Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002595.1 Hibiscus syriacus cultivar Beakdansim tig00005251_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: 104725
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6820 original size:8 final size:9
Alignment explanation
Indices: 6802--6843 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
6792 TATATTTTTG
6802 TTTTTATTT
1 TTTTTATTT
6811 TTTTTATTT
1 TTTTTATTT
6820 TTCGTTT-TATT
1 TT--TTTAT-TT
6831 TTTTTATTT
1 TTTTTATTT
6840 TTTT
1 TTTT
6844 AGCGAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 20 0.69
10 2 0.07
11 7 0.24
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTATTT
Found at i:6842 original size:21 final size:21
Alignment explanation
Indices: 6794--6841 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
6784 CATTTCGTTA
6794 TATTTTT-GTTTTTATTTTTTT
1 TATTTTTCG-TTTTATTTTTTT
6815 TATTTTTCGTTTTA-TTTTTT
1 TATTTTTCGTTTTATTTTTTT
6835 TATTTTT
1 TATTTTT
6842 TTAGCGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.50
21 12 0.46
22 1 0.04
ACGTcount: A:0.10, C:0.02, G:0.04, T:0.83
Consensus pattern (21 bp):
TATTTTTCGTTTTATTTTTTT
Found at i:6982 original size:28 final size:28
Alignment explanation
Indices: 6942--7031 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 28
6932 GAAAAAAACA
6942 GTGCAGAAAAATTGACTTGGTTCGAACT
1 GTGCAGAAAAATTGACTTGGTTCGAACT
** *
6970 GTGCAGAAAAATT--C---GAACAGAACA
1 GTGCAGAAAAATTGACTTGGTTC-GAACT
** *
6994 GTGCAGAAAAACAGATTTGGTTCGAACT
1 GTGCAGAAAAATTGACTTGGTTCGAACT
7022 GTGCAGAAAA
1 GTGCAGAAAA
7032 GTTCGAACAG
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
23 2 0.04
24 15 0.32
26 1 0.02
28 27 0.57
29 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (28 bp):
GTGCAGAAAAATTGACTTGGTTCGAACT
Found at i:7014 original size:52 final size:52
Alignment explanation
Indices: 6938--7050 Score: 190
Period size: 52 Copynumber: 2.2 Consensus size: 52
6928 ACGGGAAAAA
**
6938 AACAGTGCAGAAAAATTGACTTGGTTCGAACTGTGCAGAAAAATTCGAACAG
1 AACAGTGCAGAAAAACAGACTTGGTTCGAACTGTGCAGAAAAATTCGAACAG
* *
6990 AACAGTGCAGAAAAACAGATTTGGTTCGAACTGTGCAGAAAAGTTCGAACAG
1 AACAGTGCAGAAAAACAGACTTGGTTCGAACTGTGCAGAAAAATTCGAACAG
7042 AACAGTGCA
1 AACAGTGCA
7051 TCATCGGACA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (52 bp):
AACAGTGCAGAAAAACAGACTTGGTTCGAACTGTGCAGAAAAATTCGAACAG
Found at i:7044 original size:24 final size:24
Alignment explanation
Indices: 6965--7050 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 24
6955 GACTTGGTTC
* *
6965 GAACTGTGCAGAAAAATTCGAACA
1 GAACAGTGCAGAAAAGTTCGAACA
* **
6989 GAACAGTGCAGAAAAACAGATTTGGTTC-
1 GAACAGTGCAG--AAA-AG--TTCGAACA
*
7017 GAACTGTGCAGAAAAGTTCGAACA
1 GAACAGTGCAGAAAAGTTCGAACA
7041 GAACAGTGCA
1 GAACAGTGCA
7051 TCATCGGACA
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
23 4 0.09
24 19 0.41
25 2 0.04
26 6 0.13
27 1 0.02
28 10 0.22
29 4 0.09
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (24 bp):
GAACAGTGCAGAAAAGTTCGAACA
Found at i:8683 original size:76 final size:75
Alignment explanation
Indices: 8592--8756 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
8582 TTAAACTCAA
*
8592 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTATGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTATGTATTTTAGTTTAAATAGG-TTTTAGT
8656 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * * *
8668 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTATGTATTTTAGTTTAAATAGGTTTTAGTAT
*
8733 TTTAATTAGG
66 TTTAATTAAG
*
8743 ATTTAGAATATTAT
1 ATTTAGGATATTAT
8757 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 37 0.47
76 42 0.53
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTATGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:8742 original size:19 final size:19
Alignment explanation
Indices: 8714--8776 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
8704 TGTATTTTAG
*
8714 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
8733 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
8752 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
8773 TTTA
1 TTTA
8777 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:9413 original size:21 final size:22
Alignment explanation
Indices: 9388--9428 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9378 CTTTAATTTG
9388 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
9409 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
