Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008841.1 Hibiscus syriacus cultivar Beakdansim tig00112047_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: 204746
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6256 original size:45 final size:46
Alignment explanation
Indices: 6168--6258 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
6158 TTGAAAAAGC
* *
6168 CTGAGTACATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTACATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
* *
6214 CTGAGTGCATCGATGCATGGT-ATGTGCATTGATGCATAAAATGCA
1 CTGAGTACATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
6259 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (46 bp):
CTGAGTACATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:7197 original size:18 final size:18
Alignment explanation
Indices: 7176--7221 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
7166 ATTCTGTCGG
**
7176 TTCAGTCAGACCGGTTAT
1 TTCAGTCAGACCGGCCAT
*
7194 TTCAGTCAGATCGGCCAT
1 TTCAGTCAGACCGGCCAT
7212 TTCAGTCAGA
1 TTCAGTCAGA
7222 ACTGATTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (18 bp):
TTCAGTCAGACCGGCCAT
Found at i:19376 original size:19 final size:20
Alignment explanation
Indices: 19337--19381 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
19327 ACTGGCAATG
* *
19337 AACCGACTGAAAACCGGT-A
1 AACCGGCTGAAAACCGATAA
*
19356 AACCGGCTGAAAATCGATAA
1 AACCGGCTGAAAACCGATAA
19376 AACCGG
1 AACCGG
19382 GGTGAACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.11
Consensus pattern (20 bp):
AACCGGCTGAAAACCGATAA
Found at i:23060 original size:49 final size:49
Alignment explanation
Indices: 22984--23078 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
22974 TAAACTCCTA
* **
22984 CAGGGGCGGACCTCTATGGAGCCCGGGGTATCCCGGGCAACCCCTCATC
1 CAGGGGCGGACCTCTATAGAGCCCGGGGTATCCCAAGCAACCCCTCATC
* * *
23033 CAGGGGTGGACCTCTATAGTGCTCGGGGTATCCCAAGCAACCCCTC
1 CAGGGGCGGACCTCTATAGAGCCCGGGGTATCCCAAGCAACCCCTC
23079 CACAAGTGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.17
Consensus pattern (49 bp):
CAGGGGCGGACCTCTATAGAGCCCGGGGTATCCCAAGCAACCCCTCATC
Found at i:35478 original size:26 final size:24
Alignment explanation
Indices: 35416--35478 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
35406 CATTTTAATC
35416 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
35440 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
35463 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
35479 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:35480 original size:22 final size:23
Alignment explanation
Indices: 35450--35496 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
35440 AAAATATATT
35450 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
35473 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
35495 TA
1 TA
35497 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:35510 original size:32 final size:32
Alignment explanation
Indices: 35444--35523 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
35434 ATATTTAAAA
* *
35444 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
35476 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
35508 TATATTATAATAATAT
1 TATATT-TATTAATAT
35524 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:35610 original size:27 final size:26
Alignment explanation
Indices: 35576--35640 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
35566 AATAAATTTT
* *
35576 ATATTATTTATTAAT-TTCATAGAAATA
1 ATATTATTTATTAATAATAAT-G-AATA
*
35603 ATATTATTAAATTAATAATAATGAATA
1 ATATTATT-TATTAATAATAATGAATA
35630 ATATTATTTAT
1 ATATTATTTAT
35641 ATATTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.06
27 20 0.62
28 7 0.22
29 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (26 bp):
ATATTATTTATTAATAATAATGAATA
Found at i:35696 original size:23 final size:23
Alignment explanation
Indices: 35676--35720 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35666 AATAATATTT
35676 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
35699 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
35721 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:38057 original size:49 final size:49
Alignment explanation
Indices: 37998--38164 Score: 126
Period size: 49 Copynumber: 3.2 Consensus size: 49
37988 TTAATTTTAT
*
37998 AAATTTTATTTTTTAATATAATTCTTTTAAAATTCCTATTTTTAACATG
1 AAATTATATTTTTTAATATAATTCTTTTAAAATTCCTATTTTTAACATG
* * * * *
38047 AAATTATATTTACATCT-ATAT-TTTATTTCTAATTTAA-TGCTACGTTTTTAA-ATTTT
1 AAATTATATTT---TTTAATATAATTCTTT-TAA---AATTCCTA--TTTTTAACA--TG
*
38103 ATATATTTTATTTTTTAATATAATTCTTTTAAAATTCCTATTTTTAACATG
