT
1 AAATAATCATGCAAG-AATAT
5377337 AAATAATCAT
1 AAATAATCAT
5377347 AGAGATAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
18 2 0.03
19 18 0.25
20 34 0.47
21 15 0.21
22 4 0.05
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (20 bp):
AAATAATCATGCAAGAATAT
Found at i:5377356 original size:20 final size:20
Alignment explanation
Indices: 5377273--5377346 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
5377263 TTATACAATT
*
5377273 AATAAATAATCATGCAATTA
1 AATAAATAATCATGCAAGTA
*
5377293 ATATTAAA-AATCATGCAAGCA
1 A-A-TAAATAATCATGCAAGTA
*
5377314 TATAAATAATCATGCAAGTA
1 AATAAATAATCATGCAAGTA
5377334 AATAAATAATCAT
1 AATAAATAATCAT
5377347 AGAGATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 4 0.09
20 26 0.57
21 12 0.26
22 4 0.09
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (20 bp):
AATAAATAATCATGCAAGTA
Found at i:5378551 original size:6 final size:6
Alignment explanation
Indices: 5378540--5378573 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5378530 AATAACATTA
* *
5378540 AAATTC AAATTC AAATTC AAATTT GAATTC AAAT
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAAT
5378574 CACAATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (6 bp):
AAATTC
Found at i:5378580 original size:12 final size:12
Alignment explanation
Indices: 5378541--5378609 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
5378531 ATAACATTAA
5378541 AATTCAAATTCA-
1 AATTCAAA-TCAG
**
5378553 AATTCAAATTTG
1 AATTCAAATCAG
*
5378565 AATTCAAATCAC
1 AATTCAAATCAG
*
5378577 AATTAAAATCAG
1 AATTCAAATCAG
* *
5378589 AATTGAAATCAA
1 AATTCAAATCAG
*
5378601 AATTAAAAT
1 AATTCAAAT
5378610 ATTTGGGCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
11 1 0.02
12 45 0.98
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (12 bp):
AATTCAAATCAG
Found at i:5378580 original size:24 final size:23
Alignment explanation
Indices: 5378541--5378609 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
5378531 ATAACATTAA
* **
5378541 AATTCAAATTCAAATTCAAATTTG
1 AATTCAAA-TCAAATTAAAATCAG
5378565 AATTCAAATCACAATTAAAATCAG
1 AATTCAAATCA-AATTAAAATCAG
*
5378589 AATTGAAATCAAAATTAAAAT
1 AATTCAAATC-AAATTAAAAT
5378610 ATTTGGGCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.08
24 35 0.90
25 1 0.03
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (23 bp):
AATTCAAATCAAATTAAAATCAG
Found at i:5387318 original size:15 final size:15
Alignment explanation
Indices: 5387294--5387335 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
5387284 TTCTCTCTAT
* *
5387294 TAAAACATTTTTAAA
1 TAAAAAATTTTGAAA
*
5387309 TAAAAAATTTTGACA
1 TAAAAAATTTTGAAA
5387324 T-AAAAATTTTGA
1 TAAAAAATTTTGA
5387336 CAATCTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (15 bp):
TAAAAAATTTTGAAA
Found at i:5387328 original size:14 final size:14
Alignment explanation
Indices: 5387311--5387337 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5387301 TTTTTAAATA
5387311 AAAAATTTTGACAT
1 AAAAATTTTGACAT
5387325 AAAAATTTTGACA
1 AAAAATTTTGACA
5387338 ATCTTTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAAATTTTGACAT
Found at i:5399555 original size:30 final size:30
Alignment explanation
Indices: 5399514--5399572 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
5399504 ATTATTGGAT
* *
5399514 ATTCATGTTTTAGGTAGTTTTTAGCAAAAA
1 ATTCATGTTTTAGGCAGTTTCTAGCAAAAA
*
5399544 ATTCATTTTTTAGGCAGTTTCTAGCAAAA
1 ATTCATGTTTTAGGCAGTTTCTAGCAAAA
5399573 TGGACTACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (30 bp):
ATTCATGTTTTAGGCAGTTTCTAGCAAAAA
Found at i:5411401 original size:11 final size:11
Alignment explanation
Indices: 5411369--5411442 Score: 78
Period size: 12 Copynumber: 6.4 Consensus size: 11
5411359 CTGAAACTCA
5411369 AAAAATAAAAAG
1 AAAAA-AAAAAG
5411381 AAACAAAAAAAG
1 AAA-AAAAAAAG
*
5411393 AAAACAAAAAAT
1 AAAA-AAAAAAG
5411405 AAAAAAAAAAG
1 AAAAAAAAAAG
*
5411416 -GAAAAAAAAG
1 AAAAAAAAAAG
5411426 AACAAAAAAAGAG
1 AA-AAAAAAA-AG
5411439 AAAA
1 AAAA
5411443 CCTAGATTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.17
11 7 0.13
12 31 0.58
13 6 0.11
ACGTcount: A:0.84, C:0.04, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5411410 original size:31 final size:30
Alignment explanation
Indices: 5411367--5411434 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
5411357 GCCTGAAACT
*
5411367 CAAAAAATAAAAAGAAA-CAAAAAAAGAAAA
1 CAAAAAATAAAAAAAAAGCAAAAAAA-AAAA
* *
5411397 CAAAAAATAAAAAAAAAAGGAAAAAAAAGAA
1 CAAAAAAT-AAAAAAAAAGCAAAAAAAAAAA
5411428 CAAAAAA
1 CAAAAAA
5411435 AGAGAAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 8 0.24
31 18 0.55
32 7 0.21
ACGTcount: A:0.84, C:0.06, G:0.07, T:0.03
Consensus pattern (30 bp):
CAAAAAATAAAAAAAAAGCAAAAAAAAAAA
Found at i:5411420 original size:9 final size:9
Alignment explanation
Indices: 5411375--5411434 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
5411365 CTCAAAAAAT
5411375 AAAAAGAAA
1 AAAAAGAAA
*
5411384 CAAAA-AAA
1 AAAAAGAAA
* *
5411392 GAAAACAAA
1 AAAAAGAAA
5411401 AAATAA-AAA
1 AAA-AAGAAA
5411410 AAAAAGGAAA
1 AAAAA-GAAA
5411420 AAAAAGAACA
1 AAAAAGAA-A
5411430 AAAAA
1 AAAAA
5411435 AGAGAAAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
8 9 0.21
9 18 0.42
10 16 0.37
ACGTcount: A:0.85, C:0.05, G:0.08, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:5412761 original size:46 final size:45
Alignment explanation
