Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009447.1 Hibiscus syriacus cultivar Beakdansim tig00113547_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: 304327
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:8827 original size:12 final size:12
Alignment explanation
Indices: 8810--8834 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8800 GTCAAATAAT
8810 TTAGGCACCAAA
1 TTAGGCACCAAA
8822 TTAGGCACCAAA
1 TTAGGCACCAAA
8834 T
1 T
8835 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:11911 original size:68 final size:68
Alignment explanation
Indices: 11802--11946 Score: 238
Period size: 68 Copynumber: 2.1 Consensus size: 68
11792 GACATCGAGA
* * *
11802 ATGATTATTTCTTGATTACTTTCTGCACCTAGTCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
1 ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
11867 TGG
66 TGG
* *
11870 ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCTATCTCGGAAGGCCCT
1 ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
11935 TGG
66 TGG
11938 ATGA-TATTT
1 ATGATTATTT
11947 GGTCATTACC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
67 5 0.07
68 67 0.93
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (68 bp):
ATGATTATTTCTTGATTACCTTCCGCACCTAATCTGATTTCTTAAAGGCCATCTCGGAAAGCCCT
TGG
Found at i:15029 original size:12 final size:12
Alignment explanation
Indices: 15012--15037 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15002 AGTTTTAAGC
15012 TCTTGTTGAGGT
1 TCTTGTTGAGGT
15024 TCTTGTTGAGGT
1 TCTTGTTGAGGT
15036 TC
1 TC
15038 ACCTAGTTGT
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:0.08, C:0.12, G:0.31, T:0.50
Consensus pattern (12 bp):
TCTTGTTGAGGT
Found at i:27018 original size:14 final size:14
Alignment explanation
Indices: 26999--27025 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26989 CTTCTCCTTC
26999 AACTTGACTTGAAT
1 AACTTGACTTGAAT
27013 AACTTGACTTGAA
1 AACTTGACTTGAA
27026 GCAAATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (14 bp):
AACTTGACTTGAAT
Found at i:28341 original size:31 final size:31
Alignment explanation
Indices: 28296--28388 Score: 116
Period size: 32 Copynumber: 2.9 Consensus size: 31
28286 TTTGATATAA
*
28296 TTAATAAGATAAATTAATATTTTATTTAAAAT
1 TTAATAAG-TAAATTAATATTTTATCTAAAAT
28328 TTAAT-AGTTAAATTAATATTTTTATCTAAAAT
1 TTAATAAG-TAAATTAATA-TTTTATCTAAAAT
* * *
28360 TTAGTAAGTAAAATAGTATTTTATCTAAA
1 TTAATAAGTAAATTAATATTTTATCTAAA
28389 CATCAAAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 23 0.43
32 29 0.54
33 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (31 bp):
TTAATAAGTAAATTAATATTTTATCTAAAAT
Found at i:28812 original size:22 final size:22
Alignment explanation
Indices: 28751--28813 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
28741 CGCAACGCGA
28751 TTCTGACTATCGCATTGCGATT
1 TTCTGACTATCGCATTGCGATT
** * *
28773 TTCCAAAT-TCGCGTTGCGATT
1 TTCTGACTATCGCATTGCGATT
*
28794 TTCTGACTATCGCAATGCGA
1 TTCTGACTATCGCATTGCGA
28814 ATATGTAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.37
Consensus pattern (22 bp):
TTCTGACTATCGCATTGCGATT
Found at i:28827 original size:20 final size:20
Alignment explanation
Indices: 28802--28893 Score: 132
Period size: 20 Copynumber: 4.6 Consensus size: 20
28792 TTTTCTGACT
28802 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
28822 ATCGCAATGTGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
28842 ATCGCAATGAGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
28862 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
28882 ATCGCAATGCGA
1 ATCGCAATGCGA
28894 TTCTGACTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.02
20 65 0.98
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:28894 original size:20 final size:20
Alignment explanation
Indices: 28797--28913 Score: 96
Period size: 20 Copynumber: 5.8 Consensus size: 20
28787 TGCGATTTTC
28797 TGACTATCGCAATGCGAATA
1 TGACTATCGCAATGCGAATA
* *
28817 TGTA-AATCGCAATGTGAATA
1 TG-ACTATCGCAATGCGAATA
* *
28837 TGTA-AATCGCAATGAGAATA
1 TG-ACTATCGCAATGCGAATA
* *
28857 TGTA-AATCGCAATGCGATTA
1 TG-ACTATCGCAATGCGAATA
* *
28877 TGACTATCGCAATGCGATTC
1 TGACTATCGCAATGCGAATA
* *
28897 TGACTGTCGCAACGCGA
1 TGACTATCGCAATGCGA
28914 TTCTGACTGT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 84 0.98
21 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
TGACTATCGCAATGCGAATA
Found at i:28914 original size:20 final size:20
Alignment explanation
Indices: 28863--28929 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
28853 AATATGTAAA
* * *
28863 TCGCAATGCGATTATGACTA
1 TCGCAACGCGATTCTGACTG
*
28883 TCGCAATGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
28903 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
*
28923 TTGCAAC
1 TCGCAAC
28930 ACTTAATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTG
Found at i:30134 original size:21 final size:21
Alignment explanation
Indices: 30108--30152 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30098 GATTTCTGGG
* *
30108 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
30129 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
30150 CAA
1 CAA
30153 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:31219 original size:13 final size:14
Alignment explanation
Indices: 31191--31219 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31181 TTGAAAAGAA
31191 GATATGTGATAAGT
1 GATATGTGATAAGT
31205 GATATGTGA-AAGT
1 GATATGTGATAAGT
31218 GA
1 GA
31220 ATTACAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (14 bp):
GATATGTGATAAGT
Found at i:31499 original size:149 final size:149
Alignment explanation
Indices: 31319--31623 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
31309 AGAGTCGAGG
31319 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
1 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
*
31384 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
31449 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
31468 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
1 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
31533 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
31598 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
*
31617 TTCTACG
1 GTCTACG
31624 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAA
Found at i:31646 original size:23 final size:23
Alignment explanation
Indices: 31602--31646 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31592 ATCATTATAT
*
31602 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
31625 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
31647 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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:32688 original size:24 final size:24
Alignment explanation
Indices: 32656--32709 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32646 GTATTCGAAA
32656 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
32680 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
32704 TTTGAT
1 TTTGAT
32710 GATATTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:32928 original size:14 final size:14
Alignment explanation
Indices: 32909--32935 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32899 GAAAAAGAAA
32909 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
32923 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
32936 TGCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:34995 original size:18 final size:18
Alignment explanation
Indices: 34972--35006 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34962 AGAAAAAGGC
*
34972 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
34990 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
35007 TAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:35321 original size:140 final size:140
Alignment explanation
Indices: 35066--35331 Score: 478
Period size: 140 Copynumber: 1.9 Consensus size: 140
35056 AAACGTTGTA
*
35066 TTATGTGTAAACTTTTAACATTTTCAGATAGGCATGTATTAGTAACTTGAGTTTGAACATTGTTA
