Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001272.1 Hibiscus syriacus cultivar Beakdansim tig00002496_pilon, 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: 116934
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:6726 original size:39 final size:37
Alignment explanation
Indices: 6683--6868 Score: 173
Period size: 38 Copynumber: 4.9 Consensus size: 37
6673 TTTGAAAATG
* *
6683 AATATAGTATAGATTTTAAAACATTTTTGAAAACGGTAT
1 AATATA-TATAGTTTTTAAAACATTTTTGAAAAC-ATAT
* *
6722 -A-ATATATAGTTTTTAAAATATTTTTAGAAAAAATAT
1 AATATATATAGTTTTTAAAACATTTTT-GAAAACATAT
*
6758 -ATAATATATGGTTTTTAAAATCATTTTTTGAAAACTTATAT
1 AAT-ATATATAGTTTTTAAAA-CA-TTTTTGAAAAC--ATAT
* * *
6799 AATATATA-ATTTTTTAAAGCATTTTTGAAAACTTAT
1 AATATATATAGTTTTTAAAACATTTTTGAAAACATAT
*
6835 ATATAATATATAATTTTTAAAACATTTTTGAAAA
1 A-AT-ATATATAGTTTTTAAAACATTTTTGAAAA
6869 TTATATAGTT
Statistics
Matches: 123, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
36 27 0.22
37 10 0.08
38 33 0.27
39 29 0.24
40 13 0.11
41 9 0.07
42 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
AATATATATAGTTTTTAAAACATTTTTGAAAACATAT
Found at i:6873 original size:38 final size:38
Alignment explanation
Indices: 6631--6875 Score: 209
Period size: 39 Copynumber: 6.4 Consensus size: 38
6621 TCGTAAACGA
* * *
6631 TTTTGAAAATACATATATAATATATAGGTTTTTTAAAGGCA-
1 TTTTGAAAAT-TATATATAATATATA--ATTTTTAAA-ACAT
* * *
6672 TTTTGAAAATGA-ATATAGTATA-GA-TTTTAAAACAT
1 TTTTGAAAATTATATATAATATATAATTTTTAAAACAT
*** * *
6707 TTTTGAAAA--CGGTATAATATATAGTTTTTAAAATAT
1 TTTTGAAAATTATATATAATATATAATTTTTAAAACAT
* **
6743 TTTTAGAAAA-AATATATAATATATGGTTTTTAAAATCATT
1 TTTT-GAAAATTATATATAATATATAATTTTTAAAA-CA-T
* *
6783 TTTTGAAAACT-TATATAATATATAATTTTTTAAAGCAT
1 TTTTGAAAATTATATATAATATATAA-TTTTTAAAACAT
6821 TTTTGAAAACTTATATATAATATATAATTTTTAAAACAT
1 TTTTGAAAA-TTATATATAATATATAATTTTTAAAACAT
6860 TTTTGAAAATTATATA
1 TTTTGAAAATTATATA
6876 GTTTTTGAAA
Statistics
Matches: 170, Mismatches: 22, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
34 10 0.06
35 16 0.09
36 14 0.08
37 5 0.03
38 37 0.22
39 50 0.29
40 28 0.16
41 10 0.06
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTTGAAAATTATATATAATATATAATTTTTAAAACAT
Found at i:6894 original size:31 final size:29
Alignment explanation
Indices: 6841--6936 Score: 124
Period size: 29 Copynumber: 3.2 Consensus size: 29
6831 TTATATATAA
*
6841 TATATAATTTTTAAAACATTTTTGAAAAT
1 TATATAGTTTTTAAAACATTTTTGAAAAT
6870 TATATAGTTTTTGAAAACATTTTTTGAAAAT
1 TATATAGTTTTT-AAAACA-TTTTTGAAAAT
6901 TATATAGTTTTTTTAAAA-A-TTTTGAAAATT
1 TATATAG--TTTTTAAAACATTTTTGAAAA-T
6931 TATATA
1 TATATA
6937 TAGTATATAG
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
29 20 0.33
30 13 0.21
31 19 0.31
32 4 0.07
33 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (29 bp):
TATATAGTTTTTAAAACATTTTTGAAAAT
Found at i:7013 original size:22 final size:21
Alignment explanation
Indices: 6988--7053 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 21
6978 TTATATAGTT
6988 TTATTTATTTATTTATTTATTA
1 TTATTTATTTATTTA-TTATTA
*
7010 TTA-TTA-TCATATTATTA-TA
1 TTATTTATTTAT-TTATTATTA
**
7029 TTATTT-TTTATTACTTATT-
1 TTATTTATTTATTTATTATTA
7048 TTATTT
1 TTATTT
7054 GTTTTTCCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
19 15 0.42
20 12 0.33
21 6 0.17
22 3 0.08
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTTATTTATTTATTATTA
Found at i:8267 original size:15 final size:15
Alignment explanation
Indices: 8249--8299 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
8239 AAATTTATTT
8249 TTTATTCAATTTTTA
1 TTTATTCAATTTTTA
*
8264 TTTA-TCATTTTTTTA
1 TTTATTCA-ATTTTTA
* * *
8279 CTTGTTCCATTTTTA
1 TTTATTCAATTTTTA
8294 TTTATT
1 TTTATT
8300 TTTTAAACTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 3 0.11
15 22 0.81
16 2 0.07
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTATTCAATTTTTA
Found at i:14905 original size:2 final size:2
Alignment explanation
Indices: 14898--14936 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14888 AGGAAAAATG
14898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14937 GGAAGATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15471 original size:23 final size:23
Alignment explanation
Indices: 15403--15471 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
15393 CAACCTTAAA
* *
15403 TGGCACTTTGATGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
