Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016007.1 Corchorus capsularis cultivar CVL-1 contig16028, 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: 217828
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:303 original size:14 final size:14
Alignment explanation
Indices: 282--316 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
272 AATAAAAACT
*
282 AAAAAGAATGAAAA
1 AAAAAGAAAGAAAA
*
296 ATAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
310 AAAAAGA
1 AAAAAGA
317 CACGTCGGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:3817 original size:31 final size:31
Alignment explanation
Indices: 3779--3874 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
3769 TTGGGTTATC
*
3779 AGTCTCCAGATTTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
3810 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
3841 AGTCTCC-GAATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAG-ATCTTTAGATCTTGGATGTTTG
3872 AGT
1 AGT
3875 TTGTTCAGTT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
30 1 0.02
31 62 0.98
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.43
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:6767 original size:18 final size:20
Alignment explanation
Indices: 6726--6768 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6716 TATATGGCAA
6726 TAAATTCCGACACGTATAGC
1 TAAATTCCGACACGTATAGC
6746 TAAATT-CGAACAC-TAT-GC
1 TAAATTCCG-ACACGTATAGC
6764 TAAAT
1 TAAAT
6769 AAATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 5 0.23
20 10 0.45
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (20 bp):
TAAATTCCGACACGTATAGC
Found at i:11434 original size:162 final size:162
Alignment explanation
Indices: 11167--11475 Score: 512
Period size: 162 Copynumber: 1.9 Consensus size: 162
11157 GTGTTTCATC
* * * *
11167 TGGTTCTCAACAACATTCCCTGGAAATTCAAAAGGGTAGAGATTTGGTTTTGTGAGATTCGTGAA
1 TGGTTCTCAACAACATTCCCCGGAAATTCAAAAGGGCAAAGATTTAGTTTTGTGAGATTCGTGAA
* * * *
11232 CTGTTTTGATATTGAAAGGATTTTATATTATCTCAATCAAATATGTATTGGTAGTTTCAAAATCA
66 CTATTTTGATATGGAAAGGATTTTATATTATCTCAATCAAATATGGATCGGTAGTTTCAAAATCA
11297 GATGTTTCAAGGCTAGAATTGATAGTTTCAAA
131 GATGTTTCAAGGCTAGAATTGATAGTTTCAAA
*
11329 TGGTTCTCAATAACATTCCCCGGAAATTCAAAAGGGCAAAGATTTAGTTTTGTGAGATTCGTGAA
1 TGGTTCTCAACAACATTCCCCGGAAATTCAAAAGGGCAAAGATTTAGTTTTGTGAGATTCGTGAA
*
11394 CTATTTCT-ATATGGAAAGGATTTTATATTATCTTAATCAAATATGGATCGGTAGTTTCAAAATC
66 CTATTT-TGATATGGAAAGGATTTTATATTATCTCAATCAAATATGGATCGGTAGTTTCAAAATC
11458 AGATGTTTCAAGGCTAGA
130 AGATGTTTCAAGGCTAGA
11476 GGTCAAAGTG
Statistics
Matches: 136, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
162 135 0.99
163 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (162 bp):
TGGTTCTCAACAACATTCCCCGGAAATTCAAAAGGGCAAAGATTTAGTTTTGTGAGATTCGTGAA
CTATTTTGATATGGAAAGGATTTTATATTATCTCAATCAAATATGGATCGGTAGTTTCAAAATCA
GATGTTTCAAGGCTAGAATTGATAGTTTCAAA
Found at i:13449 original size:15 final size:15
Alignment explanation
Indices: 13425--13454 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13415 ACAAGTCCAA
*
13425 GAGAATATCCAATTT
1 GAGAAAATCCAATTT
13440 GAGAAAATCCAATTT
1 GAGAAAATCCAATTT
13455 CCGCAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
GAGAAAATCCAATTT
Found at i:14804 original size:22 final size:22
Alignment explanation
Indices: 14771--14829 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
14761 CGCCTATAAA
*
14771 GGTCATGGGCATGACCTTCTCT
1 GGTCATGTGCATGACCTTCTCT
*
14793 TGTCATGTGCATGACCTTCTCT
1 GGTCATGTGCATGACCTTCTCT
14815 GGTCATGTGCATGAC
1 GGTCATGTGCATGAC
14830 TTGTTCAGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.34
Consensus pattern (22 bp):
GGTCATGTGCATGACCTTCTCT
Found at i:15427 original size:2 final size:2
Alignment explanation
Indices: 15420--15458 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
15410 ACTAGGTTCT
15420 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15459 AAGCACCGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15796 original size:109 final size:108
Alignment explanation
Indices: 15603--15813 Score: 253
Period size: 109 Copynumber: 1.9 Consensus size: 108
15593 TTAAAGCACC
* * * * * *
15603 TTGCATACTCGTAATTTTGGTTTGTGACTGAAGCGAAGGTTGATTTTGTTATACCGAACCTCGTG
1 TTGCATACTCATAATTTTGGTTCGTGACTGAAGCGAAGGTTAATTTTGTGATACCGAACCCCATG
* **
15668 TGCTCCACTTCCCAAAAACAGTAGAGTAATTTATTAAGATGCT
66 TCCTCCACTTCCCAAAAACAACAGAGTAATTTATTAAGATGCT
* * * *
15711 TTGCATACTCATAATTTTGGTTCGTGATTGACGC-AAGGGTTAATATTTGTGATACTGAGCCCCA
1 TTGCATACTCATAATTTTGGTTCGTGACTGAAGCGAA-GGTTAAT-TTTGTGATACCGAACCCCA
** *
15775 TGTCCTCCACTTCTTAAAAACAACGGAGTAATTTATTAA
64 TGTCCTCCACTTCCCAAAAACAACAGAGTAATTTATTAA
15814 ATTCCCTGTC
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
107 2 0.02
108 36 0.42
109 47 0.55
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (108 bp):
TTGCATACTCATAATTTTGGTTCGTGACTGAAGCGAAGGTTAATTTTGTGATACCGAACCCCATG
TCCTCCACTTCCCAAAAACAACAGAGTAATTTATTAAGATGCT
Found at i:19161 original size:96 final size:96
Alignment explanation
Indices: 19036--19213 Score: 347
Period size: 96 Copynumber: 1.9 Consensus size: 96
19026 TTTTCAAGAT
19036 GAGTTCTAGATTATTGAGGCATTGATTGAAATTGTTTCCATAAACTGTGAAATCGTCCATGAAAA
1 GAGTTCTAGATTATTGAGGCATTGATTGAAATTGTTTCCATAAACTGTGAAATCGTCCATGAAAA
19101 CTTCCATCTTATCTCCTTTACCTTTGAAAAG
66 CTTCCATCTTATCTCCTTTACCTTTGAAAAG
*
19132 GAGTTCTAGATTATTGAGGCATTGATTGAAATTGTTTCCATAGACTGTGAAATCGTCCATGAAAA
