Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012776.1 Corchorus capsularis cultivar CVL-1 contig12797, 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: 55500
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2321 original size:2 final size:2
Alignment explanation
Indices: 2316--2342 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2306 ATAATATATA
2316 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2343 ATTCTTGGCT
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2699 original size:125 final size:127
Alignment explanation
Indices: 2510--2746 Score: 313
Period size: 125 Copynumber: 1.9 Consensus size: 127
2500 TACTTAAAAT
2510 TATTGGTTTATTTTTTCATCTTAATATCAAATATCAATAATACTAAATGAAAATAATTATTGTAA
1 TATTGGTTTATTTTTTCATCTTAATATCAAATAT-AATAATACTAAATGAAAATAATTATTGTAA
*
2575 CTTCCGTTATACTTTATATATGATCACCATATATATGAATTCACCTCTATAATTAATTCCTATAA
65 CTTCCGTTATACTTTATATATG---ACCATATATACGAATTCACCTCTATAATTAATTCCTATAA
2640 A
127 A
* ** ** *
2641 TATTTGTTT-TTTTTT-ATCTTAATATCAAA-AT-AT-ATTGTAAATGTCAATAATTATTGTAAT
1 TATTGGTTTATTTTTTCATCTTAATATCAAATATAATAATACTAAATGAAAATAATTATTGTAAC
* * *
2701 TTCTGTTATACTTTATATATGACTATATATACGGATTCACCTCTAT
66 TTCCGTTATACTTTATATATGACCATATATACGAATTCACCTCTAT
2747 GGCTCACTCC
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
122 22 0.23
125 42 0.44
126 2 0.02
128 2 0.02
129 14 0.15
130 6 0.06
131 8 0.08
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (127 bp):
TATTGGTTTATTTTTTCATCTTAATATCAAATATAATAATACTAAATGAAAATAATTATTGTAAC
TTCCGTTATACTTTATATATGACCATATATACGAATTCACCTCTATAATTAATTCCTATAAA
Found at i:3044 original size:2 final size:2
Alignment explanation
Indices: 3037--3064 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3027 GTTCCAATTA
3037 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
3065 TGCTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4187 original size:16 final size:16
Alignment explanation
Indices: 4168--4225 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
4158 GAACCCGCCC
4168 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
4184 GACCCGTAACCCGAGT
1 GACCCGAAACCCGAAT
* *
4200 GACCCGAGACCCGTAT
1 GACCCGAAACCCGAAT
4216 GACCCGAAAC
1 GACCCGAAAC
4226 TCAAATAACC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.31, C:0.38, G:0.22, T:0.09
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:4196 original size:32 final size:31
Alignment explanation
Indices: 4153--4223 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
4143 AAAAGTAAAC
*
4153 GACCCGAACCCGCCCGACCCGAAACCCGAAT
1 GACCCGAACCCGACCGACCCGAAACCCGAAT
** * *
4184 GACCCGTAACCCGAGTGACCCGAGACCCGTAT
1 GACCCG-AACCCGACCGACCCGAAACCCGAAT
4216 GACCCGAA
1 GACCCGAA
4224 ACTCAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.28, C:0.42, G:0.23, T:0.07
Consensus pattern (31 bp):
GACCCGAACCCGACCGACCCGAAACCCGAAT
Found at i:4237 original size:32 final size:32
Alignment explanation
Indices: 4169--4240 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
4159 AACCCGCCCG
* * * * *
4169 ACCCGAAACCCGAATGACCCGTAACCCGAGTG
1 ACCCGAGACCCGAATGACCCGAAACCCAAATA
* *
4201 ACCCGAGACCCGTATGACCCGAAACTCAAATA
1 ACCCGAGACCCGAATGACCCGAAACCCAAATA
4233 ACCCGAGA
1 ACCCGAGA
4241 AGTTAACCCG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.36, G:0.19, T:0.10
Consensus pattern (32 bp):
ACCCGAGACCCGAATGACCCGAAACCCAAATA
Found at i:5394 original size:42 final size:42
Alignment explanation
Indices: 5342--5423 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
5332 TGTTGACACA
*
5342 TACCCCACCTGATAATTAATTATATATTTAATATTCAAAACC
1 TACCCAACCTGATAATTAATTATATATTTAATATTCAAAACC
*
5384 TACCCAACCTGATAATTAATTATGTATTTAATATTCAAAA
1 TACCCAACCTGATAATTAATTATATATTTAATATTCAAAA
5424 TTAATATCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (42 bp):
TACCCAACCTGATAATTAATTATATATTTAATATTCAAAACC
Found at i:6240 original size:22 final size:22
Alignment explanation
Indices: 6165--6568 Score: 237
Period size: 22 Copynumber: 18.5 Consensus size: 22
6155 AGCATCACTA
6165 TTTTACTGATTA--TTCTTTACT
1 TTTTACTGATTACCTT-TTTACT
* *
6186 TTGTACTAATTA-CTATTTTACT
1 TTTTACTGATTACCT-TTTTACT
* *
6208 CTTGT--TGATTACCTTCTTACT
1 -TTTTACTGATTACCTTTTTACT
*
6229 TTTTACTGATTACCATTTTACT
1 TTTTACTGATTACCTTTTTACT
* * *
6251 CTTTTGCTGATTACTATTTTCTGCTCCTT
1 -TTTTACTGATTAC--CTTT-T--TAC-T
* *
6280 TTTTACTGATTA-ATCTTTAACT
