Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 11 of 31
Found at i:5703260 original size:50 final size:49
Alignment explanation
Indices: 5703201--5703354 Score: 236
Period size: 49 Copynumber: 3.1 Consensus size: 49
5703191 GTGTCACGGG
5703201 GTCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTACAAACT
1 GTCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTAC-AACT
* *
5703251 GTCTTGAATGTGTTTGTCTTGAAATTTAATTTTGAAAAGACTTACAATT
1 GTCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTACAACT
* * * *
5703300 GTCTTAAATGTGGTTGTTCTCAAATTTAATTTTGAAAAGACTTACAACT
1 GTCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTACAACT
*
5703349 ATCTTG
1 GTCTTG
5703355 TGTCACGTGG
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
49 50 0.53
50 44 0.47
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (49 bp):
GTCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTACAACT
Found at i:5703290 original size:163 final size:163
Alignment explanation
Indices: 5703089--5703399 Score: 577
Period size: 163 Copynumber: 1.9 Consensus size: 163
5703079 TGTCACGGGA
*
5703089 TCTTGAATGTGTTTATCCTGAAATTTAATTTTGAAAAGACTTACAATTTTCTTAAATGTGGTTGT
1 TCTTGAATGTGTTTATCCTGAAATTTAATTTTGAAAAGACTTACAATTGTCTTAAATGTGGTTGT
*
5703154 TCTCAAATTTAATTTTGAAAAGACTTACAACTGTCTTGTGTCACGGGGTCTTGAATGTGTTTGTC
66 TCTCAAATTTAATTTTGAAAAGACTTACAACTATCTTGTGTCACGGGGTCTTGAATGTGTTTGTC
5703219 CTGAAATTTAATTTTGAAAAGACTTACAAACTG
131 CTGAAATTTAATTTTGAAAAGACTTACAAACTG
* *
5703252 TCTTGAATGTGTTTGTCTTGAAATTTAATTTTGAAAAGACTTACAATTGTCTTAAATGTGGTTGT
1 TCTTGAATGTGTTTATCCTGAAATTTAATTTTGAAAAGACTTACAATTGTCTTAAATGTGGTTGT
*
5703317 TCTCAAATTTAATTTTGAAAAGACTTACAACTATCTTGTGTCACGTGGTCTTGAATGTGTTTGTC
66 TCTCAAATTTAATTTTGAAAAGACTTACAACTATCTTGTGTCACGGGGTCTTGAATGTGTTTGTC
5703382 CTGAAATTTAATTTTGAA
131 CTGAAATTTAATTTTGAA
5703400 NNNNNNNNNN
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
163 143 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (163 bp):
TCTTGAATGTGTTTATCCTGAAATTTAATTTTGAAAAGACTTACAATTGTCTTAAATGTGGTTGT
TCTCAAATTTAATTTTGAAAAGACTTACAACTATCTTGTGTCACGGGGTCTTGAATGTGTTTGTC
CTGAAATTTAATTTTGAAAAGACTTACAAACTG
Found at i:5703612 original size:49 final size:49
Alignment explanation
Indices: 5703555--5703700 Score: 229
Period size: 49 Copynumber: 3.0 Consensus size: 49
5703545 GAATTAAGGA
*
5703555 TGTTTGTTCTCAAATTTAATTTTGAAAAAACTTATAACTGTCTTGAATG
1 TGTTTGTTCTCAAATTTAATTTTGAAAAAACTTACAACTGTCTTGAATG
* **
5703604 TGTTTGTTCTCAAATTTAATTTTGGAATTACTTACAACTGTCTTGAATG
1 TGTTTGTTCTCAAATTTAATTTTGAAAAAACTTACAACTGTCTTGAATG
* * *
5703653 TATTTGTTCTCAAATTTAATTTTGAAAAGACTTACAACTGTCGTGAAT
1 TGTTTGTTCTCAAATTTAATTTTGAAAAAACTTACAACTGTCTTGAAT
5703701 ATGAATTCTT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (49 bp):
TGTTTGTTCTCAAATTTAATTTTGAAAAAACTTACAACTGTCTTGAATG
Found at i:5705338 original size:14 final size:12
Alignment explanation
Indices: 5705305--5705337 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5705295 TATGTTAAAG
5705305 ATATAAAAATAT
1 ATATAAAAATAT
*
5705317 GTATAAAAATAT
1 ATATAAAAATAT
5705329 ATATAAAAA
1 ATATAAAAA
5705338 ATTTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
ATATAAAAATAT
Found at i:5709571 original size:14 final size:14
Alignment explanation
Indices: 5709554--5709607 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
5709544 ATTAAAAAAA
5709554 AGAAAGAAAAAGAG
1 AGAAAGAAAAAGAG
5709568 AGAACAAGGAAAAAGAG
1 AG-A-AA-GAAAAAGAG
5709585 -GAAAGAGAAAAGA-
1 AGAAAGA-AAAAGAG
5709598 AGAAAGAAAA
1 AGAAAGAAAA
5709608 TCGCTTTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.14
14 16 0.46
15 2 0.06
16 3 0.09
17 9 0.26
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAGAG
Found at i:5725646 original size:25 final size:25
Alignment explanation
Indices: 5725618--5725672 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5725608 TTTTAATTTT
5725618 AAAAAGTAAAAAATA-TGAAAAATAA
1 AAAAAG-AAAAAATATTGAAAAATAA
* *
5725643 AAAAAGAAAAAATATTGAATATTAA
1 AAAAAGAAAAAATATTGAAAAATAA
5725668 AAAAA
1 AAAAA
5725673 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (25 bp):
AAAAAGAAAAAATATTGAAAAATAA
Found at i:5731841 original size:24 final size:24
Alignment explanation
Indices: 5731814--5731940 Score: 143
Period size: 24 Copynumber: 5.3 Consensus size: 24
5731804 CAGTCTCTGA
* *
5731814 TGATGCTTGTTTCACTGGCTCCAC
1 TGATTCTTGTTTCACAGGCTCCAC
* * *
5731838 TGATTCTAGTTCCTCAGGCTCCAC
1 TGATTCTTGTTTCACAGGCTCCAC
*
5731862 CGATTC-TGTTTGCACAGGCTCCAC
1 TGATTCTTGTTT-CACAGGCTCCAC
*
5731886 TGATTCTTGTTTCACTGGCTCCAC
1 TGATTCTTGTTTCACAGGCTCCAC
5731910 T-AGTTC-TGTTTTCACAGGCTCCAC
1 TGA-TTCTTG-TTTCACAGGCTCCAC
5731934 TGATTCT
1 TGATTCT
5731941 CGTTGCACTA
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
23 6 0.07
24 73 0.86
25 6 0.07
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.37
Consensus pattern (24 bp):
TGATTCTTGTTTCACAGGCTCCAC
Found at i:5731939 original size:72 final size:72
Alignment explanation
Indices: 5731814--5731948 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 72
5731804 CAGTCTCTGA
*
5731814 TGATGCTTGTTTCACTGGCTCCACTGATTCTAGTTCCTCAGGCTCCACCGATTCT-GTTTGCACA
1 TGATGCTTGTTTCACTGGCTCCACTGATTCTAGTTCCACAGGCTCCACCGATTCTCG-TTGCACA
5731878 GGCTCCAC
65 GGCTCCAC
* * *
5731886 TGATTCTTGTTTCACTGGCTCCACT-AGTTCT-GTTTTCACAGGCTCCACTGATTCTCGTTGCAC
1 TGATGCTTGTTTCACTGGCTCCACTGA-TTCTAG-TTCCACAGGCTCCACCGATTCTCGTTGCAC
5731949 TAGTTCCGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
71 2 0.04
72 53 0.95
73 1 0.02
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.36
Consensus pattern (72 bp):
TGATGCTTGTTTCACTGGCTCCACTGATTCTAGTTCCACAGGCTCCACCGATTCTCGTTGCACAG
GCTCCAC
Found at i:5737177 original size:166 final size:163
Alignment explanation
Indices: 5736902--5737246 Score: 498
Period size: 166 Copynumber: 2.1 Consensus size: 163
5736892 TATGCTTATA
* * * *
5736902 TATGTTGAATGCTATGGGTGAGTTTGGGAATAGTTTGGATTTTTTTTTTTTTAGTTGGGGGAACT
1 TATGTTGAATGCTGTGGGTGAGTTTGGGAATAGTTTGGATTTTTCTTTTCTTAGTTGGGGAAACT
* * * * * *
5736967 GAATAGCTTTGGATAGTGTATTTTAAATTGCAAGGTCATGAATTTGTGTAAGAAGGATTGGTGTC
66 AAAAAGCTTTGGATAGTGTATTTGAAATTGCAAGCTAATGAATTTGTATAAGAAGGATTGGTGTC
*
5737032 ATTTCTTCAATGAAAAAAATAAAGAGAGTAAATCTTG
131 ATTTCTTCAACG---AAAA-AAAGAGAGTAAATCTTG
5737069 TATGTTGAATGCTGTGGGTGAGTTTGGTG-ATAGTTTGGA-TTTTCTTTTCTTAGTTGGGGAAAC
1 TATGTTGAATGCTGTGGGTGAGTTTGG-GAATAGTTTGGATTTTTCTTTTCTTAGTTGGGGAAAC
5737132 TAAAAAGCTTTGGATAGTGTATTTGAAATTGCAAGCTAATGAATTTGTATAAGAAGGATTGGTGT
65 TAAAAAGCTTTGGATAGTGTATTTGAAATTGCAAGCTAATGAATTTGTATAAGAAGGATTGGTGT
*
5737197 CATTTCTTCAACGGAAAAAAGAGAGTAAATCTTG
130 CATTTCTTCAACGAAAAAAAGAGAGTAAATCTTG
*
5737231 T-TTTCTGAATGCTGTG
1 TATGT-TGAATGCTGTG
5737247 TGATGCTAAC
Statistics
Matches: 163, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
161 2 0.01
162 29 0.18
163 3 0.02
166 92 0.56
167 36 0.22
168 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.39
Consensus pattern (163 bp):
TATGTTGAATGCTGTGGGTGAGTTTGGGAATAGTTTGGATTTTTCTTTTCTTAGTTGGGGAAACT
AAAAAGCTTTGGATAGTGTATTTGAAATTGCAAGCTAATGAATTTGTATAAGAAGGATTGGTGTC
ATTTCTTCAACGAAAAAAAGAGAGTAAATCTTG
Found at i:5741684 original size:2 final size:2
Alignment explanation
Indices: 5741679--5741712 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5741669 CTGTGTGTCA
*
5741679 GT GT GT GT GT GT GT GT GT GT GT -T TT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
5741713 GTTCTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
GT
Found at i:5747245 original size:26 final size:26
Alignment explanation
Indices: 5747211--5747263 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
5747201 AAAAAATTCA
5747211 TAATTTATAATTAAA-ATATTAATATT
1 TAATTTATAATTAAATA-ATTAATATT
*
5747237 TAATTTATAATTTAATAATTAATATT
1 TAATTTATAATTAAATAATTAATATT
5747263 T
1 T
5747264 TATAATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TAATTTATAATTAAATAATTAATATT
Found at i:5747285 original size:20 final size:20
Alignment explanation
Indices: 5747225--5747294 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
5747215 TTATAATTAA
5747225 AATATTAATATTTAATTTAT
1 AATATTAATATTTAATTTAT
*
5747245 AAT-TTAATAATTAATATTTTAT
1 AATATTAAT-ATT--TAATTTAT
*
5747267 AATACTAATATTTAATTTAT
