Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004454.1 Hibiscus syriacus cultivar Beakdansim tig00009796_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: 368644
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:3020 original size:23 final size:23
Alignment explanation
Indices: 2990--3053 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2980 CAGCTCATAT
2990 AATTGCACTGAAGTGCCACGTAG
1 AATTGCACTGAAGTGCCACGTAG
* *
3013 AATTGCACTGGAGTGCCGCGTAG
1 AATTGCACTGAAGTGCCACGTAG
* *
3036 AATTGCACCGTAGTGCCA
1 AATTGCACTGAAGTGCCA
3054 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACTGAAGTGCCACGTAG
Found at i:3240 original size:103 final size:103
Alignment explanation
Indices: 3069--3286 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
3059 TAATGTCCAT
* * *
3069 AAGGACCATATATCATTCATTAAGAATCATATACATATACTAGGGACCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGACCAAGTATGTGTCTCACCA
3134 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
* * *
3172 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGACCAAGTATGTGTCTCACCA
*
3237 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
3275 AAGGACCACATA
1 AAGGACCACATA
3287 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGACCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
Found at i:6865 original size:15 final size:15
Alignment explanation
Indices: 6845--6874 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6835 CCTACTGTTG
6845 GAGTCTGTCGAACTC
1 GAGTCTGTCGAACTC
6860 GAGTCTGTCGAACTC
1 GAGTCTGTCGAACTC
6875 TCATCTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (15 bp):
GAGTCTGTCGAACTC
Found at i:8824 original size:23 final size:23
Alignment explanation
Indices: 8792--8855 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
8782 CAACTCATAT
*
8792 AATTGTACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
8815 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
8838 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
8856 TAAATAATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:9041 original size:103 final size:103
Alignment explanation
Indices: 8870--9087 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
8860 TAATGTCCAT
* *
8870 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
8935 GACTTCACACATGTTCCAAAGAATGCATATATGTCCCG
66 GACTTCACACATGTTACAAAGAATACATATATGTCCCG
*
8973 AATGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
9038 GACTTCACACATGTTACAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTACAAAGAATACATATATGTCCCG
9076 AAGGACCACATA
1 AAGGACCACATA
9088 GACCCTTGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTACAAAGAATACATATATGTCCCG
Found at i:9732 original size:11 final size:11
Alignment explanation
Indices: 9716--9751 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9706 GGTATGCATC
9716 GATGCACTACT
1 GATGCACTACT
9727 GATGCA-T-C-
1 GATGCACTACT
9735 GATGCACTACT
1 GATGCACTACT
9746 GATGCA
1 GATGCA
9752 TCGGTGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (11 bp):
GATGCACTACT
Found at i:9733 original size:19 final size:19
Alignment explanation
Indices: 9709--9759 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
9699 TAATGAAGGT
9709 ATGCATCGATGCACTACTG
1 ATGCATCGATGCACTACTG
9728 ATGCATCGATGCACTACTG
1 ATGCATCGATGCACTACTG
*
9747 ATGCATCGGTGCA
1 ATGCATCGATGCA
9760 TAAAATGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (19 bp):
ATGCATCGATGCACTACTG
Found at i:14560 original size:12 final size:12
Alignment explanation
Indices: 14545--14583 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
14535 ATTAAAAATG
14545 AAAAAAATGAAA
1 AAAAAAATGAAA
*
14557 AAAAAATTGAAA
1 AAAAAAATGAAA
14569 AAAAAAATGAAA
1 AAAAAAATGAAA
14581 AAA
1 AAA
14584 TGAAGTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (12 bp):
AAAAAAATGAAA
Found at i:18371 original size:22 final size:24
Alignment explanation
Indices: 18315--18371 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 24
18305 ATATATTTAT
18315 TAAAAAT-AT-TATTTCTATTCAA
1 TAAAAATAATATATTTCTATTCAA
*
18337 TAAAAATAA-ATATTTCT-TTGAA
1 TAAAAATAATATATTTCTATTCAA
18359 -AAAAATAATATAT
1 TAAAAATAATATAT
18372 AGAGTGGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 8 0.26
22 15 0.48
23 8 0.26
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAAAATAATATATTTCTATTCAA
Found at i:20907 original size:23 final size:23
Alignment explanation
Indices: 20881--20925 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20871 CACCACAGCT
*
20881 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
20904 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
20926 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:21174 original size:149 final size:149
Alignment explanation
Indices: 20904--21207 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
20894 CGAAGTGCCC
20904 CGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATAGAATTCCTTAAGAAT
*
20969 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCATACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
21034 CATATGTCCTAAAGAACCA
131 CATATGTCCTAAAGAACCA
* *
21053 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATAGAATTCCTTAAGAAT
21118 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
*
21183 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCA
21202 CGTAGA
1 CGTAGA
21208 CCCTCTACCC
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCA
Found at i:21455 original size:34 final size:29
Alignment explanation
Indices: 21376--21447 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
21366 TTTTCTGCAT
*
21376 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
21405 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
21434 ATTCATGTCATGTA
1 ATTCATGTCATGTA
21448 TCATAATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:21922 original size:67 final size:67
Alignment explanation
Indices: 21750--21900 Score: 223
Period size: 67 Copynumber: 2.3 Consensus size: 67
21740 TTTTTTCCAT
* * *
21750 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGA
21815 TGA
65 TGA
* * * *
21818 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
21882 GA
66 GA
21884 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
21901 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 23 0.30
67 41 0.54
68 12 0.16
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
GA
Found at i:29371 original size:19 final size:21
Alignment explanation
Indices: 29334--29376 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
29324 AACTTTTTTC
29334 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
29354 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
29374 TTT
1 TTT
29377 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:29382 original size:19 final size:20
Alignment explanation
Indices: 29333--29382 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
29323 TAACTTTTTT
*
29333 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
29353 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
29372 CTTTTACCTTT
1 CTTTTACCTTT
29383 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:59858 original size:4 final size:4
Alignment explanation
Indices: 59849--59916 Score: 118
Period size: 4 Copynumber: 17.0 Consensus size: 4
59839 GACTAGATCA
* *
59849 ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAT ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
59897 ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC
59917 TATGTTGCAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:63577 original size:60 final size:59
Alignment explanation
Indices: 63461--63578 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 59
63451 TAGAATGTTC
* * * *
63461 AAAAGTTTGGGACTTATTTAGAAAGAAAATCATGATTTGGGGATGAATTTGGAATATTT
1 AAAAGTTTGGGACTTATTTAGAAAGAAAATCATAATTTGAGGATGAATCTGAAATATTT
63520 AAAAGTTTTGGGACTTATTTAGAAAGAAAATCATAATTTGAGGATGAAATCT-AAATATT
1 AAAAG-TTTGGGACTTATTTAGAAAGAAAATCATAATTTGAGGATG-AATCTGAAATATT
63579 CAGAATTCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 5 0.09
60 44 0.83
61 4 0.08
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (59 bp):
AAAAGTTTGGGACTTATTTAGAAAGAAAATCATAATTTGAGGATGAATCTGAAATATTT
Found at i:64374 original size:21 final size:20
Alignment explanation
Indices: 64347--64445 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
64337 AATCAGTTTC
64347 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
64368 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
64389 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
64409 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
64430 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
64446 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:64474 original size:20 final size:20
Alignment explanation
