Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000689.1 Hibiscus syriacus cultivar Beakdansim tig00001345_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: 76884
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2198 original size:21 final size:21
Alignment explanation
Indices: 2172--2235 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
2162 TCTGTTCCCA
2172 GGGAATCGATACCCCCCAGGG
1 GGGAATCGATACCCCCCAGGG
*
2193 GGGAATCTGTTA----CC---G
1 GGGAATC-GATACCCCCCAGGG
2208 GGGAATCGATACCCCCCAGGG
1 GGGAATCGATACCCCCCAGGG
2229 GGGAATC
1 GGGAATC
2236 TGTTCCCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
14 3 0.09
15 8 0.24
18 4 0.12
21 15 0.45
22 3 0.09
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.14
Consensus pattern (21 bp):
GGGAATCGATACCCCCCAGGG
Found at i:2200 original size:36 final size:36
Alignment explanation
Indices: 2137--2242 Score: 178
Period size: 36 Copynumber: 3.0 Consensus size: 36
2127 TCATTTAGGG
*
2137 GGGAATCGATACCCCCCA-GGGGAAATCTGTTCCCA
1 GGGAATCGATACCCCCCAGGGGGGAATCTGTTCCCA
* *
2172 GGGAATCGATACCCCCCAGGGGGGAATCTGTTACCG
1 GGGAATCGATACCCCCCAGGGGGGAATCTGTTCCCA
2208 GGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1 GGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
2243 CCTGCACATA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 18 0.27
36 48 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (36 bp):
GGGAATCGATACCCCCCAGGGGGGAATCTGTTCCCA
Found at i:9093 original size:36 final size:36
Alignment explanation
Indices: 9046--9117 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
9036 TTCATTTAGG
9046 GGGGAATCGATACCC-CCCAAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCTCCC-AGGGGGAATCTGTTCCC
9082 GGGGAATCGATACCCTCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCTCCCAGGGGGAATCTGTTCCC
9118 CCTGCACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 32 0.91
37 3 0.09
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.18
Consensus pattern (36 bp):
GGGGAATCGATACCCTCCCAGGGGGAATCTGTTCCC
Found at i:15985 original size:35 final size:36
Alignment explanation
Indices: 15926--15996 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
15916 TTCATTTAGG
*
15926 GGGGAATCGATACCCCCCAAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAAGGGGGAATCTATTCCC
*
15962 GGGGAATCGATA-CCCCCAGGGGGGAATCTATTCCC
1 GGGGAATCGATACCCCCCAAGGGGGAATCTATTCCC
15997 CCTGCACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.23, C:0.30, G:0.31, T:0.17
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCAAGGGGGAATCTATTCCC
Found at i:18807 original size:21 final size:21
Alignment explanation
Indices: 18781--18839 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
18771 TAAAAGAAAT
18781 TAATTTTTAAAAATATTTTTA
1 TAATTTTTAAAAATATTTTTA
*
18802 TAA-TTTTAAAAA-ATTAATTA
1 TAATTTTTAAAAATATT-TTTA
* *
18822 TGATTTTT-TAAATATTTT
1 TAATTTTTAAAAATATTTT
18840 AAAAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 3 0.10
20 18 0.58
21 10 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATTTTTAAAAATATTTTTA
Found at i:26394 original size:3 final size:3
Alignment explanation
Indices: 26379--26408 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
26369 AAAAACCACA
*
26379 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
26409 GGTTCCCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28068 original size:18 final size:17
Alignment explanation
Indices: 28045--28096 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
28035 GATTGCTCGG
28045 ATGGTATCTATACCCCAC
1 ATGGTATCTATACCCC-C
*
28063 ATGGTATCAATACCCCC
1 ATGGTATCTATACCCCC
*
28080 AGGGGTATCTATACCCC
1 A-TGGTATCTATACCCC
28097 TGGCTGCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 28 0.93
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (17 bp):
ATGGTATCTATACCCCC
Found at i:28235 original size:20 final size:22
Alignment explanation
