Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007311.1 Hibiscus syriacus cultivar Beakdansim tig00019480_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: 85572
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1070 original size:13 final size:13
Alignment explanation
Indices: 1052--1079 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1042 GGTTGAGCAA
1052 AAATAATAATAAT
1 AAATAATAATAAT
1065 AAATAATAATAAT
1 AAATAATAATAAT
1078 AA
1 AA
1080 TACCTATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:1430 original size:2 final size:2
Alignment explanation
Indices: 1423--1448 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1413 AAAAGCATCA
1423 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
1449 TCCTTCGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2200 original size:6 final size:6
Alignment explanation
Indices: 2189--2223 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
2179 AACGAAGGGT
2189 ATGTTC ATGTTC A-GTTC ATGTTC ATGTTC ATGTTC
1 ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC
2224 GTTCGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
ATGTTC
Found at i:2211 original size:17 final size:18
Alignment explanation
Indices: 2189--2223 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2179 AACGAAGGGT
2189 ATGTTCATGTTCA-GTTC
1 ATGTTCATGTTCATGTTC
2206 ATGTTCATGTTCATGTTC
1 ATGTTCATGTTCATGTTC
2224 GTTCGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (18 bp):
ATGTTCATGTTCATGTTC
Found at i:2382 original size:24 final size:24
Alignment explanation
Indices: 2355--2400 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2345 AACGAACGTA
* *
2355 AACACAAACGAATGAATATAAACG
1 AACACAAACGAAGGAAGATAAACG
* *
2379 AACATAAATGAAGGAAGATAAA
1 AACACAAACGAAGGAAGATAAA
2401 ATTAATTGGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.13
Consensus pattern (24 bp):
AACACAAACGAAGGAAGATAAACG
Found at i:4758 original size:5 final size:5
Alignment explanation
Indices: 4743--4771 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4733 AGAAGAAGGG
4743 GAAAA -AAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
4772 ACCTTCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:13527 original size:76 final size:76
Alignment explanation
Indices: 13438--13587 Score: 300
Period size: 76 Copynumber: 2.0 Consensus size: 76
13428 AGGGACCGGG
13438 TCCCCTTTGAACCCTAACAGAACTCCGCCCCCAGAGATAACATTAAATCTAACCTCAAAGAAAAT
1 TCCCCTTTGAACCCTAACAGAACTCCGCCCCCAGAGATAACATTAAATCTAACCTCAAAGAAAAT
13503 TTAAACTTCGA
66 TTAAACTTCGA
13514 TCCCCTTTGAACCCTAACAGAACTCCGCCCCCAGAGATAACATTAAATCTAACCTCAAAGAAAAT
1 TCCCCTTTGAACCCTAACAGAACTCCGCCCCCAGAGATAACATTAAATCTAACCTCAAAGAAAAT
13579 TTAAACTTC
66 TTAAACTTC
13588 AAACAAAATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.23
Consensus pattern (76 bp):
TCCCCTTTGAACCCTAACAGAACTCCGCCCCCAGAGATAACATTAAATCTAACCTCAAAGAAAAT
TTAAACTTCGA
Found at i:20481 original size:20 final size:20
Alignment explanation
Indices: 20456--20551 Score: 165
Period size: 20 Copynumber: 4.8 Consensus size: 20
20446 ATCCTATTCC
*
20456 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCCCA
20476 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
20496 CTGATAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
20516 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
20536 CTGATAATCTTACATT
1 CTGGTAATCTTACATT
20552 TCGTGAACCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:21762 original size:15 final size:15
Alignment explanation
Indices: 21742--21772 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21732 GAAATTGAAT
21742 TGGAATCCAATTTCA
1 TGGAATCCAATTTCA
21757 TGGAATCCAATTTCA
1 TGGAATCCAATTTCA
21772 T
1 T
21773 ATTATGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (15 bp):
TGGAATCCAATTTCA
Found at i:24789 original size:24 final size:23
Alignment explanation
Indices: 24762--24809 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
24752 TTTTATATAT
24762 TTTTTTATTTTTATTGAA-ATTTTA
1 TTTTTTATTTTT-TT-AATATTTTA
24786 TTTTTTATTTTTTTAATATTTTA
1 TTTTTTATTTTTTTAATATTTTA
24809 T
1 T
24810 AAGTTCGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.09
23 9 0.39
24 12 0.52
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTTATTTTTTTAATATTTTA
Found at i:27788 original size:41 final size:42
Alignment explanation
Indices: 27693--27811 Score: 195
Period size: 41 Copynumber: 2.9 Consensus size: 42
27683 GATTCGCAAC
* *
