Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001447.1 Hibiscus syriacus cultivar Beakdansim tig00002797_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: 104406
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1265 original size:19 final size:19
Alignment explanation
Indices: 1236--1283 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1226 TGCGATTTAT
1236 TCCAA-TTCGTTGCAATAG
1 TCCAAGTTCGTTGCAATAG
*
1254 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCAATAG
*
1273 TCGAAGTTCGT
1 TCCAAGTTCGT
1284 GTTGCGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (19 bp):
TCCAAGTTCGTTGCAATAG
Found at i:2065 original size:21 final size:21
Alignment explanation
Indices: 2041--2151 Score: 70
Period size: 21 Copynumber: 5.4 Consensus size: 21
2031 AGAATAATCC
*
2041 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
*
2062 CAA--CGAA-TTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
* ** *
2082 CAACACGAGTTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
* ** *
2103 CAA--CGAATTTGGAAAATTG
1 CAACGCGAACTTGGACTATCG
2122 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
*
2143 CAATGCGAA
1 CAACGCGAA
2152 TATGTAAATC
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
18 5 0.07
19 18 0.26
20 7 0.10
21 30 0.44
22 3 0.04
23 5 0.07
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
CAACGCGAACTTGGACTATCG
Found at i:2070 original size:41 final size:41
Alignment explanation
Indices: 2024--2145 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 41
2014 ATGCACTACC
* *
2024 CGAATTTAGAATAATCCCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAATCGCAACGCGAACTTCGACTATCGCAA
* **
2065 CGAA-TTGGAATAAATCGCAACACGAGTTTCGACTATCGCAA
1 CGAATTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAA
* *
2106 CGAATTTGGAA-AATTGCAACGCGAACTTGGACTATCGCAA
1 CGAATTTGGAATAATCGCAACGCGAACTTCGACTATCGCAA
2146 TGCGAATATG
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 30 0.43
41 33 0.48
42 6 0.09
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (41 bp):
CGAATTTGGAATAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:12415 original size:25 final size:25
Alignment explanation
Indices: 12387--12458 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 25
12377 ATACAATATA
*
12387 TAAACGATATGATTCAAGGGAGTGC
1 TAAACAATATGATTCAAGGGAGTGC
**
12412 TAAACAATAT-A-T-AA---AGTTA
1 TAAACAATATGATTCAAGGGAGTGC
*
12431 TAAACTATATGATTCAAGGGAGTGC
1 TAAACAATATGATTCAAGGGAGTGC
12456 TAA
1 TAA
12459 CATGACAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 12 0.34
20 1 0.03
21 1 0.03
22 4 0.11
23 1 0.03
24 1 0.03
25 15 0.43
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (25 bp):
TAAACAATATGATTCAAGGGAGTGC
Found at i:21171 original size:2 final size:2
Alignment explanation
Indices: 21164--21194 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21154 TCGGTAAGAA
*
21164 AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21195 CCGGGAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37608 original size:24 final size:24
Alignment explanation
Indices: 37581--37628 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
37571 CTGGGGATTT
37581 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
37605 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
37629 ATTCCAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (24 bp):
TCTTCCAACAGTCAGACCTTTTAA
Found at i:38000 original size:24 final size:26
Alignment explanation
Indices: 37973--38031 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
37963 TCCTACATGG
*
37973 TTAATTT-A-CTTCACTGTAATTTGT
1 TTAATTTCATCTTCAATGTAATTTGT
37997 TTAATTGCTTCATCTTCAATGTAATTTGT
1 TTAA-T--TTCATCTTCAATGTAATTTGT
38026 TTAATT
1 TTAATT
38032 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 1 0.03
27 2 0.07
28 2 0.07
29 19 0.66
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TTAATTTCATCTTCAATGTAATTTGT
Found at i:38061 original size:39 final size:39
Alignment explanation
Indices: 38016--38122 Score: 117
Period size: 29 Copynumber: 3.0 Consensus size: 39
38006 TCATCTTCAA
38016 TGTAATTTGTTTAATTGTTTATATATTGGAAGACACAAG
