Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, 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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 4 of 14
Found at i:1286963 original size:208 final size:215
Alignment explanation
Indices: 1286556--1287153 Score: 780
Period size: 208 Copynumber: 2.8 Consensus size: 215
1286546 TCATTCATAA
* * * * * ** *
1286556 TTATATATATATGAAATTAATAATATAACTTATACGTTATGATGTTTTATATCAAAGTTTGTATA
1 TTATATATATAT-AAATCAATGACATAAATTATACATTAAAATATTTTATATCAAAGTTTGTATA
* * * * *
1286621 AATAATAAGTAATTGTAAACAATATGTTATAAAATCTAAGTTGATAGCTAATAAACTTATTAAGT
65 AATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATTAAGT
* * * * *
1286686 ATAATCACATAAATAAAGTTTATTATAAGTTATAGTAATGCTTATGTATAAATTAAATATATGTA
130 GTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATACTTAAGTATAAATTAAATATATATA
1286751 TATAT-A-ATAT-A-TTAC-T
195 TATATAATATATAATTTACAT
* * *
1286767 TTAT-TATATAT-AATCAATGATATAAATTATATATTAAAATATTTTGTATCAAAGTTTGTATAA
1 TTATATATATATAAATCAATGACATAAATTATACATTAAAATATTTTATATCAAAGTTTGTATAA
1286830 ATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATTAAGTG
66 ATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATTAAGTG
*
1286895 TAATCATATAAATAAAGTCTATTATAAGTTATAGTAATACTTAAGTATAAATTAAATATATATAT
131 TAATCATATAAATAAAGTTTATTATAAGTTATAGTAATACTTAAGTATAAATTAAATATATATAT
1286960 ATATAATATATGAATTTACTATAT
196 ATATAATATAT-AATTTAC---AT
* * * *
1286984 TTATATATATATGAAATTAATGACATAACTTATACGTTATAATATTTTATATCAAAG-TTGATAT
1 TTATATATATAT-AAATCAATGACATAAATTATACATTAAAATATTTTATATCAAAGTTTG-TAT
* * *
1287048 AAATAATAACTACTTATAAACAATATATTATAAAATCTAAGGTGATAACTAATAAAGTTATTGAG
64 AAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATTAAG
* * * *
1287113 TGTAATTATATAAATAAAGTTTATTCTAAATTAGAGTAATA
129 TGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAATA
1287154 TTTATGTACA
Statistics
Matches: 339, Mismatches: 35, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
208 166 0.49
209 1 0.00
210 11 0.03
211 4 0.01
212 1 0.00
213 4 0.01
217 5 0.01
218 7 0.02
219 3 0.01
220 137 0.40
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (215 bp):
TTATATATATATAAATCAATGACATAAATTATACATTAAAATATTTTATATCAAAGTTTGTATAA
ATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGATAACTAATAAAGTTATTAAGTG
TAATCATATAAATAAAGTTTATTATAAGTTATAGTAATACTTAAGTATAAATTAAATATATATAT
ATATAATATATAATTTACAT
Found at i:1287469 original size:2 final size:2
Alignment explanation
Indices: 1287462--1287505 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1287452 ATTCTTCTTA
* * *
1287462 AT AT AT AT A- AA AT AT AT TT AT AT AT AT AT AT AA 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
1287503 AT A
1 AT A
1287506 ACTAGTTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1296118 original size:15 final size:15
Alignment explanation
Indices: 1296106--1296234 Score: 69
Period size: 15 Copynumber: 8.2 Consensus size: 15
1296096 CCTAGGAGGT
1296106 GCAGCTCTTGGAGAA
1 GCAGCTCTTGGAGAA
*
1296121 GGAGCTCTTGGAGAA
1 GCAGCTCTTGGAGAA
* **
1296136 GCAGCTCGTGGAGGT
1 GCAGCTCTTGGAGAA
* * ***
1296151 GGAGGTGGGGGAGGAGAA
1 GCAGCT---CTTGGAGAA
*
1296169 GCAGCTCTAGGAGAA
1 GCAGCTCTTGGAGAA
*
1296184 GCAGCTCGTGGAGGGGAA
1 GCAGCTCTTGGA---GAA
** *
1296202 GTGGCTCTAGGAGAA
1 GCAGCTCTTGGAGAA
*
1296217 GCAGCTCTCGGAGAA
1 GCAGCTCTTGGAGAA
1296232 GCA
1 GCA
1296235 ACCCTAGGAG
Statistics
Matches: 84, Mismatches: 24, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
15 64 0.76
18 20 0.24
ACGTcount: A:0.26, C:0.16, G:0.43, T:0.15
Consensus pattern (15 bp):
GCAGCTCTTGGAGAA
Found at i:1296169 original size:48 final size:48
Alignment explanation
Indices: 1296115--1296234 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
1296105 TGCAGCTCTT
* * * *
1296115 GGAGAAGGAGCTCTTGGAGAAGCAGCTCGTGGAGGTGGAGGTGG-GGGA
1 GGAGAAGCAGCTCTAGGAGAAGCAGCTCGTGGAGG-GGAAGTGGCGCGA
* *
1296163 GGAGAAGCAGCTCTAGGAGAAGCAGCTCGTGGAGGGGAAGTGGCTCTA
1 GGAGAAGCAGCTCTAGGAGAAGCAGCTCGTGGAGGGGAAGTGGCGCGA
*
1296211 GGAGAAGCAGCTCTCGGAGAAGCA
1 GGAGAAGCAGCTCTAGGAGAAGCA
1296235 ACCCTAGGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
47 7 0.11
48 57 0.89
ACGTcount: A:0.27, C:0.15, G:0.45, T:0.13
Consensus pattern (48 bp):
GGAGAAGCAGCTCTAGGAGAAGCAGCTCGTGGAGGGGAAGTGGCGCGA
Found at i:1296197 original size:33 final size:33
Alignment explanation
Indices: 1296160--1296223 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1296150 TGGAGGTGGG
1296160 GGAGGAGAAGCAGCTCTAGGAGAAGCAGCTCGT
1 GGAGGAGAAGCAGCTCTAGGAGAAGCAGCTCGT
* **
1296193 GGAGGGGAAGTGGCTCTAGGAGAAGCAGCTC
1 GGAGGAGAAGCAGCTCTAGGAGAAGCAGCTC
1296224 TCGGAGAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.42, T:0.12
Consensus pattern (33 bp):
GGAGGAGAAGCAGCTCTAGGAGAAGCAGCTCGT
Found at i:1296244 original size:15 final size:15
Alignment explanation
Indices: 1296208--1296250 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1296198 GGAAGTGGCT
* *
1296208 CTAGGAGAAGCAGCT
1 CTAGGAGAAGCAACC
*
1296223 CTCGGAGAAGCAACC
1 CTAGGAGAAGCAACC
*
1296238 CTAGGAGAGGCAA
1 CTAGGAGAAGCAA
1296251 TCCTTTGAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.33, T:0.09
Consensus pattern (15 bp):
CTAGGAGAAGCAACC
Found at i:1310697 original size:20 final size:20
Alignment explanation
Indices: 1310660--1310698 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1310650 TTTAACAATT
* * *
1310660 AACATGTGATTGTGTTTTTC
1 AACATGTCAGTGTATTTTTC
1310680 AACATGTCAGTGTATTTTT
1 AACATGTCAGTGTATTTTT
1310699 ATCACACCAC
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:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (20 bp):
AACATGTCAGTGTATTTTTC
Found at i:1314713 original size:30 final size:29
Alignment explanation
Indices: 1314668--1314762 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 29
1314658 TTATATTTTA
*
1314668 TTAAATTTAATTAAATTCTTTTATTTTTATT
1 TTAAA-TTAAATAAATT-TTTTATTTTTATT
* *
1314699 TTTAATTAAATAAATTTATATATTTTTATT
1 TTAAATTAAATAAATTT-TTTATTTTTATT
1314729 TTAAATTAAATAAATTTTTTAATTATTTATT
1 TTAAATTAAATAAATTTTTT-ATT-TTTATT
1314760 TTA
1 TTA
1314763 TATCACGTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
29 3 0.05
30 40 0.71
31 13 0.23
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
TTAAATTAAATAAATTTTTTATTTTTATT
Found at i:1314811 original size:33 final size:33
Alignment explanation
Indices: 1314769--1314831 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1314759 TTTATATCAC
1314769 GTGATATGTTGACATATCATAATTGATGATTAT
1 GTGATATGTTGACATATCATAATTGATGATTAT
*
1314802 GTGATATGTTGACATATTATAATTGATGAT
1 GTGATATGTTGACATATCATAATTGATGAT
1314832 AACGTAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (33 bp):
GTGATATGTTGACATATCATAATTGATGATTAT
Found at i:1317933 original size:6 final size:6
Alignment explanation
Indices: 1317922--1317953 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1317912 AAGGAGGAGA
1317922 TGGCGG TGGCGG TGGCGG TGGCGG TGGCGG TG
1 TGGCGG TGGCGG TGGCGG TGGCGG TGGCGG TG
1317954 ATCGATCGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.66, T:0.19
Consensus pattern (6 bp):
TGGCGG
Found at i:1327603 original size:2 final size:2
Alignment explanation
Indices: 1327596--1327631 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1327586 ATGGGAGTTG
1327596 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1327632 CGGGGTGGGG
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):
GA
Found at i:1327722 original size:173 final size:174
Alignment explanation
Indices: 1327442--1327784 Score: 557
Period size: 173 Copynumber: 2.0 Consensus size: 174
1327432 TGCATCTAAT
* * ** *
1327442 GAGAGAGAGAGAGAGAGGTGGGAGGTGGGGGAGGGGTGGGTGGTGAATTTACTTGCCAATGGACT
1 GAGAGAGAGAGAGAGACGTGGGAGGGGGGGGAGGGGTGGGTGAAGAATTTAATTGCCAATGGACT
*
1327507 TTGAATAAGACATATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAA
66 TTGAAGAAGACATATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAA
*
1327572 CTGATGAGTTGTGCATGGGAGTTGGAGAGAGAGAGAGAGAGAGA
131 CTGATGAGTTGTGCATAGGAGTTGGAGAGAGAGAGAGAGAGAGA
* *
1327616 GAGAGAGAGAGAGAGACG-GGGTGGGGGGGGGGGGGTGGG-GAAAGAATTTAATTGCCAATGGAC
1 GAGAGAGAGAGAGAGACGTGGGAGGGGGGGGAGGGGTGGGTG-AAGAATTTAATTGCCAATGGAC
*
1327679 TTTGAAGAAG-CTGTATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAA
65 TTTGAAGAAGAC-ATATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAA
1327743 AACTGATGAGTTGTGCATAGGAGTTGGAGAGAGAGAGAGAGA
129 AACTGATGAGTTGTGCATAGGAGTTGGAGAGAGAGAGAGAGA
1327785 AGGGGGGGGG
Statistics
Matches: 157, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
172 2 0.01
173 138 0.88
174 17 0.11
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.24
Consensus pattern (174 bp):
GAGAGAGAGAGAGAGACGTGGGAGGGGGGGGAGGGGTGGGTGAAGAATTTAATTGCCAATGGACT
TTGAAGAAGACATATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAA
CTGATGAGTTGTGCATAGGAGTTGGAGAGAGAGAGAGAGAGAGA
Found at i:1327842 original size:146 final size:151
Alignment explanation
Indices: 1327616--1327906 Score: 484
Period size: 146 Copynumber: 1.9 Consensus size: 151
1327606 GAGAGAGAGA
*
1327616 GAGAGAGAGAGAGAGACGGGGTGGGGGGGGGGGGGTGGGGAAAGAATTTAATTGCCAATGGACTT
1 GAGAGAGAGAGAGAGACAGGGTGGGGGGGGGGGGGTGGGG--AGAATTTAATTGCCAATGGACTT
**
1327681 TGAAGAAGCTGTATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAAC
64 TGAAGAAGCCATATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAAC
1327746 TGATGAGTTGTGCATAGGAGTTG
