Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000133.1 Hibiscus syriacus cultivar Beakdansim tig00000239_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: 84036
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1987 original size:22 final size:22
Alignment explanation
Indices: 1932--1989 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
1922 CATAAACTTA
1932 ATTATTATTTTTAAATATTAAAAT
1 ATTATT-TTTTT-AATATTAAAAT
* *
1956 A--ATTTATTTATTATTAAAAT
1 ATTATTTTTTTAATATTAAAAT
1976 ATTATTTTTTTAAT
1 ATTATTTTTTTAAT
1990 TTTATTAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 11 0.39
21 4 0.14
22 12 0.43
24 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATTTTTTTAATATTAAAAT
Found at i:2182 original size:50 final size:52
Alignment explanation
Indices: 2106--2240 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 52
2096 GTATATTTAA
*
2106 ATATCTTTATTAA-AATATTATTATATTATTATTA-GATA-TA-TAAATAATAT
1 ATAT-TTTATTAATAAT-TTATTATATTATTATTATGAAATTAGTAAATAATAT
*
2156 -TATTCATTATTAATAATTTATAATATTATT-TCTATGAAATTAGTAAATAATAT
1 ATATT--TTATTAATAATTTATTATATTATTAT-TATGAAATTAGTAAATAATAT
2209 ATATTTTATTAATAATTTATTATA-TATTATTA
1 ATATTTTATTAATAATTTATTATATTATTATTA
2241 AAAAAAATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
48 1 0.01
49 4 0.05
50 21 0.29
51 12 0.16
52 21 0.29
53 10 0.14
54 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (52 bp):
ATATTTTATTAATAATTTATTATATTATTATTATGAAATTAGTAAATAATAT
Found at i:2310 original size:21 final size:23
Alignment explanation
Indices: 2284--2329 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
2274 TTGATTATTT
2284 TATTATAATATTA-AAATA-TAA
1 TATTATAATATTAGAAATATTAA
*
2305 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAGAAATATTAA
2328 TA
1 TA
2330 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAATATTAGAAATATTAA
Found at i:2336 original size:29 final size:29
Alignment explanation
Indices: 2277--2337 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
2267 AATATAATTG
* * *
2277 ATTATTTTATTATAATATTAAAATATAAT
1 ATTATATTATTAAAATATTAAAAAATAAT
*
2306 ATTATATTATTAGAAATATTAATAAAT-AT
1 ATTATATTATTA-AAATATTAAAAAATAAT
2335 ATT
1 ATT
2338 TTAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATTATATTATTAAAATATTAAAAAATAAT
Found at i:3596 original size:46 final size:46
Alignment explanation
Indices: 3499--3999 Score: 686
Period size: 46 Copynumber: 11.0 Consensus size: 46
3489 CTATTTGTAA
* * * * * * *
3499 ATTTCAGTTATGGCCTCTTTTCAGGCCTTAATACAT-CATTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
* * *
3544 ATTTTAGTTATGACATCCTTTCATGCCTTTATGCATTCATTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
* *
3590 ATTTTAGTTATGTCATCCTTTCATG-CTTTAATGCATCCGTTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGCCTTT-ATGCATCCGTTCATGC
*
3636 ATTTTAGTTATGGCATCATTTCATGCCTTTATGCATCCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
* * * *
3682 ATTTTAGTTATGACGTCCTTTCATGCATTTATGCATCTGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
* * *
3728 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCGTTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
*
3774 ATTTTAGTTATGTCATCCTTTCATGCC-TTATGCATCCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
* * * *
3819 ATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCC-ATCATGT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
*
3864 ATTTTAGTTATGGCATCCTTTCATGTCTTTATGCATCCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
* * * *
3910 ATTTTAGTTATGTCATCCTTTCATTCCTTTATGCATCCATTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
*
3956 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCAT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCAT
4000 TTTGTTATAA
Statistics
Matches: 403, Mismatches: 48, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
45 114 0.28
46 285 0.71
47 4 0.01
