Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003587.1 Hibiscus syriacus cultivar Beakdansim tig00007565_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: 85415
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:9010 original size:23 final size:23
Alignment explanation
Indices: 8976--9025 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
8966 GGAATCGACA
8976 CCCC-TTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
8998 CCCCTTTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
9021 CCCCT
1 CCCCT
9026 AGGGGAATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.20, C:0.36, G:0.24, T:0.20
Consensus pattern (23 bp):
CCCCTTTGAAGGGGAACCGATTC
Found at i:9045 original size:20 final size:19
Alignment explanation
Indices: 8984--9049 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
8974 CACCCCTTGA
*
8984 AGGGGAACCGATTCCCCCTTT
1 AGGGGAACCGA-TCCCCC-CT
*
9005 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATCCCCCCT
*
9026 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
9046 -GGGG
1 AGGGG
9050 TTCTGGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 15 0.39
20 6 0.16
21 1 0.03
22 5 0.13
23 11 0.29
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:11757 original size:19 final size:19
Alignment explanation
Indices: 11733--11769 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11723 TATGCTCGGA
*
11733 GGGTACTGATTCCCCCCAG
1 GGGTACCGATTCCCCCCAG
11752 GGGTACCGATTCCCCCCA
1 GGGTACCGATTCCCCCCA
11770 CTGTTCAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.41, G:0.24, T:0.19
Consensus pattern (19 bp):
GGGTACCGATTCCCCCCAG
Found at i:13728 original size:23 final size:23
Alignment explanation
Indices: 13693--13736 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
13683 CGATACCCCC
*
13693 TTGAAGGGGAACCAATTCCCCAT
1 TTGAAGAGGAACCAATTCCCCAT
* *
13716 TTGAAGAGTAACCGATTCCCC
1 TTGAAGAGGAACCAATTCCCC
13737 CTGTAGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
TTGAAGAGGAACCAATTCCCCAT
Found at i:15579 original size:17 final size:16
Alignment explanation
Indices: 15557--15620 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
15547 ATTTTGGATA
15557 TTTGGAATGTTTGAAT
1 TTTGGAATGTTTGAAT
* *
15573 TTGTGGATTGTTTG-AC
1 TT-TGGAATGTTTGAAT
15589 TTT-GAATTTGTTTGAAT
1 TTTGGAA--TGTTTGAAT
15606 TTATGG-ATGTTTGAA
1 TT-TGGAATGTTTGAA
15621 CTTATATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
14 2 0.05
15 1 0.03
16 19 0.50
17 13 0.34
18 2 0.05
19 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.25, T:0.52
Consensus pattern (16 bp):
TTTGGAATGTTTGAAT
Found at i:17411 original size:37 final size:36
Alignment explanation
Indices: 17364--17491 Score: 134
Period size: 37 Copynumber: 3.5 Consensus size: 36
17354 TTAATATAAA
17364 TATTATAATATTAAATTAATTTAAAAATAATTAAAAT
1 TATTATAATATTAAATTAATTTAAAAAT-ATTAAAAT
* * * * *
17401 AATTATAATATTAAATATATTTTTATACATATTAAATT
1 TATTATAATATTAAAT-TA-ATTTAAAAATATTAAAAT
* *
17439 TATTAT-ATATTAAATTTAATTTCAAAATATT-GAAT
1 TATTATAATATTAAA-TTAATTTAAAAATATTAAAAT
17474 CTATTATAATATTAAATT
1 -TATTATAATATTAAATT
17492 TTATTTTTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
35 2 0.03
36 17 0.23
37 33 0.45
38 15 0.20
39 7 0.09
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (36 bp):
TATTATAATATTAAATTAATTTAAAAATATTAAAAT
Found at i:17433 original size:21 final size:20
Alignment explanation
Indices: 17366--17540 Score: 66
Period size: 20 Copynumber: 8.9 Consensus size: 20
17356 AATATAAATA
*
17366 TTATAATATTAAAT-TAATT
1 TTATAATATTAAATATATTT
* * *
17385 TAAAAATAATTAAA-ATA--A
1 TTATAAT-ATTAAATATATTT
17403 TTATAATATTAAATATATTT
1 TTATAATATTAAATATATTT
*
17423 TTATACATATT-AA-AT-TTA
1 TTATA-ATATTAAATATATTT
* *
17441 TTAT-ATATTAAATTTAATT
1 TTATAATATTAAATATATTT
* * * *
17460 TCAAAATATTGAATCTA---
1 TTATAATATTAAATATATTT
*
17477 TTATAATATTAAATTTTATTT
1 TTATAATATTAAA-TATATTT
* *
17498 TTATACATATTGAATTTAATTT
