Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006064.1 Hibiscus syriacus cultivar Beakdansim tig00014341_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: 68645
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:483 original size:15 final size:15
Alignment explanation
Indices: 463--501 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
453 TACTTGATTG
*
463 TATGTGTATATATGC
1 TATGTGAATATATGC
*
478 TATGTGAATATATGT
1 TATGTGAATATATGC
493 TATG-GAATA
1 TATGTGAATA
502 AAGTAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44
Consensus pattern (15 bp):
TATGTGAATATATGC
Found at i:2081 original size:31 final size:32
Alignment explanation
Indices: 2008--2084 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
1998 TTGAGGGTGT
*
2008 TACACGTGACATGTGCCACATCATCATTTATG
1 TACACGTGACATGTGCAACATCATCATTTATG
* * *
2040 TACACATGACATGTGCAACATCATTA-TTGTG
1 TACACGTGACATGTGCAACATCATCATTTATG
*
2071 TACATGTGACATGT
1 TACACGTGACATGT
2085 ACCATGTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (32 bp):
TACACGTGACATGTGCAACATCATCATTTATG
Found at i:2982 original size:19 final size:19
Alignment explanation
Indices: 2928--2973 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2918 TTAGTTTACT
2928 ATTATAATTGT-AATTTTC
1 ATTATAATTGTAAATTTTC
2946 ATTATAATTGTAAATTTTC
1 ATTATAATTGTAAATTTTC
2965 ATTATAATT
1 ATTATAATT
2974 TGATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (19 bp):
ATTATAATTGTAAATTTTC
Found at i:5078 original size:31 final size:31
Alignment explanation
Indices: 4971--5060 Score: 157
Period size: 30 Copynumber: 3.0 Consensus size: 31
4961 AGAGTCGAGG
*
4971 GTTTACCTATGTTCTTCGGGACATAT-GATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5001 GTTTACCTATGTTCTTCGGGACATA-GGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5031 GTTTACCTATGTTCTTCGGGACATATGGAC
1 GTTTACCTATGTTCTTCGGGACATATGGAC
5061 AAATTACCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
30 53 0.93
31 4 0.07
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5089 original size:31 final size:31
Alignment explanation
Indices: 4973--5091 Score: 102
Period size: 30 Copynumber: 3.9 Consensus size: 31
4963 AGTCGAGGGT
* ****
4973 TTACCTATGTTCTTCGGGACATAT-GATTGT
1 TTACCTATGTTCTTCAGGACATATGGACAAA
* ***
5003 TTACCTATGTTCTTCGGGACATA-GGACTGT
1 TTACCTATGTTCTTCAGGACATATGGACAAA
*
5033 TTACCTATGTTCTTCGGGACATATGGACAAA
1 TTACCTATGTTCTTCAGGACATATGGACAAA
5064 TTACCTA-GATTCTTCAGGATC-TATGGAC
1 TTACCTATG-TTCTTCAGGA-CATATGGAC
5092 TGGTCATTCG
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
30 52 0.65
31 27 0.34
32 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCAGGACATATGGACAAA
Found at i:5969 original size:22 final size:22
Alignment explanation
Indices: 5904--5954 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
5894 TAAAATTCGG
* *
5904 TACTATTCACAGTATTGTTCAT
1 TACTGTTCACGGTATTGTTCAT
*
5926 TACTGTTCACGGTATTGCTCAT
1 TACTGTTCACGGTATTGTTCAT
5948 TACTGTT
1 TACTGTT
5955 TATGGTTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (22 bp):
TACTGTTCACGGTATTGTTCAT
Found at i:6299 original size:61 final size:61
Alignment explanation
Indices: 6198--6334 Score: 159
Period size: 61 Copynumber: 2.2 Consensus size: 61
6188 GAACATATCG
* * * * * *
6198 TCATCCGTGCCTTCGATGGGTTCTGTTTGAGCTGGCGCCACGTAAGGAAAGACGTGGATCA
1 TCATCCGCGCCTTCGATGGGTTCTATCTGAGATGGCGCCACATAAGGAAAGACATGGATCA
* * * *
6259 TCATCCGCGCCTTTG-TGAGGTTCTATCTGAGATGGTGCCACATAAGGAAAGGCATTGATCA
1 TCATCCGCGCCTTCGATG-GGTTCTATCTGAGATGGCGCCACATAAGGAAAGACATGGATCA
*
6320 TCATCTGCGCCTTCG
1 TCATCCGCGCCTTCG
6335 CGGGGTTTCT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
60 2 0.03
61 61 0.97
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (61 bp):
TCATCCGCGCCTTCGATGGGTTCTATCTGAGATGGCGCCACATAAGGAAAGACATGGATCA
Found at i:9423 original size:55 final size:55
Alignment explanation
Indices: 9351--9495 Score: 218
Period size: 55 Copynumber: 2.6 Consensus size: 55
9341 TTTGTATGAG
*
9351 TGTGTATCGGTATACTGAGAAGTGTATCGATACCCTCAAAACATCGAATGTCATT
1 TGTGTATCGGTATACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
* * * * **
9406 TGTGTATCGGTACACTGAGGAGTGTATCGACAACCTCAAAACATCGAGTGTTTTT
1 TGTGTATCGGTATACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
*
9461 TATGTATCGGTATACTGAGGAGTGTATCGATACCC
1 TGTGTATCGGTATACTGAGGAGTGTATCGATACCC
9496 CTAAGTATGA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 79 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (55 bp):
TGTGTATCGGTATACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