Indices: 5412711--5412909 Score: 191
Period size: 47 Copynumber: 4.3 Consensus size: 45
5412701 CTTTAGTGAA
* *
5412711 AAGAGCTTTTAATTTTATTTTCAAAAGTTATCAAGTCTTTAATTAG
1 AAGAGCTTTTAATTTTATTTTCAAAAGTTAT-AAGTCTCTAATGAG
**
5412757 AAGAGCTTTTAATTTTAATTTTCAAAAGTTATAGAACCTCTAATGAG
1 AAGAGCTTTTAATTTT-ATTTTCAAAAGTTATA-AGTCTCTAATGAG
* ** * *
5412804 AGGATTTTTTTAATTTTATTTTCAAAAGTTGTGAAGTCACTAATGAG
1 AAGA-GCTTTTAATTTTATTTTCAAAAGTTAT-AAGTCTCTAATGAG
* * * * * * *
5412851 AGGAGTTTTTAATTTTATTTTTAAAAGTTGTGGAGCCTCTAATGAA
1 AAGAGCTTTTAATTTTATTTTCAAAAGTTAT-AAGTCTCTAATGAG
5412897 AAGAGTCTTTTAA
1 AAGAG-CTTTTAA
5412910 AAAGTTGTGC
Statistics
Matches: 129, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
46 57 0.44
47 61 0.47
48 11 0.09
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (45 bp):
AAGAGCTTTTAATTTTATTTTCAAAAGTTATAAGTCTCTAATGAG
Found at i:5412820 original size:94 final size:93
Alignment explanation
Indices: 5412717--5412895 Score: 250
Period size: 94 Copynumber: 1.9 Consensus size: 93
5412707 TGAAAAGAGC
** *
5412717 TTTTAATTTTATTTTCAAAAGTTATCAAGTCTTTAATTAGAAGAGCTTTTAATTTTAATTTTCAA
1 TTTTAATTTTATTTTCAAAAGTTATCAAGTCACTAATGAGAAGAGCTTTTAATTTT-ATTTTCAA
5412782 AAGTTATAGAACCTCTAATGAGAGGATTT
65 AAGTTATAGAACCTCTAATGAGAGGATTT
* * * * *
5412811 TTTTAATTTTATTTTCAAAAGTTGTGAAGTCACTAATGAGAGGAGTTTTTAATTTTATTTTTAAA
1 TTTTAATTTTATTTTCAAAAGTTATCAAGTCACTAATGAGAAGAGCTTTTAATTTTATTTTCAAA
* * *
5412876 AGTTGTGGAGCCTCTAATGA
66 AGTTATAGAACCTCTAATGA
5412896 AAAGAGTCTT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
93 25 0.34
94 49 0.66
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.45
Consensus pattern (93 bp):
TTTTAATTTTATTTTCAAAAGTTATCAAGTCACTAATGAGAAGAGCTTTTAATTTTATTTTCAAA
AGTTATAGAACCTCTAATGAGAGGATTT
Found at i:5416248 original size:23 final size:23
Alignment explanation
Indices: 5416218--5416270 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
5416208 AAAAGGGTTT
5416218 AAAAAAAAAGAAAGATTTTTACA
1 AAAAAAAAAGAAAGATTTTTACA
5416241 AAAAAAAAAGAAAGATTTTTACA
1 AAAAAAAAAGAAAGATTTTTACA
5416264 AAAAAAA
1 AAAAAAA
5416271 TTGAAGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.70, C:0.04, G:0.08, T:0.19
Consensus pattern (23 bp):
AAAAAAAAAGAAAGATTTTTACA
Found at i:5419233 original size:200 final size:202
Alignment explanation
Indices: 5418812--5419393 Score: 658
Period size: 201 Copynumber: 2.9 Consensus size: 202
5418802 TTATGAATCT
* * * *
5418812 ACTGTGACAATAAAATAAAATATCACCTTATGTTTTTTTTTTTGTGAAGTTAGTTTTTGTTAGCT
1 ACTGTGACAATAAAATCAAA-ATCACCTTATGCTTTATTTTTTGTGACGTTAGTTTTTGTTAGCT
* * * * *
5418877 ATTTATGAAAAAAAAAAACCATTAAAAGCTATAATCGTCACAAAA-AAATGAGAAAATTTGATAT
65 ATTTATG-AACAAAAAAATCATTAAAGGCTATAATCGTCACAAAATAAATGATAAAATCTGATAT
* * * *
5418941 ATTAGTGATGAAAAGTAAATCATCACAGTACTAGTGACAAAATTATCATCACCAATAATTGTAAA
129 ATTAGTGATGAAAAGTAAATCATCACAGTATTGGTGACAAAATTATCATCACAAATAATCGTAAA
** *
5419006 ATAATGTCT
194 ATAACATCA
* * * *
5419015 ACTGTGACAATAAAATCAAAAGTCACCTTATGCGTTATTTTTGGTGACGCTAGTTTTCGTTAGCT
1 ACTGTGACAATAAAATCAAAA-TCACCTTATGCTTTATTTTTTGTGACGTTAGTTTTTGTTAGCT
* * *
5419080 ATTTATGAACAAAAACATCATT-AAGGCTATAATCAT-AAAAAATAAATGATAAAATCTGATATA
65 ATTTATGAACAAAAAAATCATTAAAGGCTATAATCGTCACAAAATAAATGATAAAATCTGATATA
* * * * * * **
5419143 TTAATGATGAAAAGT-AATCATCACAGTATTGGTAACACAATTATCGTTACAAATTATCGTAAGT
130 TTAGTGATGAAAAGTAAATCATCACAGTATTGGTGACAAAATTATCATCACAAATAATCGTAAAA
5419207 TAACATCAA
195 TAACATC-A
* * * *
5419216 AC-GTGACAATAAAATCAAACATCACATTATGCTTTATTTTTTTGTAACATTAGTTTTTGTTAGT
1 ACTGTGACAATAAAATCAAA-ATCACCTTATGCTTTA-TTTTTTGTGACGTTAGTTTTTGTTAGC
*** *
5419280 TATTTATGAAC--AATTGTCATTAAAGGCTATAATCGTCACAAAATAAATGATTAAAAAC-GATA
64 TATTTATGAACAAAAAAATCATTAAAGGCTATAATCGTCACAAAATAAATGA-TAAAATCTGATA
* * * *
5419342 TATTAGTGACGAAAGGTAAATCATCACAGTATTGGTGACATAATTAACATCA
128 TATTAGTGATGAAAAGTAAATCATCACAGTATTGGTGACAAAATTATCATCA
5419394 TTAAATCATA
Statistics
Matches: 317, Mismatches: 53, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
199 7 0.02
200 91 0.29
201 109 0.34
202 48 0.15
203 62 0.20
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (202 bp):
ACTGTGACAATAAAATCAAAATCACCTTATGCTTTATTTTTTGTGACGTTAGTTTTTGTTAGCTA
TTTATGAACAAAAAAATCATTAAAGGCTATAATCGTCACAAAATAAATGATAAAATCTGATATAT
TAGTGATGAAAAGTAAATCATCACAGTATTGGTGACAAAATTATCATCACAAATAATCGTAAAAT
AACATCA
Found at i:5420518 original size:65 final size:65
Alignment explanation
Indices: 5420364--5420530 Score: 252
Period size: 61 Copynumber: 2.6 Consensus size: 65
5420354 AGAAAGCCTA
* *
5420364 GATATATAATGCTTGTAACATCACAACCACAATAGAATCAATGTACCAAAAGGAACCAACAGATG
1 GATATATAATGCTTGCAACATCACAACCACAACAGAATCAATGTACCAAAAGGAACCAACAGATG
* * * *
5420429 G----ATAATGCTTGCAACATCACAACCACAACAAAATCAATGTACCAAAAGGCACCACCAGCTG
1 GATATATAATGCTTGCAACATCACAACCACAACAGAATCAATGTACCAAAAGGAACCAACAGATG
5420490 GATATATAATGCTTGCAACATCACAACCACAACAGAATCAA
1 GATATATAATGCTTGCAACATCACAACCACAACAGAATCAA
5420531 ATATATACTT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
61 55 0.60
65 36 0.40
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.18
Consensus pattern (65 bp):
GATATATAATGCTTGCAACATCACAACCACAACAGAATCAATGTACCAAAAGGAACCAACAGATG
Found at i:5425511 original size:16 final size:17
Alignment explanation
Indices: 5425475--5425515 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
5425465 TGCTATTGTT
*
