Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012099.1 Corchorus capsularis cultivar CVL-1 contig12120, 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: 33968
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:2123 original size:28 final size:26
Alignment explanation
Indices: 2074--2142 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
2064 TTTTTACTCT
2074 TTTCTTACTCT-TTTACTAATTACCC
1 TTTCTTACTCTCTTTACTAATTACCC
* *
2099 TTTCCTTACTCTCTTTCATTGATTACCAC
1 TTT-CTTACTCTCTTT-ACTAATTACC-C
2128 TTT-TTACTCTTCTTT
1 TTTCTTACTC-TCTTT
2143 TTTTCTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 9 0.24
28 13 0.35
29 4 0.11
ACGTcount: A:0.16, C:0.28, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTCTTACTCTCTTTACTAATTACCC
Found at i:2284 original size:14 final size:14
Alignment explanation
Indices: 2267--2294 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2257 ATCATTCTTC
2267 CTTTACTGATTACT
1 CTTTACTGATTACT
2281 CTTTACTGATTACT
1 CTTTACTGATTACT
2295 TTTGCCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
CTTTACTGATTACT
Found at i:2303 original size:14 final size:13
Alignment explanation
Indices: 2268--2311 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
2258 TCATTCTTCC
2268 TTTACTGATTACT
1 TTTACTGATTACT
2281 CTTTACTGATTACT
1 -TTTACTGATTACT
* *
2295 TTTGCCTGAATACT
1 TTT-ACTGATTACT
2309 TTT
1 TTT
2312 TACTACTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 3 0.11
14 24 0.89
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.52
Consensus pattern (13 bp):
TTTACTGATTACT
Found at i:2398 original size:26 final size:25
Alignment explanation
Indices: 2369--2466 Score: 97
Period size: 26 Copynumber: 3.6 Consensus size: 25
2359 CTCTTTACCG
2369 ATTACTATTTTACTCTCTTGAATTTA
1 ATTACTATTTTACTCT-TTGAATTTA
2395 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTT-ACTCTTTGAATTTA
*
2421 ATCACCATTTGTCATTTTACTCTTTGAATTTA
1 ATTA-C-----T-ATTTTACTCTTTGAATTTA
*
2453 ATTACCATTTTACT
1 ATTACTATTTTACT
2467 ATTTTATTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
25 8 0.13
26 23 0.38
27 6 0.10
31 1 0.02
32 18 0.30
33 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTACTATTTTACTCTTTGAATTTA
Found at i:2478 original size:33 final size:33
Alignment explanation
Indices: 2396--2478 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
2386 TTGAATTTAA
2396 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACTATTTT-ACTCTTTGAATTTAATCACCATT
*
2430 TGT-C-ATTTTACTCTTTGAATTTAATTACCATT
1 T-TACTATTTTACTCTTTGAATTTAATCACCATT
*
2462 TTACTATTTTATTCTTT
1 TTACTATTTTACTCTTT
2479 ACCGATTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.55
33 16 0.36
34 2 0.05
35 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.55
Consensus pattern (33 bp):
TTACTATTTTACTCTTTGAATTTAATCACCATT
Found at i:2654 original size:28 final size:30
Alignment explanation
Indices: 2577--2654 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 30
2567 ACCATTTTAC
* *
2577 TGATTACTCCTTTTACTTTACTCTTAATTCTAC
1 TGATTACTTCTTTT--TTTACTCTT-ATTCTAA
* * *
2610 TGATCACTTCCTATTTTA-TCTT-TTCTAA
1 TGATTACTTCTTTTTTTACTCTTATTCTAA
2638 TGATTACTTCTTTTTTT
1 TGATTACTTCTTTTTTT
2655 TAATTTATCC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
28 19 0.51
30 4 0.11
31 4 0.11
33 10 0.27
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (30 bp):
TGATTACTTCTTTTTTTACTCTTATTCTAA
Found at i:2880 original size:38 final size:39
Alignment explanation
Indices: 2783--2880 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
2773 TTTGACCCTT
* * * *
2783 AATTACTGATTGCTACTTTTACTTCCTCTCTTAGTTATC
1 AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
* * *
2822 AATTTACTAATTAATCCTTTTACTT-C-CTCTTAATCACC
1 AA-TTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
2860 AATTGACTGATTACTACTTTT
1 AATT-ACTGATTACTACTTTT
2881 TATCTTTTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
37 2 0.04
38 24 0.51
39 3 0.06
40 18 0.38
ACGTcount: A:0.26, C:0.22, G:0.05, T:0.47
Consensus pattern (39 bp):
AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
Found at i:6395 original size:15 final size:16
Alignment explanation
Indices: 6377--6412 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
6367 TAGGCCCAGT
6377 TTTTTTCTTTTC-TTC
1 TTTTTTCTTTTCTTTC
6392 TTTTTTCTTTTCTTTC
1 TTTTTTCTTTTCTTTC
6408 TTTTT
1 TTTTT
6413 GCGACCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTCTTTTCTTTC
Found at i:13474 original size:241 final size:241
Alignment explanation
Indices: 13051--13533 Score: 957
Period size: 241 Copynumber: 2.0 Consensus size: 241
13041 CATGAAGCTG
13051 TACATCAGGAACTTATCATCAGTGGAAAAGGGTGCCATCTTGTTCTGAAAACTGAGCACGTGGTC
1 TACATCAGGAACTTATCATCAGTGGAAAAGGGTGCCATCTTGTTCTGAAAACTGAGCACGTGGTC
13116 CCTAAGGTTTTTTTGTTCCATCGTACTTTTCAAAATCTGGCATTTTGAATTTCTGGGGGATGACT
66 CCTAAGGTTTTTTTGTTCCATCGTACTTTTCAAAATCTGGCATTTTGAATTTCTGGGGGATGACT
13181 ACCCCTTTTGCCACAGCAGTGCTTGTGATATTGGGGATTCCATAGTCCTGGATTCCATCTACACT
131 ACCCCTTTTGCCACAGCAGTGCTTGTGATATTGGGGATTCCATAGTCCTGGATTCCATCTACACT
13246 CCTTAGTCTGTCTTCTATTCGGCCTTCAATCTTCTGCCAAAACTTT
196 CCTTAGTCTGTCTTCTATTCGGCCTTCAATCTTCTGCCAAAACTTT
13292 TACATCAGGAACTTATCATCAGTGGAAAAGGGTGCCATCTTGTTCTGAAAACTGAGCACGTGGTC
1 TACATCAGGAACTTATCATCAGTGGAAAAGGGTGCCATCTTGTTCTGAAAACTGAGCACGTGGTC
13357 CCTAAGGTTTTTTTGTTCCATCGTACTTTTCAAAATCTGGCATTTTGAATTTCTGGGGGATGACT
