Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 362 of 378
Found at i:108481813 original size:40 final size:37
Alignment explanation
Indices: 108481750--108481881 Score: 164
Period size: 35 Copynumber: 3.6 Consensus size: 37
108481740 GGCAAAGTGT
*
108481750 GAAATGTAGGTATGGTA--TCATCCATACTGAGTTGT
1 GAAATGTAGGTATGGTATTTCATCCATACTGAGTTGA
*
108481785 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC--ATCCATACTGAGTTGA
* *
108481825 GAAATGTAGGTATGGCATTTC--CCATACCGAGTTGA
1 GAAATGTAGGTATGGTATTTCATCCATACTGAGTTGA
*
108481860 AAAATGTAGGTATGGTATTTCA
1 GAAATGTAGGTATGGTATTTCA
108481882 ATGAGGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
35 48 0.57
38 2 0.02
39 2 0.02
40 32 0.38
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (37 bp):
GAAATGTAGGTATGGTATTTCATCCATACTGAGTTGA
Found at i:108489230 original size:35 final size:35
Alignment explanation
Indices: 108489203--108489368 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
108489193 CATGGCAAAG
*
108489203 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
108489238 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
108489273 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
108489313 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
108489348 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
108489369 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:108489322 original size:75 final size:75
Alignment explanation
Indices: 108489203--108489373 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
108489193 CATGGCAAAG
** *
108489203 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
108489262 CCATACTGAGC
65 CCATACCGAGC
108489273 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
108489338 CATACCGAGT
66 CATACCGAGC
**
108489348 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
108489374 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:108491025 original size:17 final size:18
Alignment explanation
Indices: 108491005--108491042 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
108490995 TTAGAATCGG
*
108491005 ATTG-GAAAAATAATTTA
1 ATTGAGAAAAATAATTAA
*
108491022 ATTGAGAGAAATAATTAA
1 ATTGAGAAAAATAATTAA
108491040 ATT
1 ATT
108491043 AAATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (18 bp):
ATTGAGAAAAATAATTAA
Found at i:108491954 original size:61 final size:61
Alignment explanation
Indices: 108491845--108491966 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
108491835 AGAATAAAAA
* * * *
108491845 TATATGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGGGGGGTGGAAACTTTATAGTTT
1 TATAAGGGGATAAGAGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
108491906 TATAAGGGGATAAGAGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
1 TATAAGGGGATAAGAGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
108491967 AGAGCCACAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (61 bp):
TATAAGGGGATAAGAGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
Found at i:108496209 original size:17 final size:16
Alignment explanation
Indices: 108496189--108496223 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
108496179 ATTTTTGTTT
108496189 TTTTAGATTTTTTAAAA
1 TTTTAGA-TTTTTAAAA
*
108496206 TTTTATATTTTTAAAA
1 TTTTAGATTTTTAAAA
108496222 TT
1 TT
108496224 AGGATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTAGATTTTTAAAA
Found at i:108500219 original size:17 final size:18
Alignment explanation
Indices: 108500197--108500232 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
108500187 TCTTTATATA
108500197 TTATATTAATTTTT-ACT
1 TTATATTAATTTTTCACT
108500214 TTATATTAATTTTTCACT
1 TTATATTAATTTTTCACT
108500232 T
1 T
108500233 CTTTCTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATTAATTTTTCACT
Found at i:108500612 original size:11 final size:10
Alignment explanation
Indices: 108500594--108500631 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
108500584 GTAAAACATT
108500594 AAAAAGAAAG
1 AAAAAGAAAG
108500604 AAGAAAGAAA-
1 AA-AAAGAAAG
108500614 AAAAA-AAAG
1 AAAAAGAAAG
108500623 AAAAAGAAA
1 AAAAAGAAA
108500632 TAGTGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 8 0.32
10 7 0.28
11 7 0.28
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:108500983 original size:31 final size:31
Alignment explanation
Indices: 108500940--108501010 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
108500930 AAGGAAATAA
* * *
108500940 AAGTTTAAGCCCCAATGCGGGAACAATTACC
1 AAGTTTAGGCCCCAATACGAGAACAATTACC
* * *
108500971 TATTTTAGGCCCCAATATGAGAACAATTACC
1 AAGTTTAGGCCCCAATACGAGAACAATTACC
108501002 AAGTTTAGG
1 AAGTTTAGG
108501011 GATAATTTGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGTTTAGGCCCCAATACGAGAACAATTACC
Found at i:108504749 original size:2 final size:2
Alignment explanation
Indices: 108504742--108504766 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
108504732 GCTCTTGCAG
108504742 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
108504767 TAGAAACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:108505002 original size:6 final size:6
Alignment explanation
Indices: 108504991--108505031 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
108504981 ATCCGAAGAG
* * *
108504991 GAGGAA GAGGAA GAGGAA GAGGAC GAGGAT GAGGAT GAGGA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
108505032 GACTAAAGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.41, C:0.02, G:0.51, T:0.05
Consensus pattern (6 bp):
GAGGAA
Found at i:108505876 original size:2 final size:2
Alignment explanation
Indices: 108505869--108505903 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
108505859 AGAAATAATC
108505869 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
108505904 ACTCACATAC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:108509237 original size:10 final size:9
Alignment explanation
Indices: 108509138--108509286 Score: 88
Period size: 9 Copynumber: 15.8 Consensus size: 9
108509128 TATTTTTATC
108509138 ATAAAAATT
1 ATAAAAATT
108509147 ATAAAAATAT
1 ATAAAAAT-T
108509157 CATAAAAA--
1 -ATAAAAATT
*
108509165 ATAAATATTT
1 ATAAA-AATT
*
108509175 ACATAAAATT
1 ATA-AAAATT
*
108509185 ATAGAAATT
1 ATAAAAATT
108509194 ATAGAAAAATT
1 AT--AAAAATT
* ** *
108509205 AGAGTACTT
1 ATAAAAATT
108509214 ATAAAAA-T
1 ATAAAAATT
108509222 ATAAAAATT
1 ATAAAAATT
*
108509231 CATAAAAGGTT
1 -ATAAAA-ATT
*
108509242 ATAAATATT
1 ATAAAAATT
*
108509251 ATAAAATTTT
1 ATAAAA-ATT
108509261 ATAAAAATT
1 ATAAAAATT
*
108509270 CTAATAAATT
1 ATAA-AAATT
108509280 ATAAAAA
1 ATAAAAA
108509287 AAATAAAACA
Statistics
Matches: 105, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
7 5 0.05
8 9 0.09
9 38 0.36
10 35 0.33
11 18 0.17
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:108509244 original size:28 final size:29
Alignment explanation
Indices: 108509212--108509266 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
108509202 ATTAGAGTAC
108509212 TTATAAA-AATATAAAAATTCATAAAAGG
1 TTATAAATAATATAAAAATTCATAAAAGG
* * *
108509240 TTATAAATATTATAAAATTTTATAAAA
1 TTATAAATAATATAAAAATTCATAAAA
108509267 ATTCTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (29 bp):
TTATAAATAATATAAAAATTCATAAAAGG
Found at i:108509262 original size:19 final size:20
Alignment explanation
Indices: 108509221--108509270 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
108509211 CTTATAAAAA
108509221 TATAAAAATTCATAAAAGGT
1 TATAAAAATTCATAAAAGGT
* **
108509241 TATAAATATT-ATAAAATTT
1 TATAAAAATTCATAAAAGGT
108509260 TATAAAAATTC
1 TATAAAAATTC
108509271 TAATAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TATAAAAATTCATAAAAGGT
Found at i:108511267 original size:22 final size:21
Alignment explanation
