Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005710.1 Hibiscus syriacus cultivar Beakdansim tig00013351_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: 144954
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10590 original size:28 final size:26
Alignment explanation
Indices: 10537--10593 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
10527 TTCTTTGCTT
* *
10537 TTTCTTCTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGAGTGCTGCAATTTC
*
10563 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGCTGCAATTTC
10591 TTT
1 TTT
10594 TCCGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 7 0.27
28 15 0.58
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGCTGCAATTTC
Found at i:12643 original size:14 final size:14
Alignment explanation
Indices: 12624--12660 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
12614 TAAGATACTA
12624 TTTCCATCACCATC
1 TTTCCATCACCATC
12638 TTTCCATCACCATC
1 TTTCCATCACCATC
*
12652 -CTCCATCAC
1 TTTCCATCAC
12661 TTTCACACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.32
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:15319 original size:32 final size:33
Alignment explanation
Indices: 15281--15347 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
15271 CAAAAATTAA
15281 AAGAAA-GAAATGATTAA-AATTGAATATGGA-AG
1 AAGAAAGGAAATGA-TAAGAATTGAA-ATGGATAG
15313 AAGAAAGGAAATGATAAGAATTGAAATGGATAG
1 AAGAAAGGAAATGATAAGAATTGAAATGGATAG
15346 AA
1 AA
15348 ATGTTAACAA
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:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (33 bp):
AAGAAAGGAAATGATAAGAATTGAAATGGATAG
Found at i:15912 original size:19 final size:20
Alignment explanation
Indices: 15871--15921 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
15861 GAAACCCCTT
*
15871 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
15891 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
15910 TGAATATACATG
1 TGAAAATACATG
15922 CTCTTGGCTG
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:0.12, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:25153 original size:21 final size:20
Alignment explanation
Indices: 25128--25166 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
25118 ATGGATAATT
25128 AAGAAAGGAAATAGAAATGGA
1 AAGAAAGGAAA-AGAAATGGA
**
25149 AAGAATTGAAAAGAAATG
1 AAGAAAGGAAAAGAAATG
25167 AAATGTTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (20 bp):
AAGAAAGGAAAAGAAATGGA
Found at i:25410 original size:36 final size:35
Alignment explanation
Indices: 25317--25427 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
25307 TTGGTGGTTA
* * * *
25317 TATAGGCGTGAAATAGTGATAGAAGATGGTAATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* * *
25352 TATAGGCGTGCAATGGTAATGGAATATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
*
25387 TATAGGCCTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
25423 T-TAGG
1 TATAGG
25428 TAGTTTCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:30408 original size:15 final size:16
Alignment explanation
Indices: 30387--30444 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
30377 AAGATATGGT
30387 AATGAAATAAGAAA-A
1 AATGAAATAAGAAAGA
* *
30402 GATGAAATAATAAAGA
1 AATGAAATAAGAAAGA
*
30418 AATGAAAT-AGTAAGAA
1 AATGAAATAAGAAAG-A
30434 AATGAAGATAA
1 AATGAA-ATAA
30445 CTTACCACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 16 0.47
16 15 0.44
17 2 0.06
18 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
AATGAAATAAGAAAGA
Found at i:30424 original size:16 final size:16
Alignment explanation
Indices: 30387--30444 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
30377 AAGATATGGT
*
30387 AATGAAATAAGAAA-A
1 AATGAAATAATAAAGA
*
30402 GATGAAATAATAAAGA
1 AATGAAATAATAAAGA
*
30418 AATGAAATAGT-AAGAA
1 AATGAAATAATAAAG-A
30434 AATGAAGATAA
1 AATGAA-ATAA
30445 CTTACCACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 15 0.43
16 17 0.49
17 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
AATGAAATAATAAAGA
Found at i:31152 original size:36 final size:35
Alignment explanation
Indices: 31058--31169 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
31048 GATTGGTGGT
* *
31058 TTATAGGCGTGAAATGGTGATAGAAGATGGTAATG
