Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006765.1 Corchorus capsularis cultivar CVL-1 contig06786, 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: 68277
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1629 original size:16 final size:16
Alignment explanation
Indices: 1608--1639 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1598 CTTTGTATGG
1608 AACCTAACTAAAACCA
1 AACCTAACTAAAACCA
*
1624 AACCTAGCTAAAACCA
1 AACCTAACTAAAACCA
1640 TAAATTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.31, G:0.03, T:0.12
Consensus pattern (16 bp):
AACCTAACTAAAACCA
Found at i:2308 original size:2 final size:2
Alignment explanation
Indices: 2301--2327 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2291 AGTTTTATAA
2301 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2328 ATTTGGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3194 original size:13 final size:13
Alignment explanation
Indices: 3176--3200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3166 GCGAAGCGCA
3176 CGGGGTGAAATCG
1 CGGGGTGAAATCG
3189 CGGGGTGAAATC
1 CGGGGTGAAATC
3201 TAATTCTGTT
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:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGGTGAAATCG
Found at i:5495 original size:19 final size:19
Alignment explanation
Indices: 5477--5513 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5467 TATTAATTAT
*
5477 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
5495 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
5514 CTTAAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:5649 original size:13 final size:13
Alignment explanation
Indices: 5631--5657 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5621 AAATATAATA
5631 AATATGATTTATG
1 AATATGATTTATG
5644 AATATGATTTATG
1 AATATGATTTATG
5657 A
1 A
5658 GGTTATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Found at i:5806 original size:2 final size:2
Alignment explanation
Indices: 5799--5832 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5789 AATATGATAG
5799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5833 TCACCTTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8400 original size:31 final size:30
Alignment explanation
Indices: 8365--8460 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 30
8355 ATACAAATTG
8365 AAAGAAGATTCAAAATTATCGGAGAATTATT
1 AAAGAAGATTCAAAATTAT-GGAGAATTATT
* * * *
8396 AAAGAA-AATCCACA-GA--G-GAA-TATT
1 AAAGAAGATTCAAAATTATGGAGAATTATT
*
8420 GAAAGAAGATCCAAAATTATTGGAGAATTATT
1 -AAAGAAGATTCAAAATTA-TGGAGAATTATT
8452 AAAGAAGAT
1 AAAGAAGAT
8461 CCAAGGGAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
24 4 0.08
25 9 0.19
26 5 0.10
27 1 0.02
29 1 0.02
30 6 0.12
31 18 0.38
32 4 0.08
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (30 bp):
AAAGAAGATTCAAAATTATGGAGAATTATT
Found at i:8608 original size:41 final size:41
Alignment explanation
Indices: 8551--8632 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
8541 TTTTTGTTCG
*
8551 TTCAAAATCAAGTCATCAAAATAC-TTAAATTAAATTATCAA
1 TTCAAAATCAAGTCATCAAAA-ACATTAAATCAAATTATCAA
* * *
8592 TTCAAGATCAAGTCATCAAGACCATTAAATCAAATTATCAA
1 TTCAAAATCAAGTCATCAAAAACATTAAATCAAATTATCAA
8633 ACTCTGAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (41 bp):
TTCAAAATCAAGTCATCAAAAACATTAAATCAAATTATCAA
Found at i:9538 original size:22 final size:22
Alignment explanation
Indices: 9492--9540 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
9482 TTGCCCCTTT
* *
9492 TCTCT-CTCCTCCCACTTAATC
1 TCTCTCCTCCTCCCACTCAATA
*
9513 TCTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCCTCCCACTCAATA
9535 TCTCTC
1 TCTCTC
9541 TTCATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.12, C:0.51, G:0.00, T:0.37
Consensus pattern (22 bp):
TCTCTCCTCCTCCCACTCAATA
Found at i:9993 original size:21 final size:23
Alignment explanation
Indices: 9969--10020 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
9959 ATTAATGATA
9969 CCACGTCAGCT-CGTTGTTAT-G
1 CCACGTCAGCTGCGTTGTTATAG
* *
9990 CCACATCA-ATGCGTTGTTATAG
1 CCACGTCAGCTGCGTTGTTATAG
10012 -CACGTCAGC
1 CCACGTCAGC
10021 ACACCATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (23 bp):
