Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004380.1 Hibiscus syriacus cultivar Beakdansim tig00009606_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: 132417
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:321 original size:14 final size:15
Alignment explanation
Indices: 295--323 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
285 TAATAATAAC
295 GAACATAAACGAACA
1 GAACATAAACGAACA
310 GAACAT-AACGAACA
1 GAACATAAACGAACA
324 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.21, G:0.14, T:0.07
Consensus pattern (15 bp):
GAACATAAACGAACA
Found at i:419 original size:16 final size:16
Alignment explanation
Indices: 398--452 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
388 ATAAACAAAT
398 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
414 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
430 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
446 ATAAACG
1 ATAAACG
453 TCGGAGACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:1547 original size:24 final size:24
Alignment explanation
Indices: 1524--1609 Score: 145
Period size: 24 Copynumber: 3.6 Consensus size: 24
1514 ATAAATGAAT
*
1524 GAACATAAGCGAACATAACCGAAT
1 GAACATAAGCGAACATAACCGAAC
1548 GAACATAAGCGAACATAACCGAAC
1 GAACATAAGCGAACATAACCGAAC
*
1572 GAACATAAACGAACATAACCGAAC
1 GAACATAAGCGAACATAACCGAAC
*
1596 GAACATAACCGAAC
1 GAACATAAGCGAAC
1610 GTTCACGAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.09
Consensus pattern (24 bp):
GAACATAAGCGAACATAACCGAAC
Found at i:1553 original size:14 final size:14
Alignment explanation
Indices: 1533--1610 Score: 91
Period size: 14 Copynumber: 6.1 Consensus size: 14
1523 TGAACATAAG
1533 CGAACATAACCGAA
1 CGAACATAACCGAA
*
1547 TGAACATAA--G--
1 CGAACATAACCGAA
1557 CGAACATAACCGAA
1 CGAACATAACCGAA
1571 CGAACAT-A---AA
1 CGAACATAACCGAA
1581 CGAACATAACCGAA
1 CGAACATAACCGAA
1595 CGAACATAACCGAA
1 CGAACATAACCGAA
1609 CG
1 CG
1611 TTCACGAACG
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
10 17 0.31
11 1 0.02
12 2 0.04
13 1 0.02
14 33 0.61
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:2671 original size:16 final size:16
Alignment explanation
Indices: 2650--2690 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2640 TCAGAGCCTC
*
2650 TGAATCATTCAACATT
1 TGAATCATTCAACAGT
*
2666 TGAATCATTTAACAGT
1 TGAATCATTCAACAGT
2682 T-AATCATTC
1 TGAATCATTC
2691 TGAAATAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAACAGT
Found at i:5387 original size:154 final size:155
Alignment explanation
Indices: 5031--5942 Score: 1397
Period size: 154 Copynumber: 6.0 Consensus size: 155
5021 ACAATAAAAG
* *
5031 CATTCATTAGCTACTCTACAAACCGATATTACGTTTCAAGTCGAAAAAACATACTAGGATCGCCA
1 CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGAAAAAACATACTAGAATCGCCA
* * **
5096 AGGAGCCTGCTAAAGAGACCTAACCAAGAAAACCAGGACCCCCATGGTCTTAGTAAAACATGAAA
66 AGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATGAAA
*
5161 ATATGATCATTGGGTCCACAATCAT
131 ATATGATCATTGGGGCCACAATCAT
*
5186 CATTCATTAGCAACTCTACAAATCGATATTACGTTTCAAGTCGAAAAAACATACTAGAATCGCCA
1 CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGAAAAAACATACTAGAATCGCCA
*
5251 AGGAGCCAG-TAAAGAGACCTAACCAAGAACACCAGGACCTCCATGGTCAGAGTAAAACATGAAA
66 AGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATGAAA
5315 ATATGATCA-TGGGGCCACAATCAT
131 ATATGATCATTGGGGCCACAATCAT
* * *
5339 CATTCATTAGCAACTCTACGAATCGATATTAAGTTTCAAGTCGAAAAAACATACTAGAATCGCCA
1 CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGAAAAAACATACTAGAATCGCCA
* *
5404 AGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGA-CCCCATGGTCAGAGTAATACATGAAG
66 AGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATGAAA
* * *
5468 ATATGATCACTGGGGCGACAAACAT
131 ATATGATCATTGGGGCCACAATCAT
*
5493 CATTCATTCGCAACTCTACAAACCGATATTACGTTTCAAG-CTGAAAAAACATACTAGAATCGCC
1 CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTC-GAAAAAACATACTAGAATCGCC
5557 AAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATGAA
65 AAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATGAA
5622 AATATGATCATT--GG---------T
130 AATATGATCATTGGGGCCACAATCAT
* * * *
5637 CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCCAAAAAACATATTAGCATTGCCA
1 CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGAAAAAACATACTAGAATCGCCA
* *
5702 AGGAGCTAGCTAAAGAGACCTAACCAAGAACACCAGGACCTCCATGGTCAGAGTGAAAA-ATGAA
66 AGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGT-AAAACATGAA
5766 AATATGATCATTGGGGCCACAATCAT
130 AATATGATCATTGGGGCCACAATCAT
* * * *
5792 CATTCATTAGCAACTCTACAAACCGATATTATGTTTCAAGTCGGAAAAACCATACTAGGATAGCC
1 CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTC-GAAAAAACATACTAGAATCG-C
* * *
5857 CAAGGAGCCAGCTAAAGAGAACTAACCAAGAACACCAGGACCCCCATGGTCTGAGTAAAAAATGA
64 CAAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATGA
5922 AAATATGATCATTGGGGCCAC
129 AAATATGATCATTGGGGCCAC
5943 TATCTACAAC
Statistics
Matches: 697, Mismatches: 40, Indels: 38
0.90 0.05 0.05
