Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004915.1 Hibiscus syriacus cultivar Beakdansim tig00011065_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: 184635
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1474 original size:45 final size:45
Alignment explanation
Indices: 1260--1475 Score: 296
Period size: 45 Copynumber: 4.9 Consensus size: 45
1250 ACTCTAACAT
* * *
1260 CTTTTCTG-TGATAATTCACCCATATGCGTTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * *
1304 CTTTTATGTTGATAATGTACCCATATACATCTCAAC-C-A-TAATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGT-ATA
* * *
1347 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
*
1392 CTTTTCTGTTAATAATGCACCCATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
1437 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCT
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCT
1476 GACATCCTTT
Statistics
Matches: 152, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.01
43 38 0.25
44 8 0.05
45 105 0.69
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:1497 original size:45 final size:45
Alignment explanation
Indices: 1249--1512 Score: 281
Period size: 45 Copynumber: 6.0 Consensus size: 45
1239 ATACATTTTA
* * * *
1249 AACTCTAACAT-CTTTTCTG-TGATAATTCACCCATATGCGTTTC
1 AACTCTAGCATACTTTTCTGTTAATAATGCACCCATATGCATTTC
* * * * * * *
1292 AACTATAGTATACTTTTATGTTGATAATGTACCCATATACATCTC
1 AACTCTAGCATACTTTTCTGTTAATAATGCACCCATATGCATTTC
* * *
1337 AAC-CATA--ATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTC-TAGCATACTTTTCTGTTAATAATGCACCCATATGCATTTC
1380 AACTCTAGCATACTTTTCTGTTAATAATGCACCCATATGCATTTC
1 AACTCTAGCATACTTTTCTGTTAATAATGCACCCATATGCATTTC
* *
1425 AACTCTAGTATACTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTCTAGCATACTTTTCTGTTAATAATGCACCCATATGCATTTC
* **
1470 AACTCT-GACAT-CCTTTCATGCCAATAATGCACCCATATGCATT
1 AACTCTAG-CATACTTTTC-TGTTAATAATGCACCCATATGCATT
1513 ATTTTGTTAT
Statistics
Matches: 191, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
43 47 0.25
44 14 0.07
45 130 0.68
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (45 bp):
AACTCTAGCATACTTTTCTGTTAATAATGCACCCATATGCATTTC
Found at i:1589 original size:77 final size:79
Alignment explanation
Indices: 1476--1674 Score: 305
Period size: 78 Copynumber: 2.5 Consensus size: 79
1466 TTTCAACTCT
* *
1476 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATT-TTGTTATGCCGATAATATACTCAT
1 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTT-TTATGCCAATAATATACCCAT
1540 ATACA-ATCAGCTAA
65 ATACATATCAGCTAA
* * *
1554 GGCATCCTTTCATGCCACTAA-GCACCCATATGCATTATTCTTTTATGCCAATAATGTACCCATA
1 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCAATAATATACCCATA
1618 TACATATCAGCTAA
66 TACATATCAGCTAA
* *
1632 GACATCCTTTTATGCCAATAATGTACCCATATGCATTATTCTT
1 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTT
1675 CTATTCATTA
Statistics
Matches: 109, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
77 41 0.38
78 48 0.44
79 20 0.18
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (79 bp):
GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCAATAATATACCCATA
TACATATCAGCTAA
Found at i:1616 original size:34 final size:34
Alignment explanation
Indices: 1560--1674 Score: 88
Period size: 45 Copynumber: 3.1 Consensus size: 34
1550 CTAAGGCATC
* * *
1560 CTTTCATGCCACTAA-GCACCCATATGCATTATT
1 CTTTTATGCCAATAATGTACCCATATGCATTATT
*
1593 CTTTTATGCCAATAATGTACCCATATACATATCAGCTAAGACAT
1 CTTTTATGCCAATAATGTACCCATATGCAT-T-A--T------T
1637 CCTTTTATGCCAATAATGTACCCATATGCATTATT
1 -CTTTTATGCCAATAATGTACCCATATGCATTATT
1672 CTT
1 CTT
1675 CTATTCATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 23
0.70 0.05 0.25
Matches are distributed among these distances:
33 13 0.20
34 15 0.23
35 2 0.03
36 1 0.02
38 1 0.02
41 1 0.02
43 1 0.02
44 2 0.03
45 29 0.45
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (34 bp):
CTTTTATGCCAATAATGTACCCATATGCATTATT
Found at i:4850 original size:23 final size:23
Alignment explanation
Indices: 4824--4868 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4814 CACCATAGCT
4824 CGTATAATTGCACCGAAGTGCCG
1 CGTATAATTGCACCGAAGTGCCG
* *
4847 CGTATAATTGCACTGTAGTGCC
1 CGTATAATTGCACCGAAGTGCC
4869 ATATAATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCG
Found at i:4875 original size:21 final size:23
Alignment explanation
Indices: 4826--4875 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
4816 CCATAGCTCG
*
4826 TATAATTGCACCGAAGTGCCGCG
1 TATAATTGCACCGAAGTGCCGCA
* *
4849 TATAATTGCACTGTAGTG-C-CA
1 TATAATTGCACCGAAGTGCCGCA
4870 TATAAT
1 TATAAT
4876 GTGTCCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.29
22 1 0.04
23 16 0.67
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCGCA
Found at i:5100 original size:143 final size:141
Alignment explanation
Indices: 4836--5137 Score: 475
Period size: 143 Copynumber: 2.1 Consensus size: 141
4826 TATAATTGCA
* *
4836 CCGAAGTG-CCGCGTATAATTGCACTGTAGTGCCATATAATGTGTCCATAAGGACCACATAATTC
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGTGTCCATAAGGACCACATAATTC
*
4900 CTTAAGAACATATACATATGCTAGGGATCAGTATGTGTCTCTCAAGACTTCACACATGTTCCACA
65 CTTAAGAACATATACATA-GCTAGGGATCAGTATGTGTCTCTCAAGACTTCACACATGTTCCAAA
*
4965 GAATATATATATC
129 GAATACATATATC
4978 CCG-AGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATG-TGTCCATAAGGACCACATA--AT
*
5042 TCCTTAAGAATCATATACATA-CTAGGGATCAGTATGTGTCTTTCAAGACTTCACACATGTTCCA
63 TCCTTAAGAA-CATATACATAGCTAGGGATCAGTATGTGTCTCTCAAGACTTCACACATGTTCCA
*
5106 AAGAATACATATGTC
127 AAGAATACATATATC
5121 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
5138 CCCTCGACTC
Statistics
Matches: 148, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
140 1 0.01
141 33 0.22
142 22 0.15
143 57 0.39
144 25 0.17
145 10 0.07
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (141 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGTGTCCATAAGGACCACATAATTCC
TTAAGAACATATACATAGCTAGGGATCAGTATGTGTCTCTCAAGACTTCACACATGTTCCAAAGA
ATACATATATC
Found at i:5257 original size:14 final size:14
Alignment explanation
Indices: 5238--5265 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5228 AACTTGTAAT
5238 TCACGTATCACATA
1 TCACGTATCACATA
5252 TCACGTATCACATA
1 TCACGTATCACATA
5266 GTTTCTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:9834 original size:23 final size:23
Alignment explanation
Indices: 9808--9852 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
9798 CACCACAGCT
*
9808 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
9831 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
9853 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:10100 original size:143 final size:146
Alignment explanation
Indices: 9820--10128 Score: 493
Period size: 143 Copynumber: 2.1 Consensus size: 146
9810 TATAATTGCA
9820 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAG-ATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
9884 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
64 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
9949 CCACAG-A-ATATATATC
129 CCAAAGAATATATATATC
*
9965 CCGAAGGACCGCGTAGATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAG-ATT
1 CCGAAGGACCGCGTAGATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATT
*
10029 CCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTTC
66 CCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTTC
10093 CAAAGAATATATATATATC
130 CAAAG-A-ATATATATATC
10112 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
10129 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
143 66 0.43
144 46 0.30
145 14 0.09
