Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004438.1 Hibiscus syriacus cultivar Beakdansim tig00009735_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: 125276
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3102 original size:3 final size:3
Alignment explanation
Indices: 3094--3181 Score: 169
Period size: 3 Copynumber: 29.7 Consensus size: 3
3084 TTTCGGTTTG
3094 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3141 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3182 TAACTCAAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 82 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3689 original size:117 final size:120
Alignment explanation
Indices: 3362--3836 Score: 518
Period size: 117 Copynumber: 4.0 Consensus size: 120
3352 TAAGATCCAA
* ** *
3362 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGGAAACGTTGA-CCAAACTTTTTATGTGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-ATTGGAAATATTGATCC-ACCTTTTT-TGTGA
* * * * *
3426 TGGAATCAAACGTAATGCTA-CTGCTGATCCAAATCCTTATGTGATGGAATTGAGCGTG
63 TGGAATCAAACGTAGTGCTAGC-ACTGATCCAACTCCTTATGTGATGGAATCGAGCATG
* * * *
3484 TTGAATAAGCTCTTTTCATTATG-ACTTCTTCATTGGAAATGTTGATCCACCTTATTTTGTGATG
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGGAAATATTGATCCACCTT-TTTTGTGATG
* * * *
3548 GAATC-AACGTA-TGTTGGCAATGATCCAACTCCTTATGTGGT-GAATCGAGCATG
65 GAATCAAACGTAGTGCTAGCACTGATCCAACTCCTTATGTGATGGAATCGAGCATG
* * *
3601 TTGAATAAGTTCTTCTCGTTATGAACTTCTTCATTGG-AATATTGATCCACCTTTTTTGTGATGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGGAAATATTGATCCACCTTTTTTGTGATGG
* * * *
3665 AATC-AACGTAGTACTAGCACTGATCCAACTCCTTATGTAAT-GAATTGAGCTAAAG
66 AATCAAACGTAGTGCTAGCACTGATCCAACTCCTTATGTGATGGAATCGAGC--ATG
* * * * *
3720 TTGAACAAGTTCTTTTCATTATGAACTTCTTCATTGGAAATGTTAATTCACCTCCTTTTGTGATG
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGGAAATATTGATCCACCT-TTTTTGTGATG
* ** *
3785 GAATCAAACGTAGTGCTGGTGCCGATCCAACTCCTTATGTGATGGAATCGAG
65 GAATCAAACGTAGTGCTAGCACTGATCCAACTCCTTATGTGATGGAATCGAG
3837 TGAAAAATGT
Statistics
Matches: 300, Mismatches: 42, Indels: 21
0.83 0.12 0.06
Matches are distributed among these distances:
116 20 0.07
117 77 0.26
118 35 0.12
119 43 0.14
120 40 0.13
121 27 0.09
122 51 0.17
123 7 0.02
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (120 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCATTGGAAATATTGATCCACCTTTTTTGTGATGG
AATCAAACGTAGTGCTAGCACTGATCCAACTCCTTATGTGATGGAATCGAGCATG
Found at i:3819 original size:239 final size:239
Alignment explanation
Indices: 3362--3836 Score: 599
Period size: 239 Copynumber: 2.0 Consensus size: 239
3352 TAAGATCCAA
*
3362 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTGGAAACGTTGACCAAACTTTTTATGTGAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTATTGGAAAC-TTGACCAAACTTTTTATGTGAT
* * * * *
3427 GGAATCAAACGTAATGCTACTGCTGATCCAAATCCTTATGTGATGGAATTGAGCGTGTTGAATAA
65 GAAATCAAACGTAATACTACTACTGATCCAAATCCTTATGTAATGGAATTGAGCGTGTTGAACAA
* *
3492 GCTCTTTTCATTATGACTTCTTCATTGGAAATGTTGATCCACCTTATTTTGTGATGGAATCAACG
130 GCTCTTTTCATTATGACTTCTTCATTGGAAATGTTAATCCACCTCATTTTGTGATGGAATCAACG
* * *
3557 TATGTTGGCAATGATCCAACTCCTTATGTGGT-GAATCGAGCATG
195 TATGCTGGCAACGATCCAACTCCTTATGTGATGGAATCGAGCATG
* * *
3601 TTGAATAAGTTCTTCTCGTTATGAACTTCTTC-ATTGGAATA-TTGATCC-ACCTTTTT-TGTGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTATTGGAA-ACTTGA-CCAAACTTTTTATGTGA
* *
3662 TGAAATC-AACGTAGTACTAGC-ACTGATCCAACTCCTTATGTAAT-GAATTGAGC-TAAAGTTG
64 TGAAATCAAACGTAATACTA-CTACTGATCCAAATCCTTATGTAATGGAATTGAGCGT---GTTG
* * *
3723 AACAAGTTCTTTTCATTATGAACTTCTTCATTGGAAATGTTAATTCACCTCCTTTTGTGATGGAA
125 AACAAGCTCTTTTCATTATG-ACTTCTTCATTGGAAATGTTAATCCACCTCATTTTGTGATGGAA
***
3788 TCAAACGTAGTGCTGGTGCCGATCCAACTCCTTATGTGATGGAATCGAG
189 TC-AACGTA-TGCTGGCAACGATCCAACTCCTTATGTGATGGAATCGAG
3837 TGAAAAATGT
Statistics
Matches: 204, Mismatches: 22, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
233 1 0.00
234 9 0.04
235 30 0.15
236 34 0.17
237 53 0.26
238 14 0.07
239 55 0.27
240 8 0.04
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (239 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTATTGGAAACTTGACCAAACTTTTTATGTGATG
AAATCAAACGTAATACTACTACTGATCCAAATCCTTATGTAATGGAATTGAGCGTGTTGAACAAG
CTCTTTTCATTATGACTTCTTCATTGGAAATGTTAATCCACCTCATTTTGTGATGGAATCAACGT
ATGCTGGCAACGATCCAACTCCTTATGTGATGGAATCGAGCATG
Found at i:3861 original size:44 final size:42
Alignment explanation
Indices: 3813--3959 Score: 122
Period size: 42 Copynumber: 3.5 Consensus size: 42
3803 GTGCCGATCC
* *
3813 AACTCCTTATGTGATGGAATCGAGTGAAAAATGTAATGTTG-CCT
1 AACTCCTTATGTGATGGAAT-GAGCGAAAAATG--ATGTTGACCA
** *
3857 AACTCCTTATGTGATGG-ATGAGCGAATGATGATGTTGATCA
1 AACTCCTTATGTGATGGAATGAGCGAAAAATGATGTTGACCA
* * *
3898 AACTCCTTATGTGATGG-ATAAGTGAAATGATGATGTTGATCC-
1 AACTCCTTATGTGATGGAATGAGCGAAA-AATGATGTTGA-CCA
** *
3940 ATGTCCTTATGTAATGGAAT
1 AACTCCTTATGTGATGGAAT
3960 CAAGTCAAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
40 6 0.07
41 25 0.29
42 34 0.39
43 5 0.06
44 17 0.20
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (42 bp):
AACTCCTTATGTGATGGAATGAGCGAAAAATGATGTTGACCA
Found at i:3947 original size:42 final size:42
Alignment explanation
Indices: 3808--3999 Score: 185
Period size: 44 Copynumber: 4.5 Consensus size: 42
3798 TGCTGGTGCC
* *
3808 GATCCAACTCCTTATGTGATGGAATCGAGTGAAAAATG-TAATGTT
1 GATCCAACTCCTTATGTGATGG-AT-AAGTG--AAATGATGATGTT
* *
3853 G--CCTAACTCCTTATGTGATGGATGAGCG-AATGATGATGTT
1 GATCC-AACTCCTTATGTGATGGATAAGTGAAATGATGATGTT
*
3893 GATCAAACTCCTTATGTGATGGATAAGTGAAATGATGATGTT
1 GATCCAACTCCTTATGTGATGGATAAGTGAAATGATGATGTT
** * * *
3935 GATCCATGTCCTTATGTAATGGAATCAAGTCAAATGTTGATGTT
1 GATCCAACTCCTTATGTGATGG-AT-AAGTGAAATGATGATGTT
* *
3979 GATCCAACCCCTTCTGTGATG
1 GATCCAACTCCTTATGTGATG
4000 ATTCAAATAA
Statistics
Matches: 124, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
39 4 0.03
40 7 0.06
41 22 0.18
42 35 0.28
43 6 0.05
44 49 0.40
45 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (42 bp):
GATCCAACTCCTTATGTGATGGATAAGTGAAATGATGATGTT
Found at i:3980 original size:44 final size:42
Alignment explanation
Indices: 3857--3991 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 42
3847 AATGTTGCCT
* * * *
3857 AACTCCTTATGTGATGGATGAG-CGAATGATGATGTTGATCA
1 AACTCCTTATGTAATGGATAAGTCAAATGATGATGTTGATCC
* *
3898 AACTCCTTATGTGATGGATAAGTGAAATGATGATGTTGATCC
1 AACTCCTTATGTAATGGATAAGTCAAATGATGATGTTGATCC
** *
3940 ATGTCCTTATGTAATGGAATCAAGTCAAATGTTGATGTTGATCC
1 AACTCCTTATGTAATGG-AT-AAGTCAAATGATGATGTTGATCC
*
3984 AACCCCTT
1 AACTCCTT
3992 CTGTGATGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 21 0.27
42 30 0.38
43 2 0.03
44 26 0.33
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (42 bp):
AACTCCTTATGTAATGGATAAGTCAAATGATGATGTTGATCC
Found at i:5044 original size:21 final size:22
Alignment explanation
Indices: 5018--5059 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5008 ATCATCATTA
5018 TCATCATCAA-CATTCTTATCG
1 TCATCATCAATCATTCTTATCG
* *
5039 TCATCATTAATCATTTTTATC
1 TCATCATCAATCATTCTTATC
5060 ATATAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (22 bp):
TCATCATCAATCATTCTTATCG
Found at i:5293 original size:23 final size:23
Alignment explanation
Indices: 5263--5332 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
5253 GTGCCATATA
*