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTTATGCATCCGTTCATGC
Found at i:3815 original size:19 final size:20
Alignment explanation
Indices: 3781--3818 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3771 TGAATTTTAG
*
3781 TTATGTCATCCTTTCATGCC
1 TTATGTCATCCGTTCATGCC
3801 TTATG-CATCCGTTCATGC
1 TTATGTCATCCGTTCATGC
3819 ATTTTAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (20 bp):
TTATGTCATCCGTTCATGCC
Found at i:4501 original size:92 final size:93
Alignment explanation
Indices: 4359--4529 Score: 258
Period size: 92 Copynumber: 1.8 Consensus size: 93
4349 CCCTGATACC
* * *
4359 GATACTTCTATACTATGGTACCGATACCCCCTTTCAGTATCGATACCATTTCTA-TATTCTGTGT
1 GATACTACTATACTATGGTACCGATACCCCCTTTCAATATCGATACCATTT-TATTATTCTG-GA
4423 TACATGGTATCGATACCCTTCTCTCGGTTT
64 TACATGGTATCGATACCCTTCTCTCGGTTT
* *
4453 GATACTACTATACTATGGTA-CGATA-TCCCTTTCAATATCGATACCATTTTATTATTCTGGATC
1 GATACTACTATACTATGGTACCGATACCCCCTTTCAATATCGATACCATTTTATTATTCTGGATA
4516 CATGGTATCGATAC
66 CATGGTATCGATAC
4530 TTCCCTTGTT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
91 18 0.25
92 29 0.41
93 5 0.07
94 19 0.27
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (93 bp):
GATACTACTATACTATGGTACCGATACCCCCTTTCAATATCGATACCATTTTATTATTCTGGATA
CATGGTATCGATACCCTTCTCTCGGTTT
Found at i:10811 original size:46 final size:46
Alignment explanation
Indices: 10640--11117 Score: 595
Period size: 46 Copynumber: 10.6 Consensus size: 46
10630 AGGCCTAATA
* * **
10640 CATCCATTCATGCATTTTAGTTATGGCATCCTTTCATG-AATT-TG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
* * * *
10684 CATCAGTTCATGCATTTTAGTTATGTCATCCTTTCATGTCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
* *
10730 TATCCGTTCATGTA-TTTAGTTATGACATCCTTTCATGCCTTTATG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
* **
10775 CATCCGTTCATGCATTTTAGTTATGGCATATTTTCATGCCTTTATG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
10821 CAT-C-TTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
*
10865 CATCCATTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
* *
10911 CATCCGTTCATGCATTTTATTTATGGA-ATCCTTTCATGTCTTTATG
1 CATCCGTTCATGCATTTTAGTTAT-GACATCCTTTCATGCCTTTATG
** *
10957 CATATGCTCATGCATTTTAGTTATGACATCCTTTCATGCCTTT-TG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
* * *
11002 CATCCATTCATGCATTTTAGTTATGACATCCTTTCACGCCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
* * *
11048 AATCCG---A--CATTTTAGTTATGGCATCCTTTCATGCCTTAATG
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
* * *
11089 CATTCGTTCATACAATTTT-GTTATAACAT
1 CATCCGTTCATGC-ATTTTAGTTATGACAT
11118 AGTCAATACT
Statistics
Matches: 378, Mismatches: 42, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
41 36 0.10
43 1 0.00
44 76 0.20
45 84 0.22
46 174 0.46
47 7 0.02
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (46 bp):
CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATG
Found at i:10866 original size:90 final size:92
Alignment explanation
Indices: 10640--11117 Score: 595
Period size: 90 Copynumber: 5.3 Consensus size: 92
10630 AGGCCTAATA
* * ** *
10640 CATCCATTCATGCATTTTAGTTATGGCATCCTTTCATG-AATT-TGCATCAGTTCATGCATTTTA
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTTA
* * *
10703 GTTATGTCATCCTTTCATGTCTTAATG
66 GTTATGACATCCTTTCATGCCTTTATG
* *
10730 TATCCGTTCATGTA-TTTAGTTATGACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTTA
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTTA
* **
10794 GTTATGGCATATTTTCATGCCTTTATG
66 GTTATGACATCCTTTCATGCCTTTATG
*
10821 CAT-C-TTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATGCATCCATTCATGCATTTTA
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTTA
10884 GTTATGACATCCTTTCATGCCTTTATG
66 GTTATGACATCCTTTCATGCCTTTATG
* * ** *
10911 CATCCGTTCATGCATTTTATTTATGGA-ATCCTTTCATGTCTTTATGCATATGCTCATGCATTTT
1 CATCCGTTCATGCATTTTAGTTAT-GACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTT
10975 AGTTATGACATCCTTTCATGCCTTT-TG
65 AGTTATGACATCCTTTCATGCCTTTATG
* * * *
11002 CATCCATTCATGCATTTTAGTTATGACATCCTTTCACGCCTTAATGAATCCG---A--CATTTTA
1 CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTTA
* *
11062 GTTATGGCATCCTTTCATGCCTTAATG
66 GTTATGACATCCTTTCATGCCTTTATG
* * *
11089 CATTCGTTCATACAATTTT-GTTATAACAT
1 CATCCGTTCATGC-ATTTTAGTTATGACAT
11118 AGTCAATACT
Statistics
Matches: 341, Mismatches: 38, Indels: 21
0.85 0.09 0.05
Matches are distributed among these distances:
86 29 0.09
87 21 0.06
88 6 0.02
89 29 0.09
90 92 0.27
91 88 0.26
92 74 0.22
93 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (92 bp):
CATCCGTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTTA
GTTATGACATCCTTTCATGCCTTTATG
Found at i:11006 original size:227 final size:222
Alignment explanation
Indices: 10608--11117 Score: 632
Period size: 227 Copynumber: 2.3 Consensus size: 222
10598 CTATTTGTAA
* * * * * * *
10608 ATTTTTGTTATGGCCTCTTTTCAGGCC-TAATACATCCATTCATGCATTTTAGTTATGGCATCCT
1 ATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTATGACATCCT
** * * *
10672 TTCATGAATTTGCATCAGTTCATGCATTTTAGTTATGTCATCCTTTCATGTCTTAATGTATCCGT
66 TTCATGAATTTGCATCAGTTCATGCATTTTAGTTATGGAATCCTTTCATGTCTTAATGCATACGC
* * *
10737 TCATGTATTTAGTTATGACATCCTTTCATGCCTTTATGCATCCGTTCATGCATTTTAGTTATGGC
131 TCATGCATTTAGTTATGACATCCTTTCATGCCTTTATGCATCCATTCATGCATTTTAGTTATGAC
* * * *
10802 ATATTTTCATGCCTTTATGCATCTTC-ATGC
196 ATACTTTCACGCCTTAATGAATC--CGA--C
*
10832 ATTTTAGTTATGACATCCTTTCATGCCTTTATGCATCCATTCATGCATTTTAGTTATGACATCCT
1 ATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTATGACATCCT
** * * * *
10897 TTCATGCCTTTATGCATCCGTTCATGCATTTTATTTATGGAATCCTTTCATGTCTTTATGCATAT
66 TTCATG-AATT-TGCATCAGTTCATGCATTTTAGTTATGGAATCCTTTCATGTCTTAATGCATAC
10962 GCTCATGCATTTTAGTTATGACATCCTTTCATGCCTTT-TGCATCCATTCATGCATTTTAGTTAT
129 GCTCATGCA-TTTAGTTATGACATCCTTTCATGCCTTTATGCATCCATTCATGCATTTTAGTTAT
*
11026 GACATCCTTTCACGCCTTAATGAATCCGAC
193 GACATACTTTCACGCCTTAATGAATCCGAC
* * * * *
11056 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCGTTCATACAATTTT-GTTATAACAT
1 ATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGC-ATTTTAGTTATGACAT
11118 AGTCAATACT
Statistics
Matches: 247, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
224 73 0.30
225 46 0.19
226 3 0.01
227 97 0.39
228 28 0.11
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (222 bp):
ATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTATGACATCCT
TTCATGAATTTGCATCAGTTCATGCATTTTAGTTATGGAATCCTTTCATGTCTTAATGCATACGC
TCATGCATTTAGTTATGACATCCTTTCATGCCTTTATGCATCCATTCATGCATTTTAGTTATGAC
ATACTTTCACGCCTTAATGAATCCGAC
Found at i:11011 original size:19 final size:19
Alignment explanation
Indices: 10983--11019 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10973 TTAGTTATGA
* *
10983 CATCCTTTCATGCCTTTTG
1 CATCCATTCATGCATTTTG
11002 CATCCATTCATGCATTTT
1 CATCCATTCATGCATTTT
11020 AGTTATGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.30, G:0.08, T:0.46
Consensus pattern (19 bp):
CATCCATTCATGCATTTTG
Found at i:11516 original size:18 final size:18
Alignment explanation
Indices: 11493--11533 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
11483 TATGATACCG
*
11493 ATACCCCTTTTAGTATCA
1 ATACCCCTTTCAGTATCA
*
11511 ATACCCCTTTCAGTATCG
1 ATACCCCTTTCAGTATCA
11529 ATACC
1 ATACC
11534 ATTTCTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (18 bp):
ATACCCCTTTCAGTATCA
Found at i:14545 original size:13 final size:13
Alignment explanation
Indices: 14527--14552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14517 TACAAAACTT
14527 TTTAAAATTACAC
1 TTTAAAATTACAC
14540 TTTAAAATTACAC
1 TTTAAAATTACAC
14553 AATGGTCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAATTACAC
Found at i:15291 original size:17 final size:17
Alignment explanation
