Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002234.1 Hibiscus syriacus cultivar Beakdansim tig00004544_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: 90336
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2781 original size:29 final size:29
Alignment explanation
Indices: 2749--2806 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2739 TTGTTTAATC
*
2749 GGTTTCTAATTTGTATCTTGTATTTATTT
1 GGTTTCTAATTTGTATATTGTATTTATTT
2778 GGTTTCTAATTTGTATATTGTATTTATTT
1 GGTTTCTAATTTGTATATTGTATTTATTT
2807 CAGTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.62
Consensus pattern (29 bp):
GGTTTCTAATTTGTATATTGTATTTATTT
Found at i:19663 original size:12 final size:12
Alignment explanation
Indices: 19648--19679 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
19638 CCGACCTATG
19648 CCCATCCCTACT
1 CCCATCCCTACT
19660 CCCATCCCTACT
1 CCCATCCCTACT
19672 CCCATCCC
1 CCCATCCC
19680 ATAATCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.62, G:0.00, T:0.22
Consensus pattern (12 bp):
CCCATCCCTACT
Found at i:20116 original size:20 final size:21
Alignment explanation
Indices: 20091--20142 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
20081 TTTTCCCAAT
*
20091 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
20111 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
20132 TCGCAATGCGA
1 TCGCAATGCGA
20143 TAATACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:20743 original size:19 final size:19
Alignment explanation
Indices: 20705--20771 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
20695 TTCGAGAATG
20705 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
20725 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
20744 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
20763 AAAATCGCA
1 AAAATCGCA
20772 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:20789 original size:19 final size:19
Alignment explanation
Indices: 20767--20884 Score: 182
Period size: 19 Copynumber: 6.1 Consensus size: 19
20757 GAAACCAAAA
*
20767 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
20786 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
20805 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
20824 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
20844 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
20863 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
20883 TC
1 TC
20885 AACCAAAAGA
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 56 0.62
20 35 0.38
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:20844 original size:39 final size:38
Alignment explanation
Indices: 20767--20884 Score: 182
Period size: 39 Copynumber: 3.1 Consensus size: 38
20757 GAAACCAAAA
*
20767 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
20805 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* *
20844 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
20883 TC
1 TC
20885 AACCAAAAGA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
38 21 0.29
39 49 0.67
40 3 0.04
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:20862 original size:58 final size:59
Alignment explanation
Indices: 20772--20884 Score: 192
Period size: 58 Copynumber: 1.9 Consensus size: 59
20762 CAAAATCGCA
* *
20772 TTGCGATTTTCATTTCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTATCGCGTTGCGATTTTCATTTCGCGG
*
20830 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTATCGCGTTGCGATTTTCATTTC
20885 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 32 0.63
59 19 0.37
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.49
Consensus pattern (59 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCATTATCGCGTTGCGATTTTCATTTCGCGG
Found at i:22947 original size:42 final size:42
Alignment explanation
Indices: 22887--23009 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
22877 GCCCGACTCG
* * *
22887 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
22929 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
22971 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
23010 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:22967 original size:21 final size:21
Alignment explanation
Indices: 22943--23009 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
22933 TCATTCCTCG
22943 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
22964 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
22985 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
23006 AGAG
1 AGAG
23010 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:24389 original size:14 final size:14
Alignment explanation
Indices: 24367--24403 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
24357 TATTGTTTAA
24367 TTGATTTGTAAAAGG
1 TTGATTTGTAAAA-G
24382 TT-ATTTGTAAAAG
1 TTGATTTGTAAAAG
24395 TTGATTTGT
1 TTGATTTGT
24404 TTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 16 0.76
15 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:24568 original size:19 final size:19
