Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 5 of 29
Found at i:1405171 original size:435 final size:433
Alignment explanation
Indices: 1404361--1405663 Score: 2110
Period size: 435 Copynumber: 3.0 Consensus size: 433
1404351 GAGGTGATAC
* *
1404361 ATTAAAGTAAACATAAGGAAACCTTCCAAACAGTGGTGCCATCCGTGGGTGAATCCCTTGAGAGA
1 ATTAAAGTGAACATAAGGAAACCTTCCAAA-AGTGGTGCCATCCGTGGGTGAATCCCTTGAGAGG
* *
1404426 TTTGTGCATATGGTGGAAAATATTCAAGTGAACATGGTTGATTGTTTCTCAAATTATTAGCGTCC
65 TTTGTGCATAGGGTGGAAAATATTCAGGTGAACATGGTTGATTGTTTCTCAAATTATTAGCGTCC
* *
1404491 TGGTTTTCTAGTGGGCTAACTCTTTAGCTATTCCTTTTCCCTTGCTTAAACTCACCATCAACTCC
130 AGGTTTTCTAGTGGGCTAACTCTTTAGCCATTCCTTTTCCCTTGCTTAAACTCACCATCAACTCC
* *
1404556 ATCATTTTTGCTAGCTAATCTTTCATTTTGTTTGGAGCTGTCCATCCAGTTCAATGGATTCCTTT
195 ATCATTTTTGCTAGCTAATCTTTCA-TTTCTTTGGAGCTGTCCATCCTGTTCAATGGATTCCTTT
** * * *
1404621 GTTCCTCTTCCAAGATTTTCATTTGTCAGCAGGTATTATGCATACATTAATCATTTGGTTTAGGT
259 GTTCCTCTTCCAAGATTTTCATTTGTCAATAGGTATTATGGATACATTGATCACTTGGTTTAGGT
*
1404686 GGTAGTGCTATTTTGGGAAGCCTTTTGTAATCCTAAACATGAATTAGATGCATTGTTATTACATG
324 GGTAGAGCTATTTTGGGAAGCCTTTTGTAATCCTAAACATGAATTAGATGCATTGTTATTACATG
* *
1404751 AATGAAATGAAGAGAAATAAGACCATTGTATTTGATAAGTTTATT
389 AATGAAATGAAGAGAAATGAGACCATTGTCTTTGATAAGTTTATT
*
1404796 ATTAAAGTGAACATAAGGAAACCTTCCAATAGGTGGTGCCATCCGTGGGTGAATCCCTTGAGAGG
1 ATTAAAGTGAACATAAGGAAACCTTCCAA-AAGTGGTGCCATCCGTGGGTGAATCCCTTGAGAGG
* *
1404861 TTTGTGCATAGGGTGGAAAATATTCAGGTGAACATGGTTGATTGTTTCTCAAATTATTAACATCC
65 TTTGTGCATAGGGTGGAAAATATTCAGGTGAACATGGTTGATTGTTTCTCAAATTATTAGCGTCC
* *
1404926 AGGTTTTCTAGTGGGCCAACTCTTTAGCGATTCCTTTTCCCTTGCTTAAACTCACCATCAACTCC
130 AGGTTTTCTAGTGGGCTAACTCTTTAGCCATTCCTTTTCCCTTGCTTAAACTCACCATCAACTCC
* * * *
1404991 ATCATTTTTGCTAGCTAATCTTTCATTTCATTTGGAGCTATCCATCCTGTCCAATGGATTACTCT
195 ATCATTTTTGCTAGCTAATCTTTCATTTC-TTTGGAGCTGTCCATCCTGTTCAATGGATTCCTTT
*
1405056 GTTCCTCTTCCAAGATTTTCATTTGTCAATAAGTATTATGGATACATTGATCACTTGGTTTAGGT
259 GTTCCTCTTCCAAGATTTTCATTTGTCAATAGGTATTATGGATACATTGATCACTTGGTTTAGGT
*
1405121 GGTAGAGCTATTTTGGGAAGCCTTTTGTAATCCTAAACATGAATTAGATGCATTCTTATTACATG
324 GGTAGAGCTATTTTGGGAAGCCTTTTGTAATCCTAAACATGAATTAGATGCATTGTTATTACATG
*
1405186 AAAGAAATGAAGAGAAATGAGACCATTGTCTTTGATAAGTTTATT
389 AATGAAATGAAGAGAAATGAGACCATTGTCTTTGATAAGTTTATT
* *
1405231 ATTAAAGTGAACATAAGGAAACCTTCCAACATGTGGTGCCATCCATGGGTGAATCCCTTGAGAGG
1 ATTAAAGTGAACATAAGGAAACCTTCCAA-AAGTGGTGCCATCCGTGGGTGAATCCCTTGAGAGG
* * *
1405296 TTTGTGCATAGGGTGGAAAATATCCAGGCGAACATGGTTGATTGTTTCTCAAATTATTAGTGTCC
65 TTTGTGCATAGGGTGGAAAATATTCAGGTGAACATGGTTGATTGTTTCTCAAATTATTAGCGTCC
* * *
1405361 TA-GTTTTCTGGTGGGCTAACTCTTTAGCCATTCATTTTCCCTTGCTTAAACTCACCATCAGCTC
130 -AGGTTTTCTAGTGGGCTAACTCTTTAGCCATTCCTTTTCCCTTGCTTAAACTCACCATCAACTC
* *
1405425 CATCACTTTTGCTAGCTAATCTTTCATTTCTTCTGAAGCTGTCCATCCTGTTCAATGGATTCCTT
194 CATCATTTTTGCTAGCTAATCTTTCATTTCTT-TGGAGCTGTCCATCCTGTTCAATGGATTCCTT
*
1405490 TGTTCCTCTTCCAA-TTTTTCATTTGTCAATAGGTATTATGGATACATTGATCACTTGGATTT-G
258 TGTTCCTCTTCCAAGATTTTCATTTGTCAATAGGTATTATGGATACATTGATCACTTGG-TTTAG
* * *
1405553 GAGGTTGAGCTAATTTGGGAAGCCTTTTGTAATCCTAAACATGAATTA-ATGCATTGTTATTACA
322 GTGGTAGAGCTATTTTGGGAAGCCTTTTGTAATCCTAAACATGAATTAGATGCATTGTTATTACA
* *
1405617 CGAATGAAATGAAGAGAAATGAGACCATTGTCTTTGGTAAGTTTATT
387 TGAATGAAATGAAGAGAAATGAGACCATTGTCTTTGATAAGTTTATT
1405664 GTTATTTACA
Statistics
Matches: 808, Mismatches: 55, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
433 59 0.07
434 93 0.12
435 654 0.81
436 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (433 bp):
ATTAAAGTGAACATAAGGAAACCTTCCAAAAGTGGTGCCATCCGTGGGTGAATCCCTTGAGAGGT
TTGTGCATAGGGTGGAAAATATTCAGGTGAACATGGTTGATTGTTTCTCAAATTATTAGCGTCCA
GGTTTTCTAGTGGGCTAACTCTTTAGCCATTCCTTTTCCCTTGCTTAAACTCACCATCAACTCCA
TCATTTTTGCTAGCTAATCTTTCATTTCTTTGGAGCTGTCCATCCTGTTCAATGGATTCCTTTGT
TCCTCTTCCAAGATTTTCATTTGTCAATAGGTATTATGGATACATTGATCACTTGGTTTAGGTGG
TAGAGCTATTTTGGGAAGCCTTTTGTAATCCTAAACATGAATTAGATGCATTGTTATTACATGAA
TGAAATGAAGAGAAATGAGACCATTGTCTTTGATAAGTTTATT
Found at i:1408566 original size:18 final size:18
Alignment explanation
Indices: 1408543--1408582 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1408533 TTTCTTTCTA
1408543 ATTTATTATTATT-GTTTT
1 ATTTATT-TTATTAGTTTT
1408561 ATTTATTTTATTAGTTTT
1 ATTTATTTTATTAGTTTT
1408579 -TTTA
1 ATTTA
1408583 ACCAAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (18 bp):
ATTTATTTTATTAGTTTT
Found at i:1409872 original size:2 final size:2
Alignment explanation
Indices: 1409865--1409911 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1409855 TGTTGCTATT
*
1409865 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT 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
1409907 TC TC T
1 TC TC T
1409912 TTGCATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1412294 original size:17 final size:17
Alignment explanation
Indices: 1412258--1412295 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1412248 AGGATGGATA
*
1412258 ATTTGAATATTAAAATC
1 ATTTGAATATTAAAACC
1412275 ATTTGAATA-TATAAACC
1 ATTTGAATATTA-AAACC
1412292 ATTT
1 ATTT
1412296 TAATGCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (17 bp):
ATTTGAATATTAAAACC
Found at i:1417529 original size:38 final size:38
Alignment explanation
Indices: 1417487--1417592 Score: 194
Period size: 38 Copynumber: 2.8 Consensus size: 38
1417477 TAAACATCAA
1417487 GAGATAGTGATTGAGAATTTGACAAGCCAATTAAGGAT
1 GAGATAGTGATTGAGAATTTGACAAGCCAATTAAGGAT
*
1417525 GAGATAGTGATTGAGAATTTGACAAGCTAATTAAGGAT
1 GAGATAGTGATTGAGAATTTGACAAGCCAATTAAGGAT
1417563 GAGATAGTGATTGAGAATTCTGACAAGCCA
1 GAGATAGTGATTGAGAATT-TGACAAGCCA
1417593 GTTCAAAAGA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 56 0.86
39 9 0.14
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (38 bp):
GAGATAGTGATTGAGAATTTGACAAGCCAATTAAGGAT
Found at i:1424925 original size:50 final size:50
Alignment explanation
Indices: 1424850--1424946 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
1424840 TTAAAAAGCA
* * *
1424850 TTTTGTATGAAATCTATCAATACATTTGGGCTATGTATCAATAGATTCGC
1 TTTTGGATGAAATCTATCAATACATTTGGACCATGTATCAATAGATTCGC
*
1424900 TTTTGGATGAAATCTATCGATACATTTGGACCATGTATCAATAGATT
1 TTTTGGATGAAATCTATCAATACATTTGGACCATGTATCAATAGATT
1424947 TCTCCTATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (50 bp):
TTTTGGATGAAATCTATCAATACATTTGGACCATGTATCAATAGATTCGC
Found at i:1425320 original size:61 final size:61
Alignment explanation
Indices: 1425245--1425369 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
1425235 ATTTTCTTGC
1425245 TTTCAATGAAGTTAGAACACTAATTTATTTCATGTTATTTTGTATTATTATAATTGAACTT
1 TTTCAATGAAGTTAGAACACTAATTTATTTCATGTTATTTTGTATTATTATAATTGAACTT
*
1425306 TTTCAATGAAGTTAGAACACTAATTTATTTCATGTTATTTTGTATTATTATAATTGTACTT
1 TTTCAATGAAGTTAGAACACTAATTTATTTCATGTTATTTTGTATTATTATAATTGAACTT
1425367 TTT
1 TTT
1425370 TATCCCTCTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (61 bp):
TTTCAATGAAGTTAGAACACTAATTTATTTCATGTTATTTTGTATTATTATAATTGAACTT
Found at i:1425462 original size:59 final size:59
Alignment explanation
Indices: 1425347--1425462 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 59
1425337 ATGTTATTTT
* * * ***
1425347 GTATTATTATAATTGTACTTTTTTATCCCTCTGTTATTGCTATTAAAGGTTTAATAATG
1 GTATGATTATAATTGTACTTTTTCATCCCTCTATTATTGCTATTAAAGGAAAAATAATG
* * *
1425406 GTATGATTATAATTTTGCTTTTTCATCCCTCTATTGTTGCTATTAAAGGAAAAATAA
1 GTATGATTATAATTGTACTTTTTCATCCCTCTATTATTGCTATTAAAGGAAAAATAA
1425463 CGTTCAAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.47
Consensus pattern (59 bp):
GTATGATTATAATTGTACTTTTTCATCCCTCTATTATTGCTATTAAAGGAAAAATAATG
Found at i:1430975 original size:15 final size:15
Alignment explanation
Indices: 1430957--1431008 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
1430947 AGATTGATCA
1430957 AAAATATT-ATTTAAT
1 AAAATATTAATTT-AT
1430972 AAAAATTATTAATTTAT
1 -AAAA-TATTAATTTAT
*
1430989 TAAATATTAATTTAT
1 AAAATATTAATTTAT
1431004 AAAAT
1 AAAAT
1431009 TTTTATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 15 0.47
16 7 0.22
17 6 0.19
18 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAAATATTAATTTAT
Found at i:1431926 original size:18 final size:18
Alignment explanation
Indices: 1431886--1431931 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1431876 AATATAATAA
1431886 TAAAAAATTAAATTTGTT
1 TAAAAAATTAAATTTGTT
* *
1431904 CAAAAAATTAAATTTTTT
1 TAAAAAATTAAATTTGTT
*
1431922 TAAAATATTA
1 TAAAAAATTA
1431932 TTCTTTGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAAAAATTAAATTTGTT
Found at i:1434055 original size:10 final size:11
Alignment explanation
Indices: 1434030--1434055 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1434020 GCTATGTTTA
1434030 AAAAATGTGAC
1 AAAAATGTGAC
1434041 AAAAATGTGAC
1 AAAAATGTGAC
1434052 AAAA
1 AAAA
1434056 CTTAATGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (11 bp):
AAAAATGTGAC
Found at i:1446453 original size:59 final size:59
Alignment explanation
Indices: 1446374--1446490 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
1446364 CAATAGTCTT
* * * * *
1446374 TTTTTTTTTCCTTTTGTATTCCTAGCTCATACCTGTATATAAGCATGTACTATTGGGTC
1 TTTTTTTTACCTTTTCTATTCCCAGCTCACACCTGTATATAAGCATGTACCATTGGGTC
* **
1446433 TTTTTTTTACTTTTTCTATTCCCAGCTCACATTTGTATATAAGCATGTACCATTGGGT
1 TTTTTTTTACCTTTTCTATTCCCAGCTCACACCTGTATATAAGCATGTACCATTGGGT
1446491 AATTGAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.49
Consensus pattern (59 bp):
TTTTTTTTACCTTTTCTATTCCCAGCTCACACCTGTATATAAGCATGTACCATTGGGTC
Found at i:1447758 original size:28 final size:28
Alignment explanation
Indices: 1447723--1447777 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1447713 ATTTGAAATT
1447723 TTATTTATATTTGATGTAATGTATTTGC
1 TTATTTATATTTGATGTAATGTATTTGC
* *
1447751 TTATTTATTTTTGATGTAATTTATTTG
1 TTATTTATATTTGATGTAATGTATTTG
1447778 TTTGTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.62