Indices: 15247--15294 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
15237 GACTGAGCCA
* *
15247 TTGACTATTGACCACCT
1 TTGACCATTGACCGCCT
* *
15264 TTGAACGTTGACCGCCT
1 TTGACCATTGACCGCCT
15281 TTGACCATTGACCG
1 TTGACCATTGACCG
15295 TTGACTTTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (17 bp):
TTGACCATTGACCGCCT
Found at i:16929 original size:31 final size:31
Alignment explanation
Indices: 16891--16966 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
16881 TAAGGCGACC
** *
16891 CTTGGGTAGGCTCTGTGGCCATGAGGTTTTT
1 CTTGGGTAGGCTCTGTGGCCATGAGAATTGT
* *
16922 CTTGGGTAAGCCTCTGTGGCCTTGAGAATTGT
1 CTTGGGT-AGGCTCTGTGGCCATGAGAATTGT
16954 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
16967 ACAGGCCCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.12, C:0.18, G:0.34, T:0.36
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGTGGCCATGAGAATTGT
Found at i:25428 original size:20 final size:19
Alignment explanation
Indices: 25403--25454 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 19
25393 CACCTCTCGT
25403 ATAAAACTAAAAGCGACTTG
1 ATAAAA-TAAAAGCGACTTG
25423 ATAAAATAAAACAGCGACTTG
1 ATAAAAT-AAA-AGCGACTTG
25444 ATAAAATAAAA
1 ATAAAATAAAA
25455 CATGAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 16 0.53
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (19 bp):
ATAAAATAAAAGCGACTTG
Found at i:25440 original size:21 final size:21
Alignment explanation
Indices: 25414--25456 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
25404 TAAAACTAAA
25414 AGCGACTTGATAAAATAAAAC
1 AGCGACTTGATAAAATAAAAC
25435 AGCGACTTGATAAAATAAAAC
1 AGCGACTTGATAAAATAAAAC
25456 A
1 A
25457 TGAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (21 bp):
AGCGACTTGATAAAATAAAAC
Found at i:26891 original size:18 final size:18
Alignment explanation
Indices: 26868--26916 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
26858 TTTGGTCAAA
26868 GTCAACGGTCAACTGCCG
1 GTCAACGGTCAACTGCCG
* *
26886 GTCAACGATCAACTGTCG
1 GTCAACGGTCAACTGCCG
*
26904 ATCAACGGTCAAC
1 GTCAACGGTCAAC
26917 GGGTCGGGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (18 bp):
GTCAACGGTCAACTGCCG
Found at i:26979 original size:20 final size:19
Alignment explanation
Indices: 26940--26981 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
26930 GATTCGGGTA
* *
26940 GTCGGGTTGGATGTGTCAG
1 GTCGGGTTGGACGGGTCAG
26959 GTCGGGTTGGACCGGGTCAG
1 GTCGGGTTGGA-CGGGTCAG
26979 GTC
1 GTC
26982 AAACGGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.10, C:0.17, G:0.48, T:0.26
Consensus pattern (19 bp):
GTCGGGTTGGACGGGTCAG
Found at i:29175 original size:13 final size:13
Alignment explanation
Indices: 29157--29181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29147 TCAAAGTCAA
29157 TGAGTTGACTCAG
1 TGAGTTGACTCAG
29170 TGAGTTGACTCA
1 TGAGTTGACTCA
29182 ACCAAGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (13 bp):
TGAGTTGACTCAG
Found at i:29941 original size:131 final size:131
Alignment explanation
Indices: 29756--30252 Score: 685
Period size: 131 Copynumber: 3.8 Consensus size: 131
29746 CGATATTGAG
* * *
29756 AATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAATGCATGAGAGGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * * * *
29821 TATTCTCGATTGAAAATAATTCGATATTACCGTTTTCTCTCTAATCAATATTGATTTTTAAGACA
66 TATTCTCGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAACG
29886 A
131 A
* * * * *
29887 AATAGTAATATCTTTTCATTTCGGTTGGAATAATAAATGATTGTTTTAAGGCATGAGAGGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
*
29952 TATTCTTGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAACG
66 TATTCTCGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAACG
30017 A
131 A
* * *
30018 AATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGATGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * * * * * *
30083 TATTCTCAATTGGAAATCATT--AGATTATCGTTTTCACTCGAATCGATATTGAATTTTAAAAGG
