Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000022.1 Hibiscus syriacus cultivar Beakdansim tig00000039_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: 52469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:837 original size:19 final size:19
Alignment explanation
Indices: 813--854 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
803 TAAGTTACAG
*
813 TTGATGTAGGTGTAAGATT
1 TTGATGAAGGTGTAAGATT
* *
832 TTGATGAAGTTGTGAGATT
1 TTGATGAAGGTGTAAGATT
851 TTGA
1 TTGA
855 ATTTCATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (19 bp):
TTGATGAAGGTGTAAGATT
Found at i:970 original size:14 final size:13
Alignment explanation
Indices: 948--990 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
938 ACTTTCTATA
948 TTAATTATAATCC
1 TTAATTATAATCC
961 TTATATTATAAT-C
1 TTA-ATTATAATCC
*
974 TTAATTATAATCA
1 TTAATTATAATCC
987 TTAA
1 TTAA
991 ATTAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 8 0.30
13 11 0.41
14 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATTATAATCC
Found at i:1010 original size:17 final size:18
Alignment explanation
Indices: 988--1039 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
978 TTATAATCAT
988 TAAATTAATTTAATTAAA
1 TAAATTAATTTAATTAAA
* *
1006 T-AATTTA-TTAGATTATA
1 TAAATTAATTTA-ATTAAA
1023 TAATATTAATTTAATTA
1 TAA-ATTAATTTAATTA
1040 TTTATAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 3 0.11
17 11 0.41
18 2 0.07
19 8 0.30
20 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TAAATTAATTTAATTAAA
Found at i:1066 original size:21 final size:22
Alignment explanation
Indices: 1017--1069 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1007 AATTTATTAG
1017 ATTATATAATATTAATTTAATT
1 ATTATATAATATTAATTTAATT
1039 ATT-TATAAGT-TTAATTT-ATT
1 ATTATATAA-TATTAATTTAATT
*
1059 TTTATATAATA
1 ATTATATAATA
1070 ATGAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 6 0.22
21 17 0.63
22 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTATATAATATTAATTTAATT
Found at i:1192 original size:2 final size:2
Alignment explanation
Indices: 1185--1220 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1175 TAAAATAATG
1185 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
1221 TCACATAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1418 original size:2 final size:2
Alignment explanation
Indices: 1411--1500 Score: 63
Period size: 2 Copynumber: 49.5 Consensus size: 2
1401 CCGCCCCGAT
* * *
1411 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1451 TA T- TA -A T- TA TA TA TA TA -A TA T- TA TA TA TT TC GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1488 -A T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1501 TTTCGGGTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
1 9 0.13
2 62 0.87
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1467 original size:33 final size:32
Alignment explanation
Indices: 1416--1499 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 32
1406 CCGATTATAT
* **
1416 ATATATATATATATATATAATATTTTATATTTTT
1 ATATA-AT-TATATATATAATATTATATATTTCG
1450 ATATTAATTATATATATAATATTATATATTTCG
1 ATA-TAATTATATATATAATATTATATATTTCG
1483 ATATAATTATATATATA
1 ATATAATTATATATATA
1500 TTTTCGGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 14 0.30
33 25 0.54
34 5 0.11
35 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
ATATAATTATATATATAATATTATATATTTCG
Found at i:1496 original size:43 final size:43
Alignment explanation
Indices: 1415--1496 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
1405 CCCGATTATA
* *
1415 TATATATATATATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATATATATATATAATATTTTATAATTATATATTAAT
1458 TATATATATA-ATAT-TAT-ATATTTCGATATAATTATATAT
1 TATATATATATATATATATAATATTT---TATAATTATATAT