1 GAGTTCTAGATTATTGAGGCATTGATTGAAATTGTTTCCATAAACTGTGAAATCGTCCATGAAAA
19197 CTTCCATCTTATCTCCT
66 CTTCCATCTTATCTCCT
19214 ACATAATCTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (96 bp):
GAGTTCTAGATTATTGAGGCATTGATTGAAATTGTTTCCATAAACTGTGAAATCGTCCATGAAAA
CTTCCATCTTATCTCCTTTACCTTTGAAAAG
Found at i:23566 original size:19 final size:18
Alignment explanation
Indices: 23533--23569 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
23523 TTGAAATAAT
23533 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
23551 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
23570 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:25452 original size:21 final size:21
Alignment explanation
Indices: 25407--25454 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
25397 TCTCCTTTTG
*
25407 TTGTTGAGCCAACTTCCCCAT
1 TTGTTGAGCCAACTTCCCCAC
*
25428 TTGTTGAGCCAA-TTGCCCTAC
1 TTGTTGAGCCAACTT-CCCCAC
25449 TTGTTG
1 TTGTTG
25455 CTCAAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (21 bp):
TTGTTGAGCCAACTTCCCCAC
Found at i:28704 original size:19 final size:18
Alignment explanation
Indices: 28680--28715 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28670 TGAAGATTTC
28680 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
28699 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
28716 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:35853 original size:21 final size:21
Alignment explanation
Indices: 35827--35870 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35817 CTTTACTATG
35827 GGCCTTATCTT-GTTCTTTAAT
1 GGCCTTAT-TTCGTTCTTTAAT
*
35848 GGCCTTCTTTCGTTCTTTAAT
1 GGCCTTATTTCGTTCTTTAAT
35869 GG
1 GG
35871 GCCACTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.50
Consensus pattern (21 bp):
GGCCTTATTTCGTTCTTTAAT
Found at i:42613 original size:23 final size:23
Alignment explanation
Indices: 42585--42631 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
42575 AATTAAATTG
* *
42585 CATCAAAATAGTCACCAGTAACC
1 CATCAAAACAGTCACCACTAACC
*
42608 CATCAAAACGGTCACCACTAACC
1 CATCAAAACAGTCACCACTAACC
42631 C
1 C
42632 TCTTCCTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.15
Consensus pattern (23 bp):
CATCAAAACAGTCACCACTAACC
Found at i:47966 original size:28 final size:30
Alignment explanation
Indices: 47933--47996 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
47923 GTGCGAGTTG
47933 TGCACTTGGG-TTG-ATTCAAGTGTGGGTT
1 TGCACTTGGGATTGTATTCAAGTGTGGGTT
**
47961 TGCACTTGGGATTGTATTTGAGTGTGGGTT
1 TGCACTTGGGATTGTATTCAAGTGTGGGTT
47991 TGCACT
1 TGCACT
47997 CGGTCTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 10 0.31
29 3 0.09
30 19 0.59
ACGTcount: A:0.14, C:0.11, G:0.34, T:0.41
Consensus pattern (30 bp):
TGCACTTGGGATTGTATTCAAGTGTGGGTT
Found at i:49530 original size:27 final size:26
Alignment explanation
Indices: 49492--49544 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
49482 GAAAATAGCG
* *
49492 GCGTCTATTGAATAAAGACGCCACTAT
1 GCGTCTACTGAAGAAAG-CGCCACTAT
49519 GCGTCTACTGAAGAAAGCGCCACTAT
1 GCGTCTACTGAAGAAAGCGCCACTAT
49545 TTTCACGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (26 bp):
GCGTCTACTGAAGAAAGCGCCACTAT
Found at i:50217 original size:15 final size:15
Alignment explanation
Indices: 50216--50272 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
50206 GATTACTATT
50216 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
* *
50231 TTACTATTTT-CTGC
1 TTACTCTTTTACTGA
** *
50245 TCCCTTTTTTACTGA
1 TTACTCTTTTACTGA
50260 TTACTCTTTTACT
1 TTACTCTTTTACT
50273 TTTTACTGAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.56
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:50278 original size:15 final size:15
Alignment explanation
Indices: 50215--50279 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
50205 TGATTACTAT
50215 TTTACTCTTTTACTG
1 TTTACTCTTTTACTG
* *
50230 ATTACTATTTT-CTG
1 TTTACTCTTTTACTG
* ** *
50244 CTCCCTTTTTTACTG
1 TTTACTCTTTTACTG
* *
50259 ATTACTCTTTTACTT
1 TTTACTCTTTTACTG
50274 TTTACT
1 TTTACT
50280 GATTGCCTTT
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
14 10 0.27
15 27 0.73
ACGTcount: A:0.15, C:0.22, G:0.05, T:0.58
Consensus pattern (15 bp):
TTTACTCTTTTACTG
Found at i:50351 original size:116 final size:116
Alignment explanation
Indices: 50135--50343 Score: 257
Period size: 116 Copynumber: 1.8 Consensus size: 116
50125 ACCATTACTA
* * *
50135 TTTTACTGATTATTCTTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTTCTTACTT
1 TTTTACTGATTACTCTTTACTTTGTACTGATTACTATTTTACCCTTGTAGATTACCTTCTTACTT
** *
50200 TTTACTGATTACTATTTTACTCTTTTACTGATTACTATTTTCTGCTCCCTT
66 TTTACTGATTACTATGCTACTCTTCTACTGATTACTATTTTCTGCTCCCTT
* *
50251 TTTTACTGATTACTCTTTTACTTTTTACTGATTGCCT-TTTTACCCTT-TCAGA-TACCTT-TTC
1 TTTTACTGATTACTC-TTTACTTTGTACTGATT-ACTATTTTACCCTTGT-AGATTACCTTCTT-
* *
50312 ACTTTTTACTGATTGC-ATGCTATTCTTCTACT
62 ACTTTTTACTGATTACTATGCTACTCTTCTACT
50344 CTCTTACTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
115 14 0.18
116 36 0.46
117 27 0.34
118 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.07, T:0.55
Consensus pattern (116 bp):
TTTTACTGATTACTCTTTACTTTGTACTGATTACTATTTTACCCTTGTAGATTACCTTCTTACTT
TTTACTGATTACTATGCTACTCTTCTACTGATTACTATTTTCTGCTCCCTT
Found at i:50637 original size:34 final size:34
Alignment explanation
Indices: 50594--50711 Score: 150
Period size: 34 Copynumber: 3.4 Consensus size: 34
50584 TTAGTTATCA
50594 ATTTACTGATTACTATCTTTTTACCTGATTACTG
1 ATTTACTGATTACTATCTTTTTACCTGATTACTG
