Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 38
Found at i:6335680 original size:2 final size:2
Alignment explanation
Indices: 6335623--6335660 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6335613 CAATACATTC
6335623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6335661 TGCAAAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6337987 original size:17 final size:17
Alignment explanation
Indices: 6337962--6337998 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6337952 TATGTATTAA
*
6337962 TATACACCTTTAACAAT
1 TATACACCTTTAAAAAT
*
6337979 TATAGACCTTTAAAAAT
1 TATACACCTTTAAAAAT
6337996 TAT
1 TAT
6337999 TCCGTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (17 bp):
TATACACCTTTAAAAAT
Found at i:6340735 original size:2 final size:2
Alignment explanation
Indices: 6340728--6340760 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6340718 TAAACACTTA
6340728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6340761 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6341294 original size:5 final size:5
Alignment explanation
Indices: 6341284--6341333 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
6341274 CTATCTCCAT
*
6341284 CTTTA CTTTA C--TG CTTTA CTTTA CTTTA CTTTA CTTTA -TTT- CTTTA
1 CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA
6341330 CTTT
1 CTTT
6341334 CCCCAACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.05
4 6 0.15
5 31 0.79
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.62
Consensus pattern (5 bp):
CTTTA
Found at i:6341328 original size:18 final size:20
Alignment explanation
Indices: 6341283--6341333 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 20
6341273 GCTATCTCCA
6341283 TCTTTACTTTACTGCTTTACTT
1 TCTTTACTTTAC--CTTTACTT
6341305 TACTTTACTTTA-CTTTA-TT
1 T-CTTTACTTTACCTTTACTT
6341324 TCTTTACTTT
1 TCTTTACTTT
6341334 CCCCAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.32
19 3 0.11
20 5 0.18
22 1 0.04
23 10 0.36
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.63
Consensus pattern (20 bp):
TCTTTACTTTACCTTTACTT
Found at i:6341342 original size:28 final size:28
Alignment explanation
Indices: 6341284--6341349 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
6341274 CTATCTCCAT
***
6341284 CTTTACTTTACTGCTTTACTTTACTTTA
1 CTTTACTTTACTGCTTTACTTTACCCAA
* * *
6341312 CTTTACTTTATTTCTTTACTTTCCCCAA
1 CTTTACTTTACTGCTTTACTTTACCCAA
*
6341340 CTTTTCTTTA
1 CTTTACTTTA
6341350 GTTTACTCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.17, C:0.24, G:0.02, T:0.58
Consensus pattern (28 bp):
CTTTACTTTACTGCTTTACTTTACCCAA
Found at i:6344856 original size:57 final size:57
Alignment explanation
Indices: 6344768--6344880 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
6344758 CGTTTTCCCC
*
6344768 GGTGTCATGGCAGTCCATGCATTTATGCCCTGTGTGCCTACTTTCCGCCTGTGATCT
1 GGTGTCATGGCAGTCCATGCATTTATGCCCTGTGTGCCTACTTCCCGCCTGTGATCT
* *
6344825 GGTGTCATGGCAGTCCATGCATTTCTGCCCTGTGTGCCTGCTTCCCGCCTGTGATC
1 GGTGTCATGGCAGTCCATGCATTTATGCCCTGTGTGCCTACTTCCCGCCTGTGATC
6344881 CCTGCATGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.11, C:0.30, G:0.26, T:0.34
Consensus pattern (57 bp):
GGTGTCATGGCAGTCCATGCATTTATGCCCTGTGTGCCTACTTCCCGCCTGTGATCT
Found at i:6356476 original size:90 final size:89
Alignment explanation
Indices: 6356319--6356495 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
6356309 CCTAACACAC
*
6356319 CCTTTTATAGCCAAGTTACCCTAATCCTATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
6356384 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
*
6356408 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
6356473 ATTTAATTAATTAAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
6356496 TTCAAGATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 33 0.40
90 50 0.60
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:6356525 original size:20 final size:21
Alignment explanation
Indices: 6356457--6356526 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
6356447 TATTATTTCA
*
6356457 AATTAATTAAATC-TATATTT
1 AATTAATTAAAACATATATTT
* * *
6356477 AATTAATTAAAATTAAATATTCA
1 AATTAATTAAAA-CATATATT-T
6356500 AGATT-ATTAAAACATATATTT
1 A-ATTAATTAAAACATATATTT
6356521 AATTAA
1 AATTAA
6356527 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 14 0.37
21 2 0.05
22 11 0.29
23 8 0.21
24 3 0.08
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAACATATATTT
Found at i:6359349 original size:20 final size:20
Alignment explanation
Indices: 6359324--6359369 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6359314 AGAAAAACTC
6359324 TTGTTCGAGCAACAAACACT
1 TTGTTCGAGCAACAAACACT
*
6359344 TTGTTCGAGCAACGAACACT
1 TTGTTCGAGCAACAAACACT
6359364 TTGTTC
1 TTGTTC
6359370 TAGTTAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (20 bp):
TTGTTCGAGCAACAAACACT
Found at i:6373792 original size:17 final size:19
Alignment explanation
Indices: 6373740--6373782 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
6373730 AATAAAAGGG
6373740 TCTAAAATAGTACATGCCC
1 TCTAAAATAGTACATGCCC
6373759 TCTAAAATAGTACATGCCC
1 TCTAAAATAGTACATGCCC
6373778 TCTAA
1 TCTAA
6373783 TCTGACATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (19 bp):
TCTAAAATAGTACATGCCC
Found at i:6374360 original size:22 final size:20
Alignment explanation
Indices: 6374308--6374362 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
6374298 AGAAAGGTAT
*
6374308 GGTATCGATACTTCTTCTTG
1 GGTATCGATACTTCTTCTGG
* *
6374328 AGTTTCGATACTTCTGGTCTGG
1 GGTATCGATACTTCT--TCTGG
6374350 GGTATCGATACTT
1 GGTATCGATACTT
6374363 TCTTGAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 13 0.46
22 15 0.54
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (20 bp):
GGTATCGATACTTCTTCTGG
Found at i:6384020 original size:20 final size:20
Alignment explanation
Indices: 6383997--6384034 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6383987 TCGATATTGG
6383997 CCTCTGGATATCGATACTCA
1 CCTCTGGATATCGATACTCA
* *
6384017 CCTCTGGGTATTGATACT
1 CCTCTGGATATCGATACT
6384035 AATGACTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (20 bp):
CCTCTGGATATCGATACTCA
Found at i:6387626 original size:45 final size:45
Alignment explanation
Indices: 6387544--6387759 Score: 310
Period size: 45 Copynumber: 4.8 Consensus size: 45
6387534 ATACGCCTAT
* *
6387544 GAGCTTATGGAAT-AATGGCAAGTATATTGATAAAATAAGCTTAC
1 GAGCTTATGAAATAAATGGTAAGTATATTGATAAAATAAGCTTAC
* * * * *
6387588 GAGCTTATGGAACAAATAGTAAGCATATTGATAGAATAAGCTTAC
1 GAGCTTATGAAATAAATGGTAAGTATATTGATAAAATAAGCTTAC
*
6387633 GAGCTTATGAAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
1 GAGCTTATGAAATAAATGGTAAGTATATTGATAAAATAAGCTTAC
* *
6387678 GAGCTTATGAAATAAATGGTAAGTATGTTGGTAAAATAAGCTTA-
1 GAGCTTATGAAATAAATGGTAAGTATATTGATAAAATAAGCTTAC
* *
6387722 GAGCTTATGAAATAAATGGTAAGTATGTTGGTAAAATA
1 GAGCTTATGAAATAAATGGTAAGTATATTGATAAAATA
6387760 TTGAATATGC
Statistics
Matches: 159, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 50 0.31
45 109 0.69
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (45 bp):
GAGCTTATGAAATAAATGGTAAGTATATTGATAAAATAAGCTTAC
Found at i:6387714 original size:24 final size:24
Alignment explanation
Indices: 6387687--6387759 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
6387677 CGAGCTTATG
6387687 AAATAAATGGTAAGTATGTTGGTA
1 AAATAAATGGTAAGTATGTTGGTA
* * * *
6387711 AAAT-AA-GCTTAG-A-GCTT-ATG
1 AAATAAATGGTAAGTATG-TTGGTA
6387731 AAATAAATGGTAAGTATGTTGGTA
1 AAATAAATGGTAAGTATGTTGGTA
6387755 AAATA
1 AAATA
6387760 TTGAATATGC
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 6 0.17
21 5 0.14
22 8 0.23
23 5 0.14
24 11 0.31
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.32
Consensus pattern (24 bp):
AAATAAATGGTAAGTATGTTGGTA
Found at i:6410218 original size:30 final size:30
Alignment explanation
Indices: 6410182--6410242 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
6410172 CACTTCAACC
*
6410182 TGTACAACGAACATGAGAGTTCTATCTAAA
1 TGTACAACGAACATGAGAGTTATATCTAAA
6410212 TGTACAACGAACATGAGAGTTATATCTAAA
1 TGTACAACGAACATGAGAGTTATATCTAAA
6410242 T
1 T
6410243 AAGTTTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (30 bp):
TGTACAACGAACATGAGAGTTATATCTAAA
Found at i:6413060 original size:12 final size:12
Alignment explanation
Indices: 6413043--6413068 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6413033 AAGGCCACCA
6413043 AACATTATCTTC
1 AACATTATCTTC
6413055 AACATTATCTTC
1 AACATTATCTTC
6413067 AA
1 AA
6413069 TATACTTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (12 bp):
AACATTATCTTC
Found at i:6417816 original size:24 final size:24
Alignment explanation
Indices: 6417788--6417833 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6417778 ATCATTTTAA
*
6417788 TTACTTATCCATTTCA-TTATATCC
1 TTACTAAT-CATTTCACTTATATCC
*
6417812 TTACTAATCATTTTACTTATAT
1 TTACTAATCATTTCACTTATAT
6417834 ATATTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.52
Consensus pattern (24 bp):
TTACTAATCATTTCACTTATATCC
Found at i:6418293 original size:18 final size:17
Alignment explanation
Indices: 6418274--6418326 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
6418264 ATTTCATTCA
6418274 TTTTCCTAAATCATTTC
1 TTTTCCTAAATCATTTC
*
6418291 ATTTT--T--TTCATTTC
1 -TTTTCCTAAATCATTTC
6418305 TTTTCCTTAAATCATTTC
1 TTTTCC-TAAATCATTTC
6418323 TTTT
1 TTTT
6418327 ATCTTTCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 4 0.14