Consensus pattern (28 bp):
TTATTTATATTTGATGTAATGTATTTGC
Found at i:1448440 original size:19 final size:19
Alignment explanation
Indices: 1448413--1448455 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1448403 ATAAGATTTC
1448413 TTCTCTCCCCCTAAATACT
1 TTCTCTCCCCCTAAATACT
* *
1448432 TTCTTTCCCTCTAAATACT
1 TTCTCTCCCCCTAAATACT
1448451 TTCTC
1 TTCTC
1448456 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.37, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCTCTCCCCCTAAATACT
Found at i:1448813 original size:52 final size:53
Alignment explanation
Indices: 1448754--1448894 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 53
1448744 ATGAAAAACC
* *
1448754 ATGAATGTTCATTTCTTGAAGTGAATGTGACAAATGAG-CTAAT-AATAAAATT
1 ATGAATGTTCATTTCCTGAAGTGAATGTGACAAACGAGACTAATCAA-AAAATT
* *
1448806 ATGAATGTTTATTCCCT-ATAGTGAATGTGACAAACGAGATACTAATCAAAAAATT
1 ATGAATGTTCATTTCCTGA-AGTGAATGTGACAAACGAG--ACTAATCAAAAAATT
* *
1448861 ATAAATTCGTTCATTTCCTGAAGTGAATGCGACA
1 ATGAA-T-GTTCATTTCCTGAAGTGAATGTGACA
1448895 TCATTTAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
51 1 0.01
52 32 0.44
55 15 0.21
56 3 0.04
57 21 0.29
58 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (53 bp):
ATGAATGTTCATTTCCTGAAGTGAATGTGACAAACGAGACTAATCAAAAAATT
Found at i:1462950 original size:31 final size:29
Alignment explanation
Indices: 1462910--1462971 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1462900 ATGTACTAGT
1462910 TATTATGGATATTCAATATATCTTGCTTAGC
1 TATTATGGATATT--ATATATCTTGCTTAGC
* * *
1462941 TATTGTGGATATTGTATATCTTGTTTAGC
1 TATTATGGATATTATATATCTTGCTTAGC
1462970 TA
1 TA
1462972 CAGTGAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 16 0.57
31 12 0.43
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (29 bp):
TATTATGGATATTATATATCTTGCTTAGC
Found at i:1476422 original size:16 final size:15
Alignment explanation
Indices: 1476381--1476423 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1476371 TGATTTTAAT
1476381 TAGTTTATTTT-GCA
1 TAGTTTATTTTAGCA
*
1476395 AAGTTTTATTTTAGCA
1 TAG-TTTATTTTAGCA
1476411 TAGTTTAGTTTTA
1 TAGTTTA-TTTTA
1476424 ATTTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 12 0.50
16 10 0.42
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.56
Consensus pattern (15 bp):
TAGTTTATTTTAGCA
Found at i:1486675 original size:5 final size:5
Alignment explanation
Indices: 1486667--1486765 Score: 51
Period size: 5 Copynumber: 19.4 Consensus size: 5
1486657 TTATATTATA
* * * * * * *
1486667 TATTT TATTT TAATTT T-TTG TACTTA TATTA TATAT T-TTT TAATT TCTTA
1 TATTT TATTT T-ATTT TATTT TA-TTT TATTT TATTT TATTT TATTT TATTT
* *
1486717 TATTT TATTT TATTT TATTTT TAATTCT TATAT TATAT T-TTT TATTT
1 TATTT TATTT TATTT TA-TTT T-ATT-T TATTT TATTT TATTT TATTT
1486764 TA
1 TA
1486766 ATTATAACAT
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
4 9 0.12
5 44 0.60
6 17 0.23
7 3 0.04
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:1486681 original size:26 final size:27
Alignment explanation
Indices: 1486652--1486768 Score: 96
Period size: 30 Copynumber: 4.1 Consensus size: 27
1486642 TCTTTAATAA
1486652 AATTTTTATA-TTATATATTTTATTTT
1 AATTTTTATATTTATATATTTTATTTT
* *
1486678 AATTTTTTGTACTTATATTATATATT-TTTT
1 AA-TTTTTATA-TT-TA-TATATTTTATTTT
*
1486708 AATTTCTTATATTTTATTTTATTTTATTTTT
1 AATTT-TTATA-TTTA-TATATTTTA-TTTT
* *
1486739 AATTCTTATA-TTATATTTTTTATTTT
1 AATTTTTATATTTATATATTTTATTTT
1486765 AATT
1 AATT
1486769 ATAACATTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
26 10 0.14
27 14 0.19
28 3 0.04
29 13 0.18
30 19 0.26
31 15 0.20
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (27 bp):
AATTTTTATATTTATATATTTTATTTT
Found at i:1486753 original size:54 final size:55
Alignment explanation
Indices: 1486652--1486759 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 55
1486642 TCTTTAATAA
**
1486652 AATTTTTATATTATATATTTTATTTTAATTTTTTGTACTTATATTATATATTTTTT
1 AATTTTTATATTATATATTTTATTTTAATTTTTAATACTTATATTATAT-TTTTTT
*
1486708 AATTTCTTATATT-T-TATTTTATTTT-ATTTTTAATTCTTATATTATATTTTTT
1 AATTT-TTATATTATATATTTTATTTTAATTTTTAATACTTATATTATATTTTTT
1486760 ATTTTAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
53 5 0.10
54 19 0.40
55 11 0.23
56 6 0.12
57 7 0.15
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (55 bp):
AATTTTTATATTATATATTTTATTTTAATTTTTAATACTTATATTATATTTTTTT
Found at i:1486755 original size:20 final size:19
Alignment explanation
Indices: 1486714--1486771 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
1486704 TTTTAATTTC
1486714 TTATA-TTTT-ATTTTAT-
1 TTATATTTTTAATTTTATA
1486730 TT-TATTTTTAATTCTTATA
1 TTATATTTTTAATT-TTATA
*
1486749 TTATATTTTTTATTTTA-A
1 TTATATTTTTAATTTTATA
1486767 TTATA
1 TTATA
1486772 ACATTATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 2 0.06
16 6 0.17
17 3 0.08
18 10 0.28
19 5 0.14
20 10 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATATTTTTAATTTTATA
Found at i:1486760 original size:21 final size:18
Alignment explanation
Indices: 1486655--1486771 Score: 70
Period size: 19 Copynumber: 6.6 Consensus size: 18
1486645 TTAATAAAAT
*
1486655 TTTTATATTATATATTTTA
1 TTTTA-ATTATATTTTTTA
1486674 TTTTAATT-T-TTTGTACTTA
1 TTTTAATTATATTT-T--TTA
*
1486693 TATT-A-TATATTTTTTA
1 TTTTAATTATATTTTTTA
* *
1486709 ATTT-CTTATA--TTTTA
1 TTTTAATTATATTTTTTA
* *
1486724 TTTT-ATTTTATTTTTAA
1 TTTTAATTATATTTTTTA
1486741 TTCTTATATTATATTTTTTA
1 TT-TTA-ATTATATTTTTTA
1486761 TTTTAATTATA
1 TTTTAATTATA
1486772 ACATTATAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
15 12 0.16
16 7 0.09
17 13 0.17
18 14 0.18
19 17 0.22
20 13 0.17
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (18 bp):
TTTTAATTATATTTTTTA
Found at i:1486777 original size:26 final size:27
Alignment explanation
Indices: 1486729--1486779 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1486719 TTTTATTTTA
* * *
1486729 TTTTATTTTTAATTCTTATATTATATT
1 TTTTATTTTTAATTATAACATTATATT
1486756 TTTTA-TTTTAATTATAACATTATA
1 TTTTATTTTTAATTATAACATTATA
1486780 AAATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTATTTTTAATTATAACATTATATT
Found at i:1496025 original size:4 final size:4
Alignment explanation
Indices: 1496016--1496053 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
1496006 AAATTAGTAT
1496016 AATA AATA AATA AATA AATAA AAGTA AATA AA-A AATA A
1 AATA AATA AATA AATA AAT-A AA-TA AATA AATA AATA A
1496054 GTTGAGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 3 0.10
4 21 0.68
5 6 0.19
6 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:1503358 original size:27 final size:28
Alignment explanation
Indices: 1503274--1503359 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
1503264 AAAGCTGTCG
* *
1503274 AAAATGTAGTTGTTACATATTATGTTAA
1 AAAATGTAATTGTTACATATCATGTTAA
** * *
1503302 AAAAT-TCAATTGTTACA-CGCGTGTTGA
1 AAAATGT-AATTGTTACATATCATGTTAA
1503329 AAAATGTAATTGTTACATATCATGTTAA
1 AAAATGTAATTGTTACATATCATGTTAA
1503357 AAA
1 AAA
1503360 CTTAGTTGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
27 21 0.47
28 24 0.53
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTGTTACATATCATGTTAA
Found at i:1503368 original size:27 final size:26
Alignment explanation
Indices: 1503274--1503421 Score: 88
Period size: 27 Copynumber: 5.5 Consensus size: 26
1503264 AAAGCTGTCG
*
1503274 AAAATGTAGTTGTTACATATTATGTTAA
1 AAAAT-TAGTTGTTACATATCATGTT-A
* ** *
1503302 AAAATTCAATTGTTACA-CGCGTGTTGA
1 AAAATT-AGTTGTTACATATCATGTT-A
*
1503329 AAAATGTAATTGTTACATATCATGTTA
1 AAAAT-TAGTTGTTACATATCATGTTA
* **
1503356 AAAACTTAGTTGTTATACGTCATGTTA
1 AAAA-TTAGTTGTTACATATCATGTTA
* * *
1503383 AAGATT--TAGTTACAT-GCTATGTTA
1 AAAATTAGTTGTTACATATC-ATGTTA
1503407 AAAATTTAGTTGTTA
1 AAAA-TTAGTTGTTA
1503422 TACCCCATGT
Statistics
Matches: 92, Mismatches: 20, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
23 1 0.01
24 15 0.16
25 2 0.02
26 2 0.02
27 51 0.55
28 21 0.23
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (26 bp):
AAAATTAGTTGTTACATATCATGTTA
Found at i:1503431 original size:27 final size:27
Alignment explanation
Indices: 1503349--1503437 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
1503339 TGTTACATAT
* *
1503349 CATGTTAAAAACTTAGTTGTTATACGT
1 CATGTTAAAAATTTAGTTGTTATACGC
* * *
1503376 CATGTTAAAGATTTA---GTTACATGC
1 CATGTTAAAAATTTAGTTGTTATACGC
* *
1503400 TATGTTAAAAATTTAGTTGTTATACCC
1 CATGTTAAAAATTTAGTTGTTATACGC
*
1503427 CATGTTCAAAA
1 CATGTTAAAAA
1503438 CTGTAGTTAC
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
24 19 0.40
27 28 0.60
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (27 bp):
CATGTTAAAAATTTAGTTGTTATACGC
Found at i:1503472 original size:52 final size:53
Alignment explanation
Indices: 1503407--1503531 Score: 135
Period size: 52 Copynumber: 2.3 Consensus size: 53
1503397 TGCTATGTTA
* * * * * * *
1503407 AAAATTTAGTTGTTATACCCCATGTTCAAAACTGTAGTT-ACACATCATATTG
1 AAAATTTAATTGTTATACCCAATATTAAAAAATATAGTTAACACATCATACTG
* *
1503459 AAAATTTAATTGTTATGCGCAATATTAAAAAATATAGTTACAACACATCATACTG
1 AAAATTTAATTGTTATACCCAATATTAAAAAATATAGTT--AACACATCATACTG
*
1503514 AAGATTTAATTGTTATAC
1 AAAATTTAATTGTTATAC
1503532 ATAATGTTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
52 31 0.53
55 28 0.47
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (53 bp):
AAAATTTAATTGTTATACCCAATATTAAAAAATATAGTTAACACATCATACTG
Found at i:1503473 original size:27 final size:27
Alignment explanation
Indices: 1503443--1503572 Score: 68
Period size: 28 Copynumber: 4.7 Consensus size: 27
1503433 CAAAACTGTA
1503443 GTTACACATCATATTGAAAATTTAATT
1 GTTACACATCATATTGAAAATTTAATT
* * * *
1503470 GTTATGCGCA--ATATTAAAAAATATAGTT
1 GTTA--CACATCATATT-GAAAATTTAATT
*** * *
1503498 ACAACACATCATACTGAAGATTTAATT
1 GTTACACATCATATTGAAAATTTAATT
* * *
1503525 GTTATACATAATGTTGAAAAATTTAATT
1 GTTACACATCATATTG-AAAATTTAATT
* *
1503553 ATTATACATCATGA-TGAAAA