1 TTATGTGTAAACTTTTAACATTTTCAGATAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
35131 TGATATGTTCAGTTGTTATCAGTTATTACACATTCATTTGAATATTGCAACGCGAATTTGACTAT
66 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
35196 TATGTGTATT
131 TATGTGTATT
*
35206 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGATAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
35271 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGACTATCGCAACGCGAATTTGA
66 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
35332 TTATCGCAAC
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 120 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGATAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:35464 original size:34 final size:34
Alignment explanation
Indices: 35414--35548 Score: 128
Period size: 34 Copynumber: 3.8 Consensus size: 34
35404 GAATTTGACT
35414 ATCGCAACG-GCTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCG-TATTTGACTATCGCAACGAGAAA
* * * *
35448 ATCGCAACGCGAATTTGAGTATCGTAACGCGAATTTGA
1 ATCGCAACGCGTATTTGACTATCGCAACGAGAA----A
**
35486 TTATCGCAACGATTATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
* *
35522 ATCGCAAAGCGTATTAGACTATCGCAA
1 ATCGCAACGCGTATTTGACTATCGCAA
35549 TGCGAATTGA
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
34 50 0.62
35 1 0.01
36 1 0.01
38 1 0.01
40 27 0.34
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (34 bp):
ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
Found at i:35491 original size:74 final size:74
Alignment explanation
Indices: 35306--35556 Score: 299
Period size: 74 Copynumber: 3.3 Consensus size: 74
35296 TTACACATTC
*
35306 ATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-GCGAATTTGACTATCGCAAC-ACGAATA
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGC-TATTTGACTATCGCAACGA-G-A-A
35369 TGACTATCGCAACGCGA
62 --A--ATCGCAACGCGA
** * *
35386 ATTTTTCTATCGTAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATC
35451 GCAACGCGA
66 GCAACGCGA
* * **
35460 ATTTGAGTATCGTAACGCGAATTTGATTATCGCAACGATTATTTGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATC
* *
35525 GCAAAGCGT
66 GCAACGCGA
* *
35534 ATTAGACTATCGCAATGCGAATT
1 ATTTGACTATCGCAACGCGAATT
35557 GACTTTCGCG
Statistics
Matches: 152, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
74 97 0.64
76 1 0.01
78 1 0.01
79 1 0.01
80 49 0.32
81 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATC
GCAACGCGA
Found at i:35517 original size:20 final size:20
Alignment explanation
Indices: 35306--35516 Score: 238
Period size: 20 Copynumber: 10.8 Consensus size: 20
35296 TTACACATTC
35306 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
35326 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
35346 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
35366 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
** *
35386 ATTTTTCTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
*
35406 ATTTGACTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
35426 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
35446 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
35460 ATTTGAGTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
* ***
35480 ATTTGATTATCGCAACGATT
1 ATTTGACTATCGCAACGCGA
35500 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
35517 AGAAAATCGC
Statistics
Matches: 161, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
14 12 0.07
16 1 0.01
18 1 0.01
19 1 0.01
20 145 0.90
21 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:35565 original size:19 final size:20
Alignment explanation
Indices: 35522--35565 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
35512 CAACGAGAAA
*
35522 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
35542 ATCGCAATGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
35561 TTCGC
1 ATCGC
35566 GTGGCGATTT
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:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:35751 original size:14 final size:14
Alignment explanation
Indices: 35691--35752 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
35681 CACAAATAAG
*
35691 AATTATTTACACATC
1 AATT-TTTACAAATC
**
35706 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
35721 AACTTTTACAAATC
1 AATTTTTACAAATC
*
35735 AATTTTTATAAATC
1 AATTTTTACAAATC
35749 AATT
1 AATT
35753 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:37225 original size:42 final size:42
Alignment explanation
Indices: 37161--37271 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
37151 CTAGAATGTT
* * *
37161 GGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGT-G
1 GGGA-GGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
** *
37204 GGAGAGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG
1 GG-GAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
*
37247 GGGAGGCCTCTTGAACGATGACAGG
1 GGGAGGACTCTTGAACGATGACAGG
37272 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 46 0.82
43 8 0.14
44 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (42 bp):
GGGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
Found at i:37785 original size:18 final size:18
Alignment explanation
Indices: 37755--37821 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 18
37745 GAAACTTAAA
*
37755 ATCGCAACACGAATAACT
1 ATCGCAACGCGAATAACT
* *
37773 ATTGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATAACT
*
37793 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATAACT
37813 ATCGCAACG
1 ATCGCAACG
37822 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.21
20 34 0.79
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.16
Consensus pattern (18 bp):
ATCGCAACGCGAATAACT
Found at i:37799 original size:20 final size:20
Alignment explanation
Indices: 37770--37821 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
37760 AACACGAATA
*
37770 ACTATTGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
37790 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
37810 ACTATCGCAACG
1 ACTATCGCAACG
37822 AGAGAATCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:37894 original size:20 final size:20
Alignment explanation
Indices: 37871--37931 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
37861 TTTCGTTGTA
37871 ATAGTCATTTTCGCGTTGCG
1 ATAGTCATTTTCGCGTTGCG
*
37891 ATAGTCATTTTCACGTTGCG
1 ATAGTCATTTTCGCGTTGCG
37911 ATAGTCATTTTCGCGTTGCG
1 ATAGTCATTTTCGCGTTGCG
37931 A
1 A
37932 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
ATAGTCATTTTCGCGTTGCG
Found at i:38102 original size:18 final size:18
Alignment explanation
Indices: 38079--38128 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
38069 TTTACTAAAC
38079 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
38097 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
38115 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
38129 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:39886 original size:20 final size:20
Alignment explanation
Indices: 39863--39969 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
39853 TCTGAAACTT
39863 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
39883 AAAATAGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
39903 ACTATCGCAACGC-AAATTTG
1 AAAATCGCAACACGAAA-ATG
**
39923 ACTATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
* *
39942 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
39961 AAAATCGCA
1 AAAATCGCA
39970 TTGCGATTCT
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
19 25 0.35
20 47 0.65
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:40362 original size:20 final size:20
Alignment explanation
Indices: 40337--40386 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
40327 TCTGAGAGAT
40337 GGAGATGGACGGATTTCGTC
1 GGAGATGGACGGATTTCGTC
*
40357 GGAGATGGGGACTGATTTCGTC
1 GGAGAT--GGACGGATTTCGTC
40379 GGAGATGG
1 GGAGATGG
40387 GGACGTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
22 19 0.70
ACGTcount: A:0.20, C:0.12, G:0.44, T:0.24
Consensus pattern (20 bp):
GGAGATGGACGGATTTCGTC
Found at i:40373 original size:22 final size:22