146 1 0.01
147 26 0.17
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (146 bp):
CCGAAGGACCGCGTAGATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATT
CCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCC
AAAGAATATATATATC
Found at i:11050 original size:18 final size:18
Alignment explanation
Indices: 11029--11063 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11019 TCCCATCTAG
11029 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
11047 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
11064 AATCTCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:15186 original size:24 final size:20
Alignment explanation
Indices: 15133--15190 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
15123 TTCCCCTTGA
*
15133 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
15153 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
15176 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
15191 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:15301 original size:64 final size:63
Alignment explanation
Indices: 15178--15314 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
15168 TCTTTAACAT
* * *
15178 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAATGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTTCATTTTAA-AGA
* * * * *
15242 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTACATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTTTCAT-TTTAAAGA
15305 GTGCATCGAT
1 GTGCATCGAT
15315 ACACATTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
63 18 0.29
64 45 0.71
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:17343 original size:16 final size:16
Alignment explanation
Indices: 17322--17359 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
17312 CACGCCAAAC
17322 AATTATTAATAAAAGA
1 AATTATTAATAAAAGA
17338 AATTATTAATAAAAGA
1 AATTATTAATAAAAGA
17354 AATTAT
1 AATTAT
17360 AGTGATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
AATTATTAATAAAAGA
Found at i:18651 original size:2 final size:2
Alignment explanation
Indices: 18644--18712 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
18634 TGTCAAAAAC
18644 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
18686 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18713 TTTTTTTAGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21530 original size:3 final size:3
Alignment explanation
Indices: 21522--21551 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21512 TCCCTGGTCC
21522 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
21552 CTTGTGTGTC
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:27390 original size:11 final size:11
Alignment explanation
Indices: 27374--27400 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27364 TAATATATAT
27374 TAAAATAATAA
1 TAAAATAATAA
27385 TAAAATAATAA
1 TAAAATAATAA
27396 TAAAA
1 TAAAA
27401 GTACTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:27510 original size:14 final size:14
Alignment explanation
Indices: 27474--27512 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
27464 ACTAAAACAC
27474 ATAAAATTAAAATA
1 ATAAAATTAAAATA
**
27488 ATATGATTAAAATA
1 ATAAAATTAAAATA
*
27502 TTAAAATTAAA
1 ATAAAATTAAA
27513 GGTCATAGTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATAAAATTAAAATA
Found at i:28327 original size:16 final size:15
Alignment explanation
Indices: 28301--28333 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
28291 GCTGTTGAGA
28301 TGTGTTCCTTGTTGT
1 TGTGTTCCTTGTTGT
28316 TGTGTCTCCTTGTTGT
1 TGTGT-TCCTTGTTGT
28332 TG
1 TG
28334 GTTGTTCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.15, G:0.27, T:0.58
Consensus pattern (15 bp):
TGTGTTCCTTGTTGT
Found at i:28835 original size:3 final size:3
Alignment explanation
Indices: 28827--28919 Score: 64
Period size: 3 Copynumber: 31.3 Consensus size: 3
28817 AATTATTTAT
* * * * *
28827 TAA TAA TAA T-A TAA TAA TAT TTA TAA TAA TAA TTA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * **
28874 TAC TAA TATT TAG TAA TAA TAA TAA TAG TAA TTT TAA -AA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28919 T
1 T
28920 TTAAGTAAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
2 4 0.06
3 64 0.91
4 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:28900 original size:25 final size:23
Alignment explanation
Indices: 28867--28919 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
28857 AATTATTATT
*
28867 ATAATAATACTAATATTTAGTAATA
1 ATAATAATACTAAT-TTTA-AAATA
*
28892 ATAATAATAGTAATTTTAAAATA
1 ATAATAATACTAATTTTAAAATA
28915 ATAAT
1 ATAAT
28920 TTAAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.35
24 4 0.15
25 13 0.50
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAATAATACTAATTTTAAAATA
Found at i:29163 original size:37 final size:37
Alignment explanation
Indices: 29113--29367 Score: 135
Period size: 37 Copynumber: 6.9 Consensus size: 37
29103 TGTTTTAAGA
*
29113 AAAATAATCTCAAGTGAGATAAACTTCTGTTTCGAGTG
1 AAAACAATCTCAAGTGAGATAAA-TTCTGTTTCGAGTG
* ** * * * * ** *
29151 AATA-TGTTTCAAGCGAGACAAATTTTGTTTTAAG-A
1 AAAACAATCTCAAGTGAGATAAATTCTGTTTCGAGTG
29186 AAAACAATCTCAAGTGAGATAAAGTTCTGTTTCGAGTG
1 AAAACAATCTCAAGTGAGATAAA-TTCTGTTTCGAGTG
** ** * * ** *
29224 -AAACTGTCTCAAGCAAGACAAATTTTGTTTTAAG-A
1 AAAACAATCTCAAGTGAGATAAATTCTGTTTCGAGTG
*
29259 AAAACAATCTCAAGTGAGATAAAGTTATGTTTCGAGT-
1 AAAACAATCTCAAGTGAGATAAA-TTCTGTTTCGAGTG
* ** ** * * ** *
29296 TAAACTGTCTCAAACGAGACAAATTTTGTTTTAAG-A
1 AAAACAATCTCAAGTGAGATAAATTCTGTTTCGAGTG
* *
29332 AAAACAATATCAAGTGAGATAAATTTATGTTTCGAG
1 AAAACAATCTCAAGTGAGATAAA-TTCTGTTTCGAG
29368 AACATCCGAC
Statistics
Matches: 153, Mismatches: 56, Indels: 17
0.68 0.25 0.08
Matches are distributed among these distances:
35 3 0.02
36 73 0.48
37 74 0.48
38 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (37 bp):
AAAACAATCTCAAGTGAGATAAATTCTGTTTCGAGTG
Found at i:29186 original size:73 final size:73
Alignment explanation
Indices: 29067--29367 Score: 460
Period size: 73 Copynumber: 4.1 Consensus size: 73
29057 TGGGAATTTT
* * * * *
29067 TGTTTCTAGTGAAACTGTCTCAAGTGAGACGAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
* *
29132 TAAACTTC
66 TAAAGTTA
*
29140 TGTTTCGAGTGAATA-TGTTTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
1 TGTTTCGAGTGAA-ACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
*
29204 ATAAAGTTC
65 ATAAAGTTA
*
29213 TGTTTCGAGTGAAACTGTCTCAAGCAAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
29278 TAAAGTTA
66 TAAAGTTA
* * *
29286 TGTTTCGAGTTAAACTGTCTCAAACGAGACAAATTTTGTTTTAAGAAAAACAATATCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
*
29351 TAAATTTA
66 TAAAGTTA
29359 TGTTTCGAG
1 TGTTTCGAG
29368 AACATCCGAC
Statistics
Matches: 211, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
72 1 0.00
73 209 0.99
74 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAAGTTA
Found at i:29199 original size:36 final size:36
Alignment explanation
Indices: 29159--29363 Score: 176
Period size: 36 Copynumber: 5.6 Consensus size: 36
29149 TGAATATGTT
29159 TCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATC
1 TCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATC
* * * ** ** **
29195 TCAAGTGAGATAAAGTTCTGTTTCGAGTGAAACTGTC
1 TCAAGCGAGACAAA-TTTTGTTTTAAGAAAAACAATC
*
29232 TCAAGCAAGACAAATTTTGTTTTAAGAAAAACAATC
1 TCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATC
* * * ** ** **
29268 TCAAGTGAGATAAAGTTATGTTTCGAGTTAAACTGTC
1 TCAAGCGAGACAAA-TTTTGTTTTAAGAAAAACAATC
* *
29305 TCAAACGAGACAAATTTTGTTTTAAGAAAAACAATA
1 TCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATC
* *