Matches are distributed among these distances:
144 128 0.18
145 5 0.01
146 2 0.00
153 121 0.17
154 198 0.28
155 146 0.21
156 19 0.03
157 78 0.11
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (155 bp):
CATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGAAAAAACATACTAGAATCGCCA
AGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATGAAA
ATATGATCATTGGGGCCACAATCAT
Found at i:5752 original size:144 final size:145
Alignment explanation
Indices: 5491--5936 Score: 619
Period size: 144 Copynumber: 3.0 Consensus size: 145
5481 GGCGACAAAC
* * *
5491 ATCATTCATTCGCAACTCTACAAACCGATATTACGTTTCAAG-CTGAAAAAACATACTAGAATCG
1 ATCATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGGAAAAAACATACTAGAATAG
5555 CCAAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAACATG
66 CCAAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAA-ATG
5620 AAAATATGATCATTGG
130 AAAATATGATCATTGG
* * * *
5636 -TCATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTC-CAAAAAACATATTAGCATTG
1 ATCATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGGAAAAAACATACTAGAATAG
* *
5699 CCAAGGAGCTAGCTAAAGAGACCTAACCAAGAACACCAGGACCTCCATGGTCAGAGTGAAAAATG
66 CCAAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGT-AAAAATG
5764 AAAATATGATCATTGGGG
130 AAAATATGATCATT--GG
* *
5782 CCACAATCATCATTCATTAGCAACTCTACAAACCGATATTATGTTTCAAGTCGGAAAAACCATAC
1 --------ATCATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGGAAAAAACATAC
* * *
5847 TAGGATAGCCCAAGGAGCCAGCTAAAGAGAACTAACCAAGAACACCAGGACCCCCATGGTCTGAG
58 TAGAATAG-CCAAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAG
5912 TAAAAAATGAAAATATGATCATTGG
122 T-AAAAATGAAAATATGATCATTGG
5937 GGCCACTATC
Statistics
Matches: 268, Mismatches: 18, Indels: 20
0.88 0.06 0.07
Matches are distributed among these distances:
144 128 0.48
145 5 0.02
146 2 0.01
155 44 0.16
156 15 0.06
157 74 0.28
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (145 bp):
ATCATTCATTAGCAACTCTACAAACCGATATTACGTTTCAAGTCGGAAAAAACATACTAGAATAG
CCAAGGAGCCAGCTAAAGAGACCTAACCAAGAACACCAGGACCCCCATGGTCAGAGTAAAAATGA
AAATATGATCATTGG
Found at i:9689 original size:20 final size:20
Alignment explanation
Indices: 9660--9712 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
9650 GCAGCCTTGG
* *
9660 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGAA
9680 TGCATCGATGCACAGCAGAA
1 TGCATCGATGCACAGCAGAA
9700 TGCATCGATGCAC
1 TGCATCGATGCAC
9713 TAAGTGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGAA
Found at i:9785 original size:23 final size:20
Alignment explanation
Indices: 9732--9789 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
9722 TCGAAATGGA
9732 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
9752 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
9775 GTGCATGGATGCACT
1 GTGCATGGATGCACT
9790 TTGACACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.47
23 15 0.47
24 2 0.06
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:9903 original size:30 final size:31
Alignment explanation
Indices: 9869--9929 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
9859 AAACTTTGAA
* *
9869 TAAATTCAATT-AAGTCCAAAAATTATTTTG
1 TAAATTAAATTCAAGTCCAAAAATCATTTTG
*
9899 TAAATTAAATTCAAGTTCAAAAATCATTTTG
1 TAAATTAAATTCAAGTCCAAAAATCATTTTG
9930 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
TAAATTAAATTCAAGTCCAAAAATCATTTTG
Found at i:11687 original size:11 final size:11
Alignment explanation
Indices: 11673--11697 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11663 ATATAAATTA
11673 ATTATAGTAAT
1 ATTATAGTAAT
11684 ATTATAGTAAT
1 ATTATAGTAAT
11695 ATT
1 ATT
11698 CAACTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTATAGTAAT
Found at i:11908 original size:20 final size:20
Alignment explanation
Indices: 11836--11902 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
11826 ACATTCTCAG
*
11836 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCACACTGA
*
11856 TAATCTTTTATTCTCACTGA
1 TAATCTTTTATTCACACTGA
11876 TAATCTTTTATTCACACTGA
1 TAATCTTTTATTCACACTGA
11896 TAATCTT
1 TAATCTT
11903 ACATTCTGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.04, T:0.48
Consensus pattern (20 bp):
TAATCTTTTATTCACACTGA
Found at i:23330 original size:10 final size:10
Alignment explanation
Indices: 23300--23335 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
23290 AAAAAGAATA
23300 TATTTATGTT
1 TATTTATGTT
*
23310 TATTT-TTTT
1 TATTTATGTT
23319 TATTTATGTT
1 TATTTATGTT
23329 TATTTAT
1 TATTTAT
23336 TTATTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (10 bp):
TATTTATGTT
Found at i:23336 original size:14 final size:13
Alignment explanation
Indices: 23308--23342 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
23298 TATATTTATG
*
23308 TTTATTTTTTTTA
1 TTTATTTTATTTA
23321 TTTATGTTTATTTA
1 TTTAT-TTTATTTA
23335 TTTATTTT
1 TTTATTTT
23343 TGAAGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:24104 original size:19 final size:18
Alignment explanation
Indices: 24082--24135 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 18
