Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001917.1 Hibiscus syriacus cultivar Beakdansim tig00003880_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: 81670
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2218 original size:13 final size:13
Alignment explanation
Indices: 2200--2224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2190 TTGTTGGACT
2200 TTTTGTTAATTTA
1 TTTTGTTAATTTA
2213 TTTTGTTAATTT
1 TTTTGTTAATTT
2225 TGTTTATTAC
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTGTTAATTTA
Found at i:8388 original size:2 final size:2
Alignment explanation
Indices: 8381--8420 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8371 TACTTTACCC
8381 AT 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 AT
8421 GATGATTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11445 original size:44 final size:45
Alignment explanation
Indices: 11382--11497 Score: 144
Period size: 49 Copynumber: 2.5 Consensus size: 45
11372 CCATGCAAAT
11382 AAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGG-AAAAAA
1 AAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGTAAAAAA
* * * *
11426 AAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAAAAAT
1 AAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGGTAAAAAA
*
11475 AAGCTTATGAGCTTATGGGATAA
1 AAGCTTATGAGCTTATGGAATAA
11498 AATGTAAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
44 19 0.31
45 2 0.03
46 1 0.02
47 1 0.02
48 15 0.25
49 23 0.38
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (45 bp):
AAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGTAAAAAA
Found at i:13589 original size:2 final size:2
Alignment explanation
Indices: 13584--13693 Score: 124
Period size: 2 Copynumber: 57.5 Consensus size: 2
13574 CTTATATAAG
* * *
13584 TA TA TA -A TA TA AA TA TA -A T- TA TA TT TA TA AA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
13622 TA TA TA TA -A TA TA TA TA TA TA TA AA GTT TA T- 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
13663 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 T
13694 TTTAAGAATA
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
1 6 0.07
2 85 0.93
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13894 original size:12 final size:12
Alignment explanation
Indices: 13877--13919 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
13867 TTAAAAAATG
13877 CTCTCTCTCACA
1 CTCTCTCTCACA
*
13889 CTCTCTCCCACA
1 CTCTCTCTCACA
* *
13901 CTCTCTCTCTCT
1 CTCTCTCTCACA
13913 CTCTCTC
1 CTCTCTC
13920 GGCCCCACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.09, C:0.53, G:0.00, T:0.37
Consensus pattern (12 bp):
CTCTCTCTCACA
Found at i:15671 original size:11 final size:11
Alignment explanation
Indices: 15643--15671 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
15633 TATTTTAAAA
15643 TTAAA-TTAAT
1 TTAAATTTAAT
15653 TTAAATTTAAT
1 TTAAATTTAAT
15664 TTAAATTT
1 TTAAATTT
15672 TTCTCATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:16509 original size:19 final size:20
Alignment explanation
Indices: 16465--16509 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
16455 ATTTGTTTTT
*
16465 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
16485 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
16504 AATAAA
1 AATAAA
16510 ATATTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:22591 original size:57 final size:57
Alignment explanation
Indices: 22359--22584 Score: 344
Period size: 57 Copynumber: 4.0 Consensus size: 57
22349 CATAACCATA
