Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000657.1 Hibiscus syriacus cultivar Beakdansim tig00001271_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 120917
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5216 original size:101 final size:101
Alignment explanation
Indices: 5042--5251 Score: 379
Period size: 101 Copynumber: 2.1 Consensus size: 101
5032 AGGGTCTATG
5042 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGAGGTCTGGTGAGACACATACTTGATC
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGAGGTCTGGTGAGACACATACTTGATC
5107 CTTGGTATATGTATATGATTCTTAAGGAAT-A-ATA
66 CTTGGTATATGTATATGATTCTTAAGGAATGATATA
*
5141 TGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACA--TGTGAGGTCTGGTGAGACACATACTTGA
5206 TCCTTGGTATATGTATATGATTCTTAAGGAATGATATA
64 TCCTTGGTATATGTATATGATTCTTAAGGAATGATATA
5244 TGGTCCTT
1 TGGTCCTT
5252 ATGGACATTA
Statistics
Matches: 105, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
99 34 0.32
101 60 0.57
102 1 0.01
103 10 0.10
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (101 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGAGGTCTGGTGAGACACATACTTGATC
CTTGGTATATGTATATGATTCTTAAGGAATGATATA
Found at i:5301 original size:23 final size:23
Alignment explanation
Indices: 5268--5330 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
5258 ATTATTATAT
5268 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
5291 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
5314 GGCACTAAGGTGCAATT
1 GGCACTACGGTGCAATT
5331 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:6277 original size:23 final size:23
Alignment explanation
Indices: 6247--6333 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
6237 GCATGGCAGT
6247 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
6270 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
6292 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
6314 GATGCATCGATGCACTATTC
1 G-TGCATCGATGCAC-ATTC
6334 TGTGTATCGA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
22 3 0.06
23 17 0.33
24 13 0.25
25 4 0.08
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:6305 original size:44 final size:44
Alignment explanation
Indices: 6246--6347 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
6236 TGCATGGCAG
* * *
6246 TGTGCATCGATGCACATTC-AA-GGAGTGCATCGGTGCA-TCTTC
1 TGTGTATCGATGCACATTCAAAGGGA-TGCATCGATGCACTATTC
6288 ATGATGTATCGATGCACATTCAAAGGGATGCATCGATGCACTATTC
1 -TG-TGTATCGATGCACATTCAAAGGGATGCATCGATGCACTATTC
6334 TGTGTATCGATGCA
1 TGTGTATCGATGCA
6348 TTATGCACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
43 2 0.04
44 28 0.54
45 15 0.29
46 7 0.13
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (44 bp):
TGTGTATCGATGCACATTCAAAGGGATGCATCGATGCACTATTC
Found at i:12833 original size:17 final size:17
Alignment explanation
Indices: 12808--12855 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
12798 TTGGTTTGAC
*
12808 CCAACCCATTGATCG-AA
1 CCAAACCATTGA-CGAAA
12825 CCAAACCATTGACGAAA
1 CCAAACCATTGACGAAA
*
12842 TCAAACCAGTTGAC
1 CCAAACCA-TTGAC
12856 TATTAACTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 20 0.74
18 5 0.19
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17
Consensus pattern (17 bp):
CCAAACCATTGACGAAA
Found at i:19412 original size:30 final size:30
Alignment explanation
Indices: 19378--19437 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
19368 TGAAAGTGGC
19378 CGTCTTGTGATGATAAGCTGACTATCTGCA
1 CGTCTTGTGATGATAAGCTGACTATCTGCA
19408 CGTCTTGTGATGATAAGCTGACTATCTGCA
1 CGTCTTGTGATGATAAGCTGACTATCTGCA
19438 GATCCTCCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
CGTCTTGTGATGATAAGCTGACTATCTGCA
Found at i:31732 original size:19 final size:19
Alignment explanation
Indices: 31708--31748 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
31698 CTTGTTATAT
* *
31708 TCACTTTACTAATCCTCAA
1 TCACTTTACTAACCCACAA
*
31727 TCACTTTTCTAACCCACAA
1 TCACTTTACTAACCCACAA
31746 TCA
1 TCA
31749 TTTTTTAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (19 bp):
TCACTTTACTAACCCACAA
Found at i:32114 original size:19 final size:19
Alignment explanation
Indices: 32090--32130 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
32080 TTTGTTATAT
* *
32090 TCACTTTACTAATCCTCAA
1 TCACTTTACTAACCCACAA
*
32109 TCACTTTTCTAACCCACAA
1 TCACTTTACTAACCCACAA
32128 TCA
1 TCA
32131 TTTTTTAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (19 bp):
TCACTTTACTAACCCACAA
Found at i:32390 original size:382 final size:382
Alignment explanation
Indices: 31684--32451 Score: 1482
Period size: 382 Copynumber: 2.0 Consensus size: 382
31674 ATCTGCCTGT
31684 GAAACGGCAACATTCTTGTTATATTCACTTTACTAATCCTCAATCACTTTTCTAACCCACAATCA
1 GAAACGGCAACATTCTTGTTATATTCACTTTACTAATCCTCAATCACTTTTCTAACCCACAATCA
31749 TTTTTTAACTTCTCTTTGATTTCCATTTGCAGATATGAACGCTTCCTTAAAATTATGATTTTAAG
66 TTTTTTAACTTCTCTTTGATTTCCATTTGCAGATATGAACGCTTCCTTAAAATTATGATTTTAAG
*
31814 TGTTTTAAAGAATACCAATCGTCCAGCGAAATTCTGGTTCACAAGGAACTACTCGTCTCCTCAGT
131 TGTTTTAAAGAATACCAATCGTCCAGCGAAATTCTGGTTCACAAAGAACTACTCGTCTCCTCAGT
31879 TCAAGGTTGTATATAACTTTTTGGCATTCTTTTCGTCTTTGTCTAGCACTTTTTCCCCCTGTTAG
196 TCAAGGTTGTATATAACTTTTTGGCATTCTTTTCGTCTTTGTCTAGCACTTTTTCCCCCTGTTAG
31944 TACATGTATAATGCACGTTTGCTTTCGGGTTATGCAGGATGGTTCCACATATGGCTCAGGAATAT
261 TACATGTATAATGCACGTTTGCTTTCGGGTTATGCAGGATGGTTCCACATATGGCTCAGGAATAT
32009 GGCTTTGACTATGAACTAATCACCTACAAATGGCCTACGTGGCTGCACAAGCAGACA
326 GGCTTTGACTATGAACTAATCACCTACAAATGGCCTACGTGGCTGCACAAGCAGACA
*
32066 GAAACGGCAACATTTTTGTTATATTCACTTTACTAATCCTCAATCACTTTTCTAACCCACAATCA