9429 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:19585 original size:4 final size:4
Alignment explanation
Indices: 19576--19639 Score: 128
Period size: 4 Copynumber: 16.0 Consensus size: 4
19566 AAGAACCCTG
19576 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
19624 GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT
19640 ATGTGACTTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:19753 original size:24 final size:24
Alignment explanation
Indices: 19726--19775 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
19716 TCGATGATCG
19726 ATTTAACCTCAAGATAATGTGTGT
1 ATTTAACCTCAAGATAATGTGTGT
19750 ATTTAACCTCAAGATAATGTGTGT
1 ATTTAACCTCAAGATAATGTGTGT
19774 AT
1 AT
19776 AGCATAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (24 bp):
ATTTAACCTCAAGATAATGTGTGT
Found at i:28377 original size:42 final size:42
Alignment explanation
Indices: 28318--28432 Score: 194
Period size: 42 Copynumber: 2.7 Consensus size: 42
28308 TGGACACCAA
* * *
28318 GTGTTTGTTTCACGTAATTCATTTTTCGGAAAATATTTTCTC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCTC
*
28360 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCTC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCTC
28402 GTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAA
28433 TGTAATTCAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCTC
Found at i:28668 original size:22 final size:23
Alignment explanation
Indices: 28621--28681 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
28611 TAATTATTAA
* *
28621 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
28642 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
28665 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
28682 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:28697 original size:31 final size:32
Alignment explanation
Indices: 28632--28710 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
28622 ATATTTAAAA
28632 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
*
28664 TATATTT-TTAATA-TTAT-ATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
28695 TATATTATAATAATAT
1 TATATT-TATTAATAT
28711 AAGATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 9 0.22
30 4 0.10
31 14 0.35
32 8 0.20
33 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:28744 original size:54 final size:52
Alignment explanation
Indices: 28647--28749 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 52
28637 TTATTAATAT
*
28647 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
*
28699 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
28750 TTTTTTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 16 0.36
53 7 0.16
54 22 0.49
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:29043 original size:20 final size:20
Alignment explanation
Indices: 28965--29034 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
28955 TTTCCAGATG
28965 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
28985 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
29005 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
29025 TTTTCCAGAA
1 TTTTCCAGAA
29035 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:29043 original size:40 final size:40
Alignment explanation
Indices: 28965--29043 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
28955 TTTCCAGATG
* **
28965 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
29005 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
29044 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:29053 original size:15 final size:15
Alignment explanation
Indices: 29017--29098 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
29007 TTACAGAAAT
**
29017 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
29032 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
29046 GTAATTCATTTTCTA
1 GTAATTCAAATTCCA
29061 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
29076 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
29091 GTAATTCA
1 GTAATTCA
29099 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:29069 original size:30 final size:30
Alignment explanation
Indices: 29017--29098 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
29007 TTACAGAAAT
29017 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
29046 GTAATTCATTTTCTAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
29076 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