5263 AAATGTCCCGAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCACGTAG
*
5286 AAATGTCCCAGAA-GACCATGTAG
1 AAATGTCCC-GAAGGACCACGTAG
* * *
5309 AATTGTCCTGAAGGACCACATAG
1 AAATGTCCCGAAGGACCACGTAG
5332 A
1 A
5333 TGTCCGAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.08
23 33 0.85
24 3 0.08
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (23 bp):
AAATGTCCCGAAGGACCACGTAG
Found at i:7445 original size:36 final size:37
Alignment explanation
Indices: 7389--7569 Score: 168
Period size: 37 Copynumber: 4.9 Consensus size: 37
7379 TTGGGTTGTT
* * *
7389 ACAATTTTCTAGAGAAATGATCCTAAAAAGGACTCAA
1 ACAATTTTATAGAGAAACGATCCTAAGAAGGACTCAA
* *
7426 ACAA-TTTATAGATAAATGATCCTAAGAAGGACTCAA
1 ACAATTTTATAGAGAAACGATCCTAAGAAGGACTCAA
** * * **
7462 ACAACATTATAGAGAAACAATCTTAAGAAATACTCAA
1 ACAATTTTATAGAGAAACGATCCTAAGAAGGACTCAA
* * * *
7499 ACAATTTTCTAGAAAAACGTTCCTAAGAAGGATTCTAA
1 ACAATTTTATAGAGAAACGATCCTAAGAAGGACTC-AA
** * *
7537 TGAA-TTTATAGAGAAAAGGTCCTAAGAAGGACT
1 ACAATTTTATAGAGAAACGATCCTAAGAAGGACT
7570 TAATAATTTC
Statistics
Matches: 115, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
36 33 0.29
37 78 0.68
38 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (37 bp):
ACAATTTTATAGAGAAACGATCCTAAGAAGGACTCAA
Found at i:8622 original size:54 final size:53
Alignment explanation
Indices: 8487--9171 Score: 585
Period size: 54 Copynumber: 12.9 Consensus size: 53
8477 TTACAGATAT
* * * * * *
8487 CATCAAGAAACCCCTAAAAATTAGACTTA-ATATTTAAAAATTCATTTGATGTAAT
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCTTTAAAAATTCATTTGA---AAA
* * * *
8542 CATTAAGAAACCCCTGAAAACCAGGCTTAGCCTCTTTAAAAATCCATTTGAAGA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAG-CTCTTTAAAAATTCATTTGAAAA
* * * *
8596 TATCAAGAAACCCTTGAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGC-TCTTTAAAAATTCATTTGAAAA
* * * * *
8650 CATCAAGAAACCCCTAAAAATAAAGCTTAGCTCATTTAAACATTTATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTC-TTTAAAAATTCATTTGAAAA
* * * * * *
8704 CATC-AGAAA-TCCTAGAAAATCAAGATTAGTTGATTTCAAAATTCATTTG-AAA
1 CATCAAGAAACCCCT-GAAAATCAGGCTTAGCT-CTTTAAAAATTCATTTGAAAA
*
8756 CATAAAGAAAACCCCT-AAAATCAGGCTTAGCTCATTTAAAAATTCATTT--AAA
1 CATCAAG-AAACCCCTGAAAATCAGGCTTAGCTC-TTTAAAAATTCATTTGAAAA
* * * * * *
8808 CATTAAAAAAACCCT-AAAATCAAGCTTAGAAT-TTTCAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAG-CTCTTTAAAAATTCATTTGAAAA
* * * *
8860 CA-C---CAACCCCTAAAAATTAGGCTTAGCTCATTTAAACATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTC-TTTAAAAATTCATTTGAAAA
* * * * * * *
8910 CATCAAGAAATCCCT-AAAGTCAAGCTAAGTTTTTTCAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCTTTAAAAATTCATTTGAAAA
* * *
8962 CATCAAGAAACCCCTAAAAATCAAGCTTAGCTCATTTACAAA-TC-TTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTC-TTTAAAAATTCATTTGAAAA
* * * * *
9014 TAT-AAAAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGC-TCTTTAAAAATTCATTTGAAAA
* * * *
9067 CATTAAGAAACCCCTGAAAATTAGGCTTAGCTCATTTAAAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTC-TTTAAAAATTCATTTGAAAA
* * *
9121 CATCAAGAAACCCTTGAAAATCAGACTTAACTCCTTTAAAAATTCATTTGA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCT-CTTTAAAAATTCATTTGA
9172 TGACATCATA
Statistics
Matches: 510, Mismatches: 92, Indels: 57
0.77 0.14 0.09
Matches are distributed among these distances:
48 7 0.01
49 12 0.02
50 34 0.07
51 51 0.10
52 68 0.13
53 100 0.20
54 193 0.38
55 28 0.05
57 17 0.03
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (53 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCTTTAAAAATTCATTTGAAAA
Found at i:8888 original size:206 final size:207
Alignment explanation
Indices: 8517--9143 Score: 696
Period size: 206 Copynumber: 3.0 Consensus size: 207
8507 TTAGACTTAA
* * * *
8517 TATTTAAAAATTCATTTGATGTAATCATTAAGAAACCCCTGAAAACCAGGCTTAGCCTC-TTTAA
1 TATTTCAAAATTCATTTGA---AA-CATAAAGAAACCCCTAAAAATCAGGCTTAG-CTCATTTAA
* * * * *
8581 AAATCCATTTGAAGATATCAAGAAACCCTTGAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTG
61 AAATTCATTT-AAAATATAAAAAAACCC-TGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTG
* * *
8646 AAAACATCAAGAAACCCCTAAAAATAAAGCTTAGCTCATTTAAACATTTATTTGAAAACATC-AG
124 AAAACA-C---AAACCCCTAAAAATTAGGCTTAGCTCATTTAAACATTCATTTGAAAACATCAAG
*
8710 AAATCCTAGAAAATCAAGATTAGT
185 AAATCCT-GAAAATCAAGATAAGT
8734 TGATTTCAAAATTCATTTGAAACATAAAGAAAACCCCT-AAAATCAGGCTTAGCTCATTTAAAAA
1 T-ATTTCAAAATTCATTTGAAACATAAAG-AAACCCCTAAAAATCAGGCTTAGCTCATTTAAAAA
* **
8798 TTCATTTAAACAT-TAAAAAAACCCT-AAAATCAAGCTTAGAAT-TTTCAAAATTCATTTGAAAA
64 TTCATTTAAA-ATATAAAAAAACCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
*
8860 CACCAACCCCTAAAAATTAGGCTTAGCTCATTTAAACATTCATTTGAAAACATCAAGAAATCCCT
128 CACAAACCCCTAAAAATTAGGCTTAGCTCATTTAAACATTCATTTGAAAACATCAAGAAAT-CCT
* *
8925 -AAAGTCAAGCTAAGT
192 GAAAATCAAGATAAGT
* * * *
8940 TTTTTCAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAAGCTTAGCTCATTTACAAA-
1 TATTTCAAAATTCATTTG-AAACATAAAGAAACCCCTAAAAATCAGGCTTAGCTCATTTAAAAAT
* *
9004 TC-TTTGAAAATATAAAAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATCCATTTGTAAAC
65 TCATTT-AAAATATAAAAAAACCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTG-AAA-
* * * * * * *
9068 ATTAAGAAACCCCTGAAAATTAGGCTTAGCTCATTTAAAAATCCATTTGTAAACATCAAGAAACC
127 A--CACAAACCCCTAAAAATTAGGCTTAGCTCATTTAAACATTCATTTGAAAACATCAAGAAATC
9133 CTTGAAAATCA
190 C-TGAAAATCA
9144 GACTTAACTC
Statistics
Matches: 356, Mismatches: 36, Indels: 41
0.82 0.08 0.09
Matches are distributed among these distances:
204 5 0.01
205 40 0.11
206 107 0.30
207 21 0.06
208 6 0.02
209 2 0.01
210 24 0.07
211 67 0.19
212 7 0.02
213 14 0.04
214 35 0.10
215 10 0.03
217 1 0.00
218 17 0.05
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (207 bp):
TATTTCAAAATTCATTTGAAACATAAAGAAACCCCTAAAAATCAGGCTTAGCTCATTTAAAAATT
CATTTAAAATATAAAAAAACCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAACAC
AAACCCCTAAAAATTAGGCTTAGCTCATTTAAACATTCATTTGAAAACATCAAGAAATCCTGAAA
ATCAAGATAAGT
Found at i:10163 original size:24 final size:24
Alignment explanation
Indices: 10136--10185 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
10126 GTTTCAGCCA
10136 TCAAGTCCTTCTTCTTGTCTCTAT
1 TCAAGTCCTTCTTCTTGTCTCTAT
10160 TCAAGTCCTTCTTCTTGTCTCTAT
1 TCAAGTCCTTCTTCTTGTCTCTAT
10184 TC
1 TC
10186 TTGGGAGCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.30, G:0.08, T:0.50
Consensus pattern (24 bp):
TCAAGTCCTTCTTCTTGTCTCTAT
Found at i:10956 original size:25 final size:26
Alignment explanation
Indices: 10909--10957 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
10899 TATCTCTTCA
* *
10909 TGCAAGGAGAAGGTTATCTTGTTCCC
1 TGCAAGGAGAAGGGTATCGTGTTCCC
*
10935 TGCAA-GAGAAGGGTATGGTGTTC
1 TGCAAGGAGAAGGGTATCGTGTTC
10958 TGGTATATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (26 bp):
TGCAAGGAGAAGGGTATCGTGTTCCC
Found at i:16345 original size:11 final size:11
Alignment explanation
Indices: 16329--16370 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
16319 GAATTTGTTA
16329 GATTTGATTTT
1 GATTTGATTTT
16340 GATTTGATTTT
1 GATTTGATTTT
*
16351 --TATG-TTTT
1 GATTTGATTTT
16359 GATTTGATTTT
1 GATTTGATTTT
16370 G
1 G
16371 TGGTTGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 4 0.15
9 3 0.12
10 3 0.12
11 16 0.62
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (11 bp):
GATTTGATTTT
Found at i:16565 original size:3 final size:3
Alignment explanation
