Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 136 of 171
Found at i:42189266 original size:20 final size:19
Alignment explanation
Indices: 42189241--42189311 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 19
42189231 CGAACCTCAA
42189241 GTTTAAAGTTTAGGGTTTAG
1 GTTT-AAGTTTAGGGTTTAG
*
42189261 GTTTAAGATTTAGGGTTCAAG
1 GTTTAAG-TTTAGGGTT-TAG
42189282 GTTTAAGTTTA-GGTTTAAG
1 GTTTAAGTTTAGGGTTT-AG
42189301 GTTTAATGTTT
1 GTTTAA-GTTT
42189312 TATGTTTGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
19 15 0.33
20 21 0.47
21 9 0.20
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.46
Consensus pattern (19 bp):
GTTTAAGTTTAGGGTTTAG
Found at i:42189297 original size:12 final size:13
Alignment explanation
Indices: 42189241--42189388 Score: 75
Period size: 14 Copynumber: 10.9 Consensus size: 13
42189231 CGAACCTCAA
*
42189241 GTTTAAAGTTTAGG
1 GTTTAAGGTTTA-G
42189255 GTTT-AGGTTTAAG
1 GTTTAAGGTTT-AG
* * *
42189268 ATTTAGGGTTCAAG
1 GTTTAAGGTT-TAG
42189282 GTTTAA-GTTTAG
1 GTTTAAGGTTTAG
*
42189294 GTTTAAGGTTTAAT
1 GTTTAAGGTTT-AG
* * *
42189308 GTTTTATGTTTGGG
1 GTTTAAGGTTT-AG
*
42189322 GTTTAGGGTTTAGG
1 GTTTAAGGTTTA-G
**
42189336 GTTTAATATTTAG
1 GTTTAAGGTTTAG
* *
42189349 CATTTAAAGTTTAGG
1 -GTTTAAGGTTTA-G
*
42189364 GTTCAAGGTTTAG
1 GTTTAAGGTTTAG
*
42189377 GTTTGAGGTTTA
1 GTTTAAGGTTTA
42189389 AAGGTTATAG
Statistics
Matches: 98, Mismatches: 28, Indels: 17
0.69 0.20 0.12
Matches are distributed among these distances:
12 8 0.08
13 28 0.29
14 61 0.62
15 1 0.01
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.46
Consensus pattern (13 bp):
GTTTAAGGTTTAG
Found at i:42189340 original size:27 final size:26
Alignment explanation
Indices: 42189248--42189388 Score: 86
Period size: 27 Copynumber: 5.2 Consensus size: 26
42189238 CAAGTTTAAA
* *
42189248 GTTTAGGGTTTAGGTTTAAGATTTAGG
1 GTTTAGGGTTTAAGTTT-AGGTTTAGG
* * *
42189275 GTTCAAGGTTTAAGTTTAGGTTTAAG
1 GTTTAGGGTTTAAGTTTAGGTTTAGG
* * * *
42189301 GTTTAATGTTTTATGTTTGGGGTTTAGG
1 GTTT-AGGGTTTAAGTTT-AGGTTTAGG
* * **
42189329 GTTTAGGGTTTAATATTTAGCATTTAAA
1 GTTTAGGGTTTAA-GTTTAG-GTTTAGG
*
42189357 GTTTAGGGTTCAAGGTTTAGGTTT-GAG
1 GTTTAGGGTTTAA-GTTTAGGTTTAG-G
42189384 GTTTA
1 GTTTA
42189389 AAGGTTATAG
Statistics
Matches: 84, Mismatches: 25, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
26 10 0.12
27 39 0.46
28 35 0.42
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.46
Consensus pattern (26 bp):
GTTTAGGGTTTAAGTTTAGGTTTAGG
Found at i:42189347 original size:14 final size:14
Alignment explanation
Indices: 42189241--42189407 Score: 67
Period size: 14 Copynumber: 12.2 Consensus size: 14
42189231 CGAACCTCAA
42189241 GTTTAAAGTTTAGG
1 GTTTAAAGTTTAGG
* *
42189255 GTTT-AGGTTTAAG
1 GTTTAAAGTTTAGG
* ** * *
42189268 ATTTAGGGTTCAAG
1 GTTTAAAGTTTAGG
42189282 GTTT-AAGTTTA-G
1 GTTTAAAGTTTAGG
* **
42189294 GTTTAAGGTTTAAT
1 GTTTAAAGTTTAGG
* * *
42189308 GTTTTATGTTTGGG
1 GTTTAAAGTTTAGG
**
42189322 GTTTAGGGTTTAGG
1 GTTTAAAGTTTAGG
*
42189336 GTTTAATA-TTTAGC
1 GTTTAA-AGTTTAGG
*
42189350 ATTTAAAGTTTAGG
1 GTTTAAAGTTTAGG
* *
42189364 GTTCAAGGTTTA-G
1 GTTTAAAGTTTAGG
* * *
42189377 GTTTGAGGTTTAAAG
1 GTTTAAAGTTT-AGG
*
42189392 G-TTATAGTTTAGG
1 GTTTAAAGTTTAGG
42189405 GTT
1 GTT
42189408 CAAGGTCTAA
Statistics
Matches: 111, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
12 5 0.05
13 34 0.31
14 70 0.63
15 2 0.02
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.46
Consensus pattern (14 bp):
GTTTAAAGTTTAGG
Found at i:42189375 original size:21 final size:21
Alignment explanation
Indices: 42189351--42189413 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
42189341 ATATTTAGCA
42189351 TTTAAAGTTTAGGGTTCAAGG
1 TTTAAAGTTTAGGGTTCAAGG
* * *
42189372 TTT-AGGTTTGAGGTTTAAAGG
1 TTTAAAGTTT-AGGGTTCAAGG
*
42189393 -TTATAGTTTAGGGTTCAAGG
1 TTTAAAGTTTAGGGTTCAAGG
42189413 T
1 T
42189414 CTAAGGCTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.25, C:0.03, G:0.30, T:0.41
Consensus pattern (21 bp):
TTTAAAGTTTAGGGTTCAAGG
Found at i:42189386 original size:20 final size:20
Alignment explanation
Indices: 42189356--42189413 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
42189346 TAGCATTTAA
42189356 AGTTTAGGGTTCAAGGTT-T
1 AGTTTAGGGTTCAAGGTTAT
* *
42189375 AGGTTTGAGGTTTAAAGGTTAT
1 A-GTTT-AGGGTTCAAGGTTAT
42189397 AGTTTAGGGTTCAAGGT
1 AGTTTAGGGTTCAAGGT
42189414 CTAAGGCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 14 0.44
21 15 0.47
22 2 0.06
ACGTcount: A:0.24, C:0.03, G:0.33, T:0.40
Consensus pattern (20 bp):
AGTTTAGGGTTCAAGGTTAT
Found at i:42191064 original size:20 final size:21
Alignment explanation
Indices: 42191039--42191089 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
42191029 ACCTTGAACG
*
42191039 TTGACTTTGGT-CGTTAACCA
1 TTGACTTTGATGCGTTAACCA
*
42191059 TTGACTTTGATGCGTTAACCG
1 TTGACTTTGATGCGTTAACCA
*
42191080 TTAACTTTGA
1 TTGACTTTGA
42191090 CTATTGAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (21 bp):
TTGACTTTGATGCGTTAACCA
Found at i:42191106 original size:20 final size:19
Alignment explanation
Indices: 42191078--42191126 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
42191068 ATGCGTTAAC
42191078 CGTTAACTTTGACTATTGAA
1 CGTTAACTTTGACT-TTGAA
* *
42191098 CGTTGACTTTGACTTTGAC
1 CGTTAACTTTGACTTTGAA
*
42191117 CATTAACTTT
1 CGTTAACTTT
42191127 TTTGACCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.43
Consensus pattern (19 bp):
CGTTAACTTTGACTTTGAA
Found at i:42201961 original size:34 final size:34
Alignment explanation
Indices: 42201918--42201984 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
42201908 TATTTTGATG
42201918 ATTATTATCCTTCTCTCTTTCTCCCTTCCTTTTA
1 ATTATTATCCTTCTCTCTTTCTCCCTTCCTTTTA
42201952 ATTATTATCCTTCTCTCTTTCTCCCTTCCTTTT
1 ATTATTATCCTTCTCTCTTTCTCCCTTCCTTTT
42201985 TTAATCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (34 bp):
ATTATTATCCTTCTCTCTTTCTCCCTTCCTTTTA
Found at i:42203641 original size:140 final size:140
Alignment explanation
Indices: 42203393--42203668 Score: 313
Period size: 140 Copynumber: 2.0 Consensus size: 140
42203383 GTTAGATTTC
* * *
42203393 AAAGAAGTTATTCTTGGTTCATCCCTCAAGCATTGGAAATTTTCTGCAGCTATATAACTATCAAG
1 AAAGAAATCATTCTTGGTTCATCCCTCAAGCAGTGGAAATTTTCTGCAGCTATATAACTATCAAG
* ** * ** *
42203458 AGCACTCAGGCTTGATATGGCGTCATCATAAACGGTGCTGGTATATAAACTGTTTGAAACAGGTA
66 AGCACTCAGGCTTGATATGGCGTCATCACAAACCATGCAGGTATATAAACCATCTGAAACAGGTA
42203523 GATTTCAAAG
131 GATTTCAAAG
** * * * *
42203533 AAAGAAATCATTCTTTGGTTCATCCCTTCGTGCAGTGGAATTTTTCTTCGGCTATAT-CCTATCA
1 AAAGAAATCATTC-TTGGTTCATCCC-TCAAGCAGTGGAAATTTTCTGCAGCTATATAACTATCA
* * * * * * *
42203597 AGGGTACTC-GGCTTGATATGGTGTCATCACGAACCATGCAGGTATGTTAACCATCTGAAACAGT
64 AGAGCACTCAGGCTTGATATGGCGTCATCACAAACCATGCAGGTATATAAACCATCTGAAACAGG
42203661 TAGATTTC
129 TAGATTTC
42203669 GATGTTTTTC
Statistics
Matches: 111, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
140 62 0.56
141 25 0.23
142 24 0.22
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (140 bp):
AAAGAAATCATTCTTGGTTCATCCCTCAAGCAGTGGAAATTTTCTGCAGCTATATAACTATCAAG
AGCACTCAGGCTTGATATGGCGTCATCACAAACCATGCAGGTATATAAACCATCTGAAACAGGTA
GATTTCAAAG
Found at i:42207787 original size:17 final size:18
Alignment explanation
Indices: 42207754--42207787 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42207744 ATTTGATGAT
42207754 TTAAATAATTGAAATTTG
1 TTAAATAATTGAAATTTG
*
42207772 TTAAAT-ATTTAAATTT
1 TTAAATAATTGAAATTT
42207788 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTAAATAATTGAAATTTG
Found at i:42209379 original size:14 final size:15
Alignment explanation
Indices: 42209344--42209383 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
42209334 TATTTAATAT
42209344 TTTGTTTGTCTACAC
1 TTTGTTTGTCTACAC
*
42209359 TTT-TTTGT-TGCAC
1 TTTGTTTGTCTACAC
42209372 TTTGTTTGTCTA
1 TTTGTTTGTCTA
42209384 TTAATATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 7 0.33
14 10 0.48
15 4 0.19
ACGTcount: A:0.10, C:0.15, G:0.15, T:0.60
Consensus pattern (15 bp):
TTTGTTTGTCTACAC
Found at i:42217140 original size:10 final size:10
Alignment explanation
Indices: 42217125--42217149 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42217115 TTTAAAATAT
42217125 AAATTGTAAA
1 AAATTGTAAA
42217135 AAATTGTAAA
1 AAATTGTAAA
42217145 AAATT
1 AAATT
42217150 ATTTCAGAAT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AAATTGTAAA
Found at i:42223839 original size:3 final size:3
Alignment explanation
Indices: 42223831--42223855 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42223821 ATATTAAAAT
42223831 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
42223856 ATTACGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:42227959 original size:20 final size:20
Alignment explanation
Indices: 42227916--42227976 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
42227906 AGAACTCCTC
*
42227916 TTCTACTGATACAACTATAG
1 TTCTACCGATACAACTATAG
*
42227936 TTCTACCGATACAAGTAT-G
1 TTCTACCGATACAACTATAG
* *
42227955 TTTCTACCAAAACAACTA-AG
1 -TTCTACCGATACAACTATAG
42227975 TT
1 TT
42227977 GCAGACTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
TTCTACCGATACAACTATAG
Found at i:42230285 original size:22 final size:23
Alignment explanation
Indices: 42230248--42230295 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
42230238 CCGTTTATTT
*
42230248 GCACGTTTAGTGCTCTTCGTTTA
1 GCACGTTTAGTGCTCTTCGTCTA
42230271 GCACGTTT-GTGCTCTTCGTCTA
1 GCACGTTTAGTGCTCTTCGTCTA
42230293 GCA
1 GCA
42230296 TCTTTGTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCACGTTTAGTGCTCTTCGTCTA
Found at i:42230307 original size:22 final size:22
Alignment explanation
Indices: 42230248--42230307 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
42230238 CCGTTTATTT
* *
42230248 GCACGTTTAGTGCTCTTCGTTTA
1 GCACGTTT-GTACTCTTCGTCTA
*
42230271 GCACGTTTGTGCTCTTCGTCTA
1 GCACGTTTGTACTCTTCGTCTA