15426 CGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
15449 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
15472 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:16157 original size:36 final size:36
Alignment explanation
Indices: 16117--16202 Score: 145
Period size: 36 Copynumber: 2.4 Consensus size: 36
16107 CAACATTAAC
* *
16117 ATCATAATCATGATATCTATTATTATCCATATCCAT
1 ATCATTATCATGATATCTATTATTATCCATATCAAT
*
16153 ATCATTATCATGATATCTATTATTATCCATTTCAAT
1 ATCATTATCATGATATCTATTATTATCCATATCAAT
16189 ATCATTATCATGAT
1 ATCATTATCATGAT
16203 TTTGTAATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.44
Consensus pattern (36 bp):
ATCATTATCATGATATCTATTATTATCCATATCAAT
Found at i:16161 original size:18 final size:18
Alignment explanation
Indices: 16138--16197 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
16128 GATATCTATT
16138 ATTATCCATATCCATATC
1 ATTATCCATATCCATATC
* *
16156 ATTAT-CATGATATC-TATT
1 ATTATCCAT-AT-CCATATC
* *
16174 ATTATCCATTTCAATATC
1 ATTATCCATATCCATATC
16192 ATTATC
1 ATTATC
16198 ATGATTTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.09
18 25 0.78
19 4 0.12
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTATCCATATCCATATC
Found at i:16222 original size:15 final size:16
Alignment explanation
Indices: 16192--16231 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
16182 TTTCAATATC
16192 ATTATCATGATTTTGTA
1 ATTATCAT-ATTTTGTA
16209 ATTATCAT-TTTTGT-
1 ATTATCATATTTTGTA
16223 A-TATCATAT
1 ATTATCATAT
16232 AACACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.27
14 2 0.09
15 6 0.27
17 8 0.36
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (16 bp):
ATTATCATATTTTGTA
Found at i:16728 original size:31 final size:31
Alignment explanation
Indices: 16704--16905 Score: 309
Period size: 31 Copynumber: 6.5 Consensus size: 31
16694 CCATAGATCT
* *
16704 CGAAGAATC-TAGGTAATCAGTCCATATG-TC
1 CGAAGAA-CATAGGTAAACAATCCATATGTTC
16734 TCGAAGAACATAGGTAAACAATCCATATGTTC
1 -CGAAGAACATAGGTAAACAATCCATATGTTC
16766 CGAAGAACATAGGTAAACAATCCATATGTTC
1 CGAAGAACATAGGTAAACAATCCATATGTTC
*
16797 CGAAGAACATAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTTC
* *
16828 CGAATAACATAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTTC
* *
16859 CGAATAACATAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTTC
16890 CGAAGAACATAGGTAA
1 CGAAGAACATAGGTAA
16906 CCCTCGACTC
Statistics
Matches: 164, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
30 1 0.01
31 161 0.98
32 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.22
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAATCCATATGTTC
Found at i:22578 original size:88 final size:88
Alignment explanation
Indices: 22378--22594 Score: 335
Period size: 88 Copynumber: 2.5 Consensus size: 88
22368 ACTATGACTT
* * *
22378 GTAAGTCCTTACCGTTACTGCAAGCTCCTCTGTTATATGCAAGGGTAAGTCCTTACCGTTACCGC
1 GTAAGTCCTTACCGTTACTGTAGGCTCCTCTGCTATATGCAAGGGTAAGTCCTTACCGTTACCGC
22443 AGGCTCCTCTGCTATGTGCAAGG
66 AGGCTCCTCTGCTATGTGCAAGG
** * * *
22466 GTAAGTCCTTACTATTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTTCTTACCGTTACCGC
1 GTAAGTCCTTACCGTTACTGTAGGCTCCTCTGCTATATGCAAGGGTAAGTCCTTACCGTTACCGC
22531 AGGCTCCTCTGCTATGTGCAAGG
66 AGGCTCCTCTGCTATGTGCAAGG
* * *
22554 GTAAGTCCTTACCGTTACTATAGGCTCTTCTGCTTTATGCA
1 GTAAGTCCTTACCGTTACTGTAGGCTCCTCTGCTATATGCA
22595 CATGATAAGA
Statistics
Matches: 114, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 114 1.00
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (88 bp):
GTAAGTCCTTACCGTTACTGTAGGCTCCTCTGCTATATGCAAGGGTAAGTCCTTACCGTTACCGC
AGGCTCCTCTGCTATGTGCAAGG
Found at i:22587 original size:44 final size:44
Alignment explanation
Indices: 22378--22571 Score: 316
Period size: 44 Copynumber: 4.4 Consensus size: 44
22368 ACTATGACTT
* * * *
22378 GTAAGTCCTTACCGTTACTGCAAGCTCCTCTGTTATATGCAAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
22422 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
** *
22466 GTAAGTCCTTACTATTACCGTAGGCTCCTCTGCTATGTGCAAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
*
22510 GTAAGTTCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
22554 GTAAGTCCTTACCGTTAC
1 GTAAGTCCTTACCGTTAC
22572 TATAGGCTCT
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 138 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (44 bp):
GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
Found at i:22641 original size:39 final size:39
