Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006957.1 Hibiscus syriacus cultivar Beakdansim tig00017891_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: 93221
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:7326 original size:12 final size:11
Alignment explanation
Indices: 7303--7347 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
7293 CAAAATAAAC
7303 ATATAT-TTAT
1 ATATATATTAT
7313 ATATCATATTAT
1 ATAT-ATATTAT
7325 ATA-ATA-TAT
1 ATATATATTAT
*
7334 ATATATATTGT
1 ATATATATTAT
7345 ATA
1 ATA
7348 AACATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 6 0.20
10 10 0.33
11 7 0.23
12 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
ATATATATTAT
Found at i:8768 original size:16 final size:16
Alignment explanation
Indices: 8740--8773 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
8730 TTTTCCTATG
8740 TTTTATTTATTTCATT
1 TTTTATTTATTTCATT
8756 TTTTACTTT-TTTCATT
1 TTTTA-TTTATTTCATT
8772 TT
1 TT
8774 GTTTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTTATTTCATT
Found at i:8786 original size:14 final size:14
Alignment explanation
Indices: 8740--8801 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
8730 TTTTCCTATG
8740 TTTTATTTA-TTTCA
1 TTTTATTTAGTTT-A
*
8754 -TTT-TTTACTTT-
1 TTTTATTTAGTTTA
* *
8765 TTTCATTTTGTTTA
1 TTTTATTTAGTTTA
8779 TTTTATTTAGTTTA
1 TTTTATTTAGTTTA
8793 TTTTATTTA
1 TTTTATTTA
8802 CTTATTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
12 6 0.15
13 12 0.31
14 21 0.54
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTATTTAGTTTA
Found at i:10893 original size:19 final size:19
Alignment explanation
Indices: 10869--10919 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
10859 AAAACGTATT
10869 TATGAACAATACTATATGG
1 TATGAACAATACTATATGG
10888 TATGAACAATACTATATGG
1 TATGAACAATACTATATGG
*
10907 TATGAACAGTACT
1 TATGAACAATACT
10920 GTGAACAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (19 bp):
TATGAACAATACTATATGG
Found at i:11010 original size:21 final size:21
Alignment explanation
Indices: 10985--11026 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
10975 TGCTAGAGGG
*
10985 GTACTGATACCCTGCTACAGT
1 GTACTGATACCCTACTACAGT
11006 GTACTGATACCCTACTACAGT
1 GTACTGATACCCTACTACAGT
11027 ACTGCTACAA
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:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
GTACTGATACCCTACTACAGT
Found at i:16100 original size:24 final size:20
Alignment explanation
Indices: 16073--16128 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
16063 ATGGGTAGTG
16073 CATCGATGCACATGTTAAAGAATA
1 CATCGATGCAC-TG-T-AA-AATA
*
16097 CATCGATACACTGTAAAATA
1 CATCGATGCACTGTAAAATA
*
16117 TATCGATGCACT
1 CATCGATGCACT
16129 TCAAGGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 14 0.48
21 2 0.07
22 1 0.03
23 2 0.07
24 10 0.34
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
CATCGATGCACTGTAAAATA
Found at i:16846 original size:23 final size:24
Alignment explanation
Indices: 16815--16864 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
16805 CGGGACATAC
16815 AGTGATCCTTCGGGAT-ATTTCAT
1 AGTGATCCTTCGGGATAATTTCAT
*
16838 AGTGGTCCTTCGGGATAAATTTCAT
1 AGTGATCCTTCGGGAT-AATTTCAT
16863 AG
1 AG
16865 CCCCTAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.62
25 9 0.38
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (24 bp):
AGTGATCCTTCGGGATAATTTCAT
Found at i:20056 original size:24 final size:24
Alignment explanation
Indices: 20029--20109 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
20019 GCATGGGTAG
20029 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
20053 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
* *
20077 TACATCGATACAC-TG-T--AGAA
1 TGCATCGATGCACATGTTAAAGAA
*
20097 TGTATCGATGCAC
1 TGCATCGATGCAC
20110 TTCAAGGGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 14 0.27
22 1 0.02
23 2 0.04
24 35 0.67
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAAGAA
Found at i:23517 original size:21 final size:22
Alignment explanation
Indices: 23493--23536 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
23483 TGTAGCAGTA
*
23493 CTGTAGTA-GGGTATCGATTCC
1 CTGTAGTAGGGGAATCGATTCC
23514 CTGTAGTAGGGGAATCGATTCC
1 CTGTAGTAGGGGAATCGATTCC
23536 C
1 C
23537 CTCTTTGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (22 bp):
CTGTAGTAGGGGAATCGATTCC
Found at i:24176 original size:17 final size:17
Alignment explanation
Indices: 24133--24177 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
24123 ACAAAAATTA
*
24133 AATTTGAAAGTTAGAGT
1 AATTTGAAATTTAGAGT
*
24150 AA-TT-AAATTTGGAGT
1 AATTTGAAATTTAGAGT
24165 AATTTGAAATTTA
1 AATTTGAAATTTA
24178 AGTGATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.48
16 4 0.17
17 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (17 bp):
AATTTGAAATTTAGAGT
Found at i:37736 original size:36 final size:36
Alignment explanation