1 TTATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* * * *
31093 ATATTGGCGTGCAATGGTAATGGAAGATGGTGATG
1 TTATAGGCGTGAAATGGTGATGGAAGATGGTGATG
*
31128 TTATAGGTGTGAAAATGGTGATGGAAGATGGTGATG
1 TTATAGGCGTG-AAATGGTGATGGAAGATGGTGATG
31164 TT-TAGG
1 TTATAGG
31170 TAGTATCTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.63
36 24 0.37
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (35 bp):
TTATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Found at i:31160 original size:13 final size:13
Alignment explanation
Indices: 31106--31163 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
31096 TTGGCGTGCA
*
31106 ATGGTAATGGAAG
1 ATGGTGATGGAAG
** *
31119 ATGGTGATGTTAT
1 ATGGTGATGGAAG
*
31132 A-GGTG-T-GAAA
1 ATGGTGATGGAAG
31142 ATGGTGATGGAAG
1 ATGGTGATGGAAG
31155 ATGGTGATG
1 ATGGTGATG
31164 TTTAGGTAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.15
12 5 0.15
13 22 0.65
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:44405 original size:19 final size:20
Alignment explanation
Indices: 44359--44407 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
44349 TAATAAAGGG
44359 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
44379 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
44398 AATAAAATAA
1 AATAAAATAA
44408 ATAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:44862 original size:19 final size:21
Alignment explanation
Indices: 44819--44870 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
44809 GAAACCCCTT
*
44819 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
*
44840 TGAAAATACATTA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
*
44859 TGAAGATACATG
1 TGAAAATACATG
44871 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:47951 original size:19 final size:19
Alignment explanation
Indices: 47912--47956 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
47902 TAAAGGGAAT
*
47912 AATAATATAAGTAATAATGAA
1 AATAA-ATAAGTAAGAATG-A
47933 AATAAATAA-TAAGAATGA
1 AATAAATAAGTAAGAATGA
47951 AATAAA
1 AATAAA
47957 ATAAATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 7 0.30
20 4 0.17
21 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAATAAGTAAGAATGA
Found at i:47958 original size:19 final size:20
Alignment explanation
Indices: 47912--47960 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
47902 TAAAGGGAAT
* *
47912 AATAATATAAGTAATAATGA
1 AATAAAATAAGTAAGAATGA
47932 AA-ATAAATAA-TAAGAATGA
1 AATA-AAATAAGTAAGAATGA
47951 AATAAAATAA
1 AATAAAATAA
47961 ATAAAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAAGTAAGAATGA
Found at i:48187 original size:21 final size:21
Alignment explanation
Indices: 48139--48188 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
48129 ATTACTATCG
*
48139 CAATGCGATTTTCCAATTTCG
1 CAATGCGATTTTCCAATTTCA
**
48160 CTTTGCGATTTTCCCAA-TTCA
1 CAATGCGATTTT-CCAATTTCA
48181 CAATGCGA
1 CAATGCGA
48189 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCA
Found at i:48221 original size:21 final size:21
Alignment explanation
Indices: 48195--48250 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
48185 GCGAATAAGT
48195 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
48216 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
48237 AAATCGCAATGCGA
1 AAATCGCAATGCGA
48251 TACTGACTAT
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:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:48294 original size:21 final size:21
Alignment explanation
Indices: 48260--48326 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
48250 ATACTGACTA
* * *
48260 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
48281 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
* *
48301 TCGCGTTGCGATTCTCATAAT
1 TCGCATTGCGATTTTCATAAT
48322 TCGCA
1 TCGCA
48327 ACGCGAATAC
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:48345 original size:20 final size:20
Alignment explanation
Indices: 48316--48374 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
48306 TTGCGATTCT
*
48316 CATAATTCGCAACGCGAATA
1 CATAAATCGCAACGCGAATA
*
48336 CATAAATCGCAACGCGATTA
1 CATAAATCGCAACGCGAATA
*
48356 -AGTAAATCGCAATGCGAAT
1 CA-TAAATCGCAACGCGAAT
48375 TAGGAAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
CATAAATCGCAACGCGAATA
