Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006339.1 Hibiscus syriacus cultivar Beakdansim tig00015153_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: 234755
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5215 original size:19 final size:20
Alignment explanation
Indices: 5191--5238 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
5181 CGGCCAAGAG
5191 CATGTATCTTCA-TTAAAA-T
1 CATGTAT-TTCATTTAAAAGT
5210 CATGTATTTCATTTAAAAGT
1 CATGTATTTCATTTAAAAGT
5230 CATGTATTT
1 CATGTATTT
5239 ACAAGGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAGT
Found at i:5971 original size:22 final size:20
Alignment explanation
Indices: 5944--6006 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 20
5934 ATGGAGTACA
*
5944 AAAAGAAAGAAAATAAAAATG
1 AAAAGAAAGAAAAGAAAAA-G
*
5965 AAGAAGAAA-AGAAGAAAAAG
1 AA-AAGAAAGAAAAGAAAAAG
5985 AAAAG-AAGAAAAGAAAAAG
1 AAAAGAAAGAAAAGAAAAAG
6004 AAA
1 AAA
6007 TTCAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.05
19 16 0.43
20 3 0.08
21 10 0.27
22 6 0.16
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (20 bp):
AAAAGAAAGAAAAGAAAAAG
Found at i:5978 original size:8 final size:8
Alignment explanation
Indices: 5965--5999 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
5955 AATAAAAATG
5965 AAGAAGAA
1 AAGAAGAA
5973 AAGAAG-A
1 AAGAAGAA
5980 AA-AAGAA
1 AAGAAGAA
5987 AAGAAGAA
1 AAGAAGAA
5995 AAGAA
1 AAGAA
6000 AAAGAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 6 0.24
8 16 0.64
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:5987 original size:14 final size:13
Alignment explanation
Indices: 5944--6001 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
5934 ATGGAGTACA
*
5944 AAAAGAAAGAAAAT
1 AAAAG-AAGAAAAG
*
5958 AAAA-ATGAAGAAG
1 AAAAGAAGAA-AAG
5971 AAAAGAAGAAAAAG
1 AAAAGAAG-AAAAG
5985 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
5998 AAAA
1 AAAA
6002 AGAAATTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.11
13 15 0.39
14 17 0.45
15 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:8303 original size:17 final size:18
Alignment explanation
Indices: 8281--8317 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
8271 AACTATAGTT
*
8281 CACATCTTTATA-ATATG
1 CACATCATTATATATATG
8298 CACATCATTATATATATG
1 CACATCATTATATATATG
8316 CA
1 CA
8318 TTATATTTAT
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:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (18 bp):
CACATCATTATATATATG
Found at i:9151 original size:19 final size:21
Alignment explanation
Indices: 9129--9172 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
9119 AGCATGCATC
9129 TTCA-TTAAAA-TCATGTATT
1 TTCATTTAAAAGTCATGTATT
9148 TTCATTTAAAAGTCATGTATT
1 TTCATTTAAAAGTCATGTATT
9169 TTCA
1 TTCA
9173 AGGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 13 0.57
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (21 bp):
TTCATTTAAAAGTCATGTATT
Found at i:10637 original size:10 final size:10
Alignment explanation
Indices: 10631--10656 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
10621 TTCAAAAAAC
10631 AAAAAAATAA
1 AAAAAAATAA
10641 AAAAAAATAA
1 AAAAAAATAA
10651 AAAAAA
1 AAAAAA
10657 GCCAAAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:16397 original size:35 final size:37
Alignment explanation
Indices: 16351--16430 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
16341 TTTGAGAATT
*
16351 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
16386 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
16423 TGGGGATG
1 TGGTGATG
16431 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:22082 original size:35 final size:37
Alignment explanation
Indices: 22036--22115 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
22026 TTTGAGAATT
* *
22036 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
*
22071 TGGTGATGATATAGGCATGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
*
22108 TGGGGATG
1 TGGTGATG
22116 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
Found at i:24686 original size:22 final size:21
Alignment explanation
Indices: 24649--24689 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
24639 CCATCTCCAT
24649 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
24670 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
24690 ATTCCGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:33326 original size:11 final size:11
Alignment explanation
Indices: 33310--33357 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
33300 TTTTTTGAAA
33310 TTTTGGCTTTT
1 TTTTGGCTTTT
33321 TTTTGGCTCTTT
1 TTTTGGCT-TTT
**
33333 TTTT-TATTTT
1 TTTTGGCTTTT
*
33343 TTTTGCCTTTT
1 TTTTGGCTTTT
33354 TTTT
1 TTTT
33358 TTTTGCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 7 0.23