Indices: 108511227--108511274 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
108511217 TCATAATAGT
108511227 TCAGATAAGATGCAAAACAAA
1 TCAGATAAGATGCAAAACAAA
* * *
108511248 TCAGATACATATGCAGAACAGA
1 TCAGATA-AGATGCAAAACAAA
108511270 TCAGA
1 TCAGA
108511275 ATCAGATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (21 bp):
TCAGATAAGATGCAAAACAAA
Found at i:108512638 original size:10 final size:10
Alignment explanation
Indices: 108512623--108512655 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
108512613 AGGAAAAAAT
108512623 GAAGAAGAAG
1 GAAGAAGAAG
108512633 GAAGAAGAAG
1 GAAGAAGAAG
*
108512643 GAAGAAGAGG
1 GAAGAAGAAG
108512653 GAA
1 GAA
108512656 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:108513143 original size:20 final size:21
Alignment explanation
Indices: 108513120--108513168 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
108513110 TCGTGTCAGT
*
108513120 AAAAAAAA-GTTTGAAAAAG-A
1 AAAAAAAAGGTTAG-AAAAGCA
*
108513140 AAAACAAAGGTTAGAAAAGCA
1 AAAAAAAAGGTTAGAAAAGCA
108513161 AAAAAAAA
1 AAAAAAAA
108513169 AGGGGAGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.71, C:0.04, G:0.14, T:0.10
Consensus pattern (21 bp):
AAAAAAAAGGTTAGAAAAGCA
Found at i:108515353 original size:116 final size:116
Alignment explanation
Indices: 108515144--108515373 Score: 320
Period size: 116 Copynumber: 2.0 Consensus size: 116
108515134 AGCGTTATCC
* *
108515144 TTTTAGCACCCTGATTGATGTCTGCTTGATTTTATTTGATGAAGGTTGGGTGATTGAGATTAAAC
1 TTTTAGCACCCTGATTGATGTCTGCTTGACTTTATTTGATGAAGGTTGAGTGATTGAGATTAAAC
** * *
108515209 ATATTATTTGTAAGGGCAATAAGCGTACAAATCAC-TAGAATTCTTTAACAG
66 ATATTATTTCCAAGGACAATAAACGTACAAATCACTTA-AATTCTTTAACAG
* * * *
108515260 TTTTAGCACCCTGATTGATGAT-TGGTTGACTTTGTTTGATGAGGGTTGAGTGATTGAGATTAGA
1 TTTTAGCACCCTGATTGATG-TCTGCTTGACTTTATTTGATGAAGGTTGAGTGATTGAGATTAAA
* *
108515324 CATATTCTTTCCAAGGACAATAAATGTACAAATCACTTAAATTCTTTAAC
65 CATATTATTTCCAAGGACAATAAACGTACAAATCACTTAAATTCTTTAAC
108515374 GTAAGGATCC
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
116 97 0.97
117 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (116 bp):
TTTTAGCACCCTGATTGATGTCTGCTTGACTTTATTTGATGAAGGTTGAGTGATTGAGATTAAAC
ATATTATTTCCAAGGACAATAAACGTACAAATCACTTAAATTCTTTAACAG
Found at i:108518175 original size:18 final size:18
Alignment explanation
Indices: 108518152--108518186 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
108518142 GTTTCCATAC
108518152 ATTTTTCATA-ATTAATTA
1 ATTTTT-ATATATTAATTA
108518170 ATTTTTATATATTAATT
1 ATTTTTATATATTAATT
108518187 GAGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATATATTAATTA
Found at i:108520638 original size:25 final size:23
Alignment explanation
Indices: 108520610--108520666 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
108520600 CTCGGTGCGT
* *
108520610 TCTCTGTTTCTAAGCACGTTAGTGC
1 TCTCTGTTT-T-AGCACCTCAGTGC
*
108520635 TCTCTGTATTAGCACCTCAGTGC
1 TCTCTGTTTTAGCACCTCAGTGC
*
108520658 TCTCCGTTT
1 TCTCTGTTT
108520667 ACTTGTACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 18 0.67
24 1 0.04
25 8 0.30
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (23 bp):
TCTCTGTTTTAGCACCTCAGTGC
Found at i:108526924 original size:12 final size:12
Alignment explanation
Indices: 108526907--108526932 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
108526897 AACGATTTGC
108526907 AAAAAAAAAAGA
1 AAAAAAAAAAGA
108526919 AAAAAAAAAAGA
1 AAAAAAAAAAGA
108526931 AA
1 AA
108526933 GAAATTAGAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:108527406 original size:151 final size:148
Alignment explanation
Indices: 108527200--108527585 Score: 357
Period size: 139 Copynumber: 2.6 Consensus size: 148
108527190 TCATGCTAAT
* * * *
108527200 TGTATATATCATAATCTATTATAAAGTTAGTTACACG-TTCAGGATTTAAGATTGCATATCGTTA
1 TGTATATATTATAATCTATCATAAAGTTAGTTACATGTTTAAGG-TTTAAGATTGCATATCGTTA
*
108527264 ATATAAAAATGTACATTATAATATCATTCATAATGGTACATAA-GATTACATATCATTAATAATC
65 ATATAAAAATGTACATTATAATAT-A-T-ATAATGGTACATAAGGA-TACATATCATCAATAATC
*
108527328 TACATTGATTACGTAATGATAAC
126 TACATTGATTACATAATGATAAC
* *
108527351 TGTATATATTATAATCTATCATAAAGTTAGTTACATGTTTTAGGTTTAAGCTTGC--A--G----
1 TGTATATATTATAATCTATCATAAAGTTAGTTACATGTTTAAGGTTTAAGATTGCATATCGTTAA
* * * * * *
108527408 TATAAAAATGTACATTTTAATA-ATATAGTTGTATATAAGGATACATATCATCAATTATCTACTT
66 TATAAAAATGTACATTATAATATATATAATGGTACATAAGGATACATATCATCAATAATCTACAT
* * * *
108527472 TTATTATATAATGTTAAT
131 TGATTACATAATGATAAC
* * * * * * *
108527490 TGTATATATATTATAATGTACCATAAAATTAGTTTCATATTTAAGGTTT-AGGTTGCATATCATT
1 TG--TATATATTATAATCTATCATAAAGTTAGTTACATGTTTAAGGTTTAAGATTGCATATCGTT
* **
108527554 AATAAAAGAAATACACATTATAATAT-TATAAT
64 AATATAA-AAATGTACATTATAATATATATAAT
108527586 TGTATAATAA
Statistics
Matches: 191, Mismatches: 30, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
139 46 0.24
140 9 0.05
141 40 0.21
142 1 0.01
143 21 0.11
147 1 0.01
148 4 0.02
149 20 0.10
151 44 0.23
152 5 0.03
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (148 bp):
TGTATATATTATAATCTATCATAAAGTTAGTTACATGTTTAAGGTTTAAGATTGCATATCGTTAA
TATAAAAATGTACATTATAATATATATAATGGTACATAAGGATACATATCATCAATAATCTACAT
TGATTACATAATGATAAC
Found at i:108550428 original size:64 final size:64
Alignment explanation
Indices: 108550349--108550475 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
108550339 AGGTTTTAAC
108550349 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
1 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
*
108550413 TTGACCATAATCTGTTTTATGTTCTCTCATGTAGGTTTGAAGTCCATCTCGAGATGTTCAAAA
1 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAA
108550476 CTATCTATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (64 bp):
TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
Found at i:108551539 original size:16 final size:16
Alignment explanation
Indices: 108551518--108551549 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
108551508 CATCTAAAAG
108551518 GAAACCATGATTTTTC
1 GAAACCATGATTTTTC
108551534 GAAACCATGATTTTTC
1 GAAACCATGATTTTTC
108551550 AGGGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
GAAACCATGATTTTTC
Found at i:108556860 original size:21 final size:21
Alignment explanation
Indices: 108556823--108556863 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
108556813 AAAAAATTAA
*
108556823 AAATATATTTTTATAATTTTT
1 AAATATATTTTAATAATTTTT
108556844 AAATA-ATTTTAATTAATTTT
1 AAATATATTTTAA-TAATTTT
108556864 AACTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATATATTTTAATAATTTTT
Found at i:108557890 original size:25 final size:25
Alignment explanation
Indices: 108557844--108557913 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
108557834 GGTTTATTTT
108557844 ATTTAATATTAATA-TAATTATATTC
1 ATTTAATATTAATATTAA-TATATTC
*
108557869 ATTTAATATTAATATTAATATA-AC
1 ATTTAATATTAATATTAATATATTC
*
108557893 ATTTAA-ATT--TATTATTATATT
1 ATTTAATATTAATATTAATATATT
108557914 TTTATGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.22
23 3 0.08
24 7 0.17
25 18 0.45
26 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTAATATTAATATTAATATATTC
Found at i:108558015 original size:27 final size:25
Alignment explanation
Indices: 108557900--108558021 Score: 67
Period size: 25 Copynumber: 4.8 Consensus size: 25
108557890 AACATTTAAA
*
108557900 TTTATTATTATAT-TTTTATGAAAAT
1 TTTATT-TTATATATTTTTTGAAAAT
*
108557925 ATTTATTTT-TATATATTTT-AAAAT
1 -TTTATTTTATATATTTTTTGAAAAT
* *
108557949 TTTATATATTAT-TATTCCTTGTCAACAAT
1 TTTAT-T-TTATATATT--TTTTGAA-AAT
**
108557978 TTT-TTAAATATATTTTTTGAAAAT
1 TTTATTTTATATATTTTTTGAAAAT
108558002 ATTTATATTTATAT-TTTTTT
1 -TTTAT-TTTATATATTTTTT
108558022 ATATATTTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
