Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2652032 original size:21 final size:22
Alignment explanation
Indices: 2651991--2652041 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
2651981 CTTGATTCAA
*
2651991 TTTTTTCCTTTTTTTCATCTT-
1 TTTTTTTCTTTTTTTCATCTTC
2652012 TTTTTTTCTTTTTTT-ATTCTTC
1 TTTTTTTCTTTTTTTCA-TCTTC
2652034 TTCTTTTT
1 TT-TTTTT
2652042 TGATGAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 18 0.69
22 2 0.08
23 5 0.19
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTCATCTTC
Found at i:2654030 original size:21 final size:21
Alignment explanation
Indices: 2654004--2654049 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2653994 GTTCAAATGC
2654004 AAAAATGAAAATGCAAATATG
1 AAAAATGAAAATGCAAATATG
* **
2654025 AAAAATGCAAATGCATGTATG
1 AAAAATGAAAATGCAAATATG
2654046 AAAA
1 AAAA
2654050 GGTGTTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAATGAAAATGCAAATATG
Found at i:2654031 original size:15 final size:14
Alignment explanation
Indices: 2653998--2654036 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
2653988 CTTAAAGTTC
*
2653998 AAATGCAAAAATGA
1 AAATGCAAATATGA
2654012 AAATGCAAATATGAA
1 AAATGCAAATATG-A
2654027 AAATGCAAAT
1 AAATGCAAAT
2654037 GCATGTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.62, C:0.08, G:0.13, T:0.18
Consensus pattern (14 bp):
AAATGCAAATATGA
Found at i:2654178 original size:43 final size:44
Alignment explanation
Indices: 2654114--2654200 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 44
2654104 TGGTGCATCA
*
2654114 AACAAAACTTTTACATGTAGGGGACAACTTTCAT-TCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTC-TCTCCTAACTTC
*
2654158 AACAAAAC-TTTACATATAGGGGATAACTTTCTCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCTCTCCTAACTTC
2654201 TCTAAAGCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 1 0.03
43 31 0.77
44 8 0.20
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCTCTCCTAACTTC
Found at i:2655177 original size:30 final size:30
Alignment explanation
Indices: 2655141--2655201 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2655131 AAGGTTTTAA
2655141 TATTGTCTTAGATCAGGAGAATTTCTAGGG
1 TATTGTCTTAGATCAGGAGAATTTCTAGGG
2655171 TATTGTCTTAGATCAGGAGAATTTCTAGGG
1 TATTGTCTTAGATCAGGAGAATTTCTAGGG
2655201 T
1 T
2655202 TTATTATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (30 bp):
TATTGTCTTAGATCAGGAGAATTTCTAGGG
Found at i:2656161 original size:22 final size:23
Alignment explanation
Indices: 2656127--2656180 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
2656117 ATTCCAAGAA
2656127 AATATA-TTA-ATTTTTATAAAT
1 AATATATTTATATTTTTATAAAT
2656148 -ATATATTTATATTTTTATAAAT
1 AATATATTTATATTTTTATAAAT
*
2656170 AAGATATTTAT
1 AATATATTTAT
2656181 TTACTTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.17
21 3 0.10
22 12 0.41
23 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATATTTATATTTTTATAAAT
Found at i:2656400 original size:4 final size:4
Alignment explanation
Indices: 2656391--2656417 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2656381 TTAATATTTA
2656391 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2656418 AACATGATTA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2656706 original size:16 final size:18
Alignment explanation
Indices: 2656666--2656703 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2656656 AAGTATTGAA
2656666 AAAAT-AAAGGACAATAAT
1 AAAATAAAAGGACAAT-AT
2656684 AAAATAAAAGGACAAT-T
1 AAAATAAAAGGACAATAT
2656701 AAA
1 AAA
2656704 TAATGACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAATAAAAGGACAATAT
Found at i:2664358 original size:9 final size:9
Alignment explanation
Indices: 2664344--2664407 Score: 128
Period size: 9 Copynumber: 7.1 Consensus size: 9
2664334 TCTTGGAGCT
2664344 TTCTCTCAC
1 TTCTCTCAC
2664353 TTCTCTCAC
1 TTCTCTCAC
2664362 TTCTCTCAC
1 TTCTCTCAC
2664371 TTCTCTCAC
1 TTCTCTCAC
2664380 TTCTCTCAC
1 TTCTCTCAC
2664389 TTCTCTCAC
1 TTCTCTCAC
2664398 TTCTCTCAC
1 TTCTCTCAC
2664407 T
1 T
2664408 AGACAAGGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.11, C:0.44, G:0.00, T:0.45
Consensus pattern (9 bp):
TTCTCTCAC
Found at i:2665934 original size:12 final size:12
Alignment explanation
Indices: 2665917--2665942 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2665907 TCACTTTGCT
2665917 TTCCCTTGTTCG
1 TTCCCTTGTTCG
2665929 TTCCCTTGTTCG
1 TTCCCTTGTTCG
2665941 TT
1 TT
2665943 TACAATCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.31, G:0.15, T:0.54
Consensus pattern (12 bp):
TTCCCTTGTTCG
Found at i:2668450 original size:24 final size:24
Alignment explanation
Indices: 2668406--2668463 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
2668396 ATTTTACGTC
2668406 AAAGCTAAATTTATAAAA-TTTAAA
1 AAAG-TAAATTTATAAAATTTTAAA
* *
2668430 AAAGATAAATTTATTAGATTTTAAA
1 AAAG-TAAATTTATAAAATTTTAAA
2668455 AGAAGTAAA
1 A-AAGTAAA
2668464 AATAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.52
25 11 0.38
26 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.33
Consensus pattern (24 bp):
AAAGTAAATTTATAAAATTTTAAA
Found at i:2670446 original size:18 final size:21
Alignment explanation
Indices: 2670415--2670462 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2670405 CGACCACTGA
2670415 TATTTT-TTATTATC-C-TTT
1 TATTTTCTTATTATCACATTT
2670433 TATTTTCTTA-TATCACATTTT
1 TATTTTCTTATTATCACA-TTT
2670454 TATTTTCTT