29099 TTTTCTGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:29091 original size:45 final size:44
Alignment explanation
Indices: 29017--29104 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
29007 TTACAGAAAT
**
29017 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCTA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCTA
29061 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTCT
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTCT
29105 GGAAAACCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.34
45 27 0.66
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCTA
Found at i:30386 original size:21 final size:20
Alignment explanation
Indices: 30362--30422 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
30352 GCAAATGCGC
30362 GTTGCATTTCGCGTTGCGAT
1 GTTGCATTTCGCGTTGCGAT
* *
30382 AGTTGGAAATT-GCGTTGCGAT
1 -GTT-GCATTTCGCGTTGCGAT
* *
30403 TTTCCATTTCGCGTTGCGAT
1 GTTGCATTTCGCGTTGCGAT
30423 TTTCCTTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 13 0.41
22 4 0.12
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.39
Consensus pattern (20 bp):
GTTGCATTTCGCGTTGCGAT
Found at i:30418 original size:20 final size:20
Alignment explanation
Indices: 30393--30433 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
30383 GTTGGAAATT
30393 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
*
30413 GCGTTGCGATTTTCCTTTTC
1 GCGTTGCGATTTTCCATTTC
30433 G
1 G
30434 TGTTCCGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.24, G:0.22, T:0.46
Consensus pattern (20 bp):
GCGTTGCGATTTTCCATTTC
Found at i:30442 original size:20 final size:20
Alignment explanation
Indices: 30393--30442 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
30383 GTTGGAAATT
*
30393 GCGTTGCGATTTTCCATTTC
1 GCGTTCCGATTTTCCATTTC
* *
30413 GCGTTGCGATTTTCCTTTTC
1 GCGTTCCGATTTTCCATTTC
*
30433 GTGTTCCGAT
1 GCGTTCCGAT
30443 AGTCTACAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.08, C:0.24, G:0.22, T:0.46
Consensus pattern (20 bp):
GCGTTCCGATTTTCCATTTC
Found at i:30555 original size:5 final size:5
Alignment explanation
Indices: 30536--30568 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
30526 CGTATTACCA
30536 CGACC ACGA-C CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGA
30569 GACGGCGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.24, C:0.55, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:31404 original size:6 final size:6
Alignment explanation
Indices: 31388--31419 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
31378 TATTTTCTCG
31388 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
31420 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:31538 original size:41 final size:41
Alignment explanation
Indices: 31481--31588 Score: 162
Period size: 46 Copynumber: 2.5 Consensus size: 41
31471 CTTAAGAAAC
31481 AAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATGG
1 AAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATGG
*
31522 AAAATCGCAACGACACTGTAGTGTAGACTATCGTAACGCGAAATGG
1 AAAATCGCAACGACAC-----TGTAGACTATCGCAACGCGAAATGG
31568 AAAATCGCAACGACACTGTAG
1 AAAATCGCAACGACACTGTAG
31589 TGTAGACTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
41 21 0.34
46 40 0.66
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (41 bp):
AAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATGG
Found at i:31564 original size:46 final size:46
Alignment explanation
Indices: 31497--31608 Score: 215
Period size: 46 Copynumber: 2.4 Consensus size: 46
31487 GCAACGACAC
31497 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
31543 TGTAGACTATCGTAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
31589 TGTAGACTATCGCAACGCGA
1 TGTAGACTATCGCAACGCGA
31609 TTTTCAACTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (46 bp):
TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:31620 original size:21 final size:20
Alignment explanation
Indices: 31594--31856 Score: 92
Period size: 21 Copynumber: 12.8 Consensus size: 20
31584 TGTAGTGTAG
*
31594 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTT-A
**
31615 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCG-AATTTA
* * *
31636 A-AATCGCAACGAC-ACTGTA
1 ACTATCGCAACG-CGAATTTA
* *
31655 GACTATCACAACGCGATTTTCA
1 -ACTATCGCAACGCGAATTT-A
* *
31677 ACTATCGCAACGAC-ACTGTA
1 ACTATCGCAACG-CGAATTTA
* **
31697 GACTATCGCAACGTGAAATGGA
1 -ACTATCGCAACGCG-AATTTA