Indices: 16557--16586 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16547 TTTAGGTTTG
16557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16587 CACAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19122 original size:20 final size:20
Alignment explanation
Indices: 19097--19137 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
19087 TTTCACTCTA
19097 ATATAAAATTTGGTTTAATG
1 ATATAAAATTTGGTTTAATG
19117 ATATAAAATTTGGTTTAATG
1 ATATAAAATTTGGTTTAATG
19137 A
1 A
19138 ATGTTTTTTC
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:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
ATATAAAATTTGGTTTAATG
Found at i:21356 original size:2 final size:2
Alignment explanation
Indices: 21349--21389 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
21339 TTTATTCATA
* *
21349 AT AT AT AT AT AT AA AT AT TT 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 AT A
21390 GGATAGAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27716 original size:15 final size:14
Alignment explanation
Indices: 27696--27726 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
27686 AGAACCATGG
27696 AGGAAGAGAGAAGAA
1 AGGAAGAGA-AAGAA
27711 AGGAAGAGAAAGAA
1 AGGAAGAGAAAGAA
27725 AG
1 AG
27727 TGAATTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
AGGAAGAGAAAGAA
Found at i:30721 original size:136 final size:136
Alignment explanation
Indices: 30371--30734 Score: 475
Period size: 139 Copynumber: 2.7 Consensus size: 136
30361 TGGAATTATC
* *
30371 AAGGTTGAACAAGTTCTACTTATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTAT
* * * * ** **
30436 GAACTCTCTACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATATGACG
66 GAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGCATCACTGATTCAA---CATATATGACG
30501 AATCGAGCT
128 AATCGAGCT
* * *
30510 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTAT
*
30575 GAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGCATCACTGATTCAA-A-ATATCG-TGAA
66 GAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGCATCACTGATTCAACATATAT-GACGAA
*
30637 TTGAG-T
130 TCGAGCT
* *
30643 GATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCAT
1 -A-AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-GTCGGATGAGTTCTTCTCAT
*
30708 TATGAACTCTCCATTTGAAATGTTGAT
63 TATGAACTCTCCATTGGAAATGTTGAT
30735 TGGTTCATCT
Statistics
Matches: 200, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
133 1 0.00
134 12 0.06
135 39 0.19
136 45 0.22
139 103 0.51
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (136 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTAT
GAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGCATCACTGATTCAACATATATGACGAAT
CGAGCT
Found at i:31821 original size:20 final size:20
Alignment explanation
Indices: 31796--31833 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31786 TGCTTAAAAG
*
31796 ACTTACTGATGGCCCGAACA
1 ACTTACTAATGGCCCGAACA
31816 ACTTACTAATGGCCCGAA
1 ACTTACTAATGGCCCGAA
31834 TGACTTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (20 bp):
ACTTACTAATGGCCCGAACA
Found at i:31839 original size:20 final size:20
Alignment explanation
Indices: 31795--31840 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
31785 ATGCTTAAAA
*
31795 GACTTACTGATGGCCCGAAC
1 GACTTACTAATGGCCCGAAC
* *
31815 AACTTACTAATGGCCCGAAT
1 GACTTACTAATGGCCCGAAC
31835 GACTTA
1 GACTTA
31841 TGCTGATTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
GACTTACTAATGGCCCGAAC
Found at i:31924 original size:15 final size:16
Alignment explanation
Indices: 31897--31926 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31887 CTCAGGTGGG
31897 GTATTGTTGAATCAAA
1 GTATTGTTGAATCAAA
31913 GTATTG-TGAATCAA
1 GTATTGTTGAATCAA
31927 GTAAAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (16 bp):
GTATTGTTGAATCAAA
Found at i:32070 original size:85 final size:85
Alignment explanation
Indices: 31911--32070 Score: 248
Period size: 85 Copynumber: 1.9 Consensus size: 85
31901 TGTTGAATCA
* *
31911 AAGTATTGTGAATCAAGTAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCC
1 AAGTATTGTGAATCAAGCAAAGGAAATGTTGAAAACATCCGGCCCGAAGGTCTTATGGATGGCCC
*
31976 GAAATACTTAAGCTAATTCG
66 GAAAGACTTAAGCTAATTCG
* ** *
31996 AAGTGTTGTGAATTGAGCAAAGGAAATGTTGAAAACATCCGGCCCGAAGGTCTTATTGATGGCCC
1 AAGTATTGTGAATCAAGCAAAGGAAATGTTGAAAACATCCGGCCCGAAGGTCTTATGGATGGCCC
*
32061 GAAGGACTTA
66 GAAAGACTTA
32071 CACATCATGC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (85 bp):
AAGTATTGTGAATCAAGCAAAGGAAATGTTGAAAACATCCGGCCCGAAGGTCTTATGGATGGCCC
GAAAGACTTAAGCTAATTCG
Found at i:32076 original size:42 final size:42
Alignment explanation
Indices: 32047--32155 Score: 200
Period size: 42 Copynumber: 2.6 Consensus size: 42
32037 GCCCGAAGGT
*
32047 CTTATTGATGGCCCGAAGGACTTACACATCATGCTCAAAAGA
1 CTTATTGATGGCCCGAAGGACTTACACATCATGCTCGAAAGA
32089 CTTATTGATGGCCCGAAGGACTTACACATCATGCTCGAAAGA
1 CTTATTGATGGCCCGAAGGACTTACACATCATGCTCGAAAGA
*
32131 CTTATTGATGGCCCGAAAGACTTAC
1 CTTATTGATGGCCCGAAGGACTTAC
32156 TCATTAAGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTATTGATGGCCCGAAGGACTTACACATCATGCTCGAAAGA
Found at i:32112 original size:20 final size:20
Alignment explanation
Indices: 32084--32154 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
32074 ATCATGCTCA
32084 AAAGACTTATTGATGGCCCG
1 AAAGACTTATTGATGGCCCG
* * * *
32104 AAGGACTTACACATCAT-GCTCG
1 AAAGACTT--A-TTGATGGCCCG
32126 AAAGACTTATTGATGGCCCG
1 AAAGACTTATTGATGGCCCG
32146 AAAGACTTA
1 AAAGACTTA
32155 CTCATTAAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 3 0.08
20 21 0.54
22 12 0.31
23 3 0.08
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AAAGACTTATTGATGGCCCG
Found at i:32132 original size:22 final size:22
Alignment explanation
Indices: 32060--32134 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
32050 ATTGATGGCC
*
32060 CGAAGGACTTACACATCATGCT
1 CGAAAGACTTACACATCATGCT
* * * *
32082 CAAAAGACTT--A-TTGATGGCC
1 CGAAAGACTTACACATCAT-GCT
*
32102 CGAAGGACTTACACATCATGCT
1 CGAAAGACTTACACATCATGCT
32124 CGAAAGACTTA
1 CGAAAGACTTA
32135 TTGATGGCCC
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
19 3 0.08
20 11 0.29
22 21 0.55
23 3 0.08
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (22 bp):
CGAAAGACTTACACATCATGCT
Found at i:32756 original size:28 final size:29
Alignment explanation
Indices: 32716--32774 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
32706 TTAGGCTGAC
*
32716 TTGGGAAGGTAATGTGTTTCAAGTT-AAT
1 TTGGGAAGGTAATGGGTTTCAAGTTGAAT
* *
32744 TTGGGGAGGTAATGGGTTTCAGGTTGAAT
1 TTGGGAAGGTAATGGGTTTCAAGTTGAAT
32773 TT
1 TT
32775 TTGCGTCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.24, C:0.03, G:0.34, T:0.39
Consensus pattern (29 bp):
TTGGGAAGGTAATGGGTTTCAAGTTGAAT
Found at i:33427 original size:29 final size:28
Alignment explanation
Indices: 33395--33455 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
33385 GTTTAATCAG
*
33395 TTTTATATATTCTTTCCTTTCTTT-TTCTT
1 TTTTATATATTCTTT--ATTCTTTATTCTT
* *
33424 TTTTTTTTATTCTTTATTCTTTATTCTT
1 TTTTATATATTCTTTATTCTTTATTCTT
33452 TTTT
1 TTTT
33456 TTTCTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 9 0.32
29 13 0.46
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTATATATTCTTTATTCTTTATTCTT
Found at i:33438 original size:14 final size:14
Alignment explanation
Indices: 33419--33458 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
33409 TCCTTTCTTT