11 17 0.55
12 7 0.23
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.77
Consensus pattern (11 bp):
TTTTGGCTTTT
Found at i:33357 original size:24 final size:22
Alignment explanation
Indices: 33330--33379 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
33320 TTTTTGGCTC
*
33330 TTTTTTTTATTTTTTTTGCCTTTT
1 TTTTTTTTACTTTTTTTG--TTTT
*
33354 TTTTTTTTGCTTTTTTTGTTTT
1 TTTTTTTTACTTTTTTTGTTTT
33376 TTTT
1 TTTT
33380 GAAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
24 16 0.67
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.86
Consensus pattern (22 bp):
TTTTTTTTACTTTTTTTGTTTT
Found at i:33359 original size:15 final size:14
Alignment explanation
Indices: 33334--33376 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
33324 TGGCTCTTTT
33334 TTTTATTTTTTTTGCC
1 TTTT-TTTTTTTTG-C
33350 TTTTTTTTTTTTGC
1 TTTTTTTTTTTTGC
33364 TTTTTTTGTTTTT
1 TTTTTTT-TTTTT
33377 TTTGAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.31
15 14 0.54
16 4 0.15
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTTTGC
Found at i:33368 original size:22 final size:22
Alignment explanation
Indices: 33317--33361 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
33307 AAATTTTGGC
33317 TTTTTTTTGGCTCTTTTTTTTA
1 TTTTTTTTGGCTCTTTTTTTTA
33339 TTTTTTTT-GC-CTTTTTTTT-
1 TTTTTTTTGGCTCTTTTTTTTA
33358 TTTT
1 TTTT
33362 GCTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 2 0.09
22 8 0.35
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (22 bp):
TTTTTTTTGGCTCTTTTTTTTA
Found at i:36855 original size:26 final size:26
Alignment explanation
Indices: 36822--36896 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
36812 TATCCCTTCT
36822 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
36848 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
* *
36871 TTA-ATCATCTTCCTTTTCTTATCTTT
1 TTATTTCAT-TT-CATTTCTTATCTTT
36897 GTTGCAGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.10
23 10 0.25
24 5 0.12
25 1 0.03
26 16 0.40
27 4 0.10
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:37756 original size:10 final size:10
Alignment explanation
Indices: 37743--37781 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
37733 TGGACTAAAG
37743 GTAGCTGGAA
1 GTAGCTGGAA
37753 GTAGCTGGAA
1 GTAGCTGGAA
*
37763 GTAGTTGGGAGA
1 GTAGCT-GGA-A
37775 GTAGCTG
1 GTAGCTG
37782 AGGAGCTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 15 0.60
11 4 0.16
12 6 0.24
ACGTcount: A:0.26, C:0.08, G:0.44, T:0.23
Consensus pattern (10 bp):
GTAGCTGGAA
Found at i:44876 original size:35 final size:36
Alignment explanation
Indices: 44811--44878 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
44801 ATACAATCTG
*
44811 TCCATCACCATTATCATGCCTATATCATCACCATAT
1 TCCATCACCATTATCATGCATATATCATCACCATAT
* *
44847 TCCATCACCA-TATCATGCATGTATTATCACCA
1 TCCATCACCATTATCATGCATATATCATCACCA
44879 ACTTCTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.31, C:0.32, G:0.04, T:0.32
Consensus pattern (36 bp):
TCCATCACCATTATCATGCATATATCATCACCATAT
Found at i:45277 original size:23 final size:21
Alignment explanation
Indices: 45249--45295 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
45239 GTGCTACAAC
* *
45249 AAAAAAGCAACAAGAAAGAAGAA
1 AAAAAAACAAAAAG-AA-AAGAA
45272 AAAAAAACAAAAAGAAAAGAA
1 AAAAAAACAAAAAGAAAAGAA
45293 AAA
1 AAA
45296 GACTCCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 12 0.55
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAAAGAAAAGAA
Found at i:45294 original size:20 final size:20
Alignment explanation
Indices: 45257--45295 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
45247 ACAAAAAAGC
*
45257 AACAAGAAAGAAGAAAAAAA
1 AACAAGAAAGAAAAAAAAAA
45277 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAGAAAA-AAAAA
45296 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (20 bp):
AACAAGAAAGAAAAAAAAAA
Found at i:45381 original size:24 final size:24
Alignment explanation
Indices: 45326--45374 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
45316 AGTGCAAAAG
* *
45326 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
45350 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
45373 AA
1 AA
45375 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:45553 original size:24 final size:25
Alignment explanation
Indices: 45516--45565 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
45506 TTACTATTTC
*
45516 ATTTCCTTTTCTTTCAT-CTTTTCTT
1 ATTTCCTTTACTTT-ATCCTTTTCTT
45541 ATTT-CTTTACTTTATCCTTTTCTT
1 ATTTCCTTTACTTTATCCTTTTCTT
45565 A
1 A
45566 ACCTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 17 0.74
25 4 0.17
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (25 bp):
ATTTCCTTTACTTTATCCTTTTCTT
Found at i:46830 original size:19 final size:19