1 A-A-ATTATATTTTTTAATATAATTCTTTTAAAATTCCTATTTTTAACATG
38154 AAATTATATTT
1 AAATTATATTT
38165 ACATCCCTAT
Statistics
Matches: 88, Mismatches: 13, Indels: 34
0.65 0.10 0.25
Matches are distributed among these distances:
49 18 0.20
50 6 0.07
51 9 0.10
52 9 0.10
53 7 0.08
54 7 0.08
55 9 0.10
56 9 0.10
57 6 0.07
58 8 0.09
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (49 bp):
AAATTATATTTTTTAATATAATTCTTTTAAAATTCCTATTTTTAACATG
Found at i:38095 original size:106 final size:107
Alignment explanation
Indices: 37960--38169 Score: 404
Period size: 107 Copynumber: 2.0 Consensus size: 107
37950 AATAAATATA
37960 ATTTTATTTCTAATTTAATGCTACGTTTTT-AATTTTATAAATTTTATTTTTTAATATAATTCTT
1 ATTTTATTTCTAATTTAATGCTACGTTTTTAAATTTTATAAATTTTATTTTTTAATATAATTCTT
38024 TTAAAATTCCTATTTTTAACATGAAATTATATTTACATCTAT
66 TTAAAATTCCTATTTTTAACATGAAATTATATTTACATCTAT
*
38066 ATTTTATTTCTAATTTAATGCTACGTTTTTAAATTTTATATATTTTATTTTTTAATATAATTCTT
1 ATTTTATTTCTAATTTAATGCTACGTTTTTAAATTTTATAAATTTTATTTTTTAATATAATTCTT
38131 TTAAAATTCCTATTTTTAACATGAAATTATATTTACATC
66 TTAAAATTCCTATTTTTAACATGAAATTATATTTACATC
38170 CCTATTTATA
Statistics
Matches: 102, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 30 0.29
107 72 0.71
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.56
Consensus pattern (107 bp):
ATTTTATTTCTAATTTAATGCTACGTTTTTAAATTTTATAAATTTTATTTTTTAATATAATTCTT
TTAAAATTCCTATTTTTAACATGAAATTATATTTACATCTAT
Found at i:38678 original size:25 final size:27
Alignment explanation
Indices: 38634--38683 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
38624 AAAATCGATA
*
38634 TATATATATATTAATGATATAAAATTT
1 TATATATATATAAATGATATAAAATTT
*
38661 TATATATA-ATAAAT-ATATTAAAT
1 TATATATATATAAATGATATAAAAT
38684 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 5 0.24
27 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TATATATATATAAATGATATAAAATTT
Found at i:42090 original size:30 final size:30
Alignment explanation
Indices: 42055--42126 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
42045 TATTTAAAAT
* *
42055 ATCATTTTTTAACGTATGATAATATTTTCG
1 ATCATTTTTTAACGTATAATAATATTTTCA
* *
42085 GTCATTTTTTAACGTCTAATAATATTTTCA
1 ATCATTTTTTAACGTATAATAATATTTTCA
42115 ATCATTTTTTAA
1 ATCATTTTTTAA
42127 AAATTTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (30 bp):
ATCATTTTTTAACGTATAATAATATTTTCA
Found at i:55827 original size:20 final size:21
Alignment explanation
Indices: 55784--55827 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55774 AAAAAAAAAA
* *
55784 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATCAATATTT
55805 TTACCTAAAACATCAAT-TTT
1 TTACCTAAAACATCAATATTT
55825 TTA
1 TTA
55828 ACATATCCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (21 bp):
TTACCTAAAACATCAATATTT
Found at i:61590 original size:3 final size:3
Alignment explanation
Indices: 61582--61606 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
61572 TAAAAATATA
61582 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
61607 GCTTGCTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:61945 original size:16 final size:16
Alignment explanation
Indices: 61920--61966 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
61910 ATTCATACAG
*
61920 AGCATATGAATCATTC
1 AGCATTTGAATCATTC
*
61936 AGCATTTGAATTATTC
1 AGCATTTGAATCATTC
*
61952 AGCGTTT-AATCATTC
1 AGCATTTGAATCATTC
61967 TGAAGTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (16 bp):
AGCATTTGAATCATTC
Found at i:75052 original size:20 final size:20
Alignment explanation
Indices: 75027--75086 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
75017 CAGATTGCCT
75027 AGGGGGTACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
* *
75047 AGGGGGAACAGATTTTCCCCC
1 AGGGGGTACAGA-TTCCCCCC
* *
75068 ATGGGGTACCGATTCCCCC
1 AGGGGGTACAGATTCCCCC
75087 TGTCTAACGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.18
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:78173 original size:20 final size:20
Alignment explanation
Indices: 78148--78186 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
78138 ATCAGATTGC
*
78148 CCAGGGGGTACAGATTCCCA
1 CCAGGGGGAACAGATTCCCA
78168 CCAGGGGGAACAGATTCCC
1 CCAGGGGGAACAGATTCCC
78187 CCTCAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.31, G:0.31, T:0.13
Consensus pattern (20 bp):
CCAGGGGGAACAGATTCCCA
Found at i:79360 original size:19 final size:20
Alignment explanation
Indices: 79317--79363 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
79307 TACTTTTCTG
* *
79317 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
79337 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
