Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 14 of 20
Found at i:5603676 original size:13 final size:13
Alignment explanation
Indices: 5603658--5603683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5603648 TCTCTCTCGT
5603658 TTTTTTTTTTGGG
1 TTTTTTTTTTGGG
5603671 TTTTTTTTTTGGG
1 TTTTTTTTTTGGG
5603684 AAAGCCAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGGG
Found at i:5607396 original size:11 final size:11
Alignment explanation
Indices: 5607377--5607408 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5607367 ATGCTAACAA
5607377 GTAATAATGAT
1 GTAATAATGAT
*
5607388 GTAACAATGAT
1 GTAATAATGAT
5607399 GTAATAATGA
1 GTAATAATGA
5607409 CTTGTGTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (11 bp):
GTAATAATGAT
Found at i:5621188 original size:2 final size:2
Alignment explanation
Indices: 5621181--5621205 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5621171 AGTTTAAACT
5621181 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 T
5621206 GTGATAACCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5635159 original size:2 final size:2
Alignment explanation
Indices: 5635148--5635207 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
5635138 TTTCTTTTTC
*
5635148 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
5635189 ACT CT CC CT CT CT CT CT CT
1 -CT CT CT CT CT CT CT CT CT
5635208 AGCTCTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.96
3 1 0.02
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5656093 original size:10 final size:10
Alignment explanation
Indices: 5656063--5656112 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
5656053 ATTATATTAA
5656063 TATAATATAT
1 TATAATATAT
* *
5656073 TATTATTTAT
1 TATAATATAT
5656083 TATAATATA-
1 TATAATATAT
5656092 T-TAATATA-
1 TATAATATAT
5656100 T-TAATATAT
1 TATAATATAT
5656109 TATA
1 TATA
5656113 TCAACATGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 15 0.44
9 2 0.06
10 17 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATAATATAT
Found at i:5656098 original size:8 final size:8
Alignment explanation
Indices: 5656065--5656110 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
5656055 TATATTAATA
5656065 TAATATAT
1 TAATATAT
5656073 T-AT-TAT
1 TAATATAT
*
5656079 TTAT-TA-
1 TAATATAT
5656085 TAATATAT
1 TAATATAT
5656093 TAATATAT
1 TAATATAT
5656101 TAATATAT
1 TAATATAT
5656109 TA
1 TA
5656111 TATCAACATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 7 0.21
7 8 0.24
8 19 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TAATATAT
Found at i:5656183 original size:17 final size:17
Alignment explanation
Indices: 5656161--5656194 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5656151 AACTTTTACT
*
5656161 TATAAAAATTTACTTAA
1 TATAAAAATTTAATTAA
5656178 TATAAAAATTTAATTAA
1 TATAAAAATTTAATTAA
5656195 ACATATTAAA
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:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAAAATTTAATTAA
Found at i:5690665 original size:29 final size:29
Alignment explanation
Indices: 5690633--5690704 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
5690623 GTGAAAAGGC
*
5690633 ACAAGAAAAAAAGCTATACATGAACATGT
1 ACAAGAAAAAAAGCTATACATGAACAAGT
* *
5690662 ACAA-AATAAGAAGCTATACGTGAACAAGT
1 ACAAGAA-AAAAAGCTATACATGAACAAGT
*
5690691 ACTAGAAAAGAAAG
1 ACAAGAAAA-AAAG
5690705 TGTATGTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 28 0.80
30 5 0.14
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (29 bp):
ACAAGAAAAAAAGCTATACATGAACAAGT
Found at i:5690940 original size:35 final size:35
Alignment explanation
Indices: 5690901--5690978 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
5690891 ATATAAAGTG
* * * *
5690901 GTTATTTTGTGTGAAGTAGTGCATCACTTGTTTTA
1 GTTATTCTGTATGAAGTAATACATCACTTGTTTTA
**
5690936 GTTATTCTGTATGAAGTAATATTTCACTTGTTTTA
1 GTTATTCTGTATGAAGTAATACATCACTTGTTTTA
*
5690971 GTTGTTCT
1 GTTATTCT
5690979 CATTATTCTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (35 bp):
GTTATTCTGTATGAAGTAATACATCACTTGTTTTA
Found at i:5698444 original size:2 final size:2
Alignment explanation
Indices: 5698432--5698463 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5698422 TTCCCACAGA
*
5698432 AT AT TT 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
5698464 TCTTGATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5698907 original size:21 final size:21
Alignment explanation
Indices: 5698883--5698924 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5698873 CATGGCGGTG
5698883 TCTGCAATATGCAGTCTGCAC
1 TCTGCAATATGCAGTCTGCAC
* * *
5698904 TCTGCAGTCTGGAGTCTGCAC
1 TCTGCAATATGCAGTCTGCAC
5698925 CTATGCGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (21 bp):
TCTGCAATATGCAGTCTGCAC
Found at i:5700975 original size:2 final size:2
Alignment explanation
Indices: 5700968--5700996 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5700958 TTGATTGAGA
5700968 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
5700997 AAAGAATTCT
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:5701504 original size:131 final size:135
Alignment explanation
Indices: 5701229--5701504 Score: 443
Period size: 131 Copynumber: 2.0 Consensus size: 135
5701219 TAATTTACAA
5701229 AGATTTATACCATGACACCATTGACATGTTTCATATTCCCCATTACACACACGTCCGCCCACTTA
1 AGATTTATACCATGACACCATTGACATGTTTCATATTCCCCATTACACACAC-TCCGCCCACTTA
5701294 TTATAGTCGGCATCATACACACACATACATATATATATATATATAATGTTTTATTGAATATCATC
65 TTATAGTCGGCATCATA-ACACACA-ACA-ATATATATATATATAATGTTTTATTGAATATCATC
*
5701359 TGTTGAGTT
127 TGTTGAATT
* * * *
5701368 AGATTTATACCATGACATCATTGACGTGTTTCATATTCCCCATTATACACA-TCCGTCCACTTAT
1 AGATTTATACCATGACACCATTGACATGTTTCATATTCCCCATTACACACACTCCGCCCACTTAT
5701432 TATAGTCGGCATCAT-ACACAC-AC-ATATATATATATATAATGTTTTATTGAATATCATCTGTT
66 TATAGTCGGCATCATAACACACAACAATATATATATATATAATGTTTTATTGAATATCATCTGTT
5701494 GAATT
131 GAATT
5701499 AGATTT
1 AGATTT
5701505 GTTATCTAAT
Statistics
Matches: 132, Mismatches: 5, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
131 49 0.37
133 2 0.02
135 6 0.05
137 27 0.20
139 48 0.36
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (135 bp):
AGATTTATACCATGACACCATTGACATGTTTCATATTCCCCATTACACACACTCCGCCCACTTAT
TATAGTCGGCATCATAACACACAACAATATATATATATATAATGTTTTATTGAATATCATCTGTT
GAATT
Found at i:5704243 original size:8 final size:8
Alignment explanation
Indices: 5704230--5704254 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5704220 GAACACTTAT
5704230 ATATATAC
1 ATATATAC
5704238 ATATATAC
1 ATATATAC
5704246 ATATATAC
1 ATATATAC
5704254 A
1 A
5704255 GGGAGAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:5708893 original size:15 final size:15
Alignment explanation
Indices: 5708873--5708903 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5708863 CTCTTTCCCT
5708873 TATTTAGTAGAGGCA
1 TATTTAGTAGAGGCA
5708888 TATTTAGTAGAGGCA
1 TATTTAGTAGAGGCA
5708903 T
1 T
5708904 CAAGGATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (15 bp):
TATTTAGTAGAGGCA
Found at i:5712914 original size:2 final size:2
Alignment explanation
Indices: 5712907--5712942 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5712897 TTCAATACGT
5712907 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5712943 CCGCCTTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5723204 original size:19 final size:18
Alignment explanation
Indices: 5723176--5723212 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5723166 AATCAAGAAC
5723176 AAAGAAAGAAAGAAGAGA
1 AAAGAAAGAAAGAAGAGA
*
5723194 AAAGAAAAGAATGAAGAGA
1 AAAG-AAAGAAAGAAGAGA