5425475 AATAGAAAGTAGAACAA
1 AATAGAAACTAGAACAA
*
5425492 AATAGAAACTA-AACAG
1 AATAGAAACTAGAACAA
5425508 AATAGAAA
1 AATAGAAA
5425516 TCAAACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.66, C:0.07, G:0.15, T:0.12
Consensus pattern (17 bp):
AATAGAAACTAGAACAA
Found at i:5425987 original size:18 final size:17
Alignment explanation
Indices: 5425942--5426233 Score: 111
Period size: 18 Copynumber: 17.1 Consensus size: 17
5425932 TATATTACAA
5425942 TATATTAATAAATAATAT
1 TATATTAATAAATAAT-T
* *
5425960 TAAATGAATAAATAATT
1 TATATTAATAAATAATT
5425977 TACTATTAAT--ATAA--
1 TA-TATTAATAAATAATT
* *
5425991 TATATTAATAAAAAAAT
1 TATATTAATAAATAATT
* * *
5426008 TA-ATAAATAATATTATAA
1 TATATTAATAA-ATAAT-T
5426026 TATATTCAA-AAATAATAT
1 TATATT-AATAAATAAT-T
*
5426044 TACATTAATAAATAATATTATT
1 TATATTAAT--A-AATA--ATT
*
5426066 ATATATTAATAAAAAATAT
1 -TATATTAATAAATAAT-T
*
5426085 AATATTAATAAATAATAT
1 TATATTAATAAATAAT-T
*
5426103 TA-ATTTAATTAATAA--
1 TATA-TTAATAAATAATT
5426118 -ATATT-AT-AATAA--
1 TATATTAATAAATAATT
* *
5426130 TATATGAATAAATAATA
1 TATATTAATAAATAATT
*
5426147 TATTATTAATAAATAATA
1 TA-TATTAATAAATAATT
5426165 TACTATTAAT--ATAA--
1 TA-TATTAATAAATAATT
*
5426179 TATATTAATAAATATTAT
1 TATATTAATAAATAAT-T
*
5426197 TA-ATAAAT-AATATATT
1 TATATTAATAAATA-ATT
5426213 AATATATTAATAAATAATT
1 --TATATTAATAAATAATT
5426232 TA
1 TA
5426234 AAGAATAATA
Statistics
Matches: 212, Mismatches: 27, Indels: 71
0.68 0.09 0.23
Matches are distributed among these distances:
12 5 0.02
13 20 0.09
14 9 0.04
15 12 0.06
16 20 0.09
17 20 0.09
18 87 0.41
19 13 0.06
20 10 0.05
21 5 0.02
22 1 0.00
23 10 0.05
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
TATATTAATAAATAATT
Found at i:5426147 original size:104 final size:108
Alignment explanation
Indices: 5425980--5426230 Score: 281
Period size: 104 Copynumber: 2.4 Consensus size: 108
5425970 AATAATTTAC
* *
5425980 TATTAAT--ATAATATATTAATAAAAAAATTAATAAATAATATTATAATATATTCAAAAATAATA
1 TATTAATAAATAATATATTAAT---ATAATTAATAAATAATATAATAATATATTCAAAAATAATA
5426043 T-TACATTAATAAATAATAT-TATT-ATAT-AT-TAATAAAAAATAT
63 TAT-CATTAATAAATAATATATATTAATATAATATAATAAAAAATAT
* * *
5426085 AATATTAATAAAT-A-ATATTAATTTAATTAATAAATATTATAATAATATA-TGAATAAATAATA
1 --TATTAATAAATAATATATTAATATAATTAATAAATAATATAATAATATATTCAA-AAATAATA
* * *
5426147 TATTATTAATAAATAATATACTATTAATATAATATATTAATAAATAT
63 TATCATTAATAAATAATATA-TATTAATATAATATAATAAAAAATAT
5426194 TATTAATAAATAATATATTAATAT-ATTAATAAATAAT
1 TATTAATAAATAATATATTAATATAATTAATAAATAAT
5426231 TTAAAGAATA
Statistics
Matches: 123, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
103 3 0.02
104 47 0.38
105 1 0.01
106 4 0.03
107 30 0.24
108 16 0.13
109 22 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (108 bp):
TATTAATAAATAATATATTAATATAATTAATAAATAATATAATAATATATTCAAAAATAATATAT
CATTAATAAATAATATATATTAATATAATATAATAAAAAATAT
Found at i:5426224 original size:44 final size:41
Alignment explanation
Indices: 5425948--5426230 Score: 195
Period size: 41 Copynumber: 6.7 Consensus size: 41
5425938 ACAATATATT
* * * * *
5425948 AATAA-ATAATATTAAATGAATAAATAATTTACTATTAATA
1 AATAATATAATAATATATTAATAAATAATATATTATTAATA
* * * * *
5425988 TAAT-ATATTAATAAAAAAATTAATAAATAATATTATAATATATTC
1 -AATAATA-TAAT-AATATATTAATAAATAATA-TATTAT-TAATA
* * *
5426033 AA-AA-ATAATATTACATTAATAAATAATATTATTA-TATATT
1 AATAATATAATAATATATTAATAAATAATA-TATTATTA-ATA
*
5426073 AATAA-AAAAT-ATAATATTAATAAATAATATTAATTTAATTAATA
1 AATAATATAATAAT-ATATTAATAAATAATA-T-A-TT-ATTAATA
* *
5426117 AATATTATAATAATATATGAATAAATAATATATTATTAATA
1 AATAATATAATAATATATTAATAAATAATATATTATTAATA
* *
5426158 AATAATATACTATTAATATAATATATTAATAA-ATATTATTAATA
1 AATAATATA--A-TAATATATTA-ATAAATAATATATTATTAATA
*
5426202 AATAATATATTAATATATTAATAAATAAT
1 AATAATATAATAATATATTAATAAATAAT
5426231 TTAAAGAATA
Statistics
Matches: 194, Mismatches: 28, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
39 2 0.01
40 12 0.06
41 72 0.37
42 11 0.06
43 20 0.10
44 44 0.23
45 31 0.16
46 2 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (41 bp):
AATAATATAATAATATATTAATAAATAATATATTATTAATA
Found at i:5426225 original size:85 final size:80
Alignment explanation
Indices: 5426006--5426230 Score: 217
Period size: 81 Copynumber: 2.7 Consensus size: 80
5425996 TAATAAAAAA
* * * *
5426006 ATTAATAAATAATATT-ATAATATATTCAA-AAATAATATTACATTAATAAAT-AAT-ATTATTA
1 ATTAATAAATAATATTAAT-TTA-ATT-AATAAATAATA-TA-A-TAATATATGAATAAATAATA
5426067 TATATTAATAAAAAATATAAT
60 TATATTAATAAAAAATATAAT
*
5426088 ATTAATAAATAATATTAATTTAATTAATAAATATTATAATAATATATGAATAAATAATATATTAT
1 ATTAATAAATAATATTAATTTAATTAATAAATAATATAATAATATATGAATAAATAATATA-TAT
* *
5426153 TAATAAATAATATACT
65 TAATAAAAAATATAAT
* * *
5426169 ATTAATATAAT-ATATTAATAAATATTATTAATAAATAATATATTAATATATTAATAAATAAT
1 ATTAATA-AATAATATTAAT---T-TAATTAATAAATAATATAATAATATATGAATAAATAAT
5426231 TTAAAGAATA
Statistics
Matches: 122, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
78 7 0.06
79 4 0.03
80 11 0.09
81 42 0.34
82 21 0.17
83 2 0.02
84 1 0.01
85 34 0.28
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (80 bp):
ATTAATAAATAATATTAATTTAATTAATAAATAATATAATAATATATGAATAAATAATATATATT
AATAAAAAATATAAT
Found at i:5426346 original size:12 final size:12
Alignment explanation
Indices: 5426329--5426368 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
5426319 TTTTTAATAT
5426329 TAATAATTTTAA
