Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 6 of 187
Found at i:2148654 original size:2 final size:2
Alignment explanation
Indices: 2148647--2148676 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2148637 CAATTCTTTA
2148647 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
2148677 GAAATTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2149392 original size:31 final size:30
Alignment explanation
Indices: 2149357--2149435 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
2149347 AAAAGAAGAC
* *
2149357 TAATTTACTCTTTGATTTAG-CGTATATGAAT
1 TAATTTACTC-ATGATTT-GTCGAATATGAAT
* * *
2149388 TAATTTGCTCATGATTTGTCGAATGTGGAT
1 TAATTTACTCATGATTTGTCGAATATGAAT
*
2149418 TAATTTACTCCTGATTTG
1 TAATTTACTCATGATTTG
2149436 AGTAGAAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.75
31 9 0.22
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.47
Consensus pattern (30 bp):
TAATTTACTCATGATTTGTCGAATATGAAT
Found at i:2154123 original size:15 final size:16
Alignment explanation
Indices: 2154091--2154123 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2154081 TGCTGCTGTT
*
2154091 AGTTGCCATTCAAATG
1 AGTTGCCAATCAAATG
2154107 AGTTGCCAATC-AATG
1 AGTTGCCAATCAAATG
2154122 AG
1 AG
2154124 CTGTGTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (16 bp):
AGTTGCCAATCAAATG
Found at i:2156647 original size:30 final size:28
Alignment explanation
Indices: 2156609--2156668 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
2156599 ATTAGACCTG
*
2156609 AATTTTGAAATCTGAAAAGTAGAGG-ATTA
1 AATTTTGAAA-ATG-AAAGTAGAGGCATTA
2156638 AATTCTTGAAAATGAAAGTAGAGGCATTA
1 AATT-TTGAAAATGAAAGTAGAGGCATTA
2156667 AA
1 AA
2156669 CTCCAAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.36
29 12 0.43
30 6 0.21
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (28 bp):
AATTTTGAAAATGAAAGTAGAGGCATTA
Found at i:2166885 original size:16 final size:16
Alignment explanation
Indices: 2166864--2166898 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2166854 GTTGAGTTAA
2166864 TAAGTTAGTCGAGTAT
1 TAAGTTAGTCGAGTAT
2166880 TAAGTTAGTCGAGTAT
1 TAAGTTAGTCGAGTAT
2166896 TAA
1 TAA
2166899 TTTAATTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (16 bp):
TAAGTTAGTCGAGTAT
Found at i:2167838 original size:26 final size:27
Alignment explanation
Indices: 2167800--2167860 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
2167790 GGCCCGGCCC
* *
2167800 ATTTT-AAAAT-AAACATTAAAAAATT
1 ATTTTAAAAATAAAAAAATAAAAAATT
*
2167825 GTTTTAAAAATAAAAAAATAAAAAATT
1 ATTTTAAAAATAAAAAAATAAAAAATT
2167852 ATTTTAAAA
1 ATTTTAAAA
2167861 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.13
26 5 0.17
27 21 0.70
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
ATTTTAAAAATAAAAAAATAAAAAATT
Found at i:2168536 original size:6 final size:7
Alignment explanation
Indices: 2168503--2168534 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2168493 TAGAGAATCA
2168503 TTTTTAT
1 TTTTTAT
2168510 TTTTTAT
1 TTTTTAT
2168517 TTTTTAT
1 TTTTTAT
2168524 TTTTTAT
1 TTTTTAT
2168531 TTTT
1 TTTT
2168535 ATAAAGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:2172004 original size:60 final size:60
Alignment explanation
Indices: 2171893--2172007 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
2171883 ATAAAATATA
* * * * ** *
2171893 ATTTAGTTTTTGAACTTGACAATTTTTCTTAGCTTGGTCCCTAAACCTTTTTTAATTCAC
1 ATTTAGTTTCTGAACTTAACAACTTTTCTTAACTTAATCCCAAAACCTTTTTTAATTCAC
* **
2171953 ATTTAGTTTCTGAACTTAACAACTTTTCTTAATTTAATCCCAAAATTTTTTTTAA
1 ATTTAGTTTCTGAACTTAACAACTTTTCTTAACTTAATCCCAAAACCTTTTTTAA
2172008 ACCACAATAG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.49
Consensus pattern (60 bp):
ATTTAGTTTCTGAACTTAACAACTTTTCTTAACTTAATCCCAAAACCTTTTTTAATTCAC
Found at i:2175477 original size:2 final size:2
Alignment explanation
Indices: 2175462--2175511 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
2175452 GATTAATACA
2175462 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2175502 AT AT AT AT AT
1 AT AT AT AT AT
2175512 GACAAATAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2176803 original size:300 final size:300
Alignment explanation
Indices: 2176247--2176829 Score: 760
Period size: 300 Copynumber: 1.9 Consensus size: 300
2176237 CAATTTACTG
* * * * *** *
2176247 AGATAATAAATTGTGTATATTAAAACAAAATTGTATAAGTTATATTAAAATGAAGTTTTTGTTGA
1 AGATAATAAATTGTGTATATTAAAACAAAAATGTATAAGATATATGAAAATAAAACCTTGGTTGA
* ** * ** *
2176312 GTGGTAAATTTAATGTTTTAGTAATCCAATTGGTGCGGGTTCGAATTCCACCATATGCATATTTT
66 ATAATAAATTTAAGGTTTTAGTAATCCAATTGGCACGGGTTCAAATTCCACCATATGCATATTTT
* * * *
2176377 TATTGATTTTTGTTTAAATAAAAGACTAAAATACCCTAAAATAATTTAACTTTTTTTAATTACAA
131 AATTGATTTTTGTTAAAATAAAAGACTAAAATACCCTAAAATAATATAAATTTTTTTAATTACAA
* * *
2176442 AAGGATATTTTCATAATTTCTCAACCGAGTTGGTGATCCGGTTGAAGGTGACACCAACTCAGTTA
196 AAGGACATTTTCATAATTTCTCAACCGAGTTAGTGACCCGGTTGAAGGTGACACCAACTCAGTTA
2176507 GAAGCTTAATAAAATAGTATAGATATATAAACAACTAATGT
261 GAAGCTTAAT-AAATAGTATAGATATATAAACAACTAATGT
*
2176548 AGATAATAAATTGTGTATATTAAAACAAAAATGTATAAGATATATGAAAATAAAACCTTGGTTTA
1 AGATAATAAATTGTGTATATTAAAACAAAAATGTATAAGATATATGAAAATAAAACCTTGGTTGA
* * * *
2176613 ATAATAAATTTAAGGTTTTAGTAATTCAATTGGCATGGGTTTAAA-TCTTA-C-TATGCATATTT
66 ATAATAAATTTAAGGTTTTAGTAATCCAATTGGCACGGGTTCAAATTC-CACCATATGCATATTT
* ** *
2176675 TAATTGATTTTTGTTAAAATGAAAGGACTAAAATACCCTCGAATAATATAAATTTTTTTAATTAT
130 TAATTGATTTTTGTTAAAAT-AAAAGACTAAAATACCCTAAAATAATATAAATTTTTTTAATTAC
** ** *
2176740 GGATTGACATTTTCATAATTTC-CTAATCGAGTTAGTGACCCGGTTGAAGGTGACACCAACTCAG
194 AAAAGGACATTTTCATAATTTCTC-AACCGAGTTAGTGACCCGGTTGAAGGTGACACCAACTCAG
**
2176804 TTAGGGGCTTAATAAATAGTATAGAT
258 TTAGAAGCTTAATAAATAGTATAGAT
2176830 GCATATAATC
Statistics
Matches: 241, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
299 43 0.18
300 106 0.44
301 92 0.38
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (300 bp):
AGATAATAAATTGTGTATATTAAAACAAAAATGTATAAGATATATGAAAATAAAACCTTGGTTGA
ATAATAAATTTAAGGTTTTAGTAATCCAATTGGCACGGGTTCAAATTCCACCATATGCATATTTT
AATTGATTTTTGTTAAAATAAAAGACTAAAATACCCTAAAATAATATAAATTTTTTTAATTACAA
AAGGACATTTTCATAATTTCTCAACCGAGTTAGTGACCCGGTTGAAGGTGACACCAACTCAGTTA
GAAGCTTAATAAATAGTATAGATATATAAACAACTAATGT
Found at i:2179062 original size:5 final size:6
Alignment explanation
Indices: 2179040--2179073 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2179030 AAAAGTATTT
*
2179040 TAAAAT TAAAAA TAAAAA TAAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAAA T-AAAAA TAAAAA TAA
2179074 TATATTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
TAAAAA
Found at i:2179063 original size:13 final size:13
Alignment explanation
Indices: 2179041--2179073 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2179031 AAAGTATTTT
*
2179041 AAAATTAAAAATA
1 AAAATAAAAAATA
2179054 AAAATAAAAAATA
1 AAAATAAAAAATA
2179067 AAAATAA
1 AAAATAA
2179074 TATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:2179674 original size:13 final size:14
Alignment explanation
Indices: 2179647--2179676 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2179637 TTTGTTTCAC
2179647 TAAAAAATAACTTT
1 TAAAAAATAACTTT
2179661 TAAAAAATAA-TTT
1 TAAAAAATAACTTT
2179674 TAA
1 TAA
2179677 TGAAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAAAATAACTTT
Found at i:2179724 original size:26 final size:26
Alignment explanation
Indices: 2179695--2179775 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
2179685 TGTCAAACCA
2179695 TAAATAATATTTTAAACTAAATTATT
1 TAAATAATATTTTAAACTAAATTATT
* *
2179721 T--A-AATA--TTAAAGCATCACATT-TA
1 TAAATAATATTTTAAA-C-T-AAATTATT
*
2179744 TAAATAATATTTTATACTAAATTATT
1 TAAATAATATTTTAAACTAAATTATT
2179770 TAAATA
1 TAAATA
2179776 TTAAAGCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 18
0.64 0.08 0.28
Matches are distributed among these distances:
21 5 0.12
22 1 0.02
23 7 0.17
24 5 0.12