Found at i:10107 original size:22 final size:23
Alignment explanation
Indices: 10058--10108 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
10048 CTGGGACAAA
*
10058 TATGTGGCACTTCTGTGCAACCC
1 TATGTGACACTTCTGTGCAACCC
10081 TATGTGACACTTC-GATGCAA-CC
1 TATGTGACACTTCTG-TGCAACCC
10103 TATGTG
1 TATGTG
10109 GTCCTTTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (23 bp):
TATGTGACACTTCTGTGCAACCC
Found at i:17594 original size:64 final size:65
Alignment explanation
Indices: 17523--17684 Score: 206
Period size: 64 Copynumber: 2.5 Consensus size: 65
17513 TCCCTTGACG
* * * *
17523 GGTGCATCGATGCACTACTCATGCATCGGTGCATAAAT-CCTATTCGATGTT-TGT-ATTTTAAT
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATGCC-ATTCGATGTTAT-TAATTTAAAT
17585 CA
64 CA
* * *
17587 GGTGCATCGATGCACTCCTTATGCATCGATGCATTAATGGCATTCGATGTTCATTAATTTAAATG
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATGCCATTCGATGTT-ATTAATTTAAATC
17652 A
65 A
17653 -GTGCATCGATGCACTCCTTATGCATCGATGCA
1 GGTGCATCGATGCACTCCTTATGCATCGATGCA
17685 CCTTCAACAA
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 44 0.51
65 34 0.39
66 9 0.10
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (65 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATGCCATTCGATGTTATTAATTTAAATCA
Found at i:19071 original size:21 final size:21
Alignment explanation
Indices: 19047--19095 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
19037 GTCGAGGATC
* *
19047 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTCCGGGATAAA
19068 TATGTGGTCCTCCGGGATAAA
1 TATGTGGTCCTCCGGGATAAA
19089 TATGTGG
1 TATGTGG
19096 CACTTCAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TATGTGGTCCTCCGGGATAAA
Found at i:24979 original size:25 final size:25
Alignment explanation
Indices: 24951--24999 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
24941 TATAAATTTA
* *
24951 TATAAT-TATTTAGGTTAAACATTAC
1 TATAATAT-TTTAGATTAAAAATTAC
24976 TATAATATTTTAGATTAAAAATTA
1 TATAATATTTTAGATTAAAAATTA
25000 ACTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
TATAATATTTTAGATTAAAAATTAC
Found at i:33761 original size:27 final size:28
Alignment explanation
Indices: 33708--33761 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
33698 TATTGTTAAT
* * * *
33708 TTTTATTTATTTAATTTGTTTAGTATTA
1 TTTTATATATTTAATTTCTATAATATTA
33736 TTTTATAT-TTTAATTTCTATAATATT
1 TTTTATATATTTAATTTCTATAATATT
33762 TATTAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTTATATATTTAATTTCTATAATATTA
Found at i:35656 original size:3 final size:3
Alignment explanation
Indices: 35648--35677 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
35638 TCTTCTCCTT
35648 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
35678 GGCGTTAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:35871 original size:16 final size:15
Alignment explanation
Indices: 35850--35880 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
35840 AATTATGAAC
35850 TTCTTATTTATTTATT
1 TTCTTATTT-TTTATT
35866 TTCTTATTTTTTATT
1 TTCTTATTTTTTATT
35881 ATTTAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTATTTTTTATT
Found at i:35882 original size:26 final size:24
Alignment explanation
Indices: 35853--35929 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 24
35843 TATGAACTTC
35853 TTATTTATTTATTTTCTTATTTTTTA
1 TTATTTATTT-TTTT-TTATTTTTTA
***
35879 TTATTTAATTGTTCAAATTA-TTTTTA
1 TTATTT-ATT-TT-TTTTTATTTTTTA
35905 TTATTTAGTTTTTTTTTATTTTTTA
1 TTATTTA-TTTTTTTTTATTTTTTA
35930 GTTGTATCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
24 3 0.08
25 9 0.22
26 20 0.50
27 7 0.17
28 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (24 bp):
TTATTTATTTTTTTTTATTTTTTA
Found at i:39584 original size:38 final size:38
Alignment explanation
Indices: 39533--39612 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
39523 TACTAGGTGA
39533 ATGCAAACTCCAAATGATCAGTTTCAAGCTCATGGTTG
1 ATGCAAACTCCAAATGATCAGTTTCAAGCTCATGGTTG
39571 ATGCAAACTCCAAATGATCAGTTTCAAGCTCATGGTTG
1 ATGCAAACTCCAAATGATCAGTTTCAAGCTCATGGTTG
39609 ATGC
1 ATGC
39613 TTAAAGTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (38 bp):
ATGCAAACTCCAAATGATCAGTTTCAAGCTCATGGTTG
Found at i:41077 original size:17 final size:17
Alignment explanation
Indices: 41057--41090 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41047 GACCCGACCG
41057 TTGACCCGACCGTTGAC
1 TTGACCCGACCGTTGAC
41074 TTGACCCGACCGTTGAC
1 TTGACCCGACCGTTGAC
41091 CATTGACCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (17 bp):
TTGACCCGACCGTTGAC
Found at i:41079 original size:29 final size:30