Indices: 28197--28236 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
28187 TTTGAGCAGA
28197 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
28219 AAAAT-ATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
28237 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:29499 original size:3 final size:3
Alignment explanation
Indices: 29491--29546 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
29481 AATGGTGAAG
* *
29491 GAA GAA GAA -AA GGAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29535 GAA GAA GAA GAA
1 GAA GAA GAA GAA
29547 TGAGGAGGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:30902 original size:20 final size:20
Alignment explanation
Indices: 30879--30916 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30869 ATATGCTCTT
*
30879 AATTTTAACAATCGGTATCA
1 AATTTCAACAATCGGTATCA
*
30899 AATTTCAACAATTGGTAT
1 AATTTCAACAATCGGTAT
30917 TGCATAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTTCAACAATCGGTATCA
Found at i:31264 original size:21 final size:21
Alignment explanation
Indices: 31238--31277 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31228 CACCAATTGG
31238 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
31259 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
31278 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:31598 original size:18 final size:18
Alignment explanation
Indices: 31575--31628 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
31565 GATTGCTCGG
31575 ATGGTATCTATACCCCCC
1 ATGGTATCTATACCCCCC
*
31593 ATGGTATCGATACCCCCC
1 ATGGTATCTATACCCCCC
*
31611 AGGGGTATCTATACCCCC
1 A-TGGTATCTATACCCCC
31629 TAGCTGGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (18 bp):
ATGGTATCTATACCCCCC
Found at i:31685 original size:21 final size:21
Alignment explanation
Indices: 31659--31700 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31649 ATTTGAATTT
31659 TATGAAGGAGTACCGATACCC
1 TATGAAGGAGTACCGATACCC
*
31680 TATGAAGGGGTACCGATACCC
1 TATGAAGGAGTACCGATACCC
31701 CCTATCGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
TATGAAGGAGTACCGATACCC
Found at i:31767 original size:20 final size:22
Alignment explanation
Indices: 31729--31768 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
31719 TTTGAGCATA
31729 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
31751 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
31769 ATATAAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:35339 original size:16 final size:16
Alignment explanation
Indices: 35247--35339 Score: 82
Period size: 16 Copynumber: 5.8 Consensus size: 16
35237 TTTCAAATTG
*
35247 AAAT-TAATAACAAAT
1 AAATATAATAATAAAT
*
35262 AAATATAATAATAATT
1 AAATATAATAATAAAT
* * *
35278 AAAAATATTAA-ATATT
1 AAATATAATAATA-AAT
*
35294 AAATATAATAAATAACT
1 AAATATAAT-AATAAAT
35311 AAAATATAATAATAAAT
1 -AAATATAATAATAAAT
*
35328 AAATATAGTAAT
1 AAATATAATAAT
35340 TAAAATAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
15 5 0.08
16 39 0.61
17 10 0.16
18 10 0.16
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (16 bp):
AAATATAATAATAAAT
Found at i:35373 original size:27 final size:27
Alignment explanation
Indices: 35326--35384 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
35316 ATAATAATAA
35326 ATAAATATAGTAATTAAAATAGATATTTT
1 ATAAATATAGTAATTAAAAT--ATATTTT
*
35355 ATAAATA-A-TAATTATAATATATTTT
1 ATAAATATAGTAATTAAAATATATTTT
35380 -TAAAT
1 ATAAAT
35385 TTTGAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.17
25 7 0.24
27 9 0.31
28 1 0.03
29 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (27 bp):
ATAAATATAGTAATTAAAATATATTTT
Found at i:35458 original size:33 final size:32
Alignment explanation
Indices: 35261--35458 Score: 103
Period size: 32 Copynumber: 6.2 Consensus size: 32
35251 TAATAACAAA
* *
35261 TAAATATAATAATAATTAAAAATATTAAATAT
1 TAAATATAATAATAATTAATAATATTATATAT
* *
35293 TAAATATAATAAATAACTAA-AATA-TA-ATAA