Alignment explanation
Indices: 22577--22689 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 39
22567 GTTACTATAG
* * *
22577 GCTCTTCTGCTTTATGCACATGATAAGACCTTACCACAT
1 GCTCATCTTCTTTATGCACAAGATAAGACCTTACCACAT
* **
22616 GCTCATTTTCTTTATGCACAAGATAAGACCTTACTGCAT
1 GCTCATCTTCTTTATGCACAAGATAAGACCTTACCACAT
* * * * *
22655 GCTCCTCTTCTTTGTGCACAGGGTAAGCCCTTACC
1 GCTCATCTTCTTTATGCACAAGATAAGACCTTACC
22690 GGGTGTACAT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (39 bp):
GCTCATCTTCTTTATGCACAAGATAAGACCTTACCACAT
Found at i:23313 original size:17 final size:17
Alignment explanation
Indices: 23291--23329 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
23281 TTTAATAAAA
23291 GTTTTACATTTTCTGAG
1 GTTTTACATTTTCTGAG
23308 GTTTTACATTTTCTGAG
1 GTTTTACATTTTCTGAG
*
23325 ATTTT
1 GTTTT
23330 TATGTGGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.56
Consensus pattern (17 bp):
GTTTTACATTTTCTGAG
Found at i:28521 original size:195 final size:195
Alignment explanation
Indices: 28189--28576 Score: 679
Period size: 195 Copynumber: 2.0 Consensus size: 195
28179 TAACATTTTC
*
28189 TGTATTCTCAGGTCAGAGCTGAGAGGCAAGTTCTTGTCAAAGATTACAACAGGGGATGGGCTGTT
1 TGTATTCTCAGGTCAGAGCTGAGAGGCAAGTTCTTGTCAAAGATTACAACAGGGGAAGGGCTGTT
* * *
28254 GCATTTGATCGAAGAATACATAATGTGTTGGAGGTTTTCACCTTAGATGGATTTAAAATGTAAGT
66 GCATTTGATCAAAGAATACAGAACGTGTTGGAGGTTTTCACCTTAGATGGATTTAAAATGTAAGT
*
28319 TGATAACTAATTTCATATGTTGTTTCATGTCTCATCCTTT-TTAAAAAAGTTACTTGGTATGTTT
131 CGATAACTAATTTCATATGTTGTTTCATGTCTCATCCTTTCTT-AAAAAGTTACTTGGTATGTTT
28383 A
195 A
*
28384 TGTATTCTCAGGTCAGAGCTGAGAGGCAAGTTCTTGTCGAAGATTACAACAGGGGAAGGGCTGTT
1 TGTATTCTCAGGTCAGAGCTGAGAGGCAAGTTCTTGTCAAAGATTACAACAGGGGAAGGGCTGTT
* *
28449 GCGTTTGATTAAAGAATACAGAACGTGTTGGAGGTTTTCACCTTAGATGGATTTAAAATGTAAGT
66 GCATTTGATCAAAGAATACAGAACGTGTTGGAGGTTTTCACCTTAGATGGATTTAAAATGTAAGT
*
28514 CGATAACTGATTTCATATGTTGTTTCATGTCTCATCCTTTCTTAAAAAGTTACTTGGTATGTT
131 CGATAACTAATTTCATATGTTGTTTCATGTCTCATCCTTTCTTAAAAAGTTACTTGGTATGTT
28577 CATTATTGTC
Statistics
Matches: 183, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
195 181 0.99
196 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (195 bp):
TGTATTCTCAGGTCAGAGCTGAGAGGCAAGTTCTTGTCAAAGATTACAACAGGGGAAGGGCTGTT
GCATTTGATCAAAGAATACAGAACGTGTTGGAGGTTTTCACCTTAGATGGATTTAAAATGTAAGT
CGATAACTAATTTCATATGTTGTTTCATGTCTCATCCTTTCTTAAAAAGTTACTTGGTATGTTTA
Found at i:30207 original size:11 final size:11
Alignment explanation
Indices: 30189--30235 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
30179 AGGTTGCTAG
30189 AAGG-TTTTTT
1 AAGGCTTTTTT
* *
30199 AAAGCTTTTTC
1 AAGGCTTTTTT
30210 AAGGC-TTTTT
1 AAGGCTTTTTT
30220 AAGGCTTTTTTT
1 AAGGC-TTTTTT
30232 AAGG
1 AAGG
30236 TTGTTATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 12 0.40
11 9 0.30
12 9 0.30
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (11 bp):
AAGGCTTTTTT
Found at i:30213 original size:21 final size:21
Alignment explanation
Indices: 30189--30229 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30179 AGGTTGCTAG
*
30189 AAGGTTTTTTAAAGCTTTTTC
1 AAGGCTTTTTAAAGCTTTTTC
*
30210 AAGGCTTTTTAAGGCTTTTT
1 AAGGCTTTTTAAAGCTTTTT
30230 TTAAGGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (21 bp):
AAGGCTTTTTAAAGCTTTTTC
Found at i:30229 original size:10 final size:10
Alignment explanation
Indices: 30189--30229 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
30179 AGGTTGCTAG
*
30189 AAGGTTTTTT
1 AAGGCTTTTT
*
30199 AAAGCTTTTT
1 AAGGCTTTTT
30209 CAAGGCTTTTT
1 -AAGGCTTTTT
30220 AAGGCTTTTT
1 AAGGCTTTTT
30230 TTAAGGTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (10 bp):
AAGGCTTTTT
Found at i:30230 original size:12 final size:11
Alignment explanation
Indices: 30167--30235 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
30157 GCCTTACCTC
30167 AAGGCTTTTTT
1 AAGGCTTTTTT
* **
30178 AAGG-TTGCTAG
1 AAGGCTT-TTTT
30189 AAGG-TTTTTT
1 AAGGCTTTTTT
* *
30199 AAAGCTTTTTC
1 AAGGCTTTTTT
30210 AAGGC-TTTTT
1 AAGGCTTTTTT
30220 AAGGCTTTTTTT
1 AAGGC-TTTTTT
30232 AAGG
1 AAGG
30236 TTGTTATATT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
10 15 0.34
11 20 0.45
12 9 0.20
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.46
Consensus pattern (11 bp):
AAGGCTTTTTT
Found at i:36837 original size:16 final size:15
Alignment explanation
Indices: 36804--36845 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