Alignment explanation
Indices: 41047--41106 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
41037 GGTCTGACCC
41047 GACCCGACCGTTGACC-CGACCGTTGACTT
1 GACCCGACCGTTGACCACGACCGTTGACTT
*
41076 GACCCGACCGTTGACCATTGACCGTTGACTT
1 GACCCGACCGTTGACCA-CGACCGTTGACTT
41107 TCTTTGACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 16 0.57
31 12 0.43
ACGTcount: A:0.18, C:0.35, G:0.23, T:0.23
Consensus pattern (30 bp):
GACCCGACCGTTGACCACGACCGTTGACTT
Found at i:41091 original size:12 final size:12
Alignment explanation
Indices: 41047--41073 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41037 GGTCTGACCC
41047 GACCCGACCGTT
1 GACCCGACCGTT
41059 GACCCGACCGTT
1 GACCCGACCGTT
41071 GAC
1 GAC
41074 TTGACCCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.41, G:0.26, T:0.15
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:42720 original size:22 final size:24
Alignment explanation
Indices: 42695--42739 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
42685 AATTCAATTT
42695 TCAAA-TATCTTT-CTATTTTATC
1 TCAAAGTATCTTTACTATTTTATC
* *
42717 TCAAAGTATTTTTATTATTTTAT
1 TCAAAGTATCTTTACTATTTTAT
42740 AAACATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (24 bp):
TCAAAGTATCTTTACTATTTTATC
Found at i:44379 original size:16 final size:16
Alignment explanation
Indices: 44333--44383 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
44323 GGTATTACCC
44333 GACATGTTTTCAACCT
1 GACATGTTTTCAACCT
* ** *
44349 GACCTGTGATGAACCT
1 GACATGTTTTCAACCT
*
44365 GACATGTTTTTAACCT
1 GACATGTTTTCAACCT
44381 GAC
1 GAC
44384 TTGTAAATGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (16 bp):
GACATGTTTTCAACCT
Found at i:44435 original size:16 final size:16
Alignment explanation
Indices: 44411--44449 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
44401 TGTTATTGAT
*
44411 CTGATTTGACATTTAC
1 CTGACTTGACATTTAC
*
44427 CTGACTTGACATTTAT
1 CTGACTTGACATTTAC
44443 CTGACTT
1 CTGACTT
44450 ATATATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (16 bp):
CTGACTTGACATTTAC
Found at i:44713 original size:23 final size:24
Alignment explanation
Indices: 44671--44724 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
44661 CAATGATTAA
*
44671 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAATTTAATTT
44695 ATGTAAATT-ATATAATTTAATTT
1 ATGTAAATTAATATAATTTAATTT
44718 ATGTAAA
1 ATGTAAA
44725 GAAAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAATTTAATTT
Found at i:47853 original size:121 final size:121
Alignment explanation
Indices: 47639--47887 Score: 489
Period size: 121 Copynumber: 2.1 Consensus size: 121
47629 AAATTGTAAG
47639 ATTTTAAAACTTCGGGTCTAATTTTGAAAAATTAGAAAAGTTTAGGGACTTAGATTGAAATATCT
1 ATTTTAAAACTTCGGGTCTAATTTTGAAAAATTAGAAAAGTTTAGGGACTTAGATTGAAATATCT
47704 TGGTATTGGATTAAATAGCAAAGAAAGAAAGAAATGAAGGGTATTATGGTATTTTC
66 TGGTATTGGATTAAATAGCAAAGAAAGAAAGAAATGAAGGGTATTATGGTATTTTC
47760 ATTTTAAAACTTCGGGTCTAATTTTGAAAAATTAGAAAAGTTTAGGGACTTAGATTGAAATATCT
1 ATTTTAAAACTTCGGGTCTAATTTTGAAAAATTAGAAAAGTTTAGGGACTTAGATTGAAATATCT
*
47825 TGGTGTTGGATTAAATAGCAAAGAAAGAAAGAAATGAAGGGTATTATGGTATTTTC
66 TGGTATTGGATTAAATAGCAAAGAAAGAAAGAAATGAAGGGTATTATGGTATTTTC
47881 ATTTTAA
1 ATTTTAA
47888 TGGATACTTT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 127 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (121 bp):
ATTTTAAAACTTCGGGTCTAATTTTGAAAAATTAGAAAAGTTTAGGGACTTAGATTGAAATATCT
TGGTATTGGATTAAATAGCAAAGAAAGAAAGAAATGAAGGGTATTATGGTATTTTC
Found at i:48579 original size:35 final size:35
Alignment explanation
Indices: 48536--48605 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
48526 ATTTTTCATG
* *
48536 GGGTATCGATACCGAA-GTGGTAGTATCGGTACCAT
1 GGGTATCGATACC-AATGTAGAAGTATCGGTACCAT
48571 GGGTATCGATACCAATGTAGAAGTATCGGTACCAT
1 GGGTATCGATACCAATGTAGAAGTATCGGTACCAT
48606 TTTTTACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 2 0.06
35 30 0.94
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (35 bp):
GGGTATCGATACCAATGTAGAAGTATCGGTACCAT
Found at i:49510 original size:21 final size:21
Alignment explanation
Indices: 49452--49512 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
49442 AGGGTTCTAC
*
49452 ACGGTCCTTCGGGACATATAT
1 ACGGTCATTCGGGACATATAT
** * * **
49473 TTGATCATTTGTTACATATAT
1 ACGGTCATTCGGGACATATAT
49494 ACGGTCATTCGGGACATAT
1 ACGGTCATTCGGGACATAT
49513 TAGTGGTAAT
Statistics
Matches: 27, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (21 bp):
ACGGTCATTCGGGACATATAT
Found at i:49864 original size:16 final size:16
Alignment explanation
