Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 37
Found at i:5800755 original size:29 final size:29
Alignment explanation
Indices: 5800723--5800778 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5800713 GCGACCTACC
*
5800723 TAGGTCGTTGGGCGTGCATGGCGACCTGG
1 TAGGTCGCTGGGCGTGCATGGCGACCTGG
*
5800752 TAGGTCGCTGGGCGTGCATGGTGACCT
1 TAGGTCGCTGGGCGTGCATGGCGACCT
5800779 ACACCTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.11, C:0.21, G:0.43, T:0.25
Consensus pattern (29 bp):
TAGGTCGCTGGGCGTGCATGGCGACCTGG
Found at i:5811336 original size:17 final size:18
Alignment explanation
Indices: 5811314--5811367 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
5811304 GGGCCTTCTC
*
5811314 GGGCCTG-CTGGGTTATT
1 GGGCCTGACCGGGTTATT
*
5811331 GGGCCTGAACCGGGTTGTT
1 GGGCCTG-ACCGGGTTATT
*
5811350 GGGCCTGAACCGAGTTAT
1 GGGCCTG-ACCGGGTTAT
5811368 GGATTGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 7 0.23
19 24 0.77
ACGTcount: A:0.13, C:0.20, G:0.39, T:0.28
Consensus pattern (18 bp):
GGGCCTGACCGGGTTATT
Found at i:5811351 original size:19 final size:19
Alignment explanation
Indices: 5811323--5811367 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
5811313 CGGGCCTGCT
5811323 GGGTTATTGGGCCTGAACC
1 GGGTTATTGGGCCTGAACC
*
5811342 GGGTTGTTGGGCCTGAACC
1 GGGTTATTGGGCCTGAACC
*
5811361 GAGTTAT
1 GGGTTAT
5811368 GGATTGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.38, T:0.29
Consensus pattern (19 bp):
GGGTTATTGGGCCTGAACC
Found at i:5811445 original size:3 final size:3
Alignment explanation
Indices: 5811439--5811470 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5811429 TGTAATAATT
5811439 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5811471 TATTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5814182 original size:266 final size:254
Alignment explanation
Indices: 5813728--5814279 Score: 675
Period size: 266 Copynumber: 2.1 Consensus size: 254
5813718 TCGGGTCGGG
*
5813728 TGAAACTTTATTTTGGTCGGGTCAGGTCGGTTTTTTTAAGTGTGATATTATGGTCGGGTCGAGTT
1 TGAAACTTTATTTTGGTCGGGTCAGGTCAGTTTTTTTAAGTGTGA-ATTAT-GTCGGGTCGAGTT
* *
5813793 CGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTAACTTATATATTTAGGAAT
64 CGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTAACTTATATATTTAAGAAT
* *
5813858 AATTACAATAATACCCCTATATATATAATTTTTTCAATTAAGTCACTGCTTTTATTGAATAAAAA
129 AATTACAATAATACCCCTATATATATAATTATTTCAATTAAGTCAATGCTTTTATTGAATAAAAA
* *
5813923 TAATTTTTTTATT-ATTTCGGGTCGGGTCGGGTCAGATTTCTAATTCATTTATTCGGGTCAGTTC
194 T-ATTTTTTTATTAATTTCGGGCCGGGTC-GG---G-TTTCTAATTCATATATTCGGGTCAGTTC
5813987 GA
253 GA
* * * *
5813989 TGAAACTTTATTTTGGTTGGGTCGGGTCTATTTTTTTTAAGTGTG-A-TAT-TCGGGTCGGGTTC
1 TGAAACTTTATTTTGGTCGGGTCAGGTC-AGTTTTTTTAAGTGTGAATTATGTCGGGTCGAGTTC
*
5814051 GGGTTTAGGGTGAAAAATACCCGGCTCGACCCGACCCAAAAAATATATAATTTTACCTTATATAT
65 GGGTTTAGGGTGAAAAATA--C--C-CGACCCG----AAAAAATATATAATTTTAACTTATATAT
* *
5814116 TTAAGAATAATTATAATAATACCTCTCTATATATAT-A-TATTTCAATTAAGTCAATGTTTTTAT
121 TTAAGAATAATTACAATAATACC-C-CTATATATATAATTATTTCAATTAAGTCAATGCTTTTAT
*
5814179 TGAATAAAAATATTTTTTTATTAATTTCGGGCCTGGTCGGGTTTCTAATTCATATATTCGGGTCG
184 TGAATAAAAATATTTTTTTATTAATTTCGGGCCGGGTCGGGTTTCTAATTCATATATTCGGGTC-
* *
5814244 GGTCGGGTCGGG
248 AGT----TC-GA
5814256 TGAAACTTTATTTTGGTCGGGTCA
1 TGAAACTTTATTTTGGTCGGGTCA
5814280 AGTCGGGTCT
Statistics
Matches: 253, Mismatches: 19, Indels: 32
0.83 0.06 0.11
Matches are distributed among these distances:
257 31 0.12
259 4 0.02
260 1 0.00
261 49 0.19
262 24 0.09
265 13 0.05
266 96 0.38
267 25 0.10
268 10 0.04
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (254 bp):
TGAAACTTTATTTTGGTCGGGTCAGGTCAGTTTTTTTAAGTGTGAATTATGTCGGGTCGAGTTCG
GGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTAACTTATATATTTAAGAATAA
TTACAATAATACCCCTATATATATAATTATTTCAATTAAGTCAATGCTTTTATTGAATAAAAATA
TTTTTTTATTAATTTCGGGCCGGGTCGGGTTTCTAATTCATATATTCGGGTCAGTTCGA
Found at i:5814439 original size:4 final size:4
Alignment explanation
Indices: 5814430--5814460 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5814420 TGAAATTAAT
5814430 AATC AATC AATC AATC AATC AATC AATC AAT
1 AATC AATC AATC AATC AATC AATC AATC AAT
5814461 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
AATC
Found at i:5817906 original size:111 final size:112
Alignment explanation
Indices: 5817456--5817917 Score: 703
Period size: 112 Copynumber: 4.1 Consensus size: 112
5817446 TTATCGGTTT
* * * *
5817456 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAATAACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* * *
5817521 GGTCTATAAATGACAAAGCAAGTAAAGCGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
5817568 GTGTCGATACTTTATAAAAATATATCGATCTATAACAATATAACAGGTAAAAAAATGATAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
5817633 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
5817680 ATGAT-GATACTTTATAAAAATGTATCTATCTATAACAATATAACAGGTAAAAAAATGACAAAAT
1 GTG-TCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAT
* * *
5817744 CGATCTATAAATGACAAAACAGGTAAAGCGCTATCTGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
5817792 GTGTTGATATTTTATAAAAATGTATCGATCCATAACAATATAACATGT-AAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* *
5817856 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
5817903 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
5817918 TATAAGTATC
Statistics
Matches: 320, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
111 72 0.22
112 247 0.77
113 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:5818135 original size:162 final size:164
Alignment explanation
Indices: 5817865--5818202 Score: 549
Period size: 162 Copynumber: 2.1 Consensus size: 164
5817855 CGGTCTATAA
* * * *
5817865 ATGACAAAA-CAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCG
1 ATGACAAAATCAGATAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
* *
5817929 ACACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATGCTTTATAAAAAT
66 ACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAAT
**
5817994 GTATCGATCCATAACAATATAACAG-GTAAAAAT
131 GTATCGATCCATAACAATATAACAGAAAAAAAAT
5818027 ATGACAAAATC-GATAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
1 ATGACAAAATCAGATAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
* *
5818091 ACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCG-TCAATAAAGTGTTGATACTTTATAAAAA
66 ACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGCT-AATAAAGTGTCGATACTTTATAAAAA
5818155 TGTATCGATCCATAACAATATAACAGAAAAAAAAT
130 TGTATCGATCCATAACAATATAACAGAAAAAAAAT
5818190 ATGACAAAATCAG
1 ATGACAAAATCAG
5818203 TCTCGAAATG
Statistics
Matches: 162, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
161 1 0.01
162 142 0.88
163 18 0.11
164 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (164 bp):
ATGACAAAATCAGATAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
ACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAAT
GTATCGATCCATAACAATATAACAGAAAAAAAAT
Found at i:5818691 original size:23 final size:23
Alignment explanation
Indices: 5818658--5818705 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5818648 AAATAGGTCA
*
5818658 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTAATACATT
* *
5818681 ATATAAGCGCTACCTAATATATT
1 ATATAAACGCTACCTAATACATT
5818704 AT
1 AT
5818706 TGTACTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTAATACATT
Found at i:5822362 original size:103 final size:103
Alignment explanation
Indices: 5822142--5822354 Score: 399
Period size: 103 Copynumber: 2.1 Consensus size: 103
5822132 GGGTCTACGC
5822142 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
5822207 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
5822245 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
5822310 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
