Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001070.1 Hibiscus syriacus cultivar Beakdansim tig00002119_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: 122266
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1363 original size:42 final size:41
Alignment explanation
Indices: 1237--1481 Score: 173
Period size: 43 Copynumber: 5.9 Consensus size: 41
1227 TGTGAATGAA
1237 AAACGCCGCAATA-G-GTTGACA-TTAGCGGCGTTTTTCATAC
1 AAACGCCGCAATAGGTGTTGA-ATTTAGCGGCGTTTTT-ATAC
* * **
1277 AAACACCGCAATACGTGTT-AATTTTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAA--TTTAGCGGCGTTTTT-ATAC
*
1320 AAACGCCGCAATAGGTGTTGAATTTAGTGGCGTTTTTATCAC
1 AAACGCCGCAATAGGTGTTGAATTTAGCGGCGTTTTTAT-AC
* * * * * * *
1362 AAATGTCGCAATATGTCTTGTGATTTAGCGGCGTTTTTCTTGC
1 AAACGCCGCAATAGGTGTTG-AATTTAGCGGCGTTTTT-ATAC
*
1405 AAATGCCGC-A-AGGTGTTGAGATTTTA-CGGCGTTTTTGATAC
1 AAACGCCGCAATAGGTGTTGA-A-TTTAGCGGCGTTTTT-ATAC
* * * * *
1446 AAACGTCGCAA-AGGTATGGTATATAGCGGCGTTTTT
1 AAACGCCGCAATAGGTGTTGAATTTAGCGGCGTTTTT
1482 TCGGATACAA
Statistics
Matches: 163, Mismatches: 29, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
40 16 0.10
41 39 0.24
42 47 0.29
43 58 0.36
44 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (41 bp):
AAACGCCGCAATAGGTGTTGAATTTAGCGGCGTTTTTATAC
Found at i:1372 original size:85 final size:86
Alignment explanation
Indices: 1237--1456 Score: 224
Period size: 85 Copynumber: 2.6 Consensus size: 86
1227 TGTGAATGAA
** *
1237 AAACGCCGCAATA-G-GTTGACA-TTAGCGGCGTTTTTCATACAAACACCGCAATACGTGTTAAT
1 AAACGCCGCAATAGGTGTTGACATTTAGCGGCGTTTTTCATACAAACGTCGCAATACGTCTT-AT
*
1299 -TTTTAGCGGCGTTTTTCCCAC
65 GATTTAGCGGCGTTTTTCCCAC
* * * *
1320 AAACGCCGCAATAGGTGTTGA-ATTTAGTGGCGTTTTT-ATCACAAATGTCGCAATATGTCTTGT
1 AAACGCCGCAATAGGTGTTGACATTTAGCGGCGTTTTTCAT-ACAAACGTCGCAATACGTCTTAT
***
1383 GATTTAGCGGCGTTTTTCTTGC
65 GATTTAGCGGCGTTTTTCCCAC
* * *
1405 AAATGCCGC-A-AGGTGTTGAGATTTTA-CGGCGTTTTTGATACAAACGTCGCAA
1 AAACGCCGCAATAGGTGTTGACA-TTTAGCGGCGTTTTTCATACAAACGTCGCAA
1457 AGGTATGGTA
Statistics
Matches: 115, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
83 22 0.19
84 28 0.24
85 65 0.57
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (86 bp):
AAACGCCGCAATAGGTGTTGACATTTAGCGGCGTTTTTCATACAAACGTCGCAATACGTCTTATG
ATTTAGCGGCGTTTTTCCCAC
Found at i:1476 original size:41 final size:41
Alignment explanation
Indices: 1428--1542 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 41
1418 TGTTGAGATT
*
1428 TTACGGCGTTTTTGATACAAACGTCGC-AAAGGTATGGTATA
1 TTACGGCGTTTTTGATACAAAC-ACGCTAAAGGTATGGTATA
*
1469 -TAGCGGCGTTTTTTCGGATACAAACACGCTAAATGTATGGTATA
1 TTA-CGGCG-TTTTT--GATACAAACACGCTAAAGGTATGGTATA
* *
1513 TTATGGCGTTTTTGTTAC-AACACCGCTAAA
1 TTACGGCGTTTTTGATACAAACA-CGCTAAA
1543 TAACGCATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
40 6 0.10
41 16 0.25
42 5 0.08
43 8 0.13
44 26 0.41
45 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (41 bp):
TTACGGCGTTTTTGATACAAACACGCTAAAGGTATGGTATA
Found at i:5526 original size:11 final size:11
Alignment explanation
Indices: 5510--5544 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
5500 AAGTTTGCTA
5510 AAAATAAAATG
1 AAAATAAAATG
*
5521 AAAATAAAACG
1 AAAATAAAATG
5532 -AAATAAAATG
1 AAAATAAAATG
5542 AAA
1 AAA
5545 TGGGTTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:5537 original size:10 final size:10
Alignment explanation
Indices: 5511--5545 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5501 AGTTTGCTAA
5511 AAATAAAATG
1 AAATAAAATG
*
5521 AAAATAAAACG
1 -AAATAAAATG
5532 AAATAAAATG
1 AAATAAAATG
5542 AAAT
1 AAAT
5546 GGGTTACCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (10 bp):
AAATAAAATG
Found at i:9669 original size:21 final size:21
Alignment explanation
Indices: 9621--9671 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
9611 AGGCAATTAG
* *
9621 CTTTTCCTGGGACGTAACCAA
1 CTTTTCTTGGGACATAACCAA
9642 CTTTTCTTGGGACATAACCAA
1 CTTTTCTTGGGACATAACCAA
9663 CTTTTCTTG
1 CTTTTCTTG
9672 TGAAATTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (21 bp):
CTTTTCTTGGGACATAACCAA
Found at i:12052 original size:75 final size:75
Alignment explanation
Indices: 11841--12326 Score: 461
Period size: 75 Copynumber: 6.5 Consensus size: 75
11831 TGTCCAACTC
* ** * *
11841 CACCAGTGAAATGAATACGTAATTCAAGAACTAAACTTATCACATAATTCCTGCAGTTAAATTTA
1 CACCAGTGAAATGAATACGTAATTCCAG-ACTAAACTTATCACATAATTCCAACAGTGAAACTTA
*
11906 TCATTGACTTA
65 ACATTGACTTA
* * * * * * *
11917 CATCAGTGTAATGAATACGTAATTCAAGCACTAAACTTATCACATCATTTCAACATTGAAATTTA
1 CACCAGTGAAATGAATACGTAATTCCAG-ACTAAACTTATCACATAATTCCAACAGTGAAACTTA
11982 ACATTGACTTA
65 ACATTGACTTA
* * * *
11993 CACCAG-AAAATGAATACGTAATTCCAGAGCTAAACTTATCACATGATTCCAATAATGAAACTTA
1 CACCAGTGAAATGAATACGTAATTCCAGA-CTAAACTTATCACATAATTCCAACAGTGAAACTTA
* *
12057 TCATTAACTTA
65 ACATTGACTTA
** * *
12068 CACCAGTGATTTGAATACGTAATTCCA-AC---ACTAATCACATAATTCCTACAGTGAAACTTAA
1 CACCAGTGAAATGAATACGTAATTCCAGACTAAACTTATCACATAATTCCAACAGTGAAACTTAA
12129 CATT--CTTA
66 CATTGACTTA
* * * * * * * **
12137 CACCAATGAAATAAATACATAATTCCATCATTAAATTTATCACCTAATTCCAGTAGTGAAACTTA