23 5 0.07
24 12 0.16
25 19 0.26
26 16 0.22
27 13 0.18
28 3 0.04
29 6 0.08
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTATTTTATATATTTTTTGAAAAT
Found at i:108559171 original size:15 final size:15
Alignment explanation
Indices: 108559151--108559196 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
108559141 ATAAAATAAT
108559151 AACATAAGTGATTAA
1 AACATAAGTGATTAA
*
108559166 AACATAA-T-ATTTTA
1 AACATAAGTGA-TTAA
*
108559180 AACATAAGTGACTAA
1 AACATAAGTGATTAA
108559195 AA
1 AA
108559197 TGTTACTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 1 0.04
14 11 0.44
15 12 0.48
16 1 0.04
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (15 bp):
AACATAAGTGATTAA
Found at i:108563813 original size:22 final size:22
Alignment explanation
Indices: 108563778--108563819 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
108563768 TTAATTTTAT
*
108563778 TTTTATACTGTAAAATTAAATA
1 TTTTATACTGTAAAAATAAATA
* *
108563800 TTTTATATTTTAAAAATAAA
1 TTTTATACTGTAAAAATAAA
108563820 ATAATTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTATACTGTAAAAATAAATA
Found at i:108564818 original size:18 final size:18
Alignment explanation
Indices: 108564786--108564827 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
108564776 TAAAATTTCA
108564786 TAAAAATAATAAAAA-TT
1 TAAAAATAATAAAAACTT
*
108564803 TAAAATATATTAAAAACTT
1 TAAAA-ATAATAAAAACTT
108564822 TAAAAA
1 TAAAAA
108564828 CCGGTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 10 0.45
19 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATAATAAAAACTT
Found at i:108564882 original size:21 final size:20
Alignment explanation
Indices: 108564852--108564891 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
108564842 TCAATTGTTG
*
108564852 GATTTATTTTTTTTGGTTTCT
1 GATTTATTTTATTT-GTTTCT
*
108564873 GATTTTTTTTATTTGTTTC
1 GATTTATTTTATTTGTTTC
108564892 GAGTGATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.72
Consensus pattern (20 bp):
GATTTATTTTATTTGTTTCT
Found at i:108564890 original size:20 final size:21
Alignment explanation
Indices: 108564852--108564891 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
108564842 TCAATTGTTG
108564852 GATTTATTTTTTTTGGTTTCT
1 GATTTATTTTTTTTGGTTTCT
108564873 GATTT-TTTTTATTT-GTTTC
1 GATTTATTTTT-TTTGGTTTC
108564892 GAGTGATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.72
Consensus pattern (21 bp):
GATTTATTTTTTTTGGTTTCT
Found at i:108578326 original size:53 final size:54
Alignment explanation
Indices: 108578244--108578345 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 54
108578234 TTTATAAAAA
*
108578244 TTTTTGAGTAATCCCAAAATCTTTCAATATGTTTATAAGCCTTTTCAAAAGATT
1 TTTTTGAGTAATCCCAAAACCTTTCAATATGTTTATAAGCCTTTTCAAAAGATT
* * *
108578298 TTTTTGAGTACT-CCAAGACCTTTGAATATGTTTATAAGCCTTTTCAAA
1 TTTTTGAGTAATCCCAAAACCTTTCAATATGTTTATAAGCCTTTTCAAA
108578346 GCAGGTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 33 0.75
54 11 0.25
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (54 bp):
TTTTTGAGTAATCCCAAAACCTTTCAATATGTTTATAAGCCTTTTCAAAAGATT
Found at i:108579340 original size:13 final size:13
Alignment explanation
Indices: 108579322--108579355 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
108579312 CTTAAACCAA
108579322 AATTTTCAAAAAT
1 AATTTTCAAAAAT
* *
108579335 ACTTTTCAAAATT
1 AATTTTCAAAAAT
108579348 AATTTTCA
1 AATTTTCA
108579356 CAACACTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTTCAAAAAT
Found at i:108582818 original size:27 final size:27
Alignment explanation
Indices: 108582778--108582830 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
108582768 TGTCCACTTC
* *
108582778 TCCTAGATTAGTACTTATAATTTTTTT
1 TCCTAGATTAGTACCTAAAATTTTTTT
*
108582805 TCCTAGATTGGTACCTAAAATTTTTT
1 TCCTAGATTAGTACCTAAAATTTTTT
108582831 CCTGTCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.51
Consensus pattern (27 bp):
TCCTAGATTAGTACCTAAAATTTTTTT
Found at i:108584821 original size:15 final size:17
Alignment explanation
Indices: 108584800--108584840 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
108584790 TAATTATTTA
108584800 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
108584816 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
108584832 AAAATTATA
1 AAAATTATA
108584841 TTTCTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:108584841 original size:26 final size:26
Alignment explanation
Indices: 108584791--108584840 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
108584781 AATTTGATTT
*
108584791 AATTATTTAAAAATTATAAAAATATA
1 AATTATTTAAAAATGATAAAAATATA
*
108584817 AATTA-TT-AAAATGATAAAATTATA
1 AATTATTTAAAAATGATAAAAATATA
108584841 TTTCTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AATTATTTAAAAATGATAAAAATATA
Found at i:108596469 original size:13 final size:13
Alignment explanation
Indices: 108596451--108596480 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
108596441 TTAGTTGAAG
108596451 TGGCCACTACCAT
1 TGGCCACTACCAT
108596464 TGGCCACTACCAT
1 TGGCCACTACCAT
108596477 TGGC
1 TGGC
108596481 ACTTCGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (13 bp):
TGGCCACTACCAT
Found at i:108605619 original size:15 final size:15
Alignment explanation
Indices: 108605599--108605629 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
108605589 ACACCAAATG
108605599 ATATCAATTTACGCC
1 ATATCAATTTACGCC
*
108605614 ATATCAATTTATGCC
1 ATATCAATTTACGCC
108605629 A
1 A
108605630 AAACATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (15 bp):
ATATCAATTTACGCC
Found at i:108613296 original size:20 final size:20
Alignment explanation
Indices: 108613273--108613335 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
108613263 CTTTTTAAAT
*
108613273 AATTACACAAGATATTACCC
1 AATTACACAAAATATTACCC
* * **
108613293 AATTACAAAAAACATTACTA
1 AATTACACAAAATATTACCC
*
108613313 AATTATACAAAATATTACCC
1 AATTACACAAAATATTACCC
108613333 AAT
1 AAT
108613336 AATGAAAAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (20 bp):
AATTACACAAAATATTACCC
Found at i:108613411 original size:48 final size:49
Alignment explanation
Indices: 108613318--108613414 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 49
108613308 TACTAAATTA
* * * *
108613318 TACAAAATATTACCCAATAATGAAAAATTATTACAATATTTGTAATGTT
1 TACAAAACATTAACCAATAATGAAAAATTATTACAATACTCGTAATGTT
* *
108613367 TACAAAACATTAACCAATTAT-ACAAATTATTACAACT-CTCGTAATGTT
1 TACAAAACATTAACCAATAATGAAAAATTATTACAA-TACTCGTAATGTT
108613415 GTGCAACAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 22 0.54
49 19 0.46
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.35
Consensus pattern (49 bp):
TACAAAACATTAACCAATAATGAAAAATTATTACAATACTCGTAATGTT
Found at i:108618077 original size:67 final size:67
Alignment explanation
Indices: 108617969--108618105 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
108617959 TATCAACGGA
108617969 AGTGGAGAAGGCAGGGGATAGTGAAGAAGAAGATAATCTAATGATATGTCTGGAGTCCCTCAAGT
1 AGTGGAGAAGGCAGGGGATAGTGAAGAAGAAGATAATCTAATGATATGTCTGGAGTCCCTCAAGT
108618034 AG
66 AG
108618036 AGTGGAGAAGGCAGGGGATAGTGAAGAAGAAGATAATCTAATGATATGTCTGGAGTCCCTCAAGT
1 AGTGGAGAAGGCAGGGGATAGTGAAGAAGAAGATAATCTAATGATATGTCTGGAGTCCCTCAAGT
108618101 AG
66 AG
108618103 AGT
1 AGT
108618106 ATCTGAGGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.36, C:0.10, G:0.33, T:0.21
Consensus pattern (67 bp):
AGTGGAGAAGGCAGGGGATAGTGAAGAAGAAGATAATCTAATGATATGTCTGGAGTCCCTCAAGT
AG
Found at i:108624258 original size:31 final size:31
Alignment explanation
Indices: 108624200--108624258 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
108624190 GTTGTAATTA
* * *
108624200 TACATATGAAACTTTGATTACGGTTTAAATG
