Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002941.1 Hibiscus syriacus cultivar Beakdansim tig00006071_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: 61528
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:11 original size:6 final size:6
Alignment explanation
Indices: 1--117 Score: 211
Period size: 6 Copynumber: 19.8 Consensus size: 6
*
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TTCATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
49 TACATA TACATA TACATA TACATA TACATA TAC--A TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
95 TACATA TACATA TACATA TACAT
1 TACATA TACATA TACATA TACAT
118 TTTGATGTTG
Statistics
Matches: 107, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
4 4 0.04
6 103 0.96
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:1030 original size:12 final size:13
Alignment explanation
Indices: 1009--1050 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
999 AAAAATTAAT
1009 ATTAACTAAAATA
1 ATTAACTAAAATA
1022 ATTAA-TAAAATA
1 ATTAACTAAAATA
* *
1034 CTTTACTATAAATA
1 ATTAACTA-AAATA
1048 ATT
1 ATT
1051 TATTCTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 7 0.29
14 7 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAACTAAAATA
Found at i:6103 original size:34 final size:35
Alignment explanation
Indices: 6012--6129 Score: 166
Period size: 34 Copynumber: 3.3 Consensus size: 35
6002 ATCCCATTAT
* * *
6012 CATTTTTCAACAAACATCTACCAAACTTTAAAAAAC
1 CATTTTTCAAAAAACATTTACCAAACTTT-GAAAAC
*
6048 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAA-AAACATTTACCAAACTTTGAAAAC
6084 CA-TTTTCAAAAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAACATTTACCAAACTTTGAAAAC
6118 CAATTTTTCAAA
1 C-ATTTTTCAAA
6130 GTTGGTTGCC
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
34 25 0.34
35 9 0.12
36 23 0.31
37 17 0.23
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (35 bp):
CATTTTTCAAAAAACATTTACCAAACTTTGAAAAC
Found at i:9421 original size:15 final size:15
Alignment explanation
Indices: 9401--9432 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9391 AAAATATTTC
*
9401 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
9416 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
9431 TT
1 TT
9433 GGATCTTCCA
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:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:10670 original size:37 final size:36
Alignment explanation
Indices: 10612--10730 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
10602 TCTCATTATC
* *
10612 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
*
10648 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
10684 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
10719 AATTTTTCAAAG
1 -ATTTTTCAAAG
10731 TTGGTTGCCA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 33 0.43
36 14 0.18
37 29 0.38
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:13451 original size:35 final size:35
Alignment explanation
Indices: 13361--13456 Score: 151
Period size: 34 Copynumber: 2.8 Consensus size: 35
13351 TTATCAAATA
*
13361 TATTTTTGAATTATCTGTGAGATGTTCGAACCGTT
1 TATTTCTGAATTATCTGTGAGATGTTCGAACCGTT
