Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007805.1 Hibiscus syriacus cultivar Beakdansim tig00110123_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: 2708727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1492124 original size:21 final size:23
Alignment explanation
Indices: 1492098--1492157 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1492088 ATAACTTTCA
1492098 CCGAAGTG-CCACATA-TTTGTC
1 CCGAAGTGACCACATAGTTTGTC
1492119 CCGAAG-GACCACATAGTTTTGTC
1 CCGAAGTGACCACATAG-TTTGTC
1492142 CCGAA-TGACCACATAG
1 CCGAAGTGACCACATAG
1492158 AACCTTCGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.03
21 13 0.37
23 21 0.60
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (23 bp):
CCGAAGTGACCACATAGTTTGTC
Found at i:1503662 original size:18 final size:18
Alignment explanation
Indices: 1503639--1503677 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1503629 GAAATAAGTT
1503639 AATTAATC-AAATTAATTA
1 AATTAATCAAAATT-ATTA
1503657 AATTAATCAAAATTATTA
1 AATTAATCAAAATTATTA
1503675 AAT
1 AAT
1503678 ATTTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAATCAAAATTATTA
Found at i:1504180 original size:14 final size:12
Alignment explanation
Indices: 1504154--1504179 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1504144 TTATTATCGG
1504154 TTATATAATTTT
1 TTATATAATTTT
1504166 TTATATAATTTT
1 TTATATAATTTT
1504178 TT
1 TT
1504180 TATTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATAATTTT
Found at i:1504189 original size:14 final size:13
Alignment explanation
Indices: 1504154--1504182 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1504144 TTATTATCGG
1504154 TTATATAA-TTTT
1 TTATATAATTTTT
1504166 TTATATAATTTTT
1 TTATATAATTTTT
1504179 TTAT
1 TTAT
1504183 TTTAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATATAATTTTT
Found at i:1504436 original size:31 final size:31
Alignment explanation
Indices: 1504401--1504461 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1504391 ATTCATTCAG
* *
1504401 GTGTCTAAAGTTATAAACGTTATCATTTTAC
1 GTGTCTAAAGTTACAAACATTATCATTTTAC
* * *
1504432 GTGTCTGACGTTACAAACATTATTATTTTA
1 GTGTCTAAAGTTACAAACATTATCATTTTA
1504462 AGTATCTCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (31 bp):
GTGTCTAAAGTTACAAACATTATCATTTTAC
Found at i:1504739 original size:22 final size:23
Alignment explanation
Indices: 1504690--1504742 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1504680 CAATTAAATG
* *
1504690 AATTTAAGGGATTGAGTATTTGA
1 AATTTAAGGGATTGAGGAATTGA
* *
1504713 GATTTTAGGGATT-AGGAATTGA
1 AATTTAAGGGATTGAGGAATTGA
1504735 AATTTAAG
1 AATTTAAG
1504743 AATTTGAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (23 bp):
AATTTAAGGGATTGAGGAATTGA
Found at i:1505066 original size:31 final size:31
Alignment explanation
Indices: 1505031--1505089 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1505021 GTTAGCACCG
* *
1505031 AGGCACCTAAAATATTATCGTTTGTAACGTT
1 AGGCACCTAAAATATTAACGTTTATAACGTT
1505062 AGGCACCTAAAATATTAACGTTTATAAC
1 AGGCACCTAAAATATTAACGTTTATAAC
1505090 TTTAAGTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (31 bp):
AGGCACCTAAAATATTAACGTTTATAACGTT
Found at i:1505549 original size:18 final size:18
Alignment explanation
Indices: 1505526--1505560 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1505516 GAAATCGGTT
*
1505526 AATTAATTGAATTAACTG
1 AATTAATTAAATTAACTG
1505544 AATTAATTAAATTAACT
1 AATTAATTAAATTAACT
1505561 TTTAAATATA
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:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
AATTAATTAAATTAACTG
Found at i:1507657 original size:19 final size:20
Alignment explanation
Indices: 1507633--1507676 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
1507623 CGCATCGGCA
1507633 CGCATCGGATCGCATCA-AC
1 CGCATCGGATCGCATCAGAC
1507652 CGCATCGGATCGCATCAGAC
1 CGCATCGGATCGCATCAGAC
1507672 CGCAT
1 CGCAT
1507677 TATGTACCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (20 bp):
CGCATCGGATCGCATCAGAC
Found at i:1508541 original size:21 final size:21
Alignment explanation
Indices: 1508515--1508555 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1508505 CCGCGTAGAA
1508515 ATGTCCCGAAGGACCACATAG
1 ATGTCCCGAAGGACCACATAG
*
1508536 ATGTCCCGAATGACCACATA
1 ATGTCCCGAAGGACCACATA
1508556 TAACATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAG
Found at i:1510036 original size:16 final size:16
Alignment explanation
Indices: 1510017--1510055 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1510007 ATTTAAAGAC
1510017 AACTTAAGCTTTTCTT
1 AACTTAAGCTTTTCTT
1510033 AACTTAAGCTTTTCTT
1 AACTTAAGCTTTTCTT
1510049 AAGCTTA
1 AA-CTTA
1510056 TTTATCACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (16 bp):
AACTTAAGCTTTTCTT
Found at i:1511268 original size:54 final size:55
Alignment explanation
Indices: 1511204--1511323 Score: 224
Period size: 54 Copynumber: 2.2 Consensus size: 55
1511194 AATCCAAATA
*
1511204 ATCACTTAATCCATTAAAATACTTATTCTTAAACTCTTCCA-AAATTCTAACCAC
1 ATCATTTAATCCATTAAAATACTTATTCTTAAACTCTTCCACAAATTCTAACCAC
1511258 ATCATTTAATCCATTAAAATACTTATTCTTAAACTCTTCCACAAATTCTAACCAC
1 ATCATTTAATCCATTAAAATACTTATTCTTAAACTCTTCCACAAATTCTAACCAC
1511313 ATCATTTAATC
1 ATCATTTAATC
1511324 TTTTAACGCT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 40 0.62
55 24 0.38
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (55 bp):
ATCATTTAATCCATTAAAATACTTATTCTTAAACTCTTCCACAAATTCTAACCAC
Found at i:1523337 original size:20 final size:20
Alignment explanation
Indices: 1523312--1523365 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1523302 CTCAATTATG
1523312 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
1523332 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
1523352 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1523366 ATTTTTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.31, G:0.11, T:0.39
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1523366 original size:68 final size:68
Alignment explanation
Indices: 1523286--1523413 Score: 229
Period size: 68 Copynumber: 1.9 Consensus size: 68
1523276 TATATATGGA
**
1523286 ATCCTTTCATGCATTTCTCAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAA
1 ATCCTTTCATGCATTTCTCAATTATGGCATCCTTTCATGAATTAATGCATCCTTTCATGCCTTAA
1523351 TGC
66 TGC
*
1523354 ATCCTTTCATGCATTTTTCAATTATGGCATCCTTTCATGAATTAATGCATCCTTTCATGC
1 ATCCTTTCATGCATTTCTCAATTATGGCATCCTTTCATGAATTAATGCATCCTTTCATGC
1523414 ATTTTTCAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (68 bp):
ATCCTTTCATGCATTTCTCAATTATGGCATCCTTTCATGAATTAATGCATCCTTTCATGCCTTAA
TGC
Found at i:1523384 original size:48 final size:48
Alignment explanation
Indices: 1523332--1523476 Score: 254
Period size: 48 Copynumber: 3.0 Consensus size: 48
1523322 ATGCCTTAAT
1523332 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTCAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTCAATTATG
**
1523380 GCATCCTTTCATGAATTAATGCATCCTTTCATGCATTTTTCAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTCAATTATG
* *
1523428 GCATCCTTTCATGCCTTAATGTATCCTTTCATACATTTTTCAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTCAATTATG
1523476 G
1 G
1523477 ATTCGATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 91 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (48 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTCAATTATG
Found at i:1527979 original size:16 final size:17
Alignment explanation
Indices: 1527958--1527997 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
1527948 TGTCATTTGG
1527958 AACGGCTTCAGTGG-AA
1 AACGGCTTCAGTGGAAA
*
1527974 AACGGCTTCATTGGAAA
1 AACGGCTTCAGTGGAAA
1527991 AACGGCT
1 AACGGCT
1527998 CAACTTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (17 bp):
AACGGCTTCAGTGGAAA
Found at i:1529361 original size:28 final size:28
Alignment explanation
Indices: 1529317--1529489 Score: 144
Period size: 28 Copynumber: 6.8 Consensus size: 28
1529307 TAATATATAT
* *
1529317 AATTATGGAATCCTTTCATGTATTTCTC
1 AATTATGGCATCCTTTCATGCATTTCTC
*
1529345 AATTATGGCATCATTTCATGC----CT-
1 AATTATGGCATCCTTTCATGCATTTCTC
* * *
1529368 --TAAT-GCATCATTTCATGCATTTTTC
1 AATTATGGCATCCTTTCATGCATTTCTC
*
1529393 AATTATGGCATCCTTTCATGC----CTT
1 AATTATGGCATCCTTTCATGCATTTCTC
* *
1529417 AA-TA---CATCCTTTTATGCATTTTTC
1 AATTATGGCATCCTTTCATGCATTTCTC
*
1529441 AATTATGGCATCCTTTCATGCATTTTTC
1 AATTATGGCATCCTTTCATGCATTTCTC
1529469 AATTATGGCATCCTTTCATGC
1 AATTATGGCATCCTTTCATGC
1529490 CTTAATGCAT
Statistics
Matches: 116, Mismatches: 13, Indels: 32
0.72 0.08 0.20
Matches are distributed among these distances:
20 26 0.22
21 3 0.03
23 2 0.02
24 9 0.08
25 2 0.02
27 3 0.03
28 71 0.61
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (28 bp):
AATTATGGCATCCTTTCATGCATTTCTC
Found at i:1529395 original size:48 final size:48
Alignment explanation
Indices: 1529330--1529461 Score: 210
Period size: 48 Copynumber: 2.8 Consensus size: 48
1529320 TATGGAATCC
* * * *
1529330 TTTCATGTATTTCTCAATTATGGCATCATTTCATGCCTTAATGCATCA
1 TTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACATCA
*
1529378 TTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACATCC
1 TTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACATCA
*
1529426 TTTTATGCATTTTTCAATTATGGCATCCTTTCATGC
1 TTTCATGCATTTTTCAATTATGGCATCCTTTCATGC
1529462 ATTTTTCAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (48 bp):
TTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACATCA
Found at i:1529452 original size:76 final size:76
Alignment explanation
Indices: 1529372--1529524 Score: 272
Period size: 76 Copynumber: 2.0 Consensus size: 76