** *
50628 ATTTACTGATTACTAT-TATCTGGACTCTTGATTA-TCA
1 ATTTACTGATTACTATCT-T-TTTAC-C-TGATTACT-G
50665 ATTTACTGATTACTATCTTTTTACCTGATTACTG
1 ATTTACTGATTACTATCTTTTTACCTGATTACTG
50699 ATTTACTGATTAC
1 ATTTACTGATTAC
50712 CTTGACTCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
33 1 0.01
34 36 0.51
35 5 0.07
36 5 0.07
37 23 0.32
38 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.48
Consensus pattern (34 bp):
ATTTACTGATTACTATCTTTTTACCTGATTACTG
Found at i:50672 original size:71 final size:70
Alignment explanation
Indices: 50508--50711 Score: 254
Period size: 71 Copynumber: 2.9 Consensus size: 70
50498 GACCATTTTA
* * *
50508 ACTCTTAATTATCGATTTACTGATTACTA--TTTTTACCTAGCCTCT-TTGA-TTACTGATTAAT
1 ACTCTT-ATTATCAATTTACTGATTACTATCTTTTTACCT-G-AT-TACTGATTTACTGATT-A-
* *
50569 CTCTTACCTTG
60 CTATTACCTGG
50580 ACTCTTAGTTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
1 ACTCTTA-TTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
*
50645 ATCTGG
65 ACCTGG
50651 ACTCTTGATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTAC
1 ACTCTT-ATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTAC
50712 CTTGACTCTA
Statistics
Matches: 120, Mismatches: 6, Indels: 13
0.86 0.04 0.09
Matches are distributed among these distances:
71 69 0.57
72 32 0.27
73 10 0.08
74 9 0.08
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.48
Consensus pattern (70 bp):
ACTCTTATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTA
CCTGG
Found at i:50772 original size:55 final size:55
Alignment explanation
Indices: 50689--50836 Score: 192
Period size: 55 Copynumber: 2.7 Consensus size: 55
50679 ATCTTTTTAC
50689 CTGA-TTACTGATTTACTGATTACCTTGACTCTAATTAATCTCTTCTT-ACTTAATTA
1 CTGATTTACTGA-TTACT-ATTACCTTGACTCTAATTAATCTCTT-TTCACTTAATTA
* * * * *
50745 CTGGTTTACTGATTACTATTACTTTGACTCTGATTAGTCTCTTTTCACTTGATTA
1 CTGATTTACTGATTACTATTACCTTGACTCTAATTAATCTCTTTTCACTTAATTA
*
50800 CTGATTTACTGATTATTATTACCTTGACTCTTAATTA
1 CTGATTTACTGATTACTATTACCTTGACTC-TAATTA
50837 TCAATTTACT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
54 2 0.03
55 58 0.73
56 13 0.16
57 7 0.09
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.48
Consensus pattern (55 bp):
CTGATTTACTGATTACTATTACCTTGACTCTAATTAATCTCTTTTCACTTAATTA
Found at i:50804 original size:175 final size:173
Alignment explanation
Indices: 50599--50984 Score: 479
Period size: 175 Copynumber: 2.2 Consensus size: 173
50589 TATCAATTTA
* * *
50599 CTGATTACTATCT-TTTTACCTGATTACTGATTTACTGATTACTATTATCTGGACTCTTGATTAT
1 CTGATTA--ATCTCTTTTACTTGATTACTGATTTACTGATTACTATTACCTGGACTCTTAATTAT
* * *
50663 CAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTG-ATTACCTTGACTCTAATTAA
64 CAATTTACTGATTAATATCTTTTTACCTAATTACTGATTTACTGAATTACCTTAACTCTAATTAA
* * * *
50727 TCTCTTCTTACTTAATTACTGGTTTACTGATTACTATTACTTTGACT
129 TCTCTTCTTACTTAATTACT-GATTACT-ATTACCATTACCTTAACT
* * *
50774 CTGATTAGTCTCTTTTCACTTGATTACTGATTTACTGATTATTATTACCTTGACTCTTAATTATC
1 CTGATTAATCTCTTTT-ACTTGATTACTGATTTACTGATTACTATTACCTGGACTCTTAATTATC
* * * *
50839 AATTTACTGATTAATCTCTTTTTACTTAATTACTTATTTACTGATTACCATTACCTTAACTCTGA
65 AATTTACTGATTAATATCTTTTTACCTAATTACTGATTTACTG---A--ATTACCTTAACTCTAA
* *
50904 TTAATCTCTTTTTACTTAATTACTGATTACTATTTCCATTACCTTAACT
125 TTAATCTCTTCTTACTTAATTACTGATTACTATTACCATTACCTTAACT
*
50953 CTGATTAATCTCTTCTTACTTAATTACTGATT
1 CTGATTAATCTCTT-TTACTTGATTACTGATT
50985 ACTATTTCCT
Statistics
Matches: 181, Mismatches: 21, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
173 3 0.02
174 4 0.02
175 88 0.49
179 41 0.23
180 8 0.04
181 37 0.20
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (173 bp):
CTGATTAATCTCTTTTACTTGATTACTGATTTACTGATTACTATTACCTGGACTCTTAATTATCA
ATTTACTGATTAATATCTTTTTACCTAATTACTGATTTACTGAATTACCTTAACTCTAATTAATC
TCTTCTTACTTAATTACTGATTACTATTACCATTACCTTAACT
Found at i:50812 original size:34 final size:34
Alignment explanation
Indices: 50774--50885 Score: 93
Period size: 34 Copynumber: 3.2 Consensus size: 34
50764 TACTTTGACT
* * *
50774 CTGATTAGTCTCTTTTCACTTGATTACTGATTTA
1 CTGATTAATCTCTTTTCACTTAATTACTAATTTA
** *
50808 CTGATTATTAT-TACCTTGACTCTTAATTA-TCAATTTA
1 CTGATTA--ATCT--CTTTTCACTTAATTACT-AATTTA
* *
50845 CTGATTAATCTCTTTTTACTTAATTACTTATTTA
1 CTGATTAATCTCTTTTCACTTAATTACTAATTTA
50879 CTGATTA
1 CTGATTA
50886 CCATTACCTT
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
34 30 0.50
35 4 0.07
36 3 0.05
37 23 0.38
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (34 bp):
CTGATTAATCTCTTTTCACTTAATTACTAATTTA
Found at i:50918 original size:26 final size:26
Alignment explanation
Indices: 50893--50985 Score: 86
Period size: 26 Copynumber: 3.6 Consensus size: 26
50883 TTACCATTAC
50893 CTTAACT-CTGATTAATCTCTTTTTA
1 CTTAACTACTGATTAATCTCTTTTTA
* *
50918 CTTAATTACTGATT-A-CTATTTCCATTA
1 CTTAACTACTGATTAATCTCTTT---TTA
*
50945 CCTTAACT-CTGATTAATCTCTTCTTA
1 -CTTAACTACTGATTAATCTCTTTTTA
*
50971 CTTAATTACTGATTA
1 CTTAACTACTGATTA
50986 CTATTTCCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
24 5 0.09
25 13 0.24
26 16 0.30
27 9 0.17
28 7 0.13
29 4 0.07
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.48
Consensus pattern (26 bp):
CTTAACTACTGATTAATCTCTTTTTA
Found at i:50966 original size:53 final size:53
Alignment explanation
Indices: 50845--50993 Score: 253
Period size: 53 Copynumber: 2.8 Consensus size: 53
50835 TATCAATTTA
* *
50845 CTGATTAATCTCTTTTTACTTAATTACTTATTTACTGATTACCATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGA-TTACT-ATTTCCATTACCTTAACT
