Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005938.1 Hibiscus syriacus cultivar Beakdansim tig00013945_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: 119348
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3853 original size:20 final size:20
Alignment explanation
Indices: 3825--3902 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
3815 TTCCCATTGA
3825 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
* *
3845 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATACATTC--T-AC
* * * *
3868 ATGTGCATCGATGCACTATCC
1 A-GTGCATCGATACATTCTAC
3889 A-TGCATCGATACAT
1 AGTGCATCGATACAT
3903 AATTCACCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
19 11 0.24
20 15 0.33
21 2 0.04
22 2 0.04
23 3 0.07
24 13 0.28
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:3882 original size:24 final size:20
Alignment explanation
Indices: 3825--3882 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
3815 TTCCCATTGA
*
3825 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
3845 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
3868 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3883 CTATCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:6781 original size:70 final size:69
Alignment explanation
Indices: 6687--6816 Score: 170
Period size: 70 Copynumber: 1.9 Consensus size: 69
6677 TAAAATATCT
**
6687 ACGATCATGCAAAGAAAACAACAAACATTAAAGAAATTGTAATAACTTCAAACTATGTAATAATC
1 ACGATCATGCAAAGAAAACAACAAACATTAAAGAAATTGT-ATAACTTCAAAAAATGTAATAATC
6752 GAGAA
65 GAGAA
* * ** ** *
6757 ACGATTATGCAAAGAGAAGGACAAACATTAGCGAAATTGTATGACTTCAAAAAATGTAAT
1 ACGATCATGCAAAGAAAACAACAAACATTAAAGAAATTGTATAACTTCAAAAAATGTAAT
6817 GGCTTTAAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
69 17 0.33
70 34 0.67
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (69 bp):
ACGATCATGCAAAGAAAACAACAAACATTAAAGAAATTGTATAACTTCAAAAAATGTAATAATCG
AGAA
Found at i:8307 original size:79 final size:77
Alignment explanation
Indices: 8166--8326 Score: 196
Period size: 79 Copynumber: 2.1 Consensus size: 77
8156 TACAATCCGT
* * * * * *
8166 GAGGTCTTTTCTGAATGTTGGATTTTATTTGAATAAAAAATTACGATTTTCAACATATCTCACAT
1 GAGGTCCTTTCTGAATGTTGGATATTATTCGAATAAAAAATCACGATTTTCAACAGACCTCACAT
* *
8231 CATGTTTAACGC
66 CATCTATAACGC
* * *
8243 GAGGTCCTTTCTGAATCGTTGGATATTATTCGAATTAAAAGTCACGTCTTTTCAACAGACCTCAC
1 GAGGTCCTTTCTGAAT-GTTGGATATTATTCGAATAAAAAATCACG-ATTTTCAACAGACCTCAC
*
8308 ATCCTCTATAACGC
64 ATCATCTATAACGC
8322 GAGGT
1 GAGGT
8327 TCATTGATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
77 15 0.21
78 24 0.34
79 31 0.44
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (77 bp):
GAGGTCCTTTCTGAATGTTGGATATTATTCGAATAAAAAATCACGATTTTCAACAGACCTCACAT
CATCTATAACGC
Found at i:9568 original size:3 final size:3
Alignment explanation
Indices: 9560--9591 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
9550 AGTACCGACT
9560 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9592 TTTGTATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11421 original size:20 final size:20
Alignment explanation
Indices: 11396--11436 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
11386 AAAACTTGCC
*
11396 AAAGGTTTCGAAACCCCCTT
1 AAAGGTTTCAAAACCCCCTT
11416 AAAGGTTTCAAAACCCCCTT
1 AAAGGTTTCAAAACCCCCTT
11436 A
1 A
11437 CCCAACTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
AAAGGTTTCAAAACCCCCTT
Found at i:15885 original size:13 final size:13
Alignment explanation
Indices: 15867--15901 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
15857 ATTGTCGTGG
15867 GTAACGTGCGATA
1 GTAACGTGCGATA
15880 GTAACGTGCGATA
1 GTAACGTGCGATA
15893 GTAACGTGC
1 GTAACGTGC
15902 ATTAGCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (13 bp):