Alignment explanation
Indices: 40343--40391 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
40333 AGATGGAGAT
40343 GGACGGATTTCGTCGGAGATGG
1 GGACGGATTTCGTCGGAGATGG
*
40365 GGACTGATTTCGTCGGAGATGG
1 GGACGGATTTCGTCGGAGATGG
40387 GGACG
1 GGACG
40392 TATGTCGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GGACGGATTTCGTCGGAGATGG
Found at i:40657 original size:20 final size:20
Alignment explanation
Indices: 40564--40657 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
40554 GCGCTTTGAA
* *
40564 AATCGCATTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
40584 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
40604 AATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
40624 AATCTCGTTGCGATAATCAG
1 AATCGCGTTGCGATAGTCAG
40644 AATCGCGTTGCGAT
1 AATCGCGTTGCGAT
40658 TTACATATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:40669 original size:20 final size:20
Alignment explanation
Indices: 40646--40737 Score: 175
Period size: 20 Copynumber: 4.6 Consensus size: 20
40636 ATAATCAGAA
*
40646 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
40666 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
40686 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
40706 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
40726 TCGCATTGCGAT
1 TCGCATTGCGAT
40738 AGTCGAAAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:40675 original size:40 final size:40
Alignment explanation
Indices: 40631--40737 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
40621 CAGAATCTCG
*
40631 TTGCGATA-ATCAGAATCGCGTTGCGATTTACATATTCGCA
1 TTGCGATATA-CAGAATCGCATTGCGATTTACATATTCGCA
* * *
40671 TTGCGATTTACATATTCGCATTGCGATTTACATATTCGCA
1 TTGCGATATACAGAATCGCATTGCGATTTACATATTCGCA
* * *
40711 TTGCGATTTACATATTCGCATTGCGAT
1 TTGCGATATACAGAATCGCATTGCGAT
40738 AGTCGAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 61 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (40 bp):
TTGCGATATACAGAATCGCATTGCGATTTACATATTCGCA
Found at i:50269 original size:2 final size:2
Alignment explanation
Indices: 50262--50293 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50252 CACTAACCTA
50262 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
50294 GAATGACGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50582 original size:71 final size:70
Alignment explanation
Indices: 50465--50605 Score: 228
Period size: 71 Copynumber: 2.0 Consensus size: 70
50455 ATATGGAAGC
* *
50465 GAGTTAGGATGTTATACAATTATTGAGCGAATTTAATGGTAAAAGAAAGTATTGTTCTCTTTAAA
1 GAGTTAGGATGTTATACAATTATCGAACGAATTTAATGGTAAAAG-AAGTATTGTTCTCTTTAAA
50530 AGTTTT
65 AGTTTT
** *
50536 GAGTTAGGATGTTATACAATTATCGAACGAATTTGGTGGTAGAAGAAGTATTGTTCTCTTTAAAA
1 GAGTTAGGATGTTATACAATTATCGAACGAATTTAATGGTAAAAGAAGTATTGTTCTCTTTAAAA
50601 GTTTT
66 GTTTT
50606 AAAGCTGAGT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 25 0.38
71 40 0.62
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (70 bp):
GAGTTAGGATGTTATACAATTATCGAACGAATTTAATGGTAAAAGAAGTATTGTTCTCTTTAAAA
GTTTT
Found at i:52046 original size:2 final size:2
Alignment explanation
Indices: 52041--52072 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52031 ATTGTTATTA
52041 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
52073 GTATCTGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58572 original size:33 final size:33
Alignment explanation
Indices: 58530--58593 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
58520 GCTTCTTGCA
58530 CCGGTGAGAGGTTTCATTTGCAATTCCAGAGCG
1 CCGGTGAGAGGTTTCATTTGCAATTCCAGAGCG
58563 CCGGTGAGAGGTTTCATTTGCAATTCCAGAG
1 CCGGTGAGAGGTTTCATTTGCAATTCCAGAG
58594 TGCTCTGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (33 bp):
CCGGTGAGAGGTTTCATTTGCAATTCCAGAGCG
Found at i:72179 original size:30 final size:30
Alignment explanation
Indices: 72145--72208 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
72135 CAAAAACATA
*
72145 AACACCTTCAAAAATAAACAAGCGAACACG
1 AACACCTTCAAAAATAAACAAACGAACACG
* *
72175 AACACCTTTAAAAATAAATAAACGAACACG
1 AACACCTTCAAAAATAAACAAACGAACACG
72205 AACA
1 AACA
72209 TTATACTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.23, G:0.08, T:0.12
Consensus pattern (30 bp):
AACACCTTCAAAAATAAACAAACGAACACG
Found at i:72628 original size:27 final size:27
Alignment explanation
Indices: 72571--72628 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
72561 AACAATAATT
**
72571 TTTAAGGTTAGAGTTTAGGATATATTT
1 TTTAAGGTTAGAGTTTAGGATATATGA
72598 TTTAAGGTTAGAGTTTAGGAT-TCATGA
1 TTTAAGGTTAGAGTTTAGGATAT-ATGA
72625 TTTA
1 TTTA
72629 TGATTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (27 bp):
TTTAAGGTTAGAGTTTAGGATATATGA
Found at i:74661 original size:10 final size:10
Alignment explanation
Indices: 74633--74694 Score: 70
Period size: 11 Copynumber: 5.9 Consensus size: 10
74623 AATTATAAAA
*
74633 AATATAAAATA
1 AATA-AAAATG
74644 AATAAAAATG
1 AATAAAAATG
74654 CAATAAAAATG
1 -AATAAAAATG
74665 AATTAAAAATG
1 AA-TAAAAATG
* *
74676 AATAAAATTC
1 AATAAAAATG
74686 AATAAAAAT
1 AATAAAAAT
74695 ATAATGTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
10 21 0.47
11 24 0.53
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (10 bp):
AATAAAAATG
Found at i:74672 original size:21 final size:21
Alignment explanation
Indices: 74633--74693 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
74623 AATTATAAAA
74633 AATATAAAATAAAT-AAAAATG
1 AATA-AAAATAAATAAAAAATG
* *
74654 CAATAAAAATGAATTAAAAATG
1 -AATAAAAATAAATAAAAAATG
* *
74676 AATAAAATTCAATAAAAA
1 AATAAAAATAAATAAAAA
74694 TATAATGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.68
22 11 0.32
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AATAAAAATAAATAAAAAATG
Found at i:82182 original size:108 final size:110
Alignment explanation
Indices: 82028--82448 Score: 613
Period size: 108 Copynumber: 3.9 Consensus size: 110
82018 CGGGTTCGCT
* * * * *
82028 CCCTCTTTCTTTAGAGAGTAT-AGAACTCG-GACAATCTTTAATAATCGTGTCTGCTCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAG-CAATCTTCAACAATCGTGTCTGCCCCCTATTT
*
82091 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
64 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCC
*
82136 CCCTATTTCTTCAGAGGGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
*
82201 TCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCC
* *
82244 CCCTATTTATTCAGAGAGTATAAGACTCGAGCAATCTTCACCAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* *
82309 TCAGAGAGTATAAGACTCGAACAATTTTCAAT-GATCGCGTCTGCC
66 TCAGAGAGTATAAGACTCGAACAATCTTC-ATCAATCGCGTCTGCC
* * * **
82354 CCCTATTTCTTCAGGGAGTATAAGACTCGAACAATCTTCAACGATCGCATCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
82419 TCAGAGAGTATAAGACTCGAACAATCTTCA
66 TCAGAGAGTATAAGACTCGAACAATCTTCA
82449 ACGATCGTTG
Statistics
Matches: 288, Mismatches: 20, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
108 175 0.61
109 5 0.02
110 106 0.37
111 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (110 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCC
Found at i:82447 original size:55 final size:55
Alignment explanation
Indices: 82028--82455 Score: 587
Period size: 55 Copynumber: 7.9 Consensus size: 55
82018 CGGGTTCGCT
* * * * * * *
82028 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGACAATCTTTAATAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
82083 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
82136 CCCTATTTCTTCAGAGGGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
82191 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * *
82244 CCCTATTTATTCAGAGAGTATAAGACTCGAGCAATCTTCACCAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* **
82299 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAATGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
82354 CCCTATTTCTTCAGGGAGTATAAGACTCGAACAATCTTCAACGATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
82409 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCG
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
82456 TTGGGAAACC