129 TGATGAGTTGTGCATAGGAGTTG
*
1327769 GAGAGAGAGAGAGAGA-AGGG-GGGGGGGGGGGGGT-GTG-GAATTTAATT-CCAATGGACTTTG
1 GAGAGAGAGAGAGAGACAGGGTGGGGGGGGGGGGGTGGGGAGAATTTAATTGCCAATGGACTTTG
*
1327829 AAGAAGCCATATGTACATACTTTTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAACTG
66 AAGAAGCCATATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAACTG
1327894 ATGAGTTGTGCAT
131 ATGAGTTGTGCAT
1327907 GAGAGTGATA
Statistics
Matches: 133, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
146 88 0.66
147 10 0.08
150 2 0.02
151 14 0.11
152 3 0.02
153 16 0.12
ACGTcount: A:0.29, C:0.09, G:0.35, T:0.27
Consensus pattern (151 bp):
GAGAGAGAGAGAGAGACAGGGTGGGGGGGGGGGGGTGGGGAGAATTTAATTGCCAATGGACTTTG
AAGAAGCCATATGTACATACTTCTTTCTGTAATAGGTAACTTGATTGAACATTGGGTGAAAACTG
ATGAGTTGTGCATAGGAGTTG
Found at i:1328813 original size:151 final size:151
Alignment explanation
Indices: 1328539--1328837 Score: 510
Period size: 151 Copynumber: 2.0 Consensus size: 151
1328529 TGGATAGAAA
* *
1328539 AGTGAGGAACAGGAAATAGCACATGTTTGGAATATGTAGCTTCTGGAGAGATATTATAAAAGTTG
1 AGTGAGGAACAGGAAATAGCACATGTTTGGAATATGTAACTTCTGGAGAGATATTATAAAAGCTG
1328604 AATGGTAAATAGAAGTCCATAACTGAATGATTTAGTATCCTGTTTAGGGGGCACTGTCCCAACCA
66 AATGGTAAATAGAAGTCCATAACTGAATGATTTAGTATCCTGTTTAGGGGGCACTGTCCCAACCA
*
1328669 ATAAGATGCCTCGATGATAAC
131 ATAAGATGCCTCAATGATAAC
*
1328690 AGTGAGGAATAGGAAATAGCACATGTTTGGAATATGTAACTTCTGGAGAGATATTATAAAAGCTG
1 AGTGAGGAACAGGAAATAGCACATGTTTGGAATATGTAACTTCTGGAGAGATATTATAAAAGCTG
* * *
1328755 AATGGTAAATAGAATTCCATAACTGAATGATTTAGTATACC-GTTTAGGGGGCAGTGTCCCGACC
66 AATGGTAAATAGAAGTCCATAACTGAATGATTTAGTAT-CCTGTTTAGGGGGCACTGTCCCAACC
*
1328819 GATAAGATGCCTCAATGAT
130 AATAAGATGCCTCAATGAT
1328838 GTGTTTCAAC
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
151 137 0.99
152 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (151 bp):
AGTGAGGAACAGGAAATAGCACATGTTTGGAATATGTAACTTCTGGAGAGATATTATAAAAGCTG
AATGGTAAATAGAAGTCCATAACTGAATGATTTAGTATCCTGTTTAGGGGGCACTGTCCCAACCA
ATAAGATGCCTCAATGATAAC
Found at i:1331516 original size:2 final size:2
Alignment explanation
Indices: 1331509--1331533 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1331499 TTTATTTACT
1331509 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1331534 TTATATGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1351339 original size:17 final size:19
Alignment explanation
Indices: 1351319--1351360 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1351309 CCTTTAACAT
*
1351319 ATTTTTTAAT-AATATA-A
1 ATTTTTAAATAAATATATA
1351336 ATTTTTAAATAGAATATATA
1 ATTTTTAAATA-AATATATA
1351356 ATTTT
1 ATTTT
1351361 ACATTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTTTAAATAAATATATA
Found at i:1361935 original size:7 final size:7
Alignment explanation
Indices: 1361924--1361965 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
1361914 AAACATTGTG
*
1361924 ATTGCCG
1 ATTGCCA
1361931 ATTGCCA
1 ATTGCCA
1361938 ATTGCCA
1 ATTGCCA
1361945 ATTGCCA
1 ATTGCCA
1361952 ATTGCCA
1 ATTGCCA
1361959 ATTGCCA
1 ATTGCCA
1361966 TGATTTGGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (7 bp):
ATTGCCA
Found at i:1368487 original size:2 final size:2
Alignment explanation
Indices: 1368480--1368509 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1368470 GATGCATGTA
1368480 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
1368510 GATAGTCCGA
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):
AT
Found at i:1369025 original size:40 final size:40
Alignment explanation
Indices: 1368970--1369046 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
1368960 GTAATGAATA
1368970 TTAAGGTAAGTAAGATAAGAAAATGCAAAAGAAATAGATT
1 TTAAGGTAAGTAAGATAAGAAAATGCAAAAGAAATAGATT
1369010 TTAAGGTAAGTAAGATAAGAAAATGCAAAAGAAATAG
1 TTAAGGTAAGTAAGATAAGAAAATGCAAAAGAAATAG
1369047 CAGCTCCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (40 bp):
TTAAGGTAAGTAAGATAAGAAAATGCAAAAGAAATAGATT
Found at i:1381287 original size:3 final size:3
Alignment explanation
Indices: 1381279--1381310 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1381269 GGCTGATATG
1381279 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1381311 TTTATCGTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1407875 original size:16 final size:16
Alignment explanation
Indices: 1407836--1407878 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1407826 TTTTTTTATT
*
1407836 TTAAATAAATAAATTA
1 TTAAATTAATAAATTA
1407852 TTATAATTAAT-AATTAA
1 TTA-AATTAATAAATT-A
1407869 TTAAATTAAT
1 TTAAATTAAT
1407879 TAAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATTAATAAATTA
Found at i:1409499 original size:15 final size:15
Alignment explanation
Indices: 1409479--1409509 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1409469 AAGATAGTTG
1409479 TAATTTATTATTCCC
1 TAATTTATTATTCCC
1409494 TAATTTATTATTCCC
1 TAATTTATTATTCCC
1409509 T
1 T
1409510 TTTGTAGGTG
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:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTATTATTCCC
Found at i:1414257 original size:42 final size:40
Alignment explanation
Indices: 1414194--1414320 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 40
1414184 ATCGGATTTT
* *
1414194 TTTTACAATTTCT-AGGAAAAAGCATAAAAGGATTTGACTTTC
1 TTTTACAAATTCTAAGG-AAAAG-A-AAAAGAATTTGACTTTC
* *
1414236 TTTTACAAATTCTAAGGAAAAGAAAAA-CATTCGA-TTTC
1 TTTTACAAATTCTAAGGAAAAGAAAAAGAATTTGACTTTC
*
1414274 TCTTACAAATTCTAA-GAAAGAGAAGAGAAGAATTTGACTTTC
1 TTTTACAAATTCTAAGGAAA-AGAA-A-AAGAATTTGACTTTC
1414316 TTTTA
1 TTTTA
1414321 TTATAAAGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
37 4 0.06
38 22 0.31
39 6 0.08
40 6 0.08
41 6 0.08
42 25 0.35
43 3 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (40 bp):
TTTTACAAATTCTAAGGAAAAGAAAAAGAATTTGACTTTC
Found at i:1425944 original size:2 final size:2
Alignment explanation
Indices: 1425939--1425974 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1425929 AAGACATAAA
*
1425939 CT CT CT CT CT CT CT CT CT CT TT 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
1425975 GCTTGTGCAT
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1438965 original size:276 final size:275
Alignment explanation
Indices: 1438465--1439018 Score: 1004
Period size: 276 Copynumber: 2.0 Consensus size: 275
1438455 AAAATTGGAC
* *
1438465 GGTGCCCAAAAAAAGAACTAAATTGTTCCAATTCCTAAAATCGAGAATGAATTGATCAGATTTTC
1 GGTGCCAAAAAAAAGAACTAAATTGTTCCAATTCCTAAAATCAAGAATGAATTGATCAGATTTTC
1438530 AATATATAAATTAAATTGACGAAAATGCATGGGTATAGGATACTTTGACCATTCTTAAATTGCAT
66 AATATATAAATTAAATTGACGAAAATGCATGGGTATAGGATACTTTGACCATTCTTAAATTGCAT
1438595 AAAGTTTATCAAAATATTTATACATAGTAGAGAAGAAAATTGCAGATGAAATGTTCCCTTTCTAA
131 AAAGTTTATC-AAATATTTATACATAGTAGAGAAGAAAATTGCAGATGAAATGTTCCCTTTCTAA
*
1438660 TGTAATCTAGTTTGTTCAAATGTAATCAAATTAAATAATAAGGTAAAAGGGGCAAGAAGATCTCC
195 TCTAATCTAGTTTGTTCAAATGTAATCAAATTAAATAATAAGGTAAAAGGGGCAAGAAGATCTCC
1438725 TATACAATTTTTGTAT
260 TATACAATTTTTGTAT
*
1438741 GGTGCCAAAAAAAAGAACTAAATTGTTCCAATTCCTAAAATCAAGACTGAATTGATCAGATTTTC
1 GGTGCCAAAAAAAAGAACTAAATTGTTCCAATTCCTAAAATCAAGAATGAATTGATCAGATTTTC
1438806 AATATATAAATTAAATTGACGAAAATGCAT-GGTATAGGATTACTTTGACCATTCTTAAATTGGG
66 AATATATAAATTAAATTGACGAAAATGCATGGGTATAGGA-TACTTTGACCATTCTTAAATT--G
1438870 CATAAAGTTTATC-AATATTTATACATAGTAGAGAAGAAAATTGCAGATGAAATGTTCCCTTTCT
128 CATAAAGTTTATCAAATATTTATACATAGTAGAGAAGAAAATTGCAGATGAAATGTTCCCTTTCT
*
1438934 AATCTAATCTAGTTTGTTCAAATGTAATCAAATTAAGTAATAAGGTAAAAGGGGCAAGAAGATCT
193 AATCTAATCTAGTTTGTTCAAATGTAATCAAATTAAATAATAAGGTAAAAGGGGCAAGAAGATCT
*
1438999 CCTATACGATTTTTGTAT
258 CCTATACAATTTTTGTAT
1439017 GG
1 GG
1439019 AAAAAATCCT
Statistics
Matches: 269, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
275 9 0.03
276 246 0.91
278 14 0.05
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (275 bp):
GGTGCCAAAAAAAAGAACTAAATTGTTCCAATTCCTAAAATCAAGAATGAATTGATCAGATTTTC
AATATATAAATTAAATTGACGAAAATGCATGGGTATAGGATACTTTGACCATTCTTAAATTGCAT
AAAGTTTATCAAATATTTATACATAGTAGAGAAGAAAATTGCAGATGAAATGTTCCCTTTCTAAT
CTAATCTAGTTTGTTCAAATGTAATCAAATTAAATAATAAGGTAAAAGGGGCAAGAAGATCTCCT
ATACAATTTTTGTAT
Found at i:1441526 original size:16 final size:16
Alignment explanation
Indices: 1441486--1441528 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1441476 AAAATAAAAC
* *
1441486 ATTTTTCTTACTCTTG
1 ATTTTTTTTGCTCTTG
1441502 ATTTTTTTTGCTCTTG
1 ATTTTTTTTGCTCTTG
*
1441518 TTTTGTTTTTG
1 ATTT-TTTTTG
1441529 ATTTGATGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.07, C:0.12, G:0.12, T:0.70
Consensus pattern (16 bp):
ATTTTTTTTGCTCTTG
Found at i:1448882 original size:2 final size:2
Alignment explanation
Indices: 1448877--1448901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1448867 TATATATATA
1448877 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1448902 ATATGTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1449705 original size:2 final size:2
Alignment explanation
Indices: 1449698--1449724 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1449688 AACTGAATAC
1449698 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 A
1449725 AAATAAAAGA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1451520 original size:48 final size:48
Alignment explanation
Indices: 1451425--1451520 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
1451415 CGAAAATAAG
* *
1451425 ATAGGTTATGATGCAGTAAGCTATGAAGACACTGATACTATTGTTTAT