33419 TTCTTTTTTTTTTA
1 TTCTTTTTTTTTTA
* *
33433 TTCTTTATTCTTTA
1 TTCTTTTTTTTTTA
33447 TTCTTTTTTTTT
1 TTCTTTTTTTTT
33459 CTTTTTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (14 bp):
TTCTTTTTTTTTTA
Found at i:33439 original size:7 final size:7
Alignment explanation
Indices: 33413--33452 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
33403 ATTCTTTCCT
33413 TTCTTT-
1 TTCTTTA
*
33419 TTCTTTT
1 TTCTTTA
*
33426 TTTTTTA
1 TTCTTTA
33433 TTCTTTA
1 TTCTTTA
33440 TTCTTTA
1 TTCTTTA
33447 TTCTTT
1 TTCTTT
33453 TTTTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (7 bp):
TTCTTTA
Found at i:33463 original size:7 final size:7
Alignment explanation
Indices: 33412--33494 Score: 52
Period size: 6 Copynumber: 12.0 Consensus size: 7
33402 TATTCTTTCC
33412 TTTC-TT
1 TTTCTTT
33418 TTTCTTT
1 TTTCTTT
33425 TTT-TTT
1 TTTCTTT
33431 TATTCTTT
1 T-TTCTTT
*
33439 ATTCTTT
1 TTTCTTT
*
33446 ATTC-TT
1 TTTCTTT
33452 TTT-TTT
1 TTTCTTT
*
33458 TCT-TTT
1 TTTCTTT
33464 TTTCATTT
1 TTTC-TTT
33472 TTTCTCACTT
1 TTTCT---TT
33482 TTTC-TT
1 TTTCTTT
33488 TTTCTTT
1 TTTCTTT
33495 CTTTTTGTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
6 27 0.43
7 20 0.32
8 10 0.16
10 6 0.10
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTCTTT
Found at i:33476 original size:26 final size:26
Alignment explanation
Indices: 33416--33517 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 26
33406 CTTTCCTTTC
*
33416 TTTTTCTTTTTTTTTTATTCTTTATTCT
1 TTTTTC-TTTTTTTTTCTT-TTTATTCT
*
33444 TTATTCTTTTTTTTTCTTTTT-TTCAT
1 TTTTTCTTTTTTTTTCTTTTTATTC-T
*** *
33470 TTTTTCTCACTTTTTCTTTTTCTTTCT
1 TTTTTCTTTTTTTTTCTTTTT-ATTCT
**
33497 TTTTGT-TTTTGCTTTCTTTTT
1 TTTT-TCTTTTTTTTTCTTTTT
33518 GTGTGTTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
25 3 0.05
26 21 0.36
27 26 0.44
28 9 0.15
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTTTCTTTTTTTTTCTTTTTATTCT
Found at i:33487 original size:36 final size:34
Alignment explanation
Indices: 33416--33500 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 34
33406 CTTTCCTTTC
*
33416 TTTTTCTTT-TTTTTTTATTCTTTATTCTTTATTC
1 TTTTTCTTTCTTTTTTTATTCTTTATACTTT-TTC
* * *
33450 TTTTTTTTTCTTTTTTTCATTTTTTCTCACTTTTTC
1 TTTTTCTTTCTTTTTTT-ATTCTTTAT-ACTTTTTC
33486 TTTTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
33501 GTTTTTGCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 8 0.19
35 7 0.16
36 24 0.56
37 4 0.09
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (34 bp):
TTTTTCTTTCTTTTTTTATTCTTTATACTTTTTC
Found at i:33500 original size:17 final size:17
Alignment explanation
Indices: 33412--33517 Score: 74
Period size: 17 Copynumber: 6.1 Consensus size: 17
33402 TATTCTTTCC
*
33412 TTTCTTTTTCTTTTTTT
1 TTTCTTTTTCTTTCTTT
* *
33429 TTTATTCTTT-ATTCTTT
1 TTTCTT-TTTCTTTCTTT
* *
33446 ATTCTTTTTTTTTCTTTT
1 TTTCTTTTTCTTTC-TTT
* *
33464 TTTCATTTTT-TCTCACTT
1 TTTC-TTTTTCTTTC-TTT
33482 TTTCTTTTTCTTTCTTT
1 TTTCTTTTTCTTTCTTT
*
33499 TTGT-TTTTGCTTTCTTT
1 TT-TCTTTTTCTTTCTTT
33516 TT
1 TT
33518 GTGTGTTTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 12
0.74 0.14 0.13
Matches are distributed among these distances:
16 3 0.04
17 40 0.57
18 22 0.31
19 5 0.07
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTCTTTCTTT
Found at i:33530 original size:17 final size:16
Alignment explanation
Indices: 33411--33519 Score: 73
Period size: 16 Copynumber: 6.8 Consensus size: 16
33401 ATATTCTTTC
*
33411 CTTTCTTTTTCTTTTT
1 CTTTCTTTTTGTTTTT
* *
33427 -TTT-TTATTCTTTATT
1 CTTTCTTTTTGTTT-TT
* *
33442 CTTTATTCTTTTTTTTT
1 CTTTCTT-TTTGTTTTT
33459 CTTT-TTTTCAT-TTTTT
1 CTTTCTTTT--TGTTTTT
** *
33475 CTCACTTTTTCTTTTT
1 CTTTCTTTTTGTTTTT
33491 CTTTCTTTTTGTTTTT
1 CTTTCTTTTTGTTTTT
33507 GCTTTCTTTTTGT
1 -CTTTCTTTTTGT
33520 GTGTTTTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
14 8 0.11
15 8 0.11
16 30 0.39
17 25 0.33
18 5 0.07
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (16 bp):
CTTTCTTTTTGTTTTT
Found at i:37428 original size:23 final size:23
Alignment explanation
Indices: 37365--37429 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
37355 AGGGACATTT
*
37365 TATATGGCACTTCGGTGCAATTC
1 TATATGGCACTTCGGTGTAATTC
***
37388 TACGCGGCACTTCGGTGTAATTC
1 TATATGGCACTTCGGTGTAATTC
37411 TATATGGCACTTCGGTGTA
1 TATATGGCACTTCGGTGTA
37430 TTTATACGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (23 bp):
TATATGGCACTTCGGTGTAATTC
Found at i:47150 original size:18 final size:18
Alignment explanation
Indices: 47127--47165 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47117 ATTATTTAAA
47127 AATATAAAT-TTAATATAT
1 AATATAAATATTAA-ATAT
*
47145 AATATATATATTAAATAT
1 AATATAAATATTAAATAT
47163 AAT
1 AAT
47166 TTCTCCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATAAATATTAAATAT
Found at i:48635 original size:2 final size:2
Alignment explanation
Indices: 48628--48671 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
48618 AGATTGAATT
48628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48670 TA
1 TA
48672 ATCTTTTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49861 original size:42 final size:41
Alignment explanation
Indices: 49815--49904 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
49805 GACATATAGT
* *
49815 GGCGTTTTA-ACAACAAACGCCGTAATAGAGAAGAAATTTTGC
1 GGCGTTTTAGAC--CAAACGCCATAATAGAGAAGAAATTTAGC
* * * *
49857 GGCGTTTTAGGCCAAACGCCATAATATAGAGGTAATTTAGC
1 GGCGTTTTAGACCAAACGCCATAATAGAGAAGAAATTTAGC
49898 GGCGTTT
1 GGCGTTT
49905 ATACCTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 31 0.76
42 9 0.22
43 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (41 bp):
GGCGTTTTAGACCAAACGCCATAATAGAGAAGAAATTTAGC
Found at i:49998 original size:42 final size:41
Alignment explanation
Indices: 49952--50031 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 41
49942 ATTTTTAGAC
49952 AAACGCCACAATAA-TAT-TAATCAATAGTGGCGTTTTTTTTAT
1 AAACGCCACAA-AAGTATGTAAT--ATAGTGGCGTTTTTTTTAT
* *
49994 AAACGCCGCAAAAGTATGTGATATAGTGGCGTTTTTTT
1 AAACGCCACAAAAGTATGTAATATAGTGGCGTTTTTTT
50032 AAAAATGCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 18 0.53
42 13 0.38
43 3 0.09
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (41 bp):
AAACGCCACAAAAGTATGTAATATAGTGGCGTTTTTTTTAT
Found at i:51945 original size:143 final size:145
Alignment explanation
Indices: 51707--51992 Score: 461
Period size: 143 Copynumber: 2.0 Consensus size: 145
51697 TGAAAACGCT
* **
51707 GCAAATGTTTTTTATTTAAATGTCATTAACTTTAGACATATAACGGCGTTTTTTAATAAATGCCG
1 GCAAATGTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCGTTTTTTAATAAACACCG
*
51772 CAACAGATTAGTACTTTAGCAGCGTTTTGACAAAAATGCCGCAATAGGGTT-CACATATAGCGGC
66 CAACAGATTAGTACTTTAGCAACGTTTTGACAAAAATGCCGCAATA-GGTTGCACATATAGCGGC
* * *
51836 TTTTTGGTAACAAACC
130 GTTGTAGTAACAAACC
*
51852 GCAAATG-TTTTTATTTAAACGTCATTAACTTTAGACATATAGCGGCG-TTTTTAATAAACACCG
1 GCAAATGTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCGTTTTTTAATAAACACCG
*
51915 CAATAGATTAGTACTTTAGCAACGTTTTGACAAAAATGCCGCAATAGGTTGCACATATAGCGGCG
66 CAACAGATTAGTACTTTAGCAACGTTTTGACAAAAATGCCGCAATAGGTTGCACATATAGCGGCG
51980 TTGTAGTAACAAA
131 TTGTAGTAACAAA
51993 TGCCGTAAAT
Statistics
Matches: 131, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
142 4 0.03
143 82 0.63
144 38 0.29
145 7 0.05
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (145 bp):
GCAAATGTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCGTTTTTTAATAAACACCG
CAACAGATTAGTACTTTAGCAACGTTTTGACAAAAATGCCGCAATAGGTTGCACATATAGCGGCG
TTGTAGTAACAAACC
Found at i:52738 original size:11 final size:11
Alignment explanation
Indices: 52722--52746 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52712 TTTATGTGGT
52722 TGTTAGTCAAA
1 TGTTAGTCAAA
52733 TGTTAGTCAAA
1 TGTTAGTCAAA
52744 TGT
1 TGT
52747 CTTTTACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (11 bp):
TGTTAGTCAAA
Found at i:54183 original size:46 final size:46
Alignment explanation
Indices: 54116--54245 Score: 224
Period size: 46 Copynumber: 2.8 Consensus size: 46
54106 CTTGCAAGTT
* * * *
54116 TAGAATGCTGAATCAAGGAATCATTTTTAGCATTATTCCTTAGAAA
1 TAGAATGTTGAATCATGGAATCATTTTCAGCATTATTCCCTAGAAA
54162 TAGAATGTTGAATCATGGAATCATTTTCAGCATTATTCCCTAGAAA
1 TAGAATGTTGAATCATGGAATCATTTTCAGCATTATTCCCTAGAAA
54208 TAGAATGTTGAATCATGGAATCATTTTCAGCATTATTC
1 TAGAATGTTGAATCATGGAATCATTTTCAGCATTATTC
54246 ATTTTTTATT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (46 bp):
TAGAATGTTGAATCATGGAATCATTTTCAGCATTATTCCCTAGAAA
Found at i:55257 original size:36 final size:37
Alignment explanation
Indices: 55207--55276 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
55197 AAGGAGAACG
55207 GGTTACCTAGAATAATTAACTACACCAAT-GAATATA
1 GGTTACCTAGAATAATTAACTACACCAATCGAATATA
*
55243 GGTTACCTATAATAATTAACTACACCAATCGAAT
1 GGTTACCTAGAATAATTAACTACACCAATCGAAT
55277 TTAATTCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (37 bp):
GGTTACCTAGAATAATTAACTACACCAATCGAATATA
Found at i:58932 original size:43 final size:43
Alignment explanation
Indices: 58874--59101 Score: 262
Period size: 43 Copynumber: 5.3 Consensus size: 43
58864 AACAAAAAAT
* * *
58874 GCCGCAATATGTGTTGAGGTTTAGTGGCATTTTTCTCACAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCTCACAAAC
* * *
58917 GCCGTAATAGGTGTTGAGATTTAGTGGTATTTTTCTCACAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCTCACAAAC
* * * *
58960 GACGCAATAGGTTTTGAGATTTAGCGGCGTTTTTCACACAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCTCACAAAC
* * * * * *
59003 ACCACAATAGATGTTGAGAGTTAGCGGCGTTTTTCTCACAAAT
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCTCACAAAC
* * *
59046 GCCGTAATAGGTGTTGAGATTTAGCGGC-GTTTTCCCACAAAC
1 GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCTCACAAAC
59088 GCCGCTAA-AGGTGT
1 GCCGC-AATAGGTGT
59102 GGTATATAAC
Statistics
Matches: 156, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 21 0.13
43 135 0.87
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (43 bp):
GCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCTCACAAAC
Found at i:59130 original size:129 final size:129
Alignment explanation
Indices: 58885--59120 Score: 302
Period size: 129 Copynumber: 1.8 Consensus size: 129
58875 CCGCAATATG
* * *
58885 TGTTGAGGTTTAGTGGCATTTTTCTCACAAACGCCGTAATAGGTGTTGAGATTTAGTGGTATTTT
1 TGTTGAGGTTTAGCGGCATTTTTCTCACAAACGCCGTAATAGGTGTTGAGATTTAGCGGTAGTTT
* * * *
58950 TCTCACAAACGACGCAATAGGTTTTGAGATTTAGCGGCGTTTTTCACACAAACACCACAATAGA
66 TCCCACAAACGACGCAATAGGTTGTGAGATATAACGGCGTTTTTCACACAAACACCACAATAGA
* * *
59014 TGTTGAGAG-TTAGCGGCGTTTTTCTCACAAATGCCGTAATAGGTGTTGAGATTTAGCGG-CGTT
1 TGTTGAG-GTTTAGCGGCATTTTTCTCACAAACGCCGTAATAGGTGTTGAGATTTAGCGGTAGTT
* *
59077 TTCCCACAAACGCCGCTAA-AGG-TGTG-GTATATAACGGTGTTTTT
65 TTCCCACAAACGACGC-AATAGGTTGTGAG-ATATAACGGCGTTTTT
59121 ATGGTACAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
126 1 0.01
127 16 0.17
128 19 0.21
129 55 0.60
130 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (129 bp):
TGTTGAGGTTTAGCGGCATTTTTCTCACAAACGCCGTAATAGGTGTTGAGATTTAGCGGTAGTTT
TCCCACAAACGACGCAATAGGTTGTGAGATATAACGGCGTTTTTCACACAAACACCACAATAGA
Found at i:59546 original size:21 final size:22
Alignment explanation
Indices: 59522--59569 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
59512 GTGATGTCGC
59522 TGCTTCT-GTTGCTGCTCTCTA
1 TGCTTCTCGTTGCTGCTCTCTA
*
59543 TGCTT-TCGTTGCTGCTCTCTT
1 TGCTTCTCGTTGCTGCTCTCTA
59564 TGCTTC
1 TGCTTC
59570 CCTTGTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.02, C:0.29, G:0.19, T:0.50
Consensus pattern (22 bp):
TGCTTCTCGTTGCTGCTCTCTA
Found at i:60687 original size:19 final size:19
Alignment explanation
Indices: 60644--60694 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
60634 AAATGACCAA
* * *
60644 CAAATTCACAACACGATCT
1 CAAATTCGCAACACAAACT
60663 CAAATTCGCAACACAAACT
1 CAAATTCGCAACACAAACT
*
60682 CCAATTTCGCAAC
1 -CAAATTCGCAAC
60695 CCAGTTTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.41, C:0.33, G:0.06, T:0.20
Consensus pattern (19 bp):
CAAATTCGCAACACAAACT
Found at i:60767 original size:20 final size:20
Alignment explanation
Indices: 60740--60926 Score: 184
Period size: 20 Copynumber: 9.4 Consensus size: 20
60730 GCAACACAGA
*
60740 AGTCAAATTCGAAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
60760 ACTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
60780 ACTCAAATTCGCAACGTGAT
1 AGTCAAATTCGCAACGCGAT
* *
60800 AGTCAAATTCGCAACAC-AA
1 AGTCAAATTCGCAACGCGAT
*
60819 AGTCAAATTTGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * *
60839 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
60859 AGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACGCG-A-T
* * *
60881 TGT-AAA-TCACAACACAGA-
1 AGTCAAATTCGCAACGC-GAT
* *
60899 AGTCAAATTTGCAACGCGAA
1 AGTCAAATTCGCAACGCGAT
60919 AGTCAAAT
1 AGTCAAAT
60927 GTTTTTACGC
Statistics
Matches: 136, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 21 0.15
20 106 0.78
21 5 0.04
22 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:60839 original size:59 final size:59
Alignment explanation
Indices: 60728--60873 Score: 184
Period size: 59 Copynumber: 2.5 Consensus size: 59
60718 AATTTGTAAA
* * * * *
60728 TCGCAACACAGAAGTCAAATTCGAAACGCGATACTCAAATTCGCAACGCGATACTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACAC-AAAGTCAAATTCGCAACGCGATACTCAAAT
*** * * *
60788 TCGCAACGTGATAGTCAAATTCGCAACACAAAGTCAAATTTGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACACAAAGTCAAATTCGCAACGCGATACTCAAAT
60847 TCGCAACACAAAAGTCAAATTCGCAAC
1 TCGCAACACAAAAGTCAAATTCGCAAC
60874 GCGAATTTGT
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 49 0.69
60 22 0.31
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (59 bp):
TCGCAACACAAAAGTCAAATTCGCAACACAAAGTCAAATTCGCAACGCGATACTCAAAT
Found at i:60845 original size:79 final size:80
Alignment explanation
Indices: 60710--60926 Score: 287
Period size: 79 Copynumber: 2.7 Consensus size: 80
60700 TTCCAATTTT
* * * *
60710 GCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGAAACGCGATACTCAAATTCGCAAC
1 GCAACGCGAATTAGTAAATCGCAACACAGAAGTCAAATTTGCAACGCGATAGTCAAATTCGCAAC
* * *
60775 GCGATACTCAAATTC
66 ACAAAACTCAAATTC
*
60790 GCAACGTG-A-TAGTCAAATTCGCAACACA-AAGTCAAATTTGCAACGCGATAGTCAAATTCGCA
1 GCAACGCGAATTAGT-AAA-TCGCAACACAGAAGTCAAATTTGCAACGCGATAGTCAAATTCGCA
*
60852 ACACAAAAGTCAAATTC
64 ACACAAAACTCAAATTC
* * *
60869 GCAACGCGAATTTGTAAATCACAACACAGAAGTCAAATTTGCAACGCGAAAGTCAAAT
1 GCAACGCGAATTAGTAAATCGCAACACAGAAGTCAAATTTGCAACGCGATAGTCAAAT
60927 GTTTTTACGC
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 64 0.54
80 49 0.41
81 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (80 bp):
GCAACGCGAATTAGTAAATCGCAACACAGAAGTCAAATTTGCAACGCGATAGTCAAATTCGCAAC
ACAAAACTCAAATTC
Found at i:60918 original size:40 final size:40
