Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006318.1 Hibiscus syriacus cultivar Beakdansim tig00015098_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: 116508
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1469 original size:23 final size:23
Alignment explanation
Indices: 1440--1490 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1430 TCCGGTTAAT
**
1440 AAAAAAATCAAACAAAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAAAA
* *
1463 AAAAAAAAAAAACAAAAGAAAGA
1 AAAAAAAAAAAACAAAAAAAAAA
1486 AAAAA
1 AAAAA
1491 GGTTTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.88, C:0.06, G:0.04, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAACAAAAAAAAAA
Found at i:1546 original size:45 final size:46
Alignment explanation
Indices: 1481--1580 Score: 177
Period size: 45 Copynumber: 2.2 Consensus size: 46
1471 AAAACAAAAG
*
1481 AAAGAAAAAAGGTTTAAAGAGGGAGGGTGTAATTCTTTTCATCTTT
1 AAAGAAAAAAGGTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
1527 AAAGAAAAAA-GTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
1 AAAGAAAAAAGGTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
1572 -AAGAAAAAA
1 AAAGAAAAAA
1581 ATATTTATGC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
44 9 0.17
45 34 0.64
46 10 0.19
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGAAAAAAGGTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
Found at i:6605 original size:17 final size:17
Alignment explanation
Indices: 6585--6624 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
6575 TTTAGGGAAG
6585 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
*
6602 TAGTTCATTCATCAAAC
1 TAGTTCATTAATCAAAC
6619 TAGTTC
1 TAGTTC
6625 GTTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:8984 original size:75 final size:72
Alignment explanation
Indices: 8896--9142 Score: 231
Period size: 72 Copynumber: 3.4 Consensus size: 72
8886 TGGCTATGGT
*
8896 GACTTATACTTGTATGGCTCCTTAAGAGGAGGAGGAGAAGACTTGTACTTGTACACTGGAGGAGG
1 GACTTGTACTTGTATGGCTCCTT--GAGGAGGAGGAGAAGACTTGTACTTGTACACTGGAGGAGG
8961 TGGAGGTGGA
64 TGGA-GTGGA
* * * * * * * * *
8971 GACTTGTATTTGTATGACT-CTTTAGGATGAGGAGGAGACTTATACTTGTAGACCGGTGG-GGTT
1 GACTTGTACTTGTATGGCTCCTTGAGGAGGAGGAGAAGACTTGTACTTGTACACTGGAGGAGG-T
*
9034 GGCAGTGGT
65 GG-AGTGGA
* * *
9043 GACTTGTATTTGTATGGTTCCTTG-GGAGGAGGATGAAGA---G-ACTTGTACACTGGAGAAGGT
1 GACTTGTACTTGTATGGCTCCTTGAGGAGGAGGA-GAAGACTTGTACTTGTACACTGGAGGAGGT
9103 GGAAGTGGA
65 GG-AGTGGA
* *
9112 GATTTGTACTTGTATGGCTTCTTGA-GAGGAG
1 GACTTGTACTTGTATGGCTCCTTGAGGAGGAG
9143 TTGGAGACAT
Statistics
Matches: 139, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
69 46 0.33
70 2 0.01
71 2 0.01
72 62 0.45
73 8 0.06
74 3 0.02
75 16 0.12
ACGTcount: A:0.24, C:0.11, G:0.36, T:0.30
Consensus pattern (72 bp):
GACTTGTACTTGTATGGCTCCTTGAGGAGGAGGAGAAGACTTGTACTTGTACACTGGAGGAGGTG
GAGTGGA
Found at i:9119 original size:69 final size:68
Alignment explanation
Indices: 8942--9142 Score: 172
Period size: 69 Copynumber: 2.9 Consensus size: 68
8932 GAAGACTTGT
* ** *
8942 ACTTGTACACTGGAGGAGGTGGAGGTGGAGACTTGTATTTGTATGACTCTTTAGGATGAGGAGGA
1 ACTTGTACACTGGA-GAGGTGGAAGTGGAGACTTGTATTTGTATGGTTCCTT-GG--GAGGAGGA
** *
9007 GACTTAT
62 GACAGAG
* * * * * *
9014 ACTTGTAGACCGGTGGGGTTGGCAGTGGTGACTTGTATTTGTATGGTTCCTTGGGAGGAGGATGA
1 ACTTGTACACTGGAGAGG-TGGAAGTGGAGACTTGTATTTGTATGGTTCCTTGGGAGGAGGA-GA
9079 -AGAG
64 CAGAG
* * *
9083 ACTTGTACACTGGAGAAGGTGGAAGTGGAGATTTGTACTTGTATGGCTT-CTTGAGAGGAG
1 ACTTGTACACTGGAG-AGGTGGAAGTGGAGACTTGTATTTGTATGG-TTCCTTGGGAGGAG
9143 TTGGAGACAT
Statistics
Matches: 103, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
69 54 0.52
70 6 0.06
71 5 0.05
72 38 0.37
ACGTcount: A:0.23, C:0.10, G:0.37, T:0.30
Consensus pattern (68 bp):
ACTTGTACACTGGAGAGGTGGAAGTGGAGACTTGTATTTGTATGGTTCCTTGGGAGGAGGAGACA
GAG
Found at i:9161 original size:141 final size:144
Alignment explanation
Indices: 8892--9161 Score: 325
Period size: 141 Copynumber: 1.9 Consensus size: 144
8882 GGGGTGGCTA
8892 TGGTGACTTATACTTGTATGGCTCCTTAAGAGGAGGAGGAGAAGACTTGTACTTGTACACTGGAG
1 TGGTGACTTATACTTGTATGGCTCCTT-AGAGGAGGAGGAGAAGA--TGTACTTGTACACTGGAG
