Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008023.1 Hibiscus syriacus cultivar Beakdansim tig00110496_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: 214807
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3400 original size:11 final size:13
Alignment explanation
Indices: 3369--3397 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3359 TGGCAAAGAA
3369 GAAAAGGTATGTT
1 GAAAAGGTATGTT
3382 GAAAAGGTATG-T
1 GAAAAGGTATGTT
3394 GAAA
1 GAAA
3398 GGTTTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (13 bp):
GAAAAGGTATGTT
Found at i:10079 original size:35 final size:35
Alignment explanation
Indices: 10000--10105 Score: 140
Period size: 35 Copynumber: 3.0 Consensus size: 35
9990 ACTACCTAAA
* *
10000 CATCACCATCTTCCATCACCATTTTCAGGCCTATAA
1 CATCACCATCTTCCATCACCA-TTTCACGCCTATAT
* * *
10036 CATCACCATATTCCATTACCATTGCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
* *
10071 CATTACCATCTTCTATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
10106 AACCACCAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
35 41 0.68
36 19 0.32
ACGTcount: A:0.27, C:0.35, G:0.05, T:0.33
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:19509 original size:19 final size:20
Alignment explanation
Indices: 19485--19536 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
19475 CAGCCAAGAG
* *
19485 CATGTATATTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
19504 CATGTATTTTCATAAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
19525 CATGTATTTTCA
1 CATGTATTTTCA
19537 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:20101 original size:32 final size:33
Alignment explanation
Indices: 20060--20126 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
20050 TTGTTAACAT
20060 TTCTATCCAT-TTCAATTCTT-ATCATTTCCTTTC
1 TTCTATCCATATTCAATT-TTAATCATTT-CTTTC
20093 TTCT-TCCATATTCAATTTTAATCATTTCTTTC
1 TTCTATCCATATTCAATTTTAATCATTTCTTTC
20125 TT
1 TT
20127 TTAATTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTATCCATATTCAATTTTAATCATTTCTTTC
Found at i:22724 original size:23 final size:22
Alignment explanation
Indices: 22698--22741 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
22688 GGATAATTCA
22698 ATGGTTAAGGA-ATGGTGATGAAT
1 ATGG-TAAGGAGATGGTG-TGAAT
*
22721 ATGGTAATGAGATGGTGTGAA
1 ATGGTAAGGAGATGGTGTGAA
22742 AGTGATGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (22 bp):
ATGGTAAGGAGATGGTGTGAAT
Found at i:22771 original size:14 final size:14
Alignment explanation
Indices: 22743--22779 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
22733 TGGTGTGAAA
*
22743 GTGATGG-AGGATG
1 GTGATGGAAAGATG
22756 GTGATGGAAAGATG
1 GTGATGGAAAGATG
22770 GTGATGGAAA
1 GTGATGGAAA
22780 TAGTATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (14 bp):
GTGATGGAAAGATG
Found at i:24839 original size:28 final size:26
Alignment explanation
Indices: 24808--24864 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
24798 GAAAATCGGA
* *
24808 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAAATCAAGCACT-CAAAAG-AAG
*
24836 AAAGAAAATCCAGCACTCAAAAGAAG
1 AAAGAAAATCAAGCACTCAAAAGAAG
24862 AAA
1 AAA
24865 AAGCAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 14 0.54
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.09
Consensus pattern (26 bp):
AAAGAAAATCAAGCACTCAAAAGAAG
Found at i:33498 original size:24 final size:21
Alignment explanation
Indices: 33464--33506 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
33454 TCCACAAGAT
*
33464 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
33486 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
33507 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:36472 original size:48 final size:48
Alignment explanation
Indices: 36401--36515 Score: 221
Period size: 48 Copynumber: 2.4 Consensus size: 48
36391 TTGGGCTGCA
*
36401 AATAAGATAAGAAATAAATATGTTTAGTAATGGAAGGATAAATGGATT
1 AATAAGATAAGAAATGAATATGTTTAGTAATGGAAGGATAAATGGATT
36449 AATAAGATAAGAAATGAATATGTTTAGTAATGGAAGGATAAATGGATT
1 AATAAGATAAGAAATGAATATGTTTAGTAATGGAAGGATAAATGGATT
36497 AATAAGATAAGAAATGAAT
1 AATAAGATAAGAAATGAAT