Alignment explanation
Indices: 46806--46843 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46796 GATGCTTTAA
46806 ATGTCTTGGGAGGGGCCAC
1 ATGTCTTGGGAGGGGCCAC
46825 ATGTCTTGGGAGGGGCCAC
1 ATGTCTTGGGAGGGGCCAC
46844 GTATCTACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.42, T:0.21
Consensus pattern (19 bp):
ATGTCTTGGGAGGGGCCAC
Found at i:48956 original size:13 final size:12
Alignment explanation
Indices: 48937--49033 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
48927 TACGCCTATA
48937 TCATCACCATAT
1 TCATCACCATAT
48949 TCCATCACC--AT
1 T-CATCACCATAT
*
48960 T-ATCACGCCTAT
1 TCATCAC-CATAT
48972 ATCATCACCATAGT
1 -TCATCACCATA-T
*
48986 CCATCACC--AT
1 TCATCACCATAT
*
48996 T-ATCACGCCTAT
1 TCATCAC-CATAT
49008 ATCATCACCATAT
1 -TCATCACCATAT
49021 TCCATCACCATAT
1 T-CATCACCATAT
49034 CACGCCTATA
Statistics
Matches: 68, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
9 10 0.15
10 3 0.04
11 4 0.06
12 6 0.09
13 34 0.50
14 11 0.16
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:48968 original size:36 final size:36
Alignment explanation
Indices: 48879--49052 Score: 284
Period size: 36 Copynumber: 4.9 Consensus size: 36
48869 GATACAATCT
48879 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
48915 GT-C--CACCATTATTACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
48948 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
48984 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
49020 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
49053 ACTTATAAAT
Statistics
Matches: 129, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
33 30 0.23
34 1 0.01
35 22 0.17
36 76 0.59
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:55217 original size:16 final size:15
Alignment explanation
Indices: 55198--55240 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55188 CTTTATTATC
*
55198 TTATTTCATCTTCTGT
1 TTATTT-ATATTCTGT
*
55214 TTATTTATATTTTGT
1 TTATTTATATTCTGT
55229 TTATTT-TATTCT
1 TTATTTATATTCT
55241 AATCTTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (15 bp):
TTATTTATATTCTGT
Found at i:57217 original size:35 final size:36
Alignment explanation
Indices: 57161--57228 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
57151 ATACAATCTA
57161 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
* *
57197 TCCATCACCA-TATCACGCCTATGTTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
57229 ACTTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.29, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:61464 original size:19 final size:19
Alignment explanation
Indices: 61440--61485 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
61430 CCAGCTGAAA
*
61440 AAAAGTCTCTAGCTAGCTC
1 AAAAGTCCCTAGCTAGCTC
61459 AAAAGTCCCTAGCTAGCTC
1 AAAAGTCCCTAGCTAGCTC
61478 AAAAGTCC
1 AAAAGTCC
61486 AGCTCAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (19 bp):
AAAAGTCCCTAGCTAGCTC
Found at i:71998 original size:13 final size:12
Alignment explanation
Indices: 71979--72043 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
71969 ATATAGGCGT
71979 GATATGGTGATG
1 GATATGGTGATG
71991 GAATATGGTGAT-
1 G-ATATGGTGATG
*
72003 GATATAGGCG-T-
1 GATAT-GGTGATG
72014 GATAATGGTGATG
1 GAT-ATGGTGATG
72027 GACTATGGTGAT-
1 GA-TATGGTGATG
72039 GATAT
1 GATAT
72044 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:72034 original size:36 final size:36
Alignment explanation
Indices: 71961--72062 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
71951 ATTTATAAGT
*
71961 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
71996 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
72032 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
72063 ATATAGGCGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:72058 original size:23 final size:23
Alignment explanation
Indices: 72031--72082 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
72021 GTGATGGACT
*
72031 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTAATA
72054 ATGGTGATGATATAGGCGTAATA
1 ATGGTGATGATATAGGCGTAATA
72077 ATGGTG
1 ATGGTG
72083 GACTATGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTAATA
Found at i:72108 original size:56 final size:59
Alignment explanation
Indices: 71995--72118 Score: 218
Period size: 56 Copynumber: 2.2 Consensus size: 59
71985 GTGATGGAAT
*
71995 ATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTAATAATGGTGATGGACTATGGTGATGATATAGGCGTGATA
72054 ATGGTGATGATATAGGCGTAATAAT-G-G-TGGACTATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTAATAATGGTGATGGACTATGGTGATGATATAGGCGTGATA
72110 ATGGTGATG
1 ATGGTGATG
72119 GACAGATTGT
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
56 38 0.59
57 1 0.02
58 1 0.02
59 24 0.38
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (59 bp):