36794 TGGTTATTTT
36804 CTTTTATCTTTTCCC
1 CTTTTATCTTTTCCC
36819 CTTTTAT-TTTCTGCCC
1 CTTTTATCTTT-T-CCC
36835 CTTTTATCTTT
1 CTTTTATCTTT
36846 ATGATATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 8 0.33
16 10 0.42
17 3 0.12
ACGTcount: A:0.07, C:0.29, G:0.02, T:0.62
Consensus pattern (15 bp):
CTTTTATCTTTTCCC
Found at i:37139 original size:13 final size:13
Alignment explanation
Indices: 37121--37146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37111 ATCTTTTCAT
37121 CTTTTGTTAACTA
1 CTTTTGTTAACTA
37134 CTTTTGTTAACTA
1 CTTTTGTTAACTA
37147 GTCTGGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
CTTTTGTTAACTA
Found at i:40606 original size:201 final size:203
Alignment explanation
Indices: 40237--40655 Score: 713
Period size: 201 Copynumber: 2.1 Consensus size: 203
40227 CTTATTCATT
* * *
40237 TACTTCTGCAACTATCT-TGTGGAAACTTGAATTCAGAAATTGAAGTTTTTGTTTCAGAATAGGG
1 TACTTCTGCAACTAT-TGTATAGAAACTTGAATTCAGAAATTGAAGTTTCTGTTTCAGAATAGGG
40301 TCCAGTACGAAAATGTTATGAAAGAAAAGGTTCTTCCTCAAATTAAGGAGGCAGAGGCAGAATAT
65 TCCAGTACGAAAATGTTATGAAAGAAAAGGTTCTTCCTCAAATTAAGGAGGCAGAGGCAGAATAT
*
40366 GTGGAACTAGAAAAGAATCGTAAGGTTGATATTTATGCCTTTCAAGATATACTAACCAATTTTAG
130 GTGGAACTAGAAAAGAATCGTAAGGTTGATATTTATGCCTTTCAAGATATACTAACCAATTCTAG
40431 CCCATGTTA
195 CCCATGTTA
40440 TACTTCTGCAACTATTGTATAG-AACTTGAATTCAGAAATTGAAGTTTCTG-TTCAGAATAGGGT
1 TACTTCTGCAACTATTGTATAGAAACTTGAATTCAGAAATTGAAGTTTCTGTTTCAGAATAGGGT
*
40503 CCAGTATGAAAATGTTATGAAAGAAAAGGTTCTTCCTCAAATTAAGGAGGCAGAGGCAGAATATG
66 CCAGTACGAAAATGTTATGAAAGAAAAGGTTCTTCCTCAAATTAAGGAGGCAGAGGCAGAATATG
* * *
40568 TGGAACTAGAGAAGAATCGTAAGGTTGATATTTATGCCTTTCTAGATATACTATCCAATTCTAGC
131 TGGAACTAGAAAAGAATCGTAAGGTTGATATTTATGCCTTTCAAGATATACTAACCAATTCTAGC
40633 CCATGTTA
196 CCATGTTA
*
40641 TA-TTTTGCAAC-ATTG
1 TACTTCTGCAACTATTG
40656 CAGGAGAGCT
Statistics
Matches: 206, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
199 4 0.02
200 8 0.04
201 148 0.72
202 28 0.14
203 18 0.09
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (203 bp):
TACTTCTGCAACTATTGTATAGAAACTTGAATTCAGAAATTGAAGTTTCTGTTTCAGAATAGGGT
CCAGTACGAAAATGTTATGAAAGAAAAGGTTCTTCCTCAAATTAAGGAGGCAGAGGCAGAATATG
TGGAACTAGAAAAGAATCGTAAGGTTGATATTTATGCCTTTCAAGATATACTAACCAATTCTAGC
CCATGTTA
Found at i:47505 original size:6 final size:6
Alignment explanation
Indices: 47494--47525 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
47484 TCAAATCAAT
47494 GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GA
1 GAGGCA GAGGCA GAGGCA GAGGCA GAGGCA GA
47526 ATAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.50, T:0.00
Consensus pattern (6 bp):
GAGGCA
Found at i:56073 original size:22 final size:20
Alignment explanation
Indices: 56036--56099 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 20
56026 ACATTTTTTG
*
56036 AATTCGCAACAAGAATTTACC
1 AATTCGCAAC-TGAATTTACC
**
56057 AAATTCGCAACTCGAATTCGCC
1 -AATTCGCAACT-GAATTTACC
*
56079 AATTACGCAACTAAATTTACC
1 AATT-CGCAACTGAATTTACC
56100 GCGTTTACCT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (20 bp):
AATTCGCAACTGAATTTACC
Found at i:56209 original size:20 final size:20
Alignment explanation
Indices: 56184--56236 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
56174 ATTAAATTCA
56184 CAACTCAATTTTAAAACTCG
1 CAACTCAATTTTAAAACTCG
* * **
56204 CAACTCGAA-TTCAGATTTCG
1 CAACTC-AATTTTAAAACTCG
56224 CAACTCAATTTTA
1 CAACTCAATTTTA
56237 CCACGTTTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (20 bp):
CAACTCAATTTTAAAACTCG
Found at i:56498 original size:20 final size:22
Alignment explanation
Indices: 56454--56509 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 22
56444 AACTCGGTAA
*
56454 AATT-GAGTTGCGAAATTGGCG
1 AATTCGAGTTGCGAAATTGCCG
56475 AATTCGAGTTGCGAAA-T-CCG
1 AATTCGAGTTGCGAAATTGCCG
56495 AATTCGAGTTGCGAA
1 AATTCGAGTTGCGAA
56510 TTTGAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 17 0.52
21 5 0.15
22 11 0.33
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (22 bp):
AATTCGAGTTGCGAAATTGCCG
Found at i:56566 original size:20 final size:19
Alignment explanation
Indices: 56543--56614 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
56533 TGTAAATTCT
56543 TGTTGCGAATTCGAAAATTG
1 TGTTGCGAATTCG-AAATTG
* **
56563 TGTTGCGAATTTGACTTTCG
1 TGTTGCGAATTCGAAATT-G
*
56583 TGTTGCAAATTCGAAATTG
1 TGTTGCGAATTCGAAATTG
**
56602 AATTGCGAATTCG
1 TGTTGCGAATTCG
