Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003382.1 Hibiscus syriacus cultivar Beakdansim tig00007117_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: 149125
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4521 original size:15 final size:15
Alignment explanation
Indices: 4501--4531 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4491 AATACACTGA
4501 TGAGTGAGTATCGTC
1 TGAGTGAGTATCGTC
4516 TGAGTGAGTATCGTC
1 TGAGTGAGTATCGTC
4531 T
1 T
4532 TTACAGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.35
Consensus pattern (15 bp):
TGAGTGAGTATCGTC
Found at i:11017 original size:29 final size:29
Alignment explanation
Indices: 10978--11042 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
10968 ACTAATATAA
*
10978 AAATT-TAAATT-TTAAAGTATTTAACATAT
1 AAATTATAAATTATTAAAAT-TTTAA-ATAT
11007 -AATTATAAATTAGTTAAAATTTTAAATAT
1 AAATTATAAATTA-TTAAAATTTTAAATAT
11036 AAATTAT
1 AAATTAT
11043 TTAAAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 4 0.13
29 10 0.32
30 11 0.35
31 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
AAATTATAAATTATTAAAATTTTAAATAT
Found at i:13968 original size:24 final size:24
Alignment explanation
Indices: 13941--13986 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
13931 AATATTAAAG
13941 AATTTCAAAATAAATAACTAAATA
1 AATTTCAAAATAAATAACTAAATA
* *
13965 AATTTTAAAATAAATAATTAAA
1 AATTTCAAAATAAATAACTAAA
13987 CAAAATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTTCAAAATAAATAACTAAATA
Found at i:14626 original size:2 final size:2
Alignment explanation
Indices: 14619--14651 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14609 AATAATACTC
14619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14652 AATTAAATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15498 original size:22 final size:21
Alignment explanation
Indices: 15458--15498 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15448 AAACTATGTA
*
15458 TTTAATATTTAAATTATTATT
1 TTTAATATTTAAATAATTATT
*
15479 TTTAATCATTTTAATAATTA
1 TTTAAT-ATTTAAATAATTA
15499 AACTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAATATTTAAATAATTATT
Found at i:15973 original size:14 final size:13
Alignment explanation
Indices: 15950--15980 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
15940 CACTAAATTA
15950 ATTTATTATTGAT
1 ATTTATTATTGAT
15963 ATTTAATTATTGAT
1 ATTT-ATTATTGAT
15977 ATTT
1 ATTT
15981 TAAACCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (13 bp):
ATTTATTATTGAT
Found at i:16894 original size:17 final size:18
Alignment explanation
Indices: 16872--16914 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
16862 TAATTTAAAC
16872 TATAATAAAAATATA-AT
1 TATAATAAAAATATATAT
*
16889 TATAATAAAAATATATTT
1 TATAATAAAAATATATAT
16907 TATAATAA
1 TATAATAA
16915 CTCATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAATAAAAATATATAT
Found at i:20874 original size:28 final size:28
Alignment explanation
Indices: 20838--20891 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
20828 AATGCTCGAA
*
20838 CAAACTAAAGATACAAACAAATCTGATG
1 CAAAATAAAGATACAAACAAATCTGATG
* *
20866 CAAAATAAAGATTCGAACAAATCTGA
1 CAAAATAAAGATACAAACAAATCTGA
20892 CTACATCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.19
Consensus pattern (28 bp):
CAAAATAAAGATACAAACAAATCTGATG
Found at i:22682 original size:29 final size:29
Alignment explanation
Indices: 22625--22684 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
22615 CTTTTTCATT
* *
22625 TAAGTACCTAAACTATGTTTTGGTCAAAA
1 TAAGTACCTAAACTATGTTTTGATAAAAA
* * *
22654 TAAGTACCTAAAGTATTTTTTTATAAAAA
1 TAAGTACCTAAACTATGTTTTGATAAAAA
22683 TA
1 TA
22685 GGTATAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
TAAGTACCTAAACTATGTTTTGATAAAAA
Found at i:22816 original size:28 final size:28
Alignment explanation
Indices: 22780--22875 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
22770 GAAAATTTTG
* * *