14 7 0.25
16 2 0.07
18 15 0.54
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTCCTAAATCATTTC
Found at i:6418309 original size:31 final size:31
Alignment explanation
Indices: 6418256--6418326 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
6418246 TCACCCATTC
*
6418256 TTTCTTTGATTTCATTCATTTTCC-TAAATCA
1 TTTCTTT-TTTTCATTCATTTTCCTTAAATCA
6418287 TTTCATTTTTTTCATTTC-TTTTCCTTAAATCA
1 TTTC-TTTTTTTCA-TTCATTTTCCTTAAATCA
6418319 TTTCTTTT
1 TTTCTTTT
6418327 ATCTTTCCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 19 0.53
32 17 0.47
ACGTcount: A:0.18, C:0.18, G:0.01, T:0.62
Consensus pattern (31 bp):
TTTCTTTTTTTCATTCATTTTCCTTAAATCA
Found at i:6422809 original size:54 final size:54
Alignment explanation
Indices: 6422595--6422809 Score: 322
Period size: 54 Copynumber: 4.0 Consensus size: 54
6422585 ACATACTGTC
* * *
6422595 GAAACATTTATTCATCCACATAGGATGAATTCAGTGAAATGCACACTTAGTGTT
1 GAAACAGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCT
* * * *
6422649 GAAACAGTTACTCACCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGTT
1 GAAACAGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCT
* *
6422703 GAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCT
1 GAAACAGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCT
** *
6422757 GAAACAGTTATTCATCCACAGGGGATGAATTCTGTGAAATGCACATTTAGTGC
1 GAAACAGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGC
6422810 CTAATTGGCA
Statistics
Matches: 145, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 145 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (54 bp):
GAAACAGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCT
Found at i:6428557 original size:99 final size:98
Alignment explanation
Indices: 6428381--6428609 Score: 343
Period size: 99 Copynumber: 2.3 Consensus size: 98
6428371 CTTTGGAATT
* * *
6428381 AGCATTCGTGGTGCTGGCA-GAGCGGGGGGAGGTGATGGAGGTTGGAAACTTGTCAAGATAGCTT
1 AGCATTCGTGGTACTGG-AGGAGCAGGGGGAGGCGATGGAGGTTGGAAACTTGTCAAGATAGCTT
6428445 GGAGAGCTAGCATGAAAGCTCCAAACTCTAGAAC
65 GGAGAGCTAGCATGAAAGCTCCAAACTCTAGAAC
*
6428479 ATGCATTCGTGGTACTGGAGGAGCAGGGGGAGGCGGTGGAGGTTGGAAACTTGTCAAGATAGCTT
1 A-GCATTCGTGGTACTGGAGGAGCAGGGGGAGGCGATGGAGGTTGGAAACTTGTCAAGATAGCTT
* *
6428544 TGAGAGCTTGCATGAAAGCTCCAAACTCTAGAAC
65 GGAGAGCTAGCATGAAAGCTCCAAACTCTAGAAC
* * *
6428578 AGTTATTCGTGGTACTAGAGGAGCATGGGGAG
1 AG-CATTCGTGGTACTGGAGGAGCAGGGGGAG
6428610 AGCTTATTAT
Statistics
Matches: 119, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
98 3 0.03
99 116 0.97
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (98 bp):
AGCATTCGTGGTACTGGAGGAGCAGGGGGAGGCGATGGAGGTTGGAAACTTGTCAAGATAGCTTG
GAGAGCTAGCATGAAAGCTCCAAACTCTAGAAC
Found at i:6429456 original size:54 final size:54
Alignment explanation
Indices: 6429413--6429640 Score: 273
Period size: 54 Copynumber: 4.2 Consensus size: 54
6429403 TCATATGGTT
* *
6429413 TGCACACATAGTGTCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGTCGAAACAGTTATTCATCCACATAGGATGAATTCCATGAAA
* * **
6429467 TGCACACTTAGTGTTGAAA-TGATTATTCATCCACATAGGATGAATTCTGTGAAA
1 TGCACACTTAGTGTCGAAACAG-TTATTCATCCACATAGGATGAATTCCATGAAA
* *
6429521 TGAACACTTAGTG-CTGAAACGGTTATTCATCCACAT-GTGATGAATTCCATGAAA
1 TGCACACTTAGTGTC-GAAACAGTTATTCATCCACATAG-GATGAATTCCATGAAA
* * * ***
6429575 TGTACACTTAGTGCCGAAACAATTATTCATCCACATAGGATGAATTTTGTGAAA
1 TGCACACTTAGTGTCGAAACAGTTATTCATCCACATAGGATGAATTCCATGAAA
*
6429629 TGCACATTTAGT
1 TGCACACTTAGT
6429641 ACCTAATTGG
Statistics
Matches: 151, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
53 2 0.01
54 146 0.97
55 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (54 bp):
TGCACACTTAGTGTCGAAACAGTTATTCATCCACATAGGATGAATTCCATGAAA
Found at i:6429640 original size:108 final size:108
Alignment explanation
Indices: 6429428--6429640 Score: 320
Period size: 108 Copynumber: 2.0 Consensus size: 108
6429418 ACATAGTGTC
* ** **
6429428 GAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTTGAAATGATTAT
1 GAAACAGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAACAATTAT
6429493 TCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGCT
66 TCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGCT
* *
6429536 GAAACGGTTATTCATCCACAT-GTGATGAATTCCATGAAATGTACACTTAGTGCCGAAACAATTA
1 GAAACAGTTATTCATCCACATAG-GATGAATTCCATGAAATGCACACTTAGTGCCGAAACAATTA
* * *
6429600 TTCATCCACATAGGATGAATTTTGTGAAATGCACATTTAGT
65 TTCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGT
6429641 ACCTAATTGG
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 93 0.99
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (108 bp):
GAAACAGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAACAATTAT
TCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGCT
Found at i:6430036 original size:19 final size:21
Alignment explanation
Indices: 6429983--6430036 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
6429973 TACCTGTACC
*
6429983 ATGGTATCGATACTACTATTCT
1 ATGGTATCGATACTAC-ATGCT
* *
6430005 ATGGTACCAATAC-A-ATGCT
1 ATGGTATCGATACTACATGCT
6430024 ATGGTATCGATAC
1 ATGGTATCGATAC
6430037 CATTTTTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 15 0.56
21 1 0.04
22 11 0.41
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (21 bp):
ATGGTATCGATACTACATGCT
Found at i:6434650 original size:25 final size:21
Alignment explanation
Indices: 6434606--6434650 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 21
6434596 TTTAACATAA
6434606 AAATTATTTATAAAATATTAT
1 AAATTATTTATAAAATATTAT
6434627 AAATATATTATATCAAAATCATTA
1 AAAT-TATT-TAT-AAAAT-ATTA
6434651 AATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 3 0.15
24 5 0.25
25 4 0.20
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTATTTATAAAATATTAT
Found at i:6435066 original size:26 final size:26
Alignment explanation
Indices: 6435032--6435085 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
6435022 TATTTTTATT
* *
6435032 TTTTAAAATTTTATAAATTTATTTTC
1 TTTTAAAATTTTAAAAATTTATTGTC
6435058 TTTTAAAATTTTAAAAATTTATTGTC
1 TTTTAAAATTTTAAAAATTTATTGTC
6435084 TT
1 TT
6435086 CAAACATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTTAAAATTTTAAAAATTTATTGTC
Found at i:6439096 original size:2 final size:2
Alignment explanation
Indices: 6439089--6439129 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6439079 AAATTATAAA
6439089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6439130 ATTCTCTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6439429 original size:31 final size:31
Alignment explanation
Indices: 6439381--6439456 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
6439371 TTGAAAACAA
*
6439381 TTTGATAAATTTTAATGACTATTTTGT-ATTAG
1 TTTGAT-AAGTTTAATGACTATTTTGTAATT-G
* *
6439413 TTTGATAAGTTTAATGATTATTTTGTAATTT
1 TTTGATAAGTTTAATGACTATTTTGTAATTG
6439444 TTTGATAAGTTTA
1 TTTGATAAGTTTA
6439457 GAGAATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 31 0.77
32 9 0.22
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.55
Consensus pattern (31 bp):
TTTGATAAGTTTAATGACTATTTTGTAATTG
Found at i:6439469 original size:31 final size:31
Alignment explanation
Indices: 6439349--6439471 Score: 90
Period size: 31 Copynumber: 3.9 Consensus size: 31
6439339 TAGTGATAAA
* * **
6439349 TTTTGATAAGTTTAA-GAATCATTTGAAAACA
1 TTTTGATAAGTTTAATGAATAATTTG-TAATT
* * * *
6439380 ATTTGATAAATTTTAATGACTATTTTGT-ATT
1 TTTTGAT-AAGTTTAATGAATAATTTGTAATT
* * *
6439411 AGTTTGATAAGTTTAATGATTATTTTGTAATT
1 -TTTTGATAAGTTTAATGAATAATTTGTAATT
6439443 TTTTGATAAGTTTAGA-GAATAATTTGTAA
1 TTTTGATAAGTTTA-ATGAATAATTTGTAA
6439472 CTTTAAAAAC
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
31 49 0.67
32 17 0.23
33 7 0.10
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (31 bp):
TTTTGATAAGTTTAATGAATAATTTGTAATT
Found at i:6440087 original size:11 final size:13
Alignment explanation
Indices: 6440060--6440087 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6440050 AACGATGTTG
6440060 TATAATTATTTTA
1 TATAATTATTTTA
6440073 TATAATTATTTTA
1 TATAATTATTTTA
6440086 TA
1 TA
6440088 GTATAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATAATTATTTTA
Found at i:6440843 original size:38 final size:37
Alignment explanation
Indices: 6440780--6440909 Score: 179
Period size: 38 Copynumber: 3.5 Consensus size: 37
6440770 ATATTCACAT
* *
6440780 TTTAATTGAATATAAATTCAGAAATAATATATATGTA
1 TTTAATTAAATATAAATTCAGAAATAATATATTTGTA
* * *
6440817 TTTAATCAAATATAAATTTTAAAAATAATATATTTGTA
1 TTTAATTAAATATAAA-TTCAGAAATAATATATTTGTA
*
6440855 TTTTAATTGAATATAAATTCAGAAATAATATATTTGTA
1 -TTTAATTAAATATAAATTCAGAAATAATATATTTGTA
*
6440893 TTTAATTAAATACAAAT
1 TTTAATTAAATATAAAT
6440910 CCTTAAATAA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
37 29 0.36
38 37 0.46
39 14 0.17
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (37 bp):
TTTAATTAAATATAAATTCAGAAATAATATATTTGTA
Found at i:6440918 original size:37 final size:36
Alignment explanation
Indices: 6440780--6440921 Score: 140
Period size: 37 Copynumber: 3.8 Consensus size: 36
6440770 ATATTCACAT
* ** *
6440780 TTTAATTGAATATAAATTCAGAAATAATATATATGTA
1 TTTAATTAAATATAAA-TCTTAAATAATATATTTGTA
* *
6440817 TTTAATCAAATATAAATTTTAAAAATAATATATTTGTA
1 TTTAATTAAATATAAATCTT--AAATAATATATTTGTA
* **
6440855 TTTTAATTGAATATAAATTCAGAAATAATATATTTGTA
1 -TTTAATTAAATATAAA-TCTTAAATAATATATTTGTA
*
6440893 TTTAATTAAATACAAATCCTTAAATAATA
1 TTTAATTAAATATAAAT-CTTAAATAATA