Indices: 64412--64605 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
64402 CGATTTTCCA
* ** *
64412 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
64432 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
64452 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
64472 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
64492 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
64512 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
64532 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
64552 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
64572 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
64593 AAATCGCAACGCG
1 AAATCGCAACGCG
64606 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:64496 original size:60 final size:60
Alignment explanation
Indices: 64412--64605 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
64402 CGATTTTCCA
* ** * *
64412 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
64472 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
64532 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
64593 AAATCGCAACGCG
1 AAATCGCAACGCG
64606 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:65026 original size:33 final size:33
Alignment explanation
Indices: 64987--65057 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
64977 TTCACTTAGA
* *
64987 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
65020 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
65053 TTTCA
1 TTTCA
65058 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:65163 original size:21 final size:20
Alignment explanation
Indices: 65137--65242 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
65127 TGCAGAAGAG
65137 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
65158 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
65178 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
65199 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
65213 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
65232 TCGCAACGAGA
1 TCGCAACGAGA
65243 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:65181 original size:20 final size:21
Alignment explanation
Indices: 65135--65213 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
65125 TTTGCAGAAG
*
65135 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
65157 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
65176 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
65198 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
65214 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:65194 original size:41 final size:38
Alignment explanation
Indices: 65130--65246 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
65120 TTCAATTTGC
* *
65130 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
65168 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
65209 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
65242 AGAAT
1 AGAAT
65247 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:65219 original size:14 final size:14
Alignment explanation
Indices: 65200--65253 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
65190 AAATGAAAAG
65200 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
65214 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
65233 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
65247 CGCAACG
1 CGCAACG
65254 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:65229 original size:33 final size:33
Alignment explanation
Indices: 65189--65258 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
65179 CGCAACGAGA
65189 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
65222 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
65255 GAAA
1 GAAA
65259 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:65265 original size:33 final size:33
Alignment explanation
Indices: 65195--65269 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
65185 GAGAGAAATG
* **
65195 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
65228 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
65261 AAAATCGCA
1 AAAATCGCA
65270 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:65287 original size:19 final size:19
Alignment explanation
Indices: 65265--65362 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
65255 GAAACCAAAA
*
65265 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
65284 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
65298 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
65317 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
65331 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
65350 TCGCGTTGCGATT
1 TCGCGTTGCGATT
65363 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:65306 original size:14 final size:14
Alignment explanation
Indices: 65287--65376 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
65277 TTTCATTTCG
65287 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
65301 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
65320 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
65334 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
65351 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
65367 CGTTGCGATT
1 CGTTGCGATT
65377 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:65312 original size:33 final size:33
Alignment explanation
Indices: 65270--65384 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
65260 CAAAATCGCA
65270 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
65303 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
65336 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
65369 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
65385 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:67242 original size:93 final size:93
Alignment explanation
Indices: 67083--67463 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
67073 TAGATTGCTT
*
67083 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67148 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
67176 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67241 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
67269 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67334 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
67362 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
67427 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
67455 AGTAAATTT
1 AGTAAATTT
67464 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 285 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:67547 original size:19 final size:19
Alignment explanation
Indices: 67507--67635 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
67497 TAGTTTACTT
* *
67507 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
67527 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
67546 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
67565 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
67579 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
67598 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
67612 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
67631 TCGCA
1 TCGCA
67636 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:67586 original size:33 final size:32
Alignment explanation
Indices: 67543--67635 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
67533 CGCGAAACCA
**
67543 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
67575 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
67608 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
67636 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:67633 original size:52 final size:52
Alignment explanation
Indices: 67507--67635 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
67497 TAGTTTACTT
**
67507 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
67559 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
67612 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
67636 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:67653 original size:19 final size:19
Alignment explanation
Indices: 67631--67765 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
67621 GAAACCAAAA
*
67631 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
67650 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
67666 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
67683 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
67699 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
67716 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
67735 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
67755 TCGTGTTGCGA
1 TCGCGTTGCGA
67766 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:67672 original size:14 final size:14
Alignment explanation