1 GTTACACATCAT-ATTGAAAA
1503573 AATTATTAGA
Statistics
Matches: 72, Mismatches: 24, Indels: 14
0.65 0.22 0.13
Matches are distributed among these distances:
26 3 0.04
27 30 0.42
28 36 0.50
29 3 0.04
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
GTTACACATCATATTGAAAATTTAATT
Found at i:1503552 original size:28 final size:28
Alignment explanation
Indices: 1503517--1503573 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1503507 CATACTGAAG
* *
1503517 ATTTAATTGTTATACATAATGTTGAAAA
1 ATTTAATTATTATACATAATGATGAAAA
*
1503545 ATTTAATTATTATACATCATGATGAAAA
1 ATTTAATTATTATACATAATGATGAAAA
1503573 A
1 A
1503574 ATTATTAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (28 bp):
ATTTAATTATTATACATAATGATGAAAA
Found at i:1503564 original size:55 final size:55
Alignment explanation
Indices: 1503446--1503553 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 55
1503436 AACTGTAGTT
* * * *
1503446 ACACATCATATTGAAAATTTAATTGTTATGCGCAATATTAAAAAATATAGTTACA
1 ACACATCATACTGAAAATTTAATTGTTATACACAATATTAAAAAATATAATTACA
* * * * *
1503501 ACACATCATACTGAAGATTTAATTGTTATACATAATGTTGAAAAATTTAATTA
1 ACACATCATACTGAAAATTTAATTGTTATACACAATATTAAAAAATATAATTA
1503554 TTATACATCA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (55 bp):
ACACATCATACTGAAAATTTAATTGTTATACACAATATTAAAAAATATAATTACA
Found at i:1508055 original size:34 final size:33
Alignment explanation
Indices: 1508007--1508097 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 33
1507997 GAAGAACACT
* *
1508007 TTTTC-AAGGCTCAAGCATAACCTTTATAATTCC
1 TTTTCAAAGGATCAAGCATAACCTTTACAA-TCC
* * *
1508040 TTTTCAAAGGATCAAGTACAACCTTTACAATGC
1 TTTTCAAAGGATCAAGCATAACCTTTACAATCC
1508073 TTTTCACAAGGATCAAGCATAACCT
1 TTTTCA-AAGGATCAAGCATAACCT
1508098 CTCTACCTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 13 0.27
34 36 0.73
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (33 bp):
TTTTCAAAGGATCAAGCATAACCTTTACAATCC
Found at i:1510905 original size:16 final size:16
Alignment explanation
Indices: 1510884--1510924 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1510874 TCAAACAACC
*
1510884 AAAATTAAAG-ATACT
1 AAAATTAAAGAAAACT
1510899 GAAAATTAAAGAAAACT
1 -AAAATTAAAGAAAACT
1510916 AAAATTAAA
1 AAAATTAAA
1510925 CTAAGACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (16 bp):
AAAATTAAAGAAAACT
Found at i:1515850 original size:18 final size:20
Alignment explanation
Indices: 1515826--1515872 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
1515816 GAACATATTT
1515826 AAATATTATTTAATT-TAA-
1 AAATATTATTTAATTATAAC
*
1515844 TAATATTATTTAATTATAAC
1 AAATATTATTTAATTATAAC
1515864 AAATATTAT
1 AAATATTAT
1515873 AAAGAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 14 0.56
19 3 0.12
20 8 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATTATTTAATTATAAC
Found at i:1515889 original size:45 final size:44
Alignment explanation
Indices: 1515838--1515927 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
1515828 ATATTATTTA
*
1515838 ATTTAATAATATTATTT-AATTATAACAAATATTATAAAGAATATT
1 ATTTAATAATATTATTTGAA-TATAA-AAATATAATAAAGAATATT
* * *
1515883 ATTTAATATTATTATTTGAATATAATAATGTAATAAAGAATATT
1 ATTTAATAATATTATTTGAATATAAAAATATAATAAAGAATATT
1515927 A
1 A
1515928 CTTAGTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 17 0.43
45 21 0.52
46 2 0.05
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (44 bp):
ATTTAATAATATTATTTGAATATAAAAATATAATAAAGAATATT
Found at i:1531547 original size:76 final size:76
Alignment explanation
Indices: 1531416--1531574 Score: 237
Period size: 76 Copynumber: 2.1 Consensus size: 76
1531406 AGCCAAAAAC
* *** *
1531416 AAGTACATGATTTCATGACCATGGACTAAAAGCAATTGGAACTAAGTGCAAAGAAACACAAGTTG
1 AAGT-CATGAATTCATGACCATGGACTAAAAGCAATTGGAACTAAACACAAAGAAACACAAGTTA
1531481 CAATAACTTCCA
65 CAATAACTTCCA
* * *
1531493 AAGTCATGAATTCATGACCATGGATTGAAAGCAATTGGAACTAAACACAAAGAAACACAAGTTAT
1 AAGTCATGAATTCATGACCATGGACTAAAAGCAATTGGAACTAAACACAAAGAAACACAAGTTAC
1531558 AATAACTTCCA
66 AATAACTTCCA
1531569 AAGTCA
1 AAGTCA
1531575 ACTGCAATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 70 0.95
77 4 0.05
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (76 bp):
AAGTCATGAATTCATGACCATGGACTAAAAGCAATTGGAACTAAACACAAAGAAACACAAGTTAC
AATAACTTCCA
Found at i:1539112 original size:34 final size:34
Alignment explanation
Indices: 1539074--1539143 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1539064 CACACTTTAC
1539074 CAATTTCTTTAAGAACATTCCTCTTAAAGGAAAT
1 CAATTTCTTTAAGAACATTCCTCTTAAAGGAAAT
1539108 CAATTTCTTTAAGAACATTCCTCTTAAAGGAAAT
1 CAATTTCTTTAAGAACATTCCTCTTAAAGGAAAT
1539142 CA
1 CA
1539144 GTTCATCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (34 bp):
CAATTTCTTTAAGAACATTCCTCTTAAAGGAAAT
Found at i:1542428 original size:20 final size:20
Alignment explanation
Indices: 1542403--1542477 Score: 141
Period size: 20 Copynumber: 3.8 Consensus size: 20
1542393 CCTGCCCAAA
*
1542403 ATGTATCAATATATTAAGGG
1 ATGTATCAATACATTAAGGG
1542423 ATGTATCAATACATTAAGGG
1 ATGTATCAATACATTAAGGG
1542443 ATGTATCAATACATTAAGGG
1 ATGTATCAATACATTAAGGG
1542463 ATGTATCAATACATT
1 ATGTATCAATACATT
1542478 TTCCCCCGTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGTATCAATACATTAAGGG
Found at i:1548452 original size:34 final size:34
Alignment explanation
Indices: 1548406--1548475 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1548396 AACATCTCTA
*
1548406 AATATAAGGGCATATCATTATCCTT-AAAGTCTCC
1 AATATAAGGGCATATCATCAT-CTTCAAAGTCTCC
*
1548440 AATATGAA-GGCATATCATCATCTTCAATGTCTCC
1 AATAT-AAGGGCATATCATCATCTTCAAAGTCTCC
1548474 AA
1 AA
1548476 AGATCATCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 3 0.09
34 27 0.84
35 2 0.06
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (34 bp):
AATATAAGGGCATATCATCATCTTCAAAGTCTCC
Found at i:1548742 original size:36 final size:36
Alignment explanation
Indices: 1548696--1548778 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
1548686 CAATCGAAAG
*
1548696 AGAATTAAATCACGCAC-AGAGCAAAGCCACTAGCAA
1 AGAATCAAATCACGCACAAG-GCAAAGCCACTAGCAA
* *
1548732 AGAATCAAATCATGCACAAGGCAAAGCCACTAGCGA
1 AGAATCAAATCACGCACAAGGCAAAGCCACTAGCAA
1548768 AGAA-CAAATCA
1 AGAATCAAATCA
1548779 TGCATGTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 7 0.16
36 34 0.79
37 2 0.05
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (36 bp):
AGAATCAAATCACGCACAAGGCAAAGCCACTAGCAA
Found at i:1552248 original size:4 final size:4
Alignment explanation
Indices: 1552233--1552261 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1552223 ACTATTTTTC
1552233 TTAT TT-T TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1552262 TTATTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTAT
Found at i:1552256 original size:12 final size:11
Alignment explanation
Indices: 1552233--1552267 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1552223 ACTATTTTTC
1552233 TTATTTTTTAT
1 TTATTTTTTAT
1552244 TTATTTATTTAT
1 TTATTT-TTTAT
1552256 TTA-TTTTTAT
1 TTATTTTTTAT
1552266 TT
1 TT
1552268 TCAACAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.30
11 8 0.35
12 8 0.35
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:1555264 original size:21 final size:19
Alignment explanation
Indices: 1555238--1555278 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1555228 AATTTAAAAC
1555238 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
1555259 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
1555278 A
1 A
1555279 CTCAACATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:1562716 original size:67 final size:66
Alignment explanation
Indices: 1562596--1562759 Score: 188
Period size: 67 Copynumber: 2.5 Consensus size: 66
1562586 TGACTAATAA
* *
1562596 AGCTAAA-GTATATGCTAGATGCAACTAGTTATAATCGAATCTGCTTTGAAAGCACA-AGGCTAA
1 AGCTAAATG-ATATGCTTGATGCAACTAGTTATAATAGAATCTGCTTTGAAAGCACACA-GCTAA
1562659 TTC
64 TTC
* * * * *
1562662 AGCTAAATGATATGCTTGACTGTAATTAGTTATATTAGAATGTGCTTTGTAAGCACACAGCTAAT
1 AGCTAAATGATATGCTTGA-TGCAACTAGTTATAATAGAATCTGCTTTGAAAGCACACAGCTAAT
1562727 TC
65 TC
* * *
1562729 AGCTACATTATATGTTTGAATGCAACTAGTT
1 AGCTAAATGATATGCTTG-ATGCAACTAGTT
1562760 GATTAAATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
66 16 0.20
67 64 0.78
68 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (66 bp):
AGCTAAATGATATGCTTGATGCAACTAGTTATAATAGAATCTGCTTTGAAAGCACACAGCTAATT
C
Found at i:1566146 original size:30 final size:30
Alignment explanation
Indices: 1566081--1566150 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1566071 TTTGTTACAT
* *
1566081 TTAATTAAGTTTTTATACTTTTATTTGAAA
1 TTAAATAAGTCTTTATACTTTTATTTGAAA
* * *
1566111 CTAAATAAGTCTTTATATTTTTATTTTG-AG
1 TTAAATAAGTCTTTATACTTTTA-TTTGAAA
1566141 TTAAATAAGT
1 TTAAATAAGT
1566151 TATTTTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (30 bp):
TTAAATAAGTCTTTATACTTTTATTTGAAA
Found at i:1566461 original size:29 final size:30
Alignment explanation
Indices: 1566406--1566485 Score: 119
Period size: 29 Copynumber: 2.7 Consensus size: 30
1566396 CATCATTACT
* *
1566406 TATAAAAATTTATTTAATTTAAAATAAAA-A
1 TATAAAAATTTATTTAA-ATATAATAAAAGA
1566436 TATAAAAATTTATTTAAATATAATAAAAGA
1 TATAAAAATTTATTTAAATATAATAAAAGA
1566466 -ATAAAAATTTATTTAAATAT
1 TATAAAAATTTATTTAAATAT
1566486 TTTTAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 29 0.62
30 18 0.38
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
TATAAAAATTTATTTAAATATAATAAAAGA
Found at i:1584951 original size:71 final size:70
Alignment explanation
Indices: 1584846--1585003 Score: 158
Period size: 71 Copynumber: 2.2 Consensus size: 70
1584836 GCATTGTGGC
* * * * * * **
1584846 CCAAAATCAACTATAGGCCTTTTATAGTCAATCTTAG-GAAGGAAAAGTGCAAGAAATGTGAACA
1 CCAAGATCAACTATAGACCATTCATAGTCAATCTT-GTGAAGCAAAA-TCCAAGAAAAATGAACA
1584910 TTCTAGT
64 TTCTAGT
* * *
1584917 CCAGGATCAACTATAGACCATTCATAGT-AGATCTTGTGAAGCAAAATCCAATAAAAATGTACAT