* * *
31719 A-AATCGCAACGAC-ACTGTA
1 ACTATCGCAACG-CGAATTTA
**
31738 CACTATCGCAACGCGAAATGGA
1 -ACTATCGCAACGCG-AATTTA
* *
31760 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTT-A
* *
31780 ACTATCGCAACGCGAAATGA
1 ACTATCGCAACGCGAATTTA
* *
31800 A-AATCGCAACGAC-AATGTA
1 ACTATCGCAACG-CGAATTTA
* *
31819 GACTATCGCGACGCGATTTTCA
1 -ACTATCGCAACGCGAATTT-A
*
31841 ACTATCGCAATGCGAA
1 ACTATCGCAACGCGAA
31857 ATGTAACGTG
Statistics
Matches: 178, Mismatches: 42, Indels: 44
0.67 0.16 0.17
Matches are distributed among these distances:
19 22 0.12
20 41 0.23
21 102 0.57
22 13 0.07
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTATCGCAACGCGAATTTA
Found at i:31660 original size:41 final size:41
Alignment explanation
Indices: 31615--31834 Score: 284
Period size: 41 Copynumber: 5.4 Consensus size: 41
31605 GCGATTTTCA
31615 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* ** ** *
31656 ACTATCACAACGCGATTTTCAACTATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAA-AATCGCAACGACACTGTAG
* *
31698 ACTATCGCAACGTGAAATGGAAAATCGCAACGACACTGTAC
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* *
31739 ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTGT-AG
*
31780 ACTATCGCAACGCGAAAT-GAAAATCGCAACGACAATGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
31820 ACTATCGCGACGCGA
1 ACTATCGCAACGCGA
31835 TTTTCAACTA
Statistics
Matches: 154, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 31 0.20
41 87 0.56
42 35 0.23
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:31686 original size:62 final size:63
Alignment explanation
Indices: 31548--31688 Score: 221
Period size: 62 Copynumber: 2.2 Consensus size: 63
31538 TGTAGTGTAG
* *
31548 ACTATCGTAACGCGAAATGGAAAATCGCAACGACACTGTAGTGTAGACTATCGCAACGCGATTTT
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACAC----GTGTAGACTATCACAACGCGATTTT
31613 CA
62 CA
31615 ACTATCGCAACGCGAAATGGAAAATCGCAACGACAC-TGTAGACTATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACGTGTAGACTATCACAACGCGATTTTCA
31677 ACTATCGCAACG
1 ACTATCGCAACG
31689 ACACTGTAGA
Statistics
Matches: 72, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
62 37 0.51
67 35 0.49
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (63 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACGTGTAGACTATCACAACGCGATTTTCA
Found at i:31726 original size:20 final size:20
Alignment explanation
Indices: 31701--31810 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
31691 ACTGTAGACT
*
31701 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
31721 ATCGCAA--CGACACTGTACACT
1 ATCGCAACGCGA-AATGGA-A-A
31742 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
31762 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
31783 ATCGCAACGCGAAAT-GAAA
1 ATCGCAACGCGAAATGGAAA
31802 ATCGCAACG
1 ATCGCAACG
31811 ACAATGTAGA
Statistics
Matches: 68, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
18 2 0.03
19 13 0.19
20 25 0.37
21 21 0.31
22 4 0.06
23 3 0.04
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:31733 original size:83 final size:83
Alignment explanation
Indices: 31594--31855 Score: 343
Period size: 83 Copynumber: 3.2 Consensus size: 83
31584 TGTAGTGTAG
* *
31594 ACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACT
1 ACTATCGCAACGCGACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACT
*
31659 ATCACAACGCGATTTTCA
66 ATCGCAACGCGATTTTCA
* *
31677 ACTATCGCAACGAC-ACTGT-AGACTATCGCAACGTGAAATGGAAAATCGCAACGACACTGTACA
1 ACTATCGCAACG-CGACTGTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGA
** **
31740 CTATCGCAACGCGAAATGGA
64 CTATCGCAACGCGATTTTCA
* * * *
31760 A-AATCGCAACGCGATTTTCAACTATCGCAACGCGAAAT-GAAAATCGCAACGACAATGTAGACT
1 ACTATCGCAACGCGACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACT
*
31823 ATCGCGACGCGATTTTCA
66 ATCGCAACGCGATTTTCA
*
31841 ACTATCGCAATGCGA
1 ACTATCGCAACGCGA
31856 AATGTAACGT
Statistics
Matches: 152, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
81 38 0.25
82 41 0.27
83 72 0.47
84 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (83 bp):
ACTATCGCAACGCGACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACT
ATCGCAACGCGATTTTCA
Found at i:38162 original size:60 final size:61
Alignment explanation
Indices: 38039--38176 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 61
38029 AACAAAATGA
* * * * *
38039 ATAGTCGG-GTGACCA-ATTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAATGTCCT
1 ATAGTCGGAG-GACCATTTTTATAACTTTTAACAATCGAGAGACTCAACAAAACAATATCCT
* * * *
38099 ATAGTCGGAGGACCATTTTTATAATTTTTAACAATTGAG-GACTCAACAAAATAATATCTT
1 ATAGTCGGAGGACCATTTTTATAACTTTTAACAATCGAGAGACTCAACAAAACAATATCCT
* *
38159 ATAGTAGGAAGACCATTT
1 ATAGTCGGAGGACCATTT
38177 ATGTACTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 46 0.71
61 19 0.29
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (61 bp):
ATAGTCGGAGGACCATTTTTATAACTTTTAACAATCGAGAGACTCAACAAAACAATATCCT
Found at i:52349 original size:20 final size:20
Alignment explanation
Indices: 52326--52415 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
52316 GAATATATAA
* *
52326 ATCGCAATATGATTATGACT
1 ATCGCAACACGATTATGACT
* *
52346 ATCGCAACGCGATTCTGACT
1 ATCGCAACACGATTATGACT
* *
52366 ATCGCAACGA-GATTCTGACC
1 ATCGCAAC-ACGATTATGACT
* *
52386 ATCGCAACGCGATTCTGACT
1 ATCGCAACACGATTATGACT
*
52406 GTCGCAACAC
1 ATCGCAACAC
52416 TGAATTTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACACGATTATGACT
Found at i:52370 original size:40 final size:40
Alignment explanation
Indices: 52336--52413 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
52326 ATCGCAATAT
*
52336 GATTATGACTATCGCAACGCGATTCTGACTATCGCAACGA
1 GATTATGACCATCGCAACGCGATTCTGACTATCGCAACGA
* *
52376 GATTCTGACCATCGCAACGCGATTCTGACTGTCGCAAC
1 GATTATGACCATCGCAACGCGATTCTGACTATCGCAAC
52414 ACTGAATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GATTATGACCATCGCAACGCGATTCTGACTATCGCAACGA
Found at i:55558 original size:18 final size:18
Alignment explanation
Indices: 55535--55569 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55525 AGAAAAAGGC
55535 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
55553 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
55570 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:55881 original size:140 final size:140
Alignment explanation
Indices: 55629--55898 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
55619 AAACGTTGTA
*
55629 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTA
*
55694 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
55759 TATGTGTATT
131 TATGTGTATT
55769 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTA
55834 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
55899 CGCAACGCGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACAATGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:55894 original size:20 final size:20
Alignment explanation
Indices: 55869--56073 Score: 175
Period size: 20 Copynumber: 10.8 Consensus size: 20
55859 TTACACATTC
*
55869 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
55889 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
55909 ATTTGATTATCGTAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
55928 A----A-AATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
55943 ATTTGACTCTCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
55963 ATTTGATTACCGCAACAG-GT
1 ATTTGACTATCGCAAC-GCGA
*
55983 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
56003 A----A--ATAGCAACGCGA
1 ATTTGACTATCGCAACGCGA
56017 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
56037 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
56057 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
56074 AGAAAATCGC
Statistics
Matches: 146, Mismatches: 25, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
14 18 0.12
15 3 0.02
16 1 0.01
18 1 0.01
19 4 0.03
20 118 0.81
21 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:55994 original size:74 final size:73
Alignment explanation
Indices: 55869--56122 Score: 307
Period size: 74 Copynumber: 3.5 Consensus size: 73
55859 TTACACATTC
* * * * *
55869 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGTAACTCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACG-GTATTTGACTATCGCAAC-CAGAAAAT
*
55933 TGCAACGCGA
64 AGCAACGCGA
* * *
55943 ATTTGACTCTCGCAACGCGAATTTGATTACCGCAACAGGTATTTGACTATCGCAACGAGAAAATA
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-GGTATTTGACTATCGCAACCAGAAAATA
56008 GCAACGCGA
65 GCAACGCGA
* *
56017 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-GGTATTTGACTATCGCAACCAGAAAATA
*
56082 GCAAAGC-A
65 GCAACGCGA
* * *
56090 TATTAGACTATCGCAACGTGAA-TTGATTTTCGC
1 -ATTTGACTATCGCAACGCGAATTTGATTATCGC
56123 GTTGCGATTT
Statistics
Matches: 160, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
73 12 0.08
74 147 0.92