24072 AAATATTAAA
24082 ATAATTATTATATATATAT
1 ATAA-TATTATATATATAT
24101 ATAATATT-TATATAT-T
1 ATAATATTATATATATAT
*
24117 -TAAT-TTAAATATATAT
1 ATAATATTATATATATAT
24133 ATA
1 ATA
24136 CTCGGCCTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 2 0.06
17 9 0.29
18 4 0.13
19 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAATATTATATATATAT
Found at i:24107 original size:30 final size:32
Alignment explanation
Indices: 24073--24135 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
24063 AAGCCCGATA
*
24073 AATATTAAAATAATT-A-TTATATATATATAT
1 AATATTAAAATAATTAATTTAAATATATATAT
* * *
24103 AATATTTATATATTTAATTTAAATATATATAT
1 AATATTAAAATAATTAATTTAAATATATATAT
24135 A
1 A
24136 CTCGGCCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 12 0.44
31 1 0.04
32 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
AATATTAAAATAATTAATTTAAATATATATAT
Found at i:27960 original size:15 final size:16
Alignment explanation
Indices: 27933--27962 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27923 ATTATTCTAT
27933 TAATATATAATTAAAA
1 TAATATATAATTAAAA
27949 TAATAT-TAATTAAA
1 TAATATATAATTAAA
27963 TTAAAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATATAATTAAAA
Found at i:27966 original size:20 final size:22
Alignment explanation
Indices: 27930--27969 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
27920 ATTATTATTC
27930 TATTAATATATAATTAAAATAA
1 TATTAATATATAATTAAAATAA
27952 TATTAAT-TA-AATTAAAAT
1 TATTAATATATAATTAAAAT
27970 TTCAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTAATATATAATTAAAATAA
Found at i:28370 original size:17 final size:18
Alignment explanation
Indices: 28348--28384 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28338 CATTAGAATA
*
28348 AAATAATA-TATATTTTT
1 AAATAATATTATATTATT
28365 AAATAATATTATATTATT
1 AAATAATATTATATTATT
28383 AA
1 AA
28385 CCAAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATAATATTATATTATT
Found at i:28778 original size:49 final size:49
Alignment explanation
Indices: 28706--28804 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
28696 GCTTCACGAG
* * * *
28706 GACAATCCATTACTTCCTCAAGTATGACTCTGTTCCGACCCGAGATAAA
1 GACAATCCATCACTTCCTAAAGTATGACTCCGTTCCGACCCGAGACAAA
28755 GACAATCCATCACTTCCTAAAGTATGACTCCGTTCCGACCCGAGACAAA
1 GACAATCCATCACTTCCTAAAGTATGACTCCGTTCCGACCCGAGACAAA
28804 G
1 G
28805 TTCTCGGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.23
Consensus pattern (49 bp):
GACAATCCATCACTTCCTAAAGTATGACTCCGTTCCGACCCGAGACAAA
Found at i:31651 original size:19 final size:18
Alignment explanation
Indices: 31627--31667 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
31617 GATATATTTT
31627 TTATTTTT-ATAATAAAATA
1 TTATTTTTAATAA-AAAA-A
31646 TTATTTTTAATAAAAAAA
1 TTATTTTTAATAAAAAAA
31664 TTAT
1 TTAT
31668 AAAAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTTTTAATAAAAAAA
Found at i:33028 original size:15 final size:15
Alignment explanation
Indices: 33004--33045 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
32994 AGATACTATT
*
33004 AATAAAAATAATAAG
1 AATAAGAATAATAAG
*
33019 AATACGAATAATAAG
1 AATAAGAATAATAAG
33034 AATAAGAATAAT
1 AATAAGAATAAT
33046 CGAAAGACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (15 bp):
AATAAGAATAATAAG
Found at i:38238 original size:33 final size:33
Alignment explanation
Indices: 38171--38235 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
38161 ACGTGTTCAG
**
38171 CTTTTAACGGCGGGTACTAAAATAAAACTAAAA
1 CTTTTAACAACGGGTACTAAAATAAAACTAAAA
*
38204 CTTTTAACAACGGGTACTAAAATGAAA-TAAAA
1 CTTTTAACAACGGGTACTAAAATAAAACTAAAA
38236 ACTAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.25
Consensus pattern (33 bp):
CTTTTAACAACGGGTACTAAAATAAAACTAAAA
Found at i:45016 original size:35 final size:35
Alignment explanation
Indices: 44971--45088 Score: 209
Period size: 35 Copynumber: 3.4 Consensus size: 35
44961 TCCAAAGTAG
44971 AGTATCGGTACCAAGGGTATCGATACCAGGTTATA
1 AGTATCGGTACCAAGGGTATCGATACCAGGTTATA
* *
45006 AGTATAGGTACCAAGGGTATCTATACCAGGTTATA
1 AGTATCGGTACCAAGGGTATCGATACCAGGTTATA
45041 AGTATCGGTACCAAGGGTATCGATACCAGGTTATA
1 AGTATCGGTACCAAGGGTATCGATACCAGGTTATA
*
45076 AGTATCGATACCA
1 AGTATCGGTACCA
45089 TTTTCAGAGA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (35 bp):
AGTATCGGTACCAAGGGTATCGATACCAGGTTATA
Found at i:45052 original size:20 final size:20
Alignment explanation
Indices: 45022--45088 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
45012 GGTACCAAGG
*
45022 GTATCTATACCAGGTTATAA
1 GTATCGATACCAGGTTATAA
*
45042 GTATCGGTACCAAGG------
1 GTATCGATACC-AGGTTATAA
45057 GTATCGATACCAGGTTATAA
1 GTATCGATACCAGGTTATAA
45077 GTATCGATACCA
1 GTATCGATACCA
45089 TTTTCAGAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
14 3 0.08
15 10 0.27
20 21 0.57
21 3 0.08
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (20 bp):
GTATCGATACCAGGTTATAA
Found at i:45585 original size:29 final size:29
Alignment explanation
Indices: 45552--45651 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 29