Statistics
Matches: 333, Mismatches: 35, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
53 92 0.28
54 4 0.01
55 235 0.71
56 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:86954 original size:8 final size:8
Alignment explanation
Indices: 86941--86968 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
86931 AAAAGAAGAT
86941 ATATATAC
1 ATATATAC
86949 ATATATAC
1 ATATATAC
86957 ATATATAC
1 ATATATAC
86965 ATAT
1 ATAT
86969 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:103234 original size:47 final size:47
Alignment explanation
Indices: 103144--103355 Score: 239
Period size: 47 Copynumber: 4.4 Consensus size: 47
103134 GGTAAGAACT
*
103144 TTCATCTTTATGGTTTAGGGGTTTCATGAAAAAAAACTTTCTTCTTTTGCA
1 TTCAT-TTTAGGGTTTA-GGG-TTCATG-AAAAAAACTTTCTTCTTTTGCA
*
103195 TTCATTTTAGGGTTTAGGGTTCATGAAAAAAACTCTCTTCTTTTGCA
1 TTCATTTTAGGGTTTAGGGTTCATGAAAAAAACTTTCTTCTTTTGCA
* * * * *
103242 CTCATTTTAGGGTGTAGGGATCATGAAAAAAACTTTGTTCTTTTGCG
1 TTCATTTTAGGGTTTAGGGTTCATGAAAAAAACTTTCTTCTTTTGCA
* * * * * *
103289 TTCATTTCAGGGTTCAGGGTTCAT-TAAAAAGCTTTGTTCTTTTTC-
1 TTCATTTTAGGGTTTAGGGTTCATGAAAAAAACTTTCTTCTTTTGCA
*
103334 TCCCATTTTAGGGTTTAGGGTT
1 T-TCATTTTAGGGTTTAGGGTT
103356 TTATGCATCA
Statistics
Matches: 141, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
45 1 0.01
46 35 0.25
47 81 0.57
48 6 0.04
49 3 0.02
50 10 0.07
51 5 0.04
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.43
Consensus pattern (47 bp):
TTCATTTTAGGGTTTAGGGTTCATGAAAAAAACTTTCTTCTTTTGCA
Found at i:104423 original size:10 final size:10
Alignment explanation
Indices: 104408--104437 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
104398 AACAAAATAC
104408 ATGTATATAT
1 ATGTATATAT
104418 ATGTATATAT
1 ATGTATATAT
*
104428 ATGCATATAT
1 ATGTATATAT
104438 GAAGAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (10 bp):
ATGTATATAT
Found at i:105602 original size:3 final size:3
Alignment explanation
Indices: 105584--105618 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
105574 TAATACTAAA
*
105584 TAT T-T TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
105619 AAATTAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:109177 original size:128 final size:127
Alignment explanation
Indices: 108949--109629 Score: 1202
Period size: 128 Copynumber: 5.3 Consensus size: 127
108939 TTCATATGAA
108949 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* *
109014 TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGATTTGAAGGCGCGTTCACGGG
66 TCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTC-CGGG
*
109077 GGCGCGCCTTCCATTAATTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAAT-TCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTC-ATGTCC
* *
109141 CTCGGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTAAAGGCGCGTTCCGGG
65 CTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCGGG
*
109204 GGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* * * *
109269 TCGGGGACACTATTCATATCATTACCTATCATTTCTCAAGGGACTTGAAGGCGCGTTCCCAGG
66 TCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTT-CCGGG
109332 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
*
109397 TCGGAGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGG
66 TCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTT-CCGGG
109460 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
*
109525 TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCTGGG
66 TCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCC-GGG
109588 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
109630 ACCAAAATTT
Statistics
Matches: 530, Mismatches: 19, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
126 2 0.00
127 120 0.23
128 406 0.77
129 2 0.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (127 bp):
GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
TCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCGGG
Found at i:109408 original size:255 final size:256
Alignment explanation
Indices: 108949--109629 Score: 1222
Period size: 255 Copynumber: 2.7 Consensus size: 256
108939 TTCATATGAA
108949 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* *
109014 TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGATTTGAAGGCGCGTTCACGGGGG
66 TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGG
*
109079 CGCGCCTTCCATTAATTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAATTCCCTC
131 CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAATTCCCTC
* *
109144 GGGGACACTATTCATATCATTACCTATTATTTCTCAGGGGACTTAAAGGCGCGTT-CCGGG
196 GGAGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTAAAGGCGCGTTCCCGGG
*
109204 GGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* * * * *
109269 TCGGGGACACTATTCATATCATTACCTATCATTTCTCAAGGGACTTGAAGGCGCGTTCCCAGGGG
66 TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGG
109334 CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTC-ATGTCCCT
131 CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAAT-TCCCT
*
109398 CGGAGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGG
195 CGGAGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTAAAGGCGCGTTCCCGGG
109460 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
*
109525 TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCTGGGGG
66 TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGG
109590 CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
131 CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
109630 ACCAAAATTT
Statistics
Matches: 405, Mismatches: 19, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
254 2 0.00
255 235 0.58
256 168 0.41
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (256 bp):
GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
TCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGG
CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAATTCCCTC
GGAGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTAAAGGCGCGTTCCCGGG
Found at i:109988 original size:28 final size:28
Alignment explanation
Indices: 109957--110020 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
109947 TTTGAATATA
* *
109957 ATTTTAAATTTCAAATAATATTATTTTT
1 ATTTTAAATTTCAAATAATATAATTTGT
**
109985 ATTTTAAATTTTGAATAATATAATTTGT
1 ATTTTAAATTTCAAATAATATAATTTGT
110013 ATTTTAAA
1 ATTTTAAA
110021 AACATTTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (28 bp):
ATTTTAAATTTCAAATAATATAATTTGT
Found at i:110540 original size:21 final size:21
Alignment explanation
Indices: 110513--110624 Score: 88
Period size: 21 Copynumber: 5.3 Consensus size: 21
110503 GGTATAAAAT
110513 CCTGCGGGCTAGGCATGTAA-
1 CCTGCGGGCTAGGCATGTAAC
*
110533 CCTGGCGGGCTAGGAATGTAAC
1 CCT-GCGGGCTAGGCATGTAAC
* **
110555 CCTGCGGGCTCGAAATGTAAC
1 CCTGCGGGCTAGGCATGTAAC
* *
110576 CCTGCGGAGAT-GGCATATGAA-
1 CCTGCGG-GCTAGGCATGT-AAC
* *
110597 -CTGGTGGGCTAGGCATGTACC
1 CCT-GCGGGCTAGGCATGTAAC
110618 CCTGCGG
1 CCTGCGG
110625 CATCGACGGA
Statistics
Matches: 72, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
20 8 0.11
21 55 0.76
22 9 0.12
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.20
Consensus pattern (21 bp):
CCTGCGGGCTAGGCATGTAAC
Found at i:113048 original size:21 final size:21
Alignment explanation
Indices: 113018--113065 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
113008 GCAGGGGTAC
* *
113018 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
*
113039 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCACTTCAT
113060 ATGCCA
1 ATGCCA
113066 TCTCCGCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:113093 original size:21 final size:21
Alignment explanation
Indices: 113069--113183 Score: 142
Period size: 21 Copynumber: 5.5 Consensus size: 21
113059 TATGCCATCT
* * *
113069 CCGCAGAGTTACATTCCGATC
1 CCGCAGGGTTACATTCCTAGC
*
113090 CCGCAGGGTTACATTCCTAGA
1 CCGCAGGGTTACATTCCTAGC
* *
113111 CCGTAGGGTTACATTCCTAAC
1 CCGCAGGGTTACATTCCTAGC
* *
113132 CCACCA-GGTTACATTCCGAGC
1 CC-GCAGGGTTACATTCCTAGC
113153 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
113174 CCGCAGGGTT
