Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014974.1 Corchorus olitorius cultivar O-4 contig15007, 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: 258837
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3875 original size:31 final size:32
Alignment explanation
Indices: 3810--3875 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
3800 CCTTAATTAT
* * *
3810 TTTGTAAATTTAGGACAGATTGCCTCTTGAAC
1 TTTGAAAATTTAGGACAAATTGCCTCCTGAAC
3842 TTTGAAAATTTAGGACAAATTGCC-CCTGAAC
1 TTTGAAAATTTAGGACAAATTGCCTCCTGAAC
3873 TTT
1 TTT
3876 AAATTGTGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (32 bp):
TTTGAAAATTTAGGACAAATTGCCTCCTGAAC
Found at i:10949 original size:5 final size:5
Alignment explanation
Indices: 10939--10979 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
10929 TATATAGTAG
*
10939 TAAGA TAAGA TAAAA TAAGA TAAGA TAAGA T-AG- TAAGA TAA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAA
10980 TACATGTGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 27 0.84
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:12977 original size:25 final size:25
Alignment explanation
Indices: 12943--12991 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
12933 TAGAATAAAT
12943 TTTTATATAAATAAATTAGTGAGAA
1 TTTTATATAAATAAATTAGTGAGAA
12968 TTTTATATAAATAAATTAGTGAGA
1 TTTTATATAAATAAATTAGTGAGA
12992 TATATCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (25 bp):
TTTTATATAAATAAATTAGTGAGAA
Found at i:13623 original size:17 final size:17
Alignment explanation
Indices: 13567--13642 Score: 70
Period size: 16 Copynumber: 4.7 Consensus size: 17
13557 AATTTTGGGT
*
13567 ACCCGAACCCG-AAATT
1 ACCCGAACCCGAAAATG
* * *
13583 ACCTGAATCC--AAACG
1 ACCCGAACCCGAAAATG
13598 ACCCGAACCCGAAAATG
1 ACCCGAACCCGAAAATG
*
13615 ACCCAAACCC-AAAATG
1 ACCCGAACCCGAAAATG
*
13631 ACTCGAACCCGA
1 ACCCGAACCCGA
13643 TTAACCCGAC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
15 11 0.23
16 22 0.47
17 14 0.30
ACGTcount: A:0.41, C:0.37, G:0.13, T:0.09
Consensus pattern (17 bp):
ACCCGAACCCGAAAATG
Found at i:14323 original size:11 final size:11
Alignment explanation
Indices: 14307--14336 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
14297 AACTTAGAAT
14307 TGACCCGAAAA
1 TGACCCGAAAA
14318 TGACCCGAAAA
1 TGACCCGAAAA
14329 TGACCCGA
1 TGACCCGA
14337 TATTTGAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.30, G:0.20, T:0.10
Consensus pattern (11 bp):
TGACCCGAAAA
Found at i:14790 original size:11 final size:11
Alignment explanation
Indices: 14748--14790 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
14738 TTACTTAACC
14748 TTAACCATAGA
1 TTAACCATAGA
*
14759 CTAACCATAGA
1 TTAACCATAGA
* *
14770 TTAACTATAGC
1 TTAACCATAGA
*
14781 TTGACCATAG
1 TTAACCATAG
14791 GTTAGTAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (11 bp):
TTAACCATAGA
Found at i:19655 original size:11 final size:11
Alignment explanation
Indices: 19613--19655 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
19603 TAACTATTAC
19613 TTAACCATAGA
1 TTAACCATAGA
*
19624 CTAACCATAGA
1 TTAACCATAGA
* *
19635 TTAACTATAGC
1 TTAACCATAGA
*
19646 TTGACCATAG
1 TTAACCATAG
19656 GTTAGTTAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (11 bp):
TTAACCATAGA
Found at i:19958 original size:12 final size:13
Alignment explanation
Indices: 19935--19968 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
19925 AGAAATGTGA
19935 GTTTAGTTTATTT
1 GTTTAGTTTATTT
19948 GTTTA-TTTATTT
1 GTTTAGTTTATTT
*
19960 GATTAGTTT
1 GTTTAGTTT
19969 GTAATTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (13 bp):
GTTTAGTTTATTT
Found at i:25767 original size:13 final size:13
Alignment explanation
Indices: 25722--25770 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
25712 ATTTATTTTT
25722 AAATTAAAATA-A
1 AAATTAAAATATA
25734 AAATTAAAA-AT-
1 AAATTAAAATATA
*
25745 --ATTTAAATATA
1 AAATTAAAATATA
25756 AAATTAAAATATA
1 AAATTAAAATATA
25769 AA
1 AA
25771 TTTTTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
9 6 0.20
10 2 0.07
11 1 0.03
12 9 0.30
13 12 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTAAAATATA
Found at i:25783 original size:29 final size:28
Alignment explanation
Indices: 25716--25794 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
25706 GCCCATATTT
*
25716 ATTTTTAAAT-TAAAATAAAAATTAAAA
1 ATTTTTAAATATAAAATTAAAATTAAAA
*
25743 ATATTTAAATATAAAATTAAAA-TATAAA
1 ATTTTTAAATATAAAATTAAAATTA-AAA
*
25771 TTTTTTAACATATAACAAGTTAAA
1 ATTTTTAA-ATATAA-AA-TTAAA