Alignment explanation
Indices: 60710--60917 Score: 205
Period size: 40 Copynumber: 5.2 Consensus size: 40
60700 TTCCAATTTT
60710 GCAACGCGAATTTGTAAA-TCGCAACACAGAAGTCAAATTC
1 GCAACGCG-ATTTGTAAATTCGCAACACAGAAGTCAAATTC
* * * * *
60750 GAAACGCGATACT-CAAATTCGCAACGC-GATACTCAAATTC
1 GCAACGCGAT-TTGTAAATTCGCAACACAGA-AGTCAAATTC
* * *
60790 GCAACGTGA-TAGTCAAATTCGCAACACA-AAGTCAAATTT
1 GCAACGCGATTTGT-AAATTCGCAACACAGAAGTCAAATTC
* *
60829 GCAACGCGA-TAGTCAAATTCGCAACACAAAAGTCAAATTC
1 GCAACGCGATTTGT-AAATTCGCAACACAGAAGTCAAATTC
* *
60869 GCAACGCGAATTTGTAAA-TCACAACACAGAAGTCAAATTT
1 GCAACGCG-ATTTGTAAATTCGCAACACAGAAGTCAAATTC
60909 GCAACGCGA
1 GCAACGCGA
60918 AAGTCAAATG
Statistics
Matches: 140, Mismatches: 19, Indels: 19
0.79 0.11 0.11
Matches are distributed among these distances:
39 43 0.31
40 90 0.64
41 4 0.03
42 3 0.02
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (40 bp):
GCAACGCGATTTGTAAATTCGCAACACAGAAGTCAAATTC
Found at i:61425 original size:19 final size:20
Alignment explanation
Indices: 61403--61443 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
61393 AATTCGCAAC
61403 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
61422 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
61442 GC
1 GC
61444 AAATTTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:61456 original size:20 final size:20
Alignment explanation
Indices: 61406--61456 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
61396 TCGCAACGCG
* *
61406 ATTTTAGTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCAA
* * *
61426 TTTTCATTTTCGCGTTGCAA
1 ATTTAAGTTTCGCGTTGCAA
61446 ATTTAAGTTTC
1 ATTTAAGTTTC
61457 AGAAACTTCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCAA
Found at i:63402 original size:4 final size:4
Alignment explanation
Indices: 63393--63438 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
63383 TTTTTTGGCA
* * * *
63393 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
63439 TCAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:63629 original size:42 final size:42
Alignment explanation
Indices: 63582--63700 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
63572 GATGCACCTA
* * *
63582 TCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* * * *
63624 TCATCATTGAAGATGCCCCTCCCACCGTTCAAGAGGCCCTTG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* * *
63666 TCATCATTCAAGAGGTCCCGCCCGCCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAG
63701 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:63675 original size:21 final size:21
Alignment explanation
Indices: 63582--63680 Score: 101
Period size: 21 Copynumber: 4.7 Consensus size: 21
63572 GATGCACCTA
*
63582 TCATCATTCAAGAGGCGCCTC
1 TCATCATTCAAGAGGCCCCTC
*
63603 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCATTCAAGAGGCCCCTC
* *
63624 TCATCATTGAAGATGCCCCTC
1 TCATCATTCAAGAGGCCCCTC
* * * * *
63645 CCACCGTTCAAGAGGCCCTTG
1 TCATCATTCAAGAGGCCCCTC
63666 TCATCATTCAAGAGG
1 TCATCATTCAAGAGG
63681 TCCCGCCCGC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 59 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:65132 original size:14 final size:14
Alignment explanation
Indices: 65113--65149 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
65103 TTTTGATTAA
65113 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
65127 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
65141 TTGATTTGT
1 TTGATTTGT
65150 TTAATTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:65177 original size:75 final size:77
Alignment explanation
Indices: 65063--65213 Score: 227
Period size: 80 Copynumber: 2.0 Consensus size: 77
65053 TTTTACATTG
*
65063 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTTTTG-A-TTAATTGATTTGTAAA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGTATTTAATTGATTTGTAAA
65125 AGTTGATTTATA
66 AGTTGATTTATA
* *
65137 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTATTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTTG--TATTTAATTGATTTGT
65202 AAAAGTTGATTT
63 AAAAGTTGATTT
65214 GTTGTTTCTA
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
74 17 0.25
75 18 0.26
76 7 0.10
79 1 0.01
80 25 0.37
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.50
Consensus pattern (77 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGTATTTAATTGATTTGTAAA
AGTTGATTTATA
Found at i:65357 original size:20 final size:20
Alignment explanation
Indices: 65319--65357 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65309 GATTTTCAAT
*
65319 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTATCGCG
*
65339 TTGCGAATTTGGCTATCGC
1 TTGCGAATTTGACTATCGC
65358 AACACTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:65633 original size:39 final size:38
Alignment explanation
Indices: 65572--65657 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 38
65562 TCAAGTTGTA
65572 GATTTTGATTTCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCTTTTGCTTGGCACCATATGAGATTTG
*
65610 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTT-CTTTTGCTTGGCACCATATGAGATTTG
65649 GATTTTGAT
1 GATTTTGAT
65658 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 11 0.24
39 35 0.76
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (38 bp):
GATTTTGATTTCTTTTGCTTGGCACCATATGAGATTTG
Found at i:65956 original size:18 final size:18
Alignment explanation
Indices: 65933--65969 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
65923 CGAAATTTAT
65933 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
65951 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
65969 A
1 A
65970 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:66419 original size:20 final size:20
Alignment explanation
Indices: 66391--66455 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
66381 AAATAATGTA
* *
66391 CAACATGAAAGTTAAATTCG
1 CAACGTGAAAGTCAAATTCG
66411 CAACGTGAAAGTCAAATTCG
1 CAACGTGAAAGTCAAATTCG
* * *
66431 TAACGCGAAAGCCAAATTCG
1 CAACGTGAAAGTCAAATTCG
66451 CAACG
1 CAACG
66456 CGATTTTCGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
CAACGTGAAAGTCAAATTCG
Found at i:66505 original size:20 final size:20
Alignment explanation
Indices: 66467--66505 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66457 GATTTTCGGT
*
66467 TTGCGAATTTAACTTTCGCG
1 TTGCGAATTTAACTATCGCG
*
66487 TTGCGAATTTGACTATCGC
1 TTGCGAATTTAACTATCGC
66506 AACGCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTAACTATCGCG
Found at i:66864 original size:18 final size:18
Alignment explanation
Indices: 66824--66865 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
66814 AGGTGAAGCC
* *
66824 GATTGTGATTGTGATTTT
1 GATTTTGATTGCGATTTT
*
66842 GATTTTGATTGCGTTTTT
1 GATTTTGATTGCGATTTT
66860 GATTTT
1 GATTTT
66866 CTTTTGCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.24, T:0.60
Consensus pattern (18 bp):
GATTTTGATTGCGATTTT
Found at i:68942 original size:12 final size:12
Alignment explanation
Indices: 68925--68949 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68915 TCTTCGGGGA
68925 CTTTTTCTTCTT
1 CTTTTTCTTCTT
68937 CTTTTTCTTCTT
1 CTTTTTCTTCTT
68949 C
1 C
68950 AGGGTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:69191 original size:24 final size:24
Alignment explanation
Indices: 69140--69191 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
69130 ATCTGAGTAT
** *
69140 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
