Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015076.1 Corchorus olitorius cultivar O-4 contig15109, 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: 97251
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1857 original size:14 final size:14
Alignment explanation
Indices: 1840--1905 Score: 64
Period size: 14 Copynumber: 4.6 Consensus size: 14
1830 ATAAAAACTT
*
1840 TTTTCAAAAAAAGA
1 TTTTCAAAAAATGA
*
1854 TTTTCAAGAAACTG-
1 TTTTCAA-AAAATGA
1868 TTTTCAAAAAATGA
1 TTTTCAAAAAATGA
*
1882 CTTTC-AAAAATGA
1 TTTTCAAAAAATGA
1895 GTTTTCCAAAA
1 -TTTT-CAAAA
1906 GGTTTTGAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 13 0.31
14 21 0.50
15 5 0.12
16 3 0.07
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (14 bp):
TTTTCAAAAAATGA
Found at i:1900 original size:28 final size:28
Alignment explanation
Indices: 1834--1888 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1824 TTCAAAATAA
* *
1834 AAACTTTTTTCAAAAAAAGATTTTCAAG
1 AAACTGTTTTCAAAAAAAGACTTTCAAG
*
1862 AAACTGTTTTCAAAAAATGACTTTCAA
1 AAACTGTTTTCAAAAAAAGACTTTCAA
1889 AAATGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (28 bp):
AAACTGTTTTCAAAAAAAGACTTTCAAG
Found at i:2555 original size:8 final size:8
Alignment explanation
Indices: 2542--2603 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
2532 GAAGCAATCT
2542 AAAGAAAA
1 AAAGAAAA
2550 AAAGAAAA
1 AAAGAAAA
* *
2558 AGAGAAAGC
1 AAAGAAA-A
2567 AAAGAAAA
1 AAAGAAAA
*
2575 AAGTGAAAAA
1 AA-AG-AAAA
*
2585 AAAGAAAG
1 AAAGAAAA
2593 AAAGAAGAA
1 AAAGAA-AA
2602 AA
1 AA
2604 TCAAAAGGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
8 25 0.60
9 11 0.26
10 6 0.14
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAGAAAA
Found at i:2577 original size:18 final size:18
Alignment explanation
Indices: 2546--2603 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2536 CAATCTAAAG
2546 AAAAAAAG-AAAAAGAGA
1 AAAAAAAGAAAAAAGAGA
** *
2563 AAGCAAAGAAAAAAGTGA
1 AAAAAAAGAAAAAAGAGA
2581 AAAAAAAGAAAGAAAGAAGA
1 AAAAAAAGAAA-AAAG-AGA
2601 AAA
1 AAA
2604 TCAAAAGGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 6 0.19
18 17 0.53
19 4 0.12
20 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAAAAGAGA
Found at i:2609 original size:26 final size:27
Alignment explanation
Indices: 2554--2609 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2544 AGAAAAAAAG
* *
2554 AAAAAGAGAAAGCAAAGAAAAAAGTGA
1 AAAAAAAGAAAGCAAAGAAAAAAGTCA
2581 AAAAAAAGAAAG-AAAGAAGAAAA-TCA
1 AAAAAAAGAAAGCAAAGAA-AAAAGTCA
2607 AAA
1 AAA
2610 GGAAAAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (27 bp):
AAAAAAAGAAAGCAAAGAAAAAAGTCA
Found at i:2882 original size:87 final size:87
Alignment explanation
Indices: 2735--2904 Score: 241
Period size: 87 Copynumber: 2.0 Consensus size: 87
2725 ATGTTTGAAC
* * *
2735 ATTTCTTAAGATGAGAAATTGATCCAAAAACATCAATTGAGTTGGGAATATCAATGCATGATCAA
1 ATTTCTTAAGATGAGAAACTGATCCAAAAACATCAATTGAGTTGGGAATATCAATACATGACCAA
*
2800 ATTGGAGGAAGATTTGGGAAAT
66 ATTGGAAGAAGATTTGGGAAAT
* * * * * *
2822 ATTTCTTAAGGTGGGAAGCTGATCCAGAACCATCAGTTGAGTTGGGAATATCAATACATGACCAA
1 ATTTCTTAAGATGAGAAACTGATCCAAAAACATCAATTGAGTTGGGAATATCAATACATGACCAA
*
2887 ATTGGAAGAAGGTTTGGG
66 ATTGGAAGAAGATTTGGG
2905 GCATCAATCA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (87 bp):
ATTTCTTAAGATGAGAAACTGATCCAAAAACATCAATTGAGTTGGGAATATCAATACATGACCAA
ATTGGAAGAAGATTTGGGAAAT
Found at i:3725 original size:37 final size:37
Alignment explanation
Indices: 3684--4363 Score: 656
Period size: 37 Copynumber: 18.4 Consensus size: 37
3674 TCAAGATTTT
3684 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * **
3721 TGTTTAGGTGT-TTCATCAAAAT-CTTGTTCAAGATTTC
1 TGTTTAGGTGTCTT-ATC-AAATCCTTATTTAAGGTCCC
* *
3758 TGTTTAGGTGTCTTATCAAATCTTTGTTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * *
3795 TGTATAGGTGTCATATTAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
3832 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * *
3869 TGTTTAGGTGT-TTCATCAAAAT-CTTGTTCAAGATTCC
1 TGTTTAGGTGTCTT-ATC-AAATCCTTATTTAAGGTCCC
* *
3906 TGTTTAGGTGTCTTATCAAATCTTTGTTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * * **
3943 TATATAGGTGTCATATTAAATCCTTATTTAAGGTCAT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
3980 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * *
4017 TGTTTAGGTGTCTCATCGAAAT-CTGATTGAAGATCCC
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
** * * * *
4054 TGTTTAGGTGTCCCATCAAAAT-CTTGTTCAAGATTCC
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* * * *
4091 TGTTTAGGTTTCTTATTAAATCTTTATTTAAGGTCTC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * *
4128 TATTTAGGTGTCTTATCAAAAT-CTTGTTTAAGATCCT
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* * *
4165 TGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGCT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * ** * * *
4202 TGTTTAGGTTTCTTGTCAAAATTTTTGTTTAAGATCTC
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* * *
4240 TATTTACGTTTCTTATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
* * * ** *
4277 TGTTTAGGTGTCTCATCAAAAT-CTTGTTCAAAATTCC
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCC
* * *
4314 TGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTACC
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
*
4351 TATTTAGGTGTCT
1 TGTTTAGGTGTCT
4364 CTTCAAAATC
Statistics
Matches: 520, Mismatches: 108, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
36 24 0.05
37 445 0.86
38 51 0.10
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (37 bp):
TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
Found at i:3952 original size:148 final size:149
Alignment explanation
Indices: 3684--4296 Score: 781
Period size: 148 Copynumber: 4.1 Consensus size: 149
3674 TCAAGATTTT
3684 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATCAAAATCTTGTT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATCAAAATCTTGTT
* * *
3749 CAAGATTTCTGTTTAGGTGTCTTATC-AAATCTTTGTTTAAGGTCCCTGTATAGGTGTCATATTA
66 CAAGATTCCTGTTTAGGTGTCTTATCAAAATCTTTGTTTAAGATCCCTATATAGGTGTCATATTA
3813 AATCCTTATTTAAGGTCCC
131 AATCCTTATTTAAGGTCCC
3832 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATCAAAATCTTGTT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATCAAAATCTTGTT
*
3897 CAAGATTCCTGTTTAGGTGTCTTATC-AAATCTTTGTTTAAGGTCCCTATATAGGTGTCATATTA
66 CAAGATTCCTGTTTAGGTGTCTTATCAAAATCTTTGTTTAAGATCCCTATATAGGTGTCATATTA
**
3961 AATCCTTATTTAAGGTCAT
131 AATCCTTATTTAAGGTCCC