1497 ATATTTTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 6 0.18
41 3 0.09
42 4 0.12
43 21 0.62
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (43 bp):
TATATATATATATATATATAATATTTTATAATTATATATTAAT
Found at i:3217 original size:28 final size:28
Alignment explanation
Indices: 3173--3292 Score: 183
Period size: 28 Copynumber: 4.4 Consensus size: 28
3163 TAGAATTTGT
*
3173 CACGTAGGAC-CACTATGTCCCGTAGGAC
1 CACGTAGAACACA-TATGTCCCGTAGGAC
3201 CACGTAGAACACATATGTCCCGTAGGAC
1 CACGTAGAACACATATGTCCCGTAGGAC
* *
3229 CGCGTAGAACAC--ATGTCCCATAGGAC
1 CACGTAGAACACATATGTCCCGTAGGAC
3255 CACGTAGAACACATATGTCCCGTAGGAC
1 CACGTAGAACACATATGTCCCGTAGGAC
3283 CACGTAGAAC
1 CACGTAGAAC
3293 CCTCGACTCT
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
26 24 0.29
28 58 0.69
29 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.17
Consensus pattern (28 bp):
CACGTAGAACACATATGTCCCGTAGGAC
Found at i:3259 original size:54 final size:54
Alignment explanation
Indices: 3173--3292 Score: 195
Period size: 54 Copynumber: 2.2 Consensus size: 54
3163 TAGAATTTGT
* *
3173 CACGTAGGACCACTATGTCCCGTAGGACCACGTAGAACACATATGTCCCGTAGGAC
1 CACGTA-GAACAC-ATGTCCCATAGGACCACGTAGAACACATATGTCCCGTAGGAC
*
3229 CGCGTAGAACACATGTCCCATAGGACCACGTAGAACACATATGTCCCGTAGGAC
1 CACGTAGAACACATGTCCCATAGGACCACGTAGAACACATATGTCCCGTAGGAC
3283 CACGTAGAAC
1 CACGTAGAAC
3293 CCTCGACTCT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 50 0.83
55 5 0.08
56 5 0.08
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.17
Consensus pattern (54 bp):
CACGTAGAACACATGTCCCATAGGACCACGTAGAACACATATGTCCCGTAGGAC
Found at i:3710 original size:4 final size:4
Alignment explanation
Indices: 3701--3920 Score: 426
Period size: 4 Copynumber: 55.5 Consensus size: 4
3691 ATCCTATTTT
3701 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
3749 CACG CACG CACG CA-G CACG CACG CACG CACG CACG CACG -ACG CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
3795 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
3843 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
3891 CACG CACG CACG CACG CACG CACG CACG CA
1 CACG CACG CACG CACG CACG CACG CACG CA
3921 TACATACACG
Statistics
Matches: 214, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
3 6 0.03
4 208 0.97
ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:3926 original size:4 final size:4
Alignment explanation
Indices: 3919--4273 Score: 624
Period size: 4 Copynumber: 89.0 Consensus size: 4
3909 CGCACGCACG
** ** **
3919 CATA CATA CACG CATA CATA CACG CATA CATA CATA CATA CATA CACG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
3967 CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4015 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4063 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4110 -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4157 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4205 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4253 CATA CATAA CATA CATA CATA
1 CATA CAT-A CATA CATA CATA
4274 GGTCACATAT
Statistics
Matches: 336, Mismatches: 12, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
2 2 0.01
4 330 0.98
5 4 0.01
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:4371 original size:24 final size:25
Alignment explanation
Indices: 4344--4392 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
4334 TTTAGCACCA
4344 TATCACTACATGTTTATGC-TCAGT
1 TATCACTACATGTTTATGCTTCAGT
*
4368 TATCACTATATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
4393 ACTCCTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTTCAGT
Found at i:8489 original size:12 final size:12
Alignment explanation
Indices: 8472--8502 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
8462 GAATATAAAT