1 TTTTACTGATTACCT-TTTTACT
* *
6302 TTTTACTGATTGCC-TTTTGCT
1 TTTTACTGATTACCTTTTTACT
*
6323 TTTCACTGATTACCTTTTTACT
1 TTTTACTGATTACCTTTTTACT
* * *
6345 TCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTACCTTTTTACT
* **
6367 CTTTACTGATCGCCTTTTTAC-
1 TTTTACTGATTACCTTTTTACT
* *
6388 TCTTACTGATTTCC-TTTTACT
1 TTTTACTGATTACCTTTTTACT
* * *
6409 TCTTACTTATTACTTTTTTAC-
1 TTTTACTGATTACCTTTTTACT
* *
6430 TCTTACTGATTA-CTATTTACT
1 TTTTACTGATTACCTTTTTACT
*
6451 TTTTACTGACTA-CTATTTTA-T
1 TTTTACTGATTACCT-TTTTACT
* ** * *
6472 TCTTGTTGATGACCTTCTTACT
1 TTTTACTGATTACCTTTTTACT
6494 TTTTACTGATTA-CTATTTTACT
1 TTTTACTGATTACCT-TTTTACT
* * * *
6516 CTTTACTAATTACCATTTTACC
1 TTTTACTGATTACCTTTTTACT
* *
6538 CTTT-CAGA-TACCTTTTTACT
1 TTTTACTGATTACCTTTTTACT
6558 TTTTACTGATT
1 TTTTACTGATT
6569 GCATGCTATT
Statistics
Matches: 291, Mismatches: 66, Indels: 51
0.71 0.16 0.12
Matches are distributed among these distances:
20 28 0.10
21 101 0.35
22 122 0.42
23 19 0.07
25 4 0.01
26 3 0.01
28 13 0.04
29 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTTACTGATTACCTTTTTACT
Found at i:6241 original size:43 final size:42
Alignment explanation
Indices: 6180--6536 Score: 252
Period size: 43 Copynumber: 8.1 Consensus size: 42
6170 CTGATTATTC
* * *
6180 TTTACTTTGTACTAATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
* *
6222 TCTTACTTTTTACTGATTACCATTTTACTCTTTTGCTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTGCTGATTAC---CT
* * * * * * *
6270 TCTGCTCCTTTTTTACTGATTAATCTTTAACTTTTTACTGATTGCCT
1 T-T--TAC-TTTTTACTGATTACTATTTTAC-TCTTGCTGATTACCT
* * *
6317 TTTGCTTTTCACTGATTACCT-TTTTACTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTGCTGATTA-CCT
* ** * *
6361 TTTACTCTTTACTGATCGCCT-TTTTACTCTTACTGATTTCCT
1 TTTACTTTTTACTGAT-TACTATTTTACTCTTGCTGATTACCT
* * * *
6403 TTTACTTCTTACTTATTACTTTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
* * * *
6444 ATTTACTTTTTACTGACTACTATTTTATTCTTGTTGATGACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
* *
6487 TCTTACTTTTTACTGATTACTATTTTACTCTTTACTAATTACCAT
1 T-TTACTTTTTACTGATTACTATTTTACTC-TTGCTGATTACC-T
6532 TTTAC
1 TTTAC
6537 CCTTTCAGAT
Statistics
Matches: 246, Mismatches: 50, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
41 4 0.02
42 65 0.26
43 90 0.37
44 38 0.15
45 12 0.05
46 1 0.00
47 2 0.01
48 4 0.02
50 11 0.04
51 18 0.07
52 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.55
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
Found at i:6456 original size:14 final size:13
Alignment explanation
Indices: 6380--6457 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
6370 TACTGATCGC
*
6380 CTTTTTACTCTTA
1 CTTTTTACTTTTA
* *
6393 CTGATTTCCTTTTA
1 CT-TTTTACTTTTA
*
6407 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
6421 CTTTTTTACTCTTA
1 C-TTTTTACTTTTA
**
6435 CTGATTACTATTTA
1 CTTTTTACT-TTTA
6449 CTTTTTACT
1 CTTTTTACT
6458 GACTACTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 13 0.27
14 28 0.58
15 7 0.15
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:6822 original size:55 final size:55
Alignment explanation
Indices: 6753--7275 Score: 723
Period size: 55 Copynumber: 9.5 Consensus size: 55
6743 CATTTTAACT
6753 CTTAATTA-TCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* *
6808 CTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
*
6863 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * * *
6918 CTTAATTATTGATTTACTGATTGCCATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * *
6973 CTTAATTACTGATTTACTGATTACTATTACCTTGACTTTGATTAATTTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * * *
7028 CTTAATTATTGATTTACTGATTTCTATTACCTTGACTCTGATTAATTTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * * *
7083 ATTAATTATTGATTTACTGATTTCTATTACCTTGACTCTGATTAATTTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * * * *
7138 CTTAATTACTGATTTGCTGATTTCTATTACTCTTTA--CTGATT-ATTTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTAC-CTTGACTCTGATTAATCTCTTTTTA
* * * *
7191 CTTAATTACTGATTTACTGATTACTGTTACTTTAACTCTGATTAAT-TGTTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCT-CTTTTTA
* *
7246 CTTAATTACTGATTTGCTGACTACTATTAC
1 CTTAATTACTGATTTACTGATTACTATTAC
7276 TCTGATCCCA
Statistics
Matches: 429, Mismatches: 33, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
52 3 0.01
53 37 0.09
54 13 0.03
55 371 0.86
56 5 0.01