29341 TCAAGTGAGATAAATTTATGTTT
1 TCAAGCGAGACAAATTT-TGTTT
29364 CGAGAACATC
Statistics
Matches: 123, Mismatches: 43, Indels: 5
0.72 0.25 0.03
Matches are distributed among these distances:
36 66 0.54
37 57 0.46
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (36 bp):
TCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATC
Found at i:30105 original size:20 final size:20
Alignment explanation
Indices: 30069--30124 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 20
30059 AATAAAGCTT
30069 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTG--AAGAGAATATA
*
30091 TCATCTTTGAAGAGAATCTA
1 TCATCTTTGAAGAGAATATA
30111 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
30125 TATAGATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 24 0.73
22 9 0.27
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (20 bp):
TCATCTTTGAAGAGAATATA
Found at i:35150 original size:20 final size:20
Alignment explanation
Indices: 35056--35151 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
35046 TGTAACTATC
* *
35056 CAAAGATGCAAATGCAAATA
1 CAAAGATGCAAATACAAATG
* *
35076 CAACGATGCGGAAATAAAAATG
1 CAAAGATGC--AAATACAAATG
*
35098 CAAATTG-TGC-AATACAAAAG
1 CAAA--GATGCAAATACAAATG
* * **
35118 TAAACATAAAAATACAAATG
1 CAAAGATGCAAATACAAATG
35138 CAAAGATGCAAATA
1 CAAAGATGCAAATA
35152 AAAAAATGTA
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
19 1 0.02
20 38 0.70
22 11 0.20
23 3 0.06
24 1 0.02
ACGTcount: A:0.55, C:0.14, G:0.15, T:0.17
Consensus pattern (20 bp):
CAAAGATGCAAATACAAATG
Found at i:38441 original size:29 final size:30
Alignment explanation
Indices: 38398--38457 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
38388 AATTGCAATT
38398 TAATAGTGACTAAAACATATAAA-ATTAAAA
1 TAATAGTGACTAAAACATA-AAATATTAAAA
* *
38428 TAATA-TGATTAAAATATAAAATATTAAAA
1 TAATAGTGACTAAAACATAAAATATTAAAA
38457 T
1 T
38458 TAAAGGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 19 0.70
30 5 0.19
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (30 bp):
TAATAGTGACTAAAACATAAAATATTAAAA
Found at i:38459 original size:21 final size:20
Alignment explanation
Indices: 38417--38461 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
38407 CTAAAACATA
**
38417 TAAAATTAAAATAATATGAT
1 TAAAATTAAAATAATAAAAT
*
38437 TAAAATATAAAATATTAAAAT
1 TAAAAT-TAAAATAATAAAAT
38458 TAAA
1 TAAA
38462 GGTCATAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAATTAAAATAATAAAAT
Found at i:38461 original size:14 final size:15
Alignment explanation
Indices: 38421--38461 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
38411 AACATATAAA
*
38421 ATTAAAA-TAATATG
1 ATTAAAATTAAAATG
38435 ATTAAAATATAAAAT-
1 ATTAAAAT-TAAAATG
38450 ATTAAAATTAAA
1 ATTAAAATTAAA
38462 GGTCATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
15 8 0.33
16 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
ATTAAAATTAAAATG
Found at i:39815 original size:3 final size:3
Alignment explanation
Indices: 39807--39899 Score: 66
Period size: 3 Copynumber: 31.3 Consensus size: 3
39797 AATTATTTAT
* * *
39807 TAA TAA TAA T-A TAA TAA TAT TTA TAA TAA TAA TAA TTAC T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* * * * **
39851 TAA TAC TAA TATT TAG TAA TAA TAA TAA TAG TAA TTT TAA -AA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39896 TAA T
1 TAA T
39900 TTAAGTAAAA
Statistics
Matches: 68, Mismatches: 17, Indels: 10
0.72 0.18 0.11
Matches are distributed among these distances:
2 5 0.07
3 59 0.87
4 4 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:39833 original size:12 final size:12
Alignment explanation
Indices: 39800--39837 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39790 TATTTGTAAT
39800 TATTTATTAATAA
1 TATTTA-TAATAA
*
39813 TA-ATATAATAA
1 TATTTATAATAA
39824 TATTTATAATAA
1 TATTTATAATAA
39836 TA
1 TA
39838 ATAATTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 8 0.36
12 12 0.55
13 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATTTATAATAA
Found at i:39880 original size:25 final size:23
Alignment explanation
Indices: 39847--39899 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
39837 AATAATTACT
*
39847 ATAATAATACTAATATTTAGTAATA
1 ATAATAATACTAAT-TTTA-AAATA
*
39872 ATAATAATAGTAATTTTAAAATA
1 ATAATAATACTAATTTTAAAATA
39895 ATAAT
1 ATAAT
39900 TTAAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.35
24 4 0.15
25 13 0.50
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAATAATACTAATTTTAAAATA
Found at i:44475 original size:2 final size:2
Alignment explanation
Indices: 44468--44502 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
44458 AACTTTAAGA
44468 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 A
44503 AGTTAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46216 original size:61 final size:59
Alignment explanation
Indices: 46093--46245 Score: 175
Period size: 60 Copynumber: 2.6 Consensus size: 59
46083 TCAGGTGACT
* * *
46093 ATTTTGTAACTTTTAATAGTCGGGAACTCAACAAATCAACACCCCATAGTCGAAGGACA
1 ATTTTGTAACTTTTAATAGTCGGGAACTCAACAAATCAACAACCCATAATCAAAGGACA
* * ** *
46152 ATTTTTGTAACTTTTAATAGTCGAGGGACTCAACAATTCAACAACTTATAATCAAAGGATA
1 A-TTTTGTAACTTTTAATAGTCG-GGAACTCAACAAATCAACAACCCATAATCAAAGGACA
* * *
46213 ATTTTATAATTTTTAATAGTC--AAACTCAACAAA
1 ATTTTGTAACTTTTAATAGTCGGGAACTCAACAAA
46246 ACATTACCGT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
57 9 0.11
59 1 0.01
60 39 0.49
61 30 0.38
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCGGGAACTCAACAAATCAACAACCCATAATCAAAGGACA
Found at i:50411 original size:12 final size:12
Alignment explanation
Indices: 50394--50419 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
50384 TACTTGTTGG
50394 ATCTAGTGTCAC
1 ATCTAGTGTCAC
50406 ATCTAGTGTCAC
1 ATCTAGTGTCAC
50418 AT
1 AT
50420 TTCACTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (12 bp):
ATCTAGTGTCAC
Found at i:52003 original size:15 final size:15
Alignment explanation
Indices: 51983--52014 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
51973 AAATATTGAT
51983 ACAAAGATAATATTA
1 ACAAAGATAATATTA
*
51998 ACAAAGATAATGTTA
1 ACAAAGATAATATTA
52013 AC
1 AC
52015 TCGATTCTCA
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:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (15 bp):
ACAAAGATAATATTA
Found at i:94158 original size:94 final size:94
Alignment explanation
Indices: 94056--94374 Score: 489
Period size: 94 Copynumber: 3.4 Consensus size: 94
94046 TTTTTCTTTA
* * *
94056 ACCGTTAATCGAACCGAAATTTACTTGTAAATTATTAATCGAACCAAATTAACTAAATTTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAATCGAACCAAATTAACCAAATTTTTTTC
* *
94121 TTTAACATTAATTGAACCGAAAATATTTT
66 TTTAACATTAATCGAACCGAAAATATTTG
* *
94150 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAATCAAATTAACCAAATTTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAATCGAACCAAATTAACCAAATTTTTTTC
*
94215 TTTAACATTAATCGAACCGAAATTATTTG
66 TTTAACATTAATCGAACCGAAAATATTTG
* * * *
94244 ACCGTTAATCGAACCGAAATTTATTTAAAAATTATTAACCAAACCAAATTAACCGAA-TTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAATCGAACCAAATTAACCAAATTTTTTTC
94308 TTTAACATTAATCGAACC-AAAATTATTTG
66 TTTAACATTAATCGAACCGAAAA-TATTTG
* *
94337 ACAGTTAATCGAACCCAAATTTATTTGAAAATTATTAA
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAA
94375 CCAAATTAAC
Statistics
Matches: 206, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
92 3 0.01
93 66 0.32
94 137 0.67
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.36
Consensus pattern (94 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAATCGAACCAAATTAACCAAATTTTTTTC
TTTAACATTAATCGAACCGAAAATATTTG