1529362 ATGCCTTAAT
1529372 GCATCATTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACATCCTTTT-ATGCAT
1 GCATCATTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACAT-CTTTTCATGCAT
1529436 TTTTCAATTATG
65 TTTTCAATTATG
* *
1529448 GCATCCTTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGCATT
1 GCATCATTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATT
1529513 TTTCAATTATG
66 TTTCAATTATG
1529524 G
1 G
1529525 ATTCGATTTA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
75 5 0.07
76 69 0.93
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (76 bp):
GCATCATTTCATGCATTTTTCAATTATGGCATCCTTTCATGCCTTAATACATCTTTTCATGCATT
TTTCAATTATG
Found at i:1533999 original size:14 final size:12
Alignment explanation
Indices: 1533970--1534038 Score: 68
Period size: 12 Copynumber: 5.3 Consensus size: 12
1533960 TCGCTTGAAT
*
1533970 AAAAAAGAAATAA
1 AAAAAAGAAA-GA
1533983 AAAAATGAGAAAGAAA
1 AAAAA--AGAAAG--A
1533999 AAAAAAGAAAGA
1 AAAAAAGAAAGA
1534011 AAAAAAG-AAGA
1 AAAAAAGAAAGA
1534022 AAAAAAGAAAGA
1 AAAAAAGAAAGA
1534034 GAAAA
1 -AAAA
1534039 TAAATAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
11 11 0.22
12 12 0.24
13 9 0.18
14 6 0.12
15 5 0.10
16 6 0.12
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:1533999 original size:15 final size:14
Alignment explanation
Indices: 1533970--1534037 Score: 77
Period size: 14 Copynumber: 4.8 Consensus size: 14
1533960 TCGCTTGAAT
*
1533970 AAAAA-AGAAATAA
1 AAAAAGAGAAAGAA
1533983 AAAAATGAGAAAGAA
1 AAAAA-GAGAAAGAA
*
1533998 AAAAAAAGAAAGAA
1 AAAAAGAGAAAGAA
1534012 AAAAAGAAGAAA-AA
1 AAAAAG-AGAAAGAA
1534026 AAGAAAGAGAAA
1 AA-AAAGAGAAA
1534038 ATAAATAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
13 5 0.10
14 22 0.46
15 21 0.44
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAAAGAGAAAGAA
Found at i:1534013 original size:29 final size:28
Alignment explanation
Indices: 1533970--1534037 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
1533960 TCGCTTGAAT
*
1533970 AAAAAAGAAATAAAAAAATG-AGAAAGAAA
1 AAAAAAGAAAGAAAAAAA-GAAGAAA-AAA
1533999 AAAAAAGAAAGAAAAAAAGAAGAAAAAA
1 AAAAAAGAAAGAAAAAAAGAAGAAAAAA
*
1534027 AGAAAGAGAAA
1 A-AAAAAGAAA
1534038 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 5 0.14
29 30 0.86
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (28 bp):
AAAAAAGAAAGAAAAAAAGAAGAAAAAA
Found at i:1534028 original size:23 final size:22
Alignment explanation
Indices: 1533992--1534038 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
1533982 AAAAAATGAG
1533992 AAAGAAAAAAAAAGAAAGAAAA
1 AAAGAAAAAAAAAGAAAGAAAA
*
1534014 AAAGAAGAAAAAAAGAAAGAGAA
1 AAAGAA-AAAAAAAGAAAGAAAA
1534037 AA
1 AA
1534039 TAAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAAAGAAAGAAAA
Found at i:1535579 original size:74 final size:74
Alignment explanation
Indices: 1535453--1535591 Score: 235
Period size: 74 Copynumber: 1.9 Consensus size: 74
1535443 TTAAGAGCAG
* *
1535453 TGAATCAAATCACACTCGATTTAATCTTCCCTAAAGAGCAGCGAAGTGAATCAAAGTTTCCTCGA
1 TGAAGCAAATCACACTCGATTCAATCTTCCCTAAAGAGCAGCGAAGTGAATCAAAGTTTCCTCGA
1535518 TTCGATCTT
66 TTCGATCTT
*
1535527 TGAAGCAAATCACA-TCCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGAATCAAAGTTTCCTCG
1 TGAAGCAAATCACACT-CGATTCAATCTTCCCTAAAGAGCAGCGAAGTGAATCAAAGTTTCCTCG
1535591 A
65 A
1535592 GTCTGACCTC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 1 0.02
74 60 0.98
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (74 bp):
TGAAGCAAATCACACTCGATTCAATCTTCCCTAAAGAGCAGCGAAGTGAATCAAAGTTTCCTCGA
TTCGATCTT
Found at i:1535944 original size:136 final size:135
Alignment explanation
Indices: 1535527--1536047 Score: 665
Period size: 134 Copynumber: 3.9 Consensus size: 135
1535517 ATTCGATCTT
* * * *
1535527 TGAAGCAAATCACATCCGATTCAATCTTCCCTGAAGAGCAGCGAAGTGAATCAAAG-TTTCCTCG
1 TGAAGCAAATCACATTCGATTCAATCTTCCCTAAAGAGCAGAGAAGTGAATCAAAGTTTTTCTCG
* * *
1535591 AGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTTTTCTTTCAGATTTGATATTCTTGAAG
66 AGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTTCAGATTTGATCTTCCTGAAG
*
1535656 AGCAG
131 AACAG
* *
1535661 TGAAGCAAATCACATTCGATTCAATCTTCCC-AGAAGATG-AGCGAAGTGAATCAAA-ATTTTCT
1 TGAAGCAAATCACATTCGATTCAATCTTCCCTA-AAGA-GCAGAGAAGTGAATCAAAGTTTTTCT
* *
1535723 CAAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTTCAGATTTGATCTTTCTGA
64 CGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTTCAGATTTGATCTTCCTGA
**
1535788 AGAATTG
129 AGAACAG
* * ** *
1535795 TGAAGCAAATCACATTCGATTCAATCTTCCCTAAAGAGCAAAAAAGTTTATCAAAGTTTTTCTTG
1 TGAAGCAAATCACATTCGATTCAATCTTCCCTAAAGAGCAGAGAAGTGAATCAAAGTTTTTCTCG
* * * *
1535860 AGTCTGACCTCCTCC-AAAGAGTAGCGGAGCAAAATCCTTCTTCTTTCTGATTTGATCTACCTGA
66 AGTCTGACCTCC-CCTAAAGAGTAGCGGAGC-AGATTCTTCTTCTTTCAGATTTGATCTTCCTGA
*
1535924 AGAACAA
129 AGAACAG
** * ** * *
1535931 CAAAACAAATCACATTCGATTCAATCTTCCCTGGAGAGTAGAGAAGTGGATCAAAGTTTTTCTCG
1 TGAAGCAAATCACATTCGATTCAATCTTCCCTAAAGAGCAGAGAAGTGAATCAAAGTTTTTCTCG
* * *
1535996 AGTCAGACCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTTAGATTT
66 AGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTTCAGATTT
1536048 AGAGATAGCA
Statistics
Matches: 334, Mismatches: 44, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
133 1 0.00
134 165 0.49
135 55 0.16
136 113 0.34
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (135 bp):
TGAAGCAAATCACATTCGATTCAATCTTCCCTAAAGAGCAGAGAAGTGAATCAAAGTTTTTCTCG
AGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTTCAGATTTGATCTTCCTGAAG
AACAG
Found at i:1543705 original size:11 final size:11
Alignment explanation
Indices: 1543686--1543739 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
1543676 TTTGGCTGGC
*
1543686 ATAAAATAAAA
1 ATAATATAAAA
*
1543697 ATAATATAAAT
1 ATAATATAAAA
1543708 ATAA-AT-AAA
1 ATAATATAAAA
*
1543717 ATAATAATAATA
1 ATAAT-ATAAAA
1543729 ATAATATAAAA
1 ATAATATAAAA
1543740 TTGTCGGGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 20 0.57
12 7 0.20
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:1543715 original size:26 final size:26
Alignment explanation
Indices: 1543686--1543738 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1543676 TTTGGCTGGC
1543686 ATAAAATAAAAATAAT-ATAAATATAA
1 ATAAAATAAAAATAATAAT-AATATAA
*
1543712 ATAAAATAATAATAATAATAATATAA
1 ATAAAATAAAAATAATAATAATATAA
1543738 A
1 A
1543739 ATTGTCGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (26 bp):
ATAAAATAAAAATAATAATAATATAA
Found at i:1546348 original size:16 final size:16
Alignment explanation
Indices: 1546327--1546368 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1546317 TGTTTTATAT
1546327 GTATTAAAGTATCATG
1 GTATTAAAGTATCATG
1546343 GTATTAAAGTATCATG
1 GTATTAAAGTATCATG
*
1546359 GAATTAAAGT
1 GTATTAAAGT
1546369 GTAGATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (16 bp):
GTATTAAAGTATCATG
Found at i:1546899 original size:28 final size:28
Alignment explanation
Indices: 1546849--1546909 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
1546839 GTGTGTAATA
* *
1546849 TGCACTAGAAAGGGCCTCGTAGACAATT
1 TGCACTAGAAAGGGCATCATAGACAATT
* * *
1546877 TGCACTTGAAAGTGCATCATAGATAATT
1 TGCACTAGAAAGGGCATCATAGACAATT
1546905 TGCAC
1 TGCAC
1546910 CATAGGTTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (28 bp):
TGCACTAGAAAGGGCATCATAGACAATT
Found at i:1550913 original size:26 final size:27
Alignment explanation
Indices: 1550852--1550915 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 27
1550842 CGAGTGTGTG
1550852 TAATTTGCACTCGAAAATGCCTCGTAGA
1 TAATTTGCACTCGAAAATGCCTCG-AGA
*
1550880 TAATTTGCACTCGAAAGTGCCTC-AGA
1 TAATTTGCACTCGAAAATGCCTCGAGA
1550906 TAATTTGCAC
1 TAATTTGCAC
1550916 CATAGGTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 13 0.37
28 22 0.63
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (27 bp):
TAATTTGCACTCGAAAATGCCTCGAGA
Found at i:1556099 original size:4 final size:4
Alignment explanation
Indices: 1556090--1556118 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1556080 CACCAAATTA
1556090 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1556119 CTAGTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1556808 original size:3 final size:3
Alignment explanation
Indices: 1556790--1556889 Score: 79
Period size: 3 Copynumber: 34.7 Consensus size: 3
1556780 TTTTATCCAT
* * *
1556790 TTA TTT TTA ATA TTA TTA -TA TTA TTA TTA ATA TTA TT- TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
1556836 CTA TTA -TA TTTA TT- TTA TTA TTA -TA TT- TCA TTTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
1556879 TTA TTA TTA TT
1 TTA TTA TTA TT
1556890 TTTACATTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
2 12 0.16
3 61 0.79
4 4 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1556823 original size:17 final size:17
Alignment explanation
Indices: 1556800--1556889 Score: 87
Period size: 17 Copynumber: 5.2 Consensus size: 17
1556790 TTATTTTTAA
1556800 TATTATTATATTATTAT
1 TATTATTATATTATTAT
* *
1556817 TAATATTATTTTATT-T
1 TATTATTATATTATTAT
*
1556833 ATACTATTATATTTATT-T
1 -TATTATTATA-TTATTAT
*
1556851 TATTATTATATT-TCATT
1 TATTATTATATTATTA-T
1556868 TATTATTATTATTATTAT
1 TATTATTA-TATTATTAT
1556886 TATT
1 TATT
1556890 TTTACATTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
15 1 0.02
16 3 0.05
17 39 0.65
18 15 0.25
19 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATATTATTAT
Found at i:1558544 original size:21 final size:21
Alignment explanation
Indices: 1558501--1558542 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1558491 ATATTCTTAA
*