* * * * * * *
8957 GAGGTGGAGGTGGAGACTTGTATTTGTATGACTCTTTAGGATGAGGAGGAGACTTATACTTGTAG
63 AAGGTGGAAGTGGAGACTTGTACTTGTATGACTCTTGAGGAGGAGGAGGAGACATATAATTGTAG
9022 ACCGGTGGGGTTGGCAG
128 ACCGGTGGGGTTGGCAG
* * *
9039 TGGTGACTTGTATTTGTATGGTTCCTT-G-GGAGGAGGATGAAGA-G-ACTTGTACACTGGAGAA
1 TGGTGACTTATACTTGTATGGCTCCTTAGAGGAGGAGGA-GAAGATGTACTTGTACACTGGAGAA
* * ** *
9100 GGTGGAAGTGGAGATTTGTACTTGTATGGCTTCTTGA-GAGGAGTTGGAGACATGTAATTGTA
65 GGTGGAAGTGGAGACTTGTACTTGTATGAC-TCTTGAGGAGGAGGAGGAGACATATAATTGTA
9162 AATTGGAGGG
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
141 61 0.58
142 6 0.06
144 9 0.08
145 6 0.06
147 24 0.23
ACGTcount: A:0.24, C:0.10, G:0.35, T:0.31
Consensus pattern (144 bp):
TGGTGACTTATACTTGTATGGCTCCTTAGAGGAGGAGGAGAAGATGTACTTGTACACTGGAGAAG
GTGGAAGTGGAGACTTGTACTTGTATGACTCTTGAGGAGGAGGAGGAGACATATAATTGTAGACC
GGTGGGGTTGGCAG
Found at i:10753 original size:13 final size:13
Alignment explanation
Indices: 10735--10783 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
10725 CTTAGCATGT
10735 TTAAAAATAAAAC
1 TTAAAAATAAAAC
10748 TT-AAAATAAAA-
1 TTAAAAATAAAAC
10759 -TAAAAATGAAAAC
1 TTAAAAAT-AAAAC
* *
10772 TTGAAAAGAAAA
1 TTAAAAATAAAA
10784 GAAAAGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:10764 original size:24 final size:25
Alignment explanation
Indices: 10737--10788 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
10727 TAGCATGTTT
* *
10737 AAAAAT-AAAACTT-AAAATAAAAT
1 AAAAATGAAAACTTGAAAAGAAAAG
10760 AAAAATGAAAACTTGAAAAGAAAAG
1 AAAAATGAAAACTTGAAAAGAAAAG
10785 AAAA
1 AAAA
10789 GAAAGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 7 0.28
25 12 0.48
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (25 bp):
AAAAATGAAAACTTGAAAAGAAAAG
Found at i:11880 original size:8 final size:8
Alignment explanation
Indices: 11867--11891 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11857 CTCTATTTTC
11867 TTTTCTTT
1 TTTTCTTT
11875 TTTTCTTT
1 TTTTCTTT
11883 TTTTCTTT
1 TTTTCTTT
11891 T
1 T
11892 CAAACTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTCTTT
Found at i:16369 original size:23 final size:23
Alignment explanation
Indices: 16343--16403 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
16333 TTAGCATGTT
16343 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAA-AAAA
*
16366 TAAAAATGAAAACTTGAAAAGAAA
1 TAAAAAT-AAAACTTGAAAAAAAA
* *
16390 TGAAAAGAAAACTT
1 TAAAAATAAAACTT
16404 TATAAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 14 0.42
24 15 0.45
25 4 0.12
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.20
Consensus pattern (23 bp):
TAAAAATAAAACTTGAAAAAAAA
Found at i:16377 original size:24 final size:24
Alignment explanation
Indices: 16343--16403 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
16333 TTAGCATGTT
16343 TAAAAAT-AAAACTT-AAAATAAAA
1 TAAAAATGAAAACTTGAAAA-AAAA
*
16366 TAAAAATGAAAACTTGAAAAGAAA
1 TAAAAATGAAAACTTGAAAAAAAA
*
16390 TGAAAA-GAAAACTT
1 TAAAAATGAAAACTT
16404 TATAAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 15 0.44
24 15 0.44
25 4 0.12
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.20
Consensus pattern (24 bp):
TAAAAATGAAAACTTGAAAAAAAA
Found at i:16930 original size:26 final size:26
Alignment explanation
Indices: 16894--16945 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
16884 TATATAAGTG
16894 AATGAAAGTCTTCACGAGATGACTCT
1 AATGAAAGTCTTCACGAGATGACTCT
16920 AATGAAAGTCTTCACGAGATGACTCT
1 AATGAAAGTCTTCACGAGATGACTCT
16946 GCTTAATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (26 bp):
AATGAAAGTCTTCACGAGATGACTCT
Found at i:20808 original size:23 final size:23
Alignment explanation
Indices: 20782--20826 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20772 ATAAATTGAC
*
20782 ATGTTTAAAAAAATATCAAAATA
1 ATGTGTAAAAAAATATCAAAATA
* *
20805 ATGTGTAAAAGAATTTCAAAAT
1 ATGTGTAAAAAAATATCAAAAT
20827 CTAAACTCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (23 bp):
ATGTGTAAAAAAATATCAAAATA
Found at i:23047 original size:7 final size:7
Alignment explanation
Indices: 23035--23064 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
23025 AAACAGATAT