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
Found at i:6848 original size:29 final size:29
Alignment explanation
Indices: 6763--6905 Score: 90
Period size: 29 Copynumber: 5.1 Consensus size: 29
6753 CTTAATTATC
*
6763 GATTTACTGATTACTATTACCTTGACTCT
1 GATTTACTGATTACTATTACTTTGACTCT
* * * *
6792 GATTAATCT-CTT--T-TTAC-TTAATTACT
1 GATTTA-CTGATTACTATTACTTTGACT-CT
*
6818 GATTTACTGATTACTACTACTTTGACTCT
1 GATTTACTGATTACTATTACTTTGACTCT
* * * *
6847 GATTAATCT-CTT--T-TTAC-TTAATTACT
1 GATTTA-CTGATTACTATTACTTTGACT-CT
6873 GATTTACTGATTACTATTACTTTGACTCT
1 GATTTACTGATTACTATTACTTTGACTCT
6902 GATT
1 GATT
6906 AATCTCTTTT
Statistics
Matches: 82, Mismatches: 18, Indels: 28
0.64 0.14 0.22
Matches are distributed among these distances:
25 12 0.15
26 25 0.30
27 2 0.02
28 2 0.02
29 29 0.35
30 12 0.15
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (29 bp):
GATTTACTGATTACTATTACTTTGACTCT
Found at i:7075 original size:25 final size:25
Alignment explanation
Indices: 7047--7132 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
7037 TGATTTACTG
7047 ATTTCTATTACCTTGACTCTGATTA
1 ATTTCTATTACCTTGACTCTGATTA
* * * * *
7072 ATTTCT-TTTCAATTAATTATTGATTTA
1 ATTTCTATTAC-CTTGACT-CTGA-TTA
7099 CTGATTTCTATTACCTTGACTCTGATTA
1 ---ATTTCTATTACCTTGACTCTGATTA
7127 ATTTCT
1 ATTTCT
7133 TTTTACTTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
24 3 0.07
25 16 0.36
26 3 0.07
27 3 0.07
28 3 0.07
29 3 0.07
30 10 0.23
31 3 0.07
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.52
Consensus pattern (25 bp):
ATTTCTATTACCTTGACTCTGATTA
Found at i:8016 original size:51 final size:50
Alignment explanation
Indices: 7944--8061 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 50
7934 AACCAATCAA
** * *
7944 TTTATTTACTAATGGCCTAAAAAGTTTAAACTTCTAATTCAAAGG-TGACAT-
1 TTTATTTACTAATTACTTAAAAA-TTCAAACTT-TAATTCAAAGGTTGA-ATC
* *
7995 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTGAATC
1 TTTATTTACTAATTACTTAAAAATTCAAACTTTAATTCAAAGGTTGAATC
* *
8045 TTTATTTGCTAGTTACT
1 TTTATTTACTAATTACT
8062 CTAAGGATTC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
49 12 0.21
50 25 0.44
51 20 0.35
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAAACTTTAATTCAAAGGTTGAATC
Found at i:8079 original size:51 final size:49
Alignment explanation
Indices: 7944--8131 Score: 150
Period size: 51 Copynumber: 3.8 Consensus size: 49
7934 AACCAATCAA
** * * * *
7944 TTTATTTACTAATGGCCTAAAAAGTTTAAACTTCTAATTCAAAGGTGACAT
1 TTTATTTACTAATTACTTAAAAA-TTCAATCTT-TTATTCAAAGGTGACAT
7995 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTGA-AT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGG-TGACAT
* * ** ** *
8044 CTTTATTTGCTAGTTACTCTAAGGATTCAATCTTTTACCCAAAGATGACA-
1 -TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTGACAT
*
8094 TTT-TTTACTTAAGTTA-TTAAAAGCTTCAATCTTTTATT
1 TTTATTTAC-TAA-TTACTTAAAA-ATTCAATCTTTTATT
8132 TACAAGTTAC
Statistics
Matches: 110, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
48 7 0.06
49 30 0.27
50 31 0.28
51 42 0.38
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (49 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACAT
Found at i:9819 original size:28 final size:27
Alignment explanation
Indices: 9788--9927 Score: 114
Period size: 28 Copynumber: 5.3 Consensus size: 27
9778 GGAACTGTAA
9788 TATTTGATTATAGAAAAAATGAATCTAT
1 TATTTG-TTATAGAAAAAATGAATCTAT
* * * *
9816 TATTTG-TGTA-AAAAAAGGAATTGTAA
1 TATTTGTTATAGAAAAAATGAA-TCTAT
9842 TATTTGTTTATAG-AAAAATGAATCTAT
1 TATTTG-TTATAGAAAAAATGAATCTAT
* * * *
9869 TATTTG-TGT--AAAAAAGGAATTGTAA
1 TATTTGTTATAGAAAAAATGAA-TCTAT
9894 TATTTGTTTATAG-AAAAATGAATCTAT
1 TATTTG-TTATAGAAAAAATGAATCTAT
9921 TATTTGT
1 TATTTGT
9928 GTAAAAAAGG
Statistics
Matches: 86, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
24 8 0.09
25 20 0.23
26 13 0.15
27 20 0.23
28 25 0.29
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.41
Consensus pattern (27 bp):
TATTTGTTATAGAAAAAATGAATCTAT
Found at i:9904 original size:52 final size:52
Alignment explanation
Indices: 9755--9947 Score: 334
Period size: 52 Copynumber: 3.7 Consensus size: 52
9745 TATGGGAAAG
* * *
9755 TGAATTTATTATTTGTGT-AAAAAGGAACTGTAATATTTGATTATAGAAAAAA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAG-AAAAA
9807 TGAATCTATTATTTGTGTAAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
1 TGAATCTATTATTTGTGT-AAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