* * * * *
22359 CAACCCTGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGTAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTAAT
* * * *
22416 CAACCCCGTCACGAATAGTAAGGCTCTCAGCACAAAGCAGAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTAAT
*
22473 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAACCGAGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTAAT
**
22530 CTTCCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTA
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTA
22585 TTCTTCCTCC
Statistics
Matches: 152, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 152 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.14
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTAAT
Found at i:22689 original size:24 final size:24
Alignment explanation
Indices: 22662--22752 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
22652 CATAGTTCAG
* *
22662 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
22686 GTCAAGCATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
22710 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
22734 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
22753 ATCAAATCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
23 2 0.03
24 55 0.93
25 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:27129 original size:22 final size:22
Alignment explanation
Indices: 27074--27131 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 22
27064 TACATTCTGA
27074 ATAC-ATGGTATCGATACTTTT
1 ATACTATGGTATCGATACTTTT
* *
27095 CTCCTA--GTATCGATACTTTT
1 ATACTATGGTATCGATACTTTT
27115 ATACTATGGTATCGATA
1 ATACTATGGTATCGATA
27132 TTCCATTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 18 0.60
21 2 0.07
22 10 0.33
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (22 bp):
ATACTATGGTATCGATACTTTT
Found at i:33278 original size:54 final size:54
Alignment explanation
Indices: 33220--33531 Score: 525
Period size: 54 Copynumber: 5.8 Consensus size: 54
33210 AATACGGTCA
* * *
33220 TTCATAAACATATTATGAATTTCGTGGGTTGCACACATAGTGCCTAAATGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAATGGTTG
*
33274 TTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTAAATGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAATGGTTG
* *
33328 TTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAATGGTTG
* * *
33382 TTCATCAACATATGATGAATTCCGTGGGTTACACACATAGTGCCTAAACGGTTA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAATGGTTG
*
33436 TTCATCAACATATGATGAATTCCATGGGTTGCACACATAGTGCCTAAATGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAATGGTTG
*
33490 TTCATCAACATATGATGAATTCCATGGGTTGCACACATAGTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTG
33532 ACTATAGTAC
Statistics
Matches: 246, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 246 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAATGGTTG
Found at i:33284 original size:27 final size:27
Alignment explanation
Indices: 33254--33339 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
33244 TGGGTTGCAC
33254 ACATAGTGCCTAAATGGTTGTTCATCA
1 ACATAGTGCCTAAATGGTTGTTCATCA
* * * *
33281 ACATA-TG-ATGAATTTCGTGGGTTGCA-C-
1 ACATAGTGCCT-AA-ATGGT-TGTT-CATCA
33308 ACATAGTGCCTAAATGGTTGTTCATCA
1 ACATAGTGCCTAAATGGTTGTTCATCA
33335 ACATA
1 ACATA
33340 TGATGAATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 3 0.07
26 8 0.19
27 21 0.49
28 8 0.19
29 3 0.07
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (27 bp):
ACATAGTGCCTAAATGGTTGTTCATCA
Found at i:33473 original size:27 final size:27