1 TGTAATTTGTTTAATTGTTTATATATTGGAAGACACAAG
* * *
38055 TGTAATTTGTTTAATTGCTT-CATCTT--------CAA-
1 TGTAATTTGTTTAATTGTTTATATATTGGAAGACACAAG
38084 TGTAATTTGTTTAATTGTTTATATATTGGAAGACACAAG
1 TGTAATTTGTTTAATTGTTTATATATTGGAAGACACAAG
38123 CTTTCTTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
29 19 0.37
30 7 0.13
38 7 0.13
39 19 0.37
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (39 bp):
TGTAATTTGTTTAATTGTTTATATATTGGAAGACACAAG
Found at i:38096 original size:68 final size:68
Alignment explanation
Indices: 37987--38122 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
37977 TTTACTTCAC
37987 TGTAATTTGTTTAATTGCTTCATCTTCAATGTAATTTGTTTAATTGTTTATATATTGGAAGACAC
1 TGTAATTTGTTTAATTGCTTCATCTTCAATGTAATTTGTTTAATTGTTTATATATTGGAAGACAC
38052 AAG
66 AAG
38055 TGTAATTTGTTTAATTGCTTCATCTTCAATGTAATTTGTTTAATTGTTTATATATTGGAAGACAC
1 TGTAATTTGTTTAATTGCTTCATCTTCAATGTAATTTGTTTAATTGTTTATATATTGGAAGACAC
38120 AAG
66 AAG
38123 CTTTCTTTAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (68 bp):
TGTAATTTGTTTAATTGCTTCATCTTCAATGTAATTTGTTTAATTGTTTATATATTGGAAGACAC
AAG
Found at i:38254 original size:20 final size:20
Alignment explanation
Indices: 38197--38259 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 20
38187 ACTTGTTATT
38197 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
**
38218 TTGTTTATCTATAATCTGTTTAA
1 TTG-TTA--GGTAATCTGTTTAA
38241 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
38260 GAATTTAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 11 0.31
21 4 0.11
22 5 0.14
23 15 0.43
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:41024 original size:12 final size:12
Alignment explanation
Indices: 41009--41054 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
40999 CGGTTTTTTT
*
41009 ACCGGATAAAAA
1 ACCGGTTAAAAA
41021 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
41036 ACCGGTTAAAAA
1 ACCGGTTAAAAA
41048 ACCGGTT
1 ACCGGTT
41055 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:41036 original size:15 final size:13
Alignment explanation
Indices: 41015--41055 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
41005 TTTTACCGGA
41015 TAAAAAACCGGTT
1 TAAAAAACCGGTT
41028 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
41042 TAAAAAACCGGTT
1 TAAAAAACCGGTT
41055 T
1 T
41056 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:43370 original size:21 final size:21
Alignment explanation
Indices: 43346--43385 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43336 TTTATTTTAT
43346 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
43367 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
43386 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:43433 original size:33 final size:33
Alignment explanation
Indices: 43380--43478 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
43370 TTTGTTTCAA
43380 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
43412 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
43445 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
43478 T
1 T
43479 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:43507 original size:13 final size:13
Alignment explanation
Indices: 43464--43518 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
43454 TTGGAAGTAT
43464 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
43477 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
43491 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
43504 TTAAGTATTTGAA
1 TTAAGTATTTCAA
43517 TT
1 TT
43519 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:43978 original size:21 final size:18
Alignment explanation
Indices: 43933--43966 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43923 GGTTTTTTAT
43933 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
43950 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
43967 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:44086 original size:15 final size:17
Alignment explanation
Indices: 44060--44091 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
44050 TTCTATGGGA
44060 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