CCACGTCAGCTGCGTTGTTATAG
Found at i:11376 original size:22 final size:22
Alignment explanation
Indices: 11343--11384 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11333 GAGAATCTTT
*
11343 TTATAAATTTTTTTTAACCTTC
1 TTATAAATTTTTGTTAACCTTC
11365 TTATGAAA-TTTTGTTAACCT
1 TTAT-AAATTTTTGTTAACCT
11385 CTCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (22 bp):
TTATAAATTTTTGTTAACCTTC
Found at i:11554 original size:22 final size:23
Alignment explanation
Indices: 11529--11610 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 23
11519 AAAATCTCCT
*
11529 TATG-AATTGTT-AGTAATTACAC
1 TATGAAATTGTTGA-TAATCACAC
11551 TATGAAATT-TTGATAATCACAC
1 TATGAAATTGTTGATAATCACAC
* ***
11573 TATGAAATTG-TGATAACCTTGC
1 TATGAAATTGTTGATAATCACAC
11595 TATGAAATT-TTGATAA
1 TATGAAATTGTTGATAA
11611 ATCTTCCTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
22 46 0.90
23 5 0.10
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (23 bp):
TATGAAATTGTTGATAATCACAC
Found at i:11598 original size:44 final size:42
Alignment explanation
Indices: 11550--11863 Score: 209
Period size: 44 Copynumber: 7.4 Consensus size: 42
11540 AGTAATTACA
* *
11550 CTATGAAATTTTGATAATCACACTATGAAATTGTGATAACCTT
1 CTATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTT
** *
11593 GCTATGAAATTTTGATAAATCTTCCTACAAAATTTTGATAAACCTCC
1 -CTATGAAATTTTGAT-AATC-TCCTATGAAATTTTGAT-AACCT-T
* * * * *
11640 CTATAAAAATTTGATAACTTTCTTATGAAATCTTGATAA----
1 CTATGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACCTT
* * **
11679 CTA-AAAATTTTGATAAGCTCCCTATGATTTTTTGATAACC-T
1 CTATGAAATTTTGATAATCT-CCTATGAAATTTTGATAACCTT
* *
11720 CATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCT
1 C--TATGAAATTTTGATAATCT-CCTATGAAATTTTGATAACCTT
* *
11765 CTTATGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTT
1 C-TATGAAATTTTGATAATCT--CCTATGAAATTTTGATAACCTT
* *
11809 CATATGAAATTTTGAT-ATCCTCC-CTG-AATTTTGATATCC-T
1 C-TATGAAATTTTGATAAT-CTCCTATGAAATTTTGATAACCTT
**
11849 CCCTGAAATTTTGAT
1 CTATGAAATTTTGAT
11864 TACTCCATAA
Statistics
Matches: 218, Mismatches: 36, Indels: 37
0.75 0.12 0.13
Matches are distributed among these distances:
37 1 0.00
38 26 0.12
39 15 0.07
40 2 0.01
41 13 0.06
42 2 0.01
43 7 0.03
44 97 0.44
45 35 0.16
46 20 0.09
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (42 bp):
CTATGAAATTTTGATAATCTCCTATGAAATTTTGATAACCTT
Found at i:11627 original size:23 final size:23
Alignment explanation
Indices: 11599--11656 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
11589 CCTTGCTATG
* *
11599 AAATTTTGATAAATCTTCCTACA
1 AAATTTTGATAAACCTCCCTACA
*
11622 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTACA
*
11645 AAAATTTGATAA
1 AAATTTTGATAA
11657 CTTTCTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTACA
Found at i:11712 original size:22 final size:22
Alignment explanation
Indices: 11683--11863 Score: 160
Period size: 22 Copynumber: 8.5 Consensus size: 22
11673 TGATAACTAA
*
11683 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
11705 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
11727 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
*
11749 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
* **
11771 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
* *
11793 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATG
*
11815 AAATTTTGATATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
*
11835 -AATTTTGATATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
11854 AAATTTTGAT
1 AAATTTTGAT
11864 TACTCCATAA
Statistics
Matches: 129, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
19 19 0.15
20 11 0.09
21 4 0.03
22 91 0.71
23 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:11869 original size:19 final size:20
Alignment explanation
Indices: 11813--11863 Score: 95
Period size: 19 Copynumber: 2.6 Consensus size: 20
11803 AACCTTCATA
11813 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
11833 TG-AATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
11852 TGAAATTTTGAT
1 TGAAATTTTGAT
11864 TACTCCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:12000 original size:22 final size:22
Alignment explanation