1 CCAAGATCAACTATAGACCATTCATAGTCA-ATCTTGTGAAGCAAAATCCAAGAAAAATGAACAT
* *
1584981 TTTGGT
65 TCTAGT
1584987 CCAAGATCAACTATAGA
1 CCAAGATCAACTATAGA
1585004 GGGTCTATAG
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
70 35 0.49
71 36 0.51
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (70 bp):
CCAAGATCAACTATAGACCATTCATAGTCAATCTTGTGAAGCAAAATCCAAGAAAAATGAACATT
CTAGT
Found at i:1599124 original size:21 final size:20
Alignment explanation
Indices: 1599068--1599124 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
1599058 GAAAATAGTA
*
1599068 ATAAATAATAATAGATCTAAGG
1 ATAAA-AATAATA-ATATAAGG
1599090 -TAAAAATACA-AATATATAGG
1 ATAAAAATA-ATAATATA-AGG
1599110 ATAAAAATAATAATA
1 ATAAAAATAATAATA
1599125 AACATTTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
21 17 0.57
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (20 bp):
ATAAAAATAATAATATAAGG
Found at i:1599402 original size:2 final size:2
Alignment explanation
Indices: 1599395--1599424 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1599385 TATAGGTATG
1599395 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
1599425 ATAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1600757 original size:16 final size:15
Alignment explanation
Indices: 1600736--1600767 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1600726 TTGTTAATAG
1600736 AATAAATGATATATTA
1 AATAAATGATA-ATTA
1600752 AATAAATGATAATTA
1 AATAAATGATAATTA
1600767 A
1 A
1600768 GGAAACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (15 bp):
AATAAATGATAATTA
Found at i:1603088 original size:16 final size:17
Alignment explanation
Indices: 1603069--1603111 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1603059 AAAATCTTAA
*
1603069 TTAATTTAAATAGT-TT
1 TTAATTTAAATAATATT
*
1603085 TTAAATTAAATAATATT
1 TTAATTTAAATAATATT
1603102 TCTAATTTAA
1 T-TAATTTAA
1603112 TTAAATGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 3 0.14
18 7 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAATTTAAATAATATT
Found at i:1603534 original size:359 final size:356
Alignment explanation
Indices: 1602611--1603740 Score: 1247
Period size: 360 Copynumber: 3.2 Consensus size: 356
1602601 AATTTACTAA
* * * * * * *
1602611 AAATCTACTTATTTAATTAATTACTTAAATATTTAATTATAACACATTACATTACTTAATTGTAT
1 AAATTTACTAATTTAAATAATTGCTTAATTAATTAATTATAACACATTACATTACTTAATTATAT
* * * * * * *
1602676 AATTTTTTTTTAATTAACTCAGTCATAGCTTAATTGATTTAAATATTTTTTAAATTAAATAATAT
66 AA-ATATTTTTAATTAACTAATTCAAACCTTAATTAATTTAAATATTTTTTAAATTAAATAATAT
* * * * * *
1602741 TACAAATTTAATTAACTGCTTCAA-ATCATAAAATAATTTTTCATTTGATTAGTTTAATTCTTTA
130 TACTAATTTAATTAATTCCTT-AATAAC-TAAAACATTTTTTCATTTGATTAGTTTAATTCTTTA
* * *
1602805 GTTAATTTAATAAAACCTAATTAATTAATTCAAACAATTTAAAAAAACCCTAAATTTACTAATTT
193 ATTAATTTAATAAAA-CTAATTAATTAA-TCAAACAATTGAAAAAAACACT-AATTTACTAATTT
* * * *
1602870 AATTAATTGGTTAATTACTAATACATTATTCTTTATAATTATTTTGATTATGTGATTAATTCCCT
255 AATTAATTGATTAATTACTAATACATGATTCTTTATAATTATTTTAATTATGTAATTAATTCCCT
* *
1602935 AAACCCTAAATTAATTTAAATAAATAAGATATTATAT
320 AAACCCTAAATTAATATAAATAAATAAGAAATTATAT
*
1602972 AAATTTACTAATTTAAATAATTGCTTAATTACTTAATTATAACACATTACATTACTTAATTGA-A
1 AAATTTACTAATTTAAATAATTGCTTAATTAATTAATTATAACACATTACATTACTTAATT-ATA
* * * * * *
1603036 AAAATATTTTTAATTGACTTATTAAAATCTTAATTAATTTAAATAGTTTTTAAATTAAATAATAT
65 TAAATATTTTTAATTAACTAATTCAAACCTTAATTAATTTAAATATTTTTTAAATTAAATAATAT
* * * *
1603101 TTCTAATTTAATTAAATGCTTTAAATAA-TAAAACATTTTTTCATTTGATTAGTTTAATTATTTA
130 TACTAATTTAATT-AATTCCTT-AATAACTAAAACATTTTTTCATTTGATTAGTTTAATTCTTTA
* * * *
1603165 ACTGATTTAATAAAATCTAATTAATTAACTCAAAGAACTTGAAAAAAACACTAATTTACTAGTTT
193 ATTAATTTAATAAAA-CTAATTAATTAA-TCAAACAA-TTGAAAAAAACACTAATTTACTAATTT
* *
1603230 AATTAATTGATTAATTACTAGTACATGATTCTTTATAATTATTTTAATTATGTAATTAATTCCGT
255 AATTAATTGATTAATTACTAATACATGATTCTTTATAATTATTTTAATTATGTAATTAATTCCCT
*
1603295 AAACCCTAAATTAATATAAA-CAATAAGAAATTATAT
320 AAACCCTAAATTAATATAAATAAATAAGAAATTATAT
* * * * *
1603331 AAATTTGCTAATTTAAATGATTGCTTAATTAATTACTTATAAGATATTACATTACTTAATTATAT
1 AAATTTACTAATTTAAATAATTGCTTAATTAATTAATTATAACACATTACATTACTTAATTATAT
* *
1603396 AAATATTTTTAATTAACTAATTCAAACCTCAATTAATTTAAATATTTTTTAAATTAAATAATATC
66 AAATATTTTTAATTAACTAATTCAAACCTTAATTAATTTAAATATTTTTTAAATTAAATAATATT
* * * *
1603461 ACTTATTGAATTAATTCCTTATTAACTAAAACATTTTTTTCATTTGATTAGTTAAATTCTTTAAT
131 ACTAATTTAATTAATTCCTTAATAACTAAAACA-TTTTTTCATTTGATTAGTTTAATTCTTTAAT
* * *** * * *
1603526 TAATTTAATAAAAC--GTTAATTAATCTAAATAATTTTGAAAACCA-TATATATAGTAATTTAAT
195 TAATTTAATAAAACTAATTAATTAATC-AAACAATTGAAAAAAACACTA-ATTTACTAATTTAAT
* * *
1603588 TAATTGATTAATTACTAATACATGATTCTTTGT-A--A--TT-ACT-TG-AA-T--TT-ACTGAA
258 TAATTGATTAATTACTAATACATGATTCTTTATAATTATTTTAATTATGTAATTAATTCCCT-AA
* * * * * *
1603641 ACCCTGAATTAGTTTAAATAAATTAGATATTATGT
322 ACCCTAAATTAATATAAATAAATAAGAAATTATAT
* *
1603676 AAATTTA-TAATTTAATTAATTGCTTAATTAATTAATTAATTATAACACATTAGATTACTTAATT
1 AAATTTACTAATTTAAATAATTGC----TTAATTAATTAATTATAACACATTACATTACTTAATT
1603740 A
62 A
1603741 ACTTCAATAT
Statistics
Matches: 655, Mismatches: 99, Indels: 43
0.82 0.12 0.05
Matches are distributed among these distances:
343 1 0.00
344 33 0.05
345 18 0.03
346 1 0.00
347 2 0.00
348 36 0.05
349 2 0.00
350 2 0.00
352 1 0.00
354 3 0.00
355 53 0.08
356 13 0.02
357 4 0.01
358 15 0.02
359 177 0.27
360 217 0.33
361 76 0.12
362 1 0.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (356 bp):
AAATTTACTAATTTAAATAATTGCTTAATTAATTAATTATAACACATTACATTACTTAATTATAT
AAATATTTTTAATTAACTAATTCAAACCTTAATTAATTTAAATATTTTTTAAATTAAATAATATT
ACTAATTTAATTAATTCCTTAATAACTAAAACATTTTTTCATTTGATTAGTTTAATTCTTTAATT
AATTTAATAAAACTAATTAATTAATCAAACAATTGAAAAAAACACTAATTTACTAATTTAATTAA
TTGATTAATTACTAATACATGATTCTTTATAATTATTTTAATTATGTAATTAATTCCCTAAACCC
TAAATTAATATAAATAAATAAGAAATTATAT
Found at i:1605669 original size:2 final size:2
Alignment explanation
Indices: 1605662--1605690 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1605652 CAATTTTCTT
1605662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1605691 TTGTACCTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1615441 original size:33 final size:33
Alignment explanation
Indices: 1615371--1615442 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1615361 ACAAGCTAGG
*
1615371 TAATTAACTTCTATAAACTTAATTAAAAGAGTT
1 TAATTAACTTCTATAAACATAATTAAAAGAGTT
* *
1615404 TAATTAACTT-T-TAGACATAATTATAAATAGTT
1 TAATTAACTTCTATAAACATAATTA-AAAGAGTT
1615436 ATAATTA
1 -TAATTA
1615443 TAAGGCCTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.29
32 8 0.24
33 16 0.47
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (33 bp):
TAATTAACTTCTATAAACATAATTAAAAGAGTT
Found at i:1619127 original size:15 final size:15
Alignment explanation
Indices: 1619107--1619135 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1619097 TTCATAACTC
1619107 AATCATAAACTTTGA
1 AATCATAAACTTTGA
1619122 AATCATAAACTTTG
1 AATCATAAACTTTG
1619136 TTAAAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (15 bp):
AATCATAAACTTTGA
Found at i:1622765 original size:29 final size:28
Alignment explanation
Indices: 1622707--1622807 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 28
1622697 ATTCTCAAAA
* **
1622707 ATTTTAAAATTTTTTATTTATCATAAAT
1 ATTTTAAAATTTTTTATTTATTATTTAT
1622735 ATTTTCAAAATTTTTTAATTT-TTATTTAT
1 ATTTT-AAAATTTTTT-ATTTATTATTTAT
1622764 ATTTTTTAAAATATTTTTTATTTATTATATATAT
1 A--TTTT-AAA-ATTTTTTATTTATTAT-T-TAT
*
1622798 ATTTTTAAAT
1 ATTTTAAAAT
1622808 GATCCCTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
28 5 0.08
29 16 0.27
30 6 0.10
31 13 0.22
32 15 0.25
33 1 0.02
34 4 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTAAAATTTTTTATTTATTATTTAT
Found at i:1622780 original size:32 final size:32
Alignment explanation
Indices: 1622708--1622806 Score: 111
Period size: 32 Copynumber: 3.2 Consensus size: 32
1622698 TTCTCAAAAA
*
1622708 TTTT-AAAATTTTTTATTTATCATA-A-ATA-
1 TTTTAAAAATTTTTTATTTATTATATATATAT
* *
1622736 TTTTCAAAATTTTTTAATTT-TTATTTATAT-T
1 TTTTAAAAATTTTTT-ATTTATTATATATATAT
1622767 TTTTAAAATATTTTTTATTTATTATATATATAT
1 TTTTAAAA-ATTTTTTATTTATTATATATATAT
1622800 TTTTAAA
1 TTTTAAA
1622807 TGATCCCTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.07
29 13 0.22
30 5 0.08
31 13 0.22
32 16 0.27
33 8 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (32 bp):
TTTTAAAAATTTTTTATTTATTATATATATAT
Found at i:1623152 original size:16 final size:17
Alignment explanation
Indices: 1623121--1623154 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1623111 CTTTTTCTTT
1623121 CTATTTATATTATTTAA
1 CTATTTATATTATTTAA
1623138 CTATTTATA-TATTTAA
1 CTATTTATATTATTTAA
1623154 C
1 C
1623155 CATTGTGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
CTATTTATATTATTTAA
Found at i:1627801 original size:15 final size:16
Alignment explanation
Indices: 1627781--1627823 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
1627771 ATTCTATTTG
*
1627781 AACTAAAAATTACTC-
1 AACTAAAAATTAATCT
1627796 AACT-AAAATTAATCT
1 AACTAAAAATTAATCT
*
1627811 AATTAAAAATTAA
1 AACTAAAAATTAA
1627824 AGCGATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTAAAAATTAATCT
Found at i:1644164 original size:38 final size:38
Alignment explanation
Indices: 1644105--1644180 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
1644095 GCATAACCAC
1644105 TCTACCTTTTATCTTGATTAAGGTATAACCACTAAAGT
1 TCTACCTTTTATCTTGATTAAGGTATAACCACTAAAGT
* * *
1644143 TCTACCTTTTCAT-TTGGTTAAGGTATAACTACTTAAGT
1 TCTACCTTTT-ATCTTGATTAAGGTATAACCACTAAAGT
1644181 GAATACTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 32 0.94
39 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (38 bp):
TCTACCTTTTATCTTGATTAAGGTATAACCACTAAAGT
Found at i:1644653 original size:51 final size:50
Alignment explanation
Indices: 1644569--1644668 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 50