79356 GAAATTGA
1 GAAATTGA
79364 GCCATTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:80897 original size:19 final size:19
Alignment explanation
Indices: 80861--80930 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
80851 CATTGGGTAC
*
80861 GAATTTGAAAATTAAGTTAT
1 GAATCTGAAAA-TAAGTTAT
*
80881 GAATCTGAAAGTAAGTTAT
1 GAATCTGAAAATAAGTTAT
* *
80900 GAATCTGAAAAAAAGTTCT
1 GAATCTGAAAATAAGTTAT
*
80919 GAATCAGAAAAT
1 GAATCTGAAAAT
80931 GAATTATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 34 0.79
20 9 0.21
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (19 bp):
GAATCTGAAAATAAGTTAT
Found at i:93932 original size:3 final size:3
Alignment explanation
Indices: 93917--93948 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
93907 TTTATGAAAT
*
93917 TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
93949 GGGTAAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:94419 original size:60 final size:60
Alignment explanation
Indices: 94293--94420 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
94283 AATAGTCGTT
* * * ** *
94293 GAGATCATTTTGTAACTTTTAATAGTCGATGGACTTAATAAAACAATATTCTATAGTCGA
1 GAGATCATTTTATAACTTTTAATAATAGAAAGACTTAATAAAACAATATTCTATAATCGA
* * * *
94353 -ACGATCATTTTATAACTTTTAATAATATAAATACTTAATAAAATAGTA-TCTTATAATCGA
1 GA-GATCATTTTATAACTTTTAATAATAGAAAGACTTAATAAAACAATATTC-TATAATCGA
94413 GAGATCAT
1 GAGATCAT
94421 ATATGTACTT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
59 3 0.05
60 51 0.93
61 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (60 bp):
GAGATCATTTTATAACTTTTAATAATAGAAAGACTTAATAAAACAATATTCTATAATCGA
Found at i:95517 original size:27 final size:27
Alignment explanation
Indices: 95487--95581 Score: 145
Period size: 27 Copynumber: 3.5 Consensus size: 27
95477 TACTTGGCGG
95487 CTGCTTCTTGGCCTGGGGTGGCTGCTT
1 CTGCTTCTTGGCCTGGGGTGGCTGCTT
* * *
95514 CTGCTCCTTGGCCTGGGGAGGCTGTTT
1 CTGCTTCTTGGCCTGGGGTGGCTGCTT
* *
95541 CTGCTTCTTGGCCTGGGGTGGCGGCTG
1 CTGCTTCTTGGCCTGGGGTGGCTGCTT
95568 CTGCTTCTTGGCCT
1 CTGCTTCTTGGCCT
95582 TGGATGGCGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.01, C:0.27, G:0.37, T:0.35
Consensus pattern (27 bp):
CTGCTTCTTGGCCTGGGGTGGCTGCTT
Found at i:95589 original size:27 final size:27
Alignment explanation
Indices: 95486--95591 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
95476 CTACTTGGCG
* *
95486 GCTGCTTCTTGGCCTGGGGTGGCTGCT
1 GCTGCTTCTTGGCCTGGGATGGCGGCT
* * * *
95513 TCTGCTCCTTGGCCTGGGGA-GGCTGTT
1 GCTGCTTCTTGGCCT-GGGATGGCGGCT
* *
95540 TCTGCTTCTTGGCCTGGGGTGGCGGCT
1 GCTGCTTCTTGGCCTGGGATGGCGGCT
*
95567 GCTGCTTCTTGGCCTTGGATGGCGG
1 GCTGCTTCTTGGCCTGGGATGGCGG
95592 ACGTTCGTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 3 0.05
27 60 0.91
28 3 0.05
ACGTcount: A:0.02, C:0.25, G:0.40, T:0.33
Consensus pattern (27 bp):
GCTGCTTCTTGGCCTGGGATGGCGGCT
Found at i:96357 original size:69 final size:69
Alignment explanation
Indices: 96267--96405 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
96257 ACAACATCTG
*
96267 CAGCTTTACTAGATCTACAGGTAGCTTTTCTTGCTCCTGCTTCCCTTTAGGGTTTTCTGATTCTC
1 CAGCTTTACTAGATCTACAGGTAGCTTTTCTTGCTCCTGCTGCCCTTTAGGGTTTTCTGATTCTC
96332 CATC
66 CATC
* * *
96336 CAGCTTTACTGGATCTTCAGGTAGCTTTTCTTGCTCCTGCTGCCCTTTAGGGTTTTTTGATTCTC
1 CAGCTTTACTAGATCTACAGGTAGCTTTTCTTGCTCCTGCTGCCCTTTAGGGTTTTCTGATTCTC
96401 CATC
66 CATC
96405 C
1 C
96406 TCTTCATCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.13, C:0.27, G:0.17, T:0.42
Consensus pattern (69 bp):
CAGCTTTACTAGATCTACAGGTAGCTTTTCTTGCTCCTGCTGCCCTTTAGGGTTTTCTGATTCTC
CATC
Found at i:96833 original size:15 final size:15
Alignment explanation
Indices: 96815--96844 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
96805 AGCCTCTTAC
96815 CTTCAAGGCTCTCAT
1 CTTCAAGGCTCTCAT
*
96830 CTTCAAGGCTTTCAT
1 CTTCAAGGCTCTCAT
96845 ATTTTTCCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (15 bp):
CTTCAAGGCTCTCAT
Found at i:101096 original size:45 final size:44
Alignment explanation
Indices: 101039--101146 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 44
101029 AGAACCCGAA
101039 GAAGAGATCCGTGAAGAA-CT-CGATTTAGGTGAGACCCAAACCCAG
1 GAAGAGATCCGTGAAGAACCTGCGA---AGGTGAGACCCAAACCCAG
101084 GAAGAGATCCGTGAAGAACCTGGCGAAGGTGAGACCCAAACCCAG
1 GAAGAGATCCGTGAAGAACCT-GCGAAGGTGAGACCCAAACCCAG
* * *
101129 GGAGAGATCAGAGAAGAA
1 GAAGAGATCCGTGAAGAA
101147 GCCAGTGAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
45 52 0.91
46 2 0.04
48 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.31, T:0.11
Consensus pattern (44 bp):
GAAGAGATCCGTGAAGAACCTGCGAAGGTGAGACCCAAACCCAG