44076 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
44092 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:45582 original size:24 final size:22
Alignment explanation
Indices: 45555--45598 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
45545 CTACATTATA
45555 TTGAAACAATAATAATATATCATG
1 TTGAAACAATAA-AAT-TATCATG
*
45579 TTGAAATAATAAAATTATCA
1 TTGAAACAATAAAATTATCA
45599 AAGTGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 3 0.16
24 11 0.58
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (22 bp):
TTGAAACAATAAAATTATCATG
Found at i:49532 original size:21 final size:21
Alignment explanation
Indices: 49493--49534 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
49483 GCTAACGCTA
**
49493 CGGTGATAAAACGTGGATCAT
1 CGGTGATAAAACGCAGATCAT
49514 CGGTGATAAAACGCAGATCAT
1 CGGTGATAAAACGCAGATCAT
49535 GAAGCGCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (21 bp):
CGGTGATAAAACGCAGATCAT
Found at i:51299 original size:63 final size:66
Alignment explanation
Indices: 51181--51336 Score: 176
Period size: 63 Copynumber: 2.4 Consensus size: 66
51171 ATGCACATGA
** **
51181 AGTGCATCGATGC-ACTCTTTTAAAATACAAACATCGAATGCCATTGATGCATCGATGCAT-AAG
1 AGTGCATCGATGCAACTCCATTAAAATACAAACATCGAATAACATTGATGCATCGATGCATGAAG
51244 G
66 G
* * * *
51245 AGTGCATCGATGCAAC-CCATT-AAATACAAATATCGAATAAGATTTATGCATCGATGCATGATG
1 AGTGCATCGATGCAACTCCATTAAAATACAAACATCGAATAACATTGATGCATCGATGCATGAAG
*
51308 T
66 G
*
51309 AGTACATCGATGCATACCTCCATTAAAA
1 AGTGCATCGATGCA-A-CTCCATTAAAA
51337 GATGACAATG
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
63 33 0.43
64 31 0.41
65 3 0.04
66 1 0.01
67 5 0.07
68 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (66 bp):
AGTGCATCGATGCAACTCCATTAAAATACAAACATCGAATAACATTGATGCATCGATGCATGAAG
G
Found at i:51972 original size:23 final size:23
Alignment explanation
Indices: 51913--51977 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
51903 ACATTATTAT
* *
51913 ATGGCACTACAGTGTAATTCTAC
1 ATGGCACTTCAGTGCAATTCTAC
** *
51936 GCGGTAC-TCTAGTGCAATTCTAC
1 ATGGCACTTC-AGTGCAATTCTAC
51959 ATGGCACTTCAGTGCAATT
1 ATGGCACTTCAGTGCAATT
51978 ATACGAGCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 1 0.03
23 29 0.91
24 2 0.06
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (23 bp):
ATGGCACTTCAGTGCAATTCTAC
Found at i:58772 original size:23 final size:23
Alignment explanation
Indices: 58740--58806 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
58730 TTATTATATA
*
58740 GCACTACGGTGTAATTCTACGCG
1 GCACTACGGTGCAATTCTACGCG
* *
58763 GCACTCCGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTCTACGCG
* *
58786 GCACTTCGGTGCAATTATACG
1 GCACTACGGTGCAATTCTACG
58807 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCG
Found at i:67228 original size:22 final size:21
Alignment explanation
Indices: 67186--67225 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
67176 GAGTTTATTT
*
67186 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
67207 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
67226 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:70753 original size:24 final size:24
Alignment explanation
Indices: 70678--70761 Score: 68
Period size: 24 Copynumber: 3.6 Consensus size: 24
70668 AATTATGGGC
70678 TTTTTAT-TTATTTTGTTTCTTAA
1 TTTTTATATTATTTTGTTTCTTAA
* ** ** *
70701 TATTTATATTATTTAATTAT-GGAC
1 TTTTTATATTATTTTGTT-TCTTAA
70725 TTTTTAT-TTATTTTGTTTCTTAA
1 TTTTTATATTATTTTGTTTCTTAA
70748 TGTTTT-TATTATTT
1 T-TTTTATATTATTT
70762 AATTGTTTGA
Statistics
Matches: 44, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
22 1 0.02
23 17 0.39
24 25 0.57
25 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (24 bp):
TTTTTATATTATTTTGTTTCTTAA
Found at i:70759 original size:86 final size:84
Alignment explanation
Indices: 70592--70752 Score: 250
Period size: 86 Copynumber: 1.8 Consensus size: 84
70582 AATAGACTTG
70592 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACTTTTATTTATTTTTTTCTTAA
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACTTTTATTTATTTTTTTCTTAA
70657 TGTTTTTATTTAATTATGGGC
66 TG--TTTATTTAATTATGGGC