45542 TGATATGAAC
45552 CTATGTGATATAAGTTATATGGAAATGAT
1 CTATGTGATATAAGTTATATGGAAATGAT
* * * * *
45581 CTATGTGTGATTATATG-AAAATGTGATATGAA
1 CTA--TGTGA-TATAAGTTATATG-GAAATGAT
*
45613 CATATGTGATATAAGTTATATGGAAATAAT
1 C-TATGTGATATAAGTTATATGGAAATGAT
45643 CTATGTGAT
1 CTATGTGAT
45652 TATATGAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
29 11 0.20
30 11 0.20
31 18 0.33
32 12 0.22
33 2 0.04
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (29 bp):
CTATGTGATATAAGTTATATGGAAATGAT
Found at i:45611 original size:13 final size:15
Alignment explanation
Indices: 45593--45624 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
45583 ATGTGTGATT
45593 ATATGAA-A-ATGTG
1 ATATGAACATATGTG
45606 ATATGAACATATGTG
1 ATATGAACATATGTG
45621 ATAT
1 ATAT
45625 AAGTTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (15 bp):
ATATGAACATATGTG
Found at i:45636 original size:62 final size:59
Alignment explanation
Indices: 45539--45681 Score: 223
Period size: 62 Copynumber: 2.4 Consensus size: 59
45529 AATACATTTT
*
45539 ATGTGATATGAACCTATGTGATATAAGTTATATGGAAATGATCTATGTGTGATTATATGAAA
1 ATGTGATATGAA-CTATGTGATATAAGTTATATGGAAATAATCTA--TGTGATTATATGAAA
45601 ATGTGATATGAACATATGTGATATAAGTTATATGGAAATAATCTATGTGATTATATGAAA
1 ATGTGATATGAAC-TATGTGATATAAGTTATATGGAAATAATCTATGTGATTATATGAAA
* *
45661 ATGTGACATGAGCTATGTGAT
1 ATGTGATATGAACTATGTGAT
45682 TACATGCCTA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
59 8 0.10
60 26 0.34
61 1 0.01
62 42 0.55
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (59 bp):
ATGTGATATGAACTATGTGATATAAGTTATATGGAAATAATCTATGTGATTATATGAAA
Found at i:45679 original size:30 final size:30
Alignment explanation
Indices: 45586--45683 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
45576 ATGATCTATG
*
45586 TGTGATTATATGAAAATGTGATATGAACATA
1 TGTGATTATATGAAAATGTGAAATGAAC-TA
* * *
45617 TGTGA-TATAAGTTATATG-GAAAT-AATCTA
1 TGTGATTATATG-AAAATGTGAAATGAA-CTA
* *
45646 TGTGATTATATGAAAATGTGACATGAGCTA
1 TGTGATTATATGAAAATGTGAAATGAACTA
45676 TGTGATTA
1 TGTGATTA
45684 CATGCCTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
29 13 0.25
30 30 0.57
31 10 0.19
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (30 bp):
TGTGATTATATGAAAATGTGAAATGAACTA
Found at i:45695 original size:30 final size:30
Alignment explanation
Indices: 45638--45710 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
45628 TTATATGGAA
* *
45638 ATAATCTATGTGATTATATGAAAATGTGAC
1 ATAAGCTATGTGATTACATGAAAATGTGAC
* *** *
45668 ATGAGCTATGTGATTACATGCCTATGTGAT
1 ATAAGCTATGTGATTACATGAAAATGTGAC
*
45698 ATAAGTTATGTGA
1 ATAAGCTATGTGA
45711 AATGATATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (30 bp):
ATAAGCTATGTGATTACATGAAAATGTGAC
Found at i:45821 original size:23 final size:23
Alignment explanation
Indices: 45786--45908 Score: 106
Period size: 23 Copynumber: 5.3 Consensus size: 23
45776 GAGTCGAGAG
* *
45786 TTCTACGCGGTCCTTTGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
45809 TTCTACGTAGTCCTTCTGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* *
45832 TTCAACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
45855 TAT-TATGTGGTCCTTCGGGACAT
1 T-TCTACGTGGTCCTTCGGGACAA
* *
45878 TTCTATGT-GTCACTTCGGTACAAA
1 TTCTACGTGGTC-CTTCGGGAC-AA
45902 TTCTACG
1 TTCTACG
45909 CGACACTTCG
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
22 4 0.05
23 67 0.85
24 8 0.10
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:45868 original size:46 final size:46
Alignment explanation
Indices: 45790--45880 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
45780 CGAGAGTTCT
* *
45790 ACGCGGTCCTTTGGGACAATTCTACGTAGTCCTTCTGGACATTTCA
1 ACGCGGTCCTTCGGGACAATTCTACGTAGTCCTTCGGGACATTTCA
* *
45836 ACGCGGTCCTTCGGGACAATAT-TATGTGGTCCTTCGGGACATTTC
1 ACGCGGTCCTTCGGGACAAT-TCTACGTAGTCCTTCGGGACATTTC
45881 TATGTGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 39 0.98
47 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (46 bp):
ACGCGGTCCTTCGGGACAATTCTACGTAGTCCTTCGGGACATTTCA
Found at i:47210 original size:36 final size:36
Alignment explanation
Indices: 47163--47233 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
47153 CAAATGTCAA
47163 GATCAAAAGGAACCTCAACAACCAAGATCCAATGGT
1 GATCAAAAGGAACCTCAACAACCAAGATCCAATGGT
47199 GATCAAAAGGAACCTCAACAACCAAGATCCAATGG
1 GATCAAAAGGAACCTCAACAACCAAGATCCAATGG
47234 CGGATTACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (36 bp):
GATCAAAAGGAACCTCAACAACCAAGATCCAATGGT
Found at i:48498 original size:29 final size:29
Alignment explanation
Indices: 48450--48515 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
48440 TACTGAATGA
* *
48450 ATTTTTTAGTCAAAGTTAATAATTAAAGTT
1 ATTTTTTTGTCAAAGATAATAATTAAA-TT
**
48480 ATTTTTTTGTCAAA-ATAATGTTTAAATT
1 ATTTTTTTGTCAAAGATAATAATTAAATT
48508 ATTTTTTT
1 ATTTTTTT
48516 CATTAAGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 10 0.31
29 9 0.28
30 13 0.41
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.55
Consensus pattern (29 bp):