1 CACCAGTGAAATGAATACGTAATTCCA-GACTAAACTTATCACATAATTCCAACAGTGAAACTTA
12202 ACATTGACTTA
65 ACATTGACTTA
* ** * * * * *
12213 AACCA-TGAAATGAATACGTAATTTTAACACTAAACTTTTCACATAAGT-CAAGGAGTGAAACTG
1 CACCAGTGAAATGAATACGTAA-TTCCAGACTAAACTTATCACATAATTCCAA-CAGTGAAACTT
12276 AACATT-ACTTA
64 AACATTGACTTA
* *
12287 CACTAGTGAAATGAATACGTAATTCCAGCAATAAACTTAT
1 CACCAGTGAAATGAATACGTAATTCCAG-ACTAAACTTAT
12327 GATTTCACAT
Statistics
Matches: 335, Mismatches: 62, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
69 26 0.08
71 31 0.09
74 45 0.13
75 134 0.40
76 99 0.30
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (75 bp):
CACCAGTGAAATGAATACGTAATTCCAGACTAAACTTATCACATAATTCCAACAGTGAAACTTAA
CATTGACTTA
Found at i:12697 original size:19 final size:21
Alignment explanation
Indices: 12666--12707 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
12656 TTCCCCTCAC
12666 ATTTGTGATTCTT-A-CCTTA
1 ATTTGTGATTCTTCACCCTTA
12685 ATTTGT-ATGTCTTCACCCTTA
1 ATTTGTGAT-TCTTCACCCTTA
12706 AT
1 AT
12708 CACCTTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 1 0.05
21 7 0.35
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (21 bp):
ATTTGTGATTCTTCACCCTTA
Found at i:15803 original size:28 final size:28
Alignment explanation
Indices: 15733--15807 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
15723 ACGATTAGGT
15733 GCTCCCGTGCAAGTCACTCTAATCCTTCGG
1 GCTCCCGTGCAAGTCACTC--ATCCTTCGG
*
15763 GCTCCCGTACAAGTCACTC-TCCTTCAGG
1 GCTCCCGTGCAAGTCACTCATCCTTC-GG
15791 GCTCCCGTGCAAGTCAC
1 GCTCCCGTGCAAGTCAC
15808 CCGAAATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 6 0.14
28 18 0.43
30 18 0.43
ACGTcount: A:0.17, C:0.39, G:0.20, T:0.24
Consensus pattern (28 bp):
GCTCCCGTGCAAGTCACTCATCCTTCGG
Found at i:15951 original size:68 final size:69
Alignment explanation
Indices: 15782--15956 Score: 171
Period size: 68 Copynumber: 2.6 Consensus size: 69
15772 CAAGTCACTC
** * * * *
15782 TCCTTCAGGGCTCCCGTGCAAGTCACCCGAAATAATTATGATTAGGTGCTCCCGTGTGAGTCACT
1 TCCTTCAGGGCTCATGTGCAAGTCAACCGGAATAATCATGATTAGGTGCTCCCGTGCGAGTCACT
*
15847 CTAT
66 CTAA
* * *
15851 TCCTT-AGGGTCTTCGTGTG--AGT-AACCAAGAATAATCATGATTAGGTGCT-CCTTGCGAGTC
1 TCCTTCAGGG-C-TCATGTGCAAGTCAACC-GGAATAATCATGATTAGGTGCTCCCGTGCGAGTC
15911 ACTCTAA
63 ACTCTAA
* * *
15918 TCCTTCAAGGCTCATGTGCAAGTCATCCGGAATACTCAT
1 TCCTTCAGGGCTCATGTGCAAGTCAACCGGAATAATCAT
15957 TATTTCATAT
Statistics
Matches: 85, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
66 6 0.07
67 24 0.28
68 41 0.48
69 9 0.11
70 5 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (69 bp):
TCCTTCAGGGCTCATGTGCAAGTCAACCGGAATAATCATGATTAGGTGCTCCCGTGCGAGTCACT
CTAA
Found at i:16197 original size:76 final size:76
Alignment explanation
Indices: 16104--16265 Score: 236
Period size: 76 Copynumber: 2.1 Consensus size: 76
16094 TCACAATTCT
* *
16104 AGCAGTGAAACGTAACATTGATTTACAGC-AGTGAAATGAATACGCAATTCTAGCACTAAACTTA
1 AGCAGTGAAACGTAACATTGACTTACA-CTAGTGAAATGAATACGCAATTCAAGCACTAAACTTA
*
16168 TGACATGATTTC
65 TGACATCATTTC
* * *
16180 AGTAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCAAGCACTAAACTTAT
1 AGCAGTGAAACGTAACATTGACTTACACTAGTGAAATGAATACGCAATTCAAGCACTAAACTTAT
* *
16245 TACATCATTTT
66 GACATCATTTC
16256 AGCAGTGAAA
1 AGCAGTGAAA
16266 TTTAGCAATG
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
75 1 0.01
76 75 0.99
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (76 bp):
AGCAGTGAAACGTAACATTGACTTACACTAGTGAAATGAATACGCAATTCAAGCACTAAACTTAT
GACATCATTTC
Found at i:17118 original size:19 final size:20
Alignment explanation
Indices: 17094--17139 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
17084 AGTGAACCGG
17094 CGGTTCAAACCGGTTTT-GC
1 CGGTTCAAACCGGTTTTAGC
**
17113 CGGTTCACCCCGGTTTTCAGC
1 CGGTTCAAACCGGTTTT-AGC
17134 CGGTTC
1 CGGTTC
17140 TTCCGGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
21 8 0.35
ACGTcount: A:0.11, C:0.33, G:0.26, T:0.30
Consensus pattern (20 bp):
CGGTTCAAACCGGTTTTAGC
Found at i:17487 original size:76 final size:76
Alignment explanation
Indices: 17252--17612 Score: 473
Period size: 75 Copynumber: 4.8 Consensus size: 76
17242 CGGTTTTAAT
* * * * * * *
17252 AACATTGAAATTTAGCATTGACTTACACCAGTAAAATGAATATGTAATTCCAGCGCT-AACTTAT
1 AACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
17316 CACATAATTCC
66 CACATAATTCC
* * **
17327 AATAATGAAACTTAACATTAACTTACACCAACGAAATGAATACGT-ATTCCAACACTAAACTTAT
1 AACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
*
17391 CTCATAATTCC
66 CACATAATTCC
* *
17402 AACAATGAAACATAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
1 AACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
17467 CACATAATTCC
66 CACATAATTCC
* * * *
17478 AGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCC-A-AC--AAGTTAT
1 AACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
17539 CACATAATTCC
66 CACATAATTCC
* * * * *
17550 AGCAACGAAACTTAACATTGACTTACATCAGTGAAATGAATATGTAACTCCAACACTAAACTT
1 AACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTT
17613 TGAAGTTTAA
Statistics
Matches: 248, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