1 TATTTTCTT
2670463 CTATTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.38
19 4 0.15
21 12 0.46
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTTTCTTATTATCACATTT
Found at i:2672292 original size:29 final size:29
Alignment explanation
Indices: 2672222--2672294 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
2672212 GAGTGCTCAG
* * *
2672222 GGCCCCCATATTTTTTTATCCTTATAATTG
1 GGCCCTCA-ATTTTTTCATCCTTATAATTA
* *
2672252 GGCCCTCCATTTTTTCATCTTTATAATTA
1 GGCCCTCAATTTTTTCATCCTTATAATTA
* *
2672281 GGTCCTTAATTTTT
1 GGCCCTCAATTTTT
2672295 AAATCTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 29 0.83
30 6 0.17
ACGTcount: A:0.19, C:0.22, G:0.10, T:0.49
Consensus pattern (29 bp):
GGCCCTCAATTTTTTCATCCTTATAATTA
Found at i:2672412 original size:44 final size:41
Alignment explanation
Indices: 2672370--2672657 Score: 181
Period size: 41 Copynumber: 6.8 Consensus size: 41
2672360 ATCTCTAATT
*
2672370 TTTTTTCAATC-CCTTTTTTAACTTTATAATTGAGGTCCCTAA
1 TTTTTT-AATCTCCATTTTTAACTTTATAATTGAGG-CCCTAA
* * * **
2672412 TTTTGTAATCT-CACTTTTAACTTTATATTTGAGGCTTTTAA
1 TTTTTTAATCTCCATTTTTAACTTTATAATTGAGGC-CCTAA
* * *
2672453 GTTTTTTCAATCTCAATTTATACCTTTATAATT-ACGGCCCCTAA
1 -TTTTTT-AATCTCCATTTTTAACTTTATAATTGA-GG-CCCTAA
*
2672497 TTTTTTAATCTCACTTTTTTAACTTTATAATTGAGGCCCTTAAA
1 TTTTTTAATCTC-CATTTTTAACTTTATAATTGAGGCCC-T-AA
* * *
2672541 TTTTTTTTAATCT-CACTTTCTAACTTTCTAATTGAAGCCCCTAAGA
1 --TTTTTTAATCTCCA-TTTTTAACTTTATAATTG-AGGCCCT-A-A
* ** ** * * *
2672587 ATTTTCGATCT-CAACTATACCTTTATAATTGAGGCCCTAT
1 TTTTTTAATCTCCATTTTTAACTTTATAATTGAGGCCCTAA
* * *
2672627 TTTTTTAATCTCAATTTCTACCTTTATAATT
1 TTTTTTAATCTCCATTTTTAACTTTATAATT
2672658 AGAGAAAATA
Statistics
Matches: 190, Mismatches: 39, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
40 9 0.05
41 43 0.23
42 25 0.13
43 43 0.23
44 33 0.17
45 20 0.11
46 17 0.09
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (41 bp):
TTTTTTAATCTCCATTTTTAACTTTATAATTGAGGCCCTAA
Found at i:2672429 original size:43 final size:42
Alignment explanation
Indices: 2672338--2672657 Score: 217
Period size: 44 Copynumber: 7.5 Consensus size: 42
2672328 ATTCAATATA
* ** *
2672338 ACTTTTTATCTTTATAATTGAAATCTCTAATTTTTTTTCAATC-C
1 ACTTTTTAACTTTATAATTG-AGGCCCTAA-TTTTTTT-AATCTC
*
2672382 -CTTTTTTAACTTTATAATTGAGGTCCCTAA-TTTTGTAATCTC
1 AC-TTTTTAACTTTATAATTGAGG-CCCTAATTTTTTTAATCTC
* ** *
2672424 AC-TTTTAACTTTATATTTGAGGCTTTTAAGTTTTTTCAATCTC
1 ACTTTTTAACTTTATAATTGAGGC-CCTAA-TTTTTTTAATCTC
* * *
2672467 AATTTATACCTTTATAATT-ACGGCCCCTAA-TTTTTTAATCTC
1 ACTTTTTAACTTTATAATTGA-GG-CCCTAATTTTTTTAATCTC
2672509 ACTTTTTTAACTTTATAATTGAGGCCCTTAAATTTTTTTTAATCTC
1 AC-TTTTTAACTTTATAATTGAGGCCC-T-AA-TTTTTTTAATCTC
* * * ** **
2672555 ACTTTCTAACTTTCTAATTGAAGCCCCTAAGAATTTTCGATCTC
1 ACTTTTTAACTTTATAATTG-AGGCCCTAA-TTTTTTTAATCTC
* *
2672599 AAC--TATACCTTTATAATTGAGGCCCT-ATTTTTTTAATCTC
1 -ACTTTTTAACTTTATAATTGAGGCCCTAATTTTTTTAATCTC
* * *
2672639 AATTTCTACCTTTATAATT
1 ACTTTTTAACTTTATAATT
2672658 AGAGAAAATA
Statistics
Matches: 218, Mismatches: 38, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
39 1 0.00
40 10 0.05
41 41 0.19
42 27 0.12
43 46 0.21
44 54 0.25
45 20 0.09
46 19 0.09
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (42 bp):
ACTTTTTAACTTTATAATTGAGGCCCTAATTTTTTTAATCTC
Found at i:2672436 original size:85 final size:87
Alignment explanation
Indices: 2672338--2672530 Score: 216
Period size: 85 Copynumber: 2.2 Consensus size: 87
2672328 ATTCAATATA
* * * ** *
2672338 ACTTTTTATCTTTATAATTGAAATC-TCTAATTTTTTTTCAATC-CCTTTTTTAACTTTATAATT
1 ACTTTTTAACTTTATAATTGAAAGCTTCTAA-GTTTTTTCAATCTCAATTTATAACTTTATAATT
*
2672401 GA-GGTCCCTAATTTTGTAATCTC
65 -ACGGCCCCTAATTTTGTAATCTC
* * * *
2672424 AC-TTTTAACTTTATATTTG-AGGCTTTTAAGTTTTTTCAATCTCAATTTATACCTTTATAATTA
1 ACTTTTTAACTTTATAATTGAAAGCTTCTAAGTTTTTTCAATCTCAATTTATAACTTTATAATTA
*
2672487 CGGCCCCTAATTTTTTAATCTC
66 CGGCCCCTAATTTTGTAATCTC
2672509 ACTTTTTTAACTTTATAATTGA
1 AC-TTTTTAACTTTATAATTGA
2672531 GGCCCTTAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
84 14 0.16
85 56 0.64
86 2 0.02
87 16 0.18
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.51
Consensus pattern (87 bp):
ACTTTTTAACTTTATAATTGAAAGCTTCTAAGTTTTTTCAATCTCAATTTATAACTTTATAATTA
CGGCCCCTAATTTTGTAATCTC
Found at i:2672584 original size:88 final size:85
Alignment explanation
Indices: 2672366--2672657 Score: 251
Period size: 88 Copynumber: 3.4 Consensus size: 85
2672356 TGAAATCTCT
* *
2672366 AATTTTTTTTCAATC-C-CTTTTTTAACTTTATAATTGAGGTCCCTAATTTTGTAATCTCACTTT
1 AATTTTTTTT-AATCTCAC-TTTATAACTTTATAATTGAGGCCCCTAATTTTGTAATCTCACTTT
* * *
2672429 TAACTTTATATTTGAGGCTTTT
64 TAACTTTATAATTGAGGCCTTA
* * * * *
2672451 AAGTTTTTTCAATCTCAATTTATACCTTTATAATT-ACGGCCCCTAATTTTTTAATCTCACTTTT
1 AATTTTTTTTAATCTCACTTTATAACTTTATAATTGA-GGCCCCTAATTTTGTAATCTCAC--TT
2672515 TTAACTTTATAATTGAGGCCCTTA
63 TTAACTTTATAATTGAGG-CCTTA
* * *
2672539 AATTTTTTTTAATCTCACTTTCTAACTTTCTAATTGAAGCCCCTAAGAATTTTCG--ATCTCAAC
1 AATTTTTTTTAATCTCACTTTATAACTTTATAATTGAGGCCCCT---AATTTT-GTAATCTC-AC
* * *
2672602 -TATACCTTTATAATTGAGGCCCT-
61 TTTTAACTTTATAATTGAGGCCTTA
* * *
2672625 -A-TTTTTTTAATCTCAATTTCTACCTTTATAATT
1 AATTTTTTTTAATCTCACTTTATAACTTTATAATT
2672658 AGAGAAAATA
Statistics
Matches: 171, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
84 34 0.20
85 46 0.27
87 22 0.13
88 55 0.32
89 1 0.01
90 5 0.03
91 8 0.05