* *
3980 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCGAAATC-TGAT
1 TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATCAAAATCTTG-T
* * ** * * * * * *
4044 TGAAGATCCCTGTTTAGGTGTCCCATCAAAATC-TTGTTCAAGATTCCTGTTTAGGTTTCTTATT
65 TCAAGATTCCTGTTTAGGTGTCTTATCAAAATCTTTGTTTAAGATCCCTATATAGGTGTCATATT
* *
4108 AAATCTTTATTTAAGGTCTC
130 AAATCCTTATTTAAGGTCCC
* * * * *
4128 TATTTAGGTGTCTTATCAAAAT-CTTGTTTAAGATCCTTGTTTAGGT-TTCTTATC-AAATCCTT
1 TGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCCTGTTTAGGTGTT-TCATCAAAAT-CTT
* * * * * * * * * * * * *
4190 ATTTAAGGTGCTTGTTTAGGTTTCTTGTCAAAATTTTTGTTTAAGATCTCTATTTACGTTTCTTA
63 GTTCAAGATTCCTGTTTAGGTGTCTTATCAAAATCTTTGTTTAAGATCCCTATATAGGTGTCATA
*
4255 TCAAATCCTTATTTAAGGTCCC
128 TTAAATCCTTATTTAAGGTCCC
*
4277 TGTTTAGGTGTCTCATCAAA
1 TGTTTAGGTGTCTTATCAAA
4297 ATCTTGTTCA
Statistics
Matches: 412, Mismatches: 46, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
147 7 0.02
148 337 0.82
149 68 0.17
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (149 bp):
TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATCAAAATCTTGTT
CAAGATTCCTGTTTAGGTGTCTTATCAAAATCTTTGTTTAAGATCCCTATATAGGTGTCATATTA
AATCCTTATTTAAGGTCCC
Found at i:4411 original size:149 final size:149
Alignment explanation
Indices: 4099--4399 Score: 356
Period size: 149 Copynumber: 2.0 Consensus size: 149
4089 CCTGTTTAGG
* * * * * *
4099 TTTCTTATTAAATCTTTATTTAAGGTCTCTATTTAGGTGTCTTATCAAAATCTTGTTTAAGATCC
1 TTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAAATCC
* * * * ****
4164 TTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGCTTGTTTAGGTTTCTTGTCAAAATTTTTG
66 TTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTATTTAGGTGTCTTGTCAAAATCCCAG
** **
4229 TTTAAGATCTCTATTTACG
131 TTTAAGATCTCTATCAAAA
*
4248 TTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAAATTC
1 TTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAAA-TC
*
4313 C-TGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTACCTATTTAGGTGTCTCT-TCAAAATCCC
65 CTTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTATTTAGGTGTCT-TGTCAAAATCCC
* *
4376 AGTTT-AGGTTTCTTATCAAAA
129 AGTTTAAGATCTC-TATCAAAA
4397 TTT
1 TTT
4400 TGTTCAAAAT
Statistics
Matches: 127, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
148 5 0.04
149 118 0.93
150 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.48
Consensus pattern (149 bp):
TTTCTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTCAAAATCC
TTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTATTTAGGTGTCTTGTCAAAATCCCAG
TTTAAGATCTCTATCAAAA
Found at i:4626 original size:54 final size:54
Alignment explanation
Indices: 4470--4641 Score: 197
Period size: 54 Copynumber: 3.2 Consensus size: 54
4460 TTTCTCTAGA
* *
4470 AAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
1 AAGTTGATCAAGTGTGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
* * * * * *
4524 AAGATGACCCAGTGTGGTTTTTCATAGAAATTTTCAGAGATCTAAGTTGATCTT
1 AAGTTGATCAAGTGTGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
*
4578 AAGTTGATCAAGTGTGGTCATTCCA-AGAAGTTTAC-GATGATC-AGAGTTGATCTCT
1 AAGTTGATCAAGTGTGGTC-TTCCATAGAAGTTTTCAGA-GATCTA-AGTTGATCT-T
*
4633 AAATTGATC
1 AAGTTGATC
4642 CAATGCGGTC
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.03
54 86 0.84
55 13 0.13
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (54 bp):
AAGTTGATCAAGTGTGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
Found at i:4756 original size:33 final size:33
Alignment explanation
Indices: 4714--4791 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
4704 ATTAATTAAG
* * * *
4714 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
4747 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
4780 AAGTTCAAAATC
1 AAGTTCAAAATC
4792 CACAGTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:4956 original size:7 final size:7
Alignment explanation
Indices: 4946--5010 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
4936 AAAAATAGGC
4946 AATTCAA
1 AATTCAA
4953 AATTCAA
1 AATTCAA
*
4960 AACTCAA
1 AATTCAA
*
4967 AACTCAA
1 AATTCAA
*
4974 AACTCAA
1 AATTCAA
*
4981 AATTCAT
1 AATTCAA
**
4988 GGTTCAA
1 AATTCAA
*
4995 AAATCAA
1 AATTCAA
5002 AATTCAA
1 AATTCAA
5009 AA
1 AA
5011 CCTGCATTTC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.23
Consensus pattern (7 bp):
AATTCAA
Found at i:5993 original size:8 final size:8
Alignment explanation
Indices: 5975--6014 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
5965 TTATCATGTT
5975 TTCCAAAAA
1 TTCC-AAAA
5984 TTCCAAAA
1 TTCCAAAA
5992 TTCCAAAA
1 TTCCAAAA
6000 -T-CAAAA
1 TTCCAAAA
6006 TTCCAAAA
1 TTCCAAAA
6014 T
1 T
6015 CAAAATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.17
7 2 0.07
8 18 0.62
9 4 0.14
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (8 bp):
TTCCAAAA
Found at i:6006 original size:14 final size:14
Alignment explanation
Indices: 5987--6021 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5977 CCAAAAATTC
5987 CAAAATTCCAAAAT
1 CAAAATTCCAAAAT
6001 CAAAATTCCAAAAT
1 CAAAATTCCAAAAT
6015 CAAAATT
1 CAAAATT
6022 GTTTTCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (14 bp):
CAAAATTCCAAAAT
Found at i:7890 original size:21 final size:21
Alignment explanation
Indices: 7866--7905 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7856 GGCGCCCACA
7866 TGGTTTGCCTAAACACCCATG
1 TGGTTTGCCTAAACACCCATG
* *
7887 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTAAACACCCA
7906 GGTTACCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TGGTTTGCCTAAACACCCATG
Found at i:11854 original size:331 final size:327
Alignment explanation
Indices: 10425--13425 Score: 2396
Period size: 332 Copynumber: 9.2 Consensus size: 327
10415 ATCCCAGCCA
* ** * ** *
10425 TTGTTTTTACAAGCATCTGAATAATGTTTCGTTTTAATTAGAAATTAATTTGGAAAAAAAATAGA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATAT-GA
* * * * *
10490 AAAATGATATTATAAA-CATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATGT-T-TTTTTT
64 AAAACGATATTA-AAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTAT
* * * * * *
10552 TAGTATTGTGGCTAAAAATTAAGG-AAAAATATTTCGAGTCAATTTTTGCAAAATATTAGCCGAA
128 GAGTATTTTAGC-CAAAATTGAGGAAAAAAT-TTTCG-GTCAATTTTTGCAAAATTTTAGCCGAA
** * *
10616 ATCGTG---TAACATCACTTTTTTTTTTGCTAAAAACGC-TTTCCGGGGCCCCGAG-TCAGTTTT
190 ATCGTGTACTAACATCAC--GGTTTTTGGCTAAAAACGCGTTT-CGGGGCCTCG-GCTCAGTTTT
* * * *
10676 GCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTCTATTTATCTAATAAAATCTCAGCCACAT