1 TACACATGAAACTTTAATTACGATTTAAATG
**
108624231 TACACATGAAACTTTAATTTTGATTTAA
1 TACACATGAAACTTTAATTACGATTTAA
108624259 TCATATACGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (31 bp):
TACACATGAAACTTTAATTACGATTTAAATG
Found at i:108632326 original size:19 final size:20
Alignment explanation
Indices: 108632294--108632336 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
108632284 GACATGTAGC
108632294 AAAA-AAATATAAATAAATA
1 AAAATAAATATAAATAAATA
**
108632313 AAAATAAATA-AAATTTATA
1 AAAATAAATATAAATAAATA
108632332 AAAAT
1 AAAAT
108632337 GATTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAAATATAAATAAATA
Found at i:108632335 original size:10 final size:10
Alignment explanation
Indices: 108632322--108632409 Score: 69
Period size: 10 Copynumber: 9.3 Consensus size: 10
108632312 AAAAATAAAT
108632322 AAAATTTATA
1 AAAATTTATA
* *
108632332 AAAA-TGATT
1 AAAATTTATA
* *
108632341 AAATTTTTTA
1 AAAATTTATA
*
108632351 AAAAATTA-A
1 AAAATTTATA
108632360 AAAA--TATA
1 AAAATTTATA
* *
108632368 AAAAATTGTA
1 AAAATTTATA
*
108632378 AAATTTTATA
1 AAAATTTATA
108632388 AAAA-TTATA
1 AAAATTTATA
108632397 AAAATTTATA
1 AAAATTTATA
108632407 AAA
1 AAA
108632410 TGCATCAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 20 0.34
10 32 0.54
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAATTTATA
Found at i:108632343 original size:19 final size:18
Alignment explanation
Indices: 108632310--108632409 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 18
108632300 ATATAAATAA
*
108632310 ATAAAAATAAATAAAATTT
1 ATAAAAAT-ATTAAAATTT
*
108632329 ATAAAAATGATTAAATTTT
1 ATAAAAAT-ATTAAAATTT
* **
108632348 TTAAAAA-ATTAAAAAAT
1 ATAAAAATATTAAAATTT
108632365 ATAAAAA-ATTGTAAAATTTT
1 ATAAAAATA-T-TAAAA-TTT
*
108632385 ATAAAAATTATAAAAATTT
1 ATAAAAA-TATTAAAATTT
108632404 ATAAAA
1 ATAAAA
108632410 TGCATCAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
17 14 0.22
18 1 0.02
19 36 0.55
20 12 0.18
21 1 0.02
22 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAAATATTAAAATTT
Found at i:108635074 original size:42 final size:43
Alignment explanation
Indices: 108635010--108635101 Score: 96
Period size: 42 Copynumber: 2.1 Consensus size: 43
108635000 GCATTTATCT
* * * *
108635010 AAATATTTAACTAGACAGTTAAA-TATAATTAATTATAATTAA
1 AAATATTTAACTAGAAAATTAAAGTATAACTAACTATAATTAA
* * * *
108635052 AAATATTTAATTCGAAAATTAAAGTTTAACTAACTGTAATTAA
1 AAATATTTAACTAGAAAATTAAAGTATAACTAACTATAATTAA
108635095 AATATAT
1 AA-ATAT
108635102 ATGAAGGAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 19 0.47
43 17 0.43
44 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (43 bp):
AAATATTTAACTAGAAAATTAAAGTATAACTAACTATAATTAA
Found at i:108643807 original size:28 final size:28
Alignment explanation
Indices: 108643767--108643823 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
108643757 AGAGACGAAG
108643767 TGCAATCACAGATTCATACAATTCTTTT
1 TGCAATCACAGATTCATACAATTCTTTT
108643795 TGCAATCACAGATTCATACAATTCTTTT
1 TGCAATCACAGATTCATACAATTCTTTT
108643823 T
1 T
108643824 CCAAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (28 bp):
TGCAATCACAGATTCATACAATTCTTTT
Found at i:108644017 original size:16 final size:16
Alignment explanation
Indices: 108643996--108644028 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
108643986 CAATCTTCAA
108643996 ATGGGTAAATTACAGC
1 ATGGGTAAATTACAGC
*
108644012 ATGGGTTAATTACAGC
1 ATGGGTAAATTACAGC
108644028 A
1 A
108644029 AATGTCCTCA
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:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (16 bp):
ATGGGTAAATTACAGC
Found at i:108647885 original size:15 final size:15
Alignment explanation
Indices: 108647865--108647894 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
108647855 AACTTCTGTA
108647865 CATTATTTCACATAT
1 CATTATTTCACATAT
*
108647880 CATTATTTCAGATAT
1 CATTATTTCACATAT
108647895 TTCTCTTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTATTTCACATAT
Found at i:108655002 original size:17 final size:17
Alignment explanation
Indices: 108654982--108655015 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
108654972 ACAATATAAC
108654982 TTCTAATATCATGATTT
1 TTCTAATATCATGATTT
*
108654999 TTCTAATATCGTGATTT
1 TTCTAATATCATGATTT
108655016 CTATAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCTAATATCATGATTT
Found at i:108655022 original size:17 final size:17
Alignment explanation
Indices: 108654985--108655023 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
108654975 ATATAACTTC
* *
108654985 TAATATCATGATTTTTC
1 TAATATCATGATTTCTA
*
108655002 TAATATCGTGATTTCTA
1 TAATATCATGATTTCTA
108655019 TAATA
1 TAATA
108655024 CAGTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (17 bp):
TAATATCATGATTTCTA
Found at i:108657504 original size:80 final size:81
Alignment explanation
Indices: 108657406--108657563 Score: 282
Period size: 80 Copynumber: 2.0 Consensus size: 81
108657396 ATTATATAAT
* *
108657406 TTTTAAAAATAAAAAGTATCATTTGATAATTATGTAATAAATTTAAATTTACTATGAAAATTTTA
1 TTTTAAAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTACTATGAAAATTTTA
108657471 ATGATGTTAACAAATA
66 ATGATGTTAACAAATA
*
108657487 TTTT-AAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTATTATGAAAATTTTA
1 TTTTAAAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTACTATGAAAATTTTA
108657551 ATGATGTTAACAA
66 ATGATGTTAACAA
108657564 TTAAATTAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 70 0.95
81 4 0.05
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (81 bp):
TTTTAAAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTACTATGAAAATTTTA
ATGATGTTAACAAATA
Found at i:108660463 original size:29 final size:29
Alignment explanation
Indices: 108660402--108660463 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
108660392 TAATAATAGC
* * *
108660402 ATAAGTGACTAAAATGTAATATTTCAAAC
1 ATAAGTGACTAAAATGTAATACTTAAAAA
*
108660431 ATAAGTGACTACAATGTAAT-CTTAAATAA
1 ATAAGTGACTAAAATGTAATACTTAAA-AA
108660460 ATAA
1 ATAA
108660464 AAGTGATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (29 bp):
ATAAGTGACTAAAATGTAATACTTAAAAA
Found at i:108661000 original size:3 final size:3
Alignment explanation
Indices: 108660992--108661019 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
108660982 AAAAGCATAT
108660992 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
108661020 AAATTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:108669581 original size:2 final size:2
Alignment explanation
Indices: 108669569--108669601 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
108669559 CTAGTTCTAA
*
108669569 AT AT AT TT 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 A
108669602 ATTAAAACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:108682824 original size:27 final size:25
Alignment explanation
Indices: 108682793--108682854 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
108682783 CAAAACAAAG
*
108682793 TGGACAAAACAAAAATCACGAAAAATA
1 TGGACAAAACAAAAAT-A-AAAAAATA
* * *
108682820 TGGACAAAATAAAACTAAAAAAATG
1 TGGACAAAACAAAAATAAAAAAATA
108682845 TGGACAAAAC
1 TGGACAAAAC
108682855 CACAACGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 15 0.50
26 1 0.03
27 14 0.47
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (25 bp):
TGGACAAAACAAAAATAAAAAAATA
Found at i:108685795 original size:18 final size:18
Alignment explanation
Indices: 108685733--108685796 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
108685723 GCTCTGATGA
108685733 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGCCTTCGG
* * *
108685751 GCTTCCGTTTAGCACTTATGT
1 GCTTCAG-TTAGC-CTT-CGG
108685772 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGCCTTCGG
108685790 GCTTCAG