Indices: 37670--37742 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
37660 GTTGGAAAAT
*
37670 ATTTATATATTTTCTTTAAAAAATTTAAAATCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAAT-ATAAA
*
37707 ATTTATATATTTT-TTTACAAAATTGAAAATATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATATAAA
37742 A
1 A
37743 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 6 0.18
36 15 0.44
37 13 0.38
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATATAAA
Found at i:40069 original size:33 final size:35
Alignment explanation
Indices: 40032--40110 Score: 108
Period size: 38 Copynumber: 2.2 Consensus size: 35
40022 TTTTCACCCT
40032 AAACCCGAACC-C-GACCCGAATATCACACTTAAA
1 AAACCCGAACCACTGACCCGAATATCACACTTAAA
*
40065 AAACCCCGACCCGACTTGACCCGAATATCACACTTAAA
1 AAA-CCCGAACC-AC-TGACCCGAATATCACACTTAAA
40103 AAACCCGA
1 AAACCCGA
40111 CCCAAACAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
33 3 0.08
34 7 0.17
36 1 0.03
37 5 0.12
38 24 0.60
ACGTcount: A:0.41, C:0.37, G:0.10, T:0.13
Consensus pattern (35 bp):
AAACCCGAACCACTGACCCGAATATCACACTTAAA
Found at i:41050 original size:2 final size:2
Alignment explanation
Indices: 41043--41074 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41033 GGTTAAACTA
41043 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
41075 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42958 original size:16 final size:16
Alignment explanation
Indices: 42934--42968 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
42924 TGTTGATCGA
*
42934 CTCGTTGCTCGTTAAG
1 CTCGATGCTCGTTAAG
42950 CTCGATGCTCGTTAAG
1 CTCGATGCTCGTTAAG
42966 CTC
1 CTC
42969 ACTGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.29, G:0.23, T:0.34
Consensus pattern (16 bp):
CTCGATGCTCGTTAAG
Found at i:45099 original size:29 final size:30
Alignment explanation
Indices: 45027--45100 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
45017 CGATTTAACG
*
45027 GTTTAGTGGTATAATTGAAACGAAAATCAAA
1 GTTTAGTGGTATAATTGAAAC-AAAATAAAA
** * *
45058 GTTTAGTACTATAATTGGAA-AAATTAAAA
1 GTTTAGTGGTATAATTGAAACAAAATAAAA
45087 GTTTAGTGGTATAA
1 GTTTAGTGGTATAA
45101 ACGATACAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (30 bp):
GTTTAGTGGTATAATTGAAACAAAATAAAA
Found at i:47956 original size:18 final size:17
Alignment explanation
Indices: 47902--47950 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
47892 TTGGACCCTT
* *
47902 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
47920 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
47938 AGTGCATTCGATG
1 AGTGCA-TCGATG
47951 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:48055 original size:65 final size:65
Alignment explanation
Indices: 47922--48081 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
47912 TGCACTAAGA
* ** *
47922 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGTGTGCATCGATGTATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGTTG
* * *
47986 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGT-
48050 T-
64 TG
*
48051 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
48082 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.33
65 53 0.62
66 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGTTG
Found at i:48129 original size:65 final size:63
Alignment explanation
Indices: 47922--48131 Score: 205
Period size: 65 Copynumber: 3.3 Consensus size: 63
47912 TGCACTAAGA
* * *
47922 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGTGTGCATCGATGTATGGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTCA--GTGCATCGATGCATGGTT
47985 G
63 G
*
47986 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
48051 -
63 G
* **
48051 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
48114 TG
62 TG
* * *
48116 GTTCACCGGTGCATCA
1 GTGCATCGATGCATCA
48132 CTCTGAAAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 49 0.40
65 62 0.50
66 5 0.04
67 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:56670 original size:17 final size:17
Alignment explanation
Indices: 56638--56670 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56628 GCATGGCTGG
56638 TGCATCGATGTATCAAA
1 TGCATCGATGTATCAAA
56655 TGCATTCGATGT-TCAA
1 TGCA-TCGATGTATCAA
56671 TTTAATTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (17 bp):
TGCATCGATGTATCAAA
Found at i:58291 original size:57 final size:57
Alignment explanation
Indices: 58222--58460 Score: 361
Period size: 57 Copynumber: 4.2 Consensus size: 57
58212 ATGGCATTGA
* *
58222 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGAGCACTTT
* * *
58279 GTGTGCAAAAAGTTAAGATATTTATAATTTGTTTATGAATTTCCATATGAGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGAGCACTTT
* * **
58336 GTGTGCAAAAAGTTAAGATATTCATAATTTGTTTATGAATTTCCGTATGGGCACTGA
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGAGCACTTT
* * *
58393 GTGTGCAAAAAATTAAGAAATTCATAATTTGTTTATGAATTTCCGTATAAGAACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGAGCACTTT
*