Indices: 11970--12022 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
11960 ATCACATTTT
*
11970 GAAAATTTGATAACCTCTTT-AC
1 GAAATTTTGATAACCT-TTTAAC
11992 GAAATTTTGATAACCTTTTAAC
1 GAAATTTTGATAACCTTTTAAC
*
12014 AAAATTTTG
1 GAAATTTTG
12023 TTGATCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
GAAATTTTGATAACCTTTTAAC
Found at i:12170 original size:22 final size:22
Alignment explanation
Indices: 12015--12362 Score: 103
Period size: 22 Copynumber: 15.6 Consensus size: 22
12005 CCTTTTAACA
* * *
12015 AAATTTTGTTGATCCCTCTATG
1 AAATTTTGATAATCACTCTATG
* **
12037 AAATTCTGATAATCACAGTATG
1 AAATTTTGATAATCACTCTATG
* * * * * *
12059 TAATTTT-ATTAACCTCGCTTTA
1 AAATTTTGA-TAATCACTCTATG
*
12081 AAATTTTGATAA-CAACACTATG
1 AAATTTTGATAATC-ACTCTATG
* *
12103 AAATTTTGATATTC-TTCATAT-
1 AAATTTTGATAATCACTC-TATG
12124 AAATTTTGATAATCCGATCTCTATG
1 AAATTTTGATAAT-C-A-CTCTATG
*
12149 AAATTTCGATAATCACTCTATG
1 AAATTTTGATAATCACTCTATG
* * *
12171 AGA-TTTGATAACCA-TCTATC
1 AAATTTTGATAATCACTCTATG
* * *
12191 AAATTTTGGTACTC-CT-TATT
1 AAATTTTGATAATCACTCTATG
* *
12211 AAATTGAGACTTTTATAATC-TTCATATG
1 AAA-T-----TTTGATAATCACTC-TATG
* *
12239 AAATTTTGATAACCACAT-TATA
1 AAATTTTGATAATCAC-TCTATG
* * * *
12261 AAATTTTGATAACCTCCCCATG
1 AAATTTTGATAATCACTCTATG
*
12283 AAATATT-AGTAA-C-CTCCTAATG
1 AAATTTTGA-TAATCACT-CT-ATG
* * *
12305 AAATTTTGTTAACCACACTATG
1 AAATTTTGATAATCACTCTATG
* *
12327 AAATTCTT-ATAATCTCGCTATG
1 AAATT-TTGATAATCACTCTATG
*
12349 ACATTTTGATAATC
1 AAATTTTGATAATC
12363 TTTTTGATAA
Statistics
Matches: 237, Mismatches: 58, Indels: 62
0.66 0.16 0.17
Matches are distributed among these distances:
20 14 0.06
21 38 0.16
22 142 0.60
23 8 0.03
24 6 0.03
25 14 0.06
26 8 0.03
27 1 0.00
28 6 0.03
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAATCACTCTATG
Found at i:13439 original size:32 final size:31
Alignment explanation
Indices: 13385--13448 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
13375 ATTTAGAAAT
* * *
13385 ATATTTTTTTAAAAAAGGGGTACAATGGGAA
1 ATATGTTTTAAAAAAAGGGGTACAATCGGAA
13416 ATATGTTTTAAAAATAAGGGGTACAATCGGAA
1 ATATGTTTTAAAAA-AAGGGGTACAATCGGAA
13448 A
1 A
13449 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.30
Consensus pattern (31 bp):
ATATGTTTTAAAAAAAGGGGTACAATCGGAA
Found at i:13590 original size:30 final size:31
Alignment explanation
Indices: 13549--13610 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
13539 ATTTAGAAAT
* *
13549 ATATTTTTTAAAAA-AAGGGTACAATTGGAA
1 ATATGTTTTAAAAATAAGGATACAATTGGAA
13579 ATATGTTTTAAAAATAAGGATACAATTGGAA
1 ATATGTTTTAAAAATAAGGATACAATTGGAA
13610 A
1 A
13611 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.32
Consensus pattern (31 bp):
ATATGTTTTAAAAATAAGGATACAATTGGAA
Found at i:13647 original size:164 final size:164
Alignment explanation
Indices: 13327--13656 Score: 565
Period size: 164 Copynumber: 2.0 Consensus size: 164
13317 GGAATAATTT
* *
13327 ATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATATTTT
1 ATGATTAAAAAAATAATGGAATAATTAAAATATTATTGAGTAATGACAATTTAGAAATATATTTT
* *
13392 TTTAAAAAAGGGGTACAATGGGAAATATGTTTTAAAAATAAGGGGTACAATCGGAAAACATAAAG
66 TTTAAAAAAAGGGTACAATGGGAAATATGTTTTAAAAATAAGGGATACAATCGGAAAACATAAAG
*
13457 TTTCCCCTTATTCGTACTTTTATATATAGTATAG
131 TTTCCCCTTATTCGTACTTTTATATATAATATAG
13491 ATGATTAAAAAAATAATGGAATAATTAAAATATTATTGAGTAATGACAATTTAGAAATATA-TTT
1 ATGATTAAAAAAATAATGGAATAATTAAAATATTATTGAGTAATGACAATTTAGAAATATATTTT
* *
13555 TTTAAAAAAAGGGTACAATTGGAAATATGTTTTAAAAATAA-GGATACAATTGGAAAACATAAAG
66 TTTAAAAAAAGGGTACAATGGGAAATATGTTTTAAAAATAAGGGATACAATCGGAAAACATAAAG
13619 TTTCCCCTTATTCGTACTTTTATATATATAATATAG
131 TTTCCCCTTATTCGTAC-TTT-TATATATAATATAG
13655 AT
1 AT
13657 TAAGAAATCT
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
162 38 0.24
163 45 0.29
164 74 0.47
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (164 bp):
ATGATTAAAAAAATAATGGAATAATTAAAATATTATTGAGTAATGACAATTTAGAAATATATTTT
TTTAAAAAAAGGGTACAATGGGAAATATGTTTTAAAAATAAGGGATACAATCGGAAAACATAAAG
TTTCCCCTTATTCGTACTTTTATATATAATATAG
Found at i:14830 original size:11 final size:11
Alignment explanation
Indices: 14787--14824 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
14777 CCTATATATA
*
14787 AAATAAATTAT