9860 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
9912 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATA
9948 CTAAATGGTA
Statistics
Matches: 136, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
52 87 0.64
53 23 0.17
54 26 0.19
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (52 bp):
TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
Found at i:9920 original size:105 final size:104
Alignment explanation
Indices: 9755--9947 Score: 334
Period size: 105 Copynumber: 1.8 Consensus size: 104
9745 TATGGGAAAG
*
9755 TGAATTTATTATTTGTGTAAAAAGGAACTGTAATATTTGATTATAGAAAAAATGAATCTATTATT
1 TGAATCTATTATTTGTGTAAAAAGGAACTGTAATATTTGATTATAGAAAAAATGAATCTATTATT
9820 TGTGTAAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
66 TGTGT-AAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
* *
9860 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAG-AAAAATGAATCTATTAT
1 TGAATCTATTATTTGTGT-AAAAAGGAACTGTAATATTTGATTATAGAAAAAATGAATCTATTAT
9924 TTGTGTAAAAAAGGAATTGTAATA
65 TTGTGTAAAAAAGGAATTGTAATA
9948 CTAAATGGTA
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
104 18 0.21
105 40 0.48
106 26 0.31
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (104 bp):
TGAATCTATTATTTGTGTAAAAAGGAACTGTAATATTTGATTATAGAAAAAATGAATCTATTATT
TGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
Found at i:9921 original size:24 final size:24
Alignment explanation
Indices: 9842--9921 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
9832 GGAATTGTAA
9842 TATTTGTTTATAGAAAAATGAATC
1 TATTTGTTTATAGAAAAATGAATC
* * *
9866 TATTAT-TTGTGTA-AAAAAGGAATTGTAA
1 TATT-TGTT-TATAGAAAAATGAA---T-C
9894 TATTTGTTTATAGAAAAATGAATC
1 TATTTGTTTATAGAAAAATGAATC
9918 TATT
1 TATT
9922 ATTTGTGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
24 18 0.43
25 5 0.12
27 5 0.12
28 14 0.33
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (24 bp):
TATTTGTTTATAGAAAAATGAATC
Found at i:11305 original size:70 final size:68
Alignment explanation
Indices: 11046--11333 Score: 386
Period size: 68 Copynumber: 4.2 Consensus size: 68
11036 TCATATGAAC
* * * *
11046 TTGGCTTATGGAAAAG-CCC--CTGCTTGGATGGAACCAAGGCTAAACTAACTCATATTGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACG
11108 AGT
66 AGT
* * * *
11111 TTGGCTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGCTAAATTGACTCGTGTGGAAACG
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACG
11176 AGT
66 AGT
*
11179 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTATGGAAAC
11244 GAGT
65 GAGT
* * *
11248 TTGGCTTGTGCAAAAGCCCCTGAAC-GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCCCTG--CTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTATGGAA
11312 ACGAGT
63 ACGAGT
* *
11318 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
11334 TCGAAGCATT
Statistics
Matches: 199, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
65 14 0.07
66 2 0.01
68 82 0.41
69 43 0.22
70 57 0.29
71 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACG
AGT
Found at i:11908 original size:51 final size:50
Alignment explanation
Indices: 11842--11945 Score: 145
Period size: 51 Copynumber: 2.1 Consensus size: 50
11832 CTAAAATGCC
* * *
11842 ATTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTT
1 ATTTTGAAAAGCGAATTTTGATATTGAACTCACAAATGAAATGCAATCTT
* **
11892 ATTTTAGAAAATCGAATTTTGATATTGAACTCGTAAATGAAATGCAATCTT
1 ATTTT-GAAAAGCGAATTTTGATATTGAACTCACAAATGAAATGCAATCTT
11943 ATT
1 ATT
11946 ATAAAACTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 5 0.11
51 42 0.89
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (50 bp):
ATTTTGAAAAGCGAATTTTGATATTGAACTCACAAATGAAATGCAATCTT
Found at i:12933 original size:16 final size:16
Alignment explanation
Indices: 12914--12948 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12904 AGGCCAAGTT
12914 TTTCTTT-TCTCTTTTC
1 TTTCTTTCT-TCTTTTC
12930 TTTCTTTCTTCTTTTC
1 TTTCTTTCTTCTTTTC
12946 TTT
1 TTT
12949 GGGTTGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTTCTTTTC
Found at i:13545 original size:14 final size:13
Alignment explanation
Indices: 13522--13573 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
13512 CTCAAAAACT
*
13522 TTTTTAAAAACTCA
1 TTTTTGAAAAC-CA
*
13536 TTTTTGAAAACCT
1 TTTTTGAAAACCA
*
13549 TTTCTTGAAAACAA
1 TTT-TTGAAAACCA
13563 TTTTTTGAAAA
1 -TTTTTGAAAA