Alignment explanation
Indices: 24546--24681 Score: 157
Period size: 19 Copynumber: 7.7 Consensus size: 19
24536 CGAAATTAAA
*
24546 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
24565 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
24584 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
24603 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
24617 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
24636 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
24652 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
24669 TTCGCATTGCGAT
1 TTCGCATTGCGAT
24682 AGTAATTTCC
Statistics
Matches: 98, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
14 17 0.17
16 7 0.07
17 7 0.07
19 67 0.68
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:24570 original size:38 final size:37
Alignment explanation
Indices: 24535--24701 Score: 170
Period size: 33 Copynumber: 4.6 Consensus size: 37
24525 AAATCGCAAC
24535 GCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATT
1 GCGAAATT-AATTCGCGTTGCGATTTTCATTTCGCATT
** * *
24573 GCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
1 GCGAAATT-AATTCGCGTTGCGATTTTCATTTCGCATT
24611 GCGAAATT-A---GCGTTGCGATTTTCATTTCGCATT
1 GCGAAATTAATTCGCGTTGCGATTTTCATTTCGCATT
* *
24644 GCG--ATT--CTCTCGTTGCGATTTTCATTTCGCATT
1 GCGAAATTAATTCGCGTTGCGATTTTCATTTCGCATT
* *
24677 GCGATAGTAATTTCCGCGTTGCGAT
1 GCGAAATTAA-TT-CGCGTTGCGAT
24702 GGACATTAAG
Statistics
Matches: 107, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
31 3 0.03
33 52 0.49
35 2 0.02
38 40 0.37
39 10 0.09
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (37 bp):
GCGAAATTAATTCGCGTTGCGATTTTCATTTCGCATT
Found at i:24638 original size:71 final size:66
Alignment explanation
Indices: 24543--24680 Score: 213
Period size: 71 Copynumber: 2.0 Consensus size: 66
24533 ACGCGAAATT
* *
24543 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGC
24608 ATTGCG
61 ATTGCG
24614 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
24679 G
66 G
24680 A
1 A
24681 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
66 25 0.38
68 4 0.06
69 3 0.05
71 33 0.51
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:24690 original size:52 final size:50
Alignment explanation
Indices: 24550--24681 Score: 158
Period size: 52 Copynumber: 2.6 Consensus size: 50
24540 ATTAAATTCG
24550 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTT
* * * * * *
24600 CATTTCGCA-TTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCG-ATTTTC--ATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-T
24654 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
24682 AGTAATTTCC
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
50 8 0.12
51 1 0.02
52 44 0.69
53 2 0.03
54 9 0.14
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (50 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTT
Found at i:26989 original size:12 final size:12
Alignment explanation
Indices: 26972--26996 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26962 TCTTCGGGGA
26972 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26984 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26996 C
1 C
26997 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:27205 original size:24 final size:24
Alignment explanation
Indices: 27171--27226 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
27161 CTGAAACATC
* *
27171 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
27195 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
27219 ATCAAAAT
1 ATCAAAAT
27227 TCGAATACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:28286 original size:20 final size:20
Alignment explanation
Indices: 28261--28318 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
28251 ATTCATTTGA
28261 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
28281 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
28301 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
28319 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:28359 original size:19 final size:19
Alignment explanation
Indices: 28337--28509 Score: 258
Period size: 19 Copynumber: 9.6 Consensus size: 19
28327 GAAATGAAAA
28337 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
28356 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
28372 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
28389 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
28405 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
28422 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
28441 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
28460 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
28479 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
28498 TCGCGTTGCGAT
1 TCGCATTGCGAT
28510 AGTCTGTTTT
Statistics
Matches: 142, Mismatches: 2, Indels: 20
0.87 0.01 0.12
Matches are distributed among these distances:
14 22 0.15
16 6 0.04
17 6 0.04
19 108 0.76
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:28378 original size:14 final size:14