1 TAATAATTTTAA
5426341 TAATAATTTCT-A
1 TAATAATTT-TAA
5426353 T-AT-ATTTTAA
1 TAATAATTTTAA
5426363 TAATAA
1 TAATAA
5426369 ATAATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 1 0.04
10 6 0.25
11 4 0.17
12 12 0.50
13 1 0.04
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:5426382 original size:25 final size:25
Alignment explanation
Indices: 5426338--5426388 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
5426328 TTAATAATTT
5426338 TAATAATAATTTCTATATATTTTAA
1 TAATAATAATTTCTATATATTTTAA
*
5426363 TAATAAATAATTTTTA-ATATTTTAA
1 TAAT-AATAATTTCTATATATTTTAA
5426388 T
1 T
5426389 GTTATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TAATAATAATTTCTATATATTTTAA
Found at i:5426388 original size:22 final size:21
Alignment explanation
Indices: 5426328--5426388 Score: 59
Period size: 26 Copynumber: 2.6 Consensus size: 21
5426318 TTTTTTAATA
5426328 TTAATAATTTTAATAATAATTT
1 TTAAT-ATTTTAATAATAATTT
*
5426350 CTATATATTTTAATAATAAATAATTT
1 TTA-ATA-TTT--TAAT-AATAATTT
5426376 TTAATATTTTAAT
1 TTAATATTTTAAT
5426389 GTTATATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
22 7 0.22
23 5 0.16
24 3 0.09
25 7 0.22
26 10 0.31
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATATTTTAATAATAATTT
Found at i:5428561 original size:235 final size:230
Alignment explanation
Indices: 5428027--5428894 Score: 907
Period size: 235 Copynumber: 3.7 Consensus size: 230
5428017 AATTGTGATA
* *
5428027 TCATTAATAGTTAACTAAAGTGTTCAATTTGGGACAAAAATTAATAATGTCACCTAAAATTTATC
1 TCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAATGTCACCTAAAATCTATC
* * * *
5428092 AGAAAAAATTCATTATAGATAAAATTTTAAATTAATGACAAAATTATAACATCACATAAAAT---
66 AGAAAAAATTCATCATAGATAAAATTTTAAATTAGTGACAAAATTATAACGTCACCTAAAATAAA
*
5428154 -AA-AT-AAAAAAATTTCTCATCAAATAAATTTGGAGGTAAAAGTTTGTGATATTTAAGTTATCG
131 AAATATCAAAAAAATTT-TCACCAAATAAATTT-GAGGTAAAAGTTTGTGATATTT-AGTTATCG
* * * * *
5428216 TCATATAACACCATATATTGACA-TGAAAAAATTGCAATG
193 TC-TATAATACCATAAAAT-AAAGTGACAAAATTGCAATG
* * * * * *
5428255 TCATTAATAATTGATTAAAGTATTTAATTTGTGACAAAAATTAATATTGTCACCTAAAATCTATC
1 TCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAATGTCACCTAAAATCTATC
** * *
5428320 AGAAAAAATTTGTCATAGATAGAATTTTAAATTAGTGACAAAATTATAATGTCACCTAAAATAAA
66 AGAAAAAATTCATCATAGATAAAATTTTAAATTAGTGACAAAATTATAACGTCACCTAAAATAAA
* * * * *
5428385 AAATATCAAAAAAAACTTTCACCAAATAAAATTGACAGTAAAAGTTTATGTTATTTATGTTATCG
131 AAATATC-AAAAAAATTTTCACCAAATAAATTTGA-GGTAAAAGTTTGTGATATTTA-GTTATCG
*
5428450 TCTTATAATACCATAAAATAAAGGTGACAAAATTGTAATG
193 TC-TATAATACCATAAAATAAA-GTGACAAAATTGCAATG
* *
5428490 TCATTAATAGTTAACTAAAGTGTTTCAA-TTGTGATAAAAATTGATAATGTCACCTAAAATCTAT
1 TCATTAATAGTTAACTAAAGTG-TTCAATTTGTGACAAAAATTAATAATGTCACCTAAAATCTAT
* * *
5428554 TAGAAAAAATTCATCACAGATAAAATTTTAAATTAGTGACAAAATT-TAAATGTCACCTAAAATA
65 CAGAAAAAATTCATCATAGATAAAATTTTAAATTAGTGACAAAATTAT-AACGTCACCTAAAAT-
* * * *
5428618 AAAAAAAATGTCATAAAAATTTTCCACTAAATAAATTTGGGGGTAAAAGTTTGTGATATTTAGAT
128 --AAAAAATATCAAAAAAATTTT-CACCAAATAAATTT-GAGGTAAAAGTTTGTGATATTTAG-T
* *** * * * * * *
5428683 TATCATC-AT-ATATGGTTACATTGACGTGACGAAATTACAATG
188 TATCGTCTATAATA-CCATAAAATAAAGTGACAAAATTGCAATG
* * * *
5428725 TCATTAATAGTTAACTAAAGTGTTCAATTTATTATAAAAATTAAT-A-GTCACCTAAAATCTATA
1 TCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAATGTCACCTAAAATCTATC
* *
5428788 AGAAAAAATTCATCATAGATAAAATTTTAAATTGGTGGCAAAATTATAACGTCACCTAAATTAAA
66 AGAAAAAATTCATCATAGATAAAATTTTAAATTAGTGACAAAATTATAACGTCACC-----TAAA
* *
5428853 AGAAAAAACATCACAAAAATATTTTCCACCAAATAAATTTGA
126 ATAAAAAATATCA-AAAAA-ATTTT-CACCAAATAAATTTGA
5428895 CAGTAAAATT
Statistics
Matches: 535, Mismatches: 76, Indels: 50
0.81 0.11 0.08
Matches are distributed among these distances:
228 111 0.21
232 2 0.00
233 73 0.14
234 60 0.11
235 192 0.36
236 16 0.03
237 29 0.05
238 51 0.10
239 1 0.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (230 bp):
TCATTAATAGTTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAATGTCACCTAAAATCTATC
AGAAAAAATTCATCATAGATAAAATTTTAAATTAGTGACAAAATTATAACGTCACCTAAAATAAA
AAATATCAAAAAAATTTTCACCAAATAAATTTGAGGTAAAAGTTTGTGATATTTAGTTATCGTCT
ATAATACCATAAAATAAAGTGACAAAATTGCAATG
Found at i:5431109 original size:22 final size:22
Alignment explanation
Indices: 5431084--5431129 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5431074 AGCATGTAAC
5431084 ATAATGTGAAGCTACATGTCAT
1 ATAATGTGAAGCTACATGTCAT
5431106 ATAATGTGAAGCTACATGTCAT
1 ATAATGTGAAGCTACATGTCAT
5431128 AT
1 AT
5431130 TATGGGCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (22 bp):
ATAATGTGAAGCTACATGTCAT
Found at i:5434594 original size:1 final size:1
Alignment explanation
Indices: 5434588--5434615 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
5434578 TCCCCATTGC
5434588 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
5434616 CCATAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5434805 original size:19 final size:20
Alignment explanation
Indices: 5434765--5434805 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5434755 AATTAATACA
*
5434765 ATCAATTATTGATCCAGCCC
1 ATCAATTATTGATACAGCCC
*
5434785 ATCAATT-TTGATACAGTCC
1 ATCAATTATTGATACAGCCC
5434804 AT
1 AT
5434806 AAAAATAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCAATTATTGATACAGCCC
Found at i:5435011 original size:3 final size:3
Alignment explanation
