Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001643.1 Hibiscus syriacus cultivar Beakdansim tig00003292_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: 139279
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2003 original size:15 final size:15
Alignment explanation
Indices: 1983--2014 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1973 AAACTTTATA
1983 TAATTATATTAAAAT
1 TAATTATATTAAAAT
*
1998 TAATTATATTATAAT
1 TAATTATATTAAAAT
2013 TA
1 TA
2015 GAGTTATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATATTAAAAT
Found at i:3615 original size:20 final size:22
Alignment explanation
Indices: 3590--3631 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
3580 AACTTAGAGT
*
3590 TTTTAAA-CTTTTAAA-AATTA
1 TTTTAAATATTTTAAATAATTA
3610 TTTTAAATATTTTAAATAATTA
1 TTTTAAATATTTTAAATAATTA
3632 AATTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAATATTTTAAATAATTA
Found at i:5658 original size:20 final size:20
Alignment explanation
Indices: 5633--5681 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
5623 GGCTGCTGGA
5633 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACCGG-TTTC
5653 AACCGGTTCTGACCGGTTTC
1 AACCGGTTCTGACCGGTTTC
5673 AACCGGTTC
1 AACCGGTTC
5682 GAACCGGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (20 bp):
AACCGGTTCTGACCGGTTTC
Found at i:5670 original size:30 final size:29
Alignment explanation
Indices: 5633--5706 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
5623 GGCTGCTGGA
5633 AACCGGTTTGACCGGTTTTC-AACCGGTTCTG
1 AACCGGTTTGACCGG--TTCGAACCGG-TCTG
*
5664 -ACCGGTTTCAACCGGTTCGAACCGGTCTG
1 AACCGGTTT-GACCGGTTCGAACCGGTCTG
*
5693 AATCGGTTTGACCG
1 AACCGGTTTGACCG
5707 TTGACCCGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 11 0.30
30 21 0.57
31 5 0.14
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTCGAACCGGTCTG
Found at i:5687 original size:20 final size:19
Alignment explanation
Indices: 5633--5689 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 19
5623 GGCTGCTGGA
*
5633 AACCGGTTTGACCGGTTTTC
1 AACCGGTTCGACCGG-TTTC
5653 AACCGGTTCTGACCGGTTTC
1 AACCGGTTC-GACCGGTTTC
5673 AACCGGTTCGAACCGGT
1 AACCGGTTCG-ACCGGT
5690 CTGAATCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.03
20 27 0.79
21 6 0.18
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (19 bp):
AACCGGTTCGACCGGTTTC
Found at i:5719 original size:5 final size:5
Alignment explanation
Indices: 5709--5766 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
5699 TTTGACCGTT
* *
5709 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
5758 GACCC GACC
1 GACCC GACC
5767 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:5736 original size:22 final size:22
Alignment explanation
Indices: 5709--5773 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
5699 TTTGACCGTT
5709 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
5731 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
5753 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
5774 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:5773 original size:17 final size:17
Alignment explanation
Indices: 5702--5739 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
5692 GAATCGGTTT
5702 GACCGTTGACCCGACCC
1 GACCGTTGACCCGACCC
5719 GACCGTTGACCCGACCC
1 GACCGTTGACCCGACCC
5736 GACC
1 GACC
5740 CGACCGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCGTTGACCCGACCC
Found at i:5775 original size:7 final size:7
Alignment explanation
Indices: 5763--5793 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5753 GACCCGACCC
5763 GACCGTT
1 GACCGTT
5770 GACCGTT
1 GACCGTT
5777 GACCGTT
1 GACCGTT
5784 GACCGTT
1 GACCGTT
5791 GAC
1 GAC
5794 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:6729 original size:63 final size:63
Alignment explanation
Indices: 6661--6784 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
6651 CTAATGTGAC
* * *
6661 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
6723 T
63 T
* *
6724 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
6785 TCCTTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:6744 original size:32 final size:32
Alignment explanation
Indices: 6661--6784 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
6651 CTAATGTGAC
* * *
6661 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
6691 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
6724 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
6755 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
6785 TCCTTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:13005 original size:10 final size:9
Alignment explanation
Indices: 12970--13060 Score: 83
Period size: 10 Copynumber: 9.4 Consensus size: 9
12960 GCTGCTGGAA
12970 ACCGGTTTG
1 ACCGGTTTG
*
12979 ACCGGTTTTCA
1 ACCGG-TTT-G
12990 ACCGGTTCTG
1 ACCGGTT-TG
13000 ACCGGTTTG
1 ACCGGTTTG
*
13009 ACCGGTTTCA
1 ACCGGTTT-G
*
13019 ACCGGTTCG
1 ACCGGTTTG
13028 AACCGGTTTG
1 -ACCGGTTTG
*
13038 ACCGGTCTG
1 ACCGGTTTG
*
13047 AATCGGTTTG
1 -ACCGGTTTG
13057 ACCG
1 ACCG
13061 TTGACCCCGA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
9 26 0.39
10 34 0.52
11 6 0.09
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:13014 original size:19 final size:20
Alignment explanation
Indices: 12969--13060 Score: 102
Period size: 19 Copynumber: 4.7 Consensus size: 20
12959 GGCTGCTGGA
* *
12969 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTCTG
12989 AACCGGTTCTGACCGGTT-TG
1 AACCGGTT-TGACCGGTTCTG
*
13009 -ACCGGTTTCAACCGGTTC-G
1 AACCGGTTT-GACCGGTTCTG
13028 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
13047 AATCGGTTTGACCG
1 AACCGGTTTGACCG
13061 TTGACCCCGA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.05
19 34 0.54
20 17 0.27
21 9 0.14
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:13054 original size:29 final size:30