Found at i:48383 original size:21 final size:21
Alignment explanation
Indices: 48339--48395 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
48329 GCGAATACAT
* *
48339 AAATCGCAACGCG-ATTAAGT
1 AAATCGCAATGCGAATTAAGA
*
48359 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAAGA
48380 AAATCGCAATGCGAAT
1 AAATCGCAATGCGAAT
48396 CTGACTATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAAGA
Found at i:48949 original size:14 final size:14
Alignment explanation
Indices: 48930--48986 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
48920 TTTCATTTCG
48930 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
48944 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
48961 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
*
48977 CGTTACGATT
1 CGTTGCGATT
48987 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:48955 original size:33 final size:33
Alignment explanation
Indices: 48913--49005 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
48903 GTTGAAGTAA
48913 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
48946 TTGCGATTTTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
48979 TTACGATTTTCATTTCGCGTTGTGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
49006 TTCATTCTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:49021 original size:20 final size:20
Alignment explanation
Indices: 48937--49071 Score: 112
Period size: 20 Copynumber: 7.2 Consensus size: 20
48927 TCGCGTTGCG
48937 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
48957 ATT-TCGT-GTTGCG------
1 ATTCTC-TCGTTGCGATTTTC
*
48970 ATTCTCTCGTTACGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
48990 ATT-TCGCGTTGTGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* **
49009 ATTCTCTCGTTGTGATAGTC
1 ATTCTCTCGTTGCGATTTTC
49029 ATT-TC-CGCTTTGCGATTTTC
1 ATTCTCTCG--TTGCGATTTTC
49049 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
49069 ATT
1 ATT
49072 TCAACCAAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 28
0.71 0.08 0.22
Matches are distributed among these distances:
13 4 0.04
14 7 0.08
18 2 0.02
19 26 0.29
20 48 0.53
21 2 0.02
22 2 0.02
ACGTcount: A:0.12, C:0.21, G:0.17, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:49031 original size:39 final size:40
Alignment explanation
Indices: 48970--49073 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
48960 TCGTGTTGCG
* ** *
48970 ATTCTCTCGTTACGATTTTCATTT-CGCGTTGTGATTTTC
1 ATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTC
* *
49009 ATTCTCTCGTTGTGATAGTCATTTCCGCTTTGCGATTTTC
1 ATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTC
**
49049 ATTCTCTCGTTGCGATTTTCATTTC
1 ATTCTCTCGTTGCGATAGTCATTTC
49074 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
39 20 0.36
40 35 0.64
ACGTcount: A:0.12, C:0.22, G:0.15, T:0.50
Consensus pattern (40 bp):
ATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTC
Found at i:50949 original size:94 final size:94
Alignment explanation
Indices: 50758--51062 Score: 451
Period size: 94 Copynumber: 3.3 Consensus size: 94
50748 TAGATTGCTT
* *
50758 AGTAAATTTATTCAGTTGCTGCCAATACTGCTAAAC----TATT-TATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAG
*
50818 TATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
65 TATTTGT-ATTTGTTTTGTCTTTTGGTTGAA
*
50848 AGTAAATTTATTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
50913 ATTTGTATTTGTTTTATCTTTTGGTTGAA
66 ATTTGTATTTGTTTTGTCTTTTGGTTGAA
* * *
50942 AGTAAATTTGTTCGGTTGCTGCCAATTCTCCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
51007 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTATTTGTTTTGTCTTTTGGTTGAA
* *
51036 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
51063 GAAACTATTC
Statistics
Matches: 197, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
90 33 0.17
93 19 0.10
94 144 0.73
95 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTATTTGTTTTGTCTTTTGGTTGAA
Found at i:51530 original size:21 final size:21
Alignment explanation
Indices: 51506--51572 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
51496 TCATTCCTCG
51506 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
51527 AGAGGCCACTATCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