251 GCATGATTTTT-GCTCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA-
10741 TTG-ATTTAAGGAT
314 TTGAATTTAAGGAT
* * * *
10754 TTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAGTAGGAAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* * * * * ** * *
10819 AACGATATTAGAATCGTAAAAAACCCTTCAAAATTTTTGGTGTTGAATTATATAT-TTTTTTAGA
66 AACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTAT-GA
* * *
10883 GCATTTTAGCCAAAAATTGA-GAAAATATCTTTCCGGTCAATTTTTCCAAAATTTTAGCCGAAAT
130 GTATTTTAGCC-AAAATTGAGGAAAAAAT-TTT-CGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* * * * * * *
10947 C--GT-CT---ATTA---TTTTTGGATAAAAACGCGTTCCAGGGCCCCGGGTCAGTTTTGCATTA
192 CGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTTTGCATGA
* * * * * * * *
11003 TTTTTGGCGCTAAGACTTCTTGAGATATCCATATTCTTCTAATCAAATCTCATCCATATT-ACAT
257 TTTTT-GCTCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGA-AT
11067 TTAAGGAT
320 TTAAGGAT
* * *
11075 TTGTTTTT-CGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTTATAAAAAAATATGA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAGAAAAATATGA
* * *
11139 AAAACGATATGAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTAAATTATATATATTTCATG
64 AAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATG
* * * * *
11204 ATTATTTTAGCCAAAATTTGAGGATAAATTTTTCTGGTCATTTTTTGCAAAATTTTAGCTGAAAT
129 AGTATTTTAGCCAAAA-TTGAGGAAAAAATTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAAT
* * * * * * * *
11269 CGTGTACTAACAATCACAGTTTTTTTGCTAAAAATGCGTTTTGCGGCCCCAGCTCAGTTTTGCTT
192 CGTGTACTAAC-ATCAC-GGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTTTGCAT
* * * *
11334 GATTTTTGACGT-CGAGACTCCTTGAAATATTTATATTCATCTAATTAAATCTCAGCCACATTGC
255 GATTTTTG-C-TCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGA
11398 ATTTAAGGAT
318 ATTTAAGGAT
* * * * *
11408 TTCTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATATTAAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* * * *
11473 AACGATATTAAAAGCGTG-AAAGTCTTCCAATCATTTTGGCGTTAAATTATATATATTTTATGAG
66 AACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAG
* * *
11537 TATTTTAGCCAATAATTGACGGAAAAAATTTTCGGATCATTTATTTGCAAAATTTCAGCCCAAAA
131 TATTTTAGCCAA-AATTGA-GGAAAAAATTTTCGG-TCAATT-TTTGCAAAATTTTAG-CCGAAA
* * * *
11602 T-GTGTACTAAACATCACGGTCTTTGGCTAAAAACGCGTTTCGGGGCCTCGACTTAGTTTTGCCT
191 TCGTGTACT-AACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTTTGCAT
* * ** *
11666 GATTTTTTGCTCCGAGACTCCTTGAGATATCTATATTCATCTAATTGAATCTCAGCCACGTTGAA
255 GA-TTTTTGCTCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAA
11731 TTTAA-GAT
319 TTTAAGGAT
* * * *
11739 TTTTTTTTACGAACATCTGAATTTTGTTTCGATTT-ATTAGAAATTAATTCAGAATAATATGAAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* * * *
11803 AACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCATTGAATTATATATATTTTAATTT
66 AACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTT-A-TG
* * * * *
11868 A-TGATTACTGTGGCCAAAAATTGAGGAAAAATTTTTTTGGTCAATCTTTGCAAAATTTTAGTCG
129 AGT-ATT--T-TAGCC-AAAATTGAGGAAAAA-ATTTTCGGTCAATTTTTGCAAAATTTTAGCCG
* * *
11932 AAATCGTGTAC-AA-ATCACGGTTTTTTGGCTAAAAACGCATTTCAGGGCCTCGGGTCAGTTTTG
188 AAATCGTGTACTAACATCACGG-TTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTTTG
* * * *
11995 CATGATTTTTG-TGGCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCCACATT
252 CATGATTTTTGCT-CCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
12059 GGATTGGATTTAAGGAT
316 -GA----ATTTAAGGAT
* * * * *
12076 TTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTTA-AAATTAATTTGAAAAAAATAGGG
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA-TTAGAAATTAA-TTCAGAAAAATA-TG
* * * *
12140 AAAGAA--ATAATAGAAA-CGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAATTGTATAT-TTTT
63 AAA-AACGATATTA-AAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTT
* * * * * *
12201 ATGAGTATTGTAGCTAAAAGTTGA-GAAAAATATTATGGGTCAATTTTT-CAAAATTTTACCCAA
126 ATGAGTATTTTAGCCAAAA-TTGAGGAAAAA-ATTTTCGGTCAATTTTTGCAAAATTTTAGCCGA
* * ** * * *
12264 AATCTTGTAC---CATCATGGTTTTTTACTAAAAACGTGTTCCGGGGCC-CTGTGC-AAGTTTTG
189 AATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTC-G-GCTCAGTTTTG
* *
12324 CATGATTTTTGACACCAAGACTCCTT--AA-A---ATA-T-ATCT-AT---AT-TCA---TC--T
252 CATGATTTTTG-CTCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
*
12371 -AA-CTAAGGAT
316 GAATTTAAGGAT
** * * * * * * *
12381 TTGTTTTTACGAGTTTCTAAATCTTTTTTCGATTTAATCAAAAATTAATTTGGAAATAAAATAGG
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAGA-AAAATATG
* * * * *
12446 AAAAACGATATTAGAAGCGTGAAAAAGGCTTTCAAT-TATTTTGGCGTTGAATTATATATTTTTT
63 AAAAACGATATTAAAAGCGTG-AAAAGCCCTCCAATCT-TTTTGGCGTTGAATTATATATATTTT
* * * * *
12510 ATGATTATTTTTGCTAGAAAGTGA-GTAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
126 ATGAGTATTTTAGCCA-AAATTGAGGAAAAAAT-TTTC-GGTCAATTTTTGCAAAATTTTAGCCG
* * * *
12574 AAATCGTATACGTTAA-ATCACGGTTTTCGGCTAAAAACGC-ATTCAGCGG--TCGGGCTCAGTT
188 AAATCGTGTAC--TAACATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGGCCTC-GGCTCAGTT
* * * * *
12635 TTGCATGATTTTTGTTGGCAAGACTCTTTGAAATATCTATATTCATCTAACCAATTCTCAGCCAC
249 TTGCATGATTTTTGCT-CCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAC
12700 ATT-AGATTTAAGGAT
313 ATTGA-ATTTAAGGAT
* * * * *
12715 TTCTTTTTACGAGCATCTGAATCTTGTCTCGATTAAATTAGAAATTAATTCGGAAAAAATAGGAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAA
* * * * *** * *
12780 AAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTTATGTCGAATTATATAT-TATATAT
65 AAACGATATTAAAAGCGTGAAAAGCCCTCCAATC-TTTTTGGCGTTGAATTATATATAT-TTTAT
* * *
12844 GAGTATTCTAGCCAAAAATTGAGGAAATAACTTTTAGGTCAATTTTTGCAAAATTTTAGCCGAAA
128 GAGTATTTTAGCC-AAAATTGAGGAAA-AAATTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAA
* * * * * * *
12909 TCGTGTACTAATCGTCACGGTTTTTAGCTAAAAACACGTTCCAGGGCCACGGCTCTGTTTTGCAT
191 TCGTGTACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTTTGCAT
* * * * * *
12974 GATTTTTGGCGCCGAGACTCCTTGAATTATCTTTATTCATCTACTCAAATCTCAGCCACATTGGA
255 GATTTTT-GCTCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAA
13039 TTTAAGGAT
319 TTTAAGGAT
* * * *
13048 TGGTTTTTATGTGCATCTGAATCTTGTTTCGATATAATTAGAAATTAATTCAGAAAAAATATGAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAA
* * ** *
13113 AAACGATATCAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTATTGAATTATAAATATTTTATGA
65 AAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGA
* * * **
13178 CTATTTTTGCCAAAAAAAATGAGG-AAAAATCTTTCGAGTC-ATTTTT--ACCA---T---C---