66 CCTAAGGTTTTTTTGTTCCATCGTACTTTTCAAAATCTGGCATTTTGAATTTCTGGGGGATGACT
*
13422 ACCCCTTTTGCCACAGCAGTGCTTGTGATATTGGGGATTCCATAGTCCTGGATTCCATCTACGCT
131 ACCCCTTTTGCCACAGCAGTGCTTGTGATATTGGGGATTCCATAGTCCTGGATTCCATCTACACT
13487 CCTTAGTCTGTCTTCTATTCGGCCTTCAATCTTCTGCCAAAACTTT
196 CCTTAGTCTGTCTTCTATTCGGCCTTCAATCTTCTGCCAAAACTTT
13533 T
1 T
13534 CCTCTTCGGC
Statistics
Matches: 241, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 241 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (241 bp):
TACATCAGGAACTTATCATCAGTGGAAAAGGGTGCCATCTTGTTCTGAAAACTGAGCACGTGGTC
CCTAAGGTTTTTTTGTTCCATCGTACTTTTCAAAATCTGGCATTTTGAATTTCTGGGGGATGACT
ACCCCTTTTGCCACAGCAGTGCTTGTGATATTGGGGATTCCATAGTCCTGGATTCCATCTACACT
CCTTAGTCTGTCTTCTATTCGGCCTTCAATCTTCTGCCAAAACTTT
Found at i:14497 original size:63 final size:62
Alignment explanation
Indices: 14408--14633 Score: 220
Period size: 63 Copynumber: 3.5 Consensus size: 62
14398 GACATCCACC
* * * * *
14408 TAGTCTGGACATATCATACACTGCTGAATAATACCATAAATTCCGAGTACACAATTAAACACA
1 TAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACTCCGAGTACA-AATTAAACACA
* * *
14471 TAGTCTGAAAATAGCATCCACTGCTGAATAATACCATAAACTCCGAATACAAGTATTGAATAATA
1 TAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACTCCGAGTACAA--ATT--A-AA-C
14536 ACA
60 ACA
* * * * *
14539 TAGTCTGGAAACACCATCCCCTACTGAATAATACCATAAACTCCGAGTACATAATTAAACATA
1 TAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACTCCGAGTACA-AATTAAACACA
* *
14602 TGGTCTGAAAAATACCA-CCAACTACTGAATAA
1 TAGTCTG-AAAATACCATCC-ACTGCTGAATAA
14634 CACATTGTCT
Statistics
Matches: 135, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 55 0.41
64 23 0.17
65 1 0.01
66 1 0.01
67 5 0.04
68 48 0.36
69 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (62 bp):
TAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACTCCGAGTACAAATTAAACACA
Found at i:18155 original size:35 final size:35
Alignment explanation
Indices: 18115--18363 Score: 239
Period size: 35 Copynumber: 6.9 Consensus size: 35
18105 TAAGCCCTTT
* *
18115 ATTTACTTAATTATACCGAATTAAGTCAATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
* * * *
18150 ATTTACTTAATTATACTGAATTAAGTTGATTACCG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
* **
18185 GTTTACTTAATTACACCGAATTAAGTTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
* * *
18220 ATTTACTTAATTACACCGAATTAGGTTGATTATTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
* * * *
18255 ATTCACTTAATTACACCGGATTAAGTTAATTGCCAG
1 ATTTACTTAATTACACCGAATTAAGTTAATT-ACTG
* * *
18291 A-TTATTTAATTACCAATACCCCAAATTAAGTTGATTACTG
1 ATTTACTTAATTA-C---A--CCGAATTAAGTTAATTACTG
* *
18331 ATTTACTTAACTACACCGAATTAAGTTGATTAC
1 ATTTACTTAATTACACCGAATTAAGTTAATTAC
18364 CAAATAACTT
Statistics
Matches: 174, Mismatches: 32, Indels: 16
0.78 0.14 0.07
Matches are distributed among these distances:
35 143 0.82
36 3 0.02
37 1 0.01
39 1 0.01
40 4 0.02
41 22 0.13
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACTG
Found at i:18195 original size:70 final size:70
Alignment explanation
Indices: 18115--18377 Score: 276
Period size: 70 Copynumber: 3.7 Consensus size: 70
18105 TAAGCCCTTT
* * ** * *
18115 ATTTACTTAATTATACCGAATTAAGTCAATTACTGATTTACTTAATTATACTGAATTAAGTTGAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGAT
18180 TACCG
66 TACCG
* *
18185 GTTTACTTAATTACACCGAATTAAGTTAATTACCAATTTACTTAATTACACCGAATTAGGTTGAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGAT
**
18250 TATTG
66 TACCG
* * * * *
18255 ATTCACTTAATTACACCGGATTAAGTTAATTGCCAGA-TTATTTAATTACCAATACCCCAAATTA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCA-ATTTACTTAATTA-C---A--CCGAATTA
*
18319 AGTTGATTACTG
59 AGTTGATTACCG
* * * *
18331 ATTTACTTAACTACACCGAATTAAGTTGATTACCAAATAACTTAATT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCAATTTACTTAATT
18378 TAATTATCAG
Statistics
Matches: 160, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
70 101 0.63
71 2 0.01
74 1 0.01
75 1 0.01
76 55 0.34
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (70 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACCAATTTACTTAATTACACCGAATTAAGTTGAT
TACCG
Found at i:18215 original size:19 final size:19
Alignment explanation
Indices: 18191--18285 Score: 67
Period size: 19 Copynumber: 5.3 Consensus size: 19
18181 ACCGGTTTAC
18191 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
* *
18210 TTAATT--ACC-AATTTAC
1 TTAATTACACCGAATTAAG
*
18226 TTAATTACACCGAATTAGG
1 TTAATTACACCGAATTAAG
* ** * *
18245 TTGATT--ATTG-ATTCAC
1 TTAATTACACCGAATTAAG
*
18261 TTAATTACACCGGATTAAG
1 TTAATTACACCGAATTAAG
18280 TTAATT
1 TTAATT
18286 GCCAGATTAT
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
16 19 0.35
17 5 0.09
18 5 0.09
19 25 0.46
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
TTAATTACACCGAATTAAG
Found at i:18229 original size:16 final size:17
Alignment explanation
Indices: 18115--18233 Score: 64
Period size: 16 Copynumber: 6.8 Consensus size: 17
18105 TAAGCCCTTT
18115 ATTTACTTAATTATACCGA
1 ATTTACTTAA-T-TACCGA
* * * *
18134 ATTAAGTCAATTACTG-
1 ATTTACTTAATTACCGA
*
18150 ATTTACTTAATTATACTGA
1 ATTTACTTAA-T-TACCGA
* * *
18169 ATTAAGTTGATTACCG-
1 ATTTACTTAATTACCGA
*
18185 GTTTACTTAATTACACCGA
1 ATTTACTTAATT--ACCGA
* *
18204 ATTAAGTTAATTACC-A
1 ATTTACTTAATTACCGA
18220 ATTTACTTAATTAC
1 ATTTACTTAATTAC
18234 ACCGAATTAG
Statistics
Matches: 74, Mismatches: 20, Indels: 15
0.68 0.18 0.14