23035 ATGGAAA
1 ATGGAAA
23042 ATGGAAA
1 ATGGAAA
23049 ATGGAAA
1 ATGGAAA
23056 ATGGAAA
1 ATGGAAA
23063 AT
1 AT
23065 TTGATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (7 bp):
ATGGAAA
Found at i:23809 original size:24 final size:24
Alignment explanation
Indices: 23755--23803 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
23745 ATATATAAGG
*
23755 ACTTCAACTCGAAACATTGTAGCA
1 ACTTCAACTCGAAACATTATAGCA
*
23779 ACTTCAACTCGAGACATTATAGCA
1 ACTTCAACTCGAAACATTATAGCA
23803 A
1 A
23804 TATCAAGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (24 bp):
ACTTCAACTCGAAACATTATAGCA
Found at i:25693 original size:452 final size:452
Alignment explanation
Indices: 24439--25784 Score: 2507
Period size: 452 Copynumber: 3.0 Consensus size: 452
24429 TGGGCCAATA
*
24439 ATGGAGGAAAATTAATAGAAATTATAAAAAATATTATTTTTCATTTTACTATAATTGTCATAGTA
1 ATGGAGGAAAATTAATAGAAATTATAAAAAATATTATTTTTCATTTTACGATAATTGTCATAGTA
* * *
24504 TTGAGAGAACTCGTCATTCTTTCGTGATAGTTCTTAAAGATATTATTTTTTTAATGGGCCTGGTC
66 TTTAGAGAACTCATCATTCTTTCGTTATAGTTCTTAAAGATATTATTTTTTTAATGGGCCTGGTC
24569 A--T--G---TG--GGTCATATTAGTTTATTATTTTTCATGGAACTCGTCATTCTTTCTTGACAA
131 ACGTGGGTCATGTTGGTCATATTAGTTTATTATTTTTCATGGAACTCGTCATTCTTTCTTGACAA
* * *
24625 GTTCCATGTAATAAATTAAAAATTATTTTTTCGAATTATTTTATTTTTATTACTATTTACATTAA
196 GTTCTATGTAATTAATTAAAAATTATTTTTTTGAATTATTTTATTTTTATTACTATTTACATTAA
24690 AAAATACAGAAATCCGTCATTCTCTCTTGACTAGTTTTTTGTAGATG-CTGTTGAGTTTAAAAAT
261 AAAATACAGAAATCCGTCATTCTCTCTTGACTAGTTTTTTGTAGATGCCTGTTGAGTTTAAAAAT
* *
24754 TATAGTCGTTGATATGATTGTTTGATATATTATTTTTTTAAATTTTTAAATTTGGAACTCATCAT
326 TATAGTCGTTGATATGATTGTTTGATATATTATTTTTTAAAATTTTGAAATTTGGAACTCATCAT
*
24819 TCCCTCATGACGAGAAAAAATAGATAGATATAGTGTTGAGATTCAGAAAATGAATGCACGTG
391 TCCCTCATGACGAGAAAAAATAGATAGATATAGTGTTTAGATTCAGAAAATGAATGCACGTG
24881 ATGGAGGAAAATTAATAGAAATTATAAAAAATATTATTTTTCATTTTACGATAATTGTCATAGTA
1 ATGGAGGAAAATTAATAGAAATTATAAAAAATATTATTTTTCATTTTACGATAATTGTCATAGTA
24946 TTTAGAGAACTCATCATTCTTTCGTTATAGTTCTTAAAGATATTA-TTTTTTAATGGGCCTGGTC
66 TTTAGAGAACTCATCATTCTTTCGTTATAGTTCTTAAAGATATTATTTTTTTAATGGGCCTGGTC
25010 ACGTGGGTCATGTTGGTCATATTAGTTTATTATTTTTCATGGAACTCGTCATTCTTTCTTGACAA
131 ACGTGGGTCATGTTGGTCATATTAGTTTATTATTTTTCATGGAACTCGTCATTCTTTCTTGACAA
25075 GTTCTATGTAATTAATTAAAAATTATTTTTTTGAATTATTTTATTTTTATTACTATTTACATTAA
196 GTTCTATGTAATTAATTAAAAATTATTTTTTTGAATTATTTTATTTTTATTACTATTTACATTAA
* *
25140 AAAATACAGAAATCCGTCATTCTCTATTGACTAGTTTTTTGTAGATGCCTATTGAGTTTAAAAAT
261 AAAATACAGAAATCCGTCATTCTCTCTTGACTAGTTTTTTGTAGATGCCTGTTGAGTTTAAAAAT
25205 TATAGTCGTTGATATGATTGTTTGATATATTATTTTTTAAAATTTTGAAATTTGGAACTCATCAT
326 TATAGTCGTTGATATGATTGTTTGATATATTATTTTTTAAAATTTTGAAATTTGGAACTCATCAT
25270 TCCCTCATGACGAGAAAAAATAGATAGATATAGTGTTTAGATTCAGAAAATGAATGCACGTG
391 TCCCTCATGACGAGAAAAAATAGATAGATATAGTGTTTAGATTCAGAAAATGAATGCACGTG
25332 ATGGAGGAAAATTAATAGAAATTATAAAAAATATTATTTTTCATTTTACGATAATTGTCATAGTA
1 ATGGAGGAAAATTAATAGAAATTATAAAAAATATTATTTTTCATTTTACGATAATTGTCATAGTA
25397 TTTAGAGAACTCATCATTCTTTCGTTATAGTTCTTAAAGATATTATTTTTTTAATGGGCCTGGTC
66 TTTAGAGAACTCATCATTCTTTCGTTATAGTTCTTAAAGATATTATTTTTTTAATGGGCCTGGTC
25462 ACGTGGGTCATGTTGGTCATATTAGTTTATTATTTTTCATGGAACTCGTCATTCTTTCTTGACAA
131 ACGTGGGTCATGTTGGTCATATTAGTTTATTATTTTTCATGGAACTCGTCATTCTTTCTTGACAA
25527 GTTCTATGTAATTAATTAAAAATTATTTTTTTGAATTATTTTATTTTTATTACTATTTACATTAA
196 GTTCTATGTAATTAATTAAAAATTATTTTTTTGAATTATTTTATTTTTATTACTATTTACATTAA
25592 AAAATACAGAAATCCGTCATTCTCTCTTGACTAGTTTTTTGTAGATGCCTGTTGAGTTTAAAAAT
261 AAAATACAGAAATCCGTCATTCTCTCTTGACTAGTTTTTTGTAGATGCCTGTTGAGTTTAAAAAT
25657 TATAGTCGTTGATATGATTGTTTGATATATTATTTTTTAAAATTTTGAAATTTGGAACTCATCAT
326 TATAGTCGTTGATATGATTGTTTGATATATTATTTTTTAAAATTTTGAAATTTGGAACTCATCAT
25722 TCCCTCATGACGAGAAAAAATAGATAGATATAGTGTTTAGATTCAGAAAATGAATGCACGTG
391 TCCCTCATGACGAGAAAAAATAGATAGATATAGTGTTTAGATTCAGAAAATGAATGCACGTG
25784 A
1 A
25785 AAAATTTATG
Statistics
Matches: 879, Mismatches: 14, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
441 20 0.02
442 106 0.12
443 1 0.00
445 1 0.00
448 2 0.00
450 159 0.18
451 250 0.28
452 340 0.39