13396 TA-TTCTGAATTATCTGTGAGATGTTCGAACCGTT
1 TATTTCTGAATTATCTGTGAGATGTTCGAACCGTT
*
13430 TATTTCTGAATTAT-TCATGAGATGTTC
1 TATTTCTGAATTATCT-GTGAGATGTTC
13457 AAACATACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
34 34 0.60
35 23 0.40
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (35 bp):
TATTTCTGAATTATCTGTGAGATGTTCGAACCGTT
Found at i:17479 original size:21 final size:20
Alignment explanation
Indices: 17423--17485 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
17413 AAAATATATG
* *
17423 AAATAATAATAATATCAATCA
1 AAATAATAATAATA-AAATAA
*
17444 GAATAATAA-AATAAAATAA
1 AAATAATAATAATAAAATAA
*
17463 AAATAATATATAATAAAAGAA
1 AAATAATA-ATAATAAAATAA
17484 AA
1 AA
17486 GAAGAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 11 0.31
20 5 0.14
21 19 0.54
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
AAATAATAATAATAAAATAA
Found at i:17578 original size:20 final size:20
Alignment explanation
Indices: 17534--17578 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17524 ACTAGTACTT
*
17534 ACTATTATTATTATTTATAA
1 ACTATTATTATTATTTAAAA
* * *
17554 TCTATTATTGTTTTTTAAAA
1 ACTATTATTATTATTTAAAA
17574 ACTAT
1 ACTAT
17579 ATATATATAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (20 bp):
ACTATTATTATTATTTAAAA
Found at i:17596 original size:29 final size:27
Alignment explanation
Indices: 17565--17787 Score: 217
Period size: 27 Copynumber: 8.1 Consensus size: 27
17555 CTATTATTGT
*
17565 TTTTTAAAAACTATATATATATATAACA
1 TTTTT-AAAACTATATATATATATAATA
* *
17593 TTTTCAAAACTATATA-ATAGTATGATA
1 TTTTTAAAACTATATATATA-TATAATA
17620 TTTTTAAAACTATATATATAATATAATA
1 TTTTTAAAACTATATATAT-ATATAATA
* *
17648 TTTTCAAAACTATATAATATAGTATGATA
1 TTTTTAAAACTATAT-ATATA-TATAATA
*
17677 TTTTTAAAAC--TACATA-ATATAATA
1 TTTTTAAAACTATATATATATATAATA
* *
17701 TTTTTAAAACTATATACATATAATGTACTA
1 TTTTTAAAACTATAT--ATAT-ATATAATA
*
17731 TTTTTAAAAC--TACATA-ATATAATA
1 TTTTTAAAACTATATATATATATAATA
*
17755 TTTTCAAAACTATATAATATAATATAATA
1 TTTTTAAAACTATAT-ATAT-ATATAATA
17784 TTTT
1 TTTT
17788 ATAATGTACT
Statistics
Matches: 161, Mismatches: 18, Indels: 31
0.77 0.09 0.15
Matches are distributed among these distances:
24 31 0.19
25 1 0.01
26 13 0.08
27 36 0.22
28 32 0.20
29 32 0.20
30 16 0.10
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTTTAAAACTATATATATATATAATA
Found at i:17651 original size:55 final size:52
Alignment explanation
Indices: 17585--17770 Score: 250
Period size: 54 Copynumber: 3.5 Consensus size: 52
17575 CTATATATAT
* *
17585 ATATAACATTTTCAAAACTATATA-ATAGTATGATATTTTTAAAACTATATATATA
1 ATATAATATTTTCAAAACTATATACATAGTATGATATTTTTAAAAC----TACATA
*
17640 ATATAATATTTTCAAAACTATATAATATAGTATGATATTTTTAAAACTACATA
1 ATATAATATTTTCAAAACTATAT-ACATAGTATGATATTTTTAAAACTACATA
*
17693 ATATAATATTTTTAAAACTATATACATA-TAATGTACTATTTTTAAAACTACATA
1 ATATAATATTTTCAAAACTATATACATAGT-ATG-A-TATTTTTAAAACTACATA
17747 ATATAATATTTTCAAAACTATATA
1 ATATAATATTTTCAAAACTATATA
17771 ATATAATATA
Statistics
Matches: 121, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
51 1 0.01
52 7 0.06
53 28 0.23
54 41 0.34
55 22 0.18
56 1 0.01
57 21 0.17
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (52 bp):