6440922 AAACATTTTC
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
36 2 0.02
37 37 0.44
38 31 0.36
39 14 0.16
40 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (36 bp):
TTTAATTAAATATAAATCTTAAATAATATATTTGTA
Found at i:6442070 original size:16 final size:16
Alignment explanation
Indices: 6442049--6442079 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6442039 TACCAAAAAT
*
6442049 AATTAGTTATAAATTA
1 AATTAGTAATAAATTA
6442065 AATTAGTAATAAATT
1 AATTAGTAATAAATT
6442080 CTTTACTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AATTAGTAATAAATTA
Found at i:6456291 original size:54 final size:55
Alignment explanation
Indices: 6456145--6456303 Score: 239
Period size: 55 Copynumber: 2.9 Consensus size: 55
6456135 ATGTCACAAA
* * * *
6456145 GTGTGCAAAAACTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCATTTT
1 GTGTGC-AAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTAT
* *
6456201 GTGTGCAAAACTAGGAAATTCATACTAAGTGTATGAATTTTTGAATGGGCACTAT
1 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTAT
*
6456256 GTGTGC-GAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGG
1 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGG
6456304 AAATATATGT
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
54 39 0.41
55 49 0.52
56 6 0.06
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (55 bp):
GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTAT
Found at i:6456924 original size:68 final size:68
Alignment explanation
Indices: 6456515--6456906 Score: 597
Period size: 68 Copynumber: 5.8 Consensus size: 68
6456505 AAAGATTAAT
* *
6456515 AGGCCTAACTGTGCATTTTACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6456580 TTG
66 TTG
* * * *
6456583 AGTCCTAATTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6456648 TTG
66 TTG
* * * *
6456651 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTACCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6456716 TTG
66 TTG
* * *
6456719 AGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTACATGAAAGGTTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6456784 TTG
66 TTG
* ** *
6456787 AGGCCTAACTGTGCTTTTGACAGAAATATGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6456852 TTG
66 TTG
* *
6456855 AGG-CTGAACTATGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGGCCT-AACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
6456907 CGGTTCAATA
Statistics
Matches: 293, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 2 0.01
68 291 0.99
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:6457005 original size:81 final size:81
Alignment explanation
Indices: 6456866--6457172 Score: 398
Period size: 81 Copynumber: 3.8 Consensus size: 81
6456856 GGCTGAACTA
* ** *
6456866 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTCAATACAATTGAGTAAACG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTCAATACCGTTGAGTAAAAG
*
6456931 AAAAATGGCCTAGTTG
66 ATAAATGGCCTAGTTG
* * *
6456947 TGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTATATAAATGGTTCAATACCGTTGAGTAAAAG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTCAATACCGTTGAGTAAAAG
6457012 ATAAATGGCCTAGTTG
66 ATAAATGGCCTAGTTG
*** * * *
6457028 TATGTTTGGCAGAAATGTGTCAATTTTGCCAGTTAGATGAATGGTTCAATGCCGTTGAGTAAAAG
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTCAATACCGTTGAGTAAAAG
*
6457093 ATAAATGGCCTAGTTT
66 ATAAATGGCCTAGTTG
* * * * * * * * *
6457109 TGCATTTGGCAGAAAAGTTTCAATCATGCAAGTTAGATGAAAGGTTAAATGCCTTTGGGTAAAA
1 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTCAATACCGTTGAGTAAAA
6457173 TACTAAAGGA
Statistics
Matches: 196, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 196 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (81 bp):
TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTCAATACCGTTGAGTAAAAG
ATAAATGGCCTAGTTG
Found at i:6464187 original size:27 final size:27
Alignment explanation
Indices: 6464151--6464205 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
6464141 TGTTCCATCT
*
6464151 CGTGCTCCAAAAAAT-GTGCCATCAATG
1 CGTGCCCCAAAAAATGGT-CCATCAATG
* *
6464178 CGTGCCCCAACAGATGGTCCATCAATG
1 CGTGCCCCAAAAAATGGTCCATCAATG
6464205 C
1 C
6464206 ACGCTCCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (27 bp):
CGTGCCCCAAAAAATGGTCCATCAATG
Found at i:6469017 original size:9 final size:9
Alignment explanation
Indices: 6469000--6469051 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
6468990 ACTCTTTAAA
6469000 CTTTTTTTT
1 CTTTTTTTT
6469009 -TTCTTTTTT
1 CTT-TTTTTT
*
6469018 CTTTTCTTT
1 CTTTTTTTT
*
6469027 CCTTTTTTT
1 CTTTTTTTT
*
6469036 ATTTTTTTT
1 CTTTTTTTT
*
6469045 ATTTTTT
1 CTTTTTT
6469052 ACTAAACCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 2 0.06
9 32 0.89
10 2 0.06
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.85
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:6469021 original size:18 final size:18
Alignment explanation
Indices: 6469000--6469051 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
6468990 ACTCTTTAAA
6469000 CTTTTTTTTTTCTTTTTT
1 CTTTTTTTTTTCTTTTTT
* *
6469018 C-TTTTCTTTCCTTTTTT
1 CTTTTTTTTTTCTTTTTT
* *
6469035 -TATTTTTTTTATTTTTT
1 CTTTTTTTTTTCTTTTTT
6469052 ACTAAACCGG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.85
Consensus pattern (18 bp):
CTTTTTTTTTTCTTTTTT
Found at i:6469022 original size:12 final size:11
Alignment explanation
Indices: 6469000--6469044 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
6468990 ACTCTTTAAA
6469000 CTTTTTTTTTT
1 CTTTTTTTTTT
6469011 CTTTTTTCTTTT
1 CTTTTTT-TTTT
6469023 CTTTCCTTTTTTT
1 CTTT--TTTTTTT
*
6469036 ATTTTTTTT
1 CTTTTTTTT
6469045 ATTTTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 12 0.40
12 8 0.27
13 7 0.23
14 3 0.10
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:6484070 original size:22 final size:22
Alignment explanation
Indices: 6484040--6484081 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
6484030 TAGAAAAATA
6484040 AAAATAAAT-AATCTAAAAAGG
1 AAAATAAATAAATCTAAAAAGG
*
6484061 AAAATAAAATAAATTTAAAAA
1 AAAAT-AAATAAATCTAAAAA
6484082 TTTAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAATAAATAAATCTAAAAAGG
Found at i:6484961 original size:16 final size:18
Alignment explanation
Indices: 6484931--6484977 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
6484921 ATTATATTAG
* *
6484931 ATATTAAATAATTAGT-T
1 ATATTATATAGTTAGTAT
6484948 -TATTATATAGTTAGTAT
1 ATATTATATAGTTAGTAT
*
6484965 ATACTATATAGTT
1 ATATTATATAGTT
6484978 TACATTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 13 0.52
17 1 0.04
18 11 0.44
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (18 bp):
ATATTATATAGTTAGTAT
Found at i:6507451 original size:22 final size:20
Alignment explanation
Indices: 6507420--6507495 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 20
6507410 CCACAGTTTT
* * *
6507420 AAAGAGAAAGAAAAAGAATA
1 AAAGAAAAAGAAAAAAAAGA
6507440 AGGAAGAAAAAGAAAAAAAAGA
1 A--AAGAAAAAGAAAAAAAAGA
* *
6507462 AAAGAAAAAAGAAAAAACA-T
1 AAAG-AAAAAGAAAAAAAAGA
6507482 AAAGAAAAA-AAAAA
1 AAAGAAAAAGAAAAA
6507496 CCAAAGTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.10
19 5 0.10
20 8 0.17
21 13 0.27
22 17 0.35
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAAAGA
Found at i:6507466 original size:20 final size:19
Alignment explanation
Indices: 6507420--6507495 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 19
6507410 CCACAGTTTT
*
6507420 AAAGAGAAAGAAAAAGAATAA
1 AAAGAAAAAGAAAAA-AA-AA
*
6507441 GGAAGAAAAAGAAAAAAAAGA
1 -AAAGAAAAAGAAAAAAAA-A
* *
6507462 AAAGAAAAAAGAAAAAACAT
1 AAAG-AAAAAGAAAAAAAAA
6507482 AAAGAAAAA-AAAAA
1 AAAGAAAAAGAAAAA
6507496 CCAAAGTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
18 5 0.11
19 5 0.11
20 8 0.17
21 16 0.34
22 13 0.28
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAAAAA
Found at i:6507470 original size:21 final size:20
Alignment explanation
Indices: 6507446--6507495 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
6507436 AATAAGGAAG
6507446 AAAAAGAAAAAAAAGAAAAGA
1 AAAAAGAAAAAAAA-AAAAGA
* *
6507467 AAAAAGAAAAAACATAAAGA
1 AAAAAGAAAAAAAAAAAAGA
6507487 AAAAA-AAAA
1 AAAAAGAAAA
6507496 CCAAAGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 10 0.37
21 13 0.48
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAAAAAAAAGA
Found at i:6508428 original size:43 final size:43
Alignment explanation
Indices: 6508340--6508446 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 43
6508330 CATGTTACTC
* * *
6508340 GATCCTTCACAGAAGTAGTTGGATCAGTGAAAACCTTTCACTT
1 GATCTTTCAAAGAAGGAGTTGGATCAGTGAAAACCTTTCACTT
* * ** **
6508383 GATCTTTCATAGAAGGAGTTGGATTAGTGAAATTCTTTCGTTT
1 GATCTTTCAAAGAAGGAGTTGGATCAGTGAAAACCTTTCACTT
*
6508426 GATTCTTT-AAAAAAGGAGTTG
1 GA-TCTTTCAAAGAAGGAGTTG
6508447 AATCGACATT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 48 0.91
44 5 0.09
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (43 bp):
GATCTTTCAAAGAAGGAGTTGGATCAGTGAAAACCTTTCACTT
Found at i:6510675 original size:20 final size:20
Alignment explanation
Indices: 6510650--6510707 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
6510640 CACATGTTAA
*
6510650 AGAATGCATCGATGCACTGT
1 AGAATGCACCGATGCACTGT
*
6510670 AGAATGTACCGATGCACTGT
1 AGAATGCACCGATGCACTGT
*
6510690 AGAATGTACCGATGCACT
1 AGAATGCACCGATGCACT
6510708 TCAATGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCACCGATGCACTGT
Found at i:6511628 original size:18 final size:18
Alignment explanation
Indices: 6511605--6511649 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
6511595 GTTCTTAAGG
* *
6511605 AGTGGTCCTTTGGGACAC
1 AGTGGTCCTTCGGAACAC
*
6511623 AGTGGTCCTTCGGAACAT
1 AGTGGTCCTTCGGAACAC
6511641 AGTGGTCCT
1 AGTGGTCCT
6511650 ACAGGACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.22, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAC
Found at i:6537673 original size:36 final size:36
Alignment explanation
Indices: 6537624--6537726 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
6537614 GAGCAAATTG
* *
6537624 TTTGTCTCCCTTGAGATAGTTTCTCTT-AAAGAAAAT
1 TTTGTCTCGCTTGAGAAAGTTTCTCTTGAAA-AAAAT
* *
6537660 TTTGTTTCGCTTGAGAAAGTTTCTCTTGAAACAAAT
1 TTTGTCTCGCTTGAGAAAGTTTCTCTTGAAAAAAAT
* *
6537696 TTGGTCTCGCTTGAGACAGTTTCTCTTGAAA
1 TTTGTCTCGCTTGAGAAAGTTTCTCTTGAAA
6537727 CATAAACCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 56 0.95
37 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (36 bp):
TTTGTCTCGCTTGAGAAAGTTTCTCTTGAAAAAAAT
Found at i:6537881 original size:67 final size:68
Alignment explanation
Indices: 6537678--6537862 Score: 241
Period size: 67 Copynumber: 2.8 Consensus size: 68
6537668 GCTTGAGAAA
** * *
6537678 GTTTCTCTTG-AAACAAA-TTTGGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAG
1 GTTTCTCTTGAAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTAAAACATAAACATTTGAG
6537741 ATT
66 ATT
* * * *
6537744 GTTTCGC-TCAAAACAAAGTTTCATCTCGCTTGAGACATTTTCTCTTCAAACATAAACATTTGAG
1 GTTTCTCTTGAAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTAAAACATAAACATTTGAG
6537808 ATT
66 ATT
* ** *
6537811 GTTTCTCTTGAAAAAAAAGTTTTTTCTCGCTTGAGACAGTTTCCCTTAAAAC
1 GTTTCTCTTGAAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTAAAAC
6537863 TCAAATTTTG
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
65 1 0.01
66 13 0.13
67 50 0.50
68 37 0.37
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (68 bp):
GTTTCTCTTGAAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTAAAACATAAACATTTGAG
ATT
Found at i:6537952 original size:146 final size:143
Alignment explanation
Indices: 6537763--6538025 Score: 329
Period size: 146 Copynumber: 1.8 Consensus size: 143
6537753 AAAACAAAGT
* *
6537763 TTCATCTCGCTTGAGACATTTTCTCTTCAAACATAAACATTTGAGATTGTTTCTCTTGAAAAA-A
1 TTCATCTCGCTTGAGACATTTTCTCTTCAAACA-AAACATTTGAAATTGTTTCACTT-AAAAACA
** *
6537827 AAGTTTTTTCTCGCTTGAGACAG-TTTCCCTTAAAAC-TCAAATTTTGAAGTTGTTTTACTTGAG
64 AA-TTTCATCTCGCTTGAG--AGTTTTCCCTTAAAACGT-AAATTTTGAAATTGTTTTACTTGAG
6537890 ATTTTTTTCCTAAAAAAAA
125 ATTTTTTTCCTAAAAAAAA
* *
6537909 TTCATCTTGCTTGAGACAATTTTC-CTTCGAAAC-ACACATTTTGAAATTGTTTCACTTAAAAAC
1 TTCATCTCGCTTGAGAC-ATTTTCTCTTC-AAACAAAACA-TTTGAAATTGTTTCACTTAAAAAC
* *
6537972 AAATTTCATGTCGCTTGAGAGTTTTCCCTTGAAACGTAAATTTTGAAATTGTTT
63 AAATTTCATCTCGCTTGAGAGTTTTCCCTTAAAACGTAAATTTTGAAATTGTTT
6538026 CACTCAAAAC
Statistics
Matches: 102, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
143 2 0.02
144 28 0.27
145 23 0.23
146 39 0.38
147 10 0.10
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (143 bp):
TTCATCTCGCTTGAGACATTTTCTCTTCAAACAAAACATTTGAAATTGTTTCACTTAAAAACAAA
TTTCATCTCGCTTGAGAGTTTTCCCTTAAAACGTAAATTTTGAAATTGTTTTACTTGAGATTTTT
TTCCTAAAAAAAA
Found at i:6537970 original size:65 final size:63
Alignment explanation
Indices: 6537900--6538041 Score: 160
Period size: 65 Copynumber: 2.2 Consensus size: 63
6537890 ATTTTTTTCC
* *
6537900 TAAAAAAAATTCATCTTGCTTGAGACAATTTT-CCTTCGAAACACACATTTTGAAATTGTTTCAC
1 TAAAAAAAATTCATCTCGCTTGAG--AATTTTCCCTT-GAAACACAAATTTTGAAATTGTTTCAC
6537964 T
63 T
* * **
6537965 TAAAAACAAATTTCATGTCGCTTGAGAGTTTTCCCTTGAAACGTAAATTTTGAAATTGTTTCACT
1 TAAAAA-AAA-TTCATCTCGCTTGAGAATTTTCCCTTGAAACACAAATTTTGAAATTGTTTCACT
*
6538030 CAAAACAAAATT
1 TAAAA-AAAATT
6538042 TTATCTCACC
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
64 2 0.03
65 43 0.65
66 8 0.12
67 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (63 bp):
TAAAAAAAATTCATCTCGCTTGAGAATTTTCCCTTGAAACACAAATTTTGAAATTGTTTCACT
Found at i:6546920 original size:19 final size:19
Alignment explanation
Indices: 6546896--6546941 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
6546886 TAGTGAGGAA
6546896 CAAGGCTAGACTTGTTACT
1 CAAGGCTAGACTTGTTACT
6546915 CAAGGCTAGACTTGTTACT
1 CAAGGCTAGACTTGTTACT
6546934 CAAGGCTA
1 CAAGGCTA
6546942 TACTCAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (19 bp):
CAAGGCTAGACTTGTTACT
Found at i:6550898 original size:13 final size:13
Alignment explanation
Indices: 6550880--6550914 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
6550870 GAAGGTTTAA
*
6550880 ATGAATTTGGGGG
1 ATGAATTTGGAGG
6550893 ATGAATTTGGAGG
1 ATGAATTTGGAGG
6550906 ATGAATTTG
1 ATGAATTTG
6550915 ACTTGTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (13 bp):
ATGAATTTGGAGG
Found at i:6551900 original size:17 final size:17
Alignment explanation
Indices: 6551878--6551912 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6551868 TGCCAACACA
6551878 AAGTGAAAAAAATTCTG
1 AAGTGAAAAAAATTCTG
*
6551895 AAGTGAAAAAATTTCTG
1 AAGTGAAAAAAATTCTG
6551912 A
1 A
6551913 TATGATAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (17 bp):
AAGTGAAAAAAATTCTG
Found at i:6555803 original size:21 final size:21
Alignment explanation
Indices: 6555777--6555816 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6555767 TACGAAAGTT
*
6555777 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAATGCATCGATGC
6555798 ACTGTAGCAATGCATCGAT
1 ACTGTAGCAATGCATCGAT
6555817 ACACAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAATGCATCGATGC
Found at i:6555856 original size:12 final size:12
Alignment explanation
Indices: 6555845--6555885 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
6555835 TTTTTCACTG
*
6555845 TTCATGGTACTG
1 TTCATGGTACTA
* *
6555857 CTCATGGTATTA
1 TTCATGGTACTA
6555869 TTCATGGTACTA
1 TTCATGGTACTA
6555881 TTCAT
1 TTCAT
6555886 ACCGTATAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (12 bp):
TTCATGGTACTA
Found at i:6558947 original size:20 final size:21
Alignment explanation
Indices: 6558922--6558960 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6558912 TTTATTATCA
6558922 TTCCTTT-TTATTGATTTTTG
1 TTCCTTTCTTATTGATTTTTG
*
6558942 TTCCTTTCTTCTTGATTTT
1 TTCCTTTCTTATTGATTTT
6558961 CTCTCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (21 bp):
TTCCTTTCTTATTGATTTTTG
Found at i:6561121 original size:15 final size:14
Alignment explanation
Indices: 6561092--6561123 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
6561082 AATGGGCAGT
6561092 AATCCCTGCAAAAA
1 AATCCCTGCAAAAA
*
6561106 AATCCCTGCGAAAA
1 AATCCCTGCAAAAA
6561120 AATC
1 AATC
6561124 TATGTATATA
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:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (14 bp):
AATCCCTGCAAAAA
Found at i:6562169 original size:6 final size:7
Alignment explanation
Indices: 6562148--6562183 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
6562138 TCAAAGAAAA
*
6562148 TCAACGA
1 TCAACGG
6562155 TCAACGG
1 TCAACGG
6562162 TC-ACGG
1 TCAACGG
6562168 TCAACGG
1 TCAACGG
6562175 TCAACGG
1 TCAACGG
6562182 TC
1 TC
6562184 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.17
Consensus pattern (7 bp):
TCAACGG
Found at i:6562173 original size:13 final size:14
Alignment explanation
Indices: 6562148--6562183 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
6562138 TCAAAGAAAA
*
6562148 TCAACGATCAACGG
1 TCAACGGTCAACGG
6562162 TC-ACGGTCAACGG
1 TCAACGGTCAACGG
6562175 TCAACGGTC
1 TCAACGGTC
6562184 GGGTCGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.17
Consensus pattern (14 bp):
TCAACGGTCAACGG
Found at i:6562199 original size:17 final size:17
Alignment explanation
Indices: 6562173--6562207 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6562163 CACGGTCAAC
6562173 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
6562190 GGTCAGCGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
6562207 G
1 G
6562208 TCGAGTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.23, G:0.51, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:6563173 original size:18 final size:16
Alignment explanation
Indices: 6563150--6563190 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
6563140 AAAGTGAATT
6563150 TGAAAGTGTATATATAAG
1 TGAAAGTG--TATATAAG
*
6563168 TGAAAGTGTGTATAAG
1 TGAAAGTGTATATAAG
6563184 TGAAAGT
1 TGAAAGT
6563191 ATGAATGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.64
18 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (16 bp):
TGAAAGTGTATATAAG
Found at i:6569528 original size:16 final size:17
Alignment explanation
Indices: 6569507--6569550 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
6569497 GTTGTTTTGA
6569507 TTCGATTCGGGTTA-CT
1 TTCGATTCGGGTTATCT
** *
6569523 TTCGATTCGAATTATTT
1 TTCGATTCGGGTTATCT
6569540 TTCGATTCGGG
1 TTCGATTCGGG
6569551 CCAAATTCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (17 bp):
TTCGATTCGGGTTATCT
Found at i:6573245 original size:29 final size:29
Alignment explanation
Indices: 6573200--6573283 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
6573190 GACAGTGGCA
*
6573200 ACTAACAACAGTGATAGGTTTTGAAAGCC
1 ACTAACAACAGTAATAGGTTTTGAAAGCC
6573229 ACTAACAACAGTAATAGGTTTTGAAAGCC
1 ACTAACAACAGTAATAGGTTTTGAAAGCC