Alignment explanation
Indices: 33443--33528 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
33433 TTATTCATCA
33443 ACATATGATGAATTCCATGGGTTGCAC
1 ACATATGATGAATTCCATGGGTTGCAC
** **
33470 ACATA-G-TG-CCTAAAT-GGTTGTTCATC
1 ACATATGATGAATTCCATGGGTTG--CA-C
33496 AACATATGATGAATTCCATGGGTTGCAC
1 -ACATATGATGAATTCCATGGGTTGCAC
33524 ACATA
1 ACATA
33529 GTGACTATAG
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
23 5 0.12
24 3 0.07
25 4 0.09
26 2 0.05
27 15 0.35
28 2 0.05
29 4 0.09
30 3 0.07
31 5 0.12
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (27 bp):
ACATATGATGAATTCCATGGGTTGCAC
Found at i:34023 original size:94 final size:95
Alignment explanation
Indices: 33882--34080 Score: 256
Period size: 94 Copynumber: 2.1 Consensus size: 95
33872 CCCTACCATG
** * ** *
33882 GTATCGATACTACTATATTATGGTATTGATACCCCCTTTTAGCATCGATACCATTTCTACATTCT
1 GTATCGATACTACTATATTATGGTACCGATACCCCATTACAGCATCGATACCATTTCTACATTAT
* * *
33947 G-AATCCATGGTATCGATACTTTTCTCCTA
66 GTAATCAATGGTATCGATACCTTCCTCCTA
** * * *
33976 GTATCGATACTTTTATATTATGGTACCGATACTCCATTACAGTATCGATACCATTTCTGCATTAT
1 GTATCGATACTACTATATTATGGTACCGATACCCCATTACAGCATCGATACCATTTCTACATTAT
*
34041 GTAATCAATGGTATCGATACCTTCCTCTTA
66 GTAATCAATGGTATCGATACCTTCCTCCTA
34071 GTATCGATAC
1 GTATCGATAC
34081 CCCATCAGGA
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
94 55 0.62
95 34 0.38
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (95 bp):
GTATCGATACTACTATATTATGGTACCGATACCCCATTACAGCATCGATACCATTTCTACATTAT
GTAATCAATGGTATCGATACCTTCCTCCTA
Found at i:35227 original size:22 final size:22
Alignment explanation
Indices: 35184--35227 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35174 ATGCCGACAA
* * *
35184 GAATTGGTCTGAATGCTGATTG
1 GAATTCGTCTGAATACTAATTG
35206 GAATTCGTCTGAATACTAATTG
1 GAATTCGTCTGAATACTAATTG
35228 AACTAGGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.36
Consensus pattern (22 bp):
GAATTCGTCTGAATACTAATTG
Found at i:35710 original size:18 final size:18
Alignment explanation
Indices: 35672--35712 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
35662 AGAATCATGT
35672 TTAA-TATATTTAAGTTA
1 TTAATTATATTTAAGTTA
35689 --AATTATATTTAAGTTA
1 TTAATTATATTTAAGTTA
35705 TTAATTAT
1 TTAATTAT
35713 TACATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
18 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTAATTATATTTAAGTTA
Found at i:37123 original size:60 final size:60
Alignment explanation
Indices: 37011--37123 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
37001 ATTAATCCTC
* *
37011 CAATTATAGGACATTGCTTTGTTGAGTCATCCGACTATTAAAATATACAAAATTGTCTCT
1 CAATTATAGGAAATTGCTTTGTTGAGTCATCCGACTATTAAAATATAAAAAATTGTCTCT
37071 CAATTATAGGAAATTGCTTTGTTGAGTTC-TCCGACTATTAAAA-ATTAAAAAAT
1 CAATTATAGGAAATTGCTTTGTTGAG-TCATCCGACTATTAAAATA-TAAAAAAT
37124 GGTCATCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
59 1 0.02
60 46 0.94
61 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (60 bp):
CAATTATAGGAAATTGCTTTGTTGAGTCATCCGACTATTAAAATATAAAAAATTGTCTCT
Found at i:38674 original size:9 final size:9
Alignment explanation
Indices: 38660--38715 Score: 50
Period size: 8 Copynumber: 6.7 Consensus size: 9
38650 AATTACATCC
38660 ATATTATTA
1 ATATTATTA
38669 ATATTATT-
1 ATATTATTA
38677 ATATTATT-
1 ATATTATTA
38685 -TATT-TTA
1 ATATTATTA
*
38692 TTATT-TTA
1 ATATTATTA
38700 ATATATATTA
1 ATAT-TATTA
*
38710 TTATTA
1 ATATTA
38716 CAACCCAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 2 0.05
7 4 0.10
8 18 0.44