56615 TTGGTTATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
19 14 0.34
20 27 0.66
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (19 bp):
TGTTGCGAATTCGAAATTG
Found at i:61030 original size:26 final size:26
Alignment explanation
Indices: 61001--61083 Score: 113
Period size: 26 Copynumber: 3.4 Consensus size: 26
60991 TTTTTGATTG
61001 TTTAAAATTTTATACATTTGTCTATC
1 TTTAAAATTTTATACATTTGTCTATC
*
61027 TTTAAAATTTTATAAATTTGTCTATC
1 TTTAAAATTTTATACATTTGTCTATC
*
61053 -----GATTTTATACATTTGTCTATC
1 TTTAAAATTTTATACATTTGTCTATC
61074 TTTAAAATTT
1 TTTAAAATTT
61084 ATAAAATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
21 19 0.40
26 29 0.60
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (26 bp):
TTTAAAATTTTATACATTTGTCTATC
Found at i:61059 original size:21 final size:21
Alignment explanation
Indices: 61033--61073 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
61023 TATCTTTAAA
61033 ATTTTATAAATTTGTCTATCG
1 ATTTTATAAATTTGTCTATCG
*
61054 ATTTTATACATTTGTCTATC
1 ATTTTATAAATTTGTCTATC
61074 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTTTATAAATTTGTCTATCG
Found at i:67559 original size:14 final size:13
Alignment explanation
Indices: 67515--67575 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 13
67505 TTCATTTAAA
67515 ATTTGAAAGTTTATG
1 ATTT-AAAGTTTA-G
67530 ATTT-AAGATTTAG
1 ATTTAAAG-TTTAG
67543 ATTTAAAGTTTAGG
1 ATTTAAAGTTTA-G
*
67557 ATTTTAAAATTTAAG
1 A-TTTAAAGTTT-AG
67572 ATTT
1 ATTT
67576 GTTAACAGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 12 0.30
14 12 0.30
15 15 0.38
16 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
ATTTAAAGTTTAG
Found at i:68242 original size:60 final size:60
Alignment explanation
Indices: 68131--68243 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
68121 TTTAGTAATC
* * * * * *
68131 ATTTTGTCACTTTTATTAATTGAGAGACTTAACAAAACAATATCTTGTAGTTGGAGGATT
1 ATTTTGTAACTTTTAATAATCGAGAAACTTAACAAAACAACATCTTATAGTTGGAGGATT
* *
68191 ATTTTGTAACTTTTAATAATCGAGAAACTTAACATACCAACAT-TCTATAGTTG
1 ATTTTGTAACTTTTAATAATCGAGAAACTTAACAAAACAACATCT-TATAGTTG
68244 AAAGACTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 43 0.98
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAATCGAGAAACTTAACAAAACAACATCTTATAGTTGGAGGATT
Found at i:69501 original size:53 final size:53
Alignment explanation
Indices: 69426--69529 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
69416 TAGTCACTTG
69426 TTAATGCTGGATTCCTCTTTTAAACCAAAACATATATAAATTCCTCTTTTAAT
1 TTAATGCTGGATTCCTCTTTTAAACCAAAACATATATAAATTCCTCTTTTAAT
*
69479 TTAATGCTGGATTCCTCTTTTAAATCAAAACATATATAAATTCCTCTTTTA
1 TTAATGCTGGATTCCTCTTTTAAACCAAAACATATATAAATTCCTCTTTTA
69530 TATGGTGCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (53 bp):
TTAATGCTGGATTCCTCTTTTAAACCAAAACATATATAAATTCCTCTTTTAAT
Found at i:70596 original size:4 final size:4
Alignment explanation
Indices: 70587--70618 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
70577 TAATCACCCT
70587 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
70619 ATGTGTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:72324 original size:20 final size:20
Alignment explanation
Indices: 72301--72341 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
72291 TTTTTAAAAA
72301 ACCTAAAATTAATTTTAGAC
1 ACCTAAAATTAATTTTAGAC
72321 ACCTAAAATTAATTTTAGAC
1 ACCTAAAATTAATTTTAGAC
72341 A
1 A
72342 TTGTTTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (20 bp):
ACCTAAAATTAATTTTAGAC
Found at i:72911 original size:19 final size:19
Alignment explanation
Indices: 72887--72954 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
72877 TTTCAAAAAT
72887 TTTATATTATTGATAAGTA
1 TTTATATTATTGATAAGTA
* * *
72906 TTTATATAATCAATTTCAAAAAT-
1 TTTATAT--T--A-TTGATAAGTA
72929 TTTATATTATTGATAAGTA
1 TTTATATTATTGATAAGTA
72948 TTTATAT
1 TTTATAT
72955 AATCAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 6 0.16
19 15 0.41
21 2 0.05
23 8 0.22
24 6 0.16
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (19 bp):
TTTATATTATTGATAAGTA
Found at i:72924 original size:42 final size:42
Alignment explanation
Indices: 72877--72963 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
72867 ATTTGATTTT
72877 TTTCAAAAATTTTATATTATTGATAAGTATTTATATAATCAA
1 TTTCAAAAATTTTATATTATTGATAAGTATTTATATAATCAA
72919 TTTCAAAAATTTTATATTATTGATAAGTATTTATATAATCAA
1 TTTCAAAAATTTTATATTATTGATAAGTATTTATATAATCAA
72961 TTT
1 TTT