ATATAATATTTTCAAAACTATATACATAGTATGATATTTTTAAAACTACATA
Found at i:17662 original size:24 final size:24
Alignment explanation
Indices: 17578--17779 Score: 179
Period size: 24 Copynumber: 7.6 Consensus size: 24
17568 TTAAAAACTA
* *
17578 TATATATATATAACATTTTCAAAAC
1 TATATA-ATATAATATTTTTAAAAC
17603 TATATAATAGTATGATATTTTTAAAAC
1 TATATAATA-TA--ATATTTTTAAAAC
*
17630 TATATATATAATATAATATTTTCAAAAC
1 ----TATATAATATAATATTTTTAAAAC
17658 TATATAATATAGTATGATATTTTTAAAAC
1 TATAT-A-ATA-TA--ATATTTTTAAAAC
*
17687 TACATAATATAATATTTTTAAAAC
1 TATATAATATAATATTTTTAAAAC
17711 TATATACATATAATGTACTATTTTTAAAAC
1 TATATA-ATAT-A---A-TATTTTTAAAAC
* *
17741 TACATAATATAATATTTTCAAAAC
1 TATATAATATAATATTTTTAAAAC
17765 TATATAATATAATAT
1 TATATAATATAATAT
17780 AATATTTTAT
Statistics
Matches: 150, Mismatches: 9, Indels: 37
0.77 0.05 0.19
Matches are distributed among these distances:
24 51 0.34
25 14 0.09
26 6 0.04
27 16 0.11
28 14 0.09
29 21 0.14
30 19 0.13
31 9 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (24 bp):
TATATAATATAATATTTTTAAAAC
Found at i:17780 original size:83 final size:81
Alignment explanation
Indices: 17566--17787 Score: 238
Period size: 83 Copynumber: 2.7 Consensus size: 81
17556 TATTATTGTT
* * * * *
17566 TTTTAAAAACTATATATATATATAACATTTTCAAAACTATATAATAGTATGATATTTTTAAAACT
1 TTTTCAAAACTACATA-ATATATAATATTTTCAAAACTATATAATAATATAATATTTTTAAAACT
17631 ATATATATAATATAATA
65 ATATATATAATATAATA
* * *
17648 TTTTCAAAACTATATAATATAGTATGATATTTTTAAAAC--TA-CATAATATAATATTTTTAAAA
1 TTTTCAAAACTACATAATATA-TA--ATATTTTCAAAACTATATAATAATATAATATTTTTAAAA
* *
17710 CTATATACATATAATGTACTA
63 CTATAT--ATATAATATAATA
*
17731 TTTTTAAAACTACAT-A-ATATAATATTTTCAAAACTATATAATATAATATAATATTTT
1 TTTTCAAAACTACATAATATATAATATTTTCAAAACTATAT-A-ATAATATAATATTTT
17788 ATAATGTACT
Statistics
Matches: 118, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
78 12 0.10
80 4 0.03
81 32 0.27
82 20 0.17
83 39 0.33
84 11 0.09
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (81 bp):
TTTTCAAAACTACATAATATATAATATTTTCAAAACTATATAATAATATAATATTTTTAAAACTA
TATATATAATATAATA
Found at i:17812 original size:44 final size:45
Alignment explanation
Indices: 17755--17839 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
17745 TAATATAATA
*
17755 TTTTCAAAACTATATAATATAATATAATATTTTATA-ATGTACTGC
1 TTTTCAAAACTATATAATATAATA-AATATTTAATATATGTACTGC
*
17800 TTTT-AAATCTATATAATATAATAAATATTTAATATATGTA
1 TTTTCAAAACTATATAATATAATAAATATTTAATATATGTA
17840 ATACTGTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 10 0.27
44 23 0.62
45 4 0.11
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (45 bp):
TTTTCAAAACTATATAATATAATAAATATTTAATATATGTACTGC
Found at i:18557 original size:15 final size:15
Alignment explanation
Indices: 18523--18558 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
18513 AAATTAAGAT
18523 TTTC-TTTTTCAAAA
1 TTTCATTTTTCAAAA
18537 --TCATTTTTCAAAA
1 TTTCATTTTTCAAAA
18550 TTTCATTTT
1 TTTCATTTT
18559 GTTTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
15 7 0.37
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCATTTTTCAAAA
Found at i:18574 original size:18 final size:20
Alignment explanation