Matches are distributed among these distances:
16 28 0.38
17 12 0.16
18 11 0.15
19 23 0.31
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.41
Consensus pattern (17 bp):
ATTTACTTAATTACCGA
Found at i:18300 original size:105 final size:108
Alignment explanation
Indices: 18115--18363 Score: 279
Period size: 105 Copynumber: 2.3 Consensus size: 108
18105 TAAGCCCTTT
* ** * * * *
18115 ATTTACTTAATTATACCGAATTAAGTCAATTACTGATTTACTTAATTATACTGAATTAAGTTGAT
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTGATTCACTTAATTACACCGAATTAAGTTAAT
* * *
18180 TACCGGTTTACTTAATTA-C-A-CCGAATTAAGTTAATTACCA
66 TACCAGATTACTTAATTACCAACCCAAATTAAGTTAATTACCA
* * *
18220 ATTTACTTAATTACACCGAATTAGGTTGATTATTGATTCACTTAATTACACCGGATTAAGTTAAT
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTGATTCACTTAATTACACCGAATTAAGTTAAT
* * * **
18285 TGCCAGATTATTTAATTACCAATACCCCAAATTAAGTTGATTACTG
66 TACCAGATTACTTAATTACC-A-A-CCCAAATTAAGTTAATTACCA
*
18331 ATTTACTTAACTACACCGAATTAAGTTGATTAC
1 ATTTACTTAATTACACCGAATTAAGTTGATTAC
18364 CAAATAACTT
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
105 69 0.59
106 1 0.01
109 1 0.01
111 46 0.39
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (108 bp):
ATTTACTTAATTACACCGAATTAAGTTGATTACTGATTCACTTAATTACACCGAATTAAGTTAAT
TACCAGATTACTTAATTACCAACCCAAATTAAGTTAATTACCA
Found at i:18477 original size:43 final size:43
Alignment explanation
Indices: 18416--18531 Score: 180
Period size: 43 Copynumber: 2.7 Consensus size: 43
18406 AATTAAGCTG
* *
18416 ATTACC-ATCTTATTTAATTACACTGAATTAAGTTGTTTACCAA
1 ATTACCAAT-TTACTTAATTACACCGAATTAAGTTGTTTACCAA
*
18459 ATTGCCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAA
1 ATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAA
*
18502 ATTACCAATTTACTTAATTACGCCGAATTA
1 ATTACCAATTTACTTAATTACACCGAATTA
18532 CTTAATTACA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
43 65 0.97
44 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (43 bp):
ATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAA
Found at i:18534 original size:18 final size:18
Alignment explanation
Indices: 18511--18549 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
18501 AATTACCAAT
*
18511 TTACTTAATTACGCCGAA
1 TTACTTAATTACACCGAA
18529 TTACTTAATTACACCGAA
1 TTACTTAATTACACCGAA
18547 TTA
1 TTA
18550 AGTTGTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (18 bp):
TTACTTAATTACACCGAA
Found at i:18538 original size:61 final size:61
Alignment explanation
Indices: 18468--18952 Score: 255
Period size: 61 Copynumber: 8.0 Consensus size: 61
18458 AATTGCCAAT
*
18468 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACGCCGAA
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAA
**
18529 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCGTTTTACTTAATTACACCGAA
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAA
* * * * *** ** * * *
18590 TTAAGTT-GTT-TACCAAATTACCAT-TTTACTTAATTACACCGAATTAAGTTGATTACCATCTT
1 TT-ACTTAATTACACCGAATTAAGTTGTTTACCAAATT--ACC-AATTTACTTAATTA-CA-C--
18652 ACTTG-A
58 -C--GAA
* * * *
18658 TCTACTCAATTACACCGAATTAAGTCGTTTACCAAATTA-C--TTAATTTAA-T-CACC-AA
1 T-TACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAA
*
18714 TTTACTTAATTACACCGAATTAAGTTG--------ATTACCAATTTACTTAATTACACTGAA
1 -TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAA
* * * * * *
18768 TTACTTAATTACACCGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAA
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAA
* ** * * ** * **** *
18829 TTAAGTTGGTT--ACC-AATTTACTTAATTACAACGAATTAAGTTGTTTA-GTAGATT--ACC-A
1 TT-ACTTAATTACACCGAATTAAGTTGTTTAC--CAAATT-ACCAATTTACTTA-ATTACACCGA
18887 A
61 A
* *
18888 TTTACTTAATTACACCGAATTTAGTTGTTTACCAAATTACTAATTTACTTAATTACACCGAA
1 -TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAA
18950 TTA
1 TTA
18953 AGTTGTTTAC
Statistics
Matches: 311, Mismatches: 69, Indels: 88
0.66 0.15 0.19
Matches are distributed among these distances:
48 4 0.01
49 1 0.00
51 7 0.02
52 1 0.00
53 28 0.09
54 2 0.01
56 24 0.08
57 1 0.00
58 1 0.00
59 35 0.11
60 24 0.08
61 104 0.33
62 40 0.13
63 2 0.01
64 2 0.01
65 7 0.02
67 1 0.00
68 5 0.02
69 5 0.02
70 8 0.03
71 9 0.03
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (61 bp):
TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAA
Found at i:18549 original size:104 final size:104
Alignment explanation
Indices: 18429--18635 Score: 360
Period size: 104 Copynumber: 2.0 Consensus size: 104
18419 ACCATCTTAT
* *
18429 TTAATTACACTGAATTAAGTTGTTTACCAAATTGCCAATTTACTTAATTACACCGAATTAAGTTG
1 TTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAATTAAGTTG
*
18494 TTTACCAAATTACCAATTTACTTAATTACGCCGAATTAC
66 TTTACCAAATTACCAATTTACTTAATTACACCGAATTAC
**
18533 TTAATTACACCGAATTAAGTTGTTTACCAAATTACCGTTTTACTTAATTACACCGAATTAAGTTG
1 TTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAATTAAGTTG
*
18598 TTTACCAAATTACCATTTTACTTAATTACACCGAATTA
66 TTTACCAAATTACCAATTTACTTAATTACACCGAATTA
18636 AGTTGATTAC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 97 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (104 bp):
TTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACACCGAATTAAGTTG
TTTACCAAATTACCAATTTACTTAATTACACCGAATTAC
Found at i:18567 original size:35 final size:38
Alignment explanation
Indices: 18528--18964 Score: 175
Period size: 43 Copynumber: 10.9 Consensus size: 38