1 ATAGGTTATGATGCAGTAAGCAATGAAGACACTGATACTATTATTTAT
**
1451473 ATAGGTTATGATGCAGTAAGCAATGAAGACACTGATGTTATTATTTAT
1 ATAGGTTATGATGCAGTAAGCAATGAAGACACTGATACTATTATTTAT
1451521 CTATTACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.35
Consensus pattern (48 bp):
ATAGGTTATGATGCAGTAAGCAATGAAGACACTGATACTATTATTTAT
Found at i:1453923 original size:49 final size:46
Alignment explanation
Indices: 1453870--1453970 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 46
1453860 TTTACTATGC
* *
1453870 ATATATATATTAATGATTCTTTCAAAATTTTTGAAATTATTTATTTATT
1 ATATATATATTAATGATT-TTT--AAATTTATGAAATTATTTATTTACT
* ** *
1453919 ATATATATTTTAATGATTTTTTTATTTATGAGATTATTTATTTACT
1 ATATATATATTAATGATTTTTAAATTTATGAAATTATTTATTTACT
1453965 ATATAT
1 ATATAT
1453971 TTTTAATAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 26 0.57
48 3 0.07
49 17 0.37
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (46 bp):
ATATATATATTAATGATTTTTAAATTTATGAAATTATTTATTTACT
Found at i:1454311 original size:16 final size:16
Alignment explanation
Indices: 1454284--1454319 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1454274 TTTTTTTTAT
1454284 TTATATTATTTAACTA
1 TTATATTATTTAACTA
1454300 GTTATA-TATTTAACTA
1 -TTATATTATTTAACTA
1454316 TTAT
1 TTAT
1454320 GTAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
TTATATTATTTAACTA
Found at i:1474011 original size:2 final size:2
Alignment explanation
Indices: 1473995--1474032 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1473985 GGTAAGTGAG
*
1473995 CT CT -T CT CT -T CT CT CT CT CT CT CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1474033 TGATGGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1480719 original size:22 final size:22
Alignment explanation
Indices: 1480684--1480727 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
1480674 AGCTCTTCTT
1480684 AATTGGTTGAGATTATGATATATG
1 AATTGGTTGAGATT-TGA-ATATG
1480708 AATT-GTT-AGATTTGAATATG
1 AATTGGTTGAGATTTGAATATG
1480728 GTCTTAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 5 0.25
23 3 0.15
24 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (22 bp):
AATTGGTTGAGATTTGAATATG
Found at i:1482103 original size:21 final size:22
Alignment explanation
Indices: 1482079--1482130 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1482069 GGACCCTTAT
1482079 CTCTTCCACG-TTGGCC-TTGAA
1 CTCTTCCACGCTTGGCCATT-AA
* *
1482100 CTCTT-CAAGCTTGTCCATTAA
1 CTCTTCCACGCTTGGCCATTAA
1482121 CTCTTCCACG
1 CTCTTCCACG
1482131 GCCATCTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.17, C:0.35, G:0.13, T:0.35
Consensus pattern (22 bp):
CTCTTCCACGCTTGGCCATTAA
Found at i:1487095 original size:30 final size:32
Alignment explanation
Indices: 1487020--1487097 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
1487010 GAAAATAATG
*
1487020 ATAATGAAAAATAATTTTAATAAATTGATCTAA
1 ATAATAAAAAAT-ATTTTAATAAATTGATCTAA
* * *
1487053 ATAATAAAAAATATTTT-CTACATTTATCTAA
1 ATAATAAAAAATATTTTAATAAATTGATCTAA
1487084 ATAAT-AAAAATATT
1 ATAATAAAAAATATT
1487098 AAATTTCAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 9 0.22
31 16 0.39
32 5 0.12
33 11 0.27
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (32 bp):
ATAATAAAAAATATTTTAATAAATTGATCTAA
Found at i:1487763 original size:2 final size:2
Alignment explanation
Indices: 1487756--1487791 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1487746 TTCATAAGTT
1487756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1487792 GTTCATAAGT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1513756 original size:3 final size:3
Alignment explanation
Indices: 1513750--1513774 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1513740 ACTGGAGCTT
1513750 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
1513775 CAGTGGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1521997 original size:244 final size:243
Alignment explanation
Indices: 1521568--1522054 Score: 823
Period size: 244 Copynumber: 2.0 Consensus size: 243
1521558 AGCAGTCATC
*
1521568 CAATCAGACTATTAAACAAACCAAACAAAAACAATGCAACAACCAGATAAAAAGCTCAAGCAAAG
1 CAATCAGACTATTAAACAAACCAAACAAAAACAATGCAACAACCAGATAAAAAGCTCAAACAAAG
*
1521633 AATGCCAAGTACCTGAGTTGCCAATATATTTCCTCTCAGTCTTATCATACGGTACTTAAATAAGG
66 AATGCCAAGTACCTGAGTTGCCAATATATTTCCTCTCAGTCTTATCATAAGGTACTTAAATAAGG
* *
1521698 CTCTAGCTTTTATTGTAATTCCACTTTAAAGCATCATCAATTGCTAGAAAAATTTCCCAAAAGTA
131 CTCTAACTTTTATTCTAATTCCACTTTAAAGCATCATCAATTGCTAGAAAAATTTCCCAAAAGTA
*
1521763 AACTCTGAAGCACATAAAAGAGTCTTACTCATCTAATTAGTCCAAAATG
196 AACTCTGAAGCACAT-AAAGAGTCTTACTCATCTAATTAGCCCAAAATG
* *
1521812 CAATCAGACTATTAAACAAACCAAACAAACACAATGCAACAACCCGATAAAAAGCTCAAACAAAG
1 CAATCAGACTATTAAACAAACCAAACAAAAACAATGCAACAACCAGATAAAAAGCTCAAACAAAG
* *
1521877 AATGCCGAA-TACTTGAGTTGCCAATATATTTTCTCTCAGTCTTATCATAAGGTACTTAAATAAG
66 AATGCC-AAGTACCTGAGTTGCCAATATATTTCCTCTCAGTCTTATCATAAGGTACTTAAATAAG
* * **
1521941 TCTCTAATTTTTATTCTAATTCCGGTTTAAAGCATCATCAATTGCTAGAAAAATTTCCCAAAAGT
130 GCTCTAACTTTTATTCTAATTCCACTTTAAAGCATCATCAATTGCTAGAAAAATTTCCCAAAAGT
*
1522006 AAACTCTGAAGCACATAAAGAGTCTTACTCATCTAATTAGCCCCAAATG
195 AAACTCTGAAGCACATAAAGAGTCTTACTCATCTAATTAGCCCAAAATG
1522055 AAACATGTAA
Statistics
Matches: 228, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
243 31 0.14
244 195 0.86
245 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (243 bp):
CAATCAGACTATTAAACAAACCAAACAAAAACAATGCAACAACCAGATAAAAAGCTCAAACAAAG
AATGCCAAGTACCTGAGTTGCCAATATATTTCCTCTCAGTCTTATCATAAGGTACTTAAATAAGG
CTCTAACTTTTATTCTAATTCCACTTTAAAGCATCATCAATTGCTAGAAAAATTTCCCAAAAGTA
AACTCTGAAGCACATAAAGAGTCTTACTCATCTAATTAGCCCAAAATG
Found at i:1546409 original size:93 final size:94
Alignment explanation
Indices: 1546248--1546421 Score: 280
Period size: 93 Copynumber: 1.9 Consensus size: 94
1546238 CGGAAAGCTC
* *
1546248 TTCTACAAGACTGTTGCTATGCTTCAGTCTAAAATTGGATATACCAATACAACTTAACTATAAAA
1 TTCTACAAGAC-GTTGCTATGATTCAGTCTAAAATTGGATACACCAATACAACTTAACTATAAAA
*
1546313 AAACTTGGGTGTGAATGTCAAAAATGGGCA
65 AAACTTGGGCGTGAATGTCAAAAATGGGCA
*
1546343 TTCTACAAGAC-TTGCTATGATTCAGTGTAAAATTGGATACACCAATACAACTTAAAC-ATAAAA
1 TTCTACAAGACGTTGCTATGATTCAGTCTAAAATTGGATACACCAATACAACTT-AACTATAAAA
1546406 AAACTTGGGCGTGAAT
65 AAACTTGGGCGTGAAT
1546422 TAAAAAGTGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
93 60 0.81
94 3 0.04
95 11 0.15
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (94 bp):
TTCTACAAGACGTTGCTATGATTCAGTCTAAAATTGGATACACCAATACAACTTAACTATAAAAA
AACTTGGGCGTGAATGTCAAAAATGGGCA
Found at i:1568004 original size:20 final size:21
Alignment explanation
Indices: 1567961--1568004 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1567951 CAAAATCATA
*
1567961 TTATCATGTTATTATATTACT
1 TTATCATGTTATTATAATACT
*
1567982 TTATCAT-TTATTATAATATT
1 TTATCATGTTATTATAATACT
1568002 TTA
1 TTA
1568005 ACATACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATCATGTTATTATAATACT
Found at i:1583728 original size:31 final size:31
Alignment explanation
Indices: 1583664--1583728 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1583654 TTTTAAATTA
** *
1583664 AAAGTAAAAAATGAATTAAGTATTTTTTGTG
1 AAAGTAAAAAATGAATTAAGTATTTAATATG
1583695 AAAGT-AAAAATGAATTAAGTAATTTAATATG
1 AAAGTAAAAAATGAATTAAGT-ATTTAATATG
1583726 AAA
1 AAA
1583729 TTATAACACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (31 bp):
AAAGTAAAAAATGAATTAAGTATTTAATATG
Found at i:1595093 original size:3 final size:3
Alignment explanation
Indices: 1595085--1595119 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1595075 TTATCTTCAG
1595085 GCA GCA GCA GCA GCA GCA GCA -CA GCA GCCA GCA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA G-CA GCA GC
1595120 GCACCCCCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.31, C:0.37, G:0.31, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:1595111 original size:17 final size:17
Alignment explanation
Indices: 1595089--1595123 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1595079 CTTCAGGCAG
1595089 CAGCAG-CAGCAGCAGCA
1 CAGCAGCCAGCAGC-GCA
1595106 CAGCAGCCAGCAGCGCA
1 CAGCAGCCAGCAGCGCA
1595123 C
1 C
1595124 CCCCCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.40, G:0.29, T:0.00
Consensus pattern (17 bp):
CAGCAGCCAGCAGCGCA
Found at i:1611355 original size:169 final size:170
Alignment explanation
Indices: 1611003--1611355 Score: 397
Period size: 169 Copynumber: 2.1 Consensus size: 170
1610993 TAAACCCAAG
* * *
1611003 ACCCCTCCCTTAACTATCCACTGTGGGATTCTGTCACAATCTCTCCCAACCAAATCCACAACGCC
1 ACCCCTCCCTTACCTATCCAATGTGGGATTCTGTCACAATCTCTCCCAACCAAATCCACAACACC
*** * * *
1611068 CTCGTCACAGGTCGAGTCACCTTGCATCTTTGTCATGGGACCATTACCCTTTCCTCAAAACACTA
66 CTCGTCACAGGTCGAGTCACCTTGCATCTTTGTCACAAGACAATCACCCTCTCCTCAAAACACTA
* ** *
1611133 ACCTGATGAGATATGCAGCACCCATACATATAAGCTCAAA
131 ACCTAATGAGATACACAACACCCATACATATAAGCTCAAA
* * * *
1611173 ACCCCTCCCTTACCTATCCAATTTGGGATTCCT-TCATAGTCTCTCCC-ACCTGAATCCACAACA
1 ACCCCTCCCTTACCTATCCAATGTGGGATT-CTGTCACAATCTCTCCCAACC-AAATCCACAACA
* * * * *
1611236 CCTTTGTCGCAGGTTGGGTCACCTTG-ATCTTTGTCACAAGACAATCACCCTCTCCTCAAAACAC
64 CCCTCGTCACAGGTCGAGTCACCTTGCATCTTTGTCACAAGACAATCACCCTCTCCTCAAAACAC
* * * * * * *
1611300 TATCTTAATGGGATGCACAACACCCATGCATATAAGCTTAGA
129 TAACCTAATGAGATACACAACACCCATACATATAAGCTCAAA
*
1611342 ACCCCTTCCTTACC
1 ACCCCTCCCTTACC
1611356 CATCTGATTT
Statistics
Matches: 151, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