1 AATATTAATATTTAATTTAT
5747287 AAT-TTAAT
1 AATATTAAT
5747295 TGTTATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 9 0.21
20 16 0.38
22 13 0.31
23 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTAATATTTAATTTAT
Found at i:5747289 original size:7 final size:7
Alignment explanation
Indices: 5747205--5747292 Score: 53
Period size: 7 Copynumber: 12.9 Consensus size: 7
5747195 TTATTTAAAA
*
5747205 AATTCAT
1 AATTTAT
5747212 AATTTAT
1 AATTTAT
*
5747219 AA-TTAA
1 AATTTAT
*
5747225 AATAT-T
1 AATTTAT
5747231 AATATT-T
1 AAT-TTAT
5747238 AATTTAT
1 AATTTAT
5747245 AATTTAAT
1 AATTT-AT
*
5747253 AATTAAT
1 AATTTAT
*
5747260 ATTTTAT
1 AATTTAT
5747267 AA--TACT
1 AATTTA-T
5747273 AATATT-T
1 AAT-TTAT
5747280 AATTTAT
1 AATTTAT
5747287 AATTTA
1 AATTTA
5747293 ATTGTTATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
5 2 0.03
6 15 0.24
7 39 0.62
8 6 0.10
9 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (7 bp):
AATTTAT
Found at i:5747321 original size:21 final size:20
Alignment explanation
Indices: 5747288--5747328 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5747278 TTAATTTATA
5747288 ATTTAATTGTTATTATTATTT
1 ATTTAATTGTTATTA-TATTT
* *
5747309 ATTTATTTTTTATTATATTT
1 ATTTAATTGTTATTATATTT
5747329 TTAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTAATTGTTATTATATTT
Found at i:5747448 original size:157 final size:155
Alignment explanation
Indices: 5747150--5747448 Score: 334
Period size: 157 Copynumber: 1.9 Consensus size: 155
5747140 ATAAATATGA
* * * * ** *
5747150 TTATTTATTTTTATGTTTTTTTTTAAATTATTAATATTTTATAATTTATTTAAAAAATTCATAAT
1 TTATTTATTTTTATGTATATTTTTAAAATATTAATAATTTATAATCGATTTAAAAAATTAATAAT
* * * *
5747215 TTATAATTAAAATATTAATATTTAATTTATAATTTAATAATTAATATTTTATAATACTAATATTT
66 TGATAATTAAAATATTAATATTTAATTTATAATTTAATAATT-ATATATTAAAATACTAATAATT
*
5747280 AATTTATAATTTAATTGTTATTATTAT
130 -ATTAATAATTTAATTGTTATTATTAT
* *
5747307 TTATTTATTTTTTAT-TATATTTTTAAAATATTAATAATTTATAATCGATTTAATATATTAATAA
1 TTATTTA-TTTTTATGTATATTTTTAAAATATTAATAATTTATAATCGATTTAAAAAATTAATAA
* * * * * *
5747371 TTGATCATTTAAATATTACTATTTAATTTATACTTTAAGTGATGT-TATGATTAAAATATTAATA
65 TTGATAATTAAAATATTAATATTTAATTTATAATTTAA-TAAT-TATAT-ATTAAAATACTAATA
5747435 ATT-TTAATCAATTT
127 ATTATTAAT-AATTT
5747449 TTAAATTTAA
Statistics
Matches: 117, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
156 4 0.03
157 88 0.75
158 24 0.21
159 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (155 bp):
TTATTTATTTTTATGTATATTTTTAAAATATTAATAATTTATAATCGATTTAAAAAATTAATAAT
TGATAATTAAAATATTAATATTTAATTTATAATTTAATAATTATATATTAAAATACTAATAATTA
TTAATAATTTAATTGTTATTATTAT
Found at i:5747571 original size:41 final size:40
Alignment explanation
Indices: 5747525--5747623 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 40
5747515 ATAATTGATT
*
5747525 ATTTAAATATTAATATTTTAGTTATCATTTAATCATTAAC
1 ATTTAAATATTAATATTTTAGTTATAATTTAATCATTAAC
* *
5747565 ACTTTAAAATATGAATATTTT-TTTATAATTTAATCATTAAC
1 A-TTT-AAATATTAATATTTTAGTTATAATTTAATCATTAAC
*
5747606 ATTTTAATATT--TATTTTA
1 ATTTAAATATTAATATTTTA
5747624 TTTTTAGTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
37 6 0.12
39 5 0.10
40 4 0.08
41 22 0.43
42 14 0.27
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (40 bp):
ATTTAAATATTAATATTTTAGTTATAATTTAATCATTAAC
Found at i:5747857 original size:22 final size:21
Alignment explanation
Indices: 5747814--5747867 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
5747804 AATGATTTTA
*
5747814 ATTAATTTTTAAATTTAAAAT
1 ATTAATTTTTAAATATAAAAT
* *
5747835 ATTATTTTTTATAATATATAAT
1 ATTAATTTTTA-AATATAAAAT
*
5747857 AAGTAATTTTT
1 -ATTAATTTTT
5747868 CAAACTTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.38
22 8 0.31
23 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTAATTTTTAAATATAAAAT
Found at i:5758927 original size:15 final size:14
Alignment explanation
Indices: 5758900--5758926 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5758890 TAAAATTGTA
5758900 TTTTTTTAAAAAAG
1 TTTTTTTAAAAAAG
5758914 TTTTTTTAAAAAA
1 TTTTTTTAAAAAA
5758927 ATTCTGCTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
TTTTTTTAAAAAAG
Found at i:5759080 original size:88 final size:88
Alignment explanation
Indices: 5758914--5759081 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
5758904 TTTAAAAAAG
** *
5758914 TTTTTTTAAAAAAATTCTGCTCGTAATCTAAAGACAATTTAAAAGATCAATTCAATTGTTAGATA
1 TTTTTTTAAAAAAATTCTGCTAATAATCTAAAGACAATTTAAAAGATCAATTCAATTGTTAGAAA
*
5758979 TTTAAATACCTTTTTTCAAAATT
66 TTTAAACACCTTTTTTCAAAATT
* * * * *
5759002 TTTTTTTAAAAAGATTCTGTTAATAATTTAAAGACGATTT-AAAGAGTCAATTCAATTGTTTGAA
1 TTTTTTTAAAAAAATTCTGCTAATAATCTAAAGACAATTTAAAAGA-TCAATTCAATTGTTAGAA
* *
5759066 ATTTGAACATCTTTTT
65 ATTTAAACACCTTTTT
5759082 AATTCAAAAC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 5 0.07
88 63 0.93
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (88 bp):
TTTTTTTAAAAAAATTCTGCTAATAATCTAAAGACAATTTAAAAGATCAATTCAATTGTTAGAAA
TTTAAACACCTTTTTTCAAAATT
Found at i:5759182 original size:17 final size:17
Alignment explanation
Indices: 5759160--5759192 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5759150 CCTTATGAGG
5759160 TATTGAGTGAATTTTTA
1 TATTGAGTGAATTTTTA
5759177 TATTGAGTGAATTTTT
1 TATTGAGTGAATTTTT
5759193 GTTAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
TATTGAGTGAATTTTTA
Found at i:5769704 original size:99 final size:99
Alignment explanation
Indices: 5769526--5769708 Score: 271
Period size: 99 Copynumber: 1.8 Consensus size: 99
5769516 TCTTCAAGGC
* * * *
5769526 TAGAAGCACTGTTGATTTACAGCCTCTTTGAAAGATTATCTCCAGTAGTCTTGGCTTGAGGTAGT
1 TAGAAGCACTGTTGATTTACAACCTCTTAGAAAGATCATCTCCAATAGTCTTGGCTTGAGGTAGT
* *
5769591 ATACTAAATGAAAAACAACTTTGTCGACAGAATT
66 ATACCAAATAAAAAACAACTTTGTCGACAGAATT
*
5769625 TAGAAGCA-TAGTTGATTTACAACCTCTTAGAAAGATCATCTCGAATAGGT-TTGGCTTGAGGTA
1 TAGAAGCACT-GTTGATTTACAACCTCTTAGAAAGATCATCTCCAATA-GTCTTGGCTTGAGGTA
5769688 GTATACCAAATAAAAAACAAC
64 GTATACCAAATAAAAAACAAC
5769709 ATCGTTGGCA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
98 1 0.01
99 72 0.96
100 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (99 bp):
TAGAAGCACTGTTGATTTACAACCTCTTAGAAAGATCATCTCCAATAGTCTTGGCTTGAGGTAGT
ATACCAAATAAAAAACAACTTTGTCGACAGAATT
Found at i:5771364 original size:21 final size:21
Alignment explanation
Indices: 5771338--5771377 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5771328 ACAAACTCCC
5771338 TCTCCTTCTCC-ATCCTCTCTT
1 TCTCC-TCTCCTATCCTCTCTT
*
5771359 TCTCCTCTCCTCTCCTCTC
1 TCTCCTCTCCTATCCTCTC
5771378 CCTCCTCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.45
Consensus pattern (21 bp):
TCTCCTCTCCTATCCTCTCTT
Found at i:5771369 original size:5 final size:5
Alignment explanation
Indices: 5771336--5771389 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
5771326 CAACAAACTC
* *
5771336 CCTCT CCTTCT CC-AT CCTCT CTTTCT CCTCT CCTCT CCTCT CC-CT CCTCT
1 CCTCT CC-TCT CCTCT CCTCT C-CTCT CCTCT CCTCT CCTCT CCTCT CCTCT
5771386 CCTC
1 CCTC
5771390 CTCTACCACA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 7 0.17
5 25 0.61
6 9 0.22
ACGTcount: A:0.02, C:0.57, G:0.00, T:0.41
Consensus pattern (5 bp):
CCTCT
Found at i:5773071 original size:24 final size:23
Alignment explanation
Indices: 5773044--5773096 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5773034 AGTTAGTTAT
*
5773044 AAAAATTTATTTAATTTAAAATAA
1 AAAAATTTAATTAA-TTAAAATAA
* * *
5773068 AAAAACTTAATTAATTATAATAG
1 AAAAATTTAATTAATTAAAATAA
5773091 AAAAAT
1 AAAAAT
5773097 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAATTTAATTAATTAAAATAA
Found at i:5773094 original size:25 final size:24
Alignment explanation
Indices: 5773044--5773095 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5773034 AGTTAGTTAT
* * *
5773044 AAAAATTTATTTAATTTAAAATAA
1 AAAAACTTAATTAATTTAAAAGAA
*
5773068 AAAAACTTAATTAATTATAATAGAA
1 AAAAACTTAATTAATT-TAAAAGAA
5773093 AAA
1 AAA
5773096 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAACTTAATTAATTTAAAAGAA
Found at i:5791662 original size:26 final size:27
Alignment explanation
Indices: 5791632--5791686 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
5791622 AATAAAATTT
*
5791632 TATTTAATTCAA-AATAAAAATATAAA