36516 TTAAAAGAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (48 bp):
AATAAGATAAGAAATGAATATGTTTAGTAATGGAAGGATAAATGGATT
Found at i:37903 original size:23 final size:23
Alignment explanation
Indices: 37863--37907 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
37853 ATATATATAT
37863 ATATGAAAATAACAATCTTATAAC
1 ATATGAAAATAACAATC-TATAAC
37887 ATATG-AAATAAGC-ATCTATAA
1 ATATGAAAATAA-CAATCTATAA
37908 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (23 bp):
ATATGAAAATAACAATCTATAAC
Found at i:43104 original size:11 final size:11
Alignment explanation
Indices: 43082--43161 Score: 56
Period size: 11 Copynumber: 6.8 Consensus size: 11
43072 AAATGGAATT
43082 TGGTGATGATA
1 TGGTGATGATA
43093 TAGGTG-TGATA
1 T-GGTGATGATA
43104 TGGTGATGGACTA
1 TGGTGAT-GA-TA
*
43117 TGGTAATGATA
1 TGGTGATGATA
*
43128 TAGGCG-TGATAA
1 T-GGTGATGAT-A
*
43140 TGGTGATGGAAGA
1 TGGTGAT-G-ATA
43153 TGGTGATGA
1 TGGTGATGA
43162 ACAAATTGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
10 4 0.07
11 19 0.35
12 14 0.25
13 17 0.31
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.31
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:43126 original size:35 final size:36
Alignment explanation
Indices: 43082--43149 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
43072 AAATGGAATT
* *
43082 TGGTGATGATATAGGTGTGAT-ATGGTGATGGACTA
1 TGGTAATGATATAGGCGTGATAATGGTGATGGACTA
43117 TGGTAATGATATAGGCGTGATAATGGTGATGGA
1 TGGTAATGATATAGGCGTGATAATGGTGATGGA
43150 AGATGGTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTAATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:43156 original size:36 final size:35
Alignment explanation
Indices: 43082--43161 Score: 115
Period size: 36 Copynumber: 2.3 Consensus size: 35
43072 AAATGGAATT
* **
43082 TGGTGATGATATAGGTGTGATATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAAGA
*
43117 TGGTAATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAAGA
43153 TGGTGATGA
1 TGGTGATGA
43162 ACAAATTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.31
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAAGA
Found at i:45613 original size:35 final size:36
Alignment explanation
Indices: 45538--45617 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
45528 TGCAATCTGT
* *
45538 TCATCACCATATTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATCATCACGCCTATA
* *
45574 TCATCTCCATAGTCCATCACCA-CATCATGCCTATA
1 TCATCACCATAGTCCATCACCATCATCACGCCTATA
45609 TCATCACCA
1 TCATCACCA
45618 AATTCGATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATCATCACGCCTATA
Found at i:51177 original size:35 final size:36
Alignment explanation
Indices: 51090--51177 Score: 142
Period size: 35 Copynumber: 2.5 Consensus size: 36
51080 TACAATATGT
*
51090 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
51126 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
51161 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
51178 TTCCATTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 28 0.58
36 20 0.42
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.28
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:54835 original size:24 final size:21
Alignment explanation
Indices: 54801--54843 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
54791 TGCACAAGAT
*
54801 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
54823 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
54844 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:73382 original size:105 final size:105
Alignment explanation
Indices: 73200--73398 Score: 344
Period size: 105 Copynumber: 1.9 Consensus size: 105
73190 TTTTTTGAGC
* * *
73200 TTTCTTGTTTGTGCAGGATCCTTGTTGCTTTTCTAGATTGAAACAATCAAAGGTACAACCTTAAC
1 TTTCTTATTTGTGCAGGATCCTTGTTGCTTTCCTAGATCGAAACAATCAAAGGTACAACCTTAAC
73265 TTCACCATCCATCCAAGTGAGGCTAGGTTTAACTGTATCA
66 TTCACCATCCATCCAAGTGAGGCTAGGTTTAACTGTATCA
* *
73305 TTTCTTATTTGTGCAGGATCCTTGTTGCTTTCCTAGATCGAAACAATCAAAGGTATAACCTTGAC
1 TTTCTTATTTGTGCAGGATCCTTGTTGCTTTCCTAGATCGAAACAATCAAAGGTACAACCTTAAC
*
73370 TTCACCATCCATCGAAGTGAGGCTAGGTT
66 TTCACCATCCATCCAAGTGAGGCTAGGTT