130 GTATTTTAGCC---AAAATTGAGGAAAAAAT-TTTCG-GTCAATTTTTGCAAAATTTTAGCCGAA
** * * * **
13230 AT-G-GT--T--TTTGAC--TTTTTGGCTAAAAACGTGTTTCGGGTCCTTAGCTCAGTTTTGCAT
190 ATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTTTGCAT
* * * ** * **
13287 GATTTTTTTGCGCCTAGACTCCTTAAAATATCTATATT-ATCTAATCAAATCTCATACATATTCT
255 GA--TTTTTGCTCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGA
*
13351 ATTTAAAGAT
318 ATTTAAGGAT
* * *
13361 TTGTTTTTACGAGTAT-TTAACTCTTGTTTCGATTTAATAAGAAATTAATTCA-AAACAATATGA
1 TTGTTTTTACGAGCATCTGAA-TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAA-AATATGA
13424 AA
64 AA
13426 CAAAAATTTT
Statistics
Matches: 2172, Mismatches: 363, Indels: 291
0.77 0.13 0.10
Matches are distributed among these distances:
304 2 0.00
305 50 0.02
306 12 0.01
307 16 0.01
308 33 0.02
309 27 0.01
310 15 0.01
311 24 0.01
312 13 0.01
313 109 0.05
314 58 0.03
315 30 0.01
316 2 0.00
317 3 0.00
318 3 0.00
320 45 0.02
321 113 0.05
322 113 0.05
323 11 0.01
324 5 0.00
325 3 0.00
326 6 0.00
327 50 0.02
328 17 0.01
329 143 0.07
330 68 0.03
331 220 0.10
332 369 0.17
333 335 0.15
334 128 0.06
335 12 0.01
336 27 0.01
337 37 0.02
338 12 0.01
339 52 0.02
340 7 0.00
341 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (327 bp):
TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
AACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAG
TATTTTAGCCAAAATTGAGGAAAAAATTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
TACTAACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTT
TGCTCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGG
AT
Found at i:14429 original size:74 final size:74
Alignment explanation
Indices: 14343--14503 Score: 322
Period size: 74 Copynumber: 2.2 Consensus size: 74
14333 CTCTTTTACT
14343 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
1 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
14408 TGTTGTATA
66 TGTTGTATA
14417 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
1 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
14482 TGTTGTATA
66 TGTTGTATA
14491 AATTAATATATAT
1 AATTAATATATAT
14504 ATACATATAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 87 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (74 bp):
AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
TGTTGTATA
Found at i:18471 original size:16 final size:18
Alignment explanation
Indices: 18428--18474 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
18418 ACTTATAAAT
*
18428 AAATATTATTTAAACATA
1 AAATATTATATAAACATA
18446 AAATTAATTA-ATAAAC-TA
1 AAA-T-ATTATATAAACATA
18464 AAATATTATAT
1 AAATATTATAT
18475 TATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.16
17 3 0.12
18 8 0.32
19 6 0.24
20 4 0.16
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTATATAAACATA
Found at i:18493 original size:10 final size:11
Alignment explanation
Indices: 18476--18500 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18466 ATATTATATT
18476 ATATTTTTAAA
1 ATATTTTTAAA
18487 ATATTTTTAAA
1 ATATTTTTAAA
18498 ATA
1 ATA
18501 AAAAGATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:21593 original size:31 final size:31
Alignment explanation
Indices: 21555--21618 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
21545 TTCCTCGCTC
21555 CATCTATATATATAAACATATTCAAACAGAT
1 CATCTATATATATAAACATATTCAAACAGAT
21586 CATCTATATATATAAACATATTCAAACAGAT
1 CATCTATATATATAAACATATTCAAACAGAT
21617 CA
1 CA
21619 AAATTTCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.31
Consensus pattern (31 bp):
CATCTATATATATAAACATATTCAAACAGAT
Found at i:31766 original size:57 final size:57
Alignment explanation
Indices: 31648--31766 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 57
31638 CCTTTCGCAC
** * *
31648 AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCTTTAACAC
1 AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCTACAAAAA
*
31705 AATAAATGTTATAATAAATCCTATC-CCCCTATCTCTACTTAATTATTCTACAAAATA
1 AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCTACAAAA-A
31762 AATAA
1 AATAA
31767 TATTTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 27 0.48
57 29 0.52
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (57 bp):
AATAAATGTTAAAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCTACAAAAA
Found at i:31877 original size:42 final size:42
Alignment explanation
Indices: 31818--31898 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
31808 TAAGGATCAA
31818 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
31860 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
31899 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:36302 original size:2 final size:2
Alignment explanation
Indices: 36295--36361 Score: 51
Period size: 2 Copynumber: 37.5 Consensus size: 2
36285 GTTTAATAAT
* *
36295 TA TA TA TA T- TA T- TA TA TA TG TA -A T- TA TA TA TA TC TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
36332 TA T- TA T- TT TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36362 TTAATTATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
1 8 0.15
2 44 0.85
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:36310 original size:12 final size:12
Alignment explanation
Indices: 36293--36377 Score: 68
Period size: 12 Copynumber: 7.1 Consensus size: 12
36283 CCGTTTAATA
36293 ATTATATATATT
1 ATTATATATATT
* *
36305 ATTATATATGTA
1 ATTATATATATT
36317 ATTATATATATCT
1 ATTATATATAT-T
* *
36330 AATAT-TATTTT
1 ATTATATATATT
36341 A-TATATATATAT
1 ATTATATATAT-T
*
36353 ATAATATAT-TT
1 ATTATATATATT
*
36364 AATTATAAATATT
1 -ATTATATATATT
36377 A
1 A
36378 CTAAACGGTC
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
10 3 0.05
11 7 0.12
12 35 0.61
13 12 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (12 bp):
ATTATATATATT
Found at i:41801 original size:28 final size:26
Alignment explanation
Indices: 41765--41816 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
41755 TTTCTTTTGG
*
41765 TTATTATTCAGATTAAAGTATTTTTTTA
1 TTATAATTCAGA-TAAAGT-TTTTTTTA
41793 TTATAATTCAGATAAAGTTTTTTT
1 TTATAATTCAGATAAAGTTTTTTT
41817 CCTTATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 6 0.26
28 11 0.48
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (26 bp):
TTATAATTCAGATAAAGTTTTTTTTA
Found at i:42115 original size:16 final size:17
Alignment explanation
Indices: 42096--42131 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
42086 TATTAATGGG
42096 TTTAAGAATT-AATTTA