50900 CTGATTAATCTCTTTTTACTTAATTACTGATTACTATTTCCATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTACTATTTCCATTACCTTAACT
*
50953 CTGATTAATCTCTTCTTACTTAATTACTGATTACTATTTCC
1 CTGATTAATCTCTTTTTACTTAATTACTGATTACTATTTCC
50994 TTGACTCTGA
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 57 0.63
54 5 0.05
55 29 0.32
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (53 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTACTATTTCCATTACCTTAACT
Found at i:50972 original size:126 final size:126
Alignment explanation
Indices: 50722--50954 Score: 337
Period size: 126 Copynumber: 1.9 Consensus size: 126
50712 CTTGACTCTA
* * * * *
50722 ATTAATCTCTTCTTACTTAATTACTGGTTTACTGATTACTATTACTTTGACTCTGATTAGTCTCT
1 ATTAATCTCTTCTTACTTAATTACTGATTTACTGATTACCATTACCTTAACTCTGATTAATCTCT
* * *
50787 TTTCACTTGATTACTGATTTACTGATTATTATTACCTTGACTCTTAATTATCAATTTACTG
66 TTTCACTTAATTACTGATTTACTGATTATCATTACCTTAACTCTTAATTATCAATTTACTG
* *
50848 ATTAATCTCTTTTTACTTAATTACTTATTTACTGATTACCATTACCTTAACTCTGATTAATCTCT
1 ATTAATCTCTTCTTACTTAATTACTGATTTACTGATTACCATTACCTTAACTCTGATTAATCTCT
*
50913 TTTTACTTAATTACTGA-TTACT-ATT-TCCATTACCTTAACTCT
66 TTTCACTTAATTACTGATTTACTGATTAT-CATTACCTTAACTCT
50955 GATTAATCTC
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
123 1 0.01
124 16 0.17
125 5 0.05
126 73 0.77
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (126 bp):
ATTAATCTCTTCTTACTTAATTACTGATTTACTGATTACCATTACCTTAACTCTGATTAATCTCT
TTTCACTTAATTACTGATTTACTGATTATCATTACCTTAACTCTTAATTATCAATTTACTG
Found at i:51046 original size:50 final size:49
Alignment explanation
Indices: 50876--51068 Score: 196
Period size: 53 Copynumber: 3.9 Consensus size: 49
50866 AATTACTTAT
* * * * * *
50876 TTACTGATTACCATTACCTTAACTCTGATTAA--TCTCTTTTTACTTAA
1 TTACTGATTACTATTTCCTTGACTCTGATTAACCTTTTTTTTTACATAA
* * * * *
50923 TTACTGATTACTATTTCCATTACCTTAACTCTGATTAA--TCTCTTCTTACTTAA
1 TTACTGATTACTA--T---TT-CCTTGACTCTGATTAACCTTTTTTTTTACATAA
50976 TTACTGATTACTATTTCCTTGACTCTGATTTAACCTTTTTTTTTACATAA
1 TTACTGATTACTATTTCCTTGACTCTGA-TTAACCTTTTTTTTTACATAA
51026 TTACTGATTACTATTTCCTTGACTCTGATTAACCTTTTTTTTT
1 TTACTGATTACTATTTCCTTGACTCTGATTAACCTTTTTTTTT
51069 TTACTTAATC
Statistics
Matches: 129, Mismatches: 8, Indels: 16
0.84 0.05 0.10
Matches are distributed among these distances:
47 23 0.18
48 6 0.05
49 16 0.12
50 39 0.30
51 1 0.01
52 1 0.01
53 43 0.33
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.50
Consensus pattern (49 bp):
TTACTGATTACTATTTCCTTGACTCTGATTAACCTTTTTTTTTACATAA
Found at i:51069 original size:50 final size:50
Alignment explanation
Indices: 50968--51068 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
50958 TAATCTCTTC
*
50968 TTACTTAATTACTGATTACTATTTCCTTGACTCTGATTTAACCTTTTTTT
1 TTACATAATTACTGATTACTATTTCCTTGACTCTGATTTAACCTTTTTTT
51018 TTACATAATTACTGATTACTATTTCCTTGACTCTGA-TTAACCTTTTTTT
1 TTACATAATTACTGATTACTATTTCCTTGACTCTGATTTAACCTTTTTTT
51067 TT
1 TT
51069 TTACTTAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 15 0.30
50 35 0.70
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (50 bp):
TTACATAATTACTGATTACTATTTCCTTGACTCTGATTTAACCTTTTTTT
Found at i:52101 original size:74 final size:74
Alignment explanation
Indices: 52023--52179 Score: 278
Period size: 74 Copynumber: 2.1 Consensus size: 74
52013 TGGTCTTTTC
** *
52023 ACACTTTTCGGGTGACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGAATGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
52088 TTCGTAATT
66 TTCGTAATT
52097 ACACTTTTCGAATGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGAATGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
52162 TTCGTAATT
66 TTCGTAATT
*
52171 ACACATTTC
1 ACACTTTTC
52180 CCTTCCTTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39
Consensus pattern (74 bp):
ACACTTTTCGAATGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:53201 original size:22 final size:21
Alignment explanation
Indices: 53139--53207 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
53129 TTCGATTTAG
*
53139 AGTTT-ATAAGTTAGATTATT
1 AGTTTAATAAGATAGATTATT
** *
53159 AGTTTAATCATCATATA-TATT
1 AGTTTAAT-AAGATAGATTATT
53180 AGTTATAATAAGATAGATTATT
1 AGTT-TAATAAGATAGATTATT
53202 AGTTTA
1 AGTTTA
53208 TTATAACTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 5 0.13
21 17 0.45
22 16 0.42
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (21 bp):
AGTTTAATAAGATAGATTATT
Found at i:53459 original size:17 final size:18
Alignment explanation
Indices: 53437--53471 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53427 ACCGTTTACA
53437 ATTCGG-TTTGGTCGGTT
1 ATTCGGTTTTGGTCGGTT
53454 ATTCGGTTTTGGTCGGTT
1 ATTCGGTTTTGGTCGGTT
53472 CATGCACAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.06, C:0.11, G:0.34, T:0.49
Consensus pattern (18 bp):
ATTCGGTTTTGGTCGGTT
Found at i:64647 original size:9 final size:9
Alignment explanation
Indices: 64635--64677 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
64625 AACTACGGGA
64635 ATTCTTATC
1 ATTCTTATC
64644 ATTCTTATC
1 ATTCTTATC
* *
64653 ATTCATCTC
1 ATTCTTATC
64662 ATTCCTTATC
1 ATT-CTTATC
64672 GATTCT
1 -ATTCT
64678 ACACGTAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 19 0.68
10 6 0.21
11 3 0.11
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (9 bp):
ATTCTTATC
Found at i:75733 original size:12 final size:12
Alignment explanation
Indices: 75718--75742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75708 TCAAAACAAC