22780 AATAGTTTAGGTGCATATTTTGACATAA
1 AATACTTTAGGTACATATTTTGACAAAA
* * *
22808 AATACTTTAAGTACCTATTTTGATTAAAA
1 AATACTTTAGGTACATATTTTGA-CAAAA
* **
22837 ATATAATTTTAGGTATTTATTTTGACAAAA
1 A-AT-ACTTTAGGTACATATTTTGACAAAA
22867 AATACTTTA
1 AATACTTTA
22876 AATACTTAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 24 0.45
29 6 0.11
30 7 0.13
31 16 0.30
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (28 bp):
AATACTTTAGGTACATATTTTGACAAAA
Found at i:23287 original size:17 final size:17
Alignment explanation
Indices: 23234--23279 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
23224 ATTTTTCGTT
23234 AAATAAAATTTTATATA
1 AAATAAAATTTTATATA
23251 AAATAAAATTTTATATA
1 AAATAAAATTTTATATA
23268 AAATAAAATTTT
1 AAATAAAATTTT
23280 GTAAAAAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAAAATTTTATATA
Found at i:23610 original size:20 final size:20
Alignment explanation
Indices: 23585--23644 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
23575 TCAACACCGT
23585 GAACTGCCATGTCAGTACCA
1 GAACTGCCATGTCAGTACCA
23605 GAACTGCCATGTCAGTACCA
1 GAACTGCCATGTCAGTACCA
23625 GAACTGCCATGTCAGTACCA
1 GAACTGCCATGTCAGTACCA
23645 AAACGATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (20 bp):
GAACTGCCATGTCAGTACCA
Found at i:26821 original size:20 final size:20
Alignment explanation
Indices: 26796--26855 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
26786 TCAACACCGT
26796 GAACTGCCATGTCAGTACCA
1 GAACTGCCATGTCAGTACCA
26816 GAACTGCCATGTCAGTACCA
1 GAACTGCCATGTCAGTACCA
26836 GAACTGCCATGTCAGTACCA
1 GAACTGCCATGTCAGTACCA
26856 AAACGATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (20 bp):
GAACTGCCATGTCAGTACCA
Found at i:31061 original size:2 final size:2
Alignment explanation
Indices: 31054--31097 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
31044 AATTTCGAAC
31054 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
31096 AT
1 AT
31098 TTGACATGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33230 original size:13 final size:13
Alignment explanation
Indices: 33212--33236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33202 TCATGTAGCC
33212 TAGTAGTGGTAAT
1 TAGTAGTGGTAAT
33225 TAGTAGTGGTAA
1 TAGTAGTGGTAA
33237 AAGAGAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (13 bp):
TAGTAGTGGTAAT
Found at i:37168 original size:23 final size:23
Alignment explanation
Indices: 37118--37168 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
37108 AGGTTCAAGT
* * *
37118 TCGAACTCGAGTTCGAGCTTGAA
1 TCGAGCTCAAGTTCGAGCTTCAA
* *
37141 CCGAGCTCAAGTTTGAGCTTCAA
1 TCGAGCTCAAGTTCGAGCTTCAA
37164 TCGAG
1 TCGAG
37169 TTAAATATGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (23 bp):
TCGAGCTCAAGTTCGAGCTTCAA
Found at i:38917 original size:29 final size:28
Alignment explanation
Indices: 38879--38960 Score: 110
Period size: 29 Copynumber: 2.9 Consensus size: 28
38869 AAAAGCATAC
*
38879 CCCTAATAATAAATATTAAAAAATTAGG
1 CCCTAATAATAAATATTAAAAAATTAGA
*
38907 CCCTAGATAATAAGTATTAAAAAATTAGA
1 CCCTA-ATAATAAATATTAAAAAATTAGA
* *
38936 CCTTTAATAATAAATGTTAAAAAAT
1 CC-CTAATAATAAATATTAAAAAAT
38961 ATTGACAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
28 5 0.11
29 40 0.85
30 2 0.04
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.30
Consensus pattern (28 bp):
CCCTAATAATAAATATTAAAAAATTAGA
Found at i:39822 original size:20 final size:20
Alignment explanation
Indices: 39739--39823 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
39729 AATAACCAAT
**
39739 AAATTCGCAACGCGAACTCC
1 AAATTCGCAACGCGATTTCC
* *
39759 AATTTCGCAACAC-AGTTTCC
1 AAATTCGCAACGCGA-TTTCC
* * * **
39779 AAATTCGTAACTCAATTTTG
1 AAATTCGCAACGCGATTTCC
*
39799 AAATTCGCAACGCGATTTCA
1 AAATTCGCAACGCGATTTCC
39819 AAATT
1 AAATT
39824 AACGTCGTCG
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (20 bp):
AAATTCGCAACGCGATTTCC
Found at i:40271 original size:20 final size:20
Alignment explanation