ATGGTGATGATATAGGCGTAATAATGGTGATGGACTATGGTGATGATATAGGCGTGATA
Found at i:75355 original size:15 final size:16
Alignment explanation
Indices: 75304--75356 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
75294 AGATAGTGAA
75304 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
75321 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
75338 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
75353 ATAA
1 ATAA
75357 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:83537 original size:35 final size:36
Alignment explanation
Indices: 83490--83557 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
83480 ATTTAGAAGT
83490 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
83525 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
83558 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:83944 original size:19 final size:20
Alignment explanation
Indices: 83897--83947 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
83887 GAAACCCCTT
**
83897 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
83917 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
83936 TGAAGATACATG
1 TGAAAATACATG
83948 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:90214 original size:13 final size:13
Alignment explanation
Indices: 90192--90221 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
90182 ACTAAACACC
90192 TTTC-ACATACCT
1 TTTCAACATACCT
90204 TTTCAACATACCT
1 TTTCAACATACCT
90217 TTTCA
1 TTTCA
90222 TCTTTGGCTA
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:95014 original size:21 final size:22
Alignment explanation
Indices: 94965--95015 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
94955 AAATTTTGGC
*
94965 TTTTTTTGGCTCTTTTTTTTTG
1 TTTTTTTGCCTCTTTTTTTTTG
94987 TTTTTTTGCCT-TTTTTTTTTG
1 TTTTTTTGCCTCTTTTTTTTTG
95008 TTTTTTTG
1 TTTTTTTG
95016 AAAAAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (22 bp):
TTTTTTTGCCTCTTTTTTTTTG
Found at i:98624 original size:5 final size:5
Alignment explanation
Indices: 98610--98646 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
98600 GTGCTTCAAC
98610 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
98647 TCTTCCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:98696 original size:23 final size:25
Alignment explanation
Indices: 98639--98698 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
98629 TTTCTTTTCT
* *
98639 TTTCTTTTTCTTCCTCTTTGAGTGT
1 TTTCATTTTCTTCCTCTTTGAGTGC
*
98664 TTTCAATTTCTT-CT-TTTGAGTGC
1 TTTCATTTTCTTCCTCTTTGAGTGC
*
98687 TTTGATTTTCTT
1 TTTCATTTTCTT
98699 TGTTGGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.60
24 2 0.07
25 10 0.33
ACGTcount: A:0.08, C:0.17, G:0.12, T:0.63
Consensus pattern (25 bp):
TTTCATTTTCTTCCTCTTTGAGTGC
Found at i:104855 original size:19 final size:20
Alignment explanation
Indices: 104827--104866 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
104817 GGGTAATAAT
104827 ATAAGTAATGAATAT-AAATA
1 ATAAGTAATGAA-ATGAAATA
104847 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
104866 A
1 A
104867 ATAAAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.63
20 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:108432 original size:27 final size:26
Alignment explanation
Indices: 108393--108456 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
108383 CAAAAAGAAA
* *
108393 AGAAAAGATAAAAGGGAAAA-AAATTC
1 AGAAAAGAGAAAA-GAAAAAGAAATTC
108419 AGAAAAGAAGAAAAGAAAAAGAAATTC
1 AGAAAAG-AGAAAAGAAAAAGAAATTC
108446 A-AAAAGAGAAA
1 AGAAAAGAGAAA
108457 GCAAGCCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 5 0.15
26 17 0.50
27 12 0.35
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (26 bp):
AGAAAAGAGAAAAGAAAAAGAAATTC
Found at i:115932 original size:18 final size:19
Alignment explanation
Indices: 115911--115952 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
115901 TTTTTTGAAA
*
115911 TTTTGGCTTTTTTTGT-TT
1 TTTTGCCTTTTTTTGTGTT
*
115929 TTTTGCCTTTTTTTTTGTT
1 TTTTGCCTTTTTTTGTGTT
115948 TTTTG
1 TTTTG
115953 AAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.00, C:0.07, G:0.14, T:0.79
Consensus pattern (19 bp):
TTTTGCCTTTTTTTGTGTT
Found at i:116838 original size:22 final size:20
Alignment explanation
Indices: 116797--116846 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
116787 CAACCTTAAT
116797 TCCTAATAAAATAATAAATCTGA
1 TCCTAA-AAAATAATAAATC--A
* *
116820 TCCTAAAAGATAATTAATCA
1 TCCTAAAAAATAATAAATCA
116840 TCCTAAA
1 TCCTAAA
116847 TTAAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (20 bp):
TCCTAAAAAATAATAAATCA
Found at i:130839 original size:22 final size:23
Alignment explanation
Indices: 130814--130865 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
130804 ATTTATAAGT