Indices: 49859--49909 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
49849 GTAAACGAAC
49859 ACGAACACGAACATAA
1 ACGAACACGAACATAA
49875 ACGAACACGAACATAA
1 ACGAACACGAACATAA
*
49891 ATGAACACGAACATAA
1 ACGAACACGAACATAA
49907 ACG
1 ACG
49910 TTGGAGACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.55, C:0.24, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACACGAACATAA
Found at i:49881 original size:10 final size:10
Alignment explanation
Indices: 49839--49881 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
49829 CATTTAATAA
49839 ATAAACGAAC
1 ATAAACGAAC
*
49849 GTAAACGAAC
1 ATAAACGAAC
*
49859 ACGAACACGAAC
1 A-TAA-ACGAAC
49871 ATAAACGAAC
1 ATAAACGAAC
49881 A
1 A
49882 CGAACATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 16 0.59
11 4 0.15
12 7 0.26
ACGTcount: A:0.56, C:0.23, G:0.14, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:49903 original size:22 final size:22
Alignment explanation
Indices: 49843--49887 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
49833 TAATAAATAA
*
49843 ACGAACGTAAACGAACACGAAC
1 ACGAACATAAACGAACACGAAC
49865 ACGAACATAAACGAACACGAAC
1 ACGAACATAAACGAACACGAAC
49887 A
1 A
49888 TAAATGAACA
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:0.53, C:0.27, G:0.16, T:0.04
Consensus pattern (22 bp):
ACGAACATAAACGAACACGAAC
Found at i:52650 original size:14 final size:14
Alignment explanation
Indices: 52633--52674 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
52623 GATTGGGTTA
*
52633 AACATAAATGAACG
1 AACATAAACGAACG
*
52647 AACATAAACGAGCG
1 AACATAAACGAACG
*
52661 AACATAACCGAACG
1 AACATAAACGAACG
52675 TTCACGAACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.52, C:0.21, G:0.17, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:56185 original size:20 final size:19
Alignment explanation
Indices: 56160--56226 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
56150 TCTTCATGGG
56160 GTATCGATACCAAAGTGGTA
1 GTATCGATACCAAAGTGG-A
*
56180 GTATCGGTACC--A-TGG-
1 GTATCGATACCAAAGTGGA
*
56195 GTATCGATACCAATGTGGAA
1 GTATCGATACCAAAGTGG-A
*
56215 GTATCGGTACCA
1 GTATCGATACCA
56227 GTTTTTACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
15 10 0.26
17 3 0.08
18 4 0.11
20 21 0.55
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (19 bp):
GTATCGATACCAAAGTGGA
Found at i:56198 original size:35 final size:35
Alignment explanation
Indices: 56158--56226 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
56148 ATTCTTCATG
*
56158 GGGTATCGATACCAAAGTGGTAGTATCGGTACCAT
1 GGGTATCGATACCAAAGTGGAAGTATCGGTACCAT
*
56193 GGGTATCGATACCAATGTGGAAGTATCGGTACCA
1 GGGTATCGATACCAAAGTGGAAGTATCGGTACCA
56227 GTTTTTACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (35 bp):
GGGTATCGATACCAAAGTGGAAGTATCGGTACCAT
Found at i:57109 original size:21 final size:21
Alignment explanation
Indices: 57085--57154 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
57075 CCTTCGAGAT
57085 ATATATGTGATCCTTTGGAAC
1 ATATATGTGATCCTTTGGAAC
* * * *
57106 ATATATGCGGTTC-TTCGAGAC
1 ATATATGTGATCCTTTGGA-AC
57127 ATAT-T-T-AGTCCTTTGGAAC
1 ATATATGTGA-TCCTTTGGAAC
57146 ATATATGTG
1 ATATATGTG
57155 GTTCTTAAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 11
0.65 0.15 0.20
Matches are distributed among these distances:
19 8 0.23
20 10 0.29
21 17 0.49
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (21 bp):
ATATATGTGATCCTTTGGAAC
Found at i:58693 original size:6 final size:6
Alignment explanation
Indices: 58618--58722 Score: 70
Period size: 6 Copynumber: 17.8 Consensus size: 6
58608 GGTTTTTTAA
* * * * * ** *
58618 GGTTCG GGTTTA GATTTG GGTTCG GGTTCG GGTTTG GAATTG GGTTCG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
* * * * *
58666 GCTTT- GGTTT- GGATTG GATTTG GGTTTG GGTTTA GGTTCG GGTTTG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
*
58712 GGTTTA GGTTT
1 GGTTTG GGTTT
58723 AGGTCCGAGT
Statistics
Matches: 74, Mismatches: 24, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
5 8 0.11
6 66 0.89
ACGTcount: A:0.08, C:0.06, G:0.42, T:0.45
Consensus pattern (6 bp):
GGTTTG
Found at i:58725 original size:24 final size:24
Alignment explanation
Indices: 58684--58739 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
58674 TTGGATTGGA
* * *
58684 TTTGGGTTTGGGTTTAGGTTCGGG
1 TTTGGGTTTAGGTTTAGGTCCGAG
58708 TTTGGGTTTAGGTTTAGGTCCGAG
1 TTTGGGTTTAGGTTTAGGTCCGAG
58732 TTTGGGTT
1 TTTGGGTT
58740 ATAGAAGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.07, C:0.05, G:0.41, T:0.46
Consensus pattern (24 bp):
TTTGGGTTTAGGTTTAGGTCCGAG