1 TAAATATAAT-AATAATTAATAATATTATATAT
* *
35323 TAAATA-AATATAGTAATTAA-AATA-GATATTT
1 TAAATATAATA-A-TAATTAATAATATTATATAT
* * * *
35354 TATAA-ATAATAATTA-TAATATATTTTTAAATTT
1 TA-AATATAATAATAATTAATA-A-TATTATATAT
* * * *
35387 TGAA-ATAATGAAAAATT-ATATGTATAATATAT
1 TAAATATAAT-AATAATTAATA-ATATTATATAT
35419 TAAATATAATAAGTAATTAATAATATTATA-AT
1 TAAATATAATAA-TAATTAATAATATTATATAT
35451 TATAATAT
1 TA-AATAT
35459 TTTTTTAAAT
Statistics
Matches: 128, Mismatches: 22, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
28 1 0.01
29 7 0.05
30 23 0.18
31 9 0.07
32 43 0.34
33 41 0.32
34 4 0.03
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (32 bp):
TAAATATAATAATAATTAATAATATTATATAT
Found at i:36689 original size:16 final size:16
Alignment explanation
Indices: 36670--36701 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36660 ACCATGAAAC
36670 GTTTAACCCATTCGAT
1 GTTTAACCCATTCGAT
*
36686 GTTTAACCTATTCGAT
1 GTTTAACCCATTCGAT
36702 AATTTCTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (16 bp):
GTTTAACCCATTCGAT
Found at i:39662 original size:18 final size:18
Alignment explanation
Indices: 39628--39679 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
39618 ATTATAATCA
39628 TTATTTATAA--A-ATAT
1 TTATTTATAATTATATAT
39643 TTATTT-TAATTACTATAT
1 TTATTTATAATTA-TATAT
*
39661 TTATTTATTATTATATAT
1 TTATTTATAATTATATAT
39679 T
1 T
39680 ATTAGTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 6 0.19
16 1 0.03
18 16 0.52
19 5 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTATAATTATATAT
Found at i:44023 original size:24 final size:24
Alignment explanation
Indices: 43996--44061 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
43986 AGCTCGTATA
43996 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* *
44020 AATTTGTC-CCGAAG-GACCGCGTAG
1 AATTTG-CACCGTAGTG-CCACGTAG
44044 AA-TTGCACCGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
44062 TATAAGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 11 0.32
24 21 0.62
25 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:44092 original size:47 final size:47
Alignment explanation
Indices: 43999--44092 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
43989 TCGTATAAAT
* * * *
43999 TTGCACCGTAGTGCCACGTAGAATTTGTCCCGAAGGACCGCGTAGAA
1 TTGCACCGTAGTGCCACATAGAATTTGTCCAGAAGGACCACATAGAA
* *
44046 TTGCACCGTAGTGCCATATA-AGATTTGTCCATAAGGACCACATAGAA
1 TTGCACCGTAGTGCCACATAGA-ATTTGTCCAGAAGGACCACATAGAA
44093 ATTCCTTAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 1 0.03
47 39 0.98
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (47 bp):
TTGCACCGTAGTGCCACATAGAATTTGTCCAGAAGGACCACATAGAA
Found at i:45174 original size:150 final size:149
Alignment explanation
Indices: 44977--45284 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
44967 CACCAAAGTG
*
44977 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
* *
45042 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGTTCCACAGAA
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGTTCCAAAGAA
*
45107 TATATATATATCCCGAAGGA
130 TATACATATATCCCGAAGGA
45127 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
*
45192 AATCATATACATATACTAAGGATCTAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
45257 ATACATATGTCCCGAAGGA
131 ATACATATATCCCGAAGGA
45276 CCGCGTAGA
1 CCGCGTAGA
45285 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
149 52 0.34
150 100 0.66
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
ATACATATATCCCGAAGGA
Found at i:51945 original size:23 final size:23
Alignment explanation
Indices: 51919--51963 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
51909 CACCACAGCT
51919 CGTATAAATGCACCGAAGTGCCG
1 CGTATAAATGCACCGAAGTGCCG
* *
51942 CGTATAATTGCACCGTAGTGCC
1 CGTATAAATGCACCGAAGTGCC
51964 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTATAAATGCACCGAAGTGCCG
Found at i:54847 original size:21 final size:21