42230293 GCATC-TTTGTACTCT
1 GCA-CGTTTGTACTCT
42230308 CCATTCATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (22 bp):
GCACGTTTGTACTCTTCGTCTA
Found at i:42234717 original size:15 final size:15
Alignment explanation
Indices: 42234697--42234735 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
42234687 GATCAAAGTA
42234697 TAATTTTATTTTTAT
1 TAATTTTATTTTTAT
*
42234712 TAATTTAAATTTTTAT
1 TAATTT-TATTTTTAT
*
42234728 AAATTTTA
1 TAATTTTA
42234736 AAGAACTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTATTTTTAT
Found at i:42235455 original size:114 final size:116
Alignment explanation
Indices: 42235331--42235540 Score: 300
Period size: 116 Copynumber: 1.8 Consensus size: 116
42235321 TTTTTTGAGT
* * *
42235331 TTTTTCAACTAATGGCTGACACCAAAAAAATACGAATAAAAAAA-TA-TTTTTTGGGTGTTTGGC
1 TTTTTCAACTAATGGCCGACACCAAAAAAACACGAATAAAAAAATTATTTTTTTGGATGTTTGGC
*
42235394 AACCAAAGGTCGACATCACCTTT-TCCAACACCCCAAACAATTTTTCCCCAC
66 AACCAAAGATCGACATCACCTTTCT-CAACACCCCAAACAATTTTTCCCCAC
* *** *
42235445 TTTTTCAACTAATGGCCGACATCTGTAAAACACGAATAAAAAAATTATTTTTTTTGATGTTTGGC
1 TTTTTCAACTAATGGCCGACACCAAAAAAACACGAATAAAAAAATTATTTTTTTGGATGTTTGGC
*
42235510 AACCAATGATCGACATCACCTTTCTCAACAC
66 AACCAAAGATCGACATCACCTTTCTCAACAC
42235541 TCGAAATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
114 38 0.46
115 2 0.02
116 42 0.51
117 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.30
Consensus pattern (116 bp):
TTTTTCAACTAATGGCCGACACCAAAAAAACACGAATAAAAAAATTATTTTTTTGGATGTTTGGC
AACCAAAGATCGACATCACCTTTCTCAACACCCCAAACAATTTTTCCCCAC
Found at i:42237673 original size:17 final size:18
Alignment explanation
Indices: 42237651--42237686 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42237641 TAAATGAGTT
42237651 AATTAAGAT-TAAATTGG
1 AATTAAGATATAAATTGG
*
42237668 AATTAAGGTATAAATTGG
1 AATTAAGATATAAATTGG
42237686 A
1 A
42237687 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (18 bp):
AATTAAGATATAAATTGG
Found at i:42238633 original size:2 final size:2
Alignment explanation
Indices: 42238626--42238680 Score: 101
Period size: 2 Copynumber: 27.0 Consensus size: 2
42238616 GGTTACAAAG
42238626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42238668 AT AT AT ACT AT AT
1 AT AT AT A-T AT AT
42238681 TTTGATATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42240860 original size:13 final size:13
Alignment explanation
Indices: 42240842--42240866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42240832 TATCCACGAG
42240842 TATACATACAAAT
1 TATACATACAAAT
42240855 TATACATACAAA
1 TATACATACAAA
42240867 ACATTGTAAA
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:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (13 bp):
TATACATACAAAT
Found at i:42241050 original size:6 final size:6
Alignment explanation
Indices: 42241039--42241161 Score: 64
Period size: 6 Copynumber: 20.5 Consensus size: 6
42241029 CAAGTTGAAA
* *
42241039 TTAAAT TTAAAT TTAAA- TGAAAT TT-AAT TTAAGT TT-AAT TAATAGAAGT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T--TA-AA-T
* * *
42241088 TGAAA- TTAAAT TTAAAT TTAAA- TGAAAT TT-AAT TTAAGT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
42241132 TAATAGAAGT TGAAA- TTAAAT TTAAAT TTA
1 T--TA-AA-T TTAAAT TTAAAT TTAAAT TTA
42241162 CGTTAAAATA
Statistics
Matches: 89, Mismatches: 12, Indels: 32
0.67 0.09 0.24
Matches are distributed among these distances:
5 32 0.36
6 41 0.46
7 6 0.07
8 2 0.02
9 4 0.04
10 4 0.04
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:42241096 original size:54 final size:54
Alignment explanation
Indices: 42241030--42241161 Score: 264
Period size: 54 Copynumber: 2.4 Consensus size: 54
42241020 AAATGACTAC
42241030 AAGTTGAAATTAAATTTAAATTTAAATGAAATTTAATTTAAGTTTAATTAATAG
1 AAGTTGAAATTAAATTTAAATTTAAATGAAATTTAATTTAAGTTTAATTAATAG
42241084 AAGTTGAAATTAAATTTAAATTTAAATGAAATTTAATTTAAGTTTAATTAATAG
1 AAGTTGAAATTAAATTTAAATTTAAATGAAATTTAATTTAAGTTTAATTAATAG
42241138 AAGTTGAAATTAAATTTAAATTTA
1 AAGTTGAAATTAAATTTAAATTTA
42241162 CGTTAAAATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (54 bp):
AAGTTGAAATTAAATTTAAATTTAAATGAAATTTAATTTAAGTTTAATTAATAG
Found at i:42241129 original size:11 final size:11
Alignment explanation
Indices: 42241036--42241265 Score: 78
Period size: 11 Copynumber: 20.7 Consensus size: 11
42241026 CTACAAGTTG
*
42241036 AAATTAAATTT
1 AAATTTAATTT
* *
42241047 AAATTTAAATG
1 AAATTTAATTT
42241058 AAATTTAATTT
1 AAATTTAATTT
*
42241069 AAGTTTAA-TT
1 AAATTTAATTT
** *
42241079 -AATAGAAGTTG
1 AAATTTAA-TTT
*
42241090 AAATTAAATTT
1 AAATTTAATTT
* *
42241101 AAATTTAAATG
1 AAATTTAATTT
42241112 AAATTTAATTT
1 AAATTTAATTT
*
42241123 AAGTTTAA-TT
1 AAATTTAATTT
** *
42241133 -AATAGAAGTTG
1 AAATTTAA-TTT
*
42241144 AAATTAAATTT
1 AAATTTAATTT
**
42241155 AAATTTACGTT
1 AAATTTAATTT
* * *
42241166 AAAATAAAATT
1 AAATTTAATTT
** *
42241177 -AATACAAGTTG
1 AAATTTAA-TTT
*
42241188 AAATTAAATTT
1 AAATTTAATTT
42241199 AAATTTTGAATTT
1 AAA-TTT-AATTT
* *
42241212 TAATTTAAGTTAA
1 AAATTTAA-TT-T
42241225 AAATTTAATTT
1 AAATTTAATTT
*
42241236 GAAA-TTAAGTTG
1 -AAATTTAA-TTT
42241248 AAA-TTAATTT
1 AAATTTAATTT
*
42241258 GAATTTAA
1 AAATTTAA
42241266 ATGAAGGTTG
Statistics
Matches: 155, Mismatches: 49, Indels: 30
0.66 0.21 0.13
Matches are distributed among these distances:
9 8 0.05
10 12 0.08
11 92 0.59
12 29 0.19
13 14 0.09
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:42241224 original size:24 final size:24
Alignment explanation
Indices: 42241185--42241265 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
42241175 TTAATACAAG
* *
42241185 TTGAAATTAAATTTAAATTTTGAAT
1 TTGAAATTAAGTTAAAATTTT-AAT
* * *
42241210 TTTAATTTAAGTTAAAAATTTAAT
1 TTGAAATTAAGTTAAAATTTTAAT
*
42241234 TTGAAATTAAGTTGAAA--TTAAT
1 TTGAAATTAAGTTAAAATTTTAAT
*
42241256 TTGAATTTAA
1 TTGAAATTAA
42241266 ATGAAGGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 14 0.30
24 17 0.36
25 16 0.34
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (24 bp):
TTGAAATTAAGTTAAAATTTTAAT
Found at i:42241275 original size:28 final size:28
Alignment explanation
Indices: 42241226--42241318 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 28
42241216 TTAAGTTAAA
*
42241226 AATTT-AATTTGAAATTAAGTTGAAATT
1 AATTTGAATTTGAAATGAAGTTGAAATT
42241253 AATTTGAATTT-AAATGAAGGTTGAAATT
1 AATTTGAATTTGAAATGAA-GTTGAAATT
** * * *
42241281 AAAATGAATTTTAGATGAA-ATGAAATT
1 AATTTGAATTTGAAATGAAGTTGAAATT
**
42241308 AAAATGAATTT
1 AATTTGAATTT
42241319 AATTTGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 29 0.50
28 23 0.40
29 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (28 bp):
AATTTGAATTTGAAATGAAGTTGAAATT
Found at i:42241337 original size:22 final size:23
Alignment explanation
Indices: 42241229--42241337 Score: 60
Period size: 22 Copynumber: 4.4 Consensus size: 23
42241219 AGTTAAAAAT
* *
42241229 TTAATTTGAAATTAA-GTTGAAA
1 TTAATTTGAATTTAATATTGAAA
42241251 TTAATTTGAATTTAAATGAAGGTTGAAA
1 TTAATTTGAATTT-AAT--A--TTGAAA
** *
42241279 TTAAAATGAATTTTAGATGAAATGAAA
1 TTAATTTGAA-TTTA-AT--ATTGAAA
**
42241306 TTAAAATGAATTTAAT-TTGAAA
1 TTAATTTGAATTTAATATTGAAA
42241328 TTAATTTGAA
1 TTAATTTGAA
42241338 ATTAGATGTG
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
22 25 0.35
23 2 0.03
25 2 0.03
26 4 0.06
27 15 0.21
28 15 0.21
29 8 0.11
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (23 bp):
TTAATTTGAATTTAATATTGAAA
Found at i:42241339 original size:27 final size:27
Alignment explanation
Indices: 42241246--42241320 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
42241236 GAAATTAAGT
** *
42241246 TGAAATTAATTTGAATTTAA-ATGAAGGT
1 TGAAATTAAAATGAATTTAAGATGAA--A
*
42241274 TGAAATTAAAATGAATTTTAGATGAAA
1 TGAAATTAAAATGAATTTAAGATGAAA
42241301 TGAAATTAAAATGAATTTAA
1 TGAAATTAAAATGAATTTAA
42241321 TTTGAAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 19 0.46
28 17 0.41
29 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (27 bp):
TGAAATTAAAATGAATTTAAGATGAAA
Found at i:42248370 original size:17 final size:17
Alignment explanation
Indices: 42248348--42248386 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42248338 ACTAAACCCA
* *
42248348 ATTTTAATTTTAGATTT
1 ATTTTAAGTTTAAATTT
42248365 ATTTTAAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
*
42248382 GTTTT
1 ATTTT
42248387 TAAATTTAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
ATTTTAAGTTTAAATTT
Found at i:42253561 original size:3 final size:3
Alignment explanation
Indices: 42253550--42253580 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
42253540 TCGAAGTAGT
*
42253550 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
42253581 AAGGATGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42256191 original size:21 final size:21
Alignment explanation
Indices: 42256165--42256220 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
42256155 CGTATAGATT
42256165 CTTTTAGCTCAGCTATTCGGA
1 CTTTTAGCTCAGCTATTCGGA
* * * *
42256186 CTTTTATCTCGGCTATTTGGG
1 CTTTTAGCTCAGCTATTCGGA
* *
42256207 GTTTTAGTTCAGCT
1 CTTTTAGCTCAGCT
42256221 TTTTCAACTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (21 bp):
CTTTTAGCTCAGCTATTCGGA
Found at i:42258090 original size:29 final size:30
Alignment explanation
Indices: 42258058--42258383 Score: 180
Period size: 29 Copynumber: 11.1 Consensus size: 30
42258048 CATAGTTTGA
42258058 CCCCAAACTTTCCAAAAATTA-CATTTTAC
1 CCCCAAACTTTCCAAAAATTACCATTTTAC
42258087 CCCCAAAC-TTCTCAAAAATTA-CATTTGTAC
1 CCCCAAACTTTC-CAAAAATTACCATTT-TAC
*** *
42258117 CCTTGAACTTT--AAAAATTACCATTTTAA
1 CCCCAAACTTTCCAAAAATTACCATTTTAC
* *
42258145 CCCTAAACTTTTCC-AAAATCA-CACTTTTAC
1 CCCCAAAC-TTTCCAAAAATTACCA-TTTTAC
* * * *
42258175 CCTCGAAC-TT-CAAAAATAACCATTTTTAA
1 CCCCAAACTTTCCAAAAATTACCA-TTTTAC
* *
42258204 CCCTAAACTTTCAAAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAAATTACCATTTTAC
* * *
