Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003339.1 Hibiscus syriacus cultivar Beakdansim tig00007028_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: 152129
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10327 original size:21 final size:21
Alignment explanation
Indices: 10301--10345 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10291 GATTTCTGGG
* *
10301 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
10322 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
10343 CAA
1 CAA
10346 ACGACAGAAT
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:11151 original size:31 final size:31
Alignment explanation
Indices: 11113--11268 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
11103 AGGGTCGAGG
11113 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
11144 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
11175 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
11206 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
11237 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
11268 G
1 G
11269 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:14279 original size:21 final size:21
Alignment explanation
Indices: 14253--14297 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
14243 GATTTCTGGG
* *
14253 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
14274 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
14295 CAA
1 CAA
14298 ACGACAGAAT
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:15135 original size:31 final size:31
Alignment explanation
Indices: 15065--15219 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
15055 AGGGTCGAGG
15065 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
15096 G-TTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
15126 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
15157 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
15188 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
15219 G
1 G
15220 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 30 0.27
31 82 0.73
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:22565 original size:21 final size:20
Alignment explanation
Indices: 22539--22577 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
22529 AACCCCCAAC
22539 ACACCTCTGTTTCCATTTCCA
1 ACACCTCTGTTTCC-TTTCCA
22560 ACACCTCTGTTTCCTTTC
1 ACACCTCTGTTTCCTTTC
22578 TCCAAGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.15, C:0.38, G:0.05, T:0.41
Consensus pattern (20 bp):
ACACCTCTGTTTCCTTTCCA
Found at i:23937 original size:2 final size:2
Alignment explanation
Indices: 23932--23962 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23922 TAAATGCACT
23932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23963 TGGAATCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34700 original size:24 final size:26
Alignment explanation
Indices: 34645--34701 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
34635 AATTAAATGA
* *
34645 TCACATTGATGAAAAAATGATAGGGG
1 TCACATTGATGAAAAAATAATAGGGC
34671 TCACATTGAT-AAAAAA-AATAGAGGC
1 TCACATTGATGAAAAAATAATAG-GGC
34696 T-ACATT
1 TCACATT
34702 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.32
25 9 0.32
26 10 0.36
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (26 bp):
TCACATTGATGAAAAAATAATAGGGC
Found at i:56528 original size:12 final size:12
Alignment explanation
Indices: 56511--56546 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
56501 ATTTACCATA
*
56511 AATAATAAAAGT
1 AATAATAAAAAT
56523 AATAATAAAAAT
1 AATAATAAAAAT
56535 AATATATAAAAA
1 AATA-ATAAAAA
56547 AAACCCACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:57651 original size:44 final size:46
Alignment explanation
Indices: 57599--57768 Score: 299
Period size: 46 Copynumber: 3.7 Consensus size: 46
57589 CATTAAAAAT
* *
57599 ATATATTTTATTTTTAT-ATTAATTTT-AAATATTATAAGAATAAA
1 ATATATTTTATTTTTATCCTAAATTTTAAAATATTATAAGAATAAA
57643 ATATATTTTATTTTTATCCTAAATTTTAAAATATTATAAGAATAAA
1 ATATATTTTATTTTTATCCTAAATTTTAAAATATTATAAGAATAAA
57689 ATATATTTTATTTTTATCCTAAATTTTAAAATATTATAAGAATAAA