9 11 0.27
10 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATATTATTA
Found at i:38676 original size:3 final size:3
Alignment explanation
Indices: 38661--38715 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
38651 ATTACATCCA
* *
38661 TAT TAT TAA TAT TAT TA- TAT TATT TAT T-T TAT TAT T-T TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
38704 ATAT TAT TAT TA
1 -TAT TAT TAT TA
38716 CAACCCAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 6 0.14
3 31 0.72
4 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:38749 original size:16 final size:16
Alignment explanation
Indices: 38712--38750 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38702 ATATATTATT
*
38712 ATTACAACCCAATCCA
1 ATTACAACCCAAGCCA
* *
38728 AATACAACCCAAGCCC
1 ATTACAACCCAAGCCA
38744 ATTACAA
1 ATTACAA
38751 ATATTACCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.36, G:0.03, T:0.15
Consensus pattern (16 bp):
ATTACAACCCAAGCCA
Found at i:39968 original size:7 final size:6
Alignment explanation
Indices: 39953--40000 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
39943 TTTCTTTATT
* *
39953 TTTTTA TTTGTTA TTTTGA TTTTT- TTTTTA TTTGTTA TTTTGA TTTTT
1 TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTT
40001 TTATTTAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 5 0.14
6 18 0.51
7 12 0.34
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:39969 original size:24 final size:24
Alignment explanation
Indices: 39951--40007 Score: 105
Period size: 24 Copynumber: 2.3 Consensus size: 24
39941 ATTTTCTTTA
39951 TTTTTTTATTTGTTATTTTGATTT
1 TTTTTTTATTTGTTATTTTGATTT
39975 TTTTTTTATTTGTTATTTTGATTT
1 TTTTTTTATTTGTTATTTTGATTT
39999 TTTTATTTA
1 TTTT-TTTA
40008 AGTTTACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (24 bp):
TTTTTTTATTTGTTATTTTGATTT
Found at i:39974 original size:13 final size:13
Alignment explanation
Indices: 39953--39998 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
39943 TTTCTTTATT
*
39953 TTTTTATTTGTTA
1 TTTTGATTTGTTA
39966 TTTTGATTT-TT-
1 TTTTGATTTGTTA
*
39977 TTTTTATTTGTTA
1 TTTTGATTTGTTA
39990 TTTTGATTT
1 TTTTGATTT
39999 TTTTATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 8 0.29
12 4 0.14
13 16 0.57
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.78
Consensus pattern (13 bp):
TTTTGATTTGTTA
Found at i:40241 original size:12 final size:13
Alignment explanation
Indices: 40216--40244 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40206 ATTTTTAAAA
40216 AATTTAGTGTAAT
1 AATTTAGTGTAAT
40229 AATTTAG-GTAAT
1 AATTTAGTGTAAT
40241 AATT
1 AATT
40245 AGATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (13 bp):
AATTTAGTGTAAT
Found at i:47946 original size:19 final size:18
Alignment explanation
Indices: 47911--47951 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
47901 AGCAAATAAG
**
47911 AAAAAAACAACGAAAAGA
1 AAAAAAACAAAAAAAAGA
47929 AAAAAAACAAAAACAAAGA
1 AAAAAAACAAAAA-AAAGA
47948 AAAA
1 AAAA
47952 GAAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAGA
Found at i:50095 original size:71 final size:70
Alignment explanation
Indices: 50003--50161 Score: 212
Period size: 71 Copynumber: 2.2 Consensus size: 70
49993 CCTGGCTTTC
* *
50003 AGGGGTTTCTTGATGACGATTTTCAATGAAT-TTGTATAAGAAACTAAGCTTGAGGTACCAACAT
1 AGGGG-TTCTTGATGACGATTTTCAATGAATGTT-TATAAGAAACTAAGCTCGAGGGACCAACAT
50067 AATATGT
64 AATATGT
* * * * *
50074 AGGGGTTCATTGATGATGATTTTCAGTGAATGTTTATAAGAAACTAAGCTCGAGGGATCAACGTG
1 AGGGGTTC-TTGATGACGATTTTCAATGAATGTTTATAAGAAACTAAGCTCGAGGGACCAACATA