Found at i:105381 original size:26 final size:26
Alignment explanation
Indices: 105352--105402 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
105342 AAAAAAAAAA
*
105352 AACAAGGGTTTCAATGACTATTTAAG
1 AACAAGAGTTTCAATGACTATTTAAG
*
105378 AACAAGAGTTTCAATGACTCTTTAA
1 AACAAGAGTTTCAATGACTATTTAA
105403 TTAAATGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (26 bp):
AACAAGAGTTTCAATGACTATTTAAG
Found at i:106340 original size:24 final size:25
Alignment explanation
Indices: 106306--106353 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
106296 AAACTAAGAT
* *
106306 TTTTTTATAAATATAATATTTTTTA
1 TTTTTTATAAAAAAAATATTTTTTA
106331 TTTTTT-TAAAAAAAATATTTTTT
1 TTTTTTATAAAAAAAATATTTTTT
106354 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTTTATAAAAAAAATATTTTTTA
Found at i:106351 original size:17 final size:17
Alignment explanation
Indices: 106329--106365 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
106319 TAATATTTTT
106329 TATTTTTTTAAAAAAAA
1 TATTTTTTTAAAAAAAA
**
106346 TATTTTTTTTTAAAAAA
1 TATTTTTTTAAAAAAAA
106363 TAT
1 TAT
106366 CAGAACATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTTTTTAAAAAAAA
Found at i:111620 original size:64 final size:65
Alignment explanation
Indices: 111522--111647 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 65
111512 AATGCAGTTT
* * * * * *
111522 ATGCATTGATGCACTCAGGTTTTAATGAAAACATCGATTGCATTTTATGCATCGATGTACACACC
1 ATGCATCGATGCACTCAGGTCTTAATAAAAACATCGAATGCATTTTATGAATCGATGCACACACC
* *
111587 ATGCATCGATGCACTTAGG-CTTATTAAAAACATCGAATGCATTTTATGAATCGATGCACAC
1 ATGCATCGATGCACTCAGGTCTTAATAAAAACATCGAATGCATTTTATGAATCGATGCACAC
111648 TTAGTGCACC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
64 36 0.68
65 17 0.32
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (65 bp):
ATGCATCGATGCACTCAGGTCTTAATAAAAACATCGAATGCATTTTATGAATCGATGCACACACC
Found at i:119817 original size:15 final size:15
Alignment explanation
Indices: 119797--119827 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
119787 CATAGTATGG
*
119797 TGGAGTAAGTAGTTT
1 TGGAGTAAGTAATTT
119812 TGGAGTAAGTAATTT
1 TGGAGTAAGTAATTT
119827 T
1 T
119828 CAACTTTTCA
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:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (15 bp):
TGGAGTAAGTAATTT
Found at i:120241 original size:19 final size:19
Alignment explanation
Indices: 120217--120287 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
120207 AATGCAATTT
120217 ATGCATCGATGCACCCTCC
1 ATGCATCGATGCACCCTCC
120236 ATGCATCGATGCACCCTCC
1 ATGCATCGATGCACCCTCC
120255 ATGCATCGATGCACCCTCC
1 ATGCATCGATGCACCCTCC
120274 ATGCATCGATGCAC
1 ATGCATCGATGCAC
120288 TCAGGTTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACCCTCC
Found at i:120392 original size:64 final size:65
Alignment explanation
Indices: 120255--120399 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 65
120245 TGCACCCTCC
* * * * * * *
120255 ATGCATCGATGCACCCTCCATGCATCGATGCACTCAGGTTTTAATGAAAACATCGATTGCATTTT
1 ATGCATCGATGCACACACCATGAATCGATGCAATCAGGTCTTAATAAAAACATCGAATGCATTTT
* * *
120320 ATGTATCGATGCACACACCATGAATCGATGCAATTAGG-CTTATTAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACACACCATGAATCGATGCAATCAGGTCTTAATAAAAACATCGAATGCATTTT
120384 ATGCATCGATGCACAC
1 ATGCATCGATGCACAC
120400 TTAGTGCACC
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 37 0.54
65 32 0.46
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (65 bp):
ATGCATCGATGCACACACCATGAATCGATGCAATCAGGTCTTAATAAAAACATCGAATGCATTTT
Found at i:127626 original size:27 final size:28
Alignment explanation
Indices: 127588--127643 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
127578 CCATTCAAAC
127588 AGCCATTGACAAGAGAAAG-GAAAAAAT
1 AGCCATTGACAAGAGAAAGAGAAAAAAT
*
127615 AGCCATTGACAAGGGAAAGAGAAAAAAT
1 AGCCATTGACAAGAGAAAGAGAAAAAAT
127643 A
1 A
127644 TTCAAAAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (28 bp):
AGCCATTGACAAGAGAAAGAGAAAAAAT
Found at i:141287 original size:14 final size:15
Alignment explanation
Indices: 141256--141287 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
141246 TTTTTTAAAG
*
141256 TTTGATAAATATTTT
1 TTTGAAAAATATTTT
141271 TTTGAAAAATATTTT
1 TTTGAAAAATATTTT
141286 TT
1 TT
141288 AAAGTTTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTGAAAAATATTTT
Found at i:141293 original size:36 final size:36
Alignment explanation
Indices: 141234--141305 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
141224 GGCAACCAAC
141234 TTTGAAAAATATTTTTTTAAAGTTTGATAAATATTTT
1 TTTGAAAAATATTTTTTTAAAGTTTGATAAA-ATTTT
*
141271 TTTGAAAAATA-TTTTTTAAAGTTTGGTAAAATTTT
1 TTTGAAAAATATTTTTTTAAAGTTTGATAAAATTTT