58450 ATGTGCAAAAA
1 GTGTGCAAAAA
58461 AACTAAGAAA
Statistics
Matches: 164, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 164 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGAGCACTTT
Found at i:58500 original size:114 final size:112
Alignment explanation
Indices: 58223--58488 Score: 298
Period size: 114 Copynumber: 2.3 Consensus size: 112
58213 TGGCATTGAG
** * * **
58223 TGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAA
1 TGTGCAAAAAACTAAGAAATTCATAATTTCTTTATGAATATC--TATGGGCACTGAGTGTGCAAA
* * * * * *
58288 AAGTTAAGATATTTATAATTTGTTTATGAATTTCCATATGAGCACTTTG
64 AAATTAAGAAATTCATAATTTGTTTATGAATTTCCATATAAGAACTTTA
** * * *
58337 TGTGCAAAAAGTTAAGATATTCATAATTTGTTTATGAATTTCCGTATGGGCACTGAGTGTGCAAA
1 TGTGCAAAAAACTAAGAAATTCATAATTTCTTTATGAATAT-C-TATGGGCACTGAGTGTGCAAA
*
58402 AAATTAAGAAATTCATAATTTGTTTATGAATTTCCGTATAAGAACTTTA
64 AAATTAAGAAATTCATAATTTGTTTATGAATTTCCATATAAGAACTTTA
*
58451 TGTGCAAAAAAACTAAGAAATTATATAAATTTCTTTAT
1 TGTGC-AAAAAACTAAGAAATT-CAT-AATTTCTTTAT
58489 TGGTATTATG
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
114 107 0.80
115 14 0.11
116 2 0.02
117 10 0.08
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (112 bp):
TGTGCAAAAAACTAAGAAATTCATAATTTCTTTATGAATATCTATGGGCACTGAGTGTGCAAAAA
ATTAAGAAATTCATAATTTGTTTATGAATTTCCATATAAGAACTTTA
Found at i:59135 original size:269 final size:270
Alignment explanation
Indices: 58652--59174 Score: 798
Period size: 269 Copynumber: 1.9 Consensus size: 270
58642 ATTAATAACA
*
58652 TAACTGTGCATTTGATAGAAAGGTGTCTATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * *
58717 GCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
66 ACCTAATTGTGCATTTGATAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGCTAAGTGCCTTT
* * * * * * *
58782 GAGGCCTAACTGTGCATTTGACAGAAATATGTCAATTATATCAGTTATATGGAAGGCTAAGTACC
131 GAGGCCTAACTGTGCATTTGAAAGAAAGATGTCAATTATACCAATTAGATGAAAGGATAAGTACC
* * *
58847 TTTGAGGCCTAACTGTGCATTTGAC-AAGGTGTCTATTATTCCAGTTAGATGAAAGGCTAAGTTC
196 TTTGAGGCCTAACTGTGCATTTGACAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTTC
58911 CTTTGAGGCC
261 CTTTGAGGCC
* *
58921 TAACTGTGCATTTGATAGAGAGGTGTCAATTATGCCAGTTTGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* *
58986 ACCTAATTGTGCATTTGATAGAAATGTGTCTATTATGCCAATTAGATGAAAGGCTAAGTGCCTTT
66 ACCTAATTGTGCATTTGATAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGCTAAGTGCCTTT
* * * *
59051 GAGGCCTAACTGTGCATTTGAAAGAAAGATGTCTATTATGCCAATTAGATGAAAGGATAAGTGCT
131 GAGGCCTAACTGTGCATTTGAAAGAAAGATGTCAATTATACCAATTAGATGAAAGGATAAGTACC
*
59116 TTTGAGG-CTAAGTTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
196 TTTGAGGCCTAA-CTGTGCATTTGAC--AAAGGTGTCAATCATGCCAGTTAGATGAAAGG
59175 TTAAATACAT
Statistics
Matches: 227, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
268 4 0.02
269 195 0.86
272 28 0.12
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (270 bp):
TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
ACCTAATTGTGCATTTGATAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGCTAAGTGCCTTT
GAGGCCTAACTGTGCATTTGAAAGAAAGATGTCAATTATACCAATTAGATGAAAGGATAAGTACC
TTTGAGGCCTAACTGTGCATTTGACAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTTC
CTTTGAGGCC
Found at i:59189 original size:68 final size:68
Alignment explanation
Indices: 58652--59174 Score: 721
Period size: 68 Copynumber: 7.7 Consensus size: 68
58642 ATTAATAACA
*
58652 TAACTGTGCATTTGATAGAAAGGTGTCTATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
58717 GCC
66 GCC
**
58720 TAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
58785 GCC
66 GCC
* ** ** * * *
58788 TAACTGTGCATTTGACAGAAATATGTCAATTATATCAGTTATATGGAAGGCTAAGTACCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
58853 GCC
66 GCC
* * * *
58856 TAACTGTGCATTTG--A-CAAGGTGTCTATTATTCCAGTTAGATGAAAGGCTAAGTTCCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
58918 GCC
66 GCC
* *
58921 TAACTGTGCATTTGATAGAGAGGTGTCAATTATGCCAGTTTGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
*
58986 ACC
66 GCC
* * * *
58989 TAATTGTGCATTTGATAGAAATGTGTCTATTATGCCAATTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
59054 GCC
66 GCC
* * * * * *
59057 TAACTGTGCATTTGAAAGAAAGATGTCTATTATGCCAATTAGATGAAAGGATAAGTGCTTTTGAG
1 TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
59122 G-C
66 GCC
* * * *
59124 TAAGTTGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
1 TAA-CTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
59175 TTAAATACAT
Statistics
Matches: 402, Mismatches: 49, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
65 55 0.14
66 1 0.00
67 5 0.01
68 341 0.85
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (68 bp):
TAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
GCC
Found at i:59351 original size:81 final size:81
Alignment explanation
Indices: 59129--59440 Score: 518
Period size: 81 Copynumber: 3.8 Consensus size: 81
59119 GAGGCTAAGT
*