5723213 GAGACAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (18 bp):
AAAGAAAGAAAGAAGAGA
Found at i:5735319 original size:20 final size:23
Alignment explanation
Indices: 5735280--5735324 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5735270 TATTTAACTG
5735280 TTTATATTTAATGCATTAT-AGT
1 TTTATATTTAATGCATTATAAGT
*
5735302 TTTATATTT-A-GTATTATAAGT
1 TTTATATTTAATGCATTATAAGT
5735323 TT
1 TT
5735325 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTATATTTAATGCATTATAAGT
Found at i:5737398 original size:9 final size:9
Alignment explanation
Indices: 5737366--5737441 Score: 82
Period size: 9 Copynumber: 8.4 Consensus size: 9
5737356 TGAAGAAAGA
5737366 AGCATCAGC
1 AGCATCAGC
*
5737375 ATCATCA-C
1 AGCATCAGC
*
5737383 GAACATCAGC
1 -AGCATCAGC
5737393 AGCATCAGC
1 AGCATCAGC
* *
5737402 ATCATCAGG
1 AGCATCAGC
*
5737411 AACATCAGC
1 AGCATCAGC
5737420 AGCATCAGC
1 AGCATCAGC
*
5737429 AACATCAGC
1 AGCATCAGC
5737438 AGCA
1 AGCA
5737442 GCATCGATGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
8 1 0.02
9 53 0.96
10 1 0.02
ACGTcount: A:0.38, C:0.32, G:0.17, T:0.13
Consensus pattern (9 bp):
AGCATCAGC
Found at i:5737407 original size:18 final size:18
Alignment explanation
Indices: 5737366--5737441 Score: 91
Period size: 18 Copynumber: 4.2 Consensus size: 18
5737356 TGAAGAAAGA
*
5737366 AGCATCAGCATCATCA-C
1 AGCATCAGCAACATCAGC
* *
5737383 GAACATCAGCAGCATCAGC
1 -AGCATCAGCAACATCAGC
* *
5737402 ATCATCAGGAACATCAGC
1 AGCATCAGCAACATCAGC
5737420 AGCATCAGCAACATCAGC
1 AGCATCAGCAACATCAGC
5737438 AGCA
1 AGCA
5737442 GCATCGATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
18 49 0.98
19 1 0.02
ACGTcount: A:0.38, C:0.32, G:0.17, T:0.13
Consensus pattern (18 bp):
AGCATCAGCAACATCAGC
Found at i:5737436 original size:27 final size:27
Alignment explanation
Indices: 5737366--5737436 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
5737356 TGAAGAAAGA
*
5737366 AGCATCAGCATCATCACGAACATCAGC
1 AGCATCAGCATCATCAGGAACATCAGC
5737393 AGCATCAGCATCATCAGGAACATCAGC
1 AGCATCAGCATCATCAGGAACATCAGC
*
5737420 AGCATCAGCAACATCAG
1 AGCATCAGCATCATCAG
5737437 CAGCAGCATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.38, C:0.31, G:0.17, T:0.14
Consensus pattern (27 bp):
AGCATCAGCATCATCAGGAACATCAGC
Found at i:5739115 original size:14 final size:15
Alignment explanation
Indices: 5739098--5739127 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5739088 TATTTAACAT
5739098 AATAA-AAAATTAAA
1 AATAATAAAATTAAA
5739112 AATAATAAAATTAAA
1 AATAATAAAATTAAA
5739127 A
1 A
5739128 TCAACAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAATAAAATTAAA
Found at i:5741134 original size:12 final size:12
Alignment explanation
Indices: 5741117--5741146 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5741107 TAGCACCACC
5741117 CCACCACCTCCA
1 CCACCACCTCCA
5741129 CCACCACCTCCA
1 CCACCACCTCCA
5741141 CCACCA
1 CCACCA
5741147 TCTACACGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.67, G:0.00, T:0.07
Consensus pattern (12 bp):
CCACCACCTCCA
Found at i:5742430 original size:2 final size:2
Alignment explanation
Indices: 5742423--5742449 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5742413 AGCACTGCAC
5742423 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
5742450 TGGTACAAGC
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:5749633 original size:12 final size:12
Alignment explanation
Indices: 5749616--5749640 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5749606 CGTAAACCAA
5749616 TATTATTATTGT
1 TATTATTATTGT
5749628 TATTATTATTGT
1 TATTATTATTGT
5749640 T
1 T
5749641 GTTGTTTTTG
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTATTATTGT
Found at i:5751176 original size:13 final size:15
Alignment explanation
Indices: 5751144--5751174 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5751134 CTTTTAAGTT
*
5751144 TATTTTTATAAAATA
1 TATTTTAATAAAATA
5751159 TATTTTAATAAAATA
1 TATTTTAATAAAATA
5751174 T
1 T
5751175 TTGACAAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTAATAAAATA
Found at i:5758743 original size:2 final size:2
Alignment explanation
Indices: 5758736--5758765 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5758726 TCTTTTGCTT
5758736 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5758766 AAGAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5764766 original size:81 final size:80
Alignment explanation
Indices: 5764617--5764767 Score: 212
Period size: 81 Copynumber: 1.9 Consensus size: 80
5764607 CACTATTTGT
* * ** *
5764617 TTAATTATTTTCAGTTGATTGCTTTTGATGAATTTATTAATGTTAGGTGCAGAGAGTCGCAGGGC
1 TTAATTATCTTCACTTGATTGCTTCAGATGAATTTATAAATGTTAGGTGCAGAGAGTCGCAGGGC
5764682 AGATGGATTAATTGA
66 AGATGGATTAATTGA
* * * *
5764697 TTAATTATCTTCACTTGGTTGCTTCAGATGAATTATATAAATTTTAGGTGCAGAGTGTCTCAGGG
1 TTAATTATCTTCACTTGATTGCTTCAGATGAATT-TATAAATGTTAGGTGCAGAGAGTCGCAGGG
5764762 CAGATG
65 CAGATG
5764768 AATTTGTTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 29 0.48
81 32 0.52
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (80 bp):
TTAATTATCTTCACTTGATTGCTTCAGATGAATTTATAAATGTTAGGTGCAGAGAGTCGCAGGGC
AGATGGATTAATTGA
Found at i:5772917 original size:2 final size:2
Alignment explanation
Indices: 5772910--5772941 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5772900 GAAGACACAG
5772910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5772942 CATACTTGAA
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):
TA
Found at i:5774487 original size:27 final size:27
Alignment explanation
Indices: 5774457--5774515 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
5774447 AATGTGGTGC
* *
5774457 TTTCTTCTTCT-TTTTTGTTTTCATTTT
1 TTTCTTCTT-TATTTTTCTTTCCATTTT
*
5774484 TTTCTTCTTTATTTTTCTTTCCTTTTT
1 TTTCTTCTTTATTTTTCTTTCCATTTT
5774511 TTTCT
1 TTTCT
5774516 GATTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (27 bp):
TTTCTTCTTTATTTTTCTTTCCATTTT
Found at i:5774493 original size:24 final size:26
Alignment explanation
Indices: 5774461--5774512 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
5774451 TGGTGCTTTC
5774461 TTCTTCTTT-TTTGT-TTTCATTTTT
1 TTCTTCTTTATTTGTCTTTCATTTTT
* *
5774485 TTCTTCTTTATTTTTCTTTCCTTTTT
1 TTCTTCTTTATTTGTCTTTCATTTTT
5774511 TT
1 TT
5774513 TCTGATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 4 0.17
26 11 0.46
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (26 bp):
TTCTTCTTTATTTGTCTTTCATTTTT
Found at i:5774512 original size:14 final size:13
Alignment explanation
Indices: 5774464--5774515 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
5774454 TGCTTTCTTC
*
5774464 TTCTTTTTTGT-T
1 TTCTTTTTTTTCT
*
5774476 TTCATTTTTTTC-
1 TTCTTTTTTTTCT
5774488 TTCTTTATTTTTCT
1 TTCTTT-TTTTTCT
5774502 TTCCTTTTTTTTCT
1 TT-CTTTTTTTTCT
5774516 GATTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 14 0.42
13 6 0.18
14 9 0.27
15 4 0.12
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:5774738 original size:36 final size:36
Alignment explanation
Indices: 5774698--5774772 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
5774688 ATGACTCTTG
* * * *
5774698 ATTAAGAATATTAAATATGATAGTAATATTTTTAAA
1 ATTAAAAATATTAAATATAATAATAATATCTTTAAA
5774734 ATTAAAAATATTAAATATAATAATAATATCTTTAAA
1 ATTAAAAATATTAAATATAATAATAATATCTTTAAA
5774770 ATT
1 ATT
5774773 GATTGTTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (36 bp):
ATTAAAAATATTAAATATAATAATAATATCTTTAAA
Found at i:5794555 original size:2 final size:2
Alignment explanation
Indices: 5794548--5794578 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5794538 CATGTATTGA
5794548 TC TC TC 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 TC TC TC T