141306 AGTAGATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 5 0.15
36 18 0.53
37 11 0.32
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (36 bp):
TTTGAAAAATATTTTTTTAAAGTTTGATAAAATTTT
Found at i:141753 original size:15 final size:16
Alignment explanation
Indices: 141733--141765 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
141723 TTACTATTCA
141733 CGTGAATAGTG-AATT
1 CGTGAATAGTGAAATT
141748 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
141764 CG
1 CG
141766 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:160338 original size:21 final size:21
Alignment explanation
Indices: 160287--160339 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
160277 ATTATGACTA
*
160287 TCGCAATGTGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
160308 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
160329 TCGCAATGCGA
1 TCGCAATGCGA
160340 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:160403 original size:21 final size:21
Alignment explanation
Indices: 160369--160441 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
160359 ATACTGACTA
* *
160369 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
160390 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
160410 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
160431 TCGCAATGCGA
1 TCGCAATGCGA
160442 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:160459 original size:21 final size:21
Alignment explanation
Indices: 160431--160484 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
160421 TTTTCATAAT
*
160431 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
160452 TCGTAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
160472 TCGCAATGCGAAT
1 TCGCAATGCGAAT
160485 CTTACTATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:161097 original size:19 final size:19
Alignment explanation
Indices: 161058--161098 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
161048 GCAACGAGAG
*
161058 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
* *
161077 AATCGTAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
161096 AAT
1 AAT
161099 TGCATTGCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:161125 original size:19 final size:19
Alignment explanation
Indices: 161103--161243 Score: 140
Period size: 19 Copynumber: 7.8 Consensus size: 19
161093 CAAAATTGCA
161103 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
161122 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
161136 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
161155 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
161174 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
161188 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
161208 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
161228 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
161244 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
14 20 0.20
16 5 0.05
17 6 0.06
19 38 0.38
20 31 0.31
21 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:161181 original size:52 final size:53
Alignment explanation
Indices: 161103--161235 Score: 214
Period size: 52 Copynumber: 2.5 Consensus size: 53
161093 CAAAATTGCA
**
161103 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
161155 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
* *
161208 TTGCGATTCTCATTATCTCGTTGCGATT
1 TTGCGATTTTCATT-TCGCGTTGCGATT
161236 TTCATTTCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 46 0.61
53 17 0.23
54 12 0.16
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCG
Found at i:161190 original size:33 final size:34
Alignment explanation
Indices: 161153--161218 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
161143 TTTCATTTCG
**
161153 CGTTGCGATTTTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
161186 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
161219 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:163411 original size:21 final size:21
Alignment explanation
Indices: 163387--163456 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
163377 TCATTCCTCG
163387 AGAGTCCCCTCCCATCATTCA
1 AGAGTCCCCTCCCATCATTCA
* * ** * *
163408 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCATCATTCA
*
163429 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCATCATTCA
163450 AGA-TCCC
1 AGAGTCCC
163457 GATTCACATG
Statistics
Matches: 34, Mismatches: 13, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 30 0.88
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCATCATTCA
Found at i:163411 original size:42 final size:42
Alignment explanation