Indices: 40227--40454 Score: 182
Period size: 20 Copynumber: 11.2 Consensus size: 20
40217 AATGACCAAC
*
40227 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
40246 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
40266 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
40286 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
40306 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
40327 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
40348 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
40369 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
40390 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
40412 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
40430 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
40450 AAAAT
1 AAAAT
40455 GAGTAAATTC
Statistics
Matches: 169, Mismatches: 25, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.02
19 15 0.09
20 107 0.63
21 14 0.08
22 29 0.17
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:40354 original size:42 final size:42
Alignment explanation
Indices: 40303--40445 Score: 236
Period size: 42 Copynumber: 3.5 Consensus size: 42
40293 CAACGGTCAA
40303 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
* *
40345 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
* *
40387 CAGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
40427 AAGAAAATCGCAACGCGAT
1 AAGAAAATCGCAACGCGAT
40446 TAAGAAAATG
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 37 0.40
42 55 0.60
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
Found at i:40561 original size:6 final size:6
Alignment explanation
Indices: 40550--40636 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
40540 GACACGTATT
40550 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
40598 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
40637 CGAGACGAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:41158 original size:6 final size:6
Alignment explanation
Indices: 41142--41179 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
41132 TCTCGTCTCG
41142 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
41180 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:41368 original size:60 final size:60
Alignment explanation
Indices: 41275--41582 Score: 319
Period size: 60 Copynumber: 5.1 Consensus size: 60
41265 GAATTTACTC
*
41275 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCG
41335 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCG
* * ***
41395 A--TTCTTGGAATCGCGTTGCGATT-TTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCG
* * *
41457 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTT--TTGACCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTTAATCG--CGTTGCG
* * ** *
41519 ATTTTCTT-TTCAACGTTGCGATT-TTCTAAATCGCGTTGCGA-TTT-TTATTTCGCGTTGCG
1 ATTTTCTTAATC-GCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTTA-ATCGCGTTGCG
41578 ATTTT
1 ATTTT
41583 GTTGGTCATT
Statistics
Matches: 210, Mismatches: 21, Indels: 35
0.79 0.08 0.13
Matches are distributed among these distances:
58 7 0.03
59 17 0.08
60 104 0.50
61 10 0.05
62 50 0.24
63 5 0.02
64 17 0.08
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (60 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCG
Found at i:41518 original size:42 final size:40
Alignment explanation
Indices: 41282--41582 Score: 314
Period size: 40 Copynumber: 7.5 Consensus size: 40
41272 CTCATTTTCT
41282 GAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGA--TTCTTG
41323 -AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
41362 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
41402 GAATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
41442 GAAGATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
41484 GAATATCGCGTTGCGATTTTCTT--TTGACCGTTGCGATT-TTC
1 G-A-ATCGCGTTGCGATTTTCTTAATCG--CGTTGCGATTCTTG