1 TTATA-ATATTAAATAT-ATTT
*
17520 TAATATATATATGAAATATAT
1 T--TATA-ATATTAAATATAT
17541 ATATATTTAT
Statistics
Matches: 115, Mismatches: 23, Indels: 32
0.68 0.14 0.19
Matches are distributed among these distances:
16 5 0.04
17 18 0.16
18 18 0.16
19 10 0.09
20 25 0.22
21 13 0.11
22 12 0.10
23 2 0.02
24 12 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTATAATATTAAATATATTT
Found at i:17485 original size:74 final size:76
Alignment explanation
Indices: 17364--17525 Score: 215
Period size: 75 Copynumber: 2.1 Consensus size: 76
17354 TTAATATAAA
17364 TATTATAATATTAAATTAATTTAAAAATAATTAAAATAATTATAATATTAAA-TATATTTTTATA
1 TATTATAATATTAAATTAATTTAAAAATAATTAAAATAATTATAATATTAAATTATATTTTTATA
17428 CATATTAAATT
66 CATATTAAATT
* * * *
17439 TATTAT-ATATTAAATTTAATTTCAAAAT-ATT-GAATCTATTATAATATTAAATTTTATTTTTA
1 TATTATAATATTAAA-TTAATTTAAAAATAATTAAAAT-AATTATAATATTAAATTATATTTTTA
*
17501 TACATATTGAATT
64 TACATATTAAATT
*
17514 TAATTTTAATAT
1 T-ATTATAATAT
17526 ATATATGAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
73 3 0.04
74 25 0.33
75 40 0.53
76 4 0.05
77 4 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (76 bp):
TATTATAATATTAAATTAATTTAAAAATAATTAAAATAATTATAATATTAAATTATATTTTTATA
CATATTAAATT
Found at i:17507 original size:22 final size:21
Alignment explanation
Indices: 17477--17529 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
17467 ATTGAATCTA
*
17477 TTATAATATTAAATTTTATTT
1 TTATAATATTAAATTTAATTT
*
17498 TTATACATATTGAATTTAATTT
1 TTATA-ATATTAAATTTAATTT
*
17520 TAATATATAT
1 TTATA-ATAT
17530 ATGAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTATAATATTAAATTTAATTT
Found at i:18848 original size:14 final size:13
Alignment explanation
Indices: 18826--18886 Score: 77
Period size: 14 Copynumber: 4.4 Consensus size: 13
18816 CATCGTATAG
*
18826 CTCGCTCGGATAGC
1 CTCGGTCGGAT-GC
18840 CTCGGTCGGATGCC
1 CTCGGTCGGATG-C
18854 CTCGGTCGGATGCC
1 CTCGGTCGGATG-C
18868 CTCGGTCGGATGGC
1 CTCGGTCGGAT-GC
18882 CTCGG
1 CTCGG
18887 ATGCCCAGCG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
13 1 0.02
14 42 0.95
15 1 0.02
ACGTcount: A:0.08, C:0.34, G:0.36, T:0.21
Consensus pattern (13 bp):
CTCGGTCGGATGC
Found at i:18870 original size:28 final size:28
Alignment explanation
Indices: 18826--18886 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
18816 CATCGTATAG
*
18826 CTCGCTCGGATAGCCTCGGTCGGATGCC
1 CTCGGTCGGATAGCCTCGGTCGGATGCC
*
18854 CTCGGTCGGAT-GCCCTCGGTCGGATGGC
1 CTCGGTCGGATAG-CCTCGGTCGGATGCC
18882 CTCGG
1 CTCGG
18887 ATGCCCAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.08, C:0.34, G:0.36, T:0.21
Consensus pattern (28 bp):
CTCGGTCGGATAGCCTCGGTCGGATGCC
Found at i:29408 original size:21 final size:21
Alignment explanation
Indices: 29382--29426 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29372 TCCTCGATAC
* *
29382 CCATGCCACGAAAT-AATTTCT
1 CCATGCC-CCAAATGAAATTCT
29403 CCATGCCCCAAATGAAATTCT
1 CCATGCCCCAAATGAAATTCT
29424 CCA
1 CCA
29427 CATCTTGGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.24
Consensus pattern (21 bp):
CCATGCCCCAAATGAAATTCT
Found at i:37594 original size:12 final size:12
Alignment explanation
Indices: 37577--37601 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37567 GTCAAATAAT
37577 TTAGGCACCAAA
1 TTAGGCACCAAA
37589 TTAGGCACCAAA
1 TTAGGCACCAAA
37601 T
1 T
37602 GGTGTTTTGT
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:37943 original size:118 final size:119
Alignment explanation
Indices: 37731--37967 Score: 435
Period size: 119 Copynumber: 2.0 Consensus size: 119
37721 ATAAATACCC
37731 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGAATTTA
1 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGAATTTA
37796 GAGAGTTTCTTGAGAGTTGTTTTCTTC-TTTTTTATCTAGAGAGAATTATCATT
66 GAGAGTTTCTTGAGAGTTGTTTTCTTCTTTTTTTATCTAGAGAGAATTATCATT
37849 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCC-AATACTAGAGAGATTT