Indices: 67653--67709 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
67643 TTTCATTTCG
67653 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
67667 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
67684 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
67700 CGTTGCGATT
1 CGTTGCGATT
67710 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:67678 original size:33 final size:33
Alignment explanation
Indices: 67636--67728 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
67626 CAAAATCGCA
*
67636 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
67669 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
67702 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
67729 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:69675 original size:14 final size:14
Alignment explanation
Indices: 69656--69691 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
69646 ATTGTTTAAT
69656 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
69670 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
69684 TGATTTGT
1 TGATTTGT
69692 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:69822 original size:19 final size:19
Alignment explanation
Indices: 69798--69897 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
69788 AAAATTGACT
69798 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
69817 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
69836 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
69850 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
69869 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
69889 ATCGCAATG
1 ATCGCAATG
69898 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:69927 original size:53 final size:53
Alignment explanation
Indices: 69798--69914 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
69788 AAAATTGACT
69798 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
69850 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
69903 ATCGCAATGCGA
1 ATCGCAATGCGA
69915 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:69932 original size:19 final size:19
Alignment explanation
Indices: 69904--70052 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
69894 AATGGGAGAA
* *
69904 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
69923 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
69939 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
69956 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
69975 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
69991 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
70008 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
70024 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
70041 TCCGCATTGCGA
1 T-CGCATTGCGA
70053 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:69967 original size:52 final size:52
Alignment explanation
Indices: 69904--70020 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
69894 AATGGGAGAA
*
69904 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
69956 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
70008 TCGCATTGCGATT
1 TCGCATTGCGATT
70021 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:69998 original size:33 final size:33
Alignment explanation
Indices: 69961--70052 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
69951 TCATTTCGCA
69961 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
69994 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
70027 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
70053 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:69999 original size:14 final size:14
Alignment explanation
Indices: 69980--70034 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
69970 TCATTTCGCA
69980 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
69994 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
70011 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
70027 TTGCGATT
1 TTGCGATT
70035 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:70135 original size:19 final size:19
Alignment explanation
Indices: 70111--70227 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
70101 AAAATTGACT
70111 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
70130 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
70149 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
70168 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
70182 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
70201 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
70221 ATCGCAA
1 ATCGCAA
70228 CGAGAGAATC
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 58 0.64
20 16 0.18
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:70190 original size:33 final size:36
Alignment explanation
Indices: 70111--70227 Score: 159
Period size: 33 Copynumber: 3.2 Consensus size: 36
70101 AAAATTGACT
70111 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
70149 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
70182 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
70221 ATCGCAA
1 ATCGCAA
70228 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
33 29 0.41
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.38
39 10 0.14
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:70259 original size:53 final size:53
Alignment explanation
Indices: 70129--70246 Score: 229
Period size: 53 Copynumber: 2.2 Consensus size: 53
70119 GCGAAATGAA
70129 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
70181 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
70234 AATCGCAATGCGA
1 AATCGCAATGCGA
70247 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.46
53 35 0.54
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:71399 original size:12 final size:12
Alignment explanation
Indices: 71382--71406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71372 TCTTCGGGGA
71382 CTTTTTCTTCTT
1 CTTTTTCTTCTT
71394 CTTTTTCTTCTT
1 CTTTTTCTTCTT
71406 C
1 C
71407 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:71615 original size:24 final size:24
Alignment explanation
Indices: 71581--71627 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
71571 CTGAAACATC
71581 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
71605 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
71628 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:72338 original size:20 final size:20
Alignment explanation
Indices: 72310--72559 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
72300 AAATTTCAGT
* * *
72310 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
72330 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
72350 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
72370 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
72390 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
72410 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
72430 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
72450 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
72470 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
72490 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
72510 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
72530 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
72550 GTTGCGATTT
1 GTTGCGATTT
72560 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:72576 original size:21 final size:21
Alignment explanation
Indices: 72546--72628 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
72536 ATTTTCATAT
*
72546 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
72567 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
72588 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
72609 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
72629 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:72619 original size:42 final size:43
Alignment explanation
Indices: 72526--72624 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
72516 ATTTATGTGT
* *
72526 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
72567 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
72609 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
72625 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:73473 original size:21 final size:20
Alignment explanation
Indices: 73434--73491 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
73424 AAATTTAATC
**
73434 ATAATTTTTATTTTTATTTTT
1 ATAATTTTT-TTTCAATTTTT
73455 AATAATTTTTTTTCAATTTTT
1 -ATAATTTTTTTTCAATTTTT
73476 -TAATTTGATTTTTCAA
1 ATAATTT--TTTTTCAA
73492 ACTTTATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
21 17 0.53
22 9 0.28
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (20 bp):
ATAATTTTTTTTCAATTTTT
Found at i:74948 original size:59 final size:60