ATTTTTTTGTCAAAGATAATAATTAAATT
Found at i:48614 original size:33 final size:32
Alignment explanation
Indices: 48577--48679 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 32
48567 ACTTGGAAGA
*
48577 AAAAAATATAATAATTTAGATATTTATTTTGAT
1 AAAAAATATAATAATTTA-ATACTTATTTTGAT
* * *
48610 AAAAAAAATAATATTTTAAGTACCTATTTTGAT
1 AAAAAATATAATAATTTAA-TACTTATTTTGAT
* * *
48643 TAAAAATATAACT--TTAAATACTTACTTTGAT
1 AAAAAATATAA-TAATTTAATACTTATTTTGAT
48674 AAAAAA
1 AAAAAA
48680 AATACTTTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 16 0.28
32 5 0.09
33 36 0.62
34 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (32 bp):
AAAAAATATAATAATTTAATACTTATTTTGAT
Found at i:48659 original size:31 final size:31
Alignment explanation
Indices: 48601--48688 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
48591 TTTAGATATT
* *
48601 TATTTTGATAAAAAAAATAATATTTTAAGTACC
1 TATTTTGATAAAAAAAAT-A-ACTTTAAATACC
* * *
48634 TATTTTGATTAAAAATATAACTTTAAATACT
1 TATTTTGATAAAAAAAATAACTTTAAATACC
*
48665 TACTTTGATAAAAAAAAT-ACTTTA
1 TATTTTGATAAAAAAAATAACTTTA
48689 GGTAATTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 6 0.13
31 24 0.51
32 1 0.02
33 16 0.34
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
TATTTTGATAAAAAAAATAACTTTAAATACC
Found at i:49182 original size:20 final size:20
Alignment explanation
Indices: 49157--49210 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
49147 GTAGGCGAAC
*
49157 AACATGCCATAAGACAAGGA
1 AACATGCCATAAGACAAAGA
*
49177 AACATGTCATAAGACAAAGA
1 AACATGCCATAAGACAAAGA
* *
49197 AACGTGCTATAAGA
1 AACATGCCATAAGA
49211 GTAGAGTTAA
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:0.50, C:0.17, G:0.19, T:0.15
Consensus pattern (20 bp):
AACATGCCATAAGACAAAGA
Found at i:50627 original size:60 final size:60
Alignment explanation
Indices: 50545--50719 Score: 171
Period size: 59 Copynumber: 2.9 Consensus size: 60
50535 GTATGATTAT
* * * * *
50545 CATTTTAAATTGGTCCTTAAACTTTTAAATATTCTAATTTCATTCCTAAACTATGA-CTGC
1 CATTCTAAATTAGTCCTCAAACTTTTAAATATTCTAATTTCATTCCCAAACTATAACCT-C
* * * * *
50605 CATTCTAAATTAGTCAC-CAAAC-TTTGAGTATT-TCAATTTCATCCCCAAACGATAACCTT
1 CATTCTAAATTAGTC-CTCAAACTTTTAAATATTCT-AATTTCATTCCCAAACTATAACCTC
* *
50664 CATTCTAAATTAGTCCTCAAACTTTTTAAACATTCCAATTTCA-TCCCAAACTATAA
1 CATTCTAAATTAGTCCTCAAAC-TTTTAAATATTCTAATTTCATTCCCAAACTATAA
50720 GTATATACTA
Statistics
Matches: 92, Mismatches: 16, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
58 2 0.02
59 45 0.49
60 30 0.33
61 15 0.16
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (60 bp):
CATTCTAAATTAGTCCTCAAACTTTTAAATATTCTAATTTCATTCCCAAACTATAACCTC
Found at i:50976 original size:60 final size:57
Alignment explanation
Indices: 50862--51012 Score: 160
Period size: 60 Copynumber: 2.6 Consensus size: 57
50852 AAAAGTTAGG
* * * *
50862 GGACTAATTTAGAATGAAAGTCATAATTTGGGGATGGAATTGAAATTGTCAAAAGTTTAA
1 GGACTAATTTAAAATGAGAG-CATAATTTGGGGATGAAATTAAAATTGTCAAAAG--TAA
* * *
50922 GGACTAATTTATAATGAGAGCCATAATTTAGGGATGAAATTAAAATAT-TTAAAAGTAA
1 GGACTAATTTAAAATGAGAG-CATAATTTGGGGATGAAATTAAAAT-TGTCAAAAGTAA
* * *
50980 GGATTAATTCAAAATGAGAGTATAATTTGGGGA
1 GGACTAATTTAAAATGAGAGCATAATTTGGGGA
51013 CATACGACGT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
57 11 0.14
58 20 0.26
60 46 0.59
61 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (57 bp):
GGACTAATTTAAAATGAGAGCATAATTTGGGGATGAAATTAAAATTGTCAAAAGTAA
Found at i:52310 original size:29 final size:28
Alignment explanation
Indices: 52250--52361 Score: 125
Period size: 29 Copynumber: 3.7 Consensus size: 28
52240 TTCAGAAGTG
52250 AACTTGAACTTTTAAAAAATATATCAATGGACA
1 AACTTGAACTTTT--AAAAT-T-TCAA-GGACA
*
52283 AACTTGAACTTTTAAACTTTCAAGGGACA
1 AACTTGAACTTTTAAAATTTCAA-GGACA
* *
52312 AACTGGAACTTTTTAAAGTTTCAAGGAGCA
1 AACTTGAAC-TTTTAAAATTTCAAGGA-CA
52342 AACTTGAACTTTTAAAATTT
1 AACTTGAACTTTTAAAATTT
52362 TTATTGCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
29 30 0.42
30 24 0.34
31 4 0.06
33 13 0.18
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (28 bp):
AACTTGAACTTTTAAAATTTCAAGGACA
Found at i:52328 original size:30 final size:29
Alignment explanation
Indices: 52250--52354 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 29
52240 TTCAGAAGTG
* *
52250 AACTTGAACTTTTAAAAAATATATCAATGGACA
1 AACTTGAACTTTT-TAAACT-T-TCAA-GGACA
52283 AACTTGAAC-TTTTAAACTTTCAAGGGACA
1 AACTTGAACTTTTTAAACTTTCAA-GGACA
* *
52312 AACTGGAACTTTTTAAAGTTTCAAGGAGCA
1 AACTTGAACTTTTTAAACTTTCAAGGA-CA
52342 AACTTGAACTTTT
1 AACTTGAACTTTT
52355 AAAATTTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
29 20 0.31
30 28 0.44
31 4 0.06
32 3 0.05
33 9 0.14
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (29 bp):
AACTTGAACTTTTTAAACTTTCAAGGACA
Found at i:53181 original size:60 final size:59
Alignment explanation
Indices: 53101--53212 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
53091 GCTTGGAATG
*
53101 AAATTGAAGTGTTTAAAAGTTT-GACAACTAATTTAGAATGA-TAATCATATTTTAGGGAGA