1558501 ATAAATATATATCCTATTTTT
1 ATAAATATATATACTATTTTT
*
1558522 ATAAATTATATATATTATTTT
1 ATAAA-TATATATACTATTTT
1558543 ATTTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAAATATATATACTATTTTT
Found at i:1559243 original size:26 final size:28
Alignment explanation
Indices: 1559200--1559251 Score: 65
Period size: 26 Copynumber: 1.9 Consensus size: 28
1559190 AAATTTTTTA
1559200 ATATATACTTAATATTTTCA-TAATATTT
1 ATATATACTTAATATTTT-ATTAATATTT
*
1559228 ATATATA-TT-ATTTTTTATTAATAT
1 ATATATACTTAATATTTTATTAATAT
1559252 CTTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.05
26 12 0.55
27 2 0.09
28 7 0.32
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
ATATATACTTAATATTTTATTAATATTT
Found at i:1562521 original size:15 final size:15
Alignment explanation
Indices: 1562501--1562532 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1562491 GATCAATACC
1562501 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1562516 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1562531 TT
1 TT
1562533 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1564712 original size:162 final size:162
Alignment explanation
Indices: 1564445--1564768 Score: 648
Period size: 162 Copynumber: 2.0 Consensus size: 162
1564435 AAAGAGATAG
1564445 AGTTCTTTGAAGAAAAACCAGAAAAAAGAGAAGATAACGTTTGCGCATCAGAAGATTCTAAACCT
1 AGTTCTTTGAAGAAAAACCAGAAAAAAGAGAAGATAACGTTTGCGCATCAGAAGATTCTAAACCT
1564510 AAACAGAGAACAAGTGATCCCGTGATTATCACTGTGAAGTCATCTACAAAAAATCCTGCTCCAAT
66 AAACAGAGAACAAGTGATCCCGTGATTATCACTGTGAAGTCATCTACAAAAAATCCTGCTCCAAT
1564575 AAAGTCAAAAGTGGTTATCACAACTCCATTAC
131 AAAGTCAAAAGTGGTTATCACAACTCCATTAC
1564607 AGTTCTTTGAAGAAAAACCAGAAAAAAGAGAAGATAACGTTTGCGCATCAGAAGATTCTAAACCT
1 AGTTCTTTGAAGAAAAACCAGAAAAAAGAGAAGATAACGTTTGCGCATCAGAAGATTCTAAACCT
1564672 AAACAGAGAACAAGTGATCCCGTGATTATCACTGTGAAGTCATCTACAAAAAATCCTGCTCCAAT
66 AAACAGAGAACAAGTGATCCCGTGATTATCACTGTGAAGTCATCTACAAAAAATCCTGCTCCAAT
1564737 AAAGTCAAAAGTGGTTATCACAACTCCATTAC
131 AAAGTCAAAAGTGGTTATCACAACTCCATTAC
1564769 CATTTCCATA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (162 bp):
AGTTCTTTGAAGAAAAACCAGAAAAAAGAGAAGATAACGTTTGCGCATCAGAAGATTCTAAACCT
AAACAGAGAACAAGTGATCCCGTGATTATCACTGTGAAGTCATCTACAAAAAATCCTGCTCCAAT
AAAGTCAAAAGTGGTTATCACAACTCCATTAC
Found at i:1570047 original size:23 final size:22
Alignment explanation
Indices: 1570021--1570077 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 22
1570011 ACTTGAAGAA
1570021 GAAAAAAATGAAAAAGAAAAAAT
1 GAAAAAAATG-AAAAGAAAAAAT
1570044 GAAATGAAAA-GAAAAGAAAAAAT
1 GAAA--AAAATGAAAAGAAAAAAT
1570067 GATGAAAAAAT
1 GA--AAAAAAT
1570078 ATATATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
23 22 0.76
24 1 0.03
25 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (22 bp):
GAAAAAAATGAAAAGAAAAAAT
Found at i:1570066 original size:18 final size:17
Alignment explanation
Indices: 1570016--1570068 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
1570006 ATTATACTTG
*
1570016 AAGAAGAAAAAAATGAAA
1 AAGAAAAAAAAAATG-AA
*
1570034 AAGAAAAAATGAAATGAA
1 AAGAAAAAA-AAAATGAA
1570052 AAGAAAAGAAAAAATGA
1 AAGAAAA-AAAAAATGA
1570069 TGAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 23 0.77
19 7 0.23
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (17 bp):
AAGAAAAAAAAAATGAA
Found at i:1573049 original size:113 final size:112
Alignment explanation
Indices: 1572852--1573534 Score: 686
Period size: 113 Copynumber: 6.0 Consensus size: 112
1572842 TACTAAAGAT
* * *
1572852 TCGAATCCATCACTCAATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGA
*
1572916 AGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * *
1572964 TCGAATTCATCACTTGATGGTTCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCAGA
1 TCGAATTCATCACTCGATGGATCAACATTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGA
* * *
1573029 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGC
* * * * *
1573078 TTGAATTCATCACTCGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGA
1573143 AG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* ** * * *
1573190 AT-G-ACTCTATCACAGAAGGAGATAGATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTC
1 -TCGAATTC-ATCAC-----TCGATGGATCAACATTTCCAGGAGAGTTCATAATGAGAAGAACTC
* * *
1573253 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGT
59 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGC
* * * * * * *
1573308 TTGAATTCATCATTCGATAGATCAACTTTTCCAGAGAAAGTTCATAATGAGAATAACTTATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGA
* * *
1573373 AG-ATGAAGAAGAAGTTTATAATGAGAAGAACTTGTTCAACC-TTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* ** * *
1573419 TTG-ATTCTATCACAGAAAGAGATAGATCAACATCACCATTTCCAGAAGGAGTTCATAATGAGAA
1 TCGAATTC-ATCAC-----TCGATGGAT---CA--A-CATTTCCAGGA-GAGTTCATAATGAGAA
*
1573483 GAACTCATCT---GAA-GAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
53 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
1573535 GCCTTAATTC
Statistics
Matches: 483, Mismatches: 58, Indels: 52
0.81 0.10 0.09
Matches are distributed among these distances:
110 4 0.01
111 15 0.03
112 42 0.09
113 154 0.32
114 92 0.19
115 1 0.00
116 35 0.07
117 50 0.10
118 14 0.03
119 41 0.08
120 2 0.00
121 2 0.00
122 31 0.06
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
TCGAATTCATCACTCGATGGATCAACATTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:1573179 original size:20 final size:20
Alignment explanation
Indices: 1573117--1573180 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1573107 TCTAGAGAAA
1573117 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
1573137 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
1573156 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1573176 GTTCA
1 GTTCA
1573181 ACCTTTTGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1573290 original size:230 final size:229
Alignment explanation
Indices: 1572889--1573534 Score: 895
Period size: 230 Copynumber: 2.8 Consensus size: 229
1572879 TGCCAGGTAG
* *
1572889 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
1572954 AACCTTTTGCTCGAAT-TCATCACTTG-ATG-G-T---TCAACATTGCCAGGTAGAGTTCATAAT
65 AACCTTTTGCT-GAATCT-ATCAC-AGAAAGAGATAGATCAACATTTCCA-GAAGAGTTCATAAT
*
1573012 GAGAAGAACTCATCAGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTG
126 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTG
* *
1573077 TTTGAATTCATCACTCGATGGATCAACTTTTCTAGAGAA
191 TTTGAATTCATCACTCGATAGATCAACTTTTCCAGAGAA
1573116 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
1573181 ACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATTTCCAGAAGTGTTCATAATGAGA
66 ACCTTTTGC-TGAATCTATCACAGAAAGAGATAGATCAACATTTCCAGAAGAGTTCATAATGAGA
1573246 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTG
130 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTG
*
1573311 AATTCATCATTCGATAGATCAACTTTTCCAGAGAA
195 AATTCATCACTCGATAGATCAACTTTTCCAGAGAA
* * *
1573346 AGTTCATAATGAGAATAACTTATCTGAAGATGAAGAAGAAGTTTATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
1573411 ACC-TTTGTTTGATTCTATCACAGAAAGAGATAGATCAACATCACCATTTCCAGAAGGAGTTCAT
66 ACCTTTTG-CTGAATCTATCACAGAAAGAGATAGAT---CA--A-CATTTCCAGAA-GAGTTCAT
* *
1573475 AATGAGAAGAACTCATCTGAAGAA-TAAGAAG---TTCATAATGAGAAGAACTTGTTC-AACCTT
123 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTT
1573535 GCCTTAATTC
Statistics
Matches: 382, Mismatches: 21, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
225 1 0.00
226 54 0.14
227 31 0.08
228 1 0.00
229 28 0.07
230 177 0.46
231 17 0.04
232 24 0.06
234 1 0.00
235 17 0.04
236 31 0.08
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (229 bp):
AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTGAATCTATCACAGAAAGAGATAGATCAACATTTCCAGAAGAGTTCATAATGAGAA
GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGA
ATTCATCACTCGATAGATCAACTTTTCCAGAGAA
Found at i:1573650 original size:20 final size:19
Alignment explanation
Indices: 1573612--1573655 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1573602 AGTTCATAAT
*
1573612 AAGAAGAACTCATCTGAAA
1 AAGAAGAACTCACCTGAAA
*
1573631 AAGAAGAAGTTCACCTGAAA
1 AAGAAGAA-CTCACCTGAAA
*
1573651 GAGAA
1 AAGAA
1573656 TAATTTGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.52, C:0.14, G:0.20, T:0.14
Consensus pattern (19 bp):
AAGAAGAACTCACCTGAAA
Found at i:1573913 original size:3 final size:3
Alignment explanation
Indices: 1573895--1574011 Score: 93
Period size: 3 Copynumber: 40.3 Consensus size: 3
1573885 TTTTATCCAT
* * *
1573895 TTA TTT TTA ATA TTA TTA -TA TTA TTA TTA ATA TTA TT- TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * *
1573941 CTA TTA TTT TTA TT- TTA TTA TTA -TA TTA -CA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* *
1573984 TTA TTA TTA TTA ATA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1574012 ATTTCAGACC
Statistics
Matches: 88, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
2 10 0.11
3 75 0.85
4 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1573916 original size:17 final size:17
Alignment explanation
Indices: 1573896--1574009 Score: 61
Period size: 20 Copynumber: 6.4 Consensus size: 17
1573886 TTTATCCATT
1573896 TATTTTTAATATTATTA
1 TATTTTTAATATTATTA
*
1573913 TATTATTATTAATATTATTT
1 TA-T-TT-TTAATATTATTA
* *
1573933 TATTTATACTATTATT-
1 TATTTTTAATATTATTA
* *
1573949 TTTATTTTATTATTATATTA
1 TAT-TTTTAATA-T-TATTA
* * *
1573969 CATTATTTATTAATATTA
1 TATT-TTTAATATTATTA
*
1573987 TTATTATTAATATTATTA
1 -TATTTTTAATATTATTA
1574005 T-TTTT
1 TATTTT
1574010 ATATTTCAGA
Statistics
Matches: 74, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