1 GAAACGGCAACATTCTTGTTATATTCACTTTACTAATCCTCAATCACTTTTCTAACCCACAATCA
32131 TTTTTTAACTTCTCTTTGATTTCCATTTGCAGATATGAACGCTTCCTTAAAATTATGATTTTAAG
66 TTTTTTAACTTCTCTTTGATTTCCATTTGCAGATATGAACGCTTCCTTAAAATTATGATTTTAAG
* *
32196 TGTTTTAAAGAATACCAATCGTCCAGCGAAATTCTGGTTTACAAAGAACTACTTGTCTCCTCAGT
131 TGTTTTAAAGAATACCAATCGTCCAGCGAAATTCTGGTTCACAAAGAACTACTCGTCTCCTCAGT
32261 TCAAGGTTGTATATAACTTTTTGGCATTCTTTTCGTCTTTGTCTAGCACTTTTTCCCCCTGTTAG
196 TCAAGGTTGTATATAACTTTTTGGCATTCTTTTCGTCTTTGTCTAGCACTTTTTCCCCCTGTTAG
*
32326 TACATGTCTAATGCACGTTTGCTTTCGGGTTATGCAGGATGGTTCCACATATGGCTCAGGAATAT
261 TACATGTATAATGCACGTTTGCTTTCGGGTTATGCAGGATGGTTCCACATATGGCTCAGGAATAT
*
32391 GGCTTTGACTATGAACTAATCACCTACAAATGGCCTACGTGGCTGCACAAGCAGGCA
326 GGCTTTGACTATGAACTAATCACCTACAAATGGCCTACGTGGCTGCACAAGCAGACA
32448 GAAA
1 GAAA
32452 AGCAGCGAAT
Statistics
Matches: 380, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
382 380 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (382 bp):
GAAACGGCAACATTCTTGTTATATTCACTTTACTAATCCTCAATCACTTTTCTAACCCACAATCA
TTTTTTAACTTCTCTTTGATTTCCATTTGCAGATATGAACGCTTCCTTAAAATTATGATTTTAAG
TGTTTTAAAGAATACCAATCGTCCAGCGAAATTCTGGTTCACAAAGAACTACTCGTCTCCTCAGT
TCAAGGTTGTATATAACTTTTTGGCATTCTTTTCGTCTTTGTCTAGCACTTTTTCCCCCTGTTAG
TACATGTATAATGCACGTTTGCTTTCGGGTTATGCAGGATGGTTCCACATATGGCTCAGGAATAT
GGCTTTGACTATGAACTAATCACCTACAAATGGCCTACGTGGCTGCACAAGCAGACA
Found at i:34617 original size:29 final size:29
Alignment explanation
Indices: 34571--34664 Score: 120
Period size: 29 Copynumber: 3.2 Consensus size: 29
34561 GACCCGACCC
*
34571 AGTGACATTCTAGAAATTTTTGTGAAAAA
1 AGTGACATTCTAGGAATTTTTGTGAAAAA
* *
34600 GGTGACATTCTAGGAA-TTTTGTAAAAAAA
1 AGTGACATTCTAGGAATTTTTGT-GAAAAA
34629 AGTGACATTCT-GTGAATTTTTGTGAAAAA
1 AGTGACATTCTAG-GAATTTTTGTGAAAAA
*
34658 AATGACA
1 AGTGACA
34665 ATTTGGGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.12
29 43 0.77
30 6 0.11
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (29 bp):
AGTGACATTCTAGGAATTTTTGTGAAAAA
Found at i:41973 original size:19 final size:19
Alignment explanation
Indices: 41949--42005 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
41939 TGGTGTTATG
41949 ACCGGTTTGACCAGTCTGA
1 ACCGGTTTGACCAGTCTGA
*
41968 ACCGGTTTGACCGGT-TCGA
1 ACCGGTTTGACCAGTCT-GA
*
41987 ACCGGGTTGACCAGTCTGA
1 ACCGGTTTGACCAGTCTGA
42006 CCCGACCCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 1 0.03
19 31 0.94
20 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.25
Consensus pattern (19 bp):
ACCGGTTTGACCAGTCTGA
Found at i:41982 original size:9 final size:9
Alignment explanation
Indices: 41947--41998 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
41937 AGTGGTGTTA
41947 TGACCGGTT
1 TGACCGGTT
* *
41956 TGACCAGTC
1 TGACCGGTT
41965 TGAACCGGTT
1 TG-ACCGGTT
41975 TGACCGGTT
1 TGACCGGTT
* *
41984 CGAACCGGGT
1 TG-ACCGGTT
41994 TGACC
1 TGACC
41999 AGTCTGACCC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 20 0.59
10 14 0.41
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.25
Consensus pattern (9 bp):
TGACCGGTT
Found at i:42035 original size:17 final size:17
Alignment explanation
Indices: 42013--42045 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42003 TGACCCGACC
42013 CGACCCGACCCGTTGAT
1 CGACCCGACCCGTTGAT
42030 CGACCCGACCCGTTGA
1 CGACCCGACCCGTTGA
42046 CCCGACCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.15
Consensus pattern (17 bp):
CGACCCGACCCGTTGAT
Found at i:42147 original size:30 final size:29
Alignment explanation
Indices: 42054--42162 Score: 141
Period size: 28 Copynumber: 3.8 Consensus size: 29
42044 GACCCGACCT
* *
42054 AGTGTCATTTTGGGAATTTTTGTGAAAAA
1 AGTGACATTCTGGGAATTTTTGTGAAAAA
*
42083 GGTGACATTCTGGGAATTTTTGT-AAAAA
1 AGTGACATTCTGGGAATTTTTGTGAAAAA
42111 AGTGACATTCTGGGAATTTTTGTGAAAAAA
1 AGTGACATTCTGGGAATTTTTGTG-AAAAA
* *
42141 ATTGACAATT-TGAGAATTTTTG
1 AGTGAC-ATTCTGGGAATTTTTG
42163 AATGTGGACT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
28 27 0.38
29 20 0.28
30 21 0.30
31 3 0.04
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (29 bp):
AGTGACATTCTGGGAATTTTTGTGAAAAA
Found at i:44252 original size:2 final size:2
Alignment explanation
Indices: 44245--44315 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
44235 ATTATTAAGA
44245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
44287 AT AT AT AT AT AT AT AT AT AT -T AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44316 TTGAAATATT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:44772 original size:2 final size:2
Alignment explanation
Indices: 44765--44791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44755 ATAATAATGT
44765 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 T
44792 TTTTTATATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45821 original size:102 final size:102
Alignment explanation
Indices: 45643--45830 Score: 322
Period size: 102 Copynumber: 1.8 Consensus size: 102
45633 ATTCTTGATT
* *
45643 TAGGTGTCGTTTGTTATGCAAATCTGAACGTGAATTATCGATGAAATGGTCGATATATTTATATA
1 TAGGTGTCGTTTGTTATGCAAAACTGAACGTGAATTACCGATGAAATGGTCGATATATTTATATA
*
45708 TACGATTGAGTTATATCTTCTCCACGTTTAGGTTTTA
66 TACGATGGAGTTATATCTTCTCCACGTTTAGGTTTTA
** *
45745 TAGGTGTCGTTTGTTATGCAAAACTGAACGTGAATTACCGATGAAATGGTCTCTTTATTTATATA
1 TAGGTGTCGTTTGTTATGCAAAACTGAACGTGAATTACCGATGAAATGGTCGATATATTTATATA
45810 TACGATGGAGTTATATCTTCT
66 TACGATGGAGTTATATCTTCT
45831 TCATGTGTAG
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 80 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (102 bp):