Found at i:59489 original size:6 final size:6
Alignment explanation
Indices: 59478--59551 Score: 56
Period size: 6 Copynumber: 13.2 Consensus size: 6
59468 ACTATTTATA
*
59478 ATTAAT ATTAAT A-TAA- ATTATAT ATT-AT AATT-AT AAT-AT AATTAAT
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT -ATTAAT ATTAAT -ATTAAT
59524 ATTAAT ATTAA- ATT-AT ATTAAT A-TAAT A
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT A
59552 ATATAGTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
4 2 0.03
5 22 0.38
6 29 0.50
7 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTAAT
Found at i:59501 original size:24 final size:24
Alignment explanation
Indices: 59448--59621 Score: 89
Period size: 24 Copynumber: 7.2 Consensus size: 24
59438 ATTTCATCCC
*
59448 TATATAATTTATATTAATA-AACTAT
1 TATATAATTAATATTAATATAA--AT
59473 T-TATAATTAATATTAATATAAAT
1 TATATAATTAATATTAATATAAAT
*
59496 TATATATTATAAT-TATAATAT-AAT
1 TATATAAT-TAATAT-TAATATAAAT
*
59520 TA-AT-ATTAATATTAA-ATTATAT
1 TATATAATTAATATTAATA-TAAAT
* *
59542 TAATATAA-TAATA-TAGTTTATAAT
1 T-ATATAATTAATATTAATATA-AAT
* * *
59566 TGTAATTAATATAATATAAATAT-AGT
1 TAT-A-TAAT-TAATATTAATATAAAT
* *
59592 CTATAAAATTAATATTAATATAAAC
1 -TATATAATTAATATTAATATAAAT
59617 TATAT
1 TATAT
59622 TTTATAAATT
Statistics
Matches: 112, Mismatches: 18, Indels: 39
0.66 0.11 0.23
Matches are distributed among these distances:
20 1 0.01
21 8 0.07
22 5 0.04
23 11 0.10
24 53 0.47
25 21 0.19
26 3 0.03
27 7 0.06
28 3 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TATATAATTAATATTAATATAAAT
Found at i:59526 original size:64 final size:62
Alignment explanation
Indices: 59449--59634 Score: 163
Period size: 57 Copynumber: 3.0 Consensus size: 62
59439 TTTCATCCCT
*
59449 ATATAATTTATATTAATAAACTATTTATAATTAATATTAATATAAATTATATATTATAATTATA
1 ATATAATTAATATTAATAAA-TATTTA-AATTAATATTAATATAAATTATATATTATAATTATA
* *
59513 ATATAATTAATA-T--T-AATA-TTAAATT-ATATTAATAT-AATAATATAGTTTATAATTGTA
1 ATATAATTAATATTAATAAATATTTAAATTAATATTAATATAAATTATATA--TTATAATTATA
* * * * * *
59570 AT-TAATATAATATAAATATAGTCTATAAAATTAATATTAATATAAACTATATTTTATAAATTAT
1 ATATAAT-TAATATTAATA-AATAT-TTAAATTAATATTAATATAAATTATATATTAT-AATTAT
59634 A
62 A
59635 TAGTATAGTT
Statistics
Matches: 98, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
55 8 0.08
56 14 0.14
57 21 0.21
58 3 0.03
59 2 0.02
60 3 0.03
61 1 0.01
62 2 0.02
63 1 0.01
64 21 0.21
65 16 0.16
66 6 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (62 bp):
ATATAATTAATATTAATAAATATTTAAATTAATATTAATATAAATTATATATTATAATTATA
Found at i:59564 original size:46 final size:41
Alignment explanation
Indices: 59470--59635 Score: 134
Period size: 40 Copynumber: 4.1 Consensus size: 41
59460 ATTAATAAAC
*
59470 TATTTATAATTAATATTAATATAAATTATATATTATAATTA
1 TATTTATAATTAATATTAATATAAATTATATAATATAATTA
*
59511 TA-ATATAATTAATATTAATATTAAATTATATTAATATAATAATA
1 TATTTATAATTAATATTAATA-TAAATTATA-TAATATAAT--TA
* *
59555 TAGTTTATAATT-GTAATTAATAT-AA-TATA-AATATAGTCTA
1 TA-TTTATAATTAAT-ATTAATATAAATTATATAATATAAT-TA
* **
59595 TA---A-AATTAATATTAATATAAACTATATTTTATAAATTA
1 TATTTATAATTAATATTAATATAAATTATATAATAT-AATTA
59633 TAT
1 TAT
59636 AGTATAGTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
35 12 0.12
36 4 0.04
37 4 0.04
38 7 0.07
39 2 0.02
40 21 0.21
41 18 0.18
42 8 0.08
43 4 0.04
44 6 0.06
45 2 0.02
46 14 0.14
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (41 bp):
TATTTATAATTAATATTAATATAAATTATATAATATAATTA
Found at i:59574 original size:30 final size:30
Alignment explanation
Indices: 59450--59634 Score: 122
Period size: 30 Copynumber: 6.1 Consensus size: 30
59440 TTCATCCCTA
*
59450 TATAATTTATATTAATAA-ACTAT-TTATAAT
1 TATAATTAATA-TAATAATA-TATATTATAAT
*
59480 TA-ATATTAATATAA-ATTATATATTATAAT
1 TATA-ATTAATATAATAATATATATTATAAT
*
59509 TATAATATAAT-TAATATTA-ATATTA-AAT
1 TATAAT-TAATATAATAATATATATTATAAT
59537 TAT-ATTAATATAATAATATAGT-TTATAAT
1 TATAATTAATATAATAATATA-TATTATAAT
* *
59566 TGTAATTAATATAATATAAATATAGTCTATAAAAT
1 TATAATTAATATAATA-ATATATA-T-TAT--AAT
* *
59601 TA-ATATTAATATAA-ACTATATTTTATAAAT
1 TATA-ATTAATATAATAATATATATTAT-AAT
59631 TATA
1 TATA
59635 TAGTATAGTT
Statistics
Matches: 127, Mismatches: 9, Indels: 37
0.73 0.05 0.21
Matches are distributed among these distances:
26 4 0.03
27 9 0.07
28 14 0.11
29 31 0.24
30 36 0.28
31 8 0.06
32 2 0.02
33 7 0.06
34 2 0.02
35 14 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (30 bp):
TATAATTAATATAATAATATATATTATAAT
Found at i:59581 original size:35 final size:31
Alignment explanation
Indices: 59569--59676 Score: 87
