Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008104.1 Hibiscus syriacus cultivar Beakdansim tig00110634_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 639954
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:359779 original size:14 final size:14
Alignment explanation
Indices: 359755--359803 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
359745 ATATTTATTT
359755 TAAATAGTTTAAATAA
1 TAAATA-TTTAAA-AA
*
359771 TAAATTTTATAAAAA
1 TAAATATT-TAAAAA
*
359786 TATATATTTAAAAA
1 TAAATATTTAAAAA
359800 TAAA
1 TAAA
359804 CTCATGCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 9 0.32
15 10 0.36
16 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
TAAATATTTAAAAA
Found at i:360242 original size:31 final size:31
Alignment explanation
Indices: 360204--360267 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
360194 ATCGTATCAC
*
360204 GAAATTTTCCAGATCAGTCCATATAAAATTT
1 GAAATTTTCCAGATCAGTCCAAATAAAATTT
360235 GAAATTTTCCAGATCAGTCCAAATAAAATTT
1 GAAATTTTCCAGATCAGTCCAAATAAAATTT
360266 GA
1 GA
360268 GTAATGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (31 bp):
GAAATTTTCCAGATCAGTCCAAATAAAATTT
Found at i:361306 original size:3 final size:3
Alignment explanation
Indices: 361300--361337 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
361290 AAGGTATACT
361300 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
361338 AATTTTTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:363479 original size:20 final size:20
Alignment explanation
Indices: 363454--363495 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
363444 CCTGACTTGT
*
363454 TTGGAAGACCTGTAAATCGG
1 TTGGAAGACCTGAAAATCGG
363474 TTGGAAGACCTGAAAATCGG
1 TTGGAAGACCTGAAAATCGG
363494 TT
1 TT
363496 CCTAATTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (20 bp):
TTGGAAGACCTGAAAATCGG
Found at i:363741 original size:20 final size:20
Alignment explanation
Indices: 363716--363754 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
363706 GACTTGTTTA
*
363716 GAAGACCTGTAAATCGGTTG
1 GAAGACCTGAAAATCGGTTG
363736 GAAGACCTGAAAATCGGTT
1 GAAGACCTGAAAATCGGTT
363755 CCTAATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (20 bp):
GAAGACCTGAAAATCGGTTG
Found at i:363745 original size:259 final size:259
Alignment explanation
Indices: 363286--363807 Score: 927
Period size: 259 Copynumber: 2.0 Consensus size: 259
363276 TCCTTAAACT
* * * *
363286 TTGAATATTATCGTTAAATGTTTTGATGTCGAAAATATTTGGAACTGAAATTATGAAACCCTTAT
1 TTGAATATTATCGTTAAATGTTTTGATGTCAAAAATATTTGCAAATGAAATTATGAAACCATTAT
*
363351 GAAGTAAAAAGAGAACGGAATTAACCCGAATAGTGAAATTAACCTGATAATTCATTCTTGACCTG
66 GAAGTAAAAAGAGAACGGAAATAACCCGAATAGTGAAATTAACCTGATAATTCATTCTTGACCTG
* * *
363416 ATAGAACTACATATCTACCGACTGAACTCCTGACTTGTTTGGAAGACCTGTAAATCGGTTGGAAG
131 ATAGAACTACAGATCCACCGACTGAACTCCTGACTTGTTTAGAAGACCTGTAAATCGGTTGGAAG
*
363481 ACCTGAAAATCGGTTCCTAATTCTCGAGATCAGCAATAACTAAAATAACCCTAAAAAGTCATCA
196 ACCTGAAAATCGGTTCCTAATCCTCGAGATCAGCAATAACTAAAATAACCCTAAAAAGTCATCA
* *
363545 TTGAATATTATCGTTAAATGTTTTGATGTCAAAAATGTTTGCAAATGAAATTATGAAACCATTGT
1 TTGAATATTATCGTTAAATGTTTTGATGTCAAAAATATTTGCAAATGAAATTATGAAACCATTAT
* *
363610 GAAGTAAAAAGAGAATGGAAATAACCCGAATTGTGAAATTAACCTGATAATTCATTCTTGACCTG
66 GAAGTAAAAAGAGAACGGAAATAACCCGAATAGTGAAATTAACCTGATAATTCATTCTTGACCTG
363675 ATAGAACTACAGATCCACCGACTGAACTCCTGACTTGTTTAGAAGACCTGTAAATCGGTTGGAAG
131 ATAGAACTACAGATCCACCGACTGAACTCCTGACTTGTTTAGAAGACCTGTAAATCGGTTGGAAG
363740 ACCTGAAAATCGGTTCCTAATCCTCGAGATCAGCAATAACTAAAATAACCCTAAAAAGTCATCA
196 ACCTGAAAATCGGTTCCTAATCCTCGAGATCAGCAATAACTAAAATAACCCTAAAAAGTCATCA
363804 TTGA
1 TTGA
363808 TATGATAGAC
Statistics
Matches: 250, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
259 250 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (259 bp):
TTGAATATTATCGTTAAATGTTTTGATGTCAAAAATATTTGCAAATGAAATTATGAAACCATTAT
GAAGTAAAAAGAGAACGGAAATAACCCGAATAGTGAAATTAACCTGATAATTCATTCTTGACCTG
ATAGAACTACAGATCCACCGACTGAACTCCTGACTTGTTTAGAAGACCTGTAAATCGGTTGGAAG
ACCTGAAAATCGGTTCCTAATCCTCGAGATCAGCAATAACTAAAATAACCCTAAAAAGTCATCA
Found at i:364559 original size:3 final size:3
Alignment explanation
Indices: 364551--364619 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
364541 GGTAAATACT
364551 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
364599 TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC
364620 CTCTCCATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:364636 original size:121 final size:121
Alignment explanation
Indices: 364497--364740 Score: 470
Period size: 121 Copynumber: 2.0 Consensus size: 121
364487 GAGTTTGATA
364497 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
1 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
* *
364562 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
66 CTCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCCTTCTTCTTCTTCTTCTTCT
364618 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
1 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
364683 CTCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCCTTCTTCTTCTTCTTCTTCT
66 CTCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCCTTCTTCTTCTTCTTCTTCT
364739 TC
1 TC
364741 TTCTTCTCCT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.17, C:0.31, G:0.04, T:0.48
Consensus pattern (121 bp):
TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
CTCCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCCTTCTTCTTCTTCTTCTTCT
Found at i:364680 original size:3 final size:3
Alignment explanation
Indices: 364672--364807 Score: 222
Period size: 3 Copynumber: 45.7 Consensus size: 3
364662 GGTAAATACT
* *
364672 TTC TTC TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
364720 TTC TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC TTC TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
364767 TTC TTC TTC TT- TTC TTC TTC TTC TTCC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TT
364808 TTCCTTCAAG
Statistics
Matches: 124, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
2 4 0.03
3 117 0.94
4 3 0.02
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:364962 original size:3 final size:3
Alignment explanation
Indices: 364954--365003 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
364944 GGTAAATACT
364954 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
365002 TT
1 TT
365004 TTTTCCTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:365052 original size:3 final size:3
Alignment explanation
Indices: 365044--365082 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
365034 GGTAAATACT
365044 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
365083 CTCTCCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:365095 original size:181 final size:185
Alignment explanation
Indices: 364900--365266 Score: 654
Period size: 181 Copynumber: 2.0 Consensus size: 185
364890 GAGTTTGATA
364900 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
1 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
*
364965 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT-CT-T-C-T-TTTTTCCTTCAAGAACAAGCAA
66 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCTCTCCATAATTTTCCTTCAAGAACAAGCAA
365025 CAACATGAAGGTAAATACTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
131 CAACATGAAGGTAAATACTTT-TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
365081 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
1 TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
365146 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCTCTCCATAACATTTTCCTTCAAGAACAAGC
66 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCTCTCCAT-A-ATTTTCCTTCAAGAACAAGC
*
365211 AACAACCTGAAGGTAAATACTTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
129 AACAACATGAAGGTAAATACTTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
365267 CTTCTTCTTC
Statistics
Matches: 177, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
181 98 0.55
182 2 0.01