1 TATTTAATTAAAGAATAAAAATATAAA
*
5791658 TATTTGATTAAAGGTAATAAAAATATAAA
1 TATTTAATTAAA-G-AATAAAAATATAAA
5791687 CACTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
29 14 0.58
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (27 bp):
TATTTAATTAAAGAATAAAAATATAAA
Found at i:5791771 original size:10 final size:10
Alignment explanation
Indices: 5791756--5791790 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5791746 CTACACCCCC
5791756 TTTTTCTTTT
1 TTTTTCTTTT
*
5791766 TTTTTCTCTT
1 TTTTTCTTTT
*
5791776 TTTATCTTTT
1 TTTTTCTTTT
5791786 TTTTT
1 TTTTT
5791791 TCTCTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:5791785 original size:20 final size:20
Alignment explanation
Indices: 5791756--5791798 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
5791746 CTACACCCCC
5791756 TTTTTC-TTTTTTTTTCTCT
1 TTTTTCTTTTTTTTTTCTCT
5791775 TTTTATCTTTTTTTTTTCTCT
1 TTTT-TCTTTTTTTTTTCTCT
5791796 TTT
1 TTT
5791799 ATGAGTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.18
20 2 0.09
21 16 0.73
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTCTCT
Found at i:5793397 original size:30 final size:30
Alignment explanation
Indices: 5793361--5793426 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
5793351 CTCCCTGACA
5793361 GGAGCAAAAGCAGAGAAGACTGATACTTTT
1 GGAGCAAAAGCAGAGAAGACTGATACTTTT
5793391 GGAGCAAAAGCAGAGAAGACTGATACTTTT
1 GGAGCAAAAGCAGAGAAGACTGATACTTTT
5793421 GGAGCA
1 GGAGCA
5793427 GTAGCATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (30 bp):
GGAGCAAAAGCAGAGAAGACTGATACTTTT
Found at i:5796695 original size:1 final size:1
Alignment explanation
Indices: 5796689--5796722 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
5796679 ATTTCCCTCA
5796689 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5796723 AACCCCACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:5797153 original size:63 final size:63
Alignment explanation
Indices: 5797085--5797204 Score: 222
Period size: 63 Copynumber: 1.9 Consensus size: 63
5797075 ATTTATTTTC
**
5797085 TATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAATTATAATTATTTAAATATAG
1 TATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAACGATAATTATTTAAATATAG
5797148 TATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAACGATAATTATTTAA
1 TATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAACGATAATTATTTAA
5797205 TTCCCATTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (63 bp):
TATTAGGTATATTTAATAAACTTTTAATTAATTATTAAACCAACGATAATTATTTAAATATAG
Found at i:5801418 original size:41 final size:41
Alignment explanation
Indices: 5801361--5801440 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
5801351 TGTACATGGT
5801361 TAAAACACGTAAATATGAATAATCAACTCTAAGAAAAACTA
1 TAAAACACGTAAATATGAATAATCAACTCTAAGAAAAACTA
* * *
5801402 TAAAACATGTGAATATGAATAGTCAACTCTAAGAAAAAC
1 TAAAACACGTAAATATGAATAATCAACTCTAAGAAAAAC
5801441 GATGTACAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.23
Consensus pattern (41 bp):
TAAAACACGTAAATATGAATAATCAACTCTAAGAAAAACTA
Found at i:5814236 original size:27 final size:27
Alignment explanation
Indices: 5814198--5814249 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5814188 AAGCAACCTC
5814198 AAAAAAAATCTCAATCAAAACGAAATA
1 AAAAAAAATCTCAATCAAAACGAAATA
5814225 AAAAAAAATCTCAATCAAAACGAAA
1 AAAAAAAATCTCAATCAAAACGAAA
5814250 CCGAGGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.67, C:0.15, G:0.04, T:0.13
Consensus pattern (27 bp):
AAAAAAAATCTCAATCAAAACGAAATA
Found at i:5815861 original size:15 final size:15
Alignment explanation
Indices: 5815822--5815861 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5815812 GTGCTAAAGT
5815822 TTTTAATTTTCTTTC
1 TTTTAATTTTCTTTC
** *
5815837 TTTTCTTTTTTTTTC
1 TTTTAATTTTCTTTC
5815852 TTTTAATTTT
1 TTTTAATTTT
5815862 GTTGTATATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTAATTTTCTTTC
Found at i:5821936 original size:27 final size:28
Alignment explanation
Indices: 5821906--5821958 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
5821896 ATTATCTCAG
5821906 TTCATGAACTCAA-TTTAATTCCCAATA
1 TTCATGAACTCAAGTTTAATTCCCAATA
* *
5821933 TTCATGAATTCAAGTTTAATTTCCAA
1 TTCATGAACTCAAGTTTAATTCCCAA
5821959 CATCCTCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (28 bp):
TTCATGAACTCAAGTTTAATTCCCAATA
Found at i:5825445 original size:27 final size:26
Alignment explanation
Indices: 5825383--5825461 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 26
5825373 TAAAACCTTG
*
5825383 ATAAATTAATTTTTATTAATTAATGT
1 ATAAATTAATATTTATTAATTAATGT
*
5825409 ATAAATTAATAATTTATTAATTTAT-T
1 ATAAATTAAT-ATTTATTAATTAATGT
5825435 GATTAAA-TAATATTTAGATTAATTAAT
1 -A-TAAATTAATATTT--ATTAATTAAT
5825462 AAATTTTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
26 15 0.33
27 17 0.38
28 13 0.29
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
ATAAATTAATATTTATTAATTAATGT
Found at i:5836060 original size:21 final size:21
Alignment explanation
Indices: 5836027--5836074 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
5836017 TAGTGAAAAC
*
5836027 CTTTTTCTTTGTCATTTCATT
1 CTTTTTCTGTGTCATTTCATT
* * **
5836048 CTTTTTGTGTGTCTTTTTTTT
1 CTTTTTCTGTGTCATTTCATT
5836069 CTTTTT
1 CTTTTT
5836075 TCAAATGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.15, G:0.08, T:0.73
Consensus pattern (21 bp):
CTTTTTCTGTGTCATTTCATT
Found at i:5838342 original size:43 final size:43
Alignment explanation
Indices: 5838213--5838520 Score: 155
Period size: 43 Copynumber: 7.2 Consensus size: 43
5838203 TTATGTTATT
* * *
5838213 AAGCATAATACTTGATATCCTTAATCTATAGCG-A-TATGGTTCA
1 AAGCATAATGCTTGATATCCTTGATCTA-AG-GTACTATGGTTCC
* * * * * * * * *
5838256 AATCATTACGCTTGATATCTTTGATTTGTA-GTGCTACGCTTCC
1 AAGCATAATGCTTGATATCCTTGATCT-AAGGTACTATGGTTCC
* *
5838299 AAG-ACTAATGCTTAATATCCTTGATCTGAGGTACTATGGTTCC
1 AAGCA-TAATGCTTGATATCCTTGATCTAAGGTACTATGGTTCC
* * ** *
5838342 AAGCATAATAG-ATGATATCCTTGATATAAGGTGTTATGGTACC
1 AAGCATAAT-GCTTGATATCCTTGATCTAAGGTACTATGGTTCC
* * * *
5838385 AAGCATAATGCTTGATATCCTTAATCTATA-GTGA-TATAGTGCA
1 AAGCATAATGCTTGATATCCTTGATCTA-AGGT-ACTATGGTTCC
* * * * * * *
5838428 AATCATTATGCTTGATATCCTTGATCTATA-ATGCTACGCTTTC
1 AAGCATAATGCTTGATATCCTTGATCTA-AGGTACTATGGTTCC
* * * * * * *
5838471 AAGCCTAATGCCTGATATCTTTGATTTGAGGTACTACGATTCC
1 AAGCATAATGCTTGATATCCTTGATCTAAGGTACTATGGTTCC
5838514 AAGCATA
1 AAGCATA
5838521 TAGATGATAT
Statistics
Matches: 194, Mismatches: 59, Indels: 24
0.70 0.21 0.09
Matches are distributed among these distances:
41 1 0.01
42 4 0.02
43 186 0.96
44 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (43 bp):
AAGCATAATGCTTGATATCCTTGATCTAAGGTACTATGGTTCC
Found at i:5838350 original size:172 final size:172
Alignment explanation
Indices: 5838165--5838534 Score: 535
Period size: 172 Copynumber: 2.2 Consensus size: 172
5838155 GGGTGTTACA
* * * **
5838165 ATTCCAAGCATAATAAATGATATCCTTGATATAGGGTGTTATGTTATTAAGCATAATACTTGATA
1 ATTCCAAGCATAATAGATGATATCCTTGATATAAGGTGTTATGGTACCAAGCATAATACTTGATA
* * * * * *
5838230 TCCTTAATCTATAGCGATATGGTTCAAATCATTACGCTTGATATCTTTGATTTGTAGTGCTACGC
66 TCCTTAATCTATAGCGATATAGTGCAAATCATTACGCTTGATATCCTTGATCTATAATGCTACGC
* *
5838295 TTCCAAGACTAATGCTTAATATCCTTGATCTGAGGTACTATG
131 TTCCAAGACTAATGCCTAATATCCTTGATCTGAGGTACTACG
* *
5838337 GTTCCAAGCATAATAGATGATATCCTTGATATAAGGTGTTATGGTACCAAGCATAATGCTTGATA
1 ATTCCAAGCATAATAGATGATATCCTTGATATAAGGTGTTATGGTACCAAGCATAATACTTGATA
* *
5838402 TCCTTAATCTATAGTGATATAGTGCAAATCATTATGCTTGATATCCTTGATCTATAATGCTACGC
66 TCCTTAATCTATAGCGATATAGTGCAAATCATTACGCTTGATATCCTTGATCTATAATGCTACGC
* * * * *
5838467 TTTCAAGCCTAATGCCTGATATCTTTGATTTGAGGTACTACG
131 TTCCAAGACTAATGCCTAATATCCTTGATCTGAGGTACTACG
5838509 ATTCCAAGCAT-ATAGATGATATCCTT
1 ATTCCAAGCATAATAGATGATATCCTT
5838535 AATACTACTT
Statistics
Matches: 175, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
171 15 0.09
172 160 0.91
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (172 bp):
ATTCCAAGCATAATAGATGATATCCTTGATATAAGGTGTTATGGTACCAAGCATAATACTTGATA
TCCTTAATCTATAGCGATATAGTGCAAATCATTACGCTTGATATCCTTGATCTATAATGCTACGC
TTCCAAGACTAATGCCTAATATCCTTGATCTGAGGTACTACG
Found at i:5838358 original size:86 final size:83
Alignment explanation
Indices: 5838268--5838534 Score: 207