Found at i:94357 original size:93 final size:94
Alignment explanation
Indices: 94056--94438 Score: 482
Period size: 94 Copynumber: 4.0 Consensus size: 94
94046 TTTTTCTTTA
* * * * *
94056 ACCGTTAATCGAACCGAAATTTACTTGTAAATTATTAATCGAACCAAATTAACTAAATTTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAAATTTTTTTC
* *
94121 TTTAACATTAATTGAACCGAAAA-TATTTT
66 TTTAACATTAATCGAACC-AAAATTATTTG
* * * *
94150 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAATCAAATTAACCAAATTTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAAATTTTTTTC
*
94215 TTTAACATTAATCGAACCGAAATTATTTG
66 TTTAACATTAATCGAACCAAAATTATTTG
* *
94244 ACCGTTAATCGAACCGAAATTTATTTAAAAATTATTAACCAAACCAAATTAACCGAA-TTTTTTC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAAATTTTTTTC
94308 TTTAACATTAATCGAACCAAAATTATTTG
66 TTTAACATTAATCGAACCAAAATTATTTG
* * * * **
94337 ACAGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCAAATTAACCGAATAAAATAAATTAT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACC--A--AACCAAATTAACCAAATT-T
* *
94402 TTTTCTTTAACCATTAATCAAACCGAAATTTATTTG
61 TTTTCTTTAA-CATTAATCGAACC-AAAATTATTTG
94438 A
1 A
94439 AAATTATTAA
Statistics
Matches: 255, Mismatches: 25, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
93 75 0.29
94 133 0.52
95 1 0.00
97 11 0.04
98 1 0.00
99 11 0.04
100 12 0.05
101 11 0.04
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (94 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAAATTTTTTTC
TTTAACATTAATCGAACCAAAATTATTTG
Found at i:94374 original size:187 final size:193
Alignment explanation
Indices: 94056--94438 Score: 528
Period size: 187 Copynumber: 2.0 Consensus size: 193
94046 TTTTTCTTTA
** * * *
94056 ACCGTTAATCGAACCGAAATTTACTTGTAAATTATTAATCGAACCAAATTAACTAAATTTTTTTC
1 ACCGTTAATCGAACCGAAATTTACTTAAAAATTATTAACCAAACCAAATTAACCAAATTTTTTTC
* * *
94121 TTTAACATTAATTGAACCGAAAATATTTTACCGTTAATCGAACCAAAATTTATTTGAAAATTATT
66 TTTAACATTAATCGAACCGAAAATATTTGACAGTTAATCGAACCAAAATTTATTTGAAAATTATT
* * * * *
94186 AATCGAA-T-CAAATTAACCAAATT-TTTTTCTTTAA-CATTAATCGAACCGAAA-TTATTTG
131 AACCAAATTACAAATAAAACAAATTATTTTTCTTTAACCATTAATCAAACCGAAATTTATTTG
* *
94244 ACCGTTAATCGAACCGAAATTTATTTAAAAATTATTAACCAAACCAAATTAACCGAA-TTTTTTC
1 ACCGTTAATCGAACCGAAATTTACTTAAAAATTATTAACCAAACCAAATTAACCAAATTTTTTTC
*
94308 TTTAACATTAATCGAACC-AAAATTATTTGACAGTTAATCGAACCCAAATTTATTTGAAAATTAT
66 TTTAACATTAATCGAACCGAAAA-TATTTGACAGTTAATCGAACCAAAATTTATTTGAAAATTAT
* *
94372 TAACCAAATTAACCGAATAAAATAAATTATTTTTCTTTAACCATTAATCAAACCGAAATTTATTT
130 TAACCAAATT-A-CAAATAAAACAAATTATTTTTCTTTAACCATTAATCAAACCGAAATTTATTT
94437 G
193 G
94438 A
1 A
94439 AAATTATTAA
Statistics
Matches: 169, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
186 4 0.02
187 68 0.40
188 51 0.30
191 11 0.07
192 11 0.07
193 16 0.09
194 8 0.05
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (193 bp):
ACCGTTAATCGAACCGAAATTTACTTAAAAATTATTAACCAAACCAAATTAACCAAATTTTTTTC
TTTAACATTAATCGAACCGAAAATATTTGACAGTTAATCGAACCAAAATTTATTTGAAAATTATT
AACCAAATTACAAATAAAACAAATTATTTTTCTTTAACCATTAATCAAACCGAAATTTATTTG
Found at i:94559 original size:166 final size:164
Alignment explanation
Indices: 94248--94700 Score: 590
Period size: 166 Copynumber: 2.8 Consensus size: 164
94238 TATTTGACCG
* *
94248 TTAATCGAACCGAAATTTATTTAAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCTTTAA
1 TTAATCGAACCGAAATTTATTTAAAAATTATTAACCGAACCAAA-TAACC-ATTTTTTTCTTTAA
* * *
94313 CATTAATCGAACCAAAATTATTTGACAGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCA
64 CATTAATCGAACCAAAATTATTTGAC-CTTAATCGAACCAAAATTTATTTGAAAATTATTAACCG
94378 AATTAACCGAATAAAATAAATTA-TTTTTCTTTAACCA
128 AATTAACCGAATAAAATAAATTATTTTTTC-TTAACCA
* *
94415 TTAATCAAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCATTTTTTTCTTTAAC
1 TTAATCGAACCGAAATTTATTTAAAAATTATTAACCGAACCAAAT-AACCATTTTTTTCTTTAAC
* *
94480 GATTAATCGAACCAAAATTATTGGACCTTAATCGAATCAAAATTTATTTGAAAATTATTAACCGA
65 -ATTAATCGAACCAAAATTATTTGACCTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGA
*
94545 ATTAACAC-AATAAAATAAATTATTTTTTCTTAACCG
129 ATTAAC-CGAATAAAATAAATTATTTTTTCTTAACCA
* *
94581 TTAATGGAACTGAAATTTATTTAAAAATTATTAACCG---------A--ATTTTTTTCTTTAACC
1 TTAATCGAACCGAAATTTATTTAAAAATTATTAACCGAACCAAATAACCATTTTTTTCTTTAA-C
* * * *
94635 ATTAATCGAACCGAAATTATTTGACCATTAATCTAACCGAAATTTATTTGAAAATTATTTACCGA
65 ATTAATCGAACCAAAATTATTTGACC-TTAATCGAACCAAAATTTATTTGAAAATTATTAACCGA
94700 A
129 A
94701 CTAAATTAAC
Statistics
Matches: 260, Mismatches: 20, Indels: 24
0.86 0.07 0.08
Matches are distributed among these distances:
154 38 0.15
155 36 0.14
156 1 0.00
166 109 0.42
167 76 0.29
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (164 bp):
TTAATCGAACCGAAATTTATTTAAAAATTATTAACCGAACCAAATAACCATTTTTTTCTTTAACA
TTAATCGAACCAAAATTATTTGACCTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAAT
TAACCGAATAAAATAAATTATTTTTTCTTAACCA
Found at i:94664 original size:26 final size:27
Alignment explanation
Indices: 94632--94685 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
94622 TTTTTCTTTA
94632 ACCATTAATCGAACCGAAA-TTATTTG
1 ACCATTAATCGAACCGAAATTTATTTG
*
94658 ACCATTAATCTAACCGAAATTTATTTG
1 ACCATTAATCGAACCGAAATTTATTTG
94685 A
1 A
94686 AAATTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (27 bp):
ACCATTAATCGAACCGAAATTTATTTG
Found at i:94746 original size:94 final size:95
Alignment explanation
Indices: 94610--94793 Score: 325
Period size: 94 Copynumber: 1.9 Consensus size: 95
94600 TTTAAAAATT
* * *
94610 ATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCATTAATCTAACCGA
1 ATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCAA
*
94675 AATTTATTTGAAAATTATTTACCGAACTAA
66 AATTTATTTGAAAATTATTAACCGAACTAA
94705 ATTAACCGAATTTTTTTCTTTAA-CATTAATCGAACCAAAATTATTTGACCATTAATCGAACCAA
1 ATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCAA
94769 AATTTATTTGAAAATTATTAACCGA
66 AATTTATTTGAAAATTATTAACCGA
94794 TTAACCGTTA
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
94 62 0.73
95 23 0.27
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (95 bp):
ATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCAA
AATTTATTTGAAAATTATTAACCGAACTAA
Found at i:94757 original size:26 final size:27
Alignment explanation
Indices: 94728--94779 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
94718 TTTTCTTTAA
94728 CATTAATCGAACCAAAA-TTATTTGAC
1 CATTAATCGAACCAAAATTTATTTGAC
94754 CATTAATCGAACCAAAATTTATTTGA
1 CATTAATCGAACCAAAATTTATTTGA
94780 AAATTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (27 bp):
CATTAATCGAACCAAAATTTATTTGAC
Found at i:94785 original size:27 final size:26
Alignment explanation
Indices: 94729--94785 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
94719 TTTCTTTAAC
**
94729 ATTAATCGAACCAAAATTATTTGACC
1 ATTAATCGAACCAAAATTATTTGAAA
94755 ATTAATCGAACCAAAATTTATTTGAAA
1 ATTAATCGAACCAAAA-TTATTTGAAA
94782 ATTA
1 ATTA
94786 TTAACCGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (26 bp):
ATTAATCGAACCAAAATTATTTGAAA
Found at i:102267 original size:26 final size:26
Alignment explanation
Indices: 102192--102270 Score: 122
Period size: 26 Copynumber: 3.0 Consensus size: 26
102182 ATAAATTACG
* *
102192 AAAATGCCCCTAAAGGGTAAAATAACC
1 AAAATG-CCCTAAAGTGTAAAATGACC
102219 AAAATGCCCTAAAGTGTAAAATGACC
1 AAAATGCCCTAAAGTGTAAAATGACC
*
102245 AAAATGCCCTAAAATGTAAAATGACC
1 AAAATGCCCTAAAGTGTAAAATGACC
102271 TAAAGTACAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 43 0.88
27 6 0.12
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (26 bp):
AAAATGCCCTAAAGTGTAAAATGACC
Found at i:105021 original size:47 final size:49
Alignment explanation
Indices: 104951--105046 Score: 169