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.48
Consensus pattern (85 bp):
AATTTTTTTTAATCTCACTTTATAACTTTATAATTGAGGCCCCTAATTTTGTAATCTCACTTTTA
ACTTTATAATTGAGGCCTTA
Found at i:2672893 original size:20 final size:21
Alignment explanation
Indices: 2672868--2672960 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
2672858 TTTTCCCAAT
*
2672868 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2672888 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
2672909 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
2672929 TCGGAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2672950 TCGCAATGCGA
1 TCGCAATGCGA
2672961 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2672913 original size:41 final size:41
Alignment explanation
Indices: 2672868--2672960 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
2672858 TTTTCCCAAT
2672868 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
2672909 TCGCAATGCGAATAAGTAAATCGGAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2672950 TCGCAATGCGA
1 TCGCAATGCGA
2672961 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:2672974 original size:20 final size:20
Alignment explanation
Indices: 2672949--2673043 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
2672939 AATTGGGAAA
*
2672949 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2672969 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2672990 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2673010 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2673030 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2673044 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2672991 original size:41 final size:41
Alignment explanation
Indices: 2672946--2673023 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
2672936 GCGAATTGGG
* * *
2672946 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
2672987 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
2673024 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:2673547 original size:20 final size:20
Alignment explanation
Indices: 2673518--2673561 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2673508 GCGATTTTAG
2673518 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
2673538 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
2673558 TTTC
1 TTTC
2673562 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2674902 original size:18 final size:18
Alignment explanation
Indices: 2674881--2674925 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2674871 TCCACTTCGG
*
2674881 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2674899 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2674917 GAGCCATCA
1 GAGCCATCA
2674926 TCTGATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2675450 original size:14 final size:14
Alignment explanation
Indices: 2675431--2675488 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2675421 ATGCGAAATG
2675431 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2675445 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2675461 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2675477 AAAATCGCAACG
1 AAAATCGCAACG
2675489 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2675473 original size:32 final size:33
Alignment explanation
Indices: 2675415--2675505 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2675405 GAAAATGACT
2675415 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2675448 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2675480 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2675506 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2675541 original size:14 final size:14
Alignment explanation
Indices: 2675522--2675579 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2675512 TTGTGTTTCG
2675522 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2675536 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2675552 CACGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2675568 CGTTGCGATTTT
1 CGTTGCGATTTT
2675580 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2675561 original size:32 final size:33
Alignment explanation
Indices: 2675517--2675595 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
2675507 GCGATTTGTG
2675517 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2675549 TTTCACGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2675582 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2675596 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2675594 original size:19 final size:19
Alignment explanation
Indices: 2675568--2675634 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2675558 GCGATTTTGT
**
2675568 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
2675587 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
2675607 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
2675626 CGTTGCGAT
1 CGTTGCGAT
2675635 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:2675614 original size:20 final size:19
Alignment explanation
Indices: 2675580--2675634 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
2675570 TTGCGATTTT
*
2675580 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2675599 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
2675619 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