25 5 0.12
26 13 0.32
27 1 0.02
28 4 0.10
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (26 bp):
TAAATAATATTTTAAACTAAATTATT
Found at i:2179728 original size:23 final size:23
Alignment explanation
Indices: 2179700--2179777 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
2179690 AACCATAAAT
2179700 AATATTTTAAACTAAATTATTTA
1 AATATTTTAAACTAAATTATTTA
* **
2179723 AATA--TTAAAGCATCACATTTATAAA
1 AATATTTTAAA-C-T-A-AATTATTTA
*
2179748 TAATATTTTATACTAAATTATTTA
1 -AATATTTTAAACTAAATTATTTA
2179772 AATATT
1 AATATT
2179778 AAAGCATCAC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
21 5 0.12
22 1 0.02
23 11 0.27
24 7 0.17
25 7 0.17
26 5 0.12
27 1 0.02
28 4 0.10
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.45
Consensus pattern (23 bp):
AATATTTTAAACTAAATTATTTA
Found at i:2179749 original size:49 final size:49
Alignment explanation
Indices: 2179694--2179791 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
2179684 TTGTCAAACC
2179694 ATAAATAATATTTTAAACTAAATTATTTAAATATTAAAGCATCACATTT
1 ATAAATAATATTTTAAACTAAATTATTTAAATATTAAAGCATCACATTT
*
2179743 ATAAATAATATTTTATACTAAATTATTTAAATATTAAAGCATCACATTT
1 ATAAATAATATTTTAAACTAAATTATTTAAATATTAAAGCATCACATTT
2179792 TTTCTAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (49 bp):
ATAAATAATATTTTAAACTAAATTATTTAAATATTAAAGCATCACATTT
Found at i:2193494 original size:20 final size:20
Alignment explanation
Indices: 2193448--2193495 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2193438 AATTTAACGA
*
2193448 TTAAATTAATTTATAATTTT
1 TTAAATTTATTTATAATTTT
* *
2193468 TTGAATTTATTT-TTATTTT
1 TTAAATTTATTTATAATTTT
2193487 TATAAATTT
1 T-TAAATTT
2193496 TAATTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTAAATTTATTTATAATTTT
Found at i:2194063 original size:2 final size:2
Alignment explanation
Indices: 2194056--2194104 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
2194046 CCTAAAAATC
2194056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2194096 -T AT -T AT AT A
1 AT AT AT AT AT A
2194105 GTGNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2196484 original size:22 final size:20
Alignment explanation
Indices: 2196457--2196498 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2196447 CCGGCCCGAT
2196457 TTTTAATAAACACAAAAAAATA
1 TTTTAA-AAACA-AAAAAAATA
*
2196479 TTTTAAAAATAAAAAAAATA
1 TTTTAAAAACAAAAAAAATA
2196499 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
TTTTAAAAACAAAAAAAATA
Found at i:2198148 original size:11 final size:11
Alignment explanation
Indices: 2198080--2198214 Score: 60
Period size: 10 Copynumber: 12.7 Consensus size: 11
2198070 TAAGTGATTT
2198080 TTTAAATAATTA
1 TTTAAA-AATTA
2198092 -TTAAAGAATTA
1 TTTAAA-AATTA
**
2198103 TTTAAATTTTA
1 TTTAAAAATTA
*
2198114 TTT-AAAATTT
1 TTTAAAAATTA
2198124 TTTGATAGAAATTA
1 TTT-A-A-AAATTA
2198138 TTTAAAAATTA
1 TTTAAAAATTA
*
2198149 -TTATTAAA-T-
1 TTTA-AAAATTA
2198158 TTTAAAAAGTTA
1 TTTAAAAA-TTA
2198170 -TT-AAAATTA
1 TTTAAAAATTA
**
2198179 TTTTTAAA--A
1 TTTAAAAATTA
*
2198188 -TGAAAAA-TA
1 TTTAAAAATTA
2198197 TTTAAAAATTA
1 TTTAAAAATTA
2198208 -TTAAAAA
1 TTTAAAAA
2198215 CCACGCTTGG
Statistics
Matches: 94, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
8 4 0.04
9 8 0.09
10 33 0.35
11 33 0.35
12 6 0.06
13 2 0.02
14 8 0.09
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (11 bp):
TTTAAAAATTA
Found at i:2200920 original size:46 final size:46
Alignment explanation
Indices: 2200853--2201296 Score: 709
Period size: 46 Copynumber: 9.6 Consensus size: 46
2200843 TTTGAGTACT
2200853 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
2200899 TCTGATCAAGTGACAAAGTGATAAGTTGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
2200945 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
2200991 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
2201037 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
2201082 TCTGATCAAGTGACAAAATGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
2201128 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-TCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
2201173 TTTGATCAAGTGACAAAGTGATAAGTGGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAC------A-AAGT-GATAAGTGGTAGCTTTAGCTACACTTA
*
2201227 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
2201272 TCTGA-CCAGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
2201297 ATCATACGTA
Statistics
Matches: 375, Mismatches: 13, Indels: 23
0.91 0.03 0.06
Matches are distributed among these distances:
43 12 0.03
44 6 0.02
45 86 0.23
46 223 0.59
47 4 0.01
48 1 0.00
51 1 0.00
52 4 0.01
53 12 0.03
54 26 0.07
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:2201248 original size:54 final size:53
Alignment explanation
Indices: 2201143--2201254 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 53
2201133 TCAAGTGAAA
*
2201143 AAGT-GATAAGTGGTAGTCTAGCTACACTTATTTGATCAAGTGACAAAGTGAT
1 AAGTGGATAAGTGGTAGTCTAGCTACACTTATCTGATCAAGTGACAAAGTGAT
*
2201195 AAGTGGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGAT
1 AAGTGGATAAGTGGTAG-TCTAGCTACACTTATCTGATCAAGTGACAAAGTGAT
2201249 AAGTGG
1 AAGTGG
2201255 TAGCCTAGCT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
52 4 0.07
53 12 0.21
54 40 0.71
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (53 bp):
AAGTGGATAAGTGGTAGTCTAGCTACACTTATCTGATCAAGTGACAAAGTGAT
Found at i:2205052 original size:13 final size:13
Alignment explanation
Indices: 2205034--2205060 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2205024 ATTTAGTATT
2205034 TATATAATAAATA
1 TATATAATAAATA
2205047 TATATAATAAATA
1 TATATAATAAATA
2205060 T
1 T
2205061 TTAGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATAATAAATA
Found at i:2215088 original size:9 final size:10
Alignment explanation
Indices: 2215073--2215097 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2215063 CCATTTACAA
2215073 AAAAAAAAAG
1 AAAAAAAAAG
2215083 AAAAAAAAAG
1 AAAAAAAAAG
2215093 AAAAA
1 AAAAA
2215098 TATATTAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2215446 original size:25 final size:24
Alignment explanation
Indices: 2215401--2215448 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2215391 AAAAATACTT
*
2215401 TTTAGAGAAAATGCTTTTGAAAAG
1 TTTAGAGAAAATGCTTGTGAAAAG
2215425 TTTAGAAGAAAAGTG-TTGTGAAAA
1 TTTAG-AGAAAA-TGCTTGTGAAAA
2215449 AATGTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 14 0.67
26 2 0.10
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.31
Consensus pattern (24 bp):
TTTAGAGAAAATGCTTGTGAAAAG
Found at i:2215702 original size:15 final size:15
Alignment explanation
Indices: 2215684--2215742 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
2215674 TAAATATAAT
2215684 AATAATTTATATTTA
1 AATAATTTATATTTA
* *
2215699 AATAATCTA-ATATA
1 AATAATTTATATTTA
*
2215713 ATGATAAATTATATTTA
1 A--ATAATTTATATTTA
2215730 AATAATTTGATAT
1 AATAATTT-ATAT
2215743 AATGATACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 5 0.15
15 14 0.41
16 10 0.29
17 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (15 bp):
AATAATTTATATTTA
Found at i:2215746 original size:31 final size:31
Alignment explanation
Indices: 2215655--2215749 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
2215645 TTAATGAAAC
* *
2215655 ATAAATTAT-TTTAAA-AACTTAAATATAATA
1 ATAAATTATATTTAAATAA-TTTAATATAATG
* *
2215685 ATAATTTATATTTAAATAATCTAATATAATG
1 ATAAATTATATTTAAATAATTTAATATAATG
*
2215716 ATAAATTATATTTAAATAATTTGATATAATG
1 ATAAATTATATTTAAATAATTTAATATAATG
2215747 ATA
1 ATA
2215750 CATAAAATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
30 8 0.14
31 46 0.82
32 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (31 bp):
ATAAATTATATTTAAATAATTTAATATAATG
Found at i:2215763 original size:31 final size:31
Alignment explanation
Indices: 2215697--2215770 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
