Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000392.1 Hibiscus syriacus cultivar Beakdansim tig00000720_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: 113515
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2215 original size:18 final size:18
Alignment explanation
Indices: 2184--2225 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2174 TCACTTTTTT
2184 TAAATAAAT-AAAAATGCAA
1 TAAA-AAATAAAAAATG-AA
*
2203 TAAAAAATTAAAAATGAA
1 TAAAAAATAAAAAATGAA
2221 TAAAA
1 TAAAA
2226 TTCAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
TAAAAAATAAAAAATGAA
Found at i:3400 original size:27 final size:27
Alignment explanation
Indices: 3370--3421 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3360 TGTTATTCAT
*
3370 TTTAATAAAATTAAAATTTAATATTTA
1 TTTAATAAAATTAAAAATTAATATTTA
***
3397 TTTAATATTTTTAAAAATTAATATT
1 TTTAATAAAATTAAAAATTAATATT
3422 AGAAAGAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTAATAAAATTAAAAATTAATATTTA
Found at i:3504 original size:11 final size:11
Alignment explanation
Indices: 3471--3507 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
3461 TTTACATTAT
3471 ATTTTTATTG-
1 ATTTTTATTGC
*
3481 AATTTTATT-C
1 ATTTTTATTGC
3491 ATTTTTATTGC
1 ATTTTTATTGC
3502 ATTTTT
1 ATTTTT
3508 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (11 bp):
ATTTTTATTGC
Found at i:6695 original size:23 final size:23
Alignment explanation
Indices: 6650--6695 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6640 ACATTTTATA
*
6650 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
6673 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
6696 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:8459 original size:14 final size:14
Alignment explanation
Indices: 8440--8489 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
8430 GAAATGTGAA
8440 TAAAATAAATAAAG
1 TAAAATAAATAAAG
8454 TAAAATAAAAGTAATA-
1 TAAAAT-AAA-TAA-AG
*
8470 AAAAATAAATAAAG
1 TAAAATAAATAAAG
8484 -AAAATA
1 TAAAATA
8490 TAGATAATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
13 7 0.23
14 9 0.29
15 6 0.19
16 8 0.26
17 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (14 bp):
TAAAATAAATAAAG
Found at i:9386 original size:95 final size:95
Alignment explanation
Indices: 9223--9401 Score: 306
Period size: 95 Copynumber: 1.9 Consensus size: 95
9213 TGTAAATACC
* * * *
9223 TTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCATTTGCCTTAGAGGGACA
1 TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
9288 ACTCAAGCTTTATTGTATAGTATAATCACT
66 ACTCAAGCTTTATTGTATAGTATAATCACT
9318 TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAGAGGGAC
1 TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGGGAC
9382 AACTCAAGCTTTATTGTATA
65 AACTCAAGCTTTATTGTATA
9402 TAAATATTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 2 0.03
95 77 0.97
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (95 bp):
TTTATCAGGCTACCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
ACTCAAGCTTTATTGTATAGTATAATCACT
Found at i:13189 original size:17 final size:17
Alignment explanation
Indices: 13167--13215 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
13157 AGAAAGATGG
13167 ATAAAATAAATAAAATA
1 ATAAAATAAATAAAATA
13184 ATAAAAGT-AAT-AAATA
1 ATAAAA-TAAATAAAATA
* *
13200 A-ATAATAAAGAAAATA
1 ATAAAATAAATAAAATA
13216 TAGATAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 1 0.04
15 5 0.19
16 11 0.41
17 9 0.33
18 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
ATAAAATAAATAAAATA
Found at i:20681 original size:17 final size:17
Alignment explanation
Indices: 20659--20698 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
20649 TTGCATTACT
*
20659 TGGAATGTTAATAGAAA
1 TGGAATGTTAACAGAAA
20676 TGGAATGTTAACAGAAA
1 TGGAATGTTAACAGAAA
20693 TGGAAT
1 TGGAAT
20699 TATAAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.03, G:0.25, T:0.28
Consensus pattern (17 bp):
TGGAATGTTAACAGAAA
Found at i:24877 original size:19 final size:21