59129 TGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAA
1 TGTGCATTTGACAAAAAGGTGTCAATCATGCCAATTAGATGAAAGGTTAAATACATTTGAGTAAA
* *
59194 ATATTAATGGTCTAGC
66 AGATTAATGGCCTAGC
*
59210 TGTGCATTTGACAAAAAAGGTGTCAATCATGCCAATTAGATGAAAGGTTAAATACCTTTGAGTAA
1 TGTGCATTTGAC-AAAAAGGTGTCAATCATGCCAATTAGATGAAAGGTTAAATACATTTGAGTAA
59275 AAGATTAATGGCCTAGC
65 AAGATTAATGGCCTAGC
** *
59292 CATGCATTTGACAAAAAGGTGTCGATCATGCCAATTAGATGAAAGGTTAAATACATTTGAGTAAA
1 TGTGCATTTGACAAAAAGGTGTCAATCATGCCAATTAGATGAAAGGTTAAATACATTTGAGTAAA
59357 AGATTAATGGCCTAGC
66 AGATTAATGGCCTAGC
* *
59373 TGTGCATTTGACAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAA-AGCCTTTGAGTAA
1 TGTGCATTTGACAAAAAGGTGTCAATCATGCCAATTAGATGAAAGGTTAAATA-CATTTGAGTAA
59437 AAGA
65 AAGA
59441 CTAGATGTAT
Statistics
Matches: 216, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
80 1 0.00
81 140 0.65
82 75 0.35
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (81 bp):
TGTGCATTTGACAAAAAGGTGTCAATCATGCCAATTAGATGAAAGGTTAAATACATTTGAGTAAA
AGATTAATGGCCTAGC
Found at i:59540 original size:45 final size:46
Alignment explanation
Indices: 59466--59728 Score: 370
Period size: 45 Copynumber: 5.8 Consensus size: 46
59456 TGCATAATGT
*
59466 TGTATAAAAATGCATGAAAGGATGCCATAAATGAAACGTATAATAG
1 TGTATAAAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAG
* * *
59512 TGTAT-AAAAGGCATGAAAAGATTCCATAAATGAAACGTTTAATAG
1 TGTATAAAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAG
* * * *
59557 TGTATAAAAAGGCATGAAAGGATTCCATAAAAGAAACATATATTAG
1 TGTATAAAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAG
* * *
59603 TCTAT-AAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAG
1 TGTATAAAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAG
* * *
59648 TGTAT-AAAAGGCATGAAAAGATACCATAAATGAAACGTTTAATAG
1 TGTATAAAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAG
*
59693 TATATAAAAAGGCATGAAAGGATGCCATAAATGAAA
1 TGTATAAAAAGGCATGAAAGGATGCCATAAATGAAA
59729 TGCATATGGG
Statistics
Matches: 191, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
45 119 0.62
46 72 0.38
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (46 bp):
TGTATAAAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAG
Found at i:59644 original size:136 final size:136
Alignment explanation
Indices: 59472--59728 Score: 451
Period size: 136 Copynumber: 1.9 Consensus size: 136
59462 ATGTTGTATA
* *
59472 AAAATGCATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATAAAAGGCATGAAAAGATTCC
1 AAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATAAAAGGCATGAAAAGATACC
* *
59537 ATAAATGAAACGTTTAATAGTGTATAAAAAGGCATGAAAGGATTCCATAAAAGAAACATATATTA
66 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACATATATTA
59602 GTCTAT
131 GTCTAT
* *
59608 AAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAAGATACC
1 AAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATAAAAGGCATGAAAAGATACC
*
59673 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAATGAAA
66 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAA
59729 TGCATATGGG
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 114 1.00
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (136 bp):
AAAAGGCATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATAAAAGGCATGAAAAGATACC
ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACATATATTA
GTCTAT
Found at i:59729 original size:91 final size:91
Alignment explanation
Indices: 59466--59730 Score: 379
Period size: 91 Copynumber: 2.9 Consensus size: 91
59456 TGCATAATGT
* * *
59466 TGTATAAAAATGCATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATAAAAGGCATGAAAA
1 TGTATAAAAAGGCATGAAAGGATACCATAAATGAAACGTATAATAGTATATAAAAGGCATGAAAA
* * *
59531 GATTCCATAAATGAAACGTTTAATAG
66 GATGCCATAAATGAAATGTATAATAG
* * * * * *
59557 TGTATAAAAAGGCATGAAAGGATTCCATAAAAGAAACATATATTAGTCTATAAAAGGCATGAAAT
1 TGTATAAAAAGGCATGAAAGGATACCATAAATGAAACGTATAATAGTATATAAAAGGCATGAAAA
59622 GATGCCATAAATGAAATGTATAATAG
66 GATGCCATAAATGAAATGTATAATAG
* *
59648 TGTAT-AAAAGGCATGAAAAGATACCATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAA
1 TGTATAAAAAGGCATGAAAGGATACCATAAATGAAACGTATAATAGTATAT-AAAAGGCATGAAA
*
59712 GGATGCCATAAATGAAATG
65 AGATGCCATAAATGAAATG
59731 CATATGGGTG
Statistics
Matches: 155, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
90 38 0.25
91 117 0.75
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (91 bp):
TGTATAAAAAGGCATGAAAGGATACCATAAATGAAACGTATAATAGTATATAAAAGGCATGAAAA
GATGCCATAAATGAAATGTATAATAG
Found at i:59762 original size:136 final size:136
Alignment explanation
Indices: 59472--59775 Score: 430
Period size: 136 Copynumber: 2.2 Consensus size: 136
59462 ATGTTGTATA
* * * *
59472 AAAATGCATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATAAAAGGCATGAAAAGATTCC
1 AAAAGGCACGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAAGATACC
* * * *
59537 ATAAATGAAACGTTTAATAGTGTATAAAAAGGCATGAAAGGATTCCATAAAAGAAACATATATTA
