Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010659.1 Kokia drynarioides strain JFW-HI SEQ_125602, 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: 281457
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 226 characters in sequence are not A, C, G, or T
Found at i:323 original size:22 final size:23
Alignment explanation
Indices: 278--322 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
268 TCAACTTGTG
*
278 ATTGTTTTCTTTGATCCTCTTTT
1 ATTGTTTCCTTTGATCCTCTTTT
301 ATTGTTTCCTTTGATCCTCTTT
1 ATTGTTTCCTTTGATCCTCTTT
323 AATAGAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.09, T:0.62
Consensus pattern (23 bp):
ATTGTTTCCTTTGATCCTCTTTT
Found at i:1748 original size:6 final size:6
Alignment explanation
Indices: 1727--1807 Score: 91
Period size: 6 Copynumber: 14.0 Consensus size: 6
1717 TTTAATTTAT
*
1727 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
1773 TTTAAA -TT-AA TCTTAAA TTTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
1808 AAGTCCAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.06
5 8 0.12
6 47 0.72
7 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:1749 original size:17 final size:18
Alignment explanation
Indices: 1727--1807 Score: 91
Period size: 17 Copynumber: 4.7 Consensus size: 18
1717 TTTAATTTAT
*
1727 TTTAAATTT-GATTTAAA
1 TTTAAATTTAAATTTAAA
1744 TTTAAATTTAAA-TT-AA
1 TTTAAATTTAAATTTAAA
1760 TCTTAAATTTAAATTTAAA
1 T-TTAAATTTAAATTTAAA
1779 -TT-AATCTTAAATTTAAA
1 TTTAAAT-TTAAATTTAAA
*
1796 TTTAAAATTAAA
1 TTTAAATTTAAA
1808 AAGTCCAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
16 6 0.11
17 35 0.64
18 10 0.18
19 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (18 bp):
TTTAAATTTAAATTTAAA
Found at i:1755 original size:23 final size:23
Alignment explanation
Indices: 1739--1806 Score: 127
Period size: 23 Copynumber: 2.9 Consensus size: 23
1729 TAAATTTGAT
1739 TTAAATTTAAATTTAAATTAATC
1 TTAAATTTAAATTTAAATTAATC
1762 TTAAATTTAAATTTAAATTAATC
1 TTAAATTTAAATTTAAATTAATC
1785 TTAAATTTAAATTTAAAATTAA
1 TTAAATTTAAATTT-AAATTAA
1807 AAAGTCCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 37 0.84
24 7 0.16
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTAATC
Found at i:1775 original size:29 final size:29
Alignment explanation
Indices: 1738--1807 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
1728 TTAAATTTGA
1738 TTTAAATTTAAATTTAA-ATT-AATCTTAAA
1 TTTAAATTTAAA-TTAATATTAAAT-TTAAA
*
1767 TTTAAATTTAAATTAATCTTAAATTTAAA
1 TTTAAATTTAAATTAATATTAAATTTAAA
*
1796 TTTAAAATTAAA
1 TTTAAATTTAAA
1808 AAGTCCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 4 0.11
29 30 0.81
30 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAAATTTAAATTAATATTAAATTTAAA
Found at i:3589 original size:30 final size:28
Alignment explanation
Indices: 3517--3745 Score: 203
Period size: 29 Copynumber: 7.8 Consensus size: 28
3507 GAAGGTCCCT
3517 AAACTATCCAAAAATTACCATTTTACCCTCG
1 AAACT-TCCAAAAA-TACCATTTTACCC-CG
* *
3548 -AACTTCTAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATACCA-TTTT-ACCCCG
*
3577 AAACTTCCAAAAAATTACCATTTTACCCTTG
1 AAACTTCC-AAAAA-TACCATTTTACCC-CG
*
3608 -AACTTCCAAAAAT-CCAATTTTACCCCT
1 AAACTTCCAAAAATACC-ATTTTACCCCG
* *
3635 AAACTTCCAAAAATCCCATTTTGACCCCA
1 AAACTTCCAAAAATACCATTTT-ACCCCG
**
3664 AAACTTCCAAAAATTACCATTTTACCCTT
1 AAACTTCCAAAAA-TACCATTTTACCCCG
* *
3693 AAACTCCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATACCA-TTTT-ACCCCG
* *
3723 AAACTTCCGTAAATTACCATTTT
1 AAACTTCC-AAAAATACCATTTT
3746 TACCTCCGGA
Statistics
Matches: 165, Mismatches: 19, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.01
28 36 0.22
29 58 0.35
30 48 0.29
31 17 0.10
32 4 0.02
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (28 bp):
AAACTTCCAAAAATACCATTTTACCCCG
Found at i:3593 original size:60 final size:58
Alignment explanation
Indices: 3517--3705 Score: 199
Period size: 60 Copynumber: 3.2 Consensus size: 58
3507 GAAGGTCCCT
* *
3517 AAACTATCC-AAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCG
1 AAACT-TCCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAAT-CCAATTTT-ACCCCG
* *
3577 AAACTTCCAAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCAATTTTACCCCT
1 AAACTTCCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCAATTTTACCCCG
* * **
3635 AAACTTCC-AAAAA-TCCCATTTTGACCC-CAAAACTTCCAAAAATTACC-ATTTTACCCTT
1 AAACTTCCAAAAAATTACCATTTT-ACCCTC-GAACTTCCAAAAA-T-CCAATTTTACCCCG
*
3693 AAACTCCCAAAAA
1 AAACTTCCAAAAA
3706 TCCCATTTTT
Statistics
Matches: 114, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
56 8 0.07
57 21 0.18
58 31 0.27
59 16 0.14
60 38 0.33
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.29
Consensus pattern (58 bp):
AAACTTCCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCAATTTTACCCCG
Found at i:15549 original size:16 final size:16
Alignment explanation
Indices: 15524--15554 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15514 AAGGAGAAAG
*
15524 GGAAAGGAAAGAAAAA
1 GGAAAAGAAAGAAAAA
15540 GGAAAAGAAAGAAAA
1 GGAAAAGAAAGAAAA
15555 TGCACCCACA
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
GGAAAAGAAAGAAAAA
Found at i:20956 original size:2 final size:2
Alignment explanation
Indices: 20949--20993 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
20939 ATAACATTTC
20949 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
20991 AT A
1 AT A
20994 CACAATTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30320 original size:19 final size:18
Alignment explanation
Indices: 30296--30331 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30286 GGAATTATTG
30296 CATTTAATTTTTATTTTTC
1 CATTT-ATTTTTATTTTTC
*
30315 CATTTATTTTTGTTTTT
1 CATTTATTTTTATTTTT
30332 GATGTGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (18 bp):
CATTTATTTTTATTTTTC
Found at i:31158 original size:20 final size:21
Alignment explanation
Indices: 31133--31171 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31123 TCATTTTTTA
*
31133 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
31153 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
31172 TGCCCGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:44011 original size:10 final size:9
Alignment explanation
Indices: 43998--44042 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
43988 TGTGAATGAG
43998 AAAAAGAAA
1 AAAAAGAAA
44007 GAAAAAG-AA
1 -AAAAAGAAA
44016 AAAAAGAAA
1 AAAAAGAAA
44025 AAAGAA-AAA
1 AAA-AAGAAA
44034 AAAAAGAAA
1 AAAAAGAAA
44043 TATTGCTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.25
9 16 0.50
10 8 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:44021 original size:18 final size:18
Alignment explanation
Indices: 43998--44042 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
43988 TGTGAATGAG
*
43998 AAAAAGAAAGAAA-AAGAA
1 AAAAAGAAA-AAAGAAAAA
44016 AAAAAGAAAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
44034 AAAAAGAAA
1 AAAAAGAAA
44043 TATTGCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAGAAAAA
Found at i:44023 original size:14 final size:15
Alignment explanation
Indices: 43999--44035 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
43989 GTGAATGAGA
43999 AAAAGAAAG-AAAAAG
1 AAAA-AAAGAAAAAAG
44014 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
44029 AAAAAAA
1 AAAAAAA
44036 AAAGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:49177 original size:20 final size:21
Alignment explanation
Indices: 49138--49177 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49128 ATTTTTAGTA
*
49138 TTTTTAACTTAGTGACTGCTT
1 TTTTTAACTCAGTGACTGCTT
*
49159 TTTTTGACTCAGTGA-TGCT
1 TTTTTAACTCAGTGACTGCT
49178 CGATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTTTAACTCAGTGACTGCTT
Found at i:49618 original size:22 final size:22
Alignment explanation
Indices: 49592--49662 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
49582 CTTCCTTAAG
49592 GGCAACCTGACTGTGACGACAA
1 GGCAACCTGACTGTGACGACAA
** * **
49614 GGCAAATTG-CTCTTGACGAGGA
1 GGCAACCTGACT-GTGACGACAA
49636 -GCAAACCTGACTGTGACGACAA
1 GGC-AACCTGACTGTGACGACAA
49658 GGCAA
1 GGCAA
49663 ATTTGCTCTT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
21 4 0.11
22 27 0.77
23 4 0.11
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.15
Consensus pattern (22 bp):
GGCAACCTGACTGTGACGACAA
Found at i:49658 original size:44 final size:45
Alignment explanation
Indices: 49595--49683 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 45
49585 CCTTAAGGGC
49595 AACCTGACTGTGACGACAAGGCAAA-TTGCTCTTGACGAGGAGCA
1 AACCTGACTGTGACGACAAGGCAAATTTGCTCTTGACGAGGAGCA
49639 AACCTGACTGTGACGACAAGGCAAATTTGCTCTTGACGAGGAGCA