1 ATATATTTTATTTTTATCCTAAATTTTAAAATATTATAAGAATAAA
*
57735 ATATATTTTATTTTTATCCTAAAATTTAAAATAT
1 ATATATTTTATTTTTATCCTAAATTTTAAAATAT
57769 ATTTTATTTT
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
44 17 0.14
45 7 0.06
46 97 0.80
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (46 bp):
ATATATTTTATTTTTATCCTAAATTTTAAAATATTATAAGAATAAA
Found at i:57665 original size:23 final size:23
Alignment explanation
Indices: 57639--57759 Score: 62
Period size: 23 Copynumber: 5.3 Consensus size: 23
57629 ATTATAAGAA
57639 TAAAATATATTTTATTTTTATCC
1 TAAAATATATTTTATTTTTATCC
* * *** * * ***
57662 TAAATTTTAAAATATTATAAGAA
1 TAAAATATATTTTATTTTTATCC
57685 TAAAATATATTTTATTTTTATCC
1 TAAAATATATTTTATTTTTATCC
* * *** * * ***
57708 TAAATTTTAAAATATTATAAGAA
1 TAAAATATATTTTATTTTTATCC
57731 TAAAATATATTTTATTTTTATCC
1 TAAAATATATTTTATTTTTATCC
57754 TAAAAT
1 TAAAAT
57760 TTAAAATATA
Statistics
Matches: 58, Mismatches: 40, Indels: 0
0.59 0.41 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAATATATTTTATTTTTATCC
Found at i:57979 original size:43 final size:43
Alignment explanation
Indices: 57925--58098 Score: 233
Period size: 43 Copynumber: 4.0 Consensus size: 43
57915 AAATTATATT
* *
57925 TTTAAGTTAAATTAAAATTAAGATAAAAATAAAATGTATTTTA
1 TTTAAGTTAAATCAAAATTAAGATAAAAATAAAATATATTTTA
57968 TTTAAGTTAAATCAAAATTAAGATAAAAATAAAATATATTTTA
1 TTTAAGTTAAATCAAAATTAAGATAAAAATAAAATATATTTTA
* *
58011 TTTAAGTTAAATCAAAATTAAGATAAAAATAAAACATATTTTT
1 TTTAAGTTAAATCAAAATTAAGATAAAAATAAAATATATTTTA
* ** *
58054 TCTTATA-ATATTTTAAAATTAAGATAAAAATAATATATATATTTT
1 T-TTA-AGTTAAATCAAAATTAAGATAAAAATAA-A-ATATATTTT
58099 TAATATTAAG
Statistics
Matches: 118, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
43 83 0.70
44 25 0.21
45 2 0.02
46 8 0.07
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (43 bp):
TTTAAGTTAAATCAAAATTAAGATAAAAATAAAATATATTTTA
Found at i:58143 original size:23 final size:24
Alignment explanation
Indices: 58099--58143 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
58089 TATATATTTT
*
58099 TAATATTAAGATGTTAACTTAATA
1 TAATATTAAGATGTGAACTTAATA
* *
58123 TAATA-TAATATGTGAATTTAA
1 TAATATTAAGATGTGAACTTAA
58144 GTTAAGAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (24 bp):
TAATATTAAGATGTGAACTTAATA
Found at i:63208 original size:3 final size:3
Alignment explanation
Indices: 63200--63244 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
63190 GAGAGAAAAT
63200 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
63245 GGAGAAGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:77651 original size:19 final size:20
Alignment explanation
Indices: 77614--77653 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
77604 TATCATACTT
77614 TTTAATAAAATTAATTATTA
1 TTTAATAAAATTAATTATTA
77634 TTTAATTAAAA-T-ATTATTA
1 TTTAA-TAAAATTAATTATTA
77653 T
1 T
77654 AAATATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAATAAAATTAATTATTA
Found at i:89015 original size:21 final size:21
Alignment explanation
Indices: 88989--89078 Score: 128
Period size: 21 Copynumber: 4.3 Consensus size: 21
88979 TAGTCGTACC
88989 AAAGACGAGAAGACCGTTCAT
1 AAAGACGAGAAGACCGTTCAT
89010 AAAGACGAGAAGACCGTTCAT
1 AAAGACGAGAAGACCGTTCAT
* *
89031 AAAGATGAGAAGACCATTCAT
1 AAAGACGAGAAGACCGTTCAT
* *
89052 AGAGAC-ATGAAGACCCTTCAT
1 AAAGACGA-GAAGACCGTTCAT
89073 AAAGAC
1 AAAGAC
89079 ATGAAGGCTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 1 0.02
21 61 0.98
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (21 bp):
AAAGACGAGAAGACCGTTCAT
Found at i:89347 original size:13 final size:13
Alignment explanation
Indices: 89329--89353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89319 TAGCACCTCG
89329 TGCATTTGCATTT
1 TGCATTTGCATTT
89342 TGCATTTGCATT
1 TGCATTTGCATT
89354 GCATGTATTT
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (13 bp):
TGCATTTGCATTT
Found at i:91691 original size:13 final size:14
Alignment explanation
Indices: 91654--91720 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
91644 TTGACATCAT
91654 AAAAAGAAAGAAGAG
1 AAAAAGAAAG-AGAG
91669 AAATATAGAAAGAGA-