25795 TCTAAATGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
27 11 0.26
28 19 0.44
29 6 0.14
30 2 0.05
31 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (28 bp):
ATTTTTAAATATAAAATTAAAATTAAAA
Found at i:27212 original size:18 final size:18
Alignment explanation
Indices: 27189--27234 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
27179 TGAAATTAAT
27189 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
27207 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
27225 TTATTATTAA
1 TAATTATTAA
27235 ATTTCTAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Found at i:28685 original size:51 final size:50
Alignment explanation
Indices: 28584--28685 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
28574 GTTCTTCATA
* **
28584 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
28634 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
28685 T
1 T
28686 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:31331 original size:43 final size:42
Alignment explanation
Indices: 31283--31405 Score: 179
Period size: 43 Copynumber: 3.0 Consensus size: 42
31273 GTCATTTAAT
31283 CAATTATTTTCCTACATCTTTAATTTCTCTCAACTAGCATAGA
1 CAATTATTTTCCTACATCTTTAATTTCTCTCAACTA-CATAGA
31326 CAATTATTTTCCTACATCTTTAATTTCTCTC-A--A-AT---
1 CAATTATTTTCCTACATCTTTAATTTCTCTCAACTACATAGA
31361 CAATTATTTTCCTACATCTTTAATTTCTCTCAACTACCATAGA
1 CAATTATTTTCCTACATCTTTAATTTCTCTCAACTA-CATAGA
31404 CA
1 CA
31406 TATATATTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
35 31 0.43
36 1 0.01
38 3 0.04
40 3 0.04
42 1 0.01
43 33 0.46
ACGTcount: A:0.30, C:0.24, G:0.02, T:0.43
Consensus pattern (42 bp):
CAATTATTTTCCTACATCTTTAATTTCTCTCAACTACATAGA
Found at i:31372 original size:35 final size:35
Alignment explanation
Indices: 31326--31393 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
31316 CTAGCATAGA
31326 CAATTATTTTCCTACATCTTTAATTTCTCTCAAAT
1 CAATTATTTTCCTACATCTTTAATTTCTCTCAAAT
31361 CAATTATTTTCCTACATCTTTAATTTCTCTCAA
1 CAATTATTTTCCTACATCTTTAATTTCTCTCAA
31394 CTACCATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.49
Consensus pattern (35 bp):
CAATTATTTTCCTACATCTTTAATTTCTCTCAAAT
Found at i:33144 original size:32 final size:32
Alignment explanation
Indices: 33103--33163 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
33093 AAATATGTTT
**
33103 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAATCGATTCAATTA
*
33135 GAAAAATAAGGGTATAATAATCGATTCAA
1 GAAAAATAAGGATATAATAATCGATTCAA
33164 AAGTTTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAATCGATTCAATTA
Found at i:41311 original size:35 final size:36
Alignment explanation
Indices: 41272--41402 Score: 128
Period size: 35 Copynumber: 3.7 Consensus size: 36
41262 TAAAATGACA
41272 GGAACTTTCCCTAAATTGAAAAC-T-AAAACTTGGTG
1 GGAACTTTCCC-AAATTGAAAACTTAAAAACTTGGTG
* * * *
41307 GGAACTTTCCC-AATTCAAAAACTTTGAAAA-TCGAATG
1 GGAACTTTCCCAAATT-GAAAAC-TTAAAAACTTG-GTG
*
41344 GGAACTTTCCCAATTTGAAAACTTAAAAAC-TGGTG
1 GGAACTTTCCCAAATTGAAAACTTAAAAACTTGGTG
* *
41379 GGAACTTTCCCAATTTAAAAACTT
1 GGAACTTTCCCAAATTGAAAACTT
41403 TGACCTGATG
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
33 4 0.05
34 5 0.06
35 36 0.45
36 10 0.12
37 22 0.28
38 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (36 bp):
GGAACTTTCCCAAATTGAAAACTTAAAAACTTGGTG
Found at i:41352 original size:37 final size:37
Alignment explanation
Indices: 41296--41405 Score: 136
Period size: 35 Copynumber: 3.0 Consensus size: 37
41286 ATTGAAAACT
* *
41296 AAAACTTGGTGGGAACTTTCCCAATTCAAAAACTTTGA
1 AAAAC-TGATGGGAACTTTCCCAATTTAAAAACTTTGA
* *
41334 AAATC-GAATGGGAACTTTCCCAATTTGAAAAC-TT-A
1 AAAACTG-ATGGGAACTTTCCCAATTTAAAAACTTTGA
*
41369 AAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTGA
1 AAAACTGATGGGAACTTTCCCAATTTAAAAACTTTGA
41406 CCTGATGAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
35 28 0.46
36 6 0.10
37 23 0.38
38 4 0.07
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (37 bp):
AAAACTGATGGGAACTTTCCCAATTTAAAAACTTTGA
Found at i:41371 original size:72 final size:72
Alignment explanation
Indices: 41272--41405 Score: 218
Period size: 72 Copynumber: 1.9 Consensus size: 72
41262 TAAAATGACA
41272 GGAACTTTCCCTAAATTGAAAACT-AAAACTTGGTGGGAACTTTCCCAATTCAAAAACTTTGAAA
1 GGAACTTTCCCTAAATTGAAAACTAAAAAC-TGGTGGGAACTTTCCCAATTCAAAAACTTTGAAA
41336 ATCGAATG
65 ATCGAATG
* *
41344 GGAACTTTCCC-AATTTGAAAACTTAAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTGA
1 GGAACTTTCCCTAAATTGAAAAC-TAAAAACTGGTGGGAACTTTCCCAATTCAAAAACTTTGA