13574 ATGTCTCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.12
14 25 0.78
15 3 0.09
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTTGAAAACCA
Found at i:16328 original size:22 final size:23
Alignment explanation
Indices: 16289--16657 Score: 154
Period size: 22 Copynumber: 16.8 Consensus size: 23
16279 ATCACTATTT
16289 TACTGATTA-T-TCTTTACT-TTG
1 TACTGATTACTAT-TTTACTCTTG
*
16310 TATTGATTACTATTTTACTCTTG
1 TACTGATTACTATTTTACTCTTG
* *
16333 T--TGATTACCT-TCTTACT-TTT
1 TACTGATTA-CTATTTTACTCTTG
* *
16353 TACTGATTACCATTTTACTCTTT
1 TACTGATTACTATTTTACTCTTG
* * *
16376 TGCTGATTACTATTTTCTGCTCCTTTTT
1 TACTGATTACTA-TTT-TACT-C--TTG
*
16404 TACTGATTAC-ACTTTTACT-TTT
1 TACTGATTACTA-TTTTACTCTTG
* *
16426 TACTGATTGCCATTTT-CT-TT-
1 TACTGATTACTATTTTACTCTTG
16446 TCACTGATTACCT-TTTTACTTCTTG
1 T-ACTGATTA-CTATTTTAC-TCTTG
16471 --CTGATTAGCT-TTTTACTCTT-
1 TACTGATTA-CTATTTTACTCTTG
**
16491 TACTGATCGCCT-TTTTACTC-T-
1 TACTGAT-TACTATTTTACTCTTG
* *
16512 TACTGATTTC-CTTTTACT-TCT-
1 TACTGATTACTATTTTACTCT-TG
* *
16533 TACTTATTACTTTTTTACTC-T-
1 TACTGATTACTATTTTACTCTTG
*
16554 TACTGATTACTA-TTTACT-TTT
1 TACTGATTACTATTTTACTCTTG
* *
16575 TACTGACTACTATTTTATTCTTG
1 TACTGATTACTATTTTACTCTTG
* * *
16598 T--TGATGACCT-TCTTACT-TTT
1 TACTGATTA-CTATTTTACTCTTG
16618 TACTGATTACTATTTTACTCTT-
1 TACTGATTACTATTTTACTCTTG
* *
16640 TACTAATTACCATTTTAC
1 TACTGATTACTATTTTAC
16658 CCTTTCAGAT
Statistics
Matches: 275, Mismatches: 36, Indels: 73
0.72 0.09 0.19
Matches are distributed among these distances:
20 22 0.08
21 90 0.33
22 110 0.40
23 25 0.09
24 5 0.02
25 3 0.01
26 4 0.01
27 4 0.01
28 12 0.04
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.55
Consensus pattern (23 bp):
TACTGATTACTATTTTACTCTTG
Found at i:16360 original size:43 final size:42
Alignment explanation
Indices: 16301--16657 Score: 256
Period size: 43 Copynumber: 8.1 Consensus size: 42
16291 CTGATTATTC
* * *
16301 TTTACTTTGTATTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
* *
16343 TCTTACTTTTTACTGATTACCATTTTACTCTTTTGCTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTGCTGATTAC---CT
* * * *
16391 TCTGCTCCTTTTTTACTGATTAC-ACTTTTACTTTTTACTGATTGCCAT
1 T-T--TAC-TTTTTACTGATTACTA-TTTTAC-TCTTGCTGATTACC-T
* *
16439 TTT-CTTTTCACTGATTACCT-TTTTACTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTGCTGATTA-CCT
* ** * *
16482 TTTACTCTTTACTGATCGCCT-TTTTACTCTTACTGATTTCCT
1 TTTACTTTTTACTGAT-TACTATTTTACTCTTGCTGATTACCT
* * * *
16524 TTTACTTCTTACTTATTACTTTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
* * * *
16565 ATTTACTTTTTACTGACTACTATTTTATTCTTGTTGATGACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
* *
16608 TCTTACTTTTTACTGATTACTATTTTACTCTTTACTAATTACCAT
1 T-TTACTTTTTACTGATTACTATTTTACTC-TTGCTGATTACC-T
16653 TTTAC
1 TTTAC
16658 CCTTTCAGAT
Statistics
Matches: 250, Mismatches: 42, Indels: 44
0.74 0.12 0.13
Matches are distributed among these distances:
41 4 0.02
42 65 0.26
43 95 0.38
44 33 0.13
45 13 0.05
47 1 0.00
48 6 0.02
50 12 0.05
51 20 0.08
52 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCT
Found at i:16425 original size:21 final size:20
Alignment explanation
Indices: 16401--16657 Score: 160
Period size: 22 Copynumber: 12.0 Consensus size: 20
16391 TCTGCTCCTT
16401 TTTTACTGATTACACTTTTAC
1 TTTTACTGATTAC-CTTTTAC
*
16422 TTTTTACTGATTGCCATTTT-C
1 -TTTTACTGATTACC-TTTTAC
16443 TTTTCACTGATTACCTTTTTAC
1 TTTT-ACTGATTACC-TTTTAC
* *
16465 TTCTTGCTGATTAGCTTTTTAC
1 TT-TTACTGATTA-CCTTTTAC
**
16487 TCTTTACTGATCGCCTTTTTAC
1 T-TTTACTGATTACC-TTTTAC
* *
16509 TCTTACTGATTTCCTTTTAC
1 TTTTACTGATTACCTTTTAC
* *
16529 TTCTTACTTATTACTTTTTTAC
1 TT-TTACTGATTAC-CTTTTAC
*
16551 TCTTACTGATTA-CTATTTAC
1 TTTTACTGATTACCT-TTTAC
* *
16571 TTTTTACTGACTACTATTTTA-
1 -TTTTACTGATTAC-CTTTTAC
** *
16592 TTCTTGTTGATGACCTTCTTAC
1 TT-TTACTGATTACCTT-TTAC
*
16614 TTTTTACTGATTACTATTTTAC
1 -TTTTACTGATTAC-CTTTTAC
*
16636 TCTTTACTAATTACCATTTTAC
1 T-TTTACTGATTACC-TTTTAC
16658 CCTTTCAGAT
Statistics
Matches: 182, Mismatches: 33, Indels: 40
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.01
20 20 0.11
21 65 0.36
22 87 0.48
23 9 0.05
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTACTGATTACCTTTTAC
Found at i:16577 original size:14 final size:13
Alignment explanation
Indices: 16501--16578 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
16491 TACTGATCGC
*
16501 CTTTTTACTCTTA
1 CTTTTTACTTTTA