27693 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
* *
27735 ACGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
27776 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA
27812 CTCGAAAACT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 39 0.55
42 32 0.45
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (42 bp):
GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
Found at i:29963 original size:2 final size:2
Alignment explanation
Indices: 29956--29999 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
29946 TACTTTAACT
29956 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
29998 TA
1 TA
30000 AAGTTATTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32162 original size:17 final size:17
Alignment explanation
Indices: 32140--32181 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
32130 AATGGTCAAA
32140 ACAAACTCCTCTTCTAT
1 ACAAACTCCTCTTCTAT
32157 ACAAACTCCTCTTCTAT
1 ACAAACTCCTCTTCTAT
32174 ACAAACTC
1 ACAAACTC
32182 TTTAAGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (17 bp):
ACAAACTCCTCTTCTAT
Found at i:34776 original size:6 final size:6
Alignment explanation
Indices: 34765--34789 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34755 ATAACTACAC
34765 AATAGT AATAGT AATAGT AATAGT A
1 AATAGT AATAGT AATAGT AATAGT A
34790 GGCAACAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AATAGT
Found at i:39792 original size:15 final size:15
Alignment explanation
Indices: 39772--39801 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39762 AATTAGTATC
39772 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
39787 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
39802 ATATAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:46936 original size:16 final size:16
Alignment explanation
Indices: 46915--46956 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
46905 TAAAATAGTA
46915 AACTTTGAAACATTAG
1 AACTTTGAAACATTAG
46931 AACTTTGAAACATTAG
1 AACTTTGAAACATTAG
*
46947 AACATTGAAA
1 AACTTTGAAA
46957 ATTTTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (16 bp):
AACTTTGAAACATTAG
Found at i:55016 original size:49 final size:50
Alignment explanation
Indices: 54821--55060 Score: 410
Period size: 50 Copynumber: 4.8 Consensus size: 50
54811 TATATTTGTA
* * *
54821 AGTATGTGTTAAGTGTTATACTTTTTTATTTTAATCACATACACCGGTGT
1 AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATACACCGGTGT
54871 AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATACACCGGTGT
1 AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATACACCGGTGT
54921 AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATACACCGGTGT
1 AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATACACCGGTGT
*
54971 AGTATGTGTTAAGTGATACACTTTTTTGTTTTATTCA-ATACACCGGTGT
1 AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATACACCGGTGT
* * *
55020 AGTATATGTTAAGTGATACACTCTTTTGTTTTATTCACATA
1 AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATA
55061 ACTAAAGCTT
Statistics
Matches: 183, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
49 47 0.26
50 136 0.74
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (50 bp):
AGTATGTGTTAAGTGATATACTTTTTTGTTTTATTCACATACACCGGTGT
Found at i:58592 original size:19 final size:19
Alignment explanation
Indices: 58568--58623 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
58558 GAACGTTGGA
58568 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
58587 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
58608 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
58624 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:58603 original size:11 final size:11
Alignment explanation
Indices: 58568--58616 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
58558 GAACGTTGGA
58568 AACCGGTTTTG
1 AACCGGTTTTG
58579 -ACCGG-TTT-
1 AACCGGTTTTG
58587 AACCGGTTTTG
1 AACCGGTTTTG
58598 AACCGGTTTTG
1 AACCGGTTTTG
58609 -ACCGGTTT
1 AACCGGTTT
58617 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:58619 original size:9 final size:10
Alignment explanation
Indices: 58569--58623 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
58559 AACGTTGGAA
58569 ACCGGTTTTG
1 ACCGGTTTTG
*
58579 ACCGG-TTTA
1 ACCGGTTTTG
58588 ACCGGTTTTG
1 ACCGGTTTTG
58598 AACCGGTTTTG
1 -ACCGGTTTTG
58609 ACCGG-TTTG
1 ACCGGTTTTG
58618 ACCGGT
1 ACCGGT
58624 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:58654 original size:13 final size:13
Alignment explanation