41406 CCTGATGAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
71 10 0.17
72 43 0.74
73 5 0.09
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (72 bp):
GGAACTTTCCCTAAATTGAAAACTAAAAACTGGTGGGAACTTTCCCAATTCAAAAACTTTGAAAA
TCGAATG
Found at i:48720 original size:33 final size:33
Alignment explanation
Indices: 48678--48746 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
48668 TTATGCTCCT
48678 ATCTGAGTGAGAACTCATTGCAAGAGTTTTCTC
1 ATCTGAGTGAGAACTCATTGCAAGAGTTTTCTC
*
48711 ATCTGAGTGAGAACTCATTGCAAGAGTTTTGTC
1 ATCTGAGTGAGAACTCATTGCAAGAGTTTTCTC
48744 ATC
1 ATC
48747 AGTGGTTTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (33 bp):
ATCTGAGTGAGAACTCATTGCAAGAGTTTTCTC
Found at i:49583 original size:39 final size:39
Alignment explanation
Indices: 49505--49631 Score: 193
Period size: 39 Copynumber: 3.2 Consensus size: 39
49495 AAAAAAAACC
49505 TACACGTAACACACATGCAAGAAATTATGGAAATG-ATTACA
1 TACACGTAACACACATGCAAG-AA--ATGGAAATGAATTACA
* *
49546 TACACGTAACACACATGCAAGAAATGAAAACGAATTACA
1 TACACGTAACACACATGCAAGAAATGGAAATGAATTACA
*
49585 TACACGTAACATACATGCAAGAAATGGAAATGAATTACA
1 TACACGTAACACACATGCAAGAAATGGAAATGAATTACA
49624 TACACGTA
1 TACACGTA
49632 CGTATTACAA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
38 7 0.09
39 50 0.62
40 2 0.03
41 21 0.26
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (39 bp):
TACACGTAACACACATGCAAGAAATGGAAATGAATTACA
Found at i:52656 original size:11 final size:11
Alignment explanation
Indices: 52632--52671 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
52622 ACCTGTTCAT
52632 GGGCCGGG-TC
1 GGGCCGGGTTC
52642 GGGCCGGGTTC
1 GGGCCGGGTTC
52653 GGGCCGGGTTC
1 GGGCCGGGTTC
52664 GGGCCGGG
1 GGGCCGGG
52672 CCTAGCCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.00, C:0.28, G:0.60, T:0.12
Consensus pattern (11 bp):
GGGCCGGGTTC
Found at i:56374 original size:32 final size:32
Alignment explanation
Indices: 56328--56388 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
56318 TCAAAATAGC
56328 GGCGTTTCCGTACATAAACGCCGCTATTTAGT
1 GGCGTTTCCGTACATAAACGCCGCTATTTAGT
*
56360 GGCGTTTCCTTACATAAACGCCGCTATTT
1 GGCGTTTCCGTACATAAACGCCGCTATTT
56389 TGGCTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (32 bp):
GGCGTTTCCGTACATAAACGCCGCTATTTAGT
Found at i:56890 original size:14 final size:14
Alignment explanation
Indices: 56871--56898 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56861 ACCGAATTCC
56871 ACCCAATAAAATAA
1 ACCCAATAAAATAA
56885 ACCCAATAAAATAA
1 ACCCAATAAAATAA
56899 GTCTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
ACCCAATAAAATAA
Found at i:60509 original size:133 final size:132
Alignment explanation
Indices: 60288--60578 Score: 381
Period size: 134 Copynumber: 2.2 Consensus size: 132
60278 TTTTAAAGTA
* * * *
60288 AAACGCCACTAATTAGTGGTGTTTCTAACAAAAAAGGCCGCTAAATGTCTTACTTTACTTTTAAC
1 AAACGCCACTAAATAGTGGCGTTTCAAACAAAAAACGCCGCTAAATGTCTTACTTTACTTTTAAC
* *
60353 TTTTCCTTTAATTATTTTGGGGGGAATTTTTCCCACCAATTTTTCTAA-ATAGCGGCGTCTT-TA
66 TTTTCCTTGAATTATTTTGGGGGGAA-TTTTCCCACCAATTATTCTAATATAGCGGCGT-TTGTA
* *
60416 TATG
129 CAGG
* * *
60420 AAACGCCACTAAATAGTGGCGTTTCAAATACCAAAACGCCGCTAAATGGT-TTAGTTTATCTTTT
1 AAACGCCACTAAATAGTGGCGTTTCAAACA-AAAAACGCCGCTAAAT-GTCTTACTTTA-CTTTT
* *
60484 AACTTTTTCTTGAATTATTTTGGGGGGAATTTTCCCACCAATTATTCTAATTTAGCGGCGTTTGT
63 AACTTTTCCTTGAATTATTTTGGGGGGAATTTTCCCACCAATTATTCTAATATAGCGGCGTTTGT
*
60549 ACCGG
128 ACAGG
*
60554 AAACGCCACTATATAGTGGCGTTTC
1 AAACGCCACTAAATAGTGGCGTTTC
60579 CGGTACAAAC
Statistics
Matches: 139, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
132 26 0.19
133 43 0.31
134 70 0.50
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (132 bp):
AAACGCCACTAAATAGTGGCGTTTCAAACAAAAAACGCCGCTAAATGTCTTACTTTACTTTTAAC
TTTTCCTTGAATTATTTTGGGGGGAATTTTCCCACCAATTATTCTAATATAGCGGCGTTTGTACA
GG
Found at i:61766 original size:47 final size:48
Alignment explanation
Indices: 61679--61771 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
61669 ATTTGGTAGG
* *
61679 TAGATGGTTTATTTATGGTAGTTTCTTAGTTTGAATTGATTTCTCATT
1 TAGATGGTTTATTTATGGTAGTTTCTCAATTTGAATTGATTTCTCATT
61727 TAGATGGTTTATTTAT-GTAGTTTCTCAATTTGAGA-TGATTTCTCA
1 TAGATGGTTTATTTATGGTAGTTTCTCAATTTGA-ATTGATTTCTCA
61772 AATTGGTGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
47 25 0.60
48 17 0.40
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (48 bp):
TAGATGGTTTATTTATGGTAGTTTCTCAATTTGAATTGATTTCTCATT
Found at i:61803 original size:31 final size:29
Alignment explanation
Indices: 61768--61869 Score: 82