42258234 CCTCGAAC-ATCCAAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAAATTACCATTTTAC
*** * * **
42258263 CATTAGA-TGTCCAAAAATCATA-TTTTTTA-
1 CCCCAAACTTTCCAAAAAT--TACCATTTTAC
**
42258292 CCCTGAACTTTCCAAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAAATTACCATTTTAC
* * * * *
42258322 CCTC-GAGTGTCCAAAAATTACCGTTTTAC
1 CCCCAAACTTTCCAAAAATTACCATTTTAC
* **
42258351 CCCCGAACATTT--AAAAATTACTGTTTTAC
1 CCCCAAAC-TTTCCAAAAATTACCATTTTAC
42258380 CCCC
1 CCCC
42258384 GACATCCAAA
Statistics
Matches: 227, Mismatches: 50, Indels: 40
0.72 0.16 0.13
Matches are distributed among these distances:
27 1 0.00
28 29 0.13
29 127 0.56
30 54 0.24
31 16 0.07
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
CCCCAAACTTTCCAAAAATTACCATTTTAC
Found at i:42258251 original size:88 final size:86
Alignment explanation
Indices: 42258068--42258381 Score: 250
Period size: 88 Copynumber: 3.6 Consensus size: 86
42258058 CCCCAAACTT
* * * *
42258068 TCCAAAAATTA-CATTTTACCCCCAAACTTCTCAAAAATTACATTTGTACCCTTGAACTTT-AAA
1 TCCAAAAATTACCATTTTACCCCCGAACAT-TCAAAAATAACATTTTTACCC-TGAACTTTCAAA
* *
42258131 AATTACCATTTTAACCCT-AAACTTT
64 AATTACCATTTT-ACCCTCGAAC--A
* * *
42258156 TCC-AAAATCA-CACTTTTACCCTCGAAC-TTCAAAAATAACCATTTTTAACCCTAAACTTTCAA
1 TCCAAAAATTACCA-TTTTACCCCCGAACATTCAAAAATAA-CATTTTT-ACCCTGAACTTTC-A
42258218 AAAATTACCATTTTACCCTCGAACA
62 AAAATTACCATTTTACCCTCGAACA
*** * * *
42258243 TCCAAAAATTACCATTTTA--CCATTAGATGTCCAAAAATCATATTTTTTACCCTGAACTTTCCA
1 TCCAAAAATTACCATTTTACCCCCGAACAT-T-CAAAAATAACA-TTTTTACCCTGAACTTT-CA
***
42258306 AAAATTACCATTTTACCCTCGAGTG
62 AAAATTACCATTTTACCCTCGAACA
* * *
42258331 TCCAAAAATTACCGTTTTACCCCCGAACATTTAAAAATTAC-TGTTTTACCC
1 TCCAAAAATTACCATTTTACCCCCGAACATTCAAAAATAACAT-TTTTACCC
42258382 CCGACATCCA
Statistics
Matches: 182, Mismatches: 28, Indels: 33
0.75 0.12 0.14
Matches are distributed among these distances:
86 12 0.07
87 34 0.19
88 96 0.53
89 35 0.19
90 5 0.03
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (86 bp):
TCCAAAAATTACCATTTTACCCCCGAACATTCAAAAATAACATTTTTACCCTGAACTTTCAAAAA
TTACCATTTTACCCTCGAACA
Found at i:42258261 original size:59 final size:56
Alignment explanation
Indices: 42258068--42258261 Score: 228
Period size: 58 Copynumber: 3.3 Consensus size: 56
42258058 CCCCAAACTT
* * *
42258068 TCCAAAAATTA-CATTTTACCCCCAAACTTCTCAAAAATTACATTTGTACCCTTGAAC
1 TCCAAAAATTACCATTTTAACCCTAAACTT-TCAAAAATTACATTT-TACCCTCGAAC
** * *
42258125 TTTAAAAATTACCATTTTAACCCTAAACTTTTCCAAAATCACACTTTTACCCTCGAAC
1 TCCAAAAATTACCATTTTAACCCTAAAC-TTTCAAAAATTACA-TTTTACCCTCGAAC
* *
42258183 TTCAAAAATAACCATTTTTAACCCTAAACTTTCAAAAAATTACCATTTTACCCTCGAAC
1 TCCAAAAATTACCA-TTTTAACCCTAAACTTTC-AAAAATTA-CATTTTACCCTCGAAC
42258242 ATCCAAAAATTACCATTTTA
1 -TCCAAAAATTACCATTTTA
42258262 CCATTAGATG
Statistics
Matches: 117, Mismatches: 13, Indels: 12
0.82 0.09 0.08
Matches are distributed among these distances:
57 9 0.08
58 50 0.43
59 44 0.38
60 14 0.12
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (56 bp):
TCCAAAAATTACCATTTTAACCCTAAACTTTCAAAAATTACATTTTACCCTCGAAC
Found at i:42258278 original size:59 final size:58
Alignment explanation
Indices: 42258068--42258381 Score: 207
Period size: 58 Copynumber: 5.4 Consensus size: 58
42258058 CCCCAAACTT
* * * *
42258068 TCCAAAAATTA-CATTTTACCCCCAAACT-TCTCAAAAATTA-CATTTGTACCCTTGAAC-
1 TCCAAAAATTACCATTTTA-CCCTAGAGTGTC-CAAAAATTACCATTT-TACCCTCGAACA
** * * * *
42258125 TTTAAAAATTACCATTTTAACCCTAAACTTTTCC-AAAATCA-CACTTTTACCCTCGAAC-
1 TCCAAAAATTACCATTTT-ACCCTAGA-GTGTCCAAAAATTACCA-TTTTACCCTCGAACA
* * * * * *
42258183 TTCAAAAATAACCATTTTTAACCCTAAACTTTCAAAAAATTACCATTTTACCCTCGAACA
1 TCCAAAAATTACCA-TTTT-ACCCTAGAGTGTCCAAAAATTACCATTTTACCCTCGAACA
* ** *
42258243 TCCAAAAATTACCATTTTACCATTAGA-TGTCCAAAAATCATA-TTTTTTACCCT-GAACTT
1 TCCAAAAATTACCATTTTACC-CTAGAGTGTCCAAAAAT--TACCATTTTACCCTCGAAC-A
* * *
42258302 TCCAAAAATTACCATTTTACCCTCGAGTGTCCAAAAATTACCGTTTTACCCCCGAACA
1 TCCAAAAATTACCATTTTACCCTAGAGTGTCCAAAAATTACCATTTTACCCTCGAACA
** **
42258360 TTTAAAAATTACTGTTTTACCC
1 TCCAAAAATTACCATTTTACCC
42258382 CCGACATCCA
Statistics
Matches: 211, Mismatches: 30, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
57 11 0.05
58 91 0.43
59 91 0.43
60 18 0.09
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCTAGAGTGTCCAAAAATTACCATTTTACCCTCGAACA
Found at i:42258405 original size:28 final size:28
Alignment explanation
Indices: 42258217--42258405 Score: 87
Period size: 29 Copynumber: 6.5 Consensus size: 28
42258207 TAAACTTTCA
* *
42258217 AAAAATTACCATTTTACCCTCGAACATCC
1 AAAAATTA-CTTTTTACCCCCGAACATCC
* *** **
42258246 AAAAATTACCATTTTA-CCATTAGATGTCC
1 AAAAATTA-CTTTTTACCCCCGA-ACATCC
* * *
42258275 AAAAATCATATTTTTTA-CCCTGAACTTTCC
1 AAAAAT--TACTTTTTACCCCCGAAC-ATCC
* * ***
42258305 AAAAATTACCATTTTACCCTCGAGTGTCC
1 AAAAATTA-CTTTTTACCCCCGAACATCC
* **
42258334 AAAAATTACCGTTTTACCCCCGAACATTT
1 AAAAATTA-CTTTTTACCCCCGAACATCC
42258363 AAAAATTACTGTTTTACCCCCG-ACATCC
1 AAAAATTACT-TTTTACCCCCGAACATCC
*
42258391 AAATATTACATTTTT
1 AAAAATTAC-TTTTT
42258406 GACTCCATTT
Statistics
Matches: 123, Mismatches: 29, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
28 22 0.18
29 77 0.63
30 22 0.18
31 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAAATTACTTTTTACCCCCGAACATCC
Found at i:42258933 original size:2 final size:2
Alignment explanation
Indices: 42258926--42258962 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42258916 CAAGTTCTCA
42258926 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
42258963 ATTTTAAAGC
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:42262101 original size:16 final size:17
Alignment explanation
Indices: 42262076--42262121 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
42262066 TTGAAAATAC
*
42262076 AATAAAATAAAATACTA
1 AATAAAATAAAATACGA
*
42262093 AAT-AAAT-AAATAGGA
1 AATAAAATAAAATACGA
42262108 AATAAAATAAAATA
1 AATAAAATAAAATA
42262122 AAGTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 8 0.32
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (17 bp):
AATAAAATAAAATACGA
Found at i:42262134 original size:18 final size:18
Alignment explanation
Indices: 42262111--42262148 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42262101 AATAGGAAAT
42262111 AAAATAAAATAAAGTAAA
1 AAAATAAAATAAAGTAAA
* *
42262129 AAAATAGATTAAAGTAAA
1 AAAATAAAATAAAGTAAA
42262147 AA
1 AA
42262149 GGAGAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (18 bp):
AAAATAAAATAAAGTAAA
Found at i:42262146 original size:5 final size:5
Alignment explanation
Indices: 42262069--42262129 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
42262059 ACACGATTTG
*
42262069 AAAAT ACAAT AAAAT AAAAT ACTAAAT -AAAT -AAAT AGGAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A--AAAT AAAAT AAAAT A--AAAT AAAAT
*
42262116 AAAAT AAAGT AAAA
1 AAAAT AAAAT AAAA
42262130 AAATAGATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
4 8 0.17
5 30 0.64
7 9 0.19
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:42264810 original size:30 final size:32
Alignment explanation
Indices: 42264774--42264847 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
42264764 AATTATATTT
*
42264774 ACATTTATTGTA-TT-TATTTAATACAATAAA
1 ACATTTATTATATTTGTATTTAATACAATAAA
* *
42264804 ACATTTATTATATTTGTTTTTAATATAATAAA
1 ACATTTATTATATTTGTATTTAATACAATAAA
*
42264836 ATATTTATTATA
1 ACATTTATTATA
42264848 CTTACAGTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 11 0.29
31 2 0.05
32 25 0.66
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (32 bp):
ACATTTATTATATTTGTATTTAATACAATAAA
Found at i:42268437 original size:29 final size:29
Alignment explanation
Indices: 42268400--42268459 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
42268390 ATTTGCACTA
* * *
42268400 TTCATTTTAGGTCATTTAGGTGAATAATT
1 TTCAATTTAGATCATTTAGGTAAATAATT
*
42268429 TTCAATTTAGATCATTTATGTAAATAATT
1 TTCAATTTAGATCATTTAGGTAAATAATT
42268458 TT
1 TT
42268460 TTTTCATGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.50
Consensus pattern (29 bp):
TTCAATTTAGATCATTTAGGTAAATAATT
Found at i:42270568 original size:13 final size:13
Alignment explanation
Indices: 42270550--42270574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42270540 ATGATGATGC
42270550 TTATAATTATAAA
1 TTATAATTATAAA
42270563 TTATAATTATAA
1 TTATAATTATAA
42270575 TATTTTATTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATAATTATAAA
Found at i:42271663 original size:41 final size:43
Alignment explanation
Indices: 42271584--42271663 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
42271574 CCAAATATAA
*
42271584 TTTCGTTCTTACAAAAAACTCATAAACTAAATCCAAAATCAAT
1 TTTCGTTCTTACAAAAAACTCATAAACTAAATCAAAAATCAAT
* *
42271627 TTTCGCTTCTTA-AAAAAA-TCCTAAATTAAAT-AAAAAT
1 TTTCG-TTCTTACAAAAAACTCATAAACTAAATCAAAAAT
42271664 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 5 0.15
42 11 0.33
43 11 0.33
44 6 0.18
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (43 bp):
TTTCGTTCTTACAAAAAACTCATAAACTAAATCAAAAATCAAT
Found at i:42272268 original size:6 final size:6
Alignment explanation
Indices: 42272257--42272281 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42272247 TTAGAGGGAA
42272257 GAAGAT GAAGAT GAAGAT GAAGAT G
1 GAAGAT GAAGAT GAAGAT GAAGAT G
42272282 GAGAAAAGAG
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:42273291 original size:2 final size:2
Alignment explanation
Indices: 42273284--42273308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42273274 TCAAATCTTA
42273284 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
42273309 AAAAGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42284476 original size:31 final size:32
Alignment explanation
Indices: 42284419--42284480 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
42284409 TAATTATATA
*
42284419 TATTTAATGATATAATTTATATTTTAACAAAT
1 TATTTAATGATATAAATTATATTTTAACAAAT