183 1 0.01
184 1 0.01
185 1 0.01
187 33 0.19
188 41 0.23
ACGTcount: A:0.22, C:0.28, G:0.05, T:0.45
Consensus pattern (185 bp):
TCCTCTCCATAACATTTTCCTTCAAGAACAAGCAACAACATGAAGGTAAATACTTTCTTCTTCTT
CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCTCTCCATAATTTTCCTTCAAGAACAAGCAA
CAACATGAAGGTAAATACTTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
Found at i:365143 original size:3 final size:3
Alignment explanation
Indices: 365135--365179 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
365125 GGTAAATACT
365135 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
365180 CTCTCCATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:365242 original size:3 final size:3
Alignment explanation
Indices: 365234--365335 Score: 177
Period size: 3 Copynumber: 33.7 Consensus size: 3
365224 TAAATACTTT
365234 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC
* *
365280 TTC TTC TTC TTC TTC TTC TCC TTC TTC TTC TTC TCC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
365328 TTC TTC TT
1 TTC TTC TT
365336 TTCCTTCAAG
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
3 91 0.97
4 3 0.03
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:365490 original size:3 final size:3
Alignment explanation
Indices: 365482--365552 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
365472 GGTAAATACT
* *
365482 TTC TTC TTC ATC ATC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
365530 TTC TT- TTCC TTC TTC TTC TTC TT
1 TTC TTC TT-C TTC TTC TTC TTC TT
365553 TTCCTTCAAG
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 60 0.94
4 2 0.03
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:365560 original size:217 final size:216
Alignment explanation
Indices: 365267--365768 Score: 934
Period size: 217 Copynumber: 2.3 Consensus size: 216
365257 CTTCTTCTTC
* *
365267 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCCTTCTTCTTCTTCTCCTTCTTCTTCTTCTTCT
1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
365332 TCTTTTCCTTCAAGAACAAGCAACAACGTGAAGGTAAAAAAATGAAGAGTTATTGCATACCAACT
66 TCTTTTCCTTCAAGAACAAGCAACAACGTGAAGGTAAAAAAATGAAGAGTTATTGCATACCAACT
365397 CATTGTTCCTTCTTAGCTGCTGAGTTTGATATCCTCTCCATAACATTTTCCTTCAAGAACAAGCA
131 CATTGTTCCTTCTTAGCTGCTGAGTTTGATATCCTCTCCATAACATTTTCCTTCAAGAACAAGCA
365462 ACAACATGAAGGTAAATACTTT
196 ACAACATGAAGGTAAATAC-TT
* *
365484 CTTCTTCATCATCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT-TTCCTTCTTCTTC
1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT-CTTCTTCTTC
365548 TTCTTTTCCTTCAAGAACAAGCAACAACGTGAAGGTAAAAAAATGAAGAGTTATTGCATACCAAC
65 TTCTTTTCCTTCAAGAACAAGCAACAACGTGAAGGTAAAAAAATGAAGAGTTATTGCATACCAAC
*
365613 TCATTGTTCCTTCTTAGCTGCTGAGTTTGATATCCTCTCCATAACATTTTCCTTCAAGAACAAGT
130 TCATTGTTCCTTCTTAGCTGCTGAGTTTGATATCCTCTCCATAACATTTTCCTTCAAGAACAAGC
365678 AACAACATGAAGGTAAATACTT
195 AACAACATGAAGGTAAATACTT
365700 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
365765 TCTT
66 TCTT
365769 CTTCTTCTTC
Statistics
Matches: 276, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
216 68 0.25
217 208 0.75
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.44
Consensus pattern (216 bp):
CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
TCTTTTCCTTCAAGAACAAGCAACAACGTGAAGGTAAAAAAATGAAGAGTTATTGCATACCAACT
CATTGTTCCTTCTTAGCTGCTGAGTTTGATATCCTCTCCATAACATTTTCCTTCAAGAACAAGCA
ACAACATGAAGGTAAATACTT
Found at i:365703 original size:3 final size:3
Alignment explanation
Indices: 365697--365811 Score: 230
Period size: 3 Copynumber: 38.3 Consensus size: 3
365687 AAGGTAAATA
365697 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
365745 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
365793 CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT C
365812 GTTAATTCGA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 112 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:366204 original size:3 final size:3
Alignment explanation
Indices: 366196--366227 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
366186 GGTAAATACT
366196 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
366228 AAGCAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:366317 original size:3 final size:3
Alignment explanation
Indices: 366309--366358 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
366299 GGTAAATACT
366309 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
366357 TT
1 TT
366359 AGCTGCTGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:372577 original size:18 final size:17
Alignment explanation
Indices: 372553--372598 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
372543 GAATCAAGTT
372553 ATAAAAATATTATAATTAA
1 ATAAAAA-ATTATAA-TAA
*
372572 ATAAAAAATTATGATAA
1 ATAAAAAATTATAATAA
372589 ATAATAAAAT
1 ATAA-AAAAT
372599 ATTCAATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 11 0.44
19 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAAAAATTATAATAA
Found at i:372580 original size:20 final size:18
Alignment explanation
Indices: 372553--372592 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
372543 GAATCAAGTT
372553 ATAAAAATATTATAATTAA
1 ATAAAAATATTATAA-TAA
*
372572 ATAAAAA-ATTATGATAA
1 ATAAAAATATTATAATAA
372589 ATAA
1 ATAA
372593 TAAAATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 6 0.30
19 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
ATAAAAATATTATAATAA
Found at i:372588 original size:21 final size:19
Alignment explanation
Indices: 372555--372597 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
372545 ATCAAGTTAT
* *
372555 AAAAATATTATAATTAAATA
1 AAAAATATGATAAAT-AATA
372575 AAAAATTATGATAAATAATA
1 AAAAA-TATGATAAATAATA
372595 AAA
1 AAA
372598 TATTCAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATGATAAATAATA
Found at i:373514 original size:16 final size:15
Alignment explanation
Indices: 373477--373535 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
373467 AGATATATAT
*
373477 TTAAAT-TAAAAATA
1 TTAAATATAAAAAAA
*
373491 TAAAATATAAAAAAA
1 TTAAATATAAAAAAA
*
373506 TTAAGATATAAAATACA
1 TTAA-ATATAAAA-AAA
373523 TTAAATATAAAAA
1 TTAAATATAAAAA
373536 TGCTACAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
14 5 0.13
15 11 0.29
16 16 0.42
17 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
TTAAATATAAAAAAA
Found at i:373790 original size:24 final size:22
Alignment explanation
Indices: 373762--373808 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
373752 ACTGGAAAAA
373762 ACTTTTTATGTTTTTCATATTTTC
1 ACTTTTTATGTTTTT-AT-TTTTC
*
373786 ACTTTTTTTGTTTTTATTTTTC
1 ACTTTTTATGTTTTTATTTTTC
373808 A
1 A
373809 GAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
24 14 0.64
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (22 bp):
ACTTTTTATGTTTTTATTTTTC
Found at i:374957 original size:4 final size:4
Alignment explanation
Indices: 374948--374972 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
374938 ATTTAATTCG
374948 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
374973 TTGATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:383909 original size:21 final size:21
Alignment explanation
Indices: 383883--384038 Score: 117
Period size: 21 Copynumber: 7.4 Consensus size: 21
383873 TTTCCAAATT
*
383883 CGTTGCGATAGTCTAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
383904 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
383925 CGTTGTGATAGTACAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
383946 CGTTGCGATTTGTTCCAAATT--
1 CGTTGCGA-TAG-TCCAAGTTCG
* *
383967 CGTTGCGATAGTCGAAATTCG
1 CGTTGCGATAGTCCAAGTTCG
*
383988 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
384009 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
384030 CGTTGCGAT
1 CGTTGCGAT
384039 TTTATTCCAA
Statistics
Matches: 105, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
19 24 0.23
20 2 0.02
21 55 0.52
22 2 0.02
23 22 0.21
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:383920 original size:42 final size:42