73399 GAGCTACATC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (105 bp):
TTTCTTATTTGTGCAGGATCCTTGTTGCTTTCCTAGATCGAAACAATCAAAGGTACAACCTTAAC
TTCACCATCCATCCAAGTGAGGCTAGGTTTAACTGTATCA
Found at i:84660 original size:6 final size:6
Alignment explanation
Indices: 84645--84677 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
84635 GGATAATTAA
*
84645 GAAA-G GAAATG GAAATG GAAAAG GAAATG GAAA
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAA
84678 GAATTGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (6 bp):
GAAATG
Found at i:86084 original size:13 final size:14
Alignment explanation
Indices: 86066--86098 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
86056 TGGCGTGAAA
*
86066 GTGATGG-AGGATG
1 GTGATGGAAAGATG
86079 GTGATGGAAAGATG
1 GTGATGGAAAGATG
86093 GTGATG
1 GTGATG
86099 AAAATAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.48, T:0.24
Consensus pattern (14 bp):
GTGATGGAAAGATG
Found at i:87949 original size:13 final size:13
Alignment explanation
Indices: 87927--87956 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
87917 ACTAAGCACC
87927 TTTC-ACATACCT
1 TTTCAACATACCT
87939 TTTCAACATACCT
1 TTTCAACATACCT
87952 TTTCA
1 TTTCA
87957 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:91740 original size:19 final size:20
Alignment explanation
Indices: 91699--91747 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
91689 GAAACCCCTT
*
91699 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
91719 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
91738 TGAAGATACA
1 TGAAAATACA
91748 AGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:94920 original size:16 final size:16
Alignment explanation
Indices: 94899--94940 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
94889 TGTAGGAGTC
94899 TTTTCTTTATCTTTTT
1 TTTTCTTTATCTTTTT
*
94915 TTTTCTTCTTTCTTTTT
1 TTTTCTT-TATCTTTTT
94932 TTTCTCTTT
1 TTT-TCTTT
94941 TTGTTACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 12 0.52
18 4 0.17
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTATCTTTTT
Found at i:94939 original size:15 final size:16
Alignment explanation
Indices: 94911--94940 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
94901 TTCTTTATCT
94911 TTTTTTTTCTTCTTTC
1 TTTTTTTTCTTCTTTC
94927 TTTTTTTTC-TCTTT
1 TTTTTTTTCTTCTTT
94941 TTGTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTCTTCTTTC
Found at i:95171 original size:30 final size:33
Alignment explanation
Indices: 95135--95195 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
95125 AATGATTAAG
95135 ATGGAAAT-ATAA-ATAA-GAAATGGA-AGAATA
1 ATGGAAATGATAAGA-AAGGAAATGGATAGAATA
95165 ATGGAAATGATAAGAAAGGAAATGGATAGAA
1 ATGGAAATGATAAGAAAGGAAATGGATAGAA
95196 ATGTTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 6 0.22
32 9 0.33
33 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (33 bp):
ATGGAAATGATAAGAAAGGAAATGGATAGAATA
Found at i:95812 original size:19 final size:20
Alignment explanation
Indices: 95773--95821 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
95763 AACCCCTTTC
*
95773 AAAATACATGATTTTTGATG
1 AAAATACATGATTTTTAATG
*
95793 AAAATGCATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
*
95812 AAGATACATG
1 AAAATACATG
95822 CTATTGGCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:96567 original size:20 final size:21
Alignment explanation
Indices: 96529--96568 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
96519 GATCATCTAG
* *
96529 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
96550 AAGC-AAGATAAAAGGTATA
1 AAGCTAAGATAAAAGGTATA
96569 GGACGTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.53, C:0.07, G:0.17, T:0.23
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:99528 original size:2 final size:2
Alignment explanation
Indices: 99521--99554 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
99511 TGGAAGCGGA
99521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99555 GTTGGTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112776 original size:24 final size:21
Alignment explanation