GTAACGTGCGATA
Found at i:20079 original size:45 final size:45
Alignment explanation
Indices: 20012--20101 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
20002 CTCGAATTTA
* * *
20012 TTTATTTTTGCGAAAAGTATGCGAACTAGAGATCATGTGGTTAGG
1 TTTATTTTTGCGAAAAGCATGCGAACTAGAGACCATGCGGTTAGG
* *
20057 TTTATTTTT-CGAACAAGCATGCGAATTAGATACCATGCGGTTAGG
1 TTTATTTTTGCGAA-AAGCATGCGAACTAGAGACCATGCGGTTAGG
20102 ATTTTTTGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 4 0.10
45 35 0.90
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.34
Consensus pattern (45 bp):
TTTATTTTTGCGAAAAGCATGCGAACTAGAGACCATGCGGTTAGG
Found at i:24967 original size:14 final size:14
Alignment explanation
Indices: 24948--25021 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
24938 TTGGGCTTTG
*
24948 TAATATTTAATAAA
1 TAATATATAATAAA
24962 TAATATATAATAATTA
1 TAATATATAATAA--A
24978 TAATA-ATAATACTAA
1 TAATATATAATA--AA
*
24993 TAATA-ATAATTTTAA
1 TAATATATAA--TAAA
25008 TAATA-ATAATAAA
1 TAATATATAATAAA
25021 T
1 T
25022 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 27 0.53
16 6 0.12
17 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:24974 original size:3 final size:3
Alignment explanation
Indices: 24955--25019 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
24945 TTGTAATATT
* *
24955 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
25002 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
25020 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:25024 original size:18 final size:18
Alignment explanation
Indices: 24990--25025 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
24980 ATAATAATAC
*
24990 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
25008 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
25026 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:25278 original size:76 final size:76
Alignment explanation
Indices: 25147--25943 Score: 1409
Period size: 76 Copynumber: 10.5 Consensus size: 76
25137 GATGGAAATG
* * * *
25147 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
*
25212 CCCGAAGGCTT
66 TCCGAAGGCTT
* *
25223 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
*
25288 CCCGAAGGCTT
66 TCCGAAGGCTT
* *
25299 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAATGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
*
25364 CCCGAAGGCTT
66 TCCGAAGGCTT
25375 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25440 TCCGAAGGCTTT
66 TCCGAAGGC-TT
25452 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25517 TCCGAAGGCTT
66 TCCGAAGGCTT
*
25528 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25593 TCCGAAGGCTTT
66 TCCGAAGGC-TT
25605 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25669 TCCGAAGGCTT
66 TCCGAAGGCTT
*
25680 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25745 TCCGAAGGCTTT
66 TCCGAAGGC-TT
25757 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25822 TCCGAAGGCTT
66 TCCGAAGGCTT
* *
25833 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGC-
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25897 TCCTGAAGGCTT
66 TCC-GAAGGCTT
25909 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
25944 TGGGAAATAG
Statistics
Matches: 702, Mismatches: 14, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
75 61 0.09
76 432 0.62
77 209 0.30
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
TCCGAAGGCTT
Found at i:25703 original size:305 final size:305
Alignment explanation
Indices: 25147--25943 Score: 1445
Period size: 305 Copynumber: 2.6 Consensus size: 305
25137 GATGGAAATG
* * * *
25147 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
* * *
25212 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 TCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