42284451 TATTTAAT-ATTATAAATT-TATTTTAACAAA
1 TATTTAATGA-TATAAATTATATTTTAACAAA
42284481 CAAAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (32 bp):
TATTTAATGATATAAATTATATTTTAACAAAT
Found at i:42285086 original size:40 final size:41
Alignment explanation
Indices: 42285011--42285112 Score: 136
Period size: 40 Copynumber: 2.5 Consensus size: 41
42285001 GAAAAGCGTT
* * *
42285011 TTCACGTGAAAGCAC-TTTCCTTGAATAAGATAAAAACGCC
1 TTCACGTGGAAGCACTTTTCCTTGAATAAGACAAAAACACC
* *
42285051 TTCATGTGGAAGCACTTTTCCTTGAATGAG-CAAAAACACC
1 TTCACGTGGAAGCACTTTTCCTTGAATAAGACAAAAACACC
*
42285091 TTCACGTGGAAGCATTTTTCCT
1 TTCACGTGGAAGCACTTTTCCT
42285113 AGGAAGCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 41 0.76
41 13 0.24
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (41 bp):
TTCACGTGGAAGCACTTTTCCTTGAATAAGACAAAAACACC
Found at i:42285119 original size:16 final size:16
Alignment explanation
Indices: 42285098--42285128 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42285088 ACCTTCACGT
42285098 GGAAGCATTTTTCCTA
1 GGAAGCATTTTTCCTA
42285114 GGAAGCATTTTTCCT
1 GGAAGCATTTTTCCT
42285129 TGGATGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (16 bp):
GGAAGCATTTTTCCTA
Found at i:42286327 original size:35 final size:35
Alignment explanation
Indices: 42286281--42286350 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
42286271 AGGTTTGGTA
*
42286281 TACCTTGAACTCTAATAGTTATTAGAAATAGATCT
1 TACCTTGAACTCCAATAGTTATTAGAAATAGATCT
42286316 TACCTTGAACTCCAATAGTTATTAGAAATAGATCT
1 TACCTTGAACTCCAATAGTTATTAGAAATAGATCT
42286351 CTACTTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (35 bp):
TACCTTGAACTCCAATAGTTATTAGAAATAGATCT
Found at i:42298498 original size:18 final size:17
Alignment explanation
Indices: 42298460--42298497 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
42298450 ATGAATCAAA
42298460 TTTAAATTTAATTAAAAT
1 TTTAAATTT-ATTAAAAT
42298478 TTTAAATTT-TTAATAAT
1 TTTAAATTTATTAA-AAT
42298495 TTT
1 TTT
42298498 TTAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTAAAAT
Found at i:42298612 original size:18 final size:19
Alignment explanation
Indices: 42298576--42298628 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
42298566 GATAATTTTT
42298576 TTAAATAATTAATAA-AAAA
1 TTAAAT-ATTAATAATAAAA
*
42298595 -TCAATATTAATAATAAAA
1 TTAAATATTAATAATAAAA
42298613 TTAAATATT-ATAATAA
1 TTAAATATTAATAATAA
42298629 TATTGTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 8 0.27
18 15 0.50
19 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAATATTAATAATAAAA
Found at i:42299860 original size:67 final size:69
Alignment explanation
Indices: 42299780--42299978 Score: 230
Period size: 67 Copynumber: 2.9 Consensus size: 69
42299770 TCATGCGTTA
* *
42299780 TATGTTTAAATATT-ATGTGATTTATACTTAAATATT-ATATGATTTATGTTTAAATATTAATTT
1 TATGTTTAAATATTAATATGATTTATACTTAAATATTAATATGATTTATGTTTAAATATTAATGT
42299843 AATT
66 AATT
* * * * *
42299847 TGTGTTTAAATATTAATATCA-TTATACCTAAATATTAATATGATTTAT-TTTATATAGTAATGT
1 TATGTTTAAATATTAATATGATTTATACTTAAATATTAATATGATTTATGTTTAAATATTAATGT
42299910 AATT
66 AATT
* * * * *
42299914 TAT-TCTTAAATGTTAATATGATTTATGA-TTAATTATTAATGTGATTTATGTTGAAATATTCAT
1 TATGT-TTAAATATTAATATGATTTAT-ACTTAAATATTAATATGATTTATGTTTAAATATTAAT
42299977 GT
64 GT
42299979 GATTAATACG
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
66 1 0.01
67 59 0.54
68 37 0.34
69 12 0.11
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (69 bp):
TATGTTTAAATATTAATATGATTTATACTTAAATATTAATATGATTTATGTTTAAATATTAATGT
AATT
Found at i:42299978 original size:23 final size:23
Alignment explanation
Indices: 42299780--42299982 Score: 173
Period size: 23 Copynumber: 9.0 Consensus size: 23
42299770 TCATGCGTTA
*
42299780 TATGTTTAAATATT-ATGTGATT
1 TATGTTTAAATATTAATATGATT
**
42299802 TATACTTAAATATT-ATATGATT
1 TATGTTTAAATATTAATATGATT
* *
42299824 TATGTTTAAATATTAATTTAATT
1 TATGTTTAAATATTAATATGATT
* *
42299847 TGTGTTTAAATATTAATATCA-T
1 TATGTTTAAATATTAATATGATT
***
42299869 TATACCTAAATATTAATATGATT
1 TATGTTTAAATATTAATATGATT
* * * *
42299892 TAT-TTTATATAGTAATGTAATT
1 TATGTTTAAATATTAATATGATT
*
42299914 TAT-TCTTAAATGTTAATATGATT
1 TATGT-TTAAATATTAATATGATT
* * *
42299937 TATGATTAATTATTAATGTGATT
1 TATGTTTAAATATTAATATGATT
* * *
42299960 TATGTTGAAATATTCATGTGATT
1 TATGTTTAAATATTAATATGATT
42299983 AATACGTAAT
Statistics
Matches: 143, Mismatches: 34, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
22 65 0.45
23 78 0.55
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.51
Consensus pattern (23 bp):
TATGTTTAAATATTAATATGATT
Found at i:42300031 original size:10 final size:11
Alignment explanation
Indices: 42300016--42300129 Score: 58
Period size: 10 Copynumber: 10.2 Consensus size: 11
42300006 AAATATTCAC
42300016 GTGATTAA-AT
1 GTGATTAATAT
42300026 GTGATTAATAT
1 GTGATTAATAT
* * *
42300037 GTTATGTGATAA
1 GTGAT-TAATAT
*
42300049 ATGATTAATATT
1 GTGATTAATA-T
*
42300061 CACGTGAGTAA--T
1 ---GTGATTAATAT
42300073 GTGATTAA-AT
1 GTGATTAATAT
42300083 GTGATTAATAT
1 GTGATTAATAT
* *
42300094 GTGTTGTGACTAT
1 GTGAT-T-AATAT
42300107 GTGATTAA-AT
1 GTGATTAATAT
*
42300117 GTGATAAATAT
1 GTGATTAATAT
42300128 GT
1 GT
42300130 CTTGTGTTAA
Statistics
Matches: 78, Mismatches: 15, Indels: 21
0.68 0.13 0.18
Matches are distributed among these distances:
9 7 0.09
10 26 0.33
11 21 0.27
12 10 0.13
13 8 0.10
15 6 0.08
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (11 bp):
GTGATTAATAT
Found at i:42300032 original size:49 final size:47
Alignment explanation
Indices: 42299975--42300080 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 47
42299965 TGAAATATTC
*
42299975 ATGTGATTAATACGTAATGTGAGAAATG-TTGAAATATTCACGTGATTAA
1 ATGTGATTAATACGTAATGTGAGAAATGATT--AATATTCACGTGAGT-A
* * *
42300024 ATGTGATTAATATGTTATGTGATAAATGATTAATATTCACGTGAGTA
1 ATGTGATTAATACGTAATGTGAGAAATGATTAATATTCACGTGAGTA
42300071 ATGTGATTAA
1 ATGTGATTAA
42300081 ATGTGATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
47 11 0.21
48 14 0.27
49 25 0.48
50 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (47 bp):
ATGTGATTAATACGTAATGTGAGAAATGATTAATATTCACGTGAGTA
Found at i:42300090 original size:34 final size:34
Alignment explanation
Indices: 42300039--42300130 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 34
42300029 ATTAATATGT
*
42300039 TATGTGA-TAAA--TGATTAATAT-TCACGTGAG
1 TATGTGATTAAATGTGATTAATATGTCACGTGAC
***
42300069 TAATGTGATTAAATGTGATTAATATGTGTTGTGAC
1 T-ATGTGATTAAATGTGATTAATATGTCACGTGAC
*
42300104 TATGTGATTAAATGTGATAAATATGTC
1 TATGTGATTAAATGTGATTAATATGTC
42300131 TTGTGTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 6 0.12
32 4 0.08
34 34 0.67
35 6 0.12
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (34 bp):
TATGTGATTAAATGTGATTAATATGTCACGTGAC
Found at i:42300135 original size:34 final size:34
Alignment explanation
Indices: 42300071--42300135 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
42300061 CACGTGAGTA
* *
42300071 ATGTGATTAAATGTGATTAATATGTGTTGTGACT
1 ATGTGATTAAATGTGATAAATATGTCTTGTGACT
42300105 ATGTGATTAAATGTGATAAATATGTCTTGTG
1 ATGTGATTAAATGTGATAAATATGTCTTGTG
42300136 TTAAATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (34 bp):
ATGTGATTAAATGTGATAAATATGTCTTGTGACT
Found at i:42301494 original size:20 final size:21
Alignment explanation
Indices: 42301469--42301508 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42301459 CAAGTCAAAC
*
42301469 CATTGATCGA-CGTTGACCGG
1 CATTGACCGACCGTTGACCGG
42301489 CATTGACCGACCGTTGACCG
1 CATTGACCGACCGTTGACCG
42301509 TTGACTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.23
Consensus pattern (21 bp):
CATTGACCGACCGTTGACCGG
Found at i:42301566 original size:20 final size:20
Alignment explanation
Indices: 42301534--42301586 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
42301524 ACCGTTGAAT
42301534 TTGACTGTTGACCACTGAT-CG
1 TTGACT-TTGACCACTG-TCCG
**
42301555 TTGACTTTGACCGTTGTCCG
1 TTGACTTTGACCACTGTCCG
42301575 TTGACTTTGACC
1 TTGACTTTGACC
42301587 GTTGACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 22 0.76
21 6 0.21
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGACTTTGACCACTGTCCG
Found at i:42301587 original size:20 final size:20
Alignment explanation
Indices: 42301553--42301590 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
42301543 GACCACTGAT
42301553 CGTTGACTTTGACCGTTGTC
1 CGTTGACTTTGACCGTTGTC
42301573 CGTTGACTTTGACCGTTG
1 CGTTGACTTTGACCGTTG
42301591 ACTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.26, T:0.39
Consensus pattern (20 bp):
CGTTGACTTTGACCGTTGTC
Found at i:42302655 original size:3 final size:3
Alignment explanation
Indices: 42302643--42302678 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
42302633 TATTCTATTC
*
42302643 TAT T-T TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42302679 TTGGGATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:42308115 original size:10 final size:10
Alignment explanation
Indices: 42308100--42308134 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
42308090 TGCCCCAAAC
42308100 CTTTTTCTTT
1 CTTTTTCTTT
42308110 C-TTTT-TTT
1 CTTTTTCTTT
42308118 CTTTTTCTTT
1 CTTTTTCTTT
42308128 CTTTTTC
1 CTTTTTC
42308135 CCTTGCCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 4 0.17
9 8 0.35
10 11 0.48
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:42308635 original size:21 final size:22
Alignment explanation
Indices: 42308599--42308644 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
42308589 ACCCATTAAG
42308599 CCCAAATCCTATTTAAACCAAA
1 CCCAAATCCTATTTAAACCAAA
*
42308621 CCCAAATTC-ATTTAAACCAAA
1 CCCAAATCCTATTTAAACCAAA
42308642 CCC
1 CCC
42308645 TTTTGAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (22 bp):
CCCAAATCCTATTTAAACCAAA
Found at i:42308761 original size:13 final size:13
Alignment explanation
Indices: 42308739--42308891 Score: 106