8472 ATAAATTATGAA
1 ATAAATTATGAA
8484 ATAAATTATGAA
1 ATAAATTATGAA
8496 ATAAATT
1 ATAAATT
8503 TAAACTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (12 bp):
ATAAATTATGAA
Found at i:12894 original size:22 final size:22
Alignment explanation
Indices: 12869--12946 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
12859 TCTCTTAATG
*
12869 GAACCGTTCAACGCTGAATGCT
1 GAACCGTTCAGCGCTGAATGCT
12891 GAACCGTTCAGCGCTGAATGCT
1 GAACCGTTCAGCGCTGAATGCT
12913 GAACCGTTCAGCGCTGAATGCT
1 GAACCGTTCAGCGCTGAATGCT
12935 GAACCGTTCAGC
1 GAACCGTTCAGC
12947 ATTCAACGCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (22 bp):
GAACCGTTCAGCGCTGAATGCT
Found at i:16698 original size:3 final size:3
Alignment explanation
Indices: 16657--16684 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16647 AAAATATATA
16657 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16685 GAAGCAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17052 original size:42 final size:42
Alignment explanation
Indices: 16844--17256 Score: 409
Period size: 42 Copynumber: 9.7 Consensus size: 42
16834 AGCGCAGTCA
* * *
16844 AGATCTATAGCGGCATTTTTTGAACAAACGCCGCAAAAGATC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * **
16886 -GATACATATAGCGGCGTTTTCGGAACAAACGCAGCAAAAAATC
1 AGAT-C-TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * * *
16929 GGTATCTATAGCGGCGTTTTTGGAACAAATGTCGCAAAAGGCTG
1 AG-ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGG-TC
* * ** * *
16973 AGATATATAACAACGTTTTTTGGAA-AAACACCGCAAAAGGTT
1 AGATCTATAGCGGCG-TTTTTGGAACAAACGCCGCAAAAGGTC
* *
17015 GGATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * * * * *
17057 GATATTTATAGCGACGTTTTT-GAACAAATGCCGTAAAAGGTT
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* *
17099 AGATATATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * * * *
17141 AGATATATAGCGGCATTTTTAGAACAAACACCGTAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * **
17183 AGATCTTTAGCGGCGTTTTTGGAACAAACGCCGTAAAAAATC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
*
17225 AGATCTATAGCAGCGTTTTTGGATACAAACGC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGC
17257 TGCTAATTAT
Statistics
Matches: 303, Mismatches: 58, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
41 29 0.10
42 153 0.50
43 106 0.35
44 13 0.04
45 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (42 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
Found at i:22670 original size:15 final size:15
Alignment explanation
Indices: 22650--22681 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22640 CGCCCCGTAT
*
22650 CCGCCCCGCATCCGC
1 CCGCCCCACATCCGC
22665 CCGCCCCACATCCGC
1 CCGCCCCACATCCGC
22680 CC
1 CC
22682 ACCCAGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.69, G:0.16, T:0.06
Consensus pattern (15 bp):
CCGCCCCACATCCGC
Found at i:23928 original size:18 final size:18
Alignment explanation
Indices: 23895--23941 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
23885 TTTATATTAC
*
23895 ATAATACATATATTATACT
1 ATAATATAT-TATTATACT
*
23914 ATAATATATTATTATATT
1 ATAATATATTATTATACT
*
23932 ATTATATATT
1 ATAATATATT
23942 TCTATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAATATATTATTATACT
Found at i:23947 original size:16 final size:15
Alignment explanation
Indices: 23928--23957 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
23918 TATATTATTA
23928 TATTATTATATATTTC
1 TATTATTAT-TATTTC
23944 TATTATTATTATTT
1 TATTATTATTATTT
23958 TAAAGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTATTATTTC
Found at i:28639 original size:65 final size:64
Alignment explanation
Indices: 28548--28668 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 64
28538 CCCATTCAAC
* * ** *
28548 AGGTACTGATACCCTCTCAAACGAAAAAAATCACAGAATGTAATAAGGGTACCGATACCCTAGTT