* *
25277 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAT
131 ATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
*
25342 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
196 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAG
25407 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTT
261 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTT
25452 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
*
25517 TCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAT
66 TCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
25582 ATCAAAAAGCTTCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
131 ATCAAAAAGCTTCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
* *
25647 GGATTTGAAAATATC-AAAAGCTTCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACA
195 GGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACA
25711 GATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTT
260 GATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTT
25757 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
25822 TCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
66 TCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
25887 ATCAAAAAGC-TCCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
131 ATCAAAAAGCTTCC-GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
25944 TGGGAAATAG
Statistics
Matches: 476, Mismatches: 14, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
304 40 0.08
305 379 0.80
306 57 0.12
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (305 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
TCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
ATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAG
ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTT
Found at i:26480 original size:22 final size:22
Alignment explanation
Indices: 26455--26509 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
26445 CATAAAGCTT
26455 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
* *
26477 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
26499 TCATCTTTGAA
1 TCATCTTTGAA
26510 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:28004 original size:36 final size:34
Alignment explanation
Indices: 27964--28037 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 34
27954 TATTACTTCT
27964 TATTG-AGATGAGCCTCCAAGAATGCCCAAATATTCA
1 TATTGTAG-TGAGCCTCCAA-AATGCCCAAATATT-A
* * *
28000 TATTGTTGTGAGCCTTCAAAATGCCCCAATATTA
1 TATTGTAGTGAGCCTCCAAAATGCCCAAATATTA
28034 TATT
1 TATT
28038 TCTGGTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 5 0.15
35 13 0.38
36 15 0.44
37 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (34 bp):
TATTGTAGTGAGCCTCCAAAATGCCCAAATATTA
Found at i:38039 original size:14 final size:14
Alignment explanation
Indices: 38020--38093 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
38010 TTGGGCTTTG
*
38020 TAATATTTAATAAA
1 TAATATATAATAAA
38034 TAATATATAATAATTA
1 TAATATATAATAA--A
38050 TAATA-ATAATACTAA
1 TAATATATAATA--AA
*
38065 TAATA-ATAATTTTAA
1 TAATATATAA--TAAA
38080 TAATA-ATAATAAA
1 TAATATATAATAAA
38093 T
1 T
38094 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 27 0.53
16 6 0.12
17 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:38046 original size:3 final size:3
Alignment explanation
Indices: 38027--38091 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
38017 TTGTAATATT
* *
38027 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
38074 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
38092 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:38096 original size:18 final size:18
Alignment explanation