130814 TGGTGATAAAATAGGCGTGAT-A
1 TGGTGATAAAATAGGCGTGATAA
* *
130836 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAAAATAGGCGTGATAA
130859 TGGTGAT
1 TGGTGAT
130866 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
TGGTGATAAAATAGGCGTGATAA
Found at i:130847 original size:11 final size:11
Alignment explanation
Indices: 130831--130902 Score: 58
Period size: 11 Copynumber: 6.2 Consensus size: 11
130821 AAAATAGGCG
130831 TGATATGGTGA
1 TGATATGGTGA
*
130842 TGATATAGGCG-
1 TGATAT-GGTGA
130853 TGATAATGGTGA
1 TGAT-ATGGTGA
130865 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
130878 TGATATAGGCG-
1 TGATAT-GGTGA
130889 TGATAATGGTGA
1 TGAT-ATGGTGA
130901 TG
1 TG
130903 GACAGATTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
11 23 0.47
12 15 0.31
13 10 0.20
14 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:130874 original size:36 final size:36
Alignment explanation
Indices: 130834--130905 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
130824 ATAGGCGTGA
130834 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
130870 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
130906 AGATTGTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.06, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:132993 original size:35 final size:37
Alignment explanation
Indices: 132947--133026 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
132937 TTTGAGAATT
*
132947 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
132982 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
133019 TGGGGATG
1 TGGTGATG
133027 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:156536 original size:17 final size:18
Alignment explanation
Indices: 156514--156547 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
156504 AGATACAACA
*
156514 TCATCACCATC-TCCATT
1 TCATCAACATCATCCATT
156531 TCATCAACATCATCCAT
1 TCATCAACATCATCCAT
156548 CAAGACCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.32
Consensus pattern (18 bp):
TCATCAACATCATCCATT
Found at i:159535 original size:12 final size:12
Alignment explanation
Indices: 159499--159523 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
159489 ATGGGTTAGT
159499 AAAAAATTAAAA
1 AAAAAATTAAAA
159511 AAAAAATTAAAA
1 AAAAAATTAAAA
159523 A
1 A
159524 TTAAAAAAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATTAAAA
Found at i:159547 original size:19 final size:19
Alignment explanation
Indices: 159500--159540 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
159490 TGGGTTAGTA
*
159500 AAAAATTAAAAAAAAAATT
1 AAAAATTAAAAAAAAAATG
159519 AAAAATTAAAAAAAAAA-G
1 AAAAATTAAAAAAAAAATG
159537 AAAA
1 AAAA
159541 GTTTAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAAATTAAAAAAAAAATG
Found at i:163124 original size:2 final size:2
Alignment explanation
Indices: 163117--163154 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
163107 TGGAAGCGGA
163117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
163155 GTTGGTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:167936 original size:17 final size:15
Alignment explanation
Indices: 167906--167939 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
167896 TATTCTACCC
167906 CTATCATTACCATTT
1 CTATCATTACCATTT
167921 CTATACATTAACCATTT
1 CTAT-CATT-ACCATTT
167938 CT
1 CT
167940 TTTAAAGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (15 bp):
CTATCATTACCATTT
Found at i:175605 original size:2 final size:2
Alignment explanation
Indices: 175598--175631 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
175588 AGTTATTTTC
*
175598 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
175632 GTTATTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176716 original size:19 final size:20
Alignment explanation
Indices: 176688--176727 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
176678 GGGTAATAAT
176688 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
176708 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
176727 A
1 A
176728 AGAAAGGATA
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:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:177181 original size:19 final size:20
Alignment explanation
Indices: 177140--177190 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
177130 GAAACCCCTT
*
177140 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
177160 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
177179 TGAATATACATG
1 TGAAAATACATG
177191 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:180517 original size:34 final size:32
Alignment explanation
Indices: 180460--180531 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
180450 CTTGGCTTGC
*
180460 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TGTCT