75 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (73 bp):
ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGTATTTGACTATCGCAACCAGAAAATAG
CAACGCGA
Found at i:56142 original size:20 final size:20
Alignment explanation
Indices: 56117--56189 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
56107 GTGAATTGAT
*
56117 TTTCGCGTTGCGATTTTGTC
1 TTTCGCATTGCGATTTTGTC
*
56137 TTTCGCATTACGATTTTGTC
1 TTTCGCATTGCGATTTTGTC
*
56157 TTTTGCATTGCGATTTTGTC
1 TTTCGCATTGCGATTTTGTC
*
56177 TTTCGCGTTGCGA
1 TTTCGCATTGCGA
56190 AAGTGTGCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTGTC
Found at i:56330 original size:14 final size:14
Alignment explanation
Indices: 56270--56331 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
56260 CACAAATAAG
*
56270 AATTATTTACACATC
1 AATT-TTTACAAATC
**
56285 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
56300 AACTTTTACAAATC
1 AATTTTTACAAATC
*
56314 AATTTTTATAAATC
1 AATTTTTACAAATC
56328 AATT
1 AATT
56332 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:57808 original size:18 final size:19
Alignment explanation
Indices: 57785--57826 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
57775 CTTGAGGGAT
57785 GATAGGG-GCCTCTTGAAC
1 GATAGGGTGCCTCTTGAAC
57803 GATAGGGTATGCCTCTTGAAC
1 GATAGGG--TGCCTCTTGAAC
57824 GAT
1 GAT
57827 GACAGGTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
21 14 0.67
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (19 bp):
GATAGGGTGCCTCTTGAAC
Found at i:58341 original size:18 final size:19
Alignment explanation
Indices: 58318--58362 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
58308 GAAACTTAAA
58318 ATCGCAACACGAA-TGACT
1 ATCGCAACACGAATTGACT
*
58336 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAA-TTGACT
58356 ATCGCAA
1 ATCGCAA
58363 TGAAAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
20 12 0.50
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (19 bp):
ATCGCAACACGAATTGACT
Found at i:58434 original size:20 final size:20
Alignment explanation
Indices: 58409--58474 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
58399 GATTCTCTCA
*
58409 TTGCGATAGTCAAATTCGTG
1 TTGCGATAGTCAAATTCGCG
**
58429 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
58449 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCAAATTCGCG
58469 TTGCGA
1 TTGCGA
58475 AAGTAAACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:58690 original size:20 final size:20
Alignment explanation
Indices: 58665--58710 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
58655 TAGTTTACTT
58665 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
58685 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
58705 TCGCAA
1 TCGCAA
58711 TGAGAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:58941 original size:329 final size:328
Alignment explanation
Indices: 58428--59288 Score: 1302
Period size: 329 Copynumber: 2.6 Consensus size: 328
58418 TCAAATTCGT
** * *
58428 GTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCACGTTGCGAAAGTAAACTCTTCTTCTT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTT
**
58493 CTGCAAATTGAAACTTGAATGGATTGCATTACTTTTACCAAAAGACAACCAAAAACAAATACTAA
66 CTGCAAATTGAAACTTGAATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAA
* * *
58558 CTTCACAGGGTTAAAGAATAAACAGTTTAGCAGTATTGACAGTAACCAAATGAATTTACTAAGCA
131 CTTCACAGGGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCA
*
58623 ATCCATTTAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCG
196 ATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCG
** * * *** *
58688 CAAC-GCGAATTTGACTATCGCAATGAG-A-GA-ATTGCAATGCGATTTTCATTTCGCATTGCGA
261 CAACAG-GAAAATGACTATCACAATGAGAATGACATTGCAATGAGAGAATCA--T---AATGCGA
58749 -TTC-TTTC
320 TTTCATTTC
**
58756 GTTGCGATAGTCAAATTCGCGTTGAAAATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCT
1 GTTGCGATAGTCAAATTCGCGTTG-CGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCT
* *
58821 TCTGTAAATTGAAACTTGAATGGATTGCATTACTTCAACCAAAAGACAACAAAAAACAAATACTA
65 TCTGCAAATTGAAACTTGAATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTA
58886 ACTTCACAGGGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGC
130 ACTTCACAGGGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGC
*
58951 AATCCATTCAAGTTTCAATTTGCATAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATC
195 AATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATC
* *