Indices: 38062--38097 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38052 ATAATAATAC
*
38062 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
38080 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
38098 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:41785 original size:2 final size:2
Alignment explanation
Indices: 41778--41805 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41768 AAAGATTCTC
41778 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
41806 CTTCTCTTCC
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:53602 original size:22 final size:21
Alignment explanation
Indices: 53552--53601 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
53542 GAGGGAAACA
53552 ATTCCCCCATAGGGGGTACCG
1 ATTCCCCCATAGGGGGTACCG
53573 ATTCCCCCATAGGGGGTACCG
1 ATTCCCCCATAGGGGGTACCG
53594 ATTCCCCC
1 ATTCCCCC
53602 CTGTTCAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.20
Consensus pattern (21 bp):
ATTCCCCCATAGGGGGTACCG
Found at i:56546 original size:54 final size:54
Alignment explanation
Indices: 56409--57125 Score: 779
Period size: 54 Copynumber: 13.4 Consensus size: 54
56399 AGACATGTTT
* * *
56409 GAAGATTTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT---
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* *
56460 GAAGATGTTCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* * *
56514 GAAGATATTCGAGTTCTATTCTCCCT-GAAGAAAGAGGGAGAGAACCCGTTT---
1 GAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAA
* * * * * **
56565 GAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGAGAACGAACCTGTAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* *
56619 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGCA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* * * *
56673 GAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGAGAGCGAACCCGTTTGAA
1 GAAGA-TGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * * **
56729 GAAGATATTCGAGTTCCAAACTCCCTAGATAAAGAGGGAACGAACCCGTAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* *
56783 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCGTTTGCA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* * *
56837 GAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTT---
1 GAAGA-TGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAA
*
56890 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTT---
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* * * *
56941 GAAGATGTTCAAGTTCTATACTCCCTAGAGAAAGTGGGAGCGAAACCATTTGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* * *
56995 GAAGAT-ATCTGAGTT-TCATACT-CCTGAAAGAAGGAGGGAGCGAACCCGTTTGAA
1 GAAGATGTTC-GAGTTCT-ATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAA
* * ** * *
57049 G-AGATGTTCAAGTTCTATACTCCCTAGAGAGAGAATGAGCGAACCAGTTT-ATT
1 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGA-A
57102 GAAGATTGTTCGAG-TCTTATACTC
1 GAAGA-TGTTCGAGTTC-TATACTC
57126 TCTGAACGAA
Statistics
Matches: 558, Mismatches: 83, Indels: 46
0.81 0.12 0.07
Matches are distributed among these distances:
51 154 0.28
52 21 0.04
53 45 0.08
54 216 0.39
55 70 0.13
56 52 0.09
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (54 bp):
GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
Found at i:56559 original size:105 final size:105
Alignment explanation
Indices: 56409--57116 Score: 780
Period size: 105 Copynumber: 6.6 Consensus size: 105
56399 AGACATGTTT
* * *
56409 GAAGATTTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGT
1 GAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGT
*
56474 TCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAA
66 TCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* *
56514 GAAGATATTCGAGTTCTATTCTCCCT-GAAGAAAGAGGGAGAGAACCCGTTTGAAGATGTTCGAG