1 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGA-A-TT
37913 TAGAGAGTTTCTTGAGAGTTGTTTTC-TCTTTTTTTATCTAGAGAGAATTATCATT
64 TAGAGAGTTTCTTGAGAGTTGTTTTCTTCTTTTTTTATCTAGAGAGAATTATCATT
37968 GTTTTCTCAT
Statistics
Matches: 116, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
117 11 0.09
118 51 0.44
119 54 0.47
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (119 bp):
TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGAATTTA
GAGAGTTTCTTGAGAGTTGTTTTCTTCTTTTTTTATCTAGAGAGAATTATCATT
Found at i:42694 original size:119 final size:119
Alignment explanation
Indices: 42478--42715 Score: 435
Period size: 119 Copynumber: 2.0 Consensus size: 119
42468 ATAAATACCC
42478 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGAATTTA
1 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGAATTTA
42543 GAGAATTTCTTGAGAGTTGTTTTCTCCTTTTTTTATCTAGAGAGAATTATCATT
66 GAGAATTTCTTGAGAGTTGTTTTCTCCTTTTTTTATCTAGAGAGAATTATCATT
42597 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCC-AATACTAGAGAGATTT
1 TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGA-A-TT
*
42661 TAGAGAGTTTCTTGAGAGTTGTTTTCTCC-TTTTTTATCTAGAGAGAATTATCATT
64 TAGAGAATTTCTTGAGAGTTGTTTTCTCCTTTTTTTATCTAGAGAGAATTATCATT
42716 GTTTTCTCCT
Statistics
Matches: 116, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
118 11 0.09
119 75 0.65
120 30 0.26
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (119 bp):
TAGCTCATTTAGCTTCAAAATCATCCCAAAGCATTCTAGCTTTCTTCCAAATACTAGAGAATTTA
GAGAATTTCTTGAGAGTTGTTTTCTCCTTTTTTTATCTAGAGAGAATTATCATT
Found at i:45177 original size:202 final size:205
Alignment explanation
Indices: 44830--45238 Score: 740
Period size: 201 Copynumber: 2.0 Consensus size: 205
44820 ATGATTTCCT
44830 TAAACTTGTCCGAAGGAAAGTCATTATATACCACCACTTGTCCCCCAAAAAACATGGTCAGATGG
1 TAAACTTGTCCGAAGGAAAGTCATTATATACCACCACTTGTCCCCCAAAAAACATGGTCAGATGG
44895 AACTCTTGCCTCCACTTTTGCTGGTTTCCTAAATCAACAAAACGCTAAATACCAAGTTCATTGCC
66 AACTCTTGCCTCCACTTTTGCTGGTTTCCTAAATCAACAAAACGCTAAATACCAAGTTCATTGCC
44960 ATTTCTAACAA-TTTTTGTCAATCCTATGACTCTATGAGTATTAAACGGATAAGATCAAAT-A-T
131 ATTTCTAACAATTTTTTGTCAATCCTATGACTCTATGAGTATTAAACGGATAAGATCAAATAAGT
45022 GTATCTAAAA
196 GTATCTAAAA
45032 TAAACTTGTCCGAAGGAAAGTCA-T-TATACCACCACTTGT-CCCCAAAAAACATGGTCAGATGG
1 TAAACTTGTCCGAAGGAAAGTCATTATATACCACCACTTGTCCCCCAAAAAACATGGTCAGAT-G
45094 GAACTCTTTGCCTCCACTTTTGCTGGTTTCCTAAATCAACAAAACGCTAAATACCAAGTTTCATT
65 GAACTC-TTGCCTCCACTTTTGCTGGTTTCCTAAATCAACAAAACGCTAAATACCAAG-TTCATT
45159 GCCATTTCTAACAATTTTTTGTCAATCCTATGACTCTATGAGTATTAAACGGATAAGATCAAATA
128 GCCATTTCTAACAATTTTTTGTCAATCCTATGACTCTATGAGTATTAAACGGATAAGATCAAAT-
45224 AAGTGTATCTAAAA
192 AAGTGTATCTAAAA
45238 T
1 T
45239 TATGAATATC
Statistics
Matches: 200, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
199 21 0.10
200 22 0.11
201 52 0.26
202 43 0.22
203 49 0.25
205 1 0.00
206 12 0.06
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (205 bp):
TAAACTTGTCCGAAGGAAAGTCATTATATACCACCACTTGTCCCCCAAAAAACATGGTCAGATGG
AACTCTTGCCTCCACTTTTGCTGGTTTCCTAAATCAACAAAACGCTAAATACCAAGTTCATTGCC
ATTTCTAACAATTTTTTGTCAATCCTATGACTCTATGAGTATTAAACGGATAAGATCAAATAAGT
GTATCTAAAA
Found at i:46261 original size:10 final size:10
Alignment explanation
Indices: 46246--46272 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
46236 AATTATAATG
46246 ATTTAGAGAA
1 ATTTAGAGAA
46256 ATTTAGAGAA
1 ATTTAGAGAA
46266 ATTTAGA
1 ATTTAGA
46273 AAAAAATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (10 bp):
ATTTAGAGAA
Found at i:47771 original size:19 final size:20
Alignment explanation
Indices: 47736--47776 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
47726 TGTATTGAAT
*
47736 ATAATTTTATTTCATAT-AC
1 ATAATTTTAATTCATATCAC
47755 ATAATTATTAATT-ATATCAC
1 ATAATT-TTAATTCATATCAC
47775 AT
1 AT
47777 GTTTAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAATTTTAATTCATATCAC
Found at i:48684 original size:20 final size:21
Alignment explanation