Period size: 13 Copynumber: 12.0 Consensus size: 13
42308729 ACCGGTGTTG
*
42308739 TTTGACCGTTGAT
1 TTTGACCGTTGAC
*
42308752 TTTGATCGTTGAC
1 TTTGACCGTTGAC
* *
42308765 TTTGGCAGTTGAC
1 TTTGACCGTTGAC
42308778 -----C-GTTGAC
1 TTTGACCGTTGAC
42308785 TTTGACCGTTGACC
1 TTTGACCGTTGA-C
**
42308799 ACTGACCGTTGAC
1 TTTGACCGTTGAC
42308812 TTTGACCGTTGACC
1 TTTGACCGTTGA-C
* *
42308826 GTTGA-CTTTGA-
1 TTTGACCGTTGAC
42308837 TAGTTGACCGTTGAC
1 T--TTGACCGTTGAC
42308852 TTTGACCGTTGACC
1 TTTGACCGTTGA-C
** *
42308866 CCTGATCGTTGAC
1 TTTGACCGTTGAC
42308879 TTTGACCGTTGAC
1 TTTGACCGTTGAC
42308892 CGTTGACTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
7 6 0.06
8 1 0.01
12 1 0.01
13 68 0.63
14 31 0.29
15 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (13 bp):
TTTGACCGTTGAC
Found at i:42308795 original size:20 final size:20
Alignment explanation
Indices: 42308740--42308910 Score: 139
Period size: 20 Copynumber: 8.2 Consensus size: 20
42308730 CCGGTGTTGT
* *
42308740 TTGACCGTTGATTTTGATCG
1 TTGACCGTTGACTTTGACCG
* * *
42308760 TTGA-CTTTGGCAGTTGACCG
1 TTGACCGTTGAC-TTTGACCG
* * *
42308780 TTGA-CTTTGACCGTTGACCA
1 TTGACCGTTGA-CTTTGACCG
*
42308800 CTGACCGTTGACTTTGACCG
1 TTGACCGTTGACTTTGACCG
**
42308820 TTGACCGTTGACTTTGATAG
1 TTGACCGTTGACTTTGACCG
42308840 TTGACCGTTGACTTTGACCG
1 TTGACCGTTGACTTTGACCG
42308860 TTGACCCCTGATCGTTGACTTTGACCG
1 TTGA---C----CGTTGACTTTGACCG
*
42308887 TTGACCGTTGACTTTGACTG
1 TTGACCGTTGACTTTGACCG
42308907 TTGA
1 TTGA
42308911 TTTTTTTTTG
Statistics
Matches: 124, Mismatches: 17, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
19 4 0.03
20 93 0.75
21 6 0.05
23 1 0.01
24 1 0.01
27 19 0.15
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGACCGTTGACTTTGACCG
Found at i:42308829 original size:67 final size:67
Alignment explanation
Indices: 42308753--42308910 Score: 262
Period size: 67 Copynumber: 2.4 Consensus size: 67
42308743 ACCGTTGATT
* *
42308753 TTGATCGTTGACTTTGGCAGTTGACCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGAC
1 TTGACCGTTGACTTTGACAGTTGACCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGAC
42308818 CG
66 CG
* * *
42308820 TTGACCGTTGACTTTGATAGTTGACCGTTGACTTTGACCGTTGACCCCTGATCGTTGACTTTGAC
1 TTGACCGTTGACTTTGACAGTTGACCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGAC
42308885 CG
66 CG
*
42308887 TTGACCGTTGACTTTGACTGTTGA
1 TTGACCGTTGACTTTGACAGTTGA
42308911 TTTTTTTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 84 1.00
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (67 bp):
TTGACCGTTGACTTTGACAGTTGACCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGAC
CG
Found at i:42308863 original size:27 final size:27
Alignment explanation
Indices: 42308773--42308891 Score: 120
Period size: 27 Copynumber: 4.4 Consensus size: 27
42308763 ACTTTGGCAG
*
42308773 TTGACCGTTGACTTTGACCGTTGACCA
1 TTGACCGTTGACTTTGACCGTTGACCT
* *
42308800 CTGACCGTTGACTTTGACCGTTGACCG
1 TTGACCGTTGACTTTGACCGTTGACCT
*
42308827 TTGA-CTTTGA-TAGTTGACCGTTGA-CT
1 TTGACCGTTGACT--TTGACCGTTGACCT
** *
42308853 TTGACCGTTGACCCCTGATCGTTGA-CT
1 TTGACCGTTGA-CTTTGACCGTTGACCT
42308880 TTGACCGTTGAC
1 TTGACCGTTGAC
42308892 CGTTGACTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
25 1 0.01
26 11 0.14
27 66 0.85
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (27 bp):
TTGACCGTTGACTTTGACCGTTGACCT
Found at i:42308864 original size:47 final size:47
Alignment explanation
Indices: 42308772--42308910 Score: 172
Period size: 47 Copynumber: 3.0 Consensus size: 47
42308762 GACTTTGGCA
** * *
42308772 GTTGACCGTTGACTTTGACCGTTGACCACTGACCGTTGA-CTTTGACC
1 GTTGACCGTTGACTTTGACCGTTGACCGTTGA-CTTTGACCGTTGACC
**
42308819 GTTGACCGTTGACTTTGATAGTTGACCGTTGACTTTGACCGTTGACC
1 GTTGACCGTTGACTTTGACCGTTGACCGTTGACTTTGACCGTTGACC
** * *
42308866 CCTGATCGTTGACTTTGACCGTTGACCGTTGACTTTGACTGTTGA
1 GTTGACCGTTGACTTTGACCGTTGACCGTTGACTTTGACCGTTGA
42308911 TTTTTTTTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
46 5 0.06
47 74 0.94
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (47 bp):
GTTGACCGTTGACTTTGACCGTTGACCGTTGACTTTGACCGTTGACC
Found at i:42309972 original size:3 final size:3
Alignment explanation
Indices: 42309964--42309997 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42309954 TTCTATTCTA
42309964 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42309998 TTGGGATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42313502 original size:12 final size:12
Alignment explanation
Indices: 42313481--42313527 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
42313471 TTGTATAATT
*
42313481 AAATTAAAAATA
1 AAATTTAAAATA
42313493 AAATTTAAAATA
1 AAATTTAAAATA
*
42313505 TAAATTTAAATTA
1 -AAATTTAAAATA
*
42313518 TAA-TTAAAAT
1 AAATTTAAAAT
42313528 TTTACGTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 6 0.20
12 13 0.43
13 11 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTTAAAATA
Found at i:42313519 original size:13 final size:13
Alignment explanation
Indices: 42313480--42313520 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
42313470 TTTGTATAAT
*
42313480 TAAATTAAAAATA
1 TAAATTTAAAATA
42313493 -AAATTTAAAATA
1 TAAATTTAAAATA
*
42313505 TAAATTTAAATTA
1 TAAATTTAAAATA
42313518 TAA
1 TAA
42313521 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATTTAAAATA
Found at i:42313542 original size:62 final size:62
Alignment explanation
Indices: 42313472--42313591 Score: 172
Period size: 62 Copynumber: 1.9 Consensus size: 62
42313462 TATTTAAATT
42313472 TGTATAATTAAATTAAAAATAAAATTTAAAATATA-AATT-TAAATTATAATTAAAATTTTACG
1 TGTATAATTAAATT-AAAATAAAATTTAAAATATATAATTATAAATTA-AATTAAAATTTTACG
* * * *
42313534 TGTATAATTATATTAAATTAAAATTTATAATATATAATTATACATTAAATTAAAATTT
1 TGTATAATTAAATTAAAATAAAATTTAAAATATATAATTATAAATTAAATTAAAATTT
42313592 ATATATAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
61 18 0.35
62 28 0.54
63 6 0.12
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.43
Consensus pattern (62 bp):
TGTATAATTAAATTAAAATAAAATTTAAAATATATAATTATAAATTAAATTAAAATTTTACG
Found at i:42313555 original size:30 final size:31
Alignment explanation
Indices: 42313474--42313598 Score: 127
Period size: 31 Copynumber: 4.1 Consensus size: 31
42313464 TTTAAATTTG
* *
42313474 TATAATTA-AATTAAAAATAAAATTTAAAATA
1 TATAATTATAATT-AAATTAAAATTTATAATA
* *
42313505 TA-AATT-TAAATTATAATTAAAATTT-TACGTG
1 TATAATTAT-AATTA-AATTAAAATTTATA-ATA
42313536 TATAATTAT-ATTAAATTAAAATTTATAATA
1 TATAATTATAATTAAATTAAAATTTATAATA
42313566 TATAATTATACATTAAATTAAAATTTAT-ATA
1 TATAATTATA-ATTAAATTAAAATTTATAATA
42313597 TA
1 TA
42313599 ATTTTGAGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
30 27 0.34
31 30 0.38
32 21 0.27
33 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TATAATTATAATTAAATTAAAATTTATAATA
Found at i:42313585 original size:42 final size:42
Alignment explanation
Indices: 42313505--42313585 Score: 94
Period size: 42 Copynumber: 1.9 Consensus size: 42
42313495 ATTTAAAATA
* * *
42313505 TAAATTTAAATTATAATTAAAATTTTACGTGTATAATTATAT
1 TAAATTAAAATTATAATTAAAATTATACATGTATAATTATAT
*
42313547 TAAATTAAAATTTATAATATATAATTATACAT-TA-AATTA
1 TAAATTAAAA-TTATAAT-TAAAATTATACATGTATAATTA
42313586 AAATTTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
42 14 0.42
43 9 0.27
44 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (42 bp):
TAAATTAAAATTATAATTAAAATTATACATGTATAATTATAT
Found at i:42314544 original size:21 final size:20
Alignment explanation
Indices: 42314520--42314559 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42314510 AACAAAATGA
42314520 GTTTATCCTCCTGCTTTTGTT
1 GTTTA-CCTCCTGCTTTTGTT
* *
42314541 GTTTACTTTCTGCTTTTGT
1 GTTTACCTCCTGCTTTTGT
42314560 GCGTAGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.05, C:0.20, G:0.15, T:0.60
Consensus pattern (20 bp):
GTTTACCTCCTGCTTTTGTT
Found at i:42317172 original size:29 final size:30
Alignment explanation
Indices: 42317107--42317176 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
42317097 ATATCAAAAT
*
42317107 TATACATGAACTATGGTTTAATGTGTAATTG
1 TATACATGAACTATGGTTT-ATGTGGAATTG
* *
42317138 TATACATGAACTTTGGTTT-TGTGCGATTTG
1 TATACATGAACTATGGTTTATGTG-GAATTG
42317168 -ATACATGAA
1 TATACATGAA
42317177 ATTTTGACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.37
30 4 0.11
31 18 0.51
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (30 bp):
TATACATGAACTATGGTTTATGTGGAATTG
Found at i:42322974 original size:23 final size:23
Alignment explanation
Indices: 42322909--42323035 Score: 132
Period size: 23 Copynumber: 5.4 Consensus size: 23
42322899 GAAATGATGG
*
42322909 GTGCTCTCT-ATTTAGCAC-GTCT
1 GTGCTCTCTGA-TTAGCACTGTGT
*
42322931 CGTGCTCTTTGTTATTAGCACTGTGT
1 -GTGCTCTCTG--ATTAGCACTGTGT
*
42322957 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
42322980 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* * *
42323003 GTACTCTCTGTTTAGCATTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
42323026 GTGCTCTCTG
1 GTGCTCTCTG
42323036 TTGCCCAGCA
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
23 69 0.78
25 16 0.18
26 4 0.04
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:42323025 original size:69 final size:66
Alignment explanation
Indices: 42322945--42323081 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 66
42322935 CTCTTTGTTA
* *
42322945 TTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTC
1 TTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCT-ATTAGTACTTTG-ATACTC
42323009 TCTGT
62 TCTGT
* *
42323014 TTAGCATTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTCTTAGTACTTTGATACTCT
1 TTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTATTAGTACTTTGATACTCT
42323079 CTG
63 CTG
42323082 CTTGTTCCGT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
68 2 0.03
69 30 0.50
70 11 0.18
71 12 0.20
72 5 0.08
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (66 bp):
TTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTATTAGTACTTTGATACTCTCTG
T
Found at i:42330122 original size:25 final size:26
Alignment explanation
Indices: 42330094--42330144 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
42330084 CACTCTCTGT
42330094 TTAGCAC-GTCTCGTGCTCTCT-ATTA
1 TTAGCACTGTCT-GTGCTCTCTGATTA
*
42330119 TTAGCACTGTGTGTGCTCTCTGATTA
1 TTAGCACTGTCTGTGCTCTCTGATTA
42330145 GCACTTTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (26 bp):
TTAGCACTGTCTGTGCTCTCTGATTA
Found at i:42330144 original size:23 final size:23
Alignment explanation
Indices: 42330118--42330254 Score: 148
Period size: 23 Copynumber: 6.0 Consensus size: 23
42330108 GCTCTCTATT
*
42330118 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
*
42330141 ATTAGCACTTTGTGTGCTCACTG
1 ATTAGCACTTTGTGTGCTCTCTG
* * * *
42330164 ATTAGTAATTTGTATACTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
* *
42330187 TTTAGCACTTTGTGTGCTCACTG
1 ATTAGCACTTTGTGTGCTCTCTG
* * * *
42330210 ATTAGTAATTTGTATACTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
* *
42330233 TTTAGCACTGTGTGTGCTCTCT
1 ATTAGCACTTTGTGTGCTCTCT
42330255 ATTGCCCAGC
Statistics
Matches: 89, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 89 1.00
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.44
Consensus pattern (23 bp):
ATTAGCACTTTGTGTGCTCTCTG
Found at i:42330192 original size:46 final size:46
Alignment explanation
Indices: 42330134--42330251 Score: 218
Period size: 46 Copynumber: 2.6 Consensus size: 46
42330124 ACTGTGTGTG
*
42330134 CTCTCTGATTAGCACTTTGTGTGCTCACTGATTAGTAATTTGTATA
1 CTCTCTGTTTAGCACTTTGTGTGCTCACTGATTAGTAATTTGTATA
42330180 CTCTCTGTTTAGCACTTTGTGTGCTCACTGATTAGTAATTTGTATA
1 CTCTCTGTTTAGCACTTTGTGTGCTCACTGATTAGTAATTTGTATA
*
42330226 CTCTCTGTTTAGCACTGTGTGTGCTC
1 CTCTCTGTTTAGCACTTTGTGTGCTC
42330252 TCTATTGCCC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (46 bp):
CTCTCTGTTTAGCACTTTGTGTGCTCACTGATTAGTAATTTGTATA
Found at i:42330253 original size:69 final size:71
Alignment explanation
Indices: 42330085--42330255 Score: 177
Period size: 69 Copynumber: 2.4 Consensus size: 71
42330075 ACACTAGCGC
* * * *
42330085 ACTCTCTGTTTAGCAC-GTCTCGTGCTCTCTATTATTAGCACTGTGTGTGCTCTCTGATTAGCAC
1 ACTCTCTGTTTAGCACTGTGT-GTGCTCTCTAGTATTAGCACTGTGTGTGCTCACTGATTAGCAA
*
42330149 TTTGTGT
65 TTTGTAT
* * * * * * * * * *
42330156 GCTCACTGATTAGTAATTTGTATACTCTCT-GT-TTAGCACTTTGTGTGCTCACTGATTAGTAAT
1 ACTCTCTGTTTAGCACTGTGTGTGCTCTCTAGTATTAGCACTGTGTGTGCTCACTGATTAGCAAT
42330219 TTGTAT
66 TTGTAT
42330225 ACTCTCTGTTTAGCACTGTGTGTGCTCTCTA
1 ACTCTCTGTTTAGCACTGTGTGTGCTCTCTA
42330256 TTGCCCAGCA
Statistics
Matches: 75, Mismatches: 23, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
69 54 0.72
70 1 0.01
71 18 0.24
72 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (71 bp):
ACTCTCTGTTTAGCACTGTGTGTGCTCTCTAGTATTAGCACTGTGTGTGCTCACTGATTAGCAAT
TTGTAT
Found at i:42332151 original size:29 final size:29
Alignment explanation
Indices: 42332069--42332163 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 29
42332059 AATTTGTATG
* *
42332069 ATTAAATTAAAATTAAAATTTAAAATATATA
1 ATTAAA-TCAAATTAAAATTT-ATATATATA
*
42332100 TTTAAATCACAATTAAAACTTTATATATATA
1 ATTAAATCA-AATTAAAA-TTTATATATATA
* *
42332131 ATTACATCAAATTAAAATTTATATATACA
1 ATTAAATCAAATTAAAATTTATATATATA
42332160 ATTA
1 ATTA
42332164 TACATTAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.27
30 10 0.18
31 28 0.50
32 3 0.05
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (29 bp):
ATTAAATCAAATTAAAATTTATATATATA
Found at i:42332168 original size:31 final size:29
Alignment explanation
Indices: 42332078--42332194 Score: 101
Period size: 31 Copynumber: 3.9 Consensus size: 29
42332068 GATTAAATTA
* * *
42332078 AAATTAAAATTTAAAATATATATTTAAATC
1 AAATTAAAATTT-ATATATAAATTTACATC
42332108 ACAATTAAAACTTTATATATATAA-TTACATC
1 A-AATTAAAA-TTTATATATA-AATTTACATC
*
42332139 AAATTAAAATTTATATATACAATTATACATT
1 AAATTAAAATTTATATATA-AATT-TACATC
* ** *
42332170 AAATCAAAATCAATATATAATTTTA
1 AAATTAAAATTTATATATAAATTTA
42332195 AGATTTATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
29 14 0.19
30 13 0.18
31 42 0.58
32 4 0.05
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (29 bp):
AAATTAAAATTTATATATAAATTTACATC
Found at i:42337694 original size:18 final size:19
Alignment explanation
Indices: 42337659--42337697 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
42337649 ATTAAATATA
42337659 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
42337678 AATA-AATTGTAAA-TTAAT
1 AATACAATT-TAAATTTAAT
42337696 AA
1 AA
42337698 AAAAACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:42339238 original size:21 final size:19
Alignment explanation
Indices: 42339205--42339243 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
42339195 TTTTTAATAA
42339205 TAATTTATTTTATTAAATT
1 TAATTTATTTTATTAAATT
42339224 TAATTTAAGTTTTATTAAAT
1 TAATTT-A-TTTTATTAAAT
42339244 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TAATTTATTTTATTAAATT
Found at i:42340797 original size:28 final size:28
Alignment explanation
Indices: 42340753--42340826 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
42340743 AAAATTATAT
*
42340753 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTGAATAATTTTA
* **
42340781 TATATT-TTTTATTTATTGAATTTTTTTA
1 TATATTATTTTA-ATATTGAATAATTTTA
42340809 TAT-TGTCATTTTAATATT
1 TATAT-T-ATTTTAATATT
42340827 ATTTTAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 6 0.16
28 22 0.59
29 4 0.11
30 5 0.14
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (28 bp):
TATATTATTTTAATATTGAATAATTTTA
Found at i:42345384 original size:132 final size:132
Alignment explanation
Indices: 42345141--42345421 Score: 402
Period size: 132 Copynumber: 2.1 Consensus size: 132
42345131 GAAATGGGCC
*
42345141 TGCTCACACGAGCTATGGGTCGAGATGTGAGGCTACACGATACTGCTCACACGAGCTATGGAGAA
1 TGCTCACACGAGCTATGGGTCGAGATGTGAGGCTACACGATACTGCTCACACGAGCTATAGAGAA
* * * ** * * *
42345206 TCCGCAATAAATGTCGGACCTTAGCCATCTGTAGGACATCTGAGACCAGCGCCTATATAACCTGT
66 TCCGCAACAAATGTCGGACCTCAGCCATCGGTAGGACATCCAAGACCAGCACCCATATAACCTAT
42345271 AA
131 AA
* * * *
42345273 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACGATACTTCTCACACGAGCTGTAGAGAA
1 TGCTCACACGAGCTATGGGTCGAGATGTGAGGCTACACGATACTGCTCACACGAGCTATAGAGAA
*
42345338 TCCGCAACCAATG-CAGGACCTCAGCCATCGGTAGGACATCCAAGACCAGCACCCATATAACCTA
66 TCCGCAACAAATGTC-GGACCTCAGCCATCGGTAGGACATCCAAGACCAGCACCCATATAACCTA
42345402 TAA
130 TAA
* *
42345405 TACTCACACAAGCTATG
1 TGCTCACACGAGCTATG
42345422 AAATGGGTTT
Statistics
Matches: 131, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
131 1 0.01
132 130 0.99
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (132 bp):
TGCTCACACGAGCTATGGGTCGAGATGTGAGGCTACACGATACTGCTCACACGAGCTATAGAGAA
TCCGCAACAAATGTCGGACCTCAGCCATCGGTAGGACATCCAAGACCAGCACCCATATAACCTAT
AA
Found at i:42348015 original size:3 final size:3
Alignment explanation
Indices: 42348007--42348080 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
42347997 TGCTATCATT
* *
42348007 TTA TTA TTA -TA TTA TTA CTA -TA TTA TTA TTA TTA TTA TTTA GATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA
* * *
42348052 CTA -TA TAA TTC TTA TT- TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42348081 GTGTCGAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 8 0.14
3 45 0.78
4 5 0.09
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:42348021 original size:11 final size:11
Alignment explanation
Indices: 42348007--42348045 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
42347997 TGCTATCATT
42348007 TTATTATTATA
1 TTATTATTATA
*
42348018 TTATTACTATA
1 TTATTATTATA
42348029 TTATTATTATTA
1 TTATTATTA-TA
42348041 TTATT
1 TTATT
42348046 TAGATACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATTATTATA
Found at i:42348053 original size:28 final size:27
Alignment explanation
Indices: 42348007--42348072 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
42347997 TGCTATCATT
* *
42348007 TTATTATTATATTATTACTATATTATTA
1 TTATTATTAT-TTAATACTATATAATTA
*
42348035 TTATTATTATTTAGATACTATATAATTC
1 TTATTATTATTTA-ATACTATATAATTA
42348063 TTATT-TTATT
1 TTATTATTATT
42348073 ATTATTATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 8 0.24
28 26 0.76
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTATTATTTAATACTATATAATTA
Found at i:42349070 original size:25 final size:24
Alignment explanation
Indices: 42349031--42349080 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
42349021 AAAACCCCTC
42349031 AACCTTAAACCTAATAAAATATAA
1 AACCTTAAACCTAATAAAATATAA
*
42349055 AACCTTAACCCTTAATAAAATATAA
1 AACCTTAAACC-TAATAAAATATAA
42349080 A
1 A
42349081 TTATAACCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (24 bp):
AACCTTAAACCTAATAAAATATAA
Found at i:42350612 original size:29 final size:29
Alignment explanation
Indices: 42350570--42350688 Score: 89
Period size: 29 Copynumber: 4.1 Consensus size: 29
42350560 CAATCTTTAT
* * *
42350570 AATATTTAATAAATTTAGGTATCAAATTA
1 AATATTAAAAAAATTTAGATATCAAATTA
*
42350599 AATATTAAAAAAATACTTAGGTATCAAATTA
1 AATATTAAAAAAAT--TTAGATATCAAATTA
* * *** * *
42350630 AAAAAT-GTCAAATTTAAATATCAAATTG
1 AATATTAAAAAAATTTAGATATCAAATTA
*
42350658 AAT-TCAAAAATAATTTAGATATCAAATTA
1 AATATTAAAAA-AATTTAGATATCAAATTA
42350687 AA
1 AA
42350689 AAAAATTATC
Statistics
Matches: 68, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
28 15 0.22
29 30 0.44
30 4 0.06
31 19 0.28
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (29 bp):
AATATTAAAAAAATTTAGATATCAAATTA
Found at i:42350654 original size:59 final size:59
Alignment explanation
Indices: 42350580--42350718 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 59
42350570 AATATTTAAT
** * * *
42350580 AAATTTAGGTATCAAATTAAATATTAAAAA-AATACTTAGGTATCAAATT-AAAAAA-TGTC
1 AAATTTAAATATCAAATTAAAT-TCAAAAATAAT--TTAGATATCAAATTAAAAAAATTATC
*