Indices: 18541--18586 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
18531 TCAAAATCAT
18541 TTTTCAAAATTTCA-TTTTG
1 TTTTCAAAATTTCATTTTTG
18560 TTTTCAAAA-TTCATTTTTG
1 TTTTCAAAATTTCATTTTTG
*
18579 ATTTCAAA
1 TTTTCAAA
18587 TGAAAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTTG
Found at i:20537 original size:40 final size:40
Alignment explanation
Indices: 20490--20603 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
20480 GTCTTGCCTT
* * * * *
20490 TGGTATCGATATTACTAGAACAATATTGGTGTTGTTCATG
1 TGGTATCGATACTACAAGAACAATATCGATATTGTTCATG
*
20530 TGGTATCGATACTACCAGAACAATATCGATATTGTTCATG
1 TGGTATCGATACTACAAGAACAATATCGATATTGTTCATG
*
20570 TGGTATCGATACTACAAGAACAATATCGGTATTG
1 TGGTATCGATACTACAAGAACAATATCGATATTG
20604 CTTTGCCAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (40 bp):
TGGTATCGATACTACAAGAACAATATCGATATTGTTCATG
Found at i:29377 original size:20 final size:20
Alignment explanation
Indices: 29352--29752 Score: 118
Period size: 20 Copynumber: 17.6 Consensus size: 20
29342 TAAATTATGG
*
29352 CATCCTTTCATTCCTTAATT
1 CATCCTTTCATGCCTTAATT
*
29372 CATCCTTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
*
29396 GACATCCTTTCATGCCTTAATG
1 --CATCCTTTCATGCCTTAATT
*
29418 CATCCTTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
* *
29442 GGCATCCTTACATGCCTTAATG
1 --CATCCTTTCATGCCTTAATT
* *
29464 CATCATTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
* * *
29488 GGCATCCTTTCATGTCATAATA
1 --CATCCTTTCATGCCTTAATT
*
29510 CATCCTTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
* * *
29534 GGCATTCTTTCATGGCTTAATA
1 --CATCCTTTCATGCCTTAATT
*
29556 CATCCTTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
* *
29580 GGCATCTTTTCATGCCTTAATG
1 --CATCCTTTCATGCCTTAATT
*
29602 CATCCTTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
* * * *
29626 GATATCCCTTCATGCCTTACTG
1 --CATCCTTTCATGCCTTAATT
*
29648 CATCCTTTCATGCATTTTAATTAT
1 CATCCTTTCATGC--CTTAA-T-T
*
29672 GGCATCCTTTCATGCCTTAATA
1 --CATCCTTTCATGCCTTAATT
*
29694 CATCCTTTCATGCATTTTAACTAT
1 CATCCTTTCATGC--CTTAA-T-T
*
29718 GGCATCCTTTCATGCCTTAATG
1 --CATCCTTTCATGCCTTAATT
*
29740 CATCATTTCATGC
1 CATCCTTTCATGC
29753 TTTTTTTACA
Statistics
Matches: 280, Mismatches: 53, Indels: 96
0.65 0.12 0.22
Matches are distributed among these distances:
20 107 0.38
22 30 0.11
23 16 0.06
24 31 0.11
26 96 0.34
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATT
Found at i:29388 original size:46 final size:46
Alignment explanation
Indices: 29338--29757 Score: 651
Period size: 46 Copynumber: 9.1 Consensus size: 46
29328 TCCATTTATT
* * *
29338 CATTTAAATTATGGCATCCTTTCATTCCTTAATTCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
29384 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
29430 CATTTTAATTATGGCATCCTTACATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * *
29476 CATTTTAATTATGGCATCCTTTCATGTCATAATACATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * *
29522 CATTTTAATTATGGCATTCTTTCATGGCTTAATACATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
29568 CATTTTAATTATGGCATCTTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
** * *
29614 CATTTTAATTATGATATCCCTTCATGCCTTACTGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