Alignment explanation
Indices: 24840--24882 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
24830 TAACTTTTTC
24840 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
24860 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
24880 TTT
1 TTT
24883 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:24888 original size:19 final size:20
Alignment explanation
Indices: 24839--24888 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
24829 TTAACTTTTT
*
24839 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
24859 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
24878 CTTTTACCTTT
1 CTTTTACCTTT
24889 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:29143 original size:22 final size:22
Alignment explanation
Indices: 29118--29162 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
29108 GATTGCAAAT
29118 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
*
29140 AGGGAACTGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
29162 A
1 A
29163 ATACTGCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:29786 original size:23 final size:23
Alignment explanation
Indices: 29760--29805 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
29750 TGAAGGATCT
29760 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
29783 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
29806 TATAATATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:31530 original size:22 final size:22
Alignment explanation
Indices: 31502--31553 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
31492 CTTTATACTC
*
31502 ATTCACATTTACCATAACATAT
1 ATTCACATGTACCATAACATAT
31524 ATTCACATGTACCATAACATAT
1 ATTCACATGTACCATAACATAT
31546 ATTCACAT
1 ATTCACAT
31554 ATATTGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (22 bp):
ATTCACATGTACCATAACATAT
Found at i:32132 original size:64 final size:63
Alignment explanation
Indices: 32010--32129 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 63
32000 GCACTAACTA
* *
32010 TGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAATGGGTGCATCGATACACTTCCTG
1 TGCATCGATACACAAATCACATTCAATGTTTCCA-TTTTAAGGGGTGCATCGATACACTTCCTG
* *
32074 TGCATCGATACACAAATTACATTCAATGTTTTCA-TTTAAGGGGTGCATCGATACAC
1 TGCATCGATACACAAATCACATTCAATGTTTCCATTTTAAGGGGTGCATCGATACAC
32130 ACTAAATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 21 0.40
64 31 0.60
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (63 bp):
TGCATCGATACACAAATCACATTCAATGTTTCCATTTTAAGGGGTGCATCGATACACTTCCTG
Found at i:41986 original size:25 final size:26
Alignment explanation
Indices: 41943--41992 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
41933 TTATTTCACA
*
41943 GAAAATGTTTTTCGAAAATG-AAATT
1 GAAAATGTTTTTAGAAAATGTAAATT
41968 GAAAATGTTTTATAG-AAATGTAAAT
1 GAAAATGTTTT-TAGAAAATGTAAAT
41993 CATTTTCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.36
Consensus pattern (26 bp):
GAAAATGTTTTTAGAAAATGTAAATT
Found at i:42259 original size:15 final size:15
Alignment explanation
Indices: 42239--42267 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42229 TACACTAGTT
42239 TAGGTTTATTTTATG
1 TAGGTTTATTTTATG
42254 TAGGTTTATTTTAT
1 TAGGTTTATTTTAT
42268 ATAATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (15 bp):
TAGGTTTATTTTATG
Found at i:45930 original size:13 final size:13
Alignment explanation
Indices: 45912--45952 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
45902 ATACTGAAAA
45912 CACATATATAATC
1 CACATATATAATC
*
45925 CACATATATAAAC
1 CACATATATAATC
45938 CACATATATAATC
1 CACATATATAATC
45951 CA
1 CA
45953 TACAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (13 bp):
CACATATATAATC
Found at i:46015 original size:38 final size:41
Alignment explanation
Indices: 45937--46018 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 41
45927 CATATATAAA
45937 CCACATATATAATCCATACAAAAATTGCTATGGATGATCCACATT
1 CCACATATATAATCCATACAAAAA-T-CTAT-GA-GATCCACATT
45982 CCACATATATAATCCATACAAAAA-CTAT-A-ATCCACAT