*
6573258 ACTAACAACAATAATAGGTTTTGAAA
1 ACTAACAACAGTAATAGGTTTTGAAA
6573284 CCCGAATATC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (29 bp):
ACTAACAACAGTAATAGGTTTTGAAAGCC
Found at i:6574084 original size:20 final size:20
Alignment explanation
Indices: 6574055--6574094 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6574045 ATTTAAATGA
*
6574055 TAAACAAACATAAACAAACG
1 TAAACAAACAAAAACAAACG
* *
6574075 TAAACGAACAAAAACGAACG
1 TAAACAAACAAAAACAAACG
6574095 AACATAAACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.20, G:0.10, T:0.07
Consensus pattern (20 bp):
TAAACAAACAAAAACAAACG
Found at i:6574094 original size:14 final size:14
Alignment explanation
Indices: 6574077--6574106 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6574067 AACAAACGTA
6574077 AACGAACAAAAACG
1 AACGAACAAAAACG
*
6574091 AACGAACATAAACG
1 AACGAACAAAAACG
6574105 AA
1 AA
6574107 TAACACAAAC
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:0.63, C:0.20, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACAAAAACG
Found at i:6574417 original size:10 final size:10
Alignment explanation
Indices: 6574372--6574433 Score: 67
Period size: 10 Copynumber: 6.4 Consensus size: 10
6574362 TATTCTGTTA
6574372 GAACATAAAT
1 GAACATAAAT
6574382 GAACGA-AAAT
1 GAAC-ATAAAT
* *
6574392 -AA-ATGAAC
1 GAACATAAAT
*
6574400 GGACATAAAT
1 GAACATAAAT
6574410 GAACATAAAT
1 GAACATAAAT
6574420 GAACATAAAT
1 GAACATAAAT
6574430 GAAC
1 GAAC
6574434 GAACATATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
7 1 0.02
8 2 0.05
9 3 0.07
10 35 0.83
11 1 0.02
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (10 bp):
GAACATAAAT
Found at i:6574437 original size:24 final size:24
Alignment explanation
Indices: 6574372--6574449 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
6574362 TATTCTGTTA
*
6574372 GAACATAAATGAACGAAAATAAAT
1 GAACATAAATGAACGAACATAAAT
** * * *
6574396 GAACGGACATAAATGAACATAAAT
1 GAACATAAATGAACGAACATAAAT
6574420 GAACATAAATGAACGAACATATAAT
1 GAACATAAATGAACGAACATA-AAT
6574445 CGAAC
1 -GAAC
6574450 GTTCACGAAC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 34 0.83
25 3 0.07
26 4 0.10
ACGTcount: A:0.56, C:0.13, G:0.14, T:0.17
Consensus pattern (24 bp):
GAACATAAATGAACGAACATAAAT
Found at i:6574449 original size:16 final size:14
Alignment explanation
Indices: 6574372--6574450 Score: 68
Period size: 14 Copynumber: 5.1 Consensus size: 14
6574362 TATTCTGTTA
6574372 GAACATAAATGAAC
1 GAACATAAATGAAC
*
6574386 GAAAATAAATGAAC
1 GAACATAAATGAAC
*
6574400 GGACATAAATGAAC
1 GAACATAAATGAAC
6574414 ATAAATGAACATAAATGAAC
1 ------GAACATAAATGAAC
6574434 GAACATATAATCGAAC
1 GAACATA-AAT-GAAC
6574450 G
1 G
6574451 TTCACGAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
14 32 0.60
15 3 0.06
16 5 0.09
20 13 0.25
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.16
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:6575973 original size:17 final size:17
Alignment explanation
Indices: 6575951--6575986 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
6575941 ATTAAACTTC
6575951 TTATAA-TTTTATATAAT
1 TTATAAGTTTTATA-AAT
6575968 TTATAAGTTTTATAAAT
1 TTATAAGTTTTATAAAT
6575985 TT
1 TT
6575987 CATAGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATAAGTTTTATAAAT
Found at i:6580954 original size:24 final size:24
Alignment explanation
Indices: 6580925--6580987 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
6580915 CTGTCGAAAC
6580925 TGCCACATAGAATTTGCACCGAAG
1 TGCCACATAGAATTTGCACCGAAG
* * * *
6580949 TGCCACGTAGAATATGTACTGAAG
1 TGCCACATAGAATTTGCACCGAAG
* *
6580973 TGTCACTTAG-ATTTG
1 TGCCACATAGAATTTG
6580988 TCCCGAATGA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (24 bp):
TGCCACATAGAATTTGCACCGAAG
Found at i:6581209 original size:57 final size:57
Alignment explanation
Indices: 6581128--6581237 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
6581118 ATATAAATAG
* * *
6581128 TTCACATAGCATTATACAATTTATCATTT-TCTCACATAGAACATATACTCATAGTAT
1 TTCACATAGCATTATACAAATTATCATTTAT-TCACATAAAACATATAATCATAGTAT
* *
6581185 TTCACATAGCATTATTCAAATTATCATTTATTTACATAAAACATATAATCATA
1 TTCACATAGCATTATACAAATTATCATTTATTCACATAAAACATATAATCATA
6581238 TATGGCGTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 46 0.98
58 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (57 bp):
TTCACATAGCATTATACAAATTATCATTTATTCACATAAAACATATAATCATAGTAT
Found at i:6582866 original size:36 final size:35
Alignment explanation
Indices: 6582734--6582866 Score: 99
Period size: 36 Copynumber: 3.6 Consensus size: 35
6582724 CAAAGGTTTA
*
6582734 TGTTTCAAGAGAAAATGTCTCAAGCGAGACGAAACATT
1 TGTTTCAAGAGAAAA-ATCTCAAGCGAGAC-AAA-ATT
* * * ** *
6582772 TTTTTCGAGAGAAACAATCTTAAATGAGATC-AATTT
1 TGTTTCAAGAGAAA-AATCTCAAGCGAGA-CAAAATT
*
6582808 TGTTTCAAGAG-AATATGCCTCAAGCGAGACAAAATT
1 TGTTTCAAGAGAAAAAT--CTCAAGCGAGACAAAATT
*
6582844 TGTTTCAAAAGAAACAATCTCAA
1 TGTTTCAAGAGAAA-AATCTCAA
6582867 AGGTTTATGT
Statistics
Matches: 72, Mismatches: 16, Indels: 16
0.69 0.15 0.15
Matches are distributed among these distances:
34 2 0.03
35 3 0.04
36 38 0.53
37 4 0.06
38 23 0.32
39 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAGAAAAATCTCAAGCGAGACAAAATT
Found at i:6582944 original size:66 final size:64
Alignment explanation
Indices: 6582803--6582981 Score: 198
Period size: 66 Copynumber: 2.7 Consensus size: 64
6582793 AAATGAGATC
* *
6582803 AATTTTGTTTCAAGAG-AATATGCCTCAAGCGAGACAAAATTTGTTTCAAAAGAAACAATCTCAA
1 AATTTTGTTTCAAGAGAAAT-TGTCTCAAGTGAGACAAAATTTGTTTCAAAAGAAACAATCTCAA
* * * * *
6582867 AGGTTTATGTTTCAAGAGAAATTGTCTCAAGTGAGACGAAATTTTGTTTCAAGAGTAACAATTTC
1 A-ATTT-TGTTTCAAGAGAAATTGTCTCAAGTGAGAC-AAAATTTGTTTCAAAAGAAACAATCTC
6582932 AA
63 AA
* * * *
6582934 AATTTGTGTTTTAAGGGAAAACTATCTCAAGTGAGACAAAATTTGTTT
1 AATTT-TGTTTCAAGAG-AAATTGTCTCAAGTGAGACAAAATTTGTTT
6582982 TTAGGAAAAC
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
64 1 0.01
65 3 0.03
66 46 0.48
67 46 0.48
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (64 bp):
AATTTTGTTTCAAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTCAAAAGAAACAATCTCAA
Found at i:6582962 original size:67 final size:66
Alignment explanation
Indices: 6582804--6582981 Score: 193
Period size: 67 Copynumber: 2.7 Consensus size: 66
6582794 AATGAGATCA
*
6582804 ATTT-TGTTTCAAGAG-AA-TATGCCTCAAGCGAGACAAAATTTGTTTCAAAAGAAACAATCTCA
1 ATTTATGTTTCAAGAGAAACTAT--CTCAAGTGAGACAAAATTTGTTTCAAAAGAAACAATCTCA
6582866 AAG
64 AAG
* * * * * * *
6582869 GTTTATGTTTCAAGAGAAATTGTCTCAAGTGAGACGAAATTTTGTTTCAAGAGTAACAATTTCAA
1 ATTTATGTTTCAAGAGAAACTATCTCAAGTGAGAC-AAAATTTGTTTCAAAAGAAACAATCTCAA
6582934 A-
65 AG
* * *
6582935 ATTTGTGTTTTAAGGGAAAACTATCTCAAGTGAGACAAAATTTGTTT
1 ATTTATGTTTCAAGAG-AAACTATCTCAAGTGAGACAAAATTTGTTT
6582982 TTAGGAAAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
65 3 0.03
66 44 0.47
67 45 0.48
68 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (66 bp):
ATTTATGTTTCAAGAGAAACTATCTCAAGTGAGACAAAATTTGTTTCAAAAGAAACAATCTCAAA
G
Found at i:6582997 original size:36 final size:39
Alignment explanation
Indices: 6582931--6583005 Score: 111
Period size: 36 Copynumber: 2.0 Consensus size: 39
6582921 GTAACAATTT
* *
6582931 CAAAATTTGTGTTTTAAGGGAAAACTATCTCAAGTGAGA
1 CAAAATTTGTGTTTTAAGGGAAAACAATCTCAAATGAGA
6582970 CAAAATTTGT-TTTT-A-GGAAAACAATCTCAAATGAGA
1 CAAAATTTGTGTTTTAAGGGAAAACAATCTCAAATGAGA
6583006 TCAATTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 19 0.56
37 1 0.03
38 4 0.12
39 10 0.29
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (39 bp):
CAAAATTTGTGTTTTAAGGGAAAACAATCTCAAATGAGA
Found at i:6587075 original size:24 final size:24
Alignment explanation
Indices: 6587043--6587121 Score: 124
Period size: 24 Copynumber: 3.3 Consensus size: 24
6587033 TCGGGAAAAA
*
6587043 TCTATGTGGCACTTAGGTGCATAT
1 TCTACGTGGCACTTAGGTGCATAT
6587067 TCTACGTGGCACTTAGGTGCATAT
1 TCTACGTGGCACTTAGGTGCATAT
*
6587091 TCTACGTGGCACTTTGGTGCA-AGT
1 TCTACGTGGCACTTAGGTGCATA-T
6587115 TCTACGT
1 TCTACGT
6587122 TGTAGTGGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 51 0.98
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (24 bp):
TCTACGTGGCACTTAGGTGCATAT
Found at i:6589629 original size:16 final size:17
Alignment explanation
Indices: 6589597--6589629 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6589587 ATAGCAATCC
*
6589597 TACCCAGAAATGCTTTA
1 TACCCAGAAATGATTTA
6589614 TACCCA-AAATGATTTA
1 TACCCAGAAATGATTTA
6589630 CTTCAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (17 bp):
TACCCAGAAATGATTTA
Found at i:6590578 original size:16 final size:18
Alignment explanation
Indices: 6590557--6590591 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
6590547 TTTAAAACAA
6590557 TTTTAAGA-AA-AATTGG
1 TTTTAAGACAAGAATTGG
6590573 TTTTAAGACAAGAATTGG
1 TTTTAAGACAAGAATTGG
6590591 T
1 T
6590592 CTACATTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (18 bp):
TTTTAAGACAAGAATTGG
Found at i:6596193 original size:16 final size:16
Alignment explanation
Indices: 6596172--6596204 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6596162 TAAGCCTTGG
*
6596172 ACACTTATAACTACTT
1 ACACTTACAACTACTT
6596188 ACACTTACAACTACTT
1 ACACTTACAACTACTT
6596204 A
1 A
6596205 GAAATCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
ACACTTACAACTACTT
Found at i:6598416 original size:18 final size:18
Alignment explanation