29660 CATTTTAATTATGGCATCCTTTCATGCCTTAATACATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
29706 CATTTTAACTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
29752 CTTTTT
1 CATTTT
29758 TTACATACTC
Statistics
Matches: 341, Mismatches: 33, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 341 1.00
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (46 bp):
CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:30341 original size:95 final size:95
Alignment explanation
Indices: 30131--30351 Score: 261
Period size: 95 Copynumber: 2.3 Consensus size: 95
30121 AAGCTTAATA
* * * *
30131 GTATCGATACTAC-TACCCTGGTACCGATACT-TCTATACTATGGTACCGATACCCCCTTCGGTA
1 GTATCGATAC-CCTTACCATGGTATCGATACTATCTATACTATGGTACCGATACCCCCTTCAGTA
* * * * *
30194 TTGATACGAATTTTAAATTTGATGTTTCTTG
65 TCGATACGAATTTTAAATTCGATATTGCCTG
* * *
30225 GTATCGATACCCTTATCATGGTATCGATACTATC-CTACTATGGTACCGATACCCCCTTATAGTA
1 GTATCGATACCCTTACCATGGTATCGATACTATCTATACTATGGTACCGATACCCCCTT-CAGTA
**
30289 TCGATACTG-ATTTTGGATTCGATATTGCCTG
65 TCGATAC-GAATTTTAAATTCGATATTGCCTG
30320 GTATCGATACCCTTACCATGGTATCGATACTA
1 GTATCGATACCCTTACCATGGTATCGATACTA
30352 CCTCATAGAT
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
93 1 0.01
94 48 0.44
95 58 0.54
96 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTATCTATACTATGGTACCGATACCCCCTTCAGTAT
CGATACGAATTTTAAATTCGATATTGCCTG
Found at i:36427 original size:20 final size:20
Alignment explanation
Indices: 36398--36884 Score: 254
Period size: 20 Copynumber: 21.7 Consensus size: 20
36388 TTAAATTATG
36398 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
36418 GCATCATTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
36443 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
**
36464 GCATCCTTTCATGAATTTTAATTAT
1 GCATCCTTTCATG--CCTT-A--AT
36489 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* **
36510 ACATCCTTTCATGTATTTTAATTGT
1 GCATCCTTTCATG--CCTTAA---T
*
36535 GGCATACTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
36556 ACATCATTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
36581 GTCATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
* *
36602 ACATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
* *
36627 GGCATCCCTTCATTCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
36648 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
36673 GGCATCCCTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
36694 GCATCATTTCATGCATTTTATTAT
1 GCATCCTTTCATGC--CTTA--AT
36718 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
**
36739 AAATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
36759 ACATCCTTTAATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
36779 GCATCATTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
36804 GGGATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
36825 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
36850 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
36871 GCATCCTTTCATGC
1 GCATCCTTTCATGC
36885 ATTTTAATTA
Statistics
Matches: 362, Mismatches: 52, Indels: 106
0.70 0.10 0.20
Matches are distributed among these distances:
20 160 0.44