1 GCTTCAG
108685797 ATCACGATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 14 0.38
19 8 0.22
20 8 0.22
21 7 0.19
ACGTcount: A:0.12, C:0.27, G:0.25, T:0.36
Consensus pattern (18 bp):
GCTTCAGTTAGCCTTCGG
Found at i:108687781 original size:10 final size:10
Alignment explanation
Indices: 108687766--108687793 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
108687756 AAAGCTTAAA
108687766 TATGAAATAG
1 TATGAAATAG
108687776 TATGAAATAG
1 TATGAAATAG
108687786 TATGAAAT
1 TATGAAAT
108687794 CAAGACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (10 bp):
TATGAAATAG
Found at i:108689813 original size:26 final size:26
Alignment explanation
Indices: 108689777--108689912 Score: 245
Period size: 26 Copynumber: 5.2 Consensus size: 26
108689767 TGATACAAAT
108689777 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
108689803 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
108689829 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
108689855 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
108689881 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
108689907 TGATAA
1 TGATAA
108689913 GAATATCATG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:108691796 original size:12 final size:12
Alignment explanation
Indices: 108691779--108691804 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
108691769 AATAAGGGGC
108691779 TAAGGCCCAGTT
1 TAAGGCCCAGTT
108691791 TAAGGCCCAGTT
1 TAAGGCCCAGTT
108691803 TA
1 TA
108691805 TTATAATCTG
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:0.23, T:0.27
Consensus pattern (12 bp):
TAAGGCCCAGTT
Found at i:108695239 original size:39 final size:39
Alignment explanation
Indices: 108695193--108695293 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
108695183 GCTCTAATGA
*
108695193 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTATGT
*
108695232 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTATGT
* * *
108695271 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTTGGGCTTC
108695294 AAATCACGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.13, C:0.25, G:0.24, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTATGT
Found at i:108695275 original size:21 final size:20
Alignment explanation
Indices: 108695200--108695275 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 20
108695190 TGAGCTTCAG
*
108695200 TTAGC-CTTTGGGCTTCCGT
1 TTAGCACTTTGTGCTTCCGT
* *
108695219 TTAACACTTGTGTGCTTCAG-
1 TTAGCACTT-TGTGCTTCCGT
*
108695239 TTAGC-CTTTGGGCTTCCGT
1 TTAGCACTTTGTGCTTCCGT
108695258 TTAGCACTTATGTGCTTC
1 TTAGCACTT-TGTGCTTC
108695276 AGCTAGACTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 8 0.18
19 12 0.27
20 10 0.22
21 15 0.33
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (20 bp):
TTAGCACTTTGTGCTTCCGT
Found at i:108698883 original size:11 final size:11
Alignment explanation
Indices: 108698869--108698907 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
108698859 AAAAAAATAT
108698869 TTTTTTTGTTG
1 TTTTTTTGTTG
* *
108698880 TTTTGTTGTTA
1 TTTTTTTGTTG
*
108698891 TTTTCTTGTTG
1 TTTTTTTGTTG
108698902 TTTTTT
1 TTTTTT
108698908 AACTGTTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.03, C:0.03, G:0.15, T:0.79
Consensus pattern (11 bp):
TTTTTTTGTTG
Found at i:108699117 original size:16 final size:17
Alignment explanation
Indices: 108699084--108699122 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
108699074 GAAACATTTA
*
108699084 TTTTAATGTTTTAGTAT
1 TTTTAATGTATTAGTAT
*
108699101 TTTTGATGTATTA-TAT
1 TTTTAATGTATTAGTAT
108699117 TTTTAA
1 TTTTAA
108699123 AATTTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (17 bp):
TTTTAATGTATTAGTAT
Found at i:108713062 original size:46 final size:47
Alignment explanation
Indices: 108713002--108713229 Score: 331
Period size: 46 Copynumber: 5.0 Consensus size: 47
108712992 TTTGACATGA
* * * * * *
108713002 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*** *
108713048 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
108713094 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
108713140 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTT-ATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
108713186 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
108713230 AGAGCACACT
Statistics
Matches: 168, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
45 7 0.04
46 158 0.94
47 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:108715375 original size:11 final size:11
Alignment explanation
Indices: 108715359--108715410 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
108715349 TATACTAAAT
108715359 AAATAATAATA
1 AAATAATAATA
*
108715370 AAATAAT-ATT
1 AAATAATAATA
* *
108715380 AAATATCTCATA
1 AAATA-ATAATA
*
108715392 AAATATTAATA
1 AAATAATAATA
108715403 AAATAATA
1 AAATAATA
108715411 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:108720366 original size:46 final size:46
Alignment explanation
Indices: 108720299--108720526 Score: 341
Period size: 46 Copynumber: 5.0 Consensus size: 46
108720289 AGTGTGCTCT
108720299 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
108720345 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
108720391 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
108720437 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
108720483 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
108720527 TCATGTCAAA
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 167 0.99
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:108721569 original size:25 final size:25
Alignment explanation
Indices: 108721540--108721588 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
108721530 ATATGAACAA
*
108721540 AATAAAACTATGAAA-CAGTGGACAG
1 AATAAAACTATAAAACCA-TGGACAG
108721565 AATAAAACTATAAAACCATGGACA
1 AATAAAACTATAAAACCATGGACA
108721589 TGTGGATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.16
Consensus pattern (25 bp):
AATAAAACTATAAAACCATGGACAG
Found at i:108722460 original size:20 final size:21
Alignment explanation
Indices: 108722422--108722468 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
108722412 AGGCAATACC
*
108722422 AAAATTTTTAAAGATTTATAG
1 AAAATTTTTAAAGAGTTATAG
* *
108722443 AAAA-TTTTAAATAGTTAT-C
1 AAAATTTTTAAAGAGTTATAG
108722462 AAAATTT
1 AAAATTT
108722469 CTCAGGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 14 0.64
21 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
AAAATTTTTAAAGAGTTATAG
Found at i:108722728 original size:120 final size:120
Alignment explanation
Indices: 108722461--108722725 Score: 257
Period size: 120 Copynumber: 2.2 Consensus size: 120
108722451 AAATAGTTAT
* * * *
108722461 CAAAATTTCTCAGG-TTATATAAAAAACTTC-AAGGCTTTACCAAAATTTCTAAGAATTTATCAA
1 CAAAATTTCTAAGGATT-TAT-CAAAATTTCTAAGGCTTTACCAAAATTTCAAAGAATTTATCAA
* * * * *
108722524 TATTTTTAAAGATTTCCTTAGTTTCCCATACCCAAACAACTCAACATTTTGACATAT
64 TATTTCTAAAGATTTCCTTAGATTCCCAGACCCAAACAACACAACATTTTGACATAC
* * * * **
108722581 CAAAGTTTCTAATGATTTATCAAAATTTCTAAGGCTTTGCCATAATTTCAAAGGGTTTATCAATA
1 CAAAATTTCTAAGGATTTATCAAAATTTCTAAGGCTTTACCAAAATTTCAAAGAATTTATCAATA
* * ** * * *
108722646 TTTCTACAGATTTTCTTAGATTCTTAGACTCGACCAACACAACATTTTTTG-CATAC
66 TTTCTAAAGATTTCCTTAGATTCCCAGACCCAAACAACACAACA--TTTTGACATAC
* *
108722702 CAAAATTTCTTAGGATTTCTCAAA
1 CAAAATTTCTAAGGATTTATCAAA
108722726 TTTTTTAGGA
Statistics
Matches: 115, Mismatches: 26, Indels: 7
0.78 0.18 0.05
Matches are distributed among these distances:
119 7 0.06
120 77 0.67
121 26 0.23
122 5 0.04
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.37
Consensus pattern (120 bp):
CAAAATTTCTAAGGATTTATCAAAATTTCTAAGGCTTTACCAAAATTTCAAAGAATTTATCAATA