Period size: 31 Copynumber: 3.4 Consensus size: 29
61758 GAGATGATTT
*
61768 CTCAAATTGGTGCATTTTGATAAGGTTTA-A
1 CTCAAATTGGTGCAGTTT-A-AAGGTTTAGA
* *
61798 GCTCAATTTGGTTCAGTTTAAAGGTTTAGA
1 -CTCAAATTGGTGCAGTTTAAAGGTTTAGA
* *
61828 CTCAAATT-GAGCAAGTTGGGAAAGGTTTAGA
1 CTCAAATTGGTGC-AGTT--TAAAGGTTTAGA
*
61859 CCCAAATTGGT
1 CTCAAATTGGT
61870 CATTAGACCA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.04
29 19 0.33
30 2 0.04
31 33 0.58
32 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (29 bp):
CTCAAATTGGTGCAGTTTAAAGGTTTAGA
Found at i:62121 original size:24 final size:25
Alignment explanation
Indices: 62093--62140 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
62083 CATCGATATC
62093 TCGATATATCC-ATCAATATATCCA
1 TCGATATATCCGATCAATATATCCA
*
62117 TCGATATATCCGTTCAATATATCC
1 TCGATATATCCGATCAATATATCC
62141 GTTGATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35
Consensus pattern (25 bp):
TCGATATATCCGATCAATATATCCA
Found at i:62143 original size:13 final size:12
Alignment explanation
Indices: 62096--62140 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
62086 CGATATCTCG
62096 ATATATCCATCA
1 ATATATCCATCA
*
62108 ATATATCCATCG
1 ATATATCCATCA
*
62120 ATATATCCGTTCA
1 ATATATCC-ATCA
62133 ATATATCC
1 ATATATCC
62141 GTTGATATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (12 bp):
ATATATCCATCA
Found at i:65390 original size:75 final size:74
Alignment explanation
Indices: 65282--65457 Score: 167
Period size: 75 Copynumber: 2.4 Consensus size: 74
65272 CAATAACATT
* ** * ** * *
65282 TTCAAAATGTTGCCTATTGTCATTGGGAAGCTCAGTATTAGAATTCGAAACAGCATCCTGATTAG
1 TTCAAGATGTTGCCTATCATCATTAGGAAGCTCAAAATTAGAATTCGAAACAGAAACCTGA-TA-
65347 AA-GAATCAAC
64 AAGGAATCAAC
* * * * *
65357 TTCAAGATGTTGCCTATCATCATTATGATGCTCAAAATTTGATTTCGAATCAGAAACCTGATAAA
1 TTCAAGATGTTGCCTATCATCATTAGGAAGCTCAAAATTAGAATTCGAAACAGAAACCTGATAAA
*
65422 GTGAATCAGC
66 G-GAATCAAC
*
65432 TTCAAGATGTTG-CAACTCATCATTAG
1 TTCAAGATGTTGCCTA-TCATCATTAG
65458 AAAACTTAGT
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
73 2 0.02
74 4 0.05
75 76 0.93
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (74 bp):
TTCAAGATGTTGCCTATCATCATTAGGAAGCTCAAAATTAGAATTCGAAACAGAAACCTGATAAA
GGAATCAAC
Found at i:73979 original size:20 final size:20
Alignment explanation
Indices: 73954--73991 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
73944 CCTTTGGTTG
73954 TCAAAAATCGCTGATGTGAC
1 TCAAAAATCGCTGATGTGAC
* *
73974 TCAAAAATTGTTGATGTG
1 TCAAAAATCGCTGATGTG
73992 GCATAATGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TCAAAAATCGCTGATGTGAC
Found at i:79273 original size:6 final size:7
Alignment explanation
Indices: 79233--79295 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
79223 GTCAGCTCAA
79233 TTTCTTT
1 TTTCTTT
79240 TTTCCTTT
1 TTT-CTTT
*
79248 TTAGCTTT
1 TT-TCTTT
**
79256 TTTCCAT
1 TTTCTTT
79263 TTTC-TT
1 TTTCTTT
79269 TTTCTTT
1 TTTCTTT
79276 TTTCTTT
1 TTTCTTT
79283 TTTCTTT
1 TTTCTTT
79290 TCTTCT
1 T-TTCT
79296 CTTCTCCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
6 5 0.11
7 26 0.55
8 16 0.34
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (7 bp):
TTTCTTT
Found at i:79277 original size:20 final size:20
Alignment explanation
Indices: 79252--79290 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
79242 TCCTTTTTAG
79252 CTTTTTTCCATTTTCTTTTT
1 CTTTTTTCCATTTTCTTTTT
**
79272 CTTTTTTCTTTTTTCTTTT
1 CTTTTTTCCATTTTCTTTT
79291 CTTCTCTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
CTTTTTTCCATTTTCTTTTT
Found at i:79997 original size:40 final size:40
Alignment explanation
Indices: 79942--80020 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
79932 TTATTTTTAA
*
79942 TTGTGTTTCCAGGGTCTGAACTCTGAAGCATTACACGTTG
1 TTGTGTTTCCAGGGTCTGAACTCCGAAGCATTACACGTTG
79982 TTGTGTTTCCAGGGTCTGAACTCCGAAGCATTACACGTT
1 TTGTGTTTCCAGGGTCTGAACTCCGAAGCATTACACGTT
80021 ATTATTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (40 bp):
TTGTGTTTCCAGGGTCTGAACTCCGAAGCATTACACGTTG
Found at i:80027 original size:3 final size:3
Alignment explanation
Indices: 80019--80095 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
80009 GCATTACACG
80019 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
80067 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
80096 CCATTTTCAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:81659 original size:26 final size:26
Alignment explanation
Indices: 81623--81675 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
81613 CGGCCTGAAA
*
81623 GGATTAATCTCAGGTGCAAAGGGTAT