1 AAA-A-AGAAAGAGAG
*
91684 AAAAAGAAA-AGAT
1 AAAAAGAAAGAGAG
*
91697 AAAAA-AAATGAAATG
1 AAAAAGAAA-GAGA-G
91712 AAAAAGAAA
1 AAAAAGAAA
91721 ATAAAAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
12 6 0.14
13 10 0.23
14 3 0.07
15 11 0.26
16 7 0.16
17 6 0.14
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (14 bp):
AAAAAGAAAGAGAG
Found at i:91726 original size:24 final size:22
Alignment explanation
Indices: 91686--91785 Score: 80
Period size: 24 Copynumber: 4.4 Consensus size: 22
91676 GAAAGAGAAA
*
91686 AAAG-AAAAGATAAAAAAAATG
1 AAAGAAAAAGAAAAAAAAAATG
*
91707 AAATGAAAAAGAAAATAAAAAAGG
1 AAA-GAAAAAGAAAA-AAAAAATG
* *
91731 AAAAGAAAGAGAAAAATTGAAAATG
1 -AAAGAAAAAGAAAAA--AAAAATG
91756 --AGAAAAATGAAAAAAAAGAATG
1 AAAGAAAAA-GAAAAAAAA-AATG
91778 AAAGAAAA
1 AAAGAAAA
91786 TCGATCAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
21 5 0.08
22 11 0.18
23 15 0.24
24 23 0.37
25 8 0.13
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (22 bp):
AAAGAAAAAGAAAAAAAAAATG
Found at i:91769 original size:16 final size:16
Alignment explanation
Indices: 91739--91768 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
91729 GGAAAAGAAA
91739 GAGAAAAATTGAAAAT
1 GAGAAAAATTGAAAAT
91755 GAGAAAAA-TGAAAA
1 GAGAAAAATTGAAAA
91769 AAAAGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
GAGAAAAATTGAAAAT
Found at i:91775 original size:16 final size:16
Alignment explanation
Indices: 91683--91775 Score: 50
Period size: 16 Copynumber: 5.6 Consensus size: 16
91673 ATAGAAAGAG
91683 AAAAAAGAAAAGAT-AA
1 AAAAAAGAAAA-ATGAA
91699 AAAAAATG--AAATGAAA
1 AAAAAA-GAAAAATG-AA
* *
91715 AAGAAAATAAAAAAGGAA
1 AA-AAAA-GAAAAATGAA
91733 AAGAAAGAGAAAAATTG-A
1 AA-AAA-AGAAAAA-TGAA
**
91751 AAATGAGAAAAATGAA
1 AAAAAAGAAAAATGAA
91767 AAAAAAGAA
1 AAAAAAGAA
91776 TGAAAGAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.03
15 4 0.07
16 25 0.42
17 7 0.12
18 16 0.27
19 6 0.10
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (16 bp):
AAAAAAGAAAAATGAA
Found at i:94512 original size:36 final size:36
Alignment explanation
Indices: 94471--94676 Score: 233
Period size: 36 Copynumber: 5.7 Consensus size: 36
94461 AAATCAATCT
94471 TAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
1 TAAGCCTTCACCGAAGA-ATAGTGAAGCAAACCATCC
*
94507 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCAT-C
1 TAAGCCTTCACCGAAGAATAGTGAAGCAAACCATCC
* * *
94542 TGAAGCCTTCACCGGAGAATAGTGAAGCAATCAAT-C
1 T-AAGCCTTCACCGAAGAATAGTGAAGCAAACCATCC
* *
94578 TGAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 T-AAGCCTTCACCGAAGAATAGTGAAGCAAACCATCC
* * *
94615 TAAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGA-AGAATAGTGAAGCAAACCATCC
* *
94651 TAAGTCTTCACC-AAAAAGTAGTGAAG
1 TAAGCCTTCACCGAAGAA-TAGTGAAG
94677 TAGATCCATT
Statistics
Matches: 153, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
35 5 0.03
36 147 0.96
37 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (36 bp):
TAAGCCTTCACCGAAGAATAGTGAAGCAAACCATCC
Found at i:94584 original size:108 final size:108
Alignment explanation
Indices: 94462--94662 Score: 314
Period size: 108 Copynumber: 1.9 Consensus size: 108
94452 ATTGGAGCAA
* * *
94462 AATCAATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAAT
1 AATCAATCTGAAGCCTTCACCGAAGA-ATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAAT
94526 AGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
65 AGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
* * *
94570 AATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCATAAGTCTTCACCAGAGAGTA
1 AATCAATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATA
* *
94635 GTGAAGCAAACCATCTTAAGTCTTCACC
66 GTGAAGCAAACCATCTGAAGCCTTCACC
94663 AAAAAGTAGT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 83 0.99
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (108 bp):
AATCAATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATA
GTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:94676 original size:72 final size:70
Alignment explanation
Indices: 94471--94662 Score: 267
Period size: 72 Copynumber: 2.7 Consensus size: 70
94461 AAATCAATCT