51548 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
51569 AGAG
1 AGAG
51573 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:51530 original size:42 final size:42
Alignment explanation
Indices: 51454--51572 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 42
51444 GACTCGCTTG
* * * * * * *
51454 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCCACTA
51496 TCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCCACTA
1 TCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCCACTA
* *
51538 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
51573 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.06
42 60 0.91
43 2 0.03
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCCACTA
Found at i:56593 original size:12 final size:11
Alignment explanation
Indices: 56564--56593 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
56554 TGGCTTTGCT
56564 TTCTTTTTGAA
1 TTCTTTTTGAA
56575 TTCTTTTTGAA
1 TTCTTTTTGAA
56586 TTCTTTTT
1 TTCTTTTT
56594 CTTTTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (11 bp):
TTCTTTTTGAA
Found at i:56629 original size:15 final size:14
Alignment explanation
Indices: 56589--56636 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
56579 TTTTGAATTC
56589 TTTTTC-TTTTCTT
1 TTTTTCTTTTTCTT
* *
56602 CTTTTCTTCTTCTT
1 TTTTTCTTTTTCTT
56616 TTTTGTCTTTTTCTT
1 TTTT-TCTTTTTCTT
56631 TCTTTT
1 T-TTTT
56637 TGCACTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 11 0.39
16 3 0.11
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:56942 original size:23 final size:22
Alignment explanation
Indices: 56899--56952 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
56889 AATAAAGGGT
*
56899 AATAATATAAGTAATGAAAATA
1 AATAATATAAGAAATGAAAATA
56921 AATAATAATAATGAAATG-AAATA
1 AATAAT-ATAA-GAAATGAAAATA
56944 AATAA-ATAA
1 AATAATATAA
56953 AAAAGATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.14
22 6 0.21
23 14 0.48
24 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
AATAATATAAGAAATGAAAATA
Found at i:59366 original size:19 final size:19
Alignment explanation
Indices: 59279--59359 Score: 103
Period size: 19 Copynumber: 4.3 Consensus size: 19
59269 AAAAATGACT
*
59279 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
*
59298 ATTGCAACGCGAAA-TAAAA
1 ATCGCAACGCGAAACT-AAA
59317 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
59336 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
59355 TTCGC
1 ATCGC
59360 GTTGCGATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 55 0.98
20 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:59401 original size:33 final size:33
Alignment explanation
Indices: 59359--59452 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
59349 ACTAAATTCG
* * *
59359 CGTTGCGATTTTAATTTCTCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
59392 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
59425 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
59453 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:59418 original size:19 final size:19
Alignment explanation
Indices: 59394--59452 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
59384 GATTCCCTCG
59394 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
59413 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
59427 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
59446 TTGCGAT
1 TTGCGAT
59453 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:59518 original size:20 final size:20
Alignment explanation
Indices: 59446--59518 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
59436 TCATTTCGCA
** *
59446 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTAAGTG
*
59466 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTAAG-TG
**
59486 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTAAGTG
59507 TTGCGATAGTCA
1 TTGCGATAGTCA
59519 AATGATTGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTAAGTG
Found at i:62010 original size:24 final size:24
Alignment explanation
Indices: 61976--62029 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
61966 CTGAAACATC
*
61976 ATCAAAATCTGAGTATTGACCAAT
1 ATCAAAATCTGAGTATTGACCAAG
* *
62000 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