1 GGATTAATCTCAGGTCCAAAGGGTAT
*
81649 GGATTAGTCTCAGGTCCAAAGGGTAT
1 GGATTAATCTCAGGTCCAAAGGGTAT
81675 G
1 G
81676 AGAATACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.26
Consensus pattern (26 bp):
GGATTAATCTCAGGTCCAAAGGGTAT
Found at i:84105 original size:28 final size:28
Alignment explanation
Indices: 84074--84136 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
84064 GGCACTTGGC
**
84074 CTCTTAAATGACTTGGAATTTTTGCTAA
1 CTCTTAAATGACTTAAAATTTTTGCTAA
84102 CTCTTAAATGACTTAAAATTTTTGCTAA
1 CTCTTAAATGACTTAAAATTTTTGCTAA
*
84130 GTCTTAA
1 CTCTTAA
84137 TTGGTTCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (28 bp):
CTCTTAAATGACTTAAAATTTTTGCTAA
Found at i:84608 original size:29 final size:29
Alignment explanation
Indices: 84560--84634 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
84550 TAGGCCAATG
* *
84560 GGGCAAAACGTCCCAAAATTGAAGTTCAAA
1 GGGCAAAATGT-CCAAAATTGAAATTCAAA
**
84590 GGGCAAAATGTCCAAAATTGAAATTCATT
1 GGGCAAAATGTCCAAAATTGAAATTCAAA
84619 GGGCAAAATGTCCAAA
1 GGGCAAAATGTCCAAA
84635 CGCTACAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 31 0.76
30 10 0.24
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (29 bp):
GGGCAAAATGTCCAAAATTGAAATTCAAA
Found at i:88103 original size:25 final size:25
Alignment explanation
Indices: 88069--88118 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
88059 CAACAGGGTT
88069 CACTCGACACACAAAATATACAATC
1 CACTCGACACACAAAATATACAATC
88094 CACTCGACACACAAAATATACAATC
1 CACTCGACACACAAAATATACAATC
88119 GTAATGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.32, G:0.04, T:0.16
Consensus pattern (25 bp):
CACTCGACACACAAAATATACAATC
Found at i:94255 original size:47 final size:47
Alignment explanation
Indices: 94186--94280 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
94176 ACCCGCTTGT
94186 ATAGTCTGTTAAACTTCACTGACGGTGTATTTTATAATTTTCCATAA
1 ATAGTCTGTTAAACTTCACTGACGGTGTATTTTATAATTTTCCATAA
94233 ATAGTCTGTTAAACTTCACTGACGGTGTATTTTATAATTTTCCATAA
1 ATAGTCTGTTAAACTTCACTGACGGTGTATTTTATAATTTTCCATAA
94280 A
1 A
94281 GTATTATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (47 bp):
ATAGTCTGTTAAACTTCACTGACGGTGTATTTTATAATTTTCCATAA
Found at i:136995 original size:181 final size:177
Alignment explanation
Indices: 136627--137007 Score: 457
Period size: 181 Copynumber: 2.1 Consensus size: 177
136617 TTATAAGCTC
* *
136627 AAATTATGTAATATTAAGTAGACCATCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCATCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
* *
136692 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAAATCATGGAAC
66 TTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCATAATGAAAGTTGTAAATCATGGAAC
* * * * * *
136757 AACCTTTCATGAGACACCTGAATCATCTCAATCAGACATCTAGAGCA
131 AACCTTTAATGAGACACCTAAATCACCTCAATCAGAAACCAAGAGCA
*
136804 AAAGTTATATAATATTAAGTGGAGGACCGTCTA-TTCTCGTTAACCGAAACAACAAATT-TTTCG
1 AAA-TTATATAATATTAAGT--A-GACCATCTATTTC-CGTTAACCGAAACAACAAATTCTTT-G
* *
136867 GAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTAATGAAAGTTGTAGATC
60 GAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCATAATGAAAGTTGTAAATC
* * * **
136931 ATGGAACAATCTTTTAAT-AGACACTTAAATCACCTTAATTGGATAACCGAAGAG-A
124 ATGGAACAA-CCTTTAATGAGACACCTAAATCACCTCAATCAGA-AACC-AAGAGCA
* *
136986 AAATTATATAATGTTAAATAGA
1 AAATTATATAATATTAAGTAGA
137008 TCGTTTAACC
Statistics
Matches: 174, Mismatches: 20, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
177 3 0.02
178 17 0.10
179 1 0.01
180 11 0.06
181 126 0.72
182 12 0.07
183 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCATCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
TTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCATAATGAAAGTTGTAAATCATGGAAC
AACCTTTAATGAGACACCTAAATCACCTCAATCAGAAACCAAGAGCA
Found at i:140757 original size:9 final size:9
Alignment explanation
Indices: 140743--140776 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
140733 AACAGGTTGG
*
140743 AGAAAAGGA
1 AGAAAAGAA
140752 AGAAAAGAA
1 AGAAAAGAA
140761 AGAAAAGAA
1 AGAAAAGAA
*
140770 AAAAAAG
1 AGAAAAG
140777 GAAAAGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AGAAAAGAA
Found at i:140768 original size:14 final size:15
Alignment explanation
Indices: 140751--140788 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
140741 GGAGAAAAGG
140751 AAGAAAAGAAA-GAA
1 AAGAAAAGAAAGGAA
*
140765 AAGAAAAAAAAGGAA
1 AAGAAAAGAAAGGAA
140780 AAGGAAAAG
1 AA-GAAAAG
140789 TCAAGTGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 10 0.50
15 5 0.25