66 TATTCTCGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAACG
30146 A
131 A
* * * *
30147 AATAACT-ATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTGTAAGGCATAAGAGGTCGT
1 AAT-AGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
* * *
30211 TTATCCTCGATAGGAAATAATTAGATATTATCGTTTTCTCTC
65 TTATTCTCGATTGGAAATAATTCGATATTATCGTTTTCTCTC
30253 TTAGAATTAT
Statistics
Matches: 325, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
129 111 0.34
130 2 0.01
131 212 0.65
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (131 bp):
AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAACG
A
Found at i:30240 original size:260 final size:261
Alignment explanation
Indices: 29756--30252 Score: 683
Period size: 260 Copynumber: 1.9 Consensus size: 261
29746 CGATATTGAG
* * *
29756 AATAGTAATATCTTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAATGCATGAGAGGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * * * * *
29821 TATTCTCGATTGAAAATAATTCGATATTACCGTTTTCTCTCTAATCAATATTGATTTTTAAGACA
66 TATTCTCAATTGAAAATAATTC-AGATTACCGTTTTCACTCGAATCAATATTGAATTTTAAAACA
* * * * * * *
29886 AAATAGTAATATCTTTTCATTTCGGTTGGAATAATAAATGATTGTTTTAAGGCATGAGAGGTCAT
130 AAATACTAATATCTCTTCATTTCGATTGGAATAATAAATGACTGCTGTAAGGCATAAGAGGTCAT
* * * *
29951 TTATTCTTGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAAC
195 TTATCCTCGATAGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAAC
30016 GA
260 GA
* * *
30018 AATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGATGTCATT
1 AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * * * **
30083 TATTCTCAATTGGAAATCATT-AGATTATCGTTTTCACTCGAATCGATATTGAATTTTAAAAGGA
66 TATTCTCAATTGAAAATAATTCAGATTACCGTTTTCACTCGAATCAATATTGAATTTTAAAACAA
* *
30147 AATAACT-ATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTGTAAGGCATAAGAGGTCGT
131 AAT-ACTAATATCTCTTCATTTCGATTGGAATAATAAATGACTGCTGTAAGGCATAAGAGGTCAT
30211 TTATCCTCGATAGGAAATAATTAGATATTATCGTTTTCTCTC
195 TTATCCTCGATAGGAAATAATTAGATATTATCGTTTTCTCTC
30253 TTAGAATTAT
Statistics
Matches: 203, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
260 124 0.61
261 2 0.01
262 77 0.38
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (261 bp):
AATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
TATTCTCAATTGAAAATAATTCAGATTACCGTTTTCACTCGAATCAATATTGAATTTTAAAACAA
AATACTAATATCTCTTCATTTCGATTGGAATAATAAATGACTGCTGTAAGGCATAAGAGGTCATT
TATCCTCGATAGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAACG
A
Found at i:34997 original size:31 final size:31
Alignment explanation
Indices: 34962--35032 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
34952 TTGAATTACG
* * *
34962 ATATGATTTCTGATATGGATTCTGTTCTGAT
1 ATATGATATATGATATGAATTCTGTTCTGAT
* *
34993 ATATGATATATGATATGAATTTTGTTTTGAT
1 ATATGATATATGATATGAATTCTGTTCTGAT
* *
35024 TTCTGATAT
1 ATATGATAT
35033 CTCCGTTTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.51
Consensus pattern (31 bp):
ATATGATATATGATATGAATTCTGTTCTGAT
Found at i:39535 original size:24 final size:24
Alignment explanation
Indices: 39483--39537 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
39473 TGAATGTTTT
*
39483 ATCTGATTTCTGATTTGAATTATG
1 ATCTGATTTCTGATCTGAATTATG
* * *
39507 ATCTGATTTCTTATCTGGATTCTG
1 ATCTGATTTCTGATCTGAATTATG
*
39531 TTCTGAT
1 ATCTGAT
39538 ATATAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (24 bp):
ATCTGATTTCTGATCTGAATTATG
Found at i:39546 original size:7 final size:7
Alignment explanation
Indices: 39534--39567 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
39524 GATTCTGTTC
39534 TGATATA
1 TGATATA
*
39541 TAATATA
1 TGATATA
39548 TGATATA
1 TGATATA
39555 TGATATA
1 TGATATA
39562 TGATAT
1 TGATAT
39568 GAATTCTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TGATATA
Found at i:40562 original size:12 final size:14
Alignment explanation