59016 GCTACAGGAAAATGACTATCACAATGCGAATTTGACTATTGCAATGAGAGAATCATAATGCGATT
260 GCAACAGGAAAATGACTATCACAATGAGAA--TGAC-ATTGCAATGAGAGAATCATAATGCGA-T
59081 TTCATTTC
321 TTCATTTC
*
59089 GCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCTAAAGTAAACTATTCTTC
1 G--TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTC
*
59154 TTCTGCAAATTGAAACTTGAATGGATTGCATTACTTCAACCAAAAGACAACCAAAAATAAATACT
64 TTCTGCAAATTGAAACTTGAATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACT
* *
59219 AATTTCACAAGGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAG
129 AACTTCACAGGGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAG
59284 CAATC
194 CAATC
59289 TAAGTGAAAT
Statistics
Matches: 487, Mismatches: 33, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
328 22 0.05
329 243 0.50
330 8 0.02
332 3 0.01
333 8 0.02
334 166 0.34
335 37 0.08
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (328 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTT
CTGCAAATTGAAACTTGAATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAA
CTTCACAGGGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCA
ATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCG
CAACAGGAAAATGACTATCACAATGAGAATGACATTGCAATGAGAGAATCATAATGCGATTTCAT
TTC
Found at i:59115 original size:20 final size:20
Alignment explanation
Indices: 59086--59135 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
59076 CGATTTTCAT
*
59086 TTCGCATTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
59106 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
59126 TTCGCGTTGC
1 TTCGCGTTGC
59136 TAAAGTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:61114 original size:19 final size:20
Alignment explanation
Indices: 61026--61116 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
61016 AATAGTTTCT
* * *
61026 GAAACTTAAAATCACAACAC
1 GAAACTGAAAATCGCAACGC
*
61046 GAAAATGAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
** ** *
61066 GAATTTGACTATCGCAAAGC
1 GAAACTGAAAATCGCAACGC
61086 GAAA-TGAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
61105 GAAACT-AAAATC
1 GAAACTGAAAATC
61117 ACATTGCGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 22 0.39
20 35 0.61
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (20 bp):
GAAACTGAAAATCGCAACGC
Found at i:61793 original size:20 final size:20
Alignment explanation
Indices: 61723--61820 Score: 99
Period size: 20 Copynumber: 4.9 Consensus size: 20
61713 GCGCTTTGAA
61723 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
61743 CATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * *
61763 AATCGCGTTGTGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
61783 AATCGCATTGTGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
*
61803 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
61821 GGAAAATCGC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
19 1 0.02
20 64 0.97
21 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:62143 original size:12 final size:12
Alignment explanation
Indices: 62128--62152 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62118 AATTATCATA
62128 TATTTTATATAT
1 TATTTTATATAT
62140 TATTTTATATAT
1 TATTTTATATAT
62152 T
1 T
62153 TATTAATAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTATATAT
Found at i:64817 original size:21 final size:23
Alignment explanation
Indices: 64784--64831 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
64774 GACTCAAATT
64784 TAAAAACTAATTC-ACTTATTAC
1 TAAAAACTAATTCGACTTATTAC
* * *
64806 TAAAAA-TTATTCGAGTTATTAT
1 TAAAAACTAATTCGACTTATTAC
64828 TAAA
1 TAAA
64832 GTTATTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAAAACTAATTCGACTTATTAC
Found at i:66920 original size:17 final size:18
Alignment explanation
Indices: 66898--66931 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
66888 TCGGTTTCGG
66898 TTTT-AAAAAACCGGTTT
1 TTTTAAAAAAACCGGTTT
66915 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
66932 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTAAAAAAACCGGTTT
Found at i:68155 original size:32 final size:33
Alignment explanation
Indices: 68059--68157 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
68049 AAATCAACAT
* * *
68059 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
68092 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
68125 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
68157 A
1 A
68158 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:68176 original size:21 final size:21