42350639 AAATTTAAATATCAAATTGAATTCAAAAATAATTTAGATATCAAATTAAAAAAAATTATC
1 AAATTTAAATATCAAATTAAATTCAAAAATAATTTAGATATCAAATT-AAAAAAATTATC
42350699 AAATTTAAATATCAAATTAA
1 AAATTTAAATATCAAATTAA
42350719 GTCTAAAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
57 13 0.19
58 6 0.09
59 28 0.41
60 22 0.32
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.33
Consensus pattern (59 bp):
AAATTTAAATATCAAATTAAATTCAAAAATAATTTAGATATCAAATTAAAAAAATTATC
Found at i:42350711 original size:60 final size:56
Alignment explanation
Indices: 42350607--42350742 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 56
42350597 TAAATATTAA
* * * *
42350607 AAAAAT-ACTTAGGTATCAAATTAAAAAATGTCAAATTTAAATATCAAATTGAATTC
1 AAAAATAATTTAGATATCAAATTAAAAAATATCAAATTTAAATATCAAATT-AAGTC
42350663 AAAAATAATTTAGATATCAAATTAAAAAAAATTATCAAATTTAAATATCAAATTAAGTC
1 AAAAATAATTTAGATATCAAATT--AAAAAA-TATCAAATTTAAATATCAAATTAAGTC
* * *
42350722 TAAAA-AATTTAAAAATCAAAT
1 AAAAATAATTTAGATATCAAAT
42350743 AATATATTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
56 6 0.09
57 14 0.20
58 14 0.20
59 14 0.20
60 21 0.30
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (56 bp):
AAAAATAATTTAGATATCAAATTAAAAAATATCAAATTTAAATATCAAATTAAGTC
Found at i:42356255 original size:19 final size:22
Alignment explanation
Indices: 42356214--42356256 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
42356204 CAGCAAATGA
42356214 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTATTAAAATTATT
42356236 TTTTAAAA-TA-T-AAATTATT
1 TTTTAAAATTATTAAAATTATT
42356255 TT
1 TT
42356257 AAATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 2 0.10
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTATT
Found at i:42356261 original size:10 final size:10
Alignment explanation
Indices: 42356246--42356290 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
42356236 TTTTAAAATA
42356246 TAAATTATTT
1 TAAATTATTT
42356256 TAAATTATTT
1 TAAATTATTT
*
42356266 TAAAATTAATT
1 T-AAATTATTT
*
42356277 T-AATTTTTT
1 TAAATTATTT
42356286 TAAAT
1 TAAAT
42356291 ATAAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 7 0.23
10 14 0.47
11 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TAAATTATTT
Found at i:42356266 original size:28 final size:27
Alignment explanation
Indices: 42356219--42356306 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 27
42356209 AATGATTTTA
42356219 AAATTATTAAAATTATTTTTTAAAATAT
1 AAATTATTAAAATTA-TTTTTAAAATAT
*
42356247 AAATTATTTTAAATTA-TTTTAAAAT-T
1 AAATTA-TTAAAATTATTTTTAAAATAT
42356273 -AA-T-TT--AATT-TTTTT-AAATAT
1 AAATTATTAAAATTATTTTTAAAATAT
42356293 AAAATTATTAAAAT
1 -AAATTATTAAAAT
42356307 CATCATCATT
Statistics
Matches: 50, Mismatches: 1, Indels: 20
0.70 0.01 0.28
Matches are distributed among these distances:
19 4 0.08
20 9 0.18
22 4 0.08
23 1 0.02
24 3 0.06
25 2 0.04
26 4 0.08
27 9 0.18
28 6 0.12
29 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATTATTAAAATTATTTTTAAAATAT
Found at i:42359861 original size:3 final size:3
Alignment explanation
Indices: 42359843--42359904 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
42359833 TTAGAATACT
* *
42359843 TTA TT- TTA TTA TTTA TTA TAA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42359888 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
42359905 GGATTTTGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:42360309 original size:27 final size:26
Alignment explanation
Indices: 42360276--42360338 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
42360266 CAAAACATAA
*
42360276 AATAAAAAAATTAACAATTTAAAAGGT
1 AATAAAAAAATT-ACAATTGAAAAGGT
*
42360303 AATAAAACATAATTAGAATTGAAAAGGT
1 AATAAAA-A-AATTACAATTGAAAAGGT
42360331 AA-AAAAAA
1 AATAAAAAA
42360339 TATACATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 11 0.34
28 15 0.47
29 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.22
Consensus pattern (26 bp):
AATAAAAAAATTACAATTGAAAAGGT
Found at i:42366840 original size:104 final size:104
Alignment explanation
Indices: 42366600--42366843 Score: 271
Period size: 104 Copynumber: 2.3 Consensus size: 104
42366590 GTGCACAGAT
* * * * *
42366600 CGTGTAACTCACTGTTTGTGTATTAAGGTCACACCGATCGGGGACACGAGCATGTGTTAGATCAT
1 CGTGTAACTCACTGTTTGTGTATTAGGGCCACACGGATCGGGGACACAAGCATGCGTTAGATCAT
* * *
42366665 TTGAGGTACACGGGCTGATATAAGAGCATGTGTCTAGGC
66 GTGAGGCACACGGGCTGATACAAGAGCATGTGTCTAGGC
* * * *
42366704 CGTGTAACTTACTGTTTGTGTATTAGGCCCACACGGA-CAGGGGACACAAGCGTGCGTTAGATCG
1 CGTGTAACTCACTGTTTGTGTATTAGGGCCACACGGATC-GGGGACACAAGCATGCGTTAGATCA
* * * *
42366768 TGTGAGGCACATGGGCTGATACATA-AGCATTTGTTTAGGT
65 TGTGAGGCACACGGGCTGATACA-AGAGCATGTGTCTAGGC
*
42366808 TGTGTAACTCACTGTTT-TAG-ATATAGGGCCACACGG
1 CGTGTAACTCACTGTTTGT-GTAT-TAGGGCCACACGG
42366844 GCAGTCACGT
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
103 4 0.03
104 112 0.96
105 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (104 bp):
CGTGTAACTCACTGTTTGTGTATTAGGGCCACACGGATCGGGGACACAAGCATGCGTTAGATCAT
GTGAGGCACACGGGCTGATACAAGAGCATGTGTCTAGGC
Found at i:42371766 original size:55 final size:54
Alignment explanation
Indices: 42371678--42371806 Score: 213
Period size: 55 Copynumber: 2.3 Consensus size: 54
42371668 ATAATCCAGT
* *
42371678 GCCACTCATGGCCGCTAGTCAAATAATCTCGGATGTCCATAGTGTTATCCCGAGC
1 GCCACTCATGG-CGCTAGTCAAATAATCCCGGATGTCCATAATGTTATCCCGAGC
42371733 GCCACTCATGGTCGCTAGTCAAATAATCCCGGATGTCCATAATGTTATCCCGAGC
1 GCCACTCATGG-CGCTAGTCAAATAATCCCGGATGTCCATAATGTTATCCCGAGC
42371788 GCCACTCATGGCTGCTAGT
1 GCCACTCATGGC-GCTAGT
42371807 TAGGTTAGAG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
54 1 0.01
55 69 0.99
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (54 bp):
GCCACTCATGGCGCTAGTCAAATAATCCCGGATGTCCATAATGTTATCCCGAGC
Found at i:42387556 original size:31 final size:30
Alignment explanation
Indices: 42387511--42387577 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
42387501 AAGATTAAGT
*
42387511 ACCAACTTAAGAAAAAATGTCAAGTTTAGGA
1 ACCAAATTAAG-AAAAATGTCAAGTTTAGGA
* * * *
42387542 ACCAAATTAGGAAAAGTGTCAAGTTTGGGT
1 ACCAAATTAAGAAAAATGTCAAGTTTAGGA
42387572 ACCAAA
1 ACCAAA
42387578 ATGGATCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.22
Consensus pattern (30 bp):
ACCAAATTAAGAAAAATGTCAAGTTTAGGA
Found at i:42387575 original size:88 final size:89
Alignment explanation
Indices: 42387456--42387629 Score: 199
Period size: 89 Copynumber: 2.0 Consensus size: 89
42387446 GATTAGGTAT
* * *** *
42387456 CAAATTAAGAAAAGAATCAAGTTCAGTTACC-AAATTGAACCCCAAAAGATTAAGTACCAACTTA
1 CAAATTAAGAAAAGAATCAAGTTCAGGTACCAAAATGGAACAAAAAAAGATTAAGTACCAAATT-
*
42387520 AGAAAAAA-TGTCAAGTTTAGGAAC
65 AGAAAAAAGTGTAAAGTTTAGGAAC
* ** ** * *
42387544 CAAATTAGGAAAAGTGTCAAGTTTGGGTACCAAAATGGATCAAAAAAAGTTTAAGTACCAAATTA
1 CAAATTAAGAAAAGAATCAAGTTCAGGTACCAAAATGGAACAAAAAAAGATTAAGTACCAAATTA
42387609 GAAAAAAGTGTAAAGTTTAGG
66 GAAAAAAGTGTAAAGTTTAGG
42387630 TACTAAATAT
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
88 33 0.47
89 37 0.53
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (89 bp):
CAAATTAAGAAAAGAATCAAGTTCAGGTACCAAAATGGAACAAAAAAAGATTAAGTACCAAATTA
GAAAAAAGTGTAAAGTTTAGGAAC
Found at i:42387627 original size:31 final size:30
Alignment explanation
Indices: 42387500--42387637 Score: 102
Period size: 31 Copynumber: 4.6 Consensus size: 30
42387490 TTGAACCCCA
* * *
42387500 AAAGATTAAGTACCAACTTAAGAAAAAATGT
1 AAAGTTTAGGTACCAAATT-AGAAAAAATGT
* * * *
42387531 CAAGTTTAGGAACCAAATTAGGAAAAGTGT
1 AAAGTTTAGGTACCAAATTAGAAAAAATGT
* * * * *
42387561 CAAGTTTGGGTACCAAAATGGATCAAAA---
1 AAAGTTTAGGTACCAAATTAGA-AAAAATGT
*
42387589 AAAGTTTAAGTACCAAATTAGAAAAAAGTGT
1 AAAGTTTAGGTACCAAATTAGAAAAAA-TGT
*
42387620 AAAGTTTAGGTACTAAAT
1 AAAGTTTAGGTACCAAAT
42387638 ATTATATTAG
Statistics
Matches: 80, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
27 4 0.05
28 17 0.21
30 26 0.32
31 33 0.41
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (30 bp):
AAAGTTTAGGTACCAAATTAGAAAAAATGT
Found at i:42388656 original size:82 final size:82
Alignment explanation
Indices: 42388487--42389503 Score: 1109
Period size: 82 Copynumber: 12.5 Consensus size: 82
42388477 TAAAAATTAA
* *
42388487 AATTGAATAAATCTGTTTCGGGATTTATT-CTCGCGGTTCAACAGATTTTA---TATTTTGATTT
1 AATTGAATAAATTTGTTTCGGGATTTATTCCT-GCCGTTCAACAGATTTTATTCTATTTTGATTT
42388548 TGTTTCCAAACAAGGATT
65 TGTTTCCAAACAAGGATT
* * ***
42388566 AATTGAATAAATTTGTTTTGAGATTTATTCCTAATGTTCAACAGATTTTATTCTATTTTGATTTT
1 AATTGAATAAATTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTTT
42388631 GTTTCCAAACAAGGATT
66 GTTTCCAAACAAGGATT
* * * *
42388648 AATTGAAT-AATTCTGTTTCGGGATTTATTCCCGTCGTTCAATAGATTTTACTCTATTTTGATTT
1 AATTGAATAAATT-TGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTT
* *
42388712 TGTTTCTAAACAAGAATT
65 TGTTTCCAAACAAGGATT
* * ** * *
42388730 AATTGAATAAATATGTTTCGAGATTTATTCCTATCATTCAACAGATTTTATTCTGTTTTGATTTT
1 AATTGAATAAATTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTTT
42388795 GTTTCCAAACAAGGATT
66 GTTTCCAAACAAGGATT
* ** *
42388812 AATTGAATAAATTTGTTTCGAGATTTATTCCCACCGTTCAACAGATTTTATTTTATTTTGATTTT
1 AATTGAATAAATTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTTT
* *
42388877 GTTTTCAAATAAGGATT
66 GTTTCCAAACAAGGATT
* * * *
42388894 AATTGAAT-AATTCTGTTTAGGCATTTATT-CTCGCCGTTCAGCAGATTTTACTCTATTTTGATT
1 AATTGAATAAATT-TGTTTCGGGATTTATTCCT-GCCGTTCAACAGATTTTATTCTATTTTGATT
*
42388957 TTG-TTCCAAACAATGATT
64 TTGTTTCCAAACAAGGATT
* ** * * *
42388975 AATTGAATAATTTTGTTTCAAGATTTATTCAC-GACGTTTAACATATTTTATTCTATTTTGATTT
1 AATTGAATAAATTTGTTTCGGGATTTATTC-CTGCCGTTCAACAGATTTTATTCTATTTTGATTT
* * *
42389039 TGATTCTAAATAAGGATT
65 TGTTTCCAAACAAGGATT
* * * * *
42389057 AATTGAAT-AATTCTGTTTCGGGATTTATTCCTGTCGTTTAATAGATTTTATTCTATTCTGAGTT
1 AATTGAATAAATT-TGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTT
*
42389121 TGTTTCCAAACAAAGATT
65 TGTTTCCAAACAAGGATT
* * * * *