Indices: 48651--48689 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48641 CCGGAAATAT
48651 TAAAAAATATTAATATTTTAAA
1 TAAAAAATATTAAT-TTTTAAA
48673 TAAAAAA-A-TAATTTTTA
1 TAAAAAATATTAATTTTTA
48690 TATATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 1 0.06
22 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAAATATTAATTTTTAAA
Found at i:49536 original size:6 final size:6
Alignment explanation
Indices: 49525--49701 Score: 354
Period size: 6 Copynumber: 29.5 Consensus size: 6
49515 GACACGTATT
49525 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
49573 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
49621 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
49669 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
49702 CGAGACGAGA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 171 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:50209 original size:6 final size:6
Alignment explanation
Indices: 50193--50242 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
50183 TCTCGTCTCG
50193 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
50240 GGT
1 GGT
50243 AATGGTAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:50248 original size:6 final size:6
Alignment explanation
Indices: 50239--50281 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
50229 GTCGTGGTCG
50239 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
50282 ACGTGTCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:50248 original size:12 final size:12
Alignment explanation
Indices: 50198--50272 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 12
50188 TCTCGGGTCG
**
50198 GGTCGTGGTCGT
1 GGTCGTGGTAAT
**
50210 GGTCGTGGTCGT
1 GGTCGTGGTAAT
**
50222 GGTCGTGGTCGT
1 GGTCGTGGTAAT
50234 GGTCGTGGTAAT
1 GGTCGTGGTAAT
**
50246 GGTAATGGTAAT
1 GGTCGTGGTAAT
**
50258 GGTAATGGTAAT
1 GGTCGTGGTAAT
50270 GGT
1 GGT
50273 AATGGTAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.13, C:0.09, G:0.44, T:0.33
Consensus pattern (12 bp):
GGTCGTGGTAAT
Found at i:54281 original size:18 final size:18
Alignment explanation
Indices: 54258--54298 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
54248 TGAGATTACT
*
54258 TAAAGGAAATAAAATACC
1 TAAAGGAAATAAAACACC
*
54276 TAAAGGAAATATAACACC
1 TAAAGGAAATAAAACACC
54294 TAAAG
1 TAAAG
54299 ATAATCCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (18 bp):
TAAAGGAAATAAAACACC
Found at i:55736 original size:30 final size:30
Alignment explanation
Indices: 55674--55766 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 30
55664 AAGAAACTAA
*
55674 AATCAAACGGATCGATAACGTTAGAGACCAT
1 AATCAAACGGATCGATAACGTTGGA-ACCAT
* *
55705 AATCAAACGGATCTATAATGTTGGAACCAT
1 AATCAAACGGATCGATAACGTTGGAACCAT
* *
55735 AATCAAACAGATCGATAACATTAGGAACCAT
1 AATCAAACGGATCGATAACGTT-GGAACCAT
55766 A
1 A
55767 TACCCTTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 23 0.43
31 31 0.57
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (30 bp):
AATCAAACGGATCGATAACGTTGGAACCAT
Found at i:56221 original size:22 final size:23
Alignment explanation
Indices: 56178--56220 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
56168 AGCTAATGGT
56178 TAAATATTTATTTATAGATTTTA
1 TAAATATTTATTTATAGATTTTA
*
56201 TAAA-ATTTTTTTATA-ATTTT
1 TAAATATTTATTTATAGATTTT
56221 TTTCACCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TAAATATTTATTTATAGATTTTA
Found at i:56311 original size:37 final size:37
Alignment explanation
Indices: 56258--56330 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
56248 AATTTAATAG
* *
56258 AAAATTAAATATTAGAAGTCTTAAGCAACAAATAAAA
1 AAAATTAAATACTAGAAGTCTTAAACAACAAATAAAA
56295 AAAATTAAATACTAGAAGTCTTAAACAACAAATAAA
1 AAAATTAAATACTAGAAGTCTTAAACAACAAATAAA
56331 TAATAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (37 bp):
AAAATTAAATACTAGAAGTCTTAAACAACAAATAAAA
Found at i:57176 original size:43 final size:43
Alignment explanation