Indices: 58636--58666 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58626 CGACCCGTTT
*
58636 ACCCGTTTACCCG
1 ACCCGTTGACCCG
58649 ACCCGTTGACCCG
1 ACCCGTTGACCCG
58662 ACCCG
1 ACCCG
58667 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:58667 original size:18 final size:18
Alignment explanation
Indices: 58644--58684 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
58634 TTACCCGTTT
58644 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
58662 ACCCGACCCGTTGACTCG
1 ACCCGACCCGTTGACCCG
58680 ACCCG
1 ACCCG
58685 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:58681 original size:13 final size:13
Alignment explanation
Indices: 58665--58689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58655 TGACCCGACC
58665 CGACCCGTTGACT
1 CGACCCGTTGACT
58678 CGACCCGTTGAC
1 CGACCCGTTGAC
58690 CGTTGACCGT
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:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:58758 original size:29 final size:29
Alignment explanation
Indices: 58698--58763 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
58688 ACCGTTGACC
*** *
58698 GTGCTATTCTGGGAATTAATTCGGTTTTG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
58727 GTGCTATTCTGGGAATTAATTCGAAATGG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
58756 GTGCTATT
1 GTGCTATT
58764 TCGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (29 bp):
GTGCTATTCTGGGAATTAATTCGAAATGG
Found at i:65808 original size:19 final size:19
Alignment explanation
Indices: 65784--65839 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
65774 GAACGTTGGA
65784 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
65803 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
65824 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
65840 CACGACCGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:65819 original size:11 final size:11
Alignment explanation
Indices: 65784--65832 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
65774 GAACGTTGGA
65784 AACCGGTTTTG
1 AACCGGTTTTG
65795 -ACCGG-TTT-
1 AACCGGTTTTG
65803 AACCGGTTTTG
1 AACCGGTTTTG
65814 AACCGGTTTTG
1 AACCGGTTTTG
65825 -ACCGGTTT
1 AACCGGTTT
65833 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:65835 original size:9 final size:10
Alignment explanation
Indices: 65785--65839 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
65775 AACGTTGGAA
65785 ACCGGTTTTG
1 ACCGGTTTTG
*
65795 ACCGG-TTTA
1 ACCGGTTTTG
65804 ACCGGTTTTG
1 ACCGGTTTTG
65814 AACCGGTTTTG
1 -ACCGGTTTTG
65825 ACCGG-TTTG
1 ACCGGTTTTG
65834 ACCGGT
1 ACCGGT
65840 CACGACCGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:65869 original size:13 final size:13
Alignment explanation
Indices: 65851--65881 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
65841 ACGACCGTTT
*
65851 ACCCGTTTACCCG
1 ACCCGTTGACCCG
65864 ACCCGTTGACCCG
1 ACCCGTTGACCCG
65877 ACCCG
1 ACCCG
65882 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:65882 original size:18 final size:18
Alignment explanation
Indices: 65859--65899 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
65849 TTACCCGTTT
65859 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
65877 ACCCGACCCGTTGACTCG
1 ACCCGACCCGTTGACCCG
65895 ACCCG
1 ACCCG
65900 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:65896 original size:13 final size:13
Alignment explanation
Indices: 65880--65904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65870 TGACCCGACC
65880 CGACCCGTTGACT
1 CGACCCGTTGACT
65893 CGACCCGTTGAC
1 CGACCCGTTGAC
65905 CGTTGACCGT
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:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:65973 original size:29 final size:29
Alignment explanation
Indices: 65913--65978 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
65903 ACCGTTGACC
*** *
65913 GTGCTATTCTGGGAATTAATTCGGTTTTG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
65942 GTGCTATTCTGGGAATTAATTCGAAATGG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
65971 GTGCTATT
1 GTGCTATT
65979 TCGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (29 bp):
GTGCTATTCTGGGAATTAATTCGAAATGG
Found at i:67801 original size:20 final size:20
Alignment explanation
Indices: 67776--67815 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
67766 ATCATTAATA
* *
67776 TTAATTAGTCCTTAGGTTTT
1 TTAATTAATCCTTAGATTTT
67796 TTAATTAATCCTTAGATTTT
1 TTAATTAATCCTTAGATTTT
67816 GGGTGCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