1 AGGTACCGATACCCTCTCAAACG-AAAAAATAACAGAATACAACAAGGGTACCGATACCCTAGTT
** * *
28613 AGGTACCGATACCCTCTTGAATGAAAAACTAACAGAATACAACAAGGGTACCGATA
1 AGGTACCGATACCCTCTCAAACGAAAAAATAACAGAATACAACAAGGGTACCGATA
28669 TCTCAAGGGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
64 28 0.60
65 19 0.40
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (64 bp):
AGGTACCGATACCCTCTCAAACGAAAAAATAACAGAATACAACAAGGGTACCGATACCCTAGTT
Found at i:29743 original size:31 final size:30
Alignment explanation
Indices: 29708--29840 Score: 162
Period size: 31 Copynumber: 4.3 Consensus size: 30
29698 GAGTCGAAGG
29708 TTACCTATGTCTTTCAAGACATATGGACTGA
1 TTACCTATGTCTTTCAAGACATATGGA-TGA
*
29739 TTACCTATGTCTTTCGAGACATATGGACTGA
1 TTACCTATGTCTTTCAAGACATATGGA-TGA
* *
29770 TTACCTATGTCTTTCGAGACATATGGATAGT
1 TTACCTATGTCTTTCAAGACATATGGAT-GA
* *
29801 TTACCTATGTCCTT-AGGGACATATGGAT-A
1 TTACCTATGTCTTTCA-AGACATATGGATGA
29830 GTTACCTATGT
1 -TTACCTATGT
29841 TCTTCGAAAC
Statistics
Matches: 93, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
30 11 0.12
31 82 0.88
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (30 bp):
TTACCTATGTCTTTCAAGACATATGGATGA
Found at i:29805 original size:62 final size:61
Alignment explanation
Indices: 29707--29861 Score: 190
Period size: 62 Copynumber: 2.5 Consensus size: 61
29697 AGAGTCGAAG
* * * *
29707 GTTACCTATGTCTTTCAAGACATATGGACT-GATTACCTATGTCTTTCGAGACATATGGACT-
1 GTTACCTATGTCTTTCGAGACATATGGA-TAGTTTACCTATGTCCTTAGAGACATATGGA-TA
*
29768 GATTACCTATGTCTTTCGAGACATATGGATAGTTTACCTATGTCCTTAGGGACATATGGATA
1 G-TTACCTATGTCTTTCGAGACATATGGATAGTTTACCTATGTCCTTAGAGACATATGGATA
* *
29830 GTTACCTATGT-TCTTCGAAACTTATGGATAGT
1 GTTACCTATGTCT-TTCGAGACATATGGATAGT
29862 GGTAATTCGG
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
60 1 0.01
61 30 0.36
62 52 0.63
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (61 bp):
GTTACCTATGTCTTTCGAGACATATGGATAGTTTACCTATGTCCTTAGAGACATATGGATA
Found at i:30184 original size:20 final size:20
Alignment explanation
Indices: 30153--30191 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
30143 AAATGACTTA
30153 TATGATGATATAAGAATATGT
1 TATGATGATATAA-AATATGT
30174 TATGA-GATATAAAATATG
1 TATGATGATATAAAATATG
30192 AATGCAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (20 bp):
TATGATGATATAAAATATGT
Found at i:34384 original size:24 final size:20
Alignment explanation
Indices: 34334--34381 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
34324 TTGTGATTAC
*
34334 ATGTATATGATTAATATGAA
1 ATGTATGTGATTAATATGAA
34354 ATGTATGTGATTAATATGAA
1 ATGTATGTGATTAATATGAA
34374 ATGTATGT
1 ATGTATGT
34382 ATGCTTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (20 bp):
ATGTATGTGATTAATATGAA
Found at i:38368 original size:21 final size:21
Alignment explanation
Indices: 38344--38420 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 21
38334 TCCAGGGAGT
38344 ATCGATTCCCCTACAGGGGGA
1 ATCGATTCCCCTACAGGGGGA
* *
38365 ATCGGTTCCCCTTCAAAGGGGGA
1 ATCGATTCCCC-T-ACAGGGGGA
* * *
38388 ATCGGTTCCCCTTCAAGGGGGGT
1 ATCGATTCCCCTAC-A-GGGGGA
38411 ATCGATTCCC
1 ATCGATTCCC
38421 TCTGGACCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.22
22 3 0.07
23 33 0.72
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.23
Consensus pattern (21 bp):
ATCGATTCCCCTACAGGGGGA
Found at i:38384 original size:23 final size:23
Alignment explanation
Indices: 38358--38420 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
38348 ATTCCCCTAC
38358 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
38381 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
* * *
38404 GGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
38421 TCTGGACCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Done.