69164 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
69188 TGAC
1 TGAC
69192 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:69912 original size:14 final size:15
Alignment explanation
Indices: 69876--69913 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
69866 GAAATCATTG
69876 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
69891 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
69906 AAAAATTA
1 AAAAATTA
69914 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:70147 original size:20 final size:20
Alignment explanation
Indices: 70070--70142 Score: 96
Period size: 19 Copynumber: 3.6 Consensus size: 20
70060 ACTAAAACCT
70070 GTTGCGAATTTGAAATTCA-
1 GTTGCGAATTTGAAATTCAC
*
70089 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CAC
*
70110 GTTGCGAATTTG-ACTATCAC
1 GTTGCGAATTTGAAAT-TCAC
70130 GTTGCGAATTTGA
1 GTTGCGAATTTGA
70143 GTATCGCGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 17 0.36
20 17 0.36
21 13 0.28
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCAC
Found at i:70151 original size:40 final size:41
Alignment explanation
Indices: 70070--70164 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
70060 ACTAAAACCT
70070 GTTGCGAATTTGA-AATTCAGTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGACAATTCAGTTGCGAATTTGAAATTCCGC
* *
70110 GTTGCGAATTTGACTA-TCACGTTGCGAATTTG-AGTAT-CGC
1 GTTGCGAATTTGACAATTCA-GTTGCGAATTTGAAAT-TCCGC
*
70150 GTTTCGAATTTGACA
1 GTTGCGAATTTGACA
70165 TCTGTGTTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 34 0.71
41 14 0.29
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (41 bp):
GTTGCGAATTTGACAATTCAGTTGCGAATTTGAAATTCCGC
Found at i:70152 original size:20 final size:19
Alignment explanation
Indices: 70070--70162 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 19
70060 ACTAAAACCT
* *
70070 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGATA-TCGC
*
70089 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGATA-T-CGC
*
70110 GTTGCGAATTTGACTATCAC
1 GTTGCGAATTTGA-TATCGC
70130 GTTGCGAATTTGAGTATCGC
1 GTTGCGAATTTGA-TATCGC
*
70150 GTTTCGAATTTGA
1 GTTGCGAATTTGA
70163 CATCTGTGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
19 17 0.26
20 33 0.51
21 14 0.22
22 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGATATCGC
Found at i:79337 original size:15 final size:15
Alignment explanation
Indices: 79313--79344 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
79303 AGGCAGATCG
*
79313 AAATCTAGAACGGGA
1 AAATCAAGAACGGGA
79328 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
79343 AA
1 AA
79345 GAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.25, T:0.09
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:84134 original size:133 final size:134
Alignment explanation
Indices: 83822--84126 Score: 373
Period size: 135 Copynumber: 2.3 Consensus size: 134
83812 TATTGCGGTA
* * * * * * *
83822 TTTATGTCAAAAATGCCAATAAAGTACAATTTTTTAGCGACGTTTGGTAACAAATGCCACTAAAT
1 TTTATGTAAAAAACGCCACTAAAGTACAACTCTTTAGCGGCGTTTGGTAACAAACGCCACTAAAT
83887 TAAGAGTATTTTACGGTATTTAATTAAAAAAACGCCGCTATAAATGACAATATACAACTCTATTG
66 TAAGAGTATTTTACGGTATTTAATT-AAAAAACGCCGCTATAAATGACAATATACAACTCTATTG
83952 TGGCG
130 TGGCG
* * *
83957 TTTATGTCAAAAACGCCACTAAAGTACAACTTTTTAGCGGCGTTTGGTAATAAACGCCACTAAAT
1 TTTATGTAAAAAACGCCACTAAAGTACAACTCTTTAGCGGCGTTTGGTAACAAACGCCACTAAAT
* * * * * *
84022 TAATAGTATTTTGCGGTGTTTGATT-AAAAATGCCGCTATAAATGACAATATACAAC-C-ATTTT
66 TAAGAGTATTTTACGGTATTTAATTAAAAAACGCCGCTATAAATGACAATATACAACTCTATTGT
*
84084 ACGGTG
131 --GGCG
* * **
84090 TTTGTTTAAAAAACGCCACTAAAGTATTACTCTTTAG
1 TTTATGTAAAAAACGCCACTAAAGTACAACTCTTTAG
84127 TTGCGTTTTT
Statistics
Matches: 149, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
131 4 0.03
132 1 0.01
133 64 0.43
135 80 0.54
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (134 bp):
TTTATGTAAAAAACGCCACTAAAGTACAACTCTTTAGCGGCGTTTGGTAACAAACGCCACTAAAT
TAAGAGTATTTTACGGTATTTAATTAAAAAACGCCGCTATAAATGACAATATACAACTCTATTGT
GGCG
Found at i:87923 original size:422 final size:420
Alignment explanation
Indices: 87353--88204 Score: 1195
Period size: 422 Copynumber: 2.0 Consensus size: 420
87343 AACACCTGTA
* *
87353 AATTTTCTCTCTTTAGTAAAAGATCTGCAGCAGTCTGAAGACGTAGGCATAATTGGCCGAAATTA
1 AATTTTCTCTCTTTAGTAAAAGATCTACAGCAGTCTGAAGACGTAGGCATAATTGGCCGAAATCA
*
87418 GTTATCAATTTCAGGTATTATTATTCTGCTTTTATTTCGCATTCTCACTAATCTAGTTATAGGAA
66 GTTATCAATTTCAGGTATTATTATTCCGCTTTTATTTCGCATTCTCACTAATCTAGTTATAGGAA
* *
87483 AATTTTAGTCCCTATACTTTAGGGTATTTACAAGATTAGTCCTTAAGCTTTAACTATAAATAACC
131 AAATTTAGTCCCTATACTTTAGGGTATTTACAAGATTAGTCCTTAAGCTTCAACTATAAATAACC
* *
87548 TAACACATTTAGCTTCAAAAGCATCCCAAACCATTCTAGCTTTCTCCCAATAC-CTTGAGAGTTG
196 TAACACATTTAGCTTCAAAAGCATCACAAACCATCCTAGCTTTCTCCCAATACACTTGAGAGTTG
87612 TTTTCTTCTTTTTATCAAGAGAGAAATGTCATTATTTTCTCCTTGTTAGATCGACAGAAGTTGTA
261 TTTTCTTCTTTTTATCAAGAGAGAAATGTCATTATTTTCTCCTTGTTAGATCGACAGAAGTTGTA
* * * * *
87677 ATTCTTATTTTTTTTTCATAGTGAAATTCTTCTATCTTTACCCGTGGTTTTTACCCTATATTATT
326 ATTCCTA---TTTTCTCATAGTGAAATTATTCTACCTTTACCCGTAGTTTTTACCCTATATTATT
*
87742 TAGGGGTTTTCCATATAAAATTTAGTTTTTTTT
388 TAGGGGTTTTCCACATAAAATTTAGTTTTTTTT
* * * * *
87775 AATTTTCTCTCTTTAGTAAAAGATCTACATCAGTCTGGAGACGTAGTCATAATTGGCCGAACTCC
1 AATTTTCTCTCTTTAGTAAAAGATCTACAGCAGTCTGAAGACGTAGGCATAATTGGCCGAAATCA
* * *
87840 GTTATCAATTTCGGGTATTATTATTCCGCTTTTATTTTGCATTTTCACTAATCT-GTTTATAGGA
66 GTTATCAATTTCAGGTATTATTATTCCGCTTTTATTTCGCATTCTCACTAATCTAG-TTATAGGA
*
87904 AAAATTTAGTCCCTATACTTTAGGGTATTTACAAGATTAGTCCTTAAGCTTCAACTATAAATACC
130 AAAATTTAGTCCCTATACTTTAGGGTATTTACAAGATTAGTCCTTAAGCTTCAACTATAAATAAC
* * *
87969 CTAACCCATTTAGCTTCAAAATCATCACAAATCATCCTAGCTTTCTCCCAATACTAGAGAATTTA
195 CTAACACATTTAGCTTCAAAAGCATCACAAACCATCCTAGCTTTCTCCCAATAC-----------
* * *
88034 GAGAATTTTCTTGAGAGTTGTTTTCTTCTTTTTATCAAGAGAGAATTGTGATTGTTTTCTCCTTG
249 ----A----CTTGAGAGTTGTTTTCTTCTTTTTATCAAGAGAGAAATGTCATTATTTTCTCCTTG
* * *
88099 TTAGATCGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTATTCTACCTTTGCCCGTATT
306 TTAGATCGACAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTATTCTACCTTTACCCGTAGT
*
88164 TTTTACCCTATATTATTTAGGGGTTTTCCACGTAAAATTTA
371 TTTTACCCTATATTATTTAGGGGTTTTCCACATAAAATTTA
88205 TGTCTTCTTT
Statistics
Matches: 377, Mismatches: 32, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
421 1 0.00
422 227 0.60
439 71 0.19
442 78 0.21
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (420 bp):
AATTTTCTCTCTTTAGTAAAAGATCTACAGCAGTCTGAAGACGTAGGCATAATTGGCCGAAATCA
GTTATCAATTTCAGGTATTATTATTCCGCTTTTATTTCGCATTCTCACTAATCTAGTTATAGGAA
AAATTTAGTCCCTATACTTTAGGGTATTTACAAGATTAGTCCTTAAGCTTCAACTATAAATAACC
TAACACATTTAGCTTCAAAAGCATCACAAACCATCCTAGCTTTCTCCCAATACACTTGAGAGTTG
TTTTCTTCTTTTTATCAAGAGAGAAATGTCATTATTTTCTCCTTGTTAGATCGACAGAAGTTGTA
ATTCCTATTTTCTCATAGTGAAATTATTCTACCTTTACCCGTAGTTTTTACCCTATATTATTTAG
GGGTTTTCCACATAAAATTTAGTTTTTTTT
Found at i:90521 original size:18 final size:18
Alignment explanation
Indices: 90498--90536 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
90488 GACATGTCAA
90498 CCATAGAATCAAGTAGCT
1 CCATAGAATCAAGTAGCT
90516 CCATAGAATCAAGTAGCT
1 CCATAGAATCAAGTAGCT
90534 CCA
1 CCA
90537 ATACCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (18 bp):
CCATAGAATCAAGTAGCT
Found at i:94951 original size:60 final size:60
Alignment explanation