Period size: 47 Copynumber: 2.0 Consensus size: 49
104941 GTGCCTTGAG
*
104951 TATGTATTGGCTTGATTGATTGGTGTTTCAGTT-TTTTTTTTAATAGAA
1 TATGTATTGGCTTGATTGATTGGTGTTTCAGTTATTTCTTTTAATAGAA
104999 TATGTA-TGGCTTGATTGATTGGTGTTTCAGTTATTTCTTTTAATAGAA
1 TATGTATTGGCTTGATTGATTGGTGTTTCAGTTATTTCTTTTAATAGAA
105047 CTAGTTTGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 26 0.57
48 20 0.43
ACGTcount: A:0.22, C:0.05, G:0.21, T:0.52
Consensus pattern (49 bp):
TATGTATTGGCTTGATTGATTGGTGTTTCAGTTATTTCTTTTAATAGAA
Found at i:110876 original size:16 final size:16
Alignment explanation
Indices: 110855--110885 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
110845 ATATATGAAG
110855 AAACTTTAAATTGCAA
1 AAACTTTAAATTGCAA
110871 AAACTTTAAATTGCA
1 AAACTTTAAATTGCA
110886 GAAGTAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (16 bp):
AAACTTTAAATTGCAA
Found at i:111560 original size:18 final size:18
Alignment explanation
Indices: 111539--111575 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
111529 ATTTTATTTA
111539 GTTTTAAAATTTAAATGG
1 GTTTTAAAATTTAAATGG
*
111557 GTTTTAAAATTTAATTGG
1 GTTTTAAAATTTAAATGG
111575 G
1 G
111576 CAGTGGGCTG
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:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (18 bp):
GTTTTAAAATTTAAATGG
Found at i:111630 original size:2 final size:2
Alignment explanation
Indices: 111623--111697 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
111613 GTGGCTGAGT
111623 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
111665 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
111698 TATGTATTTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:113830 original size:51 final size:51
Alignment explanation
Indices: 113754--113854 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
113744 TAAGGAAATG
*
113754 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
113805 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
113855 CTCCCCCTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:115636 original size:16 final size:16
Alignment explanation
Indices: 115615--115645 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115605 ACCTGATACC
115615 ATGTAGAAAACAGACT
1 ATGTAGAAAACAGACT
*
115631 ATGTAGAAAATAGAC
1 ATGTAGAAAACAGAC
115646 AAGTCTGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (16 bp):
ATGTAGAAAACAGACT
Found at i:118462 original size:22 final size:23
Alignment explanation
Indices: 118419--118463 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
118409 AACGCAGACC
* *
118419 TTAATTTGTTATTTTAATTAAAA
1 TTAATTTGTTATTTAAAATAAAA
118442 TTAATTT-TTATTTAAAATAAAA
1 TTAATTTGTTATTTAAAATAAAA
118464 AACATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTTGTTATTTAAAATAAAA
Found at i:118464 original size:23 final size:23
Alignment explanation
Indices: 118419--118464 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
118409 AACGCAGACC
* *
118419 TTAATTTGTTATTTTAATTAAAA
1 TTAATTTGTTATTTAAATAAAAA
118442 TTAATTT-TTATTTAAAATAAAAA
1 TTAATTTGTTATTT-AAATAAAAA
118465 ACATTTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTGTTATTTAAATAAAAA
Found at i:120931 original size:22 final size:22
Alignment explanation
Indices: 120905--120955 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
120895 AAAAAAATGA
120905 TTAATCTTGCAGATAATGAACT
1 TTAATCTTGCAGATAATGAACT
120927 TTAATCTTGCAGATAATGAACT
1 TTAATCTTGCAGATAATGAACT
120949 TTAATCT
1 TTAATCT
120956 GATTAGAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (22 bp):
TTAATCTTGCAGATAATGAACT
Found at i:122837 original size:60 final size:60
Alignment explanation
Indices: 122719--122838 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
122709 AAACTGAGTA
* * * * *
122719 TCATAGTTTGAAGATGAATTTAGAATATTCAAAAATTTAAGAATCAATTTAGATTAAAAG
1 TCATAGTTTGAAGATAAAATTAAAATATTCAAAAATTTAAGAATCAATTTAAAATAAAAG
* * *
122779 TCATAGTTTTAGGATAAAATTAAAATATTTAAAAATTTAAGAATCAATTTAAAATAAAAG
1 TCATAGTTTGAAGATAAAATTAAAATATTCAAAAATTTAAGAATCAATTTAAAATAAAAG
122839 AATTCATCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (60 bp):
TCATAGTTTGAAGATAAAATTAAAATATTCAAAAATTTAAGAATCAATTTAAAATAAAAG
Found at i:126363 original size:23 final size:21
Alignment explanation
Indices: 126337--126396 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 21
126327 AGTCTGCATA
126337 TATGACACGTTTTTACCTGCCTT
1 TATGACACGTTTTTA--TGCCTT
126360 TATGACACGTTTTCTTATGCCTT
1 TATGACACG-TTT-TTATGCCTT
126383 T-TGACACGTTTTTA
1 TATGACACGTTTTTA
126397 AGTCGTTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.09
21 3 0.09
22 7 0.20
23 16 0.46
24 3 0.09
25 3 0.09
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (21 bp):
TATGACACGTTTTTATGCCTT
Found at i:129014 original size:57 final size:58
Alignment explanation
Indices: 128947--129059 Score: 183
Period size: 57 Copynumber: 2.0 Consensus size: 58
128937 TAGAAAGAGG
* * *
128947 GTCATAGTTTAGGGATGCAATTAGAATGTTAAAAAATTTAAGGACTAA-TTAAAATCA
1 GTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTTAAGGACTAATTTAAAATCA
*
129004 GTCATAGTTTAGGGATGAAATTAAAATATTCAAAAATTTAAGGACTAATTTAAAAT
1 GTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTTAAGGACTAATTTAAAAT
129060 GAAAGTTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 44 0.86
58 7 0.14
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (58 bp):
GTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTTAAGGACTAATTTAAAATCA
Found at i:129043 original size:29 final size:28
Alignment explanation
Indices: 128954--129043 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
128944 AGGGTCATAG
* * *
128954 TTTAGGGATGCAATTAGAATGTTAAAAAA
1 TTTAGGGATG-AATTAAAATATTCAAAAA
* * * *
128983 TTTAAGGACT-AATTAAAATCAGTC-ATAG
1 TTTAGGGA-TGAATTAAAAT-ATTCAAAAA
129011 TTTAGGGATGAAATTAAAATATTCAAAAA
1 TTTAGGGATG-AATTAAAATATTCAAAAA
129040 TTTA
1 TTTA
129044 AGGACTAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
27 1 0.02
28 20 0.44
29 23 0.51
30 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.33
Consensus pattern (28 bp):
TTTAGGGATGAATTAAAATATTCAAAAA
Found at i:129056 original size:29 final size:29
Alignment explanation
Indices: 128978--129059 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
128968 TAGAATGTTA
128978 AAAAATTTAAGGACTAATTAAAATCAGTC
1 AAAAATTTAAGGACTAATTAAAATCAGTC
* * * *
129007 -ATAGTTTAGGGA-TGAAATTAAAAT-ATTC
1 AAAAATTTAAGGACT--AATTAAAATCAGTC
129035 AAAAATTTAAGGACTAATTTAAAAT
1 AAAAATTTAAGGACTAA-TTAAAAT
129060 GAAAGTTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
27 1 0.02
28 14 0.34
29 25 0.61
30 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (29 bp):
AAAAATTTAAGGACTAATTAAAATCAGTC
Found at i:129310 original size:6 final size:6
Alignment explanation
Indices: 129282--129320 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
129272 AGTTAAAAAG
*
129282 TAAATT ATACATT TAATATT TAAATT TAAATT TAAATT T
1 TAAATT -TAAATT TAA-ATT TAAATT TAAATT TAAATT T
129321 TTATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:129316 original size:12 final size:12
Alignment explanation
Indices: 129282--129320 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
129272 AGTTAAAAAG
*
129282 TAAATTATACATT
1 TAAATT-TAAATT
129295 TAATATTTAAATT
1 TAA-ATTTAAATT
129308 TAAATTTAAATT
1 TAAATTTAAATT
129320 T
1 T
129321 TTATTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 10 0.42
13 11 0.46
14 3 0.12
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:129323 original size:20 final size:20
Alignment explanation
Indices: 129282--129320 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