* *
16514 CTGATTTCCTTTTA
1 CT-TTTTACTTTTA
*
16528 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
16542 CTTTTTTACTCTTA
1 C-TTTTTACTTTTA
**
16556 CTGATTACTATTTA
1 CTTTTTACT-TTTA
16570 CTTTTTACT
1 CTTTTTACT
16579 GACTACTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 13 0.27
14 28 0.58
15 7 0.15
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:16662 original size:22 final size:22
Alignment explanation
Indices: 16616--16662 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
16606 CTTCTTACTT
* * *
16616 TTTACTGATTACTATTTTACTC
1 TTTACTAATTACCATTTTACCC
16638 TTTACTAATTACCATTTTACCC
1 TTTACTAATTACCATTTTACCC
16660 TTT
1 TTT
16663 CAGATAGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTACTAATTACCATTTTACCC
Found at i:16943 original size:55 final size:55
Alignment explanation
Indices: 16874--17234 Score: 546
Period size: 55 Copynumber: 6.6 Consensus size: 55
16864 CATTTTAACT
16874 CTTAATTA-TCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* *
16929 CTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
*
16984 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * *
17039 CTTAATTACTGATTTACTGATTACCATTACTTTGAATCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * *
17094 CTTAATTACTGATTTACTGATTACTATTACCTTGACTTTGATTAATTTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * * * *
17149 CTTAATTA-TAGATTTACTGATTTCTATTACCTTTACTCTGATTAATTTCATTTCA
1 CTTAATTACT-GATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* *
17204 CTTAATTATTGATTTACTGATTTCTATTACC
1 CTTAATTACTGATTTACTGATTACTATTACC
17235 AGATTCTTGA
Statistics
Matches: 288, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
54 1 0.00
55 285 0.99
56 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
Found at i:16969 original size:29 final size:29
Alignment explanation
Indices: 16884--17136 Score: 96
Period size: 29 Copynumber: 9.1 Consensus size: 29
16874 CTTAATTATC
*
16884 GATTTACTGATTACTATTACCTTGACTCT
1 GATTTACTGATTACTATTACTTTGACTCT
* * * *
16913 GATTAATCT-CTT--T-TTAC-TTAATTACT
1 GATTTA-CTGATTACTATTACTTTGACT-CT
*
16939 GATTTACTGATTACTACTACTTTGACTCT
1 GATTTACTGATTACTATTACTTTGACTCT
* * * *
16968 GATTAATCT-CTT--T-TTAC-TTAATTACT
1 GATTTA-CTGATTACTATTACTTTGACT-CT
16994 GATTTACTGATTACTATTACTTTGACTCT
1 GATTTACTGATTACTATTACTTTGACTCT
* * * *
17023 GATTAATCT-CTT--T-TTAC-TTAATTACT
1 GATTTA-CTGATTACTATTACTTTGACT-CT
* *
17049 GATTTACTGATTACCATTACTTTGAATCT
1 GATTTACTGATTACTATTACTTTGACTCT
* * * *
17078 GATTAATCT-CTT--T-TTAC-TTAATTACT
1 GATTTA-CTGATTACTATTACTTTGACT-CT
* *
17104 GATTTACTGATTACTATTACCTTGACTTT
1 GATTTACTGATTACTATTACTTTGACTCT
17133 GATT
1 GATT
17137 AATTTCTTTT
Statistics
Matches: 159, Mismatches: 37, Indels: 56
0.63 0.15 0.22
Matches are distributed among these distances:
25 24 0.15
26 51 0.32
27 3 0.02
28 3 0.02
29 54 0.34
30 24 0.15
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (29 bp):
GATTTACTGATTACTATTACTTTGACTCT
Found at i:17227 original size:30 final size:30
Alignment explanation
Indices: 17138--17227 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 30
17128 ACTTTGATTA
* *
17138 ATTTCTTTTCACTTAATTATAGATTTACTG
1 ATTTCATTTCACTTAATTATTGATTTACTG
* * * *
17168 ATTTCTATTAC-CTTTACT-CTGA-TTA---
1 ATTTC-ATTTCACTTAATTATTGATTTACTG
17193 ATTTCATTTCACTTAATTATTGATTTACTG
1 ATTTCATTTCACTTAATTATTGATTTACTG
17223 ATTTC
1 ATTTC
17228 TATTACCAGA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
24 4 0.09
25 10 0.23
26 3 0.07
27 3 0.07
28 3 0.07
29 2 0.05
30 15 0.35
31 3 0.07
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.53
Consensus pattern (30 bp):
ATTTCATTTCACTTAATTATTGATTTACTG
Found at i:20318 original size:53 final size:52
Alignment explanation
Indices: 20226--20470 Score: 438
Period size: 52 Copynumber: 4.7 Consensus size: 52
20216 TATGGGAAAG
* * *
20226 TGAATTTATTATTTGTG-CAAAAAGGATTTGTAATATTTGTTTATAGAAAAAA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAG-AAAAA
20278 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
20330 TGAATCTATTATTTGTGTAAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
1 TGAATCTATTATTTGTGT-AAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
20383 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
20435 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATA
20471 CTAAATGATA
Statistics
Matches: 188, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