Indices: 112741--112783 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
112731 GGCTCATTCT
*
112741 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
112764 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
112784 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:120906 original size:23 final size:22
Alignment explanation
Indices: 120863--120906 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
120853 TTCAATTTAT
* *
120863 TAATCTTTTTTTTATCTTGTTC
1 TAATCTTTTTTTTACCGTGTTC
120885 TAATCTTTTTTCTTACCGTGTT
1 TAATCTTTTTT-TTACCGTGTT
120907 TCCAGCACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.14, C:0.16, G:0.07, T:0.64
Consensus pattern (22 bp):
TAATCTTTTTTTTACCGTGTTC
Found at i:121024 original size:25 final size:25
Alignment explanation
Indices: 120990--121040 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
120980 CATCGAGTAT
120990 AGAGCTTTCTAGGTTTGATTCTTCA
1 AGAGCTTTCTAGGTTTGATTCTTCA
121015 AGAGCTTTCTAGGTTTGATTCTTCA
1 AGAGCTTTCTAGGTTTGATTCTTCA
121040 A
1 A
121041 CAAGAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (25 bp):
AGAGCTTTCTAGGTTTGATTCTTCA
Found at i:125259 original size:10 final size:9
Alignment explanation
Indices: 125244--125303 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 9
125234 ATTGGAGTGC
125244 AAAAAGAAA
1 AAAAAGAAA
125253 GAAAAAGACAA
1 -AAAAAGA-AA
125264 AAGAAGAGAAA
1 AA-AA-AGAAA
**
125275 AATCAG-AA
1 AAAAAGAAA
125283 AAAAAGAAA
1 AAAAAGAAA
125292 AGAAAAGAAA
1 A-AAAAGAAA
125302 AA
1 AA
125304 GAAAAAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.15
9 6 0.15
10 18 0.44
11 8 0.20
12 3 0.07
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:125283 original size:27 final size:27
Alignment explanation
Indices: 125252--125303 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
125242 GCAAAAAGAA
* *
125252 AGAAAAAGACAAAAGAAGAGAAAAATC
1 AGAAAAAAACAAAAGAAAAGAAAAATC
*
125279 AGAAAAAAAGAAAAGAAAAGAAAAA
1 AGAAAAAAACAAAAGAAAAGAAAAA
125304 GAAAAAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (27 bp):
AGAAAAAAACAAAAGAAAAGAAAAATC
Found at i:130604 original size:19 final size:20
Alignment explanation
Indices: 130580--130619 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
130570 TATCATTTCT
130580 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
130599 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
130619 T
1 T
130620 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:130622 original size:19 final size:18
Alignment explanation
Indices: 130576--130622 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
130566 TCTCTATCAT
130576 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
130593 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
130612 TTACTTATATT
1 TT-CTTATATT
130623 ATTATTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:131459 original size:20 final size:19
Alignment explanation
Indices: 131434--131499 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
131424 CATTTATGCA
*
131434 TCTAGTTCATTGCATAAAG
1 TCTAGTTCATTGAATAAAG
131453 TTCTAGTTCATTGAATAAAG
1 -TCTAGTTCATTGAATAAAG
131473 T-TAGTTCATT-AATTAAA-
1 TCTAGTTCATTGAA-TAAAG
131490 -CTAGTTCATT
1 TCTAGTTCATT
131500 CATCAAACTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
17 11 0.26
18 13 0.30
19 1 0.02
20 18 0.42
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (19 bp):
TCTAGTTCATTGAATAAAG
Found at i:131496 original size:17 final size:17
Alignment explanation
Indices: 131455--131525 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
131445 GCATAAAGTT
131455 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
131472 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
131490 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
131507 CTATTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
131524 CT
1 CT
131526 TACTCTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
17 32 0.71
18 13 0.29
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:134413 original size:24 final size:25
Alignment explanation
Indices: 134378--134432 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
134368 ACTTGAAGCC