5822348 GGTCCTT
1 GGTCCTT
5822355 ATGGACATTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:5822401 original size:23 final size:23
Alignment explanation
Indices: 5822371--5822433 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
5822361 ATTATTATAT
5822371 GGCACTCCGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
5822394 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
*
5822417 GGCACTTCGGTGCAATT
1 GGCACTCCGGTGCAATT
5822434 AAACGAGCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:5823775 original size:27 final size:23
Alignment explanation
Indices: 5823687--5823771 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
5823677 ATTCAAATAC
* *
5823687 AAATTCTAATTAATAGCAAACTA
1 AAATCCTAATTAATAACAAACTA
* * * *
5823710 GAATCTTAAATAATAACAAATTA
1 AAATCCTAATTAATAACAAACTA
5823733 AAATCCTAATTAATAACAAACTA
1 AAATCCTAATTAATAACAAACTA
5823756 AAATCCTAATTAATAA
1 AAATCCTAATTAATAA
5823772 ATAATAAATC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATCCTAATTAATAACAAACTA
Found at i:5826975 original size:24 final size:24
Alignment explanation
Indices: 5826918--5827002 Score: 90
Period size: 23 Copynumber: 3.7 Consensus size: 24
5826908 TAGTCGAAAC
*
5826918 TGCCACATAGAAT-TACACCGAAG
1 TGCCACATAGAATATGCACCGAAG
* *
5826941 TGCCGCGTAGAATATGCACCGAAG
1 TGCCACATAGAATATGCACCGAAG
5826965 TGCCACATAGAA-ATGTC-CCGAAG
1 TGCCACATAGAATATG-CACCGAAG
5826988 -GACCACATAG-ATATG
1 TG-CCACATAGAATATG
5827003 TCCCGAAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
22 2 0.04
23 31 0.58
24 20 0.38
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (24 bp):
TGCCACATAGAATATGCACCGAAG
Found at i:5826987 original size:47 final size:48
Alignment explanation
Indices: 5826912--5827050 Score: 141
Period size: 46 Copynumber: 3.0 Consensus size: 48
5826902 GGGTTGTAGT
* *
5826912 CGAAACTGCCACATAG-AAT-TACACCGAAGTG-CCGCGTAGAATATG-CAC
1 CGAAAGTGCCACATAGAAATGT-C-CCGAAG-GACCACGTAGAATATGTC-C
*
5826960 CG-AAGTGCCACATAGAAATGTCCCGAAGGACCACATAG-ATATGTCC
1 CGAAAGTGCCACATAGAAATGTCCCGAAGGACCACGTAGAATATGTCC
* *
5827006 CGAAAG-ACCGCATAGAAATGTCCCGAAGGACCACGTAGAAT-TGTC
1 CGAAAGTGCCACATAGAAATGTCCCGAAGGACCACGTAGAATATGTC
5827051 ACAAAGGACC
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
46 42 0.53
47 30 0.38
48 6 0.08
49 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (48 bp):
CGAAAGTGCCACATAGAAATGTCCCGAAGGACCACGTAGAATATGTCC
Found at i:5826993 original size:23 final size:23
Alignment explanation
Indices: 5826959--5827068 Score: 132
Period size: 23 Copynumber: 4.8 Consensus size: 23
5826949 AGAATATGCA
5826959 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
*
5826982 CCGAAGGACCACATAGATATGTC
1 CCGAAGGACCACATAGAAATGTC
* *
5827005 CCGAAAGACCGCATAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
* *
5827028 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACATAGAAATGTC
* * *
5827051 ACAAAGGACCACGTAGAA
1 CCGAAGGACCACATAGAA
5827069 CCCTAGACTC
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
22 1 0.01
23 75 0.99
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:5827191 original size:15 final size:16
Alignment explanation
Indices: 5827154--5827196 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
5827144 TCACATAGCT
*
5827154 TATATCACATA-TTCA
1 TATATCACATAGATCA
5827169 TATAATCACATAGATCA
1 TAT-ATCACATAGATCA
5827186 -ATATCACATAG
1 TATATCACATAG
5827197 TATGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 10 0.40
17 3 0.12
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (16 bp):
TATATCACATAGATCA
Found at i:5829059 original size:23 final size:23
Alignment explanation
Indices: 5829033--5829110 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
5829023 CACCACAGCT
5829033 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
5829056 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * * *
5829079 CGTAGAATTGCACTGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
5829102 TATAATAAT
1 CAT-ATAAT
5829111 GTCCATAAGG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:5829290 original size:103 final size:103
Alignment explanation
Indices: 5829117--5829334 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
5829107 TAATGTCCAT
* * *
5829117 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
5829182 AACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
5829220 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
5829285 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
5829323 AAGGACCACATA
1 AAGGACCACATA
5829335 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:5835948 original size:18 final size:18
Alignment explanation
Indices: 5835927--5835962 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5835917 CTTCCATCCG
*
5835927 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5835945 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5835963 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:5837277 original size:8 final size:8
Alignment explanation
Indices: 5837235--5837289 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
5837225 TCAAAGTTTT
5837235 GGTCAACAG
1 GGTCAAC-G
5837244 TGGTCAACG
1 -GGTCAACG
5837253 CCGGTCAAC-
1 --GGTCAACG
*
5837262 GATCAACG
1 GGTCAACG
5837270 GGTCAACG
1 GGTCAACG
5837278 GGTCAACG
1 GGTCAACG
5837286 GGTC
1 GGTC
5837290 GAGTCAAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 19 0.47
9 1 0.03
10 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.33, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:5839621 original size:18 final size:18
Alignment explanation
Indices: 5839600--5839635 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5839590 CTTCCATCCG
*
5839600 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5839618 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5839636 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:5840931 original size:8 final size:8
Alignment explanation
Indices: 5840908--5840945 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
5840898 TCAAAGTTTT
5840908 GGTCAACG
1 GGTCAACG
5840916 CCGGTCAACG
1 --GGTCAACG
5840926 GGTCAACG
1 GGTCAACG
5840934 GGTCAACG
1 GGTCAACG
5840942 GGTC
1 GGTC
5840946 GAGTCAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 20 0.71
10 8 0.29
ACGTcount: A:0.21, C:0.29, G:0.37, T:0.13
Consensus pattern (8 bp):
GGTCAACG
Found at i:5843284 original size:18 final size:18
Alignment explanation
Indices: 5843263--5843298 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5843253 CTTCCATCCG
*
5843263 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5843281 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5843299 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:5844614 original size:8 final size:8
Alignment explanation
Indices: 5844572--5844626 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
5844562 TCAAAGTTTT
5844572 GGTCAACAG
1 GGTCAAC-G
5844581 TGGTCAACG
1 -GGTCAACG
5844590 CCGGTCAAC-
1 --GGTCAACG
*
5844599 GATCAACG
1 GGTCAACG
5844607 GGTCAACG
1 GGTCAACG
5844615 GGTCAACG
1 GGTCAACG
5844623 GGTC
1 GGTC
5844627 GAGTCAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 19 0.47
9 1 0.03
10 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.33, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:5844634 original size:13 final size:13
Alignment explanation
Indices: 5844616--5844640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5844606 GGGTCAACGG
5844616 GTCAACGGGTCGA
1 GTCAACGGGTCGA
5844629 GTCAACGGGTCG
1 GTCAACGGGTCG
5844641 GTCGGGTCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:5846964 original size:18 final size:18
Alignment explanation
Indices: 5846943--5846978 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5846933 CTTCCATCCG
*