Indices: 163335--163452 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
163325 GACTCGCCTG
* * *
163335 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
* * * * *
163377 TCATTCCTCGAGAGTCCCCTCCCATCATTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
** * *
163419 TCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGA
1 TCATCCCTCAAGA-GTCCACTCCCATCATTCAAGA
163453 TCCCGATTCA
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 57 0.93
43 4 0.07
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
Found at i:164829 original size:14 final size:14
Alignment explanation
Indices: 164810--164845 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
164800 ATTGTTTAAT
164810 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
164824 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
164838 TGATTTGT
1 TGATTTGT
164846 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:165018 original size:19 final size:19
Alignment explanation
Indices: 164986--165050 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
164976 AACGAGAAAA
*
164986 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
165005 TTCGCATTGTGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
165021 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
165038 TTCGCATTGCGAT
1 TTCGCATTGCGAT
165051 AGTAATTTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 5 0.14
16 7 0.19
17 7 0.19
19 17 0.47
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:167363 original size:12 final size:12
Alignment explanation
Indices: 167346--167372 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
167336 CGGGGACTTT
167346 TTCTTTTTCTTC
1 TTCTTTTTCTTC
167358 TTCTTTTTCTTC
1 TTCTTTTTCTTC
167370 TTC
1 TTC
167373 AGGATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:167581 original size:24 final size:24
Alignment explanation
Indices: 167547--167600 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
167537 CTAAAACATC
*
167547 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
167571 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
167595 ATCAAA
1 ATCAAA
167601 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:168439 original size:20 final size:20
Alignment explanation
Indices: 168406--168484 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
168396 GAATAAGTAA
* *
168406 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
168426 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
168447 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
168467 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
168485 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:168491 original size:20 final size:20
Alignment explanation
Indices: 168444--168493 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
168434 GAGATAATAC
168444 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
168464 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
168484 AAAATCGCAA
1 AAAATCGCAA
168494 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:168762 original size:20 final size:20
Alignment explanation
Indices: 168707--168753 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
168697 CAACGGGGAA
168707 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
168727 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
168747 ATCGCAA
1 ATCGCAA
168754 TGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:170846 original size:20 final size:20
Alignment explanation
Indices: 170823--170876 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
170813 GAAACTTAAA
*
170823 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
170843 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
170863 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
170877 TGCAAATCGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:170885 original size:19 final size:16
Alignment explanation
Indices: 170863--170974 Score: 76
Period size: 19 Copynumber: 6.9 Consensus size: 16
170853 GGAAATGGCT
170863 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAA---AA
170882 ATCGCAA--C-AAAAA
1 ATCGCAATGCGAAAAA
170895 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAA---AA
*
170914 ATCGCAA--CGACAAA
1 ATCGCAATGCGAAAAA
170928 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCG-AA--AAA
*
170947 ATCGCAA--CGACAAA
1 ATCGCAATGCGAAAAA
170961 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
170975 CACAAATCGC
Statistics
Matches: 76, Mismatches: 4, Indels: 29
0.70 0.04 0.27
Matches are distributed among these distances:
13 9 0.12
14 19 0.25
15 1 0.01
16 13 0.17
17 8 0.11