Alignment explanation
Indices: 12969--13043 Score: 127
Period size: 29 Copynumber: 2.5 Consensus size: 30
12959 GGCTGCTGGA
12969 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
13000 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
13028 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
13044 CTGAATCGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.65
30 14 0.33
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:13076 original size:5 final size:5
Alignment explanation
Indices: 13066--13126 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
13056 GACCGTTGAC
* * *
13066 CCCGA CCCGA CCCGA CCGTTGA CCCAA CCCGA CCCGA CCGTTGA CCCGA
1 CCCGA CCCGA CCCGA CC--CGA CCCGA CCCGA CCCGA CC--CGA CCCGA
13115 CCCGA CCCGA CC
1 CCCGA CCCGA CC
13127 GTTGACCGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 38 0.83
7 8 0.17
ACGTcount: A:0.20, C:0.54, G:0.20, T:0.07
Consensus pattern (5 bp):
CCCGA
Found at i:13098 original size:22 final size:22
Alignment explanation
Indices: 13056--13133 Score: 138
Period size: 22 Copynumber: 3.5 Consensus size: 22
13046 GAATCGGTTT
13056 GACCGTTGACCCCGACCCGACCC
1 GACCGTTGA-CCCGACCCGACCC
*
13079 GACCGTTGACCCAACCCGACCC
1 GACCGTTGACCCGACCCGACCC
13101 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
13123 GACCGTTGACC
1 GACCGTTGACC
13134 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
22 44 0.83
23 9 0.17
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.10
Consensus pattern (22 bp):
GACCGTTGACCCGACCCGACCC
Found at i:14082 original size:63 final size:63
Alignment explanation
Indices: 14014--14137 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
14004 CTAATGTGAC
* * *
14014 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
14076 T
63 T
* *
14077 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
14138 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:14097 original size:32 final size:32
Alignment explanation
Indices: 14014--14137 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
14004 CTAATGTGAC
* * *
14014 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
14044 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
14077 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
14108 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
14138 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:16850 original size:3 final size:3
Alignment explanation
Indices: 16842--16897 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
16832 ATGAAGGGAT
16842 TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
16888 TTA TTA TTA T
1 TTA TTA TTA T
16898 ATTTTATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:16906 original size:7 final size:8
Alignment explanation
Indices: 16846--16906 Score: 72
Period size: 9 Copynumber: 7.4 Consensus size: 8
16836 AGGGATTTAT
16846 TATTATTA
1 TATTATTA
16854 TTATTATTA
1 -TATTATTA
16863 -ATTATTA
1 TATTATTA
16870 TTATTATTA
1 -TATTATTA
16879 TTATTATTA
1 -TATTATTA
16888 TTATTATTA
1 -TATTATTA
16897 TATT-TTA
1 TATTATTA
16904 TAT
1 TAT
16907 ACTTATTGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
7 13 0.26
8 4 0.08
9 33 0.66
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTATTA
Found at i:21345 original size:29 final size:29
Alignment explanation
Indices: 21294--21367 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
21284 CTTCCCAGCA
* * * *
21294 TAGGTCGCCATGTC-CTCCGGGCGACCTTG
1 TAGGTCGCCATG-CACGCCAGGCGACATGG
21323 TAGGTCGCCATGCACGCCAGGCGACATGG
1 TAGGTCGCCATGCACGCCAGGCGACATGG
21352 TAGGTCGCCATGCACG
1 TAGGTCGCCATGCACG
21368 GTGGACGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.19
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCAGGCGACATGG
Found at i:21495 original size:31 final size:31
Alignment explanation
Indices: 21460--21521 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
21450 CATGGCGCAT
21460 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
**
21491 GCAAAGCTTCATCCTCTCGTCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
21522 TAGAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:23147 original size:16 final size:17
Alignment explanation
Indices: 23120--23154 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
23110 ATTAACAGTA
*
23120 TTAAAAATAATATTATT
1 TTAAAAATAATAATATT
23137 TTAAAAA-AATAATATT
1 TTAAAAATAATAATATT
23153 TT
1 TT
23155 TACTAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAAATAATAATATT
Found at i:29869 original size:21 final size:21
Alignment explanation
Indices: 29845--29934 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 21
29835 TTTGGAATAA
*
29845 ATCGCAACGCGAACTTCAACT
1 ATCGCAACGCGAACTTCGACT
* *
29866 ATCGCAATGCGATA-GTCGACT
1 ATCGCAACGCGA-ACTTCGACT
* *
29887 ATCGCAATGCAAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
29908 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTCGACT
29929 ATCGCA
1 ATCGCA
29935 TTGCGATTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:29940 original size:21 final size:20
Alignment explanation
Indices: 29863--30001 Score: 79
Period size: 21 Copynumber: 6.8 Consensus size: 20
29853 GCGAACTTCA
* * *
29863 ACTATCGCAATGCGATAGTCG
1 ACTATCGCATTGCGA-ATTTG
* * *
29884 ACTATCGCAATGCAAACTTCG
1 ACTATCGCATTGCGAA-TTTG
**
29905 ACTATCGCAACGCGAACTTTG
1 ACTATCGCATTGCGAA-TTTG
29926 ACTATCGCATTGCG-ATTT-
1 ACTATCGCATTGCGAATTTG
* * *
29944 ACATATTCGCATTGCGGTAGTCG
1 AC-TA-TCGCATTGC-GAATTTG
29967 ACTATCGCATTGCG-ATTT-
1 ACTATCGCATTGCGAATTTG
29985 ACATATTCGCATTGCGA
1 AC-TA-TCGCATTGCGA
30002 TAGTCCAAGT
Statistics
Matches: 98, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.04
19 9 0.09
20 22 0.22
21 57 0.58
22 4 0.04
23 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (20 bp):
ACTATCGCATTGCGAATTTG
Found at i:29955 original size:20 final size:20