Period size: 35 Copynumber: 3.4 Consensus size: 31
59559 TTATAATTGT
*
59569 AATTAATA-TAATAT-AAATATAGTCTATAA
1 AATTAATATTAATATAAAATATAGTTTATAA
* *
59598 AATTAATATTAATATAAACTATATTTTAT-A
1 AATTAATATTAATATAAAATATAGTTTATAA
* * * *
59628 AATTATATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAAATATAGTTTATAA
59664 AATTAATATTAAT
1 AATTAATATTAAT
59677 TAGTATATGG
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
29 8 0.13
30 12 0.19
31 14 0.22
32 1 0.02
33 4 0.06
34 1 0.02
35 18 0.29
36 5 0.08
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATAGTTTATAA
Found at i:59806 original size:36 final size:36
Alignment explanation
Indices: 59766--59844 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
59756 TAATGTAAAC
*
59766 TATAGTTTATAAACTATCTACTACATTAATACAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
* *
59802 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
59838 TATAGTT
1 TATAGTT
59845 AAGATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (36 bp):
TATAGTTTATAAACTATATACTACATTAATACAAAT
Found at i:59841 original size:15 final size:15
Alignment explanation
Indices: 59823--59873 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
59813 AACTATATAC
59823 TATATTAATATAAAT
1 TATATTAATATAAAT
*
59838 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
59853 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
59869 TATAT
1 TATAT
59874 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:59895 original size:20 final size:21
Alignment explanation
Indices: 59855--59896 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
59845 AAGATAATTA
59855 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
59877 ACATTAATATAAA-ATATAGT
1 ACATTAATATAAACATATAGT
59897 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:59958 original size:21 final size:21
Alignment explanation
Indices: 59932--60039 Score: 85
Period size: 22 Copynumber: 5.1 Consensus size: 21
59922 ATTTATAGTT
* *
59932 TACATATAAATAGATTGTATA
1 TACATATATATAGATTATATA
*
59953 TACATATACTATAGGTTATATA
1 TACATATA-TATAGATTATATA
* *
59975 TATATATATATAGTTTATATA
1 TACATATATATAGATTATATA
* * * *
59996 TA-TTATACATAGTTTATACA
1 TACATATATATAGATTATATA
*
60016 TACATGTACTATA-AGTTATATA
1 TACATATA-TATAGA-TTATATA
60038 TA
1 TA
60040 TAGTTTACAT
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
20 17 0.24
21 25 0.36
22 28 0.40
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (21 bp):
TACATATATATAGATTATATA
Found at i:59974 original size:20 final size:20
Alignment explanation
Indices: 59949--60037 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
59939 AAATAGATTG
59949 TATATACATATACTATAGGT
1 TATATACATATACTATAGGT
* * *
59969 TATATATATATATATATAGTT
1 TATATACATATA-CTATAGGT
* *
59990 TATATATATTATAC-ATAGTT
1 TATATACA-TATACTATAGGT
* *
60010 TATACATACATGTACTATAAGT
1 TAT--ATACATATACTATAGGT
60032 TATATA
1 TATATA
60038 TATAGTTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
20 23 0.41
21 18 0.32
22 15 0.27
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
TATATACATATACTATAGGT
Found at i:60273 original size:290 final size:288
Alignment explanation
Indices: 59975--60506 Score: 920
Period size: 290 Copynumber: 1.8 Consensus size: 288
59965 AGGTTATATA
* *
59975 TATATATATATAGTTTATATATATTATACATAGTTTATACATACATGTACTATAAGTTATATATA
1 TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
* *
60040 TAGTTTACATGTATACATATACTATAGGTTACATATATTAACTATTGTTTAAAGACTATAGGTTA
66 TAGTTTACATGTATACATATACTACAGGTTAAATATATTAACTATTGTTTAAAGACTATAGGTTA
60105 AGGTTACATATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAAATGTGT
131 AGGTTACATATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAAATGTGT
* * * *
60170 CTATATATATATGTAGTTTATATAGTTTAGGGTGTAGGGTTTAGGGTTTATTTTTTAAGGTTTAG
196 CTATACATATA--TAATCTATATAGTTTAGGGTGTAGGGTTTAGAGTTTATTTTTTAAGGTTTAG
60235 GGTTTCTATAAACTATATACTTTATTACTT
259 GGTTTCTATAAACTATATACTTTATTACTT
*
60265 TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTGCATATA
1 TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
* *
60330 TAGTTTATATGTATACATATACTACAGGTTAAATATATTAACTATTGTTTATAGACTATAGGTTA
66 TAGTTTACATGTATACATATACTACAGGTTAAATATATTAACTATTGTTTAAAGACTATAGGTTA
*
60395 AGGTTACATATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAATTGTGT
131 AGGTTACATATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAAATGTGT
* *
60460 CTATACATATATAATCTATATGGTTTAGGGTTTAGGGTTTAGAGTTT
196 CTATACATATATAATCTATATAGTTTAGGGTGTAGGGTTTAGAGTTT
60507 CTATAAACTA
Statistics