*
134378 TCAA-TGATCACAGCTTGTGGCACT
1 TCAAGTGATCACAGCTTGTGGAACT
* * *
134402 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAGCTTGTGGAACT
134426 TCAAGTG
1 TCAAGTG
134433 GTATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAGCTTGTGGAACT
Found at i:137207 original size:19 final size:20
Alignment explanation
Indices: 137183--137231 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
137173 ATCAAGTGCT
137183 GCAACAA-AAACAACAAAAA
1 GCAACAAGAAACAACAAAAA
* *
137202 GCAACAAGAAAGAAGAAAAA
1 GCAACAAGAAACAACAAAAA
*
137222 G-AAAAAGAAA
1 GCAACAAGAAA
137232 AGAAAAAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.73, C:0.12, G:0.14, T:0.00
Consensus pattern (20 bp):
GCAACAAGAAACAACAAAAA
Found at i:137225 original size:6 final size:6
Alignment explanation
Indices: 137197--137240 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
137187 CAAAAACAAC
*
137197 AAAAAG CAACAAG AAAGAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAAAG -AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
137241 CTCCTACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 17 0.52
7 11 0.33
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:137232 original size:11 final size:12
Alignment explanation
Indices: 137197--137240 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
137187 CAAAAACAAC
*
137197 AAAAAGCAACAAG
1 AAAAAG-AAAAAG
137210 AAAGAAGAAAAAG
1 AAA-AAGAAAAAG
137223 AAAAAG-AAAAG
1 AAAAAGAAAAAG
137234 AAAAAGA
1 AAAAAGA
137241 CTCCTACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 11 0.39
12 3 0.11
13 11 0.39
14 3 0.11
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:140560 original size:36 final size:35
Alignment explanation
Indices: 140509--140619 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 35
140499 TAAGATACTA
*
140509 CCTA-AACATTACCATCTTCCATCACCATTTTCACG
1 CCTATAACATAACCATCTTCCATCACCA-TTTCACG
** * * *
140544 CCTATAACATCTCCATCTTCCATTACTATTGCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
* * * **
140579 CCTATATCCTAACCATATTTTATCACCATTTCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
140614 CCTATA
1 CCTATA
140620 TAACCACCAA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 41 0.68
36 19 0.32
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34
Consensus pattern (35 bp):
CCTATAACATAACCATCTTCCATCACCATTTCACG
Found at i:141033 original size:19 final size:17
Alignment explanation
Indices: 141009--141049 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
140999 AAAAACAACA
*
141009 AAAAACAATAAGATAGAAG
1 AAAAACAAAAAGA-A-AAG
141028 AAAAACAAAAAGAAAAG
1 AAAAACAAAAAGAAAAG
141045 AAAAA
1 AAAAA
141050 GACTCCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
19 12 0.57
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (17 bp):
AAAAACAAAAAGAAAAG
Found at i:144442 original size:36 final size:35
Alignment explanation
Indices: 144391--144501 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
144381 TAAGATACTA
*
144391 CCTA-AACATTACCATCTTCCATCACCATTTTCACG
1 CCTATAACATAACCATCTTCCATCACCA-TTTCACG
* * * *
144426 CCTATAACATCACCATCTTCCATTACTATTGCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
* * **
144461 CCTATATCCTAACCATCTTTTATCACCATTTCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
144496 CCTATA
1 CCTATA
144502 TAACCACCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 43 0.68
36 20 0.32
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.33
Consensus pattern (35 bp):
CCTATAACATAACCATCTTCCATCACCATTTCACG
Found at i:149420 original size:24 final size:25
Alignment explanation
Indices: 149385--149439 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
149375 ACTTGAAGCC
*
149385 TCAA-TGATCACAGCTTGTGGCACT
1 TCAAGTGATCACAGCTTGTGGAACT
* * *
149409 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAGCTTGTGGAACT
149433 TCAAGTG
1 TCAAGTG
149440 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAGCTTGTGGAACT
Found at i:150627 original size:21 final size:22
Alignment explanation
Indices: 150601--150641 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
150591 GATAACATTT