Alignment explanation
Indices: 383874--384064 Score: 303
Period size: 42 Copynumber: 4.5 Consensus size: 42
383864 CAATACGATT
*
383874 TTCCAAATTCGTTGCGATAGTCTAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
* *
383916 TTCCAAATTCGTTGTGATAGTAC-AAGTTCGCGTTGCGATTTG
1 TTCCAAATTCGTTGCGATAGT-CGAAGTTCGCGTTGCGATTTA
*
383958 TTCCAAATTCGTTGCGATAGTCGAAATTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
*
384000 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTA
1 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTTA
*
384043 TTCCAAATTCGTTGGGATAGTC
1 TTCCAAATTCGTTGCGATAGTC
384065 CAAAATCGCA
Statistics
Matches: 137, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.01
42 111 0.81
43 25 0.18
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
Found at i:389764 original size:14 final size:14
Alignment explanation
Indices: 389734--389763 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
389724 AAAAAAAGTG
389734 TTTAATGTAATTTT
1 TTTAATGTAATTTT
389748 TTTAAT-TAATTTT
1 TTTAATGTAATTTT
389761 TTT
1 TTT
389764 TTGTTATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTAATGTAATTTT
Found at i:391630 original size:3 final size:3
Alignment explanation
Indices: 391622--391668 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
391612 TAGATAAGAG
391622 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
391669 TGTCTACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:392841 original size:31 final size:32
Alignment explanation
Indices: 392795--392856 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
392785 AAAGGTAAAT
392795 TATGTATTTAATACTTAAATTATTAATTTTCG
1 TATGTATTTAATACTTAAATTATTAATTTTCG
* *
392827 TATGT-TTTAGTACTTAAATTTTTAATTTTC
1 TATGTATTTAATACTTAAATTATTAATTTTC
392857 AAAATCATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (32 bp):
TATGTATTTAATACTTAAATTATTAATTTTCG
Found at i:393769 original size:2 final size:2
Alignment explanation
Indices: 393764--393792 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
393754 ATATATATAT
393764 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
393793 AAAACTACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:393884 original size:16 final size:16
Alignment explanation
Indices: 393859--393894 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
393849 GCAGAAGCCA
*
393859 TATATATATATGTATG
1 TATATATATATATATG
*
393875 TATATCTATATATATG
1 TATATATATATATATG
393891 TATA
1 TATA
393895 GAGTGTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:393888 original size:10 final size:10
Alignment explanation
Indices: 393861--393894 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
393851 AGAAGCCATA
393861 TATATATATG
1 TATATATATG
* *
393871 TATGTATATC
1 TATATATATG
393881 TATATATATG
1 TATATATATG
393891 TATA
1 TATA
393895 GAGTGTATGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:397767 original size:18 final size:17
Alignment explanation
Indices: 397744--397779 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
397734 ATACTTTGTT
*
397744 TTATAATTTTAATATATA
1 TTATAATTATAA-ATATA
397762 TTATAATTATAAATATA
1 TTATAATTATAAATATA
397779 T
1 T
397780 GTTGATGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATTATAAATATA
Found at i:401614 original size:18 final size:17
Alignment explanation
Indices: 401591--401626 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
401581 ATACTTTGTT
*
401591 TTATAATTTTAATATATA
1 TTATAATTATAA-ATATA
401609 TTATAATTATAAATATA
1 TTATAATTATAAATATA
401626 T
1 T
401627 GTTGATGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATTATAAATATA
Found at i:404128 original size:81 final size:81
Alignment explanation
Indices: 404024--404186 Score: 299
Period size: 81 Copynumber: 2.0 Consensus size: 81
404014 TAAACTATCC
404024 TGACGAGACGAACTACTAGAATCAATGTTGTCATTTTTAATCGAGACAACTTGTTCGTTCGTGTC
1 TGACGAGACGAACTACTAGAATCAATGTTGTCATTTTTAATCGAGACAACTTGTTCGTTCGTGTC
404089 TACGATTTCTATATTG
66 TACGATTTCTATATTG
* *
404105 TGACGAGACGAACTACTAGAATCAATGTTGTCATTTTTAATTGAGACCACTTGTTCGTTCGTGTC
1 TGACGAGACGAACTACTAGAATCAATGTTGTCATTTTTAATCGAGACAACTTGTTCGTTCGTGTC
*
404170 TACGATTTCTGTATTG
66 TACGATTTCTATATTG
404186 T
1 T
404187 CTCGAGAGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (81 bp):
TGACGAGACGAACTACTAGAATCAATGTTGTCATTTTTAATCGAGACAACTTGTTCGTTCGTGTC
TACGATTTCTATATTG
Found at i:407124 original size:2 final size:2
Alignment explanation
Indices: 407117--407146 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
407107 GAATACAAAG
407117 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
407147 TGCCTAAGTT
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:426077 original size:42 final size:42
Alignment explanation
Indices: 426030--426210 Score: 243
Period size: 42 Copynumber: 4.5 Consensus size: 42
426020 ATACGATTAA
*
426030 AAATCGCAACGCGAACTTGGACTATCTCAACGAATTTGGAAT
1 AAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
*
426072 AAATCGCAACGCGAACTTCGACTATCGCAAC------GGAAT
1 AAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
*
426108 AAATCGCAACGCGAACTTGGACTATCACAACGAATTTGGAAT
1 AAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
* * *
426150 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACT
1 AAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
*
426192 --ATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAACTTGGA
426211 ATAAATCGTA
Statistics
Matches: 123, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
36 34 0.28
40 17 0.14
42 72 0.59
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
AAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
Found at i:426146 original size:19 final size:20
Alignment explanation
Indices: 426032--426252 Score: 136
Period size: 21 Copynumber: 10.9 Consensus size: 20
426022 ACGATTAAAA
426032 ATCGCAACGCGAACTTGGACT
1 ATCGCAAC-CGAACTTGGACT
* * *
426053 ATCTCAA-CGAATTTGGAAT
1 ATCGCAACCGAACTTGGACT
*
426072 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAAC-CGAACTTGGACT
* *
426095 ATCGCAACGGAA--T--A-A
1 ATCGCAACCGAACTTGGACT
426110 ATCGCAACGCGAACTTGGACT
1 ATCGCAAC-CGAACTTGGACT
* * *
426131 ATCACAA-CGAATTTGGAAT
1 ATCGCAACCGAACTTGGACT
*
426150 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAAC-CGAACTTGGACT
426173 ATCGCAA-CGAACTTGGACT
1 ATCGCAACCGAACTTGGACT
* *
426192 ATCGCAACGCGAATTTGGAAT
1 ATCGCAAC-CGAACTTGGACT
* *
426213 AAATCGTAACACGAACTTTGACT
1 --ATCGCAAC-CGAACTTGGACT
*
426236 ATCGCAA-CGAATTTGGA
1 ATCGCAACCGAACTTGGA
426253 AAATCGCATT
Statistics
Matches: 153, Mismatches: 29, Indels: 38
0.70 0.13 0.17
Matches are distributed among these distances:
15 8 0.05
16 4 0.03
18 2 0.01
19 46 0.30
20 4 0.03
21 55 0.36
23 34 0.22
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACCGAACTTGGACT
Found at i:426159 original size:78 final size:78
Alignment explanation
Indices: 426030--426181 Score: 295
Period size: 78 Copynumber: 1.9 Consensus size: 78
426020 ATACGATTAA
*
426030 AAATCGCAACGCGAACTTGGACTATCTCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 AAATCGCAACGCGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
426095 ATCGCAACGGAAT
66 ATCGCAACGGAAT
426108 AAATCGCAACGCGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 AAATCGCAACGCGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
426173 ATCGCAACG
66 ATCGCAACG
426182 AACTTGGACT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (78 bp):
AAATCGCAACGCGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
ATCGCAACGGAAT
Found at i:426211 original size:63 final size:62
Alignment explanation
Indices: 426030--426252 Score: 221
Period size: 63 Copynumber: 3.6 Consensus size: 62
426020 ATACGATTAA
* * * * * *
426030 AAATCGCAACGCGAACTTGGACTATCTCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 AAATCGCAACGCGAACTT-GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAATTTGGAAT
* *
426095 --ATCGCAACG-GAA--T-A-AATCGCAACGCGAACTTGGACTATCACAA--CGAATTTGGAAT
1 AAATCGCAACGCGAACTTGACTATCGCAA--CGAACTTGGACTATCGCAACGCGAATTTGGAAT