Indices: 6598393--6598436 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
6598383 CAAGGGTGAT
6598393 ACCATAGATTGGTAGTAG
1 ACCATAGATTGGTAGTAG
6598411 ACCATAGATTGGTAGTAG
1 ACCATAGATTGGTAGTAG
6598429 ACCATAGA
1 ACCATAGA
6598437 CATGACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (18 bp):
ACCATAGATTGGTAGTAG
Found at i:6598830 original size:24 final size:24
Alignment explanation
Indices: 6598786--6598831 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6598776 CAACAAAGAA
*
6598786 ATATAAGTAAAATGATTAGTAAGG
1 ATATAAGTAAAATGATAAGTAAGG
*
6598810 ATATAA-TGAAATGGATAAGTAA
1 ATATAAGTAAAAT-GATAAGTAA
6598832 TTATAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (24 bp):
ATATAAGTAAAATGATAAGTAAGG
Found at i:6603055 original size:12 final size:12
Alignment explanation
Indices: 6603038--6603064 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6603028 TAAAAAAATT
6603038 AAAAATAGAATA
1 AAAAATAGAATA
6603050 AAAAATAGAATA
1 AAAAATAGAATA
6603062 AAA
1 AAA
6603065 CATAAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAATAGAATA
Found at i:6604689 original size:136 final size:136
Alignment explanation
Indices: 6604508--6605143 Score: 864
Period size: 136 Copynumber: 4.7 Consensus size: 136
6604498 CGAAGTGTTG
* * * *
6604508 TGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGATCTTCTTCTCCCTCTTTCGGATGAG
1 TGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAG
* * *
6604573 -TCATTCTCATTATGAACTCTCCATTTGGAATATTAATCCCTCAACCGAGGTATCACTAATTCAA
66 TTC-TTCTCATTATGAACTCTCCATTTGGAATATTAATCCCTCAAGCGAGGCATCACTGATTCAA
*
6604637 AATGTCG
130 AATGTCA
* * * *
6604644 TGAATCGAGTGATAGGTGGAACAAACTCTTCTCATTATGAACTTCTTCTCCTTCGTTT-GGATGA
1 TGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-TTTCGGATGA
* * * ** *
6604708 GTTCTTCTCATTGTGAACTCTCCATTTGGAATGTTAATCCCTCAAGCAAGGTGTCACTGATTCGA
65 GTTCTTCTCATTATGAACTCTCCATTTGGAATATTAATCCCTCAAGCGAGGCATCACTGATTCAA
*
6604773 AATGTCT
130 AATGTCA
* * *
6604780 TGAATCGAGCGATAGGTCAAACAAGCTCTTCTCATTATGAACTTCATCTCCCT-TTATTGGATGA
1 TGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTT-TCGGATGA
* * **
6604844 GTTCTTCTCATTATGAACTCTCTATTTGGAATGTTAATCCCTCAAGCGAGGCGCCACTGATTCAA
65 GTTCTTCTCATTATGAACTCTCCATTTGGAATATTAATCCCTCAAGCGAGGCATCACTGATTCAA
*
6604909 AATGTTA
130 AATGTCA
* * *
6604916 TGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTCAGATGAG
1 TGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAG
* *
6604981 TTATTCTCATTATGAACTCTCCATTTGGAATATTAATCCCTCAAGCGAGGCATCACTGATTCGAA
66 TTCTTCTCATTATGAACTCTCCATTTGGAATATTAATCCCTCAAGCGAGGCATCACTGATTCAAA
*
6605046 ATGCCA
131 ATGTCA
* * * * * * *
6605052 TGAATCAAGTGATATGTTGAACAAGCTCTTATCATTATGAACTTCTTCTCCCTCTATCAGATGAG
1 TGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAG
6605117 TTCTTCTCATTATGAACTCTCCATTTG
66 TTCTTCTCATTATGAACTCTCCATTTG
6605144 AAATTTTGAT
Statistics
Matches: 443, Mismatches: 52, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
134 2 0.00
135 1 0.00
136 434 0.98
137 6 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (136 bp):
TGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAG
TTCTTCTCATTATGAACTCTCCATTTGGAATATTAATCCCTCAAGCGAGGCATCACTGATTCAAA
ATGTCA
Found at i:6608949 original size:19 final size:19
Alignment explanation
Indices: 6608925--6608962 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6608915 ACATACAAGT
**
6608925 ATTTTGCATCTAAAGTCAA
1 ATTTTGCATAGAAAGTCAA
6608944 ATTTTGCATAGAAAGTCAA
1 ATTTTGCATAGAAAGTCAA
6608963 CTTAAACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (19 bp):
ATTTTGCATAGAAAGTCAA
Found at i:6615529 original size:40 final size:40
Alignment explanation
Indices: 6615485--6615603 Score: 220
Period size: 40 Copynumber: 3.0 Consensus size: 40
6615475 CGTAGTGCTA
6615485 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
6615525 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
* *
6615565 ACATAAGGTCGTGCCCACCATATACACCAAAGTGAATTA
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
6615604 TAAACCTGCA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (40 bp):
ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
Found at i:6619337 original size:224 final size:225
Alignment explanation
Indices: 6618963--6619414 Score: 870
Period size: 224 Copynumber: 2.0 Consensus size: 225
6618953 TCCGAAAGCA
6618963 CTTGATTCTCAACTTTTACTTGTGGACATGTCAAACATGTAACAACAAACTTAGTAATGTTTTTT
1 CTTGATTCTCAACTTTTACTTGTGGACATGTCAAACATGTAACAACAAACTTAGTAATG---TTT
6619028 TTTTCATACCTGGCCACCAAAATAACTCTTTACATCCTGATACATTCTGTTCCCACTTGTATGCA
63 TTTTCATACCTGGCCACCAAAATAACTCTTTACATCCTGATACATTCTGTTCCCACTTGTATGCA
6619093 TAGTCAGTAGACTATAATGTGCCTTAGAAAGAAAATATTTCTTCAATTCGTCATTATGAGGAATA
128 TAGTCAGTAGACTATAATGTGCCTTAGAAAGAAAATATTTCTTCAATTCGTCATTATGAGGAATA
6619158 CAAATTCTTCCTCAATAATTTCCATCAAAGTTG
193 CAAATTCTTCCTCAATAATTTCCATCAAAGTTG
6619191 CTTGATTCTCAACTTTTACTTGTGGACATGTCAAACATGTAACAACAAACTTAGTAATG-TTTTT
1 CTTGATTCTCAACTTTTACTTGTGGACATGTCAAACATGTAACAACAAACTTAGTAATGTTTTTT
6619255 TCATACCTGGCCACCAAAATAACTCTTTACATCCTGATACATTCTGTTCCCACTTGTATGCATAG
66 TCATACCTGGCCACCAAAATAACTCTTTACATCCTGATACATTCTGTTCCCACTTGTATGCATAG
6619320 TCAGTAGACTATAATGTGCCTTAGAAAGAAAATATTTCTTCAATTCGTCATTATGAGGAATACAA
131 TCAGTAGACTATAATGTGCCTTAGAAAGAAAATATTTCTTCAATTCGTCATTATGAGGAATACAA
6619385 ATTCTTCCTCAATAATTTCCATCAAAGTTG
196 ATTCTTCCTCAATAATTTCCATCAAAGTTG
6619415 ACTTCAAAGT
Statistics
Matches: 224, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
224 165 0.74
228 59 0.26
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (225 bp):
CTTGATTCTCAACTTTTACTTGTGGACATGTCAAACATGTAACAACAAACTTAGTAATGTTTTTT
TCATACCTGGCCACCAAAATAACTCTTTACATCCTGATACATTCTGTTCCCACTTGTATGCATAG
TCAGTAGACTATAATGTGCCTTAGAAAGAAAATATTTCTTCAATTCGTCATTATGAGGAATACAA
ATTCTTCCTCAATAATTTCCATCAAAGTTG
Found at i:6619503 original size:17 final size:17
Alignment explanation
Indices: 6619478--6619588 Score: 77
Period size: 17 Copynumber: 6.4 Consensus size: 17
6619468 TCATCTCTCA
6619478 TTTCTTTTCTCTTTTTCT
1 TTTC-TTTCTCTTTTTCT
* *
6619496 TTTCTTTCTCGTTTTCA
1 TTTCTTTCTCTTTTTCT
*
6619513 TTT-TTT-TCTTCTTCGT
1 TTTCTTTCTCTTTTTC-T
*
6619529 TTTCTTTTTCTTTTTCTAT
1 TTTCTTTCTCTTTTTC--T
*
6619548 TTTTTTTCTTCTGTTTT-T
1 TTTCTTTC-TCT-TTTTCT
*
6619566 TTTC-TTCTGTTTTTCT
1 TTTCTTTCTCTTTTTCT
6619582 TCTTCTT
1 T-TTCTT
6619589 CTTATAATAT
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
15 10 0.14
16 10 0.14
17 23 0.32
18 16 0.22
19 7 0.10
20 3 0.04
21 4 0.05
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTCTTTCTCTTTTTCT
Found at i:6619545 original size:21 final size:22
Alignment explanation
Indices: 6619487--6619545 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
6619477 ATTTCTTTTC
*
6619487 TCTTTTTCTTTTCTTTCTCGTTT
1 TCTTTTTCTTTT-TCTCTCGTTT
*
6619510 TCATTTTT-TTCTTCT-TCGTTT
1 TC-TTTTTCTTTTTCTCTCGTTT
6619531 TCTTTTTCTTTTTCT
1 TCTTTTTCTTTTTCT
6619546 ATTTTTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.16
21 14 0.45
22 2 0.06
23 5 0.16
24 5 0.16
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (22 bp):
TCTTTTTCTTTTTCTCTCGTTT
Found at i:6619550 original size:7 final size:6
Alignment explanation
Indices: 6619478--6619571 Score: 66
Period size: 6 Copynumber: 15.0 Consensus size: 6
6619468 TCATCTCTCA
* * * *
6619478 TTTCTT TTCTCTT TTTC-T TTTCTT TCTCGTT TTCATTTT TTTCTT CTTCGT
1 TTTCTT TT-TCTT TTTCTT TTTCTT TTTC-TT TT--TCTT TTTCTT TTTCTT
* *
6619529 TTTCTT TTTCTT TTTCTA TTT-TT TTTCTT CTGTTTTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT -T-TTCTT TTTCTT
6619572 CTGTTTTTCT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
5 9 0.13
6 39 0.57
7 11 0.16
8 8 0.12
9 1 0.01
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:6619550 original size:14 final size:14
Alignment explanation
Indices: 6619533--6619587 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
6619523 CTTCGTTTTC
*
6619533 TTTTTCTTT-TTCTA
1 TTTTT-TTTCTTCTG
6619547 TTTTTTTTCTTCTG
1 TTTTTTTTCTTCTG
6619561 TTTTTTTTCTTCTG
1 TTTTTTTTCTTCTG
*
6619575 TTTTTCTTCTTCT
1 TTTTTTTTCTTCT
6619588 TCTTATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 3 0.08
14 35 0.92
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (14 bp):
TTTTTTTTCTTCTG
Found at i:6619554 original size:12 final size:11
Alignment explanation
Indices: 6619513--6619582 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 11
6619503 CTCGTTTTCA
6619513 TTTTTTTCTTCT
1 TTTTTTTCTT-T
**
6619525 TCGTTTTCTTT
1 TTTTTTTCTTT
6619536 TTCTTTTTCTATTT
1 TT-TTTTTC--TTT
*
6619550 TTTTTCTTCTGT
1 TTTTT-TTCTTT
*
6619562 TTTTTTTCTTC
1 TTTTTTTCTTT
*
6619573 TGTTTTTCTT
1 TTTTTTTCTT
6619583 CTTCTTCTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
11 15 0.33
12 20 0.43
13 3 0.07
14 8 0.17
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:6620689 original size:6 final size:6
Alignment explanation
Indices: 6620678--6620702 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6620668 ACACTTGTAT
6620678 CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC C
6620703 TATGGGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:6622406 original size:47 final size:45
Alignment explanation
Indices: 6622336--6622461 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
6622326 TATAAAATCT
*
6622336 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
6622381 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