1644559 TAGATGTAAG
* * * * *
1644569 TATCTATCGATATATTCAACTCAAGATCATTTTGAAGTATCCTCAGGTGGC
1 TATCTATCGATAGATGCAACACAAGATCATTTTGAACTAT-CTCAAGTGGC
* * *
1644620 TATCTATCGATAGATGCAAGACAAGGTCCTTTTGAACTATCTCAAGTGG
1 TATCTATCGATAGATGCAACACAAGATCATTTTGAACTATCTCAAGTGG
1644669 ATGTTTATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 8 0.20
51 33 0.80
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (50 bp):
TATCTATCGATAGATGCAACACAAGATCATTTTGAACTATCTCAAGTGGC
Found at i:1645670 original size:28 final size:28
Alignment explanation
Indices: 1645639--1645702 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
1645629 TTATCTTAAT
*
1645639 TTAAGACAAACATGTTTTCTTGTCCAAA
1 TTAAGACAAACATGTTTTCTTATCCAAA
* * *
1645667 TTAAGAAAAATATGTTTTCTTATCTAAA
1 TTAAGACAAACATGTTTTCTTATCCAAA
1645695 TTAAGACA
1 TTAAGACA
1645703 TCATATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (28 bp):
TTAAGACAAACATGTTTTCTTATCCAAA
Found at i:1651546 original size:19 final size:19
Alignment explanation
Indices: 1651519--1651576 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
1651509 AAATCAAAAT
*
1651519 CAAAATAAAGAAAATGTAG
1 CAAACTAAAGAAAATGTAG
1651538 CAAACTAAAGAAAATGTAG
1 CAAACTAAAGAAAATGTAG
1651557 CAAACTAAAGAAAATGTAG
1 CAAACTAAAGAAAATGTAG
1651576 C
1 C
1651577 CATGAAGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.16
Consensus pattern (19 bp):
CAAACTAAAGAAAATGTAG
Found at i:1681748 original size:27 final size:27
Alignment explanation
Indices: 1681718--1681782 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1681708 GCTTAGTGGT
*
1681718 GTTCCAAGTGTAAAAGTG-CCTAGGGGC
1 GTTCCAAGTGCAAAAG-GACCTAGGGGC
* * *
1681745 GTTCCAAGCGCAGAAGGACCTAGTGGC
1 GTTCCAAGTGCAAAAGGACCTAGGGGC
1681772 GTTCCAAGTGC
1 GTTCCAAGTGC
1681783 TGAGGTGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (27 bp):
GTTCCAAGTGCAAAAGGACCTAGGGGC
Found at i:1681833 original size:27 final size:27
Alignment explanation
Indices: 1681731--1681894 Score: 102
Period size: 27 Copynumber: 6.2 Consensus size: 27
1681721 CCAAGTGTAA
* * **
1681731 AAGTGCCTAGGGGCGTTCCAAGCGCAG
1 AAGTGCCCAGAGGCGTTCCAAATGCAG
* * * *
1681758 AAG-GACCTAGTGGCGTTCCAAGTGCTG
1 AAGTG-CCCAGAGGCGTTCCAAATGCAG
* * * *
1681785 AGGTGCCCA-AGGTGTTCTAAATACAG
1 AAGTGCCCAGAGGCGTTCCAAATGCAG
*
1681811 AAGTGCCCAGGGGCGTTCCAAATGCAG
1 AAGTGCCCAGAGGCGTTCCAAATGCAG
** * * * *
1681838 AAGCACCTAGTGGCGTTCCAAGTGCTG
1 AAGTGCCCAGAGGCGTTCCAAATGCAG
* *
1681865 AAGTGCCCA-AGGTGTTCCAAATACA-
1 AAGTGCCCAGAGGCGTTCCAAATGCAG
1681890 AAGTG
1 AAGTG
1681895 TTTAGGTGTT
Statistics
Matches: 104, Mismatches: 30, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
25 5 0.05
26 31 0.30
27 67 0.64
28 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (27 bp):
AAGTGCCCAGAGGCGTTCCAAATGCAG
Found at i:1681848 original size:80 final size:79
Alignment explanation
Indices: 1681730--1681894 Score: 267
Period size: 80 Copynumber: 2.1 Consensus size: 79
1681720 TCCAAGTGTA
* * * *
1681730 AAAGTGCCTAGGGGCGTTCCAAGCGCAGAAGGACCTAGTGGCGTTCCAAGTGCTGAGGTGCCCAA
1 AAAGTGCCCAGGGGCGTTCCAAACGCAGAAGCACCTAGTGGCGTTCCAAGTGCTGAAGTGCCCAA
*
1681795 GGTGTTCTAAATAC
66 GGTGTTCCAAATAC
*
1681809 AGAAGTGCCCAGGGGCGTTCCAAATGCAGAAGCACCTAGTGGCGTTCCAAGTGCTGAAGTGCCCA
1 A-AAGTGCCCAGGGGCGTTCCAAACGCAGAAGCACCTAGTGGCGTTCCAAGTGCTGAAGTGCCCA
1681874 AGGTGTTCCAAATAC
65 AGGTGTTCCAAATAC
1681889 AAAGTG
1 AAAGTG
1681895 TTTAGGTGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 6 0.08
80 73 0.92
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.19
Consensus pattern (79 bp):
AAAGTGCCCAGGGGCGTTCCAAACGCAGAAGCACCTAGTGGCGTTCCAAGTGCTGAAGTGCCCAA
GGTGTTCCAAATAC
Found at i:1683181 original size:101 final size:98
Alignment explanation
Indices: 1683013--1683325 Score: 345
Period size: 101 Copynumber: 3.2 Consensus size: 98
1683003 TTTTCAACCA
* * * *
1683013 CAAGCTTTAATGCTCATAATTTGGCTGTAATATTACACTATTAGTCGCAAGCTTTATCGCTCACT
1 CAAGCTTTAATGCTTATAATCTGACTGTAATATTACACTATTAGCCGCAAGCTTTATCGCTCACT
*
1683078 TCTTGGCCATAGTTTGCTATTCACAAAAAGTTG
66 TCTTGGCCATAGTTTGCTATTCACAAAAAGCTG
* * * *
1683111 CAAGCTTTAATGCTTATAATCTGACTGTAATAATGTTTCGCTATTGGCCGCAAGCTTTATCGTTC
1 CAAGCTTTAATGCTTATAATCTGACTGTAAT-A--TTACACTATTAGCCGCAAGCTTTATCGCTC
1683176 ACTTCTTGGCCATAGTTTGCTATTCACAAAAAGCTG
63 ACTTCTTGGCCATAGTTTGCTATTCACAAAAAGCTG
* * * * * *
1683212 CAAGCTTTAATG-TTCATAATATGGCT-T--TA-T--ACTATTGGTCGCGAGCTTTACCGCTCAC
1 CAAGCTTTAATGCTT-ATAATCTGACTGTAATATTACACTATTAGCCGCAAGCTTTATCGCTCAC
* * *
1683270 TT-TCTAGCCATAGTTTGCTATCCATAAAAAGCTG
65 TTCT-TGGCCATAGTTTGCTATTCACAAAAAGCTG
* *
1683304 CAAACTTTAACGCTTATAATCT
1 CAAGCTTTAATGCTTATAATCT
1683326 AGCTTTATGT
Statistics
Matches: 187, Mismatches: 22, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
91 1 0.01
92 68 0.36
93 2 0.01
94 1 0.01
97 1 0.01
98 29 0.16
99 1 0.01
100 3 0.02
101 81 0.43
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (98 bp):
CAAGCTTTAATGCTTATAATCTGACTGTAATATTACACTATTAGCCGCAAGCTTTATCGCTCACT
TCTTGGCCATAGTTTGCTATTCACAAAAAGCTG
Found at i:1683323 original size:92 final size:92
Alignment explanation
Indices: 1683151--1683350 Score: 242
Period size: 92 Copynumber: 2.2 Consensus size: 92
1683141 TAATGTTTCG
* * * * *
1683151 CTATTGGCCGCAAGCTTTATCGTTCACTTCTTGGCCATAGTTTGCTATTCACAAAAAGCTGCAAG
1 CTATTGGCCGCAAGCTTTACCGCTCACTTCTTAGCCATAGTTTGCTATCCACAAAAAGCTGCAAA
* *
1683216 CTTTAATGTTCATAATATGGCTTTATA
66 CTTTAACGTTCATAATATAGCTTTATA
* * *
1683243 CTATTGGTCGCGAGCTTTACCGCTCACTT-TCTAGCCATAGTTTGCTATCCATAAAAAGCTGCAA
1 CTATTGGCCGCAAGCTTTACCGCTCACTTCT-TAGCCATAGTTTGCTATCCACAAAAAGCTGCAA
* *
1683307 ACTTTAACGCTT-ATAATCTAGCTTTATG
65 ACTTTAACG-TTCATAATATAGCTTTATA
* *
1683335 TTGTTGGCCGCAAGCT
1 CTATTGGCCGCAAGCT
1683351 ATTTACAGAA
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
91 1 0.01
92 87 0.97
93 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (92 bp):
CTATTGGCCGCAAGCTTTACCGCTCACTTCTTAGCCATAGTTTGCTATCCACAAAAAGCTGCAAA
CTTTAACGTTCATAATATAGCTTTATA
Found at i:1684544 original size:33 final size:33
Alignment explanation
Indices: 1684440--1684545 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
1684430 TAATGGCATT
* * *
1684440 CACATCATCACCATCAACTCCAGTAGCAACACC
1 CACATCATCACCACCAACTCTAGTAGCAACATC
* ** * * * *
1684473 CACATCGTCGTCACCAATTCTTGTAACAACATT
1 CACATCATCACCACCAACTCTAGTAGCAACATC
* * *
1684506 GACATCATCACCACCAGCTCTAGTAGCAGCATC
1 CACATCATCACCACCAACTCTAGTAGCAACATC
1684539 CACATCA
1 CACATCA
1684546 CCGTCATTAA
Statistics
Matches: 52, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.33, C:0.37, G:0.09, T:0.21
Consensus pattern (33 bp):
CACATCATCACCACCAACTCTAGTAGCAACATC
Found at i:1684558 original size:66 final size:66
Alignment explanation
Indices: 1684436--1684564 Score: 159
Period size: 66 Copynumber: 2.0 Consensus size: 66
1684426 TGGCTAATGG
* ** *
1684436 CATTCACATCATCACCATCAACTCCAGTAGCAACACCCACATCGTCGTCACCAATTCTTGTAACA
1 CATTCACATCATCACCACCAACTCCAGTAGCAACACCCACATCACCGTCACCAATTCCTGTAACA
1684501 A
66 A
* * * * * **
1684502 CATTGACATCATCACCACCAGCTCTAGTAGCAGCATCCACATCACCGTCATTAATTCCTGTAA
1 CATTCACATCATCACCACCAACTCCAGTAGCAACACCCACATCACCGTCACCAATTCCTGTAA
1684565 TGTCATGCAC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.32, C:0.35, G:0.09, T:0.24
Consensus pattern (66 bp):
CATTCACATCATCACCACCAACTCCAGTAGCAACACCCACATCACCGTCACCAATTCCTGTAACA
A
Found at i:1688465 original size:26 final size:26
Alignment explanation
Indices: 1688346--1688656 Score: 171
Period size: 26 Copynumber: 11.8 Consensus size: 26
1688336 CCTAAGGGCA
* * **
1688346 TTCCTAGTATAGAAGCGCTTAGTGGTG
1 TTCCAAGTGTAGAAGCGCCCAG-GGTG
* * *
1688373 TTCCAAG-GCAAAAGCACCCAGGGTG
1 TTCCAAGTGTAGAAGCGCCCAGGGTG
** * *
1688398 TTCCAAACGTAAAAGCGCCTAGGGTG
1 TTCCAAGTGTAGAAGCGCCCAGGGTG
* ** * * *
1688424 TTCTAAACGTAAAAGCACCCAGGGTA
1 TTCCAAGTGTAGAAGCGCCCAGGGTG
* *
1688450 TTCCAAGTATAGAAGCGCCCAAGGGCG
1 TTCCAAGTGTAGAAGCGCCC-AGGGTG
* *
1688477 TTCCAAGTGTAGAAGCACCCAAGGGCG
1 TTCCAAGTGTAGAAGCGCCC-AGGGTG
* * * * *
1688504 TTCTAAGTGCAAAAACACCCAGGG-G
1 TTCCAAGTGTAGAAGCGCCCAGGGTG
* *
1688529 CATTCCAAGTGTAGAAGTGCCCAAGGTG
1 --TTCCAAGTGTAGAAGCGCCCAGGGTG
* * * **
1688557 TTCCAAGCGCAAAAGCGCCCAGTGACG
1 TTCCAAGTGTAGAAGCGCCCAG-GGTG
*
1688584 TTCCAAGTGCT-GAAACGCCCAGGGTG
1 TTCCAAGTG-TAGAAGCGCCCAGGGTG
* * *
1688610 TTCCAAGTACT-GAAGTGCCCAAGGTG
1 TTCCAAGT-GTAGAAGCGCCCAGGGTG
* *
1688636 TTCCAAGTATAGAAGCACCCA
1 TTCCAAGTGTAGAAGCGCCCA
1688657 AAAGTGTTCA
Statistics
Matches: 219, Mismatches: 56, Indels: 19
0.74 0.19 0.06
Matches are distributed among these distances:
25 12 0.05
26 119 0.54
27 87 0.40
28 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (26 bp):
TTCCAAGTGTAGAAGCGCCCAGGGTG
Found at i:1688466 original size:52 final size:52
Alignment explanation
Indices: 1688331--1688468 Score: 147
Period size: 52 Copynumber: 2.6 Consensus size: 52
1688321 CATAGCATAG
* * * * * *
1688331 AAGCACCTAAGGGCATTCCTAGTATAGAAGCGCTTAGTGGTGTTCCAAGGCAA
1 AAGCACC-CAGGGTATTCCAAGTATAGAAGCGCCTAGTGGTGTTCAAACGCAA
* *
1688384 AAGCACCCAGGGTGTTCCAAACGTA-A-AAGCGCCTAG-GGTGTTCTAAACGTAA
1 AAGCACCCAGGGTATTCC-AA-GTATAGAAGCGCCTAGTGGTGTTC-AAACGCAA
1688436 AAGCACCCAGGGTATTCCAAGTATAGAAGCGCC
1 AAGCACCCAGGGTATTCCAAGTATAGAAGCGCC
1688469 CAAGGGCGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
50 3 0.04
51 10 0.14
52 46 0.65
53 9 0.13
54 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (52 bp):
AAGCACCCAGGGTATTCCAAGTATAGAAGCGCCTAGTGGTGTTCAAACGCAA
Found at i:1688480 original size:27 final size:27
Alignment explanation
Indices: 1688450--1688657 Score: 149
Period size: 27 Copynumber: 7.8 Consensus size: 27
1688440 ACCCAGGGTA
*
1688450 TTCCAAGTATAGAAGCGCCCAAGGGCG
1 TTCCAAGTGTAGAAGCGCCCAAGGGCG
*
1688477 TTCCAAGTGTAGAAGCACCCAAGGGCG
1 TTCCAAGTGTAGAAGCGCCCAAGGGCG
* * * * * * *
1688504 TTCTAAGTGCAAAAACACCCAGGGGCA
1 TTCCAAGTGTAGAAGCGCCCAAGGGCG
* *
1688531 TTCCAAGTGTAGAAGTGCCCAA-GGTG