426150 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAAT
1 AAATCGCAACGCGAACTT-GACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAAT
* * *
426213 AAATCGTAACACGAACTTTGACTATCGCAACGAATTTGGA
1 AAATCGCAACGCGAAC-TTGACTATCGCAACGAACTTGGA
426253 AAATCGCATT
Statistics
Matches: 132, Mismatches: 13, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
55 9 0.07
57 21 0.16
58 4 0.03
59 10 0.08
60 2 0.02
61 18 0.14
62 4 0.03
63 62 0.47
64 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (62 bp):
AAATCGCAACGCGAACTTGACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAAT
Found at i:426258 original size:19 final size:19
Alignment explanation
Indices: 426135--426260 Score: 56
Period size: 19 Copynumber: 6.1 Consensus size: 19
426125 TGGACTATCA
426135 CAACGAATTTGGAATAAATCG
1 CAACGAATTTGG-A-AAATCG
* * **
426156 CAACGCGAACTTCGACTATCG
1 CAA--CGAATTTGGAAAATCG
* **
426177 CAACGAACTTGGACTATCG
1 CAACGAATTTGGAAAATCG
426196 CAACGCGAATTTGGAATAAATCG
1 CAA--CGAATTTGG-A-AAATCG
* **
426219 TAACACGAACTTT-GACTATCG
1 -CA-ACGAA-TTTGGAAAATCG
426240 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
426259 CA
1 CA
426261 TTGCGATAGT
Statistics
Matches: 81, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
18 3 0.04
19 31 0.38
20 1 0.01
21 22 0.27
22 3 0.04
23 16 0.20
24 4 0.05
25 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:426289 original size:21 final size:21
Alignment explanation
Indices: 426256--426308 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
426246 ATTTGGAAAA
*
426256 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
426277 TCGCGTTGTGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
426298 TCGCGTTGCGA
1 TCGCGTTGCGA
426309 ATCTGGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:426536 original size:2 final size:2
Alignment explanation
Indices: 426529--426578 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
426519 ATGTTCCCGA
426529 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
426571 AT AT AT AT
1 AT AT AT AT
426579 GTTTACACAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429869 original size:60 final size:59
Alignment explanation
Indices: 429740--429881 Score: 180
Period size: 59 Copynumber: 2.4 Consensus size: 59
429730 TCGAGTGACT
* * *
429740 ATTTTGTAACTTTTAATAGTCGA-GGACTCAACAAATCAACACTATATAGTCAATAGTC
1 ATTTTGTAACTTTTAATAGTTGATGGACTCAACAAATCAACACTATAAAATCAATAGTC
* * * *
429798 ATTTTGTAACTTTTAGTAGTTGATGGACTCAACAAATTAATACTCTAAAATCAA-AGGGTC
1 ATTTTGTAACTTTTAATAGTTGATGGACTCAACAAATCAACACTATAAAATCAATA--GTC
*
429858 ATTTTGTAACTTTTAATAGATGAT
1 ATTTTGTAACTTTTAATAGTTGAT
429882 AAACTTAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
58 22 0.31
59 25 0.35
60 25 0.35
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTTGATGGACTCAACAAATCAACACTATAAAATCAATAGTC
Found at i:429899 original size:60 final size:60
Alignment explanation
Indices: 429795--429912 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
429785 ATAGTCAATA
* * ** *
429795 GTCATTTTGTAACTTTTAGTAGTTGATGGACTCAACAAATTAATACT-CTAAAATCAAAGG
1 GTCATTTTGTAACTTTTAATAGATGATAAACTCAACAAAATAATA-TGCTAAAATCAAAGG
* * *
429855 GTCATTTTGTAACTTTTAATAGATGATAAACTTAATAAAATAATATGCTATAATCAAA
1 GTCATTTTGTAACTTTTAATAGATGATAAACTCAACAAAATAATATGCTAAAATCAAA
429913 TACTATTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (60 bp):
GTCATTTTGTAACTTTTAATAGATGATAAACTCAACAAAATAATATGCTAAAATCAAAGG
Found at i:442343 original size:20 final size:20
Alignment explanation
Indices: 442320--442357 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
442310 CTATAGGCTA
*
442320 ATACATGTATATATATATGT
1 ATACATCTATATATATATGT
*
442340 ATACATCTATCTATATAT
1 ATACATCTATATATATAT
442358 ATATTTACAT
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:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (20 bp):
ATACATCTATATATATATGT
Found at i:445656 original size:184 final size:183
Alignment explanation
Indices: 445420--445806 Score: 609
Period size: 184 Copynumber: 2.1 Consensus size: 183
445410 AACCGAAATT
* * *
445420 AAATTTTAAATATATTATATATAACATATGGGCTTAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
445485 TTTAAGATCCAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
66 TTTAAGATCCAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAA-TT
*
445549 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTT-AATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATT-AA
* *
445604 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
* * * *
445669 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
*
445734 TTATTTTATAATTATATATTATTTAAATTAATTATACACTTTTTTTGAATTAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
* *
445787 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
445807 AATTAGAAAA
Statistics
Matches: 188, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
182 8 0.04
183 18 0.10
184 159 0.85
185 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
Found at i:446900 original size:20 final size:20
Alignment explanation
Indices: 446861--446901 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
446851 CACTTAATTT
* **
446861 TTTAAAAATAATTAGGTAAA
1 TTTAAAAATAAATAAATAAA
446881 TTTAAAAATAAATAAATAAA
1 TTTAAAAATAAATAAATAAA
446901 T
1 T
446902 GTTTGGATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TTTAAAAATAAATAAATAAA
Found at i:448141 original size:60 final size:60
Alignment explanation
Indices: 447992--448144 Score: 148
Period size: 60 Copynumber: 2.5 Consensus size: 60
447982 TGCATCATAT
* * *
447992 ATCCTTAAACTATAACCCTCATTT-TAAATTAGTCCTTAAAATTTTGAACATCCCACTTTC
1 ATCCATAAACTATGACCCTC-TTTCTAAATTAGTCCTTAAAATTTTGAACATCCCAATTTC
* * * * * * * * * *
448052 ATCCCA-AAACTACGACTCTCATCCCAAATTAGTTCTTAAACTTTTGAATATTCTAATTTC
1 AT-CCATAAACTATGACCCTCTTTCTAAATTAGTCCTTAAAATTTTGAACATCCCAATTTC
*
448112 ATCCATAAATTATGACCCTCTTTCTAAATTAGT
1 ATCCATAAACTATGACCCTCTTTCTAAATTAGT
448145 ATCCAAACTT
Statistics
Matches: 71, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
59 4 0.06
60 65 0.92
61 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (60 bp):
ATCCATAAACTATGACCCTCTTTCTAAATTAGTCCTTAAAATTTTGAACATCCCAATTTC
Found at i:449173 original size:28 final size:27
Alignment explanation
Indices: 449142--449197 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
449132 AGATTTGTAA
*
449142 ATATTAATTTTTATTATTTTATTTAAATAT
1 ATATTAACTTTT-TTA-TTTA-TTAAATAT
449172 ATATTAACTTTTTTATTTATTAAATA
1 ATATTAACTTTTTTATTTATTAAATA
449198 ATTTTTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 4 0.16
29 3 0.12
30 11 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
ATATTAACTTTTTTATTTATTAAATAT
Found at i:468718 original size:2 final size:2
Alignment explanation
Indices: 468711--468745 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
468701 AAATAAAACC
468711 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 A
468746 ATCAATCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:470968 original size:189 final size:191
Alignment explanation
Indices: 470591--471000 Score: 560
Period size: 189 Copynumber: 2.2 Consensus size: 191
470581 TTAAACAGAC
* * * * * * *
470591 AATAATATCTTTTAATTTGAAATATTCAAAATATAAAACTCCTTTTACCATTCAAACTTAAATAT
1 AATAATATCTTTTAATTTGCAATAGTCAAAAGATAAAACTCATTTCACCATTCAAACTTAAACAA
* * * *
470656 ATATTATTTTAATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAAGGT
66 ATATTATTTTAATTTGAAATATACAAAAGTAAATAATTATCTTTAACATTCAAAATTAAAAAGAT
* * * ** * *
470721 AACAAATACATTTTTAAATTGATATATTCAAAGAGTAGTTATCTTATTAATGTTCAAATTA
131 AACAAATACATTTCTAAATTGATATATTAAAAGAGTAATTATCCAACTAATATTCAAATTA
* * *
470782 AATAATAT-GTTTAATTTGCAATGGTCAAAAGAT-AAACTCATTTCACTATTCAAACTTAAACAA
1 AATAATATCTTTTAATTTGCAATAGTCAAAAGATAAAACTCATTTCACCATTCAAACTTAAACAA
*
470845 ATATTATTTTAATTTGAAATATACAAAAG-AAATAATTATCTTGTAACATTTAAAATTAAAAAGA
66 ATATTATTTTAATTTGAAATATACAAAAGTAAATAATTATCTT-TAACATTCAAAATTAAAAAGA
470909 TAACAAATACATTTCTAAATTGACT-TATTAAAAGAGTAATTATCCAACTAATATTCAAATTA