Indices: 40518--40567 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
40508 GCTACTAGAG
*
40518 ATTTCTCAATAAAT
1 ATTTATCAATAAAT
40532 ATTTATCAATAAAT
1 ATTTATCAATAAAT
*
40546 GTTTAT-AA-AAAT
1 ATTTATCAATAAAT
40558 ATTTATCAAT
1 ATTTATCAAT
40568 GTATTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 9 0.29
13 4 0.13
14 18 0.58
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (14 bp):
ATTTATCAATAAAT
Found at i:41284 original size:16 final size:16
Alignment explanation
Indices: 41253--41299 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
41243 TGCTCGACTC
* *
41253 TTGCTCGTTAAACTCG
1 TTGCTCATTAAGCTCG
*
41269 TTGTTCATTAAGCTCG
1 TTGCTCATTAAGCTCG
41285 TTGCTCATTAAGCTC
1 TTGCTCATTAAGCTC
41300 ACCATAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (16 bp):
TTGCTCATTAAGCTCG
Found at i:41507 original size:43 final size:43
Alignment explanation
Indices: 41454--41540 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
41444 CCACATATAC
41454 ACCAAAGTAACAATTCACAAATACACCAAACTAACATATTAAA
1 ACCAAAGTAACAATTCACAAATACACCAAACTAACATATTAAA
* *
41497 ACCAATGTAACAATTCACAAATACATCAAACTAACATATTAAA
1 ACCAAAGTAACAATTCACAAATACACCAAACTAACATATTAAA
41540 A
1 A
41541 ATATTCTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.21
Consensus pattern (43 bp):
ACCAAAGTAACAATTCACAAATACACCAAACTAACATATTAAA
Found at i:41543 original size:24 final size:24
Alignment explanation
Indices: 41445--41532 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
41435 AAAGGTAATC
* *
41445 CACATATACACCAAAGTAACAATT
1 CACAAATACACCAAACTAACAATT
41469 CACAAATACACCAAACTAACATATT
1 CACAAATACACCAAACTAACA-ATT
**
41494 ----AA-A-ACCAATGTAACAATT
1 CACAAATACACCAAACTAACAATT
*
41512 CACAAATACATCAAACTAACA
1 CACAAATACACCAAACTAACA
41533 TATTAAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
18 3 0.06
19 10 0.20
20 1 0.02
21 2 0.04
22 2 0.04
23 1 0.02
24 28 0.56
25 3 0.06
ACGTcount: A:0.53, C:0.25, G:0.02, T:0.19
Consensus pattern (24 bp):
CACAAATACACCAAACTAACAATT
Found at i:48010 original size:22 final size:22
Alignment explanation
Indices: 47982--48036 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
47972 AACTTTTTGG
47982 TCAAAGTCAACGCTT-GTCAAAA
1 TCAAAGTCAAC-CTTGGTCAAAA
*
48004 TCAAAGTCAACTTTGGTCAAAA
1 TCAAAGTCAACCTTGGTCAAAA
48026 TCAACAGTCAA
1 TCAA-AGTCAA
48037 GTCAATGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.73
23 6 0.20
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.24
Consensus pattern (22 bp):
TCAAAGTCAACCTTGGTCAAAA
Found at i:48095 original size:13 final size:13
Alignment explanation
Indices: 48059--48109 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
48049 TCAAAGTCAA
*
48059 CGAGTTGACTCAA
1 CGAGTTGACTCAT
*
48072 CTGACTTGACTCAT
1 C-GAGTTGACTCAT
*
48086 CGAGTTGACTGAGT
1 CGAGTTGACTCA-T
48100 -GAGTTGACTC
1 CGAGTTGACTC
48110 TATTCGACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (13 bp):
CGAGTTGACTCAT
Found at i:57769 original size:24 final size:24
Alignment explanation
Indices: 57742--57797 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
57732 CGTTCATTTA
57742 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
57766 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
57790 CGTTCGGT
1 CGTTCGGT
57798 TATGTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:57771 original size:14 final size:14
Alignment explanation
Indices: 57752--57804 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
57742 CGTTCGTGAA
57752 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
57766 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
57780 CG-T---TTATGTT
1 CGTTCGGTTATGTT
57790 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
57804 C
1 C
57805 ATTTATGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:57798 original size:24 final size:24
Alignment explanation
Indices: 57753--57814 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
