Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015664.1 Corchorus olitorius cultivar O-4 contig15697, 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: 44677
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1499 original size:16 final size:17
Alignment explanation
Indices: 1475--1547 Score: 73
Period size: 16 Copynumber: 4.5 Consensus size: 17
1465 GGGTTGATCA
1475 GGTTCGGGTCATTTT-G
1 GGTTCGGGTCATTTTCG
*
1491 GGTTTGGGTCATTTTCG
1 GGTTCGGGTCATTTTCG
* *
1508 GGTTCGGATC-GTTT-G
1 GGTTCGGGTCATTTTCG
* *
1523 GATTCGGGT-AATTTCG
1 GGTTCGGGTCATTTTCG
1539 GGTTCGGGT
1 GGTTCGGGT
1548 ACCCAAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
15 11 0.24
16 26 0.57
17 9 0.20
ACGTcount: A:0.08, C:0.12, G:0.38, T:0.41
Consensus pattern (17 bp):
GGTTCGGGTCATTTTCG
Found at i:1596 original size:17 final size:17
Alignment explanation
Indices: 1556--1596 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1546 GTACCCAAAA
1556 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
1573 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
1589 TTTCGGGT
1 TTTCGGGT
1597 TGGGCGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:4680 original size:335 final size:329
Alignment explanation
Indices: 3211--5005 Score: 1639
Period size: 334 Copynumber: 5.4 Consensus size: 329
3201 TGAAATCGTA
* * * * *
3211 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAATAAATGAAAAAACGATATTACAACCGTGAAA
1 TTGTTTTGATTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAA
* * *
3276 ACCCTTCAATCTTTTTGGCGTTG-ATTATACT-TGTTTTCTGAGTATTGTGGCAAAAAATTG-AG
65 AACCTTCAATTTTTTTGGCGTTGAATTATA-TATTTTTTCTGAGTATTGTGGCAAAAAATTGAAG
** * **
3338 -AAAA-----C--A--ATTTTCTTGTCAGTTTTTAGCCGAAATCGTGTATTAACCATCACTATTT
129 AAAAACTTTTCGGATCATTTT-TTGT-AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
* * * * *
3393 TTGGCTAAAAACGCG-TTCAGGGGTCTCCGATCAGTTTTGCATGGTTTTTGGCATC-CAGACTCC
192 TTGGCTAAAAACGCGTTTC--GGGTCGCGGCTCAGTTTTGCATGATTTTTGGCA-CAAAGACTCC
** * *
3456 TTGAAATATCTATATTCAT-GTAACCAAATCTCAGCCACATTGGATTTAAGGATTCATTTGTACA
254 TTGAAATATCTATATTCATCG-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
*
3520 AGCATCTGAATC
318 AGCATCTAAATC
* * *
3532 TTGTTTTGATTTTATTATAAATAAATTCAGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAA
1 TTGTTTTGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* *
3596 ACCTTTCAATTTTTTTGGCGATGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
66 ACC-TTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAAGA
* * * *
3661 AAAACTTTTCGGATTAGTTTTTTTGCAAAATTCTAGCCGAAATCGTGTACTAACCATCACGGCTT
130 AAAACTTTTCGGATCA--TTTTTTG-TAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
* * * * ** *
3726 TTGGCAAAAAAACGCGTTCCGGAGTCACGGCTCAATTTTATATGATTTTTGGCGCAAAGACTCCT
192 TTGGC-TAAAAACGCGTTTCGG-GTCGCGGCTCAGTTTTGCATGATTTTTGGCACAAAGACTCCT
* * * * *
3791 TCAAATATCAATATTCATCGAACCAAATCTCAGCCACATTGGATTCACGGATTTTTTTTTACGAG
255 TGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
*
3856 CACCTAAATC
320 CATCTAAATC
** *
3866 TTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAA
1 TTGTTTTGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * *
3931 ATCCTTCAATTTTTTTTGGTGTTGAGTTATGTATTTTTTTCTGAGTATTGTGGCAAAAAAATTGA
66 A-CCTTCAA-TTTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGC-AAAAAATTGA
* * * * * *
3996 AGAAAAATTTTTCGGGTCAGTTTTTCG-AAATTTTAACCGAAATCGTGCACTAACCATCACCGTT
127 AGAAAAACTTTTCGGATCA-TTTTTTGTAAATTTTAGCCGAAATCGTGTACTAACCATCA-CG-G
** * * * * ** * *
4060 TCTTTTCACTAAAAACGCGTTTCGGGACCCCAGCTTAGTTTTGCATGATTTAAGGTAGAAAGACT
189 T-TTTTGGCTAAAAACGCGTTTCGGG-TCGCGGCTCAGTTTTGCATGATTTTTGGCACAAAGACT
* ** ** * * * * * * **
4125 CCTT-AAA-AACGCGT-TTC-GGGACCCCAGCTTAGTTTTATATATATCTATATTCTCATTTAAG
252 CCTTGAAATATC-TATATTCATCGA-ACCA----A-----ATCT-CAGCCACATT-GGATTTAAG
* * *
4186 AATTTGTTTTTACGAGCATCTGAATA
304 GATTTGTTTTTACGAGCATCTAAATC
* * * *
4212 ATGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA-GGAAAAAGGATATTAAAAGCGTGAAAA
1 TTGTTTTGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * *
4276 CCCTTCAATGTTTTTGGCGTTGAATTATATATTTTTTTCTGAGTTTTCTGGCAAAGAATTGAGGA
66 ACCTTCAATTTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGAAGA
*
4341 AAAACTTTTCGGATCATTTTTTGTAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTT
130 AAAACTTTTCGGATCATTTTTTGT-AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
* * * *
4406 GGCTAAAAACGCGTTTCGGAGTGGCGGCTCAATTTTGCAAGATTTTTTGCACAAAGACTCCTTGA
194 GGCTAAAAACGCGTTTCGG-GTCGCGGCTCAGTTTTGCATGATTTTTGGCACAAAGACTCCTTGA
** * * *
4471 AATATCTATATTCATCGAAAGAAATGTCAGCTACATTGGATATATATAAGGATTTGTATTTACGA
258 AATATCTATATTCATCGAACCAAATCTCAGCCACATTGG--AT-T-TAAGGATTTGTTTTTACGA
*
4536 GCATCTCAATC
319 GCATCTAAATC
* * *
4547 TTATTTTGATTTAATTAGAAATTAATTC-GAAAACAAATGGAAAAACGATATTAGAAGCGTGAGA
1 TTGTTTTGATTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * * *
4611 AGCCTGTCAATCTTTTTGGCATTAAATTATATATTTTTTCTAAATATT-TCGCAAAAAAATT-AA
65 AACCT-TCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAA
4674 GAAAAACTTTTCTGG-TCA------GT---TTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
128 GAAAAACTTTTC-GGATCATTTTTTGTAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
* * * * *
4729 TCGGCTAAAAACGCGTTTCGGGGGCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTT
192 TTGGCTAAAAACGCGTTTC-GGGTCGCGGCTCAGTTTTGCATGATTTTTGGCACAAAGACTCCTT
* * * *
4794 GAAATATCTATATTCATCTAACCAAATCTAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGA
256 GAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
4859 ATCTAAATC
321 ATCTAAATC
* * * *
4868 TTGTTTTGATTTAATTAACTAGAAATAAATTCGGAAAAAAAAAGGAAAAACAATATTAAAAGTGT
1 TTGTTTTGATTTAA-T---TAGAAATAAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGT
* * * *
4933 GAAAAACCCGTCAATTTTTTTTGACGTTGAATTATATATTTTTTCTCAGAATTGTGG-AAAAGAA
61 GAAAAA-CCTTCAA-TTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAA-AA
*
4997 TTGAGGAAA
123 TTGAAGAAA
5006 GATAATAAAA
Statistics
Matches: 1196, Mismatches: 206, Indels: 137
0.78 0.13 0.09
Matches are distributed among these distances:
319 26 0.02
320 21 0.02
321 103 0.09
322 3 0.00
323 6 0.01
325 133 0.11
326 37 0.03
327 41 0.03
328 8 0.01
329 2 0.00
330 1 0.00
332 8 0.01
333 47 0.04
334 147 0.12