75718 AGAAAAAAAAAA
1 AGAAAAAAAAAA
75730 AGAAAAAAAAAA
1 AGAAAAAAAAAA
75742 A
1 A
75743 AGAGAGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:75764 original size:16 final size:14
Alignment explanation
Indices: 75718--75765 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 14
75708 TCAAAACAAC
75718 AGAAAAAAAAAAAG
1 AGAAAAAAAAAAAG
*
75732 AAAAAAAAAAAAGAG
1 AGAAAAAAAAAA-AG
75747 AGAAATAAAAAAACAG
1 AGAAA-AAAAAAA-AG
75763 AGA
1 AGA
75766 TTCTTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 11 0.38
15 6 0.21
16 12 0.41
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (14 bp):
AGAAAAAAAAAAAG
Found at i:76837 original size:6 final size:6
Alignment explanation
Indices: 76826--76857 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
76816 TTACCACTTC
*
76826 CCCATT CCCATT CCCATT CCCATT CCAATT CC
1 CCCATT CCCATT CCCATT CCCATT CCCATT CC
76858 TAATCTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCATT
Found at i:83333 original size:6 final size:7
Alignment explanation
Indices: 83316--83341 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
83306 ATTTGTAGGT
83316 TTTTTTG
1 TTTTTTG
83323 TTTTTTG
1 TTTTTTG
83330 TTTTTTG
1 TTTTTTG
83337 TTTTT
1 TTTTT
83342 AATAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:97978 original size:2 final size:2
Alignment explanation
Indices: 97971--98000 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
97961 ATGAACAGCA
97971 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
98001 CTTATTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98457 original size:12 final size:13
Alignment explanation
Indices: 98440--98469 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
98430 CTTTGACATT
98440 TTTTTTTCCT-TC
1 TTTTTTTCCTGTC
98452 TTTTTTTCCTGTC
1 TTTTTTTCCTGTC
98465 TTTTT
1 TTTTT
98470 GGCTTCGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTTTCCTGTC
Found at i:102909 original size:22 final size:22
Alignment explanation
Indices: 102851--102915 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
102841 GAAGATCTCA
*
102851 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
102873 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
102896 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
102916 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:103037 original size:23 final size:23
Alignment explanation
Indices: 103006--103090 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
102996 GATAACCTCG
*
103006 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
*
103029 CTATAAAATTTTGATAAA-CATCC
1 CTATAAAATTTTGATAAATC-TTC
* *
103052 CTGTAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
103074 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
103091 CTACAAATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:103145 original size:22 final size:22
Alignment explanation
Indices: 102808--103297 Score: 178
Period size: 22 Copynumber: 22.6 Consensus size: 22
102798 TTAACCTTCT
* * *
102808 TATGAAATTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * * *
102830 TAAGGAATTTTGA-AGATCTCAA
1 TATGAAATTTTGATA-ACCTCAC
*
102852 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
102875 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
102896 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
102919 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
102940 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * *
102963 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
102985 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
103007 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* * *
103030 TATAAAATTTTGATAAACATCCC
1 TATGAAATTTTGAT-AACCTCAC
* * * *
103053 TGTAAAATTTTGATAACTTTC-T
1 TATGAAATTTTGATAAC-CTCAC
*
103075 TATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
** *
103095 ----AAATTTTGATAAGTTCCC
1 TATGAAATTTTGATAACCTCAC
** *
103113 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * *
103135 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
103157 TATAAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
* *
103179 TGTGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
103201 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
* * * *
103223 AATGAAATTTTCATAATCTTTA-
1 TATGAAATTTTGATAA-CCTCAC
*
103245 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
103266 -CTG-AATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
103285 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
103298 TATTCCATAA
Statistics
Matches: 348, Mismatches: 89, Indels: 64
0.69 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
19 19 0.05
20 14 0.04
21 11 0.03
22 222 0.64
23 65 0.19
24 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:103294 original size:20 final size:20
Alignment explanation
Indices: 103247--103297 Score: 95
Period size: 19 Copynumber: 2.6 Consensus size: 20
103237 AATCTTTATA
103247 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
103267 TG-AATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
103286 TGAAATTTTGAT
1 TGAAATTTTGAT
103298 TATTCCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:103428 original size:22 final size:22
Alignment explanation
Indices: 103403--103650 Score: 170
Period size: 22 Copynumber: 11.4 Consensus size: 22
103393 AATCATATTT
*
103403 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