*
70678 TTTTTATTTATTTTGTTTCTTAATATTTATATTATTTAATTATGGACTTTTTATTTATTTTGTTT
1 TTTTTATTTATTTTGTTTCTTAAT-GTT-T-TTATTTAATTATGGAC-TTTTATTTATTTT-TTT
70743 CTTAATGTTT
61 CTTAATGTTT
70753 TTATTATTTA
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
86 24 0.35
87 2 0.03
88 1 0.01
89 19 0.28
90 13 0.19
91 10 0.14
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (84 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACTTTTATTTATTTTTTTCTTAA
TGTTTATTTAATTATGGGC
Found at i:70765 original size:47 final size:44
Alignment explanation
Indices: 70592--70757 Score: 273
Period size: 47 Copynumber: 3.8 Consensus size: 44
70582 AATAGACTTG
70592 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
*
70636 -TTTTATTTATTTT-TTTCTTAATGTTTTTATTTAATTATGGGC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
*
70678 TTTTTATTTATTTTGTTTCTTAATATTTATATTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAAT-GTT-T-TTATTTAATTATGGAC
70725 TTTTTATTTATTTTGTTTCTTAATGTTTTTATT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATT
70758 ATTTAATTGT
Statistics
Matches: 113, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
42 28 0.25
43 26 0.23
44 14 0.12
45 3 0.03
46 3 0.03
47 39 0.35
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
Found at i:70798 original size:13 final size:13
Alignment explanation
Indices: 70757--70805 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
70747 ATGTTTTTAT
*
70757 TATTTAATTGTTTG
1 TATTTAA-TATTTG
* *
70771 AATTGTAACATTTG
1 TATT-TAATATTTG
70785 TATTTAATATTTG
1 TATTTAATATTTG
70798 TATTTAAT
1 TATTTAAT
70806 TGTTTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 16 0.55
14 10 0.34
15 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (13 bp):
TATTTAATATTTG
Found at i:70824 original size:23 final size:24
Alignment explanation
Indices: 70789--70852 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
70779 CATTTGTATT
* *
70789 TAATATTTGTATTTAATT-GTTT-
1 TAATGTTTTTATTTAATTAGTTTG
*
70811 TAATTGTTTTTA-TTATTTAGTTTG
1 TAA-TGTTTTTATTTAATTAGTTTG
70835 TAATGTTTTTATTTAATT
1 TAATGTTTTTATTTAATT
70853 TTCACTTGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 8 0.24
23 18 0.53
24 8 0.24
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (24 bp):
TAATGTTTTTATTTAATTAGTTTG
Found at i:74034 original size:20 final size:20
Alignment explanation
Indices: 74009--74053 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
73999 TTATCCGGAA
*
74009 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
74029 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
74049 AAAAA
1 AAAAA
74054 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:74257 original size:22 final size:21
Alignment explanation
Indices: 74218--74258 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
74208 AGTGAAAAAA
**
74218 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
74239 CCGGATCGGATTTAAATCCG
1 CCGGATC-GATTTAAATCCG
74259 GCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:77340 original size:20 final size:18
Alignment explanation
Indices: 77315--77358 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
77305 TAAAAATTGT
77315 ATATTATTCAATATGTTTAA
1 ATATTATT-AATAT-TTTAA
*
77335 ATATTA-TAATATTTTTA
1 ATATTATTAATATTTTAA
77352 ATATTAT
1 ATATTAT
77359 ATTAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.45
18 5 0.23
19 1 0.05
20 6 0.27
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTATTAATATTTTAA
Found at i:77351 original size:18 final size:18
Alignment explanation
Indices: 77324--77377 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
77314 TATATTATTC
*
77324 AATATGTTTAAATATTAT
1 AATATTTTTAAATATTAT
77342 AATATTTTT-AATATTAT
1 AATATTTTTAAATATTAT
* * *
77359 ATTAATATTAAATA-TAT
1 AATATTTTTAAATATTAT
77376 AA
1 AA
77378 AATAATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATATTTTTAAATATTAT
Found at i:77369 original size:17 final size:17
Alignment explanation
Indices: 77334--77387 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
77324 AATATGTTTA
* *
77334 AATATTATAATATTTTT
1 AATATTATAATAATATT
*
77351 AATATTATATTAATATT