335 144 0.12
336 76 0.06
337 94 0.08
338 31 0.03
339 1 0.00
340 51 0.04
341 12 0.01
342 33 0.03
343 69 0.06
344 10 0.01
345 31 0.03
346 61 0.05
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (329 bp):
TTGTTTTGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
ACCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAAGAA
AAACTTTTCGGATCATTTTTTGTAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
CTAAAAACGCGTTTCGGGTCGCGGCTCAGTTTTGCATGATTTTTGGCACAAAGACTCCTTGAAAT
ATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTA
AATC
Found at i:13094 original size:69 final size:70
Alignment explanation
Indices: 13017--13157 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 70
13007 AAAAGAGGGA
*
13017 GTATAGATTAAGATTAAA-CCCAATTCTAACTAATGGAGGAAGAGAGGATCGTTTATCTTAGAAT
1 GTATAGATTAAGATTAAAGCCCAATTCAAACTAATGGAGGAAGAGAGGATCGTTTATCTTAGAAT
13081 TTAAC
66 TTAAC
13086 GTATAGATTAAGATTAAAGCCCAATTCAAACTAATGGAGGAAGAGAGGATCGTTTATCTTAGAAT
1 GTATAGATTAAGATTAAAGCCCAATTCAAACTAATGGAGGAAGAGAGGATCGTTTATCTTAGAAT
13151 TTAAC
66 TTAAC
13156 GT
1 GT
13158 GGCCCATCAG
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 18 0.26
70 52 0.74
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (70 bp):
GTATAGATTAAGATTAAAGCCCAATTCAAACTAATGGAGGAAGAGAGGATCGTTTATCTTAGAAT
TTAAC
Found at i:13944 original size:29 final size:32
Alignment explanation
Indices: 13901--13975 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 32
13891 ATATATTGCG
13901 TCAAGGACATTTTGTCCC-CTGAACTTT-AAA-
1 TCAA-GACATTTTGTCCCTCTGAACTTTCAAAT
13931 TCAAGACATTTTGTCCCTCTGAACTTTCCAAAT
1 TCAAGACATTTTGTCCCTCTGAACTTT-CAAAT
*
13964 TCAAAACATTTT
1 TCAAGACATTTT
13976 ACCCTTGATG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 13 0.32
30 13 0.32
32 3 0.08
33 11 0.28
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (32 bp):
TCAAGACATTTTGTCCCTCTGAACTTTCAAAT
Found at i:16407 original size:2 final size:2
Alignment explanation
Indices: 16395--16437 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
16385 CGTCCCCGAA
16395 AT AT AT A- AT AT AT -T CAT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
16435 AT A
1 AT A
16438 CATTTTATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 33 0.89
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16625 original size:29 final size:29
Alignment explanation
Indices: 16583--16638 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
16573 CCTTGTACGG
*
16583 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGGTGTTGAT
16612 TGTTGAAAACTTGTAATTGTGGTGTTG
1 TGTTGAAAACTTGTAATTGTGGTGTTG
16639 TAAACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGTGTTGAT
Found at i:17883 original size:24 final size:24
Alignment explanation
Indices: 17839--17884 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
17829 GGTTTATATT
* *
17839 CCATGCACTGTCAGTGTATAGAGG
1 CCATACACTGTCAGTGCATAGAGG
17863 CCATACACTGTCAG-GCCATAGA
1 CCATACACTGTCAGTG-CATAGA
17885 ATTATGCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
CCATACACTGTCAGTGCATAGAGG
Found at i:20657 original size:22 final size:22
Alignment explanation