5794579 GGGGTGTGTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5799565 original size:21 final size:21
Alignment explanation
Indices: 5799539--5799583 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5799529 AAGGTGTTTG
5799539 TCTGTTTTTCTACGGTCAAAA
1 TCTGTTTTTCTACGGTCAAAA
* *
5799560 TCTGTTTTTCTACTGTTAAAA
1 TCTGTTTTTCTACGGTCAAAA
5799581 TCT
1 TCT
5799584 TATTGTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (21 bp):
TCTGTTTTTCTACGGTCAAAA
Found at i:5799716 original size:37 final size:38
Alignment explanation
Indices: 5799674--5799745 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
5799664 CTAAAAGTTT
5799674 CTGCTCTGT-GGCTCTAGTTTTAGTT-TAATT-GGAGCCC
1 CTGCTCT-TCGGCTCTAGTTTT-GTTATAATTAGGAGCCC
*
5799711 CTGCTCTTCTGCTCTAGTTTTGTTATAATTAGGAG
1 CTGCTCTTCGGCTCTAGTTTTGTTATAATTAGGAG
5799746 TGTGATTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 4 0.13
37 23 0.74
38 4 0.13
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.43
Consensus pattern (38 bp):
CTGCTCTTCGGCTCTAGTTTTGTTATAATTAGGAGCCC
Found at i:5808434 original size:2 final size:2
Alignment explanation
Indices: 5808427--5808456 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5808417 AAAAATATTG
*
5808427 TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5808457 ATTTGATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5813639 original size:6 final size:6
Alignment explanation
Indices: 5813628--5813653 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5813618 AATCTGAGCA
5813628 CAGTAG CAGTAG CAGTAG CAGTAG CA
1 CAGTAG CAGTAG CAGTAG CAGTAG CA
5813654 CAAAGAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (6 bp):
CAGTAG
Found at i:5826105 original size:12 final size:12
Alignment explanation
Indices: 5826073--5826108 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5826063 AGCATAATGC
5826073 TTAAATAAAT-T
1 TTAAATAAATAT
5826084 TT-AA-AAATAT
1 TTAAATAAATAT
5826094 TTAAATAAATAT
1 TTAAATAAATAT
5826106 TTA
1 TTA
5826109 TTATTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 4 0.18
12 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAATAAATAT
Found at i:5841528 original size:32 final size:32
Alignment explanation
Indices: 5841487--5841550 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
5841477 GGTTCGATGT
*
5841487 GCTCTTCATCACTCAAACATAGGCATTCATTG
1 GCTCTTCATCACTCAAACATAGGCATGCATTG
5841519 GCTCTTCATCACTCAAACATAGGCATGCATTG
1 GCTCTTCATCACTCAAACATAGGCATGCATTG
5841551 AACCAATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (32 bp):
GCTCTTCATCACTCAAACATAGGCATGCATTG
Found at i:5846013 original size:18 final size:18
Alignment explanation
Indices: 5845992--5846046 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
5845982 AGTAGCACTT
5845992 AGAAAATGAGAATTGTCA
1 AGAAAATGAGAATTGTCA
* * *
5846010 AGAATATTGA-ACTT-ACA
1 AGAA-AATGAGAATTGTCA
5846027 CAGAAAATGAGAATTGTCA
1 -AGAAAATGAGAATTGTCA
5846046 A
1 A
5846047 AAATATTGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
17 6 0.22
18 15 0.56
19 6 0.22
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (18 bp):
AGAAAATGAGAATTGTCA
Found at i:5851599 original size:4 final size:4
Alignment explanation
Indices: 5851590--5851616 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5851580 ATGATTATAT
5851590 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
5851617 TAATGCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:5856832 original size:2 final size:2
Alignment explanation
Indices: 5856825--5856859 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5856815 TCTTAATAGA
5856825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5856860 ATACGTTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5858281 original size:19 final size:18
Alignment explanation
Indices: 5858240--5858283 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5858230 TACTTAATAA
*
5858240 TTATTT-AATTAAAGAAT
1 TTATTTAAATTAAAAAAT
5858257 TATATTTAAATTAAAAAAAT
1 T-TATTTAAATT-AAAAAAT
5858277 TTATTTA
1 TTATTTA
5858284 TTTTTTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 5 0.22
19 10 0.43
20 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTATTTAAATTAAAAAAT
Found at i:5866056 original size:12 final size:12
Alignment explanation
Indices: 5866035--5866068 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5866025 CTCATCAGTT
* *
5866035 TCGGTTTCGGAG
1 TCGGTGTCGGAA
5866047 TCGGTGTCGGAA
1 TCGGTGTCGGAA
5866059 TCGGTGTCGG
1 TCGGTGTCGG
5866069 TCCTGGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.44, T:0.29
Consensus pattern (12 bp):
TCGGTGTCGGAA
Found at i:5866110 original size:24 final size:24
Alignment explanation
Indices: 5866041--5866115 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
5866031 AGTTTCGGTT
* * *
5866041 TCGGAGTCGGTGTCGGAATCGGTG
1 TCGGATTCGGTGGCGGAATCGTTG
* **
5866065 TCGG-TCCTGGTGGCGGTGTCGTTG
1 TCGGATTC-GGTGGCGGAATCGTTG
*
5866089 TCGGATTCGGTGGCGGAATCGTCG
1 TCGGATTCGGTGGCGGAATCGTTG
5866113 TCG
1 TCG
5866116 TCGTTCAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
23 1 0.03
24 36 0.92
25 2 0.05
ACGTcount: A:0.08, C:0.20, G:0.44, T:0.28
Consensus pattern (24 bp):
TCGGATTCGGTGGCGGAATCGTTG
Found at i:5886854 original size:50 final size:50
Alignment explanation
Indices: 5886779--5886881 Score: 179
Period size: 50 Copynumber: 2.1 Consensus size: 50
5886769 CAATTGGAGT
5886779 ACAACAGAGTCACGGTTGGGTCCATTAAGCCATTCATCACCCTGAACCAC
1 ACAACAGAGTCACGGTTGGGTCCATTAAGCCATTCATCACCCTGAACCAC
** *
5886829 ACAACAGAGTTGCGGTTGGGTCCATTATGCCATTCATCACCCTGAACCAC
1 ACAACAGAGTCACGGTTGGGTCCATTAAGCCATTCATCACCCTGAACCAC
5886879 ACA
1 ACA
5886882 TCATGCTCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.21
Consensus pattern (50 bp):
ACAACAGAGTCACGGTTGGGTCCATTAAGCCATTCATCACCCTGAACCAC
Found at i:5887604 original size:65 final size:65
Alignment explanation
Indices: 5887505--5887634 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 65
5887495 TTTAAGTGAT
*
5887505 GTAGCAAGCAAAGAGGTTCACCATTCAGCAAAAGAAAATGATGCTCTAATCAGTCAGGAAAACAT
1 GTAGCAAGCAAAGAGGTTCACCATTCAGCAAAAGAAAATGATGCTCAAAT-AGTCAGGAAAACAT
5887570 A
65 A
*
5887571 GTAGCAAGCAAAGA-GTTCACCATTCAGCAAAAGAAAATGATGTTCAAATAGTCAGGAAAACATA
1 GTAGCAAGCAAAGAGGTTCACCATTCAGCAAAAGAAAATGATGCTCAAATAGTCAGGAAAACATA
5887635 CTGTACACAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 15 0.24
65 33 0.53
66 14 0.23
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.18
Consensus pattern (65 bp):
GTAGCAAGCAAAGAGGTTCACCATTCAGCAAAAGAAAATGATGCTCAAATAGTCAGGAAAACATA
Found at i:5892266 original size:34 final size:35
Alignment explanation
Indices: 5892228--5892294 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
5892218 AGCTTTTTAC
* * *
5892228 GATATTAAGTGAAA-CTTTTACAATGTTTTTTCAT
1 GATATCAAGTGAAACCTTTAACAATGGTTTTTCAT
5892262 GATATCAAGTGAAACCCTTTAACAATGGTTTTT
1 GATATCAAGTGAAA-CCTTTAACAATGGTTTTT
5892295 ACGAGCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 13 0.46
36 15 0.54
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (35 bp):
GATATCAAGTGAAACCTTTAACAATGGTTTTTCAT
Found at i:5901276 original size:36 final size:34
Alignment explanation
Indices: 5901220--5901295 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 34
5901210 AAAAGAAAAA
* * *
5901220 ATATTTTTAAATAATTATATTTATTCAAATAGTT
1 ATATTTTTAAATAAATATATTTATTCAAACAATT
*
5901254 ATATTGTTTAAAGTAAATATATTTGTTCAAACAATT
1 ATATT-TTTAAA-TAAATATATTTATTCAAACAATT
5901290 ATATTT
1 ATATTT
5901296 GTCCAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 5 0.14
35 7 0.19
36 24 0.67