1 CCGCAGGGTT
113184 TTATACCATA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
20 2 0.03
21 76 0.96
22 1 0.01
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:113756 original size:34 final size:34
Alignment explanation
Indices: 113706--113772 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
113696 AAATATTTGT
* * *
113706 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATGATATTATTCAAAATTTAAAATA
113740 AAAATAAAAATGATATTATTCAAAATTTAAAAT
1 AAAATAAAAATGATATTATTCAAAATTTAAAAT
113773 TATATTCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.34
Consensus pattern (34 bp):
AAAATAAAAATGATATTATTCAAAATTTAAAATA
Found at i:113861 original size:14 final size:14
Alignment explanation
Indices: 113842--113871 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
113832 TTTTATCATT
*
113842 AACATATATATTAA
1 AACATATACATTAA
113856 AACATATACATTAA
1 AACATATACATTAA
113870 AA
1 AA
113872 TCAACTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:114443 original size:8 final size:8
Alignment explanation
Indices: 114432--114472 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
114422 TCACAAGTTT
114432 TCAAATTC
1 TCAAATTC
114440 TCAAATTC
1 TCAAATTC
*
114448 TCAAACTC
1 TCAAATTC
114456 T-AAATTC
1 TCAAATTC
114463 TCAAATTC
1 TCAAATTC
114471 TC
1 TC
114473 TGAAAATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (8 bp):
TCAAATTC
Found at i:114462 original size:15 final size:16
Alignment explanation
Indices: 114432--114472 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
114422 TCACAAGTTT
*
114432 TCAAATTCTCAAATTC
1 TCAAACTCTCAAATTC
114448 TCAAACTCT-AAATTC
1 TCAAACTCTCAAATTC
*
114463 TCAAATTCTC
1 TCAAACTCTC
114473 TGAAAATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (16 bp):
TCAAACTCTCAAATTC
Found at i:117751 original size:34 final size:31
Alignment explanation
Indices: 117707--117795 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
117697 TTAATAATTC
*
117707 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
117741 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
117772 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
117796 AAAAATACTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.35
33 2 0.04
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:117772 original size:31 final size:33
Alignment explanation
Indices: 117707--117786 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
117697 TTAATAATTC
* *
117707 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
117741 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
117772 TATAAAATATAATAA
1 TA-AAAAAATAATAA
117787 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:117812 original size:35 final size:34
Alignment explanation
Indices: 117740--117817 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 34
117730 TATTATTTTA
* * * *
117740 ATAAAAA-AATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACAAAAAAATACTAAC
117773 ATAAAATATAATAACTATTTA-AAAAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTACAAAAAAATACTAAC
117808 ATAAAAATAA
1 ATAAAAATAA
117818 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 6 0.16
34 5 0.13
35 21 0.55
36 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACAAAAAAATACTAAC
Found at i:121909 original size:22 final size:22
Alignment explanation
Indices: 121884--121940 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
121874 TCTTCTTTCA
121884 ACCTAGTTATTTTGGCCTGTAT
1 ACCTAGTTATTTTGGCCTGTAT
*
121906 ACCTAGTTATTTTGGCCTGTCT
1 ACCTAGTTATTTTGGCCTGTAT
*
121928 ACCCAGTTATTTT
1 ACCTAGTTATTTT
121941 TCCGGATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.46
Consensus pattern (22 bp):
ACCTAGTTATTTTGGCCTGTAT
Found at i:127732 original size:55 final size:55
Alignment explanation
Indices: 127646--127753 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 55
127636 TCATTCAAAC
*
127646 TAAGAAACTTGATGAATGGGAAAGAACATATGAGAGCGACATATGGGATTTACCA
1 TAAGAAACTTGATGAATGGAAAAGAACATATGAGAGCGACATATGGGATTTACCA
* * **
127701 TAAGAATCTTGATGAATGGAAAAGAATATATGAGAGCGAGTTATGGGATTTAC
1 TAAGAAACTTGATGAATGGAAAAGAACATATGAGAGCGACATATGGGATTTAC
127754 TAGAAAACCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.25
Consensus pattern (55 bp):
TAAGAAACTTGATGAATGGAAAAGAACATATGAGAGCGACATATGGGATTTACCA
Found at i:131571 original size:36 final size:37
Alignment explanation
Indices: 131522--131600 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 37
131512 AATTTAACGT
131522 TAAATTTTGAA-CGGGATACTAAAATAAAACAAAAAC
1 TAAATTTTGAAGCGGGATACTAAAATAAAACAAAAAC
**
131558 TAAAGTTTT-AACGGCGGGATACTAAAATGGAACAAAAAC
1 TAAA-TTTTGAA--GCGGGATACTAAAATAAAACAAAAAC
131597 TAAA
1 TAAA
131601 CTGTTGGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
36 6 0.16
37 4 0.11
39 27 0.73
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (37 bp):
TAAATTTTGAAGCGGGATACTAAAATAAAACAAAAAC
Found at i:135166 original size:26 final size:26
Alignment explanation
Indices: 135135--135196 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
135125 TAAACTATTT
135135 AAACTAAAATACTAAAAACAAAAATA
1 AAACTAAAATACTAAAAACAAAAATA
* *
135161 AAACTAAAATATTAAAAACAAAGATA
1 AAACTAAAATACTAAAAACAAAAATA
*
135187 AGA-TAAAATA
1 AAACTAAAATA
135197 TAATATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 7 0.21
26 26 0.79
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (26 bp):
AAACTAAAATACTAAAAACAAAAATA
Found at i:135178 original size:15 final size:14
Alignment explanation
Indices: 135135--135179 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
135125 TAAACTATTT
135135 AAACTAAAATACTAA
1 AAACTAAAATA-TAA
135150 AAAC-AAAA-AT-A
1 AAACTAAAATATAA
135161 AAACTAAAATATTAA
1 AAACTAAAATA-TAA
135176 AAAC
1 AAAC
135180 AAAGATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 5 0.19
12 5 0.19
13 2 0.08
14 5 0.19
15 9 0.35
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACTAAAATATAA
Found at i:143385 original size:13 final size:13
Alignment explanation
Indices: 143369--143393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
143359 TTTATTTTTA
143369 TTTTTTAAATATT
1 TTTTTTAAATATT
143382 TTTTTTAAATAT
1 TTTTTTAAATAT
143394 CATATTGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTAAATATT
Found at i:143521 original size:25 final size:26
Alignment explanation
Indices: 143466--143523 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
143456 TATTCGGTAT
* *
143466 CAAAATGAATCAAAAACACCTATTTG
1 CAAAAAGAATCAAAAACACCTATTCG
* *
143492 CAAAAAGAATCAAAAGCACGTATTCG
1 CAAAAAGAATCAAAAACACCTATTCG
143518 -AAAAAG
1 CAAAAAG
143524 TGATATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.17
Consensus pattern (26 bp):
CAAAAAGAATCAAAAACACCTATTCG
Found at i:147968 original size:18 final size:19
Alignment explanation
Indices: 147931--147969 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
147921 ATTATATCGT
* *
147931 TTAAATATTTAAAGATTAA
1 TTAAATATTTAAACAATAA
147950 TTAAA-ATTTAAACAATAA
1 TTAAATATTTAAACAATAA
147968 TT
1 TT
147970 CAATGATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
TTAAATATTTAAACAATAA
Found at i:148576 original size:13 final size:14
Alignment explanation
Indices: 148499--148576 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
148489 TCCTAACTTA
*
148499 AAAC-CTAAATTAT
1 AAACTCTAAACTAT
*
148512 AAA-TCCTAAACCAT
1 AAACT-CTAAACTAT
* *
148526 AACCTCATAACCTAT
1 AAACTC-TAAACTAT
*
148541 AAACTATAAACTAT
1 AAACTCTAAACTAT
* *
148555 AAACCCTAAA-TTT
1 AAACTCTAAACTAT
148568 AAACTCTAA
1 AAACTCTAA
148577 CTTAGAATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
13 13 0.27
14 25 0.51
15 11 0.22
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACTCTAAACTAT
Found at i:150000 original size:58 final size:58
Alignment explanation
Indices: 149929--150039 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
149919 GTATAAAATC
* * *
149929 GGGTACTCAAAATTTTC-AGGTACTAAAATGTCGGCCCGTATCCCGGCCCATTATAACT
1 GGGTACTCAAAATTTTCGA-ATACCAAAATGTCGGCCCGTATCCCGACCCATTATAACT
* *
149987 GGGTAC-CAGAAATTTTCGAATACCAAAATGTCGGCCCGTGTTCCGACCCATTA