Alignment explanation
Indices: 29930--30002 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
29920 ACTTTGACTA
29930 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
29950 TCGCATTGCGGTAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
29971 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
29991 TCGCATTGCGAT
1 TCGCATTGCGAT
30003 AGTCCAAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.05
20 26 0.59
21 14 0.32
22 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:29970 original size:41 final size:41
Alignment explanation
Indices: 29925--30006 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
29915 CGCGAACTTT
*
29925 GACTATCGCATTGCGATTTACATATTCGCATTGCGGTAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
29966 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
30007 CAAGTTCGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (41 bp):
GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
Found at i:30041 original size:21 final size:21
Alignment explanation
Indices: 30015--30072 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
30005 TCCAAGTTCG
*
30015 CAAGTTCGCATTGCGATAGTC
1 CAAGTTCGCGTTGCGATAGTC
30036 CAAGTTCGCGTTGCGATAGTC
1 CAAGTTCGCGTTGCGATAGTC
*
30057 GAAGTTCGCGTTGCGA
1 CAAGTTCGCGTTGCGA
30073 ATATGAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (21 bp):
CAAGTTCGCGTTGCGATAGTC
Found at i:32561 original size:21 final size:21
Alignment explanation
Indices: 32524--32564 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32514 CAACGTTGAC
*
32524 GTGACAATTCACTATACTGAT
1 GTGACAATTCACGATACTGAT
32545 GTGACAATAT-ACGATACTGA
1 GTGACAAT-TCACGATACTGA
32565 CGTGGTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (21 bp):
GTGACAATTCACGATACTGAT
Found at i:35104 original size:21 final size:21
Alignment explanation
Indices: 35078--35127 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
35068 TACATATTCT
35078 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
35099 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
35120 CGTTGCGA
1 CATTGCGA
35128 ATCTGGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:46099 original size:51 final size:51
Alignment explanation
Indices: 46023--46126 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
46013 AATGATCCAT
46023 TGGCATAAAGAGTAAAGGAAAAACAGTAAGAGAACTTTTTACGTACTGGAA
1 TGGCATAAAGAGTAAAGGAAAAACAGTAAGAGAACTTTTTACGTACTGGAA
46074 TGGCATAAAGAGTAAAGGAAAAACAGTAAGAGAACTTTTTACGTACTGGAA
1 TGGCATAAAGAGTAAAGGAAAAACAGTAAGAGAACTTTTTACGTACTGGAA
46125 TG
1 TG
46127 ATCCAGATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (51 bp):
TGGCATAAAGAGTAAAGGAAAAACAGTAAGAGAACTTTTTACGTACTGGAA
Found at i:46514 original size:33 final size:33
Alignment explanation
Indices: 46477--46605 Score: 231
Period size: 33 Copynumber: 3.9 Consensus size: 33
46467 AGGTGGTGCA
*
46477 GGAGGACTGGCTCTAATGGGGGGAGGAGGTGGT
1 GGAGGACTGGCTCTAATGGGGGCAGGAGGTGGT
46510 GGAGGACTGGCTCTAATGGGGGCAGGAGGTGGT
1 GGAGGACTGGCTCTAATGGGGGCAGGAGGTGGT
46543 GGAGGACTGGCTCTAATGGGGGCAGGAGGTGGT
1 GGAGGACTGGCTCTAATGGGGGCAGGAGGTGGT
* *
46576 GGAGAACTGGCTCTAATTGGGGCAGGAGGT
1 GGAGGACTGGCTCTAATGGGGGCAGGAGGT
46606 TCCGGAGGAA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.19, C:0.12, G:0.50, T:0.19
Consensus pattern (33 bp):
GGAGGACTGGCTCTAATGGGGGCAGGAGGTGGT
Found at i:46613 original size:66 final size:66
Alignment explanation
Indices: 46471--46614 Score: 225
Period size: 66 Copynumber: 2.2 Consensus size: 66
46461 TTTAGGAGGT
* * *
46471 GGTGCAGGAGGACTGGCTCTAATGGGGGGAGGAGGTGGTGGAGGACTGGCTCTAATGGGGGCAGG
1 GGTGCCGGAGGACTGGCTCTAATGGGGGCAGGAGGTGGTGGAGAACTGGCTCTAATGGGGGCAGG
46536 A
66 A
** *
46537 GGTGGTGGAGGACTGGCTCTAATGGGGGCAGGAGGTGGTGGAGAACTGGCTCTAATTGGGGCAGG
1 GGTGCCGGAGGACTGGCTCTAATGGGGGCAGGAGGTGGTGGAGAACTGGCTCTAATGGGGGCAGG
46602 A
66 A
*
46603 GGTTCCGGAGGA
1 GGTGCCGGAGGA
46615 AGAGGGTCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.19, C:0.12, G:0.50, T:0.18
Consensus pattern (66 bp):
GGTGCCGGAGGACTGGCTCTAATGGGGGCAGGAGGTGGTGGAGAACTGGCTCTAATGGGGGCAGG
A
Found at i:50127 original size:60 final size:60
Alignment explanation
Indices: 50024--50139 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
50014 TTTCATCCCA
* * * *
50024 AAACTATGACCCTCGTTCTAAATTAGTCACCAGACTTTAAAATCTTACAATTTCATTCTC
1 AAACTATGACCCTCATTCTAAACTAGTCACCAAACATTAAAATCTTACAATTTCATTCTC
* * * *
50084 AAACTATGACCCTCATTCTAAACTGGTTC-CCAAACATTCAAATCTTTCAGTTTCAT
1 AAACTATGACCCTCATTCTAAACTAG-TCACCAAACATTAAAATCTTACAATTTCAT
50140 CAAAACATGC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (60 bp):
AAACTATGACCCTCATTCTAAACTAGTCACCAAACATTAAAATCTTACAATTTCATTCTC
Found at i:50377 original size:60 final size:60
Alignment explanation
Indices: 50313--50442 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
50303 AGGGTTATAG
* * *
50313 TTTGAGAA-AGAAATTAAAATGTTCAAAAGTTTACAGAAT-AATTTAAAATAAAAAACATAA
1 TTTGAGAATA-AAATCAAAATATTCAAAAATTT-CAGAATCAATTTAAAATAAAAAACATAA
* **
50373 TTTGAGAATAAAATCAAAATATTCAAAAATTTTAGAATCAATTTAAAATAAAACTCATAA
1 TTTGAGAATAAAATCAAAATATTCAAAAATTTCAGAATCAATTTAAAATAAAAAACATAA
*
50433 TTTAAGAATA
1 TTTGAGAATA
50443 TATGAATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
59 5 0.08
60 55 0.90
61 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (60 bp):
TTTGAGAATAAAATCAAAATATTCAAAAATTTCAGAATCAATTTAAAATAAAAAACATAA
Found at i:50420 original size:29 final size:28
Alignment explanation
Indices: 50326--50422 Score: 68
Period size: 29 Copynumber: 3.3 Consensus size: 28
50316 GAGAAAGAAA
* *
50326 TTAAAATGTTCAAAAGTTTACAGAATAAT
1 TTAAAATATTCAAAAATTT-CAGAATAAT
*** * *
50355 TTAAAATAAAAAACATAATTTGAGAATAAAA
1 TTAAAATATTCAA-A-AATTTCAGAAT-AAT
* *
50386 TCAAAATATTCAAAAATTTTAGAATCAAT
1 TTAAAATATTCAAAAATTTCAGAAT-AAT
50415 TTAAAATA
1 TTAAAATA