21 17 0.05
22 21 0.06
23 17 0.05
24 20 0.06
25 28 0.08
26 99 0.27
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:36435 original size:46 final size:46
Alignment explanation
Indices: 36385--36910 Score: 805
Period size: 46 Copynumber: 11.6 Consensus size: 46
36375 TCCATATATA
* *
36385 CATTTAAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
36431 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
36477 AATTTTAATTATGGCATCCTTTCATGCCTTAATACATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * * * *
36523 TATTTTAATTGTGGCATACTTTCATGCCTTAATACATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
36569 CATTTTAATTATGTCATCCTTTCATGCCTTAATACATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
36615 CATTTTAATTATGGCATCCCTTCATTCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
36661 CATTTTAATTATGGCATCCCTTCATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
**
36707 CATTTT-ATTATGGCATCCTTTCATGCCTTAATAAATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * *
36752 C--CTTAA-TA---CATCCTTTAATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
36792 CATTTTAATTATGGGATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
36838 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
36884 CATTTTAATTATGGCATCATTTCATGC
1 CATTTTAATTATGGCATCCTTTCATGC
36911 ATTTTTTACA
Statistics
Matches: 439, Mismatches: 34, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
40 29 0.07
42 4 0.01
43 6 0.01
44 1 0.00
45 36 0.08
46 363 0.83
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (46 bp):
CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:36994 original size:2 final size:2
Alignment explanation
Indices: 36987--37018 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36977 CATTATAAAC
36987 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
37019 TTAAGCATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37472 original size:95 final size:95
Alignment explanation
Indices: 37347--37530 Score: 264
Period size: 95 Copynumber: 1.9 Consensus size: 95
37337 AATTATATAT
* *
37347 TATGGTACTGATACCCCCTTCTAGTATCGATACCAATTTTAAATTCGATGTT-TCCTGGTATCGA
1 TATGGTACCGATACCCCCTTCTAATATCGATACCAATTTTAAATTCGATGTTGT-CTGGTATCGA
*
37411 TACCCTTATCATGGTATCAATACTATCCTAC
65 TACCCTTACCATGGTATCAATACTATCCTAC
* ** *
37442 TATGGTACCGATACCCGCTTAC-AATATCGATACTGATTTTAGATTCGATGTTGTCTGGTATCGA
1 TATGGTACCGATACCCCCTT-CTAATATCGATACCAATTTTAAATTCGATGTTGTCTGGTATCGA
*
37506 TACCCTTACCATGGTATCGATACTA
65 TACCCTTACCATGGTATCAATACTA
37531 CCTCGTAGGT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 77 0.97
96 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (95 bp):
TATGGTACCGATACCCCCTTCTAATATCGATACCAATTTTAAATTCGATGTTGTCTGGTATCGAT
ACCCTTACCATGGTATCAATACTATCCTAC
Found at i:37565 original size:95 final size:95
Alignment explanation
Indices: 37347--37571 Score: 246
Period size: 95 Copynumber: 2.4 Consensus size: 95
37337 AATTATATAT
* ** *
37347 TATGGTACTGATACCCCCTT-CTAGTATCGATACCAATTTTAAATTCGATGTTTCCTGGTATCGA
1 TATGGTACCGATACCCGATTAC-AGTATCGATACTAATTTTAAATTCGATGTTTCCTGGTATCGA
*
37411 TACCCTTATCATGGTATCAATACTATCCTAC
65 TACCCTTACCATGGTATCAATACTATCCTAC
* * * *