1 GGGTACTCA-AAATTTTCGAATACCAAAATGTCGGCCCGTATCCCGACCCATTA
150040 CATTAAATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 2 0.04
58 43 0.93
59 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (58 bp):
GGGTACTCAAAATTTTCGAATACCAAAATGTCGGCCCGTATCCCGACCCATTATAACT
Found at i:150338 original size:39 final size:41
Alignment explanation
Indices: 150271--150374 Score: 107
Period size: 39 Copynumber: 2.7 Consensus size: 41
150261 GAAGTTAAAA
* * *
150271 TAAATATTTTAA-AAAAT-A-ATTTAG-AATGTTAATGT-G
1 TAAATATTTTAAGAAATTAAGATTTTGAAATGTTAATCTGG
*
150307 -AAATATTTTAAGAAATTAAGATTTTGAAATGTTATTCTGG
1 TAAATATTTTAAGAAATTAAGATTTTGAAATGTTAATCTGG
150347 TAAA-A-TTTAAGAAATTAAGAATTTTGAA
1 TAAATATTTTAAGAAATTAAG-ATTTTGAA
150375 TTTTATAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
35 11 0.19
36 4 0.07
37 1 0.02
38 5 0.09
39 23 0.40
40 10 0.18
41 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.40
Consensus pattern (41 bp):
TAAATATTTTAAGAAATTAAGATTTTGAAATGTTAATCTGG
Found at i:150393 original size:39 final size:39
Alignment explanation
Indices: 150305--150398 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
150295 AATGTTAATG
* **
150305 TGAAATATTTTAAGAAATTAAGATTTTGAAATGTTATTC
1 TGAAATAATTTAAGAAATTAAGATTTTGAAATGTTATAA
* *
150344 TGGTAA-AATTTAAGAAATTAAGAATTTTG-AATTTTATAA
1 T-GAAATAATTTAAGAAATTAAG-ATTTTGAAATGTTATAA
*
150383 TGAAATAATTTGAGAA
1 TGAAATAATTTAAGAA
150399 TTATAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
38 3 0.07
39 33 0.73
40 9 0.20
ACGTcount: A:0.45, C:0.01, G:0.14, T:0.40
Consensus pattern (39 bp):
TGAAATAATTTAAGAAATTAAGATTTTGAAATGTTATAA
Found at i:151452 original size:35 final size:34
Alignment explanation
Indices: 151408--151474 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 34
151398 TAAAATGAAG
151408 TAAAAATTAAACTTTACGCATTGTATTGAAAAAAT
1 TAAAAATTAAACTTTACGCATTGTATT-AAAAAAT
151443 TAAAAATTAAACTTTACGCATTGTATTAAAAA
1 TAAAAATTAAACTTTACGCATTGTATTAAAAA
151475 TTTACGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 5 0.16
35 27 0.84
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.34
Consensus pattern (34 bp):
TAAAAATTAAACTTTACGCATTGTATTAAAAAAT
Found at i:151480 original size:20 final size:21
Alignment explanation
Indices: 151455--151497 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
151445 AAAATTAAAC
151455 TTTACGCATTGTA-TTAAAAA
1 TTTACGCATTGTATTTAAAAA
151475 TTTACGCATTGTATTTAAAAA
1 TTTACGCATTGTATTTAAAAA
151496 TT
1 TT
151498 AAACGAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TTTACGCATTGTATTTAAAAA
Found at i:165827 original size:20 final size:19
Alignment explanation
Indices: 165781--165846 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
165771 AAAATTTTAA
*
165781 AAATTGAAATTGAAATTGAAT
1 AAATTG-AATT-AAATTAAAT
165802 AGAATTGAATTAAATTAAAT
1 A-AATTGAATTAAATTAAAT
** *
165822 CAAATTTTATTAATTTAAAT
1 -AAATTGAATTAAATTAAAT
165842 AAATT
1 AAATT
165847 TAGTTTATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.13
20 23 0.59
21 6 0.15
22 5 0.13
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.39
Consensus pattern (19 bp):
AAATTGAATTAAATTAAAT
Found at i:166234 original size:13 final size:13
Alignment explanation
Indices: 166216--166241 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166206 CTAAAATGAA
166216 ACAAAACTAAAGT
1 ACAAAACTAAAGT
166229 ACAAAACTAAAGT
1 ACAAAACTAAAGT
166242 TTTTAAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
ACAAAACTAAAGT
Found at i:168991 original size:57 final size:57
Alignment explanation
Indices: 168899--169014 Score: 169
Period size: 57 Copynumber: 2.0 Consensus size: 57
168889 AATAGGAAAC
* *
168899 ATAAATATGCAAGTCGCTTCACATGGTGTGAAAAGTGGCCAAAATAACTCGGAATTG
1 ATAAATATGCAAGTCGCTTCACATGGTGTGAAAAGTAGCCAAAATAACTCAGAATTG
* * * * *
168956 ATAAATATGCAAGTTGCTTCTCATGGTGTGCAAAGTAGCCAAAGTAACTCAGCATTG
1 ATAAATATGCAAGTCGCTTCACATGGTGTGAAAAGTAGCCAAAATAACTCAGAATTG
169013 AT
1 AT
169015 GCAGATGGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (57 bp):
ATAAATATGCAAGTCGCTTCACATGGTGTGAAAAGTAGCCAAAATAACTCAGAATTG
Found at i:173901 original size:12 final size:12
Alignment explanation
Indices: 173886--173920 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
173876 GTTATTTAAA
173886 CGGGTATTGGGT
1 CGGGTATTGGGT
173898 CGGGTATTGGGT
1 CGGGTATTGGGT
173910 CGGGTATTGGG
1 CGGGTATTGGG
173921 CCGAGAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.51, T:0.31
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:173937 original size:24 final size:24
Alignment explanation
Indices: 173886--173940 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
173876 GTTATTTAAA
* * * * *
173886 CGGGTATTGGGTCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGC
173910 CGGGTATTGGGCCGAGAATCGGGC
1 CGGGTATTGGGCCGAGAATCGGGC
173934 CGGGTAT
1 CGGGTAT
173941 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGC
Found at i:174141 original size:6 final size:6
Alignment explanation
Indices: 174130--174154 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
174120 AAATGGGTTT
174130 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
174155 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:180200 original size:2 final size:2
Alignment explanation
Indices: 180195--180222 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
180185 TTTGTTTTTA
180195 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
180223 TACCAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180404 original size:2 final size:2
Alignment explanation
Indices: 180397--180494 Score: 196
Period size: 2 Copynumber: 49.0 Consensus size: 2
180387 GATTAATTCA
180397 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
180439 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
180481 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
180495 TAATTTTTTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:192868 original size:13 final size:13
Alignment explanation
Indices: 192850--192885 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
192840 CTCGGTCAAC
192850 GCCTCCATCTCCG
1 GCCTCCATCTCCG
192863 GCCTCCATCTCCG
1 GCCTCCATCTCCG
192876 GCCTCCATCT
1 GCCTCCATCT
192886 GCTTGTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.08, C:0.53, G:0.14, T:0.25
Consensus pattern (13 bp):
GCCTCCATCTCCG
Found at i:193709 original size:16 final size:16
Alignment explanation
Indices: 193665--193710 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
193655 TCAAGTCAAA
193665 TTAATATTAGATT-GG
1 TTAATATTAGATTGGG
* *
193680 TTAATTTTCGGATTGGG
1 TTAATATT-AGATTGGG
193697 TTAATATTAGATTG
1 TTAATATTAGATTG
193711 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 7 0.28
16 9 0.36
17 9 0.36
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (16 bp):
TTAATATTAGATTGGG
Found at i:193727 original size:32 final size:32
Alignment explanation
Indices: 193665--193729 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
193655 TCAAGTCAAA
* * **
193665 TTAATATTAGATTGGTTAATTTTCGGATTGGG
1 TTAATATTAGATTGCTGAATTTTCAAATTGGG
193697 TTAATATTAGATTGACTGAA-TTTCAAATTGGG
1 TTAATATTAGATTG-CTGAATTTTCAAATTGGG
193729 T
1 T
193730 CAATCTTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.45
Consensus pattern (32 bp):
TTAATATTAGATTGCTGAATTTTCAAATTGGG
Found at i:194932 original size:23 final size:23
Alignment explanation
Indices: 194906--194949 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
194896 ATTTGAAATA
*
194906 TTAATACCTAATAA-ATTTTAACC
1 TTAA-ACCCAATAATATTTTAACC
*
194929 TTAAACCCATTAATATTTTAA
1 TTAAACCCAATAATATTTTAA
194950 AACCCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAACCCAATAATATTTTAACC
Found at i:194961 original size:19 final size:16
Alignment explanation
Indices: 194931--194970 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 16
194921 TTTTAACCTT
194931 AAACCCATTAATATTTTA
1 AAACCCATT-A-ATTTTA
194949 AAACCCAATTAATTTTA
1 AAACCC-ATTAATTTTA
194966 AAACC
1 AAACC
194971 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.52