62024 ATCAAA
1 ATCAAA
62030 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:62854 original size:21 final size:21
Alignment explanation
Indices: 62828--62924 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
62818 CGAAAGTCAG
62828 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
** *
62849 TATCGCGTTGCGATAGT-TAG
1 TATCGCGTTGCGATTTTGTAT
* **
62869 TATCGCATTGCGATTTTCCAAAT
1 TATCGCGTTGCGATTTT--GTAT
*
62892 T-T-GCATTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
62911 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
62925 AGTCAGTATC
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.05
20 17 0.28
21 37 0.62
22 1 0.02
23 2 0.03
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTGTAT
Found at i:62871 original size:41 final size:41
Alignment explanation
Indices: 62748--62885 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
62738 AACTTTGAAA
* * *
62748 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
* * ** ** *
62789 ATCTCGTTGCGA--AAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGT
* *
62829 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTTAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
62870 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
62886 CCAAATTTGC
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 2 0.03
40 29 0.38
41 44 0.57
42 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
Found at i:62874 original size:20 final size:20
Alignment explanation
Indices: 62768--62944 Score: 117
Period size: 20 Copynumber: 8.7 Consensus size: 20
62758 GATTCTGTAT
*
62768 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
62788 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
62808 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
62828 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
62849 TATCGCGTTGCGATAGTTAG
1 TATCGCGTTGCGATAGTCAG
* **
62869 TATCGCATTGCGATTTTCCA-
1 TATCGCGTTGCGATAGT-CAG
* * * * *
62889 AATTTGCATTGCGATTTTGT-AT
1 TA-TCGCGTTGCGA--TAGTCAG
62911 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
62931 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
62945 TTTCCAAATT
Statistics
Matches: 126, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.05
20 79 0.63
21 35 0.28
22 3 0.02
23 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:62915 original size:62 final size:62
Alignment explanation
Indices: 62830--62968 Score: 251
Period size: 62 Copynumber: 2.2 Consensus size: 62
62820 AAAGTCAGTA
* *
62830 TCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTTAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
*
62892 TTGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
62954 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
62969 CCAAATTCGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 73 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (62 bp):
TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
Found at i:62959 original size:21 final size:21
Alignment explanation
Indices: 62871--62985 Score: 119
Period size: 21 Copynumber: 5.5 Consensus size: 21
62861 ATAGTTAGTA
62871 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* ** *
62892 TTGCATTGCGATTTT-GTATT
1 TCGCATTGCGATTTTCCAAAT
* ** *
62912 ATCGCGTTGCGATAGT-C-AGT
1 -TCGCATTGCGATTTTCCAAAT
62932 ATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATTTTCCAAAT
62954 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
62975 TCGCATTGCGA
1 TCGCATTGCGA
62986 ATTGGGAAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
20 17 0.22
21 58 0.75
22 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:62984 original size:62 final size:62
Alignment explanation
Indices: 62830--62985 Score: 206
Period size: 62 Copynumber: 2.5 Consensus size: 62
62820 AAAGTCAGTA
* ** * *
62830 TCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTTAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
* ** *
62892 TTGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
*
62954 TCGCATTGCGATTTTCCAAAT-TCGCATTGCGA
1 TCGCATTGCGATTTT-CAAATATCGCGTTGCGA
62986 ATTGGGAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
62 83 0.98
63 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (62 bp):
TCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
Found at i:62999 original size:21 final size:20
Alignment explanation
Indices: 62975--63049 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
62965 TTTTCCAAAT
*
62975 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-AGAAAA
**
62996 TCGCAACGCGAAATTAGAAAA
1 TCGCATTGCG-AATTAGAAAA
63017 TCGCATTGCG-A-TAGTAATAA
1 TCGCATTGCGAATTAG-AA-AA
*
63037 TCGCGTTGCGAAT
1 TCGCATTGCGAAT
63050 CTGGAAACTG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 3 0.07
19 3 0.07
20 11 0.26
21 22 0.51
22 4 0.09
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
TCGCATTGCGAATTAGAAAA
Found at i:63646 original size:19 final size:21
Alignment explanation
Indices: 63603--63654 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
63593 GAAACCCCTT
63603 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
63624 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
63643 TGAAGATACATG
1 TGAAAATACATG
63655 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:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:74961 original size:17 final size:17
Alignment explanation
Indices: 74941--74984 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
74931 TCTATTAATG
* *
74941 GAATGCATCCTTTGGCT
1 GAATTCATCCTTTGGCC
74958 GAATTCATCCTTTGGCC
1 GAATTCATCCTTTGGCC
74975 GAATTCATCC
1 GAATTCATCC
74985 CACCCTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.34
Consensus pattern (17 bp):
GAATTCATCCTTTGGCC
Found at i:76916 original size:16 final size:15
Alignment explanation
Indices: 76895--76924 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
76885 ATTATGAACC
76895 ATATATCTATATATTT
1 ATATATCT-TATATTT
76911 ATATATCTTATATT
1 ATATATCTTATATT
76925 ACTTAGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATCTTATATTT
Found at i:81050 original size:2 final size:2
Alignment explanation
Indices: 81039--81095 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
81029 TAACTATAGG
81039 TA TA -A 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
81080 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
81096 AATAACTATC
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:84037 original size:5 final size:5
Alignment explanation
Indices: 84027--84067 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
84017 GAACTTCTCT
*
84027 TTTTC TTTTC TTTTC TTTT- TTTTC TTTTT TTCTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC T
84068 GATTTTTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:84051 original size:9 final size:9
Alignment explanation
Indices: 84026--84057 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
84016 TGAACTTCTC
84026 TTTTTCTTT
1 TTTTTCTTT
84035 TCTTTTCTTT
1 T-TTTTCTTT
84045 TTTTTCTTT
1 TTTTTCTTT
84054 TTTT
1 TTTT
84058 CTTCTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:84052 original size:25 final size:25
Alignment explanation
Indices: 84024--84084 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
84014 TTTGAACTTC
**
84024 TCTTTTTCTTTTCTTTTCTTTTTTT
1 TCTTTTTCTTTTCTTTTCTGATTTT
84049 TCTTTTT-TTCTTCTTTTCTGATTTT
1 TCTTTTTCTT-TTCTTTTCTGATTTT
*
84074 TC-TCTTCTTTT
1 TCTTTTTCTTTT
84085 TGCACTCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (25 bp):
TCTTTTTCTTTTCTTTTCTGATTTT
Found at i:92947 original size:21 final size:21
Alignment explanation
Indices: 92901--92951 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
92891 GGCCAAGAGC
* **
92901 ATGTATCTTCATTAAAATCAT
1 ATGTATTTTCATTAAAAAAAT
92922 A--TATTTTCATTAAAAAAAT
1 ATGTATTTTCATTAAAAAAAT
92941 ATGTATTTTCA
1 ATGTATTTTCA
92952 AAGGGGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 16 0.64
21 9 0.36
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (21 bp):
ATGTATTTTCATTAAAAAAAT
Found at i:95557 original size:22 final size:23
Alignment explanation
Indices: 95529--95575 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
95519 CTTGAACATC
95529 CATGGCCGAATA-TTACAATATG
1 CATGGCCGAATATTTACAATATG
95551 CATGGCCGAATATTTACAATATG
1 CATGGCCGAATATTTACAATATG
95574 CA
1 CA
95576 AGGTTGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (23 bp):
CATGGCCGAATATTTACAATATG
Found at i:95584 original size:23 final size:22
Alignment explanation