2675635 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2677663 original size:33 final size:33
Alignment explanation
Indices: 2677618--2677728 Score: 150
Period size: 33 Copynumber: 3.4 Consensus size: 33
2677608 AAAACAGACT
* ***
2677618 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* * * *
2677651 ATCGCAATGCGAAATAAAAATCACAATGCGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
2677684 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
2677717 ATCGCAATGCGA
1 ATCGCAATGCGA
2677729 TTTTCATTTC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:2677664 original size:14 final size:14
Alignment explanation
Indices: 2677637--2677697 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
2677627 CGAAATGGCT
* *
2677637 ATCGCAACGAGAAA
1 ATCGCAATGCGAAA
2677651 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCG----AA-A
*
2677670 ATCACAATGCGAAA
1 ATCGCAATGCGAAA
2677684 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
2677698 TGAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 23 0.61
15 2 0.05
18 2 0.05
19 11 0.29
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (14 bp):
ATCGCAATGCGAAA
Found at i:2677672 original size:19 final size:18
Alignment explanation
Indices: 2677648--2677728 Score: 70
Period size: 14 Copynumber: 4.8 Consensus size: 18
2677638 TCGCAACGAG
2677648 AAAATCGCAATGCGAAAT
1 AAAATCGCAATGCGAAAT
*
2677666 AAAAATCACAATGCG----
1 -AAAATCGCAATGCGAAAT
2677681 AAAATCGCAATGCGAAAT
1 AAAATCGCAATGCGAAAT
*
2677699 GAAAATCGCAA--CG--AG
1 -AAAATCGCAATGCGAAAT
2677714 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
2677729 TTTTCATTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
14 23 0.45
15 1 0.02
16 2 0.04
17 2 0.04
19 23 0.45
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.14
Consensus pattern (18 bp):
AAAATCGCAATGCGAAAT
Found at i:2677804 original size:20 final size:20
Alignment explanation
Indices: 2677747--2677804 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2677737 TCGCATTGCG
* *
2677747 ATTTTCTCGTTGCGATAACC
1 ATTTTCACGTTGCGATAGCC
*
2677767 ATTTTCGCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
2677787 ATTTTCACGTTGCGATAG
1 ATTTTCACGTTGCGATAG
2677805 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:2678891 original size:24 final size:24
Alignment explanation
Indices: 2678864--2678917 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2678854 GTATTCGAAA
* *
2678864 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2678888 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2678912 TTTGAT
1 TTTGAT
2678918 GATGTTTCAG
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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2679109 original size:12 final size:12
Alignment explanation
Indices: 2679092--2679116 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2679082 ATATAATCCT
2679092 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2679104 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2679116 G
1 G
2679117 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2681428 original size:19 final size:19
Alignment explanation
Indices: 2681406--2681536 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
2681396 GGAAATTACT
2681406 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2681425 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2681439 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2681458 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
2681472 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2681491 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2681505 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2681524 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2681537 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2681448 original size:33 final size:33
Alignment explanation
Indices: 2681406--2681532 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
2681396 GGAAATTACT
2681406 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2681439 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2681471 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2681505 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2681533 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2681513 original size:66 final size:66
Alignment explanation
Indices: 2681407--2681539 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2681397 GAAATTACTA
*
2681407 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2681472 T
66 T
*
2681473 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2681538 T
66 T
2681539 T
1 T
2681540 AATTTCGCGG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2681554 original size:19 final size:20
Alignment explanation
Indices: 2681532--2681574 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2681522 AAATCGCAAC
2681532 GCGAATTT-AATTTCGCGGT
1 GCGAATTTCAATTTCGCGGT
* * *
2681551 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGGT
2681571 GCGA
1 GCGA
2681575 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.40
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGGT
Found at i:2681734 original size:14 final size:14
Alignment explanation
Indices: 2681715--2681751 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2681705 CATCAATTAA
2681715 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2681729 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2681743 ACAAATCAA