1 TTTAAGAATTGAATTTA
*
42112 TTTAAGAATTGATTTTA
1 TTTAAGAATTGAATTTA
42129 TTT
1 TTT
42132 TTAATATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (17 bp):
TTTAAGAATTGAATTTA
Found at i:43203 original size:28 final size:26
Alignment explanation
Indices: 43167--43224 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
43157 TTTCTTTTGG
*
43167 TTATTATTCAGATTAAAGTATTTTTTTA
1 TTATAATTCAGA-TAAAGT-TTTTTTTA
*
43195 TTATAATTCAGATAAAGTTTTTTTTC
1 TTATAATTCAGATAAAGTTTTTTTTA
43221 TTAT
1 TTAT
43225 TTTGGATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 11 0.39
27 6 0.21
28 11 0.39
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (26 bp):
TTATAATTCAGATAAAGTTTTTTTTA
Found at i:48455 original size:24 final size:24
Alignment explanation
Indices: 48404--48455 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
48394 TACCATTAGC
**
48404 AAAAGAAAAAAAGAAAAGCAAGCA
1 AAAAGAAAAAAAGAAAAGCAAAAA
*
48428 AAAAGAAAAAAGGAAAA-CAAAAA
1 AAAAGAAAAAAAGAAAAGCAAAAA
48451 GAAAA
1 -AAAA
48456 CAGAAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAGAAAAAAAGAAAAGCAAAAA
Found at i:50444 original size:54 final size:54
Alignment explanation
Indices: 50372--50946 Score: 832
Period size: 54 Copynumber: 10.6 Consensus size: 54
50362 CGATCTTTTA
50372 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
50426 AAGTTTTCAAAGGTTTAAGTTGATCTTCAGAT-AGCCCTGTGCGGACTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGA-CCCTGTGCGGTCTTTCATAG
* *
50480 AAGTTTTCAAAGATTTAAGTTGATCTTCAGATGACCTTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* *
50534 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCTTGTGCGATCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
50588 AAGTCTTCAGAGGTTTAAGTTGATCTTCAGATGACCTTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * *
50642 AAGTTTTCAGAGGTATAAGTTGAACTTCAGATAACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * * *
50696 AAGATTTCAGAGGTATAAGTTGATCTTCAGATAACCCTGTGCGATCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* *
50750 AAGATTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATGG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
50804 AAGTTTTCAAAGATTTAGGTTGATCTTCAGATGACCCTATGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * * *
50858 AAGTGTTCAGAGATCTAAGTTGAT-TTTATGATGACCCTGTGCGGACTTTCATAA
1 AAGTTTTCAGAGATTTAAGTTGATCTTCA-GATGACCCTGTGCGGTCTTTCATAG
*
50912 AAGCTTTT-AGAGATCTAAGTTGATCTTCAGATGAC
1 AAG-TTTTCAGAGATTTAAGTTGATCTTCAGATGAC
50947 TCGGGGTTGA
Statistics
Matches: 477, Mismatches: 39, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
53 4 0.01
54 466 0.98
55 7 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (54 bp):
AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
Found at i:51123 original size:106 final size:106
Alignment explanation
Indices: 50976--51687 Score: 734
Period size: 106 Copynumber: 6.7 Consensus size: 106
50966 AAGTTCTTAA
* * * *
50976 AGATCAAAGTTGATCCTCAGAAGATCCAGTGCGATCATTCCAATAAGTTTTGAATGATCAGAGTT
1 AGATCAGAGTTGATCC-CAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTGAATGATCAGAGTT
* * *
51041 GATCGCCAAATGATCTAGTGCGAT-ATTTCAAGAAGTTTTCAG
65 GATCTCCAGATGATC-AGTGCGGTCATTTCAAGAAGTTTTCAG
* * ***
51083 TGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGTAGTTTTCTTTGATCAGAGTTG
1 AGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTGAATGATCAGAGTTG
* * *
51148 ATCT--AGATGACCTAGTACGGTCA-TTCAAGAAGTTTTTAG
66 ATCTCCAGATGATC-AGTGCGGTCATTTCAAGAAGTTTTCAG
** * ***
51187 AGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAATTAGTTCTCTTTGATCAGAGTT
1 AGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTGAATGATCAGAGTT
* * *
51252 GATC-CCAGATGACCAGTACAGG-CATTCCAAGAAGTGTTT-AG
65 GATCTCCAGATGATCAGTGC-GGTCATTTCAAGAAGT-TTTCAG
* *
51293 AGATCAGAGTTGATCCCTAGATGATCCAATGCGGTCCTTCCAAGACA-TTTTCGAA-GATCAGAG
1 AGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCCAAGA-AGTTTT-GAATGATCAGAG
* * *
51356 TTGATCTCCAGATGATCCGATGCGGTCTTTTCAGGAAGTTTTC-G
63 TTGATCTCCAGATGATCAG-TGCGGTCATTTCAAGAAGTTTTCAG
* * * * * *
51400 AAGACCAGAGTTGATCTCCAGATGAT-CTG-GTGGTCATTCCAAAAAGTTTTCAATGATCAGAAT
1 -AGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTGAATGATCAGAGT
* * *
51463 TGATCTCCAGATGATCCAGTGTGGTCAATCCAAGAAGTTTTC-G
64 TGATCTCCAGATGAT-CAGTGCGGTCATTTCAAGAAGTTTTCAG
* * *
51506 AAGATCAGAGTTGATCTCCAGATGATCCGGTGCAGTCATTTCAAGAAGTTTTCGAA-GATCAGAG
1 -AGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-GAATGATCAGAG
* * *
51570 TTGATCTCTAGATGATACAGTGCGGTCGTTTCAAGAAGTTTTCAA
63 TTGATCTCCAGATGAT-CAGTGCGGTCATTTCAAGAAGTTTTCAG
* *
51615 AGATCAGAGTTGATCTCCAGATGATCCGGTGCGGTCATTTCAAGAAGTTTTCG-ATGATCAGAGT
1 AGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-GAATGATCAGAGT
51679 TGATCTCCA
64 TGATCTCCA
51688 ATTTGATACA
Statistics
Matches: 517, Mismatches: 64, Indels: 47
0.82 0.10 0.07
Matches are distributed among these distances:
104 41 0.08
105 66 0.13
106 203 0.39
107 40 0.08
108 163 0.32
109 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (106 bp):
AGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTGAATGATCAGAGTTG
ATCTCCAGATGATCAGTGCGGTCATTTCAAGAAGTTTTCAG
Found at i:51382 original size:160 final size:161
Alignment explanation
Indices: 50966--51687 Score: 764
Period size: 160 Copynumber: 4.5 Consensus size: 161
50956 ACTTTCATAA
* * * * *
50966 AAGTTCTTAAAGATCAAAGTTGATC-CTCAGAAGATCCAGTGCGATCATTCCAATAAGTTTT-GA
1 AAGTT-TTCAAGATCAGAGTTGATCTC-CAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGA
* * * * *
51029 ATGATCAGAGTTGATCGCCAAATGAT-CTAGTGCGAT-ATTTCAAGAAGTTTTC-AGTGATCAGA
64 A-GATCAGAGTTGATCTCCAGATGATCCGA-TGCGGTCATTTCAAGAAGTTTTCGA-AGATCAGA
51091 GTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAG
126 GTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAG
* ** * *
51126 TAGTTTTCTTTGATCAGAGTTGATCT--AGATGA-CCTAGTACGGTCATT-CAAGAAGTTTT-TA
1 AAGTTTTC-AAGATCAGAGTTGATCTCCAGATGATCC-AGTGCGGTCATTCCAAGAAGTTTTCGA
* * ** * ***
51186 GAGATCAGAGTTGATCCCCAGATGATCC-AGTGCGGTCATTCCAATTAGTTCTCTTTGATCAGAG
64 -AGATCAGAGTTGATCTCCAGATGATCCGA-TGCGGTCATTTCAAGAAGTTTTCGAAGATCAGAG
*
51250 TTGATC-CCAGATGA-CCAGTACAGG-CATTCCAAG
127 TTGATCTCCAGATGATCCAGTGC-GGTCATTCCAAG
* *
51283 AAGTGTTT-AGAGATCAGAGTTGATC-CCTAGATGATCCAATGCGGTCCTTCCAAGACA-TTTTC
1 AAGT-TTTCA-AGATCAGAGTTGATCTCC-AGATGATCCAGTGCGGTCATTCCAAGA-AGTTTTC
* * *
51345 GAAGATCAGAGTTGATCTCCAGATGATCCGATGCGGTCTTTTCAGGAAGTTTTCGAAGACCAGAG
62 GAAGATCAGAGTTGATCTCCAGATGATCCGATGCGGTCATTTCAAGAAGTTTTCGAAGATCAGAG