72 62 0.25
73 1 0.00
74 13 0.05
75 93 0.38
76 79 0.32
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (76 bp):
AACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
CACATAATTCC
Found at i:17610 original size:148 final size:150
Alignment explanation
Indices: 17258--17612 Score: 484
Period size: 148 Copynumber: 2.4 Consensus size: 150
17248 TAATAACATT
* * * *
17258 GAAATTTAGCATTGACTTACACCAGTAAAATGAATATGTAATTCCAGCGCT-AACTTATCACATA
1 GAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAGCACTAAACTTATCACATA
* *
17322 ATTCCAATAATGAAACTTAACATTAACTTACACCAACGAAATGAATACGTATTCCAACACTAAAC
66 ATTCCAACAATGAAACTTAACATTAACTTACACCAACAAAATGAATACGTATTCCAACAC-AAAC
* *
17387 TTATCTCATAATTCCAACAAT
130 TTATCACATAATTCCAACAAC
* *
17408 GAAACATAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATA
1 GAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAGCACTAAACTTATCACATA
* * * ** *
17473 ATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCC-A-AC-AAG
66 ATTCCAACAATGAAACTTAACATTAACTTACACCAACAAAATGAATACGT-ATTCCAACACAAAC
*
17535 TTATCACATAATTCCAGCAAC
130 TTATCACATAATTCCAACAAC
* * *
17556 GAAACTTAACATTGACTTACATCAGTGAAATGAATATGTAACTCCAACACTAAACTT
1 GAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAGCACTAAACTT
17613 TGAAGTTTAA
Statistics
Matches: 181, Mismatches: 22, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
148 72 0.40
150 47 0.26
151 57 0.31
152 5 0.03
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (150 bp):
GAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAGCACTAAACTTATCACATA
ATTCCAACAATGAAACTTAACATTAACTTACACCAACAAAATGAATACGTATTCCAACACAAACT
TATCACATAATTCCAACAAC
Found at i:17722 original size:130 final size:129
Alignment explanation
Indices: 17483--17722 Score: 288
Period size: 130 Copynumber: 1.8 Consensus size: 129
17473 ATTCCAGCAA
*
17483 TGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACAAGTTATCACATAATT
1 TGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACAACTTATCACATAATT
* *
17548 CCAGCAACGAAACTTAACATTGACTTACATCAGTGAAATGAATATGTAACTCCAACACTAAACTT
66 CCAGCAACGAAACTTAACATTGACTTACA-CAATGAAATAAATATGTAACTCCAACACTAAACTT
* * * * *
17613 TGAAGTTTAACATTGACTTACATCAGTGAAATGAATATGTAATT-TAGCACTAAACTTATCACAT
1 TGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCA--AC--AACTTATCACAT
* * ** * *
17677 AATTCCCGTAGTGAAATTTAACATTGACTTACA-AAT-AATTAAATAT
62 AATTCCAGCAACGAAACTTAACATTGACTTACACAATGAAATAAATAT
17723 TATTGTATTT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
129 1 0.01
130 48 0.52
131 4 0.04
133 39 0.42
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (129 bp):
TGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACAACTTATCACATAATT
CCAGCAACGAAACTTAACATTGACTTACACAATGAAATAAATATGTAACTCCAACACTAAACTT
Found at i:27200 original size:27 final size:27
Alignment explanation
Indices: 27142--27192 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
27132 GAAATAATTG
27142 AAATACCCTGGATATGTAAAATGACCA
1 AAATACCCTGGATATGTAAAATGACCA
*
27169 AAATACCCTGGA-ATG-GAAATGACC
1 AAATACCCTGGATATGTAAAATGACC
27193 CAAGAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 3 0.13
27 12 0.52
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (27 bp):
AAATACCCTGGATATGTAAAATGACCA
Found at i:29865 original size:31 final size:31
Alignment explanation
Indices: 29829--29933 Score: 160
Period size: 31 Copynumber: 3.4 Consensus size: 31
29819 AGATACCGGA
*
29829 CTTGGGTAGGCCCTGTGGCCCTGAGATCATT
1 CTTGGGTAGGCCCTGTGGCCCTGAGATCTTT
29860 CTTGGGTAGGCCCTGTGGCCCTGAGATCTTT
1 CTTGGGTAGGCCCTGTGGCCCTGAGATCTTT
* *
29891 CTTGGATAGG-CCTCGTGGCCCTGAGAACTTT
1 CTTGGGTAGGCCCT-GTGGCCCTGAGATCTTT
29922 CTT-GGTAGGCCC
1 CTTGGGTAGGCCC
29934 ATAGGCCCCA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
30 8 0.12
31 60 0.88
ACGTcount: A:0.12, C:0.27, G:0.31, T:0.30
Consensus pattern (31 bp):
CTTGGGTAGGCCCTGTGGCCCTGAGATCTTT
Found at i:30897 original size:23 final size:23
Alignment explanation
Indices: 30871--30920 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
30861 ATATAACACC
30871 ATTATATAAATAAATATTTATAT
1 ATTATATAAATAAATATTTATAT
* *
30894 ATTATATACATAACTATTTATAT
1 ATTATATAAATAAATATTTATAT
30917 -TTAT
1 ATTAT
30921 TTAGAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATATAAATAAATATTTATAT
Found at i:31050 original size:30 final size:29
Alignment explanation
Indices: 31014--31074 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
31004 TTTTTACTAC
31014 ATATAATTA-AATAAAAATAAAATATTATGT
1 ATATAATTACAAT-AAAATAAAAT-TTATGT
*
31044 ATATAATTACAATAAATTAAAATTTATGT
1 ATATAATTACAATAAAATAAAATTTATGT
31073 AT
1 AT
31075 TACACCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 8 0.28
30 18 0.62
31 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
ATATAATTACAATAAAATAAAATTTATGT
Found at i:35688 original size:17 final size:17
Alignment explanation
Indices: 35666--35699 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35656 ACTTTGACCA
35666 AAAAGTCAAATTTTTTG
1 AAAAGTCAAATTTTTTG
*
35683 AAAAGTCATATTTTTTG
1 AAAAGTCAAATTTTTTG