103425 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
103447 T-AATATTTTGTTGACCCCTCTA
1 TGAA-ATTTTGATAACCTCTTTA
* * * *
103469 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
103491 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** *
103513 TGAAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTCTTTA
*
103535 TGAAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
103557 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * *
103581 TGAAATTTCGATAATCACTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
103603 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
103623 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
103643 TGAAATTT
1 TGAAATTT
103651 AGACTTTTAT
Statistics
Matches: 172, Mismatches: 42, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.01
20 16 0.09
21 30 0.17
22 103 0.60
23 4 0.02
24 5 0.03
25 12 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:103557 original size:88 final size:88
Alignment explanation
Indices: 103378--103571 Score: 207
Period size: 88 Copynumber: 2.2 Consensus size: 88
103368 AGAAATACCA
* * * **
103378 CTATGAAATTTTTG-TAATCATATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCT
1 CTATGAAA-TTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAA
* * *
103442 CTTTATAATATTTTGTTGACCCCT
65 CATTATAATATTTTGATAACCCCT
* * *
103466 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
* **
103530 CATTATGAA-ATTTTGATAATCTTT
65 CATTAT-AATATTTTGATAACCCCT
103554 CTAT-AAATTTTGATAATC
1 CTATGAAATTTTGATAATC
103572 CGATCTCTAT
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
87 17 0.19
88 67 0.76
89 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ATTATAATATTTTGATAACCCCT
Found at i:103587 original size:25 final size:23
Alignment explanation
Indices: 103378--103720 Score: 149
Period size: 22 Copynumber: 15.4 Consensus size: 23
103368 AGAAATACCA
* *
103378 CTATGAAATTTTTG-TAATCATAT
1 CTATGAAA-TTTTGATAATCCTCT
* *
103401 -TTTGAAAATTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCCTCT
*
103422 TTATGAAATTTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCCTCT
* * * *
103444 TTAT-AATATTTTGTTGA-CCCCT
1 CTATGAA-ATTTTGATAATCCTCT
* *
103466 CTATGAAATTCTGATAATCAC-AT
1 CTATGAAATTTTGATAATC-CTCT
* *
103489 -TATGTAATTTTGATAA-CCTCG
1 CTATGAAATTTTGATAATCCTCT
* **
103510 CTTTGAAATTTTGATAA-CAACAT
1 CTATGAAATTTTGATAATCCTC-T
*
103533 -TATGAAATTTTGATAAT-CTTT
1 CTATGAAATTTTGATAATCCTCT
103554 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAATCC--TCT
*
103578 CTATGAAATTTCGATAATCACT-T
1 CTATGAAATTTTGATAATC-CTCT
*
103601 -TATGAGA-TTTGATAA-CCT-T
1 CTATGAAATTTTGATAATCCTCT
* * *
103620 CTATCAAATTTTGGTACT-C-CT
1 CTATGAAATTTTGATAATCCTCT
* *
103641 -TATGAAATTTAGACTTTTATAACCT-T
1 CTATGAAATTTTGA----TA-ATCCTCT
* *
103667 CATATGAAATTTTGATAA-CCACG
1 C-TATGAAATTTTGATAATCCTCT
*
103690 CTATAAAATTTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCCTCT
*
103712 CCATGAAAT
1 CTATGAAAT
103721 ATTTAATGAA
Statistics
Matches: 242, Mismatches: 48, Indels: 61
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.01
20 17 0.07
21 39 0.16
22 136 0.56
23 7 0.03
24 12 0.05
25 13 0.05
26 3 0.01
28 12 0.05
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCCTCT
Found at i:103784 original size:22 final size:22
Alignment explanation
Indices: 103726--103784 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
103716 GAAATATTTA
*
103726 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
103748 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACT
*
103770 ATGATATTTTGATAA
1 ATGAAATTTTGATAA
103785 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:103927 original size:22 final size:22
Alignment explanation
Indices: 103820--103959 Score: 120
Period size: 22 Copynumber: 6.3 Consensus size: 22
103810 TTGTGATAAT
* **
103820 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * * * *
103842 TAACCAACCCAAGAGATTTTAA
1 TAACCATCCTATGAAATTTTGA
*
103864 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTGA
* *
103888 TAACCATACTATGGAATTTTGA
1 TAACCATCCTATGAAATTTTGA
* *
103910 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTGA
*
103932 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
103954 TAACCA
1 TAACCA
103960 CATAGAGACA
Statistics
Matches: 93, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
21 3 0.03
22 71 0.76
23 3 0.03
24 16 0.17
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:104155 original size:19 final size:20
Alignment explanation
Indices: 104124--104161 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
104114 CATTGACATT
104124 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
104143 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
104162 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:104358 original size:38 final size:35
Alignment explanation
Indices: 104298--104374 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 35
104288 AATTTAAGAC
104298 CAAAGACAAAGCAAAATCAAATACAACGATTGGAAA
1 CAAAGACAAAGCAAAATCAAATACAACG-TTGGAAA
* **
104334 CAAAGACAAAATGCAAAATTAAATAGGACGTTGGAAA
1 CAAAGAC-AAA-GCAAAATCAAATACAACGTTGGAAA
104371 CAAA
1 CAAA
104375 AAGCCAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 7 0.19
37 14 0.39
38 15 0.42
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.13
Consensus pattern (35 bp):
CAAAGACAAAGCAAAATCAAATACAACGTTGGAAA
Found at i:108487 original size:14 final size:14
Alignment explanation