*** * *
41525 TTTTCAACGTTGCGATTTTCTAAATCGCGTTGCGATT-TT-
1 GAATC-GCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
41564 TATTTCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
41583 GTTGGTCATT
Statistics
Matches: 231, Mismatches: 17, Indels: 26
0.84 0.06 0.09
Matches are distributed among these distances:
38 5 0.02
39 15 0.06
40 135 0.58
41 3 0.01
42 73 0.32
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (40 bp):
GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
Found at i:41555 original size:20 final size:20
Alignment explanation
Indices: 41275--41582 Score: 260
Period size: 20 Copynumber: 15.2 Consensus size: 20
41265 GAATTTACTC
41275 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
41295 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
41315 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
41335 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
41355 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
41375 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
41395 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
41415 ATTTTCTGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
41435 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
41457 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
41477 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
41499 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
41519 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
41539 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
41559 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
41578 ATTTT
1 ATTTT
41583 GTTGGTCATT
Statistics
Matches: 238, Mismatches: 27, Indels: 47
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 22 0.09
20 167 0.70
21 18 0.08
22 27 0.11
25 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:49153 original size:3 final size:3
Alignment explanation
Indices: 49145--49220 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
49135 CATAAATTTG
49145 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
49193 TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
49221 TTTTTTGACC
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 1 0.01
3 69 0.99
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:49442 original size:39 final size:38
Alignment explanation
Indices: 49388--49527 Score: 133
Period size: 39 Copynumber: 3.5 Consensus size: 38
49378 GGATTGAACA
49388 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTT-GATG
* * **
49427 AGTTCTTCTTATTATGAAC-TCTTC--CCTGGAAATAATTGAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCT----CT--TTGATG
*
49468 ATGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATG
1 A-GTTCTTCTCATTATGAACTTCTTCTTCCTC-TTTGATG
49508 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
49528 CTCAACTGAA
Statistics
Matches: 81, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
36 3 0.04
38 5 0.06
39 37 0.46
40 5 0.06
41 3 0.04
42 20 0.25
43 5 0.06
45 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (38 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGATG
Found at i:49515 original size:81 final size:81
Alignment explanation
Indices: 49380--49529 Score: 264
Period size: 81 Copynumber: 1.9 Consensus size: 81
49370 AATGCATTGG
* *
49380 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTAGATGAGTTCTTCTTATTATGAA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGATGAGTTCTTCTCATTATGAA
49445 CTCTTCCCTGGAAATA
66 CTCTTCCCTGGAAATA
* *
49461 ATTGAACATGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGATGAGTTCTTCTCATTATGAA
49526 CTCT
66 CTCT
49530 CAACTGAAAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (81 bp):
ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGATGAGTTCTTCTCATTATGAA
CTCTTCCCTGGAAATA
Found at i:49812 original size:136 final size:136
Alignment explanation
Indices: 49614--50197 Score: 895