TTTCTAAAGATTTCCTTAGATTCCCAGACCCAAACAACACAACATTTTGACATAC
Found at i:108722818 original size:20 final size:19
Alignment explanation
Indices: 108722763--108722823 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
108722753 AGATTTTCCA
* *
108722763 AAAATTTTAAGGTTCTACC
1 AAAATTTTAATGTTTTACC
* *
108722782 AAAATTTTCAATATTTTATC
1 AAAATTTT-AATGTTTTACC
108722802 AAAATTTCTAATGTTTTACC
1 AAAATTT-TAATGTTTTACC
108722822 AA
1 AA
108722824 TATGATCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 8 0.24
20 25 0.74
21 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAATTTTAATGTTTTACC
Found at i:108722908 original size:20 final size:20
Alignment explanation
Indices: 108722848--108722908 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
108722838 CATTTTTGTG
* * *
108722848 TACTAATATTTCTAAAAATT
1 TACTAAAATTTTTAAAGATT
*
108722868 TAAT-AAA-TTTTATAAGAATT
1 TACTAAAATTTTTA-AAG-ATT
108722888 TACTAAAATTTTTAAAGATT
1 TACTAAAATTTTTAAAGATT
108722908 T
1 T
108722909 CATTAGTGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 13 0.41
21 6 0.19
22 5 0.16
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
TACTAAAATTTTTAAAGATT
Found at i:108730370 original size:19 final size:19
Alignment explanation
Indices: 108730346--108730383 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
108730336 ATAGGGATGA
108730346 AACAGAGACAAGATCCAAT
1 AACAGAGACAAGATCCAAT
*
108730365 AACAGAGGCAAGATCCAAT
1 AACAGAGACAAGATCCAAT
108730384 CTGTTCATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (19 bp):
AACAGAGACAAGATCCAAT
Found at i:108731653 original size:18 final size:19
Alignment explanation
Indices: 108731630--108731669 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
108731620 TTTAAAAAAT
*
108731630 AAAAAAT-AAGTTTTTTTA
1 AAAAAATCAAGTATTTTTA
108731648 AAAAAATCAAGTATTTTTA
1 AAAAAATCAAGTATTTTTA
108731667 AAA
1 AAA
108731670 GGTATGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAAATCAAGTATTTTTA
Found at i:108737909 original size:2 final size:2
Alignment explanation
Indices: 108737902--108737930 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108737892 TTACATTCAA
108737902 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 A
108737931 CTTGTGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108738182 original size:100 final size:100
Alignment explanation
Indices: 108737990--108738182 Score: 239
Period size: 100 Copynumber: 1.9 Consensus size: 100
108737980 TTATAGAGAA
*
108737990 TCAAAGATAATATCACATATGTGCATACCTATATGGCCAAATATGCAAGATCAAATTTAACATCA
1 TCAAAGATAATATCACATATGTGCATACCTATATGGCCAAATATGCAAGATCAAATATAACATCA
* * *
108738055 CCTAAGTACTTACTCATATGGCTGAATATACAAAT
66 CATAAGTACATACTCATATGGCCGAATATACAAAT
* * * * *
108738090 TCAAATATAATATCACTTTTGTGCATACCT-TCATGGTCAAATATTCAAGATTC-AATATAACAT
1 TCAAAGATAATATCACATATGTGCATACCTAT-ATGGCCAAATATGCAAGA-TCAAATATAACAT
* *
108738153 CACATATGTACATAC-CTATGTGGCCGAATA
64 CACATAAGTACATACTC-ATATGGCCGAATA
108738183 AATACAAGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
99 2 0.03
100 75 0.95
101 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (100 bp):
TCAAAGATAATATCACATATGTGCATACCTATATGGCCAAATATGCAAGATCAAATATAACATCA
CATAAGTACATACTCATATGGCCGAATATACAAAT
Found at i:108739184 original size:13 final size:14
Alignment explanation
Indices: 108739168--108739203 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
108739158 CAATCTCATA
108739168 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
108739181 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
108739194 TCTC-ATTTCA
1 TCTCAATTTCA
108739204 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:108739193 original size:18 final size:19
Alignment explanation
Indices: 108739155--108739195 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
108739145 TGGTTCATGT
108739155 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
108739174 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
108739192 TTTC
1 TTTC
108739196 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:108739385 original size:39 final size:38
Alignment explanation
Indices: 108739318--108739452 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
108739308 ACCAATATGG
* * *
108739318 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
108739357 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
108739395 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
108739436 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
108739453 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:108739717 original size:18 final size:19
Alignment explanation
Indices: 108739691--108739729 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
108739681 TTTCAATTCA
108739691 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
108739710 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
108739728 AT
1 AT
108739730 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:108741055 original size:5 final size:5
Alignment explanation
Indices: 108741045--108741097 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
108741035 TTACTTATTT
* *
108741045 ATATA ATATA ATATAA TATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA AT-ATA ATATA
108741093 ATATA
1 ATATA
108741098 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:108741066 original size:17 final size:17
Alignment explanation
Indices: 108741044--108741099 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
108741034 TTTACTTATT
108741044 TATATAATATAATATAA
1 TATATAATATAATATAA
*
108741061 TATATAATATACTAT-A
1 TATATAATATAATATAA
*
108741077 -ATATAATAATAATTTAA
1 TATATAAT-ATAATATAA
108741094 TATATA
1 TATATA
108741100 TTTTAACACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 15 0.45
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATAATATAATATAA
Found at i:108741947 original size:9 final size:9
Alignment explanation
Indices: 108741933--108741961 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
108741923 CATACTAGTC
108741933 CATTTATTT
1 CATTTATTT
108741942 CATTTATTT
1 CATTTATTT
108741951 CATTTATTT
1 CATTTATTT
108741960 CA
1 CA
108741962 CATTTTAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (9 bp):
CATTTATTT
Found at i:108743081 original size:23 final size:22
Alignment explanation
Indices: 108743032--108743095 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
108743022 CCTGATCAGT
*
108743032 ATACGACACATAAAGTGCCTAA
1 ATACGACACACAAAGTGCCTAA
* *
108743054 A-ACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCT-AA
*
108743076 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
108743096 GATCGATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.44
22 4 0.12
23 15 0.44
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.16
Consensus pattern (22 bp):
ATACGACACACAAAGTGCCTAA
Found at i:108743096 original size:23 final size:23
Alignment explanation
Indices: 108743032--108743097 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
108743022 CCTGATCAGT
108743032 ATACGACACATAAAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
** *
108743054 A-ACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
108743076 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
108743098 TCGATAAAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.42
22 4 0.11
23 17 0.47
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:108743493 original size:15 final size:15
Alignment explanation
Indices: 108743468--108743525 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
108743458 TCATATATAT
108743468 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
108743484 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