TAGGTGTCGTTTGTTATGCAAAACTGAACGTGAATTACCGATGAAATGGTCGATATATTTATATA
TACGATGGAGTTATATCTTCTCCACGTTTAGGTTTTA
Found at i:47980 original size:18 final size:19
Alignment explanation
Indices: 47943--47980 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
47933 TTTTTTTATA
* *
47943 AAAATAATTATTAAAGATT
1 AAAATAATTAATAAAAATT
47962 AAAATAA-TAATAAAAATT
1 AAAATAATTAATAAAAATT
47980 A
1 A
47981 TAACTTAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATAATTAATAAAAATT
Found at i:48791 original size:12 final size:11
Alignment explanation
Indices: 48769--48798 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
48759 AATAAATAAG
48769 AAATAATAATA
1 AAATAATAATA
48780 AAATATATAATA
1 AAATA-ATAATA
48792 AAATAAT
1 AAATAAT
48799 GGGTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATAATAATA
Found at i:49919 original size:4 final size:4
Alignment explanation
Indices: 49910--49934 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
49900 AAAAAATATG
49910 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
49935 TGTACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:50624 original size:106 final size:107
Alignment explanation
Indices: 50432--50642 Score: 336
Period size: 106 Copynumber: 2.0 Consensus size: 107
50422 TATTGTTCCT
* * * *
50432 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTTTGGAACTGGAAAAGTCTTTTGTTGACAG
1 AGTCCAATATCCTCCGCTGTGAAGTGGAAATTGGCTCTGAAACTGGAAAAGTCTTTTGTTGACAG
*
50497 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCG
66 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGCTGTCTCG
* *
50539 AGTCCAATATCCTTCGCTGTGAAGTGGAAATTGGCTCTGAAATTGG-AAAGT-TGTTTGTTGACA
1 AGTCCAATATCCTCCGCTGTGAAGTGGAAATTGGCTCTGAAACTGGAAAAGTCT-TTTGTTGACA
50602 GCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGCTGTCT
65 GCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGCTGTCT
50643 TAAACTGGGA
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
105 1 0.01
106 55 0.57
107 40 0.42
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (107 bp):
AGTCCAATATCCTCCGCTGTGAAGTGGAAATTGGCTCTGAAACTGGAAAAGTCTTTTGTTGACAG
CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGCTGTCTCG
Found at i:50676 original size:65 final size:65
Alignment explanation
Indices: 50583--50774 Score: 296
Period size: 65 Copynumber: 2.9 Consensus size: 65
50573 CTCTGAAATT
* * *
50583 GGAAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGCTGTCTTAAAC
1 GGAAA-TT-TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAAC
50648 TG
64 TG
* * *
50650 GGAAATTTTTGTCGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGACACTG
1 GGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTG
*
50715 GGAAA-TTTTGTTGACAACCAGTGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAA
1 GGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAA
50775 GTGGCACGAT
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
64 51 0.44
65 57 0.50
66 2 0.02
67 5 0.04
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (65 bp):
GGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTG
Found at i:51805 original size:58 final size:58
Alignment explanation
Indices: 51715--51830 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
51705 CGAGTTTTCA
51715 ATTCGGACCCATCCTTAGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAACCCACC
1 ATTCGGACCCATCCTTAGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAACCCACC
51773 ATTCGGACCCATCCTTAGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAACCCACC
1 ATTCGGACCCATCCTTAGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAACCCACC
51831 TTGTTTTTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.29
Consensus pattern (58 bp):
ATTCGGACCCATCCTTAGTTGCAAGACGCCCTTTGCGGGTTTTCATCTTGAACCCACC
Found at i:67992 original size:17 final size:14
Alignment explanation
Indices: 67954--67989 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
67944 GTGCGCCACC
67954 TCATCGGCCGCCGT
1 TCATCGGCCGCCGT
67968 TCATCGGCCGCCGT
1 TCATCGGCCGCCGT
67982 TCATCGGC
1 TCATCGGC
67990 GGCGAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.42, G:0.28, T:0.22
Consensus pattern (14 bp):
TCATCGGCCGCCGT
Found at i:69722 original size:106 final size:106
Alignment explanation
Indices: 69531--69885 Score: 575
Period size: 106 Copynumber: 3.3 Consensus size: 106
69521 ACCAGTCGTC
* * *
69531 CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAAT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
*
69596 TGTTTGTTGATAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* * * * * *
69637 CTTGCATTGTCTGGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
69702 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* * *
69743 CTTGCGTTGTCTGGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAATT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
*
69808 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
69849 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATGAA
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
69886 ATTGGGAAGT
Statistics
Matches: 228, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 228 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
Found at i:69943 original size:88 final size:88
Alignment explanation
Indices: 69794--69973 Score: 333
Period size: 88 Copynumber: 2.0 Consensus size: 88
69784 AAATTGGTTC
*
69794 TGAAATTGGGAATTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
69859 CTGGAGTCCAATATCCTTCGCTA
66 CTGGAGTCCAATATCCTTCGCTA
69882 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