169 79 0.52
170 70 0.46
171 2 0.01
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.26
Consensus pattern (170 bp):
ACCCCTCCCTTACCTATCCAATGTGGGATTCTGTCACAATCTCTCCCAACCAAATCCACAACACC
CTCGTCACAGGTCGAGTCACCTTGCATCTTTGTCACAAGACAATCACCCTCTCCTCAAAACACTA
ACCTAATGAGATACACAACACCCATACATATAAGCTCAAA
Found at i:1619323 original size:3 final size:3
Alignment explanation
Indices: 1619315--1619352 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1619305 GACACCTCAC
1619315 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1619353 ATTAGTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1620061 original size:14 final size:14
Alignment explanation
Indices: 1620042--1620071 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1620032 AATAAATTAT
1620042 TTAAATAAAGTAAA
1 TTAAATAAAGTAAA
*
1620056 TTAAATCAAGTAAA
1 TTAAATAAAGTAAA
1620070 TT
1 TT
1620072 TTTATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (14 bp):
TTAAATAAAGTAAA
Found at i:1620817 original size:7 final size:7
Alignment explanation
Indices: 1620794--1620831 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
1620784 TAACAGATTC
*
1620794 TTATTAT
1 TTATTAA
*
1620801 TTATT-T
1 TTATTAA
1620807 TTATTAA
1 TTATTAA
1620814 TTATTAA
1 TTATTAA
1620821 TTATTAA
1 TTATTAA
1620828 TTAT
1 TTAT
1620832 ACCTTTTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTATTAA
Found at i:1633635 original size:61 final size:61
Alignment explanation
Indices: 1633540--1633662 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
1633530 GAACAAAACA
1633540 ACAGAGAGAGAGAGAAAAGCTTAAGCTAAAGGTACTTAAAAATTGAGATAGACTTTATGTT
1 ACAGAGAGAGAGAGAAAAGCTTAAGCTAAAGGTACTTAAAAATTGAGATAGACTTTATGTT
1633601 ACAGAGAGAGAGAGAAAAGCTTAAGCTAAAGGTACTTAAAAATTGAGATAGACTTTATGTT
1 ACAGAGAGAGAGAGAAAAGCTTAAGCTAAAGGTACTTAAAAATTGAGATAGACTTTATGTT
1633662 A
1 A
1633663 GAACACTAGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24
Consensus pattern (61 bp):
ACAGAGAGAGAGAGAAAAGCTTAAGCTAAAGGTACTTAAAAATTGAGATAGACTTTATGTT
Found at i:1634607 original size:24 final size:25
Alignment explanation
Indices: 1634571--1634622 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
1634561 AAAAATTTAT
*
1634571 TTAATTTAAATATAAATATAAAA-AA
1 TTAATTTAAATAT-AATAAAAAATAA
1634596 TTAA-TTAAATATAATAAAAAATAA
1 TTAATTTAAATATAATAAAAAATAA
1634620 TTA
1 TTA
1634623 TTTGTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 13 0.52
25 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAATTTAAATATAATAAAAAATAA
Found at i:1634611 original size:29 final size:29
Alignment explanation
Indices: 1634561--1634619 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 29
1634551 TCTTAATTAT
* * * *
1634561 AAAAATTTATTTAATTTAAATATAAATATA
1 AAAAATTAATTAAATATAAATA-AAAAATA
1634591 AAAAATTAATTAAATAT-AATAAAAAATA
1 AAAAATTAATTAAATATAAATAAAAAATA
1634619 A
1 A
1634620 TTATTTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.28
29 4 0.16
30 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAAATTAATTAAATATAAATAAAAAATA
Found at i:1634614 original size:20 final size:18
Alignment explanation
Indices: 1634583--1634622 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1634573 AATTTAAATA
*
1634583 TAAATATAAAAAATTAAT
1 TAAATATAAAAAAATAAT
1634601 TAAATATAATAAAAAATAAT
1 TAAATAT-A-AAAAAATAAT
1634621 TA
1 TA
1634623 TTTGTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATATAAAAAAATAAT
Found at i:1641217 original size:19 final size:19
Alignment explanation
Indices: 1641168--1641218 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1641158 TTATTAATAA
1641168 TTTATTAAATTAATAATTT
1 TTTATTAAATTAATAATTT
** * *
1641187 TGTCCTT-CATTAATGATTT
1 T-TTATTAAATTAATAATTT
1641206 TTTATTAAATTAA
1 TTTATTAAATTAA
1641219 AACGTTAACT
Statistics
Matches: 23, Mismatches: 7, Indels: 4
0.68 0.21 0.12
Matches are distributed among these distances:
18 3 0.13
19 17 0.74
20 3 0.13
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTATTAAATTAATAATTT
Found at i:1653366 original size:22 final size:21
Alignment explanation
Indices: 1653329--1653369 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1653319 CTTTAGTTTT
*
1653329 AATATTATTTAAAAATATTAA
1 AATATTATATAAAAATATTAA
1653350 AATATTAATATAAAAATATT
1 AATATT-ATATAAAAATATT
1653370 TTTATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATTATATAAAAATATTAA
Found at i:1653376 original size:22 final size:21
Alignment explanation
Indices: 1653325--1653377 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
1653315 TTATCTTTAG
*
1653325 TTTTAATATTATTTAAAAATA
1 TTTTAATATTATATAAAAATA
**
1653346 TTAAAATATTAATATAAAAATA
1 TTTTAATATT-ATATAAAAATA
*
1653368 TTTTTATATT
1 TTTTAATATT
1653378 TTAATAATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAATATTATATAAAAATA
Found at i:1654241 original size:17 final size:18
Alignment explanation
Indices: 1654205--1654242 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1654195 ATTTCTTGAC
* *
1654205 AAAATAAATAATTTATTA
1 AAAATAAAAAATATATTA
1654223 AAAATAAAAAATATA-TA
1 AAAATAAAAAATATATTA
1654240 AAA
1 AAA
1654243 TCTAAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAAAAAATATATTA
Found at i:1675542 original size:17 final size:16
Alignment explanation
Indices: 1675520--1675566 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1675510 AAAGTCGGCT
*
1675520 AATAAAAAATGAATACA
1 AATAAAAAAT-AAAACA
1675537 AATAAAAATATAAAACA
1 AATAAAAA-ATAAAACA
*
1675554 AAGAAAAAA-AAAA
1 AATAAAAAATAAAA
1675567 TGGTAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 1 0.04
17 20 0.74
18 2 0.07
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (16 bp):
AATAAAAAATAAAACA
Found at i:1691909 original size:2 final size:2
Alignment explanation
Indices: 1691902--1691933 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1691892 ATTCTCATAC
1691902 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
1691934 TTCAATTACA
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:1694733 original size:23 final size:23
Alignment explanation
Indices: 1694703--1694749 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1694693 GTTGGAAAGC
1694703 TATTAAAGGCATTAATTATTTCT
1 TATTAAAGGCATTAATTATTTCT
1694726 TATTAAAGGCATTAATTATTTCT
1 TATTAAAGGCATTAATTATTTCT
1694749 T
1 T
1694750 TTGGTTGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (23 bp):
TATTAAAGGCATTAATTATTTCT
Found at i:1697306 original size:2 final size:2
Alignment explanation
Indices: 1697299--1697326 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1697289 CATGGTAGAC
1697299 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
1697327 GGGCAAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1707436 original size:20 final size:19
Alignment explanation
Indices: 1707411--1707495 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 19
1707401 AATATTTTAT
*
1707411 AATATTATAATTAAAATAAA
1 AATATTA-AAATAAAATAAA
*
1707431 AATATTAAAATAAAATATAT
1 AATATTAAAATAAAATA-AA
*
1707451 AATA-TAAGAATAAAA-ATTA
1 AATATTAA-AATAAAATA-AA
1707470 AA-A-TAAAATAAAATATAA
1 AATATTAAAATAAAATA-AA
*
1707488 AAAATTAA
1 AATATTAA
1707496 CATTTATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.13
18 9 0.16
19 17 0.31
20 22 0.40
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (19 bp):
AATATTAAAATAAAATAAA
Found at i:1707437 original size:14 final size:15
Alignment explanation
Indices: 1707420--1707813 Score: 85
Period size: 16 Copynumber: 25.7 Consensus size: 15
1707410 TAATATTATA
1707420 ATTAAAATAAAA-AT
1 ATTAAAATAAAATAT
1707434 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
* *
1707449 A-TAATATAAGAATAAAA
1 ATTAAAATAA-AAT--AT
1707466 ATTAAAATAAAATA-
1 ATTAAAATAAAATAT
*
1707480 A--AATATAAAA-A-
1 ATTAAAATAAAATAT
* **
1707491 ATTAACAT-TTATAT
1 ATTAAAATAAAATAT
* ** * *
1707505 AATATAGGTAAAACAA
1 ATTA-AAATAAAATAT
1707521 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
1707536 ATAATATAAA-AAAATAT
1 AT--TA-AAATAAAATAT
1707553 ATT--AA-AAAA-AT
1 ATTAAAATAAAATAT
1707564 A--AAAATAAAATAT
1 ATTAAAATAAAATAT
* *
1707577 ATAAAATTATAATAATAA
1 ATTAAA--ATAA-AATAT
*
1707595 ATAAAAATAAAATAT
1 ATTAAAATAAAATAT
* * *
1707610 ATGACATTAAAAATAT
1 ATTAAAAT-AAAATAT
**
1707626 ATTTAAAATATGATATT
1 A-TTAAAATAAAATA-T
*
1707643 ATATAAAA-ATTAATA-
1 AT-TAAAATA-AAATAT
1707658 A-TATAAATATAAATAT
1 ATTA-AAATA-AAATAT
1707674 ATTAAAAATAAAATAT
1 ATT-AAAATAAAATAT
* *
1707690 A-AAATATTATAATAATAA
1 ATTAA-A--ATAA-AATAT
*
1707708 ATAAAAATAAAATAT
1 ATTAAAATAAAATAT
* * *
1707723 ATGACATTAAAAATAT
1 ATTAAAAT-AAAATAT
* *
1707739 ATT-TAA-GAAATGAT
1 ATTAAAATAAAAT-AT
*
1707753 ATTATATAA-AAATTATT
1 ATTA-A-AATAAAATA-T
*
1707770 AATAAAATATAAATAT
1 ATTAAAATA-AAATAT
1707786 ATTAAAAATAAAATAT
1 ATT-AAAATAAAATAT
*
1707802 AATAATAATAAA
1 ATTAA-AATAAA
1707814 TAAAAATATA
Statistics
Matches: 284, Mismatches: 48, Indels: 94
0.67 0.11 0.22
Matches are distributed among these distances:
11 7 0.02
12 19 0.07
13 14 0.05
14 33 0.12
15 53 0.19
16 64 0.23
17 64 0.23
18 27 0.10
19 3 0.01
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:1707554 original size:50 final size:49
Alignment explanation
Indices: 1707419--1707696 Score: 145
Period size: 55 Copynumber: 5.5 Consensus size: 49
1707409 ATAATATTAT
1707419 AATTAAAATAAAA-ATAT--TA-AAATAAAATATATAATATAAGAATAAA
1 AATTAAAATAAAATATATAATATAAA-AAAATATATAATATAAGAATAAA
*
1707465 AATTAAAATAAAATA-A-AATATAAAAAATTAACATTTATATAATATAGGTAA-AACA