Indices: 108470--108501 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
108460 AATCTTATAT
108470 AGTCTTTTCGTTAC
1 AGTCTTTTCGTTAC
*
108484 AGTCTTTTTGTTAC
1 AGTCTTTTCGTTAC
108498 AGTC
1 AGTC
108502 GCAATTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (14 bp):
AGTCTTTTCGTTAC
Found at i:115134 original size:2 final size:2
Alignment explanation
Indices: 115127--115166 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
115117 TCATATTAGG
115127 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
115167 GCTAAATAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116309 original size:13 final size:13
Alignment explanation
Indices: 116293--116341 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
116283 GTATTTTCAG
116293 TTTTCCTTTTTCT
1 TTTTCCTTTTTCT
*
116306 TTTTTCTTTTT-T
1 TTTTCCTTTTTCT
*
116318 TTTTCTCGTTTTC-
1 TTTTC-CTTTTTCT
116331 TTTTCCTTTTT
1 TTTTCCTTTTT
116342 TGGGGCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTCCTTTTTCT
Found at i:117030 original size:20 final size:19
Alignment explanation
Indices: 116990--117039 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
116980 TTAGTTTGGG
116990 TTAATTAAA-AAATAATTT
1 TTAATTAAATAAATAATTT
*
117008 TTAATTAAATATATAATTTT
1 TTAATTAAATAAATAA-TTT
117028 TTAATTAAATAA
1 TTAATTAAATAA
117040 TTTTTTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 9 0.32
19 5 0.18
20 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATTAAATAAATAATTT
Found at i:117045 original size:18 final size:18
Alignment explanation
Indices: 116990--117045 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 18
116980 TTAGTTTGGG
* *
116990 TTAATTAAAAAATAATTT
1 TTAATTAAATAATATTTT
117008 TTAATTAAATATATAATTTT
1 TTAATTAAATA-AT-ATTTT
117028 TTAATTAAATAAT-TTTT
1 TTAATTAAATAATATTTT
117045 T
1 T
117046 AAACCACCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 5 0.15
18 10 0.29
19 4 0.12
20 15 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATTAAATAATATTTT
Found at i:119694 original size:6 final size:6
Alignment explanation
Indices: 119683--119708 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
119673 CTCTTCCAAC
119683 AAATCA AAATCA AAATCA AAATCA AA
1 AAATCA AAATCA AAATCA AAATCA AA
119709 GCCCATGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATCA
Found at i:126994 original size:19 final size:18
Alignment explanation
Indices: 126972--127007 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
126962 TGAAGATTTC
126972 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
126991 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
127008 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:130143 original size:294 final size:294
Alignment explanation
Indices: 129614--130201 Score: 1131
Period size: 294 Copynumber: 2.0 Consensus size: 294
129604 GATGTGCCAC
129614 CACTAATTGCTGTAATCAATGACAATCTACCAAAAGATGAGGGAATTCCAGCCGAAACCAAGGAG
1 CACTAATTGCTGTAATCAATGACAATCTACCAAAAGATGAGGGAATTCCAGCCGAAACCAAGGAG
129679 GATCAACCTACTTCATCACCAAAAGCTTCTCAACCTCATTCAAGATTCGAAGGGATGAAAAAGAT
66 GATCAACCTACTTCATCACCAAAAGCTTCTCAACCTCATTCAAGATTCGAAGGGATGAAAAAGAT
*
129744 GGAGACCATTTACGGGCCACTACCGTTTCCTCAAAGGTTTGGAAATCAACTCAATTCACTTTGAA
131 GGAGACCATTTACGGGCCACTACCGTTTCCTCAAAGGTTTGGAAATCAACTCAATTCACTTCGAA
* *
129809 ATCTAGAGGTAAACATTCCTTTGCTTGTTGAAATTGCAAAAGGGCCCAGGTACGCCTCTTTTCTC
196 ATCTAGAGGTAAACATTCCTTTGCTTGTTGAAATTGCAAAAGGGACCAAGTACGCCTCTTTTCTC
129874 AAAGAATTATGCACTACTAAGAGTAAATTTTCTG
261 AAAGAATTATGCACTACTAAGAGTAAATTTTCTG
*
129908 CACTAATTGCTGTAATCAATGACAATCTACCAAAAGATGAGGGAATTCCAGCCGAAAGCAAGGAG
1 CACTAATTGCTGTAATCAATGACAATCTACCAAAAGATGAGGGAATTCCAGCCGAAACCAAGGAG
129973 GATCAACCTACTTCATCACCAAAAGCTTCTCAACCTCATTCAAGATTCGAAGGGATGAAAAAGAT
66 GATCAACCTACTTCATCACCAAAAGCTTCTCAACCTCATTCAAGATTCGAAGGGATGAAAAAGAT
130038 GGAGACCATTTACGGGCCACTACCGTTTCCTCAAAGGTTTGGAAATCAACTCAATTCACTTCGAA
131 GGAGACCATTTACGGGCCACTACCGTTTCCTCAAAGGTTTGGAAATCAACTCAATTCACTTCGAA
*
130103 ATCTAGAGGTAAACATTCCTTTGCTTGTTGAAATTGCAAAAGTGACCAAGTACGCCTCTTTTCTC
196 ATCTAGAGGTAAACATTCCTTTGCTTGTTGAAATTGCAAAAGGGACCAAGTACGCCTCTTTTCTC
130168 AAAGAATTATGCACTACTAAGAGTAAATTTTCTG
261 AAAGAATTATGCACTACTAAGAGTAAATTTTCTG
130202 AAAAATTTGC
Statistics
Matches: 289, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
294 289 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (294 bp):
CACTAATTGCTGTAATCAATGACAATCTACCAAAAGATGAGGGAATTCCAGCCGAAACCAAGGAG
GATCAACCTACTTCATCACCAAAAGCTTCTCAACCTCATTCAAGATTCGAAGGGATGAAAAAGAT
GGAGACCATTTACGGGCCACTACCGTTTCCTCAAAGGTTTGGAAATCAACTCAATTCACTTCGAA
ATCTAGAGGTAAACATTCCTTTGCTTGTTGAAATTGCAAAAGGGACCAAGTACGCCTCTTTTCTC
AAAGAATTATGCACTACTAAGAGTAAATTTTCTG
Found at i:135860 original size:19 final size:18
Alignment explanation
Indices: 135836--135871 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
135826 TGAAGATTTC
135836 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
135855 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
135872 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:140065 original size:15 final size:15
Alignment explanation
Indices: 140044--140082 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
140034 ATAAATTTTG
140044 ATATATA-AATAAAAT
1 ATATATATAA-AAAAT
*
140059 TTATATATAAAAAAT
1 ATATATATAAAAAAT
140074 ATATATATA
1 ATATATATA
140083 TATATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATATAAAAAAT
Found at i:140066 original size:17 final size:17