130 TAACAAATACATTTCTAAATTGA-TATATTAAAAGAGTAATTATCCAACTAATATTCAAATTA
470971 AA-AATTATCTTTTAATTTGCAATAGTCAAA
1 AATAA-TATCTTTTAATTTGCAATAGTCAAA
471001 TGGACAATGA
Statistics
Matches: 191, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
188 14 0.07
189 129 0.68
190 40 0.21
191 8 0.04
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (191 bp):
AATAATATCTTTTAATTTGCAATAGTCAAAAGATAAAACTCATTTCACCATTCAAACTTAAACAA
ATATTATTTTAATTTGAAATATACAAAAGTAAATAATTATCTTTAACATTCAAAATTAAAAAGAT
AACAAATACATTTCTAAATTGATATATTAAAAGAGTAATTATCCAACTAATATTCAAATTA
Found at i:472470 original size:3 final size:3
Alignment explanation
Indices: 472462--472486 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
472452 TATTTGTAAT
472462 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
472487 CATCATCATC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:473386 original size:50 final size:51
Alignment explanation
Indices: 473261--473392 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 51
473251 CACCCGTAGC
* * *
473261 AGTAAAGCGCGCGCCCTGCAT-CGCGCTATACGCTGATTTGGTGCCACGTGG
1 AGTATAGCGCGCCCCCTG-ATCCGCGCTATACGCTGATTTGGCGCCACGTGG
* ** * * *
473312 AGTATAACGCGCCCCCTGCCCCGCGATATACGGTGATTTGGCGCCATGTGG
1 AGTATAGCGCGCCCCCTGATCCGCGCTATACGCTGATTTGGCGCCACGTGG
473363 -GTATAGCGCGCCCCCTGATCCGCGCTATAC
1 AGTATAGCGCGCCCCCTGATCCGCGCTATAC
473393 CTGGTTATCT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
50 26 0.39
51 41 0.61
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGATCCGCGCTATACGCTGATTTGGCGCCACGTGG
Found at i:473530 original size:10 final size:10
Alignment explanation
Indices: 473515--473544 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
473505 TTTATCACAC
473515 CAAATTCTCT
1 CAAATTCTCT
473525 CAAATTCTCT
1 CAAATTCTCT
*
473535 CAAATACTCT
1 CAAATTCTCT
473545 ATCTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:473624 original size:17 final size:18
Alignment explanation
Indices: 473587--473625 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
473577 ATATTATGTA
473587 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
473605 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
473622 TTTA
1 TTTA
473626 GTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:473883 original size:111 final size:111
Alignment explanation
Indices: 473689--473910 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
473679 TGGAAATCAT
* * * *
473689 ATATCTCTACACTTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTTTTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
473754 TAATTGGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
473800 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
473865 CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
473911 TTTTTGAAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
CAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:480313 original size:16 final size:17
Alignment explanation
Indices: 480263--480313 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
480253 ATAAAAAATA
480263 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
480280 GA-TT-AAA-TTATGAGT
1 AATTTGAAAGTTA-GAGT
480295 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
480311 AAT
1 AAT
480314 GAATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.11
15 8 0.29
16 10 0.36
17 4 0.14
18 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:486356 original size:20 final size:20
Alignment explanation
Indices: 486291--486560 Score: 225
Period size: 20 Copynumber: 13.8 Consensus size: 20
486281 TCAGTTTTCA
* ** *
486291 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
486311 AAATCGCAACGCGAA--CAT
1 AAATCGCAACGTGAATCCGT
*
486329 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
486349 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
*
486369 ATATCGCAACGCT--ATCCGT
1 AAATCGCAACG-TGAATCCGT
* * *
486388 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
486408 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
486428 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
486448 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
486468 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
486488 AAATCGC-ACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
486507 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
486527 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
486547 AAATCACAAC-TGAA
1 AAATCGCAACGTGAA
486561 ATTTGGGTAT
Statistics
Matches: 209, Mismatches: 29, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
18 13 0.06
19 34 0.16
20 162 0.78
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:486410 original size:59 final size:60
Alignment explanation
Indices: 486328--486556 Score: 259
Period size: 59 Copynumber: 3.9 Consensus size: 60
486318 AACGCGAACA
* * *
486328 TAAATCGCAACGTGTATCCGTATATCGCAACGCGTATCCGTATATCGCAACGCT-ATCCG
1 TAAATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
*
486387 TAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
* * * * * * *
486447 TAAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGC-ACGAGAATCTG
1 TAAATCGCAACGCGTATCCGTATATCGCAACGCGT-ATCCGTAAATCGCAACGATAATCCG
* * * * * *
486506 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGCGT-ATCCGTATATCGCAACGCGTATCCGTAAATCGCAAC
486557 TGAAATTTGG
Statistics
Matches: 146, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
59 99 0.68
60 47 0.32
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (60 bp):
TAAATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
Found at i:486427 original size:79 final size:80
Alignment explanation
Indices: 486328--486556 Score: 270
Period size: 79 Copynumber: 2.9 Consensus size: 80
486318 AACGCGAACA
* * * * *
486328 TAAATCGCAACGTGTATCCGTATATCGCAACGCGT-ATCCGTATATCGCAACG-CTATCCGTAAA
1 TAAATCGCAACGAGTATCCGTAAATCGCAACG-ATAATCCGTAAATCGCAACGACAATCCGTAAA
486391 TCGCAATGCG-T-ATCCG
65 TCGCAA--CGATAATCCG
* * * *
486407 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGACAATCCGTAAAT
486472 CGCAACGATAATCCG
66 CGCAACGATAATCCG
* * * *
486487 TAAATCGC-ACGAGAATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGACAATCCGTAAAT
*
486551 CACAAC
66 CGCAAC
486557 TGAAATTTGG
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
78 3 0.02
79 104 0.78
80 26 0.20
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (80 bp):
TAAATCGCAACGAGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGACAATCCGTAAAT
CGCAACGATAATCCG
Found at i:489260 original size:18 final size:18
Alignment explanation
Indices: 489237--489301 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
489227 TGTTTATGAG
*
489237 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGTAAA
489255 GGAATT-AGAATCTGTAAA
1 GGAATTGA-AATCTGTAAA
* * *
489273 GGAATTGGAATCTATCAA
1 GGAATTGAAATCTGTAAA
489291 -GAATTGAAATC
1 GGAATTGAAATC
489302 AAATTCCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.28
18 29 0.73
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTAAA
Found at i:489924 original size:33 final size:33
Alignment explanation
Indices: 489869--489986 Score: 134
Period size: 33 Copynumber: 3.5 Consensus size: 33
489859 TTTCCACCCT
*
489869 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCAAATATCACACTTAAAA
*
489903 AAACCCGACCTGACCCAAATATCACACTTAAAA
1 AAACCCGACCCGACCCAAATATCACACTTAAAA
*
489936 AAACCCGACCCAACTCGACCAAA-AT-ATCACTT-AAA
1 AAACCCGACCCGA--C--CCAAATATCA-CACTTAAAA
489971 AAACCCGACCCGACCC
1 AAACCCGACCCGACCC
489987 GAACAAAATA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
31 2 0.03
33 36 0.49
34 7 0.09
35 17 0.23
36 7 0.09
37 5 0.07
ACGTcount: A:0.43, C:0.37, G:0.08, T:0.12
Consensus pattern (33 bp):
AAACCCGACCCGACCCAAATATCACACTTAAAA
Found at i:489972 original size:35 final size:36
Alignment explanation
Indices: 489894--489996 Score: 108
Period size: 35 Copynumber: 3.0 Consensus size: 36
489884 CCGAATATCA
** *
489894 CACTTAAAAAAACCCGACCTGACCC--A-AATATCA-