50423 AAACTCATAA
Statistics
Matches: 50, Mismatches: 15, Indels: 6
0.70 0.21 0.08
Matches are distributed among these distances:
29 28 0.56
30 7 0.14
31 15 0.30
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (28 bp):
TTAAAATATTCAAAAATTTCAGAATAAT
Found at i:51227 original size:136 final size:137
Alignment explanation
Indices: 51074--51344 Score: 454
Period size: 136 Copynumber: 2.0 Consensus size: 137
51064 GAGATATTTC
* * *
51074 ACATCTACATGATAATTTCGATTTCATCTTTTCGATGGTAATTATAATTAAAAATTTTCAAGTTC
1 ACATCCACATGATAATTTCGATCTCATCTTTTCGATGGTAATTATAATTAAAAATTTTCAAATTC
* * * *
51139 AACTCAAATCGAACAATCTATGTAGATAAATAAGATTATTGTTA-CGTTAAAAATTTTAAATTTA
66 AACTCAAATCGAACAATCTAAGTAGATAAATAAGATTATTGTTATCATTAAAAAATTCAAATTTA
51203 AATACTT
131 AATACTT
*
51210 ACATCCACATGATAATTTCGATCTCATCTTTTCGATGGTAATTATAATTAAAATTTTTCAAATTC
1 ACATCCACATGATAATTTCGATCTCATCTTTTCGATGGTAATTATAATTAAAAATTTTCAAATTC
*
51275 AACTCAAATCGAACAATCTAAGTAGTTAAATAAGATTATTGTTATCATTAAAAAATTCAAATTTA
66 AACTCAAATCGAACAATCTAAGTAGATAAATAAGATTATTGTTATCATTAAAAAATTCAAATTTA
51340 AATAC
131 AATAC
51345 AAGATTCATA
Statistics
Matches: 125, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
136 103 0.82
137 22 0.18
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (137 bp):
ACATCCACATGATAATTTCGATCTCATCTTTTCGATGGTAATTATAATTAAAAATTTTCAAATTC
AACTCAAATCGAACAATCTAAGTAGATAAATAAGATTATTGTTATCATTAAAAAATTCAAATTTA
AATACTT
Found at i:51864 original size:32 final size:32
Alignment explanation
Indices: 51814--51886 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
51804 ACTCGTCATA
* *
51814 TTAGGGTTTTTAAGATATTTAATG-TTTAGGGT
1 TTAGGGTTTGTAAAATATTTAA-GATTTAGGGT
51846 TTAGGGTTTGTAAAATATTTAAGATTTAGGGT
1 TTAGGGTTTGTAAAATATTTAAGATTTAGGGT
51878 TTAGGGTTT
1 TTAGGGTTT
51887 ACAAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 1 0.03
32 37 0.97
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (32 bp):
TTAGGGTTTGTAAAATATTTAAGATTTAGGGT
Found at i:51914 original size:33 final size:33
Alignment explanation
Indices: 51857--51921 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
51847 TAGGGTTTGT
* * *
51857 AAAATATTTAAGATTTAGGGTTTAGGGTTTACA
1 AAAATATTTAAGATTTAAGATTTAGGATTTACA
* *
51890 AAAATATTTAGGGTTTAAGATTTAGGATTTAC
1 AAAATATTTAAGATTTAAGATTTAGGATTTAC
51922 TAATTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (33 bp):
AAAATATTTAAGATTTAAGATTTAGGATTTACA
Found at i:60238 original size:21 final size:20
Alignment explanation
Indices: 60214--60370 Score: 163
Period size: 21 Copynumber: 7.5 Consensus size: 20
60204 TTGTACCAAG
60214 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGA-CATTCATCAA
*
60235 GACGAGAATGTCATTCATCAA
1 GACGAGAA-GACATTCATCAA
*
60256 GACGAGAATGCCATTCATCAA
1 GACGAGAA-GACATTCATCAA
*
60277 GACGAGAAGGCCATTCATCAA
1 GACGAGAA-GACATTCATCAA
60298 GACGAGAAGACTATTCATCAA
1 GACGAGAAGAC-ATTCATCAA
* * *
60319 GAAGAGAAGACCCTCCAT-AA
1 GACGAGAAGA-CATTCATCAA
* * *
60339 CGACGAGAAGACCTTCGTAAA
1 -GACGAGAAGACATTCATCAA
60360 GACGAGAAGAC
1 GACGAGAAGAC
60371 CACATCGCAT
Statistics
Matches: 121, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
20 20 0.17
21 99 0.82
22 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (20 bp):
GACGAGAAGACATTCATCAA
Found at i:60273 original size:42 final size:42
Alignment explanation
Indices: 60214--60368 Score: 181
Period size: 42 Copynumber: 3.7 Consensus size: 42
60204 TTGTACCAAG
* * *
60214 GACGAGAAGAGCATTCATCAAGACGAGAATGTCATTCATCAA
1 GACGAGAAGACCATTCATCAAGACGAGAAGGCCATTCATCAA
60256 GACGAGAATG-CCATTCATCAAGACGAGAAGGCCATTCATCAA
1 GACGAGAA-GACCATTCATCAAGACGAGAAGGCCATTCATCAA
* * * * *
60298 GACGAGAAGACTATTCATCAAGAAGAGAAGACCCTCCAT-AA
1 GACGAGAAGACCATTCATCAAGACGAGAAGGCCATTCATCAA
* *
60339 CGACGAGAAGACC-TTCGTAAAGACGAGAAG
1 -GACGAGAAGACCATTCATCAAGACGAGAAG
60369 ACCACATCGC
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 17 0.17
42 80 0.82
43 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (42 bp):
GACGAGAAGACCATTCATCAAGACGAGAAGGCCATTCATCAA
Found at i:62964 original size:6 final size:6
Alignment explanation
Indices: 62949--63043 Score: 63
Period size: 6 Copynumber: 15.2 Consensus size: 6
62939 AGAGAAATAT
*
62949 AGAAAG AGAAAA AG-AAA AGATAAA A-AAAA AGAAAA TA-AAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA AGAAAA -AGAAAA AGAAAA
* *
62996 TA-AAAA AGGAAA AGAAAG AGAAAA ATTGAAAA TGAGAAAA ATGAAAA
1 -AGAAAA AGAAAA AGAAAA AGAAAA A--GAAAA --AGAAAA A-GAAAA
63043 A
1 A
63044 AAAGAATGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
5 11 0.15
6 38 0.53
7 12 0.17
8 10 0.14
10 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (6 bp):
AGAAAA
Found at i:62973 original size:12 final size:11
Alignment explanation
Indices: 62928--63020 Score: 69
Period size: 12 Copynumber: 7.8 Consensus size: 11
62918 TTGACATCAT
*
62928 AAAGAGAAAGA
1 AAAGAAAAAGA
*
62939 AGAGAAATATAGA
1 AAAGAAA-A-AGA
62952 AAGAGAAAAAGA
1 AA-AGAAAAAGA
*
62964 AAAGATAAAAAA
1 AAAGA-AAAAGA
*
62976 AAAGAAAATAAA
1 AAAGAAAA-AGA
*
62988 AAAGAAAATAAA
1 AAAGAAAA-AGA
*
63000 AAAGGAAAAGA
1 AAAGAAAAAGA
63011 AAGAGAAAAA
1 AA-AGAAAAA
63021 TTGAAAATGA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
11 15 0.22
12 44 0.64
13 5 0.07
14 5 0.07
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.05
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:62990 original size:17 final size:17
Alignment explanation
Indices: 62958--63020 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
62948 TAGAAAGAGA
*
62958 AAAAGAAAAGATAAAAA-
1 AAAAGAAAA-AAAAAAAG
*
62975 AAAAGAAAATAAAAAAG
1 AAAAGAAAAAAAAAAAG
* *
62992 AAAATAAAAAAGGAAAAG
1 AAAAGAAAAAA-AAAAAG
63010 AAAGAGAAAAA
1 AAA-AGAAAAA
63021 TTGAAAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
16 5 0.14
17 18 0.49
18 8 0.22
19 6 0.16
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAAG
Found at i:63021 original size:25 final size:24
Alignment explanation
Indices: 62934--63021 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 24
62924 TCATAAAGAG
* * * *
62934 AAAGAAGAGAAATATAGAAAGAGAA
1 AAAGAAAAGAAAAATA-AAAAAGGA
*
62959 AAAGAAAAGATAAA-AAAAAA-GA
1 AAAGAAAAGAAAAATAAAAAAGGA
* *
62981 AAATAAAAAAGAAAATAAAAAAGGA
1 AAAGAAAAGA-AAAATAAAAAAGGA
63006 AAAGAAAGAGAAAAAT
1 AAAGAAA-AGAAAAAT
63022 TGAAAATGAG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
22 9 0.18
23 7 0.14
24 7 0.14
25 24 0.49
26 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (24 bp):
AAAGAAAAGAAAAATAAAAAAGGA
Found at i:63043 original size:16 final size:16
Alignment explanation
Indices: 63013--63042 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63003 GGAAAAGAAA
63013 GAGAAAAATTGAAAAT
1 GAGAAAAATTGAAAAT
63029 GAGAAAAA-TGAAAA
1 GAGAAAAATTGAAAA
63043 AAAAGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
GAGAAAAATTGAAAAT
Found at i:64523 original size:128 final size:127
Alignment explanation
Indices: 64293--64701 Score: 599
Period size: 128 Copynumber: 3.2 Consensus size: 127
64283 AAGTTGCGAT
* * * *
64293 ATGTTGTGGCACGGCTGAACCCACATTAGGTTGAGATTACAAGATTCAGAAGAAGAAGAAGGCAT
1 ATGTTGGGGCACGACTGAACCCACATTAGGTTGAGATGA-AAAATTCAGAAGAAGAAGAAGGCAT
* *
64358 GAAGAATAAGCCTTACAATCTGAGGTGATGGGACATTTTGAAGGCTCGTACCAGTATAAGATA
65 GAAGAATAAGCCTTACAATCTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
*
64421 ATGTTGGGGCATGACTGAACCCACATTAGGTTGAGATGATAAAATTCAGAAGAAGAAGAAGGCAT
1 ATGTTGGGGCACGACTGAACCCACATTAGGTTGAGATGA-AAAATTCAGAAGAAGAAGAAGGCAT
* * *
64486 GAAGAATAAGCCTTACAAACTAAGGTGATGGGGCATTTTGAAGGCCCGTACTAGTATAAGATA
65 GAAGAATAAGCCTTACAATCTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
* * **
64549 ATGTTGGGGCACGACTGAACCCACATCACGTTGAGATGAAAAGATTCAGACCAAG--G-AGGCAT
1 ATGTTGGGGCACGACTGAACCCACATTAGGTTGAGATGAAAA-ATTCAGAAGAAGAAGAAGGCAT
* * *
64611 GAAGAATGAGCCTTACAATTTGAGGTAATAGGGGCATTTTGAAAGGCCCGTACCAGTATAAGATA
65 GAAGAATAAGCCTTACAATCTGAGGTGAT-GGGGCATTTTG-AAGGCCCGTACCAGTATAAGATA
64676 ATGTTGGGGCACGACTGAACCCACAT
1 ATGTTGGGGCACGACTGAACCCACAT
64702 CATAATGAGA
Statistics
Matches: 256, Mismatches: 22, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
125 30 0.12
126 12 0.05
127 51 0.20
128 163 0.64
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (127 bp):
ATGTTGGGGCACGACTGAACCCACATTAGGTTGAGATGAAAAATTCAGAAGAAGAAGAAGGCATG
AAGAATAAGCCTTACAATCTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
Found at i:64773 original size:127 final size:126
Alignment explanation
Indices: 64348--64763 Score: 380
Period size: 128 Copynumber: 3.3 Consensus size: 126
64338 TCAGAAGAAG
* ** * * * *
64348 AAGAAGGCATGAAGAATAAGCCTTACAA-TCTGAGGTGAT-GGGACATTTTGAAGGCTCGTACCA
1 AAGAAGGCATGAAGAATGAGCCGCACAACTC-GAAGTAATAGGGGCATTTTGAAGGCCCGTACCA
* * *** * *
64411 GTATAAGATAATGTTGGGGCATGACTGAACCCACATTAGGTTGAGATGATAAA-ATTCAGAAGAA
65 GTATAAGATAATGTTGGGGCACGACTGAACCCACATCACAATGAGAT-AAAAAGATTC---AGAC
*
64475 G
126 C
* ** * *
64476 AAGAAGGCATGAAGAATAAGCCTTACAAACT--AAGGTGAT-GGGGCATTTTGAAGGCCCGTACT
1 AAGAAGGCATGAAGAATGAGCCGCAC-AACTCGAA-GTAATAGGGGCATTTTGAAGGCCCGTACC
** *
64538 AGTATAAGATAATGTTGGGGCACGACTGAACCCACATCACGTTGAGATGAAAAGATTCAGACC
64 AGTATAAGATAATGTTGGGGCACGACTGAACCCACATCACAATGAGATAAAAAGATTCAGACC
* ** * * *
64601 AAGGAGGCATGAAGAATGAGCCTTACAATTTGAGGTAATAGGGGCATTTTGAAAGGCCCGTACCA
1 AAGAAGGCATGAAGAATGAGCCGCACAACTCGAAGTAATAGGGGCATTTTG-AAGGCCCGTACCA
*
64666 GTATAAGATAATGTTGGGGCACGACTGAACCCACATCATAATGAGA-AAATAAGATTCAGACC
65 GTATAAGATAATGTTGGGGCACGACTGAACCCACATCACAATGAGATAAA-AAGATTCAGACC
** * *
64728 AAGAAGTTATTG-AGAATGAGTCGCGCAACTCGAAGT
1 AAGAAGGCA-TGAAGAATGAGCCGCACAACTCGAAGT
64764 GTCAGGGGCA
Statistics
Matches: 247, Mismatches: 31, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
124 3 0.01
125 31 0.13
126 14 0.06
127 94 0.38
128 102 0.41
129 2 0.01
130 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.22
Consensus pattern (126 bp):
AAGAAGGCATGAAGAATGAGCCGCACAACTCGAAGTAATAGGGGCATTTTGAAGGCCCGTACCAG
TATAAGATAATGTTGGGGCACGACTGAACCCACATCACAATGAGATAAAAAGATTCAGACC
Found at i:65682 original size:36 final size:36
Alignment explanation
Indices: 65450--65715 Score: 302
Period size: 36 Copynumber: 7.4 Consensus size: 36
65440 AGCAAAGTCA
* *
65450 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAACAAACC
1 ATCTTAAGCCTTCACCGGAGA-ATAGTGAAGCAAACC
* * *
65486 ATCTGAAGCCTTCACTGGAGAATAGTGAAGTAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
65522 ATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
65558 ATCTGAAGCCTTCACCGGAGAATAGGGAAGCAATCA
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* *
65594 ATCTGAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
65630 ATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
65666 ATCTTAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCC
1 ATCTTAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACC
*
65703 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
65716 TCAGAAGAGT
Statistics
Matches: 196, Mismatches: 31, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
35 3 0.02
36 179 0.91
37 14 0.07
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
Found at i:65696 original size:108 final size:108
Alignment explanation
Indices: 65450--65715 Score: 354
Period size: 108 Copynumber: 2.5 Consensus size: 108
65440 AGCAAAGTCA
* * * *
65450 ATCTTAAGCCTTCACCGAAGAGAAGTGAAACAAACCATCTGAAGCCTTCACTGGAGAATAGTGAA
1 ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACTGGAGAATAGTGAA
* * *
65515 GTAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
66 GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
* * * *
65558 ATCTGAAGCCTTCACCGGAGAA-TAGGGAAGCAATCAATCTGAAGCCTTCACTGGAGAATAGTGA