Indices: 95532--95578 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
95522 GAACATCCAT
*
95532 GGCCGAATATTACAATATGCAT
1 GGCCGAATATTACAATATGCAA
95554 GGCCGAATATTTACAATATGCAA
1 GGCCGAATA-TTACAATATGCAA
95577 GG
1 GG
95579 TTGAATGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (22 bp):
GGCCGAATATTACAATATGCAA
Found at i:105811 original size:22 final size:23
Alignment explanation
Indices: 105783--105829 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
105773 CTTGAACATC
*
105783 CATGGCCGAATA-TTACAATATG
1 CATGGCCAAATATTTACAATATG
105805 CATGGCCAAATATTTACAATATG
1 CATGGCCAAATATTTACAATATG
105828 CA
1 CA
105830 AGGTTGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (23 bp):
CATGGCCAAATATTTACAATATG
Found at i:108348 original size:13 final size:13
Alignment explanation
Indices: 108330--108362 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
108320 CATAGTTGGA
108330 TTGAGCTGAAGAT
1 TTGAGCTGAAGAT
108343 TTGAGCTGAAGAT
1 TTGAGCTGAAGAT
108356 TTGAGCT
1 TTGAGCT
108363 ACAAGATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.30, T:0.33
Consensus pattern (13 bp):
TTGAGCTGAAGAT
Found at i:111437 original size:23 final size:25
Alignment explanation
Indices: 111409--111463 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
111399 AAATCCAGCA
111409 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAAGG
* *
111432 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAAATCAAAGCACTCAAAAAGG
111457 AAGAAAA
1 AAGAAAA
111464 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 4 0.15
25 7 0.26
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAAGG
Found at i:123492 original size:13 final size:13
Alignment explanation
Indices: 123470--123499 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
123460 ACTAAACACC
123470 TTTC-ACATACCT
1 TTTCAACATACCT
123482 TTTCAACATACCT
1 TTTCAACATACCT
123495 TTTCA
1 TTTCA
123500 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:132583 original size:23 final size:24
Alignment explanation
Indices: 132535--132584 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
132525 TTTCTTTCTT
132535 TTTCTTCTTTTCGAGTGATTTCAA
1 TTTCTTCTTTTCGAGTGATTTCAA
* *
132559 TTTCTTCTTTT-GAGTGCTTTTAA
1 TTTCTTCTTTTCGAGTGATTTCAA
132582 TTT
1 TTT
132585 ATTTGCTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGATTTCAA
Found at i:134904 original size:23 final size:25
Alignment explanation
Indices: 134876--134930 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
134866 AAATCCAGCA
134876 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAAGG
* *
134899 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAAATCAAAGCACTCAAAAAGG
134924 AAGAAAA
1 AAGAAAA
134931 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 4 0.15
25 7 0.26
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAAGG
Found at i:138529 original size:19 final size:19
Alignment explanation
Indices: 138493--138530 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
138483 ACATGTCATG
138493 TTACTTAGCTCATGCTATGT
1 TTACTTAGCTCA-GCTATGT
138513 TTACATTAGCTCA-CTATG
1 TTAC-TTAGCTCAGCTATG
138531 ATGTAAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (19 bp):
TTACTTAGCTCAGCTATGT
Found at i:138901 original size:34 final size:36
Alignment explanation
Indices: 138861--138947 Score: 115
Period size: 34 Copynumber: 2.5 Consensus size: 36
138851 TATATGTGTG
*
138861 AAATGGTGATAGAAGATAGT-ATGATATAGGCGT-G
1 AAATGGTGATAGAAGATAGTGATGATATAGGCGTAA
* * *
138895 CAATGGTGATAGAAGATGGTGATGTTATAGGCGTAA
1 AAATGGTGATAGAAGATAGTGATGATATAGGCGTAA
*
138931 AAATGGTGATGGAAGAT
1 AAATGGTGATAGAAGAT
138948 GATGAACAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 18 0.40
35 12 0.27
36 15 0.33
ACGTcount: A:0.37, C:0.03, G:0.33, T:0.26
Consensus pattern (36 bp):
AAATGGTGATAGAAGATAGTGATGATATAGGCGTAA
Found at i:141140 original size:19 final size:20
Alignment explanation
Indices: 141116--141166 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
141106 TCGGCAAGAG
*
141116 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
141135 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
141155 CATGTATTTTCA
1 CATGTATTTTCA
141167 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Done.