57743 GTTCGTGAAC
*
57753 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
57777 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
*
57801 GTTCATTTATGTTC
1 GTTCGTTTATGTTC
57815 ATTCATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.10, C:0.13, G:0.24, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:58925 original size:16 final size:16
Alignment explanation
Indices: 58904--58970 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
58894 GTCTCCAACG
58904 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
58920 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
58936 TTTATGTTCGTGGTCG
1 TTTATGTTCGTGTTCA
58952 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
58966 TTTAT
1 TTTAT
58971 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 1 0.02
16 41 0.87
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:58943 original size:32 final size:32
Alignment explanation
Indices: 58902--58962 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
58892 GGGTCTCCAA
*
58902 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGGTCATTTATGTTCGTGTT
*
58934 CGTTTATGTTCGTGGTCGTTTATGTTCGT
1 CGTTTATGTTCGTGGTCATTTATGTTCGT
58963 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.08, C:0.13, G:0.25, T:0.54
Consensus pattern (32 bp):
CGTTTATGTTCGTGGTCATTTATGTTCGTGTT
Found at i:59053 original size:16 final size:16
Alignment explanation
Indices: 59032--59064 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
59022 AAAAAAAATT
59032 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
59048 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
59064 T
1 T
59065 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:66232 original size:30 final size:30
Alignment explanation
Indices: 66192--66249 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
66182 AGAGTCGAGG
* * *
66192 GTTACTTATGTCCTTTGGGACATATGGACA
1 GTTACCTATGTCCTTCGGAACATATGGACA
*
66222 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGAACATATGGA
66250 TAGGTCATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGAACATATGGACA
Found at i:66412 original size:2 final size:2
Alignment explanation
Indices: 66400--66465 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
66390 CCTGAATACA
*
66400 AT AT GT 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 AT AT
66442 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
66466 GATGTGTGAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68679 original size:27 final size:26
Alignment explanation
Indices: 68628--68679 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
68618 ATGATCTTGA
*
68628 ATGATAAGAATGAATGATACTATTTAT
1 ATGATAAG-ATGAATGATACGATTTAT
68655 ATGATAAG-TGACATGATACGGATTT
1 ATGATAAGATGA-ATGATAC-GATTT
68680 TCAACGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 3 0.14
26 7 0.32
27 12 0.55
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (26 bp):
ATGATAAGATGAATGATACGATTTAT
Found at i:70983 original size:2 final size:2
Alignment explanation
Indices: 70976--71008 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70966 GAATATAATG
70976 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71009 GATGTGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72234 original size:19 final size:19
Alignment explanation
Indices: 72210--72256 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
72200 GATTGCGAAT
72210 TTGATAAGTAACTAAATTA
1 TTGATAAGTAACTAAATTA
*
72229 TTGATAAGTAAGTAAATTA
1 TTGATAAGTAACTAAATTA
72248 TTGATAAGT
1 TTGATAAGT
72257 TAATTTTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (19 bp):
TTGATAAGTAACTAAATTA
Found at i:74766 original size:2 final size:2
Alignment explanation
Indices: 74759--74862 Score: 208
Period size: 2 Copynumber: 52.0 Consensus size: 2
74749 GATTTAGGTG