* * *
51410 TTGATCTCCAGATGAT-CTG-GTGGTCATTCCAAA
127 TTGATCTCCAGATGATCCAGTGCGGTCATTCCAAG
* * *
51443 AAGTTTTCAATGATCAGAATTGATCTCCAGATGATCCAGTGTGGTCAATCCAAGAAGTTTTCGAA
1 AAGTTTTCAA-GATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAA
* *
51508 GATCAGAGTTGATCTCCAGATGATCCGGTGCAGTCATTTCAAGAAGTTTTCGAAGATCAGAGTTG
65 GATCAGAGTTGATCTCCAGATGATCCGATGCGGTCATTTCAAGAAGTTTTCGAAGATCAGAGTTG
* * * *
51573 ATCTCTAGATGATACAGTGCGGTCGTTTCAAG
130 ATCTCCAGATGATCCAGTGCGGTCATTCCAAG
* * *
51605 AAGTTTTCAAAGATCAGAGTTGATCTCCAGATGATCCGGTGCGGTCATTTCAAGAAGTTTTCGAT
1 AAGTTTTC-AAGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAA
51670 GATCAGAGTTGATCTCCA
65 GATCAGAGTTGATCTCCA
51688 ATTTGATACA
Statistics
Matches: 471, Mismatches: 63, Indels: 54
0.80 0.11 0.09
Matches are distributed among these distances:
157 74 0.16
158 57 0.12
159 24 0.05
160 213 0.45
161 17 0.04
162 84 0.18
163 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (161 bp):
AAGTTTTCAAGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAAG
ATCAGAGTTGATCTCCAGATGATCCGATGCGGTCATTTCAAGAAGTTTTCGAAGATCAGAGTTGA
TCTCCAGATGATCCAGTGCGGTCATTCCAAG
Found at i:51686 original size:54 final size:54
Alignment explanation
Indices: 50389--51687 Score: 813
Period size: 54 Copynumber: 24.2 Consensus size: 54
50379 CAGAGATTTA
* * * * *
50389 AGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAGAAGTTTTCAAAGGTTTA-
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCA-AGAAGTTTTCGAA-GATCAG
* * * * *
50443 AGTTGATCTTCAGAT-AGCCCTGTGCGGAC-TTTCATAGAAGTTTTCAAAGATTTA-
1 AGTTGATCTCCAGATGA-TCCTGTGCGGTCATTTCA-AGAAGTTTTCGAAGA-TCAG
* *
50497 AGTTGATCTTCAGATGA-CCTTGTGCGGTC-TTTCATAGAAGTTTTC-AGAGATTTA-
1 AGTTGATCTCCAGATGATCC-TGTGCGGTCATTTCA-AGAAGTTTTCGA-AGA-TCAG
* * * * * *
50551 AGTTGATCTTCAGATGA-CCTTGTGCGATC-TTTCATAGAAGTCTTCAGAGGTTTA-
1 AGTTGATCTCCAGATGATCC-TGTGCGGTCATTTCA-AGAAGTTTTC-GAAGATCAG
* *
50605 AGTTGATCTTCAGATGA-CCTTGTGCGGTC-TTTCATAGAAGTTTTCAGAGGTAT-A-
1 AGTTGATCTCCAGATGATCC-TGTGCGGTCATTTCA-AGAAGTTTTC-GAAG-ATCAG
* * * * * *
50659 AGTTGAACTTCAGATAACCCTGTGCGGTC-TTTCATAGAAGATTTCAGAGGTAT-A-
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCA-AGAAGTTTTC-GAAG-ATCAG
* * * * * *
50713 AGTTGATCTTCAGATAACCCTGTGCGATC-TTTCATAGAAGATTTC-AGAGATTTA-
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCA-AGAAGTTTTCGA-AGA-TCAG
* * * * *
50767 AGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATGGAAGTTTTCAAAGATTTAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCA-AGAAGTTTTCGAAGA-TCAG
* * * *
50822 -GTTGATCTTCAGATGACCCTATGCGGTC-TTTCATAGAAGTGTTC-AGAGATCTA-
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCA-AGAAGTTTTCGA-AGATC-AG
** * * * *
50875 AGTTGAT-TTTATGATGACCCTGTGCGGAC-TTTCATAAAAGCTTTTAG-AGATCTA-
1 AGTTGATCTCCA-GATGATCCTGTGCGGTCATTTCA-AGAAG-TTTTCGAAGATC-AG
* * * * *
50929 AGTTGATCTTCAGATGA--CTCG-G-GGTTGACTTTCATAAAAGTTCTT-AAAGATCAA
1 AGTTGATCTCCAGATGATCCT-GTGCGG-TCA-TTTCA-AGAAGTT-TTCGAAGATCAG
* * * * *
50983 AGTTGATC-CTCAGAAGATCCAGTGCGATCATTCCAATAAGTTTT-GAATGATCAG
1 AGTTGATCTC-CAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAA-GATCAG
* * * *
51037 AGTTGATCGCCAAATGAT-CTAGTGCGAT-ATTTCAAGAAGTTTTC-AGTGATCAG
1 AGTTGATCTCCAGATGATCCT-GTGCGGTCATTTCAAGAAGTTTTCGA-AGATCAG
* * * ***
51090 AGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGTAGTTTTCTTTGATCAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
* *
51143 AGTTGATCT--AGATGA-CCTAGTACGGTCA-TTCAAGAAGTTTT-TAGAGATCAG
1 AGTTGATCTCCAGATGATCCT-GTGCGGTCATTTCAAGAAGTTTTCGA-AGATCAG
* * * ** * ***
51194 AGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAATTAGTTCTCTTTGATCAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
* * * *
51248 AGTTGATC-CCAGATGA-CCAGTACAGG-CATTCCAAGAAGTGTTTAG-AGATCAG
1 AGTTGATCTCCAGATGATCCTGTGC-GGTCATTTCAAGAAGT-TTTCGAAGATCAG
** * *
51300 AGTTGATC-CCTAGATGATCCAATGCGGTCCTTCCAAGACA-TTTTCGAAGATCAG
1 AGTTGATCTCC-AGATGATCCTGTGCGGTCATTTCAAGA-AGTTTTCGAAGATCAG
* * *
51354 AGTTGATCTCCAGATGATCC-GATGCGGTCTTTTCAGGAAGTTTTCGAAGACCAG
1 AGTTGATCTCCAGATGATCCTG-TGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
* * *
51408 AGTTGATCTCCAGATGAT-CTG-GTGGTCATTCCAAAAAGTTTTC-AATGATCAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAA-GATCAG
* * * * *
51460 AATTGATCTCCAGATGATCCAGTGTGGTCAATCCAAGAAGTTTTCGAAGATCAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
* *
51514 AGTTGATCTCCAGATGATCCGGTGCAGTCATTTCAAGAAGTTTTCGAAGATCAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
* * * * *
51568 AGTTGATCTCTAGATGATACAGTGCGGTCGTTTCAAGAAGTTTTCAAAGATCAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
* *
51622 AGTTGATCTCCAGATGATCCGGTGCGGTCATTTCAAGAAGTTTTCGATGATCAG
1 AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
51676 AGTTGATCTCCA
1 AGTTGATCTCCA
51688 ATTTGATACA
Statistics
Matches: 1067, Mismatches: 114, Indels: 128
0.82 0.09 0.10
Matches are distributed among these distances:
50 1 0.00
51 31 0.03
52 105 0.10
53 121 0.11
54 779 0.73
55 24 0.02
56 5 0.00
57 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (54 bp):
AGTTGATCTCCAGATGATCCTGTGCGGTCATTTCAAGAAGTTTTCGAAGATCAG
Found at i:52445 original size:26 final size:27
Alignment explanation
Indices: 52415--52474 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
52405 TTTCTTTTGG
52415 TTATT-ATTCAGATTAAAGTATTTTTT-
1 TTATTAATTCAGA-TAAAGTATTTTTTC
*
52441 TTATTATAATTCAGATAAAGTTTTTTTTC
1 TTA-T-TAATTCAGATAAAGTATTTTTTC
52470 TTATT
1 TTATT
52475 TTGGATTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 3 0.10
27 2 0.07
28 14 0.48
29 10 0.34
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (27 bp):
TTATTAATTCAGATAAAGTATTTTTTC
Found at i:52452 original size:29 final size:29
Alignment explanation
Indices: 52415--52474 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
52405 TTTCTTTTGG
*
52415 TTATTATTCAGATTAAAGTATTTTTT-TTA
1 TTATAATTCAGA-TAAAGTATTTTTTCTTA
*
52444 TTATAATTCAGATAAAGTTTTTTTTCTTA
1 TTATAATTCAGATAAAGTATTTTTTCTTA
52473 TT
1 TT
52475 TTGGATTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (29 bp):
TTATAATTCAGATAAAGTATTTTTTCTTA
Found at i:52765 original size:16 final size:17
Alignment explanation
Indices: 52746--52781 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
52736 TATTAATGGG
52746 TTTAAGAATT-AATTTA
1 TTTAAGAATTGAATTTA
*
52762 TTTAAGAATTGATTTTA
1 TTTAAGAATTGAATTTA
52779 TTT
1 TTT
52782 TTAATATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (17 bp):