1 ACAAATCAA
2681752 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2683175 original size:21 final size:21
Alignment explanation
Indices: 2683109--2683175 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2683099 ATGAATCGGG
*
2683109 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2683129 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2683151 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2683172 CTCT
1 CTCT
2683176 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2683194 original size:42 final size:41
Alignment explanation
Indices: 2683109--2683231 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2683099 ATGAATCGGG
* * * * *
2683109 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
2683151 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
2683193 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
2683232 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:2685315 original size:33 final size:33
Alignment explanation
Indices: 2685258--2685356 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2685248 ACGAGATAAT
*
2685258 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
2685292 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2685325 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
2685357 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2685350 original size:19 final size:19
Alignment explanation
Indices: 2685233--2685416 Score: 165
Period size: 20 Copynumber: 10.1 Consensus size: 19
2685223 TCTTTTGGTT
*
2685233 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2685252 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2685272 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2685290 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2685306 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2685324 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2685339 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2685359 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2685378 GAAATG-AAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2685396 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2685415 GA
1 GA
2685417 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 15, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 22 0.16
19 42 0.31
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2685371 original size:39 final size:37
Alignment explanation
Indices: 2685328--2685416 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
2685318 GCGACCAGAC
2685328 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATG-AAATCGCAA-CGCGAAATAAA
*
2685367 AATCGCAACGCGAAATGAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAATCGCAACGCGAAATAAA
*
2685404 AATCGCAATGCGA
1 AATCGCAACGCGA
2685417 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 22 0.46
38 9 0.19
39 17 0.35
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (37 bp):
AATCGCAACGCGAAATGAAATCGCAACGCGAAATAAA
Found at i:2685445 original size:19 final size:19
Alignment explanation
Indices: 2685412--2685492 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
2685402 AAAATCGCAA
**
2685412 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2685431 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
2685450 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
2685464 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
2685484 TGCGATTTT
1 TGCGATTTT
2685493 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2686080 original size:21 final size:21
Alignment explanation
Indices: 2686047--2686147 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
2686037 TGCGAAAGTA
* * *
2686047 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
2686068 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
2686088 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
2686110 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
2686131 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
2686148 CCCAATTTGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:2686103 original size:20 final size:20
Alignment explanation
Indices: 2686010--2686103 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2686000 CGCTATGTAA
*
2686010 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
2686030 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2686050 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
2686071 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2686091 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2686104 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2686122 original size:41 final size:41
Alignment explanation
Indices: 2686031--2686165 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
2686021 AAAGTCAGTA
* * * ** *
2686031 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2686071 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
2686113 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
2686154 TTGCGTTGCGAT
1 TCGCGTTGCGAT
2686166 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2686136 original size:20 final size:20
Alignment explanation
Indices: 2686092--2686182 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
2686082 ATAGTCAGTA
* **