1 AACCTGACTGTGACGACAAGGCAAATTTGCTCTTGACGAGGAGCA
49684 TTCCTAATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 25 0.57
45 19 0.43
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.19
Consensus pattern (45 bp):
AACCTGACTGTGACGACAAGGCAAATTTGCTCTTGACGAGGAGCA
Found at i:62225 original size:12 final size:12
Alignment explanation
Indices: 62207--62236 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
62197 TAAATATTAC
62207 GAAGAAACAAAG
1 GAAGAAACAAAG
*
62219 TAAGAAACAAAG
1 GAAGAAACAAAG
62231 GAAGAA
1 GAAGAA
62237 CATCAAGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.23, T:0.03
Consensus pattern (12 bp):
GAAGAAACAAAG
Found at i:74536 original size:35 final size:35
Alignment explanation
Indices: 74497--74612 Score: 142
Period size: 35 Copynumber: 3.0 Consensus size: 35
74487 ATAAGGAGAG
74497 AATGAATATGAATGAACTGGAAACATCTGTTATGT
1 AATGAATATGAATGAACTGGAAACATCTGTTATGT
74532 AATGAATATGAATGAACTGGAAACATCTGTAAACATCTGTTATGT
1 AATGAATATGAATGAACT-G--------G-AAACATCTGTTATGT
74577 AATGAATATGAATGAACTGGAAACATCTGTTATGT
1 AATGAATATGAATGAACTGGAAACATCTGTTATGT
74612 A
1 A
74613 TAGGGATATC
Statistics
Matches: 71, Mismatches: 0, Indels: 20
0.78 0.00 0.22
Matches are distributed among these distances:
35 34 0.48
36 2 0.03
44 2 0.03
45 33 0.46
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (35 bp):
AATGAATATGAATGAACTGGAAACATCTGTTATGT
Found at i:74602 original size:45 final size:45
Alignment explanation
Indices: 74517--74606 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
74507 AATGAACTGG
74517 AAACATCTGTTATGTAATGAATATGAATGAACTGGAAACATCTGT
1 AAACATCTGTTATGTAATGAATATGAATGAACTGGAAACATCTGT
74562 AAACATCTGTTATGTAATGAATATGAATGAACTGGAAACATCTGT
1 AAACATCTGTTATGTAATGAATATGAATGAACTGGAAACATCTGT
74607 TATGTATAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (45 bp):
AAACATCTGTTATGTAATGAATATGAATGAACTGGAAACATCTGT
Found at i:75003 original size:17 final size:16
Alignment explanation
Indices: 74980--75039 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
74970 TTAATAAAAT
74980 TTAATATTAAATTTAA
1 TTAATATTAAATTTAA
* *
74996 TCTAATATTTATTTTAA
1 T-TAATATTAAATTTAA
*
75013 -TAAGTATTATA-TTAA
1 TTAA-TATTAAATTTAA
75028 TTTAATATTAAA
1 -TTAATATTAAA
75040 GGGATTAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
15 7 0.21
16 11 0.32
17 16 0.47
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAATATTAAATTTAA
Found at i:75446 original size:32 final size:33
Alignment explanation
Indices: 75410--75477 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
75400 TGGGGACTCA
75410 TGTGGGTAGTGGGGCAGGGATGGTTTT-AGTCT
1 TGTGGGTAGTGGGGCAGGGATGGTTTTGAGTCT
* * *
75442 TGTGGGTCGTGGGGCAGGGGTGGTTTTGAGTTT
1 TGTGGGTAGTGGGGCAGGGATGGTTTTGAGTCT
75475 TGT
1 TGT
75478 ACCCGCAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.09, C:0.06, G:0.49, T:0.37
Consensus pattern (33 bp):
TGTGGGTAGTGGGGCAGGGATGGTTTTGAGTCT
Found at i:108331 original size:24 final size:24
Alignment explanation
Indices: 108294--108341 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
108284 GCTCCATGGC
* *
108294 AGTGGTTACTTCTACTT-TTATGTT
1 AGTGGCTACATCTA-TTGTTATGTT
108318 AGTGGCTACATCTATTGTTATGTT
1 AGTGGCTACATCTATTGTTATGTT
108342 TGATTCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (24 bp):
AGTGGCTACATCTATTGTTATGTT
Found at i:125694 original size:6 final size:6
Alignment explanation
Indices: 125683--125716 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
125673 GAGCGCTATT
125683 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAA
125717 GGTTACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:131844 original size:24 final size:23
Alignment explanation
Indices: 131809--131853 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
131799 GCCTTCCTAT
*
131809 AAGGAGAGATAAGGAAGGTGAGAG
1 AAGGAGAAATAAGG-AGGTGAGAG
131833 AAGGAGAAATAAGGAGGTGAG
1 AAGGAGAAATAAGGAGGTGAG
131854 CAGGAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (23 bp):
AAGGAGAAATAAGGAGGTGAGAG
Found at i:147327 original size:19 final size:18
Alignment explanation
Indices: 147303--147341 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
147293 TATTTTAATA
*
147303 TTTAATAATTTAATAATTT
1 TTTAATAATTGAA-AATTT
*
147322 TTTAATTATTGAAAATTT
1 TTTAATAATTGAAAATTT
147340 TT
1 TT
147342 ATTTACTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAATAATTGAAAATTT
Found at i:152624 original size:55 final size:57
Alignment explanation
Indices: 152515--152634 Score: 163
Period size: 55 Copynumber: 2.1 Consensus size: 57
152505 ACATTCACTA
* * * *
152515 TTTCACATTTTGGAAGAAGTAGGTTTCGCGTGTATTAAAAGTTAGATACGATTTTTG
1 TTTCACATTTTGCAAGAAGTAGGTTTCGCGTATATTAAAAGTTACATACAATTTTTG
* *
152572 TTTCACATTTTGCAA-AA-TAGGTTTCGCGTATATTAAAAGTTACATATAATTTTTT
1 TTTCACATTTTGCAAGAAGTAGGTTTCGCGTATATTAAAAGTTACATACAATTTTTG
*
152627 TTTGACAT
1 TTTCACAT
152635 AATATCTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 40 0.71
56 2 0.04
57 14 0.25
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (57 bp):
TTTCACATTTTGCAAGAAGTAGGTTTCGCGTATATTAAAAGTTACATACAATTTTTG
Found at i:152902 original size:11 final size:11
Alignment explanation
Indices: 152888--152935 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
152878 CAAGAGAATA
*
152888 AGAAGAATAAG
1 AGAAGAAGAAG
*
152899 AGAAGAA-ATGG
1 AGAAGAAGA-AG
152910 AGAAGAAGAAG
1 AGAAGAAGAAG
*
152921 AAAAGAAGAAG
1 AGAAGAAGAAG
152932 AGAA
1 AGAA
152936 AATGGAAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 1 0.03
11 29 0.94
12 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:152904 original size:22 final size:22
Alignment explanation
Indices: 152873--152927 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
152863 TGGATAGTAA
*
152873 AAGAACAAGAGAAT-AAGAAGAAT
1 AAGAA-AAGA-AATGAAGAAGAAG
* *
152896 AAGAGAAGAAATGGAGAAGAAG
1 AAGAAAAGAAATGAAGAAGAAG
152918 AAGAAAAGAA
1 AAGAAAAGAA
152928 GAAGAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.11
22 20 0.74
23 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.27, T:0.05
Consensus pattern (22 bp):
AAGAAAAGAAATGAAGAAGAAG
Found at i:152930 original size:17 final size:16
Alignment explanation
Indices: 152871--152935 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
152861 TCTGGATAGT
* *
152871 AAAAGAACAAGAGAAT
1 AAAAGAAGAAGAGAAG
*
152887 AAGAAGAATAAGAGAAG
1 AA-AAGAAGAAGAGAAG
* *
152904 AAATGGAGAAGAAGAAG
1 AAAAGAAGAAG-AGAAG
152921 AAAAGAAGAAGAGAA
1 AAAAGAAGAAGAGAA
152936 AATGGAAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 12 0.30
17 28 0.70
ACGTcount: A:0.66, C:0.02, G:0.28, T:0.05
Consensus pattern (16 bp):
AAAAGAAGAAGAGAAG
Found at i:154518 original size:11 final size:11
Alignment explanation
Indices: 154465--154518 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
154455 TATTTGAATT
154465 TTTATGATTTT-
1 TTTA-GATTTTA
*
154476 TTTATATTTT-
1 TTTAGATTTTA
154486 TTTA-ATTTTAA
1 TTTAGATTTT-A
154497 TTT-GATTTTA
1 TTTAGATTTTA
154507 TTTAGATTTTA
1 TTTAGATTTTA
154518 T
1 T
154519 AATTTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 5 0.13
10 13 0.34
11 20 0.53
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTAGATTTTA
Found at i:155166 original size:127 final size:125
Alignment explanation
Indices: 154934--155185 Score: 310
Period size: 127 Copynumber: 2.0 Consensus size: 125
154924 GGGCGGCACT
* *
154934 TTTCTAAGTGTTGGGATAAACTTGCCAACATACGCTTTGGCCAACCCTTTGTATAAGGGTTGGGA
1 TTTCTAAGTGTCGGCATAAACTTGCCAACATACGCTTTGGCCAACCCTTTGTATAAGGGTTGGGA
* * * ** *
154999 TATGCATGTCTAAGCCAACACTTAAATTAGTGTTGGCTTTGT-TCAACACTATGCCGACAC
66 TATGCATGCCTAAGACAACACTTAAATAAGAATTGACTTTGTCT-AACACTATGCCGACAC
* * * * * *
155059 TTTCTTAAGTGTCGGCATAGACTTGCCGACATATGCTTTTGTCAACTCTTTTGTATAAGGGTTGG
1 TTTC-TAAGTGTCGGCATAAACTTGCCAACATACGCTTTGGCCAAC-CCTTTGTATAAGGGTTGG
* *
155124 GATATGCATGCCTAAGACAACGCTTAAATAAGAATCT-ACTTTGTCTAACACTATGGCGACAC
64 GATATGCATGCCTAAGACAACACTTAAATAAGAAT-TGACTTTGTCTAACACTATGCCGACAC
155186 ATTTTGGTCA
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
125 4 0.04
126 34 0.32
127 67 0.63
128 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (125 bp):
TTTCTAAGTGTCGGCATAAACTTGCCAACATACGCTTTGGCCAACCCTTTGTATAAGGGTTGGGA
TATGCATGCCTAAGACAACACTTAAATAAGAATTGACTTTGTCTAACACTATGCCGACAC
Found at i:155314 original size:140 final size:141
Alignment explanation
Indices: 155055--155318 Score: 329
Period size: 140 Copynumber: 1.9 Consensus size: 141
155045 CACTATGCCG
* * * *
155055 ACACTTTCTTAAGTGTCGGCATAGACTTGCCGACATATGCTTTTGTCAACTCTTTTGTATAAGGG
1 ACACTTTCCTAAGTGTCGGCATAGACTTGCCGACATACGCTTTGGCCAACTCTTTTGTATAAGGG
* *