72964 ATATTATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (42 bp):
TTTCAAAAATTTTATATTATTGATAAGTATTTATATAATCAA
Found at i:74143 original size:46 final size:46
Alignment explanation
Indices: 74046--74144 Score: 157
Period size: 47 Copynumber: 2.2 Consensus size: 46
74036 TTCCCTCAAA
*
74046 TTTGAGTAGTTTTTGTTCTTTTTATTGTAAAAGAGGGGAGTAGTAG
1 TTTGATTAGTTTTTGTTCTTTTTATTGTAAAAGAGGGGAGTAGTAG
74092 TTTGATTAGTTTTTTGTTCTTTTTATTGTTAAAA-AGGGGAGTAGTAG
1 TTTGATTAG-TTTTTGTTCTTTTTATTG-TAAAAGAGGGGAGTAGTAG
74139 -TTGATT
1 TTTGATT
74145 TGCTTGTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
46 14 0.28
47 31 0.62
48 5 0.10
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.49
Consensus pattern (46 bp):
TTTGATTAGTTTTTGTTCTTTTTATTGTAAAAGAGGGGAGTAGTAG
Found at i:77563 original size:2 final size:2
Alignment explanation
Indices: 77556--77623 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
77546 TGGTTATAAC
77556 AT AT AT AT 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 AT AT AT AT
77598 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
77624 CACTTCTTAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81348 original size:33 final size:33
Alignment explanation
Indices: 81311--81377 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
81301 AAACAAATAA
81311 TTGTTTAACATTATATTCCACCTACATAAAATC
1 TTGTTTAACATTATATTCCACCTACATAAAATC
*
81344 TTGTTTAACATTATATTCTACCTACATAAAATC
1 TTGTTTAACATTATATTCCACCTACATAAAATC
81377 T
1 T
81378 GTTCAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (33 bp):
TTGTTTAACATTATATTCCACCTACATAAAATC
Found at i:85687 original size:18 final size:18
Alignment explanation
Indices: 85666--85702 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
85656 TGTTTTTGTC
*
85666 CTTTAATATAAAATTATA
1 CTTTAATATAAAACTATA
85684 CTTTAATATAAAACTATA
1 CTTTAATATAAAACTATA
85702 C
1 C
85703 GTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
CTTTAATATAAAACTATA
Found at i:91553 original size:16 final size:16
Alignment explanation
Indices: 91515--91560 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
91505 ACTATTTTAT
*
91515 TTTTAAAAAAATCAGCTC
1 TTTTAAAAAAA--AACTC
*
91533 ATTTAAAAAAAAACTC
1 TTTTAAAAAAAAACTC
91549 TTTTAAAAAAAA
1 TTTTAAAAAAAA
91561 TCACAATTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 15 0.60
18 10 0.40
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (16 bp):
TTTTAAAAAAAAACTC
Found at i:91627 original size:45 final size:45
Alignment explanation
Indices: 91562--91649 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
91552 TAAAAAAAAT
* * * **
91562 CACAATTGCGGTACTTGCAATTACCGTAATAGTATTTATTATATC
1 CACAACTGCGGTACTCGCAATCACCACAATAGTATTTATTATATC
91607 CACAACTGCGGTACTCGCAATCACCACAATAGTATTTATTATA
1 CACAACTGCGGTACTCGCAATCACCACAATAGTATTTATTATA
91650 ATTATAACCG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (45 bp):
CACAACTGCGGTACTCGCAATCACCACAATAGTATTTATTATATC
Found at i:94059 original size:46 final size:46
Alignment explanation
Indices: 94007--94135 Score: 134
Period size: 46 Copynumber: 2.8 Consensus size: 46
93997 CATCATTGAT
* *
94007 ATGAGGCATGGGGTCACATAGTATCAGGAAGGTACAT-TCATTTCGG
1 ATGAGGCATGGGGTCACATAGTATCAGGAACGTACATCTCATATC-G
* * * * *
94053 ATGAGGCCTGGGATCACGTAGTATCAAGAACGTACATCTGATATCG
1 ATGAGGCATGGGGTCACATAGTATCAGGAACGTACATCTCATATCG
* * * *
94099 AGTGAGGCTTGAGGTTACATAGCATCAGGAACGTACA
1 A-TGAGGCATGGGGTCACATAGTATCAGGAACGTACA
94136 CTTGACATCA
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
46 34 0.51
47 33 0.49
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (46 bp):
ATGAGGCATGGGGTCACATAGTATCAGGAACGTACATCTCATATCG
Found at i:94166 original size:47 final size:47
Alignment explanation
Indices: 94054--94191 Score: 122
Period size: 47 Copynumber: 2.9 Consensus size: 47
94044 TCATTTCGGA
* * * *
94054 TGAGGCCTGGGATCACGTAGTATCAAGAACGTACA-TCTGATATCGAG
1 TGAGGCCTGGG-TCACATAGCATCAAGAACGTACACTCTGACATCAAG
* * *
94101 TGAGGCTTGAGGTTACATAGCATCAGGAACGTACACT-TGACATCAAG
1 TGAGGCCTG-GGTCACATAGCATCAAGAACGTACACTCTGACATCAAG
* * *
94148 TGAGGCCTAGGGTCACATA-CAATCATGAACATACAC-CAGACATC
1 TGAGGCCT-GGGTCACATAGC-ATCAAGAACGTACACTCTGACATC
94192 CATCTTTGGA
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
46 1 0.01
47 69 0.93
48 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (47 bp):
TGAGGCCTGGGTCACATAGCATCAAGAACGTACACTCTGACATCAAG
Found at i:94559 original size:78 final size:79