1 AATTAAAATAAAATATATAATAT--AAAA--AA-A--TATATAATATAAG-AATAA-A
1707520 AATTAAAATAAAATATATAATATAAAAAAATATATTAA-A-AA-AATAAA
1 AATTAAAATAAAATATATAATATAAAAAAATATA-TAATATAAGAATAAA
* * *
1707567 AA-TAAAATATATAAAATTATAATAATAAATAAAA-ATAAAATATATGACATTAAA
1 AATTAAAATA-A-AATA-TATAAT-ATAAA-AAAATATATAATATAAGA-A-TAAA
** * *
1707621 AA-TATATTTAAAATATGATATTATATAAAAAT-TAATAATATAA-ATATAAA
1 AATTA-AAATAAAATAT-ATAATATAAAAAAATAT-ATAATATAAGA-ATAAA
*
1707671 TATATTAAAAATAAAATATAAAATAT
1 -A-ATT-AAAATAAAATATATAATAT
1707697 TATAATAATA
Statistics
Matches: 180, Mismatches: 17, Indels: 64
0.69 0.07 0.25
Matches are distributed among these distances:
46 21 0.12
47 9 0.05
48 5 0.03
49 10 0.06
50 21 0.12
51 18 0.10
52 21 0.12
53 20 0.11
54 24 0.13
55 25 0.14
56 1 0.01
57 5 0.03
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (49 bp):
AATTAAAATAAAATATATAATATAAAAAAATATATAATATAAGAATAAA
Found at i:1707569 original size:6 final size:6
Alignment explanation
Indices: 1707558--1707606 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
1707548 AATATATTAA
* *
1707558 AAAAAT AAAAAT AAAATAT ATAAAAT TATAAT AATAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT AA-AAAT AAAAAT AAAA
1707607 TATATGACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 23 0.64
7 10 0.28
8 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
AAAAAT
Found at i:1707587 original size:8 final size:9
Alignment explanation
Indices: 1707527--1707724 Score: 67
Period size: 9 Copynumber: 23.2 Consensus size: 9
1707517 ACAAATTAAA
1707527 ATAAAATAT
1 ATAAAATAT
*
1707536 ATAATATA-
1 ATAAAATAT
*
1707544 AAAAAATAT
1 ATAAAATAT
*
1707553 ATTAAAA-AA
1 A-TAAAATAT
1707562 AT-AAA-A-
1 ATAAAATAT
1707568 ATAAAATAT
1 ATAAAATAT
1707577 ATAAAAT-T
1 ATAAAATAT
*
1707585 ATAATAATAA
1 ATAA-AATAT
1707595 AT-AAA-A-
1 ATAAAATAT
1707601 ATAAAATAT
1 ATAAAATAT
* *
1707610 ATGACAT-T
1 ATAAAATAT
1707618 A-AAAATAT
1 ATAAAATAT
1707626 ATTTAAAATAT
1 A--TAAAATAT
**
1707637 GATATTATAT
1 -ATAAAATAT
1707647 A-AAAAT-T
1 ATAAAATAT
* *
1707654 AATAATATAA
1 -ATAAAATAT
1707664 ATATAAATAT
1 ATA-AAATAT
*
1707674 ATTAAA-A-
1 ATAAAATAT
1707681 AT-AAA-AT
1 ATAAAATAT
1707688 ATAAAATATT
1 ATAAAATA-T
*
1707698 ATAATAATAA
1 ATAA-AATAT
1707708 AT-AAA-A-
1 ATAAAATAT
1707714 ATAAAATAT
1 ATAAAATAT
1707723 AT
1 AT
1707725 GACATTAAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 54
0.66 0.09 0.25
Matches are distributed among these distances:
6 10 0.07
7 23 0.16
8 31 0.22
9 41 0.29
10 25 0.18
11 11 0.08
12 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAAAATAT
Found at i:1707597 original size:33 final size:34
Alignment explanation
Indices: 1707524--1707611 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 34
1707514 AAAACAAATT
* * *
1707524 AAAATAAAATATATAATATAAAAAAATATATTAAA
1 AAAATAAAA-ATAAAATATATAAAAATATAATAAA
*
1707559 AAAATAAAAATAAAATATATAAAATTATAAT-AA
1 AAAATAAAAATAAAATATATAAAAATATAATAAA
*
1707592 TAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
1707612 GACATTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 21 0.44
34 18 0.38
35 9 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (34 bp):
AAAATAAAAATAAAATATATAAAAATATAATAAA
Found at i:1707622 original size:60 final size:60
Alignment explanation
Indices: 1707558--1707737 Score: 193
Period size: 60 Copynumber: 3.1 Consensus size: 60
1707548 AATATATTAA
1707558 AAAAATAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATT
1 AAAAATAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATT
* ** *
1707618 AAAAATATATTTAAAATATGAT---ATTAT-ATAA-AAATTAATAATATAAATATA--A-A-T
1 AAAAATAAAAATAAAATAT-ATAAAATTATAATAATAAA-TAAAAATA-AAATATATGACATT
* *
1707672 -ATATTAAAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATT
1 AAAAATAAAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGACATT
1707731 AAAAATA
1 AAAAATA
1707738 TATTTAAGAA
Statistics
Matches: 94, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
52 1 0.01
53 13 0.14
54 1 0.01
55 13 0.14
56 15 0.16
57 15 0.16
58 13 0.14
59 1 0.01
60 20 0.21
61 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.32
Consensus pattern (60 bp):
AAAAATAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATT
Found at i:1707623 original size:27 final size:26
Alignment explanation
Indices: 1707563--1707737 Score: 117
Period size: 27 Copynumber: 6.3 Consensus size: 26
1707553 ATTAAAAAAA
1707563 TAAAAATAAAATATATAAA-ATTATA-A-
1 TAAAAATAAAA-ATA-AAATA-TATACAT
1707589 TAATAAATAAAAATAAAATATATGACAT
1 TAA-AAATAAAAATAAAATATAT-ACAT
* ** *
1707617 TAAAAATATATTTAAAATATGATATTAT
1 TAAAAATAAAAATAAAATAT-ATA-CAT
* *
1707645 ATAAAAATTAATAATATAAATATAAATATAT
1 -TAAAAA-TAA-AA-ATAAA-ATATATACAT
1707676 TAAAAATAAAATATAAAATATTATA-A-
1 TAAAAATAAAA-ATAAAATA-TATACAT
1707702 TAATAAATAAAAATAAAATATATGACAT
1 TAA-AAATAAAAATAAAATATAT-ACAT
1707730 TAAAAATA
1 TAAAAATA
1707738 TATTTAAGAA
Statistics
Matches: 123, Mismatches: 9, Indels: 33
0.75 0.05 0.20
Matches are distributed among these distances:
25 9 0.07
26 20 0.16
27 42 0.34
28 21 0.17
29 9 0.07
30 8 0.07
31 4 0.03
32 7 0.06
33 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (26 bp):
TAAAAATAAAAATAAAATATATACAT
Found at i:1707668 original size:6 final size:6
Alignment explanation
Indices: 1707657--1707723 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
1707647 AAAAATTAAT
* *
1707657 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
1707707 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
1707724 TGACATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:1707714 original size:113 final size:112
Alignment explanation
Indices: 1707563--1707821 Score: 436
Period size: 113 Copynumber: 2.3 Consensus size: 112
1707553 ATTAAAAAAA
1707563 TAAAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATA
1 TAAAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATA
1707627 TTTAA-AATATGATATTATATAAAAATTAATAATATAAATATAAATATAT
65 TTTAAGAA-ATGATATTATATAAAAATTAATAATA-AAATATAAATATAT
1707676 TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
*
1707741 TTAAGAAATGATATTATATAAAAATTATTAATAAAATATAAATATAT
66 TTAAGAAATGATATTATATAAAAATTAATAATAAAATATAAATATAT
*
1707788 TAAAAATAAAATATAATAATAATA-AATAA-AAATA
1 TAAAAATAAAATATAA-AATATTATAATAATAAATA
1707822 TATTTAAAAA
Statistics
Matches: 141, Mismatches: 2, Indels: 8
0.93 0.01 0.05
Matches are distributed among these distances:
111 5 0.04
112 38 0.27
113 96 0.68
114 2 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (112 bp):
TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
TTAAGAAATGATATTATATAAAAATTAATAATAAAATATAAATATAT
Found at i:1707718 original size:33 final size:33
Alignment explanation
Indices: 1707560--1707821 Score: 108
Period size: 33 Copynumber: 7.3 Consensus size: 33
1707550 TATATTAAAA
1707560 AAATAAAAATAAAATATATAAA-ATTATAATAAT
1 AAATAAAAATAAAATATA-AAATATTATAATAAT
** * *
1707593 AAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAATAAAAATAAAATATAAAATATT-ATAATA-A--T
*
1707630 AAAATATGATATTATATAAAA-ATTAATAATA-TAAATATAAAT
1 -AAATA--A-A--A-ATAAAATA-TAA-AATATTATA-AT-AAT
*
1707672 ATATTAAAAATAAAATATAAAATATTATAATAAT
1 A-AATAAAAATAAAATATAAAATATTATAATAAT
** *
1707706 AAATAAAAATAAAATATATGACATTA-AA-AAT
1 AAATAAAAATAAAATATAAAATATTATAATAAT
* *
1707737 ATATTTAAGAAATGATATTATATAAAA-ATTATTAATAA-
1 A-A-ATAA-AAAT-A-A-AATATAAAATATTA-TAATAAT
*
1707775 AATATAAATATATTAAAA-ATAAAATATAATAATAAT
1 AA-ATAAA-A-A-TAAAATATAAAATATTATAATAAT
1707811 AAATAAAAATA
1 AAATAAAAATA
1707822 TATTTAAAAA
Statistics
Matches: 177, Mismatches: 19, Indels: 67
0.67 0.07 0.25
Matches are distributed among these distances:
31 4 0.02
32 6 0.03
33 46 0.26
34 14 0.08
35 25 0.14
36 24 0.14
37 16 0.09
38 10 0.06
39 4 0.02
40 2 0.01
41 2 0.01
42 4 0.02
43 5 0.03
44 12 0.07
45 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (33 bp):
AAATAAAAATAAAATATAAAATATTATAATAAT
Found at i:1707789 original size:22 final size:20
Alignment explanation
Indices: 1707756--1707868 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 20
1707746 AAATGATATT
**
1707756 ATATAAAAATTATTAATAAA
1 ATATAAAAATTAAAAATAAA
1707776 ATATAAATATATTAAAAATAAA
1 ATATAAA-A-ATTAAAAATAAA
*
1707798 ATATAATAA-TAATAAATAAA
1 ATATAAAAATTAA-AAATAAA
* *
1707818 A-AT-ATATTTAAAAAATAATA
1 ATATAAAAATT-AAAAATAA-A
*
1707838 TTATATAAAAATTAATAATACTAA
1 --ATATAAAAATTAAAAATA--AA
1707862 ATATAAA
1 ATATAAA
1707869 TATATTAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.04
19 12 0.16
20 19 0.26
21 2 0.03
22 24 0.32
23 8 0.11
24 5 0.07
25 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATAAAAATTAAAAATAAA
Found at i:1707818 original size:84 final size:85
Alignment explanation
Indices: 1707654--1707877 Score: 265
Period size: 84 Copynumber: 2.5 Consensus size: 85
1707644 TATAAAAATT
* *
1707654 AATAATATAAATATAAATATATTAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAA
1 AATAATAT-TATATAAA-A-ATTAATAATAAAATAT-AAATA-TAT--TAA-AAATAAAAATAAA
* *
1707719 ATATATGACATTAAAAATATATTTAAGA
58 ATATATGACAATAAAAATATATTTAAAA
* *
1707747 AATGATATTATATAAAAATTATTAATAAAATATAAATATATTAAAAATAAAATATAATAATA-AT
1 AATAATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAA-ATAA-AATATAT
1707811 -A-AATAAAAATATATTTAAAA
64 GACAATAAAAATATATTTAAAA
1707831 AATAATATTATATAAAAATTAATAATACTAAATATAAATATATTAAA
1 AATAATATTATATAAAAATTAATAATA--AAATATAAATATATTAAA
1707878 TTTATATTTT