TTTAAGAATTGAATTTA
Found at i:53206 original size:21 final size:23
Alignment explanation
Indices: 53182--53250 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
53172 GTTGTTTTCT
53182 TTATCTATCTA-TTTATTAT-TA
1 TTATCTATCTACTTTATTATCTA
*
53203 TTATCTATCTACTTTTTTATCTA
1 TTATCTATCTACTTTATTATCTA
* **
53226 TTTAT-TATTTACTTTCCTATCTA
1 -TTATCTATCTACTTTATTATCTA
53249 TT
1 TT
53251 TATTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 11 0.27
22 9 0.22
23 17 0.41
24 4 0.10
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATCTATCTACTTTATTATCTA
Found at i:53225 original size:12 final size:12
Alignment explanation
Indices: 53180--53256 Score: 58
Period size: 11 Copynumber: 6.8 Consensus size: 12
53170 TAGTTGTTTT
53180 CTTTATCTATCTA
1 CTTTAT-TATCTA
53193 -TTTATTAT-TA
1 CTTTATTATCTA
53203 --TTATCTATCTA
1 CTTTAT-TATCTA
*
53214 CTTTTTTATCTA
1 CTTTATTATCTA
*
53226 -TTTATTATTTA
1 CTTTATTATCTA
**
53237 CTTTCCTATCTA
1 CTTTATTATCTA
53249 -TTTATTAT
1 CTTTATTAT
53257 TATTATCTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 4 0.08
10 5 0.10
11 20 0.39
12 19 0.37
13 3 0.06
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.62
Consensus pattern (12 bp):
CTTTATTATCTA
Found at i:56529 original size:29 final size:30
Alignment explanation
Indices: 56477--56534 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
56467 GACCCGAATC
*
56477 GAAAAGTTGAGGCCCTGATTTGACATTTTT
1 GAAAAGTTGAGGCCCTGATATGACATTTTT
* * *
56507 GAAACGTT-AGGCCCTTATATGACCTTTT
1 GAAAAGTTGAGGCCCTGATATGACATTTT
56535 CCCTAAAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (30 bp):
GAAAAGTTGAGGCCCTGATATGACATTTTT
Found at i:56603 original size:2 final size:2
Alignment explanation
Indices: 56596--56626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
56586 AAAATATTCA
56596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56627 ACAGAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57975 original size:74 final size:74
Alignment explanation
Indices: 57889--58049 Score: 322
Period size: 74 Copynumber: 2.2 Consensus size: 74
57879 CTCTTTTACT
57889 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
1 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
57954 TGTTGTATA
66 TGTTGTATA
57963 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
1 AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
58028 TGTTGTATA
66 TGTTGTATA
58037 AATTAATATATAT
1 AATTAATATATAT
58050 ATACATATAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 87 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (74 bp):
AATTAATATATATTAACATCAACGAATTAATTGTTATAATCATAGGAGATTTGATTAAACCAATT
TGTTGTATA
Found at i:60039 original size:123 final size:126
Alignment explanation
Indices: 59904--60158 Score: 381
Period size: 131 Copynumber: 2.0 Consensus size: 126
59894 TATTGTTTAA
* *
59904 ACTTTTATAGTTTTACTCAATTAAAAACTCTAATTTTATTTAATTAAATCTAATA-TCTT-TA-T
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATTCTTATATT
*
59966 AATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 AATTTTTACCATTTTACTATATTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
60027 ACTTTTACAGTTTTACTCAACTAAAAGCTCTATTTTTATTTAATTAAATCTAATATTCTTAAACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATTCTT--A--
* *
60092 TATTTTATTTTTACCATTTTACTATATTAATTAAAAAACTTATATATATTAGTATTTTTTAAATA
62 TA-TTAATTTTTACCATTTTACTATATTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
60157 T
126 T
60158 A
1 A
60159 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 51 0.44
124 4 0.03
129 2 0.02
131 60 0.51
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (126 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATTCTTATATT
AATTTTTACCATTTTACTATATTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:60166 original size:13 final size:14
Alignment explanation
Indices: 60144--60182 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
60134 TATATATTAG
*
60144 TATTTTTTAAAT-A
1 TATTTCTTAAATGA
60157 TATTTCTTAAATGA
1 TATTTCTTAAATGA
*
60171 AATTTCTTAAAT
1 TATTTCTTAAAT
60183 TTTACAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (14 bp):
TATTTCTTAAATGA
Found at i:61906 original size:16 final size:16
Alignment explanation
Indices: 61867--61907 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
61857 GAAAATTCTA
* *
61867 GAACCCGATAAAACCT
1 GAACCCGAAAAAACCC
*
61883 GAATCCGAAAAAACCC
1 GAACCCGAAAAAACCC
61899 GAACCCGAA
1 GAACCCGAA
61908 CCTGAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.32, G:0.15, T:0.07
Consensus pattern (16 bp):
GAACCCGAAAAAACCC
Found at i:62163 original size:32 final size:32
Alignment explanation
Indices: 62109--62175 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
62099 AGACCGAACT
* * *
62109 CGAATCCGAATTAACCTGACCCAAAATTAATC
1 CGAACCCGAATTAACCTAACCCAAAATTAACC
** *
62141 CGAACCCGAATTAGTCTAACCCAAATTTAACC
1 CGAACCCGAATTAACCTAACCCAAAATTAACC
62173 CGA
1 CGA
62176 CCTAACTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (32 bp):
CGAACCCGAATTAACCTAACCCAAAATTAACC
Found at i:62821 original size:19 final size:18
Alignment explanation
Indices: 62784--62828 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
62774 TGAAATTTAT
62784 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
62802 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
62821 TTATTATT
1 TAATTATT
62829 AATATTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:70769 original size:39 final size:39
Alignment explanation
Indices: 70724--70804 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
70714 CTTGAAAAAG
70724 AATATGGTTAGGCTCTTGATGCACTTATGAAAAATATGA
1 AATATGGTTAGGCTCTTGATGCACTTATGAAAAATATGA
70763 AATATGGTTAGGCTCTTGATGCACTTATGAAAAATATGA
1 AATATGGTTAGGCTCTTGATGCACTTATGAAAAATATGA
70802 AAT
1 AAT
70805 GCAAGGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (39 bp):
AATATGGTTAGGCTCTTGATGCACTTATGAAAAATATGA
Found at i:72164 original size:60 final size:60
Alignment explanation
Indices: 72040--72175 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
72030 AATATTTCCC
* * * *
72040 AAAATATTCAAATAAGGACCTGAACTTTTAATTTGGCCAAATAAGGGATTAATGTTTGCA
1 AAAATACTCAAATAAGGACCTGAACTTTTAATTTGACCAAATAAGGGACTAACGTTTGCA
** ** *
72100 AAAATACTCAAATAAGGGTCTGGTCTTTTAATTTGACCAAATAA-GGACCTAACGTTAT-CG
1 AAAATACTCAAATAAGGACCTGAACTTTTAATTTGACCAAATAAGGGA-CTAACGTT-TGCA
*
72160 AAAATGCTCAAATAAG
1 AAAATACTCAAATAAG
72176 AGCCTGGCGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.05
60 60 0.94