69947 CTTGAGTCCAATATCCTTCGCTG
66 CTGGAGTCCAATATCCTTCGCTA
69970 TGAA
1 TGAA
69974 GTTGAAATTG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (88 bp):
TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTA
Found at i:69966 original size:43 final size:43
Alignment explanation
Indices: 69830--69979 Score: 112
Period size: 43 Copynumber: 3.4 Consensus size: 43
69820 ACCAGCGGTC
*
69830 CCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGCT-GTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
* * * * ** ***
69873 CCTTCGCTATGAAATTGGGAAGTT--GTT-TATTGACAACCAGCGGT
1 CCTTCGCTGTGAAGTT--GAACTTGCGTTGTCTTGA-GTCCA-ATAT
69917 CCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
1 -CCTTCGCT-GTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
69961 CCTTCGCTGTGAAGTTGAA
1 CCTTCGCTGTGAAGTTGAA
69980 ATTGGCTCTA
Statistics
Matches: 77, Mismatches: 19, Indels: 22
0.65 0.16 0.19
Matches are distributed among these distances:
42 4 0.05
43 40 0.52
44 5 0.06
45 23 0.30
46 5 0.06
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (43 bp):
CCTTCGCTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
Found at i:70026 original size:194 final size:194
Alignment explanation
Indices: 69690--70059 Score: 659
Period size: 194 Copynumber: 1.9 Consensus size: 194
69680 ATTGGCTCTA
*
69690 AAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
69755 GGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAATTTGTTTATTGACA
66 GGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTATTGACA
69820 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATG
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATG
*
69884 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
69949 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTATTGACA
66 GGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTATTGACA
70014 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
70060 GGCACGATAT
Statistics
Matches: 167, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
194 167 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (194 bp):
AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
GGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATG
Found at i:71569 original size:64 final size:64
Alignment explanation
Indices: 71501--71725 Score: 235
Period size: 64 Copynumber: 3.5 Consensus size: 64
71491 TTATTTGAAG
* * ** *
71501 GTGCATCAATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATT
*
71564 T
64 A
* *
71565 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTA
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTA
* * * * * *
71629 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATT
71693 A
64 A
*
71694 -TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCAT
71726 ACCTTCATTA
Statistics
Matches: 137, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.01
64 124 0.91
65 11 0.08
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTA
Found at i:72602 original size:103 final size:103
Alignment explanation
Indices: 72477--72699 Score: 428
Period size: 103 Copynumber: 2.2 Consensus size: 103
72467 GTCGAGGGTC
*
72477 TATGTGGTTCTTCGGGATATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
72542 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
*
72580 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
72645 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
72683 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
72700 CATTATTATA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:74365 original size:22 final size:22
Alignment explanation
Indices: 74340--74383 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
74330 CATTTTTGTC
*
74340 CATTTGATGCTCAACGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
*
74362 CATTTGATGTTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
74384 TAGGGTAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:75012 original size:20 final size:21
Alignment explanation
Indices: 74987--75037 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
74977 TTTATCCCCT
74987 TTTCTTTTTGATC-TTTGTTC
1 TTTCTTTTTGATCTTTTGTTC
* *
75007 TTTCTTTTTGTTCTTTTGTTT
1 TTTCTTTTTGATCTTTTGTTC
75028 TTTCCTTTTT
1 TTT-CTTTTT
75038 TGCTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 12 0.44
21 9 0.33
22 6 0.22
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.76
Consensus pattern (21 bp):
TTTCTTTTTGATCTTTTGTTC
Found at i:75061 original size:24 final size:24
Alignment explanation
Indices: 74998--75064 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
74988 TTCTTTTTGA
74998 TCTTTGTTCTTTCTTTTTG-TTCTTT
1 TCTTT-TT-TTTCTTTTTGCTTCTTT
* *
75023 T-GTTTTTTCCTTTTTTGCTTCTTT
1 TCTTTTTTTTC-TTTTTGCTTCTTT
75047 TCTTTTTTTTCTTTTTGC
1 TCTTTTTTTTCTTTTTGC
75065 CCTTTTTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
22 3 0.09
23 8 0.23
24 16 0.46
25 8 0.23
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.76
Consensus pattern (24 bp):
TCTTTTTTTTCTTTTTGCTTCTTT
Found at i:80342 original size:13 final size:13
Alignment explanation
Indices: 80324--80349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80314 GATGACCATG
80324 ACATATATATCAT
1 ACATATATATCAT
80337 ACATATATATCAT
1 ACATATATATCAT
80350 GCTGTATTAC
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATATATATCAT
Found at i:89390 original size:20 final size:21
Alignment explanation
Indices: 89365--89405 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
89355 GTTGTGGTCG
89365 TTTCTAGCCG-TTGGGGATGT
1 TTTCTAGCCGTTTGGGGATGT
*
89385 TTTCTAGCTGTTTGGGGATGT