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (34 bp):
ATATTTTTAAATAAATATATTTATTCAAACAATT
Found at i:5901296 original size:18 final size:18
Alignment explanation
Indices: 5901220--5901302 Score: 82
Period size: 18 Copynumber: 4.7 Consensus size: 18
5901210 AAAAGAAAAA
5901220 ATATTT-TT-AAATAATT
1 ATATTTGTTCAAATAATT
* *
5901236 ATATTTATTCAAATAGTT
1 ATATTTGTTCAAATAATT
* *
5901254 ATA-TTGTTTAAAGTAAAT
1 ATATTTGTTCAAA-TAATT
*
5901272 ATATTTGTTCAAACAATT
1 ATATTTGTTCAAATAATT
*
5901290 ATATTTGTCCAAA
1 ATATTTGTTCAAA
5901303 AAGTTTTGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
16 6 0.11
17 9 0.17
18 31 0.57
19 8 0.15
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (18 bp):
ATATTTGTTCAAATAATT
Found at i:5902058 original size:27 final size:27
Alignment explanation
Indices: 5901988--5902198 Score: 151
Period size: 27 Copynumber: 7.7 Consensus size: 27
5901978 TCATACCATA
* * * *
5901988 TTGAAAAATATAATTGTTACATGTTATA
1 TTGAAAAAT-TAATTATTACACGTCATG
* **
5902016 TTGAAAATTTTGTTATTACACGTCATG
1 TTGAAAAATTAATTATTACACGTCATG
*
5902043 TTGAAAAATTAATTATTACACATCATG
1 TTGAAAAATTAATTATTACACGTCATG
* *
5902070 TT-AAAAATTTAATTGTTACACGTTA-G
1 TTGAAAAA-TTAATTATTACACGTCATG
** ** *
5902096 TTGAAAAATGTAACCATTACAAATTATG
1 TTGAAAAAT-TAATTATTACACGTCATG
**
5902124 TT-AAAAATTTAATTATTGTACGTCATG
1 TTGAAAAA-TTAATTATTACACGTCATG
* *
5902151 TTGAAAAATATAATTATTATACATCATG
1 TTGAAAAAT-TAATTATTACACGTCATG
* *
5902179 TT-AAAGATTTAATTGTTACA
1 TTGAAA-AATTAATTATTACA
5902199 AGTTAAAAAT
Statistics
Matches: 144, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
26 9 0.06
27 98 0.68
28 37 0.26
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (27 bp):
TTGAAAAATTAATTATTACACGTCATG
Found at i:5902077 original size:54 final size:55
Alignment explanation
Indices: 5901988--5902198 Score: 228
Period size: 54 Copynumber: 3.9 Consensus size: 55
5901978 TCATACCATA
* ** * * * **
5901988 TTGAAAAATATAATTGTTACATGTTATATTGAAAATTTTGTTATTACACGTCATG
1 TTGAAAAATATAATTATTACACATCATGTTAAAAATTTAATTATTACACGTCATG
* *
5902043 TTGAAAAAT-TAATTATTACACATCATGTTAAAAATTTAATTGTTACACGTTA-G
1 TTGAAAAATATAATTATTACACATCATGTTAAAAATTTAATTATTACACGTCATG
* ** * * **
5902096 TTGAAAAATGTAACCATTACAAATTATGTTAAAAATTTAATTATTGTACGTCATG
1 TTGAAAAATATAATTATTACACATCATGTTAAAAATTTAATTATTACACGTCATG
* * *
5902151 TTGAAAAATATAATTATTATACATCATGTTAAAGATTTAATTGTTACA
1 TTGAAAAATATAATTATTACACATCATGTTAAAAATTTAATTATTACA
5902199 AGTTAAAAAT
Statistics
Matches: 126, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
53 10 0.08
54 68 0.54
55 48 0.38
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (55 bp):
TTGAAAAATATAATTATTACACATCATGTTAAAAATTTAATTATTACACGTCATG
Found at i:5902203 original size:22 final size:22
Alignment explanation
Indices: 5902178--5902220 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5902168 TATACATCAT
*
5902178 GTTAAAGATTTAATTGTTACAA
1 GTTAAAAATTTAATTGTTACAA
*
5902200 GTTAAAAATTTAGTTGTTACA
1 GTTAAAAATTTAATTGTTACA
5902221 TGTAATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (22 bp):
GTTAAAAATTTAATTGTTACAA
Found at i:5903331 original size:17 final size:17
Alignment explanation
Indices: 5903309--5903352 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
5903299 ATTTAGAAGA
5903309 AGAAGAAGAATATTTAG
1 AGAAGAAGAATATTTAG
5903326 AGAAGAAGAATATTTAG
1 AGAAGAAGAATATTTAG
5903343 AGAAGAAGAA
1 AGAAGAAGAA
5903353 ATAGTATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGAAGAATATTTAG
Found at i:5903331 original size:20 final size:20
Alignment explanation
Indices: 5903299--5903352 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 20
5903289 TTATTAAAAA
5903299 ATTTAGAAGAAGAAGAAGAAT
1 ATTTAG-AGAAGAAGAAGAAT
5903320 ATTT--AG-AGAAGAAGAAT
1 ATTTAGAGAAGAAGAAGAAT
5903337 ATTTAGAGAAGAAGAA
1 ATTTAGAGAAGAAGAA
5903353 ATAGTATGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 15 0.50
18 2 0.07
19 2 0.07
20 7 0.23
21 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (20 bp):
ATTTAGAGAAGAAGAAGAAT
Found at i:5913474 original size:18 final size:17
Alignment explanation
Indices: 5913451--5913484 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5913441 ACAATAAAAA
5913451 AAAATTAAAGAGTAGAAG
1 AAAATTAAAGAG-AGAAG
*
5913469 AAAATTAGAGAGAGAA
1 AAAATTAAAGAGAGAA
5913485 TTTAGATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (17 bp):
AAAATTAAAGAGAGAAG
Found at i:5925466 original size:16 final size:19
Alignment explanation
Indices: 5925445--5925488 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 19
5925435 TTATTGAAAA
5925445 TTAAAAATTAA-AT-TT-T
1 TTAAAAATTAATATATTAT
5925461 TTAAAAATTAATATATTAT
1 TTAAAAATTAATATATTAT
5925480 TTAAAAATT
1 TTAAAAATT
5925489 TATAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.44
17 2 0.08
18 2 0.08
19 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAAAATTAATATATTAT
Found at i:5925646 original size:19 final size:23
Alignment explanation
Indices: 5925602--5925646 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5925592 TTAATTTTAT
5925602 ATTAAATATATTTAATATAAATA
1 ATTAAATATATTTAATATAAATA
5925625 ATTAAAT-TA-TTAATA-AAA-A
1 ATTAAATATATTTAATATAAATA
5925644 ATT
1 ATT
5925647 CACCATCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 3 0.14
21 6 0.27
22 2 0.09
23 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTAAATATATTTAATATAAATA
Found at i:5925918 original size:18 final size:17
Alignment explanation
Indices: 5925895--5925930 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5925885 TTTAAAAATT
5925895 ATAAAAAATATATAAAAA
1 ATAAAAAAT-TATAAAAA
*
5925913 ATAAAAAATTTTAAAAA
1 ATAAAAAATTATAAAAA
5925930 A
1 A
5925931 GTTTTGTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAAAATTATAAAAA
Found at i:5926853 original size:2 final size:2
Alignment explanation
Indices: 5926846--5926880 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5926836 CAGTAAGAAG
5926846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5926881 TCCCTTAATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5943415 original size:2 final size:2
Alignment explanation
Indices: 5943408--5943439 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5943398 CAAGAAGTAG
5943408 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
5943440 GAAATTTTTA
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:5944002 original size:22 final size:22
Alignment explanation
Indices: 5943961--5944003 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5943951 TACGTTATTA
* *
5943961 ATTTTTAAGTATTATATGACTG
1 ATTTTTAAATATTACATGACTG
*
5943983 ATTTTTAAATATTACGTGACT
1 ATTTTTAAATATTACATGACT
5944004 AATTGATATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTTTTAAATATTACATGACTG
Found at i:5944032 original size:23 final size:22
Alignment explanation
Indices: 5943993--5944052 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
5943983 ATTTTTAAAT
**
5943993 ATTACGTGACTAATTGATATGAC
1 ATTACGTGACTGGTTGATA-GAC
**
5944016 ATTACGTGACTGGTTGATAGGT
1 ATTACGTGACTGGTTGATAGAC
*
5944038 ATTGCGTGACTGGTT
1 ATTACGTGACTGGTT
5944053 AGTAAAGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.37
Consensus pattern (22 bp):
ATTACGTGACTGGTTGATAGAC
Found at i:5944093 original size:23 final size:23
Alignment explanation
Indices: 5944016--5944094 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
5944006 TTGATATGAC
5944016 ATTACGTGACTGGTT-G-ATAGGT
1 ATTACGTGACTGGTTAGTA-AGGT
* * *
5944038 ATTGCGTGACTGGTTAGTAAAGC
1 ATTACGTGACTGGTTAGTAAGGT
* * *
5944061 ATTGCATGACTGATTAGTAAGGT
1 ATTACGTGACTGGTTAGTAAGGT
5944084 ATTACGTGACT
1 ATTACGTGACT