18 7 0.33
19 3 0.14
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
AAACCCATTAATTTTA
Found at i:196065 original size:20 final size:20
Alignment explanation
Indices: 196042--196104 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 20
196032 TTTAAATAAA
196042 AAAACCGGATTTTTTCGGAT
1 AAAACCGGATTTTTTCGGAT
* * *
196062 AAAAATCCAG-TTTTTT--TAA
1 -AAAA-CCGGATTTTTTCGGAT
196081 AAAACCGGATTTTTTCGGAT
1 AAAACCGGATTTTTTCGGAT
196101 AAAA
1 AAAA
196105 AACCAGTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
17 3 0.09
18 10 0.31
19 1 0.03
20 5 0.16
21 10 0.31
22 3 0.09
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (20 bp):
AAAACCGGATTTTTTCGGAT
Found at i:196065 original size:22 final size:21
Alignment explanation
Indices: 196018--196116 Score: 89
Period size: 22 Copynumber: 4.8 Consensus size: 21
196008 TCGGTTTGCA
***
196018 AAAAAACCGGTTTTTTTAAAT
1 AAAAAACCGGTTTTTTCGGAT
196039 AAAAAAACCGGATTTTTTCGGAT
1 -AAAAAACCGG-TTTTTTCGGAT
* *
196062 AAAAATCCAGTTTTTT----T
1 AAAAAACCGGTTTTTTCGGAT
196079 AAAAAACCGGATTTTTTCGGAT
1 AAAAAACCGG-TTTTTTCGGAT
*
196101 AAAAAACCAGTTTTTT
1 AAAAAACCGGTTTTTT
196117 ATCCGGTTTG
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
17 9 0.14
18 6 0.10
21 12 0.19
22 28 0.44
23 8 0.13
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
AAAAAACCGGTTTTTTCGGAT
Found at i:196089 original size:39 final size:39
Alignment explanation
Indices: 196040--196116 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
196030 TTTTTAAATA
*
196040 AAAAAACCGGATTTTTTCGGATAAAAATCCAGTTTTTTT
1 AAAAAACCGGATTTTTTCGGATAAAAAACCAGTTTTTTT
196079 AAAAAACCGGATTTTTTCGGATAAAAAACCAGTTTTTT
1 AAAAAACCGGATTTTTTCGGATAAAAAACCAGTTTTTT
196117 ATCCGGTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (39 bp):
AAAAAACCGGATTTTTTCGGATAAAAAACCAGTTTTTTT
Found at i:196142 original size:28 final size:28
Alignment explanation
Indices: 196101--196178 Score: 131
Period size: 27 Copynumber: 2.8 Consensus size: 28
196091 TTTTTCGGAT
*
196101 AAAAAACCAGTTTTTTATCCGGTTTG-A
1 AAAAAACCGGTTTTTTATCCGGTTTGAA
196128 AAAAAACCGGTTTTTTATCCGGTTTGAA
1 AAAAAACCGGTTTTTTATCCGGTTTGAA
*
196156 AAAAAACCGGTTTTTAATCCGGT
1 AAAAAACCGGTTTTTTATCCGGT
196179 AAAAAAATCG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 25 0.52
28 23 0.48
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (28 bp):
AAAAAACCGGTTTTTTATCCGGTTTGAA
Found at i:196185 original size:28 final size:27
Alignment explanation
Indices: 196101--196185 Score: 109
Period size: 28 Copynumber: 3.1 Consensus size: 27
196091 TTTTTCGGAT
* **
196101 AAAAAACCAGTTTTTTATCCGGTTTGA
1 AAAAAACCGGTTTTTTATCCGGTTAAA
*
196128 AAAAAACCGGTTTTTTATCCGGTTTGAA
1 AAAAAACCGGTTTTTTATCCGG-TTAAA
*
196156 AAAAAACCGGTTTTTAATCCGG-TAAA
1 AAAAAACCGGTTTTTTATCCGGTTAAA
196182 AAAA
1 AAAA
196186 TCGGTCGTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.13
27 21 0.40
28 24 0.46
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (27 bp):
AAAAAACCGGTTTTTTATCCGGTTAAA
Found at i:197919 original size:15 final size:15
Alignment explanation
Indices: 197899--197940 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
197889 AACATCTTTA
*
197899 TTTTCA-CTTATTTTG
1 TTTTCATCTT-TTATG
197914 TTTTCATCTTTTATG
1 TTTTCATCTTTTATG
*
197929 TTTTCATATTTT
1 TTTTCATCTTTT
197941 CATTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (15 bp):
TTTTCATCTTTTATG
Found at i:197957 original size:24 final size:23
Alignment explanation
Indices: 197914--197959 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
197904 ACTTATTTTG
197914 TTTTCATCTTTTATGTTTTCATA
1 TTTTCATCTTTTATGTTTTCATA
* *
197937 TTTTCATTTATTTTTGTTTTCAT
1 TTTTCATCT-TTTATGTTTTCAT
197960 TTTCTAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTCATCTTTTATGTTTTCATA
Found at i:199450 original size:237 final size:234
Alignment explanation
Indices: 199037--199486 Score: 749
Period size: 237 Copynumber: 1.9 Consensus size: 234
199027 CATAAGCATA
*
199037 CATCTTACATGTAATGATCAATATGGTTAAAACAAACAGGTTAAAAAGTATGATTTTCAAAGAAT
1 CATCTTACAAGTAATGATCAATATGGTTAAAACAAACAGGTTAAAAAGTATGATTTTCAAAGAAT
*
199102 TGAAGAGGCTATAGTATCAGACAAGCTTTCTAGGCTGCAATTTCCATCAAGAAAGCAGTTCATAA
66 TGAAGAGGCTAAAGTATCAGACAAGCTTTCTAGGCTGCAATTTCCATCAAGAAAGCAGTTCATAA
*
199167 AAGAAACTGCTCAGAGCCCAGTGCATATTTCATCATCTACATTTAGCATCCACTACAATCCATAA
131 AAGAAACTGATCAGAGCCCAGTGCATATTTCATCATCTACATTTAGCATCCACTACAATCCATAA
199232 CAAAATCCAAAACATAAATGTTGATCTATTCAACAACATG
196 CAAAATCCAAAACA-AAATGTTGATCTATTCAACAACATG
* *
199272 CATCTTACAAGTGATGATCAATATGGTTAAAACAAACAGGTTAAAAA-TAACATGATTTTCGAAG
1 CATCTTACAAGTAATGATCAATATGGTTAAAACAAACAGGTTAAAAAGT---ATGATTTTCAAAG
199336 AATTGAAGAGGCTAAAGTATCAGACAAGCTTTCTAGGCTGCAATTTCCATCAAGAAAGCAGTTCA
63 AATTGAAGAGGCTAAAGTATCAGACAAGCTTTCTAGGCTGCAATTTCCATCAAGAAAGCAGTTCA
* * * * * *
199401 TATAAGAAACTGATCAGAGCCCAGTGCATATTTCATCGTCTACATTTAGCATCTACTACAGTTCT
128 TAAAAGAAACTGATCAGAGCCCAGTGCATATTTCATCATCTACATTTAGCATCCACTACAATCCA
*
199466 TAACAAAATCCATAACAAAAT
193 TAACAAAATCCAAAACAAAAT
199487 CAGAATTTCA
Statistics
Matches: 200, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
234 1 0.00
235 45 0.22
236 4 0.02
237 150 0.75
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (234 bp):
CATCTTACAAGTAATGATCAATATGGTTAAAACAAACAGGTTAAAAAGTATGATTTTCAAAGAAT
TGAAGAGGCTAAAGTATCAGACAAGCTTTCTAGGCTGCAATTTCCATCAAGAAAGCAGTTCATAA
AAGAAACTGATCAGAGCCCAGTGCATATTTCATCATCTACATTTAGCATCCACTACAATCCATAA
CAAAATCCAAAACAAAATGTTGATCTATTCAACAACATG
Found at i:200062 original size:2 final size:2
Alignment explanation
Indices: 200055--200097 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
200045 CCATAGAAAT
200055 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
200097 T
1 T
200098 TTGAGTTGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:203840 original size:13 final size:14
Alignment explanation
Indices: 203814--203842 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
203804 CAATTTTCAA
203814 ATTAAAATAATAAT
1 ATTAAAATAATAAT
203828 ATTAAAA-AATAAT
1 ATTAAAATAATAAT
203841 AT
1 AT
203843 AAATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAAAATAATAAT
Found at i:206893 original size:22 final size:22
Alignment explanation
Indices: 206865--206913 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
206855 TTTTTTAGAG
*
206865 TATAATTTGGATCCTAACCCAA
1 TATAATTTGGACCCTAACCCAA
*
206887 TATAATTTGGACCCTGACCCAA
1 TATAATTTGGACCCTAACCCAA
206909 TATAA
1 TATAA
206914 ATTAAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (22 bp):
TATAATTTGGACCCTAACCCAA
Found at i:210867 original size:2 final size:2
Alignment explanation
Indices: 210860--210885 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
210850 TTCATGCTTA
210860 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
210886 TGCTTAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215615 original size:20 final size:20
Alignment explanation
Indices: 215579--215616 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
215569 ATCCTATTCC
**
215579 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
215599 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
215617 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:216079 original size:21 final size:22
Alignment explanation
Indices: 216053--216094 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
216043 TGGAGAGACA
*
216053 AGTTT-AATTCAAAAGTTACAG
1 AGTTTAAATACAAAAGTTACAG
*
216074 AGTTTAAATACAAGAGTTACA
1 AGTTTAAATACAAAAGTTACA
216095 AACATCTAAG
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:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (22 bp):
AGTTTAAATACAAAAGTTACAG
Found at i:217868 original size:24 final size:24
Alignment explanation
Indices: 217841--217887 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
217831 CGGCGAAGAG
* *
217841 GAGGAAGAAGACGGTGATGACGAC
1 GAGGAAGAAGACGATGACGACGAC
*
217865 GAGGACGAAGACGATGACGACGA
1 GAGGAAGAAGACGATGACGACGA
217888 AGGAGAGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.40, T:0.06
Consensus pattern (24 bp):