16 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAGGAA
Found at i:183245 original size:13 final size:13
Alignment explanation
Indices: 183227--183251 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183217 CTGGTGTGTA
183227 GGGAAGAAGAAGG
1 GGGAAGAAGAAGG
183240 GGGAAGAAGAAG
1 GGGAAGAAGAAG
183252 AGAGGAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (13 bp):
GGGAAGAAGAAGG
Found at i:185797 original size:23 final size:25
Alignment explanation
Indices: 185757--185811 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
185747 ATAAAAATAT
* *
185757 TTTTCATTTTCACTAAAT-TGC-CA
1 TTTTCATTTTCACAAAATATACTCA
185780 TTTTCATTTTC-CAAAAATATACTCA
1 TTTTCATTTTCAC-AAAATATACTCA
185805 TTTTCAT
1 TTTTCAT
185812 CGACACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 15 0.56
24 2 0.07
25 9 0.33
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTCATTTTCACAAAATATACTCA
Found at i:188463 original size:21 final size:21
Alignment explanation
Indices: 188422--188463 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
188412 GCATCTTAGG
*
188422 CAACTCCGATAAGCTTGAAAC
1 CAACTCCGATAAGCTTAAAAC
* *
188443 CAACTCCGATGAGTTTAAAAC
1 CAACTCCGATAAGCTTAAAAC
188464 TTCTTTGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (21 bp):
CAACTCCGATAAGCTTAAAAC
Found at i:193216 original size:63 final size:63
Alignment explanation
Indices: 193117--193276 Score: 302
Period size: 63 Copynumber: 2.5 Consensus size: 63
193107 ATCAGTGAAT
* *
193117 GAAGAAGGATCAGTGGAGATAGGATTAGACAGAAGGTGCAGGAAGCGTCGCAATGAGATCAAA
1 GAAGAAGGATCAGTGGAGATAGGATTAGACAAAAGGTGCAGGAAGCGTCGCAAGGAGATCAAA
193180 GAAGAAGGATCAGTGGAGATAGGATTAGACAAAAGGTGCAGGAAGCGTCGCAAGGAGATCAAA
1 GAAGAAGGATCAGTGGAGATAGGATTAGACAAAAGGTGCAGGAAGCGTCGCAAGGAGATCAAA
193243 GAAGAAGGATCAGTGGAGATAGGATTAGACAAAA
1 GAAGAAGGATCAGTGGAGATAGGATTAGACAAAA
193277 ATGAAGGGGT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 95 1.00
ACGTcount: A:0.42, C:0.10, G:0.34, T:0.14
Consensus pattern (63 bp):
GAAGAAGGATCAGTGGAGATAGGATTAGACAAAAGGTGCAGGAAGCGTCGCAAGGAGATCAAA
Found at i:193493 original size:84 final size:84
Alignment explanation
Indices: 193352--193628 Score: 475
Period size: 84 Copynumber: 3.3 Consensus size: 84
193342 TACAGGTTGC
* * *
193352 GCCTCAAAGAGAAACAA-AGATTGAAGGATGAAGAAATTGTTAGGCTATGCAGTGAACTTGAAGC
1 GCCTCAAAGAGAAAGAACA-ATTCAAGGATGAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGC
193416 AAAGAACGAAGAATGTGCAA
65 AAAGAACGAAGAATGTGCAA
*
193436 GCCTCAAAGAGAAAGAACAATTTAAGGATGAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCA
1 GCCTCAAAGAGAAAGAACAATTCAAGGATGAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCA
*
193501 AAGAACGAAGAATGTGCAT
66 AAGAACGAAGAATGTGCAA
193520 GCCTCAAAGAGAAAGAACAATTCAAGGATGAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCA
1 GCCTCAAAGAGAAAGAACAATTCAAGGATGAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCA
193585 AAGAACGAAGAATGTGCAA
66 AAGAACGAAGAATGTGCAA
* *
193604 GCCTCAAAGAGAATGAACATTTCAA
1 GCCTCAAAGAGAAAGAACAATTCAA
193629 TGAGTATCAA
Statistics
Matches: 184, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
84 183 0.99
85 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.25, T:0.18
Consensus pattern (84 bp):
GCCTCAAAGAGAAAGAACAATTCAAGGATGAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCA
AAGAACGAAGAATGTGCAA
Found at i:193595 original size:42 final size:42
Alignment explanation
Indices: 193465--193596 Score: 96
Period size: 42 Copynumber: 3.1 Consensus size: 42
193455 ATTTAAGGAT
193465 GAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCAAAGAAC
1 GAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCAAAGAAC
* * ** * * * *
193507 GAAG-AA-TGTGCATGCCT-CAAAGAGAA--AGAA-CAATTCAAGGAT
1 GAAGAAATTGT-TA-GGCTACGCAGTGAACTTGAAGC-A---AAGAAC
193549 GAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCAAAGAAC
1 GAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCAAAGAAC
193591 GAAGAA
1 GAAGAA
193597 TGTGCAAGCC
Statistics
Matches: 62, Mismatches: 16, Indels: 24
0.61 0.16 0.24
Matches are distributed among these distances:
38 1 0.02
39 4 0.06
40 3 0.05
41 9 0.15
42 28 0.45
43 9 0.15
44 3 0.05
45 4 0.06
46 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (42 bp):
GAAGAAATTGTTAGGCTACGCAGTGAACTTGAAGCAAAGAAC
Found at i:193733 original size:105 final size:105
Alignment explanation
Indices: 193570--193922 Score: 634
Period size: 105 Copynumber: 3.4 Consensus size: 105
193560 TAGGCTACGC
* *
193570 AGTGAACTTGAAGCAAAGAACGAAGAATGTGCAAGCCTCAAAGAGAATGAACATTTCAATGAGTA