5846943 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5846961 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5846979 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:5848293 original size:8 final size:8
Alignment explanation
Indices: 5848251--5848305 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
5848241 TCAAAGTTTT
5848251 GGTCAACAG
1 GGTCAAC-G
5848260 TGGTCAACG
1 -GGTCAACG
5848269 CCGGTCAAC-
1 --GGTCAACG
*
5848278 GATCAACG
1 GGTCAACG
5848286 GGTCAACG
1 GGTCAACG
5848294 GGTCAACG
1 GGTCAACG
5848302 GGTC
1 GGTC
5848306 GAGTCAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 19 0.47
9 1 0.03
10 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.33, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:5848313 original size:13 final size:13
Alignment explanation
Indices: 5848295--5848319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5848285 GGGTCAACGG
5848295 GTCAACGGGTCGA
1 GTCAACGGGTCGA
5848308 GTCAACGGGTCG
1 GTCAACGGGTCG
5848320 GTCGGGTCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:5850641 original size:18 final size:18
Alignment explanation
Indices: 5850620--5850655 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5850610 CTTCCATCCG
*
5850620 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5850638 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5850656 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:5851964 original size:8 final size:8
Alignment explanation
Indices: 5851922--5851976 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
5851912 TCAAAGTTTT
5851922 GGTCAACAG
1 GGTCAAC-G
5851931 TGGTCAACG
1 -GGTCAACG
5851940 CCGGTCAAC-
1 --GGTCAACG
*
5851949 GATCAACG
1 GGTCAACG
5851957 GGTCAACG
1 GGTCAACG
5851965 GGTCAACG
1 GGTCAACG
5851973 GGTC
1 GGTC
5851977 GAGTCAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 19 0.47
9 1 0.03
10 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.33, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:5851984 original size:13 final size:13
Alignment explanation
Indices: 5851966--5851990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5851956 GGGTCAACGG
5851966 GTCAACGGGTCGA
1 GTCAACGGGTCGA
5851979 GTCAACGGGTCG
1 GTCAACGGGTCG
5851991 GTCGGGTCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:5854314 original size:18 final size:18
Alignment explanation
Indices: 5854293--5854328 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5854283 CTTCCATCCG
*
5854293 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
5854311 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
5854329 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:5855642 original size:8 final size:8
Alignment explanation
Indices: 5855600--5855654 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
5855590 TCAAAGTTTT
5855600 GGTCAACAG
1 GGTCAAC-G
5855609 TGGTCAACG
1 -GGTCAACG
5855618 TCGGTCAAC-
1 --GGTCAACG
*
5855627 GATCAACG
1 GGTCAACG
5855635 GGTCAACG
1 GGTCAACG
5855643 GGTCAACG
1 GGTCAACG
5855651 GGTC
1 GGTC
5855655 GAGTCAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 19 0.47
9 1 0.03
10 14 0.35
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:5855662 original size:13 final size:13
Alignment explanation
Indices: 5855644--5855668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5855634 GGGTCAACGG
5855644 GTCAACGGGTCGA
1 GTCAACGGGTCGA
5855657 GTCAACGGGTCG
1 GTCAACGGGTCG
5855669 GTCGGGTCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:5857115 original size:3 final size:3
Alignment explanation
Indices: 5857109--5857142 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5857099 ATTTTATTAT
5857109 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5857143 ATCATTTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5860760 original size:29 final size:29
Alignment explanation
Indices: 5860717--5860799 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
5860707 CTCACCTAAC
5860717 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
5860747 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
5860776 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
5860800 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:5865515 original size:29 final size:29
Alignment explanation
Indices: 5865472--5865554 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
5865462 CTCACCTAAC
5865472 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
5865502 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
5865531 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
5865555 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:5868457 original size:2 final size:2
Alignment explanation
Indices: 5868450--5868480 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5868440 TAAAATAAGA
5868450 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 A
5868481 ATTTTAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5872744 original size:30 final size:29
Alignment explanation
Indices: 5872721--5872777 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5872711 TTTTATTAAC
5872721 ATAATTT-AAAAA-ATATTTTATTTTTATT
1 ATAATTTAAAAAATATATTTTA-TTTTATT
* *
5872749 TTTATTTAAAAAATATATTTTATTTTATT
1 ATAATTTAAAAAATATATTTTATTTTATT
5872778 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 12 0.48
30 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATAATTTAAAAAATATATTTTATTTTATT
Found at i:5872769 original size:19 final size:20
Alignment explanation
Indices: 5872745--5872802 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 20
5872735 ATTTTATTTT
5872745 TATTTTTATTTAAAAAATATA
1 TATTTTTATTT-AAAAATATA
*
5872766 TTTTATTTTATTTAAAAATATA
1 -TAT-TTTTATTTAAAAATATA
5872788 TATTTTTATGTTAAA
1 TATTTTTAT-TTAAA
5872803 TATTTGAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 6 0.19
21 7 0.22
22 11 0.34
23 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTTTATTTAAAAATATA
Found at i:5872785 original size:22 final size:24
Alignment explanation
Indices: 5872724--5872793 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 24
5872714 TATTAACATA
5872724 ATTTAAAAAATATTTTATTTTTATTTTT
1 ATTTAAAAAATA---TA-TTTTATTTTT
5872752 ATTTAAAAAATATATTTTA-TTTT
1 ATTTAAAAAATATATTTTATTTTT
5872775 ATTTAAAAATATATATTTT
1 ATTTAAAAA-ATATATTTT
5872794 TATGTTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.32
24 14 0.34
25 2 0.05
28 12 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTAAAAAATATATTTTATTTTT
Found at i:5872875 original size:28 final size:28
Alignment explanation
Indices: 5872844--5872936 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 28
5872834 TTAATATTTA
*
5872844 AAGAATGATATAATATATTTGGTAAATT
1 AAGAATGATATAATATATTTAGTAAATT
* * * *
5872872 AAG-ATAAAAT-GTATATTTTG-AAATT
1 AAGAATGATATAATATATTTAGTAAATT
* * *
5872897 AA-AATTATAAAATATATTTATTATAATT
1 AAGAATGATATAATATATTTAGTA-AATT
5872925 AAGTAATGATAT
1 AAG-AATGATAT
5872937 TTTTAAATTA
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 11 0.23
26 15 0.32
27 6 0.13
28 9 0.19
30 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (28 bp):
AAGAATGATATAATATATTTAGTAAATT
Found at i:5872981 original size:24 final size:24
Alignment explanation
Indices: 5872954--5873037 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 24
5872944 TTAAAATCAA
5872954 AATAAAATATTTTATTAAGTTAAT
1 AATAAAATATTTTATTAAGTTAAT
* *
5872978 AATAAAATATATTTAATAGGTTAAT
1 AATAAAATAT-TTTATTAAGTTAAT
*
5873003 -ATAAAAGTA-TTTCTTAAGTTAAT
1 AATAAAA-TATTTTATTAAGTTAAT
*
5873026 ATATATAATATT
1 A-ATAAAATATT
5873038 ATGAATTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
23 11 0.22
24 18 0.37
25 20 0.41
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (24 bp):
AATAAAATATTTTATTAAGTTAAT
Found at i:5873000 original size:25 final size:24
Alignment explanation