1 AATATTATAATAATATT
*
77368 AAATATATAAAATAATATT
1 -AATAT-TATAATAATATT
77387 A
1 A
77388 CTCATTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 14 0.47
18 6 0.20
19 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATTATAATAATATT
Found at i:77446 original size:19 final size:18
Alignment explanation
Indices: 77409--77447 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
77399 AAATTCAATA
*
77409 ATAATATTTTTAAACATT
1 ATAATATTATTAAACATT
*
77427 ATAATGATTATTAAATATT
1 ATAAT-ATTATTAAACATT
77446 AT
1 AT
77448 TTCCATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
ATAATATTATTAAACATT
Found at i:77629 original size:24 final size:24
Alignment explanation
Indices: 77602--77679 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
77592 AAACATTTAA
77602 AAATATTAAATATTATATTAATAT
1 AAATATTAAATATTATATTAATAT
77626 AAATA-TATAATA-TATTATTAATAT
1 AAATATTA-AATATTA-TATTAATAT
*
77650 -ACTATTAAAATATTATATTAATATT
1 AAATATT-AAATATTATATTAATA-T
77675 AAATA
1 AAATA
77680 CATAAATGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
23 7 0.16
24 31 0.69
25 4 0.09
26 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATATTAAATATTATATTAATAT
Found at i:77672 original size:11 final size:11
Alignment explanation
Indices: 77604--77675 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 11
77594 ACATTTAAAA
77604 ATATTAAATATT
1 ATATT-AATATT
*
77616 ATATTAATATAA
1 ATATTAATAT-T
77628 ATATATAATA-T
1 ATAT-TAATATT
77639 ATTATTAATA-T
1 A-TATTAATATT
77650 ACTATTAAAATATT
1 A-TATT--AATATT
77664 ATATTAATATT
1 ATATTAATATT
77675 A
1 A
77676 AATACATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
11 24 0.47
12 12 0.24
13 13 0.25
14 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAATATT
Found at i:82624 original size:112 final size:112
Alignment explanation
Indices: 82433--82826 Score: 646
Period size: 112 Copynumber: 3.5 Consensus size: 112
82423 GTTTGTGTCC
* * * *
82433 ATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATAACAAAA-TCGGTCT
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACT-GGTCT
* *
82497 ATAAATGACAAAACAGGTAAAGCGTTACCGGATATATTGAAAGTGTCG
65 ATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCG
* * *
82545 ATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAATGATAAAACTGATCTA
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTCTA
*
82610 TAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTATCG
66 TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCG
* *
82657 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAGACAAAACCGGTCTA
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTCTA
**
82722 TAAATGACAAAACAGGTAAAGCGCTACATGATATATTGAAAGTATCG
66 TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCG
82769 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
82827 AGGTAAAGCG
Statistics
Matches: 262, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
112 261 1.00
113 1 0.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (112 bp):
ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTCTA
TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCG
Found at i:82836 original size:92 final size:92
Alignment explanation
Indices: 82723--82918 Score: 338
Period size: 92 Copynumber: 2.1 Consensus size: 92
82713 ACCGGTCTAT
*
82723 AAATGACAAAACAGGTAAAGCGCTACATGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
*
82788 CGATCCATAACAATATAACAGGTAAAA
66 CGATCCATAACAATATAACAAGTAAAA
* * *
82815 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTTAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
*
82880 CTATCCATAACAATATAACAAGTAAAA
66 CGATCCATAACAATATAACAAGTAAAA
82907 AAATGACAAAAC
1 AAATGACAAAAC
82919 CGATCTATAA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 98 1.00
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.24
Consensus pattern (92 bp):
AAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAAGTAAAA
Found at i:82866 original size:204 final size:204
Alignment explanation
Indices: 82611--83243 Score: 845
Period size: 204 Copynumber: 3.0 Consensus size: 204
82601 ACTGATCTAT
*
82611 AAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