Indices: 57122--57234 Score: 217
Period size: 43 Copynumber: 2.6 Consensus size: 43
57112 CAACAACAAT
57122 AACAATAATTCGGTAATAAAAAAAAAGAAACAAAGACGATAAC
1 AACAATAATTCGGTAATAAAAAAAAAGAAACAAAGACGATAAC
57165 AACAATAATTCGGTAATAAAAAAAAAGAAACAAAGACGATAAC
1 AACAATAATTCGGTAATAAAAAAAAAGAAACAAAGACGATAAC
57208 AACAATAATTCGGTAATAAATAAAAAA
1 AACAATAATTCGGTAATAAA-AAAAAA
57235 CCAAGGATAA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
43 63 0.91
44 6 0.09
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (43 bp):
AACAATAATTCGGTAATAAAAAAAAAGAAACAAAGACGATAAC
Found at i:60619 original size:22 final size:22
Alignment explanation
Indices: 60594--61066 Score: 573
Period size: 22 Copynumber: 21.6 Consensus size: 22
60584 ATAATAAATT
60594 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* *
60616 TTTTAACATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
60638 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
60660 TTTTAAAATAACTCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* *
60682 TTTTAATATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
60704 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
60726 TTTTAAAAT--ATTTTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
60747 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
60769 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
60791 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
60813 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
*
60835 TTTTAAAATAAATAAATTCATA
1 TTTTAAAATAAATCAATTCATA
***
60857 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
60879 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
60901 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
60923 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
**
60945 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
60967 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* ***
60989 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
61011 TTTTAAAATAAATCAATTCGTA
1 TTTTAAAATAAATCAATTCATA
** *
61033 TTTTAAAATAAAT-TTTTTATA
1 TTTTAAAATAAATCAATTCATA
61054 TTTTAAAATAAAT
1 TTTTAAAATAAAT
61067 TTTAAAATAG
Statistics
Matches: 391, Mismatches: 49, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.01
21 36 0.09
22 339 0.87
23 11 0.03
24 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:61083 original size:11 final size:12
Alignment explanation
Indices: 61032--61080 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
61022 ATCAATTCGT
61032 ATTTTAAAATAA
1 ATTTTAAAATAA
* *
61044 ATTTT---TTAT
1 ATTTTAAAATAA
61053 ATTTTAAAATAA
1 ATTTTAAAATAA
*
61065 ATTTTAAAATAG
1 ATTTTAAAATAA
61077 ATTT
1 ATTT
61081 AAATGATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
9 7 0.24
12 22 0.76
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:61083 original size:88 final size:86
Alignment explanation
Indices: 60594--61066 Score: 651
Period size: 88 Copynumber: 5.4 Consensus size: 86
60584 ATAATAAATT
** * ***
60594 TTTTAAAATAAATCAATTCATATTTTAACATAAATCAATCCATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAAT-TTTTCATATTTTAAAATAAATCAAT-CATATTTTAAAATAAATTTTTCCAT
*
60659 ATTTTAAAATAACTCAATTCATA
64 ATTTTAAAATAAATCAATTCATA
* ** * *
60682 TTTTAATATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAAT-ATTTTTTCCAT
1 TTTTAAAATAAAT-TTTTCATATTTTAAAATAAATCAAT-CATATTTTAAAATAAATTTTTCCAT
*
60746 ATTTTAAAATAAATCAATCCATA
64 ATTTTAAAATAAATCAATTCATA
** * *
60769 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAATTTTCCAT
1 TTTTAAAATAAAT-TTTTCATATTTTAAAATAAATCAAT-CATATTTTAAAATAAATTTTTCCAT
*
60834 ATTTTAAAATAAATAAATTCATA
64 ATTTTAAAATAAATCAATTCATA
60857 TTTTAAAATAAATTTTTTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCAT
1 TTTTAAAATAAA-TTTTTCATATTTTAAAATAAATCAAT-CATATTTTAAAATAAATTTTTCCAT
60922 ATTTTAAAATAAATCAATTCATA
64 ATTTTAAAATAAATCAATTCATA
* *
60945 TTTTAAAATAAAATTTTTCATATTTTAAAATAAATCAATTCATATTTTAAAATAATTTTTTTCAT