155120 TTGGGATATGCATGCCTAAGACAACGCTTAAATAAGAATCTACTTTGTCTAACACTATGGCGACA
66 TTGGGATATGCATGCCTAAGACAACGCTTAAATAAGAATCTACTTTATCCAACACTATGGCGACA
155185 CATTTTGGTCA
131 CATTTTGGTCA
* * * *
155196 ACACTTTCCTAAGTGTTGAG-ATAGATTTGTCGGCATACGCTTTGGCCAACT-TTTTGTATAAGG
1 ACACTTTCCTAAGTGTCG-GCATAGACTTGCCGACATACGCTTTGGCCAACTCTTTTGTATAAGG
* * * * **
155259 GTTGGGATATTCATGTCTAAGGA-AACGGTTAAATAAGAGT-TGGTTTTATCCAACACTATG
65 GTTGGGATATGCATGCCTAA-GACAACGCTTAAATAAGAATCT-ACTTTATCCAACACTATG
155319 CCAACCTTTT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
139 1 0.01
140 59 0.57
141 43 0.41
142 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (141 bp):
ACACTTTCCTAAGTGTCGGCATAGACTTGCCGACATACGCTTTGGCCAACTCTTTTGTATAAGGG
TTGGGATATGCATGCCTAAGACAACGCTTAAATAAGAATCTACTTTATCCAACACTATGGCGACA
CATTTTGGTCA
Found at i:155373 original size:36 final size:36
Alignment explanation
Indices: 155314--155634 Score: 342
Period size: 36 Copynumber: 8.8 Consensus size: 36
155304 TTATCCAACA
* *
155314 CTATGCCAACCTTTTTAAGGTTGCCTTAGACATGGT
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGT
* * *
155350 CTATCCTAACCTTTTTAACGTTGCCTTAGACAATGT
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGT
155386 CTATCCCAACCTTTTTAAAAGGTTGCCTTAGACAAGGT
1 CTATCCCAACCTTTTT--AAGGTTGCCTTAGACAAGGT
* * * ** *
155424 TTATTCTAACCTTTTTAAGGTTATCTTAGACAAGAT
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGT
* * *
155460 CTATCCCAACATTTTTTATAGGTTGCCTCAAACAAGGT
1 CTATCCCAAC-CTTTTTA-AGGTTGCCTTAGACAAGGT
* *
155498 CTATCCCAACCTTTTTAAGGATGCCTTAGATAAGGT
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGT
* *
155534 CTATCCCAACATTTTTAAAGTTGCCTTAGAC-AGGT
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGT
* * *
155569 CTATCCCAACATTTTTTAAAGGTTACCTTAGACAAAG-
1 CTATCCCAAC-CTTTTT-AAGGTTGCCTTAGACAAGGT
* *
155606 CT-TGACCTAACCTTTTTAAAGTTGCCTTA
1 CTAT--CCCAACCTTTTTAAGGTTGCCTTA
155635 AACGAGTTTA
Statistics
Matches: 236, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
35 14 0.06
36 128 0.54
37 32 0.14
38 62 0.26
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (36 bp):
CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGT
Found at i:155416 original size:74 final size:72
Alignment explanation
Indices: 155314--155603 Score: 334
Period size: 74 Copynumber: 4.0 Consensus size: 72
155304 TTATCCAACA
* * * * * *
155314 CTATGCCAACCTTTTT-AAGGTTGCCTTAGACATGGTCTATCCTAACCTTTTTAACGTTGCCTTA
1 CTATCCCAACATTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTTA
155378 GACAATGT
66 GACAA-GT
* * * * *
155386 CTATCCCAACCTTTTTAAAAGGTTGCCTTAGACAAGGTTTATTCTAACCTTTTTAAGGTTATCTT
1 CTATCCCAACATTTTT-AAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTT
155451 AGACAAGAT
65 AGACAAG-T
* * * * *
155460 CTATCCCAACATTTTTTATAGGTTGCCTCAAACAAGGTCTATCCCAACCTTTTTAAGGATGCCTT
1 CTATCCCAACA-TTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTT
*
155525 AGATAAGGT
65 AGACAA-GT
*
155534 CTATCCCAACATTTTTAAA-GTTGCCTTAGAC-AGGTCTATCCCAACATTTTTTAAAGGTTACCT
1 CTATCCCAACATTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAAC-CTTTTT-AAGGTTACCT
155597 TAGACAA
64 TAGACAA
155604 AGCTTGACCT
Statistics
Matches: 186, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
71 14 0.08
72 30 0.16
73 22 0.12
74 114 0.61
75 6 0.03
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (72 bp):
CTATCCCAACATTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACCTTA
GACAAGT
Found at i:155523 original size:110 final size:110
Alignment explanation
Indices: 155314--155592 Score: 348
Period size: 110 Copynumber: 2.5 Consensus size: 110
155304 TTATCCAACA
* * * * * *
155314 CTATGCCAACCTTTTTAAGGTTGCCTTAGACATGGTCTATCCTAAC-CTTTTTAACGTTGCCTTA
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACATTTTTTAAGGTTGCCTCA
* * *
155378 GACAATGTCTATCCCAACCTTTTTAAAAGGTTGCCTTAGACAAGGT
66 AACAAGGTCTATCCCAACCTTTTT-AAAGGATGCCTTAGACAAGGT
* * * ** *
155424 TTATTCTAACCTTTTTAAGGTTATCTTAGACAAGATCTATCCCAACATTTTTTATAGGTTGCCTC
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACATTTTTTA-AGGTTGCCTC
*
155489 AAACAAGGTCTATCCCAACCTTTTT-AAGGATGCCTTAGATAAGGT
65 AAACAAGGTCTATCCCAACCTTTTTAAAGGATGCCTTAGACAAGGT
* *
155534 CTATCCCAACATTTTTAAAGTTGCCTTAGAC-AGGTCTATCCCAACATTTTTTAAAGGTT
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACATTTTTT-AAGGTT
155593 ACCTTAGACA
Statistics
Matches: 143, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
109 25 0.17
110 81 0.57
111 6 0.04
112 31 0.22
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (110 bp):
CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACATTTTTTAAGGTTGCCTCA
AACAAGGTCTATCCCAACCTTTTTAAAGGATGCCTTAGACAAGGT
Found at i:156510 original size:14 final size:14
Alignment explanation
Indices: 156491--156541 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
156481 CTTTAAACTT
*
156491 CAAACTCATAACCC
1 CAAACTCAAAACCC
*
156505 CAAACTCTAAAACCA
1 CAAACTC-AAAACCC
* *
156520 TAAACACAAAACCC
1 CAAACTCAAAACCC
156534 CAAACTCA
1 CAAACTCA
156542 TACATCATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (14 bp):
CAAACTCAAAACCC
Found at i:156680 original size:13 final size:14
Alignment explanation
Indices: 156649--156689 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
156639 TAACCTTGAG
*
156649 AGGTTTGAGGTTTA
1 AGGTTTGAGGTTCA
156663 AGGTTTGA-GTTCA
1 AGGTTTGAGGTTCA
156676 AGGTTAT-AGGTTCA
1 AGGTT-TGAGGTTCA
156690 GGGTAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.39
Consensus pattern (14 bp):
AGGTTTGAGGTTCA
Found at i:159434 original size:73 final size:72
Alignment explanation
Indices: 159349--159592 Score: 260
Period size: 73 Copynumber: 3.3 Consensus size: 72
159339 CTTAGACGTG
** *
159349 TTTATCTCAACCTTTTTAAGGTTGTTTTAGACGAACTTATTTTAATCTTTTTTATAGGTTGTCTT
1 TTTATCTCAACCTTTTTAAGGTTGTTTTAGACGAA-TTATCCTAATCTTTTTTAAAGGTTGTCTT
159414 AGACAAGA
65 AGACAAGA
* * * *
159422 TTTATCTCAACCTTTTTAAGGTTGCTTTAGACGAGTTTATCCCAA-CTTTTTTTAAAGATTG-CT
1 TTTATCTCAACCTTTTTAAGGTTGTTTTAGACGA-ATTATCCTAATC-TTTTTTAAAGGTTGTC-
*
159485 TTAGACAATA
63 TTAGACAAGA
* * * * * * *
159495 TCTATCTCAATCTTTCTAAGGTTATTTTAAACGGATCTATCCTAATCTTTTTTAAAAGGTCGTCT
1 TTTATCTCAACCTTTTTAAGGTTGTTTTAGACGAAT-TATCCTAATCTTTTTT-AAAGGTTGTCT
159560 TAGACAAG-
64 TAGACAAGA
*
159568 TTCTATCTCAACTTTTTTAAGGTTG
1 TT-TATCTCAACCTTTTTAAGGTTG
159593 CCTTAAATGG
Statistics
Matches: 138, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
72 3 0.02
73 101 0.73
74 33 0.24
75 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.45
Consensus pattern (72 bp):
TTTATCTCAACCTTTTTAAGGTTGTTTTAGACGAATTATCCTAATCTTTTTTAAAGGTTGTCTTA
GACAAGA
Found at i:159452 original size:36 final size:36
Alignment explanation
Indices: 159349--159517 Score: 146
Period size: 37 Copynumber: 4.6 Consensus size: 36
159339 CTTAGACGTG
* *
159349 TTTATCTCAACCTTTTTAAGGTTGTTTTAGACGA-A
1 TTTATCTCAACCTTTTTAAGGTTGCTTTAGACAAGA
* * * *
159384 CTTATTTTAATCTTTTTTATAGGTTG-TCTTAGACAAGA
1 TTTATCTCAA-CCTTTTTA-AGGTTGCT-TTAGACAAGA
*
159422 TTTATCTCAACCTTTTTAAGGTTGCTTTAGACGAG-
1 TTTATCTCAACCTTTTTAAGGTTGCTTTAGACAAGA
* * * *
159457 TTTATCCCAACTTTTTTTAAAGATTGCTTTAGACAATA
1 TTTATCTCAAC-CTTTTT-AAGGTTGCTTTAGACAAGA
* * *
159495 TCTATCTCAATCTTTCTAAGGTT
1 TTTATCTCAACCTTTTTAAGGTT
159518 ATTTTAAACG
Statistics
Matches: 105, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
35 17 0.16
36 32 0.30
37 40 0.38
38 16 0.15
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.46
Consensus pattern (36 bp):
TTTATCTCAACCTTTTTAAGGTTGCTTTAGACAAGA
Found at i:159577 original size:74 final size:73
Alignment explanation
Indices: 159351--159661 Score: 265
Period size: 74 Copynumber: 4.2 Consensus size: 73
159341 TAGACGTGTT
* * * *** *
159351 TATCTCAACCTTTTTAAGGTTGTTTTAGACGAACTTATTTTAATCTTTTTT-ATAGGTTGTCTTA
1 TATCTCAACCTTTTTAAGGTTGCTTTAAACGATC-TATCCCAATCTTTTTTAAAAGGTTGTCTTA
159415 GACAAGATT-
65 GACAAG-TTC
* * * *
159424 TATCTCAACCTTTTTAAGGTTGCTTTAGACGAGTTTATCCCAA-CTTTTTTTAAAGATTG-CTTT
1 TATCTCAACCTTTTTAAGGTTGCTTTAAACGA-TCTATCCCAATCTTTTTTAAAAGGTTGTC-TT
159487 AGACAA-TATC
64 AGACAAGT-TC
* * ** * *
159497 TATCTCAATCTTTCTAAGGTTATTTTAAACGGATCTATCCTAATCTTTTTTAAAAGGTCGTCTTA
1 TATCTCAACCTTTTTAAGGTTGCTTTAAAC-GATCTATCCCAATCTTTTTTAAAAGGTTGTCTTA
159562 GACAAGTTC
65 GACAAGTTC
* * * * * *
159571 TATCTCAACTTTTTTAAGGTTGCCTTAAATGGGTTTATCCCAATTTTTTTTAAAAGGTTG-CATT
1 TATCTCAACCTTTTTAAGGTTGCTTTAAA-CGATCTATCCCAATCTTTTTTAAAAGGTTGTC-TT
***
159635 AGACAAAACC
64 AGACAAGTTC
*
159645 TATCCCAACCTTTTTAA
1 TATCTCAACCTTTTTAA
159662 AGGTCGGCCT
Statistics
Matches: 192, Mismatches: 35, Indels: 21
0.77 0.14 0.08
Matches are distributed among these distances:
71 1 0.01
72 9 0.05