74759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74843 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
74863 AGCCACGTGA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75297 original size:30 final size:31
Alignment explanation
Indices: 75228--75317 Score: 128
Period size: 32 Copynumber: 2.9 Consensus size: 31
75218 AGAGTCGAGG
*
75228 GTTACCTATGTCGTTCGGGACATATGGACAT
1 GTTACCTATGTCCTTCGGGACATATGGACAT
*
75259 GATTACCTATGTCCTTCGGGATATATGGACA-
1 G-TTACCTATGTCCTTCGGGACATATGGACAT
* *
75290 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
75318 TAGGTCATTC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 24 0.45
31 2 0.04
32 27 0.51
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (31 bp):
GTTACCTATGTCCTTCGGGACATATGGACAT
Found at i:78812 original size:30 final size:30
Alignment explanation
Indices: 78778--78835 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
78768 AGATAGAAAT
78778 AGAAAAAGAAAAATAAAG-AAAAAGAGAAGA
1 AGAAAAAGAAAAA-AAAGAAAAAAGAGAAGA
* *
78808 AGAAAAAGAAGAAGAAGAAAAAAGAGAA
1 AGAAAAAGAAAAAAAAGAAAAAAGAGAA
78836 CATATCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (30 bp):
AGAAAAAGAAAAAAAAGAAAAAAGAGAAGA
Found at i:78814 original size:15 final size:14
Alignment explanation
Indices: 78793--78835 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 14
78783 AAGAAAAATA
78793 AAGAAAAAGAGAAG
1 AAGAAAAAGAGAAG
78807 AAGAAAAAGAAGAAG
1 AAGAAAAAG-AGAAG
78822 AAGAAAAAAGAGAA
1 AAG-AAAAAGAGAA
78836 CATATCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.33
15 12 0.44
16 6 0.22
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAGAAG
Found at i:78819 original size:12 final size:12
Alignment explanation
Indices: 78767--78823 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
78757 ATTCATATTC
*
78767 AAGATAGAAATAG
1 AAGA-AGAAAAAG
* *
78780 AAAAAGAAAAATA
1 AAGAAGAAAAA-G
*
78793 AAGAA-AAAGAG
1 AAGAAGAAAAAG
78804 AAGAAGAAAAAG
1 AAGAAGAAAAAG
78816 AAGAAGAA
1 AAGAAGAA
78824 GAAAAAAGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 5 0.14
12 23 0.66
13 7 0.20
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:81188 original size:41 final size:42
Alignment explanation
Indices: 81095--81198 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 42
81085 CAGGTCATCA
* * *
81095 ATAAGTCTTTCGAGCAAGATCATTAAATCCTTTGGGCCATCT
1 ATAAGTCTTTCAAGCAAGATGATTAAATCCTTTGGGCCAGCT
* * * *
81137 GTCAGTCTTTCAAGCAAGATGA-TAAGTCTTTTGGGCCAGCT
1 ATAAGTCTTTCAAGCAAGATGATTAAATCCTTTGGGCCAGCT
* *
81178 ATAAGACTTTCAGGCAAGATG
1 ATAAGTCTTTCAAGCAAGATG
81199 TTTTCATATA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 33 0.65
42 18 0.35
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
ATAAGTCTTTCAAGCAAGATGATTAAATCCTTTGGGCCAGCT
Found at i:82088 original size:19 final size:19
Alignment explanation
Indices: 82064--82110 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
82054 TGATTTGTGT
82064 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
82083 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
82102 ATCGATGCA
1 ATCGATGCA
82111 CTGTAGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (19 bp):
ATCGATGCATGGGTAGTGC
Found at i:83611 original size:61 final size:61
Alignment explanation
Indices: 83516--83652 Score: 177
Period size: 61 Copynumber: 2.2 Consensus size: 61
83506 ACATAAAGAG
* * * *
83516 ATTTTCAAATTTTCTCATTTAGTATTTTTAGAAAACG-AAATATTTGAAAAATGAGAAAGCA
1 ATTTTCAAAGTTTCTCATTTAGAATTTTCAGAAAACGAAAAT-TTTGAAAAATAAGAAAGCA
* * * **
83577 ATTTTCAAAGTTTCTCATTTAGAATTTTCAGAAAATGAAAATTTTGAAAAGTAATAAAGTG
1 ATTTTCAAAGTTTCTCATTTAGAATTTTCAGAAAACGAAAATTTTGAAAAATAAGAAAGCA
83638 ATTTTCAAAGTTTCT
1 ATTTTCAAAGTTTCT
83653 TACCTAGTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 62 0.94
62 4 0.06
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (61 bp):
ATTTTCAAAGTTTCTCATTTAGAATTTTCAGAAAACGAAAATTTTGAAAAATAAGAAAGCA
Done.