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (452 bp):
ATGGAGGAAAATTAATAGAAATTATAAAAAATATTATTTTTCATTTTACGATAATTGTCATAGTA
TTTAGAGAACTCATCATTCTTTCGTTATAGTTCTTAAAGATATTATTTTTTTAATGGGCCTGGTC
ACGTGGGTCATGTTGGTCATATTAGTTTATTATTTTTCATGGAACTCGTCATTCTTTCTTGACAA
GTTCTATGTAATTAATTAAAAATTATTTTTTTGAATTATTTTATTTTTATTACTATTTACATTAA
AAAATACAGAAATCCGTCATTCTCTCTTGACTAGTTTTTTGTAGATGCCTGTTGAGTTTAAAAAT
TATAGTCGTTGATATGATTGTTTGATATATTATTTTTTAAAATTTTGAAATTTGGAACTCATCAT
TCCCTCATGACGAGAAAAAATAGATAGATATAGTGTTTAGATTCAGAAAATGAATGCACGTG
Found at i:25957 original size:30 final size:30
Alignment explanation
Indices: 25921--25986 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
25911 AAAGGAAAAT
25921 GAAGGACGTTTAGAAGGAGCTTAAAAACTC
1 GAAGGACGTTTAGAAGGAGCTTAAAAACTC
*
25951 GAAGGACGTTTAGGAGGAGCTTAAAAACTC
1 GAAGGACGTTTAGAAGGAGCTTAAAAACTC
25981 GAAGGA
1 GAAGGA
25987 ACTTGATAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (30 bp):
GAAGGACGTTTAGAAGGAGCTTAAAAACTC
Found at i:26292 original size:17 final size:17
Alignment explanation
Indices: 26270--26302 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26260 TATGTGTAAA
26270 AAACATAATATTAAAAC
1 AAACATAATATTAAAAC
*
26287 AAACATAATCTTAAAA
1 AAACATAATATTAAAA
26303 TAGAAGCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
AAACATAATATTAAAAC
Found at i:39268 original size:13 final size:14
Alignment explanation
Indices: 39242--39270 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39232 AGGTATTTGG
39242 GCTGAAAGTTTATT
1 GCTGAAAGTTTATT
39256 GCTGAAA-TTTATT
1 GCTGAAAGTTTATT
39269 GC
1 GC
39271 CTTTTTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (14 bp):
GCTGAAAGTTTATT
Found at i:40608 original size:2 final size:2
Alignment explanation
Indices: 40590--40628 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
40580 TAAACGTTAT
* * *
40590 TA TA TA CA TA TA GA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40629 TTGAAGAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:41547 original size:30 final size:30
Alignment explanation
Indices: 41511--41576 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
41501 AAAGGAAAAT
41511 GAAGGACGTTTAGAAGGAGCTTAAAAACTC
1 GAAGGACGTTTAGAAGGAGCTTAAAAACTC
*
41541 GAAGGACGTTTAGGAGGAGCTTAAAAACTC
1 GAAGGACGTTTAGAAGGAGCTTAAAAACTC
41571 GAAGGA
1 GAAGGA
41577 ACTTGATAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (30 bp):
GAAGGACGTTTAGAAGGAGCTTAAAAACTC
Found at i:41882 original size:17 final size:17
Alignment explanation
Indices: 41860--41892 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41850 TATGTGTAAA
41860 AAACATAATATTAAAAC
1 AAACATAATATTAAAAC
*
41877 AAACATAATCTTAAAA
1 AAACATAATATTAAAA
41893 TAGAAGCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
AAACATAATATTAAAAC
Found at i:49123 original size:13 final size:13
Alignment explanation
Indices: 49105--49129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49095 AATGAAAAAA
49105 TGAAAAAAATAAT
1 TGAAAAAAATAAT
49118 TGAAAAAAATAA
1 TGAAAAAAATAA
49130 AAAAATGAAG
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
TGAAAAAAATAAT
Found at i:55024 original size:13 final size:14
Alignment explanation
Indices: 54998--55026 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54988 AGGTATTTGG
54998 GCTGAAAGTTTATT
1 GCTGAAAGTTTATT
55012 GCTGAAA-TTTATT
1 GCTGAAAGTTTATT
55025 GC
1 GC
55027 CTTTTTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (14 bp):
GCTGAAAGTTTATT
Found at i:56370 original size:4 final size:4
Alignment explanation
Indices: 56346--56390 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
56336 TAAACGTTAT
* * * *
56346 TATA TACA TACA TATA GATA TATA TATA TATA TAAA TATA TATA T
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA T
56391 TTGAAGAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:56372 original size:6 final size:6
Alignment explanation
Indices: 56346--56390 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
56336 TAAACGTTAT
* * * *
56346 TATATA CATACA TATAGA TATATA TATATA TATAAA TATATA TAT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TAT