73 84 0.44
74 96 0.50
75 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (73 bp):
TATCTCAACCTTTTTAAGGTTGCTTTAAACGATCTATCCCAATCTTTTTTAAAAGGTTGTCTTAG
ACAAGTTC
Found at i:159619 original size:147 final size:147
Alignment explanation
Indices: 159351--159657 Score: 386
Period size: 147 Copynumber: 2.1 Consensus size: 147
159341 TAGACGTGTT
* * * ** * *
159351 TATCTCAACCTTTTTAAGGTTGTTTTAGACGAACTTATTTTAATCTTTTTTATAGGTTGTCTTAG
1 TATCTCAACCTTTCTAAGGTTATTTTAAACGAACTTATCCTAATCTTTTTTAAAGGTCGTCTTAG
* *
159416 ACAAGATTTATCTCAACCTTTTTAAGGTTGCTTTAGACGAGTTTATCCCAACTTTTTTT-AAAGA
66 ACAAGATTTATCTCAACCTTTTTAAGGTTGCCTTAAACGAGTTTATCCCAACTTTTTTTAAAAGA
*
159480 TTGCTTTAGACAATATC
131 TTGCATTAGACAATATC
* *
159497 TATCTCAATCTTTCTAAGGTTATTTTAAACGGA-TCTATCCTAATCTTTTTTAAAAGGTCGTCTT
1 TATCTCAACCTTTCTAAGGTTATTTTAAACGAACT-TATCCTAATCTTTTTT-AAAGGTCGTCTT
* * * *
159561 AGACAAG-TTCTATCTCAACTTTTTTAAGGTTGCCTTAAATGGGTTTATCCCAATTTTTTTTAAA
64 AGACAAGATT-TATCTCAACCTTTTTAAGGTTGCCTTAAACGAGTTTATCCCAACTTTTTTTAAA
* * *
159625 AGGTTGCATTAGACAAAACC
128 AGATTGCATTAGACAATATC
*
159645 TATCCCAACCTTT
1 TATCTCAACCTTT
159658 TTAAAGGTCG
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
145 1 0.01
146 44 0.32
147 62 0.46
148 29 0.21
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (147 bp):
TATCTCAACCTTTCTAAGGTTATTTTAAACGAACTTATCCTAATCTTTTTTAAAGGTCGTCTTAG
ACAAGATTTATCTCAACCTTTTTAAGGTTGCCTTAAACGAGTTTATCCCAACTTTTTTTAAAAGA
TTGCATTAGACAATATC
Found at i:160537 original size:47 final size:47
Alignment explanation
Indices: 160486--160580 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
160476 AAGCTTTAAG
*
160486 AACTAATACAAGTTAAATATAATAATTTGAATGACAACAAGTATGAT
1 AACTAATACAAGTTAAATATAATAATTCGAATGACAACAAGTATGAT
*
160533 AACTAATACAAGTTAAATATAATAATTCGAATGATAACAAGTATGAT
1 AACTAATACAAGTTAAATATAATAATTCGAATGACAACAAGTATGAT
160580 A
1 A
160581 TATGATATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (47 bp):
AACTAATACAAGTTAAATATAATAATTCGAATGACAACAAGTATGAT
Found at i:162373 original size:2 final size:2
Alignment explanation
Indices: 162368--162393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
162358 TCACCTTTTC
162368 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
162394 TGTTGGAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:163766 original size:30 final size:30
Alignment explanation
Indices: 163732--164074 Score: 247
Period size: 30 Copynumber: 11.6 Consensus size: 30
163722 ATTTTCTTTA
*
163732 AAAATCACATTTTGACCCTTAAACTTTCTC
1 AAAATCACATTTTGACCCTTAAACTTTCCC
* *
163762 AAAATCACATTTTGACCCCTAAACTTTTCCA
1 AAAATCACATTTTGACCCTTAAAC-TTTCCC
*
163793 AAAATCACATTTTGACCCTTAAACTTTCCT
1 AAAATCACATTTTGACCCTTAAACTTTCCC
* *
163823 AAAATCACATTTTAACCCTCAAAC-TTCCC
1 AAAATCACATTTTGACCCTTAAACTTTCCC
* *
163852 AAAATCACA-TTTAACCCCTT-AACATTT-TC
1 AAAATCACATTTTGA-CCCTTAAAC-TTTCCC
* * * *
163881 AAAATTACATTTTAACCCCTAAACTTTCCT
1 AAAATCACATTTTGACCCTTAAACTTTCCC
* * *
163911 AAAATCACATTTTAACCC-TAAATTTTCAC
1 AAAATCACATTTTGACCCTTAAACTTTCCC
* * ** * ** *
163940 GAAGTTGCATTTTAACCCCCAAACCTTCCC
1 AAAATCACATTTTGACCCTTAAACTTTCCC
* **
163970 AAAATGACATTTTGATCCC--AAGTTTTCCC
1 AAAATCACATTTTGA-CCCTTAAACTTTCCC
* *
163999 AAAAT-ACAATTTGA-CCTCCAAACTTTCCC
1 AAAATCACATTTTGACCCT-TAAACTTTCCC
* * * * * **
164028 ATAATTACATTTTTATCCATAAACTTT-TT
1 AAAATCACATTTTGACCCTTAAACTTTCCC
*
164057 AAAATTACATTTTGACCC
1 AAAATCACATTTTGACCC
164075 CAAATTCTCT
Statistics
Matches: 252, Mismatches: 47, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
26 2 0.01
28 16 0.06
29 94 0.37
30 108 0.43
31 32 0.13
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATCACATTTTGACCCTTAAACTTTCCC
Found at i:163915 original size:59 final size:59
Alignment explanation
Indices: 163732--164075 Score: 278
Period size: 59 Copynumber: 5.8 Consensus size: 59
163722 ATTTTCTTTA
* * *
163732 AAAATCACATTTTGACCCTTAAACTTTCTCAAAATCACATTTTGACCCCTAAACTTTTCCA
1 AAAATCACATTTTAACCCTTAAACTTT-TCAAAATCACATTTTAACCCCTAAAC-TTTCCC
* *
163793 AAAATCACATTTTGACCCTTAAACTTTCCTAAAATCACATTTTAA-CCCTCAAAC-TTCCC
1 AAAATCACATTTTAACCCTTAAACTTTTC-AAAATCACATTTTAACCCCT-AAACTTTCCC
* *
163852 AAAATCACA-TTTAACCCCTT-AACATTTTCAAAATTACATTTTAACCCCTAAACTTTCCT
1 AAAATCACATTTTAA-CCCTTAAAC-TTTTCAAAATCACATTTTAACCCCTAAACTTTCCC
* ** * *
163911 AAAATCACATTTTAACCC-TAAA-TTTTCACGAAGTTGCATTTTAACCCCCAAACCTTCCC
1 AAAATCACATTTTAACCCTTAAACTTTTCA--AAATCACATTTTAACCCCTAAACTTTCCC
* * * * *
163970 AAAATGACATTTTGATCCC---AAGTTTTCCCAAAAT-ACAATTTGACCTCC-AAACTTTCCC
1 AAAATCACATTTT-AACCCTTAAACTTTT--CAAAATCACATTTTAACC-CCTAAACTTTCCC
* * * * * * * *
164028 ATAATTACATTTTTATCCATAAACTTTTTAAAATTACATTTTGACCCC
1 AAAATCACATTTTAACCCTTAAACTTTTCAAAATCACATTTTAACCCC
164076 AAATTCTCTG
Statistics
Matches: 237, Mismatches: 27, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
57 8 0.03
58 63 0.27
59 99 0.42
60 20 0.08
61 47 0.20
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAATCACATTTTAACCCTTAAACTTTTCAAAATCACATTTTAACCCCTAAACTTTCCC
Found at i:165276 original size:76 final size:76
Alignment explanation
Indices: 165196--165342 Score: 222
Period size: 76 Copynumber: 1.9 Consensus size: 76
165186 ATCTTTTATT
* * *
165196 TTTCACGTTGTTACTAAATTCATTTTAAAAAATAATTAAAATTTAAATTACAACTATTAATTGTA
1 TTTCAAGTTATTACTAAATTCATTTTAAAAAATAATTAAAATTTAAATTACAACTATTAATTATA
165261 AAAATTGTAGC
66 AAAATTGTAGC
** * * *
165272 TTTCAAGTTATTACTAGTTTCATTTTTAAAAATAATTAAAATTTAAATTAGAATTATTAATTATA
1 TTTCAAGTTATTACTAAATTCATTTTAAAAAATAATTAAAATTTAAATTACAACTATTAATTATA
165337 AAAATT
66 AAAATT
165343 ATGTTACATT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (76 bp):
TTTCAAGTTATTACTAAATTCATTTTAAAAAATAATTAAAATTTAAATTACAACTATTAATTATA
AAAATTGTAGC
Found at i:171262 original size:16 final size:15
Alignment explanation
Indices: 171216--171262 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
171206 ATTAGAGTTA
*
171216 ATTATATTAATTAATT
1 ATTATTTTAATTAA-T
171232 ATTATTTTAGA-TAAT
1 ATTATTTTA-ATTAAT
171247 ATTATTTTACATTAAT
1 ATTATTTTA-ATTAAT
171263 TGCATAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 11 0.41
16 15 0.56
17 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTATTTTAATTAAT
Found at i:171369 original size:18 final size:18
Alignment explanation
Indices: 171348--171413 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
171338 GATACATTAA
171348 TTAATAAATTAATATATT
1 TTAATAAATTAATATATT
171366 TTAATTAAATTTAATA-ATT
1 TTAA-TAAA-TTAATATATT
*
171385 TAAATAAA--AATATTATT
1 TTAATAAATTAATA-TATT
171402 TTACAT-AATTAA
1 TTA-ATAAATTAA
171414 AAATATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
15 4 0.10
17 7 0.18
18 10 0.26
19 12 0.31
20 6 0.15
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATAAATTAATATATT
Found at i:173559 original size:52 final size:52
Alignment explanation
Indices: 173473--173660 Score: 191
Period size: 52 Copynumber: 3.6 Consensus size: 52
173463 TAAACAAAAA
* * * *
173473 AGGTCCGATGACTACGTGTTATCATGAGTATATGAATCCATTT-C-AGATTATG
1 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCC-TTTACGA-ATTATG
* * *
173525 AGGTCTGGTCACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* * * * * **
173577 AGGTCCGATAACTATGTGTCATTGTGAGTGTAGGATTTCTTTTACGAATTAAA
1 AGGTCCGATAACTATGTGTCATCGTGAGTATATGA-ATCCTTTACGAATTATG
* *
173630 AGGTCCGATGACTATGTATCATCGTGAGTAT
1 AGGTCCGATAACTATGTGTCATCGTGAGTAT
173661 TAAACAAAAT
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
51 3 0.03
52 69 0.61
53 41 0.36
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
Found at i:177042 original size:139 final size:139
Alignment explanation
Indices: 176788--177066 Score: 540
Period size: 139 Copynumber: 2.0 Consensus size: 139
176778 GTTCTTGAGA
176788 AATTGTTGGATTTAATCCTATTCTTTTTCTCATAATTTTAGATTTTTGTTTGTTATTATGATGAA
1 AATTGTTGGATTTAATCCTATTCTTTTTCTCATAATTTTAGATTTTTGTTTGTTATTATGATGAA
176853 TGCTATTAATTATTTAATTAAAATGACTTAAATTCTTTAAGTGTTGGGTTGATTGTGTTTAATTG
66 TGCTATTAATTATTTAATTAAAATGACTTAAATTCTTTAAGTGTTGGGTTGATTGTGTTTAATTG
176918 CTTGTTTAT
131 CTTGTTTAT
176927 AATTGTTGGATTTAATCCTATTCTTTTTCTCATAATTTTAGATTTTTGTTTGTTATTATGATGAA
1 AATTGTTGGATTTAATCCTATTCTTTTTCTCATAATTTTAGATTTTTGTTTGTTATTATGATGAA
* *
176992 TGCTATTAATTATTTAATTAAAATGGCTTAAATTCTTTAAGTGTTTGGTTGATTGTGTTTAATTG
66 TGCTATTAATTATTTAATTAAAATGACTTAAATTCTTTAAGTGTTGGGTTGATTGTGTTTAATTG
177057 CTTGTTTAT
131 CTTGTTTAT
177066 A
1 A
177067 TTTAATCCAA
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.53
Consensus pattern (139 bp):
AATTGTTGGATTTAATCCTATTCTTTTTCTCATAATTTTAGATTTTTGTTTGTTATTATGATGAA
TGCTATTAATTATTTAATTAAAATGACTTAAATTCTTTAAGTGTTGGGTTGATTGTGTTTAATTG
CTTGTTTAT
