Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007182.1 Hibiscus syriacus cultivar Beakdansim tig00018874_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: 121377
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:56752 original size:10 final size:10
Alignment explanation
Indices: 56737--56761 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56727 TATTGGTTGA
56737 ATCAAATATT
1 ATCAAATATT
56747 ATCAAATATT
1 ATCAAATATT
56757 ATCAA
1 ATCAA
56762 GGGTAGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (10 bp):
ATCAAATATT
Found at i:81126 original size:14 final size:15
Alignment explanation
Indices: 81107--81143 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
81097 TTTTCAAGTA
81107 TTTAAATATA-ATTT
1 TTTAAATATATATTT
81121 TTTAAATATATATTT
1 TTTAAATATATATTT
*
81136 ATTAAATA
1 TTTAAATA
81144 ATTGAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATATATATTT
Found at i:84836 original size:12 final size:12
Alignment explanation
Indices: 84819--84846 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
84809 AATACAACAA
84819 AAGTGATAATTT
1 AAGTGATAATTT
84831 AAGTGATAATTT
1 AAGTGATAATTT
84843 AAGT
1 AAGT
84847 ATTAAACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (12 bp):
AAGTGATAATTT
Found at i:84980 original size:10 final size:10
Alignment explanation
Indices: 84965--85010 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
84955 AATAAATAAT
84965 ATATTTTTTC
1 ATATTTTTTC
*
84975 ATA-TTTTTA
1 ATATTTTTTC
*
84984 ATATTTTTTG
1 ATATTTTTTC
*
84994 A-AGTTTTTC
1 ATATTTTTTC
85003 ATATTTTT
1 ATATTTTT
85011 ATAGTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (10 bp):
ATATTTTTTC
Found at i:84989 original size:19 final size:19
Alignment explanation
Indices: 84965--85010 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
84955 AATAAATAAT
84965 ATATTTTTTCATA-TTTTTA
1 ATATTTTTTCA-AGTTTTTA
* *
84984 ATATTTTTTGAAGTTTTTC
1 ATATTTTTTCAAGTTTTTA
85003 ATATTTTT
1 ATATTTTT
85011 ATAGTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (19 bp):
ATATTTTTTCAAGTTTTTA
Found at i:86096 original size:10 final size:10
Alignment explanation
Indices: 86074--86105 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
86064 ATACATCTAC
86074 TATATTT-TA
1 TATATTTATA
86083 TATATTTATA
1 TATATTTATA
86093 TATATTTATA
1 TATATTTATA
86103 TAT
1 TAT
86106 TTAATTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTTATA
Found at i:87823 original size:24 final size:24
Alignment explanation
Indices: 87773--87824 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
87763 ATCTAGATAA
*
87773 AAAAAACAAATGTGATTGACTAGAT
1 AAAAAACAAATGTGATGGACTA-AT
87798 AAAAAACAAATGTGAGTGGACT-AT
1 AAAAAACAAATGTGA-TGGACTAAT
87822 AAA
1 AAA
87825 GCTTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 15 0.60
26 5 0.20
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (24 bp):
AAAAAACAAATGTGATGGACTAAT
Found at i:87977 original size:44 final size:43
Alignment explanation
Indices: 87928--88069 Score: 212
Period size: 44 Copynumber: 3.2 Consensus size: 43
87918 CGTCGGAGAC
* *
87928 AAATTCTTTACTTGTTCTAACGATCAACTTGCTTTCTTCTCAAG
1 AAATTCTTTACTTGTT-TAACAATCAACTTTCTTTCTTCTCAAG
*
87972 AAATTCTTTACTTGTTTTAACAATCAGCTTTCTTTCTTCTCAAG
1 AAATTCTTTACTTG-TTTAACAATCAACTTTCTTTCTTCTCAAG
* *
88016 AAATTCTTTACTTGTTTGAACTACCAACTTTCTTTCTTCTCAAG
1 AAATTCTTTACTTGTTT-AACAATCAACTTTCTTTCTTCTCAAG
88060 AAATTCTTTA
1 AAATTCTTTA
88070 TTTCGTTTGA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
43 3 0.03
44 85 0.94
45 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (43 bp):
AAATTCTTTACTTGTTTAACAATCAACTTTCTTTCTTCTCAAG
Found at i:89406 original size:18 final size:18
Alignment explanation
Indices: 89379--89432 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
89369 TGACCGGTCA
*
89379 CGACCTGTTTACCCGACC
1 CGACCAGTTTACCCGACC
89397 CGACCAGTTTACCCGACC
1 CGACCAGTTTACCCGACC
*
89415 CGACCCGTTTACCCGACC
1 CGACCAGTTTACCCGACC
89433 GTTGACCCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.46, G:0.17, T:0.19
Consensus pattern (18 bp):
CGACCAGTTTACCCGACC
Found at i:89428 original size:13 final size:13
Alignment explanation
Indices: 89411--89452 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
89401 CAGTTTACCC
89411 GACCCGACCCGTT
1 GACCCGACCCGTT
*
89424 TACCCGA-CCGTT
1 GACCCGACCCGTT
89436 GACCCGACCCGTT
1 GACCCGACCCGTT
89449 GACC
1 GACC
89453 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:89528 original size:29 final size:29
Alignment explanation