Indices: 5872954--5873037 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
5872944 TTAAAATCAA
*
5872954 AATAAAATATTTTATTAAGTTAAT
1 AATAAAATATTTTAATAAGTTAAT
*
5872978 AATAAAATATATTTAATAGGTTAAT
1 AATAAAATAT-TTTAATAAGTTAAT
5873003 -ATAAAAGTATTTCT--TAAGTTAAT
1 AATAAAA-TATTT-TAATAAGTTAAT
*
5873026 ATATATAATATT
1 A-ATAAAATATT
5873038 ATGAATTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
23 8 0.16
24 22 0.43
25 21 0.41
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (24 bp):
AATAAAATATTTTAATAAGTTAAT
Found at i:5873370 original size:30 final size:30
Alignment explanation
Indices: 5873311--5873373 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5873301 TGATTAAATC
*
5873311 TTAATTAAATAAAAACAAAAGACTAATATA
1 TTAATTAAATAAAAACAAAAGAATAATATA
* *
5873341 TTAATTAAATAAAAA-AAATATAATTATATA
1 TTAATTAAATAAAAACAAA-AGAATAATATA
5873371 TTA
1 TTA
5873374 TTTTTGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (30 bp):
TTAATTAAATAAAAACAAAAGAATAATATA
Found at i:5873434 original size:85 final size:88
Alignment explanation
Indices: 5873344--5873511 Score: 218
Period size: 85 Copynumber: 1.9 Consensus size: 88
5873334 TAATATATTA
* * * * * *
5873344 ATTAAATAAAA-AAAATATAATTATATATTATTTT-TGAAATCAGTAAAATA-ATTGAACAAAAT
1 ATTAAACAAAATAAAA-ATAATCATAGATTATTTTCTGAAATCAATAAAATATATTAAACAAAAC
*
5873406 ATAAA-ATAAGTGATGAATCATGC
65 AGAAATATAAGTGATGAATCATGC
* *
5873429 ATTAAACAAAATAAAAGTAATCATAGATTATTTTCTGAAATTAATAAAATATATTAAACAAAACA
1 ATTAAACAAAATAAAAATAATCATAGATTATTTTCTGAAATCAATAAAATATATTAAACAAAACA
5873494 GAAATATAAGTGATGAAT
66 GAAATATAAGTGATGAAT
5873512 ATAATTAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
85 25 0.36
86 18 0.26
87 14 0.20
88 13 0.19
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (88 bp):
ATTAAACAAAATAAAAATAATCATAGATTATTTTCTGAAATCAATAAAATATATTAAACAAAACA
GAAATATAAGTGATGAATCATGC
Found at i:5879170 original size:17 final size:18
Alignment explanation
Indices: 5879148--5879181 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5879138 TCAGCCGATC
5879148 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
5879165 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
5879182 CTAATAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:5896984 original size:35 final size:35
Alignment explanation
Indices: 5896908--5896987 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
5896898 AACACAATCA
*
5896908 TCAATTACATTCTAAACCCAAAAATCCAAAATGTT
1 TCAATTACATTCTAAACCCAAAAATCCAAAATCTT
* *
5896943 TCAATTACATTCTAAACCTC-AAATTCCTAAATACTT
1 TCAATTACATTCTAAACC-CAAAAATCCAAAAT-CTT
5896979 T-AATTACAT
1 TCAATTACAT
5896988 GCCAACCCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
35 36 0.90
36 4 0.10
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCAAAAATCCAAAATCTT
Found at i:5897438 original size:148 final size:146
Alignment explanation
Indices: 5897164--5897454 Score: 476
Period size: 148 Copynumber: 2.0 Consensus size: 146
5897154 AAATACTCAA
*
5897164 TTCAGTTTATAAAATAGTTGACTCAAACATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTAACTCAAACATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
* * * * *
5897229 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTTATTATAAATATTTATCATATTATAATAT
66 GAATTGAATTGAATTTTCGAGTCTCAGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
5897294 TATTTGATTCTAATTCAG
131 T-TTT-ATTCTAATTCAG
* *
5897312 TTCAGTTTATAAAATAGTTAACTCGAAA-TTTTTTCGATTTGATTTTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAGTTAACTC-AAACATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGT
5897376 CGAATTGAATTGAATTTTCGAGTCTCAGTTTAAATTTAATTATAAATATTTATAATACTATAATA
65 CGAATTGAATTGAATTTTCGAGTCTCAGTTTAAATTTAATTATAAATATTTATAATACTATAATA
5897441 TTTTTATTCTAATT
130 TTTTTATTCTAATT
5897455 TAAATAGTTT
Statistics
Matches: 134, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
146 9 0.07
147 3 0.02
148 119 0.89
149 3 0.02
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (146 bp):
TTCAGTTTATAAAATAGTTAACTCAAACATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
GAATTGAATTGAATTTTCGAGTCTCAGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
TTTTATTCTAATTCAG
Found at i:5897989 original size:35 final size:34
Alignment explanation
Indices: 5897934--5898028 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 34
5897924 AATGAATTAT
* *
5897934 GAATTTGGGGTTGAGCATGTAATTGAAATATTTTA
1 GAATTT-GGGTTTAGAATGTAATTGAAATATTTTA
* *
5897969 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
1 GAATTTG-GGTTTAGAATGTAATTGAAATATTTTA
*
5898004 GAATTTGGGTTTAAAATGTAATTGA
1 GAATTTGGGTTTAGAATGTAATTGA
5898029 TGACTGTGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
34 18 0.33
35 36 0.67
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (34 bp):
GAATTTGGGTTTAGAATGTAATTGAAATATTTTA
Found at i:5908698 original size:22 final size:22
Alignment explanation
Indices: 5908673--5908728 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
5908663 TATTATTTAT
5908673 TATTATAAATATATTC-CAA-TAA
1 TATTATAAATATA--CACAATTAA
5908695 TATTATGAAAT-TACACAATTAA
1 TATTAT-AAATATACACAATTAA
5908717 TATTATAAATAT
1 TATTATAAATAT
5908729 TTTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 1 0.03
21 7 0.23
22 18 0.60
23 4 0.13
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (22 bp):
TATTATAAATATACACAATTAA
Found at i:5912037 original size:17 final size:17
Alignment explanation
Indices: 5912000--5912037 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5911990 ACACTCAAAT
*
5912000 AATTTTTTTTATTTTTG
1 AATTTTTTTTATTTTTC
5912017 AATTTTTTTGTA-TTTTC
1 AATTTTTTT-TATTTTTC
5912034 AATT
1 AATT
5912038 AATTACCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (17 bp):
AATTTTTTTTATTTTTC
Found at i:5915389 original size:20 final size:18
Alignment explanation
Indices: 5915349--5915388 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5915339 AAATAAACAA
5915349 ATATTATTTATTATATAT
1 ATATTATTTATTATATAT
*
5915367 ATATATATTTATT-TATTT
1 ATAT-TATTTATTATATAT
5915385 ATAT
1 ATAT
5915389 AAATAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTATTTATTATATAT
Found at i:5916717 original size:3 final size:3
Alignment explanation
Indices: 5916709--5916772 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
5916699 GGCTTGTAAT
5916709 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5916755 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
5916773 ATATAAAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5917248 original size:113 final size:113
Alignment explanation
Indices: 5917044--5917598 Score: 977
Period size: 113 Copynumber: 4.9 Consensus size: 113
5917034 AGAATCATGC
*
5917044 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
5917109 TATGAACTCGACATGGTAATGATGATCCATCGAATGATGAATTCAAGCG
65 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
5917158 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
5917223 ATGAATTCGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
5917271 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
5917336 ATGAACTTGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
5917384 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
5917449 ATGAACTCGACCTGGTAATGTTGATCCATCAAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
5917497 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
5917562 ATGAACTCGACCT-GAAATGTTGATCCATTGAATGATG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATG
5917599 GATTTGAACT
Statistics
Matches: 426, Mismatches: 15, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
112 21 0.05
113 400 0.94
114 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:5918031 original size:22 final size:22
Alignment explanation
Indices: 5918006--5918060 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
5917996 GATAAAGCTT