Found at i:179522 original size:16 final size:17
Alignment explanation
Indices: 179501--179535 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
179491 ATTCTAAACT
179501 AAATTAAA-CTAAGTTA
1 AAATTAAATCTAAGTTA
*
179517 AAATTAAATCTATGTTA
1 AAATTAAATCTAAGTTA
179534 AA
1 AA
179536 TTTCGATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
AAATTAAATCTAAGTTA
Found at i:180161 original size:17 final size:18
Alignment explanation
Indices: 180139--180173 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
180129 CCTATAACAT
*
180139 TATAAACATG-AATTAAA
1 TATAAACAAGCAATTAAA
180156 TATAAACAAGCAATTAAA
1 TATAAACAAGCAATTAAA
180174 CACAACCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (18 bp):
TATAAACAAGCAATTAAA
Found at i:180254 original size:15 final size:12
Alignment explanation
Indices: 180222--180247 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
180212 AATTAGTTAA
180222 ATAATAGCATTC
1 ATAATAGCATTC
180234 ATAATAGCATTC
1 ATAATAGCATTC
180246 AT
1 AT
180248 TATAATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:181127 original size:19 final size:18
Alignment explanation
Indices: 181103--181186 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 18
181093 TATGTTAGAA
181103 ATTTTATCACAAATTAATT
1 ATTTTATCACAAATTAA-T
* *
181122 ATTTTATAATTAAATT-AT
1 ATTTTATCA-CAAATTAAT
*
181140 ATTTT-TCGACATTAATTAAA
1 ATTTTATC-ACA--AATTAAT
181160 ATTTTTATCACAAATTAATT
1 A-TTTTATCACAAATTAA-T
181180 ATTTTAT
1 ATTTTAT
181187 AATTAATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
17 2 0.04
18 7 0.14
19 25 0.49
20 8 0.16
21 7 0.14
22 2 0.04
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.51
Consensus pattern (18 bp):
ATTTTATCACAAATTAAT
Found at i:181194 original size:19 final size:18
Alignment explanation
Indices: 181114--181201 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 18
181104 TTTTATCACA
181114 AATTAATTATTTTATAATT
1 AATTAA-TATTTTATAATT
181133 AAATT-ATATTTT-TCGACATT
1 -AATTAATATTTTAT--A-ATT
* * **
181153 AATTAAAATTTTTATCACA
1 AATTAATA-TTTTATAATT
181172 AATTAATTATTTTATAATT
1 AATTAA-TATTTTATAATT
181191 AATT-ATATTTT
1 AATTAATATTTT
181202 TCAATATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
17 7 0.13
18 7 0.13
19 24 0.45
20 10 0.19
21 4 0.08
22 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (18 bp):
AATTAATATTTTATAATT
Found at i:181201 original size:57 final size:58
Alignment explanation
Indices: 181104--181214 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
181094 ATGTTAGAAA
*
181104 TTTTATCACAAATTAATTATTTTATAATTAAATTATATTTTTCGACATTAATTAAAAT
1 TTTTATCACAAATTAATTATTTTATAATTAAATTATATTTTTCAACATTAATTAAAAT
*
181162 TTTTATCACAAATTAATTATTTTATAATT-AATTATATTTTTCAATATTAATTA
1 TTTTATCACAAATTAATTATTTTATAATTAAATTATATTTTTCAACATTAATTA
181215 CTCAAAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 22 0.43
58 29 0.57
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (58 bp):
TTTTATCACAAATTAATTATTTTATAATTAAATTATATTTTTCAACATTAATTAAAAT
Found at i:187463 original size:22 final size:22
Alignment explanation
Indices: 187403--187467 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 22
187393 ATATTAACAA
187403 TTAAATTTAAAATATAACTAAATTC
1 TTAAATTTAAAA-A-AA-TAAATTC
**
187428 TTAAAAATATAAAAAATAAATT-
1 TTAAATTTA-AAAAAATAAATTC
187450 TTAAATTTACAAAAAATA
1 TTAAATTTA-AAAAAATA
187468 TAAAAACTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 15 0.44
23 6 0.18
24 2 0.06
25 8 0.24
26 3 0.09
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
TTAAATTTAAAAAAATAAATTC
Found at i:188490 original size:34 final size:34
Alignment explanation
Indices: 188452--188519 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
188442 TACGTGTTTA
*
188452 CAAAGTTTGTCTCATTAAGGAAAAATGAGAAACT
1 CAAAGTTTGTCTCACTAAGGAAAAATGAGAAACT
188486 CAAAGTTTGTCTCACTAAGGAAAAATGAGAAACT
1 CAAAGTTTGTCTCACTAAGGAAAAATGAGAAACT
188520 AAGCGCGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (34 bp):
CAAAGTTTGTCTCACTAAGGAAAAATGAGAAACT
Found at i:189219 original size:23 final size:23
Alignment explanation
Indices: 189192--189240 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
189182 TTTGTTTTTA
*
189192 TATAATATAAAAATTAAATATAT
1 TATAATATAAAAATTAAAAATAT
189215 TATAATATAAAAATTAAAAATAT
1 TATAATATAAAAATTAAAAATAT
189238 TAT
1 TAT
189241 TACTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAATATAAAAATTAAAAATAT
Found at i:191174 original size:138 final size:138
Alignment explanation
Indices: 190926--191203 Score: 484
Period size: 138 Copynumber: 2.0 Consensus size: 138
190916 TCTAAAAGAG
* *
190926 AACCTCTCTTCAACGAAACGATCATACTTTTTTCCCTCCTATGACCAAGTTGCCTCCGCTCCAGA
1 AACCTCTCTTCAACGAAACGAACATACTTTTTTCCCTCCTATGACCAAATTGCCTCCGCTCCAGA
190991 CAAGTTAACTTAAACTCCGTAACGAACGAGGGATGCCCGATTTTATTGGTGACTGTAGAAACTTC
66 CAAGTTAACTTAAACTCCGTAACGAACGAGGGATGCCCGATTTTATTGGTGACTGTAGAAACTTC
*
191056 CAGAATAT
131 CAGAACAT
*
191064 AACCTCTCTTCAACGAAACGAACATACTTTTTTCCCTCCTATGACCAAATTGCCTCCGCTCTAGA
1 AACCTCTCTTCAACGAAACGAACATACTTTTTTCCCTCCTATGACCAAATTGCCTCCGCTCCAGA
* * * *
191129 CGAGTTAACTTCAACTCCGTAACGAACGAGGGATGCCCGATTTTATTGGTTACTGTAGAACCTTC
66 CAAGTTAACTTAAACTCCGTAACGAACGAGGGATGCCCGATTTTATTGGTGACTGTAGAAACTTC
191194 CAGAACAT
131 CAGAACAT
191202 AA
1 AA
191204 AGACTATTAA
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 132 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (138 bp):
AACCTCTCTTCAACGAAACGAACATACTTTTTTCCCTCCTATGACCAAATTGCCTCCGCTCCAGA
CAAGTTAACTTAAACTCCGTAACGAACGAGGGATGCCCGATTTTATTGGTGACTGTAGAAACTTC
CAGAACAT
Found at i:192543 original size:2 final size:2
Alignment explanation
Indices: 192536--192587 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
192526 TGGATATTAA
192536 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
192578 AT AT AT AT AT
1 AT AT AT AT AT
192588 TAGAGTATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193660 original size:15 final size:15
Alignment explanation
Indices: 193642--193673 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
193632 CTTCCCTATT
193642 TTCTATTTCCTTTTA
1 TTCTATTTCCTTTTA
*
193657 TTCTATTTTCTTTTA
1 TTCTATTTCCTTTTA
193672 TT
1 TT
193674 TTTAATTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCTATTTCCTTTTA
Found at i:193681 original size:22 final size:21
Alignment explanation
Indices: 193637--193697 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
193627 TTTGACTTCC
**
193637 CTATTTTCTATTTCCTTTTATT
1 CTATTTTCT-TTTATTTTTATT
193659 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTT-ATT
*
193681 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
193698 CCTTAGATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (21 bp):
CTATTTTCTTTTATTTTTATT
Found at i:195420 original size:21 final size:21
Alignment explanation
Indices: 195374--195432 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
195364 AAATTAAATA
* *
195374 TTTAAATTAAA-TAATAATAG
1 TTTAATTTAAATTAATAAGAG
* *
195394 TATAATTTAAATTAATTAGAG
1 TTTAATTTAAATTAATAAGAG
* *
195415 TTTAATTCAAATAAATAA
1 TTTAATTTAAATTAATAA
195433 ATAAAATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
TTTAATTTAAATTAATAAGAG
Found at i:196010 original size:12 final size:12
Alignment explanation
Indices: 195993--196022 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
195983 TTTAAATATT
195993 TAAATAATTTAA
1 TAAATAATTTAA
*
196005 TAAATAATTTAT
1 TAAATAATTTAA
196017 TAAATA
1 TAAATA
196023 TAAATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAATAATTTAA
Found at i:196077 original size:27 final size:28
Alignment explanation
Indices: 196026--196078 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
196016 TTAAATATAA
* *
196026 ATTTTAAATACTTTTAACTACTTAATTT
1 ATTTTAAATACTTTTAAATAATTAATTT
*
196054 ATTTTAAA-ATTTTTAAATAATTAAT
1 ATTTTAAATACTTTTAAATAATTAAT
196079 ATAAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTTAAATACTTTTAAATAATTAATTT
Found at i:200327 original size:39 final size:40
Alignment explanation
Indices: 200237--200342 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 40
200227 TTTGGACAGA
* *
200237 AAACGTCGCAAAAGGTAAAGCAATAGCAGTGTTTTTCCAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTTCCAT
* *
200277 AAACGCCGCAAAAGGTAAAGCAATAGCTGCG-TTTTCTAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTTCCAT
* *
200316 AAACGCTGCAAAAGGTGAAGCAATAGC
1 AAACGCCGCAAAAGGTAAAGCAATAGC
200343 GATGTTTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 32 0.53
40 28 0.47
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTTCCAT
Found at i:202145 original size:17 final size:17
Alignment explanation
Indices: 202125--202170 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