16 5 0.07
17 18 0.24
18 19 0.26
19 11 0.15
20 21 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTAATATTATTA
Found at i:1575817 original size:2 final size:2
Alignment explanation
Indices: 1575810--1575856 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1575800 TATAAAAATA
1575810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1575852 A- AT AT
1 AT AT AT
1575857 TCTTAAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1575837 original size:143 final size:142
Alignment explanation
Indices: 1575534--1575842 Score: 345
Period size: 143 Copynumber: 2.1 Consensus size: 142
1575524 TATTACTTTA
* * **
1575534 ATTATTATTTTATATATATATTTGTTTAAATAATAATATTTATTTTTTAATATTAAGAAATGGCA
1 ATTATAATTATATATATATAAATGTTTAAATAATAATATTTATTTTTTAATATTAAGAAATGGCA
* * * * *
1575599 TGTCTTAAAGAACCTAGAAGTTCTTTTCTAATATTCTTAAATAAATAAATATCCTATTTTTATAA
66 TATCTTAAAGAACCTAGAAGATCCTTTCTAATATTCTTAAATAAATAAATATCCTATTTATAAAA
*
1575664 ATTATATATATT
131 ATAATATATATT
* * * * * *
1575676 ATTTTAATTATTTTTATATAAATGTTTTATTAATATTTATTTATTTTTTAATATTAAGAAATGGG
1 ATTATAATTATATATATATAAATGTTTAAATAATA-ATATTTATTTTTTAATATTAAGAAAT-GG
* * * *
1575741 C-TATCTTAAAGCACCTAGAA-ATCACTTTCTGATATT-TCTAAGTAAATAAATATCTTATTTAT
64 CATATCTTAAAGAACCTAGAAGATC-CTTTCTAATATTCT-TAAATAAATAAATATCCTATTTAT
1575803 AAAAATAATATATATAT
127 AAAAATAATATATAT-T
1575820 ATATATATATATATATATATATA
1 AT-TATA-AT-TATATATATATA
1575843 TATATATATA
Statistics
Matches: 136, Mismatches: 23, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
142 29 0.21
143 86 0.63
144 6 0.04
145 3 0.02
146 2 0.01
147 10 0.07
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (142 bp):
ATTATAATTATATATATATAAATGTTTAAATAATAATATTTATTTTTTAATATTAAGAAATGGCA
TATCTTAAAGAACCTAGAAGATCCTTTCTAATATTCTTAAATAAATAAATATCCTATTTATAAAA
ATAATATATATT
Found at i:1578021 original size:58 final size:58
Alignment explanation
Indices: 1577888--1578202 Score: 206
Period size: 58 Copynumber: 5.4 Consensus size: 58
1577878 GACGTTAAAG
* * * **
1577888 AAATAAAGTCAACAATTT-ATTTCTTTTTA-AAAGATATAATCATACTTGATTCTCAAG-
1 AAATAAATTCAACAATTTAATTTC-TTTTACAAACATAGAATCATACAAGATTCT-AAGA
* ** *
1577945 AAATAAATCCAATGATTTAATTTCTTTTACAAA-ATAGAATCATACAAGATTCTATGAA
1 AAATAAATTCAACAATTTAATTTCTTTTACAAACATAGAATCATACAAGATTCTAAG-A
* * * * * *
1578003 AAATAAATTTAACAATTTATTTTCTTCTAC-AAGAT-GAAATCGAT-CTAGATTTCCAAGA
1 AAATAAATTCAACAATTTAATTTCTTTTACAAACATAG-AATC-ATACAAGA-TTCTAAGA
** ** * * *
1578061 AAATAAATTTGACGTTTTAATTCCTTTTATCAAACA-A-AATCATATAAGATTCATATGA
1 AAATAAATTCAACAATTTAATTTCTTTTA-CAAACATAGAATCATACAAGATTC-TAAGA
**
1578119 AAATAAATTCAACAATTT-ATTTCCTTTT-CAAAGTTAGAATCA-ACAAAAGATTCTAAGA
1 AAATAAATTCAACAATTTAATTT-CTTTTACAAACATAGAATCATAC--AAGATTCTAAGA
1578177 TGAAATAAATTCAACAATTT-ATTTCT
1 --AAATAAATTCAACAATTTAATTTCT
1578203 ATTTTTCCAA
Statistics
Matches: 201, Mismatches: 37, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
56 6 0.03
57 49 0.24
58 104 0.52
59 17 0.08
60 25 0.12
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (58 bp):
AAATAAATTCAACAATTTAATTTCTTTTACAAACATAGAATCATACAAGATTCTAAGA
Found at i:1579764 original size:24 final size:24
Alignment explanation
Indices: 1579737--1579792 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1579727 AAAACTCTTT
*
1579737 TAATATCTATATTTAAACATATTA
1 TAATATCTAAATTTAAACATATTA
1579761 TAATATCTAAATTTAAACATATTA
1 TAATATCTAAATTTAAACATATTA
1579785 TAATATCT
1 TAATATCT
1579793 TTTAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATCTAAATTTAAACATATTA
Found at i:1579848 original size:83 final size:83
Alignment explanation
Indices: 1579761--1579977 Score: 348
Period size: 83 Copynumber: 2.6 Consensus size: 83
1579751 AAACATATTA
* *
1579761 TAATATCTAAATTTAAACATATTATAATATCTTTTAAATTTATAATATTAAACATGAGAGTTTTA
1 TAATATCTAAATTTAAACAAATTATAATATCTTTTAAATTTATAATATTAAACATAAGAGTTTTA
1579826 CTCCAACCAAAACTCTTT
66 CTCCAACCAAAACTCTTT
*
1579844 TAATATCTAAATTTAAACAAATTATAATATCTTTTAAATTTATAATATTAAACCTAAGAGTTTTA
1 TAATATCTAAATTTAAACAAATTATAATATCTTTTAAATTTATAATATTAAACATAAGAGTTTTA
*
1579909 TTCCAACCAAAACTCTTT
66 CTCCAACCAAAACTCTTT
* * *
1579927 TAATATCTAAATTTAAATAGATAATAATAT-TGTTTAAATTTA-AATATTAAA
1 TAATATCTAAATTTAAACAAATTATAATATCT-TTTAAATTTATAATATTAAA
1579978 TAAATATTTC
Statistics
Matches: 126, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
82 10 0.08
83 116 0.92
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (83 bp):
TAATATCTAAATTTAAACAAATTATAATATCTTTTAAATTTATAATATTAAACATAAGAGTTTTA
CTCCAACCAAAACTCTTT
Found at i:1579868 original size:107 final size:107
Alignment explanation
Indices: 1579677--1579875 Score: 337
Period size: 107 Copynumber: 1.9 Consensus size: 107
1579667 AAAATAAATA
* *
1579677 ATAATATTGTTTAAATTTAAAATATTAAATATGAGAGTTTTACTCTAACCAAAACTCTTTTAATA
1 ATAATATTGTTTAAATTTAAAATATTAAACATGAGAGTTTTACTCCAACCAAAACTCTTTTAATA
* *
1579742 TCTATATTTAAACATATTATAATATCTAAATTTAAACATATT
66 TCTAAATTTAAACAAATTATAATATCTAAATTTAAACATATT
*
1579784 ATAATATCT-TTTAAATTTATAATATTAAACATGAGAGTTTTACTCCAACCAAAACTCTTTTAAT
1 ATAATAT-TGTTTAAATTTAAAATATTAAACATGAGAGTTTTACTCCAACCAAAACTCTTTTAAT
1579848 ATCTAAATTTAAACAAATTATAATATCT
65 ATCTAAATTTAAACAAATTATAATATCT
1579876 TTTAAATTTA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
107 85 0.99
108 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (107 bp):
ATAATATTGTTTAAATTTAAAATATTAAACATGAGAGTTTTACTCCAACCAAAACTCTTTTAATA
TCTAAATTTAAACAAATTATAATATCTAAATTTAAACATATT
Found at i:1580656 original size:21 final size:21
Alignment explanation
Indices: 1580617--1580656 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1580607 TTTGTTAACA
*
1580617 ATAAATTCAAACACTTAAATT
1 ATAAATTCAAACAATTAAATT
1580638 ATAAA-TCAAACAATATAAA
1 ATAAATTCAAACAAT-TAAA
1580657 AATAATTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAATTCAAACAATTAAATT
Found at i:1580661 original size:20 final size:21
Alignment explanation
Indices: 1580616--1580675 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 21
1580606 ATTTGTTAAC
*
1580616 AATAAATTCAAACACTTAAAT
1 AATAAATTCAAACAATTAAAT
*
1580637 TATAAA-TCAAACAATATAAA-
1 AATAAATTCAAACAAT-TAAAT
* *
1580657 AAT-AATTCACACATTTAAA
1 AATAAATTCAAACAATTAAA
1580676 AAAAATAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 6 0.19
20 17 0.53
21 9 0.28
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAAATTCAAACAATTAAAT
Found at i:1594539 original size:45 final size:45
Alignment explanation
Indices: 1594195--1594525 Score: 387
Period size: 45 Copynumber: 7.4 Consensus size: 45
1594185 AATACACCAT
* *
1594195 TATACACTTT-AATCTATAACAT-CTTTTCTGTTGATAATGCACCCA
1 TATACA-TTTCAA-CTATAGCATACTTTTCTGTTGATAATGTACCCA
* * ** *
1594240 TATGCATTTTAACTATATTATACTTTTTTGTTGATAATGTACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* ** *
1594285 TATACATTTCAACCATAATATATTTTTCTGTTGATAATGTACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * * * *
1594330 TATACATTTCAACTCTAGCTTGCTCTTCTGTTGATAATGCACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * * *
1594375 TATGCATTTCAACTCTAGCATACATTTCTGTTGATAATGCACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* *
1594420 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * * * *
1594465 TATACATTTCAACCATAGTATACCTTTATGTTGATAATGTACTCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
1594510 TATACATTTCAACTAT
1 TATACATTTCAACTAT
1594526 GACATCCTTT
Statistics
Matches: 249, Mismatches: 35, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
44 10 0.04
45 239 0.96
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (45 bp):
TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
Found at i:1596770 original size:12 final size:12
Alignment explanation
Indices: 1596753--1596785 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1596743 GAATGGCTCC
1596753 TCTGACTGCCCA
1 TCTGACTGCCCA
1596765 TCTGACTGCCCA
1 TCTGACTGCCCA
*
1596777 TCTGTCTGC
1 TCTGACTGC
1596786 GGATGGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.39, G:0.18, T:0.30
Consensus pattern (12 bp):
TCTGACTGCCCA
Found at i:1600628 original size:45 final size:45
Alignment explanation
Indices: 1600557--1600897 Score: 373
Period size: 45 Copynumber: 7.6 Consensus size: 45
1600547 AATACACCAT
* * *
1600557 TATACACTTT-AATCTATAACAT-CTTTTCTATTGATAATGCACCCA
1 TATACA-TTTCAA-CTATAGCATACTTTTCTGTTGATAATGTACCCA
* * *
1600602 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGTACCTA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * * *
1600647 TATACATTTAAACCATAGTATACTTTTATGTTGATAATGTACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * * * *
1600692 TATACATTTCTACTCTAGCATGCTATTCTGTTGATAATGAACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * * * * *
1600737 TATGCATTTAAACTCTAGCATACATTTCTATTGATAATGCACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * *
1600782 TATGCATTTCAATTCTAGCATACTTTTCTGTTGATAATGTACCCA
1 TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
* * *
1600827 TATACATTTCAACCATAGTATACCTTTT-TGTTGATAATGTACTCA
1 TATACATTTCAACTATAGCATA-CTTTTCTGTTGATAATGTACCCA
* *
1600872 TATACATTTCAACTATGGCATCCTTT
1 TATACATTTCAACTATAGCATACTTT
1600898 CATGCCAATA
Statistics
Matches: 250, Mismatches: 43, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
44 14 0.06
45 231 0.92
46 5 0.02
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
TATACATTTCAACTATAGCATACTTTTCTGTTGATAATGTACCCA
Found at i:1601351 original size:22 final size:21
Alignment explanation
Indices: 1601315--1601374 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 21
1601305 GTCCCTTTAA
*
1601315 TATCGACAC-CCCTACCATGG
1 TATCGATACACCCTACCATGG