52 109 0.58
53 79 0.42
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (52 bp):
TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
Found at i:20409 original size:105 final size:105
Alignment explanation
Indices: 20226--20470 Score: 440
Period size: 105 Copynumber: 2.3 Consensus size: 105
20216 TATGGGAAAG
* * *
20226 TGAATTTATTATTTGTG-CAAAAAGGATTTGTAATATTTGTTTATAGAAAAAATGAATCTATTAT
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAAATGAATCTATTAT
20290 TTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
66 TTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
20330 TGAATCTATTATTTGTGTAAAAAAAGGAATTGTAATATTTGTTTATAG-AAAAATGAATCTATTA
1 TGAATCTATTATTTGTGT-AAAAAAGGAATTGTAATATTTGTTTATAGAAAAAATGAATCTATTA
20394 TTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
65 TTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
20435 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATA
1 TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATA
20471 CTAAATGATA
Statistics
Matches: 136, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
104 34 0.25
105 75 0.55
106 27 0.20
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (105 bp):
TGAATCTATTATTTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAAATGAATCTATTAT
TTGTGTAAAAAAGGAATTGTAATATTTGTTTATAGAAAAA
Found at i:23479 original size:29 final size:29
Alignment explanation
Indices: 23437--23496 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
23427 AACCGAGCCG
23437 ATTGACGAGGCCCATTTGTGTCGGTTTCA
1 ATTGACGAGGCCCATTTGTGTCGGTTTCA
23466 ATTGACGAGGCCCATTTGTGTCGGTTTCA
1 ATTGACGAGGCCCATTTGTGTCGGTTTCA
23495 AT
1 AT
23497 CGATTCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (29 bp):
ATTGACGAGGCCCATTTGTGTCGGTTTCA
Found at i:24222 original size:16 final size:17
Alignment explanation
Indices: 24203--24235 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24193 AACCCGCCCG
*
24203 AACCCTAACCC-AAAAA
1 AACCCGAACCCGAAAAA
24219 AACCCGAACCCGAAAAA
1 AACCCGAACCCGAAAAA
24236 GCTCAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.55, C:0.36, G:0.06, T:0.03
Consensus pattern (17 bp):
AACCCGAACCCGAAAAA
Found at i:24275 original size:16 final size:15
Alignment explanation
Indices: 24225--24275 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
24215 AAAAAACCCG
*
24225 AACCCGAAAAAGCTCA
1 AACCCGAAAAATCT-A
24241 AACCCGAAAAAT-TA
1 AACCCGAAAAATCTA
24255 GAACCCGAAAAATCTGA
1 -AACCCGAAAAATCT-A
24272 AACC
1 AACC
24276 AGATCCTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 1 0.03
15 13 0.42
16 16 0.52
17 1 0.03
ACGTcount: A:0.51, C:0.27, G:0.12, T:0.10
Consensus pattern (15 bp):
AACCCGAAAAATCTA
Found at i:24322 original size:20 final size:20
Alignment explanation
Indices: 24297--24337 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
24287 AAACCTGAAT
*
24297 TAAATACTAATATT-TGAAAA
1 TAAATAATAAT-TTCTGAAAA
24317 TAAATAATAATTTCTGAAAA
1 TAAATAATAATTTCTGAAAA
24337 T
1 T
24338 TTCATATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAATAATAATTTCTGAAAA
Found at i:24519 original size:32 final size:32
Alignment explanation
Indices: 24478--24589 Score: 163
Period size: 32 Copynumber: 3.5 Consensus size: 32
24468 CCAATCCGAG
* *
24478 CCCGAACCCGAATTAACCTGA-CTCAAAATTGA
1 CCCGAACCCGAATTAACCTGACCT-AAATTTAA
*
24510 CCCGAACCCGAATCAACCTGACCTAAATTTAA
1 CCCGAACCCGAATTAACCTGACCTAAATTTAA
*
24542 CCCGAACCCGAATTAACCCGACCTAAATTTAA
1 CCCGAACCCGAATTAACCTGACCTAAATTTAA
*
24574 CCCGAACCCGACTTAA
1 CCCGAACCCGAATTAA
24590 ACCCGAACCC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
32 71 0.97
33 2 0.03
ACGTcount: A:0.37, C:0.35, G:0.11, T:0.18
Consensus pattern (32 bp):
CCCGAACCCGAATTAACCTGACCTAAATTTAA
Found at i:24557 original size:16 final size:16
Alignment explanation
Indices: 24478--24602 Score: 94
Period size: 16 Copynumber: 7.8 Consensus size: 16
24468 CCAATCCGAG
24478 CCCGAACCCGAATTAA
1 CCCGAACCCGAATTAA
* ** *
24494 CCTG-ACTCAAAATTGA
1 CCCGAAC-CCGAATTAA
*
24510 CCCGAACCCGAATCAA
1 CCCGAACCCGAATTAA
* **
24526 CCTG-ACCTAAATTTAA
1 CCCGAACCCGAA-TTAA
24542 CCCGAACCCGAATTAA
1 CCCGAACCCGAATTAA
**
24558 CCCG-ACCTAAATTTAA
1 CCCGAACCCGAA-TTAA
*
24574 CCCGAACCCGACTTAAA
1 CCCGAACCCGAATT-AA
24591 CCCGAACCCGAA
1 CCCGAACCCGAA
24603 AACGACCTAA
Statistics
Matches: 80, Mismatches: 22, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