202115 CGCCATTTTA
*
202125 TTCTTCACGCCGAAATT
1 TTCTTCACGCCGAAATC
* *
202142 TTCTTCACGTCGGAATC
1 TTCTTCACGCCGAAATC
*
202159 TTCTTCATGCCG
1 TTCTTCACGCCG
202171 TTCTCTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.15, T:0.37
Consensus pattern (17 bp):
TTCTTCACGCCGAAATC
Found at i:205509 original size:7 final size:7
Alignment explanation
Indices: 205497--205527 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
205487 TTATTTTCAT
205497 ATATAAA
1 ATATAAA
205504 ATATAAA
1 ATATAAA
205511 ATATAAA
1 ATATAAA
205518 ATATAAA
1 ATATAAA
205525 ATA
1 ATA
205528 ATATTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATATAAA
Found at i:205727 original size:121 final size:120
Alignment explanation
Indices: 205602--205965 Score: 577
Period size: 110 Copynumber: 3.1 Consensus size: 120
205592 AAAAATAACC
*
205602 CAAATATTTAATTCAAAATATTAAATTATTTCATTATATTTAAATAAATATTAAATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
*
205667 CAAAAATCAATTAAAATAATTAATTATTTAATTAGTTATTTATTAAATCCTAAACT
66 CAAAAATCAATTAAAATAATTAATTA-TTAATTAGTTATTTATTAAACCCTAAACT
205723 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
* * *
205788 C----A-GAA-T-AAAT-ATTAA--AATAATTAGTTATTTATTAAACCCTAAACC
66 CAAAAATCAATTAAAATAATTAATTATTAATTAGTTATTTATTAAACCCTAAACT
205833 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
* *
205898 TAAAACTCAATTAAAATAATTAATTATTAATTAGTTATTTATTAAACCCTAAACT
66 CAAAAATCAATTAAAATAATTAATTATTAATTAGTTATTTATTAAACCCTAAACT
*
205953 CAACTATTTAATT
1 CAAATATTTAATT
205966 ATTAAAAACA
Statistics
Matches: 222, Mismatches: 11, Indels: 21
0.87 0.04 0.08
Matches are distributed among these distances:
110 91 0.41
111 1 0.00
113 5 0.02
114 4 0.02
115 3 0.01
116 3 0.01
117 5 0.02
118 5 0.02
120 40 0.18
121 65 0.29
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (120 bp):
CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
CAAAAATCAATTAAAATAATTAATTATTAATTAGTTATTTATTAAACCCTAAACT
Found at i:206011 original size:68 final size:67
Alignment explanation
Indices: 205911--206036 Score: 216
Period size: 68 Copynumber: 1.9 Consensus size: 67
205901 AACTCAATTA
* *
205911 AAATAATTAATTATTAATTAGTTATTTATTAAACCCTAAACTCAACTATTTAATTATTAAAAACA
1 AAATAATTAATTATTAATTAGTTATTTATTAAACCCTAAACCCAAATATTTAATTATTAAAAACA
205976 AC
66 AC
*
205978 AAATATTTAATTATTTAATTAGTTATTTATTAAACCCTAAACCCAAATATTTAATTATT
1 AAATAATTAATTA-TTAATTAGTTATTTATTAAACCCTAAACCCAAATATTTAATTATT
206037 TAATTATTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
67 12 0.22
68 43 0.78
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (67 bp):
AAATAATTAATTATTAATTAGTTATTTATTAAACCCTAAACCCAAATATTTAATTATTAAAAACA
AC
Found at i:215537 original size:30 final size:30
Alignment explanation
Indices: 215445--215602 Score: 151
Period size: 30 Copynumber: 5.3 Consensus size: 30
215435 AAAATTATGT
215445 TTTG-CCCC-AAACTTTCCAAAAATTCAAA
1 TTTGACCCCAAAACTTTCCAAAAATTCAAA
* ** *
215473 TTTAACCCTCAAATTTTTCGAAAAAATTCAAA
1 TTTGACCC-CAAAACTTTC-CAAAAATTCAAA
* * *
215505 TTTGACCCCAAAAATTTCCAAAAAATCTAA
1 TTTGACCCCAAAACTTTCCAAAAATTCAAA
* ***
215535 TTTGACCCCCAAACTTTCCAAAAATTTTGA
1 TTTGACCCCAAAACTTTCCAAAAATTCAAA
* *
215565 TTTGA-CCCATAAATTTTTCAAAAATTCAAA
1 TTTGACCCCA-AAACTTTCCAAAAATTCAAA
215595 TTTGACCC
1 TTTGACCC
215603 GGTTTTAATG
Statistics
Matches: 103, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
28 3 0.03
29 6 0.06
30 60 0.58
31 16 0.16
32 18 0.17
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32
Consensus pattern (30 bp):
TTTGACCCCAAAACTTTCCAAAAATTCAAA
Found at i:215571 original size:60 final size:60
Alignment explanation
Indices: 215425--215602 Score: 175
Period size: 60 Copynumber: 3.0 Consensus size: 60
215415 TTTAACCCTT
* * * * *
215425 AAACTTTTCAAAAATTATGTTTTG-CCCC-AAACTTTCCAAAAATTCAAATTTAACCCTC
1 AAACTTTCCAAAAATTATGATTTGACCCCAAAAATTTCCAAAAATTCAAATTTGACCCCC
* * * * *
215483 AAATTTTTCGAAAAAATTCA-AATTTGACCCCAAAAATTTCCAAAAAATCTAATTTGACCCCC
1 AAA-CTTTC-CAAAAATT-ATGATTTGACCCCAAAAATTTCCAAAAATTCAAATTTGACCCCC
* * *
215545 AAACTTTCCAAAAATTTTGATTTGA-CCCATAAATTTTTCAAAAATTCAAATTTGACCC
1 AAACTTTCCAAAAATTATGATTTGACCCCA-AAAATTTCCAAAAATTCAAATTTGACCC
215603 GGTTTTAATG
Statistics
Matches: 95, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
58 3 0.03
59 7 0.07
60 48 0.51
61 9 0.09
62 28 0.29
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (60 bp):
AAACTTTCCAAAAATTATGATTTGACCCCAAAAATTTCCAAAAATTCAAATTTGACCCCC
Found at i:215701 original size:16 final size:17
Alignment explanation
Indices: 215647--215703 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 17
215637 TATGCATATG
*
215647 TATGTTATTTTATTTTAT
1 TATG-TATTGTATTTTAT
215665 T-T-TATTGTATTTTAT
1 TATGTATTGTATTTTAT
*
215680 GCATGTATTGT-TTTTAT
1 -TATGTATTGTATTTTAT
215697 TATGTAT
1 TATGTAT
215704 ACTTGTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.36
16 6 0.18
17 8 0.24
18 7 0.21
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.67
Consensus pattern (17 bp):
TATGTATTGTATTTTAT
Found at i:226880 original size:50 final size:50
Alignment explanation
Indices: 226826--226954 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
226816 ATTGAAGCCA
* *
226826 CAATGGCAAATCTCATATACCTAAAGCTGTAAAGGGGCAGATTCAAGTTG
1 CAATGGCAAATCTCATATACCTAAAGCTGTAAAGGGGCAAATTCAAGTCG
* * *
226876 CAATGGCGAATCTCAT-TCACCTAAAGCTGTAGAGGGGCAAATTGAAGTCG
1 CAATGGCAAATCTCATAT-ACCTAAAGCTGTAAAGGGGCAAATTCAAGTCG
* *
226926 CAA-GG-ATGAATCTCATATTCCTGAAGCTG
1 CAATGGCA--AATCTCATATACCTAAAGCTG
226955 AAATGGAGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
49 3 0.04
50 63 0.94
51 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (50 bp):
CAATGGCAAATCTCATATACCTAAAGCTGTAAAGGGGCAAATTCAAGTCG
Found at i:227083 original size:40 final size:39
Alignment explanation
Indices: 226993--227130 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 39
226983 TTTTACCCCG
* * *
226993 ACCATGAGGCAAATTGAAG-CAATCCA-ATCACTTACCCTA
1 ACCA-GAGGCAGATTGAAGACCAT-CAGATCTCTTACCCTA
* *
227032 ACTAGAAGGCAGATTGAAGACCATCAGATCTCTTTCCCTA
1 ACCAG-AGGCAGATTGAAGACCATCAGATCTCTTACCCTA
* **
227072 ACCAGAGGGCAGATTGAAGACCATCTGATCTCTTACCCCG
1 ACCAGA-GGCAGATTGAAGACCATCAGATCTCTTACCCTA
227112 ACCATGAGGCAGATTGAAG
1 ACCA-GAGGCAGATTGAAG
227131 CAATCTAATC
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 18 0.21
40 63 0.75
41 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (39 bp):
ACCAGAGGCAGATTGAAGACCATCAGATCTCTTACCCTA
Found at i:227195 original size:40 final size:39
Alignment explanation
Indices: 227039--227205 Score: 144
Period size: 40 Copynumber: 4.2 Consensus size: 39
227029 CTAACTAGAA
* * * * ** *
227039 GGCAGATTGAAGACCATCAGATCTCTTTCCCTAACCAGAG
1 GGCAGATTAAACACCATCTGATCTCTTACCCCGACCA-TG
* *
227079 GGCAGATTGAAGACCATCTGATCTCTTACCCCGACCATG
1 GGCAGATTAAACACCATCTGATCTCTTACCCCGACCATG
* *
227118 AGGCAGATTGAAGCA--ATCTAATC-CTTTACCCCGACCATG
1 -GGCAGATT-AAACACCATCTGATCTC-TTACCCCGACCATG
227157 GGACAGATTAAACACCATAC-GATCTCTTACCCCGACCATAG
1 GG-CAGATTAAACACCAT-CTGATCTCTTACCCCGACCAT-G
227198 GGCAGATT
1 GGCAGATT
227206 GAGGCAGTCT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
38 7 0.07
39 28 0.26
40 65 0.61
41 7 0.07
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (39 bp):
GGCAGATTAAACACCATCTGATCTCTTACCCCGACCATG
Found at i:227200 original size:119 final size:118
Alignment explanation
Indices: 226985--227207 Score: 281
Period size: 119 Copynumber: 1.9 Consensus size: 118
226975 CTTGAGTATT
* * *
226985 TTACCCCGACCATGAGGCAAATTGAAGCAATCCAATCACTTACCCTAACTAGAAGGCAGATTGAA
1 TTACCCCGACCATGAGGCAAATTGAAGCAATCCAATCACTTACCCCAACCAG-AGGCAGATTAAA
* * *
227050 GACCATCAGATCTCTTTCCCTAACCAGAGGGCAGATTGAAGACCATCTGATCTC
65 CACCATCAGATCTCTTACCCCAACCAGAGGGCAGATTGAAGACCATCTGATCTC
* * *
227104 TTACCCCGACCATGAGGCAGATTGAAGCAATCTAATC-CTTTACCCCGACCATG-GGACAGATTA
1 TTACCCCGACCATGAGGCAAATTGAAGCAATCCAATCAC-TTACCCCAACCA-GAGG-CAGATTA
* *
227167 AACACCAT-ACGATCTCTTACCCCGACCATAGGGCAGATTGA
63 AACACCATCA-GATCTCTTACCCCAACCAGAGGGCAGATTGA
227208 GGCAGTCTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 84 0.94
120 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (118 bp):
TTACCCCGACCATGAGGCAAATTGAAGCAATCCAATCACTTACCCCAACCAGAGGCAGATTAAAC
ACCATCAGATCTCTTACCCCAACCAGAGGGCAGATTGAAGACCATCTGATCTC
Found at i:227277 original size:50 final size:50
Alignment explanation
Indices: 227223--227332 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
227213 TCTAATCTTT
* * * * * *
227223 TACACCTAAAGTTGTAGAGGTGCAGATTGAAGCCGCAATGGCAAATCTCA
1 TACACCTAAAGCTGTACAGGAGCAGATTAAAGCCACAAGGGCAAATCTCA
* *