* *
82676 CGATCCATAACAATATAACAGGTAAAAAAAAGACAAAACCGGTCTATAAATGACAAAACAGGTAA
66 CGATCCATAACAATATAACAAGTAAAAAAAAGACAAAACCGATCTATAAATGACAAAACAGGTAA
*
82741 AGCGCTACATGATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAA
131 AGCGCTAC-GGATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAA
82806 CAGGT-AAAA
195 CAGGTAAAAA
* *
82815 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTTAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
* *
82880 CTATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAGGTAA
66 CGATCCATAACAATATAACAAGTAAAAAAAAGACAAAACCGATCTATAAATGACAAAACAGGTAA
*
82945 AGCGCTACGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAC
131 AGCGCTACGGATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAAC
83010 AGGTAAAAA
196 AGGTAAAAA
* * *
83019 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGTGTACCGGATATATTGAAAATATCG
1 AAATGACAAAACAGG----TAAA-G------C-------G-CTACCGGATATATTGAAAGTATCG
* * * * *
83084 ATACTTTATAAAAATTTATCGATCTATAACAATATAACAAGTAAAAAAATGACAAAATCGGTCTA
47 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAAAGACAAAACCGATCTA
* * * * *
83149 TAAATGACAAAACAGGTAAAGTGCTATCAGATATGTTGATAGTGTCGATACTTTATAAAAATGTA
112 TAAATGACAAAACAGGTAAAGCGCTA-CGGATATATTGAAAGTATCGATACTTTATAAAAATGTA
* * *
83214 TCGATCCATAACAATAAAATAGTTAAAAA
176 TCGATCCATAACAATATAACAGGTAAAAA
83243 A
1 A
83244 TGACAATCGT
Statistics
Matches: 382, Mismatches: 26, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
203 59 0.15
204 149 0.39
208 4 0.01
209 1 0.00
215 1 0.00
222 1 0.00
223 105 0.27
224 62 0.16
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (204 bp):
AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAAGTAAAAAAAAGACAAAACCGATCTATAAATGACAAAACAGGTAA
AGCGCTACGGATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAAC
AGGTAAAAA
Found at i:83038 original size:112 final size:112
Alignment explanation
Indices: 82815--83313 Score: 740
Period size: 112 Copynumber: 4.5 Consensus size: 112
82805 ACAGGTAAAA
*
82815 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTTAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
* *
82880 CTATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTAT
66 CGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGGTCTAT
82927 AAATGACAAAACAGGTAAAGCGCTA-CGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
*
82991 CGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTAT
66 CGATCCATAACAATATAACAAGT-AAAAAAATGACAAAACCGGTCTAT
* * * *
83039 AAATGACAAAACAGGTAAAGTG-TACCGGATATATTGAAAATATCGATACTTTATAAAAATTTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
* *
83103 CGATCTATAACAATATAACAAGTAAAAAAATGACAAAATCGGTCTAT
66 CGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGGTCTAT
* * * * *
83150 AAATGACAAAACAGGTAAAGTGCTATCAGATATGTTGATAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
* * *
83215 CGATCCATAACAATA-AA-ATAGTTAAAAAATGAC--AATCGTTCTAT
66 CGATCCATAACAATATAACA-AGTAAAAAAATGACAAAACCGGTCTAT
* * * *
83259 AAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATAGTGTCGATAATTTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
83314 TATAAGTATC
Statistics
Matches: 359, Mismatches: 24, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
109 62 0.17
110 1 0.00
111 121 0.34
112 175 0.49
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (112 bp):
AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGGTCTAT
Found at i:83115 original size:223 final size:221
Alignment explanation
Indices: 82815--83296 Score: 734
Period size: 223 Copynumber: 2.2 Consensus size: 221
82805 ACAGGTAAAA
* * *
82815 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTTAAAGTGTCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATATCGATACTTTATAAAAATGTAT
*
82880 CTATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAGGTAA
66 CGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAGGTAA
* *
82945 AGCGCTA-CGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAA
131 AGCGCTATCAGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAA
83009 CAGGTAAAAAAAATGACAAAACCGGTCTAT
196 CA-GT-AAAAAAATGAC--AACCGGTCTAT