180491 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
180525 TTTCTTT
1 TTTCTTT
180532 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 23 0.64
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:181247 original size:20 final size:20
Alignment explanation
Indices: 181222--181260 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
181212 TTGAAACCCC
181222 TTTGAAAATACATGATTTTT
1 TTTGAAAATACATGATTTTT
181242 TTTGAAAATACATGATTTT
1 TTTGAAAATACATGATTTT
181261 AATGAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTGAAAATACATGATTTTT
Found at i:181266 original size:19 final size:20
Alignment explanation
Indices: 181224--181274 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
181214 GAAACCCCTT
**
181224 TGAAAATACATGATTTTTTT
1 TGAAAATACATGATTTTTAA
181244 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
181263 TGAAGATACATG
1 TGAAAATACATG
181275 CTCTTGACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:183176 original size:133 final size:133
Alignment explanation
Indices: 182938--183200 Score: 517
Period size: 133 Copynumber: 2.0 Consensus size: 133
182928 TATCATTTCA
182938 TAGGATATTATTATTACATGTTTCCATTTATCATTTAAGAATACCATGTTATATGATATTCATGC
1 TAGGATATTATTATTACATGTTTCCATTTATCATTTAAGAATACCATGTTATATGATATTCATGC
183003 ATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTCTTAT
66 ATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTCTTAT
183068 TCT
131 TCT
*
183071 TAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATTCATGC
1 TAGGATATTATTATTACATGTTTCCATTTATCATTTAAGAATACCATGTTATATGATATTCATGC
183136 ATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTCTTAT
66 ATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTCTTAT
183201 AATCATATTA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (133 bp):
TAGGATATTATTATTACATGTTTCCATTTATCATTTAAGAATACCATGTTATATGATATTCATGC
ATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTCTTAT
TCT
Found at i:184761 original size:10 final size:10
Alignment explanation
Indices: 184746--184771 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
184736 ACTCAAAAAG
184746 AAGAAAAGGA
1 AAGAAAAGGA
184756 AAGAAAAGGA
1 AAGAAAAGGA
184766 AAGAAA
1 AAGAAA
184772 GAAAGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:188972 original size:13 final size:12
Alignment explanation
Indices: 188956--189028 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 12
188946 GTGCAAAAAG
188956 AAAAGAAAAGACA
1 AAAAGAAAAGA-A
188969 AAAAG--AAGAA
1 AAAAGAAAAGAA
188979 AAATTCAGAAAAGAA
1 AAA---AGAAAAGAA
188994 TAAAAGAAAAG-A
1 -AAAAGAAAAGAA
**
189006 AAAAGAAAATCA
1 AAAAGAAAAGAA
189018 AAAAGAGAAAG
1 AAAAGA-AAAG
189029 CAAGACAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
10 4 0.08
11 13 0.26
12 8 0.16
13 17 0.34
15 5 0.10
16 3 0.06
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.05
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:191712 original size:21 final size:21
Alignment explanation
Indices: 191673--191712 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
191663 AAGGAAGATT
*
191673 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
191694 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
191713 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:191762 original size:22 final size:21
Alignment explanation
Indices: 191734--191775 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
191724 GGATACGAAA
191734 ATGATGGTCTTGATGGATGAAG
1 ATGATGGTCTTGAT-GATGAAG
*
191756 ATGATGGTGTTGATGATGAA
1 ATGATGGTCTTGATGATGAA
191776 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.33
Consensus pattern (21 bp):
ATGATGGTCTTGATGATGAAG
Found at i:197148 original size:24 final size:21
Alignment explanation
Indices: 197113--197155 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
197103 GGCACATTCT
*
197113 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
197136 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
197156 GTCTTGTGGA
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:201385 original size:19 final size:20
Alignment explanation
Indices: 201361--201411 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
201351 CGGCCAAGAG
* *
201361 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
201380 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
201400 CATGTATTTTCA
1 CATGTATTTTCA
201412 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:205551 original size:19 final size:20
Alignment explanation
Indices: 205527--205577 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
205517 CGGCCAAGAG
* *
205527 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
205546 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
205566 CATGTATTTTCA
1 CATGTATTTTCA