5944095 ACATAGTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 14 0.30
23 31 0.67
24 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (23 bp):
ATTACGTGACTGGTTAGTAAGGT
Found at i:5944195 original size:22 final size:22
Alignment explanation
Indices: 5944148--5944214 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
5944138 TTAGGCATGG
* * * *
5944148 CTTAAAAATTAATCACGCAGTG
1 CTTAAAAATTAATCATGTAATA
* *
5944170 CTTAAAAATTAGTTATGTAATA
1 CTTAAAAATTAATCATGTAATA
5944192 CTTAAAAATTAATCATGTAATA
1 CTTAAAAATTAATCATGTAATA
5944214 C
1 C
5944215 CTGAAACCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (22 bp):
CTTAAAAATTAATCATGTAATA
Found at i:5946994 original size:107 final size:108
Alignment explanation
Indices: 5946881--5947085 Score: 324
Period size: 107 Copynumber: 1.9 Consensus size: 108
5946871 CCCTGAACCC
*
5946881 TATATATATATATAACTTAATTAGA-AAAAAGAGATTCAATCTTCCAGATTTTTCAATGGATAGT
1 TATATATATATATAACTTAATTAGAGAAAAAG-GATTCAACCTTCCAGATTTTTCAATGGATAGT
*
5946945 -AAATAAAATTTCAAAATCATTTCATTGGTGCCTCTAAGAATTA
65 CAAATAAAATTTCAAAATCATCTCATTGGTGCCTCTAAGAATTA
* *
5946988 TATATATATATATAACTTAATTAGAGAAAAAGGATTCAACCTTTCAGATTTTTCAATGGGTAGTC
1 TATATATATATATAACTTAATTAGAGAAAAAGGATTCAACCTTCCAGATTTTTCAATGGATAGTC
* * *
5947053 AAATAAAGTTTTAAGATCATCTCATTGGTGCCT
66 AAATAAAATTTCAAAATCATCTCATTGGTGCCT
5947086 GTACTAGTTG
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 54 0.61
108 35 0.39
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (108 bp):
TATATATATATATAACTTAATTAGAGAAAAAGGATTCAACCTTCCAGATTTTTCAATGGATAGTC
AAATAAAATTTCAAAATCATCTCATTGGTGCCTCTAAGAATTA
Found at i:5955742 original size:11 final size:11
Alignment explanation
Indices: 5955726--5955751 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5955716 TATAATTTTT
5955726 AATTCAATTAG
1 AATTCAATTAG
5955737 AATTCAATTAG
1 AATTCAATTAG
5955748 AATT
1 AATT
5955752 TAGATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (11 bp):
AATTCAATTAG
Found at i:5957676 original size:22 final size:22
Alignment explanation
Indices: 5957649--5957695 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5957639 TCGCCCACCG
*
5957649 AAACGGAACAGTTCAGGCGGCT
1 AAACGGAACAGTACAGGCGGCT
*
5957671 AAACGGAACAGTACATGCGGCT
1 AAACGGAACAGTACAGGCGGCT
5957693 AAA
1 AAA
5957696 GAGACGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.13
Consensus pattern (22 bp):
AAACGGAACAGTACAGGCGGCT
Found at i:5962359 original size:27 final size:27
Alignment explanation
Indices: 5962321--5962372 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5962311 CTAGTTCACA
*
5962321 TTTTTTTAAAAAAAATGCATAATGCTT
1 TTTTTTTAAAAAAAATGAATAATGCTT
5962348 TTTTTTTAAAAAAAATGAATAATGC
1 TTTTTTTAAAAAAAATGAATAATGC
5962373 ATTAATTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (27 bp):
TTTTTTTAAAAAAAATGAATAATGCTT
Found at i:5963538 original size:2 final size:2
Alignment explanation
Indices: 5963531--5963569 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5963521 ATTACCAATA
5963531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5963570 CACTCATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5964941 original size:4 final size:4
Alignment explanation
Indices: 5964934--5964963 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
5964924 GGGTGAGGGT
5964934 GACA GACA GACA GACA GACA GACA GACA GA
1 GACA GACA GACA GACA GACA GACA GACA GA
5964964 GACAGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.27, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:5965129 original size:13 final size:13
Alignment explanation
Indices: 5965107--5965139 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5965097 CTGCAGTCTC
5965107 ACTCTCCATCTATG
1 ACTCT-CATCTATG
5965121 ACTCTCATCTATG
1 ACTCTCATCTATG
5965134 ACTCTC
1 ACTCTC
5965140 TCTTCTGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (13 bp):
ACTCTCATCTATG
Found at i:5981052 original size:2 final size:2
Alignment explanation
Indices: 5981045--5981119 Score: 120
Period size: 2 Copynumber: 39.0 Consensus size: 2
5981035 TCCTTCTTTC
5981045 CT CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT -T CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
5981085 TT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5981120 AACTTTCCAG
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
1 3 0.04
2 65 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:5996979 original size:10 final size:10
Alignment explanation
Indices: 5996964--5997001 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
5996954 AAATTAATTA
5996964 TAAAAATAAT
1 TAAAAATAAT
*
5996974 TAAAAATAAA
1 TAAAAATAAT
5996984 TAAATAATAAT
1 TAAA-AATAAT
5996995 TAAAAAT
1 TAAAAAT
5997002 TTAATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:5996992 original size:11 final size:10
Alignment explanation
Indices: 5996949--5997001 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
5996939 ACTCACTTAA
*
5996949 AAATAAAATT
1 AAATAAAAAT
5996959 AATTATAAAAAT
1 AA--ATAAAAAT
*
5996971 AATTAAAAAT
1 AAATAAAAAT
5996981 AAATAAATAAT
1 AAATAAA-AAT
*
5996992 AATTAAAAAT
1 AAATAAAAAT
5997002 TTAATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 18 0.50
11 9 0.25
12 9 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:5996994 original size:21 final size:20
Alignment explanation
Indices: 5996963--5997001 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5996953 AAAATTAATT
5996963 ATAAAAATAATTAAAAATAA
1 ATAAAAATAATTAAAAATAA
5996983 ATAAATAATAATTAAAAAT
1 ATAAA-AATAATTAAAAAT
5997002 TTAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAAATAATTAAAAATAA
Found at i:5997019 original size:29 final size:28
Alignment explanation
Indices: 5996986--5997043 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
5996976 AAAATAAATA
*
5996986 AATAAT-AATTAAAAATTTAATTAATATTT
1 AATAATAAATT-AAAATTAAATTAAT-TTT
*
5997015 AATAATAAATTTAAATTAAATTAATTTT
1 AATAATAAATTAAAATTAAATTAATTTT
5997043 A
1 A
5997044 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
29 18 0.69
30 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATAATAAATTAAAATTAAATTAATTTT
Found at i:6006796 original size:17 final size:17
Alignment explanation
Indices: 6006763--6006797 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6006753 ATATATATAT
* *
6006763 ATATGTTATGAACAATA
1 ATATGTTATAAAAAATA
6006780 ATATGTTATAAAAAATA
1 ATATGTTATAAAAAATA
6006797 A
1 A
6006798 GATAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (17 bp):
ATATGTTATAAAAAATA
Found at i:6007039 original size:21 final size:21
Alignment explanation
Indices: 6007015--6007055 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6007005 CTATAAAAGA
6007015 TTAATTAAATTTTAAA-AAAAT
1 TTAA-TAAATTTTAAATAAAAT
*
6007036 TTAATATATTTTAAATAAAA
1 TTAATAAATTTTAAATAAAA
6007056 AATTTAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAATAAATTTTAAATAAAAT
Found at i:6007450 original size:44 final size:45
Alignment explanation
Indices: 6007397--6007570 Score: 185
Period size: 44 Copynumber: 4.0 Consensus size: 45
6007387 CATGTTATAG
* * * *
6007397 TTAAATTGTTACACGTTATGTACAAAAATATGTGACACGTCA-AG
1 TTAAGTTGTTACACGTTATATACAAAAACATGTGACACGTCATAA
* * * * ** *
6007441 TTAGGTTGTTACAGGTCATATACAAAAGCACATGACACGTTATAA
1 TTAAGTTGTTACACGTTATATACAAAAACATGTGACACGTCATAA
* * *
6007486 TTAAGTTGTTGCACGCTATATACAAAAACATGTGACATGT-ATAA
1 TTAAGTTGTTACACGTTATATACAAAAACATGTGACACGTCATAA
*
6007530 TTAAATTGTT--ACGTTATATACAAAAACATGTGACACGTCAT
1 TTAAGTTGTTACACGTTATATACAAAAACATGTGACACGTCAT
6007571 GGTACACACC
Statistics
Matches: 105, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
42 26 0.25
43 2 0.02