* *
83039 AAATGACAAAACAGGTAAAGTG-TACCGGATATATTGAAAATATCGATACTTTATAAAAATTTAT
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATATCGATACTTTATAAAAATGTAT
* * *
83103 CGATCTATAACAATATAACAAGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAACAGGTAA
66 CGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAGGTAA
* * *
83168 AGTGCTATCAGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAA
131 AGCGCTATCAGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAA
* * * *
83233 TAGTTAAAAAATGACAATCGTTCTAT
196 CAGTAAAAAAATGACAACCGGTCTAT
* *
83259 AAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGA
1 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGA
83297 TAGTGTCGAT
Statistics
Matches: 235, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
220 30 0.13
221 13 0.06
222 10 0.04
223 107 0.46
224 75 0.32
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (221 bp):
AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATATCGATACTTTATAAAAATGTAT
CGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGATCTATAAATGACAAAACAGGTAA
AGCGCTATCAGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAA
CAGTAAAAAAATGACAACCGGTCTAT
Found at i:83229 original size:427 final size:427
Alignment explanation
Indices: 82427--83249 Score: 1357
Period size: 427 Copynumber: 1.9 Consensus size: 427
82417 TTGTCGGTTT
*
82427 GTGTCCATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATAACAAAATC
1 GTGTCCATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATAACAAAACC
* *
82492 GGTCTATAAATGACAAAACAGGTAAAGCGTTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* * *
82557 AATGTATCTATCCATAACAATATAACAGGTAAAAAAATGATAAAACTGATCTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTATAAATGACAAAA
* *
82622 CAGGTAAAGCGCTATCGGATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAAC
196 CAGGTAAAGCGCTACCGGATATATTGAAAATATCGATACTTTATAAAAATGTATCGATCCATAAC
*
82687 AATATAACAGGTAAAAAAAAGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACATG
261 AATATAACAAGTAAAAAAAAGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACATG
*
82752 ATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAA
326 ATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACA-GTAAAAAA
82817 ATGACAAAACAGGTAAAGCGCTACCGGATATATTTAAA
390 ATGACAAAACAGGTAAAGCGCTACCGGATATATTTAAA
* * *
82855 GTGTCGATACTTTATAAAAATGTATCT-ATCCATAACAATATAACAAGTAAAAAAATGACAAAAC
1 GTGTCCATACTTTATAAAAATATAT-TGATCCATAACAATATAACAAGTAAAAAAATAACAAAAC
82919 CGATCTATAAATGACAAAACAGGTAAAGCGCTA-CGGATATATTGAAAGTGTCGATACTTTATAA
65 CGATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
*
82983 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAA
130 AAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAACCGATCTATAAATGACAA
* * *
83048 AACAGGTAAAGTG-TACCGGATATATTGAAAATATCGATACTTTATAAAAATTTATCGATCTATA
194 AACAGGTAAAGCGCTACCGGATATATTGAAAATATCGATACTTTATAAAAATGTATCGATCCATA
* * *
83112 ACAATATAACAAGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAACAGGTAAAGTGCTATC
259 ACAATATAACAAGTAAAAAAAAGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTA-C
* * * * *
83177 A-GATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAATAGTTAAA
323 ATGATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGTAAAA
83241 AAATGACAA
388 AAATGACAA
83250 TCGTTCTATA
Statistics
Matches: 367, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
426 14 0.04
427 219 0.60
428 133 0.36
429 1 0.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (427 bp):
GTGTCCATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATAACAAAACC
GATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTATAAATGACAAAA
CAGGTAAAGCGCTACCGGATATATTGAAAATATCGATACTTTATAAAAATGTATCGATCCATAAC
AATATAACAAGTAAAAAAAAGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACATG
ATATATTGAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGTAAAAAAA
TGACAAAACAGGTAAAGCGCTACCGGATATATTTAAA
Found at i:83497 original size:182 final size:182
Alignment explanation
Indices: 83189--83639 Score: 696
Period size: 182 Copynumber: 2.5 Consensus size: 182
83179 ATATGTTGAT