56391 TTGAAGAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:60927 original size:21 final size:21
Alignment explanation
Indices: 60901--60980 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
60891 TGATTTATTA
60901 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
60922 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
60943 TTATGGATTTCAAGTTTCTTA
1 TTATGGATTTCAAGTTTCTTG
60964 TTATGGATTTCAAGTTT
1 TTATGGATTTCAAGTTT
60981 GTGTCTTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.53
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:61059 original size:27 final size:27
Alignment explanation
Indices: 61029--61089 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
61019 GCTAAATGAT
*
61029 ATTAAATTTAGGTATTGTAGAGCAGAC
1 ATTAAATTTAGGTATTGTAGAGCAGAA
*
61056 ATTAAATTTAGGTGTTGTAGAGCAGAA
1 ATTAAATTTAGGTATTGTAGAGCAGAA
61083 ATTAAAT
1 ATTAAAT
61090 ATGCAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (27 bp):
ATTAAATTTAGGTATTGTAGAGCAGAA
Found at i:61283 original size:43 final size:43
Alignment explanation
Indices: 61156--61388 Score: 265
Period size: 43 Copynumber: 5.5 Consensus size: 43
61146 AAAATGCCCA
* * ** *
61156 TATAGGTCT-GACCTTTTGCAGCGTTTGTTTGAAAAATGCCGC
1 TATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
** * * * * *
61198 TATAGATCTTTAGCTTTAGCGGTGTTT-ATCCAAAAACACCGC
1 TATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
*
61240 TATAGATGTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
1 TATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
*
61283 TATAGATCTCGACCTTTTGCGGCGTTTGTT-CAGAAAACGCTGC
1 TATAGATCTCGACCTTTTGCGGCGTTTGTTCCA-AAAACGCCGC
* * * *
61326 TATAGATCCCGGCCTTTTGCGGCGTTTGTTCTAAAAACGCCAC
1 TATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
*
61369 TATAGATCTCGACGTTTTGC
1 TATAGATCTCGACCTTTTGC
61389 AGCATTTTTT
Statistics
Matches: 158, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
42 41 0.26
43 116 0.73
44 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (43 bp):
TATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
Found at i:61788 original size:28 final size:29
Alignment explanation
Indices: 61744--61802 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
61734 CATAGAGATG
61744 GTATATTAGAGT-TTTTTCAAAATACTAT
1 GTATATTAGAGTGTTTTTCAAAATACTAT
61772 GTATATTAGAGTGTTTTTCAAAATACTAT
1 GTATATTAGAGTGTTTTTCAAAATACTAT
61801 GT
1 GT
61803 CAATATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (29 bp):
GTATATTAGAGTGTTTTTCAAAATACTAT
Found at i:65648 original size:19 final size:19
Alignment explanation
Indices: 65604--65650 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
65594 TTGTGTTCTT
*
65604 TTTTTCTTTCGAATAGTCTC
1 TTTTT-TTTCGAACAGTCTC
*
65624 TCTTTTTTCGAACAG-CTAC
1 TTTTTTTTCGAACAGTCT-C
65643 TTTTTTTT
1 TTTTTTTT
65651 TTCATTCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.15, C:0.19, G:0.09, T:0.57
Consensus pattern (19 bp):
TTTTTTTTCGAACAGTCTC
Found at i:66523 original size:13 final size:12
Alignment explanation
Indices: 66502--66537 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
66492 GCTTAATCGG
66502 AAAAAAAAAATA
1 AAAAAAAAAATA
*
66514 AAAGAAAAAATA
1 AAAAAAAAAATA
*
66526 AAAATAAAAATA
1 AAAAAAAAAATA
66538 TAACGGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (12 bp):
AAAAAAAAAATA
Found at i:87601 original size:34 final size:34
Alignment explanation
Indices: 87563--87718 Score: 142
Period size: 33 Copynumber: 4.6 Consensus size: 34
87553 AAGGTGTCTT
* * *
87563 CAAAAGTCATGATGTTTCATCAAAATGGTTCCTC
1 CAAAAGTCATGATATTTCATCAAAATAGTGCCTC
* *
87597 CAAAAAG-CATGTTTTTTCATCCAAAAT-GTGCCTC
1 C-AAAAGTCATGATATTTCAT-CAAAATAGTGCCTC
* * *
87631 CAAAAGTCA-CAAATATTCAT-AAAAAAGTGCCTC
1 CAAAAGTCATGATAT-TTCATCAAAATAGTGCCTC
* * *
87664 CAAAAGACATGTTATTTCATCCAAATAGTG-CTC
1 CAAAAGTCATGATATTTCATCAAAATAGTGCCTC
*
87697 CAAAAGTTATGATATTTCATCA
1 CAAAAGTCATGATATTTCATCA
87719 CACATTTTCA
Statistics
Matches: 97, Mismatches: 18, Indels: 15
0.75 0.14 0.12
Matches are distributed among these distances:
32 4 0.04
33 47 0.48
34 35 0.36
35 11 0.11
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (34 bp):