Alignment explanation
Indices: 68152--68193 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
68142 ACTTCAAGTT
68152 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
68173 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
68194 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:70622 original size:28 final size:29
Alignment explanation
Indices: 70584--70643 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
70574 AAAAAACCAA
* *
70584 TTTTTC-CCAAATTCAAT-TTCAAATATTT
1 TTTTTCACAAAATTAAATATTCAAAT-TTT
70612 TTTTTCACAAAATTAAATATTCAAATTTT
1 TTTTTCACAAAATTAAATATTCAAATTTT
70641 TTT
1 TTT
70644 GTGTACACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 15 0.54
30 7 0.25
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTTCACAAAATTAAATATTCAAATTTT
Found at i:74901 original size:3 final size:3
Alignment explanation
Indices: 74893--74918 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
74883 CTTGAGTTTC
74893 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
74919 TTTGAGGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:79512 original size:28 final size:28
Alignment explanation
Indices: 79480--79536 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
79470 TCGTCGTTGC
*
79480 TTTCAAGCAC-CGACTAAACGACATAATG
1 TTTCAAGCACTCG-CTAAACAACATAATG
*
79508 TTTCAAGCACTCGCTAGACAACATAATG
1 TTTCAAGCACTCGCTAAACAACATAATG
79536 T
1 T
79537 AAATGGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (28 bp):
TTTCAAGCACTCGCTAAACAACATAATG
Found at i:81928 original size:20 final size:20
Alignment explanation
Indices: 81891--81928 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
81881 ATCTTATTTA
*
81891 AATAATTAAATATTTTTATT
1 AATAATTAAATACTTTTATT
81911 AATAATATAAAT-CTTTTA
1 AATAAT-TAAATACTTTTA
81929 AATTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAATTAAATACTTTTATT
Found at i:99006 original size:50 final size:51
Alignment explanation
Indices: 98882--99009 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 51
98872 TTAGCAGTAA
** *
98882 AGCGC-GCCCTCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGGCCC-CTGCACCGCGCTATACGATGAGCTGACGCCACGTGGGGTAT
* * ** *
98933 AGCGCGCCCCCTGAACCTTGCTATACGGTGAGCTGACGCCACGT-GGGTAT
1 AGCGCGGCCCCTGCACCGCGCTATACGATGAGCTGACGCCACGTGGGGTAT
*
98983 AGCGCGGCCCCTGCAGCGCGCTATACG
1 AGCGCGGCCCCTGCACCGCGCTATACG
99010 CCACGTAGGG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
50 28 0.44
51 32 0.51
52 3 0.05
ACGTcount: A:0.16, C:0.34, G:0.31, T:0.19
Consensus pattern (51 bp):
AGCGCGGCCCCTGCACCGCGCTATACGATGAGCTGACGCCACGTGGGGTAT
Found at i:99138 original size:50 final size:51
Alignment explanation
Indices: 99021--99144 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 51
99011 CACGTAGGGG
*
99021 TATAGCGCGGATCAGGAACCGCGCTATACCTTTACTCCCGACATAATTTTA
1 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCCGACATAATTTTA
** * *
99072 TATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACT-CTGATATAATTTTA
1 TATAGCGCGGATCAGGTACCGCG-CTATACCTTTACTCCCGACATAATTTTA
99122 TATAGCGCGGATCAGGTACCGCG
1 TATAGCGCGGATCAGGTACCGCG
99145 TTTTGTATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 33 0.51
51 31 0.48
52 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (51 bp):
TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCCGACATAATTTTA
Found at i:101450 original size:20 final size:19
Alignment explanation
Indices: 101422--101460 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
101412 CCTTAAAAAG
*
101422 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
101442 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
101461 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:101627 original size:50 final size:51
Alignment explanation
Indices: 101573--101699 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
101563 AGATATACAG
* * * * **
101573 GTATAGCGCGCTGCAGGGGTCGCGCTATA-CCCACGTGGCGTCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACC
* * *
101623 GTATAGCGCGGTGCAGGGGGCGCACTATACCCCATGTGACGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACC
101674 GTATAGCGCGGTGCAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
101700 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 26 0.39
51 40 0.61
ACGTcount: A:0.18, C:0.30, G:0.35, T:0.17
Consensus pattern (51 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACC
Done.