150601 ATTTTC-ATTTCAATTCTTTTC
1 ATTTTCTATTTCAATTCTTTTC
* *
150622 ATTTTCTATTTTATTTCTTT
1 ATTTTCTATTTCAATTCTTT
150642 AATTATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTTCTATTTCAATTCTTTTC
Found at i:150851 original size:19 final size:20
Alignment explanation
Indices: 150827--150875 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
150817 ATCAAGTGCT
150827 GCAACAA-AAACAACAAAAA
1 GCAACAAGAAACAACAAAAA
* *
150846 GCAACAAGAAAGAAGAAAAA
1 GCAACAAGAAACAACAAAAA
*
150866 G-AAAAAGAAA
1 GCAACAAGAAA
150876 AGAAAAAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.73, C:0.12, G:0.14, T:0.00
Consensus pattern (20 bp):
GCAACAAGAAACAACAAAAA
Found at i:150869 original size:6 final size:6
Alignment explanation
Indices: 150841--150884 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
150831 CAAAAACAAC
*
150841 AAAAAG CAACAAG AAAGAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAAAG -AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
150885 CTCCTACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 17 0.52
7 11 0.33
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:150876 original size:11 final size:12
Alignment explanation
Indices: 150841--150884 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
150831 CAAAAACAAC
*
150841 AAAAAGCAACAAG
1 AAAAAG-AAAAAG
150854 AAAGAAGAAAAAG
1 AAA-AAGAAAAAG
150867 AAAAAG-AAAAG
1 AAAAAGAAAAAG
150878 AAAAAGA
1 AAAAAGA
150885 CTCCTACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 11 0.39
12 3 0.11
13 11 0.39
14 3 0.11
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:161986 original size:36 final size:35
Alignment explanation
Indices: 161935--162045 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 35
161925 TAAGATACTA
*
161935 CCTA-AACATTACCATCTTCCATCACCATTTTCACG
1 CCTATAACATAACCATCTTCCATCACCA-TTTCACG
** * * *
161970 CCTATAACATCTCCATCTTCCATTACTATTGCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
* * * **
162005 CCTATATCCTAACCATATTTTATCACCATTTCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
162040 CCTATA
1 CCTATA
162046 TAACCACCAA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 41 0.68
36 19 0.32
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34
Consensus pattern (35 bp):
CCTATAACATAACCATCTTCCATCACCATTTCACG
Found at i:165856 original size:36 final size:35
Alignment explanation
Indices: 165805--165915 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 35
165795 TAAGATACTA
*
165805 CCTA-AACATTACCATCTTCCATCACCATTTTCACG
1 CCTATAACATAACCATCTTCCATCACCA-TTTCACG
* * * *
165840 CCTATAACATCACCATCTTCCATTACTATTGCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
* * * **
165875 CCTATATCCTAACCATATTTTATCACCATTTCACG
1 CCTATAACATAACCATCTTCCATCACCATTTCACG
165910 CCTATA
1 CCTATA
165916 TAACCACCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 42 0.68
36 20 0.32
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.33
Consensus pattern (35 bp):
CCTATAACATAACCATCTTCCATCACCATTTCACG
Found at i:170188 original size:21 final size:22
Alignment explanation
Indices: 170146--170189 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
170136 AGCTGAATAT
* *
170146 TCTAGATTATTTTGTGGATGAA
1 TCTAGATTAATTTGAGGATGAA
*
170168 TCTAGA-TAATTTGAGGTTGAA
1 TCTAGATTAATTTGAGGATGAA
170189 T
1 T
170190 TTAGCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (22 bp):
TCTAGATTAATTTGAGGATGAA
Found at i:170923 original size:17 final size:17
Alignment explanation
Indices: 170902--171072 Score: 180
Period size: 17 Copynumber: 9.9 Consensus size: 17
170892 AATTAAGAGT
* *
170902 TAGTTTAATAAATGAAT
1 TAGTTTAATGAATGAAC
*
170919 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
**
170936 TAGTTTAATTTATGAAC
1 TAGTTTAATGAATGAAC
* * *
170953 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
* ** *
170971 TTGAAATCATGAATGAAC
1 TAG-TTTAATGAATGAAC
*
170989 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
171006 TAGTTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
171023 TAGTTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
*
171040 TAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