1 TTTCTAGCCGTTTGGGGATGT
89406 AATCTCTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.10, C:0.12, G:0.34, T:0.44
Consensus pattern (21 bp):
TTTCTAGCCGTTTGGGGATGT
Found at i:93882 original size:20 final size:21
Alignment explanation
Indices: 93851--93891 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
93841 TAGCCGTTGG
93851 TGCCTGATGGTATCAATACTA
1 TGCCTGATGGTATCAATACTA
*
93872 TGCCT-ATGGTATCGATACTA
1 TGCCTGATGGTATCAATACTA
93892 CTATGTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (21 bp):
TGCCTGATGGTATCAATACTA
Found at i:96683 original size:20 final size:20
Alignment explanation
Indices: 96654--96692 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
96644 CTTAAATAAA
*
96654 AATTATATTTAATTTAATTT
1 AATTAGATTTAATTTAATTT
*
96674 AATTAGATTTATTTTAATT
1 AATTAGATTTAATTTAATT
96693 CTCTCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AATTAGATTTAATTTAATTT
Found at i:97813 original size:40 final size:40
Alignment explanation
Indices: 97749--97830 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
97739 ATATAACTGC
* * *
97749 AATTACAAGTAAGTATTATTATACAATTAAACTTATAGTG
1 AATTACAACTAAGTATCATCATACAATTAAACTTATAGTG
* *
97789 AATTACAACTAATTATCATCATACAATTAAATTTATAGTG
1 AATTACAACTAAGTATCATCATACAATTAAACTTATAGTG
97829 AA
1 AA
97831 ATTTATTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (40 bp):
AATTACAACTAAGTATCATCATACAATTAAACTTATAGTG
Found at i:98154 original size:27 final size:27
Alignment explanation
Indices: 98115--98171 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
98105 TATTACATAC
*
98115 TAACCCATGGATTATTTGAAAGTAAAA
1 TAACCCATAGATTATTTGAAAGTAAAA
* *
98142 TAACCTATAGATTATTTGAAAGTGAAA
1 TAACCCATAGATTATTTGAAAGTAAAA
98169 TAA
1 TAA
98172 TTGAACATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.32
Consensus pattern (27 bp):
TAACCCATAGATTATTTGAAAGTAAAA
Found at i:102411 original size:2 final size:2
Alignment explanation
Indices: 102404--102457 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
102394 TTTAGGAGAA
102404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102446 AT AT AT AT AT AT
1 AT AT AT AT AT AT
102458 TAATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104057 original size:23 final size:23
Alignment explanation
Indices: 104026--104073 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
104016 ATAAGAGACG
104026 AAATCAAATATTTT-TAAAATATA
1 AAATCAAAT-TTTTATAAAATATA
* *
104049 AAATTAAATTTTTATAAAATTTA
1 AAATCAAATTTTTATAAAATATA
104072 AA
1 AA
104074 GGTTGGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATCAAATTTTTATAAAATATA
Found at i:105306 original size:21 final size:21
Alignment explanation
Indices: 105255--105307 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
105245 ATTATGACTA
105255 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
105276 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
105297 TCGCAATGCGA
1 TCGCAATGCGA
105308 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:105322 original size:20 final size:21
Alignment explanation
Indices: 105297--105348 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
105287 TTTTCCCAAT
*
105297 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
105317 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
105338 TCGCAATGCGA
1 TCGCAATGCGA
105349 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:105327 original size:41 final size:41
Alignment explanation
Indices: 105282--105450 Score: 137
Period size: 41 Copynumber: 4.1 Consensus size: 41
105272 AATTTCGCGT
*
105282 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
105323 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
105364 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
105405 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
105446 TGCGA
1 TGCGA
105451 ATGCGATTTA
Statistics
Matches: 94, Mismatches: 28, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
39 2 0.02
40 8 0.09
41 82 0.87
43 1 0.01
44 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:105392 original size:21 final size:21
Alignment explanation
Indices: 105358--105430 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
105348 ATACTGACTA
* *
105358 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
105379 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
105399 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
105420 TCGCAATGCGA
1 TCGCAATGCGA
105431 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:106044 original size:18 final size:19
Alignment explanation
Indices: 106004--106047 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
105994 GCAACAAGAG
*
106004 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
106023 AATCGCAACGCG-AACCAA
1 AATCGCAACGCGAAACAAA
106041 AATCGCA
1 AATCGCA
106048 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:106084 original size:14 final size:14
Alignment explanation
Indices: 106065--106153 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
106055 TTTCATTTCG
106065 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
106079 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
106098 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
106112 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
106131 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
106145 CGTTGCGAT
1 CGTTGCGAT
106154 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 30 0.49
16 5 0.08
17 5 0.08
19 21 0.34
ACGTcount: A:0.10, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:106090 original size:33 final size:33