1 GAAGATATTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAG
* * * * **
56578 TTCCATACTCCCTAGATAAAGAGAGAACGAACCTGTAAGAA
65 TTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* * *
56619 GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGCAGAAGATTATTC
1 GAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGA-TGTTC
* * * *
56684 GAGTTCTATACTTCCTGAAAGAAAGAGAGAGCGAACCCGTTTGAA
62 GAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * **
56729 GAAGATATTCGAGTTCCAAACTCCCTAGATAAAGAGGGAACGAACCCGTAAGAAGAAGATGTTCG
1 GAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT---TTGAAGATGTTCG
* * *
56794 AGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCGTTTGCA
63 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* *
56837 GAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGA
1 GAAGA-TATTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGA
* *
56902 GTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTT---
64 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * * *
56941 GAAGATGTTCAAGTTCTATACTCCCTAGAGAAAGTGGGAGCGAAACCATTTGAAGAAGATATCTG
1 GAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATG-T-TC-G
* * *
57006 AGTTTCATACT-CCTGAAAGAAGGAGGGAGCGAACCCGTTTGAA
63 AGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAA
* * * ** *
57049 G-AGATGTTCAAGTTCTATACTCCCTAGAGAGAGAATGAGCGAACCAGTTTATTGAAGATTGTTC
1 GAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG--T-TTGAAGA-TGTTC
57113 GAGT
62 GAGT
57117 CTTATACTCT
Statistics
Matches: 510, Mismatches: 70, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
102 27 0.05
103 19 0.04
104 10 0.02
105 169 0.33
106 1 0.00
107 88 0.17
108 39 0.08
109 58 0.11
110 98 0.19
111 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (105 bp):
GAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGT
TCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
Found at i:56793 original size:164 final size:157
Alignment explanation
Indices: 56405--57078 Score: 881
Period size: 164 Copynumber: 4.2 Consensus size: 157
56395 GAGCAGACAT
* * * * **
56405 GTTTGAAGATTTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
1 GTTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTAAGAAGATGTTC
* * *
56470 GAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATATTCGAGTTCTATTC
66 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATATTCGAGTTCTATAC
* *
56535 TCCCTG-AAGAAAGAGGGAGAGAACCC
131 TTCCTGAAAGAAAGAGGGAGCGAACCC
* * * *
56561 GTTTGAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGAGAACGAACCTGTAAGAAGAAGATG
1 GTTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGT---AAGAAGATG
* *
56626 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGCAGAAGATTATTCGAGTTCT
63 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TATTCGAGTTCT
*
56691 ATACTTCCTGAAAGAAAGAGAGAGCGAACCC
127 ATACTTCCTGAAAGAAAGAGGGAGCGAACCC
* * * *
56722 GTTTGAAGAAGATATTCGAGTTCCAAACTCCCTAGATAAAGAGGGAACGAACCCGTAAGAAGAAG
1 GTTT---GAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGT---AAGAAG
* *
56787 ATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGTGAACCCGTTTGCAGAAGATTATTCGAGT
60 ATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TATTCGAGT
56852 TCTATACTTCCTGAAAGAAAGAGGGAGCGAACCC
124 TCTATACTTCCTGAAAGAAAGAGGGAGCGAACCC
**
56886 GTTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGA-GGAAGCGAACCCGTTTGAAGATGTT
1 GTTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAA-CGAACCCGTAAGAAGATGTT
* * * *
56950 CAAGTTCTATACTCCCTAGAGAAAGTGGGAGCGAAACCATTTGAAGAAGATA-TCTGAGTT-TCA
65 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATATTC-GAGTTCT-A
*
57013 TAC-TCCTGAAAGAAGGAGGGAGCGAACCC
128 TACTTCCTGAAAGAAAGAGGGAGCGAACCC
*
57042 GTTTGAAGAGATGTTCAAGTTCTATACTCCCTAGAGA