2215687 AATTTATATT
* * *
2215697 TAAATAATCTAATATAATGATAAATTATATT
1 TAAATAATCTAATATAATGATAAATAAAATA
* * *
2215728 TAAATAATTTGATATAATGATACATAAAATA
1 TAAATAATCTAATATAATGATAAATAAAATA
2215759 TAAATTAATCTA
1 TAAA-TAATCTA
2215771 TGTAACAGCC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 29 0.85
32 5 0.15
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (31 bp):
TAAATAATCTAATATAATGATAAATAAAATA
Found at i:2216976 original size:23 final size:23
Alignment explanation
Indices: 2216932--2217000 Score: 57
Period size: 24 Copynumber: 3.0 Consensus size: 23
2216922 CACACCATAA
* * * *
2216932 CTCACAAGAGCGTCCCGTTATAG
1 CTCACATGAGCATCCTGATATAG
2216955 CTCACATGAGCATCCTGATATAAG
1 CTCACATGAGCATCCTGATAT-AG
* * * *
2216979 CTCTCTTGAGCTTTCTGATATA
1 CTCACATGAGCATCCTGATATA
2217001 TGGCTCTCCC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (23 bp):
CTCACATGAGCATCCTGATATAG
Found at i:2217206 original size:24 final size:24
Alignment explanation
Indices: 2217178--2217223 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2217168 GAGTAACCTG
2217178 TTAAGCTCGCATGAGCTTTCTAAT
1 TTAAGCTCGCATGAGCTTTCTAAT
**
2217202 TTAAGCTCTTATGAGCTTTCTA
1 TTAAGCTCGCATGAGCTTTCTA
2217224 TCATTAAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (24 bp):
TTAAGCTCGCATGAGCTTTCTAAT
Found at i:2217240 original size:25 final size:24
Alignment explanation
Indices: 2217178--2217244 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2217168 GAGTAACCTG
**
2217178 TTAAGCTCGCATGAGCTTTCTAAT
1 TTAAGCTCTAATGAGCTTTCTAAT
*
2217202 TTAAGCTCTTATGAGCTTTCT-AT
1 TTAAGCTCTAATGAGCTTTCTAAT
2217225 CATTAAGC-CTGAATGAGCTT
1 --TTAAGCTCT-AATGAGCTT
2217245 CCCGTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 2 0.05
24 21 0.57
25 14 0.38
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (24 bp):
TTAAGCTCTAATGAGCTTTCTAAT
Found at i:2223244 original size:17 final size:18
Alignment explanation
Indices: 2223222--2223255 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2223212 TCAACGTCAA
*
2223222 CCATCT-CTACATCTTCT
1 CCATCTCCTAAATCTTCT
2223239 CCATCTCCTAAATCTTC
1 CCATCTCCTAAATCTTC
2223256 GTCTTCGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (18 bp):
CCATCTCCTAAATCTTCT
Found at i:2231712 original size:21 final size:21
Alignment explanation
Indices: 2231688--2231727 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2231678 ATTTTTTTCC
*
2231688 ATTTTTAAATATATTTTTATA
1 ATTTTTAAATATATATTTATA
*
2231709 ATTTTTAATTATATATTTA
1 ATTTTTAAATATATATTTA
2231728 ATATAAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAAATATATATTTATA
Found at i:2241257 original size:30 final size:31
Alignment explanation
Indices: 2241203--2241262 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2241193 TCCTCTCAAA
* **
2241203 TTTTTAAAAATTCTCATTGTACTTT-TTAAT
1 TTTTTAAAAATTCTAATTAAACTTTCTTAAT
*
2241233 TTTTTAAAAATTTTAATTAAACTTTCTTAA
1 TTTTTAAAAATTCTAATTAAACTTTCTTAA
2241263 AATCTTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTTTAAAAATTCTAATTAAACTTTCTTAAT
Found at i:2243678 original size:3 final size:3
Alignment explanation
Indices: 2243670--2243713 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2243660 AACAATAACA
* *
2243670 ACC ACC ACC ACC ACC ACC ATC ACC ACC ATC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
2243714 AACAACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.61, G:0.00, T:0.05
Consensus pattern (3 bp):
ACC
Found at i:2246377 original size:22 final size:22
Alignment explanation
Indices: 2246343--2246385 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2246333 TATTCAAATA
2246343 ATAATAACAAAAT-AGTAGCAAT
1 ATAATAACAAAATGA-TAGCAAT
* *
2246365 ATAATAGCGAAATGATAGCAA
1 ATAATAACAAAATGATAGCAA
2246386 AACAGCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATGATAGCAAT
Found at i:2254793 original size:13 final size:13
Alignment explanation
Indices: 2254775--2254799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2254765 ATTATATTAA
2254775 TAAATTTTTAAAC
1 TAAATTTTTAAAC
2254788 TAAATTTTTAAA
1 TAAATTTTTAAA
2254800 TATTTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTTTAAAC
Found at i:2254819 original size:21 final size:22
Alignment explanation
Indices: 2254768--2254823 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
2254758 AAATATTATT
*
2254768 ATATTAATAAAT-TTTTAAACTA
1 ATATTATTAAATATTTTAAAC-A
*
2254790 A-ATTTTTAAATATTTTAAA-A
1 ATATTATTAAATATTTTAAACA
2254810 ATATTATTAAATAT
1 ATATTATTAAATAT
2254824 AATAATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 19 0.66
22 8 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTATTAAATATTTTAAACA
Found at i:2255206 original size:17 final size:18
Alignment explanation
Indices: 2255180--2255221 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2255170 ATTAAATCTA
* *
2255180 TATAAGATATTA-GTTAT
1 TATAAAATATTATCTTAT
2255197 TATAAAATATTATCTTAT
1 TATAAAATATTATCTTAT
2255215 TATAAAA
1 TATAAAA
2255222 CAAATTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (18 bp):
TATAAAATATTATCTTAT
Found at i:2268206 original size:33 final size:33
Alignment explanation
Indices: 2268169--2268231 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2268159 AGGTCTTAAC
*
2268169 TACATGTAAAATAAATTTACTTTTGATCGTAAT
1 TACATGTAAAATAAATTCACTTTTGATCGTAAT
* *
2268202 TACATGTAAAATGAATTCGCTTTTGATCGT
1 TACATGTAAAATAAATTCACTTTTGATCGT
2268232 TGTGTCTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (33 bp):
TACATGTAAAATAAATTCACTTTTGATCGTAAT
Found at i:2269760 original size:68 final size:68
Alignment explanation
Indices: 2269680--2269815 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
2269670 ACATGGCCCG
2269680 GCCTTGCCCCTTTATAATATTATATAACATAAAAATAAAATCTATAATAATCTATAATATTATAA
1 GCCTTGCCCCTTTATAATATTATATAACATAAAAATAAAATCTATAATAATCTATAATATTATAA
2269745 ATT
66 ATT
2269748 GCCTTGCCCCTTTATAATATTATATAACATAAAAATAAAATCTATAATAATCTATAATATTATAA
1 GCCTTGCCCCTTTATAATATTATATAACATAAAAATAAAATCTATAATAATCTATAATATTATAA
2269813 ATT
66 ATT
2269816 AAATATTATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (68 bp):
GCCTTGCCCCTTTATAATATTATATAACATAAAAATAAAATCTATAATAATCTATAATATTATAA
ATT
Found at i:2277735 original size:15 final size:15
Alignment explanation
Indices: 2277715--2277769 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
2277705 AAATTTTTCC
2277715 CAAAAATAAAGATAA
1 CAAAAATAAAGATAA
*
2277730 CAAAAATAAAAATAA
1 CAAAAATAAAGATAA
**
2277745 -ACCAATCAAA-ATAA
1 CAAAAAT-AAAGATAA
2277759 CAAAAATAAAG
1 CAAAAATAAAG
2277770 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.13
Consensus pattern (15 bp):
CAAAAATAAAGATAA
Found at i:2281549 original size:22 final size:22
Alignment explanation
Indices: 2281504--2281549 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2281494 TGTTTTGTCC
* * *
2281504 TTATTTTGCTACAATTTTACTA
1 TTATGTTGCTACAATTTGAATA
*
2281526 TTATGTTGCTACTATTTGAATA
1 TTATGTTGCTACAATTTGAATA
2281548 TT
1 TT
2281550 GTATAAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (22 bp):
TTATGTTGCTACAATTTGAATA
Found at i:2281616 original size:30 final size:31
Alignment explanation
Indices: 2281567--2281630 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
2281557 ACTTATTTTA
*
2281567 TTGTTAATTTTTTTTATTATTTTAAAGACAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
* *
2281598 TTGTTAA-TTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
2281628 TTG
1 TTG
2281631 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGACAT
Found at i:2291772 original size:32 final size:31
Alignment explanation
Indices: 2291736--2291806 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
2291726 AAAAAATCAT
* *
2291736 TTTAACTCTTTTTCAAAAGATTGATG-ATTAAA
1 TTTAACTCTTTGT-AAAAGATTGA-GAATCAAA
* *
2291768 TTTAATTCTTTGTAAAAGGTTGAGAATCAAA
1 TTTAACTCTTTGTAAAAGATTGAGAATCAAA
2291799 TTTAACTC
1 TTTAACTC