Period size: 86 Copynumber: 3.1 Consensus size: 83
5838258 TCATTACGCT
* * *
5838268 TGATATCTTTGATTTGTAGTGCTACGCTTCCAAGACTAATGCTTAATATCCTTGATCTGAGGTAC
1 TGATATCCTTGATAT-TAGTGCTACGCTTCCAAG-CTAATGCTTGATATCCTTGATCTGAGGTAC
5838333 TATGGTTCCAAGCATAATAGA
64 TATGGTTCCAAGCAT-ATAGA
* * * * * * *
5838354 TGATATCCTTGATATAAGGTGTTATGGTACCAAGCATAATGCTTGATATCCTTAATCT-ATAGTG
1 TGATATCCTTGATATTA-GTGCTACGCTTCCAAGC-TAATGCTTGATATCCTTGATCTGA-GGT-
* * * * *
5838418 A-TATAGTGCAAATCAT-TATGCT
62 ACTATGGTTCCAAGCATATA-G-A
* * * * * *
5838440 TGATATCCTTGATCTATAATGCTACGCTTTCAAGCCTAATGCCTGATATCTTTGATTTGAGGTAC
1 TGATATCCTTGATAT-TAGTGCTACGCTTCCAAG-CTAATGCTTGATATCCTTGATCTGAGGTAC
* *
5838505 TACGATTCCAAGCATATAGA
64 TATGGTTCCAAGCATATAGA
5838525 TGATATCCTT
1 TGATATCCTT
5838535 AATACTACTT
Statistics
Matches: 135, Mismatches: 35, Indels: 23
0.70 0.18 0.12
Matches are distributed among these distances:
84 2 0.01
85 15 0.11
86 112 0.83
87 6 0.04
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (83 bp):
TGATATCCTTGATATTAGTGCTACGCTTCCAAGCTAATGCTTGATATCCTTGATCTGAGGTACTA
TGGTTCCAAGCATATAGA
Found at i:5840155 original size:24 final size:24
Alignment explanation
Indices: 5840128--5840176 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5840118 TACTTACTTG
5840128 ATGATAAATAAGAGTTGATTACCA
1 ATGATAAATAAGAGTTGATTACCA
*
5840152 ATGATAAATAGGAGTTGATTACCA
1 ATGATAAATAAGAGTTGATTACCA
5840176 A
1 A
5840177 ATAATGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (24 bp):
ATGATAAATAAGAGTTGATTACCA
Found at i:5840569 original size:37 final size:35
Alignment explanation
Indices: 5840526--5840613 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 35
5840516 ATTGAATAAT
5840526 TTAAATATTAATATTTTAAGTTAAAAACT-TTTTAAAG
1 TTAAATATTAATATTTTAA-TTAAAAA-TATTTT-AAG
* ***
5840563 TTAAATATTGATATTTTTAATTTTTAATATTTTAAG
1 TTAAATATTAATA-TTTTAATTAAAAATATTTTAAG
5840599 TTAAATATTAATATT
1 TTAAATATTAATATT
5840614 CATCAAAGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
35 2 0.05
36 16 0.36
37 20 0.45
38 6 0.14
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (35 bp):
TTAAATATTAATATTTTAATTAAAAATATTTTAAG
Found at i:5860342 original size:24 final size:24
Alignment explanation
Indices: 5860314--5860371 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
5860304 AAATCGTAAT
*
5860314 GACATGGGCAGTCTTCACGATGAC
1 GACATGGGCAGTCTTCAAGATGAC
5860338 GACATGGGCAGTCTTCAAGATGAC
1 GACATGGGCAGTCTTCAAGATGAC
5860362 GACATGGGCA
1 GACATGGGCA
5860372 CTCTCGAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (24 bp):
GACATGGGCAGTCTTCAAGATGAC
Found at i:5861243 original size:65 final size:62
Alignment explanation
Indices: 5861132--5861261 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 62
5861122 TTTTATAAAT
5861132 TTAAATTTTCAATCAAAATATAAGATTGATCCGAATAATTAGAGTTTACTAATTAAGGTAAG
1 TTAAATTTTCAATCAAAATATAAGATTGATCCGAATAATTAGAGTTTACTAATTAAGGTAAG
*
5861194 TTAAATTTTCAATCAAAATATAAGAAGATTGATCCTAATAATTAGAGTTTACTAATTAAGGTAAG
1 TTAAATTTTCAATCAAAATAT---AAGATTGATCCGAATAATTAGAGTTTACTAATTAAGGTAAG
5861259 TTA
1 TTA
5861262 TCACTCAATG
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
62 21 0.33
65 43 0.67
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (62 bp):
TTAAATTTTCAATCAAAATATAAGATTGATCCGAATAATTAGAGTTTACTAATTAAGGTAAG
Found at i:5868336 original size:12 final size:12
Alignment explanation
Indices: 5868316--5868346 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5868306 TGCCTCTCTG
5868316 CTCTCTCTGTCT
1 CTCTCTCTGTCT
*
5868328 CTGTCTCTGTCT
1 CTCTCTCTGTCT
5868340 CTCTCTC
1 CTCTCTC
5868347 GTGCTTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.10, T:0.48
Consensus pattern (12 bp):
CTCTCTCTGTCT
Found at i:5876440 original size:22 final size:23
Alignment explanation
Indices: 5876409--5876453 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5876399 GCATGTGTTG
* *
5876409 ATATCTAT-AAAAGTTTTAATTA
1 ATATCAATAAAAAGTTTAAATTA
5876431 ATATCAATAAAAAGTTTAAATTA
1 ATATCAATAAAAAGTTTAAATTA
5876454 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
ATATCAATAAAAAGTTTAAATTA
Found at i:5890799 original size:2 final size:2
Alignment explanation
Indices: 5890792--5890833 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5890782 CAGTATAAAT
5890792 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5890833 T
1 T
5890834 TAGGATCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5890816 original size:23 final size:23
Alignment explanation
Indices: 5890785--5890833 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
5890775 GTTATTGCAG
5890785 TATAAATTATATATATATATATA
1 TATAAATTATATATATATATATA
*
5890808 TATATATTATATATATATATATA
1 TATAAATTATATATATATATATA
5890831 TAT
1 TAT
5890834 TAGGATCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAAATTATATATATATATATA
Found at i:5891614 original size:19 final size:19
Alignment explanation
Indices: 5891571--5891617 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5891561 AAAAAAAATA
*
5891571 TTAAAAA-ATTATTTTTAT
1 TTAAAAATATTATTATTAT
*
5891589 TTCAAAAATATTCTTATTAT
1 TT-AAAAATATTATTATTAT
5891609 TTAAAAATA
1 TTAAAAATA
5891618 ATTACAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 12 0.48
20 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAAATATTATTATTAT
Found at i:5896085 original size:2 final size:2
Alignment explanation
Indices: 5896078--5896109 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5896068 AAAATTAGTG
5896078 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
5896110 GAGAGAGAGA
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:5896114 original size:2 final size:2
Alignment explanation
Indices: 5896109--5896137 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5896099 ATATATATAT
5896109 AG 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 AG A
5896138 TGAAGTGAGT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5897583 original size:63 final size:64
Alignment explanation
Indices: 5897329--5897622 Score: 294
Period size: 64 Copynumber: 4.6 Consensus size: 64
5897319 TGTACCAATT
* ** * *
5897329 CGCCACACTCCCAGCGTTGCAGCGCTGTCCTCCCTTCACAAGGTAGTAGCAG-CAGCGCTGCAA
1 CGCCACACTCCCAACACTGCAGCGCTGTCCTCCCTTCACAAGGCAGTAGCAGTCAGCGCTGCAG
* ** * * *
5897392 CGTCACACTCTTAACACTGCAGCGCTAT-CTCCCTCTTCACCAA-GCAG-AACATTCAGCGCTGC
1 CGCCACACTCCCAACACTGCAGCGCTGTCCT-CC-CTTCA-CAAGGCAGTAGCAGTCAGCGCTGC
5897454 AG
63 AG
* * * * * * *
5897456 TGCCACACTCACATCTCTGCAGCACTGTCACTCCCTTCACAAGGTAGTAG-AATCAGCGCTGCAG
1 CGCCACACTCCCAACACTGCAGCGCTGTC-CTCCCTTCACAAGGCAGTAGCAGTCAGCGCTGCAG
* **
5897520 CGCCACACTCCCAGCACTGCAATGCTGTCCTCCCTTCACAAGGCAGTAGCAGT-AGCGCTGCAG
1 CGCCACACTCCCAACACTGCAGCGCTGTCCTCCCTTCACAAGGCAGTAGCAGTCAGCGCTGCAG
* *
5897583 CGCCACACTCCCAACACTGCAGCGCTATCCCCCTCTTCAC
1 CGCCACACTCCCAACACTGCAGCGCTGTCCTCC-CTTCAC
5897623 TAAGCACAAC
Statistics
Matches: 185, Mismatches: 36, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
62 2 0.01
63 86 0.46
64 89 0.48
65 6 0.03
66 2 0.01
ACGTcount: A:0.23, C:0.39, G:0.19, T:0.19
Consensus pattern (64 bp):
CGCCACACTCCCAACACTGCAGCGCTGTCCTCCCTTCACAAGGCAGTAGCAGTCAGCGCTGCAG
Found at i:5897687 original size:42 final size:42
Alignment explanation
Indices: 5897594--5897691 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 42
5897584 GCCACACTCC
*
5897594 CAACACTGCAGCGCTATCCCCCTCTTCACTAAGCACAACATT
1 CAACACTGCAGCGCTATCCCCCTCTTCACTAAGCACAACAAT
* ** *
5897636 CAACGCTGCAGCGCTATCCCTCC-CTTCAC-AAGGCAGTAGAAT
1 CAACACTGCAGCGCTATCCC-CCTCTTCACTAA-GCACAACAAT
*
5897678 CAGCACTGCAGCGC
1 CAACACTGCAGCGC
5897692 CACACTTCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (42 bp):
CAACACTGCAGCGCTATCCCCCTCTTCACTAAGCACAACAAT
Found at i:5898188 original size:19 final size:18
Alignment explanation
Indices: 5898113--5898178 Score: 132
Period size: 18 Copynumber: 3.7 Consensus size: 18
5898103 AAAATTTTAT
5898113 TTAAAATTTTTTAAATAA
1 TTAAAATTTTTTAAATAA
5898131 TTAAAATTTTTTAAATAA
1 TTAAAATTTTTTAAATAA
5898149 TTAAAATTTTTTAAATAA
1 TTAAAATTTTTTAAATAA
5898167 TTAAAATTTTTT
1 TTAAAATTTTTT
5898179 TAAAGTATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAAATTTTTTAAATAA
Found at i:5901548 original size:3 final size:3
Alignment explanation