1 AAATTGAAATGTTTAAAAGTTTAGA-AACTAATTTA-AATGAGT-ATCATATTTTAGGGAGA
* * *
53161 AAATTGAAATTTTTAAAAGTTTAGAGACTTATTTAAATGAGTATCATATTTT
1 AAATTGAAATGTTTAAAAGTTTAGAAACTAATTTAAATGAGTATCATATTTT
53213 GAGGATATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 15 0.33
60 29 0.63
61 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.39
Consensus pattern (59 bp):
AAATTGAAATGTTTAAAAGTTTAGAAACTAATTTAAATGAGTATCATATTTTAGGGAGA
Found at i:54115 original size:29 final size:29
Alignment explanation
Indices: 54072--54154 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
54062 CTCACCTAAC
54072 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
54102 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
54131 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
54155 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:57535 original size:15 final size:15
Alignment explanation
Indices: 57515--57544 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57505 CTTTCTCATA
57515 GTTATTGTTGAAATT
1 GTTATTGTTGAAATT
*
57530 GTTATTGTTGTAATT
1 GTTATTGTTGAAATT
57545 CCAGCCTCGT
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:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGAAATT
Found at i:58871 original size:29 final size:29
Alignment explanation
Indices: 58828--58910 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
58818 CTCACCTAAC
58828 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
58858 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
58887 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
58911 ATTTAGTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:62377 original size:10 final size:9
Alignment explanation
Indices: 62331--62383 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
62321 GATTAATAAT
62331 ATTTATTAA
1 ATTTATTAA
62340 ATTTATTAA
1 ATTTATTAA
*
62349 ACTATTATAAA
1 A-T-TTATTAA
*
62360 ATGGTATTTAA
1 AT-TTA-TTAA
62371 ATTTATTAA
1 ATTTATTAA
62380 ATTT
1 ATTT
62384 CATCATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 18 0.50
10 6 0.17
11 12 0.33
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (9 bp):
ATTTATTAA
Found at i:67144 original size:2 final size:2
Alignment explanation
Indices: 67137--67166 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
67127 CACTTCTTTA
*
67137 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67167 GTGAGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:80865 original size:2 final size:2
Alignment explanation
Indices: 80858--80886 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
80848 TCCTGCAATT
80858 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80887 TAGGAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100852 original size:30 final size:30
Alignment explanation
Indices: 100808--100892 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
100798 GCAAAGACTT
100808 CAATTTTTTCTAATATTTATTATTAAGGGCC
1 CAATTTTTT-TAATATTTATTATTAAGGGCC
* * * *
100839 CAATTTTTTTAATACTTACTATCT-GGGGTC
1 CAATTTTTTTAATATTTATTAT-TAAGGGCC
* * *
100869 TAATTTTTTCAATATTTTTTATTA
1 CAATTTTTTTAATATTTATTATTA
100893 GAAGCATACT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
30 32 0.74
31 10 0.23
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (30 bp):
CAATTTTTTTAATATTTATTATTAAGGGCC
Found at i:104408 original size:7 final size:7
Alignment explanation
Indices: 104396--104426 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
104386 TCATGACCTT
104396 TAAATCG
1 TAAATCG
104403 TAAATCG
1 TAAATCG
104410 TAAATCG
1 TAAATCG
104417 TAAATCG
1 TAAATCG
104424 TAA
1 TAA
104427 GCTCTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (7 bp):
TAAATCG
Found at i:108822 original size:55 final size:55
Alignment explanation
Indices: 108754--108866 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
108744 ATTTAGAATG
* * *
108754 AGATTCATTGTTTATGGATTAATTTGGGATGTTCAAAAG-GTTTGGGAATCAATTT
1 AGATTCATGGTTTATGGATTAATTTGGGAAGTTCAAAAGAG-TTGAGAATCAATTT
108809 AGATTCATGGTTTATGGATTAATTTGGGAAGTTCAAAAGAGTTGAGAATCAATTT
1 AGATTCATGGTTTATGGATTAATTTGGGAAGTTCAAAAGAGTTGAGAATCAATTT
108864 AGA
1 AGA
108867 ACACGAGTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 53 0.98
56 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (55 bp):
AGATTCATGGTTTATGGATTAATTTGGGAAGTTCAAAAGAGTTGAGAATCAATTT
Found at i:110666 original size:21 final size:21
Alignment explanation
Indices: 110640--110700 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
110630 AATCAGATTG
110640 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
110661 CCCAGGGGGAACAGATT--CC
1 CCCAGGGGGTACAGATTCCCC
*
110680 CCCA-GGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
110700 C
1 C
110701 TATCTAACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
20 3 0.09
21 16 0.46
ACGTcount: A:0.20, C:0.39, G:0.28, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:111606 original size:59 final size:59
Alignment explanation
Indices: 111529--111650 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 59