15 12 0.15
16 44 0.55
17 24 0.30
ACGTcount: A:0.37, C:0.36, G:0.11, T:0.16
Consensus pattern (16 bp):
CCCGAACCCGAATTAA
Found at i:24602 original size:23 final size:23
Alignment explanation
Indices: 24572--24632 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
24562 ACCTAAATTT
*
24572 AACCCGAACCCGACTTAAACCCG
1 AACCCGAACCCGACCTAAACCCG
**
24595 AACCCGAAAACGACCTAAACCCG
1 AACCCGAACCCGACCTAAACCCG
24618 ATGACCCGAACCCGA
1 A--ACCCGAACCCGA
24633 ACCCAACCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.38, C:0.41, G:0.15, T:0.07
Consensus pattern (23 bp):
AACCCGAACCCGACCTAAACCCG
Found at i:30529 original size:2 final size:2
Alignment explanation
Indices: 30522--30579 Score: 73
Period size: 2 Copynumber: 28.5 Consensus size: 2
30512 AGCCATTAAT
* *
30522 TA TA TA TA TA TA TA TA TA TA T- TCA CTA AA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA TA TA
30565 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
30580 CCCATGATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 1 0.02
4 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:36723 original size:25 final size:25
Alignment explanation
Indices: 36689--36737 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
36679 CCAACCAATC
**
36689 TTGAACACTCTTGCTCGGTCTCTAT
1 TTGAACACTCTCACTCGGTCTCTAT
*
36714 TTGAGCACTCTCACTCGGTCTCTA
1 TTGAACACTCTCACTCGGTCTCTA
36738 CAAACTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.37
Consensus pattern (25 bp):
TTGAACACTCTCACTCGGTCTCTAT
Found at i:40170 original size:41 final size:42
Alignment explanation
Indices: 40118--40240 Score: 135
Period size: 41 Copynumber: 3.0 Consensus size: 42
40108 TCTCTTACCC
*
40118 AATATCCAAAGTCCCCAAACACAATCCTAACACAGGAGCAACT
1 AATAT-CAAAGTCCCCAAACACAATCATAACACAGGAGCAACT
* * * * *
40161 -CTTTCAAAGTCCTCAAACACATTCATAACACA-GAGGC-ATT
1 AATATCAAAGTCCCCAAACACAATCATAACACAGGA-GCAACT
* *
40201 AATATCAAAGTCCCCAAACACAATTATAACACAGGGGCAA
1 AATATCAAAGTCCCCAAACACAATCATAACACAGGAGCAA
40241 TCCTTTCTCA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
40 4 0.06
41 56 0.88
42 4 0.06
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (42 bp):
AATATCAAAGTCCCCAAACACAATCATAACACAGGAGCAACT
Found at i:40215 original size:82 final size:83
Alignment explanation
Indices: 40118--40296 Score: 233
Period size: 82 Copynumber: 2.2 Consensus size: 83
40108 TCTCTTACCC
*
40118 AATATCCAAAGTCCCCAAACACAATCCTAACACAGGAGCAA--CTCTT-TCAAAGTCCTCAAACA
1 AATAT-CAAAGTCCCCAAACACAATCATAACACAGGAGCAATCCT-TTCTCAAAGTCCTCAAACA
*
40180 CATTCATAACACAGAGGCAT-T
64 CATTC-TAA-ACAGAGGAATCT
* * *
40201 AATATCAAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTTTCTCAAAGTCCTCAAGCACA
1 AATATCAAAGTCCCCAAACACAATCATAACACAGGAGCAATCCTTTCTCAAAGTCCTCAAACACA
*
40266 TTCTTAACAGAGGAATCT
66 TTCTAAACAGAGGAATCT
40284 -ATATCAAAGTCCC
1 AATATCAAAGTCCC
40297 TAAGCACATA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
82 54 0.63
83 10 0.12
84 22 0.26
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (83 bp):
AATATCAAAGTCCCCAAACACAATCATAACACAGGAGCAATCCTTTCTCAAAGTCCTCAAACACA
TTCTAAACAGAGGAATCT
Found at i:43061 original size:10 final size:10
Alignment explanation
Indices: 43046--43081 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
43036 AGTTATATCG
43046 AAAAAAATAA
1 AAAAAAATAA
43056 AAAAAAATAA
1 AAAAAAATAA
43066 AAAAGAAATAA
1 AAAA-AAATAA
43077 AAAAA
1 AAAAA
43082 TTTCGACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:43062 original size:11 final size:11
Alignment explanation
Indices: 43046--43081 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
43036 AGTTATATCG
43046 AAAAAAAT-AA
1 AAAAAAATAAA
43056 AAAAAAATAAA
1 AAAAAAATAAA
*
43067 AAAGAAATAAA
1 AAAAAAATAAA
43078 AAAA
1 AAAA
43082 TTTCGACCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:55481 original size:33 final size:34
Alignment explanation
Indices: 55404--55482 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 34
55394 TGCAAAGAGT
* **
55404 GTTTTAGATGTTGTTTGCAATGACACTAAATCTA
1 GTTTTAGGTGTTGTTTGCAACAACACTAAATCTA
* * *
55438 ATTTGA-GTGTTGTTTGCGACAACACTAAATC-A
1 GTTTTAGGTGTTGTTTGCAACAACACTAAATCTA
55470 GTTTTAGGTGTTG
1 GTTTTAGGTGTTG
55483 CTTGTGATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
32 5 0.14
33 27 0.75
34 4 0.11
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (34 bp):
GTTTTAGGTGTTGTTTGCAACAACACTAAATCTA
Done.