Indices: 89467--89533 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
89457 ACCGTTGACC
* ** *
89467 GGTGCTATTCTGGGAATTAATTCAGTTTT
1 GGTGCTATTCTAGGAATTAATTCAGAATG
89496 GGTGCTATTCTAGGAATTAATTC-GAAATG
1 GGTGCTATTCTAGGAATTAATTCAG-AATG
89525 GGTGCTATT
1 GGTGCTATT
89534 TTTGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTAGGAATTAATTCAGAATG
Found at i:93935 original size:42 final size:42
Alignment explanation
Indices: 93862--93959 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
93852 TAAGTAAAGA
* * *
93862 AGACGGAGAACATGGATCAAATGGAAACAACAATAGAGGCTG
1 AGACAGAGATCATAGATCAAATGGAAACAACAATAGAGGCTG
93904 AGACAGAGATCATAGATCAAATGGAAACAACAATAGAGGCTG
1 AGACAGAGATCATAGATCAAATGGAAACAACAATAGAGGCTG
93946 AGACAGAGATCATA
1 AGACAGAGATCATA
93960 ATAGAGGTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.47, C:0.14, G:0.26, T:0.13
Consensus pattern (42 bp):
AGACAGAGATCATAGATCAAATGGAAACAACAATAGAGGCTG
Found at i:95004 original size:20 final size:20
Alignment explanation
Indices: 94942--95171 Score: 214
Period size: 20 Copynumber: 11.5 Consensus size: 20
94932 TCAGTTTCCA
* ** *
94942 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
94962 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
94982 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
95002 AAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
95022 AAATAGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
95042 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
95062 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
95082 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
95102 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
95122 AAATTGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * * *
95142 AAATCACAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
95162 AAATCACAAC
1 AAATCGCAAC
95172 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:95903 original size:24 final size:24
Alignment explanation
Indices: 95864--95910 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
95854 AAATTTGGTC
95864 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
95888 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
95911 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:96102 original size:12 final size:12
Alignment explanation
Indices: 96085--96109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
96075 ATATAATCCT
96085 GAAGAAGAAAAA
1 GAAGAAGAAAAA
96097 GAAGAAGAAAAA
1 GAAGAAGAAAAA
96109 G
1 G
96110 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:98474 original size:19 final size:19
Alignment explanation
Indices: 98405--98613 Score: 250
Period size: 19 Copynumber: 11.7 Consensus size: 19
98395 GCAACGAGAG
98405 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98424 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
98438 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
98458 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98477 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98496 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
98510 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98529 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98548 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
98562 AATCGCAATACAGAAATGAA
1 AATCGCAATGC-GAAATGAA
98582 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98601 AATCGCATTGCGA
1 AATCGCAATGCGA
98614 TTCTCTCGTT
Statistics
Matches: 165, Mismatches: 8, Indels: 34
0.80 0.04 0.16
Matches are distributed among these distances:
14 32 0.19
15 2 0.01
16 4 0.02
17 6 0.04
18 1 0.01
19 92 0.56
20 28 0.17
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:98498 original size:72 final size:71
Alignment explanation
Indices: 98405--98613 Score: 280
Period size: 72 Copynumber: 2.9 Consensus size: 71
98395 GCAACGAGAG
*
98405 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCACAACATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCG
98470 AAATGAA
65 AAATGAA
* *
98477 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCACAAC-ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCG
98541 AAATGAA
65 AAATGAA
* * * * *
98548 AATCGCAACGAGAGAATCG-CAAT-ACAGAAATGAAAATCGCAATGCGAAATGAAAATCGCATTG
1 AATCGCAATGCGA-AAT-GAAAATCACA-ACATGAAAATCGCAATGCGAAATGAAAATCGCAATG
98611 CGA
63 CGA
98614 TTCTCTCGTT
Statistics
Matches: 123, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
71 41 0.33
72 80 0.65
73 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCACAACATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:98519 original size:105 final size:102