CAAAAGTCATGATATTTCATCAAAATAGTGCCTC
Found at i:87683 original size:33 final size:34
Alignment explanation
Indices: 87544--87717 Score: 126
Period size: 34 Copynumber: 5.2 Consensus size: 34
87534 GACACAATGC
* * * * *
87544 TTCATCCAAAAGGTGTCTTCAAAAGTCATGATGT
1 TTCATCCAAAAAGTGCCTCCAAAAGACATGATAT
* * * *
87578 TTCAT-CAAAATGGTTCCTCCAAAA-AGCATGTTTT
1 TTCATCCAAAA-AGTGCCTCCAAAAGA-CATGATAT
* *
87612 TTCATCCAAAATGTGCCTCCAAAAGTCACA-AATA-
1 TTCATCCAAAAAGTGCCTCCAAAAG--ACATGATAT
* *
87646 TTCAT-AAAAAAGTGCCTCCAAAAGACATGTTAT
1 TTCATCCAAAAAGTGCCTCCAAAAGACATGATAT
* **
87679 TTCATCCAAATAGTG-CTCCAAAAGTTATGATAT
1 TTCATCCAAAAAGTGCCTCCAAAAGACATGATAT
87712 TTCATC
1 TTCATC
87718 ACACATTTTC
Statistics
Matches: 111, Mismatches: 20, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
31 3 0.03
32 2 0.02
33 48 0.43
34 49 0.44
35 6 0.05
36 2 0.02
37 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (34 bp):
TTCATCCAAAAAGTGCCTCCAAAAGACATGATAT
Found at i:91108 original size:9 final size:9
Alignment explanation
Indices: 91091--91122 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
91081 TTTACTATTA
91091 TTATTGTTG
1 TTATTGTTG
*
91100 TTGTTGTTG
1 TTATTGTTG
91109 TTATTGTTG
1 TTATTGTTG
91118 TTATT
1 TTATT
91123 TTTTTGCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.09, C:0.00, G:0.22, T:0.69
Consensus pattern (9 bp):
TTATTGTTG
Found at i:98126 original size:66 final size:66
Alignment explanation
Indices: 98004--98130 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
97994 ATGAAGACAC
* *
98004 TGGCAGGTTCAGTCGCTGTGGGTAATTCCTTGTATAGGTTCTGCACCGACTTGTAATTCCTATCT
1 TGGCAGGTTCAGTCGCTGTGGGTAATTCCTTGTATAGGTTCAGCACCGAATTGTAATTCCTATCT
98069 T
66 T
* * * * * *
98070 TGGCAGGTTCAGTTGTTGTTGGTAATTCCTTTTATAGGTTCAGC-GCTAATTGGTAATTCCT
1 TGGCAGGTTCAGTCGCTGTGGGTAATTCCTTGTATAGGTTCAGCACCGAATT-GTAATTCCT
98131 TATGGACCTA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 4 0.08
66 48 0.92
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.40
Consensus pattern (66 bp):
TGGCAGGTTCAGTCGCTGTGGGTAATTCCTTGTATAGGTTCAGCACCGAATTGTAATTCCTATCT
T
Found at i:101409 original size:11 final size:11
Alignment explanation
Indices: 101393--101422 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
101383 CTAGGGTGAA
101393 TGAGCTGGAAG
1 TGAGCTGGAAG
101404 TGAGCTGGAAG
1 TGAGCTGGAAG
101415 TGAGCTGG
1 TGAGCTGG
101423 CCATAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.47, T:0.20
Consensus pattern (11 bp):
TGAGCTGGAAG
Found at i:106153 original size:3 final size:3
Alignment explanation
Indices: 106135--106208 Score: 96
Period size: 3 Copynumber: 25.0 Consensus size: 3
106125 ATTTGTTTAT
* * *
106135 TAA TAC TAA T-A TAA TAA TAA TAA TAC TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
106182 TAA TAA TAC TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
106209 GAAAAGTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:106668 original size:41 final size:42
Alignment explanation
Indices: 106600--106681 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
106590 ATTTGAAAAT
* * *
106600 ATCTTGTACTGAAGGTCTTATGTATGACCC-AAGGCTTTAAC
1 ATCTTGCACTGAAGGTCTTAAGTATGACCCGAAGGATTTAAC
106641 ATCTTGCACTGAAGGTCTTACAG-ATGACCCGAAGGATTTAA
1 ATCTTGCACTGAAGGTCTTA-AGTATGACCCGAAGGATTTAA
106682 ATTAAGAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 26 0.72
42 10 0.28
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (42 bp):
ATCTTGCACTGAAGGTCTTAAGTATGACCCGAAGGATTTAAC
Found at i:106681 original size:129 final size:130
Alignment explanation
Indices: 106423--106734 Score: 493
Period size: 129 Copynumber: 2.4 Consensus size: 130
106413 CTTTTTAGAT
* * *
106423 AATTAATAAA-CCCTGAAGGTTTGGTTTCTAAAATCTCCTTTGAAAATATCCTGCACTGAAGGTC
1 AATTAAGAAACCCCTGAAGGTTTAGTTTCTAAAATCTCATTTGAAAATATCCTGCACTGAAGGTC
* * * *
106487 TTATGGATGACCTGAAGGCTTTAACATCTTGCACTGAAGGTCTTACAGATGGCCCTAAGGTTTTA
66 TTATGGATGACCTCAAGGCTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTTA
* * *
106552 AATTAAGAAACCCCCGAAGGTTTAGTTTCTAAAATCTCATTTGAAAATATCTTGTACTGAAGGTC
1 AATTAAGAAACCCCTGAAGGTTTAGTTTCTAAAATCTCATTTGAAAATATCCTGCACTGAAGGTC
*