1 TTTTAAAAT-AAATTTTTCATATTTTAAAATAAATCAA-TCATATTTTAAAATAAATTTTTCCAT
*
61010 ATTTTAAAATAAATCAATTCGTA
64 ATTTTAAAATAAATCAATTCATA
*
61033 TTTTAAAATAAATTTTTTATATTTTAAAATAAAT
1 TTTTAAAATAAATTTTTCATATTTTAAAATAAAT
61067 TTTAAAATAG
Statistics
Matches: 358, Mismatches: 23, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
87 104 0.29
88 249 0.70
89 5 0.01
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.44
Consensus pattern (86 bp):
TTTTAAAATAAATTTTTCATATTTTAAAATAAATCAATCATATTTTAAAATAAATTTTTCCATAT
TTTAAAATAAATCAATTCATA
Found at i:66785 original size:91 final size:91
Alignment explanation
Indices: 66710--67087 Score: 560
Period size: 91 Copynumber: 4.1 Consensus size: 91
66700 TCCTGGTCTT
* * * *
66710 TCCACTGGAAATGATGATCTAAGGTTGAAGAAGTTCTTCTCATTATGAATTTCTTCTCCCTCGTT
1 TCCACTGGAAATGATGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTT
66775 GGATGAGTTCTTCTCATTATGAACTC
66 GGATGAGTTCTTCTCATTATGAACTC
** *
66801 TCCACTGGAAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGT
1 TCCACTGG-AAATGATGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT
*
66866 TGGATAAGTTCTTCTCATTATGAACTC
65 TGGATGAGTTCTTCTCATTATGAACTC
** * * * *
66893 TCCGTTGAAAATGCTGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTT
1 TCCACTGGAAATGATGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTT
66958 GGATGAGTTCTTCTCATTATGAACTC
66 GGATGAGTTCTTCTCATTATGAACTC
* *
66984 TCCACTGGAAAT-ATTGAACCAAGGCTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCGT
1 TCCACTGGAAATGA-TGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT
* *
67048 TGGACGAGTTCTTCTCATTGTGAACTC
65 TGGATGAGTTCTTCTCATTATGAACTC
*
67075 TCCACTGGCAATG
1 TCCACTGGAAATG
67088 TTGATCGGTT
Statistics
Matches: 256, Mismatches: 28, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
91 176 0.69
92 80 0.31
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (91 bp):
TCCACTGGAAATGATGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTT
GGATGAGTTCTTCTCATTATGAACTC
Found at i:67426 original size:30 final size:30
Alignment explanation
Indices: 67391--67568 Score: 103
Period size: 30 Copynumber: 5.7 Consensus size: 30
67381 AAAATTTCTA
* *
67391 GTTTCAAGGGAAA-TAATCTCAAAGGTTGGT
1 GTTTCAAGAGAAACT-ATCTCAAAGGTTAGT
* *
67421 TTTTCAAGAGAAACTGTCTCAAAGGTTAGT
1 GTTTCAAGAGAAACTATCTCAAAGGTTAGT
* *
67451 GTTTCAAGATAAACTGTCTCAAGAGAGATAAAATA-T
1 GTTTCAAGAGAAACTATCTCAA-AG-G-T----TAGT
* * * *
67487 GTTTCAAGGGAAACAATCTCAAAGATTTTGT
1 GTTTCAAGAGAAACTATCTCAAAG-GTTAGT
* * * *
67518 GTCTCAAGGGAAAC-ATTTTCAAAGTTTA-T
1 GTTTCAAGAGAAACTA-TCTCAAAGGTTAGT
*
67547 GTTTCAAGAGAAACTGTCTCAA
1 GTTTCAAGAGAAACTATCTCAA
67569 GGGAGACAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
29 18 0.15
30 49 0.42
31 24 0.20
32 1 0.01
33 1 0.01
34 1 0.01
35 3 0.03
36 19 0.16
37 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (30 bp):
GTTTCAAGAGAAACTATCTCAAAGGTTAGT
Found at i:67550 original size:96 final size:97
Alignment explanation
Indices: 67391--67597 Score: 267
Period size: 96 Copynumber: 2.1 Consensus size: 97
67381 AAAATTTCTA
* * *
67391 GTTTCAAGGGAAATAATCTCAAAGGTTGGTTTTTCAAGAGAAACTGTCTCAAAGGTTAGTGTTTC
1 GTTTCAAGGGAAACAATCTCAAAGGTTGGTGTCTCAAGAGAAACTGTCTCAAAGGTTAGTGTTTC
* *
67456 AAGATAAACTGTCTCAAGAGAGATAAAA-TAT
66 AAGAGAAACTGTCTCAAGAGAGACAAAATTAT
* * * * *
67487 GTTTCAAGGGAAACAATCTCAAAGATTTTGTGTCTCAAGGGAAACAT-TTTCAAAGTTTA-TGTT
1 GTTTCAAGGGAAACAATCTCAAAG-GTTGGTGTCTCAAGAGAAAC-TGTCTCAAAGGTTAGTGTT
* *
67550 TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
64 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTAT
67584 GTTTCAAGGGAAAC
1 GTTTCAAGGGAAAC
67598 TGTCCTAGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
96 54 0.56
97 41 0.43
98 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (97 bp):
GTTTCAAGGGAAACAATCTCAAAGGTTGGTGTCTCAAGAGAAACTGTCTCAAAGGTTAGTGTTTC
AAGAGAAACTGTCTCAAGAGAGACAAAATTAT