1 ATCTTAAGCCTTCACC-GAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACTGGAGAATAGTGA
* *
65622 AGCAAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
65 AGCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
* * * *
65666 ATCTTAAGTCTTCACCAAAAAGTAGTGAAGCAGATCCATTTTAAGCCTTC
1 ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCA-ATCCATCTGAAGCCTTC
65716 TCAGAAGAGT
Statistics
Matches: 134, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
107 3 0.02
108 114 0.85
109 17 0.13
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (108 bp):
ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACTGGAGAATAGTGAA
GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
Found at i:66165 original size:51 final size:52
Alignment explanation
Indices: 66085--66424 Score: 379
Period size: 51 Copynumber: 6.5 Consensus size: 52
66075 GTGAAGCAAA
* *
66085 TGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCAGTT
* * *
66136 TGAAGATGTTCGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCC-GTAAGA
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCAGT---T
* * * * *
66190 AGAAGATTTTTGAGTTCTATACTCCCTGAAGAAA-AAGGGAGCGAACCCAG-T
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCCAGTT
*
66241 TGAAGATGTTCAAGTTCTATACTCCTTAAAGAAAGAAGGGAGCGAACCCAG-T
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCCAGTT
66293 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCAGTT
* * * * * *
66344 TGAAGAGATGTTCGAGTTTTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTGT
1 TG-A-AGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCA-GT-T
66400 TGAAGATTGTTCGAG-TCTTATACTC
1 TGAAGA-TGTTCGAGTTC-TATACTC
66425 TCTGAAGAAA
Statistics
Matches: 248, Mismatches: 27, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
50 1 0.00
51 88 0.35
52 54 0.22
53 42 0.17
54 42 0.17
55 18 0.07
56 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (52 bp):
TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCAGTT
Found at i:66270 original size:105 final size:102
Alignment explanation
Indices: 66086--66394 Score: 388
Period size: 105 Copynumber: 3.0 Consensus size: 102
66076 TGAAGCAAAT
* *
66086 GAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGT
1 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGT
* *
66151 TCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAA
66 TCTATACTCCTTAAAGAAAGAAGGAGCGAACCC---AGAA
* * * * *
66191 GAAGATTTTTGAGTTCTATACTCCCTGAAGAAA-AAGGGAGCGAACCCAG-TTGAAGATGTTCAA
1 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCC-GTTTGAAGATGTTCGA
**
66254 GTTCTATACTCCTTAAAGAAAGAAGGGAGCGAACCCAGTT
64 GTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCCAGAA
66294 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTCGA
1 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTCGA
* * * * *
66359 GTTTTATACTCCCTAGAGAAATAGGGAGCGAACCCA
64 GTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCA
66395 TTTGTTGAAG
Statistics
Matches: 177, Mismatches: 20, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
102 1 0.01
103 45 0.25
104 17 0.10
105 102 0.58
106 12 0.07
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (102 bp):
GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGT
TCTATACTCCTTAAAGAAAGAAGGAGCGAACCCAGAA
Found at i:66423 original size:55 final size:55
Alignment explanation
Indices: 66191--66736 Score: 386
Period size: 55 Copynumber: 10.1 Consensus size: 55
66181 CCCGTAAGAA
* *
66191 GAAGATT-TTTGAGT-TCTATACTCCCTGAAGAAAAAGGGAGCGAACCCA---GTT
1 GAAGATTGTTCGAGTCT-TATACTCCCTGAAGAAATAGGGAGCGAACCCATTTGTT
* * * *
66242 GAAGA-TGTTCAAGT-TCTATACTCCTTAAAGAAAGAAGGGAGCGAACCCA---GTT
1 GAAGATTGTTCGAGTCT-TATACTCCCTGAAGAAA-TAGGGAGCGAACCCATTTGTT
* * * * * **
66294 GAAGA-TGTTCGAGT-TCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAA
1 GAAGATTGTTCGAGTCT-TATACTCCCTGAAGAAATAGGGAGCGAACCCATTTGTT
*
66348 G-AGA-TGTTCGAGTTTTATACTCCCT-AGAGAAATAGGGAGCGAACCCATTTGTT
1 GAAGATTGTTCGAGTCTTATACTCCCTGA-AGAAATAGGGAGCGAACCCATTTGTT
* * * * *
66401 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATAGTT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGA-ACCCATTTGTT
* * * * * ** *
66456 GAAGATTGTTCGGGTCTTATACTCTCTGAAGATATAGGGGGC-AGACACGGTCGTT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGA-ACCCATTTGTT
* * ** * *
66511 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGA-TTGAT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGC-GAACCCATTTGTT
* * * * * * *
66566 GAAGA-T-TACGGGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGA-ACCCATTTGTT
* * *
66619 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-AGA-CAAGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGA-ACCCA-TTTGTT
* *
66674 GAAGA-TGATTCAAGTCTTATAC-CCTCTGAAGAAATAGGGAGCGAACCCATTTTTCT
1 GAAGATTG-TTCGAGTCTTATACTCC-CTGAAGAAATAGGGAGCGAACCCATTTGT-T
66730 GAAGATT
1 GAAGATT
66737 TATTGAATTC
Statistics
Matches: 415, Mismatches: 56, Indels: 42
0.81 0.11 0.08
Matches are distributed among these distances:
50 1 0.00
51 40 0.10
52 52 0.13
53 83 0.20
54 13 0.03
55 214 0.52
56 10 0.02
57 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCGAACCCATTTGTT
Found at i:66604 original size:163 final size:163
Alignment explanation
Indices: 66414--66712 Score: 510
Period size: 163 Copynumber: 1.8 Consensus size: 163
66404 GATTGTTCGA
*
66414 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGGGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGAGTCTTATACT
* * * *
66479 CTCTGAAGATATAGGGGGCAGACACGGTCGTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGA
66 CTCTGAAGAAATAGGGGGCAGACAAGGTCGTTGAAGA-TGATTCAAGTCTTATACCCTCTGAAGA
66543 AATAGGGGGCAGATGCGATTGATGAAGATTACGG
130 AATAGGGGGCAGATGCGATTGATGAAGATTACGG
*
66577 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGAGTCTTATACT
* *
66642 CTCTGAAGAAATAGGGGGCAGACAAGTTTGTTGAAGATGATTCAAGTCTTATACCCTCTGAAGAA