106617 TTATGTATGACC-CAAGGCTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTTA
66 TTATGGATGACCTCAAGGCTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTTA
* *
106681 AATTAAGAAACCTCTGAAGGTTTAGTTTCTAAAATCTCATTTGAAAACATCCTG
1 AATTAAGAAACCCCTGAAGGTTTAGTTTCTAAAATCTCATTTGAAAATATCCTG
106735 TGTTTAAGAA
Statistics
Matches: 167, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 107 0.64
130 60 0.36
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (130 bp):
AATTAAGAAACCCCTGAAGGTTTAGTTTCTAAAATCTCATTTGAAAATATCCTGCACTGAAGGTC
TTATGGATGACCTCAAGGCTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATTTA
Found at i:106953 original size:42 final size:42
Alignment explanation
Indices: 106894--107039 Score: 211
Period size: 42 Copynumber: 3.5 Consensus size: 42
106884 CTCATTTGAA
* *
106894 AACATCCTACACTGAAGGTCTTATGGATGACCCGAAGGCTTT
1 AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTT
106936 AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTT
1 AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTT
* *** *
106978 AAAATCTTGCACTGAAGGTCTTACATATGACCCGAAGGATTT
1 AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTT
*
107020 AAACATCATGCACTGAAGGT
1 -AACATCTTGCACTGAAGGT
107040 TTTACAGATG
Statistics
Matches: 94, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 77 0.82
43 17 0.18
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTT
Found at i:107497 original size:22 final size:22
Alignment explanation
Indices: 107442--107498 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
107432 AATAAAGCTT
*
107442 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
107464 TCATATTTGAAGAGTGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
107486 TCCTCTTTGAAGA
1 TCATCTTTGAAGA
107499 ATGTAGATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:107951 original size:54 final size:54
Alignment explanation
Indices: 107863--108029 Score: 280
Period size: 54 Copynumber: 3.1 Consensus size: 54
107853 ATAATCATTA
* * * *
107863 GTTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGCTTCTGTACAGAT
*
107917 GTTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGTTTCTGTACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGCTTCTGTACAGAT
*
107971 GTTCGTAAAACATTTGACAACATATTCATTCTTTCATGTGGCTTCTGTACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGCTTCTGTACAGAT
108025 GTTCG
1 GTTCG
108030 CAATTGAAAC
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGCTTCTGTACAGAT
Found at i:108621 original size:118 final size:117
Alignment explanation
Indices: 108381--108672 Score: 413
Period size: 118 Copynumber: 2.5 Consensus size: 117
108371 TAAGCTTTCC
* * * * * * * *
108381 AAATGCCTCACATGAATCATTTATGTCTAAAATTGGCCTTCAAAATGCCCCAATATTTGTTTCTT
1 AAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCAAAATGCCCCAACATTTGCTTCTT
* **
108446 ACTAATAGGAGCTTTAAAAATACTCAAATATTCATACTAATGTGGGCCTTCA
66 ACTAATAGGAGCTTTAAAAATACCCAAATATTCATACTAACATGGGCCTTCA
* * * *
108498 AAATGCCCCACTTGGATCATTTCTGTCTGAAATGGGCTTTCGAGATGCACCAACATTTGCTTCTT
1 AAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCAAAATGCCCCAACATTTGCTTCTT
* * *
108563 ACTAATATGAGCTTTCAAAAATTCCCAAATATTCATACTGACATGGGCCTTCA
66 ACTAATAGGAGCTTT-AAAAATACCCAAATATTCATACTAACATGGGCCTTCA
108616 AAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCAAAATGCCCCAACATT
1 AAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCAAAATGCCCCAACATT
108673 CGATTTCTGA
Statistics
Matches: 152, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
117 67 0.44
118 85 0.56
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (117 bp):
AAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCAAAATGCCCCAACATTTGCTTCTT
ACTAATAGGAGCTTTAAAAATACCCAAATATTCATACTAACATGGGCCTTCA
Found at i:110110 original size:7 final size:7
Alignment explanation
Indices: 110096--110190 Score: 119
Period size: 7 Copynumber: 13.7 Consensus size: 7
110086 TCTTGATTCA
110096 TTTTTTC
1 TTTTTTC
110103 TCTTTTCTC
1 T-TTTT-TC
110112 TTTTTTC
1 TTTTTTC
110119 TTTTTTC
1 TTTTTTC
110126 --TTTTC
1 TTTTTTC
110131 TTTTTTC
1 TTTTTTC
110138 TTTTTTC
1 TTTTTTC
110145 TTTTTTC