1 AAATTAATTAT
14798 CAAA-TAATTAT
1 -AAATTAATTAT
14809 AAATTAATTAT
1 AAATTAATTAT
14820 AAATT
1 AAATT
14825 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:15340 original size:19 final size:19
Alignment explanation
Indices: 15329--15365 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
15319 AATTTTTAAG
15329 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
15348 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
15366 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:18297 original size:66 final size:66
Alignment explanation
Indices: 18191--18320 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
18181 CTAACTCCAA
*
18191 AAGCAAGCCTTGGTAGGGATTTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAT
1 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAT
18256 C
66 C
*
18257 AAGCAAGTCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGA
1 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGA
18321 CCAAAAAGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (66 bp):
AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAT
C
Found at i:18489 original size:2 final size:2
Alignment explanation
Indices: 18482--18526 Score: 58
Period size: 2 Copynumber: 22.5 Consensus size: 2
18472 TAATATGTAG
18482 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA -A TA TGA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA TA
18524 TA T
1 TA T
18527 CATAAATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 2 0.05
2 34 0.87
3 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19359 original size:66 final size:66
Alignment explanation
Indices: 19253--19378 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 66
19243 CTAATTCCAA
* *
19253 AAGCAAGCCTTGGTAGGGATTTTTTAGTAATTTCACTACTCTATTAAAGTCAATTGAGAAATGAT
1 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAT
19318 C
66 C
*
19319 AAGCAAGTCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAA
1 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAA
19379 GTGACCAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (66 bp):
AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAT
C
Found at i:19520 original size:232 final size:231
Alignment explanation
Indices: 19103--19520 Score: 563
Period size: 232 Copynumber: 1.8 Consensus size: 231
19093 ATCCTTGATG
* * *
19103 GGGATCTTTATTAATTCCACTACTCTATTCAAGTCCATTGAAAAATGACCAAAAAGATTACTTAT
1 GGGATCTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAAAAATGACCAAAAAGATTACTTAT
19168 TTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTACAAAAAGACGGAAA
66 TTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTACAAAAAGACGGAAA
* *** *
19233 AAAAAGTTCTCTAATTCCAAAAGCAAGCCTTGGTAGGGATTTTTTAGTAATTTCACTACTCTATT
131 AAAAAGTTCTCTAACTCCAAAAGCAAGCAGGGGTAGGGATATTTTAGTAATTTCACTACTCTATT
19298 AAAGTCAATTGAGAAATGATCAAGCAAGTCTTGGTA
196 AAAGTCAATTGAGAAATGATCAAGCAAGTCTTGGTA
* * *
19334 GGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAGTGACCAAAAAG-TGTAGTT
1 GGGATC-TTTAGTAATTCCACTACTCTATTAAAGTCAATTGAAAAATGACCAAAAAGAT-TACTT
* ***
19398 ATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGTCAAGTGGGAAAAGAC-GA
64 ATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTACAAAAAGACGGA
* ** ** ** * *
19462 AAAAATTTAGTTCTCTCGCTCC-TCATTAATCAGGGGTGGGGATATTTTAGTAATTTCAC
129 AAAAA--AAGTTCTCTAACTCCAAAAGCAAGCAGGGGTAGGGATATTTTAGTAATTTCAC
19521 ATGTTTATTC
Statistics
Matches: 159, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
231 14 0.09
232 134 0.84
233 11 0.07
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (231 bp):
GGGATCTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAAAAATGACCAAAAAGATTACTTAT
TTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTACAAAAAGACGGAAA
AAAAAGTTCTCTAACTCCAAAAGCAAGCAGGGGTAGGGATATTTTAGTAATTTCACTACTCTATT
AAAGTCAATTGAGAAATGATCAAGCAAGTCTTGGTA
Found at i:19593 original size:2 final size:2
Alignment explanation
Indices: 19554--19578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19544 TGTGTGTGTG
19554 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19579 CAATATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22801 original size:79 final size:76