* *
94471 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAA
1 TAAGCCTTCACCG-AGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAA
94536 ACCATC
65 ACCATC
* * * *
94542 TGAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGCA
1 T-AAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCA
94607 AACCATC
64 AACCATC
* *
94614 ATAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTTAAGTCTTCACC
1 -TAAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACC
94663 AAAAAGTAGT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
71 1 0.01
72 102 0.97
73 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (70 bp):
TAAGCCTTCACCGAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAA
CCATC
Found at i:95152 original size:51 final size:51
Alignment explanation
Indices: 95076--95661 Score: 673
Period size: 51 Copynumber: 11.3 Consensus size: 51
95066 TGAAAATATG
* *
95076 CGAGTTATATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
95127 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-T
* * * * * * * *
95179 CTAAGTTCCATACTCCATAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATC
1 C-GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
95231 CGAGTT-TCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCT-ATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * ** *
95282 CGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCATAAGAAGAAGATTTT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT---TTGAAGATGTT
* * *
95336 TGAGTTCTATACTCCCTGAAGAAA-AAGGGAGCGAACCCAG-TTGAAGATGTT
1 CGAGTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCC-GTTTGAAGATGTT
* * * *
95387 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
* *
95438 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
95489 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
95540 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
* * * * *
95593 CGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTT
1 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC--GT-TTGAAGA-TGTT
95648 CGAG-TCTTATACTC
1 CGAGTTC-TATACTC
95662 TCTGAAGAAA
Statistics
Matches: 463, Mismatches: 49, Indels: 42
0.84 0.09 0.08
Matches are distributed among these distances:
49 2 0.00
50 3 0.01
51 301 0.65
52 7 0.02
53 87 0.19
54 43 0.09
55 17 0.04
56 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (51 bp):
CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
Found at i:95542 original size:258 final size:257
Alignment explanation
Indices: 95076--95652 Score: 804
Period size: 258 Copynumber: 2.2 Consensus size: 257
95066 TGAAAATATG
* * *
95076 CGAGTTATATACTCCTTAAAGAAAGAA-TGAGCGAACCC-GTTTGAAGATGTTCGAGTTCCATAC
1 CGAGTTCTATACTCCCT-AAGAAA-AAGGGAGCGAACCCAG-TTGAAGATGTTCGAGTTCCATAC
* *
95139 TCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCATAGAGAAA
63 TCCCTAAAGAAAGAAGGAGCGAACCCG-TTGAAGAGATGTCTAAGTTCCATACTCCATAAAGAAA
*
95204 GAGGGAGCGAACCCGTGTGAAGATATCCGAGTTTCATACTCCTTAATGAAAGAAGGAGCGAACCC
127 GAGGGAGCGAACCCGTGTGAAGATATCCGAGTTTCATACTCCTTAAAGAAAGAAGGAGCGAACCC
* * *
95269 GTTTGAAGATGTTCGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCATAAGAAGAAGATT
192 GTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCATAAGAAG-AGATG
95334 TT
256 TT
*
95336 TGAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTC
1 CGAGTTCTATACTCCCT-AAGAAAAAGGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTC
* * * * *
95401 CCTAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGT-TCGAGTTCTATACTCCCTAAAGAAAGA
65 CCTAAAGAAAGAAGGAGCGAACCCGTTGAAGAGATGTCT-AAGTTCCATACTCCATAAAGAAAGA
* * *
95464 GGGAGCGAACCCGTTTGAAGATGTTCGAG-TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCG
129 GGGAGCGAACCCGTGTGAAGATATCCGAGTTTC-ATACTCCTTAAAGAAAGAAGGAGCGAACCCG
* **
95528 TTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTT
193 TTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCATAAGAAGAGATGTT
*
95593 CGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTTCGAGT
1 CGAGTTCTATACTCCCTA-AGAAAAAGGGAGCGAACCCA---GTTGAAGA-TGTTCGAGT
95653 CTTATACTCT
Statistics