61 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (60 bp):
AAAATACTCAAATAAGGACCTGAACTTTTAATTTGACCAAATAAGGGACTAACGTTTGCA
Found at i:72359 original size:60 final size:60
Alignment explanation
Indices: 72223--72359 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 60
72213 GACGTCAGAT
* *
72223 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTGGAC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCGGAC
* * * *
72283 TCTTATATGAGTATTTTCGATAACGTTAGGTCCTTATTTGGCCAAATTAAAAAATCGTG-C
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCG-GAC
* *
72343 CCTTATTTAAACATTTT
1 CCTTATTTGAGCATTTT
72360 AGCAAACGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 64 0.98
61 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCGGAC
Found at i:78933 original size:1 final size:1
Alignment explanation
Indices: 78927--78957 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
78917 ATTTGACTAT
78927 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
78958 CTTAGTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:79803 original size:195 final size:191
Alignment explanation
Indices: 79471--79853 Score: 685
Period size: 195 Copynumber: 2.0 Consensus size: 191
79461 GGATAAAATT
79471 ACCTGCAAGTATAGATTTCATTGAACTCATAATATCTATTTGGAGAGTGACACTAAAAGAAAATA
1 ACCTGCAAGTATAGATTTCATTGAACTCATAATATCTATTTGGAGAGTGACACTAAAAGAAAATA
*
79536 AATGAATATTTCATTTTCCGGAAGATATATAGTATGAAAATAGATTATTGAAAAATCTTCTCCAT
66 AATGAATATTTCATTTTCCGGAAGATATATAGAATGAAAATAGATTATTGAAAAATCTTCTCCAT
79601 AGCAAATAAGTGATCATATATATCTATAGTTTTCTTTTTTTTTAATCTAAAAATTGAATATAATG
131 AGCAAATAAGTGATC----ATATCTATAGTTTTCTTTTTTTTTAATCTAAAAATTGAATATAATG
* *
79666 ACCTGCAAGTATAGATTTCATTGACCTCATCATATCTATTTGGAGAGTGACACTAAAAGAAAATA
1 ACCTGCAAGTATAGATTTCATTGAACTCATAATATCTATTTGGAGAGTGACACTAAAAGAAAATA
*
79731 AATGAATATTTCATTTTCCGGAAGATATATAGAATGAAAATAGATTATTGAAAAATCTTTTCCAT
66 AATGAATATTTCATTTTCCGGAAGATATATAGAATGAAAATAGATTATTGAAAAATCTTCTCCAT
*
79796 AGCAAATAAGTGATCATATCTATATTTTTCTTTTTTTTTAATCTAAAAATTGAATATA
131 AGCAAATAAGTGATCATATCTATAGTTTTCTTTTTTTTTAATCTAAAAATTGAATATA
79854 TATATATATC
Statistics
Matches: 183, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
191 42 0.23
195 141 0.77
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (191 bp):
ACCTGCAAGTATAGATTTCATTGAACTCATAATATCTATTTGGAGAGTGACACTAAAAGAAAATA
AATGAATATTTCATTTTCCGGAAGATATATAGAATGAAAATAGATTATTGAAAAATCTTCTCCAT
AGCAAATAAGTGATCATATCTATAGTTTTCTTTTTTTTTAATCTAAAAATTGAATATAATG
Found at i:80354 original size:31 final size:33
Alignment explanation
Indices: 80293--80356 Score: 87
Period size: 31 Copynumber: 1.9 Consensus size: 33
80283 TCAGACACGC
80293 AAATAAACGAGAACATTCCGATTTTGTAAAATACAT
1 AAATAAACGAGAACATTCC---TTTGTAAAATACAT
80329 AAATAAACGA-AACATTCC-TTGTAAAATA
1 AAATAAACGAGAACATTCCTTTGTAAAATA
80357 TTTGTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 10 0.36
35 8 0.29
36 10 0.36
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (33 bp):
AAATAAACGAGAACATTCCTTTGTAAAATACAT
Found at i:80437 original size:19 final size:20
Alignment explanation
Indices: 80413--80452 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
80403 ATTTTTCTAG
80413 ATGGATCGATTTAT-ATTAT
1 ATGGATCGATTTATAATTAT
80432 ATGGATCGATTTATAATTAT
1 ATGGATCGATTTATAATTAT
80452 A
1 A
80453 AGAAAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATGGATCGATTTATAATTAT
Found at i:82883 original size:16 final size:17
Alignment explanation
Indices: 82851--82884 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
82841 TTTTATTTTG
*
82851 TATTTGTTAATATATAA
1 TATTTATTAATATATAA
82868 TATTTATTAA-ATATAA
1 TATTTATTAATATATAA
82884 T
1 T
82885 GTATACGTAC
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTATTAATATATAA
Found at i:87696 original size:6 final size:6
Alignment explanation
Indices: 87675--87751 Score: 93
Period size: 6 Copynumber: 12.7 Consensus size: 6
87665 CTTTTAATTA
* * *
87675 ATATCT -TATAT ATATCT ATATCTAT ATATCT ATATCT ATATCT TTATTT
1 ATATCT ATATCT ATATCT ATATC--T ATATCT ATATCT ATATCT ATATCT
*
87724 ATATCT ATATCT ATATCT ATATAT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATAT
87752 ATACTATATA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
5 4 0.07
6 51 0.84
8 6 0.10
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (6 bp):
ATATCT
Found at i:87700 original size:14 final size:13
Alignment explanation
Indices: 87685--87760 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 13
87675 ATATCTTATA
87685 TATATCTATATCT
1 TATATCTATATCT
87698 ATATATCTATATC-
1 -TATATCTATATCT
*
87711 TATATCTTTAT-T
1 TATATCTATATCT
87723 TATATCTATATC-
1 TATATCTATATCT
*
87735 TATATCTATATAT
1 TATATCTATATCT
87748 ATATATACTATAT
1 -TATAT-CTATAT
87761 AAGTCTAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
12 31 0.57
14 17 0.31
15 6 0.11
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATCTATATCT
Found at i:87752 original size:6 final size:6
Alignment explanation
Indices: 87681--87761 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
87671 ATTAATATCT
* * * * * * * *
87681 TATATA TATCTA TATCTA TATATC TATATC TATATC TTTATT TATATC
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
87729 TATATC TATATC TATATA TATATA TACTATA TA
1 TATATA TATATA TATATA TATATA TA-TATA TA
87762 AGTCTAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
6 60 0.91
7 6 0.09
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATA
Found at i:89170 original size:36 final size:36
Alignment explanation
Indices: 89123--89192 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
89113 GAGATTTTGG
*
89123 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
89159 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
89193 GGTTATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:91587 original size:3 final size:3
Alignment explanation
Indices: 91579--91616 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
91569 AATTCTTTCT
*
91579 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
91617 GCATCAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:91830 original size:22 final size:21
Alignment explanation
Indices: 91805--91848 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
91795 ATCTTTGTAA
*
91805 ACTAAATAACCAGATTTTGATG
1 ACTAAATAACCAAATTTT-ATG
* *
91827 ACTAATTAATCAAATTTTATG
1 ACTAAATAACCAAATTTTATG
91848 A
1 A
91849 AAATGAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (21 bp):
ACTAAATAACCAAATTTTATG
Done.