Alignment explanation
Indices: 28361--28418 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
28351 TCATTTCGCA
28361 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
28375 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
28392 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
28408 TTGCGATTTTC
1 TTGCGATTTTC
28419 ATTTCGCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 22 0.56
16 3 0.08
17 3 0.08
19 11 0.28
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:28509 original size:38 final size:35
Alignment explanation
Indices: 28337--28509 Score: 246
Period size: 33 Copynumber: 4.9 Consensus size: 35
28327 GAAATGAAAA
28337 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
28372 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
28405 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
28438 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ---TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
* *
28476 ATTTCGCATTGCGATTTCCATTTCGCGTTGCGAT
1 ---TCGCATTGCGATTTTCATTTCGCATTGCGAT
28510 AGTCTGTTTT
Statistics
Matches: 131, Mismatches: 2, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
33 63 0.48
35 3 0.02
36 3 0.02
38 62 0.47
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (35 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:30537 original size:20 final size:19
Alignment explanation
Indices: 30502--30568 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
30492 GAAACTTAAA
30502 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
30521 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
30541 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
30560 ATCGCAACG
1 ATCGCAACG
30569 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:30576 original size:14 final size:14
Alignment explanation
Indices: 30557--30614 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
30547 ATGCGAAATG
30557 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
30571 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
30587 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
30603 AAAATCGCAACG
1 AAAATCGCAACG
30615 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:30599 original size:32 final size:33
Alignment explanation
Indices: 30541--30619 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
30531 GGAAATGGCT
*
30541 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
30574 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
30606 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
30620 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:30648 original size:19 final size:17
Alignment explanation
Indices: 30626--30721 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
30616 GAAACACAAA
30626 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
30645 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
30661 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
30677 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
30693 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
30710 TCGCATTGCGAT
1 TCGC-TTGCGAT
30722 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:30667 original size:14 final size:14
Alignment explanation
Indices: 30648--30705 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
30638 TTTCATTTCG
30648 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
30662 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
30678 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
30694 CGTTGCGATTTT
1 CGTTGCGATTTT
30706 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:30712 original size:33 final size:33
Alignment explanation
Indices: 30631--30721 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
30621 ACAAATCGCA
30631 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
30664 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
30696 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
30722 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:30740 original size:20 final size:19
Alignment explanation
Indices: 30706--30759 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
30696 TTGCGATTTT
*
30706 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
30725 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
30745 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
30760 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:30758 original size:19 final size:19
Alignment explanation
Indices: 30694--30759 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
30684 GCGATTTTGT
**
30694 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
30713 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
30733 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
30752 TGTTGCGA
1 CGTTGCGA
30760 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:31251 original size:18 final size:18
Alignment explanation
Indices: 31225--31269 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