Matches: 284, Mismatches: 24, Indels: 17
0.87 0.07 0.05
Matches are distributed among these distances:
256 1 0.00
257 45 0.16
258 141 0.50
259 2 0.01
260 85 0.30
261 10 0.04
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (257 bp):
CGAGTTCTATACTCCCTAAGAAAAAGGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCC
CTAAAGAAAGAAGGAGCGAACCCGTTGAAGAGATGTCTAAGTTCCATACTCCATAAAGAAAGAGG
GAGCGAACCCGTGTGAAGATATCCGAGTTTCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTT
GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCATAAGAAGAGATGTT
Found at i:95671 original size:55 final size:54
Alignment explanation
Indices: 95327--96230 Score: 656
Period size: 55 Copynumber: 16.9 Consensus size: 54
95317 CCCATAAGAA
* * * *
95327 GAAGATT-TTTGAGT-TCTATACTCCCTGAAGAAAAAGGGAGCGAACCCA--GTT
1 GAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGGGCGAACCCATTGTT
* * * *
95378 GAAGA-TGTTCGAGT-TCCATACTCCCT-AGAGAAAGAGGGAGCGAACCC---G-T
1 GAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGGGCGAACCCATTGTT
* * * * * *
95427 GAAGAGATGTTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGCGAACCC-GT-TT
1 GAAGA-TTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGGGCGAACCCATTGTT
* * * * *
95480 GAAGA-TGTTCGAGT-TCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TT
1 GAAGATTGTTCGAGTCT-TATACTCTC-TGAAGAAATAGGGGGCGAACCCATTGTT
* * * * *
95531 GAAGA-TGTTCGAGT-TCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TT
1 GAAGATTGTTCGAGTCT-TATACTCTC-TGAAGAAATAGGGGGCGAACCCATTGTT
* * *
95582 GAAGAGATGTTCGAGT-TCTATACTCCCT-AGAGAAATAGGGAGCGAACCCATTTGTT
1 GAAGA-TTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGGGCGAACCCA-TTGTT
* *
95638 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGA-AC-CCATTGTT
* * * *
95693 GAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGAAC-CCATTGTT
* * **
95748 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACACAATCATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGA-AC-CCATTGTT
* *
95801 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGA-AC-CCATTGTT
* * *
95856 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGA-AC-CCATTGTT
* *
95909 GAAGATTGTTCG-GATCTTATACTCTCTGAAGAAATAGGGGGC-AGACACGATTGAT
1 GAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCGA-AC-CCATTGTT
* * * *
95964 GAAGATTGTT-G-GTCTTATACTCTCTAAAGAATTAGGGGGC-AGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGA-AC-CCATTGTT
** * *
96017 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-GAACCCATTGTT
* * * *
96072 GAAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGA-AC-CCATTGTT
*
96125 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-AGA-CAAGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGA-ACCCA--TTGTT
* *
96180 GAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACCCATT
1 GAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGAACCCATT
96231 TTTCTGAAGA
Statistics
Matches: 751, Mismatches: 62, Indels: 77
0.84 0.07 0.09
Matches are distributed among these distances:
49 6 0.01
50 4 0.01
51 179 0.24
52 3 0.00
53 225 0.30
54 16 0.02
55 302 0.40
56 15 0.02
57 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (54 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGAACCCATTGTT
Found at i:95791 original size:108 final size:108
Alignment explanation
Indices: 95637--96218 Score: 943
Period size: 108 Copynumber: 5.4 Consensus size: 108
95627 ACCCATTTGT
*
95637 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGT
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGT
* *
95702 TCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGA
64 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* *
95747 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCATTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
95812 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
95855 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
*
95920 G-GATCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGA
66 GAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* * *
95963 TGAAGATTGTTGGTCTTATACTCTCTAAAGAATTAGGGGGCAGACGCAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