Alignment explanation
Indices: 98391--98607 Score: 305
Period size: 105 Copynumber: 2.1 Consensus size: 102
98381 CGGAAATTAC
98391 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAATGAAAATCGCAA--C-G--A
*
98454 TGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
61 -GAAAATCGCAATACAGAAATGAAAATCGCAATGCGAAATGAA
*
98496 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-GC--AATGAAAATCGCAACGAGA
*
98561 GAATCGCAATACAGAAATGAAAATCGCAATGCGAAATGAA
63 AAATCGCAATACAGAAATGAAAATCGCAATGCGAAATGAA
98601 AATCGCA
1 AATCGCA
98608 TTGCGATTCT
Statistics
Matches: 103, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
104 12 0.12
105 75 0.73
107 2 0.02
108 1 0.01
110 13 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (102 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAATGAAAATCGCAACGAGAAAA
TCGCAATACAGAAATGAAAATCGCAATGCGAAATGAA
Found at i:98647 original size:53 final size:52
Alignment explanation
Indices: 98584--98699 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
98574 GAAATGAAAA
*
98584 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
98636 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
98689 TCGCATTGCGA
1 TCGCATTGCGA
98700 TTTTCATTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:98662 original size:19 final size:19
Alignment explanation
Indices: 98622--98708 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
98612 GATTCTCTCG
98622 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
98642 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
98661 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
98675 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
98694 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
98709 TTGCCTTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 7 0.12
19 25 0.42
20 15 0.25
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:98826 original size:14 final size:14
Alignment explanation
Indices: 98807--98843 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
98797 CATCAATTAC
98807 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
98821 ACAAATCATCTTTT
1 ACAAATCAACTTTT
98835 ACAAATCAA
1 ACAAATCAA
98844 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:100793 original size:19 final size:19
Alignment explanation
Indices: 100751--100923 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
100741 TAGTTTACTT
* *
100751 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
100771 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
100790 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
100809 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
100828 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
100847 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
100861 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
100880 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
100894 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
100913 TCGCAATGCGA
1 TCGCAACGCGA
100924 TTTTGGTTTC
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 82 0.64
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:100864 original size:14 final size:14
Alignment explanation
Indices: 100845--100901 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
100835 GCGAAATGAA
*
100845 AATCGCAACGACAG
1 AATCGCAACGAAAG
100859 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
100876 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
100892 AATCGCAACG
1 AATCGCAACG
100902 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:100872 original size:33 final size:33
Alignment explanation
Indices: 100826--100918 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
100816 GCGAAACCAA
100826 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
100859 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
100892 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
100919 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:100915 original size:52 final size:52
Alignment explanation
Indices: 100785--100923 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
100775 AACGCGAAAT
* * * *
100785 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
100837 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
100889 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
100924 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:100954 original size:14 final size:14
Alignment explanation
Indices: 100935--100993 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