66 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACACATATGA
59602 GTCTAT
131 GTCTAT
* *
59608 AAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAAGATACC
1 AAAAGGCACGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAAGATACC
* ** *
59673 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAATGAAATGCATATGG
66 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACACATATGA
59738 GTGC-AT
131 GT-CTAT
* ** *
59744 TATCGGCACGAAAGGATGCCATAATTGAAATG
1 AAAAGGCACGAAAGGATGCCATAAATGAAATG
59776 CATATGGGTG
Statistics
Matches: 149, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
136 148 0.99
137 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (136 bp):
AAAAGGCACGAAAGGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAAGATACC
ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACACATATGA
GTCTAT
Found at i:59764 original size:45 final size:45
Alignment explanation
Indices: 59703--59825 Score: 194
Period size: 45 Copynumber: 2.7 Consensus size: 45
59693 TATATAAAAA
59703 GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTA-T
1 GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTAGT
* *
59747 CGGCACGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTAGT
1 -GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTAGT
*
59793 GGCATGAAAGAATGCCATAAATGAAAATGCATA
1 GGCATGAAAGGATGCCATAAATG-AAATGCATA
59826 ATGGTATATT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
45 61 0.86
46 10 0.14
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTAGT
Found at i:59797 original size:136 final size:136
Alignment explanation
Indices: 59472--59818 Score: 403
Period size: 136 Copynumber: 2.6 Consensus size: 136
59462 ATGTTGTATA
* * * * * *
59472 AAAATGCATGAAAGGATGCCATAAATGAAACGTATAATAGTGTATAAAAGGCATGAAAAGATTCC
1 AAAAGGCACGAAAGGATGCCATAAATGAAATGCATAATAGTGCATAAAAGGCATGAAAAGATACC
* * * *
59537 ATAAATGAAACGTTTAATAGTGTATAAAAAGGCATGAAAGGATTCCATAAAAGAAACATATATTA
66 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACACATATGA
59602 GTCTAT
131 GTCTAT
* * * *
59608 AAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGTGTATAAAAGGCATGAAAAGATACC
1 AAAAGGCACGAAAGGATGCCATAAATGAAATGCATAATAGTGCATAAAAGGCATGAAAAGATACC
* ** *
59673 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAATGAAATGCATATGG
66 ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACACATATGA
59738 GTGC-AT
131 GT-CTAT
* ** * * * ** *
59744 TATCGGCACGAAAGGATGCCATAATTGAAATGCAT-ATGGGTGCATTAGTGGCATG-AAAGAATG
1 AAAAGGCACGAAAGGATGCCATAAATGAAATGCATAAT-AGTGCATAAAAGGCATGAAAAG-ATA
59807 CCATAAATGAAA
64 CCATAAATGAAA
59819 ATGCATAATG
Statistics
Matches: 183, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
135 6 0.03
136 176 0.96
137 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (136 bp):
AAAAGGCACGAAAGGATGCCATAAATGAAATGCATAATAGTGCATAAAAGGCATGAAAAGATACC
ATAAATGAAACGTTTAATAGTATATAAAAAGGCATGAAAGGATGCCATAAAAGAAACACATATGA
GTCTAT
Found at i:62523 original size:20 final size:20
Alignment explanation
Indices: 62500--62551 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
62490 AACGCGATCC
62500 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
62520 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
62540 CCAAAATCGCAA
1 CCAGAATCGCAA
62552 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:62632 original size:20 final size:20
Alignment explanation
Indices: 62607--62800 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
62597 TATTTTCCAT
* *
62607 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
62627 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
62647 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
62667 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
62687 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
62707 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
62727 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
62747 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
62768 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
62788 AATCGCAACGCGA
1 AATCGCAACGCGA
62801 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:62652 original size:40 final size:39
Alignment explanation
Indices: 62603--62800 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
62593 TTGCTATTTT
* ** *
62603 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
62641 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
62682 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
62722 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
62761 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
62801 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:62690 original size:60 final size:60
Alignment explanation
Indices: 62607--62799 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
62597 TATTTTCCAT
* ** * *
62607 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