35700 TTTTTTGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAAGTCAAATTTTTTG
Found at i:39629 original size:18 final size:18
Alignment explanation
Indices: 39606--39668 Score: 108
Period size: 18 Copynumber: 3.5 Consensus size: 18
39596 CCGACCCGAC
39606 CCGTTGACTGACCGTTAA
1 CCGTTGACTGACCGTTAA
**
39624 CCGTTGACTGATTGTTAA
1 CCGTTGACTGACCGTTAA
39642 CCGTTGACTGACCGTTAA
1 CCGTTGACTGACCGTTAA
39660 CCGTTGACT
1 CCGTTGACT
39669 TTGACCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (18 bp):
CCGTTGACTGACCGTTAA
Found at i:44381 original size:69 final size:69
Alignment explanation
Indices: 44293--44517 Score: 256
Period size: 69 Copynumber: 3.3 Consensus size: 69
44283 GTTCCCTTGT
*
44293 GAGTCACTCTAATTCTTCGGGGCTCCCGTGCAAGTCAACCGAAGTAATTATGATTAGGTGCTCCC
1 GAGTCACTCTAATCCTTCGGGGCTCCCGTGCAAGTCAACCGAAGTAATTATGATTAGGTGCTCCC
44358 GTGC
66 GTGC
* * ** * * *
44362 AAGTTACTCTAATCCTTCGGGGCTCCTATGCAAGTCACCCGAAATAATTATGATTAGGTTCTCCC
1 GAGTCACTCTAATCCTTCGGGGCTCCCGTGCAAGTCAACCGAAGTAATTATGATTAGGTGCTCCC
**
44427 GTAT
66 GTGC
* * ** * * *
44431 GAGTCACTCTATTCCTTAGGGGCTTTCGTGCGAGT-AACC-AAGAATAATCACGATTAGGTGCTC
1 GAGTCACTCTAATCCTTCGGGGCTCCCGTGCAAGTCAACCGAAG--TAATTATGATTAGGTGCTC
*
44494 CCTTGC
64 CCGTGC
44500 GAGTCACTCTAATCCTTC
1 GAGTCACTCTAATCCTTC
44518 AAGGCTCATG
Statistics
Matches: 125, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
67 2 0.02
68 3 0.02
69 120 0.96
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (69 bp):
GAGTCACTCTAATCCTTCGGGGCTCCCGTGCAAGTCAACCGAAGTAATTATGATTAGGTGCTCCC
GTGC
Found at i:44545 original size:69 final size:69
Alignment explanation
Indices: 44293--44545 Score: 190
Period size: 69 Copynumber: 3.7 Consensus size: 69
44283 GTTCCCTTGT
* * ** * * *
44293 GAGTCACTCTAATTCTTCGGGGCTCCCGTGCAAGTCAACC--GAAGTAATTATGATTAGGTGCTC
1 GAGTCACTCTAATCCTTCAGGGCTCATGTGCGAGTC-ACCAGGAA-TAATCACGATTAGGTGCTC
44356 CCGTGC
64 CCGTGC
* * * * * * * * * * *
44362 AAGTTACTCTAATCCTTCGGGGCTCCTATGCAAGTCACCCGAAATAATTATGATTAGGTTCTCCC
1 GAGTCACTCTAATCCTTCAGGGCTCATGTGCGAGTCACCAGGAATAATCACGATTAGGTGCTCCC
**
44427 GTAT
66 GTGC
* * * *
44431 GAGTCACTCTATTCCTT-AGGGGCT-TTCGTGCGAGTAACCAAGAATAATCACGATTAGGTGCTC
1 GAGTCACTCTAATCCTTCA-GGGCTCAT-GTGCGAGTCACCAGGAATAATCACGATTAGGTGCTC
*
44494 CCTTGC
64 CCGTGC
* * *
44500 GAGTCACTCTAATCCTTCAAGGCTCATGTGCGACTCACCTGGAATA
1 GAGTCACTCTAATCCTTCAGGGCTCATGTGCGAGTCACCAGGAATA
44546 CTCATTATTA
Statistics
Matches: 145, Mismatches: 33, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
68 4 0.03
69 137 0.94
70 4 0.03
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (69 bp):
GAGTCACTCTAATCCTTCAGGGCTCATGTGCGAGTCACCAGGAATAATCACGATTAGGTGCTCCC
GTGC
Found at i:52339 original size:28 final size:28
Alignment explanation
Indices: 52297--52364 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
52287 CAAAAGTTTT
* *
52297 ATAGAATTTGAAGTTTATGATATAATTC
1 ATAGGATTTGGAGTTTATGATATAATTC
* *
52325 ATAGGATTTGGAGTTTATGATGTAATTT
1 ATAGGATTTGGAGTTTATGATATAATTC
*
52353 ATAGGGTTTGGA
1 ATAGGATTTGGA
52365 TTAAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (28 bp):
ATAGGATTTGGAGTTTATGATATAATTC
Found at i:56392 original size:13 final size:14
Alignment explanation
Indices: 56356--56393 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
56346 AGCCTGCCCG
56356 ACTGAGTCAACTCGC
1 ACTGAGTCAACTC-C
56371 ACTGAGTCAACT-C
1 ACTGAGTCAACTCC
*
56384 ACTGGGTCAA
1 ACTGAGTCAA
56394 TCCGTTGACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
15 12 0.55
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (14 bp):
ACTGAGTCAACTCC
Found at i:58106 original size:24 final size:24
Alignment explanation
Indices: 58074--58132 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
58064 AATTCTATTT
* *
58074 TGATTTCTGATCTGGATTATGTTA
1 TGATTTCTGATATGAATTATGTTA
* * *
58098 TGATATCTGATATGAATTCTGTTT
1 TGATTTCTGATATGAATTATGTTA
58122 TGATTTCTGAT
1 TGATTTCTGAT
58133 TTCTACGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (24 bp):
TGATTTCTGATATGAATTATGTTA
Found at i:60174 original size:15 final size:14
Alignment explanation
Indices: 60154--60223 Score: 86
Period size: 15 Copynumber: 4.9 Consensus size: 14
60144 GTGTACCCGA
60154 TTGAGTCAACTCGCG
1 TTGAGTCAACTCG-G
*
60169 TTGAGTTAACTCGG
1 TTGAGTCAACTCGG
*
60183 CTGAGTCAACTCGCG
1 TTGAGTCAACTCG-G
*
60198 TTGAGTTAACTCGG
1 TTGAGTCAACTCGG
*
60212 CTGAGTCAACTC
1 TTGAGTCAACTC
60224 ACTAGGTCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
14 23 0.49
15 24 0.51
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (14 bp):
TTGAGTCAACTCGG
Found at i:60193 original size:14 final size:15
Alignment explanation
Indices: 60155--60223 Score: 88
Period size: 14 Copynumber: 4.7 Consensus size: 15
60145 TGTACCCGAT
*
60155 TGAGTCAACTCGCGT
1 TGAGTCAACTCGCGC
*
60170 TGAGTTAACTCG-GC
1 TGAGTCAACTCGCGC
*
60184 TGAGTCAACTCGCGT
1 TGAGTCAACTCGCGC
*
60199 TGAGTTAACTCG-GC
1 TGAGTCAACTCGCGC
60213 TGAGTCAACTC
1 TGAGTCAACTC
60224 ACTAGGTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
14 23 0.50
15 23 0.50
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.28
Consensus pattern (15 bp):
TGAGTCAACTCGCGC