50139 ATATGT
65 ATATGT
50145 AGGGGTTCCTTGATGAC
1 AGGGGTT-CTTGATGAC
50162 AACTAAGAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
70 3 0.04
71 71 0.92
72 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (70 bp):
AGGGGTTCTTGATGACGATTTTCAATGAATGTTTATAAGAAACTAAGCTCGAGGGACCAACATAA
TATGT
Found at i:50310 original size:41 final size:41
Alignment explanation
Indices: 50204--50321 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
50194 TCTTGTTGAG
* * *
50204 TAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCT
1 TAAGTCCTTCGGGCCATCA-TAAGTCTTTCGAGCAAGATGCA
* * * *
50246 TAAATCCTTTGGGTCATATATAAGTCTTTCGAGCAAGATG-A
1 TAAGTCCTTCGGGCCAT-CATAAGTCTTTCGAGCAAGATGCA
* *
50287 TAAGTCCTTCGGGCCATCCATAAGACCTTCGAGCA
1 TAAGTCCTTCGGGCCAT-CATAAGTCTTTCGAGCA
50322 GGATATTTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 28 0.46
42 32 0.52
43 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCAAGATGCA
Found at i:50507 original size:42 final size:41
Alignment explanation
Indices: 50461--50576 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 41
50451 AAGGGTTTCT
*
50461 TGATGAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATTA-TAAGACTTTCGAGCA
* *
50503 TGATGCGTAAGTCCTTCGGACCATTTATAAGACTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCA-TTATAAGACTTTCGAGCA
* * * *
50545 AGATGA-TATGACCTTCGGGCCATCCATAAGAC
1 TGATGAGTAAGTCCTTCGGGCCAT-TATAAGAC
50577 CTTTGGGTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 20 0.32
42 39 0.62
43 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (41 bp):
TGATGAGTAAGTCCTTCGGGCCATTATAAGACTTTCGAGCA
Found at i:50602 original size:264 final size:263
Alignment explanation
Indices: 50122--50662 Score: 814
Period size: 264 Copynumber: 2.1 Consensus size: 263
50112 AGAAACTAAG
* * * * *
50122 CTCGAGGGATCAACGTGATATGTAGGGGTTCCTTGATGACAACTAAGAAACTAAGCTTGATTTTC
1 CTCGAGGGACCAACGTAATATGTAGGGGTTCATTGATGACAACTAAGAAAATAAGATTGATTTTC
* * *
50187 AAGGGTTTCTTGTTGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATC
66 AAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATC
* ** * *
50252 CTTTGGGTCATATATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTC
131 CTTCGGACCATATATAAGACTTTCGAGCAAGATGATAAGACCTTCGGGCCATCCATAAGACCTTC
* *
50317 GAGCAGGATATTTTTAACATTTTC-GATACTCGATTCATCACATATGGAGTTGAATCAGCAAACA
196 GAGCAGGATATTTTCAACATTTTCTG-TACTCGATTCATCACATATAGAGTTGAATCAGC-AACA
50381 CCTCA
259 CCTCA
* *
50386 CTCGAGGGACCAACGTAATATGTAGGGGTTCATTGATGACAACTAAGAAAATAATATTGGTTTTC
1 CTCGAGGGACCAACGTAATATGTAGGGGTTCATTGATGACAACTAAGAAAATAAGATTGATTTTC
* *
50451 AAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCGTAAGTC
66 AAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATC
* * *
50516 CTTCGGACCATTTATAAGACTTTCGAGCAAGATGATATGACCTTCGGGCCATCCATAAGACCTTT
131 CTTCGGACCATATATAAGACTTTCGAGCAAGATGATAAGACCTTCGGGCCATCCATAAGACCTTC
* * * *
50581 GGGTAGGATGTTTTCAACATTTTCTGTACTTGATTCATCACATATAGAGTTGAATCAGCAACACC
196 GAGCAGGATATTTTCAACATTTTCTGTACTCGATTCATCACATATAGAGTTGAATCAGCAACACC
50646 TCA
261 TCA
*
50649 CTCGATGGACCAAC
1 CTCGAGGGACCAAC
50663 ATCGCCAGTA
Statistics
Matches: 249, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
263 22 0.09
264 226 0.91
265 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (263 bp):
CTCGAGGGACCAACGTAATATGTAGGGGTTCATTGATGACAACTAAGAAAATAAGATTGATTTTC
AAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATC
CTTCGGACCATATATAAGACTTTCGAGCAAGATGATAAGACCTTCGGGCCATCCATAAGACCTTC