1 CACTTAAAAAAACCCGACCCAACCCGAACAAAAT-AT
* *
489927 CACTTAAAAAAACCCGACCCAACTCGACCAAAATAT
1 CACTTAAAAAAACCCGACCCAACCCGAACAAAATAT
*
489963 CACTT-AAAAAACCCGACCCGACCCGAACAAAATA
1 CACTTAAAAAAACCCGACCCAACCCGAACAAAATA
489997 AAGTTTCACC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 22 0.38
35 27 0.47
36 9 0.16
ACGTcount: A:0.47, C:0.34, G:0.07, T:0.13
Consensus pattern (36 bp):
CACTTAAAAAAACCCGACCCAACCCGAACAAAATAT
Found at i:495481 original size:93 final size:92
Alignment explanation
Indices: 495273--495481 Score: 240
Period size: 93 Copynumber: 2.3 Consensus size: 92
495263 TTTGGTTTGT
* * *
495273 TTTAGTACCTAAACTTTCAATTTTTTTCAAAATCATACTTAACGTATAGTTATTGTCTCCTTTTA
1 TTTAGTACCTAAACTTTCAATTTTGTTCAAAATCATACATAACGTATAGTTATTGTCTCATTTTA
* *
495338 GTATCTCACCATTACAAACTTAATATG
66 GTATCTCACCATTAAAAACTTAACATG
* ** * * * * *
495365 TTTAATATTTAAACTTTCAATTTTGTTCAAAATCATACATAATGTTTAGTTTTTTGTTTTATTTT
1 TTTAGTACCTAAACTTTCAATTTTGTTCAAAATCATACATAACGTATAG-TTATTGTCTCATTTT
* *
495430 AGTATC-CAACCGTTAAAAACTTAACGTG
65 AGTATCTC-ACCATTAAAAACTTAACATG
* *
495458 TTTAGTACCTAAACTATCGATTTT
1 TTTAGTACCTAAACTTTCAATTTT
495482 AGTCCGTTTT
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
92 43 0.45
93 52 0.55
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (92 bp):
TTTAGTACCTAAACTTTCAATTTTGTTCAAAATCATACATAACGTATAGTTATTGTCTCATTTTA
GTATCTCACCATTAAAAACTTAACATG
Found at i:496400 original size:21 final size:22
Alignment explanation
Indices: 496376--496426 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
496366 TGGTGTGGGG
496376 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
* *
496397 ATGTTTTTGGTATTTTTATTTA
1 ATGTTTTTAGTATTTTTATTAA
496419 AT-TTTTTA
1 ATGTTTTTA
496427 AATAATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:501517 original size:41 final size:39
Alignment explanation
Indices: 501436--501573 Score: 158
Period size: 38 Copynumber: 3.5 Consensus size: 39
501426 TTCAGGACTG
* *
501436 AAATGTATT-GGAGAGATATATTGAAAAAAAC-ATAATT
1 AAATGTATTAGAAGAGATACATTGAAAAAAACTATAATT
* *
501473 AAATGTATTAGAAGAGATAGATTGAAAAAAAAACTATAACT
1 AAATGTATTAGAAGAGATACATTG--AAAAAAACTATAATT
501514 AAATGTATTAGGAA-AGATACATTG-AAAAAACTATAATT
1 AAATGTATTA-GAAGAGATACATTGAAAAAAACTATAATT
*
501552 AAATGCATTAGGAGAGAGATAC
1 AAATGTATTA-GA-AGAGATAC
501574 TGAAATGTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
37 9 0.10
38 37 0.42
39 1 0.01
40 14 0.16
41 24 0.27
42 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (39 bp):
AAATGTATTAGAAGAGATACATTGAAAAAAACTATAATT
Found at i:502773 original size:21 final size:21
Alignment explanation
Indices: 502744--502784 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
502734 TTATAATTAA
502744 TAAACTTTAAAATGAAAAATG
1 TAAACTTTAAAATGAAAAATG
*
502765 TAAATTTTAAAATGAAAAAT
1 TAAACTTTAAAATGAAAAAT
502785 TATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (21 bp):
TAAACTTTAAAATGAAAAATG
Found at i:516176 original size:32 final size:32
Alignment explanation
Indices: 516118--516182 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
516108 ATCACTTTGC
* *
516118 ATCAATTCGATAAAATTTGATGATCATTTTAT
1 ATCAATTCAATAAAATTTAATGATCATTTTAT
* *
516150 ATCAGTTCAATAAAATTTAATTATCATTTTAT
1 ATCAATTCAATAAAATTTAATGATCATTTTAT
516182 A
1 A
516183 GTTTTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (32 bp):
ATCAATTCAATAAAATTTAATGATCATTTTAT
Found at i:521606 original size:35 final size:35
Alignment explanation
Indices: 521567--521693 Score: 182
Period size: 35 Copynumber: 3.6 Consensus size: 35
521557 AAAACAGTCA
*
521567 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
*
521602 TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
* * *
521637 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
** *
521672 TCAATTAAATTTTAAACCCCAA
1 TCAATTTCATTCTAAACCCCAA
521694 ATTCTAAAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 84 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
Found at i:521696 original size:35 final size:35
Alignment explanation
Indices: 521567--521713 Score: 177
Period size: 35 Copynumber: 4.2 Consensus size: 35
521557 AAAACAGTCA
* * *
521567 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * *
521602 TCAATTTCATTCTAAACCCTAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
521637 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * * *
521672 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
521707 TTAATTT
1 TCAATTT
521714 AAGGTTTAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 100 1.00
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:521777 original size:35 final size:35
Alignment explanation
Indices: 521709--521783 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
521699 AAAATACTTT
* * *
521709 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
521744 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
521779 AATTT
1 AATTT
521784 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:531828 original size:10 final size:10
Alignment explanation
Indices: 531813--531838 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
531803 TATACATTAG
531813 AAAAATTATT
1 AAAAATTATT
531823 AAAAATTATT
1 AAAAATTATT
531833 AAAAAT
1 AAAAAT
531839 CAGTTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTATT
Found at i:532113 original size:15 final size:16
Alignment explanation
Indices: 532095--532129 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
532085 TAGATTATGA
*
532095 ATTTAGATA-TTAAGG
1 ATTTAGAGATTTAAGG
532110 ATTTAGAGATTTAAGG
1 ATTTAGAGATTTAAGG
532126 ATTT
1 ATTT
532130 GAGTATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
ATTTAGAGATTTAAGG
Found at i:542798 original size:15 final size:15
Alignment explanation
Indices: 542778--542816 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
542768 AAGCTAAAGA
*
542778 AGCAGCTGCTGCA-GC
1 AGCAGCAGCT-CAGGC
542793 AGCAGCAGCTCAGGC
1 AGCAGCAGCTCAGGC
542808 AGCAGCAGC
1 AGCAGCAGC
542817 AGCTAACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.26, C:0.33, G:0.33, T:0.08
Consensus pattern (15 bp):
AGCAGCAGCTCAGGC
Found at i:548176 original size:48 final size:48
Alignment explanation
Indices: 548084--548283 Score: 159
Period size: 48 Copynumber: 4.2 Consensus size: 48
548074 GCTCCACCTT
* * * * * *
548084 CTGCTGCACCAGGCATGCGAATAGGAGCATCACCTCTCAATGCACCAG
1 CTGCAGCACCAGGCATGCCAATAGGAGCACCATCTCCCGATGCACCAG
* * * * *
548132 CTGCAGCACCAGGAATGCCTATAGGAGCATCATCTCCCGGTGCACGTA-
1 CTGCAGCACCAGGCATGCCAATAGGAGCACCATCTCCCGATGCAC-CAG
* * ** * * *
548180 CTGCAACATCAGGCACACCAATAAGAGCACCATCTCCCGGTGCACCGG
1 CTGCAGCACCAGGCATGCCAATAGGAGCACCATCTCCCGATGCACCAG
* * ** * * *
548228 CTGCAACATCAGGCACACTAATAGGAGCACCATCTCCTGATGCACCGG
1 CTGCAGCACCAGGCATGCCAATAGGAGCACCATCTCCCGATGCACCAG
548276 CTGCAGCA
1 CTGCAGCA
548284 TCAAGCAAAC
Statistics
Matches: 126, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
48 125 0.99
49 1 0.01
ACGTcount: A:0.28, C:0.34, G:0.23, T:0.16
Consensus pattern (48 bp):
CTGCAGCACCAGGCATGCCAATAGGAGCACCATCTCCCGATGCACCAG
Found at i:548340 original size:48 final size:48
Alignment explanation
Indices: 548149--548340 Score: 210
Period size: 48 Copynumber: 4.0 Consensus size: 48
548139 ACCAGGAATG
* * * *
548149 CCTATAGGAGCATCATCTCCCGGTGCA-CGTACTGCAACATCAGGCACA
1 CCTATAGGAGCACCATCTCCTGGTGCACCG-GCTGCAACATCAGGCAAA
* * * *
548197 CCAATAAGAGCACCATCTCCCGGTGCACCGGCTGCAACATCAGGCACA
1 CCTATAGGAGCACCATCTCCTGGTGCACCGGCTGCAACATCAGGCAAA
* * *
548245 -CTAATAGGAGCACCATCTCCTGATGCACCGGCTGCAGCATCAAGCAAA
1 CCT-ATAGGAGCACCATCTCCTGGTGCACCGGCTGCAACATCAGGCAAA
* * *
548293 CCTATAGGATCACCA-CATCCTGGTGCAACGGCTGCAACAACAGGCAAA
1 CCTATAGGAGCACCATC-TCCTGGTGCACCGGCTGCAACATCAGGCAAA
548341 TCAATCACAA
Statistics
Matches: 123, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
47 2 0.02
48 117 0.95
49 4 0.03
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.16
Consensus pattern (48 bp):
CCTATAGGAGCACCATCTCCTGGTGCACCGGCTGCAACATCAGGCAAA