111519 GAAATATTTA
* * **
111529 AAAAGTTTTGGGACTAATTTAGAATGA-AGACATAGTTTGGGGATAAAAATAAAATGTTC
1 AAAAGTTTTGGGAATAA-TTAAAATGATAGACATAGTTTCAGGATAAAAATAAAATGTTC
* * * *
111588 AAAAG-TTTGAGGAATAATTAAAATGATAGTCATAGTTTCAGGATAAAATTGAAATGTTT
1 AAAAGTTTTG-GGAATAATTAAAATGATAGACATAGTTTCAGGATAAAAATAAAATGTTC
111647 AAAA
1 AAAA
111651 TGAGGGGCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 12 0.23
59 41 0.77
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (59 bp):
AAAAGTTTTGGGAATAATTAAAATGATAGACATAGTTTCAGGATAAAAATAAAATGTTC
Found at i:111976 original size:18 final size:19
Alignment explanation
Indices: 111953--111993 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
111943 ATGAATATAA
111953 TTTTTT-TCTTCTTTGATT
1 TTTTTTATCTTCTTTGATT
* *
111971 TTTTTTATTTTCTTTTATT
1 TTTTTTATCTTCTTTGATT
111990 TTTT
1 TTTT
111994 ACCATTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTTATCTTCTTTGATT
Found at i:112205 original size:2 final size:2
Alignment explanation
Indices: 112198--112265 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
112188 CTTATAAGAC
112198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112240 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
112266 TAAAAGGTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112919 original size:29 final size:29
Alignment explanation
Indices: 112848--112921 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
112838 ATAAGTTTTA
* * *
112848 ACTTTGGTCCCTAAATTCTATGTTAATTG
1 ACTTTAGTCCATATATTCTATGTTAATTG
112877 ACTTTAGTCCATATATTCTATGTTAATTG
1 ACTTTAGTCCATATATTCTATGTTAATTG
112906 ACTTTAGTCCATATAT
1 ACTTTAGTCCATATAT
112922 ATTATTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (29 bp):
ACTTTAGTCCATATATTCTATGTTAATTG
Found at i:113789 original size:70 final size:67
Alignment explanation
Indices: 113661--113789 Score: 168
Period size: 70 Copynumber: 1.9 Consensus size: 67
113651 GATAGTGTTG
* * * * * **
113661 GACTTGTGCTCGTTAAAAAATTTTGCTGCTCGACTCGTTGCTCGTTAAACTCGTTAAAATTGTAT
1 GACTCGTGCTCATTAAAAAATTATGCTGCTCGACTCATTGCTCATTAAACTCACTAAAATTGTAT
113726 TC
66 TC
113728 GACTCGTGCTCATTAAAAAATTAATGCTCGACTCGACTCATTGCTCATTAAACTCACTAAAA
1 GACTCGTGCTCATTAAAAAATT-ATGCT-G-CTCGACTCATTGCTCATTAAACTCACTAAAA
113790 AATTTACCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 20 0.38
68 4 0.08
69 1 0.02
70 27 0.52
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (67 bp):
GACTCGTGCTCATTAAAAAATTATGCTGCTCGACTCATTGCTCATTAAACTCACTAAAATTGTAT
TC
Found at i:115264 original size:2 final size:2
Alignment explanation
Indices: 115257--115281 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
115247 ATTTACCCTA
115257 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
115282 GGTAATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115586 original size:29 final size:29
Alignment explanation
Indices: 115553--115642 Score: 70
Period size: 29 Copynumber: 3.3 Consensus size: 29
115543 CAAAAGAATA
115553 TAAATATATTTCTTATTAATCAATTAAAT
1 TAAATATATTTCTTATTAATCAATTAAAT
*
115582 TAAAT-TAATATC--A-T-AT-AA-TAGAAT
1 TAAATAT-ATTTCTTATTAATCAATTA-AAT
* *
115606 ATAAATATATTTTTTATTAATCGATTAAAT
1 -TAAATATATTTCTTATTAATCAATTAAAT
115636 T-AATATA
1 TAAATATA
115643 ATATAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 21
0.65 0.06 0.29
Matches are distributed among these distances:
23 2 0.04
24 5 0.11
25 10 0.21
26 2 0.04
27 2 0.04
28 8 0.17
29 12 0.26
30 4 0.09
31 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (29 bp):
TAAATATATTTCTTATTAATCAATTAAAT
Found at i:115605 original size:54 final size:54
Alignment explanation
Indices: 115547--115651 Score: 167
Period size: 54 Copynumber: 1.9 Consensus size: 54
115537 GAATCACAAA
*
115547 AGAATATAAATATATTTCTTATTAATCAATTAAATTAA-ATTAATATCATATAAT
1 AGAATATAAATATATTTCTTATTAATCAATTAAATTAATA-TAATATAATATAAT
* *
115601 AGAATATAAATATATTTTTTATTAATCGATTAAATTAATATAATATAATAT
1 AGAATATAAATATATTTCTTATTAATCAATTAAATTAATATAATATAATAT
115652 TTTTTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (54 bp):
AGAATATAAATATATTTCTTATTAATCAATTAAATTAATATAATATAATATAAT
Found at i:115635 original size:24 final size:24
Alignment explanation
Indices: 115553--115635 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 24
115543 CAAAAGAATA
* *
115553 TAAATATATTTCTTATTAATCAAT
1 TAAATATATTTATTATTAATCGAT
* * *
115577 TAAATTAAATTAATATCATATAATAGAAT
1 TAAA-TATATT--TATTAT-TAATCG-AT
*
115606 ATAAATATATTTTTTATTAATCGAT
1 -TAAATATATTTATTATTAATCGAT
115631 TAAAT
1 TAAAT
115636 TAATATAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
24 9 0.20
25 7 0.16
26 5 0.11
27 8 0.18
28 4 0.09
29 7 0.16
30 4 0.09
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (24 bp):
TAAATATATTTATTATTAATCGAT
Found at i:116426 original size:19 final size:19
Alignment explanation
Indices: 116402--116440 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
116392 AGATTTTCTT
116402 TGATCCAAAGAGCAAAATC
1 TGATCCAAAGAGCAAAATC
*
116421 TGATCCAAAGTGCAAAATC
1 TGATCCAAAGAGCAAAATC