*
5918006 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
5918028 TCATCTTTAAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5918050 TCATCTTTGAA
1 TCATCTTTGAA
5918061 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5920950 original size:114 final size:114
Alignment explanation
Indices: 5920750--5920969 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
5920740 GATCATGCAG
* * * *
5920750 TTCATCTTTCAATTCCAATGATTGGTTCTAGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
5920815 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
5920864 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
5920929 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
5920970 CGAGAACGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:5925012 original size:14 final size:14
Alignment explanation
Indices: 5924995--5925060 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
5924985 GTAATTATGG
5924995 AAATATGCAAATGT
1 AAATATGCAAATGT
**
5925009 AAATA--CAAACAT
1 AAATATGCAAATGT
*
5925021 AAAAATGCAAATGT
1 AAATATGCAAATGT
**
5925035 AAATATGTGAATGT
1 AAATATGCAAATGT
5925049 AACA-ATGCAAAT
1 AA-ATATGCAAAT
5925061 TGTATAATAC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
12 9 0.23
14 29 0.74
15 1 0.03
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (14 bp):
AAATATGCAAATGT
Found at i:5925120 original size:8 final size:8
Alignment explanation
Indices: 5925107--5925136 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5925097 ACAATGAAAA
5925107 ATGCAAAG
1 ATGCAAAG
5925115 ATGCAAAG
1 ATGCAAAG
5925123 ATGCAAA-
1 ATGCAAAG
5925130 ATGCAAA
1 ATGCAAA
5925137 TGCATGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (8 bp):
ATGCAAAG
Found at i:5925128 original size:16 final size:15
Alignment explanation
Indices: 5925093--5925136 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5925083 AAGAGTATAA
* *
5925093 ATGCACAATG-AAAA
1 ATGCAAAATGCAAAG
5925107 ATGCAAAGATGCAAAG
1 ATGCAAA-ATGCAAAG
5925123 ATGCAAAATGCAAA
1 ATGCAAAATGCAAA
5925137 TGCATGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 6 0.23
15 10 0.38
16 10 0.38
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAG
Found at i:5926708 original size:28 final size:27
Alignment explanation
Indices: 5926646--5926699 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
5926636 ATACTTGCAA
* *
5926646 ATAAAATAAAATAATATATATAAATACT
1 ATAAAA-ATAATAATATATATAAAAACT
5926674 ATAAAAATAATAAGTATATATAAAAA
1 ATAAAAATAATAA-TATATATAAAAA
5926700 TTTTGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (27 bp):
ATAAAAATAATAATATATATAAAAACT
Found at i:5927520 original size:20 final size:18
Alignment explanation
Indices: 5927480--5927519 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5927470 AAATAAACAA
5927480 ATATTATTTATTATATAT
1 ATATTATTTATTATATAT
*
5927498 ATATATATTTATT-TATTT
1 ATAT-TATTTATTATATAT
5927516 ATAT
1 ATAT
5927520 AAATAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTATTTATTATATAT
Found at i:5928830 original size:3 final size:3
Alignment explanation
Indices: 5928822--5928868 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
5928812 GGCTTGTAAT
* *
5928822 TAA TAA TAAA TAA TAA TAA TAA TAA TAAA TAA TAA AAA AAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
5928869 ATATAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:5928843 original size:16 final size:16
Alignment explanation
Indices: 5928822--5928868 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
5928812 GGCTTGTAAT
5928822 TAATAATAAATAATAA
1 TAATAATAAATAATAA
5928838 TAATAAT-AATAAATAA
1 TAATAATAAAT-AATAA
*
5928854 TAA-AAAAAATAATAA
1 TAATAATAAATAATAA
5928869 ATATAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAATAAATAATAA
Found at i:5928871 original size:16 final size:16
Alignment explanation
Indices: 5928829--5928878 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
5928819 AATTAATAAT
*
5928829 AAATAAT-AATAATAA
1 AAATAATAAATAAAAA
*
5928844 TAATAA-ATAATAAAAA
1 AAATAATA-AATAAAAA
5928860 AAATAATAAATATAAAA
1 AAATAATAAATA-AAAA
5928877 AA
1 AA
5928879 CCAAATGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.18
16 16 0.57
17 7 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATAAATAAAAA
Found at i:5928878 original size:19 final size:19
Alignment explanation
Indices: 5928823--5928878 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
5928813 GCTTGTAATT
* *
5928823 AATAATAAATAATAATAAT
1 AATAATAAATAATAAAAAA
5928842 AATAATAAATAATAAAAAA
1 AATAATAAATAATAAAAAA
5928861 AATAATAAAT-ATAAAAAA
1 AATAATAAATAATAAAAAA
5928879 CCAAATGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 8 0.23
19 27 0.77
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AATAATAAATAATAAAAAA
Found at i:5946794 original size:23 final size:21
Alignment explanation
Indices: 5946754--5946796 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
5946744 TTATTTATTT
5946754 AAATTATTAATTTTATCAATC
1 AAATTATTAATTTTATCAATC
*
5946775 AAATTACTTCATTGTTATCAAT
1 AAATTA-TTAATT-TTATCAAT
5946797 TATATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTATTAATTTTATCAATC
Found at i:5946921 original size:11 final size:11
Alignment explanation
Indices: 5946905--5946937 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5946895 GTATTTTATC
5946905 AATTTAAATTT
1 AATTTAAATTT
5946916 AATTTAAATTT
1 AATTTAAATTT
5946927 AA--TAAATTT
1 AATTTAAATTT
5946936 AA
1 AA
5946938 CTAGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:5947106 original size:17 final size:18
Alignment explanation
Indices: 5947084--5947117 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5947074 AGGTTAACAA
*
5947084 TATTTT-TTGTTAAAAAC
1 TATTTTATTGATAAAAAC
5947101 TATTTTATTGATAAAAA
1 TATTTTATTGATAAAAA
5947118 TAAGGTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (18 bp):
TATTTTATTGATAAAAAC
Found at i:5953525 original size:32 final size:32
Alignment explanation
Indices: 5953478--5953544 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
5953468 CAAACTCTGA
* * *
5953478 TCTATAACTTCCACACGAGCTGCCTCATTCAT
1 TCTAGAACTTCCACACGAGCTGCATCACTCAT
*
5953510 TCTAGAACTTTCACACGAGCTGCATCACTCAT
1 TCTAGAACTTCCACACGAGCTGCATCACTCAT
5953542 TCT
1 TCT
5953545 CTCAATAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.31
Consensus pattern (32 bp):
TCTAGAACTTCCACACGAGCTGCATCACTCAT
Found at i:5960223 original size:12 final size:13
Alignment explanation
Indices: 5960206--5960234 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5960196 ATTCAACCAA
5960206 AAAATAAAA-AAT
1 AAAATAAAAGAAT
5960218 AAAATAAAAGAAT
1 AAAATAAAAGAAT
5960231 AAAA
1 AAAA
5960235 AAGTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAATAAAAGAAT
Found at i:5961515 original size:41 final size:41
Alignment explanation
Indices: 5961427--5961571 Score: 141
Period size: 41 Copynumber: 3.6 Consensus size: 41
5961417 TATAGCGGCG
* * * * * *
5961427 TAAAAACGCCGCAAAATACT-ATACTTTAGTGGCGTTTGTA
1 TAAAAACGCCGCTAAAGACTCGTAATGTAGTGGCGTTTTTA
*
5961467 TAAAAACGCCGCTAAAGAATCGTAATGTAGTGGCGTTTTTA
1 TAAAAACGCCGCTAAAGACTCGTAATGTAGTGGCGTTTTTA
* * * * *
5961508 TACAAACGCCGCTATAA-ACTAGTATTTTAGTGGTGTTTTTA
1 TAAAAACGCCGCTA-AAGACTCGTAATGTAGTGGCGTTTTTA
* *
5961549 TATAAACGCCGCTATAGACTCGT
1 TAAAAACGCCGCTAAAGACTCGT
5961572 TTTTATATAA
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
40 18 0.21
41 66 0.77
42 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (41 bp):
TAAAAACGCCGCTAAAGACTCGTAATGTAGTGGCGTTTTTA
Found at i:5963931 original size:2 final size:2
Alignment explanation
Indices: 5963887--5963917 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5963877 AACACCTAAT
5963887 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 T
5963918 TTCTCCTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 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):