Indices: 5435003--5435039 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5434993 CAACTTTAGG
5435003 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5435040 GGATCAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5435093 original size:3 final size:3
Alignment explanation
Indices: 5435085--5435119 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5435075 GAATTCTAAG
5435085 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5435120 TGGTTCATTC
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):
TAA
Found at i:5436167 original size:3 final size:3
Alignment explanation
Indices: 5436161--5436207 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5436151 GTTGTTGTTG
5436161 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5436208 GAGTTAAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5436457 original size:8 final size:8
Alignment explanation
Indices: 5436444--5436469 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5436434 TTAGTTTTAA
5436444 TATATTTT
1 TATATTTT
5436452 TATATTTT
1 TATATTTT
5436460 TATATTTT
1 TATATTTT
5436468 TA
1 TA
5436470 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TATATTTT
Found at i:5436541 original size:22 final size:22
Alignment explanation
Indices: 5436496--5436544 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5436486 TTTTATATCT
* *
5436496 AAATCTATTAAAATATATTGAA
1 AAATATATTAAAATATATTAAA
5436518 AAATATATTAAAATA-ATATAAA
1 AAATATATTAAAATATAT-TAAA
5436540 AAATA
1 AAATA
5436545 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATATATTAAAATATATTAAA
Found at i:5437078 original size:18 final size:17
Alignment explanation
Indices: 5437057--5437091 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5437047 CAAAAAATTA
*
5437057 TTATTTTTTTCATTTTTT
1 TTATCTTTTT-ATTTTTT
5437075 TTATCTTTTTATTTTTT
1 TTATCTTTTTATTTTTT
5437092 CATCTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (17 bp):
TTATCTTTTTATTTTTT
Found at i:5445760 original size:26 final size:26
Alignment explanation
Indices: 5445710--5445761 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5445700 AAATTTTTTT
5445710 GTTTTTATTTTTATTTTCTAGAAAAA
1 GTTTTTATTTTTATTTTCTAGAAAAA
* *
5445736 GTTTTTAGTTTTTGTTTTTTA-AAAAA
1 GTTTTTA-TTTTTATTTTCTAGAAAAA
5445762 CGTATTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (26 bp):
GTTTTTATTTTTATTTTCTAGAAAAA
Found at i:5446253 original size:2 final size:2
Alignment explanation
Indices: 5446246--5446278 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5446236 TTTCAAATTC
5446246 TA TA TA TA T- 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
5446279 CATACACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5447098 original size:593 final size:596
Alignment explanation
Indices: 5445974--5447115 Score: 1859
Period size: 593 Copynumber: 1.9 Consensus size: 596
5445964 TAAAAACGTC
5445974 TTTTTTTTTTCATTTTCACATTTTAACCTATTTTCATATTTATTTTCTAAAAACTTATTTTCATT
1 TTTTTTTTTTCATTTTCACATTTTAACCTATTTTCATATTTATTTTCTAAAAACTTATTTTCATT
5446039 TTTAAGTATCATGTTTTCTCTAATATTTTTCATTTTCTTAAAAAATAAAAATAAAAAATGATTCT
66 TTTAAGTATCATGTTTTCTCTAATATTTTTCATTTTCTTAAAAAATAAAAATAAAAAATG----T
5446104 ATTTTCTGAAATCAAATACTATCTTATATTTTCAATTTTTAAGATGAAATAAACCTTTTTCACAT
127 A-TTTCT-AAATCAAATACTATCTTATATTTTCAATTTTTAAGATGAAATAAACCTTTTTCACAT
*
5446169 GCGGTAAAAAAACTATCCACTCCTCGAGAAACTTCCTTTTCTTTAATTCTTTCAAAGCACAATTT
190 GCAGTAAAAAAACTATCCACTCCTCGAGAAACTTCCTTTTCTTTAATTCTTTCAAAGCACAATTT
5446234 GTTTTCAAATTCTATATATATTATATATATATATATATATATATACATACACAATCACCTATTTA
255 GTTTTCAAATTC-------------TATATATATATATATATATACA-ACACAATCACCTATTTA
5446299 GTGGATGTGTCAAAATTATAGTTTACTAATTAATCTAATAAAGTATATTATAAATAAAGGCTAAT
306 GTGGATGTGTCAAAATTATAGTTTACTAATTAATCTAATAAAGTATATTATAAATAAAGGCTAAT
*
5446364 AAAAGAGTTTATATCTCGACGAGCGGGTCCAGCTCCAAAGCCGAGATTTTTGAGGGAGGATGGTG
371 AAAAGAGTTTATATCTCGACGAGCGGGTCCAGCTCCAAAGCCGAGATTTTTGAGGGAGAATGGTG
5446429 TTCAGACTTGCTGTGGCCGTGGGCAAAACGGTTCTGGCCATGTGTAAATTTGTTTTCTTTTTAAG
436 TTCAGACTTGCTGTGGCCGTGGGCAAAACGGTTCTGGCCATGTGTAAATTTGTTTTCTTTTTAAG
5446494 AAATAAATAATTAGTTCACAAAAAAAAAATGTGCATGTAACTATCATTCAAGCTACTACTACATT
501 AAATAAATAATTAGTTCACAAAAAAAAAATGTGCATGTAACTATCATTCAAGCTACTACTACATT
5446559 TCTTGTTTTCACAATTGAAAACATCTTCTTT
566 TCTTGTTTTCACAATTGAAAACATCTTCTTT
** * * *
5446590 TTTTTTTTTTTTTTTTCACATTTTAACCTATTTTCATTTTTGTTTTTTAAAAACTTA-TTTCATT
1 TTTTTTTTTTCATTTTCACATTTTAACCTATTTTCATATTTATTTTCTAAAAACTTATTTTCATT
* * *
5446654 TTTAATTATCAAACATGTTTTCTCTAATATTTTTCGTTTTCTTAAAAAATAAAAATAAGAAATG-
66 TTTAAGTAT----CATGTTTTCTCTAATATTTTTCATTTTCTTAAAAAATAAAAATAAAAAATGT
*
5446718 A-TTCT-AATCAAATACTATCTTATATTTTCAATTTTTTAGATGAAATAAACCTTTTTCGA-ATG
127 ATTTCTAAATCAAATACTATCTTATATTTTCAATTTTTAAGATGAAATAAACCTTTTTC-ACATG
* *
5446780 CAGTAAAAAACCTATCCACTCCTCGAGAAACTTCTTTTTCTTTAATTCTTTCAAAGCACAATTTG
191 CAGTAAAAAAACTATCCACTCCTCGAGAAACTTCCTTTTCTTTAATTCTTTCAAAGCACAATTTG
* *
5446845 TTTTCAAATTC-ATATATATATATATATATAC-ACATATTCACCTATTTAGTGGATGTGTCAAAA
256 TTTTCAAATTCTATATATATATATATATATACAACACAATCACCTATTTAGTGGATGTGTCAAAA
*
5446908 -TATAGTTTACTAATTAATCTAATAAAGTATATTATAAATAAAGGCTAATAAAATAGTTTATATC
321 TTATAGTTTACTAATTAATCTAATAAAGTATATTATAAATAAAGGCTAATAAAAGAGTTTATATC
5446972 TCGACGAGCGGGTCCAGCTCCAAAGCCGAGATTTTTGAGGGAGAATGGTGTTCAGACTTGCTGTG
386 TCGACGAGCGGGTCCAGCTCCAAAGCCGAGATTTTTGAGGGAGAATGGTGTTCAGACTTGCTGTG