**
1601335 TATCGATACTACCCTACTTTGG
1 TATCGATAC-ACCCTACCATGG
*
1601357 TATCGATACCCCCTACCA
1 TATCGATACACCCTACCA
1601375 GTATCAATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 8 0.25
21 6 0.19
22 18 0.56
ACGTcount: A:0.25, C:0.37, G:0.12, T:0.27
Consensus pattern (21 bp):
TATCGATACACCCTACCATGG
Found at i:1601458 original size:94 final size:93
Alignment explanation
Indices: 1601314--1601553 Score: 243
Period size: 94 Copynumber: 2.5 Consensus size: 93
1601304 TGTCCCTTTA
* * * * *
1601314 ATATCGACACCCCTACCATGGTATCGATACTACCCTACTTTGGTATCGATACCCC-CTACCAGTA
1 ATATCGATACCCTTACCATGGTAT-GATACTA-CTTACTATGGTACCGATACCCCTCTA-CAGTA
*
1601378 TCAATACCAAAATTAGATTCAATGTGGCTCAG
63 TCAATACCAAAATTAGATTCAATGTGAC-CAG
**
1601410 -TATCGATACCCTTACCATGGTATGATACTACTATACTATGGTACCGATACCCCTCTATGGTATC
1 ATATCGATACCCTTACCATGGTATGATACTACT-TACTATGGTACCGATACCCCTCTACAGTATC
* * * * *
1601474 GATACCAAAATTAGGTTCGATGTTACCCG
65 AATACCAAAATTAGATTCAATGTGACCAG
* * * *
1601503 ATATTGGTACCCTTACCATGGTATTGATACCACTTCATTA-GGTACCGATAC
1 ATATCGATACCCTTACCATGGTA-TGATACTACTT-ACTATGGTACCGATAC
1601554 TGATTGAATA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
93 3 0.02
94 83 0.68
95 36 0.30
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (93 bp):
ATATCGATACCCTTACCATGGTATGATACTACTTACTATGGTACCGATACCCCTCTACAGTATCA
ATACCAAAATTAGATTCAATGTGACCAG
Found at i:1602901 original size:2 final size:2
Alignment explanation
Indices: 1602894--1602922 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1602884 TCAAATTAAT
1602894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1602923 TAGATTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1603907 original size:44 final size:45
Alignment explanation
Indices: 1603822--1603944 Score: 160
Period size: 44 Copynumber: 2.7 Consensus size: 45
1603812 AATATACCAT
* * * *
1603822 TATGTATTTTCATTTTGTGGCATCCATTCATGACTATAATGCACCGT
1 TATGCATTTTCA-TTTATGGCATCCTTTCATG-CTATAATGCACCGG
*
1603869 TATGCATTTTCA-TTATGG-ATCGTTTCATGCTTATAATGCACCGG
1 TATGCATTTTCATTTATGGCATCCTTTCATGC-TATAATGCACCGG
1603913 TATGCATTTTCATTTATGGCATCCTTTCATGC
1 TATGCATTTTCATTTATGGCATCCTTTCATGC
1603945 CAAAGACATT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
43 1 0.01
44 33 0.49
45 11 0.16
46 11 0.16
47 11 0.16
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (45 bp):
TATGCATTTTCATTTATGGCATCCTTTCATGCTATAATGCACCGG
Found at i:1605126 original size:7 final size:7
Alignment explanation
Indices: 1605114--1605157 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
1605104 GTGTTATGAT
1605114 TATTATA
1 TATTATA
1605121 TATTAT-
1 TATTATA
1605127 T-TTATA
1 TATTATA
1605133 TATTA-A
1 TATTATA
1605139 TTATTATA
1 -TATTATA
1605147 TATTAT-
1 TATTATA
1605153 TATTA
1 TATTA
1605158 CAAATGGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.12
6 8 0.24
7 20 0.61
8 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TATTATA
Found at i:1605127 original size:3 final size:3
Alignment explanation
Indices: 1605107--1605157 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
1605097 CGTCCAAGTG
*
1605107 TTA TGA TTA TTA TATA TTA TT- TTA TATA TTAA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TT-A TTA TTA T-TA TTA TTA
1605155 TTA
1 TTA
1605158 CAAATGGAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 2 0.05
3 27 0.66
4 12 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1605127 original size:10 final size:10
Alignment explanation
Indices: 1605112--1605155 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
1605102 AAGTGTTATG
1605112 ATTATTATAT
1 ATTATTATAT
*
1605122 ATTATTTTAT
1 ATTATTATAT
1605132 A-TA-T-TA-
1 ATTATTATAT
1605138 ATTATTATAT
1 ATTATTATAT
1605148 ATTATTAT
1 ATTATTAT
1605156 TACAAATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
6 1 0.03
7 4 0.14
8 2 0.07
9 4 0.14
10 18 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTATTATAT
Found at i:1605133 original size:12 final size:13
Alignment explanation
Indices: 1605112--1605157 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
1605102 AAGTGTTATG
1605112 ATTATTATATATT
1 ATTATTATATATT
1605125 ATT-TTATATATT
1 ATTATTATATATT
1605137 AATTATTATATATT
1 -ATTATTATATATT
1605151 ATTATTA
1 ATTATTA
1605158 CAAATGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.29
13 13 0.42
14 9 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTATATATT
Found at i:1605157 original size:16 final size:16
Alignment explanation
Indices: 1605107--1605157 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1605097 CGTCCAAGTG
*
1605107 TTATGATTAT-TATATA
1 TTATTATTATATAT-TA
1605123 TTATT-TTATATATTA
1 TTATTATTATATATTA
1605138 --ATTATTATATATTA
1 TTATTATTATATATTA
1605152 TTATTA
1 TTATTA
1605158 CAAATGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 3 0.10
14 10 0.33
15 6 0.20
16 11 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTATTATTATATATTA
Found at i:1614341 original size:23 final size:23
Alignment explanation
Indices: 1614297--1614341 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1614287 CATTTTATAT
* *
1614297 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGCTGCAATTATACGC
*
1614320 GGCACTTCGCTGCATTTATACG
1 GGCACTTCGCTGCAATTATACG
1614342 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTTCGCTGCAATTATACGC
Found at i:1616324 original size:43 final size:43
Alignment explanation
Indices: 1616270--1616380 Score: 186
Period size: 43 Copynumber: 2.6 Consensus size: 43
1616260 AAATATGAAA
1616270 CCTTCACGAAAGATTAGTGAAGCAATCCAAGTTTGAGTCTCAG
1 CCTTCACGAAAGATTAGTGAAGCAATCCAAGTTTGAGTCTCAG
* *
1616313 TCTTCATGAAAGATTAGTGAAGCAATCCAAGTTTGAGTCTCAG
1 CCTTCACGAAAGATTAGTGAAGCAATCCAAGTTTGAGTCTCAG
* *
1616356 CCTTCACGGAAGAGTAGTGAAGCAA
1 CCTTCACGAAAGATTAGTGAAGCAA
1616381 AAGAAAGAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (43 bp):
CCTTCACGAAAGATTAGTGAAGCAATCCAAGTTTGAGTCTCAG
Found at i:1616742 original size:19 final size:20
Alignment explanation
Indices: 1616718--1616757 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1616708 ATGGTTGTAA
1616718 TTGAAT-ATGTCGTGGCAAG
1 TTGAATAATGTCGTGGCAAG
1616737 TTGAATGAAATGTCGTGGCAA
1 TTGAAT--AATGTCGTGGCAA
1616758 ATTCAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
22 12 0.67
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGAATAATGTCGTGGCAAG
Found at i:1627087 original size:19 final size:19
Alignment explanation
Indices: 1627059--1627102 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
1627049 TAGTGCGGTT
1627059 GCAATTGAAT-ATGTCGTG
1 GCAATTGAATAATGTCGTG
1627077 GCAAGTTGAATGAAATGTCGTG
1 GCAA-TTGAAT--AATGTCGTG
1627099 GCAA
1 GCAA
1627103 ATTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
22 12 0.55
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (19 bp):
GCAATTGAATAATGTCGTG
Found at i:1629061 original size:3 final size:3
Alignment explanation
Indices: 1629041--1629087 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
1629031 CATCCGAGTG
*
1629041 TTA TGA TTA TTA TATA TTA TTA TATA TTAA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA T-TA TT-A TTA TTA TTA TTA TTA TTA
1629088 CAAATGGAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 2 0.05
3 27 0.71
4 9 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1629061 original size:10 final size:10
Alignment explanation
Indices: 1629046--1629085 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
1629036 GAGTGTTATG
1629046 ATTATTATAT
1 ATTATTATAT
1629056 ATTATTATAT
1 ATTATTATAT
1629066 ATTAATTATTAT
1 ATT-ATTA-TAT
1629078 ATTATTAT
1 ATTATTAT
1629086 TACAAATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.50
11 8 0.29
12 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTATTATAT
Found at i:1629075 original size:14 final size:15
Alignment explanation
Indices: 1629056--1629084 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1629046 ATTATTATAT
1629056 ATTATTATA-TATTA
1 ATTATTATATTATTA
1629070 ATTATTATATTATTA
1 ATTATTATATTATTA
1629085 TTACAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTATATTATTA
Found at i:1629087 original size:14 final size:14
Alignment explanation
Indices: 1629041--1629087 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 14
1629031 CATCCGAGTG
*
1629041 TTATGATTATTATA
1 TTATTATTATTATA
1629055 -TATTATTA-TATA
1 TTATTATTATTATA
1629067 TTA--ATTATTATA
1 TTATTATTATTATA
1629079 TTATTATTA
1 TTATTATTA
1629088 CAAATGGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
11 4 0.14
12 11 0.39
13 9 0.32
14 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:1630372 original size:25 final size:25
Alignment explanation
Indices: 1630323--1630373 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1630313 TTTAATCCCG
* * *
1630323 TATTAATATATTTGGTTAATTATAT
1 TATTAATATATATAGTTAATAATAT
*
1630348 TATTAATATATATAGTTTATAATAT
1 TATTAATATATATAGTTAATAATAT
1630373 T
1 T
1630374 TTGAAGTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TATTAATATATATAGTTAATAATAT
Found at i:1631593 original size:18 final size:19
Alignment explanation
Indices: 1631570--1631606 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1631560 AAAATGTTAA
1631570 ATATTAAAT-ATATTTTAT
1 ATATTAAATCATATTTTAT
1631588 ATATTAAATCCATATTTTA
1 ATATTAAAT-CATATTTTA
1631607 AGATCAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTAAATCATATTTTAT
Found at i:1637964 original size:20 final size:20
Alignment explanation
Indices: 1637919--1637966 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1637909 ATACCCTTTG
* *
1637919 AGTATTGATACTCTATGAAC
1 AGTATCGATACTCTATAAAC
* *
1637939 AATATCGATACTCTATAAAT