44 45 0.43
45 32 0.30
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (45 bp):
TTAAGTTGTTACACGTTATATACAAAAACATGTGACACGTCATAA
Found at i:6007509 original size:45 final size:42
Alignment explanation
Indices: 6007458--6007567 Score: 121
Period size: 42 Copynumber: 2.5 Consensus size: 42
6007448 GTTACAGGTC
* *
6007458 ATATACAAAAGCACATGACACGTTATAATTAAGTTGTTGCACGCT
1 ATATACAAAAACACATGACACG-TATAATTAAATTGTT--ACGCT
** * *
6007503 ATATACAAAAACATGTGACATGTATAATTAAATTGTTACGTT
1 ATATACAAAAACACATGACACGTATAATTAAATTGTTACGCT
**
6007545 ATATACAAAAACATGTGACACGT
1 ATATACAAAAACACATGACACGT
6007568 CATGGTACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
42 26 0.45
44 14 0.24
45 18 0.31
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (42 bp):
ATATACAAAAACACATGACACGTATAATTAAATTGTTACGCT
Found at i:6007541 original size:89 final size:87
Alignment explanation
Indices: 6007390--6007554 Score: 197
Period size: 89 Copynumber: 1.9 Consensus size: 87
6007380 TGTAGTGCAT
* * * * * **
6007390 GTTATAGTTAAATTGTTACACGTTATGTACAAAAATATGTGACACGTCAAGTTAGGTTGTTACAG
1 GTTATAATTAAATTGTTACACGCTATATACAAAAACATGTGACACGTCAAATTAAATTGTTAC--
6007455 GTCATATACAAAAGCACATGACAC
64 GTCATATACAAAAGCACATGACAC
* * *
6007479 GTTATAATTAAGTTGTTGCACGCTATATACAAAAACATGTGACATGT-ATAATTAAATTGTTACG
1 GTTATAATTAAATTGTTACACGCTATATACAAAAACATGTGACACGTCA-AATTAAATTGTTACG
*
6007543 TTATATACAAAA
65 TCATATACAAAA
6007555 ACATGTGACA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 12 0.19
88 1 0.02
89 51 0.80
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (87 bp):
GTTATAATTAAATTGTTACACGCTATATACAAAAACATGTGACACGTCAAATTAAATTGTTACGT
CATATACAAAAGCACATGACAC
Found at i:6008174 original size:21 final size:21
Alignment explanation
Indices: 6008140--6008190 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
6008130 AATTAAAAAA
*
6008140 AAATAAAAGATTAATTAAATTTT
1 AAATAAAA-TTTAA-TAAATTTT
*
6008163 AAA-AAAATTTAATATATTTT
1 AAATAAAATTTAATAAATTTT
6008183 AAATAAAA
1 AAATAAAA
6008191 AATTTAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.40
21 8 0.32
22 4 0.16
23 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATAAAATTTAATAAATTTT
Found at i:6008604 original size:45 final size:45
Alignment explanation
Indices: 6008540--6008703 Score: 143
Period size: 45 Copynumber: 3.6 Consensus size: 45
6008530 AGTTAAATTA
* * * *
6008540 TTACAGGTCATATACAAAAATATGTAACACGTCATGGTTAGGTTG
1 TTACACGTCATATACAAAAACATGTAACACGTCATGATTAAGTTG
* * * *
6008585 TTACACGTTATATACAAAAACACGTGACACG-CTATAATTAAGTTG
1 TTACACGTCATATACAAAAACATGTAACACGTC-ATGATTAAGTTG
* * * * * * * *
6008630 TTGCA-GGCTTTGTGCAAAAACATGTGACATGTTATGATTAAGTTG
1 TTACACGTC-ATATACAAAAACATGTAACACGTCATGATTAAGTTG
*
6008675 TTACACGTCATATACAAAAATATGTAACA
1 TTACACGTCATATACAAAAACATGTAACA
6008704 TATCATGGTG
Statistics
Matches: 90, Mismatches: 25, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
44 2 0.02
45 86 0.96
46 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (45 bp):
TTACACGTCATATACAAAAACATGTAACACGTCATGATTAAGTTG
Found at i:6009316 original size:21 final size:23
Alignment explanation
Indices: 6009276--6009323 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
6009266 CATGGCAAAC
* *
6009276 TAATTAAAATTTTTTTAAAAGAT
1 TAATTAAAATTTTTTAAAAAAAT
6009299 TAATT-AAA-TTTTTAAAAAAAT
1 TAATTAAAATTTTTTAAAAAAAT
6009320 TAAT
1 TAAT
6009324 ATATTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 3 0.13
23 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAATTAAAATTTTTTAAAAAAAT
Found at i:6009705 original size:45 final size:45
Alignment explanation
Indices: 6009676--6009800 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
6009666 TCATGATTCG
6009676 GTTGTTACACG-TCATACACAAAAGCATGTGACACGCTATAATTAA
1 GTTGTTACACGCT-ATACACAAAAGCATGTGACACGCTATAATTAA
** * *
6009721 GTTGTTACACGCTATGTACAAAAGCATGTGACATGTTATAATTAA
1 GTTGTTACACGCTATACACAAAAGCATGTGACACGCTATAATTAA
* * ** * *
6009766 GTTGTTATACGTTATGTACAAAAACATATGACACG
1 GTTGTTACACGCTATACACAAAAGCATGTGACACG
6009801 TCATAGTACA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
45 69 0.99
46 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (45 bp):
GTTGTTACACGCTATACACAAAAGCATGTGACACGCTATAATTAA
Found at i:6009896 original size:45 final size:45
Alignment explanation
Indices: 6009818--6009908 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
6009808 ACACACCATG
* *
6009818 TACAAAAACATGTGACATGCCATGATTAAGTTATTACACGTCATA
1 TACAAAAACATGTAACATGCAATGATTAAGTTATTACACGTCATA
* * * * * *
6009863 TACAAAAACATGTAACGTGTAATGGTTAGGTTATTATATGTCATA
1 TACAAAAACATGTAACATGCAATGATTAAGTTATTACACGTCATA
6009908 T
1 T
6009909 TGAAAAAAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (45 bp):
TACAAAAACATGTAACATGCAATGATTAAGTTATTACACGTCATA
Found at i:6013317 original size:26 final size:25
Alignment explanation
Indices: 6013288--6013339 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
6013278 ATAACCCTTC
* *
6013288 AAATATTAATGATTAAATCATAAATA
1 AAATATTAATAATTAAA-AATAAATA
6013314 AAATATTAATAATTAAAAATAAATA
1 AAATATTAATAATTAAAAATAAATA
6013339 A
1 A
6013340 TCACAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATATTAATAATTAAAAATAAATA
Found at i:6013406 original size:42 final size:42
Alignment explanation
Indices: 6013354--6013463 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
6013344 AATGACATTA
*
6013354 AAATTTTAAATAAGATATTAATATTTTTA-AATAGTAATAATT
1 AAATTATAAATAA-ATATTAATATTTTTATAATAGTAATAATT
* * *
6013396 AAATTATAAATAAAGTAGTAATA-TTTTATAATATTAATGATT
1 AAATTATAAATAAA-TATTAATATTTTTATAATAGTAATAATT
*
6013438 AAATTATAAATGAAATATCAATATTT
1 AAATTATAAAT-AAATATTAATATTT
6013464 AAATTATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
41 6 0.10
42 47 0.81
43 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (42 bp):
AAATTATAAATAAATATTAATATTTTTATAATAGTAATAATT
Found at i:6013496 original size:27 final size:28
Alignment explanation
Indices: 6013463--6013521 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
6013453 TATCAATATT
* * *
6013463 TAAATTATTAATTATTAGTATTT-TAAA
1 TAAATTATAAATTATTAATATTTAAAAA
6013490 TAAATTATAAATTATTAATATTTAAAAA
1 TAAATTATAAATTATTAATATTTAAAAA
6013518 TAAA
1 TAAA
6013522 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TAAATTATAAATTATTAATATTTAAAAA
Found at i:6013528 original size:27 final size:27
Alignment explanation
Indices: 6013463--6013528 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
6013453 TATCAATATT
* * * *
6013463 TAAATTATTAATTATTAGTATTTTAAA
1 TAAAATATAAATTATTAATATTTAAAA
*
6013490 TAAATTATAAATTATTAATATTTAAAAA
1 TAAAATATAAATTATTAATATTT-AAAA
6013518 TAAAATA-AAAT
1 TAAAATATAAAT
6013529 AAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 25 0.74
28 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAAATATAAATTATTAATATTTAAAA
Found at i:6013596 original size:197 final size:189
Alignment explanation
Indices: 6013327--6013806 Score: 481
Period size: 188 Copynumber: 2.5 Consensus size: 189
6013317 TATTAATAAT
* * * *
6013327 TAAAAATAAATAATCACAATGACATTAAAATTTTAAA-TAAGATATTAATATTTT-TAAATAG-T
1 TAAAAA-AAATAATCATAATAACATTTAAATTATAAATTAA-ATATTAATATTTTAT-AAT-GTT
* * * * *
6013389 AATAATTAAATTATAAATAAAGTAGTAATATTTTATAATATTAATGATTAA-ATT-ATAAATGAA
62 AATGATTAAATTATAAATAAAATAGTAATATTTTATAATATCAATGAATAAGATTCAAAAAT-AA
** * * ** * *
6013452 ATATCAATATTTAAATTATTAATTATTAGTATTTTAAATAAATTATAAATTATTAATA-TTTAAA
126 A-AT-AA-AAATAAA-TAATAA-TAATAACA-TTTAAAT-AA-TAAAAAATATTAATATTTTAAA
6013516 AATAAAA
183 AATAAAA
*
6013523 TAAAATAAAAATAATCATAATAATATTTAAATTATAAATTAAATATTAATATTTTATAATGTTAA
1 T-AAA-AAAAATAATCATAATAACATTTAAATTATAAATTAAATATTAATATTTTATAATGTTAA