6622428 CTTGA-CA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTT-ACCATTTATTCCATAAGCTCGTAAGCTTATTT
6622462 GCATGGCTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 36 0.50
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:6622610 original size:40 final size:40
Alignment explanation
Indices: 6622566--6622687 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
6622556 ACCGTAGTGC
6622566 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
6622606 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
6622646 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
6622686 TA
1 TA
6622688 TAAACCAGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:6626022 original size:136 final size:136
Alignment explanation
Indices: 6625778--6626030 Score: 359
Period size: 136 Copynumber: 1.9 Consensus size: 136
6625768 CGAAGTGCCA
* * ** *
6625778 AAATGGAAATTCACAAACTTACTATGAATTCCATGGATGCACATATAGTGTTGAAAGTACATATA
1 AAATGGAAATTCACAAACTCACTATGAATACCATGGATGCACATATAGTGTCAAAAGTACATACA
** *
6625843 GTACTGACATGAAAATGCACCGTTATGTATTAAACAAAATCGATCGATAACTTATACATAGTTGT
66 GTACTGACACCAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACTTATACATAGTTGT
6625908 ATATCG
131 ATATCG
* *
6625914 AAATGGTAATTCACAAACTCATTATGAATACCAT-GATTGCACATCA-AGTGTCAAAAGTACACT
1 AAATGGAAATTCACAAACTCACTATGAATACCATGGA-TGCACAT-ATAGTGTCAAAAGTACA-T
*
6625977 -CAGTACTGATACCAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACT
63 ACAGTACTGACACCAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACT
6626031 ATTATATACA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
135 2 0.02
136 99 0.96
137 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (136 bp):
AAATGGAAATTCACAAACTCACTATGAATACCATGGATGCACATATAGTGTCAAAAGTACATACA
GTACTGACACCAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACTTATACATAGTTGT
ATATCG
Found at i:6626551 original size:20 final size:22
Alignment explanation
Indices: 6626526--6626577 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
6626516 AGGTTGAATA
6626526 GTATCGATACCACT-T-CTATG
1 GTATCGATACCACTATACTATG
**
6626546 GTATCGATACTTCTATACTATG
1 GTATCGATACCACTATACTATG
6626568 GTATCGATAC
1 GTATCGATAC
6626578 TCCCTTCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.43
21 1 0.04
22 15 0.54
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (22 bp):
GTATCGATACCACTATACTATG
Found at i:6636466 original size:77 final size:79
Alignment explanation
Indices: 6636378--6636526 Score: 207
Period size: 77 Copynumber: 1.9 Consensus size: 79
6636368 TTAATAAATT
6636378 TCTTATTTAATTAATTCAAATTAAATAT-ACATT-AAAGACTTATAATCT-AAATTACAATC-TT
1 TCTTATTTAATTAATTCAAATTAAATATCA-ATTAAAAGACTTATAAT-TAAAATTACAATCTTT
6636439 TAATGTTTATTTAAAA
64 TAATGTTTATTTAAAA
* * * * *
6636455 TCTTATTTAATTATTTCGAATTAAATATCAATTAAAAGAGTTTTAATTAAAATTACATTCTTTTA
1 TCTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATTAAAATTACAATCTTTTA
6636520 ATGTTTA
66 ATGTTTA
6636527 CGTACTATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
77 30 0.48
78 22 0.35
79 11 0.17
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (79 bp):
TCTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATTAAAATTACAATCTTTTA
ATGTTTATTTAAAA
Found at i:6638089 original size:20 final size:20
Alignment explanation
Indices: 6638064--6638131 Score: 136
Period size: 20 Copynumber: 3.4 Consensus size: 20
6638054 AATATCGATA
6638064 CCATTTTTACATTCTGGAAT
1 CCATTTTTACATTCTGGAAT
6638084 CCATTTTTACATTCTGGAAT
1 CCATTTTTACATTCTGGAAT
6638104 CCATTTTTACATTCTGGAAT
1 CCATTTTTACATTCTGGAAT
6638124 CCATTTTT
1 CCATTTTT
6638132 CAATAATAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.47
Consensus pattern (20 bp):
CCATTTTTACATTCTGGAAT
Found at i:6643550 original size:29 final size:30
Alignment explanation
Indices: 6643470--6643566 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 30
6643460 ATTTAATCCT
*
6643470 CGTCCT-TATTCTGCATG-GAATTAATTCCC
1 CGTCCTGT-TTCTGCATGAGAATTATTTCCC
* * *
6643499 CATCCTGATTCTACAT-AGAATTATTTCCC
1 CGTCCTGTTTCTGCATGAGAATTATTTCCC
* *
6643528 CGTCCTGTTTCTGCATGAG-ATTATATCTC
1 CGTCCTGTTTCTGCATGAGAATTATTTCCC
*
6643557 CGTCTTGTTT
1 CGTCCTGTTT
6643567 TAGCTTGGGA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
29 53 0.96
30 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (30 bp):
CGTCCTGTTTCTGCATGAGAATTATTTCCC
Found at i:6650305 original size:58 final size:58
Alignment explanation
Indices: 6650213--6650351 Score: 215
Period size: 58 Copynumber: 2.4 Consensus size: 58
6650203 TTTAATCCTT
** *
6650213 GTCTTGTTTCTGTGTGAGATTTAATCCCCATCCTGATTCTACATAAGATTAATTCCCA
1 GTCTTGTTTCTGCATGGGATTTAATCCCCATCCTGATTCTACATAAGATTAATTCCCA
* * * *
6650271 GTCTTGTTTCTGCATGGGATTTAATCCTCGTCCTGATTCTGCATATGATTAATTCCCA
1 GTCTTGTTTCTGCATGGGATTTAATCCCCATCCTGATTCTACATAAGATTAATTCCCA
6650329 GTCTTGTTTCTGCATGGGATTTA
1 GTCTTGTTTCTGCATGGGATTTA
6650352 TCTCTTTCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 74 1.00
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (58 bp):
GTCTTGTTTCTGCATGGGATTTAATCCCCATCCTGATTCTACATAAGATTAATTCCCA
Found at i:6650349 original size:29 final size:28
Alignment explanation
Indices: 6650195--6650376 Score: 116
Period size: 29 Copynumber: 6.3 Consensus size: 28
6650185 TCCTAATTTG
**
6650195 GCATGGGATTTAATCCTTGTCTTGTTTCT
1 GCATGGGA-TTAATCCCAGTCTTGTTTCT
** * * *
6650224 GTGTGAGATTTAATCCCCA-TCCTGATTCT
1 GCATGGGA-TTAAT-CCCAGTCTTGTTTCT
* **
6650253 ACATAAGATTAATTCCCAGTCTTGTTTCT
1 GCATGGGATTAA-TCCCAGTCTTGTTTCT
* *
6650282 GCATGGGATTTAATCCTC-GTCCTGATTCT
1 GCATGGGA-TTAATCC-CAGTCTTGTTTCT
**
6650311 GCATATGATTAATTCCCAGTCTTGTTTCT
1 GCATGGGATTAA-TCCCAGTCTTGTTTCT
* * **
6650340 GCATGGGATTTATCTCTTTCTTGTTTCT
1 GCATGGGATTAATCCCAGTCTTGTTTCT
*
6650368 GCTTGGGAT
1 GCATGGGAT
6650377 CCTCATTTGA
Statistics
Matches: 117, Mismatches: 29, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
28 34 0.29
29 76 0.65
30 7 0.06
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (28 bp):
GCATGGGATTAATCCCAGTCTTGTTTCT
Found at i:6654402 original size:22 final size:22
Alignment explanation
Indices: 6654362--6654418 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
6654352 TTTTCGCCAC
* *
6654362 ATTTAATATTAATGCTATTATT
1 ATTTAATATTAATACTATTAAT
* *
6654384 ATTTAATATTATTATTATTAAT
1 ATTTAATATTAATACTATTAAT
*
6654406 A-TTACTATTAATA
1 ATTTAATATTAATA
6654419 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTAATATTAATACTATTAAT
Found at i:6654404 original size:15 final size:16
Alignment explanation
Indices: 6654377--6654415 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
6654367 ATATTAATGC
6654377 TATTATTATTTAATAT
1 TATTATTATTTAATAT
6654393 TATTATTA-TTAATAT
1 TATTATTATTTAATAT
*
6654408 TACTATTA
1 TATTATTA
6654416 ATATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATTTAATAT
Found at i:6656766 original size:22 final size:22
Alignment explanation
Indices: 6656740--6656797 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
6656730 TTTTTTCATC
6656740 TTATTTAATATTAATT-CTATTA
1 TTATTTAATATT-ATTACTATTA
*
6656762 TTATTTAATATTATTATTATTA
1 TTATTTAATATTATTACTATTA
6656784 TTACTATTAATATT
1 TTA-T-TTAATATT
6656798 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 3 0.09
22 20 0.62
23 1 0.03
24 8 0.25
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTAATATTATTACTATTA
Found at i:6656769 original size:16 final size:16
Alignment explanation
Indices: 6656750--6656799 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
6656740 TTATTTAATA
6656750 TTAATTCTATTATTAT
1 TTAATTCTATTATTAT
6656766 TTAATAT-TATTATTA-
1 TTAAT-TCTATTATTAT
*
6656781 TT-ATTACTATTAATAT
1 TTAATT-CTATTATTAT
6656797 TTA
1 TTA
6656800 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
13 1 0.04
14 2 0.07
15 9 0.32
16 15 0.54
17 1 0.04
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAATTCTATTATTAT
Found at i:6660915 original size:17 final size:17
Alignment explanation
Indices: 6660893--6660927 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6660883 GCATTTGCAC
6660893 TGCTTTAATTTAAGCAT
1 TGCTTTAATTTAAGCAT
6660910 TGCTTTAATTTAAGCAT
1 TGCTTTAATTTAAGCAT
6660927 T
1 T
6660928 TTTACATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TGCTTTAATTTAAGCAT
Found at i:6665736 original size:16 final size:15
Alignment explanation
Indices: 6665711--6665740 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6665701 TAAAATAAAA
6665711 TGCATTGCATTTAAT
1 TGCATTGCATTTAAT
6665726 TGCATTTGCATTTAA
1 TGCA-TTGCATTTAA
6665741 ACACATGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TGCATTGCATTTAAT
Found at i:6666011 original size:37 final size:37
Alignment explanation
Indices: 6665961--6666111 Score: 230
Period size: 37 Copynumber: 4.1 Consensus size: 37
6665951 TATGGAGAAA
* * *
6665961 CAAATCAATCTTAAACCTTCACGGAATAGTAGTGAAG
1 CAAATCAATCCTAAGCCTTCACGGAAGAGTAGTGAAG
* **
6665998 CAAATCAATCTTAAGCCTTCATAGAAGAGTAGTGAAG
1 CAAATCAATCCTAAGCCTTCACGGAAGAGTAGTGAAG
6666035 CAAATCAATCCTAAGCCTTCACGGAAGAGTAGTGAAG
1 CAAATCAATCCTAAGCCTTCACGGAAGAGTAGTGAAG
* *
6666072 CAAATCAATCCTAAGCTTTCACGAAAGAGTAGTGAAG
1 CAAATCAATCCTAAGCCTTCACGGAAGAGTAGTGAAG
6666109 CAA
1 CAA
6666112 GCTATCAGTA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (37 bp):
CAAATCAATCCTAAGCCTTCACGGAAGAGTAGTGAAG
Found at i:6666124 original size:74 final size:74
Alignment explanation
Indices: 6665961--6666128 Score: 214