227273 TACACCTAAAGCTGTACAGGAGCAGATTAAAGCCACAAGGGCGAATCTTA
1 TACACCTAAAGCTGTACAGGAGCAGATTAAAGCCACAAGGGCAAATCTCA
*
227323 TACTCCTAAA
1 TACACCTAAA
227333 ACTGGAAAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (50 bp):
TACACCTAAAGCTGTACAGGAGCAGATTAAAGCCACAAGGGCAAATCTCA
Found at i:228802 original size:30 final size:29
Alignment explanation
Indices: 228768--228832 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
228758 CCTTTATTTT
** *
228768 AAAATTATTTTTTAACCCCTAAACTTTTCA
1 AAAATTATACTTT-ACCCCTAAACTTTCCA
* *
228798 AAAATTATACTTTGCCCTTAAACTTTCCA
1 AAAATTATACTTTACCCCTAAACTTTCCA
228827 AAAATT
1 AAAATT
228833 CGAATCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATTATACTTTACCCCTAAACTTTCCA
Found at i:228920 original size:31 final size:30
Alignment explanation
Indices: 228778--228924 Score: 111
Period size: 30 Copynumber: 4.9 Consensus size: 30
228768 AAAATTATTT
* * *
228778 TTTAACCCCTAAACTTTTCAAAAATT-ATAC
1 TTTAACCCCAAAACTTTCCAAAAATTCA-AA
* ** *
228808 TTT-GCCCTTAAACTTTCCAAAAATTCGAA
1 TTTAACCCCAAAACTTTCCAAAAATTCAAA
* * * *
228837 TCTAA-ACCAAGAATTTTCCAAAAATTAAAA
1 TTTAACCCCAA-AACTTTCCAAAAATTCAAA
* *
228867 TTTAACCACAAAATTTTACCAAAAATTCAAA
1 TTTAACCCCAAAACTTT-CCAAAAATTCAAA
*
228898 TTTAACCCCCCAAACTTTCCAAAAATT
1 TTTAA-CCCCAAAACTTTCCAAAAATT
228925 TCGATTTGAC
Statistics
Matches: 91, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
29 24 0.26
30 29 0.32
31 29 0.32
32 9 0.10
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (30 bp):
TTTAACCCCAAAACTTTCCAAAAATTCAAA
Found at i:230868 original size:85 final size:84
Alignment explanation
Indices: 230752--230967 Score: 272
Period size: 85 Copynumber: 2.5 Consensus size: 84
230742 TATAGCGACA
* * * *
230752 TTTATGAGAAAAGCGCCGCTAAAGACGATGTTCTATAGCGGTGTTTGTGA-AGAAAGCGCCGCTA
1 TTTATG-GGAAAGCGCCACTAAAGAC-ATGTTCTATAGCGGCGTTTGTGAGA-AAAGCGCCACTA
230816 AAGACCATATTCTTTAACAGCG
63 AAGACCATATTCTTTAACAGCG
* * *
230838 TTTGTGGGAAAGCGCCACTAAAGATCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCTACTAAA
1 TTTATGGGAAAGCGCCACTAAAGA-CATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAA
* * * *
230903 GATCATGTTCTTTAGCGGCG
65 GACCATATTCTTTAACAGCG
*
230923 TTTATGGGAAAGCGCCACTAAAGACCATGTTCTACAGCGGCGTTT
1 TTTATGGGAAAGCGCCACTAAAGA-CATGTTCTATAGCGGCGTTT
230968 TTCCTCATAA
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
85 106 0.94
86 7 0.06
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (84 bp):
TTTATGGGAAAGCGCCACTAAAGACATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAG
ACCATATTCTTTAACAGCG
Found at i:230871 original size:42 final size:43
Alignment explanation
Indices: 230756--230967 Score: 257
Period size: 43 Copynumber: 5.0 Consensus size: 43
230746 GCGACATTTA
* * * * *
230756 TGAGAAAAGCGCCGCTAAAGACGATGTTCTATAGCGGTGTTTG
1 TGAGGAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGTTTG
* * * * *
230799 TGAAGAAAGCGCCGCTAAAGACCATATTCTTTAACAGCGTTTG
1 TGAGGAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGTTTG
*
230842 TG-GGAAAGCGCCACTAAAGATCATGTTCTTTAGCGGCGTTTG
1 TGAGGAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGTTTG
* * * *
230884 TGAGAAAAGCGCTACTAAAGATCATGTTCTTTAGCGGCGTTTA
1 TGAGGAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGTTTG
**
230927 TG-GGAAAGCGCCACTAAAGACCATGTTCTACAGCGGCGTTT
1 TGAGGAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGTTT
230968 TTCCTCATAA
Statistics
Matches: 146, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
42 70 0.48
43 76 0.52
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (43 bp):
TGAGGAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGTTTG
Found at i:235023 original size:16 final size:16
Alignment explanation
Indices: 235002--235047 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
234992 TGTTCCTTTC
235002 ATTTTTCT-CTCTACAA
1 ATTTTTCTACTCTA-AA
*
235018 ATTTTTCTTACCCTAAA
1 ATTTTTC-TACTCTAAA
235035 ATTTTTCTACTCT
1 ATTTTTCTACTCT
235048 TTTTATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 12 0.46
17 10 0.38
18 4 0.15
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTTCTACTCTAAA
Found at i:238235 original size:25 final size:25
Alignment explanation
Indices: 238201--238251 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
238191 AGGCTTTCCA
238201 CAATCAAGTGTTTCTTCCCAAAATT
1 CAATCAAGTGTTTCTTCCCAAAATT
238226 CAATCAAGTGTTTCTTCCCAAAATT
1 CAATCAAGTGTTTCTTCCCAAAATT
238251 C
1 C
238252 TCGAGGAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (25 bp):
CAATCAAGTGTTTCTTCCCAAAATT
Found at i:239705 original size:37 final size:39
Alignment explanation
Indices: 239628--239716 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 39
239618 TAATTTTTTT
* * * *
239628 AATTCATATTTTAATAATAATTATATTTAAAATGTTATTA
1 AATT-ATATTTTAATAATAACTATAGTTAAAATATGATTA
239668 AATTATA-TTTAATAATAACTAT-GTTAAAATATGATTA
1 AATTATATTTTAATAATAACTATAGTTAAAATATGATTA
*
239705 AATTATTTTTTA
1 AATTATATTTTA
239717 TTATTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
37 18 0.42
38 18 0.42
39 3 0.07
40 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (39 bp):
AATTATATTTTAATAATAACTATAGTTAAAATATGATTA
Found at i:240440 original size:32 final size:28
Alignment explanation
Indices: 240372--240441 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 28
240362 AATAGTTTAT
*
240372 AATTTTATCATTTTAAAAAAATTAAATT
1 AATTTTATCATTTTAAAAAAATTAAATC
*
240400 AATTTTTTATCATTTTCAAAAAAGTTTAAAGTGC
1 AA--TTTTATCATTTT-AAAAAA-ATTAAA-T-C
240434 AATTTTAT
1 AATTTTAT
240442 GAAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
28 2 0.06
30 12 0.35
31 6 0.18
32 11 0.32
33 1 0.03
34 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (28 bp):
AATTTTATCATTTTAAAAAAATTAAATC
Found at i:241152 original size:20 final size:20
Alignment explanation
Indices: 241128--241172 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
241118 AAAAATTACA
241128 AAAAAGGTTAAAATAATTTTC
1 AAAAA-GTTAAAATAATTTTC
* * *
241149 AAAAATTTTAAATAATTTTT
1 AAAAAGTTAAAATAATTTTC
241169 AAAA
1 AAAA
241173 TTCAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAAGTTAAAATAATTTTC
Found at i:241155 original size:10 final size:9
Alignment explanation
Indices: 241142--241234 Score: 50
Period size: 10 Copynumber: 10.2 Consensus size: 9
241132 AGGTTAAAAT
241142 AATTTTCAAA
1 AATTTT-AAA
241152 AATTTTAAA
1 AATTTTAAA
*
241161 TAATTTTTAA
1 -AATTTTAAA
*
241171 AA-TTCAAA
1 AATTTTAAA
241179 ATATTTATAAA
1 A-ATTT-TAAA
*
241190 AATTCT-AA
1 AATTTTAAA
*
241198 AA-TTT-AT
1 AATTTTAAA
*
241205 ATTTTTAAAA
1 AATTTT-AAA
*
241215 AATTATAAA
1 AATTTTAAA
*
241224 AATTTCAAA
1 AATTTTAAA
241233 AA
1 AA
241235 AAAATAATTC
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
7 4 0.06
8 12 0.19
9 19 0.30
10 24 0.38
11 4 0.06
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTTTAAA
Found at i:241180 original size:19 final size:19
Alignment explanation
Indices: 241137--241200 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
241127 AAAAAAGGTT
*
241137 AAAATAATTTTCAAAAATTT
1 AAAATAATTTT-AAAAATTC
* *
241157 TAAATAATTTTTAAAATTC
1 AAAATAATTTTAAAAATTC
241176 AAAAT-ATTTATAAAAATTC
1 AAAATAATTT-TAAAAATTC
241195 TAAAAT
1 -AAAAT
241201 TTATATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 15 0.41
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTC
Found at i:241189 original size:18 final size:18
Alignment explanation
Indices: 241158--241205 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
241148 CAAAAATTTT
*
241158 AAATAATTTTTAAAATTCA
1 AAAT-ATTTATAAAATTCA
*
241177 AAATATTTATAAAAATTCT
1 AAATATTTAT-AAAATTCA
241196 AAA-ATTTATA
1 AAATATTTATA
241206 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATTTATAAAATTCA
Found at i:241198 original size:27 final size:27
Alignment explanation
Indices: 241146--241201 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
241136 TAAAATAATT
*
241146 TTCAAAAATTTTAAATAATTTTTAAAA
1 TTCAAAAATTTTAAATAATTTCTAAAA
241173 TTCAAAATATTTATAAA-AA-TTCTAAAA
1 TTCAAAA-ATTT-TAAATAATTTCTAAAA
241200 TT
1 TT
241202 TATATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 16 0.62
28 6 0.23
29 4 0.15
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (27 bp):
TTCAAAAATTTTAAATAATTTCTAAAA
Found at i:245439 original size:40 final size:40
Alignment explanation
Indices: 245385--245464 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
245375 AAAATCATTA
245385 TATTATTTATATAGTTAAATAATATTATACTTCGACTATT
1 TATTATTTATATAGTTAAATAATATTATACTTCGACTATT
*
245425 TATTATTTATATAGTTAAATAATATTATACTTCGTCTATT
1 TATTATTTATATAGTTAAATAATATTATACTTCGACTATT
245465 AGTTAAATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.51