Period size: 136 Copynumber: 4.3 Consensus size: 136
49604 CCTTTAAGAC
* ** *
49614 GAGTTCTTCTCATTATGAACTCT--TTTGGAAATGTCAATCCCTCTAA-CGAGGCGTCACTGATT
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTC-AAGCGAGGTGTCACTGATT
* * *
49676 CGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGATCTTCTCATTATGAACTTCTTCTCCCTCT
65 CGAAATGCCGTGAATCGAGTGATAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT
49741 GTCGGAT
130 GTCGGAT
* **
49748 GAGTTCTTCTCATTATGAACTCTCCATTAGAAATACTGATCCCTCAAGCGAGGTGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTC
* *
49813 GAAATACCGTGAATCAAGTGATAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
66 GAAATGCCGTGAATCGAGTGATAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
49878 TCGGAT
131 TCGGAT
* ** *
49884 GAGTTCTTCTCATTATAAACTCTTTACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTC
* * *
49949 GAAATGCCGTGAATCGAGTGATAAGTCAAACAAGCTCTTCTCATTATAAACTTTTTCTCCCTCTG
66 GAAATGCCGTGAATCGAGTGATAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
50014 TCGGAT
131 TCGGAT
* * *
50020 GAGTTCTTCTCATTATGAACTCTTCACTGGAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTC
* * * * *
50085 GAAATGCCATAAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAATTTTTTCTCCCTCTG
66 GAAATGCCGTGAATCGAGTGATAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
50150 TCGGAT
131 TCGGAT
50156 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCC
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCC
50198 ATCTATTTCT
Statistics
Matches: 412, Mismatches: 35, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
134 23 0.06
135 2 0.00
136 387 0.94
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (136 bp):
GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTC
GAAATGCCGTGAATCGAGTGATAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
TCGGAT
Found at i:51081 original size:8 final size:8
Alignment explanation
Indices: 51070--51157 Score: 65
Period size: 8 Copynumber: 10.5 Consensus size: 8
51060 TCTTTTTCTC
51070 TTTTCATT
1 TTTTCATT
51078 TTTTCATT
1 TTTTCATT
51086 TCATTTCATT
1 T--TTTCATT
51096 TTTTCATT
1 TTTTCATT
51104 TCATTT--TCT
1 T--TTTCAT-T
51113 TTTTCATTT
1 TTTTCA-TT
*
51122 TTTTCACT
1 TTTTCATT
51130 TTTTCATCT
1 TTTTCAT-T
51139 TTTT-ATT
1 TTTTCATT
* *
51146 TGTTCCTT
1 TTTTCATT
51154 TTTT
1 TTTT
51158 TCTTCAAGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
7 7 0.11
8 32 0.49
9 14 0.22
10 12 0.18
ACGTcount: A:0.11, C:0.16, G:0.01, T:0.72
Consensus pattern (8 bp):
TTTTCATT
Found at i:51087 original size:13 final size:13
Alignment explanation
Indices: 51084--51124 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
51074 CATTTTTTCA
51084 TTTCATTTCATTT
1 TTTCATTTCATTT
51097 TTTCATTTCATTT
1 TTTCATTTCATTT
51110 TCTT--TTTCATTT
1 T-TTCATTTCATTT
51122 TTT
1 TTT
51125 TCACTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.07
12 9 0.33
13 14 0.52
14 2 0.07
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCATTTCATTT
Found at i:51089 original size:5 final size:5
Alignment explanation
Indices: 51071--51109 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
51061 CTTTTTCTCT
51071 TTTCA TTT-- TTTCA TTTCA TTTCA TTT-- TTTCA TTTCA TTT
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTT
51110 TCTTTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 6 0.20
5 24 0.80
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (5 bp):
TTTCA
Found at i:51094 original size:18 final size:18
Alignment explanation
Indices: 51071--51136 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
51061 CTTTTTCTCT
51071 TTTCATTTTTTCATTTCA
1 TTTCATTTTTTCATTTCA
51089 TTTCATTTTTTCATTTCA
1 TTTCATTTTTTCATTTCA
*
51107 TTT--TCTTTTTCATTT-T
1 TTTCAT-TTTTTCATTTCA
*
51123 TTTCACTTTTTCAT
1 TTTCATTTTTTCAT
51137 CTTTTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
16 4 0.09
17 18 0.42
18 21 0.49
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCATTTTTTCATTTCA
Found at i:51115 original size:17 final size:17
Alignment explanation
Indices: 51071--51136 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
51061 CTTTTTCTCT
51071 TTTCATTTTTTCATTTCA
1 TTTCA-TTTTTCATTTCA
51089 TTTCATTTTTTCATTTCA
1 TTTCA-TTTTTCATTTCA
*
51107 TTTTC-TTTTTCATTT-T
1 -TTTCATTTTTCATTTCA
51123 TTTCACTTTTTCAT
1 TTTCA-TTTTTCAT
51137 CTTTTTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
15 4 0.09
17 18 0.41
18 18 0.41
19 4 0.09
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCATTTTTCATTTCA
Found at i:51141 original size:17 final size:16
Alignment explanation
Indices: 51061--51142 Score: 60
Period size: 18 Copynumber: 4.9 Consensus size: 16
51051 TCAAACCCTT
*
51061 CTTTTTC-TCTTTTCA
1 CTTTTTCATTTTTTCA
*
51076 TTTTTTCATTTCATTTCA
1 CTTTTTCATTT--TTTCA
* *
51094 TTTTTTCATTTCATTT-T
1 CTTTTTCATTT--TTTCA
51111 CTTTTTCATTTTTTTCA
1 CTTTTTCA-TTTTTTCA
51128 CTTTTTCATCTTTTT
1 CTTTTTCAT-TTTTT
51143 ATTTGTTCCT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.11
16 6 0.11
17 20 0.36
18 24 0.43
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
CTTTTTCATTTTTTCA
Found at i:69290 original size:3 final size:3
Alignment explanation
Indices: 69284--69312 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
69274 AATAATAATA
69284 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
69313 AATTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:90092 original size:9 final size:9
Alignment explanation
Indices: 90080--90120 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
90070 AATAAATAAC
90080 TTAAAATTA
1 TTAAAATTA
*
90089 TTAAAAATA
1 TTAAAATTA
90098 -TAAAATTA
1 TTAAAATTA
90106 TT-AAATTA
1 TTAAAATTA
90114 TTTAAAA
1 -TTAAAA
90121 AGTATGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 13 0.48
9 11 0.41
10 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TTAAAATTA
Found at i:90438 original size:23 final size:24
Alignment explanation
Indices: 90412--90464 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
90402 AATCTATGTC
90412 CTTGTGACACAC-TTTTCTCTACT
1 CTTGTGACACACTTTTTCTCTACT
* *
90435 CTTGTGGCACACTTTTTCTCTGCT
1 CTTGTGACACACTTTTTCTCTACT
*
90459 ATTGTG
1 CTTGTG
90465 CAACGTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.45
Consensus pattern (24 bp):
CTTGTGACACACTTTTTCTCTACT
Found at i:96062 original size:3 final size:3
Alignment explanation
Indices: 96054--96083 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
96044 ATTTCAAATA
*
96054 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
96084 ACAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:103643 original size:66 final size:66
Alignment explanation
Indices: 103527--103664 Score: 204
Period size: 66 Copynumber: 2.1 Consensus size: 66
103517 GTTGAAGTGT
* * ** * *
103527 TGGATCCATCTCATTGTAATTTAGGAAGTTATTACTGCAAATATTTAAGGTTTTCGTTCCGGGTC
1 TGGATCCATCTCAATGTAATATAGGAAGTTATTACTGCAAATATGCAAGGTTTTCATTCAGGGTC
103592 A
66 A
* *
103593 TGGATCGATCTCAATGTAATATAGGAAGTTATTACTGCATATATGCAAGGTTTTCATTCAGGGTC
1 TGGATCCATCTCAATGTAATATAGGAAGTTATTACTGCAAATATGCAAGGTTTTCATTCAGGGTC
103658 A
66 A
103659 TGGATC
1 TGGATC
103665 AGTCTCTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (66 bp):
TGGATCCATCTCAATGTAATATAGGAAGTTATTACTGCAAATATGCAAGGTTTTCATTCAGGGTC
A
Found at i:113658 original size:16 final size:16
Alignment explanation
Indices: 113637--113667 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
113627 TGACTCGTAT
113637 CAATATTACATTCAAA
1 CAATATTACATTCAAA
*
113653 CAATATTAGATTCAA
1 CAATATTACATTCAA
113668 TATCAGTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.32
Consensus pattern (16 bp):
CAATATTACATTCAAA
Found at i:115707 original size:35 final size:35
Alignment explanation
Indices: 115661--115732 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
115651 CCAAAAAAGA
115661 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