2686092 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2686113 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2686133 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
* *
2686154 TTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2686174 TCGCATTGC
1 TCGCATTGC
2686183 AAATTGGGAA
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 29 0.54
21 25 0.46
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2686164 original size:21 final size:21
Alignment explanation
Indices: 2686092--2686167 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2686082 ATAGTCAGTA
*
2686092 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
2686113 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
2686133 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
*
2686154 TTGCGTTGCGATTT
1 TCGCGTTGCGATTT
2686168 ACTTATTCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:2686166 original size:41 final size:41
Alignment explanation
Indices: 2686092--2686182 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
2686082 ATAGTCAGTA
2686092 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
2686133 TCGCATTGCGATTTTCCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2686174 TCGCATTGC
1 TCGCATTGC
2686183 AAATTGGGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2686281 original size:19 final size:19
Alignment explanation
Indices: 2686257--2686303 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
2686247 AAAATGCAAC
*
2686257 GCGAATTTGCGATCGCGTT
1 GCGAATTTGCGATCGCATT
*
2686276 GCGAATTAGCGATCGCATT
1 GCGAATTTGCGATCGCATT
*
2686295 GCGATTTTG
1 GCGAATTTG
2686304 TTGGTCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (19 bp):
GCGAATTTGCGATCGCATT
Found at i:2687157 original size:2 final size:2
Alignment explanation
Indices: 2687150--2687205 Score: 85
Period size: 2 Copynumber: 27.0 Consensus size: 2
2687140 AATGATTTTC
2687150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
2687193 CA TA TA TCA TA TA
1 TA TA TA T-A TA TA
2687206 GAGTTGATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2698121 original size:18 final size:19
Alignment explanation
Indices: 2698086--2698122 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2698076 CACGGAATGT
2698086 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2698106 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2698123 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2698360 original size:37 final size:37
Alignment explanation
Indices: 2698287--2698361 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
2698277 ACTATAAGGT
* *
2698287 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
2698324 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
2698361 A
1 A
2698362 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:2700701 original size:41 final size:41
Alignment explanation
Indices: 2700632--2701129 Score: 562
Period size: 41 Copynumber: 12.2 Consensus size: 41
2700622 CGTTAGTAGC
* ** * * *
2700632 GGCGTTTTTAGAACAAACGTTGCTAAAGACTCCTACTATAGC
1 GGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTACTTTAGT
* * *
2700674 GGCGTTTTTATACAAATGCCGCTAAAGAAT-GTAATTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * *
2700714 GGCATTTTTATACAAACGCCGCTAAAGTCT-GTAATTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * * *
2700754 GGCATTTTTATACAAACGACGCTATAGACTTGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * *
2700795 GGCGTTTTTATACAAACGCCGATATAGACTCATGA-TTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGT-ACTTTAGT
2700836 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
** * *
2700877 GGCGTTTTTATACAAACGTTGCTATAGACTCATGA-TTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGT-ACTTTAGT
*
2700918 GGCGTTTTTATACAAACGCCACTAAAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* *
2700959 GGCGTTTTTATACAATCGCCGCTAAAGACTCATACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
*
2701000 GGCGTGTTTGT-TACAAACGCCGCTATAGACTCGTGA-TTTAGT
1 GGCGT-TTT-TATACAAACGCCGCTAAAGACTCGT-ACTTTAGT
* * * *
2701042 GGCATTTTT-TACAAACGTCGCTATAGACTCATGA-TTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGT-ACTTTAGT
* * **
2701082 GGCGTTTTTATACAAACGCCGCTATAGACTCATGTTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
2701123 GGCGTTT
1 GGCGTTT
2701130 GTGTTTACAA
Statistics
Matches: 400, Mismatches: 46, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
40 109 0.27
41 244 0.61
42 45 0.11
43 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
Found at i:2701563 original size:10 final size:11
Alignment explanation
Indices: 2701537--2701601 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 11
2701527 ATTAATCAAT
2701537 TTATTATT-AA
1 TTATTATTAAA
*
2701547 TGATTATTAAA
1 TTATTATTAAA
2701558 TT-TTATTAAA
1 TTATTATTAAA
*
2701568 TTATTATAAAA
1 TTATTATTAAA
* **
2701579 TAAACATTAAA
1 TTATTATTAAA
*
2701590 TTATTATAAAA
1 TTATTATTAAA
2701601 T
1 T
2701602 AAACATTAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
10 17 0.40
11 25 0.60
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
TTATTATTAAA
Found at i:2701577 original size:20 final size:20
Alignment explanation
Indices: 2701501--2701577 Score: 52
Period size: 22 Copynumber: 3.8 Consensus size: 20
2701491 TTAAATACCT
* *
2701501 TTAAATAATTATCAAATATTTT
1 TTAAATTATTAT-AAAT-TTTA
*
2701523 TTAAATTA--ATCAA-TTTA
1 TTAAATTATTATAAATTTTA
*
2701540 TTATTAATGATTATTAAATTTTA
1 TTA--AATTATTA-TAAATTTTA