TA
Found at i:5964870 original size:20 final size:19
Alignment explanation
Indices: 5964845--5964883 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
5964835 TTTCAGATTT
*
5964845 ATATCATTTTGTTTTATAAA
1 ATATCATTTTATTTT-TAAA
5964865 ATATCATTTTATTTTTAAA
1 ATATCATTTTATTTTTAAA
5964884 TTGTCTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (19 bp):
ATATCATTTTATTTTTAAA
Found at i:5968036 original size:37 final size:38
Alignment explanation
Indices: 5967994--5968076 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
5967984 AGAAATGTAA
**
5967994 TAAAATCACAAAT-TTTAGAGAAAAAGTT-TATAAAAGC
1 TAAAATCACAAATGTAAAGAG-AAAAGTTATATAAAAGC
* *
5968031 TAAAATCTCAAATGTAAAGAGAAAATTTATATAAAAGC
1 TAAAATCACAAATGTAAAGAGAAAAGTTATATAAAAGC
5968069 TAAAATCA
1 TAAAATCA
5968077 TATTAACGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 18 0.46
38 21 0.54
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (38 bp):
TAAAATCACAAATGTAAAGAGAAAAGTTATATAAAAGC
Found at i:5974156 original size:30 final size:29
Alignment explanation
Indices: 5974116--5974172 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
5974106 ACAACAGACA
*
5974116 ATTTTTAATAC-ATATATTATTTTATTTAAG
1 ATTTTAAATACTATA-ATT-TTTTATTTAAG
*
5974146 ATTTTAAATACTTTAATTTTTTATTTA
1 ATTTTAAATACTATAATTTTTTATTTA
5974173 CATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 13 0.54
31 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTAAATACTATAATTTTTTATTTAAG
Found at i:5985818 original size:2 final size:2
Alignment explanation
Indices: 5985811--5985851 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5985801 TACGAAAATG
5985811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5985852 AATGAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5997180 original size:10 final size:10
Alignment explanation
Indices: 5997165--5997194 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
5997155 GCATGAACCT
5997165 AAATAATTTA
1 AAATAATTTA
5997175 AAATAATTTA
1 AAATAATTTA
5997185 AAATATATTT
1 AAATA-ATTT
5997195 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATAATTTA
Found at i:6006064 original size:2 final size:2
Alignment explanation
Indices: 6006057--6006083 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6006047 CCCCCACACC
6006057 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6006084 AGATAAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6007734 original size:30 final size:32
Alignment explanation
Indices: 6007662--6007741 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
6007652 AAATAACAAT
* *
6007662 ATTTTAGGCACTGAAC-TTTAGAATTGTATTA
1 ATTTTAGGCACTAAACTTTTAGAATAGTATTA
*
6007693 ATTTTA-CCACTAAACTTTTA-AA-AG-ATTCA
1 ATTTTAGGCACTAAACTTTTAGAATAGTATT-A
6007722 ATTTTAGGCACTAAACTTTT
1 ATTTTAGGCACTAAACTTTT
6007742 TTGACAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 3 0.07
29 8 0.19
30 21 0.50
31 10 0.24
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (32 bp):
ATTTTAGGCACTAAACTTTTAGAATAGTATTA
Found at i:6010984 original size:18 final size:18
Alignment explanation
Indices: 6010961--6010995 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6010951 GCATGGATCT
6010961 AAATTACCATCTCTCCAC
1 AAATTACCATCTCTCCAC
6010979 AAATTACCATCTCTCCA
1 AAATTACCATCTCTCCA
6010996 TCTTGTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATTACCATCTCTCCAC
Found at i:6019777 original size:17 final size:17
Alignment explanation
Indices: 6019755--6019787 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6019745 AGTCATTTAA
6019755 TAAACTTGAACTTAATT
1 TAAACTTGAACTTAATT
*
6019772 TAAACTTGAATTTAAT
1 TAAACTTGAACTTAAT
6019788 AGGAATACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (17 bp):
TAAACTTGAACTTAATT
Found at i:6022807 original size:232 final size:219
Alignment explanation
Indices: 6022458--6022920 Score: 665
Period size: 232 Copynumber: 2.1 Consensus size: 219
6022448 AGTGTGATAT
* *
6022458 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGGCCCGAAAATATATATAATTTTAC
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTAC
* * * * *
6022523 CTTATATATTTAGGGATAATTACAATAATACCCCTCTATATATATTTTTTCAATTAAGTCACTGT
66 CTTATATATTTAGGAATAATTACAATAATACCCATATATATATATATTTTCAATTAAATCACTGT
*
6022588 TTTTATTAAATAAAAATAATTGTTTTATTATTTCGGGTATGGTCTGGTCGGATTTCTAATTCATA
131 TTTTATTAAATAAAAATAATTGTTTTATTATTTC----A-GGTCGGGTCGGATTTCTAATTCATA
6022653 TATTCGGGTCGGGTCGGGTGAAACTTTATTTTGG
191 TA-T----TCGGGTCGGGTGAAACTTTATTTTGG
* *
6022687 TCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCTAAAAATATATAGTTT
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGA---AAAAATATATAATTT
* *
6022752 TACCTTATATATTTAGGAATAATTACAATAATATCCATATATATATATATTTTCAATTAAATCAT
63 TACCTTATATATTTAGGAATAATTACAATAATACCCATATATATATATATTTTCAATTAAATCAC
* * * *
6022817 TGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCAGGTCGGGTCGGGTTTCTTATTCATATA
128 TGTTTTTATTAAATAAAAATAATTGTTTTATTATTTCAGGTCGGGTCGGATTTCTAATTCATATA
6022882 TTCGGGTCGGGTGAAACTTTATTTTGG
193 TTCGGGTCGGGTGAAACTTTATTTTGG
6022909 TCGGGTCGGGTC
1 TCGGGTCGGGTC
6022921 TCGGATGGAG
Statistics
Matches: 215, Mismatches: 16, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
222 38 0.18
226 1 0.00
227 24 0.11
228 1 0.00
229 45 0.21
232 106 0.49
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (219 bp):
TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTAC
CTTATATATTTAGGAATAATTACAATAATACCCATATATATATATATTTTCAATTAAATCACTGT
TTTTATTAAATAAAAATAATTGTTTTATTATTTCAGGTCGGGTCGGATTTCTAATTCATATATTC
GGGTCGGGTGAAACTTTATTTTGG
Found at i:6024650 original size:11 final size:11
Alignment explanation
Indices: 6024634--6024658 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6024624 GACCTACATG
6024634 AAAAAGAAAAA
1 AAAAAGAAAAA
6024645 AAAAAGAAAAA
1 AAAAAGAAAAA
6024656 AAA
1 AAA
6024659 GAGTGTATCA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:6028827 original size:18 final size:20
Alignment explanation
Indices: 6028804--6028842 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
6028794 AAATTTCCTT
*
6028804 TGTATCT-TTTTTCT-AAAC
1 TGTATCTCTTATTCTGAAAC
6028822 TGTATCTCTTATTCTGAAAC
1 TGTATCTCTTATTCTGAAAC
6028842 T
1 T
6028843 TGCAAGCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (20 bp):
TGTATCTCTTATTCTGAAAC
Found at i:6036470 original size:33 final size:33
Alignment explanation
Indices: 6036431--6036511 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
6036421 TCTTTTGAAC
6036431 AGGGATTGCATGTTCTTTCTTTCTTTTCGGACA
1 AGGGATTGCATGTTCTTTCTTTCTTTTCGGACA
*
6036464 AGGGATTGCATGTTCTTTCTTTCTTTTCGGGCA
1 AGGGATTGCATGTTCTTTCTTTCTTTTCGGACA
6036497 AGGGATTGCATGTTC
1 AGGGATTGCATGTTC
6036512 ATTTAACTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (33 bp):
AGGGATTGCATGTTCTTTCTTTCTTTTCGGACA
Found at i:6038999 original size:23 final size:22
Alignment explanation
Indices: 6038968--6039011 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
6038958 GTTTTCTCCG
6038968 TTATATTTTTATAT-TTTTAACA
1 TTATATTTTTA-ATCTTTTAACA
6038990 TTATATTTTTTAATCTTTTAAC
1 TTATA-TTTTTAATCTTTTAAC
6039012 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATATTTTTAATCTTTTAACA
Found at i:6042753 original size:57 final size:57
Alignment explanation
Indices: 6042634--6042779 Score: 159
Period size: 57 Copynumber: 2.6 Consensus size: 57
6042624 TTTTAGGATC
* *
6042634 CTCAGAATTGGTTTCCTCCACAATTGAAGCTTTTACGACACCAGAGTTTTCAAGATT
1 CTCAGAATTGGTTTCCTCCCCAGTTGAAGCTTTTACGACACCAGAGTTTTCAAGATT
* ** ** ***
6042691 CTCAGAACTGGTTTCCTCCCCAGTTGAAGCTTTTGTGACGTCAGAGTTTTTGGGATT
1 CTCAGAATTGGTTTCCTCCCCAGTTGAAGCTTTTACGACACCAGAGTTTTCAAGATT
* * *
6042748 TTCAGAATTGATTT-CTACCCCAGTCGAAGCTT
1 CTCAGAATTGGTTTCCT-CCCCAGTTGAAGCTT
6042780 CGGCTTCGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