Indices: 94838--94951 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
94828 TTATATGATA
* * ** *
94838 TTGCTTTATTGAGTCTCTTGACTATTAAAAGTTAATCAATGATTTCTCGACTATAGGGAG
1 TTGCTTTATTGAGTCTCTCGACTATTAAAAGTTAATAAATGATCACTCAACTATAGGGAG
* *
94898 TTGCTTTGTTGAGTCTCTCGACTATTAAAAGTT-ATAAAATGGTCACTCAACTAT
1 TTGCTTTATTGAGTCTCTCGACTATTAAAAGTTAAT-AAATGATCACTCAACTAT
94952 TCATTATGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (60 bp):
TTGCTTTATTGAGTCTCTCGACTATTAAAAGTTAATAAATGATCACTCAACTATAGGGAG
Found at i:98776 original size:2 final size:2
Alignment explanation
Indices: 98771--98833 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
98761 GAGTTGTACC
*
98771 AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
98813 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
98834 AGAAATGTCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:101304 original size:11 final size:11
Alignment explanation
Indices: 101276--101325 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 11
101266 TAATATTTAT
101276 TTAAAT-ATT-
1 TTAAATAATTA
101285 TTAAA-AATTA
1 TTAAATAATTA
101295 TTAAATAATTA
1 TTAAATAATTA
101306 TTAAAT--TTA
1 TTAAATAATTA
101315 TTAAATAATTA
1 TTAAATAATTA
101326 CAAACTATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 17 0.47
10 5 0.14
11 14 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATAATTA
Found at i:101315 original size:20 final size:20
Alignment explanation
Indices: 101265--101325 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
101255 ACTCTCAAAT
101265 TTAATATTTATTTAAAT-ATT-
1 TTAA-ATTTA-TTAAATAATTA
*
101285 TTAAAAATTATTAAATAATTA
1 TT-AAATTTATTAAATAATTA
101306 TTAAATTTATTAAATAATTA
1 TTAAATTTATTAAATAATTA
101326 CAAACTATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 6 0.17
20 26 0.72
21 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAATTTATTAAATAATTA
Found at i:103250 original size:24 final size:24
Alignment explanation
Indices: 103210--103298 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
103200 AATAATTTCA
* *
103210 AATAT-AA-TTTTTAAAAATATAT
1 AATATAAAGTTTTTGAAAACATAT
*
103232 AATATAAAGTTTTTGAAAACGTAT
1 AATATAAAGTTTTTGAAAACATAT
*
103256 AATATATAGTTTTTGAAAACATAT
1 AATATAAAGTTTTTGAAAACATAT
* *
103280 AAAATATAGTTTTTTGAAA
1 AATATAAAG-TTTTTGAAA
103299 TGGTTTTGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.09
23 2 0.03
24 42 0.72
25 9 0.16
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (24 bp):
AATATAAAGTTTTTGAAAACATAT
Found at i:103317 original size:36 final size:36
Alignment explanation
Indices: 103266--103404 Score: 160
Period size: 36 Copynumber: 3.9 Consensus size: 36
103256 AATATATAGT
* *
103266 TTTTGAAAACATATAAAATATAGTTTTTTGAAATGG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAATGG
* * *
103302 TTTTGAAAACGTATAATATATAGTTTTTAAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAATGG
* *
103338 TTTTGAAAACATATAGTATAT-GTTTTTTTTTAAAT-G
1 TTTTGAAAACATATAATATATAG--TTTTTTAAAATGG
*
103374 TTTTGAAAACGTATAATATAT--TTTTTTAAAA
1 TTTTGAAAACATATAATATATAGTTTTTTAAAA
103405 CATATAATAT
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
33 9 0.10
35 1 0.01
36 70 0.80
37 8 0.09
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTTTAAAATGG
Found at i:103342 original size:72 final size:70
Alignment explanation
Indices: 103266--103404 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 70
103256 AATATATAGT
103266 TTTTGAAAACATATAAAATATAG-TTTTTTGAAATGGTTTTGAAAACGTATAATATATAGTTTTT
1 TTTTGAAAACATATAAAATAT-GTTTTTTTGAAAT-GTTTTGAAAACGTATAATATAT-GTTTTT
103330 AAAAACGG
63 AAAAACGG
** * *
103338 TTTTGAAAACATATAGTATATGTTTTTTTTTAAATGTTTTGAAAACGTATAATATATTTTTTTAA
1 TTTTGAAAACATATAAAATATG-TTTTTTTGAAATGTTTTGAAAACGTATAATATATGTTTTTAA
103403 AA
65 AA
103405 CATATAATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
71 10 0.16
72 41 0.67
73 10 0.16
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.45
Consensus pattern (70 bp):
TTTTGAAAACATATAAAATATGTTTTTTTGAAATGTTTTGAAAACGTATAATATATGTTTTTAAA
AACGG
Found at i:103404 original size:22 final size:22
Alignment explanation
Indices: 103374--103415 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
103364 TTTTTAAATG
*
103374 TTTTGAAAACGTATAATATATT
1 TTTTGAAAACATATAATATATT
*
103396 TTTTTAAAACATATAATATA
1 TTTTGAAAACATATAATATA
103416 ATATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTTGAAAACATATAATATATT
Found at i:103502 original size:19 final size:18
Alignment explanation
Indices: 103469--103504 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
103459 TATTATATTA
103469 TTTATTTATTTATTTCAT
1 TTTATTTATTTATTTCAT
*
103487 TTTATTTTTATTATTTCA
1 TTTATTTAT-TTATTTCA
103505 GGTTCAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTATTTATTTCAT
Found at i:104492 original size:21 final size:19
Alignment explanation
Indices: 104446--104496 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
104436 ATATAAGTTT
*
104446 TATGAACAGTAAAATACGG
1 TATGAACAGTAAAATACCG
*
104465 TACGAACAGTGAACAATACCG
1 TATGAACAGT-AA-AATACCG
104486 TATGAACAGTA
1 TATGAACAGTA
104497 CCATGAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 3 0.11
21 15 0.56
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (19 bp):
TATGAACAGTAAAATACCG
Found at i:105546 original size:23 final size:23
Alignment explanation
Indices: 105519--105562 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
105509 AATACATATA
105519 TGTCCCGAAAGACCACGTAGAAT
1 TGTCCCGAAAGACCACGTAGAAT
* *
105542 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAAGACCACGTAGA
105563 CCCTCGACTC
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:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
TGTCCCGAAAGACCACGTAGAAT
Found at i:107470 original size:18 final size:18
Alignment explanation
Indices: 107457--107491 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
107447 CCTTTACTTT
107457 TTTTTATCTATTTATTTA
1 TTTTTATCTATTTATTTA
*
107475 TTTTTATTTATTT-TTTA
1 TTTTTATCTATTTATTTA
107492 ACATGTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTATCTATTTATTTA
Found at i:115633 original size:31 final size:31
Alignment explanation
Indices: 115595--115672 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
115585 TAGTTACGTC
* *
115595 AGGGACCATATTGCAAATGGACTAAATGTTG
1 AGGGACCATATTGCAAATGAAATAAATGTTG
115626 AGGGACCATATTGCAAATGAAATAAATGTTG
1 AGGGACCATATTGCAAATGAAATAAATGTTG
* **
115657 GGGGACTGTATTGCAA
1 AGGGACCATATTGCAA
115673 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.26
Consensus pattern (31 bp):
AGGGACCATATTGCAAATGAAATAAATGTTG
Found at i:120932 original size:19 final size:18
Alignment explanation
Indices: 120908--120943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
120898 AATATTGCAA
120908 TGTAATATAAACATAAAAT
1 TGTAATATAAACA-AAAAT
*
120927 TGTAATTTAAACAAAAA
1 TGTAATATAAACAAAAA
120944 CATCAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
TGTAATATAAACAAAAAT
Found at i:122787 original size:27 final size:28
Alignment explanation
Indices: 122757--122815 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
122747 AGAACAAAAT
* *
122757 ATAAACTATATGATAATGAATTATG-AG
1 ATAAACTACATGATAATGAACTATGTAG
* *
122784 ATAAATTACATGATCATGAACTATGTAG
1 ATAAACTACATGATAATGAACTATGTAG
122812 ATAA
1 ATAA
122816 CAATGATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (28 bp):
ATAAACTACATGATAATGAACTATGTAG
Done.