Alignment explanation
Indices: 74826--74951 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 60
74816 AACATAATGA
* *
74826 ATAGTCAGGTGATCGATTCATAACTTTTGATAGATTAGGGACTCAACAAAACAACTCTCT
1 ATAGTCAGGTGATCGATTCATAACTTTTAATAGATTAGGGACTCAACAAAACAACTATCT
* * *
74886 ATAGTC-GG-GATCGTTTTATAACTTTTAATA-ATTAAAGGGACTCAACAAAATAA-TATCAT
1 ATAGTCAGGTGATCGATTCATAACTTTTAATAGATT--AGGGACTCAACAAAACAACTATC-T
74945 ATAGTCA
1 ATAGTCA
74952 AGGGATCATT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
57 3 0.05
58 22 0.39
59 26 0.46
60 6 0.11
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (60 bp):
ATAGTCAGGTGATCGATTCATAACTTTTAATAGATTAGGGACTCAACAAAACAACTATCT
Found at i:76662 original size:97 final size:97
Alignment explanation
Indices: 76540--76736 Score: 376
Period size: 97 Copynumber: 2.0 Consensus size: 97
76530 TTAAAAATCT
76540 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
76605 GTAAACAAATACCCAAATTCCTGAAAAAATGG
66 GTAAACAAATACCCAAATTCCTGAAAAAATGG
* *
76637 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTTGATACCCAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
76702 GTAAACAAATACCCAAATTCCTGAAAAAATGG
66 GTAAACAAATACCCAAATTCCTGAAAAAATGG
76734 CAA
1 CAA
76737 ATCATCTTAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (97 bp):
CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
GTAAACAAATACCCAAATTCCTGAAAAAATGG
Found at i:77025 original size:118 final size:116
Alignment explanation
Indices: 76637--77206 Score: 851
Period size: 118 Copynumber: 4.9 Consensus size: 116
76627 GAAAAAATGG
* *
76637 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTTGATACCCAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
*
76702 GTAAACAAATACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGATCT
66 GTAAACAAATACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGAGCT
*
76753 CAAGTTCAAGTCATCCAATCCAACTATCATGGAACTTCATTTCAATTCAAATCTTTAGATACCAA
1 CAAGTTCAAG---T-C-ATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAA
* * *
76818 AGATAGTTAACAAATACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGATCT
61 AGATCGTAAACAAATACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGAGCT
* *
76874 CATGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATATTTAGATACCAAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
* **
76939 GTAAACAAATACCCAAATTCATGGGGGAAAATGGCAAATCATCTTAAAGAGCT
66 GTAAACAAATACCCAAATTCCT--GAAAAAATGGCAAATCATCTTAAAGAGCT
* *
76992 CAAGTTCAAGTCATCCAACTATCATGGAACTTCATTTCAATTTAAATCTTTAGATACCAAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
*
77057 GTAAACAAATACCCAAATTCCTG--AAAATGGAAAATCATCTTAAAGAGCT
66 GTAAACAAATACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGAGCT
* * ** *
77106 CAAGTTCAACTCATCTAGTTATCATGAAACTTCATTTCAATTCAAATCTTTAGATGCCAAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
* *
77171 ATAAACAAATACCC-AATTCCTG-AAAAATGACAAATC
66 GTAAACAAATACCCAAATTCCTGAAAAAATGGCAAATC
77207 TTACACAATA
Statistics
Matches: 416, Mismatches: 30, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
113 8 0.02
114 107 0.26
116 81 0.19
117 1 0.00
118 109 0.26
119 1 0.00
120 1 0.00
121 108 0.26
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (116 bp):
CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
GTAAACAAATACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGAGCT
Found at i:77180 original size:232 final size:234
Alignment explanation
Indices: 76637--77206 Score: 864
Period size: 232 Copynumber: 2.4 Consensus size: 234
76627 GAAAAAATGG
* *
76637 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTTGATACCCAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
* *
76702 GTAAACAAATACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGATCTCAAGTTCAAGTCAT
66 GTAAACAAATACCCAAATTCATGAAAAAATGGCAAATCATCTTAAAGAGCTCAAGTTCAAG--AT
*
76767 CCAATCCAACTATCATGGAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATAGTTAACAAA
129 CCAATCCAACTATCATGGAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATAGTAAACAAA
* *
76832 TACCCAAATTCCTGAAAAAATGGCAAATCATCTTAAAGATCT
194 TACCCAAATTCCTG-AAAAATGGAAAATCATCTTAAAGAGCT
* *
76874 CATGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATATTTAGATACCAAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
**
76939 GTAAACAAATACCCAAATTCATGGGGGAAAATGGCAAATCATCTTAAAGAGCTCAAGTTCAAG-T
66 GTAAACAAATACCCAAATTCAT--GAAAAAATGGCAAATCATCTTAAAGAGCTCAAGTTCAAGAT
* *
77003 -C-ATCCAACTATCATGGAACTTCATTTCAATTTAAATCTTTAGATACCAAAGATCGTAAACAAA
129 CCAATCCAACTATCATGGAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATAGTAAACAAA
77066 TACCCAAATTCCTG-AAAATGGAAAATCATCTTAAAGAGCT
194 TACCCAAATTCCTGAAAAATGGAAAATCATCTTAAAGAGCT
* * ** *
77106 CAAGTTCAACTCATCTAGTTATCATGAAACTTCATTTCAATTCAAATCTTTAGATGCCAAAGATC
1 CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
* * *
77171 ATAAACAAATACCC-AATTCCTG-AAAAATGACAAATC
66 GTAAACAAATACCCAAATTCATGAAAAAATGGCAAATC
77207 TTACACAATA
Statistics
Matches: 307, Mismatches: 24, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
228 12 0.04
229 1 0.00
231 6 0.02
232 95 0.31
234 73 0.24
235 1 0.00
236 1 0.00
237 82 0.27
239 36 0.12
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (234 bp):
CAAGTTCAAGTCATCCAACTATCATGAAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATC
GTAAACAAATACCCAAATTCATGAAAAAATGGCAAATCATCTTAAAGAGCTCAAGTTCAAGATCC
AATCCAACTATCATGGAACTTCATTTCAATTCAAATCTTTAGATACCAAAGATAGTAAACAAATA
CCCAAATTCCTGAAAAATGGAAAATCATCTTAAAGAGCT
Found at i:89729 original size:21 final size:21
Alignment explanation
Indices: 89680--89731 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
89670 TCTCCATCGC
*
89680 CGCCGCCGCCAACTTCTTCCT
1 CGCCGCCTCCAACTTCTTCCT
89701 CGCCGCCTCCAACTTCTTCCT
1 CGCCGCCTCCAACTTCTTCCT
89722 CGCCGCCTCC
1 CGCCGCCTCC
89732 TGTTAGTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.08, C:0.56, G:0.13, T:0.23
Consensus pattern (21 bp):
CGCCGCCTCCAACTTCTTCCT
Found at i:95629 original size:63 final size:63
Alignment explanation
Indices: 95551--95678 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
95541 AATTTTTTTT
95551 ATATTAGTTGTTCATTTTACTAAAGGAGCCCATATGAAATTTTATGTGTTTGCCCCATACGGA
1 ATATTAGTTGTTCATTTTACTAAAGGAGCCCATATGAAATTTTATGTGTTTGCCCCATACGGA
95614 ATATTAGTTGTTCATTTTACTAAAGGAGCCCATATGAAATTTTATGTGTTTGCCCCATACGGA
1 ATATTAGTTGTTCATTTTACTAAAGGAGCCCATATGAAATTTTATGTGTTTGCCCCATACGGA
95677 AT
1 AT
95679 TTTTTTTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (63 bp):
ATATTAGTTGTTCATTTTACTAAAGGAGCCCATATGAAATTTTATGTGTTTGCCCCATACGGA
Found at i:97066 original size:21 final size:19
Alignment explanation
Indices: 97028--97069 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
97018 ATATGGTATA
*
97028 TTTGTTTTTTTTATTATCT
1 TTTGTTTTTTTTAATATCT
97047 TTTGTTTTTTATATAATATCT
1 TTTGTTTTTT-T-TAATATCT
97068 TT
1 TT
97070 ATTTTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 1 0.05
21 9 0.45
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTGTTTTTTTTAATATCT
Found at i:98115 original size:18 final size:18
Alignment explanation
Indices: 98094--98128 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
98084 TGAAAATGTT
98094 ATTATTATAAAA-AATATA
1 ATTATT-TAAAATAATATA
98112 ATTATTTAAAATAATAT
1 ATTATTTAAAATAATAT
98129 TTAATTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATTTAAAATAATATA
Found at i:108054 original size:60 final size:60
Alignment explanation
Indices: 107982--108169 Score: 175
Period size: 60 Copynumber: 3.1 Consensus size: 60
107972 TGCATCAAAT
* * * * * *
107982 ATCCCCAAACTATAAC-CTTTATTTTCAATTAGTCCTTAAACTTTTAAAGATTCTAATTTG
1 ATCCCCAAACTATAACTC-TCATTCTAAACTAGTCCTTAAACTTTTAAACATTCTAATTTC
* * *
108042 ATCCCCAAACTATGACTCTCATTCTAAACTAGTCCTTTAACTTTTGAACATTCTAATTTC
1 ATCCCCAAACTATAACTCTCATTCTAAACTAGTCCTTAAACTTTTAAACATTCTAATTTC
* * * * ** * * *
108102 ATCCCCAAACTATGAC-AT-ATTTCTAAATTGGTCCCCAAACTTCTAAATATTCCAATTTC
1 ATCCCCAAACTATAACTCTCA-TTCTAAACTAGTCCTTAAACTTTTAAACATTCTAATTTC
108161 ATCCCCAAA
1 ATCCCCAAA
108170 TTCATCCAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
58 1 0.01
59 40 0.37
60 65 0.61
61 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (60 bp):
ATCCCCAAACTATAACTCTCATTCTAAACTAGTCCTTAAACTTTTAAACATTCTAATTTC
Found at i:108112 original size:29 final size:29
Alignment explanation
Indices: 108080--108169 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
108070 CTAGTCCTTT
* *
108080 AACTTTTGAACATTCTAATTTCATCCCCA
1 AACTTATGAATATTCTAATTTCATCCCCA
* **
108109 AAC-TATGACATATTTCTAAATTGGTCCCCA
1 AACTTATGA-ATA-TTCTAATTTCATCCCCA
* * *
108139 AACTTCTAAATATTCCAATTTCATCCCCA
1 AACTTATGAATATTCTAATTTCATCCCCA
108168 AA
1 AA
108170 TTCATCCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
28 4 0.09
29 20 0.43
30 20 0.43
31 3 0.06
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTATGAATATTCTAATTTCATCCCCA
Found at i:108126 original size:30 final size:29
Alignment explanation
Indices: 108091--108169 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
108081 ACTTTTGAAC
*
108091 ATTCTAATTTCATCCCCAAACTAT-GACAT
1 ATTCTAATTTCATCCCCAAACT-TCGAAAT
* ** *
108120 ATTTCTAAATTGGTCCCCAAACTTCTAAAT
1 A-TTCTAATTTCATCCCCAAACTTCGAAAT
*
108150 ATTCCAATTTCATCCCCAAA
1 ATTCTAATTTCATCCCCAAA
108170 TTCATCCAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
ATTCTAATTTCATCCCCAAACTTCGAAAT
Found at i:108379 original size:60 final size:60
Alignment explanation
Indices: 108315--108455 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 60
108305 GGAATGTTCA
* **
108315 AAAAGTTTAAGGACTGATTTAGAATGA-AGGT-CATAGTTTAGGGATGAAACTAAAATATTC
1 AAAAGTTTAAGGACTAATTTAGAATGATAAATACAT--TTTAGGGATGAAACTAAAATATTC
* * * *
108375 AAAAG-TTAGATGACTAATTTAGAATGATAAATACATTTTAGGGATGATATTAAAATATTT
1 AAAAGTTTA-AGGACTAATTTAGAATGATAAATACATTTTAGGGATGAAACTAAAATATTC
* *
108435 AAAAGTTTAAGAACCAATTTA
1 AAAAGTTTAAGGACTAATTTA
108456 AAATAAAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 3 0.04
60 56 0.84
61 5 0.07
62 3 0.04
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.33
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTTAGAATGATAAATACATTTTAGGGATGAAACTAAAATATTC
Found at i:109549 original size:48 final size:45
Alignment explanation
Indices: 109495--109603 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
109485 GATGATGATG
** *
109495 ATGACGACGGTGAGGATAAGAAGTCAAGATATCGAAAAAAGAAAA
1 ATGACGACGAAGAGGATAAGAAATCAAGATATCGAAAAAAGAAAA
* * *
109540 ATGACGACGAAGATGATAAGAAATCGAGATATCGAAAAAAGAAGA
1 ATGACGACGAAGAGGATAAGAAATCAAGATATCGAAAAAAGAAAA
* * *
109585 ATGATGATGACGAGGATAA
1 ATGACGACGAAGAGGATAA
109604 TGATGATAGG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.50, C:0.08, G:0.27, T:0.15
Consensus pattern (45 bp):
ATGACGACGAAGAGGATAAGAAATCAAGATATCGAAAAAAGAAAA
Found at i:111080 original size:240 final size:236
Alignment explanation
Indices: 110690--111303 Score: 684
Period size: 240 Copynumber: 2.5 Consensus size: 236
110680 GACACGATAG
* * * * * *
110690 ATCACATGTGACCTGTCGGATATTATGTCAAAAGGTTGTAACTTCCGAGAAGT-ACAAGACTCCG
1 ATCACATGCGACTTGTCGAATATTACGTCAAAAGGTTGTAGCTTCTGAGAAGTGA-AA-ACTCCG
* * * *
110754 AAAATCCTACACCTAGAGATGTTCTTTTGAGACATCAATTG-AGGATATATTTTCTGGAGGTCTT
64 AAAATCCTATACCTAGAGATGTTCTTTCGAGAC-TCAACTGCA-GATATATTTTCTAGAGGTCTT
* * *
110818 GGTATACGAAAATAATACAACAATCATACACACTAGAGCCATGATGATTATTTAAATTATAGGTT
127 GGTATAAGAAAATAATACAACAATCATACACACAAGAGCCATGATGATTA--T---TTATAGATT
* * * *
110883 GA-CACGATAGGTGGAGTTC-TCAGTTGTTAATTAATTTTAATTCTGACAT
187 GATC-CGATAGATGGAGTTCATCAGCTGTTAATTAATTTCAATTATGACAT
*
110932 ATCACATGCGACTTGTCGAATATTACGTCAAAAGGTTGTAGCTTCTGAGAAGTGAAAACTCCTAA
1 ATCACATGCGACTTGTCGAATATTACGTCAAAAGGTTGTAGCTTCTGAGAAGTGAAAACTCCGAA
* *
110997 AATCCTATACCTAGAGATGTTC-TTCGAGATCTCAACTGCCGATATATTTTCTAGAGGTCTTTGT
66 AATCCTATACCTAGAGATGTTCTTTCGAGA-CTCAACTGCAGATATATTTTCTAGAGGTCTTGGT
* *
111061 ATAAGAAAATGATACAACAATCGTACACACAAGAGCCATGATGATTATTTATAGATTGATCCGAT
130 ATAAGAAAATAATACAACAATCATACACACAAGAGCCATGATGATTATTTATAGATTGATCCGAT
*
111126 AGATGGAGTTCAATTGATATAATCAGCTGTTAATTAATTTCAGTTATGACAT
195 AGATGGAGTTC----------ATCAGCTGTTAATTAATTTCAATTATGACAT
* ** * * *
111178 ATTATGTGCGACTTGTCGAATATAACGTCAAAAGGTTGTAGCTT-TCGAGAAATGCAAGACTCCG
1 ATCACATGCGACTTGTCGAATATTACGTCAAAAGGTTGTAGCTTCT-GAGAAGTG-AAAACTCCG
* *
111242 AAAACCCTATACTTAGAGATGTTCTTTCGAGACCTCAACT-CAGATATATTTTCTAGAGGTCT
64 AAAATCCTATACCTAGAGATGTTCTTTCGAGA-CTCAACTGCAGATATATTTTCTAGAGGTCT
111304 CGATTATGGC
Statistics
Matches: 320, Mismatches: 34, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
235 24 0.08
236 1 0.00
238 1 0.00
240 77 0.24
241 29 0.09
242 49 0.15
243 1 0.00
245 1 0.00
246 73 0.23
247 50 0.16
248 14 0.04
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (236 bp):
ATCACATGCGACTTGTCGAATATTACGTCAAAAGGTTGTAGCTTCTGAGAAGTGAAAACTCCGAA
AATCCTATACCTAGAGATGTTCTTTCGAGACTCAACTGCAGATATATTTTCTAGAGGTCTTGGTA
TAAGAAAATAATACAACAATCATACACACAAGAGCCATGATGATTATTTATAGATTGATCCGATA
GATGGAGTTCATCAGCTGTTAATTAATTTCAATTATGACAT
Found at i:120837 original size:31 final size:29
Alignment explanation
Indices: 120802--120900 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 29
120792 AAATTACGTG
120802 TTTAGTATCTAAACTATTAGTTTTAGTTTGT
1 TTTAGTATCTAAACT-TTAGTTTT-GTTTGT
* * * **
120833 TTTAGTATTTTAACTTTTAATTTT-TTTAA
1 TTTAGTATCTAAAC-TTTAGTTTTGTTTGT
* *
120862 ATTA-TATCTAAAATTTAGTTTTTGTTTCGT
1 TTTAGTATCTAAACTTTAG-TTTTGTTT-GT
120892 TTTAGTATC
1 TTTAGTATC
120901 CATTCAAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
27 4 0.08
28 10 0.20
29 9 0.18
30 3 0.06
31 23 0.46
32 1 0.02
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (29 bp):
TTTAGTATCTAAACTTTAGTTTTGTTTGT
Found at i:121263 original size:2 final size:2
Alignment explanation
Indices: 121256--121299 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
121246 TTATTTTTAT
121256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
121298 TA
1 TA
121300 ACAATTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:123822 original size:18 final size:19
Alignment explanation
Indices: 123781--123822 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
123771 ATGGTTTAGA
123781 AAAAAATAATTAAATGACT
1 AAAAAATAATTAAATGACT
123800 AAAAAATAATTAAATGACT
1 AAAAAATAATTAAATGACT
123819 AAAA
1 AAAA
123823 TGAATATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAAATAATTAAATGACT
Found at i:128797 original size:6 final size:6
Alignment explanation
Indices: 128790--128874 Score: 116
Period size: 6 Copynumber: 14.2 Consensus size: 6
128780 TCTTATTTTG
* * * *
128790 TACATG TACATG TACATG TACATA TGCATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* *
128838 TACATA TAAATA TACATA TACATA TACATA TGCATA T
1 TACATA TACATA TACATA TACATA TACATA TACATA T
128875 TGCTAGTTGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:131164 original size:24 final size:25
Alignment explanation
Indices: 131109--131165 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
131099 GTTTCTACAT
131109 ACAAAAAAGTTAAATTAAAATAATC
1 ACAAAAAAGTTAAATTAAAATAATC
*
131134 ACTAAAACAGTTAAA-T-AAAT-ATC
1 AC-AAAAAAGTTAAATTAAAATAATC
131157 AACAAAAAA
1 -ACAAAAAA
131166 ATTAGTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 8 0.29
24 6 0.21
25 3 0.11
26 11 0.39
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.21
Consensus pattern (25 bp):
ACAAAAAAGTTAAATTAAAATAATC
Found at i:133937 original size:17 final size:18
Alignment explanation
Indices: 133911--133947 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
133901 CCGAAATCGG
*
133911 TTTTATCGGTTC-GGTTT
1 TTTTAACGGTTCGGGTTT
133928 TTTTAACGGTTCGGGTTT
1 TTTTAACGGTTCGGGTTT
133946 TT
1 TT
133948 CGGTTCGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.08, C:0.11, G:0.24, T:0.57
Consensus pattern (18 bp):
TTTTAACGGTTCGGGTTT
Found at i:134120 original size:12 final size:12
Alignment explanation
Indices: 134103--134127 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
134093 TGAAGCCTTT
134103 AAACCGAACCGA
1 AAACCGAACCGA
134115 AAACCGAACCGA
1 AAACCGAACCGA
134127 A
1 A
134128 CCGTTTTACT
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:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACCGAACCGA
Found at i:135963 original size:16 final size:18
Alignment explanation
Indices: 135922--135965 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
135912 AATTTTAACC
135922 TTAAACCC-ATTAATATT
1 TTAAACCCAATTAATATT
135939 TTAAAACCCAATT-A-ATT
1 TT-AAACCCAATTAATATT
135956 TTAAACCCAA
1 TTAAACCCAA
135966 ATAAAAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 7 0.28
19 3 0.12
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAACCCAATTAATATT
Found at i:137669 original size:66 final size:66
Alignment explanation
Indices: 137497--137646 Score: 284
Period size: 66 Copynumber: 2.3 Consensus size: 66
137487 TAATTTTTTA
*
137497 AAATATTTATCTTGAAAAACTATTATTATTCAAATAATTTTGATATTTGATTTTAAAAAAATAAA
1 AAATATTTAGCTTGAAAAACTATTATTATTCAAATAATTTTGATATTTGATTTTAAAAAAATAAA
137562 T
66 T
137563 AAATATTTAGCTTGAAAAACTATTATTATTCAAATAATTTTGATATTTGATTTT-AAAAAATAAA
1 AAATATTTAGCTTGAAAAACTATTATTATTCAAATAATTTTGATATTTGATTTTAAAAAAATAAA
137627 T
66 T
137628 AAATATTTAGCTTGAAAAA
1 AAATATTTAGCTTGAAAAA
137647 GTTTTATCAT
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
65 30 0.36
66 53 0.64
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (66 bp):
AAATATTTAGCTTGAAAAACTATTATTATTCAAATAATTTTGATATTTGATTTTAAAAAAATAAA
T
Found at i:140956 original size:4 final size:4
Alignment explanation
Indices: 140947--141014 Score: 90
Period size: 4 Copynumber: 18.0 Consensus size: 4
140937 CTAACCATTT
*
140947 CATA CATA CATA CATA CATA CATA CATA CATA CA-A CAAA CA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