2291807 AAAAACAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 1 0.03
31 21 0.64
32 11 0.33
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (31 bp):
TTTAACTCTTTGTAAAAGATTGAGAATCAAA
Found at i:2292288 original size:2 final size:2
Alignment explanation
Indices: 2292283--2292321 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2292273 CTGCCACATA
2292283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2292322 CTGAACTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2292711 original size:29 final size:29
Alignment explanation
Indices: 2292654--2292717 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2292644 TTGTGTATTC
* **
2292654 AGAATTTAGTCATTATATTTTTATTTTTA
1 AGAATTTAGTCATTATATTTTCAAATTTA
*
2292683 AGAATTTAGTCATTTTATTTTCAAATTTA
1 AGAATTTAGTCATTATATTTTCAAATTTA
*
2292712 AAAATT
1 AGAATT
2292718 CAACTTCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (29 bp):
AGAATTTAGTCATTATATTTTCAAATTTA
Found at i:2296747 original size:25 final size:25
Alignment explanation
Indices: 2296676--2296757 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 25
2296666 CGGGCTATAT
2296676 AAGAGCCA-TAATCAGGAAGCT-CA
1 AAGAGCCATTAATCAGGAAGCTCCA
* * * * *
2296699 TACGAGCTAATAA-CGGGTAGCTCCA
1 -AAGAGCCATTAATCAGGAAGCTCCA
*
2296724 AAGAGCCATTAATCAGGAAGCTCCG
1 AAGAGCCATTAATCAGGAAGCTCCA
*
2296749 AATAGCCAT
1 AAGAGCCAT
2296758 ATATTGGGAA
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
24 22 0.50
25 22 0.50
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (25 bp):
AAGAGCCATTAATCAGGAAGCTCCA
Found at i:2296917 original size:25 final size:25
Alignment explanation
Indices: 2296885--2296974 Score: 153
Period size: 25 Copynumber: 3.6 Consensus size: 25
2296875 TCCGAAAAGC
2296885 TATAACGGGAAGCTCGCAAGAACCA
1 TATAACGGGAAGCTCGCAAGAACCA
2296910 TATAACGGGAAGCTCGCAAGAACCA
1 TATAACGGGAAGCTCGCAAGAACCA
* *
2296935 TATAACGGGAAGCTCGTAATAACCA
1 TATAACGGGAAGCTCGCAAGAACCA
*
2296960 TATAACGGAAAGCTC
1 TATAACGGGAAGCTC
2296975 ATAAGAGCTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (25 bp):
TATAACGGGAAGCTCGCAAGAACCA
Found at i:2298895 original size:5 final size:5
Alignment explanation
Indices: 2298888--2298917 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2298878 TTTTCTTTAT
*
2298888 TTCTT TTCTC TTCTC TTCTC TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC
2298918 ACGTTACTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
TTCTC
Found at i:2301928 original size:38 final size:38
Alignment explanation
Indices: 2301875--2301959 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
2301865 AATTTGTTTC
*
2301875 AATTATTTTTATTTTATTTTATCATTATATCAT-TCTTTA
1 AATT-TTTTTATTTTATTTTAACATTATATCATCT-TTTA
*
2301914 AATTTTTTTATTTTATTTTAACATTATATTATCTTTTA
1 AATTTTTTTATTTTATTTTAACATTATATCATCTTTTA
*
2301952 AATATTTT
1 AATTTTTT
2301960 ACGTTTAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 37 0.88
39 5 0.12
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (38 bp):
AATTTTTTTATTTTATTTTAACATTATATCATCTTTTA
Found at i:2302151 original size:16 final size:15
Alignment explanation
Indices: 2302111--2302154 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2302101 ATAAATTCAG
2302111 TACTTAATTTTTTAA
1 TACTTAATTTTTTAA
2302126 T-CTTTAATTTTTTAAA
1 TAC-TTAATTTTTT-AA
*
2302142 TACTTGATTTTTT
1 TACTTAATTTTTT
2302155 TTCACATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.44
16 12 0.48
17 1 0.04
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (15 bp):
TACTTAATTTTTTAA
Found at i:2302415 original size:31 final size:31
Alignment explanation
Indices: 2302351--2302415 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2302341 GTACATGTAC
* * *
2302351 TTTAATTTTATCAATTTTAGTCTTTGTAATT
1 TTTAAGTTTATCAATTTTAGTCTCTATAATT
* *
2302382 TTTAAGTTTGTCAATTTTAGTCTCTATACTT
1 TTTAAGTTTATCAATTTTAGTCTCTATAATT
2302413 TTT
1 TTT
2302416 TTAATTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.60
Consensus pattern (31 bp):
TTTAAGTTTATCAATTTTAGTCTCTATAATT
Found at i:2311322 original size:31 final size:33
Alignment explanation
Indices: 2311262--2311333 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 33
2311252 TTAATATGTG
2311262 AAAAATA-TATAAAATTATTAAATATTAA-TTT
1 AAAAATATTATAAAATTATTAAATATTAATTTT
2311293 AAAAATATTATAAATATT-TTACAA-A-TAATTTT
1 AAAAATATTATAAA-ATTATTA-AATATTAATTTT
2311325 AAATAATAT
1 AAA-AATAT
2311334 CTACAGCCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
31 10 0.28
32 16 0.44
33 10 0.28
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
AAAAATATTATAAAATTATTAAATATTAATTTT
Found at i:2311329 original size:21 final size:20
Alignment explanation
Indices: 2311290--2311329 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2311280 TAAATATTAA
2311290 TTTAAAAATATTATAAATAT
1 TTTAAAAATATTATAAATAT
* *
2311310 TTTACAAATAATTTTAAATA
1 TTTAAAAAT-ATTATAAATA
2311330 ATATCTACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAAATATTATAAATAT
Found at i:2314820 original size:30 final size:30
Alignment explanation
Indices: 2314757--2314824 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2314747 GATGTAATAG
2314757 GTGACTGATTTCTCACTTTTAGATAAGTTA
1 GTGACTGATTTCTCACTTTTAGATAAGTTA
* * * *
2314787 GTGATTGATTTCTTATTTTTTGA-AAGTTGA
1 GTGACTGATTTCTCACTTTTAGATAAGTT-A
2314817 GTGACTGA
1 GTGACTGA
2314825 ATTTAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.46
Consensus pattern (30 bp):
GTGACTGATTTCTCACTTTTAGATAAGTTA
Found at i:2315191 original size:41 final size:41
Alignment explanation
Indices: 2315146--2315224 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
2315136 TTAAAGTGAT
*
2315146 ATTTTCAAAAGTATTTTGATGTTATAAGCCAATTTTTTAAA
1 ATTTTCAAAAGTATTATGATGTTATAAGCCAATTTTTTAAA
*
2315187 ATTTTCAAAAGTATTATGATGTTATAAGCCTATTTTTT
1 ATTTTCAAAAGTATTATGATGTTATAAGCCAATTTTTT
2315225 TAACTCACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (41 bp):
ATTTTCAAAAGTATTATGATGTTATAAGCCAATTTTTTAAA
Found at i:2316303 original size:49 final size:49
Alignment explanation
Indices: 2316231--2316356 Score: 143
Period size: 49 Copynumber: 2.6 Consensus size: 49
2316221 GTGGCATGAA
*
2316231 ACTTGAACCCGTTATCGTATAACCACTGTCAACTAGGG-G-CCTGAGTTAT
1 ACTTGAACCCGTTATCGTATAACCACCGTCAACT-GGGAGCCCT-AGTTAT
* *
2316280 ACTTGAATCCGTTA-CTGTATAACCACCGTTAACTGGGAGCCCTAGTTAT
1 ACTTGAACCCGTTATC-GTATAACCACCGTCAACTGGGAGCCCTAGTTAT
* * *
2316329 ACTTCAACCCATGATCGTAT-ACCACCGT
1 ACTTGAACCCGTTATCGTATAACCACCGT
2316357 GAATTGAGAG
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
48 12 0.18
49 50 0.76
50 4 0.06
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (49 bp):
ACTTGAACCCGTTATCGTATAACCACCGTCAACTGGGAGCCCTAGTTAT
Found at i:2323392 original size:17 final size:19
Alignment explanation
Indices: 2323365--2323401 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2323355 AAATTATAAG
2323365 TAATATTTTTGGG-TTAAA
1 TAATATTTTTGGGTTTAAA
2323383 TAAT-TTTTTGGGTTTAAA
1 TAATATTTTTGGGTTTAAA
2323401 T
1 T
2323402 TTAACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (19 bp):
TAATATTTTTGGGTTTAAA
Found at i:2325769 original size:30 final size:30
Alignment explanation
Indices: 2325735--2325800 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
2325725 AAATAATTTT
2325735 TAATATGATGATATAAAGTAAAAATTAAAA
1 TAATATGATGATATAAAGTAAAAATTAAAA
2325765 TAATATGATGATATAAAGTAAAAATTAAAA
1 TAATATGATGATATAAAGTAAAAATTAAAA
2325795 TAATAT
1 TAATAT
2325801 TCAAATTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (30 bp):
TAATATGATGATATAAAGTAAAAATTAAAA
Found at i:2326593 original size:16 final size:18
Alignment explanation
Indices: 2326567--2326602 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2326557 TTATGAATTT
2326567 TTTTAAAAATAT-TTTTA
1 TTTTAAAAATATCTTTTA
2326584 TTTT-AAAATATCTTTTA
1 TTTTAAAAATATCTTTTA
2326601 TT
1 TT
2326603 AATATGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAAAATATCTTTTA
Found at i:2344774 original size:93 final size:92
Alignment explanation
Indices: 2344613--2344834 Score: 243
Period size: 93 Copynumber: 2.4 Consensus size: 92
2344603 TATTTGGGGT
* * * * * *
2344613 CTGAACTTGGCAACTTTTCCCGCATTGGTGCTTAAACTTTTTTCTTTGTTCAAGTTAGACCTTGA
1 CTGAACTTGGCAACTATTCCCACATTGGTGCTTAAACCTTTTTCTTTGTCCAAGTTAGACCCTAA
*
2344678 ACTTGGGCAA-TTGTTCTCACATT-AGAGC
66 ACTT-GGCAATTTG-TCCCACATTGAGA-C
* * * *
2344706 CTGAACTAGACAACTATTCCCACATTGAG-GCTTGAACCTTTTTCTTTGTCCAAGTTAGTCCCTA
1 CTGAACTTGGCAACTATTCCCACATTG-GTGCTTAAACCTTTTTCTTTGTCCAAGTTAGACCCTA
* *
2344770 AACTTGGCAATTTGTCCCATATTGGGAC
65 AACTTGGCAATTTGTCCCACATTGAGAC
* * *
2344798 CTGAACTTGGCAATTATTCCCACATTGGGGCCTAAAC
1 CTGAACTTGGCAACTATTCCCACATTGGTGCTTAAAC
2344835 TCTAGGGTTT
Statistics
Matches: 107, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
91 1 0.01
92 43 0.40
93 62 0.58
94 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (92 bp):
CTGAACTTGGCAACTATTCCCACATTGGTGCTTAAACCTTTTTCTTTGTCCAAGTTAGACCCTAA
ACTTGGCAATTTGTCCCACATTGAGAC
Found at i:2344807 original size:31 final size:31
Alignment explanation
Indices: 2344766--2344835 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
2344756 CAAGTTAGTC
*
2344766 CCTAAACTTGGCAATT-TGTCCCATATTGGGA
1 CCTAAACTTGGCAATTAT-TCCCACATTGGGA
* *
2344797 CCTGAACTTGGCAATTATTCCCACATTGGGG
1 CCTAAACTTGGCAATTATTCCCACATTGGGA
2344828 CCTAAACT
1 CCTAAACT
2344836 CTAGGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (31 bp):
CCTAAACTTGGCAATTATTCCCACATTGGGA
Found at i:2351352 original size:13 final size:13
Alignment explanation
Indices: 2351330--2351359 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2351320 AAACTTAAAG
*
2351330 TAGGTGATCAAAA
1 TAGGTAATCAAAA
2351343 TAGGTAATCAAAA
1 TAGGTAATCAAAA
2351356 TAGG
1 TAGG
2351360 AACGCGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (13 bp):
TAGGTAATCAAAA
Found at i:2354393 original size:136 final size:135
Alignment explanation
Indices: 2354149--2354420 Score: 499
Period size: 136 Copynumber: 2.0 Consensus size: 135
2354139 TTTGTTAAAT
*
2354149 CACAATGCATTTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATCAGTGGCCTGTCTTAC
1 CACAATGCATTTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATCAGTGGCCTGTCTAAC
*
2354214 AGCAAAGGAACGTCCAAAGTTTCTGAACCATTAATGGTAGCCAAAATATTTACATATCTAGTGTT
66 AGCAAAGGAACGTCCAAAGTTTCTGAACCATTAATGGTAGCC-AAATATTTACATATCTAGTGAT
2354279 GGCATA
130 GGCATA
2354285 CACAATGCATTTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATCAGTGGCCTGTCTAAC
1 CACAATGCATTTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATCAGTGGCCTGTCTAAC
*
2354350 AGCAAAGGAACGTCTAAAGTTTCTGAACCATTAATGGTAGCCAAATATTTACATATCTAGTGATG
66 AGCAAAGGAACGTCCAAAGTTTCTGAACCATTAATGGTAGCCAAATATTTACATATCTAGTGATG
*
2354415 GTATA
131 GCATA
2354420 C
1 C
2354421 TATGCGATGG
Statistics
Matches: 132, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
135 27 0.20
136 105 0.80
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (135 bp):
CACAATGCATTTCTTCTGTAATCCACTGTTAAATTACTATGATTTGTATCAGTGGCCTGTCTAAC
AGCAAAGGAACGTCCAAAGTTTCTGAACCATTAATGGTAGCCAAATATTTACATATCTAGTGATG
GCATA
Found at i:2361937 original size:23 final size:23
Alignment explanation
Indices: 2361910--2361962 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2361900 AGTATCAGTG
*
2361910 TTATATATAATTAT-ATTGGTTTA
1 TTATATATAATTATAATT-ATTTA
* *
2361933 TTATATATCATTTTAATTATTTA
1 TTATATATAATTATAATTATTTA
2361956 TTATATA
1 TTATATA
2361963 CCCATCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATATATAATTATAATTATTTA
Found at i:2367668 original size:21 final size:21
Alignment explanation
Indices: 2367644--2367716 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
2367634 AAAAAACGTA
2367644 AATTAAAATGGAAAGAAAGAT
1 AATTAAAATGGAAAGAAAGAT
* * *
2367665 AATTTAAAT-GAAATGAAAAAA
1 AATTAAAATGGAAA-GAAAGAT
*
2367686 AATTAAACTGGAAAGAAAGAT
1 AATTAAAATGGAAAGAAAGAT
*
2367707 AATTTAAATG
1 AATTAAAATG
2367717 AAATAAGAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.10
21 33 0.80
22 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.23
Consensus pattern (21 bp):
AATTAAAATGGAAAGAAAGAT
Found at i:2367763 original size:49 final size:48
Alignment explanation
Indices: 2367628--2367956 Score: 393
Period size: 49 Copynumber: 6.9 Consensus size: 48
2367618 GAGAAAAATT
* **
2367628 AATATGAAAAAACGTAAATTAAAATGGAAAGAAAGATAATTTAAATGA
1 AATAAGAAAAAAATTAAATTAAAATGGAAAGAAAGATAATTTAAATGA
*
2367676 AAT--G--AAAAA--AAATTAAACTGGAAAGAAAGATAATTTAAATGA
1 AATAAGAAAAAAATTAAATTAAAATGGAAAGAAAGATAATTTAAATGA
*
2367718 AATAAGAAAAAAATTAAATTAAAATGGAAAAAAAAGATAATTTAAATGA
1 AATAAGAAAAAAATTAAATTAAAATGG-AAAGAAAGATAATTTAAATGA
* *
2367767 AATAAGAAAAAAATTAAATTAAAATGGGAAGATAGATAATTTAAATGA
1 AATAAGAAAAAAATTAAATTAAAATGGAAAGAAAGATAATTTAAATGA
* * * *
2367815 AATAAGAAACAAATTAAATTAAAATGGGAAGATAGATAATTTAAATTA
1 AATAAGAAAAAAATTAAATTAAAATGGAAAGAAAGATAATTTAAATGA
* * * * *
2367863 AATGAGGAAAGAAATTAAATTTAAATGGGAAGATAGATAATTTAAATGA
1 AAT-AAGAAAAAAATTAAATTAAAATGGAAAGAAAGATAATTTAAATGA
* * * *
2367912 AAT-GGGAAAAAATTAAATTTAAATGGAAAAAAAAGGATAATTTAA
1 AATAAGAAAAAAATTAAATTAAAATGG-AAAGAAA-GATAATTTAA
2367957 GTAAAATGGA
Statistics
Matches: 253, Mismatches: 18, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
42 35 0.14
44 5 0.02
46 6 0.02
47 21 0.08
48 85 0.34
49 101 0.40
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.24
Consensus pattern (48 bp):
AATAAGAAAAAAATTAAATTAAAATGGAAAGAAAGATAATTTAAATGA
Found at i:2367821 original size:97 final size:95
Alignment explanation
Indices: 2367628--2367956 Score: 409
Period size: 97 Copynumber: 3.5 Consensus size: 95
2367618 GAGAAAAATT
* ** *
2367628 AATATGAAAAAACGTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAAT-G--AAAAA--AAA
1 AATAAGAAAAAAATTAAATTAAAATGGAAAAAAAGATAATTTAAATGAAATAGAAAAAAATTAAA
* * *
2367688 TTAAACTGGAAAGAAAGATAATTTAAATGA
66 TTAAAATGGGAAGATAGATAATTTAAATGA
2367718 AATAAGAAAAAAATTAAATTAAAATGGAAAAAAAAGATAATTTAAATGAAATAAGAAAAAAATTA
1 AATAAGAAAAAAATTAAATTAAAATGG-AAAAAAAGATAATTTAAATGAAAT-AGAAAAAAATTA
2367783 AATTAAAATGGGAAGATAGATAATTTAAATGA
64 AATTAAAATGGGAAGATAGATAATTTAAATGA
* * * * * *
2367815 AATAAGAAACAAATTAAATTAAAATGGGAAGATAGATAATTTAAATTAAATGAGGAAAGAAATTA
1 AATAAGAAAAAAATTAAATTAAAATGGAAAAAAAGATAATTTAAATGAAAT-A-GAAAAAAATTA
*
2367880 AATTTAAATGGGAAGATAGATAATTTAAATGA
64 AATTAAAATGGGAAGATAGATAATTTAAATGA
* * *
2367912 AAT-GGGAAAAAATTAAATTTAAATGGAAAAAAAAGGATAATTTAA
1 AATAAGAAAAAAATTAAATTAAAATGG-AAAAAAA-GATAATTTAA
2367957 GTAAAATGGA
Statistics
Matches: 207, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
90 24 0.12
91 23 0.11
93 1 0.00
95 5 0.02
96 40 0.19
97 104 0.50
98 10 0.05
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.24
Consensus pattern (95 bp):
AATAAGAAAAAAATTAAATTAAAATGGAAAAAAAGATAATTTAAATGAAATAGAAAAAAATTAAA
TTAAAATGGGAAGATAGATAATTTAAATGA
Found at i:2367839 original size:22 final size:22
Alignment explanation
Indices: 2367717--2367839 Score: 79
Period size: 22 Copynumber: 5.2 Consensus size: 22
2367707 AATTTAAATG
2367717 AAATAAGAAAAAAATTAAATTA
1 AAATAAGAAAAAAATTAAATTA
* *
2367739 AAATGGAAAAAAAAGATAATTTAAA-TG
1 AAAT---AAGAAAA-A-AA-TTAAATTA
2367766 AAATAAGAAAAAAATTAAATTA
1 AAATAAGAAAAAAATTAAATTA
* * *
2367788 AAATGGGAAGATAGATAATTTAAA-TG
1 AAAT---AAGA-A-AAAAATTAAATTA
*
2367814 AAATAAGAAACAAATTAAATTA
1 AAATAAGAAAAAAATTAAATTA
2367836 AAAT
1 AAAT
2367840 GGGAAGATAG
Statistics
Matches: 78, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
21 13 0.17
22 17 0.22
23 5 0.06
24 6 0.08
25 10 0.13
26 7 0.09
27 15 0.19
28 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.11, T:0.24
Consensus pattern (22 bp):
AAATAAGAAAAAAATTAAATTA
Found at i:2367858 original size:22 final size:22
Alignment explanation
Indices: 2367833--2367908 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 22
2367823 ACAAATTAAA