Indices: 5901535--5901566 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5901525 TTATTCCAAA
*
5901535 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5901567 CTTTCCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5902625 original size:2 final size:2
Alignment explanation
Indices: 5902618--5902644 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5902608 AAACTAACTT
5902618 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5902645 GTTTTTTCTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5910389 original size:2 final size:2
Alignment explanation
Indices: 5910382--5910413 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5910372 NNNNNNNNNN
5910382 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
5910414 TAGGATCATG
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:5911192 original size:18 final size:17
Alignment explanation
Indices: 5911169--5911202 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5911159 AAAAATATTA
*
5911169 AAAAATTATTTTTATTTC
1 AAAAA-TATTCTTATTTC
5911187 AAAAATATTCTTATTT
1 AAAAATATTCTTATTT
5911203 ATTAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAAATATTCTTATTTC
Found at i:5921893 original size:25 final size:25
Alignment explanation
Indices: 5921865--5921915 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5921855 GCAGTCATCG
5921865 GATGCTTTAATTTTTCCTTTTGGTT
1 GATGCTTTAATTTTTCCTTTTGGTT
5921890 GATGCTTTAATTTTTCCTTTTGGTT
1 GATGCTTTAATTTTTCCTTTTGGTT
5921915 G
1 G
5921916 TTGATTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (25 bp):
GATGCTTTAATTTTTCCTTTTGGTT
Found at i:5929139 original size:13 final size:14
Alignment explanation
Indices: 5929116--5929149 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5929106 CCCACAAATG
*
5929116 TTTTTTATTTGTAA
1 TTTTTTATTTGGAA
5929130 TTTTTT-TTTGGAA
1 TTTTTTATTTGGAA
5929143 TTTTTTA
1 TTTTTTA
5929150 GATAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (14 bp):
TTTTTTATTTGGAA
Found at i:5930586 original size:2 final size:2
Alignment explanation
Indices: 5930553--5930577 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5930543 GAGTTAGCAG
5930553 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 A
5930578 CACATATATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5931161 original size:2 final size:2
Alignment explanation
Indices: 5931115--5931147 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5931105 ATTACCATTA
5931115 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 A
5931148 CCACTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5934615 original size:3 final size:3
Alignment explanation
Indices: 5934607--5934632 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5934597 TGCTTCTACA
5934607 AGT AGT AGT AGT AGT AGT AGT AGT AG
1 AGT AGT AGT AGT AGT AGT AGT AGT AG
5934633 AAGAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
AGT
Found at i:5953673 original size:2 final size:2
Alignment explanation
Indices: 5953666--5953691 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5953656 CTATTTTGTC
5953666 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
5953692 CTTGTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5958535 original size:4 final size:4
Alignment explanation
Indices: 5958526--5958553 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5958516 AGAGCTACAT
5958526 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5958554 TCTATGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:5959012 original size:42 final size:42
Alignment explanation
Indices: 5958953--5959048 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
5958943 ATTTTGCAAA
5958953 CAAGGGATACCATAATAGAAACAAAATACACCTTTGGCTTAG
1 CAAGGGATACCATAATAGAAACAAAATACACCTTTGGCTTAG
*
5958995 CAAGGGATACCATAATAGAAACAAAATACACCTTTTGCTTAG
1 CAAGGGATACCATAATAGAAACAAAATACACCTTTGGCTTAG
5959037 CAAGGGATACCA
1 CAAGGGATACCA
5959049 AATCATCAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.21
Consensus pattern (42 bp):
CAAGGGATACCATAATAGAAACAAAATACACCTTTGGCTTAG
Found at i:5959919 original size:2 final size:2
Alignment explanation
Indices: 5959912--5959953 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5959902 CCATACATAC
5959912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5959954 CACAGTAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5967116 original size:20 final size:20
Alignment explanation
Indices: 5967091--5967131 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5967081 AGATTTATAT
5967091 ATTTTACTAGTTGAGATGAA
1 ATTTTACTAGTTGAGATGAA
5967111 ATTTTACTAGTTGAGATGAA
1 ATTTTACTAGTTGAGATGAA
5967131 A
1 A
5967132 ACACCTCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTTTACTAGTTGAGATGAA
Found at i:5977962 original size:30 final size:30
Alignment explanation
Indices: 5977922--5977980 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
5977912 CTCCGACGCC
* *
5977922 GGCGATAAGAACGTCCCCCCCGCTACCGCG
1 GGCGAAAAGAACGTCCCCCCCGCCACCGCG
* *
5977952 GGCGAAAAGAACGTTCCCGCCGCCACCGC
1 GGCGAAAAGAACGTCCCCCCCGCCACCGC
5977981 TGGCAACGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.42, G:0.27, T:0.08
Consensus pattern (30 bp):
GGCGAAAAGAACGTCCCCCCCGCCACCGCG
Found at i:5986433 original size:4 final size:4
Alignment explanation
Indices: 5986424--5986449 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5986414 TTAAGGTGAC
5986424 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
5986450 AGCTTCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:6030212 original size:10 final size:11
Alignment explanation
Indices: 6030161--6030245 Score: 56
Period size: 10 Copynumber: 7.9 Consensus size: 11
6030151 TATTTTTTAT
*
6030161 TATTAAT-TTT
1 TATTAATATTA
*
6030171 TATTAATATCA
1 TATTAATATTA
*
6030182 TTTCTAA-A-TA
1 TAT-TAATATTA
6030192 TATTTAA-ATTA
1 TA-TTAATATTA
6030203 TA-TAATATTA
1 TATTAATATTA
*
6030213 TA-TATTATTTA
1 TATTAATA-TTA
6030224 TATTAATATTTA
1 TATTAATA-TTA
6030236 TATTAATATT
1 TATTAATATT
6030246 TACAATAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
9 3 0.05
10 23 0.38
11 16 0.26
12 19 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTAATATTA
Found at i:6030216 original size:23 final size:23
Alignment explanation
Indices: 6030189--6030239 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
6030179 TCATTTCTAA
6030189 ATATATTTAAATTATA-TAATATT
1 ATATATTT-AATTATATTAATATT
*
6030212 ATATA-TTATTTATATTAATATT
1 ATATATTTAATTATATTAATATT
6030234 -TATATT
1 ATATATT
6030240 AATATTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.40
22 10 0.40
23 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATATTTAATTATATTAATATT
Found at i:6030227 original size:9 final size:10
Alignment explanation
Indices: 6030199--6030457 Score: 64
Period size: 10 Copynumber: 27.0 Consensus size: 10
6030189 ATATATTTAA
*
6030199 ATTATATAAT
1 ATTATATATT
6030209 ATTATATATT
1 ATTATATATT
6030219 ATT-TATATT
1 ATTATATATT
* *
6030228 AATATTTA-T
1 ATTATATATT
6030237 ATTA-ATATTT
1 ATTATATA-TT
** *
6030247 ACAATAATAAT
1 ATTAT-ATATT
*
6030258 ATTTTATATT
1 ATTATATATT
*
6030268 -TTAT-TTTT
1 ATTATATATT
6030276 ATT-TA-ATT
1 ATTATATATT
*
6030284 ATTATATTACT
1 ATTATA-TATT
*
6030295 -TTATTTCATT
1 ATTATAT-ATT
6030305 -TTATAATATT
1 ATTAT-ATATT
*
6030315 TTTATAATATTT
1 ATTAT-ATA-TT
6030327 ATTA-ATA-T
1 ATTATATATT
*
6030335 ATAATA-ATTT
1 ATTATATA-TT
*
6030345 CTTAATATATT
1 ATT-ATATATT
6030356 ATTA-AT-TT
1 ATTATATATT
6030364 ATTATA-ATCT
1 ATTATATAT-T
6030374 ATTATA-ATT
1 ATTATATATT
*
6030383 A-TATAAATAT
1 ATTATATAT-T
*
6030393 ATTTATGTATAT
1 A-TTATATAT-T
*
6030405 ATTTTATATT
1 ATTATATATT
6030415 -TTATAT-TT
1 ATTATATATT
*
6030423 ACTA-AT-TT
1 ATTATATATT
6030431 ATTATA-A--
1 ATTATATATT
6030438 ATTATA-ATT
1 ATTATATATT
6030447 ATTTATATATT
1 A-TTATATATT
6030458 TATAATTTTT
Statistics
Matches: 185, Mismatches: 31, Indels: 65
0.66 0.11 0.23
Matches are distributed among these distances:
7 7 0.04
8 35 0.19
9 38 0.21
10 58 0.31
11 30 0.16
12 17 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTATATATT
Found at i:6030233 original size:12 final size:11
Alignment explanation
Indices: 6030200--6030247 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
6030190 TATATTTAAA
6030200 TTATATAATA-