Found at i:67568 original size:29 final size:29
Alignment explanation
Indices: 67484--67568 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 29
67474 AGAGATAAAA
*
67484 TATGTTTCAAGGGAAACAATCTCAAAGATT
1 TATGTTTCAAGGGAAAC-TTCTCAAAGATT
*
67514 T-TGTGTCTCAAGGGAAACATTTTCAAAG-TT
1 TATGT-T-TCAAGGGAAAC-TTCTCAAAGATT
*
67544 TATGTTTCAAGAGAAACTGTCTCAA
1 TATGTTTCAAGGGAAACT-TCTCAA
67569 GGGAGACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 1 0.02
29 18 0.38
30 6 0.13
31 22 0.47
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (29 bp):
TATGTTTCAAGGGAAACTTCTCAAAGATT
Found at i:67639 original size:15 final size:15
Alignment explanation
Indices: 67587--67640 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
67577 AAATTTTGTT
67587 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
* *
67602 -CTA--GAAACTTGTT
1 TCAAGGGAAAC-TGTC
*
67615 TCAAGAGAAACTGTC
1 TCAAGGGAAACTGTC
67630 TCAAGGGAAAC
1 TCAAGGGAAAC
67641 AAAATTCGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 4 0.13
15 13 0.43
16 5 0.17
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (15 bp):
TCAAGGGAAACTGTC
Found at i:67702 original size:66 final size:64
Alignment explanation
Indices: 67521--67807 Score: 242
Period size: 66 Copynumber: 4.3 Consensus size: 64
67511 ATTTTGTGTC
* * *
67521 TCAAGGGAAACATTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TCAAGGGAAACGTTCTCAAAGTTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-CTTGT
67586 T
64 T
* ** *
67587 TCAAGGGAAACTGTCCT-AGAA-ACTTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAA-TTCG
1 TCAAGGGAAAC-GTTCTCA-AAGTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTT-G
67649 TT
63 TT
* * *
67651 TCAAGGGGAACGTTCTCAAAGTTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGATAAAACTTGT
1 TCAAGGGAAACGTTCTCAAAG-TTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGT
67716 T
64 T
* * * *
67717 TCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTTGTTTCTAGGGAAACTGTCTCAAGAGAGACAA
1 TCAAGGGAAACGT-TCTC-A-A-AG-----TTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
*
67781 AATTTGTT
57 AACTTGTT
*
67789 TTAAGGGAAAC-TATCTCAA
1 TCAAGGGAAACGT-TCTCAA
67808 GCGAGATAAA
Statistics
Matches: 181, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
63 8 0.04
64 14 0.08
65 35 0.19
66 61 0.34
67 7 0.04
68 1 0.01
69 2 0.01
70 1 0.01
71 1 0.01
72 49 0.27
73 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (64 bp):
TCAAGGGAAACGTTCTCAAAGTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTT
Found at i:67837 original size:39 final size:39
Alignment explanation
Indices: 67677--68056 Score: 481
Period size: 39 Copynumber: 10.0 Consensus size: 39
67667 CAAAGTTTTG
* *
67677 TGTTTCAAGAGAAACTATCTCAAGGGAGATAAAA-C-T-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
67713 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
67749 TGTTTCTAGGGAAACTGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
67785 TGTTTTAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
67824 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
67863 TGTTTCGAGGAAAACTATCTCAAACGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
67902 TGTTTCGAGGGAAACTATCTCAAGCGAGGTAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
67941 TGTTTCGAGGGAAACTACCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
67980 TATTTCAAGGGAAACTACCTCGAGGGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
68019 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
68057 ATGTAAAAAC
Statistics
Matches: 310, Mismatches: 30, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
36 95 0.31
38 2 0.01
39 213 0.69
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:67910 original size:20 final size:20
Alignment explanation
Indices: 67809--67910 Score: 59
Period size: 20 Copynumber: 5.2 Consensus size: 20
67799 CTATCTCAAG
67809 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
** ****
67829 CGAG-GGAAA-CTATCTCAAG