Period size: 74 Copynumber: 2.3 Consensus size: 74
6665951 TATGGAGAAA
* * * * * *
6665961 CAAATCAATCTTAAACCTTCACGGAATAGTAGTGAAGCAAATCAATCTTAAGCCTTCATAGAAGA
1 CAAAGCAATCCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCCTAAGCCTTCAGAGAAGA
6666026 GTAGTGAAG
66 GTAGTGAAG
* *
6666035 CAAATCAATCCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCCTAAGCTTTCACGA-AAG
1 CAAAGCAATCCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCCTAAGCCTTCA-GAGAAG
6666099 AGTAGTGAAG
65 AGTAGTGAAG
* *
6666109 C-AAGCTATCAGTAAGCCTTC
1 CAAAGCAATC-CTAAGCCTTC
6666129 TGAGCATGAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
73 6 0.07
74 76 0.92
75 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (74 bp):
CAAAGCAATCCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCCTAAGCCTTCAGAGAAGA
GTAGTGAAG
Found at i:6666851 original size:233 final size:233
Alignment explanation
Indices: 6666115--6667168 Score: 1558
Period size: 233 Copynumber: 4.5 Consensus size: 233
6666105 GAAGCAAGCT
* * * * *
6666115 ATCAGTAAG-CCTTCTGAGCATGATGATTAAATCCTTTGGGTCATCTGTCAGACTTTCGAGCAAG
1 ATCAGTAAGTCTTTC-GAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAG
* * * * *
6666179 ATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGTAGGATGTTTCCACATGCCTAT-TAAAA
65 ATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTATCGAAAA
* * * * * *
6666243 TATGAGAAAGGTTTCTCATTCAAATTTGAAAATTGAGATTTTTAAAAAGTAAGAAAGGTTTCTTA
130 -ATGAGAAAGATTTCTCATTAAAATCTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTA
* * *
6666308 CCTAGTAAACTATTTCTAAAATT-TATAAGTCCTTCGGGCC
194 CCTAGTAAAATATTTC-CAAATTATATAAGTCTTTCGGGCC
* * *
6666348 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGCCATCTGTAAGTCTTTCGTGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* * **
6666413 TGATAAGTCATTCGGGACATCCATAAGACCTTCGGGCAGGATAATTTCACATGTCTATCGAAAAA
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTATCGAAAAA
* *
6666478 TGAGAAAGATTTCTCATTAAAATCTGAAAAAATGAAATTGTTGAAATGTAAGAAAGGTTTCTTAC
131 TGAGAAAGATTTCTCATTAAAATCTG-AAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTAC
*
6666543 CTAGTAAAATATTTCGAAATTATATAAGTCCTTT-GGGCC
195 CTAGTAAAATATTTCCAAATTATATAAGT-CTTTCGGGCC
*
6666582 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTATTTCGAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* *
6666647 TGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTAACATGTCTATCGAAAAA
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTATCGAAAAA
6666712 TGAGAAAGATTTCTCATTAAAATCTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACC
131 TGAGAAAGATTTCTCATTAAAATCTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACC
**
6666777 TAGTAAAATATTTCCAAATTATATAAGTCTTTCATGCC
196 TAGTAAAATATTTCCAAATTATATAAGTCTTTCGGGCC
* *
6666815 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGTAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* * *
6666880 TGATAAGTCCTTAGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCACATGTTTATCGAAAAA
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTATCGAAAAA
* * *
6666945 TGAGAAAGATTTCTCATTAAAATCTGAAAATTGAAATTTTTGAAAAGAAAGAAAGGTTTCTTACA
131 TGAGAAAGATTTCTCATTAAAATCTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACC
* * *
6667010 TAGTAAAATATTTTCAAATTATATAAGTCATTCGGGCG
196 TAGTAAAATATTTCCAAATTATATAAGTCTTTCGGGCC
* * * *
6667048 ATCAGTAAGTCTTTCGAGAATGATGTTTAAATCCTTCGGGTCATTTGTAAGTCTTTCAAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* ** *
6667113 TGATAAGTTCTTCGGGCCATTTATAAGACCTTCGGGCAGGATGTTTTCACAGGTCT
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCT
6667169 CTCTATTTCA
Statistics
Matches: 746, Mismatches: 69, Indels: 12
0.90 0.08 0.01
Matches are distributed among these distances:
232 4 0.01
233 526 0.71
234 213 0.29
235 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (233 bp):
ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTATCGAAAAA
TGAGAAAGATTTCTCATTAAAATCTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACC
TAGTAAAATATTTCCAAATTATATAAGTCTTTCGGGCC
Found at i:6666874 original size:20 final size:20
Alignment explanation
Indices: 6666800--6666875 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
6666790 CCAAATTATA
* *
6666800 TAAGTCTTTC-ATGCCATCAG
1 TAAGTCTTTCGA-GTCATCTG
*
6666820 TAAGTCTTTCGAG-CATGATG
1 TAAGTCTTTCGAGTCAT-CTG
* *
6666840 CTTAAATCCTTCGAGTCATCTG
1 --TAAGTCTTTCGAGTCATCTG
6666862 TAAGTCTTTCGAGT
1 TAAGTCTTTCGAGT
6666876 AAGATGATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
19 3 0.07
20 24 0.55
21 1 0.02
22 13 0.30
23 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
TAAGTCTTTCGAGTCATCTG
Found at i:6667706 original size:113 final size:111
Alignment explanation
Indices: 6667165--6667981 Score: 852
Period size: 112 Copynumber: 7.3 Consensus size: 111
6667155 GTTTTCACAG
* *
6667165 GTCTCTCTATTT-CAAGATTTGATATTCCCT-GAGTGACAGCGGAACAAGTCTGCCCCAATTCAA
1 GTCTCTCT-TTTCCAAGATTTGATATTCCCTAGAGTGA-AGTGGAACAAGTCTGCCCCGATTCAA
* * *
6667228 TGGATCAACTGACCCAGATCTGATATTCTATTCAGAATAAGCGGAACAA
64 TGGATCAACT-CCCCAGATCTGATATTCCATTCAGAATAAGCGGAACAT
* * * *
6667277 GT-TCCTCTCTTCCAGGATTTGATATTCCCT-GAGTGATAGCGGAACAAGTCTACCCCGATTCAA
1 GTCT-CTCTTTTCCAAGATTTGATATTCCCTAGAGTGA-AGTGGAACAAGTCTGCCCCGATTCAA
* * *
6667340 TGGATCAACTCACCCAGATCTAATATTCCCTTCAAAATAAGCGGAACAT
64 TGGATCAACTC-CCCAGATCTGATATTCCATTCAGAATAAGCGGAACAT
** * *
6667389 GTCTCTCTCTTT-CAAGATTTGATATTCCCTA-AGTGACAGCAGAACAATTCTCCCCCGATTCAA
1 GTCTCTCT-TTTCCAAGATTTGATATTCCCTAGAGTGA-AGTGGAACAAGTCTGCCCCGATTCAA
* * * *
6667452 T-GATTCAACTCACCCAGATCTGATATTCCCTTTAGAATAAGCAGAACAG
64 TGGA-TCAACTC-CCCAGATCTGATATTCCATTCAGAATAAGCGGAACAT
* * *
6667501 GTCCCTCTCTTCCAAGATTTGATATTCCCT-GAGTGACAGAGGAACAAGTCTGCCCCGATTCAAT
1 GTCTCTCTTTTCCAAGATTTGATATTCCCTAGAGTGA-AGTGGAACAAGTCTGCCCCGATTCAAT
* * *
6667565 GGATCAACTCACCCAAATCTTATATTCCATTTAGAATAAGCGGAACAT
65 GGATCAACTC-CCCAGATCTGATATTCCATTCAGAATAAGCGGAACAT
* * * *
6667613 GTCTCTCTTTTCTAAGATTTGATATTCCCTTCAGAGT-AAATGAAACAAGTCTACCCCGATTCAA
1 GTCTCTCTTTTCCAAGATTTGATATTCCC-T-AGAGTGAAGTGGAACAAGTCTGCCCCGATTCAA
* * * *
6667677 TAGATAAACTCCCCTAGATCTAATATTCCATTCAGAGA-AAGCAGAACAT
64 TGGATCAACTCCCC-AGATCTGATATTCCATTCAGA-ATAAGCGGAACAT
* * * * *
6667726 GTATTTCTTTTCAAAGATTTGATATTCCCTTCAGAGT-AAGTGGAACAAGTATGCCTCGATTCAA
1 GTCTCTCTTTTCCAAGATTTGATATTCCC-T-AGAGTGAAGTGGAACAAGTCTGCCCCGATTCAA
* * * * *
6667790 TGAATCAATTCCCCTATACCTGATATTCCATTCAGATTAAGCGGAACA-
64 TGGATCAACTCCCC-AGATCTGATATTCCATTCAGAATAAGCGGAACAT
**
6667838 GTTCTCTCTTTTCCAAGATTTGATATTCCCTTTAGAGT-AAGTGGAACAAGTCTGCCCTAATTCA
1 G-TCTCTCTTTTCCAAGATTTGATATTCCC--TAGAGTGAAGTGGAACAAGTCTGCCCCGATTCA
* * * *
6667902 ATGGATTAATTCCCTCAGATCTGATATTCCTTTCAGAGTAAGCGGAACA-
63 ATGGATCAACTCCC-CAGATCTGATATTCCATTCAGAATAAGCGGAACAT
**
6667951 GATCTCTCTCCTCCAAGATTTGATATTCCCT
1 G-TCTCTCTTTTCCAAGATTTGATATTCCCT
6667982 TCAGAAAAAG
Statistics
Matches: 607, Mismatches: 79, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
111 8 0.01
112 311 0.51
113 279 0.46
114 5 0.01
115 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (111 bp):
GTCTCTCTTTTCCAAGATTTGATATTCCCTAGAGTGAAGTGGAACAAGTCTGCCCCGATTCAATG
GATCAACTCCCCAGATCTGATATTCCATTCAGAATAAGCGGAACAT
Found at i:6667999 original size:48 final size:48
Alignment explanation
Indices: 6667918--6668025 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
6667908 TAATTCCCTC
* * **
6667918 AGATCTGATATTCCTTTCAGAGTAAGCGGAACAGATCTC-TCTCCTCCA
1 AGATTTGATATTCCCTTCAGAAAAAGCGGAACAGATC-CATCTCCTCCA
* * *
6667966 AGATTTGATATTCCCTTCAGAAAAAGTGTAACAGATCCATCTCCTTCA
1 AGATTTGATATTCCCTTCAGAAAAAGCGGAACAGATCCATCTCCTCCA
6668014 AGATTTGATATT
1 AGATTTGATATT
6668026 ATATTCCATG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAAAAAGCGGAACAGATCCATCTCCTCCA
Found at i:6668293 original size:15 final size:15
Alignment explanation
Indices: 6668273--6668327 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
6668263 TCTCATTAAA
6668273 TATTAAT-TCTATTAT
1 TATTAATAT-TATTAT
6668288 TATTAATATTATTAT
1 TATTAATATTATTAT
* * *
6668303 TATTATTAATATTAC
1 TATTAATATTATTAT
6668318 TATTAATATT
1 TATTAATATT
6668328 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 33 0.97
16 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTAATATTATTAT
Found at i:6668297 original size:6 final size:6
Alignment explanation
Indices: 6668282--6668327 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
6668272 ATATTAATTC
* * * *
6668282 TATTAT TATTAA TATTAT TATTAT TATTAA TATTAC TATTAA TATT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATT
6668328 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (6 bp):
TATTAA
Found at i:6668297 original size:9 final size:9
Alignment explanation
Indices: 6668285--6668316 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
6668275 TTAATTCTAT
6668285 TATTATTAA
1 TATTATTAA
*
6668294 TATTATTAT
1 TATTATTAA
6668303 TATTATTAA
1 TATTATTAA
6668312 TATTA
1 TATTA
6668317 CTATTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:6668305 original size:18 final size:18
Alignment explanation
Indices: 6668281--6668327 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
6668271 AATATTAATT
6668281 CTATTATTATTAATATTA
1 CTATTATTATTAATATTA
*
6668299 TTATTATTATTAATATTA
1 CTATTATTATTAATATTA
*
6668317 CTATTAATATT
1 CTATTATTATT
6668328 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
CTATTATTATTAATATTA
Done.