Indices: 20632--20705 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
20622 TTAGCTTCAG
20632 CTTCTTGGGTTAACAGTTTGCA
1 CTTCTTGGGTTAACAGTTTGCA
* * * * *
20654 CTTCTATTTTGATTCATATGTTTTCA
1 CTTC---TTGGGTTAACA-GTTTGCA
20680 TCTTCTTGGGTTAACAGTTTGCA
1 -CTTCTTGGGTTAACAGTTTGCA
20703 CTT
1 CTT
20706 TAATTTTGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
22 7 0.19
23 6 0.16
24 7 0.19
25 7 0.19
26 6 0.16
27 4 0.11
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (22 bp):
CTTCTTGGGTTAACAGTTTGCA
Found at i:20704 original size:49 final size:49
Alignment explanation
Indices: 20627--20731 Score: 185
Period size: 49 Copynumber: 2.1 Consensus size: 49
20617 TTTTGTTAGC
*
20627 TTCAGCTTCTTGGGTTAACAGTTTGCACTTCT-ATTTTGATTCATATGTT
1 TTCATCTTCTTGGGTTAACAGTTTGCACTT-TAATTTTGATTCATATGTT
20676 TTCATCTTCTTGGGTTAACAGTTTGCACTTTAATTTTGATTCATATGTT
1 TTCATCTTCTTGGGTTAACAGTTTGCACTTTAATTTTGATTCATATGTT
20725 TTCATCT
1 TTCATCT
20732 ACAACATGGG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
48 1 0.02
49 53 0.98
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.50
Consensus pattern (49 bp):
TTCATCTTCTTGGGTTAACAGTTTGCACTTTAATTTTGATTCATATGTT
Found at i:34570 original size:20 final size:20
Alignment explanation
Indices: 34545--34583 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34535 CATATAAAAT
*
34545 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
34565 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
34584 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:34692 original size:33 final size:33
Alignment explanation
Indices: 34633--34697 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
34623 AGCCGTGGTC
*
34633 GCTCGTGACTAAGCCATGGCTCGGTCGCGAGCG
1 GCTCGTGACTAAGCCACGGCTCGGTCGCGAGCG
* * * *
34666 GCTCGTGACTGAGCCGCGGCTTGGTCGTGAGC
1 GCTCGTGACTAAGCCACGGCTCGGTCGCGAGC
34698 CGCGATGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.20
Consensus pattern (33 bp):
GCTCGTGACTAAGCCACGGCTCGGTCGCGAGCG
Found at i:34836 original size:17 final size:17
Alignment explanation
Indices: 34814--34855 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
34804 AATAATTGAG
34814 ATTTGAA-AATTGAGAAA
1 ATTTGAAGAATTGA-AAA
34831 ATTTGAGAGAATTGAAAA
1 ATTTGA-AGAATTGAAAA
*
34849 TTTTGAA
1 ATTTGAA
34856 TTTTGAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (17 bp):
ATTTGAAGAATTGAAAA
Found at i:41783 original size:166 final size:166
Alignment explanation
Indices: 41504--41834 Score: 574
Period size: 166 Copynumber: 2.0 Consensus size: 166
41494 CCTGGTGTGA
* *
41504 TCATTCGAGGGTGTGCAATTGTAGAGTGTTGGGCCCTCGCACTCCACAAATTAAGTCTTGGATGT
1 TCATCCGAGGGTGTGCAATTGTAGAGTGTTGGGCCCTCGCACTCCACAAATTAAGTCTTGGATGG
*
41569 CCGGTAATTGGCCTGAATAAGTCTTGACGGAATAAGTCTTGGATGGTCGGTAATTGGCTTAAGAC
66 CCGGTAATTGGCCTGAATAAGTCTTGACGGAATAAATCTTGGATGGTCGGTAATTGGCTTAAGAC
* *
41634 TTGACGGGTTGGGCTGTACGGAGGAGAGATGAGGAT
131 TTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGAT
**
41670 TCATCCGAGGGTGTGCAATTGT-GCAGTGTTGGGCCCTCGCACTCCACGGATTAAGTCTTGGATG
1 TCATCCGAGGGTGTGCAATTGTAG-AGTGTTGGGCCCTCGCACTCCACAAATTAAGTCTTGGATG
*