Found at i:60197 original size:29 final size:29
Alignment explanation
Indices: 60155--60223 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
60145 TGTACCCGAT
60155 TGAGTCAACTCGCGTTGAGTTAACTCGGC
1 TGAGTCAACTCGCGTTGAGTTAACTCGGC
60184 TGAGTCAACTCGCGTTGAGTTAACTCGGC
1 TGAGTCAACTCGCGTTGAGTTAACTCGGC
60213 TGAGTCAACTC
1 TGAGTCAACTC
60224 ACTAGGTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.28
Consensus pattern (29 bp):
TGAGTCAACTCGCGTTGAGTTAACTCGGC
Found at i:62381 original size:24 final size:24
Alignment explanation
Indices: 62352--62444 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
62342 TTTCCTATTA
* *
62352 AATTCTGTTCTGATACCTGACCTG
1 AATTCTGTTCTGATATCTGATCTG
* *
62376 AATTCTATTCTGATTTCTGATCTG
1 AATTCTGTTCTGATATCTGATCTG
* * * *
62400 GATTCTGTTATGATATCTTATATG
1 AATTCTGTTCTGATATCTGATCTG
* *
62424 AATTCTGTTTTGATTTCTGAT
1 AATTCTGTTCTGATATCTGAT
62445 ATCTCCATTT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (24 bp):
AATTCTGTTCTGATATCTGATCTG
Found at i:62414 original size:48 final size:48
Alignment explanation
Indices: 62353--62444 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
62343 TTCCTATTAA
* *
62353 ATTCTGTTCTGATACCTGACCTGAATTCTATTCTGATTTCTGATCTGG
1 ATTCTGTTATGATACCTGACATGAATTCTATTCTGATTTCTGATCTGG
* * * * *
62401 ATTCTGTTATGATATCTTATATGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTATGATACCTGACATGAATTCTATTCTGATTTCTGAT
62445 ATCTCCATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (48 bp):
ATTCTGTTATGATACCTGACATGAATTCTATTCTGATTTCTGATCTGG
Found at i:68648 original size:7 final size:7
Alignment explanation
Indices: 68600--68664 Score: 69
Period size: 7 Copynumber: 9.3 Consensus size: 7
68590 TCTGTAACAA
68600 TAATAAT
1 TAATAAT
*
68607 TATTAAT
1 TAATAAT
**
68614 TAATGTT
1 TAATAAT
* *
68621 TATTAAA
1 TAATAAT
68628 TAA-AAT
1 TAATAAT
68634 TCAATAAT
1 T-AATAAT
68642 TAATAAT
1 TAATAAT
68649 TAATAAT
1 TAATAAT
68656 TAATAAT
1 TAATAAT
68663 TA
1 TA
68665 GTTGATTTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
6 3 0.07
7 39 0.85
8 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (7 bp):
TAATAAT
Found at i:69272 original size:69 final size:69
Alignment explanation
Indices: 69121--69283 Score: 175
Period size: 69 Copynumber: 2.4 Consensus size: 69
69111 GATAATATGC
* * * *
69121 TCCCTTGTGAGTCACTCTAATCCTTCACAACTCCCGTGCGAGTCAATCGAAATAATTTCGATTAG
1 TCCCATGTGAGTCACTCTAATCCTTCACAACTCCCGTGCAAGTCAACCGAAATAATTACGATTAG
*
69186 GTGG
66 GTGA
** ** ** * *
69190 TCCCATGCAAGTCACTCTAATCCTTCGGAGTTCCTGTGCAAGTCACCCGAAATAATTACGATTAG
1 TCCCATGTGAGTCACTCTAATCCTTCACAACTCCCGTGCAAGTCAACCGAAATAATTACGATTAG
69255 GTGCA
66 GTG-A
* *
69260 T-CCGTGTGAGTCACTCTATTCCTT
1 TCCCATGTGAGTCACTCTAATCCTT
69284 TGGGACTTTC
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
69 75 0.99
70 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (69 bp):
TCCCATGTGAGTCACTCTAATCCTTCACAACTCCCGTGCAAGTCAACCGAAATAATTACGATTAG
GTGA
Found at i:69570 original size:76 final size:76
Alignment explanation
Indices: 69482--69899 Score: 550
Period size: 76 Copynumber: 5.5 Consensus size: 76
69472 TCTAGCAGAA
* * * * *
69482 AAACTTAACATTGACTTATACCAGTGAAATGAATACATAATTCTAGCACTAAACTTATGACATGA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAA
* **
69547 TTTCAGGAGTG
66 TTCCAACAGTG
* * * * *
69558 AAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCAAGAACTATACTTATCACATCA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAA
* * *
69623 TTTCAGCAATG
66 TTCCAACAGTG
* * **
69634 -AACTTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAGCGCTAAACTTAAAACATA
1 AAAC-TTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATA
69698 ATTCCAACAGTG
65 ATTCCAACAGTG
* *
69710 AAACTTAACATTGACTTACATCAGTGAAATTAATACGTAATTCCAGCACTAAACTTATCACATAA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAA
* *
69775 TTCCATCAATG
66 TTCCAACAGTG
* * * *
69786 AAATTTAACATTGACTTAAACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAA
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAA
69851 TTCCAACAGTG
66 TTCCAACAGTG
* *
69862 AAACTTAACATTGGCTTACATCAGTGAAATGAATACGT
1 AAACTTAACATTGACTTACACCAGTGAAATGAATACGT
69900 GACTCGAGTT
Statistics
Matches: 299, Mismatches: 41, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
75 3 0.01
76 293 0.98
77 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.29
Consensus pattern (76 bp):
AAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAA
TTCCAACAGTG
Found at i:69934 original size:183 final size:183
Alignment explanation
Indices: 69725--70057 Score: 497
Period size: 183 Copynumber: 1.8 Consensus size: 183
69715 TAACATTGAC
** *
69725 TTACATCAGTGAAATTAATACGTAATTCCAGCACTAAACTTATCACATAATTC-CATCAATGAAA
1 TTACATCAGTGAAACGAATACGTAATTACAGCACTAAACTTATCACATAATTCTCAT-AATGAAA
* * *
69789 TTTAACATTGACTTAAACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTC
65 TTTAACATTGACTTAAACCAGTAAAACGAATACGTAATTCCAACACTAAACTCATCAAATAATTC
69854 CAACAGTGAAACTTAACATTGGCTTACATCAGTGAAATGAATACGTGACTCGAG
130 CAACAGTGAAACTTAACATTGGCTTACATCAGTGAAATGAATACGTGACTCGAG
* * * * * *