GAGCAGGATATTTTCAACATTTTCTGTACTCGATTCATCACATATAGAGTTGAATCAGCAACACC
TCA
Found at i:50887 original size:17 final size:17
Alignment explanation
Indices: 50865--50903 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
50855 AAAGAAATAG
50865 ATGAATTGACATTCCCA
1 ATGAATTGACATTCCCA
50882 ATGAATTGACATTCCCA
1 ATGAATTGACATTCCCA
*
50899 GTGAA
1 ATGAA
50904 GAGTTCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (17 bp):
ATGAATTGACATTCCCA
Found at i:51042 original size:3 final size:3
Alignment explanation
Indices: 51027--51081 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
51017 ATTACATCCA
* *
51027 TAT TAT TAA TAT TAT TA- TAT TAT T-T ATAT TAT TAT TCT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
51070 ATAT TAT TAT TA
1 -TAT TAT TAT TA
51082 CAACTAATCC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 5 0.12
3 34 0.79
4 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:51056 original size:23 final size:24
Alignment explanation
Indices: 51030--51074 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
51020 ACATCCATAT
51030 TATTAATATTATTATAT-TATTTA
1 TATTAATATTATTATATATATTTA
* *
51053 TATTATTATTCTTATATATATT
1 TATTAATATTATTATATATATT
51075 ATTATTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTAATATTATTATATATATTTA
Found at i:51072 original size:18 final size:18
Alignment explanation
Indices: 51035--51081 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
51025 CATATTATTA
*
51035 ATATTATTA-TATTATTT
1 ATATTATTATTATTATAT
*
51052 ATATTATTATTCTTATAT
1 ATATTATTATTATTATAT
51070 ATATTATTATTA
1 ATATTATTATTA
51082 CAACTAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTATTATTATTATAT
Found at i:52314 original size:17 final size:16
Alignment explanation
Indices: 52286--52339 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
52276 GGTCCTTGCA
* *
52286 TATTTTAATTTTCT-T
1 TATTTTTATTTTTTAT
52301 TATTTTTTATTTTTTAT
1 TA-TTTTTATTTTTTAT
*
52318 TATTTTTA-TTTTAAT
1 TATTTTTATTTTTTAT
52333 TATTTTT
1 TATTTTT
52340 TTAAAAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 15 0.44
16 16 0.47
17 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TATTTTTATTTTTTAT
Found at i:52334 original size:15 final size:16
Alignment explanation
Indices: 52304--52339 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
52294 TTTTCTTTAT
*
52304 TTTTTATTTTTTATTA
1 TTTTTATTTTTAATTA
52320 TTTTTA-TTTTAATTA
1 TTTTTATTTTTAATTA
52335 TTTTT
1 TTTTT
52340 TTAAAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTATTTTTAATTA
Found at i:53861 original size:18 final size:19
Alignment explanation
Indices: 53838--53873 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53828 TATTTTTATT
53838 TTTAATTAATT-ATCGATA
1 TTTAATTAATTAATCGATA
*
53856 TTTAATTTATTAATCGAT
1 TTTAATTAATTAATCGAT
53874 TAATTTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTAATTAATTAATCGATA
Found at i:58540 original size:26 final size:26
Alignment explanation
Indices: 58511--58568 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
58501 ATAATATTCA
* * *
58511 AATCATAGTTTGAATCAACCAATAAT
1 AATCATAATCTGAATCAAACAATAAT
*
58537 AATCATAATCTGAATCAAACAATGAT
1 AATCATAATCTGAATCAAACAATAAT
*
58563 AGTCAT
1 AATCAT
58569 GAAGTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.29
Consensus pattern (26 bp):
AATCATAATCTGAATCAAACAATAAT
Found at i:62360 original size:30 final size:30
Alignment explanation
Indices: 62324--62388 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
62314 TGGGATGGTT
62324 TTGAAGCTAAATGAGCTAGGGTATTTATAG
