Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007061.1 Hibiscus syriacus cultivar Beakdansim tig00018328_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: 58198
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3514 original size:50 final size:52
Alignment explanation
Indices: 3322--3564 Score: 266
Period size: 52 Copynumber: 4.8 Consensus size: 52
3312 CTACCAGAAA
* * **
3322 ATTGTTCGAGTTCTACTCCCTG-AG-AA-AGGGAGCGAACCTGTAGGTGGAAG
1 ATTGTTCGAGTTCTACACCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG-AG
* * * *
3372 ATTGTTCAAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGGCAAAG
1 ATTGTTCGAGTTCTACACCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAG
* * * * *
3424 ATTGTCCGAGTTTCTACTCCC-AAAGCAAGAGGGAGGGAACCCATAGGCAGA-
1 ATTGTTCGAG-TTCTACACCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAG
* *
3475 ATTGTTTGAGTTCT-CACCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAG
1 ATTGTTCGAGTTCTACACCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG-AG
*
3527 ATTGTTCGAGTTCTACTCCCTGAAGCAAGA-GGAGCGAA
1 ATTGTTCGAGTTCTACACCCTGAAGCAAGAGGGAGCGAA
3565 TGCACTGGGT
Statistics
Matches: 164, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
49 4 0.02
50 51 0.31
51 11 0.07
52 57 0.35
53 41 0.25
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (52 bp):
ATTGTTCGAGTTCTACACCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAG
Found at i:4846 original size:19 final size:18
Alignment explanation
Indices: 4821--4870 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
4811 TTATTTATTT
4821 CATTTGTTTGTTTCTTTG
1 CATTTGTTTGTTTCTTTG
*
4839 CAATTTGTTTGTTGCTTTG
1 C-ATTTGTTTGTTTCTTTG
4858 CATTTGTTTGTTT
1 CATTTGTTTGTTT
4871 GTCTTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.08, C:0.10, G:0.18, T:0.64
Consensus pattern (18 bp):
CATTTGTTTGTTTCTTTG
Found at i:5200 original size:2 final size:2
Alignment explanation
Indices: 5193--5227 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5183 ATAATTTATG
5193 TA TA TA 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 TA TA TA T
5228 GTAAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6349 original size:40 final size:43
Alignment explanation
Indices: 6261--6357 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 43
6251 GACACTACTA
6261 ATACGTGATGAAGATGTATGGTCGTCTAAGAGTGACACGGCTC
1 ATACGTGATGAAGATGTATGGTCGTCTAAGAGTGACACGGCTC
* * *
6304 CTACGTGATGAGGA-GATATGGTCG-GT-AGA-TGACACGGCTC
1 ATACGTGATGAAGATG-TATGGTCGTCTAAGAGTGACACGGCTC
6344 ATACGTGATGAAGA
1 ATACGTGATGAAGA
6358 GTTTTGGCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
40 23 0.48
41 3 0.06
42 2 0.04
43 20 0.42
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (43 bp):
ATACGTGATGAAGATGTATGGTCGTCTAAGAGTGACACGGCTC
Found at i:6604 original size:130 final size:129
Alignment explanation
Indices: 6420--6749 Score: 413
Period size: 130 Copynumber: 2.6 Consensus size: 129
6410 GACTGGTTTC
*
6420 TCTA-GGGTGACACGGCTCCTAC--GATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTATGC
1 TCTAGGGGTGATACGGCTCCTACGTGATGAGGAGGTCTGGTCGG-GGATGACACGGTTCCTA-GC
**** * * *
6482 GATGAGGA-TGGGAGACCATCTTTAGGAATGATAACACAGTTCCTACATGATGAGGAC-GATCGG
64 GATGAGGACAACAAG-CAATCTTTAGGAATGATAACACAGTTCCTACATGATAAGGACAGCT-GG
6545 TTA
127 TTA
* *
6548 TC-AGGGGTGATACGACTCCTACGTGATGAGGAGGTCTGGTCAGGGGCTGACACGGTTCCTACGC
1 TCTAGGGGTGATACGGCTCCTACGTGATGAGGAGGTCTGGTC-GGGGATGACACGGTTCCTA-GC
* *
6612 GATGAGGACAACAAGCAATCTTTAGGAGTGATAACACAGTTCCTACGTGATAAGGACAGCTGGTT
64 GATGAGGACAACAAGCAATCTTTAGGAATGATAACACAGTTCCTACATGATAAGGACAGCTGGTT
6677 A
129 A
* * *
6678 TCTAGGGTTGATACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGAAACGGTTTCTA-CG
1 TCTAGGGGTGATACGGCTCCTACGTGATGAGGAGGTCTGGTC-GGGGATGACACGGTTCCTAGCG
6742 ATGAGGAC
65 ATGAGGAC
6750 GATATGCCAT
Statistics
Matches: 176, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
127 1 0.01
128 18 0.10
129 10 0.06