1 CGAGATAAAATCT-TCTGTTT
67848 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
* ****
67868 CGAG-GAAAA-CTATCTCAAA
1 CGAGATAAAATCT-TCTGTTT
67887 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
67907 CGAG
1 CGAG
67911 GGAAACTATC
Statistics
Matches: 54, Mismatches: 22, Indels: 12
0.61 0.25 0.14
Matches are distributed among these distances:
18 4 0.07
19 21 0.39
20 25 0.46
21 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (20 bp):
CGAGATAAAATCTTCTGTTT
Found at i:68149 original size:76 final size:76
Alignment explanation
Indices: 68030--68238 Score: 234
Period size: 76 Copynumber: 2.8 Consensus size: 76
68020 GTTTCAAGGG
* *
68030 AAACTATCTCAAGCGAGACAAA--A--TCTTATGTAAAAACAATCTTGAGTAAAATGAAAT-GTC
1 AAACTATCTCAAGCGAGACAAATTATGTTTTAAG-AAAAACAATCTTGAGTAAAAT-AAATCGTC
68090 TTCTTTCGAGTAA
64 TTCTTTCGAGTAA
* * * *
68103 AAA-TCGTCTCAAGCGAGACTAATCT-TGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTC
1 AAACT-ATCTCAAGCGAGACAAAT-TATGTTTTAAGAAAAACAATCTTGAGTAAAATAAATCGTC
*
68166 TTGTTTCGAGTAA
64 TTCTTTCGAGTAA
* * * *
68179 AAACTATCTCAAGTGAGACAAATTATGTTTTAAGAAAAACAATCTTAAGTGAGATAAATC
1 AAACTATCTCAAGCGAGACAAATTATGTTTTAAGAAAAACAATCTTGAGTAAAATAAATC
68239 CTCTGTATTA
Statistics
Matches: 115, Mismatches: 12, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
72 1 0.01
73 18 0.16
75 5 0.04
76 85 0.74
77 6 0.05
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (76 bp):
AAACTATCTCAAGCGAGACAAATTATGTTTTAAGAAAAACAATCTTGAGTAAAATAAATCGTCTT
CTTTCGAGTAA
Found at i:68163 original size:36 final size:36
Alignment explanation
Indices: 68123--68238 Score: 117
Period size: 36 Copynumber: 3.1 Consensus size: 36
68113 AAGCGAGACT
* *
68123 AATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATA
1 AATCTTGTTTTAAGAAAAACAATCTTAAGTGAGATA
** * * *
68159 AATCTTCTTGTTTCGAGTAAAAACTATCTCAAGTGAGACA
1 AA---TCTTGTTTTAAG-AAAAACAATCTTAAGTGAGATA
68199 AAT-TATGTTTTAAGAAAAACAATCTTAAGTGAGATA
1 AATCT-TGTTTTAAGAAAAACAATCTTAAGTGAGATA
68235 AATC
1 AATC
68239 CTCTGTATTA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
36 25 0.40
37 8 0.13
39 10 0.16
40 19 0.31
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (36 bp):
AATCTTGTTTTAAGAAAAACAATCTTAAGTGAGATA
Found at i:80588 original size:2 final size:2
Alignment explanation
Indices: 80581--80627 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
80571 TATTTTAGTC
* *
80581 AT AT AT AT AT AT AT AT AGC AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
80624 AT AT
1 AT AT
80628 TATTTAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 39 0.98
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83682 original size:3 final size:3
Alignment explanation
Indices: 83676--83753 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
83666 TTACTCATTT
* * *
83676 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
83724 TAA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
83754 AAAAATAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:84860 original size:29 final size:28
Alignment explanation
Indices: 84806--84872 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
84796 TTAATAATTA
84806 ATATTTTAATCTGAATAGTATGTTTTAAT
1 ATATTTTAATCTGAATAGTATGTTTT-AT
* *
84835 TTATTTTAATCTG-ATA-TTTGAATTTTAT
1 ATATTTTAATCTGAATAGTATG--TTTTAT
84863 ATATTTTAAT
1 ATATTTTAAT
84873 TTAGTCACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 14 0.42
29 16 0.48
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (28 bp):
ATATTTTAATCTGAATAGTATGTTTTAT
Found at i:85330 original size:27 final size:27
Alignment explanation
Indices: 85300--85354 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
85290 ATATTTTTAA
85300 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* * *
85327 ATAAATTAATATTTTTTTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
85354 A
1 A
85355 ATTCGAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Done.