1 TTGAAGCTAAATGAGCTAGGGTATTTATAG
62354 TTGAAGCTAAATGAGCTAGGGTATTTATAG
1 TTGAAGCTAAATGAGCTAGGGTATTTATAG
62384 TTGAA
1 TTGAA
62389 ACTTAAGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (30 bp):
TTGAAGCTAAATGAGCTAGGGTATTTATAG
Found at i:62576 original size:28 final size:28
Alignment explanation
Indices: 62509--62566 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
62499 CCTTAAACTC
*
62509 TCCACCGAAATTGCATGTGGCCAACAAT
1 TCCACCGAAATTCCATGTGGCCAACAAT
62537 TCCACCGAAATTCCATGTGGCCAACAAT
1 TCCACCGAAATTCCATGTGGCCAACAAT
62565 TC
1 TC
62567 ATGCTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (28 bp):
TCCACCGAAATTCCATGTGGCCAACAAT
Found at i:67221 original size:28 final size:28
Alignment explanation
Indices: 67188--67245 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
67178 CCTTCAACTC
67188 TCCACCGAAATTGCATGTGGCCAACAAT
1 TCCACCGAAATTGCATGTGGCCAACAAT
**
67216 TCCACCGAAATTGCATGTGGTTAACAAT
1 TCCACCGAAATTGCATGTGGCCAACAAT
67244 TC
1 TC
67246 ATGCTTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (28 bp):
TCCACCGAAATTGCATGTGGCCAACAAT
Found at i:77626 original size:44 final size:42
Alignment explanation
Indices: 77578--77665 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 42
77568 ATTAGATAAG
*
77578 AAATAATAAATAAATCAAAGGGGGGAAAATAAATA-AAAAATGTA
1 AAATAATAAATAAATC-AA--GGGGAAAATAAAAATAAAAATGTA
* *
77622 AAATATTAAATAAATCAAGGGGAAAATAAAAATAAAAATTTA
1 AAATAATAAATAAATCAAGGGGAAAATAAAAATAAAAATGTA
77664 AA
1 AA
77666 TTTTAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
41 13 0.32
42 10 0.25
43 2 0.05
44 15 0.38
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.20
Consensus pattern (42 bp):
AAATAATAAATAAATCAAGGGGAAAATAAAAATAAAAATGTA
Found at i:77672 original size:41 final size:43
Alignment explanation
Indices: 77578--77673 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 43
77568 ATTAGATAAG
* *
77578 AAATAATAAATAAATCAAAGGGGGGAAAATAAATAAAAAATGTA
1 AAATATTAAATAAATCAAA-GGGGGAAAATAAAAAAAAAATGTA
*
77622 AAATATTAAATAAATC-AA-GGGGAAAATAAAAATAAAAAT-TT
1 AAATATTAAATAAATCAAAGGGGGAAAATAAAAA-AAAAATGTA
*
77663 AAATTTTAAAT
1 AAATATTAAAT
77674 TTTAAAAGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 24 0.51
42 6 0.13
43 2 0.04
44 15 0.32
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.24
Consensus pattern (43 bp):
AAATATTAAATAAATCAAAGGGGGAAAATAAAAAAAAAATGTA
Found at i:77703 original size:23 final size:23
Alignment explanation
Indices: 77677--77742 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 23
77667 TTTAAATTTT
* *
77677 AAAAGTAATAAATAAAAAAGGGA
1 AAAAATAATAAATAAAAAAGAGA
*
77700 AAAAATTATATAAA-AATAATAGAG-
1 AAAAA-TA-ATAAATAA-AAAAGAGA
77724 AAAAATAAATAAATAAAAA
1 AAAAAT-AATAAATAAAAA
77743 TTAATGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
23 12 0.35
24 12 0.35
25 10 0.29
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAATAATAAATAAAAAAGAGA
Found at i:77712 original size:25 final size:23
Alignment explanation
Indices: 77683--77742 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
77673 TTTTAAAAGT
*
77683 AATAAATAAAAAAGGGAAAAAATTA
1 AATAAATAAAAAAGAG-AAAAA-TA
* *
77708 TATAAA-AATAATAGAGAAAAATA
1 AATAAATAA-AAAAGAGAAAAATA
77731 AATAAATAAAAA
1 AATAAATAAAAA
77743 TTAATGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
23 9 0.32
24 9 0.32
25 10 0.36
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (23 bp):
AATAAATAAAAAAGAGAAAAATA
Found at i:79090 original size:19 final size:21
Alignment explanation
Indices: 79052--79092 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