* *
171057 AAGTTTAATCAATGAA
1 TAGTTTAATGAATGAA
171073 GTACTTAGTT
Statistics
Matches: 128, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
17 104 0.81
18 24 0.19
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:172700 original size:15 final size:16
Alignment explanation
Indices: 172672--172703 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
172662 CCTTGAATAA
172672 AATAATTCCCCAATTG
1 AATAATTCCCCAATTG
172688 AATAATT-CCCAATTG
1 AATAATTCCCCAATTG
172703 A
1 A
172704 TTTATGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (16 bp):
AATAATTCCCCAATTG
Found at i:176845 original size:46 final size:46
Alignment explanation
Indices: 176763--176856 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 46
176753 AACACACTAG
* *
176763 GCAAATCCTTGTTAATGTTAGAAATATAAACGATTGATTCCCTAAA
1 GCAAATCCTTGTTAATGCTAGAAATATAAACAATTGATTCCCTAAA
*
176809 GCAAAT-CTCTGTTAATGCTAGGAATCA-AAACAATTGATTCCCTAAA
1 GCAAATCCT-TGTTAATGCTAGAAAT-ATAAACAATTGATTCCCTAAA
176855 GC
1 GC
176857 GAACAAGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
45 2 0.05
46 40 0.93
47 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (46 bp):
GCAAATCCTTGTTAATGCTAGAAATATAAACAATTGATTCCCTAAA
Found at i:179004 original size:25 final size:25
Alignment explanation
Indices: 178972--179022 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
178962 GTTGTTCTTG
178972 TTGAAGAATCAAACCTAGAAAGCTC
1 TTGAAGAATCAAACCTAGAAAGCTC
178997 TTGAAGAATCAAACCTAGAAAGCTC
1 TTGAAGAATCAAACCTAGAAAGCTC
179022 T
1 T
179023 ATACTCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (25 bp):
TTGAAGAATCAAACCTAGAAAGCTC
Found at i:179713 original size:22 final size:21
Alignment explanation
Indices: 179687--179727 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
179677 ATATTAAATT
*
179687 ATATTATAAATAATCAATATAA
1 ATATTAAAAATAAT-AATATAA
*
179709 ATATTAAAAATCATAATAT
1 ATATTAAAAATAATAATAT
179728 TTACAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATTAAAAATAATAATATAA
Found at i:181345 original size:15 final size:15
Alignment explanation
Indices: 181313--181351 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
181303 CTTTATTATC
181313 TTATTTCATCTTCCGT
1 TTATTT-ATCTTCCGT
**
181329 TTATTTATCTTTTGT
1 TTATTTATCTTCCGT
181344 TTATTTAT
1 TTATTTAT
181352 TCTAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (15 bp):
TTATTTATCTTCCGT
Found at i:181719 original size:16 final size:16
Alignment explanation
Indices: 181709--181764 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
181699 AAAAACAAAA
181709 AAAAAAAAAAAAAGGC
1 AAAAAAAAAAAAAGGC
181725 AAAAAAAAAAAAAGGC
1 AAAAAAAAAAAAAGGC
*
181741 AAAAAACAAAAAAGAGCC
1 AAAAAA-AAAAAA-AGGC
181759 AAAAAA
1 AAAAAA
181765 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
16 22 0.59
17 6 0.16
18 9 0.24
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGGC
Found at i:181721 original size:18 final size:19
Alignment explanation
Indices: 181698--181737 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
181688 ATTTTTTTTC
181698 AAAAAA-CAAAAAAAAAAA
1 AAAAAAGCAAAAAAAAAAA
181716 AAAAAAGGCAAAAAAAAAAA
1 AAAAAA-GCAAAAAAAAAAA
181736 AA
1 AA
181738 GGCAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAGCAAAAAAAAAAA
Found at i:181746 original size:18 final size:18
Alignment explanation
Indices: 181707--181764 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
181697 CAAAAAACAA
181707 AAAAAAAAAAAAAAAGGC
1 AAAAAAAAAAAAAAAGGC
181725 --AAAAAAAAAAAAAGGC
1 AAAAAAAAAAAAAAAGGC
* * *
181741 AAAAAACAAAAAAGAGCC
1 AAAAAAAAAAAAAAAGGC
181759 AAAAAA
1 AAAAAA
181765 GCCAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 16 0.46
18 19 0.54
ACGTcount: A:0.81, C:0.09, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAGGC
Found at i:187557 original size:17 final size:17
Alignment explanation
Indices: 187521--187560 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
187511 CTTTCCTTAG
*
187521 TGTTCCATGAGCTACAA
1 TGTTCCATGAGATACAA
* *
187538 TGTTCCATGAGATGCCA
1 TGTTCCATGAGATACAA
187555 TGTTCC
1 TGTTCC
187561 TTGTGAGCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (17 bp):