129272 AGTTAAAAAG
*
129282 TAAATTATACATTTAATATT
1 TAAATTATAAATTTAATATT
129302 TAAATT-TAAATTTAA-ATT
1 TAAATTATAAATTTAATATT
129320 T
1 T
129321 TTATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATTATAAATTTAATATT
Found at i:130050 original size:12 final size:13
Alignment explanation
Indices: 130014--130057 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
130004 GCCCCGATTA
*
130014 CCCGATTACCCAC
1 CCCGATTACCCGC
130027 CCCGATTACCCGC
1 CCCGATTACCCGC
*
130040 CCCGA-TACCCGA
1 CCCGATTACCCGC
130052 CCCGAT
1 CCCGAT
130058 AAATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.20, C:0.52, G:0.14, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:131416 original size:30 final size:30
Alignment explanation
Indices: 131380--131438 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
131370 GCCGGAATCC
131380 AGGAAATTTATCTACTCCCATCAACCTCGG
1 AGGAAATTTATCTACTCCCATCAACCTCGG
*
131410 AGGAAATTTATCTGCTCCCATCAACCTCG
1 AGGAAATTTATCTACTCCCATCAACCTCG
131439 CCACTAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (30 bp):
AGGAAATTTATCTACTCCCATCAACCTCGG
Found at i:143374 original size:6 final size:6
Alignment explanation
Indices: 143363--143398 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
143353 GCTTTGGTGC
* *
143363 AAGAGG AAGAGG CAGAGG AAGAGG AAGGGG AAGAGG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG
143399 GCGAGCAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.03, G:0.53, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:148723 original size:21 final size:21
Alignment explanation
Indices: 148699--148738 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
148689 GCAACACAGG
*
148699 TTCCAAATTCGCAACGCGATT
1 TTCCAAATTCACAACGCGATT
148720 TTCCAAATTCACAACGCGA
1 TTCCAAATTCACAACGCGA
148739 ATAGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (21 bp):
TTCCAAATTCACAACGCGATT
Found at i:148806 original size:60 final size:60
Alignment explanation
Indices: 148723--148839 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
148713 CGCGATTTTC
148723 CAAATTCACAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCGCAACGCGAAAGT
1 CAAATTCACAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCGCAACGCGAAAGT
* * * *
148783 CAAATTCGCAACTCGAATAGGTAAATTGTAACGATAATATGTAAATCGCAACGCGAA
1 CAAATTCACAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCGCAACGCGAA
148840 TATTATTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.21
Consensus pattern (60 bp):
CAAATTCACAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCGCAACGCGAAAGT
Found at i:148842 original size:20 final size:20
Alignment explanation
Indices: 148731--148842 Score: 111
Period size: 20 Copynumber: 5.6 Consensus size: 20
148721 TCCAAATTCA
*
148731 CAACGCGAATAGGTAAATCG
1 CAACGCGAATATGTAAATCG
**
148751 CAACGATAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
148771 CAACGCGAA-A-GTCAAATTCG
1 CAACGCGAATATGT-AAA-TCG
* * *
148791 CAACTCGAATAGGTAAATTG
1 CAACGCGAATATGTAAATCG
* **
148811 TAACGATAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
148831 CAACGCGAATAT
1 CAACGCGAATAT
148843 TATTTTCAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 60 0.83
21 4 0.06
22 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:148987 original size:22 final size:22
Alignment explanation
Indices: 148962--149011 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
148952 TCACTCTCTA
* * *
148962 CGGCGAAATCTGTCCCCATCTC
1 CGGCGAAATCCGTCCACATATC
148984 CGGCGAAATCCGTCCACATATC
1 CGGCGAAATCCGTCCACATATC
149006 CGGCGA
1 CGGCGA
149012 CCCCCTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.18
Consensus pattern (22 bp):
CGGCGAAATCCGTCCACATATC
Found at i:149364 original size:20 final size:21
Alignment explanation
Indices: 149339--149391 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
149329 AATAGTTTTT
149339 GAAAATGAAAATCGCAAC-GC
1 GAAAATGAAAATCGCAACTGC
149359 GAAAATGAAAATCGCAACGTTGC
1 GAAAATGAAAATCGCAAC--TGC
149382 GAAAATGAAA
1 GAAAATGAAA
149392 TTTGCGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.60
23 12 0.40
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (21 bp):
GAAAATGAAAATCGCAACTGC
Found at i:149453 original size:20 final size:19
Alignment explanation
Indices: 149391--149446 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 19
149381 CGAAAATGAA
*
149391 ATTT-GCGTTGTGATTTTC
1 ATTTCGCGTTGCGATTTTC
149409 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
149428 ATTTTCGCGTTGCGATTTT
1 A-TTTCGCGTTGCGATTTT
149447 AAGTTTCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 4 0.11
19 14 0.40
20 17 0.49
ACGTcount: A:0.11, C:0.16, G:0.21, T:0.52
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:151272 original size:63 final size:62
Alignment explanation
Indices: 151164--151285 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 62
151154 AGGTCGGTAC
* *
151164 TTTACGTGACGACAATGGTGCATGACGTGATGAGGTACGGTCTTTAAGTGGTGAGGTAGAGGT
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTAC-GTCTTTAAGTGATGAGGTAGAGGT
* * * * *
151227 TTTACGCGATGACAATGGTGCTTTACGTGGTGAGGTATC-TACTTTACGTGATGAGGTAG
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTA-CGT-CTTTAAGTGATGAGGTAG
151286 TCGCTCTACG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.96
64 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.34, T:0.31
Consensus pattern (62 bp):
TTTACGCGACGACAATGGTGCATGACGTGATGAGGTACGTCTTTAAGTGATGAGGTAGAGGT
Found at i:151626 original size:42 final size:42
Alignment explanation
Indices: 151580--151701 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
151570 GATTCACCTG
* * *
151580 TCATCATTCAAGAGGCCTCTCCTATCGTTCAAGAAGCCCCTA
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAAGCCCCTA
* * * * *
151622 TCATCCTTCAAAAGGCCCCTCCCACCTTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAAGCCCCTA
* * * *
151664 TCATCGTTCAAGTGGTCCCTCCCACCATTCAAG-AGCCC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAAGCCC
151702 GATTCATATG
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
41 4 0.06
42 62 0.94
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.24
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAAGCCCCTA
Found at i:151694 original size:21 final size:21
Alignment explanation
Indices: 151584--151698 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 21
151574 CACCTGTCAT
* * *
151584 CATTCAAGAGGCCTCTCCTAT
1 CATTCAAGAGGCCCCTCCCAC
* * **
151605 CGTTCAAGAAGCCCCTATCATC
1 CATTCAAGAGGCCCCTCCCA-C
*
151627 C-TTCAAAAGGCCCCTCCCAC
1 CATTCAAGAGGCCCCTCCCAC
* ** *
151647 CTTTCAAGAGGCCCCTGTCAT
1 CATTCAAGAGGCCCCTCCCAC
* * *
151668 CGTTCAAGTGGTCCCTCCCAC
1 CATTCAAGAGGCCCCTCCCAC
151689 CATTCAAGAG
1 CATTCAAGAG
151699 CCCGATTCAT
Statistics
Matches: 69, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 2 0.03
21 66 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.23
Consensus pattern (21 bp):
CATTCAAGAGGCCCCTCCCAC
Found at i:153089 original size:27 final size:27
Alignment explanation
Indices: 153051--153172 Score: 94
Period size: 27 Copynumber: 4.6 Consensus size: 27
153041 CTTTTTTTGC
153051 TTGTTTAATTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATTTGTAAAAGTTGAT
* * *
153078 TTGTTTAATTGATGTGTAAATAATT-CT
1 TTGTTTAATTGATTTGTAAA-AGTTGAT
* **
153105 TAT-TTT--TTG-CTTGTTTAA-TTGAT
1 T-TGTTTAATTGATTTGTAAAAGTTGAT
** *
153128 TTGTAAAAGTTGATTTATAAAAGTTGAT
1 TTGTTTAA-TTGATTTGTAAAAGTTGAT
153156 TTGTTTAATTGATTTGT
1 TTGTTTAATTGATTTGT
153173 TGTTTAATTT
Statistics
Matches: 69, Mismatches: 17, Indels: 18
0.66 0.16 0.17
Matches are distributed among these distances:
22 3 0.04
23 4 0.06
24 4 0.06