2367833 TTAAAATGGGAAGATAGATAAT
1 TTAAAATGGGAAGATAGATAAT
2367855 TTAAATTAAATGAGGAAAGA-A-ATTAAAT
1 TT--A--AAATG-GG-AAGATAGA-T-AAT
2367883 TT-AAATGGGAAGATAGATAAT
1 TTAAAATGGGAAGATAGATAAT
2367904 TTAAA
1 TTAAA
2367909 TGAAATGGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 22
0.66 0.00 0.34
Matches are distributed among these distances:
21 9 0.21
22 8 0.19
23 6 0.14
24 1 0.02
26 6 0.14
27 4 0.09
28 9 0.21
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (22 bp):
TTAAAATGGGAAGATAGATAAT
Found at i:2367929 original size:20 final size:20
Alignment explanation
Indices: 2367904--2367943 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2367894 GATAGATAAT
2367904 TTAAA-TGAAATGGGAAAAAA
1 TTAAATTGAAAT-GGAAAAAA
*
2367924 TTAAATTTAAATGGAAAAAA
1 TTAAATTGAAATGGAAAAAA
2367944 AAGGATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (20 bp):
TTAAATTGAAATGGAAAAAA
Found at i:2368034 original size:5 final size:5
Alignment explanation
Indices: 2367960--2368017 Score: 73
Period size: 5 Copynumber: 11.2 Consensus size: 5
2367950 AATTTAAGTA
*
2367960 AAATGG AAATG AAATG AAATA AAATG AAA-G AAATG AAACTG AAATAG
1 AAAT-G AAATG AAATG AAATG AAATG AAATG AAATG AAA-TG AAAT-G
2368007 AAATG AAATG A
1 AAATG AAATG A
2368018 TAAAAAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.09
5 29 0.62
6 14 0.30
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (5 bp):
AAATG
Found at i:2368348 original size:5 final size:5
Alignment explanation
Indices: 2368340--2368437 Score: 52
Period size: 5 Copynumber: 17.4 Consensus size: 5
2368330 AAAAAAAATT
* * *
2368340 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGT AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
* *
2368392 AATGA ATATAA AATGA AATGA AATGTTA AATGA ATATAA AATGA AA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AA
2368438 AGATGATTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
5 38 0.52
6 20 0.27
7 15 0.21
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (5 bp):
AATGA
Found at i:2368405 original size:28 final size:28
Alignment explanation
Indices: 2368365--2368437 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
2368355 TAAATGAAAT
* * * *
2368365 ATGAATATGAAATGTAATGTAAT-TTGTA
1 ATGAATATAAAATGAAATGAAATGTT-AA
2368393 ATGAATATAAAATGAAATGAAATGTTAA
1 ATGAATATAAAATGAAATGAAATGTTAA
2368421 ATGAATATAAAATGAAA
1 ATGAATATAAAATGAAA
2368438 AGATGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (28 bp):
ATGAATATAAAATGAAATGAAATGTTAA
Found at i:2368531 original size:17 final size:16
Alignment explanation
Indices: 2368509--2368578 Score: 74
Period size: 17 Copynumber: 4.4 Consensus size: 16
2368499 AATTAATTTT
*
2368509 AATGAAATGGAAATGTA
1 AATGAAATGAAAATG-A
*
2368526 AATGAAATGAAAATACA
1 AATGAAATGAAAAT-GA
*
2368543 AATGAACTGAAAATG-
1 AATGAAATGAAAATGA
2368558 AA-GAAATG-AAATGA
1 AATGAAATGAAAATGA
2368572 AATGAAA
1 AATGAAA
2368579 ATATAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
13 5 0.11
14 7 0.16
15 6 0.13
17 27 0.60
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.19
Consensus pattern (16 bp):
AATGAAATGAAAATGA
Found at i:2368532 original size:11 final size:10
Alignment explanation
Indices: 2368509--2368578 Score: 63
Period size: 11 Copynumber: 6.7 Consensus size: 10
2368499 AATTAATTTT
2368509 AATGAAATGGA
1 AATGAAAT-GA
2368520 AATGTAAATGA
1 AATG-AAATGA
*
2368531 AATGAAAATACA
1 AATG-AAAT-GA
*
2368543 AATGAACTGAA
1 AATGAAATG-A
2368554 AATG-AA-GA
1 AATGAAATGA
2368562 AATGAAATGA
1 AATGAAATGA
2368572 AATGAAA
1 AATGAAA
2368579 ATATAAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
8 5 0.10
9 3 0.06
10 10 0.20
11 22 0.45
12 9 0.18
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.19
Consensus pattern (10 bp):
AATGAAATGA
Found at i:2368533 original size:5 final size:5
Alignment explanation
Indices: 2368509--2368578 Score: 63
Period size: 5 Copynumber: 13.4 Consensus size: 5
2368499 AATTAATTTT
* *
2368509 AATGA AATGGA AATGTA AATGA AATGAA AATACA AATGA ACTGAA AATG-
1 AATGA AAT-GA AATG-A AATGA AATG-A AAT-GA AATGA AATG-A AATGA
2368558 AA-GA AATGA AATGA AATGA AA
1 AATGA AATGA AATGA AATGA AA
2368579 ATATAAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
3 1 0.02
4 4 0.07
5 27 0.50
6 22 0.41
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.19
Consensus pattern (5 bp):
AATGA
Found at i:2368570 original size:41 final size:42
Alignment explanation
Indices: 2368518--2368596 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
2368508 TAATGAAATG
* *
2368518 GAAATGTAAATGAAATGAAAATACAAATGAACTGAAAATGAA
1 GAAATGTAAATGAAATGAAAATACAAATAAAATGAAAATGAA
*
2368560 GAAATG-AAATGAAATGAAAATATAAATAAAATGAAAA
1 GAAATGTAAATGAAATGAAAATACAAATAAAATGAAAA
2368597 AAATAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 28 0.82
42 6 0.18
ACGTcount: A:0.63, C:0.03, G:0.15, T:0.19
Consensus pattern (42 bp):
GAAATGTAAATGAAATGAAAATACAAATAAAATGAAAATGAA
Found at i:2368591 original size:17 final size:17
Alignment explanation
Indices: 2368525--2368597 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
2368515 ATGGAAATGT
*
2368525 AAATGAAATGAAAAT-AC
1 AAATGAAAT-AAAATGAA
*
2368542 AAATGAACTGAAAATGAA
1 AAATGAAAT-AAAATGAA
*
2368560 GAAATGAAATGAAATGAA
1 -AAATGAAATAAAATGAA
2368578 AATAT-AAATAAAATGAA
1 AA-ATGAAATAAAATGAA
2368595 AAA
1 AAA
2368598 AATAAAAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.02
17 29 0.60
18 10 0.21
19 8 0.17
ACGTcount: A:0.66, C:0.03, G:0.14, T:0.18
Consensus pattern (17 bp):
AAATGAAATAAAATGAA
Found at i:2368602 original size:18 final size:17
Alignment explanation
Indices: 2368552--2368603 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
2368542 AAATGAACTG
*
2368552 AAAATGAAGAAATGAAAT
1 AAAATGAAAAAAT-AAAT
* *
2368570 GAAATGAAAATATAAAT
1 AAAATGAAAAAATAAAT
2368587 AAAATGAAAAAAATAAA
1 AAAATG-AAAAAATAAA
2368604 AAAGGTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (17 bp):
AAAATGAAAAAATAAAT
Found at i:2368830 original size:22 final size:22
Alignment explanation
Indices: 2368797--2368839 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2368787 AATGATATTT
2368797 AAATTGACAAAAAATTTAAATA
1 AAATTGACAAAAAATTTAAATA
2368819 AAATATGA-AAAAAATTTAAAT
1 AAAT-TGACAAAAAATTTAAAT
2368840 TACCCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (22 bp):
AAATTGACAAAAAATTTAAATA
Found at i:2368911 original size:21 final size:22
Alignment explanation
Indices: 2368864--2368911 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
2368854 GAGTACTTCT
*
2368864 AATT-AATATGAAAAAATATGA
1 AATTGAATATGAAAAAAAATGA
*
2368885 AA-TGAAT-TGAAAAAAAATTA
1 AATTGAATATGAAAAAAAATGA
2368905 AATTGAA
1 AATTGAA
2368912 AAAAGATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.27
Consensus pattern (22 bp):
AATTGAATATGAAAAAAAATGA
Found at i:2369654 original size:15 final size:14
Alignment explanation
Indices: 2369635--2369662 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2369625 AATATGATAA
2369635 AAAAAATTTTACTT
1 AAAAAATTTTACTT
2369649 AAAAAATTTTACTT
1 AAAAAATTTTACTT
2369663 GTGGAAAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAAATTTTACTT
Found at i:2371996 original size:57 final size:61
Alignment explanation
Indices: 2371908--2372042 Score: 183
Period size: 57 Copynumber: 2.3 Consensus size: 61
2371898 ATTACCCATT
* *
2371908 CGGGCTAAATCCATTTT-C-CACATATTCTTCGGGAGGGTTATATC-A-A-GATCACTCGTC
1 CGGGCTAGATCC-TTTTACACACATATTCTTCGGGAGGGCTATATCGATAGGATCACTCGTC
2371965 CGGGCTAGAT-CTTTTACACACATATTCTTCGGGAGGGCTATATCAGGATAGGATCACTCGTC
1 CGGGCTAGATCCTTTTACACACATATTCTTCGGGAGGGCTATATC--GATAGGATCACTCGTC
2372027 CGGGCTAGATCCTTTT
1 CGGGCTAGATCCTTTT
2372043 TACTGTCAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
55 4 0.06
56 2 0.03
57 34 0.50
60 1 0.01
61 1 0.01
62 21 0.31
63 5 0.07
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (61 bp):