140993 CAT- GATA CA-A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA
141015 ACATGTAACC
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
3 11 0.19
4 47 0.81
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.21
Consensus pattern (4 bp):
CATA
Found at i:140993 original size:14 final size:14
Alignment explanation
Indices: 140950--141014 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
140940 ACCATTTCAT
140950 ACATACATACATACA
1 ACATACA-ACATACA
140965 TACATACATACATACA
1 -ACATACA-ACATACA
*
140981 ACAAACAACATACA
1 ACATACAACATACA
**
140995 TGATACAACATACA
1 ACATACAACATACA
141009 TACATA
1 -ACATA
141015 ACATGTAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
14 18 0.43
15 9 0.21
16 15 0.36
ACGTcount: A:0.54, C:0.25, G:0.02, T:0.20
Consensus pattern (14 bp):
ACATACAACATACA
Found at i:141002 original size:18 final size:18
Alignment explanation
Indices: 140947--141014 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
140937 CTAACCATTT
*
140947 CATACATACATACATACATA
1 CATACATACAT--ATACAAA
*
140967 CATACATACATACAACAAA
1 CATACATACATA-TACAAA
140986 CA-ACATACATGATAC-AA
1 CATACATACAT-ATACAAA
141003 CATACATACATA
1 CATACATACATA
141015 ACATGTAACC
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 5 0.12
18 19 0.45
19 7 0.17
20 11 0.26
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.21
Consensus pattern (18 bp):
CATACATACATATACAAA
Found at i:141618 original size:27 final size:27
Alignment explanation
Indices: 141563--141616 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
141553 AACGGTTTGG
141563 TTCGGTTTGGTTTTAAATGATTCGATT
1 TTCGGTTTGGTTTTAAATGATTCGATT
*
141590 TTCGGTTTGG-TTTAAATGCTTC-ATT
1 TTCGGTTTGGTTTTAAATGATTCGATT
141615 TT
1 TT
141617 TTTGATTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 5 0.19
26 11 0.42
27 10 0.38
ACGTcount: A:0.17, C:0.09, G:0.20, T:0.54
Consensus pattern (27 bp):
TTCGGTTTGGTTTTAAATGATTCGATT
Found at i:143115 original size:34 final size:34
Alignment explanation
Indices: 143072--143148 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 34
143062 TGGTCCATCC
* *
143072 GACCCGACCCGAGAATAAGGGAGATTCCACCCGA
1 GACCCGACCCGAAAATAAGGGAGACTCCACCCGA
*
143106 GACCCGACCCGAAAATAAGGGAGCCTCCACCCGA
1 GACCCGACCCGAAAATAAGGGAGACTCCACCCGA
* *
143140 AACCAGACC
1 GACCCGACC
143149 TGACTCGACC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.34, C:0.36, G:0.23, T:0.06
Consensus pattern (34 bp):
GACCCGACCCGAAAATAAGGGAGACTCCACCCGA
Found at i:144646 original size:60 final size:56
Alignment explanation
Indices: 144582--144691 Score: 132
Period size: 58 Copynumber: 1.9 Consensus size: 56
144572 GATTACAATC
*
144582 CTCATTCTAAATT-GCTCCCTAATCATTTGAATGTTCTAAATTCATCCCCAAACTATGATT
1 CTCATTCTAAATTAG--CCCGAA-CATTTGAATGTTC-AAATTCA-CCCCAAACTATGATT
* * *
144642 CTCATTCTATATTAGCCCGAACTTTTGAATGTTCCAATTCACCCCAAACT
1 CTCATTCTAAATTAGCCCGAACATTTGAATGTTCAAATTCACCCCAAACT
144692 TTTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
56 9 0.20
57 6 0.13
58 12 0.27
59 5 0.11
60 12 0.27
61 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.36
Consensus pattern (56 bp):
CTCATTCTAAATTAGCCCGAACATTTGAATGTTCAAATTCACCCCAAACTATGATT
Found at i:144926 original size:60 final size:59
Alignment explanation
Indices: 144798--144931 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 59
144788 AGAGTTTGGG
* * *
144798 GGATGAAATTAGAATGCCGAAATGTTATGGACCAATTTGGAATGAGAGTAATAATTTGA
1 GGATAAAATTAGAATGCCGAAATGTTATGGACCAAATTAGAATGAGAGTAATAATTTGA
* * * * **
144857 GGATGAAATTGGAATGCTGAAATATTTATGGACCAAATTAGAATGAGA-TACATTGTTTG-
1 GGATAAAATTAGAATGCCGAAAT-GTTATGGACCAAATTAGAATGAGAGTA-ATAATTTGA
144916 GAGATAAAATTAGAAT
1 G-GATAAAATTAGAAT
144932 TTCCAAAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 24 0.38
60 39 0.62
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (59 bp):
GGATAAAATTAGAATGCCGAAATGTTATGGACCAAATTAGAATGAGAGTAATAATTTGA
Found at i:146550 original size:60 final size:60
Alignment explanation
Indices: 146485--146625 Score: 158
Period size: 60 Copynumber: 2.4 Consensus size: 60
146475 AACGTTCAAG
* * *
146485 AGTTTGGGGATGAAATTAGAATGCCCAAATGTTTATGGACCAATTTTCAATGAGAGTA-AT
1 AGTTTGGGGATGAAATTAGAATGCCCAAATATTTATGGACCAAATTACAATGAGA-TACAT
* * *** *
146545 AGTTTGAGGATGAAATTGGAATGTTGAAATATTTATGGACCAAATTAGAATGAGATACAT
1 AGTTTGGGGATGAAATTAGAATGCCCAAATATTTATGGACCAAATTACAATGAGATACAT
* * *
146605 TGTTTGGAGATAAAATTAGAA
1 AGTTTGGGGATGAAATTAGAA
146626 CTTCCAAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
59 2 0.03
60 64 0.97
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (60 bp):
AGTTTGGGGATGAAATTAGAATGCCCAAATATTTATGGACCAAATTACAATGAGATACAT
Found at i:148313 original size:60 final size:60
Alignment explanation
Indices: 148245--148359 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
148235 GTTTGAATCG
** *
148245 TTTTCATTCTAAAGTAGTCCTCAAACTT-TTGAACATTTC-AATTTCATCGCCAAACTATGA
1 TTTTCATTCTAAACCAATCCTCAAACTTCTTGAACATTTCAAATTT-ATC-CCAAACTATGA
*
148305 TTTTCATTCTAAACCAATCTTCAAACTTCTTGAACATTTCAAATTTATCCCAAAC
1 TTTTCATTCTAAACCAATCCTCAAACTTCTTGAACATTTCAAATTTATCCCAAAC
148360 CATATGTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 30 0.61
61 14 0.29
62 5 0.10
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (60 bp):
TTTTCATTCTAAACCAATCCTCAAACTTCTTGAACATTTCAAATTTATCCCAAACTATGA
Found at i:157666 original size:3 final size:3
Alignment explanation
Indices: 157658--157698 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
157648 GATCAGAATG
157658 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
157699 TCATGGTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:166963 original size:93 final size:93
Alignment explanation
Indices: 166804--166987 Score: 368
Period size: 93 Copynumber: 2.0 Consensus size: 93
166794 ACAACGCATT
166804 ATGCTTTTAAAATTCACATCAAAGATGAAAAATTACAAAAAAGTTCAAATAAGTATTCAGACCTT
1 ATGCTTTTAAAATTCACATCAAAGATGAAAAATTACAAAAAAGTTCAAATAAGTATTCAGACCTT
166869 CCTAAACAGATTCTTCATGCCTCCACTA
66 CCTAAACAGATTCTTCATGCCTCCACTA
166897 ATGCTTTTAAAATTCACATCAAAGATGAAAAATTACAAAAAAGTTCAAATAAGTATTCAGACCTT
1 ATGCTTTTAAAATTCACATCAAAGATGAAAAATTACAAAAAAGTTCAAATAAGTATTCAGACCTT
166962 CCTAAACAGATTCTTCATGCCTCCAC
66 CCTAAACAGATTCTTCATGCCTCCAC
166988 CTGCTGAGCT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (93 bp):
ATGCTTTTAAAATTCACATCAAAGATGAAAAATTACAAAAAAGTTCAAATAAGTATTCAGACCTT
CCTAAACAGATTCTTCATGCCTCCACTA
Found at i:169197 original size:26 final size:26
Alignment explanation
Indices: 169146--169197 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
169136 AAGCTATGCC
*
169146 CAACGTTGGCTCCACAGATTTTCCAA
1 CAACGTTGGCTCCACAGATTTCCCAA
* *
169172 CAACGTTGGCTCCTCAGCTTTCCCAA
1 CAACGTTGGCTCCACAGATTTCCCAA
169198 TGTGAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (26 bp):
CAACGTTGGCTCCACAGATTTCCCAA
Found at i:175908 original size:231 final size:231
Alignment explanation
Indices: 175530--175991 Score: 702
Period size: 231 Copynumber: 2.0 Consensus size: 231
175520 TATTTTGGTC
*
175530 GGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCAGGTTTAGGGTGAAAAA
1 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC-GG-CGAGTTCAGGTTTAGGGTGAAAAA
* *
175595 TACCGGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCT
64 TACCCGACCCGAAAATATAAATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCT
* *
175660 CTCTATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTT
129 CTATATATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATTT
175725 CGGGTCGGGCCGGGTC-GGATTTCTAATTCATATATTTT
194 CGGGTCGGGCCGGGTCAGG-TTTCTAATTCATATATTTT
* * *
175763 GGGTCGGGTCGGGTTTTTTAAGTGTGGTATTCGGGTC-G-G-GTTCGGGTTTATGGTGAAAAAAA
1 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGCGAGTTCAGGTTTAGGGTG--AAAAA
175825 CTGGACCCGACCCGAAAA-A-AAATAATTTTACCTTATATATTTAGGAATAATTACAATAATACC
64 -T--ACCCGACCCGAAAATATAAATAATTTTACCTTATATATTTAGGAATAATTACAATAATACC
*
175888 TCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTA
126 CCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTA
* * *
175953 TTTCGTGTCGTGTCGGGTCAGGTTTCTAATTCATATATT
191 TTTCGGGTCGGGCCGGGTCAGGTTTCTAATTCATATATT
175992 GAATAAAAAT
Statistics
Matches: 211, Mismatches: 12, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
228 14 0.07
229 1 0.00
230 5 0.02
231 140 0.66
232 3 0.01
233 48 0.23
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (231 bp):
GGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGCGAGTTCAGGTTTAGGGTGAAAAATA
CCCGACCCGAAAATATAAATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
ATATATAATTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCG
GGTCGGGCCGGGTCAGGTTTCTAATTCATATATTTT
Found at i:176436 original size:18 final size:17
Alignment explanation
Indices: 176382--176445 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