130 88 0.50
131 59 0.34
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.24
Consensus pattern (129 bp):
TCTAGGGGTGATACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGATGACACGGTTCCTAGCGA
TGAGGACAACAAGCAATCTTTAGGAATGATAACACAGTTCCTACATGATAAGGACAGCTGGTTA
Found at i:6874 original size:34 final size:34
Alignment explanation
Indices: 6836--6941 Score: 173
Period size: 34 Copynumber: 3.2 Consensus size: 34
6826 GACAAATTCA
6836 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
1 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
6870 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
1 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
*
6904 TTTCAAGGGAAACTGACACAAAGAT--G-GTTTTG
1 TTTCAAGGGAAA-TGACTCAAAGATAGGTGTTTTG
6936 TTTCAA
1 TTTCAA
6942 AAAAACATAC
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
32 12 0.17
33 1 0.01
34 46 0.66
35 11 0.16
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (34 bp):
TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
Found at i:7052 original size:66 final size:63
Alignment explanation
Indices: 6971--7146 Score: 209
Period size: 66 Copynumber: 2.8 Consensus size: 63
6961 TTGTTCTCAA
*
6971 AAATTGTCTCAAGAGAGACAAAATTTGTTTTC-AGAGAAATAGACTCAAATATTTTTTTATCAAA
1 AAATTGTCTCAAGAGAGACAAAA-TTG-TTTCAAGAGAAATAGACTCAAAGATTTTTTT-T-AAA
*
7035 AT
62 AG
* *
7037 AAATTGTCTCAAGAGAGACAAAACTTGTTTCTAGAGAAACT-GACTCAAAGATTTTTTTTTAAAG
1 AAATTGTCTCAAGAGAGACAAAA-TTGTTTCAAGAGAAA-TAGACTCAAAGATTTTTTTTAAAAG
* *
7101 AAACTGTCTC--GAGAGACAAAATTGTTTCAAGAGAAACA-ACTCAAAG
1 AAATTGTCTCAAGAGAGACAAAATTGTTTCAAGAGAAATAGACTCAAAG
7147 GATACTGATA
Statistics
Matches: 100, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
60 8 0.08
61 14 0.14
62 11 0.11
64 12 0.12
65 5 0.05
66 49 0.49
67 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (63 bp):
AAATTGTCTCAAGAGAGACAAAATTGTTTCAAGAGAAATAGACTCAAAGATTTTTTTTAAAAG
Found at i:7266 original size:32 final size:32
Alignment explanation
Indices: 7217--7285 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
7207 TCACATCAGG
* *
7217 ATGTTGAATCCCAAAAGATACTCCAATATTCA
1 ATGTTGAATCCCAAAAGATACCCCAACATTCA
* *
7249 ATGTTGAATCTCC-AAAGATGCCCCAACATTCG
1 ATGTTGAATC-CCAAAAGATACCCCAACATTCA
7281 ATGTT
1 ATGTT
7286 TCTTGCTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (32 bp):
ATGTTGAATCCCAAAAGATACCCCAACATTCA
Found at i:12999 original size:59 final size:59
Alignment explanation
Indices: 12894--13018 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 59
12884 TACAAATAGG
*
12894 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAAACCA-A
1 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAAT-AAAACCATA
* *
12953 AATTTAAA-GAATTAAAATGGCAAAACA-A-AAA-TATAAAGGGCCAAAACAGTAACACCATA
1 AATTTAAAGGAA-TAAAATGGCAAAA-ATAGAAACT-TAAA-GGCCAAAACAATAAAACCATA
13012 AATTTAA
1 AATTTAA
13019 GGGTCTAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
57 1 0.02
58 16 0.28
59 40 0.69
60 1 0.02
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.18
Consensus pattern (59 bp):
AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAATAAAACCATA
Found at i:13047 original size:29 final size:30
Alignment explanation
Indices: 13015--13098 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
13005 CACCATAAAT
*
13015 TTAAGGGTCT-AAATAGAAAATACAGACAA-
1 TTAAGGGACTAAAATAGAAAATACAGA-AAC
*
13044 TTAAAGGACTAAAATAGAAAA-ACTAGAAAC
1 TTAAGGGACTAAAATAGAAAATAC-AGAAAC
*
13074 ATAAGGGACTAAAATAGAAAATACA
1 TTAAGGGACTAAAATAGAAAATACA
13099 AAAAAATAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGAAAATACAGAAAC
Found at i:15489 original size:30 final size:30
Alignment explanation
Indices: 15453--15526 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
15443 TTAAGGGTCT
*
15453 AAATAGAAAATACAGACAA-TTAAAGGACTA
1 AAATAGAAAATACAGA-AACATAAAGGACTA
*
15483 AAATAGAAAA-ACTAGAAACATAAGGGACTA
1 AAATAGAAAATAC-AGAAACATAAAGGACTA
15513 AAATAGAAAATACA