1 TTCCAAGTGTAGAAGCGCCCAAGGGCG
* * * *
1688557 TTCCAAGCGCAAAAGCGCCC-AGTGACG
1 TTCCAAGTGTAGAAGCGCCCAAG-GGCG
* *
1688584 TTCCAAGTGCT-GAAACGCCC-AGGGTG
1 TTCCAAGTG-TAGAAGCGCCCAAGGGCG
* * *
1688610 TTCCAAGTACT-GAAGTGCCCAA-GGTG
1 TTCCAAGT-GTAGAAGCGCCCAAGGGCG
* *
1688636 TTCCAAGTATAGAAGCACCCAA
1 TTCCAAGTGTAGAAGCGCCCAA
1688658 AAGTGTTCAA
Statistics
Matches: 140, Mismatches: 35, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
25 2 0.01
26 57 0.41
27 81 0.58
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (27 bp):
TTCCAAGTGTAGAAGCGCCCAAGGGCG
Found at i:1688592 original size:53 final size:52
Alignment explanation
Indices: 1688384--1688657 Score: 163
Period size: 53 Copynumber: 5.2 Consensus size: 52
1688374 TCCAAGGCAA
* * * * * * * ** *
1688384 AAGCACCCAGGGTGTTCCAAACGTAAAAGCGCCTAGGGTGTTCTAAACGTAA
1 AAGCGCCCAAGGTGTTCCAAGCGCAAAAGCGCCCAGGGCGTTCCAAGTGTAG
* * * *** *
1688436 AAGCACCCAGGGTATTCCAAGTATAGAAGCGCCCAAGGGCGTTCCAAGTGTAG
1 AAGCGCCCAAGGTGTTCCAAGCGCAAAAGCGCCC-AGGGCGTTCCAAGTGTAG
* * * * * * *
1688489 AAGCACCCAAGGGCGTTCTAAGTGCAAAAACACCCAGGGGCATTCCAAGTGTAG
1 AAGCGCCCAA-GGTGTTCCAAGCGCAAAAGCGCCCA-GGGCGTTCCAAGTGTAG
* *
1688543 AAGTGCCCAAGGTGTTCCAAGCGCAAAAGCGCCCAGTGACGTTCCAAGTGCT-G
1 AAGCGCCCAAGGTGTTCCAAGCGCAAAAGCGCCCAG-GGCGTTCCAAGTG-TAG
* * ** ** * * * *
1688596 AAACGCCCAGGGTGTTCCAAGTACTGAAGTGCCCAAGGTGTTCCAAGTATAG
1 AAGCGCCCAAGGTGTTCCAAGCGCAAAAGCGCCCAGGGCGTTCCAAGTGTAG
*
1688648 AAGCACCCAA
1 AAGCGCCCAA
1688658 AAGTGTTCAA
Statistics
Matches: 171, Mismatches: 45, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
51 1 0.01
52 47 0.27
53 82 0.48
54 41 0.24
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (52 bp):
AAGCGCCCAAGGTGTTCCAAGCGCAAAAGCGCCCAGGGCGTTCCAAGTGTAG
Found at i:1688657 original size:26 final size:26
Alignment explanation
Indices: 1688436--1688683 Score: 110
Period size: 27 Copynumber: 9.4 Consensus size: 26
1688426 CTAAACGTAA
* *
1688436 AAGCACCCAGGGTATTCCAAGTATAG
1 AAGCACCCAAGGTGTTCCAAGTATAG
* * *
1688462 AAGCGCCCAAGGGCGTTCCAAGTGTAG
1 AAGCACCCAA-GGTGTTCCAAGTATAG
* * ** *
1688489 AAGCACCCAAGGGCGTTCTAAGTGCAA
1 AAGCACCCAA-GGTGTTCCAAGTATAG
* * *
1688516 AAACACCC-AGGGGCATTCCAAGTGTAG
1 AAGCACCCAAGGTG--TTCCAAGTATAG
** *** *
1688543 AAGTGCCCAAGGTGTTCCAAGCGCAA
1 AAGCACCCAAGGTGTTCCAAGTATAG
* * *
1688569 AAGCGCCC-AGTGACGTTCCAAGTGCT-G
1 AAGCACCCAAG-G-TGTTCCAAGT-ATAG
* * *
1688596 AAACGCCCAGGGTGTTCCAAGTACT-G
1 AAGCACCCAAGGTGTTCCAAGTA-TAG
**
1688622 AAGTGCCCAAGGTGTTCCAAGTATAG
1 AAGCACCCAAGGTGTTCCAAGTATAG
* * *
1688648 AAGCACCCAAAAGTGTT-CAAGCATAA
1 AAGCACCC-AAGGTGTTCCAAGTATAG
1688674 AAGCACCCAA
1 AAGCACCCAA
1688684 AGAGCGTTAC
Statistics
Matches: 172, Mismatches: 39, Indels: 23
0.74 0.17 0.10
Matches are distributed among these distances:
25 8 0.05
26 79 0.46
27 80 0.47
28 5 0.03
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (26 bp):
AAGCACCCAAGGTGTTCCAAGTATAG
Found at i:1688684 original size:26 final size:28
Alignment explanation
Indices: 1688633--1688698 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
1688623 AGTGCCCAAG
* * *
1688633 GTGTTCCAAGTATAGAAGCACCCAAA-A
1 GTGTTACAAGCATAAAAGCACCCAAAGA
1688660 GTGTT-CAAGCATAAAAGCACCCAAAGA
1 GTGTTACAAGCATAAAAGCACCCAAAGA
*
1688687 GCGTTACAAGCA
1 GTGTTACAAGCA
1688699 CAGAAATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.53
27 10 0.29
28 6 0.18
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (28 bp):
GTGTTACAAGCATAAAAGCACCCAAAGA
Found at i:1696816 original size:41 final size:41
Alignment explanation
Indices: 1696760--1696853 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1696750 GTGAGAAATT
*
1696760 TTTTC-TTATAATGCTAGGTCAAAATGAACCATTATTTTTC
1 TTTTCATTATCATGCTAGGTCAAAATGAACCATTATTTTTC
*
1696800 TTTTCATTATCATGCTAGGTCAAAATGAACCGTTATTTTTC
1 TTTTCATTATCATGCTAGGTCAAAATGAACCATTATTTTTC
1696841 TTTTCATTATCAT
1 TTTTCATTATCAT
1696854 TGTATTTGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.47
Consensus pattern (41 bp):
TTTTCATTATCATGCTAGGTCAAAATGAACCATTATTTTTC
Found at i:1698284 original size:33 final size:32
Alignment explanation
Indices: 1698247--1698309 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1698237 ATACAAATTG
*
1698247 AATAAGAGTAAAATTTAGGGTAAAGGGCTTTCA
1 AATAAGAGTAAAA-TTAAGGTAAAGGGCTTTCA
* **
1698280 AATAAGATTTCAATTAAGGTAAAGGGCTTT
1 AATAAGAGTAAAATTAAGGTAAAGGGCTTT
1698310 TGAGAAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.30
Consensus pattern (32 bp):
AATAAGAGTAAAATTAAGGTAAAGGGCTTTCA
Found at i:1702294 original size:14 final size:14
Alignment explanation
Indices: 1702275--1702306 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1702265 GTTTCTTCAT
1702275 TTTTTTCCCAAATA
1 TTTTTTCCCAAATA
*
1702289 TTTTTTCCCCAATA
1 TTTTTTCCCAAATA
1702303 TTTT
1 TTTT
1702307 GCCCAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTTCCCAAATA
Found at i:1709640 original size:57 final size:58
Alignment explanation
Indices: 1709572--1709685 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 58
1709562 AATCCTTATA
* *
1709572 ATGGCTTTTAACAAGTTCAAGCACAAACCCAT-GGTTTTAATG-GGTTCACTACAAACCT
1 ATGGCTTTTAACAAGTTC-ACCACAAACCCATAGGTTTTAATGAGG-TCACCACAAACCT
** *
1709630 ATGG-TTTTAACGGGTTCACCACAAACCCATAGTTTTTAATGAGGTCACCACAAACC
1 ATGGCTTTTAACAAGTTCACCACAAACCCATAGGTTTTAATGAGGTCACCACAAACC
1709686 CATACTAACT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
56 12 0.24
57 31 0.63
58 6 0.12
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (58 bp):
ATGGCTTTTAACAAGTTCACCACAAACCCATAGGTTTTAATGAGGTCACCACAAACCT
Found at i:1709689 original size:29 final size:28
Alignment explanation
Indices: 1709593--1709688 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
1709583 CAAGTTCAAG
1709593 CACAAACCCATGGTTTTAATGGGTTCAC
1 CACAAACCCATGGTTTTAATGGGTTCAC
* * *
1709621 TACAAACCTATGGTTTTAACGGGTTCAC
1 CACAAACCCATGGTTTTAATGGGTTCAC
*
1709649 CACAAACCCATAGTTTTTAATGAGG-TCAC
1 CACAAACCCAT-GGTTTTAATG-GGTTCAC
1709678 CACAAACCCAT
1 CACAAACCCAT
1709689 ACTAACTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
28 34 0.58
29 23 0.39
30 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (28 bp):
CACAAACCCATGGTTTTAATGGGTTCAC
Found at i:1710791 original size:2 final size:2
Alignment explanation
Indices: 1710786--1710814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1710776 TATCACAATA
1710786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1710815 GATGGGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1713415 original size:29 final size:29
Alignment explanation
Indices: 1713379--1713435 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1713369 GGATATTCAA
*
1713379 TATATCTTGCTTAGCTACTGTGAATATTG
1 TATATCTTACTTAGCTACTGTGAATATTG
* *
1713408 TATATCTTATTTAGCTACTGTGGATATT
1 TATATCTTACTTAGCTACTGTGAATATT
1713436 ATAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (29 bp):
TATATCTTACTTAGCTACTGTGAATATTG
Found at i:1717108 original size:74 final size:73
Alignment explanation
Indices: 1716978--1717119 Score: 176
Period size: 74 Copynumber: 1.9 Consensus size: 73
1716968 GTGCTTAATT
* * *
1716978 TCAAATTTTTGACAGTGACCTTTTAGCTAACCAACCATACTTCTTAGTCGACTAAGTCTTCTCTG
1 TCAAATTTCTGACAGTGACCTTTTAGCTAACCAACCATACTTCTCAGTCGACTAAGTATTCTCTG
1717043 TCTCGCAG
66 TCTCGCAG
* * * * * * * *
1717051 TCAAATTCTCTGACAGTGAGCTTTTTGCTAGCTAACTATACTTCTCAGTTGATTAAGTATTCTTT
1 TCAAATT-TCTGACAGTGACCTTTTAGCTAACCAACCATACTTCTCAGTCGACTAAGTATTCTCT
1717116 GTCT
65 GTCT
1717120 TGCAATCTGT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
73 7 0.12
74 50 0.88
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (73 bp):
TCAAATTTCTGACAGTGACCTTTTAGCTAACCAACCATACTTCTCAGTCGACTAAGTATTCTCTG
TCTCGCAG
Found at i:1721557 original size:23 final size:23
Alignment explanation
Indices: 1721527--1721572 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1721517 CACGCGAGAA
1721527 GGCAACAATGCGGTAAATGGGTT
1 GGCAACAATGCGGTAAATGGGTT
* *
1721550 GGCAACAATGTGGTAGATGGGTT
1 GGCAACAATGCGGTAAATGGGTT
1721573 CGCTAAAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.37, T:0.24
Consensus pattern (23 bp):
GGCAACAATGCGGTAAATGGGTT
Found at i:1722153 original size:2 final size:2
Alignment explanation
Indices: 1722146--1722180 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1722136 AAATTAAAGA
1722146 AG AG AG 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 AG AG AG A
1722181 AAGAAAGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1723984 original size:21 final size:19
Alignment explanation
Indices: 1723960--1723999 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1723950 ATAACAGCTG
*
1723960 TAGCAACAACAATAACAAAAA
1 TAGCAA-AACAAGAA-AAAAA
1723981 TAGCAAAACAAGAAAAAAA
1 TAGCAAAACAAGAAAAAAA
1724000 CTTTTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.07
Consensus pattern (19 bp):
TAGCAAAACAAGAAAAAAA
Found at i:1729666 original size:37 final size:37
Alignment explanation
Indices: 1729633--1729712 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
1729623 GGTATTTTAG
1729633 TCATTTAATGTGTCATGTAGTTCTAAGAATATTTCTC
1 TCATTTAATGTGTCATGTAGTTCTAAGAATATTTCTC
** *
1729670 TCATTTGGTGTGTCATGTAGTTCTAAGAATATTTATC
1 TCATTTAATGTGTCATGTAGTTCTAAGAATATTTCTC
1729707 TCATTT
1 TCATTT
1729713 TTGTATATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (37 bp):
TCATTTAATGTGTCATGTAGTTCTAAGAATATTTCTC
Found at i:1730546 original size:63 final size:63
Alignment explanation
Indices: 1730452--1730585 Score: 164
Period size: 63 Copynumber: 2.1 Consensus size: 63
1730442 CTCTTTTTTG
** * * *
1730452 AATCAAACAATATCATTCATTGATTTTGAAAAACCCTTTCTTCC-TGTT-TTTTTTTTTGAATC
1 AATCAAACAATATCATTCATCAAATTAGAAAAACCATTT-TTCCATGTTCTTTTTTTTTGAATC
* *
1730514 AATCAAACTATTATCATTCATCAAATTAGAAAAACCATTTTTCCTATTTTCTTTTTTTTTGAATC
1 AATCAAAC-AATATCATTCATCAAATTAGAAAAACCATTTTTCC-ATGTTCTTTTTTTTTGAATC
1730579 AATCAAA
1 AATCAAA