79042 AAAGTAATAC
*
79052 ATAATAAAAATAATATTATAT
1 ATAATAAAAATAATAATATAT
79073 ATAAT-AAAA-AATAATATAT
1 ATAATAAAAATAATAATATAT
79092 A
1 A
79093 ATATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAATAAAAATAATAATATAT
Found at i:79275 original size:75 final size:75
Alignment explanation
Indices: 79132--79274 Score: 184
Period size: 75 Copynumber: 1.9 Consensus size: 75
79122 AAAAACATTT
* *
79132 TCGAAACTATATAATAAATATGTTTTCACAAATTAATTTTCAAAAATGTATAATATATTTTTCAA
1 TCGAAACTATATAATAAATACGTTTTCACAAATTAATTTTCAAAAATATATAATATATTTTTCAA
79197 AAATTGATTC
66 AAATTGATTC
* * *
79207 TCGAAACTATATATTATATACGTTTTCA-AAA-T-GTTTTCAAAAACTATATATTATATATATTT
1 TCGAAACTATATAATAAATACGTTTTCACAAATTAATTTTCAAAAA-TATATA--ATATAT-TTT
79269 TCAAAA
62 TCAAAA
79275 TGTAATGTCG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
72 10 0.17
73 6 0.10
74 3 0.05
75 31 0.53
76 9 0.15
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (75 bp):
TCGAAACTATATAATAAATACGTTTTCACAAATTAATTTTCAAAAATATATAATATATTTTTCAA
AAATTGATTC
Found at i:79444 original size:36 final size:37
Alignment explanation
Indices: 79118--79454 Score: 183
Period size: 36 Copynumber: 8.9 Consensus size: 37
79108 TGTAAATATG
* * * * *
79118 TCAAAAAAACATTTTCGAAACTATATAATAAATATGTTT
1 TCAAAAAATCATTTTCAAAAATATAT-AT-TATATATTT
* * * * *
79157 TCACAAATTAATTTTCAAAAATGTATAATATAT-TTT
1 TCAAAAAATCATTTTCAAAAATATATATTATATATTT
* * * * *
79193 TCAAAAATTGATTCTCGAAACTATATATTATATACGTTT
1 TCAAAAAATCATTTTCAAAAATATATATTATATA--TTT
*
79232 TC--AAAAT-GTTTTCAAAAACTATATATTATATATATTT
1 TCAAAAAATCATTTTCAAAAA-TATATA-T-TATATATTT
* *
79269 TCAAAATGTAATGTCGTTTTTCAAAACTATATGATATATATATTT
1 TCAAAA---AA--TC-ATTTTCAAAAATATAT-AT-TATATATTT
* * * *
79314 TC-GAATACCGTTTTCAAAAATATATAATATATATATTT
1 TCAAAAAATCATTTTCAAAAATATAT-AT-TATATATTT
* *
79352 TC-AAAAATCGATTTT-TAAAA-GTATATTATATATTT
1 TCAAAAAATC-ATTTTCAAAAATATATATTATATATTT
**
79387 TCAAAAAATCATTTTTTAAAATCATATATTATAT-TTT
1 TCAAAAAATCATTTTCAAAAAT-ATATATTATATATTT
*
79424 TCAAAAAAT-ATTTTCAAAAAT-TATACTATAT
1 TCAAAAAATCATTTTCAAAAATATATATTATAT
79455 TAATAATAAT
Statistics
Matches: 238, Mismatches: 39, Indels: 47
0.73 0.12 0.15
Matches are distributed among these distances:
34 9 0.04
35 16 0.07
36 60 0.25
37 34 0.14
38 48 0.20
39 37 0.16
41 1 0.00
42 2 0.01
44 3 0.01
45 18 0.08
46 10 0.04
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (37 bp):
TCAAAAAATCATTTTCAAAAATATATATTATATATTT
Found at i:80208 original size:84 final size:83
Alignment explanation
Indices: 80046--80290 Score: 339
Period size: 84 Copynumber: 2.9 Consensus size: 83
80036 CGTTTAATAG
* * *
80046 GCCCTCGAGCTGAATGAAATCGAACTCGAAAGTGTTTGTTGACATATAGCCTTTCTCGCCTTGAG
1 GCCCTTGAGCTGAATGTAATCGAACTCGAAAGT-TTTGTTGACAGATAGCC-TTCTCGCCTTGAG
**
80111 TTATGTTGTAAATTTGATAT
64 TTATACTGTAAATTTGATAT
* *
80131 GCCCTTGAGCTGAATGTAATCGAACTCGAAAGTTTTATTGACAGATAACTCTTCTCGCCTTGAGT
1 GCCCTTGAGCTGAATGTAATCGAACTCGAAAGTTTTGTTGACAGATAGC-CTTCTCGCCTTGAGT
80196 TATACTGTAAATTTGATAT
65 TATACTGTAAATTTGATAT
* *
80215 GTCCTTGAGCTGAATGTAATCGAACTC-AAAGGTTTTTGTTGATAGATAGCCCTTCTCGCCTTGA
1 GCCCTTGAGCTGAATGTAATCGAACTCGAAA-G-TTTTGTTGACAGATAG-CCTTCTCGCCTTGA
*
80279 GCTATACTGTAA
63 GTTATACTGTAA
80291 TACGCTGGGG
Statistics
Matches: 144, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
83 3 0.02
84 71 0.49
85 69 0.48
86 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (83 bp):
GCCCTTGAGCTGAATGTAATCGAACTCGAAAGTTTTGTTGACAGATAGCCTTCTCGCCTTGAGTT
ATACTGTAAATTTGATAT
Done.