Statistics
Matches: 119, Mismatches: 8, Indels: 15
0.84 0.06 0.11
Matches are distributed among these distances:
84 42 0.35
85 9 0.08
86 27 0.23
87 4 0.03
88 3 0.03
89 5 0.04
90 14 0.12
91 1 0.01
92 7 0.06
93 7 0.06
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (85 bp):
AATAATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAAATAAAATATATGA
CAATAAAAATATATTTAAAA
Found at i:1707831 original size:13 final size:16
Alignment explanation
Indices: 1707802--1707854 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1707792 AATAAAATAT
* *
1707802 AATAATAATAAATAAA
1 AATAATATTATATAAA
1707818 AAT-ATATT-TA-AAA
1 AATAATATTATATAAA
1707831 AATAATATTATATAAA
1 AATAATATTATATAAA
1707847 AATTAATA
1 AA-TAATA
1707855 ATACTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 6 0.19
14 6 0.19
15 6 0.19
16 8 0.26
17 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAATATTATATAAA
Found at i:1707838 original size:14 final size:16
Alignment explanation
Indices: 1707562--1707854 Score: 91
Period size: 14 Copynumber: 18.8 Consensus size: 16
1707552 TATTAAAAAA
*
1707562 ATAAAAATAA-AATAT
1 ATAAAAATAATATTAT
* *
1707577 ATAAAATTATAATAATAA
1 ATAAAA--ATAATATTAT
*
1707595 ATAAAAATAAAATATATGAC
1 ATAAAAAT--AATAT-T-AT
1707615 ATTAAAAAT-ATATT-T
1 A-TAAAAATAATATTAT
* *
1707630 A-AAATATGATATTAT
1 ATAAAAATAATATTAT
1707645 ATAAAAATTAATA--AT
1 ATAAAAA-TAATATTAT
*
1707660 ATAAATATAA-A-TAT
1 ATAAAAATAATATTAT
*
1707674 ATTAAAAATAA-AATAT
1 A-TAAAAATAATATTAT
* *
1707690 A-AAATATTATAATAATAA
1 ATAAA-A--ATAATATTAT
*
1707708 ATAAAAATAAAATATATGAC
1 ATAAAAAT--AATAT-T-AT
1707728 ATTAAAAAT-ATATT-T
1 A-TAAAAATAATATTAT
* *
1707743 A-AGAAATGATATTAT
1 ATAAAAATAATATTAT
1707758 ATAAAAAT--TATTA-
1 ATAAAAATAATATTAT
1707771 ATAAAATATAA-A-TAT
1 ATAAAA-ATAATATTAT
1707786 ATTAAAAATAA-A--AT
1 A-TAAAAATAATATTAT
*
1707800 ATAATAATAATA--A-
1 ATAAAAATAATATTAT
1707813 ATAAAAAT-ATATT-T
1 ATAAAAATAATATTAT
1707827 A-AAAAATAATATTAT
1 ATAAAAATAATATTAT
1707842 ATAAAAATTAATA
1 ATAAAAA-TAATA
1707855 ATACTAAATA
Statistics
Matches: 220, Mismatches: 17, Indels: 80
0.69 0.05 0.25
Matches are distributed among these distances:
12 3 0.01
13 38 0.17
14 39 0.18
15 39 0.18
16 27 0.12
17 19 0.09
18 32 0.15
19 5 0.02
20 4 0.02
21 14 0.06
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAAAAATAATATTAT
Found at i:1707855 original size:39 final size:37
Alignment explanation
Indices: 1707774--1707855 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
1707764 ATTATTAATA
* *
1707774 AAATATAAATATATTAAAAATAAAATATAATAATAAT
1 AAATAAAAATATATTAAAAATAAAATATAATAAAAAT
*
1707811 AAATAAAAATATATTTAAAAA-ATAATATTATATAAAAAT
1 AAATAAAAATATA-TTAAAAATAAAATA-TA-ATAAAAAT
*
1707850 TAATAA
1 AAATAA
1707856 TACTAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 17 0.45
38 9 0.24
39 12 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (37 bp):
AAATAAAAATATATTAAAAATAAAATATAATAAAAAT
Found at i:1707869 original size:20 final size:20
Alignment explanation
Indices: 1707831--1707869 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1707821 ATATTTAAAA
* *
1707831 AATAATATTATATAAAAATT
1 AATAATACTAAATAAAAATT
*
1707851 AATAATACTAAATATAAAT
1 AATAATACTAAATAAAAAT
1707870 ATATTAAATT
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:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAATACTAAATAAAAATT
Found at i:1711624 original size:82 final size:82
Alignment explanation
Indices: 1711487--1711652 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 82
1711477 AGTGCATAAT
* * *
1711487 ATATATACCTAGACTGTGACAAATACTAATTTTGGATTCTCAGCTATCATTTACTTAGAAACATA
1 ATATATACCTAGACTGTGACAAAGACTAATTTTCGATTCTCAGCTATCATTTACTTAGAAACACA
1711552 ATTCTCAATTCAGTAGA
66 ATTCTCAATTCAGTAGA
* *
1711569 ATATATACCTAGACTGTGACAAAGACTAATTTTCGATTCTCAGTTATCATTTACTTAGAAACGCA
1 ATATATACCTAGACTGTGACAAAGACTAATTTTCGATTCTCAGCTATCATTTACTTAGAAACACA
1711634 ATTCTCAATTCAGTAGA
66 ATTCTCAATTCAGTAGA
1711651 AT
1 AT
1711653 TGCTGATAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (82 bp):
ATATATACCTAGACTGTGACAAAGACTAATTTTCGATTCTCAGCTATCATTTACTTAGAAACACA
ATTCTCAATTCAGTAGA
Found at i:1718833 original size:14 final size:14
Alignment explanation
Indices: 1718801--1718844 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1718791 GTTTTGTTGC
*
1718801 TTTTCTGGTTTTTG
1 TTTTCTGCTTTTTG
* *
1718815 GTTTCTGCTTCTTG
1 TTTTCTGCTTTTTG
*
1718829 TTTTCTACTTTTTG
1 TTTTCTGCTTTTTG
1718843 TT
1 TT
1718845 GTTTTTATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.02, C:0.14, G:0.16, T:0.68
Consensus pattern (14 bp):
TTTTCTGCTTTTTG
Found at i:1736551 original size:24 final size:22
Alignment explanation
Indices: 1736518--1736569 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
1736508 AACATAGTAC
* *
1736518 AAATATTTTTATATTTAACATTTT
1 AAATAATTTTAAATTTAA-A-TTT
1736542 AAATAATTTTAAATTTAAATTT
1 AAATAATTTTAAATTTAAATTT
1736564 AAATAA
1 AAATAA
1736570 AAATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
23 1 0.04
24 16 0.62
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATAATTTTAAATTTAAATTT
Found at i:1751058 original size:3 final size:3
Alignment explanation
Indices: 1751050--1751078 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1751040 TATTACATTG
1751050 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1751079 CCTGTAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1751652 original size:21 final size:21
Alignment explanation
Indices: 1751626--1751665 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1751616 GGTCTTTGGA
1751626 TTGTGCACCAAAGTGTGATGT
1 TTGTGCACCAAAGTGTGATGT
1751647 TTGTGCACCAAAGTGTGAT
1 TTGTGCACCAAAGTGTGAT
1751666 TTTTCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGTGCACCAAAGTGTGATGT
Found at i:1761580 original size:14 final size:14
Alignment explanation
Indices: 1761561--1761595 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1761551 GTCCGGTCCG
1761561 GTTGTTGTATA-ATT
1 GTTGTTGTA-ACATT
1761575 GTTGTTGTAACATT
1 GTTGTTGTAACATT
1761589 GTTGTTG
1 GTTGTTG
1761596 CACTAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.05
14 19 0.95
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (14 bp):
GTTGTTGTAACATT
Found at i:1769290 original size:11 final size:10
Alignment explanation
Indices: 1769257--1769308 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
1769247 TATTTAAGTT
1769257 TATTATTAAAA
1 TATT-TTAAAA
* *
1769268 TATATCAAAA
1 TATTTTAAAA
1769278 TTATTTTAAAA
1 -TATTTTAAAA
*
1769289 T-TTTTAATA
1 TATTTTAAAA
1769298 TATTTTAAAA
1 TATTTTAAAA
1769308 T
1 T
1769309 CAAAATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
9 8 0.24
10 14 0.42
11 11 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:1778698 original size:24 final size:25
Alignment explanation
Indices: 1778664--1778715 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1778654 GTTCAAGGTA
* *
1778664 ATGGGTCTTTTCT-TCCCTCTTATG
1 ATGGGTATTTTCTCCCCCTCTTATG
*
1778688 ATGGGTATTTTCTCCCCCTCTTTTG
1 ATGGGTATTTTCTCCCCCTCTTATG
1778713 ATG
1 ATG
1778716 TTGTAGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.10, C:0.25, G:0.17, T:0.48
Consensus pattern (25 bp):
ATGGGTATTTTCTCCCCCTCTTATG
Found at i:1786549 original size:27 final size:27
Alignment explanation
Indices: 1786518--1786569 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1786508 AGATGTAAAA
*
1786518 ACTCACTAAATAATTGCATAAAATAAT
1 ACTCAATAAATAATTGCATAAAATAAT
** *
1786545 ACTCAATCGATTATTGCATAAAATA
1 ACTCAATAAATAATTGCATAAAATA
1786570 TTATTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (27 bp):
ACTCAATAAATAATTGCATAAAATAAT
Found at i:1787867 original size:2 final size:2
Alignment explanation
Indices: 1787860--1787935 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1787850 GGGTTTCAGA
1787860 TC TC TC TC TC TC TC TC TC TC TC TC 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
1787902 TC TC TC TC TC TC TC TC 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
1787936 ACTTTTTAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1790171 original size:16 final size:16
Alignment explanation
Indices: 1790150--1790181 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1790140 ATTAAATAAG
1790150 ATTGTGTCAGTTTAGT
1 ATTGTGTCAGTTTAGT
1790166 ATTGTGTCAGTTTAGT
1 ATTGTGTCAGTTTAGT
1790182 TAAGTTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
ATTGTGTCAGTTTAGT
Found at i:1811270 original size:2 final size:2
Alignment explanation
Indices: 1811263--1811290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1811253 TGTGCTAATC
1811263 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
1811291 CACATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1813787 original size:276 final size:276
Alignment explanation
Indices: 1813294--1813846 Score: 1016
Period size: 276 Copynumber: 2.0 Consensus size: 276
1813284 AATGTTAGAA
1813294 ACTCATGATGCTTATAAATTTAGGGTTTAGCAAACAATTGATTCGATCTATTCAACGTGTCATAA
1 ACTCATGATGCTTATAAATTTAGGGTTTAGCAAACAATTGATTCGATCTATTCAACGTGTCATAA
*
1813359 TTGAAAATCGAATTAAATGAAATTTAATGATAGATTCACTTATTACTTTATTATAATTTTAATAC
66 TTGAAAATCGAATTAAATGAAATTTAATGATAGATTCACTTATAACTTTATTATAATTTTAATAC
1813424 TTATAACAAGTGATTGCATTTAAGATGTCATAAAAAAATCAATTGTGATCGATTGTGGATCTAGT
131 TTATAACAAGTGATTGCATTTAAGATGTCATAAAAAAATCAATTGTGATCGATTGTGGATCTAGT
* * *
1813489 AATTTTATATACAACATGATAATATGACACGTATGTAATACAGAGTTAAATAGAGTTGGGTTTAG