* * * * *
6013588 TGATTAAATCATAAATAAAATATTCATA--TTATATTATCAATTAATAAGATTCAAAAATAAAAT
64 TGATTAAATTATAAATAAAATAGTAATATTTTATAATATCAATGAATAAGATTCAAAAATAAAAT
* *
6013651 AAAAATAAATAATCATAATAACATTTAAATTATAAAAAATATTAATATTTTTAAAAATAAAA
129 AAAAATAAATAATAATAATAACATTTAAATAATAAAAAATATTAATA-TTTTAAAAATAAAA
* * *
6013713 TTAAGAAAATAATCATAATAACATTTAAATTATAAATTAAATATTAATATTGTATAATGTTAATG
1 TAAAAAAAATAATCATAATAACATTTAAATTATAAATTAAATATTAATATTTTATAATGTTAATG
* **
6013778 ATTAAACTATGCATAAAATAGTAATATTT
66 ATTAAATTATAAATAAAATAGTAATATTT
6013807 AAATTATCAA
Statistics
Matches: 238, Mismatches: 35, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
188 91 0.38
189 3 0.01
190 22 0.09
191 5 0.02
192 4 0.02
193 5 0.02
194 2 0.01
195 17 0.07
196 8 0.03
197 75 0.32
198 6 0.03
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (189 bp):
TAAAAAAAATAATCATAATAACATTTAAATTATAAATTAAATATTAATATTTTATAATGTTAATG
ATTAAATTATAAATAAAATAGTAATATTTTATAATATCAATGAATAAGATTCAAAAATAAAATAA
AAATAAATAATAATAATAACATTTAAATAATAAAAAATATTAATATTTTAAAAATAAAA
Found at i:6013731 original size:62 final size:64
Alignment explanation
Indices: 6013496--6013763 Score: 227
Period size: 62 Copynumber: 4.2 Consensus size: 64
6013486 TAAATAAATT
* *
6013496 ATAAATTATTAATA--TTTAAAAATAAAATAAAATAAAAATAATCATAATAATATTTAAATTATA
1 ATAAA-TATTAATATTTTTAAAAATAAAATAAAA-ATAAATAATCATAATAACATTTAAATTATA
6013559 A
64 A
*** * * * * *
6013560 ATTAAATATTAATATTTTATAATGTTAATGATTAAATCATAAATAA-AAT-AT-TCATATTATAT
1 A-TAAATATTAATATTTT-TAAAAATAA--AATAAA-AATAAATAATCATAATAACAT-TTAAAT
*
6013622 TATCA
60 TATAA
* * *
6013627 AT---TAATAAGA--TTCAAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAA
1 ATAAATATTAATATTTTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAA
* *
6013686 A-AAATATTAATATTTTTAAAAATAAAATTAAGA-AAATAATCATAATAACATTTAAATTATAA
1 ATAAATATTAATATTTTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAA
6013748 ATTAAATATTAATATT
1 A-TAAATATTAATATT
6013764 GTATAATGTT
Statistics
Matches: 158, Mismatches: 28, Indels: 36
0.71 0.13 0.16
Matches are distributed among these distances:
57 8 0.05
58 7 0.04
59 12 0.08
60 8 0.05
61 8 0.05
62 30 0.19
63 22 0.14
64 22 0.14
65 4 0.03
66 5 0.03
67 18 0.11
68 2 0.01
69 12 0.08
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (64 bp):
ATAAATATTAATATTTTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAA
Found at i:6013847 original size:21 final size:20
Alignment explanation
Indices: 6013815--6013857 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
6013805 TTAAATTATC
*
6013815 AATTATAAATATTGTTAATA
1 AATTATAAATATTATTAATA
*
6013835 AATTATAAAATATTATTATTA
1 AATTAT-AAATATTATTAATA
6013856 AA
1 AA
6013858 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTATAAATATTATTAATA
Found at i:6014541 original size:19 final size:20
Alignment explanation
Indices: 6014517--6014558 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6014507 AGTTTTGAAT
6014517 ATAATTTTATA-TATTAAAA
1 ATAATTTTATATTATTAAAA
* *
6014536 ATAATTTTTTATTATTATAA
1 ATAATTTTATATTATTAAAA
6014556 ATA
1 ATA
6014559 TATATATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTTTATATTATTAAAA
Found at i:6014875 original size:16 final size:15
Alignment explanation
Indices: 6014854--6014906 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
6014844 TTTTTTCAAA
6014854 TTATATTTCATAACAT
1 TTATATTTCATAA-AT
*
6014870 TTATATTTC-T-AAG
1 TTATATTTCATAAAT
*
6014883 TTATACTTCATAATAT
1 TTATATTTCATAA-AT
6014899 TTATATTT
1 TTATATTT
6014907 TTATTATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 9 0.30
14 2 0.07
15 2 0.07
16 17 0.57
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (15 bp):
TTATATTTCATAAAT
Found at i:6024687 original size:20 final size:20
Alignment explanation
Indices: 6024662--6024700 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6024652 GGATTTTAGA
*
6024662 TTTCAATACTATTATAAAAT
1 TTTCAATACTATTAGAAAAT
6024682 TTTCAATACTATTAGAAAA
1 TTTCAATACTATTAGAAAA
6024701 ACATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (20 bp):
TTTCAATACTATTAGAAAAT
Found at i:6032875 original size:20 final size:20
Alignment explanation
Indices: 6032838--6032876 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6032828 CATACCATCA
*
6032838 ATTCAAAGTGAAATTTATTT
1 ATTCAAAGTGAAAATTATTT
* *
6032858 ATTCAAATTTAAAATTATT
1 ATTCAAAGTGAAAATTATT
6032877 GTTAATAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTCAAAGTGAAAATTATTT
Found at i:6034109 original size:24 final size:26
Alignment explanation
Indices: 6034082--6034139 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
6034072 AGTCTGTAAT
6034082 TATAAAATATA-TAAATTA-AATATA
1 TATAAAATATATTAAATTATAATATA
* * *
6034106 TATAATATATATTAATTTATTATATA
1 TATAAAATATATTAAATTATAATATA
6034132 TATAAAAT
1 TATAAAAT
6034140 TAATCACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 10 0.36
25 6 0.21
26 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TATAAAATATATTAAATTATAATATA
Found at i:6034454 original size:20 final size:21
Alignment explanation
Indices: 6034426--6034467 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6034416 ATTAATTATA
*
6034426 AATAATAT-ATTATAAAAATT
1 AATAATATAATTAAAAAAATT
*
6034446 AATATTATAATTAAAAAAATT
1 AATAATATAATTAAAAAAATT
6034467 A
1 A
6034468 TTAAGTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAATATAATTAAAAAAATT
Found at i:6034507 original size:23 final size:24
Alignment explanation
Indices: 6034481--6034566 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 24
6034471 AGTGTAATGA
6034481 TATAAATATA-ATTTATTATAAAT
1 TATAAATATATATTTATTATAAAT
*
6034504 TAT-AGTA-ATATTTATGTATAAAT
1 TATAAATATATATTTAT-TATAAAT
*
6034527 TGAATATATATAATATTTATT-T-AAT
1 T--ATAAATAT-ATATTTATTATAAAT
6034552 TAT--ATATATATTTAT
1 TATAAATATATATTTAT
6034567 AATATTTTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
20 8 0.15
21 5 0.09
22 9 0.17
23 13 0.25
25 6 0.11
26 3 0.06
27 1 0.02
28 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
TATAAATATATATTTATTATAAAT
Found at i:6034630 original size:15 final size:17
Alignment explanation
Indices: 6034587--6034631 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
6034577 ATTACGAAAT
6034587 ATTATTAAAATA-TAATA
1 ATTA-TAAAATATTAATA
*
6034604 ATTATAACATATTAAT-
1 ATTATAAAATATTAATA
6034620 A-TATAAAATATT
1 ATTATAAAATATT
6034632 TACTATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 10 0.40
16 7 0.28
17 8 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATAAAATATTAATA
Found at i:6036976 original size:12 final size:12
Alignment explanation
Indices: 6036961--6036990 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6036951 GACTGATATA
6036961 GTGGTTATGGTG
1 GTGGTTATGGTG
*
6036973 GTGGTTCTGGTG
1 GTGGTTATGGTG
6036985 GTGGTT
1 GTGGTT
6036991 TTGGCAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.03, G:0.50, T:0.43
Consensus pattern (12 bp):
GTGGTTATGGTG
Found at i:6037015 original size:30 final size:30
Alignment explanation
Indices: 6036979--6037036 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
6036969 GGTGGTGGTT
6036979 CTGGTGGTGGTTTTGGCAGTAGGGGAGGCC
1 CTGGTGGTGGTTTTGGCAGTAGGGGAGGCC
*
6037009 CTGGTGGTGGTTTTGGCAGTGGGGGAGG
1 CTGGTGGTGGTTTTGGCAGTAGGGGAGG
6037037 AATAGGCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.09, C:0.10, G:0.53, T:0.28
Consensus pattern (30 bp):
CTGGTGGTGGTTTTGGCAGTAGGGGAGGCC
Found at i:6055252 original size:41 final size:42
Alignment explanation
Indices: 6055175--6055255 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 42
6055165 TTCATAACTA
* * * * * *