1 GTTTG-A-AGATGTTCGAGTTCTATACTCCCTAGAGA
57079 GAGAATGAGC
Statistics
Matches: 466, Mismatches: 39, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
156 78 0.17
157 12 0.03
158 81 0.17
159 55 0.12
160 24 0.05
161 62 0.13
164 154 0.33
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (157 bp):
GTTTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCGTAAGAAGATGTTC
GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATATTCGAGTTCTATAC
TTCCTGAAAGAAAGAGGGAGCGAACCC
Found at i:57156 original size:55 final size:55
Alignment explanation
Indices: 57097--57226 Score: 188
Period size: 55 Copynumber: 2.4 Consensus size: 55
57087 GCGAACCAGT
* *
57097 TTATTGAAGATTGTTCGAGTCTTATACTCTCTGAACGAATAGAGAGCAGACAAGA
1 TTATTGAAGATTGTTCGAGTCTCATACTCTCTGAACGAATAGAGAGCAAACAAGA
* * *
57152 TTATTGAAGATTGTTCGTGTCTCATACTCTCTGAACGAATAGGGAGCAAACACGA
1 TTATTGAAGATTGTTCGAGTCTCATACTCTCTGAACGAATAGAGAGCAAACAAGA
* * *
57207 TTGTTAAAGATTATTCGAGT
1 TTATTGAAGATTGTTCGAGT
57227 TCCATATTCC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (55 bp):
TTATTGAAGATTGTTCGAGTCTCATACTCTCTGAACGAATAGAGAGCAAACAAGA
Found at i:68147 original size:6 final size:6
Alignment explanation
Indices: 68132--68168 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
68122 ATGCTCAACC
68132 CCCTTCT CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT
1 CCCTT-T CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT
68169 TCATGGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
CCCTTT
Found at i:88440 original size:48 final size:43
Alignment explanation
Indices: 88323--88445 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 43
88313 GAAAAAGATC
88323 TAAAAACATGAATT--AATTCATAAATATTATATTTGAAGGTA
1 TAAAAACATGAATTACAATTCATAAATATTATATTTGAAGGTA
* * * * *
88364 TGAAAGCATGAATTACACTCCATAAATATTATATTTGAAAGTTA
1 TAAAAACATGAATTACAATTCATAAATATTATATTTG-AAGGTA
*
88408 TTAAAAAAACATGATTTACAAATTCATAAATATTATAT
1 -T--AAAAACATGAATTAC-AATTCATAAATATTATAT
88446 ATAGGAAATC
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 12 0.18
43 19 0.29
44 5 0.08
45 1 0.02
47 12 0.18
48 16 0.25
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (43 bp):
TAAAAACATGAATTACAATTCATAAATATTATATTTGAAGGTA
Found at i:88822 original size:2 final size:2
Alignment explanation
Indices: 88815--88856 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
88805 ATTAACAATG
88815 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
88857 GATAATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98473 original size:760 final size:759
Alignment explanation
Indices: 96991--98509 Score: 2790
Period size: 760 Copynumber: 2.0 Consensus size: 759
96981 ATAGTTTAGA
96991 GAGTTTTCTTGTGAGTTGTGAGTGTTTTGTAAACACCTATAAATTTTCTCTCTTAGTAAAAGATC
1 GAGTTTTCTTGTGAGTTGTGAGTGTTTTGTAAACACCTATAAATTTTCTCTCTTAGTAAAAGATC
97056 TACAGCAGTCCGGAGACGTAGGCAAAATTAGCTGAATTCCGTTATCAATTTCGAGTATTATTTTT
66 TACAGCAGTCCGGAGACGTAGGCAAAATTAGCTGAATTCCGTTATCAATTTCGAGTATTATTTTT
*
97121 CTATTTTTATTTCACATTCTCACTAATCTGGTTATAGGAAAATTACTCGTTTATTTCCCAACAGT
131 CTATTTTTATTTCACATTCTCACTAATCTGGTTATAGGAAAATTACGCGTTTATTTCCCAACAGT
97186 GTTATCCCTTTTTTCTAATGAAAGTAGCCATGAAGGGCCTCCTACCTTGAGTGATATTAATCAAC
196 GTTATCCCTTTTTTCTAATGAAAGTAGCCATGAAGGGCCTCCTACCTTGAGTGATATTAATCAAC
*
97251 ATGGAATGTATTTTCTTTGTACTTGTAGCTAAGGTAAGTGTCGACACCGTTTTTTGCCTGGGCGG
261 ATGGAATGTATTTTCTTTGTACTTGTAGCTAAGGTAAGTGTCGACACCGTTTTTCGCCTGGGCGG
97316 GGAAAAGATCGATACCGACTCGAGGGTTTTATCTTTGAAAAATCGTTTCGAAATGTAAGGAGTCG
326 GGAAAAGATCGATACCGACTCGAGGGTTTTATCTTTGAAAAATCGTTTCGAAATGTAAGGAGTCG
* * *
97381 CCACCAATCATTTAAGGTGCGATTGAAACACTGTAAAAACTTGGTGATTTTAATAAAATATTTTA
391 CCACAAATCATTAAAGGTGCGATTGAAACACTGTAAAAACTGGGTGATTTTAATAAAATATTTTA