196 AATTTTATACACAACATGATAATATAACACGTATGTAATACAAAGTTAAATAGAGTTGGGTTTAG
1813554 GGCAATCGTGTTTTGT
261 GGCAATCGTGTTTTGT
* * *
1813570 ACTCATGATGCTTATAAATTTAGGGTTTAGTAAACAATTGGTTCGATCTATTCAACGTGTCATTA
1 ACTCATGATGCTTATAAATTTAGGGTTTAGCAAACAATTGATTCGATCTATTCAACGTGTCATAA
*
1813635 TTGAAAATCGAATTAAATGAAATTTAATGATAGATTCACTTATAATTTTATTATAATTTTAATAC
66 TTGAAAATCGAATTAAATGAAATTTAATGATAGATTCACTTATAACTTTATTATAATTTTAATAC
1813700 TTATAACAAGTGATTGCATTTAAGATGTCATAAAAAAATCAATTGTGATCGATTGTGGATCTAGT
131 TTATAACAAGTGATTGCATTTAAGATGTCATAAAAAAATCAATTGTGATCGATTGTGGATCTAGT
* *
1813765 AATTTTATACACAGCATGATAATATAACACGTATGTAATACAAAGTTAAATGGAGTTGGGTTTAG
196 AATTTTATACACAACATGATAATATAACACGTATGTAATACAAAGTTAAATAGAGTTGGGTTTAG
1813830 GGCAATCGTGTTTTGT
261 GGCAATCGTGTTTTGT
1813846 A
1 A
1813847 ACTTAAACAA
Statistics
Matches: 267, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
276 267 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (276 bp):
ACTCATGATGCTTATAAATTTAGGGTTTAGCAAACAATTGATTCGATCTATTCAACGTGTCATAA
TTGAAAATCGAATTAAATGAAATTTAATGATAGATTCACTTATAACTTTATTATAATTTTAATAC
TTATAACAAGTGATTGCATTTAAGATGTCATAAAAAAATCAATTGTGATCGATTGTGGATCTAGT
AATTTTATACACAACATGATAATATAACACGTATGTAATACAAAGTTAAATAGAGTTGGGTTTAG
GGCAATCGTGTTTTGT
Found at i:1815649 original size:39 final size:39
Alignment explanation
Indices: 1815598--1815679 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
1815588 CGCTCCAAAC
1815598 ACTTTCAATGTGAAAACGGAAACGGGTAGTTTCGGTCAA
1 ACTTTCAATGTGAAAACGGAAACGGGTAGTTTCGGTCAA
* *
1815637 ACTTTCAATGTGAAATCTGAAACGGGTAGTTTCGGTCAA
1 ACTTTCAATGTGAAAACGGAAACGGGTAGTTTCGGTCAA
1815676 ACTT
1 ACTT
1815680 CGGAACCGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (39 bp):
ACTTTCAATGTGAAAACGGAAACGGGTAGTTTCGGTCAA
Found at i:1820117 original size:24 final size:24
Alignment explanation
Indices: 1820090--1820145 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
1820080 ATCAGCATCA
*
1820090 GCATCAG-TTCCAGCAGCATCAACT
1 GCATCAGCTT-CAGCAGCAACAACT
1820114 GCATCAGCTTCAGCAGCAACAACT
1 GCATCAGCTTCAGCAGCAACAACT
*
1820138 GCAACAGC
1 GCATCAGC
1820146 AACAGGAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (24 bp):
GCATCAGCTTCAGCAGCAACAACT
Found at i:1820155 original size:24 final size:24
Alignment explanation
Indices: 1820100--1820157 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1820090 GCATCAGTTC
* * **
1820100 CAGCAGCATCAACTGCATCAGCTT
1 CAGCAGCAACAACTGCAACAGCAA
1820124 CAGCAGCAACAACTGCAACAGCAA
1 CAGCAGCAACAACTGCAACAGCAA
*
1820148 CAGGAGCAAC
1 CAGCAGCAAC
1820158 CACAACAGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.33, G:0.19, T:0.10
Consensus pattern (24 bp):
CAGCAGCAACAACTGCAACAGCAA
Found at i:1834746 original size:25 final size:25
Alignment explanation
Indices: 1834717--1834795 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
1834707 GTATACAAGA
1834717 GTTATGAAGGATTAGTACAATTGAT
1 GTTATGAAGGATTAGTACAATTGAT
* ** * * *
1834742 GTTATGCAA-CAACAAT-TATTTGA-
1 GTTATG-AAGGATTAGTACAATTGAT
*
1834765 GTTATGAAGGATTCGTACAATTGAT
1 GTTATGAAGGATTAGTACAATTGAT
1834790 GTTATG
1 GTTATG
1834796 CAACAACAAT
Statistics
Matches: 37, Mismatches: 13, Indels: 8
0.64 0.22 0.14
Matches are distributed among these distances:
22 2 0.05
23 8 0.22
24 10 0.27
25 15 0.41
26 2 0.05
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.37
Consensus pattern (25 bp):
GTTATGAAGGATTAGTACAATTGAT
Found at i:1834769 original size:48 final size:48
Alignment explanation
Indices: 1834715--1834810 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1834705 AAGTATACAA
1834715 GAGTTATGAAGGATTAGTACAATTGATGTTATGCAACAACAATTATTT
1 GAGTTATGAAGGATTAGTACAATTGATGTTATGCAACAACAATTATTT
*
1834763 GAGTTATGAAGGATTCGTACAATTGATGTTATGCAACAACAATTATTT
1 GAGTTATGAAGGATTAGTACAATTGATGTTATGCAACAACAATTATTT
1834811 CCCATAGACT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (48 bp):
GAGTTATGAAGGATTAGTACAATTGATGTTATGCAACAACAATTATTT
Found at i:1857900 original size:76 final size:76
Alignment explanation
Indices: 1857820--1857972 Score: 234
Period size: 76 Copynumber: 2.0 Consensus size: 76
1857810 AGTGTAATAG
* *
1857820 CAGTATTATTTTTTAACATGACATGTAACAACCTAATCATGGCGTATAACATGTTTTTGTACATG
1 CAGTATTATTTTTCAACATGACATGTAACAACCTAATCATGGCGCATAACATGTTTTTGTACATG
1857885 ACATATAACAA
66 ACATATAACAA
* * * *
1857896 CAGTATTATTTTTCAACATGACGTGTAACAATCTAATCATGGTGCATAACATGTTTTTGTATATG
1 CAGTATTATTTTTCAACATGACATGTAACAACCTAATCATGGCGCATAACATGTTTTTGTACATG
* *
1857961 ACGTGTAACAA
66 ACATATAACAA
1857972 C
1 C
1857973 CCTAACTATG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (76 bp):
CAGTATTATTTTTCAACATGACATGTAACAACCTAATCATGGCGCATAACATGTTTTTGTACATG
ACATATAACAA
Found at i:1857968 original size:45 final size:46
Alignment explanation
Indices: 1857902--1858016 Score: 128
Period size: 46 Copynumber: 2.5 Consensus size: 46
1857892 ACAACAGTAT
* *
1857902 TATTTTTCA-ACATGACGTGTAACAA-TCTAA-TCATGGTGCATAACA
1 TATTTTT-ATACATGACGTGTAACAACCCTAACT-ATGATGCATAACA
* * * **
1857947 TGTTTTTGTATATGACGTGTAACAACCCTAACTATGATGTGTAACA
1 TATTTTTATACATGACGTGTAACAACCCTAACTATGATGCATAACA
1857993 TATTTTTATACATGACGTGTAACA
1 TATTTTTATACATGACGTGTAACA
1858017 TGTTTATGTA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
45 21 0.37
46 35 0.61
47 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (46 bp):
TATTTTTATACATGACGTGTAACAACCCTAACTATGATGCATAACA
Found at i:1858012 original size:24 final size:24
Alignment explanation
Indices: 1857980--1858040 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1857970 AACCCTAACT
* *
1857980 ATGATGTGTAACATATTTTTATAC
1 ATGACGTGTAACATATTTATATAC
* *
1858004 ATGACGTGTAACATGTTTATGTAC
1 ATGACGTGTAACATATTTATATAC
1858028 ATGACGTGTAACA
1 ATGACGTGTAACA
1858041 ACTTAATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (24 bp):
ATGACGTGTAACATATTTATATAC
Found at i:1859646 original size:2 final size:2
Alignment explanation
Indices: 1859634--1859676 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1859624 GTTAAATTAA
1859634 AT AT A- 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
1859675 AT
1 AT
1859677 GAGATTCAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1868162 original size:28 final size:28
Alignment explanation
Indices: 1868129--1868481 Score: 351
Period size: 27 Copynumber: 12.8 Consensus size: 28
1868119 CTAATTAATA
* *
1868129 TTGTTACATGCCATGTTGAAAAATTTAG
1 TTGTTACACGTCATGTTGAAAAATTTAG
* ** *
1868157 TTGTTACATGTCACATT-AAAAATTTAA
1 TTGTTACACGTCATGTTGAAAAATTTAG
* ** * *
1868184 TTGTTATACACCATGTTGAAATATGTAG
1 TTGTTACACGTCATGTTGAAAAATTTAG
* *
1868212 TTATTACACATCATGTTG-AAAATTTAG
1 TTGTTACACGTCATGTTGAAAAATTTAG
*
1868239 TTGTTACATGTCATGTTG-AAAATTTAG
1 TTGTTACACGTCATGTTGAAAAATTTAG
*
1868266 TTGTTACACGTTATGTTG-AAAATTTAG
1 TTGTTACACGTCATGTTGAAAAATTTAG
** *
1868293 TTGTTACACGTCATGTTGAAAAATGGAA
1 TTGTTACACGTCATGTTGAAAAATTTAG
* *
1868321 TTGTTACTCGTCATATTG-AAAATTTAG
1 TTGTTACACGTCATGTTGAAAAATTTAG
* * *
1868348 TTGTTACATGCCATGTTG-AAAATAATAG
1 TTGTTACACGTCATGTTGAAAAAT-TTAG
* ** *
1868376 TTATTACACGTCATGTTGAAAAATGGAA
1 TTGTTACACGTCATGTTGAAAAATTTAG
** *
1868404 TTGTTACACGTCATGTT-AAGGATTTAA
1 TTGTTACACGTCATGTTGAAAAATTTAG
*
1868431 TTGTTACACGTTATGTTGAAAAATTTAG
1 TTGTTACACGTCATGTTGAAAAATTTAG
* *
1868459 TTGTTACGCGTCATGATGAAAAA
1 TTGTTACACGTCATGTTGAAAAA
1868482 ATTGTTACAC
Statistics
Matches: 265, Mismatches: 55, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
27 140 0.53
28 120 0.45
29 5 0.02
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (28 bp):
TTGTTACACGTCATGTTGAAAAATTTAG
Found at i:1868198 original size:55 final size:55
Alignment explanation
Indices: 1868129--1868481 Score: 316
Period size: 55 Copynumber: 6.4 Consensus size: 55
1868119 CTAATTAATA
* * * * * *
1868129 TTGTTACATGCCATGTTGAAAAATTTAGTTGTTACATGTCACATTAAAAATTTAA
1 TTGTTACACGCCATGTTGAAAAATGTAGTTGTTACACGTCATATTGAAAATTTAG
* * * * * *
1868184 TTGTTATACACCATGTTGAAATATGTAGTTATTACACATCATGTTGAAAATTTAG
1 TTGTTACACGCCATGTTGAAAAATGTAGTTGTTACACGTCATATTGAAAATTTAG
* * * * *
1868239 TTGTTACATGTCATGTTG-AAAATTTAGTTGTTACACGTTATGTTGAAAATTTAG
1 TTGTTACACGCCATGTTGAAAAATGTAGTTGTTACACGTCATATTGAAAATTTAG
* * * *
1868293 TTGTTACACGTCATGTTGAAAAATGGAATTGTTACTCGTCATATTGAAAATTTAG
1 TTGTTACACGCCATGTTGAAAAATGTAGTTGTTACACGTCATATTGAAAATTTAG
* * * * ** *
1868348 TTGTTACATGCCATGTTG-AAAATAATAGTTATTACACGTCATGTTGAAAAATGGAA
1 TTGTTACACGCCATGTTGAAAAAT-GTAGTTGTTACACGTCATATTG-AAAATTTAG
* ** * * * *
1868404 TTGTTACACGTCATGTT-AAGGATTTAATTGTTACACGTTATGTTGAAAAATTTAG
1 TTGTTACACGCCATGTTGAAAAATGTAGTTGTTACACGTCATATTG-AAAATTTAG
* * *
1868459 TTGTTACGCGTCATGATGAAAAA
1 TTGTTACACGCCATGTTGAAAAA
1868482 ATTGTTACAC
Statistics
Matches: 239, Mismatches: 54, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
54 53 0.22
55 159 0.67
56 27 0.11
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (55 bp):
TTGTTACACGCCATGTTGAAAAATGTAGTTGTTACACGTCATATTGAAAATTTAG
Found at i:1868270 original size:82 final size:82
Alignment explanation
Indices: 1868140--1868481 Score: 357
Period size: 82 Copynumber: 4.1 Consensus size: 82
1868130 TGTTACATGC
** * * * * * *
1868140 CATGTTGAAAAATTTAGTTGTTACATGTCACATTAAAAATTTAATTGTTATACACCATGTTGAAA
1 CATGTTGAAAAATGGAATTGTTACATGTCATATTGAAAATTTAGTTGTTACACGCCATGTTGAAA
* *
1868205 TATGTAGTTATTACACAT
66 -ATATAGTTATTACACGT
** * * **
1868223 CATGTTG-AAAATTTAGTTGTTACATGTCATGTTGAAAATTTAGTTGTTACACGTTATGTTGAAA