TTAATTAATCCTTAGATTTT
Found at i:68619 original size:15 final size:17
Alignment explanation
Indices: 68599--68637 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
68589 CATTTCAAAT
68599 ATTTTCTAAA-ATT-CG
1 ATTTTCTAAATATTCCG
68614 ATTTTCTAAATTATTCCG
1 ATTTTCTAAA-TATTCCG
68632 ATTTTC
1 ATTTTC
68638 GCCACTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
17 3 0.14
18 8 0.38
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (17 bp):
ATTTTCTAAATATTCCG
Found at i:71835 original size:77 final size:77
Alignment explanation
Indices: 71749--71903 Score: 204
Period size: 77 Copynumber: 2.0 Consensus size: 77
71739 TATTTATCTA
* * *
71749 AATGTTTTATACACCGCATGGAGCACACTGAGTTTTTTA-TCTCACTCTTTAATTTTTAATTTTT
1 AATGTTTTATACACCGCAAGGAGCACAATGAGTTTTTTAGT-TCACTCTTTAATTTTTAAATTTT
* *
71813 CATATACTTTCCG
65 CAGATACTATCCG
* * ** *
71826 AATGTTTTATACACCGTAAGGAGTACAATGTTTTTTTTAGTTTACTCTTTAATTTTTAAATTTTC
1 AATGTTTTATACACCGCAAGGAGCACAATGAGTTTTTTAGTTCACTCTTTAATTTTTAAATTTTC
71891 AGATACTATCCG
66 AGATACTATCCG
71903 A
1 A
71904 CAGTATGGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
77 66 0.99
78 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (77 bp):
AATGTTTTATACACCGCAAGGAGCACAATGAGTTTTTTAGTTCACTCTTTAATTTTTAAATTTTC
AGATACTATCCG
Found at i:72600 original size:69 final size:69
Alignment explanation
Indices: 72471--72600 Score: 172
Period size: 69 Copynumber: 1.9 Consensus size: 69
72461 TCTTAATTTT
* * *
72471 TTTATTAACTATATTTTACAATAGTTTTATATATTTATATTATTGTTAATGGAAAAAAATATTTT
1 TTTATTAACTATAATTTACAATAGTTTTACATATTTATATTATTGTTAATCGAAAAAAATATTTT
72536 TATA
66 TATA
** * * *
72540 TTTATTAACTATAATTTACAATTTTTTTACATATTTTTAATTTTTGTTAA-CGAAAGAAATA
1 TTTATTAACTATAATTTACAATAGTTTTACATATTTAT-ATTATTGTTAATCGAAAAAAATA
72601 GTTCTTAATC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 42 0.81
70 10 0.19
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (69 bp):
TTTATTAACTATAATTTACAATAGTTTTACATATTTATATTATTGTTAATCGAAAAAAATATTTT
TATA
Found at i:72791 original size:33 final size:36
Alignment explanation
Indices: 72715--72791 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
72705 TAATGGAAGA
**
72715 AATAATTTCTAATATTATATATATATATATTTGGAT
1 AATAATTTCTAATATTATATATATATATATTTAAAT
72751 AAGTAATTTCTAATATTATATATA-A-ATA-TTAAAT
1 AA-TAATTTCTAATATTATATATATATATATTTAAAT
*
72785 TATAATT
1 AATAATT
72792 AATAAATACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 5 0.14
34 5 0.14
35 3 0.08
36 3 0.08
37 21 0.57
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (36 bp):
AATAATTTCTAATATTATATATATATATATTTAAAT
Found at i:72866 original size:72 final size:69
Alignment explanation
Indices: 72767--72930 Score: 178
Period size: 72 Copynumber: 2.3 Consensus size: 69
72757 TTTCTAATAT
* *
72767 TATATATAAATA-T-TAAATTATAATTAATAAA-TACAATTCAA-AATTA-TTT-CATTAATAAA
1 TATATAAAAATATTGTAAATTATAATTAATAAATTAAAATT-AAGAATTATTTTCCATTAA-AAA
72826 CATTAAAAA
64 C--T-AAAA
*
72835 TATATAAAAAAATATTGTAAATTATAGTTAATAAATTAAAATTAAGAATTATTTTCCCATTAAAA
1 TATAT--AAAAATATTGTAAATTATAATTAATAAATTAAAATTAAGAATTATTTT-CCATTAAAA
72900 ACTAAAA
63 ACTAAAA
*
72907 TATATAAAAATGTTGTAAATTATA
1 TATATAAAAATATTGTAAATTATA
72931 TTCTAATATA
Statistics
Matches: 83, Mismatches: 4, Indels: 16
0.81 0.04 0.16
Matches are distributed among these distances:
68 5 0.06
70 24 0.29
71 1 0.01
72 28 0.34
73 12 0.14
74 3 0.04
75 4 0.05
76 6 0.07
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (69 bp):
TATATAAAAATATTGTAAATTATAATTAATAAATTAAAATTAAGAATTATTTTCCATTAAAAACT
AAAA
Found at i:74564 original size:24 final size:25
Alignment explanation
Indices: 74537--74605 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
74527 AAAGGGAAAG
74537 AGGAAG-GGAATGAAGA-GAAGGAGA
1 AGGAAGAGGAATGAAGAGGAAGGA-A
*
74561 AGGAAGTGGAA-GAAGAGGAAGGAA
1 AGGAAGAGGAATGAAGAGGAAGGAA
74585 AGGAAGAGGAACTGAAAGAGG
1 AGGAAGAGGAA-TG-AAGAGG
74606 TGGAGGGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 22 0.56
25 10 0.26
26 1 0.03
27 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.45, T:0.04
Consensus pattern (25 bp):
AGGAAGAGGAATGAAGAGGAAGGAA
Found at i:82014 original size:7 final size:7
Alignment explanation
Indices: 82002--82034 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
81992 AACATTCTCA
82002 GTTTAGG
1 GTTTAGG
82009 GTTTAGG
1 GTTTAGG
82016 GTTTAGG
1 GTTTAGG
*
82023 ATTTAGG
1 GTTTAGG
82030 GTTTA
1 GTTTA
82035 AAGTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Done.