41734 GCCGGTAATTGGCTTGAATAAGTCTTGACGGAATAAATCTTGGATGGTCGGTAATTGGCTTAAGA
65 GCCGGTAATTGGCCTGAATAAGTCTTGACGGAATAAATCTTGGATGGTCGGTAATTGGCTTAAGA
41799 CTTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGA
130 CTTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGA
41835 CTCACATGTG
Statistics
Matches: 156, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
165 1 0.01
166 155 0.99
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (166 bp):
TCATCCGAGGGTGTGCAATTGTAGAGTGTTGGGCCCTCGCACTCCACAAATTAAGTCTTGGATGG
CCGGTAATTGGCCTGAATAAGTCTTGACGGAATAAATCTTGGATGGTCGGTAATTGGCTTAAGAC
TTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGAT
Found at i:41925 original size:15 final size:15
Alignment explanation
Indices: 41905--41934 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41895 CTCGCACTCC
41905 ACGGATTAAGTCTTG
1 ACGGATTAAGTCTTG
41920 ACGGATTAAGTCTTG
1 ACGGATTAAGTCTTG
41935 GATGGCCGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
ACGGATTAAGTCTTG
Found at i:42000 original size:52 final size:52
Alignment explanation
Indices: 41922--42024 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
41912 AAGTCTTGAC
* *
41922 GGATTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCT
1 GGATTAAGTCTTGGATGGCCGATAATTGGCTTAAAACTTGACGGGTTGGGCT
*
41974 GGATTAAGTCTTGGATGGTCGATAATTGGCTTAAAACTTGACGGGTTGGGC
1 GGATTAAGTCTTGGATGGCCGATAATTGGCTTAAAACTTGACGGGTTGGGC
42025 CGCGTGGAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.21, C:0.13, G:0.35, T:0.31
Consensus pattern (52 bp):
GGATTAAGTCTTGGATGGCCGATAATTGGCTTAAAACTTGACGGGTTGGGCT
Found at i:42077 original size:211 final size:215
Alignment explanation
Indices: 41715--42192 Score: 715
Period size: 211 Copynumber: 2.2 Consensus size: 215
41705 CTCGCACTCC
* * ** *
41715 ACGGATTAAGTCTTGGATGGCCGGTAATTGGCTT--GA-AT-AAGTCTT-GACGGAATAAATCTT
1 ACGGATTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCGGAATAAATCTT
* *
41775 GGATGGTCGGTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGACTCAC
66 GGATGGTCGATAATTGGCTTAAAACTTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGACTCAC
*
41840 ATGTGAATCGGGGGAGATTTACCATCCG-GGGGGTGCAATTGTGGAGTGTTG-G-GC-C-CTCGC
131 ATGTGAATCGGGGGAGATTCACCATCCGAGGGGGTGCAATTGTGGAGTGTTGAGCGCACTCTCGC
41900 ACTCCACGGATTAAGTCTTG
196 ACTCCACGGATTAAGTCTTG
* *
41920 ACGGATTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCTGGATTAAGTCT
1 ACGGATTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGC-GGAATAAATCT
**
41985 TGGATGGTCGATAATTGGCTTAAAACTTGACGGGTTGGGCCGCGTGGAGGAGAGATGAGGACTCA
65 TGGATGGTCGATAATTGGCTTAAAACTTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGACTCA
* *
42050 CATGTGAATCGGGGGAGATTCACCATCCGAGGGTGTGCAATTGTTGAGTGTTGAGCCCTCGCACT
130 CATGTGAATCGGGGGAGATTCACCATCCGAGGGGGTGCAATTGTGGAGTGTTGAG----CGCACT
42115 CTCGCACTCCACGGATTAAGTCTTG
191 CTCGCACTCCACGGATTAAGTCTTG
42140 ACGGATTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGC
1 ACGGATTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGC
42193 CGCACGGAAG
Statistics
Matches: 244, Mismatches: 14, Indels: 15
0.89 0.05 0.05
Matches are distributed among these distances:
205 34 0.14
207 2 0.01
208 1 0.00
209 4 0.02
210 2 0.01
211 98 0.40
212 21 0.09
213 1 0.00
218 2 0.01
219 1 0.00
220 78 0.32
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (215 bp):
ACGGATTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCGGAATAAATCTT
GGATGGTCGATAATTGGCTTAAAACTTGACGGGTTGGGCCGCACGGAGGAGAGATGAGGACTCAC
ATGTGAATCGGGGGAGATTCACCATCCGAGGGGGTGCAATTGTGGAGTGTTGAGCGCACTCTCGC
ACTCCACGGATTAAGTCTTG
Found at i:42145 original size:15 final size:15
Alignment explanation
Indices: 42125--42154 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42115 CTCGCACTCC
42125 ACGGATTAAGTCTTG
1 ACGGATTAAGTCTTG
42140 ACGGATTAAGTCTTG
1 ACGGATTAAGTCTTG
42155 GATGGCCGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
ACGGATTAAGTCTTG
Found at i:42222 original size:26 final size:26
Alignment explanation
Indices: 42193--42242 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
42183 CGGGTTGGGC
42193 CGCACGGAAGAGAAATGAGGACTCGT
1 CGCACGGAAGAGAAATGAGGACTCGT
* **
42219 CGCACGGAGGAGAGGTGAGGACTC
1 CGCACGGAAGAGAAATGAGGACTC
42243 ACATGTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.40, T:0.10
Consensus pattern (26 bp):
CGCACGGAAGAGAAATGAGGACTCGT
Found at i:42623 original size:142 final size:142
Alignment explanation
Indices: 42367--42656 Score: 544
Period size: 142 Copynumber: 2.0 Consensus size: 142
42357 TCTAGACTTT
*
42367 TGGGTTAAGTCTTGGATGGCCGGTGATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGA
1 TGGGTTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGA
*
42432 GATGAGGACTCACAAGTGAATCGGGGGAGATTGTTAAGAGATTCACATGTGAGGAAACATCCCAC
66 GATGAGGACTCACAAGTGAATCGGGGGAGATTGTTAAGAGATTCACATGTGAGGAAACATCCAAC
42497 ATCATGAAGAGA
131 ATCATGAAGAGA
42509 TGGGTTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGA
1 TGGGTTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGA
* *
42574 GATGAGGACTCACAAGTGAATCGGGGGAGATTGTTAAGGGATTCACATGTGAGGAAACATTCAAC
66 GATGAGGACTCACAAGTGAATCGGGGGAGATTGTTAAGAGATTCACATGTGAGGAAACATCCAAC
42639 ATCATGAAGAGA
131 ATCATGAAGAGA
42651 TGGGTT
1 TGGGTT
42657 GTTAGAGGCC
Statistics
Matches: 144, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 144 1.00
ACGTcount: A:0.27, C:0.14, G:0.36, T:0.23
Consensus pattern (142 bp):
TGGGTTAAGTCTTGGATGGCCGGTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGA
GATGAGGACTCACAAGTGAATCGGGGGAGATTGTTAAGAGATTCACATGTGAGGAAACATCCAAC
ATCATGAAGAGA
Found at i:42989 original size:71 final size:71
Alignment explanation
Indices: 42905--43048 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 71
42895 AGAGCTAAAA
* *
42905 TTGTAAAAGCACTTAGGGATTCAAGATGAGTGATCAGGATTGAATCTTAATTTTCCTGAAGTCAA
1 TTGTAAAAACACTTAGGAATTCAAGATGAGTGATCAGGATTGAATCTTAATTTTCCTGAAGTCAA
42970 CTGGAT
66 CTGGAT
*
42976 TTGTAAAAACACTTAGGAATTCAAGATGAGTGGTCAGGATTGAATCTTAATTTTCCTGAAGTCAA
1 TTGTAAAAACACTTAGGAATTCAAGATGAGTGATCAGGATTGAATCTTAATTTTCCTGAAGTCAA
43041 CTGGAT
66 CTGGAT
43047 TT
1 TT
43049 TGATTACCTC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (71 bp):
TTGTAAAAACACTTAGGAATTCAAGATGAGTGATCAGGATTGAATCTTAATTTTCCTGAAGTCAA
CTGGAT
Done.