Alignment explanation
Indices: 22641--22809 Score: 261
Period size: 79 Copynumber: 2.2 Consensus size: 76
22631 GTTTTTTAAT
*
22641 TAAAATAGTAAAATGGTAAAATATAAGTAATAAGGATATTAGATTTAATCATATAAAAATAGAGT
1 TAAAATAGTAAAATGATAAAATATAAGTAATAAGGATATTAGATTTAATCATATAAAAATAGAGT
22706 TTTTAATTGAG
66 TTTTAATTGAG
22717 TAAAATAGTAAAATGATAAAATATAA-TAGCTATAAGGATATTAGATTTAATTACATA-AAAAAT
1 TAAAATAGTAAAATGATAAAATATAAGTA---ATAAGGATATTAGATTTAA-T-CATATAAAAAT
*
22780 AGAGTTTTTAGTTGAG
61 AGAGTTTTTAATTGAG
22796 TAAAATAGTAAAAT
1 TAAAATAGTAAAAT
22810 AAAATAGTTA
Statistics
Matches: 86, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
75 2 0.02
76 25 0.29
78 19 0.22
79 36 0.42
80 4 0.05
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.34
Consensus pattern (76 bp):
TAAAATAGTAAAATGATAAAATATAAGTAATAAGGATATTAGATTTAATCATATAAAAATAGAGT
TTTTAATTGAG
Found at i:22808 original size:71 final size:69
Alignment explanation
Indices: 22723--22877 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 69
22713 TGAGTAAAAT
* * *
22723 AGTAAAAT-GATAAAATATAATAGCTATAAGGATATTAG-ATTTAATTACATAAAAAATAGAGTT
1 AGTAAAATAG-TAAAATAAAATAGCTATAAAGATATT-GTATTGAATTA-A-AAAAAATAGAGTT
*
22786 TTTAGTTG
62 TTTAGTTA
* *
22794 AGTAAAATAGTAAAATAAAATAGTTATAAAGATATTGTATTGAATTAAATAAAATAGAGTTTTTA
1 AGTAAAATAGTAAAATAAAATAGCTATAAAGATATTGTATTGAATTAAAAAAAATAGAGTTTTTA
22859 GTTA
66 GTTA
22863 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
22878 ATCTAAACAA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
69 31 0.41
70 4 0.05
71 39 0.52
72 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (69 bp):
AGTAAAATAGTAAAATAAAATAGCTATAAAGATATTGTATTGAATTAAAAAAAATAGAGTTTTTA
GTTA
Found at i:23012 original size:19 final size:20
Alignment explanation
Indices: 22983--23023 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
22973 TAGATATATC
22983 TATATTATAAGAAACCATAA
1 TATATTATAAGAAACCATAA
*
23003 TATA-TATAAGAAGCCATAA
1 TATATTATAAGAAACCATAA
23022 TA
1 TA
23024 ATAGAAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (20 bp):
TATATTATAAGAAACCATAA
Found at i:23189 original size:95 final size:95
Alignment explanation
Indices: 23025--23213 Score: 344
Period size: 95 Copynumber: 2.0 Consensus size: 95
23015 GCCATAATAA
* *
23025 TAGAAAGTGAAATTACCTAAAAACCAATCTAACCTTAACATCTCATAAATTGAAGAATAAATGAG
1 TAGAAAGTGAAATTACCTAAAAACCAATCTAACCTTAACATCTCATAAATTGAAGAACAAATGAA
23090 GAGGGTATTTTGGTACTTTACTTTTCGGTT
66 GAGGGTATTTTGGTACTTTACTTTTCGGTT
23120 TAGAAAGTGAAATTACCTAAAAACCAAT-TCAACCTTAACATCTCATAAATTGAAGAACAAATGA
1 TAGAAAGTGAAATTACCTAAAAACCAATCT-AACCTTAACATCTCATAAATTGAAGAACAAATGA
23184 AGAGGGTATTTTGGTACTTTACTTTTCGGT
65 AGAGGGTATTTTGGTACTTTACTTTTCGGT
23214 GTTTTCATTA
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
94 1 0.01
95 90 0.99
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (95 bp):
TAGAAAGTGAAATTACCTAAAAACCAATCTAACCTTAACATCTCATAAATTGAAGAACAAATGAA
GAGGGTATTTTGGTACTTTACTTTTCGGTT
Found at i:28978 original size:29 final size:31
Alignment explanation
Indices: 28946--29012 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
28936 ACACAATTTT
*
28946 GGATATAACGTTAC-AAAA-CAAGTAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
28975 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
29006 GTATATA
1 GGATATA
29013 GTCAGTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.42
30 4 0.12
31 15 0.45
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:31662 original size:8 final size:7
Alignment explanation
Indices: 31649--31685 Score: 51
Period size: 6 Copynumber: 5.4 Consensus size: 7
31639 ATCTTATTGT
31649 TATTATA
1 TATTATA
31656 GTATTATA
1 -TATTATA
31664 TA-TATA
1 TATTATA
31670 TA-TATA
1 TATTATA
31676 TATTATA
1 TATTATA
31683 TAT
1 TAT
31686 ATCCTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.43
7 9 0.32
8 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (7 bp):
TATTATA
Found at i:34013 original size:3 final size:3
Alignment explanation
Indices: 34000--34029 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
33990 AGTACTCTAG
34000 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
34030 CTAACATGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:35193 original size:57 final size:57