1 TTATATAATAT
*
6030210 TTATATATTAT
1 TTATATAATAT
6030221 TTATATTAATAT
1 TTATA-TAATAT
6030233 TTATATTAATAT
1 TTATA-TAATAT
6030245 TTA
1 TTA
6030248 CAATAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 9 0.26
11 5 0.15
12 20 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTATATAATAT
Found at i:6030240 original size:21 final size:21
Alignment explanation
Indices: 6030200--6030240 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6030190 TATATTTAAA
6030200 TTATATAATATTATATATTAT
1 TTATATAATATTATATATTAT
6030221 TTATATTAATATT-TATATTA
1 TTATA-TAATATTATATATTA
6030241 ATATTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATAATATTATATATTAT
Found at i:6030254 original size:24 final size:22
Alignment explanation
Indices: 6030204--6030255 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
6030194 TTTAAATTAT
* *
6030204 ATAATATTATATATTATTTATA
1 ATAATATTATATAATATTTACA
*
6030226 TTAATATTTATATTAATATTTACA
1 ATAATA-TTATA-TAATATTTACA
6030250 ATAATA
1 ATAATA
6030256 ATATTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 5 0.21
23 5 0.21
24 14 0.58
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATATTATATAATATTTACA
Found at i:6030318 original size:21 final size:22
Alignment explanation
Indices: 6030269--6030319 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
6030259 TTTTATATTT
*
6030269 TATTTTTATTTAATTATTATAT
1 TATTTTTATTTAATTATTATAA
* *
6030291 TA-CTTTATTTCATT-TTATAA
1 TATTTTTATTTAATTATTATAA
6030311 TATTTTTAT
1 TATTTTTAT
6030320 AATATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.29
21 15 0.62
22 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTTATTTAATTATTATAA
Found at i:6030349 original size:18 final size:17
Alignment explanation
Indices: 6030317--6030354 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
6030307 ATAATATTTT
6030317 TATAATATTTATTAATA
1 TATAATATTTATTAATA
*
6030334 TATAATAATTTCTTAATA
1 TATAAT-ATTTATTAATA
6030352 TAT
1 TAT
6030355 TATTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAATATTTATTAATA
Found at i:6030358 original size:29 final size:29
Alignment explanation
Indices: 6030306--6030371 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
6030296 TATTTCATTT
*
6030306 TATAAT-ATTTTTATAATATTTATTAATA
1 TATAATAATTTCTATAATATTTATTAATA
*
6030334 TATAATAATTTCT-TAATATATTATTAATT
1 TATAATAATTTCTATAATAT-TTATTAATA
*
6030363 TATTATAAT
1 TATAATAAT
6030372 CTATTATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
TATAATAATTTCTATAATATTTATTAATA
Found at i:6030419 original size:50 final size:50
Alignment explanation
Indices: 6030365--6030471 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 50
6030355 TATTAATTTA
* *
6030365 TTATAATCTATTATAATTA-TATAAA-TATATTTATGTATATATTT-TATATT
1 TTAT-ATCTACTA-AATTATTATAAATTATAATTATGTATATATTTATA-ATT
* * *
6030415 TTATATTTACTAATTTATTATAAATTATAATTATTTATATATTTATAATTT
1 TTATATCTACTAAATTATTATAAATTATAATTATGTATATATTTATAA-TT
6030466 TTATAT
1 TTATAT
6030472 AATATCATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
48 4 0.08
49 12 0.25
50 22 0.46
51 10 0.21
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (50 bp):
TTATATCTACTAAATTATTATAAATTATAATTATGTATATATTTATAATT
Found at i:6030471 original size:17 final size:17
Alignment explanation
Indices: 6030400--6030472 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 17
6030390 TATATTTATG
*
6030400 TATATATTT-T-ATATT
1 TATATATTTATAATTTT
6030415 T-TATATTTACTAATTTAT
1 TATATATTTA-TAATTT-T
*
6030433 TATA-AATTATAATTATT
1 TATATATTTATAATT-TT
6030450 TATATATTTATAATTTT
1 TATATATTTATAATTTT
6030467 TATATA
1 TATATA
6030473 ATATCATTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
14 7 0.15
15 1 0.02
16 1 0.02
17 21 0.44
18 16 0.33
19 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATTTATAATTTT
Found at i:6030507 original size:16 final size:15
Alignment explanation
Indices: 6030488--6030542 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
6030478 ATTTCTAAAT
6030488 TATATTTTTATTCATA
1 TATATTTTTATT-ATA
*
6030504 TATATTTTAATT-TA
1 TATATTTTTATTATA
6030518 TTATATTATTATATT-TA
1 -TATATT-TT-TATTATA
6030535 TATATTTT
1 TATATTTT
6030543 ATTTTCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 2 0.06
15 8 0.24
16 19 0.56
17 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTTTATTATA
Found at i:6030544 original size:23 final size:24
Alignment explanation
Indices: 6030488--6030578 Score: 70
Period size: 23 Copynumber: 4.0 Consensus size: 24
6030478 ATTTCTAAAT
6030488 TATATTTT-TATTCATATATATTT-
1 TATATTTTATATTCAT-TATATTTA
6030511 TA-ATTTATTATATT-ATTATATTTA
1 TATA-TT-TTATATTCATTATATTTA
* * *
6030535 TATATTTTATTTTCATT-TCTTAA
1 TATATTTTATATTCATTATATTTA
*
6030558 TATATTTTTTATT--TTATATTT
1 TATATTTTATATTCATTATATTT
6030579 TATTTTAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
21 2 0.04
22 4 0.07
23 32 0.59
24 11 0.20
25 5 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (24 bp):
TATATTTTATATTCATTATATTTA
Found at i:6030547 original size:52 final size:49
Alignment explanation
Indices: 6030312--6030539 Score: 173
Period size: 52 Copynumber: 4.5 Consensus size: 49
6030302 ATTTTATAAT
* * * *
6030312 ATTTTTATAATATT-TATTAATATATAATA-ATTTCTTAATATATTATTA
1 ATTTTTATATTATTATATTTATATATAATATATTTATTTATATATT-TTA
* *
6030360 ATTTATTATAATCTATTATAATTATATA-AATATATTTATGTATATATTTT-
1 ATTT-TTAT-AT-TATTATATTTATATATAATATATTTATTTATATATTTTA
* *
6030410 ATATTTTATATTTACTA-ATTTAT-TATAAATTATAATTATTTATATATTTATA
1 AT-TTTTATA-TTATTATATTTATATAT-AA-TATATTTATTTATATATTT-TA
* * * * *
6030462 ATTTTTATA-TAATATCATTTCTAAATTATATTTTTATTCATATATATTTTA
1 ATTTTTATATTATTAT-ATTTATATATAATATATTTATT--TATATATTTTA
6030513 ATTTATTATATTATTATATTTATATAT
1 ATTT-TTATATTATTATATTTATATAT
6030540 TTTATTTTCA
Statistics
Matches: 142, Mismatches: 19, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
47 2 0.01
48 9 0.06
49 15 0.11
50 33 0.23
51 32 0.23
52 46 0.32
53 5 0.04
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (49 bp):
ATTTTTATATTATTATATTTATATATAATATATTTATTTATATATTTTA
Found at i:6030562 original size:31 final size:30
Alignment explanation
Indices: 6030502--6030583 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 30
6030492 TTTTTATTCA
* *
6030502 TATATATTTTAATTTATTATATTATTATATT
1 TATATATTTTATTTTATT-TATTAATATATT
*
6030533 TATATATTTTATTTTCATTTCTTAATATATT
1 TATATATTTTATTTT-ATTTATTAATATATT
*
6030564 T-TTTATTTTATATTTTATTT
1 TATATA-TTT-TATTTTATTT
6030584 TAATTTGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
30 3 0.07
31 32 0.73
32 9 0.20
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (30 bp):
TATATATTTTATTTTATTTATTAATATATT
Found at i:6030582 original size:19 final size:20
Alignment explanation
Indices: 6030529--6030584 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 20
6030519 TATATTATTA
6030529 TATTTATATATTTTA-TTTT
1 TATTTATATATTTTATTTTT
* * * *
6030548 CATTTCT-TAATATATTTTT
1 TATTTATATATTTTATTTTT
6030567 TATTT-TATATTTTATTTT
1 TATTTATATATTTTATTTT
6030585 AATTTGTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTATATATTTTATTTTT
Found at i:6030670 original size:50 final size:53
Alignment explanation
Indices: 6030555--6030670 Score: 136
Period size: 55 Copynumber: 2.2 Consensus size: 53
6030545 TTTCATTTCT
6030555 TAATA-TATTTTTTATTTTATATTTTATTTTAATTTGTTTTATCTATATTATA
1 TAATATTATTTTTTATTTTATATTTTATTTTAATTTGTTTTATCTATATTATA
* *
6030607 TAAATATTAATTTTTTATATTT-TGTTTTATTTTAATTT-TTAT-TCTTATATTATA
1 T-AATATT-ATTTTTTAT-TTTATATTTTATTTTAATTTGTTTTATC-TATATTATA
6030661 T-AT-TTATTTT
1 TAATATTATTTT
6030671 AATTATAATA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
50 5 0.09
51 2 0.04
52 3 0.05
53 6 0.11
54 14 0.25
55 24 0.42
56 3 0.05
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (53 bp):
TAATATTATTTTTTATTTTATATTTTATTTTAATTTGTTTTATCTATATTATA
Found at i:6036312 original size:39 final size:39
Alignment explanation
Indices: 6036258--6036337 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
6036248 GATTAAATAC
*
6036258 CAAAGTCAACTCCAGTATACATGTAGTTTGAAGAGAAAT
1 CAAAGTCAACTCCAGTATACACGTAGTTTGAAGAGAAAT
6036297 CAAAGTCAACTCCAGTATACACGTAGTTTGAAGAGAAAT
1 CAAAGTCAACTCCAGTATACACGTAGTTTGAAGAGAAAT
6036336 CA
1 CA
6036338 TTCTTCTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (39 bp):