Alignment explanation
Indices: 106048--106177 Score: 215
Period size: 33 Copynumber: 3.9 Consensus size: 33
106038 CAAAATCGCA
**
106048 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
**
106081 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
106114 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
106147 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
106178 ATTAACTCGT
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
33 79 0.84
34 15 0.16
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:106320 original size:25 final size:24
Alignment explanation
Indices: 106266--106320 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
106256 TTATGTTTAT
* *
106266 TGTTTTTGGTATATCTTGACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
106290 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
106316 TGTTT
1 TGTTT
106321 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:107969 original size:13 final size:13
Alignment explanation
Indices: 107951--107986 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
107941 GAAGTTAGTA
107951 TTTGTCTTTTTGT
1 TTTGTCTTTTTGT
107964 TTTGTCTTTTTGT
1 TTTGTCTTTTTGT
107977 TTTGTCTTTT
1 TTTGTCTTTT
107987 GGTTGAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (13 bp):
TTTGTCTTTTTGT
Found at i:108030 original size:104 final size:105
Alignment explanation
Indices: 107889--108079 Score: 298
Period size: 104 Copynumber: 1.8 Consensus size: 105
107879 TAGATTGCTT
* *
107889 AGTAAATTTATTTGGTTGCTGCCAATACTGCTAAAC-TGT-TT-ATTAACACTGTGAAGTTAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACGTGTATTCATTAACACTGTAAAGTTAGTA
107951 TTTGTCTTTTTGTTTTGTCTTTTTGTTTTGTCTTTTGGTTGA
66 TTTGTC--TTTGTTTTGTCTTTTTGTTTTGTCTTTTGGTTGA
* *
107993 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC-GTGTATTCATTAACACTGTAAAGTTAGT
108058 ATTTGTCTTTGTTTTGTCTTTT
65 ATTTGTCTTTGTTTTGTCTTTT
108080 GGTTGAAAGT
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
104 34 0.43
106 18 0.23
107 2 0.03
108 25 0.32
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.50
Consensus pattern (105 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACGTGTATTCATTAACACTGTAAAGTTAGTA
TTTGTCTTTGTTTTGTCTTTTTGTTTTGTCTTTTGGTTGA
Found at i:108387 original size:42 final size:42
Alignment explanation
Indices: 108304--108396 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
108294 GCCCGACTCA
* * **
108304 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTCCAAAAGGCC
* * *
108346 CCTATCATTCCTCAAGAGTCCCCTCCCACCGTCCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTCCAAAAGGCC
* *
108388 ACTGTCATC
1 CCTATCATC
108397 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.40, G:0.14, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTCCAAAAGGCC
Found at i:109803 original size:14 final size:14
Alignment explanation
Indices: 109784--109814 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
109774 GTTTAATTGA
109784 TTGTAAAAGGTGAT
1 TTGTAAAAGGTGAT
*
109798 TTGTAAAAGTTGAT
1 TTGTAAAAGGTGAT
109812 TTG
1 TTG
109815 ATTAATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (14 bp):
TTGTAAAAGGTGAT
Found at i:109975 original size:33 final size:32
Alignment explanation
Indices: 109925--109989 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
109915 AAGTACTATC
* *
109925 GCAATGCGAAATGAAAATCGCAACGAGAGAATT
1 GCAACGCGAAATAAAAATCGCAACGAGA-AATT
109958 GCAACGCGAAATAAAAATCGCAACGAGAAATT
1 GCAACGCGAAATAAAAATCGCAACGAGAAATT
109990 AAATTCGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.14
Consensus pattern (32 bp):
GCAACGCGAAATAAAAATCGCAACGAGAAATT
Found at i:109997 original size:19 final size:19
Alignment explanation
Indices: 109954--109997 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
109944 GCAACGAGAG
*
109954 AATT-GCAACGCGAAATAA
1 AATTCGCAACGAGAAATAA
* *
109972 AAATCGCAACGAGAAATTA
1 AATTCGCAACGAGAAATAA
109991 AATTCGC
1 AATTCGC
109998 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (19 bp):
AATTCGCAACGAGAAATAA
Found at i:110015 original size:19 final size:19
Alignment explanation
Indices: 109993--110077 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
109983 AGAAATTAAA
109993 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
110012 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
110027 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
110045 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
110064 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
110078 AGACATTAAG
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
14 8 0.16
16 3 0.06
17 3 0.06
19 26 0.53
20 9 0.18
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:112031 original size:24 final size:24
Alignment explanation
Indices: 111997--112050 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
111987 CTGAAACATC
*
111997 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
112021 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
112045 ATCAAA
1 ATCAAA
112051 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:112856 original size:20 final size:21
Alignment explanation
Indices: 112831--112882 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
112821 TTTTCCTAAT
*
112831 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
112851 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
112872 TCGCAATGCGA
1 TCGCAATGCGA
112883 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:112956 original size:20 final size:20
Alignment explanation