Alignment explanation
Indices: 35121--35235 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
35111 TATTTTTGTT
*
35121 TCTTTTCATCTAATGGCAGAGTTGGAACAGGCCAATGAACTTAACAATATGATGATA
1 TCTTTCCATCTAATGGCAGAGTTGGAACAGGCCAATGAACTTAACAATATGATGATA
*
35178 TCTTTCCATCTAATGGCAGAGTTGGAACAGGCCAATGAACTTAACCATATGATGATA
1 TCTTTCCATCTAATGGCAGAGTTGGAACAGGCCAATGAACTTAACAATATGATGATA
35235 T
1 T
35236 TATAAAGCTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (57 bp):
TCTTTCCATCTAATGGCAGAGTTGGAACAGGCCAATGAACTTAACAATATGATGATA
Found at i:38672 original size:24 final size:24
Alignment explanation
Indices: 38640--38729 Score: 90
Period size: 24 Copynumber: 3.5 Consensus size: 24
38630 CAGCACCGCT
38640 ACCACTTGCACCCCCACCAGCACC
1 ACCACTTGCACCCCCACCAGCACC
* *
38664 ACCAGTTGCACCTGCACCACCAGAACCGC
1 ACCACTTGCACC--C-CCACCAGCA-C-C
*
38693 TACCACTTGCACCACCACCAGCACC
1 -ACCACTTGCACCCCCACCAGCACC
*
38718 ACCAGTTGCACC
1 ACCACTTGCACC
38730 TGCATTACCG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
24 22 0.41
25 1 0.02
26 2 0.04
27 16 0.30
28 1 0.02
29 1 0.02
30 11 0.20
ACGTcount: A:0.27, C:0.50, G:0.12, T:0.11
Consensus pattern (24 bp):
ACCACTTGCACCCCCACCAGCACC
Found at i:38711 original size:54 final size:54
Alignment explanation
Indices: 38627--38933 Score: 370
Period size: 54 Copynumber: 5.9 Consensus size: 54
38617 CCTCCACCAG
* * *
38627 TACCAGCACCGCTACCACTTGCACCCCCACCAGCACCACCAGTTGCACCTGCAC
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
* * *
38681 CACCAGAACCGCTACCACTTGCACCACCACCAGCACCACCAGTTGCACCTGCAT
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
* * * *
38735 T------ACCG------CTTGCACCACCGCTAACACCTCCCGTTGCACCTGCAT
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
* * * *
38777 TACCAGAACCGCTACCGCTTGCACCACCGCCAGCACCACCAGTTGCACCTGCAT
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
* *
38831 TACCAGCACCGCTACCGCTTGCACCACCACTAACACCACCAGTTGCACCTGCAT
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
38885 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACC-GCTTGCACC
1 TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAG-TTGCACC
38934 ACCGCTTGCA
Statistics
Matches: 220, Mismatches: 20, Indels: 26
0.83 0.08 0.10
Matches are distributed among these distances:
42 33 0.15
48 8 0.04
53 1 0.00
54 178 0.81
ACGTcount: A:0.25, C:0.47, G:0.13, T:0.15
Consensus pattern (54 bp):
TACCAGCACCGCTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
Found at i:38744 original size:42 final size:42
Alignment explanation
Indices: 38693--38781 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
38683 CCAGAACCGC
*
38693 TACCACTTGCACCACCACCAGCACCACCAGTTGCACCTGCAT
1 TACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
* * * * *
38735 TACCGCTTGCACCACCGCTAACACCTCCCGTTGCACCTGCAT
1 TACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
38777 TACCA
1 TACCA
38782 GAACCGCTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.45, G:0.12, T:0.19
Consensus pattern (42 bp):
TACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCAT
Found at i:38744 original size:96 final size:98
Alignment explanation
Indices: 38638--38933 Score: 355
Period size: 96 Copynumber: 2.9 Consensus size: 98
38628 ACCAGCACCG
* * * * **
38638 CTACCACTTGCACCCCCACCAGCACCACCAGTTGCACCTGCACCACCAGAACCGCTACCACTTGC
1 CTACCGCTTGCACCACCACTAACACCACCAGTTGCACCTGCATTACCAGAACCGCTACCACTTGC
38703 ACCACCACCAGCACCACCAGTTGCACCTGCA-T
66 ACCACCACCAGCACCACCAGTTGCACCTGCATT
* * * *
38735 -TACCGCTTGCACCACCGCTAACACCTCCCGTTGCACCTGCATTACCAGAACCGCTACCGCTTGC
1 CTACCGCTTGCACCACCACTAACACCACCAGTTGCACCTGCATTACCAGAACCGCTACCACTTGC
*
38799 ACCACCGCCAGCACCACCAGTTGCACCTGCATT
66 ACCACCACCAGCACCACCAGTTGCACCTGCATT
*
38832 ACCAGCACCGCTACCGCTTGCACCACCACTAACACCACCAGTTGCACCTGCATTACCAGCACCGC
1 ----------CTACCGCTTGCACCACCACTAACACCACCAGTTGCACCTGCATTACCAGAACCGC
*
38897 TACCACTTGCACCACCACCAACACCACC-GCTTGCACC
56 TACCACTTGCACCACCACCAGCACCACCAG-TTGCACC
38934 ACCGCTTGCA
Statistics
Matches: 168, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
96 84 0.50
97 1 0.01
107 1 0.01
108 82 0.49
ACGTcount: A:0.25, C:0.47, G:0.13, T:0.15
Consensus pattern (98 bp):