31215 GTCGATCAGA
* *
31225 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
31243 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
31261 TGATGGCTC
1 TGATGGCTC
31270 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:32825 original size:22 final size:22
Alignment explanation
Indices: 32800--32843 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
32790 GATTTAGATA
32800 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
32822 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
32844 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:33102 original size:41 final size:41
Alignment explanation
Indices: 33050--33127 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
33040 CGAAAGTCAG
* * *
33050 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
33091 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
33128 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:33124 original size:20 final size:20
Alignment explanation
Indices: 33011--33124 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
33001 CGCTTTGAAA
33011 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
33031 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
33051 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
33071 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
33092 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
33112 ATCGCATTGCGAT
1 ATCGCATTGCGAT
33125 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:33143 original size:41 final size:41
Alignment explanation
Indices: 33050--33145 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
33040 CGAAAGTCAG
* * * ** *
33050 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
*
33091 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
33133 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
33146 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:34845 original size:21 final size:22
Alignment explanation
Indices: 34802--34845 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
34792 CAACTTGAAG
** *
34802 AAAAAATATATTAATTTTTTTA
1 AAAAAATATATTAATAATATTA
34824 AAAAAAT-TATTAATAATATTA
1 AAAAAATATATTAATAATATTA
34845 A
1 A
34846 CATTTACGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAAATATATTAATAATATTA
Found at i:37322 original size:5 final size:5
Alignment explanation
Indices: 37312--37336 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
37302 CGATAATTTA
37312 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
37337 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:39591 original size:2 final size:2
Alignment explanation
Indices: 39584--39614 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39574 CCCAACACAT
39584 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
39615 TTTTCTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51641 original size:4 final size:4
Alignment explanation
Indices: 51632--51690 Score: 91
Period size: 4 Copynumber: 14.8 Consensus size: 4
51622 TGATGATATA
* * *
51632 ATAG ATAG ATAT AAAG ATAG ATAG ATAG ATAT ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
51680 ATAG ATAG ATA
1 ATAG ATAG ATA
51691 AAATGATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:51975 original size:23 final size:21
Alignment explanation
Indices: 51927--51977 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
51917 TTTGGTATAA
51927 TTATATATTTGACCTTTTTAC
1 TTATATATTTGACCTTTTTAC
*
51948 TTATATATTTGATCTTTTTAC
1 TTATATATTTGACCTTTTTAC
51969 TTATATATT
1 TTATATATT
51978 CTATCAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.61
Consensus pattern (21 bp):
TTATATATTTGACCTTTTTAC
Found at i:52180 original size:16 final size:17
Alignment explanation
Indices: 52149--52181 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
52139 AGGTGCTGTC
52149 ACGTTGTTGCCAACTGG
1 ACGTTGTTGCCAACTGG
*
52166 ACGTTG-TGTCAACTGG
1 ACGTTGTTGCCAACTGG
52182 GGTAGTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.30
Consensus pattern (17 bp):
ACGTTGTTGCCAACTGG
Found at i:52994 original size:21 final size:21
Alignment explanation
Indices: 52968--53014 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
52958 AAATACGGTA
52968 GGAATTGAGAGTACTTGAATG
1 GGAATTGAGAGTACTTGAATG
52989 GGAATTGAGAGTACTTGAATG
1 GGAATTGAGAGTACTTGAATG
*
53010 CGAAT
1 GGAAT
53015 CACCCAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (21 bp):
GGAATTGAGAGTACTTGAATG
Found at i:54358 original size:167 final size:166
Alignment explanation
Indices: 54081--54466 Score: 549
Period size: 167 Copynumber: 2.3 Consensus size: 166
54071 AATATGCCCC
* * * * *
54081 TGAGCTGAATGAAATCAAACTCGAAGGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTCGCCTTGAGCTATA
* * *
54146 CTGTAAATTTGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAAC
65 CTGCAAA-TTGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTGTTGACAGATAAC
* *
54211 CCTTATAGCTTTGAGTTATGCTATAATTGATATACCTT
129 CCTTATAGCCTTGAGTTATGCTATAAATGATATACCTT