2701563 TTAAATTATTATAAA
1 TTAAATTATTATAAA
2701578 ATAAACATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
17 6 0.14
19 6 0.14
20 6 0.14
21 8 0.19
22 10 0.23
23 7 0.16
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (20 bp):
TTAAATTATTATAAATTTTA
Found at i:2701590 original size:22 final size:22
Alignment explanation
Indices: 2701562--2701613 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
2701552 ATTAAATTTT
2701562 ATTAAATTATTATAAAATAAAC
1 ATTAAATTATTATAAAATAAAC
2701584 ATTAAATTATTATAAAATAAAC
1 ATTAAATTATTATAAAATAAAC
2701606 ATTAAATT
1 ATTAAATT
2701614 TATCAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTAAATTATTATAAAATAAAC
Found at i:2702982 original size:21 final size:21
Alignment explanation
Indices: 2702956--2702997 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2702946 AACAAAGGCT
2702956 CGGTGCTGCCGGCTATAACAC
1 CGGTGCTGCCGGCTATAACAC
2702977 CGGTGCTGCCGGCTATAACAC
1 CGGTGCTGCCGGCTATAACAC
2702998 ATTTAAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.19
Consensus pattern (21 bp):
CGGTGCTGCCGGCTATAACAC
Found at i:2704278 original size:15 final size:15
Alignment explanation
Indices: 2704258--2704286 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2704248 GAGGTGAACT
2704258 AATGTGTATAGTTTC
1 AATGTGTATAGTTTC
2704273 AATGTGTATAGTTT
1 AATGTGTATAGTTT
2704287 TGTTTTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
AATGTGTATAGTTTC
Found at i:2704410 original size:43 final size:43
Alignment explanation
Indices: 2704388--2704600 Score: 329
Period size: 43 Copynumber: 5.0 Consensus size: 43
2704378 ACAAATGCCA
*
2704388 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGTCG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
**
2704431 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAATACCG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
*
2704474 CTAAATACACAGACAATAGCGGCGTTTGTAAAGAAAAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
* * * *
2704517 CTAAATATAAAGTCAATAGCGGTGTTTGTTAA-AAAAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
* *
2704559 CTAAATACACATTCAATAGCGGCGTTTGTAAAGACAAACGCC
1 CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCC
2704601 ACTATATGTC
Statistics
Matches: 152, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 37 0.24
43 115 0.76
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (43 bp):
CTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCG
Found at i:2704640 original size:128 final size:128
Alignment explanation
Indices: 2704361--2704648 Score: 319
Period size: 128 Copynumber: 2.2 Consensus size: 128
2704351 ATGGGCTTAT
* * *
2704361 TTGCGGCGTTTTTAATTACAAATGCCACTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAA
1 TTGCGGCGTTTTTAATTA-AAACGCCGCTAAATACAAAGTCAATAGCGGCGTTTGTAAAGAAAAA
* * *
2704426 CGTCGCTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAATACCGCTAAATACACAGACAA
65 CGCCGCTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACACCACTAAATACACAGACAA
* * ** * * *
2704490 TAGCGGCGTTTGTAAAGAAAAACGCCGCTAAATATAAAGTCAATAGCGGTGTTTGTTAA-AAAAA
1 TTGCGGCGTTT-TTAATTAAAACGCCGCTAAATACAAAGTCAATAGCGGCGTTTGTAAAGAAAAA
* * * * * ** *
2704554 CGCCGCTAAATACACATTCAATAGCGGCGTTTGTAAAGACAAACGCCACTATATGTC-TTGACCT
65 CGCCGCTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACACCACTAAAT-ACACAGA-CA
2704618 A
128 A
**
2704619 TTGCGGCGTTTTTTTTTAAAACGCCGCTAA
1 TTGCGGCGTTTTTAATTAAAACGCCGCTAA
2704649 CAATAGCGGC
Statistics
Matches: 129, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
128 68 0.53
129 57 0.44
130 4 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (128 bp):
TTGCGGCGTTTTTAATTAAAACGCCGCTAAATACAAAGTCAATAGCGGCGTTTGTAAAGAAAAAC
GCCGCTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACACCACTAAATACACAGACAA
Found at i:2716062 original size:129 final size:129
Alignment explanation
Indices: 2715832--2716095 Score: 456
Period size: 129 Copynumber: 2.0 Consensus size: 129
2715822 TCGTGTCAGG
* *
2715832 ATCTTTACCTGAAAATGAGGTTGCTGCTTATGATAATGCTCGTGTGATAGGTGACAACTTGAATG
1 ATCTTTACCTGAAAATGAGGTTGCTGCTCATGATAATGCTCGTGTGATAGGTGACAACTTGAATA
* *
2715897 AGGTTTTGGATGAACAAGGTCCAACAGTTCCAACTAATAGTGATTCCAGTACACAAGTATGTGA
66 AGGTTTTGGATGAACAAGGTCCAACAGCTCCAACTAATAGTGATTCCAGTACACAAGGATGTGA
* *
2715961 ATCTTTACCTGGAAATGAGGTTGCTGCTCATGATAATTCTCGTGTGATAGGTGACAACTTGAATA
1 ATCTTTACCTGAAAATGAGGTTGCTGCTCATGATAATGCTCGTGTGATAGGTGACAACTTGAATA
* *
2716026 AGGTTTTGGATGAGCAAGTTCCAACAGCTCCAACTAATAGTGATTCCAGTACACAAGGATGTGA
66 AGGTTTTGGATGAACAAGGTCCAACAGCTCCAACTAATAGTGATTCCAGTACACAAGGATGTGA
2716090 ATCTTT
1 ATCTTT
2716096 GCCTTTAATA
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (129 bp):
ATCTTTACCTGAAAATGAGGTTGCTGCTCATGATAATGCTCGTGTGATAGGTGACAACTTGAATA
AGGTTTTGGATGAACAAGGTCCAACAGCTCCAACTAATAGTGATTCCAGTACACAAGGATGTGA
Found at i:2725858 original size:23 final size:21
Alignment explanation
Indices: 2725832--2725878 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
2725822 TATTTCTGAT
2725832 AATACTAAATATTTTTAAGACAC
1 AATACTAAAT-TTTTTAA-ACAC
*
2725855 AATACTTAATTTTTTAAACAC
1 AATACTAAATTTTTTAAACAC
2725876 AAT
1 AAT
2725879 TTATCTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 7 0.30
23 9 0.39
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (21 bp):
AATACTAAATTTTTTAAACAC
Found at i:2731027 original size:23 final size:22
Alignment explanation