CTACCGCTTGCACCACCACTAACACCACCAGTTGCACCTGCATTACCAGAACCGCTACCACTTGC
ACCACCACCAGCACCACCAGTTGCACCTGCATT
Found at i:38801 original size:30 final size:30
Alignment explanation
Indices: 38765--38909 Score: 102
Period size: 30 Copynumber: 5.2 Consensus size: 30
38755 ACACCTCCCG
*
38765 TTGCACCTGCATTACCAGAACCGCTACCGC
1 TTGCACCTGCATTACCAGCACCGCTACCGC
***
38795 TTGCA-C--CACCGCCAGCA-C-C-ACCAG-
1 TTGCACCTGCATTACCAGCACCGCTACC-GC
38819 TTGCACCTGCATTACCAGCACCGCTACCGC
1 TTGCACCTGCATTACCAGCACCGCTACCGC
** *
38849 TTGCACCACCACTA--A-CA-C-C-ACCAG-
1 TTGCACCTGCATTACCAGCACCGCTACC-GC
*
38873 TTGCACCTGCATTACCAGCACCGCTACCAC
1 TTGCACCTGCATTACCAGCACCGCTACCGC
38903 TTGCACC
1 TTGCACC
38910 ACCACCAACA
Statistics
Matches: 85, Mismatches: 14, Indels: 32
0.65 0.11 0.24
Matches are distributed among these distances:
24 22 0.26
25 5 0.06
26 3 0.04
27 19 0.22
28 3 0.04
29 4 0.05
30 29 0.34
ACGTcount: A:0.24, C:0.44, G:0.14, T:0.17
Consensus pattern (30 bp):
TTGCACCTGCATTACCAGCACCGCTACCGC
Found at i:38840 original size:24 final size:24
Alignment explanation
Indices: 38813--38894 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
38803 CCGCCAGCAC
38813 CACCAGTTGCACCTGCATTACCAG
1 CACCAGTTGCACCTGCATTACCAG
** * * *
38837 CACCGCTACCGCTTGCACCACCACTAACAC
1 CA-C-C-A--G-TTGCACCTGCATTACCAG
38867 CACCAGTTGCACCTGCATTACCAG
1 CACCAGTTGCACCTGCATTACCAG
38891 CACC
1 CACC
38895 GCTACCACTT
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
24 19 0.45
25 2 0.05
26 1 0.02
27 2 0.05
28 1 0.02
29 2 0.05
30 15 0.36
ACGTcount: A:0.26, C:0.44, G:0.13, T:0.17
Consensus pattern (24 bp):
CACCAGTTGCACCTGCATTACCAG
Found at i:38913 original size:12 final size:12
Alignment explanation
Indices: 38898--38945 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
38888 CAGCACCGCT
38898 ACCACTTGCACC
1 ACCACTTGCACC
***
38910 ACCACCAACACC
1 ACCACTTGCACC
*
38922 ACCGCTTGCACC
1 ACCACTTGCACC
*
38934 ACCGCTTGCACC
1 ACCACTTGCACC
38946 TGGACTACCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.25, C:0.52, G:0.10, T:0.12
Consensus pattern (12 bp):
ACCACTTGCACC
Found at i:38938 original size:150 final size:150
Alignment explanation
Indices: 38627--38939 Score: 355
Period size: 150 Copynumber: 2.1 Consensus size: 150
38617 CCTCCACCAG
* *
38627 TACCAGCACCGCTACCACTTGCACCCCCACCAGCACCACCAGTTGCACCTGCACCACCAGAACCG
1 TACCACCACCGCTACCACTTGCACCACCACCAGCACCACCAGTTGCACCTGCACCACCAGAACCG
* **
38692 CTACCACTTGCACCACCACCAGCACCACCAGTTGCACCTGCATTACCGCTTGCACCACCGCTAAC
66 CTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCATTACCGCCCGCACCACCGCTAAC
* *****
38757 ACCTCCCGTTGCACCTGCAT
131 ACCACCAACACCACCTGCAT
** * * ** *
38777 TACCAGAACCGCTACCGCTTGCACCACCGCCAGCACCACCAGTTGCACCTGCATTACCAGCACCG
1 TACCACCACCGCTACCACTTGCACCACCACCAGCACCACCAGTTGCACCTGCACCACCAGAACCG
* * *
38842 CTACCGCTTGCACCACCACTAACACCACCAGTTGCACCTGCATTACCAGCACCGCTACCACTTGC
66 CTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCATTACC-GC-CCGC-ACCAC-CGC
*
38907 -ACCACCACCAACACCACC-GC-T
127 TAACACCACCAACACCACCTGCAT
*
38928 T-GCACCACCGCT
1 TACCACCACCGCT
38940 TGCACCTGGA
Statistics
Matches: 136, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
150 110 0.81
151 4 0.03
152 4 0.03
153 16 0.12
154 2 0.01
ACGTcount: A:0.25, C:0.47, G:0.13, T:0.15
Consensus pattern (150 bp):
TACCACCACCGCTACCACTTGCACCACCACCAGCACCACCAGTTGCACCTGCACCACCAGAACCG
CTACCACTTGCACCACCACCAACACCACCAGTTGCACCTGCATTACCGCCCGCACCACCGCTAAC
ACCACCAACACCACCTGCAT
Found at i:38989 original size:27 final size:27
Alignment explanation
Indices: 38959--39010 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
38949 ACTACCAGCA
*
38959 CCACCACTAGGAGTGGGAGTAGCACTG
1 CCACCACTAGGAGTAGGAGTAGCACTG
38986 CCACCACTAGGAGTAGGAGTAGCAC
1 CCACCACTAGGAGTAGGAGTAGCAC
39011 CGCCGGTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.31, T:0.13
Consensus pattern (27 bp):
CCACCACTAGGAGTAGGAGTAGCACTG
Found at i:39136 original size:12 final size:12
Alignment explanation
Indices: 39115--39146 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39105 ACCAATGTTG
*
39115 CCAGCACCATTA
1 CCAGCCCCATTA
39127 CCAGCCCCATTA
1 CCAGCCCCATTA
39139 CCAGCCCC
1 CCAGCCCC
39147 GCCACCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.53, G:0.09, T:0.12