Matches: 228, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
288 31 0.14
290 197 0.86
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (288 bp):
TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
TAGTTTACATGTATACATATACTACAGGTTAAATATATTAACTATTGTTTAAAGACTATAGGTTA
AGGTTACATATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAAATGTGT
CTATACATATATAATCTATATAGTTTAGGGTGTAGGGTTTAGAGTTTATTTTTTAAGGTTTAGGG
TTTCTATAAACTATATACTTTATTACTT
Found at i:60281 original size:15 final size:16
Alignment explanation
Indices: 60263--60292 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
60253 ACTTTATTAC
60263 TTTATATATA-TATAG
1 TTTATATATACTATAG
60278 TTTATATATACTATA
1 TTTATATATACTATA
60293 CATAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTATATATACTATAG
Found at i:60297 original size:20 final size:20
Alignment explanation
Indices: 60265--60308 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
60255 TTTATTACTT
*
60265 TATA-TATATATAGTTTATA
1 TATACTATACATAGTTTATA
60284 TATACTATACATAGTTTATA
1 TATACTATACATAGTTTATA
*
60304 CATAC
1 TATAC
60309 ATGTACTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (20 bp):
TATACTATACATAGTTTATA
Found at i:60618 original size:35 final size:34
Alignment explanation
Indices: 60579--60708 Score: 104
Period size: 35 Copynumber: 3.7 Consensus size: 34
60569 CTTTATTACT
*
60579 TTATATATATATATATCTATAGATACATATATTAG
1 TTATATATATATATATATATA-ATACATATATTAG
* * * * *
60614 TTATATACATATATATATATAATATAATTTATAAT
1 TTATATATATATATATATATAATA-CATATATTAG
* *
60649 TTATAAACTATAT-TATATAGTTTATACATATA-TAG
1 TTATATA-TATATATATATA--TAATACATATATTAG
60684 TT-TATATATATATACTATATCAATA
1 TTATATATATATATA-TATAT-AATA
60709 TATAGTTTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
33 6 0.08
34 11 0.15
35 44 0.60
36 8 0.11
37 4 0.05
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (34 bp):
TTATATATATATATATATATAATACATATATTAG
Found at i:60646 original size:12 final size:13
Alignment explanation
Indices: 60580--60712 Score: 72
Period size: 15 Copynumber: 9.5 Consensus size: 13
60570 TTTATTACTT
60580 TATATATATAT-A
1 TATATATATATAA
* *
60592 TATCTATAGATACA
1 TATATATATATA-A
60606 TATATTAGTTATATACA
1 TATA-TA--TATATA-A
60623 TATATATATATAA
1 TATATATATATAA
*
60636 TATA-ATTTATAA
1 TATATATATATAA
* * *
60648 TTTATAAACTATAT
1 TATATATA-TATAA
*
60662 TATATAGTTTATACA
1 TATATA-TATATA-A
*
60677 TATATAGTTTATATA
1 TATATA-TATATA-A
60692 TATATACTATATCAA
1 TATATA-TATAT-AA
60707 TATATA
1 TATATA
60713 GTTTAAAACT
Statistics
Matches: 95, Mismatches: 16, Indels: 17
0.74 0.12 0.13
Matches are distributed among these distances:
12 19 0.20
13 6 0.06
14 23 0.24
15 33 0.35
16 3 0.03
17 11 0.12
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (13 bp):
TATATATATATAA
Found at i:60661 original size:71 final size:71
Alignment explanation
Indices: 60564--60710 Score: 167
Period size: 71 Copynumber: 2.1 Consensus size: 71
60554 TTTATAAACT
* * * *
60564 ATATACTTTATTACTTTATATATATATATATCTA-TAGATACATATATTAGTTATATACATATAT
1 ATATAATTTATTAATTTATAAATATAT-TATATAGTAGATACATATA-TAGTT-TATACATATAT
60628 A-TATAT-A
63 ACTATATCA
** *
60635 ATATAATTTA-TAATTTATAAACTATATTATATAGTTTATACATATATAGTTTATATATATATAC
1 ATATAATTTATTAATTTATAAA-TATATTATATAGTAGATACATATATAGTTTATACATATATAC
60699 TATATCA
65 TATATCA
60706 ATATA
1 ATATA
60711 TAGTTTAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
69 11 0.17
70 24 0.37
71 30 0.46
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (71 bp):
ATATAATTTATTAATTTATAAATATATTATATAGTAGATACATATATAGTTTATACATATATACT
ATATCA
Found at i:60682 original size:15 final size:15
Alignment explanation
Indices: 60601--60717 Score: 77
Period size: 15 Copynumber: 8.1 Consensus size: 15
60591 ATATCTATAG
60601 ATACATATATTAGTTAT
1 ATACATATA-TAGTT-T
*
60618 ATACATATATA-TAT
1 ATACATATATAGTTT
60632 ATA-ATATA-A-TTT
1 ATACATATATAGTTT
* ***
60644 ATA-ATTTATAAACT
1 ATACATATATAGTTT
*
60658 ATA-TTATATAGTTT
1 ATACATATATAGTTT
60672 ATACATATATAGTTT
1 ATACATATATAGTTT
* * *
60687 ATATATATATACTAT
1 ATACATATATAGTTT
60702 AT-CAATATATAGTTT
1 ATAC-ATATATAGTTT
60717 A
1 A
60718 AAACTATATA
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
12 10 0.13
13 6 0.08
14 17 0.22
15 35 0.44
16 2 0.03
17 9 0.11
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (15 bp):
ATACATATATAGTTT
Found at i:60693 original size:28 final size:28
Alignment explanation
Indices: 60605--60717 Score: 83
Period size: 28 Copynumber: 4.0 Consensus size: 28
60595 CTATAGATAC
*
60605 ATATAT-TAGTTATATACATATATA-TAT
1 ATATATATAGTT-TATACATATATAGTTT