19 26 0.34
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.12
Consensus pattern (16 bp):
ATCGCAATGCGAAAAA
Found at i:170931 original size:14 final size:14
Alignment explanation
Indices: 170912--170967 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
170902 TGCGAAATGC
170912 AAATCGCAACGACA
1 AAATCGCAACGACA
*
170926 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
170945 AAATCGCAACGACA
1 AAATCGCAACGACA
170959 AAATCGCAA
1 AAATCGCAA
170968 TGCGAAACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:170934 original size:33 final size:33
Alignment explanation
Indices: 170863--170985 Score: 203
Period size: 33 Copynumber: 3.8 Consensus size: 33
170853 GGAAATGGCT
*
170863 ATCGCAATGCGAAATGCAAATCGCAAC-AAAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
170895 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
*
170928 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
**
170961 ATCGCAATGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
170986 TTGCGACTTT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
32 27 0.32
33 58 0.68
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:170983 original size:19 final size:18
Alignment explanation
Indices: 170892--170991 Score: 83
Period size: 19 Copynumber: 5.8 Consensus size: 18
170882 ATCGCAACAA
170892 AAAATCGCAATGCGAAATGC
1 AAAATCGCAATGCGAAA--C
170912 -AAATCGCAA--CG--AC
1 AAAATCGCAATGCGAAAC
*
170925 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAA-C
170944 AAAATCGCAA--CG--AC
1 AAAATCGCAATGCGAAAC
170958 AAAATCGCAATGCGAAAC
1 AAAATCGCAATGCGAAAC
*
170976 ACAAATCGCATTGCGA
1 A-AAATCGCAATGCGA
170992 CTTTCATTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 23
0.72 0.03 0.25
Matches are distributed among these distances:
13 1 0.02
14 19 0.29
15 2 0.03
16 4 0.06
17 4 0.06
18 4 0.06
19 32 0.48
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (18 bp):
AAAATCGCAATGCGAAAC
Found at i:171003 original size:19 final size:18
Alignment explanation
Indices: 170981--171044 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
170971 GAAACACAAA
170981 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
171000 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
171016 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
171033 TCGCATTGCGAT
1 TCGCATTGCGAT
171045 AGCTATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 4 0.11
19 17 0.45
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:171072 original size:20 final size:19
Alignment explanation
Indices: 171028--171072 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
171018 GTTGCGATTT
171028 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
*
171047 -CTATTTCCGCTTTGCGATAG
1 TC-ATTT-CGCATTGCGATAG
171067 TCATTT
1 TCATTT
171073 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 1 0.05
19 4 0.18
20 16 0.73
21 1 0.05
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:171585 original size:18 final size:18
Alignment explanation
Indices: 171559--171603 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
171549 GTCGATCAGA
**
171559 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGACGAGG
*
171577 TGATAGCTCTGGACGAGG
1 TGATGGCTCTGGACGAGG
171595 TGATGGCTC
1 TGATGGCTC
171604 CCGAAGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:172971 original size:20 final size:20
Alignment explanation
Indices: 172923--172981 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
172913 AATAGTTTCT
**
172923 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
172943 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
172963 GAATTTGACTATCGCAACA
1 GAAAATGACTATCGCAACA
172982 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:173286 original size:20 final size:21
Alignment explanation
Indices: 173261--173312 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
173251 TTTTCCCAAT
*
173261 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
173281 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
173302 TCGCAATGCGA
1 TCGCAATGCGA
173313 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:173326 original size:20 final size:20
Alignment explanation
Indices: 173301--173415 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
173291 AATTGGGAAA
*
173301 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
173321 ATCGCAATGAGATACTTATT
1 ATCGCAACGCGATACTGACT
* * *
173341 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
173362 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
173382 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
173402 TTCGCAACGCGATA
1 ATCGCAACGCGATA