Indices: 112867--112958 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
112857 TACGAATTTG
* *
112867 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
112887 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
112907 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
112928 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
112948 GAAAATCGCAA
1 GAAAATCGCAA
112959 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:113227 original size:20 final size:20
Alignment explanation
Indices: 113168--113231 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
113158 CGGGGAAATC
113168 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
** ***
113188 CAATTCG-AAATGAAAAATCG
1 CAACGCGAAAATG-GCTATCG
113208 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
113228 CAAC
1 CAAC
113232 TAGAAAATCG
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 5 0.16
20 22 0.69
21 5 0.16
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAATGGCTATCG
Found at i:113243 original size:34 final size:34
Alignment explanation
Indices: 113149--113251 Score: 100
Period size: 40 Copynumber: 2.9 Consensus size: 34
113139 ATTCATTTGA
** *
113149 CTATCGCAACGGGGAAATC-CAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
113182 CTATCGCAATTCGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
113222 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
113252 TGAAATCGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
33 9 0.16
34 16 0.28
35 2 0.03
36 1 0.02
38 2 0.03
39 5 0.09
40 23 0.40
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:113281 original size:14 final size:15
Alignment explanation
Indices: 113261--113332 Score: 58
Period size: 18 Copynumber: 4.5 Consensus size: 15
113251 ATGAAATCGC
113261 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
113276 -TTGCGATTTTCATTCG
1 ATTGCGATTTTC--TCG
* *
113292 CAGTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
113310 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
113326 -TTGCGAT
1 ATTGCGAT
113333 AGTCAGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
14 18 0.38
16 7 0.15
18 21 0.45
20 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:113300 original size:18 final size:19
Alignment explanation
Indices: 113277--113322 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
113267 ATTTTCTCGT
113277 TGCGATTTTCA-TTCGCAG
1 TGCGATTTTCATTTCGCAG
*
113295 TGCGA-TTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAG
113313 TGCGATTTTC
1 TGCGATTTTC
113323 TCGTTGCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 16 0.64
19 4 0.16
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAG
Found at i:113485 original size:14 final size:14
Alignment explanation
Indices: 113468--113494 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
113458 ACAATCAACA
113468 TTTACAAATCATTT
1 TTTACAAATCATTT
113482 TTTACAAATCATT
1 TTTACAAATCATT
113495 AAACAATCGA
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:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTACAAATCATTT
Found at i:115346 original size:20 final size:20
Alignment explanation
Indices: 115323--115374 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 20
115313 GAAACTTAAA
115323 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
115343 ATCGCAACGCG--AATGGCT
1 ATCGCAACGCGAAAATGACT
*
115361 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
115375 TGCAAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 16 0.57
20 12 0.43
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:115383 original size:19 final size:17
Alignment explanation
Indices: 115361--115472 Score: 80
Period size: 14 Copynumber: 6.8 Consensus size: 17
115351 GCGAATGGCT
115361 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAAT--AA
*
115380 ATCGCAA--CGACA-AA
1 ATCGCAATGCGAAATAA
115394 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT--AA
*
115413 ATCGCAA--CGACA-AA
1 ATCGCAATGCGAAATAA
115427 ATCGCAATGCGAAATAAA
1 ATCGCAATGCGAAAT-AA
*
115445 ATCGCAA--CGACA-AA
1 ATCGCAATGCGAAATAA
*
115459 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
115473 CACAAATCGC
Statistics
Matches: 76, Mismatches: 6, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
14 27 0.36
16 16 0.21
17 8 0.11
18 9 0.12
19 16 0.21
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (17 bp):
ATCGCAATGCGAAATAA
Found at i:115403 original size:33 final size:33
Alignment explanation
Indices: 115361--115472 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
115351 GCGAATGGCT
*
115361 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
115394 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
115427 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
115459 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
115473 CACAAATCGC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 30 0.39
33 47 0.61
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:115479 original size:19 final size:17
Alignment explanation
Indices: 115378--115483 Score: 86
Period size: 14 Copynumber: 6.5 Consensus size: 17
115368 TGCGAAATGC
115378 AAATCGCAA-CG--ACA
1 AAATCGCAAGCGAAACA
*
115392 AAATCGCAATGCGAAATGA
1 AAATCGCAA-GCGAAA-CA
115411 AAATCGCAA-CG--ACA
1 AAATCGCAAGCGAAACA
*
115425 AAATCGCAATGCGAAATA
1 AAATCGCAA-GCGAAACA
115443 AAATCGCAA-CG--ACA
1 AAATCGCAAGCGAAACA
115457 AAATCGCAACGCGAAACA
1 AAATCGCAA-GCGAAACA
115475 CAAATCGCA
1 -AAATCGCA
115484 TTGCGACTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 23
0.73 0.04 0.23
Matches are distributed among these distances:
14 30 0.41
15 1 0.01
16 8 0.11
17 2 0.03
18 15 0.20
19 18 0.24
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.10
Consensus pattern (17 bp):
AAATCGCAAGCGAAACA
Found at i:115480 original size:65 final size:66
Alignment explanation
Indices: 115361--115483 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 66
115351 GCGAATGGCT
* * *
115361 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
115426 A
66 A
115427 ATCGCAATGCGAAAT-AAAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
115484 TTGCGACTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 1 0.02
65 37 0.70
66 15 0.28
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.11
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:115501 original size:19 final size:18
Alignment explanation
Indices: 115479--115575 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
115469 GAAACACAAA
115479 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
115498 TCGCATTACGATTT--TG
1 TCGCATTGCGATTTCATT
115514 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
115531 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
115547 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
115564 TCGCATTGCGAT
1 TCGCATTGCGAT
115576 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 8 0.13
17 8 0.13
18 7 0.11
19 22 0.35
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:115525 original size:14 final size:14
Alignment explanation
Indices: 115506--115559 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
115496 TTTCGCATTA
115506 CGATTTTGTCGTTG
1 CGATTTTGTCGTTG
*
115520 CGATTTTCATTTCGCATTG
1 CGA-TTT--TGTCG--TTG
115539 CGATTTTGTCGTTG
1 CGATTTTGTCGTTG
115553 CGATTTT
1 CGATTTT
115560 CATTTCGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 6 0.18
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGATTTTGTCGTTG
Found at i:115528 original size:33 final size:33
Alignment explanation
Indices: 115484--115575 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
115474 ACAAATCGCA
* *
115484 TTGCGACTTTCATTTCGCATTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
115517 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
115550 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
115576 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:115582 original size:19 final size:20
Alignment explanation
Indices: 115560--115603 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
115550 TTGCGATTTT
115560 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* * *
115579 CATTTCCTCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
115599 CATTT
1 CATTT
115604 TCATGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:115611 original size:20 final size:20
Alignment explanation
Indices: 115569--115614 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
115559 TCATTTCGCA
*
115569 TTGCGATAGCCATTTCCTCG
1 TTGCGATAGCCATTTCATCG
*
115589 TTGCGATAGTCATTTTCAT-G
1 TTGCGATAGCCA-TTTCATCG
115609 TTGCGA
1 TTGCGA
115615 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTCATCG
Found at i:116121 original size:18 final size:18
Alignment explanation
Indices: 116095--116134 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
116085 GTCGATCAGA
* *
116095 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
116113 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
116131 TGAT
1 TGAT
116135 GACTCCGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:117451 original size:20 final size:20
Alignment explanation
Indices: 117426--117499 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
117416 AATAGTTTCT
*
117426 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
117446 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
117466 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
117486 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
117500 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:117751 original size:22 final size:22
Alignment explanation
Indices: 117724--117767 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
117714 GATGGAGATA
117724 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
117746 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
117768 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:118003 original size:20 final size:20
Alignment explanation
Indices: 117955--118003 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
117945 GATTATGTAT
117955 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
117975 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
117995 TATCTCGTT
1 TATCGCGTT
118004 ACAATTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:118041 original size:20 final size:20
Alignment explanation
Indices: 118016--118069 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
118006 AATTTTGTAT
*
118016 TATCGCATTACGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
118036 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
118056 TATCGCATTGCGAT
1 TATCGCATTGCGAT
118070 TTTTCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:118072 original size:61 final size:61
Alignment explanation
Indices: 117935--118072 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 61
117925 CGCTTTGAAA
* * * * *
117935 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * * *
117996 ATCTCGTTACAATTTTGTATTATCGCATTACGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
118057 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
118073 TCCAATTCGC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Done.