*
96028 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGA
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
*
96071 TGAAGATTATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
** * *
96136 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTGT
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
**
96179 TGAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGG
1 TGAAGATTG--T-GGGTCTTATACTCTCTGAAGAAATAGGG
96219 AGCGAACCCA
Statistics
Matches: 442, Mismatches: 25, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
107 2 0.00
108 402 0.91
109 3 0.01
110 35 0.08
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (108 bp):
TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
Found at i:100474 original size:60 final size:60
Alignment explanation
Indices: 100364--100479 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
100354 TAGTCGGTGA
* * **
100364 CTATTTTGTAACTTTCAATAGTCGAGAGACTTAACAAAATAATATTATATAATCGAAGGT
1 CTATTTTGAAACTTTCAATAGTCGAGAAACTTAACAAAATAATAACATATAATCGAAGGT
* * * * * *
100424 CTATTTTGAAACTTTTAATATTCGATAAACTTAAGAAAATAGTAACATATAGTCGA
1 CTATTTTGAAACTTTCAATAGTCGAGAAACTTAACAAAATAATAACATATAATCGA
100480 GAGATCATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (60 bp):
CTATTTTGAAACTTTCAATAGTCGAGAAACTTAACAAAATAATAACATATAATCGAAGGT
Found at i:103813 original size:2 final size:2
Alignment explanation
Indices: 103806--103830 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103796 ATCCTAACTC
103806 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
103831 ACTCTTTTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104167 original size:24 final size:24
Alignment explanation
Indices: 104139--104195 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
104129 CCTAAACCGA
104139 CCCAACTGAACTGGATCAACCTGG
1 CCCAACTGAACTGGATCAACCTGG
*
104163 TCCAACTGAACTGGATCAACCTGG
1 CCCAACTGAACTGGATCAACCTGG
104187 CCCAACTGA
1 CCCAACTGA
104196 GCTTAGCCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (24 bp):
CCCAACTGAACTGGATCAACCTGG
Found at i:106064 original size:12 final size:12
Alignment explanation
Indices: 106047--106071 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
106037 GTCAAATAAT
106047 TTAGACACCAAA
1 TTAGACACCAAA
106059 TTAGACACCAAA
1 TTAGACACCAAA
106071 T
1 T
106072 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:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (12 bp):
TTAGACACCAAA
Found at i:110697 original size:12 final size:12
Alignment explanation
Indices: 110680--110704 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
110670 GTCAAATAAT
110680 TTAGGCACCAAA
1 TTAGGCACCAAA
110692 TTAGGCACCAAA
1 TTAGGCACCAAA
110704 T
1 T
110705 GGTACTTTGT
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:112091 original size:23 final size:23
Alignment explanation
Indices: 112039--112091 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
112029 GACATTTTTT
*
112039 TGCCTTTATGTCTCGTTTATCTC
1 TGCCTTTATGTCTCGTTTATCTA
* *
112062 TGTCTTTGTGT-TACGTTTATCTA
1 TGCCTTTATGTCT-CGTTTATCTA
112085 TGCCTTT
1 TGCCTTT
112092 TGGTAGCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.09, C:0.21, G:0.15, T:0.55
Consensus pattern (23 bp):
TGCCTTTATGTCTCGTTTATCTA
Found at i:120913 original size:22 final size:23
Alignment explanation
Indices: 120876--120919 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
120866 GATACAATAA
*
120876 AATTTCAGGGCGGACAC-CATAG
1 AATTTCAGGGCAGACACACATAG
*
120898 AATTTCAGGGTAGACACACATA
1 AATTTCAGGGCAGACACACATA
120920 CATTAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
AATTTCAGGGCAGACACACATAG
Found at i:120951 original size:21 final size:21
Alignment explanation
Indices: 120922--120978 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
120912 CACACATACA
* *
120922 TTAATGAAGAAAATTTTGATT
1 TTAAAGAAGAAAATTTCGATT
120943 TTAAAGAAGAAAATTTCGATT
1 TTAAAGAAGAAAATTTCGATT
120964 TTAAAGAAGAAAATT
1 TTAAAGAAGAAAATT
120979 CAAATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (21 bp):
TTAAAGAAGAAAATTTCGATT