CAAAGTCAACTCCAGTATACACGTAGTTTGAAGAGAAAT
Found at i:6042900 original size:34 final size:33
Alignment explanation
Indices: 6042844--6042908 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
6042834 AGCTGGGCTA
* *
6042844 GCCCTGCCCCCCTCCTCCGGCTCCCACGAGTAG
1 GCCCTACCCCCCCCCTCCGGCTCCCACGAGTAG
6042877 GCCCTACCCGCCCCCCTCCGGCTCCCACGAGT
1 GCCCTACCC-CCCCCCTCCGGCTCCCACGAGT
6042909 CCCGGTTCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.09, C:0.57, G:0.20, T:0.14
Consensus pattern (33 bp):
GCCCTACCCCCCCCCTCCGGCTCCCACGAGTAG
Found at i:6043721 original size:27 final size:27
Alignment explanation
Indices: 6043663--6043718 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
6043653 TACTTTATTT
*
6043663 TTAAAAATTAATTTAACATTTTAATTA
1 TTAAAAATAAATTTAACATTTTAATTA
6043690 TTAAAAATAATATTTAGA-ATTTTAATTA
1 TTAAAAATAA-ATTTA-ACATTTTAATTA
6043718 T
1 T
6043719 AAATTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 16 0.62
29 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAAAATAAATTTAACATTTTAATTA
Found at i:6043955 original size:70 final size:70
Alignment explanation
Indices: 6043842--6043974 Score: 232
Period size: 70 Copynumber: 1.9 Consensus size: 70
6043832 AGAATAAATT
*
6043842 ATAATAACAATTCCTTCTTATTCCATTCTCATGAACTTAACTATATAATAATGATTCTTCCTTAA
1 ATAATAACAATTCCTTCTTATTCCATTCTCATAAACTTAACTATATAATAATGATTCTTCCTTAA
6043907 TTGTC
66 TTGTC
*
6043912 ATAATAACAATTCCTTTTTATTCCATTCTCATAAA-TCTAACTATATAATAATGATTCTTCCTT
1 ATAATAACAATTCCTTCTTATTCCATTCTCATAAACT-TAACTATATAATAATGATTCTTCCTT
6043975 TATTCTATTC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 1 0.02
70 59 0.98
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.44
Consensus pattern (70 bp):
ATAATAACAATTCCTTCTTATTCCATTCTCATAAACTTAACTATATAATAATGATTCTTCCTTAA
TTGTC
Found at i:6056928 original size:58 final size:58
Alignment explanation
Indices: 6056865--6056980 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
6056855 TCAATTTTTT
* ** *
6056865 AAGATAAATTAATTATACTTTGACATAATATTTTGCAAGTTTTTAAATTATTTTAAAA
1 AAGATAAATTAATTATAATTTGACATAATATTTTAAAAATTTTTAAATTATTTTAAAA
6056923 AAGATAAATTAATTATAATTTGACATAATATTTTAAAAATTTTTAAATTATTTTAAAA
1 AAGATAAATTAATTATAATTTGACATAATATTTTAAAAATTTTTAAATTATTTTAAAA
6056981 TTTTATCTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (58 bp):
AAGATAAATTAATTATAATTTGACATAATATTTTAAAAATTTTTAAATTATTTTAAAA
Found at i:6057188 original size:31 final size:32
Alignment explanation
Indices: 6057150--6057209 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
6057140 TATCATTAGT
* * *
6057150 TATAAAAA-TTTATTTAATTTAAAAATAAAAA
1 TATAAAAATTTTATTAAAATAAAAAATAAAAA
6057181 TATAAAAATTTTATTAAAATAAAAAATAA
1 TATAAAAATTTTATTAAAATAAAAAATAA
6057210 TTTAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (32 bp):
TATAAAAATTTTATTAAAATAAAAAATAAAAA
Found at i:6057245 original size:21 final size:22
Alignment explanation
Indices: 6057204--6057249 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
6057194 TTAAAATAAA
*
6057204 AAATAATTTAATTAATTTTTTT
1 AAATAATTTAATGAATTTTTTT
*
6057226 AAATAATTTAA-GAGTTTTTTT
1 AAATAATTTAATGAATTTTTTT
6057247 AAA
1 AAA
6057250 ATATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
AAATAATTTAATGAATTTTTTT
Found at i:6057251 original size:22 final size:23
Alignment explanation
Indices: 6057203--6057252 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
6057193 ATTAAAATAA
*
6057203 AAAATAATTTAATTAATTTTTTT
1 AAAATAATTTAATGAATTTTTTT
*
6057226 -AAATAATTTAA-GAGTTTTTTT
1 AAAATAATTTAATGAATTTTTTT
6057247 AAAATA
1 AAAATA
6057253 TTATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
AAAATAATTTAATGAATTTTTTT
Found at i:6066971 original size:20 final size:20
Alignment explanation
Indices: 6066946--6066987 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
6066936 GAGCAACAGA
6066946 TCCGATGCTCCCTTGGGAGC
1 TCCGATGCTCCCTTGGGAGC
6066966 TCCGATGCTCCCTTGGGAGC
1 TCCGATGCTCCCTTGGGAGC
6066986 TC
1 TC
6066988 AATTTGAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.36, G:0.29, T:0.26
Consensus pattern (20 bp):
TCCGATGCTCCCTTGGGAGC
Found at i:6071028 original size:197 final size:196
Alignment explanation
Indices: 6070686--6071078 Score: 644
Period size: 197 Copynumber: 2.0 Consensus size: 196
6070676 TACTATTTGG
* * *
6070686 CCATGTCAGCTGTCGTGTGGAAAGAAAATGTCAGTTGGCATTAAGTTTGATGGTTGTTAATAACC
1 CCATGTAAGCTGTCATGTGGAAAGAAAATGTCAGTTGGCAGTAAGTTTGATGGTTGTTAATAACC
* * * *
6070751 ATTAAGGATAGAATGTTAAATTTGATAGTTGATTAATATATATTAAGGGTTATTAGATATATTCA
66 ATGAAGGATAGAATATTAAATTTGATAGTTGATTAATATATATTAAGGGTTATTAGATACATGCA
6070816 TACAACAACTTGTATGCACA-ATGACGGGGGAAAGTTTTACAAATAATATAGTTACAAGGGGAGG
131 TACAACAACTTGTATGCACAGA-GAC-GGGGAAAGTTTTACAAATAATATAGTTACAAGGGGAGG
6070880 GTA
194 GTA
**
6070883 CCATGTAAGCTGTCATGTGGAAAGAAAATGTTGGTTGGCAGTAAGTTTGATGGTTGTTAATAACC
1 CCATGTAAGCTGTCATGTGGAAAGAAAATGTCAGTTGGCAGTAAGTTTGATGGTTGTTAATAACC
* *
6070948 ATGAAGGATAGAATATTAAATTTGATTGTTGATTAATATATATTAAGGGTTGTTAGATACATGCA
66 ATGAAGGATAGAATATTAAATTTGATAGTTGATTAATATATATTAAGGGTTATTAGATACATGCA
* *
6071013 TACAACAACTTGTATGCACAGAGACGGGGAAAGTTTTATAAATAATATAGTTACATGGGGAGGGT
131 TACAACAACTTGTATGCACAGAGACGGGGAAAGTTTTACAAATAATATAGTTACAAGGGGAGGGT
6071078 A
196 A
6071079 TGTCATTCTG
Statistics
Matches: 182, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
196 39 0.21
197 142 0.78
198 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (196 bp):
CCATGTAAGCTGTCATGTGGAAAGAAAATGTCAGTTGGCAGTAAGTTTGATGGTTGTTAATAACC
ATGAAGGATAGAATATTAAATTTGATAGTTGATTAATATATATTAAGGGTTATTAGATACATGCA
TACAACAACTTGTATGCACAGAGACGGGGAAAGTTTTACAAATAATATAGTTACAAGGGGAGGGT
A
Found at i:6072666 original size:18 final size:18
Alignment explanation
Indices: 6072626--6072670 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
6072616 TTACCCACAA
*
6072626 AAGCAGGAGTAGGAGCTG
1 AAGCAGGAGTAGGAGCAG
* * *
6072644 GAGCAGGAGTCGTAGCAG
1 AAGCAGGAGTAGGAGCAG
6072662 AAGCAGGAG
1 AAGCAGGAG
6072671 CCGAAGTCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.44, T:0.09
Consensus pattern (18 bp):
AAGCAGGAGTAGGAGCAG
Found at i:6073433 original size:54 final size:54
Alignment explanation
Indices: 6073284--6073448 Score: 181
Period size: 54 Copynumber: 3.1 Consensus size: 54
6073274 AAAATTTAGA
* * * * * *
6073284 GATGCAGATGCTTCATATAATGTGGAGAAATCTAGGAATGGTCTAAAATGGAGT
1 GATGCTGATGCTTCAAATGATGTGGAGAAATCTTGGACTGGTCCAAAATGGAGT
* ** *
6073338 GATGCTGATGCTTCAAATGAAGCAGAGAAATGC-TGGGCTGGTCCAAAATGGAGT
1 GATGCTGATGCTTCAAATGATGTGGAGAAAT-CTTGGACTGGTCCAAAATGGAGT
* * *
6073392 GATG-TGGATGCTTCAAATGATGTGGACAAATCTTGGACTGGTTCAAAATGGGGT
1 GATGCT-GATGCTTCAAATGATGTGGAGAAATCTTGGACTGGTCCAAAATGGAGT
6073446 GAT
1 GAT
6073449 ACAGGTACCT
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
53 2 0.02
54 88 0.97
55 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (54 bp):
GATGCTGATGCTTCAAATGATGTGGAGAAATCTTGGACTGGTCCAAAATGGAGT
Found at i:6078606 original size:2 final size:2
Alignment explanation
Indices: 6078599--6078630 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6078589 TTATTAAAGA
6078599 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
6078631 GGCGGGGGGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6079665 original size:2 final size:2
Alignment explanation
Indices: 6079658--6079693 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6079648 TTGCATCTTG
*
6079658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6079694 TTATGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6091396 original size:36 final size:34
Alignment explanation
Indices: 6091356--6091449 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 34
6091346 ACCTCCGACT
* *
6091356 CCTCCAAACGTGGCACCACCTCATTTTACTCCAGCC
1 CCTCCAAA-GT-GCACCACCTCATTATACTCCAACC
* *
6091392 CCTCCAAAAGTTGCACCACCCCATTATATTCCAACC
1 CCTCC-AAAG-TGCACCACCTCATTATACTCCAACC
6091428 CCTCCCAAAGTGCAACCACCTC
1 CCT-CCAAAGTGC-ACCACCTC
6091450 CAATGCCCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
35 3 0.06
36 40 0.82
37 6 0.12
ACGTcount: A:0.27, C:0.45, G:0.09, T:0.20
Consensus pattern (34 bp):
CCTCCAAAGTGCACCACCTCATTATACTCCAACC
Found at i:6091636 original size:17 final size:18
Alignment explanation