CGGGCTAGATCCTTTTACACACATATTCTTCGGGAGGGCTATATCGATAGGATCACTCGTC
Found at i:2375081 original size:12 final size:12
Alignment explanation
Indices: 2375066--2375101 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2375056 TTCTCTTTTA
2375066 TTTTTCTTTCCT
1 TTTTTCTTTCCT
*
2375078 TTTTTCTTTCGT
1 TTTTTCTTTCCT
*
2375090 TTTTTCTCTCCT
1 TTTTTCTTTCCT
2375102 GCTTCTCGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTTCTTTCCT
Found at i:2375656 original size:3 final size:3
Alignment explanation
Indices: 2375595--2375641 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
2375585 TTACTTTATT
* *
2375595 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2375642 TAAGACCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2383172 original size:5 final size:5
Alignment explanation
Indices: 2383162--2383187 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2383152 AATTGAAAAA
2383162 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
2383188 AAATAGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:2389383 original size:22 final size:22
Alignment explanation
Indices: 2389358--2389418 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
2389348 TATTAAACAG
2389358 AGAGCACTAAAGTGCTATACAA
1 AGAGCACTAAAGTGCTATACAA
*
2389380 AGAGCAC-AAATGTGCTATACAG
1 AGAGCACTAAA-GTGCTATACAA
*
2389402 AGAGCACTAATGTGCTA
1 AGAGCACTAAAGTGCTA
2389419 ATAATCGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 3 0.09
22 30 0.86
23 2 0.06
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (22 bp):
AGAGCACTAAAGTGCTATACAA
Found at i:2389434 original size:25 final size:25
Alignment explanation
Indices: 2389355--2389528 Score: 113
Period size: 25 Copynumber: 7.4 Consensus size: 25
2389345 CACTATTAAA
*
2389355 CAGAGAGCACTAAAGTGCT-AT-A-
1 CAGAGAGCACTAATGTGCTAATAAT
* *
2389377 CAAAGAGCACAAATGTGCT-AT-A-
1 CAGAGAGCACTAATGTGCTAATAAT
2389399 CAGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* *
2389424 CGGAGAGCACTAACGTGCTAGA-AAT
1 CAGAGAGCACTAATGTGCTA-ATAAT
* *
2389449 CAGAGAG--C-GA-GT--TAGTAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* * * *
2389468 CAGAGAGCACTGACGTGCTAATGAC
1 CAGAGAGCACTAATGTGCTAATAAT
* *
2389493 CAGAGAGCATTGATGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* *
2389518 TAGAAAGCACT
1 CAGAGAGCACT
2389529 GTAAACTCCC
Statistics
Matches: 121, Mismatches: 20, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.10
21 3 0.02
22 39 0.32
23 5 0.04
24 1 0.01
25 60 0.50
26 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (25 bp):
CAGAGAGCACTAATGTGCTAATAAT
Found at i:2399929 original size:2 final size:2
Alignment explanation
Indices: 2399922--2399968 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
2399912 AAATTTCCCC
* * *
2399922 CT CT CT CT CT CG AT CT TT C- CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2399963 CT CT CT
1 CT CT CT
2399969 GTTCTTCAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2399932 original size:21 final size:23
Alignment explanation
Indices: 2399907--2399955 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2399897 TCTTTTTTTC
2399907 CTCTC-AAATTTCC-CCCTCTCT
1 CTCTCGAAATTTCCTCCCTCTCT
** *
2399928 CTCTCGATCTTTCCTCTCTCTCT
1 CTCTCGAAATTTCCTCCCTCTCT
2399951 CTCTC
1 CTCTC
2399956 TCTCTCTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.08, C:0.47, G:0.02, T:0.43
Consensus pattern (23 bp):
CTCTCGAAATTTCCTCCCTCTCT
Found at i:2412546 original size:7 final size:7
Alignment explanation
Indices: 2412534--2412567 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2412524 ATTAAAATAG
2412534 ATTTTTA
1 ATTTTTA
2412541 ATTTTTA
1 ATTTTTA
2412548 ATTTTTA
1 ATTTTTA
2412555 ATTTTTA
1 ATTTTTA
2412562 ATTTTT
1 ATTTTT
2412568 TTTTTGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:2412789 original size:15 final size:15
Alignment explanation
Indices: 2412769--2412807 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2412759 TGACATTAAT
*
2412769 AATAATAATATTTTA
1 AATAATAATATATTA
*
2412784 AATAATAATGTATTA
1 AATAATAATATATTA
*
2412799 AATTATAAT
1 AATAATAAT
2412808 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATAATAATATATTA
Found at i:2412923 original size:36 final size:34
Alignment explanation
Indices: 2412869--2412944 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 34
2412859 TGCAACAATA
*
2412869 TTAATTTAATTATATTATAGAACATTTTAATTTAAT
1 TTAATTTAATCATATTATAGAACA--TTAATTTAAT
* *
2412905 TTAATTTAATCACT-TTATATAACATTAATTTACT
1 TTAATTTAATCA-TATTATAGAACATTAATTTAAT
2412939 TTAATT
1 TTAATT
2412945 ATCATAGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 15 0.42
36 20 0.56
37 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (34 bp):
TTAATTTAATCATATTATAGAACATTAATTTAAT
Found at i:2417765 original size:15 final size:17
Alignment explanation
Indices: 2417745--2417779 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2417735 AGATTGTGTG
2417745 AAAAATAAA-T-AAAAC
1 AAAAATAAATTAAAAAC
2417760 AAAAATAAATTAAAAAC
1 AAAAATAAATTAAAAAC
2417777 AAA
1 AAA
2417780 TTAACCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAATAAATTAAAAAC
Found at i:2419468 original size:9 final size:10
Alignment explanation
Indices: 2419441--2419467 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2419431 ATTACTTATA
2419441 TAAAAAAATT
1 TAAAAAAATT
2419451 TAAAAAAATT
1 TAAAAAAATT
2419461 TAAAAAA
1 TAAAAAA
2419468 TCGAATACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:2426190 original size:29 final size:31
Alignment explanation
Indices: 2426156--2426220 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2426146 ATAGTTCATA
*
2426156 TACCACATTAGATA-TTT-TCAAAGTATATG
1 TACCACATTAGATACTTTATCAAAGTATAGG
* *
2426185 TACCACATTGGATACTTTATGAAAGTATAGG
1 TACCACATTAGATACTTTATCAAAGTATAGG
2426216 TACCA
1 TACCA
2426221 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
30 3 0.10
31 15 0.48
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (31 bp):
TACCACATTAGATACTTTATCAAAGTATAGG
Found at i:2427721 original size:19 final size:18
Alignment explanation
Indices: 2427690--2427726 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2427680 CACATGTCCT
2427690 ATTTTCTTATATATATTA
1 ATTTTCTTATATATATTA
*
2427708 ATTTTTTTACTATATATTA
1 ATTTTCTTA-TATATATTA
2427727 TATACACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTCTTATATATATTA
Found at i:2437611 original size:16 final size:14
Alignment explanation
Indices: 2437590--2437623 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
2437580 ATAATTTTTT
2437590 TTATAAATATTATATA
1 TTATAAA-ATT-TATA
2437606 TTATAAAATTTATA
1 TTATAAAATTTATA
2437620 TTAT
1 TTAT
2437624 TTTTGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAAAATTTATA
Found at i:2437616 original size:37 final size:37
Alignment explanation
Indices: 2437575--2437650 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
2437565 AGTTTTGGAC
* *
2437575 AATTTATAATT-TTTTTTA-TAAATATTATATATTATAA
1 AATTTAT-ATTATTTTTGATTAAAT-TTACATATTATAA
*
2437612 AATTTATATTATTTTTGATTTAATTTACATATTATAA
1 AATTTATATTATTTTTGATTAAATTTACATATTATAA
2437649 AA
1 AA
2437651 AGGAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 3 0.09
37 27 0.79
38 4 0.12
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (37 bp):
AATTTATATTATTTTTGATTAAATTTACATATTATAA
Found at i:2453701 original size:2 final size:2
Alignment explanation
Indices: 2453694--2453730 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2453684 TCTTAAATTC
2453694 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 A
2453731 CATACTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2454249 original size:24 final size:23
Alignment explanation
Indices: 2454218--2454264 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2454208 TATTCACACA
2454218 TATTCTTA-CTTAATTTCAAATGT
1 TATTCTTACCTTAATTT-AAATGT
*
2454241 TATTACTTACCTTACTTTAAATGT
1 TATT-CTTACCTTAATTTAAATGT