62667 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
62727 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
62788 AATCGCAACGCG
1 AATCGCAACGCG
62800 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:63222 original size:33 final size:33
Alignment explanation
Indices: 63183--63253 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
63173 TTCACTTAGA
*
63183 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
63216 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
63249 TTTCA
1 TTTCA
63254 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:63393 original size:14 final size:14
Alignment explanation
Indices: 63374--63428 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
63364 AGAATGACTG
63374 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
63388 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
63407 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
63421 TCGCAACG
1 TCGCAACG
63429 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:63411 original size:33 final size:33
Alignment explanation
Indices: 63374--63444 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
63364 AGAATGACTG
**
63374 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
63407 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
63440 TCGCA
1 TCGCA
63445 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:63462 original size:19 final size:19
Alignment explanation
Indices: 63440--63537 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
63430 GAAACCAAAA
*
63440 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
63459 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
63473 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
63492 TCGCGTTGC-A-ATTC---
1 TCGCGTTGCGATTTTCATT
* * *
63506 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
63525 TCGCGTTGCGATT
1 TCGCGTTGCGATT
63538 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 18 0.30
15 1 0.02
16 5 0.08
17 6 0.10
18 1 0.02
19 30 0.49
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:63481 original size:14 final size:14
Alignment explanation
Indices: 63462--63551 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
63452 TTTCATTTCG
63462 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
63476 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
63495 CGTTGCAATTCTCT
1 CGTTGCGATTCTCT
63509 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
63526 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
63542 CGTTGCGATT
1 CGTTGCGATT
63552 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:63487 original size:33 final size:33
Alignment explanation
Indices: 63445--63559 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
63435 CAAAATCGCA
63445 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
63478 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
63511 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
63544 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
63560 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:65566 original size:93 final size:93
Alignment explanation
Indices: 65253--65722 Score: 894
Period size: 92 Copynumber: 5.1 Consensus size: 93
65243 TAGATTGCTT
*
65253 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65318 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
65345 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65409 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65437 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65502 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65530 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65594 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65621 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65686 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65714 AGTAAATTT
1 AGTAAATTT
65723 ATCCATTCAA
Statistics
Matches: 371, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
91 91 0.25
92 162 0.44
93 118 0.32
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:65806 original size:19 final size:19
Alignment explanation
Indices: 65766--65894 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
65756 TAGTTTACTT
* *
65766 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
65786 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
65805 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
65824 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
65838 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
65857 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
65871 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
65890 TCGCA
1 TCGCA
65895 TTGCGATTCT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:65845 original size:33 final size:32
Alignment explanation
Indices: 65802--65894 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
65792 CGCGAAACCA
**
65802 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