1 CCACATATATAATCCATACAAAAATCTATGAGATCCACAT
46019 ATTGTTCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
38 8 0.22
40 1 0.03
42 4 0.11
45 24 0.65
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (41 bp):
CCACATATATAATCCATACAAAAATCTATGAGATCCACATT
Found at i:74178 original size:35 final size:36
Alignment explanation
Indices: 74109--74178 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
74099 GGAATTTAAG
74109 GGGTACCGATACCTTGAAGAATAGTATCGATACCAA
1 GGGTACCGATACCTTGAAGAATAGTATCGATACCAA
*
74145 GGGTACCGATACCTT-AAGGAA-GGTATCGATACCA
1 GGGTACCGATACCTTGAA-GAATAGTATCGATACCA
74179 TCTTTGAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 14 0.44
36 18 0.56
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (36 bp):
GGGTACCGATACCTTGAAGAATAGTATCGATACCAA
Found at i:75315 original size:35 final size:36
Alignment explanation
Indices: 75246--75315 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
75236 GGAATTTAAG
75246 GGGTACTGATACCTTGAAGAACAGTATCGATACCAA
1 GGGTACTGATACCTTGAAGAACAGTATCGATACCAA
*
75282 GGGTACTGATACCTT-AAGGAA-GGTATCGATACCA
1 GGGTACTGATACCTTGAA-GAACAGTATCGATACCA
75316 TCTTTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 14 0.44
36 18 0.56
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (36 bp):
GGGTACTGATACCTTGAAGAACAGTATCGATACCAA
Found at i:75767 original size:2 final size:2
Alignment explanation
Indices: 75760--75784 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75750 CATGTACATT
75760 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 T
75785 TATGGTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77000 original size:35 final size:36
Alignment explanation
Indices: 76954--77023 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
76944 CGTTCAAAGA
76954 TGGTATCGATACCT-TCCTT-AAGGTATCGGTACCCT
1 TGGTATCGATA-CTGTCCTTCAAGGTATCGGTACCCT
*
76989 TGGTATCGATACTGTTCTTCAAGGTATCGGTACCC
1 TGGTATCGATACTGTCCTTCAAGGTATCGGTACCC
77024 CTAAAATTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 2 0.06
35 15 0.47
36 15 0.47
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.34
Consensus pattern (36 bp):
TGGTATCGATACTGTCCTTCAAGGTATCGGTACCCT
Found at i:82313 original size:43 final size:43
Alignment explanation
Indices: 82258--82348 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 43
82248 ACCACTAATC
82258 TCAATAACCTTTAGCTTCAATACAACAACACATTTTCCCACTT
1 TCAATAACCTTTAGCTTCAATACAACAACACATTTTCCCACTT
* * * *
82301 TCAATAACCTTTAGTTTCAATGCAGCAACTCATTTTCCCACTT
1 TCAATAACCTTTAGCTTCAATACAACAACACATTTTCCCACTT
82344 TCAAT
1 TCAAT
82349 CTTTTATTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (43 bp):
TCAATAACCTTTAGCTTCAATACAACAACACATTTTCCCACTT
Found at i:87927 original size:12 final size:12
Alignment explanation
Indices: 87910--87934 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87900 GTCAAATAAT
87910 TTAGGCACCAAA
1 TTAGGCACCAAA
87922 TTAGGCACCAAA
1 TTAGGCACCAAA
87934 T
1 T
87935 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:96332 original size:29 final size:28
Alignment explanation
Indices: 96285--96427 Score: 187
Period size: 29 Copynumber: 4.9 Consensus size: 28
96275 TCACCTTTTT
*
96285 TTTTAAGAAATATTTACGAAAATATCATCC
1 TTTTAA-AAATAATTACGAAAATATCA-CC
* *
96315 TTTTAAATATAATTACGAAACTATCACC
1 TTTTAAAAATAATTACGAAAATATCACC
*
96343 TTTTAAAAATAATTATGAAAAATATCACCC
1 TTTTAAAAATAATTACG-AAAATATCA-CC
* *
96373 TTTTAAAAATAATTACAAAAATAGCACC
1 TTTTAAAAATAATTACGAAAATATCACC
96401 ATTTTAAAAATAATTACGAAAATATCA
1 -TTTTAAAAATAATTACGAAAATATCA
96428 TTCAGTCAAC
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.19
29 57 0.58
30 23 0.23
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTTAAAAATAATTACGAAAATATCACC
Found at i:97586 original size:64 final size:62
Alignment explanation
Indices: 97480--97659 Score: 193
Period size: 65 Copynumber: 2.8 Consensus size: 62
97470 TTGGACCCTT
* * *
97480 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTCA-AAATAGCCT