18518 ATTACGCCGA
18528 ATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCGT
1 ATTACTTAATTACACCGAATTAAGTTGTTTACC-AA-TA---T
*
18571 TTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAT
1 ATTACTTAATTACACCGAATTAAGTTGTTTACC-AA-T---AT
* * *
18614 TTTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTT
1 ATTACTTAATTACACCGAATTAAGTTGTTTACCA--ATA--T
* *
18656 GATCTACTCAATTACACCGAATTAAGTCGTTTACC-A-A-
1 -AT-TACTTAATTACACCGAATTAAGTTGTTTACCAATAT
* * * *
18693 ATTACTTAATTTAATCACC-AATTTACTTAATTACACCGAAT-T
1 ATTACTTAA-TT-A-CACCGAATTAAGTT-GTT-TACC-AATAT
* * * * ** *
18735 A--AGTTGATT--ACC-AATTTACTTAATTA-CACTGA-
1 ATTACTTAATTACACCGAATTAAGTTGTTTACCAAT-AT
* *
18767 ATTACTTAATTACACCGAATCAAGTTGTTTACCAAACTACCA
1 ATTACTTAATTACACCGAATTAAGTTGTTTACC-AA-TA--T
* * * *
18809 ATTCACCTAATTAAACCAAATTAAGTTGGTTACC-A-AT
1 ATT-ACTTAATTACACCGAATTAAGTTGTTTACCAATAT
* ** *
18846 -TTACTTAATTACAACGAATTAAGTTGTTTAGTAGATTACCA
1 ATTACTTAATTACACCGAATTAAGTTGTTTACCA-A-TA--T
*
18887 ATTTACTTAATTACACCGAATTTAGTTGTTTACCAAATTACT
1 A-TTACTTAATTACACCGAATTAAGTTGTTTACC-AA-TA-T
18929 AATTTACTTAATTACACCGAATTAAGTTGTTTACCA
1 -A-TTACTTAATTACACCGAATTAAGTTGTTTACCA
18965 GTTTACTAAT
Statistics
Matches: 305, Mismatches: 47, Indels: 85
0.70 0.11 0.19
Matches are distributed among these distances:
31 2 0.01
32 2 0.01
33 1 0.00
34 8 0.03
35 41 0.13
36 9 0.03
37 17 0.06
38 7 0.02
39 9 0.03
40 7 0.02
41 2 0.01
42 8 0.03
43 162 0.53
44 29 0.10
46 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.38
Consensus pattern (38 bp):
ATTACTTAATTACACCGAATTAAGTTGTTTACCAATAT
Found at i:18582 original size:43 final size:43
Alignment explanation
Indices: 18529--18697 Score: 248
Period size: 43 Copynumber: 3.9 Consensus size: 43
18519 TTACGCCGAA
18529 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCGTT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCGTT
*
18572 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCATT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCGTT
* ** * *
18615 TTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTGAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC-CGTT
* * *
18659 CTACTCAATTACACCGAATTAAGTCGTTTACCAAATTAC
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
18698 TTAATTTAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 78 0.70
44 34 0.30
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (43 bp):
TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCGTT
Found at i:18636 original size:86 final size:87
Alignment explanation
Indices: 18529--18697 Score: 259
Period size: 87 Copynumber: 2.0 Consensus size: 87
18519 TTACGCCGAA
* * * *
18529 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC-CGTTTTACTTAATTACACCGAATTA
1 TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTCGATCTACTCAATTACACCGAATTA
*
18593 AGTTGTTTACCAAATTACCATT
66 AGTCGTTTACCAAATTACCATT
** *
18615 TTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTGATCTACTCAATTACACCGAATTA
1 TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTCGATCTACTCAATTACACCGAATTA
18680 AGTCGTTTACCAAATTAC
66 AGTCGTTTACCAAATTAC
18698 TTAATTTAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 36 0.49
87 38 0.51
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (87 bp):
TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTCGATCTACTCAATTACACCGAATTA
AGTCGTTTACCAAATTACCATT
Found at i:18758 original size:239 final size:230
Alignment explanation
Indices: 18463--18934 Score: 577
Period size: 239 Copynumber: 2.0 Consensus size: 230
18453 TACCAAATTG
*
18463 CCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTACGCCGA
1 CCAATTTACTTAATTACACCGAATTAAGTTG-------AATTACCAATTTACTTAATTACACCGA
* * ** * * * *
18528 ATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCGTTTTACTTAATTACACCGAATTA
59 ATTACTTAATTACACCGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATTA
* * ** **
18593 AGTTGTTTACCAAATTACCATTTTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTGA
124 AGTTGGTTACC-----A--A-TTTACTTAATTACAACGAATTAAGTTGATTACCAGATTAC-CAA
18658 TCTACTCAATTACACCGAATTAAGTCGTTTACCAAATTACTTAATTTAATCA
180 TCTACTCAATTACACCGAATTAAGTCGTTTACCAAATTAC-TAATTTAATCA
*
18710 CCAATTTACTTAATTACACCGAATTAAGTTG-ATTACCAATTTACTTAATTACACTGAATTACTT
1 CCAATTTACTTAATTACACCGAATTAAGTTGAATTACCAATTTACTTAATTACACCGAATTACTT
18774 AATTACACCGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATTAAGTTGGT
66 AATTACACCGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATTAAGTTGGT
* ** * *
18839 TACCAATTTACTTAATTACAACGAATTAAGTTGTTTAGTAGATTACCAATTTACTTAATTACACC
131 TACCAATTTACTTAATTACAACGAATTAAGTTGATTACCAGATTACCAATCTACTCAATTACACC
* *
18904 GAATTTAGTTGTTTACCAAATTACTAATTTA
196 GAATTAAGTCGTTTACCAAATTACTAATTTA
18935 CTTAATTACA
Statistics
Matches: 202, Mismatches: 23, Indels: 18
0.83 0.09 0.07
Matches are distributed among these distances:
229 7 0.03
230 37 0.18
231 34 0.17
232 1 0.00
234 1 0.00
239 91 0.45
247 31 0.15
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (230 bp):
CCAATTTACTTAATTACACCGAATTAAGTTGAATTACCAATTTACTTAATTACACCGAATTACTT
AATTACACCGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATTAAGTTGGT
TACCAATTTACTTAATTACAACGAATTAAGTTGATTACCAGATTACCAATCTACTCAATTACACC
GAATTAAGTCGTTTACCAAATTACTAATTTAATCA
Found at i:18773 original size:18 final size:18
Alignment explanation
Indices: 18692--18786 Score: 81