1 AGTATCGATACTCTATAAAC
1637959 AGTATCGA
1 AGTATCGA
1637967 ATATATTTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTCTATAAAC
Found at i:1639583 original size:20 final size:20
Alignment explanation
Indices: 1639567--1639604 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1639557 TCAATACTGG
*
1639567 AAGAACAGTACCGATACTAA
1 AAGAACAATACCGATACTAA
*
1639587 AAGAACAATATCGATACT
1 AAGAACAATACCGATACT
1639605 TTCTAAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAGAACAATACCGATACTAA
Found at i:1644335 original size:10 final size:10
Alignment explanation
Indices: 1644317--1644354 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1644307 AACCCATTTT
*
1644317 TTTCATTTCA
1 TTTCGTTTCA
*
1644327 TTTCGTTTCG
1 TTTCGTTTCA
1644337 TTTCGTTTCA
1 TTTCGTTTCA
1644347 TTTC-TTTC
1 TTTCGTTTC
1644355 TTTAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
9 4 0.16
10 21 0.84
ACGTcount: A:0.08, C:0.21, G:0.08, T:0.63
Consensus pattern (10 bp):
TTTCGTTTCA
Found at i:1644398 original size:21 final size:20
Alignment explanation
Indices: 1644355--1644409 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1644345 CATTTCTTTC
* *
1644355 TTTAATTTTATTTTTAGTTA
1 TTTATTTTTATTTGTAGTTA
*
1644375 TTTATTTTTATTCTGTATTTA
1 TTTATTTTTATT-TGTAGTTA
*
1644396 TTTCATTTTAATTT
1 TTT-ATTTTTATTT
1644410 TTCTTGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 11 0.38
21 10 0.34
22 8 0.28
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTATTTTTATTTGTAGTTA
Found at i:1647353 original size:3 final size:3
Alignment explanation
Indices: 1647345--1647411 Score: 53
Period size: 3 Copynumber: 22.3 Consensus size: 3
1647335 AATTGTTTAT
* * * * * * * * *
1647345 ATA ATA ATA AAA ATA ATA ATA ATA ACA ACA ACA ACA ACA ACA ACA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1647393 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
1647412 GTGTGACGGG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (3 bp):
ATA
Found at i:1647606 original size:13 final size:14
Alignment explanation
Indices: 1647573--1647638 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
1647563 TAATAATTAG
1647573 TAATA-TTTTAAAA
1 TAATATTTTTAAAA
*
1647586 TAATATTTTTAACA
1 TAATATTTTTAAAA
*
1647600 TAA-ATTTATTAAAT
1 TAATATTT-TTAAAA
*
1647614 TAATAAATTTTAAAA
1 TAAT-ATTTTTAAAA
*
1647629 -AGTATTTTTA
1 TAATATTTTTA
1647639 TTGATTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
13 15 0.36
14 19 0.45
15 5 0.12
16 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
TAATATTTTTAAAA
Found at i:1649698 original size:21 final size:20
Alignment explanation
Indices: 1649674--1649730 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1649664 AAAAACAGAG
1649674 AAGGGATCGATCCTTTTGAAA
1 AAGGGATCGATCCTTTTG-AA
*
1649695 AAGGGATTGATCCTTTTGAA
1 AAGGGATCGATCCTTTTGAA
* *
1649715 AAGAGATCAATCCTTT
1 AAGGGATCGATCCTTT
1649731 ACTGGTCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (20 bp):
AAGGGATCGATCCTTTTGAA
Found at i:1649727 original size:20 final size:21
Alignment explanation
Indices: 1649678--1649730 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1649668 ACAGAGAAGG
*
1649678 GATCGATCCTTTTGAAAAAGG
1 GATCGATCCTTTTGAAAAAGA
*
1649699 GATTGATCCTTTTG-AAAAGA
1 GATCGATCCTTTTGAAAAAGA
*
1649719 GATCAATCCTTT
1 GATCGATCCTTT
1649731 ACTGGTCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (21 bp):
GATCGATCCTTTTGAAAAAGA
Found at i:1658769 original size:12 final size:13
Alignment explanation
Indices: 1658748--1658784 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
1658738 TTAATCCTAT
1658748 TAAA-AAATTAAA
1 TAAATAAATTAAA
1658760 -AAATAAATTAAA
1 TAAATAAATTAAA
1658772 TAAAT-AATTAAA
1 TAAATAAATTAAA
1658784 T
1 T
1658785 TAAACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 16 0.70
13 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAATAAATTAAA
Found at i:1658800 original size:17 final size:16
Alignment explanation
Indices: 1658757--1658800 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1658747 TTAAAAAATT
1658757 AAAA-AATAAATTAAA
1 AAAATAATAAATTAAA
*
1658772 TAAATAATTAAATTAAA
1 AAAATAA-TAAATTAAA
1658789 CAAAATAATAAA
1 -AAAATAATAAA
1658801 CATTACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 13 0.54
18 6 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAATAAATTAAA
Found at i:1660305 original size:121 final size:120
Alignment explanation
Indices: 1660091--1660507 Score: 573
Period size: 121 Copynumber: 3.5 Consensus size: 120
1660081 TGAAACGTTG
* * * * *
1660091 ATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGTTGATGATCTACCTCGTTCTGTGATAG
1 ATCCACCTCCTTCTGTGATGGAATCGAACAAGATCTCGATGTTGATCTACCTCCTTCTGTGATAG
* * * * *
1660156 AATCAAGCAGAATGTTGAAGCTTATCCAACTCCTTATGTGCAGGATGAAAATATCT
66 AATCGA-CAAAATGTTGAAGCTGATCCAACTCCTTATGTGCTGGATGAAAATGTCT
* *
1660212 ATCCACCTCCTTCTGTGATGGAATCAAACAAGATCTCGATGTTGATCTACCTCCTTCTTTGATAG
1 ATCCACCTCCTTCTGTGATGGAATCGAACAAGATCTCGATGTTGATCTACCTCCTTCTGTGATAG
* * * * *
1660277 AATCGATAAATATGTTAAAGCTGATCCAACTCCTTATGTGTTGGATAAAAATGCCT
66 AATCGACAAA-ATGTTGAAGCTGATCCAACTCCTTATGTGCTGGATGAAAATGTCT
* * * *
1660333 ATCCACCTCCTTCTGTGATGGAATCGAACAAGATTTCGATGCTAATCTACCTTCTTCTGTGATAG
1 ATCCACCTCCTTCTGTGATGGAATCGAACAAGATCTCGATGTTGATCTACCTCCTTCTGTGATAG
* *
1660398 AATCGAGAAAATGTTGAAGTTGATCCAACTCCTTATGTGCTGGATGAAAATGTCT
66 AATCGACAAAATGTTGAAGCTGATCCAACTCCTTATGTGCTGGATGAAAATGTCT
* * * *
1660453 ATCCACCTCATTTTGTAATGGAATCGAACAAGATCTCGATGTCGATCTACCTCCT
1 ATCCACCTCCTTCTGTGATGGAATCGAACAAGATCTCGATGTTGATCTACCTCCT
1660508 ATTTCTTCTG
Statistics
Matches: 258, Mismatches: 37, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
120 89 0.34
121 169 0.66
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (120 bp):
ATCCACCTCCTTCTGTGATGGAATCGAACAAGATCTCGATGTTGATCTACCTCCTTCTGTGATAG
AATCGACAAAATGTTGAAGCTGATCCAACTCCTTATGTGCTGGATGAAAATGTCT
Found at i:1666352 original size:55 final size:55
Alignment explanation
Indices: 1666268--1666374 Score: 198
Period size: 55 Copynumber: 1.9 Consensus size: 55
1666258 TGGCAATGCA
1666268 ACGACTTTGGCTTCAAGCTTTTCCTTTTCTACCTTGGTGGACGTTTCTGGTGGCG
1 ACGACTTTGGCTTCAAGCTTTTCCTTTTCTACCTTGGTGGACGTTTCTGGTGGCG
1666323 ACGACTTTGGCTTC-AGCTTTTCCTTTTTCTACCTTGGTGGACGTTTCTGGTG
1 ACGACTTTGGCTTCAAGCTTTTCC-TTTTCTACCTTGGTGGACGTTTCTGGTG
1666375 AGTAGCATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 9 0.18
55 42 0.82
ACGTcount: A:0.10, C:0.23, G:0.24, T:0.42
Consensus pattern (55 bp):
ACGACTTTGGCTTCAAGCTTTTCCTTTTCTACCTTGGTGGACGTTTCTGGTGGCG
Found at i:1672753 original size:22 final size:22
Alignment explanation
Indices: 1672726--1672771 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1672716 TATTAATCCT
1672726 AATTAAA-AAAAATTACAAAATA
1 AATTAAATAAAAATTA-AAAATA
* *
1672748 AATTAAATAAATATTAAAATTA
1 AATTAAATAAAAATTAAAAATA
1672770 AA
1 AA
1672772 CAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATTAAATAAAAATTAAAAATA
Found at i:1673979 original size:37 final size:37
Alignment explanation
Indices: 1673861--1673967 Score: 205
Period size: 37 Copynumber: 2.9 Consensus size: 37
1673851 AATGTAGGCA
1673861 AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
1 AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
*
1673898 GATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
1 AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
1673935 AATGTGTATTGGTTACATCTTTCGTAAGTCACA
1 AATGTGTATTGGTTACATCTTTCGTAAGTCACA
1673968 CAGCAACGTG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (37 bp):
AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
Found at i:1675693 original size:23 final size:24
Alignment explanation
Indices: 1675667--1675719 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1675657 TAATCTTTTA
*
1675667 TATAATTTTATT-TTTAATATAAT
1 TATAATTTTATTATTTAAAATAAT
*
1675690 TAT-ATATTATTATTTAAAATAAT
1 TATAATTTTATTATTTAAAATAAT
1675713 T-TAATTT
1 TATAATTT
1675720 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATAATTTTATTATTTAAAATAAT
Found at i:1677874 original size:76 final size:76
Alignment explanation
Indices: 1677736--1677882 Score: 190
Period size: 76 Copynumber: 1.9 Consensus size: 76
1677726 ACAATCAATT
* ** * *
1677736 ATGTTATATACAACCTAACATTTTGGTTTCAACCTATAATATGACATTGTAGTTGTTATATGAAT
1 ATGTTATATACAACCTAACATTTTGGTTTCAACCTATAATATGAAATTACAATTCTTATATGAAT
1677801 TACAACCTACA
66 TACAACCTACA
* * *
1677812 ATGTTATATACAACCTAATATTTT-TTATTCAACCTATAATAAT-AAATTACAATTCTTTTATGA
1 ATGTTATATACAACCTAACATTTTGGT-TTCAACCTATAAT-ATGAAATTACAATTCTTATATGA
1677875 ATTACAAC
64 ATTACAAC
1677883 AAATCGTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.02
76 58 0.95
77 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (76 bp):
ATGTTATATACAACCTAACATTTTGGTTTCAACCTATAATATGAAATTACAATTCTTATATGAAT
TACAACCTACA
Found at i:1678209 original size:13 final size:13
Alignment explanation
Indices: 1678189--1678223 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1678179 AATGCGTACT
1678189 ACTTTCCCTTGAC
1 ACTTTCCCTTGAC
1678202 -CGTTTCCCTTGAC
1 AC-TTTCCCTTGAC
1678215 ACTTTCCCT
1 ACTTTCCCT
1678224 AAATATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.11, C:0.40, G:0.09, T:0.40
Consensus pattern (13 bp):
ACTTTCCCTTGAC
Found at i:1680065 original size:23 final size:24
Alignment explanation
Indices: 1680035--1680082 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1680025 GAGTACCCAT
1680035 AGCTTTA-TACTCCACGATGGGCA
1 AGCTTTATTACTCCACGATGGGCA
1680058 AGCTTTATTACTCCACGATGGGCA
1 AGCTTTATTACTCCACGATGGGCA
1680082 A
1 A