* * *
54249 TGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTCGGCAGATAACCCTTCTTGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGT-GACAGATAACCCTTCTCGCCTTGAGCTAT
* * *
54314 ATTGCAAA-TGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTGTTTTTTGACAGATAAC
64 ACTGCAAATTGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTGTTGACAGATAAC
* * *
54378 CCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCTT
129 CCTTATAGCCTTGAGTTATGCTATAAATGATATACCTT
54416 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-TGACAGATAACCCTTCT
54467 AGTGTAACAT
Statistics
Matches: 194, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
166 19 0.10
167 114 0.59
168 26 0.13
169 35 0.18
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (166 bp):
TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATAACCCTTCTCGCCTTGAGCTATAC
TGCAAATTGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTGTTGACAGATAACCC
TTATAGCCTTGAGTTATGCTATAAATGATATACCTT
Found at i:54408 original size:83 final size:83
Alignment explanation
Indices: 54081--54468 Score: 533
Period size: 83 Copynumber: 4.6 Consensus size: 83
54071 AATATGCCCC
* * * * *
54081 TGAGCTGAATGAAATCAAACTCGAAGGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
* *
54146 CTGTAAATTTGATGTGTCTT
66 CTATAAA--TGATGTGCCTT
* *
54166 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTATAGCTTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * *
54231 CTATAATTGATATACCTT
66 CTATAAATGATGTGCCTT
* * * * *
54249 TGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTCGGCAGATAACCCTTCTTGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
** **
54314 ATTGCAAATGATGTGCCTT
65 GCTATAAATGATGTGCCTT
* * *
54333 TGAGCTGAGTGAAATCGAACTCGAAGGTGTTTTTTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
54398 CTATAAATGATGTGCCTT
66 CTATAAATGATGTGCCTT
54416 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAG
54469 TGTAACATCC
Statistics
Matches: 261, Mismatches: 41, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
83 131 0.50
84 67 0.26
85 63 0.24
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (83 bp):
TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
CTATAAATGATGTGCCTT
Found at i:55272 original size:20 final size:20
Alignment explanation
Indices: 55247--55284 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55237 AGTATGTTCA
55247 GGGGGTATCGATTCCCCTGG
1 GGGGGTATCGATTCCCCTGG
55267 GGGGGTATCGATTCCCCT
1 GGGGGTATCGATTCCCCT
55285 CTAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCTGG
Found at i:56467 original size:31 final size:31
Alignment explanation
Indices: 56380--56510 Score: 131
Period size: 31 Copynumber: 4.2 Consensus size: 31
56370 AGAGTTGAGG
*
56380 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * *
56411 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
*
56443 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * * * * *
56474 ATTTACCTAGGTTCTTTGGAACCTAGGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
56505 GT-TACC
1 GTATACC
56511 GAGGATCTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
30 4 0.05
31 51 0.63
32 26 0.32
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTATGGAACATATGGACA
Found at i:56520 original size:30 final size:30
Alignment explanation
Indices: 56476--56557 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
56466 TATGGACAAT
* *
56476 TTACCTAGGTTCTTT-GGAACCTAGGGACAG
1 TTACCGAGGATCTTTAGG-ACCTAGGGACAG
* ** *
56506 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTAGGACCTAGGGACAG
*
56536 TTACCGAGGATCTTTATGACCT
1 TTACCGAGGATCTTTAGGACCT
56558 CTGGATAGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 44 0.98
31 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
TTACCGAGGATCTTTAGGACCTAGGGACAG
Found at i:56558 original size:30 final size:30
Alignment explanation
Indices: 56504--56565 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
56494 ACCTAGGGAC
56504 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
56534 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
56564 AG
1 AG
56566 GTCCTTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:61192 original size:31 final size:31
Alignment explanation
Indices: 61080--61204 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
61070 GTTGAGGGTA
*
61080 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
61112 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
61143 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * * *
61174 TACCTAGGTTCTTCGGAACCTAGGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
61205 ACCGAGGATC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
31 52 0.67
32 26 0.33
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:61235 original size:30 final size:30
Alignment explanation
Indices: 61201--61262 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
61191 ACCTAGGGAC
61201 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
61231 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