Indices: 2730976--2731027 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2730966 CCAAAAATGC
* *
2730976 TTAATGTTTTTAGCATTTGTTTC
1 TTAAT-TTTTTAGCATTTGATTA
*
2730999 TTAATTTTTTAGGATTTGATTA
1 TTAATTTTTTAGCATTTGATTA
2731021 TTGAATT
1 TT-AATT
2731028 GACTCTAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.60
Consensus pattern (22 bp):
TTAATTTTTTAGCATTTGATTA
Found at i:2733306 original size:42 final size:40
Alignment explanation
Indices: 2733233--2733318 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 40
2733223 TAGTTTGAGG
* * *
2733233 ATGAAATTTGAATATTTAAAAGTTTATGGACTAATTTAGAGA
1 ATGAAATTGGAATATTTAAAAGTCTAAGGACTAATTT-GA-A
* *
2733275 ATGATATTGGAATGTTTAAAAGTCTAAGGACTAATTTGAA
1 ATGAAATTGGAATATTTAAAAGTCTAAGGACTAATTTGAA
2733315 ATGA
1 ATGA
2733319 GGGTCATAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 5 0.13
41 2 0.05
42 32 0.82
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (40 bp):
ATGAAATTGGAATATTTAAAAGTCTAAGGACTAATTTGAA
Found at i:2733953 original size:71 final size:72
Alignment explanation
Indices: 2733865--2734008 Score: 200
Period size: 71 Copynumber: 2.0 Consensus size: 72
2733855 ACCAAAATGG
* * * *
2733865 AACCTAAACTAATCGTTAGATATAGTTTTGAAAAAAT-TCAAATTTAAGTACCAAAACAAAACAA
1 AACCTAAACTAAACGTTAGATATAATTTTAAAAAAATATAAAATTTAAGTACCAAAACAAAACAA
2733929 AATAAGA
66 AATAAGA
* *
2733936 AACCTAAACTAAACGTTAGGTATAATTTTAAAAAAATAAAATAAAATTTAAGTACCAAAACCAAA
1 AACCTAAACTAAACGTTAGATATAATTTTAAAAAAAT---ATAAAATTTAAGTACCAAAACAAAA
2734001 CAAAATAA
63 CAAAATAA
2734009 TAGTTTAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
71 33 0.52
75 30 0.48
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.24
Consensus pattern (72 bp):
AACCTAAACTAAACGTTAGATATAATTTTAAAAAAATATAAAATTTAAGTACCAAAACAAAACAA
AATAAGA
Found at i:2745867 original size:64 final size:61
Alignment explanation
Indices: 2745760--2745916 Score: 145
Period size: 65 Copynumber: 2.5 Consensus size: 61
2745750 ATTATATATT
* * **
2745760 TTTTGAAAATATTATATTATATAATTTAAAAACCTTTTGAAAATAGTA-TATTTGAAAACCA
1 TTTTGAAAATATTATATAATATAATTTAAAAACATTTCCAAAATA-TATTATTTGAAAACCA
* * * **
2745821 TTTTGAGAAATGTTATATAATATAAGTTTTGAAAACATTTCCAAAATATATTATTTTGGAAATAA
1 TTTTGA-AAATATTATATAATATAA--TTTAAAAACATTTCCAAAATATATTA-TTTGAAAACCA
*
2745886 TTTTGATAAATAGTATACGTAATATAATTTA
1 TTTTGA-AAATATTATA--TAATATAATTTA
2745917 TTATGGTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
61 6 0.08
62 16 0.21
63 2 0.03
64 19 0.25
65 25 0.33
67 8 0.11
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (61 bp):
TTTTGAAAATATTATATAATATAATTTAAAAACATTTCCAAAATATATTATTTGAAAACCA
Found at i:2753130 original size:23 final size:23
Alignment explanation
Indices: 2753064--2753133 Score: 104
Period size: 24 Copynumber: 3.0 Consensus size: 23
2753054 CACCACAGCT
*
2753064 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
2753087 CGTAGAATTTGCACCGTAGTGCCA
1 CGTAGAA-ATGCACCGAAGTGCCA
2753111 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2753134 TATAAAGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
23 20 0.49
24 21 0.51
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2755179 original size:16 final size:17
Alignment explanation
Indices: 2755152--2755184 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2755142 CTACGTGTAA
*
2755152 GTGAACTATGTGCTAAT
1 GTGAACTATGTGATAAT
2755169 GTGAA-TATGTGATAAT
1 GTGAACTATGTGATAAT
2755185 TATAAAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
GTGAACTATGTGATAAT
Found at i:2755438 original size:23 final size:23
Alignment explanation
Indices: 2755412--2755496 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
2755402 CAATCTTATA
2755412 TGGCACTACAGTGCAATTCTACG
1 TGGCACTACAGTGCAATTCTACG
* * *
2755435 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACAGTGCAATTCTACG
* * *
2755458 CGGTC-CTTC-GGGACAAATTCTACG
1 TGG-CACTACAGTG-C-AATTCTACG
2755482 TGGCACTACAGTGCA
1 TGGCACTACAGTGCA
2755497 CATTTATACG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
22 2 0.04
23 29 0.60
24 15 0.31
25 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTACAGTGCAATTCTACG
Found at i:2756235 original size:21 final size:21
Alignment explanation
Indices: 2756209--2756251 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2756199 CTATAGTAGT
2756209 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
2756230 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
2756251 A
1 A
2756252 TAATTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:2756914 original size:19 final size:19
Alignment explanation
Indices: 2756890--2756941 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
2756880 TTTAAGGGGG
2756890 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2756909 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
2756928 TGCATCAATGCACT
1 TGCATCGATGCACT
2756942 AATTGCATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:2762771 original size:28 final size:29
Alignment explanation
Indices: 2762723--2762780 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
2762713 ATATTATATA
* *
2762723 ATATAAGTTTGGAAAGCATTTTGA-AAAT
1 ATATAAGTTTGGAAAGAATTTGGATAAAT
* *
2762751 ATATAATTTTGGAAATAATTTGGATAAAT
1 ATATAAGTTTGGAAAGAATTTGGATAAAT
2762780 A
1 A
2762781 ATATGCATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.38
Consensus pattern (29 bp):
ATATAAGTTTGGAAAGAATTTGGATAAAT
Done.