Alignment explanation
Indices: 140028--140094 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
140018 AGAATTTTCA
* *
140028 ATATATATAAATTTTGAT
1 ATATAAATAAAATTT-AT
140046 ATATAAATAAAATTTAT
1 ATATAAATAAAATTTAT
*
140063 ATATAAA-AAATATATAT
1 ATATAAATAAA-ATTTAT
* *
140080 ATATATATAATATTT
1 ATATAAATAAAATTT
140095 TAAAAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
16 3 0.07
17 23 0.56
18 15 0.37
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (17 bp):
ATATAAATAAAATTTAT
Found at i:141801 original size:33 final size:33
Alignment explanation
Indices: 141719--141856 Score: 120
Period size: 33 Copynumber: 4.2 Consensus size: 33
141709 ATCCTCTGGT
* *
141719 GATGGCACGACCATGGGCGTGCCGCCCTGTTAG
1 GATGGCACGACCATGGGCGAGCCGCCCTGTCAG
* * * *
141752 GAAGGTACG-CCTATGGGCGAGCCGCCCTCTCAA
1 GATGGCACGACC-ATGGGCGAGCCGCCCTGTCAG
*
141785 GATGGCACGATCATGGGC-ATGCCGCCCTGTCAG
1 GATGGCACGACCATGGGCGA-GCCGCCCTGTCAG
* * * * *
141818 GAT-GCACGCCCATGGTCGTGCCACCCTGTAAG
1 GATGGCACGACCATGGGCGAGCCGCCCTGTCAG
*
141850 GACGGCA
1 GATGGCA
141857 TAGCTCAATT
Statistics
Matches: 82, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
32 27 0.33
33 54 0.66
34 1 0.01
ACGTcount: A:0.19, C:0.32, G:0.33, T:0.17
Consensus pattern (33 bp):
GATGGCACGACCATGGGCGAGCCGCCCTGTCAG
Found at i:152391 original size:62 final size:60
Alignment explanation
Indices: 152265--152434 Score: 299
Period size: 59 Copynumber: 2.8 Consensus size: 60
152255 TTAATTTTAA
*
152265 ACACAATATATCATATGAAAATTATTAAAAAAAATATTCCGGGGAC-GGGGCACACACAC
1 ACACAATATATTATATGAAAATTATTAAAAAAAATATTCCGGGGACGGGGGCACACACAC
152324 ACACAATATATTATATGAAAATTATTAAAAAAAATATTCCGGGGACGGGGGCACACACACAC
1 ACACAATATATTATATGAAAATTATTAAAAAAAATATTCCGGGGACGGGGG--CACACACAC
152386 ACACAATATATTATATGAAAATTATT-AAAAAAATATTCCGGGGACGGGG
1 ACACAATATATTATATGAAAATTATTAAAAAAAATATTCCGGGGACGGGG
152435 CGGGGAGGGC
Statistics
Matches: 107, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
59 45 0.42
60 4 0.04
61 23 0.21
62 35 0.33
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.22
Consensus pattern (60 bp):
ACACAATATATTATATGAAAATTATTAAAAAAAATATTCCGGGGACGGGGGCACACACAC
Found at i:159464 original size:18 final size:18
Alignment explanation
Indices: 159443--159477 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
159433 GCTAATAATA
159443 ATTATAAAATAATTATTT
1 ATTATAAAATAATTATTT
**
159461 ATTATTCAATAATTATT
1 ATTATAAAATAATTATT
159478 CCTAATTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATAAAATAATTATTT
Found at i:166573 original size:2 final size:2
Alignment explanation
Indices: 166561--166597 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
166551 ATGGTCAATG
166561 AT AT A- 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
166598 TATTAATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:182733 original size:16 final size:15
Alignment explanation
Indices: 182705--182746 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
182695 AGTTTTTAAG
*
182705 TAAAAATATAATATA
1 TAAAAATAAAATATA
182720 TAAAAATAAAA-ATA
1 TAAAAATAAAATATA
* *
182734 TAATATTAAAATA
1 TAAAAATAAAATA
182747 ATTAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATAAAATATA
Found at i:182747 original size:19 final size:21
Alignment explanation
Indices: 182705--182744 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
182695 AGTTTTTAAG
182705 TAAAAATATAATATATAAAAA
1 TAAAAATATAATATATAAAAA
182726 TAAAAATATAATAT-TAAAA
1 TAAAAATATAATATATAAAA
182745 TAATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATATAATATATAAAAA
Found at i:183670 original size:6 final size:7
Alignment explanation
Indices: 183655--183680 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
183645 TGGTTATAGC
183655 TTTTATT
1 TTTTATT
183662 TTTTATT
1 TTTTATT
183669 TTTTATT
1 TTTTATT
183676 TTTTA
1 TTTTA
183681 CTTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:198623 original size:29 final size:29
Alignment explanation
Indices: 198586--198642 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
198576 AAAATACGAG
*
198586 AGAATAAGGGGAAACCAAAATGAATTGAA
1 AGAAGAAGGGGAAACCAAAATGAATTGAA
198615 AGAAGAAGGGGAAACCAAAATGAATTGA
1 AGAAGAAGGGGAAACCAAAATGAATTGA
198643 GAGAGGAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.26, T:0.12
Consensus pattern (29 bp):
AGAAGAAGGGGAAACCAAAATGAATTGAA
Found at i:200584 original size:33 final size:33
Alignment explanation
Indices: 200541--200606 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
200531 CGCTGAGTTG
* *
200541 GAAGGTAGATTAGATGGTGTTGTAGGAGCCCTC
1 GAAGGAAGATTAGATGGTGTTGAAGGAGCCCTC
200574 GAAGGAAGATTAGATGGTGTTGAAGGAGCCCTC
1 GAAGGAAGATTAGATGGTGTTGAAGGAGCCCTC
200607 AAAGATCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.36, T:0.24
Consensus pattern (33 bp):
GAAGGAAGATTAGATGGTGTTGAAGGAGCCCTC
Found at i:202182 original size:13 final size:13
Alignment explanation
Indices: 202164--202189 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
202154 ATATTACATA
202164 TTCTGTGTATCTT
1 TTCTGTGTATCTT
202177 TTCTGTGTATCTT
1 TTCTGTGTATCTT
202190 GGGATGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (13 bp):
TTCTGTGTATCTT
Found at i:214591 original size:2 final size:2
Alignment explanation
Indices: 214584--214617 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
214574 GGGAAGACAA
214584 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
214618 TTACTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.