56 2 0.03
57 72 0.97
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (57 bp):
CTCAGAATTGGTTTCCTCCCCAGTTGAAGCTTTTACGACACCAGAGTTTTCAAGATT
Found at i:6049247 original size:32 final size:31
Alignment explanation
Indices: 6049202--6049286 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
6049192 AGAAAGTTCG
* * *
6049202 GGGCCACAGGGCCTACCTAAGAACACATCTTA
1 GGGCCGCAAGGCCTACCTAAGAA-ACATCTCA
** **
6049234 GGGCCGCAAGGCCTACCCGAGAATGATCTCA
1 GGGCCGCAAGGCCTACCTAAGAAACATCTCA
6049265 GGGCCGC-AGAGCCTACCTAAGA
1 GGGCCGCAAG-GCCTACCTAAGA
6049287 GTCACATTAG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
30 2 0.05
31 22 0.51
32 19 0.44
ACGTcount: A:0.28, C:0.32, G:0.27, T:0.13
Consensus pattern (31 bp):
GGGCCGCAAGGCCTACCTAAGAAACATCTCA
Found at i:6054524 original size:16 final size:16
Alignment explanation
Indices: 6054503--6054535 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6054493 ACCAAAAAAT
6054503 TATAATTAT-ATGATTA
1 TATAA-TATCATGATTA
6054519 TATAATATCATGATTA
1 TATAATATCATGATTA
6054535 T
1 T
6054536 TAGTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
TATAATATCATGATTA
Found at i:6054858 original size:23 final size:22
Alignment explanation
Indices: 6054807--6054860 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
6054797 AAACTGATAA
6054807 TTTAAAAAAAATTATATAAAAT
1 TTTAAAAAAAATTATATAAAAT
** * *
6054829 TAAAAAAATAAATTATATATATT
1 TTTAAAAA-AAATTATATAAAAT
6054852 TTTAAAAAA
1 TTTAAAAAA
6054861 CACACATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAAAAAATTATATAAAAT
Found at i:6056964 original size:20 final size:20
Alignment explanation
Indices: 6056927--6056964 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6056917 TTTTATGGGT
*
6056927 TTTAATAATATATAATAAGA
1 TTTAATAATATAAAATAAGA
6056947 TTTAA-AATATAAACATAA
1 TTTAATAATATAAA-ATAA
6056965 TAGTTAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
TTTAATAATATAAAATAAGA
Found at i:6060558 original size:23 final size:23
Alignment explanation
Indices: 6060508--6060563 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
6060498 TTCGTGAACA
* *
6060508 CTAAAAGAATATATTCATAAACG
1 CTAAACGAACATATTCATAAACG
* *
6060531 TTAAACGAACATATTCATAAATG
1 CTAAACGAACATATTCATAAACG
6060554 CTAAACGAAC
1 CTAAACGAAC
6060564 TAACACAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (23 bp):
CTAAACGAACATATTCATAAACG
Found at i:6064257 original size:14 final size:14
Alignment explanation
Indices: 6064238--6064265 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6064228 CTTCTAAGAA
6064238 AGTTAAGCAACAGC
1 AGTTAAGCAACAGC
6064252 AGTTAAGCAACAGC
1 AGTTAAGCAACAGC
6064266 TTGATCCATT
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:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
AGTTAAGCAACAGC
Found at i:6066764 original size:2 final size:2
Alignment explanation
Indices: 6066759--6066821 Score: 69
Period size: 2 Copynumber: 32.0 Consensus size: 2
6066749 ACACACACAC
**
6066759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT -T CG AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T
6066801 -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
6066822 CGGACTCTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.06
2 49 0.92
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6068773 original size:35 final size:35
Alignment explanation
Indices: 6068700--6068774 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
6068690 CGTCACGTCC
**
6068700 AGTAAGGCCCTGAGCACAAAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAACCGCCA
* * * *
6068735 AGTAAGGCCCTGAGCACACAGCCGATGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAACCGCCA
6068770 AGTAA
1 AGTAA
6068775 TCTTCCTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAACCGCCA
Found at i:6068963 original size:24 final size:24
Alignment explanation
Indices: 6068844--6068966 Score: 149
Period size: 24 Copynumber: 5.1 Consensus size: 24
6068834 ATCAAAACAT
* *
6068844 AATCCAGGTCAAGTATGAGATCAA
1 AATCCAGGTCAAGTATCAGATCAG
*
6068868 AATCCAGGTCAAGTATCATATCAG
1 AATCCAGGTCAAGTATCAGATCAG
* *
6068892 AATCCAAGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAG
**
6068916 AATCCCTGTC-AGATATCAGATCAG
1 AATCCAGGTCAAG-TATCAGATCAG
* *
6068940 AATCCATGTCAAGTATCATATCAG
1 AATCCAGGTCAAGTATCAGATCAG
6068964 AAT
1 AAT
6068967 TTAAATTGAA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.02
24 82 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:6080371 original size:17 final size:17
Alignment explanation
Indices: 6080349--6080383 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6080339 TGGGTCTCAT
6080349 TAAACTGATGTTAAGTG
1 TAAACTGATGTTAAGTG
6080366 TAAACTGATGTTAAGTG
1 TAAACTGATGTTAAGTG
6080383 T
1 T
6080384 GGAACATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (17 bp):
TAAACTGATGTTAAGTG
Found at i:6080694 original size:183 final size:183
Alignment explanation
Indices: 6080386--6080746 Score: 636
Period size: 183 Copynumber: 2.0 Consensus size: 183
6080376 TTAAGTGTGG
* *
6080386 AACATCAGTTTAAGAGAGGGATTGTTAAATAAATTAGTAGCAGTACACGTAAGAAAGGATTTGAG
1 AACATCAGTTTAAGAGAGGGATTGTTAAATAAATTAGTAGCAGCACACGTAAGAAAGAATTTGAG
*
6080451 TGTTCCTAGTCTTTAGGAGTTCAGTAGTTTGTTTTAATTTGTTTCCTAGTTAATAGGAGTTTGTT
66 TGTTCCTAGTCTTTAGGAGTTCAGTAGTTTGTTTAAATTTGTTTCCTAGTTAATAGGAGTTTGTT
*
6080516 GATGCACGTTGGATAGTGCCTATTTTCATGTTGCTTTCT-GTTATGTACCACAT
131 GATGCACGTTGGATAGTGACTATTTTCATGTTGCTTT-TAGTTATGTACCACAT
*
6080569 AACATCAGTTTAAGAGAGGGATTGTTAAATAAATTAGTAGCAGCACACGTAAGAAAGAATTTGGG
1 AACATCAGTTTAAGAGAGGGATTGTTAAATAAATTAGTAGCAGCACACGTAAGAAAGAATTTGAG
6080634 T-TGTCCTAGTCTTTAGGAGTTCAGTAGTTTGTTTAAATTTGTTTCCTAGTTAATAGGAGTTTGT
66 TGT-TCCTAGTCTTTAGGAGTTCAGTAGTTTGTTTAAATTTGTTTCCTAGTTAATAGGAGTTTGT
*
6080698 TTATGCACGTTGGATAGTGACTATTTTCATGTTGCTTTTAGTTATGTAC
130 TGATGCACGTTGGATAGTGACTATTTTCATGTTGCTTTTAGTTATGTAC
6080747 TTGTCTATTT
Statistics
Matches: 170, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
182 2 0.01
183 168 0.99
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.39
Consensus pattern (183 bp):
AACATCAGTTTAAGAGAGGGATTGTTAAATAAATTAGTAGCAGCACACGTAAGAAAGAATTTGAG
TGTTCCTAGTCTTTAGGAGTTCAGTAGTTTGTTTAAATTTGTTTCCTAGTTAATAGGAGTTTGTT
GATGCACGTTGGATAGTGACTATTTTCATGTTGCTTTTAGTTATGTACCACAT
Found at i:6081018 original size:23 final size:23
Alignment explanation
Indices: 6080992--6081035 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
6080982 TTATTTTTCG
6080992 TTTACAATTTTTT-TTACAAATAT
1 TTTA-AATTTTTTGTTACAAATAT
*
6081015 TTTAATTTTTTTGTTACAAAT
1 TTTAAATTTTTTGTTACAAAT
6081036 TTAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAAATTTTTTGTTACAAATAT
Found at i:6087901 original size:20 final size:20
Alignment explanation
Indices: 6087876--6087990 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
6087866 AATTGGGAAA
*
6087876 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6087896 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
6087916 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
6087937 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6087957 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
6087977 TTCGCAACGCGATA
1 ATCGCAACGCGATA
6087991 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:6087922 original size:61 final size:61
Alignment explanation
Indices: 6087855--6088004 Score: 153
Period size: 61 Copynumber: 2.5 Consensus size: 61
6087845 GAATAAGTAA
** * * * *
6087855 ATCGCAACGCGAAT-TGGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATAT-ACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * *
6087916 ATCGCAATGC-AATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGAAT-ATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* *
6087977 TTCGCAACGCG-ATAATACATAATCGCAA
1 ATCGCAACGCGAAT-ATACAAAATCGCAA
6088005 TGCAATTTTC