Alignment explanation
Indices: 94430--94595 Score: 298
Period size: 78 Copynumber: 2.1 Consensus size: 79
94420 CAAATTAATT
*
94430 ATTTAGTAGCTTATAAAAAGTAATTAATCTAATTCTGAATATCTTACAACATTTAACTCACAATC
1 ATTTACTAGCTTATAAAAAGTAATTAATCTAATTCTGAATATCTTACAACATTTAACTCACAATC
94495 TAGA-TTTTTTTTC
66 TAGATTTTTTTTTC
*
94508 ATTTACTAGCTTATAAAAAGTAATTAATCTAATTTTGAATATCTTACAACATTTAACTCACAATC
1 ATTTACTAGCTTATAAAAAGTAATTAATCTAATTCTGAATATCTTACAACATTTAACTCACAATC
94573 TAGATTTTTTTTTTC
66 TAGA-TTTTTTTTTC
94588 ATTTACTA
1 ATTTACTA
94596 TAATTAAGGA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
78 67 0.80
80 17 0.20
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (79 bp):
ATTTACTAGCTTATAAAAAGTAATTAATCTAATTCTGAATATCTTACAACATTTAACTCACAATC
TAGATTTTTTTTTC
Found at i:97768 original size:9 final size:8
Alignment explanation
Indices: 97743--97777 Score: 52
Period size: 9 Copynumber: 4.1 Consensus size: 8
97733 TTGATTTTCA
97743 ATTTTATT
1 ATTTTATT
97751 ATTTTATT
1 ATTTTATT
97759 ATTATTATT
1 ATT-TTATT
97768 ATTTTTATT
1 A-TTTTATT
97777 A
1 A
97778 AGTTAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 11 0.44
9 12 0.48
10 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTTATT
Found at i:98110 original size:42 final size:42
Alignment explanation
Indices: 98059--98227 Score: 232
Period size: 42 Copynumber: 4.0 Consensus size: 42
98049 TGCGTTAATA
** *
98059 AGACGAGAATCAAAAGTGTTATGCCTCCTTTCGTTCTACTTT
1 AGACGAGAATCAAAAGTGCGATGCCTCCTTCCGTTCTACTTT
* * *
98101 AGATGAGAATCGAAAGTGCTATGCCTCCTTCCGTTCTACTTT
1 AGACGAGAATCAAAAGTGCGATGCCTCCTTCCGTTCTACTTT
* *
98143 AGACGAGAATCGAAAGTGCGATGCCTCCTTACGTTCTACTTT
1 AGACGAGAATCAAAAGTGCGATGCCTCCTTCCGTTCTACTTT
* *
98185 AGACGAGAATCGAAAA-TGTGATGCCTCCTTCCATTCTACTTT
1 AGACGAGAATC-AAAAGTGCGATGCCTCCTTCCGTTCTACTTT
98227 A
1 A
98228 TTCACCTTTC
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
42 112 0.97
43 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (42 bp):
AGACGAGAATCAAAAGTGCGATGCCTCCTTCCGTTCTACTTT
Found at i:98209 original size:84 final size:84
Alignment explanation
Indices: 98059--98227 Score: 259
Period size: 84 Copynumber: 2.0 Consensus size: 84
98049 TGCGTTAATA
** * * *
98059 AGACGAGAATCAAAAGTGTTATGCCTCCTTTCGTTCTACTTTAGATGAGAATCGAAAGTGCTATG
1 AGACGAGAATCAAAAGTGCGATGCCTCCTTACGTTCTACTTTAGACGAGAATCGAAAATGCTATG
*
98124 CCTCCTTCCGTTCTACTTT
66 CCTCCTTCCATTCTACTTT
*
98143 AGACGAGAATCGAAAGTGCGATGCCTCCTTACGTTCTACTTTAGACGAGAATCGAAAATG-TGAT
1 AGACGAGAATCAAAAGTGCGATGCCTCCTTACGTTCTACTTTAGACGAGAATCGAAAATGCT-AT
98207 GCCTCCTTCCATTCTACTTT
65 GCCTCCTTCCATTCTACTTT
98227 A
1 A
98228 TTCACCTTTC
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
83 1 0.01
84 76 0.99
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (84 bp):
AGACGAGAATCAAAAGTGCGATGCCTCCTTACGTTCTACTTTAGACGAGAATCGAAAATGCTATG
CCTCCTTCCATTCTACTTT
Found at i:98276 original size:23 final size:23
Alignment explanation
Indices: 98234--98277 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
98224 TTTATTCACC
* *
98234 TTTCTTTCCTTTCCTGTTGTTAA
1 TTTCTTTCCTTTCATCTTGTTAA
98257 TTTCTTTCCTTTCATCTTGTT
1 TTTCTTTCCTTTCATCTTGTT
98278 CTTACCCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.23, G:0.07, T:0.64
Consensus pattern (23 bp):
TTTCTTTCCTTTCATCTTGTTAA
Found at i:103739 original size:23 final size:23
Alignment explanation
Indices: 103713--103790 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
103703 CACCATAGCT
103713 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
103736 CATATAATTGCACTGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
103759 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
103782 TATAATAAT
1 CAT-ATAAT
103791 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:107016 original size:14 final size:15
Alignment explanation
Indices: 106978--107020 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
106968 TTGATTTTTC
106978 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
106993 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
107007 GGAAAATGAATTAC
1 GGAAAATGAATTAC
107021 ATTTCTGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:107044 original size:14 final size:14
Alignment explanation
Indices: 107022--107055 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
107012 ATGAATTACA
*
107022 TTTCTGGAAAACGT
1 TTTCCGGAAAACGT
107036 TTTCCGGAAAACGT
1 TTTCCGGAAAACGT