69908 TTACATTAGTGAAACGAATACGTAATTATAGCACTAAACTTATCACATTATTCTCGTAGTGTAAT
1 TTACATCAGTGAAACGAATACGTAATTACAGCACTAAACTTATCACATAATTCTCATAATGAAAT
* * *
69973 TTAACATTGACTTACACCAGTGAAACGAATACGTAATTCCAGCACTAAACTCATCAAATAATTCC
66 TTAACATTGACTTAAACCAGTAAAACGAATACGTAATTCCAACACTAAACTCATCAAATAATTCC
**
70038 TGCAGTGAAACTTAACATTG
131 AACAGTGAAACTTAACATTG
70058 ACTTGTTGTC
Statistics
Matches: 132, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
183 130 0.98
184 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (183 bp):
TTACATCAGTGAAACGAATACGTAATTACAGCACTAAACTTATCACATAATTCTCATAATGAAAT
TTAACATTGACTTAAACCAGTAAAACGAATACGTAATTCCAACACTAAACTCATCAAATAATTCC
AACAGTGAAACTTAACATTGGCTTACATCAGTGAAATGAATACGTGACTCGAG
Found at i:69997 original size:76 final size:76
Alignment explanation
Indices: 69915--70061 Score: 206
Period size: 76 Copynumber: 1.9 Consensus size: 76
69905 GAGTTACATT
* * * * * * *
69915 AGTGAAACGAATACGTAATTATAGCACTAAACTTATCACATTATT-CTCGTAGTGTAATTTAACA
1 AGTGAAACGAATACGTAATTACAGCACTAAACTCATCAAATAATTCCT-GCAGTGAAACTTAACA
69979 TTGACTTACACC
65 TTGACTTACACC
*
69991 AGTGAAACGAATACGTAATTCCAGCACTAAACTCATCAAATAATTCCTGCAGTGAAACTTAACAT
1 AGTGAAACGAATACGTAATTACAGCACTAAACTCATCAAATAATTCCTGCAGTGAAACTTAACAT
70056 TGACTT
66 TGACTT
70062 GTTGTCGTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 60 0.97
77 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (76 bp):
AGTGAAACGAATACGTAATTACAGCACTAAACTCATCAAATAATTCCTGCAGTGAAACTTAACAT
TGACTTACACC
Found at i:75271 original size:76 final size:75
Alignment explanation
Indices: 75137--75340 Score: 223
Period size: 76 Copynumber: 2.7 Consensus size: 75
75127 CCGTCTTCCG
* * * * * * *
75137 TAACATGACTTACATCAGCGAAATGAATACATAATTCCAGCATTAAATATATATCATAATTCCAG
1 TAACATGACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTAAATATATATCATAAGTCAAG
*
75202 TAGTGAAACT
66 GAGTGAAACT
* *
75212 TAACATCGACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTACACT-TTTCA-CATAAGTC
1 TAACAT-GACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTA-AATATAT-ATCATAAGTC
75275 AAGGAGTGAAACT
63 AAGGAGTGAAACT
* * * * *
75288 GAACATTGACTTAGACTAGTGAAATGAATACGTAATTCCAGCATTAAACATAT
1 TAACA-TGACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTAAATATAT
75341 GATTTCACAT
Statistics
Matches: 107, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
75 7 0.07
76 96 0.90
77 4 0.04
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (75 bp):
TAACATGACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTAAATATATATCATAAGTCAAG
GAGTGAAACT
Found at i:79352 original size:28 final size:29
Alignment explanation
Indices: 79312--79374 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
79302 AGTTTACAAA
*
79312 ATTTGAAGTTTATGATATAATTCAT-AGG
1 ATTTGGAGTTTATGATATAATTCATAAGG
* *
79340 ATTTGGAGTTTATGATGTAATTTATAAGG
1 ATTTGGAGTTTATGATATAATTCATAAGG
79369 -TTTGGA
1 ATTTGGA
79375 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 28 0.90
29 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (29 bp):
ATTTGGAGTTTATGATATAATTCATAAGG
Found at i:81535 original size:69 final size:69
Alignment explanation
Indices: 81460--81695 Score: 251
Period size: 69 Copynumber: 3.4 Consensus size: 69
81450 TACGATAATA
*
81460 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGAGCTCCCGTGCGAGTCAACTGAAATAATTACGAT
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACTGAAATAATTACGAT
81525 TAGG
66 TAGG
** ** * * *
81529 TGCTCCCAAGCAAGTCACTCTAATCCTTCGGGGCTCCTGTGCAAGTC-ACTCGAAATAATTATGA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACT-GAAATAATTACGA
* *
81593 CTAGA
65 TTAGG
* * * ** ** * *
81598 TGCTCCCGTGTGAGTCACTCTATTCCTTAGGGGCTTTCGTGCGAGT-AACCAAGAATACTCACGA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACTGA-AATAATTACGA
81662 TTAGG
65 TTAGG
* *
81667 TGCTCTCTTATGAGTCACTCTAATCCTTC
1 TGCTCCCTTGTGAGTCACTCTAATCCTTC
81696 AAAGCTCATG
Statistics
Matches: 132, Mismatches: 32, Indels: 6
0.78 0.19 0.04
Matches are distributed among these distances:
68 4 0.03
69 128 0.97
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (69 bp):
TGCTCCCTTGTGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAACTGAAATAATTACGAT
TAGG
Found at i:83334 original size:69 final size:69
Alignment explanation
Indices: 83207--83335 Score: 152
Period size: 69 Copynumber: 1.9 Consensus size: 69
83197 AGTCACCCGA
* * ** * * * **
83207 AATAATTATGATTAGGTGCTCCCGTGTGAGTCACTCTATTCCTTAGGGGTTTTCGTGCGAGTAAC
1 AATAATCACGATTAGGTGCTCCCGTACGAGTCACTCTAATCCTTAAGGCTCATCGTGCGAGTAAC
83272 CAAG
66 CAAG
*
83276 AATAATCACGATTAGGTGCTCCCTTACGAGTCACTCTAATCCTTCAAGGCTCAT-GTGCGA
1 AATAATCACGATTAGGTGCTCCCGTACGAGTCACTCTAATCCTT-AAGGCTCATCGTGCGA
83336 CTCACCCGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
69 44 0.90
70 5 0.10
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (69 bp):
AATAATCACGATTAGGTGCTCCCGTACGAGTCACTCTAATCCTTAAGGCTCATCGTGCGAGTAAC
CAAG
Found at i:83626 original size:76 final size:76
Alignment explanation
Indices: 83509--83880 Score: 457
Period size: 76 Copynumber: 4.9 Consensus size: 76
83499 AACACATCAC
* * * * * *