5447037 GCCGTGGGCAAAACGGTTCTGGCCATGTGTAAATTTGTTTTCTTTTTAAGAAATAAATAATTAGT
451 GCCGTGGGCAAAACGGTTCTGGCCATGTGTAAATTTGTTTTCTTTTTAAGAAATAAATAATTAGT
5447102 TCACAAAAAAAAAA
516 TCACAAAAAAAAAA
5447116 AAAAAAGCTT
Statistics
Matches: 505, Mismatches: 16, Indels: 33
0.91 0.03 0.06
Matches are distributed among these distances:
593 206 0.41
594 30 0.06
596 20 0.04
610 127 0.25
611 1 0.00
612 4 0.01
614 1 0.00
615 15 0.03
616 52 0.10
619 49 0.10
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (596 bp):
TTTTTTTTTTCATTTTCACATTTTAACCTATTTTCATATTTATTTTCTAAAAACTTATTTTCATT
TTTAAGTATCATGTTTTCTCTAATATTTTTCATTTTCTTAAAAAATAAAAATAAAAAATGTATTT
CTAAATCAAATACTATCTTATATTTTCAATTTTTAAGATGAAATAAACCTTTTTCACATGCAGTA
AAAAAACTATCCACTCCTCGAGAAACTTCCTTTTCTTTAATTCTTTCAAAGCACAATTTGTTTTC
AAATTCTATATATATATATATATATACAACACAATCACCTATTTAGTGGATGTGTCAAAATTATA
GTTTACTAATTAATCTAATAAAGTATATTATAAATAAAGGCTAATAAAAGAGTTTATATCTCGAC
GAGCGGGTCCAGCTCCAAAGCCGAGATTTTTGAGGGAGAATGGTGTTCAGACTTGCTGTGGCCGT
GGGCAAAACGGTTCTGGCCATGTGTAAATTTGTTTTCTTTTTAAGAAATAAATAATTAGTTCACA
AAAAAAAAATGTGCATGTAACTATCATTCAAGCTACTACTACATTTCTTGTTTTCACAATTGAAA
ACATCTTCTTT
Found at i:5447930 original size:19 final size:19
Alignment explanation
Indices: 5447896--5447935 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5447886 TCCTTTTAAT
*
5447896 AAAATTATATATACAAGTA
1 AAAATTATATATACAACTA
5447915 AAAATTATA-ATAACAACTA
1 AAAATTATATAT-ACAACTA
5447934 AA
1 AA
5447936 TAGTGTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATTATATATACAACTA
Found at i:5456180 original size:18 final size:18
Alignment explanation
Indices: 5456140--5456180 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5456130 ATCTCTTGGA
5456140 TCAACATTGGTAGTTACT
1 TCAACATTGGTAGTTACT
*
5456158 GCAACATTGGTA-TTAACT
1 TCAACATTGGTAGTT-ACT
5456176 TCAAC
1 TCAAC
5456181 CTCTTCTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (18 bp):
TCAACATTGGTAGTTACT
Found at i:5459521 original size:2 final size:2
Alignment explanation
Indices: 5459516--5459540 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5459506 GTGTGTGTTT
5459516 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 T
5459541 TTGAGGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5463791 original size:23 final size:23
Alignment explanation
Indices: 5463761--5463813 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5463751 ATTTTTTGAA
5463761 TTTT-TTTAGTTTCA-TTTTATGG
1 TTTTATTTAGTTTCAGTTTTAT-G
* *
5463783 TTTTATTTAGTTTTAGTTTTATT
1 TTTTATTTAGTTTCAGTTTTATG
5463806 TTTTATTT
1 TTTTATTT
5463814 GATTTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 4 0.15
23 17 0.63
24 6 0.22
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (23 bp):
TTTTATTTAGTTTCAGTTTTATG
Found at i:5470955 original size:30 final size:30
Alignment explanation
Indices: 5470910--5471013 Score: 109
Period size: 37 Copynumber: 3.2 Consensus size: 30
5470900 AGCATAATAA
*
5470910 GTTTATATAATTGTTTAGATTATATATAATT
1 GTTTATAT-ATTGTTTACATTATATATAATT
*
5470941 GTTTATATATTGTTTACATTATGTATAATTGTTTATT
1 GTTTATATATTGTTTACATTA--TAT-A----TAATT
*
5470978 GTTTATATATTGTTTATATTATATATAATT
1 GTTTATATATTGTTTACATTATATATAATT
5471008 GTTTAT
1 GTTTAT
5471014 TGTTTGGCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
30 22 0.35
31 8 0.13
32 3 0.05
33 1 0.02
34 1 0.02
35 3 0.05
37 24 0.39
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.59
Consensus pattern (30 bp):
GTTTATATATTGTTTACATTATATATAATT
Found at i:5470979 original size:37 final size:37
Alignment explanation
Indices: 5470938--5471018 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
5470928 ATTATATATA
*
5470938 ATTGTTTATATATTGTTTACATTATGTATAATTGTTT
1 ATTGTTTATATATTGTTTACATTATATATAATTGTTT
*
5470975 ATTGTTTATATATTGTTTATATTATATATAATTGTTT
1 ATTGTTTATATATTGTTTACATTATATATAATTGTTT
5471012 ATTGTTT
1 ATTGTTT
5471019 GGCATTTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.62
Consensus pattern (37 bp):
ATTGTTTATATATTGTTTACATTATATATAATTGTTT
Found at i:5471013 original size:19 final size:19
Alignment explanation
Indices: 5470913--5471013 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 19
5470903 ATAATAAGTT
*
5470913 TATATAATTGTTTAGATTA
1 TATATAATTGTTTATATTA
5470932 TATATAATTG------TT-
1 TATATAATTGTTTATATTA
*
5470944 TATAT-ATTGTTTACATTA
1 TATATAATTGTTTATATTA
* *
5470962 TGTATAATTGTTTAT-TGTT
1 TATATAATTGTTTATAT-TA
5470981 TATAT-ATTGTTTATATTA
1 TATATAATTGTTTATATTA
5470999 TATATAATTGTTTAT
1 TATATAATTGTTTAT
5471014 TGTTTGGCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
11 4 0.06
12 5 0.08
13 2 0.03
17 2 0.03
18 20 0.30
19 33 0.50
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.58
Consensus pattern (19 bp):
TATATAATTGTTTATATTA
Found at i:5471925 original size:49 final size:49
Alignment explanation
Indices: 5471872--5471970 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
5471862 GGATGTTAAC
* *
5471872 TATTATGAGATTTTAAAAGACACCATTTAATTGAATTATATTGGTAGAT
1 TATTATGAGATTATAAAAGACACCATTTAATTGAATTATACTGGTAGAT
* *
5471921 TATTATGGGATTATAAAAGACATCATTTAATTGAATTATACTGGTAGAT
1 TATTATGAGATTATAAAAGACACCATTTAATTGAATTATACTGGTAGAT
5471970 T
1 T
5471971 GAAAGTTGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (49 bp):
TATTATGAGATTATAAAAGACACCATTTAATTGAATTATACTGGTAGAT
Found at i:5472878 original size:22 final size:23
Alignment explanation