100925 TTTGGTTTCG
100935 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
100949 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
100966 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
100982 CGTTGCGATTTT
1 CGTTGCGATTTT
100994 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:100961 original size:33 final size:33
Alignment explanation
Indices: 100919--101042 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
100909 AAAATCGCAA
*
100919 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
100952 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
100985 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
101018 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
101043 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:100973 original size:19 final size:18
Alignment explanation
Indices: 100919--101010 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
100909 AAAATCGCAA
100919 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
100938 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
100952 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
100971 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
100985 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
101004 TGCGATT
1 TGCGATT
101011 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:101020 original size:14 final size:14
Alignment explanation
Indices: 100968--101024 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
100958 TTTGGTTTCG
*
100968 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
100982 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
101001 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
101015 CGTTGCGATT
1 CGTTGCGATT
101025 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:101206 original size:83 final size:87
Alignment explanation
Indices: 101090--101453 Score: 472
Period size: 92 Copynumber: 4.1 Consensus size: 87
101080 ATGGATTGCA
* * **
101090 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ATTTACAGTGAGATACACAGTTTAGCA
101149 GAATTGGCAGCAACCGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
101172 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGATACACAGTTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-ACAGTG----AGATACACAGTTT
101237 AGCAGAATTGGCAGCAACCGAACAAAT
61 AGCAGAATTGGCAGCAACCGAACAAAT
101264 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-ACAGTG----AG-ATACACAGTT
101328 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
101356 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-ACAGTG----AG-ATACACAGTT
*
101421 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
101449 TTACT
1 TTACT
101454 AAGCAATCTA
Statistics
Matches: 264, Mismatches: 5, Indels: 15
0.93 0.02 0.05
Matches are distributed among these distances:
82 7 0.03
83 31 0.12
84 3 0.01
85 1 0.00
90 1 0.00
91 25 0.09
92 130 0.49
93 66 0.25
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTACAGTGAGATACACAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:101453 original size:93 final size:93
Alignment explanation
Indices: 101140--101453 Score: 605
Period size: 92 Copynumber: 3.4 Consensus size: 93
101130 TCAGGGTATT
101140 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
101205 TACTATTTCACAGTGTTAAAG-ATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
101232 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
101296 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
101324 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
101389 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
101417 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
101454 AAGCAATCTA
Statistics
Matches: 219, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
91 23 0.11
92 130 0.59
93 66 0.30
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:103170 original size:20 final size:20
Alignment explanation
Indices: 103139--103202 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
103129 TTTTGGTTGA
103139 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
103159 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
103179 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
103200 AAT
1 AAT
103203 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:103191 original size:21 final size:21
Alignment explanation
Indices: 103137--103201 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
103127 TCTTTTGGTT
103137 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