61261 AG
1 AG
61263 GTCCTTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:62359 original size:43 final size:42
Alignment explanation
Indices: 62205--62359 Score: 139
Period size: 43 Copynumber: 3.6 Consensus size: 42
62195 ACGATTCCCT
* * * * *
62205 TCGTCGTGAAGTTAAAACCGTGGTTGCGTGGGCACGATATCC
1 TCGTTGTGAAGTTGAAATCGTGGATGCGTAGGCACGATATCC
* * * * *
62247 TCTATTGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCC
1 TC-GTTGTGAAGTTGAAATCGTGGATGCGTAGGCACGATATCC
* * * * * *
62290 TCCTTCATGGAGTTGAAATAGTGGATGTGTAGGCACAATATCC
1 TCGTT-GTGAAGTTGAAATCGTGGATGCGTAGGCACGATATCC
62333 TTCGTTGTGAAGTTGAAATCGTGGATG
1 -TCGTTGTGAAGTTGAAATCGTGGATG
62360 GCCCCTTCGT
Statistics
Matches: 89, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
42 4 0.04
43 81 0.91
44 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (42 bp):
TCGTTGTGAAGTTGAAATCGTGGATGCGTAGGCACGATATCC
Found at i:69525 original size:26 final size:26
Alignment explanation
Indices: 69485--69542 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
69475 TGAATATTTT
*
69485 AAAAATAAATATAAAAACATTAAAATA
1 AAAAATAAATATAAAAA-ATAAAAATA
*
69512 AAAAAT-AATTTAAAAAATAAAAATA
1 AAAAATAAATATAAAAAATAAAAATA
69537 ATAAAA
1 A-AAAA
69543 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.32
26 13 0.46
27 6 0.21
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (26 bp):
AAAAATAAATATAAAAAATAAAAATA
Found at i:69542 original size:27 final size:27
Alignment explanation
Indices: 69484--69545 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
69474 TTGAATATTT
*
69484 TAAAAATAAATATAAAAACATTAAAATA
1 TAAAAAT-AATATAAAAACATAAAAATA
*
69512 -AAAAATAATTTAAAAA-ATAAAAATAA
1 TAAAAATAATATAAAAACATAAAAAT-A
69538 TAAAAATA
1 TAAAAATA
69546 TGAAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 7 0.23
26 10 0.33
27 13 0.43
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (27 bp):
TAAAAATAATATAAAAACATAAAAATA
Found at i:69551 original size:18 final size:17
Alignment explanation
Indices: 69506--69557 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
69496 TAAAAACATT
69506 AAAATAAAAAATAATTTAA
1 AAAAT-AAAAATAA-TTAA
69525 AAAATAAAAATAA-TAA
1 AAAATAAAAATAATTAA
* *
69541 AAATATGAAAATTATTA
1 AAA-ATAAAAATAATTA
69558 TTATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 8 0.28
18 10 0.34
19 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATAAAAATAATTAA
Found at i:69981 original size:24 final size:24
Alignment explanation
Indices: 69950--70020 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
69940 ATTCAAGTTT
69950 GAGT-TCGAGATTGAATCGAGCTC
1 GAGTCTCGAGATTGAATCGAGCTC
*
69973 GAGTCTCGAGATTGAATCGAGGTC
1 GAGTCTCGAGATTGAATCGAGCTC
* *
69997 GAGTCTCGAGCTTCAATCGAGCTC
1 GAGTCTCGAGATTGAATCGAGCTC
70021 CTGAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 4 0.09
24 39 0.91
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (24 bp):
GAGTCTCGAGATTGAATCGAGCTC
Found at i:73711 original size:2 final size:2
Alignment explanation
Indices: 73660--73694 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
73650 TCGGGCCGGG
73660 TA 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 TA T
73695 TTAAATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73806 original size:13 final size:12
Alignment explanation
Indices: 73775--73808 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
73765 TTTTAATATT
73775 TATCGGGGCGGG
1 TATCGGGGCGGG
73787 TATCGGGGCGGG
1 TATCGGGGCGGG
73799 TAATCGGGGC
1 T-ATCGGGGC
73809 AGGGATTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.12, C:0.18, G:0.53, T:0.18
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:76755 original size:32 final size:33
Alignment explanation
Indices: 76673--76756 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
76663 TATTAATATA
*
76673 TAATTAAAATAAAAAATAAATTTAAATGTTAGAG
1 TAATTAAATTAAAAAAT-AATTTAAATGTTAGAG
* *
76707 TGATTAAATT-AGAAATAATTTGAAA-GTTA-AG
1 TAATTAAATTAAAAAATAATTT-AAATGTTAGAG
76738 TAATTAAATTAAAAAATAA
1 TAATTAAATTAAAAAATAA
76757 ATTTCAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 11 0.26
32 16 0.37
33 8 0.19
34 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (33 bp):
TAATTAAATTAAAAAATAATTTAAATGTTAGAG
Found at i:77115 original size:3 final size:3
Alignment explanation
Indices: 77107--77154 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
77097 CTAGCTTTGA
77107 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
77155 TGTAGTTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:77527 original size:21 final size:23
Alignment explanation
Indices: 77485--77540 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
77475 ATATTTATCA
* *
77485 TTGTGGCACGTTTTTGTCTGCTC
1 TTGTGACACGTTTTTGTATGCTC
77508 TTGTGACAC-TTTTT-TATGCTC
1 TTGTGACACGTTTTTGTATGCTC
77529 TTGT-AGCACGTT
1 TTGTGA-CACGTT
77541 CTTTATGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 13 0.45
22 7 0.24
23 8 0.28
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (23 bp):
TTGTGACACGTTTTTGTATGCTC
Done.