25 3 0.04
26 3 0.04
27 37 0.54
28 15 0.22
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (27 bp):
TTGTTTAATTGATTTGTAAAAGTTGAT
Found at i:153142 original size:14 final size:14
Alignment explanation
Indices: 153123--153172 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
153113 GCTTGTTTAA
153123 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
153137 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
**
153151 TTGATTTGTTTAA-
1 TTGATTTGTAAAAG
153164 TTGATTTGT
1 TTGATTTGT
153173 TGTTTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 9 0.28
14 23 0.72
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:153252 original size:20 final size:20
Alignment explanation
Indices: 153227--153338 Score: 118
Period size: 20 Copynumber: 5.6 Consensus size: 20
153217 AAGGTACACT
*
153227 TTCACAACGCGAAAATCAAA
1 TTCACAACGCGAAAGTCAAA
153247 TTCACAACGCGAAAGTCAAA
1 TTCACAACGCGAAAGTCAAA
* * *
153267 ATCGCAACACGAAAGTCAAA
1 TTCACAACGCGAAAGTCAAA
** * * *
153287 ACCTCAACACCAAAGTCAAAA
1 TTCACAACGCGAAAGTC-AAA
*
153308 TT-GCAACGCGAAAGTCAAA
1 TTCACAACGCGAAAGTCAAA
153327 TTCACAACGCGA
1 TTCACAACGCGA
153339 TTTTGACTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 5 0.06
20 69 0.90
21 3 0.04
ACGTcount: A:0.46, C:0.27, G:0.13, T:0.13
Consensus pattern (20 bp):
TTCACAACGCGAAAGTCAAA
Found at i:153641 original size:20 final size:20
Alignment explanation
Indices: 153583--153715 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
153573 GCAAGTCGAA
153583 GACTTTCGCGTTGCGATTTT
1 GACTTTCGCGTTGCGATTTT
* *
153603 GATTTTC-CGTTGTTG-TTTT
1 GACTTTCGCGTTG-CGATTTT
*
153622 GACTTTCGCGTTGCGTTTTT
1 GACTTTCGCGTTGCGATTTT
* *
153642 GACTTTCACGTTGCGAATTT
1 GACTTTCGCGTTGCGATTTT
* *
153662 GATTTTCGCGTTGCGGTTTT
1 GACTTTCGCGTTGCGATTTT
***
153682 GACTTTTATGTTGCGATTTT
1 GACTTTCGCGTTGCGATTTT
153702 GACTTTCGCGTTGC
1 GACTTTCGCGTTGC
153716 AAAAGTGTAC
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
19 16 0.18
20 75 0.82
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (20 bp):
GACTTTCGCGTTGCGATTTT
Found at i:153669 original size:40 final size:40
Alignment explanation
Indices: 153583--153715 Score: 171
Period size: 40 Copynumber: 3.4 Consensus size: 40
153573 GCAAGTCGAA
* *
153583 GACTTTCGCGTTGCGATTTTGATTTTC-CGTTGTTG-TTTT
1 GACTTTCGCGTTGCGATTTTGACTTTCACGTTG-CGATTTT
* *
153622 GACTTTCGCGTTGCGTTTTTGACTTTCACGTTGCGAATTT
1 GACTTTCGCGTTGCGATTTTGACTTTCACGTTGCGATTTT
* * * *
153662 GATTTTCGCGTTGCGGTTTTGACTTTTATGTTGCGATTTT
1 GACTTTCGCGTTGCGATTTTGACTTTCACGTTGCGATTTT
153702 GACTTTCGCGTTGC
1 GACTTTCGCGTTGC
153716 AAAAGTGTAC
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 26 0.32
40 56 0.68
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (40 bp):
GACTTTCGCGTTGCGATTTTGACTTTCACGTTGCGATTTT
Found at i:153702 original size:60 final size:59
Alignment explanation
Indices: 153583--153715 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 59
153573 GCAAGTCGAA
* ** * *
153583 GACTTTCGCGTTGCGATTTTGATTTTCCGTTGTTGTTTTGACTTTCGCGTTGCGTTTTT
1 GACTTTCGCGTTGCGAATTTGATTTTCCGTTGCGGTTTTGACTTTCACGTTGCGATTTT
* * *
153642 GACTTTCACGTTGCGAATTTGATTTTCGCGTTGCGGTTTTGACTTTTATGTTGCGATTTT
1 GACTTTCGCGTTGCGAATTTGATTTTC-CGTTGCGGTTTTGACTTTCACGTTGCGATTTT
153702 GACTTTCGCGTTGC
1 GACTTTCGCGTTGC
153716 AAAAGTGTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 25 0.39
60 39 0.61
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (59 bp):
GACTTTCGCGTTGCGAATTTGATTTTCCGTTGCGGTTTTGACTTTCACGTTGCGATTTT
Found at i:154045 original size:18 final size:18
Alignment explanation
Indices: 154022--154057 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
154012 AAGTCGGTTG
*
154022 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
*
154040 TGATTGCGATTTTTATTT
1 TGATTGCGATTTTGATTT
154058 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:156231 original size:24 final size:24
Alignment explanation
Indices: 156180--156231 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
156170 ATCTGAGTAT
** *
156180 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
156204 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
156228 TGAC
1 TGAC
156232 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:157168 original size:20 final size:20
Alignment explanation
Indices: 157124--157232 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
157114 CAAAACATTT
* *
157124 GTGTTGCGAAAATAAAA-GC
1 GTGTTGCGAAATTAAAATTC
157143 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
157162 GTGTTGCG-AATCCAAAAATT-
1 GTGTTGCGAAAT--TAAAATTC
* * *
157182 GAGTTGTGAAATCAAAATTC
1 GTGTTGCGAAATTAAAATTC
* *
157202 GTGTTGCG-ATTTAGAAAATC
1 GTGTTGCGAAATTA-AAATTC
*
157222 TTGTTGCGAAA
1 GTGTTGCGAAA
157233 AGGAAACTTG
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
18 15 0.22
19 13 0.19
20 31 0.45
21 10 0.14
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:157293 original size:21 final size:20
Alignment explanation
Indices: 157256--157457 Score: 80
Period size: 20 Copynumber: 10.0 Consensus size: 20
157246 TATGAAAAAT
*
157256 AAATTCGCGTTGTGAATTTG
1 AAATTCGCGTTGCGAATTTG
*
157276 AAATTCCGTGTTGCGAATTTG
1 AAATT-CGCGTTGCGAATTTG
* * * *
157297 -ACTTATGTGTTGCG-ATTTAC
1 AAATT-CGCGTTGCGAATTT-G
*
157317 AAATTCGCATTGCG-ATTT-
1 AAATTCGCGTTGCGAATTTG
157335 ACATATTCGCGTTGCG-ATTT-
1 A-A-ATTCGCGTTGCGAATTTG
*
157355 AACTATTCACGTTGCG-ATTT-
1 AA--ATTCGCGTTGCGAATTTG
* *
157375 AACTATCCGCGCTGCGAATTTGG
1 AA--ATTCGCGTTGCGAATTT-G
* **
157398 AAATTCGCATTGC-AATTAC
1 AAATTCGCGTTGCGAATTTG
**
157417 CTATTCGCGTTGCGAATTTAG
1 AAATTCGCGTTGCGAATTT-G
* * *
157438 AAAATCGTGTTGCGATTTTG
1 AAATTCGCGTTGCGAATTTG
157458 GAACCTGTGT
Statistics
Matches: 141, Mismatches: 30, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.01
19 16 0.11
20 80 0.57
21 42 0.30
23 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:157349 original size:40 final size:41
Alignment explanation
Indices: 157258--157455 Score: 142
Period size: 40 Copynumber: 4.9 Consensus size: 41
157248 TGAAAAATAA
* ** *
157258 ATTCGCGTTGTGAATTT-GAAATTCCGTGTTGCGAATTTGACTT
1 ATTCGCGTTGCGAATTTAGAAATT-CGCATTGCG-ATTT-ACAT
* *
157301 A-T-GTGTTGCG-ATTTACAAATTCGCATTGCGATTTACAT
1 ATTCGCGTTGCGAATTTAGAAATTCGCATTGCGATTTACAT
* * *
157339 ATTCGCGTTGCG-ATTTA-ACTATTCACGTTGCGATTTA-ACT
1 ATTCGCGTTGCGAATTTAGA-AATTCGCATTGCGATTTACA-T
* * * * *
157379 ATCCGCGCTGCGAATTTGGAAATTCGCATTGC-AATTACCT
1 ATTCGCGTTGCGAATTTAGAAATTCGCATTGCGATTTACAT
* **
157419 ATTCGCGTTGCGAATTTAGAAAATCGTGTTGCGATTT
1 ATTCGCGTTGCGAATTTAGAAATTCGCATTGCGATTT
157456 TGGAACCTGT
Statistics
Matches: 121, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
38 4 0.03
39 7 0.06
40 80 0.66
41 27 0.22
42 2 0.02
43 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (41 bp):
ATTCGCGTTGCGAATTTAGAAATTCGCATTGCGATTTACAT
Found at i:157361 original size:20 final size:20
Alignment explanation
Indices: 157305--157436 Score: 103
Period size: 20 Copynumber: 6.5 Consensus size: 20
157295 TGACTTATGT
*
157305 GTTGCGATTT-ACAAATTCGC
1 GTTGCGATTTAAC-TATTCGC
*
157325 ATTGCGATTT-ACATATTCGC
1 GTTGCGATTTAAC-TATTCGC
*
157345 GTTGCGATTTAACTATTCAC
1 GTTGCGATTTAACTATTCGC
*
157365 GTTGCGATTTAACTATCCGC
1 GTTGCGATTTAACTATTCGC
*
157385 GCTGCGAATTTGGAA--ATTCGC
1 GTTGCG-ATTT--AACTATTCGC
* * *
157406 ATTGC-AATTACCTATTCGC
1 GTTGCGATTTAACTATTCGC
157425 GTTGCGAATTTA
1 GTTGCG-ATTTA
157437 GAAAATCGTG
Statistics
Matches: 90, Mismatches: 14, Indels: 15
0.76 0.12 0.13
Matches are distributed among these distances:
17 1 0.01
19 13 0.14
20 56 0.62
21 18 0.20
23 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTAACTATTCGC
Found at i:158039 original size:21 final size:22
Alignment explanation
Indices: 158013--158053 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
158003 CTAGGATAGG
158013 GAGTATCAATAC-TCCTTTAAT
1 GAGTATCAATACTTCCTTTAAT
*
158034 GAGTATCGATACTTCCTTTA
1 GAGTATCAATACTTCCTTTA
158054 TATATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (22 bp):
GAGTATCAATACTTCCTTTAAT
Found at i:161211 original size:39 final size:39
Alignment explanation
Indices: 161167--161297 Score: 219
Period size: 39 Copynumber: 3.4 Consensus size: 39
161157 TTGAATCTCT
*
161167 CTTACATGTCATATCCTTTTGAAGCTTGATTGAATTTGC
1 CTTACATGCCATATCCTTTTGAAGCTTGATTGAATTTGC
161206 CTTACATGCCATATCCTTTTGAAGCTTGATTGAATTTGC
1 CTTACATGCCATATCCTTTTGAAGCTTGATTGAATTTGC
*
161245 CTTACATGCCATATCCTTTTGAAGCTTGATTGAATCT-C
1 CTTACATGCCATATCCTTTTGAAGCTTGATTGAATTTGC
*
161283 TCTTACATGTCATAT
1 -CTTACATGCCATAT
161298 TGTTGACGGT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
38 1 0.01
39 87 0.99
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.42
Consensus pattern (39 bp):
CTTACATGCCATATCCTTTTGAAGCTTGATTGAATTTGC
Found at i:161744 original size:35 final size:35
Alignment explanation
Indices: 161698--161803 Score: 95
Period size: 44 Copynumber: 2.8 Consensus size: 35
161688 AATGTGTTTT
* *
161698 GGAAATGCTCCTCCTCTAGCTACATTGCTTGATTA
1 GGAAATACTCCTCCTCTAGCTACATTGCTTGACTA
*
161733 GGAAATACTCCTCCTACCGCTCCTATTGCTACATTGTTTGACTA
1 GGAAATA---CTCCT--C-CT-CTA--GCTACATTGCTTGACTA
*
161777 GAAAATACTCCTCCTCTAGCTACATTG
1 GGAAATACTCCTCCTCTAGCTACATTG
161804 AGTGACTGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
35 15 0.26
37 3 0.05
38 7 0.12
39 1 0.02
40 1 0.02
41 7 0.12
42 3 0.05
44 21 0.36
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (35 bp):
GGAAATACTCCTCCTCTAGCTACATTGCTTGACTA
Found at i:169715 original size:20 final size:20
Alignment explanation
Indices: 169687--169734 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
169677 AGGGTTCATA
169687 GGTCATTCGGGACATACAGT
1 GGTCATTCGGGACATACAGT
*
169707 GGTCCTTCGGGACATACAGT
1 GGTCATTCGGGACATACAGT
169727 GGTCATTC
1 GGTCATTC
169735 AGGAAATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (20 bp):
GGTCATTCGGGACATACAGT
Found at i:169751 original size:23 final size:24
Alignment explanation
Indices: 169724--169772 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
169714 CGGGACATAC
*
169724 AGTGGTCATTCAGG-AAATTTCAT
1 AGTGGTCATTCAGGAAAAATTCAT
* *
169747 AGTGGTCCTTCGGGAAAAATTCAT
1 AGTGGTCATTCAGGAAAAATTCAT
169771 AG
1 AG
169773 CCCCTAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (24 bp):
AGTGGTCATTCAGGAAAAATTCAT
Found at i:170880 original size:35 final size:36
Alignment explanation
Indices: 170805--170885 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
170795 CCTTCTTGTT
170805 GGTATCGATAACTATGGTATCGATACTACCCCTTTC
1 GGTATCGATAACTATGGTATCGATACTACCCCTTTC
*
170841 GGTATCGATAGCTATGGTATCGATACTA-CCCTTTC
1 GGTATCGATAACTATGGTATCGATACTACCCCTTTC
170876 GGTATCGATA
1 GGTATCGATA
170886 CCTTATGAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 17 0.39
36 27 0.61
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (36 bp):
GGTATCGATAACTATGGTATCGATACTACCCCTTTC
Found at i:172097 original size:31 final size:32
Alignment explanation
Indices: 172060--172120 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
172050 CGATTTTAAA
172060 AAAATTGAAAGTTTAAGTAC-TAAAACATACT
1 AAAATTGAAAGTTTAAGTACTTAAAACATACT
* * *
172091 AAAATTGATAGTTTAGGTACTTAATACATA
1 AAAATTGAAAGTTTAAGTACTTAAAACATA
172121 GTTTACCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (32 bp):
AAAATTGAAAGTTTAAGTACTTAAAACATACT
Found at i:174464 original size:16 final size:16
Alignment explanation
Indices: 174443--174474 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
174433 TTACGGAAAT
174443 AATCATTAGCTATTTG
1 AATCATTAGCTATTTG
*
174459 AATCATTAGCTGTTTG
1 AATCATTAGCTATTTG
174475 TTGCTGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (16 bp):
AATCATTAGCTATTTG
Found at i:176301 original size:68 final size:67
Alignment explanation
Indices: 176188--176316 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 67
176178 CAGATTAAAC
*
176188 GGATATGATTTCAACTAGCTATGCTAACAGAATCATATGCTTATTTCTCTT-ACAATGCTTACAG
1 GGATATGATTGCAACTAGCTATGCTAACAGAATCA-ATGCTTATTTCTCTTGA-AATGCTTACAG
176252 AAAT
64 AAAT
* *
176256 GGATATGATTGCACCTAGTTATGCTAACAGAATC-ATGCATATATTTCTCTTGAAATGCTTA
1 GGATATGATTGCAACTAGCTATGCTAACAGAATCAATGC-T-TATTTCTCTTGAAATGCTTA
176317 AATTTGTTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
66 4 0.07
67 1 0.02
68 49 0.89
69 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (67 bp):
GGATATGATTGCAACTAGCTATGCTAACAGAATCAATGCTTATTTCTCTTGAAATGCTTACAGAA
AT
Found at i:182000 original size:16 final size:16
Alignment explanation
Indices: 181975--182071 Score: 185
Period size: 16 Copynumber: 6.1 Consensus size: 16
181965 CCAACGTTTA
181975 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
181991 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
182007 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
182023 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
182039 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
182055 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
182071 T
1 T
182072 TTATTTATTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 79 1.00
ACGTcount: A:0.07, C:0.12, G:0.24, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:182010 original size:6 final size:6
Alignment explanation
Indices: 182001--182061 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
181991 TGTTCATTTA
* *
182001 TGTTCG TGTTCG T-TT-A TGTTCG TGTTCG T-TT-A TGTTCG TGTTCG
1 TGTTCG TGTTCG TGTTCG TGTTCG TGTTCG TGTTCG TGTTCG TGTTCG
*
182045 T-TT-A TGTTCG TGTTCG T
1 TGTTCG TGTTCG TGTTCG T
182062 TTATGTTCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
4 3 0.07
5 12 0.28
6 28 0.65
ACGTcount: A:0.05, C:0.13, G:0.26, T:0.56
Consensus pattern (6 bp):
TGTTCG
Found at i:182166 original size:16 final size:16
Alignment explanation
Indices: 182141--182173 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
182131 AAAAAAATTT
182141 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
182157 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
182173 T
1 T
182174 TTATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:183216 original size:2 final size:2
Alignment explanation
Indices: 183209--183242 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
183199 TCTTTTTCTA
183209 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
183243 GCACATGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:184446 original size:18 final size:18
Alignment explanation
Indices: 184423--184495 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
184413 GCACTGAATT
184423 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
184441 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
184460 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
184479 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
184496 GATAATCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 32 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:184470 original size:38 final size:38
Alignment explanation
Indices: 184422--184498 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
184412 GGCACTGAAT
*
184422 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
*
184460 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
184498 T
1 T
184499 AATCCCTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
Done.