97446 TTTTAATAAAATACCAAGTTTTAGGGTCTACAAAAATCCAGAAATCAGGTTCAGGAGTCAGTTAC
456 TTTTAATAAAATACCAAGTTTTAGGGTCTACAAAAATCCAGAAATCAGGTTCAGGAGTCAGTTAC
97511 GCGTGGGGAATGATTAGCACCCCCACAAGCGCCCAAAAATTGGTACCTAGTTGATTACCCTATAT
521 GCGTGGGGAATGATTAGCACCCCCACAAGCGCCCAAAAATTGGTACCTAGTTGATTACCCTATAT
97576 TTAAAATCAAAAATTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAAGATGCAAAGTTTG
586 TTAAAATCAAAAATTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAAGATGCAAAGTTTG
** *
97641 AAAAGGATATTCGTTTATTGAGACCGATAGATCGGTTATTTTGTCTAATAATCGAACATTGCCTC
651 AAAAGGATATTCGTTTATTGAGACCGATAGATCGACTATTTTGTCTAATAACCGAACATTGCCTC
97706 GTTTTTTAAAAACAAGATGTGGTTTTGAAAAGGATGTCGACTTAT
716 GTTTTTT-AAAACAAGATGTGGTTTTGAAAAGGATGTCGACTTAT
97751 GAGTTTTCTTGTGAGTTGTGAGTGTTTTGTAAACACCTATAAATTTTCTCTCTTAGTAAAAGATC
1 GAGTTTTCTTGTGAGTTGTGAGTGTTTTGTAAACACCTATAAATTTTCTCTCTTAGTAAAAGATC
*
97816 TACAGCAGTCCGGAGACGTAGGCAAAATTAGTTGAATTCCGTTATCAATTTCGAGTATTATTTTT
66 TACAGCAGTCCGGAGACGTAGGCAAAATTAGCTGAATTCCGTTATCAATTTCGAGTATTATTTTT
97881 CTATTTTTATTTCACATTCTCACTAATCTGGTTATAGGAAAATTACGCGTTTATTTCCCAACAGT
131 CTATTTTTATTTCACATTCTCACTAATCTGGTTATAGGAAAATTACGCGTTTATTTCCCAACAGT
* * *
97946 GTTGTCCCTTTTTTCTAATGAAAGTAGCCATGCAGGGCCTCCTGCCTTGAGTGATATTAATCAAC
196 GTTATCCCTTTTTTCTAATGAAAGTAGCCATGAAGGGCCTCCTACCTTGAGTGATATTAATCAAC
98011 ATGGAATGTATTTTCTTTGTACTTGTAGCTAAGGTAAGTGTCGACACCGTTTTTCGCCTGGGCGG
261 ATGGAATGTATTTTCTTTGTACTTGTAGCTAAGGTAAGTGTCGACACCGTTTTTCGCCTGGGCGG
*
98076 GGAAAAGATCGATACCGACTCGGGGGTTTTATCTTTGAAAAATCGTTTCGAAATGTAAGGAGTCG
326 GGAAAAGATCGATACCGACTCGAGGGTTTTATCTTTGAAAAATCGTTTCGAAATGTAAGGAGTCG
98141 CCACAAATCATTAAAGGTGCGATTGAAACACTGTAAAAACTGGGTGATTTTAATAAAATA-TTTA
391 CCACAAATCATTAAAGGTGCGATTGAAACACTGTAAAAACTGGGTGATTTTAATAAAATATTTTA
* * * *
98205 TTTTAATAAAATATCGAGTTTTGGGGTCTACGAAAATCCAGAAATCAGGTTC-GGAAGTCAGTTA
456 TTTTAATAAAATACCAAGTTTTAGGGTCTACAAAAATCCAGAAATCAGGTTCAGG-AGTCAGTTA
* *
98269 CGCGTGGGGAATGATTAGCACCCCTACAAGCGCCCAAAAATTGGTACCTAGTTGATTATCCTATA
520 CGCGTGGGGAATGATTAGCACCCCCACAAGCGCCCAAAAATTGGTACCTAGTTGATTACCCTATA
* *
98334 TTTAAAATCAGAAATTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAGGATGCAAAGTTT
585 TTTAAAATCAAAAATTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAAGATGCAAAGTTT
98399 GAAAAGGATATTCGTTTATTGAGACCGATAGATCGACTATTTTGTCTAATAACCGAACATTGCCT
650 GAAAAGGATATTCGTTTATTGAGACCGATAGATCGACTATTTTGTCTAATAACCGAACATTGCCT
* *
98464 TGTTTTTTTAAAACATGATGTGGTTTTGAAAAGGATGTCGACTTAT
715 CG-TTTTTTAAAACAAGATGTGGTTTTGAAAAGGATGTCGACTTAT
98510 TTAGGGAATT
Statistics
Matches: 734, Mismatches: 23, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
758 2 0.00
759 286 0.39
760 446 0.61
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (759 bp):
GAGTTTTCTTGTGAGTTGTGAGTGTTTTGTAAACACCTATAAATTTTCTCTCTTAGTAAAAGATC
TACAGCAGTCCGGAGACGTAGGCAAAATTAGCTGAATTCCGTTATCAATTTCGAGTATTATTTTT
CTATTTTTATTTCACATTCTCACTAATCTGGTTATAGGAAAATTACGCGTTTATTTCCCAACAGT
GTTATCCCTTTTTTCTAATGAAAGTAGCCATGAAGGGCCTCCTACCTTGAGTGATATTAATCAAC
ATGGAATGTATTTTCTTTGTACTTGTAGCTAAGGTAAGTGTCGACACCGTTTTTCGCCTGGGCGG
GGAAAAGATCGATACCGACTCGAGGGTTTTATCTTTGAAAAATCGTTTCGAAATGTAAGGAGTCG
CCACAAATCATTAAAGGTGCGATTGAAACACTGTAAAAACTGGGTGATTTTAATAAAATATTTTA
TTTTAATAAAATACCAAGTTTTAGGGTCTACAAAAATCCAGAAATCAGGTTCAGGAGTCAGTTAC
GCGTGGGGAATGATTAGCACCCCCACAAGCGCCCAAAAATTGGTACCTAGTTGATTACCCTATAT
TTAAAATCAAAAATTTTGAGTTCGATCTTTATTTAATTTAAAAATCATTAAAGATGCAAAGTTTG
AAAAGGATATTCGTTTATTGAGACCGATAGATCGACTATTTTGTCTAATAACCGAACATTGCCTC
GTTTTTTAAAACAAGATGTGGTTTTGAAAAGGATGTCGACTTAT
Found at i:99239 original size:17 final size:16
Alignment explanation
Indices: 99201--99239 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
99191 TAAATTACAA
*
99201 AATAAATTAAATAAAT
1 AATAAATTAAAAAAAT
*
99217 ACTAAATTAAAAAAAAT