Found at i:550378 original size:23 final size:23
Alignment explanation
Indices: 550352--550396 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
550342 CATTGAGTCA
* *
550352 AGTCTAAAGATTCGATTTTTTCG
1 AGTCAAAAGATTCAATTTTTTCG
550375 AGTCAAAAGATTCAATTTTTTC
1 AGTCAAAAGATTCAATTTTTTC
550397 AATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (23 bp):
AGTCAAAAGATTCAATTTTTTCG
Found at i:551344 original size:20 final size:17
Alignment explanation
Indices: 551304--551347 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
551294 GTTGGTTTTG
551304 TGCTGCTTTCTCCTCTA
1 TGCTGCTTTCTCCTCTA
551321 TGCTGCTTTCTCCTCTA
1 TGCTGCTTTCTCCTCTA
551338 TGCTGCTTTC
1 TGCTGCTTTC
551348 GACATTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.05, C:0.34, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCTGCTTTCTCCTCTA
Found at i:553658 original size:4 final size:4
Alignment explanation
Indices: 553651--553678 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
553641 TACATGCCTG
553651 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
553679 TAAAACAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:555408 original size:213 final size:211
Alignment explanation
Indices: 555043--555463 Score: 736
Period size: 213 Copynumber: 2.0 Consensus size: 211
555033 GATTTTGAGA
555043 ATTCAATCTTGTTAAGTTTAAGAATTTTTTCATTTCGAGCATCTTCGAGCTGCTCACAAGCTTCA
1 ATTCAATCTTGTTAAGTTTAAGAATTTTTTCATTTCGAGCATCTTCGAGCTGCTCACAAGCTTCA
555108 ATTCAGGATTTCGAGTTCGAGTCGAGCTTAAAAATTTTAAACTCGCGAGTTTTCGAGTCAAGTCG
66 ATTCAGGATTTCGAGTTCGAGTCGAGCTTAAAAATTTTAAACTCGCGAGTTTTCGAGTCAAGTCG
* *
555173 AGCTTCATTTCAGAGTTTTCGAGTCGAGCTCAGCAATACTCGAGCTCAACTCGGCACGTTTACAC
131 AGCTTCATTTCAGAGTTTTCGAGTCGAGCTCAGCAATACTCGAACTCAACTCGACACGTTTACAC
555238 CTCTACTATATACACG
196 CTCTACTATATACACG
* * *
555254 ATTCAATCTTGTTAAGTTTAAGATTTTTTTTTCATTTCGAGTATTTTCGAGCTGCTCACAAGCTT
1 ATTCAATCTTGTTAAGTTTAAGA--ATTTTTTCATTTCGAGCATCTTCGAGCTGCTCACAAGCTT
* * *
555319 CAATTCATGATTTCGAGTTCGAGTCGAGTTTAAAAATTTTAAGCTCGCGAGTTTTCGAGTCAAGT
64 CAATTCAGGATTTCGAGTTCGAGTCGAGCTTAAAAATTTTAAACTCGCGAGTTTTCGAGTCAAGT
555384 CGAGC-TCTATTTCAGAGTTTTCGAGTCGAGCTCAGCAATACTCGAACTCAACTCGACACGTTTA
129 CGAGCTTC-ATTTCAGAGTTTTCGAGTCGAGCTCAGCAATACTCGAACTCAACTCGACACGTTTA
555448 CACCTCTACTATATAC
193 CACCTCTACTATATAC
555464 CCCCAAAATA
Statistics
Matches: 199, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
211 23 0.12
212 2 0.01
213 174 0.87
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (211 bp):
ATTCAATCTTGTTAAGTTTAAGAATTTTTTCATTTCGAGCATCTTCGAGCTGCTCACAAGCTTCA
ATTCAGGATTTCGAGTTCGAGTCGAGCTTAAAAATTTTAAACTCGCGAGTTTTCGAGTCAAGTCG
AGCTTCATTTCAGAGTTTTCGAGTCGAGCTCAGCAATACTCGAACTCAACTCGACACGTTTACAC
CTCTACTATATACACG
Found at i:557731 original size:17 final size:17
Alignment explanation
Indices: 557709--557741 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
557699 TTTGTGTTCC
557709 TTCAATT-TGTGCTTGTT
1 TTCAATTGTGT-CTTGTT
557726 TTCAATTGTGTCTTGT
1 TTCAATTGTGTCTTGT
557742 AATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (17 bp):
TTCAATTGTGTCTTGTT
Found at i:558122 original size:7 final size:7
Alignment explanation
Indices: 558050--558136 Score: 81
Period size: 7 Copynumber: 12.6 Consensus size: 7
558040 ACTAAAATCC
558050 TAAACCA
1 TAAACCA
*
558057 TAAACTA
1 TAAACCA
*
558064 TAAACTA
1 TAAACCA
558071 TAAA-CA
1 TAAACCA
558077 CTAAACTC-
1 -TAAAC-CA
*
558085 TAAATCA
1 TAAACCA
558092 TAAACCA
1 TAAACCA
*
558099 TAAACCC
1 TAAACCA
558106 TAAA-CA
1 TAAACCA
*
558112 TAAACCC
1 TAAACCA
*
558119 TAAATCA
1 TAAACCA
558126 TAAACCA
1 TAAACCA
558133 TAAA
1 TAAA
558137 ACCTATCACA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
6 7 0.11
7 57 0.88
9 1 0.02
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:572630 original size:2 final size:2
Alignment explanation
Indices: 572618--572654 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
572608 AAAGTGATCA
572618 AT 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
572655 CATTTTCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:578050 original size:21 final size:21
Alignment explanation
Indices: 578021--578076 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
578011 GAACCCCAAT
* *
578021 GGGGTATCGATTCCCCT-GTG
1 GGGGGATCGATTCCCCTCATG
*
578041 GGGGGAATCGGTT-CCCTCATG
1 GGGGG-ATCGATTCCCCTCATG
578062 GGGGGATCGATTCCC
1 GGGGGATCGATTCCC
578077 TATGCACCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGATCGATTCCCCTCATG
Found at i:586638 original size:35 final size:36
Alignment explanation
Indices: 586581--586658 Score: 86
Period size: 37 Copynumber: 2.2 Consensus size: 36
586571 TTCACCCTAA
** *
586581 ACCCGACCCGAACAGTACA-TTTTAAAAAAAACCCG
1 ACCCGACCCGAACACAAAATTTTTAAAAAAAACCCG
* * *
586616 ACCCGACCCGAACCCAAAATTTTTTTAAAAAAATCCG
1 ACCCGACCCGAACACAAAA-TTTTTAAAAAAAACCCG
586653 ACCCGA
1 ACCCGA
586659 TCGAGTCGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 15 0.43
37 20 0.57
ACGTcount: A:0.41, C:0.32, G:0.10, T:0.17
Consensus pattern (36 bp):
ACCCGACCCGAACACAAAATTTTTAAAAAAAACCCG
Found at i:589747 original size:15 final size:15
Alignment explanation
Indices: 589727--589755 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
589717 CTATCGACAA
589727 CCAGTTAGTCTAGTC
1 CCAGTTAGTCTAGTC
589742 CCAGTTAGTCTAGT
1 CCAGTTAGTCTAGT
589756 GGGACGAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (15 bp):
CCAGTTAGTCTAGTC
Found at i:609320 original size:17 final size:18
Alignment explanation
Indices: 609298--609331 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
609288 TGAGTTGGAT
609298 TTTTTATATT-TTAAATC
1 TTTTTATATTATTAAATC
*
609315 TTTTTATTTTATTAAAT
1 TTTTTATATTATTAAAT
609332 TTTCCTTCTG
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:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATATTATTAAATC
Found at i:616970 original size:12 final size:12
Alignment explanation
Indices: 616938--616971 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
616928 TTTATTGTTC
616938 AAATCATTTTTTA
1 AAAT-ATTTTTTA
616951 AAACTATTTTTTA
1 AAA-TATTTTTTA
616964 AAATATTT
1 AAATATTT
616972 AATAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 14 0.70
14 1 0.05
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (12 bp):
AAATATTTTTTA
Found at i:618243 original size:20 final size:22
Alignment explanation
Indices: 618218--618259 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
618208 AACTTAGAGT
*
618218 TTTTAAA-CTTTTAAA-AATTA
1 TTTTAAATATTTTAAATAATTA
618238 TTTTAAATATTTTAAATAATTA
1 TTTTAAATATTTTAAATAATTA
618260 AATTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAATATTTTAAATAATTA
Found at i:620300 original size:20 final size:20
Alignment explanation
Indices: 620275--620323 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
620265 GGCTGCTGGA
620275 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACCGG-TTTC
620295 AACCGGTTCTGACCGGTTTC
1 AACCGGTTCTGACCGGTTTC
620315 AACCGGTTC
1 AACCGGTTC
620324 GAACCGGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (20 bp):
AACCGGTTCTGACCGGTTTC
Found at i:620312 original size:30 final size:29
Alignment explanation
Indices: 620275--620348 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
620265 GGCTGCTGGA
620275 AACCGGTTTGACCGGTTTTC-AACCGGTTCTG
1 AACCGGTTTGACCGG--TTCGAACCGG-TCTG
*
620306 -ACCGGTTTCAACCGGTTCGAACCGGTCTG
1 AACCGGTTT-GACCGGTTCGAACCGGTCTG
*
620335 AATCGGTTTGACCG
1 AACCGGTTTGACCG
620349 TTGACCCGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 11 0.30
30 21 0.57
31 5 0.14
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTCGAACCGGTCTG
Found at i:620329 original size:20 final size:19
Alignment explanation
Indices: 620275--620331 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 19
620265 GGCTGCTGGA
*
620275 AACCGGTTTGACCGGTTTTC
1 AACCGGTTCGACCGG-TTTC
620295 AACCGGTTCTGACCGGTTTC
1 AACCGGTTC-GACCGGTTTC
620315 AACCGGTTCGAACCGGT
1 AACCGGTTCG-ACCGGT
620332 CTGAATCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.03