GAGGAAGAAGACGATGACGACGAC
Found at i:217901 original size:21 final size:21
Alignment explanation
Indices: 217855--217902 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
217845 AAGAAGACGG
217855 TGATGACGACGAGGACGAAGA
1 TGATGACGACGAGGACGAAGA
* *
217876 CGATGACGACGAAGGA-GAGGA
1 TGATGACGACG-AGGACGAAGA
217897 TGATGA
1 TGATGA
217903 AGATGATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.12, G:0.40, T:0.10
Consensus pattern (21 bp):
TGATGACGACGAGGACGAAGA
Found at i:234165 original size:2 final size:2
Alignment explanation
Indices: 234158--234206 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
234148 ATGAATAAGT
234158 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
234200 TA TA TA T
1 TA TA TA T
234207 GATGAATCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:242809 original size:13 final size:13
Alignment explanation
Indices: 242791--242815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242781 ATTTTTTTGT
242791 TTTTTTAATTTAA
1 TTTTTTAATTTAA
242804 TTTTTTAATTTA
1 TTTTTTAATTTA
242816 TAAATTATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTAATTTAA
Found at i:243726 original size:29 final size:29
Alignment explanation
Indices: 243670--243781 Score: 127
Period size: 29 Copynumber: 3.8 Consensus size: 29
243660 GTTGACATTA
* * * * *
243670 ATCAAAGAATACTTTAAGTACCTCTTTTG
1 ATCAAAAAATATTTTAAATACTTATTTTG
243699 ATCAAAAAATATTTTAAATA-TATATTTTG
1 ATCAAAAAATATTTTAAATACT-TATTTTG
* *
243728 AACAATAAAATATTTTAAATACTTATTTTA
1 ATCAA-AAAATATTTTAAATACTTATTTTG
*
243758 ATTAAAAAATATTTTAAATACTTA
1 ATCAAAAAATATTTTAAATACTTA
243782 AATAAAAACG
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
29 46 0.65
30 24 0.34
31 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (29 bp):
ATCAAAAAATATTTTAAATACTTATTTTG
Found at i:255851 original size:16 final size:15
Alignment explanation
Indices: 255825--255855 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
255815 GTAAATATAT
255825 AATTTGATTTTATTA
1 AATTTGATTTTATTA
255840 AATTTCGATTTTATTA
1 AATTT-GATTTTATTA
255856 TTATTTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
AATTTGATTTTATTA
Found at i:257759 original size:33 final size:33
Alignment explanation
Indices: 257717--257782 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
257707 TCATATGAAA
257717 AAGTAAACATCAAAATCAAATAGAAATGGGAAT
1 AAGTAAACATCAAAATCAAATAGAAATGGGAAT
257750 AAGTAAACATCAAAATCAAATAGAAATGGGAAT
1 AAGTAAACATCAAAATCAAATAGAAATGGGAAT
257783 CAGAATTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (33 bp):
AAGTAAACATCAAAATCAAATAGAAATGGGAAT
Found at i:260396 original size:19 final size:19
Alignment explanation
Indices: 260368--260404 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
260358 TAAACTCGAT
260368 AAAATAATATTTTAAATTA
1 AAAATAATATTTTAAATTA
*
260387 AAAATTATATTTTAAATT
1 AAAATAATATTTTAAATT
260405 TTAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATAATATTTTAAATTA
Found at i:265417 original size:13 final size:13
Alignment explanation
Indices: 265401--265430 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
265391 TTACCTTTAT
265401 AATTTGATCCTAA
1 AATTTGATCCTAA
265414 AATTTGATCCTAA
1 AATTTGATCCTAA
265427 AATT
1 AATT
265431 ACAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (13 bp):
AATTTGATCCTAA
Found at i:272447 original size:19 final size:18
Alignment explanation
Indices: 272419--272458 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
272409 AGCATCTGCA
272419 TTAAAATTAATTAAATAT
1 TTAAAATTAATTAAATAT
272437 TTAATAATTAATTAAATAT
1 TTAA-AATTAATTAAATAT
272456 TTA
1 TTA
272459 CTGTTCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATTAATTAAATAT
Found at i:275845 original size:14 final size:14
Alignment explanation
Indices: 275826--275874 Score: 89
Period size: 14 Copynumber: 3.5 Consensus size: 14
275816 GCCCTCTGTT
275826 CGAACATAAATGAA
1 CGAACATAAATGAA
275840 CGAACATAAATGAA
1 CGAACATAAATGAA
275854 CGAACATAAATGAA
1 CGAACATAAATGAA
*
275868 CAAACAT
1 CGAACAT
275875 TAACGAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:275882 original size:28 final size:28
Alignment explanation
Indices: 275826--275882 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
275816 GCCCTCTGTT
* *
275826 CGAACATAAATGAACGAACATAAATGAA
1 CGAACATAAATGAACAAACATAAACGAA
*
275854 CGAACATAAATGAACAAACATTAACGAA
1 CGAACATAAATGAACAAACATAAACGAA
275882 C
1 C
275883 ATATAACCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (28 bp):
CGAACATAAATGAACAAACATAAACGAA
Found at i:276708 original size:2 final size:2
Alignment explanation
Indices: 276701--276737 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
276691 TTTTGGTTTC
276701 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
276738 GCCCTCGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:278941 original size:48 final size:48
Alignment explanation
Indices: 278868--278964 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
278858 TCAATAAACT
*
278868 TCCTAATTTATATATAATCTTATCTTATTCTCATTGTCATATATTATG
1 TCCTAATTTATATATAATCTCATCTTATTCTCATTGTCATATATTATG
*
278916 TCCTAATTTATATATAATCTCATCTTATTCTCATTGTTATATATTATG
1 TCCTAATTTATATATAATCTCATCTTATTCTCATTGTCATATATTATG
278964 T
1 T
278965 TAATAACTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (48 bp):
TCCTAATTTATATATAATCTCATCTTATTCTCATTGTCATATATTATG
Found at i:283395 original size:20 final size:20
Alignment explanation
Indices: 283352--283395 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
283342 GTGTAAATAT
* ** *
283352 AATTTCAAAAATATATTTAC
1 AATTTCAAAAATAAATAAAA
283372 AATTTCAAAAATAAATAAAA
1 AATTTCAAAAATAAATAAAA
283392 AATT
1 AATT
283396 CAGTATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTTCAAAAATAAATAAAA
Found at i:290265 original size:2 final size:2
Alignment explanation
Indices: 290258--290282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
290248 TGGATCTACT
290258 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
290283 GTTAGGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:290587 original size:188 final size:188
Alignment explanation
Indices: 290270--290647 Score: 729
Period size: 188 Copynumber: 2.0 Consensus size: 188
290260 TATATATATA
*
290270 TATATATATATATGTTAGGATCTACTTACACCTAATGTAAAATTTTTAGTTTTACACCTTTTTAT
1 TATATATATATAAGTTAGGATCTACTTACACCTAATGTAAAATTTTTAGTTTTACACCTTTTTAT
290335 AATCGTTAGATGAGAGAAAATCAACGACTAAGATTAATTCCTTTTTTTTAATGAATATCTTCTAA
66 AATCGTTAGATGAGAGAAAATCAACGACTAAGATTAATTCCTTTTTTTTAATGAATATCTTCTAA
290400 TTTCTTACTATTAATATCAACCTTTGATTTTCCCTCATCTGACGATCCTAAAAAGGTG
131 TTTCTTACTATTAATATCAACCTTTGATTTTCCCTCATCTGACGATCCTAAAAAGGTG
*
290458 TATATATATATAAGTTAGGATCTACTTACACCTAGTGTAAAATTTTTAGTTTTACACCTTTTTAT
1 TATATATATATAAGTTAGGATCTACTTACACCTAATGTAAAATTTTTAGTTTTACACCTTTTTAT
290523 AATCGTTAGATGAGAGAAAATCAACGACTAAGATTAATTCCTTTTTTTTAATGAATATCTTCTAA
66 AATCGTTAGATGAGAGAAAATCAACGACTAAGATTAATTCCTTTTTTTTAATGAATATCTTCTAA
*
290588 TTTCTTACTATTAATCTCAACCTTTGATTTTCCCTCATCTGACGATCCTAAAAAGGTG
131 TTTCTTACTATTAATATCAACCTTTGATTTTCCCTCATCTGACGATCCTAAAAAGGTG
290646 TA
1 TA
290648 AAACCTTTTA
Statistics
Matches: 187, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
188 187 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (188 bp):
TATATATATATAAGTTAGGATCTACTTACACCTAATGTAAAATTTTTAGTTTTACACCTTTTTAT
AATCGTTAGATGAGAGAAAATCAACGACTAAGATTAATTCCTTTTTTTTAATGAATATCTTCTAA
TTTCTTACTATTAATATCAACCTTTGATTTTCCCTCATCTGACGATCCTAAAAAGGTG
Found at i:298492 original size:29 final size:27
Alignment explanation
Indices: 298418--298492 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
298408 ATTTTTTTTT
* * *
298418 ATAAATTTTCGATCATTTTAGCCTCTA
1 ATAATTTTTTGATCATTTTAACCTCTA
* *
298445 ATAATTTTTTG-TTATTTTTAACGTCTA
1 ATAATTTTTTGATCA-TTTTAACCTCTA
298472 ATAATATTTTTTGATCATTTT
1 AT-A-ATTTTTTGATCATTTT
298493 TTTAAAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.05
27 21 0.55
28 1 0.03
29 12 0.32
30 2 0.05
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.55
Consensus pattern (27 bp):
ATAATTTTTTGATCATTTTAACCTCTA
Done.