107050 TTTCCG
1 TTTCCG
107056 TAAATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (14 bp):
TTTCCGGAAAACGT
Found at i:107272 original size:48 final size:50
Alignment explanation
Indices: 107176--107273 Score: 114
Period size: 48 Copynumber: 2.0 Consensus size: 50
107166 TACAAATATT
*
107176 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * *
107226 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TT-ATTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
107274 TTAATAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 21 0.50
49 13 0.31
50 8 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:107298 original size:25 final size:26
Alignment explanation
Indices: 107242--107298 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
107232 TAAAATAATT
* *
107242 TATTTATTATTAAATATTATTTTATA
1 TATTTATTAATAAATATAATTTTATA
*
107268 -ATTTTATTAATAAA-ATAATTTTGTA
1 TA-TTTATTAATAAATATAATTTTATA
107293 TATTTA
1 TATTTA
107299 GTGAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TATTTATTAATAAATATAATTTTATA
Found at i:107425 original size:22 final size:24
Alignment explanation
Indices: 107400--107574 Score: 73
Period size: 26 Copynumber: 7.2 Consensus size: 24
107390 ATCTTATTAA
107400 AATATTAT-TTA-AATATATAAAT
1 AATATTATATTATAATATATAAAT
107422 AATATTATCATTATTAATATATAAATT
1 AATATTAT-ATTA-TAATATATAAA-T
** * *
107449 TTTATTATATTATTAAAATAAAAAT
1 AATATTATATTA-TAATATATAAAT
* * *
107474 -ATAATATCTTATATTAT-TATAAT
1 AATATTATATTATAATATATA-AAT
*
107497 AATTGATTATTTTAT-ATAATATTAAA-
1 AA-T-ATTATATTATAAT-ATA-TAAAT
*
107523 AATA-TA-ATTATATTATTATAAAT
1 AATATTATATTATAATA-TATAAAT
* * *
107546 ATTAATA-AATA-AATAATATAAAT
1 AATATTATATTATAAT-ATATAAAT
107569 AATATT
1 AATATT
107575 TTTATGAAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 33
0.69 0.12 0.20
Matches are distributed among these distances:
22 18 0.16
23 28 0.24
24 19 0.16
25 4 0.03
26 36 0.31
27 9 0.08
28 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (24 bp):
AATATTATATTATAATATATAAAT
Found at i:107440 original size:26 final size:25
Alignment explanation
Indices: 107401--107540 Score: 81
Period size: 26 Copynumber: 5.4 Consensus size: 25
107391 TCTTATTAAA
107401 ATATTATTTAAATATATAAATAATATT
1 ATATTA-TT-AATATATAAATAATATT
**
107428 ATCATTATTAATATATAAATTTTTATT
1 AT-ATTATTAATATATAAA-TAATATT
* * *
107455 ATATTATTAAAATAAAAAT-ATAAT
1 ATATTATTAATATATAAATAATATT
* *
107479 ATCTTA-TATTAT-TATAATAATTGATT
1 ATATTATTAATATATA-AATAA-T-ATT
* *
107505 ATTTTATATAATAT-TAAAAATATAATT
1 ATATTAT-TAATATATAAATA-AT-ATT
107532 ATATTATTA
1 ATATTATTA
107541 TAAATATTAA
Statistics
Matches: 88, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.01
23 7 0.08
24 9 0.10
25 2 0.02
26 33 0.38
27 24 0.27
28 12 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
ATATTATTAATATATAAATAATATT
Found at i:107562 original size:32 final size:32
Alignment explanation
Indices: 107492--107562 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 32
107482 TTATATTATT
107492 ATAATAATTGATTATTTTATATAATATTAAAA
1 ATAATAATTGATTATTTTATATAATATTAAAA
107524 AT-ATAATT-A-TATTATTATA-AATATTAATAA
1 ATAATAATTGATTATT-TTATATAATATTAA-AA
107554 ATAAATAAT
1 AT-AATAAT
107563 ATAAATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
29 12 0.34
30 10 0.29
31 6 0.17
32 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
ATAATAATTGATTATTTTATATAATATTAAAA
Found at i:107815 original size:42 final size:42
Alignment explanation
Indices: 107748--107863 Score: 196
Period size: 42 Copynumber: 2.8 Consensus size: 42
107738 ATGAATTACA
*
107748 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
* *
107790 TTCCGGAAAACGAATTATGTTAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
*
107832 TTCCGAAAAACGAATTACGTGAAACAAACACG
1 TTCCGGAAAACGAATTACGTGAAACAAACACG
107864 AGAATTCGAG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.21
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
Found at i:109880 original size:33 final size:33
Alignment explanation
Indices: 109838--109905 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
109828 CGTCCGTCAC
109838 TAAGTAATTTCATCTCTCAATTTCATCATACCA
1 TAAGTAATTTCATCTCTCAATTTCATCATACCA
109871 TAAGTAATTTCATCTCTCAATTTCATCATACCA
1 TAAGTAATTTCATCTCTCAATTTCATCATACCA
109904 TA
1 TA
109906 TCACACACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (33 bp):
TAAGTAATTTCATCTCTCAATTTCATCATACCA
Done.