2454265 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGT
Found at i:2454947 original size:23 final size:22
Alignment explanation
Indices: 2454899--2454947 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
2454889 TCTTCCCCTG
*
2454899 TTTTCGTCTCTTTCTCTGTTTC
1 TTTTCGTCTCTTTCTCTGTTTA
* * *
2454921 TTTTCTGTTTCTTTGTCTTTTTA
1 TTTTC-GTCTCTTTCTCTGTTTA
2454944 TTTT
1 TTTT
2454948 ACTTACTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.02, C:0.18, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTTCGTCTCTTTCTCTGTTTA
Found at i:2454987 original size:3 final size:3
Alignment explanation
Indices: 2454979--2455026 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
2454969 TTATTTTAAC
*
2454979 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
2455025 TA
1 TA
2455027 TACTATTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2455718 original size:9 final size:8
Alignment explanation
Indices: 2455704--2455728 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2455694 CTATGTCCAC
2455704 AAAAAAAG
1 AAAAAAAG
2455712 AAAAAAAG
1 AAAAAAAG
2455720 AAAAAAAG
1 AAAAAAAG
2455728 A
1 A
2455729 TATCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2456516 original size:18 final size:18
Alignment explanation
Indices: 2456493--2456529 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2456483 CAGTTGCACG
2456493 TGGTGTGCTATATGTATC
1 TGGTGTGCTATATGTATC
2456511 TGGTGTGCTATATGTATC
1 TGGTGTGCTATATGTATC
2456529 T
1 T
2456530 CATGCTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.46
Consensus pattern (18 bp):
TGGTGTGCTATATGTATC
Found at i:2462688 original size:13 final size:13
Alignment explanation
Indices: 2462672--2462696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2462662 ATTTTATTTA
2462672 AAGAATTTAATTG
1 AAGAATTTAATTG
2462685 AAGAATTTAATT
1 AAGAATTTAATT
2462697 TATTAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AAGAATTTAATTG
Found at i:2485905 original size:34 final size:34
Alignment explanation
Indices: 2485862--2485929 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2485852 TGCCAGGTAG
2485862 TTTAATCGAATTATGAAAGAGTGAGATGAACATA
1 TTTAATCGAATTATGAAAGAGTGAGATGAACATA
2485896 TTTAATCGAATTATGAAAGAGTGAGATGAACATA
1 TTTAATCGAATTATGAAAGAGTGAGATGAACATA
2485930 CTTGCTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (34 bp):
TTTAATCGAATTATGAAAGAGTGAGATGAACATA
Found at i:2486249 original size:3 final size:3
Alignment explanation
Indices: 2486241--2486274 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2486231 TGTCCATGTC
* *
2486241 AAT AAT AAT AAA AAT AAT AAA AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2486275 GTAAGCAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:2486302 original size:4 final size:4
Alignment explanation
Indices: 2486293--2486330 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
2486283 GGTAAGTTGC
2486293 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2486331 ACCTCCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2487630 original size:18 final size:18
Alignment explanation
Indices: 2487609--2487647 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2487599 TAAGTATAAA
*
2487609 AATTTTATTGAAT-TTTTT
1 AATTTT-TTAAATATTTTT
2487627 AATTTTTTAAATATTTTT
1 AATTTTTTAAATATTTTT
2487645 AAT
1 AAT
2487648 AGTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
AATTTTTTAAATATTTTT
Found at i:2490461 original size:15 final size:15
Alignment explanation
Indices: 2490437--2490470 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2490427 AAAGGTGTTT
*
2490437 TTTTATAATTACGTA
1 TTTTAAAATTACGTA
*
2490452 TTTTAAAATTATGTA
1 TTTTAAAATTACGTA
2490467 TTTT
1 TTTT
2490471 GATTATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTTAAAATTACGTA
Found at i:2491678 original size:45 final size:45
Alignment explanation
Indices: 2491611--2491696 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
2491601 ATTACAAAAA
*
2491611 AAAATTTAAATAGTTTTTAAAAT-TAAAAATATTTATAAAAATTCC
1 AAAATTTAAATAGTTTTAAAAATATAAAAAT-TTTATAAAAATTCC
* * *
2491656 AAAATTTATATA-TTTTAAAAAATATATAAATTTTTTAAAAA
1 AAAATTTAAATAGTTTT-AAAAATATAAAAATTTTATAAAAA
2491697 AAATCTAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 4 0.11
45 25 0.71
46 6 0.17
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (45 bp):
AAAATTTAAATAGTTTTAAAAATATAAAAATTTTATAAAAATTCC
Found at i:2491705 original size:20 final size:20
Alignment explanation
Indices: 2491668--2491705 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2491658 AATTTATATA
*
2491668 TTTTAAAAAATATATAAATT
1 TTTTAAAAAAAATATAAATT
*
2491688 TTTTAAAAAAAATCTAAA
1 TTTTAAAAAAAATATAAA
2491706 GAATATATAA
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTAAAAAAAATATAAATT
Found at i:2496724 original size:30 final size:30
Alignment explanation
Indices: 2496665--2496728 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
2496655 AATCACCAAA
* *
2496665 TTTTAATTTAAATGTAAATTTTAAGATAAT
1 TTTTAATTTAAATGTAAATTTAAAAATAAT
2496695 TTTTAATTT-AATG-AAATAATTAAAAATAAT
1 TTTTAATTTAAATGTAAAT--TTAAAAATAAT
2496725 TTTT
1 TTTT
2496729 TATAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.13
29 4 0.13
30 22 0.73
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTTAATTTAAATGTAAATTTAAAAATAAT
Found at i:2498076 original size:29 final size:28
Alignment explanation
Indices: 2498031--2498120 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
2498021 AACTTTATGA
2498031 ATTAATTTAAA--AAATTATTAA-AATT
1 ATTAATTTAAACCAAATTATTAACAATT
*
2498056 ATTAA-TTAAACATCGACATTATTAACATATT
1 ATTAATTTAAAC--C-AAATTATTAACA-ATT
*
2498087 ATTATATTTAAACCAAATTATTAATAATT
1 ATTA-ATTTAAACCAAATTATTAACAATT
2498116 ATTAA
1 ATTAA
2498121 ACATCAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
24 5 0.09
25 5 0.09
28 1 0.02
29 16 0.30
30 11 0.21
31 8 0.15
32 1 0.02
33 6 0.11
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (28 bp):
ATTAATTTAAACCAAATTATTAACAATT
Found at i:2501434 original size:27 final size:29
Alignment explanation
Indices: 2501404--2501467 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
2501394 AAAGTATAAA
2501404 TTATAAA-AATAATAAAAAATTAAAA-AT
1 TTATAAATAATAATAAAAAATTAAAAGAT
* * *
2501431 TTATAAATTATTATAAAAATTTAAAAGAT
1 TTATAAATAATAATAAAAAATTAAAAGAT
*
2501460 ATATAAAT
1 TTATAAAT
2501468 TTATTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 7 0.23
28 15 0.48
29 9 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
TTATAAATAATAATAAAAAATTAAAAGAT
Found at i:2501444 original size:37 final size:39
Alignment explanation
Indices: 2501403--2501529 Score: 102
Period size: 44 Copynumber: 3.2 Consensus size: 39
2501393 AAAAGTATAA
2501403 ATTATAAAAATAATAAAAAAT-TAAAAATTTA-T-AAATT
1 ATTATAAAAAT-ATAAAAAATATAAAAATTTATTAAAATT
* * *
2501440 ATTATAAAAATTTAAAAGATATATAAATTTATTAAAATT
1 ATTATAAAAATATAAAAAATATAAAAATTTATTAAAATT
* **
2501479 ATT-TAAATATTATGAAATTATAGATATGTAAATTTATTAAAATT
1 ATTATAAA-AATAT-AAA--A-A-ATATAAAAATTTATTAAAATT
2501523 ATT-TAAA
1 ATTATAAA
2501530 TAGTATGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
36 7 0.09
37 20 0.27
38 5 0.07
39 11 0.15
40 3 0.04
42 1 0.01
44 27 0.36
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (39 bp):
ATTATAAAAATATAAAAAATATAAAAATTTATTAAAATT
Found at i:2501449 original size:20 final size:21
Alignment explanation
Indices: 2501424--2501499 Score: 60
Period size: 20 Copynumber: 3.9 Consensus size: 21
2501414 AATAAAAAAT
2501424 TAAAAATTTAT-AAATTATTA
1 TAAAAATTTATAAAATTATTA
2501444 TAAAAATTTA-AAAGA-TA-TA
1 TAAAAATTTATAAA-ATTATTA
2501463 T--AAATTTATTAAAATTATT-
1 TAAAAATTTA-TAAAATTATTA
* *
2501482 TAAATA-TTATGAAATTAT
1 TAAAAATTTATAAAATTAT
2501500 AGATATGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
17 7 0.15
18 1 0.02
19 17 0.37
20 18 0.39
21 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (21 bp):
TAAAAATTTATAAAATTATTA
Done.