103158 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
103178 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
103199 GAA
1 GAA
103202 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:103262 original size:14 final size:14
Alignment explanation
Indices: 103243--103299 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
103233 TTTGGTTTCG
103243 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
103257 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
103276 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
103290 CGTTGCGATT
1 CGTTGCGATT
103300 TTCATTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:103275 original size:33 final size:33
Alignment explanation
Indices: 103227--103306 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
103217 AAAATCGCAA
** *
103227 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
103260 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
103293 TGCGATTTTCATTT
1 TGCGATTTTCATTT
103307 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
Found at i:103312 original size:21 final size:21
Alignment explanation
Indices: 103287--103360 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
103277 GTTACGATTC
103287 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
103308 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
103329 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
103350 TCTCGTTGCGA
1 TCTCGTTGCGA
103361 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:103482 original size:33 final size:33
Alignment explanation
Indices: 103440--103510 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
103430 AATACTAACT
103440 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
103473 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
103506 TGAAA
1 TGAAA
103511 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:103914 original size:20 final size:20
Alignment explanation
Indices: 103889--104081 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
103879 CTTTAAAAAT
103889 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
103909 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
103929 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
103950 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
103970 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
103990 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
**
104010 CAAGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
104030 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
104050 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
104070 CGCGTTGCGATT
1 CGCGTTGCGATT
104082 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 130 0.88
21 18 0.12
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:109348 original size:225 final size:225
Alignment explanation
Indices: 108939--109545 Score: 907
Period size: 225 Copynumber: 2.7 Consensus size: 225
108929 ACATAACCGA
* * *
108939 TTAATTACTGGAAAATTATCAATCATAATAACAT-AC-AGATAGCGCTTATGTAACGTAATAGGT
1 TTAATTACTGGAAAATTATCAACCATAATAACATAACAAG-TAGCGCTTATTTAATGTAATAGGT
* * * * * **
109002 AACTCCTTTTTAAAGCTGACGGGGCATTAGAAATCCAACGATAACAAAATAGGTTAATTACTTGA
65 AGCTCCTGTTTAAAACTGATGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTGA
* *
109067 TTTGTTATTCAATATTATCAACATATTAGGTAGCGCCTAAAGTGTTACCGAAGTTTAAGTTGATG
130 TTTGTTA-TCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCGAAGTTTAAGCTGATG
109132 GAGCCTTAGAAATCCGACGATAACAAAATAGG
194 GAGCCTTAGAAATCCGACGATAACAAAATAGG
*
109164 TTAATTACTGGAAATATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATATGT
1 TTAATTACTGGAAA-ATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAGGT
* *
109229 TGCTCCTGTTTAAAACTGATGGGGCCTTAGAAATCTGACG-TAACAAAATATGTTAATTACTTGA
65 AGCTCCTGTTTAAAACTGATGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTGA
* *
109293 TTTGTTATCATTATTATCAACATATTAGGTAGCGCCTAAAATGTTACCTAAGTTTAAGCTGATGG
130 TTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCGAAGTTTAAGCTGATGG
* *
109358 AGCCTTGGAAATCTGACGATAACAAAATAGG
195 AGCCTTAGAAATCCGACGATAACAAAATAGG
* *
109389 TTAATTACTGGATACATTATCAACCATAATAACATAACAAGTAGCGTTTATTTAATGTAATAGGT
1 TTAATTACTGGA-AAATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAGGT
* * * * *
109454 AGCGCATG-TTAAAAGCTGATGGGGCCTTATAAATCTGATGATAACAAAATAGGTTAATTAATTG
65 AGCTCCTGTTTAAAA-CTGATGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTG
109518 ATTTGTTATCAATATTATCAACATATTA
129 ATTTGTTATCAATATTATCAACATATTA
109546 CCGTGTAAAT
Statistics