1 AATAAATT-AAAAAAAT
99234 AATAAA
1 AATAAA
99240 AATTACAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATTAAAAAAAT
Found at i:99244 original size:19 final size:19
Alignment explanation
Indices: 99220--99266 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
99210 AATAAATACT
99220 AAATTAAAAAAAATAATA-A
1 AAATTAAAAAAAATAA-AGA
* *
99239 AAATTACAAATAATAAAGA
1 AAATTAAAAAAAATAAAGA
99258 AAATTAAAA
1 AAATTAAAA
99267 TACATAGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAATTAAAAAAAATAAAGA
Found at i:101078 original size:29 final size:26
Alignment explanation
Indices: 101046--101104 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
101036 AGATTTAATT
*
101046 TAAAATATTTAAACATAAAAGAATAATAA
1 TAAAA-ATTTAAA-ATAAAAAAATAA-AA
* *
101075 TAAAAATTTCAATTAAAAAAATAAAA
1 TAAAAATTTAAAATAAAAAAATAAAA
101101 TAAA
1 TAAA
101105 GAAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.22
27 10 0.37
28 6 0.22
29 5 0.19
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (26 bp):
TAAAAATTTAAAATAAAAAAATAAAA
Found at i:115506 original size:409 final size:409
Alignment explanation
Indices: 114747--115572 Score: 1589
Period size: 409 Copynumber: 2.0 Consensus size: 409
114737 ACAATTGTAA
* *
114747 CAATGACAGTTATAACAATAAAAATAGCATTATAACTATTTCTCACTACATGATGTATATGTGAA
1 CAATGACAGTTATAACAATAAAAATAGCATTACAACTATTTCTCACTACATGATGTATATGTCAA
*
114812 ATTTTCAACTATGGAATACTACATGACCTAGAGAAAATCCAGATACATTCTTAATTTCTCTCCAA
66 ATTTTCAACTATGGAATACTACATAACCTAGAGAAAATCCAGATACATTCTTAATTTCTCTCCAA
114877 GATAAAGATAAAAAAAACTATCCGGAATGCACACAAAACCAGGTTAACATTATAACAGATAATCA
131 GATAAAGATAAAAAAAACTATCCGGAATGCACACAAAACCAGGTTAACATTATAACAGATAATCA
114942 ATTCATGTACAAAAACAAAATTTGAGTTTCTCTCATTACTTTTCTATTCACTACACTTCAAAACA
196 ATTCATGTACAAAAACAAAATTTGAGTTTCTCTCATTACTTTTCTATTCACTACACTTCAAAACA
115007 CTTTTAGCCACCATTGGTAGATATGATATTCACAAGGAGTCGGATCCTACAAATAGGTGGTTATA
261 CTTTTAGCCACCATTGGTAGATATGATATTCACAAGGAGTCGGATCCTACAAATAGGTGGTTATA
115072 ATGTGAAAACTGGAAAATATGGAGGGGAATGCAGTCACAAAGTTTTAAATAGAAATACACACAAG
326 ATGTGAAAACTGGAAAATATGGAGGGGAATGCAGTCACAAAGTTTTAAATAGAAATACACACAAG
115137 ATAAGATAAGACTATTGAT
391 ATAAGATAAGACTATTGAT
*
115156 CAATGACAGTTATAACAATAATAATAGCATTACAACTATTTCTCACTACATGATGTATATGTCAA
1 CAATGACAGTTATAACAATAAAAATAGCATTACAACTATTTCTCACTACATGATGTATATGTCAA
115221 ATTTTCAACTATGGAATACTACATAACCTAGAGAAAATCCAGATACATTCTTAATTTCTCTCCAA
66 ATTTTCAACTATGGAATACTACATAACCTAGAGAAAATCCAGATACATTCTTAATTTCTCTCCAA
*
115286 GATAAAGATAAAAAAAACTATCCGGAATGCACACAAATCCAGGTTAACATTATAACAGATAATCA
131 GATAAAGATAAAAAAAACTATCCGGAATGCACACAAAACCAGGTTAACATTATAACAGATAATCA
*
115351 ATTCATGTACAAAAACAAAATTTGAGTTTCTCTCATTACTTTTCTATTCAGTACACTTCAAAACA
196 ATTCATGTACAAAAACAAAATTTGAGTTTCTCTCATTACTTTTCTATTCACTACACTTCAAAACA
115416 CTTTTAGCCACCATTGGTAGATATGATATTCACAAGGAGTCGGATCCTACAAATAGGTGGTTATA
261 CTTTTAGCCACCATTGGTAGATATGATATTCACAAGGAGTCGGATCCTACAAATAGGTGGTTATA
115481 ATGTGAAAACTGGAAAATATGGAGGGGAATGCAGTCACAAAGTTTTAAATAGAAATACACACAAG
326 ATGTGAAAACTGGAAAATATGGAGGGGAATGCAGTCACAAAGTTTTAAATAGAAATACACACAAG
115546 ATAAGATAAGACTATTGAT
391 ATAAGATAAGACTATTGAT
*
115565 CAACGACA
1 CAATGACA
115573 TTAATTGTGT
Statistics
Matches: 410, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
409 410 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (409 bp):
CAATGACAGTTATAACAATAAAAATAGCATTACAACTATTTCTCACTACATGATGTATATGTCAA
ATTTTCAACTATGGAATACTACATAACCTAGAGAAAATCCAGATACATTCTTAATTTCTCTCCAA
GATAAAGATAAAAAAAACTATCCGGAATGCACACAAAACCAGGTTAACATTATAACAGATAATCA
ATTCATGTACAAAAACAAAATTTGAGTTTCTCTCATTACTTTTCTATTCACTACACTTCAAAACA
CTTTTAGCCACCATTGGTAGATATGATATTCACAAGGAGTCGGATCCTACAAATAGGTGGTTATA
ATGTGAAAACTGGAAAATATGGAGGGGAATGCAGTCACAAAGTTTTAAATAGAAATACACACAAG
ATAAGATAAGACTATTGAT
Done.