1 CATGTTGAAAAATGGAATTGTTACATGTCATATTGAAAATTTAGTTGTTACACGCCATGTTGAAA
* *
1868287 ATTTAGTTGTTACACGT
66 ATATAGTTATTACACGT
*
1868304 CATGTTGAAAAATGGAATTGTTAC-TCGTCATATTGAAAATTTAGTTGTTACATGCCATGTTGAA
1 CATGTTGAAAAATGGAATTGTTACAT-GTCATATTGAAAATTTAGTTGTTACACGCCATGTTGAA
1868368 AATAATAGTTATTACACGT
65 AAT-ATAGTTATTACACGT
* * * * **
1868387 CATGTTGAAAAATGGAATTGTTACACGTCATGTT-AAGGATTTAATTGTTACACGTTATGTTGAA
1 CATGTTGAAAAATGGAATTGTTACATGTCATATTGAA-AATTTAGTTGTTACACGCCATGTTG-A
* * *
1868451 AAATTTAGTTGTTACGCGT
64 AAATATAGTTATTACACGT
*
1868470 CATGATGAAAAA
1 CATGTTGAAAAA
1868482 ATTGTTACAC
Statistics
Matches: 222, Mismatches: 31, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
81 22 0.10
82 101 0.45
83 94 0.42
84 5 0.02
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (82 bp):
CATGTTGAAAAATGGAATTGTTACATGTCATATTGAAAATTTAGTTGTTACACGCCATGTTGAAA
ATATAGTTATTACACGT
Found at i:1868409 original size:83 final size:84
Alignment explanation
Indices: 1868140--1868481 Score: 358
Period size: 83 Copynumber: 4.1 Consensus size: 84
1868130 TGTTACATGC
** * * * * *
1868140 CATGTTGAAAAATTTAGTTGTTACATGTCACATTAAAAATTTAATTGTTATACACCATGTTG-AA
1 CATGTTGAAAAATGGAATTGTTACATGTCATATTGAAAATTTAATTGTTACACGCCATGTTGAAA
* *
1868204 ATATGTAGTTATTACACAT
66 ATATTTAGTTATTACACGT
** * * * **
1868223 CATGTTG-AAAATTTAGTTGTTACATGTCATGTTGAAAATTTAGTTGTTACACGTTATGTTG-AA
1 CATGTTGAAAAATGGAATTGTTACATGTCATATTGAAAATTTAATTGTTACACGCCATGTTGAAA
*
1868286 A-ATTTAGTTGTTACACGT
66 ATATTTAGTTATTACACGT
* *
1868304 CATGTTGAAAAATGGAATTGTTAC-TCGTCATATTGAAAATTTAGTTGTTACATGCCATGTTGAA
1 CATGTTGAAAAATGGAATTGTTACAT-GTCATATTGAAAATTTAATTGTTACACGCCATGTTGAA
*
1868368 AATA-ATAGTTATTACACGT
65 AATATTTAGTTATTACACGT
* * * **
1868387 CATGTTGAAAAATGGAATTGTTACACGTCATGTT-AAGGATTTAATTGTTACACGTTATGTTGAA
1 CATGTTGAAAAATGGAATTGTTACATGTCATATTGAA-AATTTAATTGTTACACGCCATGTTGAA
* *
1868451 AA-ATTTAGTTGTTACGCGT
65 AATATTTAGTTATTACACGT
*
1868470 CATGATGAAAAA
1 CATGTTGAAAAA
1868482 ATTGTTACAC
Statistics
Matches: 221, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
81 22 0.10
82 97 0.44
83 101 0.46
84 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (84 bp):
CATGTTGAAAAATGGAATTGTTACATGTCATATTGAAAATTTAATTGTTACACGCCATGTTGAAA
ATATTTAGTTATTACACGT
Found at i:1870123 original size:15 final size:15
Alignment explanation
Indices: 1870105--1870134 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1870095 TTTTATTTTA
*
1870105 ATTATTATTTCTATT
1 ATTATTATTACTATT
1870120 ATTATTATTACTATT
1 ATTATTATTACTATT
1870135 TAGAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTACTATT
Found at i:1870179 original size:9 final size:10
Alignment explanation
Indices: 1870133--1870188 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
1870123 ATTATTACTA
1870133 TTTAGAATAAT
1 TTTA-AATAAT
*
1870144 ATTTAAAGAAGT
1 -TTTAAATAA-T
*
1870156 TTATAAATTAT
1 TT-TAAATAAT
1870167 TTTAAA-AAT
1 TTTAAATAAT
1870176 TTTAAATAAT
1 TTTAAATAAT
1870186 TTT
1 TTT
1870189 TATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 8 0.22
10 10 0.27
11 9 0.24
12 10 0.27
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (10 bp):
TTTAAATAAT
Found at i:1882534 original size:26 final size:26
Alignment explanation
Indices: 1882505--1882556 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1882495 AGGCCCTTAA
1882505 ACAAACCAAGAGTTAATGGCATTTAT
1 ACAAACCAAGAGTTAATGGCATTTAT
**
1882531 ACAAACCAAGAGTTCGTGGCATTTAT
1 ACAAACCAAGAGTTAATGGCATTTAT
1882557 CAGCTTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (26 bp):
ACAAACCAAGAGTTAATGGCATTTAT
Found at i:1888978 original size:24 final size:24
Alignment explanation
Indices: 1888947--1888997 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1888937 GATAAAGCAT
1888947 TTTGATGGGTTGACATTTTATTGA
1 TTTGATGGGTTGACATTTTATTGA
1888971 TTTGATGGGTTGACATTTTATTGA
1 TTTGATGGGTTGACATTTTATTGA
1888995 TTT
1 TTT
1888998 CCTAGCACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.53
Consensus pattern (24 bp):
TTTGATGGGTTGACATTTTATTGA
Found at i:1890358 original size:5 final size:5
Alignment explanation
Indices: 1890349--1890383 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1890339 AATAAAAATA
*
1890349 AAAAG AAAAG AAAAG AAAAG AAAAG AAAGG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1890384 GCAAAACGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1896741 original size:13 final size:13
Alignment explanation
Indices: 1896723--1896747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1896713 ATTTTTCTTT
1896723 TTTTTTATTTTTA
1 TTTTTTATTTTTA
1896736 TTTTTTATTTTT
1 TTTTTTATTTTT
1896748 GAGGATAAAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:1897883 original size:17 final size:17
Alignment explanation
Indices: 1897863--1897915 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1897853 TGTTATTAAA
*
1897863 ATATTTCAAATATTTTT
1 ATATTTAAAATATTTTT
*
1897880 ATATTTAAAATATTTTA
1 ATATTTAAAATATTTTT
* *
1897897 ATATCTGAAATATATTTT
1 ATATTTAAAATAT-TTTT
1897915 A
1 A
1897916 AAAGTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
ATATTTAAAATATTTTT
Found at i:1912292 original size:2 final size:2
Alignment explanation
Indices: 1912256--1912282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1912246 AATGATTCAG
1912256 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
1912283 CAATTATATA
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:1917800 original size:21 final size:20
Alignment explanation
Indices: 1917767--1917805 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1917757 GAACCTTTGC
1917767 AGGAAAGATAGAAAGAGAAGA
1 AGGAAAGATAGAAA-AGAAGA
1917788 AGGAAAGGA-AGAAAAGAA
1 AGGAAA-GATAGAAAAGAA
1917806 AAAAATTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (20 bp):
AGGAAAGATAGAAAAGAAGA
Found at i:1920132 original size:6 final size:7
Alignment explanation
Indices: 1920116--1920141 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1920106 CTACGGCTAG
1920116 TTTTTAT
1 TTTTTAT
1920123 TTTTTAT
1 TTTTTAT
1920130 TTTTTAT
1 TTTTTAT
1920137 TTTTT
1 TTTTT
1920142 GTGCTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:1922799 original size:22 final size:22
Alignment explanation
Indices: 1922771--1922812 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1922761 TTTCATTCAA
1922771 AAAAAGAAAGA-AAAAATAAAGG
1 AAAAAGAAA-ATAAAAATAAAGG
1922793 AAAAAGAAAATAAAAATAAA
1 AAAAAGAAAATAAAAATAAA
1922813 AAAGAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAAGAAAATAAAAATAAAGG
Found at i:1925797 original size:2 final size:2
Alignment explanation
Indices: 1925790--1925815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1925780 TTTAAATTTC
1925790 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
1925816 GTTAGTTTTA
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:1928674 original size:22 final size:22
Alignment explanation
Indices: 1928646--1928688 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1928636 GCAGTGAGGT
*
1928646 AGACCAAGTACAATAGCCCAAA
1 AGACCAAGTACAATACCCCAAA
1928668 AGACCAAGTACAATACCCCAA
1 AGACCAAGTACAATACCCCAA
1928689 GATCAAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.12, T:0.09
Consensus pattern (22 bp):
AGACCAAGTACAATACCCCAAA
Found at i:1951315 original size:22 final size:22
Alignment explanation
Indices: 1951267--1951316 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1951257 GGTAAATACC
* * *
1951267 GAGATTGTGCAAGGTAGGTGTT
1 GAGATTGTGCAAGATAGATATT
*
1951289 TAGATTGTGCAAGATAGATATT
1 GAGATTGTGCAAGATAGATATT
1951311 GAGATT
1 GAGATT
1951317 ATTTAAAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (22 bp):
GAGATTGTGCAAGATAGATATT
Found at i:1951780 original size:21 final size:20
Alignment explanation
Indices: 1951754--1951826 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 20
1951744 CTTACATAAT
1951754 ATAAAAAAATATAAAACTATA
1 ATAAAAAAA-ATAAAACTATA
* *
1951775 ATAAAAAAAATTCTATACTCA-A
1 ATAAAAAAAA-T-AAAACT-ATA
1951797 TATAAAAAAACATAAAACTATA
1 -ATAAAAAAA-ATAAAACTATA
1951819 ATAAAAAA
1 ATAAAAAA
1951827 TTTTAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 1 0.02
21 19 0.45
22 10 0.24
23 11 0.26
24 1 0.02
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.23
Consensus pattern (20 bp):
ATAAAAAAAATAAAACTATA
Found at i:1953943 original size:19 final size:18
Alignment explanation
Indices: 1953915--1953951 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1953905 AGCTCTTGGG
*
1953915 AATTTGTTAAAATATTATA
1 AATTTATTAAAAT-TTATA
1953934 AATTTATTAAAATTTATA
1 AATTTATTAAAATTTATA
1953952 GTTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTTATTAAAATTTATA
Found at i:1959413 original size:17 final size:18
Alignment explanation
Indices: 1959391--1959425 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1959381 TACAATGAAC
1959391 TTCAAAATTT-ATTTTAA
1 TTCAAAATTTAATTTTAA
1959408 TTCAAAATTTAATTTTAA
1 TTCAAAATTTAATTTTAA
1959426 GTTTGTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TTCAAAATTTAATTTTAA
Found at i:1967801 original size:18 final size:18
Alignment explanation
Indices: 1967778--1967814 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1967768 TTAAGATGTT
1967778 AAATTAAAAGATTTTGGC
1 AAATTAAAAGATTTTGGC
1967796 AAATTAAAAGATTTTGGC
1 AAATTAAAAGATTTTGGC
1967814 A
1 A
1967815 GATCAACGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (18 bp):
AAATTAAAAGATTTTGGC
Done.