83189 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATA-AA-ATAGTTAAAAA-ATGAC--A
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAT-G-TAAAAATATGACAAA
* ** * *
83249 ATCGTTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATAGTGTCGATAATTTAT
64 ATCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATAATTTAT
* *
83314 TATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGAGCTAATAA
129 TATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGAGCCAATAA
* * *
83368 AGTGTCGATACTTTATAAAAATGTATCTATCTATAACAATATAACATGTAAAAATATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
* *
83433 CGATCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
66 CGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATAATTTATTA
* *
83498 TAAGTATCGACACTTTTTGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
131 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGAGCCAATAA
** *
83550 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAATAAAAATATAACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
83615 CGATCTCGAAATGACAAAACCGGTA
66 CGATCTCGAAATGACAAAACCGGTA
83640 GTAAAAAAGT
Statistics
Matches: 247, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
179 45 0.18
180 8 0.03
181 2 0.01
182 192 0.78
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
CGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATAATTTATTA
TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGAGCCAATAA
Found at i:83605 original size:15 final size:15
Alignment explanation
Indices: 83582--83612 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
83572 GTATCGATCC
*
83582 ATAACAATATAACAA
1 ATAAAAATATAACAA
83597 ATAAAAATATAACAA
1 ATAAAAATATAACAA
83612 A
1 A
83613 ATCGATCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAAATATAACAA
Found at i:89039 original size:21 final size:21
Alignment explanation
Indices: 88997--89039 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
88987 TTTCTGGGCT
*
88997 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
89018 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
89039 A
1 A
89040 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:95818 original size:21 final size:21
Alignment explanation
Indices: 95776--95818 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
95766 TTTTTGGGCT
*
95776 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
95797 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
95818 A
1 A
95819 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:96502 original size:23 final size:23
Alignment explanation
Indices: 96467--96534 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
96457 ATTATTATAT
*
96467 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* **
96490 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACGC
* *
96513 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
96535 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:100778 original size:35 final size:35
Alignment explanation
Indices: 100736--100845 Score: 86
Period size: 35 Copynumber: 3.1 Consensus size: 35
100726 TTCATCTTGG
100736 TTGGTGGCCAAACTTTGAACATGTGAATTTCATAT
1 TTGGTGGCCAAACTTTGAACATGTGAATTTCATAT
* *
100771 TTGGTGG-CTAAC-TTGTACACAT-TGGAAAATTC-T-T
1 TTGGTGGCCAAACTTTG-A-ACATGT-G-AATTTCATAT
* *
100805 TGGTAGGTAGCCAAACTTTGAACATGAGAATTTCATAT
1 T--T-GGTGGCCAAACTTTGAACATGTGAATTTCATAT
100843 TTG
1 TTG
100846 ATCCCTAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 24
0.66 0.07 0.28
Matches are distributed among these distances:
33 3 0.05
34 8 0.14
35 14 0.25
36 12 0.21
37 10 0.18
38 7 0.12
39 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (35 bp):
TTGGTGGCCAAACTTTGAACATGTGAATTTCATAT
Found at i:101424 original size:3 final size:3
Alignment explanation
Indices: 101416--101453 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
101406 GTTGTTTACA
101416 TTC TTC TTC TTTC TTC TTC TTC TTC TATC -TC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC T-TC TTC TTC TTC T
101454 GGCTCTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 25 0.78
4 5 0.16
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Done.