Consensus pattern (12 bp):
CCAGCCCCATTA
Found at i:39283 original size:6 final size:6
Alignment explanation
Indices: 39272--39298 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39262 AGCCCTCCTC
39272 CGCCAG CGCCAG CGCCAG CGCCAG CGC
1 CGCCAG CGCCAG CGCCAG CGCCAG CGC
39299 GTGCGTGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.33, T:0.00
Consensus pattern (6 bp):
CGCCAG
Found at i:41171 original size:12 final size:12
Alignment explanation
Indices: 41154--41178 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41144 GAGTTATGAG
41154 CTTATCAAGGGA
1 CTTATCAAGGGA
41166 CTTATCAAGGGA
1 CTTATCAAGGGA
41178 C
1 C
41179 GACATGGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (12 bp):
CTTATCAAGGGA
Found at i:51341 original size:2 final size:2
Alignment explanation
Indices: 51336--51361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51326 ATATATATAT
51336 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
51362 TAAAGCACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57001 original size:28 final size:29
Alignment explanation
Indices: 56947--57001 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
56937 AGCACTACAC
56947 GTAAGAGCCGCAAGAACGTATGCTTGCAA
1 GTAAGAGCCGCAAGAACGTATGCTTGCAA
56976 GTAAGAGCCGCAA-AACGTATGCTTGC
1 GTAAGAGCCGCAAGAACGTATGCTTGC
57002 TCTCTGCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (29 bp):
GTAAGAGCCGCAAGAACGTATGCTTGCAA
Found at i:61982 original size:48 final size:48
Alignment explanation
Indices: 61907--62049 Score: 180
Period size: 48 Copynumber: 3.0 Consensus size: 48
61897 ACCGCCACCC
* * * * * * *
61907 TGGAAGAGGGTTTAAATTTCGATATTGGAAGCGCTATCAGC-TCGTTGT
1 TGGAAGAGGATGTAAATTTTGACATTGGAAGCGCTACCACCAT-ATTGT
*
61955 TGGAAGAGGATGTAAATTTTGACATTGGAAGCGCTGCCACCATATTGT
1 TGGAAGAGGATGTAAATTTTGACATTGGAAGCGCTACCACCATATTGT
* *
62003 TGGAAAAGGATGTAAATTTTGACATTGGAAGCGCTGCCACCATATTG
1 TGGAAGAGGATGTAAATTTTGACATTGGAAGCGCTACCACCATATTG
62050 AAAGAAGAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 84 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (48 bp):
TGGAAGAGGATGTAAATTTTGACATTGGAAGCGCTACCACCATATTGT
Found at i:62296 original size:26 final size:23
Alignment explanation
Indices: 62254--62334 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 23
62244 AAATTTTTTT
**
62254 TTGTTGGAAGGTTGGAAGCGCCA
1 TTGTTGGACCGTTGGAAGCGCCA
*
62277 CTGTTGGATGCCAGTTGGAAGCGCCA
1 TTGTTGGA--CC-GTTGGAAGCGCCA
*
62303 TTATTGCGACCGTTGGAAGCGCCA
1 TTGTTG-GACCGTTGGAAGCGCCA
62327 TTGTTGGA
1 TTGTTGGA
62335 AGCGCCATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 9 0.19
24 18 0.38
25 2 0.04
26 17 0.35
27 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.35, T:0.27
Consensus pattern (23 bp):
TTGTTGGACCGTTGGAAGCGCCA
Found at i:62334 original size:15 final size:16
Alignment explanation
Indices: 62314--62353 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
62304 TATTGCGACC
62314 GTTGGAAGCGCCA-TT
1 GTTGGAAGCGCCATTT
62329 GTTGGAAGCGCCATTT
1 GTTGGAAGCGCCATTT
62345 GTTGGAAGC
1 GTTGGAAGC
62354 ACCAGCGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (16 bp):
GTTGGAAGCGCCATTT
Found at i:62804 original size:114 final size:115
Alignment explanation
Indices: 62588--62807 Score: 313
Period size: 114 Copynumber: 1.9 Consensus size: 115
62578 AATGGAAGAA
* * **
62588 AATATTTTCTTTGAGGTGCAACCCTAGTTTAAAGTGCGACACTCAGGAAATATTCTCTGAGATGC
1 AATATTTTCTTTGAGGTGCAACCCAAGTTTAAAGTGCAACACTCAGGAAATATTCTCCAAGATGC
62653 AACCAAAACTCTAAGGTGCAACACTTCTTACAATTTTTTTTTTGCAGGAT
66 AACCAAAACTCTAAGGTGCAACACTTCTTACAATTTTTTTTTTGCAGGAT
* *
62703 AATATTTTC-TTGAGGTGCGACCCAAGTTTAAAGTGCAATACTCAGGAAATATT-TCCCAAGATG
1 AATATTTTCTTTGAGGTGCAACCCAAGTTTAAAGTGCAACACTCAGGAAATATTCT-CCAAGATG
* * *
62766 CGA-CTAAACTCTAAGGTGCAACAC-TCTTTGCAATTTTTTTTT
65 CAACCAAAACTCTAAGGTGCAACACTTC-TTACAATTTTTTTTT
62808 AGCTCCAGAG
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
112 2 0.02
113 35 0.37
114 48 0.51
115 9 0.10
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (115 bp):
AATATTTTCTTTGAGGTGCAACCCAAGTTTAAAGTGCAACACTCAGGAAATATTCTCCAAGATGC
AACCAAAACTCTAAGGTGCAACACTTCTTACAATTTTTTTTTTGCAGGAT
Done.