176372 TATGGAATTT
176382 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
176399 GATTCTAATTCCTGACA
1 GATTCCAATTCCTGACA
*
176416 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
176434 GATTCCAATTCC
1 GATTCCAATTCC
176446 CTCAAAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 27 0.63
18 16 0.37
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:177069 original size:20 final size:20
Alignment explanation
Indices: 177039--177076 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
177029 TCGTCCCCGA
177039 ACCCGACCCG-AAATATTAT
1 ACCCGACCCGAAAATATTAT
177058 ACCCGAACCCGAAAATATT
1 ACCCG-ACCCGAAAATATT
177077 TTATATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (20 bp):
ACCCGACCCGAAAATATTAT
Found at i:177115 original size:33 final size:34
Alignment explanation
Indices: 177069--177152 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 34
177059 CCCGAACCCG
*
177069 AAAATATTTTATATATAACTAATATAAAA-ATAT
1 AAAATATTATATATATAACTAATATAAAATATAT
*
177102 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAACTAATATAAAATATAT
177136 AAAATATTATATATATA
1 AAAATATTATATATATA
177153 CAATCGGGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 27 0.56
34 21 0.44
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAACTAATATAAAATATAT
Found at i:177135 original size:9 final size:9
Alignment explanation
Indices: 177090--177142 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
177080 TATATAACTA
177090 ATATAAAA-
1 ATATAAAAT
177098 ATATAAAAT
1 ATATAAAAT
*
177107 AT-T-ATAT
1 ATATAAAAT
*
177114 ATAT-AATT
1 ATATAAAAT
177122 AATATAAAAT
1 -ATATAAAAT
177132 ATATAAAAT
1 ATATAAAAT
177141 AT
1 AT
177143 TATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.14
8 12 0.32
9 17 0.46
10 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATATAAAAT
Found at i:182895 original size:23 final size:24
Alignment explanation
Indices: 182842--182888 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
182832 AATGAATGTA
* *
182842 CTACAAGAGCATAGAAAACACATG
1 CTACAAGAGAAGAGAAAACACATG
182866 CTACAAGAGAAGAGAAAA-ACATG
1 CTACAAGAGAAGAGAAAACACATG
182889 TCACAAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (24 bp):
CTACAAGAGAAGAGAAAACACATG
Found at i:184224 original size:20 final size:20
Alignment explanation
Indices: 184199--184242 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
184189 TCCCTTTTTA
*
184199 TCTTGTTCGGATT-ACGATTT
1 TCTTGTCCGGATTGA-GATTT
*
184219 TCTTGTCCGGGTTGAGATTT
1 TCTTGTCCGGATTGAGATTT
184239 TCTT
1 TCTT
184243 TCGTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TCTTGTCCGGATTGAGATTT
Found at i:185570 original size:15 final size:15
Alignment explanation
Indices: 185550--185584 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
185540 CAAAGACAAT
185550 AAATCCGATG-GCAAG
1 AAATCCGATGCG-AAG
185565 AAATCCGATGCGAAG
1 AAATCCGATGCGAAG
185580 AAATC
1 AAATC
185585 TGATAAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (15 bp):
AAATCCGATGCGAAG
Found at i:188505 original size:3 final size:3
Alignment explanation
Indices: 188485--188531 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
188475 AAAATATTAT
* *
188485 ATA ATA TTA ATAA ATA ATA ATA ATA ATA ATA GATG ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
188532 CGATTAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:188509 original size:19 final size:19
Alignment explanation
Indices: 188485--188531 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
188475 AAAATATTAT
*
188485 ATAATATTAATAAATAATA
1 ATAATAATAATAAATAATA
* *
188504 ATAATAATAATAGATGATA
1 ATAATAATAATAAATAATA
188523 ATAATAATA
1 ATAATAATA
188532 CGATTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
ATAATAATAATAAATAATA
Found at i:189039 original size:40 final size:41
Alignment explanation
Indices: 188863--189042 Score: 113
Period size: 40 Copynumber: 4.4 Consensus size: 41
188853 TCCGCTCCTC
* * *
188863 TCCCTGAAAGATGTTGAAT-TTGGTGACGTTCTCACTTTTT
1 TCCCTGAAAGATGTTGAATCATGGTGACGATCTCACTATTT
* * * ***
188903 TCCCTGAAATATGTTGAGTCATGG-GACGATCTTACGCCTT
1 TCCCTGAAAGATGTTGAATCATGGTGACGATCTCACTATTT
* * * * *
188943 TCCCTGAAGGATGCT-AAGTCGTAT-TTCAAGCAATC-CACTCA-TT
1 TCCCTGAAAGATGTTGAA-TC--ATGGT-GA-CGATCTCACT-ATTT
* *
188986 TCTCTGAAGGATGTTGAATC-TGGTGACGATCTCACTATTT
1 TCCCTGAAAGATGTTGAATCATGGTGACGATCTCACTATTT
189026 TCCCTGAAAGATGTTGA
1 TCCCTGAAAGATGTTGA
189043 GTCGTATGAC
Statistics
Matches: 103, Mismatches: 25, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
39 6 0.06
40 65 0.63
41 4 0.04
42 2 0.02
43 20 0.19
44 6 0.06
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
TCCCTGAAAGATGTTGAATCATGGTGACGATCTCACTATTT
Found at i:189085 original size:123 final size:122
Alignment explanation
Indices: 188865--189128 Score: 332
Period size: 123 Copynumber: 2.1 Consensus size: 122
188855 CGCTCCTCTC
* * * * * *
188865 CCTGAAAGATGTTGAATTTGGTGACGTTCTCACTTTTTTCCCTGAAATATGTTGAGTCATGGGAC
1 CCTGAAGGATGTTGAATCTGGTGACGATCTCACTATTTTCCCTGAAAGATGTTGAGTCATAGGAC
** *
188930 GATCTTACGCCTTTCCCTGAAGGATGCTAAGTCGTATTTCAAGCAATCCACTCATTT
66 GATCTTACGCCTTTCCCTGAAGGACACTAAGTCGTACTTCAAGCAATCCACTCATTT
* *
188987 CTCTGAAGGATGTTGAATCTGGTGACGATCTCACTATTTTCCCTGAAAGATGTTGAGTCGTATGA
1 C-CTGAAGGATGTTGAATCTGGTGACGATCTCACTATTTTCCCTGAAAGATGTTGAGTCATAGGA
* * ** *
189052 CGATCTTA-GTCCTTTCCCTGAAGGACATTAAGTCGTACTTCGAGTGATCCACTCCTTT
65 CGATCTTACG-CCTTTCCCTGAAGGACACTAAGTCGTACTTCAAGCAATCCACTCATTT
**
189110 CCCCAAGGGATGTTGAATC
1 CCTGAA-GGATGTTGAATC
189129 GTGATTCAGG
Statistics
Matches: 121, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
122 5 0.04
123 116 0.96
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (122 bp):
CCTGAAGGATGTTGAATCTGGTGACGATCTCACTATTTTCCCTGAAAGATGTTGAGTCATAGGAC
GATCTTACGCCTTTCCCTGAAGGACACTAAGTCGTACTTCAAGCAATCCACTCATTT
Found at i:189236 original size:289 final size:289
Alignment explanation
Indices: 188717--189254 Score: 727
Period size: 289 Copynumber: 1.9 Consensus size: 289
188707 TATTTTTGCT
*
188717 TGGTGACGATCTCACTCTTTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
1 TGGTGACGATCTCACTATTTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
* * * * *
188782 AAAGGACTCTTAATCTTATTTTGACTGATCCACTCATTTCCCTAAAGGATGTTGAATCATGATTC
66 AAAGGACTATTAATCGTACTTCGACTGATCCACTCATTTCCCCAAAGGATGTTGAATCATGATTC
* * * **** * *
188847 AGGTGATCCGCTCCTCTCCCTGAAAGATGTTGAATTTGGTGACGTTCTCACTTTTTTCCCTGAAA
131 AGGTGATCCGCTCCTCTCACTGAAAGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAAA
* * * * *
188912 TATGTTGAGTCATGGGACGATCTTACGCCTTTCCCTGAAGGATGCTAAGTCGTATTTCAAGCAAT
196 GATGTTGAGTCATAGGACAATCTTACGCCTTTCCCTGAAGGATACTAAATCGTATTTCAAGCAAT
188977 CCACTCATTTCTCTGAAGGATGTTGAATC
261 CCACTCATTTCTCTGAAGGATGTTGAATC
* * * * *
189006 TGGTGACGATCTCACTATTTTCCCTGAAAGATGTTGAGTCGTATGACGATCTTAGTCCTTTCCCT
1 TGGTGACGATCTCACTATTTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
* * * * *
189071 GAAGGAC-ATTAAGTCGTACTTCGAGTGATCCACTCCTTTCCCCAAGGGATGTTGAATCGTGATT
66 AAAGGACTATTAA-TCGTACTTCGACTGATCCACTCATTTCCCCAAAGGATGTTGAATCATGATT
* * *
189135 CAGGTGATTCGCTCCTTTCACTGAAGGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAA
130 CAGGTGATCCGCTCCTCTCACTGAAAGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAA
** **
189200 AGATGTTGAGTTGTAGGACAATCTTACTTCTTTCCCTGAAGGATACTAAATCGTA
195 AGATGTTGAGTCATAGGACAATCTTACGCCTTTCCCTGAAGGATACTAAATCGTA
189255 ATTCGGGTAA
Statistics
Matches: 211, Mismatches: 37, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
288 4 0.02
289 207 0.98
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (289 bp):
TGGTGACGATCTCACTATTTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
AAAGGACTATTAATCGTACTTCGACTGATCCACTCATTTCCCCAAAGGATGTTGAATCATGATTC
AGGTGATCCGCTCCTCTCACTGAAAGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAAA
GATGTTGAGTCATAGGACAATCTTACGCCTTTCCCTGAAGGATACTAAATCGTATTTCAAGCAAT
CCACTCATTTCTCTGAAGGATGTTGAATC
Found at i:189427 original size:37 final size:36
Alignment explanation
Indices: 189316--189463 Score: 156
Period size: 36 Copynumber: 4.1 Consensus size: 36
189306 TAGGGAAACA
* * * *
189316 ATCCTAAGAAGGATTCTAATATATTTCTAGAAAATG
1 ATCCTAAGAAGGACTCAAACAAATTTCTAGAAAATG
* ** *
189352 ATCCTAAGAAGGAATTTAACAAA-TTCTAGAAAAACG
1 ATCCTAAGAAGGACTCAAACAAATTTCTAG-AAAATG
* *
189388 ATCCTAAGAATGACTCAAACAAATTTCTAGATAATCG
1 ATCCTAAGAAGGACTCAAACAAATTTCTAGAAAAT-G
*
189425 ATCCTACGAAGGACTCAAA-AGAATTTCTAGAAAATG
1 ATCCTAAGAAGGACTCAAACA-AATTTCTAGAAAATG
189461 ATC
1 ATC
189464 GACCTCACTA
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
35 6 0.06
36 51 0.54
37 37 0.39
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.26
Consensus pattern (36 bp):
ATCCTAAGAAGGACTCAAACAAATTTCTAGAAAATG
Found at i:189558 original size:44 final size:45
Alignment explanation
Indices: 189470--189641 Score: 222