1 TTTTTTC
110152 TTTTTTC
1 TTTTTTC
110159 TTTTTTC
1 TTTTTTC
110166 --TTTTC
1 TTTTTTC
110171 TTTTCTT-
1 TTTT-TTC
110178 TTATTTTC
1 TT-TTTTC
110186 TTTTT
1 TTTTT
110191 CTGATGAATG
Statistics
Matches: 79, Mismatches: 0, Indels: 18
0.81 0.00 0.19
Matches are distributed among these distances:
5 10 0.13
7 52 0.66
8 14 0.18
9 3 0.04
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:110116 original size:1 final size:1
Alignment explanation
Indices: 110112--110190 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
110102 CTCTTTTCTC
* * * * * * * * * *
110112 TTTTTTCTTTTTTCTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTCTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
110177 TTTATTTTCTTTTT
1 TTTTTTTTTTTTTT
110191 CTGATGAATG
Statistics
Matches: 54, Mismatches: 24, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:110157 original size:40 final size:41
Alignment explanation
Indices: 110096--110192 Score: 153
Period size: 40 Copynumber: 2.3 Consensus size: 41
110086 TCTTGATTCA
110096 TTTTTTCTCTTTTCTCTTTTTTCTTTTTTCTTTTCTTTT-TT
1 TTTTTTCT-TTTTCTCTTTTTTCTTTTTTCTTTTCTTTTCTT
110137 CTTTTTTCTTTTT-TCTTTTTTCTTTTTTCTTTTCTTTTCTT
1 -TTTTTTCTTTTTCTCTTTTTTCTTTTTTCTTTTCTTTTCTT
110178 TTATTTTCTTTTTCT
1 TT-TTTTCTTTTTCT
110193 GATGAATGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
40 27 0.52
41 16 0.31
42 9 0.17
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (41 bp):
TTTTTTCTTTTTCTCTTTTTTCTTTTTTCTTTTCTTTTCTT
Found at i:110192 original size:33 final size:33
Alignment explanation
Indices: 110097--110190 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
110087 CTTGATTCAT
*
110097 TTTTTCTCTTTTCTCTTTTTTCTTTTTTCTTTTC
1 TTTTT-TCTTTTCTTTTTTTTCTTTTTTCTTTTC
110131 TTTTTTCTTTT-TTCTTTTTTCTTTTTTCTTTT-
1 TTTTTTCTTTTCTT-TTTTTTCTTTTTTCTTTTC
110163 TTCTTTTCTTTTCTTTTATTTTCTTTTT
1 TT-TTTTCTTTTCTTTT-TTTTCTTTTT
110191 CTGATGAATG
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
32 3 0.05
33 35 0.64
34 17 0.31
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (33 bp):
TTTTTTCTTTTCTTTTTTTTCTTTTTTCTTTTC
Found at i:115840 original size:11 final size:11
Alignment explanation
Indices: 115824--115857 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
115814 TATATTCATG
115824 AAAATAATAAT
1 AAAATAATAAT
115835 AAAATAATAATT
1 AAAATAATAA-T
*
115847 AAATTAATAAT
1 AAAATAATAAT
115858 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:115850 original size:146 final size:145
Alignment explanation
Indices: 115565--115860 Score: 313
Period size: 146 Copynumber: 2.0 Consensus size: 145
115555 TAAATAGGGT
* * *
115565 ATTTATTTATTTAAAAATATCAGAAAATGACATCTAATTACTTTAAGACATCCCATTTCTTTGAT
1 ATTTATTTATTTAAAAATATCAGAAAATGACATATAATTACTTTAAGACAACCCATTTCTTTAAT
* * * * * *
115630 ATTAAAAAAATGAATAAATATTAATAAGAATATATAATTTTTCCTAGAAATTAATTTAAATAAAC
66 ATAAAAAAAATAAATAAATATTAATAAGAATATATAATTATTCATAGAAAATAATTAAAATAAAC
115695 TAAACTAAATATAATA
131 TAAACTAAAT-TAATA
* * *
115711 TTTTATTTATTTAAAAATATCAGAAAA-GAACATATAGTTACTTTAAGACAACCCCTTTC-TTAA
1 ATTTATTTATTTAAAAATATCAGAAAATG-ACATATAATTACTTTAAGACAACCCATTTCTTTAA
*
115774 TAATAAAAAATAAATAAATAATATTATTTAATCA-AATATAT-A-TATTCAT-GAAAATAATAAT
65 T-AT-AAAAA-AAATAAATAA-A-TA-TTAATAAGAATATATAATTATTCATAGAAAATAAT--T
*
115835 AAAAT-AA-T-AATTAAATTAATA
122 AAAATAAACTAAACTAAATTAATA
115856 ATTTA
1 ATTTA
115861 AACATATTGA
Statistics
Matches: 126, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
145 14 0.11
146 61 0.48
147 13 0.10
148 16 0.13
149 7 0.06
150 9 0.07
151 6 0.05
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (145 bp):
ATTTATTTATTTAAAAATATCAGAAAATGACATATAATTACTTTAAGACAACCCATTTCTTTAAT
ATAAAAAAAATAAATAAATATTAATAAGAATATATAATTATTCATAGAAAATAATTAAAATAAAC
TAAACTAAATTAATA
Found at i:115854 original size:12 final size:12
Alignment explanation
Indices: 115824--115858 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
115814 TATATTCATG
115824 AAAATAATAA-T
1 AAAATAATAATT
115835 AAAATAATAATT
1 AAAATAATAATT
*
115847 AAATTAATAATT
1 AAAATAATAATT
115859 TAAACATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATAATAATT
Done.