108743499 AATAATTTCAATCAA
1 TATAAATTCAATCAA
108743514 TATAAATTCAAT
1 TATAAATTCAAT
108743526 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:108744807 original size:5 final size:5
Alignment explanation
Indices: 108744794--108744835 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
108744784 TTCTTTAGTT
*
108744794 TATATA TATAA TATAA TATAA TATAA TATGA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
108744836 TAAAACATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:108744871 original size:8 final size:8
Alignment explanation
Indices: 108744858--108744886 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
108744848 TATCTTTATT
108744858 ATATAATA
1 ATATAATA
108744866 ATATAATA
1 ATATAATA
108744874 ATATAATA
1 ATATAATA
108744882 ATATA
1 ATATA
108744887 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:108746122 original size:16 final size:16
Alignment explanation
Indices: 108746098--108746130 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
108746088 AATGCTTAGT
*
108746098 AAGTTCATATAACCAA
1 AAGTACATATAACCAA
108746114 AAGTACATATAACCAA
1 AAGTACATATAACCAA
108746130 A
1 A
108746131 CTACACTTAC
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:0.55, C:0.18, G:0.06, T:0.21
Consensus pattern (16 bp):
AAGTACATATAACCAA
Found at i:108746414 original size:33 final size:33
Alignment explanation
Indices: 108746376--108746467 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 33
108746366 GAGGTGTACA
*
108746376 TTCCTTTCTAAGTGGTACACATAAAGTATACCT
1 TTCCTTTCTAAGTGGTACACACAAAGTATACCT
* *
108746409 TTCCTTT-TCATA-TGTTATACACAAAGTATACCT
1 TTCCTTTCT-A-AGTGGTACACACAAAGTATACCT
** *
108746442 AACCTTTCCAAGT-GTACACACAAAGT
1 TTCCTTTCTAAGTGGTACACACAAAGT
108746468 GTACATAACC
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
32 13 0.28
33 33 0.70
34 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (33 bp):
TTCCTTTCTAAGTGGTACACACAAAGTATACCT
Found at i:108750618 original size:27 final size:27
Alignment explanation
Indices: 108750552--108750618 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
108750542 AAAGTGTAAT
*
108750552 AAATAAAGTTTAAAAATGGATCTTTAAA
1 AAAT-AAGTATAAAAATGGATCTTTAAA
*
108750580 ATTAA-ACA-TATAAAAATGGATTTTTAAA
1 A--AATA-AGTATAAAAATGGATCTTTAAA
108750608 AAATAAGTATA
1 AAATAAGTATA
108750619 TATGTCGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
26 3 0.09
27 5 0.16
28 21 0.66
29 1 0.03
30 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATAAGTATAAAAATGGATCTTTAAA
Found at i:108751116 original size:21 final size:21
Alignment explanation
Indices: 108751092--108751138 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
108751082 ATTAAATCAT
* *
108751092 AATAATAACTATTA-CACTAAA
1 AATAATAAATATTATCAAT-AA
108751113 AATAA-AAATATTATCAATAA
1 AATAATAAATATTATCAATAA
108751133 AATAAT
1 AATAAT
108751139 TATAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAATAAATATTATCAATAA
Found at i:108751356 original size:18 final size:19
Alignment explanation
Indices: 108751333--108751377 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
108751323 TATATATATA
108751333 AATTATATTT-ATTTAATT
1 AATTATATTTAATTTAATT
*
108751351 AATTAT-TTTAATTTATTT
1 AATTATATTTAATTTAATT
108751369 AATTATATT
1 AATTATATT
108751378 CAATGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 3 0.12
18 19 0.79
19 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTATATTTAATTTAATT
Found at i:108751363 original size:9 final size:10
Alignment explanation
Indices: 108751333--108751377 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
108751323 TATATATATA
108751333 AATTATATTT
1 AATTATATTT
*
108751343 -ATT-TAATT
1 AATTATATTT
108751351 AATTAT-TTT
1 AATTATATTT
108751360 AATT-TATTT
1 AATTATATTT
108751369 AATTATATT
1 AATTATATT
108751378 CAATGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.17
9 19 0.66
10 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
AATTATATTT
Found at i:108758556 original size:15 final size:15
Alignment explanation
Indices: 108758536--108758567 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
108758526 TTGGTTGCAT
108758536 TACTACTCGAACAGA
1 TACTACTCGAACAGA
108758551 TACTACTCGAACAGA
1 TACTACTCGAACAGA
108758566 TA
1 TA
108758568 ATATTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (15 bp):
TACTACTCGAACAGA
Found at i:108762785 original size:17 final size:18
Alignment explanation
Indices: 108762765--108762802 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
108762755 TTTCACAATG
*
108762765 TAAAAAAT-ACAATAAAT
1 TAAAAAATAAAAATAAAT
*
108762782 TAAAATATAAAAATAAAT
1 TAAAAAATAAAAATAAAT
108762800 TAA
1 TAA
108762803 CAAGTTACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATAAAAATAAAT
Found at i:108762933 original size:7 final size:7
Alignment explanation
Indices: 108762916--108762950 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
108762906 TTACAATTTC
108762916 TCCCTAAA
1 TCCC-AAA
108762924 TCCCAAA
1 TCCCAAA
108762931 TCCCAAA
1 TCCCAAA
108762938 TCCCAAA
1 TCCCAAA
108762945 TCCCAA
1 TCCCAA
108762951 CCATATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 23 0.85
8 4 0.15
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (7 bp):
TCCCAAA
Found at i:108763748 original size:3 final size:3
Alignment explanation
Indices: 108763740--108763774 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
108763730 GGTGTAACAA
108763740 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
108763775 ATTATGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:108773299 original size:87 final size:87
Alignment explanation
Indices: 108773153--108773329 Score: 345
Period size: 87 Copynumber: 2.0 Consensus size: 87
108773143 AACATATTGC
108773153 ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
1 ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
*
108773218 GACTAGAATGATTTACTAATTA
66 GACTAGAATGACTTACTAATTA
108773240 ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
1 ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
108773305 GACTAGAATGACTTACTAATTA
66 GACTAGAATGACTTACTAATTA
108773327 ACA
1 ACA
108773330 TTCGAACTCA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (87 bp):
ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
GACTAGAATGACTTACTAATTA
Found at i:108776371 original size:22 final size:22
Alignment explanation
Indices: 108776343--108776388 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
108776333 GATTAAAAAT
108776343 GAGCAAAAGCCTATATCCTAAG
1 GAGCAAAAGCCTATATCCTAAG
108776365 GAGCAAAAGCCTATATCCTAAG
1 GAGCAAAAGCCTATATCCTAAG
108776387 GA
1 GA
108776389 ACTTAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (22 bp):
GAGCAAAAGCCTATATCCTAAG
Found at i:108780933 original size:16 final size:16
Alignment explanation
Indices: 108780912--108780944 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
108780902 GAACACTAAG
108780912 GCAGGAAAAAACGAAA
1 GCAGGAAAAAACGAAA
108780928 GCAGGAAAAAACGAAA
1 GCAGGAAAAAACGAAA
108780944 G
1 G
108780945 TGAAACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.12, G:0.27, T:0.00
Consensus pattern (16 bp):
GCAGGAAAAAACGAAA
Found at i:108788301 original size:18 final size:17
Alignment explanation
Indices: 108788272--108788305 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
108788262 ACAATTTATA
108788272 TTAAATTATAATTATTT
1 TTAAATTATAATTATTT
108788289 TTAAATATATAATTATT
1 TTAAAT-TATAATTATT
108788306 ACCATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTATAATTATTT
Found at i:108791317 original size:2 final size:2
Alignment explanation
Indices: 108791310--108791338 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108791300 GTAGAAATTA