66 CTCTGAAGAAATAGGGGGCAGACAAGGTCGTTGAAGATGATTCAAGTCTTATACCCTCTGAAGAA
66707 ATAGGG
131 ATAGGG
66713 AGCGAACCCA
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
162 2 0.02
163 125 0.98
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (163 bp):
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGAGTCTTATACT
CTCTGAAGAAATAGGGGGCAGACAAGGTCGTTGAAGATGATTCAAGTCTTATACCCTCTGAAGAA
ATAGGGGGCAGATGCGATTGATGAAGATTACGG
Found at i:76728 original size:31 final size:31
Alignment explanation
Indices: 76690--76938 Score: 419
Period size: 31 Copynumber: 8.0 Consensus size: 31
76680 CCCGAAGGAC
* * * *
76690 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
76721 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
76752 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
76783 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
76814 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
76845 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
76876 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
76907 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
76938 C
1 C
76939 CCTCGACCCT
Statistics
Matches: 208, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 207 1.00
32 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:77513 original size:19 final size:21
Alignment explanation
Indices: 77471--77513 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
77461 TTCATAATCA
77471 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
77492 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
77511 CAT
1 CAT
77514 CATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:77522 original size:22 final size:20
Alignment explanation
Indices: 77477--77523 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
77467 ATCACATATT
*
77477 CATATAGTTTATTATCATAT
1 CATATAGTTTATTATCATAA
*
77497 CATATGGTTTATATCATCATAA
1 CATATAGTTTAT-T-ATCATAA
77519 CATAT
1 CATAT
77524 CACATATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATATAGTTTATTATCATAA
Found at i:77911 original size:22 final size:21
Alignment explanation
Indices: 77886--77927 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
77876 TTTTCCTTTA
77886 GGGGGAATCGGTTCCCTCCTGT
1 GGGGGAATCGGTTCCC-CCTGT
*
77908 GGGGGTATCGGTTCCCCCTG
1 GGGGGAATCGGTTCCCCCTG
77928 GACATTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.07, C:0.29, G:0.38, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCCTGT
Found at i:82439 original size:16 final size:16
Alignment explanation
Indices: 82418--82450 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
82408 TTTTATAGAA
82418 TAAAATAA-TTACATTT
1 TAAAATAACTTA-ATTT
82434 TAAAATAACTTAATTT
1 TAAAATAACTTAATTT
82450 T
1 T
82451 GTTTATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATAACTTAATTT
Found at i:83232 original size:15 final size:15
Alignment explanation
Indices: 83212--83246 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
83202 GGTAGTTAGT
*
83212 GGGCGAGCGGATGCA
1 GGGCGAGCAGATGCA
*
83227 GGGCGAGCAGATGTA
1 GGGCGAGCAGATGCA
83242 GGGCG
1 GGGCG
83247 GGTAAGGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.54, T:0.09
Consensus pattern (15 bp):
GGGCGAGCAGATGCA
Found at i:87833 original size:20 final size:19
Alignment explanation
Indices: 87810--87859 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
87800 TGTGCCAACA
* *
87810 GTATCGATATTGACCCTTGG
1 GTATCGATACTCACCC-TGG
87830 GTATCGATACTCACCCTGG
1 GTATCGATACTCACCCTGG
*
87849 ATATCGATACT
1 GTATCGATACT
87860 GAAAATAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (19 bp):
GTATCGATACTCACCCTGG
Found at i:87855 original size:19 final size:20
Alignment explanation
Indices: 87811--87859 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
87801 GTGCCAACAG
* * *
87811 TATCGATATTGACCCTTGGG
1 TATCGATACTCACCCTTGGA
87831 TATCGATACTCACCC-TGGA
1 TATCGATACTCACCCTTGGA
87850 TATCGATACT
1 TATCGATACT
87860 GAAAATAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (20 bp):
TATCGATACTCACCCTTGGA
Found at i:90911 original size:20 final size:20
Alignment explanation
Indices: 90888--90960 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
90878 GATTTCAACT
*
90888 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * **
90908 ATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGAAAT-GAAAA
90929 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
90949 AACGCAACGCGA
1 ATCGCAACGCGA
90961 TTTTCAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.41, C:0.27, G:0.21, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:90932 original size:41 final size:41
Alignment explanation
Indices: 90883--90975 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
90873 GTTGCGATTT
* *
90883 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGAAAAAACGCAACGCGATCTC
* *
90924 CAACTATCGCAACGCGAAATGAAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGAAAAAACGCAACGCGATCTC
90965 CAACTATCGCA
1 CAACTATCGCA
90976 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGAAAAAACGCAACGCGATCTC
Found at i:91178 original size:31 final size:31
Alignment explanation
Indices: 91138--91196 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
91128 ACACATCAGC
* *
91138 TTAATAATTCATTCTAAATTTATATACTAAT
1 TTAAAAATTCATTCTAAATTCATATACTAAT
* *
91169 TTAAAAATTCTTTTTAAATTCATATACT
1 TTAAAAATTCATTCTAAATTCATATACT
91197 GATTATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAAAAATTCATTCTAAATTCATATACTAAT
Found at i:91207 original size:2 final size:2
Alignment explanation
Indices: 91200--91224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91190 ATATACTGAT
91200 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 T
91225 CAAATTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92002 original size:2 final size:2