1 AAATAGAAAATACA
15527 AATAAAATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 4 0.10
30 33 0.85
31 2 0.05
ACGTcount: A:0.62, C:0.09, G:0.14, T:0.15
Consensus pattern (30 bp):
AAATAGAAAATACAGAAACATAAAGGACTA
Found at i:18534 original size:31 final size:30
Alignment explanation
Indices: 18499--18564 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
18489 TGATTACATC
* *
18499 AAAAAAAAGTTAGGTACCTAACTGTACCAT
1 AAAAAAAAGTTAGGCACCTAAATGTACCAT
*
18529 AAAAAAACGTTAGGCACCTAAATGTACCAT
1 AAAAAAAAGTTAGGCACCTAAATGTACCAT
*
18559 TAAAAA
1 AAAAAA
18565 TTAGATACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (30 bp):
AAAAAAAAGTTAGGCACCTAAATGTACCAT
Found at i:18576 original size:27 final size:29
Alignment explanation
Indices: 18500--18576 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
18490 GATTACATCA
*
18500 AAAAAAAGTTAGGTACCTAACTGTACCAT
1 AAAAAAAGTTAGGTACCTAAATGTACCAT
*
18529 AAAAAAACGTTAGGCACCTAAATGTACCAT
1 AAAAAAA-GTTAGGTACCTAAATGTACCAT
* *
18559 -TAAAAA-TTAGATACCTAA
1 AAAAAAAGTTAGGTACCTAA
18577 TTACAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.24
29 12 0.29
30 20 0.48
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (29 bp):
AAAAAAAGTTAGGTACCTAAATGTACCAT
Found at i:19879 original size:17 final size:19
Alignment explanation
Indices: 19845--19882 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19835 AGATAATATC
19845 TTTTTAAAATAATAATAAT
1 TTTTTAAAATAATAATAAT
*
19864 TTTTTATAA-AAT-ATAAT
1 TTTTTAAAATAATAATAAT
19881 TT
1 TT
19883 AATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAAATAATAATAAT
Found at i:19879 original size:20 final size:21
Alignment explanation
Indices: 19831--19880 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 21
19821 TTATAGTCTT
19831 ATATAGATAATATCTTTTTAAA
1 ATATA-ATAATATCTTTTTAAA
19853 ATAATAATAAT-T-TTTTATAAA
1 AT-ATAATAATATCTTTT-TAAA
19874 ATATAAT
1 ATATAAT
19881 TTAATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.35
21 7 0.27
22 7 0.27
23 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATAATAATATCTTTTTAAA
Found at i:20346 original size:28 final size:28
Alignment explanation
Indices: 20314--20369 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
20304 TCAAACTGGT
20314 GTTAACTGAAACCCGAGTTGGAACAGGA
1 GTTAACTGAAACCCGAGTTGGAACAGGA
20342 GTTAACTGAAACCCGAGTTGGAACAGGA
1 GTTAACTGAAACCCGAGTTGGAACAGGA
20370 AATTGTGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.18
Consensus pattern (28 bp):
GTTAACTGAAACCCGAGTTGGAACAGGA
Found at i:20842 original size:16 final size:16
Alignment explanation
Indices: 20821--20865 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
20811 TTAAATTAAT
20821 TTTATTAAATAACTTA
1 TTTATTAAATAACTTA
* *
20837 TTTATTAAATTATTTA
1 TTTATTAAATAACTTA
*
20853 TTATATTATATAA
1 TT-TATTAAATAA
20866 AATTAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATTAAATAACTTA
Found at i:21215 original size:16 final size:16
Alignment explanation
Indices: 21191--21227 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
21181 ATCATTGATC
21191 ATACATAATTACATAT
1 ATACATAATTACATAT
* *
21207 ATACTTAATTACTTAT
1 ATACATAATTACATAT
21223 ATACA
1 ATACA
21228 CACTCTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (16 bp):
ATACATAATTACATAT
Found at i:22007 original size:2 final size:2
Alignment explanation
Indices: 22000--22041 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21990 TTCATCATTC
22000 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
22042 TTGATCATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23986 original size:15 final size:14
Alignment explanation
Indices: 23938--24081 Score: 61
Period size: 14 Copynumber: 10.4 Consensus size: 14
23928 CGACCGACCC
*
23938 TAATATATTAATAA
1 TAATATATTTATAA
* * *
23952 TTTAAAATAATTAAAA
1 --TAATATATTTATAA
23968 TAATATAATTTATAA
1 TAATAT-ATTTATAA
23983 TAATATATTTATAA
1 TAATATATTTATAA
* * **
23997 TTATTTATTATATTT