108791310 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
108791339 ACACACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:108795229 original size:46 final size:46
Alignment explanation
Indices: 108795176--108795269 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
108795166 ACTGGAAATG
108795176 GACCTTCAATCCTTTAAAGAAAAGCAAACATTTATCAACCATATTT
1 GACCTTCAATCCTTTAAAGAAAAGCAAACATTTATCAACCATATTT
*
108795222 GACCTTCAATCCTTTAAAGAAATGCAAACATTTATCAACCATATTT
1 GACCTTCAATCCTTTAAAGAAAAGCAAACATTTATCAACCATATTT
108795268 GA
1 GA
108795270 GAAGCCTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (46 bp):
GACCTTCAATCCTTTAAAGAAAAGCAAACATTTATCAACCATATTT
Found at i:108796683 original size:21 final size:21
Alignment explanation
Indices: 108796659--108796706 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
108796649 ACACGAGGTG
108796659 CCTGATACAACACATACAGTA
1 CCTGATACAACACATACAGTA
** * *
108796680 CCTGATATGACACATATAGTG
1 CCTGATACAACACATACAGTA
108796701 CCTGAT
1 CCTGAT
108796707 CGGCAAAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
CCTGATACAACACATACAGTA
Found at i:108798832 original size:17 final size:17
Alignment explanation
Indices: 108798812--108798845 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
108798802 TTTAACGTTT
108798812 GTTTCGATTTATTCAAG
1 GTTTCGATTTATTCAAG
108798829 GTTTCGATTTATTCAAG
1 GTTTCGATTTATTCAAG
108798846 CGGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
GTTTCGATTTATTCAAG
Found at i:108801448 original size:12 final size:12
Alignment explanation
Indices: 108801418--108801450 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
108801408 ATATTCTTTT
108801418 AAAATT-ATATA
1 AAAATTAATATA
108801429 AAAA-TAATATA
1 AAAATTAATATA
108801440 AAAATTAATAT
1 AAAATTAATAT
108801451 GGGCGGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:108809764 original size:6 final size:6
Alignment explanation
Indices: 108809753--108809805 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
108809743 CTCACTGATG
108809753 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
108809801 TTTAT
1 TTTAT
108809806 TCTGCTTGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:108818038 original size:22 final size:21
Alignment explanation
Indices: 108818013--108818053 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
108818003 TCTATTTTGC
*
108818013 CATTTATTTTATTGTTTTTTAT
1 CATTAATTTTATT-TTTTTTAT
108818035 CATTAATTTTATTTTTTTT
1 CATTAATTTTATTTTTTTT
108818054 GTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (21 bp):
CATTAATTTTATTTTTTTTAT
Found at i:108820482 original size:64 final size:64
Alignment explanation
Indices: 108820403--108820530 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
108820393 CCCAAGCTAC
108820403 TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTGTCACTTTCTTCTCA
1 TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTGTCACTTTCTTCTCA
108820467 TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTGTCACTTTCTTCTCA
1 TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTGTCACTTTCTTCTCA
108820531 ATCATCTCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.42
Consensus pattern (64 bp):
TTTGCATTCATCAGATGTCTCATCTCCTTCACAAACTTGCTTGGCTTCTGTCACTTTCTTCTCA
Found at i:108821234 original size:11 final size:11
Alignment explanation
Indices: 108821218--108821242 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
108821208 ATATATATTT
108821218 TTTTTGATATA
1 TTTTTGATATA
108821229 TTTTTGATATA
1 TTTTTGATATA
108821240 TTT
1 TTT
108821243 AAAAGTAAAT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTGATATA
Found at i:108822075 original size:2 final size:2
Alignment explanation
Indices: 108822068--108822099 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
108822058 AGAAACTTTC
108822068 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
108822100 GTATGCACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108822632 original size:82 final size:82
Alignment explanation
Indices: 108822532--108822696 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
108822522 GTTTTGAGTG
108822532 ATAGGATCTAGATATTATAGATCAACTGAGACAATTCACCGTTATTTTAGGGTTGTATTAAGAGC
1 ATAGGATCTAGATATTATAGATCAACTGAGACAATTCACCGTTATTTTAGGGTTGTATTAAGAGC
108822597 TATTTTGAAATTGTATA
66 TATTTTGAAATTGTATA
*
108822614 ATAGGATCTAGATATTATAGATCAACTGAGACAATTCACCGTTATTTTAGGGTTGTATTGAGAGC
1 ATAGGATCTAGATATTATAGATCAACTGAGACAATTCACCGTTATTTTAGGGTTGTATTAAGAGC
108822679 TATTTTGAAATTGTATA
66 TATTTTGAAATTGTATA
108822696 A
1 A
108822697 GCTAGTTATT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (82 bp):
ATAGGATCTAGATATTATAGATCAACTGAGACAATTCACCGTTATTTTAGGGTTGTATTAAGAGC
TATTTTGAAATTGTATA
Found at i:108823675 original size:32 final size:32
Alignment explanation
Indices: 108823609--108823676 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
108823599 TTTTTGTTAA
* *
108823609 TGTTGGATTCTAAAATTTTAGTTTATTATATT
1 TGTTGGATTCTAAAATTTTAGTCTATGATATT
*
108823641 TGTTGGATTCTGAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATATT
108823673 TGTT
1 TGTT
108823677 AGATATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 6 0.19
34 3 0.10
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATATT
Found at i:108824731 original size:22 final size:22
Alignment explanation
Indices: 108824663--108824751 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
108824653 GATACTTTTA
108824663 ATGTGGTGTAATATTAGTTATGC
1 ATGTGGTGTAATATTAGTTAT-C
** *
108824686 ACT-TGG-ACAATATTGTTGTTATC
1 A-TGTGGTGTAATA-T-TAGTTATC
108824709 ATGTGGTGTAATATTAGTTATC
1 ATGTGGTGTAATATTAGTTATC
*
108824731 ATATGGTGTAATATTAGTTAT
1 ATGTGGTGTAATATTAGTTAT
108824752 GCACTTGGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
22 32 0.59
23 11 0.20
24 11 0.20
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
ATGTGGTGTAATATTAGTTATC
Found at i:108824811 original size:68 final size:68
Alignment explanation
Indices: 108824666--108824814 Score: 219
Period size: 68 Copynumber: 2.2 Consensus size: 68
108824656 ACTTTTAATG
* * *
108824666 TGGTGTAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATATTAGTTATC
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
108824731 ATA
66 ATA
* * *
108824734 TGGTGTAATATTAGTTATGCACTTGGATAATGTTGTTGTTATCATGTGGTGTAATACTAATTATG
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTAT-
*
108824799 CATT
65 CATA
108824803 TGG-ATAATATTA
1 TGGTATAATATTA
108824815 TTAATTTCTA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
68 68 0.92
69 6 0.08
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (68 bp):
TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
ATA
Found at i:108830035 original size:14 final size:14
Alignment explanation
Indices: 108830016--108830068 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
108830006 CCAGAAAAGT
108830016 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
108830030 AAATCATTTTCCAAA
1 AAATCATTTTCC-AG
*
108830045 AAATTATTTTCCAG
1 AAATCATTTTCCAG
108830059 AAATCATTTT
1 AAATCATTTT
108830069 TCGAAAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:108830053 original size:15 final size:15
Alignment explanation
Indices: 108830016--108830082 Score: 68
Period size: 14 Copynumber: 4.7 Consensus size: 15
108830006 CCAGAAAAGT
*
108830016 AAATCATTTTCC-AG
1 AAATCATTTTCCAAA
108830030 AAATCATTTTCCAAA
1 AAATCATTTTCCAAA
* *
108830045 AAATTATTTTCC-AG
1 AAATCATTTTCCAAA
* *
108830059 AAATCATTTTTCGAA
1 AAATCATTTTCCAAA
108830074 AAA-CATTTT
1 AAATCATTTT
108830083 ACCTGCAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
14 29 0.64
15 16 0.36
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.39
Consensus pattern (15 bp):
AAATCATTTTCCAAA
Done.