Indices: 5472852--5472896 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
5472842 AATGTTGCAC
5472852 AATTACATTTTTTA-ATG-AATTT
1 AATTAC-TTTTTTACATGTAATTT
5472874 AATTACTTTTTTACATGTAATTT
1 AATTACTTTTTTACATGTAATTT
5472897 TTCTATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (23 bp):
AATTACTTTTTTACATGTAATTT
Found at i:5475047 original size:68 final size:68
Alignment explanation
Indices: 5474900--5475026 Score: 191
Period size: 68 Copynumber: 1.9 Consensus size: 68
5474890 GCATTACACT
* * * *
5474900 AATGAATATGATGTTTATAAAATTATTTTTGCTGGCATACAAATGGATGATTACCTTCTGTATAT
1 AATGAATAAGATGTTTATAAAATTATTTCTACTGGCATACAAATAGATGATTACCTTCTGTATAT
5474965 ATG
66 ATG
* **
5474968 AATGAATAAGATGTTTATAAAATTATTTCTACTGGTATATGAATAGATGATTACCTTCT
1 AATGAATAAGATGTTTATAAAATTATTTCTACTGGCATACAAATAGATGATTACCTTCT
5475027 TACCTTCTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 52 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (68 bp):
AATGAATAAGATGTTTATAAAATTATTTCTACTGGCATACAAATAGATGATTACCTTCTGTATAT
ATG
Found at i:5475934 original size:55 final size:54
Alignment explanation
Indices: 5475873--5476041 Score: 178
Period size: 55 Copynumber: 3.1 Consensus size: 54
5475863 AATATAATAA
* * * * *
5475873 AAAATTAAAATATATAAGTCTATATTGACAATCTCTAACAGTCGATATAGGTAAG
1 AAAATTAAAAAATACAAGTTTATACTGACAATCTCTAACTGTC-ATATAGGTAAG
** * * *
5475928 AAAATTAAAGCATACAAATTTATACTGACAGTCTCTAACTGTCAGTATAAGTAAG
1 AAAATTAAAAAATACAAGTTTATACTGACAATCTCTAACTGTCA-TATAGGTAAG
* * *
5475983 AAAATTTAAAAAATACAAGTTTATACTAACAGAT-ACTAAGTGTCATATAGGTAAG
1 AAAA-TTAAAAAATACAAGTTTATACTGACA-ATCTCTAACTGTCATATAGGTAAG
5476038 AAAA
1 AAAA
5476042 ATTACAAGTC
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
54 1 0.01
55 61 0.65
56 31 0.33
57 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (54 bp):
AAAATTAAAAAATACAAGTTTATACTGACAATCTCTAACTGTCATATAGGTAAG
Found at i:5476202 original size:55 final size:54
Alignment explanation
Indices: 5476078--5476204 Score: 141
Period size: 55 Copynumber: 2.3 Consensus size: 54
5476068 AACCGTCGAA
* *
5476078 ATAGGTAAGAAAAATTAAAACATACAAGTCTATACTGATATAAGCTAGTCATCGGT
1 ATAGGTAA-AAAAATTAAAACATACAAATCTATACTGA-ATAAGCTAGTCATCAGT
* * **
5476134 ATAGGTAAGAAAATTAAAACATACAAATCTATAGTG-ATGGGCTTTAAG-CATCAGT
1 ATAGGTAAAAAAATTAAAACATACAAATCTATACTGAATAAGC--T-AGTCATCAGT
5476189 ATAGGTAAAAAAATTA
1 ATAGGTAAAAAAATTA
5476205 CAAGTTTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
53 4 0.07
55 47 0.77
56 10 0.16
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (54 bp):
ATAGGTAAAAAAATTAAAACATACAAATCTATACTGAATAAGCTAGTCATCAGT
Found at i:5477357 original size:55 final size:54
Alignment explanation
Indices: 5477235--5477470 Score: 226
Period size: 51 Copynumber: 4.5 Consensus size: 54
5477225 AAAAATAAAA
* *
5477235 AAGGAATAAGTTAAAATATTAATTTTT-CTTAAAATAAAA--TTTTGAAAATTT
1 AAGGAAAAAGTTGAAATATTAATTTTTCCTTAAAATAAAATTTTTTGAAAATTT
* *
5477286 AAGGAAAAAGTGGAAATA-TAAGTTTTCCTTAAAATAAAATTCTTTTGAAAATATT
1 AAGGAAAAAGTTGAAATATTAATTTTTCCTTAAAATAAAATT-TTTTGAAAAT-TT
* * * *
5477341 AAGGAAAAAGTTGAAATATCAATTTTTTCTTAAATTAAACTTGTTTTGAAAATGTT
1 AAGGAAAAAGTTGAAATATTAATTTTTCCTTAAAATAAAATT-TTTTGAAAAT-TT
* * * *
5477397 ----AAAAAGTTGAAATATTAATTTTTCCTTATAAT--AAGTTTTAGAGAA-TT
1 AAGGAAAAAGTTGAAATATTAATTTTTCCTTAAAATAAAATTTTTTGAAAATTT
*
5477444 AA-GAAAAAGGTTGAAATATCAATTTTT
1 AAGGAAAAA-GTTGAAATATTAATTTTT
5477471 TTTCTAAAAT
Statistics
Matches: 154, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
47 2 0.01
49 7 0.05
50 14 0.09
51 44 0.29
52 28 0.18
54 10 0.06
55 19 0.12
56 30 0.19
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.39
Consensus pattern (54 bp):
AAGGAAAAAGTTGAAATATTAATTTTTCCTTAAAATAAAATTTTTTGAAAATTT
Found at i:5478003 original size:18 final size:20
Alignment explanation
Indices: 5477975--5478020 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
5477965 TTTTTTTAGG
*
5477975 AAATGCAAGG-AAATAGT-AA
1 AAAT-CAAGGAAAAAAGTCAA
5477994 AAATCAAGGAAAAAAGTCAA
1 AAATCAAGGAAAAAAGTCAA
5478014 AAATCAA
1 AAATCAA
5478021 CCTAAAGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.63, C:0.09, G:0.15, T:0.13
Consensus pattern (20 bp):
AAATCAAGGAAAAAAGTCAA
Found at i:5480011 original size:17 final size:17
Alignment explanation
Indices: 5479989--5480031 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
5479979 AAGATGAAAT
5479989 CTTAAAATACCTTAAAG-
1 CTTAAAATACCTT-AAGC
*
5480006 CTTAAATTACCTTAAGC
1 CTTAAAATACCTTAAGC
5480023 CTTAAAATA
1 CTTAAAATA
5480032 TCCAAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (17 bp):
CTTAAAATACCTTAAGC
Found at i:5480266 original size:32 final size:31
Alignment explanation
Indices: 5480221--5480319 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 31
5480211 TAAATTATCC
* *
5480221 AAACCTTAACCTAAGCCTAATC-CTAAGCCTT
1 AAACCTTAACCTAA-CCTAAACTCTAAACCTT
5480252 AAACCTTGAACCTAACCTAAACTCTAAACCTT
1 AAACCTT-AACCTAACCTAAACTCTAAACCTT
* *
5480284 AAACC-TAGCCTAAACCCTAAACT-TGAACC-T
1 AAACCTTAACCT-AA-CCTAAACTCTAAACCTT
5480314 AAACCT
1 AAACCT
5480320 AATGTTTAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
30 10 0.17
31 21 0.36
32 28 0.47
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.23
Consensus pattern (31 bp):
AAACCTTAACCTAACCTAAACTCTAAACCTT
Found at i:5480270 original size:25 final size:24
Alignment explanation