Matches: 346, Mismatches: 30, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
224 6 0.02
225 185 0.53
226 98 0.28
227 55 0.16
228 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (225 bp):
TTAATTACTGGAAAATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAGGTA
GCTCCTGTTTAAAACTGATGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTGAT
TTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCGAAGTTTAAGCTGATGGA
GCCTTAGAAATCCGACGATAACAAAATAGG
Found at i:109866 original size:128 final size:132
Alignment explanation
Indices: 109543--109890 Score: 342
Period size: 128 Copynumber: 2.7 Consensus size: 132
109533 TATCAACATA
* * *
109543 TTACCGTGTAAATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGAATCA
1 TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCA
* *
109608 AAACTTATATGACA---GTATCGATACTTGTATTAAGTATTGCCTATTTTCATTATATCAGTAGA
66 AAACTT-TAT-ACATGTGTATCGATACTTGTATT-AGTATTGCCTATTATCATTATACCAGTAGA
109670 AATGT
128 AATGT
* * * ** *
109675 TTACCATGTACATTGTTAATTTTCCTATTACTTTAAAGCAATAGGTTCCGAAATTGCATGTATCA
1 TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCA
* *
109740 ACACTTTATACATGTGTATTGATACTTG-A-T-GT-TTACGCCTATTATCATTATACC-GATAG-
66 AAACTTTATACATGTGTATCGATACTTGTATTAGTATT--GCCTATTATCATTATACCAG-TAGA
*
109799 ACT-T
128 AATGT
* * * * * * * *
109803 TTACCATTTTCATTGTAAATTAACCTATTACCTTATAGTAATAGATTTCGAAATTATAAGTATCG
1 TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCA
* *
109868 ATACTTTAT--ATGTGTATCAATAC
66 AAACTTTATACATGTGTATCGATAC
109891 ATTTTGCGTG
Statistics
Matches: 179, Mismatches: 31, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
126 12 0.07
128 62 0.35
129 5 0.03
130 22 0.12
131 4 0.02
132 62 0.35
133 12 0.07
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (132 bp):
TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCA
AAACTTTATACATGTGTATCGATACTTGTATTAGTATTGCCTATTATCATTATACCAGTAGAAAT
GT
Found at i:110539 original size:12 final size:12
Alignment explanation
Indices: 110493--110541 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
110483 CCCCCTACCA
110493 CATTCTCTT-TT
1 CATTCTCTTCTT
*
110504 ACCTTCTCTTCTT
1 -CATTCTCTTCTT
* *
110517 CATTATTTTCTT
1 CATTCTCTTCTT
110529 CATTCTCTTCTT
1 CATTCTCTTCTT
110541 C
1 C
110542 CTTAACTTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 28 0.93
13 2 0.07
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.59
Consensus pattern (12 bp):
CATTCTCTTCTT
Found at i:113561 original size:138 final size:137
Alignment explanation
Indices: 113304--113554 Score: 398
Period size: 138 Copynumber: 1.8 Consensus size: 137
113294 AAATTGTATC
*
113304 TAAAAGTTATCGATCGATTTTTTTAATGCATAATGGTGCATTTTCATATCAGTACAATGTGTACT
1 TAAAAGTTATCGATCGATTTTTTTAATGCATAATGGTGCATTTTCATATCAGTACAATATGTACT
* *
113369 TTCGACACTAGATGTGCAATCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGATATACAA
66 TTCGACACGAGATGTGCAATCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGATATACAA
113434 TTATGTA
131 TTATGTA
* * *
113441 TAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGTATTTTCGTATCAGTACTATATGTAC
1 TAAAAGTTATCGATCGATTTT-TTTAATGCATAATGGTGCATTTTCATATCAGTACAATATGTAC
*
113506 TTTCGGCACGATG-TGTGC-ATCCATGGAATTCATAATGAGTTTGTGAATT
65 TTTCGACACGA-GATGTGCAAT-CATGGAATTCATAATGAGTTTGTGAATT
113555 TTCATTTTGG
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
137 23 0.22
138 80 0.77
139 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (137 bp):
TAAAAGTTATCGATCGATTTTTTTAATGCATAATGGTGCATTTTCATATCAGTACAATATGTACT
TTCGACACGAGATGTGCAATCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGATATACAA
TTATGTA
Found at i:116481 original size:21 final size:21
Alignment explanation
Indices: 116444--116504 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
116434 TACCACATAC
* *
116444 CCGAAGGACAACATAGATGTCT
1 CCGAAGGACCACGTAGAT-TCT
116466 -CGAAGGACCACGTAGAATTCT
1 CCGAAGGACCACGTAG-ATTCT
*
116487 CCCGAAGGACCTCGTAGA
1 -CCGAAGGACCACGTAGA
116505 ACTCTCGACT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 16 0.48
22 3 0.09
23 14 0.42
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (21 bp):
CCGAAGGACCACGTAGATTCT
Found at i:116496 original size:23 final size:23
Alignment explanation
Indices: 116466--116510 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
116456 ATAGATGTCT
*
116466 CGAAGGACCACGTAGAATTCTCC
1 CGAAGGACCACGTAGAACTCTCC
*
116489 CGAAGGACCTCGTAGAACTCTC
1 CGAAGGACCACGTAGAACTCTC
116511 GACTCTTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (23 bp):
CGAAGGACCACGTAGAACTCTCC
Done.