1730586 TAATTTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
62 12 0.20
63 25 0.41
64 3 0.05
65 21 0.34
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (63 bp):
AATCAAACAATATCATTCATCAAATTAGAAAAACCATTTTTCCATGTTCTTTTTTTTTGAATC
Found at i:1735680 original size:22 final size:23
Alignment explanation
Indices: 1735631--1735673 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1735621 TCATAAGTGG
1735631 ATATTATAAATTAAAAAAAATTA
1 ATATTATAAATTAAAAAAAATTA
*
1735654 ATATTATATA-TAAAAAAAAT
1 ATATTATAAATTAAAAAAAAT
1735674 AGTTATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATTATAAATTAAAAAAAATTA
Found at i:1738055 original size:16 final size:16
Alignment explanation
Indices: 1738017--1738062 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1738007 GGGTCTACCG
1738017 AAAAATTAGAAAAATAT
1 AAAAA-TAGAAAAATAT
*
1738034 AAAAATATAAAAATA-
1 AAAAATAGAAAAATAT
1738049 ATAAAATAGAAAAA
1 A-AAAATAGAAAAA
1738063 AATGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 1 0.04
16 20 0.77
17 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AAAAATAGAAAAATAT
Found at i:1738062 original size:8 final size:8
Alignment explanation
Indices: 1738016--1738062 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1738006 GGGGTCTACC
1738016 GAAAAATTA
1 GAAAAA-TA
1738025 GAAAAATA
1 GAAAAATA
*
1738033 TAAAAATA
1 GAAAAATA
*
1738041 TAAAAATA
1 GAAAAATA
1738049 -ATAAAATA
1 GA-AAAATA
1738057 GAAAAA
1 GAAAAA
1738063 AATGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
7 1 0.03
8 27 0.77
9 7 0.20
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (8 bp):
GAAAAATA
Found at i:1738070 original size:16 final size:15
Alignment explanation
Indices: 1738018--1738070 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1738008 GGTCTACCGA
*
1738018 AAAATTAGAAAAATAT
1 AAAA-TAGAAAAAAAT
*
1738034 AAAAATATAAAAATAAT
1 -AAAATAGAAAAA-AAT
1738051 AAAATAGAAAAAAAT
1 AAAATAGAAAAAAAT
1738066 GAAAA
1 -AAAA
1738071 AAAAAACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 3 0.10
16 22 0.71
17 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAATAGAAAAAAAT
Found at i:1738271 original size:19 final size:19
Alignment explanation
Indices: 1738249--1738294 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1738239 CTAGGGAAAT
*
1738249 AACACAATCAAAAGCAACA
1 AACACAATCAAAAGCAAAA
*
1738268 AACACAATCACAAGCAAAA
1 AACACAATCAAAAGCAAAA
1738287 AATCACAA
1 AA-CACAA
1738295 GATAGCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.63, C:0.26, G:0.04, T:0.07
Consensus pattern (19 bp):
AACACAATCAAAAGCAAAA
Found at i:1745887 original size:35 final size:35
Alignment explanation
Indices: 1745834--1745929 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 35
1745824 TGTGGTTAAG
* *
1745834 CTTGTTAAAAACCATTGTTGAGGGTTTCGCTTACT
1 CTTGTTAAAAAGCATTGTTGAGGGTTTCACTTACT
* * * * *
1745869 CTTGTGAAAAAGCGTTGTTGAAGGTTTTACTTGCT
1 CTTGTTAAAAAGCATTGTTGAGGGTTTCACTTACT
*
1745904 CTCGTTAAAAAGCATTG-TGAGGGTTT
1 CTTGTTAAAAAGCATTGTTGAGGGTTT
1745930 AATGCTTGAT
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
34 8 0.16
35 42 0.84
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (35 bp):
CTTGTTAAAAAGCATTGTTGAGGGTTTCACTTACT
Found at i:1747476 original size:19 final size:18
Alignment explanation
Indices: 1747450--1747492 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1747440 CGAAAAAGAA
* *
1747450 AAGAAAGAAATGAGGAAG
1 AAGAAAGAAAGGAGAAAG
1747468 AATGAAAGAAAGGAGAAAG
1 AA-GAAAGAAAGGAGAAAG
1747487 AAGAAA
1 AAGAAA
1747493 AAGCTAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (18 bp):
AAGAAAGAAAGGAGAAAG
Found at i:1761058 original size:4 final size:4
Alignment explanation
Indices: 1761003--1761042 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1760993 TCCTTAGCTT
*
1761003 TTTC -TTC TTTC -TCC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1761043 CCTCCTTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 5 0.16
4 27 0.84
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:1769065 original size:2 final size:2
Alignment explanation
Indices: 1769058--1769083 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1769048 NNNNNNNNNN
1769058 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
1769084 AGCTAACACC
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):
TA
Found at i:1771671 original size:18 final size:18
Alignment explanation
Indices: 1771650--1771684 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1771640 GTCTTGTGTT
*
1771650 TGTCGGCATAATTATTGA
1 TGTCAGCATAATTATTGA
1771668 TGTCAGCATAATTATTG
1 TGTCAGCATAATTATTG
1771685 CTATTAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (18 bp):
TGTCAGCATAATTATTGA
Found at i:1793423 original size:56 final size:55
Alignment explanation
Indices: 1793301--1793450 Score: 137
Period size: 56 Copynumber: 2.7 Consensus size: 55
1793291 AATCAACAAT
* * * * **
1793301 ATTTC-AATAGAAATCAGTAAGTAATGATTAAATTACCAATGGAATTCTGTTGGTA
1 ATTTCTAATAGAATTC-GTAACTAATGACTAAATTACCAATGGAATTCTATTACTA
*
1793356 ATTTCTAATAGAAATTCG-AACATAATGAGTAAATTACCAATGGAATTAC-ATTACTA
1 ATTTCTAATAG-AATTCGTAAC-TAATGACTAAATTACCAATGGAATT-CTATTACTA
* * *
1793412 ATTT-TCCATAGAATTTGTAGCTAATGACTAAATTACCAA
1 ATTTCT-AATAGAATTCGTAACTAATGACTAAATTACCAA
1793451 ACAAAATTCC
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
55 30 0.38
56 44 0.56
57 5 0.06
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (55 bp):
ATTTCTAATAGAATTCGTAACTAATGACTAAATTACCAATGGAATTCTATTACTA
Found at i:1805632 original size:69 final size:68
Alignment explanation
Indices: 1805476--1805719 Score: 206
Period size: 69 Copynumber: 3.5 Consensus size: 68
1805466 ATTTGCTTAG
* *
1805476 CTAGACCTTGTGGTATTCTTACCCCTACACCAAGCTCTA-AAAGGAAAGAGATGGGTACATTCAC
1 CTAGACCCTGTGGTATTCTTACCCC-ACACCAAGCTTTAGAAAGGAAAGAGATGGGTACATTCAC
1805540 CCAA
65 CCAA
* * * * *
1805544 CTAGACCCTATGGTATTCTTAACCCACACCAAGCTTTAGAAAGGAGCAAGA-ATGTGTATATTCG
1 CTAGACCCTGTGGTATTCTTACCCCACACCAAGCTTTAGAAAGGA--AAGAGATGGGTACATTCA
**
1805608 TTCAA
64 CCCAA
* ** * * * * * * *
1805613 CTTGGTCCTGTGGTATTCTTACCCCCACACTAAACTTTAGAAGAAGAAA-AGGTGGATACATGCG
1 CTAGACCCTGTGGTATTCTTA-CCCCACACCAAGCTTTAGAA-AGGAAAGAGATGGGTACATTCA
1805677 CCCAA
64 CCCAA
* * * *
1805682 CTAGACCTTGTGATATTTTTACCTCCACACCAGGCTTT
1 CTAGACCCTGTGGTATTCTTACC-CCACACCAAGCTTT
1805720 TGAAGGGGNN
Statistics
Matches: 136, Mismatches: 33, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
67 12 0.09
68 31 0.23
69 69 0.51
70 21 0.15
71 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (68 bp):
CTAGACCCTGTGGTATTCTTACCCCACACCAAGCTTTAGAAAGGAAAGAGATGGGTACATTCACC
CAA
Found at i:1806497 original size:12 final size:12
Alignment explanation
Indices: 1806480--1806512 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1806470 TAGTTGAATG
1806480 ATGGTTGAAGAA
1 ATGGTTGAAGAA
1806492 ATGGTTGAAGAA
1 ATGGTTGAAGAA
1806504 ATGGTTGAA
1 ATGGTTGAA
1806513 AAAAGAGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (12 bp):
ATGGTTGAAGAA
Found at i:1807844 original size:99 final size:99
Alignment explanation
Indices: 1807680--1807865 Score: 246
Period size: 99 Copynumber: 1.9 Consensus size: 99
1807670 ATATAGCATG
* *
1807680 TAACTTGATCTCTATCTTTGTGTTTAACTAAAACATAAACTCTTGAAATTAAACACCTTACACAT
1 TAACTTGATCTCTATCTTTGTATTTAACTAAAACATAAACTCTTGAAATTAAACACCTTAAACAT
* *
1807745 GGTGTGTAACAACTTTTTTTTTCAATATGCTACA
66 GGTATATAACAACTTTTTTTTTCAATATGCTACA
* * * ** * * * *
1807779 TAACTTGGTCTCTATTTTTGTATTTCACTAGCACATAAAGTGTTGGAGTTAAACACCTTAAACAT
1 TAACTTGATCTCTATCTTTGTATTTAACTAAAACATAAACTCTTGAAATTAAACACCTTAAACAT
*
1807844 GGTATATAATAACTTTTTTTTT
66 GGTATATAACAACTTTTTTTTT
1807866 AACATGGTGT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 73 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (99 bp):
TAACTTGATCTCTATCTTTGTATTTAACTAAAACATAAACTCTTGAAATTAAACACCTTAAACAT
GGTATATAACAACTTTTTTTTTCAATATGCTACA
Found at i:1807869 original size:27 final size:29
Alignment explanation
Indices: 1807839--1807900 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
1807829 AAACACCTTA
*
1807839 AACATGGTATATAATAAC-TTTTTTTT-T
1 AACATGGTATATAACAACATTTTTTTTCT
* *
1807866 AACATGGTGTGTAACAACATTTTTTTTCT
1 AACATGGTATATAACAACATTTTTTTTCT
1807895 -ACATGG
1 AACATGG
1807901 CGTGTAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 15 0.50
28 14 0.47
29 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (29 bp):
AACATGGTATATAACAACATTTTTTTTCT
Found at i:1807889 original size:28 final size:28
Alignment explanation
Indices: 1807839--1807908 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1807829 AAACACCTTA
* * *
1807839 AACATGGTATATAATAACTTTTTTTT-T
1 AACATGGTGTGTAACAACTTTTTTTTCT
1807866 AACATGGTGTGTAACAACATTTTTTTTCT
1 AACATGGTGTGTAACAAC-TTTTTTTTCT
*
1807895 -ACATGGCGTGTAAC
1 AACATGGTGTGTAAC
1807909 TTGGTCTCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 15 0.41
28 21 0.57
29 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (28 bp):
AACATGGTGTGTAACAACTTTTTTTTCT
Found at i:1807917 original size:126 final size:124
Alignment explanation
Indices: 1807741--1807997 Score: 331
Period size: 126 Copynumber: 2.0 Consensus size: 124
1807731 AACACCTTAC
* * *
1807741 ACATGGTGTGTAACAACTTTTTTTTTCAATATGCTACATAACTTGGTCTCTATTTTTGTATTTCA
1 ACATGGTGTGTAACAACATTTTTTTTCAACATGCTA-ATAACTTGGTCTCTATCTTTGTATTTCA
** * * *
1807806 CTAGCACATAAAGT-GTTGGAGTTAAACACCTT-AAACATGGTATATAATAACTTTTTTTTTA
65 CTAAAACATAAACTCG-TGAAGTTAAACA-CTTAAAACATGGTATATAATAAC-TTTTTTTCA
* *
1807867 ACATGGTGTGTAACAACATTTTTTTTCTACATGGCGT-GTAACTTGGTCTCTATCTTTGTATTTC
1 ACATGGTGTGTAACAACATTTTTTTTCAACAT-GC-TAATAACTTGGTCTCTATCTTTGTATTTC
* *
1807931 ACTAAAACATAAACTCGTGAAGTTAAACACTTAAAACATGGTGTGTAATAACTTTTTTTCA
64 ACTAAAACATAAACTCGTGAAGTTAAACACTTAAAACATGGTATATAATAACTTTTTTTCA
1807992 ACATGG
1 ACATGG
1807998 CATGTAACTT
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