65834 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
65867 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
65895 TTGCGATTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:65892 original size:52 final size:52
Alignment explanation
Indices: 65766--65894 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
65756 TAGTTTACTT
**
65766 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
65818 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
65871 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
65895 TTGCGATTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:65914 original size:14 final size:14
Alignment explanation
Indices: 65895--65949 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
65885 CAAAATCGCA
65895 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
65909 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
*
65926 CATTGCGATTCTGTCG
1 --TTGCGATTCTTTCG
65942 TTGCGATT
1 TTGCGATT
65950 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 7 0.20
17 8 0.23
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:65932 original size:33 final size:33
Alignment explanation
Indices: 65890--65968 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
65880 GAAACCAAAA
*
65890 TCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
65923 TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
*
65956 TCGCGTTGCGATT
1 TCGCATTGCGATT
65969 TTGGTTTCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
Found at i:65933 original size:19 final size:17
Alignment explanation
Indices: 65901--65989 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 17
65891 CGCATTGCGA
65901 TTCTTTCG-TTGCGATT
1 TTCTTTCGCTTGCGATT
65917 TTCATTTCGCATTGCGA--
1 TTC-TTTCGC-TTGCGATT
*
65934 TTCTGTCG-TTGCGATT
1 TTCTTTCGCTTGCGATT
65950 TTCATTTCGCGTTGCGATT
1 TTC-TTTCGC-TTGCGATT
*
65969 TTGGTTTCGCGTTGCGATT
1 TT-CTTTCGC-TTGCGATT
65988 TT
1 TT
65990 AAGTTTCGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
14 6 0.10
16 10 0.16
17 12 0.20
19 33 0.54
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.49
Consensus pattern (17 bp):
TTCTTTCGCTTGCGATT
Found at i:65997 original size:20 final size:19
Alignment explanation
Indices: 65940--66005 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
65930 GCGATTCTGT
65940 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
65959 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
65978 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
65998 TGTTGCGA
1 CGTTGCGA
66006 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:67923 original size:14 final size:14
Alignment explanation
Indices: 67904--67939 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
67894 ATTGTTTAAT
67904 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
67918 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
67932 TGATTTGT
1 TGATTTGT
67940 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:68062 original size:19 final size:19
Alignment explanation
Indices: 68046--68147 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
68036 AAAAATGACT
68046 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
68065 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
68084 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
68098 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
68117 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
68137 ATCGCAATGCG
1 ATCGCAATGCG
68148 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:68200 original size:19 final size:19
Alignment explanation
Indices: 68176--68468 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
68166 GATTATCTCG
68176 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68195 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68214 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
68228 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68247 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68266 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68285 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68304 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
68323 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
68342 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
68356 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68375 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
68394 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
68408 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
68428 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
68442 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
68461 TTGCGATT
1 TTGCGATT
68469 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:68216 original size:52 final size:52
Alignment explanation
Indices: 68154--68468 Score: 330
Period size: 52 Copynumber: 5.9 Consensus size: 52