Found at i:120985 original size:21 final size:20
Alignment explanation
Indices: 120922--120989 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
120912 CACACATACA
* *
120922 TTAATGAAGAAAATTTTGATT
1 TTAAAGAAGAAAA-TTCGATT
120943 TTAAAGAAGAAAATTTCGATT
1 TTAAAGAAGAAAA-TTCGATT
*
120964 TTAAAGAAGAAAATTCAAATT
1 TTAAAGAAGAAAATTC-GATT
120985 TTAAA
1 TTAAA
120990 AAATTTCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 3 0.07
21 40 0.93
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (20 bp):
TTAAAGAAGAAAATTCGATT
Found at i:126803 original size:12 final size:14
Alignment explanation
Indices: 126774--126805 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
126764 TAAAAAATTA
126774 AAAATATAATGAAT
1 AAAATATAATGAAT
126788 AAAATATAA-G-AT
1 AAAATATAATGAAT
126800 AAAATA
1 AAAATA
126806 AATTTTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 1 0.06
14 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
AAAATATAATGAAT
Found at i:140963 original size:64 final size:64
Alignment explanation
Indices: 140910--141073 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
140900 CGGTGCACCA
*
140910 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
140974 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
141039 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
141074 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:141062 original size:17 final size:19
Alignment explanation
Indices: 141024--141070 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
141014 ATATTCAGAG
141024 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
141043 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
141060 TGCATTCGATG
1 TGCA-TCGATG
141071 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:141093 original size:65 final size:63
Alignment explanation
Indices: 140914--141093 Score: 184
Period size: 65 Copynumber: 2.8 Consensus size: 63
140904 GCACCAAGTG
* ****
140914 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGGAGAA
* *
140978 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAGA
141042 A
63 A
* * * *
141043 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCAT
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCAT
141094 GGTTGATGCA
Statistics
Matches: 96, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
63 2 0.02
64 35 0.36
65 53 0.55
66 4 0.04
67 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGAA
Found at i:147205 original size:23 final size:23
Alignment explanation
Indices: 147178--147222 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
147168 GATTTTGAAT
* * *
147178 TTCCACCTTTTTCAAATGTTTTG
1 TTCCAACTTTATCAAAAGTTTTG
147201 TTCCAACTTTATCAAAAGTTTT
1 TTCCAACTTTATCAAAAGTTTT
147223 AAGATCATCA
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:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (23 bp):
TTCCAACTTTATCAAAAGTTTTG
Found at i:149402 original size:64 final size:63
Alignment explanation
Indices: 149330--149538 Score: 235
Period size: 65 Copynumber: 3.2 Consensus size: 63
149320 GTGCACCAAG
*
149330 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGG-T
* * *
149394 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG-
1 TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATCCTGAGTGCATCGATGCATGGT
* * * * *
149457 AGAATGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAAT-TCACT-AATGCATCGATGCAT
1 TG--TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATATC-CTGAGTGCATCGATGCAT
149520 GGT
61 GGT
*
149523 TGATGCATCGGTGCAT
1 TG-TGCATCGATGCAT
149539 CACCTCAAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 34 0.27
65 85 0.68
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGGT
Found at i:149480 original size:17 final size:19
Alignment explanation
Indices: 149442--149488 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
149432 ATATTCAGAG
149442 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
149461 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
149478 TGCATTCGATG
1 TGCA-TCGATG
149489 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Done.