1 AGTGAACTTGAAGCAAAGAACGAAGAATGTGCAAGCCTCAAAGAGAATGAACAATTCAAGGAGTA
193635 TCAAATCAAAAGGCAGCAAGAAGAAAATGCATGGATACTT
66 TCAAATCAAAAGGCAGCAAGAAGAAAATGCATGGATACTT
* *
193675 AGTGAACTTAAAGCAAAGAACGAAGAATGTGCAAGCCTCAAAGAGAATGAACAATTCAAGGAGAA
1 AGTGAACTTGAAGCAAAGAACGAAGAATGTGCAAGCCTCAAAGAGAATGAACAATTCAAGGAGTA
193740 TCAAATCAAAAGGCAGCAAGAAGAAAATGCATGGATACTT
66 TCAAATCAAAAGGCAGCAAGAAGAAAATGCATGGATACTT
* *
193780 AGTGAACTTGAAGCAAAGAACGAAGAATGTGCAAGCCTTAAAGAGAAAGAACAATTCAAGGAGTA
1 AGTGAACTTGAAGCAAAGAACGAAGAATGTGCAAGCCTCAAAGAGAATGAACAATTCAAGGAGTA
*
193845 TCAAATCAAAAGGCAGCAAGAAGAAAATGCATGGATACTC
66 TCAAATCAAAAGGCAGCAAGAAGAAAATGCATGGATACTT
*
193885 AGTGAACTTGAAGCAAAGAAGGAAGAATGTGCAAGCCT
1 AGTGAACTTGAAGCAAAGAACGAAGAATGTGCAAGCCT
193923 ACGCAGTGAA
Statistics
Matches: 238, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 238 1.00
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.16
Consensus pattern (105 bp):
AGTGAACTTGAAGCAAAGAACGAAGAATGTGCAAGCCTCAAAGAGAATGAACAATTCAAGGAGTA
TCAAATCAAAAGGCAGCAAGAAGAAAATGCATGGATACTT
Found at i:193911 original size:42 final size:42
Alignment explanation
Indices: 193864--193962 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
193854 AAGGCAGCAA
* * *
193864 GAAGAAAATGCATGGATACTCAGTGAACTTGAAGCAAAGAAG
1 GAAGAAAATGCAAGCATACGCAGTGAACTTGAAGCAAAGAAG
** *
193906 GAAGAATGTGCAAGCCTACGCAGTGAACTTGAAGCAAAGAAG
1 GAAGAAAATGCAAGCATACGCAGTGAACTTGAAGCAAAGAAG
**
193948 GAAGAATGTGCAAGC
1 GAAGAAAATGCAAGC
193963 CTCAAAGATC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.42, C:0.14, G:0.28, T:0.15
Consensus pattern (42 bp):
GAAGAAAATGCAAGCATACGCAGTGAACTTGAAGCAAAGAAG
Found at i:193963 original size:42 final size:42
Alignment explanation
Indices: 193884--193964 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
193874 CATGGATACT
193884 CAGTGAACTTGAAGCAAAGAAGGAAGAATGTGCAAGCCTACG
1 CAGTGAACTTGAAGCAAAGAAGGAAGAATGTGCAAGCCTACG
193926 CAGTGAACTTGAAGCAAAGAAGGAAGAATGTGCAAGCCT
1 CAGTGAACTTGAAGCAAAGAAGGAAGAATGTGCAAGCCT
193965 CAAAGATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15
Consensus pattern (42 bp):
CAGTGAACTTGAAGCAAAGAAGGAAGAATGTGCAAGCCTACG
Found at i:196518 original size:21 final size:22
Alignment explanation
Indices: 196492--196534 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
196482 AAACTTTTCA
196492 TTTAATAAGATAA-AAAATATT
1 TTTAATAAGATAATAAAATATT
* *
196513 TTTAATAATATAATAATATATT
1 TTTAATAAGATAATAAAATATT
196535 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTAATAAGATAATAAAATATT
Found at i:207956 original size:29 final size:31
Alignment explanation
Indices: 207923--207983 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 31
207913 AACTAAAAAC
207923 AGAAAG-AAA-AAGAAAGTGGGTTCAAATAA
1 AGAAAGAAAAGAAGAAAGTGGGTTCAAATAA
207952 AGAAAGAAAAAAGAAGAAAGTGGGTTCAAATA
1 AGAAAG--AAAAGAAGAAAGTGGGTTCAAATA
207984 TGGAGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 6 0.21
32 3 0.11
33 19 0.68
ACGTcount: A:0.59, C:0.03, G:0.25, T:0.13
Consensus pattern (31 bp):
AGAAAGAAAAGAAGAAAGTGGGTTCAAATAA
Found at i:208896 original size:21 final size:21
Alignment explanation
Indices: 208854--208908 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
208844 TGATAAGTAC
*
208854 TAAATTTCAAAA-TTCTTTTG
1 TAAATTTGAAAAGTTCTTTTG
208874 TAAATTTGAAAAGTT-TGTTTG
1 TAAATTTGAAAAGTTCT-TTTG
208895 TAAATTTGAAAAGT
1 TAAATTTGAAAAGT
208909 CTTCGGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (21 bp):
TAAATTTGAAAAGTTCTTTTG
Found at i:211355 original size:31 final size:31
Alignment explanation
Indices: 211298--211356 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
211288 TTCAGCTCAT
* *
211298 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
211329 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
211357 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:214604 original size:11 final size:11
Alignment explanation
Indices: 214588--214613 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
214578 TTTAATCAAT
214588 AAAAAAAAACA
1 AAAAAAAAACA
214599 AAAAAAAAACA
1 AAAAAAAAACA
214610 AAAA
1 AAAA
214614 GACATAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:217234 original size:11 final size:10
Alignment explanation
Indices: 217204--217228 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
217194 GGCAAGTGAG
217204 AAAAGACAAA
1 AAAAGACAAA
217214 AAAAGACAAA
1 AAAAGACAAA
217224 AAAAG
1 AAAAG
217229 TTCAAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGACAAA
Found at i:228818 original size:16 final size:17
Alignment explanation
Indices: 228797--228830 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
228787 GTACGTATAA
*
228797 ATTATAT-TTAATAAAT
1 ATTATATATTAACAAAT
228813 ATTATATATTAACAAAT
1 ATTATATATTAACAAAT
228830 A
1 A
228831 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATATATTAACAAAT
Found at i:240082 original size:16 final size:16
Alignment explanation
Indices: 240061--240091 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
240051 GTTCATTTAT
240061 TTATTTTCCTTTTTTG
1 TTATTTTCCTTTTTTG
*
240077 TTATTTTTCTTTTTT
1 TTATTTTCCTTTTTT
240092 TATTTTCTCC
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:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (16 bp):
TTATTTTCCTTTTTTG
Found at i:250060 original size:28 final size:26
Alignment explanation
Indices: 249999--250070 Score: 110
Period size: 28 Copynumber: 2.7 Consensus size: 26
249989 TTACTTAACT
249999 AAGTATAATTTTCTTTTATATAAAAA
1 AAGTATAATTTTCTTTTATATAAAAA
250025 AAGTATAATTTTCTTTTAT-TGCCAAAAA
1 AAGTATAATTTTCTTTTATAT---AAAAA
250053 AAGTATAATTTTCTTTTA
1 AAGTATAATTTTCTTTTA
250071 AGTTTTAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
25 1 0.02
26 19 0.44
28 23 0.53
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (26 bp):
AAGTATAATTTTCTTTTATATAAAAA
Found at i:258486 original size:321 final size:319
Alignment explanation
Indices: 257812--258766 Score: 1210
Period size: 321 Copynumber: 3.0 Consensus size: 319
257802 AAAATGACCA
* * * * *
257812 AAAAGATTTTTCCTC-AATTTTTGGCAAAAACACTCATAAAAATATTTATAATTCAACGCCAAAA
1 AAAAG-TTTTTTCTCAAATTTTTGGC-ACAATACTCAGAAAAA-ATATATAATTCAACGCCAAAA
* * *
257876 AGATTGGA-GGACTTTTCACGCTTTTAATATCGTTTTT-CATATTTTGTTCTGAATTAATTTCTA
63 AGATT-GACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTT-TTCCGAATTAATTTCTA
* ** * * * *
257939 ATTAAATCGAAACAAAATTCTGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGCCT-AGAT
125 ATTAAATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGG-CTGAGAT
* ** * *
258003 TTGATT-AGACT-AATAA-AGATATTTCAAGGAGTCTCAGCACCAAAAACCATGCAAAACAGAGC
189 TTGGTTCA-A-TGAA-AATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTGAGC
* * * * * * *
258065 TGTGACCCCGGAAGGCGTTTTTAGTC-AAAATCCGTGATGGTTAGTACACGATTTCGGCTGAAAA
251 CGGGGCCCCGGAACGCGTTTTTAGCCAAAAAT-CGTGA---TTAGTACATGATTTCGGCTAAAAA
*
258129 CTGACCCG
312 CGGACCCG
* * * * *
258137 -AAA-TTTTCTCTCAATTTTTTGCCACAATACTCAGAAAAAAAATATAATTCAACTCCAAAAAGA
1 AAAAGTTTTTTCTCAAATTTTTGGCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
*
258200 TTAACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCCGAATTAATTTCTAATTAA
66 TTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTT-CCGAATTAATTTCTAATTAA
258265 ATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTT
130 ATCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTT
* * *
258330 CAATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGGCTCC
195 CAATGAAAATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCC
258395 GGAACGCGTTTTTAGCCAAAAATCGTGATATAGTACATGATTTCGGCTAAAAACGGACCCG
260 GGAACGCGTTTTTAGCCAAAAATCGTGAT-TAGTACATGATTTCGGCTAAAAACGGACCCG
*
258456 AAAAGTTTTTTCTCAAATTTTTGGCACAATACTCAGAAAAAATATATAATTCAACGGCAAAAAGA
1 AAAAGTTTTTTCTCAAATTTTTGGCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
* *
258521 TTGACGAGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAG
66 TTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAA
* * * *
258586 TCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCATATATTCAATATGACTGAGACTTGGTTC
131 TCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTC
* * * *
258651 AATGAATATAGATATTTCAAGGAGCCTTTACACCAAAAATCTTGCAAAACTGAGCCGGGGCCCCG
196 AATGAAAATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCCG
* ** * * *
258716 GAACGCGTTTTTAGCCATAAGCCGTGATGAGTAAATGATTTCGGATAAAAA
261 GAACGCGTTTTTAGCCAAAAATCGTGATTAGTACATGATTTCGGCTAAAAA
258767 TTTTACAAAA
Statistics
Matches: 555, Mismatches: 63, Indels: 30
0.86 0.10 0.05
Matches are distributed among these distances:
318 1 0.00
319 48 0.09
320 175 0.32
321 291 0.52
322 29 0.05
323 8 0.01
324 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (319 bp):
AAAAGTTTTTTCTCAAATTTTTGGCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
TTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAA
TCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTC
AATGAAAATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCCG
GAACGCGTTTTTAGCCAAAAATCGTGATTAGTACATGATTTCGGCTAAAAACGGACCCG
Done.