Period size: 18 Copynumber: 5.2 Consensus size: 18
18682 TCGTTTACCA
18692 AATTACTTAATTTAATCACC-
1 AATTACTTAA-TT-A-CACCG
18712 AATTTACTTAATTACACCG
1 AA-TTACTTAATTACACCG
* *
18731 AATTAAGTTGATT--ACC-
1 AATT-ACTTAATTACACCG
*
18747 AATTTACTTAATTACACTG
1 AA-TTACTTAATTACACCG
18766 AATTACTTAATTACACCG
1 AATTACTTAATTACACCG
18784 AAT
1 AAT
18787 CAAGTTGTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
16 8 0.13
17 5 0.08
18 26 0.42
19 11 0.18
20 4 0.06
21 8 0.13
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTACTTAATTACACCG
Found at i:18799 original size:53 final size:56
Alignment explanation
Indices: 18660--18802 Score: 195
Period size: 56 Copynumber: 2.6 Consensus size: 56
18650 TTACTTGATC
* *
18660 TACTCAATTACACCGAATTAAGTCGTTTACCAAATTACTTAATTTAATCACCAATT
1 TACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATT
* * *
18716 TACTTAATTACACCGAATTAAGTTGATTACCAATTTACTTAA-TT-A-CACTGAA-T
1 TACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCAC-CAATT
*
18769 TACTTAATTACACCGAATCAAGTTGTTTACCAAA
1 TACTTAATTACACCGAATTAAGTTGTTTACCAAA
18803 CTACCAATTC
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
53 35 0.45
54 3 0.04
55 2 0.03
56 38 0.49
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (56 bp):
TACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATT
Found at i:18835 original size:43 final size:43
Alignment explanation
Indices: 18768--18964 Score: 221
Period size: 43 Copynumber: 4.8 Consensus size: 43
18758 TTACACTGAA
* *
18768 TTACTTAATTACACCGAATCAAGTTGTTTACCAAACTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* * * * *
18811 TCACCTAATTAAACCAAATTAAGTTG--------GTTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* ** *
18846 TTACTTAATTACAACGAATTAAGTTGTTTAGTAGATTACCAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
* *
18889 TTACTTAATTACACCGAATTTAGTTGTTTACCAAATTACTAAT
1 TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
18932 TTACTTAATTACACCGAATTAAGTTGTTTACCA
1 TTACTTAATTACACCGAATTAAGTTGTTTACCA
18965 GTTTACTAAT
Statistics
Matches: 126, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
35 28 0.22
43 98 0.78
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (43 bp):
TTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAAT
Found at i:18855 original size:78 final size:78
Alignment explanation
Indices: 18766--18932 Score: 210
Period size: 78 Copynumber: 2.2 Consensus size: 78
18756 AATTACACTG
*
18766 AATTACTTAATTACACCGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATT
1 AATTACTTAATTACAACGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATT
18831 AAGTTGGTTACCA
66 AAGTTGGTTACCA
* * ** * * * * * *
18844 ATTTACTTAATTACAACGAATTAAGTTGTTTAGTAGATTACCAATTTACTTAATTACACCGAATT
1 AATTACTTAATTACAACGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATT
* *
18909 TAGTTGTTTACCA
66 AAGTTGGTTACCA
18922 AATTAC-TAATT
1 AATTACTTAATT
18933 TACTTAATTA
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
77 5 0.07
78 70 0.93
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (78 bp):
AATTACTTAATTACAACGAATCAAGTTGTTTACCAAACTACCAATTCACCTAATTAAACCAAATT
AAGTTGGTTACCA
Found at i:19034 original size:21 final size:21
Alignment explanation
Indices: 18985--19041 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
18975 TTTATCACCA
18985 ATTT-ACTTAATTA-C-ACCG
1 ATTTAACTTAATTACCAACCG
* * *
19003 AATTAAGTTAATTACCAACTG
1 ATTTAACTTAATTACCAACCG
19024 ATTTAACTTAATTACCAA
1 ATTTAACTTAATTACCAA
19042 TTTACTGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 3 0.10
19 8 0.26
20 1 0.03
21 19 0.61
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (21 bp):
ATTTAACTTAATTACCAACCG
Found at i:19053 original size:55 final size:55
Alignment explanation
Indices: 18922--19047 Score: 153
Period size: 55 Copynumber: 2.3 Consensus size: 55
18912 TTGTTTACCA
* ** ** * *
18922 AATTACTAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGTTTACTAATTT
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTAATTACCAACTGACTAACTT
* * *
18977 TATCACCAATTTACTTAATTACACCGAATTAAGTTAATTACCAACTGATTTAACTT
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTAATTACCAACTGA-CTAACTT
19033 AATTACCAATTTACT
1 AATTACCAATTTACT
19048 GATTACTATT
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
55 40 0.69
56 18 0.31
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (55 bp):
AATTACCAATTTACTTAATTACACCGAATTAAGTTAATTACCAACTGACTAACTT
Found at i:19901 original size:19 final size:19
Alignment explanation
Indices: 19877--19975 Score: 58
Period size: 19 Copynumber: 5.2 Consensus size: 19
19867 CAAACTTTTA
*
19877 ATTCAAAGGTTAAATCTTT
1 ATTCAAAGATTAAATCTTT
*** *
19896 ATTCAACCTTTTAATCTTTT
1 ATTCAAAGATTAAATC-TTT
* **
19916 ATTCAAAGATT-ACTAATT
1 ATTCAAAGATTAAATCTTT
* *
19934 ACTT-AAAAATTCAATCTTTT
1 A-TTCAAAGATTAAATC-TTT
*
19954 ATTCAAAGGTTAAATCTTT
1 ATTCAAAGATTAAATCTTT
19973 ATT
1 ATT
19976 TACTAATTAC
Statistics
Matches: 58, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
18 9 0.16
19 26 0.45
20 23 0.40
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTCAAAGATTAAATCTTT
Found at i:19971 original size:20 final size:20
Alignment explanation
Indices: 19860--19972 Score: 67
Period size: 20 Copynumber: 5.8 Consensus size: 20
19850 TTAATGGCCT
19860 AAAGGTTCAAA-CTTTTAATTC
1 AAAGGTT-AAATCTTTT-ATTC
19881 AAAGGTTAAATC-TTTATTC
1 AAAGGTTAAATCTTTTATTC