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
60 3 0.04
61 70 0.95
62 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (61 bp):
ATCGCAACGCGAATATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:6088203 original size:22 final size:22
Alignment explanation
Indices: 6088175--6088217 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6088165 CACTCTCTCA
6088175 CCATCTCCGACGAAATCCGTCC
1 CCATCTCCGACGAAATCCGTCC
*
6088197 CCATCTCCGGCGAAATCCGTC
1 CCATCTCCGACGAAATCCGTC
6088218 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.19
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCC
Found at i:6088523 original size:20 final size:20
Alignment explanation
Indices: 6088469--6088527 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
6088459 TTGCGATTCT
**
6088469 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
6088489 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
6088509 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
6088528 AGAAAACTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:6088719 original size:25 final size:24
Alignment explanation
Indices: 6088665--6088719 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
6088655 TGTTTATTAT
* *
6088665 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
6088689 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
6088715 TGTTT
1 TGTTT
6088720 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:6089841 original size:18 final size:18
Alignment explanation
Indices: 6089820--6089864 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
6089810 TCCACTTTGG
* *
6089820 GAGCCATCACCTCGCCTA
1 GAGCCATCACCTCACCCA
*
6089838 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
6089856 GAGCCATCA
1 GAGCCATCA
6089865 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:6090370 original size:20 final size:20
Alignment explanation
Indices: 6090345--6090390 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
6090335 TAGTTTACTT
6090345 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
6090365 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
6090385 TCGCAA
1 TCGCAA
6090391 TGCGAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:6090418 original size:14 final size:14
Alignment explanation
Indices: 6090399--6090455 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
6090389 AATGCGAATG
6090399 AAATCGCAACGACA
1 AAATCGCAACGACA
*
6090413 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
6090429 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
6090445 AAATCGCAACG
1 AAATCGCAACG
6090456 CGAATGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:6090436 original size:32 final size:31
Alignment explanation
Indices: 6090384--6090470 Score: 156
Period size: 32 Copynumber: 2.8 Consensus size: 31
6090374 GGAAATGGCT
6090384 ATCGCAATGCGAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAATGAAATCGCAACGACAAA
6090415 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCG-AATGAAATCGCAACGACAAA
*
6090447 ATCGCAACGCGAATGAAATCGCAA
1 ATCGCAATGCGAATGAAATCGCAA
6090471 TGCGATTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
31 24 0.44
32 30 0.56
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (31 bp):
ATCGCAATGCGAATGAAATCGCAACGACAAA
Found at i:6090506 original size:14 final size:14
Alignment explanation
Indices: 6090487--6090544 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
6090477 TTATGTTTCG
6090487 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
6090501 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
6090517 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
6090533 CGTTGCGATTTT
1 CGTTGCGATTTT
6090545 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:6090525 original size:32 final size:33
Alignment explanation
Indices: 6090482--6090560 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
6090472 GCGATTTATG
*
6090482 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
6090514 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
6090547 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
6090561 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:6090567 original size:19 final size:20
Alignment explanation
Indices: 6090545--6090588 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6090535 TTGCGATTTT
6090545 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
6090564 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
6090584 CATTT
1 CATTT
6090589 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:6090596 original size:20 final size:20
Alignment explanation
Indices: 6090554--6090600 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
6090544 TCATTTCGCA
*
6090554 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
6090574 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
6090594 TTGCGAT
1 TTGCGAT
6090601 TTTAAGTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:6092604 original size:20 final size:20
Alignment explanation
Indices: 6092575--6092612 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6092565 ATGTGAAGGC
6092575 AAAACAGACTATCGCAACAA
1 AAAACAGACTATCGCAACAA
*
6092595 AAAACTGACTATCGCAAC
1 AAAACAGACTATCGCAAC
6092613 GAGAGAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAACAGACTATCGCAACAA
Found at i:6092642 original size:19 final size:19
Alignment explanation
Indices: 6092618--6092682 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
6092608 GCAACGAGAG
6092618 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6092637 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6092656 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
6092670 AATCGCAATGCGA
1 AATCGCAATGCGA
6092683 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:6092730 original size:19 final size:20
Alignment explanation
Indices: 6092706--6092755 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
6092696 TTGCGATTTT
6092706 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
6092725 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
6092745 CGTTGCGATAG
1 CGTTGCGATAG
6092756 TCAAAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:6093768 original size:24 final size:24
Alignment explanation
Indices: 6093741--6093794 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6093731 GTATTCGAAA
*
6093741 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
6093765 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
6093789 TTTGAT
1 TTTGAT
6093795 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:6093986 original size:12 final size:12
Alignment explanation
Indices: 6093969--6093993 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6093959 ATATAATCCT
6093969 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6093981 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6093993 G
1 G
6093994 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:6096280 original size:20 final size:20
Alignment explanation
Indices: 6096250--6096306 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
6096240 CAATCATCTT
*
6096250 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
* *
6096270 AATTACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
6096289 AATGAAAATCGCAACGCG
1 AATGACTATCGCAACGCG
6096307 AATTTAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:6096339 original size:14 final size:14
Alignment explanation
Indices: 6096320--6096375 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
6096310 TTAATTTCGT
6096320 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
*
6096334 GTTGCGATTTTCATTTCGC
1 GTTGCGA--TTC---TCTC
6096353 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
6096367 GTTGCGATT
1 GTTGCGATT
6096376 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (14 bp):
GTTGCGATTCTCTC
Done.