1680083 AGGAAGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (24 bp):
AGCTTTATTACTCCACGATGGGCA
Found at i:1682685 original size:29 final size:29
Alignment explanation
Indices: 1682617--1682679 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1682607 TGGTGGTACA
*
1682617 ACACCAAG-TTCCACACTGTCATCGGCACC
1 ACACC-AGTTTCCACACTGCCATCGGCACC
*
1682646 ACACTAGTTTCCACACTGCCATCGGCACC
1 ACACCAGTTTCCACACTGCCATCGGCACC
1682675 ACACC
1 ACACC
1682680 CATTTCAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.27, C:0.43, G:0.13, T:0.17
Consensus pattern (29 bp):
ACACCAGTTTCCACACTGCCATCGGCACC
Found at i:1687159 original size:34 final size:35
Alignment explanation
Indices: 1687116--1687184 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
1687106 TTCTTTAATC
1687116 TCCTGAAGAAGAAGACGTC-ACAAACACTTCTGCT
1 TCCTGAAGAAGAAGACGTCAACAAACACTTCTGCT
1687150 TCCTGAAGAAGAAGACGTCAACAAACACTTCTGCT
1 TCCTGAAGAAGAAGACGTCAACAAACACTTCTGCT
1687185 GGCCTCTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (35 bp):
TCCTGAAGAAGAAGACGTCAACAAACACTTCTGCT
Found at i:1688142 original size:20 final size:20
Alignment explanation
Indices: 1688117--1688169 Score: 99
Period size: 19 Copynumber: 2.7 Consensus size: 20
1688107 TTTTCTAATG
1688117 TGTTGGATTTGGGGGGTGGA
1 TGTTGGATTTGGGGGGTGGA
1688137 TGTTGGATTT-GGGGGTGGA
1 TGTTGGATTTGGGGGGTGGA
1688156 TGTTGGATTTGGGG
1 TGTTGGATTTGGGG
1688170 CTATTTTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.09, C:0.00, G:0.53, T:0.38
Consensus pattern (20 bp):
TGTTGGATTTGGGGGGTGGA
Found at i:1689030 original size:20 final size:18
Alignment explanation
Indices: 1689005--1689043 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1688995 CAGTCCGTTT
1689005 ATTAATAAATCTGATTCAAA
1 ATTAATAAAT-T-ATTCAAA
*
1689025 ATTAATTAATTATTCAAA
1 ATTAATAAATTATTCAAA
1689043 A
1 A
1689044 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTAATAAATTATTCAAA
Found at i:1690310 original size:17 final size:17
Alignment explanation
Indices: 1690288--1690321 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1690278 GCATTTAGGG
1690288 GTGTGGGAGGGATGATA
1 GTGTGGGAGGGATGATA
1690305 GTGTGGGAGGGATGATA
1 GTGTGGGAGGGATGATA
1690322 TTTGAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.53, T:0.24
Consensus pattern (17 bp):
GTGTGGGAGGGATGATA
Found at i:1695247 original size:2 final size:2
Alignment explanation
Indices: 1695240--1695317 Score: 117
Period size: 2 Copynumber: 40.5 Consensus size: 2
1695230 GTAGTTATTA
* *
1695240 AT AT AT AT AT AT AT AT AT -T AT AT AG AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1695281 AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1695318 AGTAATTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
1 3 0.04
2 66 0.96
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1695358 original size:8 final size:8
Alignment explanation
Indices: 1695239--1695362 Score: 64
Period size: 8 Copynumber: 15.9 Consensus size: 8
1695229 TGTAGTTATT
1695239 AATATATA
1 AATATATA
*
1695247 TATATATA
1 AATATATA
*
1695255 TATTATATA
1 -AATATATA
*
1695264 GATATAT-
1 AATATATA
*
1695271 -ATCTATA
1 AATATATA
*
1695278 TATATATA
1 AATATATA
*
1695286 TATATATA
1 AATATATA
* *
1695294 TATATATT
1 AATATATA
1695302 AATATATA
1 AATATATA
*
1695310 TATATATA
1 AATATATA
*
1695318 AGTA-ATTA
1 AATATA-TA
*
1695326 AATGT-TA
1 AATATATA
1695333 AATA-ATTA
1 AATATA-TA
1695341 AATA-ATTA
1 AATATA-TA
1695349 AATATATA
1 AATATATA
1695357 AA-ATAT
1 AATATAT
1695363 GCACTAAATA
Statistics
Matches: 92, Mismatches: 16, Indels: 17
0.74 0.13 0.14
Matches are distributed among these distances:
6 5 0.05
7 10 0.11
8 70 0.76
9 7 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (8 bp):
AATATATA
Found at i:1703840 original size:176 final size:178
Alignment explanation
Indices: 1703509--1703862 Score: 694
Period size: 176 Copynumber: 2.0 Consensus size: 178
1703499 TCTGAAGGTT
1703509 AGCCCGTTGGCAAATCCTGTTGTCCGAATTTGATATCCAGTATGTAAGCCAGAAGCAGTTAAAGG
1 AGCCCGTTGGCAAATCCTGTTGTCCGAATTTGATATCCAGTATGTAAGCCAGAAGCAGTTAAAGG
1703574 GAGCGCCATAGCAGAATTCATTGCGAGTAGGGCTTCAGAAGAATATGAACAGTTGAATTTCGATT
66 GAGCGCCATAGCAGAATTCATTGCGAGTAGGGCTTCAGAAGAATATGAACAGTTGAATTTCGATT
1703639 TCCCGGATGAGGATTTAATGGCTATCTCGGAGGAAGAAACAATTGCTC
131 TCCCGGATGAGGATTTAATGGCTATCTCGGAGGAAGAAACAATTGCTC
1703687 AGCCCGTTGGCAAAT-CTGTTGTCCGAATTTGATATCCAGTATGTAAGCCAGAAGCAGTTAAAGG
1 AGCCCGTTGGCAAATCCTGTTGTCCGAATTTGATATCCAGTATGTAAGCCAGAAGCAGTTAAAGG
1703751 GAGCGCCATAGCAGAATTCA-TGCGAGTAGGGCTTCAGAAGAATATGAACAGTTGAATTTCGATT
66 GAGCGCCATAGCAGAATTCATTGCGAGTAGGGCTTCAGAAGAATATGAACAGTTGAATTTCGATT
1703815 TCCCGGATGAGGATTTAATGGCTATCTCGGAGGAAGAAACAATTGCTC
131 TCCCGGATGAGGATTTAATGGCTATCTCGGAGGAAGAAACAATTGCTC
1703863 TTGCCGGTAA
Statistics
Matches: 176, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
176 92 0.52
177 69 0.39
178 15 0.09
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (178 bp):
AGCCCGTTGGCAAATCCTGTTGTCCGAATTTGATATCCAGTATGTAAGCCAGAAGCAGTTAAAGG
GAGCGCCATAGCAGAATTCATTGCGAGTAGGGCTTCAGAAGAATATGAACAGTTGAATTTCGATT
TCCCGGATGAGGATTTAATGGCTATCTCGGAGGAAGAAACAATTGCTC
Found at i:1705644 original size:8 final size:7
Alignment explanation
Indices: 1705614--1705654 Score: 50
Period size: 8 Copynumber: 5.9 Consensus size: 7
1705604 GTGAAAATGA
1705614 AAAAAAT
1 AAAAAAT
1705621 AAAAAA-
1 AAAAAAT
1705627 AAAAAA-
1 AAAAAAT
1705633 AAAAAAT
1 AAAAAAT
1705640 GAAAAAAT
1 -AAAAAAT
1705648 GAAAAAA
1 -AAAAAA
1705655 GAAGGGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.38
7 6 0.19
8 14 0.44
ACGTcount: A:0.88, C:0.00, G:0.05, T:0.07
Consensus pattern (7 bp):
AAAAAAT
Found at i:1705647 original size:36 final size:39
Alignment explanation
Indices: 1705581--1705654 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 39
1705571 TTGCTTGAAG
*
1705581 AAAAAAAAAAGAAGAAAAAATGAGTGAAAATGAAAAAAAT
1 AAAAAAAAAAGAAGAAAAAATGAG-AAAAATGAAAAAAAT
1705621 AAAAAAAAAA-AA-AAAAAATGA-AAAAATGAAAAAA
1 AAAAAAAAAAGAAGAAAAAATGAGAAAAATGAAAAAA
1705655 GAAGGGTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 12 0.36
38 9 0.27
39 2 0.06
40 10 0.30
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (39 bp):
AAAAAAAAAAGAAGAAAAAATGAGAAAAATGAAAAAAAT
Found at i:1705654 original size:10 final size:10
Alignment explanation
Indices: 1705582--1705654 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 10
1705572 TGCTTGAAGA
*
1705582 AAAAAAAAAG
1 AAAAAAAATG
1705592 AAGAAAAAATG
1 AA-AAAAAATG
***
1705603 AGTGAAAATG
1 AAAAAAAATG
1705613 -AAAAAAAT-
1 AAAAAAAATG
**
1705621 AAAAAAAAAA
1 AAAAAAAATG
1705631 AAAAAAAATG
1 AAAAAAAATG
1705641 --AAAAAATG
1 AAAAAAAATG
1705649 AAAAAA
1 AAAAAA
1705655 GAAGGGTTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
8 8 0.17
9 12 0.25
10 20 0.42
11 8 0.17
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:1706672 original size:55 final size:55
Alignment explanation
Indices: 1706545--1706860 Score: 398
Period size: 55 Copynumber: 5.9 Consensus size: 55
1706535 GGTTTCCCAA
1706545 CGATCGTTGAAGATTGTTCGAGTCTT-TACTCTCTGAAGAAATAGGGGG-AG--G
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
1706596 CGATCGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1706651 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * * *
1706705 CGATCATTGAAGATTG-TCGAGTCTTATACTCTCTGAGGGAATAGGGAGCAGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * * * *
1706759 AGATTTGTTG-AGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
1 CGA-TCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * * *
1706814 CGATTGTTGAAGA-TATTCGAGT-TCTATTCTCCCTGAAGAAAGAGGGG
1 CGATCGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGG
1706861 AGCGAACCGG
Statistics
Matches: 234, Mismatches: 22, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
51 26 0.11
52 21 0.09
53 28 0.12
54 72 0.31
55 87 0.37
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:1706756 original size:108 final size:108
Alignment explanation
Indices: 1706544--1706859 Score: 410
Period size: 108 Copynumber: 2.9 Consensus size: 108
1706534 AGGTTTCCCA
*
1706544 ACGATCGTTGAAGATTGTTCGAGTCTT-TACTCTCTGAAGAAATAGGGG--GAGGCGATCGTTGA
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCGTTGA
*
1706606 AGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCAGAC
66 AGATTG-TCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGAC
* *
1706650 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCATTGA
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCGTTGA
* * *
1706715 AGATTGTCGAGTCTTATACTCTCTGAGGGAATAGGGAGCAGAC
66 AGATTGTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGAC
* * * * * *
1706758 AAGATTTGTTG-AGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 ACGA-TCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG-GCAGACGCGATCGTT
* *
1706822 GAAGATAT-TCGAGT-TCTATTCTCCCTGAAGAAAGAGGG
64 GAAGAT-TGTCGAGTCT-TATACTCCCTGAAGAAATAGGG
1706860 GAGCGAACCG
Statistics
Matches: 183, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
106 26 0.14
107 21 0.11
108 71 0.39
109 64 0.35
110 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATCGTTGA
AGATTGTCGAGTCTTATACTCCCTGAAGAAATAGGGAGCAGAC
Found at i:1706945 original size:54 final size:56
Alignment explanation
Indices: 1706822--1706978 Score: 191
Period size: 55 Copynumber: 2.9 Consensus size: 56
1706812 CACGATTGTT
* *
1706822 GAAGA-TATTCGAGTTCTATTCTCCCTGAAGA-AAGAGGGGAGCGAA-CCGGTTAGCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAA-ACAATA-GGGAGCGAACCCGGTTAGCA
*
1706877 GAAGATTCTT-GAGTTCTATACT-CCTGAAACAATAGGGAGCGAACCCGG-TAGCA