115696 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
115731 AG
1 AG
115733 GGTTTTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:116132 original size:17 final size:18
Alignment explanation
Indices: 116106--116145 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
116096 ATTATATGAA
116106 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
116122 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
116140 TATTAT
1 TATTAT
116146 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:116773 original size:42 final size:41
Alignment explanation
Indices: 116672--116863 Score: 242
Period size: 42 Copynumber: 4.5 Consensus size: 41
116662 CTATACACCA
* * *
116672 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* *
116716 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAATT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* *
116758 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGCAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
116800 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
116842 GTAAGGCTTACCTTCGCACACA
1 GTAAGGCTTACCTT-GCACACA
116864 AAAAAGTGAC
Statistics
Matches: 133, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
41 4 0.03
42 100 0.75
43 15 0.11
44 14 0.11
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:116819 original size:84 final size:84
Alignment explanation
Indices: 116672--116863 Score: 271
Period size: 84 Copynumber: 2.2 Consensus size: 84
116662 CTATACACCA
* * * *
116672 GTAAGGCTTAACCTGTGCACAAAGCAGAGGAGCCTAGGAAAACTGTAAGGTTTATCCTTGCACAC
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGAACCTAGGAAAACTGTAAGGCTTATCCTTGCACAC
*
116737 AGCAAAGGGACCTGGGAAATT
64 AGCAAAGGGACCTGGGAAACT
*
116758 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGCAAACTGTAAGGCTTA-CCTTCGCACAC
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGAACCTAGGAAAACTGTAAGGCTTATCCTT-GCACAC
116821 AGCAAAGGGACCTGGGAAACT
64 AGCAAAGGGACCTGGGAAACT
116842 GTAAGGCTTACCTTCGCACACA
1 GTAAGGCTTACCTT-GCACACA
116864 AAAAAGTGAC
Statistics
Matches: 97, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
83 8 0.08
84 59 0.61
85 18 0.19
86 12 0.12
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGAACCTAGGAAAACTGTAAGGCTTATCCTTGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:117776 original size:12 final size:12
Alignment explanation
Indices: 117759--117789 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
117749 GGTCAAAGCC
117759 GGTCAAAGTTTT
1 GGTCAAAGTTTT
117771 GGTCAAAGTTTT
1 GGTCAAAGTTTT
117783 GGTCAAA
1 GGTCAAA
117790 ATTGGTCAAC
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:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (12 bp):
GGTCAAAGTTTT
Found at i:117947 original size:18 final size:18
Alignment explanation
Indices: 117945--117985 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
117935 AACGGGTCGG
117945 GTCAACGGGTCGGGTCAA
1 GTCAACGGGTCGGGTCAA
* *
117963 GTCAACGGGTTGGGTCAT
1 GTCAACGGGTCGGGTCAA
117981 GTCAA
1 GTCAA
117986 AACCGGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCAA
Found at i:117971 original size:26 final size:26
Alignment explanation
Indices: 117911--117972 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
117901 CCCGGTCAAC
*
117911 AGTCAAC-GTTCAACGGGTCGGGTCA
1 AGTCAACGGGTCAACGGGTCGGGTCA
***
117936 ACG-GGTCGGGTCAACGGGTCGGGTCA
1 A-GTCAACGGGTCAACGGGTCGGGTCA
117962 AGTCAACGGGT
1 AGTCAACGGGT
117973 TGGGTCATGT
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.21, C:0.23, G:0.39, T:0.18
Consensus pattern (26 bp):
AGTCAACGGGTCAACGGGTCGGGTCA
Found at i:117979 original size:13 final size:13
Alignment explanation
Indices: 117920--117962 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
117910 CAGTCAACGT
117920 TCAACGGGTCGGG
1 TCAACGGGTCGGG
117933 TCAACGGGTCGGG
1 TCAACGGGTCGGG
117946 TCAACGGGTCGGG
1 TCAACGGGTCGGG
117959 TCAA
1 TCAA