205578 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:209708 original size:19 final size:19
Alignment explanation
Indices: 209684--209733 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
209674 CGGCCAAGAG
*
209684 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
209703 CATGTATTTTCATCAAAAAT
1 CATGTA-TTTCATCAAAAAT
209723 CATGTATTTCA
1 CATGTATTTCA
209734 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:209723 original size:20 final size:19
Alignment explanation
Indices: 209684--209731 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
209674 CGGCCAAGAG
* *
209684 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
209703 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
209723 CATGTATTT
1 CATGTATTT
209732 CAAAGGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:213799 original size:22 final size:21
Alignment explanation
Indices: 213773--213813 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
213763 GTTGCAGAAT
213773 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
213795 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
213814 ACGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:215603 original size:2 final size:2
Alignment explanation
Indices: 215596--215639 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
215586 AGTTATTTTC
*
215596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
215637 AT A
1 AT A
215640 GTTATTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:216926 original size:22 final size:21
Alignment explanation
Indices: 216889--216929 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
216879 CCATCTCCAT
216889 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
216910 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
216930 ATTCCATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:219602 original size:19 final size:18
Alignment explanation
Indices: 219580--219626 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
219570 GAATAATAAT
219580 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
219599 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
219618 AATA-AAGAA
1 AATATAAGAA
219627 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:220075 original size:19 final size:21
Alignment explanation
Indices: 220032--220083 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
220022 GAAACCCCTT
*
220032 TGAAAATATATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
220053 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
220072 TGAAGATACATG
1 TGAAAATACATG
220084 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:222362 original size:19 final size:18
Alignment explanation
Indices: 222316--222382 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
222306 TGAACTTCTC
*
222316 TTTTTCTTTTCTTTT--A
1 TTTTTCTCTTCTTTTGAA
*
222332 TTCTTT-TCTTCTTTTCTAA
1 TT-TTTCTCTTCTTTT-GAA
*
222351 TTTTTCTCTTCTTTTGAC
1 TTTTTCTCTTCTTTTGAA
222369 TTTTTCT-TTCTTTT
1 TTTTTCTCTTCTTTT
222383 TGCACTCCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
16 10 0.23
17 10 0.23
18 11 0.26
19 12 0.28
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (18 bp):
TTTTTCTCTTCTTTTGAA
Found at i:222670 original size:19 final size:18
Alignment explanation
Indices: 222648--222694 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
222638 GAATAATAAT
222648 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
222667 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
222686 AATA-AAGAA
1 AATATAAGAA
222695 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:223144 original size:19 final size:21
Alignment explanation
Indices: 223101--223152 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
223091 GAAACCCCTT
223101 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
223122 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
223141 TGAAGATACATG
1 TGAAAATACATG
223153 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:224887 original size:21 final size:21
Alignment explanation
Indices: 224863--224902 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
224853 TATATGCTTG
224863 CATATCAATCAATG-ATGCAAC
1 CATAT-AATCAATGAATGCAAC
*
224884 CATATAATGAATGAATGCA
1 CATATAATCAATGAATGCA
224903 CATGTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (21 bp):
CATATAATCAATGAATGCAAC
Found at i:232191 original size:19 final size:22
Alignment explanation
Indices: 232145--232189 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
232135 TCTTTCTTAC
232145 TCTTTGAGTGCTTTCAATTTCT
1 TCTTTGAGTGCTTTCAATTTCT
* *
232167 TCTTTGAGTGCTTTGATTTTCT
1 TCTTTGAGTGCTTTCAATTTCT
232189 T
1 T
232190 TGCTGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.58
Consensus pattern (22 bp):
TCTTTGAGTGCTTTCAATTTCT
Done.