83509 AATTCTAGCCGTGAAACTTAACATTGATTTACGCCAATGAAATGAATACGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAA
*
83574 ACTTATGACAT
66 ACTTATCACAT
* * *
83585 GATTTCAGCAGTGAAACTTAACGTTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAA
83650 ACTTATCACAT
66 ACTTATCACAT
* * * *
83661 CATTTCAGCAGTGAAATTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAAG-ACTA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT-CAAGCACTA
83725 AACTTATCACAT
65 AACTTATCACAT
* * * * *
83737 AATTCCAGCAATAAAAATTTAATATTGACTT--ACCAGTAAAATGAATACGTAATTCCAA-CACT
1 AATTCCAGCAGT-GAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT-CAAGCACT
83799 AAACTTATCACAT
64 AAACTTATCACAT
* * * * *
83812 AATTCCAACAGCGAAACTTAACATTGACTTACATCAGTGAAATGAATACGTGACTCCAA-CACTA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGT-AATTCAAGCACTA
83876 AACTT
65 AACTT
83881 TGAAGCTTAA
Statistics
Matches: 259, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
74 15 0.06
75 50 0.19
76 172 0.66
77 22 0.08
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (76 bp):
AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAA
ACTTATCACAT
Found at i:83833 original size:151 final size:151
Alignment explanation
Indices: 83521--83880 Score: 456
Period size: 151 Copynumber: 2.4 Consensus size: 151
83511 TTCTAGCCGT
* * * * *
83521 GAAACTTAACATTGATTTACGCCAATGAAATGAATACGTAATT-CTAGCACTAAACTTATGACAT
1 GAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAAG-ACTAAACTTATCACAT
* * * * * *
83585 GATTTCAGCAGTGAAACTTAACGTTGACTTACACCAGTGAAATGAATACGTAATTCAAGCACTAA
65 AATTCCAGCAATAAAACTTAACATTGACTTA-ACCAGTAAAATGAATACGTAATTCAAGCACTAA
* * * *
83650 ACTTATCACATCATTTCAGCAGT
129 ACTTATCACATAATTCCAACAGC
* *
83673 GAAATTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAAGACTAAACTTATCACATA
1 GAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAAGACTAAACTTATCACATA
* *
83738 ATTCCAGCAATAAAAATTTAATATTGACTT-ACCAGTAAAATGAATACGTAATTCCAA-CACTAA
66 ATTCCAGCAAT-AAAACTTAACATTGACTTAACCAGTAAAATGAATACGTAATT-CAAGCACTAA
83801 ACTTATCACATAATTCCAACAGC
129 ACTTATCACATAATTCCAACAGC
* * * *
83824 GAAACTTAACATTGACTTACATCAGTGAAATGAATACGTGACTCCAACACTAAACTT
1 GAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAAGACTAAACTT
83881 TGAAGCTTAA
Statistics
Matches: 180, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
151 98 0.54
152 65 0.36
153 17 0.09
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.28
Consensus pattern (151 bp):
GAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAAGACTAAACTTATCACATA
ATTCCAGCAATAAAACTTAACATTGACTTAACCAGTAAAATGAATACGTAATTCAAGCACTAAAC
TTATCACATAATTCCAACAGC
Found at i:84013 original size:76 final size:76
Alignment explanation
Indices: 83881--84115 Score: 260
Period size: 76 Copynumber: 3.1 Consensus size: 76
83871 CACTAAACTT
* * * ** *
83881 TGAAGCTTAACATTGACTTACATCAGTGAAATGGATACGTAATTATAGAACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
83946 AATTCCCATAG
66 AATTCCCATAG
* * *
83957 TGAAATTTAACATTGACTTACACCAGTGAAATGCATACGTAATTCCAGCACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
***
84022 AATTCCTGCAG
66 AATTCCCATAG
* ** * * *
84033 TGAAACTTAACATTAACTTACAACAGCAAAATGAAAACAG-AATTCCAGCATTAAATTTATCA-A
1 TGAAACTTAACATTGACTTACAACAGTGAAATGAATAC-GTAATTCCAGCACTAAACTTATCACA
84096 CTAATT-CCAGTAG
65 -TAATTCCCA-TAG
84109 TGAAACT
1 TGAAACT
84116 AATGTACGTG
Statistics
Matches: 134, Mismatches: 22, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
75 2 0.01
76 131 0.98
77 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
AATTCCCATAG
Found at i:84067 original size:210 final size:207
Alignment explanation
Indices: 83678--84067 Score: 552
Period size: 210 Copynumber: 1.9 Consensus size: 207
83668 GCAGTGAAAT
*
83678 TTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAAGACTAAACTTATCACATAATTCC
1 TTAACATTGACTTACACCAGTGAAATGAATACGTAATT-CAAGACTAAACTTATCACATAATTCC
*
83743 AGCAATAAAAATTTAATATTGACTTACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATC
65 A-CAATAAAAATTTAACATTGACTTACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATC
* * **
83808 ACATAATTCCAACAGCGAAACTTAACATTGACTTACATCAGTGAAATGAATACGTGACTCCAACA
129 ACATAATTCCAACAGCGAAACTTAACATTAACTTACAACAGCAAAATGAATACGTGACTCCAACA
83873 CTAAACTTTGAAGC
194 CTAAACTTTGAAGC
* *
83887 TTAACATTGACTTACATCAGTGAAATGGATACGTAATT-ATAGAACTAAACTTATCACATAATTC
1 TTAACATTGACTTACACCAGTGAAATGAATACGTAATTCA-AG-ACTAAACTTATCACATAATTC
* * * *
83951 C-C-ATAGTGAAATTTAACATTGACTTACACCAGTGAAATGCATACGTAATTCCAGCACTAAACT
64 CACAATA--AAAATTTAACATTGACTT--ACCAGTAAAATGAATACGTAATTCCAACACTAAACT
** *
84014 TATCACATAATTCCTGCAGTGAAACTTAACATTAACTTACAACAGCAAAATGAA
125 TATCACATAATTCCAACAGCGAAACTTAACATTAACTTACAACAGCAAAATGAA
84068 AACAGAATTC
Statistics
Matches: 160, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
206 3 0.02
207 2 0.01
208 18 0.11
209 57 0.36
210 80 0.50
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.28
Consensus pattern (207 bp):
TTAACATTGACTTACACCAGTGAAATGAATACGTAATTCAAGACTAAACTTATCACATAATTCCA
CAATAAAAATTTAACATTGACTTACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCAC
ATAATTCCAACAGCGAAACTTAACATTAACTTACAACAGCAAAATGAATACGTGACTCCAACACT
AAACTTTGAAGC
Found at i:85281 original size:83 final size:83
Alignment explanation
Indices: 85020--85327 Score: 255
Period size: 83 Copynumber: 3.7 Consensus size: 83
85010 TAAAAGCACT
* * * * * *
85020 TAAAGTACTATTTTGTTGCGGTGTTTGTTG-AAAAATGA-CACCATATATGAACCCTATTACAAC
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAAT-ACCACTATATATGAACCCTATTATAGC
* *
85083 ATCTATATAAAAACGCTGC
65 ATTTATATAAAAACGCCGC
* * * * * * * * * *
85102 TAAAGTACTCCACTGTTACGACGTTTGGTGGAAAAAATGCAACTATAGATGAACTC-ATTATTGA
1 TAAAGTACTACTCTGTTGCGGCGTTT-GTTGAAAAAATACCACTATATATGAACCCTATTATAG-
* * * *
85166 CTTTTGTATAAAAATGCCAC
64 CATTTATATAAAAACGCCGC
* * * *
85186 TAACA-TAATACTCTATTGCGGCGTTTGTTGAACAAATACCATTATATATGAACCCTATTATAGC
1 TAA-AGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATACCACTATATATGAACCCTATTATAGC
*
85250 ATTTATATAAAAACACCGC
65 ATTTATATAAAAACGCCGC
* * ** * *
85269 TAAAGTACTACTCTTTTGCGGCATTTGTTGAAAAAATGGCACTATAGATGAACCTTATT
1 TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATACCACTATATATGAACCCTATT
85328 GTGGTTTTTT
Statistics
Matches: 169, Mismatches: 50, Indels: 13
0.73 0.22 0.06
Matches are distributed among these distances:
82 20 0.12
83 92 0.54
84 56 0.33
85 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (83 bp):
TAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATACCACTATATATGAACCCTATTATAGCA
TTTATATAAAAACGCCGC
Found at i:87596 original size:29 final size:29
Alignment explanation
Indices: 87561--87637 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
87551 AAACTAAATT
** *
87561 GATGTCATTAATTACATCATTGAATTAAA
1 GATGTCATTGCTTACATCATTGAAGTAAA
* *
87590 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTGAAGTAAA
87619 GATGTCATTGCTTACATCA
1 GATGTCATTGCTTACATCA
87638 ATTTAGTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTGAAGTAAA
Found at i:88890 original size:24 final size:24
Alignment explanation
Indices: 88863--88913 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
88853 AACGTGGCCA
*
88863 AGGTAGAGGTAGAGGCCATGGACG
1 AGGTAGAAGTAGAGGCCATGGACG
* * * *
88887 AGGTGGAAGTCGAGGTCGTGGACG
1 AGGTAGAAGTAGAGGCCATGGACG
88911 AGG
1 AGG
88914 CTGGAATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.12, G:0.49, T:0.14
Consensus pattern (24 bp):
AGGTAGAAGTAGAGGCCATGGACG
Found at i:92348 original size:29 final size:29
Alignment explanation
Indices: 92313--92394 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
92303 AAACTAAATT
* *
92313 GATGTCATTACTTACATAATTTAATTAAA
1 GATGTCATTGCTTACATAATTTAAGTAAA
** *
92342 GATGTCATTGCTTACACCATTTAAGTAAT
1 GATGTCATTGCTTACATAATTTAAGTAAA
*
92371 GATGTCATTGTTTACATCAATTTA
1 GATGTCATTGCTTACAT-AATTTA
92395 GTTAGGTGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 39 0.89
30 5 0.11
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATAATTTAAGTAAA
Found at i:105600 original size:31 final size:31
Alignment explanation
Indices: 105565--105624 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
105555 AATAGATACT
*
105565 AACATTTTCTAAGAGAATGCAATGAAGCTTG
1 AACATTTTCTAAGAAAATGCAATGAAGCTTG
105596 AACATTTTCTAAGAAAATGCAATGAAGCT
1 AACATTTTCTAAGAAAATGCAATGAAGCT
105625 GAAAAAGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (31 bp):
AACATTTTCTAAGAAAATGCAATGAAGCTTG
Found at i:107758 original size:21 final size:20
Alignment explanation
Indices: 107729--107768 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
107719 AATTTTATTT
107729 TAATAATTTTTAATAAAAATA
1 TAATAA-TTTTAATAAAAATA
* *
107750 TAATTATTTTGATAAAAAT
1 TAATAATTTTAATAAAAAT
107769 TGGAATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAATAATTTTAATAAAAATA
Found at i:110823 original size:21 final size:20
Alignment explanation
Indices: 110798--110840 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
110788 TTTCATAAAT
110798 AAACAT-GCAATCTATGAATTC
1 AAACATAGCAAT-TATG-ATTC
*
110819 AAACATAGCACTTATGATTC
1 AAACATAGCAATTATGATTC
110839 AA
1 AA
110841 TATACATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (20 bp):
AAACATAGCAATTATGATTC
Found at i:111153 original size:31 final size:31
Alignment explanation
Indices: 111117--111196 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
111107 CCATAGATTT
* *
111117 CAAAGAACCTAGGTAATCAGTCCATATGTCC
1 CAAAGAACATAGGTAAACAGTCCATATGTCC
* *
111148 TAAAGAACATAGATAAACAGTCCATATGTCC
1 CAAAGAACATAGGTAAACAGTCCATATGTCC
*
111179 CGAAGAACATAGGTAAAC
1 CAAAGAACATAGGTAAAC
111197 CCTCGACCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (31 bp):
CAAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:121460 original size:21 final size:20
Alignment explanation
Indices: 121434--121492 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 20
121424 ATTATCCAAT
121434 AAACTTGACATCCATAACAAC
1 AAACTTGA-ATCCATAACAAC
121455 AAACTTGAAATCCATAACAAC
1 AAACTTG-AATCCATAACAAC
*
121476 CAACTTGAACTCCATAA
1 AAACTTGAA-TCCATAA
121493 TAATAAATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.05, T:0.20
Consensus pattern (20 bp):
AAACTTGAATCCATAACAAC
Done.