Alignment explanation
Indices: 91997--92046 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
91987 TTTTTAGAAA
91997 AT 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 AT
92039 AT AT AT AT
1 AT AT AT AT
92047 TAAAAGTGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92563 original size:21 final size:21
Alignment explanation
Indices: 92506--92564 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
92496 GGTTTTATGC
* * *
92506 TTTATGATTTAGGATTTGAGA
1 TTTAAGATTTTGGGTTTGAGA
* *
92527 TTT-GGAGTTTGAGGTTTGAGA
1 TTTAAGATTTTG-GGTTTGAGA
92548 TTTAAGATTTTGGGTTT
1 TTTAAGATTTTGGGTTT
92565 ACTGCGAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 5 0.17
21 19 0.63
22 6 0.20
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (21 bp):
TTTAAGATTTTGGGTTTGAGA
Found at i:93279 original size:11 final size:12
Alignment explanation
Indices: 93255--93279 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
93245 GGGGGTTTGA
93255 TTTTAGGGATTT
1 TTTTAGGGATTT
93267 TTTTAGGGATTT
1 TTTTAGGGATTT
93279 T
1 T
93280 CCATTTCTGA
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:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTTTAGGGATTT
Found at i:94877 original size:2 final size:2
Alignment explanation
Indices: 94872--94902 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
94862 ATTGATAAAT
94872 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
94903 TGTAAAAGTT
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:94947 original size:31 final size:30
Alignment explanation
Indices: 94909--95018 Score: 127
Period size: 31 Copynumber: 3.6 Consensus size: 30
94899 ATATTGTAAA
94909 AGTTTGATAAATTTAATGATCATTTTATAAT
1 AGTTTGATAAATTTAATGAT-ATTTTATAAT
*
94940 AGTTTGATAAATATAATGATGATTTTATAAT
1 AGTTTGATAAATTTAATGAT-ATTTTATAAT
* **
94971 AGATCAATAAATTTAATGATAGTTTTATAACT
1 AGTTTGATAAATTTAATGATA-TTTTATAA-T
95003 --TTTGA-AAATTTAATGA
1 AGTTTGATAAATTTAATGA
95019 CCTTTAATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
29 11 0.16
30 3 0.04
31 53 0.78
32 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (30 bp):
AGTTTGATAAATTTAATGATATTTTATAAT
Found at i:95473 original size:12 final size:12
Alignment explanation
Indices: 95452--95507 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
95442 GAACGAGCTC
*
95452 ATAAATGAACTT
1 ATAAACGAACTT
95464 ATAAACGAACTT
1 ATAAACGAACTT
** *
95476 ATGGATGAACTT
1 ATAAACGAACTT
* *
95488 ATAAACGAGCTC
1 ATAAACGAACTT
95500 ATAAACGA
1 ATAAACGA
95508 GTTTGTTTGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (12 bp):
ATAAACGAACTT
Found at i:97929 original size:18 final size:17
Alignment explanation
Indices: 97888--97931 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
97878 TCACGTTAAT
97888 TTTTTTTAAATAAAATA
1 TTTTTTTAAATAAAATA
97905 TTATTTTTAAA-AAATATAA
1 TT-TTTTTAAATAAA-AT-A
97924 TTTTTTTA
1 TTTTTTTA
97932 TTAGACACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 16 0.67
19 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTTTAAATAAAATA
Found at i:100579 original size:23 final size:23
Alignment explanation
Indices: 100529--100579 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
100519 TTGTCAAACA
100529 TTAAACAAACATGTCTACGAACG
1 TTAAACAAACATGTCTACGAACG
* *
100552 CTAAACAAACATGT-TCATGAACG
1 TTAAACAAACATGTCT-ACGAACG
100575 TTAAA
1 TTAAA
100580 TGAATAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (23 bp):
TTAAACAAACATGTCTACGAACG
Found at i:104720 original size:20 final size:20
Alignment explanation
Indices: 104645--104723 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
104635 GATATTGATT
* * *
104645 AAATATTTTAGAATATGATG
1 AAATATTTTATAACATTATG
**
104665 AAA-AGTTTTATAACACCAT-
1 AAATA-TTTTATAACATTATG
104684 AGAATATTTTATAACATTATG
1 A-AATATTTTATAACATTATG
104705 AAATATTTTATAACATTAT
1 AAATATTTTATAACATTAT
104724 TGATTATCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 2 0.04
20 45 0.92
21 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (20 bp):
AAATATTTTATAACATTATG
Found at i:106370 original size:58 final size:60
Alignment explanation
Indices: 106264--106378 Score: 153
Period size: 58 Copynumber: 1.9 Consensus size: 60
106254 CATGTGAATA
* * * * *
106264 TTTTGTAACTTTTAATAGTCGATATACTCAACAAAGCAACATCCTATAGTCGGAGGATTG
1 TTTTGTAACTTTTAATAGACGAGAGACTCAACAAAGCAAAATCATATAGTCGGAGGATTG
* *
106324 TTTTGTAA-TTTTAATAGAC-AGAGACTCAACAAAGTAAAATTATATAGTCGGAGGA
1 TTTTGTAACTTTTAATAGACGAGAGACTCAACAAAGCAAAATCATATAGTCGGAGGA
106379 CTATTTACAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 30 0.62
59 10 0.21
60 8 0.17
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (60 bp):
TTTTGTAACTTTTAATAGACGAGAGACTCAACAAAGCAAAATCATATAGTCGGAGGATTG
Found at i:113659 original size:2 final size:2
Alignment explanation
Indices: 113652--113685 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
113642 CTTAAACCCA
113652 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
113686 TGAAGGCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114999 original size:18 final size:19
Alignment explanation
Indices: 114976--115018 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
114966 CAGTAATCCT
114976 ATTCC-CTAGTAATCTTAC
1 ATTCCACTAGTAATCTTAC
*
114994 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTAGTAATCTTAC
115014 ATTCC
1 ATTCC
115019 GTAAACCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTAGTAATCTTAC
Found at i:137242 original size:30 final size:29
Alignment explanation
Indices: 137206--137263 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
137196 GTGATCGAAC
137206 AAAGTGTCATTAATGCAGAAAAAAATAATT
1 AAAGTGTCATTAATGCAG-AAAAAATAATT
*
137236 AAAGTGTTATTAATGCAGAAAAAATAAT
1 AAAGTGTCATTAATGCAGAAAAAATAAT
137264 GTGAAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (29 bp):
AAAGTGTCATTAATGCAGAAAAAATAATT
Done.