Consensus pattern (40 bp):
TATTATTTATATAGTTAAATAATATTATACTTCGACTATT
Found at i:245475 original size:36 final size:35
Alignment explanation
Indices: 245385--245475 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 35
245375 AAAATCATTA
*
245385 TATTATTTATATAGTTAAATAATATTATACTTCGAC
1 TATTA-TTAAATAGTTAAATAATATTATACTTCGAC
*
245421 TATTTATTATTTATATAGTTAAATAATATTATACTTCGTC
1 TA-TTATTA---A-ATAGTTAAATAATATTATACTTCGAC
245461 TATTAGTTAAATAGT
1 TATTA-TTAAATAGT
245476 CGGTCTATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
36 10 0.21
37 4 0.09
39 3 0.06
40 30 0.64
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (35 bp):
TATTATTAAATAGTTAAATAATATTATACTTCGAC
Found at i:246593 original size:21 final size:20
Alignment explanation
Indices: 246567--246610 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
246557 TTGATAATTA
*
246567 TTTTTATATTGAAATTTAAAT
1 TTTTTAGATTGAAA-TTAAAT
*
246588 TTTTTAGATTTAAATTAAAT
1 TTTTTAGATTGAAATTAAAT
246608 TTT
1 TTT
246611 AAATTTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTAGATTGAAATTAAAT
Found at i:252398 original size:27 final size:26
Alignment explanation
Indices: 252357--252407 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
252347 GGGATGAGAG
*
252357 GAGGGTAAAAATTTTGGAGGAAAAGT
1 GAGGGTAAAAATTTTGGAAGAAAAGT
* *
252383 GAGGAGTAAAAGTTTTTGAAGAAAA
1 GAGG-GTAAAAATTTTGGAAGAAAA
252408 ATAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (26 bp):
GAGGGTAAAAATTTTGGAAGAAAAGT
Found at i:255532 original size:80 final size:80
Alignment explanation
Indices: 255416--255574 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 80
255406 TTTTTTTCCT
255416 AGCAATGGCTTTTGGAGAGCTTCAAGTTTATGTTTATTTGCATCATTACTGCAGGTCGACTGCAA
1 AGCAATGGCTTTTGGAGAGCTTCAAGTTTATGTTTATTTGCATCATTACTGCAGGTCGACTGCAA
255481 AGTTTTCTTTCGAAA
66 AGTTTTCTTTCGAAA
*
255496 AGCAATGGCTTTTGGAGAGCTTCAAGTTTATGTTTATTTGCATCATTACTGGAGGTCGACTGCAA
1 AGCAATGGCTTTTGGAGAGCTTCAAGTTTATGTTTATTTGCATCATTACTGCAGGTCGACTGCAA
255561 AGTTTTCTTTCGAA
66 AGTTTTCTTTCGAA
255575 TATCCAAGTC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (80 bp):
AGCAATGGCTTTTGGAGAGCTTCAAGTTTATGTTTATTTGCATCATTACTGCAGGTCGACTGCAA
AGTTTTCTTTCGAAA
Found at i:256725 original size:28 final size:28
Alignment explanation
Indices: 256671--256726 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
256661 AAAAAGTGTC
* * **
256671 AAGTTTAAGTATCAAATTTGACCAAAAA
1 AAGTTTAAGTACCAAATTAGAAAAAAAA
*
256699 AAGTTTACGTACCAAATTAGAAAAAAAA
1 AAGTTTAAGTACCAAATTAGAAAAAAAA
256727 TGTCAAGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (28 bp):
AAGTTTAAGTACCAAATTAGAAAAAAAA
Found at i:261065 original size:3 final size:3
Alignment explanation
Indices: 261057--261088 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
261047 TTCTACCATC
*
261057 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
261089 ATTGGTTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:272703 original size:92 final size:91
Alignment explanation
Indices: 272517--272718 Score: 255
Period size: 92 Copynumber: 2.2 Consensus size: 91
272507 TGTAAATTAG
* * * *
272517 AAATTGACTACAAAATGTTGTTCAATTTTGGTTAATATATTGTAAAAAAATTGTTGTATAATGCT
1 AAATTGACTGCAAAATGCTGTTCAATTATGGTTAATATATTGTAAAAAAATTATTGTATAATGCT
*
272582 GCACAATCGTGGTTAGATTGCTGTCC
66 GCACAATCGTGGTTAGATGGCTGTCC
*
272608 AAATTGACGGCAAAATGCTG-TCGAATTATGGTTAATATATTGTCAAAAAAATTATTG-AGTAAT
1 AAATTGACTGCAAAATGCTGTTC-AATTATGGTTAATATATTGT-AAAAAAATTATTGTA-TAAT
* * * * *
272671 GTTGTACAATTGTGGTTAGATGGTTTTCC
63 GCTGCACAATCGTGGTTAGATGGCTGTCC
*
272700 AAATTGACTGTAAAATGCT
1 AAATTGACTGCAAAATGCT
272719 ACTCAAATGT
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
90 2 0.02
91 37 0.39
92 56 0.59
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (91 bp):
AAATTGACTGCAAAATGCTGTTCAATTATGGTTAATATATTGTAAAAAAATTATTGTATAATGCT
GCACAATCGTGGTTAGATGGCTGTCC
Found at i:272831 original size:23 final size:23
Alignment explanation
Indices: 272792--273090 Score: 175
Period size: 23 Copynumber: 13.1 Consensus size: 23
272782 GTAATGTTCC
* *
272792 ATTGAG-T-TTTAAATGCTATAA
1 ATTGAGATGTTTAAGTGCTGTAA
*
272813 ATTGAGATGTTTAAGTGCTGCAA
1 ATTGAGATGTTTAAGTGCTGTAA
* * ***
272836 ATTTAAATGTTTAAGTGCAACAA
1 ATTGAGATGTTTAAGTGCTGTAA
* *
272859 ATTGAGGTGTTTAA-TGTTGTAA
1 ATTGAGATGTTTAAGTGCTGTAA
* *
272881 ATTGA-AGTGTTTAAATGCTATAA
1 ATTGAGA-TGTTTAAGTGCTGTAA
* *
272904 ATTGTGATGTTTAAGTGCTGCAA
1 ATTGAGATGTTTAAGTGCTGTAA
* * *
272927 ATTGAGTTGTTTTAA-TGTTTTAA
1 ATTGAGATG-TTTAAGTGCTGTAA
* * *
272950 ATTGA-AGTGTTTAAATACCGTAA
1 ATTGAGA-TGTTTAAGTGCTGTAA
* * *
272973 ATTGATATGTTTAAGTGTTGCAA
1 ATTGAGATGTTTAAGTGCTGTAA
* * * *
272996 ATCGAGGTGTTTAAATGTTGTAA
1 ATTGAGATGTTTAAGTGCTGTAA
* * * *
273019 ATCGA-AGTGCTTAATTGTTGTAA
1 ATTGAGA-TGTTTAAGTGCTGTAA
* *
273042 ATTGATG-TGTATAAAG-GTTGTAA
1 ATTGA-GATGT-TTAAGTGCTGTAA
*
273065 ATTGAGATATTTAAGTGCTGTAA
1 ATTGAGATGTTTAAGTGCTGTAA
273088 ATT
1 ATT
273091 AAAGTCTATA
Statistics
Matches: 212, Mismatches: 51, Indels: 28
0.73 0.18 0.10
Matches are distributed among these distances:
21 6 0.03
22 27 0.13
23 169 0.80
24 10 0.05
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (23 bp):
ATTGAGATGTTTAAGTGCTGTAA
Found at i:273042 original size:69 final size:69
Alignment explanation
Indices: 272810--273048 Score: 270
Period size: 69 Copynumber: 3.5 Consensus size: 69
272800 TTAAATGCTA
* * * * **
272810 TAAATTG-AGATGTTTAAGTGCTGCAAATTTA-AATGTTTAAGTGCAACAAATTGAGGTGTTTAA
1 TAAATTGAAG-TGTTTAAATGCTGTAAATTGATGATGTTTAAGTGCTGCAAATTGAGGTGTTTAA
272873 TGTTG
65 TGTTG
* *
272878 TAAATTGAAGTGTTTAAATGCTATAAATTG-TGATGTTTAAGTGCTGCAAATTGAGTTGTTTTAA
1 TAAATTGAAGTGTTTAAATGCTGTAAATTGATGATGTTTAAGTGCTGCAAATTGAGGTG-TTTAA
*
272942 TGTTT
65 TGTTG
* * * *
272947 TAAATTGAAGTGTTTAAATACCGTAAATTGAT-ATGTTTAAGTGTTGCAAATCGAGGTGTTTAAA
1 TAAATTGAAGTGTTTAAATGCTGTAAATTGATGATGTTTAAGTGCTGCAAATTGAGGTGTTT-AA
273011 TGTTG
65 TGTTG
* * * *
273016 TAAATCGAAGTGCTTAATTGTTGTAAATTGATG
1 TAAATTGAAGTGTTTAAATGCTGTAAATTGATG
273049 TGTATAAAGG
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
68 49 0.34
69 93 0.65
70 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (69 bp):
TAAATTGAAGTGTTTAAATGCTGTAAATTGATGATGTTTAAGTGCTGCAAATTGAGGTGTTTAAT
GTTG
Found at i:273078 original size:69 final size:69
Alignment explanation
Indices: 272792--273095 Score: 269
Period size: 69 Copynumber: 4.4 Consensus size: 69
272782 GTAATGTTCC
* * * * * ** *
272792 ATTGA-GT-TTTAAATGCTATAAATTG-AGATGTTTAAGTGCTGCAAATTTAAATGTTTAAGTGC
1 ATTGAGGTGTTTAAATGTTGTAAATTGAAG-TGTTTAAATGCTGTAAATTGATGTGTTTAAGTGT
**
272854 AACAA
65 TGCAA
* *
272859 ATTGAGGTGTTT-AATGTTGTAAATTGAAGTGTTTAAATGCTATAAATTG-TGATGTTTAAGTGC
1 ATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGCTGTAAATTGATG-TGTTTAAGTGT
272922 TGCAA
65 TGCAA
* * * * * *
272927 ATTGAGTTGTTTTAATGTTTTAAATTGAAGTGTTTAAATACCGTAAATTGATATGTTTAAGTGTT
1 ATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGCTGTAAATTGATGTGTTTAAGTGTT
272992 GCAA
66 GCAA
* * * * * *
272996 ATCGAGGTGTTTAAATGTTGTAAATCGAAGTGCTTAATTGTTGTAAATTGATGTGTATAAAG-GT
1 ATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGCTGTAAATTGATGTGT-TTAAGTGT
*
273060 TGTAA
65 TGCAA
* * * * *
273065 ATTGAGATATTTAAGTGCTGTAAATTAAAGT
1 ATTGAGGTGTTTAAATGTTGTAAATTGAAGT
273096 CTATAGATGT
Statistics
Matches: 193, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
67 5 0.03
68 55 0.28
69 128 0.66
70 5 0.03
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (69 bp):
ATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGCTGTAAATTGATGTGTTTAAGTGTT
GCAA
Found at i:277360 original size:41 final size:41
Alignment explanation
Indices: 277303--277398 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
277293 TTGAATATAT
*
277303 TAATTCAGGCTTTGTGCCTAGCAGGCTTCACATAGGTGTAA
1 TAATTCAGGCTTTGTGCCTAGCAGGCTTCACACAGGTGTAA
*** *
277344 TAATTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTAA
1 TAATTCAGGCTTTGTGCCTAGCAGGCTTCACACAGGTGTAA
277385 TAATTCAGGCTTTG
1 TAATTCAGGCTTTG
277399 AGTGTAGTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (41 bp):
TAATTCAGGCTTTGTGCCTAGCAGGCTTCACACAGGTGTAA
Found at i:279074 original size:25 final size:24
Alignment explanation
Indices: 279017--279075 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
279007 TTTTTTTCTA
* *
279017 ATTGGGTTATTGTTGGTTTTAGGT
1 ATTGGGTTTTTATTGGTTTTAGGT
*
279041 ATTGGGTTTTTATTTGTTTTAGGGT
1 ATTGGGTTTTTATTGGTTTTA-GGT
*
279066 GTTGGGTTTT
1 ATTGGGTTTT
279076 GAAAAGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.10, C:0.00, G:0.32, T:0.58
Consensus pattern (24 bp):
ATTGGGTTTTTATTGGTTTTAGGT
Done.