125 17 0.15
126 94 0.82
127 3 0.03
128 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (124 bp):
ACATGGTGTGTAACAACATTTTTTTTCAACATGCTAATAACTTGGTCTCTATCTTTGTATTTCAC
TAAAACATAAACTCGTGAAGTTAAACACTTAAAACATGGTATATAATAACTTTTTTTCA
Found at i:1807975 original size:99 final size:98
Alignment explanation
Indices: 1807866--1808103 Score: 291
Period size: 97 Copynumber: 2.4 Consensus size: 98
1807856 CTTTTTTTTT
* *
1807866 AACATGGTGTGTAACAACATTTTTTTTCTACATGGCGTGTAACTTGGTCT-CTATCTTTGTATTT
1 AACATGGTGTGTAACAAC-TTTTTTTTCAACATGGCGTGTAACTTGGT-TGCAATCTTTGTATTT
*
1807930 CACTAAAACATAAACTCGTGAAGTTAAACACTTAA
64 CACTAAAACATAAACTAGTGAAGTTAAACACTTAA
* * *
1807965 AACATGGTGTGTAATAAC-TTTTTTTCAACATGGCATGTAACTTGGTTGCAATCTTTGTATTTTA
1 AACATGGTGTGTAACAACTTTTTTTTCAACATGGCGTGTAACTTGGTTGCAATCTTTGTATTTCA
** * * *
1808029 CTAGGACATAAACTATTGGAGTTAAACACTTTA
66 CTAAAACATAAACTAGTGAAGTTAAACACTTAA
* ** * **
1808062 AATATGGCATGTAACAATTTTTTTTTCAACATAACGTGTAAC
1 AACATGGTGTGTAACAACTTTTTTTTCAACATGGCGTGTAAC
1808104 AACATTTTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
96 1 0.01
97 80 0.68
98 20 0.17
99 17 0.14
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (98 bp):
AACATGGTGTGTAACAACTTTTTTTTCAACATGGCGTGTAACTTGGTTGCAATCTTTGTATTTCA
CTAAAACATAAACTAGTGAAGTTAAACACTTAA
Found at i:1808108 original size:223 final size:224
Alignment explanation
Indices: 1807678--1808113 Score: 576
Period size: 223 Copynumber: 1.9 Consensus size: 224
1807668 AAATATAGCA
* * *
1807678 TGTAACTTGATCTCTATCTTTGTGTTTAACTAAAACATAAACTCTTGAAATTAAACACCTTACAC
1 TGTAACTTGATCTCTATCTTTGTATTTAACTAAAACATAAACTCGTGAAATTAAACACCTTAAAC
* * *
1807743 ATGGTGTGTAACAACTTTTTTTTTCAATATGCTACATAACTTGGTCTCTATTTTTGTATTTCACT
66 ATGGTGTGTAACAAC-TTTTTTTTCAACATGCTACATAACTTGGTCTCAATCTTTGTATTTCACT
* * * * **
1807808 AGCACATAAAGTGTTGGAGTTAAACACCTTAAACATGGTATATAATAACTTTTTTTTTAACATGG
130 AGCACATAAACTATTGGAGTTAAACACCTTAAACATGGCATATAACAACTTTTTTTTTAACATAA
*
1807873 TGTGTAACAACATTTTTTTTCTACATGGCG
195 CGTGTAACAACATTTTTTTTCTACATGGCG
* * *
1807903 TGTAACTTGGTCTCTATCTTTGTATTTCACTAAAACATAAACTCGTGAAGTTAAACA-CTTAAAA
1 TGTAACTTGATCTCTATCTTTGTATTTAACTAAAACATAAACTCGTGAAATTAAACACCTT-AAA
* ** *
1807967 CATGGTGTGTAATAAC-TTTTTTTCAACATGGC-ATGTAACTTGGT-TGCAATCTTTGTATTTTA
65 CATGGTGTGTAACAACTTTTTTTTCAACAT-GCTACATAACTTGGTCT-CAATCTTTGTATTTCA
* * * *
1808029 CTAGGACATAAACTATTGGAGTTAAACACTTTAAATATGGCATGTAACAA-TTTTTTTTTCAACA
128 CTAGCACATAAACTATTGGAGTTAAACACCTTAAACATGGCATATAACAACTTTTTTTTT-AACA
1808093 TAACGTGTAACAACATTTTTT
192 TAACGTGTAACAACATTTTTT
1808114 AAACATGGCA
Statistics
Matches: 183, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
222 10 0.05
223 99 0.54
224 5 0.03
225 69 0.38
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (224 bp):
TGTAACTTGATCTCTATCTTTGTATTTAACTAAAACATAAACTCGTGAAATTAAACACCTTAAAC
ATGGTGTGTAACAACTTTTTTTTCAACATGCTACATAACTTGGTCTCAATCTTTGTATTTCACTA
GCACATAAACTATTGGAGTTAAACACCTTAAACATGGCATATAACAACTTTTTTTTTAACATAAC
GTGTAACAACATTTTTTTTCTACATGGCG
Found at i:1808146 original size:29 final size:28
Alignment explanation
Indices: 1808058--1808149 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 28
1808048 AGTTAAACAC
* *
1808058 TTTAAATATGGCATGTAACAAT-TTTTT
1 TTTAAACATGGCATGTAACAATATATTT
* ** * *
1808085 TTTCAACATAACGTGTAAC-A-ACATTT
1 TTTAAACATGGCATGTAACAATATATTT
1808111 TTTAAACATGGCATGTAACAATATATTCT
1 TTTAAACATGGCATGTAACAATATATT-T
1808140 TTTAAACATG
1 TTTAAACATG
1808150 TAACTTGGTA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
26 19 0.39
27 15 0.31
28 4 0.08
29 11 0.22
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (28 bp):
TTTAAACATGGCATGTAACAATATATTT
Found at i:1808237 original size:24 final size:24
Alignment explanation
Indices: 1808210--1808256 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1808200 AAACACCTTA
1808210 AACATGGCATGTAACAAAATTTTC
1 AACATGGCATGTAACAAAATTTTC
* *
1808234 AACATGGCGTGTAACAATATTTT
1 AACATGGCATGTAACAAAATTTT
1808257 TTTTTTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (24 bp):
AACATGGCATGTAACAAAATTTTC
Found at i:1810088 original size:22 final size:23
Alignment explanation
Indices: 1810062--1810107 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1810052 TCCATTTTCC
1810062 CTCTTC-ACACCTCTTT-TCTTCT
1 CTCTTCTACA-CTCTTTCTCTTCT
*
1810084 CTCTTCTTCACTCTTTCTCTTCT
1 CTCTTCTACACTCTTTCTCTTCT
1810107 C
1 C
1810108 CTTTTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (23 bp):
CTCTTCTACACTCTTTCTCTTCT
Found at i:1812624 original size:58 final size:58
Alignment explanation
Indices: 1812534--1812794 Score: 319
Period size: 58 Copynumber: 4.5 Consensus size: 58
1812524 TATATGGCAC
* * * ** *
1812534 ATGTAATAGGTAGGCCATAGGCAAGATTAGAAGGTATATGTCCACCCAAGATGGGTGA
1 ATGTAATGGGTAAGCCATATGCGTGATTAGAAGGCATATGTCCACCCAAGATGGGTGA
1812592 ATGTAATGGGTAAGCCATATGCGTGATTAGAAGGCATATGTCCACCCAAGATGGGTGA
1 ATGTAATGGGTAAGCCATATGCGTGATTAGAAGGCATATGTCCACCCAAGATGGGTGA
* * * *
1812650 ACGTAATGGGTAAGCCATATGCGTGATTGGAAGGCATATGTTCACCCAAGATGGGTAA
1 ATGTAATGGGTAAGCCATATGCGTGATTAGAAGGCATATGTCCACCCAAGATGGGTGA
* * * * *
1812708 ATGTATTAGG-CAGCCCATATACATGATT-GAAGGCCATATGTCCACCCAAGATGGGTGA
1 ATGTAATGGGTAAG-CCATATGCGTGATTAGAAGG-CATATGTCCACCCAAGATGGGTGA
* * *
1812766 ATGAAATGGGTTACGCCATATGTGTGATT
1 ATGTAATGGG-TAAGCCATATGCGTGATT
1812795 GTAGGGCATA
Statistics
Matches: 173, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
57 7 0.04
58 154 0.89
59 11 0.06
60 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (58 bp):
ATGTAATGGGTAAGCCATATGCGTGATTAGAAGGCATATGTCCACCCAAGATGGGTGA
Found at i:1812843 original size:116 final size:116
Alignment explanation
Indices: 1812575--1812822 Score: 270
Period size: 116 Copynumber: 2.1 Consensus size: 116
1812565 AGGTATATGT
*** * * * *
1812575 CCACCCAAGATGGGTGAATGTAATGGGTAAG-CCATATGCGTGATTAGAAGGCATATGTCCACCC
1 CCACCCAAGATGGACAAATGTAATAGG-CAGCCCATATACATGATTAGAAGGCATATGTCCACCC
* **
1812639 AAGATGGGTGAACGTAATGGGTAAGCCATATGCGTGATTGGAAGGCATATGT
65 AAGATGGGTGAACGAAATGGGTAAGCCATATGCGTGATTGGAAGGCATATAA
* ** *
1812691 TCACCCAAGATGGGTAAATGTATTAGGCAGCCCATATACATGATT-GAAGGCCATATGTCCACCC
1 CCACCCAAGATGGACAAATGTAATAGGCAGCCCATATACATGATTAGAAGG-CATATGTCCACCC
* * * * *
1812755 AAGATGGGTGAATGAAATGGGTTACGCCATATGTGTGATTGTAGGGCATATAA
65 AAGATGGGTGAACGAAATGGG-TAAGCCATATGCGTGATTGGAAGGCATATAA
1812808 CCA-CCAAGAT-GACAA
1 CCACCCAAGATGGACAA
1812823 CATGACATGG
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
115 10 0.09
116 74 0.67
117 27 0.24
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (116 bp):
CCACCCAAGATGGACAAATGTAATAGGCAGCCCATATACATGATTAGAAGGCATATGTCCACCCA
AGATGGGTGAACGAAATGGGTAAGCCATATGCGTGATTGGAAGGCATATAA
Found at i:1815696 original size:26 final size:26
Alignment explanation
Indices: 1815667--1815718 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1815657 AATTCTCCTA
* *
1815667 GAATGCCCCTAACATTTCTAAGAACT
1 GAATGCCCCTAAAATTTATAAGAACT
1815693 GAATGCCCCTAAAATTTATAAGAACT
1 GAATGCCCCTAAAATTTATAAGAACT
1815719 TCTGCCCTGT
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:0.23, G:0.12, T:0.27
Consensus pattern (26 bp):
GAATGCCCCTAAAATTTATAAGAACT
Found at i:1823537 original size:22 final size:22
Alignment explanation
Indices: 1823486--1823531 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1823476 AATATCAACC
1823486 GTGATAAACTTGGATTTTTGAA
1 GTGATAAACTTGGATTTTTGAA
1823508 GTGATAAACTTGGATTTTTGAA
1 GTGATAAACTTGGATTTTTGAA
1823530 GT
1 GT
1823532 TTTAAAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.41
Consensus pattern (22 bp):
GTGATAAACTTGGATTTTTGAA
Found at i:1824746 original size:3 final size:3
Alignment explanation
Indices: 1824726--1824775 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
1824716 CTCTTTTAAT
* *
1824726 TCA TCA TAA TCA TGCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TAA
1 TCA TCA TCA TCA T-CA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1824772 TCA T
1 TCA T
1824776 GGCTTTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:1827360 original size:14 final size:14
Alignment explanation
Indices: 1827341--1827374 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1827331 TTCATTTATA
1827341 ATTTTGCAATTAAG
1 ATTTTGCAATTAAG
*
1827355 ATTTTGCAATTATG
1 ATTTTGCAATTAAG
1827369 ATTTTG
1 ATTTTG
1827375 GTATTGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (14 bp):
ATTTTGCAATTAAG
Found at i:1828041 original size:34 final size:33
Alignment explanation
Indices: 1827997--1828094 Score: 83
Period size: 34 Copynumber: 2.9 Consensus size: 33
1827987 CACTATGAAA
* * * *
1827997 AATGCTTTTTAATAAGCTCAAGCTA-AACCTTTAC
1 AATGCCTTTTAAGAA-CTCAAGC-ACAACCCTCAC
*
1828031 AATGCCTTTTACCGAACTCAAGCACAACCCTCAC
1 AATGCCTTTTA-AGAACTCAAGCACAACCCTCAC
*
1828065 AATGCCTTTTAAGGGAA-GCAAGCACAACCC
1 AATGCCTTTTAA--GAACTCAAGCACAACCC
1828095 ACACTAACTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
33 1 0.02
34 47 0.89
35 5 0.09
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (33 bp):
AATGCCTTTTAAGAACTCAAGCACAACCCTCAC
Found at i:1847009 original size:34 final size:34
Alignment explanation
Indices: 1846964--1847032 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1846954 CCATGTCACA
1846964 CATCACAGAAGAACATAACATAAATCTATGAAGT
1 CATCACAGAAGAACATAACATAAATCTATGAAGT
*
1846998 CATCACCGAAGAACATAACATAAATCTATGAAGT
1 CATCACAGAAGAACATAACATAAATCTATGAAGT
1847032 C
1 C
1847033 GTGTCACAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (34 bp):
CATCACAGAAGAACATAACATAAATCTATGAAGT
Found at i:1849169 original size:7 final size:8
Alignment explanation
Indices: 1849152--1849177 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1849142 ATTTTTGGCA
1849152 TTTCTTTT
1 TTTCTTTT
1849160 TTTCTTTT
1 TTTCTTTT
1849168 TTTCTTTT
1 TTTCTTTT
1849176 TT
1 TT
1849178 GACCAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTCTTTT
Done.