6055175 ATAAAAGACAGCATCACTCCAAAGTTGGCGATTATTTAATGC
1 ATAAAAGAAAGCATCACACCAAAGATAGCAAATATTTAATGC
6055217 ATAAAA-AAAGCATCACACCAAAGATAGCAAATATTTAAT
1 ATAAAAGAAAGCATCACACCAAAGATAGCAAATATTTAAT
6055256 AAATTTCCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 27 0.82
42 6 0.18
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (42 bp):
ATAAAAGAAAGCATCACACCAAAGATAGCAAATATTTAATGC
Found at i:6071017 original size:20 final size:21
Alignment explanation
Indices: 6070980--6071019 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6070970 TTTCAAAATA
* *
6070980 TTATTCTGTTTTATTCTTTAT
1 TTATTCTGTTTCAATCTTTAT
6071001 TTATTCT-TTTCAATCTTTA
1 TTATTCTGTTTCAATCTTTA
6071020 CCATAATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.17, C:0.12, G:0.03, T:0.68
Consensus pattern (21 bp):
TTATTCTGTTTCAATCTTTAT
Found at i:6078815 original size:15 final size:16
Alignment explanation
Indices: 6078788--6078823 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
6078778 TTATGTTGTT
*
6078788 TTAACAGTTGATTTAA
1 TTAACAGTTGATTGAA
6078804 TTAACA-TTGATTGAA
1 TTAACAGTTGATTGAA
6078819 TTAAC
1 TTAAC
6078824 TTTTGCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (16 bp):
TTAACAGTTGATTGAA
Found at i:6081912 original size:52 final size:52
Alignment explanation
Indices: 6081851--6081953 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
6081841 CTTTAAATAT
* * * *
6081851 TTTACGTATTTTGAAATGGTTTTTAATGCATGAAGAAAAA-CTTTGGAGCATG
1 TTTAAGTATTTTGAAATGATATTTAATGCATAAAGAAAAACCTTT-GAGCATG
* *
6081903 TTTAAGTATTTTGAAGTGATATTTGATGCATAAAGAAAAACCTTTGAGCAT
1 TTTAAGTATTTTGAAATGATATTTAATGCATAAAGAAAAACCTTTGAGCAT
6081954 TTTTTATCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
52 40 0.91
53 4 0.09
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (52 bp):
TTTAAGTATTTTGAAATGATATTTAATGCATAAAGAAAAACCTTTGAGCATG
Found at i:6082103 original size:22 final size:22
Alignment explanation
Indices: 6082078--6082149 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
6082068 TGTGTAATCG
* *
6082078 ATTTTTGAGCATTGTGTGACTA
1 ATTTTTGAGCATTGCGTGATTA
* *
6082100 ATTTTT-AGATATTACGTGATTA
1 ATTTTTGAG-CATTGCGTGATTA
6082122 ATTTTTGAGCATTGCGTGATTA
1 ATTTTTGAGCATTGCGTGATTA
*
6082144 GTTTTT
1 ATTTTT
6082150 AGGTGTTGCG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (22 bp):
ATTTTTGAGCATTGCGTGATTA
Found at i:6082165 original size:44 final size:44
Alignment explanation
Indices: 6082078--6082167 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
6082068 TGTGTAATCG
* *
6082078 ATTTTTGAGCATTGTGTGACTAATTTTTAGATATTACGTGATTA
1 ATTTTTGAGCATTGCGTGACTAATTTTTAGATATTACGAGATTA
* * * * *
6082122 ATTTTTGAGCATTGCGTGATTAGTTTTTAGGTGTTGCGAGATTA
1 ATTTTTGAGCATTGCGTGACTAATTTTTAGATATTACGAGATTA
6082166 AT
1 AT
6082168 ATTTAGATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (44 bp):
ATTTTTGAGCATTGCGTGACTAATTTTTAGATATTACGAGATTA
Found at i:6082186 original size:22 final size:22
Alignment explanation
Indices: 6082093--6082213 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
6082083 TGAGCATTGT
*
6082093 GTGACTAATTTTTAGATATTAC
1 GTGATTAATTTTTAGATATTAC
* *
6082115 GTGATTAATTTTT-GAGCATTGC
1 GTGATTAATTTTTAGA-TATTAC
* * * *
6082137 GTGATTAGTTTTTAGGTGTTGC
1 GTGATTAATTTTTAGATATTAC
* *
6082159 GAGATTAATATTTAGATATTAC
1 GTGATTAATTTTTAGATATTAC
* ** *
6082181 GTGATTGATTGATACGACATTAC
1 GTGATTAATTTTTA-GATATTAC
*
6082204 GTGACTAATT
1 GTGATTAATT
6082214 GATAAGCATT
Statistics
Matches: 75, Mismatches: 21, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
21 2 0.03
22 57 0.76
23 16 0.21
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (22 bp):
GTGATTAATTTTTAGATATTAC
Found at i:6082376 original size:101 final size:101
Alignment explanation
Indices: 6082196--6082394 Score: 353
Period size: 101 Copynumber: 2.0 Consensus size: 101
6082186 TGATTGATAC
*
6082196 GACATTACGTGACTAATTGATAAGCATTGCCTGATTGGTTAGTAAGACATTGTGTGATTAGTTAA
1 GACATTACGTGACTAATTGATAAGCATTGCATGATTGGTTAGTAAGACATTGTGTGATTAGTTAA
* *
6082261 TAAGGTATAGTGTGACTTAGGCATTACTTAAAATAT
66 TAAGGTATAATGTGACTTAAGCATTACTTAAAATAT
* *
6082297 GACATTACGTGACTAATTGATAAGCATTGCATGATTGGTTAGTAAGATATTGTGTGATTAGTTGA
1 GACATTACGTGACTAATTGATAAGCATTGCATGATTGGTTAGTAAGACATTGTGTGATTAGTTAA
6082362 TAAGGTATAATGTGACTTAAGCATTACTTAAAA
66 TAAGGTATAATGTGACTTAAGCATTACTTAAAA
6082395 ATTAATCACA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.36
Consensus pattern (101 bp):
GACATTACGTGACTAATTGATAAGCATTGCATGATTGGTTAGTAAGACATTGTGTGATTAGTTAA
TAAGGTATAATGTGACTTAAGCATTACTTAAAATAT
Found at i:6082439 original size:21 final size:22
Alignment explanation
Indices: 6082391--6082441 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6082381 AGCATTACTT
* *
6082391 AAAAATTAATCACACAATGCTT
1 AAAAATTAATCACACAAAGCTC
*
6082413 AAAAATTAATCACATAAAG-TC
1 AAAAATTAATCACACAAAGCTC
6082434 AAAAATTA
1 AAAAATTA
6082442 GTTACGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAAATTAATCACACAAAGCTC
Found at i:6082459 original size:22 final size:22
Alignment explanation
Indices: 6082390--6082461 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
6082380 AAGCATTACT
* *
6082390 TAAAAATTAATCACACAATG-C
1 TAAAAATTAATCACATAAAGTC
6082411 TTAAAAATTAATCACATAAAGTC
1 -TAAAAATTAATCACATAAAGTC
* * * *
6082434 -AAAAATTAGTTACGTAATGTC
1 TAAAAATTAATCACATAAAGTC
6082455 TAAAAAT
1 TAAAAAT
6082462 CAAATACGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 17 0.40
22 24 0.57
23 1 0.02
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (22 bp):
TAAAAATTAATCACATAAAGTC
Found at i:6082500 original size:23 final size:22
Alignment explanation
Indices: 6082474--6082521 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
6082464 AATACGTAAT
* *
6082474 AATTAAGTTACGTAATGTCTAAA
1 AATTAA-TTACATAATATCTAAA
*
6082497 AATTAATTTCATAATATCTAAA
1 AATTAATTACATAATATCTAAA
6082519 AAT
1 AAT
6082522 CAAAGACACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTAATTACATAATATCTAAA
Found at i:6085166 original size:3 final size:3
Alignment explanation
Indices: 6085151--6085181 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6085141 AACTTCCTAA
*
6085151 TAT TAT GAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6085182 GTCTCTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6087181 original size:2 final size:2
Alignment explanation
Indices: 6087174--6087227 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
6087164 AGCTTTCATG
* * * * *
6087174 TC TC TC TC TC GC TC GC TC GC AC GC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6087216 TC TC TC TC TC TC
1 TC TC TC TC TC TC
6087228 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.02, C:0.50, G:0.07, T:0.41
Consensus pattern (2 bp):
TC
Found at i:6087577 original size:7 final size:7
Alignment explanation
Indices: 6087565--6087593 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
6087555 AATTGAGTTT
6087565 AGTTCCA
1 AGTTCCA
6087572 AGTTCCA
1 AGTTCCA
6087579 AGTTCCA
1 AGTTCCA
6087586 AGTTCCA
1 AGTTCCA
6087593 A
1 A
6087594 CTTTGATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (7 bp):
AGTTCCA
Found at i:6098278 original size:14 final size:13
Alignment explanation
Indices: 6098261--6098313 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
6098251 TAAGTTATTT
6098261 ATTTCAAGTTTAAA
1 ATTT-AAGTTTAAA
* *
6098275 ATTTAACATTCAAA
1 ATTTAA-GTTTAAA
*
6098289 ATTTAAGTTTTAA
1 ATTTAAGTTTAAA
6098302 ATTTAAGATTTA
1 ATTTAAG-TTTA
6098314 TAATATAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 13 0.42
14 18 0.58
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (13 bp):
ATTTAAGTTTAAA
Done.