173416 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.01
20 61 0.79
21 13 0.17
22 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:173407 original size:61 final size:61
Alignment explanation
Indices: 173298--173429 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 61
173288 GCGAATTGGG
* * * * *
173298 AAAATCGCAATGCGATACTGACTATCGCAATGAGATACTTATTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGATTATCGCAACGCGATAATAC
* * *
173359 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTT-TCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGA-TTATCGCAACGCGATAATAC
*
173420 ATAATCGCAA
1 AAAATCGCAA
173430 TGCAATTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGAGATACTGATTATCGCAACGCGATAATAC
Found at i:174188 original size:18 final size:18
Alignment explanation
Indices: 174165--174200 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
174155 TTATTACTTA
*
174165 CAAAATCTATCAAAATGG
1 CAAAATATATCAAAATGG
174183 CAAAATATATCAAAATGG
1 CAAAATATATCAAAATGG
174201 TCATAATTTT
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:0.53, C:0.14, G:0.11, T:0.22
Consensus pattern (18 bp):
CAAAATATATCAAAATGG
Found at i:184600 original size:74 final size:74
Alignment explanation
Indices: 184519--184699 Score: 231
Period size: 74 Copynumber: 2.4 Consensus size: 74
184509 GTTAAATGAC
* *
184519 TAGGGGTATCAGTACCTCTAAG-GGGGTATC-AGTACCCATTGGGCATTCTATTTTTCTAGGAGC
1 TAGGGGTATCGGTACC-CTAAGAGGGGTATCGA-TACCCATTGGGCATTATATTTTTCTAGGAGC
*
184582 TAAAATTGGCA
64 CAAAATTGGCA
* * * *
184593 TAGGGGTATCGGTACCCTATGAGGGGTATCGATACCCATTTGGCATTATGTTTTTCTCGGAGCCA
1 TAGGGGTATCGGTACCCTAAGAGGGGTATCGATACCCATTGGGCATTATATTTTTCTAGGAGCCA
184658 AAATTGGCA
66 AAATTGGCA
* *
184667 TAGGGGTATCGGTACACCCTATGAGGAGTATCG
1 TAGGGGTATCGGT--ACCCTAAGAGGGGTATCG
184700 GTACATCCCT
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
73 4 0.04
74 73 0.77
75 1 0.01
76 17 0.18
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (74 bp):
TAGGGGTATCGGTACCCTAAGAGGGGTATCGATACCCATTGGGCATTATATTTTTCTAGGAGCCA
AAATTGGCA
Found at i:187311 original size:28 final size:27
Alignment explanation
Indices: 187258--187312 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
187248 ACGACACGAG
* ** *
187258 TGAAATTTTGGGGATTTTTCGGCTAAA
1 TGAAATTTTAGGGATTTTAAGCCTAAA
187285 TGAAGATTTTAGGGATTTTAAGCCTAAA
1 TGAA-ATTTTAGGGATTTTAAGCCTAAA
187313 ACCGACAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (27 bp):
TGAAATTTTAGGGATTTTAAGCCTAAA
Found at i:187394 original size:21 final size:20
Alignment explanation
Indices: 187322--187397 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
187312 AACCGACAGG
* * *
187322 GGGTATCGGTACCCATCGAA
1 GGGTATCGATACACATTGAA
* *
187342 GGGTATCAATACACATTCAAAGA
1 GGGTATCGATACACATT--GA-A
187365 GGGTATCGATACACATTGAA
1 GGGTATCGATACACATTGAA
187385 GGGTTATCGATAC
1 GGG-TATCGATAC
187398 CTGGTGCACA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.38
21 10 0.22
22 1 0.02
23 17 0.38
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACACATTGAA
Found at i:192840 original size:54 final size:55
Alignment explanation
Indices: 192746--192858 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 55
192736 GGGGGCATCG
*
192746 GTACCCATTGGGCATTCTGTTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
1 GTACCCATTGGACATTCTGTTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
* *
192801 GTACCCATTTGACATTCTG-TTTTTCTCGGAGCCAAAATTGGCATAGGGGTATCA
1 GTACCCATTGGACATTCTGTTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
192855 GTAC
1 GTAC
192859 ACCCTATGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 38 0.69
55 17 0.31
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (55 bp):
GTACCCATTGGACATTCTGTTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCA
Found at i:193150 original size:12 final size:12
Alignment explanation
Indices: 193133--193164 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
193123 CAACAATAAT
*
193133 CACCACCATGAC
1 CACCACCATCAC
193145 CACCACCATCAC
1 CACCACCATCAC
193157 CACCACCA
1 CACCACCA
193165 CCACTTGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.56, G:0.03, T:0.06
Consensus pattern (12 bp):
CACCACCATCAC
Found at i:194094 original size:30 final size:29
Alignment explanation
Indices: 194055--194115 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
194045 GAGTTTAAGT
* *
194055 ATGACTCTCGTTAATTGTTTAACAAATTTC
1 ATGAATCTCGTTAATTGTATAAC-AATTTC
194085 ATGAATCTCGTTAATTGTATAACAATTTC
1 ATGAATCTCGTTAATTGTATAACAATTTC
194114 AT
1 AT
194116 CAAGTGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
ATGAATCTCGTTAATTGTATAACAATTTC
Done.