*** *
19900 AACCTTTTAATCTTTTATTC
1 AAAGGTTAAATCTTTTATTC
* *
19920 AAAGATT--A-CTAATTACTT-
1 AAAGGTTAAATCT-TTTA-TTC
** *
19938 AAAAATTCAATCTTTTATTC
1 AAAGGTTAAATCTTTTATTC
19958 AAAGGTTAAATCTTT
1 AAAGGTTAAATCTTT
19973 ATTTACTAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
17 2 0.03
18 10 0.14
19 16 0.23
20 33 0.46
21 10 0.14
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.43
Consensus pattern (20 bp):
AAAGGTTAAATCTTTTATTC
Found at i:22214 original size:24 final size:24
Alignment explanation
Indices: 22187--22263 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
22177 GTGAATTTAT
22187 TATTTGTGTAAAAAGGAACTGTAA
1 TATTTGTGTAAAAAGGAACTGTAA
* * * *
22211 TATTTGTTTATAGAAAAATGAA-TCTAT
1 TATTTG--TGT--AAAAAGGAACTGTAA
22238 TATTTGTGTAAAAAGGAACTGTAA
1 TATTTGTGTAAAAAGGAACTGTAA
22262 TA
1 TA
22264 CTAAATGATG
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
23 8 0.20
24 11 0.28
25 2 0.05
26 2 0.05
27 9 0.22
28 8 0.20
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (24 bp):
TATTTGTGTAAAAAGGAACTGTAA
Found at i:22243 original size:51 final size:51
Alignment explanation
Indices: 22167--22263 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
22157 TCCTTGTAAC
* * *
22167 TTATAGGAAAGTGAATTTATTATTTGTGTAAAAAGGAACTGTAATATTTGT
1 TTATAGAAAAATGAATCTATTATTTGTGTAAAAAGGAACTGTAATATTTGT
22218 TTATAGAAAAATGAATCTATTATTTGTGTAAAAAGGAACTGTAATA
1 TTATAGAAAAATGAATCTATTATTTGTGTAAAAAGGAACTGTAATA
22264 CTAAATGATG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (51 bp):
TTATAGAAAAATGAATCTATTATTTGTGTAAAAAGGAACTGTAATATTTGT
Found at i:28073 original size:33 final size:33
Alignment explanation
Indices: 27988--28080 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
27978 TTTTAGATGT
* ** * *
27988 TGTTTGCGATGATACTAAACCTAATTTGAGTGT
1 TGTTTGCGATGATACTAAATCTGTTTTAAGTGA
* **
28021 TGTTTGCAATGGCACTAAATCTGTTTTAAGTGA
1 TGTTTGCGATGATACTAAATCTGTTTTAAGTGA
*
28054 TGTTTGTGATGATACTAAATCTGTTTT
1 TGTTTGCGATGATACTAAATCTGTTTT
28081 GGATGCTAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (33 bp):
TGTTTGCGATGATACTAAATCTGTTTTAAGTGA
Found at i:28146 original size:33 final size:33
Alignment explanation
Indices: 28109--28214 Score: 151
Period size: 33 Copynumber: 3.2 Consensus size: 33
28099 AAACAAATCT
28109 GTTTTGGTTGATCATAGCATTGCAAATAATTCA
1 GTTTTGGTTGATCATAGCATTGCAAATAATTCA
* *
28142 GTTTTGGTTGATCATAGCATTGCATATAACTCTA
1 GTTTTGGTTGATCATAGCATTGCAAATAATTC-A
* * *
28176 -TTTTGGTTGATCATAACATTGAAAATAATTCT
1 GTTTTGGTTGATCATAGCATTGCAAATAATTCA
28208 GTTTTGG
1 GTTTTGG
28215 GTGAAAAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
33 63 0.98
34 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (33 bp):
GTTTTGGTTGATCATAGCATTGCAAATAATTCA
Found at i:28629 original size:30 final size:30
Alignment explanation
Indices: 28593--28651 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28583 TAAGGGGGAG
28593 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
28623 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
28652 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:31259 original size:41 final size:41
Alignment explanation
Indices: 31211--31289 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
31201 TTTGATAATC
* * *
31211 AAGAGTCAAGGTAAGAGAA-TAATCAGTGAAATTAGTAATTA
1 AAGAGTCAAAGTAAAAAAAGTAATCAGT-AAATTAGTAATTA
*
31252 AAGAGTCAAAGTAAAAAAAGTAATCAGTAAATTGGTAA
1 AAGAGTCAAAGTAAAAAAAGTAATCAGTAAATTAGTAA
31290 AGAGTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 25 0.76
42 8 0.24
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (41 bp):
AAGAGTCAAAGTAAAAAAAGTAATCAGTAAATTAGTAATTA
Found at i:31343 original size:22 final size:22
Alignment explanation
Indices: 31298--31343 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31288 AAAGAGTAAA
*
31298 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAAGAAAGT
*
31320 AATCAGTAAAGAGTAA-AATAGT
1 AATCAGTAAAAAGTAAGAA-AGT
31342 AA
1 AA
31344 AAAGTGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.20
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAGAAAGT
Found at i:31382 original size:22 final size:22
Alignment explanation
Indices: 31354--31788 Score: 200
Period size: 22 Copynumber: 19.1 Consensus size: 22
31344 AAAGTGATAA
31354 TAATCAGTAAAAAGTAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
* *
31376 TAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
*
31397 TAATCAGTAAAGAGT-AAA---
1 TAATCAGTAAAAAGTAAAATGG
31415 -AATCAGTAAAAAGTAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
* *
31436 TAATCAGTAAAGAGTAAAATCG
1 TAATCAGTAAAAAGTAAAATGG
**
31458 TAAAAAGTGATAATAATCAGTAAAA-GG
1 TAATCA--G-TAA-AA--AGTAAAATGG
*
31485 TAAAAT-GGTAATCAGTAAG-AGCACAATGG
1 T--AATCAGTAA--A--AAGTA--A-AATGG
*
31514 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
* * *
31536 TAATCAGT-AAGAGCACAATGG
1 TAATCAGTAAAAAGTAAAATGG
*
31557 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
* *
31579 TAATCAGT-AACAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
* *
31600 TAATCAGTAAAGAGTAAAATCG
1 TAATCAGTAAAAAGTAAAATGG
**
31622 TAAAAAGTGATAATAATCAGTAAAATGTAAAATGG
1 TAATCA--G-TAA-AA--AGT-AAA------ATGG
* * *
31657 TAATTAGT-AAGAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
** *
31678 TAATCAGTAAAGGGTTAAA-GG
1 TAATCAGTAAAAAGTAAAATGG
* *
31699 TAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGG
**
31720 TAATCAGTAAAGAA-TAAAATAA
1 TAATCAGTAAA-AAGTAAAATGG
31742 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAAGTAA-AATGG
* * *
31764 TTATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAAGTAAAATGG
31786 TAA
1 TAA
31789 AAAGTAATCA
Statistics
Matches: 314, Mismatches: 54, Indels: 90
0.69 0.12 0.20
Matches are distributed among these distances:
17 13 0.04
18 3 0.01
20 7 0.02
21 92 0.29
22 126 0.40
23 4 0.01
24 4 0.01
25 11 0.04
26 7 0.02
27 9 0.03
28 19 0.06
29 8 0.03
30 1 0.00
31 1 0.00
32 1 0.00
33 1 0.00
35 7 0.02
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (22 bp):
TAATCAGTAAAAAGTAAAATGG
Found at i:31407 original size:43 final size:43
Alignment explanation
Indices: 31354--31788 Score: 405
Period size: 43 Copynumber: 10.6 Consensus size: 43
31344 AAAGTGATAA
31354 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
* * *
31397 TAATCAGTAAAGAGT-AAA----AATCAGTAAAAAGTAAAATGG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGT-AAGAGCAAAATGG
* * * *
31436 TAATCAGTAAAGAGTAAAATCGTAA--A--AAGTG-ATAA---
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
* *
31471 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCACAATGG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
* *
31514 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCACAATGG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
* *
31557 TAATCAGTAAAAGGTAAAATGGTAATCAGTAACAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
* * * *
31600 TAATCAGTAAAGAGTAAAATCGTAA--A--AAGTG-ATAA---
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
* *
31635 TAATCAGTAAAATGTAAAATGGTAATTAGTAAGAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
** *
31678 TAATCAGTAAAGGGTTAAA-GGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
** * *
31720 TAATCAGTAAAGAA-TAAAATAATAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAA-AAGTAAAATGGTAATCAGT-AAGAGCAA-AATGG
* * *
31764 TTATCAGTAAAGAGTAAAATAGTAA
1 TAATCAGTAAAAAGTAAAATGGTAA
31789 AAAGTAATCA
Statistics
Matches: 327, Mismatches: 38, Indels: 53
0.78 0.09 0.13
Matches are distributed among these distances:
35 44 0.13
37 2 0.01
38 13 0.04
39 40 0.12
40 9 0.03
41 1 0.00
42 41 0.13
43 145 0.44
44 30 0.09
45 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (43 bp):
TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGG
Found at i:31420 original size:117 final size:117
Alignment explanation
Indices: 31286--31532 Score: 435
Period size: 117 Copynumber: 2.1 Consensus size: 117
31276 CAGTAAATTG
31286 GTAAAGAGTAAAAATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATAGTAAAAAGTG
1 GTAAAGAGTAAAAATCAGTAAAAAGTAA-AATGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTG
31350 ATAATAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCA
65 ATAATAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCA
*
31403 GTAAAGAGTAAAAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATCGTAAAAAGTGA
1 GTAAAGAGTAAAAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTGA
* *
31468 TAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCACAATGGTAATCA
66 TAATAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCA
31520 GTAAA-AGGTAAAA
1 GTAAAGA-GTAAAA
31533 TGGTAATCAG
Statistics
Matches: 125, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
116 3 0.02
117 122 0.98
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.21
Consensus pattern (117 bp):
GTAAAGAGTAAAAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTGA
TAATAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCA
Found at i:31514 original size:21 final size:21
Alignment explanation
Indices: 31471--31729 Score: 196
Period size: 21 Copynumber: 12.5 Consensus size: 21
31461 AAAGTGATAA
* *
31471 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAGA-GCAAAATGG
*
31493 TAATCAGTAAGAGCACAATGG
1 TAATCAGTAAGAGCAAAATGG
* *
31514 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAGA-GCAAAATGG
*
31536 TAATCAGTAAGAGCACAATGG
1 TAATCAGTAAGAGCAAAATGG
* *
31557 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAGA-GCAAAATGG
*
31579 TAATCAGTAACAGCAAAATGG
1 TAATCAGTAAGAGCAAAATGG
* *
31600 TAATCAGTAAAGAGTAAAATCG
1 TAATCAGT-AAGAGCAAAATGG
** * *
31622 TAAAAAGT--GA-TAATAATCAG
1 TAATCAGTAAGAGCAA-AAT-GG
* *
31642 T-A--A--AA-TGTAAAATGG
1 TAATCAGTAAGAGCAAAATGG
*
31657 TAATTAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGCAAAATGG
* **
31678 TAATCAGTAAAGGGTTAAA-GG
1 TAATCAGT-AAGAGCAAAATGG
31699 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGCAAAATGG
31720 TAATCAGTAA
1 TAATCAGTAA
31730 AGAATAAAAT
Statistics
Matches: 190, Mismatches: 31, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
15 2 0.01
16 4 0.02
17 4 0.02
18 4 0.02
19 6 0.03
20 11 0.06
21 89 0.47
22 70 0.37
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAGAGCAAAATGG
Found at i:31646 original size:78 final size:78
Alignment explanation
Indices: 31415--31837 Score: 380
Period size: 78 Copynumber: 5.3 Consensus size: 78
31405 AAAGAGTAAA
* *
31415 AATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAATAATCAGTA
1 AATCAGT-AAGAGCAAAATGGTAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAATAATCAGTA
31480 AAAGGTAAAATGGT
65 AAAGGTAAAATGGT
* * * *
31494 AATCAGTAAGAGCACAATGGTAATCAGTAAA-AGGTAAAATGGTAATCAGTAAGAGCACAATGGT
1 AATCAGTAAGAGCAAAATGGTAATCAGTAAAGA-GTAAAATCGTAA--A--AAGTG-ATAA---T
31558 AATCAGTAAAAGGTAAAATGGT