1 GAAGATTATTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCGGTTAGCA
** * *
1706930 GAAGATTATTCGAGTTCTATGTTCCCTGAAACGATTGGGAGCGAACCCG
1 GAAGATTATTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCG
1706979 ATGTTGAAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
53 24 0.27
54 23 0.26
55 39 0.44
56 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (56 bp):
GAAGATTATTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCGGTTAGCA
Found at i:1707238 original size:2 final size:2
Alignment explanation
Indices: 1707231--1707325 Score: 162
Period size: 2 Copynumber: 49.5 Consensus size: 2
1707221 ATGTAGTTAT
1707231 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T- TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1707270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1707312 TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1707326 CTACGGATAA
Statistics
Matches: 89, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
1 4 0.04
2 85 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1707365 original size:15 final size:16
Alignment explanation
Indices: 1707342--1707374 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1707332 ATAAGTAATT
*
1707342 AATAGTTAAATAT-TA
1 AATAATTAAATATATA
1707357 AATAATTAAATATATA
1 AATAATTAAATATATA
1707373 AA
1 AA
1707375 ATATGCACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATAATTAAATATATA
Found at i:1711433 original size:18 final size:18
Alignment explanation
Indices: 1711412--1711452 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1711402 CAGGAATGCA
* *
1711412 AACCCTGATGATAATGAT
1 AACCCTGATAATAATGAC
1711430 AACCCTGATAATAATGAC
1 AACCCTGATAATAATGAC
1711448 AACCC
1 AACCC
1711453 AAATGAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (18 bp):
AACCCTGATAATAATGAC
Found at i:1712250 original size:22 final size:23
Alignment explanation
Indices: 1712225--1712272 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
1712215 CAAATCAGGC
*
1712225 TCGAGAGCCAATTCAG-TCGAGT
1 TCGAGAGCCAATTCAGAACGAGT
1712247 TCGAGAGCCAATTCAGAACGAGT
1 TCGAGAGCCAATTCAGAACGAGT
1712270 TCG
1 TCG
1712273 GCTTAATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (23 bp):
TCGAGAGCCAATTCAGAACGAGT
Found at i:1713223 original size:2 final size:2
Alignment explanation
Indices: 1713216--1713249 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1713206 GTTCTATTTA
1713216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1713250 TTTGAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1713343 original size:37 final size:37
Alignment explanation
Indices: 1713232--1713582 Score: 420
Period size: 37 Copynumber: 9.6 Consensus size: 37
1713222 ATATATATAT
*
1713232 ATATATATATATATATA-TTTTGAAAACA-TTTTCAAA
1 ATATATATA-ATATATAGTTTTGAAAACATTTTTGAAA
*
1713268 ATATATAT-ATATATAGTTTTGAAAACATTTTT-AGA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
1713303 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
1713340 ATATATATAATATATAGTTTTGAAAGCATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
1713377 A-ATTATGTAATATATAGTTTTGAAAATATTTTTAAAA
1 ATA-TATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
1713414 ACATATATGATGTATAGTTTTGAAAACA-TTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
1713450 ATATATATAATATATAATTTTGAAAACGTTTTGGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
1713487 ATATATATAATATATA-TTTTAGAAAACA-TTTTGAAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTG-AAA
*
1713524 CATATATATAATATA-AGATTTTGAAAATATTTTTTTTG-AA
1 -ATATATATAATATATAG-TTTTGAAAACA---TTTTTGAAA
1713564 A-ATATATAATAT-TAGTTTT
1 ATATATATAATATATAGTTTT
1713583 TATAATTTTT
Statistics
Matches: 277, Mismatches: 21, Indels: 33
0.84 0.06 0.10
Matches are distributed among these distances:
34 7 0.03
35 21 0.08
36 75 0.27
37 128 0.46
38 34 0.12
39 5 0.02
40 2 0.01
42 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:1713591 original size:73 final size:75
Alignment explanation
Indices: 1713232--1713582 Score: 399
Period size: 73 Copynumber: 4.8 Consensus size: 75
1713222 ATATATATAT
* *
1713232 ATATATATATATATATA-TTTTGAAAACA--TTTTCAAAATATATAT-ATATATAGTTTTGAAAA
1 ATATATATA-ATATATAGTTTTGAAAATATTTTTTGAAAATATATATAATATATAGTTTTGAAAA
* *
1713293 CATTTT-TAGA
65 CATTTTGAAAA
* *
1713303 ATATATATAATATATAGTTTTGAAAACA-TTTTTGAAAATATATATAATATATAGTTTTGAAAGC
1 ATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATATAATATATAGTTTTGAAAAC
1713367 ATTTTTGAAAA
66 A-TTTTGAAAA
* * * * *
1713378 AT-TATGTAATATATAGTTTTGAAAATA-TTTTTAAAAACATATATGATGTATAGTTTTGAAAAC
1 ATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATATAATATATAGTTTTGAAAAC
1713441 ATTTTG-AAA
66 ATTTTGAAAA
* ** *
1713450 ATATATATAATATATAATTTTGAAAA-CGTTTTGGAAAATATATATAATATATA-TTTTAGAAAA
1 ATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATATAATATATAGTTTT-GAAAA
1713513 CATTTTGAAAA
65 CATTTTGAAAA
1713524 CATATATATAATATA-AGATTTTGAAAATATTTTTTTTG-AAA-ATATATAATAT-TAGTTTT
1 -ATATATATAATATATAG-TTTTGAAAATA--TTTTTTGAAAATATATATAATATATAGTTTT
1713583 TATAATTTTT
Statistics
Matches: 242, Mismatches: 23, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
70 7 0.03
71 20 0.08
72 24 0.10
73 76 0.31
74 63 0.26
75 29 0.12
76 15 0.06
77 3 0.01
78 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (75 bp):
ATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATATAATATATAGTTTTGAAAAC
ATTTTGAAAA
Found at i:1713649 original size:26 final size:27
Alignment explanation
Indices: 1713588--1713650 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
1713578 GTTTTTATAA
* *
1713588 TTTTTATTTACGTGTTATTTATTTCTTT
1 TTTTTATTTA-GTGTTATTAATTTCTTG
1713616 TTTATTATTT-GT-TTATTAATTTCGTTG
1 TTT-TTATTTAGTGTTATTAATTTC-TTG
1713643 TTTTTATT
1 TTTTTATT
1713651 GTTATTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 15 0.48
27 7 0.23
28 3 0.10
29 6 0.19
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.71
Consensus pattern (27 bp):
TTTTTATTTAGTGTTATTAATTTCTTG
Found at i:1714256 original size:2 final size:2
Alignment explanation
Indices: 1714249--1714275 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1714239 TAAGTTTCAA
1714249 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1714276 AATTTCCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1717715 original size:18 final size:18
Alignment explanation
Indices: 1717692--1717844 Score: 90
Period size: 18 Copynumber: 8.5 Consensus size: 18
1717682 ACAAAACCAA
1717692 TAATAATAATAATAATAG
1 TAATAATAATAATAATAG
1717710 TAATAATAATAATAAAATA-
1 TAATAATAATAAT--AATAG
1717729 TAATAA-AAT-ATAA-A-
1 TAATAATAATAATAATAG
1717743 TATATAAT-ATAAATAAGTAG
1 TA-ATAATAAT-AATAA-TAG
* * *
1717763 -AA-AAAAAGGAAAAATA-
1 TAATAATAA-TAATAATAG
1717779 TAATAGTAGTAATAATAATAG
1 TAATA--A-TAATAATAATAG
* *
1717800 CAATAGTAATAATAATAG
1 TAATAATAATAATAATAG
* *
1717818 CAATAATAAAAATAATAG
1 TAATAATAATAATAATAG
*
1717836 TAACAATAA
1 TAATAATAA
1717845 AAAAATGAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
14 3 0.03
15 8 0.08
17 12 0.11
18 58 0.55
19 8 0.08
20 11 0.10
21 6 0.06
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
TAATAATAATAATAATAG
Found at i:1717849 original size:21 final size:21
Alignment explanation
Indices: 1717807--1717849 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1717797 TAGCAATAGT
* *
1717807 AATAATAATAGCAATAATAAA
1 AATAATAATAACAATAAAAAA
*
1717828 AATAATAGTAACAATAAAAAA
1 AATAATAATAACAATAAAAAA
1717849 A
1 A
1717850 TGAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (21 bp):
AATAATAATAACAATAAAAAA
Found at i:1717860 original size:3 final size:3
Alignment explanation
Indices: 1717690--1717844 Score: 79
Period size: 3 Copynumber: 51.7 Consensus size: 3
1717680 AGACAAAACC
*
1717690 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AA- AAT -AT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
1717735 AAT -AT AAAT ATAT AAT -AT AAAT AAGT AGAA AAA AAGG AAA AAT -AT
1 AAT AAT -AAT A-AT AAT AAT -AAT AA-T A-AT AAT AA-T AAT AAT AAT
* * ** * ** *
1717780 AAT AGT AGT AAT AAT AAT AGC AAT AGT AAT AAT AAT AGC AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1717828 AAT AAT AGT AAC AAT AA
1 AAT AAT AAT AAT AAT AA
1717845 AAAAATGAAA
Statistics
Matches: 116, Mismatches: 24, Indels: 24
0.71 0.15 0.15
Matches are distributed among these distances:
2 12 0.10
3 91 0.78
4 12 0.10
5 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1720338 original size:110 final size:110
Alignment explanation
Indices: 1720145--1720549 Score: 686
Period size: 110 Copynumber: 3.7 Consensus size: 110
1720135 TTGTTTCGCT
* *
1720145 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
1720210 TGACAGTCAATCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
*
1720255 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGGTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1720320 TGACAGTCAGTCGCCCCTTCGCTT-TGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCG-TTGTGAAGTTGAGCTTGTGTTGTC
* * *
1720365 TCGAGCCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTAT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * *
1720430 TGACAGTCAGTCGCCCATTCGCTGTGAAGTTGAGCTTGTGATGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
**
1720475 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTACTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1720540 TGACAGTCAG
66 TGACAGTCAG
1720550 CTTTTCCTTA
Statistics
Matches: 277, Mismatches: 16, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
109 1 0.00
110 274 0.99
111 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
Done.