Period size: 44 Copynumber: 3.9 Consensus size: 45
189460 GATCGACCTC
* *
189470 ACTAAAAGATTGACTCCTCTGCACGAGAAAGTCAAGAATAACATT
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
*
189515 ACTAAAAGGTTGACTCCTCTTCATG-GAAAGTCAAGAATAACATT
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
* * * * * *
189559 ACTAAAAGGATGACTCCTCTTCGCGAGAAAGCCAATAATGACATC
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
* * *
189604 A-TTAAAGGTTGACTCTTCTTCACGAGAAAGTCAGGAAT
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAAT
189642 GTTTCTAGGA
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
44 71 0.65
45 38 0.35
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (45 bp):
ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
Found at i:189633 original size:89 final size:89
Alignment explanation
Indices: 189470--189641 Score: 222
Period size: 89 Copynumber: 1.9 Consensus size: 89
189460 GATCGACCTC
* *
189470 ACTAAAAGATTGACTCCTCTGCACGAGAAAGTCAAGAATAACATTACTAAAAGGTTGACTCCTCT
1 ACTAAAAGATTGACTCCTCTGCACGAGAAAGCCAAGAATAACATCACTAAAAGGTTGACTCCTCT
*
189535 TCATGGAAAGTCAAGAATAACATT
66 TCACGGAAAGTCAAGAATAACATT
* * * * * *
189559 ACTAAAAGGA-TGACTCCTCTTCGCGAGAAAGCCAATAATGACATCA-TTAAAGGTTGACTCTTC
1 ACTAAAA-GATTGACTCCTCTGCACGAGAAAGCCAAGAATAACATCACTAAAAGGTTGACTCCTC
*
189622 TTCACGAGAAAGTCAGGAAT
65 TTCACG-GAAAGTCAAGAAT
189642 GTTTCTAGGA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
88 20 0.28
89 49 0.69
90 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (89 bp):
ACTAAAAGATTGACTCCTCTGCACGAGAAAGCCAAGAATAACATCACTAAAAGGTTGACTCCTCT
TCACGGAAAGTCAAGAATAACATT
Found at i:191104 original size:13 final size:13
Alignment explanation
Indices: 191088--191114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
191078 CCTTTTTCGA
191088 TCTAATTTTTTCT
1 TCTAATTTTTTCT
191101 TCTAATTTTTTCT
1 TCTAATTTTTTCT
191114 T
1 T
191115 TCAACTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TCTAATTTTTTCT
Found at i:191670 original size:3 final size:3
Alignment explanation
Indices: 191646--191695 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
191636 CTACAAAATG
* *
191646 TAA T-A TAA TAG TAA TAAA TAA TAA TAA TAA TAA TAGA TGA T-A TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
191691 TAA TA
1 TAA TA
191696 CAATTAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:192731 original size:18 final size:18
Alignment explanation
Indices: 192708--192742 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
192698 ACTTAAAATT
192708 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
192726 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
192743 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:193008 original size:15 final size:17
Alignment explanation
Indices: 192967--193019 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
192957 AGCTTATTTT
*
192967 CATATAATTCACTTTCA
1 CATATGATTCACTTTCA
192984 CAT-TGA-TCAC-TTC-
1 CATATGATTCACTTTCA
*
192997 CATATGATTCACATGTCA
1 CATATGATTCAC-TTTCA
193015 CATAT
1 CATAT
193020 CTCATGGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.10
14 6 0.21
15 8 0.28
16 2 0.07
17 5 0.17
18 5 0.17
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (17 bp):
CATATGATTCACTTTCA
Found at i:195172 original size:2 final size:2
Alignment explanation
Indices: 195161--195220 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
195151 GTAAATTTTC
195161 AT AT -T AT AT AT AT AT AT AT -T 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
195201 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
195221 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:200740 original size:16 final size:16
Alignment explanation
Indices: 200719--200840 Score: 178
Period size: 16 Copynumber: 7.8 Consensus size: 16
200709 TTTCTCTAGC
200719 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
200735 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
*
200751 AGGTTAAAGAAGTCCG
1 AGGTTAAAGAAGTCTG
200767 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
200783 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
* *
200799 AGGTTAAAGATGCCT-
1 AGGTTAAAGAAGTCTG
* *
200814 --TTTACAGAAGTCTG
1 AGGTTAAAGAAGTCTG
200828 AGGTTAAAGAAGT
1 AGGTTAAAGAAGT
200841 TTTTGTTCAG
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
13 9 0.10
16 84 0.90
ACGTcount: A:0.37, C:0.08, G:0.30, T:0.25
Consensus pattern (16 bp):
AGGTTAAAGAAGTCTG
Found at i:204882 original size:14 final size:15
Alignment explanation
Indices: 204863--204891 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
204853 AATCTGGTGA
204863 TTTTAAAAT-TTATT
1 TTTTAAAATATTATT
204877 TTTTAAAATATTATT
1 TTTTAAAATATTATT
204892 ATAATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAATATTATT
Found at i:204949 original size:26 final size:27
Alignment explanation
Indices: 204894--204950 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
204884 ATATTATTAT
* * * *
204894 AATTATAAAAAAACCTAATTTCTCTTA
1 AATTATAAAAAAACCAAAATACTCTAA
204921 AATTATAAAAAAACCAAAATAC-CTAA
1 AATTATAAAAAAACCAAAATACTCTAA
204947 AATT
1 AATT
204951 CCCAAATCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (27 bp):
AATTATAAAAAAACCAAAATACTCTAA
Found at i:206287 original size:11 final size:11
Alignment explanation
Indices: 206271--206297 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
206261 TCTTTGGGTG
206271 TAAGGAAAGCT
1 TAAGGAAAGCT
206282 TAAGGAAAGCT
1 TAAGGAAAGCT
206293 TAAGG
1 TAAGG
206298 TGGATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.30, T:0.19
Consensus pattern (11 bp):
TAAGGAAAGCT
Found at i:207394 original size:43 final size:42
Alignment explanation
Indices: 207308--207407 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 42
207298 TATATTTCAT
*
207308 GCTATGTGATATGACTTACGTGATTATATGAAATGCGATATAA
1 GCTATGTGATATGACTTACGTAATTATATGAAATGCGA-ATAA
* *
207351 GTTATGTGATATTGAAC-TACGTAATTATATGATAATGTG-ATAA
1 GCTATGTGATA-TG-ACTTACGTAATTATATGA-AATGCGAATAA
*
207394 GCTATGTGACATGA
1 GCTATGTGATATGA
207408 TCTATGTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
41 1 0.02
42 2 0.04
43 23 0.47
44 16 0.33
45 7 0.14
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (42 bp):
GCTATGTGATATGACTTACGTAATTATATGAAATGCGAATAA
Found at i:207443 original size:14 final size:14
Alignment explanation
Indices: 207390--207445 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
207380 TGATAATGTG
*
207390 ATAAGCTATGTGAC
1 ATAAGCTATGTGAT
* *
207404 ATGATCTATGTGAT
1 ATAAGCTATGTGAT
*
207418 -TATTGTCTATGTGAT
1 ATA-AG-CTATGTGAT
207433 ATAAGCTATGTGA
1 ATAAGCTATGTGA
207446 AATGGTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
13 1 0.03
14 19 0.59
15 10 0.31
16 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (14 bp):
ATAAGCTATGTGAT
Found at i:216409 original size:21 final size:21
Alignment explanation
Indices: 216383--216438 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
216373 GATACTGACT
216383 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
216404 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
216425 ATCGCAACGCGATA
1 ATCGCAACGCGATA
216439 CTGACTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:216670 original size:22 final size:22
Alignment explanation
Indices: 216645--216702 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
216635 TCACTCTCTA
*
216645 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
216667 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
216689 CGGCGAAATCCGTC
1 CGACGAAATCCGTC
216703 TATCTCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:217074 original size:14 final size:14
Alignment explanation
Indices: 217055--217081 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
217045 AACGTGAAAT
217055 GAAAATCGCAACGA
1 GAAAATCGCAACGA
217069 GAAAATCGCAACG
1 GAAAATCGCAACG
217082 CGATTTTAGT
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:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:217135 original size:20 final size:20
Alignment explanation
Indices: 217110--217158 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
217100 ACGATTCTCT
217110 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
217130 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
217150 TGTTGCGAT
1 CGTTGCGAT
217159 TTTCATTTTC
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:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:217164 original size:20 final size:20
Alignment explanation
Indices: 217126--217181 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
217116 GATAGTCAAA
* **
217126 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
217146 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
217166 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
217182 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Done.