Indices: 5480236--5480321 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 24
5480226 TTAACCTAAG
5480236 CCTAATCCTAAGCCTTAAACCTTGAA
1 CCTAA-CCTAA-CCTTAAACCTTGAA
* *
5480262 CCTAACCTAAACTCTAAACCTTAAA
1 CCTAACCTAACCT-TAAACCTTGAA
* *
5480287 CCTAGCCTAAACCCTAAA-CTTGAA
1 CCTAACCT-AACCTTAAACCTTGAA
5480311 CCTAAACCTAA
1 CCT-AACCTAA
5480322 TGTTTAATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 12 0.24
25 30 0.60
26 8 0.16
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.23
Consensus pattern (24 bp):
CCTAACCTAACCTTAAACCTTGAA
Found at i:5480296 original size:18 final size:19
Alignment explanation
Indices: 5480265--5480319 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
5480255 CCTTGAACCT
*
5480265 AACCTAAACTCTAAACCTTA
1 AACCTGAAC-CTAAACCTTA
* *
5480285 AACCT-AGCCTAAACCCTA
1 AACCTGAACCTAAACCTTA
*
5480303 AACTTGAACCTAAACCT
1 AACCTGAACCTAAACCT
5480320 AATGTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 13 0.45
19 11 0.38
20 5 0.17
ACGTcount: A:0.42, C:0.33, G:0.04, T:0.22
Consensus pattern (19 bp):
AACCTGAACCTAAACCTTA
Found at i:5487586 original size:28 final size:27
Alignment explanation
Indices: 5487545--5487604 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
5487535 AGATGAAAGC
*
5487545 AAATAAACAATAAAGCAATAAATAAACA
1 AAATAAACAATAAAGAAATAAATAAA-A
*
5487573 AAATAAA-AATTAAAGAAATAAATAGAA
1 AAATAAACAA-TAAAGAAATAAATAAAA
5487600 AAATA
1 AAATA
5487605 TTTACAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (27 bp):
AAATAAACAATAAAGAAATAAATAAAA
Found at i:5488145 original size:17 final size:18
Alignment explanation
Indices: 5488103--5488149 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
5488093 TTTGTAACAT
*
5488103 TATTATGTGGGTTGCAAA
1 TATTATTTGGGTTGCAAA
* *
5488121 AATT-TTTGTGTTGC-AA
1 TATTATTTGGGTTGCAAA
5488137 TATTATTTGGGTT
1 TATTATTTGGGTT
5488150 TCCAAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
16 5 0.22
17 15 0.65
18 3 0.13
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.49
Consensus pattern (18 bp):
TATTATTTGGGTTGCAAA
Found at i:5490875 original size:160 final size:161
Alignment explanation
Indices: 5490655--5491443 Score: 726
Period size: 160 Copynumber: 4.9 Consensus size: 161
5490645 AAGCATGGCC
* * ** *
5490655 TTTCACACATATCAATCATG-G-AAACCAAATTCAAT-TTTTGGACAAGTTTAATATCATGTATT
1 TTTCACACATATCAA-C-TGTGAAAACCAAGTTCAATCATTTCAAAAAGTTTAATATCATGTATT
* ** * *
5490717 AAAGCTATCCAAATTGTTAAAACAGAACAATAACAGCAACGTTGTATTTTTGCCATTTAACGGCA
64 AAAGCTATCCAAACTGTTAAAACAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCA
*
5490782 AAAAAAGTCCTAAACAGAGGTAAACAATAACTT
129 AAAAAAGTCCTAAACAGATGTAAACAATAACTT
* * * * *
5490815 TTTCACATATATC-AGTGGTGAAAACTAAGTTCAATCA-TTCAAAAATTTTAATATCATGTATTG
1 TTTCACACATATCAACT-GTGAAAACCAAGTTCAATCATTTCAAAAAGTTTAATATCATGTATTA
* * * * * * *
5490878 AAGCTACCCAAACTGTTAAAACAGAACAATAATATCAATTTTGCA-TTTTACCTTTTAATGAC-A
65 AAGCTATCCAAACTGTTAAAACAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAA
* ** * *
5490941 TAAAAGTCCTAAACAGATGTAAACGTTAGCTA
130 AAAAAGTCCTAAACAGATGTAAACAATAACTT
* * * * * ** * *
5490973 TTTCACATATATTAATTGTGGAAACCAAGTTC-ATTATTTTGACAAGTTT-ATCATCATGTATTG
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTCAAAAAGTTTAAT-ATCATGTATTA
* * * * * * **
5491036 AAGCTATGCAAACTGTTACAATA-AACAATAACAACAAATTTGCATTTTTGCCTTTTAATAGCAC
65 AAGCTATCCAAACTGTTAAAACAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCA-
* *
5491100 AAAAAA-TCTTAAACAGATGTAAACGATAACTT
129 AAAAAAGTCCTAAACAGATGTAAACAATAACTT
* *
5491132 TTTCACACATATCAACTGTGGAAACCAAGTTCAATCA-TTCAAACAAGTTTAACATCATGTATT-
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTCAAA-AAGTTTAATATCATGTATTA
* * * * *
5491195 GAGCTATCCAAACTGTTAAAATAGAACAATAAAAGCAAATTTGTATTTTTACCTATTAACGGCAC
65 AAGCTATCCAAACTGTTAAAACAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAA
* * ** *
5491260 AAAAAGTCCT-TACTAAACATAAACATTAACTT
130 AAAAAGTCCTAAAC-AGATGTAAACAATAACTT
* ** * ** *
5491292 TTTCATACATATCAACTGTGAAAAATAAGTTCAATAATTTGGATAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTCAAAAAGTTTAATATCATGTATT-A
* * * * * *
5491357 AA-CTATCAAAACTATTAAAACAGAACAATAACTGTAAATTTGTATTTTTACCTTTTAACAGCAC
65 AAGCTATCCAAACTGTTAAAACAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAA
** *
5491421 AAAAAGTTGTAAACAGATATAAA
130 AAAAAGTCCTAAACAGATGTAAA
5491444 TTGCAAATTA
Statistics
Matches: 509, Mismatches: 100, Indels: 39
0.79 0.15 0.06
Matches are distributed among these distances:
157 24 0.05
158 105 0.21
159 98 0.19
160 206 0.40
161 73 0.14
162 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (161 bp):
TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTCAAAAAGTTTAATATCATGTATTAA
AGCTATCCAAACTGTTAAAACAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAAA
AAAAGTCCTAAACAGATGTAAACAATAACTT
Found at i:5497228 original size:49 final size:49
Alignment explanation
Indices: 5497175--5497275 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
5497165 TTTTGATACA
5497175 TTAAAAACCTTGATCATACCTTGAAAAGTGTGAAATTATGAAAATACCC
1 TTAAAAACCTTGATCATACCTTGAAAAGTGTGAAATTATGAAAATACCC
*
5497224 TTAAAAACCTTGATCATACCTTGAAAAGTGTGAAATTATTAAAATACCC
1 TTAAAAACCTTGATCATACCTTGAAAAGTGTGAAATTATGAAAATACCC
5497273 TTA
1 TTA
5497276 GGGTATTTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.31
Consensus pattern (49 bp):
TTAAAAACCTTGATCATACCTTGAAAAGTGTGAAATTATGAAAATACCC
Done.