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCAT-AAATGCATTCGATGTTTCATAAA-A-CCT
97543 G
62 G
* ** *
97544 AGTTCATCGATGCATGGATTGTGCATCGATGCCTCAAATGCATTCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-AAATGCATTCGATG-TTTCA-TAAAACCTG
* *
97609 AGTGCATCGATGCATGGAGAGTACATCAATGCATAAATTGCATTCGATGTT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATAAA-TGCATTCGATGTT
97660 CAATTTATTC
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
63 1 0.01
64 44 0.45
65 48 0.49
66 1 0.01
67 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATAAATGCATTCGATGTTTCATAAAACCTG
Found at i:97626 original size:65 final size:63
Alignment explanation
Indices: 97500--97707 Score: 199
Period size: 65 Copynumber: 3.2 Consensus size: 63
97490 TGCACTAAGA
* *
97500 GTGCATCGATGCATGAAGTGCATTCGATGTTTCA--AAATAGCCTGAGTTCATCGATGCATGGAT
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTCATTAAA-A-CCTGAGTGCATCGATGCATGGAT
97563 T
63 T
* **
97564 GTGCATCGATGCCTCAAATGCATTCGATGTTTTCATTAAAACCTGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCAT-AAATGCATTCGATG-TTTCATTAAAACCTGAGTGCATCGATGCATGGATT
* * * ** *
97629 GTACATCAATGCATAAATTGCATTCGATG-TTCAATTTATTCATTG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAA-TGCATTCGATGTTTC-ATTAAAAC-CTGAGTGCATCGATGCATGGAT
97692 T
63 T
*
97693 GATGCATCGGTGCAT
1 G-TGCATCGATGCAT
97708 CCCTTTGAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
63 3 0.03
64 52 0.44
65 60 0.50
66 1 0.01
67 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTCATTAAAACCTGAGTGCATCGATGCATGGATT
Found at i:97698 original size:20 final size:20
Alignment explanation
Indices: 97670--97707 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
97660 CAATTTATTC
*
97670 ATTGGTGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
97690 ATTGATGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
97708 CCCTTTGAAA
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:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:100393 original size:21 final size:22
Alignment explanation
Indices: 100332--100412 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
100322 GCATGTCCTT
100332 GTGCATCGATGCACATTCAAGA
1 GTGCATCGATGCACATTCAAGA
* * * *
100354 GTGCATTGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAAGA
* *
100375 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGA
100398 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
100413 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
21 14 0.30
22 19 0.41
23 1 0.02
24 12 0.26
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGA
Found at i:106243 original size:20 final size:20
Alignment explanation
Indices: 106218--106275 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
106208 CAATTTATTC
106218 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
106238 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
106258 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
106276 CAGTGCATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:106246 original size:65 final size:65
Alignment explanation
Indices: 106091--106255 Score: 189
Period size: 65 Copynumber: 2.6 Consensus size: 65
106081 GGTGCACTAA
*
106091 GAGTGCACCGATGCATGGATT-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAACC
1 GAGTGCATCGATGCATGGATTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATTAAAACC
106155 T
65 T
* * **
106156 GAGTGCATCGATGCATGGA--GAGTGCATTGATGCAT-AAACTGCATTCGATG-TTCAATTTATT
1 GAGTGCATCGATGCATGGATTG-GTGCATCGATGCATCAAA-TGCATTCGATGTTTC-ATTAAAA
*
106217 CATT
63 C-CT
106221 G-GTGCATCGATGCATGGATTGGTGCATCGATGCAT
1 GAGTGCATCGATGCATGGATTGGTGCATCGATGCAT
106256 GGATTGGTGC
Statistics
Matches: 86, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
63 3 0.03
64 25 0.29
65 57 0.66
66 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (65 bp):
GAGTGCATCGATGCATGGATTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATTAAAACCT
Done.