Alignment explanation
Indices: 54805--54848 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54795 CGGTAAAAAA
* *
54805 TTACCTAAAATATCATTATTT
1 TTACCTAAAACACCATTATTT
*
54826 TTACCTAAAACACCAAT-TTT
1 TTACCTAAAACACCATTATTT
54846 TTA
1 TTA
54849 ACATTTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (21 bp):
TTACCTAAAACACCATTATTT
Found at i:59892 original size:2 final size:2
Alignment explanation
Indices: 59885--59928 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
59875 GAAACTTTAA
* *
59885 AT AT AT AT AT CT AT CT 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
59927 AT
1 AT
59929 TTGTACAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60579 original size:27 final size:27
Alignment explanation
Indices: 60549--60626 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
60539 AGTACCATCT
60549 CATCAACATGTAGAGGATGAGGTGTTA
1 CATCAACATGTAGAGGATGAGGTGTTA
60576 CATCAACATGTAGAGGATGAGGTGTTA
1 CATCAACATGTAGAGGATGAGGTGTTA
*
60603 CATCAACATGTAGAGGATGGGGTG
1 CATCAACATGTAGAGGATGAGGTG
60627 CTGCATATTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (27 bp):
CATCAACATGTAGAGGATGAGGTGTTA
Found at i:60933 original size:29 final size:29
Alignment explanation
Indices: 60898--60956 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
60888 TTTTTCACAT
60898 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
60927 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
60956 A
1 A
60957 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:73617 original size:359 final size:359
Alignment explanation
Indices: 72958--73681 Score: 1331
Period size: 359 Copynumber: 2.0 Consensus size: 359
72948 TCCGGAGGAA
72958 GAGGCCGAACGAAGGCATTACACATCACTACCTACTGCAAGGGGCATGCTCTGCCAAGTGTATTG
1 GAGGCCGAACGAAGGCATTACACATCACTACCTACTGCAAGGGGCATGCTCTGCCAAGTGTATTG
* *
73023 ATCGATAATGGCTCGACCTTGAACGTGATGCCATTGGTAACATTGAAAAGGATGTCAATAGATAC
66 ATCGACAATGGCTCGACCTTGAACGTGATGCCATTGGTAACATTGAAAAGGATGCCAATAGATAC
* * * *
73088 CTTACATATGAGAACCTACCAGAACGTGGTTCAAGCATTTGACGGGACTAAGAGAGCGGTAATTG
131 CTTACATATGAGAACCTACCAAAACGTGGTTCAAGCATTTGACAGGACCAAGAGAGAGGTAATTG
* *
73153 GCAAGATTGAGGTGCCGCTAACGATCGGACCAGCCACCTACAACATTGAGTTTCTGGTGATGGAT
196 GCAAGATTGAGGTGCCGCTAACGATCGGACCAACCACCTACAACATTGAGTTTCTGGTGATAGAT
73218 ATCATGCCTTCTTACAACTGTCTTTTGGGAAGGCCATGGATTCATCAAGCAGGTGCAGTACCATC
261 ATCATGCCTTCTTACAACTGTCTTTTGGGAAGGCCATGGATTCATCAAGCAGGTGCAGTACCATC
*
73283 CACGCTGCACCAAAAAGTTAAATTTGTTATTGAC
326 CACGCTGCACCAAAAAGTTAAATTTATTATTGAC
73317 GAGGCCGAACGAAGGCATTACACATCACTACCTACTGCAAGGGGCATGCTCTGCCAAGTGTATTG
1 GAGGCCGAACGAAGGCATTACACATCACTACCTACTGCAAGGGGCATGCTCTGCCAAGTGTATTG
73382 ATCGACAATGGCTCGACCTTGAACGTGATGCCATTGGTAACATTGAAAAGGATGCCAATAGATAC
66 ATCGACAATGGCTCGACCTTGAACGTGATGCCATTGGTAACATTGAAAAGGATGCCAATAGATAC
*
73447 CTTACATATGAGAACCTACCAAAACGTGGTTTAAGCATTTGACAGGACCAAGAGAGAGGTAATTG
131 CTTACATATGAGAACCTACCAAAACGTGGTTCAAGCATTTGACAGGACCAAGAGAGAGGTAATTG
*
73512 GCAAGATTGAGGTGCCGCTAATGATCGGACCAACCACCTACAACATTGAGTTTCTGGTGATAGAT
196 GCAAGATTGAGGTGCCGCTAACGATCGGACCAACCACCTACAACATTGAGTTTCTGGTGATAGAT
*
73577 ATCATGCCTTCTTACAACTTTCTTTTGGGAAGGCCATGGATTCATCAAGCAGGTGCAGTACCATC
261 ATCATGCCTTCTTACAACTGTCTTTTGGGAAGGCCATGGATTCATCAAGCAGGTGCAGTACCATC
73642 CACGCTGCACCAAAAAGTTAAATTTATTATTGAC
326 CACGCTGCACCAAAAAGTTAAATTTATTATTGAC
*
73676 GGGGCC
1 GAGGCC
73682 TTAGTAATTA
Statistics
Matches: 352, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
359 352 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (359 bp):
GAGGCCGAACGAAGGCATTACACATCACTACCTACTGCAAGGGGCATGCTCTGCCAAGTGTATTG
ATCGACAATGGCTCGACCTTGAACGTGATGCCATTGGTAACATTGAAAAGGATGCCAATAGATAC
CTTACATATGAGAACCTACCAAAACGTGGTTCAAGCATTTGACAGGACCAAGAGAGAGGTAATTG
GCAAGATTGAGGTGCCGCTAACGATCGGACCAACCACCTACAACATTGAGTTTCTGGTGATAGAT
ATCATGCCTTCTTACAACTGTCTTTTGGGAAGGCCATGGATTCATCAAGCAGGTGCAGTACCATC
CACGCTGCACCAAAAAGTTAAATTTATTATTGAC
Done.