116440 T
1 T
116441 AAGCGAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (19 bp):
TGATCCAAAGAGCAAAATC
Found at i:122866 original size:31 final size:30
Alignment explanation
Indices: 122813--122870 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
122803 GTAAATTTTA
122813 CATTTAATACCTAAATTATTAATTTTGATC
1 CATTTAATACCTAAATTATTAATTTTGATC
*
122843 CATTTCAATATCTAAACTT-TTAATTTTG
1 CATTT-AATACCTAAA-TTATTAATTTTG
122871 TCAAAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 5 0.20
31 18 0.72
32 2 0.08
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.48
Consensus pattern (30 bp):
CATTTAATACCTAAATTATTAATTTTGATC
Found at i:123614 original size:37 final size:37
Alignment explanation
Indices: 123568--123718 Score: 135
Period size: 37 Copynumber: 4.0 Consensus size: 37
123558 AAAACAACTG
* *
123568 TTTATGTATGTTATGCATGCGGTAAAGTATCGATGTT
1 TTTAAGTATGTTATGCATGCGGGAAAGTATCGATGTT
*
123605 TTTAGGTATGTTATGCATGCATGCGGGAACA-TATCGACT-TT
1 TTTAAGTATG-T-T--ATGCATGCGGGAA-AGTATCGA-TGTT
* * * *
123646 TTGAAGTATGTTGTGCATGTGGGAACGTATCGATGTT
1 TTTAAGTATGTTATGCATGCGGGAAAGTATCGATGTT
* * * *
123683 TTTAACTATGTTATGCATTCTGGAACGTATCGATGT
1 TTTAAGTATGTTATGCATGCGGGAAAGTATCGATGT
123719 ACTGCTGTTG
Statistics
Matches: 93, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
36 1 0.01
37 58 0.62
38 1 0.01
39 2 0.02
40 1 0.01
41 28 0.30
42 2 0.02
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (37 bp):
TTTAAGTATGTTATGCATGCGGGAAAGTATCGATGTT
Found at i:123627 original size:41 final size:40
Alignment explanation
Indices: 123580--123700 Score: 126
Period size: 41 Copynumber: 3.0 Consensus size: 40
123570 TATGTATGTT
*
123580 ATGCATGCGGTAAAGTATCGATGTTTTTAGGTATGTTATGC
1 ATGCATGCGG-AAAGTATCGATGTTTTTAAGTATGTTATGC
* *
123621 ATGCATGCGGGAACA-TATCGACT-TTTTGAAGTATGTTGTGC
1 ATGCATGC-GGAA-AGTATCGA-TGTTTTTAAGTATGTTATGC
* *
123662 ATG--TG-GGAACGTATCGATGTTTTTAACTATGTTATGC
1 ATGCATGCGGAAAGTATCGATGTTTTTAAGTATGTTATGC
123699 AT
1 AT
123701 TCTGGAACGT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
36 1 0.01
37 27 0.40
39 2 0.03
41 34 0.50
42 4 0.06
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.38
Consensus pattern (40 bp):
ATGCATGCGGAAAGTATCGATGTTTTTAAGTATGTTATGC
Found at i:123791 original size:37 final size:37
Alignment explanation
Indices: 123738--123894 Score: 181
Period size: 37 Copynumber: 4.2 Consensus size: 37
123728 GAACATTTTA
* * * *
123738 ATGTTTTTAAGTATGTTAGGCATGCGGTCAAGTATCG
1 ATGTTTTTAGGCATGTTATGCATGCGGTAAAGTATCG
123775 ATGTTTTTAGGCATGTTATGCATGCGGTAAAGTATCG
1 ATGTTTTTAGGCATGTTATGCATGCGGTAAAGTATCG
*
123812 ATGTTTTTAGGCATGTTATGCATGCGGGAACA-TATCG
1 ATGTTTTTAGGCATGTTATGCATGCGGTAA-AGTATCG
** * * * * * *
123849 ACCTTTTGAAGTATGTTATGCATGTGGGAACGTATCG
1 ATGTTTTTAGGCATGTTATGCATGCGGTAAAGTATCG
123886 ATGTTTTTA
1 ATGTTTTTA
123895 ACTATGTTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
37 102 0.99
38 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.38
Consensus pattern (37 bp):
ATGTTTTTAGGCATGTTATGCATGCGGTAAAGTATCG
Found at i:123901 original size:37 final size:37
Alignment explanation
Indices: 123738--123928 Score: 174
Period size: 37 Copynumber: 5.2 Consensus size: 37
123728 GAACATTTTA
* * *
123738 ATGTTTTTAAGTATGTTAGGCATGCGGTCAA-GTATCG
1 ATGTTTTTAACTATGTTATGCATGCGG-GAACGTATCG
* * *
123775 ATGTTTTTAGGC-ATGTTATGCATGCGGTAAAGTATCG
1 ATGTTTTTA-ACTATGTTATGCATGCGGGAACGTATCG
* *
123812 ATGTTTTTAGGC-ATGTTATGCATGCGGGAACATATCG
1 ATGTTTTTA-ACTATGTTATGCATGCGGGAACGTATCG
** * * *
123849 ACCTTTTGAAGTATGTTATGCATGTGGGAACGTATCG
1 ATGTTTTTAACTATGTTATGCATGCGGGAACGTATCG
* * *
123886 ATGTTTTTAACTATGTTATGAATTCTGGG-ACGTACCG
1 ATGTTTTTAACTATGTTATGCATGC-GGGAACGTATCG
123923 ATGTTT
1 ATGTTT
123929 CTTAGATAAC
Statistics
Matches: 128, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
36 2 0.02
37 123 0.96
38 3 0.02
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (37 bp):
ATGTTTTTAACTATGTTATGCATGCGGGAACGTATCG
Found at i:124868 original size:25 final size:25
Alignment explanation
Indices: 124779--124868 Score: 69
Period size: 25 Copynumber: 3.5 Consensus size: 25
124769 AATGCCGCGC
*
124779 CACCATTTGAAAAAACTAATCATAT
1 CACCATTAGAAAAAACTAATCATAT
* * *
124804 CACCATTAGAAAGGAACAACACTCATTT
1 CACCATTAGAAA-AAACTA-A-TCATAT
124832 ACAGGCC--T-GAAAAAACTAATCATAT
1 -CA--CCATTAGAAAAAACTAATCATAT
124857 CACCATTAGAAA
1 CACCATTAGAAA
124869 GGAAGCGCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 18
0.66 0.09 0.24
Matches are distributed among these distances:
22 2 0.04
24 3 0.06
25 20 0.41
26 5 0.10
27 5 0.10
28 9 0.18
29 3 0.06
31 2 0.04
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (25 bp):
CACCATTAGAAAAAACTAATCATAT
Found at i:130682 original size:2 final size:2
Alignment explanation
Indices: 130675--130707 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
130665 GAGAAGACTT
*
130675 TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
130708 CGAAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.