TGTTCCATGAGATACAA
Found at i:191559 original size:46 final size:46
Alignment explanation
Indices: 191477--191570 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 46
191467 AACACACTAG
* *
191477 GCAAATCCTTGTTAATGTTAGAAATATAAACGATTGATTCCCTAAA
1 GCAAATCCTTGTTAATGCTAGAAATATAAACAATTGATTCCCTAAA
*
191523 GCAAAT-CTCTGTTAATGCTAGGAATCA-AAACAATTGATTCCCTAAA
1 GCAAATCCT-TGTTAATGCTAGAAAT-ATAAACAATTGATTCCCTAAA
191569 GC
1 GC
191571 GAACAAGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
45 2 0.05
46 40 0.93
47 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (46 bp):
GCAAATCCTTGTTAATGCTAGAAATATAAACAATTGATTCCCTAAA
Found at i:193720 original size:25 final size:25
Alignment explanation
Indices: 193688--193738 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
193678 GTTGTTCTTG
193688 TTGAAGAATCAAACCTAGAAAGCTC
1 TTGAAGAATCAAACCTAGAAAGCTC
193713 TTGAAGAATCAAACCTAGAAAGCTC
1 TTGAAGAATCAAACCTAGAAAGCTC
193738 T
1 T
193739 ATACTCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (25 bp):
TTGAAGAATCAAACCTAGAAAGCTC
Found at i:196437 original size:9 final size:9
Alignment explanation
Indices: 196423--196447 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
196413 TTTTTTTTTC
196423 AAAAAAACA
1 AAAAAAACA
196432 AAAAAAACA
1 AAAAAAACA
196441 AAAAAAA
1 AAAAAAA
196448 AGGCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:196458 original size:15 final size:14
Alignment explanation
Indices: 196440--196477 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
196430 CAAAAAAAAC
196440 AAAAAAAAAGGCAA
1 AAAAAAAAAGGCAA
196454 AAAAAAAAAGGCAA
1 AAAAAAAAAGGCAA
196468 AAAAACAAAA
1 AAAAA-AAAA
196478 AAAGAGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGGCAA
Found at i:196491 original size:14 final size:12
Alignment explanation
Indices: 196431--196472 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
196421 TCAAAAAAAC
196431 AAAAAAAA-CAA
1 AAAAAAAAGCAA
*
196442 AAAAAAAGGCAAA
1 AAAAAAAAGC-AA
196455 AAAAAAAAGGCAA
1 AAAAAAAA-GCAA
196468 AAAAA
1 AAAAA
196473 CAAAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 7 0.27
12 1 0.04
13 16 0.62
14 2 0.08
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGCAA
Found at i:196498 original size:20 final size:20
Alignment explanation
Indices: 196454--196491 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
196444 AAAAAGGCAA
*
196454 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
196474 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
196492 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:202278 original size:17 final size:17
Alignment explanation
Indices: 202242--202281 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
202232 CTTTCCTTAG
*
202242 TGTTCCATGAGCTACAA
1 TGTTCCATGAGATACAA
* *
202259 TGTTCCATGAGATGCCA
1 TGTTCCATGAGATACAA
202276 TGTTCC
1 TGTTCC
202282 TTGTGAGCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (17 bp):
TGTTCCATGAGATACAA
Found at i:213422 original size:17 final size:17
Alignment explanation
Indices: 213400--213537 Score: 118
Period size: 17 Copynumber: 8.1 Consensus size: 17
213390 CAATTAGAGT
*
213400 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
213417 TAGTTTGATGAATGAA-
1 TAGTTTAATGAATGAAC
*
213433 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
213450 TAACTTTATTTAATGAAC
1 T-AGTTTAATGAATGAAC
* * **
213468 TTGTAATCTTGAATGAAC
1 TAGT-TTAATGAATGAAC
*
213486 T-GTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
213502 TAGTTTAATGAATAAAC
1 TAGTTTAATGAATGAAC
* *
213519 AAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
213536 TA
1 TA
213538 CTTAGTTAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
16 25 0.26
17 46 0.47
18 26 0.27
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:214054 original size:2 final size:2
Alignment explanation
Indices: 214047--214093 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
214037 TTATAAAGGG
214047 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
214088 AT AT AT
1 AT AT AT
214094 GAATGTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.