68144 TGCGTTTATA
*
68154 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
68206 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
68258 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
68315 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
68367 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
68419 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
68469 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 9, Indels: 25
0.88 0.03 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 129 0.54
53 18 0.07
54 6 0.02
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:68324 original size:128 final size:122
Alignment explanation
Indices: 68176--68440 Score: 194
Period size: 128 Copynumber: 2.1 Consensus size: 122
68166 GATTATCTCG
*
68176 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
68238 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
68302 CA
121 CA
* * *
68304 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
68366 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
68426 CA
121 CA
68428 TTGCGATTTTCAT
1 TTGCGATTTTCAT
68441 GTTGGGATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.14
124 18 0.14
125 2 0.02
126 2 0.02
128 74 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:70982 original size:24 final size:24
Alignment explanation
Indices: 70948--70994 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
70938 CTGAAACATC
70948 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
70972 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
70995 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:71705 original size:20 final size:20
Alignment explanation
Indices: 71677--72045 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
71667 AAATTTAAGT
* * * *
71677 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
71697 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
71717 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
71737 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
71757 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
71777 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
71797 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
71817 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
71837 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
71857 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
71877 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
71897 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
71917 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
71937 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
71957 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
71977 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
71997 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
72017 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
72037 GTTGCGATT
1 GTTGCGATT
72046 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:90211 original size:193 final size:191
Alignment explanation
Indices: 89773--90291 Score: 620
Period size: 193 Copynumber: 2.7 Consensus size: 191
89763 TTGCAAAGAA
* * * *
89773 GTATCGATACATAACAATATAACAGGTTGAAGT-TGACAAAACCGGTTTCAATTTGACAAAACCG
1 GTATCGATACATGACAATATAACAGGTTAAAATATGACAAAACCGGTTTCAATATGACAAAACCG
* * * * * * *
89837 GTAGAGA-TACCTGA-ATTGTTGAAATTTGTATCGATACTTTTCTAAGTAAATATGCACCAAATT
66 GTAAAGACTACCAGATA-TGTTG-AA--GGTATCGATACTTTTATAAGT--ATATGTATCATATT
* *
89900 ATCGATACTTAGGAATTTAAAAGAATGCAGTAATAGCGCCTATAAAATATCGATAGTTTAGAAAT
125 ATCGATACTTAGGAATTTAAAAGAATGCAATAATAGCGCCTATAAAATATCGATACTTTAGAAAT
89965 AT
190 AT
* * *
89967 GTATCGATACATGACAGTATAACAGGTTAAATTATGACAAAACCAGTTTCAATATGACAAAACCG
1 GTATCGATACATGACAATATAACAGGTTAAAATATGACAAAACCGGTTTCAATATGACAAAACCG
*
90032 GCAAAGAACTACCAGATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGA
66 GTAAAG-ACTACCAGATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGA
*
90097 TACTTAAGGAATTTAAAAGAATTGCAATAATAGCGCCTATAAAGTATCGATACTTTAGAAATAT
130 TACTT-AGGAATTTAAAAGAA-TGCAATAATAGCGCCTATAAAATATCGATACTTTAGAAATAT
* ** * **
90161 GT-TCGATACATGACAATATAACATGTTAAAATATGACAAAATTGGTTTCAATATAACAAAACTA
1 GTATCGATACATGACAATATAACAGGTTAAAATATGACAAAACCGGTTTCAATATGACAAAACCG
* * * * * * *
90225 GTAAAGCGCTAGCGGATATATTGAAGGTATTG--AC-TTTAAAAGTATATGTATCATATTATTGA
66 GTAAAG-ACTACCAGATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGA
90287 TACTT
130 TACTT
90292 TTCAAAGAAA
Statistics
Matches: 284, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
190 31 0.11
191 2 0.01
192 21 0.07
193 93 0.33
194 89 0.31
195 33 0.12
196 3 0.01
197 11 0.04
198 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (191 bp):
GTATCGATACATGACAATATAACAGGTTAAAATATGACAAAACCGGTTTCAATATGACAAAACCG
GTAAAGACTACCAGATATGTTGAAGGTATCGATACTTTTATAAGTATATGTATCATATTATCGAT
ACTTAGGAATTTAAAAGAATGCAATAATAGCGCCTATAAAATATCGATACTTTAGAAATAT
Done.