37442 TATGGTACCGATACCCGCTTACAATATCGATACTGATTTTAGATTCGATGTTGT-CTGGTATCGA
1 TATGGTACCGATACCCGATTACAGTATCGATACTAATTTTAAATTCGATGTT-TCCTGGTATCGA
*
37506 TACCCTTACCATGGTATCGATACTA-CCT-C
65 TACCCTTACCATGGTATCAATACTATCCTAC
* *
37535 GTA-GGTATCGATA-CTGATTGAATCAGTATCGATACTA
1 -TATGGTACCGATACCCGATT--A-CAGTATCGATACTA
37572 CACTACTAAT
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
92 4 0.04
93 10 0.09
94 6 0.05
95 89 0.80
96 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (95 bp):
TATGGTACCGATACCCGATTACAGTATCGATACTAATTTTAAATTCGATGTTTCCTGGTATCGAT
ACCCTTACCATGGTATCAATACTATCCTAC
Found at i:52213 original size:5 final size:5
Alignment explanation
Indices: 52203--52235 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
52193 GCAAAAGACA
52203 TGAGG TGAGG TGAGG TGAGG TGAGG TGAGG TGA
1 TGAGG TGAGG TGAGG TGAGG TGAGG TGAGG TGA
52236 TAATGAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.58, T:0.21
Consensus pattern (5 bp):
TGAGG
Found at i:54020 original size:258 final size:256
Alignment explanation
Indices: 53563--54064 Score: 857
Period size: 258 Copynumber: 1.9 Consensus size: 256
53553 TATTGTTAGT
* *
53563 TTTTCAAATTTTCAGAATAATTTTAATTAAAATACATTCTGAAAATATCTTTTTATGTTTTCATA
1 TTTTCAAATTTTCAGAATAATTTTAATGAAAATA-A-TCTGAAAACATCTTTTTATGTTTTCATA
*
53628 TTTTTTTTTTGTTTTCATTTTCTCGAAATCATTTTTCAATTTTACAATCAAACATGTTTATTCAA
64 TTTTTTTTTTGTTTTCATTTTCTAGAAATCATTTTTCAATTTTACAATCAAACATGTTTATTCAA
* *
53693 CGTTTTCTATTTTCTAAGAAAATGAAAATAACATTTATTTTCTAAAATCAAACGGACCCTTAAGA
129 CGTTTTCTATTTTCTAAGAAAATGAAAATAACATTTATTTTATAAAATCAAACGGACACTTAAGA
53758 TTTTTATTTAGAAATTTGAGCTTAAAGATTTTAGGAGTTTAAAGCTACACTCATATTTCCTTA
194 TTTTTATTTAGAAATTTGAGCTTAAAGATTTTAGGAGTTTAAAGCTACACTCATATTTCCTTA
*
53821 TTTTCAAATTTTCAGAATAATTTTAATGAAAAT-A-CTGAAAACATCTTTTTATGTTTTCATCTT
1 TTTTCAAATTTTCAGAATAATTTTAATGAAAATAATCTGAAAACATCTTTTTATGTTTTCAT-AT
53884 CTTGTTTATTTTGTTTTCATTTTCTAGAAATCA-TTTTCTAATTTTACAATCAAACATGTTTATT
65 -TT-TTT-TTTTGTTTTCATTTTCTAGAAATCATTTTTC-AATTTTACAATCAAACATGTTTATT
*
53948 CAACGTTTTCTATTTTCTAAGAAAATGAAAATAACCTTTATTTTATAAAATCAAACGGACACTTA
126 CAACGTTTTCTATTTTCTAAGAAAATGAAAATAACATTTATTTTATAAAATCAAACGGACACTTA
54013 AGATTTTTATTTAGAAATTTGAGCTTAAAGATTTTAGGAGTTTAAAGCTACA
191 AGATTTTTATTTAGAAATTTGAGCTTAAAGATTTTAGGAGTTTAAAGCTACA
54065 ATTAACGGTA
Statistics
Matches: 232, Mismatches: 7, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
254 25 0.11
255 1 0.00
256 3 0.01
257 8 0.03
258 195 0.84
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.45
Consensus pattern (256 bp):
TTTTCAAATTTTCAGAATAATTTTAATGAAAATAATCTGAAAACATCTTTTTATGTTTTCATATT
TTTTTTTTGTTTTCATTTTCTAGAAATCATTTTTCAATTTTACAATCAAACATGTTTATTCAACG
TTTTCTATTTTCTAAGAAAATGAAAATAACATTTATTTTATAAAATCAAACGGACACTTAAGATT
TTTATTTAGAAATTTGAGCTTAAAGATTTTAGGAGTTTAAAGCTACACTCATATTTCCTTA
Found at i:61065 original size:21 final size:22
Alignment explanation
Indices: 61039--61079 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
61029 TCAGGATAGG
61039 GAGTATC-GATAC-TCCTTTAAT
1 GAGTATCAG-TACTTCCTTTAAT
61060 GAGTATCAGTACTTCCTTTA
1 GAGTATCAGTACTTCCTTTA
61080 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (22 bp):
GAGTATCAGTACTTCCTTTAAT
Done.