42389139 AATTGAAT-AATTCTGTTTCGAGATTTATTCCCGCCATTCAACAGATTTTACTCTATTTTTATTT
1 AATTGAATAAATT-TGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTT
**
42389203 TGTTTCCAAACAATAATT
65 TGTTTCCAAACAAGGATT
* * * * *
42389221 AATTAAATAATTTTGTTTCGGGATTTAATTTC-GCCGTGCAACAGATTTTATTCTATTTTAATTT
1 AATTGAATAAATTTGTTTCGGGATTT-ATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTT
* * *
42389285 TGTTTCTACACAAGAATT
65 TGTTTCCAAACAAGGATT
* * * * *
42389303 AATTGAAT-ATTTTGTTTCGGGATTTATTCCTGCCGTTTAACAAATTTTATTTTATTCTGATTTT
1 AATTGAATAAATTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTTT
* *
42389367 GTTTCCAAATAAGAATT
66 GTTTCCAAACAAGGATT
* * *
42389384 AATTGAATAATTTTATTTCGGGATTTATTCCTGTCGTTCAACAGA----ATT-TATTTTGATTTT
1 AATTGAATAAATTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTTT
* * *
42389444 ATTTCCAAATAAGAATT
66 GTTTCCAAACAAGGATT
* * * * * *
42389461 AATTAAAT-AATTCTATTTCAGTATTTATTCTTGTCGTTCAACA
1 AATTGAATAAATT-TGTTTCGGGATTTATTCCTGCCGTTCAACA
42389504 AAATTAATTT
Statistics
Matches: 804, Mismatches: 115, Indels: 40
0.84 0.12 0.04
Matches are distributed among these distances:
76 3 0.00
77 61 0.08
78 3 0.00
79 41 0.05
80 6 0.01
81 140 0.17
82 539 0.67
83 11 0.01
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (82 bp):
AATTGAATAAATTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTCTATTTTGATTTT
GTTTCCAAACAAGGATT
Found at i:42389084 original size:327 final size:322
Alignment explanation
Indices: 42388487--42389435 Score: 1208
Period size: 327 Copynumber: 2.9 Consensus size: 322
42388477 TAAAAATTAA
* * * *
42388487 AATTGAATAAATCTGTTTCGGGATTTATTCTCGCGGTTCAACAGATTTTA-TATTTTGATTTTGT
1 AATTGAATAAATTTGTTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTATTTTGATTTTGT
* ***
42388551 TTCCAAACAAGGATTAATTGAATAAATTTGTTTTGAGATTTATTC-CTAATGTTCAACAGATTTT
66 TTCCAAACAAGGATTAATTGAAT-AATTTGTTTAG-GATTTATTCTC-GCCGTTCAACAGATTTT
*
42388615 ATTCTATTTTGATTTTGTTTCCAAACAAGGATTAATTGAATAATTCTGTTTCGGGATTTATTCCC
128 ATTCTATTTTGATTTTGTTTCCAAACAA-GATTAATTGAATAATTTTGTTTCGGGATTTATT-CC
* * * * * * *
42388680 GTCGTTCAATAGATTTTACTCTATTTTGATTTTGTTTCTAAACAAGAATTAATTGAATAAATATG
191 GACGTTTAACAAATTTTATTCTATTTTGATTTTGTTTCTAAATAAGAATTAATTGAATAATTATG
* * * * * * *
42388745 TTTCGAGATTTATTCCTATCATTCAACAGATTTTATTCTGTTTTGATTTTGTTTCCAAACAAGGA
256 TTTCGGGATTTATTCCTGTCGTTCAACAGATTTTATTCTATTCTGAGTTTGTTTCCAAACAAAGA
42388810 TT
321 TT
*
42388812 AATTGAATAAATTTGTTTCGAGATTTATTCCCACCGTTCAACAGATTTTATTTTATTTTGATTTT
1 AATTGAATAAATTTGTTTCGAGATTTATTCCCGCCGTTCAACAGATTTTA--TTATTTTGATTTT
* * *
42388877 GTTTTCAAATAAGGATTAATTGAATAATTCTGTTTAGGCATTTATTCTCGCCGTTCAGCAGATTT
64 GTTTCCAAACAAGGATTAATTGAATAATT-TGTTTAGG-ATTTATTCTCGCCGTTCAACAGATTT
* **
42388942 TACTCTATTTTGATTTTG-TTCCAAACAATGATTAATTGAATAATTTTGTTTCAAGATTTATTCA
127 TATTCTATTTTGATTTTGTTTCCAAACAA-GATTAATTGAATAATTTTGTTTCGGGATTTATTC-
* * * *
42389006 CGACGTTTAACATATTTTATTCTATTTTGATTTTGATTCTAAATAAGGATTAATTGAATAATTCT
190 CGACGTTTAACAAATTTTATTCTATTTTGATTTTGTTTCTAAATAAGAATTAATTGAATAATTAT
* *
42389071 GTTTCGGGATTTATTCCTGTCGTTTAATAGATTTTATTCTATTCTGAGTTTGTTTCCAAACAAAG
255 GTTTCGGGATTTATTCCTGTCGTTCAACAGATTTTATTCTATTCTGAGTTTGTTTCCAAACAAAG
42389136 ATT
320 ATT
* *
42389139 AATTGAAT-AATTCTGTTTCGAGATTTATTCCCGCCATTCAACAGATTTTACTCTATTTTTATTT
1 AATTGAATAAATT-TGTTTCGAGATTTATTCCCGCCGTTCAACAGATTTTA-T-TATTTTGATTT
** * * *
42389203 TGTTTCCAAACAATAATTAATTAAATAATTTTGTTTCGGGATTTAATT-TCGCCGTGCAACAGAT
63 TGTTTCCAAACAAGGATTAATTGAATAA-TTTGTTT-AGGATTT-ATTCTCGCCGTTCAACAGAT
* * *
42389267 TTTATTCTATTTTAATTTTGTTTCTACACAAGAATTAATTGAAT-ATTTTGTTTCGGGATTTATT
125 TTTATTCTATTTTGATTTTGTTTCCAAACAAG-ATTAATTGAATAATTTTGTTTCGGGATTTATT
* * * *
42389331 CCTGCCGTTTAACAAATTTTATTTTATTCTGATTTTGTTTCCAAATAAGAATTAATTGAATAATT
189 CC-GACGTTTAACAAATTTTATTCTATTTTGATTTTGTTTCTAAATAAGAATTAATTGAATAATT
* * *
42389396 TTATTTCGGGATTTATTCCTGTCGTTCAACAGAATTTATT
253 ATGTTTCGGGATTTATTCCTGTCGTTCAACAGATTTTATT
42389436 TTGATTTTAT
Statistics
Matches: 543, Mismatches: 66, Indels: 28
0.85 0.10 0.04
Matches are distributed among these distances:
325 45 0.08
326 7 0.01
327 386 0.71
328 104 0.19
329 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (322 bp):
AATTGAATAAATTTGTTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTATTTTGATTTTGT
TTCCAAACAAGGATTAATTGAATAATTTGTTTAGGATTTATTCTCGCCGTTCAACAGATTTTATT
CTATTTTGATTTTGTTTCCAAACAAGATTAATTGAATAATTTTGTTTCGGGATTTATTCCGACGT
TTAACAAATTTTATTCTATTTTGATTTTGTTTCTAAATAAGAATTAATTGAATAATTATGTTTCG
GGATTTATTCCTGTCGTTCAACAGATTTTATTCTATTCTGAGTTTGTTTCCAAACAAAGATT
Found at i:42392076 original size:50 final size:50
Alignment explanation
Indices: 42392016--42392139 Score: 196
Period size: 50 Copynumber: 2.5 Consensus size: 50
42392006 TCAAATCTTG
* *
42392016 TTTATCTAAATTGTTTTGTTCAGATCTAGCGTTTTATATAAATATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATCTAGCGTTTTACATAAATATAAATA
* *
42392066 TTTATTTAAATTGTTTTGTTCAGATCTGGTGTTTTACATAAATATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATCTAGCGTTTTACATAAATATAAATA
*
42392116 TTTATTTATATTG-TTTGTTCAGAT
1 TTTATTTAAATTGTTTTGTTCAGAT
42392140 ATTGTATTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 11 0.16
50 58 0.84
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (50 bp):
TTTATTTAAATTGTTTTGTTCAGATCTAGCGTTTTACATAAATATAAATA
Found at i:42392170 original size:50 final size:50
Alignment explanation
Indices: 42392016--42392159 Score: 182
Period size: 50 Copynumber: 2.9 Consensus size: 50
42392006 TCAAATCTTG
* * * ** *
42392016 TTTATCTAAATTGTTTTGTTCAGATCTAGCGTTTTATATAAATATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATATGGTATTTTACATAAATATAAATA
* *
42392066 TTTATTTAAATTGTTTTGTTCAGATCTGGTGTTTTACATAAATATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATATGGTATTTTACATAAATATAAATA
* * *
42392116 TTTATTTATATTG-TTTGTTCAGATATTGTATTTTACGTAAATAT
1 TTTATTTAAATTGTTTTGTTCAGATATGGTATTTTACATAAATAT
42392160 TTTATATTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 27 0.32
50 58 0.68
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (50 bp):
TTTATTTAAATTGTTTTGTTCAGATATGGTATTTTACATAAATATAAATA
Found at i:42396779 original size:18 final size:18
Alignment explanation
Indices: 42396756--42396794 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
42396746 TTAAACTATA
42396756 TAAATTATATAACTCTTT
1 TAAATTATATAACTCTTT
42396774 TAAATTATATAACTCTTT
1 TAAATTATATAACTCTTT
42396792 TAA
1 TAA
42396795 TTCACGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATTATATAACTCTTT
Found at i:42397057 original size:19 final size:19
Alignment explanation
Indices: 42397030--42397080 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
42397020 AAATTAACTC
*
42397030 TTTTCATTTTTATAACATT-
1 TTTTAATTTTTAT-ACATTG
*
42397049 TTTTAATTTTTATATATTG
1 TTTTAATTTTTATACATTG
42397068 TTTTAAATTTTTA
1 TTTT-AATTTTTA
42397081 AAATTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 8 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAATTTTTATACATTG
Found at i:42403808 original size:10 final size:10
Alignment explanation
Indices: 42403793--42403823 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
42403783 CGAGTTAATA
42403793 TTAAAATGTT
1 TTAAAATGTT
42403803 TTAAAATG-T
1 TTAAAATGTT
42403812 TTAAAATGTT
1 TTAAAATGTT
42403822 TT
1 TT
42403824 TAAGGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (10 bp):
TTAAAATGTT
Found at i:42403816 original size:9 final size:9
Alignment explanation
Indices: 42403793--42403822 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
42403783 CGAGTTAATA
42403793 TTAAAATGTT
1 TTAAAATG-T
42403803 TTAAAATGT
1 TTAAAATGT
42403812 TTAAAATGT
1 TTAAAATGT
42403821 TT
1 TT
42403823 TTAAGGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (9 bp):
TTAAAATGT
Found at i:42404713 original size:36 final size:36
Alignment explanation
Indices: 42404661--42404730 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
42404651 AAGCCTATAA
42404661 GACTAGTCTTAAAATTAGG-CTTAAGATTAAACTTGG
1 GACTAGTCTTAAAATTAGGTC-TAAGATTAAACTTGG
*
42404697 GACTAGTCTTAGAATTAGGTCTAAGATTAAACTT
1 GACTAGTCTTAAAATTAGGTCTAAGATTAAACTT
42404731 AGAACTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (36 bp):
GACTAGTCTTAAAATTAGGTCTAAGATTAAACTTGG
Found at i:42404738 original size:36 final size:36
Alignment explanation
Indices: 42404662--42404738 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
42404652 AGCCTATAAG
* *
42404662 ACTAGTCTTAAAATTAGGCTTAAGATTAAACTTGGG
1 ACTAGTCTTAAAATTAGGCTTAAGATTAAACTTAGA
*
42404698 ACTAGTCTTAGAATTAGG-TCTAAGATTAAACTTAGA
1 ACTAGTCTTAAAATTAGGCT-TAAGATTAAACTTAGA
42404734 ACTAG
1 ACTAG
42404739 AATTAGGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (36 bp):
ACTAGTCTTAAAATTAGGCTTAAGATTAAACTTAGA
Found at i:42417947 original size:11 final size:11
Alignment explanation
Indices: 42417927--42417953 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42417917 TTAATATTTT
42417927 TTTAAATTTAA
1 TTTAAATTTAA
42417938 TTTAAATTTAA
1 TTTAAATTTAA
42417949 TTTAA
1 TTTAA
42417954 TTATTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:42418536 original size:28 final size:28
Alignment explanation
Indices: 42418494--42418548 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
42418484 AAATTCAGAT
*
42418494 TTAGTCTATATTTATTTTTGAGATTTAC
1 TTAGTCTATACTTATTTTTGAGATTTAC
42418522 TTAGTCTATACTTATTTTTGAGATTTA
1 TTAGTCTATACTTATTTTTGAGATTTA
42418549 TTTTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.56
Consensus pattern (28 bp):
TTAGTCTATACTTATTTTTGAGATTTAC
Found at i:42418956 original size:19 final size:20
Alignment explanation
Indices: 42418934--42418971 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42418924 ATTAATTTTT
42418934 TATAATATAAT-ACATATTA
1 TATAATATAATAACATATTA
*
42418953 TATAATATAGTAACATATT
1 TATAATATAATAACATATT
42418972 TTCACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TATAATATAATAACATATTA
Done.