117963 GTCAACGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:118847 original size:2 final size:2
Alignment explanation
Indices: 118842--118903 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
118832 CCTATTATTA
118842 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
118884 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
118904 TCTTAATTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118963 original size:2 final size:2
Alignment explanation
Indices: 118958--118988 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
118948 CTTATAACTT
118958 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 T
118989 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:119352 original size:9 final size:9
Alignment explanation
Indices: 119330--119381 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
119320 TATTTTTTTC
*
119330 TTATCTTATC
1 TTAT-TTATT
119340 TTATTTATT
1 TTATTTATT
119349 TTATTTATT
1 TTATTTATT
119358 TTATTT-TT
1 TTATTTATT
*
119366 TTCCTTTTATT
1 TT--ATTTATT
119377 TTATT
1 TTATT
119382 CTCTTTATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
8 4 0.11
9 21 0.58
10 7 0.19
11 4 0.11
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTATT
Found at i:119352 original size:14 final size:14
Alignment explanation
Indices: 119330--119381 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
119320 TATTTTTTTC
*
119330 TTATCTTATCTTA-T
1 TTATTTTAT-TTATT
119344 TTATTTTATTTATT
1 TTATTTTATTTATT
*
119358 TTATTTT-TTTCCTT
1 TTATTTTATTT-ATT
119372 TTATTTTATT
1 TTATTTTATT
119382 CTCTTTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 6 0.18
14 25 0.76
15 2 0.06
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:123060 original size:20 final size:20
Alignment explanation
Indices: 123031--123068 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
123021 CCCCATCAAA
*
123031 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
123051 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
123069 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:129678 original size:59 final size:60
Alignment explanation
Indices: 129596--129710 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 60
129586 GCCATGGATA
*
129596 TCATTCTAAATTAGTCCTCAAACT-TTTGAACATTTTA-ATTTCATCCCAAACTATAACCT
1 TCATTCTAAATTAATCCTCAAACTATTTGAACA-TTTAGATTTCATCCCAAACTATAACCT
* *
129655 TCATTCTAAATTAATCC-CTAAACTATTTGAGCATTTAGATTTCATCCCCAACTATA
1 TCATTCTAAATTAATCCTC-AAACTATTTGAACATTTAGATTTCATCCCAAACTATA
129711 TGTATATACT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 1 0.02
59 25 0.50
60 24 0.48
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.38
Consensus pattern (60 bp):
TCATTCTAAATTAATCCTCAAACTATTTGAACATTTAGATTTCATCCCAAACTATAACCT
Found at i:140541 original size:12 final size:12
Alignment explanation
Indices: 140524--140552 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
140514 TATTCAATTT
140524 TTTTAAATAATA
1 TTTTAAATAATA
140536 TTTTAAATAATA
1 TTTTAAATAATA
140548 TTTTA
1 TTTTA
140553 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTAAATAATA
Found at i:141307 original size:2 final size:2
Alignment explanation
Indices: 141300--141371 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
141290 GACTTGACCC
141300 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
141342 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
141372 TATTTGATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:143816 original size:21 final size:22
Alignment explanation
Indices: 143761--143816 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
143751 TCTTTCTATT
*
143761 TTTATTC-TCTATTT-TTTATC
1 TTTATTCTTCTATTTATTTAGC
143781 TTTA-TCTTCCT-TTTATTT-GC
1 TTTATTCTT-CTATTTATTTAGC
143801 TTTATTCTTCTATTTA
1 TTTATTCTTCTATTTA
143817 CATTATCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 13 0.43
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTATTCTTCTATTTATTTAGC
Done.