57 AATCAGTAAAAGGTAAAATGGT
*
31580 AATCAGTAACAGCAAAATGGTAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAATAATCAGTAA
1 AATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAATAATCAGTAA
*
31645 AATGTAAAATGGT
66 AAGGTAAAATGGT
* * * * * *
31658 AATTAGTAAGAGCAAAATGGTAATCAGTAAAGGGTTAAA-GGTAATCAGTAAGAGCAAAATGGTA
1 AATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATCGTAA--A--AAGTG-ATAA---TA
* **
31722 ATCAGT-AAAGAATAAAATAAT
58 ATCAGTAAAAG-GTAAAATGGT
* * * *
31743 AATCAGTAAAAAGTAAGAA-GGTTATCAGTAAAGAGTAAAATAGTAAAAA--G----TAATCAGT
1 AATCAGT-AAGAGCAA-AATGGTAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAATAATCAGT
*
31801 AAAAGGTAAAATAGT
64 AAAAGGTAAAATGGT
31816 AATCAGTAAGAGCAAAAATGGT
1 AATCAGTAAGAGC-AAAATGGT
31838 TATTAGAAAG
Statistics
Matches: 285, Mismatches: 34, Indels: 56
0.76 0.09 0.15
Matches are distributed among these distances:
72 6 0.02
73 28 0.10
74 4 0.01
77 5 0.02
78 89 0.31
79 8 0.03
80 1 0.00
81 8 0.03
82 11 0.04
83 5 0.02
84 4 0.01
85 22 0.08
86 87 0.31
87 7 0.02
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (78 bp):
AATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAATAATCAGTAA
AAGGTAAAATGGT
Found at i:31714 original size:42 final size:43
Alignment explanation
Indices: 31635--31788 Score: 159
Period size: 42 Copynumber: 3.6 Consensus size: 43
31625 AAAGTGATAA
** *
31635 TAATCAGTAAAATGTAAAATGGTAATTAGTAAGAGCAAAATGG
1 TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
*
31678 TAATCAGTAAAGGGTTAAA-GGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
** ** * *
31720 TAATCAGTAAAGAATAAAATAATAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAGGGTAAAATGGTAATCAGT-AAGAGCAA-AATGG
* * *
31764 TTATCAGTAAAGAGTAAAATAGTAA
1 TAATCAGTAAAGGGTAAAATGGTAA
31789 AAAGTAATCA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
42 38 0.40
43 24 0.26
44 30 0.32
45 2 0.02
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.23
Consensus pattern (43 bp):
TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
Found at i:31794 original size:22 final size:22
Alignment explanation
Indices: 31769--31824 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 22
31759 GAAGGTTATC
* *
31769 AGTAAAGAGTAAAATAGT-AAAA
1 AGTAAACAGTAAAA-AGTAAAAT
* *
31791 AGTAATCAGTAAAAGGTAAAAT
1 AGTAAACAGTAAAAAGTAAAAT
*
31813 AGTAATCAGTAA
1 AGTAAACAGTAA
31825 GAGCAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.21
Consensus pattern (22 bp):
AGTAAACAGTAAAAAGTAAAAT
Found at i:31802 original size:44 final size:43
Alignment explanation
Indices: 31713--31807 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 43
31703 CAGTAAGAGC
* **
31713 AAAATGGTAATCAGTAAAGAATAAAATAATAATCAGTAAAAAGT
1 AAAA-GGTTATCAGTAAAGAATAAAATAATAAAAAGTAAAAAGT
* * **
31757 AAGAAGGTTATCAGTAAAGAGTAAAATAGTAAAAAGTAATCAGT
1 AA-AAGGTTATCAGTAAAGAATAAAATAATAAAAAGTAAAAAGT
31801 AAAAGGT
1 AAAAGGT
31808 AAAATAGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 5 0.12
44 36 0.84
45 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (43 bp):
AAAAGGTTATCAGTAAAGAATAAAATAATAAAAAGTAAAAAGT
Found at i:31824 original size:29 final size:29
Alignment explanation
Indices: 31747--31817 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
31737 AATAATAATC
* *
31747 AGTAAAA-AGTAAGAAGGTTATCAGTAAAG
1 AGTAAAATAGTAA-AAAGTAATCAGTAAAG
31776 AGTAAAATAGTAAAAAGTAATCAGTAAA-
1 AGTAAAATAGTAAAAAGTAATCAGTAAAG
31804 AGGTAAAATAGTAA
1 A-GTAAAATAGTAA
31818 TCAGTAAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 1 0.03
29 32 0.84
30 5 0.13
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.21
Consensus pattern (29 bp):
AGTAAAATAGTAAAAAGTAATCAGTAAAG
Found at i:31833 original size:22 final size:22
Alignment explanation
Indices: 31787--31834 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31777 GTAAAATAGT
**
31787 AAAA-AGTAATCAGTAAAAGGT
1 AAAATAGTAATCAGTAAAAGCA
*
31808 AAAATAGTAATCAGTAAGAGCA
1 AAAATAGTAATCAGTAAAAGCA
31830 AAAAT
1 AAAAT
31835 GGTTATTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (22 bp):
AAAATAGTAATCAGTAAAAGCA
Found at i:31953 original size:27 final size:25
Alignment explanation
Indices: 31919--31984 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
31909 TCAGAGTAAT
*
31919 AAAA-AGTAAAAAGTGGTAATCAATA
1 AAAAGAGTAAAAAG-AGTAATCAATA
* *
31944 AAAGAGAGTAAGGAAAGAGTAATTAGTA
1 AAA-AGAGTAA--AAAGAGTAATCAATA
31972 AAAAGAGTAAAAA
1 AAAAGAGTAAAAA
31985 TGACAAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 6 0.18
26 1 0.03
27 12 0.35
28 11 0.32
29 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.21, T:0.17
Consensus pattern (25 bp):
AAAAGAGTAAAAAGAGTAATCAATA
Found at i:33330 original size:13 final size:13
Alignment explanation
Indices: 33314--33341 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33304 CCCAGGACAA
33314 GCACCCATGCCAT
1 GCACCCATGCCAT
33327 GCACCCATGCCAT
1 GCACCCATGCCAT
33340 GC
1 GC
33342 CGATGTCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.46, G:0.18, T:0.14
Consensus pattern (13 bp):
GCACCCATGCCAT
Found at i:33611 original size:8 final size:8
Alignment explanation
Indices: 33598--33622 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33588 ATCAAATCCA
33598 TCAATTTT
1 TCAATTTT
33606 TCAATTTT
1 TCAATTTT
33614 TCAATTTT
1 TCAATTTT
33622 T
1 T
33623 GTAAAAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TCAATTTT
Done.