* * ***
60632 ATA-ATATAATTTATA-ATTTATAAACT
1 ATATATATAGTTTATACATATATAGTTT
60658 ATATTATATAGTTTATACATATATAGTTT
1 ATA-TATATAGTTTATACATATATAGTTT
*
60687 ATATATATA-TACTATATCAATATATAGTTT
1 ATATATATAGT-TTATA-C-ATATATAGTTT
60717 A
1 A
60718 AAACTATATA
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
25 6 0.09
26 10 0.15
27 8 0.12
28 21 0.31
29 11 0.16
30 12 0.18
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (28 bp):
ATATATATAGTTTATACATATATAGTTT
Found at i:60727 original size:2 final size:2
Alignment explanation
Indices: 60580--60712 Score: 73
Period size: 2 Copynumber: 67.0 Consensus size: 2
60570 TTTATTACTT
* * *
60580 TA TA TA TA TA TA TA TC TA TA GA TA CA TA TA T- TA GT- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
60621 CA TA TA TA TA TA TA -A TA TA -A TT TA TA -A TT TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
60661 T- TA TA TA GTT TA TA CA TA TA TA GTT TA TA TA TA TA TA CTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
60703 TCA -A TA TA TA
1 T-A TA TA TA TA
60713 GTTTAAAACT
Statistics
Matches: 98, Mismatches: 20, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
1 7 0.07
2 84 0.86
3 7 0.07
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:60759 original size:15 final size:15
Alignment explanation
Indices: 60663--60768 Score: 58
Period size: 15 Copynumber: 6.9 Consensus size: 15
60653 AAACTATATT
* *
60663 ATATAGTTTATACAT
1 ATATAGTTTATATAC
*
60678 ATATAGTTTATATAT
1 ATATAGTTTATATAC
* * *
60693 ATATACTATATCA-AT
1 ATATAGTTTAT-ATAC
*
60708 ATATAGTTTA-AAAC
1 ATATAGTTTATATAC
*
60722 TATATACTTTTATAGTTTAC
1 -ATATA-GTTTATA---TAC
60742 ATATAGTTTATATAC
1 ATATAGTTTATATAC
60757 ATA-A-TTTATATA
1 ATATAGTTTATATA
60769 TAGGTCATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
13 9 0.12
14 2 0.03
15 44 0.59
16 5 0.07
17 1 0.01
18 6 0.08
19 5 0.07
20 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (15 bp):
ATATAGTTTATATAC
Found at i:60790 original size:26 final size:24
Alignment explanation
Indices: 60733--60826 Score: 75
Period size: 26 Copynumber: 3.8 Consensus size: 24
60723 ATATACTTTT
* * *
60733 ATAGTTTACATATAGTTTATATAC
1 ATAGTTTATATATAGTATATAAAC
*
60757 ATAATTTATATATAGGTCATATAAAC
1 ATAGTTTATATATA-GT-ATATAAAC
* *
60783 ATAGTTTATATATAACTATA-ATAAT
1 ATAGTTTATATAT-AGTATATA-AAC
60808 ATAGTTTATAGTATA-TATA
1 ATAGTTTATA-TATAGTATA
60827 GTTTATATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
24 17 0.29
25 18 0.31
26 22 0.38
27 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (24 bp):
ATAGTTTATATATAGTATATAAAC
Found at i:60854 original size:51 final size:51
Alignment explanation
Indices: 60788--60886 Score: 121
Period size: 51 Copynumber: 1.9 Consensus size: 51
60778 TAAACATAGT
* * *
60788 TTATATATAACTATAATAATATAGTTT-ATAGTATATATAGTTTATATAAAC
1 TTATATATAACTATAA-AATATACTTTAACACTATATATAGTTTATATAAAC
* *
60839 TTATATATTAA-TATAAATTATACTTTAACACTTTATATAGTTTATATA
1 TTATATA-TAACTATAAAATATACTTTAACACTATATATAGTTTATATA
60887 TTGTTTACAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 8 0.20
51 30 0.73
52 3 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (51 bp):
TTATATATAACTATAAAATATACTTTAACACTATATATAGTTTATATAAAC
Found at i:60859 original size:17 final size:19
Alignment explanation
Indices: 60821--60860 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
60811 GTTTATAGTA
*
60821 TATATAGTTTATATAAACT
1 TATATAGTTAATATAAACT
60840 TATATA-TTAATATAAA-T
1 TATATAGTTAATATAAACT
60857 TATA
1 TATA
60861 CTTTAACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TATATAGTTAATATAAACT
Found at i:61068 original size:11 final size:11
Alignment explanation
Indices: 61051--61085 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
61041 TAGGTTATTA
61051 ATAAACTACAT
1 ATAAACTACAT
*
61062 TTAAACTACAT
1 ATAAACTACAT
*
61073 ATAAACTATAT
1 ATAAACTACAT
61084 AT
1 AT
61086 TATATATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAAACTACAT
Found at i:61104 original size:2 final size:2
Alignment explanation
Indices: 61099--61134 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
61089 ATATTTGTCT
61099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61135 AATTTTTTTC
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):
TA
Found at i:65243 original size:2 final size:2
Alignment explanation
Indices: 65236--65270 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
65226 CATACCACAT
65236 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
65271 TACTTTTTGT
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
Done.