Indices: 6091590--6091637 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
6091580 CATTATATTC
6091590 CAACC-CCTCCCAAAGTG
1 CAACCACCTCCCAAAGTG
6091607 CAACCACCT-CCAAA-TG
1 CAACCACCTCCCAAAGTG
*
6091623 C-CCCATCCTCCCAAA
1 CAACCA-CCTCCCAAA
6091638 AGTACCACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.11
16 6 0.22
17 15 0.56
18 3 0.11
ACGTcount: A:0.31, C:0.50, G:0.06, T:0.12
Consensus pattern (18 bp):
CAACCACCTCCCAAAGTG
Found at i:6092861 original size:3 final size:3
Alignment explanation
Indices: 6092855--6092886 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6092845 AAATCAGGCA
6092855 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
6092887 TATTATTATT
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:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:6094207 original size:2 final size:2
Alignment explanation
Indices: 6094200--6094240 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6094190 AGATACATAC
6094200 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
6094241 AAGAGAATCA
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:6100179 original size:26 final size:28
Alignment explanation
Indices: 6100132--6100184 Score: 83
Period size: 26 Copynumber: 1.9 Consensus size: 28
6100122 GTAGATAGTG
6100132 AAAAATATTATATGATCATGTTATCATAT
1 AAAAATA-TATATGATCATGTTATCATAT
6100161 AAAAATA-ATATG-TCATGTTATCAT
1 AAAAATATATATGATCATGTTATCAT
6100185 TAATTATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 12 0.50
27 5 0.21
29 7 0.29
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (28 bp):
AAAAATATATATGATCATGTTATCATAT
Found at i:6100199 original size:25 final size:26
Alignment explanation
Indices: 6100147--6100200 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
6100137 TATTATATGA
*
6100147 TCATGTTATCATATAAAAATAATATG
1 TCATGTTATCATATAAAAATAAGATG
**
6100173 TCATGTTATCAT-TAATTATAAGATG
1 TCATGTTATCATATAAAAATAAGATG
6100198 TCA
1 TCA
6100201 ACATGTCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (26 bp):
TCATGTTATCATATAAAAATAAGATG
Found at i:6104984 original size:18 final size:18
Alignment explanation
Indices: 6104961--6104998 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6104951 AAATAAAAAA
*
6104961 ATGATTATATATTAAGAT
1 ATGATTATAAATTAAGAT
*
6104979 ATGATTGTAAATTAAGAT
1 ATGATTATAAATTAAGAT
6104997 AT
1 AT
6104999 AGTCAATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (18 bp):
ATGATTATAAATTAAGAT
Found at i:6112706 original size:22 final size:21
Alignment explanation
Indices: 6112678--6112736 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
6112668 GATATTATTA
6112678 TTATATATATATAATAAAATAT
1 TTATATATATATAATAAAA-AT
*
6112700 TTATATATCTATAATATAAAAT
1 TTATATATATATAATA-AAAAT
*
6112722 ATATATA-ATA-AATAA
1 TTATATATATATAATAA
6112737 GTAAAACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 2 0.06
22 23 0.70
23 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATATATATATAATAAAAAT
Found at i:6112706 original size:24 final size:24
Alignment explanation
Indices: 6112679--6112736 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
6112669 ATATTATTAT
*
6112679 TATATATATAT-A-ATAAAATATT
1 TATATATATATAATATAAAATATA
*
6112701 TATATATCTATAATATAAAATATA
1 TATATATATATAATATAAAATATA
*
6112725 TATA-ATAAATAA
1 TATATATATATAA
6112737 GTAAAACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 10 0.33
23 7 0.23
24 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TATATATATATAATATAAAATATA
Found at i:6112898 original size:35 final size:36
Alignment explanation
Indices: 6112811--6112900 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 36
6112801 TATAATGACC
*
6112811 AAAAAAAAAACTCATGAC-ATATTTGCCGCGAGCTCAGAA
1 AAAAAAAAAACTC--G-CGATATATGCCGCGAGCTCA-AA
*
6112850 AAAAAAAAAACTCGCGATATATGCCGCGAGCTC-CA
1 AAAAAAAAAACTCGCGATATATGCCGCGAGCTCAAA
* *
6112885 ATAAAAATAACTCGCG
1 AAAAAAAAAACTCGCG
6112901 GCATAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 15 0.33
36 1 0.02
37 17 0.37
39 13 0.28
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.17
Consensus pattern (36 bp):
AAAAAAAAAACTCGCGATATATGCCGCGAGCTCAAA
Found at i:6119197 original size:14 final size:13
Alignment explanation
Indices: 6119178--6119222 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
6119168 TGCTTTTGGC
6119178 TTCTGTTTCATGGT
1 TTCTGTTTC-TGGT
6119192 TTCTGTTTCCT-GT
1 TTCTGTTT-CTGGT
6119205 TTCCTGTTTCTGGT
1 TT-CTGTTTCTGGT
6119219 TTCT
1 TTCT
6119223 TACAACTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.29
14 19 0.68
15 1 0.04
ACGTcount: A:0.02, C:0.20, G:0.18, T:0.60
Consensus pattern (13 bp):
TTCTGTTTCTGGT
Found at i:6119206 original size:21 final size:21
Alignment explanation
Indices: 6119180--6119221 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6119170 CTTTTGGCTT
6119180 CTGTTTCATGGTTTCT-GTTTC
1 CTGTTTCAT-GTTTCTGGTTTC
*
6119201 CTGTTTCCTGTTTCTGGTTTC
1 CTGTTTCATGTTTCTGGTTTC
6119222 TTACAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.02, C:0.21, G:0.19, T:0.57
Consensus pattern (21 bp):
CTGTTTCATGTTTCTGGTTTC
Found at i:6119617 original size:26 final size:26
Alignment explanation
Indices: 6119546--6119617 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
6119536 AAAATTTTAG
6119546 ATATTAATTTTTTATAATTTATAATTAAA
1 ATATTAA-TTTTTAT--TTTATAATTAAA
* *
6119575 ATTTTAA-TTTAATTTT-TAAATATAAA
1 ATATTAATTTTTATTTTAT-AAT-TAAA
6119601 ATATTAATTTTTATTTT
1 ATATTAATTTTTATTTT
6119618 TTTATTTAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
24 1 0.03
25 6 0.17
26 10 0.28
27 13 0.36
29 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATTAATTTTTATTTTATAATTAAA
Found at i:6124637 original size:13 final size:13
Alignment explanation
Indices: 6124621--6124645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6124611 TATTTTTGTA
6124621 AAATATAAAAATG
1 AAATATAAAAATG
6124634 AAATATAAAAAT
1 AAATATAAAAAT
6124646 TATTTTAAAA
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAATATAAAAATG
Found at i:6128501 original size:29 final size:30
Alignment explanation
Indices: 6128468--6128536 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
6128458 TTATCTTATT
*
6128468 TTTATATATAT-TTTAAATATATATATGT-A
1 TTTATATATATGTATAAATATATATAT-TCA
* *
6128497 TTTATGTA-ATGTATAAATATATATATTCT
1 TTTATATATATGTATAAATATATATATTCA
6128526 TTTATATATAT
1 TTTATATATAT
6128537 ATATTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 3 0.09
29 28 0.85
30 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTATATATATGTATAAATATATATATTCA
Found at i:6134328 original size:18 final size:18
Alignment explanation
Indices: 6134305--6134353 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
6134295 TGATTTTTGC
6134305 GATTTAGGGTTTTCAATT
1 GATTTAGGGTTTTCAATT
6134323 GATTTAGGGTTTTCAATT
1 GATTTAGGGTTTTCAATT
6134341 GATTTAGGGTTTT
1 GATTTAGGGTTTT
6134354 TTTTATTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.51
Consensus pattern (18 bp):
GATTTAGGGTTTTCAATT
Found at i:6144091 original size:27 final size:28
Alignment explanation
Indices: 6144035--6144091 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
6144025 CATGCTATAT
* * *
6144035 TTAAAAAACAATATTATTACACGTCTTG
1 TTAAAAAACAAAATTATTACACGCCATG
*
6144063 TTAAAAAA-AAAATTATTACATGCCATG
1 TTAAAAAACAAAATTATTACACGCCATG
6144090 TT
1 TT
6144092 TAATATGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (28 bp):
TTAAAAAACAAAATTATTACACGCCATG
Found at i:6145698 original size:22 final size:23
Alignment explanation
Indices: 6145668--6145714 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
6145658 ATATAGAGTT
6145668 ATTTGAGCTTAATT-TTGATAGTA
1 ATTTGAGCTTAATTCTTG-TAGTA
*
6145691 ATTT-AGCTTAGTTCTTGTAGTA
1 ATTTGAGCTTAATTCTTGTAGTA
6145713 AT
1 AT
6145715 ACATAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (23 bp):
ATTTGAGCTTAATTCTTGTAGTA
Found at i:6148507 original size:11 final size:11
Alignment explanation
Indices: 6148483--6148521 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6148473 TAATAAAGTA
* *
6148483 ATATATTATAT
1 ATATATAATTT
*
6148494 ATATTTAATTT
1 ATATATAATTT
6148505 ATATATAATTT
1 ATATATAATTT
6148516 ATATAT
1 ATATAT
6148522 TTTATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATAATTT
Done.