1 TAATATATT-TATAA
* *
24012 TAA-ACAATTA-AA
1 TAATATATTTATAA
24024 TTAATATATTT-T-A
1 -TAATATATTTATAA
24037 T-ATAT-TTTATAA
1 TAATATATTTATAA
** *
24049 TTTTAATAATTA-AA
1 TAAT-ATATTTATAA
24063 TAATATATTT-TAA
1 TAATATATTTATAA
24076 TAATAT
1 TAATAT
24082 TAAAATAAAA
Statistics
Matches: 93, Mismatches: 24, Indels: 25
0.65 0.17 0.18
Matches are distributed among these distances:
10 3 0.03
11 5 0.05
12 3 0.03
13 20 0.22
14 32 0.34
15 20 0.22
16 10 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATATTTATAA
Found at i:24046 original size:42 final size:39
Alignment explanation
Indices: 23981--24079 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 39
23971 TATAATTTAT
23981 AATAATATA-TTTATAATTATTTATTATATTTTAAACAATTA
1 AATAATATATTTTATAATTATTTA-TA-ATTTT-AACAATTA
*
24022 AATTAATATATTTTAT-A-TATTTTATAATTTTAATAATTA
1 AA-TAATATATTTTATAATTA-TTTATAATTTTAACAATTA
24061 AATAATATATTTTAATAAT
1 AATAATATATTTT-ATAAT
24080 ATTAAAATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
38 11 0.22
39 11 0.22
40 6 0.12
41 6 0.12
42 12 0.24
43 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (39 bp):
AATAATATATTTTATAATTATTTATAATTTTAACAATTA
Found at i:24057 original size:9 final size:10
Alignment explanation
Indices: 24024--24082 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 10
24014 AACAATTAAA
24024 TTAATATATT
1 TTAATATATT
24034 TT-ATATATT
1 TTAATATATT
24043 TT-ATA-ATT
1 TTAATATATT
24051 TTAATA-ATT
1 TTAATATATT
*
24060 AAATAATATATT
1 --TTAATATATT
24072 TTAATAATATT
1 TTAAT-ATATT
24083 AAAATAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 5 0.12
9 18 0.43
10 6 0.14
11 10 0.24
12 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATATATT
Found at i:24074 original size:29 final size:29
Alignment explanation
Indices: 24036--24092 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
24026 AATATATTTT
* *
24036 ATATATTTT-ATAATTTTAATAATTAAATA
1 ATATATTTTAATAATATTAA-AATAAAATA
24065 ATATATTTTAATAATATTAAAATAAAAT
1 ATATATTTTAATAATATTAAAATAAAAT
24093 TCTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATATTTTAATAATATTAAAATAAAATA
Found at i:24088 original size:21 final size:21
Alignment explanation
Indices: 23972--24079 Score: 77
Period size: 21 Copynumber: 5.2 Consensus size: 21
23962 TTAAAATAAT
23972 ATAATTTATAATAATATA-TTT-
1 ATAA-TTA-AATAATATATTTTA
** *
23993 ATAATTATTTATTATATTTTAA
1 ATAATTAAATAATATATTTT-A
*
24015 ACAATTAAATTAATATATTTT-
1 ATAATTAAA-TAATATATTTTA
*
24036 ATATATT---TTATA-ATTTTA
1 ATA-ATTAAATAATATATTTTA
24054 ATAATTAAATAATATATTTTA
1 ATAATTAAATAATATATTTTA
24075 ATAAT
1 ATAAT
24080 ATTAAAATAA
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
17 8 0.12
18 7 0.10
19 6 0.09
20 10 0.15
21 17 0.25
22 9 0.13
23 10 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAATTAAATAATATATTTTA
Found at i:40003 original size:27 final size:27
Alignment explanation
Indices: 39965--40019 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
39955 CATGTCTATG
39965 TATGCAACTACTTAATTGAAAACCTCT
1 TATGCAACTACTTAATTGAAAACCTCT
* *
39992 TATGCAACTACTTGATTGAAAACTTCT
1 TATGCAACTACTTAATTGAAAACCTCT
40019 T
1 T
40020 TCTCCTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (27 bp):
TATGCAACTACTTAATTGAAAACCTCT
Found at i:43019 original size:3 final size:3
Alignment explanation
Indices: 43011--43037 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43001 TGTTTTCACT
43011 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
43038 GCAAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46747 original size:19 final size:19
Alignment explanation
Indices: 46698--46750 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
46688 TTAATTCAAG
*
46698 CATTGACTTTGACCAAGAT
1 CATTGACTTTGACCAAGAC
* *
46717 CGTTGACCTTGACCAAGAC
1 CATTGACTTTGACCAAGAC
*
46736 CATTAACTTTGACCA
1 CATTGACTTTGACCA
46751 GAGTTGACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (19 bp):
CATTGACTTTGACCAAGAC
Done.