20 27 0.79
21 6 0.18
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (19 bp):
AACCGGTTCGACCGGTTTC
Found at i:620361 original size:5 final size:5
Alignment explanation
Indices: 620351--620407 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
620341 TTTGACCGTT
* *
620351 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
620400 GACCC GAC
1 GACCC GAC
620408 TGTTGACCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 36 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:620378 original size:22 final size:22
Alignment explanation
Indices: 620351--620415 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
620341 TTTGACCGTT
620351 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
620373 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
620395 GACCCGACCCGACTGTTGACC
1 GACCCGACCCGACCGTTGACC
620416 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:620403 original size:17 final size:17
Alignment explanation
Indices: 620344--620381 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
620334 GAATCGGTTT
620344 GACCGTTGACCCGACCC
1 GACCGTTGACCCGACCC
620361 GACCGTTGACCCGACCC
1 GACCGTTGACCCGACCC
620378 GACC
1 GACC
620382 CGACCGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCGTTGACCCGACCC
Found at i:620421 original size:7 final size:7
Alignment explanation
Indices: 620409--620435 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
620399 CGACCCGACT
620409 GTTGACC
1 GTTGACC
620416 GTTGACC
1 GTTGACC
620423 GTTGACC
1 GTTGACC
620430 GTTGAC
1 GTTGAC
620436 TTTCTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (7 bp):
GTTGACC
Found at i:621372 original size:63 final size:62
Alignment explanation
Indices: 621304--621435 Score: 153
Period size: 63 Copynumber: 2.1 Consensus size: 62
621294 CTAATGTGAC
* * *
621304 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGT-
621366 T
62 T
* *
621367 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGTT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTT
*
621429 CCTTAGG
1 TCTTAGG
621436 GTAACGCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
62 8 0.13
63 48 0.80
64 4 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (62 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTT
Found at i:621387 original size:32 final size:32
Alignment explanation
Indices: 621304--621435 Score: 94
Period size: 31 Copynumber: 4.2 Consensus size: 32
621294 CTAATGTGAC
* * **
621304 TCTTAGGTAGGCTCT-GCGGCCCTGAGATCAT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTT
** * *
621335 TCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-T
* * *
621367 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTT
*
621398 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGTT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTT
*
621429 CCTTAGG
1 TCTTAGG
621436 GTAACGCTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
30 5 0.06
31 47 0.60
32 21 0.27
33 5 0.06
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTT
Found at i:627642 original size:10 final size:9
Alignment explanation
Indices: 627607--627697 Score: 83
Period size: 10 Copynumber: 9.4 Consensus size: 9
627597 GCTGCTGGAA
627607 ACCGGTTTG
1 ACCGGTTTG
*
627616 ACCGGTTTTCA
1 ACCGG-TTT-G
627627 ACCGGTTCTG
1 ACCGGTT-TG
627637 ACCGGTTTG
1 ACCGGTTTG
*
627646 ACCGGTTTCA
1 ACCGGTTT-G
*
627656 ACCGGTTCG
1 ACCGGTTTG
627665 AACCGGTTTG
1 -ACCGGTTTG
*
627675 ACCGGTCTG
1 ACCGGTTTG
*
627684 AATCGGTTTG
1 -ACCGGTTTG
627694 ACCG
1 ACCG
627698 TTGACCCTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
9 26 0.39
10 34 0.52
11 6 0.09
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:627651 original size:19 final size:20
Alignment explanation
Indices: 627606--627697 Score: 102
Period size: 19 Copynumber: 4.7 Consensus size: 20
627596 GGCTGCTGGA
* *
627606 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTCTG
627626 AACCGGTTCTGACCGGTT-TG
1 AACCGGTT-TGACCGGTTCTG
*
627646 -ACCGGTTTCAACCGGTTC-G
1 AACCGGTTT-GACCGGTTCTG
627665 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
627684 AATCGGTTTGACCG
1 AACCGGTTTGACCG
627698 TTGACCCTAC
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.05
19 34 0.54
20 17 0.27
21 9 0.14
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:627691 original size:29 final size:30
Alignment explanation
Indices: 627606--627680 Score: 127
Period size: 29 Copynumber: 2.5 Consensus size: 30
627596 GGCTGCTGGA
627606 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
627637 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
627665 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
627681 CTGAATCGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.65
30 14 0.33
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:627714 original size:5 final size:5
Alignment explanation
Indices: 627700--627762 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
627690 TTTGACCGTT
* * *
627700 GACCC TACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
627749 GACCC GACCC GACC
1 GACCC GACCC GACC
627763 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 40 0.83
7 8 0.17
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:627736 original size:27 final size:22
Alignment explanation
Indices: 627693--627769 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
627683 GAATCGGTTT
*
627693 GACCGTTGACCCTACCCGACCC
1 GACCGTTGACCCGACCCGACCC
627715 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
627737 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
627759 GACCGTTGACC
1 GACCGTTGACC
627770 GTTGACTTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.18, C:0.48, G:0.22, T:0.12
Consensus pattern (22 bp):
GACCGTTGACCCGACCCGACCC
Found at i:628727 original size:63 final size:63
Alignment explanation
Indices: 628644--628767 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
628634 CTAATGTGAC
* * * *
628644 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTCGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
628707 TCTTAGGTAGGC-CTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCT-ACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
628768 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 3 0.06
63 48 0.92
64 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCTACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:631474 original size:3 final size:3
Alignment explanation
Indices: 631466--631520 Score: 92
Period size: 3 Copynumber: 17.7 Consensus size: 3
631456 ATGAAGGGAT
631466 TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
631512 TTA TATA TT
1 TTA T-TA TT
631521 TATCATATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:631534 original size:28 final size:25
Alignment explanation
Indices: 631466--631535 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
631456 ATGAAGGGAT
*
631466 TTATTATTATTATTATTATTAATTA
1 TTATTATCATTATTATTATTAATTA
*
631491 TTATTATTATTATTATTATT-ATTA
1 TTATTATCATTATTATTATTAATTA
631515 TATATTTATCATATACTTATT
1 T-TA-TTATCAT-TA-TTATT
631536 GATGATAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
24 5 0.12
25 22 0.55
26 6 0.15
27 2 0.05
28 5 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
TTATTATCATTATTATTATTAATTA
Found at i:636074 original size:31 final size:31
Alignment explanation
Indices: 636039--636100 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
636029 CATGGCGCAT
636039 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
**
636070 GCAAAGCTTCATCCTCTCGTCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
636101 TAGAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:637696 original size:16 final size:16
Alignment explanation
Indices: 637659--637689 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
637649 TAACAGTATT
637659 AAAAATATATATTTTA
1 AAAAATATATATTTTA
637